Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014080.1 Corchorus olitorius cultivar O-4 contig14113, 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: 7475
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Found at i:3644 original size:37 final size:37
Alignment explanation
Indices: 3602--3674 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
3592 GAAGAAGCTA
* *
3602 AAAAAAAAAAAAATTAGACCTAAAATAGAAAGAGGTTT
1 AAAAAAAAAAAACTT-GACCTAAAACAGAAAGAGGTTT
* *
3640 AAAAAAAAAAAACTTGGCCTAAAACAGAGAGAGGT
1 AAAAAAAAAAAACTTGACCTAAAACAGAAAGAGGT
3675 CAGAAAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 17 0.55
38 14 0.45
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.15
Consensus pattern (37 bp):
AAAAAAAAAAAACTTGACCTAAAACAGAAAGAGGTTT
Found at i:3682 original size:37 final size:38
Alignment explanation
Indices: 3602--3689 Score: 99
Period size: 37 Copynumber: 2.3 Consensus size: 38
3592 GAAGAAGCTA
* *
3602 AAAAAAAAAAAAATTAGACCTAAAATAGAAAGAGGTTT
1 AAAAAAAAAAAAATTAGACCTAAAACAGAAAGAGGTTC
* * *
3640 AAAAAAAAAAAACTT-GGCCTAAAACAGAGAGAGG-TC
1 AAAAAAAAAAAAATTAGACCTAAAACAGAAAGAGGTTC
*
3676 AGAAAAAAGAAAAA
1 A-AAAAAAAAAAAA
3690 GGAGGGGTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
36 2 0.05
37 26 0.62
38 14 0.33
ACGTcount: A:0.64, C:0.08, G:0.16, T:0.12
Consensus pattern (38 bp):
AAAAAAAAAAAAATTAGACCTAAAACAGAAAGAGGTTC
Found at i:4593 original size:58 final size:58
Alignment explanation
Indices: 4505--5034 Score: 654
Period size: 58 Copynumber: 9.1 Consensus size: 58
4495 CTTGTTTGAG
* * *
4505 TTTCAATTTAAAATCTTATCTCGTTCCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
1 TTTCAATTCAAAATCTTATCTTGTTTCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* * * *
4563 TTTCAATTCAAAACCTTATCTCGTTTCAAAATCATGTTCGAGGTCTTTGTTAGAGAGT
1 TTTCAATTCAAAATCTTATCTTGTTTCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* **
4621 TTTCAATTTAAAATCTTATCTCATTTCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
1 TTTCAATTCAAAATCTTATCTTGTTTCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* *
4679 TTTCAATTCAAAACCTTATCTCGTTTCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
1 TTTCAATTCAAAATCTTATCTTGTTTCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* * *
4737 GTTCAATTTAAAAT-TTCATCTTGTTTCAAAATCCTGTTCAAGGTCTCTGTTAGAGAGT
1 TTTCAATTCAAAATCTT-ATCTTGTTTCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* * *
4795 TTCCAATTCAAAGTAGC-T-TCTTGATTT-AAAATCCTGTTTGAGGTCTCTGTTAGAGAGT
1 TTTCAATTCAAA--ATCTTATCTTG-TTTCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
** * * *
4853 TTTCGGTTCATAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGC
1 TTTCAATTCAAAATCTTATCTTGTTTCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* * * * * * *
4911 TTTCAATTGAAAAACTTATCTTGTTTTAAAATCCTGCTCAAGGTCTCGGCTAGAGAGT
1 TTTCAATTCAAAATCTTATCTTGTTTCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
* * ** * * *
4969 TTTCAATTGAAAATTTTATCTTGTTTTTGAAATCCTGCTCAAGGTCTCTGTTAGAGAAT
1 TTTCAATTCAAAATCTTATCTTG-TTTCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
5028 TTTCAAT
1 TTTCAAT
5035 CTTATTTTGG
Statistics
Matches: 416, Mismatches: 47, Indels: 17
0.87 0.10 0.04
Matches are distributed among these distances:
56 2 0.00
57 6 0.01
58 365 0.88
59 41 0.10
60 2 0.00
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (58 bp):
TTTCAATTCAAAATCTTATCTTGTTTCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
Found at i:5334 original size:29 final size:29
Alignment explanation
Indices: 5292--5400 Score: 164
Period size: 29 Copynumber: 3.8 Consensus size: 29
5282 ACCTTTTGTG
5292 AATCCAAGGGCATTTTGGTCATTTACGCA
1 AATCCAAGGGCATTTTGGTCATTTACGCA
