Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 10 of 328
Found at i:3016460 original size:31 final size:31
Alignment explanation
Indices: 3016402--3016549 Score: 199
Period size: 31 Copynumber: 4.8 Consensus size: 31
3016392 CTTGTCACTT
3016402 GTAGCCGAAGCTACCAC-TTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
3016432 GTAGCCGGAGCTACCATTTTTCATTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * * * *
3016463 GTAGTCGGAGCTACCATTTTTCATTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
3016494 GTAGCAGAAGCTACCACTTTTCACTAATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
3016525 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
3016550 TGTCATTTGT
Statistics
Matches: 104, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
30 15 0.14
31 89 0.86
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:3016628 original size:50 final size:50
Alignment explanation
Indices: 3016525--3016664 Score: 208
Period size: 50 Copynumber: 2.8 Consensus size: 50
3016515 CACTAATCAG
** * * *
3016525 GTAGCCGAAGCTACCACTTTTCACTTGTCATTTGTCCTTGACCAGATAAGT
1 GTAGCCGAAGCTATTACTTATCACTT-TCACTTATCCTTGACCAGATAAGT
* *
3016576 GTAGCCGAAGCTATTACTTATCACTTTTACTTATCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATTACTTATCACTTTCACTTATCCTTGACCAGATAAGT
3016626 GTAGCCGAAGCTATTACTTATCACTTTCACTTATCCTTG
1 GTAGCCGAAGCTATTACTTATCACTTTCACTTATCCTTG
3016665 TTGCCATGGT
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 58 0.72
51 23 0.28
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATTACTTATCACTTTCACTTATCCTTGACCAGATAAGT
Found at i:3018759 original size:24 final size:24
Alignment explanation
Indices: 3018732--3018780 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3018722 GTTCGTTTGG
3018732 TTACAACTCCTAAGTCTTTGAATC
1 TTACAACTCCTAAGTCTTTGAATC
3018756 TTACAACTCCTAAGTCTTTGAATC
1 TTACAACTCCTAAGTCTTTGAATC
3018780 T
1 T
3018781 CAAACTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (24 bp):
TTACAACTCCTAAGTCTTTGAATC
Found at i:3018865 original size:51 final size:51
Alignment explanation
Indices: 3018789--3018911 Score: 185
Period size: 51 Copynumber: 2.4 Consensus size: 51
3018779 CTCAAACTTA
* * *
3018789 CTTCATACTTCATCCGGAATTATTACCTTGTTGCTCTAACTTTAATAAGAG
1 CTTCATATTTCATCCGGAATAATTACCTTGTTGCTCTAACTTTAACAAGAG
* *
3018840 CTTCATATTTCATCCGGAATAATTACTTTGTTGCTCTAGCTTTAACAAGAG
1 CTTCATATTTCATCCGGAATAATTACCTTGTTGCTCTAACTTTAACAAGAG
*
3018891 CTTCATATTTTATCC-GAATAA
1 CTTCATATTTCATCCGGAATAA
3018912 CTTAGTTATG
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
50 6 0.09
51 60 0.91
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.40
Consensus pattern (51 bp):
CTTCATATTTCATCCGGAATAATTACCTTGTTGCTCTAACTTTAACAAGAG
Found at i:3020990 original size:26 final size:26
Alignment explanation
Indices: 3020961--3021044 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
3020951 TGATACAAAT
3020961 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
3020987 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3021013 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3021039 TGATAA
1 TGATAA
3021045 GAATATCATG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3023070 original size:136 final size:137
Alignment explanation
Indices: 3022825--3023110 Score: 529
Period size: 136 Copynumber: 2.1 Consensus size: 137
3022815 GAGTAGTCTC
3022825 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
3022890 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
3022955 ACTGTTA
131 ACTGTTA
*
3022962 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
3023026 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
3023091 ACTGTTA
131 ACTGTTA
**
3023098 CCTGAATGGGCTT
1 CCCAAATGGGCTT
3023111 AGGCCCAATA
Statistics
Matches: 145, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
136 125 0.86
137 20 0.14
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
ACTGTTA
Found at i:3025399 original size:30 final size:29
Alignment explanation
Indices: 3025363--3025455 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 29
3025353 GGTCAAATGG
* * *
3025363 ACTCGAACCGCCTATATCTGTGTGATATGA
1 ACTCGAACCACCTATGTCAG-GTGATATGA
*
3025393 ACTCGAACCACCCATGTCCAGGTGATATGA
1 ACTCGAACCACCTATGT-CAGGTGATATGA
* *
3025423 ACTCGAACCACCTATGTCCGGGTTATATGA
1 ACTCGAACCACCTATGT-CAGGTGATATGA
3025453 ACT
1 ACT
3025456 GCTCTGGGAC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 53 0.96
31 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (29 bp):
ACTCGAACCACCTATGTCAGGTGATATGA
Found at i:3028491 original size:18 final size:18
Alignment explanation
Indices: 3028448--3028495 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
3028438 ATAAAAAAAA
*
3028448 TATATTT-AATATATATT
1 TATATTTAAATTTATATT
*
3028465 T-T-TTAAAATTTATATT
1 TATATTTAAATTTATATT
3028481 TATATTTAAATTTAT
1 TATATTTAAATTTAT
3028496 TAATGGTCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 2 0.08
16 11 0.44
17 2 0.08
18 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATTTAAATTTATATT
Found at i:3028621 original size:21 final size:22
Alignment explanation
Indices: 3028597--3028641 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3028587 TTAAAAAAAG
*
3028597 AATT-TAAAAAGTAATATT-TAA
1 AATTGTAAAAAAT-ATATTATAA
3028618 AATTGTAAAAAATATATTATAA
1 AATTGTAAAAAATATATTATAA
3028640 AA
1 AA
3028642 CATTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (22 bp):
AATTGTAAAAAATATATTATAA
Found at i:3028626 original size:22 final size:21
Alignment explanation
Indices: 3028597--3028667 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 21
3028587 TTAAAAAAAG
*
3028597 AATTTAAAAAGTAATATT-TAA
1 AATTTAAAAAAT-ATATTATAA
3028618 AATTGTAAAAAATATATTATAAA
1 AATT-TAAAAAATATATTAT-AA
* * *
3028641 ACATTTTAAATATACATTATAA
1 A-ATTTAAAAAATATATTATAA
3028663 AATTT
1 AATTT
3028668 TTAAAATTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 13 0.31
22 11 0.26
23 15 0.36
24 3 0.07
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (21 bp):
AATTTAAAAAATATATTATAA
Found at i:3028672 original size:22 final size:22
Alignment explanation
Indices: 3028615--3028686 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 22
3028605 AAGTAATATT
* * *
3028615 TAAAATTGTAAAAAATATATTA
1 TAAAATTTTTAAAAATACATTA
* *
3028637 TAAAACATTTTAAATATACATTA
1 TAAAA-TTTTTAAAAATACATTA
* *
3028660 TAAAATTTTTAAAATTA-ATAA
1 TAAAATTTTTAAAAATACATTA
3028681 TAAAAT
1 TAAAAT
3028687 AAATAAAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
21 9 0.22
22 14 0.35
23 17 0.43
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (22 bp):
TAAAATTTTTAAAAATACATTA
Found at i:3028674 original size:23 final size:22
Alignment explanation
Indices: 3028626--3028686 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
3028616 AAAATTGTAA
*
3028626 AAAATAT-ATTATAAAACATTTT
1 AAAATATAATTATAAAA-TTTTT
3028648 -AAATATACATTATAAAATTTTT
1 AAAATATA-ATTATAAAATTTTT
*
3028670 AAAAT-TAATAATAAAAT
1 AAAATATAATTATAAAAT
3028687 AAATAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 15 0.44
22 6 0.18
23 13 0.38
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATATAATTATAAAATTTTT
Found at i:3028699 original size:17 final size:16
Alignment explanation
Indices: 3028679--3028714 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3028669 TAAAATTAAT
*
3028679 AATAAAATAAATAAAAA
1 AATAAAAT-AAGAAAAA
3028696 AATAAAATAAGAAAAA
1 AATAAAATAAGAAAAA
3028712 AAT
1 AAT
3028715 TTCAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AATAAAATAAGAAAAA
Found at i:3028788 original size:27 final size:28
Alignment explanation
Indices: 3028758--3028821 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 28
3028748 TTTAAAAAAA
* * *
3028758 TATTTAAAATATTATGATTTCTTATAT-
1 TATTTAAAAAATTATAATTTCTTAAATG
*
3028785 TA-TTAAAAAATTATAATTTTTTAAATG
1 TATTTAAAAAATTATAATTTCTTAAATG
3028812 TATTTAAAAA
1 TATTTAAAAA
3028822 TTGTATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 20 0.65
27 4 0.13
28 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (28 bp):
TATTTAAAAAATTATAATTTCTTAAATG
Found at i:3028829 original size:26 final size:26
Alignment explanation
Indices: 3028758--3028823 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
3028748 TTTAAAAAAA
* *
3028758 TATTTAAAATATTATGATTTCTTATAT
1 TATTTAAAA-ATTATAATTTCTTAAAT
* *
3028785 TATTAAAAAATTATAATTTTTTAAAT
1 TATTTAAAAATTATAATTTCTTAAAT
3028811 GTATTTAAAAATT
1 -TATTTAAAAATT
3028824 GTATTTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 14 0.42
27 19 0.58
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (26 bp):
TATTTAAAAATTATAATTTCTTAAAT
Found at i:3029037 original size:18 final size:18
Alignment explanation
Indices: 3028995--3029041 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 18
3028985 TTATAAAGTA
*
3028995 ATATTT-AATATATATTT
1 ATATTTAAATTTATATTT
*
3029012 -T-TTAAAATTTATATTT
1 ATATTTAAATTTATATTT
3029028 ATATTTAAATTTAT
1 ATATTTAAATTTAT
3029042 TAATAGTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 2 0.08
16 11 0.46
17 1 0.04
18 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATTTAAATTTATATTT
Found at i:3029425 original size:18 final size:18
Alignment explanation
Indices: 3029375--3029426 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
3029365 AAATTTTTTA
*
3029375 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
** *
3029393 AAATAAGCAAAATAAATT
1 AAATAAATAATATAAATT
3029411 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
3029427 ACTTAAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:3029452 original size:38 final size:36
Alignment explanation
Indices: 3029380--3029454 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 36
3029370 TTTTAAAATT
* *
3029380 AATAATATAAATTAAATAAGCAAAATAAATTAAGAA
1 AATAATATAAATTAAAAAAGCAAAAAAAATTAAGAA
3029416 AATAATATAAAACTTAAAAAAG-AAAAAAAATCTAAGAA
1 AATAATAT-AAA-TTAAAAAAGCAAAAAAAAT-TAAGAA
3029454 A
1 A
3029455 GAGACAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 8 0.24
37 11 0.32
38 15 0.44
ACGTcount: A:0.69, C:0.04, G:0.05, T:0.21
Consensus pattern (36 bp):
AATAATATAAATTAAAAAAGCAAAAAAAATTAAGAA
