Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold6
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: 1308201
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
File 6 of 11
Found at i:446211 original size:20 final size:20
Alignment explanation
Indices: 446180--446268 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
446170 TTGATTTATT
446180 ATATTAAA-ATATAATTTAA
1 ATATTAAATATATAATTTAA
*
446199 ATATTAAATATATAATTTTA
1 ATATTAAATATATAATTTAA
* *
446219 ATAATAAATAGAT-A-TTAA
1 ATATTAAATATATAATTTAA
*
446237 AT-TT-AATAAAT-ATTT-A
1 ATATTAAATATATAATTTAA
*
446253 ATA-AAAATATATAATT
1 ATATTAAATATATAATT
446269 AATAAAATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
16 10 0.18
17 9 0.16
18 8 0.14
19 9 0.16
20 21 0.37
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (20 bp):
ATATTAAATATATAATTTAA
Found at i:446235 original size:31 final size:33
Alignment explanation
Indices: 446199--446278 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
446189 TATAATTTAA
446199 ATATTAAATAT-AT-AAT-TTTAATAATAAATAG
1 ATATTAAATATAATAAATATTTAATAA-AAATAG
* *
446230 ATATTAAATTTAATAAATATTTAATAAAAATAT
1 ATATTAAATATAATAAATATTTAATAAAAATAG
*
446263 ATAATT-AATAAAATAA
1 AT-ATTAAATATAATAA
446279 TATGATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
31 10 0.24
32 2 0.05
33 18 0.44
34 11 0.27
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (33 bp):
ATATTAAATATAATAAATATTTAATAAAAATAG
Found at i:446261 original size:17 final size:17
Alignment explanation
Indices: 446241--446275 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
446231 TATTAAATTT
*
446241 AATAAATATTTAATAAA
1 AATAAATAATTAATAAA
*
446258 AATATATAATTAATAAA
1 AATAAATAATTAATAAA
446275 A
1 A
446276 TAATATGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAAATAATTAATAAA
Found at i:446281 original size:17 final size:17
Alignment explanation
Indices: 446241--446281 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
446231 TATTAAATTT
*
446241 AATAA-ATATTTAATAA
1 AATAATATAATTAATAA
446257 AA-ATATATAATTAATAA
1 AATA-ATATAATTAATAA
446274 AATAATAT
1 AATAATAT
446282 GATTTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 1 0.05
16 3 0.14
17 16 0.76
18 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATAATATAATTAATAA
Found at i:448480 original size:2 final size:2
Alignment explanation
Indices: 448473--448498 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
448463 TTATACAAAA
448473 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
448499 CACTTTGCAA
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:453188 original size:21 final size:21
Alignment explanation
Indices: 453142--453188 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
453132 AAAATATAAT
* *
453142 ATTAATATAAAATATTTTACA
1 ATTAATAAAAAAAATTTTACA
453163 A-TAATAAAATAAAATTTTA-A
1 ATTAATAAAA-AAAATTTTACA
453183 ATTAAT
1 ATTAAT
453189 TTAATTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTAATAAAAAAAATTTTACA
Found at i:454107 original size:18 final size:18
Alignment explanation
Indices: 454068--454107 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
454058 AGTATTTATT
*
454068 TTTTACTTAAAAAACTTA
1 TTTTACTTAAAAAACTCA
454086 TTTTA-TTAAAAAACTCA
1 TTTTACTTAAAAAACTCA
454103 CTTTT
1 -TTTT
454108 TACGTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTACTTAAAAAACTCA
Found at i:454750 original size:19 final size:17
Alignment explanation
Indices: 454704--454765 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
454694 TAAAGTAAAG
454704 AATAAAA-TTATCATTTT
1 AATAAAATTTAT-ATTTT
454721 ATATAAAATTTAAATATTTT
1 A-ATAAAATTT--ATATTTT
*
454741 AATTAAATTTATATTTT
1 AATAAAATTTATATTTT
454758 AA-AAAATT
1 AATAAAATT
454766 CACACATGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 5 0.13
17 10 0.26
18 6 0.15
19 10 0.26
20 6 0.15
21 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
AATAAAATTTATATTTT
Found at i:455398 original size:23 final size:23
Alignment explanation
Indices: 455357--455417 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
455347 TAACTTAATT
*
455357 TATTAATAATAAAAATTTAATAATA
1 TATT-ATAAT-AAAATTTAAAAATA
* *
455382 TATTTTAATAAAATTTAAAAATT
1 TATTATAATAAAATTTAAAAATA
455405 TATTATATATAAA
1 TATTATA-ATAAA
455418 TTATTCGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 18 0.58
24 9 0.29
25 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TATTATAATAAAATTTAAAAATA
Found at i:459753 original size:21 final size:22
Alignment explanation
Indices: 459712--459753 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
459702 TTTTTAGTAT
*
459712 TTTGAGTTTATTTTATCTTGAA
1 TTTGAGTTTATTTTAACTTGAA
*
459734 TTTGAG-TTATTTTAAGTTGA
1 TTTGAGTTTATTTTAACTTGA
459754 GAAATTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.57
Consensus pattern (22 bp):
TTTGAGTTTATTTTAACTTGAA
Found at i:459820 original size:22 final size:23
Alignment explanation
Indices: 459779--459844 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 23
459769 CGTTTGAGTT
*
459779 ATTTGAATTTAA--ATTATTTACA
1 ATTT-AATTTAATTATTATTTAAA
459801 ATTTAATTTAATTATT-TTTAAA
1 ATTTAATTTAATTATTATTTAAA
* * *
459823 ATTAAATTAAATTA-AATTTAAA
1 ATTTAATTTAATTATTATTTAAA
459845 TAAATTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
21 7 0.19
22 27 0.73
23 3 0.08
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTTAATTTAATTATTATTTAAA
Found at i:459839 original size:15 final size:15
Alignment explanation
Indices: 459818--459851 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
459808 TTAATTATTT
*
459818 TTAAAATTAAATTAAA
1 TTAAATTTAAA-TAAA
459834 TTAAATTTAAATAAA
1 TTAAATTTAAATAAA
459849 TTA
1 TTA
459852 TTTTATCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAATTTAAATAAA
Found at i:460578 original size:29 final size:29
Alignment explanation
Indices: 460529--460584 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
460519 AGTTTTGTTA
*
460529 AAAAATTTAAATTATTATTTATAAATAAT
1 AAAAATTAAAATTATTATTTATAAATAAT
*
460558 AAAAATTAAAAGTTATT-TTTATTAATA
1 AAAAATTAAAA-TTATTATTTATAAATA
460585 TTTTTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
AAAAATTAAAATTATTATTTATAAATAAT
Found at i:460662 original size:5 final size:6
Alignment explanation
Indices: 460618--460644 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
460608 TTTATCTCTC
460618 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
460645 ATTAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:461593 original size:29 final size:30
Alignment explanation
Indices: 461561--461623 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 30
461551 TAAATATTAA
*
461561 TTATTAAATTTAATA-ATATAATT-AATTTT
1 TTATTAAATATAATATAT-TAATTAAATTTT
* *
461590 TTA-TATATATACTATATTAATTAAATTTT
1 TTATTAAATATAATATATTAATTAAATTTT
461619 TTATT
1 TTATT
461624 TTTTAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 13 0.46
29 14 0.50
30 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (30 bp):
TTATTAAATATAATATATTAATTAAATTTT
Found at i:461633 original size:28 final size:29
Alignment explanation
Indices: 461568--461635 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
461558 TAATTATTAA
461568 ATTTAATA-ATATAATTAATTTTTTATAT
1 ATTTAATATATATAATTAATTTTTTATAT
* *
461596 ATATACTATAT-TAATTAAATTTTTTAT-T
1 ATTTAATATATATAATT-AATTTTTTATAT
*
461624 TTTTAATATATA
1 ATTTAATATATA
461636 ATGATAGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 20 0.62
29 12 0.38
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (29 bp):
ATTTAATATATATAATTAATTTTTTATAT
Found at i:461736 original size:30 final size:29
Alignment explanation
Indices: 461702--461776 Score: 86
Period size: 27 Copynumber: 2.7 Consensus size: 29
461692 ATAATTAACA
461702 TAAATAAAATATAAAA-TATATTAATCAAAT
1 TAAATAAAATATAAAATTATATTAA--AAAT
*
461732 TAAAT-AAATATAAAATTATTTTAAAAAT
1 TAAATAAAATATAAAATTATATTAAAAAT
*
461760 T--ATAAAATATAATATTA
1 TAAATAAAATATAAAATTA
461777 ATATAAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 2 0.05
27 12 0.29
28 5 0.12
29 10 0.24
30 12 0.29
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (29 bp):
TAAATAAAATATAAAATTATATTAAAAAT
Found at i:462944 original size:39 final size:38
Alignment explanation
Indices: 462869--462946 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 38
462859 TTTATTAATT
**
462869 TTAAAATTATATTAAATTATATTTAAATAAATTATTTAA
1 TTAAAATTATATTAAA-TATATAAAAATAAATTATTTAA
*
462908 TTAAAATTTTATTAAA-ATATAAAAATAAATCATATTTAA
1 TTAAAATTATATTAAATATATAAAAATAAAT--TATTTAA
462947 AATTAAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 12 0.35
39 22 0.65
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (38 bp):
TTAAAATTATATTAAATATATAAAAATAAATTATTTAA
Found at i:466009 original size:16 final size:17
