Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017531.1 Corchorus olitorius cultivar O-4 contig17564, 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: 18545
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Found at i:537 original size:3 final size:3
Alignment explanation
Indices: 531--574 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
521 ATATATAGTA
531 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
575 CTAGTTCTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1932 original size:19 final size:20
Alignment explanation
Indices: 1895--1932 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1885 AATTCAAAAC
*
1895 AAAATAAAAACTACTCATTT
1 AAAATAAAAACTACCCATTT
*
1915 AAAAT-AAAACTGCCCATT
1 AAAATAAAAACTACCCATT
1933 AGAGGATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAATAAAAACTACCCATTT
Found at i:2052 original size:226 final size:222
Alignment explanation
Indices: 1646--2279 Score: 830
Period size: 226 Copynumber: 2.8 Consensus size: 222
1636 TGAGTTTGTG
*
1646 CTCAGTTCTTAAAAATTCAAAACAAAATAAAAACTACCCATTTTAAATAAAACTACTAATTAGAG
1 CTCAGTTTTTAAAAATTCAAAACAAAATAAAAACTA-CCATTTTAAATAAAACTACTAATTAGAG
* *
1711 GATAAATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAATCACCCATTTATAAAAAATG
65 GATAAATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAAACACCCATTTA-AAAAACTG
* *
1776 TCAAAAACTACTCACGTAGTGAGTGCCCTGTGTCTTGTCTATAC-TAATTATAAAGTCAAGGCCT
129 TCAAAAACTACTCACGTAGTGAGTG-CCTGTGTCTTGT-T-TTCTTAATTATAAAGCCAAGGCCT
1840 GAGTTTGTGTCACGAGTT-ACCTCGGATACAAA
191 GAGTTTGTGTCACGAGTTGA-CTCGGATACAAA
* * **
1872 CTCAGTTTTTAAAAATTCAAAACAAAATAAAAACTACTCATTTAAAATAAAACTGCCCATTAGAG
1 CTCAGTTTTTAAAAATTCAAAACAAAATAAAAACTAC-CATTTTAAATAAAACTACTAATTAGAG
*
1937 GATAAATATAAGTATTTAAATTTTATTTATATTATTTTAAAAAAAACTACCCATTTAAAATAACT
65 GATAAATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAAAC-ACCCATTTAAAA-AACT
2002 GTCAAAAACTACTCACGTAGTGAGTGCCATGTGTCTGTGTTTTGTAATTATCTATACTAATTATA
128 GTCAAAAACTACTCACGTAGTGAGTGCC-TGTGTC------TTGT--TT-TC--T--TAATTATA
* *
2067 AAGCCAAGTCCTGAGTTTGTGTCACGAGTTGATTCGGATACAAA
179 AAGCCAAGGCCTGAGTTTGTGTCACGAGTTGACTCGGATACAAA
* *
2111 CTCAG-TTTTAAAAATTCAAAACAAAATAAAAACTACCAATTTTAAATAAAACTACTTATTAAAG
1 CTCAGTTTTTAAAAATTCAAAACAAAATAAAAACTACC-ATTTTAAATAAAACTACTAATTAGAG
2175 GATAAATATAAGTATTTAAATTTTATTTATATCATTTT-AAAAAAACAACCCATTTAAAAAAAAC
65 GATAAATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAAAC-ACCCATTT--AAAAAAC
* *
2239 TATCAAAAACTACTCAC-T-TTGAGTGACCTGTGTCTTGTTTT
127 TGTCAAAAACTACTCACGTAGTGAGTG-CCTGTGTCTTGTTTT
2280 ATTATTTCTA
Statistics
Matches: 364, Mismatches: 22, Indels: 43
0.85 0.05 0.10
Matches are distributed among these distances:
225 1 0.00
226 108 0.30
227 45 0.12
228 2 0.01
230 4 0.01
233 5 0.01
234 2 0.01
236 12 0.03
237 20 0.05
238 108 0.30
239 56 0.15
240 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (222 bp):
CTCAGTTTTTAAAAATTCAAAACAAAATAAAAACTACCATTTTAAATAAAACTACTAATTAGAGG
ATAAATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAAACACCCATTTAAAAAACTGTC
AAAAACTACTCACGTAGTGAGTGCCTGTGTCTTGTTTTCTTAATTATAAAGCCAAGGCCTGAGTT
TGTGTCACGAGTTGACTCGGATACAAA
Found at i:2190 original size:238 final size:236
Alignment explanation
Indices: 1646--2279 Score: 859
Period size: 238 Copynumber: 2.7 Consensus size: 236
1636 TGAGTTTGTG
* * * ** *
1646 CTCAGTTCTTAAAAATTCAAAACAAAATAAAAACTACCCATTTTAAATAAAACTACTAATTAGAG
1 CTCAGTTTTTAAAAATTCAAAACAAAATAAAAACTACTCATTTAAAATAAAACTACCCATTAAAG
*
