Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002371.1 Hibiscus syriacus cultivar Beakdansim tig00004844_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: 86593
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:538 original size:22 final size:22
Alignment explanation
Indices: 503--551 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
493 AATTATAATT
503 TAAAA-CTTAATTTTCTTTTAA
1 TAAAATCTTAATTTTCTTTTAA
* *
524 TAAAATCTTATTTTTTTTTTAA
1 TAAAATCTTAATTTTCTTTTAA
*
546 GAAAAT
1 TAAAAT
552 TGATAACTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (22 bp):
TAAAATCTTAATTTTCTTTTAA
Found at i:4724 original size:15 final size:15
Alignment explanation
Indices: 4704--4732 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4694 TCACTCTCAT
4704 CATTATCATCATCAC
1 CATTATCATCATCAC
4719 CATTATCATCATCA
1 CATTATCATCATCA
4733 AGAGCAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (15 bp):
CATTATCATCATCAC
Found at i:5182 original size:12 final size:12
Alignment explanation
Indices: 5150--5183 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
5140 CCAAAATGGC
5150 TTCAGTGCTGGT
1 TTCAGTGCTGGT
5162 TTCTA-TGCTGGT
1 TTC-AGTGCTGGT
5174 TTCAGTGCTG
1 TTCAGTGCTG
5184 CAGTTGAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.05
12 18 0.90
13 1 0.05
ACGTcount: A:0.09, C:0.18, G:0.29, T:0.44
Consensus pattern (12 bp):
TTCAGTGCTGGT
Found at i:5760 original size:19 final size:19
Alignment explanation
Indices: 5736--5784 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
5726 ATATAACGAT
**
5736 AATTAAAAGTAAATAATAA
1 AATTAAAAACAAATAATAA
5755 AATTAAAAACAAATAATAA
1 AATTAAAAACAAATAATAA
5774 AATTAAAAACA
1 AATTAAAAACA
5785 TATCTCTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (19 bp):
AATTAAAAACAAATAATAA
Found at i:8047 original size:11 final size:13
Alignment explanation
Indices: 8021--8061 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
8011 GTTTACATAA
*
8021 TTTTCATAATATT
1 TTTTAATAATATT
*
8034 TTTTTA-AATATT
1 TTTTAATAATATT
8046 TTTTAATAATATT
1 TTTTAATAATATT
8059 TTT
1 TTT
8062 AAAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTAATAATATT
Found at i:8715 original size:25 final size:26
Alignment explanation
Indices: 8686--8739 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
8676 AAAATATGTA
8686 TTCGTCTAT-TCTGAAATTTTATAAG
1 TTCGTCTATCTCTGAAATTTTATAAG
* *
8711 TTCGTCTCTCTTTGAAATTTTATAAG
1 TTCGTCTATCTCTGAAATTTTATAAG
8737 TTC
1 TTC
8740 ATCTCCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.50
Consensus pattern (26 bp):
TTCGTCTATCTCTGAAATTTTATAAG
Found at i:10070 original size:26 final size:25
Alignment explanation
Indices: 10032--10082 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
10022 AAGCTTTCTC
10032 CTTTTACTTTTCAAGTTCTTCATTTTT
1 CTTTTACTTTTCAAGTT-TTC-TTTTT
10059 CTTTTA-TTTTCAAGTTTTCTTTTT
1 CTTTTACTTTTCAAGTTTTCTTTTT
10083 AATATGCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 5 0.21
25 3 0.12
26 10 0.42
27 6 0.25
ACGTcount: A:0.14, C:0.16, G:0.04, T:0.67
Consensus pattern (25 bp):
CTTTTACTTTTCAAGTTTTCTTTTT
Found at i:11714 original size:36 final size:35
Alignment explanation
Indices: 11652--11730 Score: 99
Period size: 37 Copynumber: 2.3 Consensus size: 35
11642 TGCTCCATTG
* *
11652 AAAAAAAG-AAAAAAAGTAGTTTG-AAAAAGAGAA
1 AAAAAAAGAAAAAAAAGTAGTTCGAAAAAAAAGAA
*
11685 AAAAAGAAGAAAAAAAATGTTGTTCGAAAAAAAAGAA
