Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 122 of 276
Found at i:39205671 original size:63 final size:63
Alignment explanation
Indices: 39205453--39205714 Score: 211
Period size: 63 Copynumber: 4.2 Consensus size: 63
39205443 TTTAGCACAG
* * * ** * * * * *
39205453 GCAATCATTCCCTACATCAATACATACAGCAATAGTTTATTTTCCACAAGCACCTCAGCACTC
1 GCAATCATTCCCTACACCAACACATACATCACCAATTTATTTTACACAAGCACCACAACACGC
* * * * ** **
39205516 GCAATCATTCCCTACATCAACACATACAACACCAATTTATCTTCCACAAGCATTACTGCACGC
1 GCAATCATTCCCTACACCAACACATACATCACCAATTTATTTTACACAAGCACCACAACACGC
** * ** * * * *
39205579 GCAATCATTTACTACTCTGACACATTCATCACTAATTTATTTTACATAAGAACCACAACACGC
1 GCAATCATTCCCTACACCAACACATACATCACCAATTTATTTTACACAAGCACCACAACACGC
* * * *
39205642 GCAATCATTCCCTACACCAATACAGT-CATCACCACTTTATTTGACATAAGCACCACAACACGC
1 GCAATCATTCCCTACACCAACACA-TACATCACCAATTTATTTTACACAAGCACCACAACACGC
**
39205705 AAAATCATTC
1 GCAATCATTC
39205715 ACTGCACTGA
Statistics
Matches: 158, Mismatches: 40, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
63 157 0.99
64 1 0.01
ACGTcount: A:0.35, C:0.32, G:0.07, T:0.26
Consensus pattern (63 bp):
GCAATCATTCCCTACACCAACACATACATCACCAATTTATTTTACACAAGCACCACAACACGC
Found at i:39210907 original size:14 final size:12
Alignment explanation
Indices: 39210880--39210955 Score: 61
Period size: 11 Copynumber: 6.2 Consensus size: 12
39210870 ATTCCAAAAA
*
39210880 TAATA-TTATTT
1 TAATATTTATAT
39210891 TAATATTTTAATAT
1 TAATA-TTT-ATAT
39210905 TAA-ATTTA-ATT
1 TAATATTTATA-T
39210916 TAATATTTATAT
1 TAATATTTATAT
39210928 TAATAGTATTATAT
1 TAATA-T-TTATAT
*
39210942 TAAT-TTAATAT
1 TAATATTTATAT
39210953 TAA
1 TAA
39210956 AGTGATTATC
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
10 1 0.02
11 18 0.33
12 15 0.27
13 5 0.09
14 16 0.29
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (12 bp):
TAATATTTATAT
Found at i:39210928 original size:31 final size:31
Alignment explanation
Indices: 39210893--39210996 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 31
39210883 TATTATTTTA
39210893 ATATTTTAATATTAAATTTAATTTAATATTT
1 ATATTTTAATATTAAATTTAATTTAATATTT
* * *
39210924 ATATTAATAGTATTATA-TTAATTTAATATTAAAGT
1 ATATT-TTAATATTAAATTTAATTTAATATT----T
* * *
39210959 GATTATCTTAATGTTAAATTTAATTTAATGTTT
1 -A-TATTTTAATATTAAATTTAATTTAATATTT
39210992 ATATT
1 ATATT
39210997 GTAGATAAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
31 21 0.38
32 9 0.16
33 1 0.02
35 1 0.02
36 8 0.15
37 15 0.27
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (31 bp):
ATATTTTAATATTAAATTTAATTTAATATTT
Found at i:39210949 original size:5 final size:6
Alignment explanation
Indices: 39210880--39210955 Score: 52
Period size: 6 Copynumber: 12.5 Consensus size: 6
39210870 ATTCCAAAAA
* *
39210880 TAATAT T-ATTT TAATATTT TAATAT TAA-ATT TAAT-T TAATAT TTATAT
1 TAATAT TAATAT TAATA--T TAATAT TAATA-T TAATAT TAATAT TAATAT
*
39210928 TAATAGT ATTATAT TAAT-T TAATAT TAA
1 TAATA-T -TAATAT TAATAT TAATAT TAA
39210956 AGTGATTATC
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
5 15 0.27
6 28 0.51
7 2 0.04
8 10 0.18
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (6 bp):
TAATAT
Found at i:39210953 original size:25 final size:25
Alignment explanation
Indices: 39210920--39210975 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
39210910 TTAATTTAAT
39210920 ATTT-ATATTAATAGT-ATTATATTA
1 ATTTAATATTAA-AGTGATTATATTA
*
39210944 ATTTAATATTAAAGTGATTATCTTA
1 ATTTAATATTAAAGTGATTATATTA
39210969 ATGTTAA
1 AT-TTAA
39210976 ATTTAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 7 0.25
25 17 0.61
26 4 0.14
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (25 bp):
ATTTAATATTAAAGTGATTATATTA
Found at i:39212282 original size:23 final size:23
Alignment explanation
Indices: 39212254--39212357 Score: 145
Period size: 23 Copynumber: 4.5 Consensus size: 23
39212244 CTACACAAAG
39212254 AACATTTAAACACTTCAATTTAC
1 AACATTTAAACACTTCAATTTAC
* *
39212277 AGCATTTAAATACTTCAATTTAC
1 AACATTTAAACACTTCAATTTAC
*
39212300 AAAATTTAAACACTTCAATTTAC
1 AACATTTAAACACTTCAATTTAC
* * *
39212323 AATATCTACACACTTCAATTTAC
1 AACATTTAAACACTTCAATTTAC
*
39212346 AGCATTTAAACA
1 AACATTTAAACA
39212358 GCAGCAACCA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (23 bp):
AACATTTAAACACTTCAATTTAC
Found at i:39215690 original size:21 final size:21
Alignment explanation
Indices: 39215666--39215710 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
39215656 GTCAATATAC
39215666 ATGACAATCTATTGGAAGAAG
1 ATGACAATCTATTGGAAGAAG
39215687 ATGACAATCTATTGGAAGAAG
1 ATGACAATCTATTGGAAGAAG
39215708 ATG
1 ATG
39215711 GAAGCTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.24
Consensus pattern (21 bp):
ATGACAATCTATTGGAAGAAG
Found at i:39216475 original size:72 final size:73
Alignment explanation
Indices: 39216383--39216532 Score: 203
Period size: 72 Copynumber: 2.1 Consensus size: 73
39216373 TTCGGGTATA
* **
39216383 AAATAGAAGAACAGGTTGAGAAAGGCTGAGAAAAAAAAGGAAACTGGGAAAGAAAAGGGAA-TCG
1 AAATAGAAGAACAGGCTGAGAAAGGCTGAGAAAAAAAAGGAAACTGGGAAAGAAAAGAAAATTCG
39216447 GGGGAGAG
66 GGGGAGAG
* * * * * * *
39216455 AAATAGAGGAATAGGCTGAGAATGGCTGAGAAAGAAAAGGAAATTGGGAAAGAAGAGAAAATTGG
1 AAATAGAAGAACAGGCTGAGAAAGGCTGAGAAAAAAAAGGAAACTGGGAAAGAAAAGAAAATTCG
39216520 GGGGAGAG
66 GGGGAGAG
39216528 AAATA
1 AAATA
39216533 AAACGGTGTC
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 52 0.78
73 15 0.22
ACGTcount: A:0.49, C:0.04, G:0.36, T:0.11
Consensus pattern (73 bp):
AAATAGAAGAACAGGCTGAGAAAGGCTGAGAAAAAAAAGGAAACTGGGAAAGAAAAGAAAATTCG
GGGGAGAG
Found at i:39216507 original size:18 final size:18
Alignment explanation
Indices: 39216484--39216520 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
39216474 GAATGGCTGA
*
39216484 GAAAGAAAAGGAAATTGG
1 GAAAGAAAAGAAAATTGG
*
39216502 GAAAGAAGAGAAAATTGG
1 GAAAGAAAAGAAAATTGG
39216520 G
1 G
39216521 GGGAGAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.35, T:0.11
Consensus pattern (18 bp):
GAAAGAAAAGAAAATTGG
Found at i:39216669 original size:40 final size:40
Alignment explanation
Indices: 39216614--39216697 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
39216604 TAAATTGATT
* * * *
39216614 TTTTGTGGCGTTTTTATCATAAACGCTGCTATTGCTTGTC
1 TTTTGCGGCGTTTTTATCATAAACGCCGCTAATGCTTGAC
* *
39216654 TTTTGCGGTGTTTTTATCATAAACGCCGTTAATGCTTGAC
1 TTTTGCGGCGTTTTTATCATAAACGCCGCTAATGCTTGAC
39216694 TTTT
1 TTTT
39216698 TTATAATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.48
Consensus pattern (40 bp):
TTTTGCGGCGTTTTTATCATAAACGCCGCTAATGCTTGAC
Found at i:39217066 original size:17 final size:18
Alignment explanation
Indices: 39217033--39217066 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39217023 TATCTCTTAA
39217033 ATAATTTAAACTATATTG
1 ATAATTTAAACTATATTG
*
39217051 ATAATTTTAA-TATATT
1 ATAATTTAAACTATATT
39217067 AAAATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
ATAATTTAAACTATATTG
Found at i:39217497 original size:14 final size:14
Alignment explanation
Indices: 39217442--39217638 Score: 60
Period size: 14 Copynumber: 13.9 Consensus size: 14
39217432 ACTAATTAAT
*
39217442 CTAAACCTTTAACC
1 CTAAACCTTAAACC
** *
39217456 CATATCCCATAAACC
1 C-TAAACCTTAAACC
* *
39217471 C-AAAACATAAACC
1 CTAAACCTTAAACC
*
39217484 ATAAACCTTAAACCC
1 CTAAACCTTAAA-CC
* * *
39217499 CTAACCCAT-ATCC
1 CTAAACCTTAAACC
** *
39217512 CATAAACCCAAAATC
1 C-TAAACCTTAAACC
* * *
39217527 ATAAATCTTTAACCC
1 CTAAA-CCTTAAACC
*
39217542 CT-AACACTTAACCC
1 CTAAAC-CTTAAACC
*
39217556 CT-AACCTCTAACCC
1 CTAAACCT-TAAACC
39217570 CTAAACCTTAAACC
1 CTAAACCTTAAACC
* *
39217584 CCAACCCTTAAACC
1 CTAAACCTTAAACC
* * * *
39217598 ATAAATCATAATCC
1 CTAAACCTTAAACC
* *
39217612 CTAAACCCATAATCC
1 CTAAA-CCTTAAACC
*
39217627 ATAAACCTTAAA
1 CTAAACCTTAAA
39217639 ATAGTAACTC
Statistics
Matches: 132, Mismatches: 41, Indels: 20
0.68 0.21 0.10
Matches are distributed among these distances:
13 15 0.11
14 75 0.57
15 42 0.32
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (14 bp):
CTAAACCTTAAACC
Found at i:39217541 original size:43 final size:46
Alignment explanation
Indices: 39217451--39217546 Score: 126
Period size: 49 Copynumber: 2.1 Consensus size: 46
39217441 TCTAAACCTT
39217451 TAACCCATATCCCATAAACCCAAAACATAAACCATAAACCTTAAACCCC
1 TAACCCATATCCCATAAACCCAAAACAT--A-CATAAACCTTAAACCCC
* *
39217500 TAACCCATATCCCATAAACCC-AAA-AT-CATAAATCTTTAACCCC
1 TAACCCATATCCCATAAACCCAAAACATACATAAACCTTAAACCCC
39217543 TAAC
1 TAAC
39217547 ACTTAACCCC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
43 19 0.42
47 2 0.04
48 3 0.07
49 21 0.47
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (46 bp):
TAACCCATATCCCATAAACCCAAAACATACATAAACCTTAAACCCC
Found at i:39217595 original size:21 final size:21
Alignment explanation
Indices: 39217482--39217602 Score: 64
Period size: 21 Copynumber: 5.7 Consensus size: 21
39217472 AAAACATAAA
39217482 CCATAAACCTTAAACCCCTAAC
1 CCATAAACCTTAAACCCC-AAC
** * * *
39217504 CCATATCCCATAAACCCAAAA
1 CCATAAACCTTAAACCCCAAC
* * *
39217525 TCATAAATCTTTAACCCCTAAC
1 CCATAAACCTTAAACCCC-AAC
* * * * *
39217547 ACTTAACCCCT-AACCTCTAAC
1 CCATAAACCTTAAACC-CCAAC
*
39217568 CCCTAAACCTTAAACCCCAAC
1 CCATAAACCTTAAACCCCAAC
* *
39217589 CCTTAAACCATAAA
1 CCATAAACCTTAAA
39217603 TCATAATCCC
Statistics
Matches: 70, Mismatches: 26, Indels: 7
0.68 0.25 0.07
Matches are distributed among these distances:
21 43 0.61
22 27 0.39
ACGTcount: A:0.40, C:0.39, G:0.00, T:0.21
Consensus pattern (21 bp):
CCATAAACCTTAAACCCCAAC
Found at i:39217614 original size:42 final size:43
Alignment explanation
