Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 178 of 182
Found at i:54190723 original size:42 final size:39
Alignment explanation
Indices: 54190645--54190723 Score: 104
Period size: 39 Copynumber: 1.9 Consensus size: 39
54190635 TTTTCTTTGT
* *
54190645 TTGGTTAATAATTATTAGTTTTTTTTATATTTCTAAATA
1 TTGGTTAATAAATATTAGTTTTTTTTATATTACTAAATA
*
54190684 TTGGTTACTAAATATTAGTTTTTTTTTTCATATTACTAAA
1 TTGGTTAATAAATATTAG--TTTTTTTT-ATATTACTAAA
54190724 AAAATTACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 16 0.47
41 8 0.24
42 10 0.29
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (39 bp):
TTGGTTAATAAATATTAGTTTTTTTTATATTACTAAATA
Found at i:54190977 original size:22 final size:22
Alignment explanation
Indices: 54190947--54191004 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
54190937 TATATAGGTT
* **
54190947 TAAATAATATTTTTATATTTTA
1 TAAAAAATATTTTTATATGATA
* *
54190969 TAAAAAATA-CTTTATATGATC
1 TAAAAAATATTTTTATATGATA
54190990 TAAAAAATTATTTTT
1 TAAAAAA-TATTTTT
54191005 TGTATAATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 15 0.54
22 10 0.36
23 3 0.11
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (22 bp):
TAAAAAATATTTTTATATGATA
Found at i:54207053 original size:26 final size:27
Alignment explanation
Indices: 54207031--54207088 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
54207021 ATAAAAAATG
* *
54207031 TATAAAATTATTATATTTT-AAAATAA
1 TATAAAATAAATATATTTTAAAAATAA
*
54207057 TATAATATAAATATATTTTAAAAA-AA
1 TATAAAATAAATATATTTTAAAAATAA
54207083 T-TAAAA
1 TATAAAA
54207089 AGAATATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 4 0.15
26 19 0.70
27 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TATAAAATAAATATATTTTAAAAATAA
Found at i:54217309 original size:54 final size:52
Alignment explanation
Indices: 54217210--54217311 Score: 123
Period size: 54 Copynumber: 1.9 Consensus size: 52
54217200 GAATCTAATA
* * ** *
54217210 AAAATAAATAAATTATAAATTAACATATAATAAAGTTATCCTTTAATTATCT
1 AAAATAAAAAAATTATAAATTAACACATAATAAACATATACTTTAATTATCT
* *
54217262 AAAATGAAAAAAATATATAAATTAATACATAATAAACATATATTTTAATT
1 AAAAT-AAAAAAAT-TATAAATTAACACATAATAAACATATACTTTAATT
54217312 TATGAAAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 5 0.12
53 7 0.17
54 29 0.71
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (52 bp):
AAAATAAAAAAATTATAAATTAACACATAATAAACATATACTTTAATTATCT
Found at i:54217754 original size:72 final size:72
Alignment explanation
Indices: 54217633--54217790 Score: 219
Period size: 72 Copynumber: 2.2 Consensus size: 72
54217623 AAGGGTATGC
* * * *
54217633 TTATGGTTTGAGCTCGAGTTCTCCTTCTCTTCCTCTTTATCGACTGTAAAGGTATAATTCAAGTG
1 TTATGGTTTGGGCTCGAGTTATCCTTCTCTTCCTCTTTATCGAATGTAAAGGCATAATTCAAGTG
54217698 AAGATGT
66 AAGATGT
* * * *
54217705 TTATGGTTTGGGTTCGGGTTATTCTTTTCTTCCTCTTTATC-AATGGTAAAGGCATAATTCAAGT
1 TTATGGTTTGGGCTCGAGTTATCCTTCTCTTCCTCTTTATCGAAT-GTAAAGGCATAATTCAAGT
54217769 GAAGATGT
65 GAAGATGT
*
54217777 TTGTGGTTTGGGCT
1 TTATGGTTTGGGCT
54217791 TTAGTCTCGT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
71 2 0.03
72 73 0.97
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (72 bp):
TTATGGTTTGGGCTCGAGTTATCCTTCTCTTCCTCTTTATCGAATGTAAAGGCATAATTCAAGTG
AAGATGT
Found at i:54219167 original size:20 final size:20
Alignment explanation
Indices: 54219122--54219160 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
54219112 ATCATTTTAT
54219122 CTTTTTAATAATTAATTTTG
1 CTTTTTAATAATTAATTTTG
54219142 CATTTTT-ATAATTAATTTT
1 C-TTTTTAATAATTAATTTT
54219161 AGTTTTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
CTTTTTAATAATTAATTTTG
Found at i:54220946 original size:18 final size:17
Alignment explanation
Indices: 54220915--54220948 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54220905 GATTTGCTTG
*
54220915 GCCGAGCGGGGAAGTTA
1 GCCGAGCGGAGAAGTTA
54220932 GCCGAAGCGGAGAAGTT
1 GCCG-AGCGGAGAAGTT
54220949 TGTGCTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.26, C:0.18, G:0.44, T:0.12
Consensus pattern (17 bp):
GCCGAGCGGAGAAGTTA
Found at i:54232796 original size:3 final size:3
Alignment explanation
Indices: 54232788--54232815 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54232778 ATTAATTTAA
54232788 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
54232816 TTATTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54232962 original size:9 final size:8
Alignment explanation
Indices: 54232950--54233006 Score: 60
Period size: 9 Copynumber: 6.6 Consensus size: 8
54232940 ATTGATTAAA
54232950 ATTTTTATT
1 ATTTTT-TT
54232959 ATTTTTTT
1 ATTTTTTT
*
54232967 ATATTTTAT
1 AT-TTTTTT
54232976 ATTTTCTTT
1 ATTTT-TTT
54232985 ATTTTTTT
1 ATTTTTTT
*
54232993 GAATTTTTT
1 -ATTTTTTT
54233002 ATTTT
1 ATTTT
54233007 ATAATGATTG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 14 0.34
9 27 0.66
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (8 bp):
ATTTTTTT
Found at i:54232975 original size:18 final size:17
Alignment explanation
Indices: 54232950--54233006 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
54232940 ATTGATTAAA
54232950 ATTTTTATTATTTTTTT
1 ATTTTTATTATTTTTTT
54232967 ATATTTTA-TATTTTCTTT
1 AT-TTTTATTATTTT-TTT
*
54232985 ATTTTT-TTGAATTTTTT
1 ATTTTTATT-ATTTTTTT
54233002 ATTTT
1 ATTTT
54233007 ATAATGATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 21 0.60
18 14 0.40
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (17 bp):
ATTTTTATTATTTTTTT
Found at i:54232986 original size:26 final size:26
Alignment explanation
Indices: 54232957--54233006 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
54232947 AAAATTTTTA
54232957 TTATTTTTTT-ATATTTTATATTTTCT
1 TTATTTTTTTGA-ATTTTATATTTTCT
*
54232983 TTATTTTTTTGAATTTTTTATTTT
1 TTATTTTTTTGAATTTTATATTTT
54233007 ATAATGATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (26 bp):
TTATTTTTTTGAATTTTATATTTTCT
Found at i:54234491 original size:4 final size:4
Alignment explanation
Indices: 54234477--54234507 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
54234467 GATGTAGCAA
54234477 ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
54234508 TAGCTTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:54237185 original size:14 final size:16
Alignment explanation
Indices: 54237156--54237190 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
54237146 TTACACCAAA
54237156 CCTAAATTTAAACCAC
1 CCTAAATTTAAACCAC
54237172 CCTAAA-TT-AACCAC
1 CCTAAATTTAAACCAC
54237186 CCTAA
1 CCTAA
54237191 CTAGTTAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 2 0.11
16 6 0.32
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (16 bp):
CCTAAATTTAAACCAC
Found at i:54239086 original size:13 final size:13
Alignment explanation
Indices: 54239054--54239087 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
54239044 TATTCAAAGT
54239054 TTAAATATTTAAA
1 TTAAATATTTAAA
*
54239067 -AAAATATTTAAA
1 TTAAATATTTAAA
54239079 TTAAATATT
1 TTAAATATT
54239088 ATGTGTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAATATTTAAA
Found at i:54247610 original size:16 final size:16
Alignment explanation
Indices: 54247589--54247641 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
54247579 GGATCACATA
54247589 TTAAATTTGGGTCATT
1 TTAAATTTGGGTCATT
54247605 TTAAATATT-GGTCATT
1 TTAAAT-TTGGGTCATT
* **
54247621 TCAGGTTTGGGTCGATT
1 TTAAATTTGGGTC-ATT
54247638 TTAA
1 TTAA
54247642 TTAGATTAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 2 0.07
16 20 0.69
17 7 0.24
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.47
Consensus pattern (16 bp):
TTAAATTTGGGTCATT
Found at i:54256168 original size:6 final size:6
Alignment explanation
Indices: 54256159--54256183 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
54256149 AGCCCAATGT
54256159 AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA A
54256184 AAATTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:54258018 original size:30 final size:31
Alignment explanation
Indices: 54257962--54258019 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
54257952 CTTGCACCCC
* *
54257962 TAAAAATGAAAAAAATTTCAATTTAATCTCT
1 TAAAAATGAAAAAAATTGCAAGTTAATCTCT
*
54257993 TAAAAATG-ATAAAATTGCAAGTTAATC
1 TAAAAATGAAAAAAATTGCAAGTTAATC
54258020 CATGGCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAAAATGAAAAAAATTGCAAGTTAATCTCT
Found at i:54262131 original size:1 final size:1
Alignment explanation
Indices: 54262125--54262149 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
54262115 GTGGTGCAGT
54262125 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
54262150 TTAGATATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:54262945 original size:25 final size:26
Alignment explanation
Indices: 54262906--54262962 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
54262896 TTAAGTTTTT
* *
54262906 TTTTTTCATTTTTAGATTAGATGTTC
1 TTTTTTCATTGTTAGATTAGATGTTA
*
54262932 TTTTTTC-TTGTTAGATTAGATTTTA
1 TTTTTTCATTGTTAGATTAGATGTTA
54262957 TTTTTT
1 TTTTTT
54262963 TTCTTTCTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.18, C:0.05, G:0.11, T:0.67
Consensus pattern (26 bp):
TTTTTTCATTGTTAGATTAGATGTTA
Found at i:54264381 original size:6 final size:6
Alignment explanation
Indices: 54264381--54264432 Score: 61
Period size: 6 Copynumber: 8.3 Consensus size: 6
54264371 GTTTAGATTT
*
54264381 ATTTTAA ATTTAA AATTAGA TATTTAA ATTT-A ATTTAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTA-A -ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
54264431 AT
1 AT
54264433 AAAAATTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
5 5 0.12
6 25 0.62
7 6 0.15
8 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:54264444 original size:18 final size:18
Alignment explanation
Indices: 54264417--54264461 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
54264407 AATTTAATTT
*
54264417 AAATTTAAAT-TTAAATAA
1 AAATTAAAATATT-AATAA
*
54264435 AAATTAAAATATTATTAA
1 AAATTAAAATATTAATAA
54264453 AAATTAAAA
1 AAATTAAAA
54264462 GTCCAATGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATTAAAATATTAATAA
Found at i:54265526 original size:12 final size:12
Alignment explanation
Indices: 54265493--54265526 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54265483 AAAGGAGATT
54265493 AAGGAAGAAAAA
1 AAGGAAGAAAAA
*
54265505 AGGGAAGAAAAA
1 AAGGAAGAAAAA
*
54265517 AAGGAGGAAA
1 AAGGAAGAAA
54265527 GGAGCGCACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (12 bp):
AAGGAAGAAAAA
Found at i:54266147 original size:161 final size:162
Alignment explanation
Indices: 54265958--54266251 Score: 439
Period size: 161 Copynumber: 1.8 Consensus size: 162
54265948 TTATAATTTA
**
54265958 GTCCTTTGACTGTTTGACTGTGCCAGAGGTTACCACGTGTCATGTATTAGATTATTTATGCATTT
1 GTCCTTTGACTGTTTGACTGCACCAGAGGTTACCACGTGTCATGTATTAGATTATTTATGCATTT
*
54266023 AGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCC-CAAATCAACTTTGT-TTTAATTACGAAA
66 AGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTT-TATTTAATTACAAAA
