Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007976.1 Corchorus olitorius cultivar O-4 contig08003, 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, 616
Length: 1028
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Found at i:192 original size:39 final size:38
Alignment explanation
Indices: 140--221 Score: 121
Period size: 38 Copynumber: 2.1 Consensus size: 38
130 AATAATAGAC
140 AAAAAAAAAACAAAAAAACAAAAAAAACAACAA-AAAACA
1 AAAAAAAAAAC-AAAAAACAAAAAAAACAA-AACAAAACA
* *
179 AAAAAAAAAACAAAAAACAAAAAAAAGAAAACAAAAGA
1 AAAAAAAAAACAAAAAACAAAAAAAACAAAACAAAACA
217 AAAAA
1 AAAAA
222 TTGAAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
37 2 0.05
38 27 0.68
39 11 0.28
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (38 bp):
AAAAAAAAAACAAAAAACAAAAAAAACAAAACAAAACA
Found at i:214 original size:10 final size:9
Alignment explanation
Indices: 142--221 Score: 99
Period size: 9 Copynumber: 8.7 Consensus size: 9
132 TAATAGACAA
142 AAAAAAAAC
1 AAAAAAAAC
151 -AAAAAAAC
1 AAAAAAAAC
159 AAAAAAAAC
1 AAAAAAAAC
168 AACAAAAAAC
1 AA-AAAAAAC
*
178 AAAAAAAAA
1 AAAAAAAAC
187 AACAAAAAAC
1 AA-AAAAAAC
*
197 AAAAAAAAG
1 AAAAAAAAC
*
206 AAAACAAAAG
1 AAAA-AAAAC
216 AAAAAA
1 AAAAAA
222 TTGAAAAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
8 8 0.12
9 30 0.47
10 26 0.41
ACGTcount: A:0.88, C:0.10, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:219 original size:19 final size:18
Alignment explanation
Indices: 138--221 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 18
128 AAAATAATAG
138 ACAAAAAAAAAACAAAAAA
1 ACAAAAAAAAAA-AAAAAA
*
157 ACAAAAAAAACAACAAAAA
1 ACAAAAAAAA-AAAAAAAA
176 ACAAAAAAAAAAACAAAAA
1 ACAAAAAAAAAAA-AAAAA
*
195 ACAAAAAAAAGAAAACAAA
1 ACAAAAAAAA-AAAAAAAA
*
214 AGAAAAAA
1 ACAAAAAA
222 TTGAAAAATT
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
18 2 0.03
19 51 0.88
20 5 0.09
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (18 bp):
ACAAAAAAAAAAAAAAAA
Found at i:229 original size:1 final size:1
Alignment explanation
Indices: 140--221 Score: 74
Period size: 1 Copynumber: 82.0 Consensus size: 1
130 AATAATAGAC
* * * * * * *
140 AAAAAAAAAACAAAAAAACAAAAAAAACAACAAAAAACAAAAAAAAAAACAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
205 GAAAACAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAA
222 TTGAAAAATT
Statistics
Matches: 61, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:938 original size:50 final size:50
Alignment explanation
Indices: 863--1000 Score: 240
Period size: 50 Copynumber: 2.8 Consensus size: 50
853 TAAGATTGCA
* **
863 TTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAAAGTAAAACTGCT
1 TTCCATTTGTAAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAACTGCT
913 TTCCATTTGTAAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAACTGCT
1 TTCCATTTGTAAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAACTGCT
*
963 TTCCATTTGTAAGTTCAAGATCAAAATTTGCTTTTCAA
1 TTCCATTTGTAAGTTCAAGATCAAAATTCGCTTTTCAA
1001 GGTAGGATTG
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (50 bp):
TTCCATTTGTAAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAACTGCT
Found at i:1028 original size:50 final size:50
Alignment explanation
Indices: 859--1020 Score: 234
Period size: 50 Copynumber: 3.2 Consensus size: 50
849 ACAATAAGAT
* **
859 TGCATTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAAAGTAAAAC
1 TGCATTCCATTTGTAAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAAC
*
909 TGCTTTCCATTTGTAAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAAC
1 TGCATTCCATTTGTAAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAAC
* * * ** *
959 TGCTTTCCATTTGTAAGTTCAAGATCAAAATTTGCTTTTCAAGGTAGGAT
1 TGCATTCCATTTGTAAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAAC
1009 TGCATTCCATTT
1 TGCATTCCATTT
1021 ATGAGTTC
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 102 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (50 bp):
TGCATTCCATTTGTAAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAAC
Done.