Indices: 39217442--39217618 Score: 121
Period size: 42 Copynumber: 4.2 Consensus size: 43
39217432 ACTAATTAAT
* * * *
39217442 CTAAACCTTTAACCCATATCCCATAAACCCA-AAA-CATAAACC
1 CTAAACCTTAAACCCCTAACCCATAAA-CCATAAATCATAATCC
* ** * *
39217484 ATAAACCTTAAACCCCTAACCCATATCCCATAAACCCAAAAT-C
1 CTAAACCTTAAACCCCTAACCCATAAACCATAAA-TCATAATCC
* * * * * * * * *
39217527 ATAAATCTTTAACCCCTAACACTTAACCCCTAACCTC-TAACCC
1 CTAAACCTTAAACCCCTAACCCATAAACCATAA-ATCATAATCC
*
39217570 CTAAACCTTAAACCCC-AACCCTTAAACCATAAATCATAATCC
1 CTAAACCTTAAACCCCTAACCCATAAACCATAAATCATAATCC
39217612 CTAAACC
1 CTAAACC
39217619 CATAATCCAT
Statistics
Matches: 103, Mismatches: 26, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
41 5 0.05
42 51 0.50
43 43 0.42
44 4 0.04
ACGTcount: A:0.42, C:0.37, G:0.00, T:0.21
Consensus pattern (43 bp):
CTAAACCTTAAACCCCTAACCCATAAACCATAAATCATAATCC
Found at i:39217624 original size:15 final size:15
Alignment explanation
Indices: 39217586--39217633 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
39217576 CTTAAACCCC
* *
39217586 AACCCTTAAACCATA
1 AACCCATAATCCATA
* *
39217601 AA-TCATAATCCCTA
1 AACCCATAATCCATA
39217615 AACCCATAATCCATA
1 AACCCATAATCCATA
39217630 AACC
1 AACC
39217634 TTAAAATAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:39217638 original size:22 final size:21
Alignment explanation
Indices: 39217589--39217688 Score: 60
Period size: 22 Copynumber: 4.7 Consensus size: 21
39217579 AAACCCCAAC
*
39217589 CCTTAAACCATAAATCATAAT
1 CCTTAAACCATAAATCATAAA
*
39217610 CCCTAAACCCAT-AATCCATAAA
1 CCTTAAA-CCATAAAT-CATAAA
** * *
39217632 CCTTAAAATAGTAACTCCTAAA
1 CCTTAAACCA-TAAATCATAAA
* * * *
39217654 GCTTAAACCCTAAATCACATAT
1 CCTTAAACCATAAATCATA-AA
39217676 CC-TAAACCATAAA
1 CCTTAAACCATAAA
39217689 CCCTAAACTA
Statistics
Matches: 57, Mismatches: 17, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
21 26 0.46
22 29 0.51
23 2 0.04
ACGTcount: A:0.46, C:0.28, G:0.02, T:0.24
Consensus pattern (21 bp):
CCTTAAACCATAAATCATAAA
Found at i:39217693 original size:14 final size:14
Alignment explanation
Indices: 39217586--39217701 Score: 56
Period size: 14 Copynumber: 8.1 Consensus size: 14
39217576 CTTAAACCCC
39217586 AACCCTTAAACCATA
1 AACCC-TAAACCATA
* * * *
39217601 AATCATAATCCCTA
1 AACCCTAAACCATA
*
39217615 AACCCATAATCCATA
1 AACCC-TAAACCATA
*
39217630 AACCTTAAA--ATA
1 AACCCTAAACCATA
* *
39217642 GTAACTCCTAAAGCTTA
1 --AAC-CCTAAACCATA
* *
39217659 AACCCTAAATCACA
1 AACCCTAAACCATA
* *
39217673 TATCCTAAACCATA
1 AACCCTAAACCATA
*
39217687 AACCCTAAACTATA
1 AACCCTAAACCATA
39217701 A
1 A
39217702 TGATAAATAA
Statistics
Matches: 74, Mismatches: 21, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
12 3 0.04
14 46 0.62
15 23 0.31
17 2 0.03
ACGTcount: A:0.47, C:0.28, G:0.02, T:0.23
Consensus pattern (14 bp):
AACCCTAAACCATA
Found at i:39218114 original size:40 final size:40
Alignment explanation
Indices: 39218037--39218115 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
39218027 CTGCTAAAGC
39218037 TCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAATGG
1 TCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAATGG
*
39218077 TCGATCTATAGCGGCGTTTTTCTAAAAGCGCCACTAATG
1 TCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAATG
39218116 CCACTAAAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (40 bp):
TCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAATGG
Found at i:39218211 original size:40 final size:40
Alignment explanation
Indices: 39218167--39218249 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 40
39218157 TTTTGCGGTA
*
39218167 TTTTTTAAAAAGAGCCACTAATGATTGATCTATAGCGGCG
1 TTTTTTAAAAAGAGCCACTAATGATCGATCTATAGCGGCG
* * ** *
39218207 TTTTTTAAAAAGTGCCACTAGTTCTCGATCTATAGTGGCG
1 TTTTTTAAAAAGAGCCACTAATGATCGATCTATAGCGGCG
39218247 TTT
1 TTT
39218250 GGATAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (40 bp):
TTTTTTAAAAAGAGCCACTAATGATCGATCTATAGCGGCG
Found at i:39222757 original size:5 final size:5
Alignment explanation
Indices: 39222747--39222784 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
39222737 TTTAGTTGAT
*
39222747 AAATA AAATA AAATA AACA-A ATATA AAATA AAATA AAA
1 AAATA AAATA AAATA AA-ATA AAATA AAATA AAATA AAA
39222785 ACAGAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 1 0.03
5 27 0.93
6 1 0.03
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:39223654 original size:13 final size:14
Alignment explanation
Indices: 39223612--39223656 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
39223602 TAATAATGAT
39223612 TAAAGTATATTATAA
1 TAAAGTA-ATTATAA
39223627 TAATA-TAA-TATAA
1 TAA-AGTAATTATAA
39223640 TAAAGTAATTA-AA
1 TAAAGTAATTATAA
39223653 TAAA
1 TAAA
39223657 ACAAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.04
13 17 0.63
14 3 0.11
15 5 0.19
16 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
TAAAGTAATTATAA
Found at i:39225220 original size:20 final size:20
Alignment explanation
Indices: 39225191--39225237 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
39225181 GGCCTGGCCC
*
39225191 CACGGCCATGTCCCAAGCCA
1 CACGGGCATGTCCCAAGCCA
*
39225211 CACGGGCATGTCCCAGGCCA
1 CACGGGCATGTCCCAAGCCA
39225231 CACGGGC
1 CACGGGC
39225238 GTGTGCCCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.43, G:0.28, T:0.09
Consensus pattern (20 bp):
CACGGGCATGTCCCAAGCCA
Found at i:39231508 original size:42 final size:42
Alignment explanation
Indices: 39231446--39231530 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
39231436 AAAGACAAAG
*
39231446 ACTGTCTGCTATTGATTATGTGACTGTAACTGTTATACAAGT
1 ACTGACTGCTATTGATTATGTGACTGTAACTGTTATACAAGT
* * *
39231488 ACTGACTGCTATTGGTTATGTGACTGTGACTGTTATACCAGT
1 ACTGACTGCTATTGATTATGTGACTGTAACTGTTATACAAGT
39231530 A
1 A
39231531 TTGAAAGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (42 bp):
ACTGACTGCTATTGATTATGTGACTGTAACTGTTATACAAGT
Found at i:39231543 original size:42 final size:42
Alignment explanation
Indices: 39231455--39231544 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
39231445 GACTGTCTGC
** *
39231455 TATTGATTATGTGACTGTAACTGTTATACAAGTACTGACTGC
1 TATTGATTATGTGACTGTAACTGTTATACAAGTACTGAAAGA
* * * *
39231497 TATTGGTTATGTGACTGTGACTGTTATACCAGTATTGAAAGA
1 TATTGATTATGTGACTGTAACTGTTATACAAGTACTGAAAGA
39231539 TATTGA
1 TATTGA
39231545 ACGATATGAA
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:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (42 bp):
TATTGATTATGTGACTGTAACTGTTATACAAGTACTGAAAGA
Found at i:39232247 original size:20 final size:20
Alignment explanation
Indices: 39232219--39232264 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
39232209 GCCTGGCCCT
*
39232219 ACGGCCATGTCCCAAGCCAC
1 ACGGGCATGTCCCAAGCCAC
*
39232239 ACGGGCATGTCCCAGGCCAC
1 ACGGGCATGTCCCAAGCCAC
39232259 ACGGGC
1 ACGGGC
39232265 GTGTGCCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.41, G:0.28, T:0.09
Consensus pattern (20 bp):
ACGGGCATGTCCCAAGCCAC
Found at i:39232660 original size:12 final size:12
Alignment explanation
Indices: 39232643--39232668 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39232633 TATGTGAATG
39232643 CTTAGCCTCAGC
1 CTTAGCCTCAGC
39232655 CTTAGCCTCAGC
1 CTTAGCCTCAGC
39232667 CT
1 CT
39232669 CGATACACTC
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:0.15, C:0.42, G:0.15, T:0.27
Consensus pattern (12 bp):
CTTAGCCTCAGC
Found at i:39234216 original size:18 final size:17
Alignment explanation
Indices: 39234184--39234225 Score: 50
Period size: 20 Copynumber: 2.4 Consensus size: 17
39234174 CTGAGTACAC
39234184 GAGAGAAAGATAAAGGATGA
1 GAGAGAAAGA-AAA-GAT-A
39234204 GAGAGAAAG-AAAGATA
1 GAGAGAAAGAAAAGATA
39234220 GAGAGA
1 GAGAGA
39234226 GGAAAAGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.32
17 3 0.14
18 3 0.14
20 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.36, T:0.07
Consensus pattern (17 bp):
GAGAGAAAGAAAAGATA
Found at i:39234316 original size:37 final size:37
Alignment explanation
Indices: 39234253--39234324 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
39234243 GAAAGGAAAG
* * *
39234253 ATATTAAATTCCCTTTTGATTCTCTATTTTCCATAAA
1 ATATTAAATTCACTTTTCATTATCTATTTTCCATAAA
*
39234290 ATATTAAATTCAC-TTTCATATATCTATTTTTCATA
1 ATATTAAATTCACTTTTCAT-TATCTATTTTCCATA
39234325 TTTGTTAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 5 0.17
37 25 0.83
ACGTcount: A:0.32, C:0.17, G:0.01, T:0.50
Consensus pattern (37 bp):
ATATTAAATTCACTTTTCATTATCTATTTTCCATAAA
Found at i:39247783 original size:6 final size:6
Alignment explanation
Indices: 39247772--39247810 Score: 60
Period size: 6 Copynumber: 6.2 Consensus size: 6
39247762 AAAAAATTAG
39247772 TAAAAA TAAAAAA TAAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA T-AAAAA T-AAAAA TAAAAA TAAAAA TAAAAA T
39247811 CATATTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 19 0.59
7 13 0.41
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:39247785 original size:7 final size:7
Alignment explanation
Indices: 39247773--39247809 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
39247763 AAAAATTAGT
39247773 AAAAATA
1 AAAAATA
39247780 AAAAATA
1 AAAAATA
39247787 AAAAAT-
1 AAAAATA
39247793 AAAAAT-
1 AAAAATA
39247799 AAAAATA
1 AAAAATA
39247806 AAAA
1 AAAA
39247810 TCATATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:39247788 original size:13 final size:13
Alignment explanation
Indices: 39247772--39247809 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
39247762 AAAAAATTAG
39247772 TAAAAATAAAAAA
1 TAAAAATAAAAAA
39247785 TAAAAA-ATAAAAA
1 TAAAAATA-AAAAA
