Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017603.1 Corchorus olitorius cultivar O-4 contig17636, 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: 51306
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:7908 original size:15 final size:15
Alignment explanation
Indices: 7888--7920 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
7878 AGGATAGAAA
7888 ATTGTTTTTGGATTG
1 ATTGTTTTTGGATTG
7903 ATTGTTTTTGGATTG
1 ATTGTTTTTGGATTG
7918 ATT
1 ATT
7921 ATCCCCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.24, T:0.61
Consensus pattern (15 bp):
ATTGTTTTTGGATTG
Found at i:10736 original size:23 final size:22
Alignment explanation
Indices: 10702--11000 Score: 150
Period size: 22 Copynumber: 13.6 Consensus size: 22
10692 CGATCATGAT
*
10702 GTTATCAAAATTTCATAAGATTG
1 GTTATCAAAATTTCATAAG-GTG
* *
10725 GTTATCATAATTTCATGAGGTG
1 GTTATCAAAATTTCATAAGGTG
* *
10747 GTTTTCAAAATTTCAT---GAG
1 GTTATCAAAATTTCATAAGGTG
*
10766 GTTATCAAAATTTCA-AATGGAG
1 GTTATCAAAATTTCATAA-GGTG
* * * *
10788 GTTAACAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATAAGGTG
10810 GTTTAT-AAAATTTTCAT-A-GTG
1 G-TTATCAAAA-TTTCATAAGGTG
* *
10831 AGGTATCACAATTTCAT--GGTATG
1 -GTTATCAAAATTTCATAAGG--TG
* *
10854 TTTATCAAAATTTCATAATGTG
1 GTTATCAAAATTTCATAAGGTG
* * * * * * *
10876 ATTACCGATATTTTAT-CGGAAG
1 GTTATCAAAATTTCATAAGG-TG
*
10898 GTTATCAAAATTTCATAATGTG
1 GTTATCAAAATTTCATAAGGTG
* * ** *
10920 CGCTTACCAACATTTCATTGGGAG
1 -G-TTATCAAAATTTCATAAGGTG
*
10944 GTTATCAAAATTTCATAGGGTG
1 GTTATCAAAATTTCATAAGGTG
* *
10966 GTTATCAAAATTTCATTAGGTA
1 GTTATCAAAATTTCATAAGGTG
* *
10988 ATTATTAAAATTT
1 GTTATCAAAATTT
11001 TATAGGGAGT
Statistics
Matches: 207, Mismatches: 51, Indels: 37
0.70 0.17 0.13
Matches are distributed among these distances:
19 16 0.08
21 13 0.06
22 131 0.63
23 31 0.15
24 16 0.08
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGGTG
Found at i:10903 original size:44 final size:45
Alignment explanation
Indices: 10855--10960 Score: 142
Period size: 46 Copynumber: 2.4 Consensus size: 45
10845 CATGGTATGT
* * *
10855 TTATCAAAATTTCATAATGT-GATTACCGATATTTTATCGGAAGG
1 TTATCAAAATTTCATAATGTCGATTACCAACATTTCATCGGAAGG
* * *
10899 TTATCAAAATTTCATAATGTGCGCTTACCAACATTTCATTGGGAGG
1 TTATCAAAATTTCATAATGT-CGATTACCAACATTTCATCGGAAGG
10945 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
10961 GGGTGGTTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 20 0.37
46 34 0.63
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (45 bp):
TTATCAAAATTTCATAATGTCGATTACCAACATTTCATCGGAAGG
Found at i:11039 original size:22 final size:22
Alignment explanation
Indices: 10998--11040 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10988 ATTATTAAAA
*
10998 TTTTATAGGGAGTGTGACAAAC
1 TTTTATAGGGAGTGTAACAAAC
11020 TTTTATAGGGAAGT-TAACAAA
1 TTTTATAGGG-AGTGTAACAAA
11041 ATTTCATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (22 bp):
TTTTATAGGGAGTGTAACAAAC
Found at i:11112 original size:22 final size:21
Alignment explanation
Indices: 11082--11153 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
11072 TATCGTCATA
*
11082 AAAACTTTATAGTGTAATTATC
1 AAAATTTTATAGTG-AATTATC
* *
11104 AAAATTTTATATTGAGGTTATC
1 AAAATTTTATAGTGA-ATTATC
*
11126 AAAATTCTATAGTG-ATTATC
1 AAAATTTTATAGTGAATTATC
11146 -AAATTTTA
1 AAAATTTTA
