Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 130 of 214
Found at i:39555750 original size:19 final size:19
Alignment explanation
Indices: 39555713--39555750 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
39555703 CTAATTAAGT
*
39555713 TTTAATTAGATGAATTTAG
1 TTTAATTAGATGAAATTAG
39555732 TTTAATTAAGA-GAAATTAG
1 TTTAATT-AGATGAAATTAG
39555751 GAAAAATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTAATTAGATGAAATTAG
Found at i:39556022 original size:13 final size:13
Alignment explanation
Indices: 39556006--39556037 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
39555996 TGTTTGAATG
39556006 AAATTTCATAGTT
1 AAATTTCATAGTT
39556019 AAATTTCATAGTT
1 AAATTTCATAGTT
39556032 AAATTT
1 AAATTT
39556038 GAGTTTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (13 bp):
AAATTTCATAGTT
Found at i:39556634 original size:23 final size:22
Alignment explanation
Indices: 39556607--39556671 Score: 89
Period size: 23 Copynumber: 3.0 Consensus size: 22
39556597 GCCTTGCCGA
39556607 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCAC-TTATGTGTCGTATT
*
39556630 TCAGGCACCTCATGTGTCG--TT
1 TCAGGCA-CTTATGTGTCGTATT
39556651 TCAGGCACTTATGTGTCGTAT
1 TCAGGCACTTATGTGTCGTAT
39556672 ACTGATCAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 10 0.27
21 9 0.24
22 1 0.03
23 16 0.43
24 1 0.03
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (22 bp):
TCAGGCACTTATGTGTCGTATT
Found at i:39561990 original size:23 final size:22
Alignment explanation
Indices: 39561938--39562002 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 22
39561928 CCTGATCAGT
*
39561938 ATACAACACATAAGTGCCTG-A
1 ATACGACACATAAGTGCCTGAA
*
39561959 A-ACGACACATGAGGTGCCTGAA
1 ATACGACACAT-AAGTGCCTGAA
39561981 ATACGACACATAAAGTGCCTGA
1 ATACGACACAT-AAGTGCCTGA
39562003 TCGGTAAGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.22
21 9 0.24
22 2 0.05
23 18 0.49
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (22 bp):
ATACGACACATAAGTGCCTGAA
Found at i:39562948 original size:9 final size:9
Alignment explanation
Indices: 39562930--39562978 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
39562920 CTGCTGCTCT
*
39562930 TTTTGTTTC
1 TTTTCTTTC
39562939 TTTTAC-TTC
1 TTTT-CTTTC
39562948 TTTTCTTTC
1 TTTTCTTTC
39562957 TTTTCTTTC
1 TTTTCTTTC
**
39562966 TTTAGTTTC
1 TTTTCTTTC
39562975 TTTT
1 TTTT
39562979 TATTTACTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 1 0.03
9 33 0.97
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:39562951 original size:18 final size:18
Alignment explanation
Indices: 39562930--39562978 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
39562920 CTGCTGCTCT
39562930 TTTTGTTTCTTTTAC-TTC
1 TTTTGTTTCTTTT-CTTTC
*
39562948 TTTTCTTTCTTTTCTTTC
1 TTTTGTTTCTTTTCTTTC
*
39562966 TTTAGTTTCTTTT
1 TTTTGTTTCTTTT
39562979 TATTTACTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTGTTTCTTTTCTTTC
Found at i:39563234 original size:24 final size:24
Alignment explanation
Indices: 39563202--39563263 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
39563192 ATATCATCTA
* *
39563202 TACCATACACTTGTATTAAATCAT
1 TACCATACATTTGTATTAAACCAT
39563226 TACCATACATTTGTATTAAACCAT
1 TACCATACATTTGTATTAAACCAT
39563250 TACCATACATTTGT
1 TACCATACATTTGT
39563264 CTTTATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (24 bp):
TACCATACATTTGTATTAAACCAT
Found at i:39565720 original size:46 final size:46
Alignment explanation
Indices: 39565653--39565885 Score: 378
Period size: 46 Copynumber: 5.1 Consensus size: 46
39565643 ACATTGCTAT
* *
39565653 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTAATTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
*
39565699 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
*
39565745 AACTCAGTATAGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* *
39565791 AACTCAGTATGGTTTTCTTTACCGAAATACCATACTTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* * *
39565837 AACTCAGTATGGTTTTCTTCACTGAAATACCATACATACGTTTCA-
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
39565882 AACT
1 AACT
39565886 TTTCCATGGA
Statistics
Matches: 176, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
45 4 0.02
46 172 0.98
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
Found at i:39567152 original size:17 final size:17
Alignment explanation
Indices: 39567132--39567177 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
39567122 ATTCTTTTTA
39567132 AAATTACAAAATTCAAT
1 AAATTACAAAATTCAAT
* *
39567149 AAATCACAAAATTCACT
1 AAATTACAAAATTCAAT
*
39567166 AATTTA-AAAATT
1 AAATTACAAAATT
39567178 ATTCTAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATTACAAAATTCAAT
Found at i:39567772 original size:21 final size:21
Alignment explanation
Indices: 39567720--39567766 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
39567710 ATTTTCTTGT
* * *
39567720 TGCCTCTACTGCCCTTGCTGC
1 TGCCTCTGCTTCCCTCGCTGC
39567741 TGCCTCTGCTTCCCTCGCTGC
1 TGCCTCTGCTTCCCTCGCTGC
39567762 TGCCT
1 TGCCT
39567767 TCGCTTTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.45, G:0.19, T:0.34
Consensus pattern (21 bp):
TGCCTCTGCTTCCCTCGCTGC
Found at i:39568892 original size:21 final size:21
Alignment explanation
Indices: 39568868--39568908 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39568858 GCCTAAGATG
39568868 TGAATTGGATTGA-ATTGAGTA
1 TGAATTGGATT-ACATTGAGTA
*
39568889 TGAATTGTATTACATTGAGT
1 TGAATTGGATTACATTGAGT
39568909 TAAATTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.41
Consensus pattern (21 bp):
TGAATTGGATTACATTGAGTA
Found at i:39569450 original size:26 final size:26
Alignment explanation
Indices: 39569396--39569465 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
39569386 GATATATGGT
* *
39569396 TCTTCGTGAGCTTCCTGATTAAAGGC
1 TCTTTGTGAGCTTCCCGATTAAAGGC
* *
39569422 TCTTTGTGAGCTTCCCGATTAATGTC
1 TCTTTGTGAGCTTCCCGATTAAAGGC
* *
39569448 TCTCT-AGAGCTTCCCGAT
1 TCTTTGTGAGCTTCCCGAT
39569466 ATGGCTCACT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
25 12 0.32
26 26 0.68
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (26 bp):
TCTTTGTGAGCTTCCCGATTAAAGGC
Found at i:39569637 original size:25 final size:25
Alignment explanation
Indices: 39569571--39569630 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
39569561 TATGGCTCTT
**
39569571 ATGAGCTTCCCGTTATACAGCCCGG
1 ATGAGCTTCCCGTTATACAGCCCAC
* *
39569596 ATAAGCTTCCCGTTATACAGCTCAC
1 ATGAGCTTCCCGTTATACAGCCCAC
39569621 ATGAGCTTCC
1 ATGAGCTTCC
39569631 TATTATATGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATACAGCCCAC
Found at i:39581381 original size:42 final size:42
Alignment explanation
Indices: 39581335--39581424 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
39581325 GTGTCCTTAC
* * *
39581335 CCGTGTAACTCACTGAGATGCCCCACACACCCGTGTGCCAGG
1 CCGTGTAACTCACTAAGATGCCACACACACCCATGTGCCAGG
** * *
39581377 CCGTGTAACTCTTTAAGTTGCCACACACGCCCATGTGCCAGG
1 CCGTGTAACTCACTAAGATGCCACACACACCCATGTGCCAGG
*
39581419 TCGTGT
1 CCGTGT
39581425 GTTGGGCCAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.20, C:0.34, G:0.23, T:0.22
Consensus pattern (42 bp):
CCGTGTAACTCACTAAGATGCCACACACACCCATGTGCCAGG
Found at i:39582593 original size:43 final size:43
Alignment explanation
Indices: 39582317--39582593 Score: 396
Period size: 43 Copynumber: 6.4 Consensus size: 43
39582307 TTAAAGTCAA
* * * *
39582317 GACCTTTAGCGACAC-TTTCACCACAAACGCCGCTAAAGATCAA
1 GACCTTTAGCGGCGCTTTTC-CCACAAACGCCGCTAAAGACCAT
* * *
39582360 GACCTTTAGCGGCGCTCTTCCCACAAACGTCGCTAAAGACCAG
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAT
*
39582403 GACCTTTAGCGGCGGTTTTCCCACAAACGCCGCTAAAGACCAT
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAT
* *
39582446 GACTTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAAGACCAT
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCT-AAAGACCAT
* *
39582490 GACCTCTAGCGGCGCTTTTCCAAC-AACGCCGCTAAAGACCAT
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAT
*
39582532 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAACCAT
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAT
*
39582575 GACCTTTGGCGGCGCTTTT
1 GACCTTTAGCGGCGCTTTT
39582594 TTTAAAATCG
Statistics
Matches: 210, Mismatches: 21, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
42 31 0.15
43 147 0.70
44 32 0.15
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.21
Consensus pattern (43 bp):
GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAT
Found at i:39585559 original size:15 final size:15
Alignment explanation
Indices: 39585517--39585563 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
39585507 AACCCTTAAT
*
39585517 TAAA-CCATAACCCC
1 TAAATCCATAATCCC
*
39585531 T-AATCTATAATCCC
1 TAAATCCATAATCCC
*
39585545 TAAATCCATACTCCC
1 TAAATCCATAATCCC
39585560 TAAA
1 TAAA
39585564 CCTTAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 2 0.07
14 10 0.37
15 15 0.56
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:39586094 original size:85 final size:85
Alignment explanation
Indices: 39585952--39586216 Score: 399
Period size: 85 Copynumber: 3.1 Consensus size: 85
39585942 CGCTGTTGCT
* *
39585952 AACACCGCTATAGATCAGGACCTTTAGCGGTGC-TTCCCCACAAACGCCACTATAGATCAAGACC
1 AACACCGCTATAGATCAAGACCTTTAGCGGCGCTTTCCCCACAAACGCCACTATAGATCAAGACC
39586016 TTTAGCGGCGCTTTTCCACA
66 TTTAGCGGCGCTTTTCCACA
* *
39586036 AACACCGCTATAGCTCAAGATCTTTAGCGGCGCTTTCCCCACAAACGCCACTATAGATCAAGACC
