Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 6 of 163
Found at i:1827431 original size:19 final size:19
Alignment explanation
Indices: 1827407--1827445 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1827397 CAAACCAACA
1827407 TTTAAAATTGGTAGAAATG
1 TTTAAAATTGGTAGAAATG
1827426 TTTAAAATTGGTAGAAATG
1 TTTAAAATTGGTAGAAATG
1827445 T
1 T
1827446 CTAGAACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (19 bp):
TTTAAAATTGGTAGAAATG
Found at i:1828023 original size:16 final size:16
Alignment explanation
Indices: 1828002--1828039 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1827992 GAAGAGTAGA
1828002 AAAAAATTG-AAAGGAT
1 AAAAAATTGAAAAGG-T
1828018 AAAAAATTGAAAAGGT
1 AAAAAATTGAAAAGGT
1828034 AAAAAA
1 AAAAAA
1828040 ATAGAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (16 bp):
AAAAAATTGAAAAGGT
Found at i:1828047 original size:17 final size:16
Alignment explanation
Indices: 1828000--1828057 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 16
1827990 AGGAAGAGTA
1828000 GAAAAAAATTG-AAAG
1 GAAAAAAATTGAAAAG
1828015 GATAAAAAATTGAAAAG
1 GA-AAAAAATTGAAAAG
*
1828032 GTAAAAAAATAGAAAAAAG
1 G-AAAAAAATTG--AAAAG
1828051 GAAAAAA
1 GAAAAAA
1828058 TACAGATGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
15 2 0.05
16 9 0.24
17 13 0.35
18 7 0.19
19 6 0.16
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (16 bp):
GAAAAAAATTGAAAAG
Found at i:1828384 original size:47 final size:47
Alignment explanation
Indices: 1828316--1828415 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 47
1828306 AAAAAATAAA
* * * *
1828316 AAAAAATCAAATAAAGCTAAATTATAACAGAATTAATATTTGATGTT
1 AAAAAATCAAATAAAACTAAATTATAACAGAATTAACATTTAATATT
* * *
1828363 AAAAAATCAAATAAAACTAAATTGTAACGGACTTAACATTTAATATT
1 AAAAAATCAAATAAAACTAAATTATAACAGAATTAACATTTAATATT
1828410 AAAAAA
1 AAAAAA
1828416 CTGACATGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.29
Consensus pattern (47 bp):
AAAAAATCAAATAAAACTAAATTATAACAGAATTAACATTTAATATT
Found at i:1828694 original size:16 final size:16
Alignment explanation
Indices: 1828673--1828710 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1828663 AAGAGTAGAA
1828673 AAAAAATTG-AAAGGAT
1 AAAAAATTGAAAAGG-T
1828689 AAAAAATTGAAAAGGT
1 AAAAAATTGAAAAGGT
1828705 AAAAAA
1 AAAAAA
1828711 ATAGAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (16 bp):
AAAAAATTGAAAAGGT
Found at i:1828718 original size:17 final size:16
Alignment explanation
Indices: 1828672--1828728 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 16
1828662 GAAGAGTAGA
1828672 AAAAAAATTG-AAAGG
1 AAAAAAATTGAAAAGG
1828687 ATAAAAAATTGAAAAGG
1 A-AAAAAATTGAAAAGG
*
1828704 TAAAAAAATAGAAAAAAGG
1 -AAAAAAATTG--AAAAGG
1828723 AAAAAA
1 AAAAAA
1828729 TACAGATGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
15 1 0.03
16 9 0.25
17 13 0.36
18 7 0.19
19 6 0.17
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (16 bp):
AAAAAAATTGAAAAGG
Found at i:1828780 original size:671 final size:670
Alignment explanation
Indices: 1827911--1829255 Score: 2654
Period size: 671 Copynumber: 2.0 Consensus size: 670
1827901 CAAGACTAAG
1827911 AAACATTTAGTCCCCTATTTTATTATTTTAATCAAGGGATAAAATAACATTTAGGATCTAAAAAA
1 AAACATTTAGTCCCCTATTTTATTATTTTAATCAAGGGATAAAATAACATTTAGGATCTAAAAAA
1827976 CATTTAGGCTTTTTAGGAAGAGTAGAAAAAAATTGAAAGGATAAAAAATTGAAAAGGTAAAAAAA
66 CATTTAGGCTTTTTAGGAAGAGTAGAAAAAAATTGAAAGGATAAAAAATTGAAAAGGTAAAAAAA
1828041 TAGAAAAAAGGAAAAAATACAGATGTAGTTGGTAGGAATGATGGAAAAATTAAAAGAAAAATAAT
131 TAGAAAAAAGGAAAAAATACAGATGTAGTTGGTAGGAATGATGGAAAAATTAAAAGAAAAATAAT
1828106 GTTGATACATTACTTGGTAGAGTTAAATAAGTACGCAGTAAAAGAATAATCCTTTGAAAAATGCA
196 GTTGATACATTACTTGGTAGAGTTAAATAAGTACGCAGTAAAAGAATAATCCTTTGAAAAATGCA
1828171 TAATGGTGAAAGCCCTTGTCAAGCCTCTCTGTTACAGGGATTGCATCAAATCAATCCCTAAGCTA
261 TAATGGTGAAAGCCCTTGTCAAGCCTCTCTGTTACAGGGATTGCATCAAATCAATCCCTAAGCTA
* *
1828236 TTAAATGTATCATTTTGGTTCATGTATTATTTAATGAATTAGTTATCGGATTCACTTCGGTAAAT
326 TTAAATGTATCATTTTAGTTCATGTATTATTTAATGAATTAGTTATCGGATTCACTCCGGTAAAT
1828301 ATCTCAAAAAATAAAAAAAAATCAAATAAAGCTAAATTATAACAGAATTAATATTTGATGTTAAA
391 ATCTCAAAAAATAAAAAAAAATCAAATAAAGCTAAATTATAACAGAATTAATATTTGATGTTAAA
1828366 AAATCAAATAAAACTAAATTGTAACGGACTTAACATTTAATATTAAAAAACTGACATGAAAATCA
456 AAATCAAATAAAACTAAATTGTAACGGACTTAACATTTAATATTAAAAAACTGACATGAAAATCA
1828431 ATTTTTAAAATATCTTAACTTCAGCTTTTTGAGAATCAACATTAAAGCTCACATTCGTTTTATTA
521 ATTTTTAAAATATCTTAACTTCAGCTTTTTGAGAATCAACATTAAAGCTCACATTCGTTTTATTA
1828496 AAGGTCTCACATGAATACAATTTATTATCATGTAAGATAGAAAACTAAAACATCAAAGACAACAA
586 AAGGTCTCACATGAATACAATTTATTATCATGTAAGATAGAAAACTAAAACATCAAAGACAACAA
1828561 ATTAAAAACAAAACATCATT
651 ATTAAAAACAAAACATCATT
1828581 AAACATTTAGTCCCCTATTTTATTATTTTAATCAAGGGATAAAATAACATTTAGGATCTAAAAAA
1 AAACATTTAGTCCCCTATTTTATTATTTTAATCAAGGGATAAAATAACATTTAGGATCTAAAAAA
1828646 CATTTAGGCTTTTTAGGAAGAGTAGAAAAAAAATTGAAAGGATAAAAAATTGAAAAGGTAAAAAA
66 CATTTAGGCTTTTTAGGAAGAGTAG-AAAAAAATTGAAAGGATAAAAAATTGAAAAGGTAAAAAA
1828711 ATAGAAAAAAGGAAAAAATACAGATGTAGTTGGTAGGAATGATGGAAAAATTAAAAGAAAAATAA
130 ATAGAAAAAAGGAAAAAATACAGATGTAGTTGGTAGGAATGATGGAAAAATTAAAAGAAAAATAA
1828776 TGTTGATACATTACTTGGTAGAGTTAAATAAGTACGCAGTAAAAGAATAATCCTTTGAAAAATGC
195 TGTTGATACATTACTTGGTAGAGTTAAATAAGTACGCAGTAAAAGAATAATCCTTTGAAAAATGC
1828841 ATAATGGTGAAAGCCCTTGTCAAGCCTCTCTGTTACAGGGATTGCATCAAATCAATCCCTAAGCT
260 ATAATGGTGAAAGCCCTTGTCAAGCCTCTCTGTTACAGGGATTGCATCAAATCAATCCCTAAGCT
1828906 ATTAAATGTATCATTTTAGTTCATGTATTATTTAATGAATTAGTTATCGGATTCACTCCGGTAAA
325 ATTAAATGTATCATTTTAGTTCATGTATTATTTAATGAATTAGTTATCGGATTCACTCCGGTAAA
1828971 TATCTCAAAAAATAAAAAAAAATCAAATAAAGCTAAATTATAACAGAATTAATATTTGATGTTAA
390 TATCTCAAAAAATAAAAAAAAATCAAATAAAGCTAAATTATAACAGAATTAATATTTGATGTTAA
1829036 AAAATCAAATAAAACTAAATTGTAACGGACTTAACATTTAATATTAAAAAACTGACATGAAAATC
455 AAAATCAAATAAAACTAAATTGTAACGGACTTAACATTTAATATTAAAAAACTGACATGAAAATC
1829101 AATTTTTAAAATATCTTAACTTCAGCTTTTTGAGAATCAACATTAAAGCTCACATTCGTTTTATT
520 AATTTTTAAAATATCTTAACTTCAGCTTTTTGAGAATCAACATTAAAGCTCACATTCGTTTTATT
*
1829166 AGAGGTCTCACATGAATACAATTTATTATCATGTAAGATAGAAAACTAAAACATCAAAGACAACA
585 AAAGGTCTCACATGAATACAATTTATTATCATGTAAGATAGAAAACTAAAACATCAAAGACAACA
1829231 AATTAAAAACAAAACATCATT
650 AATTAAAAACAAAACATCATT
1829252 AAAC
1 AAAC
1829256 TTTTTTTTGT
Statistics
Matches: 671, Mismatches: 3, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
670 90 0.13
671 581 0.87
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (670 bp):
AAACATTTAGTCCCCTATTTTATTATTTTAATCAAGGGATAAAATAACATTTAGGATCTAAAAAA
CATTTAGGCTTTTTAGGAAGAGTAGAAAAAAATTGAAAGGATAAAAAATTGAAAAGGTAAAAAAA
TAGAAAAAAGGAAAAAATACAGATGTAGTTGGTAGGAATGATGGAAAAATTAAAAGAAAAATAAT
GTTGATACATTACTTGGTAGAGTTAAATAAGTACGCAGTAAAAGAATAATCCTTTGAAAAATGCA
TAATGGTGAAAGCCCTTGTCAAGCCTCTCTGTTACAGGGATTGCATCAAATCAATCCCTAAGCTA
TTAAATGTATCATTTTAGTTCATGTATTATTTAATGAATTAGTTATCGGATTCACTCCGGTAAAT
ATCTCAAAAAATAAAAAAAAATCAAATAAAGCTAAATTATAACAGAATTAATATTTGATGTTAAA
AAATCAAATAAAACTAAATTGTAACGGACTTAACATTTAATATTAAAAAACTGACATGAAAATCA
ATTTTTAAAATATCTTAACTTCAGCTTTTTGAGAATCAACATTAAAGCTCACATTCGTTTTATTA
AAGGTCTCACATGAATACAATTTATTATCATGTAAGATAGAAAACTAAAACATCAAAGACAACAA
ATTAAAAACAAAACATCATT
Found at i:1829055 original size:47 final size:47
Alignment explanation
Indices: 1828987--1829086 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 47
1828977 AAAAAATAAA
* * * *
1828987 AAAAAATCAAATAAAGCTAAATTATAACAGAATTAATATTTGATGTT
1 AAAAAATCAAATAAAACTAAATTATAACAGAATTAACATTTAATATT
* * *
1829034 AAAAAATCAAATAAAACTAAATTGTAACGGACTTAACATTTAATATT
1 AAAAAATCAAATAAAACTAAATTATAACAGAATTAACATTTAATATT
1829081 AAAAAA
1 AAAAAA
1829087 CTGACATGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.29
Consensus pattern (47 bp):
AAAAAATCAAATAAAACTAAATTATAACAGAATTAACATTTAATATT
Found at i:1837646 original size:17 final size:17
Alignment explanation
Indices: 1837624--1837656 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1837614 TGAAGATTAA
1837624 TTTGCATGAATCTGCTT
1 TTTGCATGAATCTGCTT
*
1837641 TTTGCATGAATGTGCT
1 TTTGCATGAATCTGCT
1837657 GTTGAAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.45
Consensus pattern (17 bp):
TTTGCATGAATCTGCTT
Found at i:1837688 original size:36 final size:36
Alignment explanation
Indices: 1837641--1837728 Score: 149
Period size: 36 Copynumber: 2.4 Consensus size: 36
1837631 GAATCTGCTT
1837641 TTTGCATGAATGTGCTGTTGAAACTATAAAGATTAA
1 TTTGCATGAATGTGCTGTTGAAACTATAAAGATTAA
* * *
1837677 TTTGCATGAATGTGTTGTTTAAACTATAAAGATTAG
1 TTTGCATGAATGTGCTGTTGAAACTATAAAGATTAA
1837713 TTTGCATGAATGTGCT
1 TTTGCATGAATGTGCT
1837729 TTTTGCATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (36 bp):
TTTGCATGAATGTGCTGTTGAAACTATAAAGATTAA
Found at i:1838978 original size:126 final size:126
Alignment explanation
Indices: 1838753--1839378 Score: 1036
Period size: 126 Copynumber: 5.0 Consensus size: 126
1838743 GTCCCTCACG
* * *
1838753 AAATGGCTGCAGCTGTTAGTCAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
1 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
* * *
1838818 CAGCTTGAAGTCCAACCATTTAACATGAATCTCGAGCAAGACACTAGTTGGTTACCTCGCA
