Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007956.1 Hibiscus syriacus cultivar Beakdansim tig00110383_pilon, whole genome shotgun sequence
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: 3102597
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:1334723 original size:23 final size:23
Alignment explanation
Indices: 1334697--1334761 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
1334687 CACCAAAGCT
* *
1334697 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTACCA
* * *
1334720 CGTAGAATTGCACCGTAGTACCG
1 CGTAGAAATGCACCGAAGTACCA
*
1334743 CGTAGAAATGCACCTAAGT
1 CGTAGAAATGCACCGAAGT
1334762 TCCATATAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTACCA
Found at i:1336454 original size:23 final size:23
Alignment explanation
Indices: 1336428--1336496 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1336418 CACCACAGCT
1336428 CGTATAAATGCACTGAAGTGCCA
1 CGTATAAATGCACTGAAGTGCCA
* * * *
1336451 CGTATAATTGCACCGTAGTGCCG
1 CGTATAAATGCACTGAAGTGCCA
*
1336474 CGTAGAAATGCACCT-AAGTGCCA
1 CGTATAAATGCA-CTGAAGTGCCA
1336497 TATAAGGTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (23 bp):
CGTATAAATGCACTGAAGTGCCA
Found at i:1337688 original size:20 final size:20
Alignment explanation
Indices: 1337663--1337700 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1337653 TTCCCCTTGA
1337663 AGTGCATCGATACATTCTAT
1 AGTGCATCGATACATTCTAT
*
1337683 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
1337701 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAT
Found at i:1337795 original size:64 final size:63
Alignment explanation
Indices: 1337708--1337869 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
1337698 TCTTTAACAT
* * *
1337708 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAA-GGG
* * * ** *
1337772 GTGCATCGATGCAGTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
* *
1337836 GTGCATTGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
1337870 CTGAACAATT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 2 0.02
64 70 0.86
65 9 0.11
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:1345305 original size:42 final size:42
Alignment explanation
Indices: 1345246--1345332 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
1345236 TGAAGAAGGG
1345246 GTAATTATTAATTACCCAATAAGTATTTTGCAGGATAAAGCA
1 GTAATTATTAATTACCCAATAAGTATTTTGCAGGATAAAGCA
1345288 GTAATTATTAATTACCCAATAAGTATTTTGCAGGATAAAGCA
1 GTAATTATTAATTACCCAATAAGTATTTTGCAGGATAAAGCA
1345330 GTA
1 GTA
1345333 TTGCTTGACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (42 bp):
GTAATTATTAATTACCCAATAAGTATTTTGCAGGATAAAGCA
Found at i:1350426 original size:21 final size:21
Alignment explanation
Indices: 1350401--1350456 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 21
1350391 AGAGAGTTTT
* *
1350401 GTAGAGAGTTTTACCGTGAGA
1 GTAGAGAGCTTTACAGTGAGA
*
1350422 TTAGAGAGAGCTTTACAGTGAGA
1 GT--AGAGAGCTTTACAGTGAGA
1350445 GTAGAGAGCTTT
1 GTAGAGAGCTTT
1350457 GCCAAGGGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.38
23 18 0.62
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.29
Consensus pattern (21 bp):
GTAGAGAGCTTTACAGTGAGA
Found at i:1350429 original size:23 final size:23
Alignment explanation
Indices: 1350403--1350452 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1350393 AGAGTTTTGT
* * *
1350403 AGAGAGTTTTACCGTGAGATTAG
1 AGAGAGCTTTACAGTGAGAGTAG
1350426 AGAGAGCTTTACAGTGAGAGTAG
1 AGAGAGCTTTACAGTGAGAGTAG
1350449 AGAG
1 AGAG
1350453 CTTTGCCAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.08, G:0.34, T:0.24
Consensus pattern (23 bp):
AGAGAGCTTTACAGTGAGAGTAG
Found at i:1354651 original size:19 final size:19
Alignment explanation
Indices: 1354602--1354651 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1354592 TGTAATTTGG
*
1354602 GTATCGATACCCAGGCAAT
1 GTATCGATACCTAGGCAAT
*
1354621 GTATCGATACCTAGGCAGT
1 GTATCGATACCTAGGCAAT
1354640 GTATCGATACCT
1 GTATCGATACCT
1354652 TAGTTAAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (19 bp):
GTATCGATACCTAGGCAAT
Found at i:1357370 original size:31 final size:31
Alignment explanation
Indices: 1357335--1357446 Score: 206
Period size: 31 Copynumber: 3.6 Consensus size: 31
1357325 ATATGTGGTC
1357335 CTTCGGGACATATGGACTGTTTACCTATGTT
1 CTTCGGGACATATGGACTGTTTACCTATGTT
1357366 CTTCGGGACATATGGACTGTTTACCTATGTT
1 CTTCGGGACATATGGACTGTTTACCTATGTT
*
1357397 CTTCGGGACATATGGACTGTTTACCTAGGTT
1 CTTCGGGACATATGGACTGTTTACCTATGTT
*
1357428 CTTCGGGATATATGGACTG
1 CTTCGGGACATATGGACTG
1357447 GTCCTTCGGG
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 79 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (31 bp):
CTTCGGGACATATGGACTGTTTACCTATGTT
Found at i:1361439 original size:31 final size:31
Alignment explanation
Indices: 1361401--1361512 Score: 172
Period size: 31 Copynumber: 3.6 Consensus size: 31
1361391 ATATGTGGTC
*
1361401 CTTCGGGACATATGGACTGTTTACCTATATT
1 CTTCGGGACATATGGACTGTTTACCTATGTT
1361432 CTTCGGGACATATGGACTGTTTACCTATGTT
1 CTTCGGGACATATGGACTGTTTACCTATGTT
* *
1361463 CTTTGGGACATATGGACTGTTTACCTAGGTT
1 CTTCGGGACATATGGACTGTTTACCTATGTT
*
1361494 CTTTGGGATC-TATGGACTG
1 CTTCGGGA-CATATGGACTG
1361513 GTCCTTCGGG
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 76 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (31 bp):
CTTCGGGACATATGGACTGTTTACCTATGTT
Found at i:1362706 original size:23 final size:23
Alignment explanation
Indices: 1362671--1362714 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1362661 GAGTCGAGGG
*
1362671 TCTACGCGGTCCTTTGGGACAAT
1 TCTACGCGGTCCTTCGGGACAAT
* *
1362694 TCTACGTGTTCCTTCGGGACA
1 TCTACGCGGTCCTTCGGGACA
1362715 TATATGTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.16, C:0.27, G:0.25, T:0.32
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGGGACAAT
Found at i:1364384 original size:30 final size:31
Alignment explanation
Indices: 1364316--1364401 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
1364306 AGAGTCGAGG
*
1364316 GTTACCTATGTCATTCGGGACATATGGACAA
1 GTTACCTATGTCCTTCGGGACATATGGACAA
*
1364347 TTTACCTATGTCCTTCGGGACATATGGAC-A
1 GTTACCTATGTCCTTCGGGACATATGGACAA
* *
1364377 GTTACCTATGTTCTTCGGAACATAT
1 GTTACCTATGTCCTTCGGGACATAT
1364402 AGATAGATCC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 23 0.46
31 27 0.54
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTACCTATGTCCTTCGGGACATATGGACAA
Found at i:1366136 original size:9 final size:9
Alignment explanation
Indices: 1366124--1366149 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1366114 ATTGTTTTTA
1366124 TCTTATTCT
1 TCTTATTCT
1366133 TCTTATTCT
1 TCTTATTCT
1366142 TCTTATTC
1 TCTTATTC
1366150 AATTTCCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (9 bp):
TCTTATTCT
Found at i:1372283 original size:20 final size:20
Alignment explanation
Indices: 1372254--1372293 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1372244 TTGGTTCACG
* *
1372254 GAATATAAGATTATCAGTGA
1 GAATAAAAGATTACCAGTGA
1372274 GAATAAAAGATTACCAGTGA
1 GAATAAAAGATTACCAGTGA
1372294 ATAGGATTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.25
Consensus pattern (20 bp):
GAATAAAAGATTACCAGTGA
Found at i:1372442 original size:17 final size:18
Alignment explanation
Indices: 1372412--1372450 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1372402 AAATTGTCCT
* *
1372412 TATTATAAATTTGTATAA
1 TATTACAAATTTGTAAAA
1372430 TATTACAAA-TTGTAAAA
1 TATTACAAATTTGTAAAA
1372447 TATT
1 TATT
1372451 TATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (18 bp):
TATTACAAATTTGTAAAA
Found at i:1372477 original size:37 final size:37
Alignment explanation
Indices: 1372443--1372512 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
1372433 TACAAATTGT
1372443 AAAATATTTATAT-ATTTTCTTTAAAAAATTAAATTC
1 AAAATATTTATATAATTTTCTTTAAAAAATTAAATTC
* * *
1372479 ATAATATTTATATAATTTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTCTTTAAAAAATTAAA
1372513 AATATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 12 0.40
37 18 0.60
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (37 bp):
AAAATATTTATATAATTTTCTTTAAAAAATTAAATTC
Found at i:1379545 original size:2 final size:2
Alignment explanation
Indices: 1379538--1379568 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1379528 AATAGCGCAA
1379538 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1379569 CACTACCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1384726 original size:18 final size:17
Alignment explanation
Indices: 1384686--1384726 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1384676 TTATCATTCT
*
