Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001838.1 Hibiscus syriacus cultivar Beakdansim tig00003721_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: 3924084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 18
Found at i:1432738 original size:59 final size:58
Alignment explanation
Indices: 1432631--1432781 Score: 178
Period size: 59 Copynumber: 2.6 Consensus size: 58
1432621 AATTAAAGGG
* * * *
1432631 AAAATAGCAATAATAGAAAGTTAAAGTG-CTAAAATAGAAAAAATAGACATTTAAAAGACT
1 AAAATAGAAAAAATAGAAACTT-AAG-GACT-AAATAGAAAAAACAGACATTTAAAAGACT
* * * *
1432691 AAAATAGTAAAAATATAAACTTAAGAGACTAAATAGAAAATACAGACATTTAAAGGACT
1 AAAATAGAAAAAATAGAAACTTAAG-GACTAAATAGAAAAAACAGACATTTAAAAGACT
*
1432750 AAAATAGAAAAAATAGAAGCTTAAGGACTAAA
1 AAAATAGAAAAAATAGAAACTTAAGGACTAAA
1432782 ATGGTATTAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
58 7 0.09
59 52 0.66
60 20 0.25
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.21
Consensus pattern (58 bp):
AAAATAGAAAAAATAGAAACTTAAGGACTAAATAGAAAAAACAGACATTTAAAAGACT
Found at i:1434165 original size:3 final size:3
Alignment explanation
Indices: 1434157--1434206 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
1434147 AAACATGATG
1434157 TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1434202 TAA TA
1 TAA TA
1434207 TTTTTATAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1434364 original size:38 final size:40
Alignment explanation
Indices: 1434290--1434369 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 40
1434280 TTTGGCAAGG
1434290 CTTTTGAAAAGTGACTTTTAAAAATGCAGTAGAAAA-TAA
1 CTTTTGAAAAGTGACTTTTAAAAATGCAGTAGAAAATTAA
* * **
1434329 CTTTT-AAAAGTGA-TATTTAGAAGTGCAGTTTAAAATTAA
1 CTTTTGAAAAGTGACT-TTTAAAAATGCAGTAGAAAATTAA
1434368 CT
1 CT
1434370 ATTTTAGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
37 1 0.03
38 24 0.69
39 10 0.29
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (40 bp):
CTTTTGAAAAGTGACTTTTAAAAATGCAGTAGAAAATTAA
Found at i:1436498 original size:54 final size:54
Alignment explanation
Indices: 1436084--1436480 Score: 578
Period size: 54 Copynumber: 7.4 Consensus size: 54
1436074 CTATGTGTAC
** * *
1436084 TATAGGCACTAAGTGTGCAAGACACGGAATTCATCATATGTTGATTAACAACCA
1 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCG
* ** *
1436138 TATAGGCACTAAGTGGGCAACCCACATAATTCATCATATGTTGATGAACAACCA
1 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCG
* * * *
1436192 TGTAGGCACTAATTGTGCAACCCACGGAATTCATTACATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCG
*
1436246 TATAGTCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCG
* *
1436300 TATAGTCACTAAGAGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCG
* * **
1436354 TATAGGCACTAAGTTTGTAACCCACGGAATTCATCATATGTTGATGAATGACCG
1 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCG
* * *
1436408 TATAGGCACTAAGTGTGTAACCCACGGAATTCATAATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCG
* *
1436462 TATCGGCACTACGTGTGCA
1 TATAGGCACTAAGTGTGCA
1436481 CACCAGAGAA
Statistics
Matches: 311, Mismatches: 32, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 311 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCG
Found at i:1439163 original size:100 final size:100
Alignment explanation
Indices: 1439029--1439233 Score: 392
Period size: 100 Copynumber: 2.0 Consensus size: 100
1439019 ATAGATGATA
* *
1439029 TTTTGGTGTATTTCAAGGAAATAAAGTTTTAAAATGCTAAAGAAGATTTTAATAGAGGCACCAGT
1 TTTTTGTGTATTTCAAGAAAATAAAGTTTTAAAATGCTAAAGAAGATTTTAATAGAGGCACCAGT
1439094 GTTTATACAACTTGAGTGGGGTAAAGATTATGTGG
66 GTTTATACAACTTGAGTGGGGTAAAGATTATGTGG
1439129 TTTTTGTGTATTTCAAGAAAATAAAGTTTTAAAATGCTAAAGAAGATTTTAATAGAGGCACCAGT
1 TTTTTGTGTATTTCAAGAAAATAAAGTTTTAAAATGCTAAAGAAGATTTTAATAGAGGCACCAGT
1439194 GTTTATACAACTTGAGTGGGGTAAAGATTATGTGG
66 GTTTATACAACTTGAGTGGGGTAAAGATTATGTGG
1439229 TTTTT
1 TTTTT
1439234 AGTGATGCAT
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 103 1.00
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (100 bp):
TTTTTGTGTATTTCAAGAAAATAAAGTTTTAAAATGCTAAAGAAGATTTTAATAGAGGCACCAGT
GTTTATACAACTTGAGTGGGGTAAAGATTATGTGG
Found at i:1442063 original size:54 final size:54
Alignment explanation
Indices: 1441999--1442124 Score: 198
Period size: 54 Copynumber: 2.3 Consensus size: 54
1441989 GTGCTTGATG
*
1441999 TTGATGAACAACCGTATAGGCACTAAGTGTGCAAGCAACAAAATTCATCACATA
1 TTGATGAACAACCGTATAGGCACTAAGTGTGCAACCAACAAAATTCATCACATA
* ** * *
1442053 TTGATGAACAACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
1 TTGATGAACAACCGTATAGGCACTAAGTGTGCAACCAACAAAATTCATCACATA
1442107 TTGATGAACAACCGTATA
1 TTGATGAACAACCGTATA
1442125 TGCAACCCCC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (54 bp):
TTGATGAACAACCGTATAGGCACTAAGTGTGCAACCAACAAAATTCATCACATA
Found at i:1442143 original size:43 final size:43
Alignment explanation
Indices: 1442082--1442167 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
1442072 GCACTAAGTG
1442082 TGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTATA
1 TGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTATA
* **
1442125 TGCAACCCCCGGAATTCATCATATGTTGATGAATGACCGTATA
1 TGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTATA
1442168 GGCACTAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (43 bp):
TGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTATA
Found at i:1442194 original size:97 final size:97
Alignment explanation
Indices: 1442040--1442221 Score: 301
Period size: 97 Copynumber: 1.9 Consensus size: 97
1442030 CAAGCAACAA
*
1442040 AATTCATCACATATTGATGAACAACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATA
1 AATTCATCACATATTGATGAACAACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATAATA
1442105 TGTTGATGAACAACCGTATATGCAACCCCCGG
66 TGTTGATGAACAACCGTATATGCAACCCCCGG
* * **
1442137 AATTCATCATATGTTGATGAATGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATAATA
1 AATTCATCACATATTGATGAACAACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATAATA
* *
1442202 TGTTGATGAACGACTGTATA
66 TGTTGATGAACAACCGTATA
1442222 GAAACTACGT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 78 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (97 bp):
AATTCATCACATATTGATGAACAACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATAATA
TGTTGATGAACAACCGTATATGCAACCCCCGG
Found at i:1442207 original size:54 final size:54
Alignment explanation
Indices: 1442125--1442236 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 54
1442115 CAACCGTATA
* * * **
1442125 TGCAACCCCCGGAATTCATCATATGTTGATGAATGACCGTATAGGCACTAAGTG
1 TGCAACCCACGGAATTCATAATATGTTGATGAACGACCGTATAGAAACTAAGTG
* *
1442179 TGCAACCCACGGAATTCATAATATGTTGATGAACGACTGTATAGAAACTACGTG
1 TGCAACCCACGGAATTCATAATATGTTGATGAACGACCGTATAGAAACTAAGTG
1442233 TGCA
1 TGCA
1442237 CACCAAAGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (54 bp):
TGCAACCCACGGAATTCATAATATGTTGATGAACGACCGTATAGAAACTAAGTG
Found at i:1443770 original size:13 final size:13
Alignment explanation
Indices: 1443752--1443785 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
1443742 TACTTCACCG
1443752 GGCGCCGTAGACT
1 GGCGCCGTAGACT
1443765 GGCGCCGTAGACT
1 GGCGCCGTAGACT
1443778 GGCGCCGT
1 GGCGCCGT
1443786 CTTTCGTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.12, C:0.32, G:0.41, T:0.15
Consensus pattern (13 bp):
GGCGCCGTAGACT
Found at i:1446433 original size:4 final size:4
Alignment explanation
Indices: 1446424--1446502 Score: 142
Period size: 4 Copynumber: 20.0 Consensus size: 4
1446414 GATTACATGA
1446424 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
1446471 TTTC TTTC TTTC TTTC TTGC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1446503 AGTTGGGTTC
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
3 3 0.04
4 69 0.96
ACGTcount: A:0.00, C:0.25, G:0.01, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:1475969 original size:2 final size:2
Alignment explanation
Indices: 1475962--1475988 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1475952 CTTCAAGTCC
1475962 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1475989 GATAATGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1476184 original size:12 final size:12
Alignment explanation
Indices: 1476167--1476196 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1476157 TTTCTAGATG
*
1476167 GAGAGAGAGACA
1 GAGAGAGAGAAA
1476179 GAGAGAGAGAAA
1 GAGAGAGAGAAA
1476191 GAGAGA
1 GAGAGA
1476197 TGTCTCTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.43, T:0.00
Consensus pattern (12 bp):
GAGAGAGAGAAA
Found at i:1480390 original size:21 final size:21
Alignment explanation
Indices: 1480364--1480403 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1480354 AGTACAGGGA
1480364 GTATCGATAATCCTTTTATAG
1 GTATCGATAATCCTTTTATAG
* *
1480385 GTATCGATACTTCTTTTAT
1 GTATCGATAATCCTTTTAT
1480404 TATTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (21 bp):
GTATCGATAATCCTTTTATAG
Found at i:1483789 original size:20 final size:20
Alignment explanation
Indices: 1483764--1483803 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1483754 GGTTGTGGTC
1483764 ATTTCTAGCCGTTGGGGATG
1 ATTTCTAGCCGTTGGGGATG
*
1483784 ATTTCTAGCCGTTTGGGATG
1 ATTTCTAGCCGTTGGGGATG
1483804 TTTTATTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.33, T:0.38
Consensus pattern (20 bp):
ATTTCTAGCCGTTGGGGATG
Found at i:1484551 original size:32 final size:32
Alignment explanation
Indices: 1484515--1484589 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
1484505 ACTGATACGG
* * *
1484515 ATTATCTAAATGCGACACTAACACTCTTGTGC
1 ATTATCTAAATGCAACAATAACACTATTGTGC
* *
1484547 ATTATCTAAATGCAACAATGACTCTATTGTGC
1 ATTATCTAAATGCAACAATAACACTATTGTGC
1484579 ATTATCTAAAT
1 ATTATCTAAAT
1484590 AAAACACTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (32 bp):
ATTATCTAAATGCAACAATAACACTATTGTGC
Found at i:1489118 original size:17 final size:17
Alignment explanation
Indices: 1489077--1489148 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
1489067 ATTCATGCAT
1489077 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
* *
1489094 GTTAGTTCACTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
1489112 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
*
1489129 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
1489146 CTA
1 CTA
1489149 ACTCTTAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
17 33 0.73
18 12 0.27
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:1490659 original size:25 final size:24
Alignment explanation
Indices: 1490623--1490669 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
1490613 CCATGTTAGT
* * *
1490623 AAAAAATTAAAATAAATCAAAATC
1 AAAAAATAAAAAAAAAACAAAATC
1490647 AAAAAATCAAAAAAAAAACAAAA
1 AAAAAAT-AAAAAAAAAACAAAA
1490670 GAAAGAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.13
Consensus pattern (24 bp):
AAAAAATAAAAAAAAAACAAAATC
Found at i:1491669 original size:28 final size:28
Alignment explanation
Indices: 1491629--1491683 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1491619 CCGAGGAAGA
1491629 ATCCAACTTCAAAGAGGAAAGTAACATT
1 ATCCAACTTCAAAGAGGAAAGTAACATT
1491657 ATCCAACTTCAAAGAGGAAAGTAACAT
1 ATCCAACTTCAAAGAGGAAAGTAACAT
1491684 ATAATATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (28 bp):
ATCCAACTTCAAAGAGGAAAGTAACATT
Found at i:1493160 original size:17 final size:17
Alignment explanation
Indices: 1493122--1493175 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
1493112 ATTCATGCAT
*
1493122 CTAGTTCATTGAA-TAAG
1 CTAGTTCATT-AATTAAA
*
1493139 TTAGTTCATTAATTAAA
1 CTAGTTCATTAATTAAA
*
1493156 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
1493173 CTA
1 CTA
1493176 ACTCTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 2 0.06
17 30 0.94
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:1495383 original size:17 final size:17
Alignment explanation
Indices: 1495361--1495413 Score: 106
Period size: 17 Copynumber: 3.1 Consensus size: 17
1495351 AAAGAAGAAA
1495361 CATCGATGCAATTGGTG
1 CATCGATGCAATTGGTG
1495378 CATCGATGCAATTGGTG
1 CATCGATGCAATTGGTG
1495395 CATCGATGCAATTGGTG
1 CATCGATGCAATTGGTG
1495412 CA
1 CA
1495414 CATGTTAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (17 bp):
CATCGATGCAATTGGTG
Found at i:1495447 original size:20 final size:20
Alignment explanation
Indices: 1495422--1495459 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1495412 CACATGTTAA
1495422 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
1495442 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
1495460 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:1496302 original size:18 final size:18
Alignment explanation
Indices: 1496279--1496412 Score: 214
Period size: 18 Copynumber: 7.4 Consensus size: 18
1496269 GAGGGTCTAC
*
1496279 GTGGTCCTTTGGGACATA
1 GTGGTCCTTCGGGACATA
1496297 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
1496315 ATGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
1496333 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
1496351 GTGGTTCTTTGGGACATA
1 GTGGTCCTTCGGGACATA
* *
1496369 ATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
1496387 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
1496405 GTGGTCCT
1 GTGGTCCT
1496413 AGGAGATAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 105 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:1498714 original size:29 final size:28
Alignment explanation
Indices: 1498654--1498712 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
1498644 AAAAGGTGGG
1498654 AAAGGAAGAAGAATAAATGAAGAGAAAT
1 AAAGGAAGAAGAATAAATGAAGAGAAAT
*
1498682 AAAGGAATGAAG-ATGAAATG-AGAGAGAT
1 AAAGGAA-GAAGAAT-AAATGAAGAGAAAT
1498710 AAA
1 AAA
1498713 AGCTCTCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (28 bp):
AAAGGAAGAAGAATAAATGAAGAGAAAT
Found at i:1501166 original size:22 final size:22
Alignment explanation
Indices: 1501138--1501184 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1501128 ATTAATTCAC
1501138 ATGGCATGATCATAAAGCATAA
1 ATGGCATGATCATAAAGCATAA
1501160 ATGGCATGATCATAAAGCATAA
1 ATGGCATGATCATAAAGCATAA
1501182 ATG
1 ATG
1501185 ATCTAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (22 bp):
ATGGCATGATCATAAAGCATAA
Found at i:1510270 original size:297 final size:297
Alignment explanation
Indices: 1509736--1510333 Score: 1151
Period size: 297 Copynumber: 2.0 Consensus size: 297
1509726 TCGGAGGTCT
*
1509736 TCTACGGAAGCTGCTCTCAACCTGGTGTTGGGGGCAGCCTACTATCTTACCTCCCCCTTATCCTA
1 TCTACGGAAGCTGCTCTCAACCTGGTGTTGGGGGCAGCCTACTATCTTACCTCCCCCTTACCCTA
1509801 TTACATATGGGAACAAAGGACACCCATTTTAATTGCTTCAATTAACTTGTTGGTCTTTGATCTTG
66 TTACATATGGGAACAAAGGACACCCATTTTAATTGCTTCAATTAACTTGTTGGTCTTTGATCTTG
*
1509866 CGCATAAGTGAAACAAGGACTAAAGTTGATCAAGTGTTTAAGCTCTAATCTCTATGTATGGAGTT
131 CACATAAGTGAAACAAGGACTAAAGTTGATCAAGTGTTTAAGCTCTAATCTCTATGTATGGAGTT
1509931 TAAACCCTCTAAACATAGCAATTTTTTTAAGTAAAACAATATTTTTATATGATCTCAATCATGTG
196 TAAACCCTCTAAACATAGCAATTTTTTTAAGTAAAACAATATTTTTATATGATCTCAATCATGTG
1509996 AGTTGTCAAGACGCATCGTATTCAATTAAGGTGCTTA
261 AGTTGTCAAGACGCATCGTATTCAATTAAGGTGCTTA
* *
1510033 TCTACGGAAGCTGCTCTCAATCTGGTGTTGGGGGCAGCCTACTATCTTACCTCCTCCTTACCCTA
1 TCTACGGAAGCTGCTCTCAACCTGGTGTTGGGGGCAGCCTACTATCTTACCTCCCCCTTACCCTA
*
1510098 TTACATATGGGAACAAGGGACACCCATTTTAATTGCTTCAATTAACTTGTTGGTCTTTGATCTTG
66 TTACATATGGGAACAAAGGACACCCATTTTAATTGCTTCAATTAACTTGTTGGTCTTTGATCTTG
1510163 CACATAAGTGAAACAAGGACTAAAGTTGATCAAGTGTTTAAGCTCTAATCTCTATGTATGGAGTT
131 CACATAAGTGAAACAAGGACTAAAGTTGATCAAGTGTTTAAGCTCTAATCTCTATGTATGGAGTT
1510228 TAAACCCTCTAAACATAGCAATTTTTTTAAGTAAAACAATATTTTTATATGATCTCAATCATGTG
196 TAAACCCTCTAAACATAGCAATTTTTTTAAGTAAAACAATATTTTTATATGATCTCAATCATGTG
1510293 AGTTGTCAAGACGCATCGTATTCAATTAAGGTGCTTA
261 AGTTGTCAAGACGCATCGTATTCAATTAAGGTGCTTA
1510330 TCTA
1 TCTA
1510334 GTTGGGAGTG
Statistics
Matches: 296, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
297 296 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (297 bp):
TCTACGGAAGCTGCTCTCAACCTGGTGTTGGGGGCAGCCTACTATCTTACCTCCCCCTTACCCTA
TTACATATGGGAACAAAGGACACCCATTTTAATTGCTTCAATTAACTTGTTGGTCTTTGATCTTG
CACATAAGTGAAACAAGGACTAAAGTTGATCAAGTGTTTAAGCTCTAATCTCTATGTATGGAGTT
TAAACCCTCTAAACATAGCAATTTTTTTAAGTAAAACAATATTTTTATATGATCTCAATCATGTG
AGTTGTCAAGACGCATCGTATTCAATTAAGGTGCTTA
Found at i:1522007 original size:29 final size:29
Alignment explanation
Indices: 1521975--1522032 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1521965 GTATAGTAAC
1521975 TGAAATAGGAGATAATAAAGTTTAGTGAG
1 TGAAATAGGAGATAATAAAGTTTAGTGAG
1522004 TGAAATAGGAGATAATAAAGTTTAGTGAG
1 TGAAATAGGAGATAATAAAGTTTAGTGAG
1522033 GAATGATGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (29 bp):
TGAAATAGGAGATAATAAAGTTTAGTGAG
Found at i:1522276 original size:3 final size:3
Alignment explanation
Indices: 1522268--1522330 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
1522258 TTTTCTTTTT
1522268 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1522316 CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC
1522331 AACAGACTCT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:1524889 original size:30 final size:30
Alignment explanation
Indices: 1524831--1524889 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1524821 ACAAGGTATA
* *
1524831 AAAAATAATAGTAATAATAAGTATTAAAAT
1 AAAAATAATAATAATAATAAGTAATAAAAT
*
1524861 AAAAATAATAATAATAGTAA-TGAATAAAA
1 AAAAATAATAATAATAATAAGT-AATAAAA
1524890 AAACAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (30 bp):
AAAAATAATAATAATAATAAGTAATAAAAT
Found at i:1526344 original size:106 final size:106
Alignment explanation
Indices: 1526140--1526355 Score: 265
Period size: 106 Copynumber: 2.0 Consensus size: 106
1526130 TCCAAGAAAG
* *
1526140 TTGTACTGCTCCGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATT
1 TTGTACTGCTCCGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGAAACTGGGAAATT
** * *
1526205 GTTTGTTGACAGTCAGTCGCCCCTTCATCGTGAAGTTGAGC
66 GTTTGTTGACAACCAGCCGCCCCTTCATCGTGAAGTTGAAC
* * * * *
1526246 TTGTACTG-TCTCGAGTCTAATATCCTTCG-CTTTGAAGTTGAAATTGACTCTGAAATTGGGAAG
1 TTGTACTGCTC-CGAGTCCAATATCCTCCGTC-GTGAAGTTGAAATTGACTCTGAAACTGGGAAA
* * * *
1526309 TTGTTTGTTGACAACCAGCCGTCTCTTCGTTGTGAAGTTGAAC
64 TTGTTTGTTGACAACCAGCCGCCCCTTCATCGTGAAGTTGAAC
1526352 TTGT
1 TTGT
1526356 GTTATCTTGA
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
105 3 0.03
106 90 0.97
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (106 bp):
TTGTACTGCTCCGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGAAACTGGGAAATT
GTTTGTTGACAACCAGCCGCCCCTTCATCGTGAAGTTGAAC
Found at i:1527015 original size:31 final size:31
Alignment explanation
Indices: 1526977--1527037 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
1526967 CCTTCGCTGC
*
1526977 GAAGTTGAAATTGGCTCTAGCTAAAACCTGT
1 GAAGTTGAAATTGGATCTAGCTAAAACCTGT
1527008 GAAGTTGAAATTGGATCTAGCTAAAACCTG
1 GAAGTTGAAATTGGATCTAGCTAAAACCTG
1527038 CAAAGTGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (31 bp):
GAAGTTGAAATTGGATCTAGCTAAAACCTGT
Found at i:1527167 original size:14 final size:14
Alignment explanation
Indices: 1527148--1527174 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1527138 CGATTGCATG
1527148 TCTGGAATCTTGAT
1 TCTGGAATCTTGAT
1527162 TCTGGAATCTTGA
1 TCTGGAATCTTGA
1527175 AGTTCTGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (14 bp):
TCTGGAATCTTGAT
Found at i:1527807 original size:8 final size:8
Alignment explanation
Indices: 1527788--1527820 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1527778 TTTTTTGTTC
1527788 TTTCTCTTT
1 TTTCT-TTT
1527797 TTTCTTTT
1 TTTCTTTT
1527805 TTTCTTTT
1 TTTCTTTT
1527813 TTT-TTTT
1 TTTCTTTT
1527820 T
1 T
1527821 AATTTTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 5 0.21
8 14 0.58
9 5 0.21
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTCTTTT
Found at i:1527809 original size:21 final size:21
Alignment explanation
Indices: 1527779--1527829 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1527769 CCCACCTTAT
*
1527779 TTTTTGTTCTTTCTCTTTTTTC
1 TTTTT-TTCTTTCTCTTTTTTA
* *
1527801 TTTTTTTCTTTTTTTTTTTTA
1 TTTTTTTCTTTCTCTTTTTTA
*
1527822 ATTTTTTC
1 TTTTTTTC
1527830 AATTTAGGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.82
Consensus pattern (21 bp):
TTTTTTTCTTTCTCTTTTTTA
Found at i:1527810 original size:15 final size:14
Alignment explanation
Indices: 1527778--1527820 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1527768 ACCCACCTTA
*
1527778 TTTTTTGTTCTTTCTC
1 TTTTTT-TT-TTTTTC
1527794 TTTTTTCTTTTTTTC
1 TTTTTT-TTTTTTTC
1527809 TTTTTTTTTTTT
1 TTTTTTTTTTTT
1527821 AATTTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 6 0.24
15 11 0.44
16 8 0.32
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTTTTTC
Found at i:1527874 original size:66 final size:67
Alignment explanation
Indices: 1527801--1527929 Score: 161
Period size: 67 Copynumber: 1.9 Consensus size: 67
1527791 CTCTTTTTTC
* * * *
1527801 TTTTTTTC-TTTTTTTTTTTTAATTTTTTCAATTTAGGGCGCCCTTTCAGGTTTTCAGCCTAAAC
1 TTTTTTTCATTTTTTCTTTTTAATTTTTTCAACTTAGGACGCCATTTCAGGTTTTCAGCCTAAAC
1527865 TT
66 TT
** ** * *
1527867 TTTTTTTCATTTTTTCTTTTTCCTTTTTTTGACTTAGGACGCCATTTCGGGTTTTCATCCTAA
1 TTTTTTTCATTTTTTCTTTTTAATTTTTTCAACTTAGGACGCCATTTCAGGTTTTCAGCCTAA
1527930 GTGAAGTATT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
66 8 0.15
67 44 0.85
ACGTcount: A:0.14, C:0.18, G:0.11, T:0.57
Consensus pattern (67 bp):
TTTTTTTCATTTTTTCTTTTTAATTTTTTCAACTTAGGACGCCATTTCAGGTTTTCAGCCTAAAC
TT
Found at i:1534311 original size:21 final size:23
Alignment explanation
Indices: 1534276--1534336 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
1534266 TTGGTGCAGA
*
1534276 GGGAATCGA-TCCCCCCATG-A-
1 GGGAACCGATTCCCCCCATGAAG
* **
1534296 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCATGAAG
1534319 GGGAACCGATTCCCCCCA
1 GGGAACCGATTCCCCCCA
1534337 CAGGGGAATC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 7 0.23
21 8 0.26
22 1 0.03
23 15 0.48
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.18
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCATGAAG
Found at i:1547032 original size:3 final size:3
Alignment explanation
Indices: 1547024--1547083 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
1547014 GGTATAAAAT
*
1547024 ATA ATA ATA ATA ATA ATA ATA AGTA TTA A-A ATA A-A A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
*
1547067 ATA ATA GTA ATGA ATA A
1 ATA ATA ATA AT-A ATA A
1547084 AAAACCAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 6 0.12
3 38 0.78
4 5 0.10
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1547085 original size:31 final size:32
Alignment explanation
Indices: 1547017--1547085 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
1547007 ATAAGAAGGT
*
1547017 ATAAAATATAATAATAATAATAATAATAAGTA
1 ATAAAATATAAAAATAATAATAATAATAAGTA
* *
1547049 TTAAAATA-AAAAATAATAATAATAGTAA-TGA
1 ATAAAATATAAAAATAATAATAATAATAAGT-A
1547080 ATAAAA
1 ATAAAA
1547086 AACCAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.03
31 24 0.75
32 7 0.22
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (32 bp):
ATAAAATATAAAAATAATAATAATAATAAGTA
Found at i:1547087 original size:28 final size:28
Alignment explanation
Indices: 1547032--1547087 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1547022 ATATAATAAT
*
1547032 AATAATAATAATAAGTATTAAAATAAAA
1 AATAATAATAATAAGTATGAAAATAAAA
1547060 AATAATAATAAT-AGTAATG--AATAAAA
1 AATAATAATAATAAGT-ATGAAAATAAAA
1547086 AA
1 AA
1547088 CCAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 9 0.35
27 3 0.12
28 14 0.54
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (28 bp):
AATAATAATAATAAGTATGAAAATAAAA
Found at i:1547094 original size:34 final size:34
Alignment explanation
Indices: 1547026--1547097 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
1547016 TATAAAATAT
* *
1547026 AATAATAATAATAATAATAAGTATTAAAATAAAA
1 AATAATAATAATAATAATAAGTATAAAAACAAAA
* *
1547060 AATAATAATAATAGTAATGAA-TA-AAAAACCAAA
1 AATAATAATAATAATAAT-AAGTATAAAAACAAAA
1547093 AATAA
1 AATAA
1547098 AAGAAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 12 0.36
34 19 0.58
35 2 0.06
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.25
Consensus pattern (34 bp):
AATAATAATAATAATAATAAGTATAAAAACAAAA
Found at i:1547137 original size:2 final size:2
Alignment explanation
Indices: 1547130--1547170 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1547120 AATCAAAGTA
1547130 AT AT AT 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 AT AT AT A
1547171 AAGTATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1547202 original size:21 final size:20
Alignment explanation
Indices: 1547178--1547225 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
1547168 ATAAAGTATA
1547178 AATGAAATAAAAAATAATAAT
1 AATGAAAT-AAAAATAATAAT
* *
1547199 AATGGAAATATAAGTAATAAT
1 AAT-GAAATAAAAATAATAAT
1547220 ATATGA
1 A-ATGA
1547226 TATTAGTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.27
Consensus pattern (20 bp):
AATGAAATAAAAATAATAAT
Found at i:1548774 original size:29 final size:29
Alignment explanation
Indices: 1548709--1548781 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 29
1548699 TTTAACACCC
*
1548709 CAATAATATAATT-A-AAAAATAAAATTT
1 CAATAATATAATTGATAAAAATAAAAATT
* * *
1548736 TAA-AGTTATAATTGATAAAATTAAAAATT
1 CAATA-ATATAATTGATAAAAATAAAAATT
*
1548765 CAATAATATAAATGATA
1 CAATAATATAATTGATA
1548782 TAACGTCTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
26 1 0.03
27 9 0.26
28 1 0.03
29 23 0.66
30 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (29 bp):
CAATAATATAATTGATAAAAATAAAAATT
Found at i:1550838 original size:229 final size:222
Alignment explanation
Indices: 1550433--1550876 Score: 744
Period size: 229 Copynumber: 2.0 Consensus size: 222
1550423 GTAAATTATC
* *
1550433 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAAT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATCTTTAAT
**
1550498 ATTGTTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATAATTTTTTGTGT
66 ATTGTTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATAAAATTTTGTGT
*
1550563 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACA
131 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAACA
1550628 TAAATTACATAACTTTCAAAAAAGTATA
196 TAAATTACATAACTTT-AAAAAAGTATA
*
1550656 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTA-T-TATCT--
*
1550721 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
61 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTAT-AAATATCAAAACAATCAAATAAAATT
* *
1550786 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
125 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
1550851 GAAACATAAATTACATAACTTTAAAA
190 GAAACATAAATTACATAACTTTAAAA
1550877 GCAGTTTTAA
Statistics
Matches: 206, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
223 36 0.17
224 16 0.08
225 1 0.00
226 4 0.02
228 41 0.20
229 108 0.52
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (222 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATCTTTAAT
ATTGTTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATAAAATTTTGTGT
AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAACA
TAAATTACATAACTTTAAAAAAGTATA
Found at i:1550965 original size:20 final size:19
Alignment explanation
Indices: 1550942--1550988 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
1550932 CGATATACCA
1550942 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1550962 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1550982 GGTAAAA
1 GGTAAAA
1550989 TTAAAAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1551131 original size:20 final size:20
Alignment explanation
Indices: 1551108--1551155 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1551098 CGATATAACA
*
1551108 GGTAAAAATATGAT-AAAACC
1 GGTAAAAA-ATGATAAAAAAC
*
1551128 GGTATCAAAATGATAAAAAAC
1 GGTA-AAAAATGATAAAAAAC
1551149 GGTAAAA
1 GGTAAAA
1551156 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.56, C:0.08, G:0.17, T:0.19
Consensus pattern (20 bp):
GGTAAAAAATGATAAAAAAC
Found at i:1553468 original size:33 final size:33
Alignment explanation
Indices: 1553426--1553491 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1553416 AAATAGATGG
*
1553426 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
1553459 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1553492 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1555308 original size:18 final size:18
Alignment explanation
Indices: 1555285--1555319 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1555275 TCGAGTTAAT
1555285 TTTGTATAAGATTTATAA
1 TTTGTATAAGATTTATAA
*
1555303 TTTGTATACGATTTATA
1 TTTGTATAAGATTTATA
1555320 TTTTTTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGTATAAGATTTATAA
Found at i:1556047 original size:199 final size:199
Alignment explanation
Indices: 1555406--1558210 Score: 5103
Period size: 199 Copynumber: 14.1 Consensus size: 199
1555396 TTAAGGGTCA
* * *
1555406 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGAATTAAAAACAAGGTGCAT
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCCAGAATGAATTAAAAACAAGGTGCAC
1555471 CAATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 CAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1555535 GTAATATGTAATTTTT-AATCTAACTGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1555599 TAATG
195 TAATG
* *
1555604 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1555669 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1555734 TAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1555798 AATG
196 AATG
* *
1555802 TGTCGACACTACTATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1555867 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1555932 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1555997 AATG
196 AATG
* *
1556001 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1556066 AATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1556130 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1556195 AATG
196 AATG
1556199 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1556264 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1556329 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1556394 TAATG
195 TAATG
* *
1556399 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1556464 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1556529 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACC-GTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1556593 AATG
196 AATG
*
1556597 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1556661 AAT-AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
1556725 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1556790 AATG
196 AATG
* *
1556794 TGTCGACACTACTATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1556859 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1556924 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1556989 AATG
196 AATG
1556993 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
* *
1557058 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1557123 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1557188 AATG
196 AATG
1557192 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1557257 CATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1557321 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1557386 AATG
196 AATG
*
1557390 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1557454 AATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1557518 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1557583 AATG
196 AATG
* *
1557587 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1557652 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
1557717 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1557782 AATG
196 AATG
* *
1557786 TGTCGACACTACTATAGTTTGTGTCGATATTTTTTTCCCAAAATGAA-TAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1557850 CAT-AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1557914 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1557979 AATG
196 AATG
1557983 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
* *
1558048 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
1558113 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1558178 AATG
196 AATG
* * *
1558182 TGTCGACAATAATATATTTTGTCTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
1558211 CTAATTTAAA
Statistics
Matches: 2542, Mismatches: 53, Indels: 23
0.97 0.02 0.01
Matches are distributed among these distances:
196 100 0.04
197 517 0.20
198 799 0.31
199 932 0.37
200 194 0.08
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:1557145 original size:793 final size:795
Alignment explanation
Indices: 1555406--1558210 Score: 5171
Period size: 793 Copynumber: 3.5 Consensus size: 795
1555396 TTAAGGGTCA
* * *
1555406 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGAATTAAAAACAAGGTGCAT
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCCAGAATGAATTAAAAACAAGGTGCAC
*
1555471 CAATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1555535 GTAATATGTAATTTTT-AATCTAACTGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
*
1555599 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT
195 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGT
*
1555664 GCATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
260 GCACCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
*
1555729 TAATGTAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTC
325 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
* *
1555793 TAAATAATGTGTCGACACTACTATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACA
390 TAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACA
* *
1555858 AGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAA
454 AGGTGCATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAA
*
1555923 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATA
519 AGTATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATA
1555988 AGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
584 AGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1556053 AACAAGGTGCATCAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
649 AACAAGGTGCATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1556117 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
714 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1556182 AATAAGTCTAAATAATG
779 AATAAGTCTAAATAATG
1556199 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1556264 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1556329 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
*
1556394 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT
195 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGT
*
1556459 GCATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
260 GCACCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
1556524 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACC-GTTTTATGAGAGAATAAGTC
325 TAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
1556588 TAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAA
390 TAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAA
1556653 GGTGCATCAAT-AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
455 GGTGCATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
*
1556717 GTATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAA
520 GTATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAA
* * *
1556782 GTCTAAATAATGTGTCGACACTACTATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAA
585 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAA
* *
1556847 ACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
650 ACAAGGTGCATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
1556912 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
715 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
*
1556977 ATATGTCTAAATAATG
780 ATAAGTCTAAATAATG
1556993 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1557058 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1557123 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1557188 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
*
1557253 CACCCATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CACCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
1557317 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
326 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
1557382 AAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAG
391 AAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAG
1557447 GTGCATCAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
456 GTGCATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
1557511 TATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAG
521 TATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAG
1557576 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAA
586 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAA
1557641 CAAGGTGCATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
651 CAAGGTGCATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
* *
1557706 AAAGTATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAA
716 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
1557771 TAAGTCTAAATAATG
781 TAAGTCTAAATAATG
* *
1557786 TGTCGACACTACTATAGTTTGTGTCGATATTTTTTTCCCAAAATGAA-TAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1557850 CAT-AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
1557914 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1557979 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
* *
1558044 CACCCATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CACCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
* * *
1558109 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCT
326 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
* * *
1558174 AAATAATGTGTCGACAATAATATATTTTGTCTCGATA
391 AAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
1558211 CTAATTTAAA
Statistics
Matches: 1961, Mismatches: 43, Indels: 17
0.97 0.02 0.01
Matches are distributed among these distances:
791 214 0.11
792 290 0.15
793 873 0.45
794 301 0.15
795 255 0.13
796 28 0.01
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (795 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
CACCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
AAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAG
GTGCATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
TATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAG
TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAA
CAAGGTGCATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
TAAGTCTAAATAATG
Found at i:1559689 original size:18 final size:18
Alignment explanation
Indices: 1559666--1559733 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
1559656 ATCGGTCGCA
1559666 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
1559684 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
1559705 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
1559726 GAAGATGA
1 GAAGATGA
1559734 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:1559690 original size:6 final size:6
Alignment explanation
Indices: 1559666--1559760 Score: 64
Period size: 6 Copynumber: 15.3 Consensus size: 6
1559656 ATCGGTCGCA
* * * * * *
1559666 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * *
1559714 GAAGCT GGCGAT GAAGAT GATGACGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GA--A-GAT GAAGAT GAAGAT GAAGAT GA
1559761 TGATCCAAAC
Statistics
Matches: 70, Mismatches: 16, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
6 64 0.91
8 1 0.01
9 5 0.07
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:1559701 original size:3 final size:3
Alignment explanation
Indices: 1559681--1559764 Score: 78
Period size: 3 Copynumber: 28.0 Consensus size: 3
1559671 TGAAGCTGAC
* * * * * ** *
1559681 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
1559729 GAT GAT GAC GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1559765 CCAAACAAGT
Statistics
Matches: 62, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:1559761 original size:12 final size:12
Alignment explanation
Indices: 1559666--1559764 Score: 72
Period size: 12 Copynumber: 8.0 Consensus size: 12
1559656 ATCGGTCGCA
* *
1559666 GAAGATGAAGCT
1 GAAGATGATGAT
* *
1559678 GACGATGAAGAT
1 GAAGATGATGAT
*
1559690 GACGATGATGAT
1 GAAGATGATGAT
* *
1559702 GATGATGACGAT
1 GAAGATGATGAT
* **
1559714 GAAGCTGGCGAT
1 GAAGATGATGAT
1559726 GAAGATGATGACGAT
1 GAAGATGAT---GAT
*
1559741 GATGATGATGAT
1 GAAGATGATGAT
1559753 GAAGATGATGAT
1 GAAGATGATGAT
1559765 CCAAACAAGT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
12 60 0.85
15 11 0.15
ACGTcount: A:0.36, C:0.07, G:0.34, T:0.22
Consensus pattern (12 bp):
GAAGATGATGAT
Found at i:1559764 original size:18 final size:18
Alignment explanation
Indices: 1559669--1559763 Score: 82
Period size: 18 Copynumber: 5.3 Consensus size: 18
1559659 GGTCGCAGAA
* * *
1559669 GATGAAGCTGACGATGAA
1 GATGAAGATGATGATGAT
*
1559687 GATGACGATGATGATGAT
1 GATGAAGATGATGATGAT
* * * **
1559705 GATGACGATGAAGCTGGC
1 GATGAAGATGATGATGAT
*
1559723 GATGAAGATGATGACGAT
1 GATGAAGATGATGATGAT
* *
1559741 GATGATGATGATGAAGAT
1 GATGAAGATGATGATGAT
1559759 GATGA
1 GATGA
1559764 TCCAAACAAG
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.22
Consensus pattern (18 bp):
GATGAAGATGATGATGAT
Found at i:1561748 original size:183 final size:184
Alignment explanation
Indices: 1561139--1562165 Score: 1988
Period size: 184 Copynumber: 5.6 Consensus size: 184
1561129 TATTATATAA
1561139 AATAGATAATTTTGTAATATAACC-GTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1561203 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
66 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
1561268 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
131 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
1561322 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1561387 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
66 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
1561452 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
131 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
1561506 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1561571 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AAAATGTGTCGA
66 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
1561635 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
131 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
1561689 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1561754 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
66 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
* *
1561819 TACAATTTAAAAAAGTGTCGACATTTTACACATCGTAACCCATAATTATAATGT
131 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
1561873 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1561938 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AAAATGTGTCGA
66 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
1562002 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
131 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
* *
1562056 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
*
1562121 CTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
1562166 CCATTTAAAA
Statistics
Matches: 835, Mismatches: 7, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
183 378 0.45
184 457 0.55
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
Found at i:1561812 original size:367 final size:367
Alignment explanation
Indices: 1561139--1562165 Score: 1993
Period size: 367 Copynumber: 2.8 Consensus size: 367
1561129 TATTATATAA
1561139 AATAGATAATTTTGTAATATAACC-GTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1561203 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
66 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AAAATGTGTCGA
1561268 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATT
130 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATT
1561333 TTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTATATCGACA
195 TTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTATATCGACA
*
1561398 CTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAA
260 CTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACAATTTAAA
1561463 AAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
325 AAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
1561506 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1561571 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATGTGTCGAT
66 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATGTGTCGAT
1561636 ACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTT
131 ACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTT
1561701 TGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTATATCGACAC
196 TGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTATATCGACAC
1561766 TTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACAATTTAAAA
261 TTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACAATTTAAAA
*
1561831 AAGTGTCGACATTTTACACATCGTAACCCATAATTATAATGT
326 AAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
1561873 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
1561938 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATGTGTCGAT
66 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATGTGTCGAT
1562003 ACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTT
131 ACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTT
* *
1562068 TGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACAC
196 TGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTATATCGACAC
*
1562133 TTTATAATATTGTGTCGGTACTTTATGTCCATA
261 TTTTTAATATTGTGTCGGTACTTTATGTCCATA
1562166 CCATTTAAAA
Statistics
Matches: 654, Mismatches: 5, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
367 562 0.86
368 92 0.14
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (367 bp):
AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAAC
CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATGTGTCGAT
ACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTT
TGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTATATCGACAC
TTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACAATTTAAAA
AAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
Found at i:1564753 original size:23 final size:23
Alignment explanation
Indices: 1564722--1564784 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1564712 ATAGGTAAAC
*
1564722 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1564745 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1564768 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
1564785 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1564792 original size:23 final size:23
Alignment explanation
Indices: 1564722--1564794 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1564712 ATAGGTAAAC
* * **
1564722 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
1564745 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
1564768 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
1564791 ATAT
1 ATAT
1564795 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:1565177 original size:23 final size:23
Alignment explanation
Indices: 1565146--1565208 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1565136 ATAGGTAAAC
*
1565146 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1565169 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1565192 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
1565209 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1565216 original size:23 final size:23
Alignment explanation
Indices: 1565146--1565218 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1565136 ATAGGTAAAC
* * **
1565146 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
1565169 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
1565192 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
1565215 ATAT
1 ATAT
1565219 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:1565640 original size:23 final size:23
Alignment explanation
Indices: 1565577--1565641 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
1565567 ATAGGTAAAC
* *
1565577 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
1565600 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
1565623 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
1565642 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:1565866 original size:18 final size:18
Alignment explanation
Indices: 1565845--1565881 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1565835 GTAATTGGAG
1565845 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1565863 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1565881 T
1 T
1565882 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1565889 original size:24 final size:24
Alignment explanation
Indices: 1565837--1565883 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1565827 TTTCATATGT
* *
1565837 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
1565861 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
1565884 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:1571915 original size:2 final size:2
Alignment explanation
Indices: 1571910--1571943 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1571900 ATATATATAT
1571910 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1571944 CCATATGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1572605 original size:22 final size:23
Alignment explanation
Indices: 1572541--1572606 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 23
1572531 AGTCGAGGGT
* *
1572541 TACATAGGTCCTTCGGGGCATAG
1 TACACAGGTCCTTCGGGACATAG
*
1572564 TAACACAGGTCCTTCAGGACATA-
1 T-ACACAGGTCCTTCGGGACATAG
* *
1572587 TACAGAGGTCATTCGGGACA
1 TACACAGGTCCTTCGGGACA
1572607 AATTTCACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 16 0.44
23 2 0.06
24 18 0.50
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
TACACAGGTCCTTCGGGACATAG
Found at i:1573319 original size:16 final size:17
Alignment explanation
Indices: 1573292--1573325 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1573282 AATTTTATTC
1573292 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
1573309 TTTTG-AAAAGTCAATG
1 TTTTGTAAAAGTAAATG
1573325 T
1 T
1573326 GACATCTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Found at i:1590322 original size:17 final size:17
Alignment explanation
Indices: 1590302--1590345 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1590292 CCTTACTTTT
1590302 TTTTCCTGTACTAATCC
1 TTTTCCTGTACTAATCC
* * *
1590319 TTTTACTATACTAATCT
1 TTTTCCTGTACTAATCC
*
1590336 TTTTCTTGTA
1 TTTTCCTGTA
1590346 TCGTTCCTTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTTCCTGTACTAATCC
Found at i:1590438 original size:17 final size:17
Alignment explanation
Indices: 1590418--1590456 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1590408 ATTAATTCGC
*
1590418 TTACTATACTGTATCTT
1 TTACTATACTATATCTT
*
1590435 TTACTATTCTATATCTT
1 TTACTATACTATATCTT
1590452 TTACT
1 TTACT
1590457 TTTGTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.18, G:0.03, T:0.56
Consensus pattern (17 bp):
TTACTATACTATATCTT
Found at i:1591749 original size:19 final size:19
Alignment explanation
Indices: 1591727--1591764 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1591717 AATTAGTCTA
1591727 AAATCAACATTTCAATATT
1 AAATCAACATTTCAATATT
* *
1591746 AAATCAATATTTTAATATT
1 AAATCAACATTTCAATATT
1591765 CGATTCCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATCAACATTTCAATATT
Found at i:1595257 original size:23 final size:21
Alignment explanation
Indices: 1595231--1595274 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1595221 CAAAAAACAA
1595231 CATTTAATGCAAAAGGGATCAAT
1 CATTTAATG--AAAGGGATCAAT
*
1595254 CATTTGATGAAAGGGATCAAT
1 CATTTAATGAAAGGGATCAAT
1595275 TCTTTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
23 8 0.40
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (21 bp):
CATTTAATGAAAGGGATCAAT
Found at i:1595372 original size:26 final size:21
Alignment explanation
Indices: 1595304--1595361 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
1595294 CGTTGCCAGA
1595304 AAGGGATTGATCCTTTAAGGG
1 AAGGGATTGATCCTTTAAGGG
1595325 AAGGGATTGATCCTTTAAGGG
1 AAGGGATTGATCCTTTAAGGG
1595346 AAGGGATTGATCCTTT
1 AAGGGATTGATCCTTT
1595362 TCATTGAGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.28, C:0.10, G:0.31, T:0.31
Consensus pattern (21 bp):
AAGGGATTGATCCTTTAAGGG
Found at i:1597423 original size:19 final size:19
Alignment explanation
Indices: 1597396--1597439 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1597386 CCACGTATCT
* *
1597396 CAAAGCTCGATATATTTAC
1 CAAAACTCGATATATATAC
1597415 CAAAACTCGATATATATAC
1 CAAAACTCGATATATATAC
1597434 CAAAAC
1 CAAAAC
1597440 CTGATGTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (19 bp):
CAAAACTCGATATATATAC
Found at i:1598898 original size:21 final size:21
Alignment explanation
Indices: 1598874--1598915 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1598864 AAAAATACAA
* *
1598874 ACTTAATAAATCTACAAAGAT
1 ACTTAAGAAATCTAAAAAGAT
*
1598895 ACTTAAGATATCTAAAAAGAT
1 ACTTAAGAAATCTAAAAAGAT
1598916 GTCTTAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (21 bp):
ACTTAAGAAATCTAAAAAGAT
Found at i:1604786 original size:16 final size:16
Alignment explanation
Indices: 1604691--1604781 Score: 146
Period size: 16 Copynumber: 5.7 Consensus size: 16
1604681 CGTTCATTTA
*
1604691 ATAAACGAAAACGAAC
1 ATAAACGAACACGAAC
*
1604707 ATAAACGAAAACGAAC
1 ATAAACGAACACGAAC
1604723 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
1604739 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
* *
1604755 ATAAGCGAACACAAAC
1 ATAAACGAACACGAAC
1604771 ATAAACGAACA
1 ATAAACGAACA
1604782 TAAACGTTGG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 71 1.00
ACGTcount: A:0.59, C:0.22, G:0.12, T:0.07
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:1605473 original size:20 final size:20
Alignment explanation
Indices: 1605450--1605517 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 20
1605440 ATAAATGAAT
1605450 GAACATAAACGAACATAACC
1 GAACATAAACGAACATAACC
* *
1605470 GAACGTTCACGAACGTAA-ATGAA-T
1 GAAC-AT-A--AACG-AACAT-AACC
1605494 GAACATAAACGAACATAACC
1 GAACATAAACGAACATAACC
1605514 GAAC
1 GAAC
1605518 GTTCGCAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
19 4 0.11
20 14 0.39
21 1 0.03
22 2 0.06
23 1 0.03
24 10 0.28
25 4 0.11
ACGTcount: A:0.50, C:0.22, G:0.15, T:0.13
Consensus pattern (20 bp):
GAACATAAACGAACATAACC
Found at i:1605504 original size:44 final size:44
Alignment explanation
Indices: 1605436--1605541 Score: 176
Period size: 44 Copynumber: 2.4 Consensus size: 44
1605426 AGATTGGGTT
*
1605436 AAACATAAATGAATGAACATAAACGAACATAACCGAACGTTCAC
1 AAACGTAAATGAATGAACATAAACGAACATAACCGAACGTTCAC
* *
1605480 GAACGTAAATGAATGAACATAAACGAACATAACCGAACGTTCGC
1 AAACGTAAATGAATGAACATAAACGAACATAACCGAACGTTCAC
*
1605524 AAACGTAAATGAACGAAC
1 AAACGTAAATGAATGAAC
1605542 GATACATATG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.50, C:0.20, G:0.15, T:0.15
Consensus pattern (44 bp):
AAACGTAAATGAATGAACATAAACGAACATAACCGAACGTTCAC
Found at i:1606394 original size:27 final size:29
Alignment explanation
Indices: 1606361--1606425 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 29
1606351 GAGAATTTTG
* * *
1606361 TAAAAAAAAACTTAATTT-TTTTATATT-
1 TAAAAAAAAACATAATTTCTCTTAAATTA
*
1606388 TAAAAAAAATCATAATTTCTCTTAAATTA
1 TAAAAAAAAACATAATTTCTCTTAAATTA
1606417 TAAAAAAAA
1 TAAAAAAAA
1606426 TATCAATCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 16 0.50
28 7 0.22
29 9 0.28
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (29 bp):
TAAAAAAAAACATAATTTCTCTTAAATTA
Found at i:1606450 original size:17 final size:17
Alignment explanation
Indices: 1606420--1606455 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1606410 TAAATTATAA
*
1606420 AAAAAATATCAATCCCT
1 AAAAAATATAAATCCCT
*
1606437 AAAAATTATAAATCCCT
1 AAAAAATATAAATCCCT
1606454 AA
1 AA
1606456 TCCTAATCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAAAATATAAATCCCT
Found at i:1607602 original size:4 final size:4
Alignment explanation
Indices: 1607595--1607647 Score: 106
Period size: 4 Copynumber: 13.2 Consensus size: 4
1607585 TGTGCATACA
1607595 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1607643 TATG T
1 TATG T
1607648 TCTTGTTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:1608882 original size:30 final size:30
Alignment explanation
Indices: 1608846--1608911 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
1608836 CCTTCACCAA
*
1608846 CGTTTCATTTAAATGAAGAGCATGCTCATT
1 CGTTTCATATAAATGAAGAGCATGCTCATT
1608876 CGTTTCATATAAATGAAGAGCATGCTCATT
1 CGTTTCATATAAATGAAGAGCATGCTCATT
1608906 CGTTTC
1 CGTTTC
1608912 TTGAATCTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (30 bp):
CGTTTCATATAAATGAAGAGCATGCTCATT
Found at i:1610038 original size:47 final size:47
Alignment explanation
Indices: 1609975--1610082 Score: 135
Period size: 47 Copynumber: 2.3 Consensus size: 47
1609965 AATTTAGTTG
* * * *
1609975 ACTAGATCCAATTTTGAGCACCTCTAACAATTCTTGAATATGTAACA
1 ACTAGAGCCAGTTTTGAGCACATCTAACAATTCTTGAATATATAACA
* * * * *
1610022 ACTAGAGCTAGTTTTGAGCATATCTAGCAATTCTTTAATGTATAACA
1 ACTAGAGCCAGTTTTGAGCACATCTAACAATTCTTGAATATATAACA
1610069 ACTAGAGCCAGTTT
1 ACTAGAGCCAGTTT
1610083 CAGGTACCTC
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (47 bp):
ACTAGAGCCAGTTTTGAGCACATCTAACAATTCTTGAATATATAACA
Found at i:1610951 original size:16 final size:17
Alignment explanation
Indices: 1610930--1610977 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 17
1610920 TAGATGAAAC
1610930 TTAAAAATAAAAAA-AA
1 TTAAAAATAAAAAATAA
*
1610946 TTAAAAAAAAACTAAATAA
1 TTAAAAATAAA--AAATAA
*
1610965 ATAAAAATAAAAA
1 TTAAAAATAAAAA
1610978 TATCAAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 10 0.38
17 2 0.08
18 3 0.12
19 11 0.42
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (17 bp):
TTAAAAATAAAAAATAA
Found at i:1610978 original size:16 final size:17
Alignment explanation
Indices: 1610930--1610979 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
1610920 TAGATGAAAC
1610930 TTAAAAATAAAAA-AAA
1 TTAAAAATAAAAATAAA
*
1610946 TTAAAAA-AAAACTAAA
1 TTAAAAATAAAAATAAA
1610962 TAAATAAAAATAAAAATA
1 T---TAAAAATAAAAATA
1610980 TCAAAGGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 4 0.15
16 11 0.41
19 6 0.22
20 6 0.22
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (17 bp):
TTAAAAATAAAAATAAA
Found at i:1614047 original size:23 final size:23
Alignment explanation
Indices: 1614021--1614084 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
1614011 CAGCTCATAT
*
1614021 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAA
* * *
1614044 AATTGCACCGGAGGGCCGCGTAA
1 AATTGCACCGAAGTGCCACGTAA
* *
1614067 AATTGCACTGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1614085 TATAATAATG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAA
Found at i:1614271 original size:103 final size:103
Alignment explanation
Indices: 1614103--1614420 Score: 582
Period size: 103 Copynumber: 3.1 Consensus size: 103
1614093 TGTCCATAAA
* * * *
1614103 GACCACATACCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
1614168 TTCACACATGTTCCAAAGAATACATATATGTCCCAAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
1614206 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1614271 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
1614309 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
1614374 TTCACACATGTTCCAAAGAATATATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
1614412 GACCACATA
1 GACCACATA
1614421 GACCCTCGAC
Statistics
Matches: 209, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 209 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
Found at i:1615291 original size:64 final size:64
Alignment explanation
Indices: 1615157--1615313 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 64
1615147 TAATGAAGGT
* * * ** *
1615157 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTTTGTTTATTAAAGAG
* * *
1615221 AAGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATT-TATT-TTAAA-A
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGT-TTGT-TTATTAAAGA
1615283 G
64 G
* * *
1615284 AGTGCATCGATGCACTTCCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
1615314 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 2 0.03
64 71 0.92
65 4 0.05
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTTTGTTTATTAAAGAG
Found at i:1615374 original size:21 final size:21
Alignment explanation
Indices: 1615348--1615406 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
1615338 TTAACCTTGA
1615348 TGCATCGATGCACTATGAATG
1 TGCATCGATGCACTATGAATG
1615369 TGCATCGATGCACTATGAATG
1 TGCATCGATGCACTATGAATG
1615390 TGCATCGATGCACTATG
1 TGCATCGATGCACTATG
1615407 CCCAGAACCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCACTATGAATG
Found at i:1620088 original size:23 final size:23
Alignment explanation
Indices: 1620062--1620125 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
1620052 CAGCTCATAT
1620062 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1620085 AATTGCACCGAAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1620108 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1620126 TATAATAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1620314 original size:103 final size:103
Alignment explanation
Indices: 1620141--1620461 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
1620131 TAATGTCCAT
* * * *
1620141 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
1620206 TACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1620244 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1620309 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1620347 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
1620412 GACTTCACACATGTTCCAAAGAATAAATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1620450 AAGGACCACATA
1 AAGGACCACATA
1620462 GACCCTCGAC
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1621331 original size:64 final size:64
Alignment explanation
Indices: 1621198--1621354 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 64
1621188 TAATGAAGGT
* * * ** *
1621198 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTTTGTTTATTAAAGAG
* *
1621262 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATT-TATT-TTAAA-A
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGT-TTGT-TTATTAAAGA
1621324 G
64 G
* * *
1621325 AGTGCATCGATGCACTTCCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
1621355 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
63 2 0.03
64 73 0.92
65 4 0.05
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTTTGTTTATTAAAGAG
Found at i:1623849 original size:85 final size:85
Alignment explanation
Indices: 1623706--1624115 Score: 509
Period size: 85 Copynumber: 4.8 Consensus size: 85
1623696 TCTCAACTTA
* * * * *
1623706 TTACAGCATAGTTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTTGAGTTCGATTATATTT
1 TTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
* *
1623771 AGCTCAAGGGCATATAAAAT
66 AGCTCAAGGACATATCAAAT
* * *
1623791 TTACAGCATAGCTCAAGTCGAGAAGAGTTATCTGTCAACAAAGACCTTTGAGTTCGATTACATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
1623856 AGCTCAAGGACATATCAAAT
66 AGCTCAAGGACATATCAAAT
* *
1623876 TTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAAAAAGACCTTCGAGTTCGATTACATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
1623941 AGCTCAAGGACATATCAAAT
66 AGCTCAAGGACATATCAAAT
* ** * * * * * *
1623961 TTACAGCATAACTCAAGGCGAGAAGGGTTATCTACCAATAAATACGTTCAAGTTCAATTCCATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
* * *
1624026 AGCTCAAGGGCATGTCATAT
66 AGCTCAAGGACATATCAAAT
* * * ** * *
1624046 TTACAGCATAGCTTAAGTCAAGAA-AATCTATCTGTCAACAAA-AACTGTCGAGTTCGATTCCAT
1 TTACAGCATAGCTCAAGGCGAGAAGGGT-TATCTGTCAACAAAGACCT-TCGAGTTCGATTACAT
1624109 TCAGCTC
64 TCAGCTC
1624116 GACAACACGT
Statistics
Matches: 286, Mismatches: 37, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
84 3 0.01
85 283 0.99
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (85 bp):
TTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
AGCTCAAGGACATATCAAAT
Found at i:1624865 original size:2 final size:2
Alignment explanation
Indices: 1624858--1624900 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1624848 TTTATTTTAT
1624858 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
1624900 T
1 T
1624901 TTTGAAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1624913 original size:11 final size:11
Alignment explanation
Indices: 1624897--1624921 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1624887 ATATATATAT
1624897 ATATTTTGAAA
1 ATATTTTGAAA
1624908 ATATTTTGAAA
1 ATATTTTGAAA
1624919 ATA
1 ATA
1624922 CATATATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
ATATTTTGAAA
Found at i:1624927 original size:36 final size:37
Alignment explanation
Indices: 1624887--1625158 Score: 167
Period size: 34 Copynumber: 7.8 Consensus size: 37
1624877 ATATATATAT
*
1624887 ATATATATATATA-TTTTGAAAATATTTTGAAAATAC
1 ATATATATATATAGTTTTGAAAACATTTTGAAAATAC
** *
1624923 ATATATAATATATAGTTTTTGAAAACATTTAAAAAAAAC
1 ATATAT-ATATATAG-TTTTGAAAACATTTTGAAAATAC
* * * **
1624962 TTATTTAGTATATAGTTTTGAAATCATTTTGAAAATTT
1 ATATATA-TATATAGTTTTGAAAACATTTTGAAAATAC
*
1625000 ATATA-ATATATAGTTTTTAAAACATTTTTG-AAA-AC
1 ATATATATATATAGTTTTGAAAACA-TTTTGAAAATAC
* * * *
1625035 ATAGT-T-T-TA-A------AACA-TTTTTGAAAACAT
1 ATA-TATATATATAGTTTTGAAAACATTTTGAAAATAC
*
1625062 ATATA-ATATATAGTTTTGAAAACATTTTTAAAA-A-
1 ATATATATATATAGTTTTGAAAACATTTTGAAAATAC
*
1625096 ATATA-ATATATAGTTTT-AAAATAGTTTTGAAAAT--
1 ATATATATATATAGTTTTGAAAACA-TTTTGAAAATAC
*
1625130 ATATAT-TATATAGTTTTTGGAAACATTTT
1 ATATATATATATAG-TTTTGAAAACATTTT
1625159 TTATATATAA
Statistics
Matches: 183, Mismatches: 28, Indels: 51
0.70 0.11 0.19
Matches are distributed among these distances:
25 5 0.03
26 4 0.02
27 8 0.04
28 2 0.01
29 1 0.01
33 6 0.03
34 39 0.21
35 16 0.09
36 38 0.21
37 13 0.07
38 21 0.11
39 30 0.16
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (37 bp):
ATATATATATATAGTTTTGAAAACATTTTGAAAATAC
Found at i:1624927 original size:38 final size:38
Alignment explanation
Indices: 1624885--1625033 Score: 160
Period size: 39 Copynumber: 3.9 Consensus size: 38
1624875 ATATATATAT
*
1624885 ATATATATATATATA-TTTTGAAAATATTTTGAAAATAC
1 ATATATA-ATATATAGTTTTGAAAACATTTTGAAAATAC
** *
1624923 ATATATAATATATAGTTTTTGAAAACATTTAAAAAAAAC
1 ATATATAATATATAG-TTTTGAAAACATTTTGAAAATAC
* * * *
1624962 TTATTTAGTATATAGTTTTGAAATCATTTTGAAAAT--
1 ATATATAATATATAGTTTTGAAAACATTTTGAAAATAC
* *
1624998 TTATATAATATATAGTTTTTAAAACATTTTTGAAAA
1 ATATATAATATATAGTTTTGAAAACA-TTTTGAAAA
1625034 CATAGTTTTA
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
36 22 0.24
37 16 0.17
38 24 0.26
39 31 0.33
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (38 bp):
ATATATAATATATAGTTTTGAAAACATTTTGAAAATAC
Found at i:1625033 original size:12 final size:11
Alignment explanation
Indices: 1625013--1625094 Score: 65
Period size: 11 Copynumber: 6.8 Consensus size: 11
1625003 TAATATATAG
1625013 TTTTTAAAACA
1 TTTTTAAAACA
1625024 TTTTTGAAAACA
1 TTTTT-AAAACA
1625036 TAGTTTTAAAACA
1 T--TTTTAAAACA
1625049 TTTTTGAAAACA
1 TTTTT-AAAACA
* * *
1625061 TATATAATATATA
1 TTTTTAA-A-ACA
*
1625074 GTTTTGAAAACA
1 -TTTTTAAAACA
1625086 TTTTTAAAA
1 TTTTTAAAA
1625095 AATATAATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
11 19 0.34
12 19 0.34
13 10 0.18
14 8 0.14
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (11 bp):
TTTTTAAAACA
Found at i:1625042 original size:25 final size:26
Alignment explanation
Indices: 1625009--1625062 Score: 101
Period size: 25 Copynumber: 2.1 Consensus size: 26
1624999 TATATAATAT
1625009 ATAGTTTTTAAAACATTTTTGAAAAC
1 ATAGTTTTTAAAACATTTTTGAAAAC
1625035 ATAG-TTTTAAAACATTTTTGAAAAC
1 ATAGTTTTTAAAACATTTTTGAAAAC
1625060 ATA
1 ATA
1625063 TATAATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (26 bp):
ATAGTTTTTAAAACATTTTTGAAAAC
Found at i:1625042 original size:62 final size:62
Alignment explanation
Indices: 1624973--1625095 Score: 185
Period size: 62 Copynumber: 2.0 Consensus size: 62
1624963 TATTTAGTAT
* ** * *
1624973 ATAGTTTTGAAATCA-TTTTGAAAATTTATATAATATATAGTTTTTAAAACATTTTTGAAAAC
1 ATAGTTTT-AAAACATTTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTTAAAAAC
1625035 ATAGTTTTAAAACATTTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTTAAAAA
1 ATAGTTTTAAAACATTTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTTAAAAA
1625096 ATATAATATA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 5 0.09
62 50 0.91
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (62 bp):
ATAGTTTTAAAACATTTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTTAAAAAC
Found at i:1626363 original size:28 final size:27
Alignment explanation
Indices: 1626332--1626391 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
1626322 ATTTTCTTTA
*
1626332 TTATTATTATTATCTTTTTCCTTCTGAT
1 TTATTATTATTATCTTTTTCCTT-TCAT
* * *
1626360 TTATAATTTTTTTCTTTTTCCTTTCAT
1 TTATTATTATTATCTTTTTCCTTTCAT
1626387 TTATT
1 TTATT
1626392 TAACATAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.68
Consensus pattern (27 bp):
TTATTATTATTATCTTTTTCCTTTCAT
Found at i:1627381 original size:30 final size:30
Alignment explanation
Indices: 1627321--1627424 Score: 158
Period size: 29 Copynumber: 3.5 Consensus size: 30
1627311 TATGGTAAAA
** * *
1627321 AATCAATGTGACCACCTAACT-TTCAATTG
1 AATCAATCAGACCACCCAACTATTTAATTG
1627350 AATCAATCAGACCACCCAACTATTTAATTG
1 AATCAATCAGACCACCCAACTATTTAATTG
1627380 AATCAATCAGACCA-CCAACTATTTAATTG
1 AATCAATCAGACCACCCAACTATTTAATTG
1627409 AATCAATCAGACCACC
1 AATCAATCAGACCACC
1627425 GGCCGTTAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
29 47 0.68
30 22 0.32
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.26
Consensus pattern (30 bp):
AATCAATCAGACCACCCAACTATTTAATTG
Found at i:1628114 original size:63 final size:68
Alignment explanation
Indices: 1627983--1628150 Score: 220
Period size: 63 Copynumber: 2.5 Consensus size: 68
1627973 CCAAAATTTG
* * *
1627983 TTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTATATTAATGGTTAAAGAAAAAAATTCGG
1 TTCGGTTCGGTTAATAATTTTCAAATTAA-TTAGGTTATATTAATGGTTAAAGAAAAAAATTCAG
1628048 TTAA
65 TTAA
* * * *
1628052 TTTGGTTCGGTTAATAATTTTCAAATTAATTAGGTTA-A-TAAT-TTTCAA-AACAAAA-TCAGT
1 TTCGGTTCGGTTAATAATTTTCAAATTAATTAGGTTATATTAATGGTTAAAGAAAAAAATTCAGT
1628112 TAA
66 TAA
*
1628115 TTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTT
1 TTCGGTTCGGTTAATAATTTTCAAATTAATTAGGTT
1628151 CGGTTAATAA
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
63 41 0.46
64 6 0.07
65 4 0.04
66 4 0.04
67 1 0.01
68 7 0.08
69 27 0.30
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (68 bp):
TTCGGTTCGGTTAATAATTTTCAAATTAATTAGGTTATATTAATGGTTAAAGAAAAAAATTCAGT
TAA
Found at i:1628295 original size:131 final size:132
Alignment explanation
Indices: 1628156--1628470 Score: 427
Period size: 139 Copynumber: 2.3 Consensus size: 132
1628146 CGGTTCGGTT
* *
1628156 AATAAATTTTGGTTCGATTAACTGAACCGAATTAACTGAATTTTTGCTTCGATTAA-TAAT-TTA
1 AATAAATTTTGGTTCGATTAACCGAACCGAATTAACCGAATTTTTGCTTCGATTAATTAATATTA
* * * * *
1628219 AAAAAAATTGTTTAATTCGGTTTAAATTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTT
66 AAAAAAATCGGTTAATTAGG-TTAAATTAATAATTTTCAAATTAATTCGGGTCGATTAATAATTT
*
1628284 TTA
130 TAA
*
1628287 AATAAATTTTGGTTCGATTAACCGAACCAAATTAACCGAATTTTTGCTTCGATTAATTCGGTTAA
1 AATAAATTTTGGTTCGATTAACCGAACCGAATTAACCGAATTTTTGCTTCGATTAA-----TTAA
* *
1628352 TAATTTAAAAAAATCGGTTAATTAGGTTCAATTAATAATTTTCAAATTAATTCGGGTCGATTAAT
61 T-ATTAAAAAAAATCGGTTAATTAGGTTAAATTAATAATTTTCAAATTAATTCGGGTCGATTAAT
1628417 AATTTTAA
125 AATTTTAA
* *
1628425 AATAAAATTTTGGTTTGATTAACCGAACCGAATTAACCAAATTTTT
1 AAT-AAATTTTGGTTCGATTAACCGAACCGAATTAACCGAATTTTT
1628471 TCTTTAACTA
Statistics
Matches: 161, Mismatches: 14, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
131 53 0.33
137 4 0.02
138 46 0.29
139 58 0.36
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (132 bp):
AATAAATTTTGGTTCGATTAACCGAACCGAATTAACCGAATTTTTGCTTCGATTAATTAATATTA
AAAAAAATCGGTTAATTAGGTTAAATTAATAATTTTCAAATTAATTCGGGTCGATTAATAATTTT
AA
Found at i:1628403 original size:29 final size:29
Alignment explanation
Indices: 1628369--1628427 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1628359 AAAAAATCGG
* *
1628369 TTAATTAGGTTCAATTAATAATTTTCAAA
1 TTAATTAGGGTCAATTAATAATTTTAAAA
* *
1628398 TTAATTCGGGTCGATTAATAATTTTAAAA
1 TTAATTAGGGTCAATTAATAATTTTAAAA
1628427 T
1 T
1628428 AAAATTTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (29 bp):
TTAATTAGGGTCAATTAATAATTTTAAAA
Found at i:1628548 original size:18 final size:18
Alignment explanation
Indices: 1628525--1628567 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1628515 CTGAACCGAA
*
1628525 TTAACCGAATTTTTTTCT
1 TTAACCAAATTTTTTTCT
1628543 TTAACCAAATTTTTTTCT
1 TTAACCAAATTTTTTTCT
1628561 TTAACCA
1 TTAACCA
1628568 TTAATTGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.19, G:0.02, T:0.51
Consensus pattern (18 bp):
TTAACCAAATTTTTTTCT
Found at i:1629618 original size:37 final size:36
Alignment explanation
Indices: 1629543--1629618 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1629533 TTTTTATATT
*
1629543 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1629579 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1629616 TTT
1 TTT
1629619 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1629800 original size:20 final size:20
Alignment explanation
Indices: 1629764--1629801 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1629754 ATCCTATTCC
**
1629764 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1629784 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1629802 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1637105 original size:21 final size:20
Alignment explanation
Indices: 1637077--1637116 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1637067 TCAAGTTGTA
*
1637077 AAATATAACTCGAATAACTT
1 AAATATAACTCAAATAACTT
*
1637097 AAATAATAATTCAAATAACT
1 AAAT-ATAACTCAAATAACT
1637117 CAACTCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (20 bp):
AAATATAACTCAAATAACTT
Found at i:1638966 original size:22 final size:23
Alignment explanation
Indices: 1638938--1638981 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1638928 CATAATTTTA
*
1638938 AATCAGTAAA-TTAGGAATCAAG
1 AATCAGTAAAGTCAGGAATCAAG
1638960 AATCAGTAAAGTCAGGAATCAA
1 AATCAGTAAAGTCAGGAATCAA
1638982 ACTTTCAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.20
Consensus pattern (23 bp):
AATCAGTAAAGTCAGGAATCAAG
Found at i:1639638 original size:27 final size:28
Alignment explanation
Indices: 1639592--1639645 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
1639582 ATAGTCTATG
*
1639592 TACTTTTAAATTAAAATTAA-AATAAAA
1 TACTTTTAAAATAAAATTAATAATAAAA
* *
1639619 TACTTTTAAAATGAAGTTAATAATAAA
1 TACTTTTAAAATAAAATTAATAATAAA
1639646 TATATTTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (28 bp):
TACTTTTAAAATAAAATTAATAATAAAA
Found at i:1643915 original size:18 final size:18
Alignment explanation
Indices: 1643894--1643936 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1643884 GTTGTTTTTA
*
1643894 AAATAAAATATAAGAATT
1 AAATAAAAGATAAGAATT
*
1643912 AAATAAAAGATAATAATT
1 AAATAAAAGATAAGAATT
*
1643930 AATTAAA
1 AAATAAA
1643937 TAAATTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:1645261 original size:16 final size:16
Alignment explanation
Indices: 1645240--1645272 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1645230 AAAATAAAAG
*
1645240 TAAAAATATAAACATA
1 TAAAAACATAAACATA
1645256 TAAAAACATAAACATA
1 TAAAAACATAAACATA
1645272 T
1 T
1645273 TTTTTCAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (16 bp):
TAAAAACATAAACATA
Found at i:1645285 original size:11 final size:11
Alignment explanation
Indices: 1645269--1645298 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
1645259 AAACATAAAC
1645269 ATATTTTTTCA
1 ATATTTTTTCA
1645280 ATA-TTTTTCA
1 ATATTTTTTCA
1645290 ATATTTTTT
1 ATATTTTTT
1645299 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (11 bp):
ATATTTTTTCA
Found at i:1649353 original size:18 final size:18
Alignment explanation
Indices: 1649330--1649373 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1649320 GTTGTTTTTA
*
1649330 AAATAAATGATAAGAATT
1 AAATAAATGAAAAGAATT
* *
1649348 AAATAAAAGAAAATAATT
1 AAATAAATGAAAAGAATT
*
1649366 AATTAAAT
1 AAATAAAT
1649374 AAATTTAAAG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (18 bp):
AAATAAATGAAAAGAATT
Found at i:1656899 original size:54 final size:54
Alignment explanation
Indices: 1656841--1657536 Score: 793
Period size: 54 Copynumber: 12.9 Consensus size: 54
1656831 TTTTCGCATG
** * *
1656841 GGCACTATGTGTGCAAC-CTATAAAATTCATCATATGTTGATGAAAAACCATTTC
1 GGCACTATGTGTGCAACTC-ACGAAATTCATCATATGTTGATGAACAACCGTTTC
* * *
1656895 GGCACTATGTGTGCAACTCACGAAATTTATCATATGTTGATGAATAACTGTTTC
1 GGCACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTC
* * ** * * *
1656949 GACACTATATGTGTTACCCAC-ATAATTCATCATATGTTGATGGACAACCGTTTT
1 GGCACTATGTGTGCAACTCACGA-AATTCATCATATGTTGATGAACAACCGTTTC
*
1657003 GACACTATGTGTGCAACTCAC-ATAATTCATCATATG-T--TGAACAACCGTTTC
1 GGCACTATGTGTGCAACTCACGA-AATTCATCATATGTTGATGAACAACCGTTTC
* * *
1657054 GGAACTATGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAACCG-TTC
1 GGCACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTC
* * *
1657107 TGGCACTATGTGTGCAACTCACGAAATTCATCATATATTGATGAACAAACATTTC
1 -GGCACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTC
* * * *
1657162 GGTACTATGTGTGCAACCCA-TATAATTCACCATATGTTGATGAACAACCGTTTC
1 GGCACTATGTGTGCAACTCACGA-AATTCATCATATGTTGATGAACAACCGTTTC
* * * * *
1657216 GGCACTATGTGTGCAACTCATGGAATTCATCATATATTGGTGAACAACCATTTC
1 GGCACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTC
* ** *
1657270 GACACTATGTGCACAACTCACGGAATTCATCATATG-TGTATGAACAACCGTTTC
1 GGCACTATGTGTGCAACTCACGAAATTCATCATATGTTG-ATGAACAACCGTTTC
* * * *
1657324 AGCACTGTGTGTGCAACTCACGAAATTCATCATATATTGATGAACAACCATTTC
1 GGCACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTC
* *
1657378 GACACTATGTGTGCAAC-CTATGAAATTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTATGTGTGCAACTC-ACGAAATTCATCATATGTTGATGAACAACCGTTTC
* * * * *
1657432 AGCACTATGTGTGAAACTCACGGAATTCATCATATGTTGATGAACAACTAG-TTA
1 GGCACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAAC-CGTTTC
* * * * *
1657486 GACACTAGGTGTGCAACCCACGAAATTCATCATATGTTTATGAATAACCGT
1 GGCACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGT
1657537 ATAGAAGGTA
Statistics
Matches: 543, Mismatches: 83, Indels: 32
0.83 0.13 0.05
Matches are distributed among these distances:
51 43 0.08
52 2 0.00
53 10 0.02
54 480 0.88
55 8 0.01
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (54 bp):
GGCACTATGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTC
Found at i:1658321 original size:54 final size:54
Alignment explanation
Indices: 1658262--1658829 Score: 634
Period size: 54 Copynumber: 10.5 Consensus size: 54
1658252 AACAACCGTT
* * * * **
1658262 ATTCATCATATATTGATGAACAACCATTTCGGCACTATGTATGAAACCCATAGA
1 ATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACGGA
* * * * * * * *
1658316 ATTCATCATATGTTGATAAACAACCGTTTCGACATTGTCTGTGCAACTTATGGA
1 ATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACGGA
* * * * * *
1658370 ATTCATCATATGTTGATGACCAACTATTTCGACACTATGTGTGTAACACACAGA
1 ATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACGGA
* *
1658424 ATTCATCATATGTTGATGAATAACTATTTCGGCACTATGTGTGCAACTCACGGA
1 ATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACGGA
* * * * * *
1658478 ATTTATCATATGTTGATGAACAACCTTTTCGACACTATGTGTGCATCCCACAGA
1 ATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACGGA
* *** * * *
1658532 ATTCATCATATGTTGATGAATAATGGTTTTGGCACTATGTGTGTAACTCACGAA
1 ATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACGGA
* * * * *
1658586 ATTCATCATATGTTAATGAACAACTATTTCAGCACTATGTATGCAACTCATGGA
1 ATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACGGA
** * *
1658640 ATTCATCATATGTTGATGAACAACCATTTCAACACTATGTGTGCAACCCACGTA
1 ATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACGGA
* *
1658694 ATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTGCAGCTCACGGA
1 ATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACGGA
* * * * * *
1658748 ATTCATCAAATGTTGATGAACAACCGTTTAGACACTAGGTGTGCAACCCACGGA
1 ATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACGGA
* * *
1658802 ATTCATAATATGTTTATG-ATAACCATTT
1 ATTCATCATATGTTGATGAACAACCATTT
1658830 TGGGAGTACG
Statistics
Matches: 429, Mismatches: 85, Indels: 1
0.83 0.17 0.00
Matches are distributed among these distances:
53 8 0.02
54 421 0.98
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (54 bp):
ATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTGCAACTCACGGA
Found at i:1659045 original size:81 final size:81
Alignment explanation
Indices: 1658925--1659090 Score: 208
Period size: 81 Copynumber: 2.0 Consensus size: 81
1658915 TCTAAAATAT
* * * * * * *
1658925 AAGATTAATGGCCTAACTGTGCATTTGGCAGAAATGTGTCAATTATGCTAGATAGATGAAAGGTT
1 AAGAATAATGACCTAACTGTGCATTTAGCAGAAAGGTGTCAATCATGCAAGATAGATGAAAGGCT
1658990 AAATACCTTCGAGTAA
66 AAATACCTTCGAGTAA
* *
1659006 AAGAATAATGACCT-ACTTGTGCATTTAGCAGGAAGGTGTCAATCATGCAAGTTAGATGAAAGGC
1 AAGAATAATGACCTAAC-TGTGCATTTAGCAGAAAGGTGTCAATCATGCAAGATAGATGAAAGGC
* * *
1659070 TAAATGCCTTTGGGTAA
65 TAAATACCTTCGAGTAA
1659087 AAGA
1 AAGA
1659091 TTAAATGCTT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 2 0.03
81 70 0.97
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (81 bp):
AAGAATAATGACCTAACTGTGCATTTAGCAGAAAGGTGTCAATCATGCAAGATAGATGAAAGGCT
AAATACCTTCGAGTAA
Found at i:1659152 original size:45 final size:45
Alignment explanation
Indices: 1659093--1659186 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 45
1659083 GTAAAAGATT
* * * * *
1659093 AAATGCTTAGTGGTGCATTAAATGCAAGAAAGGATGCCATAAATG
1 AAATGCATAATGGTGCATAAAAGGCAAGAAAGGAGGCCATAAATG
* *
1659138 AAATGCATAATGGTGCATAAAAGGTATGAAAGGAGGCCATAAATG
1 AAATGCATAATGGTGCATAAAAGGCAAGAAAGGAGGCCATAAATG
1659183 AAAT
1 AAAT
1659187 TAATGAATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (45 bp):
AAATGCATAATGGTGCATAAAAGGCAAGAAAGGAGGCCATAAATG
Found at i:1666488 original size:30 final size:30
Alignment explanation
Indices: 1666453--1666512 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1666443 ATTACAAAGT
1666453 TTAACCAAAGCAAATCACTACTTTATCTAA
1 TTAACCAAAGCAAATCACTACTTTATCTAA
*
1666483 TTAACCAAAGTAAATCACTACTTTATCTAA
1 TTAACCAAAGCAAATCACTACTTTATCTAA
1666513 GTATAGTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.22, G:0.03, T:0.32
Consensus pattern (30 bp):
TTAACCAAAGCAAATCACTACTTTATCTAA
Done.