Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold69
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: 2104606
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.31
Warning! 151874 characters in sequence are not A, C, G, or T
File 7 of 13
Found at i:1107814 original size:21 final size:23
Alignment explanation
Indices: 1107767--1107814 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
1107757 TATTATTTTT
**
1107767 TATTAATATTTATATATTTAATA
1 TATTAATATTTATATATAAAATA
1107790 -ATTAA-ATTTATATA-AAAATA
1 TATTAATATTTATATATAAAATA
1107810 TATTA
1 TATTA
1107815 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.18
21 13 0.59
22 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTAATATTTATATATAAAATA
Found at i:1108302 original size:2 final size:2
Alignment explanation
Indices: 1108295--1108359 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1108285 AAACTCTTTT
1108295 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
1108337 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1108360 GTAGAGAAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1108559 original size:22 final size:21
Alignment explanation
Indices: 1108534--1108582 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
1108524 TGGATTAAAC
1108534 TAAAATTAAATTAATTT-AATT
1 TAAAATTAAA-TAATTTAAATT
* *
1108555 GTAAATTTTAATAATTTAAATT
1 -TAAAATTAAATAATTTAAATT
1108577 TAAAAT
1 TAAAAT
1108583 ATTTAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TAAAATTAAATAATTTAAATT
Found at i:1108576 original size:15 final size:15
Alignment explanation
Indices: 1108550--1108591 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
1108540 TAAATTAATT
1108550 TAATTGTAAATTTTAA
1 TAATT-TAAATTTTAA
1108566 TAATTTAAA-TTTAA
1 TAATTTAAATTTTAA
*
1108580 AATATTTAAATT
1 TA-ATTTAAATT
1108592 AGGAGGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 6 0.26
15 11 0.48
16 6 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TAATTTAAATTTTAA
Found at i:1108640 original size:72 final size:73
Alignment explanation
Indices: 1108547--1108685 Score: 181
Period size: 72 Copynumber: 1.9 Consensus size: 73
1108537 AATTAAATTA
* ** *
1108547 ATTTAATTGTAAATTTTAATAATTTAAATTTAAAAT-ATTTAAATTAGGAGGATTAGAATGTCTG
1 ATTTAATTGTAAATTTAAATAATTTAAATTTAAAATGATTTAAATTAAAAGAATTAGAATGTCTG
1108611 ATTATCTT
66 ATTATCTT
* * * * * *
1108619 ATTTGATTTTAAATTTAAATAATTTGAGTTTAAAGTGTTTTAAATTAAAAGAATTAGAATGTCTG
1 ATTTAATTGTAAATTTAAATAATTTAAATTTAAAATGATTTAAATTAAAAGAATTAGAATGTCTG
1108684 AT
66 AT
1108686 GCAAAATATT
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
72 30 0.54
73 26 0.46
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (73 bp):
ATTTAATTGTAAATTTAAATAATTTAAATTTAAAATGATTTAAATTAAAAGAATTAGAATGTCTG
ATTATCTT
Found at i:1108967 original size:32 final size:32
Alignment explanation
Indices: 1108914--1108991 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
1108904 CAATCGATTC
* *
1108914 AGATTTGACTCACTTTCAATTTATATTATTT-T
1 AGATTTGA-TCATTTTCAATTTAAATTATTTGT
*
1108946 AGATTTGTATCATTTTGAATTTAAATTATTTGT
1 AGATTTG-ATCATTTTCAATTTAAATTATTTGT
1108979 -GATTTGGATCATT
1 AGATTT-GATCATT
1108992 CGAGTTTGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 37 0.93
33 3 0.08
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.53
Consensus pattern (32 bp):
AGATTTGATCATTTTCAATTTAAATTATTTGT
Found at i:1109606 original size:22 final size:22
Alignment explanation
Indices: 1109564--1109606 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1109554 ATGATAAGAT
* *
1109564 ATTATTATAATATAATGTATAA
1 ATTATTATAATAAAATATATAA
*
1109586 ATTATTATGATAAAATATATA
1 ATTATTATAATAAAATATATA
1109607 TATATATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTATTATAATAAAATATATAA
Found at i:1110641 original size:19 final size:21
Alignment explanation
Indices: 1110593--1110645 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
1110583 ACACCCCAAA
1110593 TGTATCGATACATATTGCTTAG
1 TGTATCGATACATATT-CTTAG
* *
1110615 TATATCGATACATATT-TT-T
1 TGTATCGATACATATTCTTAG
1110634 TGTATCGATACA
1 TGTATCGATACA
1110646 CCATAAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.39
20 2 0.07
22 15 0.54
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (21 bp):
TGTATCGATACATATTCTTAG
Found at i:1111417 original size:19 final size:19
Alignment explanation
Indices: 1111393--1111432 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1111383 GAGAGGACGT
1111393 AAGTACCGAGTTTGGATCG
1 AAGTACCGAGTTTGGATCG
1111412 AAGTACCGAGTTTGGATCG
1 AAGTACCGAGTTTGGATCG
1111431 AA
1 AA
1111433 CCTTTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (19 bp):
AAGTACCGAGTTTGGATCG
Found at i:1112445 original size:12 final size:12
Alignment explanation
Indices: 1112428--1112461 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1112418 GCAACCATAA
1112428 AAGATGATGATG
1 AAGATGATGATG
*
1112440 AAGATGATAATG
1 AAGATGATGATG
1112452 AAGATGATGA
1 AAGATGATGA
1112462 AGAGCTTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (12 bp):
AAGATGATGATG
Found at i:1113006 original size:21 final size:21
Alignment explanation
Indices: 1112955--1113007 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
1112945 AAATGAGTTG
1112955 CAAGAAGTTAATAAAGAATTAAC
1 CAAGAAG--AATAAAGAATTAAC
* *
1112978 CAATAAGAATAACGAATTAAC
1 CAAGAAGAATAAAGAATTAAC
* *
1112999 TAGGAAGAA
1 CAAGAAGAA
1113008 CATGTACTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 19 0.76
23 6 0.24
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.19
Consensus pattern (21 bp):
CAAGAAGAATAAAGAATTAAC
Found at i:1116703 original size:10 final size:10
Alignment explanation
Indices: 1116673--1116706 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
1116663 TGTGTACAAA
1116673 TTGAATGTTT
1 TTGAATGTTT
*
1116683 ATGAATGTTT
1 TTGAATGTTT
1116693 TTGAATGTTT
1 TTGAATGTTT
1116703 TTGA
1 TTGA
1116707 TTGAATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.56
Consensus pattern (10 bp):
TTGAATGTTT
Found at i:1116877 original size:13 final size:13
Alignment explanation
Indices: 1116859--1116885 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1116849 ACAAAAAAAT
1116859 TGTATCGATATAA
1 TGTATCGATATAA
1116872 TGTATCGATATAA
1 TGTATCGATATAA
1116885 T
1 T
1116886 AAAATTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATATAA
Found at i:1120054 original size:35 final size:34
Alignment explanation
Indices: 1120010--1120076 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
1120000 CGAAGTGATT
*
1120010 AAGAAGTTCTATCTTAGCCTTTATAAAAGATAGAG
1 AAGAAGTTCTATCTTAG-CTTTAGAAAAGATAGAG
* *
1120045 AAGAGGTTCTATCTTAGCTTTCGAAAAGATAG
1 AAGAAGTTCTATCTTAGCTTTAGAAAAGATAG
1120077 TGTTGTAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 13 0.45
35 16 0.55
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (34 bp):
AAGAAGTTCTATCTTAGCTTTAGAAAAGATAGAG
Found at i:1120501 original size:22 final size:22
Alignment explanation
Indices: 1120476--1120517 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1120466 ATATTTTATT
1120476 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
1120498 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
1120518 ATTATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1121167 original size:20 final size:20
Alignment explanation
Indices: 1121142--1121189 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1121132 TACCAAAATA
1121142 TATCGATACATTATACAATG
1 TATCGATACATTATACAATG
*
1121162 TATCGATACATTATTCAATG
1 TATCGATACATTATACAATG
1121182 TATCGATA
1 TATCGATA
1121190 TATACAGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (20 bp):
TATCGATACATTATACAATG
Found at i:1121638 original size:31 final size:29
Alignment explanation
Indices: 1121595--1121662 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
1121585 AATTTTGAAA
1121595 TAAATAAATTAAACTA-AATATTATAAAATTT
1 TAAATAAATTAAA-TATAATATT-T-AAATTT
* *
1121626 TAAATAATTTAAATATAATATTTTAATTT
1 TAAATAAATTAAATATAATATTTAAATTT
1121655 TAAATAAA
1 TAAATAAA
1121663 AACTAACTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 12 0.36
30 3 0.09
31 18 0.55
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
TAAATAAATTAAATATAATATTTAAATTT
Found at i:1122539 original size:23 final size:23
Alignment explanation
Indices: 1122513--1122559 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1122503 TGTACAACTT
1122513 TTTATAACTTTTTGATGTTTTTA
1 TTTATAACTTTTTGATGTTTTTA
1122536 TTTATAACTTTTTGATGTTTTTA
1 TTTATAACTTTTTGATGTTTTTA
1122559 T
1 T
1122560 CACCGTCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.04, G:0.09, T:0.66
Consensus pattern (23 bp):
TTTATAACTTTTTGATGTTTTTA
Found at i:1123454 original size:2 final size:2
Alignment explanation
Indices: 1123447--1123480 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1123437 GAACCATTTC
1123447 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
1123481 TGTTAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1124307 original size:36 final size:37
Alignment explanation
Indices: 1124248--1124346 Score: 146
Period size: 37 Copynumber: 2.6 Consensus size: 37
1124238 CTACTTTAGT
* *
1124248 TTTTAAATTTTAAAATTATTTTATTTAAA-TCTTTAATC
1 TTTT-AATTTT-AAATTATTTTATTTAAACCCTTAAATC
*
1124286 TTTTAATTTTAAATTATTTTATTTAAACCCTTAAATT
1 TTTTAATTTTAAATTATTTTATTTAAACCCTTAAATC
1124323 TTTTAATTTTAAATTATTTTATTT
1 TTTTAATTTTAAATTATTTTATTT
1124347 TTCACATGAT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
36 17 0.30
37 36 0.63
38 4 0.07
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (37 bp):
TTTTAATTTTAAATTATTTTATTTAAACCCTTAAATC
Found at i:1124565 original size:16 final size:17
Alignment explanation
Indices: 1124535--1124573 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1124525 AATTTACTTT
1124535 AAAATTATATATTTAAA
1 AAAATTATATATTTAAA
* *
1124552 AAAATTA-ATCTTTATA
1 AAAATTATATATTTAAA
1124568 AAAATT
1 AAAATT
1124574 TATGAACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATTATATATTTAAA
Found at i:1124621 original size:17 final size:17
Alignment explanation
Indices: 1124601--1124635 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1124591 TTTATATTCG
1124601 ATTTAATTAAATATTTT
1 ATTTAATTAAATATTTT
* *
1124618 ATTTTATTAATTATTTT
1 ATTTAATTAAATATTTT
1124635 A
1 A
1124636 AATTTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTAATTAAATATTTT
Found at i:1124892 original size:18 final size:17
Alignment explanation
Indices: 1124869--1124913 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1124859 AAATAAAATA
1124869 TTTA-TTTTATTAATTATT
1 TTTATTTTTA-TAATTA-T
*
1124887 TTTATTTTTATATTTAT
1 TTTATTTTTATAATTAT
1124904 TTTATTTTTA
1 TTTATTTTTA
1124914 AATGATGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 11 0.44
18 9 0.36
19 5 0.20
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTTATAATTAT
Found at i:1125683 original size:10 final size:10
Alignment explanation
Indices: 1125646--1125684 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
1125636 AAATGAAATC
1125646 ATTAAAATAA
1 ATTAAAATAA
*
1125656 ATTAATA-AA
1 ATTAAAATAA
1125665 ATATAAAATAA
1 AT-TAAAATAA
1125676 ATTAAAATA
1 ATTAAAATA
1125685 GGATATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 4 0.16
10 17 0.68
11 4 0.16
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
ATTAAAATAA
Found at i:1125684 original size:22 final size:22
Alignment explanation
Indices: 1125634--1125699 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
1125624 AACTTAATGG
*
1125634 TAAAATGAAATCATTAAAATAAAT
1 TAAAATAAAAT-A-TAAAATAAAT
1125658 T--AATAAAATATAAAATAAAT
1 TAAAATAAAATATAAAATAAAT
** *
1125678 TAAAATAGGATATAATATAAAT
1 TAAAATAAAATATAAAATAAAT
