Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold222
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: 358842
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
File 1 of 3
Found at i:333 original size:21 final size:20
Alignment explanation
Indices: 309--352 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
299 TTTATTTATG
309 TATTTTT-ATATATTATAATTA
1 TATTTTTAAT-TATTAT-ATTA
330 TATTTTTAATTATTATATTA
1 TATTTTTAATTATTATATTA
350 TAT
1 TAT
353 AAATTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 13 0.59
22 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTTTAATTATTATATTA
Found at i:341 original size:12 final size:13
Alignment explanation
Indices: 314--351 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
304 TTATGTATTT
314 TTATATATTATAA
1 TTATATATTATAA
*
327 TTATAT-TTTTAA
1 TTATATATTATAA
339 TTATTATATTATA
1 TTA-TATATTATA
352 TAAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 8 0.38
13 9 0.43
14 4 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATATATTATAA
Found at i:525 original size:19 final size:19
Alignment explanation
Indices: 501--564 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
491 TAAAATGTAA
501 TATATTTATTTTATATATT
1 TATATTTATTTTATATATT
* *
520 TATATTAATTATTTTATA-T
1 TATATTTATT-TTATATATT
* *
539 TATA-TTATATTATATTTAT
1 TATATTTATTTTATATAT-T
558 TATATTT
1 TATATTT
565 TTATGGAGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
17 5 0.14
18 3 0.09
19 19 0.54
20 8 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TATATTTATTTTATATATT
Found at i:534 original size:22 final size:23
Alignment explanation
Indices: 501--568 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 23
491 TAAAATGTAA
501 TATATTTATTTTATATATTTATAT
1 TATA-TTATTTTATATATTTATAT
525 TA-ATTATTTTATATTATATTATAT
1 TATATTATTTTATA-TAT-TTATAT
* *
549 TATATT-TATTATATTTTTAT
1 TATATTATTTTATATATTTAT
569 GGAGTAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 14 0.36
23 6 0.15
24 16 0.41
25 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TATATTATTTTATATATTTATAT
Found at i:541 original size:5 final size:5
Alignment explanation
Indices: 501--563 Score: 71
Period size: 5 Copynumber: 13.2 Consensus size: 5
491 TAAAATGTAA
* *
501 TATAT T-TAT TTTA- TATATT TATAT TA-AT TATTT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATA-T TATAT TATAT TATAT TATAT TATAT TATAT
549 TATAT T-TAT TATAT T
1 TATAT TATAT TATAT T
564 TTTATGGAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 15 0.30
5 31 0.62
6 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TATAT
Found at i:552 original size:29 final size:27
Alignment explanation
Indices: 505--560 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
495 ATGTAATATA
*
505 TTTATTTTATATATTTATATTAATTAT
1 TTTATATTATATATTTATATTAATTAT
*
532 TTTATATTATATTATATTATATTTATTAT
1 TTTATATTATA-TAT-TTATATTAATTAT
561 ATTTTTATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.40
28 3 0.12
29 12 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTATATTATATATTTATATTAATTAT
Found at i:912 original size:58 final size:52
Alignment explanation
Indices: 793--912 Score: 118
Period size: 52 Copynumber: 2.2 Consensus size: 52
783 TTTTTATTTT
* *
793 ATTTTTAAAATTTAAAATTTTTATTTATTTTATTTAATTTAATTTTTAAACTA
1 ATTTTT-AATTTTAAAATTTTTATTGATTTTATTTAATTTAATTTTTAAACTA
* *
846 A-ATATAATTTTAATAATTTTTATTGATTATTATTTAATATAAATATATTTTTAAA-TA
1 ATTTTTAATTTTAA-AATTTTTATTGATT-TTATTTAAT-T---TA-ATTTTTAAACTA
903 ATTTTTAATT
1 ATTTTTAATT
913 GTTATTAACA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
51 7 0.13
52 15 0.28
53 10 0.19
54 1 0.02
57 5 0.09
58 15 0.28
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (52 bp):
ATTTTTAATTTTAAAATTTTTATTGATTTTATTTAATTTAATTTTTAAACTA
Found at i:1468 original size:36 final size:37
Alignment explanation
Indices: 1421--1494 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
1411 GAGGGTTATG
1421 AAACCCTCAAAAG-CAAACTTCAAAATACATTTAAAA
1 AAACCCTCAAAAGACAAACTTCAAAATACATTTAAAA
* *
1457 AAACCTTCAAAAGACAACCTTCAAAATACATTTAAAA
1 AAACCCTCAAAAGACAAACTTCAAAATACATTTAAAA
1494 A
1 A
1495 TCAAAGATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 12 0.34
37 23 0.66
ACGTcount: A:0.55, C:0.22, G:0.03, T:0.20
Consensus pattern (37 bp):
AAACCCTCAAAAGACAAACTTCAAAATACATTTAAAA
Found at i:5753 original size:17 final size:18
Alignment explanation
Indices: 5733--5767 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5723 GATTAAATCA
5733 TAAAA-TTTAATAAAAAT
1 TAAAACTTTAATAAAAAT
5750 TAAAATCTTTAATAAAAA
1 TAAAA-CTTTAATAAAAA
5768 CATTCAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
19 11 0.69
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAACTTTAATAAAAAT
Found at i:6527 original size:15 final size:15
Alignment explanation
Indices: 6509--6553 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
6499 TTATTATATT
6509 TTATTTAAATTATAA
1 TTATTTAAATTATAA
6524 TTATTT-AATTCATAA
1 TTATTTAAATT-ATAA
6539 -TA-TTAAATT-TAA
1 TTATTTAAATTATAA
6551 TTA
1 TTA
6554 AAAATTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 3 0.11
13 4 0.15
14 10 0.37
15 10 0.37
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATTTAAATTATAA
Found at i:7370 original size:23 final size:25
Alignment explanation
Indices: 7332--7379 Score: 82
Period size: 23 Copynumber: 2.0 Consensus size: 25
7322 GTGAATACTA
7332 ACCGTTTGATTATGTCAGTATTTTG
1 ACCGTTTGATTATGTCAGTATTTTG
7357 ACCG-TTGA-TATGTCAGTATTTTG
1 ACCGTTTGATTATGTCAGTATTTTG
7380 GGATTAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 15 0.65
24 4 0.17
25 4 0.17
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.46
Consensus pattern (25 bp):
ACCGTTTGATTATGTCAGTATTTTG
Found at i:7569 original size:15 final size:15
Alignment explanation
Indices: 7535--7573 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
7525 AGTAATTGTG
*
7535 ATTAATAATAATTTT
1 ATTAATAATAAATTT
*
7550 A-TAATTATAAATTT
1 ATTAATAATAAATTT
7564 ATTAATAATA
1 ATTAATAATA
7574 TTTCCTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTAATAATAAATTT
Found at i:13715 original size:2 final size:2
Alignment explanation
Indices: 13705--13737 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
13695 CCTTTTTTTT
*
13705 TA TA AA 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 TA TA TA T
13738 TGAAGCTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 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):
TA
Found at i:15661 original size:2 final size:2
Alignment explanation
Indices: 15654--15678 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15644 TCATTTCCAT
15654 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
15679 TTAAAAAACT
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:21516 original size:154 final size:155
Alignment explanation
Indices: 21356--21637 Score: 347
Period size: 155 Copynumber: 1.8 Consensus size: 155
21346 TTAAAAAAAA
* * * **
21356 TTAACTTCAAAGTTTTGAAAA-TTATGTTTCGTACCTGACAG-AAAACCA-GGGATATGAAAGGT
1 TTAACTTCAAA-TTTT-AAAAGTTACGTTTCGCACCTAACAGAAAAACCAGGGGATACAAAAGGT
* * *
21418 ATTAAAATTTTTCATATCCCTAC-AGAAAATCATAGAAATAAGAAAACATGACTCGAGTGAGCAT
64 ATTAAAAATTTTCATACCCCTACGA-AAAACCATAGAAATAAGAAAACATGACTCGAGTGAGCAT
21482 AGCCGACCACGTTTTTTTTTTTTTTAAT
128 AGCCGACCACGTTTTTTTTTTTTTTAAT
* * * *
21510 TTAACTTCTAATTTTAAAAGTTACGTTTCGCACCTAACGGAAAAAGCAGGGGATACAAAAGGTGT
1 TTAACTTCAAATTTTAAAAGTTACGTTTCGCACCTAACAGAAAAACCAGGGGATACAAAAGGTAT
* * * * * *
21575 TAAAAATTTTCATACCCCTACGAAAAACCATGGGAATATGAAAGCATGACTTGAGTGGGCATA
66 TAAAAATTTTCATACCCCTACGAAAAACCATAGAAATAAGAAAACATGACTCGAGTGAGCATA
21638 AAAAGACCAT
Statistics
Matches: 106, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
152 4 0.04
153 20 0.19
154 16 0.15
155 65 0.61
156 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.30
Consensus pattern (155 bp):
TTAACTTCAAATTTTAAAAGTTACGTTTCGCACCTAACAGAAAAACCAGGGGATACAAAAGGTAT
TAAAAATTTTCATACCCCTACGAAAAACCATAGAAATAAGAAAACATGACTCGAGTGAGCATAGC
CGACCACGTTTTTTTTTTTTTTAAT
Found at i:22428 original size:12 final size:12
Alignment explanation
Indices: 22411--22435 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22401 ATGAACATAC
22411 ATGATAATAAAA
1 ATGATAATAAAA
22423 ATGATAATAAAA
1 ATGATAATAAAA
22435 A
1 A
22436 AATGCAACTA
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
ATGATAATAAAA
