Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009782.1 Corchorus olitorius cultivar O-4 contig09814, 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: 9122
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:719 original size:205 final size:201
Alignment explanation
Indices: 371--781 Score: 714
Period size: 205 Copynumber: 2.0 Consensus size: 201
361 GCTTAATAAC
*
371 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTAAATAAG
* *
436 ATACAACACATTATTATTATATATAAAACTATACCAAAAAAATTTAGTTGAACATTAGTGGTTGA
66 ATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGA
*
501 TTTATTAAATTAAATTAGATCAATGTCAAACAAATTTTCAAAATTATAAAAGATATTAAAGATCC
131 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
566 GATTTA
196 GATTTA
* *
572 TTTATCAATGGTGAATGTTATTAATTTTTTCAAGTCTAAGGTTACTATCAAAGTTGTAGTAAATA
1 TTTATCAATGGTGAATGTTATTAA-TTTTT-AAGTCTAAGATTACTAACAAAGTTGTAGTAAATA
637 AGATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGG
64 AGATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAATTAGTTGAACATTAGTGG
702 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAG
127 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAG
*
767 ATTCGATTTA
192 ATCCGATTTA
*
777 CTTAT
1 TTTAT
782 TATTAAGGAA
Statistics
Matches: 198, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
201 24 0.12
202 5 0.03
203 57 0.29
204 1 0.01
205 111 0.56
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (201 bp):
TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTAAATAAG
ATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGA
TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
GATTTA
Found at i:1484 original size:45 final size:45
Alignment explanation
Indices: 1422--1518 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
1412 AGTGCATTAC
* * * *
1422 CTAA-ATTCTAGTACTCCATTTCTAGGTAATTCATTAAAATAAAA
1 CTAATATTCTACTACTCCATCTCTAGATAATTCATCAAAATAAAA
*
1466 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTACTACTCCATCTCTAGATAATTCATCAAAATAAAA
1511 CTAATATT
1 CTAATATT
1519 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.36
Consensus pattern (45 bp):
CTAATATTCTACTACTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:4410 original size:22 final size:22
Alignment explanation
Indices: 4382--4556 Score: 112
Period size: 22 Copynumber: 7.9 Consensus size: 22
4372 TGTCTCTGTG
4382 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
4404 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
4427 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
4448 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
*
4471 -AGTTATCAAAATTTCATGGAA-A
1 TGGTTATCAAAATTTCAT--AAGA
* *
4493 T-GTTATAAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
4514 TGGTTATTAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
4536 TCAGGTTAT-AGAAATTTCATA
1 T--GGTTATCA-AAATTTCATA
4557 GTGTGATTAT
Statistics
Matches: 118, Mismatches: 20, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 1 0.01
22 92 0.78
23 5 0.04
24 18 0.15
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:4485 original size:66 final size:66
Alignment explanation
Indices: 4379--4555 Score: 189
Period size: 66 Copynumber: 2.7 Consensus size: 66
4369 TCTTGTCTCT
* * * * *
4379 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCAT-GAGGAGGTTATCAAAATTCCA
1 GTGTGGTTATCAAAATTTCATAAGATAGTTATCAAAATTTCATGGA-AAGGTTATAAAAATTCCA
4443 TA
65 TA
* * * *
4445 GTGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATGGAAATGTTATAAAAATTTCA
1 GTGTGGTTATCAAAATTTCATA-AGATAGTTATCAAAATTTCATGGAAAGGTTATAAAAATTCCA