Found at i:3029455 original size:18 final size:18
Alignment explanation
Indices: 3029434--3029476 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3029424 AAAACTTAAA
*
3029434 AAAGAAAAAAAATCTAAG
1 AAAGAAAAAAAATATAAG
* *
3029452 AAAGAGACAAAATATAAG
1 AAAGAAAAAAAATATAAG
3029470 AAA-AAAA
1 AAAGAAAA
3029477 GTAAAAAAAG
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.74, C:0.05, G:0.12, T:0.09
Consensus pattern (18 bp):
AAAGAAAAAAAATATAAG
Found at i:3029495 original size:10 final size:9
Alignment explanation
Indices: 3029470--3029494 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3029460 AAAATATAAG
3029470 AAAAAAAGT
1 AAAAAAAGT
3029479 AAAAAAAGT
1 AAAAAAAGT
3029488 AAAAAAA
1 AAAAAAA
3029495 AAATAAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (9 bp):
AAAAAAAGT
Found at i:3039674 original size:18 final size:19
Alignment explanation
Indices: 3039651--3039688 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3039641 CCGTGATTCC
3039651 TATTTTAGC-TTTCA-TTTG
1 TATTTTA-CATTTCACTTTG
3039669 TATTTTACATTTCACTTTG
1 TATTTTACATTTCACTTTG
3039688 T
1 T
3039689 TGTAAGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 12 0.67
19 5 0.28
ACGTcount: A:0.18, C:0.13, G:0.08, T:0.61
Consensus pattern (19 bp):
TATTTTACATTTCACTTTG
Found at i:3040504 original size:30 final size:31
Alignment explanation
Indices: 3040440--3040506 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
3040430 ATGTTAATGG
3040440 GTGACTGATTTGTCACTTTTTGATAATGTTA
1 GTGACTGATTTGTCACTTTTTGATAATGTTA
* *
3040471 GTGACTGATTTGTTATTTTTTGA-AA-GTTGA
1 GTGACTGATTTGTCACTTTTTGATAATGTT-A
3040501 GTGACT
1 GTGACT
3040507 AAATTCAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 3 0.09
30 9 0.27
31 21 0.64
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (31 bp):
GTGACTGATTTGTCACTTTTTGATAATGTTA
Found at i:3049370 original size:149 final size:149
Alignment explanation
Indices: 3049100--3049399 Score: 429
Period size: 149 Copynumber: 2.0 Consensus size: 149
3049090 CATTTAAATC
3049100 AAAGGGAATTTATGAGGAAGACTTCCAACATGACCATTAATGCACCACAAATAGCAACTAGCAAG
1 AAAGGGAATTTATGAGGAAGACTTCCAACATGACCATTAATGCACCACAAATAGCAACTAGCAAG
* * * * *
3049165 TTTGAAGGGAGTACTCAAAGAACTATACATCTGCGGAAGCCATTTATAGATATCAAATCTTGAAA
66 TCTGAAAGGAGTACTCAAAGAACTATACATCAGCAGAAACCATTTATAGATATCAAATCTTGAAA
*
3049230 TAAATTTCCCTCAAATTAT
131 TAAATTTACCTCAAATTAT
** ** * *
3049249 AAAGGGAATTTATGAGTTAGACTTCCAACATGACCATTAATGCACTGCATATAGCGACTAGCAAG
1 AAAGGGAATTTATGAGGAAGACTTCCAACATGACCATTAATGCACCACAAATAGCAACTAGCAAG
* * ** *
3049314 TCTGAAAGTAGTGCTCAAAGAACTATGTATCAGCAGAAACCATTTATAGATATCAAATCTTGCAA
66 TCTGAAAGGAGTACTCAAAGAACTATACATCAGCAGAAACCATTTATAGATATCAAATCTTGAAA
* *
3049379 TAAGTTTACCTCAATTTAT
131 TAAATTTACCTCAAATTAT
3049398 AA
1 AA
3049400 CTGTAATCCC
Statistics
Matches: 132, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
149 132 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (149 bp):
AAAGGGAATTTATGAGGAAGACTTCCAACATGACCATTAATGCACCACAAATAGCAACTAGCAAG
TCTGAAAGGAGTACTCAAAGAACTATACATCAGCAGAAACCATTTATAGATATCAAATCTTGAAA
TAAATTTACCTCAAATTAT
Found at i:3050193 original size:53 final size:53
Alignment explanation
Indices: 3050127--3050445 Score: 566
Period size: 53 Copynumber: 6.0 Consensus size: 53
3050117 CAATTAGATA
*
3050127 TGCCATGACCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
3050180 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
3050233 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
* *
3050286 TACCATGAGCATTGATAAAAATACATAGTAACAGTGTAACTATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
*
3050339 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATTCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
* * * *
3050392 TGTCATGAGCATTGATAACAATACATGGTAACAGTGTGACCATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
3050445 T
1 T
3050446 ATGTAATCAA
Statistics
Matches: 255, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 255 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (53 bp):
TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
Found at i:3052113 original size:25 final size:26
Alignment explanation
Indices: 3052053--3052117 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
3052043 TATATTAAAT
*
3052053 TTAATATAAATTTTAAATATAATTATA
1 TTAATAT-AATTATAAATATAATTATA
* * * *
3052080 TTGAGATAATTAT-AATATAATTTTG
1 TTAATATAATTATAAATATAATTATA
3052105 TTAATATAATTAT
1 TTAATATAATTAT
3052118 TCTAAATTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
25 21 0.68
26 5 0.16
27 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (26 bp):
TTAATATAATTATAAATATAATTATA
Found at i:3056822 original size:19 final size:19
Alignment explanation
Indices: 3056795--3056832 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3056785 TAAAGGTCCG
* *
3056795 TAATTTTTAATTTTCTTCT
1 TAATCTTTAATTTTATTCT
3056814 TAATCTTTAATTTTATTCT
1 TAATCTTTAATTTTATTCT
3056833 CAAATAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (19 bp):
TAATCTTTAATTTTATTCT
Found at i:3058218 original size:106 final size:106
Alignment explanation
Indices: 3058033--3058238 Score: 331
Period size: 106 Copynumber: 1.9 Consensus size: 106
3058023 TTAGTTATAA
* * * *
3058033 TTATTTCGGTAGCCAAAAGCTAATAACGTTAAATATAAAAGGAGTTAACTAATGAGAACTCGTCA
1 TTATTTCGGTAGCCAAAAGCTAATAACGTTAAAAATAAAAAGAGTTAACCAATGAGAACGCGTCA
* *
3058098 CGTCATCAATGACATGGCATATTGATCAACAACATAGTTTG
66 CGTCATCAATGACATAGCATATTGACCAACAACATAGTTTG
* *
3058139 TTATTTCGGTAGCTAAAAGCTAATAACGTTAAAAATAAAAAGAGTTAGCCAATGAGAACGCGTCA
1 TTATTTCGGTAGCCAAAAGCTAATAACGTTAAAAATAAAAAGAGTTAACCAATGAGAACGCGTCA
*
3058204 CGTCATCAATGACATAGCATATTGACCAACGACAT
66 CGTCATCAATGACATAGCATATTGACCAACAACAT
3058239 GATATGTTGA
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 91 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (106 bp):
TTATTTCGGTAGCCAAAAGCTAATAACGTTAAAAATAAAAAGAGTTAACCAATGAGAACGCGTCA
CGTCATCAATGACATAGCATATTGACCAACAACATAGTTTG
Found at i:3059161 original size:22 final size:22
Alignment explanation
Indices: 3059136--3059181 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3059126 TTTTTACAAC
*
3059136 TTTTA-AATATTTTAAATAATTT
1 TTTTACAAT-TTTTAAATAAATT
*
3059158 TTTTACAGTTTTTAAATAAATT
1 TTTTACAATTTTTAAATAAATT
3059180 TT
1 TT
3059182 ACAAGTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTACAATTTTTAAATAAATT
Found at i:3059323 original size:20 final size:20
Alignment explanation
Indices: 3059300--3059337 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3059290 GTCAATCTAG
*
3059300 CACGTCATTGGTCAACATTT
1 CACGTCATTGGCCAACATTT
3059320 CACGTCATTGGCCAACAT
1 CACGTCATTGGCCAACAT
3059338 GCCTACTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CACGTCATTGGCCAACATTT
Found at i:3059904 original size:59 final size:59
Alignment explanation
Indices: 3059811--3059938 Score: 154
Period size: 59 Copynumber: 2.2 Consensus size: 59
3059801 ATTGGGTGGC
* *
3059811 AAAAAAAACAATTGAATAGTTGAGTGACCATTTTGCAACT-TTTCATA-TTGGGTGACCAAA
1 AAAAAAAACTACT-AATAGTTGAGTGACCATTTTGCAA-TATTTCATAGTTGGGTGA-CAAA
* * *
3059871 AAAGAAAACTACTAATAGTTGTA-TGACTATTTTGTAATATTTCATAGTTGGGTGACAAA
1 AAAAAAAACTACTAATAGTTG-AGTGACCATTTTGCAATATTTCATAGTTGGGTGACAAA
3059930 AAAAAAAAC
1 AAAAAAAAC
3059939 CATAGTTGGG
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
58 1 0.02
59 39 0.66
60 19 0.32
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (59 bp):
AAAAAAAACTACTAATAGTTGAGTGACCATTTTGCAATATTTCATAGTTGGGTGACAAA
Found at i:3077956 original size:26 final size:28
Alignment explanation
Indices: 3077891--3077956 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
3077881 TCAAAATTCA
* *
3077891 TATATAATTTTGATATTTATTCATATAT
1 TATATAATTATGATATTTATTCATATAC
*
3077919 TATATTATATTATGGTATTT-TT-ATATAC
1 TATA-TA-ATTATGATATTTATTCATATAC
3077947 TATATAATTA
1 TATATAATTA
3077957 GTACATACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 4 0.12
27 2 0.06
28 13 0.39
29 4 0.12
30 10 0.30
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (28 bp):
TATATAATTATGATATTTATTCATATAC
Found at i:3078822 original size:2 final size:2
Alignment explanation
Indices: 3078815--3078849 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3078805 GTGAATTAAG
3078815 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3078850 ACATTATGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3087986 original size:39 final size:39
Alignment explanation
Indices: 3087943--3088107 Score: 199
Period size: 39 Copynumber: 4.2 Consensus size: 39
3087933 GGTTGCCATA
*
3087943 CATTTGCTGAGGATACATCGAACCCATCTGGCCAGCTGG
1 CATTTGCTGAGGATACATTGAACCCATCTGGCCAGCTGG
* **
3087982 CATTTGCTGAGGATACATTGAACCCATCTGGGCC-CCCAG
1 CATTTGCTGAGGATACATTGAACCCATCT-GGCCAGCTGG
* * *
3088021 CACTTGCTGAGGATACATTGAACCCATCTGGCCCGTTGG
1 CATTTGCTGAGGATACATTGAACCCATCTGGCCAGCTGG
* * * *
3088060 CATTTGATGAGGATACATGGAACTCATCTGGCCCA-CAGG
1 CATTTGCTGAGGATACATTGAACCCATCTGG-CCAGCTGG
3088099 CATTTGCTG
1 CATTTGCTG
3088108 TGGAAGCATG
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
38 4 0.04
39 96 0.91
40 6 0.06
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (39 bp):
CATTTGCTGAGGATACATTGAACCCATCTGGCCAGCTGG
Found at i:3088033 original size:78 final size:78
Alignment explanation
Indices: 3087946--3088107 Score: 236
Period size: 78 Copynumber: 2.1 Consensus size: 78
3087936 TGCCATACAT
* *
3087946 TTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGCTGAGGATACATTGAACCCATCT
1 TTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGATGAGGATACATGGAACCCATCT
*
3088011 GGGCCCCCA-GCAC
66 -GGCCCACAGGCAC
* * * *
3088024 TTGCTGAGGATACATTGAACCCATCTGGCCCGTTGGCATTTGATGAGGATACATGGAACTCATCT
1 TTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGATGAGGATACATGGAACCCATCT
*
3088089 GGCCCACAGGCAT
66 GGCCCACAGGCAC
3088102 TTGCTG
1 TTGCTG
3088108 TGGAAGCATG
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
77 7 0.09
78 68 0.91
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (78 bp):
TTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGATGAGGATACATGGAACCCATCT
GGCCCACAGGCAC
Found at i:3090282 original size:110 final size:110
