Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014197.1 Corchorus capsularis cultivar CVL-1 contig14218, 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: 12792
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Found at i:1066 original size:14 final size:14
Alignment explanation
Indices: 1049--1076 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1039 AAATTAAGGG
1049 AAGCAAATCTTAAT
1 AAGCAAATCTTAAT
1063 AAGCAAATCTTAAT
1 AAGCAAATCTTAAT
1077 TCAGCGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
AAGCAAATCTTAAT
Found at i:1275 original size:11 final size:11
Alignment explanation
Indices: 1247--1350 Score: 77
Period size: 11 Copynumber: 9.2 Consensus size: 11
1237 TAATGTCAAG
*
1247 GAAA-AAGACA
1 GAAAGAAGACT
1257 GAAA-AAGACT
1 GAAAGAAGACT
*
1267 GAAACAAGACT
1 GAAAGAAGACT
*
1278 GAAAGAGAAAACT
1 G-AA-AGAAGACT
* *
1291 GAAACAAGATT
1 GAAAGAAGACT
*
1302 GAAAGAGAAAACT
1 G-AA-AGAAGACT
*
1315 GAAAAAAGACT
1 GAAAGAAGACT
1326 GAAAGAAAGACT
1 GAAAG-AAGACT
*
1338 AAAAGAAGACT
1 GAAAGAAGACT
1349 GA
1 GA
1351 CTTATTTTCA
Statistics
Matches: 74, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
10 13 0.18
11 30 0.41
12 18 0.24
13 13 0.18
ACGTcount: A:0.61, C:0.10, G:0.21, T:0.09
Consensus pattern (11 bp):
GAAAGAAGACT
Found at i:1296 original size:24 final size:24
Alignment explanation
Indices: 1264--1350 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 24
1254 ACAGAAAAAG
1264 ACTGAAACAAGACTGAAAGAGAAA
1 ACTGAAACAAGACTGAAAGAGAAA
*
1288 ACTGAAACAAGATTGAAAGAGAAA
1 ACTGAAACAAGACTGAAAGAGAAA
* *
1312 ACTGAAAAAAGACTGAAAGA-AAG
1 ACTGAAACAAGACTGAAAGAGAAA
* *
1335 ACTAAAAGAAGACTGA
1 ACTGAAACAAGACTGA
1351 CTTATTTTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 16 0.28
24 41 0.72
ACGTcount: A:0.59, C:0.10, G:0.21, T:0.10
Consensus pattern (24 bp):
ACTGAAACAAGACTGAAAGAGAAA
Found at i:1376 original size:35 final size:35
Alignment explanation
Indices: 1337--1440 Score: 154
Period size: 35 Copynumber: 2.9 Consensus size: 35
1327 AAAGAAAGAC
* * * *
1337 TAAAAGAAGACTGACTTATTTTCAAGGAAATTAGG
1 TAAAAGAAGACTGGCTTAGTTTCAAGGAAACTAAG
1372 TAAAAGAAGACTGGCTTAGTTTCAAGGAAACTAAG
1 TAAAAGAAGACTGGCTTAGTTTCAAGGAAACTAAG
*
1407 TAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTA
1 TAAA-AGAAGACTGGCTTAGTTTCAAGGAAACTA
1441 TGACTGGCTT
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 35 0.56
36 28 0.44
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (35 bp):
TAAAAGAAGACTGGCTTAGTTTCAAGGAAACTAAG
Found at i:1457 original size:62 final size:62
Alignment explanation
Indices: 1380--1499 Score: 179
Period size: 62 Copynumber: 1.9 Consensus size: 62
1370 GGTAAAAGAA
* *
1380 GACTGGCTTAGTTTCAAGGAAACTAAGTAAAGAAAAGACTGGC-TTAGTTTCAAGGAAACTAT
1 GACTGGCTTAATTTCAAGGAAACTAAGTAAAGAAAAGACTGGCATGA-TTTCAAGGAAACTAT
* * *
1442 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGGAAAGACTGGCATGATTTCAAGGAAA
1 GACTGGCTTAATTTCAAGGAAACTAAGTAAAGAAAAGACTGGCATGATTTCAAGGAAA
