Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020689.1 Corchorus olitorius cultivar O-4 contig20722, 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: 17112
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:1343 original size:21 final size:19
Alignment explanation
Indices: 1318--1375 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
1308 GCTGCTCTAA
1318 TAATCTCATCTGTACAATACC
1 TAATCTCATCTGTACAAT--C
* * *
1339 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAATC
1358 TAATCTCATCTGTACAAT
1 TAATCTCATCTGTACAAT
1376 TGCCAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAATC
Found at i:3007 original size:23 final size:23
Alignment explanation
Indices: 2962--3008 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2952 GTACATATAG
*
2962 AAATCCAGTGAAACTCCTTAAAA
1 AAATCCAGTGAAACTCCTAAAAA
2985 AAATCCAGTGAAACATCC-AAAAA
1 AAATCCAGTGAAAC-TCCTAAAAA
3008 A
1 A
3009 TATTTAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.53, C:0.21, G:0.09, T:0.17
Consensus pattern (23 bp):
AAATCCAGTGAAACTCCTAAAAA
Found at i:3056 original size:26 final size:26
Alignment explanation
Indices: 3020--3093 Score: 148
Period size: 26 Copynumber: 2.8 Consensus size: 26
3010 ATTTAACCAA
3020 AAAAAAATCCAGTGAAGATTTTCCTC
1 AAAAAAATCCAGTGAAGATTTTCCTC
3046 AAAAAAATCCAGTGAAGATTTTCCTC
1 AAAAAAATCCAGTGAAGATTTTCCTC
3072 AAAAAAATCCAGTGAAGATTTT
1 AAAAAAATCCAGTGAAGATTTT
3094 ACTATGTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (26 bp):
AAAAAAATCCAGTGAAGATTTTCCTC
Found at i:4536 original size:12 final size:12
Alignment explanation
Indices: 4519--4543 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4509 TCAGCTTTAA
4519 GTGTTGGGGTTG
1 GTGTTGGGGTTG
4531 GTGTTGGGGTTG
1 GTGTTGGGGTTG
4543 G
1 G
4544 CCTTGGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (12 bp):
GTGTTGGGGTTG
Found at i:13533 original size:430 final size:436
Alignment explanation
Indices: 12592--13655 Score: 1279
Period size: 431 Copynumber: 2.4 Consensus size: 436
12582 CATCTGGATA
* * * ** * ** *
12592 AAAAAAATATATGAAATTAAATAGATTATCAATCGAAATCACAAAATTTCAAAAGTATTTTTTAG
1 AAAAAATTATACGATATTAAATAGACCAACAATCGAAATCA-AAAATTTCGGAAGCATTTTTTAG
* * * * * *
12657 AATTTAAACATGAAAATTAGCTTTTGAGTCTTTCATGAAAGAGTTGTAGATAATAAAATAACTTT
65 AATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATG-AA-AGTTGTAGATCATGAAATAACCTT
* *** * * *
12722 TTAATAGACACTTGAATTACCTTAATAACACAAATAGAACAAAGAAAATAAAAAATGAAGTGTTA
128 TTAATAGACACTTGAATCACCTTAATCGGACAAATAGAACAAAGAATA-AAAAAAT-AAATCTTA
*
12787 AATCGAGTAAGATAGAATTTGTAAAGAACTAAGTAGTATAAAATGTATAAAATAGAAAAGTATGA
191 AAT--AGTAAGATAGAATTTGTAAAGAACTAAG-AG-AT--AATGTATAAAATAGAAAAATATGA
* * * * *
12852 GGGTCATTTGATAACTAATTCAAATAAGAAATTATTTCTTAATGGATATCTTGAAACATAAAAAT
250 GGGTCATTTAATAAATAATCCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAAAT
* * *
12917 TCCCTTTTGAACCCTTCATGAAACTCGTAGCTCAAATTAACTTTCGGGTTCTTCATGAAAGTCGT
315 TCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTCCTTCAAGAAAGTCGT
* * * * *
12982 AGATCATACAGTAACCTTTTAACCGACACTTGAATAACTTTAATCGGACATGTGGAT
380 AAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATGTGGAC
* * * *
13039 AGAAAATTATATGGTATTAAATAGACCAACAATCGAAA-CAACCAAATTTAGGAAGCATTTTTTT
1 AAAAAATTATACGATATTAAATAGACCAACAATCGAAATCAA--AAATTTCGGAAGCA-TTTTTT
* * *
13103 A-AATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCACGAAATTACCTT
63 AGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATAACCTT
* *
13167 TTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAGAATAAAAAAATAAATCTTAAA
128 TTAATAGACACTTGAATCACCTTAATCGGACAAATAGAACAAAGAATAAAAAAATAAATCTTAAA
*
13232 T-G-AAGATAGAATTTGTAAAGAACT-A-AG-T-A-GTATAAAATAGAAAAATATGAGGGTTATT
193 TAGTAAGATAGAATTTGTAAAGAACTAAGAGATAATGTATAAAATAGAAAAATATGAGGGTCATT
* * *
13290 TAATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCAT-AAAATCTCCCTTT
258 TAATAAATAATCCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAAAT-TCCCTTT
* * *
13354 TGAGCCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGGGTCCTTCAAGAAAGTCGTAAATGA
322 TGAACCCTTCATGAAACTCGTAGATCAAA-TTAACTTTCGGGTCCTTCAAGAAAGTCGTAAATCA
* * * *
13419 TACAATAACCTTTTAACTGACATTTCAATAACTTCAATCGGATATGTGGGC
386 TACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATGTGGAC
* ** *
13470 AAAAAATTATACGATATTAAATTGACCGGCAATCAAAATCATAAAATTTCGGAAGCATTTTTTAG
1 AAAAAATTATACGATATTAAATAGACCAACAATCGAAATCA-AAAATTTCGGAAGCATTTTTTAG
* * * * * *
13535 AATCAAAACATTAAAATTGGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAATCACCTTTT
65 AATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATAACCTTTT
*
13600 AATAGACACTTGAATCACCTTAATCGGACAAATAGGAA-AAA-AATACAAAAATAAAT
130 AATAGACACTTGAATCACCTTAATCGGACAAATA-GAACAAAGAATAAAAAAATAAAT
13656 GCGAACGCGT
Statistics
Matches: 536, Mismatches: 72, Indels: 35
0.83 0.11 0.05
Matches are distributed among these distances:
429 5 0.01
430 125 0.23
431 211 0.39
432 5 0.01
433 1 0.00
434 1 0.00
436 2 0.00
438 1 0.00
439 22 0.04
440 1 0.00
443 9 0.02
444 7 0.01
445 61 0.11
446 4 0.01
447 74 0.14
448 7 0.01
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.31
Consensus pattern (436 bp):
AAAAAATTATACGATATTAAATAGACCAACAATCGAAATCAAAAATTTCGGAAGCATTTTTTAGA
ATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATAACCTTTTA
ATAGACACTTGAATCACCTTAATCGGACAAATAGAACAAAGAATAAAAAAATAAATCTTAAATAG
TAAGATAGAATTTGTAAAGAACTAAGAGATAATGTATAAAATAGAAAAATATGAGGGTCATTTAA
TAAATAATCCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAA
CCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTCCTTCAAGAAAGTCGTAAATCATACAA
TAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATGTGGAC
Found at i:14176 original size:31 final size:31
Alignment explanation
Indices: 14138--14199 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
14128 GAGTTTTGTA
*
14138 AAACTTTTGAA-CTGCCTATTATATCCTTATT
1 AAACTTTTGAATC-GCCTATTATACCCTTATT
14169 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATTATACCCTTATT
14200 TTTTGAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATTATACCCTTATT
Found at i:14394 original size:93 final size:93
Alignment explanation
Indices: 14235--14419 Score: 307
Period size: 93 Copynumber: 2.0 Consensus size: 93
14225 TTGTTTAAAT
* *
14235 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTA
* *
14300 TTTTATTTTTACCATTTTACTATTTTAC
66 TTTTATTTTTACCATATTACTAATTTAC
* *
14328 TTTTATGGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTA
*
14393 TTTTATTTTTACGATATTACTAATTTA
66 TTTTATTTTTACCATATTACTAATTTA
14420 ATTAAAAAGT
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 85 1.00
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTA
TTTTATTTTTACCATATTACTAATTTAC
Found at i:15586 original size:16 final size:16
Alignment explanation
Indices: 15565--15595 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15555 TTGACCTCAG
15565 GTCATTCGGGTTTTGA
1 GTCATTCGGGTTTTGA
*
15581 GTCATTTGGGTTTTG
1 GTCATTCGGGTTTTG
15596 GGTTTTTCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.32, T:0.48
Consensus pattern (16 bp):
GTCATTCGGGTTTTGA
Found at i:15617 original size:508 final size:507
Alignment explanation
Indices: 14698--15714 Score: 1793
Period size: 508 Copynumber: 2.0 Consensus size: 507
14688 TAAGCTGTCC
*
14698 AATCATTAATTATTCATTTTTTAAAAATAATTAAGTTAAAATTTATTGAAAATTTAATTATTGTG
1 AATCATTAATTATTCATTTTTTAAAAATAATTAAGTTAAAATTTATTGAAAATTTAATCATTGTG
* *
14763 ATTGATCTTTTCTATTTTTAGAGTGTTTGTTGGTAGTTTAATGTATTGGAGTGTATGACAAGAAT
66 ATTGATCTTTTCTATTTTTAAAGTGTTTGTTGGTAGTTTAATGTATTGGAGTGTATGAAAAGAAT
**
14828 TTAAAGTTTTTTTTTTTTTAAAAAAAAGAGTAACATGCAATTATTTCCTTTGACTTATAAGGTTA
131 TTAAAGTTTTTTTTTTTGAAAAAAAAAGAGTAACATGCAATTATTTCCTTTGACTTATAAGGTTA
* *
14893 GAGGAGTCAATTGGGCGGGTTGGACGGATTTCGGGTTCAGGTCATTAGGGTTTAGCTCAAATGAG
196 GACGAGTCAATTGGGCGGGTTGGACGGATTTCAGGTTCAGGTCATTAGGGTTTAGCTCAAATGAG
14958 TCAAGTAATTTTCTCGGGTCATTCGGATTTCGGATCATCTAAGTTCAGGTCATTCGACTCTCAAG
261 TCAAGTAATTTTCTCGGGTCATTCGGATTTCGGATCATCTAAGTTCAGGTCATTCGACTCTCAAG
* *
15023 TCTAAGGTCAGGCGGGTTCGAGTTTTGGCCTCAGGTCACTCGAGTTTTGGGTCATTTGGGTTTTG
326 TCTAAGGTCAGGCGGGTTCGAGTTTTGACCTCAGGTCACTCGAGTTTTGAGTCATTTGGGTTTTG
15088 GATTTTTCGGCTCTATGACTCGGATCAATTGGGTCAGTCTTGAATCTTTTAATGTTTAATTCTTA
