Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005768.1 Corchorus capsularis cultivar CVL-1 contig05786, 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: 3372
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Found at i:1345 original size:21 final size:21
Alignment explanation
Indices: 1300--1393 Score: 86
Period size: 21 Copynumber: 4.5 Consensus size: 21
1290 ACTCTTTGAA
* *
1300 TTACTGATCACTCTTT-ACTC
1 TTACTGATTACTATTTGACTC
*
1320 TTTACTGATTACTATTTGATTC
1 -TTACTGATTACTATTTGACTC
*
1342 TTACTAATTA-TCACTTTG-CTC
1 TTACTGATTACT-A-TTTGACTC
* *
1363 TTACTGGTTACTATTTTACTC
1 TTACTGATTACTATTTGACTC
1384 TTACTGATTA
1 TTACTGATTA
1394 TCTTTTACTA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
20 4 0.07
21 47 0.80
22 8 0.14
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.50
Consensus pattern (21 bp):
TTACTGATTACTATTTGACTC
Found at i:1367 original size:42 final size:43
Alignment explanation
Indices: 1312--1395 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
1302 ACTGATCACT
*
1312 CTTTACTCTTTACTGATTACTATTTGATTCTTACTAATTATCA
1 CTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTATCA
* * * *
1355 CTTTGCTC-TTACTGGTTACTATTTTACTCTTACTGATTATC
1 CTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTATC
1396 TTTTACTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 29 0.81
43 7 0.19
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.51
Consensus pattern (43 bp):
CTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTATCA
Found at i:1409 original size:42 final size:42
Alignment explanation
Indices: 1312--1409 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 42
1302 ACTGATCACT
* *
1312 CTTTACTCTTTACTGATTACTATTTGATTCTTACTAATTATCA
1 CTTTACT-ATTACTGATTACTATTTGACTCTTACTAATTATCA
* * * * *
1355 CTTTGCTCTTACTGGTTACTATTTTACTCTTACTGATTATC-
1 CTTTACTATTACTGATTACTATTTGACTCTTACTAATTATCA
*
1396 TTTTACTAATTACT
1 CTTTACT-ATTACT
1410 ATCTTATTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 5 0.11
42 34 0.76
43 6 0.13
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.52
Consensus pattern (42 bp):
CTTTACTATTACTGATTACTATTTGACTCTTACTAATTATCA
Found at i:1460 original size:52 final size:51
Alignment explanation
Indices: 1375--1472 Score: 151
Period size: 52 Copynumber: 1.9 Consensus size: 51
1365 ACTGGTTACT
* *
1375 ATTTTACTCTTACTGATTATCTTTTACTAATTACTATCTTATTCTTTACGG
1 ATTTTACTCTTACTGATTACCTTCTACTAATTACTATCTTATTCTTTACGG
* *
1426 ATTTTACTCTTTACTGATTACCTTCTACTGATTACTATTTTATTCTT
1 ATTTTACTC-TTACTGATTACCTTCTACTAATTACTATCTTATTCTT
1473 AATGATTGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 9 0.21
52 33 0.79
ACGTcount: A:0.22, C:0.18, G:0.05, T:0.54
Consensus pattern (51 bp):
ATTTTACTCTTACTGATTACCTTCTACTAATTACTATCTTATTCTTTACGG
Found at i:1883 original size:54 final size:55
Alignment explanation
Indices: 1829--2168 Score: 450
Period size: 54 Copynumber: 6.3 Consensus size: 55
1819 GATTACTATC
* * * ** * *
1829 TTTTACCTGATTACTGATTTACGGATTACTATTACCCTAACTCTGATTAATATCT
1 TTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCT
1884 TTTTACTTAATTACTGA-TTACTG----C---TACTTTGACTCTGATTAATCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCT
* * * *
1931 TTTTACTTAATTATTGATTTACTGATTACTGTTACTTTGACTCTGATTTACCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCT
1986 TTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTC-
1 TTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCT
* * *
2040 TTCTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTTACCTC-
1 TTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCT
*
2094 TTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTTGATTTA-CATCT
1 TTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTC-TGATTAATC-TCT
2150 TTTTACTTAATTACTGATT
1 TTTTACTTAATTACTGATT
2169 GCCCCCTTTC
Statistics
Matches: 256, Mismatches: 18, Indels: 21
0.87 0.06 0.07
Matches are distributed among these distances:
47 35 0.14
48 6 0.02
50 1 0.00
52 1 0.00
54 99 0.39
55 95 0.37
56 19 0.07
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.50
Consensus pattern (55 bp):
TTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCT
Found at i:1966 original size:29 final size:28
Alignment explanation
Indices: 1932--2022 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 28
1922 TTAATCTCTT
1932 TTTACTTAATTATTGATTTACTGATTAC
1 TTTACTTAATTATTGATTTACTGATTAC
* *
1960 TGTTACTT--TGACTCTGATTTACCT-CTT--
1 T-TTACTTAATTA-T-TGATTTA-CTGATTAC
*
1987 TTTACTTAATTACTGATTTACTGATTAC
1 TTTACTTAATTATTGATTTACTGATTAC
2015 TATTACTT
1 T-TTACTT
2023 TGACTCTGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 19
0.67 0.07 0.26
Matches are distributed among these distances:
25 2 0.04
26 15 0.31
27 3 0.06
28 5 0.10
29 21 0.44
30 2 0.04
ACGTcount: A:0.24, C:0.15, G:0.08, T:0.53
Consensus pattern (28 bp):
TTTACTTAATTATTGATTTACTGATTAC
Done.