Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019769.1 Corchorus olitorius cultivar O-4 contig19802, 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: 42786
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:6731 original size:13 final size:12
Alignment explanation
Indices: 6713--6753 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
6703 CTAGAGAAGG
6713 TTTTTCAAAACAA
1 TTTTTCAAAA-AA
6726 TTTTTC-AAAAA
1 TTTTTCAAAAAA
6737 -TTTTCAAAAAA
1 TTTTTCAAAAAA
*
6748 ATTTTC
1 TTTTTC
6754 TTTTTAAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.19
11 7 0.27
12 8 0.31
13 6 0.23
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTTTCAAAAAA
Found at i:17884 original size:68 final size:68
Alignment explanation
Indices: 17812--17947 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
17802 ACAATGAGAA
17812 TTTCGGTTTCAGTGGGTGAAAAGGTTGATGATCAACAATCAATGTGTGCAAATCTTATTAAGAAT
1 TTTCGGTTTCAGTGGGTGAAAAGGTTGATGATCAACAATCAATGTGTGCAAATCTTATTAAGAAT
17877 GAG
66 GAG
*
17880 TTTCGGTTTCAGTGGGTGAAAAGGTTGATGATCAACAATCAATGTGTGCAAGTCTTATTAAGAAT
1 TTTCGGTTTCAGTGGGTGAAAAGGTTGATGATCAACAATCAATGTGTGCAAATCTTATTAAGAAT
17945 GAG
66 GAG
17948 CAAAACAATT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (68 bp):
TTTCGGTTTCAGTGGGTGAAAAGGTTGATGATCAACAATCAATGTGTGCAAATCTTATTAAGAAT
GAG
Found at i:19228 original size:15 final size:15
Alignment explanation
Indices: 19208--19237 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19198 ATCAGGCTGC
*
19208 CACGATACACGATAT
1 CACGATACACAATAT
19223 CACGATACACAATAT
1 CACGATACACAATAT
19238 TTCAACCGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Found at i:24648 original size:21 final size:21
Alignment explanation
Indices: 24587--24648 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
24577 AAGTTTTATC
24587 AAGGGGCCAAATTCAAAAAAAA
1 AAGGGGCCAAATT-AAAAAAAA
* *
24609 AAAGGG-CAATTTTAAAAAAAA
1 AAGGGGCCAA-ATTAAAAAAAA
*
24630 AAGGGGCCAAATTAGAAAA
1 AAGGGGCCAAATTAAAAAA
24649 TTAAAATCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
21 23 0.70
22 10 0.30
ACGTcount: A:0.58, C:0.10, G:0.19, T:0.13
Consensus pattern (21 bp):
AAGGGGCCAAATTAAAAAAAA
Found at i:24907 original size:35 final size:35
Alignment explanation
Indices: 24861--24931 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
24851 GCACGCAGGC
24861 GTATGATGACAAACTCTAAAGACATAAAAGCATAA
1 GTATGATGACAAACTCTAAAGACATAAAAGCATAA
* *
24896 GTATGATGACAAACTCTAAAGAGATGAAAGCATAA
1 GTATGATGACAAACTCTAAAGACATAAAAGCATAA
24931 G
1 G
24932 ATTAAAGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (35 bp):
GTATGATGACAAACTCTAAAGACATAAAAGCATAA
Found at i:24937 original size:22 final size:23
Alignment explanation
Indices: 24912--24969 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 23
24902 TGACAAACTC
24912 TAAAGAGATG-AAAGCATAAGAT
1 TAAAGAGATGCAAAGCATAAGAT
24934 TAAAGAGATAATTGCAAAGCATAAGAT
1 TAAAGAG---A-TGCAAAGCATAAGAT
*
24961 AAAAGAGAT
1 TAAAGAGAT
24970 ATGATCTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
22 7 0.23
23 1 0.03
24 1 0.03
25 1 0.03
26 2 0.07
27 18 0.60
ACGTcount: A:0.55, C:0.05, G:0.21, T:0.19
Consensus pattern (23 bp):
TAAAGAGATGCAAAGCATAAGAT
Found at i:36285 original size:28 final size:27
Alignment explanation
Indices: 36233--36290 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
36223 TGCCTCTTGA
* * *
36233 AGAAAGAAAATCTGGATTAATTCCACC
1 AGAAAGAAAATCTGGATGAACTCCAAC
*
36260 AGAAAGAAAAGTTTGGATGAACTCCAAC
1 AGAAAGAAAA-TCTGGATGAACTCCAAC
36288 AGA
1 AGA
36291 GGGTTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (27 bp):
AGAAAGAAAATCTGGATGAACTCCAAC
Found at i:38772 original size:75 final size:75
Alignment explanation
Indices: 38605--38827 Score: 342
Period size: 75 Copynumber: 3.0 Consensus size: 75
38595 TTTGAATACC
* *
38605 CTCTGGAAATTATTGATAGCTCCAATCAAC-TTTAACGTGGGAGAACCTTTTCG-CTCGTTTTGG
1 CTCTGGAAATTATTGATAGCTCCCATCAACTTTTAACGTGGGAGAACCTTTTCGCCCCGTTTTGG
38668 TCTTTTCTCA
66 TCTTTTCTCA
* *** * *
38678 CTCTAGAAATTACCAATAGCTCCCATCAACTTTTAACGTGAGAGAACCTTTTCGCCCCGTTTCGG
1 CTCTGGAAATTATTGATAGCTCCCATCAACTTTTAACGTGGGAGAACCTTTTCGCCCCGTTTTGG
38743 TCTTTTCTCA
66 TCTTTTCTCA
* *
38753 CTCTGGAATTTATTGATAGCTCCCATCAACTTTTAATGTGGGAGAACCTTTTCGCCCCGTTTTGG
1 CTCTGGAAATTATTGATAGCTCCCATCAACTTTTAACGTGGGAGAACCTTTTCGCCCCGTTTTGG
38818 TCTTTTCTCA
66 TCTTTTCTCA
38828 ATTTACTTAA
Statistics
Matches: 132, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
73 25 0.19
74 22 0.17
75 85 0.64
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (75 bp):
CTCTGGAAATTATTGATAGCTCCCATCAACTTTTAACGTGGGAGAACCTTTTCGCCCCGTTTTGG
TCTTTTCTCA
Done.