1125700 AATTAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 11 0.31
21 1 0.03
22 23 0.64
24 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (22 bp):
TAAAATAAAATATAAAATAAAT
Found at i:1125720 original size:26 final size:26
Alignment explanation
Indices: 1125654--1125723 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 26
1125644 TCATTAAAAT
1125654 AAATTAATAAAATATAAAATAAATTAAA
1 AAATT-ATAAAATAT-AAATAAATTAAA
* ** *
1125682 ATAGGATATAATATAAAT-AATTAAA
1 AAATTATAAAATATAAATAAATTAAA
1125707 AAATTATTAAAATATAA
1 AAATTA-TAAAATATAA
1125724 CATTACAAGA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
25 10 0.30
26 13 0.39
27 8 0.24
28 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (26 bp):
AAATTATAAAATATAAATAAATTAAA
Found at i:1125813 original size:29 final size:28
Alignment explanation
Indices: 1125752--1125880 Score: 82
Period size: 29 Copynumber: 4.2 Consensus size: 28
1125742 TTAATAAAAT
*
1125752 ATAAATATATAAATATATCAAAATTTATATAAA
1 ATAAATAT-T-AATATAT-AAAAATT-T-TAAA
1125785 ATAAATTATTAATATATAAAAATTTTAAA
1 ATAAA-TATTAATATATAAAAATTTTAAA
* *
1125814 ATTAAA-ATTAAAATAAATAAAATTTT-AA
1 A-TAAATATTAATATATA-AAAATTTTAAA
* * *
1125842 GTATAATATTTATAATATAAAAATAATTAAA
1 ATA-AATATTAAT-ATATAAAAAT-TTTAAA
1125873 ATATAATA
1 ATA-AATA
1125881 AAATAAAAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
27 2 0.03
28 13 0.16
29 22 0.28
30 11 0.14
31 15 0.19
32 7 0.09
33 6 0.08
34 3 0.04
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (28 bp):
ATAAATATTAATATATAAAAATTTTAAA
Found at i:1125815 original size:40 final size:41
Alignment explanation
Indices: 1125744--1125831 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 41
1125734 AAATAATGTT
* * * *
1125744 AATAAAATATAAATATATAAATATATCAAAATTTATA-TAA
1 AATAAATTATAAATATATAAAAATATCAAAATTAAAATTAA
* * *
1125784 AATAAATTATTAATATATAAAAATTTTAAAATTAAAATTAA
1 AATAAATTATAAATATATAAAAATATCAAAATTAAAATTAA
1125825 AATAAAT
1 AATAAAT
1125832 AAAATTTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 30 0.75
41 10 0.25
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (41 bp):
AATAAATTATAAATATATAAAAATATCAAAATTAAAATTAA
Found at i:1126400 original size:16 final size:16
Alignment explanation
Indices: 1126369--1126416 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
1126359 AAGAGTCAAC
* *
1126369 AATTTAAATTTAAAAT
1 AATTTAAACTCAAAAT
*
1126385 AATTTAAACTCGAAAT
1 AATTTAAACTCAAAAT
* *
1126401 GATTTGAACTCAAAAT
1 AATTTAAACTCAAAAT
1126417 GATTCGAACT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.35
Consensus pattern (16 bp):
AATTTAAACTCAAAAT
Found at i:1126417 original size:16 final size:16
Alignment explanation
Indices: 1126380--1126426 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1126370 ATTTAAATTT
* *
1126380 AAAATAATTTAAACTC
1 AAAATGATTTGAACTC
*
1126396 GAAATGATTTGAACTC
1 AAAATGATTTGAACTC
*
1126412 AAAATGATTCGAACT
1 AAAATGATTTGAACT
1126427 TAAATTAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.30
Consensus pattern (16 bp):
AAAATGATTTGAACTC
Found at i:1127470 original size:16 final size:16
Alignment explanation
Indices: 1127449--1127522 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
1127439 CGATTGACCA
1127449 GAACTTAAAATAACCT
1 GAACTTAAAATAACCT
*
1127465 GAACTTGAAATAA-CT
1 GAACTTAAAATAACCT
** * *
1127480 CGAACTCGAAATGACTT
1 -GAACTTAAAATAACCT
*
1127497 GAACTTAAAATGATCC-
1 GAACTTAAAAT-AACCT
1127513 GAACTTAAAA
1 GAACTTAAAA
1127523 ACAATTTGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
15 2 0.04
16 42 0.91
17 2 0.04
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (16 bp):
GAACTTAAAATAACCT
Found at i:1129341 original size:23 final size:24
Alignment explanation
Indices: 1129315--1129360 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
1129305 AAAATCAGAA
*
1129315 TAAAATATTAAAAATAA-AAAAAT
1 TAAAATATGAAAAATAATAAAAAT
1129338 TAAAATATGAAAAATAATAAAAA
1 TAAAATATGAAAAATAATAAAAA
1129361 CGAGTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (24 bp):
TAAAATATGAAAAATAATAAAAAT
Found at i:1130303 original size:2 final size:2
Alignment explanation
Indices: 1130291--1130331 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1130281 GAAAATATTC
* * *
1130291 TA TA AA TA TA TA TA TA TA TA TA TG TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1130332 GAAAAAGTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1130341 original size:18 final size:18
Alignment explanation
Indices: 1130303--1130341 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1130293 TAAATATATA
* * *
1130303 TATATATATATGTATATG
1 TATATATATATGAAAAAG
1130321 TATATATATATGAAAAAG
1 TATATATATATGAAAAAG
1130339 TAT
1 TAT
1130342 TTAGAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (18 bp):
TATATATATATGAAAAAG
Found at i:1131218 original size:34 final size:34
Alignment explanation
Indices: 1131154--1131336 Score: 260
Period size: 34 Copynumber: 5.4 Consensus size: 34
1131144 TTAATGTGGG
* *
1131154 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1131187 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1131221 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
1131255 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1131289 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1131323 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1131337 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 11 0.08
34 121 0.92
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1131694 original size:19 final size:19
Alignment explanation
Indices: 1131638--1131700 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1131628 TGGTTGTCGA
**
1131638 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
1131657 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
1131676 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
1131695 GTTACT
1 GGTACT
1131701 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:1135832 original size:34 final size:34
Alignment explanation
Indices: 1135766--1135950 Score: 255
Period size: 34 Copynumber: 5.5 Consensus size: 34
1135756 AAGTGGGAGA
* *
1135766 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1135799 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1135833 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * * *
1135867 ATTATTTATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1135901 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1135935 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1135951 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 13 0.10
34 119 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1138135 original size:285 final size:283
Alignment explanation
Indices: 1137621--1138146 Score: 658
Period size: 285 Copynumber: 1.8 Consensus size: 283
1137611 TAATCTCTTA
* * * *
1137621 TATCTTATATAAATATAAAGTCTAAACTTTTAGTAAAAAAAAGTAATTATCAATTTATTTTTATT
1 TATCTTATACAAATATAAAGTCAAAACTTTTAATAAAAAAAAGTAATTATCAATTTATTATTATT
* * * * **
1137686 ACTTTACCCTAAATAGGGTTCATATATTACTTTATCCTTATTGATAACTACAATTTTAGACGGGT
66 ACTTAACCCTAAATAGGGTT-ATATATTACTTTAACCTTATTAATAACTACAATATTAGACGCAT
*
1137751 ATGGAAAAAAAAATAATATGATAAATATCTTATTAATTTTTTTAAAAAATAATATTCAAATAAAG
130 ATGGAAAAAAAAATAATATGATAAATATCTTAGTAATTTTTTTAAAAAATAATATTCAAATAAAG
*
1137816 TTTTTTATTACTTGTTGACTATTATAATTGTCTAGCATAAATTACTATAATTGTGAAATTATTAA
195 TTTTTTATTACTTGTTGACCATTATAATTGTCTAGCATAAATTACTATAATTGTGAAATTATTAA
1137881 TAATCCAATCAATTAAAATTTTAT
260 TAATCCAATCAATTAAAATTTTAT
1137905 TATCTTATACAAATATAAAAGTCAAAACTTTTAAT-AAAAAAAGTAATTATCAATTTTATTATTA
1 TATCTTATACAAATAT-AAAGTCAAAACTTTTAATAAAAAAAAGTAATTATCAA-TTTATTATTA
* * * *
1137969 TTTA-TTAACCTTAAATCA-TGTT-TATATTAGTTTAACCTTATTAATAA-TAGTC-ATATTGGA
64 -TTACTTAACCCTAAAT-AGGGTTATATATTACTTTAACCTTATTAATAACTA--CAATATTAGA
* ** * * *
1138029 TGCATATGG-AATGAATATAATGTGGTAAATAT-TTCAGTAATTTGTTTT-AAAAATAATATTCA
125 CGCATATGGAAAAAAAAATAATATGATAAATATCTT-AGTAATTT-TTTTAAAAAATAATATTCA
*
1138091 AGTAAAGTTTTATAATATTA-TGTGTTGACCATTATAATTGTCTAGCATAAATTACT
188 AATAAAGTTTT-T--TATTACT-TGTTGACCATTATAATTGTCTAGCATAAATTACT
1138147 CTTAACTTTG
Statistics
Matches: 207, Mismatches: 23, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
281 2 0.01
282 51 0.25
283 39 0.19
284 35 0.17
285 76 0.37
286 4 0.02
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (283 bp):
TATCTTATACAAATATAAAGTCAAAACTTTTAATAAAAAAAAGTAATTATCAATTTATTATTATT
ACTTAACCCTAAATAGGGTTATATATTACTTTAACCTTATTAATAACTACAATATTAGACGCATA
TGGAAAAAAAAATAATATGATAAATATCTTAGTAATTTTTTTAAAAAATAATATTCAAATAAAGT
TTTTTATTACTTGTTGACCATTATAATTGTCTAGCATAAATTACTATAATTGTGAAATTATTAAT
AATCCAATCAATTAAAATTTTAT
Found at i:1142677 original size:21 final size:21
Alignment explanation
Indices: 1142652--1142694 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1142642 GCATTTGATC
1142652 AGGCTAATTTTTGTTAGAATA
1 AGGCTAATTTTTGTTAGAATA
1142673 AGGCTAATTTTTGTTAGAATA
1 AGGCTAATTTTTGTTAGAATA
1142694 A
1 A
1142695 CAATAATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.42
Consensus pattern (21 bp):
AGGCTAATTTTTGTTAGAATA
Found at i:1142701 original size:21 final size:21
Alignment explanation
Indices: 1142656--1142702 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1142646 TTGATCAGGC
***
1142656 TAATTTTTGTTAGAATAAGGC
1 TAATTTTTGTTAGAATAACAA
1142677 TAATTTTTGTTAGAATAACAA
1 TAATTTTTGTTAGAATAACAA
1142698 TAATT
1 TAATT
1142703 CATGACGGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (21 bp):
TAATTTTTGTTAGAATAACAA
Found at i:1147647 original size:21 final size:21
Alignment explanation
Indices: 1147614--1147654 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1147604 CTAAGTAAAA
1147614 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
1147635 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
1147655 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1147719 original size:20 final size:19
Alignment explanation
Indices: 1147694--1147764 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1147684 ACCCTGAAAA
1147694 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
1147714 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
1147733 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
1147754 GTATCGATACA
1 GTATCGATACA
1147765 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:1147817 original size:53 final size:53
Alignment explanation
Indices: 1147734--1147870 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
1147724 AAATTGCATA
1147734 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
1147788 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
1147841 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
1147871 TTGGAAGTAG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
53 67 0.83
54 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:1147946 original size:21 final size:22
Alignment explanation
Indices: 1147916--1147967 Score: 97
Period size: 21 Copynumber: 2.4 Consensus size: 22
1147906 ACTATTCATT
1147916 ACTGTTCATGTATCGATACATC
1 ACTGTTCATGTATCGATACATC
1147938 ACT-TTCATGTATCGATACATC
1 ACTGTTCATGTATCGATACATC
1147959 ACTGTTCAT
1 ACTGTTCAT
1147968 AGGTCACTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (22 bp):
ACTGTTCATGTATCGATACATC
Found at i:1148022 original size:13 final size:13
Alignment explanation
Indices: 1148004--1148042 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1147994 TCACTATTCA
1148004 TTTATCGATACAT
1 TTTATCGATACAT
*
1148017 TTTATCGATACAG
1 TTTATCGATACAT
*
1148030 TGTATCGATACAT
1 TTTATCGATACAT
1148043 CATAAATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (13 bp):
TTTATCGATACAT
Found at i:1148575 original size:34 final size:35
Alignment explanation
Indices: 1148512--1148578 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1148502 CTAAGTGATT
1148512 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1148548 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1148579 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1152062 original size:32 final size:33
Alignment explanation
Indices: 1152026--1152103 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 33
1152016 TTTCCAGAGT
*
1152026 AATGTAAA-GAACACATTTTTTTAATACCTTAA
1 AATGTAAATCAACACATTTTTTTAATACCTTAA
*
1152058 AATGTTAAATCATCACATTTTTTTAATACCTTAA
1 AATG-TAAATCAACACATTTTTTTAATACCTTAA
1152092 AATGTTAAATCA
1 AATG-TAAATCA
1152104 TTATTTTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 4 0.10
33 4 0.10
34 34 0.81
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (33 bp):
AATGTAAATCAACACATTTTTTTAATACCTTAA
Found at i:1152075 original size:34 final size:34
Alignment explanation
Indices: 1152037--1152104 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1152027 ATGTAAAGAA
1152037 CACATTTTTTTAATACCTTAAAATGTTAAATCAT
1 CACATTTTTTTAATACCTTAAAATGTTAAATCAT
1152071 CACATTTTTTTAATACCTTAAAATGTTAAATCAT
1 CACATTTTTTTAATACCTTAAAATGTTAAATCAT
1152105 TATTTTCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (34 bp):
CACATTTTTTTAATACCTTAAAATGTTAAATCAT
Found at i:1153110 original size:8 final size:8
Alignment explanation
Indices: 1153098--1153176 Score: 70
Period size: 8 Copynumber: 9.8 Consensus size: 8
1153088 CAAAAAACCA
1153098 AAAAAAAGG
1 AAAAAAA-G
1153107 AAAAAGAAG
1 AAAAA-AAG
1153116 -AAAAAAG
1 AAAAAAAG
1153123 AAAAAAAG
1 AAAAAAAG
**
1153131 AAAAATGG
1 AAAAAAAG
*
1153139 AAAAAAAT
1 AAAAAAAG
* *
1153147 AATAAATG
1 AAAAAAAG
*
1153155 AAAAAGAG
1 AAAAAAAG
*
1153163 AAAAAAAT
1 AAAAAAAG
1153171 AAAAAA
1 AAAAAA
1153177 TAATAAAAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
7 3 0.05
8 44 0.80
9 6 0.11
10 2 0.04
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1153141 original size:32 final size:32
Alignment explanation
Indices: 1153099--1153184 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 32
1153089 AAAAAACCAA
1153099 AAAAAAGGAAAAAGAAGAA-AAAAGAAAAAAAG
1 AAAAAAGGAAAAA-AAGAATAAAAGAAAAAAAG
* * * *
1153131 AAAAATGGAAAAAAATAATAAATGAAAAAGAG
1 AAAAAAGGAAAAAAAGAATAAAAGAAAAAAAG
*
1153163 AAAAAA--ATAAAAAATAATAAAA
1 AAAAAAGGA-AAAAAAGAATAAAA
1153185 ATGAATGAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
30 1 0.02
31 17 0.37
32 28 0.61
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (32 bp):
AAAAAAGGAAAAAAAGAATAAAAGAAAAAAAG
Found at i:1153177 original size:24 final size:24
Alignment explanation
Indices: 1153099--1153177 Score: 92
Period size: 24 Copynumber: 3.3 Consensus size: 24
1153089 AAAAAACCAA
*
1153099 AAAAAAGGAAAAAGAAGAAAAAAGA-
1 AAAAAATGAAAAAG-AGAAAAAA-AT
1153124 AAAAAA-GAAAAATG-GAAAAAAAT
1 AAAAAATGAAAAA-GAGAAAAAAAT
*
1153147 AATAAATGAAAAAGAGAAAAAAAT
1 AAAAAATGAAAAAGAGAAAAAAAT
1153171 AAAAAAT
1 AAAAAAT
1153178 AATAAAAATG
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
22 1 0.02
23 13 0.27
24 27 0.56
25 7 0.15
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (24 bp):
AAAAAATGAAAAAGAGAAAAAAAT
Found at i:1153184 original size:16 final size:16
Alignment explanation
Indices: 1153100--1153189 Score: 69
Period size: 16 Copynumber: 5.6 Consensus size: 16
1153090 AAAAACCAAA
* * *
1153100 AAAAAGGAAAAAGAAG
1 AAAAATGAAAAAAAAT
* *
1153116 AAAAAAG-AAAAAAAG
1 AAAAATGAAAAAAAAT
*
1153131 AAAAATGGAAAAAAAT
1 AAAAATGAAAAAAAAT
1153147 AATAAATGAAAAAGAGAA-
1 AA-AAATGAAAAA-A-AAT
1153165 AAAAAT-AAAAAATAAT
1 AAAAATGAAAAAA-AAT
1153181 AAAAATGAA
1 AAAAATGAA
1153190 TGAAAACTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
15 16 0.26
16 26 0.42
17 15 0.24
18 3 0.05
19 2 0.03
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (16 bp):
AAAAATGAAAAAAAAT
Found at i:1154831 original size:13 final size:13
Alignment explanation
Indices: 1154813--1154842 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1154803 ATACATTGTT
*
1154813 CATTGTATCGATA
1 CATTGTATCAATA
1154826 CATTGTATCAATA
1 CATTGTATCAATA
1154839 CATT
1 CATT
1154843 ATGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:1154870 original size:62 final size:63
Alignment explanation
Indices: 1154763--1154891 Score: 206
Period size: 62 Copynumber: 2.1 Consensus size: 63
1154753 ATACATTATT
* * * *
1154763 CATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATTGTTCATTGTATCGATA
1 CATTGTATCAATACATTATGGGTTTTACCCAGATGTATCGATACATTGTTCAATGCATCGATA
*
1154826 CATTGTATCAATACATTATGGG-TTTACCCAGATGTATCGATACATTTTTCAATGCATCGATA
1 CATTGTATCAATACATTATGGGTTTTACCCAGATGTATCGATACATTGTTCAATGCATCGATA
1154888 CATT
1 CATT
1154892 CAGGCATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
62 41 0.67
63 20 0.33
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.39
Consensus pattern (63 bp):
CATTGTATCAATACATTATGGGTTTTACCCAGATGTATCGATACATTGTTCAATGCATCGATA
Found at i:1157434 original size:79 final size:79
Alignment explanation
Indices: 1157147--1157434 Score: 289
Period size: 79 Copynumber: 3.6 Consensus size: 79
1157137 TAGCCCCGGT
** * * * * *
1157147 TTTATTT-TCAAAACATCAATTTTTCATAATCGGAGATACTCTAA-TCCCGTTA-TTTCTAAGTG
1 TTTATTTCT-AAAACATTGATTTTTCACAATCAGAGATACTCCAACT-CCGTTATTTTC-GAGAG
1157209 GATACTCCAACCCCGAC
63 GATACTCCAACCCCGAC
* * * * * *
1157226 TTTATTTCTAAAATATTGATTTCTCACAATCAGTGATACTCCAACTCCATTATTTTGGCGAGGAT
1 TTTATTTCTAAAACATTGATTTTTCACAATCAGAGATACTCCAACTCCGTTATTTTCGAGAGGAT
1157291 ACTCCAACCCCGAC
66 ACTCCAACCCCGAC
* * * * *
1157305 TTTATTTCTAAAGCATTGATTTTCCACAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGAT
1 TTTATTTCTAAAACATTGATTTTTCACAATCAGAGATACTCCAACTCCGTTATTTTCGAGAGGAT
**
1157370 ACTCCAACCCCGGT
66 ACTCCAACCCCGAC
* * *
1157384 TTTATTT-TCAAAACACTGATTTTTCATAATC-GAGGATACTCCAGCTCCGTT
1 TTTATTTCT-AAAACATTGATTTTTCACAATCAGA-GATACTCCAACTCCGTT
1157435 TTTATCTCCA
Statistics
Matches: 172, Mismatches: 32, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
78 2 0.01
79 165 0.96
80 5 0.03
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (79 bp):
TTTATTTCTAAAACATTGATTTTTCACAATCAGAGATACTCCAACTCCGTTATTTTCGAGAGGAT
ACTCCAACCCCGAC
Found at i:1170047 original size:1 final size:1
Alignment explanation
Indices: 1170043--1170110 Score: 64
Period size: 1 Copynumber: 68.0 Consensus size: 1
1170033 TTTTTTTAAC
* * ** * * * *
1170043 AAAAAACAAAACAAAAAACCAAAAAAAAAAAAACAAAAACAAAAAAAAAAAGAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1170108 AAA
1 AAA
1170111 GAGAGAAAAG
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:1170057 original size:12 final size:12
Alignment explanation
Indices: 1170040--1170102 Score: 71
Period size: 12 Copynumber: 5.6 Consensus size: 12
1170030 TTCTTTTTTT
1170040 AACAAAAAACAA
1 AACAAAAAACAA
*
1170052 AACAAAAAACCA
1 AACAAAAAACAA
1170064 AA-AAAAAA-AA
1 AACAAAAAACAA
1170074 AAC-AAAAACAA
1 AACAAAAAACAA
* *
1170085 AAAAAAAAAGAA
1 AACAAAAAACAA
1170097 AA-AAAA
1 AACAAAA
1170103 GAAAAAAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
10 8 0.18
11 14 0.32
12 22 0.50
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (12 bp):
AACAAAAAACAA
Found at i:1170075 original size:22 final size:21
Alignment explanation
Indices: 1170043--1170110 Score: 86
Period size: 21 Copynumber: 3.2 Consensus size: 21
1170033 TTTTTTTAAC
*
1170043 AAAAAACAAAACAAAAAACCAA
1 AAAAAAAAAAACAAAAAA-CAA
1170065 AAAAAAAAAAAC-AAAAACAA
1 AAAAAAAAAAACAAAAAACAA
*
1170085 AAAAAAAAAGAA-AAAAAAGAA
1 AAAAAAAAA-AACAAAAAACAA
1170106 AAAAA
1 AAAAA
1170111 GAGAGAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
20 12 0.29
21 19 0.45
22 11 0.26
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAACAAAAAACAA
Found at i:1170078 original size:27 final size:26
Alignment explanation
Indices: 1170063--1170124 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
1170053 ACAAAAAACC
1170063 AAAAA-AAAAAAAACAAAAACAAAAAA
1 AAAAAGAAAAAAAAC-AAAACAAAAAA
* *
1170089 AAAAAGAAAAAAAAGAAAA-AAAGAGA
1 AAAAAGAAAAAAAACAAAACAAA-AAA
*
1170115 GAAAAGAAAA
1 AAAAAGAAAA
1170125 GAACCTGCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 3 0.10
26 20 0.65
27 8 0.26
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAAAAAACAAAACAAAAAA
Found at i:1170084 original size:33 final size:34
Alignment explanation
Indices: 1170044--1170109 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
1170034 TTTTTTAACA
* *
1170044 AAAAACAAAACAAAAAACCAAAAAAA-AAAAAAC
1 AAAAACAAAAAAAAAAACAAAAAAAAGAAAAAAC
*
1170077 AAAAACAAAAAAAAAAAGAAAAAAAAGAAAAAA
1 AAAAACAAAAAAAAAAACAAAAAAAAGAAAAAA
1170110 AGAGAGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 23 0.79
34 6 0.21
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (34 bp):
AAAAACAAAAAAAAAAACAAAAAAAAGAAAAAAC
Found at i:1170101 original size:21 final size:20
Alignment explanation
Indices: 1170040--1170110 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
1170030 TTCTTTTTTT
* *
1170040 AACAAAAAACAAAACAAAAA
1 AACAAAAAAAAAAAAAAAAA
* *
1170060 ACCAAAAAAAAAAAAACAAA
1 AACAAAAAAAAAAAAAAAAA
1170080 AACAAAAAAAAAAAGAAAAAA
1 AACAAAAAAAAAAA-AAAAAA
*
1170101 AAGAAAAAAA
1 AACAAAAAAA
1170111 GAGAGAAAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (20 bp):
AACAAAAAAAAAAAAAAAAA
Found at i:1170109 original size:28 final size:27
Alignment explanation
Indices: 1170043--1170110 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
1170033 TTTTTTTAAC
*
1170043 AAAAAACAAAACAAAAAACCAAAAAAAA
1 AAAAAAAAAAACAAAAAA-CAAAAAAAA
* *
1170071 AAAAACAAAAACAAAAAAAAAAAGAAAA
1 AAAAAAAAAAACAAAAAACAAAA-AAAA
1170099 AAAAGAAAAAAA
1 AAAA-AAAAAAA
1170111 GAGAGAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 4 0.12
28 24 0.71
29 6 0.18
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (27 bp):
AAAAAAAAAAACAAAAAACAAAAAAAA
Found at i:1170111 original size:17 final size:17
Alignment explanation
Indices: 1170063--1170124 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
1170053 ACAAAAAACC
*
1170063 AAAAAA-AAAAAAACAA
1 AAAAAAGAAAAAAAGAA
*
1170079 AAACAAAAAAAAAAAGAA
1 AAA-AAAGAAAAAAAGAA
*
1170097 AAAAAAGAAAAAAAGAG
1 AAAAAAGAAAAAAAGAA
*
1170114 AGAAAAGAAAA
1 AAAAAAGAAAA
1170125 GAACCTGCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
16 3 0.08
17 25 0.62
18 12 0.30
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAAGAA
Found at i:1170119 original size:10 final size:9
Alignment explanation
Indices: 1170063--1170124 Score: 67
Period size: 9 Copynumber: 7.1 Consensus size: 9
1170053 ACAAAAAACC
1170063 AAAAA-AAA
1 AAAAAGAAA
*
1170071 AAAAACAAA
1 AAAAAGAAA
1170080 AACAAA-AAA
1 AA-AAAGAAA
1170089 AAAAAGAAA
1 AAAAAGAAA
1170098 AAAAAG-AA
1 AAAAAGAAA
*
1170106 AAAAAGAGA
1 AAAAAGAAA
*
1170115 GAAAAGAAA
1 AAAAAGAAA
1170124 A
1 A
1170125 GAACCTGCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
8 16 0.35
9 27 0.59
10 3 0.07
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:1170127 original size:10 final size:10
Alignment explanation
Indices: 1170063--1170127 Score: 60
Period size: 10 Copynumber: 6.2 Consensus size: 10
1170053 ACAAAAAACC
1170063 AAAAAAAAA-
1 AAAAAAAAAG
*
1170072 AAAACAAAAAC
1 AAAA-AAAAAG
*
1170083 AAAAAAAAAA
1 AAAAAAAAAG
1170093 AGAAAAAAAAG
1 A-AAAAAAAAG
1170104 AAAAAAAGAGAG
1 AAAAAAA-A-AG
*
1170116 AAAAGAAAAG
1 AAAAAAAAAG
1170126 AA
1 AA
1170128 CCTGCTTAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
9 4 0.08
10 21 0.44
11 15 0.31
12 8 0.17
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:1171315 original size:61 final size:61
Alignment explanation
Indices: 1171138--1171440 Score: 270
Period size: 61 Copynumber: 5.1 Consensus size: 61
1171128 GAGCAGGACG
* *
1171138 CCTTTTAAAGCCTACACCAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACG------
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCTTTCT
* * * * * *
1171193 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGT-CTGTAAGGAGCAAGACGCCTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCT-CAAAGAGCAGGACGCTTTCT
* * * * *
1171254 CCTTTTAAAGCCTACACAAGTTGGTGGCACCTTTCAATCCTCAAAAAGCAGGATGCTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCTTTCT
* * * * *
1171315 -CTTTGCAAAGCCCACACAAGTTGGTGGCA-TCTTCCAATCCTCAAAGAGTAGGACACATTT-T
1 CCTTT-TAAAGCCCACACAAGTTGGTGGCACT-TTTCAGTCCTCAAAGAGCAGGACGC-TTTCT
* * * *
1171376 -CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCGAAGAGCAGGACGCTTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCTTTCT
1171437 CCTT
1 CCTT
1171441 CTTTCCTTTG
Statistics
Matches: 198, Mismatches: 34, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
54 2 0.01
55 40 0.20
56 4 0.02
60 7 0.04
61 136 0.69
62 9 0.05
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.28
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCTTTCT
Found at i:1171526 original size:42 final size:39
Alignment explanation
Indices: 1171412--1171556 Score: 130
Period size: 42 Copynumber: 3.5 Consensus size: 39
1171402 GCACTTTTTA
* **
1171412 GTCCTCGAAGAGCAGGACGCTTTTTCCTTC-TTTCCTTT
1 GTCCTCAAAGAGCAGGACGCTTTTTTTTTCTTTTCCTTT
* **
1171450 GTCCTCAAAGAGCATGACAAATTTCATTTCTTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAGGAC-GCTTT--TTT-TTTCTTTT-CC-TTT
*
1171495 GTCCTCAAAGAGCAGGATGTCTTTTTTTTTCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACG-CTTTTTTTTTC--TTTTCCTTT
*
1171537 GTCCTCAAAGAGTAGGACGC
1 GTCCTCAAAGAGCAGGACGC
1171557 ATTTCATTTC
Statistics
Matches: 85, Mismatches: 12, Indels: 17
0.75 0.11 0.15
Matches are distributed among these distances:
38 16 0.19
39 3 0.04
41 3 0.04
42 27 0.32
43 8 0.09
44 6 0.07
45 22 0.26
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (39 bp):
GTCCTCAAAGAGCAGGACGCTTTTTTTTTCTTTTCCTTT
Found at i:1171689 original size:41 final size:42
Alignment explanation
Indices: 1171434--1171725 Score: 157
Period size: 42 Copynumber: 6.8 Consensus size: 42
1171424 CAGGACGCTT
* * *
1171434 TTTCCT-TCTTTCCTTTGTCCTCAAAGAGCATGACA-AATTTCA
1 TTTCCTAT-TTTCCTTTGTCCTCAAAGAGTAGGACACACTTT-A
* * * ** * *
1171476 TTTCTTTCTTTTCCCTTTTGTCCTCAAAGAGCAGGATGTC-TTTTT
1 TTTC-CTATTTT-CC-TTTGTCCTCAAAGAGTAGGA-CACACTTTA
* * *
1171521 TTTTCTTTTTTCCTTTGTCCTCAAAGAGTAGGACGCA-TTTCA
1 TTTCCTATTTTCCTTTGTCCTCAAAGAGTAGGACACACTTT-A
** * *
1171563 TTTCCTTATTTTCTCTTCTAGTTTTCAAAGAGCATGACACACTTTA
1 TTTCC-TATTTTC-CTT-T-GTCCTCAAAGAGTAGGACACACTTTA
* *
1171609 TTCTCCT-TTTTCCTTTGTCCTCAAAAAGTAGGAAACA-TTTA
1 TT-TCCTATTTTCCTTTGTCCTCAAAGAGTAGGACACACTTTA
* * ** *
1171650 GTTT-CTATTTTCCTTTGTCTTCAAAGAGTAAGATGCATTTTA
1 -TTTCCTATTTTCCTTTGTCCTCAAAGAGTAGGACACACTTTA
* * * * *
1171692 TTTCCTTTTTTCCTTAGTCCCCAAGGAGCAGGAC
1 TTTCCTATTTTCCTTTGTCCTCAAAGAGTAGGAC
1171726 CTATTTCATT
Statistics
Matches: 193, Mismatches: 39, Indels: 36
0.72 0.15 0.13
Matches are distributed among these distances:
40 2 0.01
41 37 0.19
42 70 0.36
43 13 0.07
44 14 0.07
45 28 0.15
46 23 0.12
47 6 0.03
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.44
Consensus pattern (42 bp):
TTTCCTATTTTCCTTTGTCCTCAAAGAGTAGGACACACTTTA
Found at i:1172194 original size:16 final size:16
Alignment explanation
Indices: 1172173--1172219 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
1172163 TTCTTTTTTT
1172173 AACAAAAAAAAAGAAA
1 AACAAAAAAAAAGAAA
1172189 AACAAAAAAAAAGAAA
1 AACAAAAAAAAAGAAA
*
1172205 AAAAAGAAAAAAAGA
1 AACAA-AAAAAAAGA
1172220 GAGAAAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 20 0.69
17 9 0.31
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (16 bp):
AACAAAAAAAAAGAAA
Found at i:1172217 original size:17 final size:17
Alignment explanation
Indices: 1172178--1172231 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
1172168 TTTTTAACAA
*
1172178 AAAAAAAGAAAAACAA-
1 AAAAAAAGAAAAAAAAG
1172194 AAAAAAAGAAAAAAAAG
1 AAAAAAAGAAAAAAAAG
* *
1172211 AAAAAAAGAGAGAAAAG
1 AAAAAAAGAAAAAAAAG
1172228 AAAA
1 AAAA
1172232 GAACCTGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
16 15 0.44
17 19 0.56
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAAG
Found at i:1172226 original size:10 final size:9
Alignment explanation
Indices: 1172177--1172231 Score: 62
Period size: 8 Copynumber: 6.4 Consensus size: 9
1172167 TTTTTTAACA
1172177 AAAAAAAAG
1 AAAAAAAAG
*
1172186 -AAAAACA-
1 AAAAAAAAG
1172193 AAAAAAAAG
1 AAAAAAAAG
1172202 AAAAAAAAG
1 AAAAAAAAG
1172211 -AAAAAAAG
1 AAAAAAAAG
* *
1172219 AGAGAAAAG
1 AAAAAAAAG
1172228 AAAA
1 AAAA
1172232 GAACCTGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 20 0.54
9 17 0.46
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1172234 original size:10 final size:10
Alignment explanation
Indices: 1172176--1172234 Score: 59
Period size: 10 Copynumber: 5.9 Consensus size: 10
1172166 TTTTTTTAAC
1172176 AAAAAA-AAA
1 AAAAAAGAAA
* *
1172185 GAAAAACAAA
1 AAAAAAGAAA
1172195 AAAAAAG-AA
1 AAAAAAGAAA
1172204 AAAAAAGAAA
1 AAAAAAGAAA
1172214 AAAAGAGAGAAA
1 AAAA-A-AGAAA
*
1172226 AGAAAAGAA
1 AAAAAAGAA
1172235 CCTGATTAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
9 14 0.33
10 18 0.43
11 2 0.05
12 8 0.19
ACGTcount: A:0.85, C:0.02, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1173382 original size:61 final size:57
Alignment explanation
Indices: 1173226--1173389 Score: 158
Period size: 55 Copynumber: 2.9 Consensus size: 57
1173216 TTACCCTTTT
* * * *
1173226 GTCCTCAAAGAGCAGGATG-CCTTTTAAAGCCTACACCAGTTGGTGGC-ATTTTCCA
1 GTCCTTAAAGAGCAAGACGTCCTTTTAAAGCCTACACAAGTTGGTGGCAATTTTCCA
* * * *
1173281 GTCCTTAAAGAGCAGGACGT-CTTTCAAAGCCCACACAAGTTGGTGGCAATTTT-TA
1 GTCCTTAAAGAGCAAGACGTCCTTTTAAAGCCTACACAAGTTGGTGGCAATTTTCCA
*
1173336 GT-CTGTAAGGAGCAAGACGCCTTCTCCTTTTAAAGCCTACACAAGTTGGTGGCA
1 GTCCT-TAAAGAGCAAGACG-----TCCTTTTAAAGCCTACACAAGTTGGTGGCA
1173390 CCTTTCAATC
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
54 2 0.02
55 56 0.62
56 5 0.06
60 1 0.01
61 26 0.29
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.27
Consensus pattern (57 bp):
GTCCTTAAAGAGCAAGACGTCCTTTTAAAGCCTACACAAGTTGGTGGCAATTTTCCA
Found at i:1173543 original size:61 final size:61
Alignment explanation
Indices: 1173246--1173544 Score: 262
Period size: 61 Copynumber: 5.0 Consensus size: 61
1173236 AGCAGGATGC
* * * *
1173246 CTTTT-AAAGCCTACACCAGTTGGTGGCA-TTTTCCAGTCCTTAAAGAGCAGGACG-----T
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAATCCTCAAAGAGCAGGACGCCTTTT
* * * * * * *
1173301 C-TTTCAAAGCCCACACAAGTTGGTGGCAATTTTTAGT-CTGTAAGGAGCAAGACGCCTTCTC
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAATCCT-CAAAGAGCAGGACGCCTT-TT
* * * *
1173362 CTTTT-AAAGCCTACACAAGTTGGTGGCACCTTTCAATCCTCAAAAAGCAGGATG-CTTTCT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAATCCTCAAAGAGCAGGACGCCTTT-T
* * *
1173422 CTTTGCAAAGCCCACACAAGTTGGTGGCA-TCTTCCAATCCTCAAAGAGTAGGACGCCTTTT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACT-TTTCAATCCTCAAAGAGCAGGACGCCTTTT
* * * * *
1173483 TTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCGAAGAGCAGGACGCCTTTT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAATCCTCAAAGAGCAGGACGCCTTTT
1173544 C
1 C
1173545 CTTCTTTCCT
Statistics
Matches: 195, Mismatches: 33, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
54 5 0.03
55 37 0.19
56 4 0.02
59 1 0.01
60 7 0.04
61 131 0.67
62 10 0.05
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (61 bp):
CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAATCCTCAAAGAGCAGGACGCCTTTT
Found at i:1173570 original size:38 final size:39
Alignment explanation
Indices: 1173519--1173663 Score: 112
Period size: 42 Copynumber: 3.5 Consensus size: 39
1173509 GCACTTTTTA
*
1173519 GTCCTCGAAGAGCAGGACGC-CTTTTCCTTCTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCTCTTTTCCTTCTTTCCTTT
* * * *
1173557 GTCCTCAAAGAGCATGACACATTTCATTTCTTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAGGACGC---TCTTTTCCTTC-TTT-CC-TTT
* * * *
1173602 GTCCTCAAAGAGCAGGATGTCTTTTTTTTTCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACG-C--TCTTTTCCTTCTTTCCTTT
*
1173644 GTCCTCAAAGAGTAGGACGC
1 GTCCTCAAAGAGCAGGACGC
1173664 ACTTCATTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
38 17 0.20
41 1 0.01
42 28 0.33
43 5 0.06
44 5 0.06
45 27 0.32
46 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.16, T:0.41
Consensus pattern (39 bp):
GTCCTCAAAGAGCAGGACGCTCTTTTCCTTCTTTCCTTT
Found at i:1174466 original size:20 final size:20
Alignment explanation
Indices: 1174441--1174565 Score: 97
Period size: 20 Copynumber: 5.8 Consensus size: 20
1174431 TTTTCACGAT
1174441 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
1174461 TTGTATCGATACATTCTGGGTTTTACCCA
1 TTGTATCGATACA-T-T--G--TT---CA
* * *
1174490 GATGTATCGGTAAATTGTTCA
1 -TTGTATCGATACATTGTTCA
*
1174511 TTGTATCGATAAATTGTTCA
1 TTGTATCGATACATTGTTCA
* * *
1174531 TTGTATCGGTACATTATACA
1 TTGTATCGATACATTGTTCA
1174551 TTGTATCGATACATT
1 TTGTATCGATACATT
1174566 CTGGGTTTAC
Statistics
Matches: 85, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
20 61 0.72
21 3 0.04
22 1 0.01
24 3 0.04
26 3 0.04
28 1 0.01
29 3 0.04
30 10 0.12
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1174553 original size:90 final size:89
Alignment explanation
Indices: 1174441--1174610 Score: 268
Period size: 90 Copynumber: 1.9 Consensus size: 89
1174431 TTTTCACGAT
* * *
1174441 TTGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGGTAAATT
1 TTGTATCGATACATTATACATTGTATCGATACATTCTGGG-TTTACCCAGATGTATCGATAAATT
*
1174506 GTTCATTGTATCGATAAATTGTTCA
65 GTTCAATGTATCGATAAATTGTTCA
* * *
1174531 TTGTATCGGTACATTATACATTGTATCGATACATTCTGGGTTTACCCAGATGTATCGATACATTT
1 TTGTATCGATACATTATACATTGTATCGATACATTCTGGGTTTACCCAGATGTATCGATAAATTG
1174596 TTCAATGTATCGATA
66 TTCAATGTATCGATA
1174611 CATTCAGGCA
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 36 0.49
90 37 0.51
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (89 bp):
TTGTATCGATACATTATACATTGTATCGATACATTCTGGGTTTACCCAGATGTATCGATAAATTG
TTCAATGTATCGATAAATTGTTCA
Found at i:1177043 original size:79 final size:79
Alignment explanation
Indices: 1176910--1177208 Score: 307
Period size: 79 Copynumber: 3.8 Consensus size: 79
1176900 TTTTCATCTC
* * ** * * * *
1176910 GGGATACTCTAGCCCCGGTTTTATTTCCAAAACATTAATTTTTCATAATTGAGGATACTCCAATC
1 GGGATACTCCAACCCCGACTTTATTTCTAAAACATCAATTTTTCACAATCGAGGATACTCCAATC
1176975 CTGTTA-TTTCTAAG
66 CTGTTATTTTC-AAG
* ** * *
1176989 GGGATACTCCAACCCCGACTTTATTTCTAAAATATTGATTTCTCACAATCGAGGATACTCCAACC
1 GGGATACTCCAACCCCGACTTTATTTCTAAAACATCAATTTTTCACAATCGAGGATACTCCAATC
* *
1177054 CTGTTATTTTGATG
66 CTGTTATTTTCAAG
* * * *
1177068 AGGATACTCCAACCCTGACCTTATTTC-AAAAGCATCAATTTTTCACAATCGGGGATACTCCAAT
1 GGGATACTCCAACCCCGACTTTATTTCTAAAA-CATCAATTTTTCACAATCGAGGATACTCCAAT
*
1177132 CCCGTTATTTTCAAG
65 CCTGTTATTTTCAAG
* * * * * * *
1177147 GGGATACTCTAACCCCGATTTTATTT-TCAAAATATCGATTTTCCATAATCGGGGATACTCCA
1 GGGATACTCCAACCCCGACTTTATTTCT-AAAACATCAATTTTTCACAATCGAGGATACTCCA
1177209 GCCCCATTGT
Statistics
Matches: 182, Mismatches: 34, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
78 4 0.02
79 171 0.94
80 7 0.04
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (79 bp):
GGGATACTCCAACCCCGACTTTATTTCTAAAACATCAATTTTTCACAATCGAGGATACTCCAATC
CTGTTATTTTCAAG
Found at i:1178368 original size:41 final size:41
Alignment explanation
Indices: 1178324--1178473 Score: 149
Period size: 41 Copynumber: 3.6 Consensus size: 41
1178314 CATTGACTAG
* *
1178324 TATGGTTTTGTCTCGATCAACTCTTCTAACTTGTTGGTTTG
1 TATGGTTTCGTCTCGATCAACTCTTCTAACTTGTTGGTTTA
** * **
1178365 TATGGTTTCGTC-CTGGCCAACTATTTTCTAACTTGTTGACTTA
1 TATGGTTTCGTCTC-GATCAAC--TCTTCTAACTTGTTGGTTTA
* * *
1178408 TATGGTTTCATCTCGATCAACTCTTTTAACTTGTTGGTTCA
1 TATGGTTTCGTCTCGATCAACTCTTCTAACTTGTTGGTTTA
* * *
1178449 TATGGTTTCATCCCGACCAACTCTT
1 TATGGTTTCGTCTCGATCAACTCTT
1178474 TTCTAACTCA
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
40 1 0.01
41 54 0.61
43 32 0.36
44 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (41 bp):
TATGGTTTCGTCTCGATCAACTCTTCTAACTTGTTGGTTTA
Found at i:1178412 original size:43 final size:41
Alignment explanation
Indices: 1178347--1178840 Score: 130
Period size: 43 Copynumber: 11.7 Consensus size: 41
1178337 CGATCAACTC
* * * *
1178347 TTCTAACTTGTTGGTTTGTATGGTTTCGTCCTGGCCAACTATT
1 TTCTAACTTGTT-GCTTATATGGTTTCATCCTGACCAACT-TT
* *
1178390 TTCTAACTTGTTGACTTATATGGTTTCAT-CTCGATCAACTCT
1 TTCTAACTTGTTG-CTTATATGGTTTCATCCT-GACCAACTTT
* *
1178432 TT-TAACTTGTTGGTTCATATGGTTTCATCCCGACCAACTCTT
1 TTCTAACTTGTTGCTT-ATATGGTTTCATCCTGACCAACT-TT
** * * ** * *
1178474 TTCTAACTCATTAGTTTGTATAATTTTAT-CTCGGCCAACTGTT
1 TTCTAACTTGTT-GCTTATATGGTTTCATCCT-GACCAACT-TT
* * ** * * ** **
1178517 TTTTAATTTGTTAATTTTTATGGTTTCTTTTTGGTCAACTTT
1 TTCTAACTTGTT-GCTTATATGGTTTCATCCTGACCAACTTT
* * *
1178559 TT-TAACTTGTTAG-TTCATATGGTTTTATCC-CAGCTAACTTAT
1 TTCTAACTTGTT-GCTT-ATATGGTTTCATCCTGA-CCAACTT-T
** * * * * *
1178601 TTCTAACTCATTGGCTTGTATGGTTTCATCTTGGCTAATTCTT
1 TTCTAACTTGTT-GCTTATATGGTTTCATCCTGACCAACT-TT
* * * * * * **
1178644 TTCTAA-TTCATTAACTCATATAGTTTCGTCCTAATTAAC-TT
1 TTCTAACTT-GTT-GCTTATATGGTTTCATCCTGACCAACTTT
* ** * *
1178685 TTCTAACTTGTTGGTTCATATGGTTTTGTCCTAACCAACTCT
1 TTCTAACTTGTTGCTT-ATATGGTTTCATCCTGACCAACTTT
* * *
1178727 TT-TAACTTGTTAG-TTCATATGGTTTTAT-CTCACCCAACTCAT
1 TTCTAACTTGTT-GCTT-ATATGGTTTCATCCTGA-CCAACT-TT
* * * * * **
1178769 TTCTAACTTATTAACTTGTATGGTTTCATCCCGATCAAC-AC
1 TTCTAACTTGTT-GCTTATATGGTTTCATCCTGACCAACTTT
* *
1178810 TTCTAACTTGTTGACTTGTATGGTTTTATCC
1 TTCTAACTTGTTG-CTTATATGGTTTCATCC
1178841 AGTCAACTCT
Statistics
Matches: 337, Mismatches: 87, Indels: 56
0.70 0.18 0.12
Matches are distributed among these distances:
40 8 0.02
41 137 0.41
42 28 0.08
43 153 0.45
44 11 0.03
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (41 bp):
TTCTAACTTGTTGCTTATATGGTTTCATCCTGACCAACTTT
Found at i:1178438 original size:84 final size:83
Alignment explanation
Indices: 1178294--1178900 Score: 299
Period size: 84 Copynumber: 7.2 Consensus size: 83
1178284 TCTCATGACT
** * *
1178294 TGGCCAACTCCTTTT-TAACTCATTGAC-TAGTATGGTTTTGTCTCGATCAACTCTTCTAACTTG
1 TGGCCAACT-CTTTTCTAACTTGTT-ACTTA-TATGGTTTTATCTCGATCAACTCTTTTAACTTG
*
1178357 TTGGTTTGTATGGTTTCGTCC
63 TTGGTTTGTATGGTTTCATCC
* *
1178378 TGGCCAACTATTTTCTAACTTGTTGACTTATATGGTTTCATCTCGATCAACTCTTTTAACTTGTT
1 TGGCCAACTCTTTTCTAACTTGTT-ACTTATATGGTTTTATCTCGATCAACTCTTTTAACTTGTT
**
1178443 GGTTCATATGGTTTCATCC
65 GGTTTGTATGGTTTCATCC
* * ** * * ** ** * *
1178462 CGACCAACTCTTTTCTAACTCATTAGTTTGTATAATTTTATCTCGGCCAACTGTTTTTTAATTTG
1 TGGCCAACTCTTTTCTAACTTGTTA-CTTATATGGTTTTATCTCGATCAAC--TCTTTTAACTTG
** * * **
1178527 TTAATTTTTATGGTTTCTTTT
63 TTGGTTTGTATGGTTTCATCC
* * * * * *
1178548 TGGTCAACT-TTTT-TAACTTGTTAGTTCATATGGTTTTATC-CCAGCTAACTTATTTCTAACTC
1 TGGCCAACTCTTTTCTAACTTGTTACTT-ATATGGTTTTATCTCGATC-AAC-TCTTT-TAACTT
* * *
1178610 ATTGGCTTGTATGGTTTCATCT
62 GTTGGTTTGTATGGTTTCATCC
* * * * * ** * *
1178632 TGGCTAATTCTTTTCTAA-TTCATTAACTCATATAGTTTCGTC-CTAATTAACT-TTTCTAACTT
1 TGGCCAACTCTTTTCTAACTT-GTT-ACTTATATGGTTTTATCTC-GATCAACTCTTT-TAACTT
** **
1178694 GTTGGTTCATATGGTTTTGTCC
62 GTTGGTTTGTATGGTTTCATCC
** * *
1178716 TAACCAACTC-TTT-TAACTTGTTAGTTCATATGGTTTTATCTC-ACCCAACTCATTTCTAACTT
1 TGGCCAACTCTTTTCTAACTTGTTACTT-ATATGGTTTTATCTCGA-TCAACTC-TTT-TAACTT
* ***
1178778 ATTAACTTGTATGGTTTCATCC
62 GTTGGTTTGTATGGTTTCATCC
* ** * * ** *
1178800 CGATCAACAC--TTCTAACTTGTTGACTTGTATGGTTTTATC-C-AGTCAACTCTCATGACTTGT
1 TGGCCAACTCTTTTCTAACTTGTT-ACTTATATGGTTTTATCTCGA-TCAACTCTTTTAACTTGT
**
1178861 TGGTTTGTATGGTTTTGTCC
64 TGGTTTGTATGGTTTCATCC
* *
1178881 TAGCCAACTCCTTTCTAACT
1 TGGCCAACTCTTTTCTAACT
1178901 CATCGGTTCA
Statistics
Matches: 385, Mismatches: 115, Indels: 47
0.70 0.21 0.09
Matches are distributed among these distances:
81 29 0.08
82 20 0.05
83 37 0.10
84 231 0.60
85 16 0.04
86 49 0.13
87 3 0.01
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (83 bp):
TGGCCAACTCTTTTCTAACTTGTTACTTATATGGTTTTATCTCGATCAACTCTTTTAACTTGTTG
GTTTGTATGGTTTCATCC
Found at i:1178528 original size:127 final size:126
Alignment explanation
Indices: 1178360--1178840 Score: 402
Period size: 127 Copynumber: 3.8 Consensus size: 126
1178350 TAACTTGTTG
** * * *
1178360 GTTTGTATGGTTTCGTC-CTGGCCAACTATTTTCTAACTTGTTGACTTATATGGTTTCATCTCGA
1 GTTTGTATGGTTTTATCTC-GGCCAACTCTTTTCTAACTTATTAACTTATATGGTTTCATCTCGA
*
1178424 TCAACTCTTTTAACTTGTTGGTTCATATGGTTTCATCCCGACCAACTCTTTTCTAACTCATTA
65 TCAACTCTTTTAACTTGTTGGTTCATATGGTTTTATCCC-ACCAACTCTTTTCTAACTCATTA
** * * * * * * * * * *
1178487 GTTTGTATAATTTTATCTCGGCCAACTGTTTTTTAATTTGTTAATTTTTATGGTTTCTTTTTGGT
1 GTTTGTATGGTTTTATCTCGGCCAACTCTTTTCTAACTTATTAACTTATATGGTTTCATCTCGAT
* * * *
1178552 CAACTTTTTTAACTTGTTAGTTCATATGGTTTTATCCCAGCTAACT-TATTTCTAACTCATTG
66 CAACTCTTTTAACTTGTTGGTTCATATGGTTTTATCCCA-CCAACTCT-TTTCTAACTCATTA
* * * * * * * * *
1178614 GCTTGTATGGTTTCATCTTGGCTAATTCTTTTCTAA-TTCATTAACTCATATAGTTTCGTC-CTA
1 GTTTGTATGGTTTTATCTCGGCCAACTCTTTTCTAACTT-ATTAACTTATATGGTTTCATCTC-G
* * * **
1178677 ATTAACT-TTTCTAACTTGTTGGTTCATATGGTTTTGTCCTAACCAACTC-TTT-TAACTTGTTA
64 ATCAACTCTTT-TAACTTGTTGGTTCATATGGTTTTATCC-CACCAACTCTTTTCTAACTCATTA
** ** * * *
1178739 GTTCATATGGTTTTATCTCACCCAACTCATTTCTAACTTATTAACTTGTATGGTTTCATCCCGAT
1 GTTTGTATGGTTTTATCTCGGCCAACTCTTTTCTAACTTATTAACTTATATGGTTTCATCTCGAT
* * * *
1178804 CAACACTTCTAACTTGTTGACTT-GTATGGTTTTATCC
66 CAACTCTTTTAACTTGTTG-GTTCATATGGTTTTATCC
1178841 AGTCAACTCT
Statistics
Matches: 275, Mismatches: 67, Indels: 26
0.75 0.18 0.07
Matches are distributed among these distances:
125 77 0.28
126 17 0.06
127 179 0.65
128 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (126 bp):
GTTTGTATGGTTTTATCTCGGCCAACTCTTTTCTAACTTATTAACTTATATGGTTTCATCTCGAT
CAACTCTTTTAACTTGTTGGTTCATATGGTTTTATCCCACCAACTCTTTTCTAACTCATTA
Found at i:1178598 original size:41 final size:41
Alignment explanation
Indices: 1178553--1178755 Score: 131
Period size: 41 Copynumber: 4.9 Consensus size: 41
1178543 CTTTTTGGTC
* *
1178553 AACTTTTTTAACTTGTTAGTTCATATGGTTTTATCCCAGCT
1 AACTTTTTTAACTTGTTAGTTCATATGGTTTTATCCTAACT
** * * * * **
1178594 AACTTATTTCTAACTCATTGGCTT-GTATGGTTTCATCTTGGCT
1 AACTT-TTT-TAACTTGTTAG-TTCATATGGTTTTATCCTAACT
* * ** * ** *
1178637 AATTCTTTTCTAA-TTCATTAACTCATATAGTTTCGTCCTAATT
1 AA--CTTTTTTAACTT-GTTAGTTCATATGGTTTTATCCTAACT
* * * *
1178680 AACTTTTCTAACTTGTTGGTTCATATGGTTTTGTCCTAACC
1 AACTTTTTTAACTTGTTAGTTCATATGGTTTTATCCTAACT
*
1178721 AACTCTTTTAACTTGTTAGTTCATATGGTTTTATC
1 AACTTTTTTAACTTGTTAGTTCATATGGTTTTATC
1178756 TCACCCAACT
Statistics
Matches: 122, Mismatches: 32, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
41 64 0.52
42 7 0.06
43 44 0.36
44 4 0.03
45 3 0.02
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (41 bp):
AACTTTTTTAACTTGTTAGTTCATATGGTTTTATCCTAACT
Found at i:1178764 original size:41 final size:42
Alignment explanation
Indices: 1178680--1178918 Score: 136
Period size: 41 Copynumber: 5.8 Consensus size: 42
1178670 CGTCCTAATT
* *
1178680 AACT-TTTCTAACTTGTTGGTTCATATGGTTTTGTCCTAACC
1 AACTCTTTCTAACTTGTTAGTTCATATGGTTTTATCCTAACC
*
1178721 AACTCTTT-TAACTTGTTAGTTCATATGGTTTTAT-CTCACCC
1 AACTCTTTCTAACTTGTTAGTTCATATGGTTTTATCCT-AACC
* * * * ** *
1178762 AACTCATTTCTAACTTATTAACTT-GTATGGTTTCATCCCGATC
1 AACTC-TTTCTAACTTGTT-AGTTCATATGGTTTTATCCTAACC
* * * **
1178805 AACAC-TTCTAACTTGTTGACTT-GTATGGTTTTATCC-AGTC
1 AACTCTTTCTAACTTGTT-AGTTCATATGGTTTTATCCTAACC
* * ** * *
1178845 AACTC--TCATGACTTGTTGGTTTGTATGGTTTTGTCCTAGCC
1 AACTCTTTC-TAACTTGTTAGTTCATATGGTTTTATCCTAACC
** **
1178886 AACTCCTTTCTAACTCATCGGTTCATATGGTTT
1 AACT-CTTTCTAACTTGTTAGTTCATATGGTTT
1178919 CATTCTGGTT
Statistics
Matches: 157, Mismatches: 29, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
39 4 0.03
40 29 0.18
41 71 0.45
42 7 0.04
43 40 0.25
44 6 0.04
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.44
Consensus pattern (42 bp):
AACTCTTTCTAACTTGTTAGTTCATATGGTTTTATCCTAACC
Found at i:1179200 original size:83 final size:81
Alignment explanation
Indices: 1178995--1179375 Score: 225
Period size: 84 Copynumber: 4.6 Consensus size: 81
1178985 TATCTTAATC
* ** * *
1178995 AACTTGTTGGTTTGTATGGTTTCAATCTA-GCCAACT-CTTTTCCCTCGTTGACTTGTATAGTTT
1 AACTTGTTGGTTTGTATGGTTTC--TTTAGGCCAACTCCTTTTAACTCGTTGACTCGTATGGTTT
* * **
1179058 TATCCTGGTCAACTCTCAT
64 TATCCTAGT-AATTCTTTT
* * * * * * *
1179077 GACTTATTGGTTTGTATGATTTCATTATGGCTAACACCTTTCTAACTCGTTGACTCGTACGGTTT
1 AACTTGTTGGTTTGTATGGTTTCTTTA-GGCCAACTCCTTT-TAACTCGTTGACTCGTATGGTTT
*
1179142 CATCCTAGTAATTCTTTT
64 TATCCTAGTAATTCTTTT
* * **
1179160 AACTTGTTGGTTTGTATGGTGTCGTTTAGGCCAACTCCTTTTTAACT-TTTGGTTCGTATGGTTT
1 AACTTGTTGGTTTGTATGGTTTC-TTTAGGCCAACTCC-TTTTAACTCGTTGACTCGTATGGTTT
* * *
1179224 TATCTTAGCCAACTCCTTTTT
64 TATCCTAG-TAA-TTC-TTTT
* * * * * *
1179245 AACTT-TTGGTTTGTATGGTTT-TATCTTGGCCAACTCTTTTTTAACTCATTAACTCGAATAGTT
1 AACTTGTTGGTTTGTATGGTTTCT-T-TAGGCCAACTC-CTTTTAACTCGTTGACTCGTATGGTT
* * *
1179308 TT-GCCTTAGCAAACTCTTTT
63 TTATCC-TAG-TAATTCTTTT
** * * *
1179328 AACTTGTTGGTTCATATAGTTTCATCATGGCCAACTCCTTTTTAACTC
1 AACTTGTTGGTTTGTATGGTTTCTTTA-GGCCAACTCC-TTTTAACTC
1179376 ATTGGTTTAT
Statistics
Matches: 228, Mismatches: 53, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
80 2 0.01
82 45 0.20
83 54 0.24
84 100 0.44
85 27 0.12
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.45
Consensus pattern (81 bp):
AACTTGTTGGTTTGTATGGTTTCTTTAGGCCAACTCCTTTTAACTCGTTGACTCGTATGGTTTTA
TCCTAGTAATTCTTTT
Found at i:1179219 original size:42 final size:43
Alignment explanation
Indices: 1179156--1179413 Score: 208
Period size: 43 Copynumber: 6.1 Consensus size: 43
1179146 CTAGTAATTC
* **
1179156 TTTTAACTTGTTGGTTTGTATGGTGTCGT-TTAGGCCAACTCCT
1 TTTTAACTT-TTGGTTTGTATGGTTTTATCTTAGGCCAACTCCT
*
1179199 TTTTAACTTTTGGTTCGTATGGTTTTATCTTA-GCCAACTCCT
1 TTTTAACTTTTGGTTTGTATGGTTTTATCTTAGGCCAACTCCT
*
1179241 TTTTAACTTTTGGTTTGTATGGTTTTATCTT-GGCCAACTCTT
1 TTTTAACTTTTGGTTTGTATGGTTTTATCTTAGGCCAACTCCT
* *** * * * ** *
1179283 TTTTAACTCATTAACTCGAATAGTTTTGCCTTA-GCAAACT-C-
1 TTTTAACT-TTTGGTTTGTATGGTTTTATCTTAGGCCAACTCCT
** * * *
1179324 TTTTAACTTGTTGGTTCATATAGTTTCATCAT-GGCCAACTCCT
1 TTTTAACTT-TTGGTTTGTATGGTTTTATCTTAGGCCAACTCCT
* * * *
1179367 TTTTAACTCATTGGTTTATATGGTTTCATCCT-GGCCAACTCCT
1 TTTTAACT-TTTGGTTTGTATGGTTTTATCTTAGGCCAACTCCT
1179410 TTTT
1 TTTT
1179414 CACTCATTGA
Statistics
Matches: 174, Mismatches: 32, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
41 27 0.16
42 73 0.42
43 74 0.43
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (43 bp):
TTTTAACTTTTGGTTTGTATGGTTTTATCTTAGGCCAACTCCT
Found at i:1179260 original size:84 final size:85
Alignment explanation
Indices: 1179078--1179413 Score: 247
Period size: 84 Copynumber: 4.0 Consensus size: 85
1179068 AACTCTCATG
* * * * * * * ** * *
1179078 ACTTATTGGTTTGTATGATTTCATTATGGCTAACACCTTTCTAACTCGTTGACTCGTACGGTTTC
1 ACTTGTTGGTTTGTATGGTTTCTTTA-GGCCAACTCCTTTTTAACTCATTGGTTCGTATGGTTTT
* * *
1179143 ATCCTAG-TAA-TTC-TTTTA
65 ATCTTAGCCAACTCCTTTTTA
* *
1179161 ACTTGTTGGTTTGTATGGTGTCGTTTAGGCCAACTCCTTTTTAACT-TTTGGTTCGTATGGTTTT
