Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012106.1 Corchorus olitorius cultivar O-4 contig12139, 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: 8849
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Found at i:2705 original size:13 final size:13
Alignment explanation
Indices: 2679--2714 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
2669 AGAAAATCAT
2679 TTTTCAAGAAAAGG
1 TTTTCAA-AAAAGG
2693 TTTTCAAAAAAGG
1 TTTTCAAAAAAGG
2706 TTTTCAAAA
1 TTTTCAAAA
2715 GGTTTTGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAAAGG
Found at i:2714 original size:11 final size:12
Alignment explanation
Indices: 2687--2720 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
2677 ATTTTTCAAG
2687 AAAAGGTTTTCAA
1 AAAAGGTTTTC-A
2700 AAAAGGTTTTC-
1 AAAAGGTTTTCA
2711 AAAAGGTTTT
1 AAAAGGTTTT
2721 GGGTTTTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
13 11 0.52
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (12 bp):
AAAAGGTTTTCA
Found at i:5193 original size:64 final size:64
Alignment explanation
Indices: 5088--5463 Score: 421
Period size: 64 Copynumber: 5.9 Consensus size: 64
5078 TGCTAGAAAG
* * * * * *
5088 AATTTTCAGATGATGATCGGAAGACGATCTTGTCAAAAAGTACGCTAGAGGATGGTTTCTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
*
5152 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * ** *
5216 AGTTTTTAGAAGTACATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * ** * * * * *
5280 AGTTTTTAGAAGTACATCGGAAGACAATCTTATCAAGAAGTACGCTAGAAGATGGTTTTTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * * * *
5344 AATTTTAAGAAGTTGATCGGAAGACGATCTTGTTAAAAAGTACACCAGAAGATAGTTTCTTGAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTC-TCAAA
** ** * * * *
5409 AGGTTTCAGATTTTGGTCGGAAGACGATCTTGTTAAG-AGATGCACCAGAAAATGG
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAG-TACACCAGAAGATGG
5464 CTATTTGGAA
Statistics
Matches: 270, Mismatches: 40, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
64 224 0.83
65 46 0.17
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (64 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
Found at i:5228 original size:36 final size:36
Alignment explanation
Indices: 5187--5295 Score: 101
Period size: 36 Copynumber: 3.2 Consensus size: 36
5177 GATCTTGTCA
5187 AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTT
1 AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTT
* * * * *
5223 AGAAGTACATCGGAAGACGATCTTGTC---A------
1 AGAAGTACACCAGAAGATGGT-TTCTCAAGAGTTTTT
5251 AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTT
1 AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTT
5287 AGAAGTACA
1 AGAAGTACA
5296 TCGGAAGACA
Statistics
Matches: 53, Mismatches: 10, Indels: 20
0.64 0.12 0.24
Matches are distributed among these distances:
27 4 0.08
28 17 0.32
30 1 0.02
34 1 0.02
36 26 0.49
37 4 0.08
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (36 bp):
AGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTT
Found at i:5751 original size:51 final size:51
Alignment explanation
Indices: 5675--6055 Score: 649
Period size: 51 Copynumber: 7.5 Consensus size: 51
5665 GGTTTTCTCG
*
5675 AGATTGAATTGGAAGATAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA
1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA
*
5726 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCC-TTTTA
1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA
* * *
5776 AGATTGAATTGGAAGATAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTGA
1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA
* *
5827 AGATTGAATTGGAAGACAGTTCAAAAGATAAGCGGAAGACGGTCCTTTTAA
1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA
* *
5878 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGATGGTCCTTTTTA
1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA
5929 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC-TTTTA
1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA
*
5979 AGATTGAATTGGAAGACAGTTCAAAGGATAGGCGGAAGACGGTCCTTTTTA
1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA
*