11154 AAAAATATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 7 0.17
20 5 0.12
21 1 0.02
22 29 0.69
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (21 bp):
AAAATTTTATAGTGAATTATC
Found at i:13669 original size:439 final size:436
Alignment explanation
Indices: 12704--13679 Score: 1335
Period size: 439 Copynumber: 2.2 Consensus size: 436
12694 AGTCAAAGCG
*
12704 TTAAATCGTCCAACCTATAATTGTAAAGGATTAAATAGCATGAAACATAAAAG--TATGAGAGTC
1 TTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCAT-AAACATAAAAGTATATG-GA-TC
* * * *
12767 ATTAGATAAAT-ATCCAGCAAAAAAAATATTAGTTTATGAAGATAAAACATAAAAATTTCCTCTT
63 ATTTGATAAATAATCCAG--AAAAAAATATTTGTTTATGAAGATAAAACATAAAAATTCCCTCTC
* * * *
12831 GAATCCTCCACGAAACTCATTAATCAAATTCAACTTTCATGCCCTTAATGAAAGTTGTAGATCAC
126 GAACCCTCCACGAAACTCATTAATCAAATTCAACTTTCAGGCCCTTAATGAAAGTTATAGAACAC
*
12896 ACAATAACCTTTTAACCGACACTTGAACAACTTCAATCGAACAAGTGGACCGAAAATTATACGAT
191 ACAATAACCTTTTAACCGACACTTGAACAACTTCAATCGAACAAGTGGACCGAAAATTATACAAT
* *
12961 ATTAAATAGACCGGCAATCGAAGCCACAAAATTTAAGAAACATTTTTTAGAATCAAAGCATTAAA
256 ATTAAATAGACCGACAATCGAAGCCACAAAATTTAAGAAACATTTTTTAGAATCAAAGCATGAAA
* *
13026 ATTGGCTTCTGAGTTTTTCATGAAAGTTGTAGATCATGAGATTACCTTTTAATAGACACTTGAAT
321 ATTGGCTTCTGAGTCTTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAAT
* * ** *
13091 CATCTTCAACGGACAAATAGAACAGAAAATACAAAAATAAAAGCCGACGCG
386 CACCTTCAACGGACAAATAAAACAGAAAATACAAAAATAAAAGCCGAAACA
* *
13142 TTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAACATAAAAGTATAAGGAACAT
1 TTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCAT-AAACATAAAAGTATATGGATCAT
* *
13207 TTGATAAATAATCCAGCAAAAAATATATTTGTTTATGGAGATCAAACATAAAAATTCCCTCTCGA
65 TTGATAAATAATCCAG-AAAAAA-ATATTTGTTTATGAAGATAAAACATAAAAATTCCCTCTCGA
* * * *
13272 ACCCTCCACGAAACTCATTAATCAAATTCAGCTTTCAGGTCCTTGATGAAAGTTATAGAACATAC
128 ACCCTCCACGAAACTCATTAATCAAATTCAACTTTCAGGCCCTTAATGAAAGTTATAGAACACAC
* * *
13337 AATAACCTTTTAACCGACACTTGAACAA-TCTCAATCGGACAAGTGGATCGAGAATTATACAATA
193 AATAACCTTTTAACCGACACTTGAACAACT-TCAATCGAACAAGTGGACCGAAAATTATACAATA
* *
13401 TTAGATAGACCGACAATCG-AGACCACAAAATTTAAGAAGCATTTTTTAGAATCGAAA-CATGAA
257 TTAAATAGACCGACAATCGAAG-CCACAAAATTTAAGAAACATTTTTTAGAATC-AAAGCATGAA
*
13464 AATTGG-TT-TGCAGTCCTTT-ATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACATTTG
320 AATTGGCTTCTG-AGT-CTTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTG
* * * * *
13526 AATCACCTTGATCGGATAAGTAAAACA-AAAATA-AAAGAATTAAAGCCGAAACA
383 AATCACCTTCAACGGACAAATAAAACAGAAAATACAAA-AATAAAAGCCGAAACA
* * * * *
13579 TTCAATCGTCCAACCCAGAATTTGTGAGGGATTAAAGAGCATAAAGCATAAAAGTATATGGATCA
1 TTAAATCGTCCAACCCATAA-TTGTAAAGGATTAAATAGCATAAA-CATAAAAGTATATGGATCA
13644 TTTGATAAATAATCCAGTAAAAAAATATTTGTTTAT
64 TTTGATAAATAATCCAG-AAAAAAATATTTGTTTAT
13680 TAGGAGCGAG
Statistics
Matches: 478, Mismatches: 48, Indels: 25
0.87 0.09 0.05
Matches are distributed among these distances:
436 3 0.01
437 53 0.11
438 196 0.41
439 220 0.46
440 6 0.01
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (436 bp):
TTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAACATAAAAGTATATGGATCATT
TGATAAATAATCCAGAAAAAAATATTTGTTTATGAAGATAAAACATAAAAATTCCCTCTCGAACC
CTCCACGAAACTCATTAATCAAATTCAACTTTCAGGCCCTTAATGAAAGTTATAGAACACACAAT
AACCTTTTAACCGACACTTGAACAACTTCAATCGAACAAGTGGACCGAAAATTATACAATATTAA
