Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023210.1 Corchorus olitorius cultivar O-4 contig23243, 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: 76494
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:1279 original size:29 final size:29
Alignment explanation
Indices: 1228--1304 Score: 145
Period size: 29 Copynumber: 2.6 Consensus size: 29
1218 AAGTTCGTGT
1228 TTGAAGACCATTTGAAGATAAATTAGAGAC
1 TTGAAGACCA-TTGAAGATAAATTAGAGAC
1258 TTGAAGACCATTGAAGATAAATTAGAGAC
1 TTGAAGACCATTGAAGATAAATTAGAGAC
1287 TTGAAGACCATTGAAGAT
1 TTGAAGACCATTGAAGAT
1305 TTATTTCAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 37 0.79
30 10 0.21
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (29 bp):
TTGAAGACCATTGAAGATAAATTAGAGAC
Found at i:12418 original size:27 final size:27
Alignment explanation
Indices: 12343--12409 Score: 91
Period size: 26 Copynumber: 2.4 Consensus size: 27
12333 CTCAAGAATT
12343 TTCTCTTACTTTTTTGCGTTTTAAAAAAA
1 TTCTCTTA--TTTTTGCGTTTTAAAAAAA
**
12372 -AATCTTATTTTTGCGTTTTAAAAAAA
1 TTCTCTTATTTTTGCGTTTTAAAAAAA
12398 TTCTCTTATTTT
1 TTCTCTTATTTT
12410 CTGTTTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 19 0.58
27 9 0.27
28 5 0.15
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.54
Consensus pattern (27 bp):
TTCTCTTATTTTTGCGTTTTAAAAAAA
Found at i:17699 original size:21 final size:20
Alignment explanation
Indices: 17675--17723 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
17665 ATAGTTTAGA
* *
17675 TTTAATTTAGTTTGCTTTATT
1 TTTAATTTA-ATTGCCTTATT
*
17696 TTTAGTTTAATTGCCTTATT
1 TTTAATTTAATTGCCTTATT
17716 TTATAATT
1 TT-TAATT
17724 GTTATTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.63
Consensus pattern (20 bp):
TTTAATTTAATTGCCTTATT
Found at i:20314 original size:18 final size:19
Alignment explanation
Indices: 20279--20318 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
20269 TTGAAGATTT
20279 ATTGAAGATAATTTGAAGA
1 ATTGAAGATAATTTGAAGA
*
20298 ATTGAAGATCA-TTGAAGA
1 ATTGAAGATAATTTGAAGA
20316 ATT
1 ATT
20319 ATCTCAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.33
Consensus pattern (19 bp):
ATTGAAGATAATTTGAAGA
Found at i:20930 original size:18 final size:19
Alignment explanation
Indices: 20893--20930 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
20883 AAATTTTAGA
*
20893 TCTATTTTTCTCTTCAAGT
1 TCTAGTTTTCTCTTCAAGT
*
20912 TCTAGTTTT-TCTTCTAGT
1 TCTAGTTTTCTCTTCAAGT
20930 T
1 T
20931 TTTCCTAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.13, C:0.18, G:0.08, T:0.61
Consensus pattern (19 bp):
TCTAGTTTTCTCTTCAAGT
Found at i:30507 original size:23 final size:22
Alignment explanation
Indices: 30453--30507 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
30443 AACACTTTAA
* *
30453 TTCTATTTTCAATTTGTTTTATC
1 TTCTATTTT-TATTTGTTTGATC
*
