Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 38 of 145
Found at i:12175413 original size:25 final size:25
Alignment explanation
Indices: 12175342--12175414 Score: 103
Period size: 25 Copynumber: 3.0 Consensus size: 25
12175332 GGATACTCTT
* *
12175342 AAGAGCTAT-TAACGGGAAGCTAGC
1 AAGAACTATATAACGGGAAGCTCGC
* *
12175366 AAGAACCATATAACGGAAAGCTCGC
1 AAGAACTATATAACGGGAAGCTCGC
12175391 AAGAACTATATAACGGGAAGCTCG
1 AAGAACTATATAACGGGAAGCTCG
12175415 AGAGGGCTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 7 0.17
25 35 0.83
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.15
Consensus pattern (25 bp):
AAGAACTATATAACGGGAAGCTCGC
Found at i:12179397 original size:28 final size:28
Alignment explanation
Indices: 12179366--12179441 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
12179356 AATCATGAAC
** *
12179366 CCCAATAAAATGGGAGTTTTTTTTTAAT
1 CCCAATAAAATGGGAGTTTTGATTCAAT
*
12179394 CCCAATAAAATGAGAGTTTTGATTCAAT
1 CCCAATAAAATGGGAGTTTTGATTCAAT
*
12179422 CCCAATAAAATAGGAGTTTT
1 CCCAATAAAATGGGAGTTTT
12179442 ACTGAATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (28 bp):
CCCAATAAAATGGGAGTTTTGATTCAAT
Found at i:12186079 original size:2 final size:2
Alignment explanation
Indices: 12186072--12186102 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12186062 AAACATCAAA
12186072 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12186103 ATCATAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12187780 original size:20 final size:20
Alignment explanation
Indices: 12187738--12187781 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
12187728 CCCTAATTTC
* * *
12187738 GAAATGATACCAAAAATTCT
1 GAAATCATACCAAAAACTAT
12187758 GAAATCATACCAAAAACTAT
1 GAAATCATACCAAAAACTAT
12187778 GAAA
1 GAAA
12187782 AAAATACCCA
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:0.55, C:0.16, G:0.09, T:0.20
Consensus pattern (20 bp):
GAAATCATACCAAAAACTAT
Found at i:12187955 original size:20 final size:20
Alignment explanation
Indices: 12187930--12187974 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12187920 AAAAAGTAAA
*
12187930 AAAAATCATGCGAAAATACT
1 AAAAATCATGAGAAAATACT
* **
12187950 AAAAATTATGAGGTAATACT
1 AAAAATCATGAGAAAATACT
12187970 AAAAA
1 AAAAA
12187975 GTATACAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.22
Consensus pattern (20 bp):
AAAAATCATGAGAAAATACT
Found at i:12188538 original size:20 final size:20
Alignment explanation
Indices: 12188510--12188606 Score: 83
Period size: 20 Copynumber: 4.9 Consensus size: 20
12188500 AAAAATTCTT
* *
12188510 AGGGCATACAAAAAATTATG
1 AGGGAATACAAAAAAATATG
* *
12188530 AGGAAATACAAAAAAAAATG
1 AGGGAATACAAAAAAATATG
* *
12188550 A--GAGTACCAAAAAAATATT
1 AGGGAATA-CAAAAAAATATG
*
12188569 AGGGATTATC-AAAAAATATG
1 AGGGAATA-CAAAAAAATATG
*
12188589 AGGGAATACTAAAAAATA
1 AGGGAATACAAAAAAATA
12188607 CGAGTACCCA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
18 3 0.05
19 12 0.20
20 41 0.67
21 5 0.08
ACGTcount: A:0.58, C:0.07, G:0.16, T:0.19
Consensus pattern (20 bp):
AGGGAATACAAAAAAATATG
Found at i:12193429 original size:32 final size:32
Alignment explanation
Indices: 12193391--12193453 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
12193381 TCAAGGGGAT
12193391 CCCTTAAGCCCTTACTTATTTCTGTTCTGTGG
1 CCCTTAAGCCCTTACTTATTTCTGTTCTGTGG
12193423 CCCTTAAGCCCTTACTTATTTCTGTTCTGTG
1 CCCTTAAGCCCTTACTTATTTCTGTTCTGTG
12193454 AAGAGGGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.13, C:0.29, G:0.14, T:0.44
Consensus pattern (32 bp):
CCCTTAAGCCCTTACTTATTTCTGTTCTGTGG
Found at i:12197386 original size:2 final size:2
Alignment explanation
Indices: 12197379--12197418 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12197369 TCAAATGCCA
12197379 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
12197419 CAAAATCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12197866 original size:30 final size:29
Alignment explanation
Indices: 12197823--12197882 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 29
12197813 CTAAACCAAC
12197823 TTCATATAGTAAAAGAA-AAAAAATTATAAT
1 TTCATATAGTAAAA-AATAAAAAATT-TAAT
*
12197853 TTCATAATA-TAAAAAATAAAAAGTTTAAT
1 TTCAT-ATAGTAAAAAATAAAAAATTTAAT
12197882 T
1 T
12197883 AGACTTGCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 7 0.26
30 17 0.63
31 3 0.11
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.33
Consensus pattern (29 bp):
TTCATATAGTAAAAAATAAAAAATTTAAT
Found at i:12198312 original size:19 final size:19
Alignment explanation
Indices: 12198288--12198340 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
12198278 TATTTTATTG
12198288 TTTAAAATTAATAAAAATA
1 TTTAAAATTAATAAAAATA
12198307 TTT-AAATCTAATTAAAAATA
1 TTTAAAAT-TAA-TAAAAATA
*
12198327 -TTAATATTAATAAA
1 TTTAAAATTAATAAA
12198341 CAATCAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 8 0.27
19 11 0.37
20 11 0.37
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTAAAATTAATAAAAATA
Found at i:12199259 original size:11 final size:11
Alignment explanation
Indices: 12199243--12199285 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
12199233 TGTTTTCTCT
12199243 CTATTTTGCTA
1 CTATTTTGCTA
* *
12199254 CCATTTTACTA
1 CTATTTTGCTA
* *
12199265 TTATGTTGCTA
1 CTATTTTGCTA
12199276 CTATTTTGCT
1 CTATTTTGCT
12199286 GTTATTGTTT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.53
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:12199380 original size:29 final size:30
Alignment explanation
Indices: 12199320--12199381 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
12199310 ACTTATTTTA
12199320 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
* *
12199350 TTGTTAATTTTGTTA-TATTTTAGAGGTAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
12199379 TTG
1 TTG
12199382 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.24, C:0.02, G:0.16, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:12199448 original size:16 final size:16
Alignment explanation
Indices: 12199427--12199475 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
12199417 TTCGCTGTAT
12199427 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
12199443 TGGAATAGAGACGTAA
1 TGGAATAGAGGCGTAA
*
12199459 CGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
12199475 T
1 T
12199476 AGCAAATCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.39, C:0.08, G:0.35, T:0.18
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:12208340 original size:30 final size:30
Alignment explanation
Indices: 12208285--12208342 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
12208275 ATTACTATAA
*
12208285 AAACTACTAAAAATCATACTTTTACTAATT
1 AAACTACTAAAAATCATAATTTTACTAATT
12208315 AAACT-CTAAAAA-CATAAATTATTACTAA
1 AAACTACTAAAAATCAT-AATT-TTACTAA
12208343 AATGACTCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 3 0.12
29 10 0.40
30 12 0.48
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.33
Consensus pattern (30 bp):
AAACTACTAAAAATCATAATTTTACTAATT
Found at i:12210487 original size:28 final size:28
Alignment explanation
Indices: 12210455--12210510 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
12210445 AAGAAAGTAA
* *
12210455 ATCAAAATTGTATTATAGAAGCACAAAC
1 ATCAAAATTGAATTATAGAAGCAAAAAC
12210483 ATCAAAATTGAATTATAGAAGCAAAAAC
1 ATCAAAATTGAATTATAGAAGCAAAAAC
12210511 CGCGAAAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.54, C:0.12, G:0.11, T:0.23
Consensus pattern (28 bp):
ATCAAAATTGAATTATAGAAGCAAAAAC
Found at i:12216065 original size:50 final size:50
Alignment explanation
Indices: 12215996--12216093 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
12215986 TTCGAGCTAA
* * *
12215996 TATCGGGAAGCTCTAGAGAG-CTATTAATCGAGAAGCTCAAAAGAGCCAGT
1 TATCGAGAAGCTCTAGAGAGCCAAATAA-CGAGAAGCTCAAAAGAGCCAGT
*
12216046 TATCGAGAAGCTCGT-GAGAGCCAAATAACGAGAAGCTCAAGAGAGCCA
1 TATCGAGAAGCTC-TAGAGAGCCAAATAACGAGAAGCTCAAAAGAGCCA
12216094 TATATTGGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
50 36 0.86
51 6 0.14
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.16
Consensus pattern (50 bp):
TATCGAGAAGCTCTAGAGAGCCAAATAACGAGAAGCTCAAAAGAGCCAGT
Found at i:12216116 original size:50 final size:50
Alignment explanation
Indices: 12216024--12216125 Score: 125
Period size: 50 Copynumber: 2.0 Consensus size: 50
12216014 AGCTATTAAT
* *
12216024 CGAGAAGCTCAAAAGAGCCAGTTATCGAGAAGCTCGTGAGAGCCAAATAA
1 CGAGAAGCTCAAAAGAGCCAGTTATCGAGAAGCTCATAAGAGCCAAATAA
* * * * *
12216074 CGAGAAGCTCAAGAGAGCCA-TATATTGGGATGCTCATAAGAGCCATATAA
1 CGAGAAGCTCAAAAGAGCCAGT-TATCGAGAAGCTCATAAGAGCCAAATAA
12216124 CG
1 CG
12216126 GGACGCTCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 1 0.02
50 43 0.98
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (50 bp):
CGAGAAGCTCAAAAGAGCCAGTTATCGAGAAGCTCATAAGAGCCAAATAA
Found at i:12216128 original size:25 final size:25
Alignment explanation
Indices: 12215999--12216133 Score: 96
Period size: 25 Copynumber: 5.4 Consensus size: 25
12215989 GAGCTAATAT
* *
12215999 CGGGAAGCTCTAGAGAGCTAT-TAA
1 CGGGAAGCTCAAGAGAGCCATATAA
* * *
12216023 TCGAGAAGCTCAAAAGAGCCAGT-TAT
1 -CGGGAAGCTCAAGAGAGCCA-TATAA
* ** *
12216049 CGAGAAGCTCGTGAGAGCCAAATAA
1 CGGGAAGCTCAAGAGAGCCATATAA
* *
12216074 CGAGAAGCTCAAGAGAGCCATATAT
1 CGGGAAGCTCAAGAGAGCCATATAA
* *
12216099 TGGGATGCTCATA-AGAGCCATATAA
1 CGGGAAGCTCA-AGAGAGCCATATAA
*
12216124 CGGGACGCTC
1 CGGGAAGCTC
12216134 TTACGAGCTG
Statistics
Matches: 87, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
25 83 0.95
26 4 0.05
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.18
Consensus pattern (25 bp):
CGGGAAGCTCAAGAGAGCCATATAA
Found at i:12219004 original size:24 final size:24
Alignment explanation
Indices: 12218977--12219042 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
12218967 AAGCTCATGC
*
12218977 GAGCCAATAACGGGTAGCTCCGAA
