Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 119 of 135
Found at i:43238060 original size:16 final size:16
Alignment explanation
Indices: 43238021--43238068 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
43238011 TTGAACCCTT
43238021 TTCTTTTTTTCTT-TC
1 TTCTTTTTTTCTTCTC
*
43238036 TTCTTTTTTTCTTCTG
1 TTCTTTTTTTCTTCTC
*
43238052 TTTTTTTTTTCTTCTC
1 TTCTTTTTTTCTTCTC
43238068 T
1 T
43238069 GCTGGGCCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (16 bp):
TTCTTTTTTTCTTCTC
Found at i:43238217 original size:19 final size:19
Alignment explanation
Indices: 43238168--43238218 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
43238158 TGGGCTGCTT
* *
43238168 CTTTCTTTTTTCTGCTCTG
1 CTTTGTTTTTTTTGCTCTG
*
43238187 CTTTGTTTTTTTTGCTTTG
1 CTTTGTTTTTTTTGCTCTG
43238206 CTATT-TTTTTTTT
1 CT-TTGTTTTTTTT
43238219 CGGGCCTGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 26 0.93
20 2 0.07
ACGTcount: A:0.02, C:0.16, G:0.10, T:0.73
Consensus pattern (19 bp):
CTTTGTTTTTTTTGCTCTG
Found at i:43238332 original size:10 final size:10
Alignment explanation
Indices: 43238317--43238384 Score: 73
Period size: 10 Copynumber: 6.7 Consensus size: 10
43238307 GCTTTTTCTC
43238317 TTTTCTTTTT
1 TTTTCTTTTT
43238327 TTTTCTTTTT
1 TTTTCTTTTT
43238337 TCTTTCTTTTT
1 T-TTTCTTTTT
* *
43238348 TTCTCTCTTT
1 TTTTCTTTTT
* * *
43238358 TTCTCCTTCT
1 TTTTCTTTTT
*
43238368 TTTTCTTTCT
1 TTTTCTTTTT
43238378 TTTTCTT
1 TTTTCTT
43238385 CCTTCTTCTC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
10 40 0.80
11 10 0.20
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:43238382 original size:22 final size:22
Alignment explanation
Indices: 43238308--43238391 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 22
43238298 GTTGATTTTG
* *
43238308 CTTTTTCTCTTTTCTTTTTTTTT
1 CTTTTTCTC-CTTCTTTTTCTTT
* *
43238331 CTTTTT-TCTTTCTTTTTTTCTCT
1 CTTTTTCTCCTTC--TTTTTCTTT
43238354 CTTTTTCTCCTTCTTTTTCTTT
1 CTTTTTCTCCTTCTTTTTCTTT
43238376 CTTTTTCTTCCTTCTT
1 CTTTTTC-TCCTTCTT
43238392 CTCCTTCTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.08
22 17 0.32
23 27 0.51
24 5 0.09
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (22 bp):
CTTTTTCTCCTTCTTTTTCTTT
Found at i:43238968 original size:30 final size:30
Alignment explanation
Indices: 43238932--43239067 Score: 134
Period size: 30 Copynumber: 4.6 Consensus size: 30
43238922 AAATACAGCA
* * *
43238932 AAAGTTTTGGGGCCGAAACGTAATTTAGAG
1 AAAGTTTAGGGGTCGAAAAGTAATTTAGAG
* * *
43238962 AAAGTTTAGGGGTTGAAAGGTAATTTTGAG
1 AAAGTTTAGGGGTCGAAAAGTAATTTAGAG
* *
43238992 AAAATTTAGGGGTC-AAAAGTAATTTATA-
1 AAAGTTTAGGGGTCGAAAAGTAATTTAGAG
* * *
43239020 AAAGTTTAGGGGTTGAAATGTAATTTCGAG
1 AAAGTTTAGGGGTCGAAAAGTAATTTAGAG
**
43239050 AAAGTACAGGGGTC-AAAA
1 AAAGTTTAGGGGTCGAAAA
43239068 TGCAATTTTT
Statistics
Matches: 85, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
28 12 0.14
29 25 0.29
30 48 0.56
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.29
Consensus pattern (30 bp):
AAAGTTTAGGGGTCGAAAAGTAATTTAGAG
Found at i:43239043 original size:58 final size:59
Alignment explanation
Indices: 43238951--43239067 Score: 173
Period size: 58 Copynumber: 2.0 Consensus size: 59
43238941 GGGCCGAAAC
* **
43238951 GTAATTTAGAGAAAGTTTAGGGGTTGAAAGGTAATTTTGAGAAAATTTAGGGGTCAAAA
1 GTAATTTAGAGAAAGTTTAGGGGTTGAAAGGTAATTTCGAGAAAATACAGGGGTCAAAA
* * *
43239010 GTAATTTATA-AAAGTTTAGGGGTTGAAATGTAATTTCGAGAAAGTACAGGGGTCAAAA
1 GTAATTTAGAGAAAGTTTAGGGGTTGAAAGGTAATTTCGAGAAAATACAGGGGTCAAAA
43239068 TGCAATTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
58 43 0.83
59 9 0.17
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.30
Consensus pattern (59 bp):
GTAATTTAGAGAAAGTTTAGGGGTTGAAAGGTAATTTCGAGAAAATACAGGGGTCAAAA
Found at i:43248534 original size:17 final size:17
Alignment explanation
Indices: 43248504--43248537 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43248494 ATTTAGATCA
**
43248504 TTTAAATTTTTAAAAAT
1 TTTAAATTAGTAAAAAT
43248521 TTTAAATTAGTAAAAAT
1 TTTAAATTAGTAAAAAT
43248538 AAAATGATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTAAATTAGTAAAAAT
Found at i:43250537 original size:8 final size:8
Alignment explanation
Indices: 43250524--43250565 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
43250514 ACAATTTTAA
43250524 ATAAAATT
1 ATAAAATT
43250532 ATAAAA-T
1 ATAAAATT
43250539 ATTAAAAATAT
1 A-T-AAAAT-T
43250550 ATAAAATT
1 ATAAAATT
43250558 ATAAAATT
1 ATAAAATT
43250566 TTATTTATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
7 2 0.07
8 16 0.53
9 9 0.30
10 1 0.03
11 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATAAAATT
Found at i:43251083 original size:20 final size:20
Alignment explanation
Indices: 43251058--43251106 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
43251048 CCTACAAAAT
43251058 TAAAAAT-ACAAATTTTAT-AA
1 TAAAAATAAC-AA-TTTATCAA
43251078 TAAAAATAACAATTTATCAA
1 TAAAAATAACAATTTATCAA
43251098 TAAAAATAA
1 TAAAAATAA
43251107 GAGCAGCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.19
20 20 0.74
21 2 0.07
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAAATAACAATTTATCAA
Found at i:43251587 original size:18 final size:18
Alignment explanation
Indices: 43251556--43251609 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
43251546 TTTAAATATG
*
43251556 TTTTTATTAATTTTATAA
1 TTTTTATAAATTTTATAA
* * *
43251574 TTTATTAGAATTTTTATTA
1 TTT-TTATAAATTTTATAA
43251593 TTTTTATAAATTTTATA
1 TTTTTATAAATTTTATA
43251610 TCAATTTTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTTATAAATTTTATAA
Found at i:43261625 original size:5 final size:5
Alignment explanation
Indices: 43261615--43261639 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
43261605 ACATGTCATC
43261615 ATTAA ATTAA ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA
43261640 TAATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTAA
Found at i:43262069 original size:29 final size:31
Alignment explanation
Indices: 43261998--43262082 Score: 115
Period size: 30 Copynumber: 2.8 Consensus size: 31
43261988 AGAAATCATC
43261998 AAAATTAATA-TTGAGTGGTAAAATTTAATTA
1 AAAATTAA-AGTTGAGTGGTAAAATTTAATTA
43262029 AAAATTAAAGTTGA-TGGTAAAATTTAA-T-
1 AAAATTAAAGTTGAGTGGTAAAATTTAATTA
*
43262057 AAAATTCAAAGTTTAGTGGTAAAATT
1 AAAATT-AAAGTTGAGTGGTAAAATT
43262083 CAATCATATA
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
28 6 0.12
29 8 0.16
30 24 0.48
31 12 0.24
ACGTcount: A:0.48, C:0.01, G:0.14, T:0.36
Consensus pattern (31 bp):
AAAATTAAAGTTGAGTGGTAAAATTTAATTA
Found at i:43262446 original size:10 final size:10
Alignment explanation
Indices: 43262422--43262456 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
43262412 ATTTTTTCTA
*
43262422 TTTTTCTAAT
1 TTTTTTTAAT
43262432 GTTTTTTTAAT
1 -TTTTTTTAAT
43262443 TTTTTTTAAT
1 TTTTTTTAAT
43262453 TTTT
1 TTTT
43262457 ATAATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (10 bp):
TTTTTTTAAT
Found at i:43273554 original size:24 final size:24
Alignment explanation
Indices: 43273503--43273556 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
43273493 ATGAACCAAA
* *
43273503 AAATAAAAATAATTAAAAGTTAGT
1 AAATAAAAATAATTAAAAGATAGG
*
43273527 AAATAAAAATAATTATAAA-ATCGG
1 AAATAAAAATAATTA-AAAGATAGG
43273551 AAATAA
1 AAATAA
43273557 TATATTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATAAAAATAATTAAAAGATAGG
Found at i:43277473 original size:16 final size:16
Alignment explanation
Indices: 43277454--43277488 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43277444 TCTAATCGGG
43277454 TCATTATAGGTTTAGA
1 TCATTATAGGTTTAGA
* *
43277470 TCATTTTAGGTTTTGA
1 TCATTATAGGTTTAGA
43277486 TCA
1 TCA
43277489 CTTTAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49
Consensus pattern (16 bp):
TCATTATAGGTTTAGA
Found at i:43277493 original size:16 final size:16
Alignment explanation
Indices: 43277460--43277493 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43277450 CGGGTCATTA
*
43277460 TAGGTTTAGATCATTT
1 TAGGTTTAGATCACTT
*
43277476 TAGGTTTTGATCACTT
1 TAGGTTTAGATCACTT
43277492 TA
1 TA
43277494 ATTGTATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.50
Consensus pattern (16 bp):
TAGGTTTAGATCACTT
Found at i:43280658 original size:3 final size:3
Alignment explanation
Indices: 43280640--43280674 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
43280630 TGTTTAGAAC
* *
43280640 AGA AGA TGA GGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
43280675 GTGCAGCTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:43280899 original size:2 final size:2
Alignment explanation
Indices: 43280894--43280924 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43280884 TGCATCTCTC
43280894 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43280925 AAGTTTAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43290390 original size:25 final size:25
Alignment explanation
Indices: 43290356--43290409 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
43290346 TTTTTTTTTC
43290356 ACTTGGTCCAAGATGATAAAAATAA
1 ACTTGGTCCAAGATGATAAAAATAA
43290381 ACTTGGTCCAAGATGATAAAAATAA
1 ACTTGGTCCAAGATGATAAAAATAA
43290406 ACTT
1 ACTT
