Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008055.1 Corchorus capsularis cultivar CVL-1 contig08076, 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: 22911
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:2428 original size:19 final size:19
Alignment explanation
Indices: 2393--2430 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2383 AGACCATTGG
*
2393 TTAATCATTATTAATGAAC
1 TTAATCATCATTAATGAAC
2412 TTAATTCATCATT-ATGAAC
1 TTAA-TCATCATTAATGAAC
2431 ACATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.42
Consensus pattern (19 bp):
TTAATCATCATTAATGAAC
Found at i:3253 original size:23 final size:25
Alignment explanation
Indices: 3227--3297 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
3217 GATAATTACT
*
3227 ATAATTATCTCTAATATATAA-A-G
1 ATAATTATCTCTAATATATAACACC
*
3250 ATAATATGAT-TAATAATATATAATCACC
1 ATAAT-T-ATCT-CTAATATATAA-CACC
3278 ATAATTATCTCTAATATATA
1 ATAATTATCTCTAATATATA
3298 CATGGATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
23 5 0.13
24 2 0.05
25 12 0.32
26 11 0.29
27 3 0.08
28 5 0.13
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (25 bp):
ATAATTATCTCTAATATATAACACC
Found at i:3348 original size:55 final size:51
Alignment explanation
Indices: 3218--3352 Score: 182
Period size: 55 Copynumber: 2.6 Consensus size: 51
3208 AGGAGTCTTG
* *
3218 ATAATTACTATAATTATCTCTAATATATAAAGATAATATGATTAATAATAT
1 ATAATCACCATAATTATCTCTAATATATAAAGATAATATGATTAATAATAT
*
3269 ATAATCACCATAATTATCTCTAATATATACATGGATAATATCG-TTAATAAGTAT
1 ATAATCACCATAATTATCTCTAATATATA-A-AGATAATAT-GATTAATAA-TAT
*
3323 AATAATCACCATAATTATCTTTAATATATA
1 -ATAATCACCATAATTATCTCTAATATATA
3353 TATATATATA
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
51 27 0.36
52 1 0.01
53 15 0.20
54 4 0.05
55 28 0.37
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.39
Consensus pattern (51 bp):
ATAATCACCATAATTATCTCTAATATATAAAGATAATATGATTAATAATAT
Found at i:3374 original size:59 final size:53
Alignment explanation
Indices: 3218--3377 Score: 171
Period size: 51 Copynumber: 2.9 Consensus size: 53
3208 AGGAGTCTTG
* * * *
3218 ATAATTACTATAATTATCTCTAATATATA-A-AGATAATATGATTAATAATAT
1 ATAATCACCATAATTATCTATAATATATATATAGATAATATGGTTAATAATAT
* * * *
3269 ATAATCACCATAATTATCTCTAATATATACATGGATAATATCGTTAATAAGTAT
1 ATAATCACCATAATTATCTATAATATATATATAGATAATATGGTTAATAA-TAT
*
3323 AATAATCACCATAATTATCTTTAATATATATATATATATATAATATGGTTAATAA
1 -ATAATCACCATAATTATC--T-ATA-ATATATATATAGATAATATGGTTAATAA
3378 AGGTAATTGG
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
51 27 0.30
52 1 0.01
53 15 0.16
54 3 0.03
55 18 0.20
57 1 0.01
58 2 0.02
59 24 0.26
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (53 bp):
ATAATCACCATAATTATCTATAATATATATATAGATAATATGGTTAATAATAT
Found at i:6937 original size:62 final size:62
Alignment explanation
Indices: 6840--6969 Score: 206
Period size: 62 Copynumber: 2.1 Consensus size: 62
6830 TAGTAAAATG
* * * * *
6840 GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTTAGTTGA
1 GTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGA
*
6902 GTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGA
1 GTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGA
6964 GTAAAA
1 GTAAAA
6970 CTATAAAAAC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (62 bp):
GTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGA
Found at i:7295 original size:2 final size:2
Alignment explanation
Indices: 7290--7315 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7280 ATGAGCGCGC
7290 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
7316 TTATTGGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8566 original size:17 final size:17
Alignment explanation
Indices: 8544--8579 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
8534 GAGACAATAG
*
8544 AATATGGAGAATAAGAC
1 AATATGAAGAATAAGAC
*
8561 AATATGAAGAATGAGAC
1 AATATGAAGAATAAGAC
8578 AA
1 AA
8580 ATTGTTCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.56, C:0.06, G:0.22, T:0.17
Consensus pattern (17 bp):
AATATGAAGAATAAGAC
Found at i:8786 original size:11 final size:11
Alignment explanation
Indices: 8772--8809 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
8762 ATTCATAACA
8772 AATTTATAATT
1 AATTTATAATT
8783 AATTTATAATT
1 AATTTATAATT
8794 -ATTTGATAATT
1 AATTT-ATAATT
*
8805 TATTT
1 AATTT
8810 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:9304 original size:20 final size:20
Alignment explanation
Indices: 9267--9305 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9257 CAGTATCAAA
*
9267 AAAAATATTATATACATAAG
1 AAAAATATTAAATACATAAG
* *
9287 AAAATTATTAAATTCATAA
1 AAAAATATTAAATACATAA
9306 TAAGTCTCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAAATATTAAATACATAAG
Found at i:10628 original size:17 final size:18
Alignment explanation
Indices: 10595--10628 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10585 ACCCAACAAG
10595 AAATCAAAACATTTATTC
1 AAATCAAAACATTTATTC
*
10613 AAATCACAAC-TTTATT
1 AAATCAAAACATTTATT
10629 ATTATTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATCAAAACATTTATTC
Found at i:12946 original size:33 final size:33
Alignment explanation
Indices: 12904--12981 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
12894 GCCGCCCCAC
12904 TGGGGAGGCTCAACCACGGCGGAGCC-TCCCTAG
1 TGGGGAGGCTCAACCACGGCGGAGCCGT-CCTAG
** ** *
12937 TGGGGAGGCTCCGCCGTGGCTGAGCCGTCCTAG
1 TGGGGAGGCTCAACCACGGCGGAGCCGTCCTAG
12970 TGGGGAGGCTCA
1 TGGGGAGGCTCA
12982 GTGTAAAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 37 0.97
34 1 0.03
ACGTcount: A:0.14, C:0.29, G:0.41, T:0.15
Consensus pattern (33 bp):
TGGGGAGGCTCAACCACGGCGGAGCCGTCCTAG
Found at i:15044 original size:324 final size:319
Alignment explanation
Indices: 14662--15781 Score: 1130
Period size: 333 Copynumber: 3.5 Consensus size: 319
14652 TATATTCATC
* * *
14662 TAATCAAATCTCAGCCACATTGGATTTGAGAATTTGTTTTTACTAGCATCTAAATCTTGTTTCGA
1 TAATCAAATCTCAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCGA
** * *
14727 TTTAATTAGAAATTAATTCGGGAAAATAGGAAAAACGATATTATAAA-TGTCAAAAGCCCTTCAA
66 TTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACGATATTA-AAAGCGTGAAAAGCCCTTCAA
* ** * *
14791 TCTTTTTGGGGTTGAAATATATACTATTTATGAGTATTTTAGGTGAAAATTGAGGAAATATCTAT
130 TCTTTTTGGCGTTGAAATATATA-TATTTATGAGTATTTTATCTAAAAATTGAGGAAATATCTTT
* * * *
14856 CGGGTCGATTTTT-AAAAATTTTAACCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAA
194 CAGGTC-ATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAA
* *
14920 C-CGTTCCGGGGCCCGGA-TCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAGATATCTTC
258 CGCGTTCC-GGGCCC-AATTCAGTTTTGCATGATTTTTGGCACCAA-ACTCCTTGA-ATATCTT-
14983 GTA
318 -TA
* **
14986 TAATCAAATCTCAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTAAA
1 TAATCAAATCTCAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCGA
* * * **
15051 TTTAATTAGAATTTAATT--AAAAAATATGAAAAATGATATTAAAAGCGTGAAAAGTTC-TCAAA
66 TTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTTC-AA
* * * *
15113 TCTTTTTGACGTT-AAATTATATATATTTTATGAGTATTTTATCCAAAAATTGAGGAAAAATTTT
130 TCTTTTTGGCGTTGAAA-TATATATA-TTTATGAGTATTTTATCTAAAAATTGAGGAAATATCTT
* *
15177 TCAGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAA
193 TCAGGTCA-TTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCT-AAA
* * *
15242 AACGCGTTTCATGGCCCCAATTCAGTTTTGCATGATTTTTTGCACCAAAACTCCTTGAAATATCT
256 AACGCG-TTC-CGGGCCCAATTCAGTTTTGCATGATTTTTGGCACC-AAACTCCTTG-AATATC-
15307 ATATTCA
316 -T-TT-A
* ** * * * * * *
15314 TCAAATAAAATCTTGGCAAAACTGCATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTC
1 T--AATCAAATCTCAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTC
* * *
15379 GATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATAAAAAGCGTGAAAAGCCCTTT
64 GATTTAATTAGAAATTAATTC-GAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTTC
* * * * *
15444 AATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTCTCTAAAAATTAAGGAAATATCT
128 AATCTTTTTGGCGTTGAAATATATA-TATTTATGAGTATTTTATCTAAAAATTGAGGAAATATCT
* * * *
15509 TTCAGGTCAATTTTTGCAAACTTTTAGCCGAAATCGTATAATAATCATCACGGTTTTTGGC-GAA
192 TTCAGGTC-ATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAA
* ** * * *
15573 AACGCGTTCCGGGCCCAATTTAGTTAAGCATAACTTTTGGCACCGAAACTCCTTGAA-ATATTTA
256 AACGCGTTCCGGGCCCAATTCAGTTTTGCATGATTTTTGGCACC-AAACTCCTTGAATATCTTTA
* * * ** * * *
15637 TATTC--ATCT-A---AC--TAAATCTCAACCA-TTGTTTTTACAAGCATCTGAATCATGTTTCG
1 TAATCAAATCTCAGCCACATTGAAT-TTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCG
* *
15693 ATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAA-CATGAAAATCCCTTC
65 ATTTAATTAGAAATTAATTC-GAAAAAATAGGAAAAACGATATTA-AAAGCGTGAAAAGCCCTTC
* ** *
15757 -ATTTTTTTGGCACTGAATTATATAT
128 AATCTTTTTGGCGTTGAAATATATAT
15782 TTTCGGGTTT
Statistics
Matches: 668, Mismatches: 100, Indels: 69
0.80 0.12 0.08
Matches are distributed among these distances:
311 1 0.00
312 21 0.03
313 84 0.13
314 7 0.01
315 1 0.00
319 4 0.01
321 13 0.02
322 88 0.13
323 43 0.06
324 84 0.13
325 4 0.01
326 44 0.07
327 6 0.01
328 5 0.01
329 38 0.06
330 72 0.11
331 8 0.01
333 140 0.21
334 5 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (319 bp):
TAATCAAATCTCAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCGA
TTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAAT
CTTTTTGGCGTTGAAATATATATATTTATGAGTATTTTATCTAAAAATTGAGGAAATATCTTTCA
GGTCATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGC
GTTCCGGGCCCAATTCAGTTTTGCATGATTTTTGGCACCAAACTCCTTGAATATCTTTA
Found at i:17214 original size:334 final size:317
Alignment explanation
