Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024858.1 Corchorus olitorius cultivar O-4 contig24891, 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: 54797
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:676 original size:18 final size:19
Alignment explanation
Indices: 647--692 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
637 GAAAGGATGT
647 GCATGG-GATGCATGGAG-
1 GCATGGAGATGCATGGAGA
664 GCATGGAGATGCATGGAGA
1 GCATGGAGATGCATGGAGA
*
683 CCATGGAGAT
1 GCATGGAGAT
693 AATGATGGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 6 0.23
18 11 0.42
19 9 0.35
ACGTcount: A:0.28, C:0.13, G:0.41, T:0.17
Consensus pattern (19 bp):
GCATGGAGATGCATGGAGA
Found at i:4534 original size:12 final size:12
Alignment explanation
Indices: 4517--4542 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4507 TCAAAGCAGG
4517 CTCTTTTTTGCA
1 CTCTTTTTTGCA
4529 CTCTTTTTTGCA
1 CTCTTTTTTGCA
4541 CT
1 CT
4543 GCAAGTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.27, G:0.08, T:0.58
Consensus pattern (12 bp):
CTCTTTTTTGCA
Found at i:5076 original size:20 final size:20
Alignment explanation
Indices: 5034--5084 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5024 TTGGACATTC
* **
5034 TGGTGGCAGAGGAAGGATTT
1 TGGTGGCGGAGGAAGGAGGT
5054 TGGTGGCGGAGGAAGGAGGT
1 TGGTGGCGGAGGAAGGAGGT
*
5074 TGGTGGTGGAG
1 TGGTGGCGGAG
5085 TTTATGGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.04, G:0.55, T:0.22
Consensus pattern (20 bp):
TGGTGGCGGAGGAAGGAGGT
Found at i:19400 original size:116 final size:116
Alignment explanation
Indices: 19196--19429 Score: 441
Period size: 116 Copynumber: 2.0 Consensus size: 116
19186 TATAGGGTCC
*
19196 TGACCTTTACCCAATGTCGAACTATTCTAGAATTTTGTCTAGCTGGCATAGCATTGATATGATAA
1 TGACCTTTACCCAATGTCAAACTATTCTAGAATTTTGTCTAGCTGGCATAGCATTGATATGATAA
19261 GTTAAAATTTCATGTATGTTGATGCTAGCAAGTGGTAAAATGAATTTTACA
66 GTTAAAATTTCATGTATGTTGATGCTAGCAAGTGGTAAAATGAATTTTACA
* *
19312 TGACCTTTACCCAGTGTCAAACTATTCTAGAATTTTGTCTAGCTGGCATAGTATTGATATGATAA
1 TGACCTTTACCCAATGTCAAACTATTCTAGAATTTTGTCTAGCTGGCATAGCATTGATATGATAA
19377 GTTAAAATTTCATGTATGTTGATGCTAGCAAGTGGTAAAATGAATTTTACA
66 GTTAAAATTTCATGTATGTTGATGCTAGCAAGTGGTAAAATGAATTTTACA
19428 TG
1 TG
19430 GTTATTTCCT
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 115 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (116 bp):
TGACCTTTACCCAATGTCAAACTATTCTAGAATTTTGTCTAGCTGGCATAGCATTGATATGATAA
GTTAAAATTTCATGTATGTTGATGCTAGCAAGTGGTAAAATGAATTTTACA
Found at i:21536 original size:1 final size:1
Alignment explanation
Indices: 21530--21559 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
21520 AAGAAGAGGG
21530 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21560 GCCTTTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:24128 original size:2 final size:2
Alignment explanation
Indices: 24121--24150 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24111 AAGGATCATT
24121 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
24151 ATAGTACTTA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:25223 original size:44 final size:45
Alignment explanation
Indices: 25155--25244 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 45
25145 TCTTAACTCT
* * * *
25155 AGGAGATCGTTGGGTTCTCTCTAACGAG-CCCAAGTTTACTTAGA
1 AGGAAATCGTAGGGTACTCTCTAACGAGCCCCAAGTTTACTCAGA
*
25199 AGGAAATCGTAGGGTACTCTCTAACGAGCCCCTAGTTTACTCAGA
1 AGGAAATCGTAGGGTACTCTCTAACGAGCCCCAAGTTTACTCAGA
25244 A
1 A
25245 TCATAGGACA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 25 0.62
45 15 0.38