ATAGACCGACAATCGAAGCCACAAAATTTAAGAAACATTTTTTAGAATCAAAGCATGAAAATTGG
CTTCTGAGTCTTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCT
TCAACGGACAAATAAAACAGAAAATACAAAAATAAAAGCCGAAACA
Found at i:13867 original size:2 final size:2
Alignment explanation
Indices: 13856--13894 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
13846 CTTCACGTTT
13856 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13895 CGTTCTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22794 original size:2 final size:2
Alignment explanation
Indices: 22787--22816 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22777 AATTAAACAA
22787 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22817 GCAATTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28113 original size:42 final size:41
Alignment explanation
Indices: 28030--28114 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 41
28020 TTGACTAGAG
* * *
28030 AAAGTAATCTAAATAACCGAATGACCATCCACATGATCCGA
1 AAAGTAATCTAAATAACCGAATGACCACCCAAATGACCCGA
**
28071 AAAGTAATCTAAATGCCCCGAATGACCACCCAAATGACCCGA
1 AAAGTAATCTAAAT-AACCGAATGACCACCCAAATGACCCGA
28113 AA
1 AA
28115 TCTAAATGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
41 14 0.37
42 24 0.63
ACGTcount: A:0.44, C:0.27, G:0.13, T:0.16
Consensus pattern (41 bp):
AAAGTAATCTAAATAACCGAATGACCACCCAAATGACCCGA
Found at i:31338 original size:51 final size:50
Alignment explanation
Indices: 31237--31338 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
31227 GTTCTTCATA
**
31237 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTGTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTGTTACAGTGT
* *
31287 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACTG-TACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTGTTACA-GTGT
31338 T
1 T
31339 CTTCATTCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 7 0.16
51 37 0.82
52 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTGTTACAGTGT
Found at i:41020 original size:13 final size:13
Alignment explanation
Indices: 41002--41027 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40992 CTTGGCATGA
41002 GTGATGATTTTTG
1 GTGATGATTTTTG
41015 GTGATGATTTTTG
1 GTGATGATTTTTG
41028 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:44629 original size:99 final size:102
Alignment explanation
Indices: 44440--44657 Score: 343
Period size: 99 Copynumber: 2.2 Consensus size: 102
44430 GTGAGCTTAA
* *
44440 TTTGTAATTTGTTTGTTTGTTTATTTGGTTTATCAATAGGTATAGTTTCTAGTTTCTAGCTAGGT
1 TTTGTAATTTGTTTGTTTGTTTATTTGGTTTATCAATAGGTATAGTTTCTAG-TTCGAGATAGGT
44505 TCAAGAGCAGGTGTTATGAAATTGTTAGGGAGGGGGTT
65 TCAAGAGCAGGTGTTATGAAATTGTTAGGGAGGGGGTT
* * *
44543 TTTGTAATTTGTTTGTTTGTTTATTTGGTTTGTCAATAGGTGTAGTTTCTAG-T-GAGAT-TGTT
1 TTTGTAATTTGTTTGTTTGTTTATTTGGTTTATCAATAGGTATAGTTTCTAGTTCGAGATAGGTT
* *
44605 CAAGAGCAGGTGTTATGAGATTGTTGGGGAGGGGGTT
66 CAAGAGCAGGTGTTATGAAATTGTTAGGGAGGGGGTT
44642 TTTGTAATTTGTTTGT
1 TTTGTAATTTGTTTGT
44658 GTTGCGCCAA
Statistics
Matches: 108, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
99 54 0.50
100 3 0.03
101 1 0.01
103 50 0.46
ACGTcount: A:0.19, C:0.05, G:0.29, T:0.47
Consensus pattern (102 bp):
TTTGTAATTTGTTTGTTTGTTTATTTGGTTTATCAATAGGTATAGTTTCTAGTTCGAGATAGGTT
CAAGAGCAGGTGTTATGAAATTGTTAGGGAGGGGGTT
Done.