Found at i:22492 original size:109 final size:111
Alignment explanation
Indices: 22307--22522 Score: 391
Period size: 109 Copynumber: 2.0 Consensus size: 111
22297 TCATGAGGCA
22307 AAAAATGATAAATAAAAAAAAATGCAACTAACACCATATACAAGCTAACAAATCACATTCCTTCT
1 AAAAATGATAAAT-AAAAAAAATGCAACTAACACCATATACAAGCTAACAAATCACATTCCTTCT
22372 TCACATAATTAAATAAACTTGAAAACATGATGAACATACATGATAAT
65 TCACATAATTAAATAAACTTGAAAACATGATGAACATACATGATAAT
* *
22419 AAAAATGAT-AAT-AAAAAAATGCAACTAACACCATATATAAGCTGACAAATCACATTCCTTCTT
1 AAAAATGATAAATAAAAAAAATGCAACTAACACCATATACAAGCTAACAAATCACATTCCTTCTT
22482 CACATAATTAAATAAACTTGAAAACATGATGAACATACATG
66 CACATAATTAAATAAACTTGAAAACATGATGAACATACATG
22523 CTGATATATA
Statistics
Matches: 102, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
109 90 0.88
111 3 0.03
112 9 0.09
ACGTcount: A:0.51, C:0.17, G:0.07, T:0.25
Consensus pattern (111 bp):
AAAAATGATAAATAAAAAAAATGCAACTAACACCATATACAAGCTAACAAATCACATTCCTTCTT
CACATAATTAAATAAACTTGAAAACATGATGAACATACATGATAAT
Found at i:24201 original size:43 final size:43
Alignment explanation
Indices: 23527--24508 Score: 902
Period size: 42 Copynumber: 23.0 Consensus size: 43
23517 AGGCAGTATT
* *
23527 CAGGGTTAAAGCCGACAGGCAGACTTAGGGA-AGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * * * *
23569 CAGGGTCAAAGCTGACAAGCAGATTGAGAGATAGAAAAGTCTT
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * *
23612 CGGGGTCAAAGCCAATAGGCAGACTCAGGGA-AGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * * *
23654 AAGAGTTAAAGCCGACAGGCAGACTAAGGGATAAGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * *
23697 CAGGGTCAAAGCCAACAGACAGACTAAGGG-TAGAAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * *
23739 TAGGGTCAAAGCCGATAGGCAGACTTAGAGA-AGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * *
23781 CAGGATCAAAGCCGACAAGCAGAGTGAGGGA-AAGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * ** * * *
23823 TAGAGTCAAAGTTGACAGGCAAACTAAGGG-TAGAAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * * *
23865 CAGGATCAAAGTCAATAGGCAGACTAAGGG-TAGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
** * * * *
23907 CAGAATCAAAGCCGACAAGCAGACTTA-GGAAAGGAAAGTTTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * * *
23949 TAGGGTCAAAGCCGATAGACAGACTGAGGGA-AGAAAAGTCTT
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * *
23991 CAGAGTCAAAGCCGACAGGCAGACTGAGGGA-AGAAAAGTCTT
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* *
24033 CAGGG-CAAAGCTGACAGGCAGACTGAGGG-TAGGAAAGTATC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* *
24074 CAAGGTCAAAGCCGACAGGCAGACTGA-GGATA-GAGAAGTCTT
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGA-AAGTCTC
* * * * * *
24116 TAGGGTCAAAACCGATATGAAGATTGAGGGATAGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* *
24159 CAGGGTCAAAGCCAACAGGCAGATTGAGGGATAGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * *
24202 TAAGGTCAAAGCCGATAGACAGACTGAGGGATAGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* **
24245 CAAGGTCAAAGCCGACAAACAGACTAAAAGATAGGAAAGATAGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACT----G--AGG---GATAGGAAAGTCTC
* * * * *
24297 CATGGTCAAAGCCGACAGGCAGAATAAGGGATAAGAAAGTATC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* *
24340 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAATCTA
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * *
24383 TAGGGTCAAAGTCGATAGGCAGACTAAGGGA-AGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
* * * ** *
24425 TAGGGTCAAAGCCGATAGGTCA-ACTAATTGA-AGAAAAGTCTC
1 CAGGGTCAAAGCCGACAGG-CAGACTGAGGGATAGGAAAGTCTC
* *
24467 CAGGGTCAAAGCCGACAGGCAGACTAAGGGAT-GAAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
24509 TAGAAGTTTA
Statistics
Matches: 767, Mismatches: 149, Indels: 48
0.80 0.15 0.05
Matches are distributed among these distances:
41 43 0.06
42 426 0.56
43 254 0.33
44 2 0.00
46 3 0.00
47 1 0.00
49 3 0.00
52 35 0.05
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.15
Consensus pattern (43 bp):
CAGGGTCAAAGCCGACAGGCAGACTGAGGGATAGGAAAGTCTC
Found at i:24335 original size:52 final size:52
Alignment explanation
Indices: 24231--24335 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 52
24221 CAGACTGAGG
* *
24231 GATAGGAAAGTCTCCAAGGTCAAAGCCGACAAACAGACTAAAAGATAGGAAA
1 GATAGGAAAGTCTCCAAGGTCAAAGCCGACAAACAGAATAAAAGATAAGAAA
* ** **
24283 GATAGGAAAGTCTCCATGGTCAAAGCCGACAGGCAGAATAAGGGATAAGAAA
1 GATAGGAAAGTCTCCAAGGTCAAAGCCGACAAACAGAATAAAAGATAAGAAA
24335 G
1 G
24336 TATCCAGGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.45, C:0.16, G:0.27, T:0.12
Consensus pattern (52 bp):
GATAGGAAAGTCTCCAAGGTCAAAGCCGACAAACAGAATAAAAGATAAGAAA
Found at i:25542 original size:15 final size:15
Alignment explanation
Indices: 25522--25551 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25512 TTCATTCAAT
*
25522 TTTTTTGTTTTTTTA
1 TTTTTTATTTTTTTA
25537 TTTTTTATTTTTTTA
1 TTTTTTATTTTTTTA
25552 ATGCATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (15 bp):
TTTTTTATTTTTTTA
Found at i:32792 original size:13 final size:13
Alignment explanation
Indices: 32774--32798 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32764 AAGCAAATAT
32774 TGATGAATGAAAA
1 TGATGAATGAAAA
32787 TGATGAATGAAA
1 TGATGAATGAAA
32799 GCCATGAATA
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:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (13 bp):
TGATGAATGAAAA
Found at i:35348 original size:122 final size:121
Alignment explanation
Indices: 35132--35379 Score: 478
Period size: 122 Copynumber: 2.0 Consensus size: 121
35122 ACTAAGTTAG
35132 TATATCTTAAGAAACATATAAGTAAATTAGCAAAAGATGTAAAAAAATGTTTACGTGTCCTTAAT
1 TATATCTTAAGAAACATATAAGTAAATTAGCAAAAGATGTAAAAAAATGTTTACGTGTCCTTAAT
35197 ATCGGTGATACCTAAAGCAAAGGTACGACATTGACAAGGGCGTTGATAGGGTCTAC
66 ATCGGTGATACCTAAAGCAAAGGTACGACATTGACAAGGGCGTTGATAGGGTCTAC
35253 TATATCTTAAGAAACATATAAGTAAATTAGCAAAAGATGTAAAAACAATGTTTACGTGTCCTTAA
1 TATATCTTAAGAAACATATAAGTAAATTAGCAAAAGATGTAAAAA-AATGTTTACGTGTCCTTAA
*
35318 TATTGGTGATACCTAAAGCAAAGGTACGACATTGACAAGGGCGTTGATAGGGTCTAC
65 TATCGGTGATACCTAAAGCAAAGGTACGACATTGACAAGGGCGTTGATAGGGTCTAC
35375 TATAT
1 TATAT
35380 GTGGTTAGGG
Statistics
Matches: 125, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
121 45 0.36
122 80 0.64
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (121 bp):
TATATCTTAAGAAACATATAAGTAAATTAGCAAAAGATGTAAAAAAATGTTTACGTGTCCTTAAT
ATCGGTGATACCTAAAGCAAAGGTACGACATTGACAAGGGCGTTGATAGGGTCTAC
Found at i:41627 original size:38 final size:38
Alignment explanation
Indices: 41530--41628 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 38
41520 TAAAGTTTAG
* * * * *
41530 TATTAATTAAAATATAAAAGATATGATTAATGTATAAAT
1 TATTTATT-AAATTTAAAAAATATCAATAATGTATAAAT
* *
41569 TTTTTATTAAATTTTGAAAAATATCAATAAT-TATAAAT
1 TATTTATTAAA-TTTAAAAAATATCAATAATGTATAAAT
41607 TATTTATTAGAATTTAAAAAAT
1 TATTTATTA-AATTTAAAAAAT
41629 GTGATTAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
38 27 0.55
39 22 0.45
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (38 bp):
TATTTATTAAATTTAAAAAATATCAATAATGTATAAAT
Found at i:41717 original size:22 final size:24
Alignment explanation
Indices: 41691--41738 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
41681 AAAATTTATT
*
41691 ATAATTTTTAA-TAAA-TTAAAAA
1 ATAATATTTAATTAAATTTAAAAA
41713 ATAATATTTAATTAAATTTAAAAA
1 ATAATATTTAATTAAATTTAAAAA
41737 AT
1 AT
41739 TTATATTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.43
23 4 0.17
24 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATAATATTTAATTAAATTTAAAAA
Found at i:41766 original size:20 final size:19
Alignment explanation
Indices: 41715--41766 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
41705 ATTAAAAAAT
41715 AATATTTAATTAAATTTAA
1 AATATTTAATTAAATTTAA
*
41734 AAAATTTATATTAACATATTAA
1 AATATTTA-ATTAA-AT-TTAA
41756 AATA-TTAATTA
1 AATATTTAATTA
41767 TTATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 5 0.18
22 7 0.25
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATTTAATTAAATTTAA
Found at i:41901 original size:13 final size:13
Alignment explanation
Indices: 41883--41920 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
41873 AAACAGAATA
41883 ATTAATTTAATTT
1 ATTAATTTAATTT
*
41896 ATTAATGTAAATTT
1 ATTAAT-TTAATTT
41910 -TTAATTTAATT
1 ATTAATTTAATT
