Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015292.1 Corchorus olitorius cultivar O-4 contig15325, 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: 8780
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Found at i:263 original size:20 final size:20
Alignment explanation
Indices: 235--274 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
225 GTTCCGTTGT
*
235 TTAATATCTAACGCAACGAC
1 TTAAAATCTAACGCAACGAC
255 TTAAAATCTAACGCAACGAC
1 TTAAAATCTAACGCAACGAC
275 CTAAGTGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (20 bp):
TTAAAATCTAACGCAACGAC
Found at i:968 original size:201 final size:201
Alignment explanation
Indices: 421--988 Score: 886
Period size: 203 Copynumber: 2.8 Consensus size: 201
411 ATTTTTTTTA
* *
421 CAACCACTTCAATTGGTTACGTATAACTTTTAAAAATGATTAAATGTCGTTTCCAAAACACTTAC
1 CAACCACTTTAATTGGTTACGAATAACTTTTAAAAATGATTAAATGTCGTTTCCAAAACACTTAC
* *
486 GTAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATATCGTTGCAAAAACCCTT
66 ATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGCAAAAACCCTT
* * * *
551 ACGCAACGATGTTGTCTTGGTTGTGAAATCTTTTACGTAGCAACATTTGATTGGTTGTGTAATAA
131 ACGCAACGACGTTGTTTTGGTTGTGAAATCTTTTACATAGCAACATTTGATTGGTTGCGTAATAA
*
616 TTTTTG
196 TTTTCG
* * *
622 CAGCCACTTTTAATTGGTTACGAATAACTTTTAAAAAATGATTAAAAGTCGTTTCCAAAACAGTT
1 CAACCAC-TTTAATTGGTTACGAATAACTTTT-AAAAATGATTAAATGTCGTTTCCAAAACACTT
* * *
687 ACATAACGACCTCTCGGTAGTTGCCAAAATAATTTTAAAACGATTAAATGTCGTTGCGAAAACCC
64 ACATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGCAAAAACCC
752 TTACGCAACGACGTTGTTTTGGTTGTGAAATCTTTTACATAGCAACATTTGATTGGTTGCGTAAT
129 TTACGCAACGACGTTGTTTTGGTTGTGAAATCTTTTACATAGCAACATTTGATTGGTTGCGTAAT
817 AATTTTCG
194 AATTTTCG
* *
825 CAACCACTTTAATTGGTTATGAATAACTTTTAGAAATGATTAAATGTCGTTTCCAAAACACTTAC
1 CAACCACTTTAATTGGTTACGAATAACTTTTAAAAATGATTAAATGTCGTTTCCAAAACACTTAC
* * * * *
890 ATTACGACCTAT-GGATAGTTGCCAAAATGATTTAAAAACGATTATATGTCGTTGCAAAAACCAT
66 ATAACGACCTCTAGG-TAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGCAAAAACCCT
* *
954 TACGTAATGACGTTGTTTTGGTTGTGAAATCTTTT
130 TACGCAACGACGTTGTTTTGGTTGTGAAATCTTTT
989 GAATGGCTTT
Statistics
Matches: 335, Mismatches: 29, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
200 2 0.01
201 124 0.37
202 45 0.13
203 164 0.49
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (201 bp):
CAACCACTTTAATTGGTTACGAATAACTTTTAAAAATGATTAAATGTCGTTTCCAAAACACTTAC
ATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGCAAAAACCCTT
ACGCAACGACGTTGTTTTGGTTGTGAAATCTTTTACATAGCAACATTTGATTGGTTGCGTAATAA
TTTTCG
Found at i:1745 original size:17 final size:17
Alignment explanation
Indices: 1723--1758 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1713 ACACATTATC
1723 GATAAAATCTCATCTGA
1 GATAAAATCTCATCTGA
1740 GATAAAATCTCATCTGA
1 GATAAAATCTCATCTGA
1757 GA
1 GA
1759 GGGAAGAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (17 bp):
GATAAAATCTCATCTGA
Found at i:4109 original size:41 final size:41
Alignment explanation
Indices: 4038--4128 Score: 141
Period size: 41 Copynumber: 2.2 Consensus size: 41
4028 CATATGTTAA
*
4038 GCAACGACTAACAAAGATCGTTGCGAAAAGTTTAAGATTTC
1 GCAACGACTAACAAAGATCGCTGCGAAAAGTTTAAGATTTC
4079 GCAACGACTAACAAA-AGTCGCTGC-AGAAAGTTTAAGATTTC
1 GCAACGACTAACAAAGA-TCGCTGCGA-AAAGTTTAAGATTTC