Alignment explanation
Indices: 3090089--3090310 Score: 426
Period size: 110 Copynumber: 2.0 Consensus size: 110
3090079 ATTTTTAACA
3090089 AGTGATACTAGCAAAATCACCTTAAGGACCATGAAATAAAAAGAGAATGCCATGCAGAAAAGCAT
1 AGTGATACTAGCAAAATCACCTTAAGGACCATGAAATAAAAAGAGAATGCCATGCAGAAAAGCAT
*
3090154 GACACATTCATGAAAACAGATGATAACATCAAGTCTTCAACTTAT
66 GACACATTCATGAAAACAGATGATAACATCAAGTCATCAACTTAT
3090199 AGTGATACTAGCAAAATCACCTTAAGGACCATGAAATAAAAAGAGAATGCCATGCAGAAAAGCAT
1 AGTGATACTAGCAAAATCACCTTAAGGACCATGAAATAAAAAGAGAATGCCATGCAGAAAAGCAT
*
3090264 GACACATTCATGAAAACAGATGATACCATCAAGTCATCAACTTAT
66 GACACATTCATGAAAACAGATGATAACATCAAGTCATCAACTTAT
3090309 AG
1 AG
3090311 AGAGTATGAA
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 110 1.00
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.20
Consensus pattern (110 bp):
AGTGATACTAGCAAAATCACCTTAAGGACCATGAAATAAAAAGAGAATGCCATGCAGAAAAGCAT
GACACATTCATGAAAACAGATGATAACATCAAGTCATCAACTTAT
Found at i:3095960 original size:19 final size:19
Alignment explanation
Indices: 3095936--3095997 Score: 106
Period size: 19 Copynumber: 3.2 Consensus size: 19
3095926 AATCTTTAAG
3095936 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3095955 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3095974 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
3095995 GAT
1 GAT
3095998 CTTGTAATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 32 0.78
21 9 0.22
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3099195 original size:10 final size:10
Alignment explanation
Indices: 3099180--3099236 Score: 71
Period size: 10 Copynumber: 5.5 Consensus size: 10
3099170 TCTATTTCAC
3099180 AAAAAAAAGA
1 AAAAAAAAGA
3099190 AAAAAAAAGA
1 AAAAAAAAGA
*
3099200 AAAGAAAAGA
1 AAAAAAAAGA
3099210 AATGAAAAAA-A
1 AA--AAAAAAGA
3099221 AAGAAAAAAGA
1 AA-AAAAAAGA
3099232 AAAAA
1 AAAAA
3099237 GAAAAAATGG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
10 31 0.74
11 6 0.14
12 5 0.12
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:3099204 original size:15 final size:14
Alignment explanation
Indices: 3099180--3099243 Score: 67
Period size: 14 Copynumber: 4.4 Consensus size: 14
3099170 TCTATTTCAC
3099180 AAAAAAAAGAAAAA-
1 AAAAAAAA-AAAAAG
*
3099194 AAAAGAAAAGAAAAG
1 AAAA-AAAAAAAAAG
*
3099209 AAATGAAAAAAAAAG
1 AAA-AAAAAAAAAAG
*
3099224 AAAAAAGAAAAAAG
1 AAAAAAAAAAAAAG
3099238 AAAAAA
1 AAAAAA
3099244 TGGAGAGGCC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
14 23 0.55
15 19 0.45
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:3100387 original size:44 final size:44
Alignment explanation
Indices: 3100332--3101163 Score: 456
Period size: 44 Copynumber: 18.9 Consensus size: 44
3100322 AAATCTAAGA
* * *
3100332 TGATTTAGCATCTCTGTATTGGCAGAGAGTAGATCAAAGATGAC
1 TGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATGAC
* *
3100376 TGATTTGGCATCTCTGTATTTGGCGGATAGCAGATCGAAGACAT-AGC
1 TGATTTGGCATCTCTGTA-TTGGCAGAGAGCAGATCGAAG--ATGA-C
* * ** * * *
3100423 TGATTTGGC-TTTCATGTGTTTAC-GTTGAAGCAAATCTAAGATGA-
1 TGATTTGGCATCTC-TGTATTGGCAG-AG-AGCAGATCGAAGATGAC
* * * *
3100467 --A-TTGGCATCTTTGTATTGACAGATAGCAGATCGAAGATAAC
1 TGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATGAC
* **
3100508 AGATTTGGCATCTCTGTATTGGCAGAGAGCAGATTAAAGATGAC
1 TGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATGAC
* *
3100552 AGATTTGGCATCTCTGTATTTGGCGGAGAGCAGATCGAAGACAT-AGC
1 TGATTTGGCATCTCTGTA-TTGGCAGAGAGCAGATCGAAG--ATGA-C
* * * * **
3100599 TGATTTGGCTTCCACGTGT-TT-AC-GTTAAAGCA-AGTTTAA-A--A-
1 TGATTTGGCAT-CTC-TGTATTGGCAG--AGAGCAGA-TCGAAGATGAC
* * *
3100640 TGATTTAGCATCTCTGTATTGGCAGAGAGCAAATCGAAGAT-AA
1 TGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATGAC
*
3100683 TAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGAC
1 T-GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATGAC
* * * **
3100728 AGATTTGGCATCTCTATATTCGGCGGAGAGCAGATCGAAGACACAGC
1 TGATTTGGCATCTCTGTATT-GGCAGAGAGCAGATCGAAGA-TGA-C
* * ** *
3100775 TGATTTGGCTTCTACGTGT-TTACGTTGA-AGCA-AGTC-TA-A-GA-
1 TGATTTGGCATCT-C-TGTATT-GGCAGAGAGCAGA-TCGAAGATGAC
* * *
3100816 TGATTTGGCATCTCTGTATTGGTAGAGAGTAGATTGAAGAT-AGC
1 TGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATGA-C
* *
3100860 AGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGAC
1 TGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATGAC
* * *
3100904 AGATTTGGCATCTTTGTATTCGGCGGAGAGCAGATCGAAGACAT-AGC
1 TGATTTGGCATCTCTGTATT-GGCAGAGAGCAGATCGAAG--ATGA-C
* * * ** *
3100951 TGATTTGGCTTCCACGTGT-TTACGTTGA-AGCA-AGTC-TA-A-GA-
1 TGATTTGGCAT-CTC-TGTATT-GGCAGAGAGCAGA-TCGAAGATGAC
* * **
3100992 TGATTTGGCATCTCTGTATTGGTAGAGATCAGATCGAAGACAAC
1 TGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATGAC
* * * * * * *
3101036 AGATTTGACATCTCTATATTGACAGAGAGCAAATTGAAGAT-AA
1 TGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATGAC
*
3101079 TAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGA-
1 T-GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGAT-GAC
* * * * *
3101124 AGATTTGGCGTCTCTGTATTGTCAGAGAGTATATCGAAGA
1 TGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGA
3101164 GAAGAACAAC
Statistics
Matches: 608, Mismatches: 115, Indels: 130
0.71 0.13 0.15
Matches are distributed among these distances:
39 17 0.03
40 41 0.07
41 50 0.08
42 9 0.01
43 8 0.01
44 283 0.47
45 77 0.13
46 18 0.03
47 83 0.14
48 14 0.02
49 8 0.01
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (44 bp):
TGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATGAC
Found at i:3100457 original size:132 final size:130
Alignment explanation
Indices: 3100185--3100541 Score: 466
Period size: 132 Copynumber: 2.7 Consensus size: 130
3100175 GTATTTATAC
* * ** *
3100185 TGAAGCAGATCCAAGATGATTTGGTGTCTCTGTATTGTCA-AGGAGCAGATCGAAGATACCAGAT
1 TGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGACAGA-GAGCAGATCGAAGATA-CAGAT
* * *
3100249 TTGGCGTCTCTGTATTGGTAGG-GAGTAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTA
64 TTGGCATCTCTGTATTGG-CGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTA
3100313 CAT
128 CAT
* * * * *
3100316 TGAAGCAAATCTAAGATGATTTAGCATCTCTGTATTGGCAGAGAGTAGATCAAAGATGACTGATT
1 TGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGAT-ACAGATT
* *
3100381 TGGCATCTCTGTATTTGGCGGATAGCAGATCGAAGACATAGCTGATTTGGCTTTCATGTGTTTAC
65 TGGCATCTCTGTA-TTGGCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTAC
*
3100446 GT
129 AT
* * *
3100448 TGAAGCAAATCTAAGATGAATTGGCATCTTTGTATTGACAGATAGCAGATCGAAGATAACAGATT
1 TGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGAT-ACAGATT
*
3100513 TGGCATCTCTGTATTGGCAGAGAGCAGAT
65 TGGCATCTCTGTATTGGCGGAGAGCAGAT
3100542 TAAAGATGAC
Statistics
Matches: 196, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
131 80 0.41
132 116 0.59
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.31
Consensus pattern (130 bp):
TGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATACAGATTT
GGCATCTCTGTATTGGCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACAT
Found at i:3100521 original size:176 final size:176
Alignment explanation
Indices: 3100333--3101119 Score: 1198
Period size: 176 Copynumber: 4.5 Consensus size: 176
3100323 AATCTAAGAT
* * *
3100333 GATTTAGCATCTCTGTATTGGCAGAGAGTAGATCAAAGATGACTGATTTGGCATCTCTGTATTTG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTTG
* * * *
3100398 GCGGATAGCAGATCGAAGACATAGCTGATTTGGCTTTCATGTGTTTACGTTGAAGCAAATCTAAG
66 GCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAG
* * * *
3100463 ATGAATTGGCATCTTTGTATTGACAGATAGCAGATCGAAGATAACA
131 ATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
*
3100509 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATTAAAGATGACAGATTTGGCATCTCTGTATTTG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTTG
* * *
3100574 GCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTCCACGTGTTTACGTTAAAGCAAGTTTAAA
66 GCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAG
* * *
3100639 ATGATTTAGCATCTCTGTATTGGCAGAGAGCAAATCGAAGATAATA
131 ATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* *
3100685 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTATATTCG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTTG
* *
3100750 GCGGAGAGCAGATCGAAGACACAGCTGATTTGGCTTCTACGTGTTTACGTTGAAGCAAGTCTAAG
66 GCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAG
* * * *
3100815 ATGATTTGGCATCTCTGTATTGGTAGAGAGTAGATTGAAGATAGCA
131 ATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* *
3100861 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTTTGTATTCG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTTG
3100926 GCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAG
66 GCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAG
* * *
3100991 ATGATTTGGCATCTCTGTATTGGTAGAGATCAGATCGAAGACAACA
131 ATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
* * * * ** * * *
3101037 GATTTGACATCTCTATATTGACAGAGAGCAAATTGAAGATAATAGATTTGGCGTCTCTGTA-TTG
1 GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTTG
*
3101101 GCAGAGAGCAGATCGAAGA
66 GCGGAGAGCAGATCGAAGA
3101120 TAGAAGATTT
Statistics
Matches: 557, Mismatches: 54, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
175 20 0.04
176 537 0.96
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (176 bp):
GATTTGGCATCTCTGTATTGGCAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTTG
GCGGAGAGCAGATCGAAGACATAGCTGATTTGGCTTCCACGTGTTTACGTTGAAGCAAGTCTAAG
ATGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAACA
Found at i:3101234 original size:41 final size:40
Alignment explanation
Indices: 3101175--3101254 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 40
3101165 AAGAACAACA
* *
3101175 GATTTGGCATTTCCGTATTTGACGGGGAGCAGATCCAAGAT
1 GATTTGGCATTTCCGTATTT-ACAGGGAACAGATCCAAGAT
* * *
3101216 GATTTGGTATTTCTGTATTTACAGGGAACAGATCGAAGA
1 GATTTGGCATTTCCGTATTTACAGGGAACAGATCCAAGA
3101255 CATAGCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
40 16 0.47
41 18 0.53
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (40 bp):
GATTTGGCATTTCCGTATTTACAGGGAACAGATCCAAGAT
Found at i:3101360 original size:44 final size:44
Alignment explanation
