Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011144.1 Corchorus capsularis cultivar CVL-1 contig11165, 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: 84321
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:125 original size:31 final size:30
Alignment explanation
Indices: 52--126 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
42 GGGCAAATGT
*
52 GCAAATGGGTCCCTGAAGTGAACTTAGTGA
1 GCAATTGGGTCCCTGAAGTGAACTTAGTGA
* * *
82 GCAATTGAGTCCCTGAAGTTG-AGTTAATTGA
1 GCAATTGGGTCCCTGAAG-TGAACTT-AGTGA
*
113 GTAATTGGGTCCCT
1 GCAATTGGGTCCCT
127 CACCTAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 19 0.51
31 18 0.49
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (30 bp):
GCAATTGGGTCCCTGAAGTGAACTTAGTGA
Found at i:330 original size:29 final size:28
Alignment explanation
Indices: 297--371 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
287 TAGTTAATTC
*
297 CACTTCAGGGACTAAATTGCATATTTTTT
1 CACTTCAGGGACCAAATTGC-TATTTTTT
* *
326 CACTTGAGGGACCAATTTGCTATTTTTGCT
1 CACTTCAGGGACCAAATTGCTATTTTT--T
*
356 CCACTTGAGGGACCAA
1 -CACTTCAGGGACCAA
372 TTTTGTGCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.17
29 17 0.43
30 1 0.03
31 15 0.38
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (28 bp):
CACTTCAGGGACCAAATTGCTATTTTTT
Found at i:364 original size:31 final size:30
Alignment explanation
Indices: 294--374 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 30
284 GTTTAGTTAA
* * *
294 TTCCACTTCAGGGACTAAATTGCATATTTT
1 TTCCACTTGAGGGACCAATTTGCATATTTT
324 TT-CACTTGAGGGACCAATTTGC-TATTTT
1 TTCCACTTGAGGGACCAATTTGCATATTTT
352 TGCTCCACTTGAGGGACCAATTT
1 T--TCCACTTGAGGGACCAATTT
375 TGTGCTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.16
29 17 0.38
30 3 0.07
31 18 0.40
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (30 bp):
TTCCACTTGAGGGACCAATTTGCATATTTT
Found at i:2313 original size:11 final size:11
Alignment explanation
Indices: 2299--2421 Score: 71
Period size: 11 Copynumber: 11.8 Consensus size: 11
2289 AAATAATTTA
*
2299 TTATATATTTT
1 TTATATATATT
*
2310 TTATATATATA
1 TTATATATATT
* * *
2321 ATAAATATA-A
1 TTATATATATT
2331 TT-TATATATT
1 TTATATATATT
*
2341 TTACATATATT
1 TTATATATATT
2352 TTATATATA--
1 TTATATATATT
* * *
2361 TCATAAATA-A
1 TTATATATATT
*
2371 TTA-A-ATATA
1 TTATATATATT
*
2380 TTATATATTTT
1 TTATATATATT
*
2391 TTATATATATC
1 TTATATATATT
* *
2402 ATAAATATATT
1 TTATATATATT
2413 TTATATATA
1 TTATATATA
2422 ATAATATAAT
Statistics
Matches: 85, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
8 3 0.04
9 17 0.20
10 7 0.08
11 58 0.68
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
TTATATATATT
Found at i:6151 original size:6 final size:6
Alignment explanation
Indices: 6140--6340 Score: 132
Period size: 6 Copynumber: 35.5 Consensus size: 6
6130 GTTTCCACCA
* *
6140 TTGCCG TTGCCG TTGCCG TT---G TTGCCA TTGCCA TTGCCG TTGCCG
1 TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG
* * *
6185 TT---G TTGCCA TTGCCA TTGCCG TTGCCG TT---G TTGCCA TTGCCATTG
1 TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCC---G
* * * *
6230 TTGCCA TTGCCG TTGCCATTG TTGCCA TTGCCA TTGCCG TT---G TTGCCA