1384686 ATTTA-TTTTTATAAAT
1 ATTTATTTTTTATAAAA
1384702 A-TTATTTTTTATAAAAA
1 ATTTATTTTTTAT-AAAA
1384719 ATTTATTT
1 ATTTATTT
1384727 CTTGGCATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 8 0.38
17 4 0.19
18 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATTTTTTATAAAA
Found at i:1385519 original size:20 final size:20
Alignment explanation
Indices: 1385458--1385523 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
1385448 ATTAGCACAG
* *
1385458 AACCGG-TAAAGAACCGGAAG
1 AACCGGCTAAA-AACCAGAAA
*
1385478 AACCGGCTGAAAACCAGAAA
1 AACCGGCTAAAAACCAGAAA
1385498 AACCGGCTAAAAACC-GACAA
1 AACCGGCTAAAAACCAGA-AA
1385518 AACCGG
1 AACCGG
1385524 TTTGAACCGC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.05
20 35 0.88
21 3 0.08
ACGTcount: A:0.47, C:0.26, G:0.23, T:0.05
Consensus pattern (20 bp):
AACCGGCTAAAAACCAGAAA
Found at i:1385664 original size:31 final size:31
Alignment explanation
Indices: 1385629--1385701 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
1385619 CTCGACTCAA
1385629 ACTCGAAAACTTTAAAAGTAAGCTCAACTCG
1 ACTCGAAAACTTTAAAAGTAAGCTCAACTCG
1385660 ACTCGAAAACTTTAAAAGTAAGCTCAACTCG
1 ACTCGAAAACTTTAAAAGTAAGCTCAACTCG
*
1385691 ACTCAAAAACT
1 ACTCGAAAACT
1385702 CACGAGCTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.22
Consensus pattern (31 bp):
ACTCGAAAACTTTAAAAGTAAGCTCAACTCG
Found at i:1385818 original size:24 final size:24
Alignment explanation
Indices: 1385788--1385843 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1385778 TAGAAGTTCG
1385788 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
*
1385812 ATTGAAGTCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
1385836 ATTGAAGC
1 ATTGAAGC
1385844 GAAATAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:1397054 original size:2 final size:2
Alignment explanation
Indices: 1397049--1397075 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1397039 TAAAGAGTAT
1397049 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 T
1397076 TACTTATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1402865 original size:13 final size:14
Alignment explanation
Indices: 1402847--1402875 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1402837 CACCACCTGG
1402847 TTTT-AATTTTATA
1 TTTTAAATTTTATA
1402860 TTTTAAATTTTATA
1 TTTTAAATTTTATA
1402874 TT
1 TT
1402876 AAATAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTAAATTTTATA
Found at i:1403321 original size:38 final size:38
Alignment explanation
Indices: 1403270--1403346 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
1403260 TAAAAAATTC
1403270 AAAGTACACTGAATGAAATAGGAAAAGTGATGAATAGT
1 AAAGTACACTGAATGAAATAGGAAAAGTGATGAATAGT
1403308 AAAGTACACTGAATGAAATAGGAAAAGTGATGAATAGT
1 AAAGTACACTGAATGAAATAGGAAAAGTGATGAATAGT
1403346 A
1 A
1403347 TAATTTACCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (38 bp):
AAAGTACACTGAATGAAATAGGAAAAGTGATGAATAGT
Found at i:1403340 original size:17 final size:17
Alignment explanation
Indices: 1403282--1403341 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 17
1403272 AGTACACTGA
1403282 ATGAAATAGGAAAAGTG
1 ATGAAATAGGAAAAGTG
* *
1403299 ATG-AATAGTAAAGTACACTG
1 ATGAAATAG-GAA--A-AGTG
1403319 AATGAAATAGGAAAAGTG
1 -ATGAAATAGGAAAAGTG
1403337 ATGAA
1 ATGAA
1403342 TAGTATAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
16 5 0.15
17 10 0.30
18 3 0.09
19 2 0.06
20 3 0.09
21 5 0.15
22 5 0.15
ACGTcount: A:0.52, C:0.03, G:0.25, T:0.20
Consensus pattern (17 bp):
ATGAAATAGGAAAAGTG
Found at i:1414279 original size:19 final size:18
Alignment explanation
Indices: 1414241--1414284 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1414231 AGAATAAAGA
1414241 TTAAATTGATATAATATT
1 TTAAATTGATATAATATT
1414259 TTAAATATG-TATAATTATT
1 TTAAAT-TGATATAA-TATT
*
1414278 TTGAATT
1 TTAAATT
1414285 AGAATCGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
TTAAATTGATATAATATT
Found at i:1415394 original size:14 final size:14
Alignment explanation
Indices: 1415375--1415402 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1415365 TACTTAGCAT
1415375 ATTTAAAAACAAAG
1 ATTTAAAAACAAAG
1415389 ATTTAAAAACAAAG
1 ATTTAAAAACAAAG
1415403 TAAAAATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
ATTTAAAAACAAAG
Found at i:1421934 original size:20 final size:20
Alignment explanation
Indices: 1421909--1421953 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1421899 GTAAAAGGTT
1421909 GAAATATGAAGTATTTGTGA
1 GAAATATGAAGTATTTGTGA
1421929 GAAATATGAAGTATTTGTGA
1 GAAATATGAAGTATTTGTGA
*
1421949 TAAAT
1 GAAAT
1421954 TGAGTGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (20 bp):
GAAATATGAAGTATTTGTGA
Found at i:1422153 original size:20 final size:20
Alignment explanation
Indices: 1422128--1422178 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1422118 CGTTAAGGGA
1422128 TGTACCGATACACTATAAAG
1 TGTACCGATACACTATAAAG
1422148 TGTACCGATACACTATAAAG
1 TGTACCGATACACTATAAAG
1422168 TGTACCGATAC
1 TGTACCGATAC
1422179 TTACCTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (20 bp):
TGTACCGATACACTATAAAG
Found at i:1423043 original size:18 final size:18
Alignment explanation
Indices: 1423020--1423055 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1423010 AGGGTTCTAT
1423020 GTGGTCATTCAGGACATA
1 GTGGTCATTCAGGACATA
* *
1423038 GTGGTCCTTCGGGACATA
1 GTGGTCATTCAGGACATA
1423056 AGTGATATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (18 bp):
GTGGTCATTCAGGACATA
Found at i:1423595 original size:2 final size:2
Alignment explanation
Indices: 1423588--1423629 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1423578 ATTACATGAG
* * *
1423588 AT AT AT AT AG AT AT AT AG AT AT AT AG AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1423630 GCATTTATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1423629 original size:8 final size:8
Alignment explanation
Indices: 1423590--1423628 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
1423580 TACATGAGAT
1423590 ATATATAG
1 ATATATAG
1423598 ATATATAG
1 ATATATAG
1423606 ATATATAG
1 ATATATAG
*
1423614 ATATATAT
1 ATATATAG
1423622 ATATATA
1 ATATATA
1423629 TGCATTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (8 bp):
ATATATAG
Found at i:1432615 original size:23 final size:22
Alignment explanation
Indices: 1432579--1432643 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
1432569 AATATTGTAT
* *
1432579 TTTAATGAAATTATATTTAGATT
1 TTTAAT-AATTTATATTTAGATG
* *
1432602 TTTAACTAATTTATAATTATATG
1 TTTAA-TAATTTATATTTAGATG
*
1432625 TTTAATACTTTATAATTTA
1 TTTAATAATTTAT-ATTTA
1432644 ATAATTTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 7 0.21
23 26 0.76
24 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTAATAATTTATATTTAGATG
Found at i:1432645 original size:15 final size:15
Alignment explanation
Indices: 1432608--1432660 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1432598 GATTTTTAAC
1432608 TAATTT-ATAA-TTA
1 TAATTTAATAATTTA
* *
1432621 TATGTTTAATACTTTA
1 TA-ATTTAATAATTTA
1432637 TAATTTAATAATTTA
1 TAATTTAATAATTTA
*
1432652 TAAATTAAT
1 TAATTTAAT
1432661 TTAATAGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.06
14 3 0.09
15 22 0.69
16 5 0.16
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
TAATTTAATAATTTA
Found at i:1433697 original size:2 final size:2
Alignment explanation
Indices: 1433690--1433724 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1433680 ACGAGATTGA
1433690 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1433725 AAAGATGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1438142 original size:31 final size:31
Alignment explanation
Indices: 1438104--1438211 Score: 153
Period size: 31 Copynumber: 3.5 Consensus size: 31
1438094 GGGTCGAGAG
* *
1438104 TTACCTATGTTATTCGAGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1438135 TTACCTATGTTCTTTGGGACATATGAACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1438166 TTACCTATATTCTTCGGGACATATGGACTAT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
1438197 TTACCTAGGTTCTTC
1 TTACCTATGTTCTTC
1438212 AGAATCTATG
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.41
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1438858 original size:21 final size:22
Alignment explanation
Indices: 1438834--1438874 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1438824 CTGTAACATA
*
1438834 GTATCGGTA-CACTGTAGCAGG
1 GTATCGATACCACTGTAGCAGG
*
1438855 GTATCGATACCTCTGTAGCA
1 GTATCGATACCACTGTAGCA
1438875 TTCTGGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (22 bp):
GTATCGATACCACTGTAGCAGG
Found at i:1440247 original size:22 final size:22
