Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006889.1 Corchorus capsularis cultivar CVL-1 contig06910, 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: 8413
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:171 original size:19 final size:19
Alignment explanation
Indices: 144--186 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
134 ATTATGACCC
144 AAAGCAAAGTCC-AACAAG
1 AAAGCAAAGTCCAAACAAG
*
162 TAAAGGAAAGTCCAAACAAG
1 -AAAGCAAAGTCCAAACAAG
182 AAAGC
1 AAAGC
187 CCAAAGTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.56, C:0.19, G:0.19, T:0.07
Consensus pattern (19 bp):
AAAGCAAAGTCCAAACAAG
Found at i:738 original size:36 final size:36
Alignment explanation
Indices: 688--778 Score: 114
Period size: 36 Copynumber: 2.5 Consensus size: 36
678 AATAAGTAAC
* * *
688 TGAAGAAAAACCACCCTGGATCATTCCAAAC-TGAAA
1 TGAAGAAAGACCACCCTGGACCATTCC-AACGTAAAA
*
724 TGAA-AAATGACCACCCTCGACCATTCCAACGTAAAA
1 TGAAGAAA-GACCACCCTGGACCATTCCAACGTAAAA
760 TGAAGAAAGACCACCCTGG
1 TGAAGAAAGACCACCCTGG
779 GCCAACTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
35 6 0.13
36 38 0.81
37 3 0.06
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.15
Consensus pattern (36 bp):
TGAAGAAAGACCACCCTGGACCATTCCAACGTAAAA
Found at i:875 original size:107 final size:107
Alignment explanation
Indices: 764--960 Score: 272
Period size: 107 Copynumber: 1.8 Consensus size: 107
754 GTAAAATGAA
* * * * *
764 GAAAGACCACCCTGGGCCAACTAAAATAAACTGAAAAACGGCCACCCTCGATCATTCTGGAC-TA
1 GAAAGACCACCCTAGGCCAACTAAAACAAACTGAAAAACGACCACCCTCGATCATTC-CGACACA
828 AACTGAAGAATA-ACCACCCTCGGTCATTCTGACTCAAACTGAT
65 AACTGAAGAA-AGACCACCCTCGGTCATTCTGACTCAAACTGAT
* * * *
871 GAAAGACCGCCCTAGGTCAACTGAAACAAACTGAAGAACGACCACCCTCGATCATTCCGACACAA
1 GAAAGACCACCCTAGGCCAACTAAAACAAACTGAAAAACGACCACCCTCGATCATTCCGACACAA
*
936 ACTGAAGAAAGACCTCCCTCGGTCA
66 ACTGAAGAAAGACCACCCTCGGTCA
961 ACTGAAATAA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
106 4 0.05
107 74 0.95
ACGTcount: A:0.37, C:0.30, G:0.17, T:0.16
Consensus pattern (107 bp):
GAAAGACCACCCTAGGCCAACTAAAACAAACTGAAAAACGACCACCCTCGATCATTCCGACACAA
ACTGAAGAAAGACCACCCTCGGTCATTCTGACTCAAACTGAT
Found at i:889 original size:36 final size:36
Alignment explanation
Indices: 760--977 Score: 169
Period size: 36 Copynumber: 6.1 Consensus size: 36
750 CAACGTAAAA
* * * * * *
760 TGAAGAAAGACCACCCTGGGCCA-ACTAAAATAAAC
1 TGAAGAAAGACCACCCTCGGTCATTCTGACACAAAC
* * *
795 TGAA-AAACGGCCACCCTCGATCATTCTGGAC-TAAAC
1 TGAAGAAA-GACCACCCTCGGTCATTCT-GACACAAAC
*
831 TGAAGAATA-ACCACCCTCGGTCATTCTGACTCAAAC
1 TGAAGAA-AGACCACCCTCGGTCATTCTGACACAAAC
* * * * *
867 TGATGAAAGACCGCCCTAGGTCA-ACTGAAACAAAC
1 TGAAGAAAGACCACCCTCGGTCATTCTGACACAAAC
* * *
902 TGAAGAACGACCACCCTCGATCATTCCGACACAAAC
1 TGAAGAAAGACCACCCTCGGTCATTCTGACACAAAC
* * * *
938 TGAAGAAAGACCTCCCTCGGTCA-ACTGAAATAAAC
1 TGAAGAAAGACCACCCTCGGTCATTCTGACACAAAC
973 TGAAG
1 TGAAG
978 GATGACCGCC
Statistics
Matches: 144, Mismatches: 31, Indels: 16
0.75 0.16 0.08
Matches are distributed among these distances:
34 3 0.02
35 59 0.41
36 78 0.54
37 3 0.02
38 1 0.01
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (36 bp):
TGAAGAAAGACCACCCTCGGTCATTCTGACACAAAC
