Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014795.1 Corchorus olitorius cultivar O-4 contig14828, 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: 16638
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1550 original size:6 final size:6
Alignment explanation
Indices: 1530--1566 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
1520 GTACTTTTTA
*
1530 ATATAG -TATAA ATATAG ATATAG ATATAG ATATAG AT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG AT
1567 TAGTTGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:6226 original size:437 final size:436
Alignment explanation
Indices: 5232--6319 Score: 1185
Period size: 437 Copynumber: 2.5 Consensus size: 436
5222 TAGAATTTAG
* *
5232 ACATGAAAATTAGCTTTTGAG-TCTTTCATGAAAGAGTTGTAGATCATAAAATT-CCTTTTTAAT
1 ACATAAAAATTAGCTTTTGAGTTCTTT-ATGAAA-A-TTGTAGATCATGAAATTACC-TTTTAAT
* * * *
5295 AGACACTTAAATTAACTTAATTGGACAAATAGAACATAGAAAATAAAAAATGAAGCGTTAAA--T
62 AGACACTTAAATCAACTTAATTGGACAAATAGGA-ATA-AAAATAAAAAATAAATC-TTAAACGT
* * *
5358 GAG-T-AAGATAGAATTTGTAAATAACTAAGTAGCATAAAATATATAAAATAGAAAAGTATGAGG
124 TAGATGAAGATAGAATTTGTAAAGAACTAAGTAG---------TATAAAGTAGAAAAGTATGAGG
* * * * * * * *
5421 GTCATTTGATAACTAATTCAAATAATAAATTATTTCTTAATGGATATCTTGAAACATAAAAATTC
180 ATCATTTGATAAATAATCCAAATAAGAAAATATTTCTTAACGGAGATCTTGAAACATAAAAACTC
* * * * * *
5486 CCTTTTGAACTCTTCATGAAACTCGTAGCTCAAATTAACTTTCGGGTTCTTCATGAAAGTCATAG
245 CCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCAGGTCCTTCAAGAAAGTCATAA
* * * *
5551 ATCATACAGTAACCTTTTAACCGACACTTGAATAACTTTAATCGGACATGTGGATCGAAAATTAT
310 ATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATGTGGATCAAAAATTAT
* * * * * * **
5616 ATGGTATTAAATAGACCAACAATCGAAACGACCAAATTTAGGAAGCATTTTTTTGAATTAAA
375 ACGATATTAAATAGACCAACAATCAAAACCACCAAATTCAGGAAGCATTTTTTAGAACCAAA
* * * *
5678 ACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGAC
1 ACATAAAAATTAGCTTTTGAGTTCTTTATGAAAATTGTAGATCATGAAATTACCTTTTAATAGAC
* *
5743 ACATAAATCAACTTAATCGGACAAATA-GAATAAAGAATAAAAAAATAAATCTTAAACGTTAGAT
66 ACTTAAATCAACTTAATTGGACAAATAGGAATAAA-AAT-AAAAAATAAATCTTAAACGTTAGAT
* *
5807 GAAGATAGAATTTGTAAAGAACTAAGTAGTATAAAGTAGAAAAATATGAGGATTATTTGATAAAT
129 GAAGATAGAATTTGTAAAGAACTAAGTAGTATAAAGTAGAAAAGTATGAGGATCATTTGATAAAT
* * * * *
5872 AATCCAAATAAGAAAATGTTTGTTAACGGAGATCTTGAAGCATAAAAACTCTCTTTTGAGCCCTT
194 AATCCAAATAAGAAAATATTTCTTAACGGAGATCTTGAAACATAAAAACTCCCTTTTGAACCCTT
* * *
5937 CATGAAACTCGTAGATCAAATTTAGCTTTCAGGTCCTTCAAGAAAGTCGTAAATCATGCAATAAC
259 CATGAAACTCGTAGATCAAA-TTAACTTTCAGGTCCTTCAAGAAAGTCATAAATCATACAATAAC
*
6002 CTTTTAACCGACACTTCAATAACTTCAATCGGATATGTGGA-CAAAAAAATTATACGATATTAAA
323 CTTTTAACCGACACTTCAATAACTTCAATCGGACATGTGGATC--AAAAATTATACGATATTAAA
* ** *
6066 TTGACCGGCAATCAAAACCA-CACAATTCCGGAAGCATTTTTTAGAACCAAA
386 TAGACCAACAATCAAAACCACCA-AATTCAGGAAGCATTTTTTAGAACCAAA
* *
6117 ACATTAAAATTGGCTTTTGAGTTCTTTATGAAAATTGTAGATCATGAAATTACC-TTTAATAGAC
1 ACATAAAAATTAGCTTTTGAGTTCTTTATGAAAATTGTAGATCATGAAATTACCTTTTAATAGAC
* * * * * *