1 AACACCGCTATAGATCAAGACCTTTAGCGGCGCTTTCCCCACAAACGCCACTATAGATCAAGACC
39586101 TTTAGCGGCGCTTTTCCCACA
66 TTTAGCGGCGCTTTT-CCACA
** * * * * *
39586122 AATGCCGCTATAGAGC-AGACCTTTAGCGACGCTTTTCCCACAAACGCCGCTATAGATCAGGACC
1 AACACCGCTATAGATCAAGACCTTTAGCGGCGCTTTCCCCACAAACGCCACTATAGATCAAGACC
39586186 TTTAGCGGCGCTTTTCACACA
66 TTTAGCGGCGCTTTTC-CACA
39586207 AACACCGCTA
1 AACACCGCTA
39586217 AAAACATATC
Statistics
Matches: 163, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
84 30 0.18
85 116 0.71
86 17 0.10
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (85 bp):
AACACCGCTATAGATCAAGACCTTTAGCGGCGCTTTCCCCACAAACGCCACTATAGATCAAGACC
TTTAGCGGCGCTTTTCCACA
Found at i:39586097 original size:43 final size:43
Alignment explanation
Indices: 39585956--39586216 Score: 366
Period size: 42 Copynumber: 6.1 Consensus size: 43
39585946 GTTGCTAACA
* * *
39585956 CCGCTATAGATCAGGACCTTTAGCGGTGC-TTCCCCACAAACG
1 CCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
* *
39585998 CCACTATAGATCAAGACCTTTAGCGGCGCTTTT-CCACAAACA
1 CCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
* * *
39586040 CCGCTATAGCTCAAGATCTTTAGCGGCGCTTTCCCCACAAACG
1 CCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
* *
39586083 CCACTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAATG
1 CCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
* *
39586126 CCGCTATAGAGC-AGACCTTTAGCGACGCTTTTCCCACAAACG
1 CCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
* * *
39586168 CCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCACACAAACA
1 CCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
39586211 CCGCTA
1 CCGCTA
39586217 AAAACATATC
Statistics
Matches: 192, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
42 102 0.53
43 90 0.47
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (43 bp):
CCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACG
Found at i:39589792 original size:10 final size:10
Alignment explanation
Indices: 39589750--39589809 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
39589740 AAAATAAAAG
*
39589750 TTTAAAATCTT
1 TTTAAAAT-AT
39589761 TTTAAAA-AT
1 TTTAAAATAT
* *
39589770 TCTAAAAAAT
1 TTTAAAATAT
*
39589780 TTTAAAATCT
1 TTTAAAATAT
39589790 TTTAAAATTGAT
1 TTTAAAA-T-AT
39589802 TTTAAAAT
1 TTTAAAAT
39589810 TTTAAATCAC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
9 7 0.17
10 16 0.40
11 9 0.22
12 8 0.20
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (10 bp):
TTTAAAATAT
Found at i:39590551 original size:21 final size:21
Alignment explanation
Indices: 39590521--39590560 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39590511 ATTCACACAT
*
39590521 AACCTCTAAACCTTAAACCCC
1 AACCTCTAAACCATAAACCCC
*
39590542 AACCTTTAAACCATAAACC
1 AACCTCTAAACCATAAACC
39590561 ATAAACCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCTCTAAACCATAAACCCC
Found at i:39590558 original size:7 final size:7
Alignment explanation
Indices: 39590548--39590608 Score: 68
Period size: 7 Copynumber: 8.6 Consensus size: 7
39590538 CCCCAACCTT
39590548 TAAACCA
1 TAAACCA
39590555 TAAACCA
1 TAAACCA
39590562 TAAACCA
1 TAAACCA
*
39590569 TAACCCA
1 TAAACCA
* *
39590576 TAATCCC
1 TAAACCA
39590583 TAAACCCA
1 TAAA-CCA
*
39590591 TAATCCA
1 TAAACCA
*
39590598 TAAACCT
1 TAAACCA
39590605 TAAA
1 TAAA
39590609 ATGGCAACAC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
7 40 0.89
8 5 0.11
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCA
Found at i:39590590 original size:15 final size:15
Alignment explanation
Indices: 39590552--39590603 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
39590542 AACCTTTAAA
*
39590552 CCATAAA-CCATAAA
1 CCATAAACCCATAAT
39590566 CCAT-AACCCATAAT
1 CCATAAACCCATAAT
*
39590580 CCCTAAACCCATAAT
1 CCATAAACCCATAAT
39590595 CCATAAACC
1 CCATAAACC
39590604 TTAAAATGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 2 0.06
14 13 0.39
15 18 0.55
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (15 bp):
CCATAAACCCATAAT
Found at i:39590839 original size:66 final size:66
Alignment explanation
Indices: 39590733--39590866 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 66
39590723 CCCTAAACTA
*
39590733 TAGTGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
1 TAGTGATAATTAATTCAATAGTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
39590798 T
66 T
39590799 TAGTGATAATTAATTCAATAGTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
1 TAGTGATAATTAATTCAATAGTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
39590864 T
66 T
39590865 TA
1 TA
39590867 ATATATAAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (66 bp):
TAGTGATAATTAATTCAATAGTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
T
Found at i:39591046 original size:41 final size:41
Alignment explanation
Indices: 39590985--39591304 Score: 509
Period size: 41 Copynumber: 7.8 Consensus size: 41
39590975 CCACAGCATT
* *
39590985 ATTAGCGGCGCTTTCCCAAAAACACCGCTAAAGGCCTGGAC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGAC
*
39591026 ATTAGCGGCGCTTTCACAAAAACGACGCTAAAGGCCTGGAC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGAC
*
39591067 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGAC
*
39591108 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGAC
*
39591149 ATTAGCGGCGCTTTCACAAAACCGCCGCTAAAGGCCTGGAC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGAC
* *
39591190 ATTAGCGGCGCTTTCACAAAAAGGCTGCTAAAGGCCTAGG-C
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCT-GGAC
* *
39591231 ATTAGCGGCACTTTCACAAAAACGCCGCTAAAGGCCTGGGGC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCT-GGAC
39591273 ATTAGCGGCGCTTTC-CTAAAAACGCCGCTAAA
1 ATTAGCGGCGCTTTCAC-AAAAACGCCGCTAAA
39591305 TCCTTGAAAG
Statistics
Matches: 261, Mismatches: 15, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
41 229 0.88
42 32 0.12
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.18
Consensus pattern (41 bp):
ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGAC
Found at i:39591437 original size:40 final size:40
Alignment explanation
Indices: 39591368--39591477 Score: 145
Period size: 40 Copynumber: 2.8 Consensus size: 40
39591358 TATTGAAAAT
* *
39591368 GCCGCTAATGCT-TAT-TATTAGCGGCGTTTTCCATAAAGC
1 GCCGCTAATGCTCGATCT-TTAGCGGCGTTTTCCAAAAAGC
*
39591407 GCCGCTAAAT-CTCGATCTTTAGCGGTGTTTTCCAAAAAGC
1 GCCGCT-AATGCTCGATCTTTAGCGGCGTTTTCCAAAAAGC
*
39591447 GCCGCTAATGCTCGATCTTTAGGGGCGTTTT
1 GCCGCTAATGCTCGATCTTTAGCGGCGTTTT
39591478 TTATCCAAAC
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
39 11 0.18
40 50 0.81
41 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.33
Consensus pattern (40 bp):
GCCGCTAATGCTCGATCTTTAGCGGCGTTTTCCAAAAAGC
Found at i:39592059 original size:114 final size:113
Alignment explanation
Indices: 39591842--39592266 Score: 539
Period size: 117 Copynumber: 3.7 Consensus size: 113
39591832 ATATTTTTTA
* * *
39591842 CCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTTGTTGGGCTTAGGTTTTTTTTGCAGCGCTTTC
1 CCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG-TTTTTTTGCGGCGCTTTC
* *
39591907 TCAAAAACGCCGTTAAAGCCTTGAGCATTAGCGACGCTTTTTAAAAAACG
65 TCAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGCTTTTT-AAAAACG
* * * * *
39591957 CCGCTAAATCCACGAAAGCTCAGAAAGCCGCGTCATTGGGCTTAGGTTTTTTTGCGGCGCTTTCT
1 CCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCT
* * * * *
39592022 CAAAAACGACGCGAAATCCCTGAGCATTAGCGGCGCTTTCTTAGAAACG
66 CAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGCTTT-TTAAAAACG
* * *
39592071 CCGCTAAATCCCCAAAAGCTCACAAAACGGCATCGTTGGGCTTATGTTTTTTTTTTGCGGCGCTT
1 CCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTA-G--GTTTTTTTGCGGCGCTT
* * *
39592136 TATCAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGTTTTCTTAAAAACC
63 TCTCAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGCTTT-TTAAAAACG
* *
39592188 CCGCTAAATCCCCAAAAGCTC-GAAAAACGGCGTGGTTGGGCTTAGG-TTTTTTCCGGCGCTTTC
1 CCGCTAAATCCCCAAAAGCTCAG-AAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTC
**
39592251 TGGAAAACGCCGCTAA
65 TCAAAAACGCCGCTAA
39592267 TGCTTATTTT
Statistics
Matches: 268, Mismatches: 37, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
113 29 0.11
114 94 0.35
115 44 0.16
116 1 0.00
117 100 0.37
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (113 bp):
CCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCT
CAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGCTTTTTAAAAACG
Found at i:39596648 original size:22 final size:21
Alignment explanation
Indices: 39596612--39596671 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
39596602 GGCCCGGCCT
*
39596612 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA-AAAAA
39596634 ATTTATTTTAAAAATTAAAAAA
1 ATTTATTTTAAAAA-TAAAAAA
**
39596656 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
39596672 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 23 0.70
23 8 0.24
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTTATTTTAAAAATAAAAAA
Found at i:39596685 original size:39 final size:38
Alignment explanation
Indices: 39596641--39596746 Score: 149
Period size: 39 Copynumber: 2.7 Consensus size: 38
39596631 AAAATTTATT
*
39596641 TTAAAAATTAAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAATTAAAAAAAAATATTTT-AAAATATTTTAAAA
*
39596680 TTAAAAAATAAAAAAAAATATTTTAAAATATTTTAAAA