54266086 TTGGCCCCATAATTTTTCGAGGTTTATAAACTG
130 TTGGCCCCATAATTTTTCGAGGTTTATAAACTG
* * * * * * * *
54266119 GTCCTTTGACTTTTTGATTGCACCAGAGGTTGCCACGTGTCATTTTTTGGGTTATTTCTGCATTT
1 GTCCTTTGACTGTTTGACTGCACCAGAGGTTACCACGTGTCATGTATTAGATTATTTATGCATTT
* * *
54266184 AGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACAAAAT
66 AGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAAAT
54266249 TGG
131 TGG
54266252 TCCAAAATTT
Statistics
Matches: 117, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
161 91 0.78
162 26 0.22
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (162 bp):
GTCCTTTGACTGTTTGACTGCACCAGAGGTTACCACGTGTCATGTATTAGATTATTTATGCATTT
AGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAAAT
TGGCCCCATAATTTTTCGAGGTTTATAAACTG
Found at i:54266406 original size:30 final size:30
Alignment explanation
Indices: 54266366--54266473 Score: 164
Period size: 30 Copynumber: 3.6 Consensus size: 30
54266356 AATTGTCCAG
*
54266366 AAAA-TACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
54266395 TAAATTACATTTTGACCCCAAAGCTTTACC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
54266425 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
54266455 AAAATTACATTTTAACCCC
1 AAAATTACATTTTGACCCC
54266474 GATTTCACCG
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
29 3 0.04
30 67 0.96
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:54266501 original size:29 final size:30
Alignment explanation
Indices: 54266455--54266851 Score: 223
Period size: 30 Copynumber: 13.5 Consensus size: 30
54266445 AAACTTTTCC
*
54266455 AAAATTA-CATTTTAACCCCGATTTCACCG
1 AAAATTACCATTTTAACCCCGATTTCACCT
* * ***
54266484 AAAATTACCATTTTACCCCCGA-ATCTTTT
1 AAAATTACCATTTTAACCCCGATTTCACCT
* *
54266513 AAAATT-CCGTTTTTAACCCCGATTTCACCA
1 AAAATTACC-ATTTTAACCCCGATTTCACCT
* * ***
54266543 AAAATTACCATTTTACCCCCGA-ATCTTTT
1 AAAATTACCATTTTAACCCCGATTTCACCT
*
54266572 AAAATT-CCATTTTTAACCCCGATTTCACCA
1 AAAATTACCA-TTTTAACCCCGATTTCACCT
* * ***
54266602 AAAATTACCATTTTACCCCCGA-ATCTTTT
1 AAAATTACCATTTTAACCCCGATTTCACCT
* *
54266631 AAAATT-CCATTTTTAACCCCAATTTCACCG
1 AAAATTACCA-TTTTAACCCCGATTTCACCT
* **
54266661 AAAATTACCATTTTACCCCCGAATCTT--TTT
1 AAAATTACCATTTTAACCCCG-AT-TTCACCT
** * * *
54266691 AAAATT-CTGTTTTTAACCTCGATTTCATCA
1 AAAATTAC-CATTTTAACCCCGATTTCACCT
* ***
54266721 AAAATTACCATTTT-ACCCTCGA-ATCTTTT
1 AAAATTACCATTTTAACCC-CGATTTCACCT
* *
54266750 AAAATT-CCATTTTTAACCCCGATTTCGCCA
1 AAAATTACCA-TTTTAACCCCGATTTCACCT
* * ***
54266780 AAAATTACCATTTTACCCCCGA-ATCTTTT
1 AAAATTACCATTTTAACCCCGATTTCACCT
* *
54266809 AAAATT-CCATTTTTAACCCTGATTTTACC-
1 AAAATTACCA-TTTTAACCCCGATTTCACCT
54266838 AAAATTACCATTTT
1 AAAATTACCATTTT
54266852 GCCCCCGGGT
Statistics
Matches: 269, Mismatches: 75, Indels: 48
0.69 0.19 0.12
Matches are distributed among these distances:
28 16 0.06
29 113 0.42
30 124 0.46
31 14 0.05
32 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCCGATTTCACCT
Found at i:54266527 original size:59 final size:59
Alignment explanation
Indices: 54266425--54266858 Score: 660
Period size: 59 Copynumber: 7.4 Consensus size: 59
54266415 AAGCTTTACC
* * * *
54266425 AAAATTA-CATTTTGA-CCCCAAAACTTTTCCAAAATTACA-TTTTAACCCCGATTTCACCG
1 AAAATTACCATTTT-ACCCCCGAATCTTTT--AAAATTCCATTTTTAACCCCGATTTCACCA
*
54266484 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCA
54266543 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCA
* *
54266602 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCAATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCA
** * *
54266661 AAAATTACCATTTTACCCCCGAATCTTTTTAAAATTCTGTTTTTAACCTCGATTTCATCA
1 AAAATTACCATTTTACCCCCGAATC-TTTTAAAATTCCATTTTTAACCCCGATTTCACCA
* *
54266721 AAAATTACCATTTTACCCTCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCGCCA
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCA
* *
54266780 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCTGATTTTACC-
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCA
*
54266838 AAAATTACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
54266859 GGTATCCATA
Statistics
Matches: 346, Mismatches: 25, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
58 27 0.08
59 250 0.72
60 69 0.20
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:54266746 original size:178 final size:177
Alignment explanation
Indices: 54266425--54266858 Score: 696
Period size: 178 Copynumber: 2.5 Consensus size: 177
54266415 AAGCTTTACC
* * *
54266425 AAAATTA-CATTTTGA-CCCCAAAACTTTTCCAAAATTACA-TTTTAACCCCGATTTCACCGAAA
1 AAAATTACCATTTT-ACCCCCGAATCTTTT--AAAATTCCATTTTTAACCCCGATTTCACCGAAA
54266487 ATTACCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCACCAAAAATTACC
63 ATTACCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCACCAAAAATTACC
54266552 ATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCA
128 ATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCA
*
54266602 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCAATTTCACCGAAAATT
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATT
* * *
54266667 ACCATTTTACCCCCGAATCTTTTTAAAATTCTGTTTTTAACCTCGATTTCATCAAAAATTACCAT
66 ACCATTTTACCCCCGAATC-TTTTAAAATTCCGTTTTTAACCCCGATTTCACCAAAAATTACCAT
* *
54266732 TTTACCCTCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCGCCA
130 TTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCA
* *
54266780 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCTGATTTTACC-AAAATT
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATT
*
54266844 ACCATTTTGCCCCCG
66 ACCATTTTACCCCCG
54266859 GGTATCCATA
Statistics
Matches: 240, Mismatches: 13, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
176 8 0.03
177 72 0.30
178 160 0.67
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (177 bp):
AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATT
ACCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCACCAAAAATTACCATT
TTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:54269609 original size:17 final size:17
Alignment explanation
Indices: 54269587--54269625 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
54269577 AAGAAAAATG
54269587 GGAAATAGCAAATTCGT
1 GGAAATAGCAAATTCGT
54269604 GGAAATAGCAAATTCGT
1 GGAAATAGCAAATTCGT
54269621 GGAAA
1 GGAAA
54269626 AAGGTACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.44, C:0.10, G:0.26, T:0.21
Consensus pattern (17 bp):
GGAAATAGCAAATTCGT
Found at i:54279829 original size:69 final size:69
Alignment explanation
Indices: 54279715--54280602 Score: 1244
Period size: 69 Copynumber: 12.8 Consensus size: 69
54279705 CTGCAGGTCT
* * * *
54279715 CAACGTCATCCTCTCGAAATTGAAGTAGAGTTGGATGTTAGGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
54279780 AGAG
66 AGAG
* *
54279784 CAACGGCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
54279849 AGAG
66 AGAG
* **
54279853 CAACGTCATCCTCTCGAAATTGAAGTAGAGTTGGATATCGGGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
54279918 AGAG
66 AGAG
* * *
54279922 CAACGTCATCCTCTCGAAATTGAAGTAGAGTTGGATGTCAGGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
54279987 AGAG
66 AGAG
*
54279991 CAACGGCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
54280056 AGAG
66 AGAG
* ** *
54280060 CAACGTCATCCTCTCGAAATTGAAGTAGAGTTGGATATCGGGTCTTTATCTCTGAAATTAAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
54280125 AGAG
66 AGAG
* * *
54280129 CAACGTCATCCTCTCGAAATTGAAGTAGAGTTGGATGTCAGGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
54280194 AGAG
66 AGAG
* *
54280198 CAACGGCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
54280263 AGAG
66 AGAG
* *
54280267 CAACGTCATCCTCTCGAAATTGAAGTAGAGTTGGATATCAGGTCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
54280332 AGAG
66 AGAG
* * *
54280336 CAACGGCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCCGAGATTGAAGTA
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
54280401 AGAG
66 AGAG
* * * * * * * *
54280405 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACATA-ACGTCATCCCCTTTAAATTGAC
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCA-AGTCTTTAT-CTC-TGAAATTGAA
*
54280468 GTAGAGTGGAT
63 GTA-A---GAG
* * * * *
54280479 AACACGTATTCATCC-CTTGGAATTGAAGTAGAG-TGGATAGCACGTCTTCATCTCTGAAATTGA
1 CA-ACG---TCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGA
54280542 AGTAAGAG
62 AGTAAGAG
* * *
54280550 CAACGTCATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAAGTCTCTATCTC
1 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATC-AAGTCTTTATCTC
54280603 CCTGAAGAGC
Statistics
Matches: 737, Mismatches: 67, Indels: 29
0.88 0.08 0.03
Matches are distributed among these distances:
67 6 0.01
68 28 0.04
69 621 0.84
70 22 0.03
71 4 0.01
74 4 0.01
75 14 0.02
76 2 0.00
77 30 0.04
78 6 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (69 bp):
CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
AGAG
Found at i:54280510 original size:38 final size:39
Alignment explanation
Indices: 54280410--54280545 Score: 156
Period size: 39 Copynumber: 3.6 Consensus size: 39
54280400 AAGAGCAACG
*
54280410 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACA--TAACG
1 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGT-A-T
* *
54280449 TCATCCCCTTTAAATTGACGTAGAGTGGATAACACGTAT
1 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTAT
* * *
54280488 TCAT-CCCTTGGAATTGAAGTAGAGTGGATAGCACGTCT
1 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTAT
*
54280526 TCAT-CTC-TGAAATTGAAGTA
1 TCATCCCCTTGAAATTGAAGTA
54280546 AGAGCAACGT
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
37 12 0.14
38 35 0.41
39 36 0.42
40 1 0.01
41 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (39 bp):
TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTAT
Found at i:54280905 original size:6 final size:6
Alignment explanation
Indices: 54280896--54280934 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
54280886 TTAGATTTAT
*
54280896 TTTAAA TTTAAA ATTAGATA TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTA-A-A TTTAAA TTTAAA TTTAAA T
54280935 AAAGATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 23 0.79
7 2 0.07
8 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:54281046 original size:29 final size:28
Alignment explanation
Indices: 54280977--54281051 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
54280967 CAATGTCCAA
*
54280977 TTACAAGGGCCCAAATTGAGCCCAAATC
1 TTACAAGGACCCAAATTGAGCCCAAATC
* ** *
54281005 TTAAAAAAAACCCAAATTGAGCCCAAATT
1 TT-ACAAGGACCCAAATTGAGCCCAAATC
54281034 TTACAAGTGACCCAAATT
1 TTACAAG-GACCCAAATT
54281052 ACAATGACCC
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 5 0.14
29 32 0.86
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.21
Consensus pattern (28 bp):
TTACAAGGACCCAAATTGAGCCCAAATC
Found at i:54282027 original size:12 final size:12
Alignment explanation
Indices: 54281994--54282027 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54281984 AAAGGAGATT
54281994 AAGGAAGAAAAA
