Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold302
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: 555664
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 4 of 4
Found at i:464047 original size:185 final size:186
Alignment explanation
Indices: 463830--464207 Score: 564
Period size: 185 Copynumber: 2.0 Consensus size: 186
463820 CTTAAAAGGG
* *
463830 AAAATGGTGCCACGGAGTCATGGACTTAAAAAGAAAAGGTGCCACGGAGTTGTAGACTTAAAAGA
1 AAAAAGGTGCCACGGAGTCATGGACTTAAAAAGAAAAGGTGCCACGGAGTTATAGACTTAAAAGA
* * *
463895 AACAAGGTGCCATGGAGTTGTGGACTTAAAAAGAAAAAGATGCCACGAAGTTGTGGACTTAAAAG
66 AACAAGGTGCCATAGAGTTGTGAACTTAAAAAGAAAAAGATGCCACGAAGTTGTGAACTTAAAAG
* *
463960 GGTGCCACGGAGTTATGGACTTAAAAGGAAAAAGA-TACCACGGAGTTGT-AGACTT
131 GGTGCCACGAAGTTATGGACTTAAAAGGAAAAAGAGTACCACGGAATTGTGAG-CTT
* * *
464015 AAAAAGGTGCCA-GAGAGTCGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTATGGATTTAAAAG
1 AAAAAGGTGCCACG-GAGTCATGGACTTAAAAAGAAAAGGTGCCACGGAGTTATAGACTTAAAAG
* * * *
464079 GAACAAGGTGCCATAGAGTTGTGAACTTAAAAGGAAAAAGATGCCATGGAGTTGTGAACTTAAAA
65 AAACAAGGTGCCATAGAGTTGTGAACTTAAAAAGAAAAAGATGCCACGAAGTTGTGAACTTAAAA
* *
464144 GGGTGCCACGAAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAATTGTGAGCTT
130 GGGTGCCACGAAGTTATGGACTTAAAAGGAAAAAGAGTACCACGGAATTGTGAGCTT
*
464201 TAAAAGG
1 AAAAAGG
464208 AAAAAGGTGC
Statistics
Matches: 173, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
184 1 0.01
185 149 0.86
186 21 0.12
187 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.29, T:0.20
Consensus pattern (186 bp):
AAAAAGGTGCCACGGAGTCATGGACTTAAAAAGAAAAGGTGCCACGGAGTTATAGACTTAAAAGA
AACAAGGTGCCATAGAGTTGTGAACTTAAAAAGAAAAAGATGCCACGAAGTTGTGAACTTAAAAG
GGTGCCACGAAGTTATGGACTTAAAAGGAAAAAGAGTACCACGGAATTGTGAGCTT
Found at i:464211 original size:35 final size:33
Alignment explanation
Indices: 464140--464692 Score: 386
Period size: 34 Copynumber: 16.8 Consensus size: 33
464130 TTGTGAACTT
*
464140 AAAAGGGTGCCAC-GAAGTTGTGGACTTAAAAGG
1 AAAAAGGTGCCACGGAA-TTGTGGACTTAAAAGG
464173 AAAAAGAGTGCCACGGAATTGT-GAGCTTTAAAAGG
1 AAAAAG-GTGCCACGGAATTGTGGA-C-TTAAAAGG
* *
464208 AAAAAGGTGCCACGGAGTTGTGGACTT-ATAGG
1 AAAAAGGTGCCACGGAATTGTGGACTTAAAAGG
* * *
464240 -----GGTGCCACGTAGTTGTGGACTT-ACAGG
1 AAAAAGGTGCCACGGAATTGTGGACTTAAAAGG
* ** **
464267 AAAAACGAATGCCATAGAGGTGTAGG-CTTAAAAAGG
1 AAAAA-G-GTGCCACGGAATTGT-GGACTT-AAAAGG
* * * *
464303 AACAAGGTGCCACGGAGTCGTGGACTTAAAAAG
1 AAAAAGGTGCCACGGAATTGTGGACTTAAAAGG
* *
464336 -AAAAGGTGCCAC-GAAGTTGTAGACTTAAAAAG
1 AAAAAGGTGCCACGGAA-TTGTGGACTTAAAAGG
* *
464368 -AAAAGGTGCCACGGAGTTGTGGACTTAAAAAG
1 AAAAAGGTGCCACGGAATTGTGGACTTAAAAGG
* * * *
464400 AACAAGGTGCCACGGAGTTATGGACTT-ATAGG
1 AAAAAGGTGCCACGGAATTGTGGACTTAAAAGG
** ** *
464432 AAAAACGGATGCCATAGAGGTGTGGGCTTAAAAAGG
1 AAAAA-GG-TGCCACGGAATTGTGGACTT-AAAAGG
* * * *
464468 AACAAGGTGCCACGGAGTCGTGGACTTAAAAAG
1 AAAAAGGTGCCACGGAATTGTGGACTTAAAAGG
* * ** *
464501 -AAAAGGTGCCACAGAGTCATGGACTTAAAA-A
1 AAAAAGGTGCCACGGAATTGTGGACTTAAAAGG
*
464532 AAGTAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
1 AA--AAAGGTGCCACGGAATTGTGGACTTAAAAGG
* ** *
464567 AACAAGGTGCCATAGAGTTGTGGACTTAAAAGG
1 AAAAAGGTGCCACGGAATTGTGGACTTAAAAGG
* * *
464600 GAAAAGGTGCCACGGAGTTATGGACTTAAAAGG
1 AAAAAGGTGCCACGGAATTGTGGACTTAAAAGG
* * *
464633 -AAAATGTGCCACGGAGTTGTGGGCTTAAAAGGG
1 AAAAAGGTGCCACGGAATTGTGGACTTAAAA-GG
* *
464666 AAAAGGGTGCCAC-GAAGTCGTGGACTT
1 AAAAAGGTGCCACGGAA-TTGTGGACTT
464693 TGAAAAGAGA
Statistics
Matches: 424, Mismatches: 66, Indels: 59
0.77 0.12 0.11
Matches are distributed among these distances:
27 25 0.06
31 2 0.00
32 118 0.28
33 110 0.26
34 127 0.30
35 26 0.06
36 16 0.04
ACGTcount: A:0.36, C:0.14, G:0.31, T:0.19
Consensus pattern (33 bp):
AAAAAGGTGCCACGGAATTGTGGACTTAAAAGG
Found at i:464709 original size:31 final size:31
Alignment explanation
Indices: 464673--464850 Score: 227
Period size: 31 Copynumber: 5.6 Consensus size: 31
464663 GGGAAAAGGG
*
464673 TGCCAC-GAAGTCGTGGACTTTGAA-AAGAGA
1 TGCCACTG-AGTCGTGGACTTTGAAGAAAAGA
* *
464703 TTGCCACTGAGTCGTGGACTTTG-GGAAGAGA
1 -TGCCACTGAGTCGTGGACTTTGAAGAAAAGA
*
464734 TTGCCACTGAGTTGTGGACTTTGAAGAAAAGA
1 -TGCCACTGAGTCGTGGACTTTGAAGAAAAGA
464766 TGCCACTGAGTCGTGGACTTTGAAGAAAAGAAA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAG--A
* *
464799 TGCCACTAAGTCGTGGACTTGGAAGAAAAGGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAA-GA
464831 TGCCACTGAGTCGTGGACTT
1 TGCCACTGAGTCGTGGACTT
464851 AGAAAAGAAA
Statistics
