Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008656.1 Corchorus capsularis cultivar CVL-1 contig08677, 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: 8003
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.28
Found at i:2105 original size:27 final size:28
Alignment explanation
Indices: 2066--2141 Score: 104
Period size: 27 Copynumber: 2.8 Consensus size: 28
2056 TAAGGTCGTC
2066 CAAGGGT-ATTTTGGTCATTTTTGCAC-
1 CAAGGGTCATTTTGGTCATTTTTGCACT
* *
2092 CCAGGGTCATTTTGGTCATTTTTGTACT
1 CAAGGGTCATTTTGGTCATTTTTGCACT
*
2120 CAAGGG-CATTTTAGTCATTTTT
1 CAAGGGTCATTTTGGTCATTTTT
2142 AGGTTCACCT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 6 0.14
27 33 0.75
28 5 0.11
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.45
Consensus pattern (28 bp):
CAAGGGTCATTTTGGTCATTTTTGCACT
Found at i:5075 original size:47 final size:47
Alignment explanation
Indices: 4984--5075 Score: 105
Period size: 47 Copynumber: 2.0 Consensus size: 47
4974 TTTAGAGTGA
* * *
4984 TTAGTAAATAAAATTTTAACCTTTGATTAAAAGATCGAATTTTTAAG
1 TTAGTAAATAAAATTGTAACATTTGATTAAAAGATCGAACTTTTAAG
* * * *
5031 TTAGTAAATAAAA-TGTCACATTTGAATTAGAAGTTTGAACTTTTA
1 TTAGTAAATAAAATTGTAACATTTG-ATTAAAAGATCGAACTTTTA
5076 GGCCATTAGT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
46 8 0.22
47 29 0.78
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (47 bp):
TTAGTAAATAAAATTGTAACATTTGATTAAAAGATCGAACTTTTAAG
Found at i:5827 original size:55 final size:55
Alignment explanation
Indices: 5696--6101 Score: 582
Period size: 55 Copynumber: 7.3 Consensus size: 55
5686 GAAAGGGGGC
*
5696 AATCAGTAATTAAAGTAAAAAGAGATTAATCAAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGTAATT-AAGTAAAAAGAGATTAATC-AGAGTCAAAGTAACAGTAATCAGTA
* * *
5753 AATCAGTAATTAAG-CAAAAGAGGTAAATCAGAGTCAAAGTAACAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAACAGTAATCAGTA
*
5807 AATCAGTAATTAAGTAAAAAGAGATTAATCAAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATC-AGAGTCAAAGTAACAGTAATCAGTA
* * *
5863 AATCAGTAATTAAG-CAAAAGAGGTAAATCAGAGTCAAAGTAACAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAACAGTAATCAGTA
* * * *
5917 AATCAGTAATTAAGTAAAAAAGAGGTAAATCAGGGTCAAAGTAGCAGTAATCAGTA
1 AATCAGTAATTAAGT-AAAAAGAGATTAATCAGAGTCAAAGTAACAGTAATCAGTA
* *
5973 AATCAGTAATTAAGTAAAAAGAGATTAATCAGGGTCAAAGTAGCAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAACAGTAATCAGTA
* * * *
6028 AATCAGTAATTAAGTAAAAAGAGATTAATCAGGGTTAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAACAGTAATCAGTA
* *
6083 AATCAGTAATCAGGTAAAA
1 AATCAGTAATTAAGTAAAA
6102 GATAGTAATC
Statistics
Matches: 322, Mismatches: 23, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
54 76 0.24
55 142 0.44
56 93 0.29
57 11 0.03
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAACAGTAATCAGTA
Found at i:5973 original size:166 final size:166
Alignment explanation
Indices: 5696--6101 Score: 629
