Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold65
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: 3097370
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.31
Warning! 315397 characters in sequence are not A, C, G, or T
File 6 of 17
Found at i:1297159 original size:2 final size:2
Alignment explanation
Indices: 1297152--1297179 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1297142 TATCTTTAAA
1297152 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
1297180 TCTTTCTTTT
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:1297605 original size:3 final size:3
Alignment explanation
Indices: 1297597--1297626 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1297587 CTTCCGTATG
1297597 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1297627 ATTGTTGCTT
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):
TTA
Found at i:1297857 original size:26 final size:27
Alignment explanation
Indices: 1297814--1297885 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
1297804 ATTAATTTAA
* *
1297814 ATTATTATTTAATAAT-AAAATTTTTT
1 ATTAATATTTAATAATAAAAATATTTT
*
1297840 ATTTAA-ATTTAATTATAAAAATATTTT
1 A-TTAATATTTAATAATAAAAATATTTT
1297867 ATTAATATTTAAATAATAA
1 ATTAATATTT-AATAATAA
1297886 TTTATATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
26 14 0.37
27 17 0.45
28 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTAATATTTAATAATAAAAATATTTT
Found at i:1307040 original size:56 final size:56
Alignment explanation
Indices: 1306978--1307091 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
1306968 TAAACTTAAT
* *
1306978 AGTCAAACGTGGCAGACATAAGCATGCACATAGAACAAAGTGACTGATTTTCTTTC
1 AGTCAAACGTGGCAAAAATAAGCATGCACATAGAACAAAGTGACTGATTTTCTTTC
*
1307034 AGTCAAACGTGGCAAAAATAGGCATGCACATAGAACAAAGTGACTGATTTTCTTTC
1 AGTCAAACGTGGCAAAAATAAGCATGCACATAGAACAAAGTGACTGATTTTCTTTC
1307090 AG
1 AG
1307092 ACTTCTAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (56 bp):
AGTCAAACGTGGCAAAAATAAGCATGCACATAGAACAAAGTGACTGATTTTCTTTC
Found at i:1308434 original size:11 final size:11
Alignment explanation
Indices: 1308418--1308442 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1308408 AAAATAGCGC
1308418 TTTCAAGGTGT
1 TTTCAAGGTGT
1308429 TTTCAAGGTGT
1 TTTCAAGGTGT
1308440 TTT
1 TTT
1308443 TCTGTAACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.52
Consensus pattern (11 bp):
TTTCAAGGTGT
Found at i:1312789 original size:2 final size:2
Alignment explanation
Indices: 1312782--1312810 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1312772 CCATTGTTGA
1312782 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1312811 TGTAGAGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1313583 original size:2 final size:2
Alignment explanation
Indices: 1313576--1313610 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1313566 CAACTTCGTG
1313576 TA TA TA TA 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 TA T
1313611 TAAGATATCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1314380 original size:139 final size:139
Alignment explanation
Indices: 1314104--1314372 Score: 452
Period size: 139 Copynumber: 1.9 Consensus size: 139
1314094 TTCTTGAGTC
1314104 ACCGACTCAAATTTGAGAGATTTGAGAGCTGAAGAGAGGAAACTCTCAGTTCTGTATATTTCTCC
1 ACCGACTCAAATTTGAGAGATTTGAGAGCTGAAGAGAGGAAACTCTCAGTTCTGTATATTTCTCC
*
1314169 CTAACGTTTGTTTTTTCTCAAACGTTTCCAACGATGGCTTTCCATGTTTGTTCTTTCAAGAATGA
66 CTAACGTTTGTTTTTTCTCAAACGTTTCCAACGATGGCTTTCCATGTTTGTTCTATCAAGAATGA
1314234 TGATTGAGGG
131 T-ATTGAGGG
* *
1314244 ACCGACTC-AATTTGAGAGATTTGAGAGCTGAAGAGAGGAAACTCTCAGTTCTTTATATTTGTCC
1 ACCGACTCAAATTTGAGAGATTTGAGAGCTGAAGAGAGGAAACTCTCAGTTCTGTATATTTCTCC
*
1314308 CTAACGTTTGTTTTTTTCTCAAAACGTTTCCAAC-AGTGGCTTTCCGTGTTTGTTCTATCAAGAA
66 CTAACGTTTG-TTTTTTCTC-AAACGTTTCCAACGA-TGGCTTTCCATGTTTGTTCTATCAAGAA
1314372 T
128 T
1314373 CGTTTGAGCT
Statistics
Matches: 122, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
139 64 0.52
140 18 0.15
141 40 0.33
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (139 bp):
ACCGACTCAAATTTGAGAGATTTGAGAGCTGAAGAGAGGAAACTCTCAGTTCTGTATATTTCTCC
CTAACGTTTGTTTTTTCTCAAACGTTTCCAACGATGGCTTTCCATGTTTGTTCTATCAAGAATGA
TATTGAGGG
Found at i:1315546 original size:12 final size:12
Alignment explanation
Indices: 1315529--1315560 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1315519 AACGTAAAGG
1315529 ACACACACCCAC
1 ACACACACCCAC
1315541 ACACACACCCAC
1 ACACACACCCAC
*
1315553 ACCCACAC
1 ACACACAC
1315561 ACACTTACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.59, G:0.00, T:0.00
Consensus pattern (12 bp):
ACACACACCCAC
Found at i:1321912 original size:22 final size:22
Alignment explanation
Indices: 1321881--1321926 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1321871 GGATACCTTA
*
1321881 TTTTCGTAGCTGTTGTATGTGAT
1 TTTTCGTAGCAGTTGTATG-GAT
*
1321904 TTTTC-TAGCAGTTGTTTGGAT
1 TTTTCGTAGCAGTTGTATGGAT
1321925 TT
1 TT
1321927 CTATTAACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 11 0.52
23 5 0.24
ACGTcount: A:0.13, C:0.09, G:0.24, T:0.54
Consensus pattern (22 bp):
TTTTCGTAGCAGTTGTATGGAT
Found at i:1332897 original size:86 final size:86
Alignment explanation
Indices: 1332796--1332961 Score: 323
Period size: 86 Copynumber: 1.9 Consensus size: 86
1332786 AACCCAAAAC
1332796 ATGCTGCATTAATCTAATTAACCTTGCAGTTAAAAAAATAAAAGTAAATAAATGAGAGCAATATA
1 ATGCTGCATTAATCTAATTAACCTTGCAGTTAAAAAAATAAAAGTAAATAAATGAGAGCAATATA
1332861 TAAATATATATATATATATAT
66 TAAATATATATATATATATAT
1332882 ATGCTGCATTAATCTAATTAACCTTGCAGTTAAAAAAATAAAAGTAAATAAATGAGAGCAATATA
1 ATGCTGCATTAATCTAATTAACCTTGCAGTTAAAAAAATAAAAGTAAATAAATGAGAGCAATATA
*
1332947 TATATATATATATAT
66 TAAATATATATATAT
1332962 CTCCCAAAAC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (86 bp):
ATGCTGCATTAATCTAATTAACCTTGCAGTTAAAAAAATAAAAGTAAATAAATGAGAGCAATATA
TAAATATATATATATATATAT
Found at i:1335490 original size:3 final size:3
Alignment explanation
Indices: 1335482--1335515 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1335472 AAAGACCACA
1335482 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1335516 GAGGCAAACG
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1335959 original size:6 final size:6
Alignment explanation
Indices: 1335948--1336000 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
1335938 TCTATTTGAT
* * * * * *
1335948 ATATAC ATATAC ATATAC ATACAT ATATAT ATATAT ATATAC ACACAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1335996 ATATA
1 ATATA
1336001 TGCAGCTAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:1336001 original size:2 final size:2
Alignment explanation
Indices: 1335932--1335988 Score: 51
Period size: 2 Copynumber: 28.0 Consensus size: 2
1335922 ACCTTGATCC
* * * * * *
1335932 TA TA TA TC TA TT TGA TA TA TA CA TA TA CA TA TA CA TA CA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1335975 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1335989 CACACACATA
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
2 41 0.98
3 1 0.02
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1336594 original size:19 final size:19
Alignment explanation
Indices: 1336546--1336610 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 19
1336536 AATCTAAATA
1336546 AAAATTAAAAAAATTATTTT
1 AAAATT-AAAAAATTATTTT
