Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019611.1 Corchorus olitorius cultivar O-4 contig19644, 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: 57307
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:420 original size:16 final size:16
Alignment explanation
Indices: 383--422 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
373 AGAGGTTGAA
*
383 AGAAAGCAATTAAACT
1 AGAAAACAATTAAACT
*
399 -GAAAACAATTATACT
1 AGAAAACAATTAAACT
414 AGAAAACAA
1 AGAAAACAA
423 AACAAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.17
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:9494 original size:29 final size:30
Alignment explanation
Indices: 9460--9526 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
9450 CTATAAGCAA
* * *
9460 ATGGACAAATTGCATCATAAACTTTAATTT
1 ATGGACAAATTACACCATAAACTATAATTT
* *
9490 -TGGACAATTTACACCCTAAACTATAATTT
1 ATGGACAAATTACACCATAAACTATAATTT
9519 ATGGACAA
1 ATGGACAA
9527 TATGCAGCCC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.33
Consensus pattern (30 bp):
ATGGACAAATTACACCATAAACTATAATTT
Found at i:9823 original size:31 final size:30
Alignment explanation
Indices: 9755--9824 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
9745 GGACTGTCAC
*
9755 TTTGCACCC-AACTTTTTTATTTTGATCAT
1 TTTGCACCCTAACTGTTTTATTTTGATCAT
* *
9784 ATTGCACCCTAA-TGTTTTATTTTGCGTACAT
1 TTTGCACCCTAACTGTTTTATTTTG-AT-CAT
9815 TTTGCACCCT
1 TTTGCACCCT
9825 CTGTGACGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 19 0.56
30 3 0.09
31 12 0.35
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.47
Consensus pattern (30 bp):
TTTGCACCCTAACTGTTTTATTTTGATCAT
Found at i:10326 original size:32 final size:32
Alignment explanation
Indices: 10290--10357 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
10280 TTCAGGTTCA
** * *
10290 TTCGGGTTCGGGCTGTGTCGGGTTAGGGTATT
1 TTCGGGTTCAAGCTATGTCGGGTTAGGGTAAT
* *
10322 TTCGGGTTTAAGCTATGTCGGGTTCGGGTAAT
1 TTCGGGTTCAAGCTATGTCGGGTTAGGGTAAT
10354 TTCG
1 TTCG
10358 CTTTGGGCTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.10, C:0.13, G:0.38, T:0.38
Consensus pattern (32 bp):
TTCGGGTTCAAGCTATGTCGGGTTAGGGTAAT
Found at i:10516 original size:5 final size:5
Alignment explanation
Indices: 10506--10559 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
10496 TCATTTATTG
*
10506 ATAAT ATAAT AT-A- ATAAT ATAAT ATAAC ATAATT ATCAAT AT-AT ATATAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA-T AT-AAT ATAAT ATA-AT
10556 ATAA
1 ATAA
10560 AGATTGAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
3 2 0.05
4 6 0.15
5 21 0.51
6 10 0.24
7 2 0.05
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:10524 original size:13 final size:13
Alignment explanation
Indices: 10506--10532 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10496 TCATTTATTG
10506 ATAATATAATATA
1 ATAATATAATATA
10519 ATAATATAATATA
1 ATAATATAATATA
10532 A
1 A
10533 CATAATTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAATATAATATA
Found at i:10820 original size:21 final size:20
Alignment explanation
Indices: 10795--10841 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
10785 AATTTAAATT
* *
10795 AATTAATGCTAATTAATACTA
1 AATTAATGCAAATTAAAAC-A
*
10816 AATTATTGCAAATTAAAACA
1 AATTAATGCAAATTAAAACA
10836 AATTAA
1 AATTAA
10842 GCATTAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (20 bp):
AATTAATGCAAATTAAAACA
Found at i:29076 original size:52 final size:52
Alignment explanation
Indices: 29006--29296 Score: 453
Period size: 52 Copynumber: 5.6 Consensus size: 52
28996 ATTGAAAACT
* *
29006 AAAACCTGATGGGAACTTTCCCAATTTGAAAAGGAGCTAAATTGAATACTTTG