1 TTAAAAATTAAAAAAAAATATTTTAAAATATTTTAAAA
39596718 TTAAAAAATTTAAAAAATAAATATATTTA
1 TT-AAAAA-TTAAAAAA-AAATAT-TTTA
39596747 TTATATCGGG
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
38 16 0.27
39 27 0.45
40 7 0.12
41 6 0.10
42 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (38 bp):
TTAAAAATTAAAAAAAAATATTTTAAAATATTTTAAAA
Found at i:39596707 original size:10 final size:10
Alignment explanation
Indices: 39596694--39596718 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
39596684 AAAATAAAAA
39596694 AAAATATTTT
1 AAAATATTTT
39596704 AAAATATTTT
1 AAAATATTTT
39596714 AAAAT
1 AAAAT
39596719 TAAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AAAATATTTT
Found at i:39596708 original size:38 final size:38
Alignment explanation
Indices: 39596641--39596746 Score: 149
Period size: 38 Copynumber: 2.7 Consensus size: 38
39596631 AAAATTTATT
* *
39596641 TTAAAAATTAAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATAAAAAAAAATATTTT-AAAATATTTTAAAA
39596680 TTAAAAAATAAAAAAAAATATTTTAAAATATTTTAAAA
1 TTAAAAAATAAAAAAAAATATTTTAAAATATTTTAAAA
39596718 TTAAAAAATTTAAAAAATAAATATATTTA
1 TTAAAAAA--TAAAAAA-AAATAT-TTTA
39596747 TTATATCGGG
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
38 22 0.36
39 22 0.36
40 7 0.11
41 6 0.10
42 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (38 bp):
TTAAAAAATAAAAAAAAATATTTTAAAATATTTTAAAA
Found at i:39596723 original size:16 final size:16
Alignment explanation
Indices: 39596702--39596746 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
39596692 AAAAAATATT
*
39596702 TTAAAATATTTTAAAA
1 TTAAAATATTTAAAAA
*
39596718 TTAAAAAATTTAAAAA
1 TTAAAATATTTAAAAA
*
39596734 ATAAATATATTTA
1 TTAAA-ATATTTA
39596747 TTATATCGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAAATATTTAAAAA
Found at i:39597784 original size:45 final size:45
Alignment explanation
Indices: 39597720--39597808 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
39597710 CACGCATGAG
39597720 GTGGAGATCGAAGAGCCTGATGATCACG-GAACTACCATTCTCAAC
1 GTGGAGATCGAAGAGCCTGATGATCACGCG-ACTACCATTCTCAAC
*
39597765 GTGGAGATCGAAGAGCCTGATGATCACGCGGCTACCATTCTCAA
1 GTGGAGATCGAAGAGCCTGATGATCACGCGACTACCATTCTCAA
39597809 ACGAGTATGC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
45 41 0.98
46 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (45 bp):
GTGGAGATCGAAGAGCCTGATGATCACGCGACTACCATTCTCAAC
Found at i:39598986 original size:9 final size:9
Alignment explanation
Indices: 39598967--39599021 Score: 76
Period size: 9 Copynumber: 6.2 Consensus size: 9
39598957 TCGGGTATTT
39598967 TTCGG-TAA
1 TTCGGTTAA
39598975 TTCGGTTAA
1 TTCGGTTAA
*
39598984 TTCAGTTAA
1 TTCGGTTAA
39598993 TTCGGTTAA
1 TTCGGTTAA
*
39599002 TTCGGGTAA
1 TTCGGTTAA
*
39599011 TTCGGGTAA
1 TTCGGTTAA
39599020 TT
1 TT
39599022 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
8 5 0.12
9 38 0.88
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.42
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:39599198 original size:12 final size:12
Alignment explanation
Indices: 39599181--39599205 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39599171 AGTAATTTCG
39599181 GGTCGGTTAACC
1 GGTCGGTTAACC
39599193 GGTCGGTTAACC
1 GGTCGGTTAACC
39599205 G
1 G
39599206 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:39601318 original size:23 final size:23
Alignment explanation
Indices: 39601292--39601390 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
39601282 AGTGTTATTG
*
39601292 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
39601315 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
39601338 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
39601361 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39601384 ATCAGTG
1 ATCAGTG
39601391 TGGCACTTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:39601345 original size:46 final size:46
Alignment explanation
Indices: 39601292--39601390 Score: 189
Period size: 46 Copynumber: 2.2 Consensus size: 46
39601282 AGTGTTATTG
*
39601292 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCAGCTACAT
39601338 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCAGCTACAT
39601384 ATCAGTG
1 ATCAGTG
39601391 TGGCACTTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCAGCTACAT
Found at i:39602970 original size:30 final size:30
Alignment explanation
Indices: 39602936--39603029 Score: 118
Period size: 30 Copynumber: 3.0 Consensus size: 30
39602926 TCCCCTTTAC
39602936 ATAACAAACAAACTTATTTTTATGACTCAT
1 ATAACAAACAAACTTATTTTTATGACTCAT
*
39602966 ATAACAAATAAACTTACTTTTT-TGACTCATACT
1 ATAACAAACAAACTTA-TTTTTATGACTC--A-T
* *
39602999 ATAACAAACAAACTTACTTTTATAACTCAT
1 ATAACAAACAAACTTATTTTTATGACTCAT
39603029 A
1 A
39603030 CAAAATAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
30 23 0.42
31 6 0.11
32 5 0.09
33 21 0.38
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (30 bp):
ATAACAAACAAACTTATTTTTATGACTCAT
Found at i:39603012 original size:33 final size:33
Alignment explanation
Indices: 39602936--39603030 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
39602926 TCCCCTTTAC
39602936 ATAACAAACAAACTTA-TTTTTATGACTC--A-T
1 ATAACAAACAAACTTACTTTTT-TGACTCATACT
*
39602966 ATAACAAATAAACTTACTTTTTTGACTCATACT
1 ATAACAAACAAACTTACTTTTTTGACTCATACT
* *
39602999 ATAACAAACAAACTTACTTTTATAACTCATAC
1 ATAACAAACAAACTTACTTTTTTGACTCATAC
39603031 AAAATAATAA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
30 21 0.37
31 5 0.09
32 1 0.02
33 30 0.53
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (33 bp):
ATAACAAACAAACTTACTTTTTTGACTCATACT
Found at i:39612962 original size:35 final size:35
Alignment explanation
Indices: 39612916--39612986 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
39612906 TACGACCAGT
39612916 TTTCAATCCAACCAAACTAAACGAATGATTCAATC
1 TTTCAATCCAACCAAACTAAACGAATGATTCAATC
39612951 TTTCAATCCAACCAAACTAAACGAATGATTCAATC
1 TTTCAATCCAACCAAACTAAACGAATGATTCAATC
39612986 T
1 T
39612987 GATTCAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (35 bp):
TTTCAATCCAACCAAACTAAACGAATGATTCAATC
Found at i:39624429 original size:73 final size:73
Alignment explanation
Indices: 39624310--39624456 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
39624300 CAAAGTTTTC
39624310 AAAATTTCCCCAATTGATATCGATACCCCATGAAGGTACTGATACCAAAATTAACTTCGATGTTT
1 AAAATTTCCCCAATTGATATCGATACCCCATGAAGGTACTGATACCAAAATTAACTTCGATGTTT
39624375 CATAAAAT
66 CATAAAAT
39624383 AAAATTTCCCCAATTGATATCGATACCCCATGAAGGTACTGATACCAAAATTAACTTCGATGTTT
1 AAAATTTCCCCAATTGATATCGATACCCCATGAAGGTACTGATACCAAAATTAACTTCGATGTTT
39624448 CATAAAAT
66 CATAAAAT
39624456 A
1 A
39624457 CTTTCTTTTA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (73 bp):
AAAATTTCCCCAATTGATATCGATACCCCATGAAGGTACTGATACCAAAATTAACTTCGATGTTT
CATAAAAT
Found at i:39624998 original size:2 final size:2
Alignment explanation
Indices: 39624985--39625080 Score: 183
Period size: 2 Copynumber: 48.0 Consensus size: 2
39624975 CATATTGATT
*
39624985 CA CA CA CG CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
39625027 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
39625069 CA CA CA CA CA CA
1 CA CA CA CA CA CA
39625081 TATATATATA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.49, C:0.50, G:0.01, T:0.00
Consensus pattern (2 bp):
CA
Found at i:39642819 original size:34 final size:34
Alignment explanation
Indices: 39642776--39642843 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
39642766 CCATGTTGCA
39642776 GGATCAATATACTAGTCACCATACAGACCAATAT
1 GGATCAATATACTAGTCACCATACAGACCAATAT
*
39642810 GGATCAATATACTAGTCACTATACAGACCAATAT
1 GGATCAATATACTAGTCACCATACAGACCAATAT
39642844 AATTAGATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (34 bp):
GGATCAATATACTAGTCACCATACAGACCAATAT
Found at i:39649137 original size:40 final size:40
Alignment explanation
Indices: 39649083--39649161 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 40
39649073 AAAATGTTTA
* *
39649083 AAATTTTTATAT-AAACTTTAAAAA-TACAAAAAAAAATTT
1 AAATTATTATATAAAAC-TTAAAAACTAAAAAAAAAAATTT
39649122 AAATTATTATAATAAAACTTAAAAACTAAAAAAAAAAATT
1 AAATTATTAT-ATAAAACTTAAAAACTAAAAAAAAAAATT
39649162 GACGGTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 9 0.26
40 9 0.26
41 17 0.49
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (40 bp):
AAATTATTATATAAAACTTAAAAACTAAAAAAAAAAATTT
Found at i:39649863 original size:17 final size:17
Alignment explanation
Indices: 39649828--39649863 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39649818 TTAAGATAAG
**
39649828 TATTAAATTTAATTTAA
1 TATTAAATTTAATAAAA
39649845 TATTAAATTTAATAAAA
1 TATTAAATTTAATAAAA
39649862 TA
1 TA
39649864 ATAATATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTAAATTTAATAAAA
Found at i:39679690 original size:18 final size:21
Alignment explanation
Indices: 39679651--39679694 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
39679641 ACATGTATAA
39679651 GTATGTGTATTGATTAAAAAT
1 GTATGTGTATTGATTAAAAAT
39679672 GTATGTGTATT-A-T-AAAAT
1 GTATGTGTATTGATTAAAAAT
39679690 GTATG
1 GTATG
39679695 CATGTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.43
19 1 0.04
20 1 0.04
21 11 0.48
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.43
Consensus pattern (21 bp):
GTATGTGTATTGATTAAAAAT
Found at i:39682992 original size:16 final size:16
Alignment explanation
Indices: 39682971--39683006 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
