Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 6 of 213
Found at i:1817204 original size:21 final size:21
Alignment explanation
Indices: 1817164--1817205 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1817154 TTCAACAAAA
*
1817164 TTTTTAAAAAGTTCTTAATTT
1 TTTTTAAAAAGTTATTAATTT
1817185 TTTTTAAAAA-TTATTCAATTT
1 TTTTTAAAAAGTTATT-AATTT
1817206 AGTAATAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTTAAAAAGTTATTAATTT
Found at i:1823783 original size:61 final size:61
Alignment explanation
Indices: 1823688--1823827 Score: 147
Period size: 61 Copynumber: 2.3 Consensus size: 61
1823678 TTGGTCTAAT
** * * * * *
1823688 AATAAATTTAGCTTTTAATGTTTGCATATTTTATCAAATTGATACTAAA-TATAAAAAATCC
1 AATAAATTTAGCCCTCAATGTTTACAAAATTTATCAAATTAAT-CTAAATTATAAAAAATCC
** * **
1823749 AATAAATTTAGCCCTCAATGTTTACAAAATTTATCATTTTAATTTAAATTATAAAAAATTT
1 AATAAATTTAGCCCTCAATGTTTACAAAATTTATCAAATTAATCTAAATTATAAAAAATCC
*
1823810 AATAAATTTAACCCTCAA
1 AATAAATTTAGCCCTCAA
1823828 CATTCACAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 4 0.06
61 61 0.94
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (61 bp):
AATAAATTTAGCCCTCAATGTTTACAAAATTTATCAAATTAATCTAAATTATAAAAAATCC
Found at i:1823849 original size:61 final size:60
Alignment explanation
Indices: 1823733--1823849 Score: 137
Period size: 61 Copynumber: 1.9 Consensus size: 60
1823723 AAATTGATAC
* ** * * *
1823733 TAAATATAAAAAATCCAATAAATTTAGCCCTCAATGTTTACAAAATTTATCATTTTAATT
1 TAAATATAAAAAATCCAATAAATTTAACCCTCAACATTCACAAAATTGATAATTTTAATT
**
1823793 TAAATTATAAAAAATTTAATAAATTTAACCCTCAACATTCAC-AAATTGATAAATTTT
1 TAAA-TATAAAAAATCCAATAAATTTAACCCTCAACATTCACAAAATTGAT-AATTTT
1823850 GATTATTTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
60 11 0.23
61 36 0.77
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.38
Consensus pattern (60 bp):
TAAATATAAAAAATCCAATAAATTTAACCCTCAACATTCACAAAATTGATAATTTTAATT
Found at i:1827891 original size:4 final size:4
Alignment explanation
Indices: 1827882--1827909 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1827872 GATCTCTATC
1827882 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
1827910 AATATTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:1834465 original size:18 final size:19
Alignment explanation
Indices: 1834442--1834486 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
1834432 GGCATAGTTT
1834442 AAAATGAAAATTTTAAAG-
1 AAAATGAAAATTTTAAAGA
*
1834460 AAAATGAAGATTTTAAAGA
1 AAAATGAAAATTTTAAAGA
1834479 AAAATGAA
1 AAAATGAA
1834487 TATTGTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.24
Consensus pattern (19 bp):
AAAATGAAAATTTTAAAGA
Found at i:1841516 original size:30 final size:31
Alignment explanation
Indices: 1841481--1841541 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1841471 CAACCTTATT
* *
1841481 ACTTAAATAAAAA-ATTTAAATAGTTTAATA
1 ACTTAAATAAAAACATTTAAACAATTTAATA
*
1841511 ACTTAAATAAAAACTTTTAAACAATTTAATA
1 ACTTAAATAAAAACATTTAAACAATTTAATA
1841542 TTGTACACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (31 bp):
ACTTAAATAAAAACATTTAAACAATTTAATA
Found at i:1845075 original size:24 final size:24
Alignment explanation
Indices: 1845046--1845094 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1845036 CTTTGCTCAT
1845046 ATAAGAAAAACAACCAAATCAGCA
1 ATAAGAAAAACAACCAAATCAGCA
1845070 ATAAGAAAAACAACCAAATCAGCA
1 ATAAGAAAAACAACCAAATCAGCA
1845094 A
1 A
1845095 GTTAAGGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.63, C:0.20, G:0.08, T:0.08
Consensus pattern (24 bp):
ATAAGAAAAACAACCAAATCAGCA
Found at i:1847499 original size:9 final size:9
Alignment explanation
Indices: 1847481--1847520 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
1847471 TTTGGTTAAA
*
1847481 AATTACCCG
1 AATTAACCG
1847490 AATTAACCG
1 AATTAACCG
*
1847499 AATTACCCG
1 AATTAACCG
1847508 AATTAACCG
1 AATTAACCG
1847517 AATT
1 AATT
1847521 GAATCACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:1847504 original size:18 final size:18
Alignment explanation
Indices: 1847481--1847520 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1847471 TTTGGTTAAA
1847481 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
1847499 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
1847517 AATT
1 AATT
1847521 GAATCACTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:1849146 original size:37 final size:37
Alignment explanation
Indices: 1849085--1849231 Score: 235
Period size: 37 Copynumber: 4.0 Consensus size: 37
1849075 TACGTATGAT
* *
1849085 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
1849120 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
1849157 CACTTATCACTTTGTTTCTTGATCAGATAAGTGCAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
1849194 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1849231 C
1 C
1849232 GAAGCTATCA
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 91 0.88
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:1849316 original size:52 final size:52
Alignment explanation
Indices: 1849237--1849598 Score: 480
Period size: 52 Copynumber: 7.2 Consensus size: 52
1849227 TAGCCGAAGC
1849237 TATCACTTAT-CACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTT-TCCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
* ** **
1849290 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1849342 TATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
*
1849388 TGTCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
* ** *
1849440 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACT
1 TATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1849492 TATCACTTT--A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
* ** **
1849538 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1849590 TATCACTTT
1 TATCACTTT
1849599 ATCACTTGAT
Statistics
Matches: 271, Mismatches: 25, Indels: 27
0.84 0.08 0.08
Matches are distributed among these distances:
46 80 0.30
48 2 0.01
50 2 0.01
52 176 0.65
53 11 0.04
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
Found at i:1849326 original size:98 final size:100
Alignment explanation
Indices: 1849205--1849598 Score: 484
Period size: 98 Copynumber: 4.0 Consensus size: 100
1849195 ACTTATCACT
* *
1849205 TTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC-T-TTGTCACTTGATCAGAT
1 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTCTTGTCACTTGATCAGAT
* *
1849268 AAGTATAGCCGAAGCTATTACTTATCACTTTCCAC
66 AAGTATAGCCAAAGCTATCACTTATCACTTTCCAC
* ** *
1849303 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC-T-TTGTCACTTGATCAGAT
1 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTCTTGTCACTTGATCAGAT
* * *
1849366 AAGTATAGCCGAAGCTATTACTTGTCACTTTCCAC
66 AAGTATAGCCAAAGCTATCACTTATCACTTTCCAC
*
1849401 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATC
1 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCAC-TT---CTTGTCACTTGATC
* *
1849466 AGATAAGTGTAGCTAAAGCTATCACTTATCACTTT--A-
62 AGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCAC
*
1849502 ---TCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATC
1 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCAC-TT---CTTGTCACTTGATC
* * *
1849564 AGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
62 AGATAAGTATAGCCAAAGCTATCACTTATCACTTT
1849599 ATCACTTGAT
Statistics
Matches: 274, Mismatches: 16, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
98 229 0.84
100 1 0.00
102 1 0.00
104 43 0.16
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (100 bp):
TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTCTTGTCACTTGATCAGAT
AAGTATAGCCAAAGCTATCACTTATCACTTTCCAC
Found at i:1849447 original size:150 final size:150
Alignment explanation
Indices: 1849193--1849598 Score: 671
Period size: 150 Copynumber: 2.7 Consensus size: 150
1849183 ATAAGTGCAG
* * *
1849193 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC--T----T
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
1849252 TGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCA
66 TGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCA
1849317 GATAAGTGTAGCTAAAGCTA
131 GATAAGTGTAGCTAAAGCTA
*
1849337 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTGTCACTTTCCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
1849402 TGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCA
66 TGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCA
1849467 GATAAGTGTAGCTAAAGCTA
131 GATAAGTGTAGCTAAAGCTA
* *
1849487 TCACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
* ** **
1849552 TGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
66 TGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTT
1849599 ATCACTTGAT
Statistics
Matches: 244, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
