Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012242.1 Corchorus capsularis cultivar CVL-1 contig12263, 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: 9570
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Found at i:71 original size:27 final size:27
Alignment explanation
Indices: 35--99 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
25 AAAGAAGAGT
*
35 AAAAGTGGTAA-TAATAAAAGAGAGTAAG
1 AAAAG-GGTAATTAATAAAA-AAAGTAAG
* *
63 GAAAGGGTAATTAGTAAAAAAAGTAAG
1 AAAAGGGTAATTAATAAAAAAAGTAAG
*
90 AAAAGAGTAA
1 AAAAGGGTAA
100 AAATGATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (27 bp):
AAAAGGGTAATTAATAAAAAAAGTAAG
Found at i:1641 original size:42 final size:39
Alignment explanation
Indices: 1574--1683 Score: 100
Period size: 42 Copynumber: 2.7 Consensus size: 39
1564 AGTCAGTCAC
1574 TTGTATATATG-ATGCATTCATCATGCA-TTGTCCATCTC-T
1 TTGTATATATGTATGCA-TCATCATGCACTT-TCCAT-TCAT
1613 TTGTATATATGTTTATGCATCGATCATGCACTTTCCATTCAT
1 TTGTATATATG--TATGCATC-ATCATGCACTTTCCATTCAT
* *
1655 TAGCATATATGCTCATGCATCCATCATGC
1 TTGTATATATG-T-ATGCAT-CATCATGC
1684 TATCACTTGT
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
39 11 0.18
41 5 0.08
42 41 0.68
43 3 0.05
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.41
Consensus pattern (39 bp):
TTGTATATATGTATGCATCATCATGCACTTTCCATTCAT
Found at i:2744 original size:15 final size:14
Alignment explanation
Indices: 2724--2777 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 14
2714 TAAGAGATAT
*
2724 TTTTCAAAAAAATTG
1 TTTTCAAAAAAA-GG
*
2739 TTTTCAAGAAAAGG
1 TTTTCAAAAAAAGG
*
2753 TTTTC-AAAAATGAG
1 TTTTCAAAAAAAG-G
2767 TTTTCAAAAAA
1 TTTTCAAAAAA
2778 GTTTTTGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 5 0.15
14 12 0.36
15 16 0.48
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.35
Consensus pattern (14 bp):
TTTTCAAAAAAAGG
Found at i:2757 original size:14 final size:13
Alignment explanation
Indices: 2724--2782 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 13
2714 TAAGAGATAT
*
2724 TTTTCAAAAAAATTG
1 TTTTC-AAAAAA-GG
2739 TTTTCAAGAAAAGG
1 TTTTCAA-AAAAGG
*
2753 TTTTCAAAAATGAG
1 TTTTCAAAAAAG-G
2767 TTTTCAAAAAA-G
1 TTTTCAAAAAAGG
2779 TTTT
1 TTTT
2783 TGAGTTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 5 0.13
13 4 0.10
14 21 0.54
15 9 0.23
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (13 bp):
TTTTCAAAAAAGG
Found at i:3460 original size:14 final size:13
Alignment explanation
Indices: 3435--3497 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
3425 CAACTCACAG
3435 AAAAGAA-AAAAA
1 AAAAGAAGAAAAA
*
3447 AAAGGAAGAAAAA
1 AAAAGAAGAAAAA
*
3460 AAAAGAAGAAAGA
1 AAAAGAAGAAAAA
* *
3473 AGAAGAAGGAAAA
1 AAAAGAAGAAAAA
*
3486 AGAAGAA-AAAAA
1 AAAAGAAGAAAAA
3498 CTCAGCCTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
12 10 0.23
13 33 0.77
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAAAA
Found at i:4095 original size:13 final size:13
Alignment explanation
Indices: 4069--4116 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
4059 TATAGTGCAT
*
4069 AAAAAA-AAAGAG
1 AAAAAAGAAAAAG
4081 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
*
4094 AAAGAAAAAAAAAG
1 AAA-AAAGAAAAAG
*
4108 AAGAAAGAA
1 AAAAAAGAA
4117 GAAGCTCTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 6 0.20
13 13 0.43
14 11 0.37
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:4099 original size:17 final size:17
Alignment explanation
Indices: 4079--4116 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
4069 AAAAAAAAAG
4079 AGAAAAAAGAAA-AAGAA
1 AGAAAAAA-AAAGAAGAA
4096 AGAAAAAAAAAGAAGAA
1 AGAAAAAAAAAGAAGAA
4113 AGAA
1 AGAA
4117 GAAGCTCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAGAAGAA
Found at i:9424 original size:38 final size:39
Alignment explanation
Indices: 9382--9477 Score: 113
Period size: 38 Copynumber: 2.5 Consensus size: 39
9372 AGTGAAAAGA
* * *
9382 AAAAGAAGTAATCAGTCAATTGGTAATTAAGAG-GAAGT
1 AAAAGAAGTAATCAGTAAATTGATAACTAAGAGAGAAGT
* *
9420 AAAAGGATTAATCAGTAAATTGATAACTAAGAGAAGAAGT
1 AAAAGAAGTAATCAGTAAATTGATAACTAAGAG-AGAAGT
* *
9460 AAAAGTAGCAATCAGTAA
1 AAAAGAAGTAATCAGTAA
9478 GTAAGGGTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 28 0.58
40 20 0.42
ACGTcount: A:0.51, C:0.06, G:0.21, T:0.22
Consensus pattern (39 bp):
AAAAGAAGTAATCAGTAAATTGATAACTAAGAGAGAAGT
Found at i:9539 original size:32 final size:31
Alignment explanation
Indices: 9469--9541 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
9459 TAAAAGTAGC
*
9469 AATCAGTAAGTAAGGGTCAAAGTAAAAGGGT
1 AATCAGTAAGTAAGAGTCAAAGTAAAAGGGT
* * * *
9500 AAGTCAGTAATTAAGAGTCAAGGTAGAAGGATT
1 AA-TCAGTAAGTAAGAGTCAAAGTAAAAGG-GT
9533 AATCAGTAA
1 AATCAGTAA
9542 ATTGATAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 2 0.06
32 30 0.86
33 3 0.09
ACGTcount: A:0.45, C:0.07, G:0.26, T:0.22
Consensus pattern (31 bp):
AATCAGTAAGTAAGAGTCAAAGTAAAAGGGT
Done.