Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015908.1 Corchorus olitorius cultivar O-4 contig15941, 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: 9591
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Found at i:2967 original size:25 final size:25
Alignment explanation
Indices: 2814--2954 Score: 219
Period size: 25 Copynumber: 5.6 Consensus size: 25
2804 TAGCCTATGT
* *
2814 GTTTTCTAAACGCAAGCACAGGCTC
1 GTTTTCCAAACGCAAGCACAGGTTC
** *
2839 ACTTGCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGTTC
2864 GTTTTCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGTTC
2889 GTTTTCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGTTC
*
2914 GTTTTCCAAACGCAAGCACAGGCTC
1 GTTTTCCAAACGCAAGCACAGGTTC
*
2939 GTTTTCCAAACACAAG
1 GTTTTCCAAACGCAAG
2955 AACATGAGCG
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 106 1.00
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (25 bp):
GTTTTCCAAACGCAAGCACAGGTTC
Found at i:2967 original size:75 final size:75
Alignment explanation
Indices: 2814--2977 Score: 211
Period size: 75 Copynumber: 2.2 Consensus size: 75
2804 TAGCCTATGT
* * *
2814 GTTTTCTAAACGCAAGCACAGGCTCACTTGCCAAACGCAAGCACAGGTTCGTTTTCCAAACGCAA
1 GTTTTCCAAACGCAAGCACAGGCTCACTTGCCAAACGCAAGCACAGGCTCGTTTTCCAAACACAA
* **
2879 GCACAGGTTC
66 GAACAGGAGC
* ** *
2889 GTTTTCCAAACGCAAGCACAGGTTCGTTTTCCAAACGCAAGCACAGGCTCGTTTTCCAAACACAA
1 GTTTTCCAAACGCAAGCACAGGCTCACTTGCCAAACGCAAGCACAGGCTCGTTTTCCAAACACAA
*
2954 GAACATGAGC
66 GAACAGGAGC
* *
2964 GTTTACCCAACGCA
1 GTTTTCCAAACGCA
2978 CGTGAGTCGT
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.21
Consensus pattern (75 bp):
GTTTTCCAAACGCAAGCACAGGCTCACTTGCCAAACGCAAGCACAGGCTCGTTTTCCAAACACAA
GAACAGGAGC
Found at i:4430 original size:27 final size:27
Alignment explanation
Indices: 4392--4502 Score: 213
Period size: 27 Copynumber: 4.1 Consensus size: 27
4382 GGCACCACCT
4392 CAAGTGGCTGCGCTTCATCCGCAACCC
1 CAAGTGGCTGCGCTTCATCCGCAACCC
4419 CAAGTGGCTGCGCTTCATCCGCAACCC
1 CAAGTGGCTGCGCTTCATCCGCAACCC
4446 CAAGTGGCTGCGCTTCATCCGCAACCC
1 CAAGTGGCTGCGCTTCATCCGCAACCC
*
4473 CAAGTGGTTGCGCTTCATCCGCAACCC
1 CAAGTGGCTGCGCTTCATCCGCAACCC
4500 CAA
1 CAA
4503 TTGAATGGCC
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.20, C:0.40, G:0.22, T:0.19
Consensus pattern (27 bp):
CAAGTGGCTGCGCTTCATCCGCAACCC
Found at i:4597 original size:15 final size:15
Alignment explanation
Indices: 4546--4601 Score: 67
Period size: 15 Copynumber: 3.5 Consensus size: 15
4536 GGCACTGTTC
4546 CAGAAACAACCGTTG
1 CAGAAACAACCGTTG
* *
4561 CAAAAACATCATCCGTTT
1 CAGAAACA--A-CCGTTG
4579 CAGAAACAACCGTTG
1 CAGAAACAACCGTTG
4594 CAGAAACA
1 CAGAAACA
4602 TCATCTGGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 20 0.59
16 1 0.03
17 1 0.03
18 12 0.35
ACGTcount: A:0.43, C:0.27, G:0.14, T:0.16
Consensus pattern (15 bp):
CAGAAACAACCGTTG
Found at i:4616 original size:33 final size:33
Alignment explanation
Indices: 4546--4617 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
4536 GGCACTGTTC
* *
4546 CAGAAACAACCGTTGCAAAAACATCATCCGTTT
1 CAGAAACAACCGTTGCAAAAACATCATCCGGTG
* *
4579 CAGAAACAACCGTTGCAGAAACATCATCTGGTG
1 CAGAAACAACCGTTGCAAAAACATCATCCGGTG
4612 CAGAAA
1 CAGAAA
4618 ATTGCAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (33 bp):
CAGAAACAACCGTTGCAAAAACATCATCCGGTG
Found at i:7404 original size:25 final size:25
Alignment explanation
Indices: 7226--7391 Score: 260
Period size: 25 Copynumber: 6.6 Consensus size: 25
7216 TAGCCTATGT
* * *
7226 GTTTTCTAAACGCAGGCACAGGCTC
1 GTTTTCCAAACGCAAGCACAGGTTC
** *
7251 ACTTGCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGTTC
7276 GTTTTCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGTTC
7301 GTTTTCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGTTC
7326 GTTTTCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGTTC
*
7351 GTTTTCCAAACGCAAGCACAGGCTC
1 GTTTTCCAAACGCAAGCACAGGTTC
*
7376 GTTTTCCAAACACAAG
1 GTTTTCCAAACGCAAG
7392 AACATGAGCG
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 130 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (25 bp):
GTTTTCCAAACGCAAGCACAGGTTC
Found at i:7413 original size:75 final size:75
Alignment explanation
Indices: 7256--7414 Score: 239
Period size: 75 Copynumber: 2.1 Consensus size: 75
7246 GGCTCACTTG
* * *
7256 CCAAACGCAAGCACAGGTTCGTTTTCCAAACGCAAGCACAGGTTCGTTTTCCAAACGCAAGCACA
1 CCAAACGCAAGCACAGGTTCGTTTTCCAAACGCAAGCACAGGCTCGTTTTCCAAACACAAGAACA
** *
7321 GGTTCGTTTT
66 GGAGCGTTTA
7331 CCAAACGCAAGCACAGGTTCGTTTTCCAAACGCAAGCACAGGCTCGTTTTCCAAACACAAGAACA
1 CCAAACGCAAGCACAGGTTCGTTTTCCAAACGCAAGCACAGGCTCGTTTTCCAAACACAAGAACA
*
7396 TGAGCGTTTA
66 GGAGCGTTTA
7406 -CACAACGCA
1 CCA-AACGCA
7415 CGTGAGTCGT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
74 2 0.03
75 74 0.97
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (75 bp):
CCAAACGCAAGCACAGGTTCGTTTTCCAAACGCAAGCACAGGCTCGTTTTCCAAACACAAGAACA
GGAGCGTTTA
Done.