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 7 of 26
Found at i:922114 original size:2 final size:2
Alignment explanation
Indices: 922107--922148 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
922097 ATTTATCAAT
*
922107 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
922149 CACACACACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:922244 original size:2 final size:2
Alignment explanation
Indices: 922239--922271 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
922229 ATAGATACGT
922239 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
922272 TTTTCAAACT
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:922261 original size:105 final size:105
Alignment explanation
Indices: 922148--922356 Score: 400
Period size: 105 Copynumber: 2.0 Consensus size: 105
922138 ATATATGTAT
922148 ACACACACACACACACACATTTTCAAACTTACTAAACCATAAATATCAGTCACAGATAACAAATT
1 ACACACACACACACACACATTTTCAAACTTACTAAACCATAAATATCAGTCACAGATAACAAATT
*
922213 ATTCCTTCAATTATATATAGATACGTACACACACACACAC
66 ATTCCTTCAATTATATATAGATACATACACACACACACAC
*
922253 ACACACACACACACACACATTTTCAAACTTACTAAACCATAAATATCAGTCACAGATAACCAATT
1 ACACACACACACACACACATTTTCAAACTTACTAAACCATAAATATCAGTCACAGATAACAAATT
922318 ATTCCTTCAATTATATATAGATACATACACACACACACA
66 ATTCCTTCAATTATATATAGATACATACACACACACACA
922357 TTTTCAAACA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.45, C:0.28, G:0.03, T:0.24
Consensus pattern (105 bp):
ACACACACACACACACACATTTTCAAACTTACTAAACCATAAATATCAGTCACAGATAACAAATT
ATTCCTTCAATTATATATAGATACATACACACACACACAC
Found at i:922403 original size:85 final size:85
Alignment explanation
Indices: 922259--922414 Score: 249
Period size: 85 Copynumber: 1.8 Consensus size: 85
922249 ACACACACAC
* * *
922259 ACACACACACACATTTTCAAACTTACTAAACCATAAATATCAGTCACAGATAACCAATTATTCCT
1 ACACACACACACATTTTCAAACATACTAAAACATAAATATCAGTAACAGATAACCAATTATTCCT
922324 TCAATTATATATAGATACAT
66 TCAATTATATATAGATACAT
* * * *
922344 ACACACACACACATTTTCAAACATACTAAAACATGAATATCAGTAATATATAACGAATTATTCCT
1 ACACACACACACATTTTCAAACATACTAAAACATAAATATCAGTAACAGATAACCAATTATTCCT
922409 TCAATT
66 TCAATT
922415 GTGCTTCGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 64 1.00
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.29
Consensus pattern (85 bp):
ACACACACACACATTTTCAAACATACTAAAACATAAATATCAGTAACAGATAACCAATTATTCCT
TCAATTATATATAGATACAT
Found at i:923572 original size:3 final size:3
Alignment explanation
Indices: 923564--923594 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
923554 GAGGTAACCG
923564 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
923595 ATTATAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:923825 original size:13 final size:14
Alignment explanation
Indices: 923804--923835 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
923794 TATAGATATA
923804 AATTT-TATTTA-T
1 AATTTATATTTATT
923816 AATTTATATTTATT
1 AATTTATATTTATT
923830 AATTTA
1 AATTTA
923836 AGCATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.28
13 6 0.33
14 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AATTTATATTTATT
Found at i:928520 original size:25 final size:25
Alignment explanation
Indices: 928470--928521 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
928460 CAAACATCTC
* * **
928470 AAATAAAATTAATTTAAACTTTTAT
1 AAATAAAAATAAATTAAACTCATAT
928495 AAATAAAAATAAATTAAACTCATAT
1 AAATAAAAATAAATTAAACTCATAT
928520 AA
1 AA
928522 TCATATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (25 bp):
AAATAAAAATAAATTAAACTCATAT
Found at i:929089 original size:20 final size:20
Alignment explanation
Indices: 929064--929102 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
929054 AAACATATTT
929064 AAAAAAAATGA-TTCTAAAAA
1 AAAAAAAAT-ATTTCTAAAAA
*
929084 AAAAAACATATTTCTAAAA
1 AAAAAAAATATTTCTAAAA
929103 TTAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAAAAAATATTTCTAAAAA
Found at i:931673 original size:12 final size:13
Alignment explanation
Indices: 931651--931685 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
931641 ATTTAATTTT
931651 AAATTTATTAAAA
1 AAATTTATTAAAA
931664 AAATTT-TTAAAA
1 AAATTTATTAAAA
931676 AAATTCTATT
1 AAATT-TATT
931686 TAAGTGTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 11 0.55
13 7 0.35
14 2 0.10
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATTTATTAAAA
Found at i:931969 original size:24 final size:24
Alignment explanation
Indices: 931917--931970 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
931907 ATTTTCTATT
*
931917 TAAAAAAAATAAAAATTGAAAAGC
1 TAAAAAAAATAAAAATTGAAAAAC
*
931941 CAAAAAAAA-AAAAGATCT-AAAAAC
1 TAAAAAAAATAAAA-AT-TGAAAAAC
931965 TAAAAA
1 TAAAAA
931971 TGCTACCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 4 0.16
24 20 0.80
25 1 0.04
ACGTcount: A:0.74, C:0.07, G:0.06, T:0.13
Consensus pattern (24 bp):
TAAAAAAAATAAAAATTGAAAAAC
Found at i:934413 original size:17 final size:17
Alignment explanation
Indices: 934393--934426 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
934383 TAATTTAATT
934393 ATTT-ATAATTTTTATAA
1 ATTTAATAA-TTTTATAA
934410 ATTTAATAATTTTATAA
1 ATTTAATAATTTTATAA
934427 TTATTTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTAATAATTTTATAA
Found at i:934435 original size:25 final size:24
Alignment explanation
Indices: 934377--934435 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
934367 TTACATGATT
* *
934377 TTATTTTAATTTAATTATTTATAA
1 TTATTTAAATTTAATAATTTATAA
*
934401 TTTTTATAAATTTAATAATTTTATAA
1 TTATT-TAAATTTAATAA-TTTATAA
934427 TTATTTAAA
1 TTATTTAAA
934436 CACATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 4 0.14
25 14 0.48
26 11 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATTTAAATTTAATAATTTATAA
Found at i:934514 original size:20 final size:20
Alignment explanation
Indices: 934477--934518 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
934467 ATATATTAAA
*
934477 ATTTTATATAAATTTATAAT
1 ATTTTATATAAATCTATAAT
934497 ATTTTATATATAA-CTATAAT
1 ATTTTATATA-AATCTATAAT
934517 AT
1 AT
934519 ATAAAAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTTATATAAATCTATAAT
Found at i:934805 original size:3 final size:3
Alignment explanation
Indices: 934797--934830 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
934787 GCTGCTACTG
*
934797 TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
934831 GTGTTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:936808 original size:2 final size:2
Alignment explanation
Indices: 936797--936840 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
936787 GCTTGACATG
936797 TA TA TA -A 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
936838 TA T
1 TA T
936841 GCCTGCTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:939933 original size:13 final size:13
Alignment explanation
Indices: 939915--939939 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
939905 TTGGGGAGGC
939915 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
939928 TTTTTTGTTTTT
1 TTTTTTGTTTTT
939940 ATAGATCTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:940279 original size:23 final size:23
Alignment explanation
Indices: 940253--940297 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
940243 TATTATTAAA
*
940253 ATATA-TGTTAT-ATTAATATTT
1 ATATATTGTTATAATTAAAATTT
*
940274 ATATATTTTTATAATTAAAATTT
1 ATATATTGTTATAATTAAAATTT
940297 A
1 A
940298 AATAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 5 0.25
23 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATATTGTTATAATTAAAATTT
Found at i:947313 original size:14 final size:14
Alignment explanation
Indices: 947294--947353 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 14
947284 AAAAATAAAG
947294 AAAAGA-AAAGGAA
1 AAAAGATAAAGGAA
947307 AAGAAGA-AAATGGAAAGA
1 AA-AAGATAAA-GG--A-A
947325 AAAAGATAAAGGAA
1 AAAAGATAAAGGAA
*
947339 AAAAAATAAAGGAA
1 AAAAGATAAAGGAA
947353 A
1 A
947354 GAAACGAAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
13 2 0.05
14 22 0.55
15 3 0.08
17 7 0.17
18 6 0.15
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (14 bp):
AAAAGATAAAGGAA
Found at i:947315 original size:19 final size:20
Alignment explanation
Indices: 947291--947330 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
947281 ATAAAAAATA
*
947291 AAGAAAA-GAAAAGGAAAAG
1 AAGAAAATGAAAAGAAAAAG
*
947310 AAGAAAATGGAAAGAAAAAG
1 AAGAAAATGAAAAGAAAAAG
947330 A
1 A
947331 TAAAGGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (20 bp):
AAGAAAATGAAAAGAAAAAG
Found at i:947353 original size:31 final size:31
Alignment explanation
Indices: 947290--947357 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
947280 TATAAAAAAT
*
947290 AAAG-AAAAGAAAAGGAAAAGAAGAAAATGG
1 AAAGAAAAAGAAAAGGAAAAGAAGAAAAAGG
947320 AAAGAAAAAGATAAAGGAAAA-AA-AATAAAGG
1 AAAGAAAAAGA-AAAGGAAAAGAAGAA-AAAGG
947351 AAAGAAA
1 AAAGAAA
947358 CGAAAGAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
30 6 0.18
31 19 0.56
32 9 0.26
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (31 bp):
AAAGAAAAAGAAAAGGAAAAGAAGAAAAAGG
Found at i:947420 original size:18 final size:18
Alignment explanation
Indices: 947397--947467 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 18
947387 TATGTTGGTG
947397 TTATATTTATATAATTTT
1 TTATATTTATATAATTTT
* * *
947415 TTATATTTTTAAAATATT
1 TTATATTTATATAATTTT
* * *
947433 ATAAATTTATATAAATTT
1 TTATATTTATATAATTTT
947451 TTATATATTA-ATAATTT
1 TTATAT-TTATATAATTT
947468 ATTTTATGAA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
18 37 0.93
19 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATATTTATATAATTTT
Found at i:948509 original size:17 final size:17
Alignment explanation
Indices: 948487--948530 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
948477 ATAAAGGGGA
*
948487 AAAAGAAAGAGGAAAAG
1 AAAAGAAAGAGAAAAAG
*
948504 AAAAGAAAGAGAAAAAT
1 AAAAGAAAGAGAAAAAG
*
948521 ACAAGAAAGA
1 AAAAGAAAGA
948531 TTTGTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (17 bp):
AAAAGAAAGAGAAAAAG
Found at i:948554 original size:19 final size:19
Alignment explanation
Indices: 948530--948571 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
948520 TACAAGAAAG
*
948530 ATTTGTA-TATTTATTTTAT
1 ATTTGTATTATTT-TTTAAT
948549 ATTTGTATTATTTTTTAAT
1 ATTTGTATTATTTTTTAAT
948568 ATTT
1 ATTT
948572 TAATAGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
ATTTGTATTATTTTTTAAT
Found at i:948634 original size:20 final size:20
Alignment explanation
Indices: 948605--948656 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
948595 ATTTATATAA
**
948605 ATTTTGATATATTTTTAATTT
1 ATTTT-ATATATTTTTAAAAT
*
948626 ATTTTATATAATTTTAAAAT
1 ATTTTATATATTTTTAAAAT
948646 A-TTTATATATT
1 ATTTTATATATT
948657 CTTATTATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 9 0.33
20 13 0.48
21 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTTATATATTTTTAAAAT
Found at i:949295 original size:17 final size:18
Alignment explanation
Indices: 949275--949316 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
949265 TGTGTTAAAA
*
949275 ATATTATAAATTT-TTAT
1 ATATTAAAAATTTATTAT
*
949292 ATATTAAAAATTTATTTT
1 ATATTAAAAATTTATTAT
949310 ATATTAA
1 ATATTAA
949317 TTTTAATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATTAAAAATTTATTAT
Found at i:949373 original size:28 final size:30
Alignment explanation
Indices: 949340--949402 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 30
949330 GTATATTCTT
949340 ATCATGTTCAT-ATTATTTTTT-AT-ATTAC
1 ATCATGTT-ATAATTATTTTTTGATGATTAC
* *
949368 ATCATGTTTTAATTATTTTTTGATGATTAT
1 ATCATGTTATAATTATTTTTTGATGATTAC
949398 ATCAT
1 ATCAT
949403 AATTCATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 1 0.03
28 18 0.60
29 2 0.07
30 9 0.30
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (30 bp):
ATCATGTTATAATTATTTTTTGATGATTAC
Found at i:949731 original size:22 final size:19
Alignment explanation
Indices: 949700--949741 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
949690 ATTTTTTATT
949700 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
949721 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
949741 T
1 T
949742 TTTTTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:951568 original size:16 final size:16
Alignment explanation
Indices: 951547--951578 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
951537 TTTTTGACGC
951547 AGTTATGATTTATCCA
1 AGTTATGATTTATCCA
951563 AGTTATGATTTATCCA
1 AGTTATGATTTATCCA
951579 GTGCCTTTTA
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:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
AGTTATGATTTATCCA
Found at i:955264 original size:15 final size:15
Alignment explanation
Indices: 955246--955301 Score: 85
Period size: 15 Copynumber: 3.6 Consensus size: 15
955236 TATCAATAAA
955246 ATTTTAAATTATTAT
1 ATTTTAAATTATTAT
955261 ATTTTAAATTATTAT
1 ATTTTAAATTATTAT
*
955276 ATTTTAAGTTTATTAT
1 ATTTTAA-ATTATTAT
955292 ATTATTAAAT
1 ATT-TTAAAT
955302 ATGAATGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 22 0.59
16 11 0.30
17 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
ATTTTAAATTATTAT
Found at i:955831 original size:13 final size:13
Alignment explanation
Indices: 955813--955856 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
955803 AGTATCGTCT
955813 TAATTAATAAAAA
1 TAATTAATAAAAA
955826 TAATTAA-AATAAA
1 TAATTAATAA-AAA
955839 TAATTACATAAATAA
1 TAATTA-ATAAA-AA
955854 TAA
1 TAA
955857 AGTAAATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.07
13 16 0.59
14 2 0.07
15 7 0.26
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (13 bp):
TAATTAATAAAAA
Found at i:955851 original size:12 final size:13
Alignment explanation
Indices: 955813--955865 Score: 58
Period size: 12 Copynumber: 4.2 Consensus size: 13
955803 AGTATCGTCT
955813 TAATTAATAA-AAA
1 TAATTAA-AATAAA
955826 TAATTAAAATAAA
1 TAATTAAAATAAA
*
955839 TAATT-ACATAAA
1 TAATTAAAATAAA
*
955851 TAA-TAAAGTAAA
1 TAATTAAAATAAA
955863 TAA
1 TAA
955866 GCATTAGTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 1 0.03
12 19 0.54
13 15 0.43
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (13 bp):
TAATTAAAATAAA
Found at i:956528 original size:6 final size:6
Alignment explanation
Indices: 956517--956545 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
956507 TTGGCCCTCC
956517 GCCTTT GCCTTT GCCTTT GCCTTT GCCTT
1 GCCTTT GCCTTT GCCTTT GCCTTT GCCTT
956546 CGGCTTATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.34, G:0.17, T:0.48
Consensus pattern (6 bp):
GCCTTT
Found at i:956989 original size:3 final size:3
Alignment explanation
Indices: 956981--957006 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
956971 ATTTTATTTT
956981 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
957007 GACAACAATG
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:957243 original size:2 final size:2
Alignment explanation
Indices: 957236--957274 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
957226 ATGGCATGCA
*
957236 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
957275 GAGAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:960269 original size:2 final size:2
Alignment explanation
Indices: 960262--960402 Score: 282
Period size: 2 Copynumber: 70.5 Consensus size: 2
960252 TTATTGACAT
960262 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
960304 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
960346 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
960388 GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA G
960403 TTTTACGTGG
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 139 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:960793 original size:22 final size:25
Alignment explanation
Indices: 960737--960793 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 25
960727 ACTGTACAAC
*
960737 ATATAAAATATCATAAACATGATCT
1 ATATAAAATATCATAAACATAATCT
* *
960762 AAATATAATAT-ATAAA-A-AATCT
1 ATATAAAATATCATAAACATAATCT
960784 ATATAAAATA
1 ATATAAAATA
960794 ATTTATTAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 12 0.44
23 1 0.04
24 5 0.19
25 9 0.33
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.32
Consensus pattern (25 bp):
ATATAAAATATCATAAACATAATCT
Found at i:961778 original size:35 final size:35
Alignment explanation
Indices: 961711--961778 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
961701 ATCGACTATA
* * * *
961711 TAAAATATAAAAAGAATTAAGATACAACATAAACC
1 TAAAATATAAAAAGAACTAAAACACAAAATAAACC
961746 TAAAATATATAAAA-AACTAAAACACAAAATAAA
1 TAAAATATA-AAAAGAACTAAAACACAAAATAAA
961779 ATATAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 24 0.86
36 4 0.14
ACGTcount: A:0.68, C:0.10, G:0.03, T:0.19
Consensus pattern (35 bp):
TAAAATATAAAAAGAACTAAAACACAAAATAAACC
Found at i:964479 original size:2 final size:2
Alignment explanation
Indices: 964472--964497 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
964462 GGAAGTGTAC
964472 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
964498 TGTGAACCAC
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:965007 original size:44 final size:44
Alignment explanation
Indices: 964939--965023 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
964929 ATTGTGATAT
* *
964939 TAAAGTAATATAAATAATGATGAGATTATACAAAGATGATCCTA
1 TAAAGTAACATAAATAATGATGAGACTATACAAAGATGATCCTA
* * *
964983 TAAAGTAACATAAAT-ATTAGTGAGACTATATAAAGGTGATC
1 TAAAGTAACATAAATAATGA-TGAGACTATACAAAGATGATC
965024 TCTCTCTTGC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 3 0.09
44 32 0.91
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.29
Consensus pattern (44 bp):
TAAAGTAACATAAATAATGATGAGACTATACAAAGATGATCCTA
Found at i:969394 original size:28 final size:27
Alignment explanation
Indices: 969363--969420 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
969353 ATTTAATTTA
969363 ATTTGAATTTT-TTTAATTAATAAAAAAT
1 ATTT-AATTTTATTTAATT-ATAAAAAAT
* *
969391 ATTTTATTTTAATTTAATTATAAAATAT
1 ATTTAATTTT-ATTTAATTATAAAAAAT
969419 AT
1 AT
969421 AAATATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 14 0.54
29 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTTAATTTTATTTAATTATAAAAAAT
Found at i:969473 original size:23 final size:22
Alignment explanation
Indices: 969419--969479 Score: 74
Period size: 23 Copynumber: 2.9 Consensus size: 22
969409 TATAAAATAT
*
969419 ATAAA-TATTTTAACTTT-TAA
1 ATAAATTATTTTAAATTTATAA
*
969439 A-AAATTAATTTAAATTTATAA
1 ATAAATTATTTTAAATTTATAA
969460 ATTAAATTATTTTAAATTTA
1 A-TAAATTATTTTAAATTTA
969480 AATAAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 3 0.09
20 11 0.32
21 4 0.12
23 16 0.47
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAATTATTTTAAATTTATAA
Found at i:970062 original size:22 final size:22
Alignment explanation
Indices: 970025--970088 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
970015 TAAAAATTAC
*
970025 AAAT-TAATTTATTGATTTTAG
1 AAATATAATTTACTGATTTTAG
* * * *
970046 GACTATAATTTCCTGATTTAAG
1 AAATATAATTTACTGATTTTAG
*
970068 AAATTTAATTTACTGATTTTA
1 AAATATAATTTACTGATTTTA
970089 AGGTTGTAAT
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (22 bp):
AAATATAATTTACTGATTTTAG
Found at i:975387 original size:27 final size:28
Alignment explanation
Indices: 975327--975382 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
975317 GTTGGCCAAA
*
975327 AAAATTGAAATATACTTTTTGGAGGTTT
1 AAAATTGAAATATACTTTTTGGAGCTTT
975355 AAAATTGAAAT-TAACTTTTTGGAGCTTT
1 AAAATTGAAATAT-ACTTTTTGGAGCTTT
975383 TAATTCCAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (28 bp):
AAAATTGAAATATACTTTTTGGAGCTTT
Found at i:977761 original size:6 final size:7
Alignment explanation
Indices: 977742--977767 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
977732 TGTAGGAAAG
977742 ATAAAAA
1 ATAAAAA
977749 ATAAAAA
1 ATAAAAA
977756 ATAAAAA
1 ATAAAAA
977763 ATAAA
1 ATAAA
977768 GGTAAAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
ATAAAAA
Found at i:977988 original size:24 final size:23
Alignment explanation
Indices: 977961--978012 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
977951 ATAAAATAAC
977961 AATTCAGACAACTAAGAAATGTAT
1 AATTC-GACAACTAAGAAATGTAT
* * *
977985 AATTTCTATAACTAAGAACTGTAT
1 AA-TTCGACAACTAAGAAATGTAT
978009 AATT
1 AATT
978013 TCTATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 2 0.08
24 19 0.79
25 3 0.12
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.33
Consensus pattern (23 bp):
AATTCGACAACTAAGAAATGTAT
Found at i:978013 original size:24 final size:24
Alignment explanation
Indices: 977970--978018 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
977960 CAATTCAGAC
977970 AACTAAGAAATGTATAATTTCTAT
1 AACTAAGAAATGTATAATTTCTAT
*
977994 AACTAAGAACTGTATAATTTCTAT
1 AACTAAGAAATGTATAATTTCTAT
978018 A
1 A
978019 TAATATATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (24 bp):
AACTAAGAAATGTATAATTTCTAT
Found at i:981432 original size:2 final size:2
Alignment explanation
Indices: 981425--981469 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
981415 TCTTTTTGTA
981425 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
981467 AT A
1 AT A
981470 AACACACATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:982212 original size:11 final size:11
Alignment explanation
Indices: 982183--982216 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
982173 AAATTTATCT
982183 TAAAAAT-ATA
1 TAAAAATAATA
982193 TAAATAATAATA
1 TAAA-AATAATA
982205 TAAAAATAATA
1 TAAAAATAATA
982216 T
1 T
982217 TTTAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.18
11 11 0.50
12 7 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:984600 original size:17 final size:17
Alignment explanation
Indices: 984586--984618 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
984576 TTAAATATAT
984586 TAGTATTTTTTATATTA
1 TAGTATTTTTTATATTA
*
984603 TATTATTTTTTA-ATTA
1 TAGTATTTTTTATATTA
984619 AATTTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TAGTATTTTTTATATTA
Found at i:986016 original size:5 final size:5
Alignment explanation
Indices: 986006--986072 Score: 50
Period size: 5 Copynumber: 13.6 Consensus size: 5
985996 TAATTATACG
* * ** *
986006 AATAT AATAT AA-AT AAAAT AATTAA AATAT AATAT AA-AT ACATAT CTTAA
1 AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT A-ATAT AATAT
986056 AAT-T AATAT AATAT AAT
1 AATAT AATAT AATAT AAT
986073 TATTAACATA
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
4 10 0.21
5 33 0.69
6 5 0.10
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:986018 original size:25 final size:25
Alignment explanation
Indices: 986006--986071 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
985996 TAATTATACG
986006 AATATAATATAAATAAAATAATTAA
1 AATATAATATAAATAAAATAATTAA
* *
986031 AATATAATATAAAT-ACATATCTTAA
1 AATATAATATAAATAAAATA-ATTAA
986056 AAT-TAATATAATATAA
1 AATATAATATAA-ATAA
986072 TTATTAACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
24 12 0.33
25 23 0.64
26 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (25 bp):
AATATAATATAAATAAAATAATTAA
Found at i:986074 original size:14 final size:14
Alignment explanation
Indices: 986006--986071 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
985996 TAATTATACG
986006 AATATAATATAAAT
1 AATATAATATAAAT
*
986020 AAAATAAT-T-AA-
1 AATATAATATAAAT
986031 AATATAATATAAAT
1 AATATAATATAAAT
**
986045 ACATATCTTA-AAATT
1 A-ATATAATATAAA-T
986060 AATATAATATAA
1 AATATAATATAA
986072 TTATTAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
11 7 0.17
12 3 0.08
13 3 0.08
14 17 0.43
15 10 0.25
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
AATATAATATAAAT
Found at i:990153 original size:2 final size:2
Alignment explanation
Indices: 990146--990179 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
990136 ATCTCTTTTC
990146 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
990180 AATACTTTCA
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:990628 original size:15 final size:17
Alignment explanation
Indices: 990610--990656 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
990600 ATAAATTTCT
990610 TTAATATATAT-T-ATA
1 TTAATATATATATAATA
990625 TTAAGTTTATATATATAATA
1 TTAA---TATATATATAATA
990645 TTAATATATATA
1 TTAATATATATA
990657 CTAAACTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
15 4 0.15
17 8 0.30
18 7 0.26
19 1 0.04
20 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TTAATATATATATAATA
Found at i:991373 original size:17 final size:17
Alignment explanation
Indices: 991353--991391 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
991343 AAATTTTTAT
991353 TTTAAATAAAAAATTAA
1 TTTAAATAAAAAATTAA
* * *
991370 TTTAAATTAAGAATTTA
1 TTTAAATAAAAAATTAA
991387 TTTAA
1 TTTAA
991392 GTGTAGATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTAAATAAAAAATTAA
Found at i:992703 original size:32 final size:33
Alignment explanation
Indices: 992662--992723 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
992652 TAGCCAAACT
**
992662 TGTATCGATACA-CAAAGTATGTATCGATATAA
1 TGTATCGATACACCAAAAAATGTATCGATATAA
992694 TGTATCGATACACCAAAAAATGTATCGATA
1 TGTATCGATACACCAAAAAATGTATCGATA
992724 CATTGGCTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (33 bp):
TGTATCGATACACCAAAAAATGTATCGATATAA
Found at i:993809 original size:17 final size:18
Alignment explanation
Indices: 993757--993824 Score: 70
Period size: 17 Copynumber: 3.9 Consensus size: 18
993747 TATTAATTTG
* *
993757 TATAATTGTTTATAGT-A
1 TATAATTATTTATATTAA
*
993774 TA-AAGTATTTATATTAA
1 TATAATTATTTATATTAA
993791 TATAATTATTTAT-TTAA
1 TATAATTATTTATATTAA
* *
993808 TATAATTGTTAATATTA
1 TATAATTATTTATATTA
993825 TGAAATAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
16 10 0.24
17 20 0.48
18 12 0.29
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
TATAATTATTTATATTAA
Found at i:1000775 original size:14 final size:15
Alignment explanation
Indices: 1000751--1000783 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1000741 TTTTAATAAA
*
1000751 AATTTTAATTTTTTT
1 AATTTTAATTTATTT
1000766 AATTTT-ATTTATTT
1 AATTTTAATTTATTT
1000780 AATT
1 AATT
1000784 CATTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
AATTTTAATTTATTT
Found at i:1001212 original size:31 final size:33
Alignment explanation
Indices: 1001176--1001246 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 33
1001166 ATAATTTATC
1001176 ATAATAATTTA-ATAA-AAATAATAATTAAAAT
1 ATAATAATTTATATAATAAATAATAATTAAAAT
* * *
1001207 ATAAT-A-TTATATAATAATTAATATTTAATAT
1 ATAATAATTTATATAATAAATAATAATTAAAAT
1001238 ATCAATAAT
1 AT-AATAAT
1001247 AAAAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
29 3 0.09
30 5 0.16
31 20 0.62
32 3 0.09
33 1 0.03
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (33 bp):
ATAATAATTTATATAATAAATAATAATTAAAAT
Found at i:1001293 original size:30 final size:30
Alignment explanation
Indices: 1001209--1001303 Score: 74
Period size: 30 Copynumber: 3.2 Consensus size: 30
1001199 ATTAAAATAT
* *
1001209 AATATTATAT-AATA-ATTAATATTTAATA
1 AATATAATATAAATATATTAATATTTTATA
* * * *
1001237 TATCAATAATAAAAAAAT-TTTA-ATTTTATA
1 AAT--ATAATATAAATATATTAATATTTTATA
1001267 AATATAATATAAATATATTAATATTTTTATA
1 AATATAATATAAATATATTAATA-TTTTATA
1001298 AA-ATAA
1 AATATAA
1001304 ACTAATATGT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
28 13 0.26
29 3 0.06
30 19 0.38
31 15 0.30
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (30 bp):
AATATAATATAAATATATTAATATTTTATA
Found at i:1001799 original size:26 final size:26
Alignment explanation
Indices: 1001754--1001823 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
1001744 AAAAATTTAA
* *
1001754 ATTTAAATTTAA-TTTAATTTATT-T
1 ATTTAAAATTAATTTTTATTTATTAT
1001778 ATTTAAAATTAAATTTTTATTTATTAT
1 ATTTAAAATT-AATTTTTATTTATTAT
* *
1001805 ATTAAAAATTTATTTTTAT
1 ATTTAAAATTAATTTTTAT
1001824 ATTAAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 9 0.23
25 2 0.05
26 18 0.46
27 10 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTAAAATTAATTTTTATTTATTAT
Found at i:1001813 original size:22 final size:21
Alignment explanation
Indices: 1001788--1001851 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 21
1001778 ATTTAAAATT
1001788 AAATTTTTATTTATTATATTAA
1 AAATTTTTATTT-TTATATTAA
1001810 AAA--TTTATTTTTATATT-A
1 AAATTTTTATTTTTATATTAA
*
1001828 AAATTTATATATTTTATAATTAA
1 AAATTTTTAT-TTTTAT-ATTAA
1001851 A
1 A
1001852 TTTAAATAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
18 4 0.11
19 7 0.19
20 11 0.31
21 6 0.17
22 6 0.17
23 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATTTTTATTTTTATATTAA
Found at i:1001825 original size:19 final size:19
Alignment explanation
Indices: 1001793--1001851 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 19
1001783 AAATTAAATT
1001793 TTTATTTATTATATTAAAAA
1 TTTATTT-TTATATTAAAAA
*
1001813 TTTATTTTTATATTAAAAT
1 TTTATTTTTATATTAAAAA
1001832 TTATATATTTTATAATTAAA
1 TT-TAT-TTTTAT-ATTAAA
1001852 TTTAAATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 13 0.37
20 10 0.29
21 6 0.17
22 6 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTATTTTTATATTAAAAA
Found at i:1001832 original size:18 final size:20
Alignment explanation
Indices: 1001769--1001840 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
1001759 AATTTAATTT
*
1001769 AATTTATTTATTTAAAATTAAA
1 AATTTATTTA-TT-ATATTAAA
**
1001791 TTTTTATTTATTATATTAAA
1 AATTTATTTATTATATTAAA
1001811 AATTTATTT-TTATATT-AA
1 AATTTATTTATTATATTAAA
*
1001829 AATTTATATATT
1 AATTTATTTATT
1001841 TTATAATTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 10 0.23
19 9 0.21
20 14 0.33
21 2 0.05
22 8 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATTTATTTATTATATTAAA
Found at i:1001844 original size:21 final size:19
Alignment explanation
Indices: 1001785--1001855 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 19
1001775 TTTATTTAAA
*
1001785 ATTAAATTTTTATTTATTAT
1 ATTAAATTTATATTT-TTAT
*
1001805 ATTAAAAATT-TATTTTTAT
1 ATT-AAATTTATATTTTTAT
1001824 ATTAAAATTTATATATTTTAT
1 ATT-AAATTTATAT-TTTTAT
1001845 AATTAAATTTA
1 -ATTAAATTTA
1001856 AATAAAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
19 13 0.29
20 11 0.24
21 18 0.40
22 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTAAATTTATATTTTTAT
Found at i:1001882 original size:20 final size:18
Alignment explanation
Indices: 1001852--1001891 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 18
1001842 TATAATTAAA
1001852 TTTAAATAAAAATATATTT
1 TTTAAATAAAAATAT-TTT
1001871 TTTAATATAAAAATATTTT
1 TTTAA-ATAAAAATATTTT
1001890 TT
1 TT
1001892 AAAAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAATAAAAATATTTT
Found at i:1001886 original size:18 final size:18
Alignment explanation
Indices: 1001856--1001897 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1001846 ATTAAATTTA
1001856 AATAAAAATATATTTTTT
1 AATAAAAATATATTTTTT
1001874 AATATAAAA-ATATTTTTT
1 AATA-AAAATATATTTTTT
1001892 AA-AAAA
1 AATAAAA
1001898 TTAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.13
17 1 0.04
18 15 0.65
19 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAAAATATATTTTTT
Found at i:1002495 original size:16 final size:15
Alignment explanation
Indices: 1002453--1002496 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
1002443 CTTAAATCTA
*
1002453 AAAAAACTCGAACTT
1 AAAAAACTTGAACTT
*
1002468 GAAAAAATTTGAACTT
1 -AAAAAACTTGAACTT
1002484 AAAAGAACTTGAA
1 AAAA-AACTTGAA
1002497 TCGAAGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.23
Consensus pattern (15 bp):
AAAAAACTTGAACTT
Found at i:1002682 original size:22 final size:22
Alignment explanation
Indices: 1002657--1002706 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1002647 ATAAATGAAG
1002657 AAATTAGAAT-TTATTAAAAAGT
1 AAATTA-AATCTTATTAAAAAGT
*
1002679 AAATTATATCTTATTAAAAAGT
1 AAATTAAATCTTATTAAAAAGT
1002701 AAATTA
1 AAATTA
1002707 TATCATGAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (22 bp):
AAATTAAATCTTATTAAAAAGT
Found at i:1002707 original size:22 final size:22
Alignment explanation
Indices: 1002667--1002710 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1002657 AAATTAGAAT
1002667 TTATTAAAAAGTAAATTATATC
1 TTATTAAAAAGTAAATTATATC
1002689 TTATTAAAAAGTAAATTATATC
1 TTATTAAAAAGTAAATTATATC
1002711 ATGAGCTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (22 bp):
TTATTAAAAAGTAAATTATATC
Found at i:1003057 original size:2 final size:2
Alignment explanation
Indices: 1003052--1003084 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1003042 TTAAAAATCG
1003052 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
1003085 ATCAAGTAAC
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:1004747 original size:48 final size:48
Alignment explanation
Indices: 1004684--1004780 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
1004674 AAATCATTCT
1004684 TGAAACTTTTTTCAAACTAGATTTAAGCATTTCTTTCATTTTCTTGTG
1 TGAAACTTTTTTCAAACTAGATTTAAGCATTTCTTTCATTTTCTTGTG
1004732 TGAAACTTTTTTCAAACTAGATTTAAGCATTTCTTTCATTTTCTTGTG
1 TGAAACTTTTTTCAAACTAGATTTAAGCATTTCTTTCATTTTCTTGTG
1004780 T
1 T
1004781 AGTTATAAGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (48 bp):
TGAAACTTTTTTCAAACTAGATTTAAGCATTTCTTTCATTTTCTTGTG
Found at i:1004768 original size:24 final size:24
Alignment explanation
Indices: 1004693--1004769 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
1004683 TTGAAACTTT
1004693 TTTCAAACTAGATTTAAGCATTTC
1 TTTCAAACTAGATTTAAGCATTTC
** * * *
1004717 TTTCATTTTCTTG-TGTGAAAC-TTT-
1 TTTCA--AACTAGAT-TTAAGCATTTC
1004741 TTTCAAACTAGATTTAAGCATTTC
1 TTTCAAACTAGATTTAAGCATTTC
1004765 TTTCA
1 TTTCA
1004770 TTTTCTTGTG
Statistics
Matches: 37, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
22 7 0.19
23 4 0.11
24 15 0.41
25 4 0.11
26 7 0.19
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (24 bp):
TTTCAAACTAGATTTAAGCATTTC
Found at i:1005074 original size:2 final size:2
Alignment explanation
Indices: 1005067--1005091 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1005057 CTTCCCACAG
1005067 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1005092 TTAATCTCCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1006711 original size:14 final size:15
Alignment explanation
Indices: 1006692--1006738 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1006682 ATATATAAAT
1006692 ATAAAT-TTTAATAA
1 ATAAATATTTAATAA
1006706 ATAAATATATTAA-AA
1 ATAAATAT-TTAATAA
1006721 ATAACATATTATAATAA
1 ATAA-ATATT-TAATAA
1006738 A
1 A
1006739 AATTTACTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 6 0.21
15 8 0.29
16 11 0.39
17 3 0.11
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAAATATTTAATAA
Found at i:1006711 original size:20 final size:19
Alignment explanation
Indices: 1006668--1006714 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1006658 ATAAATTATT
* *
1006668 TAAATATTAATTATATATA
1 TAAATATAAATTATATAAA
*
1006687 TAAATATAAATTTTAATAAA
1 TAAATATAAATTAT-ATAAA
1006707 TAAATATA
1 TAAATATA
1006715 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAATATAAATTATATAAA
Found at i:1006946 original size:30 final size:31
Alignment explanation
Indices: 1006872--1006946 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
1006862 AACTCAAACC
1006872 CAAACCTAAAAAAATCCGAACTAAAATAGACT
1 CAAACCT-AAAAAATCCGAACTAAAATAGACT
* * **
1006904 CGAACCTGAAAAAT-CGAACTCGAATAGACT
1 CAAACCTAAAAAATCCGAACTAAAATAGACT
**
1006934 CAAATTTAAAAAA
1 CAAACCTAAAAAA
1006947 CCTTGAATCT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 23 0.66
31 6 0.17
32 6 0.17
ACGTcount: A:0.53, C:0.20, G:0.09, T:0.17
Consensus pattern (31 bp):
CAAACCTAAAAAATCCGAACTAAAATAGACT
Found at i:1007317 original size:34 final size:32
Alignment explanation
Indices: 1007246--1007319 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
1007236 TGATTTATTT
* *
1007246 TTTATTATTTTTATTTTATTAATAAAATATAAA
1 TTTA-TATTTGTAATTTATTAATAAAATATAAA
*
1007279 TTTATATTTGTAATTTATTGAATATAATAATAAA
1 TTTATATTTGTAATTTATT-AATAAAAT-ATAAA
1007313 TTTATAT
1 TTTATAT
1007320 AATTATATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 13 0.36
33 11 0.31
34 12 0.33
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (32 bp):
TTTATATTTGTAATTTATTAATAAAATATAAA
Found at i:1008788 original size:15 final size:15
Alignment explanation
Indices: 1008750--1008792 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1008740 GAATGATAAT
*
1008750 AATAAATTAATAATA
1 AATAAATTAAAAATA
** *
1008765 AATGTATTAAAAATG
1 AATAAATTAAAAATA
1008780 AATAAATTAAAAA
1 AATAAATTAAAAA
1008793 ATAAGAGATT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (15 bp):
AATAAATTAAAAATA
Found at i:1012083 original size:12 final size:13
Alignment explanation
Indices: 1012066--1012098 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
1012056 TAAATACATT
1012066 AAATAAAAATT-A
1 AAATAAAAATTAA
1012078 AAATAAAAATTAA
1 AAATAAAAATTAA
1012091 AAATAAAA
1 AAATAAAA
1012099 GAAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAAAATTAA
Found at i:1014109 original size:18 final size:18
Alignment explanation
Indices: 1014066--1014120 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
1014056 TTCATAATTA
1014066 TATTAAAATATTAATAT-T
1 TATTAAAAT-TTAATATAT
*
1014084 TAAATAAAATTTAATATAT
1 T-ATTAAAATTTAATATAT
*
1014103 TATTAAATTTTAAT-TAT
1 TATTAAAATTTAATATAT
1014120 T
1 T
1014121 TTTATAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.12
18 19 0.59
19 9 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTAAAATTTAATATAT
Found at i:1014887 original size:19 final size:19
Alignment explanation
Indices: 1014860--1014900 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1014850 ATCTTAATTT
*
1014860 TGATTACTATCATTTCTAC
1 TGATAACTATCATTTCTAC
*
1014879 TGATAACTATCATTTCTGC
1 TGATAACTATCATTTCTAC
1014898 TGA
1 TGA
1014901 AGTAATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.44
Consensus pattern (19 bp):
TGATAACTATCATTTCTAC
Found at i:1015588 original size:18 final size:18
Alignment explanation
Indices: 1015547--1015599 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
1015537 TATAGTATAT
1015547 TATATTTT-TTTAATTAA
1 TATATTTTATTTAATTAA
* *
1015564 T-TTTTTTATTTTATTAA
1 TATATTTTATTTAATTAA
* *
1015581 TATATTTTACTTCATTAA
1 TATATTTTATTTAATTAA
1015599 T
1 T
1015600 TCTATTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 5 0.17
17 10 0.34
18 14 0.48
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (18 bp):
TATATTTTATTTAATTAA
Found at i:1019789 original size:19 final size:18
Alignment explanation
Indices: 1019765--1019804 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
1019755 GTACTTAATA
1019765 ATTTATATATTTATATTAT
1 ATTTATATATTT-TATTAT
1019784 ATTTATATATTTTATTAT
1 ATTTATATATTTTATTAT
1019802 ATT
1 ATT
1019805 ATTATTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTATATATTTTATTAT
Found at i:1032439 original size:26 final size:25
Alignment explanation
Indices: 1032392--1032458 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
1032382 ATTTATTTAA
* *
1032392 TAAAAATTAAATTAAATTTTTATGT
1 TAAAATTTAAATTTAATTTTTATGT
* *
1032417 TTAATTTTAAATTTAATTATTTATGT
1 TAAAATTTAAATTTAATT-TTTATGT
*
1032443 TAAAATTTAAGTTTAA
1 TAAAATTTAAATTTAA
1032459 ATTAAAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
25 14 0.41
26 20 0.59
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (25 bp):
TAAAATTTAAATTTAATTTTTATGT
Found at i:1043421 original size:1 final size:1
Alignment explanation
Indices: 1043415--1043443 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
1043405 GCAAAGCTAG
1043415 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1043444 CCTTGTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1045347 original size:14 final size:15
Alignment explanation
Indices: 1045328--1045359 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1045318 ATTTATAAAA
1045328 AAAATTAAT-AATTT
1 AAAATTAATCAATTT
1045342 AAAATTAATCAATTT
1 AAAATTAATCAATTT
1045357 AAA
1 AAA
1045360 TCTAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTAATCAATTT
Found at i:1045392 original size:16 final size:16
Alignment explanation
Indices: 1045357--1045392 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1045347 TAATCAATTT
*
1045357 AAATCTAAAATGATTC
1 AAATCTAAAATGATTA
*
1045373 AAATCTAAAATTATTA
1 AAATCTAAAATGATTA
1045389 AAAT
1 AAAT
1045393 TCGAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (16 bp):
AAATCTAAAATGATTA
Found at i:1045516 original size:15 final size:16
Alignment explanation
Indices: 1045488--1045524 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
1045478 TAATTTATTT
1045488 TAATT-TCATAACTTA
1 TAATTATCATAACTTA
1045503 TAATTATCAT-ACTTA
1 TAATTATCATAACTTA
1045518 TAATTAT
1 TAATTAT
1045525 TATTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTATCATAACTTA
Found at i:1045805 original size:20 final size:20
Alignment explanation
Indices: 1045780--1045825 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
1045770 AGTTTATCAC
1045780 ATTTTTTAATCTTTTCAAT-T
1 ATTTTTTAAT-TTTTCAATAT
*
1045800 ATTTTTTTAATTTTTTAATAT
1 A-TTTTTTAATTTTTCAATAT
1045821 ATTTT
1 ATTTT
1045826 AAAAGTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTTTTAATTTTTCAATAT
Found at i:1045807 original size:21 final size:21
Alignment explanation
Indices: 1045781--1045825 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1045771 GTTTATCACA
1045781 TTTTTTAATCTTTTCAAT-TAT
1 TTTTTTAAT-TTTTCAATATAT
*
1045802 TTTTTTAATTTTTTAATATAT
1 TTTTTTAATTTTTCAATATAT
1045823 TTT
1 TTT
1045826 AAAAGTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTTAATTTTTCAATATAT
Found at i:1046005 original size:15 final size:15
Alignment explanation
Indices: 1045987--1046144 Score: 70
Period size: 15 Copynumber: 11.1 Consensus size: 15
1045977 AAGGTTTAAT
1045987 TAAAAATTTTATATG
1 TAAAAATTTTATATG
** *
1046002 TAAAAATAATAAAT-
1 TAAAAATTTTATATG
*
1046016 TAAAAAAATTTATATG
1 T-AAAAATTTTATATG
1046032 TAAAAATTTTA-AT-
1 TAAAAATTTTATATG
*
1046045 T-AAAATTATATATG
1 TAAAAATTTTATATG
* ****
1046059 CAAAAGGCCTA-AT-
1 TAAAAATTTTATATG
*
1046072 TGAAAAATCTCTAT-T-
1 T-AAAAAT-TTTATATG
*
1046087 TAAAAAATTTA-AT-
1 TAAAAATTTTATATG