Matches: 133, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
31 77 0.58
32 27 0.20
33 28 0.21
34 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAAGAAAAGA
Found at i:466074 original size:11 final size:11
Alignment explanation
Indices: 466060--466107 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
466050 TTTTTGCACT
466060 TTTTTTTGGTG
1 TTTTTTTGGTG
*
466071 TTTTTTT-GTT
1 TTTTTTTGGTG
*
466081 TTTTTTTGTTG
1 TTTTTTTGGTG
*
466092 TTTTTTTTGTG
1 TTTTTTTGGTG
466103 TTTTT
1 TTTTT
466108 ACTTTTGACT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 9 0.29
11 22 0.71
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (11 bp):
TTTTTTTGGTG
Found at i:466083 original size:21 final size:22
Alignment explanation
Indices: 466059--466107 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
466049 CTTTTTGCAC
466059 TTTTTTTTGGTG-TTTTTTTGT
1 TTTTTTTTGGTGTTTTTTTTGT
*
466080 TTTTTTTTGTTGTTTTTTTTGT
1 TTTTTTTTGGTGTTTTTTTTGT
*
466102 GTTTTT
1 TTTTTT
466108 ACTTTTGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (22 bp):
TTTTTTTTGGTGTTTTTTTTGT
Found at i:470904 original size:25 final size:25
Alignment explanation
Indices: 470855--470904 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
470845 GGTTGAAAAC
*
470855 GGGGTTGGAGTGTCCCCTCGGATGA
1 GGGGTTGGAGTGTCCCCTCGAATGA
470880 GGGGTTGGAGTGTCCCCGTC-AATGA
1 GGGGTTGGAGTGTCCCC-TCGAATGA
470905 TAACTTAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.14, C:0.20, G:0.42, T:0.24
Consensus pattern (25 bp):
GGGGTTGGAGTGTCCCCTCGAATGA
Found at i:473639 original size:13 final size:13
Alignment explanation
Indices: 473621--473645 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
473611 CATGGCACAT
473621 TGTATCGATACAA
1 TGTATCGATACAA
473634 TGTATCGATACA
1 TGTATCGATACA
473646 TGATAAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:473643 original size:33 final size:33
Alignment explanation
Indices: 473601--473665 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
473591 TACCATTGTT
* *
473601 TGTATCGATACATGGCACATTGTATCGATACAA
1 TGTATCGATACATGACAAATTGTATCGATACAA
*
473634 TGTATCGATACATGATAAATTGTATCGATACA
1 TGTATCGATACATGACAAATTGTATCGATACA
473666 TTGCTTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATGACAAATTGTATCGATACAA
Found at i:474382 original size:19 final size:20
Alignment explanation
Indices: 474358--474413 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
474348 TGTATCGATA
*
474358 CATTGTATCGATATATG-TT
1 CATTGTATCGATATATGCAT
*
474377 CATTGTATCGATACATGCAT
1 CATTGTATCGATATATGCAT
*
474397 AATTGTATCGATATATG
1 CATTGTATCGATATATG
474414 AAAATGGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.41
Consensus pattern (20 bp):
CATTGTATCGATATATGCAT
Found at i:474403 original size:20 final size:19
Alignment explanation
Indices: 474354--474414 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
474344 GCTTTGTATC
*
474354 GATACATTGTATCGATATAT
1 GATA-ATTGTATCGATACAT
* *
474374 GTTCATTGTATCGATACAT
1 GATAATTGTATCGATACAT
*
474393 GCATAATTGTATCGATATAT
1 G-ATAATTGTATCGATACAT
474413 GA
1 GA
474415 AAATGGCAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.39
Consensus pattern (19 bp):
GATAATTGTATCGATACAT
Found at i:474481 original size:33 final size:33
Alignment explanation
Indices: 474443--474507 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
474433 TACCACTATT
* *
474443 TGTATCGATACATGGCACATTGTATCGATATAA
1 TGTATCGATACATGACAAATTGTATCGATATAA
*
474476 TGTATCGATACATGATAAATTGTATCGATATA
1 TGTATCGATACATGACAAATTGTATCGATATA
474508 TTGCTTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATGACAAATTGTATCGATATAA
Found at i:476104 original size:3 final size:3
Alignment explanation
Indices: 476090--476120 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
476080 CATCAAAGAG
*
476090 GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
476121 TTGACTCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:482545 original size:44 final size:44
Alignment explanation
Indices: 482495--482581 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
482485 AAAAGGGGAG
*
482495 AAATTTTTGAAAATAAATTTTTATCAAGGGGGAGAAAATTTTTA
1 AAATTTTTGAAAATAAATTTTTATCAAAGGGGAGAAAATTTTTA
*
482539 AAATTTTTGAAAATAAATTTTTATCAAATGGGAGAAAATTTTT
1 AAATTTTTGAAAATAAATTTTTATCAAAGGGGAGAAAATTTTT
482582 TAACAAGAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (44 bp):
AAATTTTTGAAAATAAATTTTTATCAAAGGGGAGAAAATTTTTA
