Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007213.1 Corchorus capsularis cultivar CVL-1 contig07234, 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: 35726
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:893 original size:11 final size:12
Alignment explanation
Indices: 871--899 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
861 AGTTATATCG
871 AAAAATATAAAA
1 AAAAATATAAAA
883 AAAAATA-AAAA
1 AAAAATATAAAA
894 AAAAAT
1 AAAAAT
900 TTCGACCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAATATAAAA
Found at i:2478 original size:33 final size:33
Alignment explanation
Indices: 2400--2504 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
2390 TTGCAAAGAG
* *
2400 TGTTTTAGATGTTGTTTGCAATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
** *
2433 TAATTTAAGTGTTGTTTGCAATGATACTAAATC
1 TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
* * *
2466 TGTTTTAGGTGTT-ATTGCTGATGACACTAAATC
1 TGTTTTAGGTGTTGTTTGC-AATGATACTAAATC
2499 TGTTTT
1 TGTTTT
2505 GGATGCTAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 4 0.07
33 56 0.93
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
Found at i:2521 original size:33 final size:32
Alignment explanation
Indices: 2453--2540 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 32
2443 GTTGTTTGCA
* *
2453 ATGATACTAAATCTGTTTTAGGTGTTATTGCTG
1 ATGAAACTAAATCTGTTTT-GGTGTAATTGCTG
*
2486 ATGACACTAAATCTGTTTTGGATGCTAATTG-TG
1 ATGAAACTAAATCTGTTTTGG-TG-TAATTGCTG
2519 ATGAAAAC-AAATCTGTTTTGGT
1 ATG-AAACTAAATCTGTTTTGGT
2541 TGATCATAGC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
32 3 0.06
33 38 0.78
34 8 0.16
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.41
Consensus pattern (32 bp):
ATGAAACTAAATCTGTTTTGGTGTAATTGCTG
Found at i:2567 original size:33 final size:33
Alignment explanation
Indices: 2530--2638 Score: 209
Period size: 33 Copynumber: 3.3 Consensus size: 33
2520 TGAAAACAAA
2530 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
*
2563 TCTGTTTTAGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
2596 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
2629 TCTGTTTTGG
1 TCTGTTTTGG
2639 GTGAAAAGAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:3033 original size:30 final size:30
Alignment explanation
Indices: 2981--3039 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2971 CAAGGGGGAG
*
2981 GGAATGATGCGCCCAAGGCTTATCATGGAA
1 GGAATGATGCGCCCAAGACTTATCATGGAA
* *
3011 GGAATTATGCG-CCAATGACTTATTATGGA
1 GGAATGATGCGCCCAA-GACTTATCATGGA
3040 CTTGAAGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (30 bp):
GGAATGATGCGCCCAAGACTTATCATGGAA
Found at i:6533 original size:15 final size:15
Alignment explanation
Indices: 6515--6545 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6505 TTACTTTTGC
*
6515 TACTTTTATCATTTT
1 TACTTTTACCATTTT
6530 TACTTTTACCATTTT
1 TACTTTTACCATTTT
6545 T
1 T
6546 CTTACTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:6545 original size:24 final size:25
Alignment explanation
Indices: 6501--6572 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 25
6491 ACTGATTACC
* * *
6501 CTTTTTACTTTTGCTACTTTTATCA
1 CTTTTTACTTTTACCATTTTTATCA
* *
6526 -TTTTTACTTTTACCATTTTTCTTA
1 CTTTTTACTTTTACCATTTTTATCA
*
6550 CTCTTTTACTTAATACCATTTTT
1 CT-TTTTACTT-TTACCATTTTT
6573 GTTTAATACC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
24 19 0.50
25 1 0.03
26 8 0.21
27 10 0.26
ACGTcount: A:0.18, C:0.19, G:0.01, T:0.61
Consensus pattern (25 bp):
CTTTTTACTTTTACCATTTTTATCA
Found at i:6665 original size:25 final size:24
Alignment explanation
Indices: 6595--6681 Score: 83
Period size: 25 Copynumber: 3.7 Consensus size: 24
6585 CTCTTACTGG
* *
6595 ATACCATTGTTGACCCTTTTACTTA
1 ATACCATT-TTTACTCTTTTACTTA
