Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007190.1 Hibiscus syriacus cultivar Beakdansim tig00018945_pilon, whole genome shotgun sequence
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: 100138
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2714 original size:17 final size:18
Alignment explanation
Indices: 2694--2741 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
2684 TTTCCTTTTT
*
2694 TTTTTTATTTTTTC-TCA
1 TTTTTTCTTTTTTCATCA
*
2711 TTTTTTCCTTTTTCATCA
1 TTTTTTCTTTTTTCATCA
2729 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
2742 TTCTTTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTCTTTTTTCATCA
Found at i:2714 original size:18 final size:18
Alignment explanation
Indices: 2693--2745 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
2683 TTTTCCTTTT
2693 TTTTTTTATTTTTTCTCA
1 TTTTTTTATTTTTTCTCA
**
2711 -TTTTTTCCTTTTTCATCA
1 TTTTTTTATTTTTTC-TCA
*
2729 TTTTTTCTTTTTTTTCT
1 TTTTTT-TATTTTTTCT
2746 TTCTTTGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 12 0.43
18 3 0.11
19 6 0.21
20 7 0.25
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTTATTTTTTCTCA
Found at i:5576 original size:12 final size:12
Alignment explanation
Indices: 5531--5576 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
5521 GGAAATATGA
*
5531 AAATGTAAATAC
1 AAATGTAAATGC
* *
5543 AAACGTAAAAGC
1 AAATGTAAATGC
5555 AAATGTAAATGC
1 AAATGTAAATGC
5567 AAATGTAAAT
1 AAATGTAAAT
5577 ATATGAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.57, C:0.09, G:0.13, T:0.22
Consensus pattern (12 bp):
AAATGTAAATGC
Found at i:7123 original size:20 final size:20
Alignment explanation
Indices: 7098--7158 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
7088 ATAAATAATG
7098 AAATAAAATATTTGAAAATA
1 AAATAAAATATTTGAAAATA
* ***
7118 AAATAAAAAATAAAAAAATA
1 AAATAAAATATTTGAAAATA
*
7138 TAAT-AAATATTATGAAAATA
1 AAATAAAATATT-TGAAAATA
7158 A
1 A
7159 TAAGTAATAA
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
19 5 0.17
20 25 0.83
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
AAATAAAATATTTGAAAATA
Found at i:7796 original size:20 final size:19
Alignment explanation
Indices: 7761--7798 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
7751 CTTTGATATT
7761 AAAAAATAAATAATAATTA
1 AAAAAATAAATAATAATTA
7780 AAAATAAT-AATATATAATT
1 AAAA-AATAAATA-ATAATT
7799 TATAAAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAAATAAATAATAATTA
Found at i:7891 original size:118 final size:118
Alignment explanation
Indices: 7672--7891 Score: 266
Period size: 118 Copynumber: 1.9 Consensus size: 118
7662 TATATTAATT
* * * *
7672 TATATATATTTATAAATAAAATATTATTTATTTAGAAATATCAGAAAATGACTTCTAGGTGCCTT
1 TATATATATTTATAAATAAAATATTATTTATTTAAAAAGATCAGAAAATGACATCCAGGTGCCTT
* *
7737 AAGACAACTCTTTTCTTTGATATTAAAAAATAAATAATAATTAAAAATAATAA
66 AAGACAACTCCTTTCTTTAATATTAAAAAATAAATAATAATTAAAAATAATAA
** * *
7790 TATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAAGATCAGAAAATGGACATCCAGTTGT
1 TATATATATTTAT-AAATAAAATA-TTATTTATTTAAAAAGATCAGAAAAT-GACATCCAGGTGC
* ** *
7854 TTTAAGACTGC-CCTTTC-TTAATATTGAAAAATAAATAA
63 CTTAAGACAACTCCTTTCTTTAATATTAAAAAATAAATAA
7892 ATATATATTA
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
117 6 0.07
118 33 0.39
119 29 0.34
120 17 0.20
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (118 bp):
TATATATATTTATAAATAAAATATTATTTATTTAAAAAGATCAGAAAATGACATCCAGGTGCCTT
AAGACAACTCCTTTCTTTAATATTAAAAAATAAATAATAATTAAAAATAATAA
Found at i:8007 original size:14 final size:14
Alignment explanation
Indices: 7984--8016 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
7974 TTTTATTTAT
7984 ATAA-ATAATAAAA
1 ATAATATAATAAAA
*
7997 ATAATATAATAATA
1 ATAATATAATAAAA
8011 ATAATA
1 ATAATA
8017 AAAATATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAATATAATAAAA
Found at i:8505 original size:11 final size:11
Alignment explanation
Indices: 8489--8518 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
8479 CTCATTTTTC
8489 TTTCTCTCTTA
1 TTTCTCTCTTA
*
8500 TTTCTCTCTTC
1 TTTCTCTCTTA
8511 TTTCTCTC
1 TTTCTCTC
8519 AAATGAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTCTCTCTTA
Found at i:12833 original size:15 final size:16
Alignment explanation
Indices: 12799--12830 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12789 ATTTTAACTG
*
12799 ATTATTTTTTTATAAA
1 ATTATTTTTTAATAAA
12815 ATTATTTTTTAATAAA
1 ATTATTTTTTAATAAA
12831 TTAAGGTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATTTTTTAATAAA
Found at i:13290 original size:13 final size:13
Alignment explanation
Indices: 13272--13296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13262 TAATTGAACG
13272 GTCTTCATATGCA
1 GTCTTCATATGCA
13285 GTCTTCATATGC
1 GTCTTCATATGC
13297 GCGTATGTAA
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:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (13 bp):
GTCTTCATATGCA
Found at i:24723 original size:20 final size:20
Alignment explanation
Indices: 24698--24750 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
24688 GATTTTCTAG
* *
24698 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
*
24718 AATCGCAATGCGAACACATA
1 AATCGCAACGCGAACACATA
24738 AATCGCAACGCGA
1 AATCGCAACGCGA
24751 TTCTTACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.43, C:0.25, G:0.19, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:24782 original size:62 final size:62
Alignment explanation
Indices: 24716--24961 Score: 197
Period size: 60 Copynumber: 4.0 Consensus size: 62
24706 CGCGAATATG
* * *
24716 AAAATCGCAATGCG-AACACATAAATCGCAACGCG-ATTCTTACTATCGCAACGAGTATCCGTA
1 AAAATCGCAACGCGTAAC-CATAAATCGCAACGCGTATCCGTA-TATCGCAACGAGTATCCGTA
* * *
24778 AAAATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTATATCGCAACGAGTATCCGT-
1 AAAATCGCAACGCGTAACCATAAATCGCAACGCGTATCCGTATATCGCAACGAGTATCCGTA
* * * * * *
24839 -AAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGA-TAATCCGT-
1 AAAATCGCAACGCGTAA-CCATAAATCGCAACGCGTATCCGTATATCGCAACGAGT-ATCCGTA
* ** * * * *
24899 -AAATCGCAACGAG-AATCTGTAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTA
1 AAAATCGCAACGCGTAA-CCATAAATCGCAACGCGT-ATCCGTATATCGCAACGAGTATCCGTA
24960 AA
1 AA
24962 TCACAACACT
Statistics
Matches: 155, Mismatches: 20, Indels: 18
0.80 0.10 0.09
Matches are distributed among these distances:
59 3 0.02
60 98 0.63
62 47 0.30
63 7 0.05
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (62 bp):
AAAATCGCAACGCGTAACCATAAATCGCAACGCGTATCCGTATATCGCAACGAGTATCCGTA
Found at i:24804 original size:20 final size:20
Alignment explanation
Indices: 24759--24968 Score: 255
Period size: 20 Copynumber: 10.4 Consensus size: 20
24749 GATTCTTACT
24759 ATCGCAACGAGTATCCGTAAAA
1 ATCGCAACGAGTATCCGT--AA
*
24781 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* * *
24801 ATCGCAATGCGTATCCGTAT
1 ATCGCAACGAGTATCCGTAA
24821 ATCGCAACGAGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
24841 ATCGCAACGA-TAATCCGTAA
1 ATCGCAACGAGT-ATCCGTAA
* *
24861 ATCGCAACGAGAATCTGTAA
1 ATCGCAACGAGTATCCGTAA
24881 ATCGCAACGA-TAATCCGTAA
1 ATCGCAACGAGT-ATCCGTAA
* *
24901 ATCGCAACGAGAATCTGTAA
1 ATCGCAACGAGTATCCGTAA
24921 ATCGCAACGA-TAATCCGTAA
1 ATCGCAACGAGT-ATCCGTAA
* *
24941 ATCGCAACGAGAATCTGTAA
1 ATCGCAACGAGTATCCGTAA
*
24961 ATCACAAC
1 ATCGCAAC
24969 ACTGAAATTT
Statistics
Matches: 165, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.01
20 147 0.89
22 17 0.10
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:24836 original size:40 final size:40
Alignment explanation
Indices: 24736--24968 Score: 294
Period size: 40 Copynumber: 5.8 Consensus size: 40
24726 TGCGAACACA
* * *
24736 TAAATCGCAACGCGATTCT-TACTATCGCAACGAGT-ATCCG
1 TAAATCGCAACGAGAATCTGTA-AATCGCAACGA-TAATCCG
* * *
24776 TAAAAATCGCAACGCGTATCCGTAAATCGCAATGCG-T-ATCCG
1 T--AAATCGCAACGAGAATCTGTAAATCGCAA--CGATAATCCG
* * *
24818 TATATCGCAACGAGTATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
24858 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
24898 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
*
24938 TAAATCGCAACGAGAATCTGTAAATCACAAC
1 TAAATCGCAACGAGAATCTGTAAATCGCAAC
24969 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 10, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
40 140 0.80
42 29 0.16
43 2 0.01
44 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.21
Consensus pattern (40 bp):
TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
Found at i:25689 original size:24 final size:24
Alignment explanation
Indices: 25650--25696 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
25640 AAATTTGGTC
25650 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
25674 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
25697 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:25886 original size:12 final size:12
Alignment explanation
Indices: 25869--25893 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25859 TCATAATCCT
25869 GAAGAAGAAAAA