144 53 0.22
146 1 0.00
150 190 0.78
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (150 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
TGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCA
GATAAGTGTAGCTAAAGCTA
Found at i:1851912 original size:27 final size:26
Alignment explanation
Indices: 1851850--1851935 Score: 118
Period size: 26 Copynumber: 3.3 Consensus size: 26
1851840 CGGCTCGGCC
* * * **
1851850 TATTTTTAAAATAAACATTAAAAATT
1 TATTTTAAAAATAAAAAATAAAAAAA
1851876 TATTTTAAAAATAAAAAATAAAAAAA
1 TATTTTAAAAATAAAAAATAAAAAAA
1851902 TATTTTAAAAATAAAAAATAAAAAAA
1 TATTTTAAAAATAAAAAATAAAAAAA
1851928 TATATTTA
1 TAT-TTTA
1851936 TTATATTTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 50 0.93
27 4 0.07
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (26 bp):
TATTTTAAAAATAAAAAATAAAAAAA
Found at i:1856883 original size:17 final size:18
Alignment explanation
Indices: 1856861--1856897 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1856851 TGGTAAAAAT
1856861 ATAATTT-TATTATTTTA
1 ATAATTTATATTATTTTA
*
1856878 ATAATTTATATTTTTTTA
1 ATAATTTATATTATTTTA
1856896 AT
1 AT
1856898 TTTTAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATAATTTATATTATTTTA
Found at i:1859304 original size:15 final size:15
Alignment explanation
Indices: 1859284--1859321 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1859274 ACCTCATGCA
1859284 AAAAAACAAAAC-ATT
1 AAAAAA-AAAACAATT
*
1859299 AAAAAAAAAGCAATT
1 AAAAAAAAAACAATT
1859314 AAAAAAAA
1 AAAAAAAA
1859322 TATAGAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.79, C:0.08, G:0.03, T:0.11
Consensus pattern (15 bp):
AAAAAAAAAACAATT
Found at i:1860099 original size:93 final size:93
Alignment explanation
Indices: 1859917--1860111 Score: 257
Period size: 93 Copynumber: 2.1 Consensus size: 93
1859907 AACTGAAGAA
* **
1859917 GAAGAAGAAGAAGAAGAAAAAGGGTTGTTCGAAGTGAAAGAAGTGATAACATCGGAAGCCGAGTC
1 GAAGAAGAAGAAGAAGAAAAAGGGTCGTTCGAAGTGAAAGAAGTGATAACATCGGAAGCCGACCC
* *
1859982 CGGGGAGGAAGAACAAACACGTGAAGTT
66 CGGGGAAGAAGAACAAACACGTGAAATT
* *
1860010 GAAGAAGAAGAAGAAGAAAAAGGGTCGTTCGAAGTGAAAGACGTGATAACATC-GAAGGTCGACC
1 GAAGAAGAAGAAGAAGAAAAAGGGTCGTTCGAAGTGAAAGAAGTGATAACATCGGAA-GCCGACC
** * * *
1860074 CCTTGGAAGAGGAACGAACATGTGAAATT
65 CCGGGGAAGAAGAACAAACACGTGAAATT
*
1860103 AAAGAAGAA
1 GAAGAAGAA
1860112 AAAGGGTTGA
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
92 3 0.03
93 85 0.97
ACGTcount: A:0.44, C:0.11, G:0.31, T:0.13
Consensus pattern (93 bp):
GAAGAAGAAGAAGAAGAAAAAGGGTCGTTCGAAGTGAAAGAAGTGATAACATCGGAAGCCGACCC
CGGGGAAGAAGAACAAACACGTGAAATT
Found at i:1860158 original size:14 final size:14
Alignment explanation
Indices: 1860141--1860169 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1860131 AAGAAACGAA
1860141 AACATGGAAGGTCG
1 AACATGGAAGGTCG
1860155 AACATGGAAGGTCG
1 AACATGGAAGGTCG
1860169 A
1 A
1860170 TTGTTGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.34, T:0.14
Consensus pattern (14 bp):
AACATGGAAGGTCG
Found at i:1866609 original size:12 final size:12
Alignment explanation
Indices: 1866594--1866618 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1866584 ATATTTTGGA
1866594 TAATAAAATATT
1 TAATAAAATATT
1866606 TAATAAAATATT
1 TAATAAAATATT
1866618 T
1 T
1866619 CATGCTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATAAAATATT
Found at i:1869048 original size:26 final size:26
Alignment explanation
Indices: 1869008--1869059 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1868998 TAAGGATACC
*
1869008 TTAATTATAGTTTCTTATTCTACAAG
1 TTAATTATAGATTCTTATTCTACAAG
*
1869034 TTAATTTTAGATTCTTATTCTACAAG
1 TTAATTATAGATTCTTATTCTACAAG
1869060 ACTAAAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.50
Consensus pattern (26 bp):
TTAATTATAGATTCTTATTCTACAAG
Found at i:1874792 original size:13 final size:14
Alignment explanation
Indices: 1874773--1874806 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1874763 TTTGGTTTTT
1874773 TATTTTTTATATTA
1 TATTTTTTATATTA
*
1874787 -ATTTTTTATTTTA
1 TATTTTTTATATTA
1874800 TATTTTT
1 TATTTTT
1874807 AGACTGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTTTATATTA
Found at i:1877196 original size:18 final size:17
Alignment explanation
Indices: 1877167--1877200 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1877157 TTTTTATTTG
1877167 TTTATATGTATTATATT
1 TTTATATGTATTATATT
1877184 TTTATATTGTATTATAT
1 TTTATA-TGTATTATAT
1877201 GGACCATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTATATGTATTATATT
Found at i:1877209 original size:27 final size:25
Alignment explanation
Indices: 1877157--1877209 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
1877147 CAAAATTTAT
* **
1877157 TTTTTATTTGTTTATATGTATTATA
1 TTTTTATTTGTTTATATGGACCATA
1877182 TTTTTATATTGTATTATATGGACCATA
1 TTTTTAT-TTGT-TTATATGGACCATA
1877209 T
1 T
1877210 GTCAATGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 4 0.17
27 12 0.52
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.60
Consensus pattern (25 bp):
TTTTTATTTGTTTATATGGACCATA
Found at i:1886725 original size:26 final size:26
Alignment explanation
Indices: 1886689--1886742 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1886679 TTGTCAATGA
1886689 CAATGAGTAAAACATTCCTCCTTTTT
1 CAATGAGTAAAACATTCCTCCTTTTT
1886715 CAATGAGTAAAACATTCCTCCTTTTT
1 CAATGAGTAAAACATTCCTCCTTTTT
1886741 CA
1 CA
1886743 TTCGCACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.37
Consensus pattern (26 bp):
CAATGAGTAAAACATTCCTCCTTTTT
Found at i:1893913 original size:20 final size:19
Alignment explanation
Indices: 1893861--1893916 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1893851 GTGAGTGTTC
*
1893861 ACCAGTCAAAAACTGGATTG
1 ACCAGTAAAAAAC-GGATTG
* *
1893881 ACCGGTATGAAAACGGATTG
1 ACCAGTA-AAAAACGGATTG
1893901 AACCAGTAAAAAACGG
1 -ACCAGTAAAAAACGG
1893917 TTTTTTATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (19 bp):
ACCAGTAAAAAACGGATTG
Found at i:1899061 original size:5 final size:6
Alignment explanation
Indices: 1899044--1899073 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1899034 AATTAATAGT
1899044 ATAAAA ATAAAA ATAAAA AT-AAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
1899074 GTTTATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:1899061 original size:11 final size:12
Alignment explanation
Indices: 1899044--1899073 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
1899034 AATTAATAGT
1899044 ATAAAAATAAAA
1 ATAAAAATAAAA
1899056 ATAAAAAT-AAA
1 ATAAAAATAAAA
1899067 ATAAAAA
1 ATAAAAA
1899074 GTTTATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
ATAAAAATAAAA
Found at i:1910050 original size:3 final size:3
Alignment explanation
Indices: 1910042--1910076 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1910032 ATCACATGTT
1910042 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1910077 TGGATGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1910194 original size:72 final size:72
Alignment explanation
Indices: 1910077--1910332 Score: 503
Period size: 72 Copynumber: 3.6 Consensus size: 72
1910067 TATTATTATT
1910077 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1910142 TTTTAAG
66 TTTTAAG
1910149 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1910214 TTTTAAG
66 TTTTAAG
1910221 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1910286 TTTTAAG
66 TTTTAAG
*
1910293 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTT
1910333 GTCAAGTTGT
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 183 1.00
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.42
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
TTTTAAG
Found at i:1914555 original size:3 final size:3
Alignment explanation
Indices: 1914547--1914578 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1914537 ATCACATGTT
1914547 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1914579 TGGATGTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1914696 original size:72 final size:72
Alignment explanation
Indices: 1914579--1914762 Score: 359
Period size: 72 Copynumber: 2.6 Consensus size: 72
1914569 TATTATTATT
1914579 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1914644 TTTTAAG
66 TTTTAAG
1914651 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1914716 TTTTAAG
66 TTTTAAG
*
1914723 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTT
1914763 GTCAAGTTGT
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 111 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.42
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
TTTTAAG
Found at i:1917561 original size:39 final size:39
Alignment explanation
Indices: 1917507--1917636 Score: 181
