Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013675.1 Corchorus capsularis cultivar CVL-1 contig13696, 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: 9992
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Found at i:69 original size:6 final size:6
Alignment explanation
Indices: 67--100 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
57 AAGATTTCCA
67 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTC
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTC
101 TAAAAATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCAT
Found at i:336 original size:22 final size:22
Alignment explanation
Indices: 268--662 Score: 140
Period size: 22 Copynumber: 17.6 Consensus size: 22
258 AATCTCCCTG
* ** *
268 TGAAACTTTGATAACCTTAATA
1 TGAAATTTTGATAACCACACTA
*
290 TGAAATTTTGAT-ATCATC-CTA
1 TGAAATTTTGATAACCA-CACTA
* *
311 TGAAATTTTGGTTACCACACTA
1 TGAAATTTTGATAACCACACTA
*
333 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCACACTA
* * * *
355 TAAAATTGTGATAATCTCTA-TA
1 TGAAATTTTGATAACCAC-ACTA
* ** *
377 TGAAATTAATTTTGATGACCTTAATA
1 TG--A--AATTTTGATAACCACACTA
* *
403 TAAAATTTTGA-ATACCACATTAA
1 TGAAATTTTGATA-ACCACACT-A
** **** *
426 TTGCGAAAGGTTGATTTGGTACGCTA
1 -T--GAAATTTTGA-TAACCACACTA
* *
452 TGAAATTTGGATAACCATACTA
1 TGAAATTTTGATAACCACACTA
* *
474 TGAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCACACTA
* * ** *
496 TGGAATGTTGATAACTTCCCTA
1 TGAAATTTTGATAACCACACTA
* * * *
518 T-AGAATTTCGTTAATCTCACTA
1 TGA-AATTTTGATAACCACACTA
* ** *
540 TGAAGTTTTGATAAGTACAATA
1 TGAAATTTTGATAACCACACTA
* **
562 TGAAATTTTGATTA-CATTCTA
1 TGAAATTTTGATAACCACACTA
*
583 TGAAATTTTTG-TAACCACATTA
1 TGAAA-TTTTGATAACCACACTA
* * *
605 TAAAATTTTGATAACCAAATTA
1 TGAAATTTTGATAACCACACTA
*
627 TGAAATTTTGGTAGA-CACACTA
1 TGAAATTTTGATA-ACCACACTA
*
649 TGAAATTTCGATAA
1 TGAAATTTTGATAA
663 TCTGCAAAGT
Statistics
Matches: 271, Mismatches: 80, Indels: 45
0.68 0.20 0.11
Matches are distributed among these distances:
21 32 0.12
22 198 0.73
23 11 0.04
24 3 0.01
25 2 0.01
26 22 0.08
27 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (22 bp):
TGAAATTTTGATAACCACACTA
Found at i:5271 original size:22 final size:22
Alignment explanation
Indices: 5246--5929 Score: 206
Period size: 22 Copynumber: 31.9 Consensus size: 22
5236 ATGATCCCAT
5246 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
*
5268 TATGAAATTTTAATAA--TGT--
1 TATGAAATTTTGATAACCT-TCC
* *** *
5287 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
5309 TATGGAATTTCGAAAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
5331 TAT-AAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* *
5352 TATGAAATTTGGTTAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * *
5374 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
5396 TATGAAATTTTGATAA-CTTCTC
1 TATGAAATTTTGATAACCTTC-C
* ** **
5418 AATGAAATTTTGATGGCCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
5441 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
5462 ATATGATATATTGATAACC-ACAT
1 -TATGAAATTTTGATAACCTTC-C
* * *
5485 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
5506 -AT-ACCAATTGTT-AGTAA-ATACAC
1 TATGA--AATT-TTGA-TAACCTTC-C
* * *
5529 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
5551 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
5573 TATGAAATTTTGATAAAGCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
5596 TATAAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
5619 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
5641 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
5658 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** * * *
5679 TATGATTTTTTGGTAATC-TCAA
1 TATGAAATTTTGATAACCTTC-C
* * *
