Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 322 of 345
Found at i:96504400 original size:34 final size:34
Alignment explanation
Indices: 96504357--96504425 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
96504347 TTTGAACGAC
96504357 AATTATTTGGTCATGATGATATGATCCTGCACTA
1 AATTATTTGGTCATGATGATATGATCCTGCACTA
96504391 AATTATTTGGTCATGATGATATGATCCTGCACTA
1 AATTATTTGGTCATGATGATATGATCCTGCACTA
96504425 A
1 A
96504426 CTTTAACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (34 bp):
AATTATTTGGTCATGATGATATGATCCTGCACTA
Found at i:96514243 original size:46 final size:46
Alignment explanation
Indices: 96514176--96514346 Score: 188
Period size: 46 Copynumber: 3.7 Consensus size: 46
96514166 AACCTGCCCC
*
96514176 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
* *
96514222 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCA
* * * * * *
96514270 TCA-CGAACTCAGACTCAACTCAACGAGTTCAGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
96514315 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
96514347 AATGCTCAAC
Statistics
Matches: 101, Mismatches: 15, Indels: 18
0.75 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 1 0.01
45 2 0.02
46 57 0.56
47 26 0.26
48 3 0.03
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:96514289 original size:93 final size:93
Alignment explanation
Indices: 96514181--96514351 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
96514171 GCCCCTAAGT
* * * *
96514181 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
96514246 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGAATGCCTAGTTACATTTCAC
*
96514274 GAACTCAGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
96514339 CGAGTTCGAATGC
66 CGAGTTCGAATGC
96514352 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGAATGCCTAGTTACATTTCAC
Found at i:96519363 original size:93 final size:93
Alignment explanation
Indices: 96519256--96519426 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
96519246 GCCCCTAAGT
* *
96519256 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
96519321 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
96519349 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
96519414 CGAGTTCGGATGC
66 CGAGTTCGGATGC
96519427 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:96519423 original size:46 final size:46
Alignment explanation
Indices: 96519251--96519423 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
96519241 AACCTGCCCC
* * *
96519251 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
96519297 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
96519345 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
96519390 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
96519424 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 61 0.57
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:96520333 original size:22 final size:22
Alignment explanation
Indices: 96520301--96520342 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
96520291 CTATAAAGTA
* *
96520301 ATATTACTTGAATAGTTATGAG
1 ATATTAATTGAATAATTATGAG
96520323 ATATTAATTGAATAATTATG
1 ATATTAATTGAATAATTATG
96520343 TTTCTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATTAATTGAATAATTATGAG
Found at i:96524891 original size:31 final size:30
Alignment explanation
Indices: 96524856--96524923 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
96524846 TTTAACATGC
96524856 TAGTGACTTAAAT-AAATTTTTTTGAATAGTT
1 TAGTGACTTAAATGAAA--TTTTTGAATAGTT
* *
96524887 TAGTGTCTTAGATGAAATTTTTGAATAGTT
1 TAGTGACTTAAATGAAATTTTTGAATAGTT
*
96524917 TAATGAC
1 TAGTGAC
96524924 CTAATTGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 18 0.56
31 11 0.34
32 3 0.09
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (30 bp):
TAGTGACTTAAATGAAATTTTTGAATAGTT
Found at i:96534370 original size:21 final size:21
Alignment explanation
Indices: 96534330--96534401 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
96534320 ATTTCAACAA
* *
96534330 AAAATATTTAATTATATTTTTT
1 AAAATATTT-TTTTTATTTTTT
*
96534352 AAAATATTTTTTTTATTTTTG
1 AAAATATTTTTTTTATTTTTT
* *
96534373 AGATTA-TTTTTTTATTTTTAT
1 AAAATATTTTTTTTATTTTT-T
96534394 AAAA-ATTT
1 AAAATATTT
96534402 AAAATTTATA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
20 14 0.35
21 17 0.43
22 9 0.22
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
AAAATATTTTTTTTATTTTTT
Found at i:96534430 original size:20 final size:19
Alignment explanation
Indices: 96534401--96534445 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
96534391 TATAAAAATT
*
96534401 TAAAATTTATATACATTTAA
1 TAAAAATTATAT-CATTTAA
* *
96534421 TAAAAATTATATCTTTTTA
1 TAAAAATTATATCATTTAA
96534440 TAAAAA
1 TAAAAA
96534446 GAAATAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAAATTATATCATTTAA
Found at i:96535137 original size:29 final size:31
Alignment explanation
Indices: 96535105--96535176 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
96535095 AATTAGGGAT
*
96535105 ATAAATAATTATATTTATTT-GATGTA-ATA
1 ATAAATAATTATATTTATTTAAATGTATATA
96535134 ATAAATTAA-TATATTTATTTAAATGTATATA
1 ATAAA-TAATTATATTTATTTAAATGTATATA
*
96535165 ATTAA-AATTATA
1 ATAAATAATTATA
96535177 CTAAAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
29 18 0.49
30 12 0.32
31 7 0.19
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (31 bp):
ATAAATAATTATATTTATTTAAATGTATATA
Found at i:96540477 original size:2 final size:2
Alignment explanation
Indices: 96540428--96540464 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
96540418 TCTCAAATCA
96540428 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
96540465 AGTTGATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:96540953 original size:21 final size:21
Alignment explanation
Indices: 96540929--96541057 Score: 91
Period size: 21 Copynumber: 6.2 Consensus size: 21
96540919 AAAGCTGAAC
*
96540929 AGAAGCTCATGAGAGCTAAAT
1 AGAAGCTCATAAGAGCTAAAT
96540950 AGAAGCTCATAAGAGCTAACA-
1 AGAAGCTCATAAGAGCTAA-AT
* * * * * *
96540971 A-AAACCCATAAGGGTTTAAC
1 AGAAGCTCATAAGAGCTAAAT
* * *
96540991 AAAAGCTCGTAAGAGCTGAAT
1 AGAAGCTCATAAGAGCTAAAT
* * * *
96541012 AGAAACTCATATGAGTTAAAC
1 AGAAGCTCATAAGAGCTAAAT
* *
96541033 AGAAGCTCAAAAGAGCTAAAC
1 AGAAGCTCATAAGAGCTAAAT
96541054 AGAA
1 AGAA
96541058 AGTAAAACAC
Statistics
Matches: 81, Mismatches: 24, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
19 1 0.01
20 13 0.16
21 66 0.81
22 1 0.01
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.17
Consensus pattern (21 bp):
AGAAGCTCATAAGAGCTAAAT
Found at i:96541047 original size:42 final size:41
Alignment explanation
Indices: 96540921--96541058 Score: 134
Period size: 42 Copynumber: 3.3 Consensus size: 41
96540911 GAAGCCTGAA
* * *
96540921 AGCTGAACAGAAGCTCATGAGAGCTAAATAGAAGCTCATAAG
1 AGCTGAACAGAAACTCAT-AGAGTTAAACAGAAGCTCATAAG
* * * * * *
96540963 AGCT-AACAAAAACCCATAAGGGTTTAACAAAAGCTCGTAAG
1 AGCTGAACAGAAACTCAT-AGAGTTAAACAGAAGCTCATAAG
* *
96541004 AGCTGAATAGAAACTCATATGAGTTAAACAGAAGCTCAAAAG
1 AGCTGAACAGAAACTCATA-GAGTTAAACAGAAGCTCATAAG
*
96541046 AGCTAAACAGAAA
1 AGCTGAACAGAAA
96541059 GTAAAACACG
Statistics
Matches: 74, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
41 32 0.43
42 42 0.57
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.17
Consensus pattern (41 bp):
AGCTGAACAGAAACTCATAGAGTTAAACAGAAGCTCATAAG
Found at i:96544191 original size:26 final size:26
Alignment explanation
Indices: 96544145--96544197 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
96544135 TCAAACATGC
*
96544145 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAAGGGT
* *
96544171 ATTTCGGT-AATTTATCTCCTAAGGGT
1 ATTTAGGTCAATTTAAC-CCTAAGGGT
96544197 A
1 A
96544198 AAACTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAAGGGT
Found at i:96545719 original size:32 final size:32
Alignment explanation
Indices: 96545682--96545745 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
