Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011931.1 Corchorus capsularis cultivar CVL-1 contig11952, 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: 7443
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36
Found at i:277 original size:16 final size:16
Alignment explanation
Indices: 256--311 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
246 TGTGACTGAA
256 ATGCAAGAATATTGAG
1 ATGCAAGAATATTGAG
* * *
272 ATGCAA-AAAAATGCCAAA
1 ATGCAAGAATATTG---AG
290 ATGCAAGAATATTGAG
1 ATGCAAGAATATTGAG
306 ATGCAA
1 ATGCAA
312 AAAATACCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
15 5 0.17
16 13 0.43
18 7 0.23
19 5 0.17
ACGTcount: A:0.50, C:0.11, G:0.20, T:0.20
Consensus pattern (16 bp):
ATGCAAGAATATTGAG
Found at i:322 original size:33 final size:34
Alignment explanation
Indices: 254--323 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
244 TTTGTGACTG
*
254 AAATGCAAGAATATTGAGATGCAAAAAAATGCCA
1 AAATGCAAGAATATTGAGATGCAAAAAAATACCA
288 AAATGCAAGAATATTGAGATGC-AAAAAATACCA
1 AAATGCAAGAATATTGAGATGCAAAAAAATACCA
321 AAA
1 AAA
324 GTACACATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 13 0.37
34 22 0.63
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.17
Consensus pattern (34 bp):
AAATGCAAGAATATTGAGATGCAAAAAAATACCA
Found at i:464 original size:26 final size:27
Alignment explanation
Indices: 434--499 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 27
424 CTAAATATGC
434 AAATGACCAAAATACCCT-T-A-GTGCA
1 AAATGACCAAAATACCCTATGATGTG-A
*
459 AGAATGACCAAAATGCCCTATGATGTGA
1 A-AATGACCAAAATACCCTATGATGTGA
487 AAATGACCAAAAT
1 AAATGACCAAAAT
500 GCCCCTGGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
25 1 0.03
26 16 0.44
27 13 0.36
28 3 0.08
29 3 0.08
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (27 bp):
AAATGACCAAAATACCCTATGATGTGA
Found at i:498 original size:27 final size:25
Alignment explanation
Indices: 434--503 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 25
424 CTAAATATGC
*
434 AAATGACCAAAATACCCTTAGTGCA
1 AAATGACCAAAATGCCCTTAGTGCA
459 AGAATGACCAAAATGCCCTATGATGTG-A
1 A-AATGACCAAAATGCCCT-T-A-GTGCA
487 AAATGACCAAAATGCCC
1 AAATGACCAAAATGCCC
504 CTGGATGACC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
25 1 0.03
26 16 0.40
27 17 0.43
28 3 0.08
29 3 0.08
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.19
Consensus pattern (25 bp):
AAATGACCAAAATGCCCTTAGTGCA
Found at i:820 original size:45 final size:45
Alignment explanation
Indices: 749--987 Score: 374
Period size: 45 Copynumber: 5.3 Consensus size: 45
739 AGTAGTCCGT
* *
749 GGTCGACTTTGATAACTGCTG-AAACTGAAAAAGACCTGTTCTGA
1 GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGA
*
793 GGTCAACTTTGATAACTACTGAAAACTGAGAAAGACCTGTTCTGA
1 GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGA
* *
838 GGTCAACTTTGATAATTGCTGAAAACTGAGAAAGACCTGTTCTGC
1 GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGA
*
883 GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGC
1 GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGA
* *
928 GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACTTGTT-TCGG
1 GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCT-GA
*
973 GGTCGACTTTGATAA
1 GGTCAACTTTGATAA
988 TCTTATTGAA
Statistics
Matches: 183, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
44 20 0.11
45 163 0.89
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (45 bp):
GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGA
Found at i:3072 original size:10 final size:9
Alignment explanation
Indices: 3054--3086 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
3044 TTTGGCTGAG
3054 TTTTTTCTT
1 TTTTTTCTT
3063 TTTCTTTCTT
1 TTT-TTTCTT
3073 TTTTTT-TT
1 TTTTTTCTT
3081 TTTTTT
1 TTTTTT