4120 GCAACGACT
1 GCAACGACT
4129 TAATCTGTCG
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
40 2 0.04
41 45 0.96
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (41 bp):
GCAACGACTAACAAAGATCGCTGCGAAAAGTTTAAGATTTC
Found at i:4270 original size:41 final size:41
Alignment explanation
Indices: 4213--4301 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
4203 TATATTAAGC
*
4213 AACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTCGA
1 AACGACTAACAAAAGTCGCTGCGAAAAGTTTAAGATTTCGA
* * *
4254 AACGACTAACAAAAGTCGCTGCGGAAAGTTTAAGATTTTGC
1 AACGACTAACAAAAGTCGCTGCGAAAAGTTTAAGATTTCGA
4295 AACGACT
1 AACGACT
4302 TAATCTGTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (41 bp):
AACGACTAACAAAAGTCGCTGCGAAAAGTTTAAGATTTCGA
Found at i:4283 original size:173 final size:173
Alignment explanation
Indices: 4004--4443 Score: 733
Period size: 173 Copynumber: 2.5 Consensus size: 173
3994 GACTTAATTT
*
4004 GTCGCTGCGAAAATCAATTAGTAACATATGTTAAGCAACGACTAAC-AAAGATCGTTGCGAAAAG
1 GTCGCTGCGAAAATCAATTAGTAACATATATTAAGCAACGACTAACAAAAG-TCGTTGCGAAAAG
*
4068 TTTAAGATTTCGCAACGACTAACAAAAGTCGCTGCAGAAAGTTTAAGATTTCGCAACGACTTAAT
65 TTTAAGATTTCGAAACGACTAACAAAAGTCGCTGCAGAAAGTTTAAGATTTCGCAACGACTTAAT
*
4133 CTGTCGTTTCAAAAGTAATCATGTTTTTTGTAGCGACTTTCAAG
130 CTGTCGTTTCAAAAGTAATCATGTTTTTTGTAGCGACTTTAAAG
4177 GTCGCTGCGAAAATCAATTAGTAACATATATTAAGCAACGACTAACAAAAGTCGTTGCGAAAAGT
1 GTCGCTGCGAAAATCAATTAGTAACATATATTAAGCAACGACTAACAAAAGTCGTTGCGAAAAGT
* *
4242 TTAAGATTTCGAAACGACTAACAAAAGTCGCTGCGGAAAGTTTAAGATTTTGCAACGACTTAATC
66 TTAAGATTTCGAAACGACTAACAAAAGTCGCTGCAGAAAGTTTAAGATTTCGCAACGACTTAATC
4307 TGTCGTTTCAAAAGTAATCATGTTTTTTGTAGCGACTTTAAAG
131 TGTCGTTTCAAAAGTAATCATGTTTTTTGTAGCGACTTTAAAG
* * *
4350 GTCGTTGCGAAAATC-ATTAGTAACATATATTAAGCAACGACTAACAAAAGTCGTTACGAAAAGA
1 GTCGCTGCGAAAATCAATTAGTAACATATATTAAGCAACGACTAACAAAAGTCGTTGCGAAAAGT
* * * *
4414 CTATGATTTC-ACAACGACTAATAGAAGTCG
66 TTAAGATTTCGA-AACGACTAACAAAAGTCG
4444 TAGTAAAACT
Statistics
Matches: 253, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
171 1 0.00
172 71 0.28
173 177 0.70
174 4 0.02
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (173 bp):
GTCGCTGCGAAAATCAATTAGTAACATATATTAAGCAACGACTAACAAAAGTCGTTGCGAAAAGT
TTAAGATTTCGAAACGACTAACAAAAGTCGCTGCAGAAAGTTTAAGATTTCGCAACGACTTAATC
TGTCGTTTCAAAAGTAATCATGTTTTTTGTAGCGACTTTAAAG
Found at i:6277 original size:2 final size:2
Alignment explanation
Indices: 6266--6301 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6256 CCAAATCTGC
6266 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6302 CTACTACTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8373 original size:2 final size:2
Alignment explanation
Indices: 8368--8400 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8358 GCTCTGCACA
8368 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8401 AATGCTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8643 original size:13 final size:13
Alignment explanation
Indices: 8610--8642 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
8600 GATTGGTTGG
*
8610 TCTTTTTCCTTTT
1 TCTTTTTTCTTTT
8623 TCTTTTTTCTTTT
1 TCTTTTTTCTTTT
8636 T-TTTTTT
1 TCTTTTTT
8643 TACATAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TCTTTTTTCTTTT
Done.