96545672 ATGCTTATCG
96545682 TGCCCATCATCCATTAACTATTAAAATGCTAA
1 TGCCCATCATCCATTAACTATTAAAATGCTAA
*
96545714 TGCCCATCATTCATTAACTATTAAAATGCTAA
1 TGCCCATCATCCATTAACTATTAAAATGCTAA
96545746 AATGCATACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (32 bp):
TGCCCATCATCCATTAACTATTAAAATGCTAA
Found at i:96545765 original size:32 final size:31
Alignment explanation
Indices: 96545685--96545766 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 31
96545675 CTTATCGTGC
* *
96545685 CCATCATCCATTAACTATTAAAATGCTAATG
1 CCATCATTCATCAACTATTAAAATGCTAATG
*
96545716 CCCATCATTCATTAACTATTAAAATGCTAAAATG
1 -CCATCATTCATCAACTATTAAAATGCT--AATG
96545750 -CATACATT-ATCAACTAT
1 CCAT-CATTCATCAACTAT
96545767 CCATCACCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
32 37 0.82
33 4 0.09
34 4 0.09
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (31 bp):
CCATCATTCATCAACTATTAAAATGCTAATG
Found at i:96546191 original size:29 final size:30
Alignment explanation
Indices: 96546118--96546179 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
96546108 GCAGTATTTA
*
96546118 TAACTCTAAATTTAAACTTTTGAATTTTTT
1 TAACTCTAAATTTAAACTTTTAAATTTTTT
96546148 TAACTCTAAATTTAAACTTTTAAATTTTTT
1 TAACTCTAAATTTAAACTTTTAAATTTTTT
96546178 TA
1 TA
96546180 TATTCGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.53
Consensus pattern (30 bp):
TAACTCTAAATTTAAACTTTTAAATTTTTT
Found at i:96547680 original size:22 final size:22
Alignment explanation
Indices: 96547655--96547701 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
96547645 AGACTCTCGA
*
96547655 TTTTGAAGAATCAATAAACCTC
1 TTTTGAAAAATCAATAAACCTC
*
96547677 TTTTGAAAAATTAATAAACCTC
1 TTTTGAAAAATCAATAAACCTC
96547699 TTT
1 TTT
96547702 CGAGGTGTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.38
Consensus pattern (22 bp):
TTTTGAAAAATCAATAAACCTC
Found at i:96550810 original size:2 final size:2
Alignment explanation
Indices: 96550803--96550851 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
96550793 ACAAAACGTG
*
96550803 TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
96550845 TA TA TA T
1 TA TA TA T
96550852 GCCATCCACC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:96554877 original size:2 final size:2
Alignment explanation
Indices: 96554870--96554901 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
96554860 TTATGCAAAC
96554870 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
96554902 CATTCACATT
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:96560790 original size:33 final size:35
Alignment explanation
Indices: 96560694--96560791 Score: 91
Period size: 33 Copynumber: 2.9 Consensus size: 35
96560684 GTTAATATTT
*
96560694 TAATATATGAAATATAAATTTTAAATATTT--TTAAG
1 TAATATAT-AAAT-TATATTTTAAATATTTAATTAAG
* *
96560729 TAATAAATATGAATTAT-TTATAAA-ATTTAATT-AG
1 TAAT--ATATAAATTATATTTTAAATATTTAATTAAG
96560763 -AATATATAAATTATATTTTAAATATTTAA
1 TAATATATAAATTATATTTTAAATATTTAA
96560792 ATATAACAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.19
32 6 0.12
33 13 0.25
34 8 0.15
35 8 0.15
36 3 0.06
37 4 0.08
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (35 bp):
TAATATATAAATTATATTTTAAATATTTAATTAAG
Found at i:96560851 original size:19 final size:20
Alignment explanation
Indices: 96560819--96560856 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
96560809 TTGTAATTAG
96560819 TATTTTAAAAAAT-ATTTTT
1 TATTTTAAAAAATAATTTTT
**
96560838 TATTTTAATTAATAATTTT
1 TATTTTAAAAAATAATTTT
96560857 GACACATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTTAAAAAATAATTTTT
Found at i:96561902 original size:27 final size:27
Alignment explanation
Indices: 96561862--96561916 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
96561852 AACAGATAAA
*
96561862 TATAAGTCCGGAGAAAAAGGAGTGAGT
1 TATAAGTCCAGAGAAAAAGGAGTGAGT
96561889 TATAAGTCCAGAGAAAAAGGAGTGAGT
1 TATAAGTCCAGAGAAAAAGGAGTGAGT
96561916 T
1 T
96561917 CCTTCATTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.31, T:0.20
Consensus pattern (27 bp):
TATAAGTCCAGAGAAAAAGGAGTGAGT
Found at i:96567100 original size:25 final size:26
Alignment explanation
Indices: 96567051--96567101 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
96567041 AATAAATTAT
* * *
96567051 TGTGAATTAAATAAAATATAGAAACA
1 TGTGAATTAAACAAAATACACAAACA
96567077 TGTG-ATTAAACAAAATACACAAACA
1 TGTGAATTAAACAAAATACACAAACA
96567102 AAACTCACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.24
Consensus pattern (26 bp):
TGTGAATTAAACAAAATACACAAACA
Found at i:96567356 original size:7 final size:8
Alignment explanation
Indices: 96567332--96567363 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
96567322 TTTAGATTTG
96567332 AATTTAAA
1 AATTTAAA
96567340 AATTTAAA
1 AATTTAAA
96567348 AATTTAAA
1 AATTTAAA
96567356 AA-TTAAA
1 AATTTAAA
96567363 A
1 A
96567364 TTCATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AATTTAAA
Found at i:96567377 original size:16 final size:16
Alignment explanation
Indices: 96567358--96567396 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
96567348 AATTTAAAAA
96567358 TTAAAATTCAT-ATTT
1 TTAAAATTCATAATTT
*
96567373 TTTAAATTCATAATTT
1 TTAAAATTCATAATTT
96567389 TTAAAATT
1 TTAAAATT
96567397 TTATTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAAAATTCATAATTT
Found at i:96567404 original size:15 final size:16
Alignment explanation
Indices: 96567358--96567396 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
96567348 AATTTAAAAA
96567358 TTAAAATTCATATTTT
1 TTAAAATTCATATTTT
*
96567374 TT-AAATTCATAATTT
1 TTAAAATTCATATTTT
96567389 TTAAAATT
1 TTAAAATT
96567397 TTATTTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAAAATTCATATTTT
Found at i:96571283 original size:13 final size:13
Alignment explanation
Indices: 96571265--96571291 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
96571255 GTTCTGAAAA
96571265 TTCTTAACTTTAT
1 TTCTTAACTTTAT
96571278 TTCTTAACTTTAT
1 TTCTTAACTTTAT
96571291 T
1 T
96571292 AATCGAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (13 bp):
TTCTTAACTTTAT
Found at i:96576196 original size:36 final size:36
Alignment explanation
Indices: 96576152--96576220 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
96576142 TTATTACTAT
*
96576152 TATATATTATTTTCCTCAAAT-TATTAT-TATTTTTA
1 TATATATTATATT-CTCAAATATATTATATATTTTTA
*
96576187 TATATTATTATATTCTCACATATATTATATATTT
1 TATA-TATTATATTCTCAAATATATTATATATTT
96576221 ATTAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 10 0.34
36 14 0.48
37 5 0.17
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (36 bp):
TATATATTATATTCTCAAATATATTATATATTTTTA
Found at i:96576222 original size:35 final size:35
Alignment explanation
Indices: 96576142--96576235 Score: 90
Period size: 35 Copynumber: 2.7 Consensus size: 35
96576132 AGTGTTATTT
96576142 TTATTACTA-TTATATATTATT-T-TCCTCAAATTA
1 TTATTA-TATTTATATATTATTATATCCTCAAATTA
* * *
96576175 TTATTATTTTTATATATTATTATATTCTCACATATA
1 TTATTATATTTATATATTATTATATCCTCAAAT-TA
96576211 TTA-TATATTTAT-TAATTATTTATAT
1 TTATTATATTTATAT-ATTA-TTATAT
96576236 ATATATATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
32 1 0.02
33 18 0.35
34 2 0.04
35 19 0.37
36 11 0.22
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (35 bp):
TTATTATATTTATATATTATTATATCCTCAAATTA
Found at i:96576400 original size:20 final size:20
Alignment explanation
Indices: 96576367--96576405 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
96576357 TGTATCGCCA
* *
96576367 ATTATATTTTTTATGATTAC
1 ATTATATATATTATGATTAC
*
96576387 ATTATATATATTATTATTA
1 ATTATATATATTATGATTA
96576406 TTATTAAATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
ATTATATATATTATGATTAC
Found at i:96576419 original size:26 final size:24
Alignment explanation
Indices: 96576369--96576419 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
96576359 TATCGCCAAT
* *
96576369 TATATTTTTTATGATTACATTATA
1 TATATTTTTTATGATTAAATCATA
*
96576393 TATATTATTATTATTATTAAATCATA
