Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013852.1 Corchorus capsularis cultivar CVL-1 contig13873, 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: 15643
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.27
Found at i:552 original size:29 final size:29
Alignment explanation
Indices: 518--575 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
508 TTCAGTTTGG
518 CCCCTGTTTTAGATCAATTAGGTTCAAAA
1 CCCCTGTTTTAGATCAATTAGGTTCAAAA
547 CCCCTGTTTTAGATCAATTAGGTTCAAAA
1 CCCCTGTTTTAGATCAATTAGGTTCAAAA
576 GTTAATACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (29 bp):
CCCCTGTTTTAGATCAATTAGGTTCAAAA
Found at i:1963 original size:15 final size:16
Alignment explanation
Indices: 1895--1957 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
1885 TAAGAGTAAA
1895 AGTAAAAGGAGTAATC
1 AGTAAAAGGAGTAATC
*
1911 AGTAAAATG-GTAAT-
1 AGTAAAAGGAGTAATC
*
1925 --T--AA-GAGTAA-A
1 AGTAAAAGGAGTAATC
1935 AGTAAAAGGAGTAATC
1 AGTAAAAGGAGTAATC
1951 AGTAAAA
1 AGTAAAA
1958 TGGTAATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
9 1 0.03
10 6 0.16
12 2 0.05
14 2 0.05
15 11 0.30
16 15 0.41
ACGTcount: A:0.54, C:0.03, G:0.22, T:0.21
Consensus pattern (16 bp):
AGTAAAAGGAGTAATC
Found at i:2003 original size:40 final size:40
Alignment explanation
Indices: 1882--1996 Score: 214
Period size: 40 Copynumber: 2.9 Consensus size: 40
1872 TGATTAGTAG
1882 AATTAAGAGTAAAAGTAAAAGGAGTAATCAGTAAAATGGT
1 AATTAAGAGTAAAAGTAAAAGGAGTAATCAGTAAAATGGT
1922 AATTAAGAGTAAAAGTAAAAGGAGTAATCAGTAAAATGGT
1 AATTAAGAGTAAAAGTAAAAGGAGTAATCAGTAAAATGGT
1962 AATTAAGAGTAAAAGTAAAA-GAGGTAATCAGTAAA
1 AATTAAGAGTAAAAGTAAAAGGA-GTAATCAGTAAA
1997 TCGGTAAAGA
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
39 2 0.03
40 72 0.97
ACGTcount: A:0.54, C:0.03, G:0.22, T:0.22
Consensus pattern (40 bp):
AATTAAGAGTAAAAGTAAAAGGAGTAATCAGTAAAATGGT
Found at i:2100 original size:32 final size:33
Alignment explanation
Indices: 2040--2122 Score: 125
Period size: 32 Copynumber: 2.5 Consensus size: 33
2030 AGTAATCGGT
2040 AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
1 AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
*
2073 AAAGAGTAAAAT-G-ACAAATGGTGATTAAATTC
1 AAAGAGTAAAATAGTA-AAATGGTAATTAAATTC
2105 AAAGAGTGAAAATAGTAA
1 AAAGAGT-AAAATAGTAA
2123 TTAAATTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 1 0.02
32 24 0.53
33 17 0.38
34 2 0.04
35 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.18, T:0.24
Consensus pattern (33 bp):
AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
Found at i:2125 original size:26 final size:26
Alignment explanation
Indices: 2055--2144 Score: 92
Period size: 26 Copynumber: 3.2 Consensus size: 26
2045 GTAAAATAGT
2055 AAAATGGTAATTAAATTCAAAGAGTAAAATG
1 AAAATGGTAATTAAATTCAAAGAG-----TG
*
2086 ACAAATGGTGATTAAATTCAAAGAGTG
1 A-AAATGGTAATTAAATTCAAAGAGTG
*
2113 AAAATAGTAATTAAATTCAAGAGAGT-
1 AAAATGGTAATTAAATTCAA-AGAGTG
2139 AAAATG
1 AAAATG
2145 TAAATCAGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
26 22 0.42
27 8 0.15
31 1 0.02
32 22 0.42
ACGTcount: A:0.52, C:0.04, G:0.18, T:0.26
