Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017032.1 Corchorus olitorius cultivar O-4 contig17065, 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: 37809
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Found at i:600 original size:16 final size:17
Alignment explanation
Indices: 574--605 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
564 AGTGCAAATT
574 AAAATAGAAAAATAAAG
1 AAAATAGAAAAATAAAG
591 AAAA-AGAAAAATAAA
1 AAAATAGAAAAATAAA
606 ACGACAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAAATAAAG
Found at i:2876 original size:21 final size:20
Alignment explanation
Indices: 2843--2882 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2833 AAGAAATGTA
*
2843 ATAGCCTTTTCCAAAGTTTCC
1 ATAGCCTTATCC-AAGTTTCC
*
2864 ATAGGCTTATCCAAGTTTC
1 ATAGCCTTATCCAAGTTTC
2883 TAAAGACTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (20 bp):
ATAGCCTTATCCAAGTTTCC
Found at i:8082 original size:16 final size:16
Alignment explanation
Indices: 8061--8091 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
8051 TAAAATCATT
8061 TTTGGGGTTTCATTTC
1 TTTGGGGTTTCATTTC
8077 TTTGGGGTTTCATTT
1 TTTGGGGTTTCATTT
8092 GTAACGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.10, G:0.26, T:0.58
Consensus pattern (16 bp):
TTTGGGGTTTCATTTC
Found at i:8868 original size:87 final size:87
Alignment explanation
Indices: 8769--8940 Score: 344
Period size: 87 Copynumber: 2.0 Consensus size: 87
8759 TAATTTCAGA
8769 AAAAAATAATTTTAATTTGTAATAATTTGAGGCTTGGGTCTTTGGATGCGGTTTGGGCCTCCTTA
1 AAAAAATAATTTTAATTTGTAATAATTTGAGGCTTGGGTCTTTGGATGCGGTTTGGGCCTCCTTA
8834 TTTCGTTTGGGCTTTGTCTTAG
66 TTTCGTTTGGGCTTTGTCTTAG
8856 AAAAAATAATTTTAATTTGTAATAATTTGAGGCTTGGGTCTTTGGATGCGGTTTGGGCCTCCTTA
1 AAAAAATAATTTTAATTTGTAATAATTTGAGGCTTGGGTCTTTGGATGCGGTTTGGGCCTCCTTA
8921 TTTCGTTTGGGCTTTGTCTT
66 TTTCGTTTGGGCTTTGTCTT
8941 TATCCAAGTG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.44
Consensus pattern (87 bp):
AAAAAATAATTTTAATTTGTAATAATTTGAGGCTTGGGTCTTTGGATGCGGTTTGGGCCTCCTTA
TTTCGTTTGGGCTTTGTCTTAG
Found at i:11606 original size:76 final size:76
Alignment explanation
Indices: 11480--11759 Score: 357
Period size: 76 Copynumber: 3.7 Consensus size: 76
11470 ATTTACAGGT
* * *
11480 GTGCCAATCTAGGCACTCAATCGTTGAGTGAGTGGCGTCTGCGTGGACGCTCCGCCTCACTGACG
1 GTGCCAATCTAGGCACTCAACCGTTGAGTGAGTGGCATCTGCGTGGACGCTCCGCCTCACTGAAG
11545 GACGAACGGGG
66 GACGAACGGGG
* * ** * *
11556 GTGCCAATTTAGGCACTCAGCCGTTGAGTGAGTGGTGTCTGCGTGGACGCTCCGCCTAACTGATG
1 GTGCCAATCTAGGCACTCAACCGTTGAGTGAGTGGCATCTGCGTGGACGCTCCGCCTCACTGAAG
*
11621 GACGAATGGGG
66 GACGAACGGGG
* * * * ** * *
11632 GTGCCAATCTAGGCACTCAGCCGTTGAGGGAGCGGCATTTAAGTGGACGCTCCGTCTCATTGATA
1 GTGCCAATCTAGGCACTCAACCGTTGAGTGAGTGGCATCTGCGTGGACGCTCCGCCTCACTGA-A
11697 GG-CGAACGGGG
65 GGACGAACGGGG
*
11708 GTGCCAATCTAGGCACTCAACCGTTAAGT-AGGTGGCATCTGCGTGGACGCTC
1 GTGCCAATCTAGGCACTCAACCGTTGAGTGA-GTGGCATCTGCGTGGACGCTC
11760 TGTCAGGTGG
Statistics
Matches: 175, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
75 1 0.01
76 172 0.98
77 2 0.01
ACGTcount: A:0.20, C:0.25, G:0.34, T:0.22
Consensus pattern (76 bp):
GTGCCAATCTAGGCACTCAACCGTTGAGTGAGTGGCATCTGCGTGGACGCTCCGCCTCACTGAAG
GACGAACGGGG
Found at i:19373 original size:31 final size:31
Alignment explanation
Indices: 19332--19393 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
19322 TAATATATAA
*