Indices: 3101310--3101494 Score: 180
Period size: 44 Copynumber: 4.2 Consensus size: 44
3101300 GATTTTAACA
3101310 TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAGA-TTGAAGATAGCAGATT
* *
3101354 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAAACATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAGATTG--AAGATAGCAGATT
* * * * * **
3101400 TGACATTCCTGTGCTTACAGCGAAGCAGATTGAAGATTTCAGCA--
1 TGGCATCCCTGTGTTTATAGGGAA-CAGATTGAAGATAGCAG-ATT
* * *
3101444 TGGCATCCCCGTGTTCATAGGGAACA-AGTTGAAGATAGTAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAGA-TTGAAGATAGCAGATT
3101488 TGGCATC
1 TGGCATC
3101495 TCCATATTCG
Statistics
Matches: 112, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
42 2 0.02
43 12 0.11
44 52 0.46
45 8 0.07
46 32 0.29
47 6 0.05
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (44 bp):
TGGCATCCCTGTGTTTATAGGGAACAGATTGAAGATAGCAGATT
Found at i:3101458 original size:134 final size:134
Alignment explanation
Indices: 3101228--3101494 Score: 426
Period size: 134 Copynumber: 2.0 Consensus size: 134
3101218 TTTGGTATTT
*
3101228 CTGTATTTACAGGGAACAGATCGAAGACATAGCAGATCTGACATTCCCGTGCTTACAGCGAAGCA
1 CTGTATTTACAGGGAACAGATCGAAAACATAGCAGATCTGACATTCCCGTGCTTACAGCGAAGCA
* * *
3101293 GATCAAAGATTTTAACATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGC
66 GATCAAAGATTTCAACATGGCATCCCCGTGTTCATAGGGAACAAGTTGAAGATAGCAGATTTGGC
3101358 ATCC
131 ATCC
* * * *
3101362 CTGTGTTTATAGGGAACAGATCGAAAACATAGCAGATTTGACATTCCTGTGCTTACAGCGAAGCA
1 CTGTATTTACAGGGAACAGATCGAAAACATAGCAGATCTGACATTCCCGTGCTTACAGCGAAGCA
** * *
3101427 GATTGAAGATTTCAGCATGGCATCCCCGTGTTCATAGGGAACAAGTTGAAGATAGTAGATTTGGC
66 GATCAAAGATTTCAACATGGCATCCCCGTGTTCATAGGGAACAAGTTGAAGATAGCAGATTTGGC
3101492 ATC
131 ATC
3101495 TCCATATTCG
Statistics
Matches: 121, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
134 121 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (134 bp):
CTGTATTTACAGGGAACAGATCGAAAACATAGCAGATCTGACATTCCCGTGCTTACAGCGAAGCA
GATCAAAGATTTCAACATGGCATCCCCGTGTTCATAGGGAACAAGTTGAAGATAGCAGATTTGGC
ATCC
Found at i:3102089 original size:19 final size:19
Alignment explanation
Indices: 3102065--3102143 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
3102055 AATCTTTAAG
3102065 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3102084 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3102103 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3102120 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
3102141 GAT
1 GAT
3102144 CTTGTAATCT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
21 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3102095 original size:36 final size:36
Alignment explanation
Indices: 3102055--3102142 Score: 119
Period size: 36 Copynumber: 2.4 Consensus size: 36
3102045 ATGGAAATAT
3102055 AATCTTTAAGGATATG-CAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGACAATCTTAGATATGATATGC
3102091 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG--ACAATCTTAGATATGATATGC
*
3102127 AATCTTGAAGATATGA
1 AATCTTTAAGATATGA
3102143 TCTTGTAATC
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
33 6 0.13
34 1 0.02
35 2 0.04
36 29 0.63
37 1 0.02
38 7 0.15
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (36 bp):
AATCTTTAAGATATGACAATCTTAGATATGATATGC
Found at i:3106831 original size:3 final size:3
Alignment explanation
Indices: 3106802--3106844 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
3106792 AATGTCCTTG
* * * *
3106802 TTA TTT TTA TAA TTA GTA TTG TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3106845 CGTTGTTACT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3122986 original size:21 final size:20
Alignment explanation
Indices: 3122962--3123000 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3122952 GATCGCACTG
3122962 ATAACATATTAGATTTTGAAT
1 ATAACATATTAG-TTTTGAAT
* *
3122983 ATAATATTTTAGTTTTGA
1 ATAACATATTAGTTTTGA
3123001 GTTTGGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (20 bp):
ATAACATATTAGTTTTGAAT
Found at i:3123723 original size:17 final size:17
Alignment explanation
Indices: 3123701--3123734 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3123691 ACTTTCATAA
3123701 TAAAATTAAA-TTTTAAT
1 TAAAA-TAAAGTTTTAAT
3123718 TAAAATAAAGTTTTAAT
1 TAAAATAAAGTTTTAAT
3123735 CAAATTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TAAAATAAAGTTTTAAT
Found at i:3124636 original size:24 final size:23
Alignment explanation
Indices: 3124609--3124653 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3124599 TTAACACCTT
3124609 AATTGAATGTGATTTTCAATTAAA
1 AATTGAAT-TGATTTTCAATTAAA
* * *
3124633 AATTTAATTTATTTTTAATTA
1 AATTGAATTGATTTTCAATTA
3124654 TTTTAGGAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (23 bp):
AATTGAATTGATTTTCAATTAAA
Found at i:3130144 original size:253 final size:253
Alignment explanation
Indices: 3129763--3130271 Score: 928
Period size: 253 Copynumber: 2.0 Consensus size: 253
3129753 CATCAAGCAA
3129763 GCAACTGGTGAGTAATCGATCAACTAATGTTAGCATTTCATGGGAAATAAACAAAAGCAGAGGTT
1 GCAACTGGTGAGTAATCGATCAACTAATGTTAGCATTTCATGGGAAATAAACAAAAGCAGAGGTT
* *
3129828 AACATACAAGCACGCAGAAAAGCGAAATAATATAACGGTATTGGGGAGCAGTGGAACCTTACATA
66 AACATACAAGCACACAGAAAAGCGAAATAATATAACGATATTGGGGAGCAGTGGAACCTTACATA
* *
3129893 TTACAATTTTCAATAGCAGCACCATTCCCAACATTATTAGCCAAGTTCTCCAAGGTTGCTGATGA
131 TTACAATTTTCAATAGCAGCACCATTCCCAACATTATCAGCCAAATTCTCCAAGGTTGCTGATGA
*
3129958 AATTGACTGGCTTTCACTGTTCTTTATCTGCGGAGTAGGAGAGCTGATAATTATGCAT
196 AATTGACTGGCTTTCACTGTTCTTTATCTGCGGAGTAGGAGAGCTGACAATTATGCAT
*
3130016 GCAACTGGTGAGTAATCGATCAACTAATGTTAGCATTTGATGGGAAATAAACAAAAGCAGAGGTT
1 GCAACTGGTGAGTAATCGATCAACTAATGTTAGCATTTCATGGGAAATAAACAAAAGCAGAGGTT
*
3130081 AACATACAAGCACACAGAGAAGCGAAATAATATAACGATATTGGGGAGCAGTGGAACCTTACATA
66 AACATACAAGCACACAGAAAAGCGAAATAATATAACGATATTGGGGAGCAGTGGAACCTTACATA
** *
3130146 TTGTAATTTTCAATAGCAGCACCATTCCCAGCATTATCAGCCAAATTCTCCAAGGTTGCTGATGA
131 TTACAATTTTCAATAGCAGCACCATTCCCAACATTATCAGCCAAATTCTCCAAGGTTGCTGATGA
3130211 AATTGACTGGCTTTCACTGTTCTTTATCTGCGGAGTAGGAGAGCTGACAATTATGCAT
196 AATTGACTGGCTTTCACTGTTCTTTATCTGCGGAGTAGGAGAGCTGACAATTATGCAT
3130269 GCA
1 GCA
3130272 TTTCCCGAAA
Statistics
Matches: 246, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
253 246 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (253 bp):
GCAACTGGTGAGTAATCGATCAACTAATGTTAGCATTTCATGGGAAATAAACAAAAGCAGAGGTT
AACATACAAGCACACAGAAAAGCGAAATAATATAACGATATTGGGGAGCAGTGGAACCTTACATA
TTACAATTTTCAATAGCAGCACCATTCCCAACATTATCAGCCAAATTCTCCAAGGTTGCTGATGA
AATTGACTGGCTTTCACTGTTCTTTATCTGCGGAGTAGGAGAGCTGACAATTATGCAT
Found at i:3141375 original size:22 final size:21
Alignment explanation
Indices: 3141342--3141431 Score: 74
Period size: 22 Copynumber: 4.1 Consensus size: 21
3141332 TAAAGTTTAG
*
3141342 AAATTGAGAAATTGAAAAGTA
1 AAATTGAAAAATTGAAAAGTA
**
3141363 AAATTTGAAAAATATGAAATCTA
1 AAA-TTGAAAAAT-TGAAAAGTA
** * *
3141386 GAAATTGAAATTTTGAAATGTTC
1 -AAATTGAAAAATTGAAAAG-TA
3141409 AAATTGAAAAATTGAAAA-TA
1 AAATTGAAAAATTGAAAAGTA
3141429 AAA
1 AAA
3141432 AACAAAGTAT
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
20 4 0.07
21 3 0.06
22 29 0.54
23 15 0.28
24 3 0.06
ACGTcount: A:0.56, C:0.02, G:0.13, T:0.29
Consensus pattern (21 bp):
AAATTGAAAAATTGAAAAGTA
Found at i:3141402 original size:45 final size:46
Alignment explanation
Indices: 3141325--3141425 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 46
3141315 GTTTAACTAA
*
3141325 AAAAATAT-AAAGTTTAGAAATTGAGAAATTGAAAAG-TAAAATTTG
1 AAAAATATGAAAGTCTAGAAATTGAGAAATTGAAAAGTTAAAA-TTG
* * *
3141370 AAAAATATGAAA-TCTAGAAATTGA-AATTTTGAAATGTTCAAATTG
1 AAAAATATGAAAGTCTAGAAATTGAGAA-ATTGAAAAGTTAAAATTG
3141415 AAAAAT-TGAAA
1 AAAAATATGAAA
3141426 ATAAAAAACA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
44 7 0.14
45 35 0.71
46 7 0.14
ACGTcount: A:0.54, C:0.02, G:0.14, T:0.30
Consensus pattern (46 bp):
AAAAATATGAAAGTCTAGAAATTGAGAAATTGAAAAGTTAAAATTG
Found at i:3143714 original size:17 final size:17
Alignment explanation
Indices: 3143692--3143725 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3143682 TTCTTCCCTG
*
3143692 AAAAAAGGGAAAAGAAA
1 AAAAAAGAGAAAAGAAA
*
3143709 AAAAAAGAGCAAAGAAA
1 AAAAAAGAGAAAAGAAA
3143726 CTCTTCAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAAAGAGAAAAGAAA
Found at i:3147552 original size:24 final size:25
Alignment explanation
Indices: 3147507--3147556 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
3147497 TAAAAATTTA
3147507 GTTAAAAAGATTAAGTAATTTTTTTT
1 GTTAAAAAGA-TAAGTAATTTTTTTT
**
3147533 GTTAAAAAG-TAAGTTTTTTTTTTT
1 GTTAAAAAGATAAGTAATTTTTTTT
3147557 TTTGAGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
26 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (25 bp):
GTTAAAAAGATAAGTAATTTTTTTT
Found at i:3157253 original size:46 final size:44
Alignment explanation
Indices: 3157150--3157257 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
3157140 TGTCTTTGAC
** * * * *
3157150 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGCCTCCAAAGCCATATATAAT
*
3157194 ATGGACTTACATGGCTCAATCCTGCCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGCCTCCAAAGCCATA--TATAAT
3157240 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
3157258 TTTCTGTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 32 0.58
46 23 0.42
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGCCTCCAAAGCCATATATAAT
Found at i:3158920 original size:46 final size:46
Alignment explanation
Indices: 3158855--3159143 Score: 391
Period size: 46 Copynumber: 6.3 Consensus size: 46
3158845 TTATCTTTGA
* * * * * * ** *
3158855 CATGATGCCATAGTGTCTTTCAACTATAGTCTTACTCATTTTTTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
***
3158901 CATGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
3158947 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
3158993 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTGCACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
** *
3159039 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
3159084 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