Found at i:995 original size:71 final size:71
Alignment explanation
Indices: 826--995 Score: 225
Period size: 71 Copynumber: 2.4 Consensus size: 71
816 CATTCTGGAC
* * * *
826 TAAACTGAAGAATAACCACCCTCGG-TCATTCTGACTCAAACTGATGAAAGACCGCCCTAGGTCA
1 TAAACTGAAGAATGACCACCCT-GGATCATTCCGACACAAACTGAAGAAAGACCGCCCTAGGTCA
890 ACTGAAA
65 ACTGAAA
* * * * *
897 CAAACTGAAGAACGACCACCCTCGATCATTCCGACACAAACTGAAGAAAGACCTCCCTCGGTCAA
1 TAAACTGAAGAATGACCACCCTGGATCATTCCGACACAAACTGAAGAAAGACCGCCCTAGGTCAA
962 CTGAAA
66 CTGAAA
* *
968 TAAACTGAAGGATGACCGCCCTGGATCA
1 TAAACTGAAGAATGACCACCCTGGATCA
996 ATTAACTTGA
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
70 1 0.01
71 83 0.99
ACGTcount: A:0.36, C:0.29, G:0.18, T:0.17
Consensus pattern (71 bp):
TAAACTGAAGAATGACCACCCTGGATCATTCCGACACAAACTGAAGAAAGACCGCCCTAGGTCAA
CTGAAA
Found at i:3476 original size:14 final size:14
Alignment explanation
Indices: 3457--3505 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
3447 CTCAAAAAAC
3457 TTTTTGAAAACTCA
1 TTTTTGAAAACTCA
3471 TTTTTGAAAAC-C-
1 TTTTTGAAAACTCA
* *
3483 TTTTCGAAAA-TAA
1 TTTTTGAAAACTCA
3496 TTTTTGAAAA
1 TTTTTGAAAA
3506 ATACTTCTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 9 0.30
13 10 0.33
14 11 0.37
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (14 bp):
TTTTTGAAAACTCA
Found at i:3486 original size:25 final size:25
Alignment explanation
Indices: 3451--3505 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
3441 TAAAAACTCA
* * *
3451 AAAAACTTTTTGAAAACTCATTTTTG
1 AAAACCTTTTCGAAAA-TAATTTTTG
3477 AAAACCTTTTCGAAAATAATTTTTG
1 AAAACCTTTTCGAAAATAATTTTTG
3502 AAAA
1 AAAA
3506 ATACTTCTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (25 bp):
AAAACCTTTTCGAAAATAATTTTTG
Found at i:6846 original size:115 final size:116
Alignment explanation
Indices: 6623--6846 Score: 292
Period size: 115 Copynumber: 1.9 Consensus size: 116
6613 ATAAAAACAT
* * * ** *
6623 AAAAATAAACAATGATAAATAGGCATGAATTATTAAGAATAAAATGCAAACAGGCAACCAATTAT
1 AAAAATAAACAATGATAAACAGGCATGAATTA-TAACAAGAAAATGCAAACACACAACCAAATAT
* *
6688 GCAAACCCTAGTTAATACTAAACCAGTATTCAGTTCGACTCTCTGATAGGCA
65 GCAAACCCTAATCAATACTAAACCAGTATTCAGTTCGACTCTCTGATAGGCA
* *
6740 AAAAATAAACAATGATAAACAGGCATGAA-TA-AACAAGAAAATGCAAGCACACAACCCAAATCT
1 AAAAATAAACAATGATAAACAGGCATGAATTATAACAAGAAAATGCAAACACACAA-CCAAATAT
* *
6803 GGAAACCCTAATCAACT-CTAAACTAGTATTCAGTTCGACTCTCT
65 GCAAACCCTAATCAA-TACTAAACCAGTATTCAGTTCGACTCTCT
6847 AACGATCCCC
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
114 18 0.19
115 44 0.47
116 3 0.03
117 28 0.30
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.22
Consensus pattern (116 bp):
AAAAATAAACAATGATAAACAGGCATGAATTATAACAAGAAAATGCAAACACACAACCAAATATG
CAAACCCTAATCAATACTAAACCAGTATTCAGTTCGACTCTCTGATAGGCA
Found at i:7845 original size:35 final size:36
Alignment explanation
Indices: 7799--8173 Score: 448
Period size: 35 Copynumber: 10.6 Consensus size: 36
7789 TGCTTACTAA
*
7799 ACTTAATTACCCTGAATTAAGTT-ACTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGAACTC
* * *
7834 ACTTAATTACCCTGAATTAAGTTAATCA-TTAACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACTC
**
7869 ACTTAATTACCCCAAATTAAAGTTGATTACTG-ACTC