4509 TA
65 TA
* *
4511 GTGTGGTTATTAAAATTTCATAGGATCAGGTTAT-AGAAATTTCAT
1 GTGTGGTTATCAAAATTTCATAAGAT-A-GTTATCA-AAATTTCAT
4556 AGTGTGATTA
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
65 3 0.03
66 71 0.76
67 6 0.06
68 14 0.15
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (66 bp):
GTGTGGTTATCAAAATTTCATAAGATAGTTATCAAAATTTCATGGAAAGGTTATAAAAATTCCAT
A
Found at i:4504 original size:44 final size:46
Alignment explanation
Indices: 4379--4588 Score: 174
Period size: 44 Copynumber: 4.7 Consensus size: 46
4369 TCTTGTCTCT
* * *
4379 GTGTGGTTATCAAAATTTCATAAGAT--GGTTATTATAATTTCATGA
1 GTGTGGTTATCAAAATTTCATAGGATAAGGTTATAAAAATTTCAT-A
* * **
4424 G-GAGGTTATCAAAATTCCATAGTG-T--GGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATAG-GATAAGGTTATAAAAATTTCATA
*
4467 -TG-GAAGTTATCAAAATTTCAT-GGA-AATGTTATAAAAATTTCATA
1 GTGTG--GTTATCAAAATTTCATAGGATAAGGTTATAAAAATTTCATA
* * *
4511 GTGTGGTTATTAAAATTTCATAGGATCAGGTTATAGAAATTTCATA
1 GTGTGGTTATCAAAATTTCATAGGATAAGGTTATAAAAATTTCATA
* * *
4557 GTGTGATTATCACAATTTTATA-GA-AAGGTTAT
1 GTGTGGTTATCAAAATTTCATAGGATAAGGTTAT
4589 CAAAGAGATT
Statistics
Matches: 135, Mismatches: 19, Indels: 23
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.01
43 3 0.02
44 85 0.63
45 9 0.07
46 36 0.27
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (46 bp):
GTGTGGTTATCAAAATTTCATAGGATAAGGTTATAAAAATTTCATA
Found at i:4622 original size:22 final size:22
Alignment explanation
Indices: 4597--5534 Score: 262
Period size: 22 Copynumber: 42.5 Consensus size: 22
4587 ATCAAAGAGA
* *
4597 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
4619 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* *
4641 TTAACAAAATTTTATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* *
4663 TTA-CTAATATTTCATAGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
*
4685 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* * *
4707 TTATTAAAATTT-TTAAGTGTGG
1 TTATCAAAATTTCAT-AGTGAGG
4729 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
4751 TTAT-AAAAGTCTTAATTTCA-TAAGG
1 TTATCAAAA-T-TTCA--T-AGTGAGG
* * * *
4776 AGTA-C-CAATTTGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
* * * *
4796 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
4817 TTATCGAAATTTCATAGAGATTGG
1 TTATCAAAATTTCATAGTGA--GG
*
4841 ATTATCAAAATTT-ATAG-GAAGA
1 -TTATCAAAATTTCATAGTG-AGG
**
4863 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* * *
4885 TTATCAAAATCTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * **
4907 TTATCAAAATTACATAATGAAA
1 TTATCAAAATTTCATAGTGAGG
* *
4929 ATATCCAAAAATTTCAGAG-G-GG
1 TTAT-C-AAAATTTCATAGTGAGG
* * * *
4951 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGTGAGG
**
4973 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
4995 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
*
5017 TTACCAAAATTTCATAGT--GG
1 TTATCAAAATTTCATAGTGAGG
* * *
5037 TATTTCTAGGGAAGTTATCA-A---A-A
1 T-TATC-A---AAATT-TCATAGTGAGG
* *
5060 TT-TCATAGTATGGTTACCAAATTAG-GAAGC
1 TTATCA-A-AAT--TT--C--A-TAGTG-AGG
* * *
5090 TTATTAAACTTTTACTA-T-AGAG
1 TTATCAAAATTTCA-TAGTGAG-G
* *
5112 TAATCAAAATTTC--AGTGAGA
1 TTATCAAAATTTCATAGTGAGG
*
5132 ATATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
*
5154 TTATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATAG-TGAGG
* * *
5176 TTCTCAAAATTTTATA-AGAGGG
1 TTATCAAAATTTCATAGTGA-GG
* *
5198 TTATCAAAATTTCATA-TTATG
1 TTATCAAAATTTCATAGTGAGG
* *
5219 TAGATCAAAATTTCATAAG-GAGA
1 T-TATCAAAATTTCAT-AGTGAGG
** *
5242 TTAAGAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
