Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024020.1 Corchorus olitorius cultivar O-4 contig24053, 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: 27683
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:4185 original size:33 final size:32
Alignment explanation
Indices: 4101--4185 Score: 75
Period size: 32 Copynumber: 2.6 Consensus size: 32
4091 CCAAGCCGCG
* *
4101 CCGAGACACATGCCCGGCCACAGCCCGGCCAC
1 CCGAGCCATATGCCCGGCCACAGCCCGGCCAC
* * *
4133 CCGAGCCATCTACCTGGCCAC-GCCCGGACTC-C
1 CCGAGCCATATGCCCGGCCACAGCCCGG-C-CAC
*
4165 TCCGCGCCATATGCCCGGCCA
1 -CCGAGCCATATGCCCGGCCA
4186 ACCGCGCCGC
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
31 6 0.15
32 18 0.44
33 17 0.41
ACGTcount: A:0.18, C:0.49, G:0.24, T:0.09
Consensus pattern (32 bp):
CCGAGCCATATGCCCGGCCACAGCCCGGCCAC
Found at i:4463 original size:21 final size:21
Alignment explanation
Indices: 4423--4505 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
4413 TCAAGCCATT
*
4423 ACCAGCCATTCACCGTGCCACC
1 ACCAGCCATGC-CCGTGCCACC
*
4445 ACCAGCCATGCCTGTGCCACC
1 ACCAGCCATGCCCGTGCCACC
* * ** *
4466 ATCGGTTAAGCCCGTGCCACC
1 ACCAGCCATGCCCGTGCCACC
* * *
4487 ACCGGCTATGCCTGTGCCA
1 ACCAGCCATGCCCGTGCCA
4506 TCGCCATTCC
Statistics
Matches: 49, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 39 0.80
22 10 0.20
ACGTcount: A:0.19, C:0.43, G:0.20, T:0.17
Consensus pattern (21 bp):
ACCAGCCATGCCCGTGCCACC
Found at i:7769 original size:15 final size:16
Alignment explanation
Indices: 7736--7775 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
7726 TTACTTTGCT
7736 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
7752 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
7767 TTGCTTTCT
1 TTGTTTTCT
7776 TTCAATCTCT
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:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:8371 original size:60 final size:60
Alignment explanation
Indices: 8284--8404 Score: 179
Period size: 60 Copynumber: 2.0 Consensus size: 60
8274 AAACTATACT
* *
8284 AGTATAACATTTACTCATTTATTTTCCTTAAATGCATGCAATGGGCTAAAAATGGAAAGA
1 AGTACAACATTTACTCATTTACTTTCCTTAAATGCATGCAATGGGCTAAAAATGGAAAGA
* * * * *
8344 AGTACAACTTTTATTCATTTACTTTCCTTGAATGCATGGAATGGGCTAAAAGTGGAAAGA
1 AGTACAACATTTACTCATTTACTTTCCTTAAATGCATGCAATGGGCTAAAAATGGAAAGA
8404 A
1 A
8405 ACTTTGGCTT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.33
Consensus pattern (60 bp):
AGTACAACATTTACTCATTTACTTTCCTTAAATGCATGCAATGGGCTAAAAATGGAAAGA
Found at i:9731 original size:36 final size:33
Alignment explanation
Indices: 9658--9737 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 33
9648 TCAGTTGCAA
*
9658 AGGGAGAGAGAGGCTGAGGCTGCTCAGATTTAT
1 AGGGAGAGAGAGGCTGAGGCTGCTCAGATTTAG
*
9691 AGGGAGAGGGAGGCTGATGCTGCTGCTCAGAGTTT-G
1 AGGGAGAGAGAGGCTGA-G--GCTGCTCAGA-TTTAG
9727 AGGGAGCAGAG
1 AGGGAG-AGAG
9738 GGAGATAGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
33 16 0.41
34 1 0.03
36 16 0.41
37 6 0.15
ACGTcount: A:0.25, C:0.12, G:0.44, T:0.19
Consensus pattern (33 bp):
AGGGAGAGAGAGGCTGAGGCTGCTCAGATTTAG
Found at i:13930 original size:28 final size:28
Alignment explanation