1 AAAAA-AAGAAAAAAAA-GTAGTTCGAAAAAAAAGAA
11722 AAAAAAAGA
1 AAAAAAAGA
11731 CATGAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
33 5 0.13
34 3 0.08
35 7 0.18
36 10 0.26
37 14 0.36
ACGTcount: A:0.71, C:0.01, G:0.16, T:0.11
Consensus pattern (35 bp):
AAAAAAAGAAAAAAAAGTAGTTCGAAAAAAAAGAA
Found at i:19541 original size:81 final size:81
Alignment explanation
Indices: 19402--19563 Score: 279
Period size: 81 Copynumber: 2.0 Consensus size: 81
19392 TTAGGTTGAT
* *
19402 GCCAAGAAAAATGCAAGAACCAGAAACTGATCGGCGATCATCAACATTGCTTGTCCAGTCAGCGT
1 GCCAAGAAAAATCCAAGAACCAGAAACTGATCGGCGATCATCAACATTGCTTGCCCAGTCAGCGT
19467 CAACAAAGGCAATCAC
66 CAACAAAGGCAATCAC
* * *
19483 GCCAAGAAAAATCCAGGAACCATAAACTGATCGGCGGTCATCAACATTGCTTGCCCAGTCAGCGT
1 GCCAAGAAAAATCCAAGAACCAGAAACTGATCGGCGATCATCAACATTGCTTGCCCAGTCAGCGT
19548 CAACAAAGGCAATCAC
66 CAACAAAGGCAATCAC
19564 CTTACTCGAT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (81 bp):
GCCAAGAAAAATCCAAGAACCAGAAACTGATCGGCGATCATCAACATTGCTTGCCCAGTCAGCGT
CAACAAAGGCAATCAC
Found at i:23709 original size:21 final size:21
Alignment explanation
Indices: 23679--23725 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
23669 ACCGGAAACA
23679 TTATTATTTCTATCGATTTTG
1 TTATTATTTCTATCGATTTTG
* *
23700 TTATTTTTTCTATCGGTTTTG
1 TTATTATTTCTATCGATTTTG
23721 TTATT
1 TTATT
23726 GTTGGGCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.09, G:0.11, T:0.66
Consensus pattern (21 bp):
TTATTATTTCTATCGATTTTG
Found at i:23776 original size:21 final size:21
Alignment explanation
Indices: 23751--23794 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
23741 AGAAATATTA
* * *
23751 AAAAACATTGATGTTTTAGGT
1 AAAAACAATAATGTTTTAAGT
*
23772 AAAAATAATAATGTTTTAAGT
1 AAAAACAATAATGTTTTAAGT
23793 AA
1 AA
23795 TTTTTTTTAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (21 bp):
AAAAACAATAATGTTTTAAGT
Found at i:26465 original size:31 final size:30
Alignment explanation
Indices: 26430--26519 Score: 101
Period size: 31 Copynumber: 2.9 Consensus size: 30
26420 TCCCAAAAAG
*
26430 TTACAAATGATCAATGAACTTTATCAAATTA
1 TTACAAATGATCAATAAAC-TTATCAAATTA
* *
26461 TTACAGCATGATCATTAAACTTATCAAATTA
1 TTACA-AATGATCAATAAACTTATCAAATTA
*
26492 TTATAAAATGAT-AATTAAACTTATCAAA
1 TTA-CAAATGATCAA-TAAACTTATCAAA
26520 ACTTATCACT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 37 0.74
32 12 0.24
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.36
Consensus pattern (30 bp):
TTACAAATGATCAATAAACTTATCAAATTA
Found at i:29689 original size:50 final size:50
Alignment explanation
Indices: 29614--29718 Score: 210
Period size: 50 Copynumber: 2.1 Consensus size: 50
29604 AAATCCATTA
29614 GTTTTCCTTTAGGGACCCATTTGGAAAAGATGAAAAGTTAAGGGGTTGAT
1 GTTTTCCTTTAGGGACCCATTTGGAAAAGATGAAAAGTTAAGGGGTTGAT
29664 GTTTTCCTTTAGGGACCCATTTGGAAAAGATGAAAAGTTAAGGGGTTGAT
1 GTTTTCCTTTAGGGACCCATTTGGAAAAGATGAAAAGTTAAGGGGTTGAT
29714 GTTTT
1 GTTTT
29719 GAATGGATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.29, C:0.10, G:0.28, T:0.34
Consensus pattern (50 bp):
GTTTTCCTTTAGGGACCCATTTGGAAAAGATGAAAAGTTAAGGGGTTGAT
Found at i:30639 original size:26 final size:26
Alignment explanation
Indices: 30610--30660 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
30600 TAGTGCATAA
*
30610 GGTGGGCTA-GACCTTATGTGTATTAT
1 GGTGGGC-ACGACCTTACGTGTATTAT
*
30636 GGTGGGCACGATCTTACGTGTATTA
