Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold192
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2196177
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 12544 characters in sequence are not A, C, G, or T
File 14 of 14
Found at i:2152013 original size:177 final size:178
Alignment explanation
Indices: 2151716--2152078 Score: 502
Period size: 177 Copynumber: 2.0 Consensus size: 178
2151706 TCCTAATCAT
* * * *
2151716 TAGATGGTACTGATGCATCACAAAGCTTGATTTTCTCGAGGCAAGGTGTAGCCCACACATTCCTA
1 TAGATGGTACTGATGCATCACAAAGCTTGACTTTCTCGAGGCAAAGTGCAACCCACACATTCCTA
* *
2151781 ATCATATCCCTTTCATTCAACCACTAGATGGTACTGATGCATCACAAAGCCTGATTTTCCTAGGG
66 ATCATATCCCTTTCACTCAACCACTAGATGGTACTAATGCATCACAAAGCCTGATTTTCCTAGGG
* *
2151846 CAAGG-TGCAACCCACACATTC-CTAATCATATCTCCTTCATTCAACTAG
131 C-AGGATGCAACCCACACATTCAC-AATCATATCTCCTTCATTCAACCAC
* *
2151894 TAGATGGTACTGATGCATTACAAAGCTTGACTTTCTTG-GGCAAAGTGCAACCCACACATTCCTA
1 TAGATGGTACTGATGCATCACAAAGCTTGACTTTCTCGAGGCAAAGTGCAACCCACACATTCCTA
*
2151958 ATCATATCCCTCTTTC-CT-AACTACTAGATGGTACTAATGCATCACAAAGCCTGATTTTCCTAG
66 ATCATAT-CC-CTTTCACTCAACCACTAGATGGTACTAATGCATCACAAAGCCTGATTTTCCTAG
** * ** *
2152021 GGCAGGATGCGGCCCACACATTCACAATCCTATCTTTTTCTTTCAACCAC
129 GGCAGGATGCAACCCACACATTCACAATCATATCTCCTTCATTCAACCAC
2152071 TAGATGGT
1 TAGATGGT
2152079 GTGATTCAGG
Statistics
Matches: 164, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
176 3 0.02
177 117 0.71
178 39 0.24
179 5 0.03
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (178 bp):
TAGATGGTACTGATGCATCACAAAGCTTGACTTTCTCGAGGCAAAGTGCAACCCACACATTCCTA
ATCATATCCCTTTCACTCAACCACTAGATGGTACTAATGCATCACAAAGCCTGATTTTCCTAGGG
CAGGATGCAACCCACACATTCACAATCATATCTCCTTCATTCAACCAC
Found at i:2152613 original size:44 final size:43
Alignment explanation
Indices: 2152284--2152622 Score: 277
Period size: 44 Copynumber: 7.7 Consensus size: 43
2152274 TCCTTTTCTG
* *
2152284 TTTGATGTATGGTTACCACCCTTGTCAAACTTTTCTCATTTCGA
1 TTTGACGTATGGTTACCACCCTAGTCAAA-TTTTCTCATTTCGA
* * ** * *
2152328 TATGATGTATGGTTACCACCAGAGTCAAATTCTTTTCATGTCGA
1 TTTGACGTATGGTTACCACCCTAGTCAAATT-TTCTCATTTCGA
* * * ** *
2152372 TTTGGCATATAGTTACCACCC-AGGTCAAATCTGCCTCATTTCTA
1 TTTGACGTATGGTTACCACCCTA-GTCAAAT-TTTCTCATTTCGA
* *
2152416 TTTGACGTATGGTTACCACCCTGGTCAAACTTTTCTTATTTCGA
1 TTTGACGTATGGTTACCACCCTAGTCAAA-TTTTCTCATTTCGA
** * * *
2152460 TCCGATGTATGGTTACCACCCTAGTCAAATTCTTTTCGTGTT-GA
1 TTTGACGTATGGTTACCACCCTAGTCAAATT-TTCTCAT-TTCGA
* * * *** **
2152504 TTTGACATATGGTTACCACTCTGGTCAAATCCACCTCATTTTTA
1 TTTGACGTATGGTTACCACCCTAGTCAAAT-TTTCTCATTTCGA
*
2152548 TTTGATGTATGGTTACCACCCTAGTCAAACTTTTCTCATTTCGA
1 TTTGACGTATGGTTACCACCCTAGTCAAA-TTTTCTCATTTCGA
* ** *
2152592 TCTGACAAATGGTTACCACCCTAGTTAAATT
1 TTTGACGTATGGTTACCACCCTAGTCAAATT
2152623 CTTTTCGTGT
Statistics
Matches: 227, Mismatches: 58, Indels: 21
0.74 0.19 0.07
Matches are distributed among these distances:
43 9 0.04
44 213 0.94
45 5 0.02
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (43 bp):
TTTGACGTATGGTTACCACCCTAGTCAAATTTTCTCATTTCGA
Found at i:2152633 original size:132 final size:132
Alignment explanation
Indices: 2152088--2152628 Score: 674
Period size: 132 Copynumber: 4.1 Consensus size: 132
2152078 TGTGATTCAG
* * * * *
2152088 GTTAGATTCTTTTCATGTCGATTTG-CGTATGGTTATCACCTTGGTCAAATCCACCTCTTTTTTG
1 GTTAAATTCTTTTCATGTCGATTTGACATATGGTTACCACCTTGGTCAAATCCACCTCATTTTTA
* * * * *
2152152 TTTGACGTTTGGTTACCACCCTAGTCAAACTTTTCTTATTTCGGTCTAATGTATGG-TACCACTA
66 TTTGACGTATGGTTACCACCCTAGTCAAACTTTTCTCATTTCGATCTGATGTATGGTTACCACCA
*
2152216 TG
131 TA
* * * * *
2152218 GTTATATTCTTTTCATGTCAATATAACATATGGTTACCACCTTGGTCAAATCCACCTCCTTTTCT
1 GTTAAATTCTTTTCATGTCGATTTGACATATGGTTACCACCTTGGTCAAATCCACCTCATTTT-T
* * * *
2152283 GTTTGATGTATGGTTACCACCCTTGTCAAACTTTTCTCATTTCGATATGATGTATGGTTACCACC
65 ATTTGACGTATGGTTACCACCCTAGTCAAACTTTTCTCATTTCGATCTGATGTATGGTTACCACC
*
2152348 AGA
130 ATA
* * * ** ** *
2152351 GTCAAATTCTTTTCATGTCGATTTGGCATATAGTTACCACCCAGGTCAAATCTGCCTCATTTCTA
1 GTTAAATTCTTTTCATGTCGATTTGACATATGGTTACCACCTTGGTCAAATCCACCTCATTTTTA