43290410 TAATAGCACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (25 bp):
ACTTGGTCCAAGATGATAAAAATAA
Found at i:43291457 original size:22 final size:22
Alignment explanation
Indices: 43291428--43291472 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
43291418 TCTGGATGTG
*
43291428 ATTTTTTAAATAATCA-TTAAA
1 ATTTTTTTAATAATCATTTAAA
*
43291449 ATTTTTTTAATAATTATTTAAA
1 ATTTTTTTAATAATCATTTAAA
43291471 AT
1 AT
43291473 AAATTATGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTTTTTAATAATCATTTAAA
Found at i:43291713 original size:10 final size:10
Alignment explanation
Indices: 43291653--43291716 Score: 58
Period size: 10 Copynumber: 6.2 Consensus size: 10
43291643 AATTAATATT
43291653 TTTTTTATAA
1 TTTTTTATAA
*
43291663 TTTCTTATAA
1 TTTTTTATAA
* *
43291673 TTCTTAATAA
1 TTTTTTATAA
*
43291683 TTATTTA-AGTA
1 TTTTTTATA--A
43291694 TTTTTCTATAA
1 TTTTT-TATAA
43291705 TTTTTTATAA
1 TTTTTTATAA
43291715 TT
1 TT
43291717 ATCTAAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
9 1 0.02
10 28 0.65
11 11 0.26
12 2 0.05
13 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:43295826 original size:31 final size:30
Alignment explanation
Indices: 43295754--43295826 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
43295744 CTTTGATCTC
*
43295754 AATGACAAAACAATCACTCAACTTTCAGAA
1 AATGACAAATCAATCACTCAACTTTCAGAA
*
43295784 AATAACAAATCAATCACT-AACATTATC-GAA
1 AATGACAAATCAATCACTCAAC-TT-TCAGAA
43295814 AAGTGACAAATCA
1 AA-TGACAAATCA
43295827 GTCATCCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 3 0.08
30 23 0.62
31 11 0.30
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.21
Consensus pattern (30 bp):
AATGACAAATCAATCACTCAACTTTCAGAA
Found at i:43296569 original size:19 final size:20
Alignment explanation
Indices: 43296538--43296576 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
43296528 AATGATGATC
43296538 GATCATATTTCTCTTCAATT
1 GATCATATTTCTCTTCAATT
43296558 GATCAT-TTTCTCTTCAATT
1 GATCATATTTCTCTTCAATT
43296577 ATTTTGTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (20 bp):
GATCATATTTCTCTTCAATT
Found at i:43300460 original size:19 final size:19
Alignment explanation
Indices: 43300436--43300477 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
43300426 TGATATATTC
43300436 ATTTTTATG-TTATTTTATA
1 ATTTTTATGTTTATTTT-TA
*
43300455 ATTTTTTTGTTTATTTTTA
1 ATTTTTATGTTTATTTTTA
43300474 ATTT
1 ATTT
43300478 ATGTATTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (19 bp):
ATTTTTATGTTTATTTTTA
Found at i:43302109 original size:14 final size:16
Alignment explanation
Indices: 43302090--43302122 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
43302080 CCTCAATCTA
43302090 TTTTGTT-TTTGTT-T
1 TTTTGTTGTTTGTTGT
43302104 TTTTGTTGTTTGTTGT
1 TTTTGTTGTTTGTTGT
43302120 TTT
1 TTT
43302123 CACATTTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 6 0.35
16 4 0.24
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (16 bp):
TTTTGTTGTTTGTTGT
Found at i:43302435 original size:147 final size:148
Alignment explanation
Indices: 43302213--43302509 Score: 587
Period size: 147 Copynumber: 2.0 Consensus size: 148
43302203 ATAATATGTA
43302213 ATTACATTTCTATGATAAAAGAAAGTTGACTTAATTACTTTGAAATTTTATTATATATTTATATA
1 ATTACATTTCTATGATAAAAGAAAGTTGACTTAATTACTTTGAAATTTTATTATATATTTATATA
43302278 CACCCATTTTCTTTTAATCAAGTGATACCAATGTGTTAAAGGTAATAATATATATTATATACACA
66 CACCCATTTTCTTTTAATCAAGTGATACCAATGTGTTAAAGGTAATAATATATATTATATACACA
43302343 AACATAT-AATATATTTT
131 AACATATAAATATATTTT
43302360 ATTACATTTCTATGATAAAAGAAAGTTGACTTAATTACTTTGAAATTTTATTATATATTTATATA
1 ATTACATTTCTATGATAAAAGAAAGTTGACTTAATTACTTTGAAATTTTATTATATATTTATATA
43302425 CACCCATTTTCTTTTAATCAAGTGATACCAATGTGTTAAAGGTAATAATATATATTATATACACA
66 CACCCATTTTCTTTTAATCAAGTGATACCAATGTGTTAAAGGTAATAATATATATTATATACACA
43302490 AACATATAAATATATTTT
131 AACATATAAATATATTTT
43302508 AT
1 AT
43302510 ATAGATATAA
Statistics
Matches: 149, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
147 137 0.92
148 12 0.08
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (148 bp):
ATTACATTTCTATGATAAAAGAAAGTTGACTTAATTACTTTGAAATTTTATTATATATTTATATA
CACCCATTTTCTTTTAATCAAGTGATACCAATGTGTTAAAGGTAATAATATATATTATATACACA
AACATATAAATATATTTT
Found at i:43303189 original size:29 final size:27
Alignment explanation
Indices: 43303157--43303224 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
43303147 AGTGGACTTG
43303157 AAATTTTAAACCCTAAAAGTAAAGGGACT
1 AAATTTTAAA--CTAAAAGTAAAGGGACT
* * *
43303186 AAATTTCTGGAAGTAAAAGTAAATGGACT
1 AAATTT-T-AAACTAAAAGTAAAGGGACT
43303215 AAATTTTAAA
1 AAATTTTAAA
43303225 TGTAGAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 2 0.06
28 1 0.03
29 27 0.82
30 1 0.03
31 2 0.06
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.28
Consensus pattern (27 bp):
AAATTTTAAACTAAAAGTAAAGGGACT
Found at i:43304016 original size:92 final size:92
Alignment explanation
Indices: 43303859--43304043 Score: 271
Period size: 92 Copynumber: 2.0 Consensus size: 92
43303849 TGTACCGACC
* * * *
43303859 TATACAGGTTTGTAACACCCTCGACCCGACTTAGGACTTTCGGCTAAGTCGAAGGCGTTATATTG
1 TATACAAGTTTGTAACACCCTCGACCCGACTTAGGACTTTCAGCTAAGTCGAAGGCATTACATTG
* *
43303924 ATCACCGAAATGATCTTGTAAAGCCAT
66 ATCACCGAAATGATCCTATAAAGCCAT
* * * *
43303951 TATACAAGTTTGTAACACCCTCGACCCGGCTTAGGAGTTTCAGCTAGGTTGAAGGCATTACATTG
1 TATACAAGTTTGTAACACCCTCGACCCGACTTAGGACTTTCAGCTAAGTCGAAGGCATTACATTG
*
43304016 ATCACCGAAGTGATCCTATAAAGCCAT
66 ATCACCGAAATGATCCTATAAAGCCAT
43304043 T
1 T
43304044 CTTTTGCTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
92 82 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (92 bp):
TATACAAGTTTGTAACACCCTCGACCCGACTTAGGACTTTCAGCTAAGTCGAAGGCATTACATTG
ATCACCGAAATGATCCTATAAAGCCAT
Found at i:43304404 original size:3 final size:3
Alignment explanation
Indices: 43304396--43304429 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
43304386 TTGGAACTTT
43304396 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
43304430 ACGAGCAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:43306249 original size:19 final size:19
Alignment explanation
Indices: 43306203--43306240 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
43306193 GGGCCATACA
*
43306203 ACCGTGTGGAAATTCCTAG
1 ACCGTGTGGAAATGCCTAG
43306222 ACCGTGTGGAAATGCCTAG
1 ACCGTGTGGAAATGCCTAG
43306241 GCTGTGTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (19 bp):
ACCGTGTGGAAATGCCTAG
Found at i:43310454 original size:2 final size:2
Alignment explanation
Indices: 43310447--43310478 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
43310437 GCGTGAATTT
43310447 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
43310479 AACAAAGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43313995 original size:2 final size:2
Alignment explanation
Indices: 43313988--43314030 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
43313978 TTATTGTTAT
43313988 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
43314030 T
1 T
43314031 GTGGAGAGTT
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:43314409 original size:23 final size:24
Alignment explanation
Indices: 43314382--43314427 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
43314372 ATAGTTTTCG
43314382 AAAAT-ATTTTCTATTTT-TATTTA
1 AAAATAATTTT-TATTTTCTATTTA
43314405 AAAATAATTTTTATTTTCTATTT
1 AAAATAATTTTTATTTTCTATTT
43314428 TTTAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
AAAATAATTTTTATTTTCTATTTA
Found at i:43315099 original size:14 final size:14
Alignment explanation
Indices: 43315080--43315108 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
43315070 ATTCACCTTC
43315080 TTTTTTTTT-CTTT
1 TTTTTTTTTGCTTT
43315093 TTTTTTTTTGCTTT
1 TTTTTTTTTGCTTT
43315107 TT
1 TT
43315109 ATACAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.00, C:0.07, G:0.03, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTGCTTT
Found at i:43320871 original size:160 final size:160
Alignment explanation
Indices: 43320607--43320928 Score: 635
Period size: 160 Copynumber: 2.0 Consensus size: 160
43320597 GAAAACATTT
*
43320607 AAGTGATCATCTCGTTTTGCAGCGGAATTTACTAAGTTATAAGGTTTTGAAAACCGGGGTTTAAT
1 AAGTGATCATCTCGTTTTCCAGCGGAATTTACTAAGTTATAAGGTTTTGAAAACCGGGGTTTAAT
43320672 TTGCAACAAATCATTTTGCATACAGAATTATAATAGTACTTAATTCAAAAAAGTAAGTCAAAATG
66 TTGCAACAAATCATTTTGCATACAGAATTATAATAGTACTTAATTCAAAAAAGTAAGTCAAAATG
43320737 AAAAGTAAAGTCCAAAAGTCCGAAAAGTCA
131 AAAAGTAAAGTCCAAAAGTCCGAAAAGTCA
43320767 AAGTGATCATCTCGTTTTCCAGCGGAATTTACTAAGTTATAAGGTTTTGAAAACCGGGGTTTAAT
1 AAGTGATCATCTCGTTTTCCAGCGGAATTTACTAAGTTATAAGGTTTTGAAAACCGGGGTTTAAT
43320832 TTGCAACAAATCATTTTGCATACAGAATTATAATAGTACTTAATTCAAAAAAGTAAGTCAAAATG
66 TTGCAACAAATCATTTTGCATACAGAATTATAATAGTACTTAATTCAAAAAAGTAAGTCAAAATG
43320897 AAAAGTAAAGTCCAAAAGTCCGAAAAGTCA
131 AAAAGTAAAGTCCAAAAGTCCGAAAAGTCA
43320927 AA
1 AA
43320929 TTAAACATAA
Statistics
Matches: 161, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 161 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.29
Consensus pattern (160 bp):
AAGTGATCATCTCGTTTTCCAGCGGAATTTACTAAGTTATAAGGTTTTGAAAACCGGGGTTTAAT
TTGCAACAAATCATTTTGCATACAGAATTATAATAGTACTTAATTCAAAAAAGTAAGTCAAAATG