1 GGTGGGCACGACCTTACGTGTATTA
30661 GCACTTCGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.35
Consensus pattern (26 bp):
GGTGGGCACGACCTTACGTGTATTAT
Found at i:44860 original size:13 final size:13
Alignment explanation
Indices: 44842--44866 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44832 CTCCTAATAA
44842 TAAACTCGAAAAG
1 TAAACTCGAAAAG
44855 TAAACTCGAAAA
1 TAAACTCGAAAA
44867 TGAAAATCAA
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:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (13 bp):
TAAACTCGAAAAG
Found at i:46017 original size:18 final size:18
Alignment explanation
Indices: 45990--46027 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
45980 GAAATCTAAT
45990 TGCCTGGATATAATTTAA
1 TGCCTGGATATAATTTAA
*
46008 TGCCTTGATATAATTTAA
1 TGCCTGGATATAATTTAA
46026 TG
1 TG
46028 TTGAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (18 bp):
TGCCTGGATATAATTTAA
Found at i:47310 original size:21 final size:19
Alignment explanation
Indices: 47281--47319 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
47271 TGAGAGGAGA
*
47281 AAAATGGTCTTTAATAAAATT
1 AAAACGGTC-TTAA-AAAATT
47302 AAAACGGTCTTAAAAAAT
1 AAAACGGTCTTAAAAAAT
47320 ACTAGATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 4 0.24
21 8 0.47
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (19 bp):
AAAACGGTCTTAAAAAATT
Found at i:52231 original size:18 final size:19
Alignment explanation
Indices: 52199--52234 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52189 GATTTGTGGT
*
52199 TCTTTTTTTTGGTTCGAAA
1 TCTTTTCTTTGGTTCGAAA
52218 TCTTTTCTTT-GTTCGAA
1 TCTTTTCTTTGGTTCGAA
52235 TGCCCCCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.58
Consensus pattern (19 bp):
TCTTTTCTTTGGTTCGAAA
Found at i:52914 original size:2 final size:2
Alignment explanation
Indices: 52907--52955 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
52897 ACGAGTATCA
52907 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52949 AT AT AT A
1 AT AT AT A
52956 AAGCATCCGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53278 original size:2 final size:2
Alignment explanation
Indices: 53271--53306 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
53261 ATTTTATGTT
53271 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53307 ATGCAGGGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56729 original size:38 final size:37
Alignment explanation
Indices: 56541--56953 Score: 345
Period size: 38 Copynumber: 11.2 Consensus size: 37
56531 ATATATTTTT
* **
56541 ATTATAT-ATATATAGCTTGTAAAAATGTTTTTGAAAA
1 ATTATATAATATATA-CTTTTAAAAACATTTTTGAAAA
*
56578 A--ATATAATATATAATTTTCAGAAAACGATTTTCT-AAAA
1 ATTATATAATATATACTTTT-A-AAAAC-ATTTT-TGAAAA
* * * * * *
56616 TTTATATATTGTATAGTTTTGAAAATATTTTT---AA
1 ATTATATAATATATACTTTTAAAAACATTTTTGAAAA
* * *
56650 AGTATAT-ATAATATAGTTTTGAAAACA-TTTTGAAAA
1 ATTATATAAT-ATATACTTTTAAAAACATTTTTGAAAA
*
56686 ATTATATAATATATACTTTTAAAAATATTTTTGGAAAA
1 ATTATATAATATATACTTTTAAAAACATTTTT-GAAAA
*
56724 ATTATATAATATATAGTTTTTAAAAACATTTTTGAAAA
1 ATTATATAATATATA-CTTTTAAAAACATTTTTGAAAA
* *
56762 ATTATATAACATATACTTTTAAAAACATTTTTGGAAGA
1 ATTATATAATATATACTTTTAAAAACATTTTT-GAAAA
*
56800 ATTATATAATATATAGATTTTAAAAACATTTTTGAAAA
1 ATTATATAATATATA-CTTTTAAAAACATTTTTGAAAA
* * *
56838 ATTATATAATATATAGTATTAAAAATATTTTTTGAAAA
1 ATTATATAATATATACTTTTAAAAACA-TTTTTGAAAA
* * *