Alignment explanation
Indices: 465984--466016 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
465974 AAATATTAAA
*
465984 TTTTAGTATTTATAATT
1 TTTTAGTATTTAAAATT
466001 TTTTA-TATTTAAAATT
1 TTTTAGTATTTAAAATT
466017 ATAATTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTTAGTATTTAAAATT
Found at i:466035 original size:22 final size:21
Alignment explanation
Indices: 465993--466037 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
465983 ATTTTAGTAT
465993 TTATAATTTTTTATATTTAAAA
1 TTATAATTTTTTATA-TTAAAA
*
466015 TTATAATTTAATTTATATAAAAA
1 TTATAATTT--TTTATATTAAAA
466038 ATATTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATAATTTTTTATATTAAAA
Found at i:466038 original size:24 final size:22
Alignment explanation
Indices: 465993--466039 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
465983 ATTTTAGTAT
**
465993 TTATAATTTTTTATATTTAAAA
1 TTATAATTTTTTATATAAAAAA
466015 TTATAATTTAATTTATATAAAAAA
1 TTATAATTT--TTTATATAAAAAA
466039 T
1 T
466040 ATTATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
24 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATAATTTTTTATATAAAAAA
Found at i:466777 original size:13 final size:13
Alignment explanation
Indices: 466759--466784 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
466749 AGATTAATAC
466759 ATATATTTATATT
1 ATATATTTATATT
466772 ATATATTTATATT
1 ATATATTTATATT
466785 TTTTTATATT
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:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATATTTATATT
Found at i:466794 original size:16 final size:16
Alignment explanation
Indices: 466760--466838 Score: 67
Period size: 16 Copynumber: 5.0 Consensus size: 16
466750 GATTAATACA
466760 TATATTTATATTA---
1 TATATTTATATTATTT
*
466773 TATATTTATATTTTTT
1 TATATTTATATTATTT
* *
466789 TATATTTAAAATATTT
1 TATATTTATATTATTT
*
466805 TATATTTATATAAATTT
1 TATATTTATAT-TATTT
466822 TAATATATTATA-TATTT
1 T-ATAT-TTATATTATTT
466839 AAATAATTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
13 12 0.23
16 22 0.42
17 9 0.17
18 4 0.08
19 5 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATTTATATTATTT
Found at i:466826 original size:25 final size:27
Alignment explanation
Indices: 466793--466849 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
466783 TTTTTTTATA
* * *
466793 TTTAAAATATTTTATATTTATATAAAT
1 TTTAATATATTATATATTTAAATAAAT
*
466820 TTTAATATATTATATATTTAAATAATT
1 TTTAATATATTATATATTTAAATAAAT
466847 TTT
1 TTT
466850 TTAATTTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTAATATATTATATATTTAAATAAAT
Found at i:466837 original size:34 final size:32
Alignment explanation
Indices: 466759--466838 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
466749 AGATTAATAC
* * *
466759 ATATATT-TATATTATATATTTATATTTTTTT
1 ATATATTATATATTTTATATTTATATATTTTA
*
466790 ATAT-TTAAAATATTTTATATTTATATAAATTTTA
1 ATATATT-ATATATTTTATATTTATAT--ATTTTA
466824 ATATATTATATATTT
1 ATATATTATATATTT
466839 AAATAATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
30 2 0.05
31 4 0.10
32 16 0.41
34 15 0.38
35 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (32 bp):
ATATATTATATATTTTATATTTATATATTTTA
Found at i:467634 original size:2 final size:2
Alignment explanation
Indices: 467629--467653 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
467619 ACTCATTAAC
467629 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
467654 TTAGCTACCC
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:468651 original size:34 final size:35
Alignment explanation
Indices: 468595--468676 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 35
468585 TTTTATCGTG
468595 TTTAT-TTTTTTATATTTATTAAAA-T-ATAAA-A
1 TTTATATTTTTTATATTTATTAAAATTAATAAATA
468626 TTTATATTTTTTATATCTTATTTAAAATTAATAAATTA
1 TTTATATTTTTTATAT-TTA-TTAAAATTAATAAA-TA
*
468664 TTTTTATTTTTTA
1 TTTATATTTTTTA
468677 AAAAATAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
31 5 0.12
32 10 0.23
33 3 0.07
34 6 0.14
35 1 0.02
36 5 0.12
38 13 0.30
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (35 bp):
TTTATATTTTTTATATTTATTAAAATTAATAAATA
Found at i:468682 original size:21 final size:22
Alignment explanation
Indices: 468652--468705 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
468642 CTTATTTAAA
* *
468652 ATTAATAAATTAT-TTTTATTT
1 ATTAAAAAATTATATTTAATTT
* *
468673 TTTAAAAAATAATATTTAATTT
1 ATTAAAAAATTATATTTAATTT
*
468695 ATTAAGAAATT
1 ATTAAAAAATT
468706 TAATAGCGAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTAAAAAATTATATTTAATTT
Found at i:470316 original size:7 final size:7
Alignment explanation
Indices: 470304--470329 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
470294 ATAAATTTCT
470304 TTTAAAA
1 TTTAAAA
470311 TTTAAAA
1 TTTAAAA
470318 TTTAAAA
1 TTTAAAA
470325 TTTAA
1 TTTAA
470330 TAAATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:470494 original size:27 final size:27
Alignment explanation
Indices: 470461--470551 Score: 89
Period size: 27 Copynumber: 3.4 Consensus size: 27
470451 TATAATTTTA
*
470461 TTATATTATAATTGAATTTAAAATATT
1 TTATATTATAATTAAATTTAAAATATT
* *
470488 TTATATT-TATTTAAATTTTAATAATAAT
1 TTATATTATAATTAAA-TTTAA-AATATT
*
470516 TTATATTAT-A-TAAATATTAAATTATT
1 TTATATTATAATTAAAT-TTAAAATATT
*
470542 TAATATTATA
1 TTATATTATA
470552 TTTTAATTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
26 19 0.37
27 20 0.38
28 12 0.23
29 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
TTATATTATAATTAAATTTAAAATATT
Found at i:470560 original size:26 final size:26
Alignment explanation
Indices: 470531--470607 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 26
470521 TTATATAAAT
470531 ATTAAATTATTTAATATTATATTTTA
1 ATTAAATTATTTAATATTATATTTTA
*
470557 ATT--ATT-TTTTATATTATA-TTT-
1 ATTAAATTATTTAATATTATATTTTA
*
470578 ATATAATTATATTTAATATTGATAATTTTA
1 AT-TAAAT-TATTTAATATT-AT-ATTTTA
470608 TTATTTTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
21 2 0.05
22 4 0.10
23 11 0.28
24 4 0.10
25 1 0.03
26 11 0.28
27 2 0.05
28 1 0.03
29 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (26 bp):
ATTAAATTATTTAATATTATATTTTA
Found at i:470570 original size:49 final size:50
Alignment explanation
Indices: 470515--470614 Score: 134
Period size: 49 Copynumber: 2.0 Consensus size: 50
470505 TTAATAATAA
470515 TTTATATTATATAAATATTAAAT-TATTTAATATT-AT-ATTTTAATTATTT
1 TTTATATTATATAAATA-TAAATATATTTAATATTGATAATTTT-ATTATTT
** *
470564 TTTATATTATATTTATATAATTATATTTAATATTGATAATTTTATTATTT
1 TTTATATTATATAAATATAAATATATTTAATATTGATAATTTTATTATTT
470614 T
1 T
470615 GTTGTTGACA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
48 4 0.09
49 26 0.58
50 10 0.22
51 5 0.11
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (50 bp):
TTTATATTATATAAATATAAATATATTTAATATTGATAATTTTATTATTT
Found at i:470574 original size:23 final size:23
Alignment explanation
Indices: 470540--470614 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 23
470530 TATTAAATTA
470540 TTTAATATTATATTTTAATTATT
1 TTTAATATTATATTTTAATTATT
* *
470563 TTTTATATTATATTTATATAATTATA
1 TTTAATATTATA-TT-T-TAATTATT
470589 TTTAATATTGATAATTTT-ATTATT
1 TTTAATATT-AT-ATTTTAATTATT
470613 TT
1 TT
470615 GTTGTTGACA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
23 11 0.26
24 9 0.21
25 2 0.05
26 16 0.37
27 4 0.09
28 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (23 bp):
TTTAATATTATATTTTAATTATT
Found at i:475096 original size:31 final size:31
Alignment explanation
Indices: 475021--475097 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
475011 GCTCAAGTTA
*
475021 AATTTTAAAAATAAATTTAATTATTATATAAT
1 AATTTTAAAAAT-ATTTTAATTATTATATAAT
* * *
475053 AATTATAAAAATATTTTTATT-TTAATTTAAT
1 AATTTTAAAAATATTTTAATTATT-ATATAAT
*
475084 TATTTTAAAAATAT
1 AATTTTAAAAATAT
475098 ATAATAATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 2 0.05
31 25 0.66
32 11 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
AATTTTAAAAATATTTTAATTATTATATAAT
Found at i:475124 original size:16 final size:17
Alignment explanation
Indices: 475086--475124 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
475076 AATTTAATTA
475086 TTTTAAAAATATATAAT
1 TTTTAAAAATATATAAT
**
475103 AATTAAAAATA-ATAAT
1 TTTTAAAAATATATAAT
475119 TTTTAA
1 TTTTAA
475125 TAATTATTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 1
0.78 0.17 0.04
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTAAAAATATATAAT
Found at i:475145 original size:50 final size:49
Alignment explanation
Indices: 475045--475144 Score: 114
Period size: 50 Copynumber: 2.0 Consensus size: 49
475035 ATTTAATTAT
* * *
475045 TATATAATAATTATAAAAATATTTTTATTTTAATTTAATTATTTTAAAAA
1 TATATAATAATTAAAAAAATATTTTTATATTAATTTAA-TACTTTAAAAA
