Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022631.1 Corchorus olitorius cultivar O-4 contig22664, 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: 32800
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:159 original size:87 final size:85
Alignment explanation
Indices: 38--219 Score: 238
Period size: 87 Copynumber: 2.1 Consensus size: 85
28 AAAAGTCTAT
* * * * *
38 TTTTATTTAGTTAAATCTAATCACTCTATGACTATTTTATTTTTATCATTTTTACTTTTTTAATT
1 TTTT-TTTAATTAAATCTAATCACTCTATAACTATTTAATTTTTACCATTTTTACTATTTTAATT
103 AAAAAAACTTAGATATATTAGAA
65 -AAAAAACTTAGATATATTAG-A
* * *
126 TTTTTTTAATTAAATCTAATCTCTTTATAACTATTTAATTTTTACCATTTTTACTATTTTACTTA
1 TTTTTTTAATTAAATCTAATCACTCTATAACTATTTAATTTTTACCATTTTTACTATTTTAATTA
** *
191 TTAAATTTAGATATATTAGA
66 AAAAACTTAGATATATTAGA
211 TTTTTTTAA
1 TTTTTTTAA
220 ATATATTTCT
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
85 10 0.12
86 17 0.20
87 52 0.63
88 4 0.05
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (85 bp):
TTTTTTTAATTAAATCTAATCACTCTATAACTATTTAATTTTTACCATTTTTACTATTTTAATTA
AAAAACTTAGATATATTAGA
Found at i:2736 original size:16 final size:16
Alignment explanation
Indices: 2717--2767 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
2707 AAAATCCAAA
2717 ACCCAAAACCCGAATG
1 ACCCAAAACCCGAATG
*
2733 ACCCAAAATCCGAATG
1 ACCCAAAACCCGAATG
*
2749 ACCCAAAACCCGAGTG
1 ACCCAAAACCCGAATG
2765 ACC
1 ACC
2768 TGAGGCTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.41, C:0.37, G:0.14, T:0.08
Consensus pattern (16 bp):
ACCCAAAACCCGAATG
Found at i:3496 original size:93 final size:95
Alignment explanation
Indices: 3399--3588 Score: 278
Period size: 93 Copynumber: 2.0 Consensus size: 95
3389 GATTTTTAAT
** *
3399 TAAATTAGTAATTTGGTAAAAATAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAAT-A
1 TAAATTAGTAAAATGGTAAAAATAAAATAAGTATAAAGATATTAGATTTAATTAAATAAAAATAA
*
3463 GAG-TTT-TTAGTTGAGTAAAACTATAAAAG
66 G-GTTTTATTAGTTGACTAAAACTATAAAAG
* *
3492 TAAATTAGTAAAATGGTAAAAATAAAATAATTATAAGGATATTAGATTTAATTAAATAAAAATAA
1 TAAATTAGTAAAATGGTAAAAATAAAATAAGTATAAAGATATTAGATTTAATTAAATAAAAATAA
*
3557 GGTTTTAATTAGTTGACTAAAATTATAAAAG
66 GGTTTT-ATTAGTTGACTAAAACTATAAAAG
3588 T
1 T
3589 TTAAACAATG
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
93 59 0.69
94 5 0.06
96 22 0.26
ACGTcount: A:0.52, C:0.01, G:0.13, T:0.35
Consensus pattern (95 bp):
TAAATTAGTAAAATGGTAAAAATAAAATAAGTATAAAGATATTAGATTTAATTAAATAAAAATAA
GGTTTTATTAGTTGACTAAAACTATAAAAG
Found at i:3789 original size:43 final size:44
Alignment explanation
Indices: 3709--3812 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 44
3699 TGAATATTTT
* * * *
3709 TATGAAATTTTGGTAACTAGCCTATCAAATTTTGATAACCACCA
1 TATGAGATTTTGATAACTAGCCTATCAAATTGTGATAAACACCA
* *
3753 TATGAGATTTTGATAATTA-CCTA-CAAAATTGTGATAAACTCCA
1 TATGAGATTTTGATAACTAGCCTATC-AAATTGTGATAAACACCA
* *
3796 TAAGAGACTTTGATAAC
1 TATGAGATTTTGATAAC
3813 CTAACTATGA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
42 1 0.02
43 33 0.66
44 16 0.32
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (44 bp):
TATGAGATTTTGATAACTAGCCTATCAAATTGTGATAAACACCA
