Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017504.1 Corchorus olitorius cultivar O-4 contig17537, 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: 10861
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:45 original size:10 final size:10
Alignment explanation
Indices: 30--58 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
20 CCATATTAAC
30 AATTTTATTT
1 AATTTTATTT
40 AATTTTATTT
1 AATTTTATTT
50 -ATTTTATTT
1 AATTTTATTT
59 CCTTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
AATTTTATTT
Found at i:4038 original size:2 final size:2
Alignment explanation
Indices: 4002--4027 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3992 TCATCGGAAC
4002 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4028 GTTGGTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4341 original size:74 final size:74
Alignment explanation
Indices: 4244--4393 Score: 196
Period size: 74 Copynumber: 2.0 Consensus size: 74
4234 TCTTTTCATT
* * * * *
4244 ACGTCATTTTGTTGTTACTAAAAGAAGTATATTTTACGCAATAA-T-ATTGAGTTGTTGCGTAAA
1 ACGTCATTTTATTATTACTAAAAGAAGTATATTTTACGCAACAACTCAAT--CTTGTTGCGTAAA
4307 ATATTTTAACA
64 ATATTTTAACA
* * *
4318 ACGTCATTTTATTATTGCTAAAAGAATTATATTTTACGCAACAACTCAATCTTGTTGTGTAAAAT
1 ACGTCATTTTATTATTACTAAAAGAAGTATATTTTACGCAACAACTCAATCTTGTTGCGTAAAAT
4383 ATTTTAACA
66 ATTTTAACA
4392 AC
1 AC
4394 AATATATATT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
74 63 0.95
75 1 0.02
76 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (74 bp):
ACGTCATTTTATTATTACTAAAAGAAGTATATTTTACGCAACAACTCAATCTTGTTGCGTAAAAT
ATTTTAACA
Found at i:7561 original size:13 final size:13
Alignment explanation
Indices: 7519--7563 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
7509 TCATGCACCC
*
7519 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
7533 AAAACCATTT-AT
1 AAAACAATTTAAT
7545 AAAACAATTTAAT
1 AAAACAATTTAAT
7558 AAAACA
1 AAAACA
7564 GTAATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.37
13 8 0.30
14 9 0.33
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAACAATTTAAT
Found at i:8734 original size:8 final size:7
Alignment explanation
Indices: 8698--8759 Score: 63
Period size: 8 Copynumber: 8.3 Consensus size: 7
8688 ATTTCCAAAA
8698 TTCTTATT
1 TTCTT-TT
8706 TTCTTTAT
1 TTCTTT-T
8714 TTCTTTT
1 TTCTTTT
8721 TT-TTTT
1 TTCTTTT
8727 CTTCTTTT
1 -TTCTTTT
*
8735 TTTTTCTT
1 TTCTT-TT
8743 TTCTTCTT
1 TTCTT-TT
8751 TTCTTTT
1 TTCTTTT
8758 TT
1 TT
8760 TGGGTCCAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
6 4 0.08
7 14 0.29
8 30 0.62
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (7 bp):
TTCTTTT
Found at i:8734 original size:13 final size:12
Alignment explanation
Indices: 8713--8760 Score: 62
Period size: 13 Copynumber: 3.9 Consensus size: 12
8703 ATTTTCTTTA
8713 TTTC-TTTTTTT
1 TTTCTTTTTTTT
8724 TTTCTTCTTTTTT
1 TTTCTT-TTTTTT
*
8737 TTTCTTTTCTTCT
1 TTTCTTTT-TTTT
8750 TTTCTTTTTTT
1 TTTCTTTTTTT
8761 GGGTCCAGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 4 0.12
12 5 0.16
13 23 0.72
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:8738 original size:18 final size:19
Alignment explanation
Indices: 8704--8760 Score: 82
Period size: 18 Copynumber: 3.1 Consensus size: 19
