Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018403.1 Corchorus olitorius cultivar O-4 contig18436, 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: 34963
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Found at i:61 original size:10 final size:10
Alignment explanation
Indices: 26--55 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
16 CCATATTAAC
26 AATTTTATTT
1 AATTTTATTT
36 AATTTTATTT
1 AATTTTATTT
46 AATTTTATTT
1 AATTTTATTT
56 CCTTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
AATTTTATTT
Found at i:11995 original size:3 final size:3
Alignment explanation
Indices: 11987--12015 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11977 AAGCCTGCAT
11987 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
12016 TAAATCCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:13897 original size:23 final size:24
Alignment explanation
Indices: 13852--13897 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
13842 ATAAAACACA
* *
13852 TTTTTTTCTCATAAATATTTGAAG
1 TTTTTTTCTCACAAATATGTGAAG
*
13876 TTTTTTTCTTACAAA-ATGTGAA
1 TTTTTTTCTCACAAATATGTGAA
13898 ATGATGTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (24 bp):
TTTTTTTCTCACAAATATGTGAAG
Found at i:14026 original size:41 final size:42
Alignment explanation
Indices: 13981--14069 Score: 110
Period size: 45 Copynumber: 2.1 Consensus size: 42
13971 TTATCAAGCA
*
13981 ATTACATTATCA-T-ATAATCTGCAATCTATCATATAATTGCG
1 ATTACATTATCACTAATAATATG-AATCTATCATATAATTGCG
*
14022 ATTACATTATCATCTGCAATTATATGAATCTATCATATAATTGCG
1 ATTACATTATCA-CT--AATAATATGAATCTATCATATAATTGCG
14067 ATT
1 ATT
14070 GCTAATTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
41 12 0.29
43 1 0.02
45 22 0.54
46 6 0.15
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (42 bp):
ATTACATTATCACTAATAATATGAATCTATCATATAATTGCG
Found at i:14355 original size:14 final size:13
Alignment explanation
Indices: 14329--14379 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
14319 ATTTCCTCCA
*
14329 ATATATCAGTAGC
1 ATATATCAATAGC
14342 ATATAATCAATAGC
1 ATAT-ATCAATAGC
* *
14356 ATGTATCAGTAGC
1 ATATATCAATAGC
14369 ATATAATCAAT
1 ATAT-ATCAAT
14380 TTAGTAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 15 0.48
14 16 0.52
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (13 bp):
ATATATCAATAGC
Found at i:14363 original size:13 final size:13
Alignment explanation
Indices: 14329--14373 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
14319 ATTTCCTCCA
14329 ATATATCAGTAGC
1 ATATATCAGTAGC
*
14342 ATATAATCAATAGC
1 ATAT-ATCAGTAGC
*
14356 ATGTATCAGTAGC
1 ATATATCAGTAGC
14369 ATATA
1 ATATA
14374 ATCAATTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (13 bp):
ATATATCAGTAGC
Found at i:16934 original size:13 final size:14
Alignment explanation
Indices: 16897--16934 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
16887 TTTTTTTTAA
16897 ATTACTTAATTATT
1 ATTACTTAATTATT
*
16911 ATTAGTT-ATTATT
1 ATTACTTAATTATT
16924 ATTA-TTAATTA
1 ATTACTTAATTA
16935 GTTAATCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 2 0.09
13 14 0.64
14 6 0.27
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (14 bp):
ATTACTTAATTATT
Found at i:17144 original size:25 final size:25
Alignment explanation
Indices: 17094--17144 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
17084 TTGAACTTTG
*
17094 AAAGTTTGAAGGTTGAGAGAATTAA
1 AAAGTTTGAAGGTTGAGAGAAATAA
*
17119 AAAGTTTGAAGTTTGAG-GAAAATAA
1 AAAGTTTGAAGGTTGAGAG-AAATAA
17144 A
1 A
17145 GCAAAGGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.47, C:0.00, G:0.25, T:0.27
Consensus pattern (25 bp):
AAAGTTTGAAGGTTGAGAGAAATAA
Found at i:19128 original size:24 final size:25
Alignment explanation
Indices: 19082--19138 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
19072 CATATTTAGT
19082 TTTTAAAATAAAATAATAATTAAAC
1 TTTTAAAATAAAATAATAATTAAAC
*
19107 TTTTAAGAA-AAAATAA-ATTTAAAC
1 TTTTAA-AATAAAATAATAATTAAAC
*
19131 -ATTAAAAT