6181 ATTTGAATCACCTTAATTGGACAAATAGGAA-AAAAATACAAAAATAAATGC-GAACGCGTTAAA
66 ACTTAAATCAACTTAATTGGACAAATAGGAATAAAAATA-AAAAATAAAT-CTTAA-ACGTTAGA
** * * * * *
6244 TCGTCCAACCTATAA-TTGTAAAGAACTAAATAGCATAAAGTATAAAAGTATGAGGATCATTAGA
128 T-G---AAGATAGAATTTGTAAAGAACTAAGTAGTATAAAGTAGAAAAGTATGAGGATCATTTGA
6308 TAAATAATCCAA
189 TAAATAATCCAA
6320 GAAAAATATA
Statistics
Matches: 544, Mismatches: 78, Indels: 45
0.82 0.12 0.07
Matches are distributed among these distances:
436 1 0.00
437 119 0.22
438 119 0.22
439 108 0.20
441 57 0.10
442 17 0.03
443 11 0.02
444 54 0.10
445 3 0.01
446 52 0.10
447 3 0.01
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (436 bp):
ACATAAAAATTAGCTTTTGAGTTCTTTATGAAAATTGTAGATCATGAAATTACCTTTTAATAGAC
ACTTAAATCAACTTAATTGGACAAATAGGAATAAAAATAAAAAATAAATCTTAAACGTTAGATGA
AGATAGAATTTGTAAAGAACTAAGTAGTATAAAGTAGAAAAGTATGAGGATCATTTGATAAATAA
TCCAAATAAGAAAATATTTCTTAACGGAGATCTTGAAACATAAAAACTCCCTTTTGAACCCTTCA
TGAAACTCGTAGATCAAATTAACTTTCAGGTCCTTCAAGAAAGTCATAAATCATACAATAACCTT
TTAACCGACACTTCAATAACTTCAATCGGACATGTGGATCAAAAATTATACGATATTAAATAGAC
CAACAATCAAAACCACCAAATTCAGGAAGCATTTTTTAGAACCAAA
Found at i:6536 original size:2 final size:2
Alignment explanation
Indices: 6529--6557 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6519 TTGTATAATA
6529 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6558 CTAAATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11249 original size:29 final size:30
Alignment explanation
Indices: 11206--11278 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
11196 ACGGTCTGCT
* *
11206 CAAATTGAGCATAAACC-TTT-ACTCAGCAC
1 CAAATTGGGCCTAAACCATTTGA-TCAGCAC
**
11235 CAAATTGGGCCTAAACCTATTTGATGGGCAC
1 CAAATTGGGCCTAAACC-ATTTGATCAGCAC
11266 CAAATTGGGCCTA
1 CAAATTGGGCCTA
11279 TTTTTGACGG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 15 0.41
31 21 0.57
32 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (30 bp):
CAAATTGGGCCTAAACCATTTGATCAGCAC
Found at i:14248 original size:9 final size:9
Alignment explanation
Indices: 14234--14263 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
14224 CCCAAAGTTA
14234 AAAAAAATG
1 AAAAAAATG
14243 AAAAAAATG
1 AAAAAAATG
14252 AAAAAAAATG
1 -AAAAAAATG
14262 AA
1 AA
14264 TTGAGTGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Found at i:14248 original size:10 final size:10
Alignment explanation
Indices: 14233--14263 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
14223 GCCCAAAGTT
14233 AAAAAAAATG
1 AAAAAAAATG
14243 -AAAAAAATG
1 AAAAAAAATG
14252 AAAAAAAATG
1 AAAAAAAATG
14262 AA
1 AA
14264 TTGAGTGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:15713 original size:13 final size:12
Alignment explanation
Indices: 15695--15739 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
15685 ATTTTATTAC
15695 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
15708 TGTTTTATAAAT
1 TGTTTTATAAAT
*
15720 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
15734 TGTTTT
1 TGTTTT
15740 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Done.