Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold364
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: 2089110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:290607 original size:21 final size:24
Alignment explanation
Indices: 290568--290616 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
290558 GGTGAAAATA
290568 AAAAAAATAGCAAAGAATGAAAG-G
1 AAAAAAATA-CAAAGAATGAAAGTG
290592 AAAAAAATA-AAA-AATGAAAGTG
1 AAAAAAATACAAAGAATGAAAGTG
290614 AAA
1 AAA
290617 GAGTAACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.33
22 7 0.29
24 9 0.38
ACGTcount: A:0.71, C:0.02, G:0.16, T:0.10
Consensus pattern (24 bp):
AAAAAAATACAAAGAATGAAAGTG
Found at i:293225 original size:27 final size:30
Alignment explanation
Indices: 293168--293225 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 30
293158 ACTTTGCTTC
*
293168 ATGCTGTTGCTTCTGCTATTGGCGAGTTGA
1 ATGCTGTTGCTTCTGCTACTGGCGAGTTGA
293198 ATGCTGTTGC-T-T-CTACTGGCGAGTTGA
1 ATGCTGTTGCTTCTGCTACTGGCGAGTTGA
293225 A
1 A
293226 GGATTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 15 0.56
28 1 0.04
29 1 0.04
30 10 0.37
ACGTcount: A:0.16, C:0.17, G:0.29, T:0.38
Consensus pattern (30 bp):
ATGCTGTTGCTTCTGCTACTGGCGAGTTGA
Found at i:300973 original size:6 final size:6
Alignment explanation
Indices: 300962--300986 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
300952 AAAACAGAAG
300962 ATTGGA ATTGGA ATTGGA ATTGGA A
1 ATTGGA ATTGGA ATTGGA ATTGGA A
300987 GATAAGGACT
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:0.00, G:0.32, T:0.32
Consensus pattern (6 bp):
ATTGGA
Found at i:304850 original size:10 final size:10
Alignment explanation
Indices: 304822--304851 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
304812 TTTCAAATAA
*
304822 ATATATATAT
1 ATATATATGT
304832 ATATATATGT
1 ATATATATGT
304842 ATATATATGT
1 ATATATATGT
304852 GTGTGTGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (10 bp):
ATATATATGT
Found at i:312367 original size:20 final size:22
Alignment explanation
Indices: 312342--312384 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
312332 AAAATTAAAA
312342 TATTTTAA-TATTT-TAAATTT
1 TATTTTAATTATTTATAAATTT
312362 TATTTTAATTATTTATAAATTT
1 TATTTTAATTATTTATAAATTT
312384 T
1 T
312385 TTAATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.38
21 5 0.24
22 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTTTAATTATTTATAAATTT
Found at i:312388 original size:19 final size:19
Alignment explanation
Indices: 312336--312409 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
312326 TATTAAAAAA
* *
312336 TTAAAATATTTTAA-TATT
1 TTAAAATTTTTTAATTAAT
*
312354 TTAAATTTTATTTTAATT-AT
1 TTAAA-ATT-TTTTAATTAAT
312374 TTATAAATTTTTTAATTAAT
1 TTA-AAATTTTTTAATTAAT
* *
312394 TTAATATTATTTAATT
1 TTAAAATTTTTTAATT
312410 CGTGAAATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 5 0.11
19 20 0.44
20 17 0.38
21 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAAAATTTTTTAATTAAT
Found at i:317511 original size:40 final size:40
Alignment explanation
Indices: 317467--317562 Score: 165
Period size: 40 Copynumber: 2.4 Consensus size: 40
317457 ATACACGTTC
* *
317467 CAATATTTCTGGTTTCCTCTATCACATGCACTATACATTT
1 CAATATTTCTGGTTTCCTCTATCACATGCACAATACATTA
*
317507 CAATATTTCTGGTTTCCTCTATCACTTGCACAATACATTA
1 CAATATTTCTGGTTTCCTCTATCACATGCACAATACATTA
317547 CAATATTTCTGGTTTC
1 CAATATTTCTGGTTTC
317563 ATCCCAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.25, C:0.24, G:0.08, T:0.43
Consensus pattern (40 bp):
CAATATTTCTGGTTTCCTCTATCACATGCACAATACATTA
Found at i:320924 original size:19 final size:19
Alignment explanation
Indices: 320889--320937 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
320879 AGTTTAAAAG
320889 TTTAAATA-ATT-AAATTT
1 TTTAAATACATTAAAATTT
*
320906 TTTAAATTCATTAAAATTT
1 TTTAAATACATTAAAATTT
*
320925 TTTTAATACATTA
1 TTTAAATACATTA
320938 TCAATCACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 7 0.26
18 3 0.11
19 17 0.63
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAAATACATTAAAATTT
Found at i:322981 original size:2 final size:2
Alignment explanation
Indices: 322976--323003 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
322966 TTCTTTGTTC
322976 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
323004 TTCTCTGCTT
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:323186 original size:25 final size:25
Alignment explanation
Indices: 323152--323214 Score: 126
Period size: 25 Copynumber: 2.5 Consensus size: 25
323142 CAGTAAGCAA
323152 GTATTTATGCAATCCTGCAGACCCT
1 GTATTTATGCAATCCTGCAGACCCT
323177 GTATTTATGCAATCCTGCAGACCCT
1 GTATTTATGCAATCCTGCAGACCCT
323202 GTATTTATGCAAT
1 GTATTTATGCAAT
323215 AGATCAGCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (25 bp):
GTATTTATGCAATCCTGCAGACCCT
Found at i:334755 original size:3 final size:3
Alignment explanation
Indices: 334749--334781 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
334739 GTCATCATCA
334749 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
334782 GGTACCCTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:338003 original size:2 final size:2
Alignment explanation
Indices: 337996--338020 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
337986 TTATCAAATA
337996 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 A
338021 AACATAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:342470 original size:1 final size:1
Alignment explanation
Indices: 342466--342490 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
342456 TTCTTGTTTT
342466 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
342491 TTTATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:342559 original size:23 final size:21
Alignment explanation
Indices: 342509--342550 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
342499 TTTTTTACTT
342509 GTCTACACTTATATATAATTA
1 GTCTACACTTATATATAATTA
342530 GTCTACACTTATATATAATTA
1 GTCTACACTTATATATAATTA
342551 AATTCTACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (21 bp):
GTCTACACTTATATATAATTA
Found at i:346730 original size:4 final size:4
Alignment explanation
Indices: 346719--346751 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
346709 TATGTAAAAC
346719 AAAG -AAG AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
346752 TTGTTTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:357154 original size:7 final size:7
Alignment explanation
Indices: 357142--357175 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
357132 CCGCACCGCC
357142 TCTTCTT
1 TCTTCTT
357149 TCTTCTT
1 TCTTCTT
357156 TCTTCTT
1 TCTTCTT
357163 TCTTCTT
1 TCTTCTT
*
357170 GCTTCT
1 TCTTCT
357176 GCTTCACCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (7 bp):
TCTTCTT
