Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold75
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: 1998514
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
File 11 of 12
Found at i:1733514 original size:2 final size:2
Alignment explanation
Indices: 1733507--1733533 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1733497 GTTACTTTAC
1733507 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1733534 CTATGCATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1733588 original size:6 final size:6
Alignment explanation
Indices: 1733567--1733605 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
1733557 TTAATTTATA
*
1733567 TATTTT TA-TTA T-TTTT TATTTT TATTTT TATTTT TATTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTT
1733606 ACGTAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 6 0.21
6 23 0.79
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TATTTT
Found at i:1733606 original size:16 final size:17
Alignment explanation
Indices: 1733560--1733599 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1733550 AATTAATTTA
*
1733560 ATTTATATATTTTTATT
1 ATTTATTTATTTTTATT
1733577 ATTT-TTTATTTTTATT
1 ATTTATTTATTTTTATT
1733593 -TTTATTT
1 ATTTATTT
1733600 TTATTTACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 14 0.67
17 4 0.19
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
ATTTATTTATTTTTATT
Found at i:1733858 original size:2 final size:2
Alignment explanation
Indices: 1733842--1733877 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1733832 TAATTTAATT
* *
1733842 TA TA TA AA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1733878 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1733882 original size:2 final size:2
Alignment explanation
Indices: 1733877--1733910 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1733867 ATATATATAT
1733877 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1733911 CTGCCCAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1739013 original size:20 final size:19
Alignment explanation
Indices: 1738937--1739011 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
1738927 TTTTACCCAG
1738937 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTT-A
* *
1738957 ATGTATCGATACATGTATGA
1 ATGTATCGATACAT-TTTTA
1738977 ATGTATCGATACATTCTTTA
1 ATGTATCGATACATT-TTTA
*
1738997 ATGTGTCGATACATT
1 ATGTATCGATACATT
1739012 CTGTCTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.94
21 2 0.04
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (19 bp):
ATGTATCGATACATTTTTA
Found at i:1739057 original size:20 final size:20
Alignment explanation
Indices: 1739032--1739086 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
1739022 ACCTAGATGT
* *
1739032 ATGTATCTATACATTTTTCA
1 ATGTATCGATACATTTATCA
* * *
1739052 ATGTATCGACACATGTATGA
1 ATGTATCGATACATTTATCA
1739072 ATGTATCGATACATT
1 ATGTATCGATACATT
1739087 CTGTCTTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTATCA
Found at i:1739585 original size:13 final size:14
Alignment explanation
Indices: 1739562--1739590 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1739552 ATACCTTAGC
1739562 AAAAACATCAACAA
1 AAAAACATCAACAA
1739576 AAAAAC-TCAACAA
1 AAAAACATCAACAA
1739589 AA
1 AA
1739591 GTCCACTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.72, C:0.21, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAAACATCAACAA
Found at i:1741329 original size:27 final size:27
Alignment explanation
Indices: 1741299--1741368 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
1741289 TTTATTTATC
*
1741299 GGGGATACTCTAACCCTATTCTTCCGA
1 GGGGATACTCTAACCCTATTCCTCCGA
1741326 GGGGATACTCTAACCCTATTCCTCCGA
1 GGGGATACTCTAACCCTATTCCTCCGA
*
1741353 GGGGATACTCCAACCC
1 GGGGATACTCTAACCC
1741369 ACTTTTAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.24
Consensus pattern (27 bp):
GGGGATACTCTAACCCTATTCCTCCGA
Found at i:1741509 original size:97 final size:97
Alignment explanation
Indices: 1741326--1741568 Score: 407
Period size: 97 Copynumber: 2.5 Consensus size: 97
1741316 ATTCTTCCGA
* * * *
1741326 GGGGATACTCTAACCCTATTCCTCCGAGGGGATACTCCAA-CCCACTTTTAAACACATCAAAGTT
1 GGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTT
*
1741390 TAAATCTTATTCTCAATTAAATTGTCATCATC
66 TAAATCTTATTCTCAATCAAATTGTCATCATC
1741422 GGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTT
1 GGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTT
*
1741487 TAAATCTTATTCTCACTCAAATTGTCATCATC
66 TAAATCTTATTCTCAATCAAATTGTCATCATC
* *
1741519 GGGGACACTCCAACCCCATTCCTCCGAAGGGATACTCCAACCCCGTTTTT
1 GGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTT
1741569 CAATAAAAAA
Statistics
Matches: 138, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
96 37 0.27
97 101 0.73
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (97 bp):
GGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTT
TAAATCTTATTCTCAATCAAATTGTCATCATC
Found at i:1746221 original size:92 final size:91
Alignment explanation
Indices: 1746057--1746245 Score: 272
Period size: 92 Copynumber: 2.1 Consensus size: 91
1746047 ACTCATGGTG
**
1746057 TGGTATCGATATCTAGTGTGATTGTATTGATACAGCCTTAGCAGCAGCTAAAATTCAATTTTTGG
1 TGGTATCGATATCTAGTGTGATTGTACCGATACAGCCTTAGCAGCAGCTAAAATTCAATTTTTGG
*
1746122 ACAGCAAGTATCGATACATGAAGGTT
66 ACAGCAAGTATCGATACATAAAGGTT
* * *
1746148 TGGTATCGATATCTAGTGTGATTGTACCGATACAAGCCTT-GATAGTAGCTAAAATTCGATTTTT
1 TGGTATCGATATCTAGTGTGATTGTACCGATAC-AGCCTTAG-CAGCAGCTAAAATTCAATTTTT
* * *
1746212 GGATAGCAAGTATTGATACCTAAAGGTT
64 GGACAGCAAGTATCGATACATAAAGGTT
1746240 TGGTAT
1 TGGTAT
1746246 AATTACCAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
91 32 0.37
92 55 0.63
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.34
Consensus pattern (91 bp):
TGGTATCGATATCTAGTGTGATTGTACCGATACAGCCTTAGCAGCAGCTAAAATTCAATTTTTGG
ACAGCAAGTATCGATACATAAAGGTT
Found at i:1746272 original size:20 final size:21
Alignment explanation
Indices: 1746221--1746274 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
1746211 TGGATAGCAA
*
1746221 GTATTGATACCTAAAGGTTTG
1 GTATTGATACCTAAAGGTGTG
*
1746242 GTA-TAATTACC-AAAGGTGTG
1 GTATTGA-TACCTAAAGGTGTG
1746262 GTATTGATACCTA
1 GTATTGATACCTA
1746275 GTGTGATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.35
Consensus pattern (21 bp):
GTATTGATACCTAAAGGTGTG
Found at i:1747500 original size:505 final size:505
Alignment explanation
Indices: 1746529--1747522 Score: 1487
Period size: 505 Copynumber: 2.0 Consensus size: 505
1746519 AATTTAAACA
* *
1746529 CATATTTTACATTAAGAATCATCAAAAATCATACCAAGTTTCATCTTTAGGGTTGTAATTAAATT
1 CATATTTTACATCAAGAATCATCAAAAATCATACCAAGTTTCATCTTTAGGGCTGTAATTAAATT
* *
1746594 TAAAAAAGTTTCAAAACTTAATTTGCAAAAGCCAAAGGTCATTTTCAAGAGGATTAATAGTTTGT
66 TAAAAAAGTTTCAAAACATAATTTGCAAAAACCAAAGGTCATTTTCAAGAGGATTAATAGTTTGT
* * * *
1746659 TTAGGCTTTTCAGATTATAGGTAGCTACAACCTTTCAGCACACCACTTTGCATGGCAGAACCAAT
131 TTAGGCTTTTCAGATTACAAGCAGCTACAACCTTTCAACACACCACTTTGCATGGCAGAACCAAT
* * * * * * *
1746724 AGCAATAGAAGGTAGACTGAGCATATTGCTTGGATGTCTCCTTGTGTAAAGGAGAAAACCTAACA
196 AACAATAGAAGGCAAACTGAGCATATTACTTGGATGTCTCCTTGTGCAAAAGAGAAAACCGAACA
* *
1746789 ATGCCCTTAGTTTGTCTCCTAAAGTCACTGGCTGAGTATGAGGACAAATAGAGACATGGCTAGTT
261 ATGCCCTTAGTTTGTCTCCTAAAGTCACTGGCTGAGCATGAGGACAAATAAAGACATGGCTAGTT
* * *
1746854 CAGCAAAAGAGGATTCTAAAGAGAAAGAAGAGACCCCAAAATGTTTTTCAACAACCTTCAACCTA
326 CAGCAAAAGAGGATTCCAAAGAGAAAGAAGAGACCACAAAAAGTTTTTCAACAACCTTCAACCTA
* *
1746919 AAAATACTATTTCATTAACCTTTATACTTCATTCCTATAGCTTCCCAAAACCACCACTAGAAAAC
391 AAAACACTATTTCATTAACCTTTATACTTCATTCCTATAGCTTCCCAAAACCACCACCAGAAAAC
1746984 CTTCAAAAACTCAAC-TCTCCTCACACTTTCACCCAATATTCCCATAGCTT
456 CTTCAAAAACTCAACTTC-CCTCACACTTTCACCCAATATTCCCATAGCTT
* *
1747034 CATATTTTACATCAGGAATCATCAAAAATCATACCAAGTTTCATCTTTGGGGCTGTAATTAAATT
1 CATATTTTACATCAAGAATCATCAAAAATCATACCAAGTTTCATCTTTAGGGCTGTAATTAAATT
* ** * * *
1747099 TAAATAAGTTTCAAAACATAATTTTTAAAAACTAAAGGTCATTTTCAGGAGGATTAATGGTTTGT
66 TAAAAAAGTTTCAAAACATAATTTGCAAAAACCAAAGGTCATTTTCAAGAGGATTAATAGTTTGT
* * * *
1747164 TTAGGCTTTTCAGATTGCAAGCGGCTACAACCTTTCAACATATCACTTTGCATGGCAGAACCAAT
131 TTAGGCTTTTCAGATTACAAGCAGCTACAACCTTTCAACACACCACTTTGCATGGCAGAACCAAT
* *
1747229 AACAATAGAGGGCAAACTGAGCATGTTACTTGGATGTCTCCTTGTGCAAAAGAGAAAACTCGAA-
196 AACAATAGAAGGCAAACTGAGCATATTACTTGGATGTCTCCTTGTGCAAAAGAGAAAAC-CGAAC
* * * *
1747293 AATGCCCTTGGTTTGTCTTCTAAAGTCA-TTGCTTGAGCATGAGGATAAATAAAGACATGGCTAG
260 AATGCCCTTAGTTTGTCTCCTAAAGTCACTGGC-TGAGCATGAGGACAAATAAAGACATGGCTAG
* * *
1747357 CTT-AGCAAAAGAGGATTCCAGAGAGAAAGAAGAGACTACAAAAGAGTTTTTCAACAATCTTCAA
324 -TTCAGCAAAAGAGGATTCCAAAGAGAAAGAAGAGACCACAAAA-AGTTTTTCAACAACCTTCAA
* *
1747421 CCTAAAAACACTATTTCATTAACCTTTATACTTCATT-CTCGTAGCTTCCCAAAACTACCACCAG
387 CCTAAAAACACTATTTCATTAACCTTTATACTTCATTCCT-ATAGCTTCCCAAAACCACCACCAG
1747485 AAAACCTTC-AAAACTCAACTTCCCTCACACTTTCACCC
451 AAAACCTTCAAAAACTCAACTTCCCTCACACTTTCACCC
1747523 TTAAAAAGCT
Statistics
Matches: 438, Mismatches: 45, Indels: 12
0.88 0.09 0.02
Matches are distributed among these distances:
504 3 0.01
505 344 0.79
506 91 0.21
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (505 bp):
CATATTTTACATCAAGAATCATCAAAAATCATACCAAGTTTCATCTTTAGGGCTGTAATTAAATT
TAAAAAAGTTTCAAAACATAATTTGCAAAAACCAAAGGTCATTTTCAAGAGGATTAATAGTTTGT
TTAGGCTTTTCAGATTACAAGCAGCTACAACCTTTCAACACACCACTTTGCATGGCAGAACCAAT
AACAATAGAAGGCAAACTGAGCATATTACTTGGATGTCTCCTTGTGCAAAAGAGAAAACCGAACA
ATGCCCTTAGTTTGTCTCCTAAAGTCACTGGCTGAGCATGAGGACAAATAAAGACATGGCTAGTT
CAGCAAAAGAGGATTCCAAAGAGAAAGAAGAGACCACAAAAAGTTTTTCAACAACCTTCAACCTA
AAAACACTATTTCATTAACCTTTATACTTCATTCCTATAGCTTCCCAAAACCACCACCAGAAAAC
CTTCAAAAACTCAACTTCCCTCACACTTTCACCCAATATTCCCATAGCTT
Found at i:1751180 original size:20 final size:21
Alignment explanation
Indices: 1751143--1751181 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1751133 AATTGCATTG
* *
1751143 ATACAATAAGTTACTGTATCA
1 ATACAATAAGTGAATGTATCA
1751164 ATAC-ATAAGTGAATGTAT
1 ATACAATAAGTGAATGTAT
1751182 GGATACATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (21 bp):
ATACAATAAGTGAATGTATCA
Found at i:1751273 original size:20 final size:20
Alignment explanation
Indices: 1751248--1751303 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
1751238 CTGAAAAAAT
*
1751248 TGTATCGATACATTTA-CTTA
1 TGTATCGATACATTTAGC-AA
*
1751268 TGTATCGATACATGCTAGCAA
1 TGTATCGATACAT-TTAGCAA
1751289 TGTATCGATACATTT
1 TGTATCGATACATTT
1751304 TGGGTTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
21 16 0.52
22 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTAGCAA
Found at i:1753743 original size:24 final size:25
Alignment explanation
Indices: 1753691--1753740 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1753681 CCCGTTTTTA
*
1753691 CTTCTAAAACATCGAATTTTTTATC
1 CTTCTAAAACATCGAATTTTTCATC
*
1753716 CTTCTAAAACATCGCATTTTTCATC
1 CTTCTAAAACATCGAATTTTTCATC
1753741 TTCGGGGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.42
Consensus pattern (25 bp):
CTTCTAAAACATCGAATTTTTCATC
Found at i:1753815 original size:80 final size:79
Alignment explanation
Indices: 1753716--1754428 Score: 550