41921 AAATATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 5 0.23
13 11 0.50
14 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
ATTAATTTAATTT
Found at i:41933 original size:22 final size:21
Alignment explanation
Indices: 41883--41950 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 21
41873 AAACAGAATA
41883 ATTAA-TTTAATTTATT-AAT
1 ATTAATTTTAATTTATTAAAT
* *
41902 GTAAATTTTTAATTTAATTAAAT
1 ATTAA-TTTTAATTT-ATTAAAT
* *
41925 ATTAATTTTTATTTTATTAAAA
1 ATTAA-TTTTAATTTATTAAAT
41947 ATTA
1 ATTA
41951 TAATAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
19 3 0.08
21 8 0.21
22 13 0.33
23 15 0.38
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (21 bp):
ATTAATTTTAATTTATTAAAT
Found at i:42128 original size:125 final size:122
Alignment explanation
Indices: 41842--42185 Score: 401
Period size: 128 Copynumber: 2.8 Consensus size: 122
41832 ATTTGTGACT
* *
41842 TTTTTTAATTTAAAATGTTTTAATTTTTAAAAAACAGAATAATT-AA-TTTAATTTATTAATGTA
1 TTTTTT-ATTTAAAAT-TTTTTA-TTTTAAAAAACATAATAATTAAATTTTAATTTATTAATGTA
* * * *
41905 A-ATTTTTAATTTAATTAAATATTAATTTTTATTTTATTAAAAATTATAATAAAAAACTTT
63 ATTTTTTTAATTTAATTAAATATTATTTTTTATTTTATTAAAAATAATAATAAAAAAC-TC
41965 TTTTTTATTTTAAAA-TTTTTATGTTTATAAAAACATAATAATGTAAGATTTTAATTTATTAATG
1 TTTTTTA-TTTAAAATTTTTTAT-TTTA-AAAAACATAATAAT-TAA-ATTTTAATTTATTAATG
* * * * *
42029 TAATTTTTTTAAACTCAATTAAATGTTATTTTTTATTTTATTAAAAATAATAATAATAAGC-C
61 TAATTTTTTT-AATTTAATTAAATATTATTTTTTATTTTATTAAAAATAATAATAAAAAACTC
* * * *
42091 TTTTTTATTTAAAATTTTTTATTTTACAAAAATATAATAATTAATATTTAAATTTGTTAATCTGA
1 TTTTTTATTTAAAATTTTTTATTTTA-AAAAACATAATAATTAA-ATTTTAATTTATTAATGT-A
42156 ATTTTTTTAATTTAATTAAATATTATTTTT
63 ATTTTTTTAATTTAATTAAATATTATTTTT
42186 ATTAAAAATA
Statistics
Matches: 190, Mismatches: 20, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
120 1 0.01
121 9 0.05
122 14 0.07
123 14 0.07
124 38 0.20
125 34 0.18
126 32 0.17
127 5 0.03
128 43 0.23
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (122 bp):
TTTTTTATTTAAAATTTTTTATTTTAAAAAACATAATAATTAAATTTTAATTTATTAATGTAATT
TTTTTAATTTAATTAAATATTATTTTTTATTTTATTAAAAATAATAATAAAAAACTC
Found at i:42626 original size:18 final size:17
Alignment explanation
Indices: 42600--42652 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
42590 AATTTGTTAA
42600 ATTTTTTATACTTAATC
1 ATTTTTTATACTTAATC
* * *
42617 CTTATTTTATATTTAATAA
1 ATT-TTTTATACTTAAT-C
42636 ATTTTTTATACTTAATC
1 ATTTTTTATACTTAATC
42653 TTCTTATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
17 2 0.07
18 24 0.86
19 2 0.07
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTTTATACTTAATC
Found at i:42679 original size:38 final size:36
Alignment explanation
Indices: 42597--42668 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
42587 TTGAATTTGT
42597 TAAATTTTTTATACTTAATCCTTATTTTATATTTAA
1 TAAATTTTTTATACTTAATCCTTATTTTATATTTAA
*
42633 TAAATTTTTTATACTTAAT-CTTCTTATTAT-TTTAA
1 TAAATTTTTTATACTTAATCCTTATT-TTATATTTAA
42668 T
1 T
42669 TTAAAATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 11 0.32
36 23 0.68
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (36 bp):
TAAATTTTTTATACTTAATCCTTATTTTATATTTAA
Found at i:43396 original size:22 final size:22
Alignment explanation
Indices: 43354--43397 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
43344 AAAATATTTA
*
43354 ATTTTTAGTTGATTAATAAATT
1 ATTTTTAGTTGATTAACAAATT
43376 ATTTTTA-TTGATTAGACAAATT
1 ATTTTTAGTTGATTA-ACAAATT
43398 TTTATCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.52
Consensus pattern (22 bp):
ATTTTTAGTTGATTAACAAATT
Found at i:44028 original size:19 final size:20
Alignment explanation
Indices: 44006--44045 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43996 AGTATCATTT
44006 AAATTAA-ATCAGATCAACA
1 AAATTAACATCAGATCAACA
**
44025 AAATTAACATCTTATCAACA
1 AAATTAACATCAGATCAACA
44045 A
1 A
44046 GGTCAACATC
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:0.55, C:0.17, G:0.03, T:0.25
Consensus pattern (20 bp):
AAATTAACATCAGATCAACA
Found at i:44043 original size:20 final size:20
Alignment explanation
Indices: 44018--44066 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
44008 ATTAAATCAG
*
44018 ATCAACAAAATTAACATCTT
1 ATCAACAAAATCAACATCTT
**
44038 ATCAACAAGGTCAACATCTT
1 ATCAACAAAATCAACATCTT
*
44058 ATTAACAAA
1 ATCAACAAA
44067 GCCCATATCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (20 bp):
ATCAACAAAATCAACATCTT
Found at i:44204 original size:29 final size:28
Alignment explanation
Indices: 44162--44224 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
44152 TTAAATTAAA
* *
44162 ATAATAAGATAATTAAAT-TTATATAAATT
1 ATAATAAAAAAATTAAATCTTA-A-AAATT
44191 ATAATAAAAAAATTAAATCTTAAAAATT
1 ATAATAAAAAAATTAAATCTTAAAAATT
44219 -TAATAA
1 ATAATAA
44225 GGATAGAGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 6 0.19
28 5 0.16
29 17 0.55
30 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (28 bp):
ATAATAAAAAAATTAAATCTTAAAAATT
Found at i:45669 original size:18 final size:16
Alignment explanation
Indices: 45634--45668 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
45624 TCATAAAAAA
45634 ATAAATTTTTTATAAT
1 ATAAATTTTTTATAAT
* *
45650 ATAAATATTTTATATT
1 ATAAATTTTTTATAAT
45666 ATA
1 ATA
45669 TTAAAAGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATAAATTTTTTATAAT
Found at i:52961 original size:18 final size:17
Alignment explanation
Indices: 52921--52963 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
52911 TTATTTAAAT
*
52921 TTATTTTTCTTGTTTGA
1 TTATTTTTCTTATTTGA
*
52938 TATATTTTTCTTCATTTTA
1 T-TATTTTTCTT-ATTTGA
52957 TTATTTT
1 TTATTTT
52964 AACTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 16 0.73
19 5 0.23
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.72
Consensus pattern (17 bp):
TTATTTTTCTTATTTGA
Found at i:53130 original size:2 final size:2
Alignment explanation
Indices: 53123--53157 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
53113 CTTTTAAAAC
*
53123 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53158 TATTCAACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54245 original size:7 final size:7
Alignment explanation
Indices: 54233--54257 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54223 AAGTAGAAAG
54233 CAAAGTT
1 CAAAGTT
54240 CAAAGTT
1 CAAAGTT
54247 CAAAGTT
1 CAAAGTT
54254 CAAA
1 CAAA
54258 CTTTAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (7 bp):
CAAAGTT
Found at i:62877 original size:36 final size:39
Alignment explanation
Indices: 62799--62879 Score: 107
Period size: 36 Copynumber: 2.2 Consensus size: 39
62789 ATTTTTAATA
62799 AATTAATAATTTATATTATATAAATATTTAAATATTATT
1 AATTAATAATTTATATTATATAAATATTTAAATATTATT
* *
62838 AATTTATAATTTA-ATT-T-TAAATATTTAATTATTCA-T
1 AATTAATAATTTATATTATATAAATATTTAAATATT-ATT
62874 AATTAA
1 AATTAA
62880 GATTTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
36 21 0.55
37 2 0.05
38 3 0.08
39 12 0.32
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (39 bp):
AATTAATAATTTATATTATATAAATATTTAAATATTATT
Found at i:63748 original size:13 final size:13
Alignment explanation
Indices: 63730--63754 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63720 AATCTCGAAT
63730 TTAATTATTTTAG
1 TTAATTATTTTAG
63743 TTAATTATTTTA
1 TTAATTATTTTA
63755 ATTTCATTTT
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTAATTATTTTAG
Found at i:63775 original size:22 final size:23
Alignment explanation
Indices: 63729--63784 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
63719 TAATCTCGAA
*
63729 TTTAA-TTATTTTAGTTAATTAT
1 TTTAATTTATTTTAGTAAATTAT
63751 TTTAATTTCATTTT-GTAAATT-T
1 TTTAATTT-ATTTTAGTAAATTAT
63773 TTTAGATTTATT
1 TTTA-ATTTATT
63785 AGATAGATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 13 0.43
23 12 0.40
24 5 0.17
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (23 bp):
TTTAATTTATTTTAGTAAATTAT
Found at i:63781 original size:23 final size:24
Alignment explanation
Indices: 63729--63781 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
63719 TAATCTCGAA
*
63729 TTTAA-TT-ATTTTAGTTAATTAT
1 TTTAATTTCATTTTAGTAAATTAT
63751 TTTAATTTCATTTT-GTAAATT-T
1 TTTAATTTCATTTTAGTAAATTAT
63773 TTTAGATTT
1 TTTA-ATTT
63782 ATTAGATAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 10 0.37
23 12 0.44
24 5 0.19
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (24 bp):
