Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015069.1 Corchorus olitorius cultivar O-4 contig15102, 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: 45586
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:211 original size:101 final size:100
Alignment explanation
Indices: 32--216 Score: 246
Period size: 101 Copynumber: 1.8 Consensus size: 100
22 TAATTTTAGA
* ** * * *
32 TATTATAATCCGGTTTAAATTGAAAAATTTTATAATTAATTTTTAAAATAAATTTTATTAAATTT
1 TATTATAATCCAGTCAAAATT-AAAAACTTTATAATTAATTTTTAAAATAAAATATATTAAATTT
97 TAATAATGGCAATTCAGAATTAAAAGAAAGCCCATG
65 TAATAATGGCAATTCAGAATTAAAAGAAAGCCCATG
*
133 TATTATAATCCAGTCAAAATT-AAAACTTTATAATTAATTTTTAAAAATAAAAATATATTAATTT
1 TATTATAATCCAGTCAAAATTAAAAACTTTATAATTAATTTTT-AAAAT-AAAATATATTAAATT
* * *
197 TTATTAATGTCAATTTAGAA
64 TTAATAATGGCAATTCAGAA
217 ATATATATGA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
99 20 0.28
100 5 0.07
101 47 0.65
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.41
Consensus pattern (100 bp):
TATTATAATCCAGTCAAAATTAAAAACTTTATAATTAATTTTTAAAATAAAATATATTAAATTTT
AATAATGGCAATTCAGAATTAAAAGAAAGCCCATG
Found at i:4898 original size:87 final size:87
Alignment explanation
Indices: 4777--4999 Score: 319
Period size: 84 Copynumber: 2.6 Consensus size: 87
4767 CCACTATCAA
* * *
4777 ATCTTCCTCTCCTCCATGCGTTGAAATGCTCTCCTCCTTCTCATTTGATGCCATTGCTTCAACTA
1 ATCTTCCTCCCCTGCATGCTTTGAAATGCTCTCCTCCTTCTCATTTGATGCCATTGCTTCAACTA
*
4842 CCGCGACACAGGTTTCAGCCTC
66 CCGCAACACAGGTTTCAGCCTC
* *
4864 ATCTTCCTCCCCTGCATGCTTTGAAGA-GCTCTCCT-C--CTCATTCGATGCCATTGCTTTAACT
1 ATCTTCCTCCCCTGCATGCTTTGAA-ATGCTCTCCTCCTTCTCATTTGATGCCATTGCTTCAACT
* * *
4925 ACTGCAACACGGGTTTCATCCTC
65 ACCGCAACACAGGTTTCAGCCTC
*
4948 ATCTTCCTCCCCTGCATGCTTTGAAATGCTCTCCTCCTTATCATTTGATGCC
1 ATCTTCCTCCCCTGCATGCTTTGAAATGCTCTCCTCCTTCTCATTTGATGCC
5000 GCGACACTGG
Statistics
Matches: 120, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
83 1 0.01
84 75 0.62
85 1 0.01
86 1 0.01
87 41 0.34
88 1 0.01
ACGTcount: A:0.17, C:0.35, G:0.13, T:0.35
Consensus pattern (87 bp):
ATCTTCCTCCCCTGCATGCTTTGAAATGCTCTCCTCCTTCTCATTTGATGCCATTGCTTCAACTA
CCGCAACACAGGTTTCAGCCTC
Found at i:5053 original size:72 final size:72
Alignment explanation
Indices: 4931--5071 Score: 214
Period size: 72 Copynumber: 2.0 Consensus size: 72
4921 AACTACTGCA
* *
4931 ACACGGGTTTCATCCTCATCTTCCTCCCCTGCATGCTTTGAAATGCTCTCCTCCTTATCATTTGA
1 ACACGGGTTTCATCCTCATCTTCCTCCCCTGCATGCTTCGAAATGCTCTCCTCCTCATCATTTGA
4996 TGCCGCG
66 TGCCGCG
* *
5003 ACACTGGTTTCATCCTCATCTTCCTCCCCTGCATG-TATCGAAGA-GCTCTCCTCCTCCTCATTT
1 ACACGGGTTTCATCCTCATCTTCCTCCCCTGCATGCT-TCGAA-ATGCTCTCCTCCTCATCATTT
5066 GATGCC
64 GATGCC
5072 ATTGTTTCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
71 1 0.02
72 61 0.97
73 1 0.02
ACGTcount: A:0.16, C:0.36, G:0.14, T:0.34
Consensus pattern (72 bp):
ACACGGGTTTCATCCTCATCTTCCTCCCCTGCATGCTTCGAAATGCTCTCCTCCTCATCATTTGA
TGCCGCG
Found at i:5172 original size:87 final size:86
Alignment explanation
Indices: 4998--5165 Score: 198
Period size: 87 Copynumber: 1.9 Consensus size: 86
4988 TCATTTGATG
* *
4998 CCGCGACACTGGTTTCATCCTCATCTTCCTCCCCTGCATGTATCGAAGAGCTCTCCTCCTCCTCA
1 CCGCGACACGGGTTTCATCCTCATCTTCCTCCCCTGCATGTATCGAAGAGC-CTCCACCTCCTCA
* ***
5063 TTTGATGCCATTGTTTCAACTA
65 TTGGATGCCACCATTTCAACTA
* *
5085 CCGCGACACGGGTTTCATCCTCAACTTCTTCCTCCCCTGCATGTTTTGAAGAG-CT-CACCTCCT
1 CCGCGACACGGGTTTCATCCTC-A--TCTTCCTCCCCTGCATGTATCGAAGAGCCTCCACCTCCT
5148 CATTGGACT-CCACCATTT
63 CATTGGA-TGCCACCATTT
5166 GTACTACTTC
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
87 40 0.58
88 4 0.06
90 25 0.36
ACGTcount: A:0.17, C:0.36, G:0.14, T:0.32
Consensus pattern (86 bp):
CCGCGACACGGGTTTCATCCTCATCTTCCTCCCCTGCATGTATCGAAGAGCCTCCACCTCCTCAT
TGGATGCCACCATTTCAACTA
Found at i:11536 original size:11 final size:11
Alignment explanation
Indices: 11520--11544 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11510 CCCTTTATGC
11520 AAAAAGAAAAG
1 AAAAAGAAAAG
11531 AAAAAGAAAAG
1 AAAAAGAAAAG
11542 AAA
1 AAA
11545 TGCAAGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:25382 original size:6 final size:6
Alignment explanation
Indices: 25371--25406 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
25361 TTTCTTTCAT
25371 TCCAAC TCCAAC TCCAAC TCCAAC TCCAAC TCCAAC
1 TCCAAC TCCAAC TCCAAC TCCAAC TCCAAC TCCAAC
25407 CTTGCTCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
TCCAAC
Found at i:32237 original size:29 final size:29
Alignment explanation
Indices: 32164--32237 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 29
32154 GGCCTAATGT
*
32164 CCAAATTGGGCCTAAACCTTTCCAAACTTG
1 CCAAATTGGGCCTAAACCTTT-CAAACATG
* *
32194 CTCAATTTGAGCCTAAACCTTT-AAACATG
1 C-CAAATTGGGCCTAAACCTTTCAAACATG
32223 ACCAAATTGGGCCTA
1 -CCAAATTGGGCCTA
32238 GACGTTATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
29 17 0.46
30 2 0.05
31 18 0.49
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (29 bp):
CCAAATTGGGCCTAAACCTTTCAAACATG
Done.