Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021447.1 Corchorus olitorius cultivar O-4 contig21480, 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: 12088
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:43 original size:29 final size:29
Alignment explanation
Indices: 1--69 Score: 115
Period size: 28 Copynumber: 2.4 Consensus size: 29
1 TTTCCTCAAAAAAAAATAAGAGCTAATTA
1 TTTCCTCAAAAAAAAATAAGAGCTAATTA
30 TTTCCTC-AAAAAAAATAAGAGCTAATTA
1 TTTCCTCAAAAAAAAATAAGAGCTAATTA
*
58 TTCCCT-AAAAAA
1 TTTCCTCAAAAAA
70 GAGCTAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 31 0.82
29 7 0.18
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.28
Consensus pattern (29 bp):
TTTCCTCAAAAAAAAATAAGAGCTAATTA
Found at i:1749 original size:26 final size:27
Alignment explanation
Indices: 1690--1754 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
1680 CCCTAAACTG
* *
1690 TCTTATCTTTTTTTCTATCACAAACCTG
1 TCTTATC-TTTTTTCTATCAAAAACCTA
*
1718 TATTATCTTTTTTCTATCAAAAACC-A
1 TCTTATCTTTTTTCTATCAAAAACCTA
1744 TCTTATCTTTT
1 TCTTATCTTTT
1755 CTCTTCTCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 10 0.30
27 17 0.52
28 6 0.18
ACGTcount: A:0.25, C:0.22, G:0.02, T:0.52
Consensus pattern (27 bp):
TCTTATCTTTTTTCTATCAAAAACCTA
Found at i:2916 original size:70 final size:70
Alignment explanation
Indices: 2803--2933 Score: 235
Period size: 70 Copynumber: 1.9 Consensus size: 70
2793 TGGAATTTTA
** *
2803 AAAAGCATAAGGCGTTGAAAGATTGATCTAGATGCTAAGACTTGTAACGTGCTTATGGAAACTTA
1 AAAAGCATAAGGCACTGAAAGATTGATCTAGATGCTAAGACTTGTAACATGCTTATGGAAACTTA
2868 CTTTG
66 CTTTG
2873 AAAAGCATAAGGCACTGAAAGATTGATCTAGATGCTAAGACTTGTAACATGCTTATGGAAA
1 AAAAGCATAAGGCACTGAAAGATTGATCTAGATGCTAAGACTTGTAACATGCTTATGGAAA
2934 GTTATTTTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (70 bp):
AAAAGCATAAGGCACTGAAAGATTGATCTAGATGCTAAGACTTGTAACATGCTTATGGAAACTTA
CTTTG
Found at i:4520 original size:27 final size:28
Alignment explanation
Indices: 4473--4539 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
4463 GGAGAAGAGG
* *
4473 AAAGATAAGA-TGGTTTTTGATAG-AAA
1 AAAGATAAGACAGGTTTGTGATAGAAAA
*
4499 AAAGATAATACAGGTTTGTGATAGAAAA
1 AAAGATAAGACAGGTTTGTGATAGAAAA
4527 AAAGATAAGACAG
1 AAAGATAAGACAG
4540 TTTAGGGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 9 0.26
27 11 0.31
28 15 0.43
ACGTcount: A:0.51, C:0.03, G:0.22, T:0.24
Consensus pattern (28 bp):
AAAGATAAGACAGGTTTGTGATAGAAAA
Found at i:4542 original size:27 final size:26
Alignment explanation
Indices: 4473--4542 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 26
4463 GGAGAAGAGG
** *
4473 AAAGATAAGATGGTTTTTGATAGAAA
1 AAAGATAAGACAGTTTGTGATAGAAA
*
4499 AAAGATAATACAGGTTTGTGATAGAAAA
1 AAAGATAAGACA-GTTTGTGATAG-AAA
4527 AAAGATAAGACAGTTT
1 AAAGATAAGACAGTTT
4543 AGGGATTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 9 0.24
27 14 0.38
28 14 0.38
ACGTcount: A:0.49, C:0.03, G:0.21, T:0.27
Consensus pattern (26 bp):
AAAGATAAGACAGTTTGTGATAGAAA
Found at i:5502 original size:31 final size:31
Alignment explanation
Indices: 5467--5551 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
5457 TCGAACGGAA
*
5467 TTTTGGATGTTTTACCCCCTGAACTTGTATG
1 TTTTGGACGTTTTACCCCCTGAACTTGTATG
*
5498 TTTTGGACGTTTTACCCCTTGAACTTGTATG
1 TTTTGGACGTTTTACCCCCTGAACTTGTATG
*
5529 TTTTGGACGTTTTATCCCCTGAA
1 TTTTGGACGTTTTACCCCCTGAA
5552 TTTTAACTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.45
Consensus pattern (31 bp):
TTTTGGACGTTTTACCCCCTGAACTTGTATG
Found at i:7757 original size:7 final size:7
Alignment explanation
Indices: 7745--7784 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
7735 AGAGGAGGAG
7745 GAAAAAA
1 GAAAAAA
7752 GAAAAAA
1 GAAAAAA
7759 GAAAAAA
1 GAAAAAA
*
7766 GTAAAAA
1 GAAAAAA
7773 -AAAAAA
1 GAAAAAA
7779 -AAAAAA
1 GAAAAAA
7785 CCATGGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 11 0.35
7 20 0.65
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.03
Consensus pattern (7 bp):
GAAAAAA
Found at i:8896 original size:41 final size:42
Alignment explanation
Indices: 8850--8932 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
8840 AATTATCCCT
8850 CCTAAT-AATTAAGGTAATAAATTAAATCCA-AGTTTAGCCCC
1 CCTAATAAATTAAGGTAATAAATTAAATCCAGA-TTTAGCCCC
8891 CCTAATAAATTAAGGTAATAAATTAAATCCAGATTTAGCCCC
1 CCTAATAAATTAAGGTAATAAATTAAATCCAGATTTAGCCCC
8933 TAGTTATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
41 6 0.15
42 33 0.82
43 1 0.03
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (42 bp):
CCTAATAAATTAAGGTAATAAATTAAATCCAGATTTAGCCCC
Found at i:9611 original size:23 final size:23
Alignment explanation
Indices: 9580--9634 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
9570 ATAAATTAGG
*
9580 ATTTTATTATGATTATGATTCAA
1 ATTTGATTATGATTATGATTCAA
9603 ATTTGATTATGATTATGATTCAA
1 ATTTGATTATGATTATGATTCAA
9626 ATTTGATTA
1 ATTTGATTA
9635 GGTGGCATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
ATTTGATTATGATTATGATTCAA
Done.