Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007840.1 Corchorus capsularis cultivar CVL-1 contig07861, 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: 13348
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Found at i:1216 original size:9 final size:10
Alignment explanation
Indices: 1192--1256 Score: 73
Period size: 10 Copynumber: 6.4 Consensus size: 10
1182 TAATGTCAAG
1192 GAAAAAGACT
1 GAAAAAGACT
1202 GAAAAAGACT
1 GAAAAAGACT
1212 GAAAAA-A--
1 GAAAAAGACT
1219 GAAAGAAGACT
1 GAAA-AAGACT
1230 GAAAAGAAGACT
1 G-AAA-AAGACT
1242 GAAAGAAGACT
1 GAAA-AAGACT
1253 GAAA
1 GAAA
1257 GAGAATACTG
Statistics
Matches: 50, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
7 4 0.08
8 2 0.04
9 2 0.04
10 16 0.32
11 15 0.30
12 11 0.22
ACGTcount: A:0.62, C:0.08, G:0.23, T:0.08
Consensus pattern (10 bp):
GAAAAAGACT
Found at i:1217 original size:11 final size:11
Alignment explanation
Indices: 1193--1322 Score: 92
Period size: 11 Copynumber: 11.7 Consensus size: 11
1183 AATGTCAAGG
1193 AAAAAGACTG-
1 AAAAAGACTGA
1203 AAAAAGACTG-
1 AAAAAGACTGA
1213 AAAAA-A--GA
1 AAAAAGACTGA
*
1221 AAGAAGACTGA
1 AAAAAGACTGA
1232 AAAGAAGACTGA
1 AAA-AAGACTGA
*
1244 AAGAAGACTGA
1 AAAAAGACTGA
*
1255 AAGAGAATACTGA
1 AA-A-AAGACTGA
* * *
1268 AACAAGATTTA
1 AAAAAGACTGA
*
1279 AAGAGAAAACTGA
1 AA-A-AAGACTGA
1292 AAAAAGACTGA
1 AAAAAGACTGA
1303 AAGAAAGACT-A
1 AA-AAAGACTGA
1314 AAAGAAGAC
1 AAA-AAGAC
1323 CGCCTTAGTT
Statistics
Matches: 95, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
7 1 0.01
8 4 0.04
9 2 0.02
10 16 0.17
11 38 0.40
12 18 0.19
13 16 0.17
ACGTcount: A:0.61, C:0.08, G:0.21, T:0.10
Consensus pattern (11 bp):
AAAAAGACTGA
Found at i:1229 original size:18 final size:18
Alignment explanation
Indices: 1202--1239 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
1192 GAAAAAGACT
1202 GAAAAAGACTGAAAA-AA
1 GAAAAAGACTGAAAAGAA
1219 GAAAGAAGACTGAAAAGAA
1 GAAA-AAGACTGAAAAGAA
1238 GA
1 GA
1240 CTGAAAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 11 0.58
19 4 0.21
ACGTcount: A:0.66, C:0.05, G:0.24, T:0.05
Consensus pattern (18 bp):
GAAAAAGACTGAAAAGAA
Found at i:1242 original size:30 final size:27
Alignment explanation
Indices: 1192--1250 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 27
1182 TAATGTCAAG
1192 GAAAAAGACTGAAAAAGACTGAAAAAA
1 GAAAAAGACTGAAAAAGACTGAAAAAA
*
1219 GAAAGAAGACTGAAAAGAAGACTGAAAGAA
1 GAAA-AAGACTG-AAA-AAGACTGAAAAAA
1249 GA
1 GA
1251 CTGAAAGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 4 0.14
28 7 0.25
29 3 0.11
30 14 0.50
ACGTcount: A:0.63, C:0.07, G:0.24, T:0.07
Consensus pattern (27 bp):
GAAAAAGACTGAAAAAGACTGAAAAAA
Found at i:1266 original size:24 final size:24
Alignment explanation
Indices: 1219--1322 Score: 131
Period size: 24 Copynumber: 4.4 Consensus size: 24
1209 ACTGAAAAAA
1219 GAAAGAAGACTGAAA-AGAAGACT
1 GAAAGAAGACTGAAAGAGAAGACT
*
1242 GAAAGAAGACTGAAAGAGAATACT
1 GAAAGAAGACTGAAAGAGAAGACT
* * * *
1266 GAAACAAGATTTAAAGAGAAAACT
1 GAAAGAAGACTGAAAGAGAAGACT
*
1290 GAAAAAAGACTGAAAGA-AAGACT
1 GAAAGAAGACTGAAAGAGAAGACT
*
1313 AAAAGAAGAC
1 GAAAGAAGAC
1323 CGCCTTAGTT
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
23 28 0.41
24 41 0.59
ACGTcount: A:0.59, C:0.09, G:0.22, T:0.11
Consensus pattern (24 bp):
GAAAGAAGACTGAAAGAGAAGACT
Found at i:1401 original size:36 final size:36
Alignment explanation
Indices: 1326--1493 Score: 214
Period size: 36 Copynumber: 4.7 Consensus size: 36
1316 AGAAGACCGC
* *
1326 CTTAGTTTCAAGGAAATTAGGTAAA-AGAAGACTGG
1 CTTAGTTTCAAGGAAATTAGGTAAAGAAAAGACTGA
* * *
1361 CTTAGTTTCAAGGAAACTAAGTAAAGAAAAGACTAA
1 CTTAGTTTCAAGGAAATTAGGTAAAGAAAAGACTGA
* *
1397 CTTAGTTTCAAGGAAACTAGGTAAAGAAATGACTGA
1 CTTAGTTTCAAGGAAATTAGGTAAAGAAAAGACTGA
* * *
1433 CTTAATTTCAAGGAAATTAGGTAAAGGAAAGACTGG
1 CTTAGTTTCAAGGAAATTAGGTAAAGAAAAGACTGA
*
1469 CTT-GATTTCAAGGAAATTAAGTAAA
1 CTTAG-TTTCAAGGAAATTAGGTAAA
1494 AAGACACAGG
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
35 23 0.20
36 93 0.80
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (36 bp):
CTTAGTTTCAAGGAAATTAGGTAAAGAAAAGACTGA
Found at i:1559 original size:32 final size:33