Period size: 80 Copynumber: 8.9 Consensus size: 79
1753706 ATTTTTTATC
* ** *
1753716 CTTCTAAAACATCGCATTTTTCATCTTCGGGGATACTCCAACCCTACCATCTCTAAGGGGATACT
1 CTTCCAAAACATCAAATTTTTCATCTTCGGGGATACTCCAACCCTACCATCTCCAA-GGGATACT
1753781 CCAACCCCGTTTTTA
65 CCAACCCCGTTTTTA
* *
1753796 CTTCCAAAACATCAAATTTTTCATCTCCGGGGATACTCCAA-CCTCACCATCTCCGAAAGGATAC
1 CTTCCAAAACATCAAATTTTTCATCTTCGGGGATACTCCAACCCT-ACCATCTCC-AAGGGATAC
* * *
1753860 TTCAACCCTGTTTTTG
64 TCCAACCCCGTTTTTA
* ** * *
1753876 CTTTCAAAACATTGAATTTTTCATCTT-TGTGATACTCCAACCCTACCATCTCCAAGGGGATACT
1 CTTCCAAAACATCAAATTTTTCATCTTCGGGGATACTCCAACCCTACCATCTCCAA-GGGATACT
* * *
1753940 CTAACTCCATTTTTA
65 CCAACCCCGTTTTTA
* * * * * * *
1753955 TTTCTAAAACATCGAATTTTTCATC-TCTGGGGATATTCTAACCCCACCATCTCCAAAAGGATAC
1 CTTCCAAAACATCAAATTTTTCATCTTC-GGGGATACTCCAACCCTACCATCTCC-AAGGGATAC
* ***
1754019 TTCAACTTTGTTTTTA
64 TCCAACCCCGTTTTTA
* * * *
1754035 CTTCCAAAACATCAAATTTTTCATCTTTGGGGATACTCCAACCCCACCATTTTCGAAGGGATACT
1 CTTCCAAAACATCAAATTTTTCATCTTCGGGGATACTCCAACCCTACCA-TCTCCAAGGGATACT
* ***
1754100 TCAACCATATTTTTA
65 CCAACCCCGTTTTTA
* * ** **
1754115 CTTCCAAAACA-CTAAATTTTTTTATCCAT-GCAGATACTCCAATCCC-ACCATCTCCAAGAAAA
1 CTTCCAAAACATC-AAA-TTTTTCAT-CTTCGGGGATACTCCAA-CCCTACCATCTCCAAG-GGA
* *
1754177 TACTCTAACCTCGTTTTTA
61 TACTCCAACCCCGTTTTTA
* * * **
1754196 CTTCCAAAACATCAAATTTTTCATCTAT-GGGAATAGTCCAATCCC-ACCATCTCTGAAAAGATA
1 CTTCCAAAACATCAAATTTTTCATCT-TCGGGGATACTCCAA-CCCTACCATCTC-CAAGGGATA
*
1754259 CTCCAACTCCGTTTTTA
63 CTCCAACCCCGTTTTTA
* * * * *
1754276 CTTCTAAAACA-CTAAATTATTCATC-TCTGGGAATACTCTAACCCCTACC-TC-CGAAGGGATA
1 CTTCCAAAACATC-AAATTTTTCATCTTC-GGGGATACTCCAA-CCCTACCATCTCCAAGGGATA
*
1754337 CTCCAACCCCATTCTTTTTA
63 CTCCAACCCC---GTTTTTA
* * * * * ** * * *
1754357 CTTCCACAATACCGAATTCTTCATCTTTAGGGATACTCCAACCCTACTATCTCTGAGGGGATACT
1 CTTCCAAAACATCAAATTTTTCATCTTCGGGGATACTCCAACCCTACCATCTC-CAAGGGATACT
1754422 CCAACCC
65 CCAACCC
1754429 TAGTTTTCAC
Statistics
Matches: 510, Mismatches: 94, Indels: 55
0.77 0.14 0.08
Matches are distributed among these distances:
78 20 0.04
79 64 0.13
80 300 0.59
81 100 0.20
82 9 0.02
83 17 0.03
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (79 bp):
CTTCCAAAACATCAAATTTTTCATCTTCGGGGATACTCCAACCCTACCATCTCCAAGGGATACTC
CAACCCCGTTTTTA
Found at i:1754357 original size:161 final size:157
Alignment explanation
Indices: 1753716--1754426 Score: 602
Period size: 161 Copynumber: 4.5 Consensus size: 157
1753706 ATTTTTTATC
* ** *
1753716 CTTCTAAAACATCGCATTTTTCATCTTCGGGGATACTCCAACCCTACCATCTCT-AAGGGGATAC
1 CTTCCAAAACATCAAATTTTTCATCTTTGGGGATACTCCAACCCTACCATCTCTGAAGGGGATAC
* * * *
1753780 TCCAACCCCGTTTTTACTTCCAAAACATCAAATTTTTCATCTCCGGGGATACTCCAACCTCACCA
66 TCCAACTCCATTTTTACTTCCAAAACATCAAATTTTTCATCTCTGGGAATACTCCAA-C-C-CCA
* * * *
1753845 TCTCCGAAAGGATACTTCAACCCTGTTTTTG
128 CCTCCGAAAGGATACTCCAA-CCTCTTTTTA
* ** * *
1753876 CTTTCAAAACATTGAATTTTTCATCTTT-GTGATACTCCAACCCTACCATCTC-CAAGGGGATAC
1 CTTCCAAAACATCAAATTTTTCATCTTTGGGGATACTCCAACCCTACCATCTCTGAAGGGGATAC
* * * * * * *
1753939 TCTAACTCCATTTTTATTTCTAAAACATCGAATTTTTCATCTCTGGGGATATTCTAACCCCACCA
66 TCCAACTCCATTTTTACTTCCAAAACATCAAATTTTTCATCTCTGGGAATACTCCAACCCCA-C-
* * * *
1754004 TCTCCAAAAGGATACTTCAACTTTGTTTTTA
129 -CTCCGAAAGGATACTCCAAC-CTCTTTTTA
* *
1754035 CTTCCAAAACATCAAATTTTTCATCTTTGGGGATACTCCAACCCCACCAT-TTTCGAA-GGGATA
1 CTTCCAAAACATCAAATTTTTCATCTTTGGGGATACTCCAACCCTACCATCTCT-GAAGGGGATA
* * * * *
1754098 CTTCAAC-CATATTTTTACTTCCAAAACA-CTAAATTTTTTTATC-CAT-GCAGATACTCCAATC
65 CTCCAACTC-CATTTTTACTTCCAAAACATC-AAA-TTTTTCATCTC-TGGGA-ATACTCCAACC
* ** *
1754159 CCACCATCTCCAAGAAAATACTCTAACCTCGTTTTTA
125 CCACC-TC-CGAA-AGGATACTCCAACCTC-TTTTTA
* * * **
1754196 CTTCCAAAACATCAAATTTTTCATCTATGGGAATAGTCCAATCCC-ACCATCTCTGAA-AAGATA
1 CTTCCAAAACATCAAATTTTTCATCTTTGGGGATACTCCAA-CCCTACCATCTCTGAAGGGGATA
* * * *
1754259 CTCCAACTCCGTTTTTACTTCTAAAACA-CTAAATTATTCATCTCTGGGAATACTCTAACCCCTA
65 CTCCAACTCCATTTTTACTTCCAAAACATC-AAATTTTTCATCTCTGGGAATACTCCAACCCC-A
*
1754323 CCTCCGAAGGGATACTCCAACCCCATTCTTTTTA
128 CCTCCGAAAGGATACTCCAA--CC--TCTTTTTA
* * * * * * *
1754357 CTTCCACAATACCGAATTCTTCATCTTTAGGGATACTCCAACCCTACTATCTCTG-AGGGGATAC
1 CTTCCAAAACATCAAATTTTTCATCTTTGGGGATACTCCAACCCTACCATCTCTGAAGGGGATAC
1754421 TCCAAC
66 TCCAAC
1754427 CCTAGTTTTC
Statistics
Matches: 445, Mismatches: 77, Indels: 57
0.77 0.13 0.10
Matches are distributed among these distances:
156 3 0.01
157 1 0.00
158 11 0.02
159 139 0.31
160 105 0.24
161 178 0.40
162 8 0.02
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (157 bp):
CTTCCAAAACATCAAATTTTTCATCTTTGGGGATACTCCAACCCTACCATCTCTGAAGGGGATAC
TCCAACTCCATTTTTACTTCCAAAACATCAAATTTTTCATCTCTGGGAATACTCCAACCCCACCT
CCGAAAGGATACTCCAACCTCTTTTTA
Found at i:1760282 original size:2 final size:2
Alignment explanation
Indices: 1760275--1760309 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1760265 CAACCAACTT
1760275 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1760310 GTATGGTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1762792 original size:23 final size:25
Alignment explanation
Indices: 1762751--1762796 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
1762741 ATATTCAGAG
1762751 TATTATATATTTATATAAATTTTTA
1 TATTATATATTTATATAAATTTTTA
*
1762776 TATTA-AT-TTTATGTAAATTTT
1 TATTATATATTTATATAAATTTT
1762797 GACACATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 2 0.10
25 5 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TATTATATATTTATATAAATTTTTA
Found at i:1763608 original size:14 final size:14
Alignment explanation
Indices: 1763589--1763717 Score: 105
Period size: 14 Copynumber: 9.2 Consensus size: 14
1763579 TAGTACATAC
1763589 ATATATATATATAT
1 ATATATATATATAT
* *
1763603 ATATATACATACAT
1 ATATATATATATAT
* *
1763617 ATATACATATATGT
1 ATATATATATATAT
* * *
1763631 ACATATACATATCT
1 ATATATATATATAT
* *
1763645 ACATATACATATAT
1 ATATATATATATAT
* *
1763659 ATATATATATGTAC
1 ATATATATATATAT
1763673 ATATATATATATAT
1 ATATATATATATAT
** * *
1763687 ATCCATGTATGTAT
1 ATATATATATATAT
* *
1763701 ATATATAAATTTAT
1 ATATATATATATAT
1763715 ATA
1 ATA
1763718 AATAGTTATA
Statistics
Matches: 89, Mismatches: 26, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 89 1.00
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (14 bp):
ATATATATATATAT
Found at i:1763662 original size:4 final size:4
Alignment explanation
Indices: 1763589--1763717 Score: 105
Period size: 4 Copynumber: 32.2 Consensus size: 4
1763579 TAGTACATAC
* * * * *
1763589 ATAT ATAT ATAT ATAT ATAT ACAT ACAT ATAT ACAT ATAT GTAC ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * *
1763637 ACAT ATCT ACAT ATAC ATAT ATAT ATAT ATAT GTAC ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
** * * * *
1763685 ATAT CCAT GTAT GTAT ATAT ATAA ATTT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
1763718 AATAGTTATA
Statistics
Matches: 96, Mismatches: 29, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
4 96 1.00
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (4 bp):
ATAT
Found at i:1764441 original size:3 final size:3
Alignment explanation
Indices: 1764433--1764457 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1764423 TTAAGCATAC
1764433 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1764458 AAATCAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1769704 original size:21 final size:21
Alignment explanation
Indices: 1769679--1769719 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1769669 CTCCTTAAAT
1769679 TAATTTAA-ATAAATATTTATA
1 TAATTTAATA-AAATATTTATA
*
1769700 TAATTTTATAAAATATTTAT
1 TAATTTAATAAAATATTTAT
1769720 TTTAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATTTAATAAAATATTTATA
Found at i:1769790 original size:24 final size:23
Alignment explanation
Indices: 1769761--1769810 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
1769751 ATTTTTTTAT
1769761 AAAAGAGAAAAAAGTAAAAAATAA
1 AAAAGAGAAAAAAGTAAAAAA-AA
*
1769785 AAAAGAGAAAAAAGTTAAAAAAA
1 AAAAGAGAAAAAAGTAAAAAAAA
1769808 AAA
1 AAA
1769811 GATGACATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (23 bp):
AAAAGAGAAAAAAGTAAAAAAAA
Found at i:1771728 original size:37 final size:38
Alignment explanation
Indices: 1771678--1771757 Score: 119
Period size: 40 Copynumber: 2.1 Consensus size: 38
1771668 AGGTTTTAAA
1771678 TTTTTGTCATGTT-CCTTCACATAATGC-AAATCTTTTG
1 TTTTTGTCATGTTCCCTTCACATAATGCAAAAT-TTTTG
1771715 TTTTTGTCATGTTCCACCTTCACATAATGCAAAATTTTTG
1 TTTTTGTCATGTT-C-CCTTCACATAATGCAAAATTTTTG
1771755 TTT
1 TTT
1771758 AATACTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
37 13 0.33
40 22 0.56
41 4 0.10
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.49
Consensus pattern (38 bp):
TTTTTGTCATGTTCCCTTCACATAATGCAAAATTTTTG
Found at i:1773512 original size:21 final size:22
Alignment explanation
Indices: 1773488--1773528 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1773478 TATTAAAATG
1773488 TTTAATA-ATGTTTAATTTTCA
1 TTTAATATATGTTTAATTTTCA
*
1773509 TTTAATATATTTTTAATTTT
1 TTTAATATATGTTTAATTTT
1773529 TTTATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTAATATATGTTTAATTTTCA
Found at i:1773840 original size:153 final size:154
Alignment explanation
Indices: 1773561--1773867 Score: 528
Period size: 153 Copynumber: 2.0 Consensus size: 154
1773551 GCTATAATTA
* * *
1773561 TGTCGGTCAATTGCTAATATGCTTTTTTACTTCAACATTAAGAATTAAATGGCATATCGTTTTAC
1 TGTCGATCAATTGCTAATATACTTCTTTACTTCAACATTAAGAATTAAATGGCATATCGTTTTAC
* *
1773626 TTTTTGTAGTGTATGGCATTTACGTATGTGATGTGACTATAACTAACTGCTAAGTTATTCTATTT
66 TTTTTGTAGTGTATGGCATTTACATATGTGATGTGACTATAACTAACTACTAAGTTATTCTATTT
1773691 ATCTTACATTTTATAGTGTATTTT
131 ATCTTACATTTTATAGTGTATTTT
*
1773715 TGTCGATCAATTGCTAATATACTTCTTTAGTTCAACATTAAGAATTAAATGGCATATCG-TTTAC
1 TGTCGATCAATTGCTAATATACTTCTTTACTTCAACATTAAGAATTAAATGGCATATCGTTTTAC
1773779 TTTTTGTAGTGTATGGCATTTACATATGTGATGTGACTA-ACACTAACTACTAAGTTATTCTATT
66 TTTTTGTAGTGTATGGCATTTACATATGTGATGTGACTATA-ACTAACTACTAAGTTATTCTATT
*
1773843 TATCTTACCTTTTATAGTGTATTTT
130 TATCTTACATTTTATAGTGTATTTT
1773868 GGTCATACCT
Statistics
Matches: 145, Mismatches: 7, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
152 1 0.01
153 89 0.61
154 55 0.38
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (154 bp):
TGTCGATCAATTGCTAATATACTTCTTTACTTCAACATTAAGAATTAAATGGCATATCGTTTTAC
TTTTTGTAGTGTATGGCATTTACATATGTGATGTGACTATAACTAACTACTAAGTTATTCTATTT
ATCTTACATTTTATAGTGTATTTT
Found at i:1777303 original size:2 final size:2
Alignment explanation
Indices: 1777291--1777329 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1777281 ACCCTTATCC
*
1777291 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1777330 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1777861 original size:10 final size:10
Alignment explanation
Indices: 1777826--1777854 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1777816 AGTTTTGTCA
1777826 TAAAAAAATT
1 TAAAAAAATT
1777836 TAAAAAAATT
1 TAAAAAAATT
1777846 TAAAAAAAT
1 TAAAAAAAT
1777855 GAAAAAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAAAAATT
Found at i:1785855 original size:22 final size:22
Alignment explanation