TTTAATTTCATTTTAGTAAATTAT
Found at i:64243 original size:22 final size:22
Alignment explanation
Indices: 64210--64254 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
64200 CTTATCATTT
64210 TTAAAATATTATATT-TAATAAA
1 TTAAAATATTATATTAT-ATAAA
64232 TTAATAAT-TTATATTATATAAA
1 TTAA-AATATTATATTATATAAA
64254 T
1 T
64255 ATTTAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAAAATATTATATTATATAAA
Found at i:64308 original size:36 final size:39
Alignment explanation
Indices: 64230--64310 Score: 98
Period size: 36 Copynumber: 2.2 Consensus size: 39
64220 ATATTTAATA
*
64230 AATTAATAATTTATATTATATAAATATTTAAATATTATT
1 AATTAATAATTTATATTATATAAATATTTAAATATTAGT
* *
64269 AATTTATAATTTA-ATT-T-TAAATATTT-AATCATTCGT
1 AATTAATAATTTATATTATATAAATATTTAAAT-ATTAGT
64305 AATTAA
1 AATTAA
64311 GATTTTAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
35 3 0.08
36 18 0.49
37 1 0.03
38 3 0.08
39 12 0.32
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (39 bp):
AATTAATAATTTATATTATATAAATATTTAAATATTAGT
Found at i:64522 original size:16 final size:16
Alignment explanation
Indices: 64501--64628 Score: 73
Period size: 16 Copynumber: 8.5 Consensus size: 16
64491 AAAATTTTCA
64501 TATTATATTTATATAT
1 TATTATATTTATATAT
*
64517 TA-T-TATTTAT-TAG
1 TATTATATTTATATAT
* *
64530 AATTATATTTAAATTAT
1 TATTATATTTATA-TAT
64547 T-TTATATTTA-AT-T
1 TATTATATTTATATAT
*
64560 TA--ATTTTTA-ATA-
1 TATTATATTTATATAT
*
64572 TATTAATAATT-TATAT
1 TATT-ATATTTATATAT
* *
64588 TATATAAATTTAAATAT
1 TAT-TATATTTATATAT
64605 TATTATATTTATATCA-
1 TATTATATTTATAT-AT
64621 TATTATAT
1 TATTATAT
64629 CATATTTTAT
Statistics
Matches: 85, Mismatches: 13, Indels: 28
0.67 0.10 0.22
Matches are distributed among these distances:
12 10 0.12
13 5 0.06
14 9 0.11
15 15 0.18
16 35 0.41
17 11 0.13
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (16 bp):
TATTATATTTATATAT
Found at i:65075 original size:26 final size:26
Alignment explanation
Indices: 65041--65132 Score: 123
Period size: 26 Copynumber: 3.6 Consensus size: 26
65031 ATGTGTAATA
* *
65041 TAAATACAATATTATGTATACTATTT
1 TAAAAACAATATTATGTATAATATTT
*
65067 TAAAAACAATATTATGTATAAAATTT
1 TAAAAACAATATTATGTATAATATTT
*
65093 TAAATACAATATTATGTATAATATTT
1 TAAAAACAATATTATGTATAATATTT
* *
65119 TTAAATC-ATATTAT
1 TAAAAACAATATTAT
65133 AATATATTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
25 7 0.12
26 51 0.88
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (26 bp):
TAAAAACAATATTATGTATAATATTT
Found at i:65138 original size:26 final size:27
Alignment explanation
Indices: 65041--65144 Score: 108
Period size: 26 Copynumber: 4.0 Consensus size: 27
65031 ATGTGTAATA
* *
65041 TAAATACAATATTATGTATACTA-TTT
1 TAAATACAATATTATATATAATATTTT
* * *
65067 TAAAAACAATATTATGTATAA-AATTT
1 TAAATACAATATTATATATAATATTTT
*
65093 TAAATACAATATTATGTATAATATTTT
1 TAAATACAATATTATATATAATATTTT
*
65120 TAAAT-C-ATATTATAATATATTATTT
1 TAAATACAATATTAT-ATATAATATTT
65145 ATATTATATA
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
25 8 0.12
26 52 0.75
27 9 0.13
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (27 bp):
TAAATACAATATTATATATAATATTTT
Found at i:67762 original size:16 final size:16
Alignment explanation
Indices: 67741--67786 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
67731 AGTCAATCTC
67741 AAATCATTTCAAATTT
1 AAATCATTTCAAATTT
* *
67757 AGATCATTT-TAATTT
1 AAATCATTTCAAATTT
67772 AAATCATTTCAAATT
1 AAATCATTTCAAATT
67787 ATGTCATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (16 bp):
AAATCATTTCAAATTT
Found at i:67796 original size:30 final size:31
Alignment explanation
Indices: 67741--67798 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
67731 AGTCAATCTC
67741 AAATCATTTCAAATTTAGATCATTTTAATTT
1 AAATCATTTCAAATTTAGATCATTTTAATTT
67772 AAATCATTTCAAA-TTATG-TCATTTTAA
1 AAATCATTTCAAATTTA-GATCATTTTAA
67799 ATATGAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (31 bp):
AAATCATTTCAAATTTAGATCATTTTAATTT
Found at i:67800 original size:15 final size:15
Alignment explanation
Indices: 67741--67800 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
67731 AGTCAATCTC
*
67741 AAATCATTTCAAATTT
1 AAATCATTTTAAA-TT
* *
67757 AGATCATTTTAATTT
1 AAATCATTTTAAATT
*
67772 AAATCATTTCAAATT
1 AAATCATTTTAAATT
**
67787 ATGTCATTTTAAAT
1 AAATCATTTTAAAT
67801 ATGAATTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
15 25 0.71
16 10 0.29
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (15 bp):
AAATCATTTTAAATT
Found at i:68319 original size:16 final size:16
Alignment explanation
Indices: 68295--68358 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
68285 ATTTTATACT
68295 TTAAT-TTTTTTATTA
1 TTAATATTTTTTATTA
68310 TTAATATTTTTTATTA
1 TTAATATTTTTTATTA
*
68326 ATAATTATTATATTTAATTA
1 TTAA-TATT-T-TTT-ATTA
*
68346 -TAATATTTATTAT
1 TTAATATTTTTTAT
68359 ATTTATACCT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
15 7 0.17
16 15 0.36
17 5 0.12
18 5 0.12
19 6 0.14
20 4 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAATATTTTTTATTA
Found at i:68349 original size:22 final size:23
Alignment explanation
Indices: 68306--68363 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
68296 TAATTTTTTT
*
68306 ATTATTAATATTT-TTTATTAATA
1 ATTATT-ATATTTAATTATTAATA
68329 ATTATTATATTTAATTA-TAATA
1 ATTATTATATTTAATTATTAATA
*
68351 TTTATTATATTTA
1 ATTATTATATTTA
68364 TACCTACAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 23 0.72
23 9 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTATTATATTTAATTATTAATA
Found at i:69097 original size:2 final size:2
Alignment explanation
Indices: 69090--69138 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
69080 GTGTCCAAAG
69090 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
69132 TA TA TA T
1 TA TA TA T
69139 CTGCAACTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:69510 original size:192 final size:190
Alignment explanation
Indices: 69185--69565 Score: 604
Period size: 192 Copynumber: 2.0 Consensus size: 190
69175 ATTGTAGCTA
69185 TCAAAGTGCAGAAAATAATAGCAATATATGCCCCACAATCCTTTTTTTTTCCTTATTTCAGCCTT
1 TCAAAGTGCAGAAAATAATAGCAATATATGCCCCACAATCCTTTTTTTTTCCTTATTTCAGCCTT
** * * * *
69250 AAATGCAATGATCATTCAAATCGAAGTAAAGGACACGATTGCGTAGAACTTTAGACTTTGAAAGA
66 AAATGCAATGATCATTCAAATAAAAGTAAAGAACACGATAGCATAAAACTTTAGACTTTGAAAGA
*
69315 TGACTTTATGCTAGCATGGCA-TAGAAATAACTAAAAGAGCCTCAAAATTAATTCTACATG
131 TGACTTTATGCTAGCATGGCATTA-AAATAACTAAAAGAACCTCAAAATTAATTCTACATG
* * *
69375 TCAAAGTGCAGAAAATAATAGCATTATATGCCTCCCCAAT-CTTTTTTTTTTCTATATTTCAGCC
1 TCAAAGTGCAGAAAATAATAGCAATATATGCC-CCACAATCCTTTTTTTTTCCT-TATTTCAGCC
*
69439 TTAAATGCAATGGTCATTCAAATTAAAAGTAAAGAACACGATAGCATAAAACTTTAGACTTTGAA
64 TTAAATGCAATGATCATTCAAA-TAAAAGTAAAGAACACGATAGCATAAAACTTTAGACTTTGAA
*
69504 AGATGACTTTATGCTAGCATGGCATTAAAATAACTAAAAGAACTTCAAAATTAATTCTACAT
128 AGATGACTTTATGCTAGCATGGCATTAAAATAACTAAAAGAACCTCAAAATTAATTCTACAT
69566 CTTCACCGAA
Statistics
Matches: 175, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
190 43 0.25
191 37 0.21
192 93 0.53
193 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (190 bp):
TCAAAGTGCAGAAAATAATAGCAATATATGCCCCACAATCCTTTTTTTTTCCTTATTTCAGCCTT
AAATGCAATGATCATTCAAATAAAAGTAAAGAACACGATAGCATAAAACTTTAGACTTTGAAAGA
TGACTTTATGCTAGCATGGCATTAAAATAACTAAAAGAACCTCAAAATTAATTCTACATG
Found at i:74528 original size:53 final size:54
Alignment explanation
Indices: 74432--74544 Score: 192
Period size: 53 Copynumber: 2.1 Consensus size: 54
74422 ATAAGAACAA
74432 AATTAATAGTTTTAAAAAACATTAATCTTAAAAGAATACAAATTTATTTATTTT
1 AATTAATAGTTTTAAAAAACATTAATCTTAAAAGAATACAAATTTATTTATTTT
* * *
74486 AATTAATAGTTTTAAAAAATATTGATCTT-AAAGAATATAAATTTATTTATTTT
1 AATTAATAGTTTTAAAAAACATTAATCTTAAAAGAATACAAATTTATTTATTTT
74539 AATTAA
1 AATTAA
74545 AACTCATACG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 29 0.52
54 27 0.48
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (54 bp):
AATTAATAGTTTTAAAAAACATTAATCTTAAAAGAATACAAATTTATTTATTTT
Found at i:74960 original size:10 final size:10
Alignment explanation
Indices: 74945--74999 Score: 60
Period size: 10 Copynumber: 5.4 Consensus size: 10
74935 TTTTATGTAT
74945 AATTTATTAA
1 AATTTATTAA
74955 AATTTATTAAA
1 AATTTATT-AA
74966 AGATTT-TTAA
1 A-ATTTATTAA
*
74976 AATTTAATAA
1 AATTTATTAA
74986 AATATT-TTAA
1 AAT-TTATTAA
74996 AATT