39682961 CAATGATGAC
39682971 TGTTGAAGGATATTTT
1 TGTTGAAGGATATTTT
39682987 TGTTGAAGGATATTTT
1 TGTTGAAGGATATTTT
39683003 TGTT
1 TGTT
39683007 AAATAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (16 bp):
TGTTGAAGGATATTTT
Found at i:39683885 original size:55 final size:55
Alignment explanation
Indices: 39683822--39683966 Score: 236
Period size: 55 Copynumber: 2.6 Consensus size: 55
39683812 TCTTCTTAAT
* *
39683822 TGTTGGAATACTGCTTCTTTTGAATTGATTTTTTATATGTTTAAATCGATTGTCA
1 TGTTGGAATACTGCTTCTTTTGAATCGATTTTTTATATGTTTAAATCGATTATCA
* * *
39683877 TGTTGGAATACTGCTTCTTTTAAATCGATTATTTATATGTTTAAATCGATTATTA
1 TGTTGGAATACTGCTTCTTTTGAATCGATTTTTTATATGTTTAAATCGATTATCA
39683932 TGTTGGAATACTGCTTCTTTTGAATCGATTATTTT
1 TGTTGGAATACTGCTTCTTTTGAATCGATT-TTTT
39683967 TACATAGCAC
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
55 79 0.96
56 3 0.04
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (55 bp):
TGTTGGAATACTGCTTCTTTTGAATCGATTTTTTATATGTTTAAATCGATTATCA
Found at i:39690095 original size:23 final size:22
Alignment explanation
Indices: 39690052--39690095 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
39690042 TGCTGCCAAG
*
39690052 ACTGACTTTGAAAACACAAAAA
1 ACTGACTTTGAAAAAACAAAAA
*
39690074 ACTGACTTTGAAAAAACTAAAA
1 ACTGACTTTGAAAAAACAAAAA
39690096 CATAAACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.16, G:0.09, T:0.20
Consensus pattern (22 bp):
ACTGACTTTGAAAAAACAAAAA
Found at i:39692845 original size:98 final size:98
Alignment explanation
Indices: 39692666--39692862 Score: 331
Period size: 98 Copynumber: 2.0 Consensus size: 98
39692656 GTACAATAAA
*
39692666 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* * *
39692731 CCTCTAGAATCTCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCAGAATATTTCCTTT
* *
39692764 ACTTTAAAGGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
39692829 CCTTTAAAATCCCAAACTCAGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCAGAATATTTCCTTT
39692862 A
1 A
39692863 TTATTTTTAA
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCAGAATATTTCCTTT
Found at i:39693524 original size:22 final size:23
Alignment explanation
Indices: 39693499--39693542 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
39693489 ATATATATAT
39693499 GAAAATATTC-ATTTAAAAAAAG
1 GAAAATATTCGATTTAAAAAAAG
*
39693521 GAAAATATTCGTTTTAAAAAAA
1 GAAAATATTCGATTTAAAAAAA
39693543 ATATATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (23 bp):
GAAAATATTCGATTTAAAAAAAG
Found at i:39694189 original size:19 final size:19
Alignment explanation
Indices: 39694165--39694296 Score: 210
Period size: 19 Copynumber: 6.8 Consensus size: 19
39694155 AATCATATAT
39694165 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
39694184 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
39694203 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
39694222 TTTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
39694243 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
39694262 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
39694281 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
39694297 CTCAAAAATT
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
19 85 0.83
21 18 0.17
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:39694247 original size:59 final size:59
Alignment explanation
Indices: 39694161--39694295 Score: 211
Period size: 59 Copynumber: 2.3 Consensus size: 59
39694151 ACAAAATCAT
*
39694161 ATATTCTAAGATTGC--ATATCATATCTAAGATTATATATCATATCTAAGATTGCATATC
1 ATATT-TAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTGCATATC
* *
39694219 ATATTTAAGATTGCATATATCATATCTAAGATTGCATATCATATCTAGGATTGCATATC
1 ATATTTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTGCATATC
*
39694278 ATATCTAAGATTGCATAT
1 ATATTTAAGATTGCATAT
39694296 CCTCAAAAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
57 9 0.13
58 5 0.07
59 57 0.80
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.39
Consensus pattern (59 bp):
ATATTTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTGCATATC
Found at i:39694482 original size:38 final size:37
Alignment explanation
Indices: 39694440--39694589 Score: 113
Period size: 38 Copynumber: 3.9 Consensus size: 37
39694430 TTACAAGTGC
39694440 CATTTTTAAGGTTCACCTGATATTCATATCGCGGTTGT
1 CATTTTTAAGGTTC-CCTGATATTCATATCGCGGTTGT
* * * * ***
39694478 CATTTTTACGGTTCGCTTAGTATTCATATTGCAACCT-T
1 CATTTTTAAGGTTCCCTGA-TATTCATATCGC-GGTTGT
* *
39694516 CAATGTTTTAACAGTTCGCTTGATATTCATATCGCGGTTGT
1 C-AT-TTTTAA-GGTTC-CCTGATATTCATATCGCGGTTGT
* * *
39694557 CATTTTTACGGTTCGCTCAATATTCATATCGCG
1 CATTTTTAAGGTTCCCT-GATATTCATATCGCG
39694590 ACCTTCGATA
Statistics
Matches: 83, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
37 4 0.05
38 44 0.53
39 8 0.10
40 8 0.10
41 17 0.20
42 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (37 bp):
CATTTTTAAGGTTCCCTGATATTCATATCGCGGTTGT
Found at i:39694594 original size:79 final size:79
Alignment explanation
Indices: 39694457--39694651 Score: 248
Period size: 79 Copynumber: 2.5 Consensus size: 79
39694447 AAGGTTCACC
* * * *
39694457 TGATATTCATATCGCGGTTGTCATTTTTACGGTTCGCTTAGTATTCATATTGCAACCTTCAATGT
1 TGATATTCATATCGCGGTTGTCATTTTTACGGTTCGCTCAATATTCATATCGCAACCTTCAATAT
* *
39694522 TTTAACAGTTCGCT
66 TCTAACAATTCGCT
* *
39694536 TGATATTCATATCGCGGTTGTCATTTTTACGGTTCGCTCAATATTCATATCGCGACCTTCGATAT
1 TGATATTCATATCGCGGTTGTCATTTTTACGGTTCGCTCAATATTCATATCGCAACCTTCAATAT
39694601 TCTAACAATTCGCT
66 TCTAACAATTCGCT
* * * *** *
39694615 CGAT-TTAAGATCGCAACTGTCATTTTCACGGTTCGCT
1 TGATATTCATATCGCGGTTGTCATTTTTACGGTTCGCT
39694652 GATTTTAACT
Statistics
Matches: 101, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
78 27 0.27
79 74 0.73
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (79 bp):
TGATATTCATATCGCGGTTGTCATTTTTACGGTTCGCTCAATATTCATATCGCAACCTTCAATAT
TCTAACAATTCGCT
Found at i:39695874 original size:6 final size:7
Alignment explanation
Indices: 39695855--39695882 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
39695845 TTAGATGTCG
39695855 TATTTTT
1 TATTTTT
39695862 TATTTTT
1 TATTTTT
39695869 TATTTTT
1 TATTTTT
39695876 TATTTTT
1 TATTTTT
39695883 CAATTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TATTTTT
Found at i:39713781 original size:15 final size:16
Alignment explanation
Indices: 39713761--39713794 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39713751 ACGGATTGGG
39713761 TTTTTATT-TTTCTAT
1 TTTTTATTATTTCTAT
*
39713776 TTTTTATTATTTTTAT
1 TTTTTATTATTTCTAT
39713792 TTT
1 TTT
39713795 CTTCTGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTATTATTTCTAT
Found at i:39713938 original size:11 final size:11
Alignment explanation
Indices: 39713922--39713947 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39713912 TTTCAGATTT
39713922 TTTTTATTTTA
1 TTTTTATTTTA
39713933 TTTTTATTTTA
1 TTTTTATTTTA
39713944 TTTT
1 TTTT
39713948 CTTTCCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:39717115 original size:4 final size:4
Alignment explanation
Indices: 39717108--39717137 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
39717098 AATAAGTACG
39717108 TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
39717138 GCATCAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:39720253 original size:21 final size:23
Alignment explanation
Indices: 39720229--39720273 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
39720219 GGCTGTAATG
*
39720229 AGAATTT-CTAGAAATTTT-AAA
1 AGAATTTAATAGAAATTTTCAAA
39720250 AGAATTTAATAGAAATTTTCAAA
1 AGAATTTAATAGAAATTTTCAAA
39720273 A
1 A
39720274 ATCCTATGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 10 0.48
23 4 0.19
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (23 bp):
AGAATTTAATAGAAATTTTCAAA
Found at i:39720910 original size:13 final size:13
Alignment explanation
Indices: 39720892--39720955 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
39720882 AGTTCTTCAT
39720892 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
39720905 TGCTTTAGAAAAG
1 TGCTTTTGAAAAG
*
39720918 TG-TTGTGGAAAAG
1 TGCTT-TTGAAAAG
* * *
39720931 TACTTCTCAGAAA-
1 TGCTTTTGA-AAAG
39720944 TGCTTTTGAAAA
1 TGCTTTTGAAAA
39720956 ATTTGAGTGT
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
12 5 0.13
13 29 0.74
14 5 0.13
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:39720954 original size:26 final size:26
Alignment explanation
Indices: 39720892--39720955 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
39720882 AGTTCTTCAT
*
39720892 TGCTTTTGAAAAGTGCTTTAGAAAAG
1 TGCTTTTGAAAAGTACTTTAGAAAAG
*
39720918 TG-TTGTGGAAAAGTACTTCTCAG-AAA-
1 TGCTT-TTGAAAAGTACTT-T-AGAAAAG
39720944 TGCTTTTGAAAA
1 TGCTTTTGAAAA
39720956 ATTTGAGTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
25 2 0.06
26 21 0.68
27 6 0.19
28 2 0.06
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (26 bp):
TGCTTTTGAAAAGTACTTTAGAAAAG
Found at i:39723342 original size:24 final size:23
Alignment explanation
Indices: 39723303--39723379 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 23
39723293 TGGAAGAGTT
*
39723303 ACAAAGCGGTAAAGCAAAAGAGGC
1 ACAAAGCAG-AAAGCAAAAGAGGC
* **
39723327 ACAGAGCA-AAGCAGCAGCAGAGGC
1 ACAAAGCAGAA--AGCAAAAGAGGC
39723351 ACAAAGCAGTAAAGCAAAAGAGGC
1 ACAAAGCAG-AAAGCAAAAGAGGC
39723375 ACAAA
1 ACAAA
39723380 AGCCAGAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
