Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012572.1 Corchorus capsularis cultivar CVL-1 contig12593, 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: 51580
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:10311 original size:151 final size:151
Alignment explanation
Indices: 10131--10438 Score: 562
Period size: 151 Copynumber: 2.0 Consensus size: 151
10121 GGTCAATCAC
* * * *
10131 AATAACCTTTTAAATTAAAATGGTAACAATGAAATAATTATAAAAATATTGAATTTAATTAAATG
1 AATAAACTTTCAAATCAAAATGGTAACAATGAAATAATTATAAAAATATTGAATTCAATTAAATG
*
10196 AAAATAAAGTTTTTAGTAGAATCAAACTATATATTAAAAATTTTTAATATATCCAAGTTTTTAAT
66 AAAATAAAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAAT
10261 GAAAAATAGTAAAATGGTAAA
131 GAAAAATAGTAAAATGGTAAA
10282 AATAAACTTTCAAATCAAAATGGTAACAATGAAATAATTATAAAAATATTGAATTCAATTAAATG
1 AATAAACTTTCAAATCAAAATGGTAACAATGAAATAATTATAAAAATATTGAATTCAATTAAATG
*
10347 AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAAT
66 AAAATAAAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAAT
10412 GAAAAATAGTAAAATGGTAAA
131 GAAAAATAGTAAAATGGTAAA
10433 AATAAA
1 AATAAA
10439 GTAATTATAA
Statistics
Matches: 151, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
151 151 1.00
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (151 bp):
AATAAACTTTCAAATCAAAATGGTAACAATGAAATAATTATAAAAATATTGAATTCAATTAAATG
AAAATAAAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAAT
GAAAAATAGTAAAATGGTAAA
Found at i:24305 original size:1 final size:1
Alignment explanation
Indices: 24299--24323 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
24289 TATTTCATAT
24299 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
24324 CCTCCGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:27016 original size:20 final size:20
Alignment explanation
Indices: 26978--27016 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
26968 TGGGCTAGCT
*
26978 GAATTTGCTGTGGCGAAGGA
1 GAATTTGCAGTGGCGAAGGA
26998 GAATTTGACAGTGGC-AAGG
1 GAATTTG-CAGTGGCGAAGG
27017 CCTCTGGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.28, C:0.10, G:0.38, T:0.23
Consensus pattern (20 bp):
GAATTTGCAGTGGCGAAGGA
Found at i:28417 original size:4 final size:4
Alignment explanation
Indices: 28408--28433 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
28398 CTACGTGCAA
28408 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
28434 GAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:30675 original size:1 final size:1
Alignment explanation
Indices: 30669--30693 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
30659 CTTTGATTAG
30669 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
30694 GAGCAGAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:32319 original size:29 final size:29
Alignment explanation
Indices: 32287--32359 Score: 146
Period size: 29 Copynumber: 2.5 Consensus size: 29
32277 TTTTAAAGAG
32287 TTCAGGGGCTTATTTGGCTGCAATTAGAA
1 TTCAGGGGCTTATTTGGCTGCAATTAGAA
32316 TTCAGGGGCTTATTTGGCTGCAATTAGAA
1 TTCAGGGGCTTATTTGGCTGCAATTAGAA
32345 TTCAGGGGCTTATTT
1 TTCAGGGGCTTATTT
32360 AGCCGTTTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (29 bp):