AAAAGTAAAGTCCAAAAGTCCGAAAAGTCA
Found at i:43324875 original size:44 final size:43
Alignment explanation
Indices: 43324808--43324929 Score: 129
Period size: 44 Copynumber: 2.7 Consensus size: 43
43324798 CTATCTACAG
* *
43324808 TCTGCTTCACTACAACTTTAGGGAGATAGGATTAATAGCTTCAA
1 TCTGCTCCACTACAACTTCAGGGAGATA-GATTAATAGCTTCAA
* * ** *
43324852 TCTGCTCCACTGCAACTTCAGGGAGATAAAGTTGGTATCTTCAA
1 TCTGCTCCACTACAACTTCAGGGAGATAGA-TTAATAGCTTCAA
43324896 -CGTGCTCCTACTACAACTTCAGGGAGATAAGATT
1 TC-TGCTCC-ACTACAACTTCAGGGAGAT-AGATT
43324930 TGTTATATTC
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
43 2 0.03
44 41 0.63
45 20 0.31
46 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (43 bp):
TCTGCTCCACTACAACTTCAGGGAGATAGATTAATAGCTTCAA
Found at i:43325002 original size:51 final size:50
Alignment explanation
Indices: 43324937--43325099 Score: 147
Period size: 51 Copynumber: 3.3 Consensus size: 50
43324927 ATTTGTTATA
* * * *
43324937 TTCAGTTTTGATCCGCTTCGCTGCAACGCCAGGGAAACAAGATTTGCTACC
1 TTCAGCTTTAATCCG-TTCGCTGCAACGCCAGGGAAATAAGATTTGCTGCC
* * *
43324988 TTTAGCTTTAATCCG-T-GC-G--ACACCAGGGAAAATAAGATTCGCTGCC
1 TTCAGCTTTAATCCGTTCGCTGCAACGCCAGGG-AAATAAGATTTGCTGCC
* * * * * *
43325034 TTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAGATAGGAGTTGCTGCC
1 TTCAGCTTTAATCCGTT-CGCTGCAACGCCAGGGAAATAAGATTTGCTGCC
43325085 TTCAGCTTTAATCCG
1 TTCAGCTTTAATCCG
43325100 CTCTACTTCA
Statistics
Matches: 88, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
45 8 0.09
46 27 0.31
47 2 0.02
48 2 0.02
49 2 0.02
50 1 0.01
51 39 0.44
52 7 0.08
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (50 bp):
TTCAGCTTTAATCCGTTCGCTGCAACGCCAGGGAAATAAGATTTGCTGCC
Found at i:43325164 original size:72 final size:72
Alignment explanation
Indices: 43325033--43325169 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 72
43325023 GATTCGCTGC
* * * * *
43325033 CTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAGATAGGAGTTGCTGCCTTCAGCTTTAATC
1 CTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAAACAAGAGTTGCTACCTTCAGCTTTAATC
43325098 CGCTCTA
66 CGCTCTA
* ** *
43325105 CTTCAGCTTTAATCTATTCCACTGCAATGCCCGGGAAACAAGA-TTCGCTACCTTTAGCTTTAAT
1 CTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAAACAAGAGTT-GCTACCTTCAGCTTTAAT
43325169 C
65 C
43325170 TGTTCCACTG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 2 0.04
72 53 0.96
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (72 bp):
CTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAAACAAGAGTTGCTACCTTCAGCTTTAATC
CGCTCTA
Found at i:43325403 original size:132 final size:132
Alignment explanation
Indices: 43325215--43325634 Score: 725
Period size: 132 Copynumber: 3.2 Consensus size: 132
43325205 GTCTTCAATA
*
43325215 TGCTCCACTACTGCTTAAGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGA
1 TGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGA
* *
43325280 GATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTAGGAAGATAAAATTCACCGTCTTTGA
66 GATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTAGGAAGATAAGATTCACCATCTTTGA
43325345 TC
131 TC
*
43325347 TGCTTCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGA
1 TGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGA
* *
43325412 GATAGGACTGGTGGCTCAAATCTGCTTCCCTACTACCTT-GGAAAGATAAGATTCACCATCATTG
66 GATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTAGG-AAGATAAGATTCACCATCTTTG
43325476 ATC
130 ATC
*
43325479 TGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTTAACCTACTCCACTGCTGCTCAGGGA
1 TGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGA
* * *
43325544 GATAAGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTAGGAAGATAAGATTCACCATTTTTTA
66 GATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTAGGAAGATAAGATTCACCATCTTTGA
43325609 TC
131 TC
*
43325611 TGCTCCACTACTGTTTAGGGAGAC
1 TGCTCCACTACTGCTTAGGGAGAC
43325635 TTCAATCCGC
Statistics
Matches: 272, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
131 2 0.01
132 268 0.99
133 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (132 bp):
TGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGA
GATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTAGGAAGATAAGATTCACCATCTTTGA
TC
Found at i:43326848 original size:8 final size:8
Alignment explanation
Indices: 43326824--43326867 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
43326814 TGGCCTCTCC
43326824 TTTTTCTTT
1 TTTTTC-TT
43326833 TCTTTTCTT
1 T-TTTTCTT
43326842 TTTTTC--
1 TTTTTCTT
43326848 TTTTTCTT
1 TTTTTCTT
43326856 TTTTTCTT
1 TTTTTCTT
43326864 TTTT
1 TTTT
43326868 AATTTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.19
8 17 0.53
9 4 0.12
10 5 0.16
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:43326854 original size:14 final size:14
Alignment explanation
Indices: 43326830--43326866 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
43326820 CTCCTTTTTC
43326830 TTTTC-TTTTCTTT
1 TTTTCTTTTTCTTT
43326843 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
43326857 TTTTCTTTTT
1 TTTTCTTTTT
43326867 TAATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTCTTTTTCTTT
Found at i:43326874 original size:14 final size:12
Alignment explanation
Indices: 43326824--43326867 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 12
43326814 TGGCCTCTCC
*
43326824 TTTTTCTTTTCT
1 TTTTTTTTTTCT
43326836 TTTCTTTTTTTCTT
1 TTT-TTTTTTTC-T
43326850 TTTCTTTTTTTCT
1 TTT-TTTTTTTCT
43326863 TTTTT
1 TTTTT
43326868 AATTTTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 5 0.17
13 11 0.38
14 13 0.45
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTTCT
Found at i:43326987 original size:14 final size:15
Alignment explanation
Indices: 43326964--43326996 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
43326954 ATCAATGCTT
*
43326964 TTCCAGATAAGG-CC
1 TTCCACATAAGGTCC
43326978 TTCCACATAAGGTCC
1 TTCCACATAAGGTCC
43326993 TTCC
1 TTCC
43326997 GAGTTTGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.27
Consensus pattern (15 bp):
TTCCACATAAGGTCC
Found at i:43330036 original size:19 final size:19
Alignment explanation
Indices: 43330012--43330056 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
43330002 TGTGAAAATC
*
43330012 TAATGCATATG-ATGCAAT
1 TAATGCAGATGCATGCAAT
*
43330030 GTAATGCAGATGCATGGAAT
1 -TAATGCAGATGCATGCAAT
43330050 TAATGCA
1 TAATGCA
43330057 AAAAGAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (19 bp):
TAATGCAGATGCATGCAAT
Found at i:43330557 original size:5 final size:5
Alignment explanation
Indices: 43330549--43330576 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
43330539 AAGCAATCAT
43330549 AAACA AAACA AAACA AAACA AAACA AAA
1 AAACA AAACA AAACA AAACA AAACA AAA
43330577 TACGTCAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:43338624 original size:8 final size:7
Alignment explanation
Indices: 43338597--43338623 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
43338587 CTAAAAATGA
43338597 AAAAAAG
1 AAAAAAG
43338604 AAAAAAG
1 AAAAAAG
43338611 AAAAAAG
1 AAAAAAG
43338618 AAAAAA
1 AAAAAA
43338624 AATGTATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:43343926 original size:658 final size:659
Alignment explanation
Indices: 43342014--43343998 Score: 3322
Period size: 643 Copynumber: 3.0 Consensus size: 659
43342004 ACAGATTGAT
* *
43342014 CAAATCTTAATTATCAAACTCAAAAATAATCAAAATTTGAACACTCGTTTTTCATAAATCCCAAT
1 CAAATCTTAATTATCAAACTCAAAAATAATCAAAATTTGAACGCTCTTTTTTCATAAATCCCAAT
43342079 TATCAAAGTTAACAAGAAATTCAATTTACTTAAAACATTTTTCAGAGAGATTTTTGAACCCAAAA
66 TATCAAAGTTAACAAGAAATTCAATTTACTTAAAACATTTTTCAGAGAGATTTTTGAACCCAAAA
43342144 ATCACAGTCCAAGTTTTGTAACTTGGTTTTGATACCACTAAATGTAACATCCCAAACCTGGCCTA
131 ATCACAGTCCAAGTTTTGTAACTTGGTTTTGATACCACTAAATGTAACATCCCAAACCTGGCCTA
43342209 AAAGTTATAATCGAATCTGGAGAAATTGCATCGACTCACT-TGGAAAATTGATTTCAGTAAGTGT
196 AAAGTTATAATCGAATCTGGAGAAATTGCATCGACTCACTCT-GAAAATTGATTTCAGTAAGTGT
* *** *
43342273 TAAGCAAATAAGACTTTCTCAAATAATCATTAGAAACCTATTTTTTCGCTTTTAGACATTTAGTT
260 TAAGC------G--------AAA-AA--A-TAGAAACCTATTTTTTCGCTTTCAGA-AACCACTT
**
43342338 TTGTAAATTACTTAATTTACAGCAAAAACCTTTTTAGGAGTTTTAGTTTTAAAAACCAAAATCTA
306 AAG-AAATTACTTAATTTACAGCAAAAACCTTTTTAGGAGTTTTAGTTTTAAAAACCAAAATCTA
43342403 TTTTATCGACTTAAGTGATTTTGCAGTCTCACGCTAGAAAATATCAATTACCGACGAATTAAGCA
370 TTTTATCGACTTAAGTGATTTTGCAGTCTCACGCTAGAAAATATCAATTACCGACGAATTAAGCA
43342468 AAACCCAAAACGAGTTTAGAAACAGATTACAAACCCAAAAGATCAAAACATATAATTATGGAATT
435 AAACCCAAAACGAGTTTAGAAACAGATTACAAACCCAAAAGATCAAAACATATAATTATGGAATT
43342533 CATTGTATTTACATTAAGTGCAAAAATAATCTAAGCTCCCACACGCTGTCCGATCCTAAGTCTGA
500 CATTGTATTTACATTAAGTGCAAAAATAATCTAAGCTCCCACACGCTGTCCGATCCTAAGTCTGA
43342598 GGTTTACCTGAACAGACAAAGATAAAACAAAGGGGTGAGCTATGAAGCTAATTGTATAACTAAAC
565 GGTTTACCTGAACAGACAAAGATAAAACAAAGGGGTGAGCTATGAAGCTAATTGTATAACTAAAC
43342663 TCAAACAAAGATCAAACAAAACACCATATA
630 TCAAACAAAGATCAAACAAAACACCATATA
* *
43342693 CAAATCTTATTTATCAAACTCAAAAATAATTAAAATTTGAACGCTCTTTTTTCATAAATCCCAAT
1 CAAATCTTAATTATCAAACTCAAAAATAATCAAAATTTGAACGCTCTTTTTTCATAAATCCCAAT
43342758 TATCAAAGTTAACAAGAAATTCAATTTACTTAAAACATTTTTCAGAGAGATTTTTGAACCCAAAA
66 TATCAAAGTTAACAAGAAATTCAATTTACTTAAAACATTTTTCAGAGAGATTTTTGAACCCAAAA