1 TTTTAAAAT
19139 TTATATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 2 0.07
23 4 0.14
24 7 0.25
25 13 0.46
26 2 0.07
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (25 bp):
TTTTAAAATAAAATAATAATTAAAC
Found at i:19281 original size:29 final size:30
Alignment explanation
Indices: 19223--19283 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
19213 GTTATAATTA
* **
19223 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATCATATT
*
19253 ATGTATAAATAT-AATTATTTAATCATATT
1 ATGTATAAATATAAATTATTCAATCATATT
19282 AT
1 AT
19284 ATTATTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATCATATT
Found at i:20057 original size:17 final size:17
Alignment explanation
Indices: 20035--20067 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20025 TATTATGGAT
20035 ATTTAT-ATTATTAATTA
1 ATTTATAATT-TTAATTA
20052 ATTTATAATTTTAATT
1 ATTTATAATTTTAATT
20068 GATGTAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATAATTTTAATTA
Found at i:20983 original size:78 final size:78
Alignment explanation
Indices: 20877--21037 Score: 252
Period size: 78 Copynumber: 2.1 Consensus size: 78
20867 TTTATTTAAT
* * *
20877 TAAAATAATAAATGGTAAACTAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGA-
1 TAAAATAATAAATGATAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAG
20941 TTATTTAGTTGAG
66 TTATTTAGTTGAG
* *
20954 TAAAATAGTAAAATGATAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAATATAGA
1 TAAAATAAT-AAATGATAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGA
*
21019 GTTTTTTAGTTGAG
65 GTTATTTAGTTGAG
21033 TAAAA
1 TAAAA
21038 CCATAAAAGT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
77 8 0.11
78 51 0.67
79 17 0.22
ACGTcount: A:0.52, C:0.01, G:0.12, T:0.35
Consensus pattern (78 bp):
TAAAATAATAAATGATAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAG
TTATTTAGTTGAG
Found at i:21313 original size:21 final size:22
Alignment explanation
Indices: 21273--21313 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
21263 GACAAACTCG
*
21273 TAACCCGAATAACCCGAGAAAA
1 TAACCCGAATAACCCAAGAAAA
*
21295 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
21314 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.46, C:0.29, G:0.15, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAAA
Found at i:22581 original size:72 final size:72
Alignment explanation
Indices: 22452--22588 Score: 197
Period size: 72 Copynumber: 1.9 Consensus size: 72
22442 AATATATTCA
* *
22452 AAAAATAAGGGTATAATGGGCGATTCAAAAGTTTTACAAGAGTATGTACTTTTTAATATAGTATA
1 AAAAATAAAGGTATAATGGGCGATTCAAAAGTATTACAAGAGTA-GTACTTTTTAATATAGTATA
22517 GATGTTCG
65 GATGTTCG
* *
22525 AAAAATAAATGTATAATGGGGGATTC-AAAGTATTACAAGAGGTCA-TACTTTTTAATATAGTAT
1 AAAAATAAAGGTATAATGGGCGATTCAAAAGTATTACAAGA-GT-AGTACTTTTTAATATAGTAT
22588 A
64 A
22589 AATATAATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
72 32 0.55
73 25 0.43
74 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.34
Consensus pattern (72 bp):
AAAAATAAAGGTATAATGGGCGATTCAAAAGTATTACAAGAGTAGTACTTTTTAATATAGTATAG
ATGTTCG
Found at i:30821 original size:1 final size:1
Alignment explanation
Indices: 30817--30847 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
30807 TTTTTATATC
30817 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
30848 CTAATTGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:33922 original size:2 final size:2
Alignment explanation
Indices: 33915--33963 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
33905 AAACCGATCT
33915 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
33957 GA GA GA G
1 GA GA GA G
33964 TATATATATA
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34921 original size:2 final size:2
Alignment explanation
Indices: 34914--34958 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
34904 TAAACCCAAA
34914 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
34956 AG A
1 AG A
34959 AGAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.