Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 9 of 26
Found at i:1223536 original size:13 final size:14
Alignment explanation
Indices: 1223510--1223545 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1223500 ATTTTTTAAA
*
1223510 TAAATTTTATTTTT
1 TAAAATTTATTTTT
1223524 TAAAATTTA-TTTT
1 TAAAATTTATTTTT
1223537 TAAAATTTA
1 TAAAATTTA
1223546 ATATTTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TAAAATTTATTTTT
Found at i:1224765 original size:12 final size:12
Alignment explanation
Indices: 1224722--1224772 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
1224712 TGTTATTTTT
1224722 TATTATA-TT-A
1 TATTATATTTAA
*
1224732 TATTATATTTTA
1 TATTATATTTAA
*
1224744 -ATTATTTTTAA
1 TATTATATTTAA
1224755 TATTATATTTAA
1 TATTATATTTAA
*
1224767 AATTAT
1 TATTAT
1224773 CAAATTTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
10 7 0.21
11 11 0.32
12 16 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATATTTAA
Found at i:1225782 original size:17 final size:17
Alignment explanation
Indices: 1225757--1225812 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
1225747 AAATAATTTT
1225757 TTTAAAAATAAAACAAA
1 TTTAAAAATAAAACAAA
* * *
1225774 TTTACAAATTAAATAAA
1 TTTAAAAATAAAACAAA
*
1225791 TTT--AAATAAAA-AAT
1 TTTAAAAATAAAACAAA
1225805 TTTAAAAA
1 TTTAAAAA
1225813 AAATCAAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 5 0.16
15 7 0.22
16 3 0.09
17 17 0.53
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
TTTAAAAATAAAACAAA
Found at i:1226754 original size:13 final size:15
Alignment explanation
Indices: 1226738--1226776 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1226728 TTTAAATATT
*
1226738 AAAATTTAA-TAA-A
1 AAAATTAAATTAATA
1226751 AAAATTAAATTAATA
1 AAAATTAAATTAATA
1226766 AAAATTAAATT
1 AAAATTAAATT
1226777 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.35
14 3 0.13
15 12 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATTAAATTAATA
Found at i:1226784 original size:16 final size:15
Alignment explanation
Indices: 1226749--1226807 Score: 64
Period size: 16 Copynumber: 3.8 Consensus size: 15
1226739 AAATTTAATA
**
1226749 AAAAAATTAAATTAAT
1 AAAAAA-TAAATTTTT
*
1226765 AAAAATTAAATTTTT
1 AAAAAATAAATTTTT
*
1226780 AAAAAATATATTTTTT
1 AAAAAATA-AATTTTT
1226796 AAAAAATAAATT
1 AAAAAATAAATT
1226808 AAAAAATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 17 0.47
16 19 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAAAATAAATTTTT
Found at i:1230219 original size:27 final size:26
Alignment explanation
Indices: 1230155--1230229 Score: 64
Period size: 27 Copynumber: 2.8 Consensus size: 26
1230145 TATTTTTAAA
*
1230155 TTTTATATAATATAAAT-TATTAATAT
1 TTTTATATAATATAAATATA-AAATAT
* * *
1230181 ATTAAAATTAATATAAATATAAAATATT
1 TTTTATA-TAATATAAATATAAAATA-T
1230209 TTTTATATAAT-TATAATATAA
1 TTTTATATAATATA-AATATAA
1230230 TATAATATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
26 6 0.16
27 25 0.66
28 7 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTTATATAATATAAATATAAAATAT
Found at i:1230244 original size:13 final size:15
Alignment explanation
Indices: 1230159--1230256 Score: 53
Period size: 13 Copynumber: 6.6 Consensus size: 15
1230149 TTTAAATTTT
*
1230159 ATATAATATAA-ATT
1 ATATAATATAATATA
* *
1230173 AT-TAATATATTAAA
1 ATATAATATAATATA
1230187 AT-TAATATAAATATA
1 ATATAATAT-AATATA
* * * *
1230202 AAATATTTTTTATATA
1 ATATA-ATATAATATA
1230218 ATTATAATATAATATA
1 A-TATAATATAATATA
*
1230234 ATAT-ATA-AATATT
1 ATATAATATAATATA
1230247 ATATGAATAT
1 ATAT-AATAT
1230257 TCAAAATTTT
Statistics
Matches: 62, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
13 16 0.26
14 14 0.23
15 11 0.18
16 16 0.26
17 5 0.08
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (15 bp):
ATATAATATAATATA
Found at i:1230267 original size:54 final size:51
Alignment explanation
Indices: 1230152--1230267 Score: 119
Period size: 56 Copynumber: 2.2 Consensus size: 51
1230142 CAATATTTTT
*
1230152 AAATTTTATATAATATAAATTATTAATATATTAAAATTAATATAAATATAA
1 AAATTTTATATAATATAAATAATTAATATATTAAAATTAATATAAATATAA
* *
1230203 AATATTTTTTATATAATTATAATATAATATAATATA-TAAATATT-ATATGAATATTCA
1 AA-A--TTTTATATAA-TATAA-ATAAT-TAATATATTAAA-ATTAATATAAATA-TAA
1230260 AAATTTTA
1 AAATTTTA
1230268 AAGTCAGAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
51 2 0.04
52 1 0.02
54 15 0.28
55 5 0.09
56 17 0.31
57 14 0.26
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.46
Consensus pattern (51 bp):
AAATTTTATATAATATAAATAATTAATATATTAAAATTAATATAAATATAA
Found at i:1231945 original size:22 final size:23
Alignment explanation
Indices: 1231920--1231970 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
1231910 GGTAAAAGAG
** *
1231920 TTTAAATTTTTAATTTAAT-TAA
1 TTTAAATAATTAATTAAATATAA
*
1231942 TTTATATAATTAATTAAATATAA
1 TTTAAATAATTAATTAAATATAA
1231965 TTTAAA
1 TTTAAA
1231971 ATTTAAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAAATAATTAATTAAATATAA
Found at i:1233723 original size:17 final size:19
Alignment explanation
Indices: 1233681--1233723 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
1233671 GCCATGTTTA
1233681 TTAATAATAAATTAATATT
1 TTAATAATAAATTAATATT
1233700 TGATAATAATAAA-T-ATATT
1 T--TAATAATAAATTAATATT
1233719 TTAAT
1 TTAAT
1233724 TTAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.18
19 7 0.32
20 1 0.05
21 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TTAATAATAAATTAATATT
Found at i:1233741 original size:30 final size:31
Alignment explanation
Indices: 1233702--1233775 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 31
1233692 TTAATATTTG
* *
1233702 ATAATAATAAATATATTTTA-ATTTAAAATA
1 ATAAAAATAAATATAATTTACATTTAAAATA
* * * *
1233732 TTAAAAAT-AATAAAATTTACATTTTAATTA
1 ATAAAAATAAATATAATTTACATTTAAAATA
1233762 ATAAAAATAAATAT
1 ATAAAAATAAATAT
1233776 GTAAATTATT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
29 9 0.26
30 21 0.62
31 4 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (31 bp):
ATAAAAATAAATATAATTTACATTTAAAATA
Found at i:1234004 original size:1 final size:1
Alignment explanation
Indices: 1234000--1234025 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1233990 CAAAAAATTG
1234000 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1234026 CCCCAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1235528 original size:18 final size:17
Alignment explanation
Indices: 1235505--1235552 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
1235495 TTAATTGAAG
1235505 TTATAATTAAATTTATAT
1 TTATAATT-AATTTATAT
*
1235523 TTATAATT-TTTTATAT
1 TTATAATTAATTTATAT
1235539 TT-TAATTATATTTA
1 TTATAATTA-ATTTA
1235553 AAATATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 5 0.19
16 9 0.35
17 4 0.15
18 8 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATAATTAATTTATAT
Found at i:1235552 original size:10 final size:10
Alignment explanation
Indices: 1235533--1235679 Score: 64
Period size: 10 Copynumber: 15.0 Consensus size: 10
1235523 TTATAATTTT
1235533 TTATATTTTAA
1 TTATA-TTTAA
1235544 TTATATTTAA
1 TTATATTTAA
*
1235554 -AATA-TT-A
1 TTATATTTAA
1235561 -TATATTT-A
1 TTATATTTAA
*
1235569 TATAAATTTAA
1 T-TATATTTAA
*
1235580 ATATATTTAA
1 TTATATTTAA
*
1235590 TT-T-TTGTTA
1 TTATATT-TAA
*
1235599 TATAAATTTAA
