Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 2 of 143
Found at i:475279 original size:14 final size:15
Alignment explanation
Indices: 475262--475296 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
475252 GTTGCAGCTA
475262 AAAAGCAA-AAAAAG
1 AAAAGCAAGAAAAAG
475276 AAAAG-AAGAAAAAG
1 AAAAGCAAGAAAAAG
475290 AAAAGCA
1 AAAAGCA
475297 TATGTCCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 16 0.84
15 1 0.05
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAGCAAGAAAAAG
Found at i:475437 original size:12 final size:12
Alignment explanation
Indices: 475420--475461 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
475410 CATGTTCACT
475420 TATATATATATG
1 TATATATATATG
475432 TATATATATATG
1 TATATATATATG
*
475444 TATAGATATATG
1 TATATATATATG
475456 TATATA
1 TATATA
475462 CAGTGTGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (12 bp):
TATATATATATG
Found at i:478424 original size:24 final size:24
Alignment explanation
Indices: 478383--478436 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
478373 TTGATGAAAG
* *
478383 ATGAACTGTTAAATACATGCAGAA
1 ATGAACTGTTAAACACATACAGAA
* *
478407 ATGAACTGTTCAGCACATACAGAA
1 ATGAACTGTTAAACACATACAGAA
478431 A-GAACT
1 ATGAACT
478437 TACTTTTCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (24 bp):
ATGAACTGTTAAACACATACAGAA
Found at i:478739 original size:41 final size:41
Alignment explanation
Indices: 478682--478804 Score: 246
Period size: 41 Copynumber: 3.0 Consensus size: 41
478672 ACCATTAGTC
478682 CTATAAACAGTATTAAACATCGAAGAAAAAAAGAAAAAGAA
1 CTATAAACAGTATTAAACATCGAAGAAAAAAAGAAAAAGAA
478723 CTATAAACAGTATTAAACATCGAAGAAAAAAAGAAAAAGAA
1 CTATAAACAGTATTAAACATCGAAGAAAAAAAGAAAAAGAA
478764 CTATAAACAGTATTAAACATCGAAGAAAAAAAGAAAAAGAA
1 CTATAAACAGTATTAAACATCGAAGAAAAAAAGAAAAAGAA
478805 GATTAAAAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.63, C:0.10, G:0.12, T:0.15
Consensus pattern (41 bp):
CTATAAACAGTATTAAACATCGAAGAAAAAAAGAAAAAGAA
Found at i:492211 original size:24 final size:22
Alignment explanation
Indices: 492155--492212 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
492145 CATGAATATG
492155 TGTTCACGAACATTAAAGAACA
1 TGTTCACGAACATTAAAGAACA
* * * *
492177 TATTCATGAACATATAATTGATCA
1 TGTTCACGAACAT-TAA-AGAACA
492201 TGTTCACGAACA
1 TGTTCACGAACA
492213 ATGTTAATGA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 11 0.39
23 3 0.11
24 14 0.50
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (22 bp):
TGTTCACGAACATTAAAGAACA
Found at i:495887 original size:30 final size:30
Alignment explanation
Indices: 495851--495910 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
495841 AGTTCTCGTA
495851 TCCGGTATCTTTTGTGTTGCCATTGTTGTG
1 TCCGGTATCTTTTGTGTTGCCATTGTTGTG
495881 TCCGGTATCTTTTGTGTTGCCATTGTTGTG
1 TCCGGTATCTTTTGTGTTGCCATTGTTGTG
495911 CTCCCAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.07, C:0.17, G:0.27, T:0.50
Consensus pattern (30 bp):
TCCGGTATCTTTTGTGTTGCCATTGTTGTG
Found at i:498249 original size:25 final size:24
Alignment explanation
Indices: 498205--498284 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 24
498195 ATTTTATGTT
498205 TATATATT-ATATACATAAATAATTA
1 TATATATTAATATA-A-AAATAATTA
*
498230 TATATATCTAATATAAAAATAATGA
1 TATATAT-TAATATAAAAATAATTA
* *
498255 CAT-TATTTCAATATAAAAATAAATA
1 TATATA-TT-AATATAAAAATAATTA
498280 TATAT
1 TATAT
498285 TTCATGTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
24 3 0.07
25 34 0.76
26 3 0.07
27 5 0.11
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (24 bp):
TATATATTAATATAAAAATAATTA
Found at i:498495 original size:29 final size:30
Alignment explanation
Indices: 498425--498495 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 30
498415 TAAAATATGT
*
498425 TATAAGTTATTGTATTCTTCATGAATTTGAAA
1 TATAA-TTTTTGTATTCTTCATG-ATTTGAAA
* *
498457 TTTAAATTTTGTATT-TTCATG-TTTAGAAA
1 TATAATTTTTGTATTCTTCATGATTT-GAAA
498486 TATAATTTTT
1 TATAATTTTT
498496 TTTAAAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
28 3 0.09
29 12 0.36
30 6 0.18
31 8 0.24
32 4 0.12
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.54
Consensus pattern (30 bp):
TATAATTTTTGTATTCTTCATGATTTGAAA
Found at i:498656 original size:19 final size:19
Alignment explanation
Indices: 498629--498665 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
498619 ATTTGAATTT
498629 TAAAATTTTAAAAATAAAC
1 TAAAATTTTAAAAATAAAC
* *
498648 TAAATTTTTATAAATAAA
1 TAAAATTTTAAAAATAAA
498666 AATATAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATTTTAAAAATAAAC
Found at i:503896 original size:21 final size:24
Alignment explanation
Indices: 503867--503910 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
503857 TTAATTCACC
503867 TTATCTC-AA-CTTTTAA-ATTTA
1 TTATCTCAAACCTTTTAATATTTA
*
503888 TTATTTCAAACCTTTTAATATTT
1 TTATCTCAAACCTTTTAATATTT
503911 TATTTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 2 0.11
23 7 0.37
24 4 0.21
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATCTCAAACCTTTTAATATTTA
Found at i:504932 original size:22 final size:22
Alignment explanation
Indices: 504880--504932 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
504870 ATTTTTACTT
*
504880 TTATATATTTTTAAAATTATTA
1 TTATATTTTTTTAAAATTATTA
* * *
504902 TGATATTTTTTGAAAA-TATTG
1 TTATATTTTTTTAAAATTATTA
504923 TTATATTTTT
1 TTATATTTTT
504933 GTTTGAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (22 bp):
TTATATTTTTTTAAAATTATTA
Found at i:505903 original size:33 final size:30
Alignment explanation
Indices: 505848--505920 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
505838 ATGACTATAT
*
505848 AAAATAT-ATATAAAATTATTAAATATTAA
1 AAAATATAATATAAAATTATTAAAAATTAA
* *
505877 AATAATATAATATAAATATTTTTTAAAAATTTA
1 AA-AATATAATATAAA-A-TTATTAAAAATTAA
505910 AAAA-ATAATAT
1 AAAATATAATAT
505921 CTGTGGACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 2 0.05
30 5 0.14
31 14 0.38
32 3 0.08
33 13 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAATATAATATAAAATTATTAAAAATTAA
Found at i:512206 original size:244 final size:244
Alignment explanation
Indices: 511806--512295 Score: 980
Period size: 244 Copynumber: 2.0 Consensus size: 244
511796 TTTAACTTCT
511806 GATATGTTAATTATCTGGAATGTAATCGAGTTTCGGGTTGTATTCTTTCGATTTCAATATATTAT
1 GATATGTTAATTATCTGGAATGTAATCGAGTTTCGGGTTGTATTCTTTCGATTTCAATATATTAT
511871 TAAACGTGAGAAATCTATAATCTATTAATGTAGCTCTCTGCATATTCAATCTTCCCCTAGTTTCG
66 TAAACGTGAGAAATCTATAATCTATTAATGTAGCTCTCTGCATATTCAATCTTCCCCTAGTTTCG
511936 AAATGTATTGCTGGTTTTACTTGATGAACATTTTCCATGCTGCAGCTATTTATAAATTTAGTTAA
131 AAATGTATTGCTGGTTTTACTTGATGAACATTTTCCATGCTGCAGCTATTTATAAATTTAGTTAA
512001 AATAACTAGGGTATCGGTGTAGACGCACCCCTCACTGACCCTTAAATCG
196 AATAACTAGGGTATCGGTGTAGACGCACCCCTCACTGACCCTTAAATCG
512050 GATATGTTAATTATCTGGAATGTAATCGAGTTTCGGGTTGTATTCTTTCGATTTCAATATATTAT
1 GATATGTTAATTATCTGGAATGTAATCGAGTTTCGGGTTGTATTCTTTCGATTTCAATATATTAT
512115 TAAACGTGAGAAATCTATAATCTATTAATGTAGCTCTCTGCATATTCAATCTTCCCCTAGTTTCG
66 TAAACGTGAGAAATCTATAATCTATTAATGTAGCTCTCTGCATATTCAATCTTCCCCTAGTTTCG
512180 AAATGTATTGCTGGTTTTACTTGATGAACATTTTCCATGCTGCAGCTATTTATAAATTTAGTTAA
131 AAATGTATTGCTGGTTTTACTTGATGAACATTTTCCATGCTGCAGCTATTTATAAATTTAGTTAA
512245 AATAACTAGGGTATCGGTGTAGACGCACCCCTCACTGACCCTTAAATCG
196 AATAACTAGGGTATCGGTGTAGACGCACCCCTCACTGACCCTTAAATCG
512294 GA
1 GA
512296 GGAAAACCGA
Statistics
Matches: 246, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
244 246 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (244 bp):
GATATGTTAATTATCTGGAATGTAATCGAGTTTCGGGTTGTATTCTTTCGATTTCAATATATTAT
TAAACGTGAGAAATCTATAATCTATTAATGTAGCTCTCTGCATATTCAATCTTCCCCTAGTTTCG
AAATGTATTGCTGGTTTTACTTGATGAACATTTTCCATGCTGCAGCTATTTATAAATTTAGTTAA
AATAACTAGGGTATCGGTGTAGACGCACCCCTCACTGACCCTTAAATCG
Found at i:513003 original size:38 final size:38
Alignment explanation
Indices: 512961--513039 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
512951 TGATGTTCAT
* *
512961 TAAATATTATGTTAAATAG-TATTTATAAATTAAAATAA
1 TAAAT-TTATGTTAAATAGCAAATTATAAATTAAAATAA
* *
512999 TAAATTTATTTTAAATAGCAAATTATGAATTAAAATAA
1 TAAATTTATGTTAAATAGCAAATTATAAATTAAAATAA
513037 TAA
1 TAA
513040 TTATATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 12 0.33
38 24 0.67
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (38 bp):
TAAATTTATGTTAAATAGCAAATTATAAATTAAAATAA
Found at i:513006 original size:21 final size:21
Alignment explanation
Indices: 512981--513049 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
