Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024390.1 Corchorus olitorius cultivar O-4 contig24423, 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: 19129
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2984 original size:15 final size:15
Alignment explanation
Indices: 2964--2995 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2954 AAACTAAGTG
2964 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
2979 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
2994 GA
1 GA
2996 ACCCCCAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50
Consensus pattern (15 bp):
GAGCTTGTTGATTTT
Found at i:3975 original size:25 final size:24
Alignment explanation
Indices: 3938--3984 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
3928 TAGAAAAATT
3938 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
3964 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
3985 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:4627 original size:21 final size:21
Alignment explanation
Indices: 4601--4642 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4591 TTCAACAGAC
*
4601 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGAGCAGGAGTTGT
4622 CAAGTCCTGAGCAGGAGTTGT
1 CAAGTCCTGAGCAGGAGTTGT
4643 TCTGATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24
Consensus pattern (21 bp):
CAAGTCCTGAGCAGGAGTTGT
Found at i:4653 original size:71 final size:71
Alignment explanation
Indices: 4529--4711 Score: 278
Period size: 71 Copynumber: 2.6 Consensus size: 71
4519 TTTTCCGCAA
* *
4529 CAAGTCCTGGGCAGGAGTTGTCCAAGTGCTTGA-CAGGACTTGTTCTAAATTTTCTTCCGTTTTT
1 CAAGTCCTGGGCAGGAGTTGT-CAAGT-CCTGAGCAGGACTTGTTCTAAATTTTCTTCCGTCTTT
4593 CAACAGAC
64 CAACAGAC
* * *
4601 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGAGCAGGAGTTGTTCTGATTTTTCTTCCGTCTTTCA
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGAGCAGGACTTGTTCTAAATTTTCTTCCGTCTTTCA
4666 ACAGAC
66 ACAGAC
* *
4672 CAGGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTT
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGAGCAGGACTT
4712 CTCCTGTTTT
Statistics
Matches: 102, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
70 4 0.04
71 77 0.75
72 21 0.21
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (71 bp):
CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGAGCAGGACTTGTTCTAAATTTTCTTCCGTCTTTCA
ACAGAC
Found at i:7768 original size:13 final size:14
Alignment explanation
Indices: 7750--7779 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
7740 TGTCCGTATC
7750 CCTTTCTT-TTCCT
1 CCTTTCTTCTTCCT
7763 CCTTTCTTCTTCCT
1 CCTTTCTTCTTCCT
7777 CCT
1 CCT
7780 CACTTCCACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (14 bp):
CCTTTCTTCTTCCT
Found at i:8773 original size:23 final size:24
Alignment explanation
Indices: 8726--8773 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
8716 ATCAAACAAG
8726 AAAGGAAGCACAATATCAAAGAAAA
1 AAAGGAAGCACAATA-CAAAGAAAA
8751 AAAGGAAGCACAATA-AAAGAAAA
1 AAAGGAAGCACAATACAAAGAAAA
8774 TGGTAACATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 8 0.35
25 15 0.65
ACGTcount: A:0.67, C:0.10, G:0.17, T:0.06
Consensus pattern (24 bp):
AAAGGAAGCACAATACAAAGAAAA
Found at i:13251 original size:51 final size:51
Alignment explanation
Indices: 13144--13402 Score: 371
Period size: 51 Copynumber: 5.1 Consensus size: 51
13134 TGGGAACTCT
**
13144 AAAA-ACCTAAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCGTTTTG
1 AAAAGACCTAAATTGAATACTTTGAAAAC-TGATGGGAACTTTCCCAATTTG
*
13195 AAAAGACCTAAATTGAATACTTTGAAAACTTATGGGAACTTTCCCAATTTG
1 AAAAGACCTAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCAATTTG
* *
13246 AAAAGAGCTAAATTGAATACTTTGAAAACTGATGGGAACTTCCCCAATTTG
1 AAAAGACCTAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCAATTTG
* * * * *
13297 AAATTGAGCTAAATTGAATACTTTGAAAACTGATGGGAACTTTTCTAATTTT
1 AAA-AGACCTAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCAATTTG
*
13349 AAAAAAGCCT-AATTGAATACTTTGAAAACTGATGGGAACTTTCCCAA-TTG
1 AAAAGA-CCTAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCAATTTG
13399 AAAA
1 AAAA
13403 CTTTGAAAAT
Statistics
Matches: 188, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
50 6 0.03
51 110 0.59
52 72 0.38
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (51 bp):
AAAAGACCTAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCAATTTG
Found at i:13309 original size:103 final size:103
Alignment explanation
Indices: 13144--13402 Score: 382
Period size: 103 Copynumber: 2.5 Consensus size: 103
13134 TGGGAACTCT
**
13144 AAAAA-CCTAAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCGTTTTGAAAAGACCTAAAT
1 AAAAAGCCTAAATTGAATACTTTGAAAAC-TGATGGGAACTTTCCCAATTTGAAAAGACCTAAAT
*
13208 TGAATACTTTGAAAACTTATGGGAACTTTCCCAATTTGA
65 TGAATACTTTGAAAACTGATGGGAACTTTCCCAATTTGA
* * * *
13247 AAAGAG-CTAAATTGAATACTTTGAAAACTGATGGGAACTTCCCCAATTTGAAATTGAGCTAAAT
1 AAAAAGCCTAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCAATTTGAAA-AGACCTAAAT
* * *
13311 TGAATACTTTGAAAACTGATGGGAACTTTTCTAATTTTA
65 TGAATACTTTGAAAACTGATGGGAACTTTCCCAATTTGA
13350 AAAAAGCCT-AATTGAATACTTTGAAAACTGATGGGAACTTTCCCAA-TTGAAAA
1 AAAAAGCCTAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCAATTTGAAAA
13403 CTTTGAAAAT
Statistics
Matches: 140, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
102 28 0.20
103 110 0.79
104 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (103 bp):
AAAAAGCCTAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCAATTTGAAAAGACCTAAATT
GAATACTTTGAAAACTGATGGGAACTTTCCCAATTTGA
Found at i:13398 original size:35 final size:36
Alignment explanation
Indices: 13359--13439 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 36
13349 AAAAAAGCCT
* *
13359 AATTGAATACTTTGAAAA-CTGATGGGAACTTTCCC
1 AATTGAAAACTTTGAAAATCTAATGGGAACTTTCCC
*
13394 AATTGAAAACTTTGAAAATTTAATGGGAACTTTCCC
1 AATTGAAAACTTTGAAAATCTAATGGGAACTTTCCC
13430 AATTTGAAAA
1 AA-TTGAAAA
13440 TCATGAAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 17 0.41
36 17 0.41
37 7 0.17
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (36 bp):
AATTGAAAACTTTGAAAATCTAATGGGAACTTTCCC
Done.