TTCAGGGGCTTATTTGGCTGCAATTAGAA
Found at i:36977 original size:27 final size:28
Alignment explanation
Indices: 36937--37000 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
36927 ACCACCTATC
*
36937 TTGAAAATT-CAAAAAAAATCAGCAACT
1 TTGAAAATTAAAAAAAAAATCAGCAACT
36964 TTGAAAATTAAAAAAAAAATCAGCAACT
1 TTGAAAATTAAAAAAAAAATCAGCAACT
36992 TTGAAAATT
1 TTGAAAATT
37001 CATAGCCGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 9 0.26
28 26 0.74
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.25
Consensus pattern (28 bp):
TTGAAAATTAAAAAAAAAATCAGCAACT
Found at i:38578 original size:33 final size:32
Alignment explanation
Indices: 38501--38604 Score: 93
Period size: 33 Copynumber: 3.2 Consensus size: 32
38491 TTGCAAAGAG
* * *
38501 TGTTTTAGATGTTTTTGCGATGATACTAAACC
1 TGTTTTAGGTGTTTTTGCGATGAAACTAAATC
** * *
38533 TAATTT-GAGTGTTATTTGCAATGACACTAAATC
1 TGTTTTAG-GTGTT-TTTGCGATGAAACTAAATC
* *
38566 TGTTTTAGGTGTTGTTTGTGATGAAACAAAATC
1 TGTTTTAGGTGTT-TTTGCGATGAAACTAAATC
38599 TGTTTT
1 TGTTTT
38605 GGATGCTAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
31 1 0.02
32 8 0.14
33 46 0.82
34 1 0.02
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (32 bp):
TGTTTTAGGTGTTTTTGCGATGAAACTAAATC
Found at i:38705 original size:33 final size:33
Alignment explanation
Indices: 38620--38693 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
38610 CTAATTGTGA
* *
38620 TGAAAACAAATCTCTTTTGGTTGATCATAGCAT
1 TGAAAATAAATCTGTTTTGGTTGATCATAGCAT
*
38653 TGAGAATAAATCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAAATCTGTTTTGGTTGATCATAGCAT
38686 TGAAAATA
1 TGAAAATA
38694 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (33 bp):
TGAAAATAAATCTGTTTTGGTTGATCATAGCAT
Found at i:39136 original size:30 final size:30
Alignment explanation
Indices: 39084--39142 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
39074 CAATGGGGAG
*
39084 GGAATGATGCACTCAAGGCTTATCATGGAA
1 GGAATGATGCACTCAAGACTTATCATGGAA
* *
39114 GGAATGATGC-GTCAAAGACTTATTATGGA
1 GGAATGATGCACTC-AAGACTTATCATGGA
39143 CTTGAAGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (30 bp):
GGAATGATGCACTCAAGACTTATCATGGAA
Found at i:40328 original size:2 final size:2
Alignment explanation
Indices: 40323--40357 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
40313 AAAAAAAAAA
*
40323 AC AC AC AC AC AC AC AC AC TC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
40358 TATATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.49, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:43430 original size:30 final size:28
Alignment explanation
Indices: 43365--43436 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
43355 ACACAAAACG
**
43365 GCCAAATAAGCCCCTGAACTCTAATTGCA
1 GCCAAATAAGCCCCTGAACTCTAA-TAAA
43394 GCCAAATAAGCCCCTGAACTCTTTAA-AAA
1 GCCAAATAAGCCCCTGAACTC--TAATAAA
43423 TGCCAAATAAGCCC
1 -GCCAAATAAGCCC
43437 TTTTCTGATG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 22 0.58
30 13 0.34
31 3 0.08
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (28 bp):
GCCAAATAAGCCCCTGAACTCTAATAAA
Found at i:43904 original size:30 final size:30