56876 CTTATAT-A-ATAT--TTTT-AAATCA-TTTT-CAAA
1 ATTATATAATATATACTTTTAAAAACATTTTTGAAAA
* * * *
56906 ACTATATAATATATAGTTTTAAAAACTTTTTTAAAATA
1 ATTATATAATATATACTTTTAAAAACATTTTTGAAA-A
56944 TATTATATAA
1 -ATTATATAA
56954 GTTTTTAAAA
Statistics
Matches: 308, Mismatches: 41, Indels: 52
0.77 0.10 0.13
Matches are distributed among these distances:
30 8 0.03
31 5 0.02
32 4 0.01
33 9 0.03
34 29 0.09
35 11 0.04
36 39 0.13
37 44 0.14
38 105 0.34
39 40 0.13
40 14 0.05
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (37 bp):
ATTATATAATATATACTTTTAAAAACATTTTTGAAAA
Found at i:56768 original size:76 final size:73
Alignment explanation
Indices: 56541--56963 Score: 410
Period size: 76 Copynumber: 5.8 Consensus size: 73
56531 ATATATTTTT
* * * * *
56541 ATTATAT-ATATATAGCTTGTAAAAATGTTTTTGAAAAAATATAATATATAATTTTCAGAAAACG
1 ATTATATAATATATA-CTTTTAAAAATATTTTTGAAAATATATAATATATAGTTTTTA-AAAAC-
56605 ATTTTCT-AAAA
63 ATTTT-TGAAAA
* * * * * * *
56616 TTTATATATTGTATAGTTTTGAAAATATTTTT-AAAGTATAT-ATAATATAG-TTTTGAAAACA-
1 ATTATATAATATATACTTTTAAAAATATTTTTGAAAATATATAAT-ATATAGTTTTTAAAAACAT
56677 TTTTGAAAA
65 TTTTGAAAA
56686 ATTATATAATATATACTTTTAAAAATATTTTTGGAAAAATTATATAATATATAGTTTTTAAAAAC
1 ATTATATAATATATACTTTTAAAAATATTTTT-G-AAAA-TATATAATATATAGTTTTTAAAAAC
56751 ATTTTTGAAAA
63 ATTTTTGAAAA
* * *
56762 ATTATATAACATATACTTTTAAAAACATTTTTGGAAGAATTATATAATATATAGATTTTAAAAAC
1 ATTATATAATATATACTTTTAAAAATATTTTT-GAA-AA-TATATAATATATAGTTTTTAAAAAC
56827 ATTTTTGAAAA
63 ATTTTTGAAAA
* * *
56838 ATTATATAATATATAGTATTAAAAATATTTTTTGAAAACT-TAT-ATA-ATA-TTTTT-AAATCA
1 ATTATATAATATATACTTTTAAAAATA-TTTTTGAAAA-TATATAATATATAGTTTTTAAAAACA
*
56898 -TTTT-CAAA
64 TTTTTGAAAA
* * *
56906 ACTATATAATATATAGTTTTAAAAACT-TTTTT-AAAATATATTATATA-AGTTTTTAAAA
1 ATTATATAATATATACTTTTAAAAA-TATTTTTGAAAATATATAATATATAGTTTTTAAAA
56964 TATATTATAT
Statistics
Matches: 298, Mismatches: 32, Indels: 42
0.80 0.09 0.11
Matches are distributed among these distances:
65 1 0.00
66 7 0.02
67 9 0.03
68 32 0.11
69 9 0.03
70 39 0.13
71 5 0.02
72 8 0.03
73 11 0.04
74 26 0.09
75 36 0.12
76 110 0.37
77 5 0.02
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (73 bp):
ATTATATAATATATACTTTTAAAAATATTTTTGAAAATATATAATATATAGTTTTTAAAAACATT
TTTGAAAA
Found at i:56959 original size:22 final size:21
Alignment explanation
Indices: 56933--56978 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 21
56923 TTTAAAAACT
56933 TTTTTAAAATATATTATATAAG
1 TTTTTAAAATATATTATAT-AG
56955 TTTTTAAAATATATTATATAG
1 TTTTTAAAATATATTATATAG
56976 TTT
1 TTT
56979 AAAAATAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTTTAAAATATATTATATAG
Found at i:56973 original size:54 final size:55
Alignment explanation
Indices: 56909--57018 Score: 143
Period size: 54 Copynumber: 2.0 Consensus size: 55
56899 TTTCAAAACT
* * *
56909 ATATAATATATAGTTTTAAAA-ACTTTTTTAAA-ATATATTATATAAGTTTTTAAA
1 ATATAATATATAGTTTAAAAATACTTTTTGAAATATATATTATAT-AGTTTTAAAA
* * *
56963 ATATATTATATAGTTTAAAAATAGTTTTTGAAATATATGTTATATAGTTTTAAAA
1 ATATAATATATAGTTTAAAAATACTTTTTGAAATATATATTATATAGTTTTAAAA
57018 A
1 A
57019 CAAATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
54 19 0.40
55 19 0.40
56 10 0.21
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.47
Consensus pattern (55 bp):
ATATAATATATAGTTTAAAAATACTTTTTGAAATATATATTATATAGTTTTAAAA
Found at i:56983 original size:20 final size:22
Alignment explanation
