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          "seq": "-----------------------                          ----------------------------------     -     ----     -     --     -     --- -----------              ",
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          "seq": "-------------------------                         -------     -     ------------------------    --  ",
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          "val": "3.612945e-81"
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      "sequence": "CTCCTTCCCCTCCCACCTTTTTTTTGAATCANGAATCAGCCCAGGGAAATATTATTCTTATTGAAGCACAAGGAAGAACTTGAAAATGATACTGCGAAATCTTATTGAAAATGACTCTTGAGTCTATTACTGTTCCACCTGTGATGGGCCTTTATTATAAGAAACTCTTTGGCAGTGGAACAACAC",
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    {
      "germline": "TRD+",
      "id": "TTTTTATACTGATGTGTTTCACTCCTCGGGGGAACCCGTGTGACTGTGGA",
      "reads": [
        9
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      "seg_stat": {
        "3": 9
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      "sequence": 0,
      "top": 101
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    {
      "germline": "IGH",
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        9
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        "3": 9
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      "sequence": 0,
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    {
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        9
      ],
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        "3": 9
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      "sequence": 0,
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    {
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        9
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        "3": 9
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      "sequence": 0,
      "top": 104
    },
    {
      "germline": "TRG",
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        9
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        "3": 9
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      "sequence": 0,
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    {
      "germline": "TRG",
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        9
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        "3": 9
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      "top": 106
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    {
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        9
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      "top": 107
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    {
      "germline": "TRG",
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        9
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        "3": 9
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      "sequence": 0,
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    {
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        9
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        "3": 9
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    },
    {
      "germline": "TRG",
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        9
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        "3": 9
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      "sequence": 0,
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    {
      "germline": "TRG",
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        9
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        "3": 9
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      "sequence": 0,
      "top": 111
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    {
      "germline": "TRG",
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        9
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        "3": 9
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      "sequence": 0,
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    {
      "germline": "TRG",
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        9
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        "3": 9
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      "sequence": 0,
      "top": 113
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    {
      "germline": "IGH+",
      "id": "ATTGTAGTAGTACCAGCTGCTATACCTACTACTACTACTACGGTATGGAC",
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        9
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        "3": 9
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      "sequence": 0,
      "top": 114
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    {
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      "id": "TTATTACTGTGCGAGTGCGGAATATGAGATGCCTGAAGACGTCTGGGGCC",
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        8
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        "3": 8
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      "sequence": 0,
      "top": 115
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        8
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        "3": 8
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      "sequence": 0,
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    {
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        8
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        "3": 8
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      "sequence": 0,
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    {
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        8
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        8
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        8
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        "3": 8
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      "sequence": 0,
      "top": 120
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    {
      "germline": "IGH",
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        8
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        "3": 8
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      "sequence": 0,
      "top": 121
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    {
      "germline": "IGH+",
      "id": "TACAAAAACCATGCTCCCCCGGGACCCCGGGCTGTGGGTTTCTGTAGCCC",
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        8
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        "3": 8
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      "sequence": 0,
      "top": 122
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    {
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        8
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        "3": 8
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    {
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        8
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        "3": 8
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    {
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        8
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        "3": 8
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      "sequence": 0,
      "top": 125
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        8
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        "3": 8
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      "sequence": 0,
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        8
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      "sequence": 0,
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        8
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        8
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        "3": 8
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      "sequence": 0,
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        8
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      "sequence": 0,
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    {
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        7
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      "sequence": 0,
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        7
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        7
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        "3": 7
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        7
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        7
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      "sequence": 0,
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        7
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      "sequence": 0,
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    {
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        7
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      "top": 138
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        7
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        "3": 7
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      "sequence": 0,
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        7
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      "sequence": 0,
      "top": 140
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      "sequence": 0,