1 TATATT-TT-TTATGATTAAATCATA
96576419 T
1 T
96576420 TTTTAACCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 6 0.27
25 2 0.09
26 14 0.64
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (24 bp):
TATATTTTTTATGATTAAATCATA
Found at i:96583394 original size:334 final size:335
Alignment explanation
Indices: 96582754--96583423 Score: 925
Period size: 334 Copynumber: 2.0 Consensus size: 335
96582744 TATAAGAGGG
* * * * *
96582754 GAATACGAAAGTGGTGGTGTTGGACCAGGCTGATAGTAGACAAATTCTGGGTTAACCATTGGGAG
1 GAATACGAAACTGGTGGTGTTGGACCAGGATGATAGTAGACAAATTCTAGGTCAACCATCGGGAG
** * ** *
96582819 TGGTCCATCGGGGTGAAAGTGAAGTGACACTCATGGACGATTCATTTGATAAGTAATGGTGCCCT
66 TGGTCCATCAAGGTGAAAGCGAAGCAACACTCATGGACGATTCATTTGATAAGTAATGGTGCCAT
* * * *
96582884 AAAATGTTTAGCTGCTTCTAATTGTGATTTTTATAATGTCAAGAATTTTTGTATGGAATTACCAA
131 AAAATGTTTAGCTGCTTCTAATTCTAATTCTTATAATGTCAAGAATTTTTGTATGGAACTACCAA
* * * * * * *
96582949 GGTGCTGGACACTCTAATTTTGGCAGAATTATGAAGGAGTATTTATGTGAAGTAGATCCTTGTGT
196 GGTACTGGACACCCTAATTTTGGAAGAATTATAAAGGAGTATTTACGCGAAGTAGATCCCTGTGT
* *
96583014 TTTAGTTTTAATGGAAACCTGAATTAGTGGATTAAAAGCTGATAGAGTGATTAAAAGTATTAGCC
261 TGTAGTTTTAATGGAAACCTGAATTAGTGGATTAAAAGCCGATAGAGTGATTAAAAGTATTAGCC
96583079 TGCCTTACTC
326 TGCCTTACTC
* * * *
96583089 GAATATGAAACTGGTGGTGTTGGACTAGGATGATA--ACGAACAAATTCTAGGTCGACTATCGGG
1 GAATACGAAACTGGTGGTGTTGGACCAGGATGATAGTA-G-ACAAATTCTAGGTCAACCATCGGG
* * * *
96583152 AGTGGTCTATCAAGGTGAAAGCGATGCAACACTCATGGACTATTCATTTGATAAGTAATGGTGCT
64 AGTGGTCCATCAAGGTGAAAGCGAAGCAACACTCATGGACGATTCATTTGATAAGTAATGGTGCC
* * * *
96583217 ATCAAAA-GTTTGGTTGTTTCTAATTCTAATTCTTATAATGTCAAGAA-TTTTGTATGGAACTGC
129 AT-AAAATGTTTAGCTGCTTCTAATTCTAATTCTTATAATGTCAAGAATTTTTGTATGGAACTAC
96583280 CAAGGTACTGGACACCCTAATTTTGGAAGAATTATAAAGGAGTATTTACGCGAAGTAGATCCCTG
193 CAAGGTACTGGACACCCTAATTTTGGAAGAATTATAAAGGAGTATTTACGCGAAGTAGATCCCTG
* * *
96583345 TGTTGTGGTTTTGATGGAAACCTGAATTAGTGGATTAAAAGCCGATAGAGTGATTAAAAGTATTG
258 TGTTGTAGTTTTAATGGAAACCTGAATTAGTGGATTAAAAGCCGATAGAGTGATTAAAAGTATTA
*
96583410 GTCTGCCTTACTC
323 GCCTGCCTTACTC
96583423 G
1 G
96583424 CATTGGGTGG
Statistics
Matches: 292, Mismatches: 40, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
333 1 0.00
334 146 0.50
335 141 0.48
336 4 0.01
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (335 bp):
GAATACGAAACTGGTGGTGTTGGACCAGGATGATAGTAGACAAATTCTAGGTCAACCATCGGGAG
TGGTCCATCAAGGTGAAAGCGAAGCAACACTCATGGACGATTCATTTGATAAGTAATGGTGCCAT
AAAATGTTTAGCTGCTTCTAATTCTAATTCTTATAATGTCAAGAATTTTTGTATGGAACTACCAA
GGTACTGGACACCCTAATTTTGGAAGAATTATAAAGGAGTATTTACGCGAAGTAGATCCCTGTGT
TGTAGTTTTAATGGAAACCTGAATTAGTGGATTAAAAGCCGATAGAGTGATTAAAAGTATTAGCC
TGCCTTACTC
Found at i:96584943 original size:18 final size:19
Alignment explanation
Indices: 96584905--96584945 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
96584895 TGGTTCATGT
96584905 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
96584924 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
96584942 TTTC
1 TTTC
96584946 TCATTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:96585135 original size:39 final size:38
Alignment explanation
Indices: 96585068--96585202 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
96585058 ACCAATATGG
* * *
96585068 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
96585107 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
96585145 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
96585186 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
96585203 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:96585468 original size:18 final size:19
Alignment explanation
Indices: 96585442--96585480 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
96585432 TTTCAATTCA
96585442 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
96585461 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
96585479 AT
1 AT
96585481 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:96586842 original size:5 final size:5
Alignment explanation
Indices: 96586784--96586831 Score: 87
Period size: 5 Copynumber: 9.4 Consensus size: 5
96586774 TTATGTTTAT
96586784 ATATA ATATA ATATA ATATA ATAATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA ATATA ATATA AT
96586832 TAAAAATAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 37 0.88
6 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:96591337 original size:18 final size:19
Alignment explanation
Indices: 96591299--96591339 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
96591289 TGGTTCATGT
96591299 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
96591318 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
96591336 TTTC
1 TTTC
96591340 TCATTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:96591529 original size:39 final size:38
Alignment explanation
Indices: 96591462--96591596 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
96591452 ACCAATATGG
* * *
96591462 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
96591501 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
96591539 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
96591580 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
96591597 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:96591862 original size:18 final size:19
Alignment explanation
Indices: 96591836--96591874 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
96591826 TTTCAATTCA
96591836 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
96591855 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
96591873 AT
1 AT
96591875 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:96593188 original size:5 final size:5
Alignment explanation
Indices: 96593178--96593214 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
96593168 TTATGTTTAT
96593178 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
96593215 TAAAACATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:96594957 original size:24 final size:23
Alignment explanation
Indices: 96594899--96594990 Score: 107
Period size: 24 Copynumber: 3.9 Consensus size: 23
96594889 AACTCACTGT
*
96594899 AGCTCGTATGAGCTTACTGATATATC
1 AGCTCGTAAGAGCTTACTG-T-T-TC
96594925 AGCTCGTAAGAGCTTACTGTTCTC
1 AGCTCGTAAGAGCTTACTGTT-TC
*
96594949 AGCTTGTAAGAGCTTACTGTTTC
1 AGCTCGTAAGAGCTTACTGTTTC
96594972 AGCTC--AATGAGCTTACTGT
1 AGCTCGTAA-GAGCTTACTGT
96594991 CCATCAGCTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
21 2 0.03
22 11 0.18
23 6 0.10
24 23 0.38
25 1 0.02
26 18 0.30
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (23 bp):
AGCTCGTAAGAGCTTACTGTTTC
Found at i:96594967 original size:50 final size:47
Alignment explanation
Indices: 96594899--96595013 Score: 119
Period size: 50 Copynumber: 2.4 Consensus size: 47
96594889 AACTCACTGT
* *
96594899 AGCTCGTATGAGCTTACTGATATATCAGCTCGTAA-GAGCTTACTGTTC-TC
1 AGCTCGTAAGAGCTTACTG-T-T-TCAGCTC--AATGAGCTTACTGTCCATC
*
96594949 AGCTTGTAAGAGCTTACTGTTTCAGCTCAATGAGCTTACTGTCCATC
1 AGCTCGTAAGAGCTTACTGTTTCAGCTCAATGAGCTTACTGTCCATC
96594996 AGCTCAG-AAGGAGCTTAC
1 AGCTC-GTAA-GAGCTTAC
96595014 CGATCATAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
45 2 0.04
46 12 0.21
47 15 0.26
48 10 0.18
49 1 0.02
50 17 0.30
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (47 bp):
AGCTCGTAAGAGCTTACTGTTTCAGCTCAATGAGCTTACTGTCCATC
Found at i:96595013 original size:26 final size:24
Alignment explanation
Indices: 96594899--96595013 Score: 96
Period size: 26 Copynumber: 4.7 Consensus size: 24
96594889 AACTCACTGT
* *
96594899 AGCTCGTATGAGCTTACTGATATATC
1 AGCTCGTAAGAGCTTACTG-T-CATC
96594925 AGCTCGTAAGAGCTTACTGTTC-TC
1 AGCTCGTAAGAGCTTACTG-TCATC
* *
96594949 AGCTTGTAAGAGCTTACTGT-TTC
1 AGCTCGTAAGAGCTTACTGTCATC
96594972 AGCTC--AATGAGCTTACTGTCCATC
1 AGCTCGTAA-GAGCTTACTGT-CATC
96594996 AGCTCAG-AAGGAGCTTAC
1 AGCTC-GTAA-GAGCTTAC
96595014 CGATCATAGA
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
