Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008610.1 Corchorus capsularis cultivar CVL-1 contig08631, 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: 45043
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Found at i:311 original size:148 final size:148
Alignment explanation
Indices: 27--347 Score: 626
Period size: 148 Copynumber: 2.2 Consensus size: 148
17 TTTTTCCATC
27 AACTGAGGAGGAAATTTAGGCTAACATAAATTTTTCCATCATATTCTTTAGATGGATTCTCAAGT
1 AACTGAGGAGGAAATTTAGGCTAACATAAATTTTTCCATCATATTCTTTAGATGGATTCTCAAGT
92 GATTTCGGTTGACCCTATCCACTATCATGAGGGATTTGGGTGCTATCCTAATCCTGCTGTGCTAT
66 GATTTCGGTTGACCCTATCCACTATCATGAGGGATTTGGGTGCTATCCTAATCCTGCTGTGCTAT
157 TTCCCAACTTATCATGCA
131 TTCCCAACTTATCATGCA
175 AACTGAGGAGGAAATTTAGGCTAACATAAATTTTTCCATCATATTCTTTAGATGGATTCTCAAGT
1 AACTGAGGAGGAAATTTAGGCTAACATAAATTTTTCCATCATATTCTTTAGATGGATTCTCAAGT
240 GATTTCGGTTGACCCTATCCACTATCATGAGGGATTTGGGTGCTAT-CTAATCCTGCTGTGCTAT
66 GATTTCGGTTGACCCTATCCACTATCATGAGGGATTTGGGTGCTATCCTAATCCTGCTGTGCTAT
304 TTCCCCAACTTATCATGCA
131 TT-CCCAACTTATCATGCA
323 AACTGAGGAGGAAATTTAGGCTAAC
1 AACTGAGGAGGAAATTTAGGCTAAC
348 CTACTTGTTG
Statistics
Matches: 172, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
147 20 0.12
148 152 0.88
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (148 bp):
AACTGAGGAGGAAATTTAGGCTAACATAAATTTTTCCATCATATTCTTTAGATGGATTCTCAAGT
GATTTCGGTTGACCCTATCCACTATCATGAGGGATTTGGGTGCTATCCTAATCCTGCTGTGCTAT
TTCCCAACTTATCATGCA
Found at i:963 original size:13 final size:13
Alignment explanation
Indices: 945--969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
935 AAATCTAGTA
945 TACTATATATATG
1 TACTATATATATG
958 TACTATATATAT
1 TACTATATATAT
970 ACTAGATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
TACTATATATATG
Found at i:8241 original size:2 final size:2
Alignment explanation
Indices: 8234--8267 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
8224 TTTATAACAG
*
8234 AT AT AT AT AT AT AT AT AC AT AT -T AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8268 GCAAAATTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8276 original size:19 final size:17
Alignment explanation
Indices: 8239--8272 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
8229 AACAGATATA
*
8239 TATATATATATACATAT
1 TATATATATATACAAAT
8256 TATATATATATAGCAAA
1 TATATATATATA-CAAA
8273 ATTAGCATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (17 bp):
TATATATATATACAAAT
Found at i:9412 original size:2 final size:2
Alignment explanation
Indices: 9407--9435 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9397 TCAACGGGTT
9407 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9436 GAGGGAAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10902 original size:20 final size:20
Alignment explanation
Indices: 10854--10903 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 20
10844 CTCTAGAATC
10854 ATCATTAATTAGCAATCTCA
1 ATCATTAATTAGCAATCTCA
10874 ATTTGTCATTAATTAGCAATCTCA
1 A----TCATTAATTAGCAATCTCA
10898 ATCATT
1 ATCATT
10904 TTTTTTTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
20 6 0.23
24 20 0.77
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.40
Consensus pattern (20 bp):
ATCATTAATTAGCAATCTCA
Found at i:11110 original size:2 final size:2
Alignment explanation
Indices: 11066--11095 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11056 TTCTTTTTCT
11066 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11096 CACTTCCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11468 original size:20 final size:21
Alignment explanation
Indices: 11434--11474 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
11424 ATTGAATATC
* *
11434 GTTTATCGTTTATAT-TATAA
1 GTTTATCGATAATATATATAA
11454 GTTTATCGATAATATATATAA
