Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold114
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: 3219552
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 36736 characters in sequence are not A, C, G, or T
File 6 of 13
Found at i:1318683 original size:47 final size:47
Alignment explanation
Indices: 1318620--1318723 Score: 181
Period size: 47 Copynumber: 2.2 Consensus size: 47
1318610 TATAATTAAT
* *
1318620 CAAATTAATTAAATAAATTATTTTTTATAATTAATAAATTTTAAAAT
1 CAAATTAATTAAATAAATTATTTTTTATAATCAATAAATTTTAAAAA
*
1318667 TAAATTAATTAAATAAATTATTTTTTATAATCAATAAATTTTAAAAA
1 CAAATTAATTAAATAAATTATTTTTTATAATCAATAAATTTTAAAAA
1318714 CAAATTAATT
1 CAAATTAATT
1318724 GGTTCTAGAC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (47 bp):
CAAATTAATTAAATAAATTATTTTTTATAATCAATAAATTTTAAAAA
Found at i:1320729 original size:7 final size:7
Alignment explanation
Indices: 1320717--1320753 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
1320707 TGAGCGATAG
1320717 ATTTTAA
1 ATTTTAA
1320724 ATTTTAA
1 ATTTTAA
1320731 ATTTTAA
1 ATTTTAA
1320738 ATTTT-A
1 ATTTTAA
1320744 A-TTTAA
1 ATTTTAA
1320750 ATTT
1 ATTT
1320754 GATTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 3 0.11
6 4 0.14
7 21 0.75
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTTTAA
Found at i:1320734 original size:14 final size:13
Alignment explanation
Indices: 1320717--1320765 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 13
1320707 TGAGCGATAG
1320717 ATTTTAAATTTTAA
1 ATTTTAAATTTT-A
1320731 ATTTTAAATTTTA
1 ATTTTAAATTTTA
*
1320744 A-TTTAAA-TTTG
1 ATTTTAAATTTTA
1320755 A-TTTAAATTTT
1 ATTTTAAATTTT
1320766 TTAAATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
11 10 0.30
12 9 0.27
13 2 0.06
14 12 0.36
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
ATTTTAAATTTTA
Found at i:1320752 original size:6 final size:6
Alignment explanation
Indices: 1320719--1320778 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
1320709 AGCGATAGAT
* *
1320719 TTTAAA TTTTAAA TTTTAAA TTTTAA TTTAAA TTT-GA TTTAAA TTT---
1 TTTAAA -TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1320765 TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TT
1320779 ATTATTTAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
3 3 0.07
5 4 0.09
6 25 0.56
7 13 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:1320760 original size:11 final size:10
Alignment explanation
Indices: 1320733--1320774 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
1320723 AATTTTAAAT
1320733 TTTAAATTTTAA
1 TTTAAA-TTT-A
1320745 TTTAAATTTGA
1 TTTAAATTT-A
1320756 TTTAAATTT-
1 TTTAAATTTA
1320765 TTTAAATTTA
1 TTTAAATTTA
1320775 AATTATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 9 0.32
11 13 0.46
12 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:1320772 original size:26 final size:26
Alignment explanation
Indices: 1320739--1320796 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
1320729 AAATTTTAAA
1320739 TTTT-AATTTAAATT-TGATTTAAATT
1 TTTTAAATTTAAATTATGATTT-AATT
*
1320764 TTTTAAATTTAAATTATTATTTAATT
1 TTTTAAATTTAAATTATGATTTAATT
*
1320790 TATTAAA
1 TTTTAAA
1320797 AATATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 4 0.14
26 20 0.69
27 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
TTTTAAATTTAAATTATGATTTAATT
Found at i:1320805 original size:38 final size:39
Alignment explanation
Indices: 1320725--1320806 Score: 100
Period size: 38 Copynumber: 2.1 Consensus size: 39
1320715 AGATTTTAAA
*
1320725 TTTTAAATTTTAAATTTTAATTTAAATTTGATTTAAATT
1 TTTTAAATTTTAAATTTTAATTTAAATTTGATTAAAATT
1320764 TTTTAAA-TTTAAATTATT-ATTT-AATTT-ATTAAAAATAT
1 TTTTAAATTTTAAATT-TTAATTTAAATTTGATT-AAAAT-T
1320802 TTTTA
1 TTTTA
1320807 TATTAATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
36 3 0.08
37 9 0.23
38 18 0.46
39 9 0.23
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (39 bp):
TTTTAAATTTTAAATTTTAATTTAAATTTGATTAAAATT
Found at i:1320826 original size:22 final size:21
Alignment explanation
Indices: 1320798--1320839 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1320788 TTTATTAAAA
1320798 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
1320818 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1320839 A
1 A
1320840 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1321544 original size:26 final size:26
Alignment explanation
Indices: 1321515--1321596 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
1321505 AACGGCATTG
1321515 TTTTAATCA-CATTTAAA-ATTATAATA
1 TTTTAAT-ATCATTTAAATA-TATAATA
* *
1321541 TTTTCATATTATTTAAATATATAATA
1 TTTTAATATCATTTAAATATATAATA
* ** * *
1321567 TTTTTATATTTTTTCAATATATCATA
1 TTTTAATATCATTTAAATATATAATA
1321593 TTTT
1 TTTT
1321597 GGGAAATGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.02
26 46 0.96
27 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTTAATATCATTTAAATATATAATA
Found at i:1321946 original size:3 final size:3
Alignment explanation
Indices: 1321938--1321967 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1321928 TAACAGCTCC
1321938 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1321968 TAATAAAATT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1322330 original size:21 final size:21
Alignment explanation
Indices: 1322289--1322344 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1322279 ATAATAAAAA
* *
1322289 ATATTTTAA-TTTTAAAATTT
1 ATATTATAATTTTTTAAATTT
*
1322309 ATATTATAATTTTTTAATTTT
1 ATATTATAATTTTTTAAATTT
* *
1322330 AAATTATGATTTTTT
1 ATATTATAATTTTTT
1322345 TAATATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 8 0.27
21 22 0.73
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
ATATTATAATTTTTTAAATTT
Found at i:1324291 original size:6 final size:6
Alignment explanation
Indices: 1324280--1324329 Score: 75
Period size: 6 Copynumber: 8.3 Consensus size: 6
1324270 TGAGTAGTCG
*
1324280 TGGACA TGGACA T-GATCA TGGACA CGGACA TGGACA TGGACA TGGACA
1 TGGACA TGGACA TGGA-CA TGGACA TGGACA TGGACA TGGACA TGGACA
1324328 TG
1 TG
1324330 ATCATAGCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 2 0.05
6 36 0.90
7 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (6 bp):
TGGACA
Found at i:1324303 original size:18 final size:18
Alignment explanation
Indices: 1324280--1324334 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
1324270 TGAGTAGTCG
1324280 TGGACATGGACATGATCA
1 TGGACATGGACATGATCA
*
1324298 TGGACACGGACATGGA-CA
1 TGGACATGGACAT-GATCA
1324316 TGGACATGGACATGATCA
1 TGGACATGGACATGATCA
1324334 T
1 T
1324335 AGCTTTGGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 2 0.06
18 29 0.88
19 2 0.06
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (18 bp):
TGGACATGGACATGATCA
Found at i:1324525 original size:22 final size:21
Alignment explanation
Indices: 1324496--1324571 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
1324486 TATTTTTATT
1324496 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
1324517 TAAATTTTAATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
* *
1324537 -AATTTTTAATA-AAAATAAA
1 TAAATTTTAATATAAAATATA
*
1324556 TAATAATTTAA-ATAAA
1 TAA-ATTTTAATATAAA
1324572 TTAAATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
18 4 0.09
19 12 0.26
20 6 0.13
21 19 0.41
22 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:1324550 original size:17 final size:18
Alignment explanation
Indices: 1324516--1324556 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
1324506 TATAAAATAT
1324516 ATAAATTTTAATATAAAA
1 ATAAATTTTAATATAAAA
*
1324534 ATAAATTTTTA-ATAAAA
1 ATAAATTTTAATATAAAA
1324551 ATAAAT
1 ATAAAT
1324557 AATAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAATTTTAATATAAAA
Found at i:1324580 original size:15 final size:16
Alignment explanation
Indices: 1324549--1324583 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1324539 TTTTTAATAA
1324549 AAATAAATAATAATTT
1 AAATAAATAATAATTT
*
1324565 AAATAAATTA-AATTT
1 AAATAAATAATAATTT
1324580 AAAT
1 AAAT
1324584 TTTATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATAAATAATAATTT
Found at i:1331438 original size:2 final size:2
Alignment explanation
Indices: 1331431--1331468 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1331421 CAATTATTAA
*
1331431 AT AT AT AT AT AT AT AT AT AT AT AT AG 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
1331469 TCTGGTAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1331902 original size:18 final size:18
Alignment explanation
Indices: 1331881--1331917 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1331871 GAATTAAATT
1331881 ATTTATTTAA-ATTTAAAA
1 ATTTATTTAATA-TTAAAA
1331899 ATTTATTTAATATTAAAA
1 ATTTATTTAATATTAAAA
1331917 A
1 A
1331918 GGTTTGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTATTTAATATTAAAA
Found at i:1332141 original size:20 final size:21
Alignment explanation
Indices: 1332096--1332188 Score: 54
Period size: 19 Copynumber: 4.7 Consensus size: 21
1332086 TAATGAAAGT
*
1332096 TATA-TAAAATATTTTAAAAA
1 TATATTAAAATATATTAAAAA
* *
1332116 TTTATTAAAA-ATATTAATAA
1 TATATTAAAATATATTAAAAA
* * *
1332136 TATATT--TATTTATTAAAAT
1 TATATTAAAATATATTAAAAA
* *
1332155 TAAATTAAAAATATTTTAAAAA
1 TATATT-AAAATATATTAAAAA
*
1332177 -CTA-TAAAATATA
1 TATATTAAAATATA
1332189 ATATAAAGTG
Statistics
Matches: 52, Mismatches: 16, Indels: 11
0.66 0.20 0.14
Matches are distributed among these distances:
18 1 0.02
19 19 0.37
20 17 0.33
21 6 0.12
22 9 0.17
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATTAAAATATATTAAAAA
Found at i:1332168 original size:28 final size:28
Alignment explanation
Indices: 1332115--1332172 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
1332105 TATTTTAAAA
*
1332115 ATTTATTAAAAATATTAATAATATATTT
1 ATTTATTAAAAAAATTAATAATATATTT
*
1332143 ATTTATTAAAATTAAATTAAAAATAT-TTT
1 ATTTATTAAAA--AAATTAATAATATATTT
1332172 A
1 A
1332173 AAAACTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.42
29 4 0.15
30 11 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTATTAAAAAAATTAATAATATATTT
Found at i:1332441 original size:17 final size:18
Alignment explanation
Indices: 1332401--1332442 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1332391 TTATAAAATA
1332401 TATTAAA-TAAATTTATT
1 TATTAAATTAAATTTATT
*
1332418 TA-AAAATTAAA-TTATT
1 TATTAAATTAAATTTATT
1332434 TATTAAATT
1 TATTAAATT
1332443 TGATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTAAATTAAATTTATT
Found at i:1335536 original size:17 final size:17
Alignment explanation
Indices: 1335506--1335539 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1335496 TTGAGTTTTA
1335506 AAATTTTTTATTAATTT
1 AAATTTTTTATTAATTT
1335523 AAATTATTTT-TTAATTT
1 AAATT-TTTTATTAATTT
1335540 TAATAAAACT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AAATTTTTTATTAATTT
Found at i:1335541 original size:18 final size:18
Alignment explanation
Indices: 1335501--1335542 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
1335491 TGAGTTTGAG
1335501 TTTTAAAATTTTTTATTAA
1 TTTT-AAATTTTTTATTAA
1335520 -TTTAAATTATTTT-TTAA
1 TTTTAAATT-TTTTATTAA
1335537 TTTTAA
1 TTTTAA
1335543 TAAAACTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTAAATTTTTTATTAA
Found at i:1337289 original size:23 final size:23
Alignment explanation
Indices: 1337262--1337327 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
1337252 ATGAGATATA
*
1337262 AATATAATATATTTAATA-AATTT
1 AATATGATATATTTAATATAA-TT
* * *
1337285 GATATGATATATTTATTATGATT
1 AATATGATATATTTAATATAATT
1337308 AATATGATATATTTAATATA
1 AATATGATATATTTAATATA
1337328 TAATTTATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (23 bp):
AATATGATATATTTAATATAATT
Found at i:1337340 original size:23 final size:22
Alignment explanation
Indices: 1337264--1337340 Score: 61
Period size: 23 Copynumber: 3.4 Consensus size: 22
1337254 GAGATATAAA
1337264 TATAATATATTTA-ATA-AATT
1 TATAATATATTTATATATAATT
*
1337284 TGATATGATATATTTAT-TATGATT
1 T-ATA--ATATATTTATATATAATT
*
1337308 AATATGATATATTTAATATATAATT
1 --TATAATATATTT-ATATATAATT
1337333 TATAATAT
1 TATAATAT
1337341 GTATTTGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
20 1 0.02
21 3 0.07
23 26 0.59
24 5 0.11
25 8 0.18
26 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TATAATATATTTATATATAATT
Found at i:1337629 original size:2 final size:2
Alignment explanation
Indices: 1337624--1337649 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1337614 CTAGTGTGTG
1337624 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
1337650 GATTCTTGTC
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):
TA
Found at i:1338131 original size:2 final size:2
Alignment explanation
Indices: 1338085--1338119 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1338075 TACACAATAA
1338085 AT AT A- 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
1338120 GCAAAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1341885 original size:24 final size:24
Alignment explanation
Indices: 1341838--1341886 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1341828 ATTTTTTAAA
* * **
1341838 TTTTATTATCATATTTTATTTTAT
1 TTTTAATATCATATTTAAAATTAT
1341862 TTTTAATATCATATTTAAAATTAT
1 TTTTAATATCATATTTAAAATTAT
1341886 T
1 T
1341887 ATCAAAGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTAATATCATATTTAAAATTAT
Found at i:1342040 original size:28 final size:26
Alignment explanation
Indices: 1341989--1342047 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
1341979 AATTTTAATC
* *
1341989 TTAAAAATAAATTATTTTTTAATTAA
1 TTAAAAATAAAATATTTTTAAATTAA
*
1342015 TTAAAAATAAAAATATTTTTAAAATTTA
1 TTAAAAAT-AAAATATTTTT-AAATTAA
1342043 TTAAA
1 TTAAA
1342048 TATTTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 8 0.29
27 10 0.36
28 10 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TTAAAAATAAAATATTTTTAAATTAA
Found at i:1349453 original size:12 final size:12
Alignment explanation
Indices: 1349436--1349460 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1349426 AGCCTTATAC
1349436 TTTAGTCAAAGA
1 TTTAGTCAAAGA
1349448 TTTAGTCAAAGA
1 TTTAGTCAAAGA
1349460 T
1 T
1349461 GTTTATGTGA
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TTTAGTCAAAGA
Found at i:1358937 original size:24 final size:24
Alignment explanation
Indices: 1358905--1358964 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
1358895 CCAACGTCCA
1358905 AGGACTAATCTTTATGTTAGTTTT
1 AGGACTAATCTTTATGTTAGTTTT
1358929 AGGACTAATCTTTATGTTAGTTTT
1 AGGACTAATCTTTATGTTAGTTTT
1358953 AGGACTAATCTT
1 AGGACTAATCTT
1358965 GCGATGCACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (24 bp):
AGGACTAATCTTTATGTTAGTTTT
Found at i:1367269 original size:11 final size:11
Alignment explanation
Indices: 1367249--1367280 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1367239 TGTGTTGATG
*
1367249 TTATTTTTATT
1 TTATTATTATT
1367260 TTATTATTATT
1 TTATTATTATT
1367271 TTATTATTAT
1 TTATTATTAT
1367281 CATGTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTATTATTATT
Found at i:1368607 original size:17 final size:17
Alignment explanation
Indices: 1368585--1368618 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1368575 AGATAATAGA
1368585 ATAAAACATTAACAAAG
1 ATAAAACATTAACAAAG
*
1368602 ATAAAACATTAATAAAG
1 ATAAAACATTAACAAAG
1368619 TTGGATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.65, C:0.09, G:0.06, T:0.21
Consensus pattern (17 bp):
ATAAAACATTAACAAAG
Found at i:1369899 original size:21 final size:21
Alignment explanation
Indices: 1369857--1369899 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1369847 GGGTTAATAA
* *
1369857 TACTTTTTTTATAGTTGTTTT
1 TACTTTTTTTATACTTGGTTT
1369878 TACTTCTTTTT-TACTTGGTTT
1 TACTT-TTTTTATACTTGGTTT
1369899 T
1 T
1369900 GTATTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.70
Consensus pattern (21 bp):
TACTTTTTTTATACTTGGTTT
Found at i:1370480 original size:18 final size:17
Alignment explanation
Indices: 1370459--1370496 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
1370449 AATTTCATTC
1370459 TTTTTA-TAAATAAATTT
1 TTTTTACTAAAT-AATTT
1370476 TTTTTACTAAATAATTT
1 TTTTTACTAAATAATTT
1370493 TTTT
1 TTTT
1370497 AAATCTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTTACTAAATAATTT
Found at i:1370737 original size:15 final size:17
Alignment explanation
Indices: 1370695--1370734 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1370685 TATAAAAAAG
1370695 TAATATTAAAATAAATA
1 TAATATTAAAATAAATA
*
1370712 TATATATTAAAAT-TATA
1 TA-ATATTAAAATAAATA
1370729 TAATAT
1 TAATAT
1370735 AAATCATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 7 0.33
18 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATATTAAAATAAATA
Found at i:1371336 original size:2 final size:2
Alignment explanation
Indices: 1371331--1371356 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1371321 CTGCAACCCC
1371331 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1371357 TTACGTACTG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1371821 original size:3 final size:3
Alignment explanation
Indices: 1371813--1371846 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1371803 TTAGCATTTA
1371813 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1371847 CTTTTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1377924 original size:29 final size:29
Alignment explanation
Indices: 1377891--1377957 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
1377881 TCCCATTCTG
1377891 CAAAATCTGCAAAATCATTCTAATTGTTT
1 CAAAATCTGCAAAATCATTCTAATTGTTT
* *
1377920 CAAAATTTGCAAAATTATTCTAATTGTTT
1 CAAAATCTGCAAAATCATTCTAATTGTTT
1377949 CAAAATCTG
1 CAAAATCTG
1377958 AAACTTGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (29 bp):
CAAAATCTGCAAAATCATTCTAATTGTTT
Found at i:1389953 original size:334 final size:334
Alignment explanation
Indices: 1389343--1390013 Score: 1227
Period size: 334 Copynumber: 2.0 Consensus size: 334
1389333 TCTCGAGCAC
*
1389343 AACTAAGGTACTAGACTTGCTAACACTTCTTTAGCATTACAGGTGTTGATTAGATTTTGCTATAA
1 AACTAAGGTACTAGACCTGCTAACACTTCTTTAGCATTACAGGTGTTGATTAGATTTTGCTATAA
* *
1389408 TTTTGTCTTTTTGTTTTCCCATCATTGCTAGGAGTTGTTAGTTTGAATTATTGAAAGAGAAATAA
66 -TTTGTCTTTTTCTTTTCCCATCATTGCTAGGAGTTGTTAGTTTGAATTATTGAAAGAAAAATAA
*
1389473 GTTGGCATGTATTTCCCGTGTAATATCGGTAGCTTTGCCATTCTAATTTTTTGTTCCTTAAGATC
130 GTTGGCATGTATTTCCCGTGTAATATCAGTAGCTTTGCCATTCTAATTTTTTGTTCCTTAAGATC
** * *
1389538 CGAAGTCCAAGGCCTAATCTTTCGGTTAGTTTTGCAATTAAGCCGACTTTTCTTTTGCTTTAAGT
195 CGAAGTCCAAGGCCTAATCTTTCCATTAGTTTTGCAATTAAGCCAACTTTTCATTTGCTTTAAGT
1389603 CATATGCAATTTGCAGGTTTATGATTTATATTCACTCTGATTAAATATCTTTTGATCTGAACTTA
260 CATATGCAATTTGCAGGTTTATGATTTATATTCACTCTGATTAAATATCTTTTGATCTGAACTTA
1389668 GGACTCCTTT
325 GGACTCCTTT
* *
1389678 AACTAAGGTACTAGACCTGTTAACTCTTCTTTAGCATTACAGGTGTTGATTAGATTTTGCTATAA
1 AACTAAGGTACTAGACCTGCTAACACTTCTTTAGCATTACAGGTGTTGATTAGATTTTGCTATAA
1389743 -TTGTCTTTTTTCTTTTCCCATCATTGCTAGGAGTTGTTAGTTTGAATTATTGAAAGAAAAATAA
66 TTTGTC-TTTTTCTTTTCCCATCATTGCTAGGAGTTGTTAGTTTGAATTATTGAAAGAAAAATAA
1389807 GTTGGCATGTATTTCCCGTGTAATATCAGTAGCTTTGCCATTCTAATTTTTTGTTCCTTAAGATC
130 GTTGGCATGTATTTCCCGTGTAATATCAGTAGCTTTGCCATTCTAATTTTTTGTTCCTTAAGATC
1389872 CGAAGTCCAAGGCCTAATCTTTCCATTAGTTTTGCAATTAAGCCAACTTTTCATTTGCTTTAAGT
195 CGAAGTCCAAGGCCTAATCTTTCCATTAGTTTTGCAATTAAGCCAACTTTTCATTTGCTTTAAGT
1389937 CATATGCAATTTGCAGGTTTATGATTTATATTCACTCTGATTAAATATCTTTTGATCTGAACTTA
260 CATATGCAATTTGCAGGTTTATGATTTATATTCACTCTGATTAAATATCTTTTGATCTGAACTTA
1390002 GGACTCCTTT
325 GGACTCCTTT
1390012 AA
1 AA
1390014 TTCCTATGGT
Statistics
Matches: 325, Mismatches: 10, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
333 5 0.02
334 258 0.79
335 62 0.19
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (334 bp):
AACTAAGGTACTAGACCTGCTAACACTTCTTTAGCATTACAGGTGTTGATTAGATTTTGCTATAA
TTTGTCTTTTTCTTTTCCCATCATTGCTAGGAGTTGTTAGTTTGAATTATTGAAAGAAAAATAAG
TTGGCATGTATTTCCCGTGTAATATCAGTAGCTTTGCCATTCTAATTTTTTGTTCCTTAAGATCC
GAAGTCCAAGGCCTAATCTTTCCATTAGTTTTGCAATTAAGCCAACTTTTCATTTGCTTTAAGTC
ATATGCAATTTGCAGGTTTATGATTTATATTCACTCTGATTAAATATCTTTTGATCTGAACTTAG
GACTCCTTT
Found at i:1390931 original size:2 final size:2
Alignment explanation
Indices: 1390919--1390983 Score: 62
Period size: 2 Copynumber: 33.5 Consensus size: 2
1390909 GTTGAGTTGA
* * * * *
1390919 AT AT A- AT AT AT AT AT AT AT GT AT AT AT AT GT GT GT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1390960 GT AT AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1390984 GTTTAACCCT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1391696 original size:27 final size:27
Alignment explanation
Indices: 1391666--1391724 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
1391656 ATGTTCATTG
1391666 TTCATTGTCATTATAGATATAGAATTA
1 TTCATTGTCATTATAGATATAGAATTA
*
1391693 TTCACTGTCATTATAGATATAGAATTA
1 TTCATTGTCATTATAGATATAGAATTA
1391720 TTCAT
1 TTCAT
1391725 ACATTCTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (27 bp):
TTCATTGTCATTATAGATATAGAATTA
Found at i:1397027 original size:3 final size:3
Alignment explanation
Indices: 1397019--1397052 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1397009 AAATTGTATA
1397019 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1397053 GCTATAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1397755 original size:90 final size:90
Alignment explanation
Indices: 1397653--1397835 Score: 294
Period size: 90 Copynumber: 2.0 Consensus size: 90
1397643 CAATTTAATG
* * *
1397653 TTTACTTTATGTTTTATAATCGAACTATTTTAATAACTTCAAGTAAAAATTTTAATCAAAATTTT
1 TTTACTTTATGTTTTATAATCGAACTATTTTAATAACTTCAAGTAAAAAATTCAATCAAAAATTT
1397718 TTAAGTGAATGTTAAGGCTCAATTA
66 TTAAGTGAATGTTAAGGCTCAATTA
* **
1397743 TTTACTTTATGTTTTGTAATCGAACTATTTTAATAACTTTTAGTAAAAAATTCAATCAAAAATTT
1 TTTACTTTATGTTTTATAATCGAACTATTTTAATAACTTCAAGTAAAAAATTCAATCAAAAATTT
* *
1397808 TTAAGTGAATGTTGAGGCTCAGTTA
66 TTAAGTGAATGTTAAGGCTCAATTA
1397833 TTT
1 TTT
1397836 TCATATTGCT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 85 1.00
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (90 bp):
TTTACTTTATGTTTTATAATCGAACTATTTTAATAACTTCAAGTAAAAAATTCAATCAAAAATTT
TTAAGTGAATGTTAAGGCTCAATTA
Found at i:1401088 original size:39 final size:38
Alignment explanation
Indices: 1401009--1401097 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 38
1400999 GAACTTAAAT
* * *
1401009 AAATTTTGAAAAATCATCTCTTTAAAAGAAAATTGAAGAA
1 AAATTTT-AAAAATCACCTCCTTAAAAGAAAATTAAAG-A
*
1401049 AAATTTTAAAATATCACCTCCTT-AAATAAAATTAAAGA
1 AAATTTTAAAA-ATCACCTCCTTAAAAGAAAATTAAAGA
1401087 AAA-TTTAAAAA
1 AAATTTTAAAAA
1401098 GGGAAATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
36 1 0.02
37 7 0.16
38 4 0.09
39 16 0.36
40 16 0.36
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (38 bp):
AAATTTTAAAAATCACCTCCTTAAAAGAAAATTAAAGA
Found at i:1401392 original size:19 final size:19
Alignment explanation
Indices: 1401341--1401395 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
1401331 ATAAACTCTT
1401341 AATTTTTAATTTATA-TT--
1 AATTTTT-ATTTATATTTAA
* *
1401358 AATTTTT-TTAAAATTTAA
1 AATTTTTATTTATATTTAA
1401376 AATTTTTATTTATATTTAA
1 AATTTTTATTTATATTTAA
1401395 A
1 A
1401396 TAAAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 4 0.13
16 2 0.07
17 7 0.23
18 7 0.23
19 10 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTTATTTATATTTAA
Found at i:1401405 original size:18 final size:18
Alignment explanation
Indices: 1401384--1401436 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
1401374 AAAATTTTTA
1401384 TTTATATTTAAATAAAAT
1 TTTATATTTAAATAAAAT
1401402 TTTA-ATTTAAATATAAA-
1 TTTATATTTAAATA-AAAT
**
1401419 AATATATTTAAATAAAAT
1 TTTATATTTAAATAAAAT
1401437 AATATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTATATTTAAATAAAAT
Found at i:1401418 original size:23 final size:23
Alignment explanation
Indices: 1401373--1401418 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1401363 TTTTAAAATT
* * *
1401373 TAAAATTTTTATTTATATTTAAA
1 TAAAATTTTAATTTAAATATAAA
1401396 TAAAATTTTAATTTAAATATAAA
1 TAAAATTTTAATTTAAATATAAA
1401419 AATATATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAAATTTTAATTTAAATATAAA
Found at i:1401440 original size:18 final size:18
Alignment explanation
Indices: 1401386--1401446 Score: 74
Period size: 17 Copynumber: 3.5 Consensus size: 18
1401376 AATTTTTATT
**
1401386 TATATTTAAATAAAATTT
1 TATATTTAAATAAAATAA
1401404 TA-ATTTAAATATAAA-AA
1 TATATTTAAATA-AAATAA
1401421 TATATTTAAATAAAATAA
1 TATATTTAAATAAAATAA
1401439 TAT-TTTAA
1 TATATTTAA
1401447 TATTTTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 19 0.50
18 19 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATATTTAAATAAAATAA
Found at i:1401490 original size:15 final size:16
Alignment explanation
Indices: 1401464--1401493 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1401454 AATATAAAAA
1401464 TAAAATATTTATAAAT
1 TAAAATATTTATAAAT
1401480 TAAAATA-TTATAAA
1 TAAAATATTTATAAA
1401494 ATTATAATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAATATTTATAAAT
Found at i:1401495 original size:16 final size:16
Alignment explanation
Indices: 1401456--1401497 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1401446 ATATTTTAAA
*
1401456 TATAAAAATAAAATAT
1 TATAAAATTAAAATAT
1401472 T-TATAAATTAAAATAT
1 TATA-AAATTAAAATAT
1401488 TATAAAATTA
1 TATAAAATTA
1401498 TAATCGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TATAAAATTAAAATAT
Found at i:1401517 original size:2 final size:2
Alignment explanation
Indices: 1401510--1401540 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1401500 ATCGATTTAC
1401510 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1401541 AAGGGAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1402435 original size:3 final size:3
Alignment explanation
Indices: 1402392--1402419 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1402382 TTAGCGTTTG
1402392 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1402420 TCTAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1402616 original size:12 final size:12
Alignment explanation
Indices: 1402599--1402623 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1402589 AGCCTTATAC
1402599 TTTAGTCAAAGA
1 TTTAGTCAAAGA
1402611 TTTAGTCAAAGA
1 TTTAGTCAAAGA
1402623 T
1 T
1402624 GTTTATATGA
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TTTAGTCAAAGA
Found at i:1412122 original size:24 final size:24
Alignment explanation
Indices: 1412090--1412149 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
1412080 CCAACGTCCA
1412090 AGGACTAATCTTTATGTTAGTTTT
1 AGGACTAATCTTTATGTTAGTTTT
1412114 AGGACTAATCTTTATGTTAGTTTT
1 AGGACTAATCTTTATGTTAGTTTT
1412138 AGGACTAATCTT
1 AGGACTAATCTT
1412150 GCGATGCACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (24 bp):
AGGACTAATCTTTATGTTAGTTTT
Found at i:1413577 original size:19 final size:18
Alignment explanation
Indices: 1413553--1413601 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
1413543 TTTACAGATT
*
1413553 TTATTATTTAATTTATTAA
1 TTATTATTTAATCT-TTAA
*
1413572 TTATTAATTTTATCTTTAA
1 TTATT-ATTTAATCTTTAA
*
1413591 TTATTTTTTAA
1 TTATTATTTAA
1413602 GAAACATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 4 0.16
19 14 0.56
20 7 0.28
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTATTTAATCTTTAA
Found at i:1414859 original size:16 final size:18
Alignment explanation
Indices: 1414819--1414860 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1414809 CAATAAAATT
1414819 ATATAATTTTTTATTTATA
1 ATAT-ATTTTTTATTTATA
1414838 ATATATTTTTTATTTATA
1 ATATATTTTTTATTTATA
1414856 ATATA
1 ATATA
1414861 ATTATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATATTTTTTATTTATA
Found at i:1414960 original size:16 final size:17
Alignment explanation
Indices: 1414934--1414969 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1414924 TTTTAAGAGT
1414934 TTTTATAGGTCTTATTG
1 TTTTATAGGTCTTATTG
1414951 TTTT-TAGGTCTTATTG
1 TTTTATAGGTCTTATTG
1414967 TTT
1 TTT
1414970 AATTTACCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.14, C:0.06, G:0.17, T:0.64
Consensus pattern (17 bp):
TTTTATAGGTCTTATTG
Found at i:1424411 original size:12 final size:13
Alignment explanation
Indices: 1424394--1424426 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1424384 AAAAAGTTAA
1424394 AAAAATT-AAAAT
1 AAAAATTAAAAAT
1424406 AAAAATTAAAAAT
1 AAAAATTAAAAAT
1424419 AAATAATT
1 AAA-AATT
1424427 GATAAAGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 8 0.42
14 4 0.21
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAAATTAAAAAT
Found at i:1424952 original size:21 final size:21
Alignment explanation
Indices: 1424928--1424973 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
1424918 TTAATTAACT
1424928 AAGTTTTAAGTGAATTTTGAA
1 AAGTTTTAAGTGAATTTTGAA
1424949 AAG-TTTAAGTGAATTTTGAA
1 AAGTTTTAAGTGAATTTTGAA
*
1424969 GAGTT
1 AAGTT
1424974 GAATGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (21 bp):
AAGTTTTAAGTGAATTTTGAA
Found at i:1425142 original size:21 final size:25
Alignment explanation
Indices: 1425090--1425144 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 25
1425080 ATATATTTTT
*
1425090 TTATTATTAAATATATTTATTGAGAA
1 TTATAATT-AATATATTTATTGAGAA
1425116 TTATAATTAATA-ATTT-TTGA-AA
1 TTATAATTAATATATTTATTGAGAA
1425138 -TATAATT
1 TTATAATT
1425145 TTTTTTACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 7 0.25
22 2 0.07
23 4 0.14
24 4 0.14
25 4 0.14
26 7 0.25
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (25 bp):
TTATAATTAATATATTTATTGAGAA
Found at i:1425450 original size:22 final size:21
Alignment explanation
Indices: 1425419--1425463 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
1425409 ATATAAATAT
*
1425419 TTATTTATAAAATATAAAAAAA
1 TTATTAATAAAAT-TAAAAAAA
* *
1425441 TTATTAATAATATTAAATAAA
1 TTATTAATAAAATTAAAAAAA
1425462 TT
1 TT
1425464 TTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTATTAATAAAATTAAAAAAA
Found at i:1425462 original size:21 final size:21
Alignment explanation
Indices: 1425401--1425463 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
1425391 GTGTATTAAA
*
1425401 ATTATATAATA-TAAAT-ATTT
1 ATTA-ATAATATTAAATAAATT
* * *
1425421 ATTTATAAAATATAAAAAAATT
1 ATTAATAATAT-TAAATAAATT
1425443 ATTAATAATATTAAATAAATT
1 ATTAATAATATTAAATAAATT
1425464 TTTTATATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
19 5 0.15
20 3 0.09
21 13 0.39
22 12 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTAATAATATTAAATAAATT
Found at i:1426728 original size:12 final size:12
Alignment explanation
Indices: 1426711--1426735 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1426701 AGCCTTATAC
1426711 TTTAGTCAAAGA
1 TTTAGTCAAAGA
1426723 TTTAGTCAAAGA
1 TTTAGTCAAAGA
1426735 T
1 T
1426736 GTTTATATGA
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TTTAGTCAAAGA
Found at i:1444216 original size:2 final size:2
Alignment explanation
Indices: 1444209--1444250 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1444199 CATAGAGTGT
*
1444209 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG 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
1444251 AATAAAAGGC
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:1445923 original size:229 final size:229
Alignment explanation
Indices: 1445511--1445973 Score: 711
Period size: 229 Copynumber: 2.0 Consensus size: 229
1445501 AGGCATTGAC
* *
1445511 AACCAGTTCTAGGAAGGAAACTGGTGAAAGAGGTTTTCTGAATGATTTGTCCATTTTTCCAAGCT
1 AACCAGTTCTAGAAAGGAAACTGGTGAAAGAGGTTTTCTGAATGATTCGTCCA-TTTTCCAAGCT
* * *
1445576 GTTCTTTTTATGAACCCAATCGATTTAGAGTAAGTAGGCAAGTTGCTGGATTGGCCTTGGTGTTC
65 ATTCTTTTGATGAACCCAATCGATTTAGAGTAAGTAGGCAAGGTGCTGGATTGGCCTTGGTGTTC
*
1445641 CAGATTTCTTTTTTATTTTAATTTTAAAAGGTTTCTTTTTATAATGTATTCTGCTTGCCTTCTTG
130 CAGATTTCTTTTTTATTTTAATTTTAAAAGGTTTCTTTTTATAATGCATTCTGCTTGCCTTCTTG
1445706 TA-GTTAGATAGGCCAAGTGGAAGACAATGAAGCA
195 TATGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
* *
1445740 AACCAGTTCTAGAAAGGATACTGGTGAAAG-GGTTTGTTTGAATGATTCGTCCA-TTTCCAAGCT
1 AACCAGTTCTAGAAAGGAAACTGGTGAAAGAGGTTT-TCTGAATGATTCGTCCATTTTCCAAGCT
*
1445803 ATTCTTTTGATGAACCCAATTGA-TTAGAGTAAGTAGGCAAGGTGCTGGATTTGGCCTTGGTGTT
65 ATTCTTTTGATGAACCCAATCGATTTAGAGTAAGTAGGCAAGGTGCTGGA-TTGGCCTTGGTGTT
*
1445867 CCGGATTTC-TTTTTATTTTAATTTTAAAAGGTTTCTTTTTTTTATAATGCATTCTGCTTGCCTT
129 CCAGATTTCTTTTTTATTTTAATTTTAAAAGGTTTC---TTTTTATAATGCATTCTGCTTGCCTT
*
1445931 CTTGTAGTTTGTTAGATAGGCCAAGTGGTAGACAATGAAGCA
191 CTTGTA---TGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
1445973 A
1 A
1445974 TGGATTTTGC
Statistics
Matches: 214, Mismatches: 11, Indels: 14
0.90 0.05 0.06
Matches are distributed among these distances:
226 51 0.24
227 52 0.24
228 5 0.02
229 74 0.35
233 32 0.15
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.39
Consensus pattern (229 bp):
AACCAGTTCTAGAAAGGAAACTGGTGAAAGAGGTTTTCTGAATGATTCGTCCATTTTCCAAGCTA
TTCTTTTGATGAACCCAATCGATTTAGAGTAAGTAGGCAAGGTGCTGGATTGGCCTTGGTGTTCC
AGATTTCTTTTTTATTTTAATTTTAAAAGGTTTCTTTTTATAATGCATTCTGCTTGCCTTCTTGT
ATGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
Found at i:1446766 original size:18 final size:19
Alignment explanation
Indices: 1446736--1446777 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1446726 AAAATGCTTT
* *
1446736 ATTTTCTTTGGTTTACTTG
1 ATTTTCTTTGGTTCACTTA
1446755 ATTTTC-TTGGTTCACTTA
1 ATTTTCTTTGGTTCACTTA
1446773 ATTTT
1 ATTTT
1446778 TCTCAAGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.62
Consensus pattern (19 bp):
ATTTTCTTTGGTTCACTTA
Found at i:1456080 original size:31 final size:31
Alignment explanation
Indices: 1456044--1456136 Score: 186
Period size: 31 Copynumber: 3.0 Consensus size: 31
1456034 TTGCAGATTA
1456044 TCCTGCCTTAGACTCTCTTATATCGTTAATC
1 TCCTGCCTTAGACTCTCTTATATCGTTAATC
1456075 TCCTGCCTTAGACTCTCTTATATCGTTAATC
1 TCCTGCCTTAGACTCTCTTATATCGTTAATC
1456106 TCCTGCCTTAGACTCTCTTATATCGTTAATC
1 TCCTGCCTTAGACTCTCTTATATCGTTAATC
1456137 CTAGGTAAAC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.19, C:0.29, G:0.10, T:0.42
Consensus pattern (31 bp):
TCCTGCCTTAGACTCTCTTATATCGTTAATC
Found at i:1459916 original size:67 final size:67
Alignment explanation
Indices: 1459808--1459942 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
1459798 CAATATTCTT
* *
1459808 TTAAAGGGAGTTATGTCCATGTTTAATAGTTAAACTGCTTTGTTTCTTGGTTATCTATAGTTCAT
1 TTAAAGGGAGCTATGTCCATGTTTAACAGTTAAACTGCTTTGTTTCTTGGTTATCTATAGTTCAT
1459873 TA
66 TA
1459875 TTAAAGGGAGCTATGTCCATGTTTAACAGTTAAACTGCTTTGTTTCTTGGTTATCTATAGTTCAT
1 TTAAAGGGAGCTATGTCCATGTTTAACAGTTAAACTGCTTTGTTTCTTGGTTATCTATAGTTCAT
1459940 TA
66 TA
1459942 T
1 T
1459943 CTTAAGAGAC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (67 bp):
TTAAAGGGAGCTATGTCCATGTTTAACAGTTAAACTGCTTTGTTTCTTGGTTATCTATAGTTCAT
TA
Found at i:1460652 original size:103 final size:103
Alignment explanation
Indices: 1460473--1460674 Score: 305
Period size: 103 Copynumber: 2.0 Consensus size: 103
1460463 CAAGACTTTG
* * *
1460473 TCAGATATTTTGGTCAAAATAGTCTATTGGCATCTTTGCTTATTCTATTTCCTGTAAGATAATGA
1 TCAGATATTTTGGTCAAAATAGTCTATTGGCATCTTAGCTTATTCTATTGCCTATAAGATAATGA
*
1460538 CTAGTGTCTCAAATATGTTTGGTTGCAGGATATTTTTT
66 CTAGTGTCTCAAATATGTCTGGTTGCAGGATATTTTTT
* * * * * * *
1460576 TCAGATTTTTTGGTTAAAATGGTTTGTTGGTATCTTAGCTTATTCTATTGCGTATAAGATAATGA
1 TCAGATATTTTGGTCAAAATAGTCTATTGGCATCTTAGCTTATTCTATTGCCTATAAGATAATGA
1460641 CTAGTGTCTCAAATATGTCTGGTTGCAGGATATT
66 CTAGTGTCTCAAATATGTCTGGTTGCAGGATATT
1460675 CATACTTCCT
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
103 88 1.00
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.44
Consensus pattern (103 bp):
TCAGATATTTTGGTCAAAATAGTCTATTGGCATCTTAGCTTATTCTATTGCCTATAAGATAATGA
CTAGTGTCTCAAATATGTCTGGTTGCAGGATATTTTTT
Found at i:1461371 original size:37 final size:39
Alignment explanation
Indices: 1461321--1461399 Score: 126
Period size: 40 Copynumber: 2.1 Consensus size: 39
1461311 GGTTGGAATG
*
1461321 CTGTTC-TTTTTTTTTT-GTGTTTGACTCATCACTCGCT
1 CTGTTCTTTTTTTTTTTGGTGTTTGACTCATCACACGCT
1461358 CTGTTCTTTTTTTTTTTTGGTGTTTGACTCATCACACGCT
1 CTGTTC-TTTTTTTTTTTGGTGTTTGACTCATCACACGCT
1461398 CT
1 CT
1461400 ATTGCTTATG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
37 6 0.16
39 10 0.26
40 22 0.58
ACGTcount: A:0.09, C:0.22, G:0.14, T:0.56
Consensus pattern (39 bp):
CTGTTCTTTTTTTTTTTGGTGTTTGACTCATCACACGCT
Found at i:1462188 original size:23 final size:24
Alignment explanation
Indices: 1462162--1462208 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1462152 GCATTAAAGG
* *
1462162 TAGTAAAAT-TGTATGTGTTTTTT
1 TAGTAAAATCTGTATATATTTTTT
1462185 TAGTAAAATCTGTATATATTTTTT
1 TAGTAAAATCTGTATATATTTTTT
1462209 CTTTATTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.55
Consensus pattern (24 bp):
TAGTAAAATCTGTATATATTTTTT
Found at i:1462344 original size:16 final size:16
Alignment explanation
Indices: 1462323--1462354 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1462313 TTATATTTTC
1462323 TCATATTACTGTTATA
1 TCATATTACTGTTATA
1462339 TCATATTACTGTTATA
1 TCATATTACTGTTATA
1462355 GAGATGTAAT
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:0.06, T:0.50
Consensus pattern (16 bp):
TCATATTACTGTTATA
Found at i:1462439 original size:2 final size:2
Alignment explanation
Indices: 1462434--1462460 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1462424 TTAGTGCTTT
1462434 TA 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 TA T
1462461 TTACATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1467419 original size:15 final size:15
Alignment explanation
Indices: 1467399--1467428 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1467389 TCATTGTTTT
1467399 TGATTTTGCTTTGGA
1 TGATTTTGCTTTGGA
1467414 TGATTTTGCTTTGGA
1 TGATTTTGCTTTGGA
1467429 GCAAGATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.27, T:0.53
Consensus pattern (15 bp):
TGATTTTGCTTTGGA
Found at i:1468718 original size:31 final size:32
Alignment explanation
Indices: 1468647--1468719 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 32
1468637 TGATTTATGA
* *
1468647 TAAAAAAATTCTTTTAATCTTATCATTTTATC
1 TAAATAAATTCTTTTAATCTTATCATTATATC
* * * * *
1468679 TAATTAAATT-TTTTAATTTTTTGATTATATT
1 TAAATAAATTCTTTTAATCTTATCATTATATC
1468710 TAAATAAATT
1 TAAATAAATT
1468720 AATAATTTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 25 0.76
32 8 0.24
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.55
Consensus pattern (32 bp):
TAAATAAATTCTTTTAATCTTATCATTATATC
Found at i:1468787 original size:18 final size:18
Alignment explanation
Indices: 1468766--1468801 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1468756 TTAATTTGTA
1468766 TTTAAATTTTATAAAAAT
1 TTTAAATTTTATAAAAAT
* *
1468784 TTTAATTTTTATCAAAAT
1 TTTAAATTTTATAAAAAT
1468802 AAATTTTTTA
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:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAATTTTATAAAAAT
Found at i:1468810 original size:24 final size:23
Alignment explanation
Indices: 1468802--1468846 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1468792 TTATCAAAAT
1468802 AAATTTTTTATTTATATATAAAC
1 AAATTTTTTATTTATATATAAAC
*
1468825 AAA-TTTTTATTTTAAATATAAA
1 AAATTTTTTA-TTTATATATAAA
1468847 AATCTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTTTTTATTTATATATAAAC
Found at i:1468834 original size:22 final size:22
Alignment explanation
Indices: 1468780--1468846 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
1468770 AATTTTATAA
* * *
1468780 AAATTTTAATTTTTATCA-AAAT
1 AAATTTTTATTTATAT-ATAAAC
1468802 AAATTTTTTATTTATATATAAAC
1 AAA-TTTTTATTTATATATAAAC
*
1468825 AAATTTTTATTTTAAATATAAA
1 AAATTTTTA-TTTATATATAAA
1468847 AATCTATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
22 10 0.26
23 28 0.74
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTTTTATTTATATATAAAC
Found at i:1469238 original size:2 final size:2
Alignment explanation
Indices: 1469233--1469264 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1469223 TCTCTCCAAC
1469233 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1469265 TTACGTACTG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1475018 original size:4 final size:4
Alignment explanation
Indices: 1475011--1475035 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1475001 TTTTTTTGTC
1475011 TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT T
1475036 ATTTTCCGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:1480388 original size:67 final size:67
Alignment explanation
Indices: 1480280--1480410 Score: 253
Period size: 67 Copynumber: 2.0 Consensus size: 67
1480270 CAATATTCTT
*
1480280 TTAAAGGGAGCTATGTCCATGTTTAACAGTTAGACTGCTTTGTTTCTTGGTTATCTATAGTTCAT
1 TTAAAGGGAGCTATGTCCATGTTTAACAGTTAAACTGCTTTGTTTCTTGGTTATCTATAGTTCAT
1480345 TA
66 TA
1480347 TTAAAGGGAGCTATGTCCATGTTTAACAGTTAAACTGCTTTGTTTCTTGGTTATCTATAGTTCA
1 TTAAAGGGAGCTATGTCCATGTTTAACAGTTAAACTGCTTTGTTTCTTGGTTATCTATAGTTCA
1480411 ATATCTTTTA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (67 bp):
TTAAAGGGAGCTATGTCCATGTTTAACAGTTAAACTGCTTTGTTTCTTGGTTATCTATAGTTCAT
TA
Found at i:1489603 original size:26 final size:26
Alignment explanation
Indices: 1489544--1489593 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1489534 AATTTACATT
1489544 AAATAAATTTTTAATTTTTAATTTCA
1 AAATAAATTTTTAATTTTTAATTTCA
* *
1489570 AAATAAATTTTTTATTTTTTATTT
1 AAATAAATTTTTAATTTTTAATTT
1489594 ATATTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
AAATAAATTTTTAATTTTTAATTTCA
Found at i:1491597 original size:16 final size:18
Alignment explanation
Indices: 1491560--1491599 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1491550 TTAAATCAAT
1491560 AAATTGTTTTATTAAAGTA
1 AAATTGTTTTA-TAAAGTA
1491579 AAATTGTTTTA-AAAG-A
1 AAATTGTTTTATAAAGTA
1491595 AAATT
1 AAATT
1491600 TAAAATTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 4 0.19
19 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (18 bp):
AAATTGTTTTATAAAGTA
Found at i:1491642 original size:13 final size:14
Alignment explanation
Indices: 1491616--1491646 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1491606 TTTGAAATTG
1491616 AAAAAATAATTATT
1 AAAAAATAATTATT
1491630 AAAAAATAA-TATT
1 AAAAAATAATTATT
1491643 AAAA
1 AAAA
1491647 TAAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAAAATAATTATT
Found at i:1491681 original size:15 final size:15
Alignment explanation
Indices: 1491645--1491686 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1491635 ATAATATTAA
*
1491645 AATAAAAAATATATGT
1 AATATAAAAT-TATGT
1491661 -AT-TAAAATTATGT
1 AATATAAAATTATGT
1491674 AATATAAAATTAT
1 AATATAAAATTAT
1491687 TTATAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 5 0.22
14 7 0.30
15 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
AATATAAAATTATGT
Found at i:1491696 original size:19 final size:18
Alignment explanation
Indices: 1491674--1491723 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 18
1491664 AAAATTATGT
*
1491674 AATATAAAATTATTTATAA
1 AATATAAAATTATTAAT-A
1491693 AATACATAAAAATTATTAATA
1 AAT--AT-AAAATTATTAATA
1491714 AATATAAAAT
1 AATATAAAAT
1491724 AAAATATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
21 6 0.22
22 11 0.41
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATAAAATTATTAATA
Found at i:1492221 original size:26 final size:27
Alignment explanation
Indices: 1492192--1492246 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
1492182 CTTCTTTACC
1492192 TTTTGTGTTTTTACTCC-TCCTTTGTT
1 TTTTGTGTTTTTACTCCTTCCTTTGTT
* * **
1492218 TTTTTTTTTTTTTTTCCTTCCTTTGTT
1 TTTTGTGTTTTTACTCCTTCCTTTGTT
1492245 TT
1 TT
1492247 GTCGAGTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.02, C:0.16, G:0.07, T:0.75
Consensus pattern (27 bp):
TTTTGTGTTTTTACTCCTTCCTTTGTT
Found at i:1492616 original size:3 final size:3
Alignment explanation
Indices: 1492573--1492600 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1492563 TTAGCATTTG
1492573 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1492601 TCTAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1492797 original size:12 final size:12
Alignment explanation
Indices: 1492780--1492804 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1492770 AGCCTTATAC
1492780 TTTAGTCAAAGA
1 TTTAGTCAAAGA
1492792 TTTAGTCAAAGA
1 TTTAGTCAAAGA
1492804 T
1 T
1492805 GTTTTTATGA
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TTTAGTCAAAGA
Found at i:1510629 original size:2 final size:2
Alignment explanation
Indices: 1510622--1510666 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1510612 CATAGAATGT
1510622 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
1510664 TA T
1 TA T
1510667 GTTAGGCTCC
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:1512113 original size:233 final size:233
Alignment explanation
Indices: 1511703--1512169 Score: 756
Period size: 233 Copynumber: 2.0 Consensus size: 233
1511693 AGGCATTGAC
* * *
1511703 AACCAGTTCTAGAAAGGAAACTGGTGAAAGAGGTTTTCTAAATGATTTGTCCATTTCCAAGCTGT
1 AACCAGTTATAGAAAGGAAACCGGTGAAAGAGGTTTTCTAAATGATTTGTCCATTTCCAAGCTAT
1511768 TCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGATGGATTTGGCCTTGGTGTTCT
66 TCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGATGGATTTGGCCTTGGTGTTCT
*
1511833 GGATTTCTTTTTTATTTTAATCTTAGAAGGTTTCTTTCTTATAATGTATCCTCCTTGCCTTCTTG
131 GGATTTCTTTTCTATTTTAATCTTAGAAGGTTTCTTTCTTATAATGTATCCTCCTTGCCTTCTTG
*
1511898 TAGTTTGTTCGATAGGCCAAGTGGAAGACAATGAAGCA
196 TAGTTTGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
* * * *
1511936 AACCAGTTATAGAAAGGATACCGGTGAAAGAGTTTTTTTGAATGATTTGTCCATTTCCAAGCTAT
1 AACCAGTTATAGAAAGGAAACCGGTGAAAGAGGTTTTCTAAATGATTTGTCCATTTCCAAGCTAT
* *
1512001 TCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGCTGGATTTGGCCTTGGTGTTGT
66 TCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGATGGATTTGGCCTTGGTGTTCT
* * * * * *
1512066 GGATTTGTTTTCTATTTTAATTTTA-AGAGGTTTCTTTTTTGTAATGTATTCTGCTTGCCTTCTT
131 GGATTTCTTTTCTATTTTAATCTTAGA-AGGTTTCTTTCTTATAATGTATCCTCCTTGCCTTCTT
*
1512130 GTAGTTTGTTAGATAGGCCAAGTGGCAGACAATGAAGCA
195 GTAGTTTGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
1512169 A
1 A
1512170 TGGATTTTGC
Statistics
Matches: 215, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
232 1 0.00
233 214 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.39
Consensus pattern (233 bp):
AACCAGTTATAGAAAGGAAACCGGTGAAAGAGGTTTTCTAAATGATTTGTCCATTTCCAAGCTAT
TCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGATGGATTTGGCCTTGGTGTTCT
GGATTTCTTTTCTATTTTAATCTTAGAAGGTTTCTTTCTTATAATGTATCCTCCTTGCCTTCTTG
TAGTTTGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
Found at i:1513473 original size:18 final size:19
Alignment explanation
Indices: 1513439--1513474 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1513429 TGGCTTGCAA
*
1513439 ATTCATATTTGTTTTCCAT
1 ATTCATATTTCTTTTCCAT
1513458 ATTCATA-TTCTTTTCCA
1 ATTCATATTTCTTTTCCA
1513475 GCATGTGAGA
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:0.22, C:0.19, G:0.03, T:0.56
Consensus pattern (19 bp):
ATTCATATTTCTTTTCCAT
Found at i:1513651 original size:12 final size:12
Alignment explanation
Indices: 1513634--1513705 Score: 81
Period size: 12 Copynumber: 5.8 Consensus size: 12
1513624 GTTGGCTTAT
*
1513634 TATATACATACA
1 TATATATATACA
*
1513646 TATATATATATA
1 TATATATATACA
1513658 TATATATACATACA
1 TATATAT--ATACA
1513672 TATATATATACA
1 TATATATATACA
* *
1513684 TACATATATCCA
1 TATATATATACA
*
1513696 TACATATATA
1 TATATATATA
1513706 TACACACACA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
12 41 0.79
14 11 0.21
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (12 bp):
TATATATATACA
Found at i:1513655 original size:16 final size:16
Alignment explanation
Indices: 1513637--1513707 Score: 83
Period size: 16 Copynumber: 4.6 Consensus size: 16
1513627 GGCTTATTAT
*
1513637 ATACATACATATAT--
1 ATACATATATATATAC
*
1513651 ATATATATATATATAC
1 ATACATATATATATAC
1513667 ATACATATATATATAC
1 ATACATATATATATAC
**
1513683 ATACATATATCCATAC
1 ATACATATATATATAC
*
1513699 ATATATATA
1 ATACATATA
1513708 CACACACACA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
14 12 0.24
16 37 0.76
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (16 bp):
ATACATATATATATAC
Found at i:1513706 original size:4 final size:4
Alignment explanation
Indices: 1513634--1513707 Score: 67
Period size: 4 Copynumber: 18.5 Consensus size: 4
1513624 GTTGGCTTAT
* * * *
1513634 TATA TACA TACA TATA TATA TATA TATA TATA CATA CATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * *
1513682 CATA CATA TATC CATA CATA TATA TA
1 TATA TATA TATA TATA TATA TATA TA
1513708 CACACACACA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (4 bp):
TATA
Found at i:1520310 original size:21 final size:22
Alignment explanation
Indices: 1520258--1520315 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
1520248 TATTACGACA
*
1520258 ATTATTTTATTATTGAAATTTT
1 ATTAATTTATTATTGAAATTTT
* *
1520280 ATTAATTTATTATTTAATTTTT
1 ATTAATTTATTATTGAAATTTT
1520302 A-T-ATCTTATTATTG
1 ATTAAT-TTATTATTG
1520316 TAAGAAGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 2 0.06
21 9 0.29
22 20 0.65
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (22 bp):
ATTAATTTATTATTGAAATTTT
Found at i:1530141 original size:32 final size:33
Alignment explanation
Indices: 1530080--1530141 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
1530070 CACATTTCTA
*
1530080 TATGAAACTTTGCAAATCCAAATCGTTTTTCAG
1 TATGAAACTTTGCAAATCCAAATAGTTTTTCAG
* *
1530113 TATGAAAC-TTGCAAATTCAAATATTTTTT
1 TATGAAACTTTGCAAATCCAAATAGTTTTT
1530142 GAATTGTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 18 0.69
33 8 0.31
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (33 bp):
TATGAAACTTTGCAAATCCAAATAGTTTTTCAG
Found at i:1532805 original size:54 final size:54
Alignment explanation
Indices: 1532743--1532849 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
1532733 CCCCCATGCA
1532743 ATTGAGACATACTAGGAATATTTAATTAAAGCCAATAAGGTGGGCAGGGCAGGT
1 ATTGAGACATACTAGGAATATTTAATTAAAGCCAATAAGGTGGGCAGGGCAGGT
1532797 ATTGAGACATACTAGGAATATTTAATTAAAGCCAATAAGGTGGGCAGGGCAGG
1 ATTGAGACATACTAGGAATATTTAATTAAAGCCAATAAGGTGGGCAGGGCAGG
1532850 GTATAAGGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.23
Consensus pattern (54 bp):
ATTGAGACATACTAGGAATATTTAATTAAAGCCAATAAGGTGGGCAGGGCAGGT
Found at i:1540163 original size:19 final size:19
Alignment explanation
Indices: 1540110--1540166 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1540100 ATACAAAGAC
1540110 AATTTTTT-AT-TTATATTT
1 AATTTTTTAATATTAT-TTT
* * *
1540128 AA-TTATTAAAATAATTTT
1 AATTTTTTAATATTATTTT
1540146 AATTTTTTAATATTATTTT
1 AATTTTTTAATATTATTTT
1540165 AA
1 AA
1540167 ATAAAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 4 0.13
18 8 0.27
19 18 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AATTTTTTAATATTATTTT
Found at i:1540680 original size:24 final size:25
Alignment explanation
Indices: 1540653--1540713 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 25
1540643 TGTTTTAGAT
1540653 ATAATATGAAAAT-AAAATATGATG
1 ATAATATGAAAATAAAAATATGATG
* *
1540677 ATAATATGTTAATATAAAAATATTATG
1 ATAATATG--AAAATAAAAATATGATG
1540704 ATAAATATGA
1 AT-AATATGA
1540714 TATAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 8 0.26
26 5 0.16
27 12 0.39
28 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (25 bp):
ATAATATGAAAATAAAAATATGATG
Found at i:1540696 original size:27 final size:30
Alignment explanation
Indices: 1540666--1540721 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 30
1540656 ATATGAAAAT
1540666 AAAATATGATGAT-AATATG-T-TAATATA
1 AAAATATGATGATAAATATGATATAATATA
*
1540693 AAAATATTATGATAAATATGATATAATAT
1 AAAATATGATGATAAATATGATATAATAT
1540722 TTTATATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 12 0.48
28 6 0.24
29 1 0.04
30 6 0.24
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.38
Consensus pattern (30 bp):
AAAATATGATGATAAATATGATATAATATA
Found at i:1544563 original size:2 final size:2
Alignment explanation
Indices: 1544558--1544585 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1544548 ATAATTTGTG
1544558 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
1544586 TTTTTGTAAA
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:1552330 original size:2 final size:2
Alignment explanation
Indices: 1552323--1552360 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1552313 CATTAATAGC
1552323 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
1552361 TTACATCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1553071 original size:21 final size:21
Alignment explanation
Indices: 1553045--1553095 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1553035 AAGCTAACTA
1553045 GCTAAATTCCATTTACAGACC
1 GCTAAATTCCATTTACAGACC
*