Found at i:3861 original size:21 final size:22
Alignment explanation
Indices: 3817--3875 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
3807 GATAACCTAA
3817 CTATGAAGTTTTAATAAACTTTC
1 CTATGAA-TTTTAATAAACTTTC
* *
3840 CTATGAATTTT-GTAACCTTTC
1 CTATGAATTTTAATAAACTTTC
*
3861 CTAT-AATTTTTATAA
1 CTATGAATTTTAATAA
3876 TCTCTCTCTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 6 0.19
21 15 0.47
22 4 0.12
23 7 0.22
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (22 bp):
CTATGAATTTTAATAAACTTTC
Found at i:5427 original size:6 final size:6
Alignment explanation
Indices: 5416--5442 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5406 TTTTTTTGGC
5416 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
5443 GCAATCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:6324 original size:49 final size:50
Alignment explanation
Indices: 6249--6368 Score: 136
Period size: 49 Copynumber: 2.4 Consensus size: 50
6239 ACTAAAAACT
**
6249 CTATTTTAATTTAATTAAATTCAATATTTTTATAAATATTTTA-TTTTAC
1 CTATTTTAATTTAATTAAATTCAATATCCTTATAAATATTTTATTTTTAC
* * **
6298 CTATTTTTATTTGATTAAA-TCTAATATCCTTATACCTATTTTATTTTTAC
1 CTATTTTAATTTAATTAAATTC-AATATCCTTATAAATATTTTATTTTTAC
*
6348 CGTATTACTAATTTAATTAAA
1 C-TATT-TTAATTTAATTAAA
6369 AAGCTTAGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
48 2 0.03
49 34 0.59
50 7 0.12
51 4 0.07
52 11 0.19
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (50 bp):
CTATTTTAATTTAATTAAATTCAATATCCTTATAAATATTTTATTTTTAC
Found at i:6466 original size:227 final size:225
Alignment explanation
Indices: 6071--6523 Score: 782
Period size: 227 Copynumber: 2.0 Consensus size: 225
6061 ACTACAAACT
6071 CTATTTTTATTTGATTAAATCTAATATCCTTATACATATTTTATTTTTACCATATTACTAATTTA
1 CTATTTTTATTTGATTAAATCTAATATCCTTATACATATTTTATTTTTACCATATTACTAATTTA
6136 ATTAAAAAGCTTAGATATATTAGAACTTTAAAATATATTTCTTAAATGACATTTGTTTAAATTTT
66 ATTAAAAAGCTTAGATATATTAGAACTTTAAAATATATTTCTTAAATGACATTTGTTTAAATTTT
6201 ACAGTTTTTTGTTAGAAATAAACTTTCACAGTTATTCAACTAAAAACTCTATTTTAATTTAATTA
131 ACAGTTTTTTGTTAGAAATAAACTTTCACAGTTATTCAACTAAAAACTCTATTTTAATTTAATTA
6266 AATTCAATATTTTTATAAATATTTTATTTTAC
196 AATTCAATA--TTTATAAATATTTTATTTTAC
* *
6298 CTATTTTTATTTGATTAAATCTAATATCCTTATACCTATTTTATTTTTACCGTATTACTAATTTA
1 CTATTTTTATTTGATTAAATCTAATATCCTTATACATATTTTATTTTTACCATATTACTAATTTA
* * * *
6363 ATTAAAAAGCTTAGATATATTAGAATTTTTCAAATATATTTGTTAAATGATA-TTGTTTAAATTT
66 ATTAAAAAGCTTAGATATATTAGAA-CTTTAAAATATATTTCTTAAATGACATTTGTTTAAATTT
* *
6427 TACAGTTTTTTGTTAGAAATAAACTTTTACAGTTATTCAACTAAAAACTCTATTTTTATTTAATT
130 TACAGTTTTTTGTTAGAAATAAACTTTCACAGTTATTCAACTAAAAACTCTATTTTAATTTAATT
* *
6492 AAATTTAATATTTATAGATATTTTATTTTAC
195 AAATTCAATATTTATAAATATTTTATTTTAC
6523 C
1 C
6524 ACTATCATTT
Statistics
Matches: 215, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
225 21 0.10
227 172 0.80
228 22 0.10
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.49
Consensus pattern (225 bp):
CTATTTTTATTTGATTAAATCTAATATCCTTATACATATTTTATTTTTACCATATTACTAATTTA
ATTAAAAAGCTTAGATATATTAGAACTTTAAAATATATTTCTTAAATGACATTTGTTTAAATTTT