1 T-TATATTTAA
*
1235610 -TATATTTAT
1 TTATATTTAA
*
1235619 TTATA-TTATT
1 TTATATTTA-A
1235629 TTATATTTTAA
1 TTATA-TTTAA
*
1235640 TTATTTTTATA
1 TTATATTTA-A
1235651 TTATATTTAA
1 TTATATTTAA
*
1235661 -AAT-TATTAA
1 TTATAT-TTAA
1235670 TTATATTTAA
1 TTATATTTAA
1235680 AATTTTCTCG
Statistics
Matches: 104, Mismatches: 16, Indels: 33
0.68 0.10 0.22
Matches are distributed among these distances:
7 4 0.04
8 8 0.08
9 23 0.22
10 42 0.40
11 22 0.21
12 5 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (10 bp):
TTATATTTAA
Found at i:1235634 original size:22 final size:21
Alignment explanation
Indices: 1235604--1235660 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
1235594 TGTTATATAA
* *
1235604 ATTTAATATATTTATTTATATT
1 ATTTTATATATTTAATTAT-TT
1235626 ATTTTATAT-TTTAATTATTT
1 ATTTTATATATTTAATTATTT
*
1235646 -TTATATTATATTTAA
1 ATTTTA-TATATTTAA
1235661 AATTATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 4 0.13
20 5 0.17
21 13 0.43
22 8 0.27
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTATATATTTAATTATTT
Found at i:1235642 original size:16 final size:18
Alignment explanation
Indices: 1235618--1235652 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1235608 AATATATTTA
1235618 TTTATATTA-TTTTATAT
1 TTTATATTATTTTTATAT
1235635 TTTA-ATTATTTTTATAT
1 TTTATATTATTTTTATAT
1235652 T
1 T
1235653 ATATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATATTATTTTTATAT
Found at i:1235653 original size:27 final size:30
Alignment explanation
Indices: 1235616--1235678 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1235606 TTAATATATT
*
1235616 TATTTATATTAT-TTT-ATATT-TTAATTA
1 TATTTATATTATATTTAAAATTATTAATTA
*
1235643 TTTTTATATTATATTTAAAATTATTAATTA
1 TATTTATATTATATTTAAAATTATTAATTA
1235673 TATTTA
1 TATTTA
1235679 AAATTTTCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 11 0.37
28 3 0.10
29 4 0.13
30 12 0.40
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
TATTTATATTATATTTAAAATTATTAATTA
Found at i:1235677 original size:32 final size:27
Alignment explanation
Indices: 1235601--1235678 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 27
1235591 TTTTGTTATA
1235601 TAAA-TTTAATATATTTATTTATATTATTT
1 TAAATTTTAAT-TA-TT-TTTATATTATTT
*
1235630 TATATTTTAATTATTTTTATATTATATT
1 TAAATTTTAATTATTTTTATATTAT-TT
*
1235658 TAAAATTATTAATTATATTTA
1 T-AAATT-TTAATTATTTTTA
1235679 AAATTTTCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 10 0.24
28 5 0.12
29 9 0.21
30 18 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TAAATTTTAATTATTTTTATATTATTT
Found at i:1236361 original size:2 final size:2
Alignment explanation
Indices: 1236354--1236393 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1236344 GAAACTCATA
1236354 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1236394 GTAAACCAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1237646 original size:26 final size:26
Alignment explanation
Indices: 1237604--1237687 Score: 64
Period size: 26 Copynumber: 3.0 Consensus size: 26
1237594 ATCGTTTTTA
*
1237604 AATATTT-TACTATATTTAAAATATTT
1 AATATTTATA-TAAATTTAAAATATTT
*
1237630 AATATTTATATAAATTTTAAAA-AATT
1 AATATTTATATAAA-TTTAAAATATTT
*
1237656 AATAATTCGTTATATAATTTTTAAAATATTT
1 AAT-A-T--TTATATAA-ATTTAAAATATTT
1237687 A
1 A
1237688 TATAGTCGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
26 16 0.35
27 10 0.22
28 1 0.02
30 15 0.33
31 4 0.09
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (26 bp):
AATATTTATATAAATTTAAAATATTT
Found at i:1242787 original size:86 final size:86
Alignment explanation
Indices: 1242638--1242808 Score: 236
Period size: 86 Copynumber: 2.0 Consensus size: 86
1242628 TTAATATATT
* * * * *
1242638 AATTATTATCACTAATATGTATAAGATAGATTCATAAATTATAAAAGGTATATTTGTATATAATG
1 AATTATAATCACTAATATATATAAAATAGATTCATAAATTATAAAAGGTACATTTGTATATAATA
*
1242703 ATTAAATTTATATTAAATAAC
66 ATTAAACTTATATTAAATAAC
* * *
1242724 AATTATAATCACTAATATATATAAAATCGATTCATGAATTATAAAAGTTACATTTGTGA-ATAAT
1 AATTATAATCACTAATATATATAAAATAGATTCATAAATTATAAAAGGTACATTTGT-ATATAAT
*
1242788 AATTAAACTTATATTGAATAA
65 AATTAAACTTATATTAAATAA
1242809 TAATGAATAG
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
86 73 0.99
87 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (86 bp):
AATTATAATCACTAATATATATAAAATAGATTCATAAATTATAAAAGGTACATTTGTATATAATA
ATTAAACTTATATTAAATAAC
Found at i:1244888 original size:10 final size:10
Alignment explanation
Indices: 1244873--1244898 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1244863 TATGCAGATA
1244873 TGAAGAGCTT
1 TGAAGAGCTT
1244883 TGAAGAGCTT
1 TGAAGAGCTT
1244893 TGAAGA
1 TGAAGA
1244899 TGAAGAACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (10 bp):
TGAAGAGCTT
Found at i:1245325 original size:2 final size:2
Alignment explanation
Indices: 1245318--1245362 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
1245308 TTTTCGCTTC
* * * *
1245318 AT AT AT AT AT AT AT AT TT TT AT AT AT AT GT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1245360 AT A
1 AT A
1245363 GAATAATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (2 bp):
AT
Found at i:1245342 original size:14 final size:14
Alignment explanation
Indices: 1245318--1245362 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
1245308 TTTTCGCTTC
*
1245318 ATATATATATATAT
1 ATATTTATATATAT
*
1245332 ATTTTTATATATAT
1 ATATTTATATATAT
*
1245346 GTATTTATATATAT
1 ATATTTATATATAT
1245360 ATA
1 ATA
1245363 GAATAATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
ATATTTATATATAT
Found at i:1245342 original size:16 final size:16
Alignment explanation
Indices: 1245319--1245362 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
1245309 TTTCGCTTCA
1245319 TATATATATATATATT
1 TATATATATATATATT
* *
1245335 TTTATATATATGTATT
1 TATATATATATATATT
1245351 TATATATATATA
1 TATATATATATA
1245363 GAATAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TATATATATATATATT
Found at i:1245343 original size:20 final size:20
Alignment explanation
Indices: 1245318--1245433 Score: 64
Period size: 18 Copynumber: 6.0 Consensus size: 20
1245308 TTTTCGCTTC
1245318 ATATATATATATATATTTTT
1 ATATATATATATATATTTTT
* * *
1245338 ATATATATGTAT-T-TATAT
1 ATATATATATATATATTTTT
*
1245356 ATATATAGA-ATA-ATTTTT
1 ATATATATATATATATTTTT
* * * *
1245374 TTATTTAAATATATAGTGTCTT
1 ATATATATATATATA-T-TTTT
*
1245396 ATTTAT-TATAT-TATTTTT
1 ATATATATATATATATTTTT
* *
1245414 ATATTTATTAAATATATTTT
1 ATATATA-TATATATATTTT
1245434 CTCATGTTTA
Statistics
Matches: 68, Mismatches: 19, Indels: 17
0.65 0.18 0.16
Matches are distributed among these distances:
17 2 0.03
18 26 0.38
19 5 0.07
20 18 0.26
21 11 0.16
22 6 0.09
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (20 bp):
ATATATATATATATATTTTT
Found at i:1245940 original size:25 final size:25
Alignment explanation
Indices: 1245919--1245971 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1245909 TATTTAACAG
*
1245919 TAGCATTGTTTCTTTAAATTAAAAC
1 TAGCATTATTTCTTTAAATTAAAAC
1245944 TAGCATTATTTCTTTAAATTAAAAC
1 TAGCATTATTTCTTTAAATTAAAAC
1245969 TAG
1 TAG
1245972 TTAGATAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (25 bp):
TAGCATTATTTCTTTAAATTAAAAC
Found at i:1246014 original size:39 final size:39
Alignment explanation
Indices: 1245960--1246037 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
1245950 TATTTCTTTA
1245960 AATTAAAACTAGTTAGATAAGACATGTTATATATGATCT
1 AATTAAAACTAGTTAGATAAGACATGTTATATATGATCT
1245999 AATTAAAACTAGTTAGATAAGACATGTTATATATGATCT
1 AATTAAAACTAGTTAGATAAGACATGTTATATATGATCT
1246038 GAGAATTTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.36
Consensus pattern (39 bp):
AATTAAAACTAGTTAGATAAGACATGTTATATATGATCT
Found at i:1248859 original size:2 final size:2
Alignment explanation
Indices: 1248852--1248883 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1248842 GACTTAGAAA
*
1248852 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1248884 GCCCGGCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1250438 original size:2 final size:2
Alignment explanation
Indices: 1250431--1250464 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1250421 CTTTTCCTTT
1250431 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
1250465 ATGGATATTT
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):
TA
Found at i:1251153 original size:2 final size:2
Alignment explanation
Indices: 1251148--1251189 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1251138 AATATAAAAA
1251148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1251190 GATAGGTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1252153 original size:22 final size:22
Alignment explanation
Indices: 1252125--1252171 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
1252115 AAAACTCATT
1252125 TATTATTTA-ATTATAATAA-TAA
1 TATTATTTATATT-TAA-AATTAA
1252147 TATTATTTATATTTAAAATTAA
1 TATTATTTATATTTAAAATTAA
1252169 TAT
1 TAT
1252172 ATATATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 2 0.09
22 18 0.78
23 3 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATTTATATTTAAAATTAA
Found at i:1252602 original size:24 final size:26
Alignment explanation
Indices: 1252562--1252640 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
1252552 TAGAATATAT
* *
1252562 AAAATATAA-ATAAATATATGAT-TTT
1 AAAATATAATATATATATAT-ATATTA
*
1252587 AGAATATAATATATATATATATATTA
1 AAAATATAATATATATATATATATTA
* *
1252613 AAAATATAATATATAGA-ATATTTTA
1 AAAATATAATATATATATATATATTA
1252638 AAA
1 AAA
1252641 GGCAAAGTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
25 20 0.43
26 26 0.57
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
AAAATATAATATATATATATATATTA
Found at i:1255485 original size:24 final size:24
Alignment explanation
Indices: 1255436--1255495 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
1255426 ACAAGCGATT
*
1255436 AATAAAAA-CAAAATTATTAATATA
1 AATAAAAATC-AAATTATCAATATA
1255460 AATAAAAATCAAATTATCAAGT-TA
1 AATAAAAATCAAATTATCAA-TATA
*
1255484 AATGAAAATCAA
1 AATAAAAATCAA
1255496 TCTTACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (24 bp):
AATAAAAATCAAATTATCAATATA
Found at i:1257423 original size:1 final size:1
Alignment explanation
Indices: 1257417--1257483 Score: 62
Period size: 1 Copynumber: 67.0 Consensus size: 1
1257407 CAAATCTTCA
* * *** * * *
1257417 TTTTTTTTTTGTTTTTTTTCTTTTTTTTTACCTTTTCTTTTTTTTTTCTTTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1257482 TT
1 TT
1257484 ACAATTGCCA
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.01, C:0.09, G:0.01, T:0.88
Consensus pattern (1 bp):
T
Found at i:1257442 original size:17 final size:16
Alignment explanation
Indices: 1257420--1257483 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 16
1257410 ATCTTCATTT
1257420 TTTTTTTGTTTTTTTTC
1 TTTTTTT-TTTTTTTTC
**
1257437 TTTTTTTTTACCTTTTC
1 TTTTTTTTT-TTTTTTC
1257454 TTTTTTTTTTCTTTTTC
1 TTTTTTTTTT-TTTTTC
1257471 TTTTTTTTTTTTT
1 TTTTTTTTTTTTT
1257484 ACAATTGCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 5 0.12
17 36 0.88
ACGTcount: A:0.02, C:0.09, G:0.02, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTTTTTTTC
Found at i:1258103 original size:22 final size:21
Alignment explanation
Indices: 1258067--1258138 Score: 135
Period size: 21 Copynumber: 3.4 Consensus size: 21
1258057 ACAAAAACAA
1258067 AAACACAATTTTTTTTTAGAG
1 AAACACAATTTTTTTTTAGAG
1258088 AAACACAATTTTTTTTTTAGAG
1 AAACACAA-TTTTTTTTTAGAG
1258110 AAACACAATTTTTTTTTAGAG
1 AAACACAATTTTTTTTTAGAG
1258131 AAACACAA
1 AAACACAA
1258139 CCTAAAAACC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 29 0.58
22 21 0.42
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (21 bp):
AAACACAATTTTTTTTTAGAG
Found at i:1271385 original size:28 final size:28
Alignment explanation
Indices: 1271349--1271404 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1271339 ATCATTAATT
*
1271349 GTATTTTATTATTACAATTTCAATTTAA
1 GTATCTTATTATTACAATTTCAATTTAA
* * *
1271377 GTATCTTATTTTTATAATTTTAATTTAA
1 GTATCTTATTATTACAATTTCAATTTAA
1271405 TTTTTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.57
Consensus pattern (28 bp):
GTATCTTATTATTACAATTTCAATTTAA
Found at i:1271435 original size:17 final size:18
Alignment explanation
Indices: 1271415--1271452 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1271405 TTTTTAAATA
1271415 AATTTATAATATC-ATTT
1 AATTTATAATATCAATTT
*
1271432 AATTTATGATATCAATTT
1 AATTTATAATATCAATTT
1271450 AAT
1 AAT
1271453 AAGATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTTATAATATCAATTT
Found at i:1280217 original size:2 final size:2
Alignment explanation
Indices: 1280168--1280204 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1280158 AATAAAAGAA
1280168 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1280205 CCATCTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1282378 original size:21 final size:19
Alignment explanation
Indices: 1282347--1282403 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
1282337 TTAAATATAA
1282347 ATTTTTTTAATTTTAAATTT
1 ATTTTTTTAA-TTTAAATTT
1282367 ATTTTATTTAATTTAAA-TT
1 ATTTT-TTTAATTTAAATTT
*
1282386 ATTATTTAATAATTTAAA
1 ATT-TTT-TTAATTTAAA
1282404 ATATTATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 6 0.18
20 22 0.67
21 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTTTTAATTTAAATTT
Found at i:1282390 original size:17 final size:17
Alignment explanation
Indices: 1282344--1282395 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
1282334 ATCTTAAATA
1282344 TAAATT-TT-TTTAATTT
1 TAAATTATTATTTAA-TT
1282360 TAAATTTATTTTATTTAATT
1 TAAA-TTA--TTATTTAATT
1282380 TAAATTATTATTTAAT
1 TAAATTATTATTTAAT
1282396 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
16 4 0.13
17 11 0.35
19 3 0.10
20 8 0.26
21 5 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TAAATTATTATTTAATT
Found at i:1282660 original size:10 final size:8
Alignment explanation
Indices: 1282637--1282710 Score: 50
Period size: 7 Copynumber: 9.2 Consensus size: 8
1282627 TAAATACTGA
1282637 ATAAATAT
1 ATAAATAT
1282645 ATAAATAT
1 ATAAATAT
*
1282653 ATCAAAATTT
1 AT--AAATAT
1282663 ATATAATAT
1 ATA-AATAT
1282672 A-AAATAT
1 ATAAATAT
1282679 -T-AATAT
1 ATAAATAT
*
1282685 ATCAAAATTT
1 AT--AAATAT
1282695 ATAAA-AT
1 ATAAATAT
1282702 ATAAA-AT
1 ATAAATAT
1282709 AT
1 AT
1282711 TTTAAATAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
6 5 0.09
7 16 0.30
8 15 0.28
9 5 0.09
10 13 0.24
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAAATAT
Found at i:1282665 original size:18 final size:17
Alignment explanation
Indices: 1282639--1282741 Score: 72
Period size: 18 Copynumber: 6.0 Consensus size: 17
1282629 AATACTGAAT
*
1282639 AAATATATAAATATATCA
1 AAATTTATAAATATAT-A
*
1282657 AAATTTATATA-ATATA
1 AAATTTATAAATATATA
*
1282673 AAA--TATTAATATATCA
1 AAATTTATAAATATAT-A
1282689 AAATTTATAAA-ATATA
1 AAATTTATAAATATATA
*
1282705 AAATATTTTAAATAATATGA
1 AAAT-TTATAAAT-ATAT-A
*
1282725 TAATATTATAAA-ATATA
1 AAAT-TTATAAATATATA
1282742 TGAATAGAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
14 4 0.06
15 4 0.06
16 13 0.19
17 15 0.22
18 18 0.26
19 4 0.06
20 11 0.16
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (17 bp):
AAATTTATAAATATATA
Found at i:1282741 original size:37 final size:32
Alignment explanation
Indices: 1282637--1282711 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
1282627 TAAATACTGA
* *
1282637 ATAAATATATAAATATATCAAAATTTATATAAT
1 ATAAA-ATATTAATATATCAAAATTTATAAAAT
1282670 ATAAAATATTAATATATCAAAATTTATAAAAT
1 ATAAAATATTAATATATCAAAATTTATAAAAT
1282702 ATAAAATATT
1 ATAAAATATT
1282712 TTAAATAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 35 0.88
33 5 0.12
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (32 bp):
ATAAAATATTAATATATCAAAATTTATAAAAT
Found at i:1283265 original size:22 final size:22
Alignment explanation
Indices: 1283237--1283283 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1283227 ATTAAATATT
1283237 AAAATAT-TAAAT-ATAAGTAA
1 AAAATATATAAATAATAAGTAA
*
1283257 AAAATATATATATAATAAGTAA
1 AAAATATATAAATAATAAGTAA
1283279 AAAAT
1 AAAAT
1283284 TTTAACAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 7 0.29
21 4 0.17
22 13 0.54
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAATATATAAATAATAAGTAA
Found at i:1283491 original size:30 final size:30
Alignment explanation
Indices: 1283418--1283480 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
1283408 TTAACCCAAA
1283418 AATCAAACTAAAATTCTATTGTTAATAAATT
1 AATCAAA-TAAAATTCTATTGTTAATAAATT
* *
1283449 AATCAAATAAAATTTTATT-TTAATTAATT
1 AATCAAATAAAATTCTATTGTTAATAAATT
1283478 AAT
1 AAT
1283481 TTAATTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.40
30 11 0.37
31 7 0.23
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (30 bp):
AATCAAATAAAATTCTATTGTTAATAAATT
Found at i:1285451 original size:15 final size:15
Alignment explanation
Indices: 1285431--1285467 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1285421 TAAAGTAAAA
1285431 AAAATTAT-AAATGTT
1 AAAATTATAAAAT-TT
1285446 AAAATT-TAAAATTT
1 AAAATTATAAAATTT
1285460 AAAATTAT
1 AAAATTAT
1285468 TGAATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AAAATTATAAAATTT
Found at i:1286862 original size:3 final size:3
Alignment explanation
Indices: 1286850--1286897 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
1286840 GGTAGCTCAA
*
1286850 TCT T-T TCT TCT TCA TCT TCT TCT TCT TCT TCT T-T CTCT TCT ATCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT -TCT
1286895 TCT
1 TCT
1286898 GCTCGTCATC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 3 0.08
3 32 0.82
4 4 0.10
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:1289265 original size:2 final size:2
Alignment explanation
Indices: 1289260--1289304 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1289250 TTTTCTTAGC
1289260 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
1289302 TA T
1 TA T
1289305 TTCTAACCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1289999 original size:37 final size:37
Alignment explanation
Indices: 1289954--1290090 Score: 140
Period size: 37 Copynumber: 3.8 Consensus size: 37
1289944 TATTATAAAC
1289954 ATAT-TTAAAATATTATATATTTTTATATAAATTTTA
1 ATATATTAAAATATTATATATTTTTATATAAATTTTA
* * *
1289990 ATATATTAAAATACTATATATTTTTATACAACTTTTA
1 ATATATTAAAATATTATATATTTTTATATAAATTTTA
* * *
1290027 ATATATT-AAATA--ATTTATCTTTA-ATATATTTTA
1 ATATATTAAAATATTATATATTTTTATATAAATTTTA
* * *
1290060 ATATATTTATATATTTATATAATTTTCATAT
1 ATATATTAAAATA-TTATAT-ATTTTTATAT
1290091 TATATTATGT
Statistics
Matches: 82, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
33 14 0.17
34 13 0.16
36 9 0.11
37 39 0.48
38 5 0.06
39 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (37 bp):
ATATATTAAAATATTATATATTTTTATATAAATTTTA
Found at i:1290451 original size:2 final size:2
Alignment explanation
Indices: 1290444--1290480 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1290434 TTTGTTCGTC
1290444 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1290481 GATGTGAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1290973 original size:2 final size:2
Alignment explanation
Indices: 1290966--1291005 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1290956 ATAAATAGAT
*
1290966 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG A- AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1291006 CCAAAACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1293467 original size:12 final size:12
Alignment explanation
Indices: 1293452--1293493 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1293442 TTAATTATAA
*
1293452 AATATAAAATAT
1 AATATAAATTAT
1293464 AATAT-AATTAT
1 AATATAAATTAT
*
1293475 TATATAAATTATT
1 AATATAAATTA-T
1293488 AATATA
1 AATATA
1293494 TTAAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 9 0.36
12 10 0.40
13 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AATATAAATTAT
Found at i:1293491 original size:29 final size:27
Alignment explanation
Indices: 1293446--1293519 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
1293436 CAAAAATTAA
** *
1293446 TTATA-AAATATAAAATATAATATAATT
1 TTATATAAATATTTAATATAATA-AAAT
*
1293473 ATTATATAAAT-TATTAATATATTAAAAT
1 -TTATATAAATAT-TTAATATAATAAAAT
1293501 TTATATAAATATTTAATAT
1 TTATATAAATATTTAATAT
1293520 TTTATATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 17 0.44
28 10 0.26
29 12 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TTATATAAATATTTAATATAATAAAAT
Found at i:1293511 original size:20 final size:21
Alignment explanation
Indices: 1293465--1293558 Score: 74
Period size: 20 Copynumber: 4.6 Consensus size: 21
1293455 ATAAAATATA
*
1293465 ATAT-AAT-TATTATATAAATT
1 ATATAAATATATTA-ATAATTT
1293485 AT-T-AATATATTAA-AATTT
1 ATATAAATATATTAATAATTT
*
1293503 ATATAAATAT-TTAATATTTT
1 ATATAAATATATTAATAATTT
* *
1293523 ATATAAAATTATAATACATAAATT
1 ATAT-AAA-TATATTA-ATAATTT
1293547 ATATAAATATAT
1 ATATAAATATAT
1293559 AATTTATCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
18 6 0.10
19 10 0.17
20 20 0.33
21 3 0.05
22 7 0.12
23 5 0.08
24 9 0.15
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATAAATATATTAATAATTT
Found at i:1295453 original size:20 final size:20
Alignment explanation
Indices: 1295428--1295467 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1295418 ATCATAATCC
1295428 ATCATTAATTTTAATCTCAT
1 ATCATTAATTTTAATCTCAT
* *
1295448 ATCATTATTTTTAATTTCAT
1 ATCATTAATTTTAATCTCAT
1295468 GTTTGCCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (20 bp):
ATCATTAATTTTAATCTCAT
Found at i:1297669 original size:49 final size:49
Alignment explanation
Indices: 1297589--1297684 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 49
1297579 GTACAGTTTA
* *
1297589 GCGCTTCGCAATACCATTTTGTTGAGCCGAATAAGGAGCAATGGTTTTT
1 GCGCTTCGCAATACCATTTTGTTAAGCCGAATAAGGAACAATGGTTTTT
* *
1297638 GCGC-TCGACAATATCATTTTGTTAAGTCGAATAAGGAACAATGGTTT
1 GCGCTTCG-CAATACCATTTTGTTAAGCCGAATAAGGAACAATGGTTT
1297685 GATGGATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 3 0.07
49 39 0.93
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (49 bp):
GCGCTTCGCAATACCATTTTGTTAAGCCGAATAAGGAACAATGGTTTTT
Found at i:1298770 original size:13 final size:13
Alignment explanation
Indices: 1298752--1298777 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1298742 TTATGCTTTT
1298752 TATCGATACATTG
1 TATCGATACATTG
1298765 TATCGATACATTG
1 TATCGATACATTG
1298778 ACAATTGTAT
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):
TATCGATACATTG
Found at i:1298850 original size:20 final size:20
Alignment explanation
Indices: 1298825--1298878 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1298815 CTACCACTGT
1298825 TTGTATCGATACAT-AGGACA
1 TTGTATCGATACATGAGGA-A
* *
1298845 TTGTATCGATATATGATGAA
1 TTGTATCGATACATGAGGAA
*
1298865 TTGTATTGATACAT
1 TTGTATCGATACAT
1298879 TGCTTATAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGAGGAA
Found at i:1300576 original size:20 final size:20
Alignment explanation
Indices: 1300548--1300622 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1300538 TCATACCCTG
1300548 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1300568 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1300588 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1300608 ATGTATCGATACATT
1 ATGTATCGATACATT
1300623 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1300615 original size:40 final size:39
Alignment explanation
Indices: 1300548--1300625 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1300538 TCATACCCTG
* *
1300548 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1300588 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1300626 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1305672 original size:16 final size:16
Alignment explanation
Indices: 1305653--1305685 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1305643 ATATAAAGGG
1305653 TATTTT-ATATAATTAA
1 TATTTTAATA-AATTAA
1305669 TATTTTAATAAATTAA
1 TATTTTAATAAATTAA
1305685 T
1 T
1305686 TATTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTTAATAAATTAA
Found at i:1305782 original size:16 final size:16
Alignment explanation
Indices: 1305763--1305804 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1305753 TATACATAAA
1305763 ATAAAATAAATAAAAT
1 ATAAAATAAATAAAAT
* *
1305779 ATAAATTAAATTAAAT
1 ATAAAATAAATAAAAT
*
1305795 A-AATATAAAT
1 ATAAAATAAAT
1305805 TTTATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAAATAAATAAAAT
Found at i:1305782 original size:21 final size:20
Alignment explanation
Indices: 1305758--1305803 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
1305748 CTTGATATAC
1305758 ATAAAATAAAATAAATAAAAT
1 ATAAAATAAAATAAAT-AAAT
* *
1305779 ATAAATTAAATTAAATAAAT
1 ATAAAATAAAATAAATAAAT
1305799 ATAAA
1 ATAAA
1305804 TTTTATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAAAATAAAATAAATAAAT
Found at i:1305789 original size:20 final size:20
Alignment explanation
Indices: 1305761--1305822 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
1305751 GATATACATA
*
1305761 AAATAAAATAAATAAAATAT
1 AAATTAAATAAATAAAATAT
1305781 AAATTAAATTAAAT-AAATAT
1 AAATTAAA-TAAATAAAATAT
**
1305801 AAATTTTAT-AA-AAAATAT
1 AAATTAAATAAATAAAATAT
1305819 AAAT
1 AAAT
1305823 ATATAAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 12 0.32
19 1 0.03
20 19 0.51
21 5 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATTAAATAAATAAAATAT
Found at i:1305789 original size:25 final size:26
Alignment explanation
Indices: 1305752--1305825 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 26
1305742 ATAAAACTTG
*
1305752 ATATACATAAAATAAAATAAATA-AA
1 ATATAAATAAAATAAAATAAATATAA
* *
1305777 ATATAAATTAAATTAAATAAATATAA
1 ATATAAATAAAATAAAATAAATATAA
** *
1305803 AT-TTTATAAAA-AATATAAATATA
1 ATATAAATAAAATAAAATAAATATA
1305826 TAAAATTAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
24 10 0.25
25 26 0.65
26 4 0.10
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (26 bp):
ATATAAATAAAATAAAATAAATATAA
Found at i:1305842 original size:36 final size:38
Alignment explanation
Indices: 1305774--1305846 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 38
1305764 TAAAATAAAT
*
1305774 AAAATATAAATTAAATTAAATAAATATAAATTTTATAA
1 AAAATATAAATTAAATAAAATAAATATAAATTTTATAA
* * *
1305812 AAAATATAAA-TATATAAAATTAAT-TTAATTTTATA
1 AAAATATAAATTAAATAAAATAAATATAAATTTTATA
1305847 TTTATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 10 0.32
37 11 0.35
38 10 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (38 bp):
AAAATATAAATTAAATAAAATAAATATAAATTTTATAA
Found at i:1309118 original size:2 final size:2
Alignment explanation
Indices: 1309111--1309135 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1309101 AGTATAGTAA
1309111 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1309136 GAAATTTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1310028 original size:16 final size:17
Alignment explanation
Indices: 1310004--1310038 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1309994 TTGAATTTGA
1310004 TTTGGATATT-TTATAT
1 TTTGGATATTATTATAT
*
1310020 TTTGTATATTATTATAT
1 TTTGGATATTATTATAT
1310037 TT
1 TT
1310039 AAATTATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (17 bp):
TTTGGATATTATTATAT
Found at i:1312030 original size:2 final size:2
Alignment explanation
Indices: 1312023--1312058 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1312013 TTTTTCCCTA
1312023 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1312059 CAATTAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1316265 original size:31 final size:31
Alignment explanation
Indices: 1316229--1316400 Score: 102
Period size: 31 Copynumber: 5.2 Consensus size: 31
1316219 TTCGAATATT
1316229 TTAAAATTATATAATATAAATTAATAATAAA
1 TTAAAATTATATAATATAAATTAATAATAAA
*
1316260 TTAAAATTTATATAAATATAAAATAACTTAAATACAA
1 TTAAAA-TTATAT-AATATAAATTAA--T-AATA-AA
* * * *
1316297 TTATAACA-TAAACAA-AAAAATTAATACACAAATA
1 TTA-AA-ATTATATAATATAAATTAATA-A-TAA-A
1316331 TTTTAAAAATTATATAATATAAATTAAT-ATCAAA
1 --TT-AAAATTATATAATATAAATTAATAAT-AAA
*
1316365 TTAAAATT-TATATATATATATGTAA-AATAAA
1 TTAAAATTATATA-ATATAAAT-TAATAATAAA
1316396 TTAAA
1 TTAAA
1316401 TATAATTATA
Statistics
Matches: 110, Mismatches: 11, Indels: 40
0.68 0.07 0.25
Matches are distributed among these distances:
30 4 0.04
31 27 0.25
32 14 0.13
33 14 0.13
34 3 0.03
35 12 0.11
36 15 0.14
37 18 0.16
38 2 0.02
39 1 0.01
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (31 bp):
TTAAAATTATATAATATAAATTAATAATAAA
Found at i:1316281 original size:17 final size:17
Alignment explanation
Indices: 1316230--1316283 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
1316220 TCGAATATTT
1316230 TAAAA-TTATAT-AATA
1 TAAAATTTATATAAATA
*
1316245 T-AAATTAATAATAAAT-
1 TAAAATTTAT-ATAAATA
1316261 TAAAATTTATATAAATA
1 TAAAATTTATATAAATA
1316278 TAAAAT
1 TAAAAT
1316284 AACTTAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 3 0.09
15 4 0.12
16 9 0.28
17 16 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:1317845 original size:2 final size:2
Alignment explanation
Indices: 1317840--1317882 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1317830 ACAGAAAAAT
1317840 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1317882 G
1 G
1317883 GTGCAGAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1319958 original size:136 final size:135
Alignment explanation
Indices: 1319714--1319983 Score: 443
Period size: 136 Copynumber: 2.0 Consensus size: 135
1319704 TTTATATCCA
*
1319714 GCAACCAATAATCTGAAAATTGACAATATTCCAGTATGTAACATATGCTACATCATTTTAGCAGT
1 GCAACCAATAATCTGAAAATTGACAATATTCCAGTATGTAACATATGCTACATAATTTTAGCAGT
* *
1319779 CCCAAATTCATTTGTCTGGTTAAAGACAAAATGATCAGAAAAAAACAATGACCTCGATAGAATAA
66 CCCAAATTCATTTGTCTAGCTAAAGACAAAATGATCAGAAAAAAACAATGACCTCGATAGAAT-A
1319844 ATTCCG
130 ATTCCG
* ** *
1319850 GCAACCAATAATCTGAAAAATT-ATAATATTCCAGTATGTAGGATATGCTTCATAATTTTAGCAG
1 GCAACCAATAATCTG-AAAATTGACAATATTCCAGTATGTAACATATGCTACATAATTTTAGCAG
*
1319914 TCCCAAATTCATTTGTCTAGCTAAAGACAAAATGATCAGAAAAAAACAATGACCTTGATAGAATA
65 TCCCAAATTCATTTGTCTAGCTAAAGACAAAATGATCAGAAAAAAACAATGACCTCGATAGAATA
1319979 ATTCC
130 ATTCC
1319984 ACCTAATAAG
Statistics
Matches: 125, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
135 6 0.05
136 113 0.90
137 6 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (135 bp):
GCAACCAATAATCTGAAAATTGACAATATTCCAGTATGTAACATATGCTACATAATTTTAGCAGT
CCCAAATTCATTTGTCTAGCTAAAGACAAAATGATCAGAAAAAAACAATGACCTCGATAGAATAA
TTCCG
Found at i:1321995 original size:21 final size:22
Alignment explanation
Indices: 1321971--1322015 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1321961 TATTATTTAA
1321971 AATATAAAAATATTTTAT-ATT
1 AATATAAAAATATTTTATAATT
** *
1321992 AATATTTATATATTTTATAATT
1 AATATAAAAATATTTTATAATT
1322014 AA
1 AA
1322016 ATTTAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATAAAAATATTTTATAATT
Found at i:1322019 original size:21 final size:21
Alignment explanation
Indices: 1321980--1322020 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1321970 AAATATAAAA
1321980 ATATTTTATATTAATATTTAT
1 ATATTTTATATTAATATTTAT
1322001 ATATTTTATAATTAA-ATTTA
1 ATATTTTAT-ATTAATATTTA
1322021 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATATTAATATTTAT
Found at i:1323560 original size:17 final size:17
Alignment explanation
Indices: 1323538--1323582 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
1323528 AATTAATTTA
*
1323538 ATTTAATTTAAATTATT
1 ATTTAATTTAAAATATT
1323555 ATTTAATAATTAAAATATT
1 ATTTAAT--TTAAAATATT
*
1323574 TTTTAATTT
1 ATTTAATTT
1323583 TAACTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 9 0.38
19 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAATTTAAAATATT
Found at i:1323612 original size:22 final size:22
Alignment explanation
Indices: 1323577--1323649 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
1323567 AAATATTTTT
*
1323577 TAATTTTAACTATAATAATAA-A
1 TAATATTAA-TATAATAATAATA
*
1323599 TCAATATTAATATAAAAATAATA
1 T-AATATTAATATAATAATAATA
** *
1323622 TTTTATTAATATTATAATAATAA
1 TAATATTAATATAATAATAAT-A
1323645 TAATA
1 TAATA
1323650 ATAAATTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
22 27 0.68
23 13 0.32
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATATTAATATAATAATAATA
Found at i:1323619 original size:28 final size:28
Alignment explanation
Indices: 1323588--1323655 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
1323578 AATTTTAACT
1323588 ATAATAATAAATCAATATTA-ATATAAAA
1 ATAATAATAAATCAATATTATA-ATAAAA
* ** * *
1323616 ATAATATTTTATTAATATTATAATAATA
1 ATAATAATAAATCAATATTATAATAAAA
1323644 ATAATAATAAAT
1 ATAATAATAAAT
1323656 TTTTGGATTG
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (28 bp):
ATAATAATAAATCAATATTATAATAAAA
Found at i:1324229 original size:2 final size:2
Alignment explanation
Indices: 1324222--1324261 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1324212 TTTCATATTT
1324222 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
1324262 AAGTAATACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1326086 original size:16 final size:16
Alignment explanation
Indices: 1326065--1326096 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1326055 CTATAGGGGC
1326065 ACAGCTAGGCGGTGCA
1 ACAGCTAGGCGGTGCA
1326081 ACAGCTAGGCGGTGCA
1 ACAGCTAGGCGGTGCA
1326097 GGCAGAGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (16 bp):
ACAGCTAGGCGGTGCA
Found at i:1326643 original size:3 final size:3
Alignment explanation
Indices: 1326635--1326667 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1326625 AGCCAATGCA
1326635 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1326668 TTGCGTTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1331385 original size:2 final size:2
Alignment explanation
Indices: 1331378--1331421 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1331368 CATGTGCCAT
1331378 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
1331420 TA
1 TA
1331422 CACACACCTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1333428 original size:19 final size:17
Alignment explanation
Indices: 1333396--1333430 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
1333386 CTATTAAAGA
1333396 AAAAGAAAAAAATATTT
1 AAAAGAAAAAAATATTT
1333413 AAAAGTAAAAATAATATT
1 AAAAG-AAAAA-AATATT
1333431 CTTTGTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAAGAAAAAAATATTT
Found at i:1337026 original size:1 final size:1
Alignment explanation
Indices: 1337020--1337046 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1337010 TTTCAAAACA
1337020 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1337047 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1337889 original size:22 final size:22
Alignment explanation
Indices: 1337863--1337905 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1337853 ATTTTATATA
*
1337863 AAAAAAGTCT-GTAAAAAGTAT
1 AAAAAAGTATGGTAAAAAGTAT
*
1337884 ATAAAAGTATGGTAAAAAGTAT
1 AAAAAAGTATGGTAAAAAGTAT
1337906 GAAACTAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.56, C:0.02, G:0.16, T:0.26
Consensus pattern (22 bp):
AAAAAAGTATGGTAAAAAGTAT
Found at i:1337903 original size:12 final size:11
Alignment explanation
Indices: 1337864--1337906 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1337854 TTTTATATAA
*
1337864 AAAAAGTCTGT
1 AAAAAGTATGT
*
1337875 AAAAAGTATAT
1 AAAAAGTATGT
1337886 -AAAAGTATGGT
1 AAAAAGTAT-GT
1337897 AAAAAGTATG
1 AAAAAGTATG
1337907 AAACTAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 8 0.30
11 11 0.41
12 8 0.30
ACGTcount: A:0.53, C:0.02, G:0.19, T:0.26
Consensus pattern (11 bp):
AAAAAGTATGT
Found at i:1340183 original size:16 final size:17
Alignment explanation
Indices: 1340162--1340195 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1340152 AATTTTAATA
1340162 ATTTTT-ATATAATTTT
1 ATTTTTGATATAATTTT
1340178 ATTTTTGATATAATTTT
1 ATTTTTGATATAATTTT
1340195 A
1 A
1340196 ATATTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
ATTTTTGATATAATTTT
Found at i:1340194 original size:11 final size:10
Alignment explanation
Indices: 1340150--1340219 Score: 67
