Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009770.1 Corchorus olitorius cultivar O-4 contig09802, 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: 2860
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:1223 original size:33 final size:33
Alignment explanation
Indices: 1179--1309 Score: 167
Period size: 33 Copynumber: 4.0 Consensus size: 33
1169 ATAAAACTGG
*
1179 GAGGCGCGCCCAGAGGGCGCCA-CTGCCATGGCG
1 GAGGCGCGCCCAGAGGGCGCCACCT-CCATGGCA
* *
1212 GAGGCGTGCCCAGAGGGTGCCACCTCCATGGCA
1 GAGGCGCGCCCAGAGGGCGCCACCTCCATGGCA
* * **
1245 GAGGCACACCCAGAGGATGCCACCTCCATGGCA
1 GAGGCGCGCCCAGAGGGCGCCACCTCCATGGCA
1278 GAGGCGCGCCCAGAGGGCGCCA-CTACCATGGC
1 GAGGCGCGCCCAGAGGGCGCCACCT-CCATGGC
1310 TATGGCGTGA
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
32 2 0.02
33 81 0.95
34 2 0.02
ACGTcount: A:0.20, C:0.36, G:0.36, T:0.08
Consensus pattern (33 bp):
GAGGCGCGCCCAGAGGGCGCCACCTCCATGGCA
Found at i:2009 original size:29 final size:30
Alignment explanation
Indices: 1953--2021 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
1943 ACTAAATACC
* *
1953 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTCATGTTTT-CTTTTGGGA
1984 CAAAATAATCCCTCATGTTTT-TTTTGGGA
1 CAAAATAATCCCTCATGTTTTCTTTTGGGA
*
2013 CAAATTAAT
1 CAAAATAAT
2022 TTCTTACATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 16 0.46
31 19 0.54
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (30 bp):
CAAAATAATCCCTCATGTTTTCTTTTGGGA
Found at i:2225 original size:31 final size:30
Alignment explanation
Indices: 2176--2260 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 30
2166 AAGGGTCTAA
2176 TTTGT-CCAAAA-AAAAACATAAGGATTTTT
1 TTTGTCCCAAAAGAAAAACATAAGGA-TTTT
2205 TTTGTCCCAAAAGAAAAACATAAAGGATTTT
1 TTTGTCCCAAAAGAAAAACAT-AAGGATTTT
*
2236 TTTGTCCCAAAAGAAAAATATAAGG
1 TTTGTCCCAAAAGAAAAACATAAGG
2261 GAAATTTTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
29 5 0.10
30 10 0.19
31 32 0.62
32 5 0.10
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (30 bp):
TTTGTCCCAAAAGAAAAACATAAGGATTTT
Found at i:2269 original size:32 final size:31
Alignment explanation
Indices: 2176--2270 Score: 124
Period size: 31 Copynumber: 3.1 Consensus size: 31
2166 AAGGGTCTAA
*
2176 TTTGT-CCAAAA-AAAAACATAAGGATTTTT
1 TTTGTCCCAAAAGAAAAACATAAGGAATTTT
2205 TTTGTCCCAAAAGAAAAACATAAAGG-ATTTT
1 TTTGTCCCAAAAGAAAAACAT-AAGGAATTTT
* *
2236 TTTGTCCCAAAAGAAAAATATAAGGGAAATTT
1 TTTGTCCCAAAAGAAAAACATAA-GGAATTTT
2268 TTT
1 TTT
2271 AGTCTATAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
29 5 0.09
30 8 0.14
31 34 0.59
32 11 0.19
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGAATTTT
Found at i:2786 original size:172 final size:172
Alignment explanation
Indices: 2414--2841 Score: 547
Period size: 172 Copynumber: 2.4 Consensus size: 172
2404 AATTCCCTAA
* * *
2414 AAAATGGTAAAGATAAAATAGTTATAAAAATATTAAATTTAATTAAATAAAAATAGAATTTTTGA
1 AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTAATTAAATAAAAATAGAA-TTTT--
** * * * ***
2479 TAAAATAAAATTGTAAAAGTTTAAATAATGTCATTTAAGAAATATATTTAGAATCTCGTCAAAAA
63 T--AAT-TGA--GTAAAAGTTTAAACAAAGGCATTTAAGAAATATATTTAGAA-CAAATCAAAAA
*
2544 AGAAATATATTTAGAAAATTCTAATATATCTAATTTTTTAATTAAAATAGT
122 AGAAATATATTTAAAAAATTCTAATATATCTAATTTTTTAATTAAAATAGT
*
2595 AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTTATTAAATAAAAATAGAATTTTTAA
1 AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTAATTAAATAAAAATAGAATTTTTAA
**
2660 TTGAGTAAAAGTTTAAACAAAGGCATTTAAGAAATATATTT-GAA-AAAT-AAGGGTAAGAAATA
66 TTGAGTAAAAGTTTAAACAAAGGCATTTAAGAAATATATTTAGAACAAATCAA--AAAAGAAATA
2722 TATTTAAAAAATTCTAATATATCTAAGTTTTTTAATTAAAATAGT
129 TATTTAAAAAATTCTAATATATCTAA-TTTTTTAATTAAAATAGT
* * * * *
2767 AAAATGGTAAAAATAAAATATTTATAAATATATTAGATTAAATTAAATAAAAGTAGAGTTTTTAG
1 AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTAATTAAATAAAAATAGAATTTTTAA
2832 TTGAGTAAAA
66 TTGAGTAAAA
2842 CTATAAAAAT
Statistics
Matches: 223, Mismatches: 21, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
169 2 0.01
170 1 0.00
171 33 0.15
172 90 0.40
173 34 0.15
175 1 0.00
176 3 0.01
178 1 0.00
180 4 0.02
181 54 0.24
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (172 bp):
AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTAATTAAATAAAAATAGAATTTTTAA
TTGAGTAAAAGTTTAAACAAAGGCATTTAAGAAATATATTTAGAACAAATCAAAAAAGAAATATA
TTTAAAