Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold206
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: 2736418
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 22040 characters in sequence are not A, C, G, or T
File 13 of 20
Found at i:1593208 original size:21 final size:20
Alignment explanation
Indices: 1593183--1593221 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1593173 TGAATAAAGA
1593183 AAAAAAATGCAAATATTATT
1 AAAAAAATGCAAATATTATT
*
1593203 AAAAAAATGCAAATGTTAT
1 AAAAAAATGCAAATATTAT
1593222 CTCAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (20 bp):
AAAAAAATGCAAATATTATT
Found at i:1594068 original size:23 final size:22
Alignment explanation
Indices: 1594041--1594091 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1594031 AAATTAAATG
**
1594041 TTAAAGGTTTATTTTGATATAAA
1 TTAAAGG-TTATTTAAATATAAA
* *
1594064 TTAAAAGTTCTTTAAATATAAA
1 TTAAAGGTTATTTAAATATAAA
1594086 TTAAAG
1 TTAAAG
1594092 ATTAAGAGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (22 bp):
TTAAAGGTTATTTAAATATAAA
Found at i:1594887 original size:17 final size:19
Alignment explanation
Indices: 1594861--1594898 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1594851 TTAAATTATT
1594861 TTTATAAAAAT-T-AATAA
1 TTTATAAAAATGTAAATAA
*
1594878 TTTATTAAAATGTAAATAA
1 TTTATAAAAATGTAAATAA
1594897 TT
1 TT
1594899 ATTTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 1 0.06
19 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
TTTATAAAAATGTAAATAA
Found at i:1597396 original size:22 final size:21
Alignment explanation
Indices: 1597342--1597398 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1597332 ATTAATAATT
1597342 ATAA-TTAAATTTAAATAAAA
1 ATAATTTAAATTTAAATAAAA
** **
1597362 ATAATTTTTATTTACTTAAATA
1 ATAATTTAAATTTAAATAAA-A
1597384 ATAATTTAAATTTAA
1 ATAATTTAAATTTAA
1597399 CTGATCCAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 4 0.14
21 11 0.39
22 13 0.46
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAATTTAAATTTAAATAAAA
Found at i:1598119 original size:29 final size:29
Alignment explanation
Indices: 1598073--1598141 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
1598063 CGAACACAAT
* *
1598073 ATGAAAA-ATAGTTAAAATA-TGACATGAC
1 ATGAAAATATAATTAAAATACAG-CATGAC
*
1598101 ATGAAAATATAATTAAAATACAGCCTGAC
1 ATGAAAATATAATTAAAATACAGCATGAC
1598130 ATGAAAAT-TAAT
1 ATGAAAATATAAT
1598142 ATGATTACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 11 0.31
29 24 0.67
30 1 0.03
ACGTcount: A:0.54, C:0.09, G:0.12, T:0.26
Consensus pattern (29 bp):
ATGAAAATATAATTAAAATACAGCATGAC
Found at i:1599828 original size:2 final size:2
Alignment explanation
Indices: 1599821--1599847 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1599811 TAACAGAAGA
1599821 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
1599848 AACATTTAAA
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:1602236 original size:20 final size:20
Alignment explanation
Indices: 1602211--1602252 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1602201 AATACGTTTG
1602211 ATTGATACAAAAATAATTTA
1 ATTGATACAAAAATAATTTA
1602231 ATTGATACAAAAATAATTTA
1 ATTGATACAAAAATAATTTA
1602251 AT
1 AT
1602253 AAATATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
ATTGATACAAAAATAATTTA
Found at i:1602696 original size:14 final size:15
Alignment explanation
Indices: 1602672--1602700 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1602662 AAAAAATAAT
1602672 ATTTAATAATTTTAA
1 ATTTAATAATTTTAA
1602687 ATTTAA-AATTTTAA
1 ATTTAATAATTTTAA
1602701 TATCTGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTAATAATTTTAA
Found at i:1604025 original size:32 final size:31
Alignment explanation
Indices: 1603972--1604055 Score: 82
Period size: 32 Copynumber: 2.6 Consensus size: 31
1603962 ATTATGAATG
*
1603972 TAATATAAATATATGAATATATTAA-ATTTATA
1 TAATAAAAAT-TATGAATATA-TAATATTTATA
*
1604004 TAATAAAAATTATTAACTATATAATATTTATA
1 TAATAAAAATTATGAA-TATATAATATTTATA
* *
1604036 TAAATAATAATT-TAAATATA
1 T-AATAAAAATTATGAATATA
1604056 ATTATATATG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
31 12 0.27
32 24 0.53
33 9 0.20
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (31 bp):
TAATAAAAATTATGAATATATAATATTTATA
Found at i:1604149 original size:6 final size:6
Alignment explanation
Indices: 1604103--1604145 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
1604093 AATAGAAGTT
*
1604103 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GATGGA G
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA G
1604146 ATGGGAAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.19, C:0.00, G:0.65, T:0.16
Consensus pattern (6 bp):
GGTGGA
Found at i:1608191 original size:11 final size:11
Alignment explanation
Indices: 1608169--1608199 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
1608159 TTAAATATGC
1608169 ATAAATATTCAT
1 ATAAA-ATTCAT
1608181 ATAAAATTCAT
1 ATAAAATTCAT
1608192 ATAAAATT
1 ATAAAATT
1608200 AAGCCAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (11 bp):
ATAAAATTCAT
Found at i:1611402 original size:29 final size:30
Alignment explanation
Indices: 1611369--1611438 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 30
1611359 TTTACCCCAC
*
1611369 TAAGCCCTTATACTTTTATT-GTATCTAAA
1 TAAGCCCTTATACTTTTATTAGTATCCAAA
* *
1611398 TAAGCCCTCATCCTTTTATTAGTATCCAAA
1 TAAGCCCTTATACTTTTATTAGTATCCAAA
1611428 TAAGCCCTTAT
1 TAAGCCCTTAT
1611439 TTCAAATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 18 0.50
30 18 0.50
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (30 bp):
TAAGCCCTTATACTTTTATTAGTATCCAAA
Found at i:1612471 original size:34 final size:34
Alignment explanation
Indices: 1612428--1612496 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1612418 CATGCAAGAA
1612428 CATACCGCCTTCACCTCCTGGGCATCCAACTATT
1 CATACCGCCTTCACCTCCTGGGCATCCAACTATT
1612462 CATACCGCCTTCACCTCCTGGGCATCCAACTATT
1 CATACCGCCTTCACCTCCTGGGCATCCAACTATT
1612496 C
1 C
1612497 TCTTGTCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.20, C:0.42, G:0.12, T:0.26
Consensus pattern (34 bp):
CATACCGCCTTCACCTCCTGGGCATCCAACTATT
Found at i:1615045 original size:14 final size:14
Alignment explanation
Indices: 1615012--1615051 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1615002 TATAATATTC
1615012 TAATTAT-TTTATA
1 TAATTATATTTATA
*
1615025 AATATTATATTTATA
1 TA-ATTATATTTATA
1615040 TAATTATATTTA
1 TAATTATATTTA
1615052 AAGTTGTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 1 0.04
14 15 0.65
15 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATTATATTTATA
Found at i:1615869 original size:101 final size:101
Alignment explanation
Indices: 1615682--1615885 Score: 336
Period size: 101 Copynumber: 2.0 Consensus size: 101
1615672 TGCCTCGATG
*
1615682 CATATAAGATAACCACAGCCTTATAATCAAGTCTAAGTCCAACCTCAAACTATTTCTTTCTTTTG
1 CATATAAGATAACCACAGCCTTATAATCAAGTCTAAGTCCAACCTCAAACTATTTCTTTCCTTTG
* * *
1615747 CATTTGCATGAGCTATGTGACCAAACTCCTCAGCTT
66 CATTTGCATAAGCTATATGACCAAACTCCTCAACTT
* *
1615783 CATATAAGATAACCCCAGCCTTATAGTCAAGTCTAAGTCCAACCTCAAACTATTTCTTTCCTTTG
1 CATATAAGATAACCACAGCCTTATAATCAAGTCTAAGTCCAACCTCAAACTATTTCTTTCCTTTG
* *
1615848 TATTTGCATAAGCTGTATGACCAAACTCCTCAACTT
66 CATTTGCATAAGCTATATGACCAAACTCCTCAACTT
1615884 CA
1 CA
1615886 GAAGCTTTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 95 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.32
Consensus pattern (101 bp):
CATATAAGATAACCACAGCCTTATAATCAAGTCTAAGTCCAACCTCAAACTATTTCTTTCCTTTG
CATTTGCATAAGCTATATGACCAAACTCCTCAACTT
Found at i:1616694 original size:33 final size:33
Alignment explanation
Indices: 1616651--1616715 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1616641 TTTGAAGCAA
1616651 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATGTC-TCATGTATCGATACAT
* *
1616684 TGTATGGATACAATGTCTCATGTATTGATACA
1 TGTATCGATACAATGTCTCATGTATCGATACA
1616716 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAATGTCTCATGTATCGATACAT
Found at i:1616967 original size:21 final size:22
Alignment explanation
Indices: 1616920--1616971 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1616910 ATTTTTACTT
*
1616920 AAAAACATTTGATTTAAAGTTC
1 AAAAACATTTGATTTAAAGCTC
1616942 AAAAACATTTG-TTTATAA-CTC
1 AAAAACATTTGATTTA-AAGCTC
*
1616963 TAAAACATT
1 AAAAACATT
1616972 CATTGATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.37
Consensus pattern (22 bp):
AAAAACATTTGATTTAAAGCTC
Found at i:1617909 original size:22 final size:22
Alignment explanation
Indices: 1617884--1617926 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1617874 TCTTTACATG
*
1617884 ATATAAATTATATACTATATAT
1 ATATAAATAATATACTATATAT
*
1617906 ATATAAATAATATATTATATA
1 ATATAAATAATATACTATATA
1617927 ATTTGTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATAAATAATATACTATATAT
Found at i:1618429 original size:13 final size:13
Alignment explanation
Indices: 1618411--1618435 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1618401 TTTTACAATT
1618411 TGTATCGATACAA
1 TGTATCGATACAA
1618424 TGTATCGATACA
1 TGTATCGATACA
1618436 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1618448 original size:19 final size:19
Alignment explanation
Indices: 1618424--1618476 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1618414 ATCGATACAA
*
1618424 TGTATCGATACATAAGT-TT
1 TGTATCGATACATAA-TCAT
*
1618443 TGTATCGATACACTTATCAT
1 TGTATCGATACA-TAATCAT
1618463 TGTATCGATACATA
1 TGTATCGATACATA
1618477 CAGGTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATAATCAT
Found at i:1624855 original size:18 final size:18
Alignment explanation
Indices: 1624832--1624870 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1624822 CCCGAAGGAT
1624832 GCTTTTTTCATTACTTTG
1 GCTTTTTTCATTACTTTG
1624850 GCTTTTTTCATTACTTTG
1 GCTTTTTTCATTACTTTG
1624868 GCT
1 GCT
1624871 CCAAAGACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (18 bp):
GCTTTTTTCATTACTTTG
Found at i:1625028 original size:32 final size:33
Alignment explanation
Indices: 1624976--1625046 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 33
1624966 TTTTATACTT
**
1624976 TATTTTTAAAAATTTACTAAGTGTCATCATTAA
1 TATTTTTAAAAATTTACTAAGTGTCATCACAAA
*
1625009 TATTTTT-AAAATTTCCTAAGTGTCATCACAAA
1 TATTTTTAAAAATTTACTAAGTGTCATCACAAA
1625041 TATTTT
1 TATTTT
1625047 GCTTTATGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 28 0.80
33 7 0.20
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (33 bp):
TATTTTTAAAAATTTACTAAGTGTCATCACAAA
Found at i:1625713 original size:21 final size:20
Alignment explanation
Indices: 1625660--1625717 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1625650 ATATATTTTG
1625660 CATTGTATTGATACATTACT
1 CATTGTATTGATACATTACT
*
1625680 CATTGTATTGATACATTGCT
1 CATTGTATTGATACATTACT
*
1625700 CATATGTATCGATACATT
1 CAT-TGTATTGATACATT
1625718 CAAGCATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (20 bp):
CATTGTATTGATACATTACT
Found at i:1636458 original size:23 final size:23
Alignment explanation
Indices: 1636427--1636470 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1636417 TGAATCGATT
*
1636427 TTTTTTAATTATATAATATATTA
1 TTTTGTAATTATATAATATATTA
*
1636450 TTTTGTAATTATATATTATAT
1 TTTTGTAATTATATAATATAT
1636471 AATTCATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTGTAATTATATAATATATTA
Found at i:1636505 original size:20 final size:20
Alignment explanation
Indices: 1636469--1636525 Score: 50
Period size: 19 Copynumber: 3.0 Consensus size: 20
1636459 TATATATTAT
*
1636469 ATAATTCATATCA-TATAAAA
1 ATAATT-ATATAATTATAAAA
*
1636489 ATAATTATATAATTAT-ATA
1 ATAATTATATAATTATAAAA
1636508 ATATATT-T-TAATTATAAA
1 ATA-ATTATATAATTATAAA
1636526 CAATTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 7 0.23
19 12 0.39
20 12 0.39
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAATTATATAATTATAAAA
Found at i:1637194 original size:16 final size:16
Alignment explanation
Indices: 1637173--1637209 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1637163 AATATTATAT
*
1637173 ATTTAAATTTTTTAAA
1 ATTTAAAATTTTTAAA
1637189 ATTTAAAATTTTTAAA
1 ATTTAAAATTTTTAAA
1637205 ATTTA
1 ATTTA
1637210 TCAATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTAAAATTTTTAAA
Found at i:1638820 original size:2 final size:2
Alignment explanation
Indices: 1638813--1638843 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1638803 GCTGAACTAA
1638813 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1638844 CTAAGCTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1648177 original size:32 final size:32
Alignment explanation
Indices: 1648141--1648204 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1648131 GTTCTCAAAA
1648141 GAACAAATAAATTATATTACATAGCATTCAAG
1 GAACAAATAAATTATATTACATAGCATTCAAG
1648173 GAACAAATAAATTATATTACATAGCATTCAAG
1 GAACAAATAAATTATATTACATAGCATTCAAG
1648205 ATTTTGAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.28
Consensus pattern (32 bp):
GAACAAATAAATTATATTACATAGCATTCAAG
Found at i:1648981 original size:15 final size:15
Alignment explanation
Indices: 1648961--1649020 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
1648951 ATTTAATTCG
1648961 ATAAATTTAATTTAT
1 ATAAATTTAATTTAT
*
1648976 ATAAATTAAATTTTAT
1 ATAAATTTAA-TTTAT
**
1648992 ATAAAATTTTAATAAAT
1 AT-AAA-TTTAATTTAT
1649009 ATAAATTTAATT
1 ATAAATTTAATT
1649021 AATTTAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
15 15 0.41
16 10 0.27
17 8 0.22
18 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAAATTTAATTTAT
Found at i:1648992 original size:16 final size:15
Alignment explanation
Indices: 1648961--1648996 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1648951 ATTTAATTCG
*
1648961 ATAAATTTAATTTAT
1 ATAAATTAAATTTAT
1648976 ATAAATTAAATTTTAT
1 ATAAATTAAA-TTTAT
1648992 ATAAA
1 ATAAA
1648997 ATTTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAAATTAAATTTAT
Found at i:1649051 original size:18 final size:19
Alignment explanation
Indices: 1648967--1649051 Score: 69
Period size: 17 Copynumber: 4.8 Consensus size: 19
1648957 TTCGATAAAT
1648967 TTAATTT-ATATAAA-TTA
1 TTAATTTAATATAAATTTA
* *
1648984 --AATTTTATATAAAATT-
1 TTAATTTAATATAAATTTA
*
1649000 TTAA-TAAATATAAATTTAA
1 TTAATTTAATATAAATTT-A
1649019 TTAATTTAATATAAATTT-
1 TTAATTTAATATAAATTTA
1649037 TT-ATTTAATTATAAA
1 TTAATTTAA-TATAAA
1649052 ATAATATTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
15 5 0.09
16 7 0.12
17 18 0.32
18 10 0.18
19 4 0.07
20 12 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAATTTAATATAAATTTA
Found at i:1649058 original size:48 final size:48
Alignment explanation
Indices: 1648961--1649058 Score: 110
Period size: 48 Copynumber: 2.0 Consensus size: 48
1648951 ATTTAATTCG
* * *
1648961 ATAAATTTAATTTATATAAATTAAATTTTATATAAAATTTTAATAAAT
1 ATAAATTTAATTAATATAAATTAAATTTTATATAAAATTATAAAAAAT
* **
1649009 ATAAATTTAATTAAT-TTAATATAAATTTT-TATTTAATTATAAAATAAT
1 ATAAATTTAATTAATATAAAT-TAAATTTTATATAAAATTATAAAA-AAT
1649057 AT
1 AT
1649059 TTTTATTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
47 15 0.36
48 27 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (48 bp):
ATAAATTTAATTAATATAAATTAAATTTTATATAAAATTATAAAAAAT
Found at i:1649906 original size:12 final size:12
Alignment explanation
Indices: 1649878--1649911 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1649868 ATATATAATT
1649878 TAAAAATAAA-A
1 TAAAAATAAATA
1649889 TAAAAATAAATA
1 TAAAAATAAATA
*
1649901 TTAAAATAAAT
1 TAAAAATAAAT
1649912 TTATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
TAAAAATAAATA
Found at i:1650135 original size:19 final size:19
Alignment explanation
Indices: 1650111--1650156 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1650101 TTTTAAAAAT
1650111 AAAATAAAAATAATTTAAC
1 AAAATAAAAATAATTTAAC
*
1650130 AAAATAAAAATAATTTAAT
1 AAAATAAAAATAATTTAAC
1650149 AAAATAAA
1 AAAATAAA
1650157 TTCTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAATAAAAATAATTTAAC
Found at i:1653158 original size:17 final size:17
Alignment explanation
Indices: 1653122--1653154 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1653112 CTTGAAAAAA
1653122 ATTTCATTAAAATATTT
1 ATTTCATTAAAATATTT
*
1653139 ATTTTATT-AAATATTT
1 ATTTCATTAAAATATTT
1653155 TATTAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTCATTAAAATATTT
Found at i:1654483 original size:6 final size:6
Alignment explanation
Indices: 1654472--1654501 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1654462 AAAAATACTT
*
1654472 TTATAA TTATAA TAATAA TTATAA TTATAA
1 TTATAA TTATAA TTATAA TTATAA TTATAA
1654502 AACTTTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TTATAA
Found at i:1654819 original size:3 final size:3
Alignment explanation
Indices: 1654811--1654857 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
1654801 AAAGTCAAAA
* * *
1654811 AAT AAT AAT AA- AAA AAT AACT AAT AAA AAT AAT AAA AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
1654856 AA
1 AA
1654858 AAGAGAGAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (3 bp):
AAT
Found at i:1654825 original size:15 final size:15
Alignment explanation
Indices: 1654807--1654851 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
1654797 ATCAAAAGTC
1654807 AAAAAATAATAAT-A
1 AAAAAATAATAATAA
1654821 AAAAAATAACTAATAA
1 AAAAAATAA-TAATAA
* *
1654837 AAATAATAAAAATAA
1 AAAAAATAATAATAA
1654852 TAATAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 9 0.33
15 9 0.33
16 9 0.33
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAAATAATAATAA
Found at i:1654835 original size:21 final size:21
Alignment explanation
Indices: 1654811--1654859 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
1654801 AAAGTCAAAA
*
1654811 AATAATAATAA-AAAAATAACT
1 AATAAAAATAATAAAAATAA-T
1654832 AATAAAAATAATAAAAATAAT
1 AATAAAAATAATAAAAATAAT
1654853 AATAAAA
1 AATAAAA
1654860 GAGAGAGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (21 bp):
AATAAAAATAATAAAAATAAT
Found at i:1654857 original size:15 final size:14
Alignment explanation
Indices: 1654782--1654851 Score: 65
Period size: 15 Copynumber: 4.9 Consensus size: 14
1654772 CTTAATTAAT
1654782 AAAA-AATAA-AAA
1 AAAATAATAATAAA
*
1654794 AAAATCAA-AAGTCAA
1 AAAAT-AATAA-TAAA
1654809 AAAATAATAATAAA
1 AAAATAATAATAAA
1654823 AAAATAACTAATAAA
1 AAAATAA-TAATAAA
*
1654838 AATAATAAAAATAA
1 AA-AATAATAATAA
1654852 TAATAAAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
12 4 0.08
13 2 0.04
14 14 0.29
15 23 0.48
16 5 0.10
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.17
Consensus pattern (14 bp):
AAAATAATAATAAA
Found at i:1655802 original size:54 final size:53
Alignment explanation
Indices: 1655736--1655840 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 53
1655726 ACAAGCTTTT
* *
1655736 AACAGCTTGCAGCTC-GCACGTCCCACGACTGACAGTAGCTTCCAGCCCACGTCC
1 AACAGCTTGCAGCACAGCA--TCCCACGACCGACAGTAGCTTCCAGCCCACGTCC
* *
1655790 AACAGTTTGCAGCACATGCATCCCACGACCGACAGTAGCTTTCAGCCCACG
1 AACAGCTTGCAGCACA-GCATCCCACGACCGACAGTAGCTTCCAGCCCACG
1655841 ACCAGCACCA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
54 42 0.93
56 3 0.07
ACGTcount: A:0.25, C:0.38, G:0.20, T:0.17
Consensus pattern (53 bp):
AACAGCTTGCAGCACAGCATCCCACGACCGACAGTAGCTTCCAGCCCACGTCC
Found at i:1656647 original size:27 final size:27
Alignment explanation
Indices: 1656608--1656662 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1656598 GATTTTATTG
1656608 ATTAAGGACTAAAATGTAAACAT-GAAA
1 ATTAAGGACTAAAATGTAAA-ATGGAAA
* * *
1656635 ATTAGGGATTAAATTGTAAAATGGAAA
1 ATTAAGGACTAAAATGTAAAATGGAAA
1656662 A
1 A
1656663 ATTTTGATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.25
Consensus pattern (27 bp):
ATTAAGGACTAAAATGTAAAATGGAAA
Found at i:1658454 original size:30 final size:30
Alignment explanation
Indices: 1658418--1658521 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
1658408 ATTAATTTAT
*
1658418 ATTAAAATTTTATTTAAAT-ATAAATTAAAA
1 ATTAAAAATTTATTT-AATCATAAATTAAAA
*
1658448 ATTAAAAATTTATTTTATCATAAATTAAAA
1 ATTAAAAATTTATTTAATCATAAATTAAAA
* * * * *
1658478 CTCAAAAAGTTATTT-TTTAT-AA-TAAAA
1 ATTAAAAATTTATTTAATCATAAATTAAAA
*
1658505 ATATAAAAATGTATTTA
1 AT-TAAAAATTTATTTA
1658522 CACTAATATA
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
27 6 0.10
28 12 0.20
29 5 0.08
30 37 0.62
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (30 bp):
ATTAAAAATTTATTTAATCATAAATTAAAA
Found at i:1659487 original size:11 final size:11
Alignment explanation
Indices: 1659447--1659502 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
1659437 GACATTATAA
*
1659447 AAAAATAAAAT
1 AAAAATAATAT
*
1659458 ATAAA-AATAT
1 AAAAATAATAT
*
1659468 -AATATAATAT
1 AAAAATAATAT
1659478 AAAAATAATAT
1 AAAAATAATAT
* *
1659489 AAATATGATAT
1 AAAAATAATAT
1659500 AAA
1 AAA
1659503 TATATAAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
9 2 0.06
10 9 0.25
11 25 0.69
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:1659503 original size:11 final size:10
Alignment explanation
Indices: 1659451--1659580 Score: 79
Period size: 9 Copynumber: 13.7 Consensus size: 10
1659441 TTATAAAAAA
1659451 ATAAA-ATAT
1 ATAAATATAT
*
1659460 AAAAATATA-
1 ATAAATATAT
1659469 ATATAATATA-
1 ATA-AATATAT
1659479 A-AAATA-AT
1 ATAAATATAT
1659487 ATAAATATGAT
1 ATAAATAT-AT
1659498 AT-AA-ATAT
1 ATAAATATAT
1659506 ATAAATAT-T
1 ATAAATATAT
* *
1659515 TTAAA-ATTT
1 ATAAATATAT
1659524 ATATAA-ATAT
1 ATA-AATATAT
1659534 A-AAATAT-T
1 ATAAATATAT
*
1659542 TTAAATATAATT
1 ATAAATAT-A-T
1659554 ATAAA-ATAT
1 ATAAATATAT
1659563 ATAAATATGAT
1 ATAAATAT-AT
1659574 ATAAATA
1 ATAAATA
1659581 CATAAATTAT
Statistics
Matches: 97, Mismatches: 7, Indels: 32
0.71 0.05 0.24
Matches are distributed among these distances:
7 1 0.01
8 14 0.14
9 39 0.40
10 23 0.24
11 15 0.15
12 5 0.05
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
ATAAATATAT
Found at i:1659509 original size:8 final size:8
Alignment explanation
Indices: 1659454--1659570 Score: 69
Period size: 8 Copynumber: 13.8 Consensus size: 8
1659444 TAAAAAAATA
*
1659454 AAATATAA
1 AAATATAT
1659462 AAATATAAT
1 AAATAT-AT
*
1659471 ATAATATAA
1 A-AATATAT
1659480 AAATAATAT
1 AAAT-ATAT
1659489 AAATATGATAT
1 -AA-AT-ATAT
1659500 AAATATAT
1 AAATATAT
*
1659508 AAATATTTT
1 AAATA-TAT
1659517 AAAATTTATAT
1 -AAA--TATAT
1659528 AAATATA-
1 AAATATAT
*
1659535 AAATATTT
1 AAATATAT
*
1659543 TAA-ATAT
1 AAATATAT
*
1659550 AATTATA-
1 AAATATAT
1659557 AAATATAT
1 AAATATAT
1659565 AAATAT
1 AAATAT
1659571 GATATAAATA
Statistics
Matches: 85, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
7 16 0.19
8 33 0.39
9 11 0.13
10 15 0.18
11 8 0.09
12 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (8 bp):
AAATATAT
Found at i:1659510 original size:55 final size:56
Alignment explanation
Indices: 1659440--1659579 Score: 142
Period size: 55 Copynumber: 2.5 Consensus size: 56
1659430 AAAATTGGAC
* * *
1659440 ATTATAAAAAAATAAA-ATATAAAAATATAATAT-AATATAAAAATAATATAAATATG
1 ATTATAAATATATAAATATATAAAAAT-TAATATAAATAT-AAAATAATATAAATATA
* * * * *
1659496 A-TATAAATATATAAATATTTTAAAATTTATATAAATATAAAATATTTTAAATATA
1 ATTATAAATATATAAATATATAAAAATTAATATAAATATAAAATAATATAAATATA
*
1659551 ATTATAAAATATATAAATATGATATAAAT
1 ATTAT-AAATATATAAATAT-ATAAAAAT
1659580 ACATAAATTA
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
55 32 0.47
56 17 0.25
57 14 0.21
58 5 0.07
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (56 bp):
ATTATAAATATATAAATATATAAAAATTAATATAAATATAAAATAATATAAATATA
Found at i:1659519 original size:28 final size:28
Alignment explanation
Indices: 1659462--1659570 Score: 125
Period size: 28 Copynumber: 3.9 Consensus size: 28
1659452 TAAAATATAA
* * *
1659462 AAATATAATAT-AATATAAAAATAATAT
1 AAATATAATATAAATATATAAATATTTT
*
1659489 AAATATGATATAAATATATAAATATTTT
1 AAATATAATATAAATATATAAATATTTT
*
1659517 AAA-ATTTATATAAATATA-AAATATTTT
1 AAATA-TAATATAAATATATAAATATTTT
1659544 AAATATAATTATAAAATATATAAATAT
1 AAATATAA-TAT-AAATATATAAATAT
1659571 GATATAAATA
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
27 25 0.36
28 32 0.46
29 7 0.10
30 6 0.09
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (28 bp):
AAATATAATATAAATATATAAATATTTT
Found at i:1659549 original size:22 final size:22
Alignment explanation
Indices: 1659496--1659578 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 22
1659486 TATAAATATG
1659496 ATATAAATATATAAATATTTTAAAA
1 ATATAAATATA-AAATATTTT--AA
1659521 TTTATATAAATATAAAATATTTTAA
1 ---ATATAAATATAAAATATTTTAA
* *
1659546 ATATAATTATAAAATA-TATAA
1 ATATAAATATAAAATATTTTAA
*
1659567 ATAT-GATATAAA
1 ATATAAATATAAA
1659579 TACATAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.12
21 8 0.16
22 15 0.29
25 2 0.04
27 9 0.18
28 11 0.22
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (22 bp):
ATATAAATATAAAATATTTTAA
Found at i:1659557 original size:48 final size:49
Alignment explanation
Indices: 1659496--1659617 Score: 110
Period size: 48 Copynumber: 2.5 Consensus size: 49
1659486 TATAAATATG
* * *
1659496 ATATAAATATATAAATATTTTAAAAT-TTATATAAATATA-AAATATTTTAA
1 ATAT-AAT-TATAAATATTTTAAAATATGATATAAATACATAAAT-TATTAA
*
1659546 ATATAATTATAAA-A-TATATAAATATGATATAAATACATAAATTATTAA
1 ATATAATTATAAATATTTTA-AAATATGATATAAATACATAAATTATTAA
*
1659594 AT-TTATTAATAAATAATTTTAAAA
1 ATATAATT-ATAAAT-ATTTTAAAA
1659618 AATATAAACA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
46 3 0.05
47 9 0.15
48 29 0.49
49 7 0.12
50 8 0.14
51 3 0.05
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (49 bp):
ATATAATTATAAATATTTTAAAATATGATATAAATACATAAATTATTAA
Found at i:1659961 original size:36 final size:35
Alignment explanation
Indices: 1659882--1659962 Score: 83
Period size: 36 Copynumber: 2.2 Consensus size: 35
1659872 AAATAATTTA
* * **
1659882 TTATATTTTAAAATATTTTTATATTATTTTATTTAT
1 TTATA-TTTAAAATATTTTAATATTATATTATAAAT
1659918 TTGATATTTAAAA-ATTTTAAATATTAATATTATAAAT
1 TT-ATATTTAAAATATTTT-AATATT-ATATTATAAAT
1659955 TTATATTT
1 TTATATTT
1659963 GATATTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
35 5 0.13
36 20 0.53
37 13 0.34
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (35 bp):
TTATATTTAAAATATTTTAATATTATATTATAAAT
Found at i:1662624 original size:2 final size:2
Alignment explanation
Indices: 1662619--1662651 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1662609 AATATGAGCA
1662619 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 A
1662652 AGGATTCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1662719 original size:13 final size:13
Alignment explanation
Indices: 1662701--1662725 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1662691 ATTTTACATA
1662701 TTTATATAATTTT
1 TTTATATAATTTT
1662714 TTTATATAATTT
1 TTTATATAATTT
1662726 ATATTTTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTATATAATTTT
Found at i:1663263 original size:16 final size:17
Alignment explanation
Indices: 1663221--1663263 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
1663211 TTTAATATTT
*
1663221 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
1663238 ATAAAA-TTATAA-TAA
1 ATAAAATTTATAATTAA
1663253 ATAAAATTTAT
1 ATAAAATTTAT
1663264 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 9 0.38
16 9 0.38
17 6 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:1663698 original size:23 final size:23
Alignment explanation
Indices: 1663646--1663698 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
1663636 GAAACACGAA
* *
1663646 ATGAACACAACATAGAAAATAAT
1 ATGAATACAACATAAAAAATAAT
* *
1663669 -TAAAATACAGCATAAAAAATAAT
1 AT-GAATACAACATAAAAAATAAT
1663692 ATGAATA
1 ATGAATA
1663699 TAATACAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
22 1 0.04
23 21 0.91
24 1 0.04
ACGTcount: A:0.62, C:0.09, G:0.08, T:0.21
Consensus pattern (23 bp):
ATGAATACAACATAAAAAATAAT
Found at i:1664553 original size:58 final size:59
Alignment explanation
Indices: 1664474--1664586 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
1664464 CAATTTTTTT
* * *
1664474 AATTAAATCATTATAACAAATTATG-AAAAAATGTCACGAATTGAGATATGATACATTA
1 AATTAAATCATTATAAAAAATTATGTAAAAAATGTCACGAATGGAGATACGATACATTA
* * *
1664532 AATTAAATTATTA-AGAAAAATTATGTAAAATATGTCATGAATGGAGATACGATAC
1 AATTAAATCATTATA-AAAAATTATGTAAAAAATGTCACGAATGGAGATACGATAC
1664587 GAATATGACA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 1 0.02
58 21 0.45
59 25 0.53
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (59 bp):
AATTAAATCATTATAAAAAATTATGTAAAAAATGTCACGAATGGAGATACGATACATTA
Found at i:1665332 original size:8 final size:8
Alignment explanation
Indices: 1665319--1665377 Score: 55
Period size: 8 Copynumber: 6.9 Consensus size: 8
1665309 AATACAAATA
1665319 TTTTTCTT
1 TTTTTCTT
1665327 TTTTTCTCCT
1 TTTTTCT--T
*
1665337 TTCTTTTTT
1 TT-TTTCTT
*
1665346 TTCTTTTTT
1 TT-TTTCTT
1665355 TTTTTCTT
1 TTTTTCTT
1665363 TTTTTCTT
1 TTTTTCTT
*
1665371 TCTTTCT
1 TTTTTCT
1665378 CTCCTGCCGA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
8 26 0.58
9 12 0.27
10 3 0.07
11 4 0.09
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1665341 original size:15 final size:14
Alignment explanation
Indices: 1665321--1665377 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 14
1665311 TACAAATATT
1665321 TTTCTTTTTTTCTCC
1 TTTCTTTTTTTCT-C
1665336 TTTCTTTTTTT-TC
1 TTTCTTTTTTTCTC
1665349 TTT-TTTTTTT-TC
1 TTTCTTTTTTTCTC
*
1665361 TTT-TTTTCTT-TC
1 TTTCTTTTTTTCTC
1665373 TTTCT
1 TTTCT
1665378 CTCCTGCCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
12 23 0.57
13 5 0.12
14 1 0.03
15 11 0.28
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTCTTTTTTTCTC
Found at i:1665348 original size:24 final size:22
Alignment explanation
Indices: 1665319--1665379 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 22
1665309 AATACAAATA
1665319 TTTTTCTTTTTTTCTCCTTTCTTT
1 TTTTTCTTTTTTTCT-CTTTC-TT
1665343 TTTTTCTTTTTTT-T-TTTCTT
1 TTTTTCTTTTTTTCTCTTTCTT
*
1665363 TTTTTCTTTCTTTCTCT
1 TTTTTCTTTTTTTCTCT
1665380 CCTGCCGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
20 14 0.41
21 5 0.15
22 1 0.03
23 1 0.03
24 13 0.38
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTCTTTTTTTCTCTTTCTT
Found at i:1665671 original size:27 final size:28
Alignment explanation
Indices: 1665620--1665672 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
1665610 ATATTTTAAA
* *
1665620 AATTAAAAAATAATATTAATTTTAATTT
1 AATTAAAAAATAATATAAATATTAATTT
*
1665648 AATTATAAAAT-ATATAAATATTAAT
1 AATTAAAAAATAATATAAATATTAAT
1665673 ATAAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
AATTAAAAAATAATATAAATATTAATTT
Found at i:1665672 original size:22 final size:23
Alignment explanation
Indices: 1665646--1665692 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1665636 TAATTTTAAT
1665646 TTAAT-TATAAAATA-TATAAATA
1 TTAATATA-AAAATATTATAAATA
*
1665668 TTAATATAAAAATATTTTAAATA
1 TTAATATAAAAATATTATAAATA
1665691 TT
1 TT
1665693 TTATTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAATATAAAAATATTATAAATA
Found at i:1665919 original size:2 final size:2
Alignment explanation
Indices: 1665912--1665947 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1665902 TTTGACTTCA
1665912 AT AT AT AT -T 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 A
1665948 ATTTCAAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1666408 original size:20 final size:20
Alignment explanation
Indices: 1666371--1666409 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1666361 AACTAATAAA
*
1666371 ATAAAATTATAATTATTATT
1 ATAAAATTATAATAATTATT
1666391 ATAAAA-TATATATAATTAT
1 ATAAAATTATA-ATAATTAT
1666410 ATTTTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAAAATTATAATAATTATT
Found at i:1666408 original size:29 final size:27
Alignment explanation
Indices: 1666375--1666434 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 27
1666365 AATAAAATAA
1666375 AATTATAATTATTAT-TATAAAATATATAT
1 AATTAT-ATT-TTATATATAAAATAT-TAT
1666404 AATTATATTTTATAATATAAAATATTAT
1 AATTATATTTTAT-ATATAAAATATTAT
1666432 AAT
1 AAT
1666435 AAAAATATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 4 0.14
28 9 0.31
29 16 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
AATTATATTTTATATATAAAATATTAT
Found at i:1666431 original size:15 final size:15
Alignment explanation
Indices: 1666390--1666442 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 15
1666380 TAATTATTAT
1666390 TATAAAATATATATAA
1 TATAAAATAT-TATAA
* *
1666406 T-T-ATATTTTATAA
1 TATAAAATATTATAA
1666419 TATAAAATATTATAA
1 TATAAAATATTATAA
1666434 TA-AAAATAT
1 TATAAAATAT
1666443 GATTTGAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
13 6 0.19
14 12 0.39
15 12 0.39
16 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAAAATATTATAA
Found at i:1666502 original size:19 final size:17
Alignment explanation
Indices: 1666473--1666520 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
1666463 TATTTTTAAA
1666473 AATTTTTATTTAAAATTT
1 AATTTTTATTTAAAA-TT
1666491 AATTTATTATTT-AAATT
1 AATTT-TTATTTAAAATT
1666508 AATTTTT-TTTAAA
1 AATTTTTATTTAAA
1666521 TTTTTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.11
16 4 0.14
17 7 0.25
18 8 0.29
19 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTTTTATTTAAAATT
Found at i:1666547 original size:18 final size:18
Alignment explanation
Indices: 1666524--1666560 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1666514 TTTTAAATTT
1666524 TTTTAAAAATTAAATAAA
1 TTTTAAAAATTAAATAAA
*
1666542 TTTTAAAATTTAAATAAA
1 TTTTAAAAATTAAATAAA
1666560 T
1 T
1666561 GTATCAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTTAAAAATTAAATAAA
Found at i:1667130 original size:18 final size:17
Alignment explanation
Indices: 1667099--1667135 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1667089 CAAAAGTTTC
1667099 TTTCTTTTCTTTTCTTT
1 TTTCTTTTCTTTTCTTT
*
1667116 TTTCTTTTTTCTTTCTTT
1 TTTCTTTTCT-TTTCTTT
1667134 TT
1 TT
1667136 GTTGTTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTCTTTTCTTTTCTTT
Found at i:1676118 original size:19 final size:20
Alignment explanation
Indices: 1676094--1676136 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1676084 TTCATCTAAT
1676094 AAAAAATAT-T-TTAATTATA
1 AAAAAATATATATTAA-TATA
1676113 AAAAAATATATATTAATATA
1 AAAAAATATATATTAATATA
1676133 AAAA
1 AAAA
1676137 TAAAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
20 9 0.41
21 4 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAATATATATTAATATA
Found at i:1676118 original size:21 final size:20
Alignment explanation
Indices: 1676094--1676141 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1676084 TTCATCTAAT
*
1676094 AAAAAATATTTTAATTATAAA
1 AAAAAATATATTAA-TATAAA
*
1676115 AAAATATATATTAATATAAA
1 AAAAAATATATTAATATAAA
1676135 AATAAAA
1 AA-AAAA
1676142 ATAAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATATATTAATATAAA
Found at i:1676137 original size:18 final size:19
Alignment explanation
Indices: 1676092--1676138 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
1676082 TATTCATCTA
*
1676092 ATAAAAA-ATATTTTAATT
1 ATAAAAATATATATTAATT
1676110 ATAAAAAAATATATATTAA-T
1 AT--AAAAATATATATTAATT
1676130 ATAAAAATA
1 ATAAAAATA
1676139 AAAATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 9 0.36
20 8 0.32
21 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAAAATATATATTAATT
Found at i:1676579 original size:2 final size:2
Alignment explanation
Indices: 1676572--1676601 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1676562 AAGTAAAGCT
1676572 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
1676602 GGAACTAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1677518 original size:21 final size:19
Alignment explanation
Indices: 1677493--1677538 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
1677483 TAAAATTTTT
1677493 TTAAATTCATCATAATATAAA
1 TTAAATTCATCA-AAT-TAAA
*
1677514 TTAAATTTATCAAATTAAA
1 TTAAATTCATCAAATTAAA
1677533 -TAAATT
1 TTAAATT
1677539 ATTTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 4 0.17
20 3 0.12
21 11 0.46
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (19 bp):
TTAAATTCATCAAATTAAA
Found at i:1678858 original size:33 final size:35
Alignment explanation
Indices: 1678742--1678858 Score: 120
Period size: 33 Copynumber: 3.5 Consensus size: 35
1678732 ATTAATTAAA
* * *
1678742 TTATTATTTAACATAAATATCATTTTAATAAT-TT
1 TTATTATTTAATATAAATATAATTTTAATTATATT
* * *
1678776 TTAATTATATAACAT--ATATAATTTTATTTATATT
1 TT-ATTATTTAATATAAATATAATTTTAATTATATT
1678810 TTATTATTTAATATAAATATAATTTTAATT-T-TT
1 TTATTATTTAATATAAATATAATTTTAATTATATT
1678843 TTATTA-TTAATTATAA
1 TTATTATTTAA-TATAA
1678859 CGACATATAT
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
32 4 0.06
33 36 0.51
34 7 0.10
35 24 0.34
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (35 bp):
TTATTATTTAATATAAATATAATTTTAATTATATT
Found at i:1679394 original size:18 final size:17
Alignment explanation
Indices: 1679355--1679398 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1679345 TTTTAAATTT
* *
1679355 ATTTAACATTTAAAAAT
1 ATTTAACATTCAAAAAC
*
1679372 GTTTACACATTCAAAAAC
1 ATTTA-ACATTCAAAAAC
1679390 ATTTAACAT
1 ATTTAACAT
1679399 ATTATTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (17 bp):
ATTTAACATTCAAAAAC
Found at i:1682716 original size:23 final size:23
Alignment explanation
Indices: 1682685--1682734 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1682675 TTTACTTACA
* * *
1682685 TATAATAGCGTAATTAGTTAAAT
1 TATAATAGCATAATTACTAAAAT
*
1682708 TATAGTAGCATAATTACTAAAAT
1 TATAATAGCATAATTACTAAAAT
1682731 TATA
1 TATA
1682735 TAAGTAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (23 bp):
TATAATAGCATAATTACTAAAAT
Found at i:1685501 original size:21 final size:21
Alignment explanation
Indices: 1685459--1685497 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1685449 TATTTTTATT
1685459 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
1685480 TAAATATTAA-TA-AAAATA
1 TAAAT-TTAATTATAAAATA
1685498 ATATTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:1685886 original size:20 final size:20
Alignment explanation
Indices: 1685854--1685893 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1685844 ATTTTTATTT
*
1685854 AAATTTAATTATAAATTATA
1 AAATTTAATTATAAAATATA
1685874 AAATATTAA-TATAAAATATA
1 AAAT-TTAATTATAAAATATA
1685894 TTTTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATTTAATTATAAAATATA
Found at i:1685944 original size:30 final size:30
Alignment explanation
Indices: 1685872--1685950 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 30
1685862 TTATAAATTA
* *
1685872 TAAAATATTAATATAAAATATATTTTTTAT
1 TAAATTATAAATATAAAATATATTTTTTAT
** * *
1685902 TATTTTATAAATATTAAATTTATTTTTTAAT
1 TAAATTATAAATATAAAATATATTTTTT-AT
1685933 TAAATTA-AAATA-AAAATA
1 TAAATTATAAATATAAAATA
1685951 AATATAACTA
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
29 4 0.11
30 27 0.71
31 7 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TAAATTATAAATATAAAATATATTTTTTAT
Found at i:1687122 original size:2 final size:2
Alignment explanation
Indices: 1687117--1687151 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1687107 TCTGTGAGTA
* *
1687117 TG TG TG TG CG TG TA TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1687152 ATAAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.03, G:0.46, T:0.49
Consensus pattern (2 bp):
TG
Found at i:1691635 original size:3 final size:3
Alignment explanation
Indices: 1691627--1691658 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1691617 CCCTTTTTCA
1691627 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1691659 ATGGGTACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1693102 original size:1 final size:1
Alignment explanation
Indices: 1693096--1693121 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1693086 AAGCCACGAG
1693096 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1693122 CACCTGTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1698888 original size:3 final size:3
Alignment explanation
Indices: 1698880--1698940 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
1698870 CTCCAACATG
1698880 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1698928 ATT ATT ACT ATT A
1 ATT ATT ATT ATT A
1698941 ATCTGCACTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1700250 original size:11 final size:11
Alignment explanation
Indices: 1700230--1700261 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1700220 ATTAATTTTA
*
1700230 TTATTATAATT
1 TTATTTTAATT
1700241 TTATTTTAATT
1 TTATTTTAATT
1700252 TTATTTTAAT
1 TTATTTTAAT
1700262 ATTTTAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTTTAATT
Found at i:1700351 original size:2 final size:2
Alignment explanation
Indices: 1700346--1700383 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1700336 TGGGGGGTCG
1700346 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1700384 GAAGATTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1700712 original size:29 final size:29
Alignment explanation
Indices: 1700656--1700712 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1700646 GTTTTAATAT
** *
1700656 CAAAAAATTATTTCATATTAAAAGAAAAC
1 CAAAAAATTAAATCATATTAAAAAAAAAC
1700685 CAAAAAATTAAAT-ATATTAAGAAAAAAA
1 CAAAAAATTAAATCATATTAA-AAAAAAA
1700713 GTTTTAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.65, C:0.07, G:0.04, T:0.25
Consensus pattern (29 bp):
CAAAAAATTAAATCATATTAAAAAAAAAC
Found at i:1701104 original size:24 final size:24
Alignment explanation
Indices: 1701070--1701117 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1701060 AAGCCCGTAA
*
1701070 CCCCCTTCCCTTCAACCCTGATGG
1 CCCCCTCCCCTTCAACCCTGATGG
*
1701094 CCCCCTCCCCTTCAACCTTGATGG
1 CCCCCTCCCCTTCAACCCTGATGG
1701118 TATAGAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.12, C:0.50, G:0.12, T:0.25
Consensus pattern (24 bp):
CCCCCTCCCCTTCAACCCTGATGG
Found at i:1702846 original size:20 final size:22
Alignment explanation
Indices: 1702804--1702850 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
1702794 TATTCTTATG
1702804 TTAT-TTTTTATATATAAAATT
1 TTATATTTTTATATATAAAATT
*
1702825 TTATATTTTTATA-AT-AATTT
1 TTATATTTTTATATATAAAATT
1702845 TTATAT
1 TTATAT
1702851 ATATAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 10 0.42
21 6 0.25
22 8 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATATTTTTATATATAAAATT
Found at i:1702846 original size:34 final size:35
Alignment explanation
Indices: 1702784--1702861 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 35
1702774 GTAAAAGAAA
** *
1702784 AAAATTTATATATTCTTATGTTATTTTTTATATAT
1 AAAATTTATATATTCTTATAATAATTTTTATATAT
*
1702819 AAAATTT-TATATTTTTATAATAATTTTTATATAT
1 AAAATTTATATATTCTTATAATAATTTTTATATAT
*
1702853 ATAATTTAT
1 AAAATTTAT
1702862 TTTATTTCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 29 0.78
35 8 0.22
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (35 bp):
AAAATTTATATATTCTTATAATAATTTTTATATAT
Found at i:1702864 original size:18 final size:18
Alignment explanation
Indices: 1702809--1702866 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 18
1702799 TTATGTTATT
*
1702809 TTTTATATATAAAATTTTA
1 TTTTATATATATAA-TTTA
*
1702828 TATTTTTATA-ATAA--T-
1 T-TTTATATATATAATTTA
1702843 TTTTATATATATAATTTA
1 TTTTATATATATAATTTA
1702861 TTTTAT
1 TTTTAT
1702867 TTCATGTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 11
0.69 0.07 0.24
Matches are distributed among these distances:
14 7 0.23
15 5 0.16
16 1 0.03
17 1 0.03
18 6 0.19
19 4 0.13
20 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATATATATAATTTA
Found at i:1704336 original size:44 final size:43
Alignment explanation
Indices: 1704288--1704423 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 43
1704278 ATATCAAATT
* *
1704288 TTTAAATATTTTAATTTTATTTAAATTTAATTAATTTATATAAA
1 TTTAAATATTTTAATTTTATTAAAATTTAATTAA-TAATATAAA
**
1704332 TTT--A-A-TTTAATTTT-TATAAAAAATAATTAATAATATAAA
1 TTTAAATATTTTAATTTTAT-TAAAATTTAATTAATAATATAAA
* *
1704371 TTTAAAATAATTTAAATTTA--AAATATTTAACTTAATAATATAAA
1 TTT-AAATATTTTAATTTTATTAAA-ATTTAA-TTAATAATATAAA
1704415 TTTAAATAT
1 TTTAAATAT
1704424 AAAATAATCT
Statistics
Matches: 75, Mismatches: 8, Indels: 19
0.74 0.08 0.19
Matches are distributed among these distances:
39 12 0.16
40 20 0.27
41 1 0.01
42 5 0.07
43 10 0.13
44 27 0.36
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (43 bp):
TTTAAATATTTTAATTTTATTAAAATTTAATTAATAATATAAA
Found at i:1704349 original size:20 final size:20
Alignment explanation
Indices: 1704297--1704351 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1704287 TTTTAAATAT
*
1704297 TTTAATTTTATTTAAATTTAA
1 TTTAATTTT-TATAAATTTAA
*
1704318 -TTAATTTATATAAATTTAA
1 TTTAATTTTTATAAATTTAA
1704337 TTTAATTTTTATAAA
1 TTTAATTTTTATAAA
1704352 AAATAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATTTTTATAAATTTAA
Found at i:1704361 original size:20 final size:19
Alignment explanation
Indices: 1704315--1704362 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1704305 TATTTAAATT
**
1704315 TAATTAATTTATATAAATT
1 TAATTAATTTATATAAAAA
*
1704334 TAATTTAATTTTTATAAAAAA
1 TAA-TTAATTTATAT-AAAAA
1704355 TAATTAAT
1 TAATTAAT
1704363 AATATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.12
20 15 0.62
21 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATTAATTTATATAAAAA
Found at i:1704379 original size:16 final size:16
Alignment explanation
Indices: 1704360--1704468 Score: 114
Period size: 16 Copynumber: 6.8 Consensus size: 16
1704350 AAAAATAATT
*
1704360 AATAATATAAATTTAA
1 AATAATTTAAATTTAA
1704376 AATAATTTAAATTTAA
1 AATAATTTAAATTTAA
*
1704392 AAT-ATTTAACTTAATAA
1 AATAATTTAAATT--TAA
* *
1704409 TATAAATTTAAATATAA
1 AAT-AATTTAAATTTAA
*
1704426 AATAATCTAAATTTAA
1 AATAATTTAAATTTAA
*
1704442 AATAATTTAAATTTTA
1 AATAATTTAAATTTAA
*
1704458 TA-AATTTAAAT
1 AATAATTTAAAT
1704469 ATTTAAATCC
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
15 17 0.22
