Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016267.1 Corchorus olitorius cultivar O-4 contig16300, 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: 50407
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:403 original size:49 final size:47
Alignment explanation
Indices: 326--466 Score: 151
Period size: 49 Copynumber: 2.9 Consensus size: 47
316 CAAGCAATCA
* *
326 TTTACTTTTCACTGCACTTTTTATCAATTTTTACTACAAAATTGAACT
1 TTTAATTTTCATTGCACTTTTTATCAATTTTTA-TACAAAATTGAACT
* * * * *
374 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTAAAGACAAAATTGATCT
1 TTTAATTTTCA-TTGCA-CTTTTTATCAATTTT-TATACAAAATTGAACT
*
423 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTTAATTTTCATTGCACTTTTTATCAATTTTTAT-ACAAAATTGA
467 TTGGCACGCT
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
47 15 0.20
48 21 0.28
49 33 0.43
50 7 0.09
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.50
Consensus pattern (47 bp):
TTTAATTTTCATTGCACTTTTTATCAATTTTTATACAAAATTGAACT
Found at i:13380 original size:32 final size:31
Alignment explanation
Indices: 13329--13390 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
13319 GTTTTTTTTC
*
13329 TTTTTTTTTTGCAATAAAACTTATCACAAGA
1 TTTTTTTTTTGCAATAAAACTCATCACAAGA
13360 TTTTTTTTTTGGC-ATCAAAACTCATCACAAG
1 TTTTTTTTTT-GCAAT-AAAACTCATCACAAG
13391 TTTATAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (31 bp):
TTTTTTTTTTGCAATAAAACTCATCACAAGA
Found at i:14417 original size:35 final size:35
Alignment explanation
Indices: 14378--14449 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
14368 AGGAAAACAG
14378 AACTAGAATGTTAATAGTTTACCCATGAAAGAGTC
1 AACTAGAATGTTAATAGTTTACCCATGAAAGAGTC
14413 AACTAGAATGTTAATAGTTTACCCATGAAAGAGTC
1 AACTAGAATGTTAATAGTTTACCCATGAAAGAGTC
14448 AA
1 AA
14450 ATGATGTAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (35 bp):
AACTAGAATGTTAATAGTTTACCCATGAAAGAGTC
Found at i:26584 original size:3 final size:3
Alignment explanation
Indices: 26576--26613 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
26566 CGTTAACACC
*
26576 CTT CTT CTT CTT CGT CTGT -TT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CT
26614 CTTTCGCCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 29 0.94
4 1 0.03
ACGTcount: A:0.00, C:0.32, G:0.05, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:30238 original size:2 final size:2
Alignment explanation
Indices: 30227--30270 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
30217 ATAATTGAAG
*
30227 AT AT AT -T AT AT A- AT AT A- AT AT A- AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30265 AT AT AT
1 AT AT AT
30271 GGCCTAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
1 4 0.11
2 32 0.89
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30263 original size:8 final size:8
Alignment explanation
Indices: 30227--30270 Score: 51
Period size: 7 Copynumber: 6.0 Consensus size: 8
30217 ATAATTGAAG
30227 ATATAT-T
1 ATATATAT
30234 ATATA-AT
1 ATATATAT
30241 ATA-ATAT
1 ATATATAT
30248 A-ATATAT
1 ATATATAT
*
30255 ATGTATAT
1 ATATATAT
30263 ATATATAT
1 ATATATAT
30271 GGCCTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
6 2 0.06
7 17 0.55
8 12 0.39
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (8 bp):
ATATATAT
Found at i:31878 original size:22 final size:22
Alignment explanation
Indices: 31845--31891 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
31835 TTAAGTGAAT
*
31845 AAAAATATTTTTTAATTA-TTA
1 AAAAATAATTTTTAATTACTTA
31866 AAAAAGTAATTTTTAATTACTTA
1 AAAAA-TAATTTTTAATTACTTA
31889 AAA
1 AAA
31892 TAAAAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 12 0.52
23 6 0.26
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
AAAAATAATTTTTAATTACTTA
Found at i:31911 original size:18 final size:17
Alignment explanation
Indices: 31888--31931 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
31878 TTAATTACTT
*
31888 AAAATAAAAAAGAAAACG
1 AAAATAAAAAA-AAAAAG
31906 AAAATAAATAAAAAAAAG
1 AAAATAAA-AAAAAAAAG
31924 AAAA-AAAA
1 AAAATAAAA
31932 GTAACAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 1 0.04
17 3 0.12
18 17 0.71
19 3 0.12
ACGTcount: A:0.84, C:0.02, G:0.07, T:0.07
Consensus pattern (17 bp):
AAAATAAAAAAAAAAAG
Found at i:33606 original size:16 final size:16
Alignment explanation
Indices: 33585--33618 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
33575 TCTTTTCTGG
33585 TTAAATTAAATT-AATT
1 TTAAA-TAAATTAAATT
33601 TTAAATAAATTAAATT
1 TTAAATAAATTAAATT
33617 TT
1 TT
33619 TTTTCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATAAATTAAATT
Found at i:33622 original size:20 final size:21
Alignment explanation
Indices: 33586--33627 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
33576 CTTTTCTGGT
33586 TAAATTAAATTAATTTT-AAA
1 TAAATTAAATTAATTTTCAAA
**
33606 TAAATTAAATTTTTTTTCAAA
1 TAAATTAAATTAATTTTCAAA
33627 T
1 T
33628 TTTTACTGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTAAATTAATTTTCAAA
Found at i:33776 original size:29 final size:31
Alignment explanation
Indices: 33709--33778 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 31
33699 ATAGACGGTC
* * *
33709 TACCCCAAATTGACGCGAATTGAAAACGTTT
1 TACCCCAAATAGACGCAAATTGAAAACGTTG
*
33740 TGA-TCCAAATAGAC-CAAATTG-AAACGTTG
1 T-ACCCCAAATAGACGCAAATTGAAAACGTTG
33769 TACCCCAAAT
1 TACCCCAAAT
33779 TAAGCCGACT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 1 0.03
29 14 0.44
30 6 0.19
31 10 0.31
32 1 0.03
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (31 bp):
TACCCCAAATAGACGCAAATTGAAAACGTTG
Found at i:50377 original size:2 final size:2
Alignment explanation
Indices: 50370--50397 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
50360 AAGACAGTGA
50370 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
50398 GTAGGTTAAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.