1 AAAA-CTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
* *
29059 AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAGATTAAATACTTTG
1 AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
* *
29111 AAAACTGGTGGGAACTTTCGCAATTTGAAAAAAAGAGCTAGATTGAATACTTTG
1 AAAACTGGTGGGAACTTTCCCAATTTG--AAAAAGAGCTAAATTGAATACTTTG
29165 AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTG-A-ACTTTG
1 AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
*
29215 AAAACAGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
1 AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
* *
29267 -AAACTGATGGGAACTTTCCTAATTTGAAAA
1 AAAACTGGTGGGAACTTTCCCAATTTGAAAA
29297 CTTAAATTGA
Statistics
Matches: 222, Mismatches: 12, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
50 48 0.22
51 29 0.13
52 91 0.41
53 4 0.02
54 50 0.23
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (52 bp):
AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
Found at i:29198 original size:106 final size:102
Alignment explanation
Indices: 29006--29296 Score: 449
Period size: 106 Copynumber: 2.8 Consensus size: 102
28996 ATTGAAAACT
* *
29006 AAAACCTGATGGGAACTTTCCCAATTTGAAAAGGAGCTAAATTGAATACTTTGAAAACTGGTGGG
1 AAAA-CTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGGG
*
29071 AACTTTCCCAATTTGAAAAAGAGCTAGATTAAATACTTTG
65 AACTTTCCCAATTTGAAAAAGAGCTAAATT-AA-ACTTTG
* *
29111 AAAACTGGTGGGAACTTTCGCAATTTGAAAAAAAGAGCTAGATTGAATACTTTGAAAACTGGTGG
1 AAAACTGGTGGGAACTTTCCCAATTTG--AAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGG
*
29176 GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAACTTTG
64 GAACTTTCCCAATTTGAAAAAGAGCTAAATTAAACTTTG
* *
29215 AAAACAGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG-AAACTGATGGGA
1 AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGGGA
*
29279 ACTTTCCTAATTTGAAAA
66 ACTTTCCCAATTTGAAAA
29297 CTTAAATTGA
Statistics
Matches: 173, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
101 28 0.16
102 24 0.14
104 52 0.30
105 5 0.03
106 64 0.37
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (102 bp):
AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGGGA
ACTTTCCCAATTTGAAAAAGAGCTAAATTAAACTTTG
Found at i:31648 original size:21 final size:21
Alignment explanation
Indices: 31598--31642 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31588 GTGACATTGC
* *
31598 CCACCTGGGTTCTCAAGCAAA
1 CCACATGGGTGCTCAAGCAAA
*
31619 CCACATGGGTGCTCAAGGAAA
1 CCACATGGGTGCTCAAGCAAA
31640 CCA
1 CCA
31643 TGTGGGCGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (21 bp):
CCACATGGGTGCTCAAGCAAA
Found at i:44915 original size:15 final size:16
Alignment explanation
Indices: 44891--44930 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
44881 AGAGGTTGAA
*
44891 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
44906 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
44922 AGAAAACAA
1 AGAAAACAA
44931 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:45736 original size:17 final size:18
Alignment explanation
Indices: 45699--45736 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
45689 ACCCTTGCCT
*
45699 AAAACTAGAAGAAAACTA
1 AAAACTAGAAGAAAACGA
45717 AAAACTAGAAGAAAA-GA
1 AAAACTAGAAGAAAACGA
45734 AAA
1 AAA
45737 TATCTATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.71, C:0.08, G:0.13, T:0.08
Consensus pattern (18 bp):
AAAACTAGAAGAAAACGA
Found at i:48312 original size:21 final size:21
Alignment explanation
Indices: 48265--48313 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
48255 TTGGAATGGC
* *
48265 GATGGCACAGGCATAGCCGGT
1 GATGGCACAGGCATAACCAGT
* * *
48286 GGTGGCACGGGCTTAACCAGT