Found at i:357698 original size:2 final size:2
Alignment explanation
Indices: 357691--357720 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
357681 TCTAAAAAGA
*
357691 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
357721 TATTATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:358255 original size:22 final size:22
Alignment explanation
Indices: 358220--358283 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
358210 CTCAAATAAC
358220 TATTAAATAATAAAAATATTTAAA
1 TATT-AAT-ATAAAAATATTTAAA
*
358244 T-TTAATTATAAAAATA-TAAAA
1 TATTAA-TATAAAAATATTTAAA
*
358265 TATTCATATAAAAATATTT
1 TATTAATATAAAAATATTT
358284 TTATTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
21 15 0.44
22 15 0.44
23 3 0.09
24 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TATTAATATAAAAATATTTAAA
Found at i:364317 original size:14 final size:13
Alignment explanation
Indices: 364294--364339 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
364284 TTTACTTGGT
364294 AAAATTAAAAAAA
1 AAAATTAAAAAAA
364307 AAAAGTTAAAAAAGA
1 AAAA-TTAAAAAA-A
*
364322 TAAATTAAAATAAA
1 AAAATTAAAA-AAA
364336 AAAA
1 AAAA
364340 AGTGAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 4 0.14
14 18 0.64
15 6 0.21
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.17
Consensus pattern (13 bp):
AAAATTAAAAAAA
Found at i:366921 original size:2 final size:2
Alignment explanation
Indices: 366914--366953 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
366904 ATCTCCCTTC
366914 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
366954 AGTTTCCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:368411 original size:2 final size:2
Alignment explanation
Indices: 368404--368433 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
368394 GGGGCAATAA
368404 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
368434 GTAGCGAGCC
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:370758 original size:36 final size:33
Alignment explanation
Indices: 370711--370783 Score: 83
Period size: 36 Copynumber: 2.1 Consensus size: 33
370701 GATGTTTATA
* * *
370711 GTTTTTCTTTTTCTTTTTCTTTTTTTTTTGGTCGTT
1 GTTTTTCTTTTT-TATTTC-TTATTTTATGGT-GTT
*
370747 GTTTTTGTTTTTTATTTCTTATTTTATGGTGTT
1 GTTTTTCTTTTTTATTTCTTATTTTATGGTGTT
370780 GTTT
1 GTTT
370784 CCTGTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 7 0.21
34 10 0.30
35 5 0.15
36 11 0.33
ACGTcount: A:0.04, C:0.07, G:0.14, T:0.75
Consensus pattern (33 bp):
GTTTTTCTTTTTTATTTCTTATTTTATGGTGTT
Found at i:371728 original size:16 final size:15
Alignment explanation
Indices: 371691--371728 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
371681 CTATAGGAAA
*
371691 ATTAAATATTATTAT
1 ATTAAATATAATTAT
371706 A-TAAATATAATATAT
1 ATTAAATATAAT-TAT
371721 ATTAAATA
1 ATTAAATA
371729 ATTAAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 5 0.25
16 6 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAAATATAATTAT
Found at i:373164 original size:18 final size:19
Alignment explanation
Indices: 373141--373178 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
373131 ATTCATGGTC
373141 CCAGCCAGGTG-GGCAGGT
1 CCAGCCAGGTGCGGCAGGT
* *
373159 CCAGCCTGTTGCGGCAGGT
1 CCAGCCAGGTGCGGCAGGT
373178 C
1 C
373179 GGTCTCAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.13, C:0.32, G:0.39, T:0.16
Consensus pattern (19 bp):
CCAGCCAGGTGCGGCAGGT
Found at i:377540 original size:14 final size:16
Alignment explanation
Indices: 377510--377550 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
377500 AATTTATTTT
377510 TATAT-TTTAATAAGA
1 TATATATTTAATAAGA
377525 TA-ATATTTAA-AAGA
1 TATATATTTAATAAGA
377539 TATATA-TTAATA
1 TATATATTTAATA
377551 TCTATATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (16 bp):
TATATATTTAATAAGA
Found at i:378598 original size:14 final size:15
Alignment explanation
Indices: 378581--378610 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
378571 AATTGAAATA
378581 TAAAAAAA-TTATTT
1 TAAAAAAAGTTATTT
378595 TAAAAAAAGTTATTT
1 TAAAAAAAGTTATTT
378610 T
1 T
378611 TAAGTAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
TAAAAAAAGTTATTT
Found at i:378853 original size:2 final size:2
Alignment explanation
Indices: 378846--378873 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
378836 ACCAAAACAA
378846 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
378874 GTAAAAGACA
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:380202 original size:27 final size:28
Alignment explanation
Indices: 380135--380202 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 28
380125 AATTAAAAAG
* * *
380135 TAAATAAAAATAATATTTAATTTGATTTA
1 TAAATAAAAATTATAATT-ATTTAATTTA
*
380164 -AATTAAATAATTATAATT-TTTAATTTA
1 TAAATAAA-AATTATAATTATTTAATTTA
380191 TAAATAAAAATT
1 TAAATAAAAATT
380203 CAAGCTAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
27 12 0.38
28 12 0.38
29 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
TAAATAAAAATTATAATTATTTAATTTA
Found at i:384816 original size:26 final size:26
Alignment explanation
Indices: 384787--384843 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
384777 ATATTCTCTG
* *
384787 TTATGCTATTTGAATTAATATAAGTT
1 TTATGCTATTTGAATGAATATAAATT
**
384813 TTATATTATTTGAATGAATATAAATT
1 TTATGCTATTTGAATGAATATAAATT
384839 TTATG
1 TTATG
384844 TTTGATATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.51
Consensus pattern (26 bp):
TTATGCTATTTGAATGAATATAAATT
Found at i:386524 original size:6 final size:6
Alignment explanation
Indices: 386515--386554 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
386505 GGGATTGGGA
*
386515 TGGGGG TGGGGG TGGGGG TGGGGG TGGGGG TAGGGG TGGG
1 TGGGGG TGGGGG TGGGGG TGGGGG TGGGGG TGGGGG TGGG
386555 AGAGGGAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.80, T:0.17
Consensus pattern (6 bp):
TGGGGG
Found at i:386576 original size:18 final size:20
Alignment explanation
Indices: 386552--386597 Score: 78
Period size: 18 Copynumber: 2.4 Consensus size: 20
386542 GGGTAGGGGT
386552 GGGAGAGGGAGAGGGAGA-A
1 GGGAGAGGGAGAGGGAGAGA
386571 -GGAGAGGGAGAGGGAGAGA
1 GGGAGAGGGAGAGGGAGAGA
386590 GGGAGAGG
1 GGGAGAGG
386598 TGACGAGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 17 0.68
19 1 0.04
20 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (20 bp):
GGGAGAGGGAGAGGGAGAGA
Found at i:386597 original size:6 final size:6
Alignment explanation
Indices: 386552--386588 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
386542 GGGTAGGGGT
*
386552 GGGAGA GGGAGA GGGAGA AGGAGA GGGAGA GGGAGA G
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA G
386589 AGGGAGAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:388234 original size:3 final size:3
Alignment explanation
Indices: 388226--388263 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