30476 TTTTATTTTTATTTCGTTTGATC
1 TTCTATTTTTATTT-GTTTGATC
*
30499 TTCTCTTTT
1 TTCTATTTT
30508 CTTGGATTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.13, C:0.13, G:0.05, T:0.69
Consensus pattern (22 bp):
TTCTATTTTTATTTGTTTGATC
Found at i:31731 original size:182 final size:183
Alignment explanation
Indices: 31390--31754 Score: 687
Period size: 182 Copynumber: 2.0 Consensus size: 183
31380 CCTTGTTGAA
*
31390 CAAAGCTAATATTAATATTATCTCTAACCCCTCTAACCCTTATATGAATTGTGATTGGTGTTCAG
1 CAAAGCTAATATTAATACTATCTCTAACCCCTCTAACCCTTATATGAATTGTGATTGGTGTTCAG
31455 AATATCATGATAGTTCTGAGTGTCCACAGTTAGAACAGGCTCAATTCGTTGCTAATACTGGAAGG
66 AATATCATGATAGTTCTGAGTGTCCACAGTTAGAACAGGCTCAATTCGTTGCTAATACTGGAAGG
*
31520 TAGCAAAACAATCCTTACTCCAACACTTACAATCCAAGGATGAGAAATCACCC
131 CAGCAAAACAATCCTTACTCCAACACTTACAATCCAAGGATGAGAAATCACCC
*
31573 CAAAGCTAATATTAATGCTATCTCTAACCCCTCTAACCCTTATATGAATTGTGATTGGTGTTCAG
1 CAAAGCTAATATTAATACTATCTCTAACCCCTCTAACCCTTATATGAATTGTGATTGGTGTTCAG
31638 AATATCATGATAGTT-TGAGTGTCCACAGTTAGAACAGGCTCAATTCGTTGCTAATACTGGAAGG
66 AATATCATGATAGTTCTGAGTGTCCACAGTTAGAACAGGCTCAATTCGTTGCTAATACTGGAAGG
*
31702 CAGCAAAACAATCCTTACTCCAACACTTACAATCCAGGGATGAGAAATCACCC
131 CAGCAAAACAATCCTTACTCCAACACTTACAATCCAAGGATGAGAAATCACCC
31755 TAATTCTTCT
Statistics
Matches: 178, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
182 100 0.56
183 78 0.44
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.28
Consensus pattern (183 bp):
CAAAGCTAATATTAATACTATCTCTAACCCCTCTAACCCTTATATGAATTGTGATTGGTGTTCAG
AATATCATGATAGTTCTGAGTGTCCACAGTTAGAACAGGCTCAATTCGTTGCTAATACTGGAAGG
CAGCAAAACAATCCTTACTCCAACACTTACAATCCAAGGATGAGAAATCACCC
Found at i:43308 original size:32 final size:32
Alignment explanation
Indices: 43214--43316 Score: 107
Period size: 32 Copynumber: 3.2 Consensus size: 32
43204 TTTTTTCGAG
* * **
43214 TTCGGGTCAAATTCAGGTCAGGTCAATTCAGA
1 TTCGGGTCAATTTCAGGTCAGGTTAATTTGGA
* * * **
43246 TTCGGATAAATTTCAGGTCAGATTTTTTTGGA
1 TTCGGGTCAATTTCAGGTCAGGTTAATTTGGA
* *
43278 TTCGGGTCAATTTTAGGTCAGGTTAATTTGGG
1 TTCGGGTCAATTTCAGGTCAGGTTAATTTGGA
43310 TTCGGGT
1 TTCGGGT
43317 TGGATTTTGG
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (32 bp):
TTCGGGTCAATTTCAGGTCAGGTTAATTTGGA
Found at i:50179 original size:7 final size:7
Alignment explanation
Indices: 50167--50199 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
50157 AACAATTAAA
50167 TAAAATT
1 TAAAATT
50174 TAAAATT
1 TAAAATT
50181 TAAAATT
1 TAAAATT
*
50188 CAAAA-T
1 TAAAATT
50194 TAAAAT
1 TAAAAT
50200 ATCTTAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (7 bp):
TAAAATT
Found at i:56133 original size:5 final size:6
Alignment explanation
Indices: 56108--56132 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
56098 CTATATATTC
56108 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