Indices: 56933--56985 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
56923 TTTAAAAACT
*
56933 TTTTTAAAATATATTATATAAG
1 TTTTAAAAATATATTATATAAG
*
56955 TTTTTAAAATATATTATAT-AG
1 TTTTAAAAATATATTATATAAG
56976 -TTTAAAAATA
1 TTTTAAAAATA
56986 GTTTTTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (22 bp):
TTTTAAAAATATATTATATAAG
Found at i:56990 original size:32 final size:35
Alignment explanation
Indices: 56953--57018 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
56943 ATATTATATA
56953 AGTTTTT-AAA-ATATATTATATAG-TTTAAAAAT
1 AGTTTTTGAAATATATATTATATAGTTTTAAAAAT
*
56985 AGTTTTTGAAATATATGTTATATAGTTTTAAAAA
1 AGTTTTTGAAATATATATTATATAGTTTTAAAAA
57019 CAAATTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 7 0.23
33 3 0.10
34 12 0.40
35 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (35 bp):
AGTTTTTGAAATATATATTATATAGTTTTAAAAAT
Found at i:57038 original size:2 final size:2
Alignment explanation
Indices: 57033--57077 Score: 56
Period size: 2 Copynumber: 22.0 Consensus size: 2
57023 TTTTTTTAAA
*
57033 AT AT AT AT AT -T GT AT AGT AT AT CAT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT AT AT
57076 AT
1 AT
57078 CATTTTATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
1 1 0.03
2 34 0.87
3 4 0.10
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57063 original size:23 final size:23
Alignment explanation
Indices: 57033--57080 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
57023 TTTTTTTAAA
*
57033 ATATATATAT-TGTATAGTATATC
1 ATATATATATATATATA-TATATC
57056 ATATATATATATATATATATATC
1 ATATATATATATATATATATATC
57079 AT
1 AT
57081 TTTATTATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
ATATATATATATATATATATATC
Found at i:57110 original size:17 final size:18
Alignment explanation
Indices: 57080--57120 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
57070 ATATATATCA
57080 TTTTATTATGTTATTTAT
1 TTTTATTATGTTATTTAT
57098 TTTTATTAT-TTATTTAT
1 TTTTATTATGTTATTTAT
57115 TATTTA
1 T-TTTA
57121 CTCGTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTATTATGTTATTTAT
Found at i:58374 original size:2 final size:2
Alignment explanation
Indices: 58367--58431 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
58357 CATTTCTATC
58367 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58409 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
58432 CCTCAGATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58690 original size:18 final size:18
Alignment explanation
Indices: 58669--58703 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
58659 TCCCATCTAG
58669 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
58687 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
58704 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:62101 original size:149 final size:149
Alignment explanation
Indices: 61831--62145 Score: 544
Period size: 149 Copynumber: 2.1 Consensus size: 149
61821 TATAATTGCA
*
61831 CCGAAGTACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
*
61896 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTATCCAGACTTCACACATGTTC
*
61961 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
61980 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
* *
62045 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCAT-CAGGCTTCACACATGT
66 TCCTTAAGAATCATATACATATACTAGGGATCA-AGTATGTGTCT-ATCCAGACTTCACACATGT