*
1336566 AATATATAAAAAA-TATTTAT
1 AAAAT-TAAAAAATTATTT-T
*
1336586 AAAATTAAAAGATAGTATTTT
1 AAAATTAAAA-A-ATTATTTT
1336607 AAAA
1 AAAA
1336611 AATATTTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 10 0.26
20 16 0.42
21 7 0.18
22 5 0.13
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
AAAATTAAAAAATTATTTT
Found at i:1340599 original size:3 final size:3
Alignment explanation
Indices: 1340591--1340628 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1340581 ACAAACAATT
*
1340591 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1340629 TCAGTATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1340895 original size:5 final size:5
Alignment explanation
Indices: 1340872--1340946 Score: 50
Period size: 5 Copynumber: 15.4 Consensus size: 5
1340862 CTAAAGAAAG
* * * * * *
1340872 AATAT AA-AA AATA- AATAT AATAT AAAAA AATTAA AATAT AACAT AAAAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT
1340921 AATAT AAATAT AATAT AA-AT -ATAT AA
1 AATAT -AATAT AATAT AATAT AATAT AA
1340947 AAAAATTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
3 1 0.02
4 11 0.20
5 35 0.62
6 9 0.16
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.29
Consensus pattern (5 bp):
AATAT
Found at i:1340908 original size:21 final size:20
Alignment explanation
Indices: 1340872--1340939 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
1340862 CTAAAGAAAG
1340872 AATAT-AAAAAAT-AAATAT
1 AATATAAAAAAATAAAATAT
1340890 AATATAAAAAAATTAAAATAT
1 AATATAAAAAAA-TAAAATAT
* *
1340911 AACATAAAATAATATAAATAT
1 AATATAAAAAAATA-AAATAT
1340932 AATATAAA
1 AATATAAA
1340940 TATATAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 5 0.12
19 6 0.14
20 3 0.07
21 29 0.67
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (20 bp):
AATATAAAAAAATAAAATAT
Found at i:1341635 original size:6 final size:6
Alignment explanation
Indices: 1341595--1341637 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1341585 ATCCATCTTT
* * * *
1341595 ATATTT ATATTT ATATTA ATATAA ATATAA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA A
1341638 AGTTTTTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
ATATTA
Found at i:1341718 original size:23 final size:24
Alignment explanation
Indices: 1341658--1341718 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
1341648 TGTCTTTAAG
1341658 TAAATTATCTTTTTACATATTTATTT
1 TAAA-TAT-TTTTTACATATTTATTT
* *
1341684 TTAAT-TTCTTTTA-ATTTTTATTT
1 TAAATATT-TTTTACATATTTATTT
1341707 TAAATATTTTTT
1 TAAATATTTTTT
1341719 TTACTCAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
23 18 0.60
24 8 0.27
25 1 0.03
26 3 0.10
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (24 bp):
TAAATATTTTTTACATATTTATTT
Found at i:1342276 original size:28 final size:28
Alignment explanation
Indices: 1342228--1342288 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1342218 TTTTAATTAT
* *
1342228 TTAATTTTTTTAAAAATATTATATCAAA
1 TTAATTTTTTTAAAAATATTAAAACAAA
*
1342256 TTAATTATTTTTATAAA-ATTAAAACAAA
1 TTAATT-TTTTTAAAAATATTAAAACAAA
1342284 TTAAT
1 TTAAT
1342289 ATGCTTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
TTAATTTTTTTAAAAATATTAAAACAAA
Found at i:1354859 original size:41 final size:41
Alignment explanation
Indices: 1354802--1354882 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
1354792 AAGAAACCTA
1354802 GTTTGTAACCTTTACCTCTATCTTGAATAACCAAAAAGTTG
1 GTTTGTAACCTTTACCTCTATCTTGAATAACCAAAAAGTTG
1354843 GTTTGTAACCTTTACCTCTATCTTGAATAACCAAAAAGTT
1 GTTTGTAACCTTTACCTCTATCTTGAATAACCAAAAAGTT
1354883 CTACTATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (41 bp):
GTTTGTAACCTTTACCTCTATCTTGAATAACCAAAAAGTTG
Found at i:1356135 original size:14 final size:14
Alignment explanation
Indices: 1356106--1356135 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1356096 AATAGGAGAG
*
1356106 AAGGAAAAAACAAA
1 AAGGAAAAAAAAAA
1356120 AAGGAAAAAAAAAA
1 AAGGAAAAAAAAAA
1356134 AA
1 AA
1356136 AAAGAGAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (14 bp):
AAGGAAAAAAAAAA
Found at i:1363696 original size:2 final size:2
Alignment explanation
Indices: 1363689--1363722 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1363679 TACTGGACTC
* *
1363689 TA TA TA TA CA TA TA TA TA TA TA TA TA TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1363723 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1366617 original size:6 final size:6
Alignment explanation
Indices: 1366606--1366630 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1366596 ATCCTACTAA
1366606 ACATGC ACATGC ACATGC ACATGC A
1 ACATGC ACATGC ACATGC ACATGC A
1366631 TTACATGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
ACATGC
Found at i:1371669 original size:54 final size:54
Alignment explanation
Indices: 1371580--1371735 Score: 257
Period size: 54 Copynumber: 2.9 Consensus size: 54
1371570 TAGAACCTAT
1371580 ATCAAGCTTTGAT-T--TTTTTTAATCAAAAAAA-TTTCTCCAACTGTTCAATAA
1 ATCAAGCTTTGATATGCTTTTTTAA-CAAAAAAATTTTCTCCAACTGTTCAATAA
1371631 ATCAAGCTTTGATATGCTTTTTTAACAAAAAAATTTTCTCCAACTGTTCAATAA
1 ATCAAGCTTTGATATGCTTTTTTAACAAAAAAATTTTCTCCAACTGTTCAATAA
**
1371685 ATCAAGCTTTGATATGCTTTTTTAATTAAAAAATTTTCTCCAACTGTTCAA
1 ATCAAGCTTTGATATGCTTTTTTAACAAAAAAATTTTCTCCAACTGTTCAA
1371736 CAAGAAACAT
Statistics
Matches: 99, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
51 13 0.13
52 1 0.01
53 8 0.08
54 77 0.78
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (54 bp):
ATCAAGCTTTGATATGCTTTTTTAACAAAAAAATTTTCTCCAACTGTTCAATAA
Found at i:1375447 original size:21 final size:21
Alignment explanation
Indices: 1375423--1375464 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1375413 ATATTTTTTA
*
1375423 TAATATAAAAAAAAATTAAAT
1 TAATATAAAAAAAAATAAAAT
* *
1375444 TAATTTAAAATAAAATAAAAT
1 TAATATAAAAAAAAATAAAAT
1375465 AAAATTCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TAATATAAAAAAAAATAAAAT
Found at i:1377081 original size:15 final size:15
Alignment explanation
Indices: 1377061--1377090 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1377051 ATTTTTCTCA
*
1377061 TTTGGATTAGGAAAT
1 TTTGGATAAGGAAAT
1377076 TTTGGATAAGGAAAT
1 TTTGGATAAGGAAAT
1377091 GATGGAGGAC
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:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (15 bp):
TTTGGATAAGGAAAT
Found at i:1383554 original size:24 final size:25
Alignment explanation
Indices: 1383507--1383555 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1383497 TATGTTATTT
*
1383507 TTATTTGAAAATAAATTAATTATAA
1 TTATTTGAAAATAAATTAAATATAA
* *
1383532 TTATTTTAAAA-AATTTAAATATAA
1 TTATTTGAAAATAAATTAAATATAA
1383556 AATATTGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
TTATTTGAAAATAAATTAAATATAA
Found at i:1384060 original size:29 final size:29
Alignment explanation
Indices: 1383974--1384074 Score: 98
Period size: 29 Copynumber: 3.5 Consensus size: 29
1383964 ACTTAGTAAT
* * * *
1383974 AATAATTATATTTTTTATCAAATTTGAAA
1 AATAAATATATTTTTTATAAAAATTAAAA
* * * *
1384003 AGTAAGTGA-ATATTTT-TAAATATTAAAAA
1 AATAAAT-ATATTTTTTATAAAAATT-AAAA
1384032 AATAAATATATTTTTTATAAAAATTAAAA
1 AATAAATATATTTTTTATAAAAATTAAAA
1384061 AATAAATATATTTT
1 AATAAATATATTTT
1384075 ATTTTTGTCA
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
28 6 0.11
29 43 0.75
30 8 0.14