Alignment explanation
Indices: 1440219--1440270 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
1440209 GAGTCGAGGG
* *
1440219 ATTCATAGGTCCTTCGGGACAT
1 ATTCATAGGTCCTTAGGGACAA
1440241 ATTCATAGGTCCTTAGGGACAA
1 ATTCATAGGTCCTTAGGGACAA
1440263 ATTTCATA
1 A-TTCATA
1440271 TGCCACTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (22 bp):
ATTCATAGGTCCTTAGGGACAA
Found at i:1446417 original size:17 final size:17
Alignment explanation
Indices: 1446397--1446457 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
1446387 GGAAAATAAA
1446397 AAAAACAAAGAGCAAAG
1 AAAAACAAAGAGCAAAG
1446414 AAAAACAAAGAGCAAAG
1 AAAAACAAAGAGCAAAG
* *
1446431 AGAAAAGAAACA--AAAG
1 A-AAAACAAAGAGCAAAG
*
1446447 AAAAATAAAGA
1 AAAAACAAAGA
1446458 AAAAAAGAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
15 8 0.21
16 5 0.13
17 18 0.46
18 8 0.21
ACGTcount: A:0.74, C:0.08, G:0.16, T:0.02
Consensus pattern (17 bp):
AAAAACAAAGAGCAAAG
Found at i:1448018 original size:39 final size:39
Alignment explanation
Indices: 1447889--1448167 Score: 314
Period size: 39 Copynumber: 7.2 Consensus size: 39
1447879 TTAAAAAAAT
* * *
1447889 ATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAAAGAAG
1 ATTTTATCTCGCTTGAGATAATTTCCCTTGAAACAGAAG
* *
1447928 A-TTTATCTCGCTTGAGATAGTTTCCCTTGAAACCA-ATG
1 ATTTTATCTCGCTTGAGATAATTTCCCTTGAAA-CAGAAG
* * * ** *
1447966 A-TTTATCTTGCTTGAGACAATTTCTCTCAAAACATAAG
1 ATTTTATCTCGCTTGAGATAATTTCCCTTGAAACAGAAG
* * *
1448004 ATTTTATCTTGCTTGAGATAGTTTTCCCTTGAAACAAAAG
1 ATTTTATCTCGCTTGAGATA-ATTTCCCTTGAAACAGAAG
* *
1448044 ATTTTGTCTCGCTTGAGATAATTTCCATTGAAACA-AACG
1 ATTTTATCTCGCTTGAGATAATTTCCCTTGAAACAGAA-G
* * *
1448083 ATTTTGTCTCACTTGAGATAGTTTCCCTTGAAACAGAAG
1 ATTTTATCTCGCTTGAGATAATTTCCCTTGAAACAGAAG
* *
1448122 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAG
1 ATTTTATCTCGCTTGAGATAATTTCCCTTGAAACAGAAG
1448161 ATTTTAT
1 ATTTTAT
1448168 AAGAAACTAA
Statistics
Matches: 208, Mismatches: 26, Indels: 12
0.85 0.11 0.05
Matches are distributed among these distances:
37 2 0.01
38 63 0.30
39 109 0.52
40 34 0.16
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (39 bp):
ATTTTATCTCGCTTGAGATAATTTCCCTTGAAACAGAAG
Found at i:1448113 original size:78 final size:78
Alignment explanation
Indices: 1447884--1448167 Score: 349
Period size: 78 Copynumber: 3.7 Consensus size: 78
1447874 TGTTCTTAAA
* * * * *
1447884 AAAATATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAAAGAAGA-TTTATCTCGCTTGAGATAG
1 AAAAGATTTTATCTCGCTTGAGATAATTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAG
1447948 TTTCCCTTGAAAC
66 TTTCCCTTGAAAC
* * * * * * * *
1447961 CAATGA-TTTATCTTGCTTGAGACAATTTCTCTCAAAACATAAGATTTTATCTTGCTTGAGATAG
1 AAAAGATTTTATCTCGCTTGAGATAATTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAG
1448025 TTTTCCCTTGAAAC
66 -TTTCCCTTGAAAC
* * * * *
1448039 AAAAGATTTTGTCTCGCTTGAGATAATTTCCATTGAAACA-AACGATTTTGTCTCACTTGAGATA
1 AAAAGATTTTATCTCGCTTGAGATAATTTCCCTCGAAACAGAA-GATTTTATCTCGCTTGAGATA
1448103 GTTTCCCTTGAAAC
65 GTTTCCCTTGAAAC
* *
1448117 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTAT
1 AAAAGATTTTATCTCGCTTGAGATAATTTCCCTCGAAACAGAAGATTTTAT
1448168 AAGAAACTAA
Statistics
Matches: 171, Mismatches: 31, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
76 29 0.17
77 21 0.12
78 74 0.43
79 47 0.27
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (78 bp):
AAAAGATTTTATCTCGCTTGAGATAATTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAG
TTTCCCTTGAAAC
Found at i:1448454 original size:42 final size:42
Alignment explanation
Indices: 1448389--1448502 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 42
1448379 AAGGGTTTCT
1448389 TGATGAGTAAGTCCTTCGAGCCATC-AGTAAGTCTTTCGAGTA
1 TGATGAGTAAGTCCTTCGAGCCATCTA-TAAGTCTTTCGAGTA
* *
1448431 TGATGTGTAAGTCCTTC-AGGCCATCTATAAGTCTTTCGAGCA
1 TGATGAGTAAGTCCTTCGA-GCCATCTATAAGTCTTTCGAGTA
* * *
1448473 AGATGA-TAAGCCCTTCGAGCCATCCATAAG
1 TGATGAGTAAGTCCTTCGAGCCATCTATAAG
1448503 ACCTTCGGGC
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
41 21 0.33
42 41 0.65
43 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (42 bp):
TGATGAGTAAGTCCTTCGAGCCATCTATAAGTCTTTCGAGTA
Found at i:1448724 original size:20 final size:21
Alignment explanation
Indices: 1448684--1448724 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1448674 CTTTAAGACA
1448684 GTTTCCCTTGAAACAAATTTC
1 GTTTCCCTTGAAACAAATTTC
*
1448705 GTTTCTCTTGAAAC-AATTTC
1 GTTTCCCTTGAAACAAATTTC
1448725 CCTTGAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (21 bp):
GTTTCCCTTGAAACAAATTTC
Found at i:1448783 original size:30 final size:30
Alignment explanation
Indices: 1448721--1448784 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
1448711 CTTGAAACAA
* *
1448721 TTTCCCTTGAAACACAAATCTTTTAGATTG
1 TTTCCCTTAAAACACAAATCTTTGAGATTG
1448751 TTTCCCTTAAAACATC-AATCTTTGA-ATCTG
1 TTTCCCTTAAAACA-CAAATCTTTGAGAT-TG
1448781 TTTC
1 TTTC
1448785 TCTCGAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 2 0.07
30 27 0.90
31 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (30 bp):
TTTCCCTTAAAACACAAATCTTTGAGATTG
Found at i:1449220 original size:91 final size:91
Alignment explanation
Indices: 1449082--1449442 Score: 596
Period size: 91 Copynumber: 4.0 Consensus size: 91
1449072 AGAGAACCGA
1449082 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
1449147 ATGAGAAGAACTTGTTTAACCTTGGT
66 ATGAGAAGAACTTGTTCAACCTTGGT
* * *
1449173 TCAACGTTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTAACGAGGGAGAAGAAATTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
* * *
1449238 ATGAGAAGAATTTGTTTAACCTTGGC
66 ATGAGAAGAACTTGTTCAACCTTGGT
* *
1449264 TCAAAATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAACAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
1449329 ATGAGAAGAACTTGTTCAACCTTAGT
66 ATGAGAAGAACTTGTTCAACCTTGGT
* * * *
1449355 TCATCATTTCCATTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAACTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1449420 ATGAGAAGAACTTGTTCAACCTT
66 ATGAGAAGAACTTGTTCAACCTT
1449443 CACTCGATTC
Statistics
Matches: 250, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 250 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (91 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGGT
Found at i:1449424 original size:21 final size:21
Alignment explanation
Indices: 1449383--1449424 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1449373 AGTTCATAAT
1449383 GAGAAGAACTCATCCAATGAGG
1 GAGAAGAACTCAT-CAATGAGG
1449405 GAGAAGAACTTCAT-AATGAG
1 GAGAAGAAC-TCATCAATGAG
1449425 AAGAACTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.17
Consensus pattern (21 bp):
GAGAAGAACTCATCAATGAGG
Found at i:1449609 original size:139 final size:139
Alignment explanation
Indices: 1449359--1449886 Score: 759
Period size: 139 Copynumber: 3.8 Consensus size: 139
1449349 CTTAGTTCAT
* * *
1449359 CATTTCCATTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAACTTCATAATGA
1 CATTTCCAGTGGAAAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGA
* * * *
1449424 GAAGAACTTGTTCAACCTTCACTCGATTCGTCGCATATGGAGTTGAATCAGCAACACCTCACTCG
66 GAAGAACTTGTTCAACCTTCACTCGATTCATCACATATGGAGTTGAATCAACAACACCTCACTTG
1449489 AGGGATCAA
131 AGGGATCAA
* * * *
1449498 CATTTCCAATGGAGAGTTCACAATGAGAAGAACTCATCCAATGAGGGAGAAAAAGTTCATAATGA
1 CATTTCCAGTGGAAAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGA
* * * *
1449563 GAAGAACTTGTTCAACGTTCGCTTGATTCATCACATATGGAGTTGAATCAATAACACCTCACTTG
66 GAAGAACTTGTTCAACCTTCACTCGATTCATCACATATGGAGTTGAATCAACAACACCTCACTTG
1449628 AGGGATCAA
131 AGGGATCAA
* * *
1449637 CATTTTCAGTGAAAAGTTCATAATGACAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGA
1 CATTTCCAGTGGAAAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGA
** *
1449702 GAAGAACTTGTTCAACCTTTGCTCGATTCATCACATATGGAGTTAAATCAACAACACCTCACTTG
66 GAAGAACTTGTTCAACCTTCACTCGATTCATCACATATGGAGTTGAATCAACAACACCTCACTTG
1449767 AGGGATCAA
131 AGGGATCAA
* * * * * *
1449776 TATTTTCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGATAAGGAAGAAGAAGTTCATAATAA
1 CATTTCCAGTGGAAAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGA
* * * * *
1449841 GAAGAACTTGTTCAATCTTAACTTGTTTCCATCACATACGGAGTTG
66 GAAGAACTTGTTCAACCTTCACTCGATT-CATCACATATGGAGTTG
1449887 GAACATCACC
Statistics
Matches: 350, Mismatches: 38, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
139 335 0.96
140 15 0.04
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (139 bp):
CATTTCCAGTGGAAAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTTCACTCGATTCATCACATATGGAGTTGAATCAACAACACCTCACTTG
AGGGATCAA
