Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017937.1 Corchorus olitorius cultivar O-4 contig17970, 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: 5001
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Found at i:1614 original size:98 final size:99
Alignment explanation
Indices: 1451--1629 Score: 261
Period size: 98 Copynumber: 1.8 Consensus size: 99
1441 AAAAAAATTG
* * *
1451 AAGATATGATTCGAATTTTTCATTTTAAAAGAATAAAAAAAATATCAATTAATTGAATAAATAGA
1 AAGATATGATTCGAATTTGTCATTTCAAAAGAATAAAAAAAATATCAATTAATTGAACAAATAGA
*
1516 TCTTTTATTCATAAGACACGTTGCCACAAAAACA
66 TCTCTTATTCATAAGACACGTTGCCACAAAAACA
* * * * * *
1550 AAGATATGATTTGAATTTGTCGTTTCAAAATAAT-ACAAAAATATCCATTAATTGAACAATTAGA
1 AAGATATGATTCGAATTTGTCATTTCAAAAGAATAAAAAAAATATCAATTAATTGAACAAATAGA
1614 TCTCTTATTCATAAGA
66 TCTCTTATTCATAAGA
1630 TAAGATGCGA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
98 41 0.59
99 29 0.41
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (99 bp):
AAGATATGATTCGAATTTGTCATTTCAAAAGAATAAAAAAAATATCAATTAATTGAACAAATAGA
TCTCTTATTCATAAGACACGTTGCCACAAAAACA
Found at i:1911 original size:41 final size:41
Alignment explanation
Indices: 1829--1915 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
1819 AAAAGAATAC
*
1829 AAAAAAGTATTCATGAATTGAATAAATAGATCTCTTATAAA
1 AAAAAAGTATTCATGAATTGAATAAATAGATCTCATATAAA
* * * * *
1870 AAAAAAGTA-TCAATTAATTTAATAAATATATCTGATGTAAA
1 AAAAAAGTATTC-ATGAATTGAATAAATAGATCTCATATAAA
1911 AAAAA
1 AAAAA
1916 TCAAATAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 2 0.05
41 37 0.95
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (41 bp):
AAAAAAGTATTCATGAATTGAATAAATAGATCTCATATAAA
Found at i:2760 original size:170 final size:172
Alignment explanation
Indices: 2552--2894 Score: 557
Period size: 170 Copynumber: 2.0 Consensus size: 172
2542 CTTTTACAGT
* *
2552 TTTACTGTTGCCAAAAAATAGTTTATAGTTTTATTACTATATTATTAGAATTTTTACATATATTT
1 TTTACTGTTGCCAAAAAAAAGTTTACAGTTTTATTACTATATTATTAGAATTTTTACATATATTT
* * **
2617 CTTAAATGACATTGTTTAAACTTTTACAGTTATACTGTTT-CAAAAAAAAATTTTTTACAGTTTT
66 CTTAAATGACATTGTTTAAACTTTTAAAGTTATACTGTTTAAAAAAAAAAAACTTTTACAGTTTT
*
2681 ATTCTATTAAAAACTATA-TTTTTATTTAATTAAATTCAATA
131 ATTCTACTAAAAACTATATTTTTTATTTAATTAAATTCAATA
*
2722 TTTACTGTTG-CAAAAAAAACTTTTACAGTTTTATTACTATATTATTAGAATTTTTACATATATT
1 TTTACTGTTGCCAAAAAAAA-GTTTACAGTTTTATTACTATATTATTAGAATTTTTACATATATT
* *
2786 TCTTAAATGATATTGTTTAAACTTTTAAAGTTTTACTGTTTGAAAAAAAAAAAACTTTTACAGTT
65 TCTTAAATGACATTGTTTAAACTTTTAAAGTTATACTGTTT-AAAAAAAAAAAACTTTTACAGTT
2851 TTATTCTACTAAAAACTATATTTTTTATTTAATTAAATTCAATA
129 TTATTCTACTAAAAACTATATTTTTTATTTAATTAAATTCAATA
2895 AAAACTCTAT
Statistics
Matches: 159, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
169 8 0.05
170 90 0.57
172 38 0.24
173 23 0.14
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.48
Consensus pattern (172 bp):
TTTACTGTTGCCAAAAAAAAGTTTACAGTTTTATTACTATATTATTAGAATTTTTACATATATTT
CTTAAATGACATTGTTTAAACTTTTAAAGTTATACTGTTTAAAAAAAAAAAACTTTTACAGTTTT
ATTCTACTAAAAACTATATTTTTTATTTAATTAAATTCAATA
Found at i:2908 original size:32 final size:33
Alignment explanation
Indices: 2860--2921 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
2850 TTTATTCTAC
2860 TAAAAACTATATTTTTTATTTAATTAAATTCAA
1 TAAAAACTATATTTTTTATTTAATTAAATTCAA
*
2893 TAAAAACTCTA-TTTTTATTTAATTAAATT
1 TAAAAACTATATTTTTTATTTAATTAAATT
2922 TATAAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (33 bp):
TAAAAACTATATTTTTTATTTAATTAAATTCAA
Found at i:3433 original size:137 final size:137
Alignment explanation
Indices: 3289--3537 Score: 374
Period size: 137 Copynumber: 1.8 Consensus size: 137
3279 TATAAAAGTC
* *
3289 CGAATGTTGTAAAACTTCTGAATAAACAATTATACTCTTATCTTTT-TAATATATTTCTTAAATG
1 CGAATGTTGTAAAACTTCTGAATAAACAATTATACCCTTAT-TTTTCGAATATATTTCTTAAATG
*
3353 TCATTATTTAAACTTTTATAGTTCCACTCTACTAAAAACACTATTTTTTTAATCTATACTATATA
65 TCATTATTTAAACTTTTATAGTTCCACTCAACTAAAAACACTATTTTTTTAATCTATACTATATA
3418 TGAAATTA
130 TGAAATTA
* **
3426 CGAATGTTGTAAAACTTTTGAATCGACAATTATACCCTTATTTTTCGAATATATTTCTTAAATGT
1 CGAATGTTGTAAAACTTCTGAATAAACAATTATACCCTTATTTTTCGAATATATTTCTTAAATGT
* * * ** *
3491 CATTGTTTAGATTTTTATAGTTTTACTCAACTAAAAACTCTATTTTT
66 CATTATTTAAACTTTTATAGTTCCACTCAACTAAAAACACTATTTTT
3538 ATTTAATTAA
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
136 4 0.04
137 95 0.96
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (137 bp):
CGAATGTTGTAAAACTTCTGAATAAACAATTATACCCTTATTTTTCGAATATATTTCTTAAATGT
CATTATTTAAACTTTTATAGTTCCACTCAACTAAAAACACTATTTTTTTAATCTATACTATATAT
GAAATTA
Done.