388216 TAGTCGGTAG
388226 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
388264 AAAATATGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:399516 original size:22 final size:22
Alignment explanation
Indices: 399491--399540 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
399481 TTTTAAATAT
* *
399491 TAATTTTTATAAATATAAAAAA
1 TAATTTTTAAAAATACAAAAAA
*
399513 TAATATTTAAAAATACAAAAAA
1 TAATTTTTAAAAATACAAAAAA
399535 TAATTT
1 TAATTT
399541 AAAATAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TAATTTTTAAAAATACAAAAAA
Found at i:399750 original size:2 final size:2
Alignment explanation
Indices: 399743--399768 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
399733 TTACCAGTAA
399743 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
399769 TCTTATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:406346 original size:10 final size:10
Alignment explanation
Indices: 406328--406359 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
406318 GTTTCTCATA
*
406328 ATATATATAT
1 ATATGTATAT
406338 ATATGTATAT
1 ATATGTATAT
406348 ATATGTATAT
1 ATATGTATAT
406358 AT
1 AT
406360 GCACAAACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
ATATGTATAT
Found at i:408194 original size:2 final size:2
Alignment explanation
Indices: 408187--408218 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
408177 GGCAAATAAT
*
408187 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
408219 AACAAATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:414038 original size:16 final size:16
Alignment explanation
Indices: 414019--414073 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 16
414009 TAAAAATATA
414019 TAATTATTTTATAATT
1 TAATTATTTTATAATT
414035 TAA-T-TTTTAT-ATT
1 TAATTATTTTATAATT
*
414048 T-TTTATTTTA-AATT
1 TAATTATTTTATAATT
414062 TATATTATTTTA
1 TA-ATTATTTTA
414074 CTCATACACT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 5 0.16
14 15 0.47
15 1 0.03
16 11 0.34
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TAATTATTTTATAATT
Found at i:414047 original size:21 final size:23
Alignment explanation
Indices: 414012--414073 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 23
414002 ATAATATTAA
*
414012 AAATATATAATTATTTTATAATTT
1 AAATTTAT-ATTATTTTATAATTT
*
414036 AATTTTTATATT-TTTTAT--TTT
1 AA-ATTTATATTATTTTATAATTT
414057 AAATTTATATTATTTTA
1 AAATTTATATTATTTTA
414074 CTCATACACT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 8 0.24
21 10 0.30
23 6 0.18
24 5 0.15
25 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
AAATTTATATTATTTTATAATTT
Found at i:415272 original size:4 final size:4
Alignment explanation
Indices: 415263--415293 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
415253 AAGGTTGCCT
415263 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
415294 TGCTGATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:415596 original size:14 final size:15
Alignment explanation
Indices: 415577--415606 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
415567 AAAACTTAAA
415577 TTTAT-AAATCATAT
1 TTTATAAAATCATAT
415591 TTTATAAAATCATAT
1 TTTATAAAATCATAT
415606 T
1 T
415607 ACTATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTATAAAATCATAT
Found at i:415629 original size:15 final size:16
Alignment explanation
Indices: 415581--415630 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
415571 CTTAAATTTA
415581 TAAATCATATTTTA-T
1 TAAATCATATTTTATT
* *
415596 AAAATCATATTACTATT
1 TAAATCATATT-TTATT
415613 TAAAT-ATATTTTATT
1 TAAATCATATTTTATT
415628 TAA
1 TAA
415631 TACTATTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 17 0.59
16 7 0.24
17 5 0.17
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATCATATTTTATT
Found at i:417169 original size:25 final size:25
Alignment explanation
Indices: 417124--417171 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
417114 TTTTTATTTT
417124 TTAATATAAATATAAATAATTAATA
1 TTAATATAAATATAAATAATTAATA
*
417149 TTAATAT-AATTTAAATAAATTAA
1 TTAATATAAATATAAAT-AATTAA
417172 ATTTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TTAATATAAATATAAATAATTAATA
Found at i:417180 original size:24 final size:23
Alignment explanation
Indices: 417136--417184 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
417126 AATATAAATA
417136 TAAATAATTAATATTAATATAATT
1 TAAATAATTAATATTAATAT-ATT
**
417160 TAAATAAATTAA-ATTTTTATATT
1 TAAAT-AATTAATATTAATATATT
417183 TA
1 TA
417185 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 5 0.23
24 11 0.50
25 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAATAATTAATATTAATATATT
Found at i:417194 original size:18 final size:17
Alignment explanation
Indices: 417171--417206 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
417161 AAATAAATTA
417171 AATTTTTATATTTATTTT
1 AATTTTTATA-TTATTTT
417189 AATTTTTATATTATTTT
1 AATTTTTATATTATTTT
417206 A
1 A
417207 TATATTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
AATTTTTATATTATTTT
Found at i:417214 original size:18 final size:18
Alignment explanation
Indices: 417175--417215 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
417165 AAATTAAATT
*
417175 TTTATATTTATTTTAATT
1 TTTATATTTATTTTAATA
417193 TTTATA-TTATTTTATATA
1 TTTATATTTATTTTA-ATA
417211 TTTAT
1 TTTAT
417216 CATAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATATTTATTTTAATA
Found at i:418244 original size:225 final size:225
Alignment explanation
Indices: 417802--418285 Score: 641
Period size: 225 Copynumber: 2.2 Consensus size: 225
417792 GAATAATTAG
* * * * *
417802 ACATGTCAAAATTTACATAAAATTAAGTATTAGTGTTCTAAAGTTTTTGTAAATAATATTTTAAA
1 ACATATCAAAATTTACATAAAATTAATTATTAATGTTCTAAAGTTTTTATAAATAATATCTTAAA
* * * * *
417867 TATGATTTTGACATGAAAAGTAATACTAACATGATGATACATGATATAAAATTAAGAGTTATTAA
66 TATGATTATAACATGAAAAGTAATACCAACATCATGACACATGATATAAAATTAAGAGTTATTAA
* * * * * *
417932 TGGTATCAATCAGACTTGATAATTTCAAACATAATATCAGAAAAATAATTAAATATGATATAATA
131 TGGTATCAACCAAACTTAAAAATTTAAAACATAATATCAGAAAAATAATTAAATATGACATAATA
*
417997 TAAAAAAATAAACATAATATAAATTTATAA
196 TAAAAAAATAAACATAATATAAATATATAA
*
418027 ATATATCAAAATTTACATAAAATTAATTATTAATGTT-TCAAAGTTTTTATAAATAATATCTTAA
1 ACATATCAAAATTTACATAAAATTAATTATTAATGTTCT-AAAGTTTTTATAAATAATATCTTAA
* * *
418091 ATATGATTATAACATGAAAAGTAATACCAATATCATGACACATGTTATAAAATTGAGAGTTATTG
65 ATATGATTATAACATGAAAAGTAATACCAACATCATGACACATGATATAAAATTAAGAGTTATT-
* * *
418156 AATGGTGTCAACCAAACTTAAAAATTTAAAATATAATATGAGAAAAATAATTAAAATATGACAT-
129 AATGGTATCAACCAAACTTAAAAATTTAAAACATAATATCAGAAAAATAATT-AAATATGACATA
* ** * *
418220 AT-TATAAGCATAAATATTATATAAATATATAA
193 ATATAAAAAAATAAACATAATATAAATATATAA
* *
418252 ACATGTCAAAATTTACATAAAATAAATTATTAAT
1 ACATATCAAAATTTACATAAAATTAATTATTAAT
418286 AAATTAAATT
Statistics
