Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007185.1 Corchorus capsularis cultivar CVL-1 contig07206, 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: 17100
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Found at i:104 original size:15 final size:14
Alignment explanation
Indices: 53--145 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
43 TTATGATTAG
*
53 TTTTAATTAGTTAA
1 TTTTAATTAGTTTA
** *
67 TTAAAATTA-CTTA
1 TTTTAATTAGTTTA
*
80 GTTT-ATTAGTTTA
1 TTTTAATTAGTTTA
93 TGTTTAATTAG--TA
1 T-TTTAATTAGTTTA
*
106 -TCTAATTAGTTTA
1 TTTTAATTAGTTTA
119 TTATTAATTAG--TA
1 TT-TTAATTAGTTTA
132 -TTTAATTAGTTTA
1 TTTTAATTAGTTTA
145 T
1 T
146 GATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 20
0.65 0.12 0.22
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.24
14 11 0.19
15 12 0.21
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (14 bp):
TTTTAATTAGTTTA
Found at i:113 original size:26 final size:26
Alignment explanation
Indices: 84--151 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
74 TACTTAGTTT
84 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
110 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
136 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
152 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:195 original size:24 final size:25
Alignment explanation
Indices: 161--219 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
151 AAATGAAGGA
*
161 AAATGAA-TTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
184 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
209 AAATGAAGTTT
1 AAATGAAGTTT
220 ATAGTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
25 19 0.58
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.36
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:1562 original size:23 final size:23
Alignment explanation
Indices: 1536--1584 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
1526 TATAGCAATA
1536 ATAAATTA-ATAATTATATATAAT
1 ATAAATTACATAATTA-ATATAAT
*
1559 AT-AATTACCATAATTAGTATAAT
1 ATAAATTA-CATAATTAATATAAT
1582 ATA
1 ATA
1585 TTAAGACTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
22 5 0.23
23 10 0.45
24 7 0.32
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAAATTACATAATTAATATAAT
Found at i:3138 original size:20 final size:20
Alignment explanation
Indices: 3109--3146 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3099 AGTTCAAAGG
3109 GGGGGCGGTACTTAGTAAAA
1 GGGGGCGGTACTTAGTAAAA
* *
3129 GGGGGTGGTATTTAGTAA
1 GGGGGCGGTACTTAGTAA
3147 TCCCCTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.05, G:0.42, T:0.26
Consensus pattern (20 bp):
GGGGGCGGTACTTAGTAAAA
Found at i:7067 original size:17 final size:18
Alignment explanation
Indices: 7042--7075 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
7032 AAGTAGTTAT
*
7042 TTTTGGCCTAA-AGAGTG
1 TTTTAGCCTAAGAGAGTG
7059 TTTTAGCCTAAGAGAGT
1 TTTTAGCCTAAGAGAGT
7076 TAATTAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (18 bp):
TTTTAGCCTAAGAGAGTG
Done.