21 2 0.03
22 11 0.14
23 7 0.09
24 27 0.36
26 29 0.38
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (24 bp):
AGCTCGTAAGAGCTTACTGTCATC
Found at i:96595183 original size:19 final size:19
Alignment explanation
Indices: 96595159--96595238 Score: 81
Period size: 19 Copynumber: 4.2 Consensus size: 19
96595149 AAAAGCTATG
96595159 TGTTATACGGATGAATTAC
1 TGTTATACGGATGAATTAC
* **
96595178 TGTTATATGGATGAGGTAC
1 TGTTATACGGATGAATTAC
* *
96595197 TATTTATACGGATGAGTTAC
1 T-GTTATACGGATGAATTAC
* *
96595217 TGTTAT-TGAATGAATTAC
1 TGTTATACGGATGAATTAC
96595235 TGTT
1 TGTT
96595239 TATATGATTG
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
18 13 0.26
19 21 0.42
20 16 0.32
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.41
Consensus pattern (19 bp):
TGTTATACGGATGAATTAC
Found at i:96595209 original size:20 final size:19
Alignment explanation
Indices: 96595159--96595222 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
96595149 AAAAGCTATG
*
96595159 TGTTATACGGATGAATTAC
1 TGTTATACGGATGAGTTAC
* *
96595178 TGTTATATGGATGAGGTAC
1 TGTTATACGGATGAGTTAC
*
96595197 TATTTATACGGATGAGTTAC
1 T-GTTATACGGATGAGTTAC
96595217 TGTTAT
1 TGTTAT
96595223 TGAATGAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
19 21 0.57
20 16 0.43
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (19 bp):
TGTTATACGGATGAGTTAC
Found at i:96595500 original size:49 final size:49
Alignment explanation
Indices: 96595444--96595542 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
96595434 AAAAGGTAAG
96595444 TTAAAATCTGAATTATATGGGCCTACTAAGCTATAAAGCTTACTCTGTT
1 TTAAAATCTGAATTATATGGGCCTACTAAGCTATAAAGCTTACTCTGTT
96595493 TTAAAATCTGAATTATATGGGCCTACTAAGCTATAAAGCTTACTCTGTT
1 TTAAAATCTGAATTATATGGGCCTACTAAGCTATAAAGCTTACTCTGTT
96595542 T
1 T
96595543 CTTTTTCCAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (49 bp):
TTAAAATCTGAATTATATGGGCCTACTAAGCTATAAAGCTTACTCTGTT
Found at i:96599521 original size:12 final size:12
Alignment explanation
Indices: 96599504--96599531 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
96599494 CACCACACAA
96599504 CCGTGTGGTAGG
1 CCGTGTGGTAGG
96599516 CCGTGTGGTAGG
1 CCGTGTGGTAGG
96599528 CCGT
1 CCGT
96599532 ATGCCCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.21, G:0.46, T:0.25
Consensus pattern (12 bp):
CCGTGTGGTAGG
Found at i:96607075 original size:19 final size:20
Alignment explanation
Indices: 96607051--96607089 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
96607041 CACTATGAAC
96607051 CCAAAAGATA-ATAAAAAAA
1 CCAAAAGATATATAAAAAAA
*
96607070 CCAAAATATATATAAAAAAA
1 CCAAAAGATATATAAAAAAA
96607090 GTCCCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.72, C:0.10, G:0.03, T:0.15
Consensus pattern (20 bp):
CCAAAAGATATATAAAAAAA
Found at i:96612692 original size:27 final size:26
Alignment explanation
Indices: 96612655--96612769 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
96612645 AGCATGGCTG
* *
96612655 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
96612681 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
96612709 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
96612736 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
96612763 CCAGAAC
1 CCAGAAC
96612770 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:96612714 original size:54 final size:54
Alignment explanation
Indices: 96612655--96612769 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
96612645 AGCATGGCTG
*
96612655 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
96612709 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
96612763 CCAGAAC
1 CCAGAAC
96612770 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:96614425 original size:26 final size:26
Alignment explanation
Indices: 96614390--96614499 Score: 159
Period size: 26 Copynumber: 4.2 Consensus size: 26
96614380 CATGAAATTC
*
96614390 TTATCATGAAACATTTACCTAACCCC
1 TTATCATGAAACATTTACCTAACCCA
96614416 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
96614442 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
96614468 TTATCATTG-AATATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
96614494 TTATCA
1 TTATCA
96614500 ATTTGTACCA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
26 77 0.97
27 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:96615417 original size:2 final size:2
Alignment explanation
Indices: 96615410--96615453 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
96615400 AAACCTATTG
96615410 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96615452 AT
1 AT
96615454 GGAATAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96620026 original size:36 final size:36
Alignment explanation
Indices: 96619981--96620055 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
96619971 AAATACAGAG
96619981 AAAAACGCTTCCAGCATTTTTCTGAATTTTCCCTGA
1 AAAAACGCTTCCAGCATTTTTCTGAATTTTCCCTGA
96620017 AAAAACGCTTCCAGCATTTTTCTGAATTTTCCCTGA
1 AAAAACGCTTCCAGCATTTTTCTGAATTTTCCCTGA
96620053 AAA
1 AAA
96620056 CATTTCCAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.35
Consensus pattern (36 bp):
AAAAACGCTTCCAGCATTTTTCTGAATTTTCCCTGA
Found at i:96632006 original size:15 final size:15
Alignment explanation
Indices: 96631986--96632016 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
96631976 CATATTCATC
96631986 AAAATAGTTTGGATA
1 AAAATAGTTTGGATA
96632001 AAAATAGTTTGGATA
1 AAAATAGTTTGGATA
96632016 A
1 A
96632017 CAACAGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (15 bp):
AAAATAGTTTGGATA
Found at i:96634697 original size:21 final size:22
Alignment explanation
Indices: 96634668--96634723 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
96634658 CACGGCCTAG
* *
96634668 CACACGGGCGTGTCCCAAGG-T
1 CACATGGGCGTGTCCCAAGGAC
* **
96634689 CACATGGGCATGTCCCTTGGAC
1 CACATGGGCGTGTCCCAAGGAC
96634711 CACATGGGCGTGT
1 CACATGGGCGTGT
96634724 GAGCCCTGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.18, C:0.30, G:0.32, T:0.20
Consensus pattern (22 bp):
CACATGGGCGTGTCCCAAGGAC
Found at i:96635925 original size:21 final size:22
Alignment explanation
Indices: 96635882--96635936 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
96635872 ATACCCAAGT
*
96635882 CCAAAATTCAAAATAACAAGGC
1 CCAAAATACAAAATAACAAGGC
* *
96635904 CCAAAATACAAATTAA-ATGGC
1 CCAAAATACAAAATAACAAGGC
*
96635925 CCAATA-ACAAAA
1 CCAAAATACAAAA
96635937 AAAAAAACAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 5 0.18
21 9 0.32
22 14 0.50
ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (22 bp):
CCAAAATACAAAATAACAAGGC
Found at i:96636841 original size:17 final size:17
Alignment explanation
Indices: 96636819--96636853 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
96636809 CTTTAACCCC
*
96636819 TGTGCATTTGTACTCAT
1 TGTGCATTGGTACTCAT
*
96636836 TGTGCATTGGTCCTCAT
1 TGTGCATTGGTACTCAT
96636853 T
1 T
96636854 TTAATTTCAA
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:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (17 bp):
TGTGCATTGGTACTCAT
Found at i:96637717 original size:23 final size:22
Alignment explanation
Indices: 96637683--96637726 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
96637673 GTTTTTTAAA
*
96637683 TTCATCAATTCATATATTATGTG
1 TTCATCAATTCAT-CATTATGTG
*
96637706 TTCATCAGTTCATCATTATGT
1 TTCATCAATTCATCATTATGT
96637727 TAAATCTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (22 bp):
TTCATCAATTCATCATTATGTG
Found at i:96639533 original size:20 final size:20
Alignment explanation
Indices: 96639494--96639533 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
96639484 CAAACCCCCA
*
96639494 AAACTTTTTATTTTCTCCCT
1 AAACTTTTTATTTTCACCCT
96639514 AAAC-TTTTATTTCTCACCCT
1 AAACTTTTTATTT-TCACCCT
96639534 TTACCCCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.50
Consensus pattern (20 bp):
AAACTTTTTATTTTCACCCT
Found at i:96647063 original size:35 final size:34
Alignment explanation