39247798 TAAAAATAAAAA
1 TAAAAATAAAAA
39247810 TCATATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.04
13 21 0.91
14 1 0.04
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:39254922 original size:36 final size:36
Alignment explanation
Indices: 39254875--39254947 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
39254865 TCTTTAACAG
39254875 TACAAATGAATGAAAATTTTTAACAGAAATGATCAA
1 TACAAATGAATGAAAATTTTTAACAGAAATGATCAA
39254911 TACAAATGAATGAAAATTTTTAACAGAAATGATCAA
1 TACAAATGAATGAAAATTTTTAACAGAAATGATCAA
39254947 T
1 T
39254948 TTACTCTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (36 bp):
TACAAATGAATGAAAATTTTTAACAGAAATGATCAA
Found at i:39257313 original size:22 final size:20
Alignment explanation
Indices: 39257285--39257329 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 20
39257275 TATTTGATTT
39257285 TGATCTATTCTGCATCTATATC
1 TGATCTATT-TGCATCT-TATC
39257307 TGATCTATTTGCATCTTATC
1 TGATCTATTTGCATCTTATC
39257327 TGA
1 TGA
39257330 ACTGTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.30
21 7 0.30
22 9 0.39
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (20 bp):
TGATCTATTTGCATCTTATC
Found at i:39258810 original size:18 final size:19
Alignment explanation
Indices: 39258789--39258827 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
39258779 AATCTCAGTG
39258789 ATTTT-TAAAAAAAAATTA
1 ATTTTATAAAAAAAAATTA
*
39258807 ATTTTGATAAAGAAAAATTA
1 ATTTT-ATAAAAAAAAATTA
39258827 A
1 A
39258828 ACTAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
20 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
ATTTTATAAAAAAAAATTA
Found at i:39260053 original size:17 final size:18
Alignment explanation
Indices: 39260002--39260059 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 18
39259992 TTTATTTGTG
*
39260002 TTTTTTTAATATACAACA
1 TTTTTTTAATATACAATA
* *
39260020 -TTTATT-ATATGATAATA
1 TTTTTTTAATAT-ACAATA
39260037 TTTTTTTAATATA-AATA
1 TTTTTTTAATATACAATA
39260054 CTTTTT
1 -TTTTT
39260060 AATGTTTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 4 0.12
17 13 0.41
18 11 0.34
19 4 0.12
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTTTTAATATACAATA
Found at i:39262008 original size:40 final size:39
Alignment explanation
Indices: 39261964--39262068 Score: 111
Period size: 40 Copynumber: 2.7 Consensus size: 39
39261954 GAATAAGTGT
* *
39261964 TCTTGATAGCACTAGGGTGCTCCTGACAGTACTTTCGTAC
1 TCTTGATAGCACTACGGTGCTCCTGACAGTAC-TTCATAC
** * * *
39262004 TCTTGATAGCACTATAGTGCTTCTAATAGTACTTCATAC
1 TCTTGATAGCACTACGGTGCTCCTGACAGTACTTCATAC
* * *
39262043 TCCTGTTAGTACTACGGTGCTCCTGA
1 TCTTGATAGCACTACGGTGCTCCTGA
39262069 TAGCATATTC
Statistics
Matches: 52, Mismatches: 13, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
39 25 0.48
40 27 0.52
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (39 bp):
TCTTGATAGCACTACGGTGCTCCTGACAGTACTTCATAC
Found at i:39262148 original size:20 final size:20
Alignment explanation
Indices: 39262105--39262149 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39262095 TACGGTGCCT
* *
39262105 TGATTGTACTTTTATGCCCT
1 TGATTGCACTTTTATGCCCC
* *
39262125 TGATTGCACTTTTGTTCCCC
1 TGATTGCACTTTTATGCCCC
39262145 TGATT
1 TGATT
39262150 TTTCTTCGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.13, C:0.22, G:0.16, T:0.49
Consensus pattern (20 bp):
TGATTGCACTTTTATGCCCC
Found at i:39265539 original size:19 final size:20
Alignment explanation
Indices: 39265499--39265540 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
39265489 TTTAGAATCC
*
39265499 ACCTCTTAAAAAAAATAGAA
1 ACCTCTTAAAAAAAATAAAA
39265519 ACCT-TTAAAAATAAA-AAAA
1 ACCTCTTAAAAA-AAATAAAA
39265538 ACC
1 ACC
39265541 CTCTACTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.62, C:0.17, G:0.02, T:0.19
Consensus pattern (20 bp):
ACCTCTTAAAAAAAATAAAA
Found at i:39266463 original size:16 final size:16
Alignment explanation
Indices: 39266442--39266474 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39266432 GTTTGAGAAC
39266442 ATGAAATAAGAAATTT
1 ATGAAATAAGAAATTT
39266458 ATGAAATAAGAAATTT
1 ATGAAATAAGAAATTT
39266474 A
1 A
39266475 AATTTTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (16 bp):
ATGAAATAAGAAATTT
Found at i:39270742 original size:6 final size:6
Alignment explanation
Indices: 39270731--39270755 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39270721 TCGTCCAAAC
39270731 AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA A
39270756 AAAGGAAACT
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:39280424 original size:43 final size:43
Alignment explanation
Indices: 39280377--39280542 Score: 190
Period size: 43 Copynumber: 3.9 Consensus size: 43
39280367 TATCACATAT
** * * *
39280377 CGATGCCGCTGTCCCAGATAGGGTCTTACACGAAATCGAATAA
1 CGATGCCAATGTCCCAGACATGGTCTTACACGTAATCGAATAA
* *
39280420 CGATGCTAATGTCCCAGACATGGTTTTACACGTAATCGAATAA
1 CGATGCCAATGTCCCAGACATGGTCTTACACGTAATCGAATAA
* *
39280463 CGATGCCAATGTCCCAGACATGGTCTTAAACGTAATCACAAT-A
1 CGATGCCAATGTCCCAGACATGGTCTTACACGTAATC-GAATAA
* * ** *
39280506 CAATGCCAATGTCCTAGACACAGTCTTACATGTAATC
1 CGATGCCAATGTCCCAGACATGGTCTTACACGTAATC
39280543 ACATTTCAAT
Statistics
Matches: 105, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
43 102 0.97
44 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
CGATGCCAATGTCCCAGACATGGTCTTACACGTAATCGAATAA
Found at i:39282828 original size:30 final size:30
Alignment explanation
Indices: 39282794--39282852 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
39282784 ACAAGTTATA
* *
39282794 ATTT-ACTTACTAAATTATTTGAAAGTTTTC
1 ATTTAACTCACTAAACTATTT-AAAGTTTTC
*
39282824 ATTTAAGTCACTAAACTATTTAAAGTTTT
1 ATTTAACTCACTAAACTATTTAAAGTTTT
39282853 TTTTAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (30 bp):
ATTTAACTCACTAAACTATTTAAAGTTTTC
Found at i:39286838 original size:25 final size:25
Alignment explanation
Indices: 39286810--39286860 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
39286800 AATAGACATG
39286810 TTTATTCACAATTCATGCAATCATA
1 TTTATTCACAATTCATGCAATCATA
39286835 TTTATTCACAATTCATGCAATCATA
1 TTTATTCACAATTCATGCAATCATA
39286860 T
1 T
39286861 AAATATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (25 bp):
TTTATTCACAATTCATGCAATCATA
Found at i:39289755 original size:17 final size:17
Alignment explanation
Indices: 39289730--39289767 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
39289720 ATAGTAATTT
* *
39289730 TTTTTATAACTTTAATA
1 TTTTGATAACTTCAATA
39289747 TTTTGATAACTTCAATA
1 TTTTGATAACTTCAATA
39289764 TTTT
1 TTTT
39289768 TTTTACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTTGATAACTTCAATA
Found at i:39292573 original size:46 final size:46
Alignment explanation
Indices: 39292523--39292698 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
39292513 TGATTGAGCA
39292523 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
39292569 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
39292614 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
39292662 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39292699 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 61 0.55
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:39292679 original size:93 final size:93
Alignment explanation
Indices: 39292520--39292691 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
39292510 GGATGATTGA
*
39292520 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
39292585 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
39292613 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
39292677 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
39292692 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:39300149 original size:46 final size:46
Alignment explanation
Indices: 39300099--39300274 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
39300089 TGGTTGAGCA
39300099 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
39300145 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
39300190 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
39300238 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39300275 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:39300255 original size:93 final size:93
Alignment explanation
Indices: 39300096--39300267 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
39300086 GGATGGTTGA
* *
39300096 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39300161 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
39300189 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39300254 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
39300268 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:39313377 original size:39 final size:40
Alignment explanation
Indices: 39313173--39313393 Score: 232
Period size: 40 Copynumber: 5.5 Consensus size: 40
39313163 TTGAATGCTG
* * * * * *
39313173 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
39313213 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
39313253 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
39313293 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
39313333 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
39313372 ACCGGGCTATGTCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCA
39313394 CTTGAACGAG
Statistics
Matches: 159, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 33 0.21
40 118 0.74
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:39313415 original size:79 final size:80
Alignment explanation
Indices: 39313248--39313430 Score: 210