66 CAGCTTGAAGTCCAATCATTTGACACGAATCTCGAGCAAGACACTAGTTGGTTACCTCGCA
* *
1838879 AAATGGCTGAACCTGTTACTGAACCCATTAGTATGGTTGCACCACCTGTTTATGATCAATATGAA
1 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
1838944 CAGCTTGAAGTCCAATCATTTGACACGAATCTCGAGCAAGACACTAGTTGGTTACCTCGCA
66 CAGCTTGAAGTCCAATCATTTGACACGAATCTCGAGCAAGACACTAGTTGGTTACCTCGCA
1839005 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
1 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
* * *
1839070 CAGTTTGAAATCCAATCATTTGACACGATTCTCGAGCAAGACACTAGTTGGTTACCTCGCA
66 CAGCTTGAAGTCCAATCATTTGACACGAATCTCGAGCAAGACACTAGTTGGTTACCTCGCA
*
1839131 AAATGGTTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
1 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
* * *
1839196 CAACTTGAAGTCCAATCATTTGACACGATTCTCGAGCAAGACACTAGTCGGTTACCTCGCA
66 CAGCTTGAAGTCCAATCATTTGACACGAATCTCGAGCAAGACACTAGTTGGTTACCTCGCA
* *
1839257 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGCTGCACCACCTGTTTATGTTCAATATGAA
1 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
* * * * * * *
1839322 CAGCTTGAAGTTCAACCATTTAACATGAATCTCGAACAAGACACTAATTGCTTACCT
66 CAGCTTGAAGTCCAATCATTTGACACGAATCTCGAGCAAGACACTAGTTGGTTACCT
1839379 GAAGAAGACA
Statistics
Matches: 469, Mismatches: 31, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 469 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (126 bp):
AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
CAGCTTGAAGTCCAATCATTTGACACGAATCTCGAGCAAGACACTAGTTGGTTACCTCGCA
Found at i:1841506 original size:14 final size:14
Alignment explanation
Indices: 1841463--1841506 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1841453 CTCATAAGTG
1841463 TTATGTTTAAATAA
1 TTATGTTTAAATAA
*
1841477 TT-T-TTTAAAGAA
1 TTATGTTTAAATAA
*
1841489 TTATGTTTAAATAT
1 TTATGTTTAAATAA
1841503 TTAT
1 TTAT
1841507 TTGACTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 10 0.40
13 2 0.08
14 13 0.52
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
TTATGTTTAAATAA
Found at i:1842602 original size:78 final size:78
Alignment explanation
Indices: 1842507--1842773 Score: 464
Period size: 78 Copynumber: 3.4 Consensus size: 78
1842497 CTTATAATGG
* * *
1842507 TGGTGGCAACTCAAAGTCAGGATCTTGATTGAACTGATCAAGATGTGAGAAATCAAAATCACTTG
1 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGGGAAATCAAAATCACTTG
*
1842572 GGGGCTGAACATT
66 GGGGCTGAACACT
1842585 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGGGAAATCAAAATCACTTG
1 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGGGAAATCAAAATCACTTG
1842650 GGGGCTGAACACT
66 GGGGCTGAACACT
1842663 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGGGAAATCAAAATCACTTG
1 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGGGAAATCAAAATCACTTG
1842728 GGAGG-TGAACACT
66 GG-GGCTGAACACT
* *
1842741 TGGTGGCAACCCAGAGTCAGGATCTTGAATGAA
1 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAA
1842774 GGAGCAATCT
Statistics
Matches: 182, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
78 180 0.99
79 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.23
Consensus pattern (78 bp):
TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGGGAAATCAAAATCACTTG
GGGGCTGAACACT
Found at i:1843047 original size:15 final size:15
Alignment explanation
Indices: 1843010--1843041 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1843000 ATACATTAAT
1843010 TAAGCTAAATGAATC
1 TAAGCTAAATGAATC
*
1843025 TAAGCTAAATGCATC
1 TAAGCTAAATGAATC
1843040 TA
1 TA
1843042 CTCTAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (15 bp):
TAAGCTAAATGAATC
Found at i:1847442 original size:15 final size:15
Alignment explanation
Indices: 1847405--1847436 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1847395 ATACATTAAT
1847405 TAAGCTAAATGCATC
1 TAAGCTAAATGCATC
1847420 TAAGCTAAATGCATC
1 TAAGCTAAATGCATC
1847435 TA
1 TA
1847437 TTCTAATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (15 bp):
TAAGCTAAATGCATC
Found at i:1847805 original size:81 final size:81
Alignment explanation
Indices: 1847686--1847981 Score: 502
Period size: 81 Copynumber: 3.7 Consensus size: 81
1847676 TCCATTGTAT
* * * *
1847686 GGTAGAATTGCACCTGTATCAGCTTCACCTTCACCTTCCTCTTGATGACCTTCTTGTTGAACCAT
1 GGTACAATTGCACTTGTATCAGCTTCAGCTTCAGCTTCCTCTTGATGACCTTCTTGTTGAACCAT
1847751 TTGGGTTTCATCATAA
66 TTGGGTTTCATCATAA
*
1847767 GGTACAATTGCACTTGTATCAGCTTCAGTTTCAGCTTCCTCTTGATGACCTTCTTGTTGAACCAT
1 GGTACAATTGCACTTGTATCAGCTTCAGCTTCAGCTTCCTCTTGATGACCTTCTTGTTGAACCAT
* *
1847832 TTAGGTTTCATCGTAA
66 TTGGGTTTCATCATAA
* *
1847848 GGTACAATTGCACTTGTATAAGCTTCAGTTTCAGCTTCCTCTTGATGACCTTCTTGTTGAACCAT
1 GGTACAATTGCACTTGTATCAGCTTCAGCTTCAGCTTCCTCTTGATGACCTTCTTGTTGAACCAT
*
1847913 TTGGGTTTGATCATAA
66 TTGGGTTTCATCATAA
1847929 GGTACAATTGCACTTGTATCAGCTTCAGCTTCAGCTTCCTCTTGATGACCTTC
1 GGTACAATTGCACTTGTATCAGCTTCAGCTTCAGCTTCCTCTTGATGACCTTC
1847982 CTGTAAGTTT
Statistics
Matches: 202, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 202 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (81 bp):
GGTACAATTGCACTTGTATCAGCTTCAGCTTCAGCTTCCTCTTGATGACCTTCTTGTTGAACCAT
TTGGGTTTCATCATAA
Found at i:1849779 original size:163 final size:163
Alignment explanation
Indices: 1849509--1849826 Score: 487
Period size: 163 Copynumber: 2.0 Consensus size: 163
1849499 TCTCTTTTGG
* *
1849509 ATTCTGAGTTTGGCATGCCACCACAATCCAAGTTTTGTTGAATATTTGGAGAGGGGTGTGAAAGC
1 ATTCTGAGTTTGGCATGCCACCACAATCCAAGTTTTATTGAAAATTTGGAGAGGGGTGTGAAAGC
* * * * *
1849574 TTGTCTAATTAAACCGGTTTTCTTTGATTAGACACGCTTTCACATTTTCTCTCTAAAATCGATTT
66 GTGTCTAATTAAACCGGTTTTCTTTGATTAGACACGCTTTCACACTATCTATCCAAAATCGATTT
* *
1849639 ATTTTTTTAAATCATCATAAAAACAATTTGATT
131 ATTTTTTAAAATCATCAGAAAAACAATTTGATT
* *
1849672 ATTCTGAGTTTGGCATGCCACCACCATCCGAA-TTTTATTGAAAATTTGGAG-GATGGTGTGAAA
1 ATTCTGAGTTTGGCATGCCACCACAATCC-AAGTTTTATTGAAAATTTGGAGAG-GGGTGTGAAA
* *
1849735 GCGTGTCTAATTAAACCGGTTTTCTTTTATTAGACACGCTTTCACACTATCTATCCAAAATTGAT
64 GCGTGTCTAATTAAACCGGTTTTCTTTGATTAGACACGCTTTCACACTATCTATCCAAAATCGAT
1849800 TTATTTTTTAAAATCATCAGAAAAACA
129 TTATTTTTTAAAATCATCAGAAAAACA
1849827 GTTATCAACT
Statistics
Matches: 140, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
162 1 0.01
163 137 0.98
164 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (163 bp):
ATTCTGAGTTTGGCATGCCACCACAATCCAAGTTTTATTGAAAATTTGGAGAGGGGTGTGAAAGC
GTGTCTAATTAAACCGGTTTTCTTTGATTAGACACGCTTTCACACTATCTATCCAAAATCGATTT
ATTTTTTAAAATCATCAGAAAAACAATTTGATT
Found at i:1851451 original size:14 final size:14
Alignment explanation
Indices: 1851408--1851451 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1851398 CTCATAAGTG
1851408 TTATGTTTAAATAA
1 TTATGTTTAAATAA
*
1851422 TT-T-TTTAAAGAA
1 TTATGTTTAAATAA
*
1851434 TTATGTTTAAATAT
1 TTATGTTTAAATAA
1851448 TTAT
1 TTAT
1851452 TTGACTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 10 0.40
13 2 0.08
14 13 0.52
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
TTATGTTTAAATAA
Found at i:1852265 original size:17 final size:17
Alignment explanation
Indices: 1852243--1852275 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1852233 TGAAGATTAA
1852243 TTTGCATGAATCTGCTT
1 TTTGCATGAATCTGCTT
*
1852260 TTTGCATGAATGTGCT
1 TTTGCATGAATCTGCT
1852276 GTTGAAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.45
Consensus pattern (17 bp):
TTTGCATGAATCTGCTT
Found at i:1852307 original size:36 final size:36
Alignment explanation
Indices: 1852260--1852347 Score: 149
Period size: 36 Copynumber: 2.4 Consensus size: 36
1852250 GAATCTGCTT
1852260 TTTGCATGAATGTGCTGTTGAAACTATAAAGATTAA
1 TTTGCATGAATGTGCTGTTGAAACTATAAAGATTAA
* * *
1852296 TTTGCATGAATGTGTTGTTTAAACTATAAAGATTAG
1 TTTGCATGAATGTGCTGTTGAAACTATAAAGATTAA
1852332 TTTGCATGAATGTGCT
1 TTTGCATGAATGTGCT
1852348 TTTTGCATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (36 bp):
TTTGCATGAATGTGCTGTTGAAACTATAAAGATTAA
Found at i:1853641 original size:28 final size:28
Alignment explanation
Indices: 1853582--1853641 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1853572 AAATTGTTAG
* * **
1853582 TTTTTCAATATTTAAGAAAATATTTCAT
1 TTTTTAAATATTTAAAAAAATAAATCAT
1853610 TTTTTAAATATTTAAAAAAATAAATCGAT
1 TTTTTAAATATTTAAAAAAATAAATC-AT
1853639 TTT
1 TTT
1853642 AAAGAGATGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (28 bp):
TTTTTAAATATTTAAAAAAATAAATCAT
Found at i:1855589 original size:88 final size:89
Alignment explanation
Indices: 1855496--1855674 Score: 224
Period size: 88 Copynumber: 2.0 Consensus size: 89
1855486 AGCTTTTTTT
* *
1855496 TTTTTTTTGCACTCAATT-GA-GCTGA-ACTTTCAAAATACATAAAAAAAAGTC-CTCAAATTTT
1 TTTTTTTT-CACTCAATTGGATACTGATACTTTCAAAATACATAAAAAAAA--CACTCAAAATTT
*
1855557 TTCAAAAAAAGCAATTAAGCCCTTG-TC
63 TTC-AAAAAAGCAATTAAACCCTTGCTC
* * * *
1855584 TTTTTTTTCACTCAATTGGATACTTATACTTTCAAAATGCATCAAAAATACACTCAAAATTTTTC
1 TTTTTTTTCACTCAATTGGATACTGATACTTTCAAAATACATAAAAAAAACACTCAAAATTTTTC
1855649 AAAAAAGCAATTAAACCCTTGCTC
66 AAAAAAGCAATTAAACCCTTGCTC
1855673 TT
1 TT
1855675 ATTAAAAATT
Statistics
Matches: 79, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
87 9 0.11
88 31 0.39
89 19 0.24
90 20 0.25