512971 GTTAAATAGT
512981 ATTTATAAATTAAAATAATAA
1 ATTTATAAATTAAAATAATAA
* **
513002 ATTTAT---TTTAAATAGCAA
1 ATTTATAAATTAAAATAATAA
*
513020 A-TTATGAATTAAAATAAT-A
1 ATTTATAAATTAAAATAATAA
513039 ATTATATAAAT
1 ATT-TATAAAT
513050 CTCATATGAT
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
17 4 0.11
18 10 0.28
19 2 0.06
20 8 0.22
21 12 0.33
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (21 bp):
ATTTATAAATTAAAATAATAA
Found at i:513255 original size:25 final size:27
Alignment explanation
Indices: 513206--513256 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
513196 AATAATAAAA
*
513206 TTATATTTGTATTAATTATATTGAAAG
1 TTATATTTATATTAATTATATTGAAAG
*
513233 TTATATTTATTTTAATT-TA-TGAAA
1 TTATATTTATATTAATTATATTGAAA
513257 TATATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
26 2 0.09
27 15 0.68
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (27 bp):
TTATATTTATATTAATTATATTGAAAG
Found at i:517461 original size:1 final size:1
Alignment explanation
Indices: 517457--517491 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
517447 TGAATTTAGA
* *
517457 TTTTTTTCTGTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
517492 GTAACCCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.03, T:0.94
Consensus pattern (1 bp):
T
Found at i:521267 original size:1 final size:1
Alignment explanation
Indices: 521261--521287 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
521251 GAGAGAGAGA
521261 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
521288 CCATGCCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:530248 original size:30 final size:29
Alignment explanation
Indices: 530202--530259 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
530192 TTTATTTTAT
530202 TTTAAAATAATTTTTATTAGGATTTAATA
1 TTTAAAATAATTTTTATTAGGATTTAATA
* *
530231 TTTAAAGAT-ATTATTTATTTGTATTTAAT
1 TTTAAA-ATAATT-TTTATTAGGATTTAAT
530260 TTATGTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (29 bp):
TTTAAAATAATTTTTATTAGGATTTAATA
Found at i:531085 original size:22 final size:22
Alignment explanation
Indices: 531046--531106 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
531036 TTCGACTTCC
*
531046 CTATTTTCTATTT-CTTTTAACT
1 CTATTTTCT-TTTATTTTTAACT
*
531068 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAACT
*
531090 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
531107 CCTCAGATCG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.15, C:0.13, G:0.02, T:0.70
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAACT
Found at i:538427 original size:19 final size:21
Alignment explanation
Indices: 538405--538443 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
538395 TGAGTTTTAG
538405 AGAGCTAA-TTGAT-TTTGAA
1 AGAGCTAATTTGATATTTGAA
*
538424 AGAGTTAATTTGATATTTGA
1 AGAGCTAATTTGATATTTGA
538444 GTTTGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.41
Consensus pattern (21 bp):
AGAGCTAATTTGATATTTGAA
Found at i:538683 original size:17 final size:16
Alignment explanation
Indices: 538657--538688 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
538647 ATCTTTACTA
538657 ATTTAAAATTTAAAAT
1 ATTTAAAATTTAAAAT
538673 ATTTAAAAATTTAAAA
1 ATTT-AAAATTTAAAA
538689 GGACCTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTTAAAATTTAAAAT
Found at i:538686 original size:8 final size:8
Alignment explanation
Indices: 538656--538688 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
538646 TATCTTTACT
538656 AATTT-AA
1 AATTTAAA
538663 AATTTAAA
1 AATTTAAA
538671 ATATTTAAA
1 A-ATTTAAA
538680 AATTTAAA
1 AATTTAAA
538688 A
1 A
538689 GGACCTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 5 0.21
8 11 0.46
9 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AATTTAAA
Found at i:545751 original size:15 final size:15
Alignment explanation
Indices: 545731--545762 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
545721 ATCTACTGTG
545731 ACAAGTTAACTGGCC
1 ACAAGTTAACTGGCC
*
545746 ACAAGTTAACTTGCC
1 ACAAGTTAACTGGCC
545761 AC
1 AC
545763 GTCACCTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (15 bp):
ACAAGTTAACTGGCC
Found at i:547317 original size:6 final size:6
Alignment explanation
Indices: 547306--547334 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
547296 TTGCCATACA
547306 ACCCTC ACCCTC ACCCTC ACCCTC ACCCT
1 ACCCTC ACCCTC ACCCTC ACCCTC ACCCT
547335 AACTTATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.66, G:0.00, T:0.17
Consensus pattern (6 bp):
ACCCTC
Found at i:550699 original size:21 final size:20
Alignment explanation
Indices: 550675--550721 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
550665 AATTATAATT
550675 TTATATATTTTAATAATTTAA
1 TTATATATTTT-ATAATTTAA
* *
550696 TTATTATATTTTATATTTTAT
1 TTA-TATATTTTATAATTTAA
550717 TTATA
1 TTATA
550722 CATATCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 13 0.57
22 8 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATATATTTTATAATTTAA
Found at i:550699 original size:29 final size:29
Alignment explanation
Indices: 550657--550715 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
550647 TTTGACCTCA
*
550657 AATAGTTTAATTATAAT-TTTATATATTTT
1 AATAATTTAATTATAATATTT-TATATTTT
*
550686 AATAATTTAATTATTATATTTTATATTTT
1 AATAATTTAATTATAATATTTTATATTTT
550715 A
1 A
550716 TTTATACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
AATAATTTAATTATAATATTTTATATTTT
Found at i:550779 original size:26 final size:27
Alignment explanation
Indices: 550745--550795 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
550735 GTATAAATTA
* *
550745 AAAAAATTT-AATTATTTATTTTATGT
1 AAAAAATTTCAATCATTAATTTTATGT
550771 AAAAAATTTCAATCATTAATTTTAT
1 AAAAAATTTCAATCATTAATTTTAT
550796 ATTAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAAATTTCAATCATTAATTTTATGT
Found at i:552164 original size:15 final size:16
Alignment explanation
Indices: 552140--552179 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
552130 CAACCTTTAA
*
552140 CCATTAAAGTCTAAAC
1 CCATTAAAGTCCAAAC
552156 CCATT-AAGTCCAAAC
1 CCATTAAAGTCCAAAC
552171 CCATCTAAA
1 CCAT-TAAA
552180 AGCCCAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 13 0.62
16 6 0.29
17 2 0.10
ACGTcount: A:0.42, C:0.30, G:0.05, T:0.23
Consensus pattern (16 bp):
CCATTAAAGTCCAAAC
Found at i:556910 original size:82 final size:88
Alignment explanation
Indices: 556741--556918 Score: 233
Period size: 82 Copynumber: 2.1 Consensus size: 88
556731 TCCAAAAGAA
* **
556741 AAAATTCCATCCCATCCCACCCCACCTCAACTCACTCCACATCCATTTTTCAAAAAGCAAAAATC
1 AAAA-TCCATCCCATCCCACCCCACCTC-ACTCACTCCACATCCATCTTTCAAAAAAAAAAAATC
*
556806 CACTTCATTCGAAACGGATCGATTC
64 CACTTCATTCGAAACAGATCGATTC
*
556831 AAAATCCATCCCATCCCACCCCA-C-C-C-CACTCCACATCCA-CTTT-AAAAAAAAAAAATCCT
1 AAAATCCATCCCATCCCACCCCACCTCACTCACTCCACATCCATCTTTCAAAAAAAAAAAATCCA
*
556890 CTTCATTTGAAACAGATCGATTC
66 CTTCATTCGAAACAGATCGATTC
*
556913 GAAATC
1 AAAATC
556919 TATTGAGAGT
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
82 39 0.48
83 3 0.04
84 13 0.16
85 1 0.01
87 1 0.01
88 1 0.01
89 19 0.23
90 4 0.05
ACGTcount: A:0.37, C:0.36, G:0.05, T:0.22
Consensus pattern (88 bp):
AAAATCCATCCCATCCCACCCCACCTCACTCACTCCACATCCATCTTTCAAAAAAAAAAAATCCA
CTTCATTCGAAACAGATCGATTC
Found at i:560243 original size:17 final size:17
Alignment explanation
Indices: 560221--560259 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
560211 AGGTGGAGAA
* *
560221 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
*
560238 CTTGTTTGTAGAGAATT
1 CTTGTTCGTAGAGAATT
560255 CTTGT
1 CTTGT
560260 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:560306 original size:41 final size:41
Alignment explanation
Indices: 560249--560344 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
560239 TTGTTTGTAG
*
560249 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTAAGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTAAGTGACT
**
560290 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTAAGTGACT
*
560331 AGAATTATTGTTAA
1 AGAATTCTTGTTAA
560345 AATAAAATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.36
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTAAGTGACT
Found at i:563911 original size:2 final size:2
Alignment explanation
Indices: 563904--563937 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
563894 CAAGATTGTT
563904 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
563938 GATACATAGA
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):
TA