1 AAGGAAGAAAAA
*
54282006 AGGGAAGAAAAA
1 AAGGAAGAAAAA
*
54282018 AAGGAGGAAA
1 AAGGAAGAAA
54282028 GGAGCGCACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (12 bp):
AAGGAAGAAAAA
Found at i:54282637 original size:161 final size:162
Alignment explanation
Indices: 54282458--54282765 Score: 458
Period size: 161 Copynumber: 1.9 Consensus size: 162
54282448 TTATAATTTA
**
54282458 GTCCTTTGACTGTTTGACTGTGCCAGAGGTTGCCACGTGTCATGTATTAGATTATTTATGCATTT
1 GTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATGTATTAGATTATTTATGCATTT
*
54282523 AGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCC-CAAATCAACTTTGT-TTTAATTACGAAA
66 AGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTT-TATTTAATTACAAAA
* *
54282586 TTGGCCCCATAATTTTTCGAGGTTTATAAACTG
130 TTGGCCCAAAAATTTTTCGAGGTTTATAAACTG
* * * * * *
54282619 GTCCTTTGACTTTTTGACTGCACCAGAGGTTGCCACGTGTCATTTTTTGGGTTATTTCTGCATTT
1 GTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATGTATTAGATTATTTATGCATTT
* * *
54282684 AGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACAAAAT
66 AGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAAAT
*
54282749 TGGTCCAAAAATTTTTC
131 TGGCCCAAAAATTTTTC
54282766 AAGATTTTCA
Statistics
Matches: 130, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
161 93 0.72
162 37 0.28
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (162 bp):
GTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATGTATTAGATTATTTATGCATTT
AGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAAAT
TGGCCCAAAAATTTTTCGAGGTTTATAAACTG
Found at i:54282821 original size:161 final size:160
Alignment explanation
Indices: 54282480--54282797 Score: 397
Period size: 161 Copynumber: 2.0 Consensus size: 160
54282470 TTTGACTGTG
*
54282480 CCAGAGGTTGCCACGTGTCATGTATTAGATTATTTATGCATTTAGTCCTTTTCATTTTTAATTTG
1 CCAGAGGCTGCCACGTGTCATGTATTAGATTATTTATGCATTTAGTCCTTTTCATTTTTAATTTG
* * * * *
54282545 TTTTAATTTAATCCCAAATCAACTTTGTTTTAATTACGAAATTGGCCCCATAATTTTTCGAGGTT
66 TTTTAATTTAATCCCAAATCAACTTTGTTTTAATTACAAAATTGGCCCAAAAATTTTTCAAGATT
* * * *
54282610 TATAAACTGGTCCTTTGACTTTTTGACTGCA
131 TATAAACTGGTCCCTTGACCTCTGGACT-CA
* * * * * * *
54282641 CCAGAGGTTGCCACGTGTCATTTTTTGGGTTATTTCTGCATTTAGTCCTTTTTATTTTTAATTTG
1 CCAGAGGCTGCCACGTGTCATGTATTAGATTATTTATGCATTTAGTCCTTTTCATTTTTAATTTG
* * *
54282706 TTTTAATTTAATCCTTAAATCGACTTT-TATTTAATTACAAAATTGGTCCAAAAATTTTTCAAGA
66 TTTTAATTTAATCC-CAAATCAACTTTGT-TTTAATTACAAAATTGGCCCAAAAATTTTTCAAGA
*
54282770 TTT-TCAAATTGGTCCCTTGACCTCTGGA
129 TTTAT-AAACTGGTCCCTTGACCTCTGGA
54282798 TACCTGTGGG
Statistics
Matches: 135, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
161 75 0.56
162 60 0.44
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (160 bp):
CCAGAGGCTGCCACGTGTCATGTATTAGATTATTTATGCATTTAGTCCTTTTCATTTTTAATTTG
TTTTAATTTAATCCCAAATCAACTTTGTTTTAATTACAAAATTGGCCCAAAAATTTTTCAAGATT
TATAAACTGGTCCCTTGACCTCTGGACTCA
Found at i:54282904 original size:30 final size:30
Alignment explanation
Indices: 54282866--54282973 Score: 173
Period size: 30 Copynumber: 3.6 Consensus size: 30
54282856 AATTGTCCAG
54282866 AAAA-TACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
54282895 TAAATTACATTTTGACCCCAAAGCTTTACC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
54282925 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
54282955 AAAATTACATTTTAACCCC
1 AAAATTACATTTTGACCCC
54282974 GATTTCACCG
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
29 3 0.04
30 68 0.96
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:54283030 original size:59 final size:59
Alignment explanation
Indices: 54282925--54283415 Score: 731
Period size: 59 Copynumber: 8.4 Consensus size: 59
54282915 AAGCTTTACC
* * *
54282925 AAAATTA-CATTTTGA-CCCCAAAACTTTTCCAAAATTACA-TTTTAACCCCGATTTCACCG
1 AAAATTACCATTTT-ACCCCCGAATCTTTT--AAAATTCCATTTTTAACCCCGATTTCACCG
* *
54282984 AAAATTACCATTTTACCCTCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
54283043 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
* *
54283102 AAAATTACCATTTTACCCTCGAATCTTTTAAAATTCTATTTTTAACCCCGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
* *
54283161 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCTGATTTTACCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * ***
54283220 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCTGATTGCATTA
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
** *
54283279 AAAATTACCATTTTACCCCTAAATCTTTCAAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
* *
54283338 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCA-TTTTAACCCTGATTTTACC-
1 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
*
54283395 AAAATTACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
54283416 GGTATCCATA
Statistics
Matches: 395, Mismatches: 34, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
57 20 0.05
58 25 0.06
59 334 0.85
60 16 0.04
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.37
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
Found at i:54290151 original size:30 final size:30
Alignment explanation
Indices: 54290101--54290166 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
54290091 AATTTTCAAG
*
54290101 AAAA-TTTTAAAATTTGAATTAGA-TCTTC
1 AAAATTTTTAAAATTTGAATTAGACCCTTC
54290129 AAAATTTTTGAAAATTAT-AATTAGACCCTTC
1 AAAATTTTT-AAAATT-TGAATTAGACCCTTC
54290160 AAAATTT
1 AAAATTT
54290167 AATGCCAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 4 0.12
29 4 0.12
30 13 0.39
31 12 0.36
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (30 bp):
AAAATTTTTAAAATTTGAATTAGACCCTTC
Found at i:54298044 original size:18 final size:18
Alignment explanation
Indices: 54298021--54298060 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
54298011 AAAACTGCTT
54298021 GAAAATGGAAGAAGAAAA
1 GAAAATGGAAGAAGAAAA
* *
54298039 GAAAATGGAAGGAGAGAA
1 GAAAATGGAAGAAGAAAA
54298057 GAAA
1 GAAA
54298061 GGAAAAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.05
Consensus pattern (18 bp):
GAAAATGGAAGAAGAAAA
Found at i:54298920 original size:30 final size:30
Alignment explanation
Indices: 54298870--54298935 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
54298860 AATTTTCAAG
*
54298870 AAAA-TTTTAAAATTTGAATTAGA-TCTTC
1 AAAATTTTTAAAATTTGAATTAGACCCTTC
54298898 AAAATTTTTGAAAATTAT-AATTAGACCCTTC
1 AAAATTTTT-AAAATT-TGAATTAGACCCTTC
54298929 AAAATTT
1 AAAATTT
54298936 AATGCCAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 4 0.12
29 4 0.12
30 13 0.39
31 12 0.36
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (30 bp):
AAAATTTTTAAAATTTGAATTAGACCCTTC
Found at i:54303807 original size:30 final size:30
Alignment explanation
Indices: 54303773--54303874 Score: 73
Period size: 30 Copynumber: 3.2 Consensus size: 30
54303763 AACCCTCTAA
54303773 AATTATACTCATAAATTTTCTTAAAATTTT
1 AATTATACTCATAAATTTTCTTAAAATTTT
* *
54303803 AATTAGA-TCCTAAAATTTT-TTGAAAAATTTAATT
1 AATTATACTCAT-AAATTTTCTT--AAAA-TT--TT
* *
54303837 AGACCCTATACTCATAAATTTTCTTAAAAGTTT
1 A-A--TTATACTCATAAATTTTCTTAAAATTTT
54303870 AATTA
1 AATTA
54303875 AACCCTCTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 22
0.65 0.08 0.27
Matches are distributed among these distances:
29 5 0.09
30 15 0.28
31 4 0.07
32 3 0.06
33 3 0.06
34 3 0.06
35 2 0.04
36 4 0.07
37 10 0.19
38 5 0.09
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (30 bp):
AATTATACTCATAAATTTTCTTAAAATTTT
Found at i:54304958 original size:105 final size:105
Alignment explanation
Indices: 54304837--54305053 Score: 335
Period size: 105 Copynumber: 2.1 Consensus size: 105
54304827 GCCTAAATCA
* * *
54304837 CTCCACATGGCTTGCCACACTACCGTGTCTCCACTGTAGCTTAATTTTACATGTTCCACATGGAC
1 CTCCACATGGCCTGCCACACTACCGTGTCTCCACTGTAACTTAATTTTACATGTTCCACAAGGAC
* * * *
54304902 ATAGTTTGTTACATGGCCTGGCTACACGATCATGTAACTC
66 ACAGTCTGTTACATGGCCTGGCCACACGATCATGTAACCC
* * * *
54304942 CTCCACATGGCCTGCCACATTACCGTGTCTCCCCTGTAACTTAATTTTACATGTTCCATAAGGCC
1 CTCCACATGGCCTGCCACACTACCGTGTCTCCACTGTAACTTAATTTTACATGTTCCACAAGGAC
54305007 ACAGTCTGTTACATGGCCTGGCCACACGATCATGTAACCC
66 ACAGTCTGTTACATGGCCTGGCCACACGATCATGTAACCC
54305047 CTCCACA
1 CTCCACA
54305054 CGGCTTAAGG
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 101 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (105 bp):
CTCCACATGGCCTGCCACACTACCGTGTCTCCACTGTAACTTAATTTTACATGTTCCACAAGGAC
ACAGTCTGTTACATGGCCTGGCCACACGATCATGTAACCC
Found at i:54306661 original size:30 final size:30
Alignment explanation
Indices: 54306617--54306758 Score: 257
Period size: 30 Copynumber: 4.7 Consensus size: 30
54306607 TTAGGAGATT
* *
54306617 TTTTTGGGTTAAAATGTAATTTTGGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
*
54306647 TTTTGGGGTCAAAATATAATTTTGGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
54306677 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
54306707 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
54306737 TTTTGGGGTCAAAATGTAATTT
1 TTTTGGGGTCAAAATGTAATTT
54306759 CTAGATTGTT
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 108 1.00
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (30 bp):
TTTTGGGGTCAAAATGTAATTTTGGAAAAG
Found at i:54306701 original size:19 final size:19
Alignment explanation
Indices: 54306677--54306731 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
54306667 TTTGGAAAAG
54306677 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
54306696 TTTT--GG--AAAA-G---
1 TTTTGGGGTCAAAATGTAA
54306707 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
54306726 TTTTGG
1 TTTTGG
54306732 AAAAGTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
13 2 0.07
14 1 0.04
15 8 0.29
16 1 0.04
17 2 0.07
19 10 0.36
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (19 bp):
TTTTGGGGTCAAAATGTAA
Found at i:54308627 original size:6 final size:6
Alignment explanation
Indices: 54308603--54308711 Score: 82
Period size: 6 Copynumber: 18.0 Consensus size: 6
54308593 ACATTGGACT
* * **
54308603 TTTAAA TTTTTAA TGTTAAA TTTAATA TTTTAA TTTTTA TTTAAA TTTAAA
1 TTTAAA -TTTAAA T-TTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
* * *
54308654 TTCAAA -TTAAA TTTAAATA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTT-AA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
54308702 --TAAA TTTAAA
1 TTTAAA TTTAAA
54308712 ATCAATTTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 48 0.58
7 19 0.23
8 4 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:54308675 original size:25 final size:25
Alignment explanation
Indices: 54308647--54308696 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
54308637 TTTTATTTAA
* *
54308647 ATTTAAATTCAAATTAAATTTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
*
54308672 ATTTAAATTTAAAATAAATCTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
54308697 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAATTCAAAATAAATCTAAAT
Found at i:54308675 original size:31 final size:31
Alignment explanation
Indices: 54308640--54308703 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
