Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010142.1 Corchorus capsularis cultivar CVL-1 contig10163, 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: 29984
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2139 original size:41 final size:41
Alignment explanation
Indices: 2082--2164 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
2072 ATATGCTGTC
2082 ATGCTACTCAACTCAGATTCTAGAATGTCAGTTAGTGAGGA
1 ATGCTACTCAACTCAGATTCTAGAATGTCAGTTAGTGAGGA
2123 ATGCTACTCAACTCAGATTCTAGAATGTCAGTTAGTGAGGA
1 ATGCTACTCAACTCAGATTCTAGAATGTCAGTTAGTGAGGA
2164 A
1 A
2165 AAGATATGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (41 bp):
ATGCTACTCAACTCAGATTCTAGAATGTCAGTTAGTGAGGA
Found at i:8378 original size:2 final size:2
Alignment explanation
Indices: 8371--8396 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8361 CATTACTCGA
8371 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
8397 GTGGCACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12217 original size:110 final size:109
Alignment explanation
Indices: 12085--12361 Score: 414
Period size: 110 Copynumber: 2.5 Consensus size: 109
12075 AAAATATATA
*
12085 TATAAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
12149 AAAA-AATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAATT
65 AAAACAA-TTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAA-T
12195 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
* *
12260 AAACAATTTAGTATATCCAATTTTTTTGGTAAAAATAAAGTAAT
66 AAACAATTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
* * *
12304 TATAAAGATATTAGATTTAATTTAATTGAAGAAAAATAGAATTTCTAGTAGAATAAAA
1 TATAAAGATATTAGATTTAA-TTAA---ATG-AAAATAGAGTTTTTAGTAGAATAAAA
12362 CTATAATAGT
Statistics
Matches: 154, Mismatches: 6, Indels: 10
0.91 0.04 0.06
Matches are distributed among these distances:
109 21 0.14
110 104 0.68
111 3 0.02
113 2 0.01
114 24 0.16
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAACAATTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:14053 original size:19 final size:19
Alignment explanation
Indices: 14029--14065 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
14019 ACTTTTATAT
14029 ATAGTATAGATATAGATAG
1 ATAGTATAGATATAGATAG
*
14048 ATAGTATAGATATGGATA
1 ATAGTATAGATATAGATA
14066 TCCAATGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (19 bp):
ATAGTATAGATATAGATAG
Found at i:16046 original size:20 final size:21
Alignment explanation
Indices: 16018--16057 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
16008 TTATTATGTG
16018 AAAGAATAGGAC-ATTTGAAGA
1 AAAGAATA-GACAATTTGAAGA
16039 AAAG-ATAGACAATTTGAAG
1 AAAGAATAGACAATTTGAAG
16058 GTTAAGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 11 0.61
21 4 0.22
ACGTcount: A:0.53, C:0.05, G:0.23, T:0.20
Consensus pattern (21 bp):
AAAGAATAGACAATTTGAAGA
Found at i:20974 original size:45 final size:44
Alignment explanation
Indices: 20902--20995 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
20892 ACAAAAAAAA
*
20902 AAAAGCAGACACTCATGGGGTTCTCTTTTTGTTGTTCAAGCAGT
1 AAAAGCAGAAACTCATGGGGTTCTCTTTTTGTTGTTCAAGCAGT
* *
20946 GAAAAGCAGAAACTGATGGAGGTT-TCTTTTTGTTGTTTAAGCAGT
1 -AAAAGCAGAAACTCATGG-GGTTCTCTTTTTGTTGTTCAAGCAGT
20991 AAAAG
1 AAAAG
20996 GCATTAGATT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 5 0.11
45 36 0.80
46 4 0.09
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (44 bp):
AAAAGCAGAAACTCATGGGGTTCTCTTTTTGTTGTTCAAGCAGT
Found at i:23670 original size:17 final size:15
Alignment explanation
Indices: 23648--23687 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
23638 ACCAATTTTT
*
23648 TTTTTTAAAATTATATA
1 TTTTTTAAAA-AAT-TA
23665 TTTTTTAAAAAATTA
1 TTTTTTAAAAAATTA
23680 TTTTTTAA
1 TTTTTTAA
23688 TCAAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.45
16 2 0.09
17 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTTAAAAAATTA
Found at i:24284 original size:16 final size:16
Alignment explanation
Indices: 24263--24294 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
24253 TCAGAAAGCG
24263 GAAAAGCTCTGAAGTA
1 GAAAAGCTCTGAAGTA
24279 GAAAAGCTCTGAAGTA
1 GAAAAGCTCTGAAGTA
24295 TTTCAGATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (16 bp):
GAAAAGCTCTGAAGTA
Found at i:26618 original size:73 final size:74
Alignment explanation
Indices: 26519--26663 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 74
26509 CAACCCAAAA
* *
26519 AAAAAAAAAAAGGCTCGCTAAGTTGAAAATTCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCA-
1 AAAAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGCAC
26583 AAAAAAAGC
66 AAAAAAAGC
*
26592 AAAACAAAAAAGGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGCAC
1 AAAAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGCAC
26657 AAAAAAA
66 AAAAAAA
26664 AATGAACTAC
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
73 61 0.90
74 7 0.10
ACGTcount: A:0.49, C:0.16, G:0.21, T:0.14
Consensus pattern (74 bp):
AAAAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGCAC
AAAAAAAGC
Found at i:27451 original size:16 final size:16
Alignment explanation
Indices: 27427--27461 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
27417 ACAATTCAGA
*
27427 AAGCGGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
27443 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
27459 AAG
1 AAG
27462 TATTTCAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.29, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:28403 original size:27 final size:27
Alignment explanation
Indices: 28365--28432 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
28355 ACTAGAGAGT
*
28365 GACAATTAAAAAGGATCAAAA-GATTG
1 GACAATTAAAAAGGAACAAAAGGATTG
*
28391 AGACAATTAAAAAGGAACAAAAGGTTTG
1 -GACAATTAAAAAGGAACAAAAGGATTG
*
28419 GATAATTAAAAAGG
1 GACAATTAAAAAGG
28433 TACCCTAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 33 0.89
28 4 0.11
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (27 bp):
GACAATTAAAAAGGAACAAAAGGATTG
Found at i:29116 original size:18 final size:18
Alignment explanation
Indices: 29093--29127 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29083 TTGACTCGCC
29093 CCACTCACCTCTCCGATT
1 CCACTCACCTCTCCGATT
*
29111 CCACTCCCCTCTCCGAT
1 CCACTCACCTCTCCGAT
29128 CCGACCAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.54, G:0.06, T:0.26
Consensus pattern (18 bp):
CCACTCACCTCTCCGATT
Done.