Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017095.1 Corchorus olitorius cultivar O-4 contig17128, 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: 14871
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:2133 original size:339 final size:333
Alignment explanation
Indices: 1511--2185 Score: 1099
Period size: 339 Copynumber: 2.0 Consensus size: 333
1501 GAGTCAGTCT
*
1511 AAACATGTTTGTGGGTATCGTCCTAGTTAAGTAAACCCTCAGGAGACTATAACTCCTCCAGTGTA
1 AAACATGTTTGTGGGTATCGTCCTAGTTAAGTAAACCCTCAGGAGACTATAACACCTCCA-TGTA
*
1576 GACATACATTGGTTTAAAGGCTTGCGTCACGTGCTAAGTGCCGCCGTACACCTACGAAAGTGGAA
65 GACATACATTGGTTTAAAGGCTTGCGTCACGTGCTAAGTGACGCCGTACACCTACGAAAGTGGAA
* *
1641 TCTTTATTTGCATTAGTTTTTGTTTTTGTTTTCTTAGTTTTTCTGTACTAGTTTGCTAGGGACTA
130 TCTTAATTTGCATTAGTCTTTGTTTTTGTTTTCTTAGTTTTTCTGTACTAGTTTGCTAGGGACTA
*
1706 GCAAAGATTTAGTGTGGGGAAAATTATGATCGAGCTAAAAAAGACCCTATTTTTATGATCATTTT
195 GCAAAGATTTAGTGTGGGGAAAATTATGATCGACCTAAAAAAGACCCTATTTTTATGATCATTTT
*
1771 CCTATGCTTTTTACTATTTTTATGTGGAATTTAACCCTATTTTATAAGTATTTGTGTTTTTAGGT
260 CCTATGCTTTTTACTATTTTTATGTGGAATTTAACCCTATTTTATAAGTATTTGTGTTTATAGGT
1836 CTTGAAGAC
325 CTTGAAGAC
* *
1845 AAACATGTTTGTGGGTATCGTCCTAGTTAAGTAAACCCTCATGTGAC-ATAACACCTCC-TG-AG
1 AAACATGTTTGTGGGTATCGTCCTAGTTAAGTAAACCCTCAGGAGACTATAACACCTCCATGTAG
* *
1907 CACCTCTATCAGTCTCAGGTTTAAATGGCTTGCGTCACGTGCTAAGTGACGCCGTACACCTATGA
66 -A-C-ATA-CA-T-T--GGTTTAAA-GGCTTGCGTCACGTGCTAAGTGACGCCGTACACCTACGA
1972 AAGTGGAATCTTAATTTGCATTAGTCTTTGTTTTTG-TTTCTTAAGTTTTTCTGTACTAGTTTGC
122 AAGTGGAATCTTAATTTGCATTAGTCTTTGTTTTTGTTTTCTT-AGTTTTTCTGTACTAGTTTGC
*
2036 TAGGGACTAGCAAAGATTTAGTGTGGGGGAAATTATGATCGACCTAAAAAAGACCCTATTTTTAT
186 TAGGGACTAGCAAAGATTTAGTGTGGGGAAAATTATGATCGACCTAAAAAAGACCCTATTTTTAT
*
2101 GATCATTTTCCTATGCTTTTTTACTA-TTTTATGTGGAATTTAACCCTATTTTGTAAGTATTTGT
251 GATCATTTTCCTATGC-TTTTTACTATTTTTATGTGGAATTTAACCCTATTTTATAAGTATTTGT
2165 GTTTATAGGTCTTGAAGAC
315 GTTTATAGGTCTTGAAGAC
2184 AA
1 AA
2186 GAAAAGTGGA
Statistics
Matches: 318, Mismatches: 12, Indels: 17
0.92 0.03 0.05
Matches are distributed among these distances:
330 2 0.01
331 3 0.01
332 1 0.00
333 12 0.04
334 47 0.15
335 1 0.00
336 1 0.00
338 14 0.04
339 228 0.72
340 9 0.03
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (333 bp):
AAACATGTTTGTGGGTATCGTCCTAGTTAAGTAAACCCTCAGGAGACTATAACACCTCCATGTAG
ACATACATTGGTTTAAAGGCTTGCGTCACGTGCTAAGTGACGCCGTACACCTACGAAAGTGGAAT
CTTAATTTGCATTAGTCTTTGTTTTTGTTTTCTTAGTTTTTCTGTACTAGTTTGCTAGGGACTAG
CAAAGATTTAGTGTGGGGAAAATTATGATCGACCTAAAAAAGACCCTATTTTTATGATCATTTTC
CTATGCTTTTTACTATTTTTATGTGGAATTTAACCCTATTTTATAAGTATTTGTGTTTATAGGTC
TTGAAGAC
Found at i:4140 original size:25 final size:24
Alignment explanation
Indices: 4085--4167 Score: 94
Period size: 25 Copynumber: 3.2 Consensus size: 24
4075 TATTTTTTTA
*
4085 TTTGCGTTTTTGAAAAAAAAATTTGTGT
1 TTTGTGTTTTTGAAAAAAAAA---GT-T
4113 TTTGTGTTTTTGAAAAAAAAGAGTT
1 TTTGTGTTTTTGAAAAAAAA-AGTT
*
4138 TTTGTGTTTTCTAAAAAAAAAAGTT
1 TTTGTGTTTT-TGAAAAAAAAAGTT
4163 TTTGT
1 TTTGT
4168 TTCTGCGTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
25 20 0.39
26 11 0.22
28 19 0.37
29 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (24 bp):
TTTGTGTTTTTGAAAAAAAAAGTT
Found at i:6459 original size:21 final size:21
Alignment explanation
Indices: 6435--6476 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
6425 GATGACTTAT
6435 ATGCGAT-AATTGCTATGATTG
1 ATGCGATGAATTGCT-TGATTG
**
6456 ATGCTTTGAATTGCTTGATTG
1 ATGCGATGAATTGCTTGATTG
6477 GGTCGACACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.43
Consensus pattern (21 bp):
ATGCGATGAATTGCTTGATTG
Done.