1 TTGCCG TTGCCG TTGCC---G TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG
*
6278 TTGCCG TTGCCG TT---G TTGCCG TTGCCG TTGCCA TTGCCG TTGCCG
1 TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG
6323 TT---G TTGCCG TTGCCG TTG
1 TTGCCG TTGCCG TTGCCG TTG
6341 TTGCCTTTGC
Statistics
Matches: 157, Mismatches: 14, Indels: 48
0.72 0.06 0.22
Matches are distributed among these distances:
3 18 0.11
6 128 0.82
9 11 0.07
ACGTcount: A:0.06, C:0.29, G:0.27, T:0.38
Consensus pattern (6 bp):
TTGCCG
Found at i:6170 original size:21 final size:21
Alignment explanation
Indices: 6167--6309 Score: 187
Period size: 21 Copynumber: 6.8 Consensus size: 21
6157 GTTGTTGCCA
6167 TTGCCATTGCCGTTGCCGTTG
1 TTGCCATTGCCGTTGCCGTTG
*
6188 TTGCCATTGCCATTGCCGTTG
1 TTGCCATTGCCGTTGCCGTTG
** *** * *
6209 CCGTTGTTGCCATTGCCATTG
1 TTGCCATTGCCGTTGCCGTTG
*
6230 TTGCCATTGCCGTTGCCATTG
1 TTGCCATTGCCGTTGCCGTTG
*
6251 TTGCCATTGCCATTGCCGTTG
1 TTGCCATTGCCGTTGCCGTTG
6272 TTGCCATTGCCGTTGCCGTTG
1 TTGCCATTGCCGTTGCCGTTG
*
6293 TTGCCGTTGCCGTTGCC
1 TTGCCATTGCCGTTGCC
6310 ATTGCCGTTG
Statistics
Matches: 105, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 105 1.00
ACGTcount: A:0.07, C:0.29, G:0.26, T:0.38
Consensus pattern (21 bp):
TTGCCATTGCCGTTGCCGTTG
Found at i:6176 original size:27 final size:27
Alignment explanation
Indices: 6137--6336 Score: 235
Period size: 27 Copynumber: 7.3 Consensus size: 27
6127 AGGGTTTCCA
*
6137 CCATTGCCGTTGCCGTTGCCGTTGTTG
1 CCATTGCCATTGCCGTTGCCGTTGTTG
6164 CCATTGCCATTGCCGTTGCCGTTGTTG
1 CCATTGCCATTGCCGTTGCCGTTGTTG
6191 CCATTGCCATTGCCGTTGCCGTTGTTG
1 CCATTGCCATTGCCGTTGCCGTTGTTG
*
6218 CCATTGCCATT---GTTGCCATTGCCGTTG
1 CCATTGCCATTGCCGTTGCCGTT---GTTG
*
6245 CCATTGTTGCCATTGCCATTGCCGTTGTTG
1 CCA---TTGCCATTGCCGTTGCCGTTGTTG
* ** **
6275 CCATTGCCGTTGCCGTTGTTGCCGTTG
1 CCATTGCCATTGCCGTTGCCGTTGTTG
*
6302 CCGTTGCCATTGCCGTTGCCGTTGTTG
1 CCATTGCCATTGCCGTTGCCGTTGTTG
*
6329 CCGTTGCC
1 CCATTGCC
6337 GTTGTTGCCT
Statistics
Matches: 148, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
24 8 0.05
27 118 0.80
30 15 0.10
33 7 0.05
ACGTcount: A:0.07, C:0.30, G:0.27, T:0.37
Consensus pattern (27 bp):
CCATTGCCATTGCCGTTGCCGTTGTTG
Found at i:6351 original size:21 final size:21
Alignment explanation
Indices: 6293--6340 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
6283 GTTGCCGTTG
6293 TTGCCGTTGCC---GTTGCCA
1 TTGCCGTTGCCGTTGTTGCCA
*
6311 TTGCCGTTGCCGTTGTTGCCG
1 TTGCCGTTGCCGTTGTTGCCA
6332 TTGCCGTTG
1 TTGCCGTTG
6341 TTGCCTTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.42
21 15 0.58
ACGTcount: A:0.02, C:0.29, G:0.31, T:0.38
Consensus pattern (21 bp):
TTGCCGTTGCCGTTGTTGCCA
Found at i:10367 original size:1 final size:1
Alignment explanation
Indices: 10363--10388 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
10353 AAAAAAAGCC
10363 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
10389 GATTTGCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12540 original size:103 final size:101
Alignment explanation
Indices: 12361--12565 Score: 329
Period size: 103 Copynumber: 2.0 Consensus size: 101
12351 TTTCAAACTT
* * * *
12361 AAGCACAATTTTTTTTTATTACAATCGTATAGGAAGACCTGTACACCGGTACATGATTAGCTATT