1 GAGCCAATAACGGGAAGCTCCGAA
* *
12219001 GAGCCATTAACGGGAAGCTCCGGA
1 GAGCCAATAACGGGAAGCTCCGAA
* *
12219025 TAGCCATATATCGGGAAG
1 GAGCCA-ATAACGGGAAG
12219043 TTCAAGTGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 26 0.74
25 9 0.26
ACGTcount: A:0.32, C:0.23, G:0.30, T:0.15
Consensus pattern (24 bp):
GAGCCAATAACGGGAAGCTCCGAA
Found at i:12219659 original size:29 final size:29
Alignment explanation
Indices: 12219617--12219677 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
12219607 CGAGAATACA
12219617 TAAAAACGGGACAAGAATACATACCTAAT
1 TAAAAACGGGACAAGAATACATACCTAAT
12219646 TAAAAACGGGACAAGAATACATACCTAAT
1 TAAAAACGGGACAAGAATACATACCTAAT
12219675 TAA
1 TAA
12219678 GCAAAATAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.52, C:0.16, G:0.13, T:0.18
Consensus pattern (29 bp):
TAAAAACGGGACAAGAATACATACCTAAT
Found at i:12221601 original size:17 final size:18
Alignment explanation
Indices: 12221579--12221613 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12221569 TTTCTAATAA
*
12221579 TTAAAT-ATAAAACTCCT
1 TTAAATAATAAAAATCCT
12221596 TTAAATAATAAAAATCCT
1 TTAAATAATAAAAATCCT
12221614 AAAATAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAATAATAAAAATCCT
Found at i:12231665 original size:21 final size:22
Alignment explanation
Indices: 12231634--12231685 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
12231624 GATGGAAGTA
*
12231634 ATAAA-TTTATATAT-TAAAAT
1 ATAAATTTTATAAATATAAAAT
12231654 ATAAATTTTATAAATATAAAAT
1 ATAAATTTTATAAATATAAAAT
12231676 -TAAAATTTTA
1 AT-AAATTTTA
12231686 GTTGAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 5 0.18
21 9 0.32
22 14 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAAATTTTATAAATATAAAAT
Found at i:12237409 original size:17 final size:18
Alignment explanation
Indices: 12237387--12237424 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
12237377 TTGTAATAGA
12237387 AAATATATT-ATTTTCGT
1 AAATATATTAATTTTCGT
*
12237404 AAATATGTTACATTTTCGT
1 AAATATATTA-ATTTTCGT
12237423 AA
1 AA
12237425 TTAGTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (18 bp):
AAATATATTAATTTTCGT
Found at i:12243874 original size:4 final size:4
Alignment explanation
Indices: 12243865--12243908 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
12243855 GGCCACCATT
* *
12243865 ATAC ATAC ATAC ATAC ATAC --AC ATGC ATGC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
12243909 TCACTCATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
4 34 0.94
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:12244360 original size:28 final size:26
Alignment explanation
Indices: 12244328--12244380 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 26
12244318 AAACAACAAA
12244328 AAAAACAAAAGAAGAAGAAAACAAAAGCC
1 AAAAA-AAAAGAA-AAGAAAA-AAAAGCC
12244357 AAAAAAAAAGAAAAGAAAAAAAAG
1 AAAAAAAAAGAAAAGAAAAAAAAG
12244381 ATGAACTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 5 0.21
27 7 0.29
28 7 0.29
29 5 0.21
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (26 bp):
AAAAAAAAAGAAAAGAAAAAAAAGCC
Found at i:12244364 original size:16 final size:15
Alignment explanation
Indices: 12244324--12244379 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 15
12244314 GTTTAAACAA
12244324 CAAAAAAAACAAAAG
1 CAAAAAAAACAAAAG
12244339 -AAGAAGAAAACAAAAG
1 CAA-AA-AAAACAAAAG
*
12244355 CCAAAAAAAAAGAAAAG
1 -C-AAAAAAAACAAAAG
12244372 -AAAAAAAA
1 CAAAAAAAA
12244380 GATGAACTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
14 10 0.29
15 2 0.06
16 10 0.29
17 9 0.26
18 2 0.06
19 2 0.06
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (15 bp):
CAAAAAAAACAAAAG
Found at i:12244367 original size:22 final size:23
Alignment explanation
Indices: 12244333--12244375 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
12244323 ACAAAAAAAA
*
12244333 CAAAAGAAGAAGAAAACAAAAGC
1 CAAAAGAAAAAGAAAACAAAAGC
*
12244356 CAAAA-AAAAAGAAAAGAAAA
1 CAAAAGAAAAAGAAAACAAAA
12244376 AAAAGATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.77, C:0.09, G:0.14, T:0.00
Consensus pattern (23 bp):
CAAAAGAAAAAGAAAACAAAAGC
Found at i:12249387 original size:235 final size:237
Alignment explanation
Indices: 12248966--12249438 Score: 923
Period size: 235 Copynumber: 2.0 Consensus size: 237
12248956 TTCTACAAGG
12248966 TCAGCATTCCCTTCTTAAATTCTTGCCTCCTGTTTTTTTTTTTTCCCCTTTTTGCATGCATTTTT
1 TCAGCATTCCCTTCTTAAATTCTTGCCTCCTGTTTTTTTTTTTTCCCCTTTTTGCATGCATTTTT
*
12249031 CTTATCTGGGTCATCTTCCTTTTGCCTTCTTCTGGGATGGTTTAAAATGGTGAAAATTAGAGGAA
66 CTTATCTGGGTCATCTTCCTTTTGCCTTCTTCTGGGATGGTTTAAAATGGTGAAAATGAGAGGAA
12249096 ATTGTTAAATTCAGGTTTTTGTCCATTAAGTTTTGGGGGGGAAAACTGATTCTTTACTCTTTATA
131 ATTGTTAAATTCAGGTTTTTGTCCATTAAGTTTTGGGGGGGAAAACTGATTCTTTACTCTTTATA
12249161 TAAAGATGACACTTTTGCTTTTACTTTGTTAAATTTATATAC
196 TAAAGATGACACTTTTGCTTTTACTTTGTTAAATTTATATAC
12249203 TCAGCATT-CCTTCTTAAATTCTTGCCTCCTG-TTTTTTTTTTTCCCCTTTTTGCATGCATTTTT
1 TCAGCATTCCCTTCTTAAATTCTTGCCTCCTGTTTTTTTTTTTTCCCCTTTTTGCATGCATTTTT
12249266 CTTATCTGGGTCATCTTCCTTTTGCCTTCTTCTGGGATGGTTTAAAATGGTGAAAATGAGAGGAA
66 CTTATCTGGGTCATCTTCCTTTTGCCTTCTTCTGGGATGGTTTAAAATGGTGAAAATGAGAGGAA
12249331 ATTGTTAAATTCAGGTTTTTGTCCATTAAGTTTTGGGGGGGAAAACTGATTCTTTACTCTTTATA
131 ATTGTTAAATTCAGGTTTTTGTCCATTAAGTTTTGGGGGGGAAAACTGATTCTTTACTCTTTATA
12249396 TAAAGATGACACTTTTGCTTTTACTTTGTTAAATTTATATAC
196 TAAAGATGACACTTTTGCTTTTACTTTGTTAAATTTATATAC
12249438 T
1 T
12249439 TTTTTCAATT
Statistics
Matches: 235, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
235 204 0.87
236 23 0.10
237 8 0.03
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (237 bp):
TCAGCATTCCCTTCTTAAATTCTTGCCTCCTGTTTTTTTTTTTTCCCCTTTTTGCATGCATTTTT
CTTATCTGGGTCATCTTCCTTTTGCCTTCTTCTGGGATGGTTTAAAATGGTGAAAATGAGAGGAA
ATTGTTAAATTCAGGTTTTTGTCCATTAAGTTTTGGGGGGGAAAACTGATTCTTTACTCTTTATA
TAAAGATGACACTTTTGCTTTTACTTTGTTAAATTTATATAC
Found at i:12251884 original size:45 final size:45
Alignment explanation
Indices: 12251835--12251974 Score: 153
Period size: 45 Copynumber: 3.1 Consensus size: 45
12251825 AACAATATTA
*
12251835 ATCTTACATCTGAAACTGATACTATTTTGGAAGAAAAGAGGATTG
1 ATCTTACATCTGAAACTGATACTCTTTTGGAAGAAAAGAGGATTG
* * * *
12251880 ATCTTGCATCCATTG--AC-AATACTCTTTTGGAAGAAAGGAGAATTG
1 ATCTTACAT-C--TGAAACTGATACTCTTTTGGAAGAAAAGAGGATTG
* *
12251925 ATCTTACATC-AAATAATGATACTCTTTTGGAAGAAAAGAGGATTG
1 ATCTTACATCTGAA-ACTGATACTCTTTTGGAAGAAAAGAGGATTG
12251970 ATCTT
1 ATCTT
12251975 GAAGAGTATA
Statistics
Matches: 77, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
44 2 0.03
45 70 0.91
46 3 0.04
48 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (45 bp):
ATCTTACATCTGAAACTGATACTCTTTTGGAAGAAAAGAGGATTG
Found at i:12255788 original size:21 final size:21
Alignment explanation
Indices: 12255747--12255788 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
12255737 ACGTCAAATT
* *
12255747 TTATTTTTATTTATTTTATAA
1 TTATTTTTATTTATATGATAA
12255768 TTATTTTTATTT-TAATGATAA
1 TTATTTTTATTTAT-ATGATAA
12255789 AAATCAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATTTTTATTTATATGATAA
Found at i:12256009 original size:16 final size:16
Alignment explanation
Indices: 12255985--12256015 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12255975 ATTTTTGTTC
12255985 TAAAAATATAAATAAA
1 TAAAAATATAAATAAA
*
12256001 TAAATATATAAATAA
1 TAAAAATATAAATAA
12256016 CGTCATTTCC
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAAATATAAATAAA
Found at i:12258513 original size:107 final size:107
Alignment explanation
Indices: 12258314--12258624 Score: 435
Period size: 107 Copynumber: 2.9 Consensus size: 107
12258304 AAATTAAGAA
* **
12258314 GATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCA-AATTCTCTCGAA
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC-CTCGAA
* * *
12258378 TTTCCAAACGCAAAACATTGCCTCATTTTGAAAGTTTAAAAAT
65 TTTCCAAACGCAAAATATTGCCTTATTTTGAAAGTTTAAAAAG
* * *
12258421 GATATTTGGCTATTTGGTCGAACGAGGAATCGAAACCCAACACGTTAGGGCACGTTTCCTCGATT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGAAT
* * *
12258486 TTCCAAACGCGAAATATTACCTTATTTTAAAAGTTTAAAAAG
66 TTCCAAACGCAAAATATTGCCTTATTTTGAAAGTTTAAAAAG
* * * * *
12258528 GATATTTGGCTATTTGGCCAAACGAGTAATCGAAACCGAGCACGTTAGGGCACGTTTTCTCGAAT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGAAT
* *
12258593 TTCTAAACGCAAAATATTGCCTTATTTAGAAA
66 TTCCAAACGCAAAATATTGCCTTATTTTGAAA
12258625 AATTTTCTTT
Statistics
Matches: 179, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
107 176 0.98
108 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (107 bp):
GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGAAT
TTCCAAACGCAAAATATTGCCTTATTTTGAAAGTTTAAAAAG
Found at i:12259026 original size:3 final size:3
Alignment explanation
Indices: 12259018--12259057 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
12259008 ACAGTTTAAG
12259018 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12259058 CAGACCCAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:12259886 original size:24 final size:23
Alignment explanation
Indices: 12259849--12259900 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
12259839 ATAGTACGCA
12259849 CAAAAAAGAAAAAAGATA-AAAT
1 CAAAAAAGAAAAAAGATAGAAAT
*
12259871 CAAAAAAGAAGCAAAAGTTAGAAAT
1 CAAAAAAGAA--AAAAGATAGAAAT
12259896 -AAAAA
1 CAAAAA
12259901 TATCAACCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 10 0.38
24 12 0.46
25 4 0.15
ACGTcount: A:0.73, C:0.06, G:0.12, T:0.10
Consensus pattern (23 bp):
CAAAAAAGAAAAAAGATAGAAAT
Found at i:12259900 original size:25 final size:22
Alignment explanation
Indices: 12259850--12259900 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
12259840 TAGTACGCAC
*
12259850 AAAAAAGAAAAAAGATAAAATC
1 AAAAAAGAAAAAAGATAAAATA
*
12259872 AAAAAAGAAGCAAAAGTTAGAAATA
1 AAAAAAGAA--AAAAGATA-AAATA
12259897 AAAA
1 AAAA