Period size: 39 Copynumber: 3.3 Consensus size: 39
1917497 AAATTAAAAC
*
1917507 AAAAATTAAAAAAAGTATTTTAAAAAAAATTTAAAATTAA
1 AAAAATT-AAAAAAGTATTTTAAAAAAATTTTAAAATTAA
**
1917547 AAAAATTAAAAAAGTATTTTAAAAAAATTTTAAAATTTT
1 AAAAATTAAAAAAGTATTTTAAAAAAATTTTAAAATTAA
* * **
1917586 AAAATTTTAAAAAGTATTTTAAAAGTATTTTAAAATTAA
1 AAAAATTAAAAAAGTATTTTAAAAAAATTTTAAAATTAA
1917625 AAAAA-TAAAAAA
1 AAAAATTAAAAAA
1917637 TAAAAAAATT
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
38 6 0.08
39 66 0.84
40 7 0.09
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (39 bp):
AAAAATTAAAAAAGTATTTTAAAAAAATTTTAAAATTAA
Found at i:1917570 original size:11 final size:11
Alignment explanation
Indices: 1917556--1917620 Score: 68
Period size: 11 Copynumber: 6.4 Consensus size: 11
1917546 AAAAAATTAA
1917556 AAAAGTATTTT
1 AAAAGTATTTT
**
1917567 AAAAAAATTTT
1 AAAAGTATTTT
1917578 -AAA--ATTTT
1 AAAAGTATTTT
*
1917586 AAAA-T-TTTA
1 AAAAGTATTTT
1917595 AAAAGTATTTT
1 AAAAGTATTTT
1917606 AAAAGTATTTT
1 AAAAGTATTTT
1917617 AAAA
1 AAAA
1917621 TTAAAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 5 0.11
9 10 0.22
10 4 0.09
11 27 0.59
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:1917583 original size:8 final size:8
Alignment explanation
Indices: 1917570--1917597 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1917560 GTATTTTAAA
1917570 AAAATTTT
1 AAAATTTT
1917578 AAAATTTT
1 AAAATTTT
1917586 AAAATTTT
1 AAAATTTT
1917594 AAAA
1 AAAA
1917598 AGTATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
AAAATTTT
Found at i:1929701 original size:13 final size:14
Alignment explanation
Indices: 1929683--1929712 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1929673 CTTTGTTGGG
1929683 TTTGTATT-AGTTT
1 TTTGTATTAAGTTT
1929696 TTTGTATTAAGTTT
1 TTTGTATTAAGTTT
1929710 TTT
1 TTT
1929713 TTTTTTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.70
Consensus pattern (14 bp):
TTTGTATTAAGTTT
Found at i:1940046 original size:4 final size:4
Alignment explanation
Indices: 1940039--1940081 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
1940029 TCTATCTATA
* *
1940039 TATG TATG TATG TATG TATG TATG --TG TATT TATA TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1940082 GGTTGTGGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.06
4 32 0.94
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (4 bp):
TATG
Found at i:1941761 original size:27 final size:24
Alignment explanation
Indices: 1941731--1941781 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
1941721 TTTATTAATA
1941731 TGGTATATAAAAAATATATAATAAATT
1 TGGTAT-TAAAAAAT-TATAA-AAATT
*
1941758 TGGTATTATAAAATTATAAAAATT
1 TGGTATTAAAAAATTATAAAAATT
1941782 ATAATTTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 5 0.22
26 7 0.30
27 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (24 bp):
TGGTATTAAAAAATTATAAAAATT
Found at i:1944737 original size:37 final size:37
Alignment explanation
Indices: 1944695--1944842 Score: 251
Period size: 37 Copynumber: 4.0 Consensus size: 37
1944685 AGCTAAAGCT
*
1944695 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTA
* *
1944732 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTA
**
1944769 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTA
1944806 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTA
1944843 GCTAAAACTA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (37 bp):
ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTA
Found at i:1950474 original size:220 final size:220
Alignment explanation
Indices: 1950092--1950532 Score: 882
Period size: 220 Copynumber: 2.0 Consensus size: 220
1950082 TCAAGTGTGA
1950092 CACCTATAAAGTTATCACAACAAATGAAGTCAGCCAAAGATTCAATTCAGGCTCGCCATTGATCA
1 CACCTATAAAGTTATCACAACAAATGAAGTCAGCCAAAGATTCAATTCAGGCTCGCCATTGATCA
1950157 AGCACGCCTTCTAGTAGGCAACAGATTGCTAAGATTCCCCATAGAAACTGCACCCAAGTTCCTAA
66 AGCACGCCTTCTAGTAGGCAACAGATTGCTAAGATTCCCCATAGAAACTGCACCCAAGTTCCTAA
1950222 CAATCTGGAACCTAACCTAACCTTATCATTTCTTTATAAAAGCCTGTAACCTCAGTTTCCAATCA
131 CAATCTGGAACCTAACCTAACCTTATCATTTCTTTATAAAAGCCTGTAACCTCAGTTTCCAATCA
1950287 ATTCCCCATACAAATTACATCTGAG
196 ATTCCCCATACAAATTACATCTGAG
1950312 CACCTATAAAGTTATCACAACAAATGAAGTCAGCCAAAGATTCAATTCAGGCTCGCCATTGATCA
1 CACCTATAAAGTTATCACAACAAATGAAGTCAGCCAAAGATTCAATTCAGGCTCGCCATTGATCA
1950377 AGCACGCCTTCTAGTAGGCAACAGATTGCTAAGATTCCCCATAGAAACTGCACCCAAGTTCCTAA
66 AGCACGCCTTCTAGTAGGCAACAGATTGCTAAGATTCCCCATAGAAACTGCACCCAAGTTCCTAA
1950442 CAATCTGGAACCTAACCTAACCTTATCATTTCTTTATAAAAGCCTGTAACCTCAGTTTCCAATCA
131 CAATCTGGAACCTAACCTAACCTTATCATTTCTTTATAAAAGCCTGTAACCTCAGTTTCCAATCA
1950507 ATTCCCCATACAAATTACATCTGAG
196 ATTCCCCATACAAATTACATCTGAG
1950532 C
1 C
1950533 TCCTTACATT
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
220 221 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.26
Consensus pattern (220 bp):
CACCTATAAAGTTATCACAACAAATGAAGTCAGCCAAAGATTCAATTCAGGCTCGCCATTGATCA
AGCACGCCTTCTAGTAGGCAACAGATTGCTAAGATTCCCCATAGAAACTGCACCCAAGTTCCTAA
CAATCTGGAACCTAACCTAACCTTATCATTTCTTTATAAAAGCCTGTAACCTCAGTTTCCAATCA
ATTCCCCATACAAATTACATCTGAG
Found at i:1953063 original size:19 final size:19
Alignment explanation
Indices: 1953039--1953076 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1953029 CCTCTTTCCC
1953039 TTTAAAATCTCATTCTACG
1 TTTAAAATCTCATTCTACG
1953058 TTTAAAATCTCATTCTACG
1 TTTAAAATCTCATTCTACG
1953077 AAGAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (19 bp):
TTTAAAATCTCATTCTACG
Found at i:1953083 original size:19 final size:19
Alignment explanation
Indices: 1953042--1953084 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1953032 CTTTCCCTTT
***
1953042 AAAATCTCATTCTACGTTT
1 AAAATCTCATTCTACGAAG
1953061 AAAATCTCATTCTACGAAG
1 AAAATCTCATTCTACGAAG
1953080 AAAAT
1 AAAAT
1953085 ATCTCATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.33
Consensus pattern (19 bp):
AAAATCTCATTCTACGAAG
Found at i:1958024 original size:20 final size:20
Alignment explanation
Indices: 1957999--1958036 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1957989 CGTAAAATGA
*
1957999 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
1958019 TTTCTGTAAAATGATTTA
1 TTTCTGGAAAATGATTTA
1958037 TTGGAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:1958028 original size:34 final size:35
Alignment explanation
Indices: 1957984--1958050 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1957974 CGGTAAAATA
*
1957984 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
* *
1958018 TTTTCTGTAAAATGATTTATTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
1958051 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:1961309 original size:27 final size:27
Alignment explanation
Indices: 1961258--1961308 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1961248 ACCAAAAATT
1961258 TATTTTAAAAATAAAAAATATAAAAGG
1 TATTTTAAAAATAAAAAATATAAAAGG
*
1961285 TATTTTAAAATTAAAAAA-ATAAAA
1 TATTTTAAAAATAAAAAATATAAAA
1961309 AATAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (27 bp):
TATTTTAAAAATAAAAAATATAAAAGG
Found at i:1973323 original size:15 final size:15
Alignment explanation
Indices: 1973302--1973337 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1973292 ATTTTGAGAA
1973302 AAAAATAAATATTGT
1 AAAAATAAATATTGT
* *
1973317 TAAAATAAATGTTGT
1 AAAAATAAATATTGT
1973332 AAAAAT
1 AAAAAT
1973338 CATGATTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (15 bp):
AAAAATAAATATTGT
Found at i:1977990 original size:39 final size:40
Alignment explanation
Indices: 1977938--1978060 Score: 214
Period size: 39 Copynumber: 3.1 Consensus size: 40
1977928 AATTTATTTT
*
1977938 AAAAATTAA-AAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAAATAATAAAAAGTATTTTAAAAATATTTTAAAATTA
*
1977977 AAAAAA-AATAAAAAGTGTTTTAAAAATATTTTAAAATTA
1 AAAAAATAATAAAAAGTATTTTAAAAATATTTTAAAATTA
1978016 AAAAAATAATAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAAATAATAAAAAGTATTTTAAAAATATTTTAAAATTA
1978056 AAAAA
1 AAAAA
1978061 TTTAAAAAAT
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
38 2 0.03
39 40 0.51
40 37 0.47
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (40 bp):
AAAAAATAATAAAAAGTATTTTAAAAATATTTTAAAATTA
Found at i:1978020 original size:40 final size:40
Alignment explanation
Indices: 1977947--1978060 Score: 203
Period size: 40 Copynumber: 2.9 Consensus size: 40
1977937 TAAAAATTAA
1977947 AAAAAGTATTTTAAAAATATTTTAAAATT-AAAAAAAAAT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAAAT
* *
1977986 AAAAAGTGTTTTAAAAATATTTTAAAATTAAAAAAATAAT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAAAT
1978026 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAA
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAA
1978061 TTTAAAAAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 28 0.39