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (45 bp):
AGGAAATCGTAGGGTACTCTCTAACGAGCCCCAAGTTTACTCAGA
Found at i:25463 original size:44 final size:44
Alignment explanation
Indices: 25400--25483 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
25390 TATGAATCTG
*
25400 AGTAAACTAGGGCTCGTTAGAGAGAACCCTACGATCTCCTTCTA
1 AGTAAACTAGGGCTCGTTAGAGAGAACCCAACGATCTCCTTCTA
* * *
25444 AGTAAACTTGGGCTTGTTAGAGAGAACCCAATGATCTCCT
1 AGTAAACTAGGGCTCGTTAGAGAGAACCCAACGATCTCCT
25484 AGAGAAGTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (44 bp):
AGTAAACTAGGGCTCGTTAGAGAGAACCCAACGATCTCCTTCTA
Found at i:25633 original size:22 final size:22
Alignment explanation
Indices: 25605--25649 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
25595 CAGCAACTAA
*
25605 ACTACCCTCCTAGAACACAGCC
1 ACTACCCTCCTAAAACACAGCC
25627 ACTACCCTCCTAAAACACAGCC
1 ACTACCCTCCTAAAACACAGCC
25649 A
1 A
25650 TAAAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.44, G:0.07, T:0.13
Consensus pattern (22 bp):
ACTACCCTCCTAAAACACAGCC
Found at i:25715 original size:8 final size:8
Alignment explanation
Indices: 25702--25726 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
25692 CAATAATCTA
25702 AACATAAC
1 AACATAAC
25710 AACATAAC
1 AACATAAC
25718 AACATAAC
1 AACATAAC
25726 A
1 A
25727 CACTATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.24, G:0.00, T:0.12
Consensus pattern (8 bp):
AACATAAC
Found at i:31224 original size:121 final size:128
Alignment explanation
Indices: 31073--31322 Score: 361
Period size: 121 Copynumber: 2.0 Consensus size: 128
31063 CATTGTTTAA
*
31073 ACTTTTATAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-C-T-T-TA
1 ACTTTTACAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCATATCTA
* *
31134 -TAATTTTTACGATTTTACTATTTTAATTAAAAAAATTATATAT-T-AGAATTTTTTAAATAT
66 TTAATTTTTACCATTTTAATATTTTAATTAAAAAAATTATATATATAAGAATTTTTTAAATAT
* *
31194 ACTTTTACAGTTTTATTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCATATACC
1 ACTTTTACAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCATAT--C
* *
31259 TATTTTATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATAAGAATTTTTTAAAT
64 TA-TTAATTTTTACCATTTTAATATTTTAATTAAAAAAATTATATATATAAGAATTTTTTAAAT
31323 TTATTTCTTA
Statistics
Matches: 112, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
121 53 0.47
122 1 0.01
123 1 0.01
124 1 0.01
127 2 0.02
129 39 0.35
130 1 0.01
131 14 0.12
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (128 bp):
ACTTTTACAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCATATCTA
TTAATTTTTACCATTTTAATATTTTAATTAAAAAAATTATATATATAAGAATTTTTTAAATAT
Found at i:40004 original size:24 final size:24
Alignment explanation
Indices: 39977--40022 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
39967 GTTAGAAATT
39977 ATTTATATAAGCATTTTCAAGTTC
1 ATTTATATAAGCATTTTCAAGTTC
* *
40001 ATTTATATATGCCTTTTCAAGT
1 ATTTATATAAGCATTTTCAAGT
40023 GTTAAACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (24 bp):
ATTTATATAAGCATTTTCAAGTTC
Found at i:42234 original size:42 final size:42
Alignment explanation
Indices: 42187--42272 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 42
42177 TTCTCTCCCC
* *
42187 AACGCAGAT-TCGAGTCCAAGTATTTCATAAGAAAGAAACAAG
1 AACGCAGATCT-GAGTACAAGTATTTCATAAGAAAAAAACAAG
42229 AACGCAGATCTGAGTACAAGTATTTCATAAGAAAAAAACAAG
1 AACGCAGATCTGAGTACAAGTATTTCATAAGAAAAAAACAAG
42271 AA
1 AA
42273 ATCATATGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 40 0.98
43 1 0.02
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (42 bp):
AACGCAGATCTGAGTACAAGTATTTCATAAGAAAAAAACAAG
