Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014845.1 Corchorus olitorius cultivar O-4 contig14878, 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: 7820
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1573 original size:2 final size:2
Alignment explanation
Indices: 1566--1593 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1556 GCATTAGACA
1566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1594 GAGGGAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2728 original size:433 final size:426
Alignment explanation
Indices: 1748--2732 Score: 1213
Period size: 433 Copynumber: 2.3 Consensus size: 426
1738 GGTGGGTCCC
* * ** * *
1748 ATCTCCATCAACAAAAATTTTTTTGGATTATTTATGGAATTACCC-CATACTTTTCAACTTTATG
1 ATCTCCATCAACAAACATTTTTTTGAATTATTTATCAAATGACCCTCATACTTTTCAACTTTATA
* * * ** * *** * *
1812 CTATTTAGTCCTTTACGAATT-GAT-TTAA-CGCTTTTGGTATTTTTTTTCATTTTTTTTCTATT
66 CTACTTAGTCCTTTACAAATTCCATCTTAATC-AATTT--AACGCTTATTAATTTTTTTTCTATT
* * *
1874 TGTCCCATTAAGGTGATTCAGGTGTCTATTAAAAGGTAATTTCATGATTTACAACTTTCATGAAA
128 TGTCCCATTAAGCTGATTCAGGTGTCGATTAAAAGGTAATTTCATGATTTACAACTTTCATAAAA
* * ** *
1939 GACTTAAAAGCCAATTTTTATGTTTCAATTCAAAAAAATGCTTCCGAAATTTAGTGATTTTGATT
193 AACTCAAAAGCCAATTTTTACATTTCAATTCAAAAAAATGCTTCCCAAATTTAGTGATTTTGATT
*
2004 GTCGATCTATTTAAAATCATATAATTTTCAATCAACATGTTCGATTAATGTTTCTCAAGTGTCAG
258 GTCGATCTATTTAAAATCATATAATTTTCAATCAACATGTTCGATTAAAGTTTCTCAAGTGTCAG
* * * *
2069 TTAAAAGGTTATTGCATGATCTACGACTTTCTTGAAGGACCCTAAAGGTAAATTTAATCTACGAG
323 TTAAAAGGTTATTGCATGATCTACGACTTTCATGAAGGACCCAAAAGCTAAATTTAATCTACAAG
* * *
2134 TTTCATTAAGTGTTCGAAAGGGAATTTTTATGTTTCAAG
388 TTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAG
* * * *
2173 ATCTCCATCAACAAACATTTTTTTGGATTATTTATGAAATGACCCTCATATTTTTCTACTTTATA
1 ATCTCCATCAACAAACATTTTTTTGAATTATTTATCAAATGACCCTCATACTTTTCAACTTTATA
* * * *
2238 CTACTTAGTCCTTTACTAATTCTATCTTAATCGATTTAACGCTTAAACTTTATTTTTTTTCTATT
66 CTACTTAGTCCTTTACAAATTCCATCTTAATCAATTTAACGCTT--A-TTAATTTTTTTTCTATT
* *
2303 TGTCCGATTAAGCTGATTCAGGTGTCGATTAAAAGGTAATTTCATGATTTCCAACTTTCATAAAA
128 TGTCCCATTAAGCTGATTCAGGTGTCGATTAAAAGGTAATTTCATGATTTACAACTTTCATAAAA
* *
2368 AACTCAAAAGCCAATTTTTACATTTCAATTCAAAGAAAAATGCTTCCCAAATTTTGTGGTTTTGA
193 AACTCAAAAGCCAATTTTTACATTTCAATTC-AA-AAAAATGCTTCCCAAATTTAGTGATTTTGA
*
2433 TTGTC-AGTCTATTTAATACCAT-ATATAATTTT-ACATCCACATG-TCTGATTAAAGTAATT-T
256 TTGTCGA-TCTATTTAA-A--ATCATATAATTTTCA-ATCAACATGTTC-GATTAAAGT--TTCT
* *
2493 -AAGTGTCGGTTAAAAGGTTATTGCGTGATCTACGACTTTCATGAAGTG-CCCAAAAGCTAAATT
313 CAAGTGTCAGTTAAAAGGTTATTGCATGATCTACGACTTTCATGAAG-GACCCAAAAGCTAAATT
* *
2556 TGATCTACAAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTGAAG
377 TAATCTACAAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAG
*
2606 ATCTCTATCAACAAACATTTTCTTATTTGAATTATTTATCAAATGACCCTCATACTTTTCAACTT
1 ATCTCCATCAACAAACA--TT-TT-TTTGAATTATTTATCAAATGACCCTCATACTTTTCAACTT
*
2671 TATACTACTTAGTCCTTTACAAATTCCATCTTTACTCAATTTAACGC-T-TTAATTTTTTTTCT
62 TATACTACTTAGTCCTTTACAAATTCCATC-TTAATCAATTTAACGCTTATTAATTTTTTTTCT
2733 TTGTTCTATT
Statistics
Matches: 485, Mismatches: 52, Indels: 38
0.84 0.09 0.07
Matches are distributed among these distances:
425 42 0.09
426 38 0.08
427 2 0.00
428 7 0.01
429 104 0.21
430 3 0.01
431 41 0.08
432 4 0.01
433 155 0.32
434 4 0.01
435 4 0.01
436 2 0.00
437 65 0.13
438 14 0.03
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.42
Consensus pattern (426 bp):
ATCTCCATCAACAAACATTTTTTTGAATTATTTATCAAATGACCCTCATACTTTTCAACTTTATA
CTACTTAGTCCTTTACAAATTCCATCTTAATCAATTTAACGCTTATTAATTTTTTTTCTATTTGT
CCCATTAAGCTGATTCAGGTGTCGATTAAAAGGTAATTTCATGATTTACAACTTTCATAAAAAAC
TCAAAAGCCAATTTTTACATTTCAATTCAAAAAAATGCTTCCCAAATTTAGTGATTTTGATTGTC
GATCTATTTAAAATCATATAATTTTCAATCAACATGTTCGATTAAAGTTTCTCAAGTGTCAGTTA
AAAGGTTATTGCATGATCTACGACTTTCATGAAGGACCCAAAAGCTAAATTTAATCTACAAGTTT
CATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAG
Found at i:7311 original size:29 final size:28
Alignment explanation
Indices: 7278--7338 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 28
7268 TTAGTAGTCC
7278 AATTTGCAATCAATTAATCAATCAGTTAT
1 AATTTGCAATCAATTAATCAATCA-TTAT
*
7307 AATTTGCAATCAATTAATCAATCATTTT
1 AATTTGCAATCAATTAATCAATCATTAT
7335 AATT
1 AATT
7339 GTTGTAGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (28 bp):
AATTTGCAATCAATTAATCAATCATTAT
Done.