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (89 bp):
TTTTTTTTCACTCAATTGGATACTGATACTTTCAAAATACATAAAAAAAACACTCAAAATTTTTC
AAAAAAGCAATTAAACCCTTGCTC
Found at i:1855738 original size:19 final size:18
Alignment explanation
Indices: 1855705--1855759 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
1855695 TTATAAAAAA
*
1855705 TAAATTTTAGA-AAAATTAT
1 TAAATTTTA-ATAAAAAT-T
1855724 TAAATTTTAATAAAAATT
1 TAAATTTTAATAAAAATT
* *
1855742 TAAAATTTATTAAAAATT
1 TAAATTTTAATAAAAATT
1855760 CAAAATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 18 0.56
19 14 0.44
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TAAATTTTAATAAAAATT
Found at i:1855750 original size:18 final size:18
Alignment explanation
Indices: 1855723--1855767 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1855713 AGAAAAATTA
*
1855723 TTAAATTTTAATAAAAAT
1 TTAAAATTTAATAAAAAT
*
1855741 TTAAAATTTATTAAAAAT
1 TTAAAATTTAATAAAAAT
*
1855759 TCAAAATTT
1 TTAAAATTT
1855768 TTTATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAATTTAATAAAAAT
Found at i:1856032 original size:9 final size:9
Alignment explanation
Indices: 1856018--1856226 Score: 70
Period size: 9 Copynumber: 22.0 Consensus size: 9
1856008 TTTTCGTATG
1856018 ATAATTTTT
1 ATAATTTTT
1856027 ATAATTCTTT
1 ATAATT-TTT
*
1856037 -TACGAATTTT
1 ATA--ATTTTT
*
1856047 ATATTTCTTT
1 ATAATT-TTT
1856057 AT-ATTTTGT
1 ATAATTTT-T
1856066 ATAATTTTCTT
1 ATAA-TTT-TT
*
1856077 ATGATTTTAT
1 ATAATTTT-T
*
1856087 AAAATTTTAT
1 ATAATTTT-T
*
1856097 AATAAAATTTT
1 -AT-AATTTTT
1856108 AT-ATTTTT
1 ATAATTTTT
1856116 AT-ATATTTT
1 ATAAT-TTTT
1856125 ATAAATTTTT
1 AT-AATTTTT
***
1856135 ACGGTTTTT
1 ATAATTTTT
*
1856144 ATAAAATTTT
1 AT-AATTTTT
*
1856154 ACAATTTTT
1 ATAATTTTT
*
1856163 TTATATTTTT
1 ATA-ATTTTT
**
1856173 ACGATTTTT
1 ATAATTTTT
*
1856182 ATATTTTTT
1 ATAATTTTT
1856191 A-AATTTTT
1 ATAATTTTT
1856199 ACT-ATTTTT
1 A-TAATTTTT
* * *
1856208 TTAAATTTA
1 ATAATTTTT
1856217 ATAATATTTT
1 ATAAT-TTTT
1856227 TAGCTTTTGT
Statistics
Matches: 145, Mismatches: 34, Indels: 41
0.66 0.15 0.19
Matches are distributed among these distances:
8 19 0.13
9 60 0.41
10 45 0.31
11 15 0.10
12 6 0.04
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:1856076 original size:21 final size:21
Alignment explanation
Indices: 1856050--1856094 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1856040 GAATTTTATA
* *
1856050 TTTCTTTAT-ATTTTGTATAAT
1 TTTC-TTATGATTTTATAAAAT
1856071 TTTCTTATGATTTTATAAAAT
1 TTTCTTATGATTTTATAAAAT
1856092 TTT
1 TTT
1856095 ATAATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTCTTATGATTTTATAAAAT
Found at i:1856103 original size:13 final size:13
Alignment explanation
Indices: 1856085--1856110 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1856075 TTATGATTTT
1856085 ATAAAATTTTATA
1 ATAAAATTTTATA
1856098 ATAAAATTTTATA
1 ATAAAATTTTATA
1856111 TTTTTATATA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAAAATTTTATA
Found at i:1856146 original size:59 final size:61
Alignment explanation
Indices: 1856041--1856154 Score: 155
Period size: 59 Copynumber: 1.9 Consensus size: 61
1856031 TTCTTTTACG
* *
1856041 AATTTTATATTTCTTTATATTTTGTATAATTTTCTTATGATTTTATAAAATTTTATAATAA
1 AATTTTATATTTCTTTATATTTTGTATAAATTTCTTAGGATTTTATAAAATTTTATAATAA
*
1856102 AATTTTATA-TT-TTTATATATTT-TATAAATTT-TTACGGTTTTTATAAAATTTTA
1 AATTTTATATTTCTTTATAT-TTTGTATAAATTTCTTA-GGATTTTATAAAATTTTA
1856155 CAATTTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
58 3 0.06
59 31 0.65
60 5 0.10
61 9 0.19
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.60
Consensus pattern (61 bp):
AATTTTATATTTCTTTATATTTTGTATAAATTTCTTAGGATTTTATAAAATTTTATAATAA
Found at i:1856190 original size:19 final size:19
Alignment explanation
Indices: 1856107--1856228 Score: 92
Period size: 19 Copynumber: 6.5 Consensus size: 19
1856097 AATAAAATTT
*
1856107 TATATTTTTA-TATATTTTA
1 TATATTTTTACAAT-TTTTA
* **
1856126 TAAATTTTTACGGTTTTTA
1 TATATTTTTACAATTTTTA
* * *
1856145 TAAAATTTTACAATTTTTT
1 TATATTTTTACAATTTTTA
*
1856164 TATATTTTTACGATTTTTA
1 TATATTTTTACAATTTTTA
1856183 TAT-TTTTTA-AATTTTTA
1 TATATTTTTACAATTTTTA
* *
1856200 CTATTTTTTTA-AA-TTTAA
1 -TATATTTTTACAATTTTTA
1856218 TAATATTTTTA
1 T-ATATTTTTA
1856229 GCTTTTGTTG
Statistics
Matches: 85, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
17 8 0.09
18 21 0.25
19 55 0.65
20 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.63
Consensus pattern (19 bp):
TATATTTTTACAATTTTTA
Found at i:1856434 original size:88 final size:90
Alignment explanation
Indices: 1856267--1856436 Score: 200
Period size: 88 Copynumber: 1.9 Consensus size: 90
1856257 TTTTTAAGAT
* * * * * *
1856267 TTAATTGCTTTTTTTTAAAAAAAGGTTTGAGGGTTTTTTTAATACATTTTAAAAGTTTAAGTATC
1 TTAATTACTTTTTTTT-AAAAAAGGTTTGAGGATCTTTTTAATACATTTCAAAAGTTCAAGTACC
* * * *
1856332 CAATTGAGTGCAAAAAAAATAGGGGC
65 CAAATAAATACAAAAAAAATAGGGGC
* * *
1856358 TTAATTAC-TTTTTTT-AAAAAGGTTTGAGGATCTTTTTGATGCATTTCGAAAGTTCAAGTACCC
1 TTAATTACTTTTTTTTAAAAAAGGTTTGAGGATCTTTTTAATACATTTCAAAAGTTCAAGTACCC
1856421 AAATAAATACAAAAAA
66 AAATAAATACAAAAAA
1856437 GGGACTTAAT
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
88 52 0.79
90 7 0.11
91 7 0.11
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (90 bp):
TTAATTACTTTTTTTTAAAAAAGGTTTGAGGATCTTTTTAATACATTTCAAAAGTTCAAGTACCC
AAATAAATACAAAAAAAATAGGGGC
Found at i:1858460 original size:126 final size:126
Alignment explanation
Indices: 1857835--1858449 Score: 1050
Period size: 126 Copynumber: 4.9 Consensus size: 126
1857825 GTCCCTCACG
* * *
1857835 AAATGGCTGCAGCTGTTAGTCAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
1 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
* *
1857900 CAGCTTGAAGTCCAACCATTTAACATGAATCTCGAGCAAGACACTAGTTGGTTACCTCGCA
66 CAGCTTGAAGTCCAATCATTTGACATGAATCTCGAGCAAGACACTAGTTGGTTACCTCGCA
* *
1857961 AAATGGCTGAACCTGTTACTGAACCCATTAGTATGGTTGCACCACCTGTTTATGATCAATATGAA
1 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
*
1858026 CAGCTTGAAGTCCAATCATTTGACACGAATCTCGAGCAAGACACTAGTTGGTTACCTCGCA
66 CAGCTTGAAGTCCAATCATTTGACATGAATCTCGAGCAAGACACTAGTTGGTTACCTCGCA
1858087 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
1 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
* * *
1858152 CAGTTTGAAATCCAATCATTTGACATGATTCTCGAGCAAGACACTAGTTGGTTACCTCGCA
66 CAGCTTGAAGTCCAATCATTTGACATGAATCTCGAGCAAGACACTAGTTGGTTACCTCGCA
1858213 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
1 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
* * *
1858278 CAGCTTAAAGTCCAATCATTTGACACGATTCTCGAGCAAGACACTAGTTGGTTACCTCGCA
66 CAGCTTGAAGTCCAATCATTTGACATGAATCTCGAGCAAGACACTAGTTGGTTACCTCGCA
* *
1858339 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGCTGCACCACCTGTTTATGTTCAATATGAA
1 AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
* * * *
1858404 CAGCTTGAAGTTCAACCATTTAACATGAATCTCGAACAAGACACTA
66 CAGCTTGAAGTCCAATCATTTGACATGAATCTCGAGCAAGACACTA
1858450 ACTGCTTACC
Statistics
Matches: 462, Mismatches: 27, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 462 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (126 bp):
AAATGGCTGAACCTGTTAGTGAACCCATTAATATGGTTGCACCACCTGTTTATGATCAATATGAA
CAGCTTGAAGTCCAATCATTTGACATGAATCTCGAGCAAGACACTAGTTGGTTACCTCGCA
Found at i:1859203 original size:22 final size:21
Alignment explanation
Indices: 1859178--1859228 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1859168 ATAATTTATA
*
1859178 TATTTATATAAAACTCTTATTT
1 TATTAATATAAAA-TCTTATTT
* *
1859200 TATTAATTTAAAATTTTATTT
1 TATTAATATAAAATCTTATTT
*
1859221 TGTTAATA
1 TATTAATA
1859229 AATTTTAACA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (21 bp):
TATTAATATAAAATCTTATTT
Found at i:1860587 original size:14 final size:14
Alignment explanation
Indices: 1860544--1860587 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1860534 CTCATAAGTG
1860544 TTATGTTTAAATAA
1 TTATGTTTAAATAA
*
1860558 TT-T-TTTAAAGAA
1 TTATGTTTAAATAA
*
1860570 TTATGTTTAAATAT
1 TTATGTTTAAATAA
1860584 TTAT
1 TTAT
1860588 TTGACTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 10 0.40
13 2 0.08
14 13 0.52
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
TTATGTTTAAATAA
Found at i:1861689 original size:78 final size:78
Alignment explanation
Indices: 1861590--1861860 Score: 445
Period size: 78 Copynumber: 3.5 Consensus size: 78
1861580 CTTATAATGG
* * *
1861590 TGGTGGCAACTCAAAGTCAGGATCTTGATTGAACTGATCAAGATGTGAGAAATCAAAATCACTTG
1 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGGGAAATCAAAATCACTTG
*
1861655 GGGGCTGAACATT
66 GGGGCTGAACACT
* *
1861668 TGGTGGCAACCCAATGTCAGGATCTTGGTTGAACTGATCAAGAGGTGGGAAATCAAAATCACTTG
1 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGGGAAATCAAAATCACTTG
1861733 GGGGCTGAACACT
66 GGGGCTGAACACT
1861746 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGGGAAATCAAAATCACTTG
1 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGGGAAATCAAAATCACTTG
1861811 GGAGG-TGAACACT
66 GG-GGCTGAACACT
* * *
1861824 TGGTGGCAACCCAGAGTCAGGATCTTGAATGACCTGA
1 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGA
1861861 ATTGGATTAC
Statistics
Matches: 181, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
78 179 0.99
79 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.23
Consensus pattern (78 bp):
TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGGGAAATCAAAATCACTTG
GGGGCTGAACACT
Found at i:1862149 original size:15 final size:15
Alignment explanation
Indices: 1862112--1862143 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1862102 ATACATTAAT
1862112 TAAGCTAAATGAATC
1 TAAGCTAAATGAATC
*
1862127 TAAGCTAAATGCATC
1 TAAGCTAAATGAATC
1862142 TA
1 TA
1862144 CTCTAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (15 bp):
TAAGCTAAATGAATC
Found at i:1863987 original size:12 final size:12
Alignment explanation
Indices: 1863948--1863978 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1863938 AAGTATATGT
1863948 ATGTATGCATGC
1 ATGTATGCATGC
*
1863960 ATGCATGCATGC
1 ATGTATGCATGC
1863972 ATGTATG
1 ATGTATG
1863979 TATTCATGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (12 bp):
ATGTATGCATGC
Found at i:1865851 original size:21 final size:22
Alignment explanation
Indices: 1865825--1865865 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1865815 TAAACTTAAA
1865825 TTTT-AAATTTTTTAATTTTAT
1 TTTTAAAATTTTTTAATTTTAT
*
1865846 TTTTAAAATTTTTTTATTTT
1 TTTTAAAATTTTTTAATTTT
1865866 TTAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTAAAATTTTTTAATTTTAT
Found at i:1865862 original size:17 final size:17
Alignment explanation
Indices: 1865840--1865873 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1865830 AATTTTTTAA
1865840 TTTTATTTTTAAAATTT
1 TTTTATTTTTAAAATTT
*
1865857 TTTTATTTTTTAAATTT
1 TTTTATTTTTAAAATTT
1865874 AAAATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTTTTAAAATTT
Found at i:1865867 original size:24 final size:23
Alignment explanation
Indices: 1865823--1865880 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
1865813 CGTAAACTTA
1865823 AATTTT-AAA-TTTTTTAATTTT
1 AATTTTAAAATTTTTTTAATTTT
* *
1865844 ATTTTTAAAATTTTTTTATTTTTT
1 AATTTTAAAATTTTTTTA-ATTTT
*
1865868 AAATTTAAAATTT
1 AATTTTAAAATTT
1865881 AAATTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 5 0.17
22 3 0.10
23 7 0.23
24 15 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
AATTTTAAAATTTTTTTAATTTT
Found at i:1866408 original size:21 final size:21
Alignment explanation
Indices: 1866384--1866426 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1866374 ATTTAATGTT
1866384 ATATCAATATTTTCATCATAA
1 ATATCAATATTTTCATCATAA
* *
1866405 ATATTAATATTTTCATCTTAA
1 ATATCAATATTTTCATCATAA
1866426 A
1 A
1866427 AAAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATCAATATTTTCATCATAA
Found at i:1867294 original size:18 final size:18
Alignment explanation
Indices: 1867271--1867305 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1867261 CCTGATCACA
1867271 ATGATGATGGTGTTGATG
1 ATGATGATGGTGTTGATG
1867289 ATGATGATGGTGTTGAT
1 ATGATGATGGTGTTGAT
1867306 AATCCAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (18 bp):
ATGATGATGGTGTTGATG
Found at i:1867394 original size:4 final size:4
Alignment explanation
Indices: 1867385--1867414 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1867375 GAGGTATAAT
*
1867385 ATAC ATAC ATAC ATAC ATAC ATGC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1867415 GCATGCATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:1867415 original size:8 final size:8
Alignment explanation
Indices: 1867385--1867427 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
1867375 GAGGTATAAT
*
1867385 ATACATAC
1 ATACATGC
*
1867393 ATACATAC
1 ATACATGC
1867401 ATACATGC
1 ATACATGC
1867409 ATACATGC
1 ATACATGC
*
1867417 ATGCATGC
1 ATACATGC
1867425 ATA
1 ATA
1867428 ACTTTCTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (8 bp):
ATACATGC
Found at i:1867419 original size:12 final size:12
Alignment explanation
Indices: 1867385--1867427 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
1867375 GAGGTATAAT
*
1867385 ATACATACATAC
1 ATACATACATGC
1867397 ATACATACATGC
1 ATACATACATGC
*
1867409 ATACATGCATGC
1 ATACATACATGC
*
1867421 ATGCATA
1 ATACATA
1867428 ACTTTCTTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (12 bp):
ATACATACATGC
Found at i:1870026 original size:32 final size:32
Alignment explanation
Indices: 1869937--1870028 Score: 88
Period size: 32 Copynumber: 3.0 Consensus size: 32
1869927 CTTTTTGTTT
*
1869937 TTTTTTTCATTTTTTTAACGTAAATT--TTTTTA
1 TTTTTTT-ATTTTTTTAA-ATAAATTAATTTTTA
* *
1869969 TGTTTTTCA-TTTGTT--A-AAATTAATTTTTA
1 T-TTTTTTATTTTTTTAAATAAATTAATTTTTA
1869998 TTTTTTTATTTTTTTAAATAAATTAATTTTT
1 TTTTTTTATTTTTTTAAATAAATTAATTTTT
1870029 TTCGAGTGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
27 5 0.10
28 6 0.12
29 12 0.25
31 6 0.12
32 14 0.29
33 5 0.10
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (32 bp):
TTTTTTTATTTTTTTAAATAAATTAATTTTTA
Found at i:1870029 original size:28 final size:28
Alignment explanation
Indices: 1869934--1870030 Score: 88
Period size: 28 Copynumber: 3.3 Consensus size: 28
1869924 TCTCTTTTTG
*
1869934 TTTTTTTTTTCATTTTTTTAACGTAAATTT
1 TTTTTTTTTTCATTTTTTTAA-ATAAA-TT
* * *
1869964 TTTTATGTTTTTCATTTGTTAAAATTAATT
1 TTTT-T-TTTTTCATTTTTTTAAATAAATT
1869994 TTTATTTTTTT-ATTTTTTTAAATAAATT
1 TTT-TTTTTTTCATTTTTTTAAATAAATT
**
1870022 AATTTTTTT
1 TTTTTTTTT
1870031 CGAGTGAGTC
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
27 6 0.11
28 15 0.27
29 5 0.09
30 10 0.18
31 5 0.09
32 14 0.25
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTTTTTTTTCATTTTTTTAAATAAATT
Found at i:1870150 original size:11 final size:11
Alignment explanation
Indices: 1870136--1870168 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1870126 AAAGAGAATG
1870136 AAAAAAATTAA
1 AAAAAAATTAA
*
1870147 AAAAACA-TAA
1 AAAAAAATTAA
1870157 AAAAAAATTAA
1 AAAAAAATTAA
1870168 A
1 A
1870169 TTACTCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATTAA
Found at i:1870447 original size:21 final size:22
Alignment explanation
Indices: 1870410--1870475 Score: 89
Period size: 21 Copynumber: 2.9 Consensus size: 22
1870400 TTTACCGTTG
1870410 AAATTATATATAAATAAAATATAT
1 AAATTATA-A-AAATAAAATATAT
1870434 AAATTA-AAAAATAAAATATAT
1 AAATTATAAAAATAAAATATAT
1870455 AAATTATAAAATTATAAAATA
1 AAATTATAAAA--ATAAAATA
1870476 ATTAAACATT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
21 19 0.49
22 5 0.13
23 1 0.03
24 14 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATTATAAAAATAAAATATAT
Found at i:1870466 original size:8 final size:8
Alignment explanation
Indices: 1870423--1870474 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
1870413 TTATATATAA
1870423 ATAAAA-T
1 ATAAAATT
1870430 ATATAAATT
1 ATA-AAATT
1870439 A-AAAA--
1 ATAAAATT
1870444 ATAAAA-T
1 ATAAAATT
1870451 ATATAAATT
1 ATA-AAATT
1870460 ATAAAATT
1 ATAAAATT
1870468 ATAAAAT
1 ATAAAAT
1870475 AATTAAACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
5 1 0.03
6 4 0.10
7 9 0.23
8 19 0.49
9 6 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
ATAAAATT
Found at i:1872745 original size:15 final size:15
Alignment explanation
Indices: 1872725--1872754 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1872715 ATATTTATTG
1872725 TTAATTTCATTTGTT
1 TTAATTTCATTTGTT
1872740 TTAATTTCATTTGTT
1 TTAATTTCATTTGTT
1872755 AAAATATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (15 bp):
TTAATTTCATTTGTT
Found at i:1873361 original size:57 final size:56
Alignment explanation
Indices: 1873270--1873387 Score: 166
Period size: 57 Copynumber: 2.1 Consensus size: 56
1873260 CTGCATGTTC
*
1873270 TTAGGATTTTATTTCTTTTAGGGACAAAATTTATTTATTTTATTCATTAGGCCAAT
1 TTAGGATTTTATTTCTTTTAGGGACAAAATTTATTAATTTTATTCATTAGGCCAAT
* * * *
1873326 TTAGGATTTTTTTTTTTTTGAGGGACAAGAA-TTATTAATTTTGTTCATTAGGTCAAT
1 TTAGGATTTTATTTCTTTT-AGGGACAA-AATTTATTAATTTTATTCATTAGGCCAAT
1873383 TTAGG
1 TTAGG
1873388 TTATCATATT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
56 17 0.31
57 36 0.65
58 2 0.04
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.50
Consensus pattern (56 bp):
TTAGGATTTTATTTCTTTTAGGGACAAAATTTATTAATTTTATTCATTAGGCCAAT
Found at i:1873829 original size:22 final size:22
Alignment explanation
Indices: 1873789--1873830 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1873779 TCAAGTCAGG
* *
1873789 ATTTTCTACCTAAATTTGTGCA
1 ATTTTCTACATAAACTTGTGCA
*
1873811 ATTTTCTACATATACTTGTG
1 ATTTTCTACATAAACTTGTG
1873831 GCTCTTCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.48
Consensus pattern (22 bp):
ATTTTCTACATAAACTTGTGCA
Found at i:1875923 original size:6 final size:6
Alignment explanation
Indices: 1875912--1875950 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1875902 TGATCAAAAT
* * *
1875912 TGAAAG TGAAAG TGAAAG TAAAAT TGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
1875951 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:1876445 original size:32 final size:32
Alignment explanation
Indices: 1876409--1876472 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1876399 ATAAAATTAA