* *
43342823 ATCACAGTCCAAGTTTTGTAACTTGGTTTTGATGCAACTAAATGTAACATCCCAAACCTGGCCTA
131 ATCACAGTCCAAGTTTTGTAACTTGGTTTTGATACCACTAAATGTAACATCCCAAACCTGGCCTA
* *
43342888 AAAGTTATAATTGAATCTGGAGAAATTGAATCGACTCACTCTGAAAATTGATTTCAGTAA--G-T
196 AAAGTTATAATCGAATCTGGAGAAATTGCATCGACTCACTCTGAAAATTGATTTCAGTAAGTGTT
* *
43342950 ----G------T---AACCTACTTTTTCGCTTTCAGAAACCACTTAAGAAATTACTTAATTTGCA
261 AAGCGAAAAAATAGAAACCTATTTTTTCGCTTTCAGAAACCACTTAAGAAATTACTTAATTTACA
* *
43343002 GAAAAAACCTTTTTAGGAGTTGTAGTTTTAAAAACCAAAATCTATTTTATCGACTTAAGTGATTT
326 GCAAAAACCTTTTTAGGAGTTTTAGTTTTAAAAACCAAAATCTATTTTATCGACTTAAGTGATTT
*
43343067 TGCAGTCTCACGCTAGAAAATATCAATTACCAACGAATTAAGCAAAACCCAAAACGAGTTTAGAA
391 TGCAGTCTCACGCTAGAAAATATCAATTACCGACGAATTAAGCAAAACCCAAAACGAGTTTAGAA
43343132 ACAGATTACAAACCCAAAAGATCAAAACATATAATTATGGAATTCATTGTATTTACATTAAGTGC
456 ACAGATTACAAACCCAAAAGATCAAAACATATAATTATGGAATTCATTGTATTTACATTAAGTGC
43343197 AAAAATAATCTAAGCTCCCACACGCTGTCCGATCCTAAGTCTGAGGTTTACCTGAACAGACAAAG
521 AAAAATAATCTAAGCTCCCACACGCTGTCCGATCCTAAGTCTGAGGTTTACCTGAACAGACAAAG
* * *
43343262 ATAAAACAAAGGGGTGAGCTATAAAGCTAATTGTATAACTAAACTCAAACAAAGATAAAATAAAA
586 ATAAAACAAAGGGGTGAGCTATGAAGCTAATTGTATAACTAAACTCAAACAAAGATCAAACAAAA
43343327 CACCATATA
651 CACCATATA
* *
43343336 CAAATCTTAATTATCAAACTCAAAAATAATCAAAATATGAACGCTCTTTTTTCATAAACCCCAAT
1 CAAATCTTAATTATCAAACTCAAAAATAATCAAAATTTGAACGCTCTTTTTTCATAAATCCCAAT
43343401 TATCAAAG-TAACAAGAAATTCAATTTACTTAAAACATTTTTCAGAGAGATTTTTGAACCCAAAA
66 TATCAAAGTTAACAAGAAATTCAATTTACTTAAAACATTTTTCAGAGAGATTTTTGAACCCAAAA
* *
43343465 ATCACAGTCCAAGTTTCGTAGCTTGGTTTTGATACCACTAAATGTAACATCCCAAACCTGGCCTA
131 ATCACAGTCCAAGTTTTGTAACTTGGTTTTGATACCACTAAATGTAACATCCCAAACCTGGCCTA
* * *
43343530 AAAGTTATAACCGAATCTGGAGAATTTGCATTGACTCACTCTGAAAATTGATTTCAGTAAGTGTT
196 AAAGTTATAATCGAATCTGGAGAAATTGCATCGACTCACTCTGAAAATTGATTTCAGTAAGTGTT
*
43343595 AAGCGAAAAAATAGAAACCTATTTTTTCACTTTCAGAAACCACTTAAGAAATTACTTAATTTACA
261 AAGCGAAAAAATAGAAACCTATTTTTTCGCTTTCAGAAACCACTTAAGAAATTACTTAATTTACA
43343660 GCAAAAACCTTTTTAGGAGTTTTAGTTTTAAAAACCAAAATCTATTTTATCGACTTAAGTGATTT
326 GCAAAAACCTTTTTAGGAGTTTTAGTTTTAAAAACCAAAATCTATTTTATCGACTTAAGTGATTT
*
43343725 TGCAGTCTCACGCTAGAAAATATCAATTACCGATGAATTAAGCAAAACCCAAAACGAGTTTAGAA
391 TGCAGTCTCACGCTAGAAAATATCAATTACCGACGAATTAAGCAAAACCCAAAACGAGTTTAGAA
* * *
43343790 ACAAATTACAAACCCAAAAGACCAAAACATATAATTATGGAATTCATTGTATTTACACTAAGTGC
456 ACAGATTACAAACCCAAAAGATCAAAACATATAATTATGGAATTCATTGTATTTACATTAAGTGC
* *
43343855 AAAAATAATCTAAGCTCCCACACGCCGTCCGATCCTAAGTCTGAGGTTTACCTGAATAGACAAAG
521 AAAAATAATCTAAGCTCCCACACGCTGTCCGATCCTAAGTCTGAGGTTTACCTGAACAGACAAAG
43343920 ATAAAACAAAGGGGTGAGCTATGAAGCTAATTGTATAACTAAACTCAAACAAAGATCAAACAAAA
586 ATAAAACAAAGGGGTGAGCTATGAAGCTAATTGTATAACTAAACTCAAACAAAGATCAAACAAAA
43343985 CACCATATA
651 CACCATATA
43343994 CAAAT
1 CAAAT
43343999 AAGAGTAACA
Statistics
Matches: 1238, Mismatches: 51, Indels: 55
0.92 0.04 0.04
Matches are distributed among these distances:
642 172 0.14
643 413 0.33
644 6 0.00
645 21 0.02
648 1 0.00
649 1 0.00
655 1 0.00
658 374 0.30
666 1 0.00
676 1 0.00
677 1 0.00
679 245 0.20
680 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (659 bp):
CAAATCTTAATTATCAAACTCAAAAATAATCAAAATTTGAACGCTCTTTTTTCATAAATCCCAAT
TATCAAAGTTAACAAGAAATTCAATTTACTTAAAACATTTTTCAGAGAGATTTTTGAACCCAAAA
ATCACAGTCCAAGTTTTGTAACTTGGTTTTGATACCACTAAATGTAACATCCCAAACCTGGCCTA
AAAGTTATAATCGAATCTGGAGAAATTGCATCGACTCACTCTGAAAATTGATTTCAGTAAGTGTT
AAGCGAAAAAATAGAAACCTATTTTTTCGCTTTCAGAAACCACTTAAGAAATTACTTAATTTACA
GCAAAAACCTTTTTAGGAGTTTTAGTTTTAAAAACCAAAATCTATTTTATCGACTTAAGTGATTT
TGCAGTCTCACGCTAGAAAATATCAATTACCGACGAATTAAGCAAAACCCAAAACGAGTTTAGAA
ACAGATTACAAACCCAAAAGATCAAAACATATAATTATGGAATTCATTGTATTTACATTAAGTGC
AAAAATAATCTAAGCTCCCACACGCTGTCCGATCCTAAGTCTGAGGTTTACCTGAACAGACAAAG
ATAAAACAAAGGGGTGAGCTATGAAGCTAATTGTATAACTAAACTCAAACAAAGATCAAACAAAA
CACCATATA
Found at i:43346676 original size:21 final size:21
Alignment explanation
Indices: 43346649--43346703 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
43346639 GTAACTCGGT
*
43346649 CACATGGGCATGTGTCTCTTT
1 CACATGGGCATGTGTCTCTTC
* * *
43346670 CATATGGCCATGTGTTTCTTC
1 CACATGGGCATGTGTCTCTTC
*
43346691 CACACGGGCATGT
1 CACATGGGCATGT
43346704 ATATCTTGCA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (21 bp):
CACATGGGCATGTGTCTCTTC
Found at i:43349020 original size:3 final size:3
Alignment explanation
Indices: 43348965--43349002 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
43348955 CAAAAAAAAT
43348965 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
43349003 AAAAAATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:43354994 original size:15 final size:15
Alignment explanation
Indices: 43354972--43355014 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
43354962 TTACACATTT
43354972 TATTTTAGTCACTTA
1 TATTTTAGTCACTTA
*
43354987 -ATTTTTAGATCACTTT
1 TA-TTTTAG-TCACTTA
43355003 TATTTTAGTCAC
1 TATTTTAGTCAC
43355015 CGAAAGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
14 1 0.04
15 10 0.42
16 12 0.50
17 1 0.04
ACGTcount: A:0.26, C:0.14, G:0.07, T:0.53
Consensus pattern (15 bp):
TATTTTAGTCACTTA
Found at i:43355008 original size:16 final size:15
Alignment explanation
Indices: 43354969--43355014 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
43354959 TGTTTACACA
43354969 TTTTATTTTAGTCAC
1 TTTTATTTTAGTCAC
*
43354984 -TTAATTTTTAGATCAC
1 TTTTA-TTTTAG-TCAC
43355000 TTTTATTTTAGTCAC
1 TTTTATTTTAGTCAC
43355015 CGAAAGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 3 0.12
15 10 0.38
16 10 0.38
17 3 0.12
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTTATTTTAGTCAC
Found at i:43364004 original size:29 final size:29
Alignment explanation
Indices: 43363972--43364027 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
43363962 CACACGGACG
* * *
43363972 TGTGTCTGGCCATGTAGGCCACACGAGTA
1 TGTGTCTGGACATATAGACCACACGAGTA
*
43364001 TGTGTCTGGACGTATAGACCACACGAG
1 TGTGTCTGGACATATAGACCACACGAG
43364028 CTCGTCAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (29 bp):
TGTGTCTGGACATATAGACCACACGAGTA
Found at i:43371436 original size:10 final size:10
Alignment explanation
Indices: 43371421--43371496 Score: 61
Period size: 10 Copynumber: 7.6 Consensus size: 10
43371411 TTTAAAATAC
43371421 TTTTTTAAAA
1 TTTTTTAAAA
*
43371431 TTTTTTAAAT
1 TTTTTTAAAA
43371441 TTTTTTAAAA
1 TTTTTTAAAA
*
43371451 TACTTTTT-TAA
1 T--TTTTTAAAA
*
43371462 TTTTTT-TAA
1 TTTTTTAAAA
43371471 --TTTTAAAA
1 TTTTTTAAAA
43371479 TATTTTTAAAA
1 T-TTTTTAAAA
43371490 TATTTTT
1 T-TTTTT
43371497 TTAATTTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
7 4 0.07
8 2 0.04
9 8 0.14
10 19 0.34
11 18 0.32
12 5 0.09
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:43371465 original size:72 final size:70
Alignment explanation
Indices: 43371384--43371530 Score: 206
Period size: 72 Copynumber: 2.1 Consensus size: 70
43371374 ATAATAAATA
43371384 TTTTTATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTAAAATTT-TTTAAATTTTTTTA
1 TTTTTATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTAAAATTTGTTTAAA--TTTTTA
*
43371448 AAATACT
64 AAATAAT
* * ** *
43371455 TTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTAATTTTTGTTTTAATTTTTAA
1 TTTTT-ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTAAAATTTGTTTAAATTTTTAA
43371520 AATAAT
65 AATAAT
43371526 TTTTT
1 TTTTT
43371531 GGTATTTATT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
71 22 0.32
72 41 0.60
73 5 0.07
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (70 bp):
TTTTTATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTAAAATTTGTTTAAATTTTTAAA
ATAAT
Found at i:43371468 original size:11 final size:11
Alignment explanation
Indices: 43371399--43371497 Score: 70
Period size: 11 Copynumber: 9.5 Consensus size: 11
43371389 ATTTTTTTAA
* *
43371399 TTTTAAAATAC
1 TTTTTAAATAT
*
43371410 TTTTAAAATACT
1 TTTTTAAATA-T
43371422 TTTTTAAA-AT
1 TTTTTAAATAT
43371432 TTTTTAAAT-T
1 TTTTTAAATAT
43371442 TTTTTAAAATACT
1 TTTTT-AAATA-T
43371455 TTTTT-AAT-T
1 TTTTTAAATAT
43371464 TTTTT--A-A-
1 TTTTTAAATAT
*
43371471 TTTTAAAATAT
1 TTTTTAAATAT
*
43371482 TTTTAAAATAT
1 TTTTTAAATAT
43371493 TTTTT
1 TTTTT
43371498 TAATTTTTGT
Statistics
Matches: 74, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
7 4 0.05
8 1 0.01
9 7 0.09
10 16 0.22
11 33 0.45
12 7 0.09
13 6 0.08
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTTAAATAT
Found at i:43376726 original size:334 final size:334
Alignment explanation
Indices: 43376112--43376784 Score: 1339
Period size: 334 Copynumber: 2.0 Consensus size: 334
43376102 TCATATTGAC
43376112 GATGA-AGATCAGGCTATGCTATTATTGTGCTCTTTACCCCCTTCATATAAGTCTTTCAGGGGGA
1 GATGATAGATCAGGCTATGCTATTATTGTGCTCTTTACCCCCTTCATATAAGTCTTTCAGGGGGA
43376176 CCCTGATTTATGGTAGAGACAAACTCTCGTTTGAAAATGTGAAGGGTCATTTGTTGAGTAGAGAC
66 CCCTGATTTATGGTAGAGACAAACTCTCGTTTGAAAATGTGAAGGGTCATTTGTTGAGTAGAGAC
43376241 AAACTCGACAATGAGTTTGGTTTGGATAGCAAGGCAGATAGGCAAGCTTCTATTTTGTTAGCATC
131 AAACTCGACAATGAGTTTGGTTTGGATAGCAAGGCAGATAGGCAAGCTTCTATTTTGTTAGCATC
43376306 AAAGAAACGAGACAAAAGGTGTCGCTATTGTAAAAAGTTAGGTCACATCAAAGCAGATTGTTATA