475095 TATATAATAATTAAAAATAATAATTTTTAATAATT-ATTTAA-ACTTTAAAA
1 TATATAATAATTAAAAA-AAT-ATTTTT-AT-ATTAATTTAATACTTTAAAA
475145 TTAAATCTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
50 16 0.37
51 11 0.26
52 6 0.14
53 8 0.19
54 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (49 bp):
TATATAATAATTAAAAAAATATTTTTATATTAATTTAATACTTTAAAAA
Found at i:475524 original size:5 final size:6
Alignment explanation
Indices: 475509--475533 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
475499 AAGAAATAAA
475509 CCCCCT CCCCCT CCCCCT CCCCCT C
1 CCCCCT CCCCCT CCCCCT CCCCCT C
475534 ATTGACCAAA
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:0.00, C:0.84, G:0.00, T:0.16
Consensus pattern (6 bp):
CCCCCT
Found at i:475990 original size:2 final size:2
Alignment explanation
Indices: 475983--476016 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
475973 CCTTTTTCCA
475983 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
476017 TCAATCATTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:486415 original size:36 final size:33
Alignment explanation
Indices: 486375--486471 Score: 86
Period size: 36 Copynumber: 2.8 Consensus size: 33
486365 ATTTTAAATA
486375 AAATTTTTATAAATTTATATAAATATGATTTAATTT
1 AAATTTTTATAAATTTATATAAATAT-ATTT--TTT
* ** * *
486411 AAATTATTATTTATTAATAAAAATATATTTTTT
1 AAATTTTTATAAATTTATATAAATATATTTTTT
**
486444 AAATTTAATTATAAAAATATATAAATAT
1 AAATTT--TTATAAATTTATATAAATAT
486472 TAATATAAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
33 8 0.17
35 18 0.38
36 21 0.45
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (33 bp):
AAATTTTTATAAATTTATATAAATATATTTTTT
Found at i:486469 original size:22 final size:22
Alignment explanation
Indices: 486443--486485 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
486433 ATATATTTTT
486443 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
*
486465 TAAATATTAATATAAATATAT
1 TAAATATTAATATAAAAATAT
486486 TTTTAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:486755 original size:2 final size:2
Alignment explanation
Indices: 486748--486790 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
486738 TAATGGTCAA
486748 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
486790 A
1 A
486791 AAGGATTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:491693 original size:20 final size:20
Alignment explanation
Indices: 491668--491726 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
491658 TACCCAGATG
491668 TATCGATACATTTTTCAATA
1 TATCGATACATTTTTCAATA
* * *
491688 TATCGATACATGTATGAATA
1 TATCGATACATTTTTCAATA
* *
491708 TATGGATACATTCTTCAAT
1 TATCGATACATTTTTCAAT
491727 GTATTGATAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (20 bp):
TATCGATACATTTTTCAATA
Found at i:491735 original size:20 final size:20
Alignment explanation
Indices: 491668--491741 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
491658 TACCCAGATG
*
491668 TATCGATACATTTTTCAATA
1 TATCGATACATTCTTCAATA
* *
491688 TATCGATACATGT-ATGAATA
1 TATCGATACAT-TCTTCAATA
* *
491708 TATGGATACATTCTTCAATG
1 TATCGATACATTCTTCAATA
* *
491728 TATTGATATATTCT
1 TATCGATACATTCT
491742 GTCTTTTTAC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (20 bp):
TATCGATACATTCTTCAATA
Found at i:492625 original size:20 final size:20
Alignment explanation
Indices: 492597--492671 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
492587 TCATACCCTG
492597 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
492617 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
492637 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
492657 ATGTATCGATACATT
1 ATGTATCGATACATT
492672 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:492664 original size:40 final size:39
Alignment explanation
Indices: 492597--492674 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
492587 TCATACCCTG
* *
492597 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
492637 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
492675 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:499772 original size:15 final size:17
Alignment explanation
Indices: 499736--499778 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
499726 AAAGTCAAAA
*
499736 GCAAAAGCACAAAAGAT
1 GCAAAAGCAAAAAAGAT
499753 G-AAAAG-AAAAAAG-T
1 GCAAAAGCAAAAAAGAT
499767 GCAAAAGCAAAA
1 GCAAAAGCAAAA
499779 TAAAAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 9 0.39
17 1 0.04
ACGTcount: A:0.65, C:0.12, G:0.19, T:0.05
Consensus pattern (17 bp):
GCAAAAGCAAAAAAGAT
Found at i:499784 original size:22 final size:22
Alignment explanation
Indices: 499759--499808 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
499749 AGATGAAAAG
499759 AAAAAAGTGCAA-AAGC-AAAATA
1 AAAAAAG-GCAACAA-CAAAAATA
*
499781 AAAAAAGGGAACAACAAAAATA
1 AAAAAAGGCAACAACAAAAATA
499803 AAAAAA
1 AAAAAA
499809 ACGAGGACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.74, C:0.08, G:0.12, T:0.06
Consensus pattern (22 bp):
AAAAAAGGCAACAACAAAAATA
Found at i:499800 original size:37 final size:36
Alignment explanation
Indices: 499723--499800 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 36
499713 CAAAATGACA
* * * *
499723 AAAAAAGTCAAAAGCAAAAGCACAAAAGATGAAAAG
1 AAAAAAGTCAAAAGCAAAAGAAAAAAAGAGGAAAAC
*
499759 AAAAAAGTGCAAAAGCAAAATAAAAAAAG-GGAACAAC
1 AAAAAAGT-CAAAAGCAAAAGAAAAAAAGAGGAA-AAC
499796 AAAAA
1 AAAAA
499801 TAAAAAAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
36 11 0.31
37 24 0.69
ACGTcount: A:0.69, C:0.10, G:0.15, T:0.05
Consensus pattern (36 bp):
AAAAAAGTCAAAAGCAAAAGAAAAAAAGAGGAAAAC
Found at i:501126 original size:27 final size:27
Alignment explanation
Indices: 501087--502233 Score: 1817
Period size: 27 Copynumber: 42.0 Consensus size: 27
501077 AGTGTGACCT
* *
501087 CTTTAAAGCCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
501114 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
501141 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * *
501169 CTTTTAAGTCTACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
501196 CTTTTAAAGTCCACAACTCCGTGGCATT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
501224 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
501251 CTTTTAAATCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
501278 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
501306 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
501333 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
501360 CTTTTAAGTCCATAACTCTGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
501388 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
501415 CTTTTTAAGTCCACAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCACC
501443 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
501470 CTTTTAAGTCCATAACTTCGCGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
501497 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
501525 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
501552 CTTTTAAGTCCACAACTCCGTGACACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
501579 CTTTTAAGTCCACAACTCCGTGGCATAT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
501607 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
501634 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
501662 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
501689 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
501716 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
501743 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
501771 CTTTTAAGTCCACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
501798 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
501825 CTTTTAAGTCCACAACTCCGGGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
501852 CTTTTAAGTCCATAACTCCGCGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
501879 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
501907 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
501934 CTTTTAAGTCCACAACTCCGCGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
501961 CTTTTAAGTCCACAACTCCGCGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
501988 CTTTTAAGTCCACAACTTCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
502016 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
502043 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
502070 CTTTTAAGTCCACAACTCCGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
502097 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
502124 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
502151 CTTTTAAGTCCATAACTCCGTGACATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
502179 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
502206 CTTTTAAAATCCATAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
502234 ATTTCAAAGC
Statistics
Matches: 1039, Mismatches: 68, Indels: 25
0.92 0.06 0.02
Matches are distributed among these distances:
27 718 0.69
28 321 0.31
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.27
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:501257 original size:82 final size:81
Alignment explanation
Indices: 501087--502233 Score: 1817
Period size: 82 Copynumber: 14.0 Consensus size: 81
501077 AGTGTGACCT
* *
501087 CTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
501152 ACAACTCCGTGGCATCC
66 ACAACTCCGTGGCA-CC
* * * **
501169 CTTTTAAGTCTACAACTTCGTGGCATCCTTTTAAAGTCCACAACTCCGTGGCATTCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
501234 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
501251 CTTTTAAATCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGAC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
501316 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* * *
501333 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCTGTGGCATCTCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
501398 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
501415 CTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 C-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* * *
501480 CATAACTTCGCGGCACC
65 CACAACTCCGTGGCACC
*
501497 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
501562 CACAACTCCGTGACACC
65 CACAACTCCGTGGCACC
** *
501579 CTTTTAAGTCCACAACTCCGTGGCATATCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
501644 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
501662 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
501727 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
* *
501743 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
501808 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* * *
501825 CTTTTAAGTCCACAACTCCGGGGCACCCTTTTAAGTCCATAACTCCGCGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
501890 ACAACTCCGTGGCATCC
66 ACAACTCCGTGGCA-CC
* *
501907 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGCGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
501972 ACAACTCCGCGGCACC
66 ACAACTCCGTGGCACC
* * *
501988 CTTTTAAGTCCACAACTTCGTGGCATCTCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
502053 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
502070 CTTTTAAGTCCACAACTCCGTGGTACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
502135 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
* * * * *
502151 CTTTTAAGTCCATAACTCCGTGACATCTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAAT
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
* *
502216 CCATAACTCTGTGGCACC
64 CCACAACTCCGTGGCACC
502234 ATTTCAAAGC
Statistics
Matches: 986, Mismatches: 69, Indels: 19
0.92 0.06 0.02
Matches are distributed among these distances:
81 241 0.24
82 587 0.60
83 158 0.16
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.27
Consensus pattern (81 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACC
Found at i:501347 original size:109 final size:108
Alignment explanation
Indices: 501087--502233 Score: 1817
Period size: 109 Copynumber: 10.5 Consensus size: 108
501077 AGTGTGACCT
* *
501087 CTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * *
501152 ACAACTCCGTGGCATCCCTTTTAAGTCTACAACTTCGTGGCATC
66 ACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
** *
501196 CTTTTAAAGTCCACAACTCCGTGGCATTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAATC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
501261 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
*
501306 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * *
501371 ATAACTCTGTGGCATCTCTTTTAAGTCCACAACTCCGTGGCACC
66 ACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
501415 CTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 C-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* * *
501480 CATAACTTCGCGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* *
501525 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGACACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
** *
501590 ACAACTCCGTGGCATATCTTTTAAGTCCACAACTCTGTGGCACC
66 ACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
501634 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
501699 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
501743 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
501808 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGGGGCACC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
501852 CTTTTAAGTCCATAACTCCGCGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGAC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
*
501917 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGCGGCACC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * * *
501961 CTTTTAAGTCCACAACTCCGCGGCACCCTTTTAAGTCCACAACTTCGTGGCATCTCTTTTAAGAC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
502026 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
65 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
502070 CTTTTAAGTCCACAACTCCGTGGTACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * *
502135 ACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGACATCT
66 ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* * * *
502179 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAATCCATAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACC
502234 ATTTCAAAGC
Statistics
Matches: 969, Mismatches: 58, Indels: 21
0.92 0.06 0.02
Matches are distributed among these distances:
108 97 0.10
109 578 0.60
110 294 0.30
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.27
Consensus pattern (108 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:502269 original size:32 final size:32
Alignment explanation
Indices: 502232--502801 Score: 753
Period size: 32 Copynumber: 18.3 Consensus size: 32
502222 CTCTGTGGCA
502232 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
502264 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
502296 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
**
502328 CTTTTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
502360 CCATTTCAAAGCCCACACAAGTCGGTGGCAA-
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
502391 CCATTTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CCA-TTTCAAAGCCCACACAAGTCGGTGGCAAC
*
502424 CCTTTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
502456 CCATTTCAAAGCCCACACAAGTCGGTGGCAA-
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
502487 CCATTTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CCA-TTTCAAAGCCCACACAAGTCGGTGGCAAC
*
502520 CCTTTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
*
502552 CCATTCCAAAGCCCACACAAGTCGGTGGCAAC
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
*
502584 CCATTTCAAAGCCCACACAAGTTGGTGGCAAC
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * *
502616 CCTTTTCAAAGCCCACACAAGTCAGTGG-TA-
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
502646 CCTTTTCAAAG-CC-CACAAGTCAGTGGC-AC
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * *
502675 TC-TTTCAAAG-CC-CACAAGTCAGTGGC-AT
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* ** *
502703 CC-TTTCAAAG-CC-CACGAGTTAGTGGC-AT
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * *
502731 TC-TTTCAAAGCCCACGCAAGTCAGTGGC-AC
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* ** **
502761 CC-TTTTAAAGCCCATGCAAGTCAATGGCAAC
1 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
*
502792 CCTTTTCAAA
1 CCATTTCAAA
502802 TCATCACTGT
Statistics
Matches: 498, Mismatches: 30, Indels: 20
0.91 0.05 0.04
Matches are distributed among these distances:
28 73 0.15
29 5 0.01
30 47 0.09
31 11 0.02
32 358 0.72
33 4 0.01
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (32 bp):
CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
Found at i:503343 original size:20 final size:20
Alignment explanation
Indices: 503315--503389 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
503305 TCATACCCTG
503315 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
503335 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
503355 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
503375 ATGTATCGATACATT
1 ATGTATCGATACATT
503390 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:503382 original size:40 final size:39
Alignment explanation
Indices: 503315--503392 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
503305 TCATACCCTG
* *
503315 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
