Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011263.1 Corchorus capsularis cultivar CVL-1 contig11284, 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: 32083
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:624 original size:16 final size:16
Alignment explanation
Indices: 600--650 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
590 TGTAAAAAGT
600 AATTCATTTTAAGGGTA
1 AATT-ATTTTAAGGGTA
**
617 AATTATTTTTTTGGGTA
1 AATTA-TTTTAAGGGTA
*
634 CA-TATTTTAAGGGTA
1 AATTATTTTAAGGGTA
649 AA
1 AA
651 CTATGAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 10 0.37
16 3 0.11
17 14 0.52
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (16 bp):
AATTATTTTAAGGGTA
Found at i:829 original size:110 final size:108
Alignment explanation
Indices: 637--905 Score: 324
Period size: 111 Copynumber: 2.5 Consensus size: 108
627 TTGGGTACAT
** * * *
637 ATTTTAAGGGTAAACTATGAAATTAAAGATTTATTAGTATAGGGTTTTAGAAAAAATAGAATCAA
1 ATTTTAAGGGTAAGTTATCAAATTAAAGATTTATTAGTATAGGGTTTTAGAAAAAATAAAAACAA
* *
702 CCAATTTCGCTAAGTTTAGCCCCAAATTAAAAA-TTTTAATTC
66 CCAATTTCACTAAGTTTAGCCCCAAATTAAAAACATTTAATTC
* *
744 ATTTTAAGGGTAAGTTATCAAATTAAAGATTTATTATTAATTAGTGTTTTAGAAAAAAATAAAAA
1 ATTTTAAGGGTAAGTTATCAAATTAAAGATTTATTAGT-A-TAGGGTTTTAG-AAAAAATAAAAA
* * **
809 CAACCAATTTCACTATGTTTAGTCTTAAATTAAAAACATTTAATTC
63 CAACCAATTTCACTAAGTTTAGCCCCAAATTAAAAACATTTAATTC
* * ** *
855 ATTTCAAGGGTAAGTTGTCAAATTAAATTTTTTTATTATTATAGGGTTTTA
1 ATTTTAAGGGTAAGTTATCAAATTAAA--GATTTATTAGTATAGGGTTTTA
906 TGGAAAATAA
Statistics
Matches: 138, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
107 34 0.25
108 1 0.01
109 10 0.07
110 41 0.30
111 42 0.30
112 1 0.01
113 9 0.07
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (108 bp):
ATTTTAAGGGTAAGTTATCAAATTAAAGATTTATTAGTATAGGGTTTTAGAAAAAATAAAAACAA
CCAATTTCACTAAGTTTAGCCCCAAATTAAAAACATTTAATTC
Found at i:917 original size:110 final size:110
Alignment explanation
Indices: 637--905 Score: 314
Period size: 110 Copynumber: 2.5 Consensus size: 110
627 TTGGGTACAT
* ** * * * *
637 ATTTTAAGGGTAAACTATGAAATTAAAGA---TTTATTAGTATAGGGTTTTAGAAAAAATAGAAT
1 ATTTCAAGGGTAAGTTATCAAATTAAAGATTTTTTATTAATATAGGGTTTTAGAAAAAATAAAAA
* *
699 CAACCAATTTCGCTAAGTTTAGCCCCAAATTAAAAATTTTAATTC
66 CAACCAATTTCACTAAGTTTAGCCCCAAATTAAAAAATTTAATTC
* * *
744 ATTTTAAGGGTAAGTTATCAAATTAAAGATTTATTATTAAT-TAGTGTTTTAGAAAAAAATAAAA
1 ATTTCAAGGGTAAGTTATCAAATTAAAGATTTTTTATTAATATAGGGTTTTAG-AAAAAATAAAA
* * **
808 ACAACCAATTTCACTATGTTTAGTCTTAAATTAAAAACATTTAATTC
65 ACAACCAATTTCACTAAGTTTAGCCCCAAATTAAAAA-ATTTAATTC
* * *
855 ATTTCAAGGGTAAGTTGTCAAATTAAA-TTTTTTTATTATTATAGGGTTTTA
1 ATTTCAAGGGTAAGTTATCAAATTAAAGATTTTTTATTAATATAGGGTTTTA
906 TGGAAAATAA
Statistics
Matches: 136, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
107 26 0.19
109 10 0.07
110 58 0.43
111 42 0.31
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (110 bp):
ATTTCAAGGGTAAGTTATCAAATTAAAGATTTTTTATTAATATAGGGTTTTAGAAAAAATAAAAA
CAACCAATTTCACTAAGTTTAGCCCCAAATTAAAAAATTTAATTC