196 AAAGAAACGAGACAAAAGGTGTCGCTATTGTAAAAAGTTAGGTCACATCAAAGCAGATTGTTATA
43376371 AACTGCAAAATAAAAGAATTGCTAAGAGTAATAAGGAAGATGTAGATGGTGCTAATTTGGCCGAT
261 AACTGCAAAATAAAAGAATTGCTAAGAGTAATAAGGAAGATGTAGATGGTGCTAATTTGGCCGAT
43376436 GAAAGCGGT
326 GAAAGCGGT
43376445 GATGATAGATCAGGCTATGCTATTATTGTGCTCTTTACCCCCTTCATATAAGTCTTTCAGGGGGA
1 GATGATAGATCAGGCTATGCTATTATTGTGCTCTTTACCCCCTTCATATAAGTCTTTCAGGGGGA
43376510 CCCTGATTTATGGTAGAGACAAACTCTCGTTTGAAAATGTGAAGGGTCATTTGTTGAGTAGAGAC
66 CCCTGATTTATGGTAGAGACAAACTCTCGTTTGAAAATGTGAAGGGTCATTTGTTGAGTAGAGAC
43376575 AAACTCGACAATGAGTTTGGTTTGGATAGCAAGGCAGATAGGCAAGCTTCTATTTTGTTAGCATC
131 AAACTCGACAATGAGTTTGGTTTGGATAGCAAGGCAGATAGGCAAGCTTCTATTTTGTTAGCATC
43376640 AAAGAAACGAGACAAAAGGTGTCGCTATTGTAAAAAGTTAGGTCACATCAAAGCAGATTGTTATA
196 AAAGAAACGAGACAAAAGGTGTCGCTATTGTAAAAAGTTAGGTCACATCAAAGCAGATTGTTATA
43376705 AACTGCAAAATAAAAGAATTGCTAAGAGTAATAAGGAAGATGTAGATGGTGCTAATTTGGCCGAT
261 AACTGCAAAATAAAAGAATTGCTAAGAGTAATAAGGAAGATGTAGATGGTGCTAATTTGGCCGAT
43376770 GAAAGCGGT
326 GAAAGCGGT
43376779 GATGAT
1 GATGAT
43376785 TTTTTGTTAG
Statistics
Matches: 339, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
333 5 0.01
334 334 0.99
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.28
Consensus pattern (334 bp):
GATGATAGATCAGGCTATGCTATTATTGTGCTCTTTACCCCCTTCATATAAGTCTTTCAGGGGGA
CCCTGATTTATGGTAGAGACAAACTCTCGTTTGAAAATGTGAAGGGTCATTTGTTGAGTAGAGAC
AAACTCGACAATGAGTTTGGTTTGGATAGCAAGGCAGATAGGCAAGCTTCTATTTTGTTAGCATC
AAAGAAACGAGACAAAAGGTGTCGCTATTGTAAAAAGTTAGGTCACATCAAAGCAGATTGTTATA
AACTGCAAAATAAAAGAATTGCTAAGAGTAATAAGGAAGATGTAGATGGTGCTAATTTGGCCGAT
GAAAGCGGT
Found at i:43377489 original size:27 final size:27
Alignment explanation
Indices: 43377448--43377506 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
43377438 TGCATAGTTC
43377448 AAGATAGGCCTGTGGCGGACTTTGGCA
1 AAGATAGGCCTGTGGCGGACTTTGGCA
*
43377475 AAGATAGG-CTCGTGGCGGGCTTTGGCA
1 AAGATAGGCCT-GTGGCGGACTTTGGCA
43377502 AAGAT
1 AAGAT
43377507 GACGTTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.22
Consensus pattern (27 bp):
AAGATAGGCCTGTGGCGGACTTTGGCA
Found at i:43378563 original size:94 final size:94
Alignment explanation
Indices: 43378402--43378589 Score: 340
Period size: 94 Copynumber: 2.0 Consensus size: 94
43378392 TTAAAACAAC
*
43378402 GTGTTATAAATTTTCTGAAATCCCCACTTTTACCTCCACTCAACGTGCATGGATCGGAGCTTAAC
1 GTGTTATAAATTTTCTGAAATCCCCACTTTTACCGCCACTCAACGTGCATGGATCGGAGCTTAAC
43378467 AATGTGGAATTAAACGTGGAAGTAAAATT
66 AATGTGGAATTAAACGTGGAAGTAAAATT
*
43378496 GTGTTATAAATTTTCTGAAATCCCCACTTTTGCCGCCACTCAACGTGCATGGATCGGAGCTTAAC
1 GTGTTATAAATTTTCTGAAATCCCCACTTTTACCGCCACTCAACGTGCATGGATCGGAGCTTAAC
* *
43378561 AATGTGGATTTAAATGTGGAAGTAAAATT
66 AATGTGGAATTAAACGTGGAAGTAAAATT
43378590 ACGGTTTCTA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (94 bp):
GTGTTATAAATTTTCTGAAATCCCCACTTTTACCGCCACTCAACGTGCATGGATCGGAGCTTAAC
AATGTGGAATTAAACGTGGAAGTAAAATT
Found at i:43379333 original size:3 final size:3
Alignment explanation
Indices: 43379325--43379370 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
43379315 CTTTCCTCGG
43379325 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
43379371 GATNNNNNNN
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:43379763 original size:3 final size:3
Alignment explanation
Indices: 43379755--43379802 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
43379745 TACTTTCCTC
43379755 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
43379803 GATTGGTGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:43388153 original size:33 final size:33
Alignment explanation
Indices: 43388081--43388153 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
43388071 CTAAATAATC
* * *
43388081 ACATCTTTAG-AAGAGATATAATTATTCAACTA
1 ACATCTCTAGTAAGAGATACAACTATTCAACTA
* *
43388113 ATATCTCTAGTAAGAGATACAACTATTCAATTA
1 ACATCTCTAGTAAGAGATACAACTATTCAACTA
*
43388146 ACCTCTCT
1 ACATCTCT
43388154 TAAATAAACA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
32 8 0.24
33 25 0.76
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (33 bp):
ACATCTCTAGTAAGAGATACAACTATTCAACTA
Found at i:43389120 original size:46 final size:46
Alignment explanation
Indices: 43389053--43389145 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
43389043 TTACCGATTC
43389053 ACCAAAGAGATCGAAGATGAACTTGAGAACATCTACCATAACAACA
1 ACCAAAGAGATCGAAGATGAACTTGAGAACATCTACCATAACAACA
43389099 ACCAAAGAGATCGAAGATGAACTTGAGAACATCTACCATAACAACA
1 ACCAAAGAGATCGAAGATGAACTTGAGAACATCTACCATAACAACA
43389145 A
1 A
43389146 TAATGCCGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15
Consensus pattern (46 bp):
ACCAAAGAGATCGAAGATGAACTTGAGAACATCTACCATAACAACA
Found at i:43398845 original size:18 final size:18
Alignment explanation
Indices: 43398822--43398856 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43398812 TTACTTGTAA
43398822 AAATAATAATTATATTTG
1 AAATAATAATTATATTTG
* *
43398840 AAATAATTATTTTATTT
1 AAATAATAATTATATTT
43398857 TACAATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AAATAATAATTATATTTG
Found at i:43399725 original size:21 final size:21
Alignment explanation
Indices: 43399690--43399740 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
43399680 ATAACAAGTT
* *
43399690 CAAACCATGCTTATCATAATA
1 CAAATCATACTTATCATAATA
*
43399711 CGAATCATACTTATCATAATA
1 CAAATCATACTTATCATAATA
43399732 CAAATCATA
1 CAAATCATA
43399741 TTAAGCATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.22, G:0.04, T:0.29
Consensus pattern (21 bp):
CAAATCATACTTATCATAATA
Found at i:43399749 original size:21 final size:21
Alignment explanation
Indices: 43399690--43399749 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
43399680 ATAACAAGTT
* * *
43399690 CAAACCATGCTTATCATAATA
1 CAAATCATACTTAGCATAATA
* *
43399711 CGAATCATACTTATCATAATA
1 CAAATCATACTTAGCATAATA
43399732 CAAATCATA-TTAAGCATA
1 CAAATCATACTT-AGCATA
43399750 TAACATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (21 bp):
CAAATCATACTTAGCATAATA
Found at i:43399790 original size:41 final size:42
Alignment explanation
Indices: 43399744--43399825 Score: 130
Period size: 43 Copynumber: 2.0 Consensus size: 42
43399734 AATCATATTA
*
43399744 AGCATATAAC-ATTAATCATGCGTACATAAATCGTATTTATG
1 AGCATATAACAATTAATCATGCATACATAAATCGTATTTATG
*
43399785 AGCATATAACATATTAATCATGCATACATAAATTGTATTTA
1 AGCATATAACA-ATTAATCATGCATACATAAATCGTATTTA
43399826 ACACAAATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 10 0.27
43 27 0.73
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.35
Consensus pattern (42 bp):
AGCATATAACAATTAATCATGCATACATAAATCGTATTTATG
Found at i:43402466 original size:5 final size:5
Alignment explanation
Indices: 43402456--43402481 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
43402446 TGAGCATTCG
43402456 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
43402482 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:43403252 original size:28 final size:29
Alignment explanation
Indices: 43403212--43403266 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
43403202 GGGTTGGGAG
* *
43403212 GGGAGAGGAGTAAAAGTTTTGGGGGAAGT
1 GGGAGAGGAGTAAAAATTTTGAGGGAAGT
43403241 GGGA-AGGAGTAAAAATTTTGAGGGAA
1 GGGAGAGGAGTAAAAATTTTGAGGGAA
43403267 AAATAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.20
Consensus pattern (29 bp):
GGGAGAGGAGTAAAAATTTTGAGGGAAGT
Found at i:43405114 original size:5 final size:5
Alignment explanation
Indices: 43405104--43405128 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
43405094 TTGGGGGGTT
43405104 GGGAG GGGAG GGGAG GGGAG GGGAG
1 GGGAG GGGAG GGGAG GGGAG GGGAG
43405129 TAAAAGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (5 bp):
GGGAG
Found at i:43405332 original size:9 final size:9
Alignment explanation
Indices: 43405315--43405345 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43405305 TTGAGTTGAT
43405315 TCGAATAAC
1 TCGAATAAC
*
43405324 TCGATTAAC
1 TCGAATAAC
43405333 TCGAATAAC
1 TCGAATAAC
43405342 TCGA
1 TCGA
43405346 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:43405450 original size:18 final size:18
Alignment explanation
Indices: 43405427--43405463 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
43405417 ATTTCTCATC
43405427 CCCGATTCCCTTTTCTTT
1 CCCGATTCCCTTTTCTTT
43405445 CCCGATTCCCTTTTCTTT
1 CCCGATTCCCTTTTCTTT
43405463 C
1 C
43405464 TCAGCCTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.41, G:0.05, T:0.49
Consensus pattern (18 bp):
CCCGATTCCCTTTTCTTT
Found at i:43406544 original size:21 final size:21
Alignment explanation
Indices: 43406520--43406564 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
43406510 TATAAAAGAA
43406520 CTGAATTGTATGGACTTGAGC
1 CTGAATTGTATGGACTTGAGC
43406541 CTGAATTGTATGGACTTGAGC
1 CTGAATTGTATGGACTTGAGC
43406562 CTG
1 CTG
43406565 CCCTGCCCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (21 bp):
CTGAATTGTATGGACTTGAGC
Found at i:43408924 original size:9 final size:9
Alignment explanation
Indices: 43408910--43408969 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
43408900 AATAATCACT
43408910 TTACATAAC
1 TTACATAAC
43408919 TTACATAAC
1 TTACATAAC
43408928 TTACATAA-