3087 AAGTTGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 6 0.26
10 9 0.39
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:4921 original size:42 final size:38
Alignment explanation
Indices: 4842--4951 Score: 96
Period size: 42 Copynumber: 2.7 Consensus size: 38
4832 ACAAGTGATA
* * * *
4842 GCATGATGGATGCATGAGCATATATGCTAATGAATGGATAGT
1 GCATGAT-GATGCAT-A-CATATATAC-AAAGAATGGACAAT
4884 GCATGATCGATGCATAAACATATATACAAAGAGATGGACAAT
1 GCATGAT-GATGCAT--ACATATATACAAAGA-ATGGACAAT
4926 GCATGATGAATGCAT-CATATATACAA
1 GCATGATG-ATGCATACATATATACAA
4952 GTGACTGACT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
39 11 0.19
41 5 0.08
42 42 0.71
43 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (38 bp):
GCATGATGATGCATACATATATACAAAGAATGGACAAT
Found at i:6426 original size:16 final size:16
Alignment explanation
Indices: 6391--6448 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
6381 TCTTCTATCC
* *
6391 TTTTTATTAACTACCA
1 TTTTTACTAATTACCA
*
6407 TTTTTACTAATTATCCT
1 TTTTTACTAATTA-CCA
*
6424 TTTCTTACTGATTACCA
1 TTT-TTACTAATTACCA
6441 TTTTTACT
1 TTTTTACT
6449 TTTGCTACCT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 16 0.46
17 10 0.29
18 9 0.26
ACGTcount: A:0.24, C:0.19, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTTTACTAATTACCA
Found at i:6444 original size:18 final size:17
Alignment explanation
Indices: 6391--6445 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
6381 TCTTCTATCC
* *
6391 TTTTTATTAACTACCA-
1 TTTTTACTAATTACCAT
6407 TTTTTACTAATTATCC-T
1 TTTTTACTAATTA-CCAT
*
6424 TTTCTTACTGATTACCAT
1 TTT-TTACTAATTACCAT
6442 TTTT
1 TTTT
6446 ACTTTTGCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 11 0.34
17 8 0.25
18 13 0.41
ACGTcount: A:0.24, C:0.18, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTTTACTAATTACCAT
Found at i:6516 original size:13 final size:13
Alignment explanation
Indices: 6470--6517 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
6460 TATCATTTTT
6470 TCTCTTTTCTTAC
1 TCTCTTTTCTTAC
* *
6483 TCT-TTTTACTAAT
1 TCTCTTTT-CTTAC
6496 TACTCTTTTCTTAC
1 T-CTCTTTTCTTAC
6510 TCTCTTTT
1 TCTCTTTT
6518 ATTTATTACC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
12 4 0.14
13 14 0.50
14 6 0.21
15 4 0.14
ACGTcount: A:0.12, C:0.25, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTCTTTTCTTAC
Found at i:6532 original size:29 final size:28
Alignment explanation
Indices: 6473--6545 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
6463 CATTTTTTCT
*
6473 CTTTTCTTACTCT-TTTTACTAATTACT
1 CTTTTCTTACTCTCTTTTACTAATTACA
* *
6500 CTTTTCTTACTCTCTTTTATTTATTACCA
1 CTTTTCTTACTCTCTTTTACTAATTA-CA
6529 C-TTT-TTACTCTTCTTTT
1 CTTTTCTTACTC-TCTTTT
6546 TTCTTATACT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 19 0.47
28 19 0.47
29 2 0.05
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (28 bp):
CTTTTCTTACTCTCTTTTACTAATTACA
Found at i:6618 original size:22 final size:22
Alignment explanation
Indices: 6590--6865 Score: 180
Period size: 21 Copynumber: 12.6 Consensus size: 22
6580 ACTGATCACC
*
6590 TTTTACTCTTTACTGATTATTA
1 TTTTACTCTTTACTGATTACTA
* *
6612 TTTTACTC-TTACTAATTACCA
1 TTTTACTCTTTACTGATTACTA
* * *
6633 CTTTGCTC-TTACTAATTACTA
1 TTTTACTCTTTACTGATTACTA
*
6654 TTTTACTC-TTACTGATTAC-C
1 TTTTACTCTTTACTGATTACTA
*** *
6674 TTTTACGGATTACT-ATTTTACTCT
1 TTTTACTCTTTACTGA--TTACT-A
*
6698 TTGTTGATTACCTTCTACTGATTACTA
1 TT-TT-ACT--CTT-TACTGATTACTA
6725 TTTTACTCTTTACTGATTACCT-
1 TTTTACTCTTTACTGATTA-CTA
* *
6747 TCTTACTTTTTACTGATTACTA
1 TTTTACTCTTTACTGATTACTA
*
6769 TTTTACTCTTTACTGATTACCA
1 TTTTACTCTTTACTGATTACTA
**
6791 TTTTGGTC-TTACTGATTACTA
1 TTTTACTCTTTACTGATTACTA
*
6812 TTTTTC-CTTTTACTGATTA-TCA
1 TTTTACTC-TTTACTGATTACT-A
* *
6834 --TTACTTTTTACTGATTAC-C
1 TTTTACTCTTTACTGATTACTA
*
6853 CTTTACTCTTTAC