5701 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
5723 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
*
5745 TATGAAATTTTGATAACCCT-C
1 TATGAAATTTTGATAACCTTCC
* **
5766 TAATGAAATTTTGA-AAACTAAAC
1 T-ATGAAATTTTGATAACCT-TCC
*
5789 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
*
5811 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
5832 -ATG-AATTTTGAT-ATCATCC
1 TATGAAATTTTGATAACCTTCC
*
5851 T-TGAAATTTTGATTA-C-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
5870 ATAATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACCTTCC
* * *
5894 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
5911 TATGAAATTTTGATAACCT
1 TATGAAATTTTGATAACCT
5930 CCCCAGAAAT
Statistics
Matches: 490, Mismatches: 117, Indels: 110
0.68 0.16 0.15
Matches are distributed among these distances:
16 11 0.02
17 12 0.02
18 3 0.01
19 35 0.07
20 19 0.04
21 42 0.09
22 290 0.59
23 71 0.14
24 6 0.01
25 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:5292 original size:19 final size:19
Alignment explanation
Indices: 5268--5304 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5258 ATAACCTTCC
5268 TATGAAATTTTAATAATGT
1 TATGAAATTTTAATAATGT
5287 TATGAAATTTTAATAATG
1 TATGAAATTTTAATAATG
5305 ATACTATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (19 bp):
TATGAAATTTTAATAATGT
Found at i:5603 original size:23 final size:23
Alignment explanation
Indices: 5533--5634 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 23
5523 ATACACTCTG
* * * *
5533 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAAGCTCCCTATA
* * * *
5555 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAAGCTCCCTATA
*
5577 AAATTTTGATAAAGCTTCCTATA
1 AAATTTTGATAAAGCTCCCTATA
*
5600 AAATTTTGATAAATCTCCCTATA
1 AAATTTTGATAAAGCTCCCTATA
5623 AAATTTTGATAA
1 AAATTTTGATAA
5635 CTTTCTTATG
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
22 27 0.40
23 41 0.60
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (23 bp):
AAATTTTGATAAAGCTCCCTATA
Found at i:5655 original size:45 final size:45
Alignment explanation
Indices: 5550--5656 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 45
5540 GATAATCACA
* *
5550 CTATGAAATTGTGAT-AACCTCGCTATGAAATTTTGATAAAGCTTC
1 CTATGAAATT-TGATAAACCTCCCTATAAAATTTTGATAAAGCTTC
* *
5595 CTATAAAATTTTGATAAATCTCCCTATAAAATTTTGAT-AA-CTTTC
1 CTATGAAA-TTTGATAAACCTCCCTATAAAATTTTGATAAAGC-TTC
*
5640 TTATGAAATCTTGATAA
1 CTATGAAAT-TTGATAA
5657 CTACAAATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
44 2 0.04
45 29 0.56
46 21 0.40
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39
Consensus pattern (45 bp):
CTATGAAATTTGATAAACCTCCCTATAAAATTTTGATAAAGCTTC
Found at i:5860 original size:20 final size:20
Alignment explanation
Indices: 5812--5863 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
5802 TAACCTTCAT
*
5812 ATGAAATTTTGATATCCTCC
1 ATGAAATTTTGATATCATCC
5832 ATG-AATTTTGATATCATCC
1 ATGAAATTTTGATATCATCC
*
5851 TTGAAATTTTGAT
1 ATGAAATTTTGAT
5864 TACTCCATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGAAATTTTGATATCATCC
Found at i:6759 original size:31 final size:31
Alignment explanation
Indices: 6724--6789 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
6714 TGGCAATTTA
* *
6724 GAAATATGTTTTAAAGAA-AAGGGTACAATTG
1 GAAATATGTTTTAAA-AATAAGGATACAATCG
6755 GAAATATGTTTTAAAAATAAGGATACAATCG
1 GAAATATGTTTTAAAAATAAGGATACAATCG
6786 GAAA
1 GAAA
6790 ATATAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGATACAATCG
Found at i:9969 original size:2 final size:2
Alignment explanation
Indices: 9962--9990 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9952 AATACTCATA
9962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9991 AA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.