40 43 0.61
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (40 bp):
AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAAAT
Found at i:1978070 original size:17 final size:17
Alignment explanation
Indices: 1978036--1978068 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1978026 AAAAAGTATT
*
1978036 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
1978053 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTAAAAA
1978069 ATATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:1982058 original size:40 final size:39
Alignment explanation
Indices: 1981987--1982065 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 39
1981977 CTACAGCTGA
*
1981987 AATGAACTTGAAATGACTCAAACCGAGAATGATTTGAAT
1 AATGAACTTGAAATGACTCAAACCGAGAATGATTAGAAT
*
1982026 AATGTAACTTGAAATGAC-CTGAACCTGA-AATGATTAGAAT
1 AATG-AACTTGAAATGACTC-AAACC-GAGAATGATTAGAAT
1982066 CCAAAATGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 5 0.14
40 28 0.80
41 2 0.06
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.27
Consensus pattern (39 bp):
AATGAACTTGAAATGACTCAAACCGAGAATGATTAGAAT
Found at i:1986293 original size:105 final size:105
Alignment explanation
Indices: 1986090--1986332 Score: 382
Period size: 105 Copynumber: 2.3 Consensus size: 105
1986080 CCTTCATAAA
* *
1986090 CGGTGATCACAGGATTATTTCTGGCCAATTTATGGAAATGTTAAAATAATTGTCTTTACGCTTGT
1 CGGTGATCACAGTATTATTTCTGGCCAATTTATGGAAATGTTAAAACAATTGTCTTTACGCTTGT
* * *
1986155 TGCTTCGTTGCAAGCAACTCAATCATTTTCACCAATCCAT
66 TGCTTCATTACAAGCAACTCAACCATTTTCACCAATCCAT
* *
1986195 TGGTGATCACAGTATTACTTCTGG-CAATTTATGGAAATGTTAAAACAATTGTCTTTACGCTTGT
1 CGGTGATCACAGTATTATTTCTGGCCAATTTATGGAAATGTTAAAACAATTGTCTTTACGCTTGT
1986259 TGCTTCCATTACAAGCAACTCAACCATTTTCACCAATCCAT
66 TGCTT-CATTACAAGCAACTCAACCATTTTCACCAATCCAT
*
1986300 CGTTGATCACA-TAATTATTTCTGGCCAATTTAT
1 CGGTGATCACAGT-ATTATTTCTGGCCAATTTAT
1986333 CTTAACGCTT
Statistics
Matches: 125, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
104 45 0.36
105 72 0.58
106 8 0.06
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (105 bp):
CGGTGATCACAGTATTATTTCTGGCCAATTTATGGAAATGTTAAAACAATTGTCTTTACGCTTGT
TGCTTCATTACAAGCAACTCAACCATTTTCACCAATCCAT
Found at i:1989276 original size:29 final size:30
Alignment explanation
Indices: 1989217--1989288 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
1989207 ACATTTACAG
* **
1989217 TCACTAAACTATTAATAACTTTACATTTTGA
1 TCACTAAACT-TTAAAAACTTTACAAATTGA
*
1989248 TCACTCAACTTTAAAAAC-TTACAAATTGA
1 TCACTAAACTTTAAAAACTTTACAAATTGA
*
1989277 TCACTGAACTTT
1 TCACTAAACTTT
1989289 TCGAATGTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 20 0.56
30 7 0.19
31 9 0.25
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.38
Consensus pattern (30 bp):
TCACTAAACTTTAAAAACTTTACAAATTGA
Found at i:1994808 original size:10 final size:11
Alignment explanation
Indices: 1994780--1994806 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1994770 ATTTTAAAAA
1994780 TAAAAATATTT
1 TAAAAATATTT
1994791 TAAAAATATTT
1 TAAAAATATTT
1994802 TAAAA
1 TAAAA
1994807 TAAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:1995636 original size:49 final size:48
Alignment explanation
Indices: 1995532--1995634 Score: 165
Period size: 46 Copynumber: 2.2 Consensus size: 48
1995522 TTCATCCTTG
*
1995532 TATTATTAATGTTATGTGGTGAAAGAACTTAGCAAGTCTCTAGTCTTAT
1 TATTATTAATGTTATGTGGTG-AAGAACCTAGCAAGTCTCTAGTCTTAT
*
1995581 TATTATTGATGTTATGTGGTG-A-AACCTAGCAAGTCTCTAGTCTTAT
1 TATTATTAATGTTATGTGGTGAAGAACCTAGCAAGTCTCTAGTCTTAT
1995627 TATTATTA
1 TATTATTA
1995635 TTAGGATAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
46 30 0.59
47 1 0.02
49 20 0.39
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (48 bp):
TATTATTAATGTTATGTGGTGAAGAACCTAGCAAGTCTCTAGTCTTAT
Found at i:1997535 original size:21 final size:18
Alignment explanation
Indices: 1997496--1997540 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
1997486 CAAATAATTT
1997496 AAAAATTATAAAATATTC
1 AAAAATTATAAAATATTC
1997514 AAAAATATATATAAATAGTTC
1 AAAAAT-TATA-AAATA-TTC
1997535 ATAAAA
1 A-AAAA
1997541 AAAATGAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.26
19 4 0.17
20 5 0.22
21 4 0.17
22 4 0.17
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAAATTATAAAATATTC
Found at i:1999126 original size:196 final size:197
Alignment explanation
Indices: 1998792--1999181 Score: 595
Period size: 196 Copynumber: 2.0 Consensus size: 197
1998782 GATTATGATA
* * *
1998792 GTGGTATGCTTTTGGATCACTATCTTCTTTGGTTGAATGCCCTTTATTCTTTTGAGCATATATCT
1 GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCCCTTTATGCTTTTGAGCATATATCT
* * *
1998857 GTATGTCTGTGTATTCTCAATGGTTATAATGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
66 CTATGTCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
* * * *
1998922 TAAATCCAACATTGTCTCC-AAAACAATGAGTGATTAAATTGAATGG-CATGGTAAGAAGATTGG
131 TAAATCCAACATTATCTCCAAAAACAATGAGTGACTAAATGGAATGGTC-TGATAAGAAGATTGG
1998985 GTT
195 GTT
* * * * *
1998988 GTGGTATGCTTTTAGATCATTTTCATCTTTGGTTGAATGCTCTTTATGCTTTTGAGCATATGTTT
1 GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCCCTTTATGCTTTTGAGCATATATCT
* *
1999053 CTATGTCAGTGTATTCTCAATTGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATGT
66 CTATGTCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
*
1999118 TAAATCCAACATTATCTCCAAAAACAATGTGTGACTAAATGGAATGGTCTGATAAGAAGATTGG
131 TAAATCCAACATTATCTCCAAAAACAATGAGTGACTAAATGGAATGGTCTGATAAGAAGATTGG
1999182 ATTGCATTCA
Statistics
Matches: 174, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
196 135 0.78
197 38 0.22
198 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (197 bp):
GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCCCTTTATGCTTTTGAGCATATATCT
CTATGTCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
TAAATCCAACATTATCTCCAAAAACAATGAGTGACTAAATGGAATGGTCTGATAAGAAGATTGGG
TT
Found at i:2011786 original size:46 final size:45
Alignment explanation
Indices: 2011761--2011924 Score: 145
Period size: 46 Copynumber: 3.4 Consensus size: 45
2011751 GATCAAGTGA
* * *
2011761 CAAGTGGA-AAGTGATAAGTAATAGCT-TCGGCTATACTTATCTGAT
1 CAAGT-GACAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGAT
*
2011806 CAAGTGACAAAGTGATAAGTGATAGCT-TCGGCTACACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGAT
*
2011852 CAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGAC-------AAGTGATAAGTGATAGCTATAGCTACACTTATCTGAT
*
2011904 CAAGAGACAAAGTGATAAGTG
1 CAAGTGAC-AAGTGATAAGTG
2011925 GCTACACTTA
Statistics
Matches: 106, Mismatches: 4, Indels: 17
0.83 0.03 0.13
Matches are distributed among these distances:
44 2 0.02
45 5 0.05
46 56 0.53
52 42 0.40
53 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (45 bp):
CAAGTGACAAGTGATAAGTGATAGCTATAGCTACACTTATCTGAT
Found at i:2011787 original size:52 final size:51
Alignment explanation
Indices: 2011716--2011924 Score: 275
Period size: 52 Copynumber: 4.1 Consensus size: 51
2011706 ATCAAGTGAC
* *
2011716 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-G
* * *
2011768 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
2011814 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
2011865 AAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTG
1 -AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGTG
2011918 ATAAGTG
1 A-AAGTG
2011925 GCTACACTTA
Statistics
Matches: 139, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
46 44 0.32
52 85 0.61
53 10 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:2011822 original size:98 final size:98
Alignment explanation
Indices: 2011702--2011925 Score: 367
Period size: 98 Copynumber: 2.3 Consensus size: 98
2011692 TTTGAGTACT
*
2011702 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* * *
2011767 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCAGCTACACTTA
* *
2011800 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
2011865 AAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 AAAAGTGATAAGTAATAGCTTCAGCTACACTTA
*
2011898 TCTGATCAAGAGACAAAGTGATAAGTGG
1 TCTGATCAAGTGACAAAGTGATAAGTGG
2011926 CTACACTTAT
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 116 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCAGCTACACTTA
Found at i:2011932 original size:37 final size:37
Alignment explanation
Indices: 2011888--2011996 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
2011878 GATAGCTTTA
2011888 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
2011925 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
2011962 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
2011997 ATCATACGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:2012689 original size:22 final size:22
Alignment explanation