Found at i:483290 original size:13 final size:13
Alignment explanation
Indices: 483272--483296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
483262 CATGGCACAT
483272 TGTATCGATACAA
1 TGTATCGATACAA
483285 TGTATCGATACA
1 TGTATCGATACA
483297 TGATAAATTA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:484345 original size:178 final size:178
Alignment explanation
Indices: 484046--484402 Score: 714
Period size: 178 Copynumber: 2.0 Consensus size: 178
484036 TTTCTCCTCG
484046 ACACTTCCTTGTCGAGTATATACCACAACTCACTACTAGAATGGTTTACCTTTAAGGCAAAGGTA
1 ACACTTCCTTGTCGAGTATATACCACAACTCACTACTAGAATGGTTTACCTTTAAGGCAAAGGTA
484111 TACCTTACAACACTTATCTTTTGAAAGCTAAGATAAAAGCCTCTCAATCTCTCTAAGAATTATAC
66 TACCTTACAACACTTATCTTTTGAAAGCTAAGATAAAAGCCTCTCAATCTCTCTAAGAATTATAC
484176 CCAAAATCCTTGAGAGATTGTGTCCTAAGATTGAATACAACCTTTACA
131 CCAAAATCCTTGAGAGATTGTGTCCTAAGATTGAATACAACCTTTACA
484224 ACACTTCCTTGTCGAGTATATACCACAACTCACTACTAGAATGGTTTACCTTTAAGGCAAAGGTA
1 ACACTTCCTTGTCGAGTATATACCACAACTCACTACTAGAATGGTTTACCTTTAAGGCAAAGGTA
484289 TACCTTACAACACTTATCTTTTGAAAGCTAAGATAAAAGCCTCTCAATCTCTCTAAGAATTATAC
66 TACCTTACAACACTTATCTTTTGAAAGCTAAGATAAAAGCCTCTCAATCTCTCTAAGAATTATAC
484354 CCAAAATCCTTGAGAGATTGTGTCCTAAGATTGAATACAACCTTTACA
131 CCAAAATCCTTGAGAGATTGTGTCCTAAGATTGAATACAACCTTTACA
484402 A
1 A
484403 TACAAAGAGA
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
178 179 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.30
Consensus pattern (178 bp):
ACACTTCCTTGTCGAGTATATACCACAACTCACTACTAGAATGGTTTACCTTTAAGGCAAAGGTA
TACCTTACAACACTTATCTTTTGAAAGCTAAGATAAAAGCCTCTCAATCTCTCTAAGAATTATAC
CCAAAATCCTTGAGAGATTGTGTCCTAAGATTGAATACAACCTTTACA
Found at i:484881 original size:46 final size:46
Alignment explanation
Indices: 484814--484905 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
484804 ACATTTTAAG
484814 TATGTATCGATACTTTGTATCGATAAAAAGGGAGTTTTAGCTACTT
1 TATGTATCGATACTTTGTATCGATAAAAAGGGAGTTTTAGCTACTT
484860 TATGTATCGATACTTTGTATCGATAAAAAGGGAGTTTTAGCTACTT
1 TATGTATCGATACTTTGTATCGATAAAAAGGGAGTTTTAGCTACTT
484906 CCAGTTTCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (46 bp):
TATGTATCGATACTTTGTATCGATAAAAAGGGAGTTTTAGCTACTT
Found at i:484978 original size:32 final size:33
Alignment explanation
Indices: 484934--484996 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
484924 ATAATTCAAT
*
484934 ATGTATCAATACTAAG-AATATGTATCGATATA
1 ATGTATCAATACTAAGCAATATATATCGATATA
*
484966 ATGTATCGATACTAAGCAATATATATCGATA
1 ATGTATCAATACTAAGCAATATATATCGATA
484997 CATCTGGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (33 bp):
ATGTATCAATACTAAGCAATATATATCGATATA
Found at i:486369 original size:51 final size:51
Alignment explanation
Indices: 486314--486412 Score: 141
Period size: 51 Copynumber: 1.9 Consensus size: 51
486304 GAGTATCCTT
*
486314 GATTATAGAAAA-TTGGTGTTTT-GAAAATAAAATCG-GAGTTGGAGTATCTCC
1 GATTAT-GAAAATTTGGTATTTTAG-AAATAAAATCGAG-GTTGGAGTATCTCC
486365 GATTATGAAAATTTGGTATTTTAGAAATAAAATCGAGGTTGGAGTATC
1 GATTATGAAAATTTGGTATTTTAGAAATAAAATCGAGGTTGGAGTATC
486413 CCCTCGAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
50 5 0.11
51 37 0.84
52 2 0.05
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.34
Consensus pattern (51 bp):
GATTATGAAAATTTGGTATTTTAGAAATAAAATCGAGGTTGGAGTATCTCC
Found at i:486602 original size:51 final size:50
Alignment explanation
Indices: 486539--486682 Score: 184
Period size: 51 Copynumber: 2.8 Consensus size: 50
486529 AAATAACGGG
486539 GTTGGAGTATCCCCAATTGTGAAAAATT-AGTGTTTTGAAAATAAAATCAGA
1 GTTGGAGTATCCCCAATTG-GAAAAATTGA-TGTTTTGAAAATAAAATCAGA
* * *
486590 GTTGGAGTATCCCCAATTGCAATAAATCGATGCTTTT-AAAAAAAAATCAGA
1 GTTGGAGTATCCCCAATTGGAA-AAATTGATG-TTTTGAAAATAAAATCAGA
* *
486641 GTTGGAGTATCCCCAATTAAGAAAAATTGATGTTTTGGAAAT
1 GTTGGAGTATCCCCAATT-GGAAAAATTGATGTTTTGAAAAT
486683 GGAACCGGGA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
50 6 0.08
51 67 0.84
52 7 0.09
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.31
Consensus pattern (50 bp):
GTTGGAGTATCCCCAATTGGAAAAATTGATGTTTTGAAAATAAAATCAGA
Found at i:489023 original size:20 final size:19
Alignment explanation
Indices: 488998--489154 Score: 104
Period size: 20 Copynumber: 7.8 Consensus size: 19
488988 AAAATGCCTG
*
488998 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AA
*
489018 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
489038 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
* *
489058 AATATATCGATACATCTGGGTAA
1 AATGTATCGATACA-AT--G-AA