12259901 TATCAACCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.38
24 7 0.29
25 8 0.33
ACGTcount: A:0.75, C:0.04, G:0.12, T:0.10
Consensus pattern (22 bp):
AAAAAAGAAAAAAGATAAAATA
Found at i:12261373 original size:17 final size:18
Alignment explanation
Indices: 12261341--12261376 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
12261331 TTAATAAAGA
12261341 AACCTAAAGTTTTTCTAT
1 AACCTAAAGTTTTTCTAT
*
12261359 AACCTAACG-TTTTCTAT
1 AACCTAAAGTTTTTCTAT
12261376 A
1 A
12261377 GTTCATTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (18 bp):
AACCTAAAGTTTTTCTAT
Found at i:12292409 original size:21 final size:21
Alignment explanation
Indices: 12292380--12292419 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12292370 ACCACTATAA
12292380 CTTTATTTTTAATTAAATATC
1 CTTTATTTTTAATTAAATATC
* **
12292401 CTTTTTTTTTGGTTAAATA
1 CTTTATTTTTAATTAAATA
12292420 AAAATGGTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (21 bp):
CTTTATTTTTAATTAAATATC
Found at i:12299257 original size:47 final size:47
Alignment explanation
Indices: 12299189--12299329 Score: 187
Period size: 47 Copynumber: 3.0 Consensus size: 47
12299179 TTCGTTTTCT
12299189 CGATGCCATAGT-CCA-ACTATGGTCTTACACGGAATCACATATCACAC
1 CGATGCCATA-TCCCAGA-TATGGTCTTACACGGAATCACATATCACAC
* ** * *
12299236 CGATGTCATATCCCAGATATGGTCTTACATAGTAGCACATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTACACGGAATCACATATCACAC
*
12299283 CGATGCCATATCCCAGATATGGTCTTACACGAAAATCACATATCACA
1 CGATGCCATATCCCAGATATGGTCTTACACG-GAATCACATATCACA
12299330 TATTGCCATG
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
46 1 0.01
47 66 0.82
48 13 0.16
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTACACGGAATCACATATCACAC
Found at i:12300645 original size:22 final size:22
Alignment explanation
Indices: 12300602--12300670 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
12300592 TATGCACTAT
* * * *
12300602 TAAACAGAGATCACTAAAGTGC
1 TAAACAAAGAGCACGAATGTGC
*
12300624 TATACAAAGAGCACGAATGTGC
1 TAAACAAAGAGCACGAATGTGC
* *
12300646 TAAACAGAGAGCACTAATGTGC
1 TAAACAAAGAGCACGAATGTGC
12300668 TAA
1 TAA
12300671 TAATCAGAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.19
Consensus pattern (22 bp):
TAAACAAAGAGCACGAATGTGC
Found at i:12300688 original size:19 final size:19
Alignment explanation
Indices: 12300664--12300701 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12300654 GAGCACTAAT
12300664 GTGCTAATAATCAGAGAGC
1 GTGCTAATAATCAGAGAGC
*
12300683 GTGCTAGTAATCAGAGAGC
1 GTGCTAATAATCAGAGAGC
12300702 ACTGACGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (19 bp):
GTGCTAATAATCAGAGAGC
Found at i:12300710 original size:25 final size:25
Alignment explanation
Indices: 12300650--12300778 Score: 189
Period size: 25 Copynumber: 5.4 Consensus size: 25
12300640 ATGTGCTAAA
* *
12300650 CAGAGAGCACTAATGTGCTAATAAT
1 CAGAGAGCACTGACGTGCTAATAAT
*
12300675 C--AGAG-A--G-CGTGCTAGTAAT
1 CAGAGAGCACTGACGTGCTAATAAT
12300694 CAGAGAGCACTGACGTGCTAATAAT
1 CAGAGAGCACTGACGTGCTAATAAT
12300719 CAGAGAGCACTGACGTGCTAATAAT
1 CAGAGAGCACTGACGTGCTAATAAT
12300744 CAGAGAGCACTGACGTGCTAATAAT
1 CAGAGAGCACTGACGTGCTAATAAT
12300769 CAGAGAGCAC
1 CAGAGAGCAC
12300779 GCTAAACTCC
Statistics
Matches: 94, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
19 11 0.12
21 4 0.04
22 2 0.02
23 4 0.04
24 1 0.01
25 72 0.77
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.19
Consensus pattern (25 bp):
CAGAGAGCACTGACGTGCTAATAAT
Found at i:12306026 original size:21 final size:21
Alignment explanation
Indices: 12306000--12306072 Score: 128
Period size: 21 Copynumber: 3.5 Consensus size: 21
12305990 TTGTGCACAG
*
12306000 TATTCACCAAATGGTTCAACA
1 TATTCACCACATGGTTCAACA
*
12306021 TATTCACCACATGATTCAACA
1 TATTCACCACATGGTTCAACA
12306042 TATTCACCACATGGTTCAACA
1 TATTCACCACATGGTTCAACA
12306063 TATTCACCAC
1 TATTCACCAC
12306073 CACGATCACT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (21 bp):
TATTCACCACATGGTTCAACA
Found at i:12312939 original size:21 final size:21
Alignment explanation
Indices: 12312889--12312942 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
12312879 GAAATCTCAG
*
12312889 ACGCCCATGTGGCTAAGGGAC
1 ACGCCCATGTGGCTAAGGCAC
** *
12312910 ACGATCATGTGTCTAAGGCAC
1 ACGCCCATGTGGCTAAGGCAC
*
12312931 ATGCCCATGTGG
1 ACGCCCATGTGG
12312943 AAATTGAAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.26, G:0.30, T:0.20
Consensus pattern (21 bp):
ACGCCCATGTGGCTAAGGCAC
Found at i:12313524 original size:21 final size:21
Alignment explanation
Indices: 12313500--12313556 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
12313490 GTGGAAATCT
*
12313500 CACACGCCCATGTGGCTAAGG
1 CACACGCCCATATGGCTAAGG
* * *
12313521 CACACGGCCGTATGTCTAAGG
1 CACACGCCCATATGGCTAAGG
* *
12313542 CACACGTCCTTATGG
1 CACACGCCCATATGG
12313557 AAATCGACAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (21 bp):
CACACGCCCATATGGCTAAGG
Found at i:12316149 original size:13 final size:13
Alignment explanation
Indices: 12316133--12316166 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
12316123 GGGGGTAGGA
12316133 TTCTGTATATCTG
1 TTCTGTATATCTG
*
12316146 TTCTGCATATCTG
1 TTCTGTATATCTG
12316159 TATCTGTA
1 T-TCTGTA
12316167 AAGGATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.50
Consensus pattern (13 bp):
TTCTGTATATCTG
Found at i:12321437 original size:11 final size:11
Alignment explanation
Indices: 12321420--12321457 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
12321410 TTTTTAATCA
12321420 AATATATATTT
1 AATATATATTT
* *
12321431 TATATATATTA
1 AATATATATTT
12321442 AATATATATTT
1 AATATATATTT
12321453 AATAT
1 AATAT
12321458 GGGCCGGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATATATATTT
Found at i:12322379 original size:93 final size:94
Alignment explanation
Indices: 12322268--12322461 Score: 372
Period size: 93 Copynumber: 2.1 Consensus size: 94
12322258 TTGTGTTAAT
12322268 AATATTTTGTATTATTTTTTTATTATCTAAGTATAATTTTTAAATTAAAATTATCTTTTAATTGT
1 AATATTTTGTATTATTTTTTTATTATCTAAGTATAATTTTTAAATTAAAATTATCTTTTAATTGT
12322333 TTAATTTATTGCAAAATATAATTTATTTA
66 TTAATTTATTGCAAAATATAATTTATTTA
12322362 AATATTTTGT-TTATTTTTTTATTATCTAAGTATAATTTTTAAATTAAAATTATCTTTTAATTGT
1 AATATTTTGTATTATTTTTTTATTATCTAAGTATAATTTTTAAATTAAAATTATCTTTTAATTGT
*
12322426 TTAATTTATTGCAAAATATAATTTATTTT
66 TTAATTTATTGCAAAATATAATTTATTTA
12322455 AATATTT
1 AATATTT
12322462 ATATAATATA
Statistics
Matches: 99, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
93 89 0.90
94 10 0.10
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (94 bp):
AATATTTTGTATTATTTTTTTATTATCTAAGTATAATTTTTAAATTAAAATTATCTTTTAATTGT
TTAATTTATTGCAAAATATAATTTATTTA
Found at i:12322855 original size:19 final size:19
Alignment explanation
Indices: 12322831--12322884 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
12322821 AATCTTCAAG
*
12322831 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAC
*
12322850 GATATGTAATCTTAGATAC
1 GATATGCAATCTTAGATAC
12322869 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
12322885 AAATATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAC
Found at i:12322875 original size:38 final size:40
Alignment explanation
Indices: 12322831--12322907 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
12322821 AATCTTCAAG
12322831 GATATGCAATCTTAG-ATATGA-TATGTAATCTTAGATAC
1 GATATGCAATCTTAGAATATGATTATGTAATCTTAGATAC
*
12322869 GATATGCAATCTTAGAAAATATGATTTTGTAATCTTAGA
1 GATATGCAATCTTAG--AATATGATTATGTAATCTTAGA
12322908 GATTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 15 0.44
41 6 0.18
42 13 0.38
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (40 bp):
GATATGCAATCTTAGAATATGATTATGTAATCTTAGATAC
Found at i:12324936 original size:24 final size:24
Alignment explanation
Indices: 12324899--12324951 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
12324889 TAGTACTAAA
* * *
12324899 TTGCGGTTGCGGTGTCTGTCGCGG
1 TTGCGATTGCGGTGTCTATCGCAG
*
12324923 TTGCGATTGTGGTGTCTATCGCAG
1 TTGCGATTGCGGTGTCTATCGCAG
12324947 TTGCG
1 TTGCG
12324952 GATGATGCGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.06, C:0.19, G:0.40, T:0.36
Consensus pattern (24 bp):
TTGCGATTGCGGTGTCTATCGCAG
Found at i:12325371 original size:168 final size:169
Alignment explanation
Indices: 12325173--12325509 Score: 631
Period size: 168 Copynumber: 2.0 Consensus size: 169
12325163 AAATATTATC
*
12325173 ATACTAAATAATTGATAATAACAACCATAATTTTAATGAGTAACATATAAATAGTCTCATATTAG
1 ATACTAAATAATTGATAATAACAACCATAATTTTAATGAGTAACATATAAATAGTCTCACATTAG
12325238 AAAAAGCATATAAATATTCTCACATTTTAACATGAAAAAGTTCATGTTACATAACTTAAAAAATA
66 AAAAAGCATATAAATATTCTCACATTTTAACATGAAAAAGTTCATGTTACATAACTTAAAAAATA
*
12325303 CATAAATACAAATATGGAAACTTCATTTCTTACAATTCA
131 CATAAATACAAATATGAAAACTTCATTTCTTACAATTCA
*
12325342 ATACTAAAT-ATTGATAATAACATCCATAATTTTAATGAGTAACATATAAATAGTCTCACATTAG
1 ATACTAAATAATTGATAATAACAACCATAATTTTAATGAGTAACATATAAATAGTCTCACATTAG
*
12325406 AAAAAGCATATAAATATTCTCACATTTTAACATGAAAAAGTTCATTTTACATAACTTAAAAAATA
66 AAAAAGCATATAAATATTCTCACATTTTAACATGAAAAAGTTCATGTTACATAACTTAAAAAATA
12325471 CATAAATACAAATATGAAAACTTCATTTCTTACAATTCA
131 CATAAATACAAATATGAAAACTTCATTTCTTACAATTCA
12325510 CCACCAAATT
Statistics
Matches: 164, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
168 155 0.95
169 9 0.05
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (169 bp):
ATACTAAATAATTGATAATAACAACCATAATTTTAATGAGTAACATATAAATAGTCTCACATTAG
AAAAAGCATATAAATATTCTCACATTTTAACATGAAAAAGTTCATGTTACATAACTTAAAAAATA
CATAAATACAAATATGAAAACTTCATTTCTTACAATTCA
Found at i:12327447 original size:15 final size:15
Alignment explanation
Indices: 12327427--12327456 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12327417 TTTTGGTGAT
*
12327427 TTTTCAAAGTCACAC
1 TTTTCAAAGACACAC
12327442 TTTTCAAAGACACAC
1 TTTTCAAAGACACAC