Indices: 13858--14099 Score: 153
Period size: 33 Copynumber: 7.8 Consensus size: 28
13848 TTTAAATTAA
13858 ATTGACACCAGAAGTTGTCAT-ATTAAATT
1 ATTGACACCAGAAGTTGTCATGA--AAATT
13887 ATCTTGACACCAGAAGTTGTCATGAAAATT
1 A--TTGACACCAGAAGTTGTCATGAAAATT
* *
13917 ATTGACACCAGAAGTTCTCATATCAAATTATT
1 ATTGACACCAGAAGTTGTC--ATGAAA--ATT
* * *
13949 ATCTTGATACCAGGAGTTTTCATGAAAATT
1 A--TTGACACCAGAAGTTGTCATGAAAATT
* * *
13979 ATTGACACCAGGAGTTTTCATATCAAATTATT
1 ATTGACACCAGAAGTTGTC--ATGAAA--ATT
*
14011 ATCTTGACACCAAAAGTTGTCATGCTGAGGAAATT
1 A--TTGACACCAGAAGTTGTCA---TGA--AAATT
*
14046 ATTGACACTAGAAGTTGTCATGCTGAGTAAATT
1 ATTGACACCAGAAGTTGTCA---TGA--AAATT
14079 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
14100 CCTAAGATTG
Statistics
Matches: 177, Mismatches: 16, Indels: 39
0.76 0.07 0.17
Matches are distributed among these distances:
28 34 0.19
29 1 0.01
30 21 0.12
31 20 0.11
32 15 0.08
33 48 0.27
34 30 0.17
35 6 0.03
37 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (28 bp):
ATTGACACCAGAAGTTGTCATGAAAATT
Found at i:13981 original size:62 final size:62
Alignment explanation
Indices: 13858--14066 Score: 262
Period size: 62 Copynumber: 3.3 Consensus size: 62
13848 TTTAAATTAA
* *
13858 ATTGACACCAGAAGTTGTCATAT-TAA--ATTATCTTGACACCAGAAGTTGTCATGAAAATT
1 ATTGACACCAGAAGTTCTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
* * *
13917 ATTGACACCAGAAGTTCTCATATCAAATTATTATCTTGATACCAGGAGTTTTCATGAAAATT
1 ATTGACACCAGAAGTTCTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
* * *
13979 ATTGACACCAGGAGTTTTCATATCAAATTATTATCTTGACACCAAAAGTTGTCATGCTGAGGAAA
1 ATTGACACCAGAAGTTCTCATATCAAATTATTATCTTGACACCAGAAGTTGTCA---TGA--AAA
14044 TT
61 TT
* *
14046 ATTGACACTAGAAGTTGTCAT
1 ATTGACACCAGAAGTTCTCAT
14067 GCTGAGTAAA
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
59 22 0.17
60 2 0.02
62 78 0.61
65 3 0.02
67 23 0.18
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (62 bp):
ATTGACACCAGAAGTTCTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
Found at i:23910 original size:21 final size:22
Alignment explanation
Indices: 23881--23933 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
23871 CTAAAAAAAT
23881 AACTTTATTAATCTCTT-TGTA
1 AACTTTATTAATCTCTTATGTA
23902 AA-TATTATTAATCTCTTATGTA
1 AACT-TTATTAATCTCTTATGTA
23924 AACTTTATTA
1 AACTTTATTA
23934 TTTTGCATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 1 0.03
21 15 0.52
22 12 0.41
23 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (22 bp):
AACTTTATTAATCTCTTATGTA
Found at i:26071 original size:32 final size:32
Alignment explanation
Indices: 26035--26097 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
26025 CCAGTATCAT
26035 TGATTTTTGTTGAATTGTTTGAATAAATAATA
1 TGATTTTTGTTGAATTGTTTGAATAAATAATA
26067 TGATTTTTGTTGAATTGTTTGAATAAATAAT
1 TGATTTTTGTTGAATTGTTTGAATAAATAAT
26098 TACTTTTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (32 bp):
TGATTTTTGTTGAATTGTTTGAATAAATAATA
Found at i:27657 original size:2 final size:2
Alignment explanation
Indices: 27650--27683 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
27640 AGTTAGTGGT
27650 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.