Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013505.1 Corchorus olitorius cultivar O-4 contig13538, 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: 35792
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:4586 original size:10 final size:10
Alignment explanation
Indices: 4571--4601 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
4561 GAATATTAGC
4571 TTTATTTTGA
1 TTTATTTTGA
4581 TTTATTTTGA
1 TTTATTTTGA
4591 TTTATTTTGA
1 TTTATTTTGA
4601 T
1 T
4602 AAATTACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (10 bp):
TTTATTTTGA
Found at i:10491 original size:2 final size:2
Alignment explanation
Indices: 10484--10510 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10474 TCTTCTCCTT
10484 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
10511 TTAATAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12198 original size:27 final size:28
Alignment explanation
Indices: 12142--12199 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
12132 TCTTTTGACT
*
12142 ACATTTACCAGGTATTTTTTTTTTCACCA
1 ACATTTACCAGGTATTTTTTATTT-ACCA
*
12171 ACATTTACTAGGTATTTTTTATTT-CCA
1 ACATTTACCAGGTATTTTTTATTTACCA
12198 AC
1 AC
12200 TTTTTCCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 5 0.19
29 22 0.81
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (28 bp):
ACATTTACCAGGTATTTTTTATTTACCA
Found at i:15497 original size:24 final size:23
Alignment explanation
Indices: 15470--15519 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
15460 TTTTGTGCAA
*
15470 TCTC-CTTCTCCTTGTATGGAGTTT
1 TCTCACTT-TCCTAGTAT-GAGTTT
15494 TCTCATCTTTCCTAGTATGAGTTT
1 TCTCA-CTTTCCTAGTATGAGTTT
15518 TC
1 TC
15520 CATGAGCTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 12 0.52
25 8 0.35
26 3 0.13
ACGTcount: A:0.12, C:0.24, G:0.14, T:0.50
Consensus pattern (23 bp):
TCTCACTTTCCTAGTATGAGTTT
Found at i:21508 original size:21 final size:21
Alignment explanation
Indices: 21467--21510 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
21457 AAATTTTGTT
**
21467 TTTATTTATTTATTTTTAATA
1 TTTATTTATTTATTTACAATA
21488 TTTA-TTATTTAATTTACAATA
1 TTTATTTATTT-ATTTACAATA
21509 TT
1 TT
21511 AACCTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTATTTATTTATTTACAATA
Found at i:23415 original size:22 final size:23
Alignment explanation
Indices: 23376--23418 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
23366 AATTCTAATC
23376 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
23399 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
23419 ACTCTTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:29710 original size:20 final size:20
Alignment explanation
Indices: 29685--29723 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
29675 AATGCTTCAA
29685 ACACGCTTCGACAGCTACAC
1 ACACGCTTCGACAGCTACAC
*
29705 ACACGCTTCTACAGCTACA
1 ACACGCTTCGACAGCTACA
29724 AACTTGTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.38, G:0.13, T:0.18
Consensus pattern (20 bp):
ACACGCTTCGACAGCTACAC
Found at i:29778 original size:22 final size:22
Alignment explanation
Indices: 29746--29799 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
29736 GCAAAAAACC
*
29746 AAGCTCTGTGCTTATTCTCTCA
1 AAGCTCCGTGCTTATTCTCTCA
* *
29768 AAGCTCCGTGCTTTTTCTCTGA
1 AAGCTCCGTGCTTATTCTCTCA
*
29790 AATCTCCGTG
1 AAGCTCCGTG
29800 ATTTCCTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (22 bp):
AAGCTCCGTGCTTATTCTCTCA
Found at i:31305 original size:2 final size:2
Alignment explanation
Indices: 31288--31326 Score: 60
Period size: 2 Copynumber: 18.5 Consensus size: 2
31278 AGTCCACTAG
31288 AT AT AT CAT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
31327 AATTCTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 31 0.89
3 4 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:35187 original size:30 final size:30
Alignment explanation
Indices: 35153--35212 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
35143 ATGAAAGATA
* *
35153 AATTATTTTGAGAAG-CTAAAAAGAAAAAAG
1 AATTAGTTTAAGAAGTC-AAAAAGAAAAAAG
*
35183 AATTAGTTTAAGGAGTCAAAAAGAAAAAAG
1 AATTAGTTTAAGAAGTCAAAAAGAAAAAAG
35213 TTCAACGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.57, C:0.03, G:0.18, T:0.22
Consensus pattern (30 bp):
AATTAGTTTAAGAAGTCAAAAAGAAAAAAG
Found at i:35531 original size:72 final size:71
Alignment explanation
Indices: 35381--35527 Score: 197
Period size: 71 Copynumber: 2.1 Consensus size: 71
35371 TAAATTTTTA
* * *
35381 GGGGTCAAATTAGAAACTTTCGAATTTTTTTAGTTGAAATGCATATATATGAAAGAATTCTTAGC
1 GGGGCCAAATTAGAAACTTTCCAATTTTTTCAGTTGAAAT-CATATATATGAAAGAATTCTTAGC
35446 AATTTGG
65 AATTTGG
* * * *
35453 GGGGCCAAATTATAAATTTTCCAATTTTTTCATTTGAATAT-ATATATATGAAAGAATTCTTGGC
1 GGGGCCAAATTAGAAACTTTCCAATTTTTTCAGTTGAA-ATCATATATATGAAAGAATTCTTAGC
*
35517 AGTTTGG
65 AATTTGG
35524 GGGG
1 GGGG
35528 GCCATGGCCC
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
71 32 0.48
72 32 0.48
73 2 0.03
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (71 bp):
GGGGCCAAATTAGAAACTTTCCAATTTTTTCAGTTGAAATCATATATATGAAAGAATTCTTAGCA
ATTTGG
Done.