* * * *
2152416 TTTGACGTATGGTTACCACCCTGGTCAAACTTTTCTTATTTCGATCCGATGTATGGTTACCACCC
66 TTTGACGTATGGTTACCACCCTAGTCAAACTTTTCTCATTTCGATCTGATGTATGGTTACCACCA
2152481 TA
131 TA
* * *
2152483 GTCAAATTCTTTTCGTGTTGATTTGACATATGGTTACCA-CTCTGGTCAAATCCACCTCATTTTT
1 GTTAAATTCTTTTCATGTCGATTTGACATATGGTTACCACCT-TGGTCAAATCCACCTCATTTTT
* ***
2152547 ATTTGATGTATGGTTACCACCCTAGTCAAACTTTTCTCATTTCGATCTGACAAATGGTTACCACC
65 ATTTGACGTATGGTTACCACCCTAGTCAAACTTTTCTCATTTCGATCTGATGTATGGTTACCACC
*
2152612 CTA
130 ATA
2152615 GTTAAATTCTTTTC
1 GTTAAATTCTTTTC
2152629 GTGTTTGTCG
Statistics
Matches: 352, Mismatches: 55, Indels: 6
0.85 0.13 0.01
Matches are distributed among these distances:
130 21 0.06
131 35 0.10
132 239 0.68
133 57 0.16
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (132 bp):
GTTAAATTCTTTTCATGTCGATTTGACATATGGTTACCACCTTGGTCAAATCCACCTCATTTTTA
TTTGACGTATGGTTACCACCCTAGTCAAACTTTTCTCATTTCGATCTGATGTATGGTTACCACCA
TA
Found at i:2153696 original size:79 final size:79
Alignment explanation
Indices: 2153607--2154000 Score: 313
Period size: 79 Copynumber: 5.0 Consensus size: 79
2153597 ATAAAAATGG
2153607 GGTTAGAGTATTCCCTCAGAAATAACGGGGTTGGAGTATCCCGGATGGTGAAAAATCAGTGTTTT
1 GGTTAGAGTATTCCCTCAGAAATAACGGGGTTGGAGTATCCCGGATGGTGAAAAATCAGTGTTTT
*
2153672 GGAAATAAAATCGA
66 AGAAATAAAATCGA
* * * * * *
2153686 GGTTGGAGTATCCCCT-TGAAAATAACGGGGTTGGAATATCTCCAAGTAT-G-AAAAAAT-AGTG
1 GGTTAGAGTATTCCCTCAG-AAATAACGGGGTTGGAGTATC-CC--GGATGGTGAAAAATCAGTG
* * *
2153747 TTTTAAAAATAAAACCAA
62 TTTTAGAAATAAAATCGA
* * * * * *
2153765 GGTTAGAATA-TCTCCACAGAAATAACGGGGTTAGAGTATCTCTGATTGTGAAAAATCAGTGTTT
1 GGTTAGAGTATTC-CCTCAGAAATAACGGGGTTGGAGTATCCCGGATGGTGAAAAATCAGTGTTT
*
2153829 TAGAAATAAAA-CTA
65 TAGAAATAAAATCGA
* ** * * * *
2153843 GGGTTGGAAAATTCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGATGAAAAAT-TGATGTT
1 -GGTTAGAGTATTCCCTCAGAAATAACGGGGTTGGAGTATCCCGGATGGTGAAAAATCAG-TGTT
* * * *
2153907 TCAAAAATAAAATTGG
64 TTAGAAATAAAATCGA
* ** * * *
2153923 GGTTAAAGTA-TCCTCTC-GAAAATAACGAAGTTGGAGTAT-CCTGATGGTGAAAAGTCAATGTT
1 GGTTAGAGTATTCC-CTCAG-AAATAACGGGGTTGGAGTATCCCGGATGGTGAAAAATCAGTGTT
* *
2153985 TAAGAAAGAAAATCGA
64 TTAGAAATAAAATCGA
2154001 TGTTTTAGAA
Statistics
Matches: 244, Mismatches: 55, Indels: 33
0.73 0.17 0.10
Matches are distributed among these distances:
76 2 0.01
77 1 0.00
78 43 0.18
79 183 0.75
80 11 0.05
81 1 0.00
82 3 0.01
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (79 bp):
GGTTAGAGTATTCCCTCAGAAATAACGGGGTTGGAGTATCCCGGATGGTGAAAAATCAGTGTTTT
AGAAATAAAATCGA
Found at i:2153927 original size:158 final size:157
Alignment explanation
Indices: 2153597--2153997 Score: 420
Period size: 158 Copynumber: 2.5 Consensus size: 157
2153587 TATTTTGGAG
* *
2153597 ATAAAAATGGGGTTAGAGTAT-TCCCTCAGAAATAACGGGGTTGGAGTATCCCGGATGGTGAAAA
1 ATAAAAATGGGGTTAGAATATCT-CCTCAGAAATAACGGGGTTGGAGTAT-CCTGATGGTGAAAA
* * ** **
2153661 ATCAGTGTTTTGGAAATAAAATCGAGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAATATC
64 ATCAGTGTTTTAGAAATAAAATAGAGGTTGGAAAATCCCCTCAAAAATAACGGGGTTGGAATATC
* *
2153726 TCCAAGTATGAAAAAATAGTGTTTTAAAA
129 CCCAAGTATGAAAAAATAGTGTTTCAAAA
**** * * *
2153755 ATAAAACCAAGGTTAGAATATCTCCACAGAAATAACGGGGTTAGAGTATCTCTGATTGTGAAAAA
1 ATAAAAATGGGGTTAGAATATCTCCTCAGAAATAACGGGGTTGGAGTATC-CTGATGGTGAAAAA
* *
2153820 TCAGTGTTTTAGAAATAAAACTAG-GGTTGGAAAATTCCCTCAAAAATAACGGGGTTGGAGTATC
65 TCAGTGTTTTAGAAATAAAA-TAGAGGTTGGAAAATCCCCTCAAAAATAACGGGGTTGGAATATC
* *
2153884 CCCGA-TGATG-AAAAATTGATGTTTCAAAA
129 CCCAAGT-ATGAAAAAATAG-TGTTTCAAAA
* **
2153913 ATAAAATTGGGGTTA-AAGTATC-CTCTC-GAAAATAACGAAGTTGGAGTATCCTGATGGTGAAA
1 ATAAAAATGGGGTTAGAA-TATCTC-CTCAG-AAATAACGGGGTTGGAGTATCCTGATGGTGAAA
* * * *
2153975 AGTCAATGTTTAAGAAAGAAAAT
63 AATCAGTGTTTTAGAAATAAAAT
2153998 CGATGTTTTA
Statistics
Matches: 201, Mismatches: 34, Indels: 18
0.79 0.13 0.07
Matches are distributed among these distances:
156 1 0.00
157 42 0.21
158 155 0.77
159 3 0.01
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (157 bp):
ATAAAAATGGGGTTAGAATATCTCCTCAGAAATAACGGGGTTGGAGTATCCTGATGGTGAAAAAT