22 2 0.05
24 38 0.90
26 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.27, T:0.03
Consensus pattern (23 bp):
ACAAAGCAGAAAGCAAAAGAGGC
Found at i:39726916 original size:15 final size:15
Alignment explanation
Indices: 39726896--39726927 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
39726886 TCTTCGAAGG
39726896 TTTAGGGTTTAAGTT
1 TTTAGGGTTTAAGTT
39726911 TTTAGGGTTTAAGTT
1 TTTAGGGTTTAAGTT
39726926 TT
1 TT
39726928 GACCCGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.25, T:0.56
Consensus pattern (15 bp):
TTTAGGGTTTAAGTT
Found at i:39728835 original size:31 final size:30
Alignment explanation
Indices: 39728770--39728856 Score: 122
Period size: 30 Copynumber: 2.8 Consensus size: 30
39728760 TAAATATATA
39728770 TTTTTTATTTTTAAAA-ATATTTTAAAATAC
1 TTTTTTATTTTTAAAATAT-TTTTAAAATAC
39728800 TTTTTTATTTTTAAAATATTTTTAAAATAC
1 TTTTTTATTTTTAAAATATTTTTAAAATAC
39728830 TTTTTTTAATTTTCTAAAATTATTTTT
1 -TTTTTT-ATTTT-TAAAA-TATTTTT
39728857 GTGTTTATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
30 27 0.52
31 8 0.15
32 5 0.10
33 5 0.10
34 7 0.13
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTTATTTTTAAAATATTTTTAAAATAC
Found at i:39731284 original size:31 final size:31
Alignment explanation
Indices: 39731249--39731331 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 31
39731239 TAGCCAAGTA
*
39731249 ACTTAAATAAAAACTTTCGAATAATTCGATG
1 ACTTAAATAAAAACTTTCAAATAATTCGATG
* *
39731280 ACTTAAATAAAAACTTTCAAATAGTTCGGTG
1 ACTTAAATAAAAACTTTCAAATAATTCGATG
* **
39731311 ACTAAAATGGAAACTTTCAAA
1 ACTTAAATAAAAACTTTCAAA
39731332 CAGTCAAGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAATTCGATG
Found at i:39737735 original size:16 final size:16
Alignment explanation
Indices: 39737711--39737752 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
39737701 TAGTTCACTG
39737711 TAATCGAATAGAGCTA
1 TAATCGAATAGAGCTA
* *
39737727 TAATTGAATAGAGCTG
1 TAATCGAATAGAGCTA
*
39737743 TAATGGAATA
1 TAATCGAATA
39737753 AAGTTGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (16 bp):
TAATCGAATAGAGCTA
Found at i:39737760 original size:16 final size:16
Alignment explanation
Indices: 39737708--39737762 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
39737698 GTTTAGTTCA
* *
39737708 CTGTAATCGAATAGAG
1 CTGTAATGGAATAAAG
* * *
39737724 CTATAATTGAATAGAG
1 CTGTAATGGAATAAAG
39737740 CTGTAATGGAATAAAG
1 CTGTAATGGAATAAAG
*
39737756 TTGTAAT
1 CTGTAAT
39737763 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAAAG
Found at i:39737951 original size:22 final size:22
Alignment explanation
Indices: 39737924--39737975 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
39737914 ATTGTTATTG
39737924 TTATTAAATTTTAATAAGATTA
1 TTATTAAATTTTAATAAGATTA
*
39737946 TTATTAAATTTTAATAAGGTTA
1 TTATTAAATTTTAATAAGATTA
39737968 TTATTAAA
1 TTATTAAA
39737976 AATACTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (22 bp):
TTATTAAATTTTAATAAGATTA
Found at i:39738081 original size:58 final size:58
Alignment explanation
Indices: 39737969--39738083 Score: 151
Period size: 58 Copynumber: 2.0 Consensus size: 58
39737959 ATAAGGTTAT
* * *
39737969 TATTAAAAATACTTTAATAAAAATAATAAATAATTTAACCATATTTTAACATAATTAC
1 TATTAAAAATAATTTAATAAAAATAATAAATAATTTAACAAAATTTTAACATAATTAC
* * * *
39738027 TATTAAATATAATTTAAT-AAAATAATATATAATTTAATAAAATTCTTAATATAATTA
1 TATTAAAAATAATTTAATAAAAATAATAAATAATTTAACAAAATT-TTAACATAATTA
39738084 TTATATGAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
57 22 0.45
58 27 0.55
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (58 bp):
TATTAAAAATAATTTAATAAAAATAATAAATAATTTAACAAAATTTTAACATAATTAC
Found at i:39738132 original size:23 final size:23
Alignment explanation
Indices: 39738096--39738141 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
39738086 ATATGAATTA
*
39738096 AAAAATCATAATATATAATACTAT
1 AAAAATAATAATATATAAT-CTAT
39738120 AAAAATAAT-ATATATAATCTAT
1 AAAAATAATAATATATAATCTAT
39738142 TTTATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 9 0.43
24 8 0.38
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAAATAATAATATATAATCTAT
Found at i:39747849 original size:14 final size:14
Alignment explanation
Indices: 39747830--39747860 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
39747820 ATCAAATCGA
39747830 TAAGAAAATATTAC
1 TAAGAAAATATTAC
39747844 TAAGAAAATATTAC
1 TAAGAAAATATTAC
39747858 TAA
1 TAA
39747861 ACTTTCAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (14 bp):
TAAGAAAATATTAC
Found at i:39748859 original size:33 final size:29
Alignment explanation
Indices: 39748821--39748895 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 29
39748811 CAACTATAAG
39748821 TGCCGAATGCACATAT-TCACTTATACCTACCTA
1 TGCCGAATGCACATATAT-A--TAT-CC-ACCTA
39748854 TGCCGAATGCATACATATATATATCCACCTA
1 TGCCGAATGC--ACATATATATATCCACCTA
39748885 TGCCGAATGCA
1 TGCCGAATGCA
39748896 TACATATACA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
29 1 0.03
31 15 0.38
32 2 0.05
33 13 0.33
35 7 0.18
36 1 0.03
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (29 bp):
TGCCGAATGCACATATATATATCCACCTA
Found at i:39748872 original size:27 final size:27
Alignment explanation
Indices: 39748842--39748904 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 27
39748832 CATATTCACT
39748842 TATACCTACCTATGCCGAATGCATACATATA
1 TATACC-ACCTATGCCGAATGCATAC--A-A
39748873 TATATCCACCTATGCCGAATGCATAC-A
1 TATA-CCACCTATGCCGAATGCATACAA
39748900 TATAC
1 TATAC
39748905 ACACTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
26 1 0.03
27 5 0.16
31 23 0.74
32 2 0.06
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.29
Consensus pattern (27 bp):
TATACCACCTATGCCGAATGCATACAA
Found at i:39749300 original size:41 final size:41
Alignment explanation
Indices: 39749091--39749277 Score: 277
Period size: 41 Copynumber: 4.6 Consensus size: 41
39749081 TTTAAGCAGA
* * * * *
39749091 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTCTAATTCCG
1 TTCACCGGCACTT-AGCCTGCTAGGCTTATAGCCTGATTCAG
* *
39749132 TTCATCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
*
39749173 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
*
39749214 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
39749255 TTCACCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAG
39749278 ACGTATAGTC
Statistics
Matches: 135, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 1 0.01
41 134 0.99
ACGTcount: A:0.19, C:0.29, G:0.22, T:0.30
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
Found at i:39750823 original size:26 final size:26
Alignment explanation
Indices: 39750793--39750848 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
39750783 TTGATTTGTT
*
39750793 ATATTAAACATATATTAACC-TTATTA
1 ATATTAAAC-TATATTAACCTTTACTA
**
39750819 ATATTTTACTATATTAACCTTTACTA
1 ATATTAAACTATATTAACCTTTACTA
39750845 ATAT
1 ATAT
39750849 ATATATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATTAAACTATATTAACCTTTACTA
Found at i:39755515 original size:29 final size:29
Alignment explanation
Indices: 39755427--39756261 Score: 1299
Period size: 29 Copynumber: 28.9 Consensus size: 29
39755417 TAAAAAAAAT
*
39755427 CCTAATTTAATTAAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
* *
39755457 CCTAATTTAATTTAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
*
39755487 CCTAATTTAATTAAAAACCTTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
39755516 CCTAATTTAATTAAAAACCCTAACCCTGA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
39755545 CTTAATTTAATTAAAAACCCTAACCCTAG
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
39755574 CTTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
39755603 CCTAATTTAATTAAAAATCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
* *
39755633 CCTAATTTAATTAAAAACTCTAACTCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
39755662 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
39755691 CTTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
39755720 CTTAATTTAATTAAAAATCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
39755749 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
39755779 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
39755808 CCTAATTTAATTAAAAACCCTAA-CCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
39755836 CCTAATTTAATTAAAAACCCTAAACTCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
*
39755866 CCTAATTTAATTAAAAACCCTAACTCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
39755895 CCTAATTTAATT--AAA----AACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
39755918 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
39755947 CCTAATTTAAGTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
39755976 CTTAATTTAATT-AAAACTCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
39756004 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* * *
39756033 CTTAATTTAATTAAAAAACCTAACCTTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
39756062 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
39756091 CTTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
39756120 CTTAATTTAATTGAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
39756149 CCTAATTTAATTAAAAACCCTAACCCTAG
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
39756178 CTTGATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