1 ACTTGTTGGTTTGTATGGTTTC-TTTAGGCCAACTCCTTTTTAACTCATTGGTTCGTATGGTTTT
1179225 ATCTTAGCCAACTCCTTTTTA
65 ATCTTAGCCAACTCCTTTTTA
* * *** * *
1179246 ACTT-TTGGTTTGTATGGTTT-TATCTTGGCCAACTCTTTTTTAACTCATTAACTCGAATAGTTT
1 ACTTGTTGGTTTGTATGGTTTCT-T-TAGGCCAACTCCTTTTTAACTCATTGGTTCGTATGGTTT
** *
1179309 TGCCTTAGCAAACT-C-TTTTA
64 TATCTTAGCCAACTCCTTTTTA
** * * * ** *
1179329 ACTTGTTGGTTCATATAGTTTCATCATGGCCAACTCCTTTTTAACTCATTGGTTTATATGGTTTC
1 ACTTGTTGGTTTGTATGGTTTCTTTA-GGCCAACTCCTTTTTAACTCATTGGTTCGTATGGTTTT
* *
1179394 ATCCTGGCCAACTCCTTTTT
65 ATCTTAGCCAACTCCTTTTT
1179414 CACTCATTGA
Statistics
Matches: 194, Mismatches: 47, Indels: 21
0.74 0.18 0.08
Matches are distributed among these distances:
82 20 0.10
83 47 0.24
84 91 0.47
85 32 0.16
86 4 0.02
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.46
Consensus pattern (85 bp):
ACTTGTTGGTTTGTATGGTTTCTTTAGGCCAACTCCTTTTTAACTCATTGGTTCGTATGGTTTTA
TCTTAGCCAACTCCTTTTTA
Found at i:1179364 original size:41 final size:41
Alignment explanation
Indices: 1179314--1179536 Score: 130
Period size: 41 Copynumber: 5.3 Consensus size: 41
1179304 AGTTTTGCCT
*
1179314 TAGCAAACTCTTTTAACTTGTTGGTTCATATAGTTTCATCA
1 TAGCCAACTCTTTTAACTTGTTGGTTCATATAGTTTCATCA
* ** * * *
1179355 TGGCCAACTCCTTTTTAACTCATTGGTTTATATGGTTTCATCC
1 TAGCCAACT-C-TTTTAACTTGTTGGTTCATATAGTTTCATCA
* * ** * * * *
1179398 TGGCCAACTCCTTTTTCACTCATTGACTT-GTATAGTTTCGT-T
1 TAGCCAACT-C-TTTTAACTTGTTG-GTTCATATAGTTTCATCA
* ** *
1179440 TCAGTCAACTCTCCTAACTTGTTAGTTCATA-AGGTTTCATC-
1 T-AGCCAACTCTTTTAACTTGTTGGTTCATATA-GTTTCATCA
** * * *
1179481 TCAGTTAACTCTTCTAACTTGTTGGTTCATATGGTTTCATCC
1 T-AGCCAACTCTTTTAACTTGTTGGTTCATATAGTTTCATCA
1179523 TAGCCAACTCTTTT
1 TAGCCAACTCTTTT
1179537 CTAACTCATT
Statistics
Matches: 142, Mismatches: 31, Indels: 18
0.74 0.16 0.09
Matches are distributed among these distances:
40 3 0.02
41 68 0.48
42 4 0.03
43 65 0.46
44 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.43
Consensus pattern (41 bp):
TAGCCAACTCTTTTAACTTGTTGGTTCATATAGTTTCATCA
Found at i:1179381 original size:43 final size:43
Alignment explanation
Indices: 1179188--1179422 Score: 210
Period size: 43 Copynumber: 5.6 Consensus size: 43
1179178 GTGTCGTTTA
* *
1179188 GGCCAACTCCTTTTTAACT-TTTGGTTCGTATGGTTTTATCTT
1 GGCCAACTCCTTTTTAACTCATTGGTTCATATGGTTTTATCTT
* * **
1179230 AGCCAACTCCTTTTTAACT-TTTGGTTTGTATGGTTTTATCTT
1 GGCCAACTCCTTTTTAACTCATTGGTTCATATGGTTTTATCTT
* *** * **
1179272 GGCCAACTCTTTTTTAACTCATTAACTCGA-ATAGTTTTGCCTT
1 GGCCAACTCCTTTTTAACTCATTGGTTC-ATATGGTTTTATCTT
* * ** * * *
1179315 AGCAAACT-C-TTTTAACTTGTTGGTTCATATAGTTTCATCAT
1 GGCCAACTCCTTTTTAACTCATTGGTTCATATGGTTTTATCTT
* * *
1179356 GGCCAACTCCTTTTTAACTCATTGGTTTATATGGTTTCATCCT
1 GGCCAACTCCTTTTTAACTCATTGGTTCATATGGTTTTATCTT
*
1179399 GGCCAACTCCTTTTTCACTCATTG
1 GGCCAACTCCTTTTTAACTCATTG
1179423 ACTTGTATAG
Statistics
Matches: 155, Mismatches: 33, Indels: 9
0.79 0.17 0.05
Matches are distributed among these distances:
40 1 0.01
41 27 0.17
42 58 0.37
43 69 0.45
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.46
Consensus pattern (43 bp):
GGCCAACTCCTTTTTAACTCATTGGTTCATATGGTTTTATCTT
Found at i:1179402 original size:127 final size:125
Alignment explanation
Indices: 1179199--1179551 Score: 367
Period size: 127 Copynumber: 2.8 Consensus size: 125
1179189 GCCAACTCCT
* * * * *
1179199 TTTTAACTT-TTGGTTCGTATGGTTTTATCTTAGCCAACTCCTTTTTAACTTTTGGTTTGTATGG
1 TTTTAACTTGTTGGTTCATATAGTTTCATC-TAGCCAACTCCTTTTTAACTATTGGTTTATATGG
* * * *
1179263 TTTTATCTTGGCCAACTCTTTTTTAACTCATTAACTCGAATAGTTTTGCCTT-AG-CAAACTC
65 TTTCATCCTGGCCAACTCTTTTTTAACTCATTGACTCGAATAGTTTCG-CTTCAGTC-AACTC
*
1179324 TTTTAACTTGTTGGTTCATATAGTTTCATCATGGCCAACTCCTTTTTAACTCATTGGTTTATATG
1 TTTTAACTTGTTGGTTCATATAGTTTCATC-TAGCCAACTCCTTTTTAACT-ATTGGTTTATATG
* * * * *
1179389 GTTTCATCCTGGCCAACTCCTTTTTCACTCATTGACTTGTATAGTTTCGTTTCAGTCAACTC
64 GTTTCATCCTGGCCAACTCTTTTTTAACTCATTGACTCGAATAGTTTCGCTTCAGTCAACTC
** * ** * * *
1179451 TCCTAACTTGTTAGTTCATA-AGGTTTCATCTCAGTTAACT-C-TTCTAACTTGTTGGTTCATAT
1 TTTTAACTTGTTGGTTCATATA-GTTTCATCT-AGCCAACTCCTTTTTAAC-TATTGGTTTATAT
* *
1179513 GGTTTCATCCTAGCCAACTCTTTTCTAACTCATTGACTC
63 GGTTTCATCCTGGCCAACTCTTTTTTAACTCATTGACTC
1179552 ATATGGTTTT
Statistics
Matches: 191, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
125 59 0.31
126 42 0.22
127 89 0.47
128 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.45
Consensus pattern (125 bp):
TTTTAACTTGTTGGTTCATATAGTTTCATCTAGCCAACTCCTTTTTAACTATTGGTTTATATGGT
TTCATCCTGGCCAACTCTTTTTTAACTCATTGACTCGAATAGTTTCGCTTCAGTCAACTC
Found at i:1179554 original size:43 final size:42
Alignment explanation
Indices: 1179189--1179560 Score: 156
Period size: 43 Copynumber: 8.8 Consensus size: 42
1179179 TGTCGTTTAG
* * * * *
1179189 GCCAACTCCTTTTTAACT-TTTGGTTCGTATGGTTTTATCTTA
1 GCCAACT-CTTTTTAACTCATTGATTCATATGGTTTCATCCTA
* * ** * * *
1179231 GCCAACTCCTTTTTAACT-TTTGGTTTGTATGGTTTTATCTTG
1 GCCAACT-CTTTTTAACTCATTGATTCATATGGTTTCATCCTA
* * *
1179273 GCCAACTCTTTTTTAACTCATTAACTCGA-ATAGTTT--TGCCTTA
1 GCCAACTC-TTTTTAACTCATTGATTC-ATATGGTTTCAT-CC-TA
* ** * * * *
1179316 GCAAACTC-TTTTAACTTGTTGGTTCATATAGTTTCATCATG
1 GCCAACTCTTTTTAACTCATTGATTCATATGGTTTCATCCTA
* * *
1179357 GCCAACTCCTTTTTAACTCATTGGTTTATATGGTTTCATCCTG
1 GCCAACT-CTTTTTAACTCATTGATTCATATGGTTTCATCCTA
* * * * *
1179400 GCCAACTCCTTTTTCACTCATTGACTT-GTATAGTTTCGT-TTCA
1 GCCAACT-CTTTTTAACTCATTGA-TTCATATGGTTTCATCCT-A
* ** ** *
1179443 GTCAACTC-TCCTAACTTGTT-AGTTCATAAGGTTTCAT-CTCA
1 GCCAACTCTTTTTAACTCATTGA-TTCATATGGTTTCATCCT-A
** * ** *
1179484 GTTAACTC-TTCTAACTTGTTGGTTCATATGGTTTCATCCTA
1 GCCAACTCTTTTTAACTCATTGATTCATATGGTTTCATCCTA
*
1179525 GCCAACTCTTTTCTAACTCATTGACTCATATGGTTT
1 GCCAACTCTTTT-TAACTCATTGATTCATATGGTTT
1179561 TATTTTATTT
Statistics
Matches: 258, Mismatches: 55, Indels: 33
0.75 0.16 0.10
Matches are distributed among these distances:
40 4 0.02
41 85 0.33
42 65 0.25
43 102 0.40
44 2 0.01
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (42 bp):
GCCAACTCTTTTTAACTCATTGATTCATATGGTTTCATCCTA
Found at i:1179583 original size:125 final size:125
Alignment explanation
Indices: 1179377--1179645 Score: 310
Period size: 125 Copynumber: 2.2 Consensus size: 125
1179367 TTTTAACTCA
* * ** *
1179377 TTGGTTTATATGGTTTCATCCTGGCCAACTCCTTTTTCACTCATTGACTTGTATAGTTTCGTTTC
1 TTGGTTTATATGGTTTCATCCTAGCCAACTCCTTTTTAACTCATTGACTCATATAGTTTCATTTC
* *
1179442 AGTCAACTCTCCTAACTTGTT-AGTTCATAAGGTTTCAT-CTCAGTTAACTCTTCTAACTTG
66 AGTCAACCCTCCTAACTTGTTGA-TTCATAAGGTTTCATCCT-AGTAAACTCTTCTAACTTG
* * *
1179502 TTGGTTCATATGGTTTCATCCTAGCCAACT-CTTTTCTAACTCATTGACTCATATGGTTTTATTT
1 TTGGTTTATATGGTTTCATCCTAGCCAACTCCTTTT-TAACTCATTGACTCATATAGTTTCATTT
* * * * * * * * *
1179566 TATTTAACCCTCTTAACTTGTTGATTCGTATGGTTTCGTCCTTGTAAACTTTTCTAACTTG
65 CAGTCAACCCTCCTAACTTGTTGATTCATAAGGTTTCATCCTAGTAAACTCTTCTAACTTG
*
1179627 TTGGTTTGTATGGTTTCAT
1 TTGGTTTATATGGTTTCAT
1179646 TTTGACGAAC
Statistics
Matches: 120, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
124 5 0.04
125 112 0.93
126 3 0.03
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.46
Consensus pattern (125 bp):
TTGGTTTATATGGTTTCATCCTAGCCAACTCCTTTTTAACTCATTGACTCATATAGTTTCATTTC
AGTCAACCCTCCTAACTTGTTGATTCATAAGGTTTCATCCTAGTAAACTCTTCTAACTTG
Found at i:1180048 original size:84 final size:80
Alignment explanation
Indices: 1179953--1180253 Score: 281
Period size: 84 Copynumber: 3.7 Consensus size: 80
1179943 TTAACTTTTC
* * *
1179953 TGACTTATTGGTTCATATGGTTTCGTCTTGGCCAACTCCTTTCTAACTTGTTGACTCATGTGGTC
1 TGACTTGTTGGTTCATATGGTTTCATCCTGGCCAACTCCTTTCTAACTTGTTGACTC-T-TGGT-
1180018 TTGTCTTCATCAACTCTCT
63 TTGT-TTCATCAACTCTCT
* * * * * *
1180037 TAACTTGTTGGTTCGTATGG-TTCTATCCCGACCAACTCATTTCTAACTTATTGACTC---GTAT
1 TGACTTGTTGGTTCATATGGTTTC-ATCCTGGCCAACTCCTTTCTAACTTGTTGACTCTTGGT-T
* *
1180098 GGTTTCATCCACTCTCT
64 TGTTTCATCAACTCTCT
** * *
1180115 TGACTTGTTAATTCATATGGTTTCATGCTGGCCAACTCCTTTCTAACTTGTTAACTCGTATGGTT
1 TGACTTGTTGGTTCATATGGTTTCATCCTGGCCAACTCCTTTCTAACTTGTTGACTC-T-TGGTT
* *
1180180 TCATAGT-AGTCAACTCTCT
64 T-GT-TTCA-TCAACTCTCT
* * *
1180199 TGACTTGTTCGTTCGTATGGTTTCATCCTAGCCAACT-CTTTCTAACTTGTTGACT
1 TGACTTGTTGGTTCATATGGTTTCATCCTGGCCAACTCCTTTCTAACTTGTTGACT
1180254 TGTATGATTT
Statistics
Matches: 175, Mismatches: 32, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
78 56 0.32
79 8 0.05
82 1 0.01
83 24 0.14
84 86 0.49
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.43
Consensus pattern (80 bp):
TGACTTGTTGGTTCATATGGTTTCATCCTGGCCAACTCCTTTCTAACTTGTTGACTCTTGGTTTG
TTTCATCAACTCTCT
Found at i:1180149 original size:162 final size:161
Alignment explanation
Indices: 1179964--1180259 Score: 395
Period size: 162 Copynumber: 1.8 Consensus size: 161
1179954 GACTTATTGG
* * * * **
1179964 TTCATATGGTTTCGTCTTGGCCAACTCCTTTCTAACTTGTTGACTCATGTGGTCTT-GTCTTCA-
1 TTCATATGGTTTCATCTTGGCCAACTCCTTTCTAACTTGTTAACTCATATGGT-TTCATAGT-AG
*
1180027 TCAACTCTCTTAACTTGTTGGTTCGTATGG-TTCTATCCCGA-CCAACTCATTTCTAACTTATTG
64 TCAACTCTCTTAACTTGTTCGTTCGTATGGTTTC-AT-CCGAGCCAACTC-TTTCTAACTTATTG
1180090 ACTCGTATGGTTTCATCCACTCTCTTGACTTGTTAA
126 ACTCGTATGGTTTCATCCACTCTCTTGACTTGTTAA
*
1180126 TTCATATGGTTTCATGC-TGGCCAACTCCTTTCTAACTTGTTAACTCGTATGGTTTCATAGTAGT
1 TTCATATGGTTTCAT-CTTGGCCAACTCCTTTCTAACTTGTTAACTCATATGGTTTCATAGTAGT
* * * *
1180190 CAACTCTCTTGACTTGTTCGTTCGTATGGTTTCATCCTAGCCAACTCTTTCTAACTTGTTGACTT
65 CAACTCTCTTAACTTGTTCGTTCGTATGGTTTCATCCGAGCCAACTCTTTCTAACTTATTGACTC
1180255 GTATG
130 GTATG
1180260 ATTTTGTCTT
Statistics
Matches: 117, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
161 27 0.23
162 86 0.74
163 4 0.03
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.43
Consensus pattern (161 bp):
TTCATATGGTTTCATCTTGGCCAACTCCTTTCTAACTTGTTAACTCATATGGTTTCATAGTAGTC
AACTCTCTTAACTTGTTCGTTCGTATGGTTTCATCCGAGCCAACTCTTTCTAACTTATTGACTCG
TATGGTTTCATCCACTCTCTTGACTTGTTAA
Found at i:1180178 original size:43 final size:42
Alignment explanation
Indices: 1180068--1180259 Score: 150
Period size: 41 Copynumber: 4.7 Consensus size: 42
1180058 TCTATCCCGA
* *
1180068 CCAACTCATTTCTAACTTATTGACTCGTATGGTTTCA---T--
1 CCAACTC-TTTCTAACTTGTTAACTCGTATGGTTTCATGCTAG
* * * * *
1180106 CC-ACTCTCT-TGACTTGTTAATTCATATGGTTTCATGCTGG
1 CCAACTCTTTCTAACTTGTTAACTCGTATGGTTTCATGCTAG
1180146 CCAACTCCTTTCTAACTTGTTAACTCGTATGGTTTCATAG-TAG
1 CCAACT-CTTTCTAACTTGTTAACTCGTATGGTTTCAT-GCTAG
* * * *** *
1180189 TCAACTCTCT-TGACTTGTTCGTTCGTATGGTTTCATCCTAG
1 CCAACTCTTTCTAACTTGTTAACTCGTATGGTTTCATGCTAG
* *
1180230 CCAACTCTTTCTAACTTGTTGACTTGTATG
1 CCAACTCTTTCTAACTTGTTAACTCGTATG
1180260 ATTTTGTCTT
Statistics
Matches: 118, Mismatches: 25, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
35 20 0.17
36 2 0.02
37 4 0.03
38 3 0.03
40 2 0.02
41 36 0.31
42 20 0.17
43 30 0.25
44 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (42 bp):
CCAACTCTTTCTAACTTGTTAACTCGTATGGTTTCATGCTAG
Found at i:1182644 original size:20 final size:21
Alignment explanation
Indices: 1182597--1182644 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
1182587 AGTGTTTTTT
*
1182597 GCTTTTTTAAACATGTTTTAG
1 GCTTTTTTAAACATGTTTAAG
*
1182618 GCATTTTT-AACAT-TTTAAG
1 GCTTTTTTAAACATGTTTAAG
1182637 GACTTTTT
1 G-CTTTTT
1182645 GTAATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 6 0.26
20 10 0.43
21 7 0.30
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.52
Consensus pattern (21 bp):
GCTTTTTTAAACATGTTTAAG
Found at i:1183631 original size:13 final size:13
Alignment explanation
Indices: 1183613--1183638 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1183603 TAATTTTTTG
1183613 TGTATCGATACAT
1 TGTATCGATACAT
1183626 TGTATCGATACAT
1 TGTATCGATACAT
