Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023593.1 Corchorus olitorius cultivar O-4 contig23626, 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: 15479
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:140 original size:36 final size:35
Alignment explanation
Indices: 5--170 Score: 278
Period size: 35 Copynumber: 4.7 Consensus size: 35
1 GGCG
*
5 CGCGCCAGGCCTGGGCGCTGGGCCATGCGCTGGCG
1 CGCGCCAGGCCTGGGCGCTGGGCCATGCGCTGGCC
40 CGCGCCAGGCCTGGGCGCTGGGCCATGCGCTGGCC
1 CGCGCCAGGCCTGGGCGCTGGGCCATGCGCTGGCC
75 CGCGCCAGGCCTGGGCGCTGGGCCATGCGCTGGCC
1 CGCGCCAGGCCTGGGCGCTGGGCCATGCGCTGGCC
* *
110 CGCGCCTGGCCTGGGCGCTTGGGCCATGCGCTGGAC
1 CGCGCCAGGCCTGGGCGC-TGGGCCATGCGCTGGCC
*
146 CGCGCCTGGCCTGGGCGCTTGGGCC
1 CGCGCCAGGCCTGGGCGC-TGGGCC
171 GCGCCAGGCC
Statistics
Matches: 127, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
35 86 0.68
36 41 0.32
ACGTcount: A:0.05, C:0.39, G:0.43, T:0.13
Consensus pattern (35 bp):
CGCGCCAGGCCTGGGCGCTGGGCCATGCGCTGGCC
Found at i:173 original size:24 final size:23
Alignment explanation
Indices: 137--183 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
127 CTTGGGCCAT
*
137 GCGCTGGACCGCGCCTGGCCTGG
1 GCGCTGGACCGCGCCAGGCCTGG
*
160 GCGCTTGGGCCGCGCCAGGCCTGG
1 GCGC-TGGACCGCGCCAGGCCTGG
184 CCCAAGAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.04, C:0.38, G:0.45, T:0.13
Consensus pattern (23 bp):
GCGCTGGACCGCGCCAGGCCTGG
Found at i:2661 original size:23 final size:23
Alignment explanation
Indices: 2635--2694 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
2625 CAACACTATA
*
2635 AATAAACATAATACTCACA-TATT
1 AATAAACATAATA-TCACATTAAT
*
2658 AAT-AATATAAATATCACATTAAT
1 AATAAACAT-AATATCACATTAAT
2681 AATAAACATAATAT
1 AATAAACATAATAT
2695 ATATATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 9 0.29
23 18 0.58
24 4 0.13
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.32
Consensus pattern (23 bp):
AATAAACATAATATCACATTAAT
Found at i:5826 original size:25 final size:26
Alignment explanation
Indices: 5782--5830 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
5772 GACAAAATAG
*
5782 CCCTCAAACTTTATAAAAAAAAAAAC
1 CCCTCAAACTTTAGAAAAAAAAAAAC
*
5808 CCCTCAAACTTT-GACAAAAAAAA
1 CCCTCAAACTTTAGAAAAAAAAAA
5831 TATATATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.55, C:0.24, G:0.02, T:0.18
Consensus pattern (26 bp):
CCCTCAAACTTTAGAAAAAAAAAAAC
Found at i:6668 original size:20 final size:20
Alignment explanation
Indices: 6643--6682 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
6633 ATACACCTAC
*
6643 GCATATGTAAGCATTATGCT
1 GCATATGTAAGAATTATGCT
6663 GCATATGTAAGAATTATGCT
1 GCATATGTAAGAATTATGCT
6683 CTGTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (20 bp):
GCATATGTAAGAATTATGCT
Found at i:10980 original size:22 final size:22
Alignment explanation
Indices: 10914--11079 Score: 109
Period size: 22 Copynumber: 7.7 Consensus size: 22
10904 CACATAGAGA
10914 TTATCAAAA--TCATA-GTAAGG
1 TTATCAAAATTTCATAGGT-AGG
* *
10934 TTAT-AAAA-TTCATAGGAAAGT
1 TTATCAAAATTTCATAGG-TAGG
*
10955 TTATTAAAATTTCATAGGTAGG
1 TTATCAAAATTTCATAGGTAGG
* *
10977 TTATCAAACTTT-ATTATGG-AGT
1 TTATCAAAATTTCA-TA-GGTAGG
* * *
10999 TTATCACAATTTTATAGGTA-A
1 TTATCAAAATTTCATAGGTAGG
*
11020 TTATCAAAATTTCATATG-ATGG
1 TTATCAAAATTTCATAGGTA-GG
* *
11042 TTATCAAAATTTAATAGGGT-GA
1 TTATCAAAATTTCATA-GGTAGG
11064 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
