Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007456.1 Corchorus capsularis cultivar CVL-1 contig07477, 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: 16388
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:3557 original size:21 final size:21
Alignment explanation
Indices: 3531--3573 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3521 ACGCTGGCAT
3531 CCATGTCAGCATGTCAGAGCG
1 CCATGTCAGCATGTCAGAGCG
*
3552 CCATGTCAGCTTGTCAGAGCG
1 CCATGTCAGCATGTCAGAGCG
3573 C
1 C
3574 GTGTAAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.30, G:0.28, T:0.21
Consensus pattern (21 bp):
CCATGTCAGCATGTCAGAGCG
Found at i:6451 original size:21 final size:21
Alignment explanation
Indices: 6427--6478 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
6417 TTGTCATAGA
* * *
6427 TTTAGATTACTTTGTTTTGTT
1 TTTAGATTAATTTGCTTTCTT
*
6448 TTTAGTTTAATTTGCTTTCTT
1 TTTAGATTAATTTGCTTTCTT
6469 TTTA-ATTAAT
1 TTTAGATTAAT
6479 CTCTTTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.19, C:0.06, G:0.10, T:0.65
Consensus pattern (21 bp):
TTTAGATTAATTTGCTTTCTT
Found at i:8416 original size:6 final size:6
Alignment explanation
Indices: 8405--8429 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
8395 TTTTTAGTCT
8405 AGATAA AGATAA AGATAA AGATAA A
1 AGATAA AGATAA AGATAA AGATAA A
8430 ACCCAAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AGATAA
Found at i:8790 original size:11 final size:11
Alignment explanation
Indices: 8774--8803 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
8764 ATCCTCATTC
8774 CTTCTCCTTTT
1 CTTCTCCTTTT
8785 CTTCTCCTTTT
1 CTTCTCCTTTT
8796 CTTCTCCT
1 CTTCTCCT
8804 CTCCAATTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (11 bp):
CTTCTCCTTTT
Found at i:13502 original size:39 final size:39
Alignment explanation
Indices: 13459--13574 Score: 223
Period size: 39 Copynumber: 3.0 Consensus size: 39
13449 TATGATAACA
13459 TGTATATATTATTATGAGATTATTATGTAAGCTACATTT
1 TGTATATATTATTATGAGATTATTATGTAAGCTACATTT
13498 TGTATATATTATTATGAGATTATTATGTAAGCTACATTT
1 TGTATATATTATTATGAGATTATTATGTAAGCTACATTT
*
13537 TGTATATATTATTAAGAGATTATTATGTAAGCTACATT
1 TGTATATATTATTATGAGATTATTATGTAAGCTACATT
13575 ATAGATTTAT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 76 1.00
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.47
Consensus pattern (39 bp):
TGTATATATTATTATGAGATTATTATGTAAGCTACATTT
Found at i:16091 original size:21 final size:22
Alignment explanation
Indices: 16048--16097 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
16038 TTAGAACCGA
16048 CGGGTCGGTTCCGTCGCGTTCT
1 CGGGTCGGTTCCGTCGCGTTCT
*
16070 CGGGTCGGTTCCG-CGGGTTCT
1 CGGGTCGGTTCCGTCGCGTTCT
16091 CGGGTCG
1 CGGGTCG
16098 AGTCGAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.00, C:0.30, G:0.42, T:0.28
Consensus pattern (22 bp):
CGGGTCGGTTCCGTCGCGTTCT
Found at i:16174 original size:15 final size:15
Alignment explanation
Indices: 16143--16267 Score: 61
Period size: 15 Copynumber: 8.5 Consensus size: 15
16133 TATAAAAGTA
*
16143 AATATATATTTATTAT
1 AATATATA-TAATTAT
16159 AATATATATAATTAT
1 AATATATATAATTAT
* *
16174 AATTATAATTTATATAAT
1 AA-TAT-ATATA-ATTAT
*
16192 AAATATATATAAAGTA-
1 -AATATATAT-AATTAT
* *
16208 AATATATTTACTT-T
1 AATATATATAATTAT
16222 -ATATATAT--TTAT
1 AATATATATAATTAT
*
16234 --TATATA-AAGTA-
1 AATATATATAATTAT
*
16245 AATACATATAATTAT
1 AATATATATAATTAT
16260 AATATATA
1 AATATATA
16268 ATTTATATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 27
0.67 0.11 0.22
Matches are distributed among these distances:
11 8 0.10
12 3 0.04
13 12 0.15
14 6 0.07
15 23 0.28
16 11 0.13
17 9 0.11
18 8 0.10
19 2 0.02
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
AATATATATAATTAT
Found at i:16275 original size:37 final size:37
Alignment explanation
Indices: 16177--16267 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
16167 TAATTATAAT
* *
16177 TATAATTTATATA-ATAAATATATATAAAGTAAATATA
1 TATAATTTATATATATATAT-TATATAAAGTAAATACA
* * *
16214 TTTACTTTATATATATTTATTATATAAAGTAAATACA
1 TATAATTTATATATATATATTATATAAAGTAAATACA
16251 TATAA-TTATA-ATATATA
1 TATAATTTATATATATATA
16268 ATTTATATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 6 0.13
36 5 0.11
37 30 0.67
38 4 0.09
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (37 bp):
TATAATTTATATATATATATTATATAAAGTAAATACA
Done.