39756207 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
*
39756237 CTTAATTTAATTAAAAACCCTAACC
1 CCTAATTTAATTAAAAACCCTAACC
39756262 ATTAACAAAA
Statistics
Matches: 747, Mismatches: 46, Indels: 25
0.91 0.06 0.03
Matches are distributed among these distances:
23 19 0.03
25 3 0.00
27 3 0.00
28 52 0.07
29 513 0.69
30 157 0.21
ACGTcount: A:0.45, C:0.25, G:0.01, T:0.30
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:39756229 original size:23 final size:23
Alignment explanation
Indices: 39755857--39755942 Score: 109
Period size: 23 Copynumber: 3.5 Consensus size: 23
39755847 TAAAAACCCT
*
39755857 AAACTCTAACCTAATTTAATTAA
1 AAACCCTAACCTAATTTAATTAA
39755880 AAACCCTAACTCTAACCTAATTTAATTAA
1 AAA--C---C-CTAACCTAATTTAATTAA
39755909 AAACCCTAACCTAATTTAATTAA
1 AAACCCTAACCTAATTTAATTAA
39755932 AAACCCTAACC
1 AAACCCTAACC
39755943 CTAACCTAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
23 32 0.57
24 1 0.02
25 1 0.02
27 1 0.02
29 21 0.38
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (23 bp):
AAACCCTAACCTAATTTAATTAA
Found at i:39759676 original size:124 final size:124
Alignment explanation
Indices: 39759456--39759735 Score: 481
Period size: 124 Copynumber: 2.3 Consensus size: 124
39759446 CCACGAGGGC
*
39759456 GCGATTTTATACTATTTGCTCAGAAACGTTAAAAAAAATTATTTCTTACATGACCAACTGTAGCG
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCG
*
39759521 AAATCGCGTCCACAAGGGCACGATTTCACAATTTCTTCTCAGATAGCATCCTAGTAGAA
66 AAATCGCGTCCACAAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
* * *
39759580 GCGATTTTATATTATTTGCTCACAAACGTCAAAAAAAATTATTTTTTACATGACCAACTGTAGCG
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCG
* *
39759645 AAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTATAA
66 AAATCGCGTCCACAAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
39759704 GCGATTTTATACTATTTGAC-CAGAAACGTCAA
1 GCGATTTTATACTATTTG-CTCAGAAACGTCAA
39759736 CTCGAAATAA
Statistics
Matches: 146, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
124 145 0.99
125 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (124 bp):
GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCG
AAATCGCGTCCACAAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
Found at i:39762908 original size:11 final size:12
Alignment explanation
Indices: 39762892--39762924 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
39762882 CAGTTTGACT
39762892 ATTAAATAAA-A
1 ATTAAATAAATA
39762903 ATTAAATAAATA
1 ATTAAATAAATA
39762915 ATTAAA-AAAT
1 ATTAAATAAAT
39762925 TAAAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
ATTAAATAAATA
Found at i:39762929 original size:26 final size:25
Alignment explanation
Indices: 39762895--39762945 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
39762885 TTTGACTATT
* *
39762895 AAATAAAAATTAAATAAATAATTAAA
1 AAATAAAAAATAAAAAAAT-ATTAAA
*
39762921 AAATTAAAAATAAAAAAATATTAAA
1 AAATAAAAAATAAAAAAATATTAAA
39762946 CCAGTTCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (25 bp):
AAATAAAAAATAAAAAAATATTAAA
Found at i:39774624 original size:54 final size:54
Alignment explanation
Indices: 39774566--39774668 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
39774556 TTATAATTTA
* *
39774566 TTTTTTAGTCACTCAACTATG-AAAATTACAAAATGGTCATTCAACTATTAGTAT
1 TTTTTTA-TCACTCAAATATGAAAAATTACAAAATGGTCACTCAACTATTAGTAT
* * *
39774620 TTTTTTATCACTCAAATATGAAAAATTATAGAATGGTCACTCAATTATT
1 TTTTTTATCACTCAAATATGAAAAATTACAAAATGGTCACTCAACTATT
39774669 TAATTTTGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 12 0.28
54 31 0.72
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (54 bp):
TTTTTTATCACTCAAATATGAAAAATTACAAAATGGTCACTCAACTATTAGTAT
Found at i:39778747 original size:29 final size:29
Alignment explanation
Indices: 39778715--39778777 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
39778705 TCATGTGTAT
* *
39778715 AATTGT-ACTAAATCAAAGTTCATGTATCA
1 AATTGTAACTAAACCAAAGTTCATATAT-A
*
39778744 AATTGTAAATTAAACCAAAGTTCATATATA
1 AATTGT-AACTAAACCAAAGTTCATATATA
39778774 AATT
1 AATT
39778778 TGATATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 6 0.21
30 5 0.17
31 18 0.62
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (29 bp):
AATTGTAACTAAACCAAAGTTCATATATA
Found at i:39780317 original size:27 final size:28
Alignment explanation
Indices: 39780268--39780320 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
39780258 AAAAAATCAA
* *
39780268 CTTTTAAGGGGCTCAAAAGTTTTTTTAG
1 CTTTTAAGAGCCTCAAAAGTTTTTTTAG
*
39780296 CTTTTAAGAGCCT-AAAATTTTTTTT
1 CTTTTAAGAGCCTCAAAAGTTTTTTT
39780321 TACCAACTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.47
Consensus pattern (28 bp):
CTTTTAAGAGCCTCAAAAGTTTTTTTAG
Found at i:39780373 original size:32 final size:32
Alignment explanation
Indices: 39780296--39780376 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
39780286 GTTTTTTTAG
* *
39780296 CTTTTAAGAGCCT-AAAATTTTTTTTTACCAA
1 CTTTTAAGAACCTAAAAATTTTTTTCTACCAA
* * *
39780327 CTTTTGAGGGACCTAAAAATTTTTTTCT-CTAA
1 CTTTT-AAGAACCTAAAAATTTTTTTCTACCAA
39780359 CTTTTAAAGAACCTAAAA
1 CTTTT-AAGAACCTAAAA
39780377 CTCCATTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
31 5 0.12
32 23 0.57
33 12 0.30
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.41
Consensus pattern (32 bp):
CTTTTAAGAACCTAAAAATTTTTTTCTACCAA
Found at i:39789651 original size:2 final size:2
Alignment explanation
Indices: 39789644--39789668 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39789634 TGAAGGAAGA
39789644 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39789669 GCAGGTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39803686 original size:25 final size:26
Alignment explanation
Indices: 39803652--39803705 Score: 92
Period size: 27 Copynumber: 2.1 Consensus size: 26
39803642 AGTACCAAAA
39803652 GTCTGCCGTA-TTGGCACGTTTCTTT
1 GTCTGCCGTATTTGGCACGTTTCTTT
39803677 GTCTGCCGTATTTTGGCACGTTTCTTT
1 GTCTGCCGTA-TTTGGCACGTTTCTTT
39803704 GT
1 GT
39803706 TTTTCTAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 10 0.37
27 17 0.63
ACGTcount: A:0.07, C:0.22, G:0.24, T:0.46
Consensus pattern (26 bp):
GTCTGCCGTATTTGGCACGTTTCTTT
Found at i:39811706 original size:13 final size:13
Alignment explanation
Indices: 39811688--39811728 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
39811678 CTCAATTTTC
39811688 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
39811701 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
* *
39811714 TC-CTTCTTTCCT
1 TCTTTTCTTTCTT
39811726 TCT
1 TCT
39811729 CTGTTTCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TCTTTTCTTTCTT
Found at i:39831843 original size:25 final size:25
Alignment explanation
Indices: 39831825--39831954 Score: 88
Period size: 25 Copynumber: 5.2 Consensus size: 25
39831815 GAAGCTTTAG
39831825 AGAGCCA-TTAATCGGGAAGCTCATA
1 AGAGCCAGTT-ATCGGGAAGCTCATA
**
39831850 AGAGCCAGTTATCGGGAAGCTCCGA
1 AGAGCCAGTTATCGGGAAGCTCATA
* **
39831875 AGAGCCAATTAT-GGAGAAGCTCGCA
1 AGAGCCAGTTATCGG-GAAGCTCATA
* * *
39831900 GGAACCA-TATAAT-GGGAAGCTCGTA
1 AGAGCCAGT-T-ATCGGGAAGCTCATA
** * *
39831925 AGAGCCAAATATCGGGACGCTTATA
1 AGAGCCAGTTATCGGGAAGCTCATA
39831950 AGAGC
1 AGAGC
39831955 TGTGGTGTGT
Statistics
Matches: 85, Mismatches: 14, Indels: 12
0.77 0.13 0.11
Matches are distributed among these distances:
24 5 0.06
25 74 0.87
26 6 0.07
ACGTcount: A:0.35, C:0.20, G:0.28, T:0.18
Consensus pattern (25 bp):
AGAGCCAGTTATCGGGAAGCTCATA
Found at i:39834990 original size:2 final size:2
Alignment explanation
Indices: 39834985--39835016 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39834975 TTTTCCAGGG
39834985 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39835017 CTTTCAGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:39842334 original size:103 final size:103
Alignment explanation
Indices: 39842155--39842351 Score: 274
Period size: 103 Copynumber: 1.9 Consensus size: 103
39842145 TATCAAGACC
* * *
39842155 GTATCAATACTTTGTAGGTTTTGTGAGAAACATAATGCTATTTTGGTATCGCTTTTAAGAATAGG
1 GTATCAATACTTTGTAGGTTTTGTGAAAAACATAATACCATTTTGGTATCGCTTTTAAGAATAGG
*
39842220 TATCGATAATTCAGAAAATATCGATACTTAATCAAAAG
66 TATCGATAATTCAGAAAATATCAATACTTAATCAAAAG
* *
39842258 GTATCTATACTTAT-TAGGTTTTGTGAAAAACGA-AATACCATTTTGGTATCGTTTTTAAGAGA-
1 GTATCAATACTT-TGTAGGTTTTGTGAAAAAC-ATAATACCATTTTGGTATCGCTTTTAAGA-AT
* *
39842320 AGGTATTGATAATTCATAAAATATCAATACTT
63 AGGTATCGATAATTCAGAAAATATCAATACTT
39842352 GGCCAAAAAG
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
103 80 0.96
104 3 0.04
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (103 bp):
GTATCAATACTTTGTAGGTTTTGTGAAAAACATAATACCATTTTGGTATCGCTTTTAAGAATAGG
TATCGATAATTCAGAAAATATCAATACTTAATCAAAAG
Found at i:39848934 original size:43 final size:43
Alignment explanation
Indices: 39848854--39848936 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 43
39848844 GACTCCGATA
*
39848854 TGTGTTTTTGTGTAAGACCACGTCTGGGATGTCGGCATCGACT
1 TGTGTTTTTGTGTAAGACCACGTCTGGGAAGTCGGCATCGACT
39848897 TGTGTTTTTGTGTAAGACC-CTGTCTGGGACAGT-GGCATCG
1 TGTGTTTTTGTGTAAGACCAC-GTCTGGGA-AGTCGGCATCG
39848937 GTATGTGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
42 1 0.03
43 34 0.92
44 2 0.05
ACGTcount: A:0.16, C:0.18, G:0.31, T:0.35
Consensus pattern (43 bp):
TGTGTTTTTGTGTAAGACCACGTCTGGGAAGTCGGCATCGACT
Found at i:39849324 original size:47 final size:47
Alignment explanation
Indices: 39849234--39849548 Score: 449
