Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021071.1 Corchorus olitorius cultivar O-4 contig21104, 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: 23140
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1557 original size:132 final size:129
Alignment explanation
Indices: 1310--1564 Score: 350
Period size: 129 Copynumber: 2.0 Consensus size: 129
1300 ATTATTCTTT
* * *
1310 TTTTGTACATGAATATTTTCCTTCTCGCAATTACTGCAACTCTCATTTATATATGTTAAACCTAA
1 TTTTGTACATGAATATTTTCCTTCTCGCAATTACTGCAACTCTCATTTACATATATTAAACATAA
* *
1375 ATCACAAAACATGAAACCTCCTATACAAAGCTTTGTTCGATTATACTAACTTTTGTAAAATATC
66 ACCACAAAACATGAAACCTCCTATACAAAGCTTTCTTCGATTATACTAACTTTTGTAAAATATC
* * * * * * *
1439 TTTTGTACCTGATTATTTTCTTTCTCGGAATTATTGCAATTCTCATTTACATATATTGAACTTAT
1 TTTTGTACATGAATATTTTCCTTCTCGCAATTACTGCAACTCTCATTTACATATATT-AA---AC
*
1504 ATAAACCACAAAACATG-AACCTCCTATACAAAGCTTTCTTCGATTATATTAACTTTTGTAA
62 ATAAACCACAAAACATGAAACCTCCTATACAAAGCTTTCTTCGATTATACTAACTTTTGTAA
1565 TATAAGTTTA
Statistics
Matches: 109, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
129 49 0.45
130 2 0.02
132 42 0.39
133 16 0.15
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (129 bp):
TTTTGTACATGAATATTTTCCTTCTCGCAATTACTGCAACTCTCATTTACATATATTAAACATAA
ACCACAAAACATGAAACCTCCTATACAAAGCTTTCTTCGATTATACTAACTTTTGTAAAATATC
Found at i:4248 original size:15 final size:14
Alignment explanation
Indices: 4230--4268 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
4220 AGAACTTGAC
4230 TTTTTTTTTAGAGTT
1 TTTTTTTTTAGA-TT
*
4245 TTTTTTTTAAGATT
1 TTTTTTTTTAGATT
*
4259 TATTTTTTTA
1 TTTTTTTTTA
4269 AAAGGATTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTAGATT
Found at i:4269 original size:15 final size:15
Alignment explanation
Indices: 4230--4269 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
4220 AGAACTTGAC
4230 TTTTTTTTT-AGAGT
1 TTTTTTTTTAAGAGT
4244 TTTTTTTTTAAGA-T
1 TTTTTTTTTAAGAGT
4258 TTATTTTTTTAA
1 TT-TTTTTTTAA
4270 AAGGATTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.72
Consensus pattern (15 bp):
TTTTTTTTTAAGAGT
Found at i:4284 original size:24 final size:24
Alignment explanation
Indices: 4256--4302 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
4246 TTTTTTTAAG
*
4256 ATTTATTTTTTTAAAAGGATTAGT
1 ATTTATTTTTGTAAAAGGATTAGT
4280 ATTTATTTTTGTAAAAGGATTAG
1 ATTTATTTTTGTAAAAGGATTAG
4303 GGTATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
ATTTATTTTTGTAAAAGGATTAGT
Found at i:4310 original size:24 final size:24
Alignment explanation
Indices: 4259--4310 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
4249 TTTTAAGATT
* * *
4259 TATTTTTTTAAAAGGATTAGTATT
1 TATTTTTGTAAAAGGATTAGGATA
*
4283 TATTTTTGTAAAAGGATTAGGGTA
1 TATTTTTGTAAAAGGATTAGGATA
4307 TATT
1 TATT
4311 AAGAGATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (24 bp):
TATTTTTGTAAAAGGATTAGGATA
Found at i:5052 original size:13 final size:13
Alignment explanation
Indices: 5019--5044 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5009 AGAACTTGAC
5019 GTTTTTTTTAGAT
1 GTTTTTTTTAGAT
5032 GTTTTTTTTAGAT
1 GTTTTTTTTAGAT
5045 TTATTTTTGT
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:0.15, T:0.69
Consensus pattern (13 bp):
GTTTTTTTTAGAT
Found at i:5075 original size:23 final size:23
Alignment explanation
Indices: 5039--5086 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 23
5029 GATGTTTTTT
5039 TTAGATTTATTTTTGTAAAAGGA
1 TTAGATTTATTTTTGTAAAAGGA
5062 TTAGTATTTATTTTTGTAAAAGGA
1 TTAG-ATTTATTTTTGTAAAAGGA
5086 T
1 T
5087 GAGGGTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (23 bp):
TTAGATTTATTTTTGTAAAAGGA
Found at i:5097 original size:24 final size:24
