Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014685.1 Corchorus olitorius cultivar O-4 contig14718, 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: 35010
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:496 original size:105 final size:103
Alignment explanation
Indices: 313--521 Score: 341
Period size: 105 Copynumber: 2.0 Consensus size: 103
303 ATAAAGGTGA
*
313 AAGACTAAAACGCCTAAACTTTTCTTTATTATAATTGAACTGACTCCATTAGAGCTTTAGGACAT
1 AAGACTAAAACACCTAAACTTTTCTTTATTATAATTGAACTGACTCCATTAGAGCTTTAGGACAT
*
378 TTATGAGGAGAAACTACTAATATGATCAGTAGCTAAGAATG
66 TAATGAGGAGAAACTACT-A-AT-ATCAGTAGCTAAGAATG
419 AAGACTAAAACACCTAAAC-TTTCTTTATTATAATTGAACCT-ACTCCATTAGAGCTTTAGGACA
1 AAGACTAAAACACCTAAACTTTTCTTTATTATAATTGAA-CTGACTCCATTAGAGCTTTAGGACA
*
482 TTAATGAGGAGAAACTTCTAATATCAGTAGCTAAGAATG
65 TTAATGAGGAGAAACTACTAATATCAGTAGCTAAGAATG
521 A
1 A
522 TGTAATTAGA
Statistics
Matches: 99, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
102 18 0.18
103 2 0.02
104 1 0.01
105 58 0.59
106 20 0.20
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (103 bp):
AAGACTAAAACACCTAAACTTTTCTTTATTATAATTGAACTGACTCCATTAGAGCTTTAGGACAT
TAATGAGGAGAAACTACTAATATCAGTAGCTAAGAATG
Found at i:3759 original size:246 final size:246
Alignment explanation
Indices: 3320--4055 Score: 1032
Period size: 246 Copynumber: 3.0 Consensus size: 246
3310 CTTTTAATTG
* * * ***
3320 ACCTCAGATTCCTTACCAGATGAAGCATTTTCAGTAACC-TTAGAATCTTG-GCCACTCTCATTT
1 ACCTCAGATTCCTTCCCTGATGAAGCATTTTCAGCAACCTTTA-AATC-TGATTTACTCTCATTT
* ** * ** **
3383 GACACTGATAACCCATCCTCTTAGTGATCTTTGGCTTGTCGACGCCTTTGCTTCATCCTTGCAGC
64 GCCACTGATAATTCATGCTCTTCCTGATCTTTGATTTGTCGACGCCTTTGCTTCATCCTTGCAGC
* * * * * *
3448 AATACTGTCTGGGCTATGTTCCATCGCAGAGGCAGGCCT-CTTCTTAACCTTTGGGCTAGTCTCT
129 AATACTGTCTGGGCTATGATCCGTAGCAGAAGCA-GCCTGCTTCTTAAGCTTTGGGCTACTCTCT
* * * *
3512 GAAGCAATATAGCTTTCAGCTTTATTGTCATTAGCATT-GTGCATTTCCTTCTTA
193 GATGCAATATAGCTTTCACCTTTATTGTCATTGGC-TTCATGCATTTCCTTCTTA
* *
3566 ACCTCAGATTCCTTCCCTGATAAAGCATTTTCAGCAACCTTTAAATCTGATTTACTCTCCTTTGC
1 ACCTCAGATTCCTTCCCTGATGAAGCATTTTCAGCAACCTTTAAATCTGATTTACTCTCATTTGC
*
3631 CACTGATAATTCATGTTCTTCCTGATCTTTGATTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
66 CACTGATAATTCATGCTCTTCCTGATCTTTGATTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
* * *
3696 CACTGTCTGGGGTTTGATCCGTAGCAGAAGCAGCCTGCTTCTTAAGCTTTGGGCTACTCTCTGAT
131 TACTGTCTGGGCTATGATCCGTAGCAGAAGCAGCCTGCTTCTTAAGCTTTGGGCTACTCTCTGAT
*
3761 GCAATATAGCCTTCACCTTTATTGTCATTGGCTTCATGCATTTCCTTCTTA
196 GCAATATAGCTTTCACCTTTATTGTCATTGGCTTCATGCATTTCCTTCTTA
* *
3812 ACCTCAGATTCTTTCCCTGATGAAGCATTTTCAGCAACCTTTGAATCTGATTTACTCTCATTTGC
1 ACCTCAGATTCCTTCCCTGATGAAGCATTTTCAGCAACCTTTAAATCTGATTTACTCTCATTTGC
* *
3877 CACTGATAGTTCATGCTCTTCCTGATCTTTGCTTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
66 CACTGATAATTCATGCTCTTCCTGATCTTTGATTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
* * * * *
3942 TACTGTTTGGGCTCTGATACGTAGCAGAAGTAGGCTGCTTCTTAAGCTTTGGGCTACTCTCTGAT
131 TACTGTCTGGGCTATGATCCGTAGCAGAAGCAGCCTGCTTCTTAAGCTTTGGGCTACTCTCTGAT
4007 GCAATATAG-TCTTCACCTTTATTGTCATTGGCTTCATGCATTTCCTTCT
196 GCAATATAGCT-TTCACCTTTATTGTCATTGGCTTCATGCATTTCCTTCT
4056 CTTGGACTAG
Statistics
Matches: 439, Mismatches: 46, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
245 8 0.02
246 428 0.97
247 3 0.01
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (246 bp):
ACCTCAGATTCCTTCCCTGATGAAGCATTTTCAGCAACCTTTAAATCTGATTTACTCTCATTTGC
CACTGATAATTCATGCTCTTCCTGATCTTTGATTTGTCGACGCCTTTGCTTCATCCTTGCAGCAA
TACTGTCTGGGCTATGATCCGTAGCAGAAGCAGCCTGCTTCTTAAGCTTTGGGCTACTCTCTGAT
GCAATATAGCTTTCACCTTTATTGTCATTGGCTTCATGCATTTCCTTCTTA
Found at i:18578 original size:21 final size:21
Alignment explanation
Indices: 18519--18579 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
18509 GCAGTTACAA
* * *
18519 TTTCCACAGCAACAGCAACCG
1 TTTCAACAGCAGCAGCAGCCG
18540 TTTCAACAGCAGCAGCAGCCG
1 TTTCAACAGCAGCAGCAGCCG
*
18561 TTTCAGCAGCAGCAGCAGC
1 TTTCAACAGCAGCAGCAGC
18580 AGCAGCTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.30, C:0.34, G:0.21, T:0.15
Consensus pattern (21 bp):
TTTCAACAGCAGCAGCAGCCG
Found at i:18600 original size:3 final size:3
Alignment explanation
Indices: 18588--18624 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
18578 GCAGCAGCTT
*
18588 CAA CAG CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA C
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA C
18625 TGTTTCTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.35, G:0.03, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:32702 original size:18 final size:16
Alignment explanation
Indices: 32670--32708 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
32660 TTCTTATTTG
32670 AGTTTGTTTTTGAGTC
1 AGTTTGTTTTTGAGTC
*
32686 GGTTTGTTTTTTCGAGTC
1 AGTTTG-TTTTT-GAGTC
32704 AGTTT
1 AGTTT
32709 CGAGTCTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.10, C:0.08, G:0.26, T:0.56
Consensus pattern (16 bp):
AGTTTGTTTTTGAGTC
Done.