1 GAAGAAGAAAAA
25881 GAAGAAGAAAAA
1 GAAGAAGAAAAA
25893 G
1 G
25894 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:27293 original size:33 final size:33
Alignment explanation
Indices: 27251--27321 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
27241 AATACTAACT
*
27251 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* * *
27284 TGAAAATCGCAACGACAGAATCGTAACGTGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
27317 TGAAA
1 TGAAA
27322 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:27556 original size:22 final size:22
Alignment explanation
Indices: 27504--27558 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
27494 TGGTTGTGAG
**
27504 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
27526 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
27548 GGATTTCTTCG
1 GGATTTCTTCG
27559 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:27833 original size:40 final size:40
Alignment explanation
Indices: 27705--27859 Score: 195
Period size: 40 Copynumber: 3.9 Consensus size: 40
27695 GCTTTAAATA
*
27705 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** *
27746 TATCGTTGCGATTTACGGATACGCGTTGCGATTTACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
27786 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
27826 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
27860 TGGAAAATCG
Statistics
Matches: 98, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
40 68 0.69
41 30 0.31
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.38
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:27860 original size:20 final size:20
Alignment explanation
Indices: 27706--27859 Score: 177
Period size: 20 Copynumber: 7.7 Consensus size: 20
27696 CTTTAAATAT
27706 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
27726 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
27748 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
27767 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
27787 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
27807 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
27827 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
27847 CGCGTTGCGATTT
1 CGCGTTGCGATTT
27860 TGGAAAATCG
Statistics
Matches: 115, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.02
20 96 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:27876 original size:21 final size:21
Alignment explanation
Indices: 27846--27928 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
27836 ATTTTCATAT
*
27846 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
27867 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
27888 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
27909 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
27929 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:27919 original size:42 final size:43
Alignment explanation
Indices: 27826--27924 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
27816 ATTTATGTGT
* *
27826 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
27867 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
27909 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
27925 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:31485 original size:30 final size:30
Alignment explanation
Indices: 31449--31512 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
31439 TTGTATTTGG
31449 AATTTGAGACCATGAATTCCAAATATAAGA
1 AATTTGAGACCATGAATTCCAAATATAAGA
31479 AATTTGAGACCATGAATTCCAAATATAAGA
1 AATTTGAGACCATGAATTCCAAATATAAGA
31509 AATT
1 AATT
31513 AATTTCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (30 bp):
AATTTGAGACCATGAATTCCAAATATAAGA
Found at i:33218 original size:23 final size:23
Alignment explanation
Indices: 33188--33257 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
33178 AGTGCCACAT
* *
33188 ATTTTTCCTGAAGGACCATATAG
1 ATTTTTCCCGAAGGACCACATAG
*
33211 ATTTTTCCCGAAGAACCACATAG
1 ATTTTTCCCGAAGGACCACATAG
*
33234 ATTTTTCCCAAAGGACCACATAG
1 ATTTTTCCCGAAGGACCACATAG
33257 A
1 A
33258 CCCTCGATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (23 bp):
ATTTTTCCCGAAGGACCACATAG
Found at i:33468 original size:27 final size:27
Alignment explanation
Indices: 33422--33482 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
33412 TGTTCCATAG
* *
33422 AACATATTCACTTAGCACA-TGTTCACAT
1 AACAT-TTCACGTAGAACATTG-TCACAT
33450 AACATTTCACGTAGAACATTGTCACAT
1 AACATTTCACGTAGAACATTGTCACAT