*
62108 TCCAAAGAATATATATATATC
129 TCCAAAGAATATACATATATC
62129 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
62146 CCCTCGACTC
Statistics
Matches: 158, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
149 156 0.99
150 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTATCCAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:62791 original size:2 final size:2
Alignment explanation
Indices: 62784--62820 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
62774 ATTTCATTTC
62784 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62821 CCTCAAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:63083 original size:18 final size:18
Alignment explanation
Indices: 63062--63096 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
63052 TCCCATCTAG
63062 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
63080 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
63097 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:70515 original size:5 final size:6
Alignment explanation
Indices: 70503--70528 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
70493 TATATTAAAA
70503 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
70529 TCATTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:79953 original size:27 final size:27
Alignment explanation
Indices: 79915--80030 Score: 214
Period size: 27 Copynumber: 4.3 Consensus size: 27
79905 CACCAACCAT
79915 CGCCTTCGTCAATGTAGTCCTGGTCCC
1 CGCCTTCGTCAATGTAGTCCTGGTCCC
79942 CGCCTTCGTCAATGTAGTCCTGGTCCC
1 CGCCTTCGTCAATGTAGTCCTGGTCCC
*
79969 CGCCTTCGTCAATGTAGTCCTGATCCC
1 CGCCTTCGTCAATGTAGTCCTGGTCCC
*
79996 CACCTTCGTCAATGTAGTCCTGGTCCC
1 CGCCTTCGTCAATGTAGTCCTGGTCCC
80023 CGCCTTCG
1 CGCCTTCG
80031 ACGAACAACC
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 85 1.00
ACGTcount: A:0.12, C:0.38, G:0.21, T:0.29
Consensus pattern (27 bp):
CGCCTTCGTCAATGTAGTCCTGGTCCC
Found at i:82200 original size:22 final size:23
Alignment explanation
Indices: 82175--82236 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
82165 TGGGACAAAT
*
82175 TTCTACGTGGTCCTTCGAGAC-A
1 TTCTATGTGGTCCTTCGAGACAA
* *
82197 TTCTATGTGGTCTTTCGGGACAA
1 TTCTATGTGGTCCTTCGAGACAA
* *
82220 ATCTATGTGGTACTTCG
1 TTCTATGTGGTCCTTCG
82237 GTGCATATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 18 0.55
23 15 0.45
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGAGACAA
Found at i:82228 original size:23 final size:23
Alignment explanation
Indices: 82162--82230 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
82152 GTTCTACGCG
*
82162 CTTT-GGGACAAATTTCTACGTGGT
1 CTTTCGGGACAAA--TCTATGTGGT
* * *
82186 CCTTCGAGAC-ATTCTATGTGGT
1 CTTTCGGGACAAATCTATGTGGT
82208 CTTTCGGGACAAATCTATGTGGT
1 CTTTCGGGACAAATCTATGTGGT
82231 ACTTCGGTGC
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
22 17 0.47
23 11 0.31
24 4 0.11
25 4 0.11
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (23 bp):
CTTTCGGGACAAATCTATGTGGT
Found at i:82789 original size:11 final size:11
Alignment explanation
Indices: 82773--82802 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
82763 ATGGTTGATC
82773 ACTAAAAGAAT
1 ACTAAAAGAAT
82784 ACTAAAAGAAT
1 ACTAAAAGAAT
*
82795 AATAAAAG
1 ACTAAAAG
82803 GTTTAAATTA
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:0.67, C:0.07, G:0.10, T:0.17
Consensus pattern (11 bp):
ACTAAAAGAAT
Done.