Indices: 1785830--1785892 Score: 56
Period size: 24 Copynumber: 2.7 Consensus size: 22
1785820 TAAATTATAG
1785830 AAATTTTGCACATATTAATTCA
1 AAATTTTGCACATATTAATTCA
*
1785852 AAATTATTGCCAGCATA-TGATTCA
1 AAATT-TTG-CA-CATATTAATTCA
* *
1785876 AAACTTTTTCATATATT
1 AAA-TTTTGCACATATT
1785893 TCAACATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
22 8 0.24
23 6 0.18
24 13 0.39
25 6 0.18
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.41
Consensus pattern (22 bp):
AAATTTTGCACATATTAATTCA
Found at i:1788808 original size:36 final size:35
Alignment explanation
Indices: 1788739--1788817 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 35
1788729 GTTATGCAAA
* *
1788739 ATTTA-ATTTAATTTAAAATATAAATTTTTAATTT
1 ATTTATATTTAATTTAAAATATAAAATTTAAATTT
1788773 A-TTATATTTATATTTATAAATA-AATAATTTAAATTT
1 ATTTATATTTA-ATTTA-AAATATAA-AATTTAAATTT
1788809 ATTTATATT
1 ATTTATATT
1788818 CGTTTATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
33 3 0.08
34 6 0.16
35 7 0.18
36 15 0.39
37 7 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
ATTTATATTTAATTTAAAATATAAAATTTAAATTT
Found at i:1788846 original size:12 final size:12
Alignment explanation
Indices: 1788829--1788873 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1788819 GTTTATATTA
1788829 TATTTTTTAAAT
1 TATTTTTTAAAT
1788841 TATTTTTTAAATT
1 TATTTTTTAAA-T
*
1788854 TAATTTTT-AAT
1 TATTTTTTAAAT
*
1788865 AATTTTTTA
1 TATTTTTTA
1788874 TTAAATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 7 0.25
12 13 0.46
13 8 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTTTTAAAT
Found at i:1788860 original size:13 final size:12
Alignment explanation
Indices: 1788832--1788885 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
1788822 TATATTATAT
*
1788832 TTTTTAAATTAT
1 TTTTTAAATTAA
1788844 TTTTTAAATTTAA
1 TTTTTAAA-TTAA
1788857 TTTTT-AA-TAA
1 TTTTTAAATTAA
*
1788867 TTTTT-TATTAA
1 TTTTTAAATTAA
*
1788878 ATTTTAAA
1 TTTTTAAA
1788886 ATATTTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 9 0.26
11 7 0.20
12 11 0.31
13 8 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTTTAAATTAA
Found at i:1788868 original size:27 final size:26
Alignment explanation
Indices: 1788830--1788881 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
1788820 TTTATATTAT
*
1788830 ATTTTTTAAATTATTTT-TTAAATTTA
1 ATTTTTAAAATT-TTTTATTAAATTTA
1788856 ATTTTTAATAATTTTTTATTAAATTT
1 ATTTTTAA-AATTTTTTATTAAATTT
1788882 TAAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
ATTTTTAAAATTTTTTATTAAATTTA
Found at i:1788883 original size:46 final size:47
Alignment explanation
Indices: 1788820--1788938 Score: 120
Period size: 46 Copynumber: 2.5 Consensus size: 47
1788810 TTTATATTCG
* *
1788820 TTTATATTATATTTTTTAAATTATTTTTTAAATTTA-A-TTTTTAATAA
1 TTTATATTATA-ATTTTAAATTATTTTATAAATTTATATTTTTTAAT-A
* * *
1788867 TTTTTTATTA-AATTTTAAAATA-TTTATAACTTTATATTTTTTAATA
1 -TTTATATTATAATTTTAAATTATTTTATAAATTTATATTTTTTAATA
*
1788913 TTTATATTATAATATTAAATATATTT
1 TTTATATTATAATTTTAAAT-TATTT
1788939 ATTTTTTATA
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
45 18 0.31
46 19 0.33
47 11 0.19
48 10 0.17
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (47 bp):
TTTATATTATAATTTTAAATTATTTTATAAATTTATATTTTTTAATA
Found at i:1789003 original size:19 final size:19
Alignment explanation
Indices: 1788956--1789005 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1788946 ATATAATAAA
1788956 AATTATATAA--AATATAT
1 AATTATATAATTAATATAT
* *
1788973 AAATATAAAATTAATATAT
1 AATTATATAATTAATATAT
*
1788992 ATTTATATAATTAA
1 AATTATATAATTAA
1789006 AAATAAGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 8 0.31
19 18 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTATATAATTAATATAT
Found at i:1789330 original size:38 final size:38
Alignment explanation
Indices: 1789275--1789362 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 38
1789265 TTGACATGAA
* * *
1789275 ATTTTTTTTATTGTTTATTA-TATAATTTAAATAATAAT
1 ATTTTTTATATTGTTTATAATTA-AATTTAAATAAAAAT
1789313 ATTTTTATATATT-TTTATAATTAAATTTAAATAAAAAT
1 ATTTTT-TATATTGTTTATAATTAAATTTAAATAAAAAT
1789351 ATTATTTT-TATT
1 ATT-TTTTATATT
1789363 AGTAATTTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
37 4 0.09
38 30 0.68
39 10 0.23
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (38 bp):
ATTTTTTATATTGTTTATAATTAAATTTAAATAAAAAT
Found at i:1790323 original size:18 final size:19
Alignment explanation
Indices: 1790281--1790317 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1790271 AAATAAATAT
1790281 TTTAT-AAATTATTTAAAA
1 TTTATAAAATTATTTAAAA
1790299 TTTATAAAATTAATTTAAA
1 TTTATAAAATT-ATTTAAA
1790318 TTATAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 5 0.29
20 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTATAAAATTATTTAAAA
Found at i:1790846 original size:10 final size:9
Alignment explanation
Indices: 1790789--1790853 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
1790779 GACAGAATTC
*
1790789 AATTTAAAA
1 AATTAAAAA
*
1790798 AA-TAAATAT
1 AATTAAA-AA
1790807 AATTAAGAAA
1 AATTAA-AAA
*
1790817 TATTAAAAA
1 AATTAAAAA
*
1790826 AATTTCAAAA
1 AA-TTAAAAA
*
1790836 AATTAATAA
1 AATTAAAAA
1790845 AATTAAAAA
1 AATTAAAAA
1790854 TAAAATAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
8 3 0.07
9 22 0.51
10 17 0.40
11 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (9 bp):
AATTAAAAA
Found at i:1792189 original size:16 final size:16
Alignment explanation
Indices: 1792170--1792244 Score: 73
Period size: 16 Copynumber: 4.8 Consensus size: 16
1792160 ATTGATTTAT
1792170 TTTTAGATTTAAATTA
1 TTTTAGATTTAAATTA
* *
1792186 TTTTAAATTTATATTA
1 TTTTAGATTTAAATTA
* *
1792202 TTTTAGATTTATA-TC
1 TTTTAGATTTAAATTA
* *
1792217 TTTTAGAGTCAAATGTA
1 TTTTAGATTTAAAT-TA
1792234 TTTT-GATTTAA
1 TTTTAGATTTAA
1792245 GTTTTTCATA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
15 11 0.23
16 31 0.66
17 5 0.11
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (16 bp):
TTTTAGATTTAAATTA
Found at i:1792196 original size:22 final size:22
Alignment explanation
Indices: 1792154--1792196 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1792144 AAATAAATGA
**
1792154 ATTTAAATTGATTTATTTTTAG
1 ATTTAAATTGATTTAAATTTAG
1792176 ATTTAAATT-ATTTTAAATTTA
1 ATTTAAATTGA-TTTAAATTTA
1792197 TATTATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
ATTTAAATTGATTTAAATTTAG
Found at i:1792590 original size:2 final size:2
Alignment explanation
Indices: 1792585--1792616 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1792575 TATAAGTTTG
1792585 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1792617 CTACTTATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1792701 original size:28 final size:28
Alignment explanation
Indices: 1792664--1792736 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
1792654 TTTTATTATT
*
1792664 TTACAATTAATAATTATTAGGTTACATAC
1 TTACAATTAATAATTATTA-CTTACATAC
* *
1792693 TTA-TATTAATAATTATTACTTATATAC
1 TTACAATTAATAATTATTACTTACATAC
*
1792720 TTACAATTAATACTTAT
1 TTACAATTAATAATTAT
1792737 AAACAATTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
27 10 0.26
28 25 0.66
29 3 0.08
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.47
Consensus pattern (28 bp):
TTACAATTAATAATTATTACTTACATAC
Found at i:1792744 original size:17 final size:18
Alignment explanation
Indices: 1792722--1792771 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
1792712 TTATATACTT
*
1792722 ACAATTAATACTTAT-AA
1 ACAATTAATAATTATAAA
1792739 ACAATTAATAATTATAAA
1 ACAATTAATAATTATAAA
1792757 ACAATTAATAATTAT
1 ACAATTAATAATTAT
1792772 TTGGTTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 14 0.45
18 17 0.55
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (18 bp):
ACAATTAATAATTATAAA
Found at i:1793085 original size:22 final size:22
Alignment explanation
Indices: 1793049--1793090 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1793039 TTATTTTTTA
1793049 TTTTTATTTATTTTATTATATT
1 TTTTTATTTATTTTATTATATT
1793071 TTTTTAGTTTA-TTTATTATA
1 TTTTTA-TTTATTTTATTATA
1793091 ACTTTTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTTATTTATTTTATTATATT
Found at i:1793096 original size:22 final size:22
Alignment explanation
Indices: 1793049--1793098 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1793039 TTATTTTTTA
**
1793049 TTTTTATTTATTTTATTATATT
1 TTTTTATTTATTTTATTATAAC
1793071 TTTTTAGTTTA-TTTATTATAAC
1 TTTTTA-TTTATTTTATTATAAC
1793093 TTTTTA
1 TTTTTA
1793099 AGATTGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTTATTTATTTTATTATAAC
Found at i:1793141 original size:19 final size:19
Alignment explanation
Indices: 1793113--1793149 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1793103 TGAATTTGAA
1793113 AATTTGAATTTCAAAAATC
1 AATTTGAATTTCAAAAATC
*
1793132 AATTTTAATTTCAAAAAT
1 AATTTGAATTTCAAAAAT
1793150 AATGTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (19 bp):
AATTTGAATTTCAAAAATC
Found at i:1793159 original size:18 final size:19
Alignment explanation
Indices: 1793119--1793159 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1793109 TGAAAATTTG
* *
1793119 AATTTCAAAAATCAATTTT
1 AATTTCAAAAATCAATGTA
1793138 AATTTCAAAAAT-AATGTA
1 AATTTCAAAAATCAATGTA
1793156 AATT
1 AATT
1793160 ATGTAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (19 bp):
AATTTCAAAAATCAATGTA
Found at i:1793924 original size:6 final size:7
Alignment explanation
Indices: 1793903--1793934 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1793893 TATTGTTTAC
1793903 TTTATTT
1 TTTATTT
1793910 TTTATTT
1 TTTATTT
1793917 TTTATTT
1 TTTATTT
*
1793924 TTTATAT
1 TTTATTT
1793931 TTTA
1 TTTA
1793935 ATTTACAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTATTT
Found at i:1794455 original size:22 final size:21
Alignment explanation
Indices: 1794430--1794477 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
1794420 TTATTTATAC
1794430 TTTTACATTAAATAATTCAAGT
1 TTTTACATTAAA-AATTCAAGT
** * *
1794452 TTTTGGATTATAAATTCGAGT
1 TTTTACATTAAAAATTCAAGT
1794473 TTTTA
1 TTTTA
1794478 TGAAATTCAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.50
Consensus pattern (21 bp):
TTTTACATTAAAAATTCAAGT
Found at i:1795233 original size:15 final size:15
Alignment explanation
Indices: 1795215--1795288 Score: 87
Period size: 15 Copynumber: 4.8 Consensus size: 15
1795205 TTTAAATTAG
1795215 TTTAAATTAAAATAA
1 TTTAAATTAAAATAA
*
1795230 TTTAAATTTAAAAAAA
1 TTTAAA-TTAAAATAA
1795246 TTTAAATTCAAAAT-A
1 TTTAAATT-AAAATAA
*
1795261 TCTAAATCTAAAATAA
1 TTTAAAT-TAAAATAA
*
1795277 TTTAACTTAAAA
1 TTTAAATTAAAA
1795289 CTTTTCTAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
15 25 0.50
16 25 0.50
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTAAATTAAAATAA
Found at i:1795240 original size:31 final size:30
Alignment explanation
Indices: 1795203--1795288 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 30
1795193 TCTAATCCTG
* * *
1795203 AATTTAAATTAGTTTAAATTAAAATAATTTA
1 AATTTAAAATAATTTAAATTAAAAT-ATCTA
*
1795234 AATTTAAAAAAATTTAAATTCAAAATATCTA
1 AATTTAAAATAATTTAAATT-AAAATATCTA
* *
1795265 AATCTAAAATAATTTAACTTAAAA