Period size: 10 Copynumber: 7.2 Consensus size: 10
1340140 TATCTATAAA
1340150 ATAATTTTA-
1 ATAATTTTAT
1340159 ATAATTTTTAT
1 ATAA-TTTTAT
1340170 ATAATTTTAT
1 ATAATTTTAT
*
1340180 -T--TTTGAT
1 ATAATTTTAT
1340187 ATAATTTTAAT
1 ATAATTTT-AT
* *
1340198 ATTATTTAAT
1 ATAATTTTAT
1340208 ATAATTTTAT
1 ATAATTTTAT
1340218 AT
1 AT
1340220 CAGAATTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
7 5 0.10
8 1 0.02
9 5 0.10
10 26 0.53
11 12 0.24
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (10 bp):
ATAATTTTAT
Found at i:1340202 original size:23 final size:21
Alignment explanation
Indices: 1340150--1340216 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
1340140 TATCTATAAA
1340150 ATAATTTTAATAATT-TTT-AT
1 ATAATTTTAAT-ATTATTTAAT
*
1340170 ATAA-TTT--TATT-TTTGAT
1 ATAATTTTAATATTATTTAAT
1340187 ATAATTTTAATATTATTTAAT
1 ATAATTTTAATATTATTTAAT
1340208 ATAATTTTA
1 ATAATTTTA
1340217 TATCAGAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
16 6 0.15
17 7 0.17
18 3 0.07
19 3 0.07
20 8 0.20
21 14 0.34
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (21 bp):
ATAATTTTAATATTATTTAAT
Found at i:1342460 original size:18 final size:19
Alignment explanation
Indices: 1342439--1342474 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1342429 AATTATATTT
*
1342439 ATACAATATA-ATTAAATA
1 ATACAAAATAGATTAAATA
1342457 ATACAAAATAGATTAAAT
1 ATACAAAATAGATTAAAT
1342475 TATTCAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (19 bp):
ATACAAAATAGATTAAATA
Found at i:1345051 original size:3 final size:3
Alignment explanation
Indices: 1345045--1345074 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1345035 TATTTATTAT
1345045 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1345075 ATAAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1345079 original size:4 final size:4
Alignment explanation
Indices: 1345070--1345106 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
1345060 TAATAATAAT
1345070 AATA AATA AATA AATA AATA AATA AATA AAT- AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
1345107 ATCTAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:1345108 original size:12 final size:12
Alignment explanation
Indices: 1345049--1345108 Score: 63
Period size: 12 Copynumber: 4.9 Consensus size: 12
1345039 TATTATTAAT
1345049 AATAATAATAAT-
1 AATAATAA-AATA
1345061 AATAATAATAATA
1 AATAATAA-AATA
1345074 AATAA-ATAAATA
1 AATAATA-AAATA
1345086 AATAA-ATAAATA
1 AATAATA-AAATA
1345098 AATAATAAAAT
1 AATAATAAAAT
1345109 CTAATATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
12 38 0.84
13 7 0.16
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AATAATAAAATA
Found at i:1345483 original size:19 final size:20
Alignment explanation
Indices: 1345450--1345491 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1345440 AAATTCAAAT
1345450 ATAAATTATAAAATAATAAA
1 ATAAATTATAAAATAATAAA
*
1345470 ATAAA-TATATAATAATAAA
1 ATAAATTATAAAATAATAAA
1345489 ATA
1 ATA
1345492 CATCTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAAATTATAAAATAATAAA
Found at i:1345641 original size:23 final size:24
Alignment explanation
Indices: 1345601--1345646 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
1345591 ACCTATCACT
1345601 ATTATTTATAAAAAAATTAAAAAA
1 ATTATTTATAAAAAAATTAAAAAA
1345625 ATTATTTAT-AAAAAATTAAAAA
1 ATTATTTATAAAAAAATTAAAAA
1345647 TTTATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
ATTATTTATAAAAAAATTAAAAAA
Found at i:1345937 original size:12 final size:12
Alignment explanation
Indices: 1345920--1345944 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1345910 AATCAGAGTT
1345920 AAATATAAATAA
1 AAATATAAATAA
1345932 AAATATAAATAA
1 AAATATAAATAA
1345944 A
1 A
1345945 TAAATATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATATAAATAA
Found at i:1347511 original size:20 final size:22
Alignment explanation
Indices: 1347476--1347526 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 22
1347466 AGATTTTAAA
*
1347476 ATATTTAAAT-TTTTAAAAATT
1 ATATTTATATATTTTAAAAATT
1347497 -T-TTTATATATTTTAAAAATT
1 ATATTTATATATTTTAAAAATT
1347517 ATATTTATAT
1 ATATTTATAT
1347527 TTATATCCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.23
20 12 0.46
21 1 0.04
22 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTTATATATTTTAAAAATT
Found at i:1347710 original size:2 final size:2
Alignment explanation
Indices: 1347703--1347734 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1347693 AGCTCCCATA
1347703 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
1347735 TTCTTGACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1348679 original size:20 final size:20
Alignment explanation
Indices: 1348656--1348693 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1348646 AATTACAAAA
1348656 AAAAAAAAAAAAAAAAGAGG
1 AAAAAAAAAAAAAAAAGAGG
* *
1348676 AAAAGAAAAAGAAAAAGA
1 AAAAAAAAAAAAAAAAGA
1348694 AAAGTTAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAGAGG
Found at i:1348697 original size:5 final size:6
Alignment explanation
Indices: 1348652--1348696 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
1348642 AGAAAATTAC
1348652 AAAAA- AAAAA- AAAAA- AAAAAG AGGAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG A--AAAAG AAAAAG AAAAAG AAAA
1348697 GTTAAAGCAC
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 15 0.41
6 16 0.43
8 6 0.16
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1349498 original size:22 final size:22
Alignment explanation
Indices: 1349473--1349519 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1349463 AACTTTCCTC
* * *
1349473 TTTTTTCTTTTTTTTTTTTTAT
1 TTTTTTCATTTCTTTTTATTAT
1349495 TTTTTTCATTTCTTTTTATTAT
1 TTTTTTCATTTCTTTTTATTAT
1349517 TTT
1 TTT
1349520 AATTTATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (22 bp):
TTTTTTCATTTCTTTTTATTAT
Found at i:1349510 original size:19 final size:19
Alignment explanation
Indices: 1349488--1349524 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1349478 TCTTTTTTTT
* *
1349488 TTTTTATTTTTTTCATTTC
1 TTTTTATTATTTTAATTTC
1349507 TTTTTATTATTTTAATTT
1 TTTTTATTATTTTAATTT
1349525 ATGTAAAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTATTATTTTAATTTC
Found at i:1355257 original size:2 final size:2
Alignment explanation
Indices: 1355252--1355299 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1355242 TTTTTTTTTG
*
1355252 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CC
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1355294 CT CT CT
1 CT CT CT
1355300 GTTTCTCTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1357998 original size:2 final size:2
Alignment explanation
Indices: 1357991--1358024 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1357981 CCTCAATTAT
1357991 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1358025 AAAGAATAAC
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1360570 original size:26 final size:27
Alignment explanation
Indices: 1360530--1360594 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 27
1360520 AATTATTATT
* *
1360530 TATTTAATTAAATAATATTTTTAAA-AA
1 TATTTAATTATATAA-AATTTTAAATAA
1360557 T-TTTAATTATATAAAATTTTAAATAA
1 TATTTAATTATATAAAATTTTAAATAA
1360583 TATTTAAATTAT
1 TATTT-AATTAT