Matches: 224, Mismatches: 32, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
224 1 0.00
225 167 0.75
226 46 0.21
227 10 0.04
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.35
Consensus pattern (225 bp):
ACATATCAAAATTTACATAAAATTAATTATTAATGTTCTAAAGTTTTTATAAATAATATCTTAAA
TATGATTATAACATGAAAAGTAATACCAACATCATGACACATGATATAAAATTAAGAGTTATTAA
TGGTATCAACCAAACTTAAAAATTTAAAACATAATATCAGAAAAATAATTAAATATGACATAATA
TAAAAAAATAAACATAATATAAATATATAA
Found at i:418379 original size:24 final size:23
Alignment explanation
Indices: 418334--418385 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
418324 ATTATAATAT
* * *
418334 AAAAATAATATAAACATAACACG
1 AAAAATAAAATAAAAATAACACA
*
418357 AAAAATAAAATAAAAAATCACACA
1 AAAAATAAAAT-AAAAATAACACA
418381 AAAAA
1 AAAAA
418386 ATTCAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.73, C:0.12, G:0.02, T:0.13
Consensus pattern (23 bp):
AAAAATAAAATAAAAATAACACA
Found at i:427013 original size:2 final size:2
Alignment explanation
Indices: 427008--427032 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
426998 TATGGAAACT
427008 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
427033 TTAATTCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:428619 original size:53 final size:53
Alignment explanation
Indices: 428556--428660 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
428546 ATTTTACGAA
428556 ATCTTATACTTATCTATCTCATTTGGAGTACTTGATGGGAAATTACGATTGAC
1 ATCTTATACTTATCTATCTCATTTGGAGTACTTGATGGGAAATTACGATTGAC
* * *
428609 ATCTTCTACTTATCTATCTCATTTGGAGTACTTGATGGGACATTACTATTGA
1 ATCTTATACTTATCTATCTCATTTGGAGTACTTGATGGGAAATTACGATTGA
428661 TCCTTCCTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (53 bp):
ATCTTATACTTATCTATCTCATTTGGAGTACTTGATGGGAAATTACGATTGAC
Found at i:428752 original size:29 final size:29
Alignment explanation
Indices: 428719--428776 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
428709 TCAAAAGTTG
428719 GATTCTAATACCAGTTATCA-AGAGATCAT
1 GATTCTAATACCAGTTATCAGAG-GATCAT
* *
428748 GATTCTATTACCATTTATCAGAGGATCAT
1 GATTCTAATACCAGTTATCAGAGGATCAT
428777 TACTCTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (29 bp):
GATTCTAATACCAGTTATCAGAGGATCAT
Found at i:432557 original size:21 final size:21
Alignment explanation
Indices: 432519--432559 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
432509 TAGTCTTACC
*
432519 AATAAATTTATTTATAAATTA
1 AATAAATTTAGTTATAAATTA
432540 AATAAATTATAGTT-TAAATT
1 AATAAATT-TAGTTATAAATT
432560 TTTTTAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
AATAAATTTAGTTATAAATTA
Found at i:432598 original size:17 final size:17
Alignment explanation
Indices: 432550--432598 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
432540 AATAAATTAT
432550 AGTTTAAATTTT-TTTA
1 AGTTTAAATTTTATTTA
* **
432566 AGTTTGAATTAAATTTA
1 AGTTTAAATTTTATTTA
*
432583 AGTTAAAATTTTATTT
1 AGTTTAAATTTTATTT
432599 TATTTTATTA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (17 bp):
AGTTTAAATTTTATTTA
Found at i:432697 original size:18 final size:18
Alignment explanation
Indices: 432636--432697 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
432626 TATTTTTATA
432636 ATTAATTTAAA-TAAAAT
1 ATTAATTTAAATTAAAAT
* *
432653 TTTAATTTATTATT-AAAT
1 ATTAATTTA-AATTAAAAT
* *
432671 AATACTTTAAATTAAAAT
1 ATTAATTTAAATTAAAAT
*
432689 CTTAATTTA
1 ATTAATTTA
432698 TAAAAGTTTT
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
17 11 0.33
18 21 0.64
19 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTAATTTAAATTAAAAT
Found at i:433674 original size:2 final size:2
Alignment explanation
Indices: 433667--433709 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
433657 TTTAAAACTT
*
433667 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
433710 ATTATATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:433716 original size:8 final size:9
Alignment explanation
Indices: 433666--433719 Score: 53
Period size: 8 Copynumber: 6.4 Consensus size: 9
433656 TTTTAAAACT
433666 TTATATATA
1 TTATATATA
433675 -TATATATA
1 TTATATATA
433683 -TATATATA
1 TTATATATA
433691 -TATATATA
1 TTATATATA
* *
433699 TGATAAATA
1 TTATATATA
*
433708 TAAT-TATA
1 TTATATATA
433716 TTAT
1 TTAT
433720 TAAATTTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
8 30 0.77
9 9 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (9 bp):
TTATATATA
Found at i:434961 original size:16 final size:17
Alignment explanation
Indices: 434936--434968 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
434926 TTCATTTTTT
434936 ATTATAA-TTTTAATTA
1 ATTATAATTTTTAATTA
*
434952 ATTATCATTTTTAATTA
1 ATTATAATTTTTAATTA
434969 TCACCTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATAATTTTTAATTA
Found at i:452219 original size:20 final size:18
Alignment explanation
Indices: 452169--452220 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
452159 ACCATAATTT
452169 TATTT-AAAATATTTAATA
1 TATTTAAAAAT-TTTAATA
* *
452187 T-TTTAATAATTTATATTA
1 TATTTAAAAATTT-TAATA
452205 TATTTAAAAATTTTAA
1 TATTTAAAAATTTTAA
452221 AAATATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
17 5 0.19
18 12 0.44
19 10 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTTAAAAATTTTAATA
Found at i:452231 original size:28 final size:28
Alignment explanation
Indices: 452177--452237 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
452167 TTTATTTAAA
* *
452177 ATATTTAATATTTTAATAATTTATA-TT
1 ATATTTAAAATTTTAAAAATTTATATTT
452204 ATATTTAAAAATTTTAAAAATATT-TATTT
1 ATATTT-AAAATTTTAAAAAT-TTATATTT
452233 ATATT
1 ATATT
452238 ATATTTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.21
28 14 0.48
29 9 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATATTTAAAATTTTAAAAATTTATATTT
Found at i:457373 original size:2 final size:2
Alignment explanation
Indices: 457366--457392 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
457356 TTTATGAATC
457366 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
457393 CCTAATCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:461556 original size:18 final size:18
Alignment explanation
Indices: 461535--461569 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
461525 AAAATAATAT
*
461535 ATTTTTTTACTTTTTAAA
1 ATTTATTTACTTTTTAAA
*
461553 ATTTATTTATTTTTTAA
1 ATTTATTTACTTTTTAA
461570 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTATTTACTTTTTAAA
Found at i:461580 original size:30 final size:31
Alignment explanation
Indices: 461546--461608 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
461536 TTTTTTTACT
*
461546 TTTTAAAAT-TTATTTATTTTTTAAT-TTAAA
1 TTTTAAAATATT-TTTATTATTTAATATTAAA
461576 TTTTAAAATATTTTTATTATTTAATATTAAA
1 TTTTAAAATATTTTTATTATTTAATATTAAA
461607 TT
1 TT
461609 AATTAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 21 0.70