Found at i:1452825 original size:40 final size:40
Alignment explanation
Indices: 1452741--1452833 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
1452731 AACACAAGCA
* * * *
1452741 CCACTAAAGTACGAGTCTTTAGCGGGGTTTGTATAAAAATG
1 CCACTAAAGTA-TAGTCTTTAGCGGCGTTTATATAAAAACG
* *
1452782 CCACTAAAGTATAGTCTTTAGTGGCGTTTATATGAAAACG
1 CCACTAAAGTATAGTCTTTAGCGGCGTTTATATAAAAACG
1452822 CCACTAAAGTAT
1 CCACTAAAGTAT
1452834 GAATATTTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 35 0.76
41 11 0.24
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (40 bp):
CCACTAAAGTATAGTCTTTAGCGGCGTTTATATAAAAACG
Found at i:1458470 original size:42 final size:43
Alignment explanation
Indices: 1458415--1458495 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 43
1458405 GAATGTTTTT
* *
1458415 AATATGTTAGTTTGATTTATTTATGGATTGTTA-TTTGGTTTA
1 AATATGTTAGTTTGATATATTTATAGATTGTTACTTTGGTTTA
*
1458457 AATATGTTAGTTTGATATATTTGTAGATTGTTACTTTGG
1 AATATGTTAGTTTGATATATTTATAGATTGTTACTTTGG
1458496 AGTTTAGACT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 30 0.86
43 5 0.14
ACGTcount: A:0.25, C:0.01, G:0.20, T:0.54
Consensus pattern (43 bp):
AATATGTTAGTTTGATATATTTATAGATTGTTACTTTGGTTTA
Found at i:1461907 original size:6 final size:6
Alignment explanation
Indices: 1461898--1461922 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1461888 GGGATGATAA
1461898 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
1461923 AAACCCATTT
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:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:1462017 original size:14 final size:13
Alignment explanation
Indices: 1461986--1462030 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1461976 GCCCCGATTA
1461986 CCCGATTACCCGC
1 CCCGATTACCCGC
1461999 CCCGATTACCCGCC
1 CCCGATTACCCG-C
*
1462013 CCCGA-TACCCGA
1 CCCGATTACCCGC
1462025 CCCGAT
1 CCCGAT
1462031 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 5 0.17
13 18 0.62
14 6 0.21
ACGTcount: A:0.18, C:0.53, G:0.16, T:0.13
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:1462161 original size:12 final size:12
Alignment explanation
Indices: 1462146--1462180 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1462136 CGATTCTCGG
1462146 CCCAATACCCGA
1 CCCAATACCCGA
*
1462158 CCCAATACCCGG
1 CCCAATACCCGA
1462170 CCCAATACCCG
1 CCCAATACCCG
1462181 TTTAAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:1463324 original size:2 final size:2
Alignment explanation
Indices: 1463317--1463342 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1463307 TTTAGAGGTA
1463317 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
1463343 TAAATTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1463834 original size:3 final size:3
Alignment explanation
Indices: 1463826--1463859 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1463816 TGAAGCACCA
1463826 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1463860 GGCTTCCAAG
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1466711 original size:15 final size:16
Alignment explanation
Indices: 1466686--1466715 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1466676 ATTTAGGTTA
1466686 TTATGGAAAGAAAATT
1 TTATGGAAAGAAAATT
1466702 TTAT-GAAAGAAAAT
1 TTATGGAAAGAAAAT
1466716 GCTGTTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (16 bp):
TTATGGAAAGAAAATT
Found at i:1469273 original size:2 final size:2
Alignment explanation
Indices: 1469266--1469297 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1469256 TAATTGGTGA
1469266 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1469298 GCATGTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1474246 original size:15 final size:16
Alignment explanation
Indices: 1474226--1474255 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1474216 TTTTTTTATA
1474226 ATTATAA-TTATAATT
1 ATTATAATTTATAATT
1474241 ATTATAATTTATAAT
1 ATTATAATTTATAAT
1474256 AAGTTGTGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTATAATTTATAATT
Found at i:1474591 original size:24 final size:23
Alignment explanation
Indices: 1474559--1474604 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
1474549 GCTGATTAGC
*
1474559 TGTAACTGTTTCTGGTTAAGTTGT
1 TGTAACTGTTCCTGGTT-AGTTGT
1474583 TGTAACTGTTCCTGGTTAGTTG
1 TGTAACTGTTCCTGGTTAGTTG
1474605 GGCCGTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.15, C:0.11, G:0.26, T:0.48
Consensus pattern (23 bp):
TGTAACTGTTCCTGGTTAGTTGT
Found at i:1475475 original size:24 final size:23
Alignment explanation
Indices: 1475443--1475488 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
1475433 GCTGATTAGC
*
1475443 TGTAACTGTTTCTGGTTAAGTTGT
1 TGTAACTGTTCCTGGTT-AGTTGT
1475467 TGTAACTGTTCCTGGTTAGTTG
1 TGTAACTGTTCCTGGTTAGTTG
1475489 GGTCGTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.15, C:0.11, G:0.26, T:0.48
Consensus pattern (23 bp):
TGTAACTGTTCCTGGTTAGTTGT
Found at i:1475502 original size:19 final size:19
Alignment explanation
Indices: 1475478--1475526 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1475468 GTAACTGTTC
1475478 CTGGTTAGTTGGGTCGTTT
1 CTGGTTAGTTGGGTCGTTT
1475497 CTGGTTAGTTGGGTCGTTT
1 CTGGTTAGTTGGGTCGTTT
1475516 CTGGTTAGTTG
1 CTGGTTAGTTG
1475527 AGCTAGTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.06, C:0.10, G:0.37, T:0.47
Consensus pattern (19 bp):
CTGGTTAGTTGGGTCGTTT
Found at i:1478041 original size:98 final size:98
Alignment explanation
Indices: 1477872--1478070 Score: 398
Period size: 98 Copynumber: 2.0 Consensus size: 98
1477862 AATAGGCTGG
1477872 AAACAATTAAAAACATAATATTAATATCAATTTATTTCTTCGATCATTTTATTTAATTATAGATT
1 AAACAATTAAAAACATAATATTAATATCAATTTATTTCTTCGATCATTTTATTTAATTATAGATT
1477937 GGATATTAATTTAGTTGACATTATTATAATTAA
66 GGATATTAATTTAGTTGACATTATTATAATTAA
1477970 AAACAATTAAAAACATAATATTAATATCAATTTATTTCTTCGATCATTTTATTTAATTATAGATT
1 AAACAATTAAAAACATAATATTAATATCAATTTATTTCTTCGATCATTTTATTTAATTATAGATT
1478035 GGATATTAATTTAGTTGACATTATTATAATTAA
66 GGATATTAATTTAGTTGACATTATTATAATTAA
1478068 AAA
1 AAA
1478071 AGTTTTTATA
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 101 1.00
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (98 bp):
AAACAATTAAAAACATAATATTAATATCAATTTATTTCTTCGATCATTTTATTTAATTATAGATT
GGATATTAATTTAGTTGACATTATTATAATTAA
Found at i:1479395 original size:14 final size:14
Alignment explanation
Indices: 1479376--1479403 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1479366 CCCCCTTACT
1479376 TTAACACTTCTCCC
1 TTAACACTTCTCCC
1479390 TTAACACTTCTCCC
1 TTAACACTTCTCCC
1479404 CCTTTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAACACTTCTCCC
Found at i:1481665 original size:45 final size:44
Alignment explanation
Indices: 1481573--1481670 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 44
1481563 GGCTCTGTGA
* * *
1481573 ATCGATGCACATTCAAGGCGTGCATCGGTGCATCTTCATGATGT
1 ATCGATGCACATTCAAGGCGTACATCGATGCACCTTCATGATGT
*
1481617 ATCGATGCACATTCATAGG-GATACATCGATGCACCTTTAT-AGTGT
1 ATCGATGCACATTCA-AGGCG-TACATCGATGCACCTTCATGA-TGT
1481662 ATCGATGCA
1 ATCGATGCA
1481671 TTATGCACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
44 17 0.36
45 30 0.64
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGCGTACATCGATGCACCTTCATGATGT
Found at i:1481667 original size:21 final size:21
Alignment explanation
Indices: 1481614--1481670 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 21
1481604 ATCTTCATGA
1481614 TGTATCGATGCACATTCATAG
1 TGTATCGATGCACATTCATAG
* * *
1481635 GGATACATCGATGCACCTTTATAG
1 TG-T--ATCGATGCACATTCATAG
1481659 TGTATCGATGCA
1 TGTATCGATGCA
1481671 TTATGCACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 10 0.34
22 1 0.03
23 1 0.03
24 17 0.59
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (21 bp):
TGTATCGATGCACATTCATAG
Found at i:1488540 original size:29 final size:30
Alignment explanation
Indices: 1488498--1488569 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
1488488 CCCGAATGAC
*
1488498 CTATCCAGAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCCCGGCAA
* *
1488527 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCCCGGCAA
* *
1488557 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1488570 CCGACGAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCCCGGCAA
Found at i:1488593 original size:31 final size:31
Alignment explanation
Indices: 1488555--1488619 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
1488545 GAACCTCGGC
*
1488555 AACTGTCCATAGGTCCCGACGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1488586 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1488617 AAC
1 AAC