1 AATT
75000 ATTTATCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 5 0.13
10 23 0.59
11 7 0.18
12 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (10 bp):
AATTTATTAA
Found at i:74995 original size:20 final size:21
Alignment explanation
Indices: 74946--74999 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
74936 TTTATGTATA
*
74946 ATTTATTAAAATTTATTAAAAG
1 ATTT-TTAAAATTTAATAAAAG
*
74968 ATTTTTAAAATTTAATAAAAT
1 ATTTTTAAAATTTAATAAAAG
74989 A-TTTTAAAATT
1 ATTTTTAAAATT
75000 ATTTATCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 10 0.33
21 16 0.53
22 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATTTTTAAAATTTAATAAAAG
Found at i:75469 original size:17 final size:17
Alignment explanation
Indices: 75447--75490 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 17
75437 GTTCACATTT
75447 TTATAATTCACGACACA
1 TTATAATTCACGACACA
*
75464 TTATAATTTTTACGACACA
1 TTATAA--TTCACGACACA
75483 TTATAATT
1 TTATAATT
75491 TTTAATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.33
19 16 0.67
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.41
Consensus pattern (17 bp):
TTATAATTCACGACACA
Found at i:75480 original size:19 final size:19
Alignment explanation
Indices: 75456--75494 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
75446 TTTATAATTC
75456 ACGACACATTATAATTTTT
1 ACGACACATTATAATTTTT
75475 ACGACACATTATAATTTTT
1 ACGACACATTATAATTTTT
75494 A
1 A
75495 ATTTATTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.41
Consensus pattern (19 bp):
ACGACACATTATAATTTTT
Found at i:75962 original size:40 final size:39
Alignment explanation
Indices: 75886--75963 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 39
75876 AATAAAATCT
* * *
75886 AAAAATACTTTGAAAAATTGTAATAAGTTTTATTCATTC
1 AAAAATACTCTAAAAAATTCTAATAAGTTTTATTCATTC
*
75925 AAAAATACTCTAAAAACATTCTTATAAGTATTT-TTCATT
1 AAAAATACTCTAAAAA-ATTCTAATAAGT-TTTATTCATT
75964 ATTAAATGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 14 0.42
40 16 0.48
41 3 0.09
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (39 bp):
AAAAATACTCTAAAAAATTCTAATAAGTTTTATTCATTC
Found at i:76201 original size:16 final size:16
Alignment explanation
Indices: 76148--76211 Score: 62
Period size: 16 Copynumber: 4.0 Consensus size: 16
76138 TATTCTGCTT
76148 TGTATCGATACAT---
1 TGTATCGATACATGCA
*
76161 TGTATTGATACATGTTCA
1 TGTATCGATACATG--CA
76179 TTGTATCGATACATGCA
1 -TGTATCGATACATGCA
*
76196 TGTATCAATACATGCA
1 TGTATCGATACATGCA
76212 CAATTATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
13 12 0.29
16 15 0.36
17 2 0.05
19 13 0.31
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (16 bp):
TGTATCGATACATGCA
Found at i:83814 original size:6 final size:6
Alignment explanation
Indices: 83790--83838 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
83780 GTGGATGGGG
* * * * *
83790 GGTGAT GGTGAG GGGGAA GGTGAA GGTGAA TGTGAA GGTGAA GGGGAA
1 GGTGAA GGTGAA GGTGAA GGTGAA GGTGAA GGTGAA GGTGAA GGTGAA
83838 G
1 G
83839 CAGAGAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.29, C:0.00, G:0.55, T:0.16
Consensus pattern (6 bp):
GGTGAA
Found at i:85935 original size:35 final size:35
Alignment explanation
Indices: 85890--86010 Score: 113
Period size: 35 Copynumber: 3.4 Consensus size: 35
85880 ACATGAAAGT
*
85890 ATAAAATAAATATAACTAT-ATACATTTAAATATA
1 ATAAAATAAATATAAATATAATACATTTAAATATA
* * *
85924 ATAAATATAAATAT-ATTGTAATACATATAATAATATA
1 ATAAA-ATAAATATAAATATAATACAT-TTA-AATATA
* * *
85961 ATATAATAAATATAAATATAATTCATTTAAATACA
1 ATAAAATAAATATAAATATAATACATTTAAATATA
*
85996 AT-TAATATAATATAA
1 ATAAAATA-AATATAA
86011 TAATATTAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
34 13 0.18
35 28 0.39
36 12 0.17
37 19 0.26
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (35 bp):
ATAAAATAAATATAAATATAATACATTTAAATATA
Found at i:85951 original size:20 final size:20
Alignment explanation
Indices: 85918--85982 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 20
85908 TATACATTTA
85918 AATATAATAAATATAAATAT
1 AATATAATAAATATAAATAT
* * *
85938 ATTGTAATACATATAATAATAT
1 AATATAATAAATAT-A-AATAT
85960 AATATAATAAATATAAATAT
1 AATATAATAAATATAAATAT
85980 AAT
1 AAT
85983 TCATTTAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 19 0.51
21 2 0.05
22 16 0.43
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
AATATAATAAATATAAATAT
Found at i:85963 original size:5 final size:5
Alignment explanation
Indices: 85918--86012 Score: 63
Period size: 5 Copynumber: 18.8 Consensus size: 5
85908 TATACATTTA
* * *
85918 AATAT AATA- AATAT AAATAT ATTGT AATAC ATATAAT AATAT AATAT
1 AATAT AATAT AATAT -AATAT AATAT AATAT A-AT-AT AATAT AATAT
* * *
85965 AATA- AATAT AAATAT AAT-T CATTT AAATAC AAT-T AATAT AATAT AATA
1 AATAT AATAT -AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AATA
86013 ATATTAATTT
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
4 14 0.20
5 38 0.54
6 16 0.23
7 2 0.03
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:85992 original size:57 final size:57
Alignment explanation
Indices: 85898--86016 Score: 134
Period size: 57 Copynumber: 2.1 Consensus size: 57
85888 GTATAAAATA
* * * * *
85898 AATATAACTATATACATTTAAATATAATAAATATAAATATATTGTAATA-CATATAAT
1 AATATAACTATATAAATATAAATATAATAAATATAAATACAAT-TAATATAATATAAT
** *
85955 AATATAA-TATAATAAATATAAATATAATTCATTTAAATACAATTAATATAATATAAT
1 AATATAACTAT-ATAAATATAAATATAATAAATATAAATACAATTAATATAATATAAT
86012 AATAT
1 AATAT
86017 TAATTTTATT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
56 8 0.15
57 44 0.85
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (57 bp):
AATATAACTATATAAATATAAATATAATAAATATAAATACAATTAATATAATATAAT
Found at i:86455 original size:37 final size:36
Alignment explanation
Indices: 86388--86470 Score: 100
Period size: 37 Copynumber: 2.4 Consensus size: 36
86378 AATTAATATT
* *
86388 TTTATATATA-T-AATTAATTTTTAATTTATAAAAA
1 TTTATATATATTAAATTAAATATTAATTTATAAAAA
*
86422 TTTATATATATTAAATATAAATATTAATTTATAATAA
1 TTTATATATATTAAAT-TAAATATTAATTTATAAAAA
*
86459 TTTTTAT-TATTA
1 TTTATATATATTA
86471 TATTTTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 10 0.24
35 1 0.02
36 8 0.19
37 23 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (36 bp):
TTTATATATATTAAATTAAATATTAATTTATAAAAA
Found at i:86539 original size:21 final size:20
Alignment explanation
Indices: 86503--86544 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
86493 TAAATTTTAC
*
86503 TTAAAAAATTAAAATATAAT
1 TTAAAAAATTAAAATAAAAT
86523 TTAAAAAA-TAATTAATAAAAT
1 TTAAAAAATTAA--AATAAAAT
86544 T
1 T
86545 AATATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 3 0.16
20 8 0.42
21 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TTAAAAAATTAAAATAAAAT
Found at i:86587 original size:73 final size:72
Alignment explanation
Indices: 86498--86635 Score: 231
Period size: 73 Copynumber: 1.9 Consensus size: 72
86488 TCATTTAAAT
*
86498 TTTACTTAAAAAATTAAAATATAATTTAAAAAATAATTAATAAAATTAATATATTATATTAAATT
1 TTTACTAAAAAAATTAAAATATAATTTAAAAAATAATTAATAAAATTAATATATTATATTAAATT
86563 TAATAAG
66 TAATAAG
* * *
86570 TTTACTAAAAAAGATTAAAATATAATTTAAAAAGTAATTAATGAAATTAATTTATTATATTAAAT
1 TTTACTAAAAAA-ATTAAAATATAATTTAAAAAATAATTAATAAAATTAATATATTATATTAAAT
86635 T
65 T
86636 CAACAAATGA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
72 11 0.18
73 50 0.82
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (72 bp):
TTTACTAAAAAAATTAAAATATAATTTAAAAAATAATTAATAAAATTAATATATTATATTAAATT
TAATAAG
Found at i:87080 original size:13 final size:13
Alignment explanation
Indices: 87062--87086 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
87052 AAATAAATGA
87062 AATAAAATTAATT
1 AATAAAATTAATT
87075 AATAAAATTAAT
1 AATAAAATTAAT
87087 ATTATACATA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATAAAATTAATT
Found at i:88500 original size:16 final size:17
Alignment explanation
Indices: 88479--88510 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
88469 ATATTTTTTT
88479 AATATATTTT-TAAAAA
1 AATATATTTTATAAAAA
88495 AATATATTTTATAAAA
1 AATATATTTTATAAAA
88511 TGTAACCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATATTTTATAAAAA
Found at i:93118 original size:167 final size:166
Alignment explanation
Indices: 92883--93285 Score: 517
Period size: 163 Copynumber: 2.4 Consensus size: 166
92873 TGCTATATGT
* * ** *