* *
6620 ACACCA-TTTT--T-TTTTAATTA
1 ATACCATTTTTACTCTTTTACTTA
6640 ATACCATTCTTTACTCTTTTACTTA
1 ATACCATT-TTTACTCTTTTACTTA
6665 ATACCATTTTTTACTCT
1 ATACCA-TTTTTACTCT
6682 ACACCATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
20 13 0.26
21 1 0.02
22 3 0.06
23 2 0.04
24 2 0.04
25 27 0.54
26 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.02, T:0.51
Consensus pattern (24 bp):
ATACCATTTTTACTCTTTTACTTA
Found at i:6678 original size:17 final size:16
Alignment explanation
Indices: 6656--6739 Score: 50
Period size: 17 Copynumber: 5.2 Consensus size: 16
6646 TTCTTTACTC
6656 TTTTACTTAATACCATT
1 TTTTACTT-ATACCATT
*
6673 TTTTACTCTACACCATT
1 TTTTACT-TATACCATT
*
6690 TTTT--TTTTGACC--T
1 TTTTACTTAT-ACCATT
* *
6703 TCTTACTCAATACCATT
1 TTTTACT-TATACCATT
*
6720 TTTCACTTGATACCATT
1 TTTTACTT-ATACCATT
6737 TTT
1 TTT
6740 GACCTTCTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 16
0.67 0.12 0.21
Matches are distributed among these distances:
13 4 0.08
14 1 0.02
15 8 0.16
16 1 0.02
17 35 0.70
18 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.02, T:0.52
Consensus pattern (16 bp):
TTTTACTTATACCATT
Found at i:6769 original size:14 final size:13
Alignment explanation
Indices: 6747--6831 Score: 66
Period size: 14 Copynumber: 6.3 Consensus size: 13
6737 TTTGACCTTC
6747 TTACTGATTACTT
1 TTACTGATTACTT
6760 TTACCTGATTACTTT
1 TTA-CTGATTAC-TT
*
6775 TTACT-ACT-CTT
1 TTACTGATTACTT
** **
6786 TGCCATTTTTACTTT
1 TTAC-TGATTAC-TT
6801 TTACTGATTACTCT
1 TTACTGATTACT-T
6815 TTACTGATTACTT
1 TTACTGATTACTT
6828 TTAC
1 TTAC
6832 CTTTTTACTG
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
11 4 0.07
12 2 0.04
13 12 0.21
14 29 0.52
15 9 0.16
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.54
Consensus pattern (13 bp):
TTACTGATTACTT
Found at i:6825 original size:21 final size:21
Alignment explanation
Indices: 6801--6847 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
6791 TTTTTACTTT
6801 TTACTGATTA-CTCTTTACTGA
1 TTACT-ATTACCTCTTTACTGA
* *
6822 TTACTTTTACCTTTTTACTGA
1 TTACTATTACCTCTTTACTGA
6843 TTACT
1 TTACT
6848 CTTAGCTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.53
Consensus pattern (21 bp):
TTACTATTACCTCTTTACTGA
Found at i:7147 original size:29 final size:29
Alignment explanation
Indices: 7076--7167 Score: 96
Period size: 29 Copynumber: 3.0 Consensus size: 29
7066 TTCTTAATTA
*
7076 TTAATTTACTGATTAGTCCTTTTTACTTCCTTTC
1 TTAA-TTACTGATTAAT-CTTTTTACTT-C--TC
7110 TTAATTACTGATTAATCTTTTTACTTCTC
1 TTAATTACTGATTAATCTTTTTACTTCTC
* *
7139 TTAATTACTTATTACTC-TTTTACTCTCTC
1 TTAATTACTGATTAATCTTTTTACT-TCTC
7168 CCTTAAGTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
28 7 0.13
29 21 0.39
31 1 0.02
32 10 0.19
33 11 0.20
34 4 0.07
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.55
Consensus pattern (29 bp):
TTAATTACTGATTAATCTTTTTACTTCTC
Found at i:7553 original size:38 final size:38
Alignment explanation
Indices: 7169--7543 Score: 537
Period size: 38 Copynumber: 9.9 Consensus size: 38
7159 TACTCTCTCC
* * *
7169 CTTAAGTATCAA-TTTACTGATTA--A-TCCCTTGACT
1 CTTAATTATCAATTTTACTGATTACTATTACTTTGACT
* *
7203 CTTAATTA-CTGA-TTTACTGATTACTATTTTTACCTTGACT
1 CTTAATTATC-AATTTTACTGATTACTA---TTACTTTGACT
* * *
7243 CTTGATTATCAATTTTACTGATTATTCTTACTTTGACT
1 CTTAATTATCAATTTTACTGATTACTATTACTTTGACT
7281 CTTAATTATCAATTTTACTGATTACTATTACTTTGACT
1 CTTAATTATCAATTTTACTGATTACTATTACTTTGACT
* * *
7319 CTTAATTATCAATTTTACTGATTATTCTTACTTCGACT
1 CTTAATTATCAATTTTACTGATTACTATTACTTTGACT
* *
7357 CTTAATTATCAATTTTACTGATTATTCTTACTTTGACT
1 CTTAATTATCAATTTTACTGATTACTATTACTTTGACT
7395 CTTAATTATCAATTTTACTGATTACTATTACTTTGACT
1 CTTAATTATCAATTTTACTGATTACTATTACTTTGACT
7433 CTTAATTATCAATTTTACTGATTACTATTACTTTGACT