8694 AAAATTCTTA
8704 TTTTCTT-TATTTCTTTTTT
1 TTTTCTTCT-TTTCTTTTTT
*
8723 TTTTCTTCTTTT-TTTTTC
1 TTTTCTTCTTTTCTTTTTT
8741 TTTTCTTCTTTTCTTTTTT
1 TTTTCTTCTTTTCTTTTTT
8760 T
1 T
8761 GGGTCCAGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 17 0.50
19 16 0.47
20 1 0.03
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTCTTCTTTTCTTTTTT
Found at i:8878 original size:18 final size:18
Alignment explanation
Indices: 8857--8917 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
8847 TGGGCCTGCG
8857 CTGGCTCGCGCGCCTGGC
1 CTGGCTCGCGCGCCTGGC
* *
8875 CTGGCGCGCCTGGGCCT-GC
1 CTGGCTCG-C-GCGCCTGGC
* *
8894 GCTGGCTTGCGTGCCTGGC
1 -CTGGCTCGCGCGCCTGGC
8913 CTGGC
1 CTGGC
8918 ACGCCTGGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
18 17 0.50
19 6 0.18
20 11 0.32
ACGTcount: A:0.00, C:0.39, G:0.41, T:0.20
Consensus pattern (18 bp):
CTGGCTCGCGCGCCTGGC
Found at i:8892 original size:15 final size:14
Alignment explanation
Indices: 8864--8930 Score: 54
Period size: 14 Copynumber: 5.0 Consensus size: 14
8854 GCGCTGGCTC
8864 GCGCGCCTGGCCTG
1 GCGCGCCTGGCCTG
8878 GCGCGCCTGGGCCT-
1 GCGCGCCT-GGCCTG
*
8892 --GCG-CTGG-CTT
1 GCGCGCCTGGCCTG
*
8902 GCGTGCCTGGCCTG
1 GCGCGCCTGGCCTG
*
8916 GCACGCCTGGGCCTG
1 GCGCGCCT-GGCCTG
8931 CGCTAGGCCC
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
9 2 0.05
10 2 0.05
11 2 0.05
12 5 0.12
13 4 0.10
14 16 0.38
15 11 0.26
ACGTcount: A:0.01, C:0.39, G:0.42, T:0.18
Consensus pattern (14 bp):
GCGCGCCTGGCCTG
Found at i:8897 original size:38 final size:38
Alignment explanation
Indices: 8846--8943 Score: 151
Period size: 38 Copynumber: 2.6 Consensus size: 38
8836 AGCCAGGCCG
*
8846 CTGGGCCTGCGCTGGCTCGCGCGCCTGGCCTGGCGCGC
1 CTGGGCCTGCGCTGGCTCGCGCGCCTGGCCTGGCACGC
* *
8884 CTGGGCCTGCGCTGGCTTGCGTGCCTGGCCTGGCACGC
1 CTGGGCCTGCGCTGGCTCGCGCGCCTGGCCTGGCACGC
*
8922 CTGGGCCTGCGCTAGGCCCGCG
1 CTGGGCCTGCGCT-GGCTCGCG
8944 TGCTATGACT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 48 0.89
39 6 0.11
ACGTcount: A:0.02, C:0.40, G:0.41, T:0.17
Consensus pattern (38 bp):
CTGGGCCTGCGCTGGCTCGCGCGCCTGGCCTGGCACGC
Found at i:9910 original size:131 final size:131
Alignment explanation
Indices: 9738--9991 Score: 386
Period size: 131 Copynumber: 1.9 Consensus size: 131
9728 TGGTATTACA
* * * * *
9738 GTTACGAATAGGTTATGATTTCGCAATGACTTTGTTTTTGTTGTTACAAAAATTGTAAGCATTGG
1 GTTACGAATAGATTATGATTTCACAACGACTTTGTTTTTGTTGTTACAAAAACTATAAGCATTGG
* *
9803 CAACGAA-TAAAAAA-GTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGACTTTATAAAA
66 CAAC-AATTAAAAAATGTGTTGAGTAAAATACCATCAAAATCACTAAGGCAACGACTTTATAAAA
9866 TT
130 TT
* *
9868 GTTACGAATTAGATTATGATTTCACAGCGACTTTGTTTTTGTTGTTACGAAAACTATAAGCATTG
1 GTTACGAA-TAGATTATGATTTCACAACGACTTTGTTTTTGTTGTTACAAAAACTATAAGCATTG
*
9933 GCAACAATTAAAAAATTTGTTGAGTAAAATACCATCAAAATCACTAAGGCAACGACTTT
65 GCAACAATTAAAAAATGTGTTGAGTAAAATACCATCAAAATCACTAAGGCAACGACTTT
9992 TAATTATTGT
Statistics
Matches: 111, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
130 10 0.09
131 61 0.55
132 40 0.36
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (131 bp):
GTTACGAATAGATTATGATTTCACAACGACTTTGTTTTTGTTGTTACAAAAACTATAAGCATTGG
CAACAATTAAAAAATGTGTTGAGTAAAATACCATCAAAATCACTAAGGCAACGACTTTATAAAAT
T
Done.