Alignment explanation
Indices: 1522--1629 Score: 141
Period size: 32 Copynumber: 3.2 Consensus size: 33
1512 CAGGAAAGGA
1522 AATTAAGTAA-AATAAAGAACTTAATTCAGGGT
1 AATTAAGTAAGAATAAAGAACTTAATTCAGGGT
*
1554 AATTAAGTAAGGTCAATAAA-AGGCTTAATTCAGGGT
1 AATTAAGTAA-G--AATAAAGA-ACTTAATTCAGGGT
*
1590 AATTAAG-AAGAATAAAGAACTTAATTCAAGGT
1 AATTAAGTAAGAATAAAGAACTTAATTCAGGGT
1622 AATTAAGT
1 AATTAAGT
1630 GAAGTCGATA
Statistics
Matches: 66, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
32 35 0.53
33 1 0.02
34 1 0.02
35 3 0.05
36 26 0.39
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (33 bp):
AATTAAGTAAGAATAAAGAACTTAATTCAGGGT
Found at i:1572 original size:36 final size:35
Alignment explanation
Indices: 1532--1650 Score: 147
Period size: 36 Copynumber: 3.4 Consensus size: 35
1522 AATTAAGTAA
1532 AATAAAGAACTTAATTCAGGGTAATTAAGTAAGGTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGTAA-GTC
*
1568 AATAAA-AGGCTTAATTCAGGGTAATTAAG-AAG--
1 AATAAAGA-ACTTAATTCAGGGTAATTAAGTAAGTC
*
1600 AATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGT-AAGTC
* *
1636 GATAAACAACTTAAT
1 AATAAAGAACTTAAT
1651 CTAAAAAGAG
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
32 25 0.35
33 1 0.01
34 4 0.06
35 3 0.04
36 39 0.54
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (35 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTAAGTC
Found at i:1649 original size:68 final size:68
Alignment explanation
Indices: 1522--1650 Score: 183
Period size: 68 Copynumber: 1.9 Consensus size: 68
1512 CAGGAAAGGA
* *
1522 AATTAAGTAAAATAAAGAACTTAATTCAGGGTAATTAAGTAAGGTCAATAAAAGGCTTAATTCAG
1 AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTAAGGTCAATAAAAGACTTAATTCAG
1587 GGT
66 GGT
*
1590 AATTAAG-AAGAATAAAGAACTTAATTCAAGGTAATTAAGTGAA-GTCGATAAACA-ACTTAAT
1 AATTAAGTAA-AATAAAGAACTTAATTCAAGGTAATTAAGT-AAGGTCAATAAA-AGACTTAAT
1651 CTAAAAAGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
67 2 0.04
68 50 0.91
69 3 0.05
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (68 bp):
AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTAAGGTCAATAAAAGACTTAATTCAG
GGT
Found at i:6740 original size:10 final size:10
Alignment explanation
Indices: 6725--6771 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
6715 TTTTTTATTT
6725 TTCTTCCATC
1 TTCTTCCATC
6735 TTCTTCC-TC
1 TTCTTCCATC
*
6744 GATTCTT-CTTC
1 --TTCTTCCATC
6755 TTCTTCCATC
1 TTCTTCCATC
6765 TTCTTCC
1 TTCTTCC
6772 TCTATGCTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
9 7 0.22
10 18 0.56
11 7 0.22
ACGTcount: A:0.06, C:0.38, G:0.02, T:0.53
Consensus pattern (10 bp):
TTCTTCCATC
Found at i:6760 original size:30 final size:30
Alignment explanation
Indices: 6725--6782 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
6715 TTTTTTATTT
*
6725 TTCTTCCATCTTCTTCCTCGATTCTTCTTC
1 TTCTTCCATCTTCTTCCTCGATGCTTCTTC
*
6755 TTCTTCCATCTTCTTCCTCTATGCTTCT
1 TTCTTCCATCTTCTTCCTCGATGCTTCT
6783 CCATCTCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.07, C:0.36, G:0.03, T:0.53
Consensus pattern (30 bp):
TTCTTCCATCTTCTTCCTCGATGCTTCTTC
Found at i:7438 original size:22 final size:21
Alignment explanation
Indices: 7410--7451 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
7400 TCTAGGTTTG
7410 GTTGAATCCT-GTATTGTATTTC
1 GTTGAAT-CTGGTATT-TATTTC
7432 GTTGAATCTGGTATTTATTT
1 GTTGAATCTGGTATTTATTT
7452 GTGGCTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (21 bp):
GTTGAATCTGGTATTTATTTC
Found at i:7902 original size:2 final size:2
Alignment explanation
Indices: 7895--7929 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7885 GTCAGAAAGG
7895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7930 AAGAAAGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9869 original size:21 final size:21
Alignment explanation
Indices: 9845--9884 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9835 CCACTTTTAG
9845 ACAAAATCAGCAA-AATGGAGA
1 ACAAAATC-GCAACAATGGAGA
*
9866 ACAAACTCGCAACAATGGA
1 ACAAAATCGCAACAATGGA
9885 AGAGGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.53, C:0.20, G:0.17, T:0.10
Consensus pattern (21 bp):
ACAAAATCGCAACAATGGAGA
Done.