Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020600.1 Corchorus olitorius cultivar O-4 contig20633, 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: 32868
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:223 original size:10 final size:10
Alignment explanation
Indices: 208--237 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
198 GTTGTTTTAC
208 TTGAATGATT
1 TTGAATGATT
218 TTGAATGATT
1 TTGAATGATT
228 TTGAATGATT
1 TTGAATGATT
238 GAGCTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (10 bp):
TTGAATGATT
Found at i:1254 original size:51 final size:51
Alignment explanation
Indices: 1127--1275 Score: 156
Period size: 51 Copynumber: 2.9 Consensus size: 51
1117 TTCTCCAACT
* * * * *
1127 TTAAAATTATCAAGACTCAACATTTACCACCTAAAGACCCAATTTTTATTG
1 TTAAAATTACCAAGACTCAAAATTTGCTACCTAAAGATCCAATTTTTATTG
* * * *
1178 TTAAAGTTACCAAGATTCAAAATTTGTTACCTAAAGATCCAATTTTTCTTG
1 TTAAAATTACCAAGACTCAAAATTTGCTACCTAAAGATCCAATTTTTATTG
* ** * *
1229 TTAAAATTACCGCA-ACTCATCATTTGCTACTTAAAAATCCAATTTTT
1 TTAAAATTACC-AAGACTCAAAATTTGCTACCTAAAGATCCAATTTTT
1276 GTTATCCAAA
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
51 79 0.99
52 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (51 bp):
TTAAAATTACCAAGACTCAAAATTTGCTACCTAAAGATCCAATTTTTATTG
Found at i:3348 original size:17 final size:17
Alignment explanation
Indices: 3326--3361 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3316 TGATTTGCAA
3326 AGTTTGTTACACCAGAT
1 AGTTTGTTACACCAGAT
* *
3343 AGTTTGTTATACTAGAT
1 AGTTTGTTACACCAGAT
3360 AG
1 AG
3362 CTCTATGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (17 bp):
AGTTTGTTACACCAGAT
Found at i:3598 original size:18 final size:18
Alignment explanation
Indices: 3556--3599 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
3546 TCATCAATGG
3556 CTGCTGCAAACACCACCA
1 CTGCTGCAAACACCACCA
3574 C-GCCTGCAAACACCACCA
1 CTG-CTGCAAACACCACCA
3592 CTGCTGCA
1 CTGCTGCA
3600 GGATTTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.30, C:0.45, G:0.14, T:0.11
Consensus pattern (18 bp):
CTGCTGCAAACACCACCA
Found at i:3680 original size:18 final size:18
Alignment explanation
Indices: 3615--3683 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
3605 TACAAAATAT
3615 TGTTCCACTGCCGCAGGA
1 TGTTCCACTGCCGCAGGA
* * * *
3633 TGTTCTACTACTGCAGAA
1 TGTTCCACTGCCGCAGGA
* *
3651 TGTTGCATTGCCGCAGGA
1 TGTTCCACTGCCGCAGGA
*
3669 TGTTCCGCTGCCGCA
1 TGTTCCACTGCCGCA
3684 ATCCTCAGAT
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.28
Consensus pattern (18 bp):
TGTTCCACTGCCGCAGGA
Found at i:5457 original size:17 final size:17
Alignment explanation
Indices: 5435--5470 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5425 TGATTTGTAA
5435 AGTTTGTTACACCAGAT
1 AGTTTGTTACACCAGAT
* *
5452 AGTTTGTTATACTAGAT
1 AGTTTGTTACACCAGAT
5469 AG
1 AG
5471 CTCTATGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (17 bp):
AGTTTGTTACACCAGAT
Found at i:6989 original size:14 final size:14
Alignment explanation
Indices: 6970--7006 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
6960 AGATGTTAAA
*
6970 AGAATTTATAGTGG
1 AGAATTTATAATGG
6984 AGAATTTATAATGG
1 AGAATTTATAATGG
6998 AGAATTTAT
1 AGAATTTAT
7007 GTAACGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (14 bp):
AGAATTTATAATGG
Found at i:7230 original size:18 final size:19
Alignment explanation
Indices: 7207--7248 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
7197 AATTGAAAAT
7207 ATATAACGTTAAGAATT-A
1 ATATAACGTTAAGAATTAA
*
7225 ATATAACGTTAATAATTAA
1 ATATAACGTTAAGAATTAA
7244 ATATA
1 ATATA
7249 TCATCATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (19 bp):
ATATAACGTTAAGAATTAA
Found at i:7675 original size:11 final size:11
Alignment explanation
Indices: 7659--7687 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
7649 ATAACATCTG
7659 ACATGTGTCTT
1 ACATGTGTCTT
7670 ACATGTGTCTT
1 ACATGTGTCTT
7681 ACATGTG
1 ACATGTG
7688 GTTATAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (11 bp):
ACATGTGTCTT
Found at i:17551 original size:12 final size:13
Alignment explanation
Indices: 17524--17556 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
17514 GAGAGAACAA
*
17524 AAAAGAAACTAAG
1 AAAAGAAACAAAG
17537 AAAAGAAA-AAAG
1 AAAAGAAACAAAG
17549 AAAAGAAA
1 AAAAGAAA
17557 GAACTTAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAAGAAACAAAG
Done.