1 TTACATAAC
43408936 -TACATAA-
1 TTACATAAC
* * *
43408943 ATATATATC
1 TTACATAAC
*
43408952 ATATCATAAC
1 TTA-CATAAC
43408962 TTACATAA
1 TTACATAA
43408970 AAACTTGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
7 7 0.16
8 5 0.12
9 25 0.58
10 6 0.14
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (9 bp):
TTACATAAC
Found at i:43409097 original size:7 final size:7
Alignment explanation
Indices: 43409085--43409109 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43409075 ACACCCATTA
43409085 GATACTT
1 GATACTT
43409092 GATACTT
1 GATACTT
43409099 GATACTT
1 GATACTT
43409106 GATA
1 GATA
43409110 TATATTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (7 bp):
GATACTT
Found at i:43413973 original size:84 final size:84
Alignment explanation
Indices: 43413832--43414000 Score: 329
Period size: 84 Copynumber: 2.0 Consensus size: 84
43413822 AAAGATCACT
43413832 TTCATTTTACAATGGTGAACTTCTCTCGATAAATTCACACTGGACAACAATTGATAAACGAGTCG
1 TTCATTTTACAATGGTGAACTTCTCTCGATAAATTCACACTGGACAACAATTGATAAACGAGTCG
*
43413897 TATGTATTTTTTTCTCAAG
66 TATGTATTTTCTTCTCAAG
43413916 TTCATTTTACAATGGTGAACTTCTCTCGATAAATTCACACTGGACAACAATTGATAAACGAGTCG
1 TTCATTTTACAATGGTGAACTTCTCTCGATAAATTCACACTGGACAACAATTGATAAACGAGTCG
43413981 TATGTATTTTCTTCTCAAG
66 TATGTATTTTCTTCTCAAG
43414000 T
1 T
43414001 CAAACAAATT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (84 bp):
TTCATTTTACAATGGTGAACTTCTCTCGATAAATTCACACTGGACAACAATTGATAAACGAGTCG
TATGTATTTTCTTCTCAAG
Found at i:43435774 original size:17 final size:16
Alignment explanation
Indices: 43435752--43435794 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
43435742 TCTTAAAATA
43435752 TTAATTAATAACTTAAT
1 TTAATTAATAA-TTAAT
*
43435769 TTAATTAACTAATTAGT
1 TTAATTAA-TAATTAAT
*
43435786 TAAATTAAT
1 TTAATTAAT
43435795 TTCACAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 1 0.04
17 19 0.83
18 3 0.13
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (16 bp):
TTAATTAATAATTAAT
Found at i:43435776 original size:21 final size:21
Alignment explanation
Indices: 43435743--43435795 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
43435733 TTTTCTATTT
* *
43435743 CTTAAAAT-ATTAATTAATAA
1 CTTAAATTAATTAACTAATAA
* *
43435763 CTTAATTTAATTAACTAATTA
1 CTTAAATTAATTAACTAATAA
*
43435784 GTTAAATTAATT
1 CTTAAATTAATT
43435796 TCACAATTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (21 bp):
CTTAAATTAATTAACTAATAA
Found at i:43436660 original size:12 final size:12
Alignment explanation
Indices: 43436643--43436667 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43436633 ACATACTCCC
43436643 TTATCCATTCAA
1 TTATCCATTCAA
43436655 TTATCCATTCAA
1 TTATCCATTCAA
43436667 T
1 T
43436668 ATTAAAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (12 bp):
TTATCCATTCAA
Found at i:43437012 original size:27 final size:27
Alignment explanation
Indices: 43436982--43437034 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
43436972 TTAATAGTGA
43436982 GTATTTTATATGTCAAACTTAATCAAT
1 GTATTTTATATGTCAAACTTAATCAAT
*
43437009 GTATTTTATATGTCAAACTTCATCAA
1 GTATTTTATATGTCAAACTTAATCAA
43437035 AATTAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (27 bp):
GTATTTTATATGTCAAACTTAATCAAT
Found at i:43442811 original size:15 final size:15
Alignment explanation
Indices: 43442791--43442834 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
43442781 CATACATAAG
43442791 CAGGGTTTGCACATA
1 CAGGGTTTGCACATA
*
43442806 CAGGGTTCGCACATA
1 CAGGGTTTGCACATA
* *
43442821 TA-GGATTGCACATA
1 CAGGGTTTGCACATA
43442835 TGGGTTAGCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (15 bp):
CAGGGTTTGCACATA
Found at i:43442858 original size:29 final size:29
Alignment explanation
Indices: 43442792--43442894 Score: 109
Period size: 29 Copynumber: 3.6 Consensus size: 29
43442782 ATACATAAGC
* *
43442792 AGGGTTTGCACATACAGGGTTCGCACATAT
1 AGGGTTTGCACATA-TGGGTTCGCACATGT
* * *
43442822 A-GGATTGCACATATGGGTTAGCGCATGT
1 AGGGTTTGCACATATGGGTTCGCACATGT
* * *
43442850 AGGGTTTGCACCTAGGGGTTCGTACATGT
1 AGGGTTTGCACATATGGGTTCGCACATGT
*
43442879 AGGGTTCGCACATATG
1 AGGGTTTGCACATATG
43442895 CTTCAGTTCG
Statistics
Matches: 58, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
28 12 0.21
29 45 0.78
30 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.28
Consensus pattern (29 bp):
AGGGTTTGCACATATGGGTTCGCACATGT
Found at i:43445909 original size:2 final size:2
Alignment explanation
Indices: 43445898--43445928 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
43445888 GCCATTGGTT
43445898 TA TA -A 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
43445929 ATACGTGTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:43447166 original size:15 final size:15
Alignment explanation
Indices: 43447146--43447183 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
43447136 TTATTCTATC
43447146 TTTTAT-CCTTTATAT
1 TTTTATACC-TTATAT
43447161 TTTTATACCTTATAT
1 TTTTATACCTTATAT
43447176 TTTATATA
1 TTT-TATA
43447184 TATGTGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTATACCTTATAT
Found at i:43451841 original size:20 final size:20
Alignment explanation
Indices: 43451812--43451851 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
43451802 TTCACCTCAT
*
43451812 GCATCGCATCATATGCATTA
1 GCATCACATCATATGCATTA
43451832 GCATCACATCATATGCATTA
1 GCATCACATCATATGCATTA
43451852 AAGACCTTTA
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:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (20 bp):
GCATCACATCATATGCATTA
Found at i:43458418 original size:14 final size:14
Alignment explanation
Indices: 43458399--43458427 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43458389 CCGACCCAGA
43458399 GAATTTCACGAGGG
1 GAATTTCACGAGGG
43458413 GAATTTCACGAGGG
1 GAATTTCACGAGGG
43458427 G
1 G
43458428 GACCTGGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.38, T:0.21
Consensus pattern (14 bp):
GAATTTCACGAGGG
Found at i:43459681 original size:50 final size:51
Alignment explanation
Indices: 43459546--43459684 Score: 131
Period size: 50 Copynumber: 2.8 Consensus size: 51
43459536 TTGAAAAGTA
* * * *
43459546 AAAAGATTGAAGCCACAACGGCGGATTTTACTT-CCTTAGCAGTGCAGCGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGAGCAGTACAACGG
* * * * * * ***
43459596 AACAGATTGAAGCTACGACGGCGGATC-TAGTTTCCCTGA-TATTACAATTT
1 AAAAGATTGAAGCCACAACGGCGGATCTTA-CTTCCCTGAGCAGTACAACGG
43459646 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGA
43459685 CAATGCGGGG
Statistics
Matches: 69, Mismatches: 17, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
49 2 0.03
50 61 0.88
51 6 0.09
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (51 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGAGCAGTACAACGG
Found at i:43460688 original size:15 final size:15
Alignment explanation
Indices: 43460668--43460705 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
43460658 TTATTCTATC
43460668 TTTTAT-CCTTTATAT
1 TTTTATACC-TTATAT
43460683 TTTTATACCTTATAT
1 TTTTATACCTTATAT
43460698 TTTATATA
1 TTT-TATA
43460706 TATGTGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTATACCTTATAT
Found at i:43462091 original size:2 final size:2
Alignment explanation
Indices: 43462084--43462120 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
43462074 CCTTTAAATA
*
43462084 AT AT AT AT AT AT AT AT AT GT 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
43462121 GGTTTTGAAN
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43464551 original size:3 final size:3
Alignment explanation
Indices: 43464543--43464572 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
43464533 TACAAGAGAG
43464543 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
43464573 AACTACGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:43464880 original size:18 final size:18
Alignment explanation
Indices: 43464857--43464898 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
43464847 TTCTTTTTGG
43464857 AATTTTAGGTTTGTAGAA
1 AATTTTAGGTTTGTAGAA
* *
43464875 AATTTTAGGTTTTTATAA
1 AATTTTAGGTTTGTAGAA
43464893 AATTTT
1 AATTTT
43464899 GGAATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (18 bp):
AATTTTAGGTTTGTAGAA
Found at i:43464984 original size:21 final size:21
Alignment explanation
Indices: 43464960--43465001 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43464950 AAATCCTAAG
43464960 TAAAAATTACCATAAAATTCT
1 TAAAAATTACCATAAAATTCT
* **
43464981 TAAAATTTTTCATAAAATTCT
1 TAAAAATTACCATAAAATTCT
43465002 ATATTTTTAT
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:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAATTACCATAAAATTCT
Found at i:43474067 original size:71 final size:72
Alignment explanation
Indices: 43473951--43474097 Score: 287
Period size: 71 Copynumber: 2.1 Consensus size: 72
43473941 AACTGGATGG
43473951 AAAAATTAATGTTTGTTAACTTTATTACTATGGCATCCACGTATGTGCCACGTTAACAATTAA-T
1 AAAAATTAATGTTTGTTAACTTTATTACTATGGCATCCACGTATGTGCCACGTTAACAATTAATT
43474015 AATTTTT
66 AATTTTT
43474022 AAAAATTAATGTTTGTTAACTTTATTACTATGGCATCCACGTATGTGCCACGTTAACAATTAATT
1 AAAAATTAATGTTTGTTAACTTTATTACTATGGCATCCACGTATGTGCCACGTTAACAATTAATT
43474087 AATTTTT
66 AATTTTT
43474094 AAAA
1 AAAA