1500 TTAAGTAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
62 50 0.96
63 2 0.04
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (62 bp):
GACTGGCTTAATTTCAAGGAAACTAAGTAAAGAAAAGACTGGCATGATTTCAAGGAAACTAT
Found at i:1522 original size:97 final size:97
Alignment explanation
Indices: 1345--1530 Score: 252
Period size: 97 Copynumber: 1.9 Consensus size: 97
1335 ACTAAAAGAA
* *
1345 GACTGACTTATTTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAACTAAGTAA
1 GACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTGAGTTTCAAGGAAACTAAGTAA
* *
1410 AGAAAAGACTGGCTTAGTTTCAAGGAAACTAT
66 AGAAAACACTGGCTTAATTTCAAGGAAACTAT
* * *
1442 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGGAAAGACTGGCATGA-TTTCAAGGAAATTAAGT
1 GACTGACTTAATTTCAAGGAAATTAGGTAAAAG-AAGACTGGC-TGAGTTTCAAGGAAACTAAGT
*
1506 AAA-AAGACACAT-GCTTAATTTCAAG
64 AAAGAAAACAC-TGGCTTAATTTCAAG
1531 AAAGGAAATT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
97 47 0.60
98 29 0.37
99 2 0.03
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (97 bp):
GACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTGAGTTTCAAGGAAACTAAGTAA
AGAAAACACTGGCTTAATTTCAAGGAAACTAT
Found at i:1596 original size:36 final size:33
Alignment explanation
Indices: 1537--1644 Score: 141
Period size: 32 Copynumber: 3.2 Consensus size: 33
1527 CAAGAAAGGA
1537 AATTAAGTAA-AATAAAGAACTTAATTCAGGGT
1 AATTAAGTAAGAATAAAGAACTTAATTCAGGGT
*
1569 AATTAAGTAAGGTCAATAAA-AGGCTTAATTCAGGGT
1 AATTAAGTAA-G--AATAAAGA-ACTTAATTCAGGGT
*
1605 AATTAAG-AAGAATAAAGAACTTAATTCAAGGT
1 AATTAAGTAAGAATAAAGAACTTAATTCAGGGT
1637 AATTAAGT
1 AATTAAGT
1645 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:1663 original size:36 final size:36
Alignment explanation
Indices: 1547--1665 Score: 142
Period size: 36 Copynumber: 3.4 Consensus size: 36
1537 AATTAAGTAA
1547 AATAAAGAACTTAATTCAGGGTAATTAAGT-AAGGTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGAA-GTC
*
1583 AATAAA-AGGCTTAATTCAGGGTAATTAA--GAAG--
1 AATAAAGA-ACTTAATTCAGGGTAATTAAGTGAAGTC
*
1615 AATAAAGAACTTAATTCAAGGTAATTAAGTGAAGTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGAAGTC
* *
1651 GATAAACAACTTAAT
1 AATAAAGAACTTAAT
1666 CTAAAAAGAG
Statistics
Matches: 71, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
32 24 0.34
33 1 0.01
34 5 0.07
35 3 0.04
36 38 0.54
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (36 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTGAAGTC
Found at i:1664 original size:68 final size:68
Alignment explanation
Indices: 1537--1665 Score: 183
Period size: 68 Copynumber: 1.9 Consensus size: 68
1527 CAAGAAAGGA
* *
1537 AATTAAGTAAAATAAAGAACTTAATTCAGGGTAATTAAGTAAGGTCAATAAAAGGCTTAATTCAG
1 AATTAAGTAAAATAAAGAACTTAATTCAAGGTAATTAAGTAAGGTCAATAAAAGACTTAATTCAG
1602 GGT
66 GGT
*
1605 AATTAAG-AAGAATAAAGAACTTAATTCAAGGTAATTAAGTGAA-GTCGATAAACA-ACTTAAT
1 AATTAAGTAA-AATAAAGAACTTAATTCAAGGTAATTAAGT-AAGGTCAATAAA-AGACTTAAT
1666 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
Done.