Indices: 96647018--96647088 Score: 124
Period size: 35 Copynumber: 2.1 Consensus size: 34
96647008 TCTAACTAGC
96647018 TTCGATTTTATTGTAAGCTCTTAAATATTGTGAT
1 TTCGATTTTATTGTAAGCTCTTAAATATTGTGAT
*
96647052 TTCGAATTTTATTGTAAGCTCTTAGATATTGTGAT
1 TTCG-ATTTTATTGTAAGCTCTTAAATATTGTGAT
96647087 TT
1 TT
96647089 TGAGTGAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 4 0.11
35 31 0.89
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.51
Consensus pattern (34 bp):
TTCGATTTTATTGTAAGCTCTTAAATATTGTGAT
Found at i:96664733 original size:34 final size:35
Alignment explanation
Indices: 96664652--96664740 Score: 108
Period size: 36 Copynumber: 2.5 Consensus size: 35
96664642 AGTACATTGA
* ** *
96664652 TAATCCAACCGAAACACATTAGATGCTCATAAGAGC
1 TAATCCATCCGAAACACACCA-CTGCTCATAAGAGC
* *
96664688 TAATCCATCCGAGACACACCACTGCTCATAAGATC
1 TAATCCATCCGAAACACACCACTGCTCATAAGAGC
96664723 T-ATCCATCCGAAACACAC
1 TAATCCATCCGAAACACAC
96664741 TAAAAAAGGA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
34 16 0.35
35 13 0.28
36 17 0.37
ACGTcount: A:0.38, C:0.31, G:0.11, T:0.19
Consensus pattern (35 bp):
TAATCCATCCGAAACACACCACTGCTCATAAGAGC
Found at i:96665665 original size:30 final size:30
Alignment explanation
Indices: 96665631--96665690 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
96665621 GAATTTGATT
96665631 AATGTTTCAATTTGTTTCATTAAATTTTAA
1 AATGTTTCAATTTGTTTCATTAAATTTTAA
96665661 AATGTTTCAATTTGTTTCATTAAATTTTAA
1 AATGTTTCAATTTGTTTCATTAAATTTTAA
96665691 CTTATTTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (30 bp):
AATGTTTCAATTTGTTTCATTAAATTTTAA
Found at i:96669670 original size:20 final size:21
Alignment explanation
Indices: 96669625--96669671 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
96669615 ACGGTAAGTG
*
96669625 ACTTA-ATGAAAAGTTTCATA
1 ACTTATATGAAAAGGTTCATA
96669645 AC-TATATGAAAAGGTTCAT-
1 ACTTATATGAAAAGGTTCATA
*
96669664 GCTTATAT
1 ACTTATAT
96669672 CATGTATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (21 bp):
ACTTATATGAAAAGGTTCATA
Found at i:96670806 original size:2 final size:2
Alignment explanation
Indices: 96670799--96670839 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
96670789 GGAAATGGCA
96670799 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
96670840 TTAGGTAAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:96676875 original size:16 final size:16
Alignment explanation
Indices: 96676854--96676886 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
96676844 TAACTCAAGA
96676854 TCATGCGTTGGATAGT
1 TCATGCGTTGGATAGT
96676870 TCATGCGTTGGATAGT
1 TCATGCGTTGGATAGT
96676886 T
1 T
96676887 GCCCTCATAC
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:0.18, C:0.12, G:0.30, T:0.39
Consensus pattern (16 bp):
TCATGCGTTGGATAGT
Found at i:96688507 original size:30 final size:30
Alignment explanation
Indices: 96688466--96688532 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
96688456 CCACTGGATT
* *
96688466 TGAAACTTCACACATATTTGAATTTAAATA
1 TGAATCTTCACACATATTTGAATCTAAATA
96688496 TGAATCTTCACACATATTTGAATCTAAATA
1 TGAATCTTCACACATATTTGAATCTAAATA
96688526 TGAATCT
1 TGAATCT
96688533 ATCTTTGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.37
Consensus pattern (30 bp):
TGAATCTTCACACATATTTGAATCTAAATA
Found at i:96688519 original size:18 final size:18
Alignment explanation
Indices: 96688463--96688520 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
96688453 TCACCACTGG
*
96688463 ATTTGAAACTTCACACAT
1 ATTTGAATCTTCACACAT
96688481 ATTTGAAT-TT-A-A-AT
1 ATTTGAATCTTCACACAT
96688495 A--TGAATCTTCACACAT
1 ATTTGAATCTTCACACAT
96688511 ATTTGAATCT
1 ATTTGAATCT
96688521 AAATATGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
12 5 0.15
13 2 0.06
14 4 0.12
15 2 0.06
16 4 0.12
17 2 0.06
18 14 0.42
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.40
Consensus pattern (18 bp):
ATTTGAATCTTCACACAT
Found at i:96690670 original size:34 final size:34
Alignment explanation
Indices: 96690632--96690714 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
96690622 AACTACTAAG
96690632 CTAGCAGGGCCTATTCAATCAACTAGTCATTAAC
1 CTAGCAGGGCCTATTCAATCAACTAGTCATTAAC
* ** * *
96690666 CTAGCAAGTTCTATTCAATGAACTAGTTATTAAC
1 CTAGCAGGGCCTATTCAATCAACTAGTCATTAAC
*
96690700 CTAGTAGGGCCTATT
1 CTAGCAGGGCCTATT
96690715 GGCATTCCAC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (34 bp):
CTAGCAGGGCCTATTCAATCAACTAGTCATTAAC
Found at i:96696309 original size:23 final size:23
Alignment explanation
Indices: 96696282--96696342 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
96696272 ATAGAAAATG
*
96696282 GAAATAAAAACTACAATTGAAAA
1 GAAATAAAAACTAAAATTGAAAA
** * *
96696305 GAAATCTAAATTAAAATTGAAAG
1 GAAATAAAAACTAAAATTGAAAA
*
96696328 GAAAATTAAAACTAA
1 G-AAATAAAAACTAA
96696343 GTAAAAAGTC
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (23 bp):
GAAATAAAAACTAAAATTGAAAA
Found at i:96699974 original size:12 final size:11
Alignment explanation
Indices: 96699897--96699982 Score: 50
Period size: 11 Copynumber: 7.7 Consensus size: 11
96699887 TTTATTTCGC
*
96699897 TATTATATTA-
1 TATTTTATTAT
96699907 TATTGTTATTAT
1 TATT-TTATTAT
*
96699919 T-TTAATATTAT
1 TATT-TTATTAT
* *
96699930 TATTTGAATAT
1 TATTTTATTAT
* * * *
96699941 TATATAACTCT
1 TATTTTATTAT
96699952 TATTTTATTAT
1 TATTTTATTAT
*
96699963 TAATTTTGTTAT
1 T-ATTTTATTAT
96699975 TATTTTAT
1 TATTTTAT
96699983 AAATATTTAC
Statistics
Matches: 56, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
10 4 0.07
11 39 0.70
12 13 0.23
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.63
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:96700117 original size:22 final size:23
Alignment explanation
Indices: 96700091--96700140 Score: 93
Period size: 22 Copynumber: 2.2 Consensus size: 23
96700081 TTTTTAGTGT
96700091 ATTTAATATATTATA-TTTTAAA
1 ATTTAATATATTATATTTTTAAA
96700113 ATTTAATATATTATATTTTTAAA
1 ATTTAATATATTATATTTTTAAA
96700136 ATTTA
1 ATTTA
96700141 TTTTTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTAATATATTATATTTTTAAA
Found at i:96702089 original size:12 final size:12
Alignment explanation
Indices: 96702072--96702110 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
96702062 GTTATTAATA
96702072 TAATTTAGTTCT
1 TAATTTAGTTCT
96702084 TAATTTAGTTC-
1 TAATTTAGTTCT
96702095 TAATTT-GTT-T
1 TAATTTAGTTCT
96702105 TAATTT
1 TAATTT
96702111 TTTAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.35
11 6 0.23
12 11 0.42
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.62
Consensus pattern (12 bp):
TAATTTAGTTCT
Found at i:96703181 original size:13 final size:13
Alignment explanation
Indices: 96703165--96703230 Score: 80
Period size: 13 Copynumber: 5.1 Consensus size: 13
96703155 TTTAAACCAA
*
96703165 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
*
96703178 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
*
96703191 ACTTTTTC-ACAGC
1 AC-TTTTCAAAAGC
*
96703204 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
96703217 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
96703230 A
1 A
96703231 ATGAAGAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
12 4 0.09
13 36 0.82
14 4 0.09
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:96703194 original size:26 final size:26
Alignment explanation
Indices: 96703165--96703230 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
96703155 TTTAAACCAA
96703165 ACTTTTTAAAAGCACTTCTCAAAAGC
1 ACTTTTTAAAAGCACTTCTCAAAAGC
* *
96703191 ACTTTTTCACAGCACTTCTCAAAAGC
1 ACTTTTTAAAAGCACTTCTCAAAAGC
*
96703217 ACTTTTCAAAAGCA
1 ACTTTTTAAAAGCA
96703231 ATGAAGAACT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (26 bp):
ACTTTTTAAAAGCACTTCTCAAAAGC
Found at i:96703842 original size:18 final size:18
Alignment explanation
Indices: 96703818--96703857 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
96703808 AGTGCGACCC
96703818 ATTTTTTT-AATAATATA
1 ATTTTTTTAAATAATATA
* *
