Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014428.1 Corchorus olitorius cultivar O-4 contig14461, 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: 30329
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:822 original size:56 final size:56
Alignment explanation
Indices: 736--846 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
726 TAAGGGACAA
736 GTGACCAACTTATCCTTCATCTTAAATTCAATATTTGATTTGTAAAGTTGTTACAC
1 GTGACCAACTTATCCTTCATCTTAAATTCAATATTTGATTTGTAAAGTTGTTACAC
*
792 GTGACCAACTTATCTTTCATCTTAAATTCAATATTTGATTTGTAAAGTTGTTACA
1 GTGACCAACTTATCCTTCATCTTAAATTCAATATTTGATTTGTAAAGTTGTTACA
847 GCAGATAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (56 bp):
GTGACCAACTTATCCTTCATCTTAAATTCAATATTTGATTTGTAAAGTTGTTACAC
Found at i:2201 original size:29 final size:29
Alignment explanation
Indices: 2159--2219 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
2149 AATGTCTCTG
2159 TTGATGCTGACAAATTTTTGGTGAAGGAT
1 TTGATGCTGACAAATTTTTGGTGAAGGAT
*
2188 TTGATGCTGACAAATTTTTGGTTAAGGAT
1 TTGATGCTGACAAATTTTTGGTGAAGGAT
2217 TTG
1 TTG
2220 TAGACTCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (29 bp):
TTGATGCTGACAAATTTTTGGTGAAGGAT
Found at i:3413 original size:30 final size:30
Alignment explanation
Indices: 3378--3465 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
3368 ATGTATAGGC
*
3378 AGATGTTCCATTGCCACAGGATTTACA-AA
1 AGATGTTCCATTGCCGCAGGATTTACAGAA
* * * *
3407 TTGATGTTCC-TCTGCTGCATGATGTACAGAA
1 -AGATGTTCCAT-TGCCGCAGGATTTACAGAA
*
3438 AAATGTTCCATTGCCGCAGGATTTACAG
1 AGATGTTCCATTGCCGCAGGATTTACAG
3466 TTAGCTGTTA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
29 1 0.02
30 41 0.91
31 3 0.07
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (30 bp):
AGATGTTCCATTGCCGCAGGATTTACAGAA
Found at i:18526 original size:28 final size:28
Alignment explanation
Indices: 18490--18556 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
18480 TTCATAGTAC
* * *
18490 AAGGTTAAAACTGTAAATTTA-ACCTTCT
1 AAGGGTAAAACGGT-AATTTATACATTCT
*
18518 AAGGGTAAAACGGTAATTTATTCATTCT
1 AAGGGTAAAACGGTAATTTATACATTCT
*
18546 TAGGGTAAAAC
1 AAGGGTAAAAC
18557 AATAATTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 6 0.18
28 27 0.82
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (28 bp):
AAGGGTAAAACGGTAATTTATACATTCT
Found at i:24571 original size:28 final size:29
Alignment explanation
Indices: 24535--24618 Score: 95
Period size: 28 Copynumber: 3.0 Consensus size: 29
24525 TTCAAAGTAC
* *
24535 AAGGTTAAAACTGTAAATTTAAC-C-TTCT
1 AAGGGTAAAACAGT-AATTTAACTCATTCT
*
24563 AAGGGTAAAACGGTAATTT-ACTCATTCT
1 AAGGGTAAAACAGTAATTTAACTCATTCT
*
24591 TAGGGTAAAACAGTAATTT-ACTCATTCT
1 AAGGGTAAAACAGTAATTTAACTCATTCT
24619 TAGGTGCCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.04
27 6 0.12
28 42 0.84
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (29 bp):
AAGGGTAAAACAGTAATTTAACTCATTCT
Found at i:24619 original size:28 final size:28
Alignment explanation
Indices: 24559--24622 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
24549 AAATTTAACC
* *
24559 TTCTAAGGGTAAAACGGTAATTTACTCA
1 TTCTTAGGGTAAAACAGTAATTTACTCA
24587 TTCTTAGGGTAAAACAGTAATTTACTCA
1 TTCTTAGGGTAAAACAGTAATTTACTCA
24615 TTCTTAGG
1 TTCTTAGG
24623 TGCCAAGCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (28 bp):
TTCTTAGGGTAAAACAGTAATTTACTCA
Found at i:24728 original size:2 final size:2
Alignment explanation
Indices: 24723--24751 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24713 TTTTTTTCTT
24723 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24752 TAAACTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29175 original size:20 final size:20
Alignment explanation
Indices: 29137--29178 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29127 CTTGTTCTTT
* *
29137 TGGCACCTGAATTCTTGATG
1 TGGCACCTGAACTCGTGATG
*
29157 TGGCACCTGAACTGGTGATG
1 TGGCACCTGAACTCGTGATG
29177 TG
1 TG
29179 TACTAAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (20 bp):
TGGCACCTGAACTCGTGATG
Done.