6030 AGATTGAATTGGAAGATAGTTCAAAG
1 AGATTGAATTGGAAGACAGTTCAAAG
6056 AAATTGATCG
Statistics
Matches: 310, Mismatches: 18, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
50 96 0.31
51 214 0.69
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.25
Consensus pattern (51 bp):
AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA
Found at i:5789 original size:101 final size:101
Alignment explanation
Indices: 5675--6055 Score: 663
Period size: 101 Copynumber: 3.8 Consensus size: 101
5665 GGTTTTCTCG
* *
5675 AGATTGAATTGGAAGATAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGAATTGGAA
1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTTAAGATTGAATTGGAA
*
5740 GACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTA
66 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
* *
5776 AGATTGAATTGGAAGATAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTGAAGATTGAATTGGAA
1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTTAAGATTGAATTGGAA
*
5841 GACAGTTCAAAAGATAAGCGGAAGACGGTCCTTTTAA
66 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT-A
*
5878 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGATGGTCCTTTTTAAGATTGAATTGGAA
1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTTAAGATTGAATTGGAA
5943 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
66 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
* *
5979 AGATTGAATTGGAAGACAGTTCAAAGGATAGGCGGAAGACGGTCCTTTTTAAGATTGAATTGGAA
1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTTAAGATTGAATTGGAA
*
6044 GATAGTTCAAAG
66 GACAGTTCAAAG
6056 AAATTGATCG
Statistics
Matches: 267, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
101 170 0.64
102 97 0.36
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.25
Consensus pattern (101 bp):
AGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTTAAGATTGAATTGGAA
GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
Found at i:5893 original size:28 final size:28
Alignment explanation
Indices: 5810--5894 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 28
5800 AGGATAAGCA
*
5810 GAAGACGGTCCTTTTGAAGATTGAATTG
1 GAAGACGGTCCTTTTAAAGATTGAATTG
* ** **
5838 GAAGACAG---TTCAAAAGA-T-AAGCG
1 GAAGACGGTCCTTTTAAAGATTGAATTG
5861 GAAGACGGTCCTTTTAAAGATTGAATTG
1 GAAGACGGTCCTTTTAAAGATTGAATTG
5889 GAAGAC
1 GAAGAC
5895 AGTTCAAAGG
Statistics
Matches: 41, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
23 10 0.24
24 1 0.02
25 6 0.15
26 7 0.17
27 1 0.02
28 16 0.39
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (28 bp):
GAAGACGGTCCTTTTAAAGATTGAATTG
Found at i:6024 original size:203 final size:203
Alignment explanation
Indices: 5675--6054 Score: 679
Period size: 203 Copynumber: 1.9 Consensus size: 203
5665 GGTTTTCTCG
* *
5675 AGATTGAATTGGAAGATAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGAATTGGAA
1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTTAAGATTGAATTGGAA
*
5740 GACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTAAGATTGAATTGGAAGATAGTTCAAAGGAT
66 GACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGAT
5805 AAGCAGAAGACGGTCCTTTTGAAGATTGAATTGGAAGACAGTTCAAAAGATAAGCGGAAGACGGT
131 AAGCAGAAGACGGTCCTTTTGAAGATTGAATTGGAAGACAGTTCAAAAGATAAGCGGAAGACGGT
5870 CCTTTTAA
196 CCTTTTAA
*
5878 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGATGGTCCTTTTTAAGATTGAATTGGAA
1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTTAAGATTGAATTGGAA
*
5943 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGAT
66 GACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGAT
* * * *
6008 AGGCGGAAGACGGTCCTTTTTAAGATTGAATTGGAAGATAGTTCAAA
131 AAGCAGAAGACGGTCCTTTTGAAGATTGAATTGGAAGACAGTTCAAA
6055 GAAATTGATC
Statistics
Matches: 168, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
203 168 1.00
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.26
Consensus pattern (203 bp):
AGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTTAAGATTGAATTGGAA
GACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTAAGATTGAATTGGAAGACAGTTCAAAGGAT
AAGCAGAAGACGGTCCTTTTGAAGATTGAATTGGAAGACAGTTCAAAAGATAAGCGGAAGACGGT
CCTTTTAA
Done.