1 AATTTAAAATAATTTAAATTAAAA
1795289 CTTTTCTAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
30 4 0.09
31 38 0.81
32 5 0.11
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (30 bp):
AATTTAAAATAATTTAAATTAAAATATCTA
Found at i:1797820 original size:14 final size:15
Alignment explanation
Indices: 1797801--1797830 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1797791 GATAATCACA
1797801 ACTTAAAT-TTTTTT
1 ACTTAAATGTTTTTT
1797815 ACTTAAATGTTTTTT
1 ACTTAAATGTTTTTT
1797830 A
1 A
1797831 GTGTTTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (15 bp):
ACTTAAATGTTTTTT
Found at i:1798428 original size:48 final size:47
Alignment explanation
Indices: 1798310--1798428 Score: 116
Period size: 48 Copynumber: 2.4 Consensus size: 47
1798300 AAGAGGGCTA
*
1798310 TATATACATATTTTTGATATTTTAAAAATTTAAAATTTAATTTAATTAATT
1 TATATA-ATATTTTT-ATA-TTTAAAAATTTAAAATTTAATTT-ATTAAGT
* **
1798361 TAAATAAT-TAATTAGTATTTAAAAATTTTAAAATTTAAATTT-TTAAGT
1 TATATAATATTTTTA-TATTTAAAAA-TTTAAAATTT-AATTTATTAAGT
*
1798409 TATATAATATTTTTTTATTT
1 TATATAATATTTTTATATTT
1798429 TTAAAATATA
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
48 26 0.46
49 18 0.32
50 7 0.12
51 5 0.09
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (47 bp):
TATATAATATTTTTATATTTAAAAATTTAAAATTTAATTTATTAAGT
Found at i:1798435 original size:49 final size:48
Alignment explanation
Indices: 1798310--1798435 Score: 116
Period size: 49 Copynumber: 2.6 Consensus size: 48
1798300 AAGAGGGCTA
* *
1798310 TATATACATATTTTTGATATTTTAAAAATTTAAAATTTAATTTAATTAAT
1 TATATA-ATATTTTTTATATTTTAAAATTTTAAAATTTAATTT-ATTAAT
** *
1798360 T-TA-AATAATTAATTAGTATTTAAAAATTTTAAAATTTAAATTT-TTAAGT
1 TATATAAT-ATTTTTTA-TATTTTAAAATTTTAAAATTT-AATTTATTAA-T
1798409 TATATAATATTTTTT-TATTTTTAAAAT
1 TATATAATATTTTTTATA-TTTTAAAAT
1798436 ATATTTTTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 15
0.73 0.10 0.18
Matches are distributed among these distances:
47 2 0.03
48 12 0.20
49 31 0.51
50 13 0.21
51 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (48 bp):
TATATAATATTTTTTATATTTTAAAATTTTAAAATTTAATTTATTAAT
Found at i:1799229 original size:22 final size:24
Alignment explanation
Indices: 1799182--1799236 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1799172 GGGAGAGGTT
1799182 TTTTTTTAATTATAATAATAATAA
1 TTTTTTTAATTATAATAATAATAA
*
1799206 TTTTTTTAATTCTGAA-AAT-A-AA
1 TTTTTTTAATTAT-AATAATAATAA
1799228 TTTTTTTAA
1 TTTTTTTAA
1799237 AAATATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 11 0.38
23 1 0.03
24 15 0.52
25 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTTTTAATTATAATAATAATAA
Found at i:1799245 original size:13 final size:13
Alignment explanation
Indices: 1799225--1799261 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1799215 TTCTGAAAAT
1799225 AAAT-TTTTTTAA
1 AAATATTTTTTAA
*
1799237 AAATA-TTTTTCA
1 AAATATTTTTTAA
1799249 AAATATTTTTTAA
1 AAATATTTTTTAA
1799262 TCATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (13 bp):
AAATATTTTTTAA
Found at i:1799420 original size:18 final size:18
Alignment explanation
Indices: 1799397--1799443 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1799387 TTTTTAATAA
1799397 AATTAAGAAAAAAAATTT
1 AATTAAGAAAAAAAATTT
***
1799415 AATTAAGTTTAAAAATTT
1 AATTAAGAAAAAAAATTT
1799433 ATATTAA-AAAA
1 A-ATTAAGAAAA
1799444 TTAAATTATT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (18 bp):
AATTAAGAAAAAAAATTT
Found at i:1799470 original size:75 final size:78
Alignment explanation
Indices: 1799315--1799480 Score: 193
Period size: 75 Copynumber: 2.2 Consensus size: 78
1799305 ATCTGATATG
* * *
1799315 ATAAAATTAAAAAAATAAAATTTAATTAAATTTTAAAAAATTTATATTGAAATCAATATATTAAT
1 ATAAAATTAAAAAAATAAAATTTAATTAAAGTTTAAAAAATTTATATTAAAATAAATATATTAAT
*
1799380 CATCAATTTTTTA
66 CATCAATTATTTA
*
1799393 ATAAAATTAAGAAAA-AAAATTTAATT-AAGTTT-AAAAATTTATATTAAAAAATTAAAT-TATT
1 ATAAAATTAAAAAAATAAAATTTAATTAAAGTTTAAAAAATTTATATT--AAAA-TAAATATATT
* *
1799454 AATTAT-TA-TATTTA
63 AATCATCAATTATTTA
1799468 ATAAAA-TAAAAAA
1 ATAAAATTAAAAAA
1799481 TTTTAAACTA
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
74 6 0.08
75 24 0.31
76 6 0.08
77 23 0.30
78 18 0.23
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (78 bp):
ATAAAATTAAAAAAATAAAATTTAATTAAAGTTTAAAAAATTTATATTAAAATAAATATATTAAT
CATCAATTATTTA
Found at i:1799508 original size:16 final size:15
Alignment explanation
Indices: 1799469--1799508 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
1799459 TTATATTTAA
1799469 TAAAATAAAAAATTT
1 TAAAATAAAAAATTT
*
1799484 TAAACTAAAAAATTT
1 TAAAATAAAAAATTT
1799499 TAAAAGTAAA
1 TAAAA-TAAA
1799509 GATCATAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (15 bp):
TAAAATAAAAAATTT
Found at i:1799637 original size:25 final size:24
Alignment explanation
Indices: 1799609--1799676 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
1799599 TAATTCTATG
1799609 AGTTTAATTTATTTTTATTTATAAA
1 AGTTTAATTTATTTTTATTT-TAAA
*
1799634 AGTTTAATTT-TGTTTTATTTTAAG
1 AGTTTAATTTAT-TTTTATTTTAAA
* *
1799658 GGATT-ATTTATTTTTATTT
1 AGTTTAATTTATTTTTATTT
1799677 GTAAGATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
23 12 0.32
24 8 0.21
25 18 0.47
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (24 bp):
AGTTTAATTTATTTTTATTTTAAA
Found at i:1799780 original size:73 final size:72
Alignment explanation
Indices: 1799695--1801243 Score: 1332
Period size: 73 Copynumber: 21.5 Consensus size: 72
1799685 AATTTACTTA
** * *
1799695 AAGGTAGT-ATTTATTTTTATTAATAGAATTTTAAATTTGTTTGTATGGTATGATTATACGAGTT
1 AAGGTA-TAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTT-TTTGGTATGATTATACGAGTT
*
1799759 TAAATTTTG
64 TAAATTTTT
* * * * * *
1799768 AAGGTATAATTTATTTTTATTTGTAAAAGTTTAACA-TTGTTTTTT-ATTTGATTATGCAAGTAT
1 AAGGTATAATTTATTTTTATTTGTAGAAGTTTAA-ATTTGTTTTTTGGTATGATTATACGAGTTT
1799831 AAATTTTT
65 AAATTTTT
* * * *
1799839 -AGGATATAATTTATTTTGATTTGTA-AATGTTTAAATATGTTTTTAGGTATGATTATATGAGTT
1 AAGG-TATAATTTATTTTTATTTGTAGAA-GTTTAAATTTGTTTTTTGGTATGATTATACGAGTT
*
1799902 TAAAATTTTG
64 T-AAATTTTT
* * * * ** * * * *
1799912 AAAGTGTAATTTA-TTTTATTTGTAAAAGTTTACATTTAATTTTTAGTTTGATTATGCAAGTTTA
1 AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTTGGTATGATTATACGAGTTTA
1799976 AATTTTT
66 AATTTTT
* * * * * * * *
1799983 AAGGTATTATTCATCTTTATTTGTAGAAGTTTAAATTTATTTTTTAAGTATCATCACACGAGTTT
1 AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTT-GGTATGATTATACGAGTTT
1800048 AAATTTTT
65 AAATTTTT
** * *
1800056 AAAATATAATTTATTTTTATTTATAGAAGTTTAAATGTAT-TTTTTTGGTATGATTATAAGAGTT
1 AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAAT-T-TGTTTTTTGGTATGATTATACGAGTT
*
1800120 TATATTTTT
64 TAAATTTTT
* * * * * * *
1800129 GATGGCAT-A---A-TTTTATTTGTAAAAGTTTAAATTTATTTTTTGGTTTAATTATACAAGTTT
1 -AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTTGGTATGATTATACGAGTTT
*
1800189 AGATTTTT
65 AAATTTTT
* * * * * * *
1800197 -AGGCTATTATTTATCTTCA--T-T--AAGTTTAAATTTATTTTTTGGGTTTGATTATATGAATT
1 AAGG-TATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTT-GGTATGATTATACGAGTT
1800256 TAAA-TTTT
64 TAAATTTTT
* * *
1800264 ATAGGTATAATTTATTTTTACTTATAGAAGTTTAAATGTGTTTTTTGGGGTATGATTATACGAGT
1 A-AGGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTT--GGTATGATTATACGAGT
*
1800329 TCAAATTTTT
63 TTAAATTTTT
* * * * *
1800339 ATGGTATAATTTATTTTTATTTGTAGATGTTTAAATGTGTGTTTCTCGATATGATTATACGAGTT
1 AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAAT-T-TGTTTTTTGGTATGATTATACGAGTT
*
1800404 TATATTTTT
64 TAAATTTTT
* * * *
1800413 ATA-GTATAATTTATCTTTATTTGTAGAAATATAAATTTATTTTTTTGGT-TGATTATACGAGTT
1 A-AGGTATAATTTATTTTTATTTGTAGAAGTTTAAATTT-GTTTTTTGGTATGATTATACGAGTT
1800476 TAAATTTTT
64 TAAATTTTT
* * * * * **
1800485 -AGGCTATTATTTATCTTTATCTGTAGAAGTTTAAATTTATTTTTTTTGGTATTATTATATAAGT
1 AAGG-TATAATTTATTTTTATTTGTAGAAGTTTAAA-TT-TGTTTTTTGGTATGATTATACGAGT
1800549 TTAAATTTTT
63 TTAAATTTTT
** * *
1800559 AAAATATAATTTATTTTTATTTGCAGAAGTTT-GATTGTGTTTTTTGGGTATGATTATACGAGTT
1 AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATT-TGTTTTTT-GGTATGATTATACGAGTT
*
1800623 TATATTTTT
64 TAAATTTTT
* *
1800632 GATGATATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTTGAGT-TGATTATAC-AGTT
1 -AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTTG-GTATGATTATACGAGTT
1800695 TAAATTTTT
64 TAAATTTTT
* * * *
1800704 -AGGATATATTTTATTTTT-TTT-CAGAAGTTTAAATATGTTTTTTGGGTATGATTATACAAGTT
1 AAGG-TATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTT-GGTATGATTATACGAGTT
* *
1800766 TATATTCTT
64 TAAATTTTT
* * * *
1800775 AATGGTGTAATTTATTTTTATTTATAGAAGTTTAAATTT-TTTTTGGGTCA--ATTATACGATTT
1 AA-GGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTTGGT-ATGATTATACGAGTT
1800837 TAAATTTTT
64 TAAATTTTT
* * * * * ** *
1800846 -AGCGTATTATTTATCTTTATTTGTAGAAGTTTAAATTTATTTTTTTGTATAATTATATAAATTT
1 AAG-GTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTTGGTATGATTATACGAGTTT
*
1800910 AAA-TTTC
65 AAATTTTT
* * * *** *
1800917 AGGGTATAATTTATTTTTATTTATAGAAATTTAAATACCTTTTTGGGT-TGATTATACGAGTTTA
1 AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTTGGTATGATTATACGAGTTTA
1800981 AATTTTT
66 AATTTTT
* ** * *
1800988 AAGGTATTATTTATCATTATTTGTAGAAGTTTAAATTTATTTTTTGGGTATGATTATATGAGTTT
1 AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTT-GGTATGATTATACGAGTTT
1801053 AAATTTTT
65 AAATTTTT
* * * *** ** * * *
1801061 AAGATATACTTTATTTTTATTTGTAAAAGTTTAAATACATTTTTTAGAAATGATTGTGCAAGTTT
1 AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTT-GGTATGATTATACGAGTTT
*
1801126 ATATTTTTT
65 A-AATTTTT
* * * * *
1801135 ATGGTATAATTTATTTTTATTTCTAAAAGTTTATATTTGTTTTTTGGT-TGATTATACGATTTTA
1 AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTTGGTATGATTATACGAGTTTA
*
1801199 TATTTTT
66 AATTTTT
* * * *
1801206 AGGGTATTATTTATCTTTATTTGTAAAAGTTTAAATTT
1 AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATTT
1801244 TCATTTAAAT
Statistics
Matches: 1189, Mismatches: 224, Indels: 128
0.77 0.15 0.08
Matches are distributed among these distances:
66 2 0.00
67 26 0.02
68 59 0.05
69 47 0.04
70 71 0.06
71 235 0.20
72 197 0.17
73 279 0.23
74 257 0.22
75 10 0.01
76 6 0.01
ACGTcount: A:0.30, C:0.03, G:0.13, T:0.53
Consensus pattern (72 bp):
AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTTGGTATGATTATACGAGTTTA
AATTTTT
Found at i:1800495 original size:502 final size:491
Alignment explanation
Indices: 1799741--1801222 Score: 1651
Period size: 502 Copynumber: 3.0 Consensus size: 491
1799731 TTGTTTGTAT
* * *
1799741 GGTATGATTATACGAGTTTAAATTTTGAAGGTATAATTTATTTTTATTTGTAAAAGTTTAACATT
1 GGTATGATTATA-GAATTTAAATTTT-AAGGTATAATTTATTTTTATTTATAGAAGTTTAA-ATT
* * * * * *
1799806 GTTTTTT--ATTTGATTATGCAAGTATAAATTTTTAGGATATAATTTATTTTGATTTGTAAATGT
63 GTTTTTTGGGTATGATTATACGAGT-TAAATTTTTAGG-TATAATTTATTTTTATTTGTAGATGT
* *
1799869 TTAAATATGTTTTTAGGTATGATTATATGAGTTTAAAATTTTGAAAGTGTAATTTATTTTATTTG
126 TTAAATATGTTTTTA-GTATGATTATATGAGTTT--AATTTTCAAAGTATAATTTATTTTATTTG
* * * * *
1799934 TA-AAAGTTTACATTTAATTTTTAGTTTGATTATGCAAGTTTAAATTTTTAAGGTATTATTCATC
188 TAGAAA-TTTAAATTTAATTTTTAGGTTGATTATACGAGTTTAAATTTTTAAGGTATTATTTATC