1 TTTTACTCTTTAC
6866 CATTCTTCCT
Statistics
Matches: 201, Mismatches: 33, Indels: 41
0.73 0.12 0.15
Matches are distributed among these distances:
20 22 0.11
21 78 0.39
22 74 0.37
23 5 0.02
24 2 0.01
25 4 0.02
26 3 0.01
27 2 0.01
28 6 0.03
29 4 0.02
30 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (22 bp):
TTTTACTCTTTACTGATTACTA
Found at i:6721 original size:36 final size:36
Alignment explanation
Indices: 6642--6789 Score: 172
Period size: 36 Copynumber: 3.9 Consensus size: 36
6632 ACTTTGCTCT
* *
6642 TACTAATTACTATTTTACTC-TTACTGATTACCTTT
1 TACTGATTACTATTTTACTCTTTACTGATTACCTTC
* **
6677 TACGGATTACTATTTTACTCTTTGTTGATTACCTTC
1 TACTGATTACTATTTTACTCTTTACTGATTACCTTC
6713 TACTGATTACTATTTTACTCTTTACTGATTACCTTCTTAC
1 TACTGATTACTATTTTACTCTTTACTGATTA-C--CTT-C
6753 TTTTTACTGATTACTATTTTACTCTTTACTGATTACC
1 ----TACTGATTACTATTTTACTCTTTACTGATTACC
6790 ATTTTGGTCT
Statistics
Matches: 96, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
35 18 0.19
36 40 0.42
37 1 0.01
39 3 0.03
40 1 0.01
41 1 0.01
43 1 0.01
44 31 0.32
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.51
Consensus pattern (36 bp):
TACTGATTACTATTTTACTCTTTACTGATTACCTTC
Found at i:6761 original size:44 final size:44
Alignment explanation
Indices: 6713--6865 Score: 176
Period size: 44 Copynumber: 3.6 Consensus size: 44
6703 GATTACCTTC
6713 TACTGATTACTATTTTACTCTTTACTGATTACCTTCTTACTTTT
1 TACTGATTACTATTTTACTCTTTACTGATTACCTTCTTACTTTT
** *
6757 TACTGATTACTATTTTACTCTTTACTGATTACCATT-TT-GGTCT
1 TACTGATTACTATTTTACTCTTTACTGATTACC-TTCTTACTTTT
*
6800 TACTGATTACTATTTTTC-CTTTTACTGATTA---TCATTACTTTT
1 TACTGATTACTATTTTACTC-TTTACTGATTACCTTC-TTACTTTT
**
6842 TACTGATTAC-CCTTTACTCTTTAC
1 TACTGATTACTATTTTACTCTTTAC
6866 CATTCTTCCT
Statistics
Matches: 93, Mismatches: 10, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
39 1 0.01
41 11 0.12
42 14 0.15
43 30 0.32
44 35 0.38
45 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (44 bp):
TACTGATTACTATTTTACTCTTTACTGATTACCTTCTTACTTTT
Found at i:6856 original size:35 final size:33
Alignment explanation
Indices: 6828--6939 Score: 127
Period size: 35 Copynumber: 3.2 Consensus size: 33
6818 CTTTTACTGA
6828 TTATCATTACTTTTTACTGATTACCCTTTACTCT
1 TTATCATT-CTTTTTACTGATTACCCTTTACTCT
* * *
6862 TTACCATTCTTCCTTTACTGATTACTCTTTACTTT
1 TTATCATTCTT--TTTACTGATTACCCTTTACTCT
*
6897 TTATCATTCTTCTTTTACTGATTACTCTTTACT-T
1 TTATCATTC-T-TTTTACTGATTACCCTTTACTCT
6931 TCTATCATT
1 T-TATCATT
6940 TTACTCTTTA
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
33 3 0.04
34 9 0.13
35 55 0.80
36 1 0.01
37 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.55
Consensus pattern (33 bp):
TTATCATTCTTTTTACTGATTACCCTTTACTCT
Found at i:7079 original size:16 final size:17
Alignment explanation
Indices: 7055--7089 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
7045 ACTGATTACC
7055 TTTTACTCTTTACC-AT
1 TTTTACTCTTTACCGAT
*
7071 TTTTGCTCTTTACCGAT
1 TTTTACTCTTTACCGAT
7088 TT
1 TT
7090 ACTGATTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.14, C:0.23, G:0.06, T:0.57
Consensus pattern (17 bp):
TTTTACTCTTTACCGAT
Found at i:7124 original size:40 final size:39
Alignment explanation
Indices: 7080--7186 Score: 126
Period size: 40 Copynumber: 2.6 Consensus size: 39
7070 TTTTTGCTCT
7080 TTACCGATTTACTGATTACTTCTTTTACTCGT-ACTCTTAA
1 TTACC-ATTTACTGATTACTTCTTTTACT-GTGACTCTTAA
*
7120 TTACCATTCTACTGATTACTTCTTTTACTTTGACTCTTAA
1 TTACCATT-TACTGATTACTTCTTTTACTGTGACTCTTAA
* * *
7160 TTATCAAATTACTGATTAATCTCTTTT
1 TTA-CCATTTACTGATTACT-TCTTTT
7187 TACTTAATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
39 4 0.07
40 46 0.78
41 9 0.15
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.50
Consensus pattern (39 bp):
TTACCATTTACTGATTACTTCTTTTACTGTGACTCTTAA
Done.