Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014834.1 Corchorus olitorius cultivar O-4 contig14867, 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: 28686
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2157 original size:19 final size:19
Alignment explanation
Indices: 2133--2179 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
2123 AGAATATTTT
2133 GTTTTAACGAACAACAACG
1 GTTTTAACGAACAACAACG
2152 GTTTTAACGAACAACAACG
1 GTTTTAACGAACAACAACG
2171 GTTTTAACG
1 GTTTTAACG
2180 TTTTAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (19 bp):
GTTTTAACGAACAACAACG
Found at i:2394 original size:195 final size:190
Alignment explanation
Indices: 2040--2413 Score: 515
Period size: 195 Copynumber: 1.9 Consensus size: 190
2030 TATTTATTTA
*
2040 TTTTTTTTTTATGAAACTTTTGTGAAATAATGCTTTTGTGGTTATAGGTATGATAAACCGTTATG
1 TTTTTTTTTTATGAAACTTTTGTGAAATAATGCTTTTGTGGTTATAGGCATGATAAACCGTTAT-
2105 AAATTATTTTATGAAACAAGAATATTTTGTTTTAACGAACAACAACGGTTTTAACGAACAACAAC
65 -AATTATTTTATGAAACAAGAATATTTTGTTTTAACGAACAACAACGGTTTTAACGAACAACAAC
*
2170 GGTTTTAACGTTTTAAACAATAAACTACTTTTAATTTTTTCCAAATTAAGTTACCAAATAAAGTT
129 GGTTTTAACGTTTTAAACAATAAACTAC-TTT--TTTTTTCCAAATAAAGTTACCAAATAAAGTT
* *
2235 TTTTTTTTTTAAATGAAACTTTTGTGAAATAATGTTTTTGTGGTTGTAGGCATG-TAAACCG-T-
1 TTTTTTTTTT--ATGAAACTTTTGTGAAATAATGCTTTTGTGGTTATAGGCATGATAAACCGTTA
* *
2297 T-ATTATTTTATGAAACAAGAATATTTTGTTTTAACGAACACCAACAGTTTGTTTTAAACG-ATA
64 TAATTATTTTATGAAACAAGAATATTTTGTTTTAACGAACAACAAC-G---GTTTT-AACGAACA
* * **
2360 ATATCGGTTTTAACGTTTTAAACGGTAAACTACTTTTTTTTTCCAAATAAAGTT
124 ACAACGGTTTTAACGTTTTAAACAATAAACTACTTTTTTTTTCCAAATAAAGTT
2414 TAAATTGCAT
Statistics
Matches: 162, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
191 43 0.27
192 18 0.11
194 4 0.02
195 47 0.29
196 11 0.07
197 39 0.24
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (190 bp):
TTTTTTTTTTATGAAACTTTTGTGAAATAATGCTTTTGTGGTTATAGGCATGATAAACCGTTATA
ATTATTTTATGAAACAAGAATATTTTGTTTTAACGAACAACAACGGTTTTAACGAACAACAACGG
TTTTAACGTTTTAAACAATAAACTACTTTTTTTTTCCAAATAAAGTTACCAAATAAAGTT
Found at i:16024 original size:3 final size:3
Alignment explanation
Indices: 16016--16042 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
16006 GTTGCCTACT
16016 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
16043 CCCTTTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:25754 original size:27 final size:27
Alignment explanation
Indices: 25723--25779 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
25713 GATCTCTCCA
25723 TTAGTGGAAAGGATCCTCACCCATGTT
1 TTAGTGGAAAGGATCCTCACCCATGTT
* * *
25750 TTAGTGTAAAGGATCCTTACCTATGTT
1 TTAGTGGAAAGGATCCTCACCCATGTT
25777 TTA
1 TTA
25780 ATTATAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (27 bp):
TTAGTGGAAAGGATCCTCACCCATGTT
Done.