1046100 TAAAAATTTTATATG
1 TAAAAATTTTATATG
* * *
1046115 TAAAGAGTCTA-ATG
1 TAAAAATTTTATATG
1046129 -AAAAATTTTATATG
1 TAAAAATTTTATATG
1046143 TA
1 TA
1046145 CAAGGTTTAA
Statistics
Matches: 103, Mismatches: 27, Indels: 26
0.66 0.17 0.17
Matches are distributed among these distances:
12 8 0.08
13 24 0.23
14 22 0.21
15 48 0.47
16 1 0.01
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (15 bp):
TAAAAATTTTATATG
Found at i:1046118 original size:28 final size:28
Alignment explanation
Indices: 1045981--1046144 Score: 136
Period size: 28 Copynumber: 5.8 Consensus size: 28
1045971 AATAAAAAGG
1045981 TTTAATTAAAAATTTTATATGTAAAAATA
1 TTTAATTAAAAATTTTATATGTAAAAA-A
* * * *
1046010 ATAAATTAAAAAAATTTATATGTAAAAAT
1 TTTAATT-AAAAATTTTATATGTAAAAAA
* * **
1046039 TTTAATT-AAAATTATATATGCAAAAGG
1 TTTAATTAAAAATTTTATATGTAAAAAA
** *
1046066 CCTAATTGAAAAATCTCTAT-T-TAAAAAA
1 TTTAATT-AAAAAT-TTTATATGTAAAAAA
* *
1046094 TTTAATTAAAAATTTTATATGTAAAGAG
1 TTTAATTAAAAATTTTATATGTAAAAAA
* *
1046122 TCTAATGAAAAATTTTATATGTA
1 TTTAATTAAAAATTTTATATGTA
1046145 CAAGGTTTAA
Statistics
Matches: 105, Mismatches: 24, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
26 4 0.04
27 27 0.26
28 35 0.33
29 16 0.15
30 23 0.22
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.39
Consensus pattern (28 bp):
TTTAATTAAAAATTTTATATGTAAAAAA
Found at i:1046154 original size:56 final size:56
Alignment explanation
Indices: 1045973--1046156 Score: 178
Period size: 56 Copynumber: 3.2 Consensus size: 56
1045963 TTAATTAAAA
* * * *
1045973 TAAAAAGGTTTAATTAAAAATTTTATATGTAAAAATAATAAATTAAAAAAATTTATATG
1 TAAAAA-GTTTAATTAAAAATTTTATATGTAAAAGT-CT-AATTGAAAAATTTTATATG
* * * * *
1046032 TAAAAATTTTAATT-AAAATTATATATGCAAAAGGCCTAATTGAAAAATCTCTAT-T-
1 TAAAAAGTTTAATTAAAAATTTTATATGTAAAA-GTCTAATTGAAAAAT-TTTATATG
*
1046087 TAAAAAATTTAATTAAAAATTTTATATGTAAAGAGTCTAA-TGAAAAATTTTATATG
1 TAAAAAGTTTAATTAAAAATTTTATATGTAAA-AGTCTAATTGAAAAATTTTATATG
* *
1046143 TACAAGGTTTAATT
1 TAAAAAGTTTAATT
1046157 TTAAAAATCT
Statistics
Matches: 102, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
54 4 0.04
55 22 0.22
56 41 0.40
57 22 0.22
58 7 0.07
59 6 0.06
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (56 bp):
TAAAAAGTTTAATTAAAAATTTTATATGTAAAAGTCTAATTGAAAAATTTTATATG
Found at i:1046401 original size:23 final size:23
Alignment explanation
Indices: 1046370--1046414 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1046360 TGGATAAAGT
*
1046370 AAAAGTTTAA-TAGAAAATCATAA
1 AAAAATTTAATTAGAAAA-CATAA
1046393 AAAAATTTAATTAGAAAACATA
1 AAAAATTTAATTAGAAAACATA
1046415 TTAAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (23 bp):
AAAAATTTAATTAGAAAACATAA
Found at i:1047462 original size:25 final size:26
Alignment explanation
Indices: 1047433--1047482 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
1047423 AGTAAAAATA
1047433 TTTTATTATTTT-CACGTTTTTTAAT
1 TTTTATTATTTTACACGTTTTTTAAT
*
1047458 TTTTATTATTTTACACTTTTTTTAA
1 TTTTATTATTTTACACGTTTTTTAA
1047483 AAAAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTTATTATTTTACACGTTTTTTAAT
Found at i:1047838 original size:23 final size:23
Alignment explanation
Indices: 1047803--1047866 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
1047793 TATTAAAATT
* *
1047803 TATTTTTAT-ATT-AATATTTATA
1 TATTTTTATAATTAAATA-TAAAA
1047825 TATTTTTATAATTAAATATAAAA
1 TATTTTTATAATTAAATATAAAA
1047848 TATTTTTATTAATTAAATA
1 TATTTTTA-TAATTAAATA
1047867 ATTATTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.24
23 14 0.38
24 14 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTTTTATAATTAAATATAAAA
Found at i:1047895 original size:20 final size:18
Alignment explanation
Indices: 1047858--1047915 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 18
1047848 TATTTTTATT
1047858 AATTAAAT-AATTATTTA
1 AATTAAATAAATTATTTA
1047875 AATTAAATCAAATTAATTTA
1 AATTAAAT-AAATT-ATTTA
*
1047895 AATTAAAAAAAATTATTTA
1 AATT-AAATAAATTATTTA
1047914 AA
1 AA
1047916 CCTAATTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 8 0.22
19 11 0.31
20 14 0.39
21 3 0.08
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTAAATAAATTATTTA
Found at i:1048802 original size:26 final size:26
Alignment explanation
Indices: 1048773--1048822 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1048763 ATTTTATGTA
* *
1048773 ATTATATTGTGTTCATATTTTTTTTT
1 ATTATATTATGTTAATATTTTTTTTT
*
1048799 ATTATTTTATGTTAATATTTTTTT
1 ATTATATTATGTTAATATTTTTTT
1048823 ATGTTATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (26 bp):
ATTATATTATGTTAATATTTTTTTTT
Found at i:1048822 original size:16 final size:16
Alignment explanation
Indices: 1048798--1048828 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1048788 TATTTTTTTT
1048798 TATTATTTTATGTTAA
1 TATTATTTTATGTTAA
*
1048814 TATTTTTTTATGTTA
1 TATTATTTTATGTTA
1048829 TGTTGGTACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TATTATTTTATGTTAA
Found at i:1049088 original size:17 final size:17
Alignment explanation
Indices: 1049055--1049088 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1049045 TGTATTTAAA
*
1049055 TAAGCTAAGAGTTTATT
1 TAAGCTAAGAGTATATT
*
1049072 TAAGTTAAGAGTATATT
1 TAAGCTAAGAGTATATT
1049089 GATTTAAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TAAGCTAAGAGTATATT
Found at i:1049178 original size:30 final size:30
Alignment explanation
Indices: 1049114--1049201 Score: 101
Period size: 30 Copynumber: 2.9 Consensus size: 30
1049104 TTTGCCTAAT
* *
1049114 TAAAGATTAAGAGTTTATTTAG-CTAAAAC
1 TAAAGATTAAGAGCTTATTTAGTGTAAAAC
1049143 TTAAAGATTAAGAGCTTATTTAAGTGTAAAA-
1 -TAAAGATTAAGAGCTTATTT-AGTGTAAAAC
1049174 TAAAGATTAATG-GCTTATTTGAGTGTAA
1 TAAAGATTAA-GAGCTTATTT-AGTGTAA
1049202 TAAAAGTATA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
30 44 0.85
31 3 0.06
32 5 0.10
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.36
Consensus pattern (30 bp):
TAAAGATTAAGAGCTTATTTAGTGTAAAAC
Found at i:1049578 original size:17 final size:17
Alignment explanation
Indices: 1049552--1049586 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1049542 ATTATAAGTA
* *
1049552 TTTTATTTTAATTTATT
1 TTTTAATTTAATTAATT
1049569 TTTTAATTTAATTAATT
1 TTTTAATTTAATTAATT
1049586 T
1 T
1049587 ATATAATATT
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTAATTTAATTAATT
Found at i:1049599 original size:21 final size:21
Alignment explanation
Indices: 1049538--1049622 Score: 55
Period size: 21 Copynumber: 3.9 Consensus size: 21
1049528 ATAGAAGCTT
*
1049538 ATTTATTATAAGTATTTTATTTTA
1 ATTTA-TATAA-TATTTTA-ATTA
* ** *
1049562 ATTTATTTTTTAATTTAATTA
1 ATTTATATAATATTTTAATTA
*
1049583 ATTTATATAATATTTTAA-AA
1 ATTTATATAATATTTTAATTA
*
1049603 ATTATATTTAATATATTTAA
1 ATT-TATATAATAT-TTTAA
1049623 ATTTAAATCT
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
20 4 0.08
21 26 0.54
22 11 0.23
23 2 0.04
24 5 0.10
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (21 bp):
ATTTATATAATATTTTAATTA
Found at i:1052744 original size:18 final size:18
Alignment explanation