54308630 TTTTAATTTT
*
54308640 TATTTAAATTTAAATTCAAAT-TAAATTTAAA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAAA
54308671 TATTTAAATTTAAAATAAATCTAAATTTAAA
1 TATTTAAATTTAAAATAAATCTAAATTTAAA
54308702 TA
1 TA
54308704 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAAA
Found at i:54308690 original size:42 final size:43
Alignment explanation
Indices: 54308618--54308711 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 43
54308608 ATTTTTAATG
* * ** *
54308618 TTAAATTT-AATATTTTAATTTTTATTTAAATTTAAATTCAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
*
54308660 TTAAATTTAAATA-TTTAAATTTAAAATAAATCTAAATTTAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
54308702 -TAAATTTAAA
1 TTAAATTTAAA
54308712 ATCAATTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 10 0.22
42 31 0.69
43 4 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (43 bp):
TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
Found at i:54308713 original size:17 final size:16
Alignment explanation
Indices: 54308641--54308711 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 16
54308631 TTTAATTTTT
54308641 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAA-T-AA
54308659 A-TTAAATTTAAAT--
1 ATTTAAATTTAAATAA
54308672 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
*
54308689 ATCTAAATTTAAATAA
1 ATTTAAATTTAAATAA
54308705 ATTTAAA
1 ATTTAAA
54308712 ATCAATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 4 0.09
16 13 0.28
17 20 0.43
18 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:54309157 original size:90 final size:90
Alignment explanation
Indices: 54308997--54309165 Score: 239
Period size: 90 Copynumber: 1.9 Consensus size: 90
54308987 TGGTGGTATA
* * * *
54308997 TCCACAAAATTTACTGGTAACTTTGATCTACAAACTCGTTGTGTATTCACAACCACTAACAGCGT
1 TCCACAAAATTTACTGGTAACTTTCATCTACAAACCCGTTGTATATTCACAACCACTAACAGCAT
54309062 ATTAACCTACAACATTGGTGGCTTG
66 ATTAACCTACAACATTGGTGGCTTG
* * * * **
54309087 TCCACAATATTTACTGGTAGCTTTCATCTGCAAACCCGTTGTATATTCACAACTACTGGCAGCAT
1 TCCACAAAATTTACTGGTAACTTTCATCTACAAACCCGTTGTATATTCACAACCACTAACAGCAT
*
54309152 CTTAACCTACAACA
66 ATTAACCTACAACA
54309166 CTTGTGGTTC
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
90 68 1.00
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (90 bp):
TCCACAAAATTTACTGGTAACTTTCATCTACAAACCCGTTGTATATTCACAACCACTAACAGCAT
ATTAACCTACAACATTGGTGGCTTG
Found at i:54311282 original size:22 final size:22
Alignment explanation
Indices: 54311254--54311299 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
54311244 CGTTAAATAT
*
54311254 ATTGATA-AAGATAATATTTCAG
1 ATTGATATAAGATAA-ATATCAG
*
54311276 ATTGATATAATATAAATATCAG
1 ATTGATATAAGATAAATATCAG
54311298 AT
1 AT
54311300 CAGTTTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (22 bp):
ATTGATATAAGATAAATATCAG
Found at i:54313125 original size:30 final size:31
Alignment explanation
Indices: 54313091--54313148 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
54313081 TAAAATCTTT
*
54313091 AAAATTTTAATTA-AATCCTCAGAACTTTTG
1 AAAATTTTAATTAGAATCCTCAAAACTTTTG
*
54313121 AAAATTTTAATTAGACTCCTCAAAACTT
1 AAAATTTTAATTAGAATCCTCAAAACTT
54313149 AATACCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (31 bp):
AAAATTTTAATTAGAATCCTCAAAACTTTTG
Found at i:54313513 original size:15 final size:16
Alignment explanation
Indices: 54313486--54313515 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54313476 ATAATAATAC
54313486 CAATCGAACTAAAATT
1 CAATCGAACTAAAATT
54313502 CAATCG-ACTAAAAT
1 CAATCGAACTAAAAT
54313516 GTAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.23
Consensus pattern (16 bp):
CAATCGAACTAAAATT
Found at i:54315206 original size:20 final size:21
Alignment explanation
Indices: 54315167--54315209 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
54315157 AAAAAATAAT
54315167 ATTTAAATATATTATAATTAA
1 ATTTAAATATATTATAATTAA
* *
54315188 ATTTAACTA-ATTATTATTAA
1 ATTTAAATATATTATAATTAA
54315208 AT
1 AT
54315210 AATAATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTAAATATATTATAATTAA
Found at i:54317289 original size:29 final size:29
Alignment explanation
Indices: 54317229--54317365 Score: 82
Period size: 29 Copynumber: 4.7 Consensus size: 29
54317219 TATGGATACC
* * * *
54317229 CGGGGGCAAAATGGTAATTTTAG-TGTAAT
1 CGGGGGTAAAATGGCAATTTTAGAAG-ATT
* *
54317258 CGGGGTTAAAAATGG-AATTTTAAAAGATT
1 CGGGGGT-AAAATGGCAATTTTAGAAGATT
* ** *
54317287 CGGGGGTAAAATGGCAATTTTTGGTGAAAT
1 CGGGGGTAAAATGGCAATTTTAGAAG-ATT
* * * *
54317317 CGAGGTTAAAAAT-GAAATTTTAGAAGCTT
1 CGGGGGT-AAAATGGCAATTTTAGAAGATT
*
54317346 CGGGGGTAAAATGGTAATTT
1 CGGGGGTAAAATGGCAATTT
54317366 CGGTGAAATC
Statistics
Matches: 80, Mismatches: 22, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
28 12 0.15
29 39 0.49
30 24 0.30
31 5 0.06
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (29 bp):
CGGGGGTAAAATGGCAATTTTAGAAGATT
Found at i:54317336 original size:59 final size:58
Alignment explanation
Indices: 54317229--54317544 Score: 370
Period size: 59 Copynumber: 5.4 Consensus size: 58
54317219 TATGGATACC
* * * *
54317229 CGGGGGCAAAATGGTAA-TTTTAGTGTAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATC-GGGTTAAAAATGAAATTTTAAAAGATT
* * *
54317287 CGGGGGTAAAATGGCAATTTTTGGTGAAATCGAGGTTAAAAATGAAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCG-GGTTAAAAATGAAATTTTAAAAGATT
* * ** *
54317346 CGGGGGTAAAATGGTAA-TTTCGGTGAAATCCGGGTTAAAAA-CAGAATTTTGTAAGTTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAAT-CGGGTTAAAAATGA-AATTTTAAAAGATT
* * * * ** *
54317404 CGAGGGTAAAATGGTAATTTTCGGTGAAATCCGGGTTAAAAACGGAATTTTGTAAGTTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAAT-CGGGTTAAAAATGAAATTTTAAAAGATT
54317463 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAT-AGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATC-GGGTTAAAAATGA-AATTTTAAAAGATT
54317522 CGGGGGTAAAATGGTAATTTTTG
1 CGGGGGTAAAATGGTAATTTTTG
54317545 AAAATTTTGG
Statistics
Matches: 227, Mismatches: 23, Indels: 15
0.86 0.09 0.06
Matches are distributed among these distances:
57 1 0.00
58 64 0.28
59 162 0.71
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (58 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGTTAAAAATGAAATTTTAAAAGATT
Found at i:54317357 original size:117 final size:117
Alignment explanation
Indices: 54317229--54317544 Score: 447
Period size: 117 Copynumber: 2.7 Consensus size: 117
54317219 TATGGATACC
* * * *
54317229 CGGGGGCAAAATGGTAATTTTAGTGTAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATAGAATTTTAAAAGATTCGGGGGT
* *
54317294 AAAATGGCAATTTTTGGTGAAAT-CGAGGTTAAAAATGAAATTTTAG-AAGCTT
66 AAAATGGTAATTTTTGGTGAAATCCG-GGTTAAAAACGAAATTTT-GTAAGCTT
* * * ** * *
54317346 CGGGGGTAAAATGGTAATTTCGGTGAAATCCGGGTTAAAAACAGAATTTTGTAAGTTTCGAGGGT
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATAGAATTTTAAAAGATTCGGGGGT
* * *
54317411 AAAATGGTAATTTTCGGTGAAATCCGGGTTAAAAACGGAATTTTGTAAGTTT
66 AAAATGGTAATTTTTGGTGAAATCCGGGTTAAAAACGAAATTTTGTAAGCTT
54317463 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTAAAAGATTCGGGGG
1 CGGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATAGAATTTTAAAAGATTCGGGGG
54317528 TAAAATGGTAATTTTTG
65 TAAAATGGTAATTTTTG
54317545 AAAATTTTGG
Statistics
Matches: 172, Mismatches: 24, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
116 1 0.01
117 113 0.66
118 58 0.34
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (117 bp):
CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATAGAATTTTAAAAGATTCGGGGGT
AAAATGGTAATTTTTGGTGAAATCCGGGTTAAAAACGAAATTTTGTAAGCTT
Found at i:54317384 original size:29 final size:29
Alignment explanation
Indices: 54317352--54317444 Score: 75
Period size: 30 Copynumber: 3.2 Consensus size: 29
54317342 GCTTCGGGGG
54317352 TAAAATGGTAATTTCGGTGAAATCCGGGT
1 TAAAATGGTAATTTCGGTGAAATCCGGGT
** * * * *
54317381 TAAAAACAG-AATTT-TGT-AAGTTTCGAGGG
1 T-AAAATGGTAATTTCGGTGAA-ATCCG-GGT
54317410 TAAAATGGTAATTTTCGGTGAAATCCGGGT
1 TAAAATGGTAA-TTTCGGTGAAATCCGGGT
54317440 TAAAA
1 TAAAA
54317445 ACGGAATTTT
Statistics
Matches: 45, Mismatches: 12, Indels: 13
0.64 0.17 0.19
Matches are distributed among these distances:
27 2 0.04
28 10 0.22
29 11 0.24
30 15 0.33
31 5 0.11
32 2 0.04
ACGTcount: A:0.35, C:0.09, G:0.25, T:0.31
Consensus pattern (29 bp):
TAAAATGGTAATTTCGGTGAAATCCGGGT
Found at i:54317481 original size:29 final size:30
Alignment explanation
Indices: 54317390--54317572 Score: 91
Period size: 30 Copynumber: 6.2 Consensus size: 30
54317380 TTAAAAACAG
*
54317390 AATTTTGTAAGTTTCGAGGGT-AAAATGGT
1 AATTTTGTAAGTTTCGGGGGTAAAAATGGT
* * * *
54317419 AATTTTCGGTGAA--ATCCGGGTTAAAAACGG-
1 AATTTT--GT-AAGTTTCGGGGGTAAAAATGGT
54317449 AATTTTGTAAGTTTCGGGGGT-AAAATGGT
1 AATTTTGTAAGTTTCGGGGGTAAAAATGGT
* * *
54317478 AATTTTTGGTGAA--ATCGGGGTTAAAAATAG-
1 AA-TTTT-GT-AAGTTTCGGGGGTAAAAATGGT
** *
54317508 AATTTTAAAAGATTCGGGGGT-AAAATGGT
1 AATTTTGTAAGTTTCGGGGGTAAAAATGGT
* * * *
54317537 AATTTTTGAAAATTT-TGGGGTCAAAAT-GT
1 AA-TTTTGTAAGTTTCGGGGGTAAAAATGGT
54317566 AATTTTG
1 AATTTTG
54317573 GGAAAGTTTT
Statistics
Matches: 117, Mismatches: 21, Indels: 33
0.68 0.12 0.19
Matches are distributed among these distances:
27 4 0.03
28 19 0.16
29 36 0.31
30 38 0.32
31 16 0.14
32 4 0.03
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (30 bp):
AATTTTGTAAGTTTCGGGGGTAAAAATGGT
Found at i:54317622 original size:29 final size:30
Alignment explanation
Indices: 54317524--54317635 Score: 156
Period size: 30 Copynumber: 3.7 Consensus size: 30
54317514 AAAAGATTCG
*
54317524 GGGGT-AAAATGGTAATTTTTGAAAA-TTTT
1 GGGGTCAAAAT-GTAATTTTGGAAAAGTTTT
*
54317553 GGGGTCAAAATGTAATTTTGGGAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
54317583 AGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
54317613 GGGGTCAAATTGTAATTTCTGGA
1 GGGGTCAAAATGTAATTT-TGGA
54317636 CAATTTAGAG
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
29 17 0.23
30 53 0.72
31 4 0.05
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.38
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTTGGAAAAGTTTT
Found at i:54317956 original size:162 final size:162
Alignment explanation
Indices: 54317728--54318041 Score: 490
Period size: 162 Copynumber: 1.9 Consensus size: 162
54317718 ATTTGAAAAT
*
54317728 CTTGAAAAAATTTTGGACCAATTTTGTAATTAAATAAAAGTCGATTTAAGGATTAAATTAAAACA
1 CTTGAAAAAATTTTGGACCAATTTCGTAATTAAATAAAAGTCGATTTAAGGATTAAATTAAAACA
* * *
54317793 AATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAGATGACAGGTGGCAACCTCTGGT
66 AATAAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAG-TGACACGTGGCAACCTATGGT
*
54317858 GCAGTCAAACAGTCAAAGGACTAGTTTATAAAC
130 ACAGTCAAACAGTCAAAGGACTAGTTTATAAAC
* * *
54317891 CTTG-AAAAATTATTGGGCCAATTTCGTAATTAAA-ATAAAGTTGATTT-GGGATTAAATTAAAA
1 CTTGAAAAAATT-TTGGACCAATTTCGTAATTAAATA-AAAGTCGATTTAAGGATTAAATTAAAA
* *
54317953 CAAATAAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAGTTACACGTGGCAGCCTATGG
64 CAAATAAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAGTGACACGTGGCAACCTATGG
54318018 TACAGTCAAACAGTCAAAGGACTA
129 TACAGTCAAACAGTCAAAGGACTA
54318042 AATTGAAAAG
Statistics
Matches: 139, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
161 39 0.28
162 66 0.47
163 34 0.24
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.25
Consensus pattern (162 bp):
CTTGAAAAAATTTTGGACCAATTTCGTAATTAAATAAAAGTCGATTTAAGGATTAAATTAAAACA
AATAAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAGTGACACGTGGCAACCTATGGTA
CAGTCAAACAGTCAAAGGACTAGTTTATAAAC
Found at i:54318121 original size:162 final size:161
Alignment explanation
Indices: 54317775--54318124 Score: 404
Period size: 162 Copynumber: 2.2 Consensus size: 161
54317765 AAGTCGATTT
*
54317775 AAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAGATGA
1 AAGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAGATGA
* * * * * * **
54317840 CAGGTGGCAACCTCTGGTGCAGTCAAACAGTCAAAGGACTAGTTTATAAACCTTGAAAAATTATT
66 CACGTGGCAACCTATGGTACAGTCAAACAGTCAAAGGACTAATTGATAAACATT-AAAAATTACA
* * * * **
54317905 GGGCCAATTTCGTAATTAAAATAAAGTTGATT
130 GGGCAAATTTCGCAAATAAAATAAAGATGAAA
** *
54317937 TGGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAG-TTA
1 AAGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAGATGA
*
54318001 CACGTGGCAGCCTATGGTACAGTCAAACAGTCAAAGGACTAAATTGA-AAAGCAATT-AAAATTA
66 CACGTGGCAACCTATGGTACAGTCAAACAGTCAAAGGACT-AATTGATAAA-C-ATTAAAAATTA
54318064 CAGGGCAAATTT-GCAAATAATTAA-AAAGATGCAAA
128 CAGGGCAAATTTCGCAAATAA--AATAAAGATG-AAA
* * *
54318099 AAGGACTAAATTGAAGCAAATAAAAA
1 AAGGATTAAATTAAAACAAATAAAAA
54318125 TGCGGAAGGA
Statistics
Matches: 158, Mismatches: 24, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
160 6 0.04
161 63 0.40
162 87 0.55
163 2 0.01
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (161 bp):
AAGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAGATGA
CACGTGGCAACCTATGGTACAGTCAAACAGTCAAAGGACTAATTGATAAACATTAAAAATTACAG
GGCAAATTTCGCAAATAAAATAAAGATGAAA
Found at i:54318197 original size:22 final size:22
Alignment explanation
Indices: 54318169--54318220 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
54318159 CTAAAAACAC
54318169 GCGGATCCCAGGGGTCCGTGGG
1 GCGGATCCCAGGGGTCCGTGGG
*
54318191 GCGGATCCCAGGGGTCCGTTGG
1 GCGGATCCCAGGGGTCCGTGGG
*
54318213 TCGGATCC
1 GCGGATCC
54318221 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.10, C:0.29, G:0.44, T:0.17
Consensus pattern (22 bp):
GCGGATCCCAGGGGTCCGTGGG
Found at i:54319561 original size:6 final size:6
Alignment explanation
Indices: 54319522--54319641 Score: 97
Period size: 6 Copynumber: 20.2 Consensus size: 6
54319512 CTTTGGACTC
* ** *
54319522 TTAAATT TTTAAT TTAATAT TTAAAT TTTTAT TTAAAT TTAAAT TCAAA-
1 TTAAA-T TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
54319571 TTAAAT TTAAATAT TTAAAT TTAAAT TTAAA- ATAAAT CTAAAT TTAAA-
1 TTAAAT TT-AA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
54319619 -TAAAT TTAAA- ATCAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT T
54319642 CAAAAGTCCA
Statistics
Matches: 90, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
4 4 0.04
5 11 0.12
6 57 0.63
7 14 0.16
8 4 0.04
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:54319576 original size:17 final size:17
Alignment explanation
Indices: 54319554--54319641 Score: 85
Period size: 17 Copynumber: 5.4 Consensus size: 17
54319544 AAATTTTTAT
54319554 TTAAATTTAAATTCAAA
1 TTAAATTTAAATTCAAA
*
54319571 TTAAATTTAAA-T--AT
1 TTAAATTTAAATTCAAA
*
54319585 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTCAAA
* * *
54319602 ATAAATCTAAATTTAAA
1 TTAAATTTAAATTCAAA
* *
54319619 -TAAATTTAAAATCAAT
1 TTAAATTTAAATTCAAA
54319635 TTAAATT
1 TTAAATT
54319642 CAAAAGTCCA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
14 12 0.20
15 1 0.02
16 13 0.22
17 33 0.56
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAATTTAAATTCAAA
Found at i:54320607 original size:20 final size:21
Alignment explanation
Indices: 54320573--54320628 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
54320563 ATAAATAATT
54320573 TAAAAATTATAAAATA-TTCAA
1 TAAAAATTATAAAATAGTTC-A
54320594 TAAAAATTAT-AAATAGTTCA
1 TAAAAATTATAAAATAGTTCA
*
54320614 TAAAAAATTTTAAAA
1 T-AAAAATTATAAAA
54320629 AAATTAGCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 7 0.23
21 21 0.68
22 3 0.10
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAAAATTATAAAATAGTTCA
Found at i:54320924 original size:23 final size:22
Alignment explanation
Indices: 54320894--54320937 Score: 54
Period size: 25 Copynumber: 1.9 Consensus size: 22
54320884 AATATATGAT
54320894 AAAATTAT-ATTTTAATCCCTAA
1 AAAATTATAATTTTAA-CCCTAA
54320916 AAAATTTATCAATTTTAACCCT
1 AAAA-TTAT-AATTTTAACCCT
54320938 TCTAAGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.21
23 4 0.21
24 4 0.21
25 7 0.37
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTATAATTTTAACCCTAA
Found at i:54322296 original size:13 final size:12
Alignment explanation
Indices: 54322268--54322312 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 12
54322258 AGTGTCTTTA
*
54322268 AAAATTATTTTGG
1 AAAAGTATTTT-G
54322281 AAAAGTGATTTTG
1 AAAAGT-ATTTTG
54322294 AAAAGTACTTTTG
1 AAAAGTA-TTTTG
54322307 AAAAGT
1 AAAAGT
54322313 TTGGTTTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 1 0.03
13 23 0.79
14 5 0.17
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (12 bp):
AAAAGTATTTTG
Found at i:54326198 original size:30 final size:31
Alignment explanation
Indices: 54326135--54326195 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
54326125 TTCCGTTTTA
*
54326135 TAATTAAATTTACAAATATAATATAATCATT
1 TAATTAAATTTACAAATATAATATAATAATT
**
54326166 TAATTAAA-TTACTGATATAAT-TAATAATT
1 TAATTAAATTTACAAATATAATATAATAATT
54326195 T
1 T
54326196 TAAAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 8 0.30
30 11 0.41
31 8 0.30
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (31 bp):
TAATTAAATTTACAAATATAATATAATAATT
Found at i:54326258 original size:26 final size:25
Alignment explanation
Indices: 54326210--54326259 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
54326200 ATTAATTTCT
* * *
54326210 TATATAAATATATTTATATATAATA
1 TATATAAAAATATTTAAAAATAATA
54326235 TATATGAAAAATATTTAAAAATAAT
1 TATAT-AAAAATATTTAAAAATAAT
54326260 GATTAATCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
TATATAAAAATATTTAAAAATAATA
Found at i:54327257 original size:14 final size:15
Alignment explanation
Indices: 54327224--54327259 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
54327214 AAAATTTAAA
* *
54327224 AAAAATGAATTTTGT
1 AAAAATGAATGTTAT
54327239 AAAAATGAATGTTAT
1 AAAAATGAATGTTAT
54327254 AAAAAT
1 AAAAAT
54327260 CTTGGTCTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (15 bp):
AAAAATGAATGTTAT
Found at i:54333104 original size:31 final size:31
Alignment explanation
Indices: 54333069--54333137 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
54333059 TTACATTTTT
*
54333069 TCAAGTTCAAGGATCAAAATGGACCTAATTG
1 TCAAGTTCAAGGATCAAAATGAACCTAATTG
* * *
54333100 TCAAGTACAAGTATCAAAGTGAACCTAATTG
1 TCAAGTTCAAGGATCAAAATGAACCTAATTG
*
54333131 CCAAGTT
1 TCAAGTT
54333138 TAGAGGCCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (31 bp):
TCAAGTTCAAGGATCAAAATGAACCTAATTG
Found at i:54351528 original size:2 final size:2
Alignment explanation
Indices: 54351521--54351583 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
54351511 ATTATGTCAA
54351521 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
54351563 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
54351584 GTATGATTAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54356688 original size:3 final size:3
Alignment explanation
Indices: 54356680--54356717 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
54356670 TTTAAATTGG
* *
54356680 GAT GAT GAT GAT GAT GTT GAT GCT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
54356718 GAAGTCACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.34, T:0.34
Consensus pattern (3 bp):
GAT
Found at i:54370472 original size:16 final size:15
Alignment explanation
Indices: 54370451--54370490 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
54370441 CGTTTGGTTC
*
54370451 GCTGTAATGGAATAG
1 GCTGTAATAGAATAG
54370466 AGCTGTAATAGAATAG
1 -GCTGTAATAGAATAG
54370482 GACTGTAAT
1 G-CTGTAAT
54370491 CAGTAATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (15 bp):
GCTGTAATAGAATAG
Found at i:54370724 original size:58 final size:59
Alignment explanation
Indices: 54370660--54370800 Score: 207
Period size: 58 Copynumber: 2.4 Consensus size: 59
54370650 AATTTTAATG
* *
54370660 ATTATTATTAAATATAATTTAATAAAAATATTA-ATTAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATA-TAATTTAATAATATTTTTAACATA
*
54370718 ATTATTATTAAATATAATTTAAT-AAAATAATATATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAATATTTTTAACATA
*
54370776 ATTATTATTAAAATATAAATTAATA
1 ATTATTATT-AAATATAATTTAATA
54370801 TATAACCTAA
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
57 20 0.27
58 42 0.56
59 13 0.17
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.48
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAATATTTTTAACATA
Found at i:54370736 original size:32 final size:28
Alignment explanation
Indices: 54370660--54370805 Score: 104
Period size: 29 Copynumber: 5.0 Consensus size: 28
54370650 AATTTTAATG
54370660 ATTATTATTAAATATAATTTAATAAA-A
1 ATTATTATTAAATATAATTTAATAAATA
* *
54370687 A-TATTAATT-AATTTAATTATATTTTAACATA
1 ATTATT-ATTAAATATAATT-TA--ATAA-ATA
54370718 ATTATTATTAAATATAATTTAATAAAATA
1 ATTATTATTAAATATAATTTAAT-AAATA
* * *
54370747 ATATATAATTTAATA-ATATTT-TTAATATA
1 AT-TATTATTAAATATA-ATTTAATAA-ATA
* *
54370776 ATTATTATTAAAATATAAATTAATATATA
1 ATTATTATT-AAATATAATTTAATAAATA
54370805 A
1 A
54370806 CCTAATTTAT
Statistics
Matches: 92, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
26 12 0.13
27 6 0.07
28 8 0.09
29 27 0.29
30 20 0.22
31 7 0.08
32 12 0.13
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTATTATTAAATATAATTTAATAAATA
Found at i:54379526 original size:5 final size:5
Alignment explanation
Indices: 54379516--54379544 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
54379506 CTCAAAATTG
54379516 AAGTC AAGTC AAGTC AAGTC AAGTC AAGT
1 AAGTC AAGTC AAGTC AAGTC AAGTC AAGT
54379545 GACAAATGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (5 bp):
AAGTC
Found at i:54414195 original size:46 final size:45
Alignment explanation
Indices: 54414138--54414231 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 45
54414128 CGGTAACATG
*
54414138 GATGCTATTTAAATTTTAAAATATTTTAATTAATATTATATCAATAA
1 GATGCTATTTAAATTTT-AAATATTTTAATT-ATACTATATCAATAA
*
54414185 GATG-TATTTAAATTTTAAATATTTTAATTATGCTATATCAATAA
1 GATGCTATTTAAATTTTAAATATTTTAATTATACTATATCAATAA
54414229 GAT
1 GAT
54414232 CATTTAGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
44 16 0.36
45 13 0.29
46 12 0.27
47 4 0.09