CAGTGTTTTAGAAATAAAATAGAGGTTGGAAAATCCCCTCAAAAATAACGGGGTTGGAATATCCC
CAAGTATGAAAAAATAGTGTTTCAAAA
Found at i:2153995 original size:21 final size:20
Alignment explanation
Indices: 2153971--2154019 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2153961 TCCTGATGGT
2153971 GAAAAGTCAATGTTTAAGAAA
1 GAAAA-TCAATGTTTAAGAAA
* *
2153992 GAAAATCGATGTTTTAGAAA
1 GAAAATCAATGTTTAAGAAA
*
2154012 TAAAATCA
1 GAAAATCA
2154020 GGGTTGGAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (20 bp):
GAAAATCAATGTTTAAGAAA
Found at i:2154138 original size:76 final size:76
Alignment explanation
Indices: 2153992--2154171 Score: 222
Period size: 76 Copynumber: 2.3 Consensus size: 76
2153982 GTTTAAGAAA
* ** *
2153992 GAAAATCGATGTTTTAGAAATAAAATCAGGGTTGGAGTATCTTCTCAGAAATAACGGGGTTAGAG
1 GAAAATCGATGTTTTAGAAATAAAAT-A-GATTGGAGTATCCCCTCAGAAATAACGGAGTTAGAG
2154057 CATCCCCGATGGT
64 CATCCCCGATGGT
* *
2154070 GGAAAATCGATGTTTTAAAAATAAAAT-GATTGGAGTATCCCCTTAGAAATAACGGAGTT-GAAG
1 -GAAAATCGATGTTTTAGAAATAAAATAGATTGGAGTATCCCCTCAGAAATAACGGAGTTAG-AG
*
2154133 TATCCCCGATGGT
64 CATCCCCGATGGT
2154146 GAAAACTC-AGTGTTTTAGAAATAAAA
1 GAAAA-TCGA-TGTTTTAGAAATAAAA
2154172 ACATAAATGA
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
75 7 0.08
76 58 0.64
79 25 0.28
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (76 bp):
GAAAATCGATGTTTTAGAAATAAAATAGATTGGAGTATCCCCTCAGAAATAACGGAGTTAGAGCA
TCCCCGATGGT
Found at i:2157092 original size:47 final size:47
Alignment explanation
Indices: 2156982--2157131 Score: 203
Period size: 47 Copynumber: 3.2 Consensus size: 47
2156972 AAATCCACCT
* * * *
2156982 CCTCATTTGACTATATTAGCGTTAGGACCTAGTCAAA-CTTTTTCAC
1 CCTCGTTTGACTATATTGGCGTTAAGACCTAGTCAAACCCTTTTCAC
* *
2157028 CCTAGTTTGACTGTATTGGCGTTAAGACCTAGTCAAACCCTTTTCAC
1 CCTCGTTTGACTATATTGGCGTTAAGACCTAGTCAAACCCTTTTCAC
* * *
2157075 CCTCGTTTGACTATATTGGCATTAAGACCTGGTCAAACTCTTTTCAC
1 CCTCGTTTGACTATATTGGCGTTAAGACCTAGTCAAACCCTTTTCAC
*
2157122 CCTTGTTTGA
1 CCTCGTTTGA
2157132 TTGCATTAGC
Statistics
Matches: 91, Mismatches: 12, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
46 32 0.35
47 59 0.65
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (47 bp):
CCTCGTTTGACTATATTGGCGTTAAGACCTAGTCAAACCCTTTTCAC
Found at i:2157154 original size:47 final size:46
Alignment explanation
Indices: 2157013--2157221 Score: 161
Period size: 47 Copynumber: 4.5 Consensus size: 46
2157003 TTAGGACCTA
* * * * * *
2157013 GTCAAACT-TTTTCACCCTAGTTTGACTGTATTGGCGTTAAGACCTA
1 GTCAAACTCTTTTCACCCTTGTTTGACTGCATTAGCCTT-AGTCCTG
* * ** * * *
2157059 GTCAAACCCTTTTCACCCTCGTTTGACTATATTGGCATTAAGACCTG
1 GTCAAACTCTTTTCACCCTTGTTTGACTGCATTAGCCTT-AGTCCTG
* *
2157106 GTCAAACTCTTTTCACCCTTGTTTGATTGCATTAGCCTTGGGGT-CTG
1 GTCAAACTCTTTTCACCCTTGTTTGACTGCATTAGCCTT--AGTCCTG
* ** * * **
2157153 GTCAAACTCTTCTCACTTTTTTTTGACTGCATTGGTGTTAGTCCTG
1 GTCAAACTCTTTTCACCCTTGTTTGACTGCATTAGCCTTAGTCCTG
*
2157199 GTCAAACTCTTTTCATCCTTGTT
1 GTCAAACTCTTTTCACCCTTGTT
2157222 CGATGTGATG
Statistics
Matches: 131, Mismatches: 29, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
45 2 0.02
46 28 0.21
47 100 0.76
48 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (46 bp):
GTCAAACTCTTTTCACCCTTGTTTGACTGCATTAGCCTTAGTCCTG
Found at i:2158518 original size:20 final size:20
Alignment explanation
Indices: 2158481--2158534 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
2158471 TTCTATAATT
*
2158481 TGTATCGATACAATAAGTTAA
1 TGTATCGATAC-ATAAGTGAA
*
2158502 TGTATTGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
*
2158522 TTTATCGATACAT
1 TGTATCGATACAT
2158535 GCTTGAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:2158660 original size:20 final size:20
Alignment explanation
Indices: 2158635--2158677 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2158625 TATTTGGGGT
2158635 TATTCTTCAATGTATCGATA
1 TATTCTTCAATGTATCGATA
2158655 TATTCTTCAATGTATCGATA
1 TATTCTTCAATGTATCGATA
2158675 TAT
1 TAT
2158678 CAGCCAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (20 bp):
TATTCTTCAATGTATCGATA
Found at i:2161004 original size:97 final size:93
