Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016139.1 Corchorus capsularis cultivar CVL-1 contig16160, 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: 4662
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Found at i:126 original size:22 final size:22
Alignment explanation
Indices: 76--476 Score: 245
Period size: 22 Copynumber: 17.8 Consensus size: 22
66 TTGATTATTA
*
76 TTTACT-TTGTACTTGATTACAATT
1 TTTACTCTT-TAC-TGATTAC-CTT
*
100 TTTACTCTTTATTGATTACCTT
1 TTTACTCTTTACTGATTACCTT
* *
122 TTTACTTTTTTACTGATTTACCAT
1 TTTAC-TCTTTACTGA-TTACCTT
*
146 TTTACTCTTTTACTGATTACTATT
1 TTTACTC-TTTACTGATTAC-CTT
*
170 TTCTGCTCCTTTTTTACTGATTACTCTT
1 TT-TACT-C---TTTACTGATTAC-CTT
* *
198 TTTACTTTTTACTGATTTGCCCTT
1 TTTACTCTTTACTGA-TT-ACCTT
* *
222 TTTGCTTTTTTATCTGATTACCTT
1 TTTAC-TCTTTA-CTGATTACCTT
*
246 TTTACTTCTTGT--TGATTAGCTTT
1 TTTAC-TCTT-TACTGATTA-CCTT
*
269 TTTACTCTTTACTGATCACCTT
1 TTTACTCTTTACTGATTACCTT
*
291 TTTACTC-TTACTGATTTCC-T
1 TTTACTCTTTACTGATTACCTT
* *
311 TTTACT-TCTTACTTATTACTTT
1 TTTACTCT-TTACTGATTACCTT
*
333 TTTACTC-TTACTGATTA-CTA
1 TTTACTCTTTACTGATTACCTT
* * *
353 TTTACTTTTTACTGACTA-TTAT
1 TTTACTCTTTACTGATTACCT-T
375 TTTACTCTTGT--TGATTACCTT
1 TTTACTCTT-TACTGATTACCTT
* *
396 CTTACTTTTTACTGATTA-CTAT
1 TTTACTCTTTACTGATTACCT-T
* *
418 TTTACTCTTTACTAATTACCAT
1 TTTACTCTTTACTGATTACCTT
* *
440 TTTACCCTTT-CAGA-TACCTT
1 TTTACTCTTTACTGATTACCTT
* *
460 CTTACTTTTTACTGATT
1 TTTACTCTTTACTGATT
477 GCACGCTATT
Statistics
Matches: 297, Mismatches: 49, Indels: 64
0.72 0.12 0.16
Matches are distributed among these distances:
20 27 0.09
21 59 0.20
22 76 0.26
23 43 0.14
24 51 0.17
25 15 0.05
26 5 0.02
27 3 0.01
28 18 0.06
ACGTcount: A:0.18, C:0.19, G:0.06, T:0.56
Consensus pattern (22 bp):
TTTACTCTTTACTGATTACCTT
Found at i:171 original size:15 final size:15
Alignment explanation
Indices: 147--199 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
137 ATTTACCATT
147 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
162 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
175 CTCCTTTTTTACTGA
1 TTACTCTTTTACTGA
190 TTACTCTTTT
1 TTACTCTTTT
200 TACTTTTTAC
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 7 0.24
14 6 0.21
15 16 0.55
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.58
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:335 original size:42 final size:42
Alignment explanation
Indices: 180--444 Score: 219
Period size: 42 Copynumber: 6.0 Consensus size: 42
170 TTCTGCTCCT
* * *
180 TTTTTACTGATTACTCTTTTTACTTTTTACTGATTTGCCCTTTTTGC
1 TTTTTACTGATTACT-TTTTTAC-TCTTACTGA-TT-ACC-TTTTAC
* ** *
227 TTTTTTATCTGATTACCTTTTTACTTCTTGTTGATTAGCTTTTTTAC
1 -TTTTTA-CTGATTACTTTTTTAC-TCTTACTGATTA-C-CTTTTAC
* * * *
274 TCTTTACTGATCACCTTTTTACTCTTACTGATTTCCTTTTAC
1 TTTTTACTGATTACTTTTTTACTCTTACTGATTACCTTTTAC
* *
316 TTCTTACTTATTACTTTTTTACTCTTACTGATTA-CTATTTAC
1 TTTTTACTGATTACTTTTTTACTCTTACTGATTACCT-TTTAC
* **