* * * *
1799998 TTTATTTGTAGAAGTTTAAATTTATTTTTTAAGTATCATCACACGAGTTTAAATTTTTAAAATAT
252 TTTATTTGTAGAAGTTTAAATTTATTTTTTAGGTATCATTATATGAGTTTAAATTTTTAAAATAT
* *
1800063 AATTTATTTTTATTTATAGAAGTTTAAATGTATTTTTTTGGTATGATTATAAGAGTTTATATTTT
317 AATTTATTTTTATTTGTAGAAGTTTAAATGTATTTTTTAGGTATGATTATAAGAGTTTATATTTT
* * *
1800128 TGATGGCAT-A-A-TTTTATTTGTAAAAGTTTAAATTTATTTTTTGGTTTAATTATACAAGTTTA
382 TGATGGTATAATATTTTTATTTGTAAAAGTTTAAATTTGTTTTTTGG-TTGATTATAC-AGTTTA
* * * *
1800190 GATTTTTAGGCTATTATTTATCTTCATTAAGTTTAAATTTATTTTTTG
445 AATTTTTAGGATATTATTTATCTTCA-GAAGTTTAAATATATTTTTTG
* *
1800238 GGTTTGATTATATGAATTTAAATTTTATAGGTATAATTTATTTTTACTTATAGAAGTTTAAATGT
1 GGTATGATTATA-GAATTTAAATTTTA-AGGTATAATTTATTTTTATTTATAGAAGTTTAAAT-T
1800303 GTTTTTTGGGGTATGATTATACGAGTTCAAATTTTTATGGTATAATTTATTTTTATTTGTAGATG
63 GTTTTTT-GGGTATGATTATACGAGTT-AAATTTTTA-GGTATAATTTATTTTTATTTGTAGATG
* * * * *
1800368 TTTAAATGTGTGTTTCTCGATATGATTATACGAGTTTATATTTTTATAGTATAATTTATCTTTAT
125 TTTAAATATGT-TTT-TAG-TATGATTATATGAGTTTA-ATTTTCAAAGTATAATTTAT-TTTAT
* * *
1800433 TTGTAGAAATATAAATTTATTTTTTTGGTTGATTATACGAGTTTAAATTTTT-AGGCTATTATTT
185 TTGTAGAAATTTAAATTTAATTTTTAGGTTGATTATACGAGTTTAAATTTTTAAGG-TATTATTT
* * * *
1800497 ATCTTTATCTGTAGAAGTTTAAATTTATTTTTTTTGGTATTATTATATAAGTTTAAATTTTTAAA
249 ATCTTTATTTGTAGAAGTTTAAATTTA-TTTTTTAGGTATCATTATATGAGTTTAAATTTTTAAA
* * * * * *
1800562 ATATAATTTATTTTTATTTGCAGAAGTTTGATTGTGTTTTTTGGGTATGATTATACGAGTTTATA
313 ATATAATTTATTTTTATTTGTAGAAGTTTAAATGTATTTTTTAGGTATGATTATAAGAGTTTATA
* *
1800627 TTTTTGATGATATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTTTTGAGTTGATTATACA
378 TTTTTGATGGTATAA--TATTTTTATTTGTAAAAGTTTAAATTTGTTTTTTG-GTTGATTATACA
* * *
1800692 GTTTAAATTTTTAGGATATATTTTATTTTTTTTCAGAAGTTTAAATATGTTTTTTG
440 GTTTAAATTTTTAGG--ATA--TTATTTATCTTCAGAAGTTTAAATATATTTTTTG
* * *
1800748 GGTATGATTATACAAGTTTATATTCTTAATGGTGTAATTTATTTTTATTTATAGAAGTTTAAATT
1 GGTATGATTATAGAA-TTTAAATT-TTAA-GGTATAATTTATTTTTATTTATAGAAGTTTAAATT
* * * *
1800813 -TTTTTTGGGTCA--ATTATACGATTTTAAATTTTTAGCGTATTATTTATCTTTATTTGTAGAAG
63 GTTTTTTGGGT-ATGATTATACGA-GTTAAATTTTTAG-GTATAATTTATTTTTATTTGTAGATG
* * * * * **
1800875 TTTAAATTTAT-TTTTTTGTATAATTATATAAATTTAAATTTCAGGGTATAATTTATTTTTATTT
125 TTTAAA--TATGTTTTTAGTATGATTATATGAGTTTAATTTTCAAAGTATAATTTA-TTTTATTT
* * *
1800939 ATAGAAATTTAAA--TACCTTTTTGGGTTGATTATACGAGTTTAAATTTTTAAGGTATTATTTAT
187 GTAGAAATTTAAATTTA-ATTTTTAGGTTGATTATACGAGTTTAAATTTTTAAGGTATTATTTAT
* * * *
1801002 CATTATTTGTAGAAGTTTAAATTTATTTTTTGGGTATGATTATATGAGTTTAAATTTTTAAGATA
251 CTTTATTTGTAGAAGTTTAAATTTATTTTTTAGGTATCATTATATGAGTTTAAATTTTTAAAATA
* * ** ** * *
1801067 TACTTTATTTTTATTTGTAAAAGTTTAAATACATTTTTTAGAAATGATTGTGCA-AGTTTATATT
316 TAATTTATTTTTATTTGTAGAAGTTTAAATGTATTTTTTAGGTATGATTAT-AAGAGTTTATATT
* * * *
1801131 TTTTATGGTATAATTTATTTTTATTTCTAAAAGTTTATATTTGTTTTTTGGTTGATTATACGATT
380 TTTGATGGTATAA--TATTTTTATTTGTAAAAGTTTAAATTTGTTTTTTGGTTGATTATAC-AGT
* *
1801196 TTATATTTTTAGGGTATTATTTATCTT
442 TTAAATTTTTAGGATATTATTTATCTT
1801223 TATTTGTAAA
Statistics
Matches: 841, Mismatches: 106, Indels: 75
0.82 0.10 0.07
Matches are distributed among these distances:
496 3 0.00
497 61 0.07
498 9 0.01
499 1 0.00
500 57 0.07
501 37 0.04
502 242 0.29
503 166 0.20
504 37 0.04
505 15 0.02
506 3 0.00
507 66 0.08
508 46 0.05
509 14 0.02
510 38 0.05
511 46 0.05
ACGTcount: A:0.30, C:0.03, G:0.13, T:0.53
Consensus pattern (491 bp):
GGTATGATTATAGAATTTAAATTTTAAGGTATAATTTATTTTTATTTATAGAAGTTTAAATTGTT
TTTTGGGTATGATTATACGAGTTAAATTTTTAGGTATAATTTATTTTTATTTGTAGATGTTTAAA
TATGTTTTTAGTATGATTATATGAGTTTAATTTTCAAAGTATAATTTATTTTATTTGTAGAAATT
TAAATTTAATTTTTAGGTTGATTATACGAGTTTAAATTTTTAAGGTATTATTTATCTTTATTTGT
AGAAGTTTAAATTTATTTTTTAGGTATCATTATATGAGTTTAAATTTTTAAAATATAATTTATTT
TTATTTGTAGAAGTTTAAATGTATTTTTTAGGTATGATTATAAGAGTTTATATTTTTGATGGTAT
AATATTTTTATTTGTAAAAGTTTAAATTTGTTTTTTGGTTGATTATACAGTTTAAATTTTTAGGA
TATTATTTATCTTCAGAAGTTTAAATATATTTTTTG
Found at i:1802556 original size:12 final size:13
Alignment explanation
Indices: 1802541--1802572 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
1802531 TTGTAGCCGT
1802541 TGGAGTTGATT-A
1 TGGAGTTGATTAA
1802553 TGGAGTTGATTAA
1 TGGAGTTGATTAA
1802566 TGGAGTT
1 TGGAGTT
1802573 TCTAGCCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (13 bp):
TGGAGTTGATTAA
Found at i:1802733 original size:13 final size:13
Alignment explanation
Indices: 1802715--1802740 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1802705 CAATTTTTTA
1802715 TGTATCGATACAT
1 TGTATCGATACAT
1802728 TGTATCGATACAT
1 TGTATCGATACAT
1802741 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1805064 original size:15 final size:14
Alignment explanation
Indices: 1805029--1805067 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1805019 ATTAATAATA
1805029 AAATATTATATTTT
1 AAATATTATATTTT
*
1805043 ATTATATTATATTTTT
1 A-AATATTATA-TTTT
1805059 AAATATTAT
1 AAATATTAT
1805068 TTTAGTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 1 0.05
15 15 0.71
16 5 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AAATATTATATTTT
Found at i:1805085 original size:31 final size:30
Alignment explanation
Indices: 1805029--1805146 Score: 86
Period size: 28 Copynumber: 4.0 Consensus size: 30
1805019 ATTAATAATA
* *
1805029 AAATATTATATTTTATTATATTATATTTTT
1 AAATATTATATTTTATTATAATATATTATT
1805059 AAATATTAT-TTTAGTATTATAATATATTATT
1 AAATATTATATTT--TATTATAATATATTATT
* * *
1805090 AAACA-TAAATATTTATTAT-GT-TATTATT
1 AAATATTATAT-TTTATTATAATATATTATT
** * *
1805118 ATTTA-TAAATTTTAATATAATA-ATTATT
1 AAATATTATATTTTATTATAATATATTATT
1805146 A
1 A
1805147 TTTTAAAGTT
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
27 7 0.10
28 22 0.31
29 4 0.06
30 17 0.24
31 20 0.28
32 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (30 bp):
AAATATTATATTTTATTATAATATATTATT
Found at i:1805175 original size:28 final size:27
Alignment explanation
Indices: 1805111--1805175 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 27
1805101 TTTATTATGT
1805111 TATTATTATTTATAAATTTTAATATAA
1 TATTATTATTTATAAATTTTAATATAA
*
1805138 TAATTATTATTT-TAAAGTTATTAAATTTAA
1 T-ATTATTATTTATAAA-TT-TT-AATATAA
1805168 TATT-TTAT
1 TATTATTAT
1805176 AATAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 5 0.15
28 16 0.48
29 5 0.15
30 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
TATTATTATTTATAAATTTTAATATAA
Found at i:1811126 original size:21 final size:21
Alignment explanation
Indices: 1811084--1811149 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
1811074 TGTCAAGCCC
*
1811084 ATAAAATTTGTTTTATTATTAAA
1 ATAAAA-TTATTTTA-TATTAAA
1811107 ATAAAATTATTTTATATTAATA
1 ATAAAATTATTTTATATTAA-A
*
1811129 ATTAAA-TATTTTATAGTTAAA
1 ATAAAATTATTTTATA-TTAAA
1811150 TTTTAAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 16 0.41
22 17 0.44
23 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
ATAAAATTATTTTATATTAAA
Found at i:1811156 original size:22 final size:21
Alignment explanation
Indices: 1811094--1811148 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 21
1811084 ATAAAATTTG
*
1811094 TTTTATTATTAA-AATAAAATTA
1 TTTTA-TATTAATAATTAAA-TA
1811116 TTTTATATTAATAATTAAATA
1 TTTTATATTAATAATTAAATA
1811137 TTTTATAGTTAA
1 TTTTATA-TTAA
1811149 ATTTTAAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTATATTAATAATTAAATA
Found at i:1811417 original size:17 final size:18
Alignment explanation
Indices: 1811392--1811426 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1811382 GCATTTATTT
*
1811392 ATTTTTTTAT-ATTTTTA
1 ATTTATTTATAATTTTTA
1811409 ATTTATTTATAATTTTTA
1 ATTTATTTATAATTTTTA
1811427 TCTTTTACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTATTTATAATTTTTA
Found at i:1811418 original size:25 final size:26
Alignment explanation
Indices: 1811384--1811432 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1811374 TCAATGATGC
*
1811384 ATTTATTTAT-TTTTTTATATTTTTA
1 ATTTATTTATAATTTTTATATTTTTA
*
1811409 ATTTATTTATAATTTTTATCTTTT
1 ATTTATTTATAATTTTTATATTTT
1811433 ACTTAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (26 bp):
ATTTATTTATAATTTTTATATTTTTA
Found at i:1811433 original size:25 final size:25
Alignment explanation
Indices: 1811384--1811433 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1811374 TCAATGATGC
* *
1811384 ATTTATTTATTTTTTTATATTTTTA
1 ATTTATTTATATTTTTATACTTTTA
1811409 ATTTATTTATAATTTTTAT-CTTTTA
1 ATTTATTTAT-ATTTTTATACTTTTA
1811434 CTTAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (25 bp):
ATTTATTTATATTTTTATACTTTTA
Found at i:1811489 original size:9 final size:10
Alignment explanation
Indices: 1811468--1811497 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1811458 TTATATATTT
1811468 AAATTTTTAA
1 AAATTTTTAA
1811478 AAATTTTTAA
1 AAATTTTTAA
*
1811488 AAATTATTAA
1 AAATTTTTAA
1811498 TAAAATTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AAATTTTTAA
Found at i:1812099 original size:14 final size:14
Alignment explanation
Indices: 1812074--1812117 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1812064 TTAAGTATGA
1812074 ATAAAAATATTATTT
1 ATAAAAA-ATTATTT
* *
1812089 TTAAAAAATTATTA
1 ATAAAAAATTATTT
*
1812103 ATAAATAATTATTT
1 ATAAAAAATTATTT
1812117 A
1 A
1812118 AATAAATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATAAAAAATTATTT
Found at i:1812139 original size:12 final size:12
Alignment explanation
Indices: 1812094--1812160 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
1812084 TATTTTTAAA
*
1812094 AAATTATTA-AT
1 AAATAATTATAT
*
1812105 AAATAATTATTT
1 AAATAATTATAT
*
1812117 AAATAAATATAT
1 AAATAATTATAT
1812129 AAAT-ATT-TAT
1 AAATAATTATAT
1812139 AAATTTATATTAT-T
1 AAA--TA-ATTATAT
1812153 AAATAATT
1 AAATAATT
1812161 TTTATAATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
10 6 0.13
11 13 0.29
12 18 0.40
14 7 0.16
15 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAATAATTATAT
Found at i:1812160 original size:17 final size:17
Alignment explanation
Indices: 1812140--1812173 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1812130 AATATTTATA
*
1812140 AATTTATATTATTAAAT
1 AATTTATATAATTAAAT
*
1812157 AATTTTTATAATTAAAT
1 AATTTATATAATTAAAT
1812174 TAATATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTATATAATTAAAT
Found at i:1826404 original size:3 final size:3
Alignment explanation
Indices: 1826396--1826424 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1826386 ATTGGATTAA
1826396 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1826425 ATTGAAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1828391 original size:29 final size:29
Alignment explanation
Indices: 1828359--1828415 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1828349 CAGCGAAAGA
1828359 AATATTTTAATCTTTATATTATTAAATTT
1 AATATTTTAATCTTTATATTATTAAATTT
* * *
1828388 AATATTTTAATTTTTATGTTTTTAAATT
1 AATATTTTAATCTTTATATTATTAAATT
1828416 ATTGTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (29 bp):
AATATTTTAATCTTTATATTATTAAATTT
Found at i:1828776 original size:25 final size:26
Alignment explanation
Indices: 1828733--1828782 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1828723 AATCTTAGTA
