Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010408.1 Corchorus olitorius cultivar O-4 contig10440, 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: 18013
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:627 original size:13 final size:13
Alignment explanation
Indices: 609--633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
599 TTAGAATTCC
609 AAATAATATTTAT
1 AAATAATATTTAT
622 AAATAATATTTA
1 AAATAATATTTA
634 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:7388 original size:19 final size:16
Alignment explanation
Indices: 7359--7409 Score: 102
Period size: 16 Copynumber: 3.2 Consensus size: 16
7349 GACCCTGCTC
7359 ATCATGTTTATTATTA
1 ATCATGTTTATTATTA
7375 ATCATGTTTATTATTA
1 ATCATGTTTATTATTA
7391 ATCATGTTTATTATTA
1 ATCATGTTTATTATTA
7407 ATC
1 ATC
7410 TGATTAGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.55
Consensus pattern (16 bp):
ATCATGTTTATTATTA
Found at i:9170 original size:22 final size:22
Alignment explanation
Indices: 9145--9189 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
9135 ACATAAACCC
9145 TTTATTTGTCATAATTGGTAAA
1 TTTATTTGTCATAATTGGTAAA
9167 TTTATTTGTCATAATTGGTAAA
1 TTTATTTGTCATAATTGGTAAA
9189 T
1 T
9190 ATTTAACCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.51
Consensus pattern (22 bp):
TTTATTTGTCATAATTGGTAAA
Found at i:10241 original size:20 final size:20
Alignment explanation
Indices: 10216--10254 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
10206 CATATAAAAT
*
10216 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
10236 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
10255 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:10483 original size:105 final size:105
Alignment explanation
Indices: 10290--10485 Score: 241
Period size: 105 Copynumber: 1.8 Consensus size: 105
10280 GCACATGGCC
* * * *
10290 GGTCGCGAGCCATGGTCGCTCGTGACTAAGCCATGGCTCGGTCGCGAGCGGCTCGCGACTGAGTC
1 GGTCGCAAGCCATAGTCGCTCGCGACTAAGCCATGGCTCGGTCGCGAGCGGCTCGCGACTGAGCC
* **
10355 GCGGCTTGGTCGTGAGCCACGCGCGATCGAGCCGCGGCTT
66 GCGGCCTGGTCGCAAGCCACGCGCGATCGAGCCGCGGCTT
* * * *
10395 GGTCGCAAGCCTTAGTCGCTCGCGAGC-AAGCCATGGCTCGGTCGTGCGCGGTTCGCGACTGAGC
1 GGTCGCAAGCCATAGTCGCTCGCGA-CTAAGCCATGGCTCGGTCGCGAGCGGCTCGCGACTGAGC
* *
10459 CGCGGCGGCTGGTTGCAAGCCGCGCGC
65 CGCGGC--CTGGTCGCAAGCCACGCGC
10486 AACCAAGCCT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
105 60 0.80
106 1 0.01
107 14 0.19
ACGTcount: A:0.12, C:0.32, G:0.38, T:0.17
Consensus pattern (105 bp):
GGTCGCAAGCCATAGTCGCTCGCGACTAAGCCATGGCTCGGTCGCGAGCGGCTCGCGACTGAGCC
GCGGCCTGGTCGCAAGCCACGCGCGATCGAGCCGCGGCTT
Found at i:10632 original size:17 final size:18
Alignment explanation
Indices: 10607--10653 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
10597 ATTGAGGTTT
*
10607 GAAAGTTTGAA-AATTGA
1 GAAAATTTGAAGAATTGA
10624 GAAAATTTGAGAGAATTGA
1 GAAAATTTGA-AGAATTGA
*
10643 -AAAATATGAAG
1 GAAAATTTGAAG
10654 TTAGAAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 11 0.42
18 9 0.35
19 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (18 bp):
GAAAATTTGAAGAATTGA
Found at i:12495 original size:2 final size:2
Alignment explanation
Indices: 12490--12526 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
12480 TATAAGTCTG
12490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12527 CGAGAATGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16664 original size:56 final size:57
Alignment explanation
Indices: 16563--16677 Score: 214
Period size: 56 Copynumber: 2.0 Consensus size: 57
16553 TTTATTTTGT
*
16563 AGAATAATTAAGTAGAGATATGGGGTATAAGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATATGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
16620 AGAATAATTAAGTAGAGATA-GGGGGATAAGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATATGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
16676 AG
1 AG
16678 GAAACATATA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 37 0.65
57 20 0.35
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.35
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGATATGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
Done.