1876409 GCAATAAATAAATAATCGTCTATTATGCTTGT
1 GCAATAAATAAATAATCGTCTATTATGCTTGT
1876441 GCAATAAATAAATAATCGTCTATTATGCTTGT
1 GCAATAAATAAATAATCGTCTATTATGCTTGT
1876473 AGTGCTTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (32 bp):
GCAATAAATAAATAATCGTCTATTATGCTTGT
Found at i:1881229 original size:58 final size:58
Alignment explanation
Indices: 1881147--1881258 Score: 138
Period size: 58 Copynumber: 1.9 Consensus size: 58
1881137 TTAAGGCTTG
** **
1881147 AATTTAGTAATTTTTCTTACATTAGGGT-TCAATTTTTTTTTGTTTAAATTAGGCTTTA
1 AATTTAGTAATTTTTCTTACATTAGGGTCT-AAACTTTTTTTGTCCAAATTAGGCTTTA
* *
1881205 AATTTGGTAATTATTT-TTATATTAGGGTCTAAACTTTTTTTGTCCAAATTAGGC
1 AATTTAGTAATT-TTTCTTACATTAGGGTCTAAACTTTTTTTGTCCAAATTAGGC
1881259 GTTGAACTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 42 0.91
59 4 0.09
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (58 bp):
AATTTAGTAATTTTTCTTACATTAGGGTCTAAACTTTTTTTGTCCAAATTAGGCTTTA
Found at i:1886430 original size:24 final size:25
Alignment explanation
Indices: 1886403--1886459 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 25
1886393 ATCAACGAGC
1886403 AATTTAATTTTTTT-TTTTGTTAAA
1 AATTTAATTTTTTTCTTTTGTTAAA
*
1886427 AATTTTATTTTTTTCTTTTGTTAAA
1 AATTTAATTTTTTTCTTTTGTTAAA
1886452 AA-TTAATT
1 AATTTAATT
1886460 CTTGTACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 18 0.60
25 12 0.40
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (25 bp):
AATTTAATTTTTTTCTTTTGTTAAA
Found at i:1886439 original size:25 final size:25
Alignment explanation
Indices: 1886405--1886455 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1886395 CAACGAGCAA
*
1886405 TTTAATTTTTTTTTTTGTTAAAAAT
1 TTTAATTTTTTCTTTTGTTAAAAAT
*
1886430 TTTATTTTTTTCTTTTGTTAAAAAT
1 TTTAATTTTTTCTTTTGTTAAAAAT
1886455 T
1 T
1886456 AATTCTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTAATTTTTTCTTTTGTTAAAAAT
Found at i:1890977 original size:30 final size:31
Alignment explanation
Indices: 1890943--1891002 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1890933 AACAACTTAG
1890943 TGACTT-AATAAAAACTTTT-ATATAGTTCAA
1 TGACTTAAATAAAAACTTTTGA-ATAGTTCAA
* *
1890973 TGACTTAAATGATAACTTTTGAATAGTTCA
1 TGACTTAAATAAAAACTTTTGAATAGTTCA
1891003 GTAACAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 6 0.23
31 19 0.73
32 1 0.04
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAGTTCAA
Found at i:1891366 original size:29 final size:29
Alignment explanation
Indices: 1891333--1891392 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
1891323 AGAATAAAAT
1891333 CAAATCAAAATTTCATATATAAAATTGCA
1 CAAATCAAAATTTCATATATAAAATTGCA
** * *
1891362 CAAATTTAAATTTTATGTATAAAATTGCA
1 CAAATCAAAATTTCATATATAAAATTGCA
1891391 CA
1 CA
1891393 TTAGACCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (29 bp):
CAAATCAAAATTTCATATATAAAATTGCA
Found at i:1895883 original size:17 final size:17
Alignment explanation
Indices: 1895847--1895884 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1895837 ATGGGTATAA
*
1895847 TTTTCTTTTTTCTTTTC
1 TTTTCTTTTTTCTTTCC
1895864 TTTTCTTTTCTT-TTTCC
1 TTTTCTTTT-TTCTTTCC
1895881 TTTT
1 TTTT
1895885 TGAATGGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTCTTTTTTCTTTCC
Found at i:1899856 original size:2 final size:2
Alignment explanation
Indices: 1899849--1899881 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1899839 TGATCCTTCC
1899849 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 T
1899882 CCTTTGAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1907587 original size:3 final size:3
Alignment explanation
Indices: 1907579--1907612 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1907569 CATTTTGCTC
1907579 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1907613 TCTTTAGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1907751 original size:5 final size:5
Alignment explanation
Indices: 1907741--1907801 Score: 95
Period size: 5 Copynumber: 11.8 Consensus size: 5
1907731 ATTGTTTTAT
*
1907741 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA CATAAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT-AA
1907792 TATAAA TATA
1 TAT-AA TATA
1907802 TTTTATATTC
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
5 43 0.81
6 10 0.19
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (5 bp):
TATAA
Found at i:1917952 original size:11 final size:11
Alignment explanation
Indices: 1917936--1917978 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
1917926 ACTGGACCAA
*
1917936 TAAATTTATTT
1 TAAATTTAATT
1917947 TAAATTTAAATT
1 TAAATTT-AATT
1917959 TAAATTTAATT
1 TAAATTTAATT
*
1917970 TAATTTTAA
1 TAAATTTAA
1917979 AATTAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TAAATTTAATT
Found at i:1917962 original size:23 final size:23
Alignment explanation
Indices: 1917936--1917984 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1917926 ACTGGACCAA
* *
1917936 TAAATTTATTTTAAATTTAAATT
1 TAAATTTAATTTAAATTTAAAAT
*
1917959 TAAATTTAATTTAATTTTAAAAT
1 TAAATTTAATTTAAATTTAAAAT
1917982 TAA
1 TAA
1917985 TATAAATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAATTTAATTTAAATTTAAAAT
Found at i:1917969 original size:17 final size:17
Alignment explanation
Indices: 1917936--1917991 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
1917926 ACTGGACCAA
*
1917936 TAAATTT-ATTTTAAATT
1 TAAATTTAAATTT-AATT
1917953 TAAATTTAAATTTAATT
1 TAAATTTAAATTTAATT
* * *
1917970 TAATTTTAAAATTAATA
1 TAAATTTAAATTTAATT
1917987 TAAAT
1 TAAAT
1917992 GTTCAAATAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
17 29 0.88
18 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAATTTAAATTTAATT
Found at i:1917971 original size:5 final size:6
Alignment explanation
Indices: 1917936--1917984 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
1917926 ACTGGACCAA
* * *
1917936 TAAATT T-ATTT TAAATT TAAATT TAAATT T-AATT TAATTT TAAAAT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
1917982 TAA
1 TAA
1917985 TATAAATGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 9 0.25
6 27 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TAAATT
Found at i:1917985 original size:12 final size:12
Alignment explanation
Indices: 1917936--1917984 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
1917926 ACTGGACCAA
*
1917936 TAAATTT-ATTT
1 TAAATTTAAATT
1917947 TAAATTTAAATT
1 TAAATTTAAATT
1917959 TAAATTT-AATT
1 TAAATTTAAATT
* *
1917970 TAATTTTAAAAT
1 TAAATTTAAATT
1917982 TAA
1 TAA
1917985 TATAAATGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
11 17 0.52
12 16 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TAAATTTAAATT
Found at i:1918746 original size:14 final size:14
Alignment explanation
Indices: 1918713--1918742 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1918703 TTAATGATAA
1918713 TAATAATATTTTAT
1 TAATAATATTTTAT
1918727 TAATAATA-TTTAT
1 TAATAATATTTTAT
1918740 TAA
1 TAA
1918743 ATAAATAATA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATAATATTTTAT
Found at i:1918749 original size:18 final size:18
Alignment explanation
Indices: 1918728--1918765 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1918718 ATATTTTATT
*
1918728 AATAATATTTATTAAATA
1 AATAATAATTATTAAATA
1918746 AATAATAATTATTAAATA
1 AATAATAATTATTAAATA
1918764 AA
1 AA
1918766 AAAAAGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAATAATTATTAAATA
Found at i:1928599 original size:29 final size:29
Alignment explanation
Indices: 1928423--1928583 Score: 261
Period size: 29 Copynumber: 5.6 Consensus size: 29
1928413 TGATCGGCAA
*
1928423 GTATTAGTGGAGGAATATTATTAGTTTAT
1 GTATTAGTGGAGGAATATTAATAGTTTAT
*
1928452 GTATTAGTGGAGGAATATTATTAGTTTAT
1 GTATTAGTGGAGGAATATTAATAGTTTAT
*
1928481 GTATTAGTGGAGGAATATTAATATTTTAT
1 GTATTAGTGGAGGAATATTAATAGTTTAT
*
1928510 GTATTAGTGGAGGAATATTTATAGTTTAT
1 GTATTAGTGGAGGAATATTAATAGTTTAT
*
1928539 GTATTAGTGG-GGAATATTAATATTTTAT
1 GTATTAGTGGAGGAATATTAATAGTTTAT
*
1928567 ATATTAGTGGAGGAATA
1 GTATTAGTGGAGGAATA
1928584 AAATTTTTTA
Statistics
Matches: 124, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 25 0.20
29 99 0.80
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (29 bp):
GTATTAGTGGAGGAATATTAATAGTTTAT
Found at i:1934628 original size:29 final size:29
Alignment explanation
Indices: 1934571--1934660 Score: 101
Period size: 29 Copynumber: 3.0 Consensus size: 29
1934561 AATTCATGAG
* *
1934571 AATTAGATTAAAAT-AAAATTTCATGTATAA
1 AATTAGA-CAAAATCAAAATTT-ATATATAA
1934601 AATTAGACAAAATCAAAATTTATATATAA
1 AATTAGACAAAATCAAAATTTATATATAA
* *
1934630 AATTACACATTAAACCAAAATTTATATATAA
1 AATTAGACA--AAATCAAAATTTATATATAA
1934661 TTTTGAGATT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
29 20 0.38
30 14 0.26
31 19 0.36
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (29 bp):
AATTAGACAAAATCAAAATTTATATATAA
Found at i:1934652 original size:31 final size:29
Alignment explanation
Indices: 1934585--1934660 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 29
1934575 AGATTAAAAT
* * *
1934585 AAAATTTCATGTATAAAATTAGACAAAATC
1 AAAATTT-ATATATAAAATTACACAAAACC