92883 TATTTAGATACCAATAAATATTGAATATAAATATGTGTTTAATATAGGTAGATATATTTAATATT
1 TATTTAGATACAAATAAATATTGAATATAAATATATGTTTAATATAAATAAATATATTTAATATT
* *
92948 TTTTATATTTTTTTATATATTTAAAATATTATAATTTTATGATTATATTTAAATACATATCATAT
66 TTTTATA-TTTTTTATATATGTAAAATATTATAATTTTATGATTATATTCAAATACATATCATAT
* * **
93013 ATAAATATAAAAAATAAATA-TTTAAAAAATTAAGTAA
130 AT-AACATAAAAAATAAAAATTTTAAAAAATTAAAAAA
* * * *
93050 TATTTAGATACGAATGAATATTGAATATGATTATATGTTTAATATAAATAAATATATTTAATA-T
1 TATTTAGATACAAATAAATATTGAATATAAATATATGTTTAATATAAATAAATATATTTAATATT
* * * *
93114 TTTT-TA-TTTTTATATATGTGAAATATTATAATTTTATGATTATATTCAAATACGTGTTATATA
66 TTTTATATTTTTTATATATGTAAAATATTATAATTTTATGATTATATTCAAATACATATCATATA
*
93177 TAACATAAAAAATAAAAATTTTACAAAATTAAAAAA
131 TAACATAAAAAATAAAAATTTTAAAAAATTAAAAAA
* * * ** * *
93213 TATTTAAATAAAAATAAATATTAAATATAAATATACATTTAATATAAATAAATATATTTTATATA
1 TATTTAGATACAAATAAATATTGAATATAAATATATGTTTAATATAAATAAATATATTTAATATT
93278 TTTTATAT
66 TTTTATAT
93286 ATTTAAAATA
Statistics
Matches: 202, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
162 15 0.07
163 119 0.59
164 4 0.02
165 4 0.02
166 5 0.02
167 55 0.27
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (166 bp):
TATTTAGATACAAATAAATATTGAATATAAATATATGTTTAATATAAATAAATATATTTAATATT
TTTTATATTTTTTATATATGTAAAATATTATAATTTTATGATTATATTCAAATACATATCATATA
TAACATAAAAAATAAAAATTTTAAAAAATTAAAAAA
Found at i:93238 original size:17 final size:17
Alignment explanation
Indices: 93202--93267 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
93192 AAATTTTACA
93202 AAAT-TAAA-AAATATTT
1 AAATATAAATAAATA-TT
*
93218 AAATAAAAATAAATATT
1 AAATATAAATAAATATT
* *
93235 AAATATAAATATACATT
1 AAATATAAATAAATATT
*
93252 TAATATAAATAAATAT
1 AAATATAAATAAATAT
93268 ATTTTATATA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
16 4 0.10
17 32 0.78
18 5 0.12
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATATAAATAAATATT
Found at i:93276 original size:19 final size:20
Alignment explanation
Indices: 93239--93277 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
93229 AATATTAAAT
93239 ATAAATATACATTTAATATAA
1 ATAAATATA-ATTTAATATAA
*
93260 ATAAATAT-ATTTTATATA
1 ATAAATATAATTTAATATA
93278 TTTTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAATATAATTTAATATAA
Found at i:93286 original size:11 final size:9
Alignment explanation
Indices: 93264--93289 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
93254 ATATAAATAA
93264 ATATATTTT
1 ATATATTTT
93273 ATATATTTT
1 ATATATTTT
93282 ATATATTT
1 ATATATTT
93290 AAAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATATATTTT
Found at i:93331 original size:24 final size:24
Alignment explanation
Indices: 93304--93357 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
93294 TATTATAGTT
* *
93304 ATATAATTATATTT-AAATATAAAA
1 ATATAAATAT-TTTAAAAAATAAAA
93328 ATATAAATATTTTAAAAAATAAAA
1 ATATAAATATTTTAAAAAATAAAA
93352 A-ATAAA
1 ATATAAA
93358 ATAGTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
ATATAAATATTTTAAAAAATAAAA
Found at i:93860 original size:23 final size:22
Alignment explanation
Indices: 93834--93880 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
93824 TTAATTATCA
93834 TTAAAAATTAATATTTGATAATT
1 TTAAAAATTAATATTT-ATAATT
** *
93857 TTAAATTTTAATATTTATATTT
1 TTAAAAATTAATATTTATAATT
93879 TT
1 TT
93881 TTTTCAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTAAAAATTAATATTTATAATT
Found at i:100093 original size:2 final size:2
Alignment explanation
Indices: 100086--100131 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
100076 TCAAATTAAG
100086 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
100128 AT AT
1 AT AT
100132 TCTCTTCTCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:106332 original size:35 final size:35
Alignment explanation
Indices: 106286--106388 Score: 111
Period size: 35 Copynumber: 2.8 Consensus size: 35
106276 GCAACAAACA
*
106286 AACAATCAAACAAAAC-AATAATA-TTATCAGCATTG
1 AACAAACAAAC-AAACTAATAATAGTT-TCAGCATTG
* *
106321 AACAAACAAACAATCTAATAATAGTTTCAGTATTG
1 AACAAACAAACAAACTAATAATAGTTTCAGCATTG
106356 AACAAACAAATAAACAAACTAATAATAGTTTCA
1 AACAAAC----AAACAAACTAATAATAGTTTCA
106389 ACTAAAATAA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
34 3 0.05
35 32 0.55
36 2 0.03
39 21 0.36
ACGTcount: A:0.54, C:0.16, G:0.06, T:0.24
Consensus pattern (35 bp):
AACAAACAAACAAACTAATAATAGTTTCAGCATTG
Found at i:106428 original size:25 final size:25
Alignment explanation
Indices: 106367--106444 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 25
106357 ACAAACAAAT
* * *
106367 AAACAAACTAATAATAGTTTCAACTA
1 AAAC-AACCAATAACAGTTTCAACAA
* *
106393 AAATAAGCCAATAACAGTTTCAGCAA
1 AAACAA-CCAATAACAGTTTCAACAA
* *
106419 AAACAACCAATAACAATATCAACAA
1 AAACAACCAATAACAGTTTCAACAA
106444 A
1 A
106445 CATTGTTATT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
25 19 0.45
26 23 0.55
ACGTcount: A:0.56, C:0.19, G:0.05, T:0.19
Consensus pattern (25 bp):
AAACAACCAATAACAGTTTCAACAA
Found at i:106509 original size:54 final size:55
Alignment explanation
Indices: 106426--106533 Score: 139
Period size: 54 Copynumber: 2.0 Consensus size: 55
106416 CAAAAACAAC
* * * *
106426 CAATAACAATATCAACAAACATTGTTATTTCGATTTA-AAACTTTAAACTCTAAAT
1 CAATAACAATATCAACAAACACTATTATTTCAATTTACAAA-TTTAAACCCTAAAT
* *
106481 CAATAAC-ATCTCAACAAACACTATTATTTCAATTTACATATTTAAACCCTAAA
1 CAATAACAATATCAACAAACACTATTATTTCAATTTACAAATTTAAACCCTAAA
106534 ATAAACTAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
54 37 0.80
55 9 0.20
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.33
Consensus pattern (55 bp):
CAATAACAATATCAACAAACACTATTATTTCAATTTACAAATTTAAACCCTAAAT
Found at i:106656 original size:16 final size:16
Alignment explanation
Indices: 106635--106688 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
106625 AGTCAAAAAT
106635 TCGAACCCGAAATTA-C
1 TCGAACCCGAAA-TAGC
106651 TCGAACCCGAAATAGC
1 TCGAACCCGAAATAGC
* *
106667 ACGAACCCGAGATAGC
1 TCGAACCCGAAATAGC
106683 TCGAAC
1 TCGAAC
106689 TCGATAAAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
15 2 0.06
16 32 0.94
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.13
Consensus pattern (16 bp):
TCGAACCCGAAATAGC
Found at i:106737 original size:16 final size:16
Alignment explanation
Indices: 106718--106768 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
106708 AAAAACCCCA
106718 AACCAGAAAGAACCCG
1 AACCAGAAAGAACCCG
*
106734 AACCCGAAAGAACCCG
1 AACCAGAAAGAACCCG
* * *
106750 TACCTGAAAGAACTCG
1 AACCAGAAAGAACCCG
106766 AAC
1 AAC
106769 TTGAGACCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.45, C:0.31, G:0.18, T:0.06
Consensus pattern (16 bp):
AACCAGAAAGAACCCG
Found at i:110019 original size:13 final size:13
Alignment explanation
Indices: 110001--110026 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
109991 AGATTTGAAG
110001 TTTTTTTATTTTA
1 TTTTTTTATTTTA
110014 TTTTTTTATTTTA
1 TTTTTTTATTTTA
110027 ATTGAGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTATTTTA
Found at i:110314 original size:20 final size:18
Alignment explanation
Indices: 110279--110317 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
110269 ATTATTTGAA
110279 AAATTAATTTTATATAAT
1 AAATTAATTTTATATAAT
110297 AAATTAATTTTATAT-AT
1 AAATTAATTTTATATAAT
110314 AAAT
1 AAAT
110318 ATAGATTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTAATTTTATATAAT
Found at i:111487 original size:3 final size:3
Alignment explanation
Indices: 111479--111552 Score: 100
Period size: 3 Copynumber: 25.7 Consensus size: 3
111469 AAGCTAGCAT
*
111479 TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TC
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
111525 TTC TTA -AA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
111553 GTTTTTTTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
2 4 0.06
3 60 0.94
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:111931 original size:3 final size:3
Alignment explanation
Indices: 111923--111948 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
111913 ATTTCATATA
111923 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
111949 ATATATTTTA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:112409 original size:2 final size:2
Alignment explanation
Indices: 112402--112431 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