Period size: 79 Copynumber: 2.3 Consensus size: 80
39313238 GTGCGAGATA
* * *
39313248 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
39313313 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
39313328 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
39313392 CACTT-GAACGAGGAG
66 CA-TTCGAACGAGGAG
* * *
39313407 CTATATCC-GGTTAAATTCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
39313431 TACGTGATTT
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
78 13 0.15
79 44 0.51
80 29 0.34
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:39317016 original size:13 final size:13
Alignment explanation
Indices: 39316998--39317022 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39316988 GTATTGATCA
39316998 TGTGTTCACACCT
1 TGTGTTCACACCT
39317011 TGTGTTCACACC
1 TGTGTTCACACC
39317023 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:39323899 original size:50 final size:49
Alignment explanation
Indices: 39323824--39324049 Score: 224
Period size: 50 Copynumber: 4.5 Consensus size: 49
39323814 TGAATACACG
* *
39323824 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTGTTCAGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TGTTCAGTCACA
* * *
39323874 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCA-ATGACTTC-GATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAGATG--TTCAG-TCACA
* * * * * *
39323925 TGTGTAGTATTAAGTGCAGGCTACTATGTGTATCAGATGATGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGTTCA-GTCACA
* *
39323975 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TGTTCAGTCACA
* * *
39324024 TGTGTACTATTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
39324050 TGCATATCAG
Statistics
Matches: 149, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
49 30 0.20
50 74 0.50
51 45 0.30
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGTTCAGTCACA
Found at i:39324058 original size:99 final size:100
Alignment explanation
Indices: 39323874--39324061 Score: 247
Period size: 99 Copynumber: 1.9 Consensus size: 100
39323864 TTCAGTCGCA
* * *
39323874 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCAATGACTTCGATCACGTGTGTAGTATTAAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACTCAATGA-TTCGATCACATGTGTACTATTAAG
**
39323939 TGCAGGCTACTATGTGTATCAGATGATGAGGTCACG
65 TGCAGGCTACTATGCATATCAGATGATGAGGTCACG
* * * *
39323975 TGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAGATTG-TT-GGTCGCATGTGTACTATTAT
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACTCA-A-TGATTCGATCACATGTGTACTATTAA
39324037 GTGCAGGCTACTATGCATATCAGAT
64 GTGCAGGCTACTATGCATATCAGAT
39324062 AGCTTCGGCT
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
99 38 0.50
100 4 0.05
101 32 0.42
102 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (100 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGCGTACTCAATGATTCGATCACATGTGTACTATTAAGT
GCAGGCTACTATGCATATCAGATGATGAGGTCACG
Found at i:39324641 original size:16 final size:17
Alignment explanation
Indices: 39324620--39324656 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
39324610 TGGTTGTTGG
39324620 AATTCTGTATAGGGA-A
1 AATTCTGTATAGGGAGA
39324636 AATTCTGTATAGGGAGA
1 AATTCTGTATAGGGAGA
39324653 AATT
1 AATT
39324657 TGGTTTGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.32
Consensus pattern (17 bp):
AATTCTGTATAGGGAGA
Found at i:39326645 original size:30 final size:30
Alignment explanation
Indices: 39326589--39326646 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39326579 TTTTCGAGCA
* *
39326589 TAGGGGTAAAATGGTCATTTCGCCAAAGTC
1 TAGGGGAAAAATGGTCATTTCACCAAAGTC
* *
39326619 TAGGGGAAAAATGTTCATTTTACCAAAG
1 TAGGGGAAAAATGGTCATTTCACCAAAG
39326647 ATGTGAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (30 bp):
TAGGGGAAAAATGGTCATTTCACCAAAGTC
Found at i:39327060 original size:47 final size:47
Alignment explanation
Indices: 39326997--39327303 Score: 202
Period size: 49 Copynumber: 6.5 Consensus size: 47
39326987 GCTAGTGCAT
* *
39326997 GACATGTTTGGCACATGCATCGGCCACA-ATATGATAGCCAGTGTAA
1 GACATGTCTGGGACATGCATCGGCCACAGATATGATAGCCAGTGTAA
* *
39327043 GACCATGTCTGGGACATGGCATCGG-CATAGAGAATGAGT-GCCAGTGTAA
1 GA-CATGTCTGGGACAT-GCATCGGCCACAGA-TATGA-TAGCCAGTGTAA
* ** * *
39327092 GACATGTCTGGGACATGTATCAACCTC-GACGATGATAGCCAGTGTAA
1 GACATGTCTGGGACATGCATCGGCCACAGA-TATGATAGCCAGTGTAA
* * * *
39327139 GACGTGTCTGGGACACGCATCGGCTA-AGAGT-TG-T-GCTAGTGTAA
1 GACATGTCTGGGACATGCATCGGCCACAGA-TATGATAGCCAGTGTAA
* * * * * * *
39327183 GACATGTTTGGGACATGCATCAG-TACATATAGATGAGAGCTAGTATAA
1 GACATGTCTGGGACATGCATCGGCCACAGAT--ATGATAGCCAGTGTAA
* * *
39327231 GACCATGTCTGGGACATGGCATCAGCCTC-GATGATGATAGCTAGTGTAA
1 GA-CATGTCTGGGACAT-GCATCGGCCACAGAT-ATGATAGCCAGTGTAA
* *
39327280 GAACATGTCCGAGACATGGCATCG
1 G-ACATGTCTGGGACAT-GCATCG
39327304 ACAACATATC
Statistics
Matches: 206, Mismatches: 37, Indels: 33
0.75 0.13 0.12
Matches are distributed among these distances:
43 3 0.01
44 30 0.15
45 1 0.00
46 7 0.03
47 56 0.27
48 34 0.17
49 63 0.31
50 11 0.05
51 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (47 bp):
GACATGTCTGGGACATGCATCGGCCACAGATATGATAGCCAGTGTAA
Found at i:39327195 original size:91 final size:96
Alignment explanation
Indices: 39327027--39327253 Score: 268
Period size: 91 Copynumber: 2.4 Consensus size: 96
39327017 CGGCCACAAT
*
39327027 ATGATAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGAATGAGTGCCAGTGTAA
1 ATGATAGCCAGTGTAAGACCATGTCTGGGACATCGCATCGGCATAGAGAATGAGTGCCAGTGTAA
*
39327092 GACATGTCTGGGACATGTATCAACCTCGACG
66 GACATGTCTGGGACATGCATCAACCTCGACG
* * * *
39327123 ATGATAGCCAGTGTAAGA-CGTGTCTGGGACA-CGCATCGGC-TA-AGAGT-TGTGCTAGTGTAA
1 ATGATAGCCAGTGTAAGACCATGTCTGGGACATCGCATCGGCATAGAGAATGAGTGCCAGTGTAA
* * **
39327183 GACATGTTTGGGACATGCATCAGTACATATA-G
66 GACATGTCTGGGACATGCATCA--ACCTCGACG
* * * *
39327215 ATGAGAGCTAGTATAAGACCATGTCTGGGACATGGCATC
1 ATGATAGCCAGTGTAAGACCATGTCTGGGACATCGCATC
39327254 AGCCTCGATG
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
91 31 0.28
92 20 0.18
93 18 0.16
94 13 0.12
95 12 0.11
96 18 0.16
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (96 bp):
ATGATAGCCAGTGTAAGACCATGTCTGGGACATCGCATCGGCATAGAGAATGAGTGCCAGTGTAA
GACATGTCTGGGACATGCATCAACCTCGACG
Found at i:39328143 original size:42 final size:42
Alignment explanation
Indices: 39328096--39328175 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
39328086 CGGGTAGGCC
* *
39328096 ACACGGGCATGTGTCATGGCCGTGTTTTAAATTCAGTGCTGT
1 ACACGGGCATGTGTCATGGCCATGTTTTAAAGTCAGTGCTGT
*
39328138 ACACGGGCGTGTGTCATGGCCATGTTTTAAAGTCAGTG
1 ACACGGGCATGTGTCATGGCCATGTTTTAAAGTCAGTG
39328176 TTGCACACAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (42 bp):
ACACGGGCATGTGTCATGGCCATGTTTTAAAGTCAGTGCTGT
Found at i:39333735 original size:80 final size:80
Alignment explanation
Indices: 39333602--39333763 Score: 315
Period size: 80 Copynumber: 2.0 Consensus size: 80
39333592 TATTCATATT
39333602 TGATTGGCCTACATATGCTGTTGCATGCTTGACTAAATTAATTAGTAATGACTAAAGTTATTCAA
1 TGATTGGCCTACATATGCTGTTGCATGCTTGACTAAATTAATTAGTAATGACTAAAGTTATTCAA
39333667 AATTCATAGAATGTA
66 AATTCATAGAATGTA
*
39333682 TGATTGGCCTACATATGTTGTTGCATGCTTGACTAAATTAATTAGTAATGACTAAAGTTATTCAA
1 TGATTGGCCTACATATGCTGTTGCATGCTTGACTAAATTAATTAGTAATGACTAAAGTTATTCAA
39333747 AATTCATAGAATGTA
66 AATTCATAGAATGTA
39333762 TG
1 TG
39333764 CTTGTTTGAA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (80 bp):
TGATTGGCCTACATATGCTGTTGCATGCTTGACTAAATTAATTAGTAATGACTAAAGTTATTCAA
AATTCATAGAATGTA
Found at i:39334369 original size:104 final size:105
Alignment explanation
Indices: 39334235--39334444 Score: 368
Period size: 104 Copynumber: 2.0 Consensus size: 105
39334225 TGAAAGGGGG
* *
39334235 AAGAGTTGTAATAGCCCAATATTTGGTCTAGCTGGAACAGACGTTTCAGGACTGTAAAATCTAAG
1 AAGAGTTGTAATAGCCCAATATTGGGTCTAGCTGGAACAGACGTTTCAGGACTGCAAAATCTAAG
39334300 ATAGAAATAATTATTTTATGATTATTTTGAGGTCTATGAT
66 ATAGAAATAATTATTTTATGATTATTTTGAGGTCTATGAT
* * *
39334340 AAGAGTT-TAATAGCCCAATATTGGGTCTAGTTGGAACAGAGGTTTCAGGACTGCAAAATCTGAG
1 AAGAGTTGTAATAGCCCAATATTGGGTCTAGCTGGAACAGACGTTTCAGGACTGCAAAATCTAAG
39334404 ATAGAAATAATTATTTTATGATTATTTTGAGGTCTATGAT
66 ATAGAAATAATTATTTTATGATTATTTTGAGGTCTATGAT
39334444 A
1 A
39334445 TGATTGCATG
Statistics
Matches: 100, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
104 93 0.93
105 7 0.07
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (105 bp):
AAGAGTTGTAATAGCCCAATATTGGGTCTAGCTGGAACAGACGTTTCAGGACTGCAAAATCTAAG
ATAGAAATAATTATTTTATGATTATTTTGAGGTCTATGAT
Found at i:39336001 original size:68 final size:67
Alignment explanation
Indices: 39335929--39336075 Score: 165
Period size: 67 Copynumber: 2.2 Consensus size: 67
39335919 CATCATGTGT
* * * *
39335929 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
39335991 ATGTAG
62 ATGTAG
** * *
39335997 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
39336062 AG
66 AG
39336064 ACAAGAGAGCTA
1 ACAAGAGAGCTA
39336076 ATAGATAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 24 0.35
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.22
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:39336034 original size:64 final size:64
Alignment explanation
Indices: 39335953--39336137 Score: 169
Period size: 67 Copynumber: 2.9 Consensus size: 64
39335943 AGACATTATG
* * *
39335953 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTAAGAGATAA
* * * * * * *
39336017 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTAATAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTAAGAGAT
39336082 AA
63 AA
* * * * *
39336084 AT-TGGCTAGGTCACATGGGTGGTATTGA-GTGTTCACCATGT-GTACAAGAGAGCT