Alignment explanation
Indices: 43868--43945 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
43858 CATCAGAAAA
43868 GGGCTTATTTGGCCTTTTTAA-AGAGTTCAG
1 GGGCTTATTTGGCC-TTTTAATAGAGTTCAG
**
43898 GGGCTTATTTGG-C-TGCAATTAGAGTTCAG
1 GGGCTTATTTGGCCTTTTAA-TAGAGTTCAG
43927 GGGCTTATTTGGCCGTTTT
1 GGGCTTATTTGGCC-TTTT
43946 GTGTAAGTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.08
29 22 0.56
30 13 0.33
32 1 0.03
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (30 bp):
GGGCTTATTTGGCCTTTTAATAGAGTTCAG
Found at i:47111 original size:15 final size:15
Alignment explanation
Indices: 47088--47118 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
47078 TATCATTTGA
*
47088 ATTATTAATTTATTT
1 ATTAATAATTTATTT
47103 ATTAATAATTTATTT
1 ATTAATAATTTATTT
47118 A
1 A
47119 ACTCAGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTAATAATTTATTT
Found at i:48013 original size:19 final size:19
Alignment explanation
Indices: 47961--48030 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
47951 AGTTTAAAAC
47961 TTTAAATGATGAAGTTCAG
1 TTTAAATGATGAAGTTCAG
* * *
47980 TTTACTAT-TTAAAGTTCAG
1 TTTA-AATGATGAAGTTCAG
*
47999 TTTAAATGATGAAGTTCGG
1 TTTAAATGATGAAGTTCAG
48018 TTTAAATGATGAA
1 TTTAAATGATGAA
48031 TGAAGCTTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
18 2 0.05
19 38 0.90
20 2 0.05
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.40
Consensus pattern (19 bp):
TTTAAATGATGAAGTTCAG
Found at i:48685 original size:49 final size:49
Alignment explanation
Indices: 48625--48726 Score: 141
Period size: 49 Copynumber: 2.1 Consensus size: 49
48615 ACTTGGAAAC
* * * * * *
48625 AACTGATGAAAAACCGCCCTGGGTCGACTGAATCGATCATTCTGACATA
1 AACTGAAGAAAAACCACCCTGGGTCAACGGAATCAATCATTCTAACATA
*
48674 AACTGAAGAAAAACCACCTTGGGTCAACGGAATCAATCATTCTAACATA
1 AACTGAAGAAAAACCACCCTGGGTCAACGGAATCAATCATTCTAACATA
48723 AACT
1 AACT
48727 TAGAATAAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.22
Consensus pattern (49 bp):
AACTGAAGAAAAACCACCCTGGGTCAACGGAATCAATCATTCTAACATA
Found at i:48952 original size:154 final size:155
Alignment explanation
Indices: 48671--49002 Score: 531
Period size: 154 Copynumber: 2.1 Consensus size: 155
48661 TCATTCTGAC
* * * *
48671 ATAAACTGAAGAAAAACCACCTTGGGTCAACGGAATCAATCATTCTAACATAAACTTAGAATAAA
1 ATAAACTAAAGAAAGACCACCCTAGGTCAACGGAATCAATCATTCTAACATAAACTTAGAATAAA
48736 CTTGAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAA
66 CTTGAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAA
* *
48801 GAAAGACCACCCTGGGTCAATCGAA
131 GAAAGACCACCCTAGGTCAACCGAA
* * * *
48826 ATAAACTAAAGAAAGACCACCCTAGGTCAACTGAATCGATCATTCTGACATAAACTT-GGATAAA
1 ATAAACTAAAGAAAGACCACCCTAGGTCAACGGAATCAATCATTCTAACATAAACTTAGAATAAA
* *
48890 CTTGAAAACAATTGAAGAAAGACCGCCCTGGGTTGACTGAATCGATCATTCTGACATAAACTGAA
66 CTTGAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAA
* *
48955 GAAAGACCGCCCTAGGTCAACCGAG
131 GAAAGACCACCCTAGGTCAACCGAA
48980 ATAAACTAAAGAAAGACCACCCT
1 ATAAACTAAAGAAAGACCACCCT
49003 CGATCATTCC
Statistics
Matches: 163, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
154 113 0.69
155 50 0.31