358 TTTTTACTGACTA-TTATTTTACTCTTGTTGATTACCTTCTTAC
1 TTTTTACTGATTACTT-TTTTACTCTTACTGATTACCTT-TTAC
* *
401 TTTTTACTGATTACTATTTTACTCTTTACTAATTACCATTTTAC
1 TTTTTACTGATTACTTTTTTACTC-TTACTGATTACC-TTTTAC
445 CCTTTCAGAT
Statistics
Matches: 178, Mismatches: 29, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
41 4 0.02
42 66 0.37
43 27 0.15
44 23 0.13
45 17 0.10
46 5 0.03
47 8 0.04
48 20 0.11
49 8 0.04
ACGTcount: A:0.18, C:0.19, G:0.06, T:0.57
Consensus pattern (42 bp):
TTTTTACTGATTACTTTTTTACTCTTACTGATTACCTTTTAC
Found at i:364 original size:14 final size:13
Alignment explanation
Indices: 288--365 Score: 57
Period size: 14 Copynumber: 5.7 Consensus size: 13
278 TACTGATCAC
*
288 CTTTTTACTCTTA
1 CTTTTTACTTTTA
* *
301 CTGATTTCCTTTTA
1 CT-TTTTACTTTTA
*
315 CTTCTTACTTATTA
1 CTTTTTACTT-TTA
*
329 CTTTTTTACTCTTA
1 C-TTTTTACTTTTA
**
343 CTGATTACTATTTA
1 CTTTTTACT-TTTA
357 CTTTTTACT
1 CTTTTTACT
366 GACTATTATT
Statistics
Matches: 48, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
13 13 0.27
14 28 0.58
15 7 0.15
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.59
Consensus pattern (13 bp):
CTTTTTACTTTTA
Found at i:458 original size:64 final size:64
Alignment explanation
Indices: 340--476 Score: 179
Period size: 64 Copynumber: 2.1 Consensus size: 64
330 TTTTTTACTC
* * ** * *
340 TTACTGATTACTATTTACTTTTTACTGACTATTATTTTACTCTTGTTGATTACCTTCTTACTTT
1 TTACTGATTACTATTTACTCTTTACTAACTACCATTTTACCCTTGTAGATTACCTTCTTACTTT
*
404 TTACTGATTACTATTTTACTCTTTACTAATTACCATTTTACCCTT-TCAGA-TACCTTCTTACTT
1 TTACTGATTACTA-TTTACTCTTTACTAACTACCATTTTACCCTTGT-AGATTACCTTCTTACTT
467 T
64 T
468 TTACTGATT
1 TTACTGATT
477 GCACGCTATT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
64 37 0.58
65 27 0.42
ACGTcount: A:0.22, C:0.20, G:0.05, T:0.53
Consensus pattern (64 bp):
TTACTGATTACTATTTACTCTTTACTAACTACCATTTTACCCTTGTAGATTACCTTCTTACTTT
Found at i:722 original size:55 final size:55
Alignment explanation
Indices: 661--938 Score: 459
Period size: 55 Copynumber: 5.1 Consensus size: 55
651 AATTTTAACT
* *
661 CTTAATTA-TCGATTTACTGATTACTATTACCTTCACTCTGATTAATCTCTTTTTA
1 CTTAATTACT-GATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* *
716 CTTAATTACTGATTTACTGATTACTACTACTTTGACTCTGATTAATATCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
771 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* *
826 CTTAATTACTGATTTACTGATTACTATTTCCTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* * *
881 CTTAATTACTGATTTACTGATTACTGTTACTTTGACTCTGATTTACCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
936 CTT
1 CTT
939 TTTAGATTTC
Statistics
Matches: 209, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
55 208 1.00
56 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.50
Consensus pattern (55 bp):
CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
Found at i:756 original size:29 final size:28
Alignment explanation