1 CTTAATTATCAATTTTACTGATTACTATTACTTTGACT
7471 CTTAATTATCAATTTTACTGATTACTATTACTTTGACT
1 CTTAATTATCAATTTTACTGATTACTATTACTTTGACT
* *
7509 CTTAATTATCAATTTTACTGATTGCTATTATTTTG
1 CTTAATTATCAATTTTACTGATTACTATTACTTTG
7544 GTCCTTAATT
Statistics
Matches: 313, Mismatches: 19, Indels: 14
0.90 0.05 0.04
Matches are distributed among these distances:
33 1 0.00
34 19 0.06
36 1 0.00
38 262 0.84
40 17 0.05
41 13 0.04
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.50
Consensus pattern (38 bp):
CTTAATTATCAATTTTACTGATTACTATTACTTTGACT
Found at i:8196 original size:14 final size:14
Alignment explanation
Indices: 8177--8208 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
8167 TAACTTTGAC
8177 TTATCATGAATCTA
1 TTATCATGAATCTA
8191 TTATCATGAATCTA
1 TTATCATGAATCTA
8205 TTAT
1 TTAT
8209 TATATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.47
Consensus pattern (14 bp):
TTATCATGAATCTA
Found at i:10894 original size:20 final size:20
Alignment explanation
Indices: 10869--10907 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10859 AAAAAAAGAA
*
10869 CCAATTTGCAAATCAAATGT
1 CCAATTCGCAAATCAAATGT
*
10889 CCAATTCGTAAATCAAATG
1 CCAATTCGCAAATCAAATG
10908 CCTTGTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (20 bp):
CCAATTCGCAAATCAAATGT
Found at i:13572 original size:20 final size:21
Alignment explanation
Indices: 13547--13594 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
13537 TAAAATTATC
* *
13547 AATTAAAAAGAAAGC-AATTA
1 AATTAAAAACAAAGCAAAGTA
13567 AATTAAAAACAAAGCAAAGTA
1 AATTAAAAACAAAGCAAAGTA
13588 AATTAAA
1 AATTAAA
13595 TCTAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (21 bp):
AATTAAAAACAAAGCAAAGTA
Found at i:14344 original size:18 final size:18
Alignment explanation
Indices: 14321--14356 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
14311 CACCCTCAAC
14321 CTAAAACTAGAAGAAAAA
1 CTAAAACTAGAAGAAAAA
14339 CTAAAACTAGAAGAAAAA
1 CTAAAACTAGAAGAAAAA
14357 TAGATGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (18 bp):
CTAAAACTAGAAGAAAAA
Found at i:14991 original size:19 final size:18
Alignment explanation
Indices: 14958--14996 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
14948 TTGAAATAAT
14958 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
14976 TCTTCAAGTTATCTTCAAA
1 TCTTCAA-TGATCTTCAAA
14995 TC
1 TC
14997 ACGAGCTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:19443 original size:20 final size:21
Alignment explanation
Indices: 19418--19465 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
19408 TAAAATTATC
* * *
19418 AATTAAAAAGAAAGC-AATTA
1 AATTAAAAACAAAACAAAGTA
19438 AATTAAAAACAAAACAAAGTA
1 AATTAAAAACAAAACAAAGTA
19459 AATTAAA
1 AATTAAA
19466 TCTAAATCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (21 bp):
AATTAAAAACAAAACAAAGTA
Found at i:20223 original size:18 final size:17
Alignment explanation
Indices: 20196--20231 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
20186 CTCAACCTAA
20196 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
*
20214 AACTATAAGAAAAATAG
1 AACTAGAAGAAAAATAG
20231 A
1 A
20232 TGAAGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.64, C:0.08, G:0.14, T:0.14
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:26708 original size:22 final size:22
Alignment explanation
Indices: 26657--26715 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
26647 TTTCTTACCC
26657 TTATCTTTTATTTTTCGTTATTT
1 TTAT-TTTTATTTTTCGTTATTT
**
26680 TCCTTTTTATTTTTCGTT-TTGT
1 TTATTTTTATTTTTCGTTATT-T
26702 TTATTTTCTATTTT
1 TTATTTT-TATTTT
26716 CTTTGGTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 2 0.07
22 20 0.67
23 8 0.27
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.75
Consensus pattern (22 bp):
TTATTTTTATTTTTCGTTATTT
Done.