1934615 AAAATTTATATATAAAATTACACATTAAACC
1 AAAATTTATATATAAAATTACACA--AAACC
1934646 AAAATTTATATATAA
1 AAAATTTATATATAA
1934661 TTTTGAGATT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
29 15 0.37
30 7 0.17
31 19 0.46
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATTTATATATAAAATTACACAAAACC
Found at i:1936266 original size:45 final size:46
Alignment explanation
Indices: 1936190--1936289 Score: 161
Period size: 45 Copynumber: 2.2 Consensus size: 46
1936180 CATCCAAAAG
*
1936190 CAGC-AAATGTGCACACATATGCGGCATTTTACTCAACAAAAACAA
1 CAGCAAAATGTGCACACATATGCGACATTTTACTCAACAAAAACAA
*
1936235 CAGCAAAATGTGCACACATATGCGACA-TTTACTCAACAAAAACAG
1 CAGCAAAATGTGCACACATATGCGACATTTTACTCAACAAAAACAA
1936280 CAG-AAAATGT
1 CAGCAAAATGT
1936290 TCATTACATC
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
44 7 0.13
45 24 0.46
46 21 0.40
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.19
Consensus pattern (46 bp):
CAGCAAAATGTGCACACATATGCGACATTTTACTCAACAAAAACAA
Found at i:1938239 original size:6 final size:6
Alignment explanation
Indices: 1938228--1938256 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1938218 CACGACCTCC
1938228 TCACCA TCACCA TCACCA TCACCA TCACC
1 TCACCA TCACCA TCACCA TCACCA TCACC
1938257 CTGCAACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.52, G:0.00, T:0.17
Consensus pattern (6 bp):
TCACCA
Found at i:1939502 original size:26 final size:26
Alignment explanation
Indices: 1939473--1939524 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1939463 TATATGTGAT
* *
1939473 ATAAATTATATTATACAAAAT-TAAAA
1 ATAAAATATATTACA-AAAATATAAAA
1939499 ATAAAATATATTACAAAAATATAAAA
1 ATAAAATATATTACAAAAATATAAAA
1939525 TTAAGTCGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
ATAAAATATATTACAAAAATATAAAA
Found at i:1945045 original size:3 final size:3
Alignment explanation
Indices: 1945037--1945081 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1945027 TAATTTACCC
1945037 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1945082 AAATGGAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1945363 original size:25 final size:23
Alignment explanation
Indices: 1945298--1945368 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
1945288 TATAGAGGGT
1945298 AAATAATAGAGTAGAAGAGAGCG
1 AAATAATAGAGTAGAAGAGAGCG
* * * * *
1945321 TAATAAAAGATTAAAAGAGATCAAG
1 AAATAATAGAGTAGAAGAGAGC--G
1945346 AAATAATAGAGTAGAAGAGAGCG
1 AAATAATAGAGTAGAAGAGAGCG
1945369 TATTTTTCAA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
23 18 0.50
25 18 0.50
ACGTcount: A:0.55, C:0.04, G:0.25, T:0.15
Consensus pattern (23 bp):
AAATAATAGAGTAGAAGAGAGCG
Found at i:1947587 original size:33 final size:32
Alignment explanation
Indices: 1947550--1947614 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
1947540 TAGACAACTA
*
1947550 TATATTATCTA-ATGTTTAATATTTACATAATAT
1 TATATTAT-TATATATTTAAT-TTTACATAATAT
*
1947583 TATATTATTATATATTTAATTTTATATAATAT
1 TATATTATTATATATTTAATTTTACATAATAT
1947615 AAATTACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (32 bp):
TATATTATTATATATTTAATTTTACATAATAT
Found at i:1949817 original size:24 final size:24
Alignment explanation
Indices: 1949785--1949830 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1949775 AGCTTGTTCG
1949785 GTTCATTTATTGACTCGTTTATAA
1 GTTCATTTATTGACTCGTTTATAA
*
1949809 GTTCGTTTATTGACTCGTTTAT
1 GTTCATTTATTGACTCGTTTAT
1949831 TTATTTGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.13, G:0.15, T:0.52
Consensus pattern (24 bp):
GTTCATTTATTGACTCGTTTATAA
Found at i:1949826 original size:12 final size:12
Alignment explanation
Indices: 1949790--1949831 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1949780 GTTCGGTTCA
1949790 TTTATTGACTCG
1 TTTATTGACTCG
* *
1949802 TTTA-TAAGTTCG
1 TTTATTGA-CTCG
1949814 TTTATTGACTCG
1 TTTATTGACTCG
1949826 TTTATT
1 TTTATT
1949832 TATTTGCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.55
Consensus pattern (12 bp):
TTTATTGACTCG
Found at i:1949938 original size:12 final size:12
Alignment explanation
Indices: 1949916--1949960 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1949906 ATTATTCATT
1949916 AACATTGTTCGTG
1 AACA-TGTTCGTG
*
1949929 AACATGTTCGTC
1 AACATGTTCGTG
*
1949941 TA-ATGTTCGTG
1 AACATGTTCGTG
1949952 AACATGTTC
1 AACATGTTC
1949961 AATTAAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 9 0.33
12 14 0.52
13 4 0.15
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (12 bp):
AACATGTTCGTG
Found at i:1950220 original size:19 final size:18
Alignment explanation
Indices: 1950196--1950232 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
1950186 GTCAATTTTG
1950196 AAAATTTTAAATATTTATA
1 AAAATTTTAAAT-TTTATA
1950215 AAAATTTTAAATTTTATA
1 AAAATTTTAAATTTTATA
1950233 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAATTTTAAATTTTATA
Found at i:1950251 original size:26 final size:26
Alignment explanation
Indices: 1950197--1950251 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
1950187 TCAATTTTGA
* *
1950197 AAATTTTAAATATTTATAAAAATTTT
1 AAATTTTAAATATTTATAAAAAATCT
* *
1950223 AAATTTTATATATTTTTAAAAAATCT
1 AAATTTTAAATATTTATAAAAAATCT
1950249 AAA
1 AAA
1950252 GAATATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
AAATTTTAAATATTTATAAAAAATCT
Found at i:1951843 original size:20 final size:20
Alignment explanation
Indices: 1951818--1951856 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1951808 GTCATGTCGC
*
1951818 TAAAAATTTTAAAAATATAG
1 TAAAAATATTAAAAATATAG
*
1951838 TAAAAATATTAAAATTATA
1 TAAAAATATTAAAAATATA
1951857 CATAATTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAAAATATTAAAAATATAG
Found at i:1952557 original size:16 final size:17
Alignment explanation
Indices: 1952536--1952577 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1952526 CATGATTATG
*
1952536 TAATAAAAA-ATTAATA
1 TAATAAAAATATAAATA
*
1952552 TAATAATAAATATAAATT
1 TAATAA-AAATATAAATA
1952570 TAATAAAA
1 TAATAAAA
1952578 TATTTTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 5 0.23
18 11 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAATAAAAATATAAATA
Found at i:1954936 original size:19 final size:19
Alignment explanation
Indices: 1954912--1954949 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1954902 GCATATTCAT
1954912 TGATGCCTCAGAGGTTTTG
1 TGATGCCTCAGAGGTTTTG
*
1954931 TGATGCCTCCGAGGTTTTG
1 TGATGCCTCAGAGGTTTTG
1954950 CAATTGGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.32, T:0.37
Consensus pattern (19 bp):
TGATGCCTCAGAGGTTTTG
Found at i:1970351 original size:22 final size:21
Alignment explanation
Indices: 1970326--1970379 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1970316 TAGGTCCATC
1970326 TATATTAATTTTTTTAAATATT
1 TATATTAATTTTTTT-AATATT
*
1970348 TATATTATATTATTTTAATATT
1 TATATTA-ATTTTTTTAATATT
*
1970370 TA-ATAAATTT
1 TATATTAATTT
1970380 ATGCATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 3 0.11
21 3 0.11
22 15 0.54
23 7 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATTAATTTTTTTAATATT
Found at i:1971800 original size:26 final size:26
Alignment explanation
Indices: 1971768--1971820 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1971758 AGTTTAAAAT
1971768 TACATTCTTTCTCAATCAGAAATTAC
1 TACATTCTTTCTCAATCAGAAATTAC
1971794 TACATTCTTTCTCAATCAGAAATTAC
1 TACATTCTTTCTCAATCAGAAATTAC
1971820 T
1 T
1971821 CTCTAAGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.40
Consensus pattern (26 bp):
TACATTCTTTCTCAATCAGAAATTAC
Found at i:1973013 original size:249 final size:249
Alignment explanation
Indices: 1972575--1973075 Score: 975
Period size: 249 Copynumber: 2.0 Consensus size: 249
1972565 ACCCAAGAGA
*
1972575 AGCAAAGCAAAGACAGAAAACCCCAGACGAAGGGAACAAAGATGAAGCTGATAGAGGTGCAATCG
1 AGCAAAGCAAAGACAGAAAACCCCAGAAGAAGGGAACAAAGATGAAGCTGATAGAGGTGCAATCG
*
1972640 TACCTCACGAAATGGCTGCACCTGTTAGTCAACCTCAACCCATTAATATGGTTGCACTAACTGTT
66 TACCTCACGAAATGGCTGCACCTGTTAGTCAACCTCAACCCATTAATATGGTTGCACCAACTGTT
1972705 CGTGATCAATATGAACAGCTTGAAGTTCAACCCTTTAACATGAACATTAGACAAGACACTAGATG
131 CGTGATCAATATGAACAGCTTGAAGTTCAACCCTTTAACATGAACATTAGACAAGACACTAGATG
1972770 GGTACCTCACGAAATGGCTGCACATGTTAGTGAACCCATTAATATGGTTGCACC
196 GGTACCTCACGAAATGGCTGCACATGTTAGTGAACCCATTAATATGGTTGCACC
1972824 AGCAAAGCAAAGACAGAAAACCCCAGAAGAAGGGAACAAAGATGAAGCTGATAGAGGTGCAATCG
1 AGCAAAGCAAAGACAGAAAACCCCAGAAGAAGGGAACAAAGATGAAGCTGATAGAGGTGCAATCG
1972889 TACCTCACGAAATGGCTGCACCTGTTAGTCAACCTCAACCCATTAATATGGTTGCACCAACTGTT
66 TACCTCACGAAATGGCTGCACCTGTTAGTCAACCTCAACCCATTAATATGGTTGCACCAACTGTT
*
1972954 CGTGATCAATATGAACAGCTTGAAGTTCAACCGTTTAACATGAACATTAGACAAGACACTAGATG
131 CGTGATCAATATGAACAGCTTGAAGTTCAACCCTTTAACATGAACATTAGACAAGACACTAGATG
1973019 GGTACCTCACGAAATGGCTGCACATGTTAGTGAACCCATTAATATGGTTGCACC
196 GGTACCTCACGAAATGGCTGCACATGTTAGTGAACCCATTAATATGGTTGCACC
1973073 AGC
1 AGC
1973076 TGTTTATGAT
Statistics
Matches: 249, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
249 249 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (249 bp):
AGCAAAGCAAAGACAGAAAACCCCAGAAGAAGGGAACAAAGATGAAGCTGATAGAGGTGCAATCG