1 ATGTAGCTAGGTCGCATGGGTGATACT-ATGTGTACACCATGTAG-ACAAGAGAGCT
39336138 GAACTATATG
Statistics
Matches: 96, Mismatches: 20, Indels: 11
0.76 0.16 0.09
Matches are distributed among these distances:
62 1 0.01
63 20 0.21
64 21 0.22
65 6 0.06
66 18 0.19
67 30 0.31
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTAAGAGATAA
Found at i:39340479 original size:64 final size:64
Alignment explanation
Indices: 39340399--39340581 Score: 174
Period size: 67 Copynumber: 2.8 Consensus size: 64
39340389 AGACATTATG
* *
39340399 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGGGAGCTACGAGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * * * *
39340463 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGATACCATGTAGACCAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
39340528 AA
63 AA
* * * *
39340530 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAG
1 ATGTAGCTAGGTCGCATGGGTGATACT-ATGTGTACACCATGTAG-ACAAGAGAG
39340582 TCGACCTATA
Statistics
Matches: 93, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
62 1 0.01
63 16 0.17
64 21 0.23
65 7 0.08
66 18 0.19
67 30 0.32
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:39344854 original size:68 final size:66
Alignment explanation
Indices: 39344782--39344953 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
39344772 CATCATGTGT
* * * *
39344782 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
39344845 TGTAG
62 TGTAG
** * *
39344850 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
39344915 AG
65 AG
* * * *
39344917 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
39344954 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:39344887 original size:64 final size:64
Alignment explanation
Indices: 39344806--39344989 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
39344796 AGACATTATG
* * *
39344806 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
39344870 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
39344935 AA
63 AA
* * *
39344937 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
39344990 CGAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 33 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:39351327 original size:49 final size:49
Alignment explanation
Indices: 39351163--39351327 Score: 181
Period size: 50 Copynumber: 3.3 Consensus size: 49
39351153 ATATGACGAA
* ** * *
39351163 TAAGTGCAGGCTACTAGCGTACCCGATAACTTCGATCACGTGTGTAGTAC
1 TAAGTGCAGGCTACTAGTGTACTAGATAA-TTAGGTCACGTGTGTAGTAC
**
39351213 TAAGTGCAGGCTACTAAGTGTA-TCAGATTGTTAGGTCACGTGTGTAGTAC
1 TAAGTGCAGGCTACT-AGTGTACT-AGATAATTAGGTCACGTGTGTAGTAC
* * * *
39351263 TAAGTGCAGGTTACTACGTGTACTGGATAATT-GGCCACATGTGTAGTAC
1 TAAGTGCAGGCTACTA-GTGTACTAGATAATTAGGTCACGTGTGTAGTAC
39351312 TAAGTGCAGGCTACTA
1 TAAGTGCAGGCTACTA
39351328 TGCGTACCAG
Statistics
Matches: 97, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
49 31 0.32
50 57 0.59
51 9 0.09
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
TAAGTGCAGGCTACTAGTGTACTAGATAATTAGGTCACGTGTGTAGTAC
Found at i:39355935 original size:50 final size:50
Alignment explanation
Indices: 39355881--39355980 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
39355871 TAGACTCATA
39355881 TATATATTTAATAATTGTTTTCTAGAATTTTTGGTTGAGCCAATTAGTAC
1 TATATATTTAATAATTGTTTTCTAGAATTTTTGGTTGAGCCAATTAGTAC
39355931 TATATATTTAATAATTGTTTTCTAGAATTTTTGGTTGAGCCAATTAGTAC
1 TATATATTTAATAATTGTTTTCTAGAATTTTTGGTTGAGCCAATTAGTAC
39355981 AGTTTATTAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (50 bp):
TATATATTTAATAATTGTTTTCTAGAATTTTTGGTTGAGCCAATTAGTAC
Found at i:39357209 original size:93 final size:93
Alignment explanation
Indices: 39357050--39357220 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
39357040 GCCCCTAAGT
* * * *
39357050 GAACTCGGAATCAACTTAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCGGAATCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39357115 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
39357143 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGAATCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39357208 CGAGTTCGGATGC
66 CGAGTTCGGATGC
39357221 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.23
Consensus pattern (93 bp):
GAACTCGGAATCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:39357217 original size:46 final size:46
Alignment explanation
Indices: 39357045--39357217 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
39357035 AACCCGCCCC
* * * * *
39357045 TAAGTGAACTCGGAATCAACTTAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
39357091 TAAGTGAACTTGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
39357139 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
39357184 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
39357218 TGCTCAACCA
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 58 0.56
47 28 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:39357674 original size:30 final size:30
Alignment explanation
Indices: 39357640--39357699 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
39357630 ATTTAATACG
39357640 AACTTTGGAAAAATTACACTATTGCCCCTA
1 AACTTTGGAAAAATTACACTATTGCCCCTA
* * * *
39357670 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTATTGCCCCTA
39357700 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.35
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTATTGCCCCTA
Found at i:39360549 original size:40 final size:40
Alignment explanation
Indices: 39360426--39360648 Score: 218
Period size: 40 Copynumber: 5.6 Consensus size: 40
39360416 TATTCGAATG
* * * *
39360426 ATATCCGGGCTAAGTCCTGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GCGACT
* * * * * * *
39360467 ATAACCGGACTAAGA-TCAAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-CGACT
*
39360506 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
* *
39360546 ATATCCAGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
* * * *
39360586 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
* **
39360626 ACAT-CAAGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
39360649 CTTGCGCAAG
Statistics
Matches: 149, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
39 33 0.22
40 104 0.70
41 12 0.08
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
Found at i:39363649 original size:93 final size:93
Alignment explanation
Indices: 39363490--39363674 Score: 361
Period size: 93 Copynumber: 2.0 Consensus size: 93
39363480 TTCCAAATCA
*
39363490 TGAGTAGGATAATTCCTCTCATGAGGTTTTAACTGCCTTGAAGCATAAGCCACCATTTTTCCTTC
1 TGAGTAGGATAATTCCTCTCATGAGGTTTTAACTGCCTTGAAGCATAAGCCACCACTTTTCCTTC
39363555 TTGCATGAGTACACACCCCAAACCATTG
66 TTGCATGAGTACACACCCCAAACCATTG
39363583 TGAGTAGGATAATTCCTCTCATGAGGTTTTAACTGCCTTGAAGCATAAGCCACCACTTTTCCTTC
1 TGAGTAGGATAATTCCTCTCATGAGGTTTTAACTGCCTTGAAGCATAAGCCACCACTTTTCCTTC
39363648 TTGCATGAGTACACACCCCAAACCATT
66 TTGCATGAGTACACACCCCAAACCATT
39363675 TAGAGAAGCA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (93 bp):
TGAGTAGGATAATTCCTCTCATGAGGTTTTAACTGCCTTGAAGCATAAGCCACCACTTTTCCTTC
TTGCATGAGTACACACCCCAAACCATTG
Found at i:39366093 original size:13 final size:13
Alignment explanation
Indices: 39366075--39366100 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39366065 ATATTATAAT
39366075 TATTTTATGTTAA
1 TATTTTATGTTAA
39366088 TATTTTATGTTAA
1 TATTTTATGTTAA
39366101 AAATAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:39367267 original size:30 final size:30
Alignment explanation
Indices: 39367231--39367319 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
39367221 AACGGTGATA
39367231 TAATGATTCTACTTGAATTATATATCGAGG
1 TAATGATTCTACTTGAATTATATATCGAGG
39367261 TAATGATTCTACTTGAATTATATAT-----
1 TAATGATTCTACTTGAATTATATATCGAGG
39367286 TAATGATTCTACTTGAATTATATATCGAGG
1 TAATGATTCTACTTGAATTATATATCGAGG
39367316 TAAT
1 TAAT
39367320 TAGTTATACT
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
25 25 0.46
30 29 0.54
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (30 bp):
TAATGATTCTACTTGAATTATATATCGAGG
Found at i:39367290 original size:25 final size:26
Alignment explanation
Indices: 39367231--39367310 Score: 117
Period size: 25 Copynumber: 3.0 Consensus size: 26
39367221 AACGGTGATA
39367231 TAATGATTCTACTTGAATTATATATCGAGG
1 TAATGATTCTACTTGAATTATATAT----G
39367261 TAATGATTCTACTTGAATTATATAT-
1 TAATGATTCTACTTGAATTATATATG
39367286 TAATGATTCTACTTGAATTATATAT
1 TAATGATTCTACTTGAATTATATAT
39367311 CGAGGTAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
25 25 0.50
30 25 0.50
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (26 bp):
TAATGATTCTACTTGAATTATATATG
Found at i:39367574 original size:40 final size:40
Alignment explanation
Indices: 39367526--39367731 Score: 324
Period size: 40 Copynumber: 5.2 Consensus size: 40
39367516 GGACTAAGAT
*
39367526 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
39367566 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
* * *
39367606 CCGAAGGCATCTGTGCTAGTTACTAAATCTGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
*
39367646 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
* * * *
39367686 CCGAAGGCATTTGTGCGAGTTGCTATATCC-AGCTAAATC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
39367725 CCGAAGG
1 CCGAAGG
39367732 TACTTGGGTT
Statistics
Matches: 155, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
39 14 0.09
40 141 0.91
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
Found at i:39370094 original size:46 final size:47
Alignment explanation
Indices: 39370044--39370181 Score: 156