1488620 CCTCGACTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACCTAGGTA
Found at i:1489579 original size:20 final size:22
Alignment explanation
Indices: 1489554--1489611 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
1489544 TTCCCCTTGA
1489554 AGTGCATCGATGCATGC-T-AC
1 AGTGCATCGATGCATGCTTAAC
* *
1489574 AGTGCATCAATGCATTCTTTAAC
1 AGTGCATCGATGCATGC-TTAAC
1489597 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1489612 CTACCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATGCTTAAC
Found at i:1489677 original size:64 final size:63
Alignment explanation
Indices: 1489599--1489739 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
1489589 TCTTTAACAT
* *
1489599 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * *
1489662 GATGCATCGATGCACTCCTTATGCATCGATGCACCATTTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
1489726 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1489740 ATTGAATGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 21 0.31
64 46 0.69
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:1492858 original size:35 final size:35
Alignment explanation
Indices: 1492789--1492859 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
1492779 GTTGAAAAAT
*
1492789 ATTTATATATTTTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTTTAAAAAAATTAAAATCATAAA
* *
1492824 ATTTATATATTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTTTAAAAAAATT-AAAATCATAAA
1492859 A
1 A
1492860 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 28 0.88
36 4 0.12
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (35 bp):
ATTTATATATTTTTTAAAAAAATTAAAATCATAAA
Found at i:1500123 original size:21 final size:21
Alignment explanation
Indices: 1500093--1500299 Score: 160
Period size: 21 Copynumber: 10.0 Consensus size: 21
1500083 CGATTACATA
*
1500093 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
1500114 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** *
1500135 TTCGCGTTGTGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
1500156 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
1500175 TTCGCGTTGCAATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
1500198 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1500217 TTCGCGTTGTGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
1500240 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
1500259 TTCGCATTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
1500282 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
1500300 AATCGCAACG
Statistics
Matches: 144, Mismatches: 30, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
19 39 0.27
21 79 0.55
23 26 0.18
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:1500306 original size:42 final size:42
Alignment explanation
Indices: 1500118--1500296 Score: 290
Period size: 42 Copynumber: 4.3 Consensus size: 42
1500108 TCCAAGTTCG
*
1500118 CGTTGCGATAGTCGAAGTTCGCGTTGTGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
1500158 CGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* * *
1500200 CGTTGCGATAGTCCAAGTTCGCGTTGTGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
1500242 CGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1500284 CGTTGCGATAGTC
1 CGTTGCGATAGTC
1500297 CAAAATCGCA
Statistics
Matches: 127, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
40 27 0.21
41 2 0.02
42 98 0.77
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:1501142 original size:40 final size:42
Alignment explanation
Indices: 1501022--1501198 Score: 308
Period size: 40 Copynumber: 4.3 Consensus size: 42
1501012 TGCGATTTTG
1501022 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
1501064 GACTATCGCAATGAATTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1501106 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1501146 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1501186 GACTATCGCAACG
1 GACTATCGCAACG
1501199 CGAACTTGGA
Statistics
Matches: 131, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
40 71 0.54
41 1 0.01
42 59 0.45
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:1501193 original size:21 final size:21
Alignment explanation
Indices: 1501047--1501217 Score: 156
Period size: 21 Copynumber: 8.3 Consensus size: 21
1501037 TTTGGAATAA
1501047 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * * *
1501068 ATCGCAA--TGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
*
1501087 AAATCGCAATGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * **
1501110 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
1501129 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
1501150 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
1501169 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
1501190 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
1501211 ATCGCAA
1 ATCGCAA
1501218 TGCAAATATG
Statistics
Matches: 117, Mismatches: 25, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
19 38 0.32
21 71 0.61
23 8 0.07
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:1501261 original size:21 final size:21
Alignment explanation
Indices: 1501232--1501284 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1501222 AATATGTAAA
*
1501232 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
1501253 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
1501274 TCGCGTTGCGA
1 TCGCGTTGCGA
1501285 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:1505953 original size:2 final size:2
Alignment explanation
Indices: 1505946--1506005 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
1505936 TACATAGTTT
1505946 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1505988 TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1506006 CACAGTAGGA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1507134 original size:16 final size:16
Alignment explanation
Indices: 1507113--1507143 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1507103 GCTGTATTTT
*
1507113 ATAAAATTATTTAAAG
1 ATAAAATTAATTAAAG
1507129 ATAAAATTAATTAAA
1 ATAAAATTAATTAAA
1507144 CCGATTGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
ATAAAATTAATTAAAG
Found at i:1511165 original size:18 final size:19
Alignment explanation
Indices: 1511142--1511183 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1511132 CCGTTATTAG
1511142 TGAACCGGAAG-GAATCGT
1 TGAACCGGAAGTGAATCGT
**
1511160 TGAACCGGTTGTGAATCGT
1 TGAACCGGAAGTGAATCGT
1511179 TGAAC
1 TGAAC
1511184 GGTTGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.24
Consensus pattern (19 bp):
TGAACCGGAAGTGAATCGT
Found at i:1511177 original size:19 final size:18
Alignment explanation
Indices: 1511153--1511188 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
1511143 GAACCGGAAG
1511153 GAATCGTTGAACCGGTTGT
1 GAATCGTTGAA-CGGTTGT
1511172 GAATCGTTGAACGGTTG
1 GAATCGTTGAACGGTTG
1511189 AAAATCGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.14, G:0.33, T:0.31
Consensus pattern (18 bp):
GAATCGTTGAACGGTTGT
Found at i:1511194 original size:18 final size:19
Alignment explanation
Indices: 1511154--1511195 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1511144 AACCGGAAGG
**
1511154 AATCGTTGAACCGGTTGTG
1 AATCGTTGAACCGGTTGAA
1511173 AATCGTTGAA-CGGTTGAA
1 AATCGTTGAACCGGTTGAA
1511191 AATCG
1 AATCG
1511196 GTTTTGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (19 bp):
AATCGTTGAACCGGTTGAA
Found at i:1513607 original size:16 final size:16
Alignment explanation
Indices: 1513586--1513704 Score: 193
Period size: 16 Copynumber: 7.4 Consensus size: 16
1513576 GGTATTACCC
1513586 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
1513602 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
* *
1513618 GACTTGTTTTTAACCT
1 GACCTGTTTTCAACCT
*
1513634 GACATGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
1513650 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
1513666 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
1513682 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
1513698 GACCTGT
1 GACCTGT
1513705 AAATGATCCA
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 95 1.00
ACGTcount: A:0.19, C:0.27, G:0.13, T:0.40
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:1514207 original size:14 final size:14
Alignment explanation
Indices: 1514184--1514254 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
1514174 TCCATTTAAA
*
1514184 TTAGGATTTATGGT
1 TTAGGGTTTATGGT
*
1514198 TTAGTGTTTATGGT
1 TTAGGGTTTATGGT
** **
1514212 TTAAAGTTTA-GAA
1 TTAGGGTTTATGGT
*
1514225 TTAGGGTTTATGAT
1 TTAGGGTTTATGGT