TACCTCACGAAATGGCTGCACCTGTTAGTCAACCTCAACCCATTAATATGGTTGCACCAACTGTT
CGTGATCAATATGAACAGCTTGAAGTTCAACCCTTTAACATGAACATTAGACAAGACACTAGATG
GGTACCTCACGAAATGGCTGCACATGTTAGTGAACCCATTAATATGGTTGCACC
Found at i:1973119 original size:126 final size:127
Alignment explanation
Indices: 1972888--1973139 Score: 398
Period size: 126 Copynumber: 2.0 Consensus size: 127
1972878 AGGTGCAATC
*
1972888 GTACCTCACGAAATGGCTGCACCTGTTAGTCAACCTCAACCCATTAATATGGTTGCACCAACTGT
1 GTACCTCACGAAATGGCTGCACATGTTAG-----CTCAACCCATTAATATGGTTGCACCAACTGT
* *
1972953 TCGTGATCAATATGAACAGCTTGAAGTTCAACCGTTTAACATGAACATTAGACAAGACACTAGAT
61 TCATGATCAATATGAACAGCTTGAAGTTCAACCATTTAACATGAACATTAGACAAGACACTAGAT
1973018 GG
126 GG
* * *
1973020 GTACCTCACGAAATGGCTGCACATGTTAG-TGAACCCATTAATATGGTTGCACCAGCTGTTTATG
1 GTACCTCACGAAATGGCTGCACATGTTAGCTCAACCCATTAATATGGTTGCACCAACTGTTCATG
1973084 ATCAATATGAACAGCTTGAAGTTCAACCATTTAACATGAACATTAGACAAGACACT
66 ATCAATATGAACAGCTTGAAGTTCAACCATTTAACATGAACATTAGACAAGACACT
1973140 GGTTGGATAG
Statistics
Matches: 114, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
126 86 0.75
132 28 0.25
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (127 bp):
GTACCTCACGAAATGGCTGCACATGTTAGCTCAACCCATTAATATGGTTGCACCAACTGTTCATG
ATCAATATGAACAGCTTGAAGTTCAACCATTTAACATGAACATTAGACAAGACACTAGATGG
Found at i:1977563 original size:25 final size:25
Alignment explanation
Indices: 1977529--1977579 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1977519 CGAACTATAT
1977529 ACTTTTGAAACATTAACATGTTTCC
1 ACTTTTGAAACATTAACATGTTTCC
1977554 ACTTTTGAAACATTAACATGTTTCC
1 ACTTTTGAAACATTAACATGTTTCC
1977579 A
1 A
1977580 TTGTTCCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (25 bp):
ACTTTTGAAACATTAACATGTTTCC
Found at i:1980287 original size:147 final size:147
Alignment explanation
Indices: 1979936--1980583 Score: 653
Period size: 147 Copynumber: 4.4 Consensus size: 147
1979926 ATCATTCATA
* * * * * * * *
1979936 CATACATGCATAAAGATTTATGCTGATAGTATAATTGGTTAAAGATAACGATGATGATGATGAAA
1 CATACATACATACATATTCATGCTGATAATCTAATTGGTTAATGATAATG-T-ATGATGATGAAA
* * * * * * *
1980001 ACTGCAGAATGATGGTATTGTCATGTAATCTTTAGAAGTTCGTACCACCAAACTCATGTCCAAAC
64 ACTACAGAATGATTGTATTGCCATGTAATCTTTAGAAGGTCATATCACCATACTCATG-------
*
1980066 TCCAAATATGAAACAAACATGGATGT
122 TCCAAATATGCAACAAACATGGATGT
1980092 CATTCATTCATACATACATATTCATGCTGATAATCTAATTGGTTAATGATAATGTCATGATGATG
1 CA-T-A--CATACATACATATTCATGCTGATAATCTAATTGGTTAATGATAATGT-ATGATGATG
* *
1980157 AAAACTACAGAATGATTGTATTGCTATGTAATCTTTAGAAGGTCATATCCCCATA-TCATGTCCA
61 AAAACTACAGAATGATTGTATTGCCATGTAATCTTTAGAAGGTCATATCACCATACTCATGTCCA
*
1980221 AATATGCAACAAACATGGTTGT
126 AATATGCAACAAACATGGATGT
* * *
1980243 CATTCATACATACATATTCATGCTGATAATCTAATTGGTCAATGATAATGTCATGATGATGAAAG
1 CATACATACATACATATTCATGCTGATAATCTAATTGGTTAATGATAATGT-ATGATGATGAAAA
* *
1980308 CTACACAATGATTGTATTGCCATGTAATCTTTAGAAGGCCATATCACCATA-TCATGTCCAAATA
65 CTACAGAATGATTGTATTGCCATGTAATCTTTAGAAGGTCATATCACCATACTCATGTCCAAATA
* *
1980372 TGCAATAAACATGGATGC
130 TGCAACAAACATGGATGT
*** *
1980390 CATACATACATACATA--CATAAAGAT--TC--A-T-GTGTCATG---ATG-ATGATGATGAAAA
1 CATACATACATACATATTCATGCTGATAATCTAATTGGT-TAATGATAATGTATGATGATGAAAA
* * * * * *
1980443 TTGCATAATGATCGAATTGCCATGTAATCTTTAGAAGGTCATATCACCATACTCATGTTCAAATA
65 CTACAGAATGATTGTATTGCCATGTAATCTTTAGAAGGTCATATCACCATACTCATGTCCAAATA
* *
1980508 TGCAAACGAACATGAATG-
130 TGC-AACAAACATGGATGT
* * *
1980526 CAGGACATACATACATATTCATGCTGATAATCTAACTGGTTAATGACAATG-ATGATGA
1 CA-TACATACATACATATTCATGCTGATAATCTAATTGGTTAATGATAATGTATGATGA
1980584 AAAGTGCAGG
Statistics
Matches: 421, Mismatches: 52, Indels: 47
0.81 0.10 0.09
Matches are distributed among these distances:
135 57 0.14
136 17 0.04
137 27 0.06
139 8 0.02
140 4 0.01
141 3 0.01
143 3 0.01
144 5 0.01
145 8 0.02
147 159 0.38
150 1 0.00
151 26 0.06
156 2 0.00
157 1 0.00
158 6 0.01
159 56 0.13
160 38 0.09
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (147 bp):
CATACATACATACATATTCATGCTGATAATCTAATTGGTTAATGATAATGTATGATGATGAAAAC
TACAGAATGATTGTATTGCCATGTAATCTTTAGAAGGTCATATCACCATACTCATGTCCAAATAT
GCAACAAACATGGATGT
Found at i:1981055 original size:14 final size:14
Alignment explanation
Indices: 1981036--1981071 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
1981026 TAATCCTATT
1981036 TTTATTTCAAGAAA
1 TTTATTTCAAGAAA
1981050 TTTATTTCAAGAAA
1 TTTATTTCAAGAAA
1981064 TTTATTTC
1 TTTATTTC
1981072 CTTTACTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (14 bp):
TTTATTTCAAGAAA
Found at i:1984960 original size:25 final size:24
Alignment explanation
Indices: 1984932--1984979 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1984922 AATATATGTT
*
1984932 ATTAATTAGACTTTAATTTTTAAAA
1 ATTAATCA-ACTTTAATTTTTAAAA
* *
1984957 ATTAATCAATTTTGATTTTTAAA
1 ATTAATCAACTTTAATTTTTAAA
1984980 TTAGACAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (24 bp):
ATTAATCAACTTTAATTTTTAAAA
Found at i:1986096 original size:13 final size:13
Alignment explanation
Indices: 1986056--1986097 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1986046 GAATAGGGGC
1986056 ATTTATTTTGTAAA
1 ATTTATTTTGT-AA
*
1986070 ATTTAGATTT-TAA
1 ATTTA-TTTTGTAA
1986083 ATTTATTTTGTAA
1 ATTTATTTTGTAA
1986096 AT
1 AT
1986098 ATGCAAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 3 0.12
13 12 0.50
14 6 0.25
15 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (13 bp):
ATTTATTTTGTAA
Found at i:1990988 original size:16 final size:16
Alignment explanation
Indices: 1990967--1990999 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1990957 AATTTGATTC
1990967 AATCATGCACATTTAA
1 AATCATGCACATTTAA
1990983 AATCATGCACATTTAA
1 AATCATGCACATTTAA
1990999 A
1 A
1991000 GAAATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.30
Consensus pattern (16 bp):
AATCATGCACATTTAA
Found at i:1991164 original size:29 final size:30
Alignment explanation
Indices: 1991119--1991177 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1991109 GAATTTGATC
* *
1991119 AAATCAAAATATCATATATAATATTACACA
1 AAATCAAAATATCATATATAAAAATACACA
1991149 AAATCAAAATA-CATATATAAAAATACACA
1 AAATCAAAATATCATATATAAAAATACACA
1991178 TTAAGTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (30 bp):
AAATCAAAATATCATATATAAAAATACACA
Found at i:1993038 original size:16 final size:15
Alignment explanation
Indices: 1993017--1993060 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1993007 AAGTGATTAT
1993017 AATTCAAAATAATTCG
1 AATTCAAAA-AATTCG
*
1993033 AATTCATAACAATTCG
1 AATTCA-AAAAATTCG
1993049 -ATTCAAAAAATT
1 AATTCAAAAAATT
1993061 AAATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 12 0.48
17 2 0.08
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.32
Consensus pattern (15 bp):
AATTCAAAAAATTCG
Found at i:1998397 original size:2 final size:2
Alignment explanation
Indices: 1998390--1998419 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1998380 TTATTTGCTA
1998390 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
1998420 GTGTGTGCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2005287 original size:150 final size:150
Alignment explanation
Indices: 2005016--2005465 Score: 891
Period size: 150 Copynumber: 3.0 Consensus size: 150
2005006 TATTCAAAGG
2005016 TCAAACCCCAAATTTATGATATCAGACAATAGTGATGTTTCCCAAACCAAACATGGGATGTTGTT
1 TCAAACCCCAAATTTATGATATCAGACAATAGTGATGTTTCCCAAACCAAACATGGGATGTTGTT
*
2005081 ATCCGATTACACCCCACTTTCAACTTTCTCACTCCAACTCAACAATTTCTAATCATAAATATGAA
66 ATCCGATTACACCCCACTTTCAACTTTCTCACTCCAACTCAACTATTTCTAATCATAAATATGAA
2005146 TAATTTATTAGTATTTATAT
131 TAATTTATTAGTATTTATAT
2005166 TCAAACCCCAAATTTATGATATCAGACAATAGTGATGTTTCCCAAACCAAACATGGGATGTTGTT
1 TCAAACCCCAAATTTATGATATCAGACAATAGTGATGTTTCCCAAACCAAACATGGGATGTTGTT
2005231 ATCCGATTACACCCCACTTTCAACTTTCTCACTCCAACTCAACTATTTCTAATCATAAATATGAA
66 ATCCGATTACACCCCACTTTCAACTTTCTCACTCCAACTCAACTATTTCTAATCATAAATATGAA
2005296 TAATTTATTAGTATTTATAT
131 TAATTTATTAGTATTTATAT
2005316 TCAAACCCCAAATTTATGATATCAGACAATAGTGATGTTTCCCAAACCAAACATGGGATGTTGTT
1 TCAAACCCCAAATTTATGATATCAGACAATAGTGATGTTTCCCAAACCAAACATGGGATGTTGTT
2005381 ATCCGATTACACCCCACTTTCAACTTTCTCACTCCAACTCAACTATTTCTAATCATAAATATGAA
66 ATCCGATTACACCCCACTTTCAACTTTCTCACTCCAACTCAACTATTTCTAATCATAAATATGAA
2005446 TAATTTATTAGTATTTATAT
131 TAATTTATTAGTATTTATAT
2005466 ATTTTCTAGC
Statistics
Matches: 299, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 299 1.00
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (150 bp):
TCAAACCCCAAATTTATGATATCAGACAATAGTGATGTTTCCCAAACCAAACATGGGATGTTGTT
ATCCGATTACACCCCACTTTCAACTTTCTCACTCCAACTCAACTATTTCTAATCATAAATATGAA
TAATTTATTAGTATTTATAT
Found at i:2007541 original size:25 final size:25
Alignment explanation
Indices: 2007513--2007568 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
2007503 TGATTAAATG
*
2007513 TTATTGAATCTTATTCTTAACTCAA
1 TTATTAAATCTTATTCTTAACTCAA
2007538 TTATTAAATCTTATTCTTAACTCAA
1 TTATTAAATCTTATTCTTAACTCAA
2007563 TTATTA
1 TTATTA
2007569 TTGTTCCTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.50
Consensus pattern (25 bp):
TTATTAAATCTTATTCTTAACTCAA
Found at i:2008389 original size:29 final size:26