Alignment explanation
Indices: 2160794--2161038 Score: 217
Period size: 97 Copynumber: 2.6 Consensus size: 93
2160784 TTTATTCATT
* * * *
2160794 GGGGATACTCTAACCTAATTCTTCCGAAGG-GATATTCTAACCCCATTTTTAAACTTGTCTTTAA
1 GGGGATACTCTAACCTCATTCTTCTG-AGGAGATACTCCAACCCCATTTTTAAACTTGTCTTTAA
* ** *
2160858 ATCTTATTTTTGCTTAAATTGTCACCATC
65 ATATTATTTTTGCCCAAATTATCACCATC
*** * *
2160887 AAAGATACTCCAATCC-CATTCTTCTGAGGAGATACTCCAACCCCATTTTTGAACTTGTCAAGAT
1 GGGGATACTCTAA-CCTCATTCTTCTGAGGAGATACTCCAACCCCATTTTTAAACTTGTC----T
* *
2160951 TTAAATATTATTTTTGCCCAAATTATCATCGTC
61 TTAAATATTATTTTTGCCCAAATTATCACCATC
* * * * * *
2160984 GGGGATATTCTAACCTCATTCCTCTGA-AAGGATACTTCAACCCTATTTTTCAACT
1 GGGGATACTCTAACCTCATTCTTCTGAGGA-GATACTCCAACCCCATTTTTAAACT
2161039 AAAAATTAAA
Statistics
Matches: 119, Mismatches: 25, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
92 3 0.03
93 43 0.36
94 2 0.02
96 3 0.03
97 68 0.57
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (93 bp):
GGGGATACTCTAACCTCATTCTTCTGAGGAGATACTCCAACCCCATTTTTAAACTTGTCTTTAAA
TATTATTTTTGCCCAAATTATCACCATC
Found at i:2165760 original size:21 final size:21
Alignment explanation
Indices: 2165719--2165776 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
2165709 ATAAAAGTTA
*
2165719 CATTTTTTCATTTAAAAAACG
1 CATTTTTTCATTCAAAAAACG
* **
2165740 TATTTTTTCATTCAACCAACG
1 CATTTTTTCATTCAAAAAACG
**
2165761 CATCCTTTCATTCAAA
1 CATTTTTTCATTCAAA
2165777 TATACCTTTT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.41
Consensus pattern (21 bp):
CATTTTTTCATTCAAAAAACG
Found at i:2165889 original size:52 final size:53
Alignment explanation
Indices: 2165786--2165897 Score: 208
Period size: 52 Copynumber: 2.1 Consensus size: 53
2165776 ATATACCTTT
2165786 TTATAAAGAATGGAGTCTATATACTTTTTTTATCTAAAGTGATTATTAAATGG
1 TTATAAAGAATGGAGTCTATATACTTTTTTTATCTAAAGTGATTATTAAATGG
*
2165839 TTATAAAGAATGGTGTCTATATAC-TTTTTTATCTAAAGTGATTATTAAATGG
1 TTATAAAGAATGGAGTCTATATACTTTTTTTATCTAAAGTGATTATTAAATGG
2165891 TTATAAA
1 TTATAAA
2165898 TAAATTTGTA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 35 0.60
53 23 0.40
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (53 bp):
TTATAAAGAATGGAGTCTATATACTTTTTTTATCTAAAGTGATTATTAAATGG
Found at i:2174097 original size:32 final size:32
Alignment explanation
Indices: 2174043--2174103 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2174033 GTCAAGGTGA
*
2174043 TTTTTTCAATAAAAATACACAAATAAAATAAT
1 TTTTTTCAATAAAAATACACAAAAAAAATAAT
* *
2174075 TTTTTTGCAAT-AATATATACAAAAAAAAT
1 TTTTTT-CAATAAAAATACACAAAAAAAAT
2174104 GAAAAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 21 0.84
33 4 0.16
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.36
Consensus pattern (32 bp):
TTTTTTCAATAAAAATACACAAAAAAAATAAT
Found at i:2174565 original size:18 final size:19
Alignment explanation
Indices: 2174542--2174579 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2174532 TAATTGAATT
*
2174542 AATTAAATA-AAATTAAAA
1 AATTAAAAATAAATTAAAA
2174560 AATTAAAAATAAATTAAAA
1 AATTAAAAATAAATTAAAA
2174579 A
1 A
2174580 TATATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AATTAAAAATAAATTAAAA
Found at i:2174580 original size:18 final size:18
Alignment explanation
Indices: 2174542--2174593 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
2174532 TAATTGAATT
*
2174542 AATTAAATAAAATTAAAA
1 AATTAAAAAAAATTAAAA
2174560 AATTAAAAATAAATTAAAA
1 AATTAAAAA-AAATTAAAA
2174579 ATATATATAAAAAAA
1 A-AT-TA-AAAAAAA
2174594 ATCAATCACA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.28
19 10 0.34
20 2 0.07
21 5 0.17
22 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AATTAAAAAAAATTAAAA
Found at i:2175544 original size:16 final size:17
Alignment explanation
Indices: 2175515--2175548 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
2175505 TTTAACAAAT
2175515 AAATATATGAATTATAAA
1 AAATATAT-AATTATAAA
2175533 AAATATAT-ATTATAAA
1 AAATATATAATTATAAA
2175549 TTGTTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AAATATATAATTATAAA
Found at i:2178972 original size:21 final size:21