Found at i:2894 original size:11 final size:11
Alignment explanation
Indices: 2875--2905 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2865 GAAAGTCTAT
*
2875 TATATTATATA
1 TATAGTATATA
2886 TATAGTATATA
1 TATAGTATATA
2897 TATAGTATA
1 TATAGTATA
2906 AATTAGAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (11 bp):
TATAGTATATA
Found at i:3284 original size:15 final size:17
Alignment explanation
Indices: 3249--3286 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
3239 AACTGAAAAC
3249 GACCC-AACCCAGAATT
1 GACCCGAACCCAGAATT
3265 GACCCGAACCCA-AA-T
1 GACCCGAACCCAGAATT
3280 GACCCGA
1 GACCCGA
3287 CATTTGATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.37, C:0.39, G:0.16, T:0.08
Consensus pattern (17 bp):
GACCCGAACCCAGAATT
Found at i:3987 original size:22 final size:22
Alignment explanation
Indices: 3953--4003 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 22
3943 ACTCAGTTAC
3953 TCCTTCTCTCTCTTATTTTCATTT
1 TCCTTCTCTCTC--ATTTTCATTT
3977 TCCTTCTCTCTCATTTTCATTT
1 TCCTTCTCTCTCATTTTCATTT
3999 TCCTT
1 TCCTT
4004 TTGTTTCTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 15 0.56
24 12 0.44
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.61
Consensus pattern (22 bp):
TCCTTCTCTCTCATTTTCATTT
Found at i:5125 original size:20 final size:20
Alignment explanation
Indices: 5096--5134 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5086 GAGAAGACAT
*
5096 TTGACCAATTGACATCATTC
1 TTGACAAATTGACATCATTC
5116 TTGACAAATTGACATCATT
1 TTGACAAATTGACATCATT
5135 GCAGATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (20 bp):
TTGACAAATTGACATCATTC
Found at i:5649 original size:16 final size:16
Alignment explanation
Indices: 5630--5676 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
5620 GTCTTATGTT
5630 TTACTTATTGTTATTG
1 TTACTTATTGTTATTG
*
5646 TTACTTAGTGTTATTG
1 TTACTTATTGTTATTG
*
5662 TTACTCATTGTTATT
1 TTACTTATTGTTATT
5677 TATTTTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.19, C:0.09, G:0.13, T:0.60
Consensus pattern (16 bp):
TTACTTATTGTTATTG
Found at i:5982 original size:24 final size:24
Alignment explanation
Indices: 5955--6001 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
5945 CATAGTCCAT
5955 CATCAACTTCACAAAACAACAATG
1 CATCAACTTCACAAAACAACAATG
*
5979 CATCAACTTCAGAAAACAACAAT
1 CATCAACTTCACAAAACAACAAT
6002 CCAAAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.51, C:0.28, G:0.04, T:0.17
Consensus pattern (24 bp):
CATCAACTTCACAAAACAACAATG
Found at i:6664 original size:31 final size:31
Alignment explanation
Indices: 6622--6700 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
6612 CGTTTCAATT
*
6622 TTTAGGCTCAAATTGGTC-ACTATTTGAAAGG
1 TTTAGGCTCAAATTGGTCAACT-TTTAAAAGG
* * *
6653 TTTAGGTTCAAATTGGGCAACTTTTAAAATG
1 TTTAGGCTCAAATTGGTCAACTTTTAAAAGG
6684 TTTAGGCTCAAATTGGT
1 TTTAGGCTCAAATTGGT
6701 GGCTAAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 38 0.93
32 3 0.07
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (31 bp):
TTTAGGCTCAAATTGGTCAACTTTTAAAAGG
Done.