503355 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
503393 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:509888 original size:224 final size:223
Alignment explanation
Indices: 509492--509913 Score: 580
Period size: 224 Copynumber: 1.9 Consensus size: 223
509482 AATAGTATTG
* * * *
509492 TAGTTTCTTATAAATTTTCTATAATAGTCAACCAATTTCAAAAGGCCTTTAAAGAAATTTAAGGT
1 TAGTTCCTTATAAATTTTCTATAATACTCAACCAATTTCAAAAAGCCTCTAAAGAAATTTAAGGT
* * *
509557 TTAAGAAATGGCTAGTTTTTGATAGCTTCCACCTTTGCAGGATTAGTTGAGACTTTTTGTGATGA
66 TTAAGAAATGGCCAGTTCTTGATAGCTTCCACCTTTGCAGGATCAGTTGAGACTTTTTGTGATGA
* * * *
509622 GATGATAAGGCCTATGTATTGCAATTGCCTTTGGCCAAAAAAAACACTTGCTTC-TCTTAATATA
131 GATGATAAGGCATAGGTATTGCAATTGCCTTTGGCC-AAAAAAACAATT-ATTCTTCTTAATATA
509686 TAATCTGTGAGGGGTTTTTTAATAACATTA
194 TAATCTGTGAGGGGTTTTTTAATAACATTA
* * *
509716 TAGTTCCTTATAAATTTTCTATAATAACT-AGCCAATTTTAAAAAGCCTCTAAAGAACTTTAAGG
1 TAGTTCCTTATAAATTTTCTATAAT-ACTCAACCAATTTCAAAAAGCCTCTAAAGAAATTTAAGG
**
509780 TTTAAGAAATGGCCAGTTCTTGATAGCTTCCATTTTTGCAGGATCAGTTGAGACTTTTTGTGATG
65 TTTAAGAAATGGCCAGTTCTTGATAGCTTCCACCTTTGCAGGATCAGTTGAGACTTTTTGTGATG
* * * * ** *
509845 AGATGATATGGTATAGGTATT-CTATTTGCTTTTGGGTAAAAAAACAATTATTCTTCTTGATATA
130 AGATGATAAGGCATAGGTATTGC-AATTGCCTTTGGCCAAAAAAACAATTATTCTTCTTAATATA
509909 TAATC
194 TAATC
509914 CGTGTGCTCT
Statistics
Matches: 172, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
222 3 0.02
223 26 0.15
224 141 0.82
225 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.39
Consensus pattern (223 bp):
TAGTTCCTTATAAATTTTCTATAATACTCAACCAATTTCAAAAAGCCTCTAAAGAAATTTAAGGT
TTAAGAAATGGCCAGTTCTTGATAGCTTCCACCTTTGCAGGATCAGTTGAGACTTTTTGTGATGA
GATGATAAGGCATAGGTATTGCAATTGCCTTTGGCCAAAAAAACAATTATTCTTCTTAATATATA
ATCTGTGAGGGGTTTTTTAATAACATTA
Found at i:512575 original size:20 final size:18
Alignment explanation
Indices: 512537--512575 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
512527 ATTCTATGAG
*
512537 ATGCTGAAAATATTAAAA
1 ATGCTGAAAATAATAAAA
512555 ATGCATGAAACATAATAAAA
1 ATGC-TGAAA-ATAATAAAA
512575 A
1 A
512576 AAATGCATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 9 0.50
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.23
Consensus pattern (18 bp):
ATGCTGAAAATAATAAAA
Found at i:513523 original size:20 final size:19
Alignment explanation
Indices: 513494--513568 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
513484 AAAAAGACAT
513494 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
513513 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
513534 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
513554 AATGTATCGATACAT
1 AATGTATCGATACAT
513569 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:513551 original size:40 final size:39
Alignment explanation
Indices: 513491--513568 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
513481 GGCAAAAAGA
*
513491 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
513530 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
513569 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:514263 original size:26 final size:26
Alignment explanation
Indices: 514204--514255 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
514194 GGAAGCAAAT
*
514204 AAACTTTAAAGAAAGTGGCATTGCTA
1 AAACCTTAAAGAAAGTGGCATTGCTA
514230 AAACCTTAAAGAAAGTGGCATTGCTA
1 AAACCTTAAAGAAAGTGGCATTGCTA
514256 TAGCCTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.25
Consensus pattern (26 bp):
AAACCTTAAAGAAAGTGGCATTGCTA
Found at i:517012 original size:43 final size:44
Alignment explanation
Indices: 516940--517025 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 44
516930 AATGATGAGG
* *
516940 GATTGTTGGAGCATTTTTAAAAATAAGTAAATGATTATATCTTA
1 GATTGCTGGAACATTTTTAAAAATAAGTAAATGATTATATCTTA
*
516984 GATTGCTGGAACA-TTTTCAAAATAAGTAAATGATTATATCTT
1 GATTGCTGGAACATTTTTAAAAATAAGTAAATGATTATATCTT
517026 TCATAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (44 bp):
GATTGCTGGAACATTTTTAAAAATAAGTAAATGATTATATCTTA
Found at i:518381 original size:42 final size:42
Alignment explanation
Indices: 518322--518420 Score: 198
Period size: 42 Copynumber: 2.4 Consensus size: 42
518312 TGACGAGAGA
518322 CTAAAATCCATAATTTTGACAACTACATAAACGAAATCTGTT
1 CTAAAATCCATAATTTTGACAACTACATAAACGAAATCTGTT
518364 CTAAAATCCATAATTTTGACAACTACATAAACGAAATCTGTT
1 CTAAAATCCATAATTTTGACAACTACATAAACGAAATCTGTT
518406 CTAAAATCCATAATT
1 CTAAAATCCATAATT
518421 CTGCAGGAAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.31
Consensus pattern (42 bp):
CTAAAATCCATAATTTTGACAACTACATAAACGAAATCTGTT
Found at i:522680 original size:22 final size:21
Alignment explanation
Indices: 522653--522696 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
522643 TATTTATTAT
*
522653 AATTTTATTTAATTTAAATTTA
1 AATTTTAATTAATTT-AATTTA
*
522675 AATTTTAATTACTTTAATTTA
1 AATTTTAATTAATTTAATTTA
522696 A
1 A
522697 TGGAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTTTAATTAATTTAATTTA
Found at i:522683 original size:28 final size:27
Alignment explanation
Indices: 522635--522696 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
522625 ATATTTGATA
*
522635 AATTTAAATATTTATTATAATTTTA-TTT
1 AATTTAAATATTAATTATAA--TTACTTT
*
522663 AATTTAAAT-TTAAATTTTAATTACTTT
1 AATTTAAATATT-AATTATAATTACTTT
522690 AATTTAA
1 AATTTAA
522697 TGGAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 3 0.10
27 12 0.40
28 15 0.50
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
AATTTAAATATTAATTATAATTACTTT
Found at i:523195 original size:11 final size:10
Alignment explanation
Indices: 523179--523241 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 10
523169 GTTATTTGAG
523179 TTTTAATTAAT
1 TTTTAATT-AT
523190 TTTTAA-TAT
1 TTTTAATTAT
523199 TTTTAA-T-T
1 TTTTAATTAT
523207 TTTTAA-TAT
1 TTTTAATTAT
523216 TTTTATATT-T
1 TTTTA-ATTAT
*
523226 TTATAATTAT
1 TTTTAATTAT
*
523236 ATTTAA
1 TTTTAA
523242 AAATAAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
8 8 0.18
9 18 0.40
10 12 0.27
11 7 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTAATTAT
Found at i:523202 original size:9 final size:9
Alignment explanation
Indices: 523188--523228 Score: 68
Period size: 8 Copynumber: 4.8 Consensus size: 9
523178 GTTTTAATTA
523188 ATTTTTAAT
1 ATTTTTAAT
523197 ATTTTTAAT
1 ATTTTTAAT
523206 -TTTTTAAT
1 ATTTTTAAT
523214 ATTTTT-AT
1 ATTTTTAAT
523222 ATTTTTA
1 ATTTTTA
523229 TAATTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 16 0.53
9 14 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:523211 original size:17 final size:17
Alignment explanation
Indices: 523185--523232 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
523175 TGAGTTTTAA
523185 TTAA-TTTTTAATATTT
1 TTAATTTTTTAATATTT
523201 TTAATTTTTTAATATTT
1 TTAATTTTTTAATATTT
523218 TTATATTTTTATAAT
1 TTA-ATTTTT-TAAT
523233 TATATTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.14
17 15 0.52
18 6 0.21
19 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTAATTTTTTAATATTT
Found at i:523770 original size:16 final size:16
Alignment explanation
Indices: 523749--523779 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
523739 AAATTAAGTT
523749 ATAAATAAAAATAAAA
1 ATAAATAAAAATAAAA
*
523765 ATAAATAAATATAAA
1 ATAAATAAAAATAAA
523780 TTTTAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
ATAAATAAAAATAAAA
Found at i:523894 original size:2 final size:2
Alignment explanation
Indices: 523887--523913 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
523877 ATTATATTTG
523887 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
523914 AAGAATTTCG
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:525399 original size:13 final size:12
Alignment explanation
Indices: 525350--525400 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
525340 ACCTTCACTG
525350 TTTCAAATTGAA
1 TTTCAAATTGAA
*
525362 TTTCAACATTTACTA
1 TTTCAA-ATTGA--A
525377 TTTCAAATTGAA
1 TTTCAAATTGAA
525389 TTTCAAAATTGA
1 TTTC-AAATTGA
525401 CGGCACAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 11 0.33
13 11 0.33
14 4 0.12
15 7 0.21
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (12 bp):
TTTCAAATTGAA
Found at i:530307 original size:22 final size:23
Alignment explanation
Indices: 530262--530307 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
530252 AAAATTATAA
*
530262 AAAATTATTTTTTAATAATTTTT
1 AAAATTATTTTTTAATAATCTTT
530285 AAAATT-TTATTTT-ATAATCTTT
1 AAAATTATT-TTTTAATAATCTTT
530307 A
1 A
530308 TATAGGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
AAAATTATTTTTTAATAATCTTT
Found at i:531202 original size:17 final size:18
Alignment explanation
Indices: 531162--531202 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
531152 ATGTTAAGGT
*