16 44 0.56
17 10 0.13
19 7 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATTTAAATTTAA
Found at i:1704382 original size:39 final size:41
Alignment explanation
Indices: 1704303--1704425 Score: 114
Period size: 39 Copynumber: 3.0 Consensus size: 41
1704293 ATATTTTAAT
* **
1704303 TTTATTT-AAAT-T-TAATTAATTTATATAAATTTAATTTAA
1 TTTATTTAAAATATATAATTAA-TAATATAAATTTAAAATAA
1704342 TTT-TTATAAAA-A-ATAATTAATAATATAAATTTAAAATAA
1 TTTATT-TAAAATATATAATTAATAATATAAATTTAAAATAA
*
1704381 TTTAAATTTAAAATATTTAACTTAATAATATAAATTTAAATATAA
1 TTT--ATTTAAAATATATAA-TTAATAATATAAATTTAAA-ATAA
1704426 AATAATCTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
38 2 0.03
39 23 0.33
40 10 0.14
41 5 0.07
42 3 0.04
43 3 0.04
44 19 0.28
45 4 0.06
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (41 bp):
TTTATTTAAAATATATAATTAATAATATAAATTTAAAATAA
Found at i:1704427 original size:50 final size:47
Alignment explanation
Indices: 1704367--1704470 Score: 138
Period size: 50 Copynumber: 2.1 Consensus size: 47
1704357 ATTAATAATA
* * *
1704367 TAAATTTAAAATAATTTAAATTTAAAAT-ATTTAACTTAATAATATAAATT
1 TAAATATAAAATAATCTAAATTTAAAATAATTTAAATT--T--TATAAATT
1704417 TAAATATAAAATAATCTAAATTTAAAATAATTTAAATTTTATAAATT
1 TAAATATAAAATAATCTAAATTTAAAATAATTTAAATTTTATAAATT
1704464 TAAATAT
1 TAAATAT
1704471 TTAAATCCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
47 15 0.30
49 1 0.02
50 26 0.52
51 8 0.16
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (47 bp):
TAAATATAAAATAATCTAAATTTAAAATAATTTAAATTTTATAAATT
Found at i:1704616 original size:13 final size:13
Alignment explanation
Indices: 1704598--1704643 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
1704588 GACATGATAT
1704598 TATAATATATAAA
1 TATAATATATAAA
*
1704611 TATAATATATCTAA
1 TATAATATAT-AAA
1704625 TA-AATATA-AAA
1 TATAATATATAAA
1704636 -ATAATATA
1 TATAATATA
1704644 ATTAACATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 1 0.03
11 8 0.28
13 16 0.55
14 4 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
TATAATATATAAA
Found at i:1707371 original size:2 final size:2
Alignment explanation
Indices: 1707364--1707388 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1707354 TGATTTCAAA
1707364 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1707389 TTTAATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1707666 original size:15 final size:15
Alignment explanation
Indices: 1707646--1707679 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1707636 TAGATAAATT
1707646 TTTAAATATT-TATTA
1 TTTAAAT-TTATATTA
1707661 TTTAAATTTATATTA
1 TTTAAATTTATATTA
1707676 TTTA
1 TTTA
1707680 TATAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAAATTTATATTA
Found at i:1708426 original size:47 final size:47
Alignment explanation
Indices: 1708372--1708464 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
1708362 CCACCCTATT
** *
1708372 GCATATTTTTTTGATTATACGTAAATCTTTTC-GATAATAAATTCAAC
1 GCATATTTCCTTGATTATACGTAAATC-TTTCAAATAATAAATTCAAC
* **
1708419 GCATATTTCCTTGATTATTCGTATTTCTTTCAAATAATAAATTCAA
1 GCATATTTCCTTGATTATACGTAAATCTTTCAAATAATAAATTCAA
1708465 TAATAAGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 4 0.10
47 35 0.90
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (47 bp):
GCATATTTCCTTGATTATACGTAAATCTTTCAAATAATAAATTCAAC
Found at i:1712544 original size:72 final size:72
Alignment explanation
Indices: 1712428--1712581 Score: 211
Period size: 72 Copynumber: 2.1 Consensus size: 72
1712418 CATTCATCAG
* * * * *
1712428 CAGCTCCTGTACAATCCCCTGGTTGGCAAGCACTTCAAGCCCATGTCATGGGGCATGGCTTGCAA
1 CAGCTCCTGCACAATCCCCTGGGTGGCAACCACTTCAAGACCATGTCATCGGGCATGGCTTGCAA
*
1712493 TATTCAT
66 CATTCAT
1712500 CAGCTCCTGCACAATCCCC-GAGGTGGCAACCACTTCAAGACCATGTCATCGGGCATGGCTTGCA
1 CAGCTCCTGCACAATCCCCTG-GGTGGCAACCACTTCAAGACCATGTCATCGGGCATGGCTTGCA
* *
1712564 GCATTTAT
65 ACATTCAT
*
1712572 CAGCCCCTGC
1 CAGCTCCTGC
1712582 GTGGCAAGCA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
71 1 0.01
72 71 0.99
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.23
Consensus pattern (72 bp):
CAGCTCCTGCACAATCCCCTGGGTGGCAACCACTTCAAGACCATGTCATCGGGCATGGCTTGCAA
CATTCAT
Found at i:1712634 original size:60 final size:60
Alignment explanation
Indices: 1712522--1712635 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
1712512 AATCCCCGAG
* *
1712522 GTGGCAACCACTTCAAGACCATGTCATCGGGCATGGCTTGCAGCATTTATCAGCCCCTGC
1 GTGGCAACCACGTCAAGACCATGTCATCGGGCATGGCTTGCAGCATTCATCAGCCCCTGC
* *
1712582 GTGGCAAGCACGTCAAG-CTCATGTCAT-GGGCCATGGCTTGCTAG-GTTCATCAGC
1 GTGGCAACCACGTCAAGAC-CATGTCATCGGG-CATGGCTTGC-AGCATTCATCAGC
1712636 TCCTTCACAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
59 4 0.09
60 41 0.87
61 2 0.04
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.24
Consensus pattern (60 bp):
GTGGCAACCACGTCAAGACCATGTCATCGGGCATGGCTTGCAGCATTCATCAGCCCCTGC
Found at i:1712680 original size:132 final size:132
Alignment explanation
Indices: 1712443--1712696 Score: 336
Period size: 132 Copynumber: 1.9 Consensus size: 132
1712433 CCTGTACAAT
* * *
1712443 CCCCTGGTTGGCAAGCACTTCAAGCCCATGTCATGGGGCATGGCTTGCAATATTCATCAGCTCCT
1 CCCCTGGTTGGCAAGCACGTCAAGCCCATGTCATGGGCCATGGCTTGCAAGATTCATCAGCTCCT
* *
1712508 GCACAATCCCCGAGGTGGCAACCACTTCAAGACCATGTCATCGGG-CATGGCTTGCAGCATTTAT
66 GCACAATCCCCGAGGTGGCAACCACTTCAAGACCAGGTCAT-GGGCCACGGCTTGCAGCATTTAT
1712572 CAG
130 CAG
* * *
1712575 CCCCTGCG-TGGCAAGCACGTCAAGCTCATGTCATGGGCCATGGCTTGCTAGGTTCATCAGCTCC
1 CCCCTG-GTTGGCAAGCACGTCAAGCCCATGTCATGGGCCATGGCTTGCAAGATTCATCAGCTCC
* * * *
1712639 TTCACATTCCCCTG-GTTGGCAAGCACTTCAAG-CTCAGGTCATGGGCCACGGCTTGCAG
65 TGCACAATCCCC-GAGGTGGCAACCACTTCAAGAC-CAGGTCATGGGCCACGGCTTGCAG
1712697 TATTCTTCTA
Statistics
Matches: 106, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
131 4 0.04
132 100 0.94
133 2 0.02
ACGTcount: A:0.20, C:0.31, G:0.25, T:0.24
Consensus pattern (132 bp):
CCCCTGGTTGGCAAGCACGTCAAGCCCATGTCATGGGCCATGGCTTGCAAGATTCATCAGCTCCT
GCACAATCCCCGAGGTGGCAACCACTTCAAGACCAGGTCATGGGCCACGGCTTGCAGCATTTATC
AG
Found at i:1716022 original size:24 final size:23
Alignment explanation
Indices: 1715992--1716056 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 23
1715982 CTTGACTTAT
1715992 TTATTTTTTAATTATATAATATA
1 TTATTTTTTAATTATATAATATA
1716015 TTA-TTTTT-ATT-TAT-ATATA
1 TTATTTTTTAATTATATAATATA
*
1716034 TTATTTAATTTAAATATATAATA
1 TTATTT--TTTAATTATATAATA
1716057 ATAATAACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
19 8 0.23
20 5 0.14
21 3 0.09
22 8 0.23
23 5 0.14
24 3 0.09
25 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTATTTTTTAATTATATAATATA
Found at i:1716045 original size:22 final size:21
Alignment explanation
Indices: 1715993--1716053 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 21
1715983 TTGACTTATT
*
1715993 TATTTTTTAA-TTATATAATA
1 TATTATTTAATTTATATAATA
*
1716013 TATTA-TT--TTTATTTATATA
1 TATTATTTAATTTATATA-ATA
*
1716032 TATTATTTAATTTAAAT-ATA
1 TATTATTTAATTTATATAATA
1716052 TA
1 TA
1716054 ATAATAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
18 6 0.19
19 10 0.31
20 11 0.34
22 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTATTTAATTTATATAATA
Found at i:1716050 original size:18 final size:18
Alignment explanation
Indices: 1715993--1716052 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
1715983 TTGACTTATT
*
1715993 TATTTTTTAATTATATAATA
1 TATTATTTAATT-TA-AATA
* *
1716013 TATTATTTTTATTTATATA
1 TATTA-TTTAATTTAAATA
1716032 TATTATTTAATTTAAATA
1 TATTATTTAATTTAAATA
1716050 TAT
1 TAT
1716053 AATAATAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 14 0.41
19 8 0.24
20 6 0.18