96703835 ATTTTTTTAAATATTATT
1 ATTTTTTTAAATAATATA
96703853 ATTTT
1 ATTTT
96703858 ATTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTTTAAATAATATA
Found at i:96703847 original size:15 final size:16
Alignment explanation
Indices: 96703818--96703864 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
96703808 AGTGCGACCC
96703818 ATTTTTTTAATAATATA
1 ATTTTTTT-ATAATATA
*
96703835 ATTTTTTTA-AATATT
1 ATTTTTTTATAATATA
* *
96703850 ATTATTTTATTATAT
1 ATTTTTTTATAATAT
96703865 TTTAATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 13 0.50
16 5 0.19
17 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTTTATAATATA
Found at i:96710802 original size:3 final size:3
Alignment explanation
Indices: 96710790--96710846 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
96710780 CTTTCTCCTC
* *
96710790 CTT CTC CTT CTT CTT CTT CTT CTT CTT TTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
96710838 -TT CTCT CTT
1 CTT CT-T CTT
96710847 TGCTGCTGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:96710847 original size:9 final size:10
Alignment explanation
Indices: 96710777--96710843 Score: 56
Period size: 9 Copynumber: 7.2 Consensus size: 10
96710767 ACATTTTTTC
96710777 CTTCTT-TCT
1 CTTCTTCTCT
*
96710786 CCTCCTTCTC-
1 -CTTCTTCTCT
96710796 CTTCTTCT-T
1 CTTCTTCTCT
96710805 CTTCTTCT-T
1 CTTCTTCTCT
*
96710814 CTTTTTCT-T
1 CTTCTTCTCT
96710823 CTTCTTCT-T
1 CTTCTTCTCT
*
96710832 CTTCTTTTCT
1 CTTCTTCTCT
96710842 CT
1 CT
96710844 CTTTGCTGCT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
9 39 0.80
10 8 0.16
11 2 0.04
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (10 bp):
CTTCTTCTCT
Found at i:96711108 original size:16 final size:15
Alignment explanation
Indices: 96711071--96711109 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
96711061 TAAAATATAA
96711071 TAAAATAATAATATTT
1 TAAAA-AATAATATTT
*
96711087 TAAAAAATTATATTAT
1 TAAAAAATAATATT-T
96711103 TAAAAAA
1 TAAAAAA
96711110 ATGGGTCGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAAAATAATATTT
Found at i:96712898 original size:25 final size:23
Alignment explanation
Indices: 96712856--96712904 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 23
96712846 ATAATTCTAC
*
96712856 TTGTCTGTCTTATGACGTGTTCT
1 TTGTCTGTCTTATGACGTATTCT
96712879 TTGTCTGTCTTATGACACGTATTCT
1 TTGTCTGTCTTATG--ACGTATTCT
96712904 T
1 T
96712905 CTTTTTGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.61
25 9 0.39
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.51
Consensus pattern (23 bp):
TTGTCTGTCTTATGACGTATTCT
Found at i:96712916 original size:15 final size:15
Alignment explanation
Indices: 96712898--96712949 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
96712888 TTATGACACG
96712898 TATTCTTCTTTTTGA
1 TATTCTTCTTTTTGA
*
96712913 TATTCTTCTTTTTTA
1 TATTCTTCTTTTTGA
*
96712928 TTTTCTT-TTGTTTGA
1 TATTCTTCTT-TTTGA
*
96712943 TTTTCTT
1 TATTCTT
96712950 TTGTCTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
14 2 0.06
15 31 0.94
ACGTcount: A:0.10, C:0.12, G:0.06, T:0.73
Consensus pattern (15 bp):
TATTCTTCTTTTTGA
Found at i:96715728 original size:47 final size:47
Alignment explanation
Indices: 96715659--96715924 Score: 206
Period size: 47 Copynumber: 5.6 Consensus size: 47
96715649 TATAATGCCA
* **
96715659 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATGAAGTTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTCATCCATGAAGCCG
* * *
96715706 ATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCGAAACCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTCATC--CA-TGAAGCCG
** * * *
96715755 ACACCATGTCTCAGACATGGTCTTACACTAGCCCTTACAT--ATTCGTA-CCG
1 ATGCCATGTCCCAGACATGGTCTTACACT-G-AC-T-CATCCA-T-GAAGCCG
* * * * *
96715805 ATGGCATGTCCCAGACATGGTCTTACACTGACACATCTATCG-TGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTCATCCAT-GAAGCCG
* * * *
96715852 ATGCCATGTCCCAGATATGGTCTTACACTGACACAT-CTTGTAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTCATCCATGAAGCCG
96715898 ATG-CATGTCCCAGACAT-GTCTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
96715925 AGCTCTTGTC
Statistics
Matches: 177, Mismatches: 29, Indels: 29
0.75 0.12 0.12
Matches are distributed among these distances:
44 10 0.06
45 14 0.08
46 13 0.07
47 71 0.40
48 3 0.02
49 31 0.18
50 30 0.17
51 2 0.01
52 1 0.01
54 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (47 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACTCATCCATGAAGCCG
Found at i:96729180 original size:26 final size:26
Alignment explanation
Indices: 96729149--96729256 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
96729139 TGAAATTCCC
*
96729149 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
96729175 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
96729201 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
96729227 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
96729253 ATCA
1 ATCA
96729257 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:96736203 original size:26 final size:26
Alignment explanation
Indices: 96736172--96736278 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
96736162 TGAAATTCCC
*
96736172 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
96736198 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
96736224 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
96736250 ATCATGGAA-ATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
96736275 ATCA
1 ATCA
96736279 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
25 19 0.25
26 58 0.75
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:96739487 original size:16 final size:15
Alignment explanation
Indices: 96739453--96739486 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
96739443 ACAGTAATCC
96739453 AAAATAAAATTTCCA
1 AAAATAAAATTTCCA
96739468 AAAATAACAA-TTCCA
1 AAAATAA-AATTTCCA
96739483 AAAA
1 AAAA
96739487 AATCATCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATAAAATTTCCA
Found at i:96744540 original size:12 final size:13
Alignment explanation
Indices: 96744518--96744555 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
96744508 AACCCACGAG
96744518 TATTAATTTTTTA
1 TATTAATTTTTTA
96744531 TATT-ATTTTTTA
1 TATTAATTTTTTA
* *
96744543 TATAAAATTTTTA
1 TATTAATTTTTTA
96744556 AAATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTAATTTTTTA
Found at i:96744788 original size:12 final size:12
Alignment explanation
Indices: 96744771--96744822 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
96744761 AAATGGTAGC
96744771 AAAATAGTAAAA
1 AAAATAGTAAAA
* *
96744783 AAAATAG-CAAC
1 AAAATAGTAAAA
*
96744794 AAAACAGTAAAA
1 AAAATAGTAAAA
* *
96744806 AAAATACTTAAA
1 AAAATAGTAAAA
96744818 AAAAT
1 AAAAT
96744823 CATTTTTTAT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
11 8 0.26
12 23 0.74
ACGTcount: A:0.71, C:0.08, G:0.06, T:0.15
Consensus pattern (12 bp):
AAAATAGTAAAA
Found at i:96747270 original size:43 final size:43
Alignment explanation
Indices: 96747124--96747274 Score: 146
Period size: 43 Copynumber: 3.5 Consensus size: 43
96747114 GATTACCGAG
** * *
96747124 ATGAGATTACATGTAAGAAAATCTCTGGGACATTGGCATTG-T
1 ATGAGATTACATGTAAGACCATGTCTGGGACATTGGCATCGAT
* **
96747166 ACTGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATC-ATT
1 A-TGAGATTACATGTAAGACCATGTCTGGGACATTGGCATCGA-T
* * * *
96747210 AT-ATGATTTCGTTTAAGACCATGTCTAGGACATTGGCATCGAT
1 ATGA-GATTACATGTAAGACCATGTCTGGGACATTGGCATCGAT
*
96747253 ATGAGATAACATGTAAGACCAT
1 ATGAGATTACATGTAAGACCAT
96747275 ATTTGGGATA
Statistics
Matches: 87, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
42 1 0.01
43 82 0.94
44 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32
Consensus pattern (43 bp):
ATGAGATTACATGTAAGACCATGTCTGGGACATTGGCATCGAT
Found at i:96751202 original size:46 final size:46
Alignment explanation
Indices: 96751121--96751302 Score: 267
Period size: 46 Copynumber: 4.0 Consensus size: 46
96751111 TTTGACATGA