*
1828733 AATTTTTACCACTAAAAAATTAAATT
1 AATTTTTACCACTAAAAAATCAAATT
1828759 AATTTTT-CCA-TAAAAAAATCAAAT
1 AATTTTTACCACT-AAAAAATCAAAT
1828783 ACAAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 14 0.64
26 7 0.32
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (26 bp):
AATTTTTACCACTAAAAAATCAAATT
Found at i:1829240 original size:20 final size:20
Alignment explanation
Indices: 1829215--1829271 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
1829205 ATTAATTATT
1829215 TATTTAAATAA-AATTTTAAA
1 TATTTAAATAATAATTTT-AA
1829235 TATTTAAA-AATTAATTTTAA
1 TATTTAAATAA-TAATTTTAA
*
1829255 TATTAAATATAATAATT
1 TATTTAA-ATAATAATT
1829272 AATAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 2 0.06
20 16 0.50
21 12 0.38
22 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTTAAATAATAATTTTAA
Found at i:1829403 original size:42 final size:43
Alignment explanation
Indices: 1829356--1829440 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
1829346 TAAAAAAATA
*
1829356 CATATAAAATAAATTAA-TTATTTATCAATTTTATATAATATT
1 CATATAAAACAAATTAATTTATTTATCAATTTTATATAATATT
* *
1829398 CATATAAAACAAATTAATTTTTTTATCAGTTTTATATAATATT
1 CATATAAAACAAATTAATTTATTTATCAATTTTATATAATATT
1829441 TCAGATCGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 16 0.41
43 23 0.59
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (43 bp):
CATATAAAACAAATTAATTTATTTATCAATTTTATATAATATT
Found at i:1832184 original size:2 final size:2
Alignment explanation
Indices: 1832177--1832212 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1832167 ACCCCATCTT
1832177 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1832213 TTTTCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1833668 original size:16 final size:18
Alignment explanation
Indices: 1833620--1833668 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
1833610 ATATTATAAT
1833620 TTAAATTAATTTTATAAAAA
1 TTAAA-TAA-TTTATAAAAA
1833640 TTAAATAATTTATAAAAA
1 TTAAATAATTTATAAAAA
1833658 -TAAAT-ATTTAT
1 TTAAATAATTTAT
1833669 TTAATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.21
17 5 0.17
18 10 0.34
19 3 0.10
20 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAAATAATTTATAAAAA
Found at i:1834599 original size:15 final size:17
Alignment explanation
Indices: 1834566--1834598 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1834556 TTTTATATTT
1834566 ATTTATAAAAATATAAA
1 ATTTATAAAAATATAAA
*
1834583 ATTTAAAAAAAT-TAAA
1 ATTTATAAAAATATAAA
1834599 TAAATAGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTTATAAAAATATAAA
Found at i:1835482 original size:13 final size:13
Alignment explanation
Indices: 1835464--1835488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1835454 TTATTAAATA
1835464 TAAAAAATATAAT
1 TAAAAAATATAAT
1835477 TAAAAAATATAA
1 TAAAAAATATAA
1835489 AAAATAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAAAAATATAAT
Found at i:1835979 original size:2 final size:2
Alignment explanation
Indices: 1835967--1836010 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
1835957 TGCATACATG
* *
1835967 TA TA TA AA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1836008 TA T
1 TA T
1836011 TCATTTTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1837284 original size:15 final size:14
Alignment explanation
Indices: 1837260--1837298 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1837250 ATTTAATTAT
*
1837260 AAATATTTTATTTAA
1 AAATA-TTTATTCAA
1837275 AAACTATTTATTCAA
1 AAA-TATTTATTCAA
1837290 AAATATTTA
1 AAATATTTA
1837299 AATAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 6 0.27
15 14 0.64
16 2 0.09
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (14 bp):
AAATATTTATTCAA
Found at i:1840073 original size:24 final size:24
Alignment explanation
Indices: 1840046--1840100 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
1840036 GAAATATTAT
1840046 AATA-AATAAAATATAATATATTTA
1 AATATAAT-AAATATAATATATTTA
* *
1840070 AATATAATTAATATAATATGTTTA
1 AATATAATAAATATAATATATTTA
1840094 ATATATA
1 A-ATATA
1840101 TTAATTATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
AATATAATAAATATAATATATTTA
Found at i:1840103 original size:24 final size:24
Alignment explanation
Indices: 1840055--1840117 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
1840045 TAATAAATAA
1840055 AATATAATATATTTAAATATAATT
1 AATATAATATATTTAAATATAATT
*
1840079 AATATAATATGTTT-AATATATATT
1 AATATAATATATTTAAATATA-ATT
*
1840103 AAT-T-ATGTATTTAAA
1 AATATAATATATTTAAA
1840118 ATTTTGACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 6 0.18
23 9 0.26
24 19 0.56
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (24 bp):
AATATAATATATTTAAATATAATT
Found at i:1843912 original size:28 final size:28
Alignment explanation
Indices: 1843877--1843932 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
1843867 AATTTTGAAG
1843877 ATAACTTTTTAGTGGCTCGTACTAGATT
1 ATAACTTTTTAGTGGCTCGTACTAGATT
* *
1843905 ATAACTTTTTTGTGGCTTGTACTAGATT
1 ATAACTTTTTAGTGGCTCGTACTAGATT
1843933 TCTTTATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.46
Consensus pattern (28 bp):
ATAACTTTTTAGTGGCTCGTACTAGATT
Found at i:1845717 original size:21 final size:21
Alignment explanation
Indices: 1845688--1845729 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1845678 ATAGTTATAA
1845688 AAGTGCATTGTATCATCTAAT
1 AAGTGCATTGTATCATCTAAT
* *
1845709 AAGTTCATTGTTTCATCTAAT
1 AAGTGCATTGTATCATCTAAT
1845730 TGATACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (21 bp):
AAGTGCATTGTATCATCTAAT
Found at i:1846157 original size:18 final size:19
Alignment explanation
Indices: 1846124--1846159 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1846114 TAAATAGATA
*
1846124 TTTAATAAATTCATAAATT
1 TTTAATAAAATCATAAATT
1846143 TTTAA-AAAATCATAAAT
1 TTTAATAAAATCATAAAT
1846160 GTTACATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAATAAAATCATAAATT
Found at i:1848594 original size:27 final size:27
Alignment explanation
Indices: 1848562--1848638 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
1848552 AACCTGAATT
1848562 TTTTAAAAAATTATAAATATTATTTTA
1 TTTTAAAAAATTATAAATATTATTTTA
* * *
1848589 TTTTAAAATATTTTAAA-ATGATTTTTA
1 TTTTAAAAAATTATAAATATTA-TTTTA
* *
1848616 TTTTTAAAAATTA-AAATTTTATT
1 TTTTAAAAAATTATAAATATTATT
1848639 AAAATATTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
26 8 0.20
27 32 0.80
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
TTTTAAAAAATTATAAATATTATTTTA
Found at i:1849285 original size:20 final size:21
Alignment explanation
Indices: 1849262--1849313 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
1849252 TATGGAAATC
1849262 TTATTATTTAATCA-TAG-ATA
1 TTATTATTTAAT-ATTAGTATA
*
1849282 TTATTA-ATAATATTAGTATA
1 TTATTATTTAATATTAGTATA
1849302 TTATTATATTAA
1 TTATTAT-TTAA
1849314 GTAAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 1 0.04
19 7 0.27
20 15 0.58
22 3 0.12
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (21 bp):
TTATTATTTAATATTAGTATA
Found at i:1851626 original size:32 final size:33
Alignment explanation
Indices: 1851588--1851666 Score: 126
Period size: 33 Copynumber: 2.4 Consensus size: 33
1851578 TTCTAAAGCT
1851588 GTTAACTTTGATCATA-G-ATTTATACACTTTTG
1 GTTAACTTTGATCATAGGTATTT-TACACTTTTG
*
1851620 GTTAACTTTAATCATAGGTATTTTACACTTTTG
1 GTTAACTTTGATCATAGGTATTTTACACTTTTG
1851653 GTTAACTTTGATCA
1 GTTAACTTTGATCA
1851667 AATTTTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
32 15 0.35
33 24 0.56
34 4 0.09
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (33 bp):
GTTAACTTTGATCATAGGTATTTTACACTTTTG
Found at i:1856080 original size:13 final size:12
Alignment explanation
Indices: 1856050--1856082 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1856040 AATATATCAT
1856050 TTAAAAATTAAA
1 TTAAAAATTAAA
1856062 -TAAAAATGTAAA
1 TTAAAAAT-TAAA
1856074 TTAAAAATT
1 TTAAAAATT
1856083 TTTAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.37
12 5 0.26
13 7 0.37
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
TTAAAAATTAAA
Found at i:1857011 original size:6 final size:6
Alignment explanation
Indices: 1857002--1857028 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1856992 CCAAACATAA
1857002 ACAACT ACAACT ACAACT ACAACT ACA
1 ACAACT ACAACT ACAACT ACAACT ACA
1857029 GTTTGTCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (6 bp):
ACAACT
Found at i:1862082 original size:51 final size:52
Alignment explanation
Indices: 1861959--1862093 Score: 159
Period size: 51 Copynumber: 2.6 Consensus size: 52
1861949 GCCTACATGC
*
1861959 ATCGATAC-ATTAAAGAATGTATCGATACATTTGGGTTAAAAAGCCAGAATAT
1 ATCGATACAATTAAA-AATGTATCGATACATTTGGGTTAAAAAGCCAAAATAT
* * * * *
1862011 ATCGATACAATTAAGAATGTATTGATATATTTGGG-TCAAAA-CTCAAAATGT
1 ATCGATACAATTAAAAATGTATCGATACATTTGGGTTAAAAAGC-CAAAATAT
* *
1862062 ATCGATACAATGAAAAATGTATCAATACATTT
1 ATCGATACAATTAAAAATGTATCGATACATTT
1862094 TTATTTCAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
50 1 0.01
51 38 0.54
52 26 0.37
53 5 0.07
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (52 bp):
ATCGATACAATTAAAAATGTATCGATACATTTGGGTTAAAAAGCCAAAATAT
Found at i:1863133 original size:16 final size:16
Alignment explanation
Indices: 1863112--1863147 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1863102 TGTCAAACTT
*
1863112 AAATAATTTAAATTTA
1 AAATAATCTAAATTTA
1863128 AAATAATCTAAATTTA
1 AAATAATCTAAATTTA
1863144 AAAT
1 AAAT
1863148 TATTCAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATAATCTAAATTTA
Found at i:1864562 original size:60 final size:60
Alignment explanation
Indices: 1864458--1864570 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
1864448 TGATTATGCC
** *
1864458 AAACGACATCTGCAATCATTAATGTCATGTAGGAAAATAGTATGAGGAATATTATACCCT
1 AAACGACATCCACAATCATTAATGTCATGTAGGAAAATAGTATGAGAAATATTATACCCT
* *
1864518 AAACGACATCCACGATCATTAATGTCATGTTCGGAAAATA-TATGAGAAATATT
1 AAACGACATCCACAATCATTAATGTCATG-TAGGAAAATAGTATGAGAAATATT
1864571 GTATCTTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 38 0.81
61 9 0.19
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (60 bp):
AAACGACATCCACAATCATTAATGTCATGTAGGAAAATAGTATGAGAAATATTATACCCT
Found at i:1865332 original size:57 final size:56
Alignment explanation
Indices: 1865223--1865334 Score: 170
Period size: 57 Copynumber: 2.0 Consensus size: 56
1865213 ACATATTAAG
* * * *
1865223 ATCAATATTCTACCTAATTAGTTTTTTTCAATTAATTAATTATTGTATTATCCAAT
1 ATCAATATCCTACCTAATTAGTTTTTTTCAATTAATTAATCACTATATTATCCAAT
*
1865279 ATCAATATCCTACCTAATTAGTTTTTTTTCAATTAATTACTCACTATATTATCCAA
1 ATCAATATCCTACCTAATTAG-TTTTTTTCAATTAATTAATCACTATATTATCCAA
1865335 GAATTTAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 20 0.40
57 30 0.60
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (56 bp):
ATCAATATCCTACCTAATTAGTTTTTTTCAATTAATTAATCACTATATTATCCAAT
Found at i:1869006 original size:22 final size:22
Alignment explanation
Indices: 1868975--1869022 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1868965 TAAGAATTTA
*
1868975 TTTA-AAAATAATAATTATTAT
1 TTTATAAAATAATAATTAATAT
**
1868996 TTTATAAAATAATTTTTAATAT
1 TTTATAAAATAATAATTAATAT