31 9 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTAAAATATTTTTATTATTTAATATTAAA
Found at i:461605 original size:24 final size:24
Alignment explanation
Indices: 461560--461606 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
461550 AAAATTTATT
*
461560 TATTTTTTAATTTAAATTTTAAAA
1 TATTTTTTAATTTAAATATTAAAA
*
461584 TATTTTTATTATTT-AATATTAAA
1 TATTTTT-TAATTTAAATATTAAA
461607 TTAATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTTTTTAATTTAAATATTAAAA
Found at i:461627 original size:21 final size:21
Alignment explanation
Indices: 461596--461645 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
461586 TTTTTATTAT
*
461596 TTAAT-ATTAAATTAATTAAA
1 TTAATAATTAAATCAATTAAA
461616 TTAATAATTAAATCAATTAAA
1 TTAATAATTAAATCAATTAAA
461637 TTAA-AATTA
1 TTAATAATTA
461646 TGATTCAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAATAATTAAATCAATTAAA
Found at i:466579 original size:3 final size:3
Alignment explanation
Indices: 466571--466609 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
466561 GTTGTACATG
466571 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
466610 GAGGTAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:474554 original size:2 final size:2
Alignment explanation
Indices: 474547--474572 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
474537 ATAAATCTTC
474547 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
474573 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:474577 original size:2 final size:2
Alignment explanation
Indices: 474572--474601 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
474562 TATATATATA
*
474572 TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
474602 CGTATATTGT
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:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:474871 original size:2 final size:2
Alignment explanation
Indices: 474864--474921 Score: 55
Period size: 2 Copynumber: 29.0 Consensus size: 2
474854 AAAACTAGTG
* * * *
474864 TA TA TA TA TA TA TA TA TA TA TA TA TA TC T- TT TG TA TCA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
*
474906 TA AA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
474922 GATAGATATG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
1 1 0.02
2 44 0.94
3 2 0.04
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:475453 original size:2 final size:2
Alignment explanation
Indices: 475446--475478 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
475436 ACATTTTTAA
*
475446 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
475479 AAAAATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:487097 original size:63 final size:63
Alignment explanation
Indices: 487024--487150 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
487014 TATGTTTTTT
* *
487024 AAGTAAAGGGAAGATATATTTCATTGTTTACTAAAATATTAAGCTAAAGGCATTTTCATGTAA
1 AAGTAAAGGGAAGATATATTTCATTGTTCACTAAAATATTAAGCTAAAGGCACTTTCATGTAA
487087 AAGTAAAGGGAAGATATATTTCATTGTTCACTAAAATATTAAGCTAAAGGCACTTTCATGTAA
1 AAGTAAAGGGAAGATATATTTCATTGTTCACTAAAATATTAAGCTAAAGGCACTTTCATGTAA
487150 A
1 A
487151 GCTACTTCAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (63 bp):
AAGTAAAGGGAAGATATATTTCATTGTTCACTAAAATATTAAGCTAAAGGCACTTTCATGTAA
Found at i:488083 original size:50 final size:50
Alignment explanation
Indices: 488008--488107 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
487998 CCCTTGTGAC
488008 TCCCCAATATAGCAGAGGATTATCATTCTTCATATAGGCTTGATCTTGAA
1 TCCCCAATATAGCAGAGGATTATCATTCTTCATATAGGCTTGATCTTGAA
*
488058 TCCCCATTATAGCAGAGGATTATCATTCTTCATATAGGCTTGATCTTGAA
1 TCCCCAATATAGCAGAGGATTATCATTCTTCATATAGGCTTGATCTTGAA
488108 GTGAAGAGAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (50 bp):
TCCCCAATATAGCAGAGGATTATCATTCTTCATATAGGCTTGATCTTGAA
Found at i:499015 original size:16 final size:17
Alignment explanation
Indices: 498983--499015 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
498973 CTTCCTTTTC
498983 AAATTTTAAATCAAATT
1 AAATTTTAAATCAAATT
499000 AAATTTTAAA-CAAATT
1 AAATTTTAAATCAAATT
499016 TTAAAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTTTAAATCAAATT
Found at i:506819 original size:2 final size:2
Alignment explanation
Indices: 506812--506849 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
506802 GGAAAGGAAC
506812 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
506850 AACCCTAGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:507933 original size:20 final size:20
Alignment explanation
Indices: 507898--507943 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
507888 TTATAATTTA
507898 ATTAA-ATTTTTATTATCAT
1 ATTAATATTTTTATTATCAT
*
507917 ATTAATATTTATT-TTATTAT
1 ATTAATATTT-TTATTATCAT
507937 ATTAATA
1 ATTAATA
507944 CGAAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 5 0.21
20 17 0.71
21 2 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTAATATTTTTATTATCAT
Found at i:509588 original size:2 final size:2
Alignment explanation
Indices: 509581--509606 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
509571 TGCCTTTTTA
509581 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
509607 TGTTTTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:511635 original size:3 final size:3
Alignment explanation
Indices: 511627--511653 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
511617 ACAAAATGAT
511627 GCA GCA GCA GCA GCA GCA GCA GCA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA
511654 TCCGGAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:512064 original size:22 final size:19
Alignment explanation
Indices: 512029--512070 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
512019 TTAATAAAAA
512029 ATTATTTTATATTAATATTT
1 ATTATTTTATATTAA-ATTT
512049 ATTATATTTATGATTAAATTT
1 ATTAT-TTTAT-ATTAAATTT
512070 A
1 A
512071 AATAAAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTATTTTATATTAAATTT
Found at i:514624 original size:2 final size:2
Alignment explanation
Indices: 514617--514645 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
514607 AAAAATCATT
514617 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
514646 GATCTGATGT
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:516634 original size:118 final size:119
Alignment explanation
Indices: 516510--516799 Score: 298
Period size: 118 Copynumber: 2.4 Consensus size: 119
516500 AAAAAATTTG
* * *
516510 AAATTATTTTATTAATTAATATTTTTA-TTTATTTTAAATAATTTATTTAAAAGGTTGATCCGTA
1 AAATTATTTTATTAATTAATATTTTTATTTTATTTTAAATAATTTATTTAAAAAGTTAATCCGCA
*
516574 -AGTTAACTCG-TGAGTCAATTTAAAATTCGCACCTGACTTGCT-T-AAAAAA-TTAAA
66 TA-TTAACTCGCGGA-TCAATTTAAAA-TC-CACC-GACTTGCTCTAAAAAAATTTAAA
* * * *
516628 AAATTATTTTATTAA-T--TATTTTAATTTTATTTTTAAATTATATATTTAAAAAAGTTAATCTG
