Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007800.1 Corchorus capsularis cultivar CVL-1 contig07821, 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: 30019
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:5983 original size:19 final size:19
Alignment explanation
Indices: 5959--6021 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
5949 TTCCACTTTG
5959 TCAATTTCAGTTTTGTTCT
1 TCAATTTCAGTTTTGTTCT
* *
5978 TCAATTTGCA-CTTT-TT-G
1 TCAATTT-CAGTTTTGTTCT
5995 TCAATTTCAGTTTTGTTCT
1 TCAATTTCAGTTTTGTTCT
*
6014 TCATTTTC
1 TCAATTTC
6022 CACTTTTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 2 0.06
17 10 0.29
18 4 0.11
19 17 0.49
20 2 0.06
ACGTcount: A:0.16, C:0.17, G:0.10, T:0.57
Consensus pattern (19 bp):
TCAATTTCAGTTTTGTTCT
Found at i:6001 original size:36 final size:36
Alignment explanation
Indices: 5943--6029 Score: 133
Period size: 36 Copynumber: 2.5 Consensus size: 36
5933 TTTTAGTTGG
*
5943 TTCAAGTTCCAC--TTTGTCAATTTCAGTTTTGTTC
1 TTCAATTTCCACTTTTTGTCAATTTCAGTTTTGTTC
*
5977 TTCAATTTGCACTTTTTGTCAATTTCAGTTTTGTTC
1 TTCAATTTCCACTTTTTGTCAATTTCAGTTTTGTTC
*
6013 TTCATTTTCCACTTTTT
1 TTCAATTTCCACTTTTT
6030 ATCAGTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
34 10 0.21
36 37 0.79
ACGTcount: A:0.16, C:0.20, G:0.09, T:0.55
Consensus pattern (36 bp):
TTCAATTTCCACTTTTTGTCAATTTCAGTTTTGTTC
Found at i:6175 original size:29 final size:29
Alignment explanation
Indices: 6103--6194 Score: 103
Period size: 29 Copynumber: 3.2 Consensus size: 29
6093 GCTTTGTTGA
6103 TGTTTATTTGGGTTTTGATATGATAGGAC
1 TGTTTATTTGGGTTTTGATATGATAGGAC
*** ****
6132 TGAAAATGACTGTTTTGATATGATAGGAC
1 TGTTTATTTGGGTTTTGATATGATAGGAC
* *
6161 TGTTTATTTGGGTTTTAATATGATAGGAT
1 TGTTTATTTGGGTTTTGATATGATAGGAC
6190 TGTTT
1 TGTTT
6195 TGTAGTTGGC
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (29 bp):
TGTTTATTTGGGTTTTGATATGATAGGAC
Found at i:7043 original size:32 final size:32
Alignment explanation
Indices: 7007--7219 Score: 255
Period size: 32 Copynumber: 6.7 Consensus size: 32
6997 CTAAAATTGG
* *
7007 GGCGTTTATTGAACAAAACGCCACCATATCGA
1 GGCGTTTAATGAACAAAACGCCACCATATAGA
* *
7039 GGCGTTCAATGAACAAAACACCACCATATAGA
1 GGCGTTTAATGAACAAAACGCCACCATATAGA
* * * * *
7071 GACGTTTAAAGAACAAGACACCACCATATAGT
1 GGCGTTTAATGAACAAAACGCCACCATATAGA
* *
7103 GGCATTCAATGAACAAAACGCCACCATATAGA
1 GGCGTTTAATGAACAAAACGCCACCATATAGA
* * * *
7135 GACGTTTAAAGAACAAAACACCACCATATAGT
1 GGCGTTTAATGAACAAAACGCCACCATATAGA
* * *
7167 GGCATTCAATGAACAAAACGCCACCATATAGG
1 GGCGTTTAATGAACAAAACGCCACCATATAGA
*
7199 GGTGTTTAATGAACAAAACGC
1 GGCGTTTAATGAACAAAACGC
7220 TGGTAAATTT
Statistics
Matches: 150, Mismatches: 31, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 150 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (32 bp):
GGCGTTTAATGAACAAAACGCCACCATATAGA