1869018 TTTAT
1 TTTAT
1869023 TATAATTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTATAAAATAATAATTAATAT
Found at i:1869096 original size:20 final size:19
Alignment explanation
Indices: 1869073--1869122 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1869063 TTAAAAAAAT
*
1869073 GATAATTTTTATACGATGTG
1 GATAATTTTTATA-GAAGTG
*
1869093 GATAAATTTTTTTAGAAGTG
1 GAT-AATTTTTATAGAAGTG
*
1869113 GATAGTTTTT
1 GATAATTTTT
1869123 TAAAAAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 6 0.23
20 11 0.42
21 9 0.35
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (19 bp):
GATAATTTTTATAGAAGTG
Found at i:1869141 original size:24 final size:24
Alignment explanation
Indices: 1869114--1869161 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1869104 TTAGAAGTGG
1869114 ATAGTT-TTTTAAAAAACTATTTTA
1 ATAGTTATTTT-AAAAACTATTTTA
*
1869138 ATAGTTATTTTAAATACTATTTTA
1 ATAGTTATTTTAAAAACTATTTTA
1869162 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (24 bp):
ATAGTTATTTTAAAAACTATTTTA
Found at i:1871565 original size:16 final size:16
Alignment explanation
Indices: 1871544--1871578 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1871534 GAAGATAGGT
1871544 AAAACACAAGGTAAAA
1 AAAACACAAGGTAAAA
1871560 AAAACACAAGGTAAAA
1 AAAACACAAGGTAAAA
1871576 AAA
1 AAA
1871579 TTTAAGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.71, C:0.11, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAACACAAGGTAAAA
Found at i:1874330 original size:180 final size:180
Alignment explanation
Indices: 1874021--1874382 Score: 559
Period size: 180 Copynumber: 2.0 Consensus size: 180
1874011 AGTTCTTTGT
* *
1874021 ATTAGACAACTTTGATAGAAAAGCATAACAAAGGGAAAAAGCAATGAAACAGGTGGTCAATTAAA
1 ATTAGACAACTTTGATAGAAAAGCATAACAAAGGGAAAAAGCAAAGAAACAGGTGGACAATTAAA
* * *
1874086 TCTCAGAAACTTAAATCAGAATCAGCAACCAACAAATCCTTTAGCTAGTAACCAGCAACCTTTTC
66 TCTCAGAAACTTAAATCAGAATCAGCAACCAACAAATCATTTAGCCAGTAACCAGAAACCTTTTC
*
1874151 CAAAAGTTTCTATGATTCAAAGAGAATTTTCACTG-TCTATATTCTTACAC
131 CAAAAGTTTCTATGATTCAAAGAGAATTTTCACTGCT-TATATTCCTACAC
* *
1874201 ATTAGATAACTTTGATAGAAAAGCATAACAAAGGGAAAAAGCAAAGAAACAGGTGGACAATTCAA
1 ATTAGACAACTTTGATAGAAAAGCATAACAAAGGGAAAAAGCAAAGAAACAGGTGGACAATTAAA
* *
1874266 TCTCAGACGA-TTAAATCAGAATCAGCAACCAGCAAATCATTCT-GCCAGTAACCAGAAACCTTT
66 TCTCAGA-AACTTAAATCAGAATCAGCAACCAACAAATCATT-TAGCCAGTAACCAGAAACCTTT
* * *
1874329 TCCAAATGTTTCTTTGATTCAAAGAGAATTTTCACTGCTTGTATTCCTACAC
129 TCCAAAAGTTTCTATGATTCAAAGAGAATTTTCACTGCTTATATTCCTACAC
1874381 AT
1 AT
1874383 GATATAAATG
Statistics
Matches: 166, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
180 163 0.98
181 3 0.02
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (180 bp):
ATTAGACAACTTTGATAGAAAAGCATAACAAAGGGAAAAAGCAAAGAAACAGGTGGACAATTAAA
TCTCAGAAACTTAAATCAGAATCAGCAACCAACAAATCATTTAGCCAGTAACCAGAAACCTTTTC
CAAAAGTTTCTATGATTCAAAGAGAATTTTCACTGCTTATATTCCTACAC
Found at i:1876173 original size:16 final size:16
Alignment explanation
Indices: 1876152--1876184 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1876142 CAAGCATAGG
1876152 AGAGAGAGAGACAGAA
1 AGAGAGAGAGACAGAA
*
1876168 AGAGAGAGAGAGAGAA
1 AGAGAGAGAGACAGAA
1876184 A
1 A
1876185 TAATACCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.39, T:0.00
Consensus pattern (16 bp):
AGAGAGAGAGACAGAA
Found at i:1882613 original size:20 final size:20
Alignment explanation
Indices: 1882584--1882631 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1882574 TGACCTCCTC
*
1882584 TTTTCAAATTCAAATTAGAT
1 TTTTCTAATTCAAATTAGAT
***
1882604 TTTTCTAATTCTTTTTAGAT
1 TTTTCTAATTCAAATTAGAT
1882624 TTTTCTAA
1 TTTTCTAA
1882632 ATCTATAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTCTAATTCAAATTAGAT
Found at i:1883742 original size:32 final size:30
Alignment explanation
Indices: 1883653--1884568 Score: 721
Period size: 28 Copynumber: 31.1 Consensus size: 30
1883643 AAATTGGTGA
* *
1883653 TTTGAAAAGGGTTGCCACTGACTTGCATAGGC
1 TTTGAAAAGAGTTGCCACTGACTTG--TGGGC
* * * * *
1883685 TTTTAAAAAAATATGCCACTAACTTATGTAGGC
1 TTTGAAAAGAGT-TGCCACTGAC-T-TGTGGGC
*
1883718 TTTGAAAAGAGTTGCCACCGACTTACGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTT--GTGGGC
* * *
1883750 TTTG-AAAG-GGTGGCACTGACTTGTAGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
* *
1883778 TTTGAAAAAAGAGTTGCCAC-CACTTATATGGGC
1 TTTG--AAAAGAGTTGCCACTGAC-T-TGTGGGC
* *
1883811 TTTG-AAAG-GATGTCACTGACTTGT-GGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
1883838 TTTGAAAAGA--TGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
* *
1883866 TTTGAAAA-AG-TGCTACTAACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
*
1883894 TTTG-AAAGGGTATGCCACTGACTTGTGGGC
1 TTTGAAAAGAGT-TGCCACTGACTTGTGGGC
* *
1883924 TTTG-AAAG-GGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
* *
1883952 TTTGGAAAG-G-TGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
* *
1883980 TTTGGAAAG-G-TGCCACCGA-TT-T--G-
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
* * * *
1884003 TGTGAAAAGAGTTGCCACCGACTTATGTGAC
1 TTTGAAAAGAGTTGCCACTGACTTGTG-GGC
1884034 TTTGAAAAGAGTTGCCACTGACTTGTGTGGAC
1 TTTGAAAAGAGTTGCCACTGACTTGTG-GG-C
*
1884066 TTTGAAAATAGTTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
* *
1884096 TTTGAAAAG-GGTGCCATTGACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
1884125 TTTGAAAAGAG-TGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
*
1884154 TTTG-AAAGGGTATGCCACTGACTTGTGGG-
1 TTTGAAAAGAGT-TGCCACTGACTTGTGGGC
* * * *
1884183 TTTTAAAAG-GGTGCCACTGACTGGTGAGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
* *
1884212 TTT-AAAAGAG-TGTCACAGACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
*
1884240 TTTG-AAAG-GATGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
* * *
1884268 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAAAGAGTTGCCACTGAC-T-TGTGGGC
* * *
1884300 TTTGAAATGGGTTGCCACCGACTTGTATGGGC
1 TTTGAAAAGAGTTGCCACTGACTTG--TGGGC
* *
1884332 TTTCAAATGAGTTGCCA-TCGACTTGTATGGGC
1 TTTGAAAAGAGTTGCCACT-GACTTG--TGGGC
* * *
1884364 TTTCAAATGAGTTGCCACTAACTTGTGTAGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTG--GGC
* * *
1884396 TTTGAAATGAGTTACCACCGACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
* *
1884426 TTTGAAATGA--TGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
* *
1884454 TTTGAAATG-G-TGCCACTGACTTGTGGGT
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
*
1884482 TTTGAAATGA--TGCCA-TGGACTTGTGGGC
1 TTTGAAAAGAGTTGCCACT-GACTTGTGGGC
* * *
1884510 TTTG-AAAG-GATGCCATTAACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
* * *
1884538 TTTGAAATGA--TGCCACGGACTTGTGGAC
1 TTTGAAAAGAGTTGCCACTGACTTGTGGGC
1884566 TTT
1 TTT
1884569 AAAGGGTGCC
Statistics
Matches: 746, Mismatches: 83, Indels: 114
0.79 0.09 0.12
Matches are distributed among these distances:
23 7 0.01
24 2 0.00
25 9 0.01
26 3 0.00
27 32 0.04
28 271 0.36
29 76 0.10
30 100 0.13
31 41 0.05
32 169 0.23
33 33 0.04
34 1 0.00
35 2 0.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.31
Consensus pattern (30 bp):
TTTGAAAAGAGTTGCCACTGACTTGTGGGC
Found at i:1883779 original size:28 final size:28
Alignment explanation
Indices: 1883715--1885167 Score: 717
Period size: 28 Copynumber: 51.2 Consensus size: 28
1883705 AACTTATGTA
* *
1883715 GGCTTTGAAAAGAGTTGCCACCGACTTACGTG
1 GGCTTTG-AAAG-GGTGCCACTGACTT--GTG
* *
1883747 GGCTTTGAAAGGGTGGCACTGACTTGTA
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * *
1883775 GGCTTTGAAAAAAGAGTTGCCAC-CACTTATATG
1 GGCTTTG---AAAG-GGTGCCACTGAC-T-TGTG
* *
1883808 GGCTTTGAAAGGATGTCACTGACTTGT-
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* *
1883835 GGCTTTGAAAAGATGCCACTGACTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
** * *
1883863 GGCTTTGAAAAAGTGCTACTAACTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
1883891 GGCTTTGAAAGGGTATGCCACTGACTTGTG
1 GGCTTTGAAAGGG--TGCCACTGACTTGTG
*
1883921 GGCTTTGAAAGGGTGCCACTGATTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
*
1883949 GGCTTTGGAAA-GGTGCCACTAACTTGTG
1 GGCTTT-GAAAGGGTGCCACTGACTTGTG
*
1883977 GGCTTTGGAAA-GGTGCCACCGA-TT-T-
1 GGCTTT-GAAAGGGTGCCACTGACTTGTG
* * * *
1884002 -G-TGTGAAAAGAGTTGCCACCGACTTATG
1 GGCTTTG-AAAG-GGTGCCACTGACTTGTG
* *
1884030 TGACTTTGAAAAGAGTTGCCACTGACTTGTG
1 -GGCTTTG-AAAG-GGTGCCACTGACTTGTG
* *
1884061 TGGACTTTGAAAATAGTTGCCACTGACTTGTG
1 -GG-CTTTG-AAA-GGGTGCCACTGACTTGTG
*
1884093 GGCTTTGAAAAGGGTGCCATTGACTTGTG
1 GGCTTTG-AAAGGGTGCCACTGACTTGTG
*
1884122 GGCTTTGAAAAGAGTGCCACTGACTTGTG
1 GGCTTTG-AAAGGGTGCCACTGACTTGTG
1884151 GGCTTTGAAAGGGTATGCCACTGACTTGTG
1 GGCTTTGAAAGGG--TGCCACTGACTTGTG
* * *
1884181 GGTTTTAAAAGGGTGCCACTGACTGGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * * * *
1884209 AGCTTTAAAAGAGTGTCACAGACTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
*
1884237 GGCTTTGAAAGGATGCCACTGACTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
*
1884265 GGCTTTGAAATGGGTTGCCACCGACTTGTGTG
1 GGCTTTGAAA-GGG-TGCCACTGAC-T-TGTG
*
1884297 GGCTTTGAAATGGGTTGCCACCGACTTGTATG
1 GGCTTTGAAA-GGG-TGCCACTGACTTG--TG
* *
1884329 GGCTTTCAAATGAGTTGCCA-TCGACTTGTATG
1 GGCTTTGAAA-G-GGTGCCACT-GACTTG--TG
* * *
1884361 GGCTTTCAAATGAGTTGCCACTAACTTGTG
1 GGCTTTGAAA-G-GGTGCCACTGACTTGTG
* * *
1884391 TAGGCTTTGAAATGAGTTACCACCGACTTGTG
1 --GGCTTTGAAA-G-GGTGCCACTGACTTGTG
* * *
1884423 GGCTTTGAAATGATGCCACTAACTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
*
1884451 GGCTTTGAAATGGTGCCACTGACTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * *
1884479 GGTTTTGAAATGATGCCA-TGGACTTGTG
1 GGCTTTGAAAGGGTGCCACT-GACTTGTG
* * *
1884507 GGCTTTGAAAGGATGCCATTAACTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * *
1884535 GGCTTTGAAATGATGCCACGGACTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * *
1884563 GACTTT-AAAGGGTGCCACGGAGTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * * *
1884590 GAC-TTAAAAGGGTGCCACGGAGTTGT-
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * * * * *
1884616 GGATCTAAAAGGGTACCA-TGGAGTGGTG
1 GGCTTTGAAAGGGTGCCACT-GACTTGTG
* * * * ** *
1884644 GACTTTAAAAGAGTACCACAAAGTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * *** * *
1884672 GAC-TTAAAAATATGCCACGGAGTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * * * *
1884699 GACTTTAAAAGGGTGCCACGGAGTTGTA
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * * * *
1884727 GAC-CTAAAAGGGTACCA-TGGA---GTA
1 GGCTTTGAAAGGGTGCCACT-GACTTGTG
** * * * * *
1884751 AACTTTAAAAGAGTGCCACAGAGTTATG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
** * * *
1884779 AAC-TTAAAAGAGTGCCACAGACTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * * * * * *
1884806 GAC-CTAAAAGGGTGCTACGGAGTGGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
** * * *
1884833 AAC-TTAAAAGGGTGCCACAGAGTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * * *
1884860 GAC-TTCAAAGGATGCCA-TGGAGTTGTG
1 GGCTTTGAAAGGGTGCCACT-GACTTGTG
** *
1884887 GGCTTAAAAAGGGATGCTACTGACTTGTG
1 GGCTTTGAAAGGG-TGCCACTGACTTGTG
**
1884916 GGCTTTGGGAGGGTGCCACTGACTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * * * * *
1884944 AGC-TTAAAATGATGCCACGGAGTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* ** * * * *