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (45 bp):
GATGCTATTTAAATTTTAAATATTTTAATTATACTATATCAATAA
Found at i:54415395 original size:24 final size:24
Alignment explanation
Indices: 54415367--54415417 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
54415357 GAATTGACTC
* *
54415367 AAACAACTAAACAAAGTTTAATTG
1 AAACAAATAAACAAAGTTTAACTG
*
54415391 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAAAGTTTAACTG
54415415 AAA
1 AAA
54415418 AATTATTTTT
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:0.57, C:0.12, G:0.10, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAACTG
Found at i:54416332 original size:30 final size:30
Alignment explanation
Indices: 54416259--54416338 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 30
54416249 ATATCAAAAC
* *
54416259 TATACATGAATTTTGGTTTAGTGTGTAATTT
1 TATACATGAATTTTGATTTA-TGTGTAAATT
54416290 TATACATGAATTTTGATTT-TGTGTAAATT
1 TATACATGAATTTTGATTTATGTGTAAATT
54416319 TATACATGAAATTTTGATTT
1 TATACATG-AATTTTGATTT
54416339 GATCTAATTC
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 17 0.37
30 11 0.24
31 18 0.39
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.51
Consensus pattern (30 bp):
TATACATGAATTTTGATTTATGTGTAAATT
Found at i:54418912 original size:33 final size:34
Alignment explanation
Indices: 54418865--54418939 Score: 93
Period size: 33 Copynumber: 2.2 Consensus size: 34
54418855 ATTAAATTAC
* *
54418865 TTTTATCAAGAATTA-T-ATTTTTATGATAA-AAAG
1 TTTTATCAAAAATTATTAATGTTTAT--TAACAAAG
54418898 TTTTATCAAAAATTATTAATGTTTATTAACAAAG
1 TTTTATCAAAAATTATTAATGTTTATTAACAAAG
54418932 TTTTATCA
1 TTTTATCA
54418940 TTATTGATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
33 17 0.46
34 13 0.35
35 7 0.19
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (34 bp):
TTTTATCAAAAATTATTAATGTTTATTAACAAAG
Found at i:54422089 original size:72 final size:72
Alignment explanation
Indices: 54421969--54422104 Score: 209
Period size: 72 Copynumber: 1.9 Consensus size: 72
54421959 ATGCAATGGG
* *
54421969 AACATCTAAAAAATCTGCAAAGGCTTTCTCTCGCTAATTTTCCCAATTTAACATCGCTTCCGGAG
1 AACATCTAAAAAATCTACAAAGGCTTTCTCTCGCTAATTTGCCCAATTTAACATCGCTTCCGGAG
54422034 TGGATTC
66 TGGATTC
* * * * *
54422041 AACATCTAATAAATCTACAAAGGCTTTCTCTCGTTGATTTGCCTAATTTAACATCGTTTCCGGA
1 AACATCTAAAAAATCTACAAAGGCTTTCTCTCGCTAATTTGCCCAATTTAACATCGCTTCCGGA
54422105 TGAGATGCGT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (72 bp):
AACATCTAAAAAATCTACAAAGGCTTTCTCTCGCTAATTTGCCCAATTTAACATCGCTTCCGGAG
TGGATTC
Found at i:54430801 original size:105 final size:105
Alignment explanation
Indices: 54430619--54430822 Score: 309
Period size: 105 Copynumber: 1.9 Consensus size: 105
54430609 CTAAATTGAA
* * ** *
54430619 TAATTTATTTACTTAGTATTTTGATCCATAAAAATCCCTAAATTATGTTAATATTTCTTACAAAA
1 TAATTTATTTACTTAGTATCTTGATCCATAAAAAACCCTAAATTATACTAATATCTCTTACAAAA
* *
54430684 GTAAGAGCAATTGATTTTAGGTTTATTAATTAAACTTGCG
66 GTAAAAGCAATTGATTTTAAGTTTATTAATTAAACTTGCG
* * *
54430724 TAATTTATTTACTTAGTATCTTGATTCATAAAAAACCTTAAATTATACTAATATCTCTTACAAGA
1 TAATTTATTTACTTAGTATCTTGATCCATAAAAAACCCTAAATTATACTAATATCTCTTACAAAA
*
54430789 GTAAAAGTAATTGATTTTAAGTTTATTAATTAAA
66 GTAAAAGCAATTGATTTTAAGTTTATTAATTAAA
54430823 ATTTCTTTCT
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 88 1.00
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.43
Consensus pattern (105 bp):
TAATTTATTTACTTAGTATCTTGATCCATAAAAAACCCTAAATTATACTAATATCTCTTACAAAA
GTAAAAGCAATTGATTTTAAGTTTATTAATTAAACTTGCG
Found at i:54433390 original size:12 final size:12
Alignment explanation
Indices: 54433375--54433400 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54433365 AATATTAAAA
54433375 TAATTAAAAAGC
1 TAATTAAAAAGC
54433387 TAATTAAAAAGC
1 TAATTAAAAAGC
54433399 TA
1 TA
54433401 CTACCATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (12 bp):
TAATTAAAAAGC
Found at i:54434705 original size:23 final size:24
Alignment explanation
Indices: 54434678--54434724 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
54434668 TATATTATAT
54434678 AATTTA-GAATATATTAAAA-AATA
1 AATTTATGAA-ATATTAAAATAATA
*
54434701 AATTTATTAAATATTAAAATAATA
1 AATTTATGAAATATTAAAATAATA
54434725 TAAATAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AATTTATGAAATATTAAAATAATA
Found at i:54441220 original size:6 final size:6
Alignment explanation
Indices: 54441165--54441221 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
54441155 AAATAGTATA
* * * *
54441165 TTTATT TTCATT TTCATT TTTAGT TTTATT TTTATT TTAATT TGCATTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT T---TTATT
54441216 TTTATT
1 TTTATT
54441222 CCTATGATTG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
6 37 0.88
9 5 0.12
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.72
Consensus pattern (6 bp):
TTTATT
Found at i:54442156 original size:18 final size:19
Alignment explanation
Indices: 54442135--54442171 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
54442125 AGAAAAAATT
54442135 TTGA-AAAAAAAAAGAAAA
1 TTGAGAAAAAAAAAGAAAA
*
54442153 TTGAGAAAAAAGAAGAAAA
1 TTGAGAAAAAAAAAGAAAA
54442172 AAAAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (19 bp):
TTGAGAAAAAAAAAGAAAA
Found at i:54442172 original size:20 final size:19
Alignment explanation
Indices: 54442121--54442172 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
54442111 TATTATTTAG
*
54442121 AAAAAGAA-AAAATTTTGAA
1 AAAAAGAAGAAAA-ATTGAA
*
54442140 AAAAAAAAG-AAAATTGAGA
1 AAAAAGAAGAAAAATTGA-A
54442159 AAAAAGAAGAAAAA
1 AAAAAGAAGAAAAA
54442173 AAAAACAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 4 0.15
19 19 0.70
20 4 0.15
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (19 bp):
AAAAAGAAGAAAAATTGAA
Found at i:54443071 original size:4 final size:4
Alignment explanation
Indices: 54443062--54443087 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
54443052 GGGACGGGTA
54443062 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
54443088 TCATCATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:54451409 original size:3 final size:3
Alignment explanation
Indices: 54451401--54451428 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54451391 TACCATTACA
54451401 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
54451429 CCCAATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:54472713 original size:173 final size:174
Alignment explanation
Indices: 54472372--54472748 Score: 413
Period size: 173 Copynumber: 2.2 Consensus size: 174
54472362 AGGGATTGAA
* * * * * *
54472372 TTTTTT-TCTAAGTTAATCTCTGAACTTCGCACTTGTTTTCATATTGAGGCTTGGATTAGGCAAT
1 TTTTTTGTCTAAGTTAATCT-TAAACTTGGCACTTGTTCTCACATTGAGGCTTGGACTAGACAAT
* * *
54472436 TGATCTCACTTTGGAGCTTGGACGTTTCTTTGTCTAAGTTAATCTCTCAACTTAGAAATTATTCC
65 TGATCTCACTTTGGAGCTTAGACGTTTCTTTGTCCAAGTTAATCTCTAAACTTAGAAATTATTCC
*
54472501 CACATTAGGGTCTAGACTAGAGAACTATTCCCATGGCTTAGAC-T
130 CACATTAAGGTCTAGACTAGAGAACTATTCCCATGGCTTAGACTT
* *
54472545 TTTTTTGTCCAAGTTAATCCTTAAACTTGGCACTTGTTCTCACATTGGGGCTTGGACTAGACAAT
1 TTTTTTGTCTAAGTTAAT-CTTAAACTTGGCACTTGTTCTCACATTGAGGCTTGGACTAGACAAT
* * * * * * *
54472610 TGCTCTCATTTTGGGGTTTAGA-TTTTTTTTGTCCAAGTTAATCTCTAAACTTA-ATAATTGTTC
65 TGATCTCACTTTGGAGCTTAGACGTTTCTTTGTCCAAGTTAATCTCTAAACTTAGA-AATTATTC
* * * * * * * *
54472673 CCACATTAAGTTCTGGA-TTGGGCAATTGTTCTCGTGGCTTAGACTT
129 CCACATTAAGGTCTAGACTAGAG-AACTATTCCCATGGCTTAGACTT
*
54472719 TTCTTTTGTCTAAATTAATTCTTAAACTTG
1 TT-TTTTGTCTAAGTTAA-TCTTAAACTTG
54472749 ATAATTATTT
Statistics
Matches: 168, Mismatches: 29, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
172 4 0.02
173 71 0.42
174 67 0.40
175 25 0.15
176 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (174 bp):
TTTTTTGTCTAAGTTAATCTTAAACTTGGCACTTGTTCTCACATTGAGGCTTGGACTAGACAATT
GATCTCACTTTGGAGCTTAGACGTTTCTTTGTCCAAGTTAATCTCTAAACTTAGAAATTATTCCC
ACATTAAGGTCTAGACTAGAGAACTATTCCCATGGCTTAGACTT
Found at i:54474433 original size:30 final size:30
Alignment explanation
Indices: 54474335--54474550 Score: 130
Period size: 29 Copynumber: 7.3 Consensus size: 30
54474325 TGCAATTTAG
54474335 TTACCATTTTTAACCTCGATTTCACCAAAA
1 TTACCATTTTTAACCTCGATTTCACCAAAA
* * *
54474365 TTTACC-GTTTTACCCCCGAACTTTCA--AAAA
1 -TTACCATTTTTAACCTCG-A-TTTCACCAAAA
*
54474395 TT-CCATTTTTAAGCTCGATTTCACCAAAA
1 TTACCATTTTTAACCTCGATTTCACCAAAA
* * * *
54474424 TTA-CAATTTTACCCCCGAATCTT--TCAAAA
1 TTACCATTTTTAACCTCG-AT-TTCACCAAAA
* *
54474453 TT-CCATTTTTGACCTCGATTCCACCAAAA
1 TTACCATTTTTAACCTCGATTTCACCAAAA
* * ** *
54474482 TTACC-GTTTTACCCTTAAACTTC-CCAAAA
1 TTACCATTTTTAACC-TCGATTTCACCAAAA
* * *
54474511 CT-CTATTTTTAACCTCGATTTCACTAAAAA
1 TTACCATTTTTAACCTCGATTTCAC-CAAAA
54474541 TTACCATTTT
1 TTACCATTTT
54474551 ACCCCCGAAC
Statistics
Matches: 133, Mismatches: 35, Indels: 34
0.66 0.17 0.17
Matches are distributed among these distances:
27 6 0.05
28 11 0.08
29 71 0.53
30 26 0.20
31 14 0.11
32 5 0.04
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.37
Consensus pattern (30 bp):
TTACCATTTTTAACCTCGATTTCACCAAAA
Found at i:54474462 original size:58 final size:57
Alignment explanation
Indices: 54474338--54474578 Score: 293
Period size: 58 Copynumber: 4.1 Consensus size: 57
54474328 AATTTAGTTA
*
54474338 CCATTTTTAACCTCGATTTCACCAAAATTTACCGTTTTACCCCCGAACTTTCAAAAATT
1 CCATTTTTAACCTCGATTTCACCAAAA-TTACCATTTTACCCCCGAACTTTC-AAAATT
* *
54474397 CCATTTTTAAGCTCGATTTCACCAAAATTACAATTTTACCCCCGAATCTTTCAAAATT
1 CCATTTTTAACCTCGATTTCACCAAAATTACCATTTTACCCCCGAA-CTTTCAAAATT
* * * *** * *
54474455 CCATTTTTGACCTCGATTCCACCAAAATTACCGTTTTACCCTTAAACTTCCCAAAACT
1 CCATTTTTAACCTCGATTTCACCAAAATTACCATTTTACCCCCGAACTT-TCAAAATT
* * * *
54474513 CTATTTTTAACCTCGATTTCACTAAAAATTACCATTTTACCCCCGAACCTTCCAAATT
1 CCATTTTTAACCTCGATTTCAC-CAAAATTACCATTTTACCCCCGAACTTTCAAAATT
54474571 ACCATTTT
1 -CCATTTT
54474579 GTTCTCGAAT
Statistics
Matches: 152, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
57 3 0.02
58 91 0.60
59 58 0.38
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.36
Consensus pattern (57 bp):
CCATTTTTAACCTCGATTTCACCAAAATTACCATTTTACCCCCGAACTTTCAAAATT
Found at i:54474510 original size:117 final size:117
Alignment explanation
Indices: 54474335--54474578 Score: 323
Period size: 117 Copynumber: 2.1 Consensus size: 117
54474325 TGCAATTTAG
* * * *
54474335 TTACCATTTTTAACCTCGATTTCACCAAAATTTACCGTTTTACCCCCGAACTTTCAAAAATTCCA
1 TTACCATTTTTAACCTCGATTCCACCAAAATTTACCGTTTTACCCCCAAAC-TTCCAAAACTCCA
* * *
54474400 TTTTTAAGCTCGATTTCAC-CAAAATTACAATTTTACCCCCGAATCTTTCAAAA
65 TTTTTAACCTCGATTTCACTAAAAATTACAATTTTACCCCCGAA-CCTTCAAAA
* ** *
54474453 TT-CCATTTTTGACCTCGATTCCACCAAAA-TTACCGTTTTACCCTTAAACTTCCCAAAACTCTA
1 TTACCATTTTTAACCTCGATTCCACCAAAATTTACCGTTTTACCCCCAAACTT-CCAAAACTCCA
* *
54474516 TTTTTAACCTCGATTTCACTAAAAATTACCATTTTACCCCCGAACCTTCCAAA
65 TTTTTAACCTCGATTTCACTAAAAATTACAATTTTACCCCCGAACCTTCAAAA
54474569 TTACCATTTT
1 TTACCATTTT
54474579 GTTCTCGAAT
Statistics
Matches: 110, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
115 2 0.02
116 52 0.47
117 54 0.49