Period size: 46 Copynumber: 2.9 Consensus size: 47
39370034 TTACACTAAC
*
39370044 ACATCTCGTA-GCCGATGCATGTCCCAGACATGTCTTACACTGGCT-T
1 ACATCTCG-AGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT
* * *
39370090 ACATCTCGAGGCTGATGCATGTCCTAGACATGTCTTACTCTAGCTCT
1 ACATCTCGAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT
* * * *
39370137 -CATTTCAATGCCAATGTCATGTCCCAGACATGGTCTTACACTAGC
1 ACATCTCGAGGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGC
39370182 GCACAAATGA
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
45 1 0.01
46 50 0.65
47 14 0.18
48 12 0.16
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (47 bp):
ACATCTCGAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT
Found at i:39374493 original size:21 final size:21
Alignment explanation
Indices: 39374467--39374506 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39374457 GGACTAAACT
*
39374467 GAAAACTTTGAAAAGTTTCAG
1 GAAAACTTAGAAAAGTTTCAG
*
39374488 GAAAACTTAGAAAATTTTC
1 GAAAACTTAGAAAAGTTTC
39374507 CCATGAAACA
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:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (21 bp):
GAAAACTTAGAAAAGTTTCAG
Found at i:39378828 original size:49 final size:50
Alignment explanation
Indices: 39378754--39378880 Score: 141
Period size: 49 Copynumber: 2.6 Consensus size: 50
39378744 TCAATTCGAT
* * * *
39378754 GCCAAGTCCCAGACATAGTCTTACACTGGCTATCAAAAATGAG-GCCA-AC
1 GCCATGTCCCAGACATGGTCTTACACTAGCTATCAAAAATCAGTG-CAGAC
* * * * * *
39378803 GCCATGTCCCAGACATGGTCATACACTAGCTCTCACATATCTGTGCAGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTATCAAAAATCAGTGCAGAC
39378853 GCCATGTCCCAGACATGGTCTTACACTA
1 GCCATGTCCCAGACATGGTCTTACACTA
39378881 ACACATCTCG
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 36 0.55
50 29 0.45
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACACTAGCTATCAAAAATCAGTGCAGAC
Found at i:39391911 original size:20 final size:20
Alignment explanation
Indices: 39391868--39391913 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
39391858 AAAATAATCT
* *
39391868 TCATTTTTCTCATTTTACTT
1 TCATTTTGCTCATTTTACTA
39391888 TCATTTTGCTCATTATT-CTA
1 TCATTTTGCTCATT-TTACTA
39391908 TCATTT
1 TCATTT
39391914 AAATTGCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.17, C:0.20, G:0.02, T:0.61
Consensus pattern (20 bp):
TCATTTTGCTCATTTTACTA
Found at i:39392014 original size:23 final size:23
Alignment explanation
Indices: 39391988--39392034 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
39391978 CATTCGATTT
*
39391988 TCATACTCATGCCATTACTATGC
1 TCATACTCATGCCATTACCATGC
* * *
39392011 TCATTCTTATGCTATTACCATGC
1 TCATACTCATGCCATTACCATGC
39392034 T
1 T
39392035 AATGTCATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (23 bp):
TCATACTCATGCCATTACCATGC
Found at i:39396400 original size:190 final size:190
Alignment explanation
Indices: 39396077--39396456 Score: 760
Period size: 190 Copynumber: 2.0 Consensus size: 190
39396067 CAACCCTAGG
39396077 AAGTTAATTAGAAAGAGATTTCAATTATTCAACCTAGGGTTAGACGTTGTTAGTCTTGAGAGGGA
1 AAGTTAATTAGAAAGAGATTTCAATTATTCAACCTAGGGTTAGACGTTGTTAGTCTTGAGAGGGA
39396142 TAATAATATAACTTAGGGATTCCTACGGAATAAGTTAAATGAATAAATCGTCCGATTTGGAGTCA
66 TAATAATATAACTTAGGGATTCCTACGGAATAAGTTAAATGAATAAATCGTCCGATTTGGAGTCA
39396207 GAATAACAAGTGAAGTCTAGGTGAATTTTTCCTTAGGTATTGTCTTAATTCAATCGTTTT
131 GAATAACAAGTGAAGTCTAGGTGAATTTTTCCTTAGGTATTGTCTTAATTCAATCGTTTT
39396267 AAGTTAATTAGAAAGAGATTTCAATTATTCAACCTAGGGTTAGACGTTGTTAGTCTTGAGAGGGA
1 AAGTTAATTAGAAAGAGATTTCAATTATTCAACCTAGGGTTAGACGTTGTTAGTCTTGAGAGGGA
39396332 TAATAATATAACTTAGGGATTCCTACGGAATAAGTTAAATGAATAAATCGTCCGATTTGGAGTCA
66 TAATAATATAACTTAGGGATTCCTACGGAATAAGTTAAATGAATAAATCGTCCGATTTGGAGTCA
39396397 GAATAACAAGTGAAGTCTAGGTGAATTTTTCCTTAGGTATTGTCTTAATTCAATCGTTTT
131 GAATAACAAGTGAAGTCTAGGTGAATTTTTCCTTAGGTATTGTCTTAATTCAATCGTTTT
39396457 TCCAAAAGTA
Statistics
Matches: 190, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 190 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.35
Consensus pattern (190 bp):
AAGTTAATTAGAAAGAGATTTCAATTATTCAACCTAGGGTTAGACGTTGTTAGTCTTGAGAGGGA
TAATAATATAACTTAGGGATTCCTACGGAATAAGTTAAATGAATAAATCGTCCGATTTGGAGTCA
GAATAACAAGTGAAGTCTAGGTGAATTTTTCCTTAGGTATTGTCTTAATTCAATCGTTTT
Found at i:39399909 original size:55 final size:55
Alignment explanation
Indices: 39399791--39399929 Score: 145
Period size: 55 Copynumber: 2.5 Consensus size: 55
39399781 CTTGGCCGTC
* ** * *
39399791 GTCGAACCTGCCAAAACAACACGGGCGTGCGACACGCCCGTGCCTTGAAGCTGTG
1 GTCGAACCTGTCAAATTAACACGGGCGTGAGACACGCCCGTGCCTAGAAGCTGTG
* * * * *
39399846 GCCAAACCTGTCAAATTAACATGGGCGTGAGACACGCCCGTGTCTAGCA-CTCGTG
1 GTCGAACCTGTCAAATTAACACGGGCGTGAGACACGCCCGTGCCTAGAAGCT-GTG
* **
39399901 GTCGAACCTATTGAATTAACACGGGCGTG
1 GTCGAACCTGTCAAATTAACACGGGCGTG
39399930 GGACTACATA
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
54 2 0.03
55 65 0.97
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (55 bp):
GTCGAACCTGTCAAATTAACACGGGCGTGAGACACGCCCGTGCCTAGAAGCTGTG
Found at i:39400363 original size:20 final size:20
Alignment explanation
Indices: 39400322--39400365 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
39400312 AATAATCTTT
* *
39400322 ATTTTTCTCATTTTACTTTC
1 ATTTTGCTCATTTTACTATC
39400342 ATTTTGCTCATTATT-CTATC
1 ATTTTGCTCATT-TTACTATC
39400362 ATTT
1 ATTT
39400366 AAATTGCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.18, C:0.18, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTTGCTCATTTTACTATC
Found at i:39400460 original size:7 final size:7
Alignment explanation
Indices: 39400448--39400473 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39400438 CCTAGATGAA
39400448 TTGGGCT
1 TTGGGCT
39400455 TTGGGCT
1 TTGGGCT
39400462 TTGGGCT
1 TTGGGCT
39400469 TTGGG
1 TTGGG
39400474 TTTCATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.46, T:0.42
Consensus pattern (7 bp):
TTGGGCT
Found at i:39401765 original size:29 final size:28
Alignment explanation
Indices: 39401710--39401824 Score: 122
Period size: 29 Copynumber: 4.0 Consensus size: 28
39401700 GTGAGCATGA
* *
39401710 ATATAAATGTGACTGGGCCTAACGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
39401738 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * ** *
39401767 ATATACAGGTGATTTACGCCTAATAGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * *
39401796 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
39401824 A
1 A
39401825 GATACAGGTA
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
28 25 0.35
29 46 0.65
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:39404409 original size:19 final size:18
Alignment explanation
Indices: 39404385--39404430 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
39404375 GTTTAAAAAC
*
39404385 TTTTATTTATTATTTATTA
1 TTTTATTTATTACTT-TTA
*
39404404 TTTTATGTTTTTACTTTTA
1 TTTTAT-TTATTACTTTTA
39404423 TTTTATTT
1 TTTTATTT
39404431 TAAGACTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 15 0.62
20 7 0.29
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTATTTATTACTTTTA
Found at i:39409158 original size:7 final size:7
Alignment explanation
Indices: 39409146--39409176 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
39409136 GAAATGGAAG
39409146 GATATTT
1 GATATTT
39409153 GATATTT
1 GATATTT
39409160 GATATTT
1 GATATTT
39409167 GATATTT
1 GATATTT
39409174 GAT
1 GAT
39409177 GGTTCTGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (7 bp):
GATATTT
Found at i:39410811 original size:26 final size:26
Alignment explanation
Indices: 39410782--39410834 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
39410772 AAAACGCCAT
39410782 AGGAGGGTTCTCTAAGCTGGTATTTC
1 AGGAGGGTTCTCTAAGCTGGTATTTC
39410808 AGGAGGGTTCTCTAAGCTGGTATTTC
1 AGGAGGGTTCTCTAAGCTGGTATTTC
39410834 A
1 A
39410835 TAATTTTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.34
Consensus pattern (26 bp):
AGGAGGGTTCTCTAAGCTGGTATTTC
Found at i:39411343 original size:54 final size:54
Alignment explanation
Indices: 39411270--39411410 Score: 282
Period size: 54 Copynumber: 2.6 Consensus size: 54
39411260 GTAATTGTCG
39411270 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATA
1 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATA
39411324 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATA
1 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATA
39411378 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCG
1 TTGCAGGGGATTTAGCCTGGACTGGTAATCCCG
39411411 CTGCAAGGTT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 87 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (54 bp):
TTGCAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATA
Found at i:39413847 original size:8 final size:8
Alignment explanation
Indices: 39413836--39413860 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
39413826 AGTTTTCTTC
39413836 CTTAACAT
1 CTTAACAT
39413844 CTTAACAT
1 CTTAACAT
39413852 CTTAACAT
1 CTTAACAT
39413860 C
1 C
39413861 AGAATCCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.28, G:0.00, T:0.36
Consensus pattern (8 bp):
CTTAACAT
Found at i:39430245 original size:20 final size:20
Alignment explanation
Indices: 39430189--39430250 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
39430179 TTTAGTCATA
*
39430189 TAATAAATTA-TTAATATAAT
1 TAATAAATTATTTAATAT-TT
* *
39430209 AAATAAA--ATTTATTATTT
1 TAATAAATTATTTAATATTT
39430227 TAATAAATTATTTAATATTT
1 TAATAAATTATTTAATATTT
39430247 TAAT
1 TAAT
39430251 TTTATTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 20 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATAAATTATTTAATATTT
Found at i:39430863 original size:14 final size:14
Alignment explanation
Indices: 39430841--39430892 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
39430831 CCAGGAATAT
39430841 AAATTATTTTTCAA
1 AAATTATTTTTCAA
*
39430855 AAATCA-TTTTCAAA
1 AAATTATTTTTC-AA
*
39430869 AAATTATTTTTCGA
1 AAATTATTTTTCAA
39430883 AAATTATTTT
1 AAATTATTTT
39430893 CAGTTTAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 5 0.15
14 23 0.70
15 5 0.15
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (14 bp):
AAATTATTTTTCAA
Found at i:39430885 original size:28 final size:28
Alignment explanation
Indices: 39430841--39430894 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
39430831 CCAGGAATAT
39430841 AAATTATTTTTCAAAAATCATTTTCAAA
1 AAATTATTTTTCAAAAATCATTTTCAAA
* *
39430869 AAATTATTTTTCGAAAATTATTTTCA
1 AAATTATTTTTCAAAAATCATTTTCA
39430895 GTTTAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (28 bp):
AAATTATTTTTCAAAAATCATTTTCAAA
Found at i:39431581 original size:13 final size:13
Alignment explanation
Indices: 39431562--39431623 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
39431552 TAAATCAAAA
39431562 TTTTTAAAAATAC
1 TTTTTAAAAATAC
* **
39431575 TTCTTAAATTTAC
1 TTTTTAAAAATAC
*
39431588 TTTTTAAAAATAT
1 TTTTTAAAAATAC
*
39431601 TTTTTAAAAGTAC
1 TTTTTAAAAATAC
*
39431614 TTTCTAAAAA
1 TTTTTAAAAA
39431624 CAATGCTTAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (13 bp):
TTTTTAAAAATAC
Found at i:39431598 original size:26 final size:26
Alignment explanation
Indices: 39431562--39431623 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
39431552 TAAATCAAAA
**
39431562 TTTTTAAAAATACTTCTTAAATTTAC
1 TTTTTAAAAATACTTCTTAAAAGTAC
* *
39431588 TTTTTAAAAATATTTTTTAAAAGTAC
1 TTTTTAAAAATACTTCTTAAAAGTAC
*
39431614 TTTCTAAAAA
1 TTTTTAAAAA
39431624 CAATGCTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTTTAAAAATACTTCTTAAAAGTAC
Found at i:39434025 original size:3 final size:3
Alignment explanation
Indices: 39434017--39434067 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
39434007 CTGTTGACCT
39434017 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39434065 TTA
1 TTA
39434068 CTTCAAATGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39438254 original size:16 final size:17
Alignment explanation
Indices: 39438228--39438265 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
39438218 TTTTGCCCCT
*
39438228 TTTTTTAAGGTTTAGGG
1 TTTTTTAAGGTTTAAGG
39438245 TTTTTT-AGGTTTAAGG
1 TTTTTTAAGGTTTAAGG
39438261 TTTTT
1 TTTTT
39438266 GGTGGGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.61
Consensus pattern (17 bp):
TTTTTTAAGGTTTAAGG
Found at i:39438408 original size:22 final size:24
Alignment explanation
Indices: 39438380--39438435 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
39438370 AATAATTAAA
*
39438380 TTAGGGTTTTGAGTT-TTTTA-GG
1 TTAGGGTTTTGAATTGTTTTAGGG
*
39438402 TTAGGGTTTTTAATTGTTTTAGGG
1 TTAGGGTTTTGAATTGTTTTAGGG
*
39438426 TTAGAGTTTT
1 TTAGGGTTTT
39438436 AGTGATTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 13 0.45
23 5 0.17
24 11 0.38
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.55
Consensus pattern (24 bp):
TTAGGGTTTTGAATTGTTTTAGGG
Found at i:39438527 original size:159 final size:160
Alignment explanation
Indices: 39438290--39438640 Score: 523
Period size: 159 Copynumber: 2.2 Consensus size: 160
39438280 TTTAGAGTTA
*
39438290 TTTAATA-TTTTTAAAGGGA-AAATTTAATGAACACTTAGAGTTGATGGTTAATTAATTAAATTA
1 TTTAATAGTTTTT-AAGGGAGAAA-TTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTA
* * *
39438353 ACTATGAAAATAAAAAAAAT-AATTAAATTAGGGTTTTGAGTTTTTT-AGGTTAGGGTTTTTAAT
64 ACTATGAAAAT-AAAAAAATCAATTAAATTAAGGTTTTAAGTTTTTTAAGGTTAGGGTTTCTAAT
* *
39438416 TGTTTTAGGGTTAGAGTTTTAGTGATTTGGGGTT
128 TATTTTAGGGTTAGAGTTTTAGTGATTTAGGG-T
* *
39438450 TTTAGTGGTTTTTAAGGGAGAAATTAATGAACACTTAGAGTT-AGGGTTAATTAATTAAATTAAC
1 TTTAATAGTTTTTAAGGGAGAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAAC
* * *
39438514 TATGAGAATAAAAAACTCAATTAAATTAAGGTTTTAAGTTTTTTAAGGTTAGGGTTTCTGATTAT
66 TATGAAAATAAAAAAATCAATTAAATTAAGGTTTTAAGTTTTTTAAGGTTAGGGTTTCTAATTAT
*
39438579 TTTAGGGTTAGAGTTTTAGTGGTTTAGGGT
131 TTTAGGGTTAGAGTTTTAGTGATTTAGGGT
39438609 TTTAATAGTTTTTAAGGGAGAAATTAATGAAC
1 TTTAATAGTTTTTAAGGGAGAAATTAATGAAC
39438641 GCTCAGAAAT
Statistics
Matches: 173, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
158 7 0.04
159 84 0.49
160 74 0.43
161 8 0.05
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.42
Consensus pattern (160 bp):
TTTAATAGTTTTTAAGGGAGAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAAC
TATGAAAATAAAAAAATCAATTAAATTAAGGTTTTAAGTTTTTTAAGGTTAGGGTTTCTAATTAT
TTTAGGGTTAGAGTTTTAGTGATTTAGGGT
Found at i:39438569 original size:23 final size:23
Alignment explanation
Indices: 39438543--39438596 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
39438533 ATTAAATTAA
39438543 GGTTTTAAGTT-TTTTAAGGTTAG
1 GGTTTTAA-TTATTTTAAGGTTAG
* *
39438566 GGTTTCTGATTATTTTAGGGTTAG
1 GGTTT-TAATTATTTTAAGGTTAG
*
39438590 AGTTTTA
1 GGTTTTA
39438597 GTGGTTTAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.20, C:0.02, G:0.26, T:0.52
Consensus pattern (23 bp):
GGTTTTAATTATTTTAAGGTTAG
Found at i:39438898 original size:125 final size:126
Alignment explanation
Indices: 39438657--39439117 Score: 680
Period size: 125 Copynumber: 3.7 Consensus size: 126
39438647 AAATTAATGC
* * * * * * *
39438657 ACACATTCAAGAATGATGCATTTTTAGCAAATTTTTAAAAAAAAGCTTCCACGTGGACGCTCTTT
1 ACAC-TTCAAGAAGGATGCACTTTCAGCAAAATTTCAAAAAAAAGCTCCCACGTGAACGCTCTTT
*
39438722 TGCTATAGTGGTATCTGATAAAATAATTTTGAAAAGATGTTTCTGAACAAATAGTGTCAAAA
65 TGCTATAGTGGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAA
* * * *
39438784 ACGCTTCAAGAAGGATGCACTTTCAGCAAAATTTCAGAAAAAAGCTTCCACGTGAATGCTCTTTT
1 ACACTTCAAGAAGGATGCACTTTCAGCAAAATTTCAAAAAAAAGCTCCCACGTGAACGCTCTTTT
*
39438849 GCTA-CGTGGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTC-AAA
66 GCTATAGTGGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAA
* *
39438908 ACACTTCAAGAAGGGTGCACTTTCAGCAAAATTTCAAAAAAAAGCTCCCACGTGAACGTTCTTTT
1 ACACTTCAAGAAGGATGCACTTTCAGCAAAATTTCAAAAAAAAGCTCCCACGTGAACGCTCTTTT
* * *
39438973 GCTACAGTGGTCTCTGATAAAATAATTTTAAGAAGATGTTTCTGAACAAATAGTGTCAAAA
66 GCTATAGTGGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAA
* * * *
39439034 ACACTTTAAGAAGGATGCACTTTCAGCAAAATTTC-AGAAAAAGCTCCCACGTGGACGCTATTTT
1 ACACTTCAAGAAGGATGCACTTTCAGCAAAATTTCAAAAAAAAGCTCCCACGTGAACGCTCTTTT
39439098 GCTATAGTGGT-TCTGA-AAAA
66 GCTATAGTGGTATCTGATAAAA
39439118 GCCTTAGACT
Statistics
Matches: 305, Mismatches: 27, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
123 4 0.01
124 71 0.23
125 134 0.44
126 93 0.30
127 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (126 bp):
ACACTTCAAGAAGGATGCACTTTCAGCAAAATTTCAAAAAAAAGCTCCCACGTGAACGCTCTTTT
GCTATAGTGGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAA
Found at i:39442723 original size:18 final size:18
Alignment explanation
Indices: 39442697--39442740 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
39442687 GACTGGGAAA
* *
39442697 AGGAAACATAAAAGGGTT
1 AGGATACATAAAAGGGCT
*
39442715 AGGATACATATAAGGGCT
1 AGGATACATAAAAGGGCT
39442733 AGGATACA
1 AGGATACA
39442741 CACCTGGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.09, G:0.27, T:0.18
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:39443369 original size:7 final size:7
Alignment explanation
Indices: 39443357--39443402 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
39443347 TTATATAGGT
39443357 AATACTA
1 AATACTA
39443364 AATACTA
1 AATACTA
39443371 AATACTA
1 AATACTA
39443378 AATACTA
1 AATACTA
39443385 AATACTA
1 AATACTA
39443392 AATACTA
1 AATACTA
39443399 AATA
1 AATA
39443403 TGAAATGACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:39444586 original size:22 final size:21
Alignment explanation
Indices: 39444554--39444600 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
39444544 ACACAGCTTT
39444554 TTTG-CAAAAATT-AGAGACAA
1 TTTGACAAAAATTGAGAGA-AA
39444574 CTTTGACAAAAATTGAGAGAAA
1 -TTTGACAAAAATTGAGAGAAA
39444596 TTTGA
1 TTTGA
39444601 GAGAATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.38
22 10 0.42
23 5 0.21
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.28
Consensus pattern (21 bp):
TTTGACAAAAATTGAGAGAAA
Found at i:39452586 original size:20 final size:20
Alignment explanation
Indices: 39452564--39452605 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
39452554 CTTTAGAATT
*
39452564 TTTTTTAT-AA-ATTTTGGA
1 TTTTTTATAAATATTTTGAA
39452582 TTTTTTATAAATATTTTGAA
1 TTTTTTATAAATATTTTGAA
39452602 TTTT
1 TTTT
39452606 GAAAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 2 0.10
20 11 0.52
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (20 bp):
TTTTTTATAAATATTTTGAA
Found at i:39456135 original size:28 final size:27
Alignment explanation
Indices: 39456095--39456156 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
39456085 CATCACAGAC
* * * *
39456095 ACAGTATCAGGTGGGCTTTAGCCCATT
1 ACAGAATCAGGTGGGCCTAAGCCCAAT
39456122 AACAGAATCAGGTGGGCCTAAGCCCAAT
1 -ACAGAATCAGGTGGGCCTAAGCCCAAT
39456150 ACAGAAT
1 ACAGAAT
39456157 TAGTATCAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (27 bp):
ACAGAATCAGGTGGGCCTAAGCCCAAT
Found at i:39480855 original size:140 final size:140
Alignment explanation
Indices: 39480598--39480878 Score: 526
Period size: 140 Copynumber: 2.0 Consensus size: 140
39480588 TGGTCCCTAC
39480598 AAGGATTTTTCATGAAAATCACCTAGGAAAAGATGTTTAACACATATTCATCTTTCATTGTTCCT