5264 TTATCACAAA-ATCATAGGGAGG
1 TTATCA-AAATTTCATAGTGAGG
5286 TTATCAAAA-TT--T-GT-A-G
1 TTATCAAAATTTCATAGTGAGG
*
5302 TTATCAAGATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* *
5324 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
5346 TTTATCAAAATTTTATAGCGAGG
1 -TTATCAAAATTTCATAGTGAGG
* *
5369 TTATCACAATTTCATAGTGTA-A
1 TTATCAAAATTTCATAGTG-AGG
* *
5391 TTATCAAAATTTCAGAGTGTA-A
1 TTATCAAAATTTCATAGTG-AGG
5413 TTA-CTAACAA-TTCATA-TGGAGG
1 TTATC-AA-AATTTCATAGT-GAGG
* * * ** *
5435 TTTTTAAATTTTCATAACGTGG
1 TTATCAAAATTTCATAGTGAGG
* *
5457 TTATCAATATATCATA-TGGAGG
1 TTATCAAAATTTCATAGT-GAGG
* * *
5479 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAGTG-AGG
5502 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
5524 TCT-TCAAAATT
1 T-TATCAAAATT
5535 CCTTAAGGAG
Statistics
Matches: 676, Mismatches: 152, Indels: 176
0.67 0.15 0.18
Matches are distributed among these distances:
16 9 0.01
17 3 0.00
18 2 0.00
19 6 0.01
20 41 0.06
21 59 0.09
22 427 0.63
23 72 0.11
24 18 0.03
25 22 0.03
26 8 0.01
27 2 0.00
29 2 0.00
30 3 0.00
31 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:5335 original size:82 final size:83
Alignment explanation
Indices: 5222--5380 Score: 196
Period size: 82 Copynumber: 1.9 Consensus size: 83
5212 TATTATGTAG
* * *
5222 ATCAAAATTTCATAAGGAGATTAAGAAAATTTCATAATGAGG-TTATCACAAA-ATCATAGGGAG
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCA-AAATATCATAGCGAG
5285 GTTATCAAAATTTGTAGTT
65 GTTATCAAAATTTGTAGTT
* * * * * * *
5304 ATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGCGAGG
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAATATCATAGCGAGG
*
5369 TTATCACAATTT
66 TTATCAAAATTT
5381 CATAGTGTAA
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
82 38 0.59
83 26 0.41
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.34
Consensus pattern (83 bp):
ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAATATCATAGCGAGG
TTATCAAAATTTGTAGTT
Found at i:6124 original size:9 final size:9
Alignment explanation
Indices: 6112--6143 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
6102 GGGTCAGATT
6112 GGTTGGATG
1 GGTTGGATG
6121 GGTTGGATG
1 GGTTGGATG
*
6130 GGTTGGACG
1 GGTTGGATG
6139 GGTTG
1 GGTTG
6144 AACGGGTCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.09, C:0.03, G:0.56, T:0.31
Consensus pattern (9 bp):
GGTTGGATG
Found at i:6150 original size:18 final size:18
Alignment explanation
Indices: 6112--6150 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6102 GGGTCAGATT
* * *
6112 GGTTGGATGGGTTGGATG
1 GGTTGGACGGGTTGAACG
6130 GGTTGGACGGGTTGAACG
1 GGTTGGACGGGTTGAACG
6148 GGT
1 GGT
6151 CGGATGCATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.05, G:0.54, T:0.28
Consensus pattern (18 bp):
GGTTGGACGGGTTGAACG
Found at i:7068 original size:16 final size:16
Alignment explanation
Indices: 7047--7090 Score: 63
Period size: 16 Copynumber: 2.7 Consensus size: 16
7037 AAAGAAAAAC
7047 TAAATTTTTATATTTA
1 TAAATTTTTATATTTA
7063 TAAATTATTTA-ATTTA
1 TAAATT-TTTATATTTA
7079 TCAAATTTTTAT
1 T-AAATTTTTAT
7091 TTAATTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TAAATTTTTATATTTA
Found at i:7113 original size:20 final size:20
Alignment explanation
Indices: 7067--7104 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
7057 TATTTATAAA
7067 TTATTTAATTTATCAAATTT
1 TTATTTAATTTATCAAATTT
7087 TTATTTAA-TTA-CAAATTT
1 TTATTTAATTTATCAAATTT
7105 CCTTATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 8 0.44
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTTAATTTATCAAATTT
Done.