118 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.36
Consensus pattern (117 bp):
TTACCATTTTTAACCTCGATTCCACCAAAATTTACCGTTTTACCCCCAAACTTCCAAAACTCCAT
TTTTAACCTCGATTTCACTAAAAATTACAATTTTACCCCCGAACCTTCAAAA
Found at i:54474586 original size:116 final size:117
Alignment explanation
Indices: 54474338--54474578 Score: 324
Period size: 116 Copynumber: 2.1 Consensus size: 117
54474328 AATTTAGTTA
* * * * *
54474338 CCATTTTTAACCTCGATTTCACCAAAATTTACCGTTTTACCCCCGAACTTTCAAAAATTCCATTT
1 CCATTTTTGACCTCGATTCCACCAAAATTTACCGTTTTACCCCCAAACTTCCAAAAACTCCATTT
* * *
54474403 TTAAGCTCGATTTCACCAAAATTACAATTTTACCCCCGAATCTTTCAAAATT
66 TTAACCTCGATTTCACAAAAATTACAATTTTACCCCCGAATCCTTCAAAATT
** * *
54474455 CCATTTTTGACCTCGATTCCACCAAAA-TTACCGTTTTACCCTTAAACTTCCCAAAACTCTATTT
1 CCATTTTTGACCTCGATTCCACCAAAATTTACCGTTTTACCCCCAAACTTCCAAAAACTCCATTT
* *
54474519 TTAACCTCGATTTCACTAAAAATTACCATTTTACCCCCGAA-CCTTCCAAATT
66 TTAACCTCGATTTCAC-AAAAATTACAATTTTACCCCCGAATCCTTCAAAATT
54474571 ACCATTTT
1 -CCATTTT
54474579 GTTCTCGAAT
Statistics
Matches: 108, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
116 54 0.50
117 54 0.50
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.36
Consensus pattern (117 bp):
CCATTTTTGACCTCGATTCCACCAAAATTTACCGTTTTACCCCCAAACTTCCAAAAACTCCATTT
TTAACCTCGATTTCACAAAAATTACAATTTTACCCCCGAATCCTTCAAAATT
Found at i:54474616 original size:29 final size:27
Alignment explanation
Indices: 54474554--54474637 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 27
54474544 CCATTTTACC
* *
54474554 CCCGAACCTTCCAAATTACCATTTTGTT
1 CCCGAATCTTCCAAAATACCATTTT-TT
* *
54474582 CTCGAATCTTCCAAAATCCCATTTTTAAT
1 CCCGAATCTTCCAAAATACCATTTTT--T
*
54474611 CCCGAATTTTTCCAAAATTA-CATTTTT
1 CCCGAA-TCTTCCAAAA-TACCATTTTT
54474638 GCCCCCGGGT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.02
28 21 0.47
29 6 0.13
30 16 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.39
Consensus pattern (27 bp):
CCCGAATCTTCCAAAATACCATTTTTT
Found at i:54479315 original size:17 final size:16
Alignment explanation
Indices: 54479278--54479324 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
54479268 ACAGAAAAAC
*
54479278 TTCGATAAATGAAT-A
1 TTCGATAAATTAATAA
54479293 TTCGATAAATTAATAA
1 TTCGATAAATTAATAA
54479309 TTTCGATTAAA-TAATA
1 -TTCGA-TAAATTAATA
54479325 TTTTTTCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 13 0.46
16 1 0.04
17 10 0.36
18 4 0.14
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (16 bp):
TTCGATAAATTAATAA
Found at i:54482377 original size:47 final size:47
Alignment explanation
Indices: 54482308--54482397 Score: 171
Period size: 47 Copynumber: 1.9 Consensus size: 47
54482298 TGTTTTGTCA
*
54482308 AGGTGGTTTTTTGCCATATTTGTAATAATTGATTGAGCAAAAATATT
1 AGGTGGTTTTTTGCCATATTTGTAATAATTGATTGAGAAAAAATATT
54482355 AGGTGGTTTTTTGCCATATTTGTAATAATTGATTGAGAAAAAA
1 AGGTGGTTTTTTGCCATATTTGTAATAATTGATTGAGAAAAAA
54482398 AATATTAACA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (47 bp):
AGGTGGTTTTTTGCCATATTTGTAATAATTGATTGAGAAAAAATATT
Found at i:54483945 original size:19 final size:19
Alignment explanation
Indices: 54483921--54483963 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54483911 AAACATGAAT
54483921 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
54483940 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
54483959 TAAAT
1 TAAAT
54483964 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:54485041 original size:44 final size:47
Alignment explanation
Indices: 54484951--54485044 Score: 158
Period size: 44 Copynumber: 2.1 Consensus size: 47
54484941 CGGTAACATG
54484951 GATGCTATTTAAATTTTAAAATATTTTAATTAATATTATATCAATAA
1 GATGCTATTTAAATTTTAAAATATTTTAATTAATATTATATCAATAA
*
54484998 GATG-TATTTAAATTTT-AAATATTTTAGTT-ATATTATATCAATAA
1 GATGCTATTTAAATTTTAAAATATTTTAATTAATATTATATCAATAA
54485042 GAT
1 GAT
54485045 CATTTAGTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
44 18 0.39
45 12 0.26
46 12 0.26
47 4 0.09
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (47 bp):
GATGCTATTTAAATTTTAAAATATTTTAATTAATATTATATCAATAA
Found at i:54485526 original size:16 final size:18
Alignment explanation
Indices: 54485494--54485526 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54485484 ATGGTATTAT
54485494 TTATATTTTTATATAAAG
1 TTATATTTTTATATAAAG
54485512 TTAT-TTTTTAT-TAAA
1 TTATATTTTTATATAAA
54485527 TATTCTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TTATATTTTTATATAAAG
Found at i:54486131 original size:31 final size:29
Alignment explanation
Indices: 54486093--54486171 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 29
54486083 ATCTCAAAAC
*
54486093 TATACATGAACTTTGGCTTAGTGTGTAATTT
1 TATACATGAA-TTTGGATT-GTGTGTAATTT
* *
54486124 TATACATGAATTTTGATTTTGTGTAATTT
1 TATACATGAATTTGGATTGTGTGTAATTT
*
54486153 TATACATGAAATTTCGATT
1 TATACATG-AATTTGGATT
54486172 TGATCTAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 18 0.42
30 15 0.35
31 10 0.23
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (29 bp):
TATACATGAATTTGGATTGTGTGTAATTT
Found at i:54486152 original size:29 final size:30
Alignment explanation
Indices: 54486114--54486172 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
54486104 TTTGGCTTAG
*
54486114 TGTGTAATTTTATACATG-AATTTTGATTT
1 TGTGTAATTTTATACATGAAATTTCGATTT
54486143 TGTGTAATTTTATACATGAAATTTCGATTT
1 TGTGTAATTTTATACATGAAATTTCGATTT
54486173 GATCTAATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.53
Consensus pattern (30 bp):
TGTGTAATTTTATACATGAAATTTCGATTT
Found at i:54486181 original size:30 final size:29
Alignment explanation
Indices: 54486118--54486181 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
54486108 GCTTAGTGTG
* *
54486118 TAATTTTATACATGAATTTTGATTTTGTG
1 TAATTTTATACATGAATTTCGATTTTGTC
54486147 TAATTTTATACATGAAATTTCGA-TTTGATC
1 TAATTTTATACATG-AATTTCGATTTTG-TC
54486177 TAATT
1 TAATT
54486182 CTCACAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (29 bp):
TAATTTTATACATGAATTTCGATTTTGTC
Found at i:54491987 original size:72 final size:72
Alignment explanation
Indices: 54491867--54492002 Score: 200
Period size: 72 Copynumber: 1.9 Consensus size: 72
54491857 ATGCAATGGG
* * *
54491867 AACATCTAAAAAATCTGCAAAGGCTTTCTCTCGCTAATTTTCCCAATTTAACATCGCTTCCGGAG
1 AACATCTAAAAAATCTACAAAGGCTTTCTCTCGCTAACTTGCCCAATTTAACATCGCTTCCGGAG
54491932 TGGATTC
66 TGGATTC
* * * * *
54491939 AACATCTAATAAATCTACAAAGGCTTTCTCTCGTTGACTTGCCTAATTTAACATCGTTTCCGGA
1 AACATCTAAAAAATCTACAAAGGCTTTCTCTCGCTAACTTGCCCAATTTAACATCGCTTCCGGA
54492003 TGAGATGCAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (72 bp):
AACATCTAAAAAATCTACAAAGGCTTTCTCTCGCTAACTTGCCCAATTTAACATCGCTTCCGGAG
TGGATTC
Found at i:54503626 original size:23 final size:22
Alignment explanation
Indices: 54503596--54503763 Score: 133
Period size: 23 Copynumber: 7.3 Consensus size: 22
54503586 ACACTAGCGC
* * *
54503596 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCAC-TTTTGT
54503619 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
*
54503642 GCTCTTTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
*
54503665 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
* * *
54503688 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACT-TTTGT
*
54503711 GCTCTCTG-TTGCCCAGCACTTATGT
1 GCTCTCTGATT----AGCACTTTTGT
* *
54503736 GCTCTCTG-TTAGTACTTTGGT
1 GCTCTCTGATTAGCACTTTTGT
*
54503757 ACTCTCT
1 GCTCTCT
54503764 TCTTGTTCCG
Statistics
Matches: 123, Mismatches: 16, Indels: 14
0.80 0.10 0.09
Matches are distributed among these distances:
21 14 0.11
22 4 0.03
23 84 0.68
24 1 0.01
25 14 0.11
26 6 0.05
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTTTTGT
Found at i:54503667 original size:46 final size:46
Alignment explanation
Indices: 54503597--54503718 Score: 165
Period size: 46 Copynumber: 2.7 Consensus size: 46
54503587 CACTAGCGCG
* * *
54503597 CTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGATTAGCACTTTGTGTG
1 CTCTCTGATTAGCACTGTGT-GTGCTCTCTGATTAGCACTTTGTGTA
* * *
54503643 CTCTTTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTA
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTA
*
54503689 CTCTCTGTTTAGCACTGTGTGTGCTCTCTG
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTG
54503719 TTGCCCAGCA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
46 64 0.97
47 2 0.03
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (46 bp):
CTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTA
Found at i:54503710 original size:69 final size:66
Alignment explanation
Indices: 54503620--54503763 Score: 182
Period size: 69 Copynumber: 2.1 Consensus size: 66
54503610 ACGTCTCGTG
* * *
54503620 CTCTCTGATTAGCACTTTGTGTGCTCTTTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACTTT
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCTG-TTAGTACTTT
54503684 GTGTA
63 G-GTA
*
54503689 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTT
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTGTTAGTACTTT
54503754 GGTA
63 GGTA
54503758 CTCTCT
1 CTCTCT
54503764 TCTTGTTCCG
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
68 2 0.03
69 36 0.54
70 11 0.16
71 13 0.19
72 5 0.07
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.44
Consensus pattern (66 bp):
CTCTCTGATTAGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTGTTAGTACTTTGGT
A
Found at i:54506149 original size:6 final size:6
Alignment explanation
Indices: 54506140--54506174 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
54506130 GGTTTGGGTT
54506140 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGA
1 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGA
54506175 ATATAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.00, G:0.66, T:0.17
Consensus pattern (6 bp):
TGGGAG
Found at i:54512323 original size:20 final size:23
Alignment explanation
Indices: 54512270--54512325 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
54512260 TTAAATTTTT
*
54512270 AAATAATTAATATTAATTACTTAG
1 AAAT-ATTAAAATTAATTACTTAG
54512294 AAATATTTAAAATTAA-TA-TTA-
1 AAATA-TTAAAATTAATTACTTAG
54512315 AAATATTAAAA
1 AAATATTAAAA
54512326 ATAAGTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.20
21 5 0.17
22 3 0.10
23 3 0.10
24 13 0.43
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
AAATATTAAAATTAATTACTTAG
Found at i:54513281 original size:27 final size:27
Alignment explanation
Indices: 54513228--54513281 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
54513218 AATATGAATC
** *
54513228 AATAATCTAAAAATATCACCTATAAAA
1 AATAATCTAAAAATATCAAATAAAAAA
54513255 AATAATCTAAAAATATCAAATAAAAAA
1 AATAATCTAAAAATATCAAATAAAAAA
54513282 TTAAGCATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (27 bp):
AATAATCTAAAAATATCAAATAAAAAA
Found at i:54513867 original size:31 final size:31
Alignment explanation
Indices: 54513805--54513867 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
54513795 CATTATTTAT
* * *
54513805 ATACTTCCATTTTACATATATGTATAGATTA