* * * *
489081 ACCTAGAAT-G-TACCGAT-AT
1 A-AT-GTATCGATA-CAATGAA
*
489100 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
489120 AATGTATCGATACAATGAA
1 AATGTATCGATACAATGAA
489139 CAATGTATCGATACAA
1 -AATGTATCGATACAA
489155 ATTGTGAAAA
Statistics
Matches: 107, Mismatches: 17, Indels: 26
0.71 0.11 0.17
Matches are distributed among these distances:
17 3 0.03
18 5 0.05
19 6 0.06
20 79 0.74
21 2 0.02
23 7 0.07
24 3 0.03
25 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:489975 original size:68 final size:68
Alignment explanation
Indices: 489861--490017 Score: 260
Period size: 68 Copynumber: 2.3 Consensus size: 68
489851 ACTCCCCTTT
* * *
489861 AACAACTTTTCTCCCCTTTAACAAAATATTTAGTACTCCCCCTTAACAAATTGTCCCTCTTTTAT
1 AACAACTTTTCTCCCCCTTAACAAAATATTTAGTACTCCCCATTAACAAATTATCCCTCTTTTAT
489926 AAA
66 AAA
* *
489929 AATAACTTTTCTCCCCCTTAACAAAATATTTAGTACTTCCCATTAACAAATTATCCCTCTTTTAT
1 AACAACTTTTCTCCCCCTTAACAAAATATTTAGTACTCCCCATTAACAAATTATCCCTCTTTTAT
*
489994 ATA
66 AAA
489997 AACAACTTTTCTCCCCCTTAA
1 AACAACTTTTCTCCCCCTTAA
490018 TTTATTACAC
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 82 1.00
ACGTcount: A:0.32, C:0.28, G:0.02, T:0.38
Consensus pattern (68 bp):
AACAACTTTTCTCCCCCTTAACAAAATATTTAGTACTCCCCATTAACAAATTATCCCTCTTTTAT
AAA
Found at i:492102 original size:21 final size:20
Alignment explanation
Indices: 492068--492110 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
492058 TTAAACATCA
*
492068 AATACATCAATAATTAAGCAC
1 AATACAACAATAA-TAAGCAC
* *
492089 AATACAACATTAATAATCAC
1 AATACAACAATAATAAGCAC
492109 AA
1 AA
492111 AATCACAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.56, C:0.19, G:0.02, T:0.23
Consensus pattern (20 bp):
AATACAACAATAATAAGCAC
Found at i:493616 original size:13 final size:13
Alignment explanation
Indices: 493598--493623 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
493588 TACAGCAAGT
493598 ATGTATCGATACA
1 ATGTATCGATACA
493611 ATGTATCGATACA
1 ATGTATCGATACA
493624 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:495869 original size:21 final size:21
Alignment explanation
Indices: 495836--495880 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
495826 TTGCAAGTTG
*
495836 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
495858 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
495878 AAA
1 AAA
495881 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:497704 original size:15 final size:15
Alignment explanation
Indices: 497684--497714 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
497674 TAAAAATGTC
*
497684 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
497699 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
497714 C
1 C
497715 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:499812 original size:13 final size:13
Alignment explanation
Indices: 499794--499819 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
499784 CATTTTTTCT
499794 TTGTATCGATACA
1 TTGTATCGATACA
499807 TTGTATCGATACA
1 TTGTATCGATACA
499820 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:502391 original size:13 final size:13
Alignment explanation
Indices: 502373--502398 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
502363 TACAGTAAGT
502373 ATGTATCGATACA
1 ATGTATCGATACA
502386 ATGTATCGATACA
1 ATGTATCGATACA
502399 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:504887 original size:17 final size:18
Alignment explanation
Indices: 504853--504893 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
504843 AAAAAAATAA
504853 AATTTTTATAATTTAAATT
1 AATTTTTATAATTTAAA-T
504872 AATTTTTA-AA-TTAAAT
1 AATTTTTATAATTTAAAT
504888 AATTTT
1 AATTTT
504894 ATTATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 5 0.23
18 2 0.09
19 8 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTTTATAATTTAAAT
Found at i:504900 original size:8 final size:9
Alignment explanation
Indices: 504889--504945 Score: 59
Period size: 8 Copynumber: 6.7 Consensus size: 9
504879 AAATTAAATA
504889 ATTTTAT-T
1 ATTTTATAT
504897 ATTTT-TAT
1 ATTTTATAT
*
504905 ATTTT-TAA
1 ATTTTATAT
504913 ATATTTAT-T
1 AT-TTTATAT
504922 ATTTTATAT
1 ATTTTATAT
*
504931 ATTTTTTAT
1 ATTTTATAT
504940 ATTTTA
1 ATTTTA
504946 AATTTTTACA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
7 1 0.02
8 20 0.49
9 19 0.46
10 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
ATTTTATAT
Found at i:504908 original size:16 final size:17
Alignment explanation