1553066 GCTAAATTCCATTTACAGGCC
1 GCTAAATTCCATTTACAGACC
*
1553087 ACTAAATTC
1 GCTAAATTC
1553096 ATGTATATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.29
Consensus pattern (21 bp):
GCTAAATTCCATTTACAGACC
Found at i:1556634 original size:2 final size:2
Alignment explanation
Indices: 1556627--1556669 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1556617 GCCCCTACAA
* *
1556627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1556669 A
1 A
1556670 AATTGTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1557127 original size:12 final size:13
Alignment explanation
Indices: 1557098--1557155 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 13
1557088 AATATAAATA
1557098 TATTTTTCATCATT
1 TATTTTTCAT-ATT
1557112 TATTTTTCAT-TT
1 TATTTTTCATATT
* *
1557124 TATTATTCATATA
1 TATTTTTCATATT
* *
1557137 TATATAT-ATATT
1 TATTTTTCATATT
1557149 TATTTTT
1 TATTTTT
1557156 TATCCATCTT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
12 20 0.57
13 5 0.14
14 10 0.29
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTTTTCATATT
Found at i:1557735 original size:23 final size:23
Alignment explanation
Indices: 1557709--1557752 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1557699 GATTTAATAA
*
1557709 TTTA-TATATTTATAGTTATATAT
1 TTTATTATA-TTATAATTATATAT
1557732 TTTATTATATTATAATTATAT
1 TTTATTATATTATAATTATAT
1557753 TTAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTATTATATTATAATTATATAT
Found at i:1557753 original size:21 final size:20
Alignment explanation
Indices: 1557726--1557856 Score: 66
Period size: 21 Copynumber: 6.0 Consensus size: 20
1557716 ATTTATAGTT
1557726 ATATATTTTATTATATTATA
1 ATATATTTTATTATATTATA
*
1557746 ATTATATTTAAAATATTTATATTTTA
1 A-TATATTT----TA-TTATATTATA
*
1557772 AT-TAATTTTAATATATTAATA
1 ATAT-ATTTTATTATATT-ATA
* * * *
1557793 ATCTATGTTATATAAATTTAAAA
1 ATATATTTTAT-TATA-TT-ATA
1557816 ATATATTTATATTATATTATA
1 ATATATTT-TATTATATTATA
* *
1557837 ATAAATTTTTATTATTTTAT
1 ATATA-TTTTATTATATTAT
1557857 GTGTTATATT
Statistics
Matches: 85, Mismatches: 13, Indels: 25
0.69 0.11 0.20
Matches are distributed among these distances:
20 7 0.08
21 34 0.40
22 9 0.11
23 14 0.16
24 4 0.05
25 7 0.08
26 10 0.12
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.56
Consensus pattern (20 bp):
ATATATTTTATTATATTATA
Found at i:1557765 original size:26 final size:26
Alignment explanation
Indices: 1557736--1557788 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1557726 ATATATTTTA
1557736 TTATATTATAATT-ATATTTAAAATAT
1 TTATATTATAATTAAT-TTTAAAATAT
* *
1557762 TTATATTTTAATTAATTTTAATATAT
1 TTATATTATAATTAATTTTAAAATAT
1557788 T
1 T
1557789 AATAATCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTATATTATAATTAATTTTAAAATAT
Found at i:1557836 original size:32 final size:35
Alignment explanation
Indices: 1557781--1557844 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 35
1557771 AATTAATTTT
*
1557781 AATATATTAATAATCTATGTTAT-ATAAATTTAAA
1 AATATATTAATAATCTATATTATAATAAATTTAAA
*
1557815 AATATATTTAT-AT-TATATTATAATAAATTT
1 AATATATTAATAATCTATATTATAATAAATTT
1557845 TTATTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 7 0.26
33 10 0.37
34 10 0.37
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (35 bp):
AATATATTAATAATCTATATTATAATAAATTTAAA
Found at i:1565838 original size:2 final size:2
Alignment explanation
Indices: 1565831--1565860 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1565821 TTCTTTCAAT
1565831 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1565861 CAACTTGCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1572258 original size:36 final size:36
Alignment explanation
Indices: 1572218--1572292 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
1572208 ACCTCCGTTC
*
1572218 AGACAGTGGAAAGAATCGCATTACTTTGATGGCTCA
1 AGACAGTGGAAAGAATCGCATTACTTTGATGGCCCA
*
1572254 AGACAGTGGAAAGCATCGCATTACTTTGATGGCCCA
1 AGACAGTGGAAAGAATCGCATTACTTTGATGGCCCA
1572290 AGA
1 AGA
1572293 ATCCCATGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (36 bp):
AGACAGTGGAAAGAATCGCATTACTTTGATGGCCCA
Found at i:1576400 original size:19 final size:21
Alignment explanation
Indices: 1576376--1576421 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1576366 TATTTAATTT
* *
1576376 TTTAAAAT-TTTTA-TATATA
1 TTTAAAATATTATATTACATA
1576395 TTTAAAATATTATATTACATA
1 TTTAAAATATTATATTACATA
1576416 TTTAAA
1 TTTAAA
1576422 TTTATTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
20 4 0.17
21 11 0.48
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTAAAATATTATATTACATA
Found at i:1576418 original size:21 final size:19
Alignment explanation
Indices: 1576376--1576426 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1576366 TATTTAATTT
* *
1576376 TTTAAAATTTTTATATATA
1 TTTAAAATTTATATACATA
1576395 TTTAAAATATTATATTACATA
1 TTTAAAAT-TTATA-TACATA
1576416 TTT-AAATTTAT
1 TTTAAAATTTAT
1576427 TTTGAAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 12 0.43
20 8 0.29
21 8 0.29
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAAATTTATATACATA
Found at i:1576462 original size:13 final size:13
Alignment explanation
Indices: 1576444--1576468 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1576434 TGTGTAAAAG
1576444 ATAAATATTTAAC
1 ATAAATATTTAAC
1576457 ATAAATATTTAA
1 ATAAATATTTAA
1576469 AACAATAAAT
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAAATATTTAAC
Found at i:1577168 original size:16 final size:17
Alignment explanation
Indices: 1577143--1577201 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 17
1577133 CTGAATTTAA
*
1577143 ATAATATTAATA-GTAT
1 ATAATTTTAATATGTAT
*
1577159 ATAATTTTAATATTTAT
1 ATAATTTTAATATGTAT
1577176 ATAATTTATAATAAT-TAT
1 ATAATTT-TAAT-ATGTAT
1577194 ATTAATTT
1 A-TAATTT
1577202 ATATTGATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
16 11 0.30
17 10 0.27
18 8 0.22
19 8 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATAATTTTAATATGTAT
Found at i:1577184 original size:9 final size:9
Alignment explanation
Indices: 1577156--1577205 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
1577146 ATATTAATAG
1577156 TATATAATT
1 TATATAATT
1577165 T-TA-ATATT
1 TATATA-ATT
1577173 TATATAATT
1 TATATAATT
1577182 TATAATAA-T
1 TAT-ATAATT
1577191 TATATTAATT
1 TATA-TAATT
1577201 TATAT
1 TATAT
1577206 TGATTAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
7 1 0.03
8 7 0.20
9 17 0.49
10 10 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATATAATT
Found at i:1577211 original size:19 final size:18
Alignment explanation
Indices: 1577156--1577204 Score: 73
Period size: 17 Copynumber: 2.7 Consensus size: 18
1577146 ATATTAATAG
*
1577156 TATATAATTT-TAATATT
1 TATATAATTTATAATAAT
1577173 TATATAATTTATAATAAT
1 TATATAATTTATAATAAT
1577191 TATATTAATTTATA
1 TATA-TAATTTATA
1577205 TTGATTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 10 0.34
18 10 0.34
19 9 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATAATTTATAATAAT
Found at i:1577392 original size:15 final size:15
Alignment explanation
Indices: 1577374--1577437 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 15
1577364 AAAAATATAA
1577374 TATATTTTAAATATT
1 TATATTTTAAATATT
*
1577389 TATATATT---TATT
1 TATATTTTAAATATT
* *
1577401 TAGATATTAAATATT
1 TATATTTTAAATATT
1577416 TATAATTTTAAA-ATT
1 TAT-ATTTTAAATATT
1577431 TATATTT
1 TATATTT
1577438 ATATATGGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
12 11 0.27
14 4 0.10
15 19 0.46
16 7 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TATATTTTAAATATT
Done.