1360595 TATATAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 8 0.24
26 15 0.45
27 4 0.12
28 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TATTTAATTATATAAAATTTTAAATAA
Found at i:1360601 original size:19 final size:18
Alignment explanation
Indices: 1360568--1360612 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1360558 TTTAATTATA
*
1360568 TAAAATTTTAAATAATAT
1 TAAAATTTTAAATAAGAT
* *
1360586 TTAAATTATTATATAAGAT
1 TAAAATT-TTAAATAAGAT
1360605 TAAAATTT
1 TAAAATTT
1360613 GATTTTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TAAAATTTTAAATAAGAT
Found at i:1360816 original size:30 final size:30
Alignment explanation
Indices: 1360782--1360864 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 30
1360772 TTAAATTATT
*
1360782 ATTTAATTAATAAATAATATTTTTATTTAA
1 ATTTAATTAATAAATAATATTTTTATATAA
* * *
1360812 ATTTAATT-ATAAA-ACTATTTTAATATAT
1 ATTTAATTAATAAATAATATTTTTATATAA
*
1360840 TTTTAATTAATAAAATAA-ATTTTTA
1 ATTTAATTAAT-AAATAATATTTTTA
1360865 AATATGATGA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
28 18 0.42
29 7 0.16
30 17 0.40
31 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTTAATTAATAAATAATATTTTTATATAA
Found at i:1361354 original size:2 final size:2
Alignment explanation
Indices: 1361347--1361412 Score: 105
Period size: 2 Copynumber: 33.0 Consensus size: 2
1361337 TTCCCCACAA
* *
1361347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1361389 AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
1361413 CAAAAATTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1365662 original size:2 final size:2
Alignment explanation
Indices: 1365655--1365682 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1365645 TAATTACATA
1365655 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
1365683 GGAGCCGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1365820 original size:2 final size:2
Alignment explanation
Indices: 1365813--1365845 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1365803 AATTTGAATC
1365813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1365846 AGAGAAAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1366101 original size:18 final size:19
Alignment explanation
Indices: 1366078--1366113 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1366068 TCATATGTAC
1366078 ACGTGATA-AAAAAAATAT
1 ACGTGATAGAAAAAAATAT
1366096 ACGTGATAGAAAAAAATA
1 ACGTGATAGAAAAAAATA
1366114 CAATTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.61, C:0.06, G:0.14, T:0.19
Consensus pattern (19 bp):
ACGTGATAGAAAAAAATAT
Found at i:1367422 original size:21 final size:19
Alignment explanation
Indices: 1367392--1367432 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1367382 TTAAGTTGTT
1367392 ATAGTTAATTTTTCTTAATG
1 ATAGTTAA-TTTTCTTAATG
*
1367412 ATAGTTTAATTTTCTTCATG
1 ATAG-TTAATTTTCTTAATG
1367432 A
1 A
1367433 AATATGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (19 bp):
ATAGTTAATTTTCTTAATG
Found at i:1368702 original size:155 final size:153
Alignment explanation
Indices: 1368343--1368738 Score: 371
Period size: 155 Copynumber: 2.5 Consensus size: 153
1368333 TACTTAACAG
* * * * ** * *
1368343 GTATTTTGATAATTTCTCCTAAAACCGAGTTTGATTTATTTATCTGGATGCTCTTATGCCAAAGG
1 GTATTTTGATAATTTCT-C-AAAAACAAGTTTGATCTAATTATCAAGATGCTTTTATGCCAAAAG
* * * * * *
1368408 CGTGCATTTAGGATAAGTTCACTCTTCCATGACTATTCTCGAGTCTTTTAGGGTAATCAGGATAT
64 TGTGCATTTAGGATAAGTTCACTCTTCCATGAATATTCTCGAGTCCTTGAGGATAATCAGGATAC
* * *
1368473 TTTCATATCGAAAGCATACCCCAAG
129 TTTCATATCAAAAGCATACCCAAAA
* * * * * * * *
1368498 GCATTTTGATAATTTCCCCTAGAAGCAAGTTTGATCTAATTTTCGAGATGTTTTTATGTCAAAAG
1 GTATTTTGATAATTT-CTC-AAAAACAAGTTTGATCTAATTATCAAGATGCTTTTATGCCAAAAG
* *** * * *
1368563 TGTGCATTTAAGATAAGTTCACTCTTTTGTGAATATTTTTGATTCCTTGAGGATAA-CTAGGATA
64 TGTGCATTTAGGATAAGTTCACTCTTCCATGAATATTCTCGAGTCCTTGAGGATAATC-AGGATA
*
1368627 CTTTCATATCAAAAGTATATCCCAAAA
128 CTTTCATATCAAAAGCATA-CCCAAAA
* * * *
1368654 GTATTTTGATAATTTCTCAAAAACTAAGTTTGATGTAGTCATCAAGATGCTTTTATACCAAAAGT
1 GTATTTTGATAATTTCTCAAAAAC-AAGTTTGATCTAATTATCAAGATGCTTTTATGCCAAAAGT
* *
1368719 GTGTATTTAGGACAAGTTCA
65 GTGCATTTAGGATAAGTTCA
1368739 TAATTCTATG
Statistics
Matches: 191, Mismatches: 46, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
154 5 0.03
155 166 0.87
156 20 0.10
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (153 bp):
GTATTTTGATAATTTCTCAAAAACAAGTTTGATCTAATTATCAAGATGCTTTTATGCCAAAAGTG
TGCATTTAGGATAAGTTCACTCTTCCATGAATATTCTCGAGTCCTTGAGGATAATCAGGATACTT
TCATATCAAAAGCATACCCAAAA
Found at i:1369192 original size:152 final size:154
Alignment explanation
Indices: 1368961--1369239 Score: 388
Period size: 152 Copynumber: 1.8 Consensus size: 154
1368951 GTTGTAGTCT
* * *
1368961 CTAAAGGCATTTTGGTAATTTCCTCTAGAATCAAGTCGGATGTAATCACTAAGATAATTTTATGT
1 CTAAAGACATTTGGGTAATTT-CTCTAGAATCAAGTCGGATATAATCACTAAGATAATTTTATGT
* * * * *
1369026 TAAAGATATGTATTTAGGATA-GATTCATCCTTTTATGATTTGTTTTTGAGTCCTTTAGGATTAT
65 CAAAAATATGTATTTAGGATATG-TTCATCATTTTATAATATGTTTTTGAGTCCTTTA-GATTAT
1369090 CAATATACTTCATATCGAAAGTATATC
128 CAATATACTTCATATCGAAAGTATATC
* **
1369117 CTAAAGACATTTGGGTAATTT-T-TAGAATCAAGT-GCGATATAGTCAC-AAGATGCTTTTATGT
1 CTAAAGACATTTGGGTAATTTCTCTAGAATCAAGTCG-GATATAATCACTAAGATAATTTTATGT
1369178 CAAAAATATGTATTTAGGATATGTTCATCATTTTATAATATGTTTTTGAGTCCTTTAGATTA
65 CAAAAATATGTATTTAGGATATGTTCATCATTTTATAATATGTTTTTGAGTCCTTTAGATTA
1369240 CTAAGATATT
Statistics
Matches: 110, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
151 5 0.05
152 64 0.58
153 21 0.19
154 1 0.01
156 19 0.17
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (154 bp):
CTAAAGACATTTGGGTAATTTCTCTAGAATCAAGTCGGATATAATCACTAAGATAATTTTATGTC
AAAAATATGTATTTAGGATATGTTCATCATTTTATAATATGTTTTTGAGTCCTTTAGATTATCAA
TATACTTCATATCGAAAGTATATC
Found at i:1370131 original size:2 final size:2
Alignment explanation
Indices: 1370091--1370116 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1370081 TGACTTCTAA
1370091 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
1370117 GAAATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1370333 original size:2 final size:2
Alignment explanation
Indices: 1370326--1370376 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1370316 AATTCAAATG
1370326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1370368 AT AT AT AT A
1 AT AT AT AT A
1370377 CCCACTAGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1370551 original size:15 final size:17
Alignment explanation
Indices: 1370532--1370566 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1370522 ATAAGTTAAT
*
1370532 TTTTTAA-ATAATTATA
1 TTTTTAATATAAATATA
1370548 TTTTTAATATAAATATA
1 TTTTTAATATAAATATA
1370565 TT
1 TT
1370567 ATTTCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTTAATATAAATATA
Found at i:1370710 original size:22 final size:22
Alignment explanation
Indices: 1370683--1370739 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1370673 TATCTTCAAA
1370683 TATTTATTATTATATTAACA-AT
1 TATTTATTATTATATT-ACATAT
* *
1370705 TATTTATTTTTATATTGCATAT
1 TATTTATTATTATATTACATAT
*
1370727 CATTTATTATTAT
1 TATTTATTATTAT
1370740 TTTATTCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (22 bp):
TATTTATTATTATATTACATAT
Done.