1 AAATTATTTTATTAATTAATATTTTTATTTTA-TTTTAAATAATTTATTT-AAAAAGTTAATCCG
* * *
516690 CATATTAACTCGCGGATTAATTTAAAATCCATCGATTTGCTCTGAAAAAAATTTAAA
64 CATATTAACTCGCGGATCAATTTAAAATCCACCGACTTGCTCT-AAAAAAATTTAAA
516747 AAATT-TTATT-TT-ATTAATAATTTTTATTTTAATTTTAAATAATTTATTTAAAA
1 AAATTATT-TTATTAATTAAT-ATTTTTATTTT-ATTTTAAATAATTTATTTAAAA
516800 TTATTGATCT
Statistics
Matches: 143, Mismatches: 14, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
115 14 0.10
116 8 0.06
117 19 0.13
118 56 0.39
119 15 0.10
120 5 0.03
121 25 0.17
122 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (119 bp):
AAATTATTTTATTAATTAATATTTTTATTTTATTTTAAATAATTTATTTAAAAAGTTAATCCGCA
TATTAACTCGCGGATCAATTTAAAATCCACCGACTTGCTCTAAAAAAATTTAAA
Found at i:516789 original size:22 final size:22
Alignment explanation
Indices: 516749--516791 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
516739 AATTTAAAAA
516749 ATTTTATTTTATTAATAATTTTT
1 ATTTTATTTTA-TAATAATTTTT
516772 ATTTTAATTTTA-AATAATTT
1 ATTTT-ATTTTATAATAATTT
516792 ATTTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 5 0.26
24 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTTATTTTATAATAATTTTT
Found at i:516995 original size:29 final size:26
Alignment explanation
Indices: 516959--517034 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 26
516949 TAATTTTAAA
*
516959 TATAAAATTTAAATATATAATTATTATTT
1 TATAAAATTT-AATATAAAATTA-T-TTT
*
516988 TATAAAATTTAATTTAAAATTATTTT
1 TATAAAATTTAATATAAAATTATTTT
*
517014 TATAAATACTTAAT-TAAAATT
1 TATAAA-ATTTAATATAAAATT
517035 TATAAAGAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 16 0.37
27 7 0.16
28 10 0.23
29 10 0.23
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (26 bp):
TATAAAATTTAATATAAAATTATTTT
Found at i:530180 original size:2 final size:2
Alignment explanation
Indices: 530173--530202 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
530163 AAACATGCGC
530173 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
530203 AAACTAAATA
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):
TA
Found at i:530857 original size:18 final size:19
Alignment explanation
Indices: 530834--530875 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
530824 AAATTATTTA
530834 AAAAATTA-AAATAAAATT
1 AAAAATTATAAATAAAATT
*
530852 ATAAA-TATAAATAAAATT
1 AAAAATTATAAATAAAATT
530870 AAAAAT
1 AAAAAT
530876 ATTTAAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATTATAAATAAAATT
Found at i:530876 original size:18 final size:18
Alignment explanation
Indices: 530842--530877 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
530832 TAAAAAATTA
*
530842 AAATAAAATTATAAATAT
1 AAATAAAATTAAAAATAT
530860 AAATAAAATTAAAAATAT
1 AAATAAAATTAAAAATAT
530878 TTAAATCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAAAATTAAAAATAT
Found at i:531068 original size:118 final size:118
Alignment explanation
Indices: 530844--531057 Score: 374
Period size: 118 Copynumber: 1.8 Consensus size: 118
530834 AAAAATTAAA
* *
530844 ATAAAATTATAAATATAAATAAAATTAAAAATATTTAAATCTTTTGATCATAAAAATAACAACCA
1 ATAAAATTATAAATATAAATAAAATTAAAAATACTTAAATCTTTTGATCATAAAAACAACAACCA
*
530909 AAAAAGTTAATTTTTAATATATCTTTTAATTTTTAGAAAAAAATTATTTATTT
66 AAAAAATTAATTTTTAATATATCTTTTAATTTTTAGAAAAAAATTATTTATTT
* * *
530962 ATAAAATTATAAATATATATAAAATTAAAAGTACTTAAATCTTTTGATCATAAAAGCAACAACCA
1 ATAAAATTATAAATATAAATAAAATTAAAAATACTTAAATCTTTTGATCATAAAAACAACAACCA
531027 AAAAAATTAATTTTTAATATATCTTTTAATT
66 AAAAAATTAATTTTTAATATATCTTTTAATT
531058 CTTTTAAAAA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 90 1.00
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (118 bp):
ATAAAATTATAAATATAAATAAAATTAAAAATACTTAAATCTTTTGATCATAAAAACAACAACCA
AAAAAATTAATTTTTAATATATCTTTTAATTTTTAGAAAAAAATTATTTATTT
Found at i:533885 original size:34 final size:34
Alignment explanation
Indices: 533839--534023 Score: 248
Period size: 34 Copynumber: 5.5 Consensus size: 34
533829 GTAAAAACCA
*
533839 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
533873 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
533907 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
533941 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
533975 CCATTTAGTCAATAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
534008 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
534024 TCTCCCACTT
Statistics
Matches: 133, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
33 17 0.13
34 112 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:538116 original size:19 final size:19
Alignment explanation
Indices: 538089--538151 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
538079 TCACGTGTAC
* *
538089 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
538108 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
538127 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
538146 AGTACC
1 AGTACC
538152 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:538503 original size:34 final size:34
Alignment explanation
Indices: 538457--538639 Score: 226
Period size: 34 Copynumber: 5.4 Consensus size: 34
538447 GTAAAAACCA
*
538457 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
538491 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* * * *
538525 TCATTTAATCAATAATGGTAAGCTACTAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
538559 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
538593 CCATTTAGTCAATAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
538626 CCATTTAATCAACA
1 CCATTTAATCAACA
538640 CTCTAAATGT
Statistics
Matches: 127, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
33 15 0.12
34 108 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:539888 original size:10 final size:10
Alignment explanation
Indices: 539859--539898 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
539849 TATTAAAAAT
539859 TATAGTAATA
1 TATAGTAATA
**
539869 T-TTTTAATA
1 TATAGTAATA
539878 TATAGTAATA
1 TATAGTAATA
539888 TATAGTAATA
1 TATAGTAATA
539898 T
1 T
539899 TTTTATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 7 0.28
10 18 0.72
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (10 bp):
TATAGTAATA
Found at i:542671 original size:14 final size:15
Alignment explanation
Indices: 542646--542683 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
542636 TAATCAAACG
542646 TAATATATTTATATA
1 TAATATATTTATATA
542661 TAATA-ATTTATATA
1 TAATATATTTATATA
542675 TAAATATAT
1 T-AATATAT
542684 GTATTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.48
15 9 0.43
16 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATATATTTATATA
Found at i:545355 original size:34 final size:34
Alignment explanation
Indices: 545316--545498 Score: 217
Period size: 34 Copynumber: 5.4 Consensus size: 34
