Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015037.1 Corchorus capsularis cultivar CVL-1 contig15058, 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: 30811
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:2546 original size:330 final size:331
Alignment explanation
Indices: 1857--2770 Score: 867
Period size: 332 Copynumber: 2.8 Consensus size: 331
1847 TTTTGTCTTA
* * * * * *
1857 CGACACTCCTTGAAATATCTATATTCTTCTAATAAAATCTTAGTCATACTGCATTTAAAGATTTG
1 CGACACTCCTTAAAATATCTATATTCATCTAATAAAATCTCAGCCACACTGCATTTAAAAATTTG
* * * *
1922 TTTTACGAGCATCTAAATCTTGTTTCGATTCAATTAGAATTTAATTCAGAAAAAATATGAAAAAT
66 TTTTACAAGCATCTAAATCTTATTTCGATTCAATTAGAAATTAATTCAGAAAAAATATGAAAAAC
* * ** * * *
1987 GATATTAAAAGCGTGAAAAGCCCTTCAATCTCTTTAGCGTTGAATTATATATTTTTTTTATGAGT
131 GATATTAAAAACGTGAAAAGCCCTCCAATCTCTTTAGCACTAAATTATATATTTTTATGATGAGT
* ** * *
2052 TTTATGGATAAAAATTAAGGAAATATCTTTCGGGTCAATTTTTGCTAAATTTTAGCCGAAATCGT
196 TTTAT-GATAAAAATTAAGGAAAAATCTTTCAAGTCAATTTTTGCAAAATTTTAGCCAAAATCGT
* * * * *
2117 GTAATAATCATCATGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGATTCAGTTTTGAATGATTT
260 GTAATAACCATCATGATTTTTGACTAAAAACGCATTCCGGGGCCCGACTCAGTTTTGAATGATTT
*
2182 TTGGCTC
325 TTGGCAC
* * * * *
2189 CAAGACTCCTTAAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTG
1 CGACACTCCTTAAAATATCTATATTCATCTAATAAAATCTCAGCCACACTGCATTTAAAAATTTG
* * * * *
2254 TTTTTATAAGCATCTGAATCTTATTTTGATTTAATTAGAAATTAATTCTG-AAAAATATGAAAAA
66 -TTTTACAAGCATCTAAATCTTATTTCGATTCAATTAGAAATTAATTCAGAAAAAATATGAAAAA
* * * * *
2318 CGATATTAAAAATGTGAGAAGTCCTCCAATCAT-TTTGGCACTAAATTATATATATTTTATGATT
130 CGATATTAAAAACGTGAAAAGCCCTCCAATC-TCTTTAGCACTAAATTATATAT-TTTTATGATG
* * ** *
2382 A-TTTTAT-CTAAAAATTGAGGAAAAAT-TTTCAAGTCGTTTTTTGCAAAATTTTAGCCAAAATT
193 AGTTTTATGATAAAAATTAAGGAAAAATCTTTCAAGTCAATTTTTGCAAAATTTTAGCCAAAATC
* * * *
2444 GTGTACTAACCATCATGATTTTTGACTAAAAACGTATTTCGGGGCCCTGACTCAGTTTTGCATGA
258 GTGTAATAACCATCATGATTTTTGACTAAAAACGCATTCCGGGGCCC-GACTCAGTTTTGAATGA
2509 TTTTTGGCAC
322 TTTTTGGCAC
* ** * * * * **
2519 CGACACTCCTTTAAATATCTATATTCATCTAATAAAATCTTGGTCATATTGCGTTTAAGGATTT-
1 CGACACTCCTTAAAATATCTATATTCATCTAATAAAATCTCAGCCACACTGCATTTAAAAATTTG
* *
2583 TTTTACGAGCATCTAAATCTTGTTTCGA-T---TT---AATT-A---AGAAAAAAT-TGAAAAAC
66 TTTTACAAGCATCTAAATCTTATTTCGATTCAATTAGAAATTAATTCAGAAAAAATATGAAAAAC
* * * * * * * ** *** * * * *
2636 AATATTAAAAGCGTGAAAATCTCTTCAATCTTTTTCGCGTTGGTTTTTATATTTTTTTTATGAGC
131 GATATTAAAAACGTGAAAAGCCCTCCAATCTCTTTAGCACTAAATTATATATTTTTATGATGAGT
* * * * **