Period size: 166 Copynumber: 2.4 Consensus size: 166
5686 GAAAGGGGGC
5696 AATCAGTAATTAAAGTAAAAAGAGATTAATCAAGAGTCAAAGTAATAGTAATCAGTAAATCAGTA
1 AATCAGTAATT-AAGTAAAAAGAGATTAATC-AGAGTCAAAGTAATAGTAATCAGTAAATCAGTA
*
5761 ATTAAG--CAAAAGAGGTAAATCAGAGTCAAAGTAACAGTAATCAGTAAATCAGTAATTAAGTAA
64 ATTAAGTAAAAAAGAGGTAAATCAGAGTCAAAGTAACAGTAATCAGTAAATCAGTAATTAAGTAA
*
5824 AAAGAGATTAATCAAGAGTCAAAGTAATAGTAATCAGTA
129 AAAGAGATTAATC-AGAGTCAAAGTAACAGTAATCAGTA
* * * *
5863 AATCAGTAATTAAG-CAAAAGAGGTAAATCAGAGTCAAAGTAACAGTAATCAGTAAATCAGTAAT
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAAT
* *
5927 TAAGTAAAAAAGAGGTAAATCAGGGTCAAAGTAGCAGTAATCAGTAAATCAGTAATTAAGTAAAA
66 TAAGTAAAAAAGAGGTAAATCAGAGTCAAAGTAACAGTAATCAGTAAATCAGTAATTAAGTAAAA
* *
5992 AGAGATTAATCAGGGTCAAAGTAGCAGTAATCAGTA
131 AGAGATTAATCAGAGTCAAAGTAACAGTAATCAGTA
* * *
6028 AATCAGTAATTAAGTAAAAAGAGATTAATCAGGGTTAAGGTAATAGTAATCAGTAAATCAGTAAT
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAAT
* *
6093 CAGGTAAAA
66 TAAGTAAAA
6102 GATAGTAATC
Statistics
Matches: 217, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
164 38 0.18
165 48 0.22
166 120 0.55
167 11 0.05
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (166 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAAT
TAAGTAAAAAAGAGGTAAATCAGAGTCAAAGTAACAGTAATCAGTAAATCAGTAATTAAGTAAAA
AGAGATTAATCAGAGTCAAAGTAACAGTAATCAGTA
Found at i:6213 original size:22 final size:24
Alignment explanation
Indices: 6178--6221 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
6168 AATGGTAATC
6178 AGTGAATCGATAATTAAGAGTTAA
1 AGTGAATCGATAATTAAGAGTTAA
6202 AGTG-ATC-ATAATTAAGAGTT
1 AGTGAATCGATAATTAAGAGTT
6222 GAGTGGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 3 0.15
24 4 0.20
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (24 bp):
AGTGAATCGATAATTAAGAGTTAA
Found at i:6463 original size:22 final size:21
Alignment explanation
Indices: 6424--6693 Score: 129
Period size: 22 Copynumber: 12.3 Consensus size: 21
6414 AATCATAGAC
*
6424 AGTAAATA-GTAATCAGTAAG
1 AGTAAAAAGGTAATCAGTAAG
*
6444 AGTAAAAAGGGTAATAAGTAAG
1 AGTAAAAA-GGTAATCAGTAAG
* * *
6466 AAG-CAAAAGGAAATTAGTAAG
1 -AGTAAAAAGGTAATCAGTAAG
6487 AGTAAAAAGGTAATCAGTAAAG
1 AGTAAAAAGGTAATCAGT-AAG
* * *
6509 AGTAAAAAGCTAATCAGCAAAA
1 AGTAAAAAGGTAATCAG-TAAG
*
6531 AGTAAAAAGGTAATC-GATGAAA
1 AGTAAAAAGGTAATCAG-T-AAG
* * *
6553 AG-CAAAAGGCAATCAGTAAAA
1 AGTAAAAAGGTAATCAGT-AAG
* **
6574 ACT-AAAAGAGTAATCAAAAAAAGG
1 AGTAAAAAG-GTAATC--AGTAA-G
* *
6598 AGCAGAAAATAGTAATCAGTAAAAG
1 AGTA-AAAA-GGTAATCAGT--AAG
* *
6623 AGTAAAATGGTAATCAGTAAAA
1 AGTAAAAAGGTAATCAGT-AAG
* **
6645 AGTAAGAAGGTAATCAACAAG
1 AGTAAAAAGGTAATCAGTAAG
*
6666 AGTAAAATA-GTAATCAGTACAA
1 AGTAAAA-AGGTAATCAGTA-AG
6688 AGTAAA
1 AGTAAA
6694 GAATAATCAG
Statistics
Matches: 190, Mismatches: 40, Indels: 38
0.71 0.15 0.14
Matches are distributed among these distances:
20 9 0.05
21 60 0.32
22 86 0.45
23 13 0.07
24 6 0.03