391 GATTTTTCGGCTCTATGACTCGGATCAATTGGGTCAGTCTTGAATCTTTTAATGTTTAATTCTTA
*
15153 AATTTATTTAATATCTTTATTATTCGATTTATTTTACAATTGACTACCGATG
456 AATTTATTTAATATCTTTATTATTCGATTTATTTTACAATCGACTACCGATG
*
15205 AATCATTAATTATTCATTTTTTAAAAATAATTAATTTAAAATTTATTGAAAATTTAATCATTGTG
1 AATCATTAATTATTCATTTTTTAAAAATAATTAAGTTAAAATTTATTGAAAATTTAATCATTGTG
15270 ATTGATCTTTTTCTATTTTTAAAGTGTTTGTTGGTAGTTTAATGTATTGGAGTGTATGAAAAGAA
66 ATTGATC-TTTTCTATTTTTAAAGTGTTTGTTGGTAGTTTAATGTATTGGAGTGTATGAAAAGAA
15335 TTTAAAGTTTTTTTTTTTAGAAAAAAAAAGAGTAACATGCAATTATTTCCTTTGACTTATAAGGT
130 TTTAAAGTTTTTTTTTTT-GAAAAAAAAAGAGTAACATGCAATTATTTCCTTTGACTTATAAGGT
*** * *
15400 TAG-CTTTTCAATTGGGCGGGTTGGGCGGGTTTCAGGTTCAGGTCATTAGGGTTTAGCTCAAATG
194 TAGACGAGTCAATTGGGCGGGTTGGACGGATTTCAGGTTCAGGTCATTAGGGTTTAGCTCAAATG
* * *
15464 AGTCAGGTAATTTTCTCGGGTCATTCGGATTTCGGATCATCTAGGTTCAGGTCATTCGGCTCTCA
259 AGTCAAGTAATTTTCTCGGGTCATTCGGATTTCGGATCATCTAAGTTCAGGTCATTCGACTCTCA
* *
15529 AGTCTAAGGTCAGGCGGGTTCGAGTTTTGACCTCAGGTCATTCGGGTTTTGAGTCATTTGGGTTT
324 AGTCTAAGGTCAGGCGGGTTCGAGTTTTGACCTCAGGTCACTCGAGTTTTGAGTCATTTGGGTTT
* *
15594 TGGGTTTTTCGGCTCTATGACTCGGATCAATTGGGTCAGTCTTGAATTTTTTAATGTTTAATTCT
389 TGGATTTTTCGGCTCTATGACTCGGATCAATTGGGTCAGTCTTGAATCTTTTAATGTTTAATTCT
*
15659 TAAATTTATTTAATATCTTTATTATTGGATTTATTTTACAATCGACTACCGATG
454 TAAATTTATTTAATATCTTTATTATTCGATTTATTTTACAATCGACTACCGATG
15713 AA
1 AA
15715 GTTTAGCAAA
Statistics
Matches: 484, Mismatches: 24, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
507 70 0.14
508 367 0.76
509 47 0.10
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (507 bp):
AATCATTAATTATTCATTTTTTAAAAATAATTAAGTTAAAATTTATTGAAAATTTAATCATTGTG
ATTGATCTTTTCTATTTTTAAAGTGTTTGTTGGTAGTTTAATGTATTGGAGTGTATGAAAAGAAT
TTAAAGTTTTTTTTTTTGAAAAAAAAAGAGTAACATGCAATTATTTCCTTTGACTTATAAGGTTA
GACGAGTCAATTGGGCGGGTTGGACGGATTTCAGGTTCAGGTCATTAGGGTTTAGCTCAAATGAG
TCAAGTAATTTTCTCGGGTCATTCGGATTTCGGATCATCTAAGTTCAGGTCATTCGACTCTCAAG
TCTAAGGTCAGGCGGGTTCGAGTTTTGACCTCAGGTCACTCGAGTTTTGAGTCATTTGGGTTTTG
GATTTTTCGGCTCTATGACTCGGATCAATTGGGTCAGTCTTGAATCTTTTAATGTTTAATTCTTA
AATTTATTTAATATCTTTATTATTCGATTTATTTTACAATCGACTACCGATG
Found at i:16512 original size:26 final size:29
Alignment explanation
Indices: 16483--16552 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
16473 TTGGGTTTGT
16483 AAACTCAAATTTATGG-T-TGGC-AAAAA
1 AAACTCAAATTTATGGTTCTGGCAAAAAA
16509 AAACTCAAATTTATGGTTCTGGCAAAAAA
1 AAACTCAAATTTATGGTTCTGGCAAAAAA
16538 AAACTCAAATTTATG
1 AAACTCAAATTTATG
16553 TATAGAGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
26 16 0.39
27 1 0.02
28 4 0.10
29 20 0.49
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.29
Consensus pattern (29 bp):
AAACTCAAATTTATGGTTCTGGCAAAAAA
Done.