Period size: 47 Copynumber: 7.0 Consensus size: 47
39849224 TAAAAAAAAT
*
39849234 TATATATGTATATGCTGTCAA-TTTTGATGTACAAATGCAGTCCAAA
1 TATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAAA
*
39849280 TATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAAT
1 TATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAAA
* * * * *
39849327 TATATAAGTATATGCTGTTAATTTTTTATGTAT-AAGGCAGTCCAAT
1 TATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAAA
* *
39849373 TATATATGTATATGCTGTCAATTTTTGACGTATAAATGCAGTCCAAT
1 TATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAAA
*
39849420 TATATATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAAA
1 TATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAAA
39849467 TATATATGTATATGCTGTCAA--TTT--T-T-T--AT---GTCCAAA
1 TATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAAA
39849503 TATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAA
1 TATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAA
39849549 TTTTGTAAAT
Statistics
Matches: 241, Mismatches: 15, Indels: 25
0.86 0.05 0.09
Matches are distributed among these distances:
36 28 0.12
38 3 0.01
39 2 0.01
40 1 0.00
41 1 0.00
42 2 0.01
43 1 0.00
44 2 0.01
45 3 0.01
46 62 0.26
47 136 0.56
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (47 bp):
TATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAAA
Found at i:39849390 original size:93 final size:94
Alignment explanation
Indices: 39849231--39849548 Score: 464
Period size: 93 Copynumber: 3.5 Consensus size: 94
39849221 TTTTAAAAAA
39849231 AATTATATATGTATATGCTGTCAA-TTTTGATGTACAAATGCAGTCCAAATATATATGTATATGC
1 AATTATATATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAAATATATATGTATATGC
39849295 TGTCAATTTTTGATGTATAAATGCAGTCC
66 TGTCAATTTTTGATGTATAAATGCAGTCC
* * * * * *
39849324 AATTATATAAGTATATGCTGTTAATTTTTTATGTA-TAAGGCAGTCCAATTATATATGTATATGC
1 AATTATATATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAAATATATATGTATATGC
*
39849388 TGTCAATTTTTGACGTATAAATGCAGTCC
66 TGTCAATTTTTGATGTATAAATGCAGTCC
39849417 AATTATATATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAAATATATATGTATATGC
1 AATTATATATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAAATATATATGTATATGC
39849482 TGTCAA--TTT--T-T-T--AT---GTCC
66 TGTCAATTTTTGATGTATAAATGCAGTCC
* *
39849500 AAATATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAA
1 AATTATATATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAA
39849549 TTTTGTAAAT
Statistics
Matches: 207, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
83 51 0.25
86 2 0.01
88 1 0.00
89 1 0.00
92 3 0.01
93 108 0.52
94 41 0.20
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (94 bp):
AATTATATATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAAATATATATGTATATGC
TGTCAATTTTTGATGTATAAATGCAGTCC
Found at i:39849482 original size:140 final size:130
Alignment explanation
Indices: 39849231--39849550 Score: 471
Period size: 140 Copynumber: 2.4 Consensus size: 130
39849221 TTTTAAAAAA
* *
39849231 AATTATATATGTATATGCTGTCAA-TTTTGATGTACAAATGCAGTCCAAATATATATGTATATGC
1 AATTATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAATTATATATGTATATGC
* * *
39849295 TGTCAATTTTTGATGTATAAATGCAGTCCAATTATATAAGTATATGCTGTTAATTTTTTATGTAT
66 TGTCAATTTTTGATGTACAAATGCAGTCCAAATATATAAGTATATGCTGTCAA--TTTT-T-TAT
39849360 AAGGCAGTCC
127 ------GTCC
*
39849370 AATTATATATGTATATGCTGTCAATTTTTGACGTATAAATGCAGTCCAATTATATATGTATATGC
1 AATTATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAATTATATATGTATATGC
*
39849435 TGTCAATTTTTGATGTACAAATGCAGTCCAAATATATATGTATATGCTGTCAATTTTTTATGTCC
66 TGTCAATTTTTGATGTACAAATGCAGTCCAAATATATAAGTATATGCTGTCAATTTTTTATGTCC
*
39849500 AAATATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAATT
1 AATTATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAATT
39849551 TTGTAAATAT
Statistics
Matches: 171, Mismatches: 9, Indels: 11
0.90 0.05 0.06
Matches are distributed among these distances:
130 53 0.31
136 3 0.02
137 1 0.01
138 4 0.02
139 24 0.14
140 86 0.50
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (130 bp):
AATTATATATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAATTATATATGTATATGC
TGTCAATTTTTGATGTACAAATGCAGTCCAAATATATAAGTATATGCTGTCAATTTTTTATGTCC
Found at i:39849500 original size:36 final size:36
Alignment explanation
Indices: 39849460--39849533 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
39849450 TACAAATGCA
*
39849460 GTCCAAATATATATGTATATGCTGTCAATTTTTTAT
1 GTCCAAATATATATGTATATGCTGTCAATTTTTGAT
39849496 GTCCAAATATATATGTATATGCTGTCAATTTTTGAT
1 GTCCAAATATATATGTATATGCTGTCAATTTTTGAT
39849532 GT
1 GT
39849534 ATAAATGCAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (36 bp):
GTCCAAATATATATGTATATGCTGTCAATTTTTGAT
Found at i:39849912 original size:12 final size:12
Alignment explanation
Indices: 39849895--39849919 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39849885 TATCTGTTTA
39849895 TATATATATATG
1 TATATATATATG
39849907 TATATATATATG
1 TATATATATATG
39849919 T
1 T
39849920 GGAATGAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TATATATATATG
Found at i:39850159 original size:25 final size:24
Alignment explanation
Indices: 39850083--39850173 Score: 101
Period size: 25 Copynumber: 3.7 Consensus size: 24
39850073 GCCTTGTAAA
*
39850083 GGGAAGCTCATAAGAGCCATAATC
1 GGGAAGCTCATAAGAGCCATTATC
* * * *
39850107 GGGAAGTTCACAAGAACCATATAAC
1 GGGAAGCTCATAAGAGCCAT-TATC
*
39850132 GGGAAGCTCATGAGAGCCAATTATC
1 GGGAAGCTCATAAGAGCC-ATTATC
*
39850157 GGGATGCTCATAAGAGC
1 GGGAAGCTCATAAGAGC
39850174 TACTAACTGG
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
24 17 0.32
25 34 0.64
26 2 0.04
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (24 bp):
GGGAAGCTCATAAGAGCCATTATC
Found at i:39851739 original size:21 final size:21
Alignment explanation
Indices: 39851710--39851766 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
39851700 AATTCTGGAA
* *
39851710 TTTTAAAAAATTATTTTGAAT
1 TTTTGAAAAATTATTTTAAAT
39851731 TTTTGAAAAATTATTTTAAAT
1 TTTTGAAAAATTATTTTAAAT
39851752 TTTTGAAAAATTATT
1 TTTTGAAAAATTATT
39851767 GTTTGATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTTGAAAAATTATTTTAAAT
Found at i:39851776 original size:21 final size:21
Alignment explanation
Indices: 39851710--39851777 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
39851700 AATTCTGGAA
*
39851710 TTTTAAAAAATTA-TTTTGAAT
1 TTTTGAAAAATTATTTTTG-AT
**
39851731 TTTTGAAAAATTATTTTAAAT
1 TTTTGAAAAATTATTTTTGAT
39851752 TTTTGAAAAATTATTGTTTGAT
1 TTTTGAAAAATTATT-TTTGAT
39851774 TTTT
1 TTTT
39851778 TTTGTAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
21 29 0.73
22 11 0.28
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTGAAAAATTATTTTTGAT
Found at i:39853834 original size:31 final size:30
Alignment explanation
Indices: 39853796--39853865 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
39853786 GGTTTGGAGT
*
39853796 TTTTAAAAATTTTGAAA-AATCTAATTAAAAA
1 TTTTAAAAACTTTGAAAGAAT-TAATT-AAAA
*
39853827 TTTTAAAAACTTTGAAAGGATTAATTAAAA
1 TTTTAAAAACTTTGAAAGAATTAATTAAAA
39853857 TTTCTAAAA
1 TTT-TAAAA
39853866 TTGAAGGGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 7 0.20
31 26 0.74
32 2 0.06
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (30 bp):
TTTTAAAAACTTTGAAAGAATTAATTAAAA
Found at i:39857794 original size:6 final size:6
Alignment explanation
Indices: 39857783--39857817 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
39857773 GTTTTAAGCA
39857783 TATATG TATATG TATATG TATATG TATATG TATAT
1 TATATG TATATG TATATG TATATG TATATG TATAT
39857818 ATGAAAATCA
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:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:39861813 original size:27 final size:27
Alignment explanation
Indices: 39861783--39861838 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
39861773 TTTAAGGGCC
39861783 AAAATTTTTTTT-TACCAACTTTTAAGT
1 AAAATTTTTTTTCT-CCAACTTTTAAGT
39861810 AAAATTTTTTTTCTCCAACTTTTAAGT
1 AAAATTTTTTTTCTCCAACTTTTAAGT
39861837 AA
1 AA
39861839 CTTAAAACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.04, T:0.50
Consensus pattern (27 bp):
AAAATTTTTTTTCTCCAACTTTTAAGT
Found at i:39873595 original size:11 final size:11
Alignment explanation
Indices: 39873570--39873638 Score: 67
Period size: 11 Copynumber: 6.5 Consensus size: 11
39873560 ATTTTTTAAA
39873570 TTTTAAAATACTT
1 TTTTAAAATA--T
39873583 TTTTAAAAT-T
1 TTTTAAAATAT
*
39873593 TTTT--TA-AT
1 TTTTAAAATAT
39873601 T-TTAAAATAT
1 TTTTAAAATAT
39873611 TTTTAAAATAT
1 TTTTAAAATAT
*
39873622 TTTTAAAATAC
1 TTTTAAAATAT
39873633 TTTTAA
1 TTTTAA
39873639 TTTTTTTAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
7 2 0.04
8 3 0.06
9 1 0.02
10 8 0.17
11 25 0.52
13 9 0.19
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:39873596 original size:30 final size:28
Alignment explanation
Indices: 39873560--39873628 Score: 102
Period size: 30 Copynumber: 2.4 Consensus size: 28
39873550 TTATTTATTT
39873560 ATTTTTTAAATTTTAAAATACTTTTTTAAA
1 ATTTTTTAAATTTTAAAATA--TTTTTAAA
*
39873590 ATTTTTTTAATTTTAAAATATTTTTAAA
1 ATTTTTTAAATTTTAAAATATTTTTAAA
39873618 ATATTTTTAAA
1 AT-TTTTTAAA
39873629 ATACTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 10 0.28
29 7 0.19
30 19 0.53
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTTTTTAAATTTTAAAATATTTTTAAA