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (29 bp):
AATAAATATATTTTTTATAAAAATTAAAA
Found at i:1388730 original size:2 final size:2
Alignment explanation
Indices: 1388725--1388763 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1388715 TGCGCGTGTG
1388725 TA TA TA TA TA TA 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 TA TA TA T
1388764 GTGTGTGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1391379 original size:3 final size:3
Alignment explanation
Indices: 1391371--1391417 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1391361 TACCTACATC
1391371 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1391418 TCAAAACAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1395465 original size:2 final size:2
Alignment explanation
Indices: 1395458--1395488 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1395448 TACCCTATGC
1395458 TA TA 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 T
1395489 GTCTTTTTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1397279 original size:14 final size:14
Alignment explanation
Indices: 1397260--1397320 Score: 81
Period size: 14 Copynumber: 4.4 Consensus size: 14
1397250 GAAATGATAA
1397260 AAATAATAATATTT
1 AAATAATAATATTT
1397274 AAATAAT-ATATTTT
1 AAATAATAATA-TTT
1397288 AAAATAATAATATTT
1 -AAATAATAATATTT
*
1397303 TAATAATAA-ATTT
1 AAATAATAATATTT
1397316 AAATA
1 AAATA
1397321 TTAAGGTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
13 11 0.26
14 18 0.43
15 10 0.24
16 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATAATAATATTT
Found at i:1397298 original size:29 final size:29
Alignment explanation
Indices: 1397259--1397315 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1397249 AGAAATGATA
*
1397259 AAAATAATAATATTTAAATAATATATTTT
1 AAAATAATAATATTTAAATAATAAATTTT
*
1397288 AAAATAATAATATTTTAATAATAAATTT
1 AAAATAATAATATTTAAATAATAAATTT
1397316 AAATATTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAATAATAATATTTAAATAATAAATTTT
Found at i:1401088 original size:33 final size:33
Alignment explanation
Indices: 1401051--1401116 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
1401041 AAATTTTATT
*
1401051 AAAA-TATTAATTTT-TTATAATTATATTTAAATA
1 AAAATTATT-ATTTTATTAAAATTA-ATTTAAATA
1401084 AAAATTATTATTTTAATTAAAATTAATTTAAAT
1 AAAATTATTATTTT-ATTAAAATTAATTTAAAT
1401117 TATAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 9 0.31
34 12 0.41
35 8 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
AAAATTATTATTTTATTAAAATTAATTTAAATA
Found at i:1401105 original size:18 final size:17
Alignment explanation
Indices: 1401043--1401108 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
1401033 TATTATTTAA
1401043 ATTTTATTAAAA-TATT
1 ATTTTATTAAAATTATT
*
1401059 AATTTT-TTATAATTA-T
1 -ATTTTATTAAAATTATT
* *
1401075 ATTTAAATAAAAATTATT
1 ATTT-TATTAAAATTATT
1401093 ATTTTAATTAAAATTA
1 ATTTT-ATTAAAATTA
1401109 ATTTAAATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
15 4 0.11
16 6 0.16
17 14 0.37
18 14 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTATTAAAATTATT
Found at i:1410432 original size:13 final size:13
Alignment explanation
Indices: 1410414--1410438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1410404 ATTTAATATT
1410414 AAATAAATTAATC
1 AAATAAATTAATC
1410427 AAATAAATTAAT
1 AAATAAATTAAT
1410439 ATCGTTTCAT
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:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATAAATTAATC
Found at i:1414131 original size:14 final size:14
Alignment explanation
Indices: 1414021--1414131 Score: 73
Period size: 15 Copynumber: 7.9 Consensus size: 14
1414011 ATTAGATATG
*
1414021 TATAAATATTTTGA
1 TATAAATATTTTAA
*
1414035 TATAAATATTTGAA
1 TATAAATATTTTAA
* **
1414049 -ACAGGTATTTTAA
1 TATAAATATTTTAA
*
1414062 TATAGATA-TTTAA
1 TATAAATATTTTAA
*
1414075 TATAAATAGTTTTAG
1 TATAAATA-TTTTAA
* ***
1414090 CACGTATATCTTTAA
1 TATAAATAT-TTTAA
*
1414105 TATAGATACTTTTAA
1 TATAAATA-TTTTAA
1414120 TATAAATATTTT
1 TATAAATATTTT
1414132 TGACACAAAT
Statistics
Matches: 72, Mismatches: 20, Indels: 10
0.71 0.20 0.10
Matches are distributed among these distances:
13 21 0.29
14 22 0.31
15 28 0.39
16 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (14 bp):
TATAAATATTTTAA
Found at i:1414144 original size:45 final size:43
Alignment explanation
Indices: 1414057--1414145 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 43
1414047 AAACAGGTAT
**
1414057 TTTAATATAGATATTTAATATAAATAGTTTTAGCACGTATATC
1 TTTAATATAGATATTTAATATAAATAGTTTTAGCACAAATATC
*
1414100 TTTAATATAGATACTTTTAATATAAATA-TTTTTGACACAAATATC
1 TTTAATATAGATA--TTTAATATAAATAGTTTTAG-CACAAATATC
1414145 T
1 T
1414146 GTCAAAGACA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
43 13 0.32
44 5 0.12
45 22 0.55
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (43 bp):
TTTAATATAGATATTTAATATAAATAGTTTTAGCACAAATATC
Found at i:1414240 original size:14 final size:14
Alignment explanation
Indices: 1414223--1414265 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1414213 TAAGACATAG
1414223 GTACTTTAATATAA
1 GTACTTTAATATAA
* * *
1414237 GTACTTTGACATAT
1 GTACTTTAATATAA
1414251 GTACTTTTAATATAA
1 GTAC-TTTAATATAA
1414266 ATATTTTGAC
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (14 bp):
GTACTTTAATATAA
Found at i:1414249 original size:28 final size:29
Alignment explanation
Indices: 1414216--1414277 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
1414206 AAGGTATTAA
*
1414216 GACATAGGTAC-TTTAATATAAGTACTTT
1 GACATAGGTACTTTTAATATAAATACTTT
* *
1414244 GACATATGTACTTTTAATATAAATATTTT
1 GACATAGGTACTTTTAATATAAATACTTT
1414273 GACAT
1 GACAT
1414278 TAGCACATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 10 0.33
29 20 0.67
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (29 bp):
GACATAGGTACTTTTAATATAAATACTTT
Found at i:1414845 original size:24 final size:24
Alignment explanation
Indices: 1414818--1414866 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
1414808 CTGCTATCAT
1414818 ATTTATTTT-TTAAT-ATTTACTTTA
1 ATTT-TTTTCTTAATCATTT-CTTTA
*
1414842 ATTTTTTTCTTCATCATTTCTTTA
1 ATTTTTTTCTTAATCATTTCTTTA
1414866 A
1 A
1414867 CACAACGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 4 0.18
24 14 0.64
25 4 0.18
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTTTTTTCTTAATCATTTCTTTA
Found at i:1415713 original size:2 final size:2
Alignment explanation
Indices: 1415653--1415697 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1415643 GTCTTGAATT
1415653 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1415695 AC A
1 AC A
1415698 TATATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1422963 original size:2 final size:2
Alignment explanation
Indices: 1422956--1422988 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1422946 AAAAGAAATC
*
1422956 TA TA TA TA TA TA TA TA CA 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
1422989 GTGCGTGAGA
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1425097 original size:2 final size:2
Alignment explanation
Indices: 1425090--1425123 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1425080 ATGTTGCTAT
1425090 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1425124 GTTACTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1426046 original size:20 final size:21