*
5321 AATCCAAGGGCATTTTGGTCATTTCCGCA
1 AATCCAAGGGCATTTTGGTCATTTACGCA
* **
5350 TATCCAAGGGCATTTTGGTCATTTTGGCA
1 AATCCAAGGGCATTTTGGTCATTTACGCA
* *
5379 CATCCAAGGGCATTTTTGTCAT
1 AATCCAAGGGCATTTTGGTCAT
5401 GTTTGCACAA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 74 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (29 bp):
AATCCAAGGGCATTTTGGTCATTTACGCA
Found at i:5420 original size:30 final size:29
Alignment explanation
Indices: 5293--5424 Score: 158
Period size: 29 Copynumber: 4.5 Consensus size: 29
5283 CCTTTTGTGA
** *
5293 ATCCAAGGGCATTTTGGTCATTTACGCAA
1 ATCCAAGGGCATTTTGGTCATTTTGGCAC
** *
5322 ATCCAAGGGCATTTTGGTCATTTCCGCAT
1 ATCCAAGGGCATTTTGGTCATTTTGGCAC
5351 ATCCAAGGGCATTTTGGTCATTTTGGCAC
1 ATCCAAGGGCATTTTGGTCATTTTGGCAC
*
5380 ATCCAAGGGCATTTTTGTCATGTTT-GCAC
1 ATCCAAGGGCATTTTGGTCAT-TTTGGCAC
* *
5409 AATTCAGGGGCATTTT
1 -ATCCAAGGGCATTTT
5425 CTTTGTTTTT
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
29 77 0.83
30 16 0.17
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (29 bp):
ATCCAAGGGCATTTTGGTCATTTTGGCAC
Found at i:5525 original size:30 final size:29
Alignment explanation
Indices: 5473--5625 Score: 234
Period size: 29 Copynumber: 5.2 Consensus size: 29
5463 TTACAGATCC
* * *
5473 GGGGACATTATGGTCATTTTTGCATATCCA
1 GGGG-CATTATGATAATTTTTGCATATCTA
5503 GGGGCATTATGATAATTTTTTGCATATCTA
1 GGGGCATTATGATAA-TTTTTGCATATCTA
*
5533 GGGGCATTATGATAATTTCTGCATATCTA
1 GGGGCATTATGATAATTTTTGCATATCTA
*
5562 GGGGCATTATGATAATTTCTGCATATCTA
1 GGGGCATTATGATAATTTTTGCATATCTA
*
5591 GGGGCATTATGGTAATTTTTGCATATCTA
1 GGGGCATTATGATAATTTTTGCATATCTA
5620 GGGGCA
1 GGGGCA
5626 ATTCGGTCAC
Statistics
Matches: 116, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
29 84 0.72
30 32 0.28
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (29 bp):
GGGGCATTATGATAATTTTTGCATATCTA
Found at i:5640 original size:29 final size:29
Alignment explanation
Indices: 5483--5673 Score: 156
Period size: 29 Copynumber: 6.6 Consensus size: 29
5473 GGGGACATTA
*
5483 TGGTCATTTTTGCATATCCAGGGGC-ATT
1 TGGTCATTTTTGCATATCTAGGGGCAATT
* *
5511 ATGATAATTTTTTGCATATCTAGGGGC-ATT
1 -TGGTCA-TTTTTGCATATCTAGGGGCAATT
* * *
5541 ATGATAATTTCTGCATATCTAGGGGC-ATT
1 -TGGTCATTTTTGCATATCTAGGGGCAATT
* * *
5570 ATGATAATTTCTGCATATCTAGGGGC-ATT
1 -TGGTCATTTTTGCATATCTAGGGGCAATT
*
5599 ATGGTAATTTTTGCATATCTAGGGGCAATT
1 -TGGTCATTTTTGCATATCTAGGGGCAATT
* ** * * * *
5629 CGGTCACCTTTGTATGTCCAGGGGCATTT
1 TGGTCATTTTTGCATATCTAGGGGCAATT
5658 TGGTCATTTTTGCATA
1 TGGTCATTTTTGCATA
5674 CTCTGGGTTC
Statistics
Matches: 141, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
29 110 0.78
30 31 0.22
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (29 bp):
TGGTCATTTTTGCATATCTAGGGGCAATT
Found at i:5652 original size:58 final size:58
Alignment explanation
Indices: 5469--5673 Score: 200
Period size: 58 Copynumber: 3.5 Consensus size: 58
5459 GTGTTTACAG
* * * * *
5469 ATCC-GGGGACATTATGGTCATTTTTGCATATCCAGGGGCATTATGATAATTTTTTGCAT
1 ATCCAGGGG-CATTATGGTAATTTTTGCATATCTAGGGGCATTACGATAA-CTTCTGCAT
* * * * *
5528 ATCTAGGGGCATTATGATAATTTCTGCATATCTAGGGGCATTATGATAATTTCTGCAT
1 ATCCAGGGGCATTATGGTAATTTTTGCATATCTAGGGGCATTACGATAACTTCTGCAT
* * * *
5586 ATCTAGGGGCATTATGGTAATTTTTGCATATCTAGGGGCAATT-CGGTCACCTT-TGTAT
1 ATCCAGGGGCATTATGGTAATTTTTGCATATCTAGGGGC-ATTACGAT-AACTTCTGCAT
* * *
5644 GTCCAGGGGCATTTTGGTCATTTTTGCATA
1 ATCCAGGGGCATTATGGTAATTTTTGCATA
5674 CTCTGGGTTC
Statistics
Matches: 126, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
58 77 0.61
59 45 0.36
60 4 0.03
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (58 bp):
ATCCAGGGGCATTATGGTAATTTTTGCATATCTAGGGGCATTACGATAACTTCTGCAT
Done.