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.19
Consensus pattern (155 bp):
ATAAACTAAAGAAAGACCACCCTAGGTCAACGGAATCAATCATTCTAACATAAACTTAGAATAAA
CTTGAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAA
GAAAGACCACCCTAGGTCAACCGAA
Found at i:49035 original size:36 final size:36
Alignment explanation
Indices: 48931--49038 Score: 130
Period size: 35 Copynumber: 3.0 Consensus size: 36
48921 GTTGACTGAA
* *
48931 TCGATCATTCTGACATAAACTGAAGAAAGACCGCCC
1 TCGATCATTCCGACATAAACTGAAGAAAGACCACCC
* * * * *
48967 TAGGTCA-ACCGAGATAAACTAAAGAAAGACCACCC
1 TCGATCATTCCGACATAAACTGAAGAAAGACCACCC
49002 TCGATCATTCCGACATAAACTGAAGACAA-ACCACCC
1 TCGATCATTCCGACATAAACTGAAGA-AAGACCACCC
49038 T
1 T
49039 GGGTCAACTG
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
35 28 0.48
36 28 0.48
37 2 0.03
ACGTcount: A:0.40, C:0.29, G:0.15, T:0.17
Consensus pattern (36 bp):
TCGATCATTCCGACATAAACTGAAGAAAGACCACCC
Found at i:49104 original size:53 final size:54
Alignment explanation
Indices: 49031--49137 Score: 180
Period size: 53 Copynumber: 2.0 Consensus size: 54
49021 CTGAAGACAA
*
49031 ACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGG-ATAAACTTG
1 ACCACCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGAATAAACTTG
* *
49084 ACCACCCTGGGTCGACTGAATCGATCATTTTAACATAAACTTGGAATAAACTTG
1 ACCACCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGAATAAACTTG
49138 GAAACAACTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
53 41 0.82
54 9 0.18
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (54 bp):
ACCACCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGAATAAACTTG
Found at i:49178 original size:124 final size:123
Alignment explanation
Indices: 48840--49209 Score: 359
Period size: 124 Copynumber: 3.0 Consensus size: 123
48830 ACTAAAGAAA
* * * *
48840 GACCACCCTAGGTCAACTGAATCGATCATTCTGACATAAACTTGGATAAACTTGAAAACAATTGA
1 GACCACCCTAGGTCAACTGAATCGATCATTTTAACATAAACTTGGATAAACTTGGAAACAACTGA
* *
48905 AGAAAGACCGCCCTGGGTTGACTGAATCGATCATTCTGACATAAAC-TGAAGAAA---
66 AGAAAGACCGCCCTGGGTAGACTGAATCGATCATTCTGACATAAACTTGAATAAACTT
* * * ** * * * * * * *
48959 GACCGCCCTAGGTCAACCG-A--GATAAACTAAAGAAAGACCACCCTCGAT-CA-TTCCGACATA
1 GACCACCCTAGGTCAACTGAATCGATCATTTTAACATA-A--A-CTTGGATAAACTT-GGA-A-A
* *
49019 -AACTGAAGACAA-ACCACCCTGGGTCA-ACTGAATCGATCATTCTGACATAAACTTGGATAAAC
59 CAACTGAAGA-AAGACCGCCCTGGGT-AGACTGAATCGATCATTCTGACATAAACTTGAATAAAC
49081 TT
122 TT
* *
49083 GACCACCCTGGGTCGACTGAATCGATCATTTTAACATAAACTTGGAATAAACTTGGAAACAACTG
1 GACCACCCTAGGTCAACTGAATCGATCATTTTAACATAAACTTGG-ATAAACTTGGAAACAACTG
49148 AAGAAAGACCGCCCTGGGTAGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
65 AAGAAAGACCGCCCTGGGTAGACTGAATCGATCATTCTGACATAAACTT-GAATAAACTT
49208 GA
1 GA
49210 AAACAACTGA
Statistics
Matches: 192, Mismatches: 36, Indels: 40
0.72 0.13 0.15
Matches are distributed among these distances:
116 7 0.04
117 1 0.01
118 3 0.02
119 20 0.10
120 51 0.27
121 9 0.05
123 7 0.04
124 67 0.35
125 15 0.08
126 3 0.02
127 9 0.05
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (123 bp):
GACCACCCTAGGTCAACTGAATCGATCATTTTAACATAAACTTGGATAAACTTGGAAACAACTGA