*
33477 AGCATT
1 AACATT
33483 ATCATATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (27 bp):
AACATTTCACGTAGAACATTGTCACAT
Found at i:49329 original size:23 final size:23
Alignment explanation
Indices: 49272--49368 Score: 105
Period size: 23 Copynumber: 4.3 Consensus size: 23
49262 CACCACTGCT
49272 CACATA-ATTTG-CACCGAAGTG-C
1 CACATAGATTTGTC-CCGAAG-GAC
49294 CACAT--ATTTGTCCCGAAGGAC
1 CACATAGATTTGTCCCGAAGGAC
*
49315 CACATAGATTTGTCCCGAAGAAC
1 CACATAGATTTGTCCCGAAGGAC
* * *
49338 CACATAGATTTTTCACAAAGGAC
1 CACATAGATTTGTCCCGAAGGAC
49361 CACATAGA
1 CACATAGA
49369 CCCTTGACTC
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.02
21 17 0.26
22 6 0.09
23 42 0.64
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (23 bp):
CACATAGATTTGTCCCGAAGGAC
Found at i:49584 original size:27 final size:27
Alignment explanation
Indices: 49538--49598 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
49528 TATTCCATAG
* *
49538 AACATATTCACTTAGCACA-TGTTCACAT
1 AACAT-TTCACGTAGAACATTG-TCACAT
49566 AACATTTCACGTAGAACATTGTCACAT
1 AACATTTCACGTAGAACATTGTCACAT
*
49593 AGCATT
1 AACATT
49599 ATCAGATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (27 bp):
AACATTTCACGTAGAACATTGTCACAT
Found at i:51378 original size:12 final size:12
Alignment explanation
Indices: 51361--51385 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51351 AAACTATTTA
51361 TATTTAATTATT
1 TATTTAATTATT
51373 TATTTAATTATT
1 TATTTAATTATT
51385 T
1 T
51386 TATTCTTATC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTAATTATT
Found at i:56372 original size:3 final size:3
Alignment explanation
Indices: 56364--56451 Score: 86
Period size: 3 Copynumber: 28.7 Consensus size: 3
56354 TTCATTTAAA
* * * * * *
56364 TAT TAT TAT AAT TAT TAT TAT AAT TAT TAT TAT AAT TAT AAT TAC TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
56412 TAT TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
56452 CAAACGGGCC
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
3 63 0.91
4 6 0.09
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:56381 original size:12 final size:12
Alignment explanation
Indices: 56364--56451 Score: 98
Period size: 12 Copynumber: 7.7 Consensus size: 12
56354 TTCATTTAAA
56364 TATTATTATAAT
1 TATTATTATAAT
56376 TATTATTATAAT
1 TATTATTATAAT
56388 TATTATTATAAT
1 TATTATTATAAT
*
56400 TATAATTACTAA-
1 TATTATTA-TAAT
56412 TATTATTAT--T
1 TATTATTATAAT
*
56422 TATTA--CTAA-
1 TATTATTATAAT
56431 TATTATTATTAAT
1 TATTATTA-TAAT
56444 TATTATTA
1 TATTATTA
56452 CAAACGGGCC
Statistics
Matches: 64, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
8 1 0.02
9 5 0.08
10 5 0.08
11 1 0.02
12 41 0.64
13 11 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTATTATAAT
Found at i:57726 original size:23 final size:19
Alignment explanation
Indices: 57700--57751 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 19
57690 GATTTTTAAT
57700 TTTATTTTCACTATATTTAGTCA
1 TTTATTTT-A-TATATTT--TCA
*
57723 TTTATTTTATATGTTTTCA
1 TTTATTTTATATATTTTCA
57742 TTTATTTTAT
1 TTTATTTTAT
57752 TGTTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 13 0.46
21 6 0.21
22 1 0.04
23 8 0.29
ACGTcount: A:0.23, C:0.08, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTATTTTATATATTTTCA
Found at i:57758 original size:19 final size:19
Alignment explanation
Indices: 57720--57757 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
57710 CTATATTTAG
57720 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
57739 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
57757 T
1 T
57758 TAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:57870 original size:13 final size:13
Alignment explanation
Indices: 57852--57890 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
57842 GTAATTAAAT
57852 TTTTAAATATTTA
1 TTTTAAATATTTA
*
57865 TTTTAAATGAATTA
1 TTTTAAAT-ATTTA
57879 TTTT-AATATTTA
1 TTTTAAATATTTA
57891 GCTTTCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTTAAATATTTA
Found at i:58538 original size:20 final size:21
Alignment explanation
Indices: 58515--58566 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
58505 AGAAATTAAA
58515 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
58535 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
58557 -ATT-ATTTATT
1 AATTCATTTATT
58567 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:60008 original size:15 final size:14
Alignment explanation
Indices: 59983--60024 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