112392 ACTATACACA
*
112402 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
112432 TTGAGATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116382 original size:17 final size:17
Alignment explanation
Indices: 116362--116400 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
116352 TAATATTCGG
116362 TAAATATACAAATTCAT
1 TAAATATACAAATTCAT
** *
116379 TAAATATTTAAATTTAT
1 TAAATATACAAATTCAT
116396 TAAAT
1 TAAAT
116401 TATTTTTTTA
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:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATATACAAATTCAT
Found at i:118109 original size:139 final size:138
Alignment explanation
Indices: 117827--118109 Score: 297
Period size: 139 Copynumber: 2.0 Consensus size: 138
117817 AAAAAATTTC
* *
117827 TTTTCCTTTTCTTGCCTCCATTGCTGCTGCATCAGGCTATAGCTTCAAGCATTGTAATCAACTCT
1 TTTTCCTTTTCTTGCCTCCATTGCTGCAGCATCAGGCTATAGCTTCAAACATTGTAATCAACTCT
** ** * * * * **
117892 ACATTCCAGATTTCCACAGACATTTGAGGCGTGCAGTTTATACCGCAACAATGAAGTTAAAAGAA
66 ACATTCCAGATTTCCACAGACATTAAAAACATGAAGTTAAAAAAGCAACAATGAAGTT-AAAGAA
* * *
117957 AAAAGATTC
130 AAAACAATA
117966 TTTTCCTTTTCTTGCCTCCATTGCTGCAGCATCAGGCTATAGCTTCAAACATTGTAATCAACTCT
1 TTTTCCTTTTCTTGCCTCCATTGCTGCAGCATCAGGCTATAGCTTCAAACATTGTAATCAACTCT
** *
118031 ACATTCCAGATTTCCATTG-CGA-TAAAAACTATGAAG-TAAAAAAGAGAATCAATAGAA-TT-A
66 ACATTCCAGATTTCCACAGAC-ATTAAAAAC-ATGAAGTTAAAAAAG-CAA-CAAT-GAAGTTAA
*
118091 TGATAAAAACAATA
126 AGA-AAAAACAATA
118105 TTTTC
1 TTTTC
118110 GATAAAAGAA
Statistics
Matches: 119, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
138 11 0.09
139 99 0.83
140 6 0.05
141 3 0.03
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (138 bp):
TTTTCCTTTTCTTGCCTCCATTGCTGCAGCATCAGGCTATAGCTTCAAACATTGTAATCAACTCT
ACATTCCAGATTTCCACAGACATTAAAAACATGAAGTTAAAAAAGCAACAATGAAGTTAAAGAAA
AAACAATA
Found at i:128952 original size:21 final size:19
Alignment explanation
Indices: 128911--128947 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
128901 TTTTCATATT
128911 TATATATTTATATCTATAA
1 TATATATTTATATCTATAA
128930 TATATATTTATATCTATA
1 TATATATTTATATCTATA
128948 TAATAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TATATATTTATATCTATAA
Found at i:128957 original size:21 final size:19
Alignment explanation
Indices: 128914--128957 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
128904 TCATATTTAT
*
128914 ATATTTATATCTATAATAT
1 ATATTTATATCTATAATAA
128933 ATATTTATATCTATATAATAA
1 ATATTTATATC--TATAATAA
128954 ATAT
1 ATAT
128958 AAAATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
21 11 0.50
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATTTATATCTATAATAA
Found at i:129318 original size:46 final size:46
Alignment explanation
Indices: 129267--129360 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
129257 TTATAATATT
129267 AATTAATAGATATAAATTCATTAAATCTAAATCTTAACACTAATGA
1 AATTAATAGATATAAATTCATTAAATCTAAATCTTAACACTAATGA
129313 AATTAATAGATATAAATTCATTAAATCTAAATCTTAACACTAATGA
1 AATTAATAGATATAAATTCATTAAATCTAAATCTTAACACTAATGA
129359 AA
1 AA
129361 CCCTTGAATC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.34
Consensus pattern (46 bp):
AATTAATAGATATAAATTCATTAAATCTAAATCTTAACACTAATGA
Found at i:131405 original size:20 final size:21
Alignment explanation
Indices: 131377--131415 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
131367 TAAAATTTTT
131377 TATAAATTAAAA-ATTAATTA
1 TATAAATTAAAATATTAATTA
*
131397 TATATATTAAAATATTAAT
1 TATAAATTAAAATATTAAT
131416 AATACATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATAAATTAAAATATTAATTA
Found at i:131700 original size:12 final size:12
Alignment explanation
Indices: 131685--131726 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
131675 ATTAAATTTG
131685 ATAATATTAAAA
1 ATAATATTAAAA
131697 ATAATA-TAAAA
1 ATAATATTAAAA
*
131708 A-AATATATAAAT
1 ATAATAT-TAAAA
131720 ATAATAT
1 ATAATAT
131727 AAATACATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 4 0.15
11 6 0.23
12 11 0.42
13 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAATATTAAAA
Found at i:131723 original size:23 final size:22
Alignment explanation
Indices: 131687--131729 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
131677 TAAATTTGAT
131687 AATATTAAAAATAATATAAAAA
1 AATATTAAAAATAATATAAAAA
*
131709 AATATATAAATATAATATAAA
1 AATAT-TAAAAATAATATAAA
131730 TACATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AATATTAAAAATAATATAAAAA
Found at i:131731 original size:11 final size:11
Alignment explanation
Indices: 131685--131729 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
131675 ATTAAATTTG
131685 ATAATATTAAAA
1 ATAATA-TAAAA
131697 ATAATATAAAA
1 ATAATATAAAA
131708 A-AATATATAAA
1 ATAATATA-AAA
131719 TATAATATAAA
1 -ATAATATAAA
131730 TACATAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.20
11 9 0.30
12 9 0.30
13 6 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:149121 original size:33 final size:34
Alignment explanation
Indices: 149079--149147 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
149069 CAACGATTTG
149079 TATCGATACATA-AAGTGTTGTATCGATACAATT
1 TATCGATACATATAAGTGTTGTATCGATACAATT
*** *
149112 TATCGATACATATTTTTTTTGTATCGATACAATT
1 TATCGATACATATAAGTGTTGTATCGATACAATT
149146 TA
1 TA
149148 AGCTACTGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 12 0.39
34 19 0.61
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (34 bp):
TATCGATACATATAAGTGTTGTATCGATACAATT
Found at i:149201 original size:13 final size:13
Alignment explanation
Indices: 149185--149209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
149175 ATCATTTAAA
149185 TGTATCGATACAT
1 TGTATCGATACAT
149198 TGTATCGATACA
1 TGTATCGATACA
149210 CTAATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:149259 original size:52 final size:50
Alignment explanation
Indices: 149198--149346 Score: 208
Period size: 52 Copynumber: 2.9 Consensus size: 50
149188 ATCGATACAT
149198 TGTATCGATACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-AT-TTTGTATCGATACATGCAGGCAAATTTGCCCAGA
* **
149250 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TTTGTATCGATACATGCAGGCAAATTTGCCCAGA
*
149302 TGTATCGATACACTATTTAATGTATCGAAACATGCAGGCAAATTT
1 TGTATCGATACACTATTT--TGTATCGATACATGCAGGCAAATTT
149347 TCATATTTCG
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (50 bp):
TGTATCGATACACTATTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:151486 original size:24 final size:27
Alignment explanation
Indices: 151459--151509 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
151449 TCAAAATTTT
151459 ATTC-ACCG-GAG-ACACTCCAACCCC
1 ATTCTACCGAGAGAACACTCCAACCCC
* *
151483 ATTCTTCCGAGGGAACACTCCAACCCC
1 ATTCTACCGAGAGAACACTCCAACCCC
151510 GTTTTCAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 4 0.18
25 3 0.14
26 2 0.09
27 13 0.59
ACGTcount: A:0.27, C:0.43, G:0.14, T:0.16
Consensus pattern (27 bp):
ATTCTACCGAGAGAACACTCCAACCCC
Found at i:152561 original size:2 final size:2
Alignment explanation
Indices: 152549--152601 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
152539 TCTAATGGGT
152549 TA TA T- 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
*
152590 TA TA TA TG TA TA
1 TA TA TA TA TA TA
152602 AAATGAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:155265 original size:28 final size:27
Alignment explanation
Indices: 155234--155286 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
155224 AAAGTCACTT
*
155234 TTTGTATTTGCCAAAAAATGGTGGTTCC
1 TTTGTATTTG-CAAAAAATAGTGGTTCC
* *
155262 TTTGTGTTTGTAAAAAATAGTGGTT
1 TTTGTATTTGCAAAAAATAGTGGTT
155287 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (27 bp):
TTTGTATTTGCAAAAAATAGTGGTTCC
Found at i:155284 original size:27 final size:26
Alignment explanation
Indices: 155246--155305 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
155236 TGTATTTGCC
*
155246 AAAAAATGGTGGTTCCTTTGTGTTTGT
1 AAAAAATAGTGGTT-CTTTGTGTTTGT
* * *
155273 AAAAAATAGTGGTTTTTTTTTTTTGT
1 AAAAAATAGTGGTTCTTTGTGTTTGT
155299 AAAAAAT
1 AAAAAAT
155306 TGTGACTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 16 0.55
27 13 0.45
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (26 bp):
AAAAAATAGTGGTTCTTTGTGTTTGT
Found at i:155931 original size:21 final size:20
Alignment explanation
Indices: 155901--155939 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