2701 ATAAGGGATAAAAATTGA-GAAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCG
196 TTTA-TGATAAAAATTAAGGAAAA-ATCTTTCAAGTCAATTTTTGCAAAATTTTAGCCAAAATCG
2765 TGTAAT
259 TGTAAT
2771 TTGGATGAAA
Statistics
Matches: 472, Mismatches: 99, Indels: 34
0.78 0.16 0.06
Matches are distributed among these distances:
316 9 0.02
317 46 0.10
318 11 0.02
319 12 0.03
320 38 0.08
321 4 0.01
324 2 0.00
327 1 0.00
328 23 0.05
329 69 0.15
330 92 0.19
332 115 0.24
333 50 0.11
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (331 bp):
CGACACTCCTTAAAATATCTATATTCATCTAATAAAATCTCAGCCACACTGCATTTAAAAATTTG
TTTTACAAGCATCTAAATCTTATTTCGATTCAATTAGAAATTAATTCAGAAAAAATATGAAAAAC
GATATTAAAAACGTGAAAAGCCCTCCAATCTCTTTAGCACTAAATTATATATTTTTATGATGAGT
TTTATGATAAAAATTAAGGAAAAATCTTTCAAGTCAATTTTTGCAAAATTTTAGCCAAAATCGTG
TAATAACCATCATGATTTTTGACTAAAAACGCATTCCGGGGCCCGACTCAGTTTTGAATGATTTT
TGGCAC
Found at i:3782 original size:437 final size:438
Alignment explanation
Indices: 2977--3805 Score: 1209
Period size: 437 Copynumber: 1.9 Consensus size: 438
2967 TGGGTCCCAA
*
2977 TCTCAATAAACAAATCATTTTTTTGCTGGATTATTTATCAAATGATCCTCATACTTTTATGCTTT
1 TCTCAATAAACAAATCATTTTTTTGCTGGATTATTTATCAAATGATCATCATACTTTTATGCTTT
* *
3042 ATGCTATTTAATCCTTTACAGTTATGGGTTGGACGACTGAACGTTTCGGCTTTAATTCTTCTATG
66 ATGCTATTTAATCCTTTACAATTATGGGTTGGACGACTGAACGGTTCGGCTTTAATTCTTCTATG
* * * * *
3107 TTTTGTTTTGCTTGTCCTATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATTCACA
131 TTTTGTTCTACTTATCCGATCAAGGTGATTCAAGTGTCTATTAAAAGATAATTTCATGATTCACA
* *
3172 ACTTCCATGAAAGACTCAAAAACCAATTTTAATGTTTTGATTCTAAAAAATGCTTCTGAAATTTT
196 ACTTCCATGAAAGACTCAAAAACCAATTATAATGTTTTGATTCTAAAAAATACTTCTGAAATTTT
* * *
3237 GTGGTCTCGATTGCCAGTCTATCTAATATTATATAATTTTCAGTCCAATTGTCCGATTGAGGTTG
261 GTGGTCTCGATTGACAGTCTATCTAATATTATATAAATTTCAGTCCAATTGTCCGATTGAGATTG
** * * * *
3302 TTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCATTAAGGGCTTGAAAGCTGAAT
326 TTCAAGTGTCGGTTAAAAGGTTATTGCATGATCAACGACTTTCA-TAAGGACATGAAAACTGAAT
3367 TTGATTAATGAGTTTCGTGGAGGATTCAAGAGGTAATTTTTATATTAGG
390 TTGATTAATGAGTTTCGTGGAGGATTCAAGAGGTAATTTTTATATTAGG
* *
3416 TCTCCATAAACAAAT-ATTTTTTTTGCTGGATTATTTATCAAATGATCATCATACTTTTATGTTT
1 TCTCAATAAACAAATCA-TTTTTTTGCTGGATTATTTATCAAATGATCATCATACTTTTATGCTT
* * * * * *
3480 TATTCTATTTAATCCTTTACAATTATGGGTTGGACGATTTAACGCGTT-GGCTTTTATTTTTGTA
65 TATGCTATTTAATCCTTTACAATTATGGGTTGGACGACTGAACG-GTTCGGCTTTAATTCTTCTA
* * * *
3544 T-TTTTGTTCTATTTATCCGATTAAGGTGATTTAAGTGTCTATTAAAAGATAATTTCATGATTTA
129 TGTTTTGTTCTACTTATCCGATCAAGGTGATTCAAGTGTCTATTAAAAGATAATTTCATGATTCA