531162 AATAAAATAATTTTATTA
1 AATAAAATAATCTTATTA
*
531180 AA-AAAATTATCTT-TTA
1 AATAAAATAATCTTATTA
531196 AATAAAA
1 AATAAAA
531203 AAATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 5 0.25
17 13 0.65
18 2 0.10
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAAAATAATCTTATTA
Found at i:532077 original size:13 final size:14
Alignment explanation
Indices: 532058--532091 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
532048 CTAAACTATT
*
532058 TAAATATATAAAAA
1 TAAATATAAAAAAA
532072 -AAATATAAAAAAA
1 TAAATATAAAAAAA
532085 TAAATAT
1 TAAATAT
532092 TTTTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAATATAAAAAAA
Found at i:534937 original size:18 final size:18
Alignment explanation
Indices: 534914--535022 Score: 141
Period size: 18 Copynumber: 6.1 Consensus size: 18
534904 AAATAATAGA
534914 TTTTAAGAATCACAGATT
1 TTTTAAGAATCACAGATT
534932 TTTTAAGAATC-CTAGATT
1 TTTTAAGAATCAC-AGATT
534950 TTTTAAGAATCACAGATT
1 TTTTAAGAATCACAGATT
*
534968 TTTTAAGAATCATTAGATT
1 TTTTAAGAATCA-CAGATT
* *
534987 TTATAAGAATCACA-ACT
1 TTTTAAGAATCACAGATT
* *
535004 TTTTAAAAATCATAGATT
1 TTTTAAGAATCACAGATT
535022 T
1 T
535023 CTGTAATTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
17 14 0.18
18 48 0.61
19 17 0.22
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.41
Consensus pattern (18 bp):
TTTTAAGAATCACAGATT
Found at i:534957 original size:36 final size:36
Alignment explanation
Indices: 534914--535022 Score: 166
Period size: 36 Copynumber: 3.0 Consensus size: 36
534904 AAATAATAGA
*
534914 TTTTAAGAATCACAGATTTTTTAAGAATCCTAGATT
1 TTTTAAGAATCACAGATTTTTTAAGAATCATAGATT
534950 TTTTAAGAATCACAGATTTTTTAAGAATCATTAGATT
1 TTTTAAGAATCACAGATTTTTTAAGAATCA-TAGATT
* * *
534987 TTATAAGAATCACA-ACTTTTTAAAAATCATAGATT
1 TTTTAAGAATCACAGATTTTTTAAGAATCATAGATT
535022 T
1 T
535023 CTGTAATTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
35 7 0.10
36 42 0.62
37 19 0.28
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.41
Consensus pattern (36 bp):
TTTTAAGAATCACAGATTTTTTAAGAATCATAGATT
Found at i:537381 original size:18 final size:18
Alignment explanation
Indices: 537321--537393 Score: 69
Period size: 18 Copynumber: 4.1 Consensus size: 18
537311 AGTATAAATT
* *
537321 ATAGA-TTTTAAGGTATC
1 ATAGATTTTTTAGGAATC
* *
537338 ACAGATTTTTTAGAAAT-
1 ATAGATTTTTTAGGAATC
*
537355 ATTAAATTTTTTAGGAATC
1 A-TAGATTTTTTAGGAATC
*
537374 ATAGATTTTTTAAGAATC
1 ATAGATTTTTTAGGAATC
537392 AT
1 AT
537394 TTAATTTTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
17 5 0.11
18 38 0.86
19 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.44
Consensus pattern (18 bp):
ATAGATTTTTTAGGAATC
Found at i:537400 original size:19 final size:19
Alignment explanation
Indices: 537342--537401 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 19
537332 GGTATCACAG
*
537342 ATTTTTT-AGAAAT-ATTAA
1 ATTTTTTAAG-AATCATTTA
*
537360 ATTTTTTAGGAATCA--TA
1 ATTTTTTAAGAATCATTTA
537377 GATTTTTTAAGAATCATTTA
1 -ATTTTTTAAGAATCATTTA
537397 ATTTT
1 ATTTT
537402 ATGAATAGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
17 1 0.03
18 24 0.71
19 7 0.21
20 2 0.06
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.52
Consensus pattern (19 bp):
ATTTTTTAAGAATCATTTA
Found at i:538532 original size:14 final size:14
Alignment explanation
Indices: 538513--538552 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
538503 ACGATAATAT
*
538513 TAAATATAATTATG
1 TAAATATAATTATA
538527 TAAATATAATCTATA
1 TAAATATAAT-TATA
538542 TAAA-ATAATTA
1 TAAATATAATTA
538553 AAATGACACG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 2 0.08
14 15 0.62
15 7 0.29
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (14 bp):
TAAATATAATTATA
Found at i:538847 original size:3 final size:3
Alignment explanation
Indices: 538839--538880 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
538829 CAAAGTAGTG
538839 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
538881 CTTTTAATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:539350 original size:23 final size:23
Alignment explanation
Indices: 539324--539394 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
539314 TTTTCACGTA
539324 ATTTATATATTTATATTATATTT
1 ATTTATATATTTATATTATATTT
* **
539347 ATTTAT-TTTATTATATTATAAAT
1 ATTTATATAT-TTATATTATATTT
* *
539370 ATATTATA-AATTATTTTATATTT
1 AT-TTATATATTTATATTATATTT
539393 AT
1 AT
539395 ATAAATTGTA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
22 2 0.05
23 31 0.84
24 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTATATATTTATATTATATTT
Found at i:539395 original size:23 final size:24
Alignment explanation
Indices: 539334--539453 Score: 75
Period size: 23 Copynumber: 4.9 Consensus size: 24
539324 ATTTATATAT
**
539334 TTATATTATATTTAT-TTATTTTA
1 TTATATTATATTTATATTATTAAA
**
539357 TTATATTATAAATATATTA-TAAA
1 TTATATTATATTTATATTATTAAA
* * *
539380 TTATTTTATATTTATATAAATTGTAA
1 TTATATTATATTTATAT-TATT-AAA
539406 -TATATTAATAATTTATATTATATAAA
1 TTATATT-AT-ATTTATATTAT-TAAA
* **
539432 TTTTAAAATAATTTATATTATT
1 TTATATTAT-ATTTATATTATT
539454 TTATATTATT
Statistics
Matches: 74, Mismatches: 15, Indels: 14
0.72 0.15 0.14
Matches are distributed among these distances:
23 29 0.39
24 4 0.05
25 7 0.09
26 22 0.30
27 12 0.16
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (24 bp):
TTATATTATATTTATATTATTAAA
Found at i:539408 original size:18 final size:16
Alignment explanation
Indices: 539384--539434 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
539374 TATAAATTAT
539384 TTTATATTTATATAAA
1 TTTATATTTATATAAA
539400 TTGTAATATATTA-AT-AA
1 TT-T-ATAT-TTATATAAA
539417 TTTATA-TTATATAAA
1 TTTATATTTATATAAA
539432 TTT
1 TTT
539435 TAAAATAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
13 3 0.10
14 2 0.07
15 8 0.27
16 3 0.10
17 5 0.17
18 6 0.20
19 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTATATTTATATAAA
Found at i:539428 original size:20 final size:20
Alignment explanation
Indices: 539368--539429 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 20
539358 TATATTATAA
*
539368 ATATATT-ATAAATTATTTT
1 ATATATTAATAAATTATATT
*
539387 ATAT-TTATATAAATTGTA--
1 ATATATTA-ATAAATTATATT
*
539405 ATATATTAATAATTTATATT
1 ATATATTAATAAATTATATT
539425 ATATA
1 ATATA
539430 AATTTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
18 14 0.41
19 7 0.21
20 13 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATATATTAATAAATTATATT
Found at i:539433 original size:15 final size:13
Alignment explanation
Indices: 539406--539451 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
539396 TAAATTGTAA
539406 TATATTAATAATT
1 TATATTAATAATT
539419 TATATTATATAAATT
1 TATATTA-AT-AATT
*
539434 T-TA-AAATAATT
1 TATATTAATAATT
539445 TATATTA
1 TATATTA
539452 TTTTATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
11 5 0.19
12 4 0.15
13 9 0.33
14 4 0.15
15 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATTAATAATT
Found at i:546930 original size:13 final size:13
Alignment explanation
Indices: 546895--546949 Score: 60
Period size: 12 Copynumber: 4.2 Consensus size: 13
546885 AATTAATTAT
546895 TTTTAATATTTTTA
1 TTTT-ATATTTTTA
*
546909 ATTTA-ATTTTTA
1 TTTTATATTTTTA
546921 TTTTATATTTTTA
1 TTTTATATTTTTA
*
546934 -TTTAAATTTTTTA
1 TTTTATA-TTTTTA
546947 TTT
1 TTT
546950 ATTAAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
12 16 0.46
13 14 0.40
14 5 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTATATTTTTA
Found at i:546941 original size:25 final size:27
Alignment explanation
Indices: 546895--546949 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
546885 AATTAATTAT
546895 TTTTAATATTTTTAATTTAA-TTTTTA
1 TTTTAATATTTTTAATTTAATTTTTTA
546921 TTTT-ATATTTTT-ATTTAAATTTTTTA
1 TTTTAATATTTTTAATTT-AATTTTTTA
546947 TTT
1 TTT
546950 ATTAAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 4 0.15
25 10 0.37
26 13 0.48
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTTAATATTTTTAATTTAATTTTTTA
Found at i:546951 original size:25 final size:25
Alignment explanation
Indices: 546874--546949 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 25
546864 TAAAATTAAA
* *
546874 TTATATTTATGAA-TTAATTATT-TT
1 TTATATTT-TTAATTTAATTTTTATT
*
546898 TAATATTTTTAATTTAATTTTTATT
1 TTATATTTTTAATTTAATTTTTATT
546923 TTATATTTTT-ATTTAAATTTTTTATT
1 TTATATTTTTAATTT-AA-TTTTTATT
546949 T
1 T
546950 ATTAAATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
23 3 0.07
24 19 0.43
25 13 0.30
26 9 0.20
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (25 bp):
TTATATTTTTAATTTAATTTTTATT
Found at i:546965 original size:17 final size:17
Alignment explanation
Indices: 546920--546972 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
546910 TTTAATTTTT