Alignment explanation
Indices: 1426007--1426046 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1425997 TGGTTAATTT
* *
1426007 AAATATTTTATTTATTTATAA
1 AAATAATTTAATTATTTATAA
1426028 AAATAATTTAATT-TTTATA
1 AAATAATTTAATTATTTATA
1426047 TATTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AAATAATTTAATTATTTATAA
Found at i:1426109 original size:15 final size:16
Alignment explanation
Indices: 1426084--1426114 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1426074 ATGAATTATC
1426084 AAATATATTAAAAAAT
1 AAATATATTAAAAAAT
1426100 AAAT-TATTAAAAAAT
1 AAATATATTAAAAAAT
1426115 TCAGTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATATATTAAAAAAT
Found at i:1426372 original size:3 final size:3
Alignment explanation
Indices: 1426366--1426420 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
1426356 AAAATAAAAA
*
1426366 ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1426414 ATT ATT A
1 ATT ATT A
1426421 CTTGTAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1427258 original size:20 final size:20
Alignment explanation
Indices: 1427233--1427286 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1427223 GTTTGAGATA
* *
1427233 ATGTATCGATACAATTTTTC
1 ATGTATCGATACAATATATC
*
1427253 ATGTATCGATATAATATATC
1 ATGTATCGATACAATATATC
1427273 ATGTATCGATACAA
1 ATGTATCGATACAA
1427287 ACAGTGGTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACAATATATC
Found at i:1427694 original size:23 final size:25
Alignment explanation
Indices: 1427668--1427714 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
1427658 TAATAATTTT
1427668 TATT-ATAAAATTA-AAATATAATA
1 TATTAATAAAATTATAAATATAATA
*
1427691 TATTAATAAAATTATATATATAAT
1 TATTAATAAAATTATAAATATAAT
1427715 TTAATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 9 0.43
25 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TATTAATAAAATTATAAATATAATA
Found at i:1433008 original size:3 final size:3
Alignment explanation
Indices: 1433000--1433049 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
1432990 AACTTTTTAC
* **
1433000 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT ATAT TGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
1433046 AAT A
1 AAT A
1433050 TTAGGCTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
3 38 0.95
4 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:1441517 original size:44 final size:45
Alignment explanation
Indices: 1441439--1441530 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
1441429 TAAAACTATT
* * *
1441439 TTTTTTCCCTTTGACAGTATACTAGTATTTAGCTGAAATAGTCTC
1 TTTTTTACCTTTGACAATATAATAGTATTTAGCTGAAATAGTCTC
1441484 TTTTTTACCTTTGACAATATAATAGTA-TTAGCTGAAATAGTCTC
1 TTTTTTACCTTTGACAATATAATAGTATTTAGCTGAAATAGTCTC
1441528 TTT
1 TTT
1441531 AGTTGCATAG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 20 0.45
45 24 0.55
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (45 bp):
TTTTTTACCTTTGACAATATAATAGTATTTAGCTGAAATAGTCTC
Found at i:1441613 original size:4 final size:4
Alignment explanation
Indices: 1441606--1441644 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
1441596 TATATATGTA
* * *
1441606 TATG TATG TATG TATG CATG CATG CATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1441645 AATATACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.44
Consensus pattern (4 bp):
TATG
Found at i:1441655 original size:4 final size:4
Alignment explanation
Indices: 1441648--1441684 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
1441638 TATGTATAAT
*
1441648 ATAC ATAC ATAC ATAC ATGC ATAC --AC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1441685 TATATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.07
4 27 0.93
ACGTcount: A:0.49, C:0.24, G:0.03, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:1441677 original size:14 final size:14
Alignment explanation
Indices: 1441648--1441684 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1441638 TATGTATAAT
1441648 ATACATACAT--AC
1 ATACATACATACAC
*
1441660 ATACATGCATACAC
1 ATACATACATACAC
1441674 ATACATACATA
1 ATACATACATA
1441685 TATATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 9 0.43
14 12 0.57
ACGTcount: A:0.49, C:0.24, G:0.03, T:0.24
Consensus pattern (14 bp):
ATACATACATACAC
Found at i:1448789 original size:2 final size:2
Alignment explanation
Indices: 1448782--1448821 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1448772 GAGGAGCCCC
1448782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1448822 CATTCGATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1449450 original size:2 final size:2
Alignment explanation
Indices: 1449443--1449468 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1449433 TATATCAGCC
1449443 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
1449469 ATTTGTTTGT
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:1450049 original size:39 final size:39
Alignment explanation
Indices: 1449992--1450071 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
1449982 TCAATCATAA
1449992 ATTATTCCTCTAAACTGCCAGGGTCCAAGCAGTGTGTGT
1 ATTATTCCTCTAAACTGCCAGGGTCCAAGCAGTGTGTGT
* * *
1450031 ATTATTCCTCTAACCTGCCGGGGTCCAAGTAGTGTGTGT
1 ATTATTCCTCTAAACTGCCAGGGTCCAAGCAGTGTGTGT
1450070 AT
1 AT
1450072 CTTCTCATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.33
Consensus pattern (39 bp):
ATTATTCCTCTAAACTGCCAGGGTCCAAGCAGTGTGTGT
Found at i:1453099 original size:5 final size:5
Alignment explanation
Indices: 1453087--1453121 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
1453077 ATTTATATTT
1453087 AAAT- AAATA AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA A
1453122 TTTTAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:1453801 original size:47 final size:52
Alignment explanation
Indices: 1453730--1453832 Score: 137
Period size: 49 Copynumber: 2.1 Consensus size: 52
1453720 CTTTCTCTTC
* *
1453730 ATTTTACGAGTAATTGACTATAAAG-T-TATATAA-TTATTACCAAAATATT
1 ATTTTACGAGTAATTAAATATAAAGTTATATATAATTTATTACCAAAATATT
*
1453779 ATTTTA-GA-TAATTAAATATAAAGTTATATATAATTTATTATCAAAATATT
1 ATTTTACGAGTAATTAAATATAAAGTTATATATAATTTATTACCAAAATATT
1453829 -TTTT
1 ATTTT
1453833 CATATTTAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
47 13 0.27
48 3 0.06
49 17 0.35
50 15 0.31
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.46
Consensus pattern (52 bp):
ATTTTACGAGTAATTAAATATAAAGTTATATATAATTTATTACCAAAATATT
Found at i:1454193 original size:15 final size:16
Alignment explanation
Indices: 1454174--1454216 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1454164 TTTATTTTCT
*
1454174 TTTTATTTTTTTTA-C
1 TTTTATTTTTTTCATC
1454189 TTTTACTTTTTTTCATC
1 TTTTA-TTTTTTTCATC
1454206 TTTCTATTTTT
1 TTT-TATTTTT
1454217 CTACTCTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.21
16 8 0.33
17 9 0.38
18 2 0.08
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTTTTTTCATC
Found at i:1454539 original size:2 final size:2
Alignment explanation
Indices: 1454532--1454560 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1454522 GACACCAACA
1454532 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 A
1454561 ATGAGGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1456292 original size:2 final size:2
Alignment explanation