1884971 GAC-TCAAAAGAGTGCCACAGAGTTGTA
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * *
1884998 GAC-TTAAAAGGGTGCCAC-GAAGTTGTG
1 GGCTTTGAAAGGGTGCCACTG-ACTTGTG
**
1885025 GGCTTAAAAAGGGATGCCACTGACTTGTG
1 GGCTTTGAAAGGG-TGCCACTGACTTGTG
* *
1885054 GGTTTTGGAAGGGTGCCACTGACTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * *
1885082 GGC-TTAAAAGGATGCCA-TGGAGTTGTG
1 GGCTTTGAAAGGGTGCCACT-GACTTGTG
* * * * *
1885109 GAC-TTAAAAGAGTGCCACGGAGTTGTG
1 GGCTTTGAAAGGGTGCCACTGACTTGTG
* * *
1885136 GAC-TTAAAAGGGTGCCA-TGGAGTTGTG
1 GGCTTTGAAAGGGTGCCACT-GACTTGTG
1885163 GGCTT
1 GGCTT
1885168 AAAAGGATGC
Statistics
Matches: 1173, Mismatches: 187, Indels: 126
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.00
23 5 0.00
24 6 0.01
25 23 0.02
26 8 0.01
27 337 0.29
28 387 0.33
29 104 0.09
30 103 0.09
31 40 0.03
32 148 0.13
33 11 0.01
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCTTTGAAAGGGTGCCACTGACTTGTG
Found at i:1883839 original size:60 final size:62
Alignment explanation
Indices: 1883711--1883845 Score: 206
Period size: 61 Copynumber: 2.2 Consensus size: 62
1883701 CACTAACTTA
* *
1883711 TGTAGGCTTTG--AAAAGAGTTGCCACCGACTTACGTGGGCTTTGAAAGGGTGGCACTGACT
1 TGTAGGCTTTGAAAAAAGAGTTGCCACCGACTTACATGGGCTTTGAAAGGATGGCACTGACT
* *
1883771 TGTAGGCTTTGAAAAAAGAGTTGCCACC-ACTTATATGGGCTTTGAAAGGATGTCACTGACT
1 TGTAGGCTTTGAAAAAAGAGTTGCCACCGACTTACATGGGCTTTGAAAGGATGGCACTGACT
1883832 TGT-GGCTTTGAAAA
1 TGTAGGCTTTGAAAA
1883846 GATGCCACTG
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
60 22 0.32
61 32 0.46
62 15 0.22
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (62 bp):
TGTAGGCTTTGAAAAAAGAGTTGCCACCGACTTACATGGGCTTTGAAAGGATGGCACTGACT
Found at i:1884018 original size:25 final size:25
Alignment explanation
Indices: 1883990--1884062 Score: 74
Period size: 31 Copynumber: 2.7 Consensus size: 25
1883980 TTTGGAAAGG
1883990 TGCCACCGATTTGTGTGAAAAGAGT
1 TGCCACCGATTTGTGTGAAAAGAGT
1884015 TGCCACCGACTTATGTGACTTTGAAAAGAGT
1 TGCCACCGA-TT-TGTG----TGAAAAGAGT
* *
1884046 TGCCACTGACTTGTGTG
1 TGCCACCGATTTGTGTG
1884063 GACTTTGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
25 11 0.28
26 2 0.05
27 4 0.10
29 4 0.10
30 1 0.03
31 18 0.45
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (25 bp):
TGCCACCGATTTGTGTGAAAAGAGT
Found at i:1884588 original size:27 final size:27
Alignment explanation
Indices: 1884548--1885315 Score: 583
Period size: 27 Copynumber: 27.9 Consensus size: 27
1884538 TTTGAAATGA
* *
1884548 TGCCACGGACTTGTGGACTTTAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
1884575 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
1884602 TGCCACGGAGTTGTGGA-TCTAAAAGGG
1 TGCCACGGAGTTGTGGACT-TAAAAGGG
* * * *
1884629 TACCATGGAGTGGTGGACTTTAAAAGAG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* ** ***
1884657 TACCACAAAGTTGTGGACTTAAAAATA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
1884684 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
1884712 TGCCACGGAGTTGTAGACCTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * ** *
1884739 TACCATGGA---GTAAACTTTAAAAGAG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * * *
1884764 TGCCACAGAGTTATGAACTTAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
1884791 TGCCACAGACTTGTGGACCTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
1884818 TGCTACGGAGTGGTGAACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
1884845 TGCCACAGAGTTGTGGACTTCAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
1884872 TGCCATGGAGTTGTGGGCTTAAAAAGGG
1 TGCCACGGAGTTGTGGACTT-AAAAGGG
* * * * ***
1884900 ATGCTACTGACTTGTGGGCTTTGGGAGGG
1 -TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * * *
1884929 TGCCACTGACTTGT-GAGCTTAAAATGA
1 TGCCACGGAGTTGTGGA-CTTAAAAGGG
* *
1884956 TGCCACGGAGTTGTGGACTCAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
1884983 TGCCACAGAGTTGTAGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
1885010 TGCCACGAAGTTGTGGGCTTAAAAAGGG
1 TGCCACGGAGTTGTGGACTT-AAAAGGG
* * ** **
1885038 ATGCCACTGACTTGTGGGTTTTGGAAGGG
1 -TGCCACGGAGTTGT-GGACTTAAAAGGG
* * * *
1885067 TGCCACTGACTTGTGGGCTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
1885094 TGCCATGGAGTTGTGGACTTAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
1885121 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
1885148 TGCCATGGAGTTGTGGGCTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
** *
1885175 TGCCATAGAGTTGTGGACTTGGACTTAAAAGGA
1 TGCCACGGAG-T-T-G---TGGACTTAAAAGGG
** * * *
1885208 TGCCATAGAGTTGTAGACTTTCAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
1885236 TGCCACGGAGTTGTGGACTTAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * * * *
1885263 TGCCATGAAATTGTAGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
1885291 TACCACAGAGTTGTGGACTTAAAAG
1 TGCCACGGAGTTGTGGACTTAAAAG
1885316 AGATTAGAGT
Statistics
Matches: 593, Mismatches: 124, Indels: 48
0.78 0.16 0.06
Matches are distributed among these distances:
24 5 0.01
25 13 0.02
26 1 0.00
27 371 0.63
28 134 0.23
29 36 0.06
30 8 0.01
31 1 0.00
32 1 0.00
33 23 0.04
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:1884669 original size:82 final size:82
Alignment explanation
Indices: 1884550--1884722 Score: 222
Period size: 82 Copynumber: 2.1 Consensus size: 82
1884540 TGAAATGATG
* * * * ** * *
1884550 CCACGGACTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTG
1 CCACGGAGTGGTGGACTTTAAAGAGTACCACAAAGTTGTGGACTTAAAAAGATGCCACGGAGTTG
1884615 TGGA-TCTAAAAGGGTA
66 TGGACTCTAAAAGGGTA
* *
1884631 CCATGGAGTGGTGGACTTTAAAAGAGTACCACAAAGTTGTGGACTTAAAAATATGCCACGGAGTT
1 CCACGGAGTGGTGGACTTT-AAAGAGTACCACAAAGTTGTGGACTTAAAAAGATGCCACGGAGTT
* *
1884696 GTGGACTTTAAAAGGGTG
65 GTGGACTCTAAAAGGGTA
1884714 CCACGGAGT
1 CCACGGAGT
1884723 TGTAGACCTA
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 16 0.21
82 43 0.56
83 18 0.23
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.24
Consensus pattern (82 bp):
CCACGGAGTGGTGGACTTTAAAGAGTACCACAAAGTTGTGGACTTAAAAAGATGCCACGGAGTTG
TGGACTCTAAAAGGGTA
Found at i:1884828 original size:79 final size:80
Alignment explanation
Indices: 1884684--1884856 Score: 197
Period size: 79 Copynumber: 2.1 Consensus size: 80
1884674 CTTAAAAATA
* * * * * * *
1884684 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTAGACCTAAAAGGGTACCATGGA-
1 TGCCACAGAGTTATGAACTTTAAAAGAGTGCCACAGACTTGTAGACCTAAAAGGGTACCACGGAG
1884748 GTAAACTTTAAAAGAG
66 GTAAAC-TTAAAAGAG
* * *
1884764 TGCCACAGAGTTATGAAC-TTAAAAGAGTGCCACAGACTTGTGGACCTAAAAGGGTGCTACGGAG
1 TGCCACAGAGTTATGAACTTTAAAAGAGTGCCACAGACTTGTAGACCTAAAAGGGTACCACGGA-
* *
1884828 TGGTGAACTTAAAAGGG
65 -GGTAAACTTAAAAGAG
1884845 TGCCACAGAGTT
1 TGCCACAGAGTT
1884857 GTGGACTTCA
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
79 38 0.49
80 15 0.19
81 20 0.26
82 5 0.06
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.22
Consensus pattern (80 bp):
TGCCACAGAGTTATGAACTTTAAAAGAGTGCCACAGACTTGTAGACCTAAAAGGGTACCACGGAG
GTAAACTTAAAAGAG
Found at i:1884986 original size:138 final size:137
Alignment explanation
Indices: 1884490--1885179 Score: 648
Period size: 138 Copynumber: 5.1 Consensus size: 137
1884480 GTTTTGAAAT
* * * * * *
1884490 GATGCCA-TGGACTTGTGGGCTTTGAAAGGATGCCATTAACTTGTGGGCTTTGAAATGATGCCAC
1 GATGCCACT-GACTTGTGGGCTTTGGAAGGGTGCCACTGACTTGT-GGC-TTAAAAGGATGCCAC
* * * * *
1884554 GGACTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGT-GG
63 GGAGTTGTGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGG
*
1884618 ATCT-AAAAGG
128 CT-TAAAAAGG
* * * * ** * * ** * **
1884628 G-TACCA-TGGAGTGGTGGACTTTAAAAGAGTACCACAAAGTTGTGGACTTAAAAATATGCCACG
1 GATGCCACT-GACTTGTGGGCTTTGGAAGGGTGCCACTGACTTGTGG-CTTAAAAGGATGCCACG
* * * * * ***
1884691 GAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTAGACCTAAAAGGGTACCATGGA---GTAAA
64 GAGTTGTGGAC-TTAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGG
* *
1884753 CTTTAAAAGA
128 CTTAAAAAGG
* * * ** ** * * * * *
1884763 G-TGCCACAGAGTTATGAAC-TTAAAAGAGTGCCACAGACTTGTGGACCTAAAAGGGTGCTACGG
1 GATGCCACTGACTTGTGGGCTTTGGAAGGGTGCCACTGACTTGTGG-CTTAAAAGGATGCCACGG
* * * * *
1884826 AGTGGTGAACTTAAAAGGGTGCCACAGAGTTGTGGACTTCAAAGGATGCCATGGAGTTGTGGGCT
65 AGTTGTGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGGCT
1884891 TAAAAAGG
130 TAAAAAGG
* * *
1884899 GATGCTACTGACTTGTGGGCTTTGGGAGGGTGCCACTGACTTGTGAGCTTAAAATGATGCCACGG
1 GATGCCACTGACTTGTGGGCTTTGGAAGGGTGCCACTGACTTGTG-GCTTAAAAGGATGCCACGG
* * * *
1884964 AGTTGTGGACTCAAAAGAGTGCCACAGAGTTGTAGACTTAAAAGGGTGCCACGAAGTTGTGGGCT
65 AGTTGTGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGGCT
1885029 TAAAAAGG
130 TAAAAAGG
* *
1885037 GATGCCACTGACTTGTGGGTTTTGGAAGGGTGCCACTGACTTGTGGGCTTAAAAGGATGCCATGG
1 GATGCCACTGACTTGTGGGCTTTGGAAGGGTGCCACTGACTTGT-GGCTTAAAAGGATGCCACGG
*
1885102 AGTTGTGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGGCT
65 AGTTGTGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGGCT
1885167 T-AAAA-G
130 TAAAAAGG
1885173 GATGCCA
1 GATGCCA
1885180 TAGAGTTGTG
Statistics
Matches: 456, Mismatches: 84, Indels: 26
0.81 0.15 0.05
Matches are distributed among these distances:
133 39 0.09
134 47 0.10
135 19 0.04
136 44 0.10
137 88 0.19
138 217 0.48
139 2 0.00
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.25
Consensus pattern (137 bp):
GATGCCACTGACTTGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGCTTAAAAGGATGCCACGGA
GTTGTGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGGCTT
AAAAAGG
Found at i:1885207 original size:33 final size:33
Alignment explanation
Indices: 1885134--1885227 Score: 119
Period size: 33 Copynumber: 3.0 Consensus size: 33
1885124 CACGGAGTTG
* *
1885134 TGGACTTAAAAGGGTGCCATGGAGTTGT-G---
1 TGGACTTAAAAGGATGCCATAGAGTTGTAGACT
*
1885163 -GG-CTTAAAAGGATGCCATAGAGTTGTGGACT
1 TGGACTTAAAAGGATGCCATAGAGTTGTAGACT
1885194 TGGACTTAAAAGGATGCCATAGAGTTGTAGACT
1 TGGACTTAAAAGGATGCCATAGAGTTGTAGACT
1885227 T
1 T
1885228 TCAAAGGATG
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
27 22 0.39
28 3 0.05
32 2 0.04
33 29 0.52
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.28
Consensus pattern (33 bp):
TGGACTTAAAAGGATGCCATAGAGTTGTAGACT
Found at i:1885265 original size:88 final size:87
Alignment explanation
Indices: 1885107--1885268 Score: 227
Period size: 88 Copynumber: 1.9 Consensus size: 87
1885097 CATGGAGTTG
* * * * *
1885107 TGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGGCTTAAAA
1 TGGACTTAAAAGAGTGCCACAGAGTTGTAGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAA
*
1885172 GGATGCCATAGAGTTGTGGACT
66 AGATGCCATAGAGTTGTGGACT
* *
1885194 TGGACTTAAAAG-GATGCCATAGAGTTGTAGACTTTCAAAGGATGCCACGGAGTTGTGGACTTAA
1 TGGACTTAAAAGAG-TGCCACAGAGTTGTAGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTAA
1885258 AAAGATGCCAT
64 AAAGATGCCAT
1885269 GAAATTGTAG
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
86 1 0.02
87 27 0.42
88 37 0.57
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.25
Consensus pattern (87 bp):
TGGACTTAAAAGAGTGCCACAGAGTTGTAGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAA
AGATGCCATAGAGTTGTGGACT
Done.