Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021178.1 Corchorus olitorius cultivar O-4 contig21211, 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: 5227
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1450 original size:30 final size:29
Alignment explanation
Indices: 1406--1501 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 29
1396 AAACTTACCA
*
1406 ATTTTATTAATTTCCAAAATCTTTTTTCGG
1 ATTTTATTATTTTCCAAAATCTTTTTT-GG
* *
1436 ATTTTTTTATTTTCCAAAATCTCCTTTTGGGG
1 ATTTTATTATTTTCCAAAATCT--TTTT-TGG
***
1468 ATTACCTTATTTTCCAAAATCTTCTTTTGG
1 ATTTTATTATTTTCCAAAATCTT-TTTTGG
1498 ATTT
1 ATTT
1502 GCTTAAGAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
30 26 0.48
31 3 0.06
32 25 0.46
ACGTcount: A:0.23, C:0.16, G:0.08, T:0.53
Consensus pattern (29 bp):
ATTTTATTATTTTCCAAAATCTTTTTTGG
Found at i:1658 original size:19 final size:20
Alignment explanation
Indices: 1634--1675 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
1624 TTATTGCGTC
1634 TTTTTAT-TTTCTGAT-TTTT
1 TTTTTATATTT-TGATCTTTT
1653 TTTTTATATTTTGATCTTTT
1 TTTTTATATTTTGATCTTTT
1673 TTT
1 TTT
1676 ATCTCTAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTATATTTTGATCTTTT
Found at i:3529 original size:26 final size:26
Alignment explanation
Indices: 3455--3536 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
3445 TCGTCTCCCG
3455 ATCAATCTTCTTTGAATTGTCTTCCA
1 ATCAATCTTCTTTGAATTGTCTTCCA
** *
3481 ATTCAATCTTCTGGGAATCGTCTTCCGA
1 A-TCAATCTTCTTTGAATTGTCTTCC-A
*
3509 ATCAA-CTTCTTTGTATTGTCTTCCA
1 ATCAATCTTCTTTGAATTGTCTTCCA
3534 ATC
1 ATC
3537 CAATATTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
25 4 0.09
26 16 0.34
27 25 0.53
28 2 0.04
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (26 bp):
ATCAATCTTCTTTGAATTGTCTTCCA
Found at i:3556 original size:53 final size:51
Alignment explanation
Indices: 3525--3849 Score: 512
Period size: 51 Copynumber: 6.4 Consensus size: 51
3515 TTCTTTGTAT
* * * *
3525 TGTCTTCCAATCCAATATT-AAAAGGACCGTCTCCCACTTATCCTTTGAAC
1 TGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAAC
3575 TGTCTTCCAATTCAATCTT--AAAGGACCGTCTTCCGCTTATCCTTTGAAC
1 TGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAAC
* ** *
3624 TGTCTTCCAATCCAATCTTAAAAAAAAAACCGTCTTCCGATTATCCTTTGAAC
1 TGTCTTCCAATTCAATCTT--AAAAAGGACCGTCTTCCGCTTATCCTTTGAAC
* *
3677 TGTCTTCCAATTCAATCTTAAAAAGGATCGTCTTCCACTTATCCTTTGAAC
1 TGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAAC
3728 TGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAAC
1 TGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAAC
*
3779 TGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCTGCTTATCCTTTGAAC
1 TGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAAC
3830 TGTCTTCCAATTCAATCTTA
1 TGTCTTCCAATTCAATCTTA
3850 GGAAAATCGT
Statistics
Matches: 254, Mismatches: 17, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
49 46 0.18
50 17 0.07
51 146 0.57
53 45 0.18
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (51 bp):
TGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAAC
Found at i:4529 original size:65 final size:64
Alignment explanation
Indices: 4113--4797 Score: 823
Period size: 64 Copynumber: 10.6 Consensus size: 64
4103 TCGAGAAGCT
* * * * * * *
4113 ATCTTCTGGTGT-GCTTTTTAACATGATCATCTTCCGAGCAACTTCTGAAAACTCTTGAGAAACC
1 ATCTTCTGGTGTAG-TTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACC
* * * * *
4177 ATCTTCTGGTGTAATTTTTGACAAGATCGTCTTCCGAGCAACTTCTGAAAACTCTTGAGAAACC
1 ATCTTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACC
* * * * *
4241 ATCTTCTGGTGTAATTTTTGACAAGATCCTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACC
1 ATCTTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACC
* * * * * * *
4305 ATCTTCTGGTGTAATTTTTGACAAGGTCGTCTTCCGATCAACTTCTAAAAACTCTTAAGAAACC
1 ATCTTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACC
* * * * * *
4369 ATCTTCTAGTGTACTTCTTGACAAGATCGTCTTTCGATCGACTTCTGAAAATTTTTGAGAACCC
1 ATCTTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACC
* * * * * *
4433 ATCTTCCGGCGTAGTTGTTGACAAGATCGTCTTCCGTTCATCTTCTGACAATTGTTGAGAAAACC
1 ATCTTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAG-AAACC
* * * *
4498 ATCTCCTGGAGTAGTTCTTGACAAGATCGTCTTCCGATCATCTTTTGAAAATTGTTGAGAAAACC
1 ATCTTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAG-AAACC
* * * * *
4563 ATCTTCTAGTGTACTTCTTGACAAGATCGTCTTTCGATCATCTTCAGAAAATTGTTGAGAAAACC
1 ATCTTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAG-AAACC
* * * *
4628 ATCTCCTGGAGTAGTTCTTGACAAGATCGTCTTCTGATCATCTTCTGAAAATTGTTGAGAAAACC
1 ATCTTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAG-AAACC
* * * * *
4693 ATCTTCTAGTGTACTTCTTGATAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAACCC
1 ATCTTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACC
*
4757 ATCTTCTGGTGTAGTTCTTGACAAGATCGTCTTCTGATCAA
1 ATCTTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAA
4798 ACCAAAATGA
Statistics
Matches: 552, Mismatches: 67, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
64 323 0.59
65 229 0.41
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (64 bp):
ATCTTCTGGTGTAGTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACC
Done.