43474098 TTTTTAAAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 63 0.84
72 12 0.16
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (72 bp):
AAAAATTAATGTTTGTTAACTTTATTACTATGGCATCCACGTATGTGCCACGTTAACAATTAATT
AATTTTT
Found at i:43474101 original size:9 final size:9
Alignment explanation
Indices: 43474087--43474152 Score: 55
Period size: 9 Copynumber: 6.8 Consensus size: 9
43474077 ACAATTAATT
43474087 AATTTTTAA
1 AATTTTTAA
43474096 AATTTTTAAAA
1 AATTTTT--AA
43474107 TATATTTTTAA
1 -A-ATTTTTAA
43474118 AATTTTTAA
1 AATTTTTAA
43474127 AATGATTTT-A
1 AAT--TTTTAA
43474137 AA-TTTTAA
1 AATTTTTAA
43474145 AATATTTT
1 AAT-TTTT
43474153 TTTATATATT
Statistics
Matches: 48, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
7 4 0.08
8 3 0.06
9 18 0.38
10 8 0.17
11 8 0.17
12 1 0.02
13 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
AATTTTTAA
Found at i:43475546 original size:18 final size:17
Alignment explanation
Indices: 43475508--43475546 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
43475498 AATTTTTCAT
*
43475508 AATTTCGTAAATTACTA
1 AATTTCGTAAAATACTA
*
43475525 AATTTCGTAAAAATACTG
1 AATTTCGT-AAAATACTA
43475543 AATT
1 AATT
43475547 ACTAAAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (17 bp):
AATTTCGTAAAATACTA
Found at i:43475561 original size:26 final size:28
Alignment explanation
Indices: 43475517--43475577 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
43475507 TAATTTCGTA
**
43475517 AATTACTAAATTTCGTAAA-AA-TACTG
1 AATTACTAAAACTCGTAAAGAATTACTG
* *
43475543 AATTACTAAAACTCTTAAAGAATTATTG
1 AATTACTAAAACTCGTAAAGAATTACTG
43475571 AATTACT
1 AATTACT
43475578 GATAGAATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 16 0.55
27 2 0.07
28 11 0.38
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (28 bp):
AATTACTAAAACTCGTAAAGAATTACTG
Found at i:43479336 original size:21 final size:21
Alignment explanation
Indices: 43479312--43479351 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
43479302 AGAAAGACAC
43479312 GCTTCTCTC-CTTTGACATTAA
1 GCTTCTCTCTCTTT-ACATTAA
*
43479333 GCTTCTTTCTCTTTACATT
1 GCTTCTCTCTCTTTACATT
43479352 TGGAACATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.15, C:0.28, G:0.07, T:0.50
Consensus pattern (21 bp):
GCTTCTCTCTCTTTACATTAA
Found at i:43486688 original size:15 final size:15
Alignment explanation
Indices: 43486665--43486699 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
43486655 GGGTTTAGGC
* *
43486665 TAGTCGGGCTTGGTG
1 TAGTTGGGCTAGGTG
43486680 TAGTTGGGCTAGGTG
1 TAGTTGGGCTAGGTG
43486695 TAGTT
1 TAGTT
43486700 TAATTGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.11, C:0.09, G:0.43, T:0.37
Consensus pattern (15 bp):
TAGTTGGGCTAGGTG
Found at i:43494092 original size:21 final size:21
Alignment explanation
Indices: 43494066--43494105 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
43494056 GGTATCAGCA
43494066 ATTTTATACTATTTCCTCACG
1 ATTTTATACTATTTCCTCACG
43494087 ATTTTATACTATTTCCTCA
1 ATTTTATACTATTTCCTCA
43494106 GAAAACGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.23, G:0.03, T:0.50
Consensus pattern (21 bp):
ATTTTATACTATTTCCTCACG
Found at i:43494222 original size:145 final size:145
Alignment explanation
Indices: 43493940--43494224 Score: 367
Period size: 145 Copynumber: 2.0 Consensus size: 145
43493930 CACGAGGGTG
* *
43493940 CGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAAATATTTCCTACATGACCAACTGTAGTGA
1 CGATTTGACACTATTTCCTCAGAAACGTCAAAAAAAAATATTTCCTACATGACCAACTGTAGCGA
*** * * **
43494005 AATCACGTCCACGAGGGTGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAGCAATTT
66 AATCACGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAAGCAATTT
* *
43494070 TATACTATTTCCTCA
131 CACACTATTTCCTCA
* * *
43494085 CGATTTTATACTATTTCCTCAGAAAACGTCAAAAAAAATTATTT-CTCACATGACC-ACTGTAGC
1 CGATTTGACACTATTTCCTCAG-AAACGTCAAAAAAAAATATTTCCT-ACATGACCAACTGTAGC
* * * *
43494148 GAAATCGCGTCCACGAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTAGTAGAAGCGAT
64 GAAATCACGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAAGCAAT
*
43494213 TTCCCACTATTT
129 TTCACACTATTT
43494225 AACCAGAAAC
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
145 91 0.76
146 28 0.24
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (145 bp):
CGATTTGACACTATTTCCTCAGAAACGTCAAAAAAAAATATTTCCTACATGACCAACTGTAGCGA
AATCACGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAAGCAATTT
CACACTATTTCCTCA
Found at i:43496241 original size:28 final size:29
Alignment explanation
Indices: 43496198--43496271 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
43496188 AAAAGCTTTG
*
43496198 TTTTAATTTATTTTATAA-AATTTTATGAT
1 TTTTAA-TTAATTTATAATAATTTTATGAT
*
43496227 TTTTAATTAATTTATAATAATTTTATTAT
1 TTTTAATTAATTTATAATAATTTTATGAT
*
43496256 TTTTTA-TAATTT-TAAT
1 TTTTAATTAATTTATAAT
43496272 TATTCTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
27 4 0.10
28 16 0.39
29 21 0.51
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (29 bp):
TTTTAATTAATTTATAATAATTTTATGAT
Found at i:43496249 original size:10 final size:9
Alignment explanation
Indices: 43496227--43496287 Score: 59
Period size: 9 Copynumber: 6.4 Consensus size: 9
43496217 ATTTTATGAT
43496227 TTTTAATTAA
1 TTTTAA-TAA
43496237 TTTATAATAA
1 TTT-TAATAA
* *
43496247 TTTTATTAT
1 TTTTAATAA
*
43496256 TTTTTATAA
1 TTTTAATAA
*
43496265 TTTTAATTA
1 TTTTAATAA
43496274 TTCTTAATAA
1 TT-TTAATAA
43496284 TTTT
1 TTTT
43496288 TTTTGTTTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
9 21 0.51
10 17 0.41
11 3 0.07
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTAATAA
Found at i:43496257 original size:18 final size:18
Alignment explanation
Indices: 43496227--43496287 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 18
43496217 ATTTTATGAT
43496227 TTTTAATTAATTTATAATAA
1 TTTTAATT-ATTT-TAATAA
*
43496247 TTTT-ATTATTTTTTATAA
1 TTTTAATTA-TTTTAATAA
43496265 TTTTAATTATTCTTAATAA
1 TTTTAATTATT-TTAATAA
43496284 TTTT
1 TTTT
43496288 TTTTGTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
18 12 0.33
19 20 0.56
20 4 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTAATTATTTTAATAA
Found at i:43498913 original size:2 final size:2
Alignment explanation
Indices: 43498906--43498940 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
43498896 AAATTGTAAA
43498906 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
43498941 CCAAATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:43512247 original size:22 final size:22
Alignment explanation
Indices: 43512222--43512271 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
43512212 ATTTTGGGAA
43512222 AAAAATAAAATAAGATAAAAAT
1 AAAAATAAAATAAGATAAAAAT
* ** *
43512244 AAAAATAAATTAATCTCAAAAT
1 AAAAATAAAATAAGATAAAAAT
43512266 AAAAAT
1 AAAAAT
43512272 CCCACTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAAATAAAATAAGATAAAAAT
Found at i:43512757 original size:18 final size:18
Alignment explanation
Indices: 43512734--43512777 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
43512724 ATCCTCCTAT
*
43512734 TTATGGGTTGGGGAGGGG
1 TTATGGGTTGAGGAGGGG
43512752 TTATGGGTTGAGGAGGGG
1 TTATGGGTTGAGGAGGGG
*
43512770 CTATGGGT
1 TTATGGGT
43512778 AGTTCTAGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.14, C:0.02, G:0.55, T:0.30
Consensus pattern (18 bp):
TTATGGGTTGAGGAGGGG
Found at i:43513194 original size:14 final size:14
Alignment explanation
Indices: 43513175--43513209 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
43513165 AAGCTTTATT
43513175 TTAAATTCATCAAG
1 TTAAATTCATCAAG
*
43513189 TTAAATTTATCAAG
1 TTAAATTCATCAAG
*
43513203 TCAAATT
1 TTAAATT
43513210 TTGAGTTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (14 bp):
TTAAATTCATCAAG
Found at i:43514021 original size:28 final size:31
Alignment explanation
Indices: 43513963--43514021 Score: 88
Period size: 28 Copynumber: 2.0 Consensus size: 31
43513953 TTTTTTTAAA
43513963 ATTTAAAAAATTCAAAATATTATAAAATTAT
1 ATTTAAAAAATTCAAAATATTATAAAATTAT
*
43513994 ATTT-AAAAATT-AAAA-ATTATTAAATTAT
1 ATTTAAAAAATTCAAAATATTATAAAATTAT
43514022 TAAAAAATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 12 0.44
29 4 0.15
30 7 0.26
31 4 0.15
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (31 bp):
ATTTAAAAAATTCAAAATATTATAAAATTAT
Found at i:43517356 original size:15 final size:17
Alignment explanation
Indices: 43517326--43517363 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
43517316 TAAATTAATA
*
43517326 TAAAATACATTAAAAAT
1 TAAAATACATTAAAAAC
43517343 TAAAATA-ATT-AAAAC
1 TAAAATACATTAAAAAC
43517358 TAAAAT
1 TAAAAT
43517364 TGATTCATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 3 0.15
17 7 0.35
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAATACATTAAAAAC
Found at i:43517661 original size:18 final size:20
Alignment explanation
Indices: 43517638--43517682 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
43517628 CAAGCCTAAT
*
43517638 TTACAAAT-AAATACAAA-A
1 TTACAAATCAAATAAAAATA
43517656 TTACAAATCCAAATAAAAATA
1 TTACAAAT-CAAATAAAAATA
43517677 TTACAA
1 TTACAA
43517683 GCCCAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
20 8 0.35
21 7 0.30
