Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024113.1 Corchorus olitorius cultivar O-4 contig24146, 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: 26774
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:6777 original size:13 final size:13
Alignment explanation
Indices: 6759--6784 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6749 CTTGGCATGA
6759 GTGATGATTTTTG
1 GTGATGATTTTTG
6772 GTGATGATTTTTG
1 GTGATGATTTTTG
6785 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:8628 original size:51 final size:50
Alignment explanation
Indices: 8527--8630 Score: 115
Period size: 51 Copynumber: 2.1 Consensus size: 50
8517 GTTCTTCATA
* **
8527 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
*
8577 TTTTCTCTTGTTTCA-ATCTTGTCTCCA-GACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCT-CAGGACAAACAAACACTCGTACA-GTGT
8628 TTT
1 TTT
8631 CATTCATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
50 7 0.15
51 36 0.78
52 3 0.07
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:13700 original size:14 final size:14
Alignment explanation
Indices: 13681--13714 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
13671 TTTTATAATT
13681 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
13695 ATTTTATTTTTACT
1 ATTTTATTTTTACC
13709 ATTTTA
1 ATTTTA
13715 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:15125 original size:2 final size:2
Alignment explanation
Indices: 15118--15150 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
15108 GTGTAGTAGA
*
15118 AT AT AT AT AT AT AT AT AT AT AT AG A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15151 TTCCAAGTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:16781 original size:18 final size:17
Alignment explanation
Indices: 16754--16807 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
16744 GAACGGGTAG
*
16754 AGAAGGAGAAGGAAAAGA
1 AGAAGAAGAA-GAAAAGA
16772 AGAAGAAGAAGAAAAGA
1 AGAAGAAGAAGAAAAGA
*
16789 TAGGAA-AAAAAGAAAAGA
1 -A-GAAGAAGAAGAAAAGA
16807 A
1 A
16808 ATAGGAGTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 8 0.25
18 21 0.66
19 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.02
Consensus pattern (17 bp):
AGAAGAAGAAGAAAAGA
Found at i:17143 original size:56 final size:56
Alignment explanation
Indices: 17061--17173 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 56
17051 TCCTTTAAAC
* *
17061 GAATAGACACGTCTCCAATTAAAGATGTAATCTCTCAT-GCAAAGACACCTTTTCAT
1 GAATAGACACGTCTCCAATTAAAGATGCAATCTCTCATAG-AAAGACACATTTTCAT
* * *
17117 GAATAGACATGTCTCCGATTAGAGATGCAATCTCTCATAGAAAGACACATTTTCAT
1 GAATAGACACGTCTCCAATTAAAGATGCAATCTCTCATAGAAAGACACATTTTCAT
17173 G
1 G
17174 TTTGAAACAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
56 50 0.98
57 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.28
Consensus pattern (56 bp):
GAATAGACACGTCTCCAATTAAAGATGCAATCTCTCATAGAAAGACACATTTTCAT
Found at i:17866 original size:162 final size:161
Alignment explanation
Indices: 17678--17995 Score: 458
Period size: 162 Copynumber: 2.0 Consensus size: 161
17668 TACCCTTTAT
* * * *
17678 GCATGGTTTATTTTAAAAAGGACTAAACCTTGGGCTGAAATTGGGACTT-AATTTTAGGACTTTA
1 GCATGGTTTATTTCAAAAAGGACTAAACCTTAGGCTAAAATTAGGA-TTAAATTTTAGGACTTTA
* ** * *
17742 TTTGACATGGCATAATTTTAATGGTTAGTCCCATGGATGACGTGGTGGGACAGTCCCAATAATTT
65 TTTGACATGACATAATTTTAATGGTTAGT-CCATAAATAACGTGATGGGACAGTCCCAATAATTT
*
17807 CTCGTTTGTAAAATGAGAAAGAGAAGAAATATC
129 CTCATTTGTAAAATGAGAAAGAGAAGAAATATC
* *
17840 GCATGGTTTATTTCAAAAGGGACTAAACCTTAGGCTAAAATTATGATTAAATTTTAGGACTTTAT
1 GCATGGTTTATTTCAAAAAGGACTAAACCTTAGGCTAAAATTAGGATTAAATTTTAGGACTTTAT
* **
17905 TTGACATGACATAATTTTAATGGTTAGTCTATAAATAACGTGATGGGATTGTCCCAATAATTTCT
66 TTGACATGACATAATTTTAATGGTTAGTCCATAAATAACGTGATGGGACAGTCCCAATAATTTCT
* *
17970 CATTTGTAGAGTGAGAAAGAGAAGAA
131 CATTTGTAAAATGAGAAAGAGAAGAA
17996 GCATCGCCAT
Statistics
Matches: 138, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
161 55 0.40
162 83 0.60
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (161 bp):
GCATGGTTTATTTCAAAAAGGACTAAACCTTAGGCTAAAATTAGGATTAAATTTTAGGACTTTAT
TTGACATGACATAATTTTAATGGTTAGTCCATAAATAACGTGATGGGACAGTCCCAATAATTTCT
CATTTGTAAAATGAGAAAGAGAAGAAATATC
Found at i:21403 original size:3 final size:3
Alignment explanation
Indices: 21395--21456 Score: 108
Period size: 3 Copynumber: 20.7 Consensus size: 3
21385 TTATCAGACC
21395 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
21443 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
21457 GTATATATGA
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:23012 original size:15 final size:15
Alignment explanation
Indices: 22992--23022 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22982 TATCAGGCTG
*
22992 TCACGATACACGATA
1 TCACGATACACAATA
23007 TCACGATACACAATA
1 TCACGATACACAATA
23022 T
1 T
23023 TTCAACCGTA
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:0.42, C:0.26, G:0.10, T:0.23
Consensus pattern (15 bp):
TCACGATACACAATA
Done.