59973 TTTTCATGCA
59983 TACAT-TTGCATTT
1 TACATCTTGCATTT
59996 TACATCCTTGCATTT
1 TACAT-CTTGCATTT
* *
60011 TTCATTTTGCATTT
1 TACATCTTGCATTT
60025 ATACTGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 12 0.48
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (14 bp):
TACATCTTGCATTT
Found at i:66815 original size:50 final size:50
Alignment explanation
Indices: 66735--66835 Score: 152
Period size: 50 Copynumber: 2.0 Consensus size: 50
66725 AATGATTGAG
*
66735 ACATCTGAGCAGAATACACAGAAAAGGATGAATGTGTTGTCAAATGTTTT
1 ACATCTGAGCAGAATACACAGAAAAGGATGAATGTATTGTCAAATGTTTT
*
66785 ACATCTGAGTAGAA-ACCACATGAAAA-GATGAATGTATTGTCAAATGTTTT
1 ACATCTGAGCAGAATA-CACA-GAAAAGGATGAATGTATTGTCAAATGTTTT
66835 A
1 A
66836 TGAACCAGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
49 1 0.02
50 41 0.87
51 5 0.11
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.29
Consensus pattern (50 bp):
ACATCTGAGCAGAATACACAGAAAAGGATGAATGTATTGTCAAATGTTTT
Found at i:67238 original size:22 final size:22
Alignment explanation
Indices: 67207--67261 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
67197 ATCTACACTC
*
67207 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
67229 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
67251 TTCAAAGATGA
1 TTCAAAGATGA
67262 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:68318 original size:24 final size:23
Alignment explanation
Indices: 68275--68319 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
68265 GTTCATAATG
*
68275 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
68298 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
68320 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:68463 original size:116 final size:114
Alignment explanation
Indices: 67660--68801 Score: 1644
Period size: 113 Copynumber: 10.0 Consensus size: 114
67650 TTAGCAAAGA
* * *
67660 TTTAAATCCATCA-TTCGATGGATCAGCATTACCAGAGAA-AGTTCATAATGAGAAGAACTCATC
1 TTTAAATTCATCACTT-GATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATC
67723 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
65 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
* * * ***
67773 CTCAAA-TCTATCACTTGATGGATTATTTTTGCCAGAGAA-AGTTCATAATGAGAAGAACTCATC
1 TTTAAATTC-ATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATC
67836 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
65 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
* * * ***
67886 TCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAG-GTTCATAATGAGAAGAACTCATCT
1 TTTAAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATCT
67950 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
* * * *** *
67999 CTCAAA-TCTATCACTTGATGGATTATTTTTGCCTGAGAA-AGTTCATAATGAGAAGAACTCATC
1 TTTAAATTC-ATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATC
68062 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
65 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
* * * ***
68112 TCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAG-GTTCATAATGAGAAGAACTCATCT
1 TTTAAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATCT
68176 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
* * * * *
68225 TTTAAATTCATCACTTGATGGATCAGCTTTTCCAGA-AAAAGTTCATAATGAGAAGAATTCATCT
1 TTTAAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATCT
68289 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
*
68338 TTTAAATTCATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCGTCA
1 TTTAAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAA--C-TCA
** *
68402 TCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTATG
63 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
*
68454 TTTAAATTCATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCGTCA
1 TTTAAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAA--C-TCA
68518 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
63 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
*
68570 TTTAAATTCATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCATCA
1 TTTAAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATC-
*
68634 TTTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTG
65 --TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
*
68686 TTTAAATTCATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCGTCA
1 TTTAAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAA--C-TCA
** ** *
68750 TCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