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (20 bp):
TTACAAATCAAATAAAAATA
Found at i:43517688 original size:21 final size:20
Alignment explanation
Indices: 43517646--43517690 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
43517636 ATTTACAAAT
* *
43517646 AAATACAAAATTACAAATCC
1 AAATAAAAAATTACAAACCC
*
43517666 AAATAAAAATATTACAAGCCC
1 AAATAAAAA-ATTACAAACCC
43517687 AAAT
1 AAAT
43517691 GTAAAAAGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.60, C:0.18, G:0.02, T:0.20
Consensus pattern (20 bp):
AAATAAAAAATTACAAACCC
Found at i:43520336 original size:18 final size:18
Alignment explanation
Indices: 43520315--43520349 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43520305 AGAATTATAG
43520315 ATAATAT-TACATATAAGC
1 ATAATATATACAT-TAAGC
43520333 ATAATATATACATTAAG
1 ATAATATATACATTAAG
43520350 GATGTGGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (18 bp):
ATAATATATACATTAAGC
Found at i:43520990 original size:105 final size:100
Alignment explanation
Indices: 43520748--43521010 Score: 300
Period size: 105 Copynumber: 2.6 Consensus size: 100
43520738 GAATTGAGGG
* * * * *
43520748 ATAAGACCGTAACTAGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGC-A-GTGTT
1 ATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATATGTA
* *
43520811 TATATGTAAGACCATAGCTGGGCTATAGCTTTCTA
66 CATATGTAAGACCATAGCTGGGCTATAGCTTTATA
*
43520846 ATGAGACCATAACTGGGTTATGGCACCT-TGAACGTAAGACCATGGTTGGACCATGGCAATATAG
1 ATAAGACCATAACTGGGTTATGGCA-CTATGAACGTAAGACCATGGTTGGACCATGGCAATAT-G
*
43520910 ATACATGTGTAAGACCATAGCTGGGCTAT-GACATTCTGATA
64 -TACATATGTAAGACCATAGCTGGGCTATAG-C-TT-T-ATA
** * * * *
43520951 ATAAGACCATAACTGGGTTATGGCACTACAAATGTAAGACCATGGTAGGGCCATGACAAT
1 ATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAAT
43521011 GTATGTGTAA
Statistics
Matches: 139, Mismatches: 16, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
98 50 0.36
99 3 0.02
100 1 0.01
101 2 0.01
102 26 0.19
103 2 0.01
104 3 0.02
105 52 0.37
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (100 bp):
ATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATATGTA
CATATGTAAGACCATAGCTGGGCTATAGCTTTATA
Found at i:43524504 original size:35 final size:35
Alignment explanation
Indices: 43524453--43524523 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 35
43524443 ATTATATAAG
43524453 TAAAATGAAATAGGTGAAAAAGATGAATCTAAGGT
1 TAAAATGAAATAGGTGAAAAAGATGAATCTAAGGT
43524488 TAAAATGAAA-ATGGTGAAAAAGATGAATCTAAGGT
1 TAAAATGAAATA-GGTGAAAAAGATGAATCTAAGGT
43524523 T
1 T
43524524 CATGCCATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 1 0.03
35 34 0.97
ACGTcount: A:0.51, C:0.03, G:0.23, T:0.24
Consensus pattern (35 bp):
TAAAATGAAATAGGTGAAAAAGATGAATCTAAGGT
Found at i:43525854 original size:26 final size:25
Alignment explanation
Indices: 43525825--43525909 Score: 61
Period size: 26 Copynumber: 3.5 Consensus size: 25
43525815 AGGAGAACTT
*
43525825 AAATTCAAGAAAACAAAGTGCATGAG
1 AAATACAA-AAAACAAAGTGCATGAG
** ** *
43525851 AAATACAAAAAA-GGAGAAC-T--T
1 AAATACAAAAAACAAAGTGCATGAG
*
43525872 AAATTCAAGAAAACAAAGTGCATGAG
1 AAATACAA-AAAACAAAGTGCATGAG
43525898 AAATACAAAAAA
1 AAATACAAAAAA
43525910 GGAGAACTTA
Statistics
Matches: 41, Mismatches: 13, Indels: 11
0.63 0.20 0.17
Matches are distributed among these distances:
21 7 0.17
22 4 0.10
23 4 0.10
24 4 0.10
25 8 0.20
26 14 0.34
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.14
Consensus pattern (25 bp):
AAATACAAAAAACAAAGTGCATGAG
Found at i:43525862 original size:47 final size:47
Alignment explanation
Indices: 43525809--43525935 Score: 254
Period size: 47 Copynumber: 2.7 Consensus size: 47
43525799 TATTTGAAGT
43525809 CAAAAAAGGAGAACTTAAATTCAAGAAAACAAAGTGCATGAGAAATA
1 CAAAAAAGGAGAACTTAAATTCAAGAAAACAAAGTGCATGAGAAATA
43525856 CAAAAAAGGAGAACTTAAATTCAAGAAAACAAAGTGCATGAGAAATA
1 CAAAAAAGGAGAACTTAAATTCAAGAAAACAAAGTGCATGAGAAATA
43525903 CAAAAAAGGAGAACTTAAATTCAAGAAAACAAA
1 CAAAAAAGGAGAACTTAAATTCAAGAAAACAAA
43525936 TATGGAAAAC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 80 1.00
ACGTcount: A:0.59, C:0.11, G:0.16, T:0.14
Consensus pattern (47 bp):
CAAAAAAGGAGAACTTAAATTCAAGAAAACAAAGTGCATGAGAAATA
Found at i:43527337 original size:15 final size:15
Alignment explanation
Indices: 43527317--43527351 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
43527307 GATACAATAG
43527317 TCAACCTTGTCATTT
1 TCAACCTTGTCATTT
43527332 TCAACCTTGTCATTT
1 TCAACCTTGTCATTT
43527347 TCAAC
1 TCAAC
43527352 TTCTATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.43
Consensus pattern (15 bp):
TCAACCTTGTCATTT
Found at i:43557925 original size:89 final size:89
Alignment explanation
Indices: 43557766--43558522 Score: 1010
Period size: 89 Copynumber: 8.5 Consensus size: 89
43557756 GAACAGATTA
* *
43557766 AAAGATAA-CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCT
1 AAAGA-AAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCT
43557830 TCCCATACTGGTGGCGAAGCAGATC
65 TCCCATACTGGTGGCGAAGCAGATC
* *
43557855 AAAGAAAGCAGATCTTGTCTTCATGTACAGGCGTGAAGTAGATCAAAGATAACAGATCTTGTC-T
1 AAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTT
* * *
43557919 CTCCATACTGGTGGTGGAGTAGATC
66 C-CCATACTGGTGGCGAAGCAGATC
* * * *
43557944 GAAGAGAA-CAGACCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCT
1 AAAGA-AAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCT
*
43558008 TCCCATACTAGTGGCGAAGCAGATC
65 TCCCATACTGGTGGCGAAGCAGATC
* * *
43558033 AAAGAAAGTAGATCTTTTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTT
1 AAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTT
*
43558098 CCCATACTGGTGGCGAAGCGGATC
66 CCCATACTGGTGGCGAAGCAGATC
* * * * * *
43558122 GAAGAAAACAAATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGGTAACAGGTCTTGCCTT
1 AAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTT
43558187 CCCATACTGGTGGCGAAGCAGATC
66 CCCATACTGGTGGCGAAGCAGATC
* * *
43558211 AAAGAAAGCAGATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAGATAACAGATATTGTCTT
1 AAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTT
*
43558276 CCCATACTGGTGGCGAAACAGATC
66 CCCATACTGGTGGCGAAGCAGATC
* * * *
43558300 GAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAATAGATCGTGTCTT
1 AAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTT
*
43558365 CCCATACTGGTGGCGAAGTAGATC
66 CCCATACTGGTGGCGAAGCAGATC
* * * *
43558389 GAAGGAAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGACAACAGATCTTGT
1 -AA--AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGC
* * *
43558454 C-TCTCCATACTGGTGGGGGAGTAGATC
63 CTTC-CCATACTGGTGGCGAAGCAGATC
* * *
43558481 GAAGAGAA-CAGACCTTGTTTTCA--T--TGGCGTGAAGTAGATCAA
1 AAAGA-AAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAA
43558523 GCGCAGCAGA
Statistics
Matches: 595, Mismatches: 63, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
85 18 0.03
87 1 0.00
88 6 0.01
89 483 0.81
90 7 0.01
91 3 0.01
92 77 0.13
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (89 bp):
AAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTT
CCCATACTGGTGGCGAAGCAGATC
Found at i:43560428 original size:19 final size:18
Alignment explanation
Indices: 43560387--43560428 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
43560377 ATACATATGC
*
43560387 ATTTTCTTTTATACTTTT
1 ATTTTCTTTTATACTGTT
43560405 ATTTTCTTTTTATACATGTT
1 ATTTTC-TTTTATAC-TGTT
43560425 -TTTT
1 ATTTT
43560429 GTTTGTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 12 0.57
20 3 0.14
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTTCTTTTATACTGTT
Found at i:43560550 original size:135 final size:137
Alignment explanation
Indices: 43560397--43560668 Score: 458
Period size: 135 Copynumber: 2.0 Consensus size: 137
43560387 ATTTTCTTTT
* *
43560397 ATACTTTTATTTTCTTTTTATACATGTTTTTTGTTTGTTTTATTGGATATATTTCATTTCTTCTA
1 ATACTTTTATTTTATTTTTATACATGTTTTTTGTTTGTTTTATTGGATATATTTCATTCCTTCTA
* * * *
43560462 TTTGCATGTATACTTGTATATGTGTTTTTGATATA-TGTG-TACATATGTTTGCAACTTTATTGT
66 TTTGCATGTATACTTGTATATGTGTGTTAGATATAGTGTGTTACATATGCTTGCAACTTTACTGT
43560525 TATATTA
131 TATATTA
43560532 ATACTTTTATTTTATTTTTATACATGTTTTTTGTTTGTTTTATTGGATATATTTCATTCCTTCTA
1 ATACTTTTATTTTATTTTTATACATGTTTTTTGTTTGTTTTATTGGATATATTTCATTCCTTCTA
*
43560597 TTTGCATGTATACTTGTATATGTGTGTTAGATATATGTGTGTTAGATATGCTTGCAACTTTACTG
66 TTTGCATGTATACTTGTATATGTGTGTTAGATATA-GTGTGTTACATATGCTTGCAACTTTACTG
43560662 TTATATT
130 TTATATT
43560669 GTATTTATAT
Statistics
Matches: 127, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
135 96 0.76
137 4 0.03
138 27 0.21
ACGTcount: A:0.22, C:0.08, G:0.13, T:0.57
Consensus pattern (137 bp):
ATACTTTTATTTTATTTTTATACATGTTTTTTGTTTGTTTTATTGGATATATTTCATTCCTTCTA
TTTGCATGTATACTTGTATATGTGTGTTAGATATAGTGTGTTACATATGCTTGCAACTTTACTGT
TATATTA
Found at i:43560633 original size:15 final size:15
Alignment explanation
Indices: 43560613--43560645 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
43560603 TGTATACTTG
43560613 TATATGTGTGTTAGA
1 TATATGTGTGTTAGA
43560628 TATATGTGTGTTAGA
1 TATATGTGTGTTAGA
43560643 TAT
1 TAT
43560646 GCTTGCAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.48
Consensus pattern (15 bp):
TATATGTGTGTTAGA
Done.