3159130 CAGGTTGCCATGGT
1 CATGTTGCCATGGT
3159144 CATATCAGGT
Statistics
Matches: 216, Mismatches: 26, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
45 41 0.19
46 175 0.81
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:3159059 original size:25 final size:25
Alignment explanation
Indices: 3159031--3159105 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
3159021 GTCTTGCACA
3159031 TTTCATATCATGTTGCCATGGTATC
1 TTTCATATCATGTTGCCATGGTATC
* *
3159056 TTTCA-ACCATG--GTC-T--TATTC
1 TTTCATATCATGTTGCCATGGTA-TC
* *
3159076 TTTCATGTCACGTTGCCATGGTATC
1 TTTCATATCATGTTGCCATGGTATC
3159101 TTTCA
1 TTTCA
3159106 ACCATGGTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
19 2 0.05
20 7 0.19
21 4 0.11
22 2 0.05
23 2 0.05
24 6 0.16
25 12 0.32
26 2 0.05
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.44
Consensus pattern (25 bp):
TTTCATATCATGTTGCCATGGTATC
Found at i:3159124 original size:91 final size:91
Alignment explanation
Indices: 3158855--3159603 Score: 699
Period size: 91 Copynumber: 8.0 Consensus size: 91
3158845 TTATCTTTGA
* * * * * * **
3158855 CATGATGCCATAGTGTCTTTCAACTATAGTCTTACTCATTTTTTGTCATGTTGCCATGGTATCTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTCATGTCATGTTGCCATGGTATCTT
***
3158920 TCAACCATGGTCTTGTTCATTTCATAT
65 TCAACCATGGTCTTACACATTTCATAT
* ** * *
3158947 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTCATGTCATGTTGCCATGGTATCTT
*
3159012 TCAACCATGGTCTTGCACATTTCATAT
65 TCAACCATGGTCTTACACATTTCATAT
*
3159039 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTCATGTCACGTTGCCATGGTATCTTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTCATGTCATGTTGCCATGGTATCTTT
3159104 CAACCATGGTCTTACACATTTCATAT
66 CAACCATGGTCTTACACATTTCATAT
* * * * *** **
3159130 CAGGTTGCCATGG--TCATATCAGGTTGCCATGGTATCT-TTCAACCATAGTCTTAT-TCTTTCA
1 CATGTTGCCATGGTATC-TTTCA----ACCATGGTCT-TATTCTTTCAT-GTC--ATGT-TGCCA
* *
3159191 T-GTCA-CGTT--GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
56 TGGT-ATCTTTCAACCATGG------T----C-T-----TACACATTTCATAT
* ** *
3159240 CATGTTGCCATGGTATCTTTCAACCATGATCTTACACATTTC-TAATCATGTTGCCATGGTATCT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTCAT-GTCATGTTGCCATGGTATCT
* * *
3159304 TTAAACCATGGTCTTGCACATTTTATAT
64 TTCAACCATGGTCTTACACATTTCATAT
**
3159332 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTCATGTCACATTGCCATGGTATCTTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTCATGTCATGTTGCCATGGTATCTTT
*
3159397 CAACCATGGTCTTACACATTTCATGT
66 CAACCATGGTCTTACACATTTCATAT
* *
3159423 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTCATGTCATGTTCCCATGGTATCTTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTCATGTCATGTTGCCATGGTATCTTT
*
3159488 CAACCATGGTCTTGCACATTTCATAT
66 CAACCATGGTCTTACACATTTCATAT
* * * * *
3159514 CATGTTGTCATGGTATCTTTCAACCATGGTCTTACATATTTC-TAATCATGTTGTCATGGTATCT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTA-TTCTTTCAT-GTCATGTTGCCATGGTATCT
*
3159578 TTCAACCATGGTCATACACATTTCAT
64 TTCAACCATGGTCTTACACATTTCAT
3159604 TTCAGAGAGC
Statistics
Matches: 545, Mismatches: 73, Indels: 78
0.78 0.10 0.11
Matches are distributed among these distances:
89 2 0.00
90 4 0.01
91 226 0.41
92 206 0.38
94 20 0.04
95 4 0.01
96 6 0.01
97 7 0.01
98 1 0.00
100 1 0.00
102 1 0.00
104 1 0.00
105 8 0.01
106 7 0.01
107 12 0.02
108 7 0.01
110 26 0.05
111 4 0.01
112 2 0.00
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (91 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTCATGTCATGTTGCCATGGTATCTTT
CAACCATGGTCTTACACATTTCATAT
Found at i:3159135 original size:137 final size:138
Alignment explanation
Indices: 3158860--3159603 Score: 897
Period size: 137 Copynumber: 5.3 Consensus size: 138
3158850 TTTGACATGA
* * * * * ** *
3158860 TGCCATAGTGTCTTTCAACTATAGTCTTACTCATTTTTTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
*
3158925 CATGGTCTTGTTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
66 CATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
3158990 TATCAGGT
131 TATCAGGT
*
3158998 TGCCATGGTATCTTTCAACCATGGTCTTGCACATTTCATATCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
*
3159063 CATGGTCTTATTC-TTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
66 CATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
3159127 TATCAGGT
131 TATCAGGT
* ** * *
3159135 TGCCATGGTCATATCAGGTTGCCATGGTATCTTTCAACCATAGTCTTATTC-TTTCATGTCACGT
1 TGCCATGG-----T-A---T--C--------TTTCAACCATGGTCTTACACATTTCATATCATGT
** *
3159199 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
47 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAAC
* *
3159264 CATGATCTTACACATTTC-TAATCATGT
112 CATGGTCTTACACATTTCAT-ATCAGGT
* * *
3159291 TGCCATGGTATCTTTAAACCATGGTCTTGCACATTTTATATCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
* *
3159356 CATGGTCTTATTC-TTTCATGTCACATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
66 CATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
*
3159420 TGTCAGGT
131 TATCAGGT
** * *
3159428 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTCATGTCATGTTCCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
*** * * *
3159492 CATGGTCTTGCACATTTCATATCATGTTGTCATGGTATCTTTCAACCATGGTCTTACATATTTC-
66 CATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
*
3159556 TAATCATGT
131 T-ATCAGGT
* *
3159565 TGTCATGGTATCTTTCAACCATGGTCATACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
3159604 TTCAGAGAGC
Statistics
Matches: 520, Mismatches: 60, Indels: 52
0.82 0.09 0.08
Matches are distributed among these distances:
136 40 0.08
137 238 0.46
138 115 0.22
142 1 0.00
143 1 0.00
145 1 0.00
146 1 0.00
147 1 0.00
148 1 0.00
150 1 0.00
151 1 0.00
155 42 0.08
156 77 0.15
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (138 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
TATCAGGT
Found at i:3159148 original size:19 final size:19
Alignment explanation
Indices: 3159124--3159162 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3159114 CTTACACATT
3159124 TCATATCAGGTTGCCATGG
1 TCATATCAGGTTGCCATGG
3159143 TCATATCAGGTTGCCATGG
1 TCATATCAGGTTGCCATGG
3159162 T
1 T
3159163 ATCTTTCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.33
Consensus pattern (19 bp):
TCATATCAGGTTGCCATGG
Found at i:3159161 original size:65 final size:64
Alignment explanation
Indices: 3159078--3159207 Score: 188
Period size: 65 Copynumber: 2.0 Consensus size: 64
3159068 TCTTATTCTT
* * *
3159078 TCATGTCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
1 TCATATCACGTTGCCATGGTATCTTTCAACCATAGTCTTACAC-TTTCATATCACGTTGCCATGG
* ** *
3159143 TCATATCAGGTTGCCATGGTATCTTTCAACCATAGTCTTATTCTTTCATGTCACGTTGCCATGG
1 TCATATCACGTTGCCATGGTATCTTTCAACCATAGTCTTACACTTTCATATCACGTTGCCATGG
3159207 T
1 T
3159208 ATCTTTCAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
64 20 0.34
65 38 0.66
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.38
Consensus pattern (64 bp):
TCATATCACGTTGCCATGGTATCTTTCAACCATAGTCTTACACTTTCATATCACGTTGCCATGG
Found at i:3159161 original size:110 final size:110
Alignment explanation
Indices: 3159033--3159253 Score: 415
Period size: 110 Copynumber: 2.0 Consensus size: 110
3159023 CTTGCACATT
* *
3159033 TCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTCATGTCACGTTGCCATGGT
1 TCATATCAGGTTGCCATGGTATCTTTCAACCATAGTCTTATTCTTTCATGTCACGTTGCCATGGT
3159098 ATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
66 ATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
3159143 TCATATCAGGTTGCCATGGTATCTTTCAACCATAGTCTTATTCTTTCATGTCACGTTGCCATGGT
1 TCATATCAGGTTGCCATGGTATCTTTCAACCATAGTCTTATTCTTTCATGTCACGTTGCCATGGT
*
3159208 ATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGG
66 ATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
3159253 T
1 T
3159254 ATCTTTCAAC
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 108 1.00
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (110 bp):
TCATATCAGGTTGCCATGGTATCTTTCAACCATAGTCTTATTCTTTCATGTCACGTTGCCATGGT
ATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
Found at i:3159253 original size:46 final size:46
Alignment explanation
Indices: 3159143--3159603 Score: 635
Period size: 46 Copynumber: 10.1 Consensus size: 46
3159133 GTTGCCATGG
* * **
3159143 TCATATCAGGTTGCCATGGTATCTTTCAACCATAGTCTTATTC-TT
1 TCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
* *
3159188 TCATGTCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
1 TCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
*
3159234 TCATATCATGTTGCCATGGTATCTTTCAACCATGATCTTACACATT
1 TCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
* *
3159280 TC-TAATCATGTTGCCATGGTATCTTTAAACCATGGTCTTGCACATT
1 TCAT-ATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
* **
3159326 TTATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTC-TT
1 TCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
* **
3159371 TCATGTCACATTGCCATGGTATCTTTCAACCATGGTCTTACACATT
1 TCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
* * **
3159417 TCATGTCAGGTTGCCATGGTATCTTTCAACCATGGTCTTATTC-TT
1 TCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
* * *
3159462 TCATGTCATGTTCCCATGGTATCTTTCAACCATGGTCTTGCACATT
1 TCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
* *
3159508 TCATATCATGTTGTCATGGTATCTTTCAACCATGGTCTTACATATT
1 TCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
* *
3159554 TC-TAATCATGTTGTCATGGTATCTTTCAACCATGGTCATACACATT
1 TCAT-ATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
3159600 TCAT
1 TCAT
3159604 TTCAGAGAGC
Statistics
Matches: 371, Mismatches: 38, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
45 119 0.32
46 250 0.67
47 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
TCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
Found at i:3159534 original size:25 final size:25
Alignment explanation
Indices: 3159506--3159581 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
3159496 GTCTTGCACA
3159506 TTTCATATCATGTTGTCATGGTATC
1 TTTCATATCATGTTGTCATGGTATC
* *** *
3159531 TTTCA-ACCATG--GTC-TTACATA
1 TTTCATATCATGTTGTCATGGTATC
3159552 TTTC-TAATCATGTTGTCATGGTATC
1 TTTCAT-ATCATGTTGTCATGGTATC