56133 TGCTGGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:58251 original size:511 final size:512
Alignment explanation
Indices: 57283--58302 Score: 1212
Period size: 511 Copynumber: 2.0 Consensus size: 512
57273 CAAAGCATAA
* *
57283 TGATGCACCCAAGGTTGATCATGGACTTGAAGATGACAATGGAGAGCAAGGAAAGGAAGAGGATG
1 TGATGCACCCAAGGTTGATCATGGACTTGAAGATGACAATGGAGAGCAAGAAAAGGAAGAGGAAG
** * * ** * *
57348 GGCTGCAAGGAAGCATGAAGATGCATGGAGATCAACGAGTCATCGATGAGGTTGTAACAATAGCT
66 AACTGCAAGGAAGCATGAAGATGCATGGAGATCAAAGAGTCATCGATAAGCATGTAACAACAGCC
* * * *
57413 AAGAAGGTGTCATTTGATCCATTAAGTATGTCATCGGGTCCTATGACAAGATCAATAGTTAAAAG
131 AAGAAGGTGTCATTCGATCCATTAAGTATGTCATCGGGTCCGATGACAAGAGCAAGAGTTAAAAG
* * * ** * *
57478 GTTCAAGGATACACTTATGGGCCTTATTCGAACTCAAATTGAAGACATGAAGGTCATTGATGTGC
196 ATTCAAGGATACACTCATGGGCCTTATTCGAACTCAAATAGAAGACATGAAGACCATCGAAGTGC
* * ** *
57543 AATTGAAGAGGTTTGGTGATGATTTGAGCAAGCATTCATCCATTGATTCCAAGATCATCACCTTA
261 AATTGAAGAGCTTTGGTGATGATTTGAGCAAGAAGACATCCATCGATTCCAAGATCATCACCTTA
* * * * *
57608 CTTGCAATCGACATGTAGTTGGGCTTGCATAGGTCAATTCGGCCTTCTGTGGGCTTAATTCTATC
326 CTTGCAATCGACATGTAATTGGGCTTGCATAGATCAATTCGGCCTTATGAGGCCTTAATTCTATC
* ** * * *
57673 TTAGATTAGCTTATTTTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTAATTTAGTCCAATCC
391 TTAGATTAGCTTATTTTAAGTTTAGATGACATTAGGGTTGGGCCTTGTTTAACTAAGTCCAATCC
* * * *
57738 TTGTTTAATTTTGTCTT-TTATTTCCTTTTCCTAGTTGGGCTTGGACTAGTTTTACC
456 TTGTTTAATTATGCCTTGTTATTTACTTTTCCTAGTTGGACTTGGACTAGTTTTACC
* * * * *
57794 TGATGCGCCCAAGGTTGATCATGGACTTGAAGATGACGATGGAGAGCATGAAAAGGATGTGGAAG
1 TGATGCACCCAAGGTTGATCATGGACTTGAAGATGACAATGGAGAGCAAGAAAAGGAAGAGGAAG
* **
57859 AACTGCAAGGAAGCATGTAGATGCATGGAGATCATGAAGA-T-ATCGATAAGCATGTTCCAAGCA
66 AACTGCAAGGAAGCATGAAGATGCATGGAGATCA--AAGAGTCATCGATAAGCATGTAACAA-CA
* *
57922 -CCAA-AAGGATGTCATTCGATCCATTAAAG-ATGCTTAT-TGGTCCGATGACAAGAGCAAGAGT
128 GCCAAGAAGG-TGTCATTCGATCCATT-AAGTATG-TCATCGGGTCCGATGACAAGAGCAAGAGT
* * * ** * **
57983 TAAGAGATTCAAGGATGCACTCATGGGCCTTGTTCGAACTCATCTAGATGGTATGAAGACCATCG
190 TAAAAGATTCAAGGATACACTCATGGGCCTTATTCGAACTCAAATAGAAGACATGAAGACCATCG
* * * *
58048 AAGTTCAATTGAAGAGCTTTGGTGATGATTTGGGCAAGAAGACTTCCATCGATTCCAAGCTCATC
255 AAGTGCAATTGAAGAGCTTTGGTGATGATTTGAGCAAGAAGACATCCATCGATTCCAAGATCATC
* * * ** * **
58113 ACTTTGCTTGCAATTGATGTGTAATTGGGCTTG-ATTGCATGTATTCGGCCTTATGAGGCCTT-A
320 ACCTTACTTGCAATCGACATGTAATTGGGCTTGCATAG-ATCAATTCGGCCTTATGAGGCCTTAA
* * * *
58176 TTCTATCTTAGATTAGCTTATCTTTATGTTTAGATGACATTAGGGTTGTGTCTTGTTTGACTAAG
384 TTCTATCTTAGATTAGCTTAT-TTTAAGTTTAGATGACATTAGGGTTGGGCCTTGTTTAACTAAG
* *
58241 TCCAATCCTTGTTTAATTATGCCTTGTTATTTATTTTTCCTAGTTGGACTTGGATTAGTTTT
448 TCCAATCCTTGTTTAATTATGCCTTGTTATTTACTTTTCCTAGTTGGACTTGGACTAGTTTT
58303 CCTTGTCTTT
Statistics
Matches: 423, Mismatches: 77, Indels: 17
0.82 0.15 0.03
Matches are distributed among these distances:
510 29 0.07
511 351 0.83
512 40 0.09
513 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (512 bp):
TGATGCACCCAAGGTTGATCATGGACTTGAAGATGACAATGGAGAGCAAGAAAAGGAAGAGGAAG
AACTGCAAGGAAGCATGAAGATGCATGGAGATCAAAGAGTCATCGATAAGCATGTAACAACAGCC
AAGAAGGTGTCATTCGATCCATTAAGTATGTCATCGGGTCCGATGACAAGAGCAAGAGTTAAAAG
ATTCAAGGATACACTCATGGGCCTTATTCGAACTCAAATAGAAGACATGAAGACCATCGAAGTGC
AATTGAAGAGCTTTGGTGATGATTTGAGCAAGAAGACATCCATCGATTCCAAGATCATCACCTTA
CTTGCAATCGACATGTAATTGGGCTTGCATAGATCAATTCGGCCTTATGAGGCCTTAATTCTATC
TTAGATTAGCTTATTTTAAGTTTAGATGACATTAGGGTTGGGCCTTGTTTAACTAAGTCCAATCC
TTGTTTAATTATGCCTTGTTATTTACTTTTCCTAGTTGGACTTGGACTAGTTTTACC
Found at i:60056 original size:68 final size:68
Alignment explanation
Indices: 59947--60085 Score: 278
Period size: 68 Copynumber: 2.0 Consensus size: 68
59937 ACTATCAATA
59947 GTGATTAGAGGGTCGGCCAAACCCACATAGTTGTGTGCAAACACGAGTGCAAATTGTGGTAAACA
1 GTGATTAGAGGGTCGGCCAAACCCACATAGTTGTGTGCAAACACGAGTGCAAATTGTGGTAAACA
60012 CGT
66 CGT
60015 GTGATTAGAGGGTCGGCCAAACCCACATAGTTGTGTGCAAACACGAGTGCAAATTGTGGTAAACA
1 GTGATTAGAGGGTCGGCCAAACCCACATAGTTGTGTGCAAACACGAGTGCAAATTGTGGTAAACA
60080 CGT
66 CGT
60083 GTG
1 GTG
60086 TGTGTGGGGG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (68 bp):
GTGATTAGAGGGTCGGCCAAACCCACATAGTTGTGTGCAAACACGAGTGCAAATTGTGGTAAACA
CGT
Found at i:67812 original size:4 final size:4
Alignment explanation
Indices: 67803--67828 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
67793 TCCTCTTACA
67803 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
67829 CCTGCAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:68314 original size:26 final size:27
Alignment explanation
Indices: 68278--68332 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 27
68268 TTCAAATGTT
*
68278 AAGACATCATGAAGAAGTCAC-GTTGC
1 AAGACATCATGAAGAAGCCACGGTTGC
68304 AAGACATCATGAAGAAGCCACGGTTGC
1 AAGACATCATGAAGAAGCCACGGTTGC
68331 AA
1 AA
68333 ACTGCACCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 20 0.74
27 7 0.26
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (27 bp):
AAGACATCATGAAGAAGCCACGGTTGC
Found at i:73822 original size:16 final size:16
Alignment explanation
Indices: 73801--73835 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
73791 AGATGTCCTT
73801 CGATGACCTCCTTTGA
1 CGATGACCTCCTTTGA
**
73817 CGATGATTTCCTTTGA
1 CGATGACCTCCTTTGA
73833 CGA
1 CGA
73836 CCTGAAGCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (16 bp):
CGATGACCTCCTTTGA
Found at i:76431 original size:18 final size:17
Alignment explanation
Indices: 76405--76438 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
76395 ATTTTGTCTC
76405 ACATGAGCATGGCAATTA
1 ACATGAGCATGG-AATTA
*
76423 ACATTAGCATGGAATT
1 ACATGAGCATGGAATT
76439 CAAACATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (17 bp):
ACATGAGCATGGAATTA
Done.