21 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTATTTAATTTAAATA
Found at i:1717222 original size:39 final size:39
Alignment explanation
Indices: 1717156--1717238 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
1717146 TATAAATATT
* * *
1717156 TTTAAAAATATTTTCATTATATCTAAATTCGAATTTTAA
1 TTTAAAAATATTTTCATTATATATAAATTCAAAATTTAA
* * * * *
1717195 TTTATAAATTTTTTTATTCTATATAAATTTAAAATTTAA
1 TTTAAAAATATTTTCATTATATATAAATTCAAAATTTAA
1717234 TTTAA
1 TTTAA
1717239 TTGATTCATA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (39 bp):
TTTAAAAATATTTTCATTATATATAAATTCAAAATTTAA
Found at i:1717961 original size:14 final size:15
Alignment explanation
Indices: 1717934--1717962 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1717924 TAGATAAGAT
1717934 ATCGATCTTAATTAA
1 ATCGATCTTAATTAA
1717949 ATCGATC-TAATTAA
1 ATCGATCTTAATTAA
1717963 TCAATTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (15 bp):
ATCGATCTTAATTAA
Found at i:1721728 original size:117 final size:117
Alignment explanation
Indices: 1721521--1721757 Score: 402
Period size: 117 Copynumber: 2.0 Consensus size: 117
1721511 CAGCTCGTAC
* *
1721521 CTTATTTATGTAATCACTTCCTCCATATGCGAAATCCAATTCACCAAGAGTATGGTTGAAAGAAT
1 CTTATTTATGTAATCACTTCCTCCACATGCGAAATCCAATTCACCAAAAGTATGGTTGAAAGAAT
*
1721586 AAACCACCGGCATTCAAGGTACCGCTGAACCAACAATGGAACATAGCTAATA
66 AAACCACCGGCATTCAAAGTACCGCTGAACCAACAATGGAACATAGCTAATA
* *
1721638 CTTATTTATGTAATCACTTCCTTCACATGCGAAATCCAATTCACCAAAAGTATGGTTGAGAGAAT
1 CTTATTTATGTAATCACTTCCTCCACATGCGAAATCCAATTCACCAAAAGTATGGTTGAAAGAAT
* * *
1721703 AAACTACCGGGATTCAAAGTGCCGCTGAACCAACAATGGAACATAGCTAATA
66 AAACCACCGGCATTCAAAGTACCGCTGAACCAACAATGGAACATAGCTAATA
1721755 CTT
1 CTT
1721758 TTCCAAGATC
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 112 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (117 bp):
CTTATTTATGTAATCACTTCCTCCACATGCGAAATCCAATTCACCAAAAGTATGGTTGAAAGAAT
AAACCACCGGCATTCAAAGTACCGCTGAACCAACAATGGAACATAGCTAATA
Found at i:1722201 original size:159 final size:159
Alignment explanation
Indices: 1721912--1722227 Score: 623
Period size: 159 Copynumber: 2.0 Consensus size: 159
1721902 TCGGTAAACA
1721912 AACGAAGAGTCGTCCTTCCATCCTCCAAAAAATGACTATGGATCAAATATACAAAAACTTAGCAC
1 AACGAAGAGTCGTCCTTCCATCCTCCAAAAAATGACTATGGATCAAATATACAAAAACTTAGCAC
1721977 ATTTGATAAAACTTCCTCTCCTTTCTCTCTTATAAAAGTTCAAATATCGAATAGTTTCTGCTATA
66 ATTTGATAAAACTTCCTCTCCTTTCTCTCTTATAAAAGTTCAAATATCGAATAGTTTCTGCTATA
1722042 ATTACCATGCAAGGGTTGACATCATGAAC
131 ATTACCATGCAAGGGTTGACATCATGAAC
1722071 AACGAAGAGTCGTCCTTCCATCCTCCAAAAAATGACTATGGATCAAATATACAAAAACTTAGCAC
1 AACGAAGAGTCGTCCTTCCATCCTCCAAAAAATGACTATGGATCAAATATACAAAAACTTAGCAC
*
1722136 ATTTGATAAACCTTCCTCTCCTTTCTCTCTTATAAAAGTTCAAATATCGAATAGTTTCTGCTATA
66 ATTTGATAAAACTTCCTCTCCTTTCTCTCTTATAAAAGTTCAAATATCGAATAGTTTCTGCTATA
1722201 ATTACCATGCAAGGGTTGACATCATGA
131 ATTACCATGCAAGGGTTGACATCATGA
1722228 CTTAATTTGC
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 156 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.30
Consensus pattern (159 bp):
AACGAAGAGTCGTCCTTCCATCCTCCAAAAAATGACTATGGATCAAATATACAAAAACTTAGCAC
ATTTGATAAAACTTCCTCTCCTTTCTCTCTTATAAAAGTTCAAATATCGAATAGTTTCTGCTATA
ATTACCATGCAAGGGTTGACATCATGAAC
Found at i:1723778 original size:18 final size:19
Alignment explanation
Indices: 1723757--1723792 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1723747 AATTATACTT
*
1723757 ATACAATATA-ATTAAATA
1 ATACAAAATAGATTAAATA
1723775 ATACAAAATAGATTAAAT
1 ATACAAAATAGATTAAAT
1723793 TATTTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (19 bp):
ATACAAAATAGATTAAATA
Found at i:1726626 original size:3 final size:3
Alignment explanation
Indices: 1726618--1726657 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1726608 TTATTTATGT
1726618 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1726658 AATCTAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1726678 original size:18 final size:19
Alignment explanation
Indices: 1726622--1726676 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 19
1726612 TTATGTATAA
*
1726622 TAATAATAATAATAATAATAA
1 TAATAATAATAATAA-AAT-C
1726643 TAATAATAATAATAAAATC
1 TAATAATAATAATAAAATC
1726662 TAAT-ATAAT-ATAAAA
1 TAATAATAATAATAAAA
1726677 ATTCATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 4 0.12
20 3 0.09
21 15 0.45
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAATAATAATAAAATC
Found at i:1727017 original size:45 final size:45
Alignment explanation
Indices: 1726938--1727027 Score: 103
Period size: 45 Copynumber: 2.0 Consensus size: 45
1726928 TAATTTTTTT
* *
1726938 AATTATTTAAATTTAAAATAATAAAAATACAAATACCAAAATAAA
1 AATTATTTAAAATTAAAATAATAAAAATACAAATAACAAAATAAA
* * *
1726983 AATTATTTCAAAATTCAAAT-ATAAATTATA-AAATAATAAAATAAA
1 AATTATTT-AAAATTAAAATAATAAA-AATACAAATAACAAAATAAA
1727028 TATATAATAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
45 26 0.68
46 12 0.32
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (45 bp):
AATTATTTAAAATTAAAATAATAAAAATACAAATAACAAAATAAA
Found at i:1729234 original size:20 final size:19
Alignment explanation
Indices: 1729192--1729232 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1729182 AACTCAAATT
1729192 AAATAAAGTAAATAAGTAA
1 AAATAAAGTAAATAAGTAA
*
1729211 AAATAAGAGTAAA-AGGTAA
1 AAATAA-AGTAAATAAGTAA
1729230 AAA
1 AAA
1729233 ATGTGTCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (19 bp):
AAATAAAGTAAATAAGTAA
Found at i:1733202 original size:21 final size:20
Alignment explanation
Indices: 1733155--1733208 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
1733145 CATTTGAGAC
*
1733155 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTA
1733175 ATGTATCGATACATTCACTA
1 ATGTATCGATACATTCACTA
1733195 ATTGTATCGATACA
1 A-TGTATCGATACA
1733209 AATCGTAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 20 0.62
21 12 0.38
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:1738422 original size:13 final size:13
Alignment explanation
Indices: 1738403--1738433 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1738393 ACAATTCATC
1738403 ATGTATCGATACA
1 ATGTATCGATACA
*
1738416 TTGTATCGATACA
1 ATGTATCGATACA
1738429 ATGTA
1 ATGTA
1738434 CCATGTATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1738428 original size:33 final size:33
Alignment explanation
Indices: 1738386--1738448 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1738376 TGAAGCAATA
*
1738386 TATCGATACAAT-TCATCATGTATCGATACATTG
1 TATCGATACAATGT-ACCATGTATCGATACATTG
1738419 TATCGATACAATGTACCATGTATCGATACA
1 TATCGATACAATGTACCATGTATCGATACA
1738449 AACAGTGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (33 bp):
TATCGATACAATGTACCATGTATCGATACATTG
Found at i:1738501 original size:20 final size:20
Alignment explanation
Indices: 1738476--1738534 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
1738466 TGCTGCCGGT
1738476 TTCATGTATCGATACAATTG
1 TTCATGTATCGATACAATTG
*
1738496 TTCATGTATCGATACAA-CG
1 TTCATGTATCGATACAATTG
**
1738515 AACATGTATCGATAC-ATTG
1 TTCATGTATCGATACAATTG
1738534 T
1 T
1738535 ATCGATATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 1 0.03
19 15 0.45
20 17 0.52
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (20 bp):
TTCATGTATCGATACAATTG
Found at i:1738522 original size:19 final size:20
Alignment explanation
Indices: 1738478--1738530 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
1738468 CTGCCGGTTT
* **
1738478 CATGTATCGATACAATTGTT
1 CATGTATCGATACAATCGAA
1738498 CATGTATCGATACAA-CGAA
1 CATGTATCGATACAATCGAA
1738517 CATGTATCGATACA
1 CATGTATCGATACA
1738531 TTGTATCGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATCGAA
Done.