11080 AAAATATTCA
Statistics
Matches: 115, Mismatches: 18, Indels: 24
0.73 0.11 0.15
Matches are distributed among these distances:
19 4 0.03
20 10 0.09
21 25 0.22
22 64 0.56
23 12 0.10
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGTAGG
Found at i:11144 original size:2 final size:2
Alignment explanation
Indices: 11137--11197 Score: 51
Period size: 2 Copynumber: 32.0 Consensus size: 2
11127 GTAAAACTAG
* *
11137 TA TA TA TA -A AA TA TA TA TA TA TA TA TA TA TA -A CTA -A TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
11177 TA TA T- TA TA -A TA GTA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA
11198 CTACAATACG
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
1 5 0.10
2 41 0.84
3 3 0.06
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:11963 original size:32 final size:32
Alignment explanation
Indices: 11927--11995 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
11917 TTGAATCAGG
* * *
11927 TCGGGTTAAATTTGGGTCAGGTTGATTCGGGT
1 TCGGGTCAAATTTGGGTCAAGTTAATTCGGGT
* *
11959 TCGGGTCAATTTTGGGTCAAGTTAATTCTGGT
1 TCGGGTCAAATTTGGGTCAAGTTAATTCGGGT
11991 TCGGG
1 TCGGG
11996 CTGGATTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.16, C:0.12, G:0.35, T:0.38
Consensus pattern (32 bp):
TCGGGTCAAATTTGGGTCAAGTTAATTCGGGT
Found at i:12009 original size:32 final size:31
Alignment explanation
Indices: 11935--12009 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 31
11925 GGTCGGGTTA
* * *
11935 AATTTGGGTCAGGTTGATTCGGGTTCGGGTC
1 AATTTTGGTCAAGTTAATTCGGGTTCGGGTC
* *
11966 AATTTTGGGTCAAGTTAATTCTGGTTCGGGCTG
1 AATTTT-GGTCAAGTTAATTCGGGTTCGGG-TC
*
11999 GATTTTGGTCA
1 AATTTTGGTCA
12010 GATCATTCCC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
31 5 0.14
32 25 0.69
33 6 0.17
ACGTcount: A:0.16, C:0.12, G:0.33, T:0.39
Consensus pattern (31 bp):
AATTTTGGTCAAGTTAATTCGGGTTCGGGTC
Found at i:12161 original size:20 final size:20
Alignment explanation
Indices: 12128--12166 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12118 CATAAATGAA
* *
12128 ATTTTCAGAGATTATTATTT
1 ATTTTCAAAGATTAATATTT
*
12148 ATTTTCAAATATTAATATT
1 ATTTTCAAAGATTAATATT
12167 GAATTCGGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAAAGATTAATATTT
Found at i:12218 original size:16 final size:16
Alignment explanation
Indices: 12199--12241 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
12189 GGGTTCGTGT
*
12199 TTTTTCGGGTTTTAGA
1 TTTTTCGGGTTATAGA
* * *
12215 TTTTCCGGGTTATGGT
1 TTTTTCGGGTTATAGA
12231 TTTTTCGGGTT
1 TTTTTCGGGTT
12242 CGGATTCAGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.07, C:0.09, G:0.28, T:0.56
Consensus pattern (16 bp):
TTTTTCGGGTTATAGA
Found at i:15143 original size:16 final size:16
Alignment explanation
Indices: 15107--15150 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
15097 TCCCGAACCC
*
15107 ACCCAAGCCCGAAAAT
1 ACCCGAGCCCGAAAAT
15123 ACCCGAGCCCGAAAAT
1 ACCCGAGCCCGAAAAT
*
15139 ACCCGAACCCGA
1 ACCCGAGCCCGA
15151 CTCGAACCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.39, C:0.41, G:0.16, T:0.05
Consensus pattern (16 bp):
ACCCGAGCCCGAAAAT
Found at i:15341 original size:2 final size:2
Alignment explanation
Indices: 15334--15371 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
15324 GCTAAACTAC
15334 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15372 AAGCAAAAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.