Found at i:564705 original size:31 final size:31
Alignment explanation
Indices: 564652--564719 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
564642 CGCTACCCCA
*
564652 AAAAATAAAAAATTTCCTATTTTAGACCCTCT
1 AAAAATAAAAAAATTCCTATTTTAGACCCT-T
*
564684 AAAAATAAAAAAAATT-C-ATTTTAGTCCCTT
1 AAAAAT-AAAAAAATTCCTATTTTAGACCCTT
564714 AAAAAT
1 AAAAAT
564720 TATGAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 7 0.21
31 11 0.33
32 7 0.21
33 8 0.24
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAAATAAAAAAATTCCTATTTTAGACCCTT
Found at i:589136 original size:58 final size:59
Alignment explanation
Indices: 589074--589239 Score: 210
Period size: 58 Copynumber: 2.8 Consensus size: 59
589064 ATAATATTTG
* *
589074 GTACCTGAACTTGACACTTTTTTCTAATTTGGTAATTAAACTTTTTT-GAGCCAATTCA
1 GTACCTAAACTTGACACTTTTTTCTAATTTGGTACTTAAACTTTTTTGGAGCCAATTCA
* * *
589132 GTACCTAAACTTGACAC-TTTTTCTTAATTTGATACCTAAACTTTTTTTGGATCCAATTCA
1 GTACCTAAACTTGACACTTTTTTC-TAATTTGGTACTTAAAC-TTTTTTGGAGCCAATTCA
** * *
589192 GTACCTAAACTTGGTATTTTTTTCCTAATTTGGTACTTAAGCTTTTTT
1 GTACCTAAACTTGACACTTTTTT-CTAATTTGGTACTTAAACTTTTTT
589240 TTAGATTCAA
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
57 6 0.07
58 30 0.33
59 6 0.07
60 30 0.33
61 19 0.21
62 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (59 bp):
GTACCTAAACTTGACACTTTTTTCTAATTTGGTACTTAAACTTTTTTGGAGCCAATTCA
Found at i:589530 original size:32 final size:32
Alignment explanation
Indices: 589463--589554 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 32
589453 TGGTCCCTAA
* * *
589463 AAAGTTTAAGTACCAACTTA--AAAAAAGTAT
1 AAAGTTTAGGTACCAAATTAGTAAAAAAATAT
*
589493 AAAGTTTAGGTACCAAATTAGTAAAAAAATGT
1 AAAGTTTAGGTACCAAATTAGTAAAAAAATAT
* *
589525 CAAGTTT-GAGTACCAAATTGGATAAAAAAA
1 AAAGTTTAG-GTACCAAATTAG-TAAAAAAA
589555 ATTAAGTACC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
30 18 0.35
31 1 0.02
32 25 0.48
33 8 0.15
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (32 bp):
AAAGTTTAGGTACCAAATTAGTAAAAAAATAT
Found at i:593578 original size:141 final size:142
Alignment explanation
Indices: 593376--594237 Score: 1009
Period size: 140 Copynumber: 6.0 Consensus size: 142
593366 CTAAAGTCTC
593376 GAAGAACGTGAA-TTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCAT
1 GAAGAACGT-AATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCAT
* * *
593440 GAATTCAAATTTCAACGTCAATTGGAAGAACTTTG-ATGAAAAATGGGGTAAAGAACTCAAATAC
65 GAATTCAAATTTCAACGTCAATTTGAAGAACTTTGAATGAAAAATGAGGTAAAGAACTCAATTAC
593504 ACACAGATCAAAA
130 ACACAGATCAAAA
*
593517 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATT-GATATCGGACTCAT
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGA-ATCGGACTCAT
* *
593581 GAATTCAAATTTCCACG-CAATTTTGAAGAACTTGGAATG-AAAATGAGGTAAAGAACTCAATTA
65 GAATTCAAATTTCAACGTCAA-TTTGAAGAACTTTGAATGAAAAATGAGGTAAAGAACTCAATTA
593644 CACACAGATC-AAA
129 CACACAGATCAAAA
* * * *
593657 GAAGAACGCAATGTCGAATTCAAATCTAAAATTACAAAAGCGTTCGCATTGGAATCGGACTCATG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* * * * * *
593722 AATTCAAATGTCAACGTAAATTTGAAGAACTTTG-ACGAAAACTGAGGTAAAGCACTCGATTACA
66 AATTCAAATTTCAACGTCAATTTGAAGAACTTTGAATGAAAAATGAGGTAAAGAACTCAATTACA
593786 CACAGATC--AA
131 CACAGATCAAAA
* **
593796 -AAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCAAACTCATG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* * *
593860 AATTCAAATTTCGAC-TTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAACTCAATTTA
66 AATTCAAATTTCAACGTCAA-TTTGAAGAACTTTGAATGAAAAATGAGGTAAAGAACTCAA-TTA
593924 CACACAGATCAAAA
129 CACACAGATCAAAA
* * * * * *
593938 CAAGAGCGTGACTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCAGA-TACAT
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACT-CAT
* * * *
594002 GAATTCAAATTTCGACGTGATTTTGAAGAACTTGGAATGAAAATGGAATGAAAAATGAGCTAAAG
65 GAATTCAAATTTCAACGTCAATTTGAAGAAC-T----T-----T-GAATGAAAAATGAGGTAAAG
594067 AACTCAAATT--ACACAGATCAAAA
119 AACTC-AATTACACACAGATCAAAA
* * * * * * * *
594090 CAATAACGTGACTTTGAATTCAAATCCAAAACTACAAATGCATTCGCATTGGAATCGAACTCATG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* * * * * *
594155 TATTCAAATTTCCACGTGATTTTGAAGAACTAT-AATGAAAGAA-GAGGTCAAGAACTCAATTAC
66 AATTCAAATTTCAACGTCAATTTGAAGAACTTTGAATGAAA-AATGAGGTAAAGAACTCAATTAC
594218 ACACAGATCAGAAA
130 ACACAGATCA-AAA
*
594232 GGAGAA
1 GAAGAA
594238 AACAAGCAGT
Statistics
Matches: 631, Mismatches: 58, Indels: 63
0.84 0.08 0.08
Matches are distributed among these distances:
137 3 0.00
138 83 0.13
139 29 0.05
140 157 0.25
141 133 0.21
142 13 0.02
143 83 0.13
144 3 0.00
148 1 0.00
151 1 0.00
152 96 0.15
153 1 0.00
154 26 0.04
155 2 0.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.25
Consensus pattern (142 bp):
GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
AATTCAAATTTCAACGTCAATTTGAAGAACTTTGAATGAAAAATGAGGTAAAGAACTCAATTACA
CACAGATCAAAA
Found at i:593959 original size:281 final size:282
Alignment explanation
Indices: 593377--594227 Score: 1094
Period size: 281 Copynumber: 3.0 Consensus size: 282
593367 TAAAGTCTCG
593377 AAGAACGTGAATTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATGA
1 AAGAACGTGAATTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATGA
* * * *
593442 ATTCAAATTTCAACGTCAATTGGAAGAACTTTGATGAAAAATGGGGTAAAGAACTCAAATACACA
66 ATTCAAATTTCAACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACACA
* * *
593507 CAGATCAAAAGAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGATAT
131 CAGATC-AAACAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAAT
* *
593572 CGGACTCATGAATTCAAATTTCCACGCAATTTTGAAGAACTTGGAATG-AAAATGAGGTAAAGAA
195 CGAACTCATGAATTCAAATTTCCACGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAA
*
593636 CTCAATTACACACAGATC-AAAG
260 CTCAATTACACACAGATCAAAAC
* * *
593658 AAGAACG-CAATGTCGAATTCAAATCTAAAATTACAAAAGCGTTCGCATTGGAATCGGACTCATG
1 AAGAACGTGAAT-TTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* * * * *
593722 AATTCAAATGTCAACGTAAATTTGAAGAACTTTGACGAAAACTGAGGTAAAGCACTCGATTACAC
65 AATTCAAATTTCAACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACAC
593787 ACAGATC-AA-AAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAAT
130 ACAGATCAAACAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAAT
* * *
593850 CAAACTCATGAATTCAAATTTCGACTTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAA
195 CGAACTCATGAATTCAAATTTCCACGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAA
593915 CTCAATTTACACACAGATCAAAAC
260 CTCAA-TTACACACAGATCAAAAC
* * * *
593939 AAGAGCGTGACTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCAGA-TACATG
1 AAGAACGTGAATTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACT-CATG
* * * *
594003 AATTCAAATTTCGACGTGATTTTGAAGAACTTGGAATGAAAATGGAATGAAAAATGAGCTAAAGA
65 AATTCAAATTTCAACGTAAATTTGAAGAAC-T----T-----T-G-ATGAAAAATGAGGTAAAGA
* * * * * *
594068 ACTCAAATT--ACACAGATCAAAACAATAACGTGACTTTGAATTCAAATCCAAAACTACAAATGC
118 ACTC-AATTACACACAGATC-AAACAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGC
* * *
594131 ATTCGCATTGGAATCGAACTCATGTATTCAAATTTCCACGTGATTTTGAAGAACTAT--AATGAA
181 ATTCGCATTGAAATCGAACTCATGAATTCAAATTTCCACGTAATTTTGAAGAACT-TGGAATGAA
*
594194 AGAA-GAGGTCAAGAACTCAATTACACACAGATCA
245 A-AATGAGGTAAAGAACTCAATTACACACAGATCA
594228 GAAAGGAGAA
Statistics
Matches: 497, Mismatches: 49, Indels: 36
0.85 0.08 0.06
Matches are distributed among these distances:
278 95 0.19
279 23 0.05
280 17 0.03
281 201 0.40
282 3 0.01
286 1 0.00
291 1 0.00
292 10 0.02
293 33 0.07
294 27 0.05
295 85 0.17
296 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (282 bp):
AAGAACGTGAATTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATGA
ATTCAAATTTCAACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACACA
CAGATCAAACAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATC
GAACTCATGAATTCAAATTTCCACGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAAC
TCAATTACACACAGATCAAAAC
Found at i:594172 original size:152 final size:153
Alignment explanation
Indices: 593891--594185 Score: 452
Period size: 152 Copynumber: 1.9 Consensus size: 153
593881 TTGAAGAACT
* * *
593891 TGGAATGAAAAATGAGGTAAAGAACTCAATTTACACACAGATCAAAACAAGAGCGTGACTTTGAA
1 TGGAATGAAAAATGAGCTAAAGAACTCAAATTA-ACACAGATCAAAACAAGAACGTGACTTTGAA
* * *
593956 TTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCAGATACATGAATTCAAATTTCGACGTG
65 TTCAAATCCAAAACTACAAAAGCATTCGCATTGAAATCAGATACATGAATTCAAATTTCCACGTG
594021 ATTTTGAAGAACTTGGAATGAAAA
130 ATTTTGAAGAACTTGGAATGAAAA
*