Alignment explanation
Indices: 2178932--2178973 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2178922 TATATATTTT
*
2178932 ATTTTAAAATTATTATTATTA
1 ATTTTAAAATTATTAATATTA
2178953 ATTTTAAAATGT-TTAATATTA
1 ATTTTAAAAT-TATTAATATTA
2178974 GAGATCTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTTAAAATTATTAATATTA
Found at i:2179349 original size:17 final size:19
Alignment explanation
Indices: 2179322--2179361 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2179312 AATTTTTTAT
2179322 AATTTTATATTTA-AATTA
1 AATTTTATATTTATAATTA
*
2179340 AATTTT-TATTTATTATTA
1 AATTTTATATTTATAATTA
2179358 AATT
1 AATT
2179362 GATTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTATATTTATAATTA
Found at i:2183812 original size:89 final size:89
Alignment explanation
Indices: 2183702--2183879 Score: 329
Period size: 89 Copynumber: 2.0 Consensus size: 89
2183692 AACTTTTAGG
*
2183702 ATGTGCATGGTGCGCATGAACAATGGCATGCAAAGATTAATTCCAATGAAATTAAGGTTTTTAGA
1 ATGTGCATGGTGCGCATGAACAATGGCATGCAAAGATTAATTCCAACGAAATTAAGGTTTTTAGA
2183767 TGAAAATTTTCATAAAAAAAAAGT
66 TGAAAATTTTCATAAAAAAAAAGT
2183791 ATGTGCATGGTGCGCATGAACAATGGCATGCAAAGATTAATTCCAACGAAATTAAGGTTTTTAGA
1 ATGTGCATGGTGCGCATGAACAATGGCATGCAAAGATTAATTCCAACGAAATTAAGGTTTTTAGA
* *
2183856 TGAAAATTTTCTTTAAAAAAAAGT
66 TGAAAATTTTCATAAAAAAAAAGT
2183880 CAATATTTTT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (89 bp):
ATGTGCATGGTGCGCATGAACAATGGCATGCAAAGATTAATTCCAACGAAATTAAGGTTTTTAGA
TGAAAATTTTCATAAAAAAAAAGT
Found at i:2184742 original size:29 final size:30
Alignment explanation
Indices: 2184676--2184750 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
2184666 GGATACTTAT
* *
2184676 TTAAATAAATTATTAATTTTTAATTTGTAC
1 TTAAATAAACTATTAATATTTAATTTGTAC
*
2184706 TTCAATAAACTATTAATATTTAA-TTGTAC
1 TTAAATAAACTATTAATATTTAATTTGTAC
*
2184735 TTAAATAAACTTTTAA
1 TTAAATAAACTATTAA
2184751 CATATAGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 20 0.50
30 20 0.50
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.48
Consensus pattern (30 bp):
TTAAATAAACTATTAATATTTAATTTGTAC
Found at i:2184801 original size:15 final size:17
Alignment explanation
Indices: 2184767--2184827 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 17
2184757 GATTAAATTT
2184767 TTATTTAGAATAAAAAA
1 TTATTTAGAATAAAAAA
*
2184784 TTATTTA-AAT-ACAAA
1 TTATTTAGAATAAAAAA
** *
2184799 TTA-AAAG-GTAAAAAA
1 TTATTTAGAATAAAAAA
2184814 TTATTTAG-ATAAAA
1 TTATTTAGAATAAAA
2184828 TAAAAATATA
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
14 2 0.06
15 14 0.42
16 10 0.30
17 7 0.21
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (17 bp):
TTATTTAGAATAAAAAA
Found at i:2184813 original size:30 final size:29
Alignment explanation
Indices: 2184777--2184833 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
2184767 TTATTTAGAA
*
2184777 TAAAAAATTATTTAAATACAAATTAAAAGG
1 TAAAAAATTATTTAAATA-AAATAAAAAGG
*
2184807 TAAAAAATTATTTAGATAAAATAAAAA
1 TAAAAAATTATTTAAATAAAATAAAAA
2184834 TATATCTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (29 bp):
TAAAAAATTATTTAAATAAAATAAAAAGG
Found at i:2186338 original size:15 final size:15
Alignment explanation
Indices: 2186283--2186338 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
2186273 ATAATTATAA
2186283 TTATAATAATCA-ATT
1 TTATAATAAT-ATATT
*
2186298 ATATATATAATTATTATT
1 TTATA-ATAA-TA-TATT
2186316 TT-TAATAATATATT
1 TTATAATAATATATT
2186330 TTATAATAA
1 TTATAATAA
2186339 AAATAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
15 12 0.35
16 9 0.26
17 3 0.09
18 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATAATAATATATT
Found at i:2186689 original size:14 final size:16
Alignment explanation
Indices: 2186672--2186704 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
2186662 TATAAAAATA
2186672 ATAAAAT-TAT-TTTT
1 ATAAAATATATATTTT
2186686 ATAAAATATATATTTT
1 ATAAAATATATATTTT
2186702 ATA
1 ATA
2186705 TTAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 3 0.18
16 7 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATAAAATATATATTTT
Found at i:2193355 original size:21 final size:22