12327457 AACTGTTGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
TTTTCAAAGACACAC
Found at i:12327568 original size:25 final size:26
Alignment explanation
Indices: 12327511--12327561 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
12327501 ATAATTTCAC
*
12327511 TTTTTCACTATCTCAGTTCCATTGAA
1 TTTTTCACTATCTCAGTTCCAATGAA
12327537 TTTTTCAC-ATCTCA-TTCCAAT-AA
1 TTTTTCACTATCTCAGTTCCAATGAA
12327560 TT
1 TT
12327562 CATTTCAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 6 0.25
25 6 0.25
26 8 0.33
ACGTcount: A:0.25, C:0.24, G:0.04, T:0.47
Consensus pattern (26 bp):
TTTTTCACTATCTCAGTTCCAATGAA
Found at i:12327838 original size:51 final size:50
Alignment explanation
Indices: 12327778--12327920 Score: 198
Period size: 50 Copynumber: 2.8 Consensus size: 50
12327768 ATACCCGATT
*
12327778 CACATAGTAGCCTGCACATAGTACTACACACGTGATCGAAGC-TATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCAAGCAT-TCCGGTA
* * * * *
12327829 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAGCATTCCGGTA
*
12327879 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAGCA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAGCA
12327921 ACTTCACTCG
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
50 46 0.58
51 33 0.42
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAGCATTCCGGTA
Found at i:12332564 original size:124 final size:123
Alignment explanation
Indices: 12332422--12332719 Score: 426
Period size: 124 Copynumber: 2.4 Consensus size: 123
12332412 TCATACTCAA
* *
12332422 TTTTTTCTCTTTATTTGTTGAATTATTGTACCAAAAGATTCTATCGTAGTTTT-CTATTTCTATC
1 TTTTTTC-CTTTATTTGTTGAATAATTGTACCAAAAGATTCTATCGTAGTTTTCCAATTT-TATC
* *
12332486 AAATACTTCAAAACAAAATTTACAC-AGTTTACTTTAGCCCTTTACTTACATTTTA-CCCT
64 AAACACTTCAAAACAAAATTTACACTA-TTTACTTTAGCCCTTTACTTACATATTACCCCT
* *
12332545 TTTTTTCCCCTTTATTTGTTGAATAATTGTACCAAAAGATTCTATCGCAGTTTTCCAATTTTTTC
1 TTTTTT--CCTTTATTTGTTGAATAATTGTACCAAAAGATTCTATCGTAGTTTTCCAATTTTATC
*
12332610 AAACACTTCAAAACAAAATTTACACTATTTACTTTAGTCCTTTACTTACATATTACCCCT
64 AAACACTTCAAAACAAAATTTACACTATTTACTTTAGCCCTTTACTTACATATTACCCCT
* * *
12332670 TTTTTT--TGTATTTGTTGAATGATTGTACTAAAAGATTCTATCGTAGTTTT
1 TTTTTTCCTTTATTTGTTGAATAATTGTACCAAAAGATTCTATCGTAGTTTT
12332720 TCAAACACTT
Statistics
Matches: 159, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
121 40 0.25
123 6 0.04
124 96 0.60
125 17 0.11
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (123 bp):
TTTTTTCCTTTATTTGTTGAATAATTGTACCAAAAGATTCTATCGTAGTTTTCCAATTTTATCAA
ACACTTCAAAACAAAATTTACACTATTTACTTTAGCCCTTTACTTACATATTACCCCT
Found at i:12333710 original size:2 final size:2
Alignment explanation
Indices: 12333705--12333751 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
12333695 CATATATAAT
12333705 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12333747 AC AC A
1 AC AC A
12333752 TATATAGGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12349153 original size:40 final size:41
Alignment explanation
Indices: 12349107--12349189 Score: 141
Period size: 40 Copynumber: 2.0 Consensus size: 41
12349097 TAACGAAATT
*
12349107 AATCTTTTAAACAGCTGCATATATTTTTAGAAAATTTG-CC
1 AATCTTTTAAACAACTGCATATATTTTTAGAAAATTTGTCC
*
12349147 AATCTTTTAAAGAACTGCATATATTTTTAGAAAATTTGTCC
1 AATCTTTTAAACAACTGCATATATTTTTAGAAAATTTGTCC
12349188 AA
1 AA
12349190 CATAATAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (41 bp):
AATCTTTTAAACAACTGCATATATTTTTAGAAAATTTGTCC
Found at i:12350132 original size:21 final size:22
Alignment explanation
Indices: 12350107--12350150 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
12350097 CACTCTTCCT
12350107 TTTCTTCATCGATTATTGCAGG
1 TTTCTTCATCGATTATTGCAGG
12350129 TTCTTCTTCATCGATTATTGCA
1 -T-TTCTTCATCGATTATTGCA
12350151 CTGTTCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.48
Consensus pattern (22 bp):
TTTCTTCATCGATTATTGCAGG
Found at i:12350165 original size:24 final size:24
Alignment explanation
Indices: 12350114--12350168 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
12350104 CCTTTTCTTC
* *
12350114 ATCGATTATTGCAGGTTCTTCTTC
1 ATCGATTATTGCAGGTTCTACTTA
*
12350138 ATCGATTATTGCACTGTTC-ACTTA
1 ATCGATTATTGCA-GGTTCTACTTA
12350162 ATCGATT
1 ATCGATT
12350169 TCCCTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.44
Consensus pattern (24 bp):
ATCGATTATTGCAGGTTCTACTTA
Found at i:12351560 original size:16 final size:15
Alignment explanation
Indices: 12351528--12351571 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12351518 GTGTTCGATT
* *
12351528 TTATTTACTTATTTA
1 TTATTTATTTTTTTA
12351543 TTATTTAGTTTTTTTA
1 TTATTTA-TTTTTTTA
*
12351559 TTTTTTATTTTTT
1 TTATTTATTTTTT
12351572 CTCTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (15 bp):
TTATTTATTTTTTTA
Found at i:12352915 original size:16 final size:15
Alignment explanation
Indices: 12352883--12352926 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12352873 GTGTTCGATT
* *
12352883 TTATTTACTTATTTA
1 TTATTTATTTTTTTA
12352898 TTATTTAGTTTTTTTA
1 TTATTTA-TTTTTTTA
*
12352914 TTTTTTATTTTTT
1 TTATTTATTTTTT
12352927 CTCTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (15 bp):
TTATTTATTTTTTTA
Found at i:12353843 original size:34 final size:34
Alignment explanation
Indices: 12353801--12353886 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
12353791 TATTTTTATC
*
12353801 TTAT-TTTCATAATTTTCACATACATATATATTT
1 TTATATTTCATAATTTTAACATACATATATATTT
* * * *
12353834 TTATATTTCATGATTTAAACATGCATGTATATTT
1 TTATATTTCATAATTTTAACATACATATATATTT
* *
12353868 TTTTATGTTTATAATTTTA
1 TTATAT-TTCATAATTTTA
12353887 TTCATTTTCT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
33 4 0.10
34 29 0.69
35 9 0.21
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (34 bp):
TTATATTTCATAATTTTAACATACATATATATTT
Found at i:12355913 original size:277 final size:276
Alignment explanation
Indices: 12355419--12355972 Score: 1009
Period size: 277 Copynumber: 2.0 Consensus size: 276
12355409 TAAATAGAGA
*
12355419 GCTTGTCATAAGAAAATGAGTTTCTTGATAAAGTAGATGACAATATGGTTGTCCGAATATGTTCC
1 GCTTGTCATAAGAAAATGAGTTTCTTGATAAAGTAGATGACAATATGGTTGTCCGAATATGGTCC
* * *
12355484 AAGAACAAATGATAAGAGAATGATTATAATTTAATGGAGGGCTACACGACTATGGCTCCGTTGCC
66 AAGAACAAATGATAAGAGAAGGATGATAATTTAATGGAGGACTACACGACTATGGCTCCGTTGCC
12355549 CAAGGATTCAAGATGGCAAAGATTATTCGAGAGCTGCTGAACCTTCTTAAAGAGAAGCCAACGAG
131 CAAGGATTCAAGATGGCAAAGATTATTCGAGAGCTGCTGAACCTTCTTAAAGAGAAGCCAACGAG
12355614 TATCACGAGGATGAGTGAGCAACAAGTTACGACCTGGATCGAGCAAAAAGGAGATAGAAGAGATG
196 TATCACGAGGATGAGTGAGCAACAAGTTACGACCTGGATCGAGCAAAAAGGAGATAGAAGAGATG
*
12355679 TTTTTTTTAAAGAGTTC
261 -GTTTTTTAAAGAGTTC
* *
12355696 GCTTGTCATAAGAAAATGGGTTTCTTGATAAAGTGGATGACAATATGGTTGTCCGAATATGGTCC
1 GCTTGTCATAAGAAAATGAGTTTCTTGATAAAGTAGATGACAATATGGTTGTCCGAATATGGTCC
* *
12355761 AAGAACACATGATAAGGGAAGGATGATAATTTAATGGAGGACTACACGACTATGGCTCCGTTGCC
66 AAGAACAAATGATAAGAGAAGGATGATAATTTAATGGAGGACTACACGACTATGGCTCCGTTGCC
12355826 CAAGGATTCAAGATGGCAAAGATTATTCGAGAGCTGCTGAACCTTCTTAAAGAGAAGCCAACGAG
131 CAAGGATTCAAGATGGCAAAGATTATTCGAGAGCTGCTGAACCTTCTTAAAGAGAAGCCAACGAG
12355891 TATCACGAGGATGAGTGAGCAACAAGTTACGACCTGGATCGAGCAAAAAGGAGATAGAAGAGATG
196 TATCACGAGGATGAGTGAGCAACAAGTTACGACCTGGATCGAGCAAAAAGGAGATAGAAGAGATG
*
12355956 GTTTTTTGAAGAGTTC
261 GTTTTTTAAAGAGTTC
12355972 G
1 G
12355973 TGAGATTTAT
Statistics
Matches: 267, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
276 15 0.06
277 252 0.94
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.25
Consensus pattern (276 bp):
GCTTGTCATAAGAAAATGAGTTTCTTGATAAAGTAGATGACAATATGGTTGTCCGAATATGGTCC
AAGAACAAATGATAAGAGAAGGATGATAATTTAATGGAGGACTACACGACTATGGCTCCGTTGCC
CAAGGATTCAAGATGGCAAAGATTATTCGAGAGCTGCTGAACCTTCTTAAAGAGAAGCCAACGAG
TATCACGAGGATGAGTGAGCAACAAGTTACGACCTGGATCGAGCAAAAAGGAGATAGAAGAGATG
GTTTTTTAAAGAGTTC
Found at i:12360446 original size:88 final size:88
Alignment explanation
Indices: 12360297--12361080 Score: 985
Period size: 88 Copynumber: 8.9 Consensus size: 88
12360287 TAAATCACAA
* * *
12360297 AGCCTTGTCTCCCTGGGTCGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACCGA
* *
12360362 CAGCGAAACAGATCAAAGATACC
66 CAGCGAAGCAGATCGAAGATACC
** *
12360385 AGCCTTGCCTCCCTGGGTCATAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACCGA
12360450 CAGCGAAGCAGATCGAAGATACC
66 CAGCGAAGCAGATCGAAGATACC
** * * * * *
12360473 AGCCTTGCCTCATTGGGTTGTAGTGGAGCAGGTTGAAGACAGTAGATTTTGCCTTACTGCATCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACCGA
* * * * *
12360538 TAGCGAAGCAAACCGAATATATC
66 CAGCGAAGCAGATCGAAGATACC
* * *
12360561 AGCTTTGCCTCCCTGGGTCGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACCGA
*
12360626 CAGCGAAACAGATCGAAGATACC
66 CAGCGAAGCAGATCGAAGATACC
* *
12360649 AGCCTTGCCTCTCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACCGA
* * *
12360714 TAGTGAAGTAGATCGAAGATACC
66 CAGCGAAGCAGATCGAAGATACC
* * * * * *
12360737 AGCCTTGCCTCCCTGGGTTGCAGGGGAGCAAGTTGAAGATAACAGATCTTGACTTCCTGTACCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACCGA
* * *
12360802 GAGAGAAGCAGATCGAAGACACC
66 CAGCGAAGCAGATCGAAGATACC
** ** * * * * *
12360825 AGCCTTGCCTCCCTGGGTTACAACGGAGCAGGTTAAAAATAGTAGATCTTGCTTTCCTGCACTGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACCGA
*
12360890 CAGCGAAGCAGATCGAAGACACC
66 CAGCGAAGCAGATCGAAGATACC
* * * ** *
12360913 ATCCTTGCCTCCCTAGGTTGCAGCAGAGCAGGTT-AAAACTAGCAGATCTTGCCTTCCTGCACCG
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGA-TAGCAGATCTTGCCTTCCTGCACCG
* *
12360977 ACAGCGAAGCAAATCGAAGACACC
65 ACAGCGAAGCAGATCGAAGATACC
* * * *
12361001 AGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAAAATAGCAGATCTTGCCTTCCTGCACC
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTT--GAAGATAGCAGATCTTGCCTTCCTGCACC
*
12361066 GACAGCGAAACAGAT
64 GACAGCGAAGCAGAT
12361081 TAATGACCCG
Statistics
Matches: 614, Mismatches: 78, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