Indices: 504889--504953 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 17
504879 AAATTAAATA
504889 ATTTTAT-TATTTTTAT
1 ATTTTATATATTTTTAT
* *
504905 ATTTT-TAAATATTTATT
1 ATTTTATATATTTTTA-T
504922 ATTTTATATATTTTTTAT
1 ATTTTATATA-TTTTTAT
504940 ATTTTA-A-ATTTTTA
1 ATTTTATATATTTTTA
504954 CAAAATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
15 7 0.17
16 12 0.29
17 7 0.17
18 10 0.24
19 5 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTATATATTTTTAT
Found at i:504931 original size:26 final size:27
Alignment explanation
Indices: 504882--504936 Score: 87
Period size: 25 Copynumber: 2.1 Consensus size: 27
504872 AATTTTTAAA
504882 TTAAATAATTTTATTATTTTTATATTT
1 TTAAATAATTTTATTATTTTTATATTT
504909 TTAAAT-A-TTTATTATTTTATATATTT
1 TTAAATAATTTTATTATTTT-TATATTT
504935 TT
1 TT
504937 TATATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 11 0.41
26 10 0.37
27 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTAAATAATTTTATTATTTTTATATTT
Found at i:504952 original size:8 final size:8
Alignment explanation
Indices: 504890--504953 Score: 58
Period size: 8 Copynumber: 7.6 Consensus size: 8
504880 AATTAAATAA
504890 TTTTATTAT
1 TTTTA-TAT
504899 TTTTATAT
1 TTTTATAT
*
504907 TTTTAAAT
1 TTTTATAT
*
504915 ATTTATTAT
1 TTTTA-TAT
504924 TTTATATAT
1 TTT-TATAT
504933 TTTT-TAT
1 TTTTATAT
*
504940 ATTTTAAAT
1 -TTTTATAT
504949 TTTTA
1 TTTTA
504954 CAAAATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
7 3 0.07
8 24 0.52
9 17 0.37
10 2 0.04
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTATAT
Found at i:505454 original size:33 final size:32
Alignment explanation
Indices: 505417--505488 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 32
505407 TATTTAATTA
*
505417 TTAATTTTAAAAAATTATATACGTAT-TATTTTT
1 TTAATTTTAAAAAA-TAT-TAAGTATATATTTTT
*
505450 TTAA--TTAAAAAATATTAATTATATATTTTT
1 TTAATTTTAAAAAATATTAAGTATATATTTTT
*
505480 TAAATTTTA
1 TTAATTTTA
505489 TTTTTAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
29 5 0.15
30 13 0.39
31 8 0.24
32 3 0.09
33 4 0.12
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (32 bp):
TTAATTTTAAAAAATATTAAGTATATATTTTT
Found at i:505522 original size:14 final size:14
Alignment explanation
Indices: 505462--505522 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
505452 AATTAAAAAA
505462 TATTAATTATATATT
1 TATTAATTA-ATATT
* *
505477 TTTTAAATT-TTATT
1 TATT-AATTAATATT
*
505491 T-TTAATTAATATG
1 TATTAATTAATATT
*
505504 CATTAATTAATATT
1 TATTAATTAATATT
505518 TATTA
1 TATTA
505523 TTATCATTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
12 4 0.11
13 5 0.14
14 20 0.56
15 3 0.08
16 4 0.11
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (14 bp):
TATTAATTAATATT
Found at i:505525 original size:3 final size:3
Alignment explanation
Indices: 505517--505560 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
505507 TAATTAATAT
* *
505517 TTA TTA TTA TCA TTA TTTA TTTA TTT TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA
505561 CAAGAAACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 29 0.81
4 7 0.19
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:505539 original size:20 final size:20
Alignment explanation
Indices: 505514--505553 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
505504 CATTAATTAA
505514 TATTTATTATTATCATTATT
1 TATTTATTATTATCATTATT
* *
505534 TATTTATTTTTATTATTATT
1 TATTTATTATTATCATTATT
505554 ATTATTACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTTATTATTATCATTATT
Found at i:509050 original size:3 final size:3
Alignment explanation
Indices: 509036--509094 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
509026 TTCCTTATTA
*
509036 AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
509084 AAT AAT AAT AA
1 AAT AAT AAT AA
509095 ACGAAAGAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:509933 original size:5 final size:5
Alignment explanation
Indices: 509923--509954 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
509913 CTATCTCTCT
*
509923 TCTTC TCTTC TCGTC TCTTC TCTTC TCTTC TC
1 TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TC
509955 CCCTCCTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.41, G:0.03, T:0.56
Consensus pattern (5 bp):
TCTTC
Found at i:509939 original size:10 final size:9
Alignment explanation
Indices: 509916--509954 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
509906 TCAATTTCTA
509916 TCTCTCTTC
1 TCTCTCTTC
509925 T-TCTCTTC