Alignment explanation
Indices: 2193310--2193363 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2193300 TGGACATGTT
2193310 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
2193332 AAAAATGCATGAAACATAAT-A
1 AAAAATGCATGAAACATAATAA
2193353 AAAAATGCATG
1 AAAAATGCATG
2193364 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:2194326 original size:20 final size:20
Alignment explanation
Indices: 2194279--2194353 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
2194269 AAAAAGACAT
* ** *
2194279 AATGTATCGATATATTGTAG
1 AATGTATCGATACATTAAAA
* * *
2194299 AATATATCGATACATTCATA
1 AATGTATCGATACATTAAAA
* *
2194319 CATGTATCGATATATTAAAA
1 AATGTATCGATACATTAAAA
2194339 AATGTATCGATACAT
1 AATGTATCGATACAT
2194354 CAAGGTAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTAAAA
Found at i:2194347 original size:40 final size:39
Alignment explanation
Indices: 2194276--2194353 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
2194266 GGTAAAAAGA
** *
2194276 CATAATGTATCGATATATTGTAGAATATATCGATACATT
1 CATAATGTATCGATATATTAAAAAATATATCGATACATT
*
2194315 CATACATGTATCGATATATTAAAAAATGTATCGATACAT
1 CATA-ATGTATCGATATATTAAAAAATATATCGATACAT
2194354 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATATATTAAAAAATATATCGATACATT
Found at i:2195062 original size:28 final size:28
Alignment explanation
Indices: 2194961--2196109 Score: 1162
Period size: 28 Copynumber: 40.0 Consensus size: 28
2194951 CACTGACACA
* **
2194961 TGTGGGCTTTGAAAAGAGTGTTACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
2194990 TGCGTGGGCTTTAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTGAAAGGATGCCACTGACT
2195020 TGCGTGGGCTTTGAAAGGATGCCACTGA-T
1 T--GTGGGCTTTGAAAGGATGCCACTGACT
2195049 TCGTGGGCTTTGAAA-GAGTGCCACTGACT
1 T-GTGGGCTTTGAAAGGA-TGCCACTGACT
2195078 TGTGGGCTTTGAAAGG-TGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2195105 CGTGGGCTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
** *
2195133 CATGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
2195160 TGTGGGCTTTGAAA-GAGTGTCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
2195188 CGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
2195216 TGCGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGGA-TGCCACTGAC-T
* *
2195248 GTGTGGGCTTTGAAAGGGTGCCACTAACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
*
2195277 CGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
2195305 TGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
2195333 CGTGGGCTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * *
2195361 TGTGTGAGCTTTAAAAAGAGTGCCACTAACT
1 TGTG-G-GCTTTGAAAGGA-TGCCACTGACT
*
2195392 TGTGGGCTTTGAAA-GAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
2195420 TGTGGGCATCGCAATGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
2195448 TGTGGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
2195476 TGTGGGCTCTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
2195504 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2195532 TGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
2195561 TGTGGGCTTTGAAAAGAGTGCCACTCACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
2195590 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
2195619 TGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 TGTGGGCTTTGAAAGGA-TGCCACTGAC-T
* *
2195649 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2195678 TGTGCGCTTTGAAA-GAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
2195706 TGTGGGCTTCGCAATGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * *
2195734 TGTAGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
2195762 TGCGTGGGCTTTGAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTG-AAAGGATGCCACTGACT
* *
2195793 TGTGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
2195821 TGTGAGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * **
2195850 TGTGGGCTTTAAAAGGGTGCCACCAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
2195878 TGCGTGGGCTTTGAAAGGGGTGCCACTGACT
1 T--GTGGGCTTTGAAA-GGATGCCACTGACT
* *