1 GATGGCACAGGCATAACCAGT
48307 GATGGCA
1 GATGGCA
48314 TGGTGAATGC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.39, T:0.16
Consensus pattern (21 bp):
GATGGCACAGGCATAACCAGT
Found at i:48721 original size:17 final size:18
Alignment explanation
Indices: 48684--48721 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
48674 ACCCTTGCCT
*
48684 AAAACTAGAAGAAAACTA
1 AAAACTAGAAGAAAACGA
48702 AAAACTAGAAGAAAA-GA
1 AAAACTAGAAGAAAACGA
48719 AAA
1 AAA
48722 TACCTATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.71, C:0.08, G:0.13, T:0.08
Consensus pattern (18 bp):
AAAACTAGAAGAAAACGA
Found at i:50529 original size:26 final size:28
Alignment explanation
Indices: 50485--50546 Score: 92
Period size: 26 Copynumber: 2.3 Consensus size: 28
50475 TGGGACGTCA
50485 TCCCTCTTGATGGAAGATGG-CAATTT-
1 TCCCTCTTGATGGAAGATGGACAATTTC
* *
50511 TCCTTCTTGATGGACGATGGACAATTTC
1 TCCCTCTTGATGGAAGATGGACAATTTC
50539 TCCCTCTT
1 TCCCTCTT
50547 CTTATAGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 18 0.58
27 6 0.19
28 7 0.23
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.37
Consensus pattern (28 bp):
TCCCTCTTGATGGAAGATGGACAATTTC
Found at i:54060 original size:20 final size:20
Alignment explanation
Indices: 54037--54085 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
54027 TTGAAAAACT
54037 AATTGAAAAATGCAAAACAG
1 AATTGAAAAATGCAAAACAG
*
54057 AATTGAAAAATGCAAAACAT
1 AATTGAAAAATGCAAAACAG
54077 AATTGAAAA
1 AATTGAAAA
54086 GTAAAACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.61, C:0.08, G:0.12, T:0.18
Consensus pattern (20 bp):
AATTGAAAAATGCAAAACAG
Found at i:54098 original size:31 final size:31
Alignment explanation
Indices: 54062--54178 Score: 198
Period size: 31 Copynumber: 3.8 Consensus size: 31
54052 AACAGAATTG
*
54062 AAAAATGCAAAACATAATTGAAAAGTAAAAC
1 AAAAATGCAAAACAGAATTGAAAAGTAAAAC
54093 AAAAATGCAAAACAGAATTGAAAAGTAAAAC
1 AAAAATGCAAAACAGAATTGAAAAGTAAAAC
*
54124 AGAAATGCAAAACAGAATTGAAAAGTAAAAC
1 AAAAATGCAAAACAGAATTGAAAAGTAAAAC
* *
54155 AGAAATGCAAAACAAAATTGAAAA
1 AAAAATGCAAAACAGAATTGAAAA
54179 ACATAATTGA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 83 1.00
ACGTcount: A:0.64, C:0.09, G:0.13, T:0.14
Consensus pattern (31 bp):
AAAAATGCAAAACAGAATTGAAAAGTAAAAC
Found at i:54124 original size:18 final size:18
Alignment explanation
Indices: 54037--54171 Score: 85
Period size: 18 Copynumber: 7.8 Consensus size: 18
54027 TTGAAAAACT
54037 AATTGAAAAATGCAAAACAG
1 AATTG-AAAA-GCAAAACAG
*
54057 AATTGAAAAATGCAAAACAT
1 AATTG-AAAA-GCAAAACAG
*
54077 AATTGAAAAGTAAAAC--
1 AATTGAAAAGCAAAACAG
*
54093 AA---AAATGCAAAACAG
1 AATTGAAAAGCAAAACAG
*
54108 AATTGAAAAGTAAAAC--
1 AATTGAAAAGCAAAACAG
*
54124 -A--GAAATGCAAAACAG
1 AATTGAAAAGCAAAACAG
*
54139 AATTGAAAAGTAAAACAG
1 AATTGAAAAGCAAAACAG
*
54157 AAATGCAAAA-CAAAA
1 AATTG-AAAAGCAAAA
54172 TTGAAAAACA
Statistics
Matches: 92, Mismatches: 12, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
13 19 0.21
15 3 0.03
16 3 0.03
18 35 0.38
19 8 0.09
20 24 0.26
ACGTcount: A:0.63, C:0.10, G:0.13, T:0.14
Consensus pattern (18 bp):
AATTGAAAAGCAAAACAG
Found at i:54179 original size:13 final size:13
Alignment explanation
Indices: 54150--54213 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
54140 ATTGAAAAGT
*
54150 AAAACAGAAA-TGC
1 AAAACA-AAATTGA
54163 AAAACAAAATTGA
1 AAAACAAAATTGA
*
54176 AAAACATAATTGA
1 AAAACAAAATTGA
* **
54189 AAAATAGTATTGA
1 AAAACAAAATTGA
*
54202 AAAACAGAATTG
1 AAAACAAAATTG
54214 TACCTGAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
12 3 0.07
13 40 0.93
ACGTcount: A:0.61, C:0.08, G:0.12, T:0.19
Consensus pattern (13 bp):
AAAACAAAATTGA
Done.