3159577 TTTCA
1 TTTCA
3159582 ACCATGGTCA
Statistics
Matches: 35, Mismatches: 10, Indels: 11
0.62 0.18 0.20
Matches are distributed among these distances:
21 7 0.20
22 8 0.23
24 8 0.23
25 12 0.34
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.46
Consensus pattern (25 bp):
TTTCATATCATGTTGTCATGGTATC
Found at i:3161753 original size:3 final size:3
Alignment explanation
Indices: 3161739--3161787 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
3161729 TTTTATATTA
*
3161739 AAT AATT AAT AAT AA- AAT AAT AAT GA- AAT AAT AAT AA- AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3161782 AA- AAT A
1 AAT AAT A
3161788 TCTTATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3161761 original size:11 final size:11
Alignment explanation
Indices: 3161745--3161783 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
3161735 ATTAAATAAT
3161745 TAATAATAAAA
1 TAATAATAAAA
*
3161756 TAATAATGAAA
1 TAATAATAAAA
3161767 TAATAATAAAA
1 TAATAATAAAA
3161778 TAATAA
1 TAATAA
3161784 AATATCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:3161770 original size:19 final size:19
Alignment explanation
Indices: 3161746--3161787 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3161736 TTAAATAATT
*
3161746 AATAATAAAATAATAATGA
1 AATAATAAAATAATAATAA
3161765 AATAATAATAA-AATAATAA
1 AATAATAA-AATAATAATAA
3161784 AATA
1 AATA
3161788 TCTTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAATAAAATAATAATAA
Found at i:3161810 original size:20 final size:21
Alignment explanation
Indices: 3161757--3161832 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 21
3161747 ATAATAAAAT
* *
3161757 AATAATGAAATA-ATAA-TAA
1 AATAATAAAATATCTAATTAA
*
3161776 AATAATAAAATATCTTATTAA
1 AATAATAAAATATCTAATTAA
*
3161797 AATAAT-ATATATCTAATTAAA
1 AATAATAAAATATCTAATT-AA
*
3161818 TAATCATAAAATATC
1 -AATAATAAAATATC
3161833 ATCGAAATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 11 0.24
20 12 0.27
21 11 0.24
22 5 0.11
23 6 0.13
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.34
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:3163020 original size:37 final size:37
Alignment explanation
Indices: 3162970--3163044 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
3162960 ACAAAAAAAA
3162970 GTATGAAAATAAGTTTAACTCCAGAGCAATGTAGAAC
1 GTATGAAAATAAGTTTAACTCCAGAGCAATGTAGAAC
3163007 GTATGAAAATAAGTTTAACTCCAGAGCAATGTAGAAC
1 GTATGAAAATAAGTTTAACTCCAGAGCAATGTAGAAC
3163044 G
1 G
3163045 ACCACTTCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (37 bp):
GTATGAAAATAAGTTTAACTCCAGAGCAATGTAGAAC
Found at i:3165694 original size:14 final size:15
Alignment explanation
Indices: 3165675--3165706 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3165665 AAGATGTTTT
3165675 AAGAAAAGAAAAA-A
1 AAGAAAAGAAAAAGA
3165689 AAGAAAAGAAAAAGA
1 AAGAAAAGAAAAAGA
3165704 AAG
1 AAG
3165707 CCTTACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAAAAAGA
Found at i:3181862 original size:121 final size:118
Alignment explanation
Indices: 3181724--3181967 Score: 425
Period size: 121 Copynumber: 2.0 Consensus size: 118
3181714 TTATTTACCT
* *
3181724 TAATTATATAAAGTGAAATTATATTGTAGGTTGAATATGTTGAAAATGCTTTAATTATGATTCAA
1 TAATTATATAAAGTGAAATTATATTATAAGTTGAATATGTTGAAAATGCTTTAATTATGATTC-A
3181789 ATTTTTTTATTATAATATCTGAATTAATAAGTTAATATATTTTAATTATATTTAA
65 ATTTTTTT-TTATAATATCTGAATTAATAAGTTAATATATTTTAATTATATTTAA
3181844 TAATTATTATAAAGTGAAATTATATTATAAGTTGAATATGTTGAAAATGCTTTAATTATGATTCA
1 TAATTA-TATAAAGTGAAATTATATTATAAGTTGAATATGTTGAAAATGCTTTAATTATGATTCA
* *
3181909 ATTTTTTTTTATAATATTTGAATTGATAAGTTAATATATTTTAATTATATTTAA
65 ATTTTTTTTTATAATATCTGAATTAATAAGTTAATATATTTTAATTATATTTAA
3181963 TAATT
1 TAATT
3181968 TAAATATAAA
Statistics
Matches: 119, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
119 49 0.41
120 15 0.13
121 55 0.46
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (118 bp):
TAATTATATAAAGTGAAATTATATTATAAGTTGAATATGTTGAAAATGCTTTAATTATGATTCAA
TTTTTTTTTATAATATCTGAATTAATAAGTTAATATATTTTAATTATATTTAA
Found at i:3182156 original size:13 final size:14
Alignment explanation
Indices: 3182125--3182155 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3182115 TCGACTAAAA
*
3182125 TTTTATTTAAATTT
1 TTTTATATAAATTT
3182139 TTTTATATAAATTT
1 TTTTATATAAATTT
3182153 TTT
1 TTT
3182156 ACTCACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATATAAATTT
Found at i:3187010 original size:14 final size:14
Alignment explanation
Indices: 3186991--3187020 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3186981 GTAGATAAGC
3186991 AAGTATGAAGGAAG
1 AAGTATGAAGGAAG
3187005 AAGTATGAAGGAAG
1 AAGTATGAAGGAAG
3187019 AA
1 AA
3187021 ATACAATCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.13
Consensus pattern (14 bp):
AAGTATGAAGGAAG
Found at i:3188169 original size:39 final size:39
Alignment explanation
Indices: 3188071--3188169 Score: 103
Period size: 39 Copynumber: 2.6 Consensus size: 39
3188061 TATGGTATTT
* * * *
3188071 AAATATATATAT-ATATATATGTATATAATAGTATTTAA
1 AAATATATACATAATATATATATATATAATAGCATTAAA
* * * *
3188109 GAATATATACATAAGAAATATATA-ACTAATGGCATTAAA
1 AAATATATACATAATATATATATATA-TAATAGCATTAAA
3188148 AAATATATACATAATATATATA
1 AAATATATACATAATATATATA
3188170 AAATACCTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
38 11 0.23
39 37 0.77
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (39 bp):
AAATATATACATAATATATATATATATAATAGCATTAAA
Found at i:3188683 original size:19 final size:19
Alignment explanation
Indices: 3188654--3188714 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 19
3188644 GGCTAGGTTT
3188654 TTTTATCTTTTTTTGTTAGG
1 TTTT-TCTTTTTTTGTTAGG
* *
3188674 TTTTTC-TTTTTTCTT--C
1 TTTTTCTTTTTTTGTTAGG
*
3188690 TTTTTTTTTTTTTGGTTAGG
1 TTTTTCTTTTTTT-GTTAGG
3188710 TTTTT
1 TTTTT
3188715 TTTGGGGTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
16 5 0.16
17 6 0.19
18 10 0.31
19 2 0.06
20 9 0.28
ACGTcount: A:0.05, C:0.07, G:0.11, T:0.77
Consensus pattern (19 bp):
TTTTTCTTTTTTTGTTAGG
Found at i:3188713 original size:16 final size:16
Alignment explanation
Indices: 3188694--3188780 Score: 69
Period size: 16 Copynumber: 5.7 Consensus size: 16
3188684 TTCTTCTTTT
3188694 TTTTTTTTTGGTTAGG
1 TTTTTTTTTGGTTAGG
* *
3188710 TTTTTTTTGGGGTAGG
1 TTTTTTTTTGGTTAGG
3188726 TTTTTCTTTT--TT---
1 TTTTT-TTTTGGTTAGG
* * *
3188738 TTTTTTTTT-CTTTGT
1 TTTTTTTTTGGTTAGG
3188753 TTTTTTTTTGGGTTAGG
1 TTTTTTTTT-GGTTAGG
3188770 TTTTTTTTTGG
1 TTTTTTTTTGG
3188781 GGGGCTTAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
11 4 0.07
12 7 0.12
15 10 0.18
16 21 0.37
17 15 0.26
ACGTcount: A:0.03, C:0.02, G:0.21, T:0.74
Consensus pattern (16 bp):
TTTTTTTTTGGTTAGG
Found at i:3188738 original size:44 final size:44
Alignment explanation
Indices: 3188681--3188778 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
3188671 AGGTTTTTCT
*
3188681 TTTTTCTTCTTTTTTTTTTTTTGGTTAG-GTTTTTTTTGGGGTAGG
1 TTTTTCTT-TTTTTTTTTTTTT-CTTAGTGTTTTTTTTGGGGTAGG
* * *
3188726 TTTTTCTTTTTTTTTTTTTTTCTTTGTTTTTTTTTTGGGTTAGG
1 TTTTTCTTTTTTTTTTTTTTTCTTAGTGTTTTTTTTGGGGTAGG
3188770 TTTTT-TTTT
1 TTTTTCTTTT
3188779 GGGGGGCTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
43 7 0.15
44 33 0.69
45 8 0.17
ACGTcount: A:0.03, C:0.04, G:0.16, T:0.77
Consensus pattern (44 bp):
TTTTTCTTTTTTTTTTTTTTTCTTAGTGTTTTTTTTGGGGTAGG
Found at i:3188744 original size:15 final size:16
Alignment explanation
Indices: 3188726--3188761 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3188716 TTGGGGTAGG
*
3188726 TTTTTCTTTTTTTTTT
1 TTTTTCTTTTGTTTTT
3188742 TTTTTC-TTTGTTTTT
1 TTTTTCTTTTGTTTTT
3188757 TTTTT
1 TTTTT
3188762 GGGTTAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.92
Consensus pattern (16 bp):
TTTTTCTTTTGTTTTT
Found at i:3194404 original size:2 final size:2
Alignment explanation
Indices: 3194397--3194428 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3194387 AATGAATTGC
3194397 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
3194429 CGCTCGTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3198266 original size:21 final size:21
Alignment explanation
Indices: 3198237--3198294 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
3198227 TTATTTAAAA
*
3198237 TAATATAAATCTAAATATTTT
1 TAATTTAAATCTAAATATTTT
3198258 TAATTTAAATAC-AAATATTTT
1 TAATTTAAAT-CTAAATATTTT
* *
3198279 TATTATTAAATATAAA
1 TAAT-TTAAATCTAAA
3198295 ATTAAGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATTTAAATCTAAATATTTT
Found at i:3198287 original size:22 final size:21
Alignment explanation
Indices: 3198249--3198290 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3198239 ATATAAATCT
3198249 AAATATTTTTAATTTAAATAC
1 AAATATTTTTAATTTAAATAC
*
3198270 AAATATTTTTATTATTAAATA
1 AAATATTTTTAAT-TTAAATA
3198291 TAAAATTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATATTTTTAATTTAAATAC
Found at i:3198661 original size:2 final size:2
Alignment explanation
Indices: 3198619--3198651 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3198609 TAAATATAAT
3198619 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3198652 GCAATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3202281 original size:27 final size:27
Alignment explanation
Indices: 3202251--3202309 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
3202241 TAAATTAAAT
3202251 AGTTAGTTTGTTAAAATACATACAGAG
1 AGTTAGTTTGTTAAAATACATACAGAG
3202278 AGTTAGTTTGTTAAAATACATACAGAG
1 AGTTAGTTTGTTAAAATACATACAGAG
3202305 AGTTA
1 AGTTA
3202310 TATATGTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.34
Consensus pattern (27 bp):
AGTTAGTTTGTTAAAATACATACAGAG
Found at i:3202527 original size:54 final size:57
Alignment explanation
Indices: 3202432--3202537 Score: 148
Period size: 54 Copynumber: 1.9 Consensus size: 57
3202422 CTATGTCATA
* *
3202432 ATTATTACTTATCTCTTAATTAATTTAAATATTAAGCGATAAATAATAAATAAATAT
1 ATTATTACTTATCTCTTAATTAATTTAAATAATAAGAGATAAATAATAAATAAATAT
*
3202489 ATTATTA-TT-TCTC-TAATTAA-TTAAATTAATATGAGATAAATAATAAATA
1 ATTATTACTTATCTCTTAATTAATTTAAA-TAATAAGAGATAAATAATAAATA
3202538 GATGAGAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