Indices: 1456285--1456314 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1456275 GTATTATCCA
1456285 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1456315 TATATAACAA
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1457200 original size:18 final size:18
Alignment explanation
Indices: 1457177--1457212 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1457167 CAGTCGTTAA
1457177 TCCAAACCCAGAACCACT
1 TCCAAACCCAGAACCACT
* *
1457195 TCCAAAGCCAGTACCACT
1 TCCAAACCCAGAACCACT
1457213 GCTAGAAATG
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:0.36, C:0.42, G:0.08, T:0.14
Consensus pattern (18 bp):
TCCAAACCCAGAACCACT
Found at i:1457371 original size:25 final size:25
Alignment explanation
Indices: 1457342--1457396 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
1457332 TACATAACTG
*
1457342 TTGAAAAATCAT-TACAAATCAGGTA
1 TTGAAAAATC-TCTACAAATCAGGGA
*
1457367 TTGAAAAATCTCTAGAAATCAGGGA
1 TTGAAAAATCTCTACAAATCAGGGA
1457392 TTGAA
1 TTGAA
1457397 TTCCCTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (25 bp):
TTGAAAAATCTCTACAAATCAGGGA
Found at i:1459849 original size:10 final size:9
Alignment explanation
Indices: 1459837--1459878 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
1459827 CGTTTTGTTG
1459837 AAAAAG-AA
1 AAAAAGAAA
*
1459845 AGAAAGAATA
1 AAAAAGAA-A
1459855 AAAAAGAAA
1 AAAAAGAAA
1459864 AAAAAGGAAA
1 AAAAA-GAAA
1459874 AAAAA
1 AAAAA
1459879 AAGGAAAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 5 0.17
9 7 0.24
10 17 0.59
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:1459874 original size:17 final size:17
Alignment explanation
Indices: 1459854--1459894 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1459844 AAGAAAGAAT
1459854 AAAAAAGAAAA-AAAAGG
1 AAAAAA-AAAAGAAAAGG
*
1459871 AAAAAAAAAAGGAAAGG
1 AAAAAAAAAAGAAAAGG
1459888 AAAAAAA
1 AAAAAAA
1459895 TTATATGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAGG
Found at i:1459892 original size:12 final size:12
Alignment explanation
Indices: 1459861--1459885 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1459851 AATAAAAAAG
1459861 AAAAAAAAGGAA
1 AAAAAAAAGGAA
1459873 AAAAAAAAGGAA
1 AAAAAAAAGGAA
1459885 A
1 A
1459886 GGAAAAAAAT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGGAA
Found at i:1459953 original size:16 final size:15
Alignment explanation
Indices: 1459932--1459982 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
1459922 TGTATTTAAA
1459932 ATATTATATTTTGTAT
1 ATATTATATTTT-TAT
1459948 ATATTAATAATTTATT-T
1 ATATT-AT-ATTT-TTAT
1459965 -TATTATATTTTTAT
1 ATATTATATTTTTAT
1459979 ATAT
1 ATAT
1459983 AATTATATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
13 2 0.07
14 5 0.17
15 5 0.17
16 9 0.30
17 3 0.10
18 5 0.17
19 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
ATATTATATTTTTAT
Found at i:1460297 original size:4 final size:4
Alignment explanation
Indices: 1460282--1460329 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
1460272 TTAGGAGGGA
* *
1460282 AAAG AGAG AAAG AAAG AAAT AAGGAG AAA- AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AA--AG AAAG AAAG AAAG AAAG AAAG AAA
1460330 AAGAGAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
3 3 0.08
4 31 0.84
6 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:1460320 original size:29 final size:27
Alignment explanation
Indices: 1460281--1460340 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 27
1460271 TTTAGGAGGG
*
1460281 AAAAGAGAGAAAGAAAGAAATAAGGAGAA
1 AAAAGAAAGAAAGAAAGAAA-AA-GAGAA
1460310 AAAAGAAAGAAAGAAAGAAAAAGAGAA
1 AAAAGAAAGAAAGAAAGAAAAAGAGAA
1460337 AAAA
1 AAAA
1460341 ATTACGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 9 0.30
28 2 0.07
29 19 0.63
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (27 bp):
AAAAGAAAGAAAGAAAGAAAAAGAGAA
Found at i:1460753 original size:15 final size:14
Alignment explanation
Indices: 1460733--1460766 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1460723 GAGAAATATC
1460733 GAAAGAAAAAAAAA
1 GAAAGAAAAAAAAA
*
1460747 GGAAAGAAAGAAAAA
1 -GAAAGAAAAAAAAA
1460762 GAAAG
1 GAAAG
1460767 TGAGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
GAAAGAAAAAAAAA
Found at i:1461340 original size:15 final size:16
Alignment explanation
Indices: 1461322--1461355 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1461312 TATTTTATAA
*
1461322 AAAGAGAGAAAAAG-G
1 AAAGAAAGAAAAAGAG
1461337 AAAGAAAGAAAAAGAG
1 AAAGAAAGAAAAAGAG
1461353 AAA
1 AAA
1461356 AAATTTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAAAAGAG
Found at i:1461907 original size:16 final size:17
Alignment explanation
Indices: 1461880--1461920 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1461870 ATTTTTAAAT
1461880 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
1461895 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
1461912 AAATTTTAT
1 AAATTTTAT
1461921 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:1462319 original size:12 final size:12
Alignment explanation
Indices: 1462289--1462322 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1462279 GAGCTATTTG
1462289 AATAATATTAAAA
1 AATAAT-TTAAAA
1462302 AA-AATTTAAAA
1 AATAATTTAAAA
1462313 AATAATTTAA
1 AATAATTTAA
1462323 CTTAATTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.40
12 10 0.50
13 2 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAATTTAAAA
Found at i:1465597 original size:41 final size:40
Alignment explanation
Indices: 1465552--1465655 Score: 95
Period size: 42 Copynumber: 2.5 Consensus size: 40
1465542 TTATTAAATT
1465552 AAATAAATATAAATAATATAA-AAAAATTATGTAAATATTTA
1 AAATAAATATAAATAATATAATAAAAATTA-GTAAA-ATTTA
* ** *
1465593 AAATAAA-ATTAATTTTGTATAATTAAAATTAGTAAAATTTA
1 AAATAAATA-TAA-ATAATATAATAAAAATTAGTAAAATTTA
*
1465634 AAATTAAATATATATATATATA
1 AAA-TAAATATAAATA-ATATA
1465656 TATATATAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
40 1 0.02
41 19 0.39
42 21 0.43
43 8 0.16
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (40 bp):
AAATAAATATAAATAATATAATAAAAATTAGTAAAATTTA
Found at i:1466583 original size:19 final size:19
Alignment explanation
Indices: 1466559--1466631 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 19
1466549 TTTAACAAAT
1466559 ATTTTTTAATAAAATTAAA
1 ATTTTTTAATAAAATTAAA
1466578 A-TTTTTACATATAAATTAGATAA
1 ATTTTTTA-ATA-AAATT--A-AA
1466601 ATTTTATTAATAATAA--AAA
1 ATTTT-TTAATAA-AATTAAA
*
1466620 ATTTTATAATAA
1 ATTTTTTAATAA
1466632 TATAATTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 17
0.71 0.02 0.27
Matches are distributed among these distances:
18 12 0.27
19 11 0.24
20 6 0.13
22 1 0.02
23 4 0.09
24 8 0.18
25 3 0.07
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (19 bp):
ATTTTTTAATAAAATTAAA
Found at i:1466630 original size:15 final size:16
Alignment explanation
Indices: 1466599--1466641 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 16
1466589 TAAATTAGAT
1466599 AAATTTTATTAATAATAAA
1 AAATTTTA-TAATAAT--A
1466618 AAATTTTATAATAATA
1 AAATTTTATAATAATA
*
1466634 TAATTTTA
1 AAATTTTA
1466642 GTAAATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 8 0.35
18 7 0.30
19 8 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTTTATAATAATA
Found at i:1466887 original size:2 final size:2
Alignment explanation
Indices: 1466870--1466906 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1466860 AAAGATTTTT