Found at i:39873605 original size:17 final size:17
Alignment explanation
Indices: 39873583--39873616 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39873573 TAAAATACTT
*
39873583 TTTTAAAATTTTTTTAA
1 TTTTAAAATATTTTTAA
39873600 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
39873617 AATATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:39873666 original size:48 final size:51
Alignment explanation
Indices: 39873570--39873674 Score: 162
Period size: 48 Copynumber: 2.1 Consensus size: 51
39873560 ATTTTTTAAA
*
39873570 TTTTAAAATACTTTTTTAAAATTTTTTTAATTTTAAAATATTTTTAAAAT-AT
1 TTTTAAAATAC-TTTTT-AAATTTTTTTAATTTTAAAATATTATTAAAATAAT
39873622 TTTTAAAATAC-TTTT-AATTTTTTTAATTTTAAAATATTATTAAAATAAT
1 TTTTAAAATACTTTTTAAATTTTTTTAATTTTAAAATATTATTAAAATAAT
39873671 TTTT
1 TTTT
39873675 TTATTTTTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
48 30 0.59
49 6 0.12
50 4 0.08
52 11 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (51 bp):
TTTTAAAATACTTTTTAAATTTTTTTAATTTTAAAATATTATTAAAATAAT
Found at i:39873682 original size:37 final size:34
Alignment explanation
Indices: 39873611--39873708 Score: 103
Period size: 37 Copynumber: 2.8 Consensus size: 34
39873601 TTTAAAATAT
* *
39873611 TTTTAAAATATTTTTAAAATACTTTTAATTTTTTTAA
1 TTTTAAAATA-TTTTAAAATAATTTT--TTTTTTTTA
*
39873648 TTTTAAAATATTATTAAAATAATTTTTTTATTTTTG
1 TTTTAAAATATT-TTAAAATAATTTTTTT-TTTTTA
39873684 TTTT--AAT-TTTTAAAATAATTTTTTT
1 TTTTAAAATATTTTAAAATAATTTTTTT
39873709 GGTATTTATT
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
32 16 0.29
33 2 0.04
34 3 0.05
35 3 0.05
36 10 0.18
37 22 0.39
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (34 bp):
TTTTAAAATATTTTAAAATAATTTTTTTTTTTTA
Found at i:39873721 original size:32 final size:32
Alignment explanation
Indices: 39873661--39873721 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
39873651 TAAAATATTA
* *
39873661 TTAAAATAATTTTTTTATTTTTGTTTTAATTT
1 TTAAAATAATTTTTTTATATTTGATTTAATTT
*
39873693 TTAAAATAATTTTTTTGGTATTT-ATTTAA
1 TTAAAATAATTTTTTT-ATATTTGATTTAA
39873722 AAAAACGGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 21 0.84
33 4 0.16
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (32 bp):
TTAAAATAATTTTTTTATATTTGATTTAATTT
Found at i:39874983 original size:31 final size:29
Alignment explanation
Indices: 39874943--39875012 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
39874933 ATTTTTTTTG
* *
39874943 AGTTAAATTTAATTATCAATCTTTTAACAAA
1 AGTTGAATTTAATCATCAA-CTTTTAA-AAA
* * *
39874974 AGTTGAATTTGATCCTCAACTTTTCAAAA
1 AGTTGAATTTAATCATCAACTTTTAAAAA
39875003 AGTTGAATTT
1 AGTTGAATTT
39875013 TTGTTTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 13 0.38
30 6 0.18
31 15 0.44
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (29 bp):
AGTTGAATTTAATCATCAACTTTTAAAAA
Found at i:39880202 original size:27 final size:27
Alignment explanation
Indices: 39880172--39880240 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
39880162 CGCCTATCTC
39880172 AGAGGCGCCAATGGTGGTCCCAATG-TG
1 AGAGGCGCCAATGGTGGTCCC-ATGTTG
* * *
39880199 AGAGGCGCCATTAGTGGTGCCATGTTG
1 AGAGGCGCCAATGGTGGTCCCATGTTG
*
39880226 AAAGGCGCCAATGGT
1 AGAGGCGCCAATGGT
39880241 CTGATTTTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 3 0.09
27 32 0.91
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.20
Consensus pattern (27 bp):
AGAGGCGCCAATGGTGGTCCCATGTTG
Found at i:39880323 original size:21 final size:19
Alignment explanation
Indices: 39880298--39880343 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
39880288 CAGAGAAACG
* *
39880298 GAAGAAATAAGAAGGAAGACA
1 GAAGAAAAAAAAAGGAA-A-A
39880319 GAAGAAAAAAAAAGGAAAA
1 GAAGAAAAAAAAAGGAAAA
39880338 GAAGAA
1 GAAGAA
39880344 GAAGGATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 1 0.04
21 15 0.65
ACGTcount: A:0.70, C:0.02, G:0.26, T:0.02
Consensus pattern (19 bp):
GAAGAAAAAAAAAGGAAAA
Found at i:39882332 original size:44 final size:46
Alignment explanation
Indices: 39882267--39882395 Score: 138
Period size: 49 Copynumber: 2.7 Consensus size: 46
39882257 ATGCACTAAT
* * *
39882267 GAACAGAGAGCACTAAAGTGCTATA-CAGAGAGCA-CAGATGTGCTA
1 GAACAGAGAGCACTAACGTGCTAAATCAGAGAGCACCA-ACGTGCTA
*
39882312 -AACAGAGAGCACTGACGTGCTAAAATCAGAGAGCACCAACGTGCTA
1 GAACAGAGAGCACTAACGTGCT-AAATCAGAGAGCACCAACGTGCTA
*
39882358 GTAGTCAGAGAGCACTAACGTGCTAATAATCAGAGAGC
1 G-A-ACAGAGAGCACTAACGTGCT-A-AATCAGAGAGC
39882396 GCGCTAAAGT
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
44 19 0.27
45 2 0.03
46 16 0.23
47 2 0.03
48 1 0.01
49 20 0.28
50 11 0.15
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.16
Consensus pattern (46 bp):
GAACAGAGAGCACTAACGTGCTAAATCAGAGAGCACCAACGTGCTA
Found at i:39882371 original size:25 final size:24
Alignment explanation
Indices: 39882270--39882395 Score: 136
Period size: 22 Copynumber: 5.3 Consensus size: 24
39882260 CACTAATGAA
*
39882270 CAGAGAGCACTAAAGTGCTAT-A-
1 CAGAGAGCACTAACGTGCTATAAT
*
39882292 CAGAGAGCAC-AGATGTGCTA-AA-
1 CAGAGAGCACTA-ACGTGCTATAAT
* *
39882314 CAGAGAGCACTGACGTGCTAAAAT
1 CAGAGAGCACTAACGTGCTATAAT
* *
39882338 CAGAGAGCACCAACGTGCTAGTAGT
1 CAGAGAGCACTAACGTGCTA-TAAT
39882363 CAGAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCT-ATAAT
39882388 CAGAGAGC
1 CAGAGAGC
39882396 GCGCTAAAGT
Statistics
Matches: 88, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
21 1 0.01
22 35 0.40
23 2 0.02
24 18 0.20
25 31 0.35
26 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (24 bp):
CAGAGAGCACTAACGTGCTATAAT
Found at i:39883480 original size:16 final size:16
Alignment explanation
Indices: 39883459--39883495 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
39883449 GTTTTATCTA
39883459 TATAATAATATAATAT
1 TATAATAATATAATAT
39883475 TATAATAATATAATAT
1 TATAATAATATAATAT
*
39883491 AATAA
1 TATAA
39883496 CTTACTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAATAATATAATAT
Found at i:39883495 original size:8 final size:8
Alignment explanation
Indices: 39883458--39883489 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
39883448 TGTTTTATCT
39883458 ATATAATA
1 ATATAATA
39883466 ATATAATA
1 ATATAATA
*
39883474 TTATAATA
1 ATATAATA
39883482 ATATAATA
1 ATATAATA
39883490 TAATAACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAATA
Found at i:39883495 original size:13 final size:13
Alignment explanation
Indices: 39883458--39883538 Score: 53
Period size: 13 Copynumber: 6.1 Consensus size: 13
39883448 TGTTTTATCT
39883458 ATATAATAATATAA
1 ATATAATAATAT-A
39883472 TATTATAATAATATA
1 -A-TATAATAATATA
39883487 ATATAATAACT-TA
1 ATATAATAA-TATA
* *
39883500 CT-TATTAAT-TA
1 ATATAATAATATA
*
39883511 AT-TAAATAACATA
1 ATAT-AATAATATA
39883524 ATATAATATATATA
1 ATATAATA-ATATA
39883538 A
1 A
39883539 CTTAAATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
11 5 0.09
12 9 0.17
13 19 0.35
14 8 0.15
15 2 0.04
16 11 0.20
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATAATAATATA
Found at i:39883555 original size:37 final size:39
Alignment explanation
Indices: 39883479--39883555 Score: 88
Period size: 42 Copynumber: 1.9 Consensus size: 39
39883469 TAATATTATA
*
39883479 ATAATATAATATAATAACTTACTTATTAATTAATTAAATAAC
1 ATAATATAATATAATAACTTAC-AATTAA-TAA-TAAATAAC
39883521 ATAATATAATATATATAACTTA-AATTAA-AA-AAATA
1 ATAATATAATATA-ATAACTTACAATTAATAATAAATA
39883556 TCTTAGATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
37 5 0.15
39 2 0.06
41 5 0.15
42 13 0.39
43 8 0.24
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (39 bp):
ATAATATAATATAATAACTTACAATTAATAATAAATAAC
Found at i:39887785 original size:60 final size:60
Alignment explanation
Indices: 39887711--39887832 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
39887701 ATACTAAACT
* * * * *
39887711 AAACACAACAATTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
39887771 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
39887831 AA
1 AA
39887833 TATTCATACA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 4 0.07
60 52 0.93
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:39887998 original size:61 final size:61
Alignment explanation
Indices: 39887855--39887998 Score: 261
Period size: 61 Copynumber: 2.4 Consensus size: 61
39887845 AAATTACAAT
*
39887855 ATTACAATATTCATACAAAATACTAATCCAAAACTATAAAAACAAAATTAATTATAAAATA
1 ATTACAATATTCATACAAAATTCTAATCCAAAACTATAAAAACAAAATTAATTATAAAATA
* *
39887916 ATTACAATATTCATACAAAATTCTCATCCAAAACTATAAATACAAAATTAATTATAAAATA
1 ATTACAATATTCATACAAAATTCTAATCCAAAACTATAAAAACAAAATTAATTATAAAATA
39887977 ATTACAATATTCATACAAAATT
1 ATTACAATATTCATACAAAATT
39887999 ACAATATTCA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 80 1.00
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.31
Consensus pattern (61 bp):
ATTACAATATTCATACAAAATTCTAATCCAAAACTATAAAAACAAAATTAATTATAAAATA
Found at i:39888000 original size:19 final size:19
Alignment explanation
Indices: 39887976--39888037 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
39887966 ATTATAAAAT
39887976 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
39887995 AATTACAATATTCATACAAAA
1 AATTACAATATTCATAC--AA
*
39888016 AATTAGAATATTCATACAA
1 AATTACAATATTCATACAA
39888035 AAT
1 AAT
39888038 ACTAATCCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 22 0.55
21 18 0.45
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.31
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Done.