1 ATACTTCCATTTTAAAAATATATATAGATTA
*
54513836 ATACTTTCATTTTGAAAAATATATATA-ATTA
1 ATACTTCCATTTT-AAAAATATATATAGATTA
54513867 A
1 A
54513868 ATCAACATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (31 bp):
ATACTTCCATTTTAAAAATATATATAGATTA
Found at i:54513889 original size:31 final size:31
Alignment explanation
Indices: 54513854--54513937 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 31
54513844 ATTTTGAAAA
54513854 ATATATATAATTAAATCAACATTAAAACTTC
1 ATATATATAATTAAATCAACATTAAAACTTC
* * * * *
54513885 ATATATACATTTAAACCATA-ATTAAAATTTT
1 ATATATATAATTAAATCA-ACATTAAAACTTC
* *
54513916 ATTTATATAATTATATCGAACA
1 ATATATATAATTAAATC-AACA
54513938 AAAATTTATG
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
31 37 0.93
32 3 0.08
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (31 bp):
ATATATATAATTAAATCAACATTAAAACTTC
Found at i:54518884 original size:29 final size:30
Alignment explanation
Indices: 54518811--54518884 Score: 78
Period size: 35 Copynumber: 2.3 Consensus size: 30
54518801 ATTTCCACAA
*
54518811 AAAAGAAATGTTTACAGTATTCTTAGTAAT
1 AAAAGAAATGTTTACAGTATTCATAGTAAT
*
54518841 AAACACCATTAAATGTTTACAGTATTCATAGTAAT
1 -AA-A--A-GAAATGTTTACAGTATTCATAGTAAT
54518876 -AAAGAAATG
1 AAAAGAAATG
54518885 AAAATATAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
29 5 0.14
30 1 0.03
31 2 0.06
32 2 0.06
33 1 0.03
34 1 0.03
35 24 0.67
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (30 bp):
AAAAGAAATGTTTACAGTATTCATAGTAAT
Found at i:54519636 original size:20 final size:20
Alignment explanation
Indices: 54519620--54519667 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
54519610 TTGTATCGTC
54519620 TTAAAAATATCGATATCATA
1 TTAAAAATATCGATATCATA
* * *
54519640 TTAGAAATATTGATATCACA
1 TTAAAAATATCGATATCATA
54519660 TTAAAAAT
1 TTAAAAAT
54519668 TTGGTTTGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.35
Consensus pattern (20 bp):
TTAAAAATATCGATATCATA
Found at i:54522126 original size:810 final size:809
Alignment explanation
Indices: 54520668--54522985 Score: 3984
Period size: 810 Copynumber: 2.9 Consensus size: 809
54520658 AGTGGAAATG
*
54520668 AAATAATAGGGAGGGAGGAGGATAAAAGAGCTCTTTTAGATCTTATTTTAGGGTTTGAAAGTGAA
1 AAATAATAGGGAGGGAGGAGGATAAAAGAGCTCTTTTAGCTCTTATTTTAGGGTTTGAAAGTGAA
*
54520733 GAGAATGTTTACGTCGTTCCTATTGTGGGGTTTGGAGGGTTAGGGAAGACTGCGTTGGCACAGAT
66 GAGAATGTTTACGTCATTCCTATTGTGGGGTTTGGAGGGTTAGGGAAGACTGCGTTGGCACAGAT
54520798 TATTTTCAATAATGAAATGGTCCTTAATCATTTTGAATTGAGAATGTGGGTGTGTGTTTCAGATA
131 TATTTTCAATAATGAAATGGTCCTTAATCATTTTGAATTGAGAATGTGGGTGTGTGTTTCAGATA
*
54520863 TTTTTGATGTCAAAATAATTGTAGAAAGCATTATCAAATCTGCAACTGGCCAAGCACCAGATAAA
196 TTTTTGATGTCAAAATAATTGTAGAAAGCATTATCAAATCTGCAACTGGCCAAGCACCTGATAAA
* *
54520928 AATCTTGAAATGGATCAATTGCAAAGACAACTTCGAGATATAATTGGTGGGAAAAAATATTTACT
261 AATCTTCAAATGGATCAATTGCAAAGACAACTTCGAGATATAATTGGTGGG-AAAAATATTTGCT
*
54520993 TGTTTTGGATGACATTTGGAATGAAGAGAGGGAAGAATGGGTTAGTTTAATGGAGTTATTGATGG
325 TGTTTTGGATGACATTTGGAATGAAGAGAGGGAAGAATGGGTTAGTTTAAAGGAGTTATTGATGG
*
54521058 GTGGGGCTAAAGGAAGTAGAATAATAGTAACTACTCGCTCTTTTAAGGTAGCTAAGATCACTAGT
390 GTGGGGCTAAAGGAAGTAGAATAATAGTAACTACTCGCTCTTTTAAGGTAGCAAAGATCACTAGT
*
54521123 AAATGTCAACCTCATGTTCTGAAAGGCTTGTCTGATGACGATGCTTGGTTTTTGTTCAATAAAAT
455 AAATGTCAACCTCATGTTCTGAAAGGCTTGTCTGATGACGATGCTTGGTTTTTGTTCAAAAAAAT
*
54521188 AGCATTTGAGCAAAGATATGCAGACTCAACAAATCCAGCTTTTGTGGAAATAGGGAAACAAATTT
520 AGCATTTGAGCAAAGATATGCAGACTCAACAAATCCAGCCTTTGTGGAAATAGGGAAACAAATTT
* *
54521253 TGGAGAAGTGTGGTGGGGTTCCCTTAGTCATAAGGAGCATAGCAAGTGAATTATCTTACAAAGAA
585 TGGAAAAGTGTGGTGGGGTTCCCTTAGTCATAAGGAGAATAGCAAGTGAATTATCTTACAAAGAA
54521318 ACTGAAAATGAGTGGCGTTCTTTCAAAGATAATGAACTTGCTAGAATATCACAAATTATAAGTGA
650 ACTGAAAATGAGTGGCGTTCTTTCAAAGATAATGAACTTGCTAGAATATCACAAATTATAAGTGA
*
54521383 GGACAAGTTCGACTTGGTAGAGCGTGAACGCCTCATGGAAACCTCTTCCATGACTAAAAAGAGGC
715 GGACAAGTTCGACTTGGTAAAGCGTGAACGCCTCATGGAAACCTCTTCCATGACTAAAAAGAGGC
54521448 GGGAAACACACTCTTTTGTGAATGAAGGTC
780 GGGAAACACACTCTTTTGTGAATGAAGGTC
54521478 AAATAATAGGGAGGGAGGAGGATAAAAGAGCTCTTTTAGCTCTTATTTTAGGGTTTGAAAGTGAA
1 AAATAATAGGGAGGGAGGAGGATAAAAGAGCTCTTTTAGCTCTTATTTTAGGGTTTGAAAGTGAA
* *
54521543 GAGAATGTTTACGTTATTCCTATTGTGGGGTTCGGAGGGTTAGGGAAGACTGCGTTGGCACAGAT
66 GAGAATGTTTACGTCATTCCTATTGTGGGGTTTGGAGGGTTAGGGAAGACTGCGTTGGCACAGAT
54521608 TATTTTCAATAATGAAATGGTCCTTAATCATTTTGAATTGAGAATGTGGGTGTGTGTTTCAGATA
131 TATTTTCAATAATGAAATGGTCCTTAATCATTTTGAATTGAGAATGTGGGTGTGTGTTTCAGATA
54521673 TTTTTGATGTCAAAATAATTGTAGAAAGCATTATCAAATCTGCAACTGGCCAAGCACCTGATAAA
196 TTTTTGATGTCAAAATAATTGTAGAAAGCATTATCAAATCTGCAACTGGCCAAGCACCTGATAAA
*
54521738 AATC-TCAATATGGATCAATTGCAAAGACAACTTCGACATATAATTGGTGGGAAAAGATATTTGC
261 AATCTTCAA-ATGGATCAATTGCAAAGACAACTTCGAGATATAATTGGTGGGAAAA-ATATTTGC
*
54521802 TTGTTTTGGATGACATTTGGGATGAAGAGAGGGAAGAATGGGTTAGTTTAAAGGAGTTATTGATG
324 TTGTTTTGGATGACATTTGGAATGAAGAGAGGGAAGAATGGGTTAGTTTAAAGGAGTTATTGATG
* * * *
54521867 GGTGGGGCTAAAAGAAGTAAAATAATAGTAACTACTAGCTCTTTTAAGGTAGCCAAGATCACTAG
389 GGTGGGGCTAAAGGAAGTAGAATAATAGTAACTACTCGCTCTTTTAAGGTAGCAAAGATCACTAG
*
54521932 TAAATGTCAGCCTCATGTTCTGAAAGGCTTGTCTGATGACGATGCTTGGTTTTTGTTCAAAAAAA
454 TAAATGTCAACCTCATGTTCTGAAAGGCTTGTCTGATGACGATGCTTGGTTTTTGTTCAAAAAAA
*
54521997 TAGCATTTGATCAAAGATATGCAGACTCAACAAATCCAGCCTTTGTGGAAATAGGGAAACAAATT
519 TAGCATTTGAGCAAAGATATGCAGACTCAACAAATCCAGCCTTTGTGGAAATAGGGAAACAAATT
*
54522062 TTGGAAAAGTGTGGTGGGGTTCCCTTAGTCATAAGGAGGATAGCAAGTGAATTATCTTACAAAGA
584 TTGGAAAAGTGTGGTGGGGTTCCCTTAGTCATAAGGAGAATAGCAAGTGAATTATCTTACAAAGA
54522127 AACTGAAAATGAGTGGCGTTCTTTCAAAGATAATGAACTTGCTAGAATATCACAAATTATAAGTG
649 AACTGAAAATGAGTGGCGTTCTTTCAAAGATAATGAACTTGCTAGAATATCACAAATTATAAGTG
*
54522192 AGGACAAGTTCGACTTGGTAAAGCGTGAACGCCTCATGGAAACCTCTTTCATGACTAAAAAGAGG
714 AGGACAAGTTCGACTTGGTAAAGCGTGAACGCCTCATGGAAACCTCTTCCATGACTAAAAAGAGG
54522257 CGGGAAACACACTCTTTTGTGAATGAAGGTC
779 CGGGAAACACACTCTTTTGTGAATGAAGGTC
54522288 AAATAATAGGGAGGGAGGAGGATAAAAGAGCTCTTTTAGCTCTTATTTTAGGGTTTGAAAGTGAA
1 AAATAATAGGGAGGGAGGAGGATAAAAGAGCTCTTTTAGCTCTTATTTTAGGGTTTGAAAGTGAA
* *
54522353 GAGAATGTTTACGTCATTCCTATTGTGGGGTTTGGAGGGTCAGGGAAGACTGCGTTGGCACAGTT
66 GAGAATGTTTACGTCATTCCTATTGTGGGGTTTGGAGGGTTAGGGAAGACTGCGTTGGCACAGAT
* *
54522418 TATTTTCAATAATGAGATGGTCCTTGATCATTTTGAATTGAGAATGTGGGTGTGTGTTTCAGATG
131 TATTTTCAATAATGAAATGGTCCTTAATCATTTTGAATTGAGAATGTGGGTGTGTGTTTCAGAT-
* *
54522483 A-TTTTGATGTCAAAAGAATTGTAGAAAGCATTATCAAATCTGCAACTGGCCAAGCAGCAT-ATA
195 ATTTTTGATGTCAAAATAATTGTAGAAAGCATTATCAAATCTGCAACTGGCCAAGCA-CCTGATA
* * *
54522546 AAAATCTTTC-AATGGACCAATTGCAAAAACAACTTCGAGATAAAATTGGTGGGACAAAATATTT
259 AAAATC-TTCAAATGGATCAATTGCAAAGACAACTTCGAGATATAATTGGTGGGA-AAAATATTT
* * * * *
54522610 GCTTGTTTTGGATGACATTTGGAATGAAGATGAGAG-TGCATGGGTTTA-CTTAAAGGAGGTATT
322 GCTTGTTTTGGATGACATTTGGAATGAAGA-GAGGGAAGAATGGG-TTAGTTTAAAGGAGTTATT
* * * * * * *
54522673 GATGAGTGGGGCTAAAGGAAGTAGGATAATAGTAACTACTCGCTCTATGAGGGTAGCAAAGGTTA
385 GATGGGTGGGGCTAAAGGAAGTAGAATAATAGTAACTACTCGCTCTTTTAAGGTAGCAAAGATCA
* * *
54522738 CTAGTAAATGTGAACCTCAAGTTGTGAAAGGCTTGTCTGATGACGATGCTTGGTTTTTGTTCAAA
450 CTAGTAAATGTCAACCTCATGTTCTGAAAGGCTTGTCTGATGACGATGCTTGGTTTTTGTTCAAA
** *
54522803 GTAATAGCATTTGAGCAAAGATATGCAGACTCAACAAATCCAGCCTTCGTGGAAATAGGGAAACA
515 AAAATAGCATTTGAGCAAAGATATGCAGACTCAACAAATCCAGCCTTTGTGGAAATAGGGAAACA
* * *
54522868 GATTTTGAAAAAGTGTGGTGGGGTTCCCTTAGTCATAAGGACAATAGCAAGT-ACATTATCTTAC
580 AATTTTGGAAAAGTGTGGTGGGGTTCCCTTAGTCATAAGGAGAATAGCAAGTGA-ATTATCTTAC
* * *
54522932 AAAGAAACTGCATATGAGTGGCGTTCTTTCAAAGATAATGAACTTGTTAGAATA
644 AAAGAAACTGAAAATGAGTGGCGTTCTTTCAAAGATAATGAACTTGCTAGAATA
54522986 CTTCAAAACG
Statistics
Matches: 1432, Mismatches: 66, Indels: 20
0.94 0.04 0.01
Matches are distributed among these distances:
809 8 0.01
810 1408 0.98
811 14 0.01
812 2 0.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (809 bp):
AAATAATAGGGAGGGAGGAGGATAAAAGAGCTCTTTTAGCTCTTATTTTAGGGTTTGAAAGTGAA
GAGAATGTTTACGTCATTCCTATTGTGGGGTTTGGAGGGTTAGGGAAGACTGCGTTGGCACAGAT
TATTTTCAATAATGAAATGGTCCTTAATCATTTTGAATTGAGAATGTGGGTGTGTGTTTCAGATA
TTTTTGATGTCAAAATAATTGTAGAAAGCATTATCAAATCTGCAACTGGCCAAGCACCTGATAAA
AATCTTCAAATGGATCAATTGCAAAGACAACTTCGAGATATAATTGGTGGGAAAAATATTTGCTT
GTTTTGGATGACATTTGGAATGAAGAGAGGGAAGAATGGGTTAGTTTAAAGGAGTTATTGATGGG
TGGGGCTAAAGGAAGTAGAATAATAGTAACTACTCGCTCTTTTAAGGTAGCAAAGATCACTAGTA
AATGTCAACCTCATGTTCTGAAAGGCTTGTCTGATGACGATGCTTGGTTTTTGTTCAAAAAAATA
GCATTTGAGCAAAGATATGCAGACTCAACAAATCCAGCCTTTGTGGAAATAGGGAAACAAATTTT
GGAAAAGTGTGGTGGGGTTCCCTTAGTCATAAGGAGAATAGCAAGTGAATTATCTTACAAAGAAA
CTGAAAATGAGTGGCGTTCTTTCAAAGATAATGAACTTGCTAGAATATCACAAATTATAAGTGAG
GACAAGTTCGACTTGGTAAAGCGTGAACGCCTCATGGAAACCTCTTCCATGACTAAAAAGAGGCG
GGAAACACACTCTTTTGTGAATGAAGGTC
Found at i:54530309 original size:18 final size:17
Alignment explanation
Indices: 54530267--54530309 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
54530257 TTTTTTAGTT
*
54530267 TGTAATGTTTTATATTA
1 TGTAATTTTTTATATTA
54530284 TGCT-ATTTTTGTATATTA
1 TG-TAATTTTT-TATATTA
54530302 TGTAATTT
1 TGTAATTT
54530310 ATAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (17 bp):
TGTAATTTTTTATATTA
Found at i:54531035 original size:26 final size:26
Alignment explanation
Indices: 54530983--54531031 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
54530973 AGATTACTAT
*
54530983 TTTCTTATTTTTTTTTTTACTTTAGA
1 TTTCTTATTTTTTTTTCTACTTTAGA
54531009 TTTCTT-TTTTCTTTTTCT-CTTTA
1 TTTCTTATTTT-TTTTTCTACTTTA
54531032 AGATAAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (26 bp):
TTTCTTATTTTTTTTTCTACTTTAGA
Found at i:54531852 original size:169 final size:168
Alignment explanation
Indices: 54531562--54531891 Score: 398
Period size: 169 Copynumber: 2.0 Consensus size: 168
54531552 AGGTCCCCCC
* * * *
54531562 AAAAAATATTTTTTCAACTTTTAATGTGGGAAAAAAAATTCATACTAAAATAAAATAATTAAATG
1 AAAAAATATTTATTCAACTTTTAATGTGGGAAAAAAAACTCAGACTAAAATAAAATAAGTAAATG
** * ** * * *
54531627 CTTAGAACTTTCAATTTTTCACCATAAATGTTTTTTCTTCTAAAGCCCCCAAAAATTTTCAGCTT
66 CCCAGAACTTTCAATTTTTCACCATAAATCTTCATTCTTCTAAAG-CCCAAAAAAATTTCAACTT
**
54531692 TTATTGTATTACATTTTATATATATTTTTAAAAGATGCCCA
130 TTATAATATTACATTTTA-A-ATATTTTTAAAAGATGCCCA
* * *
54531733 AAAAAATATTTATTCAGCTTTTAATGTGGG-AAAAAAACT-AGACTGAAATAAATTAAGTAAATG
1 AAAAAATATTTATTCAACTTTTAATGTGGGAAAAAAAACTCAGACTAAAATAAAATAAGTAAATG
** *
54531796 CCCAGGGCTTTCAATTTTTCACCATAAATACTTCATT-TTCT-AGGACCCAAAAAAATTTCAACT
66 CCCAGAACTTTCAATTTTTCACCATAAAT-CTTCATTCTTCTAAAG-CCCAAAAAAATTTCAACT
*
54531859 TTTATAATATTACATTTTAAATTTTTTTAAAAG
129 TTTATAATATTACATTTTAAATATTTTTAAAAG
54531892 GGACCCAGTT
Statistics
Matches: 136, Mismatches: 22, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
166 12 0.09
167 1 0.01
168 34 0.25
169 49 0.36
170 12 0.09
171 28 0.21
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (168 bp):
AAAAAATATTTATTCAACTTTTAATGTGGGAAAAAAAACTCAGACTAAAATAAAATAAGTAAATG
CCCAGAACTTTCAATTTTTCACCATAAATCTTCATTCTTCTAAAGCCCAAAAAAATTTCAACTTT
TATAATATTACATTTTAAATATTTTTAAAAGATGCCCA
Done.