Indices: 2012644--2012687 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
2012634 TAAAACGCAA
2012644 TAAATAAAAAAATATTAAATAT
1 TAAATAAAAAAATATTAAATAT
*
2012666 TAAATTAAAATAAATATAAAAT
1 TAAA-TAAAA-AAATATTAAAT
2012688 TATATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 5 0.26
24 10 0.53
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAATAAAAAAATATTAAATAT
Found at i:2022980 original size:27 final size:27
Alignment explanation
Indices: 2022942--2023008 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
2022932 GACAGCACTG
2022942 ATAGGCGGCACCAAAGGTGCCATTCCC
1 ATAGGCGGCACCAAAGGTGCCATTCCC
* *
2022969 ATAGGCGGCACCGATGGTGCCATTCCC
1 ATAGGCGGCACCAAAGGTGCCATTCCC
* *
2022996 ATGGGTGGCACCA
1 ATAGGCGGCACCA
2023009 CTCGTGTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.30, T:0.16
Consensus pattern (27 bp):
ATAGGCGGCACCAAAGGTGCCATTCCC
Found at i:2023071 original size:11 final size:11
Alignment explanation
Indices: 2023044--2023073 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
2023034 CCAGCTGAAG
2023044 GAGAAAAATAA
1 GAGAAAAATAA
2023055 GAAGAAAAATAA
1 G-AGAAAAATAA
2023067 GAGAAAA
1 GAGAAAA
2023074 GAAGAGGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (11 bp):
GAGAAAAATAA
Found at i:2024503 original size:17 final size:17
Alignment explanation
Indices: 2024481--2024541 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
2024471 TATATTTATT
2024481 TTTTTAATTTTAAAATA
1 TTTTTAATTTTAAAATA
** *
2024498 TTTTTACATACTTTTTAATT
1 TTTTTA-AT--TTTAAAATA
*
2024518 TTTTTAATTTCAAAATA
1 TTTTTAATTTTAAAATA
2024535 TTTTTAA
1 TTTTTAA
2024542 AATACTTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 18 0.53
18 2 0.06
19 2 0.06
20 12 0.35
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTTAATTTTAAAATA
Found at i:2024519 original size:37 final size:39
Alignment explanation
Indices: 2024478--2024574 Score: 153
Period size: 37 Copynumber: 2.5 Consensus size: 39
2024468 AAATATATTT
*
2024478 ATTTTTTTAATTTTAAAATATTTTT-ACATACTTTTT-A
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
*
2024515 ATTTTTTTAATTTCAAAATATTTTTAAAATACTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
2024554 ATTTTTTTAATTTTTAAAATA
1 ATTTTTTTAA-TTTTAAAATA
2024575 AAAATGGGCC
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
37 24 0.44
38 10 0.19
39 11 0.20
40 9 0.17
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
Found at i:2026558 original size:11 final size:11
Alignment explanation
Indices: 2026542--2026568 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2026532 GTTTATGCTT
2026542 AAATTGTATCC
1 AAATTGTATCC
2026553 AAATTGTATCC
1 AAATTGTATCC
2026564 AAATT
1 AAATT
2026569 AAGTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (11 bp):
AAATTGTATCC
Found at i:2029890 original size:43 final size:44
Alignment explanation
Indices: 2029843--2029973 Score: 149
Period size: 44 Copynumber: 3.0 Consensus size: 44
2029833 CTTTTTTTTT
*
2029843 CTTTCCTCCCCTCTT-CTTCTTCTTCTTTTTTTTTTC-TCTTCTC
1 CTTTCCTCCCCT-TTCCTTCTTCTTCTTTCTTTTTTCTTCTTCTC
*** *
2029886 CTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTTCTTCTTCTC
1 CTTTCCTCCCCTTTCCTTCTTCTTCTTTCTTTTTTCTTCTTCTC
*** *
2029930 CTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCTTTCTTCTTCT
1 CTTTCCTCCCCTTTCCTTCTTCTTCTTTCTTT-TTTCTTCTTCT
2029974 TCCCCTCTCC
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
42 2 0.03
43 28 0.35
44 39 0.49
45 11 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (44 bp):
CTTTCCTCCCCTTTCCTTCTTCTTCTTTCTTTTTTCTTCTTCTC
Found at i:2029895 original size:20 final size:21
Alignment explanation
Indices: 2029856--2029973 Score: 91
Period size: 24 Copynumber: 5.5 Consensus size: 21
2029846 TCCTCCCCTC
* *
2029856 TTCTTCTTCTTCTTT-TTTTT
1 TTCTTCTTCTCCTTTCCTTTT
2029876 TTC-TCTTCTCCTTTCCTTTTCT
1 TTCTTCTTCTCCTTTCC-TTT-T
* *
2029898 TTCCTTCTTTTTCTTT-CTTTT
1 TT-CTTCTTCTCCTTTCCTTTT
2029919 TTCTTCTTCTCCTTTCCTTTTCT
1 TTCTTCTTCTCCTTTCC-TTT-T
* *
2029942 TTCCTTCTTTTTCTTT-CTTTCT
1 TT-CTTCTTCTCCTTTCCTTT-T
2029964 TTCTTCTTCT
1 TTCTTCTTCT
2029974 TCCCCTCTCC
Statistics
Matches: 80, Mismatches: 9, Indels: 17
0.75 0.08 0.16
Matches are distributed among these distances:
19 10 0.12
20 14 0.17
21 14 0.17
22 16 0.20
23 6 0.08
24 20 0.25
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
TTCTTCTTCTCCTTTCCTTTT
Found at i:2029901 original size:10 final size:11
Alignment explanation
Indices: 2029875--2029974 Score: 84
Period size: 10 Copynumber: 9.2 Consensus size: 11
2029865 TTCTTTTTTT
*
2029875 TTTCTCTTCTCC
1 TTTC-CTTCTTC
2029887 TTTCCTT-TTC
1 TTTCCTTCTTC
2029897 TTTCCTTCTT-
1 TTTCCTTCTTC
* *
2029907 TTTCTTTCTTT
1 TTTCCTTCTTC
*
2029918 TTTCTTCTTCTCC
1 TTTC--CTTCTTC
2029931 TTTCCTT-TTC
1 TTTCCTTCTTC
2029941 TTTCCTTCTT-
1 TTTCCTTCTTC
*
2029951 TTTCTTTCTTTC
1 TTTCCTTC-TTC
2029963 TTT-CTTCTTC
1 TTTCCTTCTTC
2029973 TT
1 TT
2029975 CCCCTCTCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
10 39 0.53
11 19 0.26
12 7 0.10
13 8 0.11
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTCCTTCTTC
Found at i:2029911 original size:14 final size:14
Alignment explanation
Indices: 2029892--2029971 Score: 90
Period size: 14 Copynumber: 5.5 Consensus size: 14
2029882 TCTCCTTTCC
2029892 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
*
2029906 TTTTCTTT-CTTTT
1 TTTTCTTTCCTTCT
*
2029919 TTCTTCTTCTCCTTTCC
1 TT-TTCTT-TCC-TTCT
2029936 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
*
2029950 TTTTCTTTCTTTCT
1 TTTTCTTTCCTTCT
2029964 TTCTTCTT
1 TT-TTCTT
2029972 CTTCCCCTCT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
13 6 0.11
14 31 0.55
15 9 0.16
16 6 0.11
17 4 0.07
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCTTTCCTTCT
Found at i:2029914 original size:4 final size:4
Alignment explanation
Indices: 2029893--2029968 Score: 56
Period size: 4 Copynumber: 19.5 Consensus size: 4
2029883 CTCCTTTCCT
*
2029893 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC -TTC TTCTCC TTTCC TTTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C -TTTC
*
2029941 TTTC CTTC -TT- TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
2029969 CTTCTTCCCC
Statistics
Matches: 61, Mismatches: 2, Indels: 18
0.75 0.02 0.22
Matches are distributed among these distances:
3 14 0.23
4 36 0.59
5 5 0.08
6 6 0.10
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:2029934 original size:44 final size:44
Alignment explanation
Indices: 2029858--2029973 Score: 198
Period size: 44 Copynumber: 2.6 Consensus size: 44
2029848 CTCCCCTCTT
* *
2029858 CTTCTTCTTCTTTTTTTTTTC-TCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
2029901 CTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
2029945 CTTCTTTTTCTTTCTTTCTTTCTTCTTCT
1 CTTCTTTTTCTTTCTTT-TTTCTTCTTCT
2029974 TCCCCTCTCC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
43 19 0.28
44 39 0.57
45 11 0.16
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (44 bp):
CTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
Found at i:2029960 original size:34 final size:34
Alignment explanation
Indices: 2029896--2029976 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 34
2029886 CTTTCCTTTT
*
2029896 CTTTCCTTCTTTTTCTTTCTTTTTTCTTCTTCTC
1 CTTTCCTTCTTTTTCCTTCTTTTTTCTTCTTCTC
2029930 CTTTCCTT-TTCTTTCCTTC-TTTTTCTTTCTT-T-
1 CTTTCCTTCTT-TTTCCTTCTTTTTTC-TTCTTCTC
*
2029962 CTTT-CTTCTTCTTCC
1 CTTTCCTTCTTTTTCC
2029977 CCTCTCCTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
31 7 0.17
32 6 0.14
33 9 0.21
34 20 0.48
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (34 bp):
CTTTCCTTCTTTTTCCTTCTTTTTTCTTCTTCTC
Found at i:2029963 original size:48 final size:47
Alignment explanation
Indices: 2029855--2029990 Score: 174
Period size: 48 Copynumber: 3.0 Consensus size: 47
2029845 TTCCTCCCCT
*
2029855 CTTCTTCTTC-TTCTTTTTTTTTTC-TCTTCTCCTTTCCTTTTCTTTC
1 CTTCTT-TTCTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
2029901 CTTC--TT-TTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTCTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
* * * *
2029945 CTTCTTTTTCTTTCTTTCTTTCTTCTTCTTCCCCTCTCCTTCTCTT
1 CTTC-TTTTCTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTT
2029991 CCCCCCACCC
Statistics
Matches: 79, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
43 15 0.19
44 26 0.33
46 4 0.05
47 2 0.03
48 32 0.41
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (47 bp):
CTTCTTTTCTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
Found at i:2029974 original size:14 final size:14
Alignment explanation
Indices: 2029859--2029971 Score: 79
Period size: 14 Copynumber: 7.8 Consensus size: 14
2029849 TCCCCTCTTC
*
2029859 TTCTTCTTCTTTTT
1 TTCTTCTTCTTTCT
*