2195909 TGTGGGCTTTGAAAGGGTGCCACCGACTT
1 TGTGGGCTTTGAAAGGATGCCACTGAC-T
2195938 GTGTGGGCTTTGAAAGGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
*
2195967 TGTGGGCTTTGAAA-GAGTGTCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
2195995 CGTGGACTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * *
2196023 TGCGTGAGCTTTAAAAAGGAGTGCCACTAACT
1 T--GTGGGCTTT-GAAAGGA-TGCCACTGACT
*
2196055 TGTGGGCTTTGAAA-GAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
2196083 TGTGGGCTTCGCAATGG-TGCCACTGAC
1 TGTGGGCTTTG-AAAGGATGCCACTGAC
2196110 GTTGGTGCGT
Statistics
Matches: 966, Mismatches: 101, Indels: 107
0.82 0.09 0.09
Matches are distributed among these distances:
26 5 0.01
27 55 0.06
28 472 0.49
29 183 0.19
30 142 0.15
31 97 0.10
32 11 0.01
33 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:2195385 original size:87 final size:85
Alignment explanation
Indices: 2194910--2196109 Score: 1297
Period size: 87 Copynumber: 13.9 Consensus size: 85
2194900 TTTTTAAAAA
* * *
2194910 AAAATGTGCCACT-AGCTTGTGTAGGCTTTGAAAAAAGTTGCCACTGACACATGTGGGCTTTGAA
1 AAAAGGTGCCACTGA-CTTGTG--GGCTTTGAAAAGAG-TGCCACTG--ACTTGTGGGCTTTG-A
**
2194974 AAGAGTGTTACTGACTTGCGTGGGCTTT-
59 AAGAGTGCCACTGACTT--GTGGGCTTTG
*
2195002 AAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGA-TGCCACTGA-TTCGTGGGCTTTGAAAG
1 AAAA-GGTGCCACTGACTT--GTGGGCTTTGAAAAGAGTGCCACTGACTT-GTGGGCTTTGAAAG
2195065 AGTGCCACTGACTTGTGGGCTTTG
62 AGTGCCACTGACTTGTGGGCTTTG
* * ** *
2195089 -AAAGGTGCCACTGACTCGTGGGCTTTGAAAAG-GTACCACTGACTCATGGGC-TTGAAAGGGTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTG
2195151 CCACTGACTTGTGGGCTTTG
66 CCACTGACTTGTGGGCTTTG
* *
2195171 -AAAGAGTGTCACTGACTCGTGGGCTTTGAAAAG-GTGCCACTGACTTGCGTGGGCTTTGAAAGG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAA-G
2195234 AGTGCCACTGACTTGTGTGGGCTTTG
62 AGTGCCACTGAC-T-TGTGGGCTTTG
* * * *
2195260 AAAGGGTGCCACTAACTCGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGAGTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTG
*
2195324 CCACTGACTCGTGGGCTTTG
66 CCACTGACTTGTGGGCTTTG
* * *
2195344 AAAAGGTACCACTGACTTGTGTGAGCTTTAAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGAG
1 AAAAGGTGCCACTGACTTGTG-G-GCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAG
* * *
2195409 TGCCACTGAATTGTGGGCATCG
64 TGCCACTGACTTGTGGGCTTTG
* * * * * *
2195431 CAATGGTGCCACTGACTTGTGGGCTTCG-AAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTG
*
2195495 CCACTAACTTGTGGGCTTTG
66 CCACTGACTTGTGGGCTTTG
* *
2195515 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGT
1 AAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGT
*
2195580 GCCACTCACTTGTGGGCTTTG
65 GCCACTGACTTGTGGGCTTTG
* * * *
2195601 AAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGA
*
2195666 GTGCCACTGACTTGTGCGCTTTG
63 GTGCCACTGACTTGTGGGCTTTG
* * * * * * *
2195689 -AAAGAGTGCCACTGAATTGTGGGCTTCGCAATG-GTGCCACTGACTTGTAGGCTTCGAAAGGGT
1 AAAAG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGT
2195752 GCCACTGACTTGCGTGGGCTTTG
65 GCCACTGACTT--GTGGGCTTTG
* *
2195775 AAAAGGGTGCCACTGACTTGTGGGCTTT-AAAAGGGTGCCACTGACTTGTGAGCTTTGAAAAGAG
1 AAAA-GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGAG
*
2195839 TGCCACTAACTTGTGGGCTTT-
64 TGCCACTGACTTGTGGGCTTTG
** * * *
2195860 AAAAGGGTGCCACCAACTTGCGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGG
1 AAAA-GGTGCCACTGACTT--GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGA
*
2195925 GTGCCACCGACTTGTGTGGGCTTTG
63 GTGCCACTGAC-T-TGTGGGCTTTG
* * *
2195950 -AAAGGATGCCACTGACTTGTGGGCTTTG-AAAGAGTGTCACTGACTCGTGGACTTTGAAA-AGG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGA-G
* * *
2196012 TACCACTGACTTGCGTGAGCTTTA
64 TGCCACTGACTT--GTGGGCTTTG
* * * *
2196036 AAAAGGAGTGCCACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGAATTGTGGGCTTCGCAATG-
1 AAAA-G-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGA
2196099 GTGCCACTGAC
63 GTGCCACTGAC
2196110 GTTGGTGCGT
Statistics
Matches: 957, Mismatches: 105, Indels: 96
0.83 0.09 0.08
Matches are distributed among these distances:
82 34 0.04