Found at i:45676 original size:4 final size:4
Alignment explanation
Indices: 45667--45693 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
45657 TTAACCCCCT
45667 CTCC CTCC CTCC CTCC CTCC CTCC CTC
1 CTCC CTCC CTCC CTCC CTCC CTCC CTC
45694 TTTCTTCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.74, G:0.00, T:0.26
Consensus pattern (4 bp):
CTCC
Found at i:47248 original size:19 final size:19
Alignment explanation
Indices: 47224--47260 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
47214 AATCTATCTG
47224 TATTATATTGAAAAGTATA
1 TATTATATTGAAAAGTATA
47243 TATTATATTGAAAAGTAT
1 TATTATATTGAAAAGTAT
47261 GACTTCTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (19 bp):
TATTATATTGAAAAGTATA
Found at i:47581 original size:2 final size:2
Alignment explanation
Indices: 47574--47600 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47564 CGATGAAGAT
47574 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
47601 TAATTAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48820 original size:21 final size:21
Alignment explanation
Indices: 48795--48852 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
48785 AGGAGATCAT
48795 TTCCAAGCTCATTGGAGAAGG
1 TTCCAAGCTCATTGGAGAAGG
48816 TTCCAAGCTCATTGGAGAAGG
1 TTCCAAGCTCATTGGAGAAGG
48837 -TCTCAAGCTCATTGGA
1 TTC-CAAGCTCATTGGA
48853 ATTGCCTAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 2 0.06
21 34 0.94
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TTCCAAGCTCATTGGAGAAGG
Found at i:52994 original size:14 final size:14
Alignment explanation
Indices: 52975--53016 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
52965 TTTCTTCAAC
52975 TAGAGTTATAAAGT
1 TAGAGTTATAAAGT
*
52989 TAGAGTTATAGAGT
1 TAGAGTTATAAAGT
*
53003 TAGGAATTATAAAG
1 TA-GAGTTATAAAG
53017 AGGGAGTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (14 bp):
TAGAGTTATAAAGT
Found at i:54419 original size:37 final size:36
Alignment explanation
Indices: 54345--54419 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
54335 TTAAGTTTTT
*** **
54345 AAATTGGGAAAGTTCCCACCAGTTTTTTAAGTTTTC
1 AAATTGGGAAAGTTCCCACCAGTTTCCAAAGCATTC
*
54381 AAATTGGGAAAGTTCCCATTCAGTTTCCAAAGCATTC
1 AAATTGGGAAAGTTCCCA-CCAGTTTCCAAAGCATTC
54418 AA
1 AA
54420 TCTATCTCTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 18 0.56
37 14 0.44
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (36 bp):
AAATTGGGAAAGTTCCCACCAGTTTCCAAAGCATTC
Found at i:54506 original size:52 final size:52
Alignment explanation
Indices: 54376--54619 Score: 339
Period size: 52 Copynumber: 4.6 Consensus size: 52
54366 GTTTTTTAAG
* *
54376 TTTTCAAATTGGGAAAGTTCCCATTCAGTTTCCAAAGCATTCAATCTATCTCTCTT
1 TTTTCAAATTGGGAAAGTTCCCA-TCAGTTTTCAAAGCATTCAATCTA--GCTC-T
*
54432 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGCATTCAGTCTAGCTCT
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGCATTCAATCTAGCTCT
54484 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGCATTCAATCTAGCTCT
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGCATTCAATCTAGCTCT
* * * *
54536 TTTTTAAATTGGGAAAGTTCCCATCAAGTTTCCAAAGTATTCAATTTAGCTCT
1 TTTTCAAATTGGGAAAGTTCCCATC-AGTTTTCAAAGCATTCAATCTAGCTCT
* *
54589 TTTT-AATTTAGGGAAAGTTCCCGTCA-TTTTC
1 TTTTCAAATT-GGGAAAGTTCCCATCAGTTTTC
54620 GATTTTAGTT
Statistics
Matches: 175, Mismatches: 11, Indels: 9
0.90 0.06 0.05
Matches are distributed among these distances:
51 4 0.02
52 81 0.46
53 45 0.26
55 22 0.13
56 23 0.13
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (52 bp):
TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGCATTCAATCTAGCTCT
Done.