1711 GATAAATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAATC-ACCCATTTATAAAAAA-
66 GATAAATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAA-CAACCCATTTAAAAAAAAC
* * * * *
1774 TGTCAAAAACTACTCAC-GT-AGTGA---GTGCCCTG---TGT-CTTGTCTATACTAATTATAAA
130 TATCAAAAACTACTCACTGTGAGTGACCTGTGTCTTGTTTTGTAATTATCTATACTAATTATAAA
*
1830 GTCAAGGCCTGAGTTTGTGTCACGAGTTACCTCGGATACAAA
195 GCCAAGGCCTGAGTTTGTGTCACGAGTTACCTCGGATACAAA
* *
1872 CTCAGTTTTTAAAAATTCAAAACAAAATAAAAACTACTCATTTAAAATAAAACTGCCCATTAGAG
1 CTCAGTTTTTAAAAATTCAAAACAAAATAAAAACTACTCATTTAAAATAAAACTACCCATTAAAG
* * *
1937 GATAAATATAAGTATTTAAATTTTATTTATATTATTTTAAAAAAAACTACCCATTT-AAAATAAC
66 GATAAATATAAGTATTTAAATTTTATTTATATCATTTT-AAAAAAACAACCCATTTAAAAAAAAC
*
2001 TGTCAAAAACTACTCACGTAGTGAGTG-CCATGTGTCTGTGTTTTGTAATTATCTATACTAATTA
130 TATCAAAAACTACTCAC-T-GTGAGTGACC-TGTGTCT-TGTTTTGTAATTATCTATACTAATTA
* *
2065 TAAAGCCAAGTCCTGAGTTTGTGTCACGAGTTGA-TTCGGATACAAA
191 TAAAGCCAAGGCCTGAGTTTGTGTCACGAGTT-ACCTCGGATACAAA
* **
2111 CTCAG-TTTTAAAAATTCAAAACAAAATAAAAACTAC-CAATTTTAAATAAAACTACTTATTAAA
1 CTCAGTTTTTAAAAATTCAAAACAAAATAAAAACTACTC-ATTTAAAATAAAACTACCCATTAAA
2174 GGATAAATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAACAACCCATTTAAAAAAAAC
65 GGATAAATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAACAACCCATTTAAAAAAAAC
*
2239 TATCAAAAACTACTCACTTTGAGTGACCTGTGTCTTGTTTT
130 TATCAAAAACTACTCACTGTGAGTGACCTGTGTCTTGTTTT
2280 ATTATTTCTA
Statistics
Matches: 362, Mismatches: 26, Indels: 31
0.86 0.06 0.07
Matches are distributed among these distances:
226 102 0.28
227 32 0.09
230 2 0.01
231 4 0.01
234 4 0.01
235 8 0.02
236 13 0.04
237 20 0.06
238 115 0.32
239 61 0.17
240 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (236 bp):
CTCAGTTTTTAAAAATTCAAAACAAAATAAAAACTACTCATTTAAAATAAAACTACCCATTAAAG
GATAAATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAACAACCCATTTAAAAAAAACT
ATCAAAAACTACTCACTGTGAGTGACCTGTGTCTTGTTTTGTAATTATCTATACTAATTATAAAG
CCAAGGCCTGAGTTTGTGTCACGAGTTACCTCGGATACAAA
Found at i:3383 original size:21 final size:21
Alignment explanation
Indices: 3354--3406 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
3344 TGAAGCACCG
*
3354 TGGGACTCTGTTCACTCAACC
1 TGGGTCTCTGTTCACTCAACC
3375 TGGGTCTCTGTTCACTCAACC
1 TGGGTCTCTGTTCACTCAACC
3396 TGGGTCTCTGT
1 TGGGTCTCTGT
3407 GGATGGATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.13, C:0.30, G:0.23, T:0.34
Consensus pattern (21 bp):
TGGGTCTCTGTTCACTCAACC
Found at i:13507 original size:30 final size:31
Alignment explanation
Indices: 13468--13535 Score: 111
Period size: 30 Copynumber: 2.2 Consensus size: 31
13458 GAGTATGACG
13468 AGGAGGAAGATTCCGATCTCTTTG-TTTGTGA
1 AGGA-GAAGATTCCGATCTCTTTGTTTTGTGA
*
13499 AGGAGAAGATTCTGATCTCTTTGTTTTGTGA
1 AGGAGAAGATTCCGATCTCTTTGTTTTGTGA
13530 AGGAGA
1 AGGAGA
13536 GAATTCTGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 18 0.51
31 17 0.49
ACGTcount: A:0.25, C:0.10, G:0.29, T:0.35
Consensus pattern (31 bp):
AGGAGAAGATTCCGATCTCTTTGTTTTGTGA
Found at i:13527 original size:31 final size:30
Alignment explanation
Indices: 13468--13545 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 30
13458 GAGTATGACG
*
13468 AGGAGGAAGATTCCGATCTCTTTGTTTGTGA
1 AGGA-GAAGATTCTGATCTCTTTGTTTGTGA
13499 AGGAGAAGATTCTGATCTCTTTGTTTTGTGA
1 AGGAGAAGATTCTGATCTCTTTG-TTTGTGA
13530 AGGAG-AGAATTCTGAT
1 AGGAGAAG-ATTCTGAT
13546 TTTGTCATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
30 20 0.45
31 24 0.55
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (30 bp):
AGGAGAAGATTCTGATCTCTTTGTTTGTGA
Done.