*
546920 ATTTTATATTTTTATTTAA
1 ATTTTA-ATATTTA-TTAA
*
546939 ATTTT-TTATTTATTAA
1 ATTTTAATATTTATTAA
546955 ATTTTAATATTTA-TAA
1 ATTTTAATATTTATTAA
546971 AT
1 AT
546973 AATATAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 14 0.47
17 11 0.37
19 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTAATATTTATTAA
Found at i:547013 original size:13 final size:13
Alignment explanation
Indices: 546896--547017 Score: 66
Period size: 13 Copynumber: 9.6 Consensus size: 13
546886 ATTAATTATT
546896 TTTAATATTTTTAA
1 TTTAATA-TTTTAA
546910 TTTAAT-TTTT-A
1 TTTAATATTTTAA
* *
546921 TTTTATATTTTTA
1 TTTAATATTTTAA
546934 TTTAA-A-TTT--
1 TTTAATATTTTAA
546943 TTT-AT-TTATTAAA
1 TTTAATATT-TT-AA
546956 TTTTAATATTTATAA
1 -TTTAATATTT-TAA
* *
546971 -ATAATATAATTAA
1 TTTAATAT-TTTAA
*
546984 TTTAA-ATTTAAA
1 TTTAATATTTTAA
546996 TTTTAATATTTTAA
1 -TTTAATATTTTAA
547010 TTTAATAT
1 TTTAATAT
547018 AAAATATAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 33
0.67 0.06 0.26
Matches are distributed among these distances:
8 1 0.01
9 4 0.05
10 2 0.02
11 9 0.11
12 12 0.14
13 29 0.35
14 19 0.23
15 5 0.06
16 3 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTAATATTTTAA
Found at i:547080 original size:8 final size:9
Alignment explanation
Indices: 547033--547087 Score: 58
Period size: 9 Copynumber: 6.1 Consensus size: 9
547023 ATAAAATATA
547033 AAAAATTAT
1 AAAAATTAT
*
547042 AAAATTTAT
1 AAAAATTAT
*
547051 AATAATTAT
1 AAAAATTAT
*
547060 ATAAATT-T
1 AAAAATTAT
*
547068 AAAAATTAA
1 AAAAATTAT
547077 AAAAATCTAT
1 AAAAAT-TAT
547087 A
1 A
547088 TCCAAATCTC
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
8 7 0.19
9 26 0.72
10 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAAATTAT
Found at i:547087 original size:27 final size:27
Alignment explanation
Indices: 547035--547088 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
547025 AAAATATAAA
* * *
547035 AAATTATAAAATTTATAATAATTATAT
1 AAATTATAAAAATTAAAAAAATTATAT
547062 AAATT-TAAAAATTAAAAAAATCTATAT
1 AAATTATAAAAATTAAAAAAAT-TATAT
547089 CCAAATCTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
AAATTATAAAAATTAAAAAAATTATAT
Found at i:552208 original size:54 final size:54
Alignment explanation
Indices: 552137--552346 Score: 187
Period size: 54 Copynumber: 3.8 Consensus size: 54
552127 GGGTCGTTTT
*
552137 GTGGCGATCTCGA-TTTGAATGACTTA-GCGTCACTTAGTGTTTGGGATTGCCTTG
1 GTGGCGATCT-GAGTTTGAATGAC-AAGGCGTCACTTAGTGTTTGGGATTGCCTTG
* *
552191 GTGGCGATCTGAGTTTGAGTGACAAGGCGTCACTTAGTGTTT-GAATTTGGGTCGCTTTG
1 GTGGCGATCTGAGTTTGAATGACAAGGCGTCACTTAGTGTTTGGGA-TT--G-C-C-TTG
* * ** * *
552250 GTGGTGATTTGAGTTT-AAGTGACTTGGCGTCACTTAGT-TTCTAGGATTGCCTTA
1 GTGGCGATCTGAGTTTGAA-TGACAAGGCGTCACTTAGTGTT-TGGGATTGCCTTG
* * *
552304 GTGGCAATTTGAGTTTGAATGACAAGGTGTCACTTAGTGTTTG
1 GTGGCGATCTGAGTTTGAATGACAAGGCGTCACTTAGTGTTTG
552347 AATTTGGGTC
Statistics
Matches: 127, Mismatches: 16, Indels: 26
0.75 0.09 0.15
Matches are distributed among these distances:
53 5 0.04
54 70 0.55
55 5 0.04
56 2 0.02
57 2 0.02
58 4 0.03
59 37 0.29
60 2 0.02
ACGTcount: A:0.19, C:0.13, G:0.30, T:0.38
Consensus pattern (54 bp):
GTGGCGATCTGAGTTTGAATGACAAGGCGTCACTTAGTGTTTGGGATTGCCTTG
Found at i:552271 original size:59 final size:59
Alignment explanation
Indices: 552188--552382 Score: 210
Period size: 59 Copynumber: 3.4 Consensus size: 59
552178 TGGGATTGCC
* *
552188 TTGGTGGCGATCTGAGTTTGAGTGACAAGGCGTCACTTAGTGTTTGAATTTGGGTCGCT
1 TTGGTGGCGATTTGAGTTTAAGTGACAAGGCGTCACTTAGTGTTTGAATTTGGGTCGCT
* ** *
552247 TTGGTGGTGATTTGAGTTTAAGTGACTTGGCGTCACTTAGT-TTCTAGGA-TT--G-C-C-
1 TTGGTGGCGATTTGAGTTTAAGTGACAAGGCGTCACTTAGTGTT-T-GAATTTGGGTCGCT
* * *
552301 TTAGTGGCAATTTGAGTTTGAA-TGACAAGGTGTCACTTAGTGTTTGAATTTGGGTCG-T
1 TTGGTGGCGATTTGAGTTT-AAGTGACAAGGCGTCACTTAGTGTTTGAATTTGGGTCGCT
*
552359 TTGGTGGCGATTTGAGTTTGAGTG
1 TTGGTGGCGATTTGAGTTTAAGTG
552383 GAGTCGCATT
Statistics
Matches: 109, Mismatches: 16, Indels: 23
0.74 0.11 0.16
Matches are distributed among these distances:
53 2 0.02
54 35 0.32
55 5 0.05
56 2 0.02
57 3 0.03
58 21 0.19
59 39 0.36
60 2 0.02
ACGTcount: A:0.18, C:0.11, G:0.32, T:0.39
Consensus pattern (59 bp):
TTGGTGGCGATTTGAGTTTAAGTGACAAGGCGTCACTTAGTGTTTGAATTTGGGTCGCT
Found at i:552287 original size:113 final size:112
Alignment explanation
Indices: 552127--552382 Score: 356
Period size: 113 Copynumber: 2.3 Consensus size: 112
552117 ATTTTGATAG
* * *
552127 GGGTCGTTTTGTGGCGATCTCGA-TTTGAA-TGACTTAGCGTCACTTAGTGTT-TGGGATTGCCT
1 GGGTCGTTTGGTGGCGAT-TTGAGTTT-AAGTGACTTAGCGTCACTTAGT-TTCTAGGATTGCCT
* * *
552189 TGGTGGCGATCTGAGTTTGAGTGACAAGGCGTCACTTAGTGTTTGAATTT
63 TAGTGGCAATCTGAGTTTGAATGACAAGGCGTCACTTAGTGTTTGAATTT
* *
552239 GGGTCGCTTTGGTGGTGATTTGAGTTTAAGTGACTTGGCGTCACTTAGTTTCTAGGATTGCCTTA
1 GGGTCG-TTTGGTGGCGATTTGAGTTTAAGTGACTTAGCGTCACTTAGTTTCTAGGATTGCCTTA
* *
552304 GTGGCAATTTGAGTTTGAATGACAAGGTGTCACTTAGTGTTTGAATTT
65 GTGGCAATCTGAGTTTGAATGACAAGGCGTCACTTAGTGTTTGAATTT
*
552352 GGGTCGTTTGGTGGCGATTTGAGTTTGAGTG
1 GGGTCGTTTGGTGGCGATTTGAGTTTAAGTG
552383 GAGTCGCATT
Statistics
Matches: 128, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
112 36 0.28
113 92 0.72
ACGTcount: A:0.17, C:0.12, G:0.32, T:0.39
Consensus pattern (112 bp):
GGGTCGTTTGGTGGCGATTTGAGTTTAAGTGACTTAGCGTCACTTAGTTTCTAGGATTGCCTTAG
TGGCAATCTGAGTTTGAATGACAAGGCGTCACTTAGTGTTTGAATTT
Found at i:557589 original size:14 final size:15
Alignment explanation
Indices: 557567--557600 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
557557 AAATTTATAT
*
557567 TAAATAATAAT-AAA
1 TAAAAAATAATAAAA
557581 TAAAAAATAATAAAA
1 TAAAAAATAATAAAA
557596 TAAAA
1 TAAAA
557601 TTAAACTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAAAAATAATAAAA
Found at i:558794 original size:2 final size:2
Alignment explanation
Indices: 558787--558827 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
558777 ACTTTGGTTA
558787 AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A- AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
558825 AT A
1 AT A
558828 AGACTAACTG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 4 0.11
2 31 0.89
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:558800 original size:8 final size:8
Alignment explanation
Indices: 558787--558827 Score: 54
Period size: 7 Copynumber: 5.6 Consensus size: 8
558777 ACTTTGGTTA
558787 ATATATAT
1 ATATATAT
558795 ATATATAT
1 ATATATAT
558803 ATATA-AT
1 ATATATAT
558810 ATA-ATAT
1 ATATATAT
558817 A-ATATA-
1 ATATATAT
558823 ATATA
1 ATATA
558828 AGACTAACTG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
6 3 0.10
7 14 0.47
8 13 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
ATATATAT
Found at i:558813 original size:5 final size:5
Alignment explanation
Indices: 558785--558828 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
558775 TAACTTTGGT
558785 TAATA T-ATA TATATA TATATA TAATA TAATA TAATA TAATA TAA
1 TAATA TAATA TA-ATA TA-ATA TAATA TAATA TAATA TAATA TAA
558829 GACTAACTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.11
5 22 0.59
6 11 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TAATA
Found at i:559424 original size:21 final size:22
Alignment explanation
Indices: 559398--559439 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
559388 TATCTAGTTC
* *
559398 ACTAATTATGTAT-AAATATAT
1 ACTAATAATATATCAAATATAT
559419 ACTAATAATATATCAAATATA
1 ACTAATAATATATCAAATATA
559440 AATTCATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (22 bp):
ACTAATAATATATCAAATATAT
Found at i:559640 original size:18 final size:18
Alignment explanation
Indices: 559588--559641 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
559578 AAAATAAAAT
559588 TATTATTT-ATTT-TTAA
1 TATTATTTAATTTATTAA
* ** *
559604 AATTATTTAATGAAATAA
1 TATTATTTAATTTATTAA
559622 TATTATTTAATTTATTAA
1 TATTATTTAATTTATTAA
559640 TA
1 TA
559642 ATATATAGAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 7 0.25
17 2 0.07
18 19 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TATTATTTAATTTATTAA
Found at i:559674 original size:25 final size:25
Alignment explanation
Indices: 559642--559693 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
559632 TTTATTAATA
*
559642 ATATATAGATATATATACTGTCAAT
1 ATATATAGATATATATACTATCAAT
559667 ATATATAGATATATATACTATCAAT
1 ATATATAGATATATATACTATCAAT
559692 AT
1 AT
559694 TTATTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (25 bp):
ATATATAGATATATATACTATCAAT
Found at i:563351 original size:16 final size:17
Alignment explanation
Indices: 563330--563365 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
563320 CATATTATGA
563330 TTATATTTA-AAAAATT
1 TTATATTTATAAAAATT
*
563346 TTATATTTATATAAATT
1 TTATATTTATAAAAATT
563363 TTA
1 TTA