Found at i:7077 original size:64 final size:64
Alignment explanation
Indices: 7017--7217 Score: 312
Period size: 64 Copynumber: 3.1 Consensus size: 64
7007 GGCGTTTATT
* * * * *
7017 GAACAAAACGCCACCATATCGAGGCGTTCAATGAACAAAACACCACCATATAGAGACGTTTAAA
1 GAACAAAACACCACCATATAGTGGCATTCAATGAACAAAACGCCACCATATAGAGACGTTTAAA
*
7081 GAACAAGACACCACCATATAGTGGCATTCAATGAACAAAACGCCACCATATAGAGACGTTTAAA
1 GAACAAAACACCACCATATAGTGGCATTCAATGAACAAAACGCCACCATATAGAGACGTTTAAA
* ** *
7145 GAACAAAACACCACCATATAGTGGCATTCAATGAACAAAACGCCACCATATAGGGGTGTTTAAT
1 GAACAAAACACCACCATATAGTGGCATTCAATGAACAAAACGCCACCATATAGAGACGTTTAAA
7209 GAACAAAAC
1 GAACAAAAC
7218 GCTGGTAAAT
Statistics
Matches: 126, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 126 1.00
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17
Consensus pattern (64 bp):
GAACAAAACACCACCATATAGTGGCATTCAATGAACAAAACGCCACCATATAGAGACGTTTAAA
Found at i:8523 original size:21 final size:21
Alignment explanation
Indices: 8473--8512 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
8463 AGCTCATCGA
8473 AATCAAATTAGGGTTCTTGAG
1 AATCAAATTAGGGTTCTTGAG
*
8494 TATCAAATTAGGGTTCTTG
1 AATCAAATTAGGGTTCTTG
8513 GAACTGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.38
Consensus pattern (21 bp):
AATCAAATTAGGGTTCTTGAG
Found at i:12098 original size:10 final size:10
Alignment explanation
Indices: 12083--12115 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
12073 ACTGGCAATT
12083 GGGCGGGTTC
1 GGGCGGGTTC
12093 GGGCGGGTTC
1 GGGCGGGTTC
12103 GGGCGGGTTC
1 GGGCGGGTTC
12113 GGG
1 GGG
12116 TATTTTCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.64, T:0.18
Consensus pattern (10 bp):
GGGCGGGTTC
Found at i:13241 original size:13 final size:14
Alignment explanation
Indices: 13223--13251 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
13213 ATAACCGGAC
13223 TTTGCATTCAT-CA
1 TTTGCATTCATGCA
13236 TTTGCATTCATGCA
1 TTTGCATTCATGCA
13250 TT
1 TT
13252 GAGTAGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTGCATTCATGCA
Found at i:13356 original size:13 final size:13
Alignment explanation
Indices: 13338--13362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13328 AAGTTTTTTT
13338 TTTTCAAAAAATG
1 TTTTCAAAAAATG
13351 TTTTCAAAAAAT
1 TTTTCAAAAAAT
13363 CATGTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAAATG
Found at i:25969 original size:29 final size:29
Alignment explanation
Indices: 25892--25949 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
25882 TTTGATTTCT
*
25892 TGTTGATTCAAGTGCAGGTTGTGCACTTG
1 TGTTGATTCAAGTGCGGGTTGTGCACTTG
25921 TGTTGATTCAAGTGCGGGTTGTGCACTTG
1 TGTTGATTCAAGTGCGGGTTGTGCACTTG
25950 GATTGGTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.16, C:0.14, G:0.33, T:0.38
Consensus pattern (29 bp):
TGTTGATTCAAGTGCGGGTTGTGCACTTG
Done.