Indices: 16517--17299 Score: 821
Period size: 334 Copynumber: 2.4 Consensus size: 317
16507 TTGGCCAGAC
* *
16517 CTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTAAATCATGTTTCGATTTAATTAG
1 CTTAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTAAAT-TTGTTTCGATTTAATTAG
* *
16582 AAATTAATTTGAAAAAAA-AGGGAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATCTTTTTG
64 AAATTAATTTGAAAAAAATA-GGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTG
* * * * *
16646 GCGTTGAATTATATATTTTTTTTGAGTATTGTGGCTAAAAGTTGAGAAAAATATTTCGGGTCAAT
128 GCGTTGAATTATATATGTTTTATGAGTATTGTCGCTAAAAGTGGAGAAAAATATTTCGGATCAAT
* * *
16711 TTTTACCGAAATCGTGTACAATCACGGTTTTTTGGCTAAAAACGAATTATGGGGCCCCGAGCCAC
193 TTTTACCGAAATCGTGTACAATCACGATTTTTTGGCTAAAAACGAATTACGGGGCCCCGAGCAAC
*
16776 TTTTGCATGATTTTTGGAACCAAGACTCCTTAAAATATATCTATATTCATCTAACCAAAT
258 TTTTGCATGATTTTTGGAACCAAAACTCCTTAAAATATATCTATATTCATCTAACCAAAT
* * *
16836 CTCAGCCACATTGTGTTTAAGGATTTGTTTTTACGAGTATCTAAATTGTGTTTCGATTTAATTAG
1 CTTAGCCACATTG-ATTTAAGGATTTGTTTTTACGAGCATCTAAATT-TGTTTCGATTTAATTAG
*** * *
16901 AAATTAATTTAGAAATAAAATAGGAAAATTTATATTAGAAGCGTGAAAAGGCTTTCAAT-TTTTC
64 AAATTAATTT-GAAA-AAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTT-
*
16965 TGGCGTTGAATTATATATGTTTTATGAGTATTTTCGCTAGAAATTGTGGA-AAAAAT-TTTCGGA
126 TGGCGTTGAATTATATATGTTTTATGAGTATTGTCGCTA-AAA--GTGGAGAAAAATATTTCGGA
17028 TCAATTTTTGCAAAATTTCAGCCGAAATCGTGTACTAA-CTATC-ATATTTTTCGGCTAAAAAC-
188 TCAA---TT------TTT-A-CCGAAATCGTGTAC-AATC-A-CGAT-TTTTT-GGCTAAAAACG
* * * ** * *** **
17090 ACGTTCCGGGG-CCTGCTCAATTTTTTGCATGATTTTTGGTGTCAAAACTCCTT-GTA-ATATCT
237 A-ATTACGGGGCCCCGAGCAA-CTTTTGCATGATTTTTGGAACCAAAACTCCTTAAAATATATCT
* **
17152 ATATTTATCTAATTAAAT
300 ATATTCATCTAACCAAAT
* * *
17170 CTTAGCCACATTAGATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTATTTTGATTTAATTAG
1 CTTAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTAAAT-TTGTTTCGATTTAATTAG
** *
17235 AAATTAACTCGGAAAAAAATAGGAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCCTTTTT
64 AAATTAA-TTTGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAAT-CTTTTT
17300 AATGTCGAAT
Statistics
Matches: 383, Mismatches: 49, Indels: 49
0.80 0.10 0.10
Matches are distributed among these distances:
318 1 0.00
319 67 0.17
320 8 0.02
321 70 0.18
322 14 0.04
323 6 0.02
324 4 0.01
325 2 0.01
331 3 0.01
332 1 0.00
333 52 0.14
334 92 0.24
335 20 0.05
336 43 0.11
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (317 bp):
CTTAGCCACATTGATTTAAGGATTTGTTTTTACGAGCATCTAAATTTGTTTCGATTTAATTAGAA
ATTAATTTGAAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCG
TTGAATTATATATGTTTTATGAGTATTGTCGCTAAAAGTGGAGAAAAATATTTCGGATCAATTTT
TACCGAAATCGTGTACAATCACGATTTTTTGGCTAAAAACGAATTACGGGGCCCCGAGCAACTTT
TGCATGATTTTTGGAACCAAAACTCCTTAAAATATATCTATATTCATCTAACCAAAT
Found at i:22473 original size:21 final size:21
Alignment explanation
Indices: 22447--22489 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
22437 TACCTCACGG
22447 AATGACTTTGAGAGATCATCC
1 AATGACTTTGAGAGATCATCC
22468 AATGACTTTGAGAGATCATCC
1 AATGACTTTGAGAGATCATCC
22489 A
1 A
22490 TTGTCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (21 bp):
AATGACTTTGAGAGATCATCC
Done.