Consensus pattern (26 bp):
AAAATGGTAATTAAATTCAAAGAGTG
Found at i:2182 original size:14 final size:14
Alignment explanation
Indices: 2147--2222 Score: 75
Period size: 14 Copynumber: 5.4 Consensus size: 14
2137 GTAAAATGTA
*
2147 AATCAGTAAAGAGG
1 AATCAGTAAAGAGT
**
2161 AAAAAGTAAAGAGT
1 AATCAGTAAAGAGT
2175 AATCAGTAAA-AGT
1 AATCAGTAAAGAGT
**
2188 AAAAATGGTAAA-AGT
1 AATCA--GTAAAGAGT
2203 AATCAGTAAAGAGT
1 AATCAGTAAAGAGT
2217 AATCAG
1 AATCAG
2223 CGAAAAGTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
13 11 0.22
14 28 0.56
15 11 0.22
ACGTcount: A:0.55, C:0.05, G:0.21, T:0.18
Consensus pattern (14 bp):
AATCAGTAAAGAGT
Found at i:2192 original size:28 final size:29
Alignment explanation
Indices: 2136--2218 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 29
2126 AATTCAAGAG
*
2136 AGTAAAATGTAAATCAGTAAAGAG-GAAAA-
1 AGTAAAA-GT-AATCAGTAAAGAGTAAAAAT
2165 AGTAAAGAGTAATCAGTAAA-AGTAAAAAT
1 AGTAAA-AGTAATCAGTAAAGAGTAAAAAT
*
2194 GGTAAAAGTAATCAGTAAAGAGTAA
1 AGTAAAAGTAATCAGTAAAGAGTAA
2219 TCAGCGAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.04
28 27 0.56
29 18 0.38
30 1 0.02
ACGTcount: A:0.57, C:0.04, G:0.20, T:0.19
Consensus pattern (29 bp):
AGTAAAAGTAATCAGTAAAGAGTAAAAAT
Found at i:2231 original size:14 final size:13
Alignment explanation
Indices: 2172--2232 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 13
2162 AAAAGTAAAG
*
2172 AGTAATCAGTAAA
1 AGTAATCAGGAAA
**
2185 AGTAAAAATGGTAAA
1 AGTAATCA-GG-AAA
*
2200 AGTAATCAGTAAA
1 AGTAATCAGGAAA
2213 GAGTAATCAGCGAAA
1 -AGTAATCAG-GAAA
2228 AGTAA
1 AGTAA
2233 AAATAGGCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
13 9 0.24
14 16 0.43
15 12 0.32
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.20
Consensus pattern (13 bp):
AGTAATCAGGAAA
Found at i:2286 original size:14 final size:14
Alignment explanation
Indices: 2269--2296 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2259 TTCAGGCAAA
2269 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
2283 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
2297 GAAGAATGAT
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:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:2466 original size:22 final size:22
Alignment explanation
Indices: 2428--2496 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
2418 CGGTAAAATG
2428 GTAAAAAGTAAAA-GGTAATCA
1 GTAAAAAGTAAAATGGTAATCA
** *
2449 GTAAAGGGTAAAATGGTAATTA
1 GTAAAAAGTAAAATGGTAATCA
* *
2471 GTAAAAAGTAAGATGGCAATCA
1 GTAAAAAGTAAAATGGTAATCA
2493 GTAA
1 GTAA
2497 GAAGAGGATA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 11 0.28
22 28 0.72
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.22
Consensus pattern (22 bp):
GTAAAAAGTAAAATGGTAATCA
Found at i:6548 original size:16 final size:16
Alignment explanation
Indices: 6523--6553 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6513 AAAAAAGGAT
*
6523 AATAATAAATAATAAG
1 AATAAAAAATAATAAG
6539 AATAAAAAATAATAA
1 AATAAAAAATAATAA
6554 CGATTTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AATAAAAAATAATAAG
Done.