1 TCTCTCTTC
509933 TCGTCTCTTC
1 TC-TCTCTTC
509943 TCTTCTCTTC
1 TC-TCTCTTC
509953 TC
1 TC
509955 CCCTCCTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 8 0.30
9 1 0.04
10 18 0.67
ACGTcount: A:0.00, C:0.41, G:0.03, T:0.56
Consensus pattern (9 bp):
TCTCTCTTC
Found at i:510468 original size:2 final size:2
Alignment explanation
Indices: 510461--510494 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
510451 TTACAACCAG
510461 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
510495 CATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:510655 original size:6 final size:6
Alignment explanation
Indices: 510638--510676 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
510628 ACCTCCAGTT
* *
510638 TGCTGC TGCTAC TCCTAC TGCTAC TGCTAC TGCTAC TGC
1 TGCTAC TGCTAC TGCTAC TGCTAC TGCTAC TGCTAC TGC
510677 GACTAGACAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.13, C:0.36, G:0.18, T:0.33
Consensus pattern (6 bp):
TGCTAC
Found at i:513328 original size:16 final size:16
Alignment explanation
Indices: 513309--513344 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
513299 AAATAACTCG
513309 AACCCGAAATGATCCA
1 AACCCGAAATGATCCA
*
513325 AACCCGAAATGATTCA
1 AACCCGAAATGATCCA
513341 AACC
1 AACC
513345 TAAAGTAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.31, G:0.11, T:0.14
Consensus pattern (16 bp):
AACCCGAAATGATCCA
Found at i:513698 original size:22 final size:21
Alignment explanation
Indices: 513659--513700 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
513649 TAACTTTTAT
*
513659 CATATAAATATAAATATATAG
1 CATATAAAAATAAATATATAG
*
513680 CATATAAAGAATAACTATATA
1 CATATAAA-AATAAATATATA
513701 TAACATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (21 bp):
CATATAAAAATAAATATATAG
Found at i:515060 original size:4 final size:4
Alignment explanation
Indices: 515051--515077 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
515041 ATGTTTTTAG
515051 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
515078 CTAGGCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:515588 original size:2 final size:2
Alignment explanation
Indices: 515581--515611 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
515571 TTTCATTTTC
515581 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
515612 TATGTGGAAA
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:516207 original size:2 final size:2
Alignment explanation
Indices: 516200--516229 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
516190 CCCTTCCATA
*
516200 AT AT AT AT AC 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
516230 TAATAAGAGG
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:516782 original size:2 final size:2
Alignment explanation
Indices: 516775--516804 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
516765 AGTATAAGCA
516775 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
516805 TTTTCAAAAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:519267 original size:23 final size:21
Alignment explanation
Indices: 519233--519289 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
519223 CATTACTAAT
*
519233 TTGTTATCAATTTATTTATTATG
1 TTGTTAT-AATTGATTTA-TATG
519256 TTGTTCATAATTGATTTATATG
1 TTGTT-ATAATTGATTTATATG
*
519278 TTATTGATAATT
1 TTGTT-ATAATT
519290 ATCATAAGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.47
23 14 0.47
24 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.58
Consensus pattern (21 bp):
TTGTTATAATTGATTTATATG
Found at i:519287 original size:22 final size:23
Alignment explanation
Indices: 519241--519289 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
519231 ATTTGTTATC
* *
519241 AATTTATTTATTATGTTGTTCAT
1 AATTGATTTATTATGTTATTCAT
*
519264 AATTGATTTA-TATGTTATTGAT
1 AATTGATTTATTATGTTATTCAT
519286 AATT
1 AATT
519290 ATCATAAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (23 bp):
AATTGATTTATTATGTTATTCAT
Found at i:519422 original size:50 final size:50
Alignment explanation
Indices: 519363--519498 Score: 202
Period size: 50 Copynumber: 2.7 Consensus size: 50
519353 TGGAAAGTAT
* * *
519363 CTTTGACAATAGAGAGAGGTGGTCATAATTGTTGATGATTCTTCACAAAC
1 CTTTGACAATAAAGAGAGGTGGCCATAATTGTTGACGATTCTTCACAAAC
*
519413 CTTTGACAATATAAG-GAGGTGGCCATAATTGTTGACGATTCTTCACCAAC
1 CTTTGACAATA-AAGAGAGGTGGCCATAATTGTTGACGATTCTTCACAAAC
* *
519463 CTTTGACAATAAAGGGAGGTGACCATAATTGTTGAC
1 CTTTGACAATAAAGAGAGGTGGCCATAATTGTTGAC
519499 TCTAAATATA