2029873 TTTTTC-TCTTCTCCT
1 TTCTTCTTCTT-T-CT
*
2029888 TTCCTT-TTCTTTCC
1 TT-CTTCTTCTTTCT
*
2029902 TTCTTTTTCTTTCT
1 TTCTTCTTCTTTCT
*
2029916 TTTTTCTTCTTCTCCT
1 TTCTTCTTCTT-T-CT
*
2029932 TTCCTT-TTCTTTCC
1 TT-CTTCTTCTTTCT
*
2029946 TTCTTTTTCTTTCT
1 TTCTTCTTCTTTCT
2029960 TTCTTTCTTCTT
1 TTC-TTCTTCTT
2029972 CTTCCCCTCT
Statistics
Matches: 78, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
13 10 0.13
14 38 0.49
15 13 0.17
16 15 0.19
17 2 0.03
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TTCTTCTTCTTTCT
Found at i:2030554 original size:19 final size:20
Alignment explanation
Indices: 2030525--2030585 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
2030515 ATTTAATAAA
2030525 ATAAAATATTTATTATATTT
1 ATAAAATATTTATTATATTT
** *
2030545 AT-TTATATTT-TTA-ATATA
1 ATAAAATATTTATTATAT-TT
2030563 ATAAAATATTTATTATATTT
1 ATAAAATATTTATTATATTT
2030583 ATA
1 ATA
2030586 GTAGCATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
17 2 0.06
18 6 0.19
19 12 0.39
20 9 0.29
21 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATAAAATATTTATTATATTT
Found at i:2030605 original size:38 final size:38
Alignment explanation
Indices: 2030516--2030604 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 38
2030506 TAAAATTATA
* * *
2030516 TTTAATAAAATAAAATATTTATTATATTTATTTATATT
1 TTTAATATAATAAAATATTTATTATATTTATGTACATT
2030554 TTTAATATAATAAAATATTTATTATATTTATAGTAGCATTT
1 TTTAATATAATAAAATATTTATTATATTTAT-GTA-CA-TT
2030595 TTTAATATAA
1 TTTAATATAA
2030605 ATATTTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 30 0.67
39 2 0.04
40 1 0.02
41 12 0.27
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (38 bp):
TTTAATATAATAAAATATTTATTATATTTATGTACATT
Found at i:2030710 original size:42 final size:42
Alignment explanation
Indices: 2030658--2030743 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
2030648 GTATTTAATG
2030658 TATTATAATTTTAAAAAAAACATTTTTAAATAAAATTAATCT
1 TATTATAATTTTAAAAAAAACATTTTTAAATAAAATTAATCT
*
2030700 TATTATAATTTTTAAAAAAACATTTTTAAATAAAATTAATCT
1 TATTATAATTTTAAAAAAAACATTTTTAAATAAAATTAATCT
2030742 TA
1 TA
2030744 AAAATCAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (42 bp):
TATTATAATTTTAAAAAAAACATTTTTAAATAAAATTAATCT
Found at i:2031664 original size:25 final size:24
Alignment explanation
Indices: 2031610--2031667 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
2031600 AATTAGTGTT
** *
2031610 AATTGAATTAATTAAAATTTTTAAT
1 AATT-AATTAATTAAAATTTAAAAA
*
2031635 TATTAATTAAATTAAAATTTAAAAA
1 AATTAATT-AATTAAAATTTAAAAA
2031660 AATTAATT
1 AATTAATT
2031668 GAATCGAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
AATTAATTAATTAAAATTTAAAAA
Found at i:2032552 original size:20 final size:21
Alignment explanation
Indices: 2032515--2032558 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
2032505 TAATAATATC
*
2032515 AGTAATTATTATTTTTAA-TT
1 AGTAATTATTATTCTTAACTT
2032535 AGTAATTCATTA-TCTTAACTT
1 AGTAATT-ATTATTCTTAACTT
2032556 AGT
1 AGT
2032559 TACTAGGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (21 bp):
AGTAATTATTATTCTTAACTT
Found at i:2033203 original size:25 final size:22
Alignment explanation
Indices: 2033158--2033212 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 22
2033148 AAAAATCCAG
2033158 TTTAATTTTTATTTTAATTAAT
1 TTTAATTTTTATTTTAATTAAT
*
2033180 TTTGATTTTTATAATTTAATTTAAT
1 TTTAATTTTTAT--TTTAA-TTAAT
2033205 TTTAATTT
1 TTTAATTT
2033213 AAAAATGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 11 0.39
24 5 0.18
25 12 0.43
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTAATTTTTATTTTAATTAAT
Found at i:2034612 original size:8 final size:8
Alignment explanation
Indices: 2034601--2034643 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
2034591 ATAATAAAAA
2034601 TATAATTT
1 TATAATTT
2034609 TATAATTT
1 TATAATTT
2034617 TA-ATATTT
1 TATA-ATTT
*
2034625 TATATTTT
1 TATAATTT
2034633 TATAAATTT
1 TAT-AATTT
2034642 TA
1 TA
2034644 AAAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
7 1 0.03
8 22 0.73
9 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATAATTT
Found at i:2037640 original size:4 final size:4
Alignment explanation
Indices: 2037633--2037680 Score: 80
Period size: 4 Copynumber: 12.0 Consensus size: 4
2037623 CTTTCTTTGC
2037633 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- ATGT GATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT -ATGT
2037681 TCCCCATGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.07
4 35 0.83
5 4 0.10
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:2039715 original size:6 final size:6
Alignment explanation
Indices: 2039704--2039741 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
2039694 CCCTTTTTCG
* *
2039704 AACCTT AACCTT AACCCT AACCCT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AA
2039742 TTTTTCCCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (6 bp):
AACCCT
Found at i:2042715 original size:14 final size:15
Alignment explanation
Indices: 2042696--2042729 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2042686 TGTTTTTAAA
2042696 TTTTAA-AATACGGG
1 TTTTAAGAATACGGG
*
2042710 TTTTAAGAATATGGG
1 TTTTAAGAATACGGG
2042725 TTTTA
1 TTTTA
2042730 TTTGATAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.44
Consensus pattern (15 bp):
TTTTAAGAATACGGG
Found at i:2044269 original size:45 final size:45
Alignment explanation
Indices: 2044203--2044292 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
2044193 CTTATCTTTC
2044203 CATTAGTAATTTAATGATTGGTGACCAAAAAAGAAAAATTCGAAT
1 CATTAGTAATTTAATGATTGGTGACCAAAAAAGAAAAATTCGAAT
* *
2044248 CATTAGTAATTTAATGGTTGGTGATCAAAAAAGAAAAATTCGAAT
1 CATTAGTAATTTAATGATTGGTGACCAAAAAAGAAAAATTCGAAT
2044293 GGTTGAGTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.30
Consensus pattern (45 bp):
CATTAGTAATTTAATGATTGGTGACCAAAAAAGAAAAATTCGAAT
Found at i:2051752 original size:23 final size:23
Alignment explanation
Indices: 2051722--2052134 Score: 358
Period size: 23 Copynumber: 16.2 Consensus size: 23
2051712 TAAGATTATC
* *
2051722 AAATTAGGTTAGAGTTTTTAACT
1 AAATTAGGTTAGGGTTTTTAATT
* *
2051745 AATTTAGGTTAGGGTTTTTAACT
1 AAATTAGGTTAGGGTTTTTAATT
2051768 AAATTAGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
2051796 AAATTAGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
2051824 AAATTAGGGTTAGGGTTTTTAATT
1 AAATTA-GGTTAGGGTTTTTAATT
*
2051848 AAATTGGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
*
2051876 AAATTAGGTTAGGGTTTTTAAAT
1 AAATTAGGTTAGGGTTTTTAATT
2051899 AAATTATGGTTAGGGTTTTTAATT
1 AAATTA-GGTTAGGGTTTTTAATT
2051923 AAATTAGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
2051951 AAATTAGAGTTAGGGTTTTTAATTAAATT
1 AAATTAG-GTTAGGG-T-TT--TT-AATT
2051980 AAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
*
2052003 AAATTAGGTTAGGGTTTAGGATTTTTAAAT
1 AAATTAGGTTA--G----GG-TTTTTAATT
2052033 AAATTAGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
**
2052061 AAATTAGGTTAGAATTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
*
2052084 AAATTATGGTTACGGTTTTTAATT
1 AAATTA-GGTTAGGGTTTTTAATT
*
2052108 AAATTAGGTTAGGGTTTTTAATC
1 AAATTAGGTTAGGGTTTTTAATT
2052131 AAAT
1 AAAT
2052135 AATATCAAAA
Statistics
Matches: 341, Mismatches: 18, Indels: 62
0.81 0.04 0.15
Matches are distributed among these distances:
23 103 0.30
24 59 0.17
25 15 0.04
26 8 0.02
27 12 0.04
28 90 0.26
29 35 0.10
30 19 0.06
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (23 bp):
AAATTAGGTTAGGGTTTTTAATT
Found at i:2051779 original size:28 final size:26
Alignment explanation
Indices: 2051724--2052134 Score: 407
Period size: 28 Copynumber: 16.0 Consensus size: 26
2051714 AGATTATCAA
* *
2051724 ATTAGGTTAGAGTTTTTAACT-AA-T
1 ATTAGGTTAGGGTTTTTAATTAAATT
*
2051748 -TTAGGTTAGGGTTTTTAACT-AA--
1 ATTAGGTTAGGGTTTTTAATTAAATT
2051770 ATTAGGTTAGGGTTTTTAATTAAATT
1 ATTAGGTTAGGGTTTTTAATTAAATT
2051796 AAATTAGGTTAGGGTTTTTAATTAAATT
1 --ATTAGGTTAGGGTTTTTAATTAAATT
2051824 AAATTAGGGTTAGGGTTTTTAATT-AA--
1 --ATTA-GGTTAGGGTTTTTAATTAAATT
*
2051850 ATTGGGTTAGGGTTTTTAATTAAATT
1 ATTAGGTTAGGGTTTTTAATTAAATT
*
2051876 AAATTAGGTTAGGGTTTTTAAATAAATT
1 --ATTAGGTTAGGGTTTTTAATTAAATT
2051904 A-T-GGTTAGGGTTTTTAATT-AA--
1 ATTAGGTTAGGGTTTTTAATTAAATT
2051925 ATTAGGTTAGGGTTTTTAATTAAATT
1 ATTAGGTTAGGGTTTTTAATTAAATT
2051951 AAATTAGAGTTAGGGTTTTTAATTAAATT
1 --ATTAG-GTTAGGGTTTTTAATTAAATT
2051980 AAATTAGGTTAGGGTTTTTAATTAAATT
1 --ATTAGGTTAGGGTTTTTAATTAAATT
* *
2052008 AGGTTAGGGTTTAGGATTTTTAAAT-AA--
1 A--TTA-GG-TTAGGGTTTTTAATTAAATT
2052035 ATTAGGTTAGGGTTTTTAATTAAATT
1 ATTAGGTTAGGGTTTTTAATTAAATT
**
2052061 AAATTAGGTTAGAATTTTTAATTAAATT
1 --ATTAGGTTAGGGTTTTTAATTAAATT
*
2052089 A-T-GGTTACGGTTTTTAATT-AA--
1 ATTAGGTTAGGGTTTTTAATTAAATT
*
2052110 ATTAGGTTAGGGTTTTTAATCAAAT