25 4 0.02
26 12 0.06
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.17
Consensus pattern (21 bp):
AGTAAAAAGGTAATCAGTAAG
Found at i:6574 original size:43 final size:42
Alignment explanation
Indices: 6434--6644 Score: 142
Period size: 43 Copynumber: 4.8 Consensus size: 42
6424 AGTAAATAGT
* * *
6434 AATCAGT-AAGAGTAAAAAGGGTAATAAGTAAGAAGCAAAAGGA
1 AATCAGTAAAAAGTAAAAA-GGTAATCAGTAA-AAGCAAAAGGC
* * * *
6477 AATTAGT-AAGAGTAAAAAGGTAATCAGTAAAGAGTAAAAAGC
1 AATCAGTAAAAAGTAAAAAGGTAATCAGTAAA-AGCAAAAGGC
*
6519 TAATCAGCAAAAAGTAAAAAGGTAATC-GATGAAAAGCAAAAGGC
1 -AATCAGTAAAAAGTAAAAAGGTAATCAG-T-AAAAGCAAAAGGC
* ** * *
6563 AATCAGTAAAAACT-AAAAGAGTAATCAAAAAAAGGAGCAGAAAATAGT
1 AATCAGTAAAAAGTAAAAAG-GTAATC-AGTAAA--AGC--AAAA-GGC
*
6611 AATCAGTAAAAGAGTAAAATGGTAATCAGTAAAA
1 AATCAGTAAAA-AGTAAAAAGGTAATCAGTAAAA
6645 AGTAAGAAGG
Statistics
Matches: 133, Mismatches: 20, Indels: 27
0.74 0.11 0.15
Matches are distributed among these distances:
41 1 0.01
42 23 0.17
43 44 0.33
44 26 0.20
45 6 0.05
46 1 0.01
47 4 0.03
48 16 0.12
49 8 0.06
50 4 0.03
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.16
Consensus pattern (42 bp):
AATCAGTAAAAAGTAAAAAGGTAATCAGTAAAAGCAAAAGGC
Found at i:6681 original size:114 final size:112
Alignment explanation
Indices: 6496--6702 Score: 263
Period size: 114 Copynumber: 1.8 Consensus size: 112
6486 GAGTAAAAAG
** *
6496 GTAATCAGTAAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGGTAATCGATGAAAAGCAAAAG
1 GTAATCAGTAAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGGTAATCGAACAAAAGCAAAAA
*
6561 GCAATCAGTAAAAACTAAAAGAGTAATCAAAAAAAGGAGCAGAAAATA
66 GCAATCAGTAAAAACT-AAAGAATAATCAAAAAAAGGAGCAGAAAATA
* * * * * *
6609 GTAATCAGTAAAAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATC-AACAAGAGTAAAA
1 GTAATCAGT-AAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGGTAATCGAACAAAAGCAAAA
* * *
6673 TAGTAATCAGTACAAAGTAAAGAATAATCA
65 -AGCAATCAGTAAAAACTAAAGAATAATCA
6703 GTGAAATAGT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
113 29 0.37
114 50 0.63
ACGTcount: A:0.56, C:0.09, G:0.18, T:0.17
Consensus pattern (112 bp):
GTAATCAGTAAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGGTAATCGAACAAAAGCAAAAA
GCAATCAGTAAAAACTAAAGAATAATCAAAAAAAGGAGCAGAAAATA
Found at i:6700 original size:21 final size:22
Alignment explanation
Indices: 6608--6704 Score: 80
Period size: 21 Copynumber: 4.5 Consensus size: 22
6598 AGCAGAAAAT
*
6608 AGTAATCAGTAAAAGAGTAAA-A
1 AGTAATCAGTACAA-AGTAAAGA
* *
6630 TGGTAATCAGTAAAAAGT-AAGA
1 -AGTAATCAGTACAAAGTAAAGA
6652 AGGTAATCA--ACAAGAGTAAA-A
1 A-GTAATCAGTACAA-AGTAAAGA
6673 TAGTAATCAGTACAAAGTAAAGA
1 -AGTAATCAGTACAAAGTAAAGA
6696 A-TAATCAGT
1 AGTAATCAGT
6705 GAAATAGTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
20 3 0.05
21 21 0.33
22 21 0.33
23 18 0.29
ACGTcount: A:0.54, C:0.07, G:0.19, T:0.21
Consensus pattern (22 bp):
AGTAATCAGTACAAAGTAAAGA
Done.