Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020859.1 Corchorus olitorius cultivar O-4 contig20892, 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: 29383
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:871 original size:15 final size:16
Alignment explanation
Indices: 830--869 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 16
820 TGAAAGAAAA
830 AAAAGAAGAAAAAACTG
1 AAAA-AAGAAAAAACTG
847 TCAAAAAAGAAAAAACTG
1 --AAAAAAGAAAAAACTG
865 AAAAA
1 AAAAA
870 GAGTGTAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
18 12 0.57
19 4 0.19
ACGTcount: A:0.72, C:0.07, G:0.12, T:0.07
Consensus pattern (16 bp):
AAAAAAGAAAAAACTG
Found at i:2219 original size:29 final size:30
Alignment explanation
Indices: 2124--2227 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 30
2114 TTTATAATAT
2124 GTAAAATGTCTTGAATTTAGAAAGTTC-AGGA
1 GTAAAATGTCTT-AATTT-GAAAGTTCAAGGA
* *
2155 GATAAAATGTCGTAAATTTGAAAATTCAA-GA
1 G-TAAAATGTC-TTAATTTGAAAGTTCAAGGA
*
2186 GGTAAAATGTCTTTATTTG-AAGTTCAAGGA
1 -GTAAAATGTCTTAATTTGAAAGTTCAAGGA
*
2216 GTAAAACGTCTT
1 GTAAAATGTCTT
2228 TGATGTAATA
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
29 18 0.29
30 8 0.13
31 19 0.31
32 16 0.26
33 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (30 bp):
GTAAAATGTCTTAATTTGAAAGTTCAAGGA
Found at i:2228 original size:29 final size:30
Alignment explanation
Indices: 2170--2228 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
2160 AATGTCGTAA
*
2170 ATTTGAAAATTCAAGAGGTAAAATGTCTTT
1 ATTTGAAAATTCAAGAGGTAAAACGTCTTT
*
2200 ATTTG-AAGTTCAAG-GAGTAAAACGTCTTT
1 ATTTGAAAATTCAAGAG-GTAAAACGTCTTT
2229 GATGTAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 1 0.04
29 20 0.77
30 5 0.19
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (30 bp):
ATTTGAAAATTCAAGAGGTAAAACGTCTTT
Found at i:3277 original size:15 final size:14
Alignment explanation
Indices: 3251--3284 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
3241 TCAAGATTTC
3251 ATACTATAAATATA
1 ATACTATAAATATA
*
3265 CTACTACTAAATATA
1 ATACTA-TAAATATA
3280 ATACT
1 ATACT
3285 TGTATCATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (14 bp):
ATACTATAAATATA
Found at i:8763 original size:20 final size:20
Alignment explanation
Indices: 8728--8765 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8718 GTTTGTCTCT
**
8728 TGAAAATTTTGTATTTTGAA
1 TGAAAATTTTCAATTTTGAA
8748 TGAAAATTTTCAATTTTG
1 TGAAAATTTTCAATTTTG
8766 CATTTTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (20 bp):
TGAAAATTTTCAATTTTGAA
Found at i:26341 original size:67 final size:67
Alignment explanation
Indices: 26233--26367 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
26223 CAGGTTAGAA
26233 TCTTTAGATTCATTTCTGTCTTTTACTTGATGTCCAAGGAACATAAATTTACTGATAATTGTTTA
1 TCTTTAGATTCATTTCTGTCTTTTACTTGATGTCCAAGGAACATAAATTTACTGATAATTGTTTA
26298 TG
66 TG
26300 TCTTTAGATTCATTTCTGTCTTTTACTTGATGTCCAAGGAACATAAATTTACTGATAATTGTTTA
1 TCTTTAGATTCATTTCTGTCTTTTACTTGATGTCCAAGGAACATAAATTTACTGATAATTGTTTA
26365 TG
66 TG
26367 T
1 T
26368 TGTGGAATCT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (67 bp):
TCTTTAGATTCATTTCTGTCTTTTACTTGATGTCCAAGGAACATAAATTTACTGATAATTGTTTA
TG
Found at i:28186 original size:2 final size:2
Alignment explanation
Indices: 28179--28208 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28169 GCATGAATGA
28179 AT 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 AT
28209 GTTTATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29086 original size:18 final size:19
Alignment explanation
Indices: 29044--29088 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
29034 ATACGTTTAG
29044 TCGTGT-TCGTGTTTGACTTA
1 TCGTGTCTCGTGTTTGA--TA
29064 TCGTGTCTCGTGTTTGA-A
1 TCGTGTCTCGTGTTTGATA
29082 TCGTGTC
1 TCGTGTC
29089 GGACACGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.33
20 6 0.25
21 10 0.42
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.47
Consensus pattern (19 bp):
TCGTGTCTCGTGTTTGATA
Found at i:29108 original size:42 final size:43
Alignment explanation
Indices: 29061--29143 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
29051 CGTGTTTGAC
* *
29061 TTATCGTGTCTCGTGT-TTGAATCGTGTC-GGACACGATTAAGA
1 TTATCGTGTCTCGTGTCCT-AATCGTGTCAAGACACGATTAAGA
*
29103 TTATCGTGTTTCGTGTCCTAATCGTGTCAAGACACGATTAA
1 TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAA
29144 CACGTTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 24 0.67
43 12 0.33
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (43 bp):
TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAAGA
Done.