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
49 3 0.04
50 74 0.94
51 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (50 bp):
CTTTGACAATAAAGAGAGGTGGCCATAATTGTTGACGATTCTTCACAAAC
Found at i:519683 original size:14 final size:14
Alignment explanation
Indices: 519664--519699 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
519654 GTGCTTGTTT
519664 TTCATTTTTCTATC
1 TTCATTTTTCTATC
*
519678 TTCATTTTTCTATT
1 TTCATTTTTCTATC
519692 TTCATTTT
1 TTCATTTT
519700 AGCTGTGACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (14 bp):
TTCATTTTTCTATC
Found at i:522851 original size:146 final size:146
Alignment explanation
Indices: 522587--522884 Score: 596
Period size: 146 Copynumber: 2.0 Consensus size: 146
522577 AACTGCATTT
522587 CTTCATGGAGAACTTGAAGAAGAAATTTATATGCTCCAACCAGAAGGTTTTGCTGAAATAGGCAA
1 CTTCATGGAGAACTTGAAGAAGAAATTTATATGCTCCAACCAGAAGGTTTTGCTGAAATAGGCAA
522652 GGAGAACTTGGTTTGCAGGTTTAACAAATCTCTATACGGTCTCAAGCAGGCACCGAGGTGTTGGT
66 GGAGAACTTGGTTTGCAGGTTTAACAAATCTCTATACGGTCTCAAGCAGGCACCGAGGTGTTGGT
522717 ATAAGAGAGTTGATTC
131 ATAAGAGAGTTGATTC
522733 CTTCATGGAGAACTTGAAGAAGAAATTTATATGCTCCAACCAGAAGGTTTTGCTGAAATAGGCAA
1 CTTCATGGAGAACTTGAAGAAGAAATTTATATGCTCCAACCAGAAGGTTTTGCTGAAATAGGCAA
522798 GGAGAACTTGGTTTGCAGGTTTAACAAATCTCTATACGGTCTCAAGCAGGCACCGAGGTGTTGGT
66 GGAGAACTTGGTTTGCAGGTTTAACAAATCTCTATACGGTCTCAAGCAGGCACCGAGGTGTTGGT
522863 ATAAGAGAGTTGATTC
131 ATAAGAGAGTTGATTC
522879 CTTCAT
1 CTTCAT
522885 TATGAGCCTT
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
146 152 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (146 bp):
CTTCATGGAGAACTTGAAGAAGAAATTTATATGCTCCAACCAGAAGGTTTTGCTGAAATAGGCAA
GGAGAACTTGGTTTGCAGGTTTAACAAATCTCTATACGGTCTCAAGCAGGCACCGAGGTGTTGGT
ATAAGAGAGTTGATTC
Found at i:524789 original size:22 final size:22
Alignment explanation
Indices: 524759--524841 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 22
524749 TATTTTTTAC
* *
524759 ATGTCATTAATCATTTATTATT
1 ATGTTATTAATCATTTACTATT
* *
524781 ATGTTATTAGTCATATACTATT
1 ATGTTATTAATCATTTACTATT
*** *
524803 GCATTATTAATCTTTTACTATT
1 ATGTTATTAATCATTTACTATT
*
524825 AT-TATATTCATCATTTA
1 ATGT-TATTAATCATTTA
524842 ATATATATCA
Statistics
Matches: 46, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
21 1 0.02
22 45 0.98
ACGTcount: A:0.31, C:0.11, G:0.05, T:0.53
Consensus pattern (22 bp):
ATGTTATTAATCATTTACTATT
Found at i:527556 original size:2 final size:2
Alignment explanation
Indices: 527549--527592 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
527539 GAGGTTGAGG
527549 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
527591 AT
1 AT
527593 GTTGCACCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:528832 original size:13 final size:13
Alignment explanation
Indices: 528814--528838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
528804 CAATTCAACA
528814 TGTATCGATACAT
1 TGTATCGATACAT
528827 TGTATCGATACA
1 TGTATCGATACA
528839 ATGTGCCATG
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:528836 original size:33 final size:33
Alignment explanation
Indices: 528794--528858 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
528784 TTAGAAGCAA
528794 TGTATCGATACAAT-T-CAACATGTATCGATACAT
1 TGTATCGATACAATGTGC--CATGTATCGATACAT
528827 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTGCCATGTATCGATACA
528859 AACAGTAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCGATACAT
Found at i:528926 original size:13 final size:13
Alignment explanation
Indices: 528908--528934 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
528898 TACAATGAAC
528908 ATGTATCGATACA
1 ATGTATCGATACA
528921 ATGTATCGATACA
1 ATGTATCGATACA
528934 A
1 A
528935 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:528930 original size:32 final size:33
Alignment explanation
Indices: 528889--528951 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
528879 TGCCAGTTTT
*
528889 ATGTATCGATACAATG-A-ACATGTATCGATACA
1 ATGTATCGATACAAAGCATA-ATGTATCGATACA
528921 ATGTATCGATACAAAGCATAATGTATCGATA
1 ATGTATCGATACAAAGCATAATGTATCGATA
528952 TATCTGGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.54
33 12 0.43
34 1 0.04
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATACA
Found at i:529534 original size:16 final size:16
Alignment explanation
Indices: 529486--529534 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
529476 TTTAATTTGT
529486 TAAAAATAAA-ATTT-
1 TAAAAATAAATATTTA
* *
529500 TAATAATATAATA-TGA