1 GTTTATCGATAATATATATAA
11475 TATAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (21 bp):
GTTTATCGATAATATATATAA
Found at i:11487 original size:13 final size:14
Alignment explanation
Indices: 11462--11496 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
11452 AAGTTTATCG
11462 ATAATATATATAAT
1 ATAATATATATAAT
11476 ATAATA-ATATAAT
1 ATAATATATATAAT
*
11489 GTAATATA
1 ATAATATA
11497 ATAGCGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (14 bp):
ATAATATATATAAT
Found at i:11495 original size:18 final size:17
Alignment explanation
Indices: 11462--11499 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
11452 AAGTTTATCG
11462 ATAATATATATAATATA
1 ATAATATATATAATATA
*
11479 ATAATATAATGTAATATA
1 ATAATAT-ATATAATATA
11497 ATA
1 ATA
11500 GCGAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATAATATATATAATATA
Found at i:12000 original size:15 final size:15
Alignment explanation
Indices: 11980--12008 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11970 ATCTCATGTA
11980 TTTAATTAATTATAC
1 TTTAATTAATTATAC
11995 TTTAATTAATTATA
1 TTTAATTAATTATA
12009 AGGGTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAATTAATTATAC
Found at i:16477 original size:27 final size:27
Alignment explanation
Indices: 16439--16507 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
16429 TAGACTTAAG
* *
16439 ATGACCAAAATGCCCCTAAATGTGCGA
1 ATGACCAAAATGCCCCTAAACGTGCAA
**
16466 ATGACCAAAATGCCCCTGGACGTGCAA
1 ATGACCAAAATGCCCCTAAACGTGCAA
*
16493 ATGACCAGAATGCCC
1 ATGACCAAAATGCCC
16508 TTAATTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.35, C:0.29, G:0.20, T:0.16
Consensus pattern (27 bp):
ATGACCAAAATGCCCCTAAACGTGCAA
Found at i:18130 original size:28 final size:28
Alignment explanation
Indices: 18073--18131 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
18063 TTTTTTTGTG
** *
18073 ATACACAATTGATATTTTTTTGGGTGAA
1 ATACACAATTGATATTTTGATGGGTCAA
18101 ATACACAATTGATA-TTTGATGGGATCAA
1 ATACACAATTGATATTTTGATGGG-TCAA
18129 ATA
1 ATA
18132 ATGTTTATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.37
Consensus pattern (28 bp):
ATACACAATTGATATTTTGATGGGTCAA
Found at i:21319 original size:90 final size:90
Alignment explanation
Indices: 21166--21344 Score: 295
Period size: 90 Copynumber: 2.0 Consensus size: 90
21156 AGGAAAAGCC
* *
21166 GAGATGTAGCCACTGCCAAAAGATGGGGCATACCAAGGACCGATGTTATGAAATCCTTGGATATC
1 GAGATGTAGCCACTGCCAAAAGATAGGGCATACCAAGGACCGATGTTATAAAATCCTTGGATATC
*
21231 CAGCGGTGTGGCGTAAAAACCTGCT
66 CAGCGGGGTGGCGTAAAAACCTGCT
* * *
21256 GAGATGTGGCCACTGCCAGAAGATAGGGCATACCAAGGACTGATGTTATAAAATCCTTGGATATC
1 GAGATGTAGCCACTGCCAAAAGATAGGGCATACCAAGGACCGATGTTATAAAATCCTTGGATATC
*
21321 CTGCGGGGTGGCGTAAAAACCTGC
66 CAGCGGGGTGGCGTAAAAACCTGC
21345 GGAATAAGGG
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (90 bp):
GAGATGTAGCCACTGCCAAAAGATAGGGCATACCAAGGACCGATGTTATAAAATCCTTGGATATC
CAGCGGGGTGGCGTAAAAACCTGCT
Found at i:26002 original size:16 final size:15
Alignment explanation
Indices: 25976--26005 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
25966 TTGATGAGAT
25976 TTTCTCCTCTCTTTC
1 TTTCTCCTCTCTTTC
25991 TTTCTCCCTCTCTTT
1 TTTCT-CCTCTCTTT
26006 GAAAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTCTCCTCTCTTTC
Found at i:28370 original size:1 final size:1
Alignment explanation
Indices: 28364--28391 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
28354 GGTACTGAGG
28364 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
28392 GCAAAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:31565 original size:424 final size:419
Alignment explanation
Indices: 30657--31646 Score: 1092
Period size: 424 Copynumber: 2.3 Consensus size: 419
30647 TATTTTTGAA
* *