1 AAGCACAATTTTTTTTTATTACAAACGCATAGGAAGACCCGTACACCGCTACATGATTAGCTATT
*
12426 ACAAAACCCTTCCCCAACAAATACAATTGAAATCTC
66 ACAAAACCCTTCCCCAACAAATACAATCGAAATCTC
12462 AAGCACAAATTTTTTTTTTATTACAAACGCATAGGAAGACCCGTACACCGCTACATGATTAGCTA
1 AAGCAC-AA-TTTTTTTTTATTACAAACGCATAGGAAGACCCGTACACCGCTACATGATTAGCTA
* *
12527 TTACAAAATCCTTCCCTAACAAATACAATCGAAATCTC
64 TTACAAAACCCTTCCCCAACAAATACAATCGAAATCTC
12565 A
1 A
12566 TAACAAATAC
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 6 0.06
102 2 0.02
103 87 0.92
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (101 bp):
AAGCACAATTTTTTTTTATTACAAACGCATAGGAAGACCCGTACACCGCTACATGATTAGCTATT
ACAAAACCCTTCCCCAACAAATACAATCGAAATCTC
Found at i:12570 original size:23 final size:23
Alignment explanation
Indices: 12543--12593 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
12533 AATCCTTCCC
12543 TAACAAATACAATCGAAATCTCA
1 TAACAAATACAATCGAAATCTCA
12566 TAACAAATACAATCGAAATCTCA
1 TAACAAATACAATCGAAATCTCA
12589 TAACA
1 TAACA
12594 CCTGCTCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.22, G:0.04, T:0.22
Consensus pattern (23 bp):
TAACAAATACAATCGAAATCTCA
Found at i:20702 original size:24 final size:25
Alignment explanation
Indices: 20675--20723 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
20665 ATTTAGAATG
20675 ATAAAG-ATTAATCTAAGGTTTGTA
1 ATAAAGAATTAATCTAAGGTTTGTA
20699 ATAAAGATAATTAATCTAAGGTTTG
1 ATAAAG--AATTAATCTAAGGTTTG
20724 GTAAACGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.27
27 16 0.73
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (25 bp):
ATAAAGAATTAATCTAAGGTTTGTA
Found at i:21398 original size:38 final size:38
Alignment explanation
Indices: 21347--21420 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
21337 ATTGATGCTA
*
21347 AAGTTGTTATTGATCTTGTTAATAATGCTAATGTTCTG
1 AAGTTGTTATTGATCTTGTCAATAATGCTAATGTTCTG
21385 AAGTTGTTATTGATCTTGTCAATAATGCTAATGTTC
1 AAGTTGTTATTGATCTTGTCAATAATGCTAATGTTC
21421 ATACTCATCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.46
Consensus pattern (38 bp):
AAGTTGTTATTGATCTTGTCAATAATGCTAATGTTCTG
Found at i:21477 original size:51 final size:51
Alignment explanation
Indices: 21396--21497 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
21386 AGTTGTTATT
21396 GATCTTGTCAATAATGCTAATGTTCATACTCATCCACTGACCCTGATGAAA
1 GATCTTGTCAATAATGCTAATGTTCATACTCATCCACTGACCCTGATGAAA
*
21447 GATCTTGTCAATAATGCTAATGTTCTTACTCATCCACTGACCCTGATGAAA
1 GATCTTGTCAATAATGCTAATGTTCATACTCATCCACTGACCCTGATGAAA
21498 TGCTTCCGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
GATCTTGTCAATAATGCTAATGTTCATACTCATCCACTGACCCTGATGAAA
Found at i:23375 original size:43 final size:43
Alignment explanation
Indices: 23322--23410 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
23312 TTATTTTCTA
23322 ATGGAAAACAATTGTCAGACACAGAAGATAATTAACACATTAG
1 ATGGAAAACAATTGTCAGACACAGAAGATAATTAACACATTAG
23365 ATGGAAAACAATTGTCAGACACAGAAGATAATTAACACATTAG
1 ATGGAAAACAATTGTCAGACACAGAAGATAATTAACACATTAG
23408 ATG
1 ATG
23411 ATACTACTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.21
Consensus pattern (43 bp):
ATGGAAAACAATTGTCAGACACAGAAGATAATTAACACATTAG
Found at i:40940 original size:17 final size:18