63 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
68802 AATGACTCTA
Statistics
Matches: 961, Mismatches: 49, Indels: 35
0.92 0.05 0.03
Matches are distributed among these distances:
112 5 0.01
113 571 0.59
114 7 0.01
116 372 0.39
118 1 0.00
119 5 0.01
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (114 bp):
TTTAAATTCATCACTTGATGGATCAACATTGCCAGAGAAGAGTTCATAATGAGAAGAACTCATCT
GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
Found at i:69031 original size:3 final size:3
Alignment explanation
Indices: 69025--69112 Score: 86
Period size: 3 Copynumber: 28.7 Consensus size: 3
69015 TTCATTTAAA
* * * * * *
69025 TAT TAT TAT AAT TAT TAT TAT AAT TAT TAT TAT AAT TAT AAT TAC TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
69073 TAT TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
69113 CAAACGAGCC
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
3 63 0.91
4 6 0.09
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:69042 original size:12 final size:12
Alignment explanation
Indices: 69025--69112 Score: 98
Period size: 12 Copynumber: 7.7 Consensus size: 12
69015 TTCATTTAAA
69025 TATTATTATAAT
1 TATTATTATAAT
69037 TATTATTATAAT
1 TATTATTATAAT
69049 TATTATTATAAT
1 TATTATTATAAT
*
69061 TATAATTACTAA-
1 TATTATTA-TAAT
69073 TATTATTAT--T
1 TATTATTATAAT
*
69083 TATTA--CTAA-
1 TATTATTATAAT
69092 TATTATTATTAAT
1 TATTATTA-TAAT
69105 TATTATTA
1 TATTATTA
69113 CAAACGAGCC
Statistics
Matches: 64, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
8 1 0.02
9 5 0.08
10 5 0.08
11 1 0.02
12 41 0.64
13 11 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTATTATAAT
Found at i:70419 original size:19 final size:19
Alignment explanation
Indices: 70381--70418 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
70371 TATAATTTAG
70381 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
70400 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
70418 T
1 T
70419 TAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:70536 original size:13 final size:13
Alignment explanation
Indices: 70518--70556 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
70508 GTAATTAAAT
70518 TTTTAAATATTTA
1 TTTTAAATATTTA
*
70531 TTTTAAATGAATTA
1 TTTTAAAT-ATTTA
70545 TTTT-AATATTTA
1 TTTTAAATATTTA
70557 GCTTTCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTTAAATATTTA
Found at i:74789 original size:27 final size:27
Alignment explanation
Indices: 74744--74803 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
74734 AAAAAGTCGA
* *
74744 AAAAAAACTGTTCATTGTTTCAAACAG
1 AAAAAAACTGTTAAATGTTTCAAACAG
*
74771 CAAAAAAA-TGTTAAATGTTTCGAACAG
1 -AAAAAAACTGTTAAATGTTTCAAACAG
74798 AAAAAA
1 AAAAAA
74804 GAAAAAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 6 0.21
27 16 0.55
28 7 0.24
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.25
Consensus pattern (27 bp):
AAAAAAACTGTTAAATGTTTCAAACAG
Found at i:75778 original size:21 final size:23
Alignment explanation
Indices: 75752--75804 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
75742 AGTATTTTAA
75752 TTAGGATTTAT-TTT-CTTTATT
1 TTAGGATTTATCTTTACTTTATT
*
75773 TTAGGA-TTATCTTTACCTTTTTT
1 TTAGGATTTATCTTTA-CTTTATT
75796 TTAGGATTT
1 TTAGGATTT
75805 TGAAGGCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.15
21 9 0.33
23 12 0.44
24 2 0.07
ACGTcount: A:0.19, C:0.08, G:0.11, T:0.62
Consensus pattern (23 bp):
TTAGGATTTATCTTTACTTTATT
Found at i:76557 original size:12 final size:12
Alignment explanation
Indices: 76534--76578 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
76524 CTTTATCTCA
76534 ATTTATTTTGTTT
1 ATTTA-TTTGTTT
76547 ATTTATTTGTTT
1 ATTTATTTGTTT
*
76559 ATTTAATT-TTT
1 ATTTATTTGTTT
76570 ATTTCATTT
1 ATTT-ATTT
76579 TATTTCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 7 0.24
12 17 0.59
13 5 0.17
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (12 bp):
ATTTATTTGTTT
Found at i:80247 original size:17 final size:17
Alignment explanation
Indices: 80225--80275 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
80215 ACATTATACT
80225 TATAATATATATAAGTA
1 TATAATATATATAAGTA
*
80242 TATAATATAAGTATCAAGTG
1 TATAATAT-A-TAT-AAGTA
80262 TATATATATATATA
1 TATA-ATATATATA
80276 CATACACGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 8 0.28
18 2 0.07
19 6 0.21
20 9 0.31
21 4 0.14
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (17 bp):
TATAATATATATAAGTA
Found at i:80705 original size:17 final size:15