* * *
3608 CAACTTTCATG-AAGAACTCAGAAGCCAATTATAATGTTTTGATTCT-AAAAATACTTCTGAAAT
194 CAACTTCCATGAAAG-ACTCAAAAACCAATTATAATGTTTTGATTCTAAAAAATACTTCTGAAAT
** * * *
3671 TTTGTGGTCTCGATTGATGGTCTATCTAGTATTATATAAATTTCGGTCCATTTGTCCGATTGAGA
258 TTTGTGGTCTCGATTGACAGTCTATCTAATATTATATAAATTTCAGTCCAATTGTCCGATTGAGA
** *
3736 TTGTTCAAGTGTCGGTTAAAAGGTTATTGCATGATCAATTACTTTCATAAGGACATGAAAACTTA
323 TTGTTCAAGTGTCGGTTAAAAGGTTATTGCATGATCAACGACTTTCATAAGGACATGAAAACTGA
3801 ATTTG
388 ATTTG
3806 TTACTTTTAT
Statistics
Matches: 345, Mismatches: 42, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
436 19 0.06
437 118 0.34
438 93 0.27
439 113 0.33
440 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.42
Consensus pattern (438 bp):
TCTCAATAAACAAATCATTTTTTTGCTGGATTATTTATCAAATGATCATCATACTTTTATGCTTT
ATGCTATTTAATCCTTTACAATTATGGGTTGGACGACTGAACGGTTCGGCTTTAATTCTTCTATG
TTTTGTTCTACTTATCCGATCAAGGTGATTCAAGTGTCTATTAAAAGATAATTTCATGATTCACA
ACTTCCATGAAAGACTCAAAAACCAATTATAATGTTTTGATTCTAAAAAATACTTCTGAAATTTT
GTGGTCTCGATTGACAGTCTATCTAATATTATATAAATTTCAGTCCAATTGTCCGATTGAGATTG
TTCAAGTGTCGGTTAAAAGGTTATTGCATGATCAACGACTTTCATAAGGACATGAAAACTGAATT
TGATTAATGAGTTTCGTGGAGGATTCAAGAGGTAATTTTTATATTAGG
Found at i:10106 original size:338 final size:334
Alignment explanation
Indices: 9485--10351 Score: 802
Period size: 338 Copynumber: 2.6 Consensus size: 334
9475 GGTGTTGAAT
* * * * * * * *
9485 TATATATTTTTTATGAGTATTTTAGTCGAAAATTGAGGAAATATCTTTCGTGTCAATTTTTCCAA
1 TATATATATATTATGAGTATTTAAGTCAAAAATTGAGAAAACATCTTTCGGGTCAATTTTTCAAA
* * **
9550 ATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTGGATAAAAATGCGTTTTAGGAACTGGCT
66 ATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTGGATAAAAACGCGTTTTAGGAACTAACT
* * * * *
9615 CAATTTTGCATGATTTTTGGCGCCAAGACTTCTTTAGATATCCATATTCATCTAATCAAATCTCA
131 CAATTTTGCATGATTTTTGGCACCAACACTCCTTGAAATATCCATATTCATCTAATCAAATCTCA
* * * * * * * *
9680 TCCACATTGGATTTAAGAATTTGTTTTTACAAGCATTTGAATCTTGTTTCTATTTAATTAGAAAT
196 GCCACATTGCATTTAAGAATTTGTTTTTACAACCATCTGAATCTTATTTCGATTCAAATAGAAAT
* * *
9745 TAATTCAGGAAAATATGAAAAACGATATTAAAAGCTTGAAAAGTCCTCCAATCTTTCTGACGTTA
261 TAATTCAGAAAAATATCAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTCTGACGTTA
9810 AAATATATA
326 AAATATATA
* * * *
9819 TATATATATATTATGATTATTTAATTCAAAAATTGAGAAAACATTTTTCGGGTCATTTTTTTACA
1 TATATATATATTATGAGTATTTAAGTCAAAAATTGAGAAAACATCTTTCGGGTCA-ATTTTT-CA
* * * * * * **
9884 AAATTTTAGCTAAAATCGTGTACTAACCATCATAGTTTTTGGCTAATAACGCGTTTTGGGGCCCT