545306 ATAAAAACCA
* *
545316 CCATTTAATCAAAAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
545350 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* * * *
545384 TCATTTAATCAATAATGGTAAGCTACTAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
545418 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
545452 CCATTTAGTCAATAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
545485 CCATTTAATCAACA
1 CCATTTAATCAACA
545499 CTCTAAATGT
Statistics
Matches: 126, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
33 15 0.12
34 107 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:545430 original size:68 final size:68
Alignment explanation
Indices: 545316--545498 Score: 242
Period size: 68 Copynumber: 2.7 Consensus size: 68
545306 ATAAAAACCA
* * * *
545316 CCATTTAATCAAAAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAATAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
545381 CAC
66 CAC
* * * * *
545384 TCATTTAATCAATAATGGTAAGCTACTAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAATAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
**
545449 TTC
66 CAC
* *
545452 CCATTTAGTCAATAATGGTAAACTACCAAATC-ACCATTTAATCAACA
1 CCATTTAATCAATAATGGTAAACTACCAAATCTCCCATTTAATCAACA
545499 CTCTAAATGT
Statistics
Matches: 100, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
67 14 0.14
68 86 0.86
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (68 bp):
CCATTTAATCAATAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
CAC
Found at i:546747 original size:10 final size:10
Alignment explanation
Indices: 546718--546757 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
546708 TATTAAAAAT
546718 TATAGTAATA
1 TATAGTAATA
**
546728 T-TTTTAATA
1 TATAGTAATA
546737 TATAGTAATA
1 TATAGTAATA
546747 TATAGTAATA
1 TATAGTAATA
546757 T
1 T
546758 TTTTATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 7 0.28
10 18 0.72
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (10 bp):
TATAGTAATA
Found at i:549530 original size:14 final size:15
Alignment explanation
Indices: 549505--549542 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
549495 TAATCAAACG
549505 TAATATATTTATATA
1 TAATATATTTATATA
549520 TAATA-ATTTATATA
1 TAATATATTTATATA
549534 TAAATATAT
1 T-AATATAT
549543 GTATTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.48
15 9 0.43
16 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATATATTTATATA
Found at i:560105 original size:2 final size:2
Alignment explanation
Indices: 560098--560124 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
560088 AACATTCAAG
560098 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 A
560125 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:560129 original size:2 final size:2
Alignment explanation
Indices: 560124--560164 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
560114 ATATATATAT
560124 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
560165 AAGAAAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:565525 original size:2 final size:2
Alignment explanation
Indices: 565518--565542 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
565508 TTGGAATTGC
565518 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
565543 CTAATATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:574323 original size:3 final size:3
Alignment explanation
Indices: 574315--574340 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
574305 GGGGGTTTCA
574315 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
574341 AATATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:574803 original size:2 final size:2
Alignment explanation
Indices: 574796--574841 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
574786 TGTTATTGGA
574796 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
574838 AT AT
1 AT AT
574842 TAGAAGGCTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:576257 original size:2 final size:2
Alignment explanation
Indices: 576250--576288 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
576240 CTTTAAGTCC
576250 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
576289 ACTTTGGTTG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:590496 original size:50 final size:50
Alignment explanation
Indices: 590437--590645 Score: 337
Period size: 50 Copynumber: 4.2 Consensus size: 50
590427 TATACTTAGA
* *
590437 GTCAACAATTATGGCCACCTCCCTCTATTATCAAAAGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
590487 GTCAACAATTATGGCCACTTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
590537 GTCAACAATTATGGCCACGTCCCTCTATTGTCAAAGGTTTGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
590587 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
590637 GTCAACAAT
1 GTCAACAAT
590646 GACAACAACT
Statistics
Matches: 147, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 147 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:595219 original size:50 final size:50
Alignment explanation
Indices: 595011--595205 Score: 311
Period size: 50 Copynumber: 3.9 Consensus size: 50
595001 TATATTTAGA
* *
595011 GTCAACAATTATGGCCACTTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGATGAAGAATC
*
595061 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAAGTT-AGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGA-TGAAGAATC
*
595111 GTCAACAATTATGGCCACCTCCCTTTATTGTCAAAGGTTGATGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGATGAAGAATC
* * *
595161 GTCAATAATTATGGTCACCTCTCTCTATTGTCAAAGGTTGATGAA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGATGAA
595206 AGATAGTTAA
Statistics
Matches: 134, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
50 133 0.99
51 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGATGAAGAATC
Found at i:599386 original size:3 final size:3
Alignment explanation
Indices: 599378--599424 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
599368 TGTCACCCAT
*
599378 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC GTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
599425 TCCCTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:599559 original size:12 final size:13
Alignment explanation
Indices: 599541--599575 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
599531 TTTGGATTCT
599541 GAGAAAAAAAAAA
1 GAGAAAAAAAAAA
599554 -AGAAAAAAAAAA
1 GAGAAAAAAAAAA
599566 GAGAACAAAA
1 GAGAA-AAAA
599576 CGGATGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.60
13 4 0.20
14 4 0.20
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (13 bp):
GAGAAAAAAAAAA
Found at i:599987 original size:3 final size:3
Alignment explanation
Indices: 599979--600005 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
599969 TCTGAGGAGT