53 5 0.11
54 27 0.60
55 4 0.09
56 2 0.04
57 7 0.16
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (57 bp):
ATTATTACTTATCTCTTAATTAATTTAAATAATAAGAGATAAATAATAAATAAATAT
Found at i:3207268 original size:14 final size:15
Alignment explanation
Indices: 3207251--3207279 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3207241 TTAAAATTTA
3207251 TAAAATT-AAAAAAT
1 TAAAATTCAAAAAAT
3207265 TAAAATTCAAAAAAT
1 TAAAATTCAAAAAAT
3207280 ATTAAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAAATTCAAAAAAT
Found at i:3207863 original size:18 final size:18
Alignment explanation
Indices: 3207842--3207876 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3207832 ATTAATAAAT
3207842 TTAA-ATTTTATATTAATA
1 TTAATATTTT-TATTAATA
3207860 TTAATATTTTTATTAAT
1 TTAATATTTTTATTAAT
3207877 GATTCACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATATTTTTATTAATA
Found at i:3211020 original size:17 final size:17
Alignment explanation
Indices: 3210987--3211021 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3210977 TAACCAATTC
* *
3210987 AATTAAAAATTATTAAA
1 AATTAAAAATAAATAAA
3211004 AATTAAAAATAAATAAA
1 AATTAAAAATAAATAAA
3211021 A
1 A
3211022 TAAATAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATTAAAAATAAATAAA
Found at i:3214375 original size:157 final size:157
Alignment explanation
Indices: 3214089--3214401 Score: 608
Period size: 157 Copynumber: 2.0 Consensus size: 157
3214079 TTTTGAAATA
3214089 CAAAAGTATAACTTGCAAGTAACCCAAAGAATACCATTCTTGATCCATTCAACTTGAAAAGTTCA
1 CAAAAGTATAACTTGCAAGTAACCCAAAGAATACCATTCTTGATCCATTCAACTTGAAAAGTTCA
3214154 GCAGGGGTGCCTAAAAAGATACATCATAATCCCTAACACATCAAAAAAAAATCAAAACAAATATA
66 GCAGGGGTGCCTAAAAAGATACATCATAATCCCTAACACATCAAAAAAAAATCAAAACAAATATA
3214219 TGCTATGTGAAGGAGAGGCCACATATT
131 TGCTATGTGAAGGAGAGGCCACATATT
3214246 CAAAAGTATAACTTGCAAGTAACCCAAAGAATACCATTCTTGATCCATTCAACTTGAAAAGTTCA
1 CAAAAGTATAACTTGCAAGTAACCCAAAGAATACCATTCTTGATCCATTCAACTTGAAAAGTTCA
**
3214311 GCAGGGGTGCCTAAAAAGATACATCATAATCCCTAACACATCAAAAAATTATCAAAACAAATATA
66 GCAGGGGTGCCTAAAAAGATACATCATAATCCCTAACACATCAAAAAAAAATCAAAACAAATATA
3214376 TGCTATGTGAAGGAGAGGCCACATAT
131 TGCTATGTGAAGGAGAGGCCACATAT
3214402 GACAATTATT
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (157 bp):
CAAAAGTATAACTTGCAAGTAACCCAAAGAATACCATTCTTGATCCATTCAACTTGAAAAGTTCA
GCAGGGGTGCCTAAAAAGATACATCATAATCCCTAACACATCAAAAAAAAATCAAAACAAATATA
TGCTATGTGAAGGAGAGGCCACATATT
Found at i:3217522 original size:2 final size:2
Alignment explanation
Indices: 3217515--3217540 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3217505 AAATTTAACA
3217515 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
3217541 CTGAATTTTA
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:3225088 original size:20 final size:20
Alignment explanation
Indices: 3225063--3225102 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3225053 TATTGGAGAA
*
3225063 AGGGAGAAAATTAAACAGAG
1 AGGGAGAAAAATAAACAGAG
3225083 AGGGAGAAAAATAAACAGAG
1 AGGGAGAAAAATAAACAGAG
3225103 GAAGAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.30, T:0.07
Consensus pattern (20 bp):
AGGGAGAAAAATAAACAGAG
Found at i:3225109 original size:20 final size:20
Alignment explanation
Indices: 3225066--3225111 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3225056 TGGAGAAAGG
* *
3225066 GAGAAAATTAAACAGAGAGG
1 GAGAAAAATAAACAGAGAGA
3225086 GAGAAAAATAAACAGAG-GAA
1 GAGAAAAATAAACAGAGAG-A
3225106 GAGAAA
1 GAGAAA
3225112 TAACCAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.61, C:0.04, G:0.28, T:0.07
Consensus pattern (20 bp):
GAGAAAAATAAACAGAGAGA
Found at i:3226888 original size:24 final size:24
Alignment explanation
Indices: 3226824--3226904 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 24
3226814 ATTATTATTG
3226824 TTAAATTATATTTAATAATAATTTTA
1 TTAAATTATATTT-A-AATAATTTTA
* **
3226850 TTAAAATATGA-TTAAATTTTTTTA
1 TTAAATTAT-ATTTAAATAATTTTA
*
3226874 TTAAATTATATTTAATAATAATCTTA
1 TTAAATTATATTT-A-AATAATTTTA
3226900 TTAAA
1 TTAAA
3226905 ATTTAATAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
23 1 0.02
24 18 0.41
25 2 0.05
26 22 0.50
27 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (24 bp):
TTAAATTATATTTAAATAATTTTA
Found at i:3227437 original size:20 final size:19
Alignment explanation
Indices: 3227390--3227448 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 19
3227380 AATGAAAATT
3227390 TATTAAAATCTTAAAAAAAC
1 TATTAAAAT-TTAAAAAAAC
*
3227410 -ATAAAAAATATTAAAAAAAC
1 TAT-TAAAAT-TTAAAAAAAC
3227430 TATTAAAATTTCAAAAAAA
1 TATTAAAATTT-AAAAAAA
3227449 ATATATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.12
20 27 0.82
21 2 0.06
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (19 bp):
TATTAAAATTTAAAAAAAC
Found at i:3227490 original size:20 final size:21
Alignment explanation
Indices: 3227402--3227493 Score: 73
Period size: 22 Copynumber: 4.4 Consensus size: 21
3227392 TTAAAATCTT
*
3227402 AAAAAAACATAAA-AAATATTA
1 AAAAAAATATAAAGAAATA-TA
* * *
3227423 AAAAAACTAT-TA-AAATTTCA
1 AAAAAAATATAAAGAAATAT-A
* * *
3227443 AAAAAAATATATATATATATA
1 AAAAAAATATAAAGAAATATA
3227464 AAGAAAAATATAAAGAAATATA
1 AA-AAAAATATAAAGAAATATA
3227486 AAAAAAAT
1 AAAAAAAT
3227494 TAGTAATGCC
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 15 0.26
21 19 0.33
22 22 0.39
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAAAAATATAAAGAAATATA
Found at i:3229435 original size:15 final size:15
Alignment explanation
Indices: 3229412--3229460 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3229402 GGTTAAACGG
*
3229412 TTATGATTTTTTATA
1 TTATTATTTTTTATA
3229427 TTATTATTTTTTATGA
1 TTATTATTTTTTAT-A
3229443 TT-TT-TTTATTTA-A
1 TTATTATTT-TTTATA
3229456 TTATT
1 TTATT
3229461 TTTGAACTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 3 0.10
14 5 0.17
15 19 0.63
16 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (15 bp):
TTATTATTTTTTATA
Found at i:3229446 original size:25 final size:26
Alignment explanation
Indices: 3229412--3229463 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
3229402 GGTTAAACGG
3229412 TTATGA-TTTTTTATATT-ATTATTTT
1 TTATGATTTTTTTAT-TTAATTATTTT
3229437 TTATGATTTTTTTATTTAATTATTTT
1 TTATGATTTTTTTATTTAATTATTTT
3229463 T
1 T
3229464 GAACTGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (26 bp):
TTATGATTTTTTTATTTAATTATTTT
Found at i:3229458 original size:26 final size:25
Alignment explanation
Indices: 3229412--3229463 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 25
3229402 GGTTAAACGG
3229412 TTATGATTTTTTATATTATTATTTT
1 TTATGATTTTTTATATTATTATTTT
3229437 TTATGATTTTTT-TATTTAATTATTTT
1 TTATGATTTTTTATA-TT-ATTATTTT
3229463 T
1 T
3229464 GAACTGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 2 0.08
25 14 0.56
26 9 0.36
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (25 bp):
TTATGATTTTTTATATTATTATTTT
Found at i:3234042 original size:94 final size:94
Alignment explanation
Indices: 3233938--3234121 Score: 287
Period size: 94 Copynumber: 2.0 Consensus size: 94
3233928 TAATTGAGAA
* * * *
3233938 AAAAAAGTACCTGCTGCAAGAATGGTATCACGAACTCTAGAATTTCAAAAACAAAAAGGGAAGCG
1 AAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGGAAGCA
3234003 CACAGAGGCAATGAAAGAGGAAGCATGAG
66 CACAGAGGCAATGAAAGAGGAAGCATGAG
* ** *
3234032 AAAAAGGTACCTACTGCAAGAATGGTATTGCCAGCTCTAGAACTTCAAAAACAAAAAGGGAAGCA
1 AAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGGAAGCA
*
3234097 CGCAGAGGCAATGAAAGAGGAAGCA
66 CACAGAGGCAATGAAAGAGGAAGCA
3234122 CTCAGGCTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
94 81 1.00
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (94 bp):
AAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGGAAGCA
CACAGAGGCAATGAAAGAGGAAGCATGAG
Found at i:3238535 original size:28 final size:28
Alignment explanation
Indices: 3238495--3238550 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3238485 TTTTCCAAGG
3238495 ATGGAATTCAAACAACCTAGGAGATCTT
1 ATGGAATTCAAACAACCTAGGAGATCTT
3238523 ATGGAATTCAAACAACCTAGGAGATCTT
1 ATGGAATTCAAACAACCTAGGAGATCTT
3238551 TCCTTTTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (28 bp):
ATGGAATTCAAACAACCTAGGAGATCTT
Found at i:3239962 original size:20 final size:20
Alignment explanation
Indices: 3239937--3239977 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3239927 CAAGATCTGT
*
3239937 CCCATC-ACAGACATCCTCGC
1 CCCATCGACA-ACATCCACGC
3239957 CCCATCGACAACATCCACGC
1 CCCATCGACAACATCCACGC
3239977 C
1 C
3239978 ATTCATTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.27, C:0.51, G:0.10, T:0.12
Consensus pattern (20 bp):
CCCATCGACAACATCCACGC
Found at i:3243650 original size:46 final size:44
Alignment explanation
Indices: 3243546--3243653 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
3243536 TGTCTTTGAC
** * * *
3243546 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
3243590 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
3243636 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
3243654 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:3245182 original size:47 final size:47
Alignment explanation
Indices: 3245124--3245228 Score: 140
Period size: 47 Copynumber: 2.2 Consensus size: 47
3245114 TTACACGGAT
* * **
3245124 CACATATCACACTGATGCCATATCCC-ATATATGGTATTATACATTAG
1 CACATATCACACCGATGCCATACCCCGA-ATATGGTATTATACAGAAG
* *
3245171 CACATATCACACCGATGCCATACCCCGAATATGGTCTTATACGGAAG
1 CACATATCACACCGATGCCATACCCCGAATATGGTATTATACAGAAG
3245218 CACATATCACA
1 CACATATCACA
3245229 TTTCTCCGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
47 50 0.98
48 1 0.02
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (47 bp):
CACATATCACACCGATGCCATACCCCGAATATGGTATTATACAGAAG
Found at i:3247943 original size:28 final size:27
Alignment explanation
Indices: 3247906--3248006 Score: 103
Period size: 28 Copynumber: 3.6 Consensus size: 27
3247896 TCAATGTCTT
* *
3247906 GCACGCTAAGTGCTATACCGGATGTTTC
1 GCACACTAAGTGCCAT-CCGGATGTTTC
* * **
3247934 ACACACTAAGTGCCATCCTCGATACTTC
1 GCACACTAAGTGCCATCC-GGATGTTTC
*
3247962 GCACACTAAGTGCCATTTCGGATGTTTC
1 GCACACTAAGTGCCA-TCCGGATGTTTC
*
3247990 GCACACTAAGTGTCATC