1 ACTTAATTACCCTGAATT-AAGTTGATTACTGAACTC
*
7905 ACTTAATTACCCTGAATTAAGTTGATTACTGAA-TT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACTC
7940 ACTTAATTACCCTGAATTAAGTTGATTACTG-ACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACTC
*
7975 ACTTAATTACCCTGAATTAAGTTGATTACTGAA-TT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACTC
8010 ACTTAATTACCCTGAATTAAGTTGATTACTG-ACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACTC
* * *
8045 ACTTAATTACCTTGAATGAAGTTGATTACTGAA-TT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACTC
* * * * *
8080 ACTTAATTACCCTGAATTAAATTAATAACT-AAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGAACTC
* * * * *
8115 ACTTAATTACCTTGAATTAATTTAATTACTCTAA-TG
1 ACTTAATTACCCTGAATTAAGTTGATTACT-GAACTC
*
8151 ACTTAATTACCATGAATTAAGTT
1 ACTTAATTACCCTGAATTAAGTT
8174 ACTTATTACT
Statistics
Matches: 301, Mismatches: 27, Indels: 23
0.86 0.08 0.07
Matches are distributed among these distances:
34 9 0.03
35 235 0.78
36 54 0.18
37 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.39
Consensus pattern (36 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGAACTC
Found at i:7998 original size:70 final size:70
Alignment explanation
Indices: 7799--8173 Score: 495
Period size: 70 Copynumber: 5.3 Consensus size: 70
7789 TGCTTACTAA
* * *
7799 ACTTAATTACCCTGAATTAAGTT-ACTTATTGAACT-ACTTAATTACCCTGAATTAAGTTAATCA
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTG-ACTCACTTAATTACCCTGAATTAAGTTGATTA
* *
7862 -TTAACTC
64 CTGAA-TT
**
7869 ACTTAATTACCCCAAATTAAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTAC
1 ACTTAATTACCCTGAATT-AAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTAC
7934 TGAATT
65 TGAATT
7940 ACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACT
8005 GAATT
66 GAATT
* *
8010 ACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCTTGAATGAAGTTGATTACT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACT
8075 GAATT
66 GAATT
* * * * * * * * *
8080 ACTTAATTACCCTGAATTAAATTAATAACTAAATTACTTAATTACCTTGAATTAATTTAATTACT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACT
* *
8145 CTAATG
66 -GAATT
*
8151 ACTTAATTACCATGAATTAAGTT
1 ACTTAATTACCCTGAATTAAGTT
8174 ACTTATTACT
Statistics
Matches: 276, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
70 195 0.71
71 77 0.28
72 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.39
Consensus pattern (70 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATTACT
GAATT
Found at i:8149 original size:9 final size:8
Alignment explanation
Indices: 8069--8160 Score: 58
Period size: 8 Copynumber: 10.6 Consensus size: 8
8059 AATGAAGTTG
*
8069 ATTACTGA
1 ATTACTTA
8077 ATTACTTA
1 ATTACTTA
*
8085 ATTACCCTGA
1 ATTA--CTTA
*
8095 ATTAAATTA
1 ATT-ACTTA
* *
8104 ATAACTAA
1 ATTACTTA
8112 ATTACTTA
1 ATTACTTA
8120 ATTACCTTGA
1 ATTA-CTT-A
*
8130 ATTAATTTA
1 ATT-ACTTA
8139 ATTACTCTA
1 ATTACT-TA
*
8148 ATGACTTA
1 ATTACTTA
8156 ATTAC
1 ATTAC
8161 CATGAATTAA
Statistics
Matches: 64, Mismatches: 13, Indels: 14
0.70 0.14 0.15
Matches are distributed among these distances:
8 32 0.50
9 18 0.28
10 12 0.19
11 2 0.03
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.41
Consensus pattern (8 bp):
ATTACTTA
Done.