594045 TGGAATGAAAAATGAGCTAAAGAACTCAAATT-ACACAGATCAAAACAATAACGTGACTTTGAAT
1 TGGAATGAAAAATGAGCTAAAGAACTCAAATTAACACAGATCAAAACAAGAACGTGACTTTGAAT
* * *
594109 TCAAATCCAAAACTACAAATGCATTCGCATTGGAATC-GA-ACTCATGTATTCAAATTTCCACGT
66 TCAAATCCAAAACTACAAAAGCATTCGCATTGAAATCAGATA--CATGAATTCAAATTTCCACGT
594172 GATTTTGAAGAACT
129 GATTTTGAAGAACT
594186 ATAATGAAAG
Statistics
Matches: 129, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
150 1 0.01
151 2 0.02
152 96 0.74
154 30 0.23
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (153 bp):
TGGAATGAAAAATGAGCTAAAGAACTCAAATTAACACAGATCAAAACAAGAACGTGACTTTGAAT
TCAAATCCAAAACTACAAAAGCATTCGCATTGAAATCAGATACATGAATTCAAATTTCCACGTGA
TTTTGAAGAACTTGGAATGAAAA
Found at i:594851 original size:23 final size:22
Alignment explanation
Indices: 594825--594868 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
594815 CAAAAGAAAC
*
594825 AGATATAATCAAAAATTATAATG
1 AGAT-TAATCAAAAATAATAATG
**
594848 AGATTGTTCAAAAATAATAAT
1 AGATTAATCAAAAATAATAAT
594869 ATCTGCGTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.32
Consensus pattern (22 bp):
AGATTAATCAAAAATAATAATG
Found at i:595351 original size:33 final size:32
Alignment explanation
Indices: 595274--595353 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 32
595264 TTAGTTCAAT
* *
595274 TTGGTACTCAAACTTGACACCTTTTTCCTAAT
1 TTGGTACTTAAACTTGACACCTTTTTCCTAAG
* * * **
595306 TTGATACCTAAACTTGACACTTTTTTTTTAAAG
1 TTGGTACTTAAACTTGACACCTTTTTCCT-AAG
595339 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
595354 TTTAGGGTCC
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
32 23 0.61
33 15 0.39
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.44
Consensus pattern (32 bp):
TTGGTACTTAAACTTGACACCTTTTTCCTAAG
Found at i:595352 original size:65 final size:59
Alignment explanation
Indices: 595215--595353 Score: 145
Period size: 61 Copynumber: 2.3 Consensus size: 59
595205 AATATAATAT
* * * * *
595215 TTGGTACTTGAACTTGATATTTTTCCTAATTTGGTACCTAAACTTTTTTTTAGTTCAAT
1 TTGGTACTTAAACTTGACATTTTTCCTAATTTGATACCTAAACTTTTTTTTAGTTAAAG
* *
595274 TTGGTACTCAAACTTGACACCTTTTTCCTAATTTGATACCTAAACTTGACACTTTTTT-TTTAAA
1 TTGGTACTTAAACTTGACA--TTTTTCCTAATTTGATACCTAAACTT-----TTTTTTAGTTAAA
595338 G
59 G
595339 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
595354 TTTAGGGTCC
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
59 16 0.25
61 25 0.38
65 18 0.28
66 6 0.09
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.47
Consensus pattern (59 bp):
TTGGTACTTAAACTTGACATTTTTCCTAATTTGATACCTAAACTTTTTTTTAGTTAAAG
Found at i:595691 original size:60 final size:62
Alignment explanation
Indices: 595558--595691 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 62
595548 TACTACATTT
* * **
595558 AGGTACCAAATTGAATCTAAAACAAAGCTTAGGTGCCAAATTAGGGGAAAAATGCCAAGTTA
1 AGGTACCAAATTGAATCCAAAACAAAGCTTAGGTACCAAATTAGGAAAAAAATGCCAAGTTA
* ** * * *
595620 ATGTACCAAATTGGGTCCAAAA-AAAGTTTAGGTACCAAATTA-GAAAAAAATGTCAAGTTC
1 AGGTACCAAATTGAATCCAAAACAAAGCTTAGGTACCAAATTAGGAAAAAAATGCCAAGTTA
*
595680 AGGTACAAAATT
1 AGGTACCAAATT
595692 TTATATTAAG
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 24 0.40
61 18 0.30
62 18 0.30
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (62 bp):
AGGTACCAAATTGAATCCAAAACAAAGCTTAGGTACCAAATTAGGAAAAAAATGCCAAGTTA
Found at i:596390 original size:20 final size:20
Alignment explanation
Indices: 596365--596438 Score: 53
Period size: 20 Copynumber: 3.7 Consensus size: 20
596355 TAATAAATAA
596365 TATAAAAAATTAAAAACAAT
1 TATAAAAAATTAAAAACAAT
* * *
596385 T-T-TAAATTTCAGAAAATAAT
1 TATAAAAAATT-A-AAAACAAT
* *
596405 TATAAAAAATTCATAACAAT
1 TATAAAAAATTAAAAACAAT
* *
596425 TCTAAAAAAGTAAA
1 TATAAAAAATTAAA
596439 GTAAACGTGA
Statistics
Matches: 38, Mismatches: 12, Indels: 8
0.66 0.21 0.14
Matches are distributed among these distances:
18 5 0.13
19 2 0.05
20 25 0.66
21 1 0.03
22 5 0.13
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.30
Consensus pattern (20 bp):
TATAAAAAATTAAAAACAAT
Found at i:597293 original size:13 final size:14
Alignment explanation
Indices: 597277--597306 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
597267 ATCTGTAATT
597277 TTTTTCA-ATAAAA
1 TTTTTCACATAAAA
597290 TTTTTCACATAAAA
1 TTTTTCACATAAAA
597304 TTT
1 TTT
597307 ATATATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTTCACATAAAA
Found at i:597752 original size:17 final size:17
Alignment explanation
Indices: 597708--597752 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
597698 ATTCAATCGA
597708 AAACTAATTAAAAAATC
1 AAACTAATTAAAAAATC
* * *
597725 AATCCAATTAAAAAATT
1 AAACTAATTAAAAAATC
*
597742 AAACTAGTTAA
1 AAACTAATTAA
597753 CTCATGAATC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.27
Consensus pattern (17 bp):
AAACTAATTAAAAAATC
Found at i:602423 original size:15 final size:14
Alignment explanation
Indices: 602403--602446 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 14
602393 TGTGACATAA
602403 TTTAAAATAAAAAAC
1 TTTAAAA-AAAAAAC
*
602418 TTTAAAAAAAAAATA
1 TTTAAAAAAAAAA-C
602433 TTGTAAAAAAAAAA
1 TT-TAAAAAAAAAA
602447 AAATTTGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 6 0.23
15 9 0.35
16 11 0.42
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (14 bp):
TTTAAAAAAAAAAC
Found at i:602430 original size:16 final size:16
Alignment explanation
Indices: 602401--602448 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
602391 TATGTGACAT
*
602401 AATT-TAAAATAAAAA
1 AATTGTAAAAAAAAAA
*
602416 ACTT-TAAAAAAAAAA
1 AATTGTAAAAAAAAAA
*
602431 TATTGTAAAAAAAAAA
1 AATTGTAAAAAAAAAA
602447 AA
1 AA
602449 ATTTGTGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (16 bp):
AATTGTAAAAAAAAAA
Found at i:603608 original size:19 final size:20
Alignment explanation
Indices: 603584--603629 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
603574 CGTGATACGT
*
603584 TTAAATTA-AAAAAATTAAA
1 TTAAATTACAAAAAATCAAA
603603 TTAAATTACAAAAAATCAAA
1 TTAAATTACAAAAAATCAAA
*
603623 TTTAATT
1 TTAAATT
603630 TAATTGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
TTAAATTACAAAAAATCAAA
Found at i:605663 original size:16 final size:16
Alignment explanation
Indices: 605642--605673 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
605632 TTTTCTTCCC
605642 CTACACTTGCTACTTA
1 CTACACTTGCTACTTA
605658 CTACACTTGCTACTTA
1 CTACACTTGCTACTTA
605674 AAACACCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.06, T:0.38
Consensus pattern (16 bp):
CTACACTTGCTACTTA
Found at i:605679 original size:16 final size:16
Alignment explanation
Indices: 605644--605679 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
605634 TTCTTCCCCT
**
605644 ACACTTGCTACTTACT
1 ACACTTGCTACTTAAA
605660 ACACTTGCTACTTAAA
1 ACACTTGCTACTTAAA
605676 ACAC
1 ACAC
605680 CAAAACTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.31
Consensus pattern (16 bp):
ACACTTGCTACTTAAA
Found at i:613049 original size:17 final size:17
Alignment explanation
Indices: 613023--613061 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
613013 ATATTTCAAT
613023 TATATAATAAATAA-TAA
1 TATATAAT-AATAATTAA
*
613040 TATATGATAATAATTAA
1 TATATAATAATAATTAA
613057 TATAT
1 TATAT
613062 TATGTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TATATAATAATAATTAA
Found at i:613065 original size:20 final size:19
Alignment explanation
Indices: 613020--613065 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
613010 AGCATATTTC
613020 AATTAT-ATAATAAATAAT
1 AATTATGATAATAAATAAT
*
613038 AATATATGATAATAATTAAT
1 AAT-TATGATAATAAATAAT
613058 ATATTATG
1 A-ATTATG
613066 TATTATTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 3 0.12
19 3 0.12
20 16 0.67
21 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
AATTATGATAATAAATAAT
Found at i:615697 original size:24 final size:25
Alignment explanation
Indices: 615663--615712 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
615653 AGTTTCATAT
615663 ATATAATTACACTAAACCAAAATTC
1 ATATAATTACACTAAACCAAAATTC
* * *
615688 ATAT-ATTACATTGAATCAAAATTC
1 ATATAATTACACTAAACCAAAATTC
615712 A
1 A
615713 ATCAAAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.32
Consensus pattern (25 bp):
ATATAATTACACTAAACCAAAATTC
Found at i:627574 original size:18 final size:20
Alignment explanation
Indices: 627536--627576 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
627526 TAAACATGGT
627536 TTAAATATGAGAACACCTAA
1 TTAAATATGAGAACACCTAA
*
627556 TTAAATAT-AG-ACACTTAA
1 TTAAATATGAGAACACCTAA
627574 TTA
1 TTA
627577 TCAGTCATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 2 0.10
20 8 0.40
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (20 bp):
TTAAATATGAGAACACCTAA
Found at i:628894 original size:18 final size:20
Alignment explanation
Indices: 628871--628913 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
628861 TAAAATTAAT
*
628871 AAAATAATATTTT-TT-TTA
1 AAAATAAAATTTTATTATTA
628889 AAAATAAAATTTTATTATTA
1 AAAATAAAATTTTATTATTA
628909 AAAAT
1 AAAAT
628914 TATGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.55
19 2 0.09
20 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATAAAATTTTATTATTA
Found at i:632817 original size:138 final size:138
Alignment explanation
Indices: 632569--632845 Score: 545
Period size: 138 Copynumber: 2.0 Consensus size: 138
632559 CATGACATTA
632569 ATAAATTGTCAATATGGGTTGATTCAGTTGATTGAGTATTCATTAATATTTTCAGCAGACTCATT
1 ATAAATTGTCAATATGGGTTGATTCAGTTGATTGAGTATTCATTAATATTTTCAGCAGACTCATT
*
632634 CAATATGTGATTTGTAAGTATCAATTTCAATCCTATATGAAATCAAATGAATACCCTAACCCTGA
66 CAATATGTGATTTGTAAGTATCAATTTCAACCCTATATGAAATCAAATGAATACCCTAACCCTGA
632699 ACTAGAAT
131 ACTAGAAT
632707 ATAAATTGTCAATATGGGTTGATTCAGTTGATTGAGTATTCATTAATATTTTCAGCAGACTCATT
1 ATAAATTGTCAATATGGGTTGATTCAGTTGATTGAGTATTCATTAATATTTTCAGCAGACTCATT
632772 CAATATGTGATTTGTAAGTATCAATTTCAACCCTATATGAAATCAAATGAATACCCTAACCCTGA
66 CAATATGTGATTTGTAAGTATCAATTTCAACCCTATATGAAATCAAATGAATACCCTAACCCTGA
632837 ACTAGAAT
131 ACTAGAAT
632845 A
1 A
632846 ATCCAACTAA
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 138 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (138 bp):
ATAAATTGTCAATATGGGTTGATTCAGTTGATTGAGTATTCATTAATATTTTCAGCAGACTCATT
CAATATGTGATTTGTAAGTATCAATTTCAACCCTATATGAAATCAAATGAATACCCTAACCCTGA
ACTAGAAT
Found at i:634380 original size:17 final size:15
Alignment explanation
Indices: 634331--634381 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 15
634321 TAATTGGGTG
634331 AAAATAATTTAGTTTT
1 AAAATAATTTA-TTTT
634347 AAAACT-ATTTATGTTT
1 AAAA-TAATTTAT-TTT
634363 AAAATTAATTTGATTTT
1 AAAA-TAATTT-ATTTT
634380 AA
1 AA
634382 TTAGAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 1 0.03
16 17 0.57
17 10 0.33
18 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (15 bp):
AAAATAATTTATTTT
Found at i:641723 original size:17 final size:17
Alignment explanation
Indices: 641701--641745 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
641691 TCTAGGCATT
641701 TTGTCACCAATATAGCA
1 TTGTCACCAATATAGCA
641718 TTGTCACCAATATAGCA
1 TTGTCACCAATATAGCA
641735 TTGTCACCAAT
1 TTGTCACCAAT
641746 GACGGTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.31
Consensus pattern (17 bp):
TTGTCACCAATATAGCA
Found at i:652450 original size:32 final size:31
Alignment explanation
Indices: 652390--652455 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
652380 GAGAAATTTG
* * *
652390 ACTCTTTTTTAAATGTTGATAGTTAAATTCA
1 ACTCTTTTGTAAATGTTGAGAGTCAAATTCA
* *
652421 ACTCTTTTGTAAATGGTTGAGGGTCAAATTTA
1 ACTCTTTTGTAAAT-GTTGAGAGTCAAATTCA
652453 ACT
1 ACT
652456 AGAGAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (31 bp):
ACTCTTTTGTAAATGTTGAGAGTCAAATTCA
Found at i:653892 original size:51 final size:51
Alignment explanation
Indices: 653831--653962 Score: 160
Period size: 51 Copynumber: 2.6 Consensus size: 51
653821 ATGTTGACAA
* * *
653831 AATATATAAATTTTGTGAGTTAATTTTGTTAAGTCAAGATC-AAATTGATAG
1 AATATGTAAATTTTGTGAGTTAAATTTGTTAAATCAAGA-CAAAATTGATAG
* * *
653882 AATATGTAAATATTGT-AGGTTAAAGTTGTTAAATCAAGACAAAATTGGTAG
1 AATATGTAAATTTTGTGA-GTTAAATTTGTTAAATCAAGACAAAATTGATAG
* *
653933 AATATGTAAACTTTGAGAGTTAAATTTGTT
1 AATATGTAAATTTTGTGAGTTAAATTTGTT
653963 TTATACCAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
50 2 0.03
51 65 0.96
52 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.39
Consensus pattern (51 bp):
AATATGTAAATTTTGTGAGTTAAATTTGTTAAATCAAGACAAAATTGATAG
Found at i:659562 original size:30 final size:30
Alignment explanation
Indices: 659458--659891 Score: 676
Period size: 30 Copynumber: 14.4 Consensus size: 30
659448 TTTGAGGGTG
*
659458 AAATGGTAATTTTTG-AAAGTTTTGGGGT-A
1 AAAT-GTAATTTTGGAAAAGTTTTGGGGTCA
* *
659487 GAAATGCAATTTTTAGAAAAGTTTTGGGGTCA
1 -AAATGTAA-TTTTGGAAAAGTTTTGGGGTCA
* * * *
659519 AAACGTAATTTTGGAAAGGTTTTAGGGTTA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
* *
659549 AAATGTAACTTTGGAAAGGTTTTGGGGTCA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
*
659579 AAATATAATTTTGGAAAAGTTTTGGGGTCA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
659609 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
659639 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
659669 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
*
659699 AAATGTAATTTTGGAAAAGTTTTAGGGTCA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
*
659729 AAATGTAATTTTGGAAAAGCTTTGGGGTCA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
659759 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
*
659789 AAATATAA-TTTGTGAAAAGTTTTGGGGTCAA
1 AAATGTAATTTTG-GAAAAGTTTTGGGGTC-A
659820 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
*
659850 AAATGTAATTTTGGAAAAGTTTTAGGGTCA
1 AAATGTAATTTTGGAAAAGTTTTGGGGTCA
659880 AAATGTAATTTT
1 AAATGTAATTTT
659892 TGGATGATTT
Statistics
Matches: 375, Mismatches: 23, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
29 7 0.02
30 320 0.85
31 43 0.11
32 5 0.01
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (30 bp):
AAATGTAATTTTGGAAAAGTTTTGGGGTCA
Found at i:661869 original size:6 final size:6
Alignment explanation
Indices: 661860--661959 Score: 91
Period size: 6 Copynumber: 16.8 Consensus size: 6
661850 TTTTTTAATG
* ** * *
661860 TTAAAT TTAATAT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA- GTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
661908 TTAAAT AATTAAAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAA- -TAAAT
1 TTAAAT --TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
661955 TTAAA
1 TTAAA
661960 ATCAATTTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
4 4 0.05
5 7 0.09
6 55 0.71
7 5 0.06
8 6 0.08
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:661906 original size:17 final size:16
Alignment explanation
Indices: 661886--661964 Score: 90
Period size: 17 Copynumber: 4.9 Consensus size: 16
661876 AATTTTTATT
661886 TAAATTTAAATTCAAA
1 TAAATTTAAATTCAAA
*
661902 GTAAATTTAAA-T-AAT
1 -TAAATTTAAATTCAAA
*
661917 TAAATTTAAATTTAAAA
1 TAAATTTAAA-TTCAAA
*
661934 TAAATTTAAATTTAAA
1 TAAATTTAAATTCAAA
*
661950 TAAATTTAAAATCAA
1 TAAATTTAAATTCAA
661965 TTTAACTCTA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
14 10 0.19
15 2 0.04
16 20 0.37
17 22 0.41
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (16 bp):
TAAATTTAAATTCAAA
Found at i:661920 original size:31 final size:32
Alignment explanation
Indices: 661885--661964 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
661875 TAATTTTTAT
*
661885 TTAAATTTAAATTCAAAGTAAATTTAAA-TAA
1 TTAAATTTAAATTCAAAATAAATTTAAATTAA
*
661916 TTAAATTTAAATTTAAAATAAATTTAAATTTAA
1 TTAAATTTAAATTCAAAATAAATTTAAA-TTAA
* *
661949 ATAAATTTAAAATCAA
1 TTAAATTTAAATTCAA
661965 TTTAACTCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 26 0.62
33 16 0.38
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (32 bp):
TTAAATTTAAATTCAAAATAAATTTAAATTAA
Found at i:661976 original size:27 final size:28
Alignment explanation
Indices: 661886--661982 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 28
661876 AATTTTTATT
* * *
661886 TAAATTTAAATTCAAAGTAAATTTAAATAAT
1 TAAA-TTAAATTTAAAATAAATTTAAAT--C
*
661917 TAAATTTAAATTTAAAATAAATTTAAATT
1 TAAA-TTAAATTTAAAATAAATTTAAATC
* *
661946 TAAA-TAAATTTAAAATCAATTTAACTC
1 TAAATTAAATTTAAAATAAATTTAAATC
661973 TAAATTAAAT
1 TAAATTAAAT
661983 GAAAAGTCCA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.40
28 5 0.08
29 5 0.08
31 26 0.43
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (28 bp):
TAAATTAAATTTAAAATAAATTTAAATC
Found at i:661987 original size:27 final size:27
Alignment explanation
Indices: 661923--661987 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
661913 TAATTAAATT
* *
661923 TAAATTTAAAATAAATTTAAATTTAAA
1 TAAATTGAAAATAAATTTAAATCTAAA
* * *
661950 TAAATTTAAAATCAATTTAACTCTAAA
1 TAAATTGAAAATAAATTTAAATCTAAA
661977 TTAAA-TGAAAA
1 -TAAATTGAAAA
661988 GTCCAAGCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 29 0.88
28 4 0.12
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (27 bp):
TAAATTGAAAATAAATTTAAATCTAAA
Found at i:666140 original size:25 final size:25
Alignment explanation
Indices: 666112--666167 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
666102 CTTGGTAACC
* *
666112 TTTAGTACTTGGTATCTAAATTTTT
1 TTTAGTAATTGGTAGCTAAATTTTT
*
666137 TTTATCTAATTGGTAGCTAAATTTTT
1 TTTA-GTAATTGGTAGCTAAATTTTT
666163 TTTAG
1 TTTAG
666168 ATGTAATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.55
Consensus pattern (25 bp):
TTTAGTAATTGGTAGCTAAATTTTT
Found at i:666184 original size:28 final size:26
Alignment explanation
Indices: 666127--666185 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
666117 TACTTGGTAT
** *
666127 CTAAATTTTTTTTATCTAATTGGTAG
1 CTAAATTTTTTTTATCTAATTAATAC
*
666153 CTAAATTTTTTTTAGATGTAATTAATAC
1 CTAAATTTTTTTT--ATCTAATTAATAC
666181 CTAAA
1 CTAAA
666186 CTTAAAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 13 0.48
28 14 0.52
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.49
Consensus pattern (26 bp):
CTAAATTTTTTTTATCTAATTAATAC
Found at i:668126 original size:83 final size:83
Alignment explanation
Indices: 667987--668156 Score: 340
Period size: 83 Copynumber: 2.0 Consensus size: 83
667977 GAAAATTACA
667987 AGTTGGCACGGTATTACACATACGATAATATATTTGCCGTGTTGGATTTTGGAAATAACATAACT
1 AGTTGGCACGGTATTACACATACGATAATATATTTGCCGTGTTGGATTTTGGAAATAACATAACT
668052 TAATTGAATGAATTTAAT
66 TAATTGAATGAATTTAAT
668070 AGTTGGCACGGTATTACACATACGATAATATATTTGCCGTGTTGGATTTTGGAAATAACATAACT
1 AGTTGGCACGGTATTACACATACGATAATATATTTGCCGTGTTGGATTTTGGAAATAACATAACT
668135 TAATTGAATGAATTTAAT
66 TAATTGAATGAATTTAAT
668153 AGTT
1 AGTT
668157 ATTGTTCGGT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 87 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (83 bp):
AGTTGGCACGGTATTACACATACGATAATATATTTGCCGTGTTGGATTTTGGAAATAACATAACT
TAATTGAATGAATTTAAT
Found at i:669592 original size:29 final size:29
Alignment explanation
Indices: 669557--669623 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
669547 TCCGAAATTT
* *
669557 GGAATTTAGTCCCTATGTTTTTATTTCTA
1 GGAATTTAGTCCCTATATTTTTATTTCCA
669586 GGAATTTAGTCCCTATATTTTTATTTCCA
1 GGAATTTAGTCCCTATATTTTTATTTCCA
669615 GGAATTTAG
1 GGAATTTAG
669624 AAGGTCCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (29 bp):
GGAATTTAGTCCCTATATTTTTATTTCCA
Found at i:671663 original size:29 final size:30
Alignment explanation
Indices: 671630--671716 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 30
671620 CAAATGATTA
671630 ATTTGTTACTTTTCAAAAATATTAGTGAT-
1 ATTTGTTACTTTTCAAAAATATTAGTGATG
* * * * *
671659 ATTTGTCACTTTTCATAAACATCAATGATTG
1 ATTTGTTACTTTTCAAAAATATTAGTGA-TG
* *
671690 ATTTATTACTTTT--AAAATTTTAGTGAT
1 ATTTGTTACTTTTCAAAAATATTAGTGAT
671717 TGAAATGTTA
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
28 1 0.02
29 31 0.70
30 1 0.02
31 11 0.25
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (30 bp):
ATTTGTTACTTTTCAAAAATATTAGTGATG
Found at i:671702 original size:31 final size:30
Alignment explanation
Indices: 671622--671706 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 30
671612 AATGAATTCA
* *
671622 AATGATTAATTTGTTACTTTTCAAAAATATT
1 AATGATT-ATTTGTTACTTTTCAAAAACATC
* * *
671653 AGTGA-TATTTGTCACTTTTCATAAACATC
1 AATGATTATTTGTTACTTTTCAAAAACATC
*
671682 AATGATTGATTTATTACTTTT-AAAA
1 AATGATT-ATTTGTTACTTTTCAAAA
671707 TTTTAGTGAT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
29 23 0.53
30 5 0.12
31 15 0.35
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.46
Consensus pattern (30 bp):
AATGATTATTTGTTACTTTTCAAAAACATC
Found at i:681129 original size:21 final size:21
Alignment explanation
Indices: 681105--681146 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
681095 TAATTCAACA
681105 AAAAACTGGTGGATTTAATGC
1 AAAAACTGGTGGATTTAATGC
681126 AAAAACTGGTGGATTTAATGC
1 AAAAACTGGTGGATTTAATGC
681147 TTCTTTTCCC
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:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
AAAAACTGGTGGATTTAATGC
Found at i:682181 original size:16 final size:17
Alignment explanation
Indices: 682160--682195 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
682150 TTGGGATGAT
682160 AATAAATTT-TTAATTG
1 AATAAATTTATTAATTG
682176 AATAAATTTAATTAATTG
1 AATAAATTT-ATTAATTG
682194 AA
1 AA
682196 AATTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
AATAAATTTATTAATTG
Found at i:682192 original size:18 final size:18
Alignment explanation
Indices: 682160--682210 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
682150 TTGGGATGAT
682160 AATAAATTT--TTAATTG
1 AATAAATTTAATTAATTG
682176 AATAAATTTAATTAATTG
1 AATAAATTTAATTAATTG
*
682194 AA-AATTTTAAATTAATT
1 AATAAATTT-AATTAATT
682211 ACAACTGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 9 0.29
17 5 0.16
18 17 0.55
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (18 bp):
AATAAATTTAATTAATTG
Found at i:683404 original size:98 final size:98
Alignment explanation
Indices: 683129--683370 Score: 441
Period size: 97 Copynumber: 2.5 Consensus size: 98
683119 ACAGTATCTC
*
683129 AACTTTTACAATGTCATTGATTAACTCAAATACTTTATTTTGATTAAGACTCTCATGTAACTTTT
1 AACTTTTACAATGTCATTGATTAGCTCAAATACTTTATTTTGATTAAGACTCTCATGTAACTTTT
683194 ATGAGTTGTA-TTTTTACATAATTGGGTAATTT
66 ATGAGTTGTATTTTTTACATAATTGGGTAATTT
*
683226 AACTTTTTCAATGTCATTGATTAGCTCAAATACTTTATTTTGATTAAGACTCTCATGTAACTTTT
1 AACTTTTACAATGTCATTGATTAGCTCAAATACTTTATTTTGATTAAGACTCTCATGTAACTTTT
683291 ATGAGTTGTATTTTTTACATAATTGGGTAATTT
66 ATGAGTTGTATTTTTTACATAATTGGGTAATTT
* *
683324 AACTTTTCCAATGTCATTGATTAGCTCAAATATTTTATTTTGATTAA
1 AACTTTTACAATGTCATTGATTAGCTCAAATACTTTATTTTGATTAA
683371 AATGTTGACG
Statistics
Matches: 140, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
97 73 0.52
98 67 0.48
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (98 bp):
AACTTTTACAATGTCATTGATTAGCTCAAATACTTTATTTTGATTAAGACTCTCATGTAACTTTT
ATGAGTTGTATTTTTTACATAATTGGGTAATTT
Found at i:687641 original size:36 final size:36
Alignment explanation
Indices: 687595--687666 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
687585 GTATAGCTAG
* *
687595 AGAGCGTTAGATGTTTCTAGGATTCTTTCCTCGTCT
1 AGAGCATTAGATGTTTCTAGGATTATTTCCTCGTCT
*
687631 AGAGCATTAGATGTTTCTAGGATTATTTTCTCGTCT
1 AGAGCATTAGATGTTTCTAGGATTATTTCCTCGTCT
687667 CGAATTCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (36 bp):
AGAGCATTAGATGTTTCTAGGATTATTTCCTCGTCT
Found at i:687904 original size:31 final size:31
Alignment explanation
Indices: 687869--687943 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
687859 TGTTAAAAAA
* *
687869 ATTTAA-TTCATTGAATTATTCGAAGGTT-TT
1 ATTTAAGTT-ATTGAACTATTCGAAAGTTGTT
*
687899 CATTTAAGTTATTGAACTATTTGAAAGTTGTT
1 -ATTTAAGTTATTGAACTATTCGAAAGTTGTT
687931 ATTTAAGTTATTG
1 ATTTAAGTTATTG
687944 GGTTAATGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 35 0.90
32 4 0.10
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (31 bp):
ATTTAAGTTATTGAACTATTCGAAAGTTGTT
Found at i:689025 original size:15 final size:17
Alignment explanation
Indices: 688992--689029 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
688982 GGATGCCGAT
*
688992 ATAAAAAAATTCAATAA
1 ATAAAAAAATTCAAAAA
689009 ATAAAAAAA-T-AAAAA
1 ATAAAAAAATTCAAAAA
689024 ATAAAA
1 ATAAAA
689030 TATTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 1 0.05
17 9 0.45
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
ATAAAAAAATTCAAAAA
Found at i:696080 original size:27 final size:28
Alignment explanation
Indices: 696025--696086 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
696015 CATTGAAACC
**
696025 AAACTT-AAGTACCAAATTTGGATTAAA
1 AAACTTCAAGTACCAAATTTGGACAAAA
*
696052 AAATTTCAAGTACCAAA-TTGGACAAAA
1 AAACTTCAAGTACCAAATTTGGACAAAA
696079 AAACTTCA
1 AAACTTCA
696087 CGGTGCCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 20 0.67
28 10 0.33
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.26
Consensus pattern (28 bp):
AAACTTCAAGTACCAAATTTGGACAAAA
Found at i:697499 original size:20 final size:20
Alignment explanation
Indices: 697474--697517 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
697464 TCATATTAAT
* * *
697474 ATAATTTAAATTATAAATTA
1 ATAATTTAAAATAAAAATAA
697494 ATAATTTAAAATAAAAATAA
1 ATAATTTAAAATAAAAATAA
697514 ATAA
1 ATAA
697518 AATAATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAATTTAAAATAAAAATAA
Found at i:700114 original size:21 final size:21
Alignment explanation
Indices: 700085--700125 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