Alignment explanation
Indices: 5046--5097 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5036 TTTTTAGATT
* * *
5046 TATTTTTGTAAAAGGATTAGTATT
1 TATTTTTGTAAAAGGATGAGGATA
*
5070 TATTTTTGTAAAAGGATGAGGGTA
1 TATTTTTGTAAAAGGATGAGGATA
5094 TATT
1 TATT
5098 AAGAGATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (24 bp):
TATTTTTGTAAAAGGATGAGGATA
Found at i:5232 original size:6 final size:6
Alignment explanation
Indices: 5214--5243 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
5204 GTTTAGACTT
5214 ATATAG TATATAG ATATAG ATATAG ATATA
1 ATATAG -ATATAG ATATAG ATATAG ATATA
5244 TATAATTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:5238 original size:12 final size:13
Alignment explanation
Indices: 5214--5247 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
5204 GTTTAGACTT
5214 ATATAGTATATAG
1 ATATAGTATATAG
5227 ATATAG-ATATAG
1 ATATAGTATATAG
5239 ATATA-TATA
1 ATATAGTATA
5248 ATTCGTCGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (13 bp):
ATATAGTATATAG
Found at i:15009 original size:68 final size:68
Alignment explanation
Indices: 14899--15029 Score: 217
Period size: 68 Copynumber: 1.9 Consensus size: 68
14889 CAACTAAGGA
* * * *
14899 AAAAAATGGTGGGAGCACCATTAATTACATCTCAATGCTAAAATTACATATAAAGACAATGCACT
1 AAAAAATGGTAGGAACAACATTAATTACATCTAAATGCTAAAATTACATATAAAGACAATGCACT
14964 AAG
66 AAG
*
14967 AAAAAATGGTAGGAACAACATTAATTACATCTAAATGTTAAAATTACATATAAAGACAATGCA
1 AAAAAATGGTAGGAACAACATTAATTACATCTAAATGCTAAAATTACATATAAAGACAATGCA
15030 TTTCAAGCAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (68 bp):
AAAAAATGGTAGGAACAACATTAATTACATCTAAATGCTAAAATTACATATAAAGACAATGCACT
AAG
Found at i:16632 original size:16 final size:16
Alignment explanation
Indices: 16607--16655 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
16597 TACCCATTTC
16607 AATTATAATATAAACT
1 AATTATAATATAAACT
*
16623 AATT-TGAATA-AAA-A
1 AATTAT-AATATAAACT
16637 AATTATAATATAAACT
1 AATTATAATATAAACT
16653 AAT
1 AAT
16656 AAAAGTCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
15 8 0.30
16 11 0.41
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (16 bp):
AATTATAATATAAACT
Found at i:16646 original size:14 final size:16
Alignment explanation
Indices: 16607--16651 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
16597 TACCCATTTC
*
16607 AATTATAATATAAACT
1 AATTATAATATAAACA
16623 AATT-TGAATA-AAA-A
1 AATTAT-AATATAAACA
16637 AATTATAATATAAAC
1 AATTATAATATAAAC
16652 TAATAAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
14 8 0.33
15 8 0.33
16 8 0.33
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (16 bp):
AATTATAATATAAACA
Found at i:19529 original size:24 final size:24
Alignment explanation
Indices: 19502--19547 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
19492 CAAGTTTTGG
* *
19502 AAATATGTATCCACTATTATAAGA
1 AAATATGCATCCACTAGTATAAGA
19526 AAATATGCATCCACTAGTATAA
1 AAATATGCATCCACTAGTATAA
19548 TATTTGTTTA
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:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (24 bp):
AAATATGCATCCACTAGTATAAGA
Found at i:21437 original size:27 final size:28
Alignment explanation
Indices: 21399--21455 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
21389 ATTAAATCTA
*
21399 ATATCTTTATACCT-TTTT-TTTTTCATC
1 ATATCCTTATACCTATTTTATTTTT-ATC
21426 ATATCCTTATACCTATTTTATTTTTATC
1 ATATCCTTATACCTATTTTATTTTTATC
21454 AT
1 AT
21456 TTTACTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 13 0.48
28 9 0.33
29 5 0.19
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.60
Consensus pattern (28 bp):
ATATCCTTATACCTATTTTATTTTTATC
Done.