1183639 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1184998 original size:3 final size:3
Alignment explanation
Indices: 1184990--1185015 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1184980 GCTAAAAGCT
1184990 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1185016 GTTTTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1185437 original size:28 final size:28
Alignment explanation
Indices: 1185406--1185459 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1185396 CTAAATTACG
1185406 ACAAATAAAAATTATATTAAAACTTATC
1 ACAAATAAAAATTATATTAAAACTTATC
*
1185434 ACAAATAAAAATTTTATTAAAACTTA
1 ACAAATAAAAATTATATTAAAACTTA
1185460 CGCACCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.33
Consensus pattern (28 bp):
ACAAATAAAAATTATATTAAAACTTATC
Found at i:1185523 original size:27 final size:28
Alignment explanation
Indices: 1185479--1185533 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
1185469 AGAGGGTTAG
* * *
1185479 TTAAAACTTTACTTATGTTAAAACTCAA
1 TTAAAACTTTAATCATGTAAAAACTCAA
*
1185507 TTAAAA-TTTAATCATGTAAAAATTCAA
1 TTAAAACTTTAATCATGTAAAAACTCAA
1185534 AAAAAAAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (28 bp):
TTAAAACTTTAATCATGTAAAAACTCAA
Found at i:1185846 original size:19 final size:21
Alignment explanation
Indices: 1185806--1185847 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1185796 CTGATTTACT
1185806 ATGAATTTAATAAAAATATTTG
1 ATGAATTT-ATAAAAATATTTG
1185828 ATGAATTT-TAAAAAT-TTTG
1 ATGAATTTATAAAAATATTTG
1185847 A
1 A
1185848 ACTAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
22 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (21 bp):
ATGAATTTATAAAAATATTTG
Found at i:1185921 original size:154 final size:152
Alignment explanation
Indices: 1185756--1186073 Score: 376
Period size: 154 Copynumber: 2.1 Consensus size: 152
1185746 ATATTTACAA
* * * * *
1185756 AAAAAAT-TAAAACTCATGAAATAAAT-TAAATCTTCTAAAACTGATTTACTATGAATTTAATAA
1 AAAAAATCTAAAACTCATAAAATAAATCAAAATCTTC-AAAACTGATTTAATA-GAAATTAAAAA
* * *
1185819 AA-ATATTTGATGAATTTTAAAAATTTTGAACTAAGAAAAATCGAAT-CAAAAAAATTTACGAAG
64 AAGATATTTGAAGAATTTTAAAAATTATAAACTAAGAAAAATC--ATCCAAAAAAATTTACGAAG
*
1185882 TAGAAAACTCCATATTTTGGAAATAG
127 TAGAAAACTCCATATTTTAGAAATAG
* *
1185908 AAAAAATTCTAAAACTCATAAAATAAATCAAAATTTTCAAAATTGATTTAATAGAAATTAAAAAA
1 AAAAAA-TCTAAAACTCATAAAATAAATCAAAATCTTCAAAACTGATTTAATAGAAATTAAAAAA
* * ** * **
1185973 ATGATATTTGAAGAATTTTTAAAATTATAAACTTAGAGTAATCCTCCCGAAAAATTTACGAAGTA
65 A-GATATTTGAAGAATTTTAAAAATTATAAACTAAGAAAAATCATCCAAAAAAATTTACGAAGTA
*
1186038 GGAAACTCCATATTTTAGAAATAG
129 GAAAACTCCATATTTTAGAAATAG
1186062 -AAAAATCTAAAA
1 AAAAAATCTAAAA
1186074 GACAAATGCA
Statistics
Matches: 141, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
152 13 0.09
153 18 0.13
154 70 0.50
155 40 0.28
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (152 bp):
AAAAAATCTAAAACTCATAAAATAAATCAAAATCTTCAAAACTGATTTAATAGAAATTAAAAAAA
GATATTTGAAGAATTTTAAAAATTATAAACTAAGAAAAATCATCCAAAAAAATTTACGAAGTAGA
AAACTCCATATTTTAGAAATAG
Found at i:1188658 original size:16 final size:16
Alignment explanation
Indices: 1188637--1188669 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1188627 CATGACCCTT
1188637 TTCTTTTCGGAGAGGC
1 TTCTTTTCGGAGAGGC
1188653 TTCTTTTCGGAGAGGC
1 TTCTTTTCGGAGAGGC
1188669 T
1 T
1188670 AGTGTGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.18, G:0.30, T:0.39
Consensus pattern (16 bp):
TTCTTTTCGGAGAGGC
Found at i:1189271 original size:6 final size:6
Alignment explanation
Indices: 1189260--1189290 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1189250 AATCTAAAAT
1189260 ATTATA ATTATA ATTATA ATTATA ATTATA A
1 ATTATA ATTATA ATTATA ATTATA ATTATA A
1189291 AAATTAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTATA
Found at i:1190860 original size:79 final size:79
Alignment explanation
Indices: 1190722--1191161 Score: 700
Period size: 79 Copynumber: 5.6 Consensus size: 79
1190712 AAAATAAAAT
* * *
1190722 CGGGGTTAGAGTATCCCCGATTATGAAAAATTAATGTTTTATAAATAAAACCGGCGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1190787 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
* * *
1190801 CAGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1190866 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
* *
1190880 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1190945 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
* * * *
1190959 CGGGGTTGGAGTATCCCTGATTATGAAAAATTAATATTTTAGAAATAAAATCAGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
1191024 CCCCTCGAAAATAA
66 CCCCTCGGAAATAA
**
1191038 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
**
1191103 CCCCTCAAAAATAA
66 CCCCTCGGAAATAA
* * *
1191117 TGGGGTTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGAAA
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAA
1191162 CTTAACAAAA
Statistics
Matches: 335, Mismatches: 26, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 335 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
CCCCTCGGAAATAA
Found at i:1192431 original size:35 final size:35
Alignment explanation
Indices: 1192366--1192548 Score: 277
Period size: 35 Copynumber: 5.4 Consensus size: 35
1192356 TCATTTTTAT
1192366 CCATCATTCCATGCCTTCA-TTTTTTATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
*
1192400 CCATCATTCTATGCCTTCATTTTTTTATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
* *
1192435 CCATCATTCCATGCCTTCATTTTTATATTCCAAGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
* *
1192470 CCATCATCCCATG--TT--TTTTTTTATTTCATGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
*
1192501 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
1192536 CCATCATTCCATG
1 CCATCATTCCATG
1192549 TTTTTTATTT
Statistics
Matches: 133, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
31 25 0.19
33 4 0.03
34 18 0.14
35 86 0.65
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (35 bp):
CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
Found at i:1192509 original size:66 final size:66
Alignment explanation
Indices: 1192366--1192554 Score: 299
Period size: 66 Copynumber: 2.8 Consensus size: 66
1192356 TCATTTTTAT
*
1192366 CCATCATTCCATGCCTTCATTTTT-TATTCCATGCCCATCATTCTATGCCTTCATTTTTTTATTC
1 CCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATG--TT--TTTTTTTATTC
1192430 CATGC
62 CATGC
* * *
1192435 CCATCATTCCATGCCTTCATTTTTATATTCCAAGCCCATCATCCCATGTTTTTTTTTATTTCATG
1 CCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATGTTTTTTTTTATTCCATG
1192500 C
66 C
1192501 CCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATGTTTTTT
1 CCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATGTTTTTT
1192555 ATTTCTTGAT
Statistics
Matches: 113, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
66 67 0.59
68 2 0.02
69 24 0.21
70 20 0.18
ACGTcount: A:0.19, C:0.30, G:0.06, T:0.46
Consensus pattern (66 bp):
CCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATGTTTTTTTTTATTCCATG
C
Found at i:1193216 original size:40 final size:41
Alignment explanation
Indices: 1193170--1193301 Score: 153
Period size: 42 Copynumber: 3.2 Consensus size: 41
1193160 TCCCACTTTT
*
1193170 TTGAGGACAAAGAAAAAGAGAATGAAATAG-GTCCTGCTCC
1 TTGAGGACAAAGAAAAAGAGAAAGAAATAGTGTCCTGCTCC
* *
1193210 TTGAGGACAAAGGAAAAGAAGAAAAGAAA-AGTGTCCTGCTTC
1 TTGAGGACAAAGAAAAAG-AG-AAAGAAATAGTGTCCTGCTCC
* * *
1193252 TTGAGGACAAAGTGAAAAAGGGAAAGAAGT-GTGTCCTGCTCT
1 TTGAGGACAAA--GAAAAAGAGAAAGAAATAGTGTCCTGCTCC
1193294 TTGAGGAC
1 TTGAGGAC
1193302 TGAAAAGTGC
Statistics
Matches: 78, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
40 17 0.22
41 4 0.05
42 50 0.64
43 1 0.01
44 6 0.08
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19
Consensus pattern (41 bp):
TTGAGGACAAAGAAAAAGAGAAAGAAATAGTGTCCTGCTCC
Found at i:1193377 original size:61 final size:60
Alignment explanation
Indices: 1193284--1193601 Score: 384
Period size: 61 Copynumber: 5.3 Consensus size: 60
1193274 AAAGAAGTGT
* * *
1193284 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGTCTTTGAAAAGAAAAGGT
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAA-AAAAGGC
* * *
1193345 GTCCTGCTCTTTGAGGACTTGAAGA-TGCCACCAACTAGTGTGGGATTTGCAAAAAGAAA-GC
1 GTCCTGCTCTTTGAGGAC-TGAAAAGTGCCACCAACTTGTGTGGGCTTTG-AAAAA-AAAGGC
* * *
1193406 ATCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-ACAAAAAGAAAGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGA-AAAAA-AAGGC
* *
1193467 ATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAATGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAA--AAAAAGGC
* *
1193529 GTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGCGGGCTTTG-----AAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAGGC
1193583 GTCCTGCTCTTTGAGGACT
1 GTCCTGCTCTTTGAGGACT
1193602 AAAGGGTGAG
Statistics
Matches: 231, Mismatches: 16, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
54 25 0.11
59 2 0.01
60 11 0.05
61 155 0.67
62 36 0.16
63 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (60 bp):
GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAGGC
Found at i:1193689 original size:94 final size:93
Alignment explanation
Indices: 1193529--1193700 Score: 283
Period size: 94 Copynumber: 1.8 Consensus size: 93
1193519 TGGAAAAGGC
* *
1193529 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGCGGGCTTTGAAAGGCGTCCTGCTCTT
1 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGCGGGCTTTAAAAGGAGTCCTGCTCTT
1193594 TGAGGACTAAAGGGTGAGAGAAGAGAGT
66 TGAGGACTAAAGGGTGAGAGAAGAGAGT
*
1193622 GTCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCCTGCTC
1 GTCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGCGGGCTTTAAAAGGAGTCCTGCTC
*
1193686 TTTGAGGACTGAAGG
64 TTTGAGGACTAAAGG
1193701 TGCCACCAAC
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
93 19 0.26
94 51 0.70
95 3 0.04
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (93 bp):
GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGCGGGCTTTAAAAGGAGTCCTGCTCTT
TGAGGACTAAAGGGTGAGAGAAGAGAGT
Found at i:1193718 original size:54 final size:54
Alignment explanation
Indices: 1193622--1193915 Score: 491
Period size: 54 Copynumber: 5.4 Consensus size: 54
1193612 AGAAGAGAGT
*
1193622 GTCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 GTCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
*
1193677 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
1193731 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
* *
1193785 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
1 GTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
* *
1193840 GTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
*
1193894 GTCCTACTCTTTGAGGACTGAA
1 GTCCTGCTCTTTGAGGACTGAA
1193916 AGGGTGAAAG
Statistics
Matches: 227, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
53 3 0.01
54 155 0.68
55 69 0.30
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (54 bp):
GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
Found at i:1193832 original size:109 final size:109
Alignment explanation
Indices: 1193622--1194311 Score: 628
Period size: 109 Copynumber: 6.2 Consensus size: 109
1193612 AGAAGAGAGT
*
1193622 GTCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCCTGCTC
1 GTCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTC
*
1193686 TTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
64 TTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
1193731 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTT
1 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTT
1193796 TGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
66 TGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
* * *