155891 GGAAGACTAT
155901 CAATCGATTGGCATGTGGTA
1 CAATCGATTGGCATGTGGTA
155921 CAATCCGATTGGCATGTGG
1 CAAT-CGATTGGCATGTGG
155940 CATGTGGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (20 bp):
CAATCGATTGGCATGTGGTA
Found at i:159840 original size:27 final size:27
Alignment explanation
Indices: 159809--159887 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
159799 AAAGCCACAA
159809 TTTGTATTTGTCAAAAATGGTGGTTAC
1 TTTGTATTTGTCAAAAATGGTGGTTAC
* *
159836 TTTGTATTTATCAAAAATGGTGGTTCC
1 TTTGTATTTGTCAAAAATGGTGGTTAC
* * *
159863 TTTTTGTTTGTCAAAAATTGTGGTT
1 TTTGTATTTGTCAAAAATGGTGGTT
159888 TGTTGTTTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (27 bp):
TTTGTATTTGTCAAAAATGGTGGTTAC
Found at i:159897 original size:28 final size:27
Alignment explanation
Indices: 159815--159902 Score: 101
Period size: 27 Copynumber: 3.4 Consensus size: 27
159805 ACAATTTGTA
* *
159815 TTTGTCAAAAATGGTGGTTACTTTGTA
1 TTTGTCAAAAATGGTGGTTACTTTTTG
* *
159842 TTTATCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAAATGGTGGTTACTTTTTG
* *
159869 TTTGTCAAAAATTGTGG-T--TTGTTG
1 TTTGTCAAAAATGGTGGTTACTTTTTG
159893 TTTGTCAAAA
1 TTTGTCAAAA
159903 TTTGTGGCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
24 15 0.28
26 1 0.02
27 38 0.70
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.47
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTTTG
Found at i:165192 original size:11 final size:12
Alignment explanation
Indices: 165168--165200 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
165158 TTTTTATTAA
165168 TTAATTATTATAT
1 TTAA-TATTATAT
165181 TTAATATT-TAT
1 TTAATATTATAT
165192 TTAATATTA
1 TTAATATTA
165201 AAATTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
12 4 0.21
13 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTAATATTATAT
Found at i:165641 original size:17 final size:17
Alignment explanation
Indices: 165603--165644 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
165593 AATATTAAAT
*
165603 TTAAAAAATAAATTTAG
1 TTAAAAAATAAACTTAG
*
165620 ATAAAAAATGAAACTTA-
1 TTAAAAAAT-AAACTTAG
165637 TTAAAAAA
1 TTAAAAAA
165645 ATAGGTTGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (17 bp):
TTAAAAAATAAACTTAG
Found at i:165852 original size:22 final size:23
Alignment explanation
Indices: 165827--165869 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
165817 AGAAAATCAA
*
165827 TAAAAATT-TAATAAAAAAATGT
1 TAAAAATTAAAATAAAAAAATGT
*
165849 TAAAGATTAAAATAAAAAAAT
1 TAAAAATTAAAATAAAAAAAT
165870 AAAAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (23 bp):
TAAAAATTAAAATAAAAAAATGT
Found at i:166948 original size:30 final size:29
Alignment explanation
Indices: 166908--167016 Score: 82
Period size: 30 Copynumber: 3.8 Consensus size: 29
166898 TCCATCACCA
* *
166908 CCACCGCCACCTATTCCAAAGGCAAAGGCT
1 CCACCTCCACCTACTCCAAA-GCAAAGGCT
* *** *
166938 CCACCTCCACCTGCTCCAAAGC-TTCG-A
1 CCACCTCCACCTACTCCAAAGCAAAGGCT
*
166965 CCA-CTACCACCTATTCCGATAA-CAAAGGCT
1 CCACCT-CCACCTACTCC-A-AAGCAAAGGCT
166995 CCACCTCCACCTACTCCAAAGC
1 CCACCTCCACCTACTCCAAAGC
167017 TTACACCACC
Statistics
Matches: 58, Mismatches: 14, Indels: 15
0.67 0.16 0.17
Matches are distributed among these distances:
26 2 0.03
27 12 0.21
28 5 0.09
29 7 0.12
30 30 0.52
31 2 0.03
ACGTcount: A:0.28, C:0.44, G:0.11, T:0.17
Consensus pattern (29 bp):
CCACCTCCACCTACTCCAAAGCAAAGGCT
Found at i:166968 original size:57 final size:57
Alignment explanation
Indices: 166906--167032 Score: 179
Period size: 57 Copynumber: 2.2 Consensus size: 57
166896 TTTCCATCAC
* *
166906 CACCACCGCCACCTATTCC-A-AAGGCAAAGGCTCCACCTCCACCTGCTCCAAAGCTT-
1 CACCACCACCACCTATTCCGATAA--CAAAGGCTCCACCTCCACCTACTCCAAAGCTTA
*
166962 CGACCACTACCACCTATTCCGATAACAAAGGCTCCACCTCCACCTACTCCAAAGCTTA
1 C-ACCACCACCACCTATTCCGATAACAAAGGCTCCACCTCCACCTACTCCAAAGCTTA
167020 CACCACCACCACC
1 CACCACCACCACC
167033 ACTTATTCCC
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
56 1 0.02
57 58 0.92
58 2 0.03
59 2 0.03
ACGTcount: A:0.29, C:0.46, G:0.09, T:0.16
Consensus pattern (57 bp):
CACCACCACCACCTATTCCGATAACAAAGGCTCCACCTCCACCTACTCCAAAGCTTA
Found at i:167014 original size:24 final size:24
Alignment explanation
Indices: 166987--167131 Score: 114
Period size: 24 Copynumber: 5.8 Consensus size: 24
166977 ATTCCGATAA
*
166987 CAAAGGCTCCACCTCCACCTACTC
1 CAAAGGCTCCACCACCACCTACTC
*
167011 CAAA-GCTTACACCACCACCACCACTTATTC
1 CAAAGGC-T---CCACCACCA-C-C-TACTC
* *
167041 CCAAGGCTCCACCACCATCTACTC
1 CAAAGGCTCCACCACCACCTACTC
* * *
167065 CAAA-CCTTCCACCAACACCTATTC
1 CAAAGGC-TCCACCACCACCTACTC
* *
167089 CAAAGGTTCCATCACCACCTACTC
1 CAAAGGCTCCACCACCACCTACTC
*
167113 CAAAGGCTCCACCTCCACC
1 CAAAGGCTCCACCACCACC
167132 ACCACGACGA
Statistics
Matches: 93, Mismatches: 18, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
23 3 0.03
24 60 0.65
25 1 0.01
27 17 0.18
28 1 0.01
29 1 0.01
30 8 0.09
31 2 0.02
ACGTcount: A:0.29, C:0.47, G:0.06, T:0.18
Consensus pattern (24 bp):
CAAAGGCTCCACCACCACCTACTC
Found at i:167125 original size:48 final size:48
Alignment explanation
Indices: 166987--167116 Score: 143
Period size: 48 Copynumber: 2.6 Consensus size: 48
166977 ATTCCGATAA
* * *
166987 CAAAGGCTCCACCTCCACCTACTCCAAAGCTTACACCACCACCACCACTTATTC
1 CAAAGGCTCCACCACCACCTACTCCAAACCTT---CCACCA--A-CACCTATTC
* *
167041 CCAAGGCTCCACCACCATCTACTCCAAACCTTCCACCAACACCTATTC
1 CAAAGGCTCCACCACCACCTACTCCAAACCTTCCACCAACACCTATTC
* *
167089 CAAAGGTTCCATCACCACCTACTCCAAA
1 CAAAGGCTCCACCACCACCTACTCCAAA
167117 GGCTCCACCT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
48 32 0.48
49 1 0.01
51 6 0.09
54 28 0.42
ACGTcount: A:0.31, C:0.45, G:0.05, T:0.18
Consensus pattern (48 bp):
CAAAGGCTCCACCACCACCTACTCCAAACCTTCCACCAACACCTATTC
Found at i:167208 original size:18 final size:18
Alignment explanation
Indices: 167185--167224 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
167175 CATCGTCATT
167185 ATGATTGCCCGCCATGTC
1 ATGATTGCCCGCCATGTC
**
167203 ATGATTGCGTGCCATGTC
1 ATGATTGCCCGCCATGTC
167221 ATGA
1 ATGA
167225 CCCTTAACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (18 bp):
ATGATTGCCCGCCATGTC
Found at i:167844 original size:6 final size:6
Alignment explanation
Indices: 167825--167859 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
167815 GAAATTAGTT
* *
167825 TTTATG TTTGTG TTTATG TTTATT TTTATG TTTAT
1 TTTATG TTTATG TTTATG TTTATG TTTATG TTTAT
167860 CTCTGTCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (6 bp):
TTTATG
Found at i:168503 original size:20 final size:19
Alignment explanation
Indices: 168462--168504 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
168452 AAGTATAATT
*
168462 TAAAAATATATTAAATTAA
1 TAAAAATATATTAAAATAA
168481 TAAAAATAATATTTAAAAT-A
1 TAAAAAT-ATA-TTAAAATAA
168501 TAAA
1 TAAA
168505 TTATTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 8 0.38
21 6 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATATTAAAATAA
Found at i:169218 original size:19 final size:17
Alignment explanation
Indices: 169204--169257 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
169194 AATATTCATA
169204 ATTTATATTTTTATTAAT
1 ATTT-TATTTTTATTAAT
* *
169222 ATTTTATTTTTGTTACT
1 ATTTTATTTTTATTAAT
*
169239 TTTTTATAATTTTATTAAT
1 ATTTTAT--TTTTATTAAT
169258 TGAAATAGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 17 0.59
18 4 0.14
19 8 0.28
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (17 bp):
ATTTTATTTTTATTAAT
Found at i:170790 original size:18 final size:18
Alignment explanation
Indices: 170767--170802 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
170757 TATATTTAAA
* *
170767 TTAATTAATTTTAATTTT
1 TTAATTAAATTAAATTTT
170785 TTAATTAAATTAAATTTT
1 TTAATTAAATTAAATTTT
170803 AATTTAAATG
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTAATTAAATTAAATTTT
Found at i:170807 original size:30 final size:31
Alignment explanation
Indices: 170762--170825 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
170752 TATTTTATAT
* ***
170762 TTAAATTAATTAATTTTAATTTTTTAATTAAA
1 TTAAATT-ATTAATTTAAATGAATTAATTAAA
170794 TTAAATT-TTAATTTAAATGAATTAATTAAA
1 TTAAATTATTAATTTAAATGAATTAATTAAA
170824 TT
1 TT
170826 TTTTATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 21 0.75
32 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (31 bp):
TTAAATTATTAATTTAAATGAATTAATTAAA
Done.