599979 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
600006 ATAACTTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:601599 original size:25 final size:27
Alignment explanation
Indices: 601540--601595 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 27
601530 CATAGCTGCC
601540 TAAAATAAGATATATTAATTTTAAATA
1 TAAAATAAGATATATTAATTTTAAATA
* *
601567 TAATATAA-TTATA-TAA-TTTAAATA
1 TAAAATAAGATATATTAATTTTAAATA
601591 TAAAA
1 TAAAA
601596 ATAAAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 12 0.46
25 3 0.12
26 4 0.15
27 7 0.27
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (27 bp):
TAAAATAAGATATATTAATTTTAAATA
Found at i:605244 original size:2 final size:2
Alignment explanation
Indices: 605237--605267 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
605227 CCCTTTCATG
605237 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
605268 CCTGCTAGAT
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:606469 original size:2 final size:2
Alignment explanation
Indices: 606462--606505 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
606452 TGAAATGTCA
* * * *
606462 AT AT AT AT GT AT AT AT TT GT GT 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
606504 AT
1 AT
606506 CAACCGATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (2 bp):
AT
Found at i:613285 original size:50 final size:50
Alignment explanation
Indices: 613231--613419 Score: 256
Period size: 50 Copynumber: 3.8 Consensus size: 50
613221 TATACTTAGA
* * * *
613231 GTCAACAATTATGACCACCTTTTTCTATTGTTAAAGGTTGATGAAGAATC
1 GTCAACAATTATGACCACCTCTCTCTATTATCAAAGGTTGATGAAGAATC
* *
613281 GTCAACAATTATAACCACCTCTCTTCTATTGTCAAAGGTT-AGTGAAGAATC
1 GTCAACAATTATGACCACCTCTC-TCTATTATCAAAGGTTGA-TGAAGAATC
* * *
613332 GTCAACAATTATGGCCACCTCTCTCTATTATCAAAGGTTGGTAAAGAATC
1 GTCAACAATTATGACCACCTCTCTCTATTATCAAAGGTTGATGAAGAATC
613382 GTCAACAATTAT-AGCCACCTCTCTCTATTATCAAAGGT
1 GTCAACAATTATGA-CCACCTCTCTCTATTATCAAAGGT
613420 ACTTTCCACC
Statistics
Matches: 125, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
50 80 0.64
51 45 0.36
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (50 bp):
GTCAACAATTATGACCACCTCTCTCTATTATCAAAGGTTGATGAAGAATC
Found at i:617827 original size:50 final size:50
Alignment explanation
Indices: 617767--617916 Score: 176
Period size: 50 Copynumber: 3.0 Consensus size: 50
617757 TATACTTAGA
* * * * *
617767 GTCAACAATTATGATCACCTTTCTCTATTGTCAAAAATTGGTGAAGAATT
1 GTCAATAATTATGATCACCTCTCTCTATTGTCAAAAATTAGTAAAGAATC
* *
617817 GTCAATAATTATGA-CTACCTCTCTCTATTATCAAAAGTTAGTAAAGAATC
1 GTCAATAATTATGATC-ACCTCTCTCTATTGTCAAAAATTAGTAAAGAATC
* * * * *
617867 GTCAATAATTACGATCATCTCTCTTTATTGTCAAAAATTAATAAAAAATC
1 GTCAATAATTATGATCACCTCTCTCTATTGTCAAAAATTAGTAAAGAATC
617917 ATTAACAATG
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
49 1 0.01
50 82 0.98
51 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (50 bp):
GTCAATAATTATGATCACCTCTCTCTATTGTCAAAAATTAGTAAAGAATC
Found at i:632349 original size:2 final size:2
Alignment explanation
Indices: 632342--632370 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
632332 CATAAATTCT
632342 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 T
632371 GAGTTACACA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:633182 original size:2 final size:2
Alignment explanation
Indices: 633175--633202 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
633165 CTAGTCGTGG
633175 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
633203 AAACTAATTA
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):
TA
Found at i:639153 original size:3 final size:3
Alignment explanation
Indices: 639145--639176 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
639135 TTAATTTGAA
*
639145 AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
639177 GACTTCTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:639312 original size:2 final size:2
Alignment explanation
Indices: 639272--639298 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
639262 TGGACTATTA
639272 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 T
639299 GCAGTTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:642030 original size:23 final size:22
Alignment explanation
Indices: 642004--642050 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
641994 AATAAATTTT
* *
642004 TAAAATTTTATATAATATTTTAA
1 TAAAATTATATA-AATAATTTAA
*
642027 TAAAGTTATATAAATAATTTAA
1 TAAAATTATATAAATAATTTAA
642049 TA
1 TA
642051 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TAAAATTATATAAATAATTTAA
Found at i:644447 original size:19 final size:19
Alignment explanation
Indices: 644425--644472 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
644415 ATTTTTATAA
*
644425 TAAATTAATTTAATCAATT
1 TAAATTAATTTAATCAAAT
644444 TAAATTAATTTAATCAAAT
1 TAAATTAATTTAATCAAAT
644463 TAAATTAATT
1 TAAATTAATT
644473 AAACTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATTAATTTAATCAAAT
Found at i:644730 original size:2 final size:2
Alignment explanation
Indices: 644723--644769 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
644713 CCATGACAGT
644723 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
644765 AA GA G
1 GA GA G
644770 GCAGAAAGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:650071 original size:17 final size:17
Alignment explanation
Indices: 650051--650101 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
650041 AATTTGAATA
650051 AAAATAAAATAATTTTT
1 AAAATAAAATAATTTTT
* *
650068 AAAAATAAATTAA-ATTT
1 -AAAATAAAATAATTTTT
650085 AAAATAAAAT-ATTTTT
1 AAAATAAAATAATTTTT
650101 A
1 A
650102 TTTAGATTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 1 0.04
16 13 0.46
17 3 0.11
18 11 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATAAAATAATTTTT
Found at i:650172 original size:19 final size:20
Alignment explanation
Indices: 650145--650193 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
650135 TTATTTAAAA
650145 AATTAATTTTTAAAAAATAA-T
1 AATT-ATTTTT-AAAAATAATT
*
650166 AA-TATTTTTTAAAATAATT
1 AATTATTTTTAAAAATAATT
650185 AATTATTTT
1 AATTATTTT
650194 AAGAGTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 7 0.28
21 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTATTTTTAAAAATAATT
Found at i:650179 original size:18 final size:19
Alignment explanation
Indices: 650131--650193 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 19
650121 ATTATTAAGT
650131 ATATTTATTTAAAA-AATTA
1 ATATTT-TTTAAAATAATTA
**
650150 AT-TTTTAAAAAATAA-TA
1 ATATTTTTTAAAATAATTA
650167 ATATTTTTTAAAATAATTA
1 ATATTTTTTAAAATAATTA
650186 ATTATTTT
1 A-TATTTT
650194 AAGAGTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
17 9 0.25
18 16 0.44
19 5 0.14
20 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTTTTTAAAATAATTA
Done.