30657 TTTTTTT-TTCTAGTTGTCCGATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCT
1 TTTTTTTGTTCTATTTGTCCGATTAAGGTGATTC-AGTGTCTATTAAAAGGTAATTTCATGATCT
* * * * * *
30721 ATAATTTTCATGAAGAAGTCAAAAGCCAATTTTAATGTTTTGATTTTAAAAAATGCTTCCGAAAT
65 ACAACTTTCATGAAGAACTCAAAAGCAAATTTTAATGTTTTAATTCTAAAAAATGCTTCCGAAAT
* * * * * ***** *
30786 TTTGTGGTTTTGATTGTCGGTCAATTTAATATCGTATAATTTTGTGGTTTTGATTGAAGTGTCAG
130 TTGGTCGTTTCGATTGTCGGTCAATTTAATACCATATAATTTTGTCCACATGATCGAAGTGTCAG
** * *
30851 TTAAAAGGTTGTTGCATGATTTACGACTTTCATGAAGGACCCGAAAGCTAAATTTGATCTACGAG
195 TTAAAAGGTTACTGCATGATGTACGACTTTCATGAAGAACCCGAAAGCTAAATTTGATCTACGAG
** * *
30916 TTTCATGAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATCTTCATTAACAAACATTTTTTATT
260 TTTCATGAAGGGTTCAAAAGAAAATTTTTATGCTTCAAGATATCCATTAACAAACATTTTTTATT
* * * * *
30981 TGGATTATTTATCAAATGACCCTCATATTTTTCTACTTTATACTACTTTGTACTTTACAAATTCT
325 TGAATTAGTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTTCTACTTTACAAATGCT
** * *
31046 AGTTTTTAATCTAACGTTTAAGATATTTTTTTT
390 AG-ACTTAATCT-ACGTTTAAGATA-TATTTTC
*
31079 TATTTTTTGTTCTATTTGTCCGATTAA-GTCGATTC--TGTCTATTAAAAGGTAGTTTCATGATC
1 T-TTTTTTGTTCTATTTGTCCGATTAAGGT-GATTCAGTGTCTATTAAAAGGTAATTTCATGATC
* * *
31141 TACAACTTTCATGAAGAACTCAAAAGCAAATTTTTATGTTTTAATTCAAAAAAATGCTTCCTAAA
64 TACAACTTTCATGAAGAACTCAAAAGCAAATTTTAATGTTTTAATTCTAAAAAATGCTTCCGAAA
* *
31206 TTTGGTCGTTTCGATTGTTGGTCTATTTAATACCATATAATTTTCGATCCACATG-TCCGATAGT
129 TTTGGTCGTTTCGATTGTCGGTCAATTTAATACCATATAATTTT-G-TCCACATGAT-CGA-AGT
* * * * *
31270 GTCGGTTAAAAGGTTACTGTATGATGTACGACTTTCATGAAGAATCTGAAAG-TTAATTTGATCT
190 GTCAGTTAAAAGGTTACTGCATGATGTACGACTTTCATGAAGAACCCGAAAGCTAAATTTGATCT
* *
31334 ACGAGTTTCATGAAGGGTTCAAAAGAAAATTTTTATGTTTCAAGATATCCATTAAGAAA-ATTTT
255 ACGAGTTTCATGAAGGGTTCAAAAGAAAATTTTTATGCTTCAAGATATCCATTAACAAACATTTT
* *
31398 GCTTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTATTTTATGCTACTTATACT-CATT
320 --TTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTT-T-CTAC-TT
*
31462 TACAAATGCTA-ACTT-AT-T-CGATTTAACGCT-TCATTTTC
380 TACAAATGCTAGACTTAATCTACG-TTTAA-GATAT-ATTTTC
* * * *
31500 TTTTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTGTCTATTAAAAAGTAATTTTATGATC
1 TTTT-TTTGTTCTATTTGTCCGATTAAGGTGATTCA-GTGTCTATTAAAAGGTAATTTCATGATC
* * * * * * **
31565 TACAACTTTCAT-AAAAGATTCAAAAGCTAATTTTCATGTTTCAATTCTAAAAAATACTTTTGAA
64 TACAACTTTCATGAAGA-ACTCAAAAGCAAATTTTAATGTTTTAATTCTAAAAAATGCTTCCGAA
*
31629 ATTTTGT-GATTTCGATTG
128 ATTTGGTCG-TTTCGATTG
31647 ACAATCTATT
Statistics
Matches: 478, Mismatches: 68, Indels: 42
0.81 0.12 0.07
Matches are distributed among these distances:
420 6 0.01
421 154 0.32
422 13 0.03
423 82 0.17
424 208 0.44
425 2 0.00
426 13 0.03
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (419 bp):
TTTTTTTGTTCTATTTGTCCGATTAAGGTGATTCAGTGTCTATTAAAAGGTAATTTCATGATCTA
CAACTTTCATGAAGAACTCAAAAGCAAATTTTAATGTTTTAATTCTAAAAAATGCTTCCGAAATT
TGGTCGTTTCGATTGTCGGTCAATTTAATACCATATAATTTTGTCCACATGATCGAAGTGTCAGT
TAAAAGGTTACTGCATGATGTACGACTTTCATGAAGAACCCGAAAGCTAAATTTGATCTACGAGT
TTCATGAAGGGTTCAAAAGAAAATTTTTATGCTTCAAGATATCCATTAACAAACATTTTTTATTT
GAATTAGTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTTCTACTTTACAAATGCTA
GACTTAATCTACGTTTAAGATATATTTTC
Found at i:42507 original size:27 final size:29
Alignment explanation
Indices: 42469--42531 Score: 94
Period size: 27 Copynumber: 2.2 Consensus size: 29
42459 AAAAAAAAAA
42469 AAAAAAAGTGAATATG-A-GCCTTTTACT
1 AAAAAAAGTGAATATGAATGCCTTTTACT
*
42496 AAAAAAAGTGAATATGAATGTCTTTTACT
1 AAAAAAAGTGAATATGAATGCCTTTTACT
*
42525 ACAAAAA
1 AAAAAAA
42532 TCCAAGTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 16 0.50
28 1 0.03
29 15 0.47
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.29
Consensus pattern (29 bp):
AAAAAAAGTGAATATGAATGCCTTTTACT
Done.