64 AAATTTTAGCCAAAATCGTGTAATAACCATCACAG-TTTTGGATAAAAACGCGTTTT-AGGAACT
* * ** * *
9949 AACTCAGTTTTGTATGATTTTTGGCACTGACACTCCTTGAAATATCTATATTCATCT-ATTAAGA
127 AACTCAATTTTGCATGATTTTTGGCACCAACACTCCTTGAAATATCCATATTCATCTAATCAA-A
* *
10013 TCTTAGCCACATTGCATTTAA-ATATTTGTTTTTACGACCATCTGAATCTTATTTCGATTCAAAT
191 TCTCAGCCACATTGCATTTAAGA-ATTTGTTTTTACAACCATCTGAATCTTATTTCGATTCAAAT
* * * * *
10077 AGAAATTAATTTAGAAAAATATCAAAAACGATATTAAAAGCGTGAAAAGCCCTTCATTCTTTTTG
255 AGAAATTAATTCAGAAAAATATCAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTCTG
**
10142 --GATTTGAAT-TATA
320 ACG-TTAAAATATATA
* * * * * ** *
10155 TAT-T-T-T-TTATGAGTA-TTATGGTTAAAGATTGAGGAAATATCTTTCTAGTTAATTTTTTCA
1 TATATATATATTATGAGTATTTA-AGTCAAAAATTGAGAAAACATCTTTCGGGTCAA-TTTTTCA
* * * * * * * *
10215 AAATTTTAGCCGAAATCATGTAATAATCATCACGATTTTTGGCTAAAATCGCG-TTTCGGGACTC
64 AAATTTTAGCCAAAATCGTGTAATAACCATCAC-AGTTTTGGATAAAAACGCGTTTTAGGAACT-
* * * * * * * * ** * *
10279 AGCTCAGTTTTGAATGATTTTTGACGCCGAGACTCCTTGAAAAATATATATTCATTTAACCAAAT
127 AACTCAATTTTGCATGATTTTTGGCACCAACACTCCTTGAAATATCCATATTCATCTAATCAAAT
*
10344 CCCAGCCA
192 CTCAGCCA
10352 TTTTTTTTAC
Statistics
Matches: 429, Mismatches: 92, Indels: 28
0.78 0.17 0.05
Matches are distributed among these distances:
329 4 0.01
330 59 0.14
331 50 0.12
332 36 0.08
333 1 0.00
334 46 0.11
335 6 0.01
336 40 0.09
337 28 0.07
338 159 0.37
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (334 bp):
TATATATATATTATGAGTATTTAAGTCAAAAATTGAGAAAACATCTTTCGGGTCAATTTTTCAAA
ATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTGGATAAAAACGCGTTTTAGGAACTAACT
CAATTTTGCATGATTTTTGGCACCAACACTCCTTGAAATATCCATATTCATCTAATCAAATCTCA
GCCACATTGCATTTAAGAATTTGTTTTTACAACCATCTGAATCTTATTTCGATTCAAATAGAAAT
TAATTCAGAAAAATATCAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTCTGACGTTA
AAATATATA
Found at i:11769 original size:40 final size:40
Alignment explanation
Indices: 11713--11803 Score: 137
Period size: 40 Copynumber: 2.3 Consensus size: 40
11703 TTTGATAATT
* * ** *
11713 TTTGGCATGACTAAATGATTTTTCCCCTAAACTGGATCTG
1 TTTGGAATGACAAAATGATTTGCCCCCTAAACTAGATCTG
11753 TTTGGAATGACAAAATGATTTGCCCCCTAAACTAGATCTG
1 TTTGGAATGACAAAATGATTTGCCCCCTAAACTAGATCTG
11793 TTTGGAATGAC
1 TTTGGAATGAC
11804 TATACTAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (40 bp):
TTTGGAATGACAAAATGATTTGCCCCCTAAACTAGATCTG
Found at i:12410 original size:49 final size:49
Alignment explanation
Indices: 12338--12435 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
12328 GGTACATTGG