83 65 0.07
84 128 0.13
85 68 0.07
86 148 0.15
87 232 0.24
88 146 0.15
89 95 0.10
90 3 0.00
91 8 0.01
92 4 0.00
93 22 0.02
94 1 0.00
95 3 0.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.27
Consensus pattern (85 bp):
AAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTG
CCACTGACTTGTGGGCTTTG
Found at i:2196175 original size:116 final size:115
Alignment explanation
Indices: 2194962--2196167 Score: 1209
Period size: 115 Copynumber: 10.5 Consensus size: 115
2194952 ACTGACACAT
* ** * *
2194962 GTGGGCTTTGAAAAGAGTGTTACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGG
1 GTGGGCTTTGAAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAGGGTGCCACTAACTT--GTGG
*
2195027 GCTTTGAAAG-GATGCCACTG-ATTCGTGGGCTTTGAAAGAGTGCCACTGACTT--
62 GCTTTGAAAGAG-TGCCACTGAATT-GTGGGCTTTGAAAGGGTGCCACTGACTTGC
* * * * **
2195079 GTGGGCTTTG-AAA-GGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCATGGGC-T
1 GTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
* * * *
2195141 TGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGTCACTGAC-T-C
66 TGAAAGAGTGCCACTGAATTGTGGGCTTTGAAAGGGTGCCACTGACTTGC
*
2195189 GTGGGCTTTGAAAA-GGTGCCACTGACTTGCGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTG
1 GTGGGCTTTGAAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAGG-GTGCCACTAAC-T-TGTG
* * *
2195253 GGCTTTGAAAGGGTGCCACT-AACTCGTGGGCTTTGAAAGGATGCCACTGACTT--
61 GGCTTTGAAAGAGTGCCACTGAA-TTGTGGGCTTTGAAAGGGTGCCACTGACTTGC
* * * * *
2195306 GTGGGCTTTG-AAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTTGTGTGAGC
1 GTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTG-G-GC
* * *
2195370 TTTAAAAAGAGTGCCACT-AACTTGTGGGCTTTGAAAGAGTGCCACTGAATT--
64 TTT-GAAAGAGTGCCACTGAA-TTGTGGGCTTTGAAAGGGTGCCACTGACTTGC
* * * * * * *
2195421 GTGGGCATCG-CAATGGTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTC
1 GTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
*
2195485 TGAAAGGGTGCCACT-AACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--
66 TGAAAGAGTGCCACTGAA-TTGTGGGCTTTGAAAGGGTGCCACTGACTTGC
* * * *
2195533 GTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTCACTTGTGGGCT
1 GTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCT
* *
2195598 TTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGT
65 TTGAAA-GAGTGCCACTGAATTGTGGGCTTTGAAAGG-GTGCCACTGACTTGC
* *
2195651 GTGGGCTTT-AAAAGGGTGCCACTGACTTGTGCGCTTTGAAAGAGTGCCACTGAA-TTGTGGGCT
1 GTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT-AACTTGTGGGCT
* * * * *
2195714 TCGCAATG-GTGCCACTGACTTGTAGGCTTCGAAAGGGTGCCACTGACTTGC
65 TTG-AAAGAGTGCCACTGAATTGTGGGCTTTGAAAGGGTGCCACTGACTTGC
* * *
2195765 GTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGAGCTT
1 GTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
* **
2195830 TGAAAAGAGTGCCACT-AACTTGTGGGCTTTAAAAGGGTGCCACCAACTTGC
66 TG-AAAGAGTGCCACTGAA-TTGTGGGCTTTGAAAGGGTGCCACTGACTTGC
* **
2195881 GTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGC
1 GTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAAC-T-TGTGGGC
* * *
2195946 TTTGAAAG-GATGCCACTGACTTGTGGGCTTTGAAAGAGTGTCACTGAC-T-C
64 TTTGAAAGAG-TGCCACTGAATTGTGGGCTTTGAAAGGGTGCCACTGACTTGC
* * * *
2195996 GTGGACTTTGAAAA-GGTACCACTGACTTGCGTGAGCTTTAAAAAGGAGTGCCACTAACTTGTGG
1 GTGGGCTTTGAAAAGGGTGCCACTGACTT--GTGGGCTTT-GAAAGG-GTGCCACTAACTTGTGG
* * *
2196060 GCTTTGAAAGAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACGTTG-
62 GCTTTGAAAGAGTGCCACTGAATTGTGGGCTTTGAAAGGGTGCCACTGAC-TTGC
* * * * *
2196114 GTGCG-TTCGAAATGGGGGTGCCA-TGGACGTGTGGGCTATGAAAGGGTG-CACTAA
1 GTGGGCTTTGAAA--AGGGTGCCACT-GACTTGTGGGCTTTGAAAGGGTGCCACTAA
2196168 TATTGTGGCT
Statistics
Matches: 932, Mismatches: 112, Indels: 92
0.82 0.10 0.08
Matches are distributed among these distances:
109 1 0.00
110 50 0.05
111 24 0.03
112 55 0.06
113 67 0.07
114 91 0.10
115 240 0.26
116 198 0.21
117 154 0.17
118 41 0.04
119 1 0.00
120 10 0.01
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (115 bp):
GTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
TGAAAGAGTGCCACTGAATTGTGGGCTTTGAAAGGGTGCCACTGACTTGC
Done.