19332 TGAAATACGTATGTACTTAGTTTTTATTTCT
1 TGAAACACGTATGTACTTAGTTTTTATTTCT
*
19363 TGAAACACGTATGTACTTAGTTTTTGTTTCT
1 TGAAACACGTATGTACTTAGTTTTTATTTCT
19394 CTTTTTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50
Consensus pattern (31 bp):
TGAAACACGTATGTACTTAGTTTTTATTTCT
Found at i:23210 original size:13 final size:13
Alignment explanation
Indices: 23192--23218 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23182 ACCCTTAACA
23192 TTCAAAAGTTGTT
1 TTCAAAAGTTGTT
23205 TTCAAAAGTTGTT
1 TTCAAAAGTTGTT
23218 T
1 T
23219 AAAACATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TTCAAAAGTTGTT
Found at i:25913 original size:16 final size:16
Alignment explanation
Indices: 25894--25938 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
25884 CTACTCCACC
* *
25894 CTCCTCCCCCTCCCTA
1 CTCCTCCCCCACCCCA
25910 CTCC-CCCCCACCCCA
1 CTCCTCCCCCACCCCA
25925 CTCCT-CCCCACCCC
1 CTCCTCCCCCACCCC
25939 CCCTTGAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.09, C:0.76, G:0.00, T:0.16
Consensus pattern (16 bp):
CTCCTCCCCCACCCCA
Found at i:34338 original size:29 final size:30
Alignment explanation
Indices: 34278--34343 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
34268 TTTTTTTTTG
34278 TTTTTTTGGCCAAAACAACAGATCTACTTT
1 TTTTTTTGGCCAAAACAACAGATCTACTTT
*
34308 TTTTTTTGG-CAGAAGCAACAGATCTACTTT
1 TTTTTTTGGCCA-AAACAACAGATCTACTTT
*
34338 TGTTTT
1 TTTTTT
34344 GCCTTATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 2 0.06
30 31 0.94
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.44
Consensus pattern (30 bp):
TTTTTTTGGCCAAAACAACAGATCTACTTT
Found at i:36666 original size:31 final size:32
Alignment explanation
Indices: 36604--36664 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
36594 ATCTACTCAC
36604 ATATATCATAAGAACCGAGAAAAAAAAAAACT
1 ATATATCATAAGAACCGAGAAAAAAAAAAACT
36636 ATATATCATAAGAACCGAGAAAAAAAAAA
1 ATATATCATAAGAACCGAGAAAAAAAAAA
36665 CTCTATAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.64, C:0.11, G:0.10, T:0.15
Consensus pattern (32 bp):
ATATATCATAAGAACCGAGAAAAAAAAAAACT
Found at i:36995 original size:17 final size:17
Alignment explanation
Indices: 36973--37012 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
36963 TTTTCTTTCC
36973 ATATTACAAAATCTAAA
1 ATATTACAAAATCTAAA
36990 ATATTACAAAATCTAAA
1 ATATTACAAAATCTAAA
37007 ATATTA
1 ATATTA
37013 GTAGCAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATTACAAAATCTAAA
Found at i:37068 original size:15 final size:14
Alignment explanation
Indices: 37044--37086 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
37034 ACCTCTTATT
*
37044 ATTATAATTATTAA
1 ATTATTATTATTAA
*
37058 ACTTATTATTATTAT
1 A-TTATTATTATTAA
37073 ATTAATTATTATTA
1 ATT-ATTATTATTA
37087 GTGGTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 22 0.88
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTATTATTATTAA
Found at i:37081 original size:18 final size:21
Alignment explanation
Indices: 37038--37086 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
37028 CGTTAAACCT
37038 CTTATTATTATAATTATTAAA
1 CTTATTATTATAATTATTAAA
*
37059 CTTATTATTATTA-TATT-AA
1 CTTATTATTATAATTATTAAA
37078 -TTATTATTA
1 CTTATTATTA
37087 GTGGTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.33
19 2 0.07
20 4 0.15
21 12 0.44
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
CTTATTATTATAATTATTAAA
Done.