1 GCACACTAAGTGCCATC
3248007 ATCAATACTT
Statistics
Matches: 58, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
27 3 0.05
28 53 0.91
29 2 0.03
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (27 bp):
GCACACTAAGTGCCATCCGGATGTTTC
Found at i:3247997 original size:56 final size:56
Alignment explanation
Indices: 3247906--3248085 Score: 231
Period size: 56 Copynumber: 3.2 Consensus size: 56
3247896 TCAATGTCTT
* * ** * *
3247906 GCACGCTAAGTGCTATACCGGATGTTTCACACACTAAGTGCCATCCTCGATACTTC
1 GCACACTAAGTGCCATTTCGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTC
* *
3247962 GCACACTAAGTGCCATTTCGGATGTTTCGCACACTAAGTGTCATCATCAATACTTC
1 GCACACTAAGTGCCATTTCGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTC
** *
3248018 ATACACT--GTGTCATTTCGGATGTCTT-GCACACTAAGTGCCATCCTCAATACTTC
1 GCACACTAAGTGCCATTTCGGATGT-TTCGCACACTAAGTGCCATCCTCAATACTTC
3248072 GCACACTAAGTGCC
1 GCACACTAAGTGCC
3248086 GTTCGTTTGG
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
54 46 0.44
55 2 0.02
56 57 0.54
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (56 bp):
GCACACTAAGTGCCATTTCGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTC
Found at i:3248054 original size:54 final size:55
Alignment explanation
Indices: 3247924--3248085 Score: 211
Period size: 54 Copynumber: 2.9 Consensus size: 55
3247914 AGTGCTATAC
* * *
3247924 CGGATGTTTCACACACTAAGTGCCATCCTCGATACTTCGCACACTAAGTGCCATTT
1 CGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTCACACACT-AGTGCCATTT
* * * *
3247980 CGGATGTTTCGCACACTAAGTGTCATCATCAATACTTCATACACT-GTGTCATTT
1 CGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTCACACACTAGTGCCATTT
*
3248034 CGGATGTCTT-GCACACTAAGTGCCATCCTCAATACTTCGCACACTAAGTGCC
1 CGGATGT-TTCGCACACTAAGTGCCATCCTCAATACTTCACACACT-AGTGCC
3248086 GTTCGTTTGG
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
54 46 0.51
55 2 0.02
56 43 0.47
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (55 bp):
CGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTCACACACTAGTGCCATTT
Found at i:3248084 original size:28 final size:28
Alignment explanation
Indices: 3247935--3248085 Score: 132
Period size: 28 Copynumber: 5.5 Consensus size: 28
3247925 GGATGTTTCA
3247935 CACACTAAGTGCCATCCTCGATACTTCG
1 CACACTAAGTGCCATCCTCGATACTTCG
* **
3247963 CACACTAAGTGCCAT-TTCGGATGTTTCG
1 CACACTAAGTGCCATCCTC-GATACTTCG
* * * *
3247991 CACACTAAGTGTCATCATCAATACTTCA
1 CACACTAAGTGCCATCCTCGATACTTCG
* * * *
3248019 TACACT--GTGTCAT-TTCGGATGTCTT-G
1 CACACTAAGTGCCATCCTC-GAT-ACTTCG
*
3248045 CACACTAAGTGCCATCCTCAATACTTCG
1 CACACTAAGTGCCATCCTCGATACTTCG
3248073 CACACTAAGTGCC
1 CACACTAAGTGCC
3248086 GTTCGTTTGG
Statistics
Matches: 96, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
25 2 0.02
26 14 0.15
27 8 0.08
28 68 0.71
29 4 0.04
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (28 bp):
CACACTAAGTGCCATCCTCGATACTTCG
Found at i:3250795 original size:47 final size:47
Alignment explanation
Indices: 3250697--3250844 Score: 154
Period size: 47 Copynumber: 3.2 Consensus size: 47
3250687 ATAGTCACAT
* * * ** * * *
3250697 ATATCATACCGAGGCCATAGCCCAGCCATGGTCTTACAC-GGATCAC
1 ATATCACACCGATGCCATATCCCAGATATGGTCTTATACAGAAGCAC
* * * * *
3250743 ATATCACACTGATGTCATATCCCATATATGGTCTTATATAGTAGCAC
1 ATATCACACCGATGCCATATCCCAGATATGGTCTTATACAGAAGCAC
* *
3250790 ATATCACACCGATGCCATATCCCGGATATGGTCTTATACGGAAGCAC
1 ATATCACACCGATGCCATATCCCAGATATGGTCTTATACAGAAGCAC
3250837 ATATCACA
1 ATATCACA
3250845 TTTCTCCGAA
Statistics
Matches: 82, Mismatches: 19, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
46 29 0.35
47 53 0.65
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (47 bp):
ATATCACACCGATGCCATATCCCAGATATGGTCTTATACAGAAGCAC
Found at i:3257781 original size:13 final size:15
Alignment explanation
Indices: 3257763--3257800 Score: 53
Period size: 13 Copynumber: 2.6 Consensus size: 15
3257753 TTTAAACAAA
3257763 ATTTTAAATT-TAT-
1 ATTTTAAATTATATC
3257776 ATTTTAAATTATATC
1 ATTTTAAATTATATC
3257791 ATATTTAAAT
1 AT-TTTAAAT
3257801 AAATATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.45
14 3 0.14
15 2 0.09
16 7 0.32
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTAAATTATATC
Found at i:3262691 original size:28 final size:28
Alignment explanation
Indices: 3262660--3262717 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3262650 CTTTGTAATC
3262660 ACATTTGAAAGGAGACCTTTATTTATTT
1 ACATTTGAAAGGAGACCTTTATTTATTT
3262688 ACATTTGAAAGGAGACCTTTATTTATTT
1 ACATTTGAAAGGAGACCTTTATTTATTT
3262716 AC
1 AC
3262718 TTATCATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (28 bp):
ACATTTGAAAGGAGACCTTTATTTATTT
Found at i:3266279 original size:11 final size:11
Alignment explanation
Indices: 3266263--3266292 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
3266253 ATTTAATAGT
3266263 TTGGTTTCTGC
1 TTGGTTTCTGC
3266274 TTGGTTTCTGC
1 TTGGTTTCTGC
3266285 TTGGTTTC
1 TTGGTTTC
3266293 AGGTATTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.17, G:0.27, T:0.57
Consensus pattern (11 bp):
TTGGTTTCTGC
Found at i:3284065 original size:24 final size:24
Alignment explanation
Indices: 3284038--3284088 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3284028 ACTGAGCTAT
*
3284038 GATGTTTCGTACAAGAAATACGAA
1 GATGTTTCATACAAGAAATACGAA
* *
3284062 GATGTTTTATACAAGAAATGCGAA
1 GATGTTTCATACAAGAAATACGAA
3284086 GAT
1 GAT
3284089 TGCAAGCTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (24 bp):
GATGTTTCATACAAGAAATACGAA
Found at i:3286280 original size:21 final size:19
Alignment explanation
Indices: 3286224--3286280 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 19
3286214 AAAAAAAATC
3286224 TTAATAAAA-ATATT-ATT
1 TTAATAAAATATATTAATT
3286241 TTAATAAAATAT-TTAAATT
1 TTAATAAAATATATT-AATT
3286260 TTATATAAAAATATATTAATT
1 TTA-AT-AAAATATATTAATT
3286281 ATATTTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
17 11 0.32
18 2 0.06
19 6 0.18
20 2 0.06
21 11 0.32
22 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAAAATATATTAATT
Found at i:3287404 original size:60 final size:60
Alignment explanation
Indices: 3287290--3287404 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
3287280 TTGTAGAATC
* * * * *
3287290 TAATTAAAAATTTTAAAAATTTTCAAAAGTTTAATATTAATTTTTAAAACTTTTGGGATG
1 TAATTAAAAATTTTAAAAATTTTCAAAAGTATAATATAAAGTTTCAAAAATTTTGGGATG
3287350 TAATT-AAAATTTTCAAAAAATTTT-AAAAGTATAACTA-AAAGTTTCAAAAATTTTG
1 TAATTAAAAATTTT--AAAAATTTTCAAAAGTATAA-TATAAAGTTTCAAAAATTTTG
3287405 AGAAGGCAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
59 8 0.17
60 28 0.60
61 11 0.23
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (60 bp):
TAATTAAAAATTTTAAAAATTTTCAAAAGTATAATATAAAGTTTCAAAAATTTTGGGATG
Found at i:3287622 original size:20 final size:20
Alignment explanation
Indices: 3287597--3287637 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3287587 TTTTTATATG
*
3287597 TTTTTGACTTTATTTTAATT
1 TTTTTGACTTTATATTAATT
3287617 TTTTTGACTTTATATTAATT
1 TTTTTGACTTTATATTAATT
3287637 T
1 T
3287638 AATCCTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTGACTTTATATTAATT
Found at i:3293675 original size:33 final size:30
Alignment explanation
Indices: 3293609--3293676 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 30
3293599 AAATGATATT
*
3293609 TTTTGATTAAATAAAAAAAGAAGAAGCTAG
1 TTTTGATTAAATAAAAAAAGAAGAAGATAG
*
3293639 TTTTGATTAAAGTAATGAAAGAGAAGAGAGAT-G
1 TTTTGATTAAA-TAA--AAAAAGAAGA-AGATAG
3293672 TTTTG
1 TTTTG
3293677 TGTTTTTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 11 0.34
31 3 0.09
33 15 0.47
34 3 0.09
ACGTcount: A:0.46, C:0.01, G:0.22, T:0.31
Consensus pattern (30 bp):
TTTTGATTAAATAAAAAAAGAAGAAGATAG
Found at i:3295908 original size:3 final size:3
Alignment explanation
Indices: 3295838--3295867 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3295828 TAATTAAATA
3295838 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3295868 ACTAACATAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3296010 original size:2 final size:2
Alignment explanation
Indices: 3295973--3295997 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3295963 TTACATGTAC
3295973 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3295998 CATTTGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3296141 original size:3 final size:3
Alignment explanation
Indices: 3296133--3296260 Score: 73
Period size: 3 Copynumber: 41.7 Consensus size: 3
3296123 TATTTCTAAC
* *
3296133 TAT TAT TAT TTT TAT GTAT ATAT TAT TAT T-T ATAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* * * * * * * *
3296180 TAC TAT TACT AAA TAT TTT TAT TAT TAC TAT TAT TTT TGT TCCT T-T
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
* *
3296226 TAT TAT TGTT TAT TAT CAT TA- TAT TAT TAT TAT TA
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA
3296261 CTCCTTTTTT
Statistics
Matches: 95, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
2 5 0.05
3 77 0.81
4 13 0.14
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3296216 original size:18 final size:18
Alignment explanation
Indices: 3296136--3296346 Score: 89
Period size: 18 Copynumber: 11.6 Consensus size: 18
3296126 TTCTAACTAT
3296136 TATTATTTTTATGTA-TA-
1 TATTATTTTTAT-TATTAC
*
3296153 TATTATTATTTA-TATTAT
1 TATTATT-TTTATTATTAC
* * *
3296171 TGTTATTATTACTATTAC
1 TATTATTTTTATTATTAC
*
3296189 TAAATATTTTTATTATTAC
1 T-ATTATTTTTATTATTAC
* * *
3296208 TATTATTTTTGTTCCTT-T
1 TATTATTTTTATT-ATTAC
* *
3296226 TATTATTGTTTATTATCAT
1 TATTATT-TTTATTATTAC
*
3296245 TA-TATTATTATTATTAC
1 TATTATTTTTATTATTAC
** * *
3296262 TCCT-TTTTT-GTACTAC
1 TATTATTTTTATTATTAC
* * *
3296278 CATTATTGTTCATACATATAC
1 TATTATT-TTTAT-TAT-TAC
3296299 GTTATTATTTATTATTATTAC
1 --TATTATTT-TTATTATTAC
3296320 TA-TATTTTTTATTATTAC
1 TATTA-TTTTTATTATTAC
3296338 TA-TATTTTT
1 TATTATTTTT
3296347 GTATTCTTTC
Statistics
Matches: 145, Mismatches: 31, Indels: 36
0.68 0.15 0.17
Matches are distributed among these distances:
16 8 0.06
17 32 0.22
18 57 0.39
19 29 0.20
20 1 0.01
21 6 0.04
22 3 0.02
23 9 0.06
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.61
Consensus pattern (18 bp):
TATTATTTTTATTATTAC
Done.