* *
1466870 TA TA TT TA TA TT 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 TA TA T
1466907 GAGTATTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:1466999 original size:25 final size:23
Alignment explanation
Indices: 1466950--1467000 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
1466940 AATCATATTT
* *
1466950 TTATTTATTTTAAAAATATATAA
1 TTATATATTTTAAAAATATAAAA
*
1466973 TTATATATTTTATAAATAATTAAAA
1 TTATATATTTTAAAAAT-A-TAAAA
1466998 TTA
1 TTA
1467001 AAAAATGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 15 0.65
24 1 0.04
25 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTATATATTTTAAAAATATAAAA
Found at i:1468190 original size:18 final size:20
Alignment explanation
Indices: 1468153--1468190 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1468143 GTCCTTTTGC
*
1468153 CTTTTTTATTTTTAGTTTAT
1 CTTTTTTATTTTTAGATTAT
1468173 CTTTTTT-TTTTTA-ATTAT
1 CTTTTTTATTTTTAGATTAT
1468191 TAATCTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (20 bp):
CTTTTTTATTTTTAGATTAT
Found at i:1468482 original size:20 final size:22
Alignment explanation
Indices: 1468451--1468492 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1468441 TTTTAATTGT
1468451 TTATTATATTTAATA-TTAAAA
1 TTATTATATTTAATATTTAAAA
1468472 TTATT-TATTTAATATTTAAAA
1 TTATTATATTTAATATTTAAAA
1468493 ATTTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATTATATTTAATATTTAAAA
Found at i:1468498 original size:20 final size:20
Alignment explanation
Indices: 1468452--1468503 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1468442 TTTAATTGTT
*
1468452 TATTATATTTAATATTAAAAT
1 TATT-TATTTAATATTAAAAA
1468473 TATTTATTTAATATTTAAAAA
1 TATTTATTTAATA-TTAAAAA
*
1468494 T-TTTAATTAA
1 TATTTATTTAA
1468504 ATAATCCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTATTTAATATTAAAAA
Found at i:1470019 original size:31 final size:31
Alignment explanation
Indices: 1469974--1470045 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
1469964 ATAATATTAT
1469974 TTTATA-TATAAATTTTAATATATCCATA-A
1 TTTATATTATAAATTTTAATATATCCATATA
**
1470003 TTTATATTGATAAATTTTAATATATTTATATA
1 TTTATATT-ATAAATTTTAATATATCCATATA
1470035 TTTATATTATA
1 TTTATATTATA
1470046 TTAATATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 6 0.16
30 1 0.03
31 22 0.58
32 9 0.24
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (31 bp):
TTTATATTATAAATTTTAATATATCCATATA
Found at i:1470028 original size:18 final size:18
Alignment explanation
Indices: 1470005--1470075 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
1469995 ATCCATAATT
* *
1470005 TATATTGATAAATTTTAA
1 TATATTAATATATTTTAA
* *
1470023 TATATTTATATATTTATAT
1 TATATTAATATATTT-TAA
*
1470042 TATATTAATATTTTTTAA
1 TATATTAATATATTTTAA
*
1470060 TAT-TATATTATATTTT
1 TATAT-TAATATATTTT
1470076 TATTACTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
17 1 0.02
18 27 0.63
19 15 0.35
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (18 bp):
TATATTAATATATTTTAA
Found at i:1470045 original size:37 final size:39
Alignment explanation
Indices: 1470004--1470078 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 39
1469994 TATCCATAAT
*
1470004 TTATATTGATAAATTTTAATA-TAT-TTATATATTTATA
1 TTATATTAATAAATTTTAATATTATATTATATATTTATA
** *
1470041 TTATATTAATATTTTTTAATATTATATTATATTTTTAT
1 TTATATTAATAAATTTTAATATTATATTATATATTTAT
1470079 TACTTTTCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 18 0.56
38 3 0.09
39 11 0.34
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (39 bp):
TTATATTAATAAATTTTAATATTATATTATATATTTATA
Found at i:1470062 original size:21 final size:20
Alignment explanation
Indices: 1470017--1470076 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
1470007 TATTGATAAA
1470017 TTTTAATA-TAT-TTATA-T
1 TTTTAATATTATATTATATT
*
1470034 ATTT-ATATTATATTAATATT
1 TTTTAATATTATATT-ATATT
1470054 TTTTAATATTATATTATATT
1 TTTTAATATTATATTATATT
1470074 TTT
1 TTT
1470077 ATTACTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.08
17 6 0.17
18 2 0.06
19 3 0.08
20 12 0.33
21 10 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTAATATTATATTATATT
Found at i:1470072 original size:26 final size:27
Alignment explanation
Indices: 1470019--1470073 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
1470009 TTGATAAATT
1470019 TTAATATATTTATATATTTATATTATA
1 TTAATATATTTATATATTTATATTATA
*
1470046 TTAATAT-TTTTTA-ATATTATATTATA
1 TTAATATATTTATATAT-TTATATTATA
1470072 TT
1 TT
1470074 TTTATTACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 2 0.08
26 17 0.65
27 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TTAATATATTTATATATTTATATTATA
Found at i:1473985 original size:28 final size:28
Alignment explanation
Indices: 1473952--1474030 Score: 140
Period size: 28 Copynumber: 2.8 Consensus size: 28
1473942 CAAATGTCAC
1473952 CCTTTGTATTTGTCAAATATGGTAGTTT
1 CCTTTGTATTTGTCAAATATGGTAGTTT
*
1473980 TCTTTGTATTTGTCAAATATGGTAGTTT
1 CCTTTGTATTTGTCAAATATGGTAGTTT
*
1474008 CCTTTATATTTGTCAAATATGGT
1 CCTTTGTATTTGTCAAATATGGT
1474031 GGTTATTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.23, C:0.10, G:0.16, T:0.51
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTAGTTT
Found at i:1474063 original size:27 final size:27
Alignment explanation
Indices: 1474022--1474091 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 27
1474012 TATATTTGTC
1474022 AAATATGGTGG-TTATTTTTGTTTGTAA
1 AAAT-TGGTGGCTTATTTTTGTTTGTAA
*
1474049 AAATTGGTGGCTTA---TTGTTTGTCA
1 AAATTGGTGGCTTATTTTTGTTTGTAA
*
1474073 AAATTGGTGGCTAATTTTT
1 AAATTGGTGGCTTATTTTT
1474092 ATTAGAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
24 22 0.59
26 6 0.16
27 9 0.24
ACGTcount: A:0.24, C:0.04, G:0.23, T:0.49
Consensus pattern (27 bp):
AAATTGGTGGCTTATTTTTGTTTGTAA
Found at i:1478657 original size:28 final size:28
Alignment explanation
Indices: 1478578--1478660 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
1478568 CAAATGCCAC
*
1478578 CCTTTGTATTTGTCAAATATGGTAGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
1478606 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
*
1478634 CCTTTATATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
1478661 ATTTTTGTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:1478701 original size:24 final size:24
Alignment explanation
Indices: 1478665--1478710 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1478655 GTGGTTATTT
1478665 TTGTTTGTAAAAATTGGTGGCTTG
1 TTGTTTGTAAAAATTGGTGGCTTG
*
1478689 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTAAAAATTGGTGGCT
1478711 AATTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.46
Consensus pattern (24 bp):
TTGTTTGTAAAAATTGGTGGCTTG
Found at i:1479119 original size:73 final size:73
Alignment explanation
Indices: 1479036--1479181 Score: 229
Period size: 73 Copynumber: 2.0 Consensus size: 73
1479026 TATATGATAT
1479036 GATTAAAAATATTTTTACAATCACAATTTAAATATTTAAATACATATAATATAGCAGAACAGTAA
1 GATTAAAAATATTTTTACAATCACAATTTAAATATTTAAATACATATAATATAGCAGAACAGTAA
1479101 TATAACAA
66 TATAACAA
* * * ** * *
1479109 GATTAAAAATATTTTTAGAATCATAATTTAAATATTTGAATTTATATAGTATAGCAGAACAGTAG
1 GATTAAAAATATTTTTACAATCACAATTTAAATATTTAAATACATATAATATAGCAGAACAGTAA
1479174 TATAACAA
66 TATAACAA
1479182 AAATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (73 bp):