* * * * *
96751121 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*
96751167 TACCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
96751213 TGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
96751259 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
96751303 AGAGCACACT
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.03
46 120 0.97
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:96754318 original size:105 final size:100
Alignment explanation
Indices: 96754140--96754336 Score: 272
Period size: 105 Copynumber: 1.9 Consensus size: 100
96754130 GAATTGACGG
* * *
96754140 ATAAGACCATGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTGGGCTATGCCATTTCAG
1 ATAAGACCATGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTGGGCTATGACATCTCAA
96754205 TGGAAAGACCATAACTGGGTTATGGCACCGTGAAC
66 TGGAAAGACCATAACTGGGTTATGGCACCGTGAAC
* *
96754240 ATAAGACCATAGTTGGACCTTGGCAGTATGTGTATAAGTGTAAGACCATAGCTGGGCTATGACAT
1 ATAAGACCAT-GTTGGACCATGGCAATAT-T-TA-AA-TGTAAGACCATAGCTGGGCTATGACAT
96754305 C-CTAAT-GATAAGACCATAACTGGGTTATGGCA
61 CTC-AATGGA-AAGACCATAACTGGGTTATGGCA
96754337 TTACGAGTGT
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
100 10 0.12
101 16 0.19
102 1 0.01
103 2 0.02
104 5 0.06
105 51 0.60
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (100 bp):
ATAAGACCATGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTGGGCTATGACATCTCAA
TGGAAAGACCATAACTGGGTTATGGCACCGTGAAC
Found at i:96754350 original size:33 final size:32
Alignment explanation
Indices: 96754276--96754355 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
96754266 TATGTGTATA
* * *
96754276 AGTGTAAGACCATAGCTGGGCTATGACATCCT
1 AGTGTAAGACCATAACTGGGCTATGACATACG
* * *
96754308 AATGATAAGACCATAACTGGGTTATGGCATTACG
1 AGTG-TAAGACCATAACTGGGCTATGACA-TACG
96754342 AGTGTAAGACCATA
1 AGTGTAAGACCATA
96754356 GCAATATATG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 3 0.08
33 31 0.79
34 5 0.13
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (32 bp):
AGTGTAAGACCATAACTGGGCTATGACATACG
Found at i:96755004 original size:2 final size:2
Alignment explanation
Indices: 96754997--96755021 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
96754987 TTATTTAGTC
96754997 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
96755022 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:96763125 original size:6 final size:6
Alignment explanation
Indices: 96763109--96763142 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
96763099 TACTAAACAC
*
96763109 TCTTCTT TCTTTT TCTTTT TCTTTT TTTTTT TCT
1 TCTT-TT TCTTTT TCTTTT TCTTTT TCTTTT TCT
96763143 GTCACGATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TCTTTT
Found at i:96770472 original size:20 final size:20
Alignment explanation
Indices: 96770447--96770484 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
96770437 AAAAGGTCAA
*
96770447 ACAAACAACAGAATATTCTG
1 ACAAACAAAAGAATATTCTG
*
96770467 ACAAACAAAAGTATATTC
1 ACAAACAAAAGAATATTC
96770485 AGATGCGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.18, G:0.08, T:0.21
Consensus pattern (20 bp):
ACAAACAAAAGAATATTCTG
Found at i:96771149 original size:21 final size:21
Alignment explanation
Indices: 96771119--96771181 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
96771109 GGTCGTGTAG
96771119 AGGTC-TACACGCCCATGTGA
1 AGGTCATACACGCCCATGTGA
* * *
96771139 AGGTCATACACACCCGTGTAA
1 AGGTCATACACGCCCATGTGA
** * *
96771160 AGGGGACACATGCCCATGTGA
1 AGGTCATACACGCCCATGTGA
96771181 A
1 A
96771182 CAGCCCATGA
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
20 5 0.16
21 27 0.84
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.17
Consensus pattern (21 bp):
AGGTCATACACGCCCATGTGA
Found at i:96773792 original size:20 final size:20
Alignment explanation
Indices: 96773755--96773792 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
96773745 TAAAAAGTAG
*
96773755 TATTTTTTTATAAGTTTAAA
1 TATTTTTTTAAAAGTTTAAA
*
96773775 TATTTTTTTAAAATTTTA
1 TATTTTTTTAAAAGTTTA
96773793 TATAGAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
TATTTTTTTAAAAGTTTAAA
Found at i:96775041 original size:29 final size:30
Alignment explanation
Indices: 96774994--96775052 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
96774984 GAATTGGATC
*
96774994 AAATCAAAATTTCAAGTATAAAATTGCACA
1 AAATCAAAATTTCAAGTATAAAATTACACA
* *
96775024 AAATCAAAA-TTCATGTATAGAATTACACA
1 AAATCAAAATTTCAAGTATAAAATTACACA
96775053 TTAAATCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.27
Consensus pattern (30 bp):
AAATCAAAATTTCAAGTATAAAATTACACA
Found at i:96783899 original size:32 final size:32
Alignment explanation
Indices: 96783862--96783922 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
96783852 ATGCATTTTA
96783862 CATTTTAATAGTTAATGGATGATGGGCATTAG
1 CATTTTAATAGTTAATGGATGATGGGCATTAG
96783894 CATTTTAATAGTTAATGGATGATGGGCAT
1 CATTTTAATAGTTAATGGATGATGGGCAT
96783923 GGTAAGCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.38
Consensus pattern (32 bp):
CATTTTAATAGTTAATGGATGATGGGCATTAG
Found at i:96785432 original size:26 final size:26
Alignment explanation
Indices: 96785403--96785455 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
96785393 TTTACAGTTT
96785403 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
96785429 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
96785455 T
1 T
96785456 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:96792903 original size:32 final size:32
Alignment explanation
Indices: 96792867--96792931 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
96792857 TGTATGTATT
*
96792867 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAATTAATGGATGATGGGCA
96792899 TTAGCATTTTAATAATTAATGGATGATGGGCA
1 TTAGCATTTTAATAATTAATGGATGATGGGCA
96792931 T
1 T
96792932 GGTAAGCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAATTAATGGATGATGGGCA
Found at i:96795618 original size:36 final size:36
Alignment explanation
Indices: 96795571--96795643 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
96795561 GTTTTTTCAA
96795571 TAATATCAAACTTAAAAATATATTGAAATCTTGATG
1 TAATATCAAACTTAAAAATATATTGAAATCTTGATG
96795607 TAATATCAAACTTAAAAATATATTGAAATCTTGATG
1 TAATATCAAACTTAAAAATATATTGAAATCTTGATG
96795643 T
1 T
96795644 TCTTACCTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (36 bp):
TAATATCAAACTTAAAAATATATTGAAATCTTGATG
Found at i:96803552 original size:29 final size:31
Alignment explanation
Indices: 96803497--96803565 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
96803487 TCAACCTTAA
* * *
96803497 AATATTTGCACTATTAGTCCTTCAAATTTT-
1 AATATTTACACTATTAATCCCTCAAATTTTG
*
96803527 TATATTTACACT-TTAATCCCTCAAATTTTG
1 AATATTTACACTATTAATCCCTCAAATTTTG
96803557 AATATTTAC
1 AATATTTAC
96803566 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 15 0.45
30 18 0.55
ACGTcount: A:0.32, C:0.17, G:0.04, T:0.46
Consensus pattern (31 bp):
AATATTTACACTATTAATCCCTCAAATTTTG
Found at i:96804423 original size:25 final size:23
Alignment explanation
Indices: 96804393--96804450 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
96804383 GAGACATGGC
96804393 CAGTAAGCTCTT-CATGAGCTGATAA
1 CAGTAAGCTCTTCCA--AGCTGA-AA
*
96804418 CAGTAAACTCTTCCAAGCTGAAA
1 CAGTAAGCTCTTCCAAGCTGAAA
*
96804441 CAATAAGCTC
1 CAGTAAGCTC
96804451 ATACGAGCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 10 0.34
24 6 0.21
25 11 0.38
26 2 0.07
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (23 bp):
CAGTAAGCTCTTCCAAGCTGAAA
Found at i:96810406 original size:22 final size:22
Alignment explanation
Indices: 96810379--96810420 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
96810369 ACAGAAGTAC
96810379 TTTTTC-CTTCGTTTTCTTTTCT
1 TTTTTCACTTCG-TTTCTTTTCT
*
96810401 TTTTTCATTTCGTTTCTTTT
1 TTTTTCACTTCGTTTCTTTT
96810421 AATCCGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.74
Consensus pattern (22 bp):
TTTTTCACTTCGTTTCTTTTCT