Alignment explanation
Indices: 40903--40941 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
40893 AATTTTTAGG
*
40903 GAAAAGAAATAAAAGGGA
1 GAAAAAAAATAAAAGGGA
40921 GAAAAAAAATAAAA-GGA
1 GAAAAAAAATAAAAGGGA
40938 GAAA
1 GAAA
40942 GCTTTGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (18 bp):
GAAAAAAAATAAAAGGGA
Found at i:53137 original size:74 final size:74
Alignment explanation
Indices: 53059--53215 Score: 199
Period size: 74 Copynumber: 2.1 Consensus size: 74
53049 TGGTCTTTTC
* * * * * * * *
53059 ACACTTTTCGGGTGACTAAAAAACCCCTCTATGAGTTTTCTC-TATTCCTTTTCCTTCTACCCTT
1 ACACTTTTCAGATGACTAAAAAACCCATCTATAAG-TTTCCCACATTCATTTTCCTTCTACCATT
*
53123 TTTTGTAATT
65 TTTCGTAATT
*
53133 ACACTTTTCAGATGACTAAAAAGCCCATCTATAAGTTTCCCACATTCATTTTCCTTCTACCATTT
1 ACACTTTTCAGATGACTAAAAAACCCATCTATAAGTTTCCCACATTCATTTTCCTTCTACCATTT
53198 TTCGTAATT
66 TTCGTAATT
*
53207 ACACATTTC
1 ACACTTTTC
53216 CCTTCCATTG
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
73 5 0.07
74 66 0.93
ACGTcount: A:0.25, C:0.26, G:0.08, T:0.41
Consensus pattern (74 bp):
ACACTTTTCAGATGACTAAAAAACCCATCTATAAGTTTCCCACATTCATTTTCCTTCTACCATTT
TTCGTAATT
Found at i:82764 original size:14 final size:14
Alignment explanation
Indices: 82722--82764 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 14
82712 AGAACTAAAC
82722 TAATAACAATAGAG
1 TAATAACAATAGAG
*
82736 TAATTGCACCAATAGAG
1 TAA-T--AACAATAGAG
82753 TAATAACAATAG
1 TAATAACAATAG
82765 GTGTGAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.42
15 1 0.04
16 1 0.04
17 12 0.50
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.23
Consensus pattern (14 bp):
TAATAACAATAGAG
Found at i:83544 original size:16 final size:16
Alignment explanation
Indices: 83523--83553 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
83513 CATTTGACTA
*
83523 AGTAAGTTAACAAAAC
1 AGTAAGTAAACAAAAC
83539 AGTAAGTAAACAAAA
1 AGTAAGTAAACAAAA
83554 AAACAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.10, G:0.13, T:0.16
Consensus pattern (16 bp):
AGTAAGTAAACAAAAC
Found at i:84015 original size:2 final size:2
Alignment explanation
Indices: 84010--84099 Score: 51
Period size: 2 Copynumber: 44.5 Consensus size: 2
84000 TTTCTGATGC
* * * * *
84010 TA TA TA TA TT TT TCA TA TA TA TGA TA TA TA AA AA T- TA TA AA TA
1 TA TA TA TA TA TA T-A TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
* * *
84053 TA TA TA TC TC TGA TGC TA TA -A TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA T-A T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
84095 TA TA T
1 TA TA T
84100 TTTTTTTAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
1 3 0.04
2 63 0.88
3 6 0.08
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:84268 original size:18 final size:18
Alignment explanation
Indices: 84245--84297 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
84235 CACCATTTAC
84245 TAATCGGTTCGGTCGGTG
1 TAATCGGTTCGGTCGGTG
84263 TAATCGGTTCGGTCGGTG
1 TAATCGGTTCGGTCGGTG
*
84281 TAATCGGTTCGTTCGGT
1 TAATCGGTTCGGTCGGT
84298 TTATGATCAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.11, C:0.17, G:0.36, T:0.36
Consensus pattern (18 bp):
TAATCGGTTCGGTCGGTG
Done.