12338 GAACATTACAATTAAAGGGGGGTGAAATAGGAAGGTTGTTAGCTTTTCC
1 GAACATTACAATTAAAGGGGGGTGAAATAGGAAGGTTGTTAGCTTTTCC
*
12387 GAACATTACAATT-AGGAGGGGGTGAAATAGGAAGGTTGTTAGCTTTTCC
1 GAACATTACAATTAAAG-GGGGGTGAAATAGGAAGGTTGTTAGCTTTTCC
12436 TCTGTTTAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 2 0.04
49 45 0.96
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.29
Consensus pattern (49 bp):
GAACATTACAATTAAAGGGGGGTGAAATAGGAAGGTTGTTAGCTTTTCC
Found at i:15124 original size:19 final size:19
Alignment explanation
Indices: 15100--15136 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
15090 ATACAGTACC
15100 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
15119 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
15137 TGCTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:30665 original size:16 final size:16
Alignment explanation
Indices: 30644--30699 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
30634 GCCGCCCAAC
30644 TTGGGCGGCGTCACCA
1 TTGGGCGGCGTCACCA
30660 TTGGGCAGGCCG-C-CCAA
1 TTGGGC-GG-CGTCACC-A
30677 CTTGGGCGGCGTCACCA
1 -TTGGGCGGCGTCACCA
30694 TTGGGC
1 TTGGGC
30700 AGGCCGCCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
16 16 0.47
17 8 0.24
18 10 0.29
ACGTcount: A:0.12, C:0.32, G:0.38, T:0.18
Consensus pattern (16 bp):
TTGGGCGGCGTCACCA
Found at i:30672 original size:34 final size:34
Alignment explanation
Indices: 30614--30725 Score: 165
Period size: 34 Copynumber: 3.4 Consensus size: 34
30604 CGCCCCAAGA
* *
30614 GGGCGGC-TTACCA-TGGGGAGGCCGCCCAACTT
1 GGGCGGCGTCACCATTGGGCAGGCCGCCCAACTT
30646 GGGCGGCGTCACCATTGGGCAGGCCGCCCAACTT
1 GGGCGGCGTCACCATTGGGCAGGCCGCCCAACTT
* *
30680 GGGCGGCGTCACCATTGGGCAGGCCGCCCCACTG
1 GGGCGGCGTCACCATTGGGCAGGCCGCCCAACTT
*
30714 GGGCGGCTTCAC
1 GGGCGGCGTCAC
30726 TATGAATAGG
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
32 7 0.10
33 5 0.07
34 61 0.84
ACGTcount: A:0.13, C:0.35, G:0.38, T:0.14
Consensus pattern (34 bp):
GGGCGGCGTCACCATTGGGCAGGCCGCCCAACTT
Found at i:30782 original size:31 final size:31
Alignment explanation
Indices: 30733--30810 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
30723 CACTATGAAT
* *
30733 AGGCCGCCCCGGTTGGGCGGCTTCGCCAGGGC
1 AGGCCG-CCCGGTGGGGCGGCTTCGCCACGGC
*
30765 AGGCCGCCCGGTGGGGCGGCTTCGCCACGGT
1 AGGCCGCCCGGTGGGGCGGCTTCGCCACGGC
30796 AGGCCGCACCGGTGG
1 AGGCCGC-CCGGTGG
30811 C
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
31 29 0.69
32 13 0.31
ACGTcount: A:0.08, C:0.36, G:0.45, T:0.12
Consensus pattern (31 bp):
AGGCCGCCCGGTGGGGCGGCTTCGCCACGGC
Done.