GATTAAAAATATTTTTACAATCACAATTTAAATATTTAAATACATATAATATAGCAGAACAGTAA
TATAACAA
Found at i:1480620 original size:13 final size:13
Alignment explanation
Indices: 1480602--1480637 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1480592 AATTGTTTTT
1480602 ATTTATTAAATAA
1 ATTTATTAAATAA
*
1480615 ATTTATTTAATAA
1 ATTTATTAAATAA
*
1480628 ATTTAATAAA
1 ATTTATTAAA
1480638 AATTTATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTATTAAATAA
Found at i:1480651 original size:19 final size:21
Alignment explanation
Indices: 1480610--1480662 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
1480600 TTATTTATTA
*
1480610 AATAAATTTATTTAATAAATTT
1 AATAAA-TAATTTAATAAATTT
*
1480632 AATAAA-AATTT-ATAATTTT
1 AATAAATAATTTAATAAATTT
1480651 AATAAATAATTT
1 AATAAATAATTT
1480663 TATTTACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 13 0.46
20 9 0.32
22 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATAAATAATTTAATAAATTT
Found at i:1481815 original size:3 final size:3
Alignment explanation
Indices: 1481807--1481836 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1481797 CTTTAAATCA
1481807 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1481837 GGCATAAAAA
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:1482041 original size:2 final size:2
Alignment explanation
Indices: 1482036--1482068 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1482026 TAGTGTCGAC
1482036 TA TA TA 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
1482069 TTCTTTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1482134 original size:20 final size:20
Alignment explanation
Indices: 1482109--1482150 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1482099 CTCTACTTTT
* *
1482109 TCCAACAATATTAAGGCATA
1 TCCAACAATATAAAGACATA
*
1482129 TCCAACGATATAAAGACATA
1 TCCAACAATATAAAGACATA
1482149 TC
1 TC
1482151 ACGTTATGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.24
Consensus pattern (20 bp):
TCCAACAATATAAAGACATA
Found at i:1483908 original size:24 final size:23
Alignment explanation
Indices: 1483876--1483921 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1483866 TTGTCATTAT
*
1483876 TATTTTTAAAATTATTTATAATG
1 TATTTTTAAAAATATTTATAATG
*
1483899 TATTTATTAAAAATATTTTTAAT
1 TATTT-TTAAAAATATTTATAAT
1483922 AAAATTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TATTTTTAAAAATATTTATAATG
Found at i:1484210 original size:365 final size:362
Alignment explanation
Indices: 1483543--1484270 Score: 1145
Period size: 365 Copynumber: 2.0 Consensus size: 362
1483533 TAATAATTAT
* *
1483543 TTAAAAATATTTTTAATAAAATTTTATACACGCAAATTATAGATAAGAATCGCACGATACTCTTT
1 TTAAAAATATTTTTAATAAAATTTCATACACGCAAATTATAGATAAAAATCGCACGATACTCTTT
** * * **
1483608 ATTATATTTTAAGTATCGTAAGTGTTTCGTGTGAGCATGGATAAGTTTTAAATTTTTATTTTTAT
66 AAGATACTTTAAGTATCGCAAGTGTTTCGTGTGAAAATGGATAAGTTTTAAATTTTTATTTTTAT
*
1483673 TAATTTTTAATATTTTTTTACTGCAACAAAACAATAACTTAAAAAGTAAAAAACTTTAATAGTAC
131 TAATTTTTAATATTTTTTTACTGCAACAAAACAACAACTTAAAAAGTAAAAAACTTTAATAGTAC
* *
1483738 GTTTAATAAGCTAACGTAATTGTTAATTCTCATTAATTCATCATTAACCATATATAGGAGTTATC
196 GTTTAACAAGCTAACATAATTGTTAATTCTCATTAATTCATCATTAACCATATATAGGAGTTATC
*
1483803 GCCACCAGGGATCGCTTTCGATTCACAATTGCTTGCCATGCAATATAGCCACTTGTCCTTTTATT
261 GCCACCAGGGATCGCTTTCGATTCACAATTGCTTGCCATGCAATATAGCCAATTGTCCTTTTATT
1483868 GTCATTATTATTTTTAAAATTATTTATAATGTATTTA
326 GTCATTATTATTTTTAAAATTATTTATAATGTATTTA
* * *
1483905 TTAAAAATATTTTTAATAAAATTTCATACACGTAAATTATAGATAAAAATCGCAC-ATATTTTTT
1 TTAAAAATATTTTTAATAAAATTTCATACACGCAAATTATAGATAAAAATCGCACGATACTCTTT
* * *
1483969 AAGATACTTTAAGTATCGCAAGTGTTTCGTGTGATAAATCCTGAT-AGATTTTGAATTTTTGTTT
66 AAGATACTTTAAGTATCGCAAGTGTTTCGTGTGA-AAAT--GGATAAG-TTTTAAATTTTTATTT
* * * * *
1484033 TTGTTAGTTTTTAATATTTTTTTAACTGCACCAAAACGACAACTTAAAAAGTAAGAAACTTTAAT
127 TTATTAATTTTTAATATTTTTTT-ACTGCAACAAAACAACAACTTAAAAAGTAAAAAACTTTAAT
* *
1484098 GGTATGTTTAACAAGCTAACATAATTGTTAATTCTCATTAATTCATCATTAACCATATATAGGAG
191 AGTACGTTTAACAAGCTAACATAATTGTTAATTCTCATTAATTCATCATTAACCATATATAGGAG
* *
1484163 TTATCGCCACCAGGGATCGCTTTTGATTCACAATTGCTTGCCATGCAATATGGCCAATTGTCCTT
256 TTATCGCCACCAGGGATCGCTTTCGATTCACAATTGCTTGCCATGCAATATAGCCAATTGTCCTT
*
1484228 TTATTGTCATTATTATTTTTAAAATTATTTGTAATGTATTTA
321 TTATTGTCATTATTATTTTTAAAATTATTTATAATGTATTTA
1484270 T
1 T
1484271 ATATTTTTTG
Statistics
Matches: 333, Mismatches: 28, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
361 37 0.11
362 54 0.16
363 2 0.01
364 38 0.11
365 202 0.61
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.41
Consensus pattern (362 bp):
TTAAAAATATTTTTAATAAAATTTCATACACGCAAATTATAGATAAAAATCGCACGATACTCTTT
AAGATACTTTAAGTATCGCAAGTGTTTCGTGTGAAAATGGATAAGTTTTAAATTTTTATTTTTAT
TAATTTTTAATATTTTTTTACTGCAACAAAACAACAACTTAAAAAGTAAAAAACTTTAATAGTAC
GTTTAACAAGCTAACATAATTGTTAATTCTCATTAATTCATCATTAACCATATATAGGAGTTATC
GCCACCAGGGATCGCTTTCGATTCACAATTGCTTGCCATGCAATATAGCCAATTGTCCTTTTATT
GTCATTATTATTTTTAAAATTATTTATAATGTATTTA
Found at i:1484374 original size:37 final size:37
Alignment explanation
Indices: 1484333--1484408 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 37
1484323 ATTAATAATC
* *
1484333 TATATTGATAGATTTTAATATATTTATG-TATTTATAT
1 TATATTAATAGATTTTAATAT-TATATGATATTTATAT
** *
1484370 TATATTAATATTTTTTAATATTATATGATATTTTTAT
1 TATATTAATAGATTTTAATATTATATGATATTTATAT
1484407 TA
1 TA
1484409 CTCTTCGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
36 5 0.15
37 28 0.85
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (37 bp):
TATATTAATAGATTTTAATATTATATGATATTTATAT
Found at i:1484390 original size:21 final size:20
Alignment explanation
Indices: 1484366--1484404 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1484356 TTATGTATTT
1484366 ATATTATATTAATATTTTTTA
1 ATATTATA-TAATATTTTTTA
*
1484387 ATATTATATGATATTTTT
1 ATATTATATAATATTTTT
1484405 ATTACTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
ATATTATATAATATTTTTTA
Found at i:1485026 original size:19 final size:19
Alignment explanation
Indices: 1485004--1485051 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1484994 ATTTTATTTT
1485004 AAAAATTATTAT-TAAATTA
1 AAAAATT-TTATATAAATTA
*
1485023 AAAAATTTTATATAATTTA
1 AAAAATTTTATATAAATTA
*
1485042 TAAAATTTTA
1 AAAAATTTTA
1485052 AATTTATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAAATTTTATATAAATTA
Found at i:1485046 original size:20 final size:19
Alignment explanation
Indices: 1484999--1485059 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
1484989 TTTATATTTT
1484999 ATTT-TAAAAATTATTATTA
1 ATTTATAAAAATT-TTATTA
*
1485018 AATTA-AAAAATTTTATATA
1 ATTTATAAAAATTTTAT-TA
1485037 ATTTAT-AAAATTTTA--A
1 ATTTATAAAAATTTTATTA
1485053 ATTTATA
1 ATTTATA
1485060 TGATATCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
16 7 0.19
18 4 0.11
19 25 0.69
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTATAAAAATTTTATTA
Found at i:1486461 original size:37 final size:37
Alignment explanation
Indices: 1486376--1486462 Score: 88
Period size: 37 Copynumber: 2.3 Consensus size: 37
1486366 TATTAATATT
* * **
1486376 ATATATTTTTTATTTATTTTTAAAAAATATATTTTTA
1 ATATATTTTTTATTTAATTTTAAAAAATAAATACTTA
*
1486413 AT-TAATATTTTTA-TTAATTTTAAAATATAAATAACTTA
1 ATAT-AT-TTTTTATTTAATTTTAAAAAATAAAT-ACTTA
1486451 ATATATTTTTTA
1 ATATATTTTTTA