Alignment explanation
Indices: 80674--80768 Score: 66
Period size: 17 Copynumber: 5.7 Consensus size: 15
80664 AATAGACCAC
*
80674 TGTTTT-TTGTTTTT
1 TGTTTTATTTTTTTT
80688 TGTTTTATGCTTTTTTTT
1 TGTTTTA---TTTTTTTT
80706 TGTTTTTTATTTTATTTT
1 TG--TTTTATTTT-TTTT
*
80724 TCTTTCTATTTTTTATT
1 TGTTT-TATTTTTT-TT
80741 TGTTTTATATTTTTATT
1 TGTTTTAT-TTTTT-TT
*
80758 TGTTTTCTTTT
1 TGTTTTATTTT
80769 ATTCATTATT
Statistics
Matches: 67, Mismatches: 4, Indels: 18
0.75 0.04 0.20
Matches are distributed among these distances:
14 6 0.09
16 11 0.16
17 31 0.46
18 14 0.21
20 5 0.07
ACGTcount: A:0.08, C:0.04, G:0.07, T:0.80
Consensus pattern (15 bp):
TGTTTTATTTTTTTT
Found at i:80706 original size:18 final size:17
Alignment explanation
Indices: 80683--80763 Score: 83
Period size: 17 Copynumber: 4.6 Consensus size: 17
80673 CTGTTTTTTG
*
80683 TTTTTTGTTTTATGCTTT
1 TTTTTTGTTTTAT-ATTT
*
80701 TTTTTTGTTTTTTATTT
1 TTTTTTGTTTTATATTT
*
80718 TATTTTTCTTTCTAT-TTT
1 T-TTTTTGTTT-TATATTT
*
80736 TTATTTGTTTTATATTT
1 TTTTTTGTTTTATATTT
*
80753 TTATTTGTTTT
1 TTTTTTGTTTT
80764 CTTTTATTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
16 3 0.06
17 25 0.46
18 24 0.44
19 2 0.04
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.80
Consensus pattern (17 bp):
TTTTTTGTTTTATATTT
Found at i:80744 original size:35 final size:34
Alignment explanation
Indices: 80698--80798 Score: 107
Period size: 38 Copynumber: 2.9 Consensus size: 34
80688 TGTTTTATGC
80698 TTTTTT-TTTGTTTTTTATTTTATTTTTCTTTCTA
1 TTTTTTATTTGTTTTTTATTTTATTTTTCTTT-TA
*
80732 TTTTTTATTTGTTTTATATTTTTATTTGTTTTCTTTTA
1 TTTTTTATTTGTTTTTTA-TTTTA--T-TTTTCTTTTA
** *
80770 TTCATTATTT-TCTTTTATTTTATTTTTCT
1 TTTTTTATTTGTTTTTTATTTTATTTTTCT
80799 CTTTTTTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
33 6 0.11
34 7 0.12
35 10 0.18
36 10 0.18
37 5 0.09
38 11 0.19
39 8 0.14
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.79
Consensus pattern (34 bp):
TTTTTTATTTGTTTTTTATTTTATTTTTCTTTTA
Found at i:80757 original size:24 final size:24
Alignment explanation
Indices: 80702--80794 Score: 66
Period size: 24 Copynumber: 3.9 Consensus size: 24
80692 TTATGCTTTT
* * *
80702 TTTTTGTTTTTTATTTTATTTTTC
1 TTTTTATTTTTTATTTTATTTATA
*
80726 TTTCTATTTTTTATTTGT-TTTATA
1 TTTTTATTTTTTATTT-TATTTATA
* *
80750 TTTTTATTTGTTTTCTTTTATTCAT-
1 TTTTTA-TT-TTTTATTTTATTTATA
* *
80775 TATTT-TCTTTTATTTTATTT
1 TTTTTATTTTTTATTTTATTT
80795 TTCTCTTTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
22 11 0.20
23 1 0.02
24 23 0.43
25 8 0.15
26 11 0.20
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.78
Consensus pattern (24 bp):
TTTTTATTTTTTATTTTATTTATA
Found at i:81111 original size:17 final size:18
Alignment explanation
Indices: 81083--81130 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
81073 TAAAAGGTAT
81083 ATTGATAAAGTTGTT-ACA
1 ATTGA-AAAGTTGTTCACA
*
81101 ATTGAAAAGTT-TTCGCA
1 ATTGAAAAGTTGTTCACA
81118 ATTGAAAAGTTGT
1 ATTGAAAAGTTGT
81131 CTTGTGATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 2 0.07
17 19 0.70
18 6 0.22
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (18 bp):
ATTGAAAAGTTGTTCACA
Found at i:82196 original size:22 final size:22
Alignment explanation
Indices: 82178--82236 Score: 118
Period size: 22 Copynumber: 2.7 Consensus size: 22
82168 TTAGACTTGG
82178 TCTGAATGTTGACTGGACTTAA
1 TCTGAATGTTGACTGGACTTAA
82200 TCTGAATGTTGACTGGACTTAA
1 TCTGAATGTTGACTGGACTTAA
82222 TCTGAATGTTGACTG
1 TCTGAATGTTGACTG
82237 TAATTCGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (22 bp):
TCTGAATGTTGACTGGACTTAA
Found at i:82250 original size:44 final size:44
Alignment explanation
Indices: 82178--82273 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 44
82168 TTAGACTTGG
*
82178 TCTGAATGTTGACTGGACTTAATCTGAATGTTGACTGGACTTAA
1 TCTGAATGTTGACTGGAATTAATCTGAATGTTGACTGGACTTAA
* ** * ** * *
82222 TCTGAATGTTGACTGTAATTCGTTTGAATGTTGGTTGGATTTGA
1 TCTGAATGTTGACTGGAATTAATCTGAATGTTGACTGGACTTAA
82266 TCTGAATG
1 TCTGAATG
82274 ATGAATTGAT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (44 bp):
TCTGAATGTTGACTGGAATTAATCTGAATGTTGACTGGACTTAA
Found at i:82634 original size:18 final size:18
Alignment explanation
Indices: 82596--82636 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
82586 AGAATTATGT
82596 TTAA-TATATTTAAGTTA
1 TTAATTATATTTAAGTTA
82613 --AATTATATTTAAGTTA
1 TTAATTATATTTAAGTTA
82629 TTAATTAT
1 TTAATTAT
82637 TACTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.10