563366 ATATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTTATAAAAATT
Found at i:563377 original size:18 final size:17
Alignment explanation
Indices: 563330--563377 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
563320 CATATTATGA
*
563330 TTATAT-TTAAAAAATT
1 TTATATATTAATAAATT
563346 TTATAT-TTATATAAATT
1 TTATATATTA-ATAAATT
563363 TTAATATATTAATAA
1 TT-ATATATTAATAA
563378 TTAGTATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 9 0.32
17 8 0.29
18 8 0.29
19 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATATATTAATAAATT
Found at i:564295 original size:2 final size:2
Alignment explanation
Indices: 564288--564325 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
564278 TCCCTATACC
564288 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
564326 TTGCTGGAAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:565836 original size:21 final size:21
Alignment explanation
Indices: 565797--565870 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 21
565787 AATTAATATT
565797 TTATAATAAAT-TATAAATTTAA
1 TTATAA-AAATATAT-AATTTAA
*
565819 TTATAAAAATATATAATTATTA
1 TTATAAAAATATATAATT-TAA
565841 TTATAAAAATA-AT-ATTTAATA
1 TTATAAAAATATATAATTT-A-A
565862 TTATAAAAA
1 TTATAAAAA
565871 ATAATTAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 20 0.43
22 22 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTATAAAAATATATAATTTAA
Found at i:565871 original size:22 final size:21
Alignment explanation
Indices: 565787--565878 Score: 82
Period size: 21 Copynumber: 4.3 Consensus size: 21
565777 TTTCAACTTA
*
565787 AATTAATATTTTATAATAAATTAT
1 AATTAATA--TTATAA-AAATAAT
*
565811 AAATTTA-ATTATAAAAATATAT
1 -AATTAATATTATAAAAATA-AT
*
565833 AATTATTATTATAAAAATAAT
1 AATTAATATTATAAAAATAAT
*
565854 ATTTAATATTAT-AAAA-AAT
1 AATTAATATTATAAAAATAAT
565873 AATTAA
1 AATTAA
565879 ATAAACTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
19 8 0.14
20 4 0.07
21 20 0.34
22 20 0.34
24 1 0.02
25 5 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTAATATTATAAAAATAAT
Found at i:566750 original size:15 final size:15
Alignment explanation
Indices: 566706--566751 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
566696 CCTTCCTTTC
566706 TCTTTTTTTTC-TTT
1 TCTTTTTTTTCATTT
566720 TCTTTTTTTTTCCATTT
1 TC-TTTTTTTT-CATTT
*
566737 TCTTTCTTTTCATTT
1 TCTTTTTTTTCATTT
566752 CATTCCTCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.07
15 13 0.46
16 8 0.29
17 5 0.18
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.78
Consensus pattern (15 bp):
TCTTTTTTTTCATTT
Found at i:566752 original size:21 final size:22
Alignment explanation
Indices: 566712--566752 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
566702 TTTCTCTTTT
**
566712 TTTTCTTTTCTTTTTTTTTCCA
1 TTTTCTTTTCTTTTCATTTCCA
566734 TTTTC-TTTCTTTTCATTTC
1 TTTTCTTTTCTTTTCATTTC
566753 ATTCCTCTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTCTTTTCTTTTCATTTCCA
Found at i:567369 original size:3 final size:3
Alignment explanation
Indices: 567356--567404 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
567346 AACAAAATAC
567356 AAT AA- 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
567403 AA
1 AA
567405 AGAGAAATAG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:568011 original size:27 final size:29
Alignment explanation
Indices: 567948--568025 Score: 80
Period size: 27 Copynumber: 2.9 Consensus size: 29
567938 AAAATATTTT
567948 ATTTAAAT-TTATTT-T-AATT--TAAAA
1 ATTTAAATATTATTTATAAATTAATAAAA
567972 ATTTAAATTATTATTTATAAATTAATAAAA
1 ATTTAAA-TATTATTTATAAATTAATAAAA
* *
568002 A-TTAAA-ATTATTTTTATATTAATA
1 ATTTAAATATTATTTATAAATTAATA
568026 TTTAAATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
24 7 0.15
25 1 0.02
26 6 0.13
27 17 0.37
28 4 0.09
29 5 0.11
30 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTTAAATATTATTTATAAATTAATAAAA
Found at i:568033 original size:29 final size:29
Alignment explanation
Indices: 567956--568025 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 29
567946 TTATTTAAAT
*
567956 TTATTT-TAATT--TAAAAATTTAAATTA
1 TTATTTATAATTAATAAAAATTAAAATTA
567982 TTATTTATAAATTAATAAAAATTAAAATTA
1 TTATTTAT-AATTAATAAAAATTAAAATTA
568012 TT-TTTAT-ATTAATA
1 TTATTTATAATTAATA
568026 TTTAAATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 6 0.15
27 8 0.21
28 4 0.10
29 5 0.13
30 16 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TTATTTATAATTAATAAAAATTAAAATTA
Found at i:568036 original size:20 final size:20
Alignment explanation
Indices: 568011--568052 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
568001 AATTAAAATT
568011 ATTTTTAT-ATTAATATTTAA
1 ATTTTTATAATTAA-ATTTAA
568031 ATTTTTATAATTAAATTTAA
1 ATTTTTATAATTAAATTTAA
568051 AT
1 AT
568053 AAAAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTATAATTAAATTTAA
Found at i:568046 original size:53 final size:55
Alignment explanation
Indices: 567950--568058 Score: 127
Period size: 53 Copynumber: 2.0 Consensus size: 55
567940 AATATTTTAT
* *
567950 TTAAATTTATTTTAATTTAAAAATTTAAATTATTATTTATAAA-TT-AATAAAAA
1 TTAAAATTATTTTAATTTAAAAATTTAAATTATTATATATAAATTTAAATAAAAA
* * *
568003 TTAAAATTATTTTTATATT-AATATTTAAATTTTTATA-ATTAAATTTAAATAAAAA
1 TTAAAATTATTTTAAT-TTAAAAATTTAAATTATTATATA-TAAATTTAAATAAAAA
568058 T
1 T
568059 ATTTTTATTC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
52 1 0.02
53 33 0.70
54 4 0.09
55 9 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (55 bp):
TTAAAATTATTTTAATTTAAAAATTTAAATTATTATATATAAATTTAAATAAAAA
Found at i:569585 original size:2 final size:2
Alignment explanation
Indices: 569578--569609 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
569568 GCATTTACAC
569578 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
569610 ATACTAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:573848 original size:26 final size:24
Alignment explanation
Indices: 573794--573848 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
573784 TATTGATTAC
** *
573794 AATGATATTTATAAAAATGTTATC
1 AATGATATTTATAAAAAAATTATA
*
573818 GATGATATTTATAGAAAAAATTAATA
1 AATGATATTTATA-AAAAAATT-ATA
573844 AATGA
1 AATGA
573849 AAATCAGTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 12 0.50
25 6 0.25
26 6 0.25
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (24 bp):
AATGATATTTATAAAAAAATTATA
Found at i:574014 original size:3 final size:3
Alignment explanation
Indices: 574008--574040 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
573998 ACAAAAAAAG
574008 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
574041 GCATTTCTAG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:580578 original size:24 final size:24
Alignment explanation
Indices: 580532--580581 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
580522 TTTGGTAAGA
*
580532 TTGATTTTCATTTAACTTGATAAT
1 TTGATTTTCATTTAACTTAATAAT
*
580556 TTGATTTTTATTTATA-TTAATAAT
1 TTGATTTTCATTTA-ACTTAATAAT
580580 TT
1 TT
580582 TGCTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (24 bp):
TTGATTTTCATTTAACTTAATAAT
Found at i:582142 original size:21 final size:21
Alignment explanation
Indices: 582097--582143 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
582087 TCAATTTCAA
* *
582097 CAGGAAACAAGAGCCAACATT
1 CAGGAAACAAGAGACAACATC
582118 CAGGAAACAAG-GACAAGCATC
1 CAGGAAACAAGAGACAA-CATC
582139 CAGGA
1 CAGGA
582144 TTTAGGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.47, C:0.23, G:0.23, T:0.06
Consensus pattern (21 bp):
CAGGAAACAAGAGACAACATC
Found at i:587370 original size:14 final size:13
Alignment explanation
Indices: 587351--587401 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
587341 TGGCAATTGG
587351 AAAAAAAAAGGTAA
1 AAAAAAAAAGG-AA
*
587365 AAAAAAAAAGAAA
1 AAAAAAAAAGGAA
**
587378 AAAGAAAAAAACAA
1 AAA-AAAAAAGGAA
587392 AAAAAAAAAG
1 AAAAAAAAAG
587402 TGAAGATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.34
14 21 0.66
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAGGAA
Found at i:589372 original size:24 final size:24
Alignment explanation
Indices: 589326--589375 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
589316 TTTGGTAAGA
*
589326 TTGATTTTCATTTAACTTGATAAT
1 TTGATTTTCATTTAACTTAATAAT
*
589350 TTGATTTTTATTTATA-TTAATAAT
1 TTGATTTTCATTTA-ACTTAATAAT
589374 TT
1 TT
589376 TGCTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (24 bp):
TTGATTTTCATTTAACTTAATAAT
Found at i:592122 original size:12 final size:12
Alignment explanation
Indices: 592105--592129 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
592095 TATAACTTAA
592105 TAAAAATTAATT
1 TAAAAATTAATT
592117 TAAAAATTAATT
1 TAAAAATTAATT
592129 T
1 T
592130 TTATACCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAATTAATT
Done.