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      "top": 142
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        7
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      "sequence": 0,
      "top": 144
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    {
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        7
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        "3": 7
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      "sequence": 0,
      "top": 145
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      "germline": "IGH",
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        7
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        "3": 7
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      "sequence": 0,
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    {
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      "sequence": 0,
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    {
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        6
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        "3": 6
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      "sequence": 0,
      "top": 148
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    {
      "germline": "IGH",
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        6
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        "3": 6
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      "sequence": 0,
      "top": 149
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      "germline": "IGH",
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        6
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        "3": 6
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      "top": 150
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    {
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        6
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        "3": 6
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      "sequence": 0,
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    {
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        6
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        "3": 6
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        6
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        "3": 6
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        6
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        "3": 6
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      "top": 154
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    {
      "germline": "IGH",
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        6
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        "3": 6
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      "sequence": 0,
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    {
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        6
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        "3": 6
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      "sequence": 0,
      "top": 156
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    {
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        6
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        "3": 6
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      "sequence": 0,
      "top": 157
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    {
      "germline": "IGH",
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        6
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        "3": 6
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      "sequence": 0,
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    {
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        6
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        "3": 6
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    {
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        6
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        "3": 6
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      "sequence": 0,
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    {
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        6
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        "3": 6
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      "sequence": 0,
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        6
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        "3": 6
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      "sequence": 0,
      "top": 163
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    {
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        6
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        "3": 6
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      "sequence": 0,
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        6
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        "3": 6
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        6
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        "3": 6
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      "sequence": 0,
      "top": 166
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      "germline": "TRG",
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        6
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        "3": 6
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      "sequence": 0,
      "top": 167
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    {
      "germline": "TRG",
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        6
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        "3": 6
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      "sequence": 0,
      "top": 168
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    {
      "germline": "TRG",
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        6
      ],
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        "3": 6
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      "sequence": 0,
      "top": 169
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    {
      "germline": "TRG",
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        6
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      "seg_stat": {
        "3": 6
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      "sequence": 0,
      "top": 170
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    {
      "germline": "TRG",
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        6
      ],
      "seg_stat": {
        "3": 6
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      "sequence": 0,
      "top": 171
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    {
      "germline": "TRG",
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        6
      ],
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        "3": 6
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      "sequence": 0,
      "top": 172
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    {
      "germline": "TRG",
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        6
      ],
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        "3": 6
      },
      "sequence": 0,
      "top": 173
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    {
      "germline": "TRG",
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        6
      ],
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        "3": 6
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      "sequence": 0,
      "top": 174
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    {
      "germline": "TRG",
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        6
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        "3": 6
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      "sequence": 0,
      "top": 175
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    {
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        6
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        "3": 6
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        6
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        "3": 6
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    {
      "germline": "TRG",
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        5
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        "3": 5
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      "sequence": 0,
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    {
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        5
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        "3": 5
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      "sequence": 0,
      "top": 179
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    {
      "germline": "IGH",
      "id": "TTACTGTGCGAGAGGTGACTATGGTTCGGGGAGAGCATACTACTACTACG",
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        5
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      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 180
    },
    {
      "germline": "TRG",
      "id": "TCTGGAGTCTATTACTATGCCTACTGGGATGGGCCTTTATTATAAGAAAC",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 181
    },
    {
      "germline": "TRG",