*
1514239 TTAGGGTTTAGGGT
1 TTAGGGTTTATGGT
1514253 TT
1 TT
1514255 CTATAAACTA
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
13 9 0.20
14 36 0.80
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:1514242 original size:41 final size:40
Alignment explanation
Indices: 1514178--1514254 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 40
1514168 TGCTAGTCCA
* * *
1514178 TTTAAATTAGGATTTATGGTTTAGTGTTTATGGTTTAAAG
1 TTTAAATTAGGATTTATGATTTAGGGTTTAGGGTTTAAAG
*
1514218 TTTAGAATTAGGGTTTATGATTTAGGGTTTAGGGTTT
1 TTTA-AATTAGGATTTATGATTTAGGGTTTAGGGTTT
1514255 CTATAAACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 4 0.12
41 28 0.88
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (40 bp):
TTTAAATTAGGATTTATGATTTAGGGTTTAGGGTTTAAAG
Found at i:1514349 original size:15 final size:15
Alignment explanation
Indices: 1514329--1514365 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
1514319 TAATTTACTT
1514329 TATATAGTTTATATA
1 TATATAGTTTATATA
1514344 TATATAGTTTATATA
1 TATATAGTTTATATA
1514359 TACTATA
1 TA-TATA
1514366 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:1514754 original size:14 final size:14
Alignment explanation
Indices: 1514732--1514795 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 14
1514722 TTCATTTAAA
1514732 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
*
1514746 TTAGTGTTTATGGT
1 TTAGGGTTTATGGT
** **
1514760 TTAAAGTTTA-GAA
1 TTAGGGTTTATGGT
*
1514773 TTAGGGTTTATGAT
1 TTAGGGTTTATGGT
*
1514787 TTAAGGTTT
1 TTAGGGTTT
1514796 CTATAAACTA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
13 9 0.22
14 31 0.77
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:1515176 original size:546 final size:541
Alignment explanation
Indices: 1514106--1515275 Score: 1938
Period size: 546 Copynumber: 2.1 Consensus size: 541
1514096 TTTTGGCAAT
* * *
1514106 ACATTAGTTTACAAAGG-CCAGTACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTG
1 ACATTAGTTTACATAGGCCCAATGC--AAGCCCACTCTTTTATTACAAATATATATGCATTAGTG
1514170 CTAGTCCATTTAAATTAGGATTTATGGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAGGGTTTA
64 CTAGTCCATTTAAATTAGGATTTATGGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAGGGTTTA
* *
1514235 TGATTTAGGGTTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCTCAGTG
129 TGATTTA--G---AGGGTTTCTATAAACTATATATTTTACTACTTTATATAGTGTA--CTCAGTG
1514300 TTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATAGTTTATATATACTAT
187 TTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATAGTTTATATATACTAT
*
1514365 ACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTA
252 ACATGGTTTATACATACATAATATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTA
*
1514430 AATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACAATGCATATTATATGGT
317 AATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACAATCCATATTATATGGT
*
1514495 TCATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAG
382 TCATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTAGTATTTTAGTTGCATGTTAG
* * *
1514560 GTTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACTCAAAAAT
447 GTTAATTCACATTAATAGCACATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAAT
1514625 AAGTCCATTTGCAATAGTGCTAGTCCATTA
512 AAGTCCATTTGCAATAGTGCTAGTCCATTA
1514655 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
* *
1514720 AGTTCATTTAAATTAGGGTTTATGGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAGGGTTTATG
66 AGTCCATTTAAATTAGGATTTATGGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAGGGTTTATG
1514785 ATTTA-A-GGTTTCTATAAACTATATATTTTACTACTTTATATA-TGTA-T-AGTGTTTCTATAA
131 ATTTAGAGGGTTTCTATAAACTATATATTTTACTACTTTATATAGTGTACTCAGTGTTTCTATAA
1514845 ACTATATAAGTAATTTACTTTATATAGTTTATATATATATATATATATATAGTTTATATATACTA
196 ACTATATAAGTAATTTACTTTATATAG--------T-T-TATATATATATAGTTTATATATACTA
1514910 TACATGGTTTATACATACATAATATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGT
251 TACATGGTTTATACATACATAATATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGT
*
1514975 AAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCCATATTATATGG
316 AAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACAATCCATATTATATGG
* *
1515040 TTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTA
381 TTCATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTAGTATTTTAGTTGCATGTTA
*
1515105 GGTTAATTCACATTAATAGCACATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAT
446 GGTTAATTCACATTAATAGCACATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAA
1515170 TAAGTCCATTTGCAATAGTGCTAGTCCATTA
511 TAAGTCCATTTGCAATAGTGCTAGTCCATTA
* * * *
1515201 ACATTAATTTAGATAGGCCCAATGTAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGAT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
1515266 AGTCCATTTA
66 AGTCCATTTA
1515276 CATTTTAAAT
Statistics
Matches: 588, Mismatches: 22, Indels: 25
0.93 0.03 0.04
Matches are distributed among these distances:
536 40 0.07
537 1 0.00
540 3 0.01
541 35 0.06
542 1 0.00
544 1 0.00
545 1 0.00
546 377 0.64
548 108 0.18
549 16 0.03
550 5 0.01
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (541 bp):
ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
AGTCCATTTAAATTAGGATTTATGGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAGGGTTTATG
ATTTAGAGGGTTTCTATAAACTATATATTTTACTACTTTATATAGTGTACTCAGTGTTTCTATAA
ACTATATAAGTAATTTACTTTATATAGTTTATATATATATAGTTTATATATACTATACATGGTTT
ATACATACATAATATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATATA
AAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACAATCCATATTATATGGTTCATAAATA
GTAGTACATGTCATATTAATTTAAATTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCA
CATTAATAGCACATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATT
TGCAATAGTGCTAGTCCATTA
Found at i:1516683 original size:40 final size:40
Alignment explanation
Indices: 1516611--1516697 Score: 93
Period size: 40 Copynumber: 2.2 Consensus size: 40
1516601 TTTACAACAT
* * *
1516611 CGAATTTAAAATTCATAACACATAATTGAAATTCACGTTG
1 CGAATTTAAAATTCACAACACAGAATTAAAATTCACGTTG
* * * **
1516651 CGAATTTGAAATTCGCAACACAGGATTAAAATTTGCGTTG
1 CGAATTTAAAATTCACAACACAGAATTAAAATTCACGTTG
*
1516691 TGAATTT
1 CGAATTT
1516698 CAGAAATGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (40 bp):
CGAATTTAAAATTCACAACACAGAATTAAAATTCACGTTG
Found at i:1517610 original size:20 final size:19
Alignment explanation
Indices: 1517564--1517615 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
1517554 AATTCTAAAT
*
1517564 TTTATGTTTGAATTTAGAA
1 TTTATGTTTGAAATTAGAA
* * *
1517583 ATTGTGTTATGAAATTAGAG
1 TTTATGTT-TGAAATTAGAA
1517603 TTTATGTTGTGAA
1 TTTATGTT-TGAA
1517616 TTTATTGGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (19 bp):
TTTATGTTTGAAATTAGAA
Found at i:1518136 original size:3 final size:3
Alignment explanation
Indices: 1518128--1518153 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1518118 ACATGGACTA
1518128 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1518154 GTATGACGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1527520 original size:51 final size:51
Alignment explanation
Indices: 1527444--1527546 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
1527434 AAAGTGTTAA
*
1527444 TATGATTATTTTCTCATCTAAAGTGAATGTTAAAGTGCTCCGTAGAAGACG
1 TATGATTATTTTCTCATCTAAAGTGAATGTTAAAGTGCTCCATAGAAGACG
1527495 TATGATTATTTTCTCATCTAAAGTGAATGTTAAAGTGCTCCATAGAAGACG
1 TATGATTATTTTCTCATCTAAAGTGAATGTTAAAGTGCTCCATAGAAGACG
1527546 T
1 T
1527547 CCAAAAGATC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (51 bp):
TATGATTATTTTCTCATCTAAAGTGAATGTTAAAGTGCTCCATAGAAGACG
Found at i:1531909 original size:21 final size:20
Alignment explanation
Indices: 1531885--1531930 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
1531875 AATGTGCTAG
1531885 TATATGCACTGAAGCTCATAC
1 TATAT-CACTGAAGCTCATAC
1531906 TATAATCACTGAAGCTCATAC
1 TAT-ATCACTGAAGCTCATAC
1531927 TATA
1 TATA
1531931 ATCCCAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 1 0.04
21 21 0.88
22 2 0.08
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (20 bp):
TATATCACTGAAGCTCATAC
Found at i:1531931 original size:21 final size:21
Alignment explanation
Indices: 1531891--1531933 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1531881 CTAGTATATG
1531891 CACTGAAGCTCATACTATAAT
1 CACTGAAGCTCATACTATAAT
1531912 CACTGAAGCTCATACTATAAT
1 CACTGAAGCTCATACTATAAT
1531933 C
1 C
1531934 CCAACAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.28
Consensus pattern (21 bp):
CACTGAAGCTCATACTATAAT
Found at i:1532151 original size:12 final size:12
Alignment explanation