AGAAAGACCGCCCTGGGTAGACTGAATCGATCATTCTGACATAAACTTGAATAAACTT
Found at i:49204 original size:71 final size:71
Alignment explanation
Indices: 49083--49237 Score: 256
Period size: 71 Copynumber: 2.2 Consensus size: 71
49073 GGATAAACTT
* * * * *
49083 GACCACCCTGGGTCGACTGAATCGATCATTTTAACATAAACTTGGAATAAACTTGGAAACAACTG
1 GACCGCCCTGGGTAGACTGAATCGATCATTCTAACATAAACTTCGAATAAACTTGAAAACAACTG
49148 AAGAAA
66 AAGAAA
*
49154 GACCGCCCTGGGTAGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAACAACTG
1 GACCGCCCTGGGTAGACTGAATCGATCATTCTAACATAAACTTCGAATAAACTTGAAAACAACTG
49219 AAGAAA
66 AAGAAA
49225 GACCGCCCTGGGT
1 GACCGCCCTGGGT
49238 CGATTGAAGC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 78 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (71 bp):
GACCGCCCTGGGTAGACTGAATCGATCATTCTAACATAAACTTCGAATAAACTTGAAAACAACTG
AAGAAA
Found at i:50678 original size:16 final size:13
Alignment explanation
Indices: 50641--50680 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
50631 CAATTTTCAC
50641 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
50654 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
*
50667 TTTTTTACTTCTT
1 TTTTTTTCTTCTT
50680 T
1 T
50681 ATCGACTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:51056 original size:45 final size:45
Alignment explanation
Indices: 51002--51109 Score: 155
Period size: 45 Copynumber: 2.4 Consensus size: 45
50992 AAAACACAAC
* *
51002 TTTGGAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTT
1 TTTGAAAAACCATTTTATCAAAACCTTTTGAAAACAATGACTCTT
* *
51047 TTTGAAAAACCATTTTGTCCAAACCTTTTGAAAACAATGACTCTT
1 TTTGAAAAACCATTTTATCAAAACCTTTTGAAAACAATGACTCTT
*
51092 TTT-TAAAACCATTATTAT
1 TTTGAAAAACCATT-TTAT
51110 TATTTTTCTT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 9 0.16
45 47 0.84
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (45 bp):
TTTGAAAAACCATTTTATCAAAACCTTTTGAAAACAATGACTCTT
Found at i:51141 original size:17 final size:18
Alignment explanation
Indices: 51111--51165 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
51101 CATTATTATT
*
51111 ATTTTTC-TTGTTTTCTC
1 ATTTTTCTTTCTTTTCTC
*
51128 -TTTTTCTTTCTTTTTTC
1 ATTTTTCTTTCTTTTCTC
51145 ATTTTT-TTTCATTTT-TC
1 ATTTTTCTTTC-TTTTCTC
51162 ATTT
1 ATTT
51166 CCATTTATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 6 0.18
17 18 0.55
18 9 0.27
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (18 bp):
ATTTTTCTTTCTTTTCTC
Found at i:51235 original size:17 final size:18
Alignment explanation
Indices: 51213--51251 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
51203 TTAGGCCAAG
51213 TTTTTCT-TTCCTCTTTT
1 TTTTTCTCTTCCTCTTTT
*
51230 TTTTTCTCTTTCTCTTTT
1 TTTTTCTCTTCCTCTTTT
51248 TTTT
1 TTTT
51252 AGAATGGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTCTCTTCCTCTTTT
Found at i:51539 original size:2 final size:2
Alignment explanation
Indices: 51532--51578 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
51522 ATAGTAGAAA
* *
51532 AT AT AT AT GT AT AT AT AT TT 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
51574 AT AT A
1 AT AT A
51579 CA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Done.