87 4 0.01
88 569 0.93
90 37 0.06
91 4 0.01
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (88 bp):
AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACCGA
CAGCGAAGCAGATCGAAGATACC
Found at i:12360511 original size:43 final size:42
Alignment explanation
Indices: 12360297--12360777 Score: 188
Period size: 44 Copynumber: 11.0 Consensus size: 42
12360287 TAAATCACAA
* *
12360297 AGCCTTGTCTCCCTGGGTCGTAGTGGAGCAGGTTGAAGATAGC
1 AGCCTTGCCT-CCTGGGTCGTAGTGGAGCAGGTTGAAGATACC
* ** * * * * * **
12360340 AGATCTTGCCTTCCTGCATCGACAGCGAAACAGATCAAAGATACC
1 AG-CCTTGCC-TCCTGGGTCG-TAGTGGAGCAGGTTGAAGATACC
* *
12360385 AGCCTTGCCTCCCTGGGTCATAGTGGAGCAGGTTGAAGATAGC
1 AGCCTTGCCT-CCTGGGTCGTAGTGGAGCAGGTTGAAGATACC
* ** * * * * *
12360428 AGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATACC
1 AG-CCTTGCC-TCCTGGGTCG-TAGTGGAGCAGGTTGAAGATACC
* * * **
12360473 AGCCTTGCCTCATTGGGTTGTAGTGGAGCAGGTTGAAGACAGT
1 AGCCTTGCCTC-CTGGGTCGTAGTGGAGCAGGTTGAAGATACC
** * ** * * **** * *
12360516 AGATTTTGCCTTACTGCATCGATAGCGAAGCAAACCGAATATATC
1 AG-CCTTGCC-TCCTGGGTCG-TAGTGGAGCAGGTTGAAGATACC
* *
12360561 AGCTTTGCCTCCCTGGGTCGTAGTGGAGCAGGTTGAAGATAGC
1 AGCCTTGCCT-CCTGGGTCGTAGTGGAGCAGGTTGAAGATACC
* ** * * * * * *
12360604 AGATCTTGCCTTCCTGCATCGACAGCGAAACAGATCGAAGATACC
1 AG-CCTTGCC-TCCTGGGTCG-TAGTGGAGCAGGTTGAAGATACC
* *
12360649 AGCCTTGCCTCTCTGGGTTGTAGTGGAGCAGGTTGAAGATAGC
1 AGCCTTGCCTC-CTGGGTCGTAGTGGAGCAGGTTGAAGATACC
* *** * * * *
12360692 AGATCTTGCCTTCCTGTACCGATAGTGAAGTAGATCGAAGATACC
1 AG-CCTTGCC-TCCTGGGTCG-TAGTGGAGCAGGTTGAAGATACC
* * * *
12360737 AGCCTTGCCTCCCTGGGTTGCAGGGGAGCAAGTTGAAGATA
1 AGCCTTGCCT-CCTGGGTCGTAGTGGAGCAGGTTGAAGATA
12360778 ACAGATCTTG
Statistics
Matches: 298, Mismatches: 120, Indels: 40
0.65 0.26 0.09
Matches are distributed among these distances:
43 92 0.31
44 111 0.37
45 95 0.32
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (42 bp):
AGCCTTGCCTCCTGGGTCGTAGTGGAGCAGGTTGAAGATACC
Found at i:12361321 original size:43 final size:44
Alignment explanation
Indices: 12361096--12361323 Score: 185
Period size: 44 Copynumber: 5.2 Consensus size: 44
12361086 ACCCGAGCCC
* *
12361096 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATCT
* * * * * *
12361140 TATCTCCCCGGTCAGCAGTGGAGTAGGTTAAAAATT-ACAGATTT
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGA-ATCT
* * * ** * * **** **
12361184 TATCTCTCTAAGT-AGTAGTGGAGCAGATCGAAG-TCCCCAGCCT
1 TATCTCCCT-GGTCAGCAGTGGAATAGGTTGAAGATTGAGAATCT
* *
12361227 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATCT
*
12361271 TATCTCCCTGGTCAGTAGTGGAATA-GTTGAAGATTGAGAATCT
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATCT
*
12361314 TACCTCCCTG
1 TATCTCCCTG
12361324 AAGTTGCAGT
Statistics
Matches: 139, Mismatches: 40, Indels: 11
0.73 0.21 0.06
Matches are distributed among these distances:
42 2 0.01
43 51 0.37
44 84 0.60
45 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATCT
Found at i:12361367 original size:131 final size:130
Alignment explanation
Indices: 12361094--12361334 Score: 324
Period size: 131 Copynumber: 1.8 Consensus size: 130
12361084 TGACCCGAGC
12361094 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCCGGTCAGCAGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCCGGTCAGCAGT
* * * * * * *
12361159 GGAGTAGGTTAAAAATTACAGATTTTATCTCTCTAAGTAGTAGTGGAGCAGATCGAAGTCCCCAG
66 GGAATAGGTTAAAAATTACAGATCTTACCTCCCTAAGTAGCAGTGGAGCAGATCGAAGGCCCAAG
* *
12361224 CCTTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTGGTCAGTAG
1 CC-TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCCGGTCAGCAG
* * * *
12361289 TGGAATA-GTTGAAGATT-GAGAATCTTACCTCCCTGAAGTTGCAGTG
65 TGGAATAGGTTAAAAATTACAG-ATCTTACCTCCCT-AAGTAGCAGTG
12361335 TAGTAGATTA
Statistics
Matches: 97, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
129 2 0.02
130 20 0.21
131 75 0.77
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (130 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCCGGTCAGCAGT
GGAATAGGTTAAAAATTACAGATCTTACCTCCCTAAGTAGCAGTGGAGCAGATCGAAGGCCCAAG
Found at i:12362233 original size:16 final size:15
Alignment explanation
Indices: 12362201--12362244 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12362191 GTGTTCGATT
* *
12362201 TTATTTACTTATTTA
1 TTATTTATTTTTTTA
12362216 TTATTTAGTTTTTTTA
1 TTATTTA-TTTTTTTA
*
12362232 TTTTTTATTTTTT
1 TTATTTATTTTTT
12362245 CTCTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (15 bp):
TTATTTATTTTTTTA
Found at i:12362987 original size:3 final size:3
Alignment explanation
Indices: 12362979--12363030 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
12362969 GTTAACATTG
* * * *
12362979 TTA TTA TTA TTT TTA TGA TTA TTG TTA TTG TTA -TA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
12363024 TTA TTA T
1 TTA TTA T
12363031 ATCTACATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:12363002 original size:24 final size:24
Alignment explanation
Indices: 12362975--12363030 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
12362965 TTTTGTTAAC
*
12362975 ATTGTTATTATTAT-TTTTATGATT
1 ATTGTTATTATTATATTATAT-ATT
*
12362999 ATTGTTATTGTTATATTATATATT
1 ATTGTTATTATTATATTATATATT
*
12363023 ATTATTAT
1 ATTGTTAT
12363031 ATCTACATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (24 bp):
ATTGTTATTATTATATTATATATT
Found at i:12363024 original size:18 final size:17
Alignment explanation
Indices: 12362979--12363032 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
12362969 GTTAACATTG
*
12362979 TTATTATTATTTTTATGA
1 TTATTATTATTATTAT-A
* *
12362997 TTATTGTTATTGTTATA
1 TTATTATTATTATTATA
12363014 TTATATATTATTATTATA
1 TTAT-TATTATTATTATA
12363032 T
1 T
12363033 CTACATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 5 0.16
18 26 0.84
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TTATTATTATTATTATA
Found at i:12363165 original size:34 final size:34
Alignment explanation
Indices: 12363123--12363208 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
12363113 TATTTTTATC
*
12363123 TTAT-TTTCATAATTTTCACATACATATATATTT
1 TTATATTTCATAATTTTAACATACATATATATTT
* * * *
12363156 TTATATTTCATGATTTAAACATGCATGTATATTT
1 TTATATTTCATAATTTTAACATACATATATATTT
* *
12363190 TTTTATGTTTATAATTTTA
1 TTATAT-TTCATAATTTTA
12363209 TTCATTTTCT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
33 4 0.10
34 29 0.69
35 9 0.21
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (34 bp):
TTATATTTCATAATTTTAACATACATATATATTT
Found at i:12364578 original size:22 final size:22
Alignment explanation
Indices: 12364537--12364625 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 22
12364527 TTCAATGAAA
12364537 CTGGAAATTG--TTGCATTTGTT
1 CTGGAAATTGTTTTG-ATTTGTT
* *
12364558 -TTGATATTGTTCTTGATTTGTT
1 CTGGAAATTGTT-TTGATTTGTT
*
12364580 CTGGAAATTGTTTTGA-TAGTCT
1 CTGGAAATTGTTTTGATTTGT-T
12364602 GCTGGAAATTGTTCTTGATTTGTT
1 -CTGGAAATTGTT-TTGATTTGTT
12364626 AGTGAGTAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
20 7 0.13
21 3 0.06
22 12 0.22
23 24 0.44
24 5 0.09
25 3 0.06
ACGTcount: A:0.18, C:0.08, G:0.22, T:0.52
Consensus pattern (22 bp):
CTGGAAATTGTTTTGATTTGTT
Found at i:12364717 original size:107 final size:107
Alignment explanation
Indices: 12364531--12364760 Score: 415
Period size: 107 Copynumber: 2.1 Consensus size: 107
12364521 GCTATTTTCA
*
12364531 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
1 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTAA
* *
12364596 TAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTGAGTAGAAG
66 TAATCTGCTGGAAATTGTCCTTGATTTGTTAGTGAGTAGAAG
*
12364638 ATGAAACTGGAAATTGTTGCATTTGTTTTTATATTGTTCTTGATTTGTTCTGGAAATTGTTTTAA
1 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTAA
12364703 TAATCTGCTGGAAATTGTCCTTGATTTGTTAGTGAGTAGAAG
66 TAATCTGCTGGAAATTGTCCTTGATTTGTTAGTGAGTAGAAG
*
12364745 ATGAAAGTGGAAATTG
1 ATGAAACTGGAAATTG
12364761 CAAGTATAGT
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 118 1.00
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.44
Consensus pattern (107 bp):
ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTAA
TAATCTGCTGGAAATTGTCCTTGATTTGTTAGTGAGTAGAAG
Found at i:12369164 original size:18 final size:17
Alignment explanation
Indices: 12369136--12369170 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12369126 NNTATTAAGA
*
12369136 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12369153 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12369171 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:12369405 original size:16 final size:16
Alignment explanation
Indices: 12369384--12369416 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12369374 TTGATTTGCT
12369384 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
12369400 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
12369416 A
1 A
12369417 ATACAGCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:12375455 original size:16 final size:16
Alignment explanation
Indices: 12375434--12375466 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12375424 GGAGATTCCA
12375434 AACATGTTGCCTTGAT
1 AACATGTTGCCTTGAT
12375450 AACATGTTGCCTTGAT
1 AACATGTTGCCTTGAT
12375466 A
1 A
12375467 CATTTGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (16 bp):
AACATGTTGCCTTGAT
Found at i:12382837 original size:74 final size:75
Alignment explanation
Indices: 12382744--12382892 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 75
12382734 CATATGAATT
12382744 TAGCCTATAAATAGACTCTTTTACAACCTTAGAAACAACACCCATTAGAGATTAGAACTCATAAC
1 TAGCCTATAAATAGACTCTTTTACAACCTTAGAAACAACACCCATTAGAGATTAGAACTCATAAC
12382809 ACATTTAGAG
66 ACATTTAGAG
12382819 TAGCCTAT-AATAGACTCTTTTACAACCTTAGAAACAACACCCATTAGAGATTAGAACTCATAAC
1 TAGCCTATAAATAGACTCTTTTACAACCTTAGAAACAACACCCATTAGAGATTAGAACTCATAAC
12382883 ACATTTAGAG