Indices: 1532134--1532168 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
1532124 TCAATAAACT
1532134 ACAACTTGCAGG
1 ACAACTTGCAGG
1532146 ACAACTTGCAGG
1 ACAACTTGCAGG
1532158 ACAACTTGCAG
1 ACAACTTGCAG
1532169 TATCGTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (12 bp):
ACAACTTGCAGG
Found at i:1534402 original size:19 final size:20
Alignment explanation
Indices: 1534368--1534406 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1534358 ATAACTAACT
*
1534368 CTTAACAGTCCTTAACTGCA
1 CTTAACACTCCTTAACTGCA
1534388 CTTAACACT-CTTAACTGCA
1 CTTAACACTCCTTAACTGCA
1534407 TAACAACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (20 bp):
CTTAACACTCCTTAACTGCA
Found at i:1538978 original size:19 final size:20
Alignment explanation
Indices: 1538941--1538979 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1538931 ATAACTAACT
* *
1538941 CTTAACAGTCCTTAGCTGCA
1 CTTAACACTCCTTAACTGCA
1538961 CTTAACACT-CTTAACTGCA
1 CTTAACACTCCTTAACTGCA
1538980 TAACAACCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (20 bp):
CTTAACACTCCTTAACTGCA
Found at i:1541514 original size:29 final size:29
Alignment explanation
Indices: 1541480--1541538 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1541470 CCTAAATTAA
*
1541480 TTTGATGTCATTACTTACATCAATTTAGT
1 TTTGATATCATTACTTACATCAATTTAGT
*
1541509 TTTGATATCATTGCTTACATCAATTTAGT
1 TTTGATATCATTACTTACATCAATTTAGT
1541538 T
1 T
1541539 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (29 bp):
TTTGATATCATTACTTACATCAATTTAGT
Found at i:1543940 original size:21 final size:21
Alignment explanation
Indices: 1543914--1543956 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
1543904 CTACAGTGCA
1543914 TGCATCGATGCAT-TGCTACAG
1 TGCATCGATGC-TCTGCTACAG
1543935 TGCATCGATGCTCTGCTACAG
1 TGCATCGATGCTCTGCTACAG
1543956 T
1 T
1543957 ACTGCTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (21 bp):
TGCATCGATGCTCTGCTACAG
Found at i:1544709 original size:31 final size:30
Alignment explanation
Indices: 1544671--1544826 Score: 188
Period size: 31 Copynumber: 5.0 Consensus size: 30
1544661 CCTGAAAGAC
* *
1544671 CAGTCCATAGATTCCGAAGAACCTAGGTAAT
1 CAGTCCATAG-TTCCGAAGAACATAGGTAAA
*
1544702 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GTTCCGAAGAACATAGGTAAA
* *
1544733 CAATCCATATTTCCCGAAGAACATAGGTAAA
1 CAGTCCATAGTT-CCGAAGAACATAGGTAAA
1544764 CAGTCCATA-TGTCTCGAAGAACATAGGTAAA
1 CAGTCCATAGT-TC-CGAAGAACATAGGTAAA
* *
1544795 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GTTCCGAAGAACATAGGTAAA
1544826 C
1 C
1544827 CCTTGACCCT
Statistics
Matches: 110, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
30 3 0.03
31 104 0.95
32 2 0.02
33 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (30 bp):
CAGTCCATAGTTCCGAAGAACATAGGTAAA
Found at i:1544771 original size:62 final size:62
Alignment explanation
Indices: 1544684--1544826 Score: 250
Period size: 62 Copynumber: 2.3 Consensus size: 62
1544674 TCCATAGATT
* * *
1544684 CCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATTTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATGTC
*
1544746 CCGAAGAACATAGGTAAACAGTCCATATGTCTCGAAGAACATAGGTAAACAATCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATGTC
1544808 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
1544827 CCTTGACCCT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 77 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.20
Consensus pattern (62 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATGTC
Found at i:1547666 original size:16 final size:18
Alignment explanation
Indices: 1547631--1547667 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1547621 TTTACATTCC
1547631 TTTCATATCATTTATACT
1 TTTCATATCATTTATACT
*
1547649 TTTCAT-TC-TTTATCCT
1 TTTCATATCATTTATACT
1547665 TTT
1 TTT
1547668 ACTTCTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTCATATCATTTATACT
Found at i:1549560 original size:21 final size:21
Alignment explanation
Indices: 1549536--1549578 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1549526 AGCCAATTTA
*
1549536 TGCATCGATGCATTGCTACAG
1 TGCATCGATGCACTGCTACAG
1549557 TGCATCGATGCACTGCTACAG
1 TGCATCGATGCACTGCTACAG
1549578 T
1 T
1549579 ACTGCTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCACTGCTACAG
Found at i:1550331 original size:31 final size:31
Alignment explanation
Indices: 1550307--1550479 Score: 301
Period size: 31 Copynumber: 5.6 Consensus size: 31
1550297 CCATAGATTT
* *
1550307 CGAAGAACCTAGGTAATCAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
1550338 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
* *
1550369 CAAAGAACATAGATAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
*
1550400 CGAAGAACATAGGTAAACAGTCCGTATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
1550431 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
1550462 CGAAGAACATAGGTAAAC
1 CGAAGAACATAGGTAAAC
1550480 CCTCGACCCT
Statistics
Matches: 134, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 134 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAGTCCATATGTCC
Found at i:1554488 original size:29 final size:29
Alignment explanation
Indices: 1554454--1554512 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1554444 CCTAAATTAA
*
1554454 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTAATTGCTTACATCAATTTAGT
*
1554483 TTTGATGTAATTGTTTACATCAATTTAGT
1 TTTGATGTAATTGCTTACATCAATTTAGT
1554512 T
1 T
1554513 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.10, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTAATTGCTTACATCAATTTAGT
Found at i:1554523 original size:29 final size:29
Alignment explanation
Indices: 1554463--1554520 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1554453 ATTTGATGTC
* *
1554463 ATTGCTTACATCAATTTAGTTTTGATGTA
1 ATTGCTTACATCAATTTAGTTTAGATGAA
* *
1554492 ATTGTTTACATCAATTTAG-TTAGGTGAA
1 ATTGCTTACATCAATTTAGTTTAGATGAA
1554520 A
1 A
1554521 ATTAAGTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.45
Consensus pattern (29 bp):
ATTGCTTACATCAATTTAGTTTAGATGAA
Found at i:1556122 original size:59 final size:60
Alignment explanation
Indices: 1555991--1556122 Score: 139
Period size: 59 Copynumber: 2.2 Consensus size: 60
1555981 ATATGGTGAC
* * * *
1555991 CATTTTG-AACCTTTAATAGTCGAGGGACTCAACAAATCAACTTCCTATAGTCGGGGGAT
1 CATTTTGTAACTTTTAATAATCGAGGGACTCAACAAATCAACTTCCTATAGCCAGGGGAT
* * *
1556050 TATTTTGTAACTTTTAATAATCG-GGGACTTAACAAAGT-AA-TATCCTATAGCCAGTGGAT
1 CATTTTGTAACTTTTAATAATCGAGGGACTCAACAAA-TCAACT-TCCTATAGCCAGGGGAT
1556109 CATTTGTGT-ACTTT
1 CATTT-TGTAACTTT
1556123 ACCCTAAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
58 1 0.02
59 43 0.70
60 17 0.28
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAATCGAGGGACTCAACAAATCAACTTCCTATAGCCAGGGGAT
Found at i:1566458 original size:28 final size:28
Alignment explanation
Indices: 1566414--1566472 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
1566404 CATTTCATCT
*
1566414 TGATTAATTAATGTATATGTAAAAGAAC
1 TGATTAATTAATATATATGTAAAAGAAC
*
1566442 TGATTAATTAATATATATGTAGAAGAAC
1 TGATTAATTAATATATATGTAAAAGAAC
1566470 TGA
1 TGA
1566473 AGGGATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (28 bp):
TGATTAATTAATATATATGTAAAAGAAC
Found at i:1572474 original size:21 final size:20
Alignment explanation
Indices: 1572448--1572545 Score: 74
Period size: 21 Copynumber: 4.8 Consensus size: 20
1572438 ATCAGTTTCC
1572448 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
1572469 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
**
1572488 ACAAATTCGCATTGCGATTTT-
1 A-AAA-TCGCAACGCGATTTTG
* *
1572509 ACAGAATCGCAACGCGAATATG
1 A-A-AATCGCAACGCGATTTTG
1572531 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1572546 ACACATAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 17 0.27
21 42 0.67
22 3 0.05
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:1572607 original size:20 final size:20
Alignment explanation
Indices: 1572513--1572741 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
1572503 GATTTTACAG
* ** *
1572513 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1572533 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1572553 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1572573 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1572593 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1572613 AATCGCAATGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1572633 TATCGTAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1572653 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1572673 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1572693 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1572713 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1572733 AATCACAAC