700075 AAAATAAAAA
**
700085 ATTGCTTTTGCTGTTGTTTTC
1 ATTGCTTTTGCAATTGTTTTC
*
700106 ATTGTTTTTGCAATTGTTTT
1 ATTGCTTTTGCAATTGTTTT
700126 ATCACTGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.10, G:0.17, T:0.63
Consensus pattern (21 bp):
ATTGCTTTTGCAATTGTTTTC
Found at i:702806 original size:22 final size:21
Alignment explanation
Indices: 702788--702830 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
702778 TGATATTGTT
702788 TTGCTATCATTTTATTATTATA
1 TTGCTA-CATTTTATTATTATA
*
702810 TTGCTACTATTTTATTGTTAT
1 TTGCTAC-ATTTTATTATTAT
702831 TGTTTGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.60
Consensus pattern (21 bp):
TTGCTACATTTTATTATTATA
Found at i:710616 original size:34 final size:34
Alignment explanation
Indices: 710578--710646 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
710568 GAGCAATGAC
710578 AAGCAATAATGAAAAAGACTCAGTTTGGAGATTT
1 AAGCAATAATGAAAAAGACTCAGTTTGGAGATTT
710612 AAGCAATAATGAAAAAGACTCAGTTTGGAGATTT
1 AAGCAATAATGAAAAAGACTCAGTTTGGAGATTT
710646 A
1 A
710647 GTAATCACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.26
Consensus pattern (34 bp):
AAGCAATAATGAAAAAGACTCAGTTTGGAGATTT
Found at i:714390 original size:17 final size:17
Alignment explanation
Indices: 714347--714391 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
714337 CTGTTCAATT
*
714347 AAATAAATAATTTTTAAA
1 AAATAAA-AACTTTTAAA
*
714365 ATTATAAAAACTTTTAAA
1 A-AATAAAAACTTTTAAA
714383 AAATAAAAA
1 AAATAAAAA
714392 TTCGATTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 7 0.30
18 11 0.48
19 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAAAACTTTTAAA
Found at i:718308 original size:4 final size:4
Alignment explanation
Indices: 718299--718323 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
718289 TCCAATATGA
718299 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
718324 TATATTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:722170 original size:16 final size:16
Alignment explanation
Indices: 722149--722179 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
722139 TTATTTTTAC
722149 ATAAATAAAATAAAAT
1 ATAAATAAAATAAAAT
*
722165 ATAAATCAAATAAAA
1 ATAAATAAAATAAAA
722180 GAAATAAAAT
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:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
ATAAATAAAATAAAAT
Found at i:726245 original size:2 final size:2
Alignment explanation
Indices: 726238--726263 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
726228 GTAGCTTTAA
726238 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
726264 TAGATTAATA
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:727687 original size:3 final size:3
Alignment explanation
Indices: 727679--727742 Score: 103
Period size: 3 Copynumber: 21.7 Consensus size: 3
727669 AGGCAAGAAC
* *
727679 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATC ATA ATC ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
727727 ATA ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA AT
727743 TTGCAGTATT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:729618 original size:31 final size:31
Alignment explanation
Indices: 729578--729644 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
729568 AGAAGATTTG
*
729578 AGTTAAATTTGA-CATCCAACATTTTAAAAAA
1 AGTTAAATTTGACCAT-CAACATTTCAAAAAA
* *
729609 AGTTGAATTTGACCATTAACATTTCAAAAAA
1 AGTTAAATTTGACCATCAACATTTCAAAAAA
729640 AGTTA
1 AGTTA
729645 TTGTTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (31 bp):
AGTTAAATTTGACCATCAACATTTCAAAAAA
Found at i:730279 original size:19 final size:19
Alignment explanation
Indices: 730255--730291 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
730245 GCTCAATATT
730255 ATTTTA-ATAAAACATTTAA
1 ATTTTATATAAAA-ATTTAA
730274 ATTTTATATAAAAATTTA
1 ATTTTATATAAAAATTTA
730292 TTAATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTTATATAAAAATTTAA
Found at i:730336 original size:21 final size:21
Alignment explanation
Indices: 730295--730336 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
730285 AAATTTATTA
*
730295 ATAATATTTTATTAAATAAAT
1 ATAATATTTTAATAAATAAAT
730316 ATAATA-TTTAATAAATGAAAT
1 ATAATATTTTAATAAAT-AAAT
730337 TACATTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
ATAATATTTTAATAAATAAAT
Found at i:730427 original size:14 final size:14
Alignment explanation
Indices: 730408--730434 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
730398 TAAATATTTA
730408 TTATAATTTTTAAT
1 TTATAATTTTTAAT
730422 TTATAATTTTTAA
1 TTATAATTTTTAA
730435 AAATTCAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATAATTTTTAAT
Found at i:733363 original size:51 final size:51
Alignment explanation
Indices: 733303--733404 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
733293 TATTTCATAA
*
733303 TCTCTTCATATAGACCATAACAATATTCTTAACTGACATCCATCGCTCTAC
1 TCTCTTCATATAGACCATAACAATATTCTTAACTAACATCCATCGCTCTAC
* *
733354 TCTCTTCATATAGACCCTAACAATATTCTTAGCTAACATCCATCGCTCTAC
1 TCTCTTCATATAGACCATAACAATATTCTTAACTAACATCCATCGCTCTAC
733405 CCTATACACT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (51 bp):
TCTCTTCATATAGACCATAACAATATTCTTAACTAACATCCATCGCTCTAC
Found at i:739326 original size:29 final size:30
Alignment explanation
Indices: 739270--739336 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
739260 ATAAAATAAT
* **
739270 TATTGAATTATTCAAAAATTTTAATTTAAG
1 TATTAAATTATTCAAAAAAATTAATTTAAG
739300 ATATTAAATTATT-AAAAAAATT-ATTTAAG
1 -TATTAAATTATTCAAAAAAATTAATTTAAG
739329 TCATTAAA
1 T-ATTAAA
739337 CTATCCCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.03
29 13 0.41
30 7 0.22
31 11 0.34
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (30 bp):
TATTAAATTATTCAAAAAAATTAATTTAAG
Found at i:742336 original size:31 final size:30
Alignment explanation
Indices: 742300--742406 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 30
742290 GTTATAAAAT
742300 AGTCACTGAATTATTAGAAAGTTTTCATTTA
1 AGTCACTGAATTATTAGAAAGTTTT-ATTTA
* *
742331 AGTCACTGAACTATT-GAAAAGTTTT-TATA
1 AGTCACTGAATTATTAG-AAAGTTTTATTTA
* * ** *
742360 AGTCATTGAAATATTCCAAAATTTGTATTTA
1 AGTCACTGAATTATTAGAAAGTTT-TATTTA
742391 AGTCACT-AAGTTATTA
1 AGTCACTGAA-TTATTA
742407 AGTTTTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
29 22 0.36
30 4 0.07
31 35 0.57
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.40
Consensus pattern (30 bp):
AGTCACTGAATTATTAGAAAGTTTTATTTA
Found at i:745138 original size:31 final size:31
Alignment explanation
Indices: 745090--745158 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
745080 GAAAATCCTA
* *
745090 AAGTTTAGGCTCTAATGTGGGAACAATTGCC
1 AAGTTCAGGCTCTAATGTGGGAACAATTACC
*
745121 AAGTTCAGGC-CTCAATGTGGGAGCAATTACC
1 AAGTTCAGGCTCT-AATGTGGGAACAATTACC
745152 AAGTTCA
1 AAGTTCA
745159 AGAACTAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (31 bp):
AAGTTCAGGCTCTAATGTGGGAACAATTACC
Found at i:763157 original size:24 final size:23
Alignment explanation
Indices: 763105--763175 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
763095 GGTGGGAGGA
763105 ATTTTTT-TAATATAATTATAATT
1 ATTTTTTGTAATATAA-TATAATT
*
763128 ATTTTTTTGTGAATTTAATATAATT
1 A-TTTTTTGT-AATATAATATAATT
*
763153 ATTTTTAGTTAATATAATA-AATT
1 ATTTTTTG-TAATATAATATAATT
763176 TAAATTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.12
24 20 0.49
25 10 0.24
26 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (23 bp):
ATTTTTTGTAATATAATATAATT
Found at i:763181 original size:6 final size:6
Alignment explanation
Indices: 763170--763196 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
763160 GTTAATATAA
763170 TAAATT TAAATT TAAATT TAAATT TAA
1 TAAATT TAAATT TAAATT TAAATT TAA
763197 TAATTTTTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:768477 original size:54 final size:55
Alignment explanation
Indices: 768419--768539 Score: 136
Period size: 59 Copynumber: 2.1 Consensus size: 55
768409 GAACAAAAAG
* * * *
768419 AAACTCAAGTAGCAAATT-GAAAAAAACTTAGGTACCAAAGTGAATATTGAAGTC
1 AAACTCAAGTAGCAAATTAGAAAAAAACTTAAGTACCAAAGTAAATATTCAAGCC
* * *
768473 AAACTCAGGTATCAAATTGGAACGAAAAAAACTTAAGTACCAAATTAAATATTCAAGCC
1 AAACTCAAGTAGCAAATT---A-GAAAAAAACTTAAGTACCAAAGTAAATATTCAAGCC
768532 AAACTCAA
1 AAACTCAA
768540 CTCGGGTACC
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
54 16 0.30
59 38 0.70
ACGTcount: A:0.50, C:0.16, G:0.13, T:0.21
Consensus pattern (55 bp):
AAACTCAAGTAGCAAATTAGAAAAAAACTTAAGTACCAAAGTAAATATTCAAGCC
Found at i:769016 original size:31 final size:30