Found at i:96811988 original size:40 final size:40
Alignment explanation
Indices: 96811942--96812023 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
96811932 CTAGTATTTG
96811942 GAGTACATTAATGCGTCTAAGGTTCTTTATTATTTGATAA
1 GAGTACATTAATGCGTCTAAGGTTCTTTATTATTTGATAA
96811982 GAGTACATTAATGCGTCTAAGGTTCTTTATTATTTGATAA
1 GAGTACATTAATGCGTCTAAGGTTCTTTATTATTTGATAA
96812022 GA
1 GA
96812024 TATTTTCTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.41
Consensus pattern (40 bp):
GAGTACATTAATGCGTCTAAGGTTCTTTATTATTTGATAA
Found at i:96812013 original size:22 final size:22
Alignment explanation
Indices: 96811948--96812013 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 22
96811938 TTTGGAGTAC
96811948 ATTAATGCGTCTAAGGTTCTTT
1 ATTAATGCGTCTAAGGTTCTTT
** * *
96811970 ATT-ATTTG-ATAAGAGTAC---
1 ATTAATGCGTCTAAG-GTTCTTT
96811988 ATTAATGCGTCTAAGGTTCTTT
1 ATTAATGCGTCTAAGGTTCTTT
96812010 ATTA
1 ATTA
96812014 TTTGATAAGA
Statistics
Matches: 30, Mismatches: 8, Indels: 12
0.60 0.16 0.24
Matches are distributed among these distances:
18 3 0.10
19 6 0.20
20 8 0.27
21 6 0.20
22 7 0.23
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.44
Consensus pattern (22 bp):
ATTAATGCGTCTAAGGTTCTTT
Found at i:96827302 original size:17 final size:15
Alignment explanation
Indices: 96827278--96827314 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
96827268 AATCAATTAA
96827278 TTAAAATTTAATATTT
1 TTAAAATTTAAT-TTT
96827294 TTAACAATTTAATTTT
1 TTAA-AATTTAATTTT
96827310 TTAAA
1 TTAAA
96827315 TATATTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 11 0.55
17 8 0.40
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAAAATTTAATTTT
Found at i:96828367 original size:25 final size:25
Alignment explanation
Indices: 96828339--96828393 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
96828329 ATATCTAAAG
*
96828339 GTTATTGCATCCA-CTATAAAAGAAA
1 GTTATTGCACCCATC-ATAAAAGAAA
*
96828364 GTTATTGCACCCATCATAAAAGAAT
1 GTTATTGCACCCATCATAAAAGAAA
96828389 GTTAT
1 GTTAT
96828394 ACCTTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (25 bp):
GTTATTGCACCCATCATAAAAGAAA
Found at i:96828960 original size:20 final size:20
Alignment explanation
Indices: 96828910--96828963 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
96828900 TAATTAGATT
*
96828910 TATATTTT-AATTTTAATTT
1 TATATTTTCAATTTTAATTA
** *
96828929 TAATATAATCAATTTTTATTA
1 T-ATATTTTCAATTTTAATTA
96828950 TATATTTTCAATTT
1 TATATTTTCAATTT
96828964 GTGTATTGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 1 0.04
20 16 0.59
21 10 0.37
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATTTTCAATTTTAATTA
Found at i:96828993 original size:40 final size:40
Alignment explanation
Indices: 96828949--96829029 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
96828939 AATTTTTATT
96828949 ATATATTTTCAATTTGTGTATTGTTTTAAGAATTGTTTTA
1 ATATATTTTCAATTTGTGTATTGTTTTAAGAATTGTTTTA
** * * * *
96828989 ATATATTTTTTATTTGTTTCTTGTTTTAATATTTGTTTTA
1 ATATATTTTCAATTTGTGTATTGTTTTAAGAATTGTTTTA
96829029 A
1 A
96829030 ATGTATTTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.63
Consensus pattern (40 bp):
ATATATTTTCAATTTGTGTATTGTTTTAAGAATTGTTTTA
Found at i:96829416 original size:18 final size:18
Alignment explanation
Indices: 96829393--96829428 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
96829383 TTTATGACCA
* *
96829393 TTTTAATATTATTTTTAT
1 TTTTAAGATAATTTTTAT
96829411 TTTTAAGATAATTTTTAT
1 TTTTAAGATAATTTTTAT
96829429 CTTTGGAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTAAGATAATTTTTAT
Found at i:96831709 original size:53 final size:53
Alignment explanation
Indices: 96831577--96831727 Score: 196
Period size: 53 Copynumber: 2.8 Consensus size: 53
96831567 ATAAGTGCGC
* ** *
96831577 CCGTTTAAGACCATAGTTGGGCTATGGCATCGGTGCAATGTAATAATGTGACT
1 CCGTATAAGACCATAGTTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
96831630 CCGTATAAGACCATAGTTGCGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGTTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
96831683 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAGT-TGGGCTATGGCATCGGTAT-A-ATGTGA
96831728 ACCGTGTAAG
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
52 2 0.02
53 77 0.90
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (53 bp):
CCGTATAAGACCATAGTTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:96837853 original size:10 final size:10
Alignment explanation
Indices: 96837838--96837894 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 10
96837828 TGAGTTAAGC
96837838 AAGAATTTAA
1 AAGAATTTAA
*
96837848 AAGAATTTAT
1 AAGAATTTAA
* * *
96837858 TAG--GTCAA
1 AAGAATTTAA
96837866 AAGAATTTAA
1 AAGAATTTAA
*
96837876 AATAATTTAA
1 AAGAATTTAA
96837886 AAGAATTTA
1 AAGAATTTA
96837895 TTAGTGATTT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
8 4 0.11
10 31 0.89
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (10 bp):
AAGAATTTAA
Found at i:96845406 original size:31 final size:31
Alignment explanation
Indices: 96845371--96845436 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
96845361 TATAAAATAA
* *
96845371 TTATTAAATTATTCAAAAAATTTTATTTAAG
1 TTATTAAACTACTCAAAAAATTTTATTTAAG
* **
96845402 TTATTAAACTACTCAGAAGTTTTTATTTAAG
1 TTATTAAACTACTCAAAAAATTTTATTTAAG
96845433 TTAT
1 TTAT
96845437 AAGGATGTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (31 bp):
TTATTAAACTACTCAAAAAATTTTATTTAAG
Found at i:96853570 original size:28 final size:28
Alignment explanation
Indices: 96853520--96853580 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
96853510 CATTATCAAT
96853520 CCCATAAGTTATAAATCTCTTCCTATAC
1 CCCATAAGTTATAAATCTCTTCCTATAC
* *
96853548 CCCATAAGTTATGAGA-CTTTTCCTATAC
1 CCCATAAGTTAT-AAATCTCTTCCTATAC
96853576 CCCAT
1 CCCAT
96853581 TAATATGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.93
29 2 0.07
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.34
Consensus pattern (28 bp):
CCCATAAGTTATAAATCTCTTCCTATAC
Found at i:96853674 original size:26 final size:26
Alignment explanation
Indices: 96853638--96853689 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
96853628 TTAGAGAGTT
96853638 ACTTTTAACCCCTATATATATGGGGC
1 ACTTTTAACCCCTATATATATGGGGC
96853664 ACTTTTAACCCCTATATATATGGGGC
1 ACTTTTAACCCCTATATATATGGGGC
96853690 TCATGTACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (26 bp):
ACTTTTAACCCCTATATATATGGGGC
Found at i:96857010 original size:48 final size:48
Alignment explanation
Indices: 96856939--96857035 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
96856929 CATGACTGAA
96856939 AGAATAGTTTCAGAAGAAAATCAGGTACCTGACAATGAAGAGATCTCT
1 AGAATAGTTTCAGAAGAAAATCAGGTACCTGACAATGAAGAGATCTCT
96856987 AGAATAGTTTCAGAAGAAAATCAGGTACCTGACAATGAAGAGATCTCT
1 AGAATAGTTTCAGAAGAAAATCAGGTACCTGACAATGAAGAGATCTCT
96857035 A
1 A
96857036 TTGATTATGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (48 bp):
AGAATAGTTTCAGAAGAAAATCAGGTACCTGACAATGAAGAGATCTCT
Found at i:96859054 original size:28 final size:28
Alignment explanation
Indices: 96859004--96859064 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
96858994 CATTATCAAC
*
96859004 CCCATAAGTTATAAAACTCTTCCTATAT
1 CCCATAAGTTATAAAACTCTTCCTATAA
* * *
96859032 CCCATAAGTTATGAGACTTTTCCTATAA
1 CCCATAAGTTATAAAACTCTTCCTATAA
96859060 CCCAT
1 CCCAT
96859065 TAATATGGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (28 bp):
CCCATAAGTTATAAAACTCTTCCTATAA
Found at i:96859546 original size:8 final size:9
Alignment explanation
Indices: 96859502--96859549 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
96859492 CTTCTGCTTG
96859502 AAAAATATA
1 AAAAATATA
96859511 AAAAATATA
1 AAAAATATA
96859520 AAAAATATA
1 AAAAATATA
* *
96859529 TAAATTATTA
1 AAAAATA-TA
96859539 AAAAAT-TA
1 AAAAATATA
96859547 AAA
1 AAA
96859550 TTACAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
8 5 0.15
9 23 0.68
10 6 0.18
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAAATATA
Done.