1 AATCGCAAC
1572742 AATGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1573473 original size:24 final size:24
Alignment explanation
Indices: 1573434--1573480 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1573424 AAATTTGGTC
1573434 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1573458 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1573481 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1573672 original size:12 final size:12
Alignment explanation
Indices: 1573655--1573679 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1573645 ATATAATCCT
1573655 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1573667 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1573679 G
1 G
1573680 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1576043 original size:53 final size:52
Alignment explanation
Indices: 1575975--1576197 Score: 367
Period size: 53 Copynumber: 4.2 Consensus size: 52
1575965 GCAACGAGAG
* *
1575975 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
*
1576028 AATCGCAATGTGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
1576081 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
1576133 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
1576185 AATCGCATTGCGA
1 AATCGCAATGCGA
1576198 TTCTCTCGTT
Statistics
Matches: 163, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
52 71 0.44
53 91 0.56
54 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:1576044 original size:19 final size:19
Alignment explanation
Indices: 1575975--1576197 Score: 225
Period size: 19 Copynumber: 12.7 Consensus size: 19
1575965 GCAACGAGAG
1575975 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1575994 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1576008 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1576028 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1576047 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1576061 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1576081 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1576100 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1576114 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1576133 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1576152 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1576166 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1576185 AATCGCATTGCGA
1 AATCGCAATGCGA
1576198 TTCTCTCGTT
Statistics
Matches: 170, Mismatches: 12, Indels: 44
0.75 0.05 0.19
Matches are distributed among these distances:
14 42 0.25
15 3 0.02
16 6 0.04
17 7 0.04
18 2 0.01
19 82 0.48
20 28 0.16
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1576118 original size:86 final size:84
Alignment explanation
Indices: 1575961--1576140 Score: 233
Period size: 86 Copynumber: 2.1 Consensus size: 84
1575951 CGGAAATTAC
1575961 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAA-GCGG-AATG
*
1576026 AAAATCGCAATGTGAAATGAA
64 AAAATCGCAATGCGAAATGAA
*
1576047 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAAGCGG
*
1576110 -A-GAGAATCGCAATGCGAAATGAA
60 AATGAAAATCGCAATGCGAAATGAA
1576133 AATCGCAA
1 AATCGCAA
1576141 TGCGAAATGA
Statistics
Matches: 85, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
86 53 0.62
87 16 0.19
89 2 0.02
90 1 0.01
92 13 0.15
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (84 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAAGCGGAATGAA
AATCGCAATGCGAAATGAA
Found at i:1576137 original size:33 final size:33
Alignment explanation
Indices: 1575961--1576140 Score: 161
Period size: 33 Copynumber: 5.2 Consensus size: 33
1575951 CGGAAATTAC
*
1575961 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
*
1575994 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
* * * * *
1576028 AATCGCAATGTG-AAAT-GAAAAT-CGCAACGAGA
1 AATCGCAACGAGAAAATCG-CAATGCGAAATGA-A
1576060 GAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAA--C-G--A-GAAAATCGCAATGCGAAATGAA
*
1576100 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
1576133 AATCGCAA
1 AATCGCAA
1576141 TGCGAAATGA
Statistics
Matches: 118, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
31 5 0.04
32 4 0.03
33 65 0.55
34 17 0.14
36 2 0.02
37 1 0.01
39 9 0.08
40 8 0.07
41 7 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:1576170 original size:33 final size:33
Alignment explanation
Indices: 1576028--1576191 Score: 154
Period size: 33 Copynumber: 4.8 Consensus size: 33
1576018 CGGAAATGAA
*
1576028 AATCGCAATGTGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
1576061 AATCGCAATGCGGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
* * * *
1576094 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
1576133 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
1576166 AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
1576192 TTGCGATTCT
Statistics
Matches: 106, Mismatches: 13, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
31 5 0.05
32 3 0.03
33 51 0.48
34 20 0.19
35 1 0.01
36 2 0.02
38 10 0.09
39 7 0.07
40 7 0.07
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:1576300 original size:52 final size:53
Alignment explanation
Indices: 1576187--1576303 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1576177 GAAATTAAAA
1576187 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1576240 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1576292 TCGCATTGCGAT
1 TCGCATTGCGAT
1576304 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1576311 original size:19 final size:19
Alignment explanation
Indices: 1576206--1576303 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1576196 GATTCTCTCG
1576206 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1576226 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1576245 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1576259 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1576278 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1576297 TTGCGAT
1 TTGCGAT
1576304 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1576429 original size:14 final size:14
Alignment explanation
Indices: 1576410--1576446 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1576400 CATCAATTAC
1576410 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1576424 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1576438 ACAAATCAA
1 ACAAATCAA
1576447 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1578483 original size:14 final size:14
Alignment explanation
Indices: 1578464--1578520 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1578454 GCGAAATGAA
1578464 AATCGCAACGACAG
1 AATCGCAACGACAG
*
1578478 AATCGCAATGCGAAATG
1 AATCGCAA--CGACA-G
1578495 AAAATCGCAACGACAG
1 --AATCGCAACGACAG
*
1578511 AATCGTAACG
1 AATCGCAACG
1578521 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 5 0.14
19 8 0.23
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (14 bp):
AATCGCAACGACAG
Found at i:1578491 original size:33 final size:33
Alignment explanation
Indices: 1578445--1578534 Score: 162
Period size: 33 Copynumber: 2.7 Consensus size: 33
1578435 GCGAAACCAA
1578445 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
*
1578478 AATCGCAATGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
*
1578511 AATCGTAACGCGAAATGAAAATCG
1 AATCGCAACGCGAAATGAAAATCG
1578535 TAATGCGATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:1578542 original size:19 final size:19
Alignment explanation
Indices: 1578370--1578534 Score: 143
Period size: 19 Copynumber: 9.2 Consensus size: 19
1578360 TAGTTTACTT
* *
1578370 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
1578390 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
1578409 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
1578428 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1578447 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1578466 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1578480 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1578499 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1578513 TCGTAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1578532 TCG
1 TCG
1578535 TAATGCGATT
Statistics
Matches: 120, Mismatches: 15, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 15 0.12
16 10 0.08
17 10 0.08
19 73 0.61
20 12 0.10
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Done.