1 AAGGATTTTTCATGAAAATCACCTAGGAAAAGATGTTTAACACATATTCATCTTTCATTGTTCCT
* *
39480663 CCATAATCCATCAAAATACAAGTTACTCATGCATGGGTAAATTTTTAAACATGAACCTTAGCATG
66 CCATAATCCATCAAAATACAAATGACTCATGCATGGGTAAATTTTTAAACATGAACCTTAGCATG
39480728 AAATATGGGT
131 AAATATGGGT
*
39480738 AAGGGTTTTTCATGAAAATCACCTAGGAAAAGATGTTTAACACATATTCATCTTTCATTGTTCCT
1 AAGGATTTTTCATGAAAATCACCTAGGAAAAGATGTTTAACACATATTCATCTTTCATTGTTCCT
*
39480803 CTATAATCCATCAAAATACAAATGACTCATGCATGGGTAAATTTTTAAACATGAACCTTAGCATG
66 CCATAATCCATCAAAATACAAATGACTCATGCATGGGTAAATTTTTAAACATGAACCTTAGCATG
39480868 AAATATGGGT
131 AAATATGGGT
39480878 A
1 A
39480879 CAAATGGAGA
Statistics
Matches: 137, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 137 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.33
Consensus pattern (140 bp):
AAGGATTTTTCATGAAAATCACCTAGGAAAAGATGTTTAACACATATTCATCTTTCATTGTTCCT
CCATAATCCATCAAAATACAAATGACTCATGCATGGGTAAATTTTTAAACATGAACCTTAGCATG
AAATATGGGT
Found at i:39494750 original size:40 final size:40
Alignment explanation
Indices: 39494693--39494800 Score: 139
Period size: 40 Copynumber: 2.7 Consensus size: 40
39494683 TTGAATGATG
* * *
39494693 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGA-GTGACCAAA
* *
39494733 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTGACCAAA
39494773 TCCGGACTAAGATCCGAAGGCATTTGTG
1 TCCGGACTAAGATCCGAAGGCATTTGTG
39494801 TATACGAATG
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
40 52 0.85
41 9 0.15
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTGACCAAA
Found at i:39494909 original size:40 final size:41
Alignment explanation
Indices: 39494854--39494959 Score: 155
Period size: 40 Copynumber: 2.6 Consensus size: 41
39494844 TTGAATGATG
*
39494854 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTTACTA-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTATAA
*
39494894 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39494935 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39494960 AACGAGTAGC
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
40 50 0.83
41 10 0.17
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:39494913 original size:161 final size:161
Alignment explanation
Indices: 39494641--39494959 Score: 527
Period size: 161 Copynumber: 2.0 Consensus size: 161
39494631 CGAAAATGAA
39494641 ATACGAATGTGCCATGATTTGTTGTTAAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAGTC
1 ATACGAATGTGCCATGATTTGTTGTTAAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAGTC
*
39494706 CCGAAGGCTTTGTGCTAGGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTA
66 CCGAAGGCTTTGTGCTAGGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTA
39494771 -AATCCGGACTAAGAT-CCGAAGGCATTTGTGT
131 TAA-CCGGACTAAG-TCCCGAAGGCATTTGTGT
39494802 ATACGAATGTGCCATGATTTGTTGTTAAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAGTC
1 ATACGAATGTGCCATGATTTGTTGTTAAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAGTC
* * **
39494867 CCGAAGGCTTTGTGCTAGGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACT
66 CCGAAGGCTTTGTGCTAGGTGACCAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACT
* *
39494931 ATAACCGGGCTATGTCCCGAAGGCATTTG
130 ATAACCGGACTAAGTCCCGAAGGCATTTG
39494960 AACGAGTAGC
Statistics
Matches: 148, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
160 2 0.01
161 144 0.97
162 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (161 bp):
ATACGAATGTGCCATGATTTGTTGTTAAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAGTC
CCGAAGGCTTTGTGCTAGGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTA
TAACCGGACTAAGTCCCGAAGGCATTTGTGT
Found at i:39502889 original size:79 final size:81
Alignment explanation
Indices: 39502753--39502937 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
39502743 TTGAATGATG
*
39502753 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
39502817 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
39502832 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
39502894 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
39502912 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39502938 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:39502951 original size:40 final size:40
Alignment explanation
Indices: 39502754--39502937 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
39502744 TGAATGATGT
* * * *
39502754 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
39502794 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
39502834 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39502872 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39502913 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
39502938 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:39502959 original size:79 final size:79
Alignment explanation
Indices: 39502806--39502970 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
39502796 GGACTAAGAT
* **
39502806 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
39502871 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
39502885 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
39502948 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
39502964 CCGAAGG
1 CCGAAGG
39502971 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:39517249 original size:55 final size:53
Alignment explanation
Indices: 39517160--39517415 Score: 247
Period size: 55 Copynumber: 4.8 Consensus size: 53
39517150 CATTAGGGTT
**
39517160 CAAGGATACCATGTAAGACCATG-CTAAGGTATGGCAATTGGTAAGGTTTCTAAGG
1 CAAGGATACCATGTAAGACCATGTC-AAGACATGGC-ATTGGTAA-GTTTCTAAGG
* * * * *
39517215 CAAGGAAATCATGTAAGACCTTGTCAAGACATGGCATTGATAAGTTACTATAAGG
1 CAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTT--TCTAAGG
* * * *
39517270 CAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGG
1 C-AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTC-TAAGG
*
39517323 CAAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTTTC-AA--
1 CAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCTAAGG
* ** * *
39517373 -AAGGATACCACGTAAGACCATAACAAGTCATGGCAATGGTAAG
1 CAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAG
39517416 GTACCTGTGT
Statistics
Matches: 169, Mismatches: 25, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
49 39 0.23
52 7 0.04
53 42 0.25
54 11 0.07
55 65 0.38
56 5 0.03
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (53 bp):
CAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCTAAGG
Found at i:39517367 original size:108 final size:110
Alignment explanation
Indices: 39517168--39517368 Score: 300
Period size: 108 Copynumber: 1.8 Consensus size: 110
39517158 TTCAAGGATA
* * *
39517168 CCATGTAAGACCATGCTAAGGTATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
* *
39517233 CCTTGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* *
39517278 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
39517340 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
39517369 TCAAAAGGAT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.57
109 7 0.09
110 25 0.30
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:39519136 original size:3 final size:3
Alignment explanation
Indices: 39519128--39519159 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
39519118 CCATAAAACT
39519128 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
39519160 CTAACTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:39522387 original size:47 final size:47
Alignment explanation
Indices: 39522295--39522569 Score: 180
Period size: 47 Copynumber: 5.9 Consensus size: 47
39522285 GTGGGTAAGG
*
39522295 TGTCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCATATCTCA
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCA
* *
39522342 TGTCGATGCCATGTCCTAGACATAGG-CTTATACT-GACT-ATCATCTCA
1 TGTCGATGCCATGTCCCAGACAT-GGTCTTACACTAG-CTCAT-ATCTCA
* * * * *
39522389 TAGCCGATG-CATGTCCCAGACAT-GTCTTACATTGGCTTATGTCTCGA
1 T-GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTC-A
* * * * *
39522436 GGCCGATG-TATGTCCCAGACAT-GTCTTACACTAGCAC-TCGTCTCGA
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCAT-ATCTC-A
* * * * * *
39522482 TGCCGATACCATGTCTCAAACATGGTCTTACACTGGCTC---TCATAA
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATC-TCA
*
39522527 TGTGGCTGATG-CATGTCCCAGACAT-GTCTTACACTAGCCCATA
1 TGT--C-GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATA
39522570 ATAACCCACA
Statistics
Matches: 182, Mismatches: 28, Indels: 34
0.75 0.11 0.14
Matches are distributed among these distances:
45 7 0.04
46 73 0.40
47 78 0.43
48 24 0.13
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (47 bp):
TGTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCA
Found at i:39522479 original size:46 final size:46
Alignment explanation
Indices: 39522391--39522564 Score: 165
Period size: 46 Copynumber: 3.7 Consensus size: 46
39522381 TCATCTCATA
* *
39522391 GCCGATGCATGTCCCAGACATGTCTTACATTGGCTTA-T-GTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC--ACTCGTCTCGAG
* *
39522437 GCCGATGTATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGAG
* * * * * * * *
39522483 GCCGATACCATGTCTCAAACATGGTCTTACACTGGCTCTCATAAT-GTG
1 GCCGAT-GCATGTCCCAGACAT-GTCTTACACTAGCACTCGT-CTCGAG
*
39522531 GCTGATGCATGTCCCAGACATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
39522565 CCATAATAAC
Statistics
Matches: 104, Mismatches: 19, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
44 1 0.01
45 1 0.01
46 56 0.54
47 23 0.22
48 22 0.21
49 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGAG
Done.