Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013321.1 Corchorus olitorius cultivar O-4 contig13354, 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: 48403
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:6670 original size:2 final size:2
Alignment explanation
Indices: 6665--6727 Score: 78
Period size: 2 Copynumber: 32.0 Consensus size: 2
6655 TATATATCCG
*
6665 TA TA TA CTA TA TA TA TA TA -A TA TA -A TA TA TA TA GTA AA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
6707 -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
6728 CTAAGCATAA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
1 3 0.06
2 47 0.87
3 4 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:6693 original size:18 final size:18
Alignment explanation
Indices: 6666--6725 Score: 86
Period size: 18 Copynumber: 3.3 Consensus size: 18
6656 ATATATCCGT
*
6666 ATATACTATATATATATA
1 ATATAATATATATATATA
6684 ATATAATATATATAGTA-A
1 ATATAATATATATA-TATA
6702 ATATAATATATATATATA
1 ATATAATATATATATATA
6720 TATATA
1 -ATATA
6726 TACTAAGCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
17 2 0.05
18 29 0.76
19 7 0.18
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
ATATAATATATATATATA
Found at i:13090 original size:2 final size:2
Alignment explanation
Indices: 13083--13113 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13073 GTCCCGAGCT
13083 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13114 TGTTGCGCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14926 original size:15 final size:15
Alignment explanation
Indices: 14906--14936 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14896 TTCAATAAAA
*
14906 TAATAATTATTTAAT
1 TAATAATTAATTAAT
14921 TAATAATTAATTAAT
1 TAATAATTAATTAAT
14936 T
1 T
14937 TCAGCCCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATAATTAATTAAT
Found at i:14931 original size:19 final size:18
Alignment explanation
Indices: 14883--14933 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
14873 CATAAAATTT
14883 TTAATAATAATTATTCAA
1 TTAATAATAATTATTCAA
* *
14901 TAAAATAATAATTATTTAA
1 T-TAATAATAATTATTCAA
14920 TTAATAATTAATTA
1 TTAATAA-TAATTA
14934 ATTTCAGCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAATAATAATTATTCAA
Found at i:15305 original size:13 final size:13
Alignment explanation
Indices: 15287--15311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15277 AGGTAACAAC
15287 AAAAATCATCACA
1 AAAAATCATCACA
15300 AAAAATCATCAC
1 AAAAATCATCAC
15312 TCATGCCAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATCATCACA
Found at i:16577 original size:9 final size:9
Alignment explanation
Indices: 16563--16589 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
16553 TCGAGCCCTT
16563 AATTGCAAA
1 AATTGCAAA
16572 AATTGCAAA
1 AATTGCAAA
16581 AATTGCAAA
1 AATTGCAAA
16590 TTGGGCGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTGCAAA
Found at i:32594 original size:15 final size:15
Alignment explanation
Indices: 32574--32604 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
32564 TTCAATAAAA
*
32574 TAATAATTATTTAAT
1 TAATAATTAATTAAT
32589 TAATAATTAATTAAT
1 TAATAATTAATTAAT
32604 T
1 T
32605 TCAGCCCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATAATTAATTAAT
Found at i:32599 original size:19 final size:18
Alignment explanation
Indices: 32551--32601 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
32541 CATAAGATTT
32551 TTAATAATAATTATTCAA
1 TTAATAATAATTATTCAA
* *
32569 TAAAATAATAATTATTTAA
1 T-TAATAATAATTATTCAA
32588 TTAATAATTAATTA
1 TTAATAA-TAATTA
32602 ATTTCAGCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAATAATAATTATTCAA
Found at i:34284 original size:17 final size:18
Alignment explanation
Indices: 34249--34285 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
34239 CTTACATTAT
34249 AATATATTTTTTTGTATA
1 AATATATTTTTTTGTATA
34267 AATAT-TTTTTATTG-ATA
1 AATATATTTTT-TTGTATA
34284 AA
1 AA
34286 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
AATATATTTTTTTGTATA
Found at i:34341 original size:19 final size:19
Alignment explanation
Indices: 34317--34355 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34307 ATAAAGTACA
34317 TATAATA-ATTATTTTTATT
1 TATAATATA-TATTTTTATT
*
34336 TATAATTTATATTTTTATT
1 TATAATATATATTTTTATT
34355 T
1 T
34356 CTTTCCCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATAATATATATTTTTATT
Found at i:41882 original size:30 final size:30
Alignment explanation
Indices: 41831--41898 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
41821 TTAATTTTGG
* *
41831 AAAACGC--AAAAACACATTTTTTTTTTCA
1 AAAACGCAAAAAAAAACAATTTTTTTTTCA
41859 AAAACGCAAAAAAAAACAATTTTTTTTTCA
1 AAAACGCAAAAAAAAACAATTTTTTTTTCA
41889 AAAACGCAAA
1 AAAACGCAAA
41899 TTTTTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 7 0.19
30 29 0.81
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.28
Consensus pattern (30 bp):
AAAACGCAAAAAAAAACAATTTTTTTTTCA
Done.