1 ATTAGGTTAGGGTTTTTAATTAAAT
2052135 AATATCAAAA
Statistics
Matches: 337, Mismatches: 17, Indels: 65
0.80 0.04 0.16
Matches are distributed among these distances:
21 2 0.01
22 2 0.01
23 106 0.31
24 45 0.13
25 5 0.01
26 3 0.01
27 1 0.00
28 111 0.33
29 49 0.15
30 13 0.04
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.46
Consensus pattern (26 bp):
ATTAGGTTAGGGTTTTTAATTAAATT
Found at i:2051870 original size:52 final size:51
Alignment explanation
Indices: 2051722--2052134 Score: 422
Period size: 52 Copynumber: 8.0 Consensus size: 51
2051712 TAAGATTATC
* * * *
2051722 AAATTAGGTTAGAGTTTTTAACTAATTTAGGTTAGGG--TTT--TT-AACT
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATT
2051768 AAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATTAAATTAGGTTAGGGTTTTTAATTAAATT
*
2051824 AAATTAGGGTTAGGGTTTTTAATTAAATTGGGTTAGGGTTTTTAATTAAATT
1 AAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATT
*
2051876 AAATTAGGTTAGGGTTTTTAAATAAATTATGGTTAGGG--TTT--TT-AATT
1 AAATTAGGTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTTTTAATTAAATT
2051923 AAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGAGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATTAAATTAG-GTTAGGGTTTTTAATTAAATT
*
2051980 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGATT-TTTAAA-T
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT----TTAATTAAATT
** ** *
2052033 AAATTAGGTTAGGGTTTTTAATTAAATTAAATTA-GG-TTAGAATTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA--TTAAATT
* *
2052084 AAATTATGGTTACGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATCAAAT
1 AAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAAT
2052135 AATATCAAAA
Statistics
Matches: 311, Mismatches: 22, Indels: 62
0.79 0.06 0.16
Matches are distributed among these distances:
46 13 0.04
47 18 0.06
48 5 0.02
49 3 0.01
50 9 0.03
51 59 0.19
52 103 0.33
53 42 0.14
54 12 0.04
55 10 0.03
56 11 0.04
57 26 0.08
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (51 bp):
AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATT
Found at i:2052353 original size:21 final size:21
Alignment explanation
Indices: 2052304--2052353 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2052294 CTTCCTCTAG
* *
2052304 CTTCCGGCGGTGGTTGTTCTT
1 CTTCCGGTGGTGATTGTTCTT
* *
2052325 CCTCCGGTGGTGATTGTTGTT
1 CTTCCGGTGGTGATTGTTCTT
2052346 CTTCCGGT
1 CTTCCGGT
2052354 TCGGCATCTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.24, G:0.32, T:0.42
Consensus pattern (21 bp):
CTTCCGGTGGTGATTGTTCTT
Found at i:2053310 original size:7 final size:7
Alignment explanation
Indices: 2053300--2053324 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2053290 ACATATACAT
2053300 AATACTA
1 AATACTA
2053307 AATACTA
1 AATACTA
2053314 AATACTA
1 AATACTA
2053321 AATA
1 AATA
2053325 TCAATCCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:2054442 original size:27 final size:28
Alignment explanation
Indices: 2054410--2054465 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
2054400 TTGAAAATAT
2054410 TAAAAAT-TTTAAAATTATT-TTAAAAAA
1 TAAAAATATTTAAAATT-TTCTTAAAAAA
2054437 TAAAAATATTTAAAATTTTCTTAAAAAA
1 TAAAAATATTTAAAATTTTCTTAAAAAA
2054465 T
1 T
2054466 GAAATTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TAAAAATATTTAAAATTTTCTTAAAAAA
Found at i:2054524 original size:22 final size:21
Alignment explanation
Indices: 2054499--2054549 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
2054489 TAATATGGAT
*
2054499 TTGAGAGATTTTTTGAAGGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
*
2054521 TTGAGAGGATTTTGGAAGGAAT
1 TTGAGA-GATTTTGGAAGGAAA
2054543 TTGAGAG
1 TTGAGAG
2054550 TTTAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:2056262 original size:73 final size:73
Alignment explanation
Indices: 2056175--2056360 Score: 354
Period size: 73 Copynumber: 2.5 Consensus size: 73
2056165 CCAACTTGAC
*
2056175 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCAACACCTACTAC
2056240 CACTAACA
66 CACTAACA
2056248 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCAACACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCAACACCTACTAC
2056313 CACTAACA
66 CACTAACA
*
2056321 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
2056361 AATAATAATA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 111 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCAACACCTACTAC
CACTAACA
Found at i:2056369 original size:3 final size:3
Alignment explanation
Indices: 2056361--2056410 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
2056351 ATTACATCCA
2056361 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2056409 AA
1 AA
2056411 AACATGTGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2060746 original size:3 final size:3
Alignment explanation
Indices: 2060740--2060786 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2060730 ATTACATCCA
2060740 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2060787 AACATGTGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2077550 original size:24 final size:24
Alignment explanation
Indices: 2077517--2077563 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2077507 TGTTTCCATG
2077517 AAAGAGGGTGACATA-TTCTTTGGT
1 AAAGAGGGTGACA-AGTTCTTTGGT
*
2077541 AAAGATGGTGACAAGTTCTTTGG
1 AAAGAGGGTGACAAGTTCTTTGG
2077564 ACTGTGCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (24 bp):
AAAGAGGGTGACAAGTTCTTTGGT
Found at i:2080192 original size:29 final size:29
Alignment explanation
Indices: 2080137--2080193 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2080127 TATTGAATTA
* *
2080137 TTTTATAAATTTTAAATATGTTCTTTAAT
1 TTTTATAAATTTTAAATATATTATTTAAT
*
2080166 TTTTATGAAATTTTAATTA-ATTATTTAA
1 TTTTAT-AAATTTTAAATATATTATTTAA
2080194 AATTTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (29 bp):
TTTTATAAATTTTAAATATATTATTTAAT
Found at i:2080200 original size:30 final size:29
Alignment explanation
Indices: 2080136--2080200 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
2080126 ATATTGAATT
* *
2080136 ATTTTATAAATTTTAAATATGTTCTTTAA
1 ATTTTATAAATTTTAAATATATTATTTAA
* *
2080165 TTTTTATGAAATTTTAATTA-ATTATTTAAA
1 ATTTTAT-AAATTTTAAATATATTATTT-AA
2080195 ATTTTA
1 ATTTTA
2080201 AATAATTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (29 bp):
ATTTTATAAATTTTAAATATATTATTTAA
Found at i:2085671 original size:18 final size:17
Alignment explanation
Indices: 2085619--2085673 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
2085609 TGAATAAATT
2085619 ACTCATCTTAATTAATTGA
1 ACTCATCTTAATTAA-T-A
**
2085638 GTTCATCTTAATTAATA
1 ACTCATCTTAATTAATA
2085655 ACTCATCTTAGATTAATA
1 ACTCATCTTA-ATTAATA
2085673 A
1 A
2085674 ATGAGTTGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 9 0.29
18 9 0.29
19 13 0.42
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (17 bp):
ACTCATCTTAATTAATA
Found at i:2088218 original size:17 final size:17
Alignment explanation
Indices: 2088196--2088230 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2088186 GGAAATATGC
2088196 TTGTGATCATGAAAGGG
1 TTGTGATCATGAAAGGG
2088213 TTGTGATCATGAAAGGG
1 TTGTGATCATGAAAGGG
2088230 T
1 T
2088231 GGTAAGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.34, T:0.31
Consensus pattern (17 bp):
TTGTGATCATGAAAGGG
Found at i:2091751 original size:46 final size:46
Alignment explanation
Indices: 2091674--2091855 Score: 312
Period size: 46 Copynumber: 4.0 Consensus size: 46
2091664 ACATTGCTAT
*
2091674 AACTCAGTATGG-TTTCTTCATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
2091719 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
* *
2091765 AACTCAGTATGGTTTTCTTCATTAAAACACCATACTTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
* *
2091811 AACTCAGTATGATTTTCTTCACTGAAACACCATACCTACTTTTCA
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCA
2091856 AAATTTGCCA
Statistics
Matches: 129, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 12 0.09
46 117 0.91
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
Found at i:2093117 original size:16 final size:17
Alignment explanation
Indices: 2093071--2093115 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2093061 AAATTCTTTT
*
2093071 TAAATCACAAAATTCAA
1 TAAATCAAAAAATTCAA
*
2093088 TAAATCAAAAAATTCAC
1 TAAATCAAAAAATTCAA
*
2093105 TAATTCAAAAA
1 TAAATCAAAAA
2093116 TTATTCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAATCAAAAAATTCAA
Found at i:2094763 original size:23 final size:23
Alignment explanation
Indices: 2094737--2094926 Score: 283
Period size: 23 Copynumber: 8.3 Consensus size: 23
2094727 ATAAGTGCCA
2094737 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * * *
2094760 CACTGATACGTAGACGAAGTTAT
1 CACTGATATGTAGCCGAAGCTAC
* * *
2094783 CACTAAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