1 TAAAAATA-AATATTTA
529516 TAAAAATAAATATTTA
1 TAAAAATAAATATTTA
529532 TAA
1 TAA
529535 TCTTTATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 7 0.26
15 7 0.26
16 13 0.48
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
TAAAAATAAATATTTA
Found at i:534553 original size:13 final size:13
Alignment explanation
Indices: 534535--534560 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
534525 CAATTTTTTG
534535 TGTATCGATACAT
1 TGTATCGATACAT
534548 TGTATCGATACAT
1 TGTATCGATACAT
534561 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:537123 original size:13 final size:13
Alignment explanation
Indices: 537105--537143 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
537095 ATAATCACCC
*
537105 TGTATCGATACAG
1 TGTATCGATACAA
537118 TGTATCGATACAA
1 TGTATCGATACAA
537131 TGTATCGATACAA
1 TGTATCGATACAA
537144 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:537154 original size:20 final size:20
Alignment explanation
Indices: 537129--537207 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
537119 GTATCGATAC
537129 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
537149 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
537174 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
537194 CATGTATCGATACA
1 AATGTATCGATACA
537208 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:539242 original size:15 final size:15
Alignment explanation
Indices: 539222--539252 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
539212 ATTTCGTTTG
*
539222 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
539237 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
539252 G
1 G
539253 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:540626 original size:13 final size:13
Alignment explanation
Indices: 540608--540633 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
540598 CAATTTTTTG
540608 TGTATCGATACAT
1 TGTATCGATACAT
540621 TGTATCGATACAT
1 TGTATCGATACAT
540634 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:543198 original size:13 final size:13
Alignment explanation
Indices: 543180--543216 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
543170 AATCACCCTA
*
543180 TATCGATACAGTG
1 TATCGATACAATG
543193 TATCGATACAATG
1 TATCGATACAATG
543206 TATCGATACAA
1 TATCGATACAA
543217 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:543227 original size:20 final size:20
Alignment explanation
Indices: 543202--543280 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
543192 GTATCGATAC
543202 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
543222 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
543247 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
543267 CATGTATCGATACA
1 AATGTATCGATACA
543281 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:545315 original size:15 final size:15
Alignment explanation
Indices: 545295--545325 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
545285 ATTTCGTTTG
*
545295 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
545310 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
545325 G
1 G
545326 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:547158 original size:21 final size:21
Alignment explanation
Indices: 547129--547173 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
547119 AAGTTTTCAT
*
547129 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
547149 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
547171 TTT
1 TTT
547174 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:549878 original size:19 final size:21
Alignment explanation
Indices: 549854--549895 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
549844 AGCTCATGGA
549854 TTTTGTTG-ATATAT-TTGAT
1 TTTTGTTGTATATATGTTGAT
*
549873 TTTTGTTGTATTTATGTTGAT
1 TTTTGTTGTATATATGTTGAT
549894 TT
1 TT
549896 CCATTGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 5 0.25
21 7 0.35
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (21 bp):
TTTTGTTGTATATATGTTGAT
Found at i:554213 original size:19 final size:20
Alignment explanation
Indices: 554178--554232 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
554168 AAAAACCCCG
*
554178 AATGTATCGATACAATGAGA
1 AATGTATCGAAACAATGAGA
554198 AATGTATC-AAACAATGAGA
1 AATGTATCGAAACAATGAGA
*
554217 AATGTATCGATACAAT
1 AATGTATCGAAACAAT
554233 TATAGTATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.25
Consensus pattern (20 bp):
AATGTATCGAAACAATGAGA
Done.