Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010496.1 Corchorus capsularis cultivar CVL-1 contig10517, 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: 24380
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:1234 original size:19 final size:19
Alignment explanation
Indices: 1210--1247 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1200 ACCTATCTTC
1210 TTTTTCAAAGCAATAATGA
1 TTTTTCAAAGCAATAATGA
1229 TTTTTCAAAGCAATAATGA
1 TTTTTCAAAGCAATAATGA
1248 GAACCGTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
TTTTTCAAAGCAATAATGA
Found at i:8282 original size:12 final size:12
Alignment explanation
Indices: 8260--8292 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
8250 CCCTATTAGT
8260 TTTTGCATTCTCA
1 TTTT-CATTCTCA
8273 TTTTCATTCTCA
1 TTTTCATTCTCA
8285 TTTTCATT
1 TTTTCATT
8293 TCTTACTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.15, C:0.21, G:0.03, T:0.61
Consensus pattern (12 bp):
TTTTCATTCTCA
Found at i:18037 original size:19 final size:18
Alignment explanation
Indices: 18013--18051 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
18003 TTCCAGTCAA
18013 TTTTTTGAGTCAGTTCAGT
1 TTTTTTGAGTCAGTT-AGT
18032 TTTTTTGAGTCAGTTAGT
1 TTTTTTGAGTCAGTTAGT
18050 TT
1 TT
18052 GAGTCTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.15, C:0.08, G:0.21, T:0.56
Consensus pattern (18 bp):
TTTTTTGAGTCAGTTAGT
Found at i:18983 original size:3 final size:3
Alignment explanation
Indices: 18977--19022 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
18967 AATAATCTTG
18977 TTA TTA TTA TTA -TA TTA TATA TATA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA
19022 T
1 T
19023 ATATAGTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 29 0.73
4 7 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:18993 original size:28 final size:29
Alignment explanation
Indices: 18962--19033 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 29
18952 TATGTTTAAG
* *
18962 ATTATAATA-ATCTTGTTATTATTATTAT
1 ATTATAATATATATTATTATTATTATTAT
18990 ATTAT-ATATATATTATTATTATTATTAT
1 ATTATAATATATATTATTATTATTATTAT
19018 ATTATATATAGTATAT
1 ATTATA-ATA-TATAT
19034 CGCAATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 3 0.08
28 27 0.71
30 3 0.08
31 5 0.13
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (29 bp):
ATTATAATATATATTATTATTATTATTAT
Found at i:18994 original size:11 final size:10
Alignment explanation
Indices: 18978--19033 Score: 60
Period size: 11 Copynumber: 5.3 Consensus size: 10
18968 ATAATCTTGT
18978 TATTATTATTA
1 TATTA-TATTA
18989 TATTATATATA
1 TATTATAT-TA
19000 TATTATTATTA
1 TATTA-TATTA
19011 TTATTATATTA
1 -TATTATATTA
*
19022 TA-TATAGTA
1 TATTATATTA
19031 TAT
1 TAT
19034 CGCAATATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
9 8 0.20
10 5 0.12
11 19 0.47
12 8 0.20
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
TATTATATTA
Found at i:18999 original size:9 final size:9
Alignment explanation
Indices: 18984--19033 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
18974 TTGTTATTAT
18984 TATTATAT-
1 TATTATATA
18992 TA-TATATA
1 TATTATATA
19000 TATTAT-TA
1 TATTATATA
19008 TTATTAT-TA
1 -TATTATATA
19017 TATTATATA
1 TATTATATA
*
19026 TAGTATAT
1 TATTATAT
19034 CGCAATATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
7 5 0.14
8 12 0.32
9 20 0.54
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (9 bp):
TATTATATA
Found at i:19032 original size:14 final size:13
Alignment explanation
Indices: 18978--19033 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
18968 ATAATCTTGT
18978 TATTAT-TAT-TA
1 TATTATATATATA
18989 TATTATATATATA
1 TATTATATATATA
19002 TTATTAT-TATTATTA
1 -TATTATATA-TA-TA
19017 TATTATATATAGTA
1 TATTATATATA-TA
19031 TAT
1 TAT
19034 CGCAATATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
11 6 0.16
12 3 0.08
13 4 0.11
14 21 0.55
15 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
TATTATATATATA
Found at i:21178 original size:6 final size:6
Alignment explanation
Indices: 21167--21204 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
21157 ACACGAAGAC
21167 ATCTCT ATCTCT ATCTCT ATCTCT ATCTCT ATCTCT AT
1 ATCTCT ATCTCT ATCTCT ATCTCT ATCTCT ATCTCT AT
21205 ATTATAGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTCT
Done.