2094806 CACTGAAATGTAGCCG-AGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
2094828 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
2094851 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
2094874 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
2094897 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
2094920 CACTGAT
1 CACTGAT
2094927 CAATAACACT
Statistics
Matches: 150, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
22 22 0.15
23 128 0.85
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:2094893 original size:91 final size:92
Alignment explanation
Indices: 2094737--2094925 Score: 281
Period size: 91 Copynumber: 2.1 Consensus size: 92
2094727 ATAAGTGCCA
* * * *
2094737 CACTGATATGTAGCCGAAGCTACCACTGATACGTAGACGAAGTTATCACTAAAATGTAGCTGAAG
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGACGAAGCTACCACTAAAATGTAGCCGAAG
2094802 CTACCACTGAAATGTAGCCG-AGCTAC
66 CTACCACTGAAATGTAGCCGAAGCTAC
* * * * *
2094828 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGATATGTAGCCGAAG
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGACGAAGCTACCACTAAAATGTAGCCGAAG
*
2094893 CTACCACTGATATGTAGCCGAAGCTAC
66 CTACCACTGAAATGTAGCCGAAGCTAC
2094920 CACTGA
1 CACTGA
2094926 TCAATAACAC
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
91 75 0.86
92 12 0.14
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (92 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGACGAAGCTACCACTAAAATGTAGCCGAAG
CTACCACTGAAATGTAGCCGAAGCTAC
Found at i:2097575 original size:21 final size:23
Alignment explanation
Indices: 2097543--2097585 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
2097533 GAGCGATTAT
*
2097543 GGTGCTTAAAAA-TGGTAGCAAG
1 GGTGCTTAAAAATTGGCAGCAAG
2097565 GGTGC-TAAAAATTGGCAGCAA
1 GGTGCTTAAAAATTGGCAGCAA
2097586 AAAGGGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (23 bp):
GGTGCTTAAAAATTGGCAGCAAG
Found at i:2100775 original size:6 final size:6
Alignment explanation
Indices: 2100764--2100790 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2100754 TTTTATCTAC
2100764 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
2100791 AATATTTAAA
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:2100798 original size:18 final size:18
Alignment explanation
Indices: 2100764--2100798 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2100754 TTTTATCTAC
* *
2100764 TTTTATTTTTATTTTTAT
1 TTTTATTTTAATATTTAT
2100782 TTTTATTTTAATATTTA
1 TTTTATTTTAATATTTA
2100799 AAATTTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTATTTTAATATTTAT
Found at i:2128573 original size:22 final size:21
Alignment explanation
Indices: 2128546--2128606 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
2128536 TTCTAATAAA
2128546 AATATAAATATATATTTAATC
1 AATATAAATATATATTTAATC
* *
2128567 AACTAT-AATATAAAATTAAATC
1 AA-TATAAATAT-ATATTTAATC
*
2128589 AATATAAA-ATATAATTAA
1 AATATAAATATATATTTAA
2128607 CAAAAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 5 0.16
21 12 0.38
22 15 0.47
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
AATATAAATATATATTTAATC
Found at i:2128577 original size:21 final size:20
Alignment explanation
Indices: 2128546--2128606 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
2128536 TTCTAATAAA
2128546 AATATAAATATATATTTAATC
1 AATAT-AATATATATTTAATC
* *
2128567 AACTATAATATAAAATTAAATC
1 AA-TATAATAT-ATATTTAATC
* *
2128589 AATATAAAATATAATTAA
1 AATATAATATATATTTAA
2128607 CAAAAAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 5 0.16
21 14 0.44
22 13 0.41
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AATATAATATATATTTAATC
Found at i:2128951 original size:6 final size:6
Alignment explanation
Indices: 2128940--2128964 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2128930 CCGAATATAA
2128940 TATATT TATATT TATATT TATATT T
1 TATATT TATATT TATATT TATATT T
2128965 TTAATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:2128985 original size:20 final size:20
Alignment explanation
Indices: 2128962--2129004 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
2128952 TATATTTATA
2128962 TTTTTAATTTTAAAAT-AAT
1 TTTTTAATTTTAAAATAAAT
*
2128981 TTTTTATTTTTAAAATAAAT
1 TTTTTAATTTTAAAATAAAT
2129001 TTTT
1 TTTT
2129005 GGTGTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTAATTTTAAAATAAAT
Found at i:2129012 original size:20 final size:19
Alignment explanation
Indices: 2128961--2129012 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
2128951 TTATATTTAT
*
2128961 ATTTTTAAT-TTTAAAATA
1 ATTTTTGATGTTTAAAATA
* *
2128979 ATTTTTTATTTTTAAAATAA
1 ATTTTTGATGTTTAAAAT-A
*
2128999 ATTTTTGGTGTTTA
1 ATTTTTGATGTTTA
2129013 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 8 0.29
19 8 0.29
20 12 0.43
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (19 bp):
ATTTTTGATGTTTAAAATA
Found at i:2129413 original size:13 final size:13
Alignment explanation
Indices: 2129395--2129419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2129385 AAAAAAGTAA
2129395 TTAAATTTTTTAG
1 TTAAATTTTTTAG
2129408 TTAAATTTTTTA
1 TTAAATTTTTTA
2129420 TCAATTTTTA
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTAAATTTTTTAG
Found at i:2129849 original size:23 final size:23
Alignment explanation
Indices: 2129823--2129883 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
2129813 AAAAATAAAT
2129823 TTTAAAATTTATGTTTTT-TATTG
1 TTTAAAATTTAT-TTTTTGTATTG
* *
2129846 TTT-AAATCTCATTTTTTGTATTT
1 TTTAAAAT-TTATTTTTTGTATTG
2129869 TTTAAAGATTTATTT
1 TTTAAA-ATTTATTT
2129884 ATTAGCTTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 9 0.29
23 13 0.42
24 7 0.23
25 2 0.06
ACGTcount: A:0.26, C:0.03, G:0.07, T:0.64
Consensus pattern (23 bp):
TTTAAAATTTATTTTTTGTATTG
Found at i:2132312 original size:13 final size:13
Alignment explanation
Indices: 2132272--2132322 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
2132262 TTTTTCATTA
2132272 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* ** *
2132285 CTGTAAAAAAATG
1 CTTTTGAAAAGTG
*
2132298 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
2132311 CTTTTGAAAAGT
1 CTTTTGAAAAGT
2132323 TTGGTTTAAA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:2136202 original size:25 final size:23
Alignment explanation
Indices: 2136157--2136204 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
2136147 AGCAAAGCAA
*
2136157 AGCAAAACCCATTATTAATCTAC
1 AGCAAAACCCATTAGTAATCTAC
*
2136180 AGCAAAACCACCATTAGTCATCTAC
1 AGCAAAA-C-CCATTAGTAATCTAC
2136205 TACAGTTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 1 0.05
25 13 0.62
ACGTcount: A:0.42, C:0.29, G:0.06, T:0.23
Consensus pattern (23 bp):
AGCAAAACCCATTAGTAATCTAC
Found at i:2136700 original size:26 final size:26
Alignment explanation
Indices: 2136648--2136700 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2136638 ATGAGATTAA
*
2136648 TATTCAAAAACAAATCCATAATATTG
1 TATTCAAAAACAAATCCAGAATATTG
*
2136674 TATTCAATAACAAATCCGAGAAT-TTG
1 TATTCAAAAACAAATCC-AGAATATTG
2136700 T
1 T
2136701 TGTTGGAGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (26 bp):
TATTCAAAAACAAATCCAGAATATTG
Found at i:2139367 original size:19 final size:20
Alignment explanation
Indices: 2139334--2139388 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
2139324 AATTTAGTCT
*
2139334 TTAATATTTGTATTTTTTTAA
1 TTAA-ATTTGGATTTTTTTAA
*
2139355 TT-AATTTGGATTTTTTTAG
1 TTAAATTTGGATTTTTTTAA
2139374 TTAAATTTGG-TTTTT
1 TTAAATTTGGATTTTT
2139389 AATTTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 21 0.68
20 8 0.26
21 2 0.06
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.65
Consensus pattern (20 bp):
TTAAATTTGGATTTTTTTAA
Found at i:2148861 original size:38 final size:38
Alignment explanation
Indices: 2148818--2148894 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
2148808 TTGAGTTCAT
2148818 AAGTTTATATCTAAGAAGATAAATTTAGCCCCATTCTG
1 AAGTTTATATCTAAGAAGATAAATTTAGCCCCATTCTG
*
2148856 AAGTTTATATCTAAGAAGATAAATTTAGTCCCATTCTG
1 AAGTTTATATCTAAGAAGATAAATTTAGCCCCATTCTG
2148894 A
1 A
2148895 TACTTTGATC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (38 bp):
AAGTTTATATCTAAGAAGATAAATTTAGCCCCATTCTG
Found at i:2151056 original size:31 final size:32
Alignment explanation
Indices: 2150992--2151061 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
2150982 TAACAGAGAA
*
2150992 TGACT-AAAATAGAAATGATCTAAATCGTGAG
1 TGACTAAAAATAGAAATGATCTAAATCATGAG
* *
2151023 TGA-TAAAAATAGAAATTATCTAAAAT-ATTAG
1 TGACTAAAAATAGAAATGATCT-AAATCATGAG
2151054 TGACTAAA
1 TGACTAAA
2151062 TTAAATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 1 0.03
31 24 0.73
32 8 0.24
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (32 bp):
TGACTAAAAATAGAAATGATCTAAATCATGAG
Done.