16 13 0.62
18 6 0.29
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
TTAATTATATTTAAGTTA
Found at i:82749 original size:19 final size:19
Alignment explanation
Indices: 82725--82763 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
82715 ATAAATATAG
*
82725 AAAATAAATTTTGTACTAT
1 AAAATAAATTTTGTAATAT
82744 AAAATAAATTTTGTAATAT
1 AAAATAAATTTTGTAATAT
82763 A
1 A
82764 GGGATCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
AAAATAAATTTTGTAATAT
Found at i:83672 original size:109 final size:109
Alignment explanation
Indices: 83481--83698 Score: 330
Period size: 109 Copynumber: 2.0 Consensus size: 109
83471 CATACGTGTT
* * * * *
83481 TTTTCAAATTGGTAAAGTGTAGAAGTCTAAACATCATCCATCAACTATAATTGCAATTTCATACA
1 TTTTCAAATTGGTAAACTGTAGAAGTCCAAACATCATCCATCAAATAAAATTGCAATTACATACA
*
83546 CTTTTTGCTGCCTAATGCTTCCTTCAGTTTCCTTCCCAATGCAA
66 CTTTTTACTGCCTAATGCTTCCTTCAGTTTCCTTCCCAATGCAA
* *
83590 TTTTCAAATTGGTAAACTGTAGAAGTCCCAAC-TACATCCATCAAATAAAATTGCAGTTACATAC
1 TTTTCAAATTGGTAAACTGTAGAAGTCCAAACAT-CATCCATCAAATAAAATTGCAATTACATAC
* *
83654 ACTTTTTACTGTCTAATGCTTCCTTCAGTTTTCTTCCCAATGCAA
65 ACTTTTTACTGCCTAATGCTTCCTTCAGTTTCCTTCCCAATGCAA
83699 ATGCCAAAGG
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 1 0.01
109 97 0.99
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (109 bp):
TTTTCAAATTGGTAAACTGTAGAAGTCCAAACATCATCCATCAAATAAAATTGCAATTACATACA
CTTTTTACTGCCTAATGCTTCCTTCAGTTTCCTTCCCAATGCAA
Found at i:85515 original size:24 final size:24
Alignment explanation
Indices: 85483--85531 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
85473 ATCAGTAAAA
85483 GCAGAAGGTTCGACAAAGTGCTTT
1 GCAGAAGGTTCGACAAAGTGCTTT
*
85507 GCAGAAGGTTGGACAAAGTGCTTT
1 GCAGAAGGTTCGACAAAGTGCTTT
85531 G
1 G
85532 GAAAAAAGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (24 bp):
GCAGAAGGTTCGACAAAGTGCTTT
Found at i:97271 original size:65 final size:65
Alignment explanation
Indices: 97159--97411 Score: 314
Period size: 65 Copynumber: 3.9 Consensus size: 65
97149 TAAGGATTTA
* * **
97159 TTTCAAGAGAAATTGTCTCAAGAAAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATAATG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATAATG
* * * *
97224 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTAAAAGGAAACTATCTCAAAGATGATG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATAATG
* * **
97289 TTTCAAGAGAAACTGTCTCATGAGAGACAAAATTCTTTTCAAGGGAAACGATCTCAAAGATCTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGAT-AAT
97354 G
65 G
* * * * *
97355 TTTCAAGAGAAATTGTTTC-A-AGAGACAAAACTT-GTTTCAAGGGAAACAATCTTAAAG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAG
97412 GTTTTCTTTT
Statistics
Matches: 165, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
64 31 0.19
65 115 0.70
66 19 0.12
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.27
Consensus pattern (65 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATAATG
Found at i:97816 original size:36 final size:37
Alignment explanation
Indices: 97751--97850 Score: 121
Period size: 36 Copynumber: 2.7 Consensus size: 37
97741 CATCTTAAAG
* * *
97751 GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAGA
1 GAAAACTGTCTCAAGTGAGATGAAATTTGTTTTGAGA
* * * *
97788 G-AAATTGTTTCAAGTGAGATGAAGTTTGTTTTTAGA
1 GAAAACTGTCTCAAGTGAGATGAAATTTGTTTTGAGA
*
97824 GAAAACTGTCTCAAGTGAGATAAAATT
1 GAAAACTGTCTCAAGTGAGATGAAATT
97851 ATTTCGAGAG
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
36 30 0.58
37 22 0.42
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (37 bp):
GAAAACTGTCTCAAGTGAGATGAAATTTGTTTTGAGA
Found at i:99022 original size:16 final size:16
Alignment explanation
Indices: 99003--99054 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
98993 TTTTATTTTT
*
99003 CTTTGCTTTTTCTTTG
1 CTTTTCTTTTTCTTTG
*
99019 CTTTTCTTTTTCTTTA
1 CTTTTCTTTTTCTTTG
*
99035 CTTTTTTTCTTTCTTTG
1 CTTTTCTT-TTTCTTTG
99052 CTT
1 CTT
99055 CGATGTGATC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 21 0.68
17 10 0.32
ACGTcount: A:0.02, C:0.19, G:0.06, T:0.73
Consensus pattern (16 bp):
CTTTTCTTTTTCTTTG
Found at i:99040 original size:11 final size:11
Alignment explanation
Indices: 98998--99027 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
98988 TTGTCTTTTA
98998 TTTTTCTTTGC
1 TTTTTCTTTGC
99009 TTTTTCTTTGC
1 TTTTTCTTTGC
99020 -TTTTCTTT
1 TTTTTCTTT
99028 TTCTTTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.77
Consensus pattern (11 bp):
TTTTTCTTTGC
Done.