Indices: 724--813 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 28
714 TACTTAATTA
724 CTGATTTACTGATTACTACTACTTTGACT
1 CTGATTTACTGATTACTA-TACTTTGACT
** *
753 CTGATTAATATCTTTTTACT-TA-ATT-A--
1 CTGATT--TA-CTGATTACTATACTTTGACT
779 CTGATTTACTGATTACTATTACTTTGACT
1 CTGATTTACTGATTACTA-TACTTTGACT
808 CTGATT
1 CTGATT
814 AATCTCTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 18
0.66 0.09 0.26
Matches are distributed among these distances:
23 7 0.15
24 2 0.04
25 2 0.04
26 8 0.17
27 1 0.02
28 1 0.02
29 14 0.30
30 2 0.04
31 2 0.04
32 7 0.15
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (28 bp):
CTGATTTACTGATTACTATACTTTGACT
Found at i:1776 original size:101 final size:101
Alignment explanation
Indices: 1624--1889 Score: 403
Period size: 101 Copynumber: 2.7 Consensus size: 101
1614 ACTTCTAATT
* * * *
1624 CAAAGGTGACA-TTTTATTTACTAA--ACTTAAAAGTTCAATCTTTTATTCAAAGGTAAAATCTT
1 CAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTT
* *
1686 TATTTACTAATTACTCAAAAAATTCAGTCTTTTACC
66 TATTTACTAATTACTCAAAAAATTCAATCTTTTAAC
1722 CAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTT
1 CAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTT
*
1787 TATTTACTAATTACTCTAAAAATTCAATCTTTTAAC
66 TATTTACTAATTACTCAAAAAATTCAATCTTTTAAC
* * * * *
1823 CTAAGATGACATTTTTATTTAGCAATTACTTAAAAATCCAATCTTTTATTTAAAGGTTACATCTT
1 CAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTT
1888 TA
66 TA
1890 GCCAAATATC
Statistics
Matches: 153, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
98 10 0.07
99 12 0.08
101 131 0.86
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.42
Consensus pattern (101 bp):
CAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTT
TATTTACTAATTACTCAAAAAATTCAATCTTTTAAC
Found at i:1789 original size:50 final size:50
Alignment explanation
Indices: 1586--1889 Score: 310
Period size: 50 Copynumber: 6.1 Consensus size: 50
1576 AACTAATCAA
** * * * *
1586 TTTATTTACTAATGGCCTAAAAGTTCAAACTTCTAATTCAAAGGTGACAT-
1 TTTATTTACTAATTACTTAAAAATTCAATCTT-TTATTCAAAGGTGACATC
* * *
1636 TTTATTTACTAA--ACTTAAAAGTTCAATCTTTTATTCAAAGGTAAAATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTGACATC
* * ** * *
1684 TTTATTTACTAATTACTCAAAAAATTCAGTCTTTTACCCAAAGATGACATT
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGGTGACATC
* * *
1735 TTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTGACATC
** * * *
1785 TTTATTTACTAATTACTCTAAAAATTCAATCTTTTAACCTAAGATGACATT
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGGTGACATC
* * *
1836 TTTATTTAGC-AATTACTTAAAAATCCAATCTTTTATTTAAAGGTTACATC
1 TTTATTTA-CTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTGACATC
1886 TTTA
1 TTTA
1890 GCCAAATATC
Statistics
Matches: 208, Mismatches: 40, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
47 14 0.07
48 27 0.13
50 85 0.41
51 81 0.39
52 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (50 bp):
TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTGACATC
Done.