1486463 ATATTCATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
36 1 0.02
37 26 0.63
38 13 0.32
39 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (37 bp):
ATATATTTTTTATTTAATTTTAAAAAATAAATACTTA
Found at i:1486530 original size:18 final size:19
Alignment explanation
Indices: 1486493--1486530 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1486483 ATTTATTATT
*
1486493 ATATAATAAAAATAACATA
1 ATATAATAAAAATAAAATA
*
1486512 ATAT-ATAAAATTAAAATA
1 ATATAATAAAAATAAAATA
1486530 A
1 A
1486531 AAATATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
ATATAATAAAAATAAAATA
Found at i:1486542 original size:24 final size:24
Alignment explanation
Indices: 1486489--1486556 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 24
1486479 ATATATTTAT
*
1486489 TATTATATAATAAAAATAACATAATA
1 TATTATATAATTAAAATAA-A-AATA
1486515 TA-TA-A-AATTAAAATAAAAATA
1 TATTATATAATTAAAATAAAAATA
1486536 TATTATATAATTAAAAATAAA
1 TATTATATAATT-AAAATAAA
1486557 TCAAACACCA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 6 0.16
22 3 0.08
23 11 0.30
24 5 0.14
25 10 0.27
26 2 0.05
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (24 bp):
TATTATATAATTAAAATAAAAATA
Found at i:1487228 original size:25 final size:25
Alignment explanation
Indices: 1487193--1487240 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1487183 TATCTAATAA
* *
1487193 ATAATTAAATATTTTTAATTTATTT
1 ATAATTAAATATGTATAATTTATTT
*
1487218 ATAATTTAATATGTATAATTTAT
1 ATAATTAAATATGTATAATTTAT
1487241 ATGAACAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
ATAATTAAATATGTATAATTTATTT
Found at i:1487315 original size:12 final size:11
Alignment explanation
Indices: 1487275--1487321 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
1487265 ATCAAATTAA
*
1487275 TAAATATAAAT
1 TAAATAAAAAT
*
1487286 AAAATAAAAAT
1 TAAATAAAAAT
*
1487297 TATATAAATAAT
1 TAAATAAA-AAT
1487309 TAAAT-AAAAT
1 TAAATAAAAAT
1487319 TAA
1 TAA
1487322 TTTTTTATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
10 6 0.20
11 17 0.57
12 7 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAATAAAAAT
Found at i:1487331 original size:28 final size:26
Alignment explanation
Indices: 1487249--1487318 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 26
1487239 ATATGAACAG
*
1487249 AATATAAAATATAATAATCAAATTA-ATA
1 AATAT-AAATAAAATAA--AAATTATATA
1487277 AATATAAATAAAATAAAAATTATATA
1 AATATAAATAAAATAAAAATTATATA
1487303 AATAATTAAATAAAAT
1 AAT-A-TAAATAAAAT
1487319 TAATTTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
25 6 0.16
26 6 0.16
27 11 0.29
28 15 0.39
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (26 bp):
AATATAAATAAAATAAAAATTATATA
Found at i:1487841 original size:18 final size:20
Alignment explanation
Indices: 1487804--1487841 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1487794 ATATATAAGT
*
1487804 TAAATAAATTTTATTAATAA
1 TAAATAAATTATATTAATAA
1487824 TAAA-AAATTATA-TAATAA
1 TAAATAAATTATATTAATAA
1487842 CAATTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAATAAATTATATTAATAA
Found at i:1488127 original size:74 final size:74
Alignment explanation
Indices: 1488045--1488194 Score: 246
Period size: 74 Copynumber: 2.0 Consensus size: 74
1488035 AACAATGAAT
* *
1488045 ATTTTTATAATTCAAAAGATTCTTTATATTTTTACTTTTATATAAATTAGTATTTATTATCATAT
1 ATTTTTATAATTCAAAAGATTCTTTATATTCTTACTTTTATATAAATTAGTATTTATAATCATAT
1488110 ACATAATAC
66 ACATAATAC
* * * *
1488119 ATTTTTATAATTTAAAAGATTTTTTATATTCTTACTTTTATATATATTAGTATTTGTAATCATAT
1 ATTTTTATAATTCAAAAGATTCTTTATATTCTTACTTTTATATAAATTAGTATTTATAATCATAT
1488184 ACATAATAC
66 ACATAATAC
1488193 AT
1 AT
1488195 GAATGCTCTA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.52
Consensus pattern (74 bp):
ATTTTTATAATTCAAAAGATTCTTTATATTCTTACTTTTATATAAATTAGTATTTATAATCATAT
ACATAATAC
Found at i:1488310 original size:17 final size:19
Alignment explanation
Indices: 1488290--1488330 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 19
1488280 TGATTTAATT
1488290 TAAAATTAA-AATT-TATA
1 TAAAATTAACAATTCTATA
1488307 T-AAA-TAACAATTCTATA
1 TAAAATTAACAATTCTATA
1488324 TAAAATT
1 TAAAATT
1488331 TAATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
15 3 0.15
16 7 0.35
17 6 0.30
18 3 0.15
19 1 0.05
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAATTAACAATTCTATA
Found at i:1489396 original size:20 final size:20
Alignment explanation
Indices: 1489371--1489412 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1489361 CTCTACTTTT
1489371 TCCAACAATATAAAGACATA
1 TCCAACAATATAAAGACATA
*
1489391 TCCAACGATATAAAGACATA
1 TCCAACAATATAAAGACATA
1489411 TC
1 TC
1489413 ACGTTATGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (20 bp):
TCCAACAATATAAAGACATA
Found at i:1490829 original size:25 final size:23
Alignment explanation
Indices: 1490799--1490846 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1490789 AAGTCTGAAC
*
1490799 TTATTTATAAGTAATATTTTAATAA
1 TTATTTA-AAATAAT-TTTTAATAA
*
1490824 TTATTTAAAATTATTTTTAATAA
1 TTATTTAAAATAATTTTTAATAA
1490847 AATTTTATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 5 0.24
25 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TTATTTAAAATAATTTTTAATAA
Found at i:1491270 original size:31 final size:31
Alignment explanation
Indices: 1491220--1491297 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
1491210 ACATTATTTT
*
1491220 ATATATTT-TATATATAAATTTTAATATATTA
1 ATATATTTATAT-TATAAATTTTAACATATTA
*
1491251 ATA-ATTTATATTGATAAATTTTAACATATTT
1 ATATATTTATATT-ATAAATTTTAACATATTA
*
1491282 ATATATTTGTATTATA
1 ATATATTTATATTATA
1491298 TTAATATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 5 0.12
31 28 0.68
32 8 0.20
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (31 bp):
ATATATTTATATTATAAATTTTAACATATTA
Found at i:1491289 original size:18 final size:18
Alignment explanation
Indices: 1491217--1491329 Score: 68
Period size: 19 Copynumber: 6.7 Consensus size: 18
1491207 ATAACATTAT
1491217 TTTATATATTTT-ATATA
1 TTTATATATTTTAATATA
1491234 --TA-A-ATTTTAATATA
1 TTTATATATTTTAATATA
*
1491248 -TTA-ATA-ATT--TATA
1 TTTATATATTTTAATATA
* * *
1491261 TTGATAAATTTTAACATA
1 TTTATATATTTTAATATA
*
1491279 TTTATATATTTGTATTATA
1 TTTATATATTT-TAATATA
*
1491298 TTAATATATTTTAATATTA
1 TTTATATATTTTAATA-TA
1491317 TATTATAT-TTTTA
1 T-TTATATATTTTA
1491330 TTTTTTCATA
Statistics
Matches: 73, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
13 9 0.12
14 8 0.11
15 9 0.12
16 3 0.04
18 16 0.22
19 23 0.32
20 5 0.07
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTATATATTTTAATATA
Found at i:1491335 original size:26 final size:26
Alignment explanation
Indices: 1491291--1491350 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
1491281 TATATATTTG
1491291 TATTATATTAATATATTTTAATATTA
1 TATTATATTAATATATTTTAATATTA
** * *
1491317 TATTATATTTTTATTTTTTCATATTA
1 TATTATATTAATATATTTTAATATTA
*
1491343 TATCATAT
1 TATTATAT
1491351 CATGTCTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (26 bp):
TATTATATTAATATATTTTAATATTA
Found at i:1492517 original size:3 final size:3
Alignment explanation
Indices: 1492511--1492543 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1492501 GATGGAAAAA
1492511 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1492544 GAGCAGCAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Done.