Indices: 1052721--1052761 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1052711 TGCAGATCAG
1052721 AAGATAACATGTGTTAAA
1 AAGATAACATGTGTTAAA
1052739 AAGATAACATGTGTTAAA
1 AAGATAACATGTGTTAAA
1052757 AAGAT
1 AAGAT
1052762 GATCTTGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (18 bp):
AAGATAACATGTGTTAAA
Found at i:1062145 original size:17 final size:17
Alignment explanation
Indices: 1062123--1062159 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1062113 TTATCCTTTC
1062123 TAAATTAAACATTTAAT
1 TAAATTAAACATTTAAT
**
1062140 TAAATTAAATGTTTAAT
1 TAAATTAAACATTTAAT
1062157 TAA
1 TAA
1062160 TTTATTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (17 bp):
TAAATTAAACATTTAAT
Found at i:1062765 original size:19 final size:19
Alignment explanation
Indices: 1062741--1062803 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
1062731 TAAAAATAAA
1062741 ATTTATATATTTATTT-TAT
1 ATTTATATA-TTATTTATAT
1062760 ATTTATATATTATTTATAT
1 ATTTATATATTATTTATAT
* *
1062779 ATCTCATAATTTTATTTAATAT
1 AT-TTAT-ATATTATTT-ATAT
1062801 ATT
1 ATT
1062804 ATTATTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 6 0.16
19 14 0.37
20 3 0.08
21 9 0.24
22 6 0.16
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTATATATTATTTATAT
Found at i:1064510 original size:21 final size:19
Alignment explanation
Indices: 1064486--1064528 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
1064476 TTATTTAAAG
1064486 TTAATACTTATTATAATATTA
1 TTAATACTTATT-T-ATATTA
**
1064507 TTAATTTTTATTTATATTA
1 TTAATACTTATTTATATTA
1064526 TTA
1 TTA
1064529 TAATGTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 1 0.05
21 10 0.50
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAATACTTATTTATATTA
Found at i:1064527 original size:22 final size:21
Alignment explanation
Indices: 1064496--1064538 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1064486 TTAATACTTA
*
1064496 TTATAATATTATTAATTTTTAT
1 TTATAATATTA-TAATGTTTAT
*
1064518 TTATATTATTATAATGTTTAT
1 TTATAATATTATAATGTTTAT
1064539 ATTTTACTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTATAATATTATAATGTTTAT
Found at i:1067139 original size:19 final size:20
Alignment explanation
Indices: 1067115--1067167 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
1067105 TTTGTATCAA
1067115 ATATAATATAATTATAAA-C
1 ATATAATATAATTATAAATC
* *
1067134 ATATAA-AT-ATTTTAAATTT
1 ATATAATATAATTATAAA-TC
1067153 ATATAATATAATTAT
1 ATATAATATAATTAT
1067168 TAATAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 7 0.26
18 2 0.07
19 12 0.44
20 2 0.07
21 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATAATATAATTATAAATC
Found at i:1067203 original size:10 final size:10
Alignment explanation
Indices: 1067188--1067228 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1067178 GAAAATTTAT
1067188 AAATATAATA
1 AAATATAATA
1067198 AAATAT-AT-
1 AAATATAATA
1067206 AAATATAATA
1 AAATATAATA
*
1067216 TAATATAAATA
1 AAATAT-AATA
1067227 AA
1 AA
1067229 TAATTACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 6 0.23
9 4 0.15
10 11 0.42
11 5 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATATAATA
Found at i:1067206 original size:18 final size:18
Alignment explanation
Indices: 1067179--1067222 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1067169 AATAAAAATG
*
1067179 AAAATTTATAAATATAAT
1 AAAATATATAAATATAAT
1067197 AAAATATATAAATATAAT
1 AAAATATATAAATATAAT
*
1067215 ATAATATA
1 AAAATATA
1067223 AATAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATATATAAATATAAT
Found at i:1067230 original size:10 final size:9
Alignment explanation
Indices: 1067186--1067230 Score: 56
Period size: 9 Copynumber: 4.8 Consensus size: 9
1067176 ATGAAAATTT
1067186 ATAAATATA
1 ATAAATATA
1067195 ATAAA-ATA
1 ATAAATATA
1067203 TATAAATATA
1 -ATAAATATA
1067213 ATATAATATAA
1 ATA-AATAT-A
1067224 ATAAATA
1 ATAAATA
1067231 ATTACTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 3 0.09
9 13 0.41
10 12 0.38
11 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAAATATA
Found at i:1067480 original size:3 final size:3
Alignment explanation
Indices: 1067472--1067506 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1067462 ACAAAAATTT
1067472 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1067507 TCATGATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1067575 original size:18 final size:18
Alignment explanation
Indices: 1067549--1067584 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1067539 CCCTCCAACC
*
1067549 AATATTGTGTCGCTGTTT
1 AATACTGTGTCGCTGTTT
*
1067567 AATACTGTGTTGCTGTTT
1 AATACTGTGTCGCTGTTT
1067585 CAAATTACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.11, G:0.22, T:0.50
Consensus pattern (18 bp):
AATACTGTGTCGCTGTTT
Found at i:1068599 original size:2 final size:2
Alignment explanation
Indices: 1068594--1068672 Score: 51
Period size: 2 Copynumber: 40.5 Consensus size: 2
1068584 AGTTCTTTAG
* * *
1068594 TA TA TA TA -A TA TA CA TA TA AA AA TA TA TA -A TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1068633 T- TA GCA TA TA TA TGA TT TA -A GTA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA T-A TA TA TA -TA TA TA TA TA TA TA TA TA T
1068673 TAAAAATATA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
1 5 0.08
2 52 0.85
3 4 0.07
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1068643 original size:17 final size:18
Alignment explanation
Indices: 1068623--1068668 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
1068613 AAAATATATA
1068623 ATATATAATATT-AGCAT
1 ATATATAATATTAAGCAT
* *
1068640 ATATATGAT-TTAAGTAT
1 ATATATAATATTAAGCAT
1068657 ATATATATATAT
1 ATATATA-ATAT
1068669 ATATTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 2 0.09
17 18 0.78
18 2 0.09
19 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (18 bp):
ATATATAATATTAAGCAT
Found at i:1068681 original size:23 final size:23
Alignment explanation
Indices: 1068638--1068682 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1068628 TAATATTAGC
**
1068638 ATATATATGATTTAAGTATATAT
1 ATATATATGATTTAAAAATATAT
1068661 ATATATAT-ATATTAAAAATATA
1 ATATATATGAT-TTAAAAATATA
1068683 AAATATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
ATATATATGATTTAAAAATATAT
Found at i:1069508 original size:17 final size:16
Alignment explanation
Indices: 1069474--1069507 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1069464 TTTTAATTAT
1069474 AATTATAATTATAAAA
1 AATTATAATTATAAAA
1069490 AATTATAGATT-TAAAA
1 AATTATA-ATTATAAAA
1069506 AA
1 AA
1069508 AACTATCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
AATTATAATTATAAAA
Found at i:1070092 original size:23 final size:23
Alignment explanation
Indices: 1070051--1070094 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1070041 ATTATAGTAC
* **
1070051 AAAATAATATTAATTTAATTAAT
1 AAAATAATATAAAAATAATTAAT
1070074 AAAATAATATAAAAATAATTA
1 AAAATAATATAAAAATAATTA
1070095 TATTTTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATAATATAAAAATAATTAAT
Done.