Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021428.1 Corchorus olitorius cultivar O-4 contig21461, 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: 16939
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2233 original size:23 final size:22
Alignment explanation
Indices: 2193--2235 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
2183 AAATTACCAT
2193 AAAAAATAAAAAAGAAAAAGTG
1 AAAAAATAAAAAAGAAAAAGTG
2215 AAAATAATAAAAGAA-AAAAAG
1 AAAA-AATAAAA-AAGAAAAAG
2236 AAAGGGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 13 0.68
24 2 0.11
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (22 bp):
AAAAAATAAAAAAGAAAAAGTG
Found at i:2238 original size:21 final size:20
Alignment explanation
Indices: 2195--2238 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
2185 ATTACCATAA
**
2195 AAAATAAAAAAGAAAAAGTG
1 AAAATAAAAAAGAAAAAAAG
2215 AAAATAATAAAAGAAAAAAAG
1 AAAATAA-AAAAGAAAAAAAG
2236 AAA
1 AAA
2239 GGGAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (20 bp):
AAAATAAAAAAGAAAAAAAG
Found at i:2340 original size:14 final size:14
Alignment explanation
Indices: 2307--2356 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
2297 CAAGAGACGT
*
2307 TTTTCAAGAAAATTG
1 TTTTCAAGAAAA-GG
2322 TTTTCAAGAAAAGG
1 TTTTCAAGAAAAGG
*
2336 TTTTCAA-AAATGAG
1 TTTTCAAGAAAAG-G
2350 TTTTCAA
1 TTTTCAA
2357 AAGGTTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
13 4 0.12
14 16 0.50
15 12 0.38
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (14 bp):
TTTTCAAGAAAAGG
Found at i:3053 original size:10 final size:10
Alignment explanation
Indices: 3038--3068 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3028 GGTGCATGGT
3038 GAAAAAAAAA
1 GAAAAAAAAA
3048 GAAAAAAAAA
1 GAAAAAAAAA
*
3058 GAAAAGAAAA
1 GAAAAAAAAA
3068 G
1 G
3069 GATAAAGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:6599 original size:2 final size:2
Alignment explanation
Indices: 6592--6623 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6582 TAATCACTTA
6592 AT AT AT 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 AT AT AT
6624 GAAAAATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6661 original size:12 final size:13
Alignment explanation
Indices: 6642--6671 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6632 AAAAAGTTTG
*
6642 ATTTTTTTCGAAA
1 ATTTTTTTCAAAA
6655 ATTTTTTTCAAAA
1 ATTTTTTTCAAAA
6668 ATTT
1 ATTT
6672 CATGCATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (13 bp):
ATTTTTTTCAAAA
Found at i:6959 original size:20 final size:21
Alignment explanation
Indices: 6934--6973 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
6924 TATCAATTAT
6934 AAAAAAAAAACCAAT-TAAAC
1 AAAAAAAAAACCAATGTAAAC
* *
6954 AAAAAATAAAGCAATGTAAA
1 AAAAAAAAAACCAATGTAAA
6974 TTAAATCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.72, C:0.10, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAAAAAAAACCAATGTAAAC
Found at i:10220 original size:2 final size:2
Alignment explanation
Indices: 10213--10242 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10203 TAATCACTTA
10213 AT AT 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 AT AT
10243 GAAAAATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11454 original size:2 final size:2
Alignment explanation
Indices: 11447--11474 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11437 TAATCACTTA
11447 AT 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 AT
11475 GAAAAATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16063 original size:22 final size:22
Alignment explanation
Indices: 16021--16063 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
16011 TTTCTAATTA
**
16021 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
16043 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
16064 AATTATTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Done.