66 ACATTTAGAG
12382893 AATTTTCTAT
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 66 0.89
75 8 0.11
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (75 bp):
TAGCCTATAAATAGACTCTTTTACAACCTTAGAAACAACACCCATTAGAGATTAGAACTCATAAC
ACATTTAGAG
Found at i:12388364 original size:43 final size:43
Alignment explanation
Indices: 12388298--12388466 Score: 215
Period size: 43 Copynumber: 4.0 Consensus size: 43
12388288 GACTCGTACA
*
12388298 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
12388341 ATGCC-ACTGTCCCAGACAG-GGTCTTACACG-AATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
* * *
12388382 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATA-TCG
12388425 ATGCCAACGTCCCAGACGTGGTCTTACACGATAA-CACATATC
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-TAATCACATATC
12388467 AGAAATCCTA
Statistics
Matches: 109, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
41 28 0.26
42 16 0.15
43 60 0.55
44 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:12388439 original size:84 final size:84
Alignment explanation
Indices: 12388298--12388455 Score: 232
Period size: 84 Copynumber: 1.9 Consensus size: 84
12388288 GACTCGTACA
* * *
12388298 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACTGTCCCAGACAG-GG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCACTGTCCCAGAC-GTGG
12388362 TCTTACACGAATCAAATACG
65 TCTTACACGAATCAAATACG
*
12388382 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCGATGCCAAC-GTCCCAGACGTG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATA-TCGATGCC-ACTGTCCCAGACGTG
12388445 GTCTTACACGA
64 GTCTTACACGA
12388456 TAACACATAT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
83 2 0.03
84 63 0.94
85 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCACTGTCCCAGACGTGGT
CTTACACGAATCAAATACG
Found at i:12393874 original size:51 final size:50
Alignment explanation
Indices: 12393813--12393912 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 50
12393803 AGTCTAGTAT
*
12393813 GTGTACCGGATAGT-TTCGATCACATGTGTAGTACTATGTGCAGGCTACTAC
1 GTGTACCGGATAGTAAT-GATCACATGTGTAGTACTATG-GCAGGCTACTAC
* * * *
12393864 GTGTATCGGATGGTAATGGTCACATGTGTAGTACTCTGGCAGGCTACTA
1 GTGTACCGGATAGTAATGATCACATGTGTAGTACTATGGCAGGCTACTA
12393913 TGTGAACCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 11 0.26
51 31 0.72
52 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (50 bp):
GTGTACCGGATAGTAATGATCACATGTGTAGTACTATGGCAGGCTACTAC
Found at i:12397407 original size:2 final size:2
Alignment explanation
Indices: 12397400--12397439 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
12397390 ACTAACTTTG
12397400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
12397440 GACTTTCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12403231 original size:52 final size:52
Alignment explanation
Indices: 12403169--12403272 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
12403159 ACTGCAATGA
12403169 AACCTATACATTGGTGTTAAAACTGAAGGAATGTTTTTTTTATACTAGTTGG
1 AACCTATACATTGGTGTTAAAACTGAAGGAATGTTTTTTTTATACTAGTTGG
12403221 AACCTATACATTGGTGTTAAAACTGAAGGAATGTTTTTTTTATACTAGTTGG
1 AACCTATACATTGGTGTTAAAACTGAAGGAATGTTTTTTTTATACTAGTTGG
12403273 TTAACAGCTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (52 bp):
AACCTATACATTGGTGTTAAAACTGAAGGAATGTTTTTTTTATACTAGTTGG
Found at i:12406267 original size:36 final size:36
Alignment explanation
Indices: 12406220--12406307 Score: 151
Period size: 36 Copynumber: 2.4 Consensus size: 36
12406210 CGACGAACGA
12406220 GATGGAGTTCCCGAACTCCTCGAAGGTGGTGGTCGC
1 GATGGAGTTCCCGAACTCCTCGAAGGTGGTGGTCGC
*
12406256 GATGGATTTCCCGAACTCCTCGAAGGTGGTGGTCGC
1 GATGGAGTTCCCGAACTCCTCGAAGGTGGTGGTCGC
12406292 GATGGAG-TCCCTGAAC
1 GATGGAGTTCCC-GAAC
12406308 CTCTTGGAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
35 4 0.08
36 45 0.92
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (36 bp):
GATGGAGTTCCCGAACTCCTCGAAGGTGGTGGTCGC
Found at i:12410574 original size:41 final size:41
Alignment explanation
Indices: 12410529--12410695 Score: 334
Period size: 41 Copynumber: 4.1 Consensus size: 41
12410519 ACGACACAAG
12410529 TAAGCTACAATTAAGCTTAGTAAGTTCATAGGCTGAAATGA
1 TAAGCTACAATTAAGCTTAGTAAGTTCATAGGCTGAAATGA
12410570 TAAGCTACAATTAAGCTTAGTAAGTTCATAGGCTGAAATGA
1 TAAGCTACAATTAAGCTTAGTAAGTTCATAGGCTGAAATGA
12410611 TAAGCTACAATTAAGCTTAGTAAGTTCATAGGCTGAAATGA
1 TAAGCTACAATTAAGCTTAGTAAGTTCATAGGCTGAAATGA
12410652 TAAGCTACAATTAAGCTTAGTAAGTTCATAGGCTGAAATGA
1 TAAGCTACAATTAAGCTTAGTAAGTTCATAGGCTGAAATGA
12410693 TAA
1 TAA
12410696 AACATACAAT
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 126 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (41 bp):
TAAGCTACAATTAAGCTTAGTAAGTTCATAGGCTGAAATGA
Found at i:12415043 original size:22 final size:22
Alignment explanation
Indices: 12415007--12415066 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
12414997 GTGCCCACTG
*
12415007 TTAAGCACTTCGGTGCCTATTAT
1 TTAA-CACTTTGGTGCCTATTAT
* * *
12415030 TTAACATTTTGGTGTCTATTGT
1 TTAACACTTTGGTGCCTATTAT
12415052 TTAACACTTTGGTGC
1 TTAACACTTTGGTGC
12415067 TTACTTCTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.45
Consensus pattern (22 bp):
TTAACACTTTGGTGCCTATTAT
Found at i:12415754 original size:32 final size:29
Alignment explanation
Indices: 12415692--12415747 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
12415682 CCTATTTGGA
**
12415692 ATGTGTTTATGATATGTATATAGGAGGTG
1 ATGTGTTTACAATATGTATATAGGAGGTG
12415721 ATGTGTTTACAATATGTATATAGGAGG
1 ATGTGTTTACAATATGTATATAGGAGG
12415748 AGGTGATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.02, G:0.29, T:0.39
Consensus pattern (29 bp):
ATGTGTTTACAATATGTATATAGGAGGTG
Found at i:12440971 original size:20 final size:20
Alignment explanation
Indices: 12440946--12440991 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
12440936 CACATGCCCG
*
12440946 CGTGTGGACAGGCACACATC
1 CGTGTGGACAGGCACACATA
12440966 CGTGTGGACAGGCACACATA
1 CGTGTGGACAGGCACACATA
12440986 CGTGTG
1 CGTGTG
12440992 AAAATCACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.26, G:0.33, T:0.17
Consensus pattern (20 bp):
CGTGTGGACAGGCACACATA
Found at i:12443692 original size:21 final size:18
Alignment explanation
Indices: 12443668--12443721 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 18
12443658 TTTTTATTAC
12443668 AAAATCAAAGTTTTCTTTAAA
1 AAAATCAAAGTTTTC-TT--A
* *
12443689 AAAATCACTACTTTTCTTA
1 AAAATCA-AAGTTTTCTTA
12443708 AAAATCAAAGTTTT
1 AAAATCAAAGTTTT
12443722 ATTTTGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 5 0.18
19 8 0.29
21 9 0.32
22 6 0.21
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.39
Consensus pattern (18 bp):
AAAATCAAAGTTTTCTTA
Found at i:12443977 original size:22 final size:24
Alignment explanation
Indices: 12443944--12443988 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
12443934 TTTATCATAT
*
12443944 TTTTATTTTAAAAA-TCTAAACTA
1 TTTTATTTTAAAAAGTCAAAACTA
12443967 TTTT-TTTTAAAAAGTCAAAACT
1 TTTTATTTTAAAAAGTCAAAACT
12443989 TTTCCTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTTATTTTAAAAAGTCAAAACTA
Found at i:12444278 original size:22 final size:18
Alignment explanation
Indices: 12444234--12444270 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12444224 TTTTCTTTCA
12444234 TTTCATGTATATATATAT
1 TTTCATGTATATATATAT
12444252 TTTCATGTATATATATAT
1 TTTCATGTATATATATAT
12444270 T
1 T
12444271 GTTTTTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTCATGTATATATATAT
Found at i:12444848 original size:42 final size:42
Alignment explanation
Indices: 12444801--12444895 Score: 163
Period size: 42 Copynumber: 2.3 Consensus size: 42
12444791 CTTCATATAC
* *
12444801 AATGCAATGAAAAGTAGATGGACCTTCACACCTGGGCCTCTA
1 AATGCAATGAAAAGTAAATAGACCTTCACACCTGGGCCTCTA
*
12444843 AATGCAATGAAAAGTAAATAGACCTTCACACTTGGGCCTCTA
1 AATGCAATGAAAAGTAAATAGACCTTCACACCTGGGCCTCTA
12444885 AATGCAATGAA
1 AATGCAATGAA
12444896 TGCTTTTCTT
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:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (42 bp):
AATGCAATGAAAAGTAAATAGACCTTCACACCTGGGCCTCTA
Found at i:12452622 original size:101 final size:102
Alignment explanation
Indices: 12452503--12452687 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
12452493 AAAGTGATGG
*
12452503 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCA-A-AATGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAATGAT-GGTCACATGTGTAGT
* *
12452566 ATTATGTGCAGGCTACTATGCGTACCGGATAACTTCGA
65 ACTATGTGCAGGATACTATGCGTACCGGATAACTTCGA
* *
12452604 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAATGATGGTCACATGTGTAGTA
*
12452669 CTATGTGTAGGATACTATG
66 CTATGTGCAGGATACTATG
12452688 TGAACCGGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 39 0.51
102 32 0.42
103 5 0.07
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAATGATGGTCACATGTGTAGTA
CTATGTGCAGGATACTATGCGTACCGGATAACTTCGA
Found at i:12452630 original size:51 final size:49
Alignment explanation
Indices: 12452503--12452685 Score: 154
Period size: 51 Copynumber: 3.6 Consensus size: 49
12452493 AAAGTGATGG
* *
12452503 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAAAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCAAAAT-ATAGA
* * * * * *
12452553 TCGCATGTGTAGTATTATGTGCAGGCTACTATGCGTACCGGATAACT-TCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACC--A-AAATATAGA
* * * *
12452604 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATC-AGATAGTGATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCAAAATA-T-A-GA
* * *
12452655 TCACATGTGTAGTACTATGTGTAGGATACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTA
12452686 TGTGAACCGG
Statistics
Matches: 105, Mismatches: 21, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
47 2 0.02
49 1 0.01
50 34 0.32
51 64 0.61
52 1 0.01