      "id": "TATTACTTTGCCTCCTGGGATGGGCCTTTATTATAAGAAACTCTTTGCCA",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 182
    },
    {
      "germline": "TRG",
      "id": "TATTACTGTGCCACCTGAGATGGGCCTTTATTANAAGAAANTCTTTGGCA",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 183
    },
    {
      "germline": "TRG",
      "id": "TATTACTGTCCCTCCTGGGATGGGCCTTTATTANAAGAAACTCTTTGGCA",
      "reads": [
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      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 184
    },
    {
      "germline": "TRG",
      "id": "TATTACTGTCCCACCTGGGATGGGCCTTTATTATAAGAAACTCTTTGNCA",
      "reads": [
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      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 185
    },
    {
      "germline": "TRG",
      "id": "TATTACTATGCCTCCTGGGATGGGCCTTTATTATAAGAAACTCTTTGGCA",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 186
    },
    {
      "germline": "TRG",
      "id": "TACTACTGTGCTGCGTGGGATGAGGCTGGCTATTATAAGAAACTCTTTGG",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 187
    },
    {
      "germline": "IGH+",
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      "reads": [
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      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 188
    },
    {
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      "reads": [
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      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 189
    },
    {
      "germline": "TRG",
      "id": "GTTTCTATTACTGTGCCACCTCGAGCTCTTAATTATAAGAAACTCTTTGG",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 190
    },
    {
      "germline": "TRG",
      "id": "GTCTATTACTGTGCCACATCGAGCTCTTAATTANAAGAAACTCTTTGGCA",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 191
    },
    {
      "germline": "TRG",
      "id": "GTCTATTACTGTGCCACATAGAGCTCTTAATTANAAGAAACTCTTTGGCA",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 192
    },
    {
      "germline": "TRG",
      "id": "GGTCTATTACTGTGCCACCTGGAGCTCTTAATTATAAGAAACTCTTTTGC",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 193
    },
    {
      "germline": "TRG",
      "id": "GGTCTATTACTGTGCCACCTGGAGCTCTTAATTATAAGAAACTCTTTGGT",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 194
    },
    {
      "germline": "TRG",
      "id": "GGGTTCTATTACTTTGCCACCTGGAGCTCTTAATTATAAGAAACTCTTTG",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 195
    },
    {
      "germline": "TRG",
      "id": "GGGTCTATTACTGTTCCACCTAGAGCTCTTAATTATAAGAAACTCTTTGG",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 196
    },
    {
      "germline": "TRG",
      "id": "GGGGTCTATTACTTTGCCACCTAGAGCTCTTAATTATAAGAAACTCTTTG",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 197
    },
    {
      "germline": "TRG",
      "id": "GGGGTCTATTACTGTGCCACATCGAGCTCTTAATTATAAGAAACTCTTTG",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 198
    },
    {
      "germline": "TRG",
      "id": "GGGATCTATTACTGTGCCACATGGAGCTCTTAATTATAAGAAACTCTTTG",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 199
    },
    {
      "germline": "IGH+",
      "id": "GGCTGAGCTGAGAACCACTGTGCCCAGGGACTACTGGGGCCAGGGAACCC",
      "reads": [
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      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 200
    },
    {
      "germline": "TRG",
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      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 201
    },
    {
      "germline": "TRG",
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      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 202
    },
    {
      "germline": "TRG",
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      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 203
    },
    {
      "germline": "TRG",
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      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 204
    },
    {
      "germline": "TRG",
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      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 205
    },
    {
      "germline": "TRG",
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      "reads": [
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      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 206
    },
    {
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      "reads": [
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      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 207
    },
    {
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      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 208
    },
    {
      "germline": "IGH",
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      "reads": [
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      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 209
    },
    {
      "germline": "TRG",
      "id": "CTCTATTACTGTGCCATCTGGGATGGGCCTTTATTATAAGAAACTCTTTG",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 210
    },
    {
      "germline": "TRG",
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      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 211
    },
    {
      "germline": "TRG",
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      "reads": [
        5
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      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 212
    },
    {
      "germline": "TRG",
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      "reads": [
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      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 213
    },
    {
      "germline": "TRG",
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      "reads": [
        5
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      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 214
    },
    {
      "germline": "IGH",
      "id": "CATGGTCGTGTATTCCTGTGACTGGATAGTAGTGGACCTACTGGGGCCAG",
      "reads": [
        5
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      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 215
    },
    {
      "germline": "IGH+",
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      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 216
    },
    {
      "germline": "TRG",
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      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 217
    },
    {
      "germline": "IGH+",
      "id": "AAACCATGCTCCCCCGGGACCCCGGGCTGTGGGTTTCTGTAGCCCCTGGC",
      "reads": [
        5
      ],
      "seg_stat": {
        "3": 5
      },
      "sequence": 0,
      "top": 218
    }
  ],
  "diversity": {
    "index_Ds_diversity": 0.978837490081787,
    "index_E_equitability": 0.685247778892517,
    "index_H_entropy": 6.55956835928373
  },
  "germlines": {
    "custom": {
      "3": [],
      "4": [],
      "5": [],
      "shortcut": "X"
    }
  },
  "reads": {
    "germline": {
      "IGH": [
        1806
      ],
      "IGH+": [
        531
      ],
      "IGK": [
        0
      ],
      "IGK+": [
        54
      ],
      "IGL": [
        0
      ],
      "TRA": [
        0
      ],
      "TRA+D": [
        3
      ],
      "TRB": [
        0
      ],
      "TRB+": [
        0
      ],
      "TRD": [
        31
      ],
      "TRD+": [
        47
      ],
      "TRG": [
        11893
      ]
    },
    "segmented": [
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    "total": [
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    ]
  },
  "samples": {
    "commandline": [
      "./vidjil -g germline/ -i ../vidjil/data/Data/Mat(786)Clean.fastq "
    ],
    "log": [
      "  ==> junction detected in 14383 reads (31.6%)\n  ==> found 5461 50-windows in 14365 reads (31.5% of 45564 reads)\n  ! There are not so many CDR3 windows found in this set of reads.\n  ! Please check the unsegmentation causes below and refer to the documentation.\n                          reads av. len     clones clo/rds\n  IGH               ->     1806   200.0       1557   0.862\n  IGH+              ->      531   200.0        434   0.817\n  IGK               ->        0       -          0       -\n  IGK+              ->       54   200.0         53   0.981\n  IGL               ->        0       -          0       -\n  TRA               ->        0       -          0       -\n  TRA+D             ->        3   200.0          3   1.000\n  TRB               ->        0       -          0       -\n  TRB+              ->        0       -          0       -\n  TRD               ->       31   200.0         30   0.968\n  TRD+              ->       47   200.0         32   0.681\n  TRG               ->    11893   200.0       3352   0.282\n\n  SEG               ->    14365   200.0\n  SEG_+             ->        0       -\n  SEG_-             ->    14365   200.0\n\n  UNSEG too short   ->        0       -\n  UNSEG strand      ->     1617   200.0\n  UNSEG too few V/J ->      246   200.0\n  UNSEG only V/5'   ->     1913   200.0\n  UNSEG only J/3'   ->    27381   200.0\n  UNSEG < delta_min ->        0       -\n  UNSEG ambiguous   ->       24   200.0\n  UNSEG too short w ->       18   200.0\n"
    ],
    "number": 1,
    "original_names": [
      "../vidjil/data/Data/Mat(786)Clean.fastq"
    ],
    "producer": [
      "vidjil 2016.09"
    ],
    "run_timestamp": [
      "2017-01-03 17:57:35"
    ]
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