ACAGTTTTTTGTTAGAAATAAACTTTCACAGTTATTCAACTAAAAACTCTATTTTAATTTAATTA
AATTCAATATTTATAAATATTTTATTTTAC
Found at i:6989 original size:16 final size:16
Alignment explanation
Indices: 6943--6983 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
6933 TGTCACTCAG
6943 GTTTTGGGTCATTCGA
1 GTTTTGGGTCATTCGA
6959 GTTTTGGGTCATTCGA
1 GTTTTGGGTCATTCGA
6975 GTTTTGGGT
1 GTTTTGGGT
6984 TTTTCGGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.10, C:0.10, G:0.34, T:0.46
Consensus pattern (16 bp):
GTTTTGGGTCATTCGA
Found at i:10287 original size:16 final size:16
Alignment explanation
Indices: 10266--10296 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10256 TTAAAAATAG
10266 TTTGATTTATTTATAA
1 TTTGATTTATTTATAA
10282 TTTGATTTATTTATA
1 TTTGATTTATTTATA
10297 TGCACATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTGATTTATTTATAA
Found at i:10322 original size:35 final size:35
Alignment explanation
Indices: 10276--10343 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
10266 TTTGATTTAT
10276 TTATAATTTGATTTATTTATATGCACATATATAGA
1 TTATAATTTGATTTATTTATATGCACATATATAGA
*
10311 TTATAATTTGATTTATTTATATGTACATATATA
1 TTATAATTTGATTTATTTATATGCACATATATA
10344 TTCTTTTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.51
Consensus pattern (35 bp):
TTATAATTTGATTTATTTATATGCACATATATAGA
Found at i:14158 original size:10 final size:11
Alignment explanation
Indices: 14141--14165 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
14131 TACTTCATTT
14141 CAAAAAAAGAA
1 CAAAAAAAGAA
14152 CAAAAAAAGAA
1 CAAAAAAAGAA
14163 CAA
1 CAA
14166 TGAATATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.12, G:0.08, T:0.00
Consensus pattern (11 bp):
CAAAAAAAGAA
Found at i:15412 original size:23 final size:23
Alignment explanation
Indices: 15386--15434 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
15376 CTAAATTTCT
* * *
15386 AAGTTTAAATAGTCATCTCTATA
1 AAGTTTAAACAATCAACTCTATA
15409 AAGTTTAAACAATCAACTCTATA
1 AAGTTTAAACAATCAACTCTATA
15432 AAG
1 AAG
15435 CTAAATTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (23 bp):
AAGTTTAAACAATCAACTCTATA
Found at i:23076 original size:21 final size:20
Alignment explanation
Indices: 22996--23087 Score: 130
Period size: 21 Copynumber: 4.4 Consensus size: 20
22986 CTTAGGCAAT
*
22996 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAA-CTTC
23017 TCCAATGAGCTTGGAACATTC
1 TCCAATGAGCTTGGAAC-TTC
23038 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTT-C
23059 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTT-C
*
23080 CCCAATGA
1 TCCAATGA
23088 ACTCCTAGCA
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 64 0.96
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (20 bp):
TCCAATGAGCTTGGAACTTC
Found at i:27138 original size:19 final size:18
Alignment explanation
Indices: 27105--27140 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
27095 TGGAAATAAT
27105 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
27123 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
27141 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Done.