Alignment explanation
Indices: 768920--769020 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 30
768910 AAAGTCAAAT
* *
768920 TCAGATATCAAATTGAATATTAAAACTAAAC
1 TCAGATACCAAATTGAATACTAAAA-TAAAC
* *
768951 TCA-AGTACCAAATTGGA-AC--AGA-AAAC
1 TCAGA-TACCAAATTGAATACTAAAATAAAC
* *
768977 TTAAATACCAAATTGAATACTAAAATTAAAC
1 TCAGATACCAAATTGAATACTAAAA-TAAAC
769008 TCAGATACCAAAT
1 TCAGATACCAAAT
769021 AATATATTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
26 17 0.31
27 3 0.06
28 2 0.04
29 2 0.04
30 2 0.04
31 28 0.52
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.25
Consensus pattern (30 bp):
TCAGATACCAAATTGAATACTAAAATAAAC
Found at i:771776 original size:5 final size:5
Alignment explanation
Indices: 771766--771790 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
771756 GGAAGTGATG
771766 GGTTA GGTTA GGTTA GGTTA GGTTA
1 GGTTA GGTTA GGTTA GGTTA GGTTA
771791 TGATTTGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
GGTTA
Found at i:778054 original size:23 final size:23
Alignment explanation
Indices: 778024--778077 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
778014 ATCTTTGAAT
* *
778024 TTTA-ATTTAATTATTTCAAGGA
1 TTTATATTTAATTATTTAAAGAA
* *
778046 TTTATATTTGATTCTTTAAAGAA
1 TTTATATTTAATTATTTAAAGAA
*
778069 ATTATATTT
1 TTTATATTT
778078 GATACGTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
TTTATATTTAATTATTTAAAGAA
Found at i:778554 original size:18 final size:18
Alignment explanation
Indices: 778531--778565 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
778521 TTATCTTTTT
*
778531 TTAAAAAAAATAGAATAA
1 TTAAAAAAAATAAAATAA
*
778549 TTAAAACAAATAAAATA
1 TTAAAAAAAATAAAATA
778566 TACACAATAA
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:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
TTAAAAAAAATAAAATAA
Found at i:779395 original size:26 final size:28
Alignment explanation
Indices: 779366--779429 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
779356 GATTTAAAAA
779366 TTAATTAAATT-AATTTTAATTATTTT-T
1 TTAATTAAATTGAATTTTAA-TATTTTAT
* * *
779393 TAAATT-TATTGATTTTTAATATTTTAT
1 TTAATTAAATTGAATTTTAATATTTTAT
779420 TTAATTAAAT
1 TTAATTAAAT
779430 CGGACGAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
26 9 0.31
27 18 0.62
28 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
TTAATTAAATTGAATTTTAATATTTTAT
Found at i:791339 original size:22 final size:22
Alignment explanation
Indices: 791314--791357 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
791304 GAGAATAGTT
791314 TGTTAAATAAAAAATAAAATAA
1 TGTTAAATAAAAAATAAAATAA
*** *
791336 TGTTTTTTAAAAAGTAAAATAA
1 TGTTAAATAAAAAATAAAATAA
791358 AATAATATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (22 bp):
TGTTAAATAAAAAATAAAATAA
Found at i:791663 original size:31 final size:33
Alignment explanation
Indices: 791590--791665 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
791580 TTAACTACAA
*
791590 AAATAGTTTAA-AGATTTGTTTAAATAAAATGT
1 AAATAGTTTAAGAGACTTGTTTAAATAAAATGT
*
791622 AATATAGTTTAAGAG-CTTGTTTAAATAAAGTGT
1 AA-ATAGTTTAAGAGACTTGTTTAAATAAAATGT
791655 -AATAGTTTAAG
1 AAATAGTTTAAG
791666 GTTTTTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 10 0.25
32 3 0.08
33 25 0.62
34 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.16, T:0.39
Consensus pattern (33 bp):
AAATAGTTTAAGAGACTTGTTTAAATAAAATGT
Found at i:794005 original size:31 final size:31
Alignment explanation
Indices: 793970--794029 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
793960 ACAAAATAAT
793970 CATTGAAATATTT-AAAAGTTTTTATTGAAAC
1 CATTGAAATATTTGAAAA-TTTTTATTGAAAC
*
794001 CATTGAATTATTTGAAAATTTTTATTGAA
1 CATTGAAATATTTGAAAATTTTTATTGAA
794030 GTCACTAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (31 bp):
CATTGAAATATTTGAAAATTTTTATTGAAAC
Found at i:795635 original size:27 final size:28
Alignment explanation
Indices: 795588--795644 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
795578 GGTATGATGC
**
795588 TTTAGAAATTATATATATTTAGGATTTT
1 TTTAGAAATTATATATATTTAAAATTTT
*
795616 TTTAG-AATTTTATGAT-TTTAAAATTTT
1 TTTAGAAATTATAT-ATATTTAAAATTTT
795643 TT
1 TT
795645 CACTAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (28 bp):
TTTAGAAATTATATATATTTAAAATTTT
Found at i:797343 original size:3 final size:3
Alignment explanation
Indices: 797335--797364 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
797325 ATCCTTTGCT
797335 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
797365 GTCGATCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:800419 original size:42 final size:42
Alignment explanation
Indices: 800360--800454 Score: 172
Period size: 42 Copynumber: 2.3 Consensus size: 42
800350 CAGGATTATC
800360 TCTTGGGAACAGCTTTCCGTACTAAAAAAGTTGCGGAACTAA
1 TCTTGGGAACAGCTTTCCGTACTAAAAAAGTTGCGGAACTAA
* *
800402 TCTTGAGAACAGCTTTCCGTACTGAAAAAGTTGCGGAACTAA
1 TCTTGGGAACAGCTTTCCGTACTAAAAAAGTTGCGGAACTAA
800444 TCTTGGGAACA
1 TCTTGGGAACA
800455 AAACTATGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (42 bp):
TCTTGGGAACAGCTTTCCGTACTAAAAAAGTTGCGGAACTAA
Found at i:803917 original size:29 final size:27
Alignment explanation
Indices: 803882--803951 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
803872 ATGAATAATT
803882 AAATTAAATTTTAAAATTTAAAAAATAAA
1 AAATTAAATTTTAAAA--TAAAAAATAAA
*
803911 AAATTAAATTTCTAAAATAAAATATAAA
1 AAATTAAATTT-TAAAATAAAAAATAAA
* *
803939 AAGTTTAATTTTA
1 AAATTAAATTTTA
803952 TCAACAACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.05
28 19 0.51
29 11 0.30
30 5 0.14
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (27 bp):
AAATTAAATTTTAAAATAAAAAATAAA
Found at i:804642 original size:29 final size:31
Alignment explanation
Indices: 804593--804658 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 31
804583 TCAAAGATTT
*
804593 AGAATTT-AATCTCTATATTTTT-ATTTTTA
1 AGAATTTAAATCTCTATATTTTTAAATTTTA
* *
804622 AGAATTTAAATTTTTAT-TTTTTAAATTTTA
1 AGAATTTAAATCTCTATATTTTTAAATTTTA
804652 A-AATTTA
1 AGAATTTA
804659 GGTCTAACGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (31 bp):
AGAATTTAAATCTCTATATTTTTAAATTTTA
Found at i:813888 original size:22 final size:22
Alignment explanation
Indices: 813856--813897 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
813846 ATATAGTTAA
*
813856 CATTTATTATTTAAAAAAATAT
1 CATTTAGTATTTAAAAAAATAT
*
813878 CATTTAGTATTTAACAAAAT
1 CATTTAGTATTTAAAAAAAT
813898 TAATATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (22 bp):
CATTTAGTATTTAAAAAAATAT
Found at i:816293 original size:18 final size:17
Alignment explanation
Indices: 816265--816326 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
816255 TTCATGCTAT
816265 TTTTTTAATTTTTATGAAA
1 TTTTTT-ATTTTTAT-AAA
816284 TTTTTTA-TTTTATAAA
1 TTTTTTATTTTTATAAA
816300 TATTTTTATTATTT-TAAA
1 T-TTTTTATT-TTTATAAA
*
816318 TTATTTATT
1 TTTTTTATT
816327 GACATATCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
16 4 0.10
17 19 0.49
18 7 0.18
19 9 0.23
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTTTTATTTTTATAAA
Found at i:816323 original size:19 final size:19
Alignment explanation
Indices: 816262--816315 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
816252 CATTTCATGC
*
816262 TATTTTTTTAATTTTTATGAA
1 TATTTTTTT-A-TTTTATAAA
816283 -A-TTTTTTATTTTATAAA
1 TATTTTTTTATTTTATAAA
816300 TATTTTTATTATTTTA
1 TATTTTT-TTATTTTA
816316 AATTATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 8 0.28
18 2 0.07
19 10 0.34
20 9 0.31
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TATTTTTTTATTTTATAAA
Found at i:816940 original size:2 final size:2
Alignment explanation
Indices: 816933--816958 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
816923 CCAATTTGTA
816933 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
816959 GGATTTAAAG
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:822812 original size:2 final size:2
Alignment explanation
Indices: 822800--822836 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
822790 GAATTGAACC
*
822800 AT AT GT 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 A
822837 GCACTAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:826451 original size:14 final size:15
Alignment explanation
Indices: 826428--826456 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
826418 GAAATTTTAT
826428 TTTTTATTAATTAAA
1 TTTTTATTAATTAAA
826443 TTTTT-TTAATTAAA
1 TTTTTATTAATTAAA
826457 GTATTTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTATTAATTAAA
Done.