53 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (49 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCAAAATATAGA
Found at i:12452934 original size:16 final size:16
Alignment explanation
Indices: 12452913--12452944 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12452903 TGATTGAAAG
*
12452913 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
12452929 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
12452945 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:12455446 original size:151 final size:153
Alignment explanation
Indices: 12455159--12455446 Score: 463
Period size: 153 Copynumber: 1.9 Consensus size: 153
12455149 AAAATCAATG
* * *
12455159 TTTTCTTTAAAAAAATCACTACTTTTCTTAAAAATCAAAGCTTTATTTCGAAATAGTTCAAAAAT
1 TTTTCTTTAAAAAAATCACTACTTTTCTTAAAAATCAAAACTTTATTTCAAAATAGTTCAAAAAG
*
12455224 ATCAAAACTTTGTTTTAAAAATTTTAAACTTTTCCTTTAAAATGACTAAAAAACATATTTTTATT
66 ATCAAAACTTTGTTTTAAAAATTTTAAAATTTTCCTTTAAAATGACTAAAAAACATATTTTTATT
*
12455289 TTAAAAATCTAACATTTCTCTTT
131 TAAAAAATCTAACATTTCTCTTT
* ** *
12455312 TTTTTTTTAAAAAAATCACTGTTTTTCTTAAAAATCAAAACTTTATTTCAAAATAGTT-GAAAAG
1 TTTTCTTTAAAAAAATCACTACTTTTCTTAAAAATCAAAACTTTATTTCAAAATAGTTCAAAAAG
* *
12455376 ATCAAAACTTTGTTTTAAAAA-TTTAAAATTTTCCTTTAATATGACTAAAAATCATATTTTTATT
66 ATCAAAACTTTGTTTTAAAAATTTTAAAATTTTCCTTTAAAATGACTAAAAAACATATTTTTATT
12455440 TAAAAAA
131 TAAAAAA
12455447 AAATCTAAAC
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
151 46 0.37
152 25 0.20
153 53 0.43
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (153 bp):
TTTTCTTTAAAAAAATCACTACTTTTCTTAAAAATCAAAACTTTATTTCAAAATAGTTCAAAAAG
ATCAAAACTTTGTTTTAAAAATTTTAAAATTTTCCTTTAAAATGACTAAAAAACATATTTTTATT
TAAAAAATCTAACATTTCTCTTT
Found at i:12460441 original size:34 final size:34
Alignment explanation
Indices: 12460375--12460440 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
12460365 TGTTAGTATA
*
12460375 CATTGAAACTAATTTCACATTCCTACGAAAAATT
1 CATTGAAACTAATTTCACATTCCTAAGAAAAATT
*
12460409 CATTGAAACTAATTTCACATTGCTCAAGAAAA
1 CATTGAAACTAATTTCACATTCCT-AAGAAAA
12460441 TCAATAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 23 0.79
35 6 0.21
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (34 bp):
CATTGAAACTAATTTCACATTCCTAAGAAAAATT
Found at i:12467917 original size:12 final size:12
Alignment explanation
Indices: 12467896--12467926 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
12467886 GAGAGCTTTT
*
12467896 TCTCTCTCTCTC
1 TCTCTTTCTCTC
12467908 TCTCTTTCTCTC
1 TCTCTTTCTCTC
12467920 TCTCTTT
1 TCTCTTT
12467927 TTTGATTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (12 bp):
TCTCTTTCTCTC
Found at i:12470340 original size:26 final size:26
Alignment explanation
Indices: 12470304--12470389 Score: 118
Period size: 26 Copynumber: 3.2 Consensus size: 26
12470294 ATTGTACCAA
*
12470304 ATATCATGCTTGACGTGCAAAGAAAG
1 ATATAATGCTTGACGTGCAAAGAAAG
*
12470330 ATATAATGCTTGACGTGTAAAGAAAG
1 ATATAATGCTTGACGTGCAAAGAAAG
* *
12470356 TTATATCATGCTTGACATGCAAAGAAAG
1 --ATATAATGCTTGACGTGCAAAGAAAG
12470384 ATATAA
1 ATATAA
12470390 CAAGTCTGGA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 29 0.56
28 23 0.44
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.27
Consensus pattern (26 bp):
ATATAATGCTTGACGTGCAAAGAAAG
Found at i:12470370 original size:28 final size:27
Alignment explanation
Indices: 12470304--12470388 Score: 118
Period size: 28 Copynumber: 3.1 Consensus size: 27
12470294 ATTGTACCAA
12470304 ATATCATGCTTGACGTGCAAAGAAAG-
1 ATATCATGCTTGACGTGCAAAGAAAGT
* *
12470330 ATATAATGCTTGACGTGTAAAGAAAGTT
1 ATATCATGCTTGACGTGCAAAGAAAG-T
*
12470358 ATATCATGCTTGACATGCAAAGAAAGAT
1 ATATCATGCTTGACGTGCAAAGAAAG-T
12470386 ATA
1 ATA
12470389 ACAAGTCTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
26 24 0.47
28 27 0.53
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (27 bp):
ATATCATGCTTGACGTGCAAAGAAAGT
Found at i:12473935 original size:18 final size:18
Alignment explanation
Indices: 12473912--12473948 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12473902 AGTAAAATTT
12473912 TGAGCTCATAAGGTTGTA
1 TGAGCTCATAAGGTTGTA
12473930 TGAGCTCATAAGGTTGTA
1 TGAGCTCATAAGGTTGTA
12473948 T
1 T
12473949 ACTGACATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (18 bp):
TGAGCTCATAAGGTTGTA
Found at i:12476092 original size:43 final size:43
Alignment explanation
Indices: 12476030--12476125 Score: 140
Period size: 43 Copynumber: 2.3 Consensus size: 43
12476020 TGAGTTTCCA
*
12476030 TTTAACCC-TAATGGGTTTCCGTTCAGCTCTTTTGAGCTTCAG
1 TTTAACCCTTAATGGGTTTCCGTTCAGCTCTTATGAGCTTCAG
* * *
12476072 TTTAACCCTTATTGGGTTTCCGTTCAGCTCTTATGAGGTTCCG
1 TTTAACCCTTAATGGGTTTCCGTTCAGCTCTTATGAGCTTCAG
*
12476115 TTCAACCCTTA
1 TTTAACCCTTA
12476126 CAAGTTTTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 8 0.17
43 40 0.83
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.41
Consensus pattern (43 bp):
TTTAACCCTTAATGGGTTTCCGTTCAGCTCTTATGAGCTTCAG
Found at i:12476111 original size:22 final size:22
Alignment explanation
Indices: 12476043--12476118 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 22
12476033 AACCCTAATG
*
12476043 GGTTTCCGTTCAGCTCTTTTGA
1 GGTTTCCGTTCAGCTCTTATGA
* * * * *
12476065 -GCTTCAGTTTAACCCTTATTG-
1 GGTTTCCGTTCAGCTCTTA-TGA
12476086 GGTTTCCGTTCAGCTCTTATGA
1 GGTTTCCGTTCAGCTCTTATGA
12476108 GG-TTCCGTTCA
1 GGTTTCCGTTCA
12476119 ACCCTTACAA
Statistics
Matches: 40, Mismatches: 11, Indels: 7
0.69 0.19 0.12
Matches are distributed among these distances:
21 23 0.57
22 17 0.43
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (22 bp):
GGTTTCCGTTCAGCTCTTATGA
Found at i:12476125 original size:21 final size:21
Alignment explanation
Indices: 12476018--12476125 Score: 67
Period size: 21 Copynumber: 5.1 Consensus size: 21
12476008 AGTTAACTCA
* * *
12476018 TATGAGTTTCCATTTAACCCT
1 TATGAGGTTCCGTTCAACCCT
* * *
12476039 AATG-GGTTTCCGTTCAGCTCT
1 TATGAGG-TTCCGTTCAACCCT
* * * *
12476060 TTTGAGCTTCAGTTTAACCCT
1 TATGAGGTTCCGTTCAACCCT
* *
12476081 TATTG-GGTTTCCGTTCAGCTCT
1 TA-TGAGG-TTCCGTTCAACCCT
12476103 TATGAGGTTCCGTTCAACCCT
1 TATGAGGTTCCGTTCAACCCT
12476124 TA
1 TA
12476126 CAAGTTTTCT
Statistics
Matches: 61, Mismatches: 21, Indels: 10
0.66 0.23 0.11
Matches are distributed among these distances:
20 1 0.02
21 43 0.70
22 17 0.28
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (21 bp):
TATGAGGTTCCGTTCAACCCT
Found at i:12477206 original size:28 final size:29
Alignment explanation
Indices: 12477116--12477212 Score: 88
Period size: 28 Copynumber: 3.2 Consensus size: 29
12477106 CAACATGCAG
* * *
12477116 AATCAGTCTGGGCCTGAGCCCTATACAGT
1 AATCAGTGTGGGCCTTAGCCCAATACAGT
* *
12477145 ATCAGTATAGTGTGGGCCTTAGCCCATTACAGT
1 A--A-T-CAGTGTGGGCCTTAGCCCAATACAGT
**
12477178 AA-CAGTGTGGGCCTTAGCCCAATGTAGT
1 AATCAGTGTGGGCCTTAGCCCAATACAGT
12477206 AATCAGT
1 AATCAGT
12477213 ACAATGCAGT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
28 24 0.44
29 5 0.09
31 2 0.04
32 1 0.02
33 22 0.41
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.27
Consensus pattern (29 bp):
AATCAGTGTGGGCCTTAGCCCAATACAGT
Found at i:12477564 original size:27 final size:27
Alignment explanation
Indices: 12477543--12477791 Score: 185
Period size: 27 Copynumber: 9.3 Consensus size: 27
12477533 GGGGGTACAA
12477543 CAGTCATTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
* * *
12477570 CGGTCATTTTA-CCTTTGGGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
*
12477596 CAGTCATTTTACCCT-TCAAGGGTATTT
1 CAGTCATTTTACCCTAT-AGGGGTATTT
* *
12477623 CGGTCATTTTACCC-ATCGAGGGTATTT
1 CAGTCATTTTACCCTATAG-GGGTATTT
* *
12477650 CGGTCATTTTACCCT-TCGAGGGTATTT
1 CAGTCATTTTACCCTATAG-GGGTATTT
* *
12477677 CGGTTATTTTACCCT-TCCA-GGGTATTT
1 CAGTCATTTTACCCTAT--AGGGGTATTT
** * **
12477704 TGGTAATTTTACCCT-TCAAAGGTATTT
1 CAGTCATTTTACCCTAT-AGGGGTATTT
* * *
12477731 CGGCCATTTTA-CCTATTGAGGGTATTT
1 CAGTCATTTTACCCTATAG-GGGTATTT
12477758 C-GATCATTTTACCCT-TAGGGGTATTT
1 CAG-TCATTTTACCCTATAGGGGTATTT
*
12477784 CGGTCATT
1 CAGTCATT
12477792 AACCCACAAT
Statistics
Matches: 187, Mismatches: 22, Indels: 27
0.79 0.09 0.11
Matches are distributed among these distances:
26 44 0.24
27 140 0.75
28 3 0.02
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (27 bp):
CAGTCATTTTACCCTATAGGGGTATTT
Found at i:12477663 original size:54 final size:54
Alignment explanation
Indices: 12477545--12477791 Score: 311
Period size: 54 Copynumber: 4.6 Consensus size: 54
12477535 GGGTACAACA
* * * * *
12477545 GTCATTTTACCCTAT-AGGGGTATTTCGGTCATTTTA-CCTTTGGGGGTATTTCA
1 GTCATTTTACCCT-TCAAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCG
12477598 GTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCG
* * * * *
12477652 GTCATTTTACCCTTCGAGGGTATTTCGGTTATTTTACCCTTCCAGGGTATTTTG
1 GTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCG
* * * * *
12477706 GTAATTTTACCCTTCAAAGGTATTTCGGCCATTTTACCTATTGAGGGTATTTCG
1 GTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCG
* *
12477760 ATCATTTTACCCTT-AGGGGTATTTCGGTCATT
1 GTCATTTTACCCTTCAAGGGTATTTCGGTCATT
12477792 AACCCACAAT
Statistics
Matches: 167, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
52 1 0.01
53 48 0.29
54 118 0.71
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.42
Consensus pattern (54 bp):
GTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCG
Found at i:12477713 original size:81 final size:80
Alignment explanation
Indices: 12477548--12477787 Score: 313
Period size: 81 Copynumber: 3.0 Consensus size: 80
12477538 TACAACAGTC
* * *
12477548 ATTTTACCCTATAG-GGGTATTTCGGTCATTTTACCTTTGGGGGTATTTCAGTCATTTTACCCTT
1 ATTTTACCC-ATCGAGGGTATTTCGGTCATTTTACCTTTGAGGGTATTTCGGTCATTTTACCCTT
*
12477612 CAAGGGTATTTCGGTC
65 CAAGGGTATTTCGGTA
* *
12477628 ATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGGTTATTTTACCCTT
1 ATTTTACCCATCGAGGGTATTTCGGTCATTTTA-CCTTTGAGGGTATTTCGGTCATTTTACCCTT
* *
12477693 CCAGGGTATTTTGGTA
65 CAAGGGTATTTCGGTA
* * * * *
12477709 ATTTTACCCTTCAAAGGTATTTCGGCCATTTTACCTATTGAGGGTATTTCGATCATTTTACCCTT
1 ATTTTACCCATCGAGGGTATTTCGGTCATTTTACCT-TTGAGGGTATTTCGGTCATTTTACCCTT
*
12477774 -AGGGGTATTTCGGT
65 CAAGGGTATTTCGGT
12477788 CATTAACCCA
Statistics
Matches: 139, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
79 3 0.02
80 42 0.30
81 94 0.68
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.42
Consensus pattern (80 bp):
ATTTTACCCATCGAGGGTATTTCGGTCATTTTACCTTTGAGGGTATTTCGGTCATTTTACCCTTC
AAGGGTATTTCGGTA
Found at i:12483977 original size:27 final size:27
Alignment explanation
Indices: 12483918--12484155 Score: 223
Period size: 27 Copynumber: 8.9 Consensus size: 27
12483908 GGGTATAACA
*
12483918 GTCATTTTACCCTTTG-GGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
12483944 GTTATTTTACCCTTCAAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
12483971 GTCATTTTACCCTTTGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
12483998 ATCATTTTATCCATCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * * *
12484025 GTCACTTTACACATCAAGGATATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
12484052 GTTATCTTACCCTTTGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
12484079 GTTATTTTA-CCTATTGAGGGTATTTCG
1 GTCATTTTACCCT-TCGAGGGTATTTCG
* * *
12484106 GCCATTTTACCCAT-GAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
12484132 GTTATTTTACCATT-GGGGGTATTT
1 GTCATTTTACCCTTCGAGGGTATTT
12484156 TAGTCATTAG
Statistics
Matches: 173, Mismatches: 36, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
26 46 0.27
27 125 0.72
28 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGGGTATTTCG
Found at i:12484042 original size:81 final size:81
Alignment explanation
Indices: 12483934--12484155 Score: 279
Period size: 81 Copynumber: 2.8 Consensus size: 81
12483924 TTACCCTTTG
* * *
12483934 GGGTATTTCGGTTATTTTACCCTTCAAGGGTATTTTGGTCATTTTACCCTTTGAGGGTATTTCGA
1 GGGTATTTCGGTCATTTTACCCATCAAGGGTATTTTGGTTATTTTACCCTTTGAGGGTATTTCGA
12483999 TCATTTTATCC-ATCGA
66 TCATTTTA-CCTATCGA
* * * * * *
12484015 GGGTATTTCGGTCACTTTACACATCAAGGATATTTCGGTTATCTTACCCTTTGAGGGTATTTCGG
1 GGGTATTTCGGTCATTTTACCCATCAAGGGTATTTTGGTTATTTTACCCTTTGAGGGTATTTCGA
* *
12484080 TTATTTTACCTATTGA
66 TCATTTTACCTATCGA
* * * *
12484096 GGGTATTTCGGCCATTTTACCCAT-GAGGGTATTTTGGTTATTTTA-CCATTGGGGGTATTT
1 GGGTATTTCGGTCATTTTACCCATCAAGGGTATTTTGGTTATTTTACCCTTTGAGGGTATTT
12484156 TAGTCATTAG
Statistics
Matches: 120, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
79 13 0.11
80 19 0.16
81 88 0.73
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (81 bp):
GGGTATTTCGGTCATTTTACCCATCAAGGGTATTTTGGTTATTTTACCCTTTGAGGGTATTTCGA
TCATTTTACCTATCGA
Found at i:12487981 original size:36 final size:36
Alignment explanation
Indices: 12487926--12488025 Score: 94
Period size: 36 Copynumber: 2.7 Consensus size: 36
12487916 TTATCCACTG
* * *
12487926 ATATACTGAAAGAATCTCAACCGAGCAAAATCTACGG
1 ATATACTGAAA-AAGCTCAAACGAGCAAAATCTACGA
* ** *
12487963 A-ATACTGAACAAAGCTCAATCGAGTGAAATCTACTA
1 ATATACTGAA-AAAGCTCAAACGAGCAAAATCTACGA
*
12487999 ATATACTGAGTAAAGCTCAAACGAGCA
1 ATATACTGA-AAAAGCTCAAACGAGCA
12488026 TTATCCATAG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
36 28 0.56
37 22 0.44
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (36 bp):
ATATACTGAAAAAGCTCAAACGAGCAAAATCTACGA
Found at i:12494339 original size:140 final size:141
Alignment explanation
Indices: 12494181--12494462 Score: 557
Period size: 140 Copynumber: 2.0 Consensus size: 141
12494171 AATTTAATTC
12494181 TATTTTCAAACTTCAATTAATTAATTAATTAATTAATAATTCGAAAAATCATAAATTAATTCTCA
1 TATTTTCAAACTTCAATTAATTAATTAATTAATTAATAATTCGAAAAATCATAAATTAATTCTCA
12494246 AGTCATTTCCATAGTGAGAAAATCACATTCATTTTCGAATATTTCTCATTTCTCTAACTTTACCA
66 AGTCATTTCCATAGTGAGAAAATCACATTCATTTTCGAATATTTCTCATTTCTCTAACTTTACCA
12494311 TTTCCATCCAT
131 TTTCCATCCAT
12494322 TATTTTCAAAC-TCAATTAATTAATTAATTAATTAATAATTCGAAAAATCATAAATTAATTCTCA
1 TATTTTCAAACTTCAATTAATTAATTAATTAATTAATAATTCGAAAAATCATAAATTAATTCTCA
12494386 AGTCATTTCCATAGTGAGAAAATCACATTCATTTTCGAATATTTCTCATTTCTCTAACTTTACCA
66 AGTCATTTCCATAGTGAGAAAATCACATTCATTTTCGAATATTTCTCATTTCTCTAACTTTACCA
12494451 TTTCCATCCAT
131 TTTCCATCCAT
12494462 T
1 T
12494463 TATGTTCATT
Statistics
Matches: 141, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
140 130 0.92
141 11 0.08
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (141 bp):
TATTTTCAAACTTCAATTAATTAATTAATTAATTAATAATTCGAAAAATCATAAATTAATTCTCA
AGTCATTTCCATAGTGAGAAAATCACATTCATTTTCGAATATTTCTCATTTCTCTAACTTTACCA
TTTCCATCCAT
Found at i:12497238 original size:27 final size:27
Alignment explanation
Indices: 12497186--12497238 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
12497176 CTCTACTTTC
*
12497186 AACCAACTCCTCGTTTTATCCATCCAA
1 AACCAACTCCTCGTTTTAGCCATCCAA
12497213 AACCAACCTCCTCGTTTTAGCC-TCCA
1 AACCAA-CTCCTCGTTTTAGCCATCCA
12497239 CACTTCCCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.26, C:0.40, G:0.06, T:0.28
Consensus pattern (27 bp):
AACCAACTCCTCGTTTTAGCCATCCAA
Found at i:12502343 original size:12 final size:14
Alignment explanation
Indices: 12502304--12502339 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
12502294 GACTCTATTT
12502304 TAATTATATTAAGA
1 TAATTATATTAAGA
12502318 TAATTAATATTAAGA
1 TAATT-ATATTAAGA
12502333 TAATTAT
1 TAATTAT
12502340 TAAGGATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (14 bp):
TAATTATATTAAGA
Found at i:12509148 original size:20 final size:20
Alignment explanation
Indices: 12509125--12509196 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
12509115 AAATCTTTTT
*
12509125 AAAATATGAAAAAAATAAAA
1 AAAATATGAAAAAAATATAA
** *
12509145 AAAATACCAAAAAATATTTAA
1 AAAATATGAAAAAA-ATATAA
* *
12509166 AAAAT-T-AAAAAATTATTA
1 AAAATATGAAAAAAATATAA
12509184 AAAATATGAAAAA
1 AAAATATGAAAAA
12509197 TAGAAAAGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
18 8 0.20
19 7 0.17
20 17 0.41
21 9 0.22
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (20 bp):
AAAATATGAAAAAAATATAA
Found at i:12512227 original size:23 final size:23
Alignment explanation
Indices: 12512201--12512247 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
12512191 TTATTAGGTG
12512201 ATAAATGTCACACCCCAAAATAT
1 ATAAATGTCACACCCCAAAATAT
** *
12512224 ATAAATGTCATGCCTCAAAATAT
1 ATAAATGTCACACCCCAAAATAT
12512247 A
1 A
12512248 GGAGGTTAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (23 bp):
ATAAATGTCACACCCCAAAATAT
Found at i:12513329 original size:29 final size:29
Alignment explanation
Indices: 12513262--12513329 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 29
12513252 AAATTTATGG
*
12513262 TTTTG-CCCTTATTTTTTAGATTTTAAAA
1 TTTTGTCCCCTATTTTTTAGATTTTAAAA
*
12513290 TTTT-TCCCCTATTTTTTAGATTTTATAA
1 TTTTGTCCCCTATTTTTTAGATTTTAAAA
12513318 TTTTGTCCCCTA
1 TTTTGTCCCCTA
12513330 CTTTACAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 29 0.81
29 7 0.19
ACGTcount: A:0.21, C:0.16, G:0.06, T:0.57
Consensus pattern (29 bp):
TTTTGTCCCCTATTTTTTAGATTTTAAAA
Found at i:12515177 original size:20 final size:20
Alignment explanation
Indices: 12515140--12515177 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12515130 TATATACTTT
*
12515140 ATAATTTTATTCTATTTTTA
1 ATAATTTTATACTATTTTTA
12515160 ATAATTTTAATACT-TTTT
1 ATAATTTT-ATACTATTTT
12515178 CAATTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
ATAATTTTATACTATTTTTA
Found at i:12518681 original size:47 final size:47
Alignment explanation
Indices: 12518621--12518714 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 47
12518611 CAGTTCAACT
* * * *
12518621 GCAATGTCGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTCC
1 GCAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTAAATCTATTCC
* *
12518668 GCAATGTCAGGGAAGCAAGATTCGCCGTTGTAGTTTAAATCTGTTCC
1 GCAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTAAATCTATTCC
12518715 ACTGCGCTGC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (47 bp):
GCAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTAAATCTATTCC
Found at i:12518742 original size:50 final size:50
Alignment explanation
Indices: 12518607--12519059 Score: 329
Period size: 50 Copynumber: 9.1 Consensus size: 50
12518597 CTGTCATCTC
* * *
12518607 CAATCAGTTCAACTGCAATG-TCGGGG-AAGTAAGATTCGCTGTTGTAGCTT
1 CAATCTGTTCCACTGCAATGCT-GGGGAAAG-AAGATTCGCCGTTGTAGCTT
* * *
12518657 CAATCTATT-C-C-GCAATG-TCAGGG-AAGCAAGATTCGCCGTTGTAGTTT
1 CAATCTGTTCCACTGCAATGCT-GGGGAAAG-AAGATTCGCCGTTGTAGCTT
* ** * * * *
12518704 AAATCTGTTCCACTGCGCTGCTGGGGAAATATGATTCGCCGTTGTGGCCT
1 CAATCTGTTCCACTGCAATGCTGGGGAAAGAAGATTCGCCGTTGTAGCTT
* ** * *
12518754 CAATCTTTTTTATTGCAATGTTGGGGAAAGAAGATTCGCCGTTGTAGCTT
1 CAATCTGTTCCACTGCAATGCTGGGGAAAGAAGATTCGCCGTTGTAGCTT
*** * *
12518804 CAATCTGTTCCACTGC-AT-CACCGGAGAAGTAAGATTCGCCATTGTGGCTT
1 CAATCTGTTCCACTGCAATGCTGGGGA-AAG-AAGATTCGCCGTTGTAGCTT
* ** * * * *
12518854 CAATCTTTTTGATTGCAATGTTGGGGAAAGAAGATTCGCCGTTGCAACTT
1 CAATCTGTTCCACTGCAATGCTGGGGAAAGAAGATTCGCCGTTGTAGCTT
*** *
12518904 CAATCTGTTCCACTGC-AT-CACCGGAGAAGTAAGATTCGCCGTTGTGGCTT
1 CAATCTGTTCCACTGCAATGCTGGGGA-AAG-AAGATTCGCCGTTGTAGCTT
* ** * *
12518954 CAATCTTTTTGATTGCAATGTTGGGGAAAGAAGATTCGCCGTTGTAGCTT
1 CAATCTGTTCCACTGCAATGCTGGGGAAAGAAGATTCGCCGTTGTAGCTT
* * * * *
12519004 CAATCTGTTCCACTGC-ATCGCCGGAG-AAGTAAGATTCGTCATTGTGGCTT
1 CAATCTGTTCCACTGCAAT-GCTGGGGAAAG-AAGATTCGCCGTTGTAGCTT
12519054 CAATCT
1 CAATCT
12519060 TTTTAATTAC
Statistics
Matches: 307, Mismatches: 81, Indels: 30
0.73 0.19 0.07
Matches are distributed among these distances:
47 39 0.13
48 8 0.03
49 16 0.05
50 225 0.73
51 13 0.04
52 6 0.02
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (50 bp):
CAATCTGTTCCACTGCAATGCTGGGGAAAGAAGATTCGCCGTTGTAGCTT
Done.