Alignment explanation
Indices: 2008345--2008420 Score: 71
Period size: 29 Copynumber: 2.7 Consensus size: 26
2008335 CAAAAAAAAT
* * *
2008345 ATTTTTTTATATTTTTAAAATAATTTTA
1 ATTTTTTAAT-TTTTTAAAA-AACTATA
2008373 ATGATTTTTAATTTTTTCAAAAAACTATA
1 AT--TTTTTAATTTTTT-AAAAAACTATA
2008402 ATTTTTTAAATTTTTTAAA
1 ATTTTTT-AATTTTTTAAA
2008421 TTTTAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 8 0.20
28 10 0.24
29 12 0.29
30 11 0.27
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (26 bp):
ATTTTTTAATTTTTTAAAAAACTATA
Found at i:2015651 original size:23 final size:23
Alignment explanation
Indices: 2015624--2015706 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
2015614 CGTTTGTTTA
2015624 ATGTTCACGAACATTAATCGAAC
1 ATGTTCACGAACATTAATCGAAC
* *
2015647 ATGTTCACAAACATTAAACGAAC
1 ATGTTCACGAACATTAATCGAAC
*** * **
2015670 ATGCAAATGAACATATAATTAAAC
1 ATGTTCACGAACAT-TAATCGAAC
2015694 ATGTTCACGAACA
1 ATGTTCACGAACA
2015707 ATGTTAATAA
Statistics
Matches: 45, Mismatches: 14, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
23 30 0.67
24 15 0.33
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (23 bp):
ATGTTCACGAACATTAATCGAAC
Found at i:2015821 original size:12 final size:11
Alignment explanation
Indices: 2015793--2015862 Score: 59
Period size: 12 Copynumber: 6.0 Consensus size: 11
2015783 TCATTAATAA
*
2015793 ATAAACGAGCT
1 ATAAACGAGTT
2015804 ATAAACGAGTT
1 ATAAACGAGTT
2015815 AATAAACGAGCTT
1 -ATAAACGAG-TT
* **
2015828 ATGAACGAGCCA
1 ATAAACGAG-TT
2015840 ATAAACGAGCTT
1 ATAAACGAG-TT
*
2015852 TTAAACGAGTT
1 ATAAACGAGTT
2015863 TGTTCGTGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 12 0.24
12 35 0.71
13 2 0.04
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.23
Consensus pattern (11 bp):
ATAAACGAGTT
Found at i:2015842 original size:24 final size:24
Alignment explanation
Indices: 2015792--2015860 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
2015782 ATCATTAATA
**
2015792 AATAAACGAGC-TATAAACGAGTT
1 AATAAACGAGCTTATAAACGAGCC
*
2015815 AATAAACGAGCTTATGAACGAGCC
1 AATAAACGAGCTTATAAACGAGCC
*
2015839 AATAAACGAGCTTTTAAACGAG
1 AATAAACGAGCTTATAAACGAG
2015861 TTTGTTCGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 11 0.28
24 29 0.73
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.20
Consensus pattern (24 bp):
AATAAACGAGCTTATAAACGAGCC
Found at i:2016715 original size:15 final size:13
Alignment explanation
Indices: 2016687--2016721 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 13
2016677 TTCAAAAAAA
2016687 TATTTTTATTATT
1 TATTTTTATTATT
2016700 TATTATTTATTTATT
1 TATT-TTTA-TTATT
2016715 TATTTTT
1 TATTTTT
2016722 GGGAGAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 7 0.35
15 9 0.45
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTTTTATTATT
Found at i:2018058 original size:26 final size:24
Alignment explanation
Indices: 2018005--2018061 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 24
2017995 ATCGAGTTAA
*
2018005 AATTTAATTAATTTAAATAAAAAT
1 AATTTAATGAATTTAAATAAAAAT
*
2018029 AATTTATATGAATTTAAATTTAAAAT
1 AATTTA-ATGAATTTAAA-TAAAAAT
2018055 AATTTAA
1 AATTTAA
2018062 AATATAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 6 0.21
25 11 0.38
26 12 0.41
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
AATTTAATGAATTTAAATAAAAAT
Found at i:2028661 original size:12 final size:12
Alignment explanation
Indices: 2028644--2028669 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2028634 CAAAGATCAT
2028644 AACTGGAAAGCA
1 AACTGGAAAGCA
2028656 AACTGGAAAGCA
1 AACTGGAAAGCA
2028668 AA
1 AA
2028670 GATTTGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.15, G:0.23, T:0.08
Consensus pattern (12 bp):
AACTGGAAAGCA
Found at i:2028771 original size:13 final size:13
Alignment explanation
Indices: 2028753--2028806 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
2028743 GATGATGATT
2028753 ATAATTTTAAAAA
1 ATAATTTTAAAAA
*
2028766 ATAATTTTAATAATTT
1 ATAATTTTAA-AA--A
* *
2028782 ATATTTTTTAAAA
1 ATAATTTTAAAAA
2028795 ATAATTTTAAAA
1 ATAATTTTAAAA
2028807 CTATTTGCTG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
13 20 0.62
14 2 0.06
15 2 0.06
16 8 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATAATTTTAAAAA
Found at i:2029830 original size:59 final size:57
Alignment explanation
Indices: 2029661--2029810 Score: 169
Period size: 59 Copynumber: 2.5 Consensus size: 57
2029651 TTGGTATCTA
* * * * * *
2029661 AACTTCACATTTTTTCTTAATTTAGTATTTAAATTTTTTTTGATCCAATTTGGTACTTG
1 AACTTGACTTTTTTTC-TAATTTGGTATCT-AATTTTTTTTGATCCAATTTGCTACCTG
2029720 AACTTGATACTTTTTTT-TAATTTGGTA-CATAATTTTTTTTGAATCCAATTTGCTACCTG
1 AACTTG--ACTTTTTTTCTAATTTGGTATC-TAATTTTTTTTG-ATCCAATTTGCTACCTG
2029779 AACTTGACTTTTTTTCCTAATTTGGTATCTAA
1 AACTTGACTTTTTTT-CTAATTTGGTATCTAA
2029811 CTTTCTTAAG
Statistics
Matches: 78, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
57 9 0.12
58 11 0.14
59 49 0.63
60 1 0.01
61 8 0.10
ACGTcount: A:0.25, C:0.13, G:0.09, T:0.52
Consensus pattern (57 bp):
AACTTGACTTTTTTTCTAATTTGGTATCTAATTTTTTTTGATCCAATTTGCTACCTG
Found at i:2044248 original size:3 final size:3
Alignment explanation
Indices: 2044242--2044287 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
2044232 AAATTCTTCT
*
2044242 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2044288 AACCAAACGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2044748 original size:8 final size:7
Alignment explanation
Indices: 2044729--2044759 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
2044719 ATTTATATAT
2044729 TAAAAAA
1 TAAAAAA
2044736 TAAAAAA
1 TAAAAAA
2044743 TAAAAAA
1 TAAAAAA
2044750 TAAAATAA
1 TAAAA-AA
2044758 TA
1 TA
2044760 GCGGTGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.83
8 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAAAAA
Found at i:2045235 original size:5 final size:5
Alignment explanation
Indices: 2045225--2045252 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2045215 AATACTAACA
2045225 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
2045253 AATAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:2045262 original size:15 final size:15
Alignment explanation
Indices: 2045225--2045264 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2045215 AATACTAACA
*
2045225 AAATTAAATTAAATT
1 AAATTAAATTAAAAT
2045240 AAATTAAATTAAAAAT
1 AAATTAAATT-AAAAT
2045256 AAA-TAAATT
1 AAATTAAATT
2045265 TACTTTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATTAAATTAAAAT
Found at i:2045327 original size:25 final size:27
Alignment explanation
Indices: 2045299--2045354 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
2045289 TTGCTCTACT
*
2045299 AAATAAAAAAATTAAA-T-AACAAATC
1 AAATAAAAAAATTAAATTAAACAAAAC
2045324 AAAT--AAAAATTAAATTAAACAAAAC
1 AAATAAAAAAATTAAATTAAACAAAAC
2045349 AAATAA
1 AAATAA
2045355 TTTAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 10 0.38
24 1 0.04
25 15 0.58
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (27 bp):
AAATAAAAAAATTAAATTAAACAAAAC
Found at i:2046533 original size:21 final size:22
Alignment explanation
Indices: 2046509--2046558 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
2046499 TTATCAATCA
*
2046509 ATATTTTTTA-AATTTATTTGT
1 ATATTTTTTAGAATTTATTTAT
*
2046530 ATATATTTTTAGATTTTATTTAT
1 ATAT-TTTTTAGAATTTATTTAT
2046553 A-ATTTT
1 ATATTTT
2046559 AAAATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.28
22 8 0.32
23 10 0.40
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (22 bp):
ATATTTTTTAGAATTTATTTAT
Found at i:2046545 original size:22 final size:22
Alignment explanation
Indices: 2046509--2046566 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
2046499 TTATCAATCA
2046509 ATATTTTTTAAA-TTTATTTGT
1 ATATTTTTTAAATTTTATTTGT
*
2046530 ATATATTTTTAGATTTTA-TT-T
1 ATAT-TTTTTAAATTTTATTTGT
* *
2046551 ATAATTTTAAAATTTT
1 ATATTTTTTAAATTTT
2046567 TAGATGATGC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 10 0.32
21 8 0.26
22 9 0.29
23 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (22 bp):
ATATTTTTTAAATTTTATTTGT
Found at i:2058490 original size:54 final size:54
Alignment explanation
Indices: 2058408--2058524 Score: 216
Period size: 54 Copynumber: 2.2 Consensus size: 54
2058398 ACTAATTAAA
*
2058408 AAATTAGTATGGTTTCCTACTCATGCTTTGCGTTGAGTTAACTATTTTTGGACT
1 AAATTATTATGGTTTCCTACTCATGCTTTGCGTTGAGTTAACTATTTTTGGACT
*
2058462 AAATTATTATGGTTTTCTACTCATGCTTTGCGTTGAGTTAACTATTTTTGGACT
1 AAATTATTATGGTTTCCTACTCATGCTTTGCGTTGAGTTAACTATTTTTGGACT
2058516 AAATTATTA
1 AAATTATTA
2058525 AAAGGGATAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46
Consensus pattern (54 bp):
AAATTATTATGGTTTCCTACTCATGCTTTGCGTTGAGTTAACTATTTTTGGACT
Found at i:2061647 original size:16 final size:15
Alignment explanation
Indices: 2061621--2061650 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2061611 CTCAAATTTA
2061621 AATTTACTTGAACCC
1 AATTTACTTGAACCC
2061636 AATTTGACTTGAACC
1 AATTT-ACTTGAACC
2061651 AGATATAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (15 bp):
AATTTACTTGAACCC
Done.