Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014317.1 Corchorus capsularis cultivar CVL-1 contig14338, 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: 23079
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1867 original size:8 final size:8
Alignment explanation
Indices: 1854--1887 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1844 CACCTTCTTG
1854 AAAAATTC
1 AAAAATTC
1862 AAAAATTC
1 AAAAATTC
*
1870 AGAAACTTC
1 A-AAAATTC
1879 AAAAATTC
1 AAAAATTC
1887 A
1 A
1888 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:1976 original size:5 final size:5
Alignment explanation
Indices: 1966--1991 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1956 ATCGAAAAAT
1966 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
1992 AAATTTTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:3575 original size:33 final size:32
Alignment explanation
Indices: 3524--3628 Score: 106
Period size: 33 Copynumber: 3.3 Consensus size: 32
3514 CTAATTGTGA
* * *
3524 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
1 TGAAAATAATCCTATTTTGGTTG-ACATAGCAT
* **
3557 TAAAAATAATTTTATTTTGGTTGATCATAGCAT
1 TGAAAATAATCCTATTTTGGTTGA-CATAGCAT
* *
3590 TGCAAATAATCCTGTTTTGGTTG--ATAGCAT
1 TGAAAATAATCCTATTTTGGTTGACATAGCAT
3620 TGAAAATAA
1 TGAAAATAA
3629 ATCTGTTTTG
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
30 15 0.25
32 1 0.02
33 45 0.74
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (32 bp):
TGAAAATAATCCTATTTTGGTTGACATAGCAT
Found at i:4054 original size:30 final size:30
Alignment explanation
Indices: 4018--4076 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
4008 CAAGGGGGAG
4018 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
*
4048 GGAATGATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
4077 CTTGAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:8288 original size:32 final size:32
Alignment explanation
Indices: 8223--8325 Score: 125
Period size: 32 Copynumber: 3.2 Consensus size: 32
8213 TTGAGTTAGG
* *
8223 TCGGGTTAAATTTGGGTTAGGTTGATTCGGGT
1 TCGGGTTAAATTTGGGTCAGGTTGATTCAGGT
*
8255 TCGGGTTAAATTTGGGTCAGGTTGATTTAGGT
1 TCGGGTTAAATTTGGGTCAGGTTGATTCAGGT
* * * * *
8287 TCGAGTCAATTTTGGGTCGGGTTAATTCAGGT
1 TCGGGTTAAATTTGGGTCAGGTTGATTCAGGT
*
8319 TTGGGTT
1 TCGGGTT
8326 TAGACTGAGT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.17, C:0.08, G:0.35, T:0.41
Consensus pattern (32 bp):
TCGGGTTAAATTTGGGTCAGGTTGATTCAGGT
Found at i:8313 original size:16 final size:16
Alignment explanation
Indices: 8221--8313 Score: 62
Period size: 16 Copynumber: 5.8 Consensus size: 16
8211 GCTTGAGTTA
*
8221 GGTCGGGTTAAATTTG
1 GGTCGGGTTAATTTTG
** * *
8237 GGTTAGGTTGA-TTCG
1 GGTCGGGTTAATTTTG
*
8252 GGTTCGGGTTAAATTTG
1 GG-TCGGGTTAATTTTG
* * *
8269 GGTCAGGTTGATTTAG
1 GGTCGGGTTAATTTTG
* * *
8285 GTTCGAGTCAATTTTG
1 GGTCGGGTTAATTTTG
8301 GGTCGGGTTAATT
1 GGTCGGGTTAATT
8314 CAGGTTTGGG
Statistics
Matches: 54, Mismatches: 21, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
15 5 0.09
16 44 0.81
17 5 0.09
ACGTcount: A:0.17, C:0.08, G:0.35, T:0.40
Consensus pattern (16 bp):
GGTCGGGTTAATTTTG
Found at i:10003 original size:39 final size:37
Alignment explanation
Indices: 9952--10025 Score: 121
Period size: 39 Copynumber: 1.9 Consensus size: 37
9942 CTTTGAAAAA
*
9952 TTAGTTGTAGTTTCTTCTAGATTTAACTAATTGGGGTAG
1 TTAGTGGTAGTTTCTTCTAGATTTAACT--TTGGGGTAG
9991 TTAGTGGTAGTTTCTTCTAGATTTAACTTTGGGGT
1 TTAGTGGTAGTTTCTTCTAGATTTAACTTTGGGGT
10026 GGTTTTCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 7 0.21
39 27 0.79
ACGTcount: A:0.20, C:0.08, G:0.24, T:0.47
Consensus pattern (37 bp):
TTAGTGGTAGTTTCTTCTAGATTTAACTTTGGGGTAG
Found at i:17075 original size:23 final size:23
Alignment explanation
Indices: 17049--17095 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
17039 TTAATCTAAC
17049 GCTTAGTTTGGTATTGATATTGA
1 GCTTAGTTTGGTATTGATATTGA
17072 GCTTAGTTTGGTATTGATATTGA
1 GCTTAGTTTGGTATTGATATTGA
17095 G
1 G
17096 ATTGCAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.04, G:0.28, T:0.47
Consensus pattern (23 bp):
GCTTAGTTTGGTATTGATATTGA
Done.