1193840 GTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTACTCTT
1 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTT
* * ** ** * * *
1193905 TGAGGACTGAAAGGGTG-AAAGAA-GAGAGT-GTC-CT-----GC
66 TGAGGACTGAAA-AGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
** ** * * *
1193941 -T-CT--T-TGAGGACTA-GGAA-GTGCCACCAACTTATGTGGGCTTTGAAAGGCGTCCTGCTCT
1 GTCCTGCTCT-TTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCT
* *
1193999 TTGAGGACTGAAAAGTGCCACCAACTCGTGTGGTCTTTGAAAAGAAAAGGC
65 TTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGC
* * * *
1194050 GTCCTGCTCTTTGAGGACTGGAAGATGCCACCAACTAGTGTGGGATTTGCAAAAAGAAAGCATCC
1 GTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT---AAAAG---GCGTCC
* * * *
1194115 TGCTCTTTGAAGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTACAAAAAAAAAGC
59 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT------GAAAGGC
* * *
1194172 ATCTTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAATGGAAAATGG-GT
1 GTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGC-TT----T--AAAA-GGCGT
*
1194236 CCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
57 CCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
*
1194288 GTCCTGCTCTTTGAGGACTAAAGG
1 GTCCTGCTCTTTGAGGACTGAAGG
1194312 GTGAGAGAAG
Statistics
Matches: 473, Mismatches: 67, Indels: 76
0.77 0.11 0.12
Matches are distributed among these distances:
94 3 0.01
95 54 0.11
96 6 0.01
97 7 0.01
98 1 0.00
99 2 0.00
100 1 0.00
101 2 0.00
106 1 0.00
107 5 0.01
108 53 0.11
109 131 0.28
110 4 0.01
111 2 0.00
113 4 0.01
114 1 0.00
115 6 0.01
116 42 0.09
119 4 0.01
121 1 0.00
122 113 0.24
123 23 0.05
124 1 0.00
126 4 0.01
127 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (109 bp):
GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTT
TGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
Found at i:1194002 original size:95 final size:94
Alignment explanation
Indices: 1193840--1194011 Score: 283
Period size: 95 Copynumber: 1.8 Consensus size: 94
1193830 TTTGAAAGGC
*
1193840 GTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTACTCTT
1 GTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGCGTCCTACTCTT
1193905 TGAGGACTGAAAGGGTGAAAGAAGAGAGT
66 TGAGGACTGAAAGGGTGAAAGAAGAGAGT
* * *
1193934 GTCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTATGTGGGCTTTGAAAGGCGTCCTGCTC
1 GTCCTACTCTTTGAGGACTA--AAGGTGCCACCAACTTATGTGGGCTTTAAAAGGCGTCCTACTC
1193998 TTTGAGGACTGAAA
64 TTTGAGGACTGAAA
1194012 AGTGCCACCA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
94 19 0.26
95 51 0.71
96 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (94 bp):
GTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGCGTCCTACTCTT
TGAGGACTGAAAGGGTGAAAGAAGAGAGT
Found at i:1194079 original size:61 final size:60
Alignment explanation
Indices: 1193934--1194306 Score: 400
Period size: 61 Copynumber: 6.3 Consensus size: 60
1193924 AGAAGAGAGT
* *
1193934 GTCCTGCTCTTTGAGGACT-AGGAAGTGCCACCAACTTATGTGGGCTTT----G-AAAGGC
1 GTCCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
* *
1193989 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGTCTTTGAAAAGAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGC
* * *
1194050 GTCCTGCTCTTTGAGGACTG-GAAGATGCCACCAACTAGTGTGGGATTTGCAAAA-AGAAA-GC
1 GTCCTGCTCTTTGAGGACTGAAAAG-TGCCACCAACTTGTGTGGGCTTT--AAAAGA-AAAGGC
* * * * *
1194111 ATCCTGCTCTTTGAAGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTACAAAAAAAAAGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTA-AAAGAAAAGGC
* * *
1194172 ATCTTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAATGGAAAATGG-
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAA-AGAAAA-GGC
*
1194234 GTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
1194288 GTCCTGCTCTTTGAGGACT
1 GTCCTGCTCTTTGAGGACT
1194307 AAAGGGTGAG
Statistics
Matches: 276, Mismatches: 24, Indels: 37
0.82 0.07 0.11
Matches are distributed among these distances:
53 2 0.01
54 22 0.08
55 43 0.16
56 1 0.00
59 1 0.00
60 10 0.04
61 163 0.59
62 33 0.12
63 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (60 bp):
GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
Found at i:1194264 original size:183 final size:177
Alignment explanation
Indices: 1193935--1194577 Score: 568
Period size: 154 Copynumber: 3.8 Consensus size: 177
1193925 GAAGAGAGTG
* ** * * *
1193935 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTATGTGGGCTTTGAAAGGCGTCCTGCTCTT
1 TCCTGCTCTTTGAAGACTAAAAAGTGCCACCAACTTATGTGGGCTTTAAAAAGCATCCTGCTCTT
*
1194000 TGAGGACTGAAAAGTGCCACCAACTCGTGTGGTCTTTGAAAAGAAAAGGCGTCCTGCTCTTTGAG
66 TGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCGTCCTGCTCTTTGAG
1194065 GACTGGAAGATGCCACCAACTAGTGTGGGATTTGCAAAAAGAAAGCA
131 GACTGGAAGATGCCACCAACTAGTGTGGGATTTGCAAAAAGAAAGCA
* *
1194112 TCCTGCTCTTTGAAGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTACAAAAAAAAAGCATCTT
1 TCCTGCTCTTTGAAGACTAAAAAGTGCCACCAACTTATGTGGGCTTT------AAAAAGCATCCT
* *
1194177 GCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAATGGAAAATGG-GTCCTGC
60 GCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA-AGAAAA-GGCGTCCTGC
* * * *
1194241 TCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTG---AAAG---GCG
123 TCTTTGAGGACTGGAAGATGCCACCAACTAGTGTGGGATTTGCAAAAAGAAAGCA
* ** * * * *
1194289 TCCTGCTCTTTGAGGACTAAAGGGTG--A-GAGA---A-GAGAG---T-----G--TCCCGCTCT
1 TCCTGCTCTTTGAAGACTAAAAAGTGCCACCA-ACTTATGTGGGCTTTAAAAAGCATCCTGCTCT
* **
1194337 TTGAGGACT-AGGAAGTGCCACCAACTTATGTGGGCTTT-AAAAGGAAAAGGCGTCCTGCTCTTT
65 TTGAGGACTGA-AAAGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAGGCGTCCTGCTCTTT
* * *
1194400 GAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTG---AAAG---GCA
128 GAGGACTGGAAGATGCCACCAACTAGTGTGGGATTTGCAAAAAGAAAGCA
* * * * *
1194443 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCT
1 TCCTGCTCTTTGAAGACT-AAAAAGTGCCACCAACTTATGTGGGCTTTAAAAAGCATCCTGCTCT
* * * *
1194507 TTGAGGACT-AAATGGTGCCACCAAGTTGTGTGGGCTTT-AAAAGGAAAAGGCGTCCTACTCTTT
65 TTGAGGACTGAAA-AGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAGGCGTCCTGCTCTTT
1194570 GAGGACTG
128 GAGGACTG
1194578 AAGGGCTAAA
Statistics
Matches: 393, Mismatches: 41, Indels: 70
0.78 0.08 0.14
Matches are distributed among these distances:
153 2 0.01
154 83 0.21
155 43 0.11
156 2 0.01
157 2 0.01
160 3 0.01
163 1 0.00
168 2 0.01
169 1 0.00
170 71 0.18
171 3 0.01
174 1 0.00
175 2 0.01
177 68 0.17
180 4 0.01
183 79 0.20
184 24 0.06
185 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (177 bp):
TCCTGCTCTTTGAAGACTAAAAAGTGCCACCAACTTATGTGGGCTTTAAAAAGCATCCTGCTCTT
TGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCGTCCTGCTCTTTGAG
GACTGGAAGATGCCACCAACTAGTGTGGGATTTGCAAAAAGAAAGCA
Found at i:1194369 original size:94 final size:95
Alignment explanation
Indices: 1194234--1194411 Score: 254
Period size: 100 Copynumber: 1.8 Consensus size: 95
1194224 TGGAAAATGG
* *
1194234 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-G-AAAGGCGTCCTGCTC
1 GTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTATGTGGGCTTTAGAAAAGGCGTCCTGCTC
1194297 TTTGAGGACTAAAGGGTGAGAGAAGAGAGT
66 TTTGAGGACTAAAGGGTGAGAGAAGAGAGT
1194327 GTCCCGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCGTC
1 GTCCCGCTCTTTGAGGACT--GAAGGTGCCACCAACTTATGTGGGCTTT---A-GAAAAGGCGTC
*
1194391 CTGCTCTTTGAGGACTGAAGG
60 CTGCTCTTTGAGGACTAAAGG
1194412 TGCCACCAAC
Statistics
Matches: 74, Mismatches: 3, Indels: 9
0.86 0.03 0.10
Matches are distributed among these distances:
93 18 0.24
94 23 0.31
95 3 0.04
99 1 0.01
100 29 0.39
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (95 bp):
GTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTATGTGGGCTTTAGAAAAGGCGTCCTGCTC
TTTGAGGACTAAAGGGTGAGAGAAGAGAGT
Found at i:1194495 original size:55 final size:54
Alignment explanation
Indices: 1194327--1194550 Score: 279
Period size: 55 Copynumber: 4.0 Consensus size: 54
1194317 AGAAGAGAGT
* * *
1194327 GTCCCGCTCTTTGAGGACTAGGAAGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT------AAAAGGC
* *
1194388 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
* *
1194442 ATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGC
1 GTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
*
1194497 GTCCTGCTCTTTGAGGACT-AAATGGTGCCACCAAGTTGTGTGGGCTTTAAAAGG
1 GTCCTGCTCTTTGAGGACTGAAA--GTGCCACCAACTTGTGTGGGCTTTAAAAGG
1194551 AAAAGGCGTC
Statistics
Matches: 148, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
53 3 0.02
54 24 0.16
55 78 0.53
60 25 0.17
61 18 0.12
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (54 bp):
GTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
Found at i:1200736 original size:51 final size:51
Alignment explanation
Indices: 1200594--1200738 Score: 168
Period size: 53 Copynumber: 2.8 Consensus size: 51
1200584 CTGACGAGAA
* * *
1200594 AAAAATTGGTATTTTAGAGATAACAACGGGGCTAGAGTATCCCCGATTATGG
1 AAAAATTGGTGTTTTAGAAATAA-AACGGGGTTAGAGTATCCCCGATTATGG
* *
1200646 AAAAA-TGGTGTTCTAAAAAAATAAAATCGGGGTTAGAGTATCCCCGATTAT-G
1 AAAAATTGGTGTT-T-TAGAAATAAAA-CGGGGTTAGAGTATCCCCGATTATGG
* *
1200698 AAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
1 AAAAATTGGTGTTTTAGAAATAAAA-CGGGGTTAGAGTATC
1200739 ACCTCAAAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
51 29 0.37
52 15 0.19
53 35 0.44
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAAATTGGTGTTTTAGAAATAAAACGGGGTTAGAGTATCCCCGATTATGG
Found at i:1201113 original size:79 final size:79
Alignment explanation
Indices: 1200673--1201112 Score: 709
Period size: 79 Copynumber: 5.6 Consensus size: 79
1200663 AAAATAAAAT
*
1200673 CGGGGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
* **
1200738 CACCTCAAAAATAA
66 CCCCTCGGAAATAA
* *
1200752 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTGAAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1200817 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
* *
1200831 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACCAGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1200896 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
* *
1200910 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
1200975 CCCCTCGAAAATAA
66 CCCCTCGGAAATAA
* * *
1200989 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAACAAAACCGGGGTTAGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1201054 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
* * * * *
1201068 CGGGGTTGGAGTATTCTCGATTGTGAAAAATTAATATTTTAGAAA
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAA
1201113 CTTAACAAAA
Statistics
Matches: 336, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 336 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
CCCCTCGGAAATAA
Found at i:1202375 original size:35 final size:35
Alignment explanation
Indices: 1202310--1202492 Score: 277
Period size: 35 Copynumber: 5.4 Consensus size: 35
1202300 TCATTTTTAT
1202310 CCATCATTCCATGCCTTCA-TTTTTTATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
*
1202344 CCATCATTCTATGCCTTCATTTTTTTATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
*
1202379 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
* * *
1202414 CCATCATCCCATG---T-GTTTTTTTATTTCATGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
*
1202445 CCATCATTCCATGCCTTCATTTTTATATTCCATGC
1 CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
1202480 CCATCATTCCATG
1 CCATCATTCCATG
1202493 TTTTTTATTT
Statistics
Matches: 133, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
31 26 0.20
32 1 0.01
34 19 0.14
35 87 0.65
ACGTcount: A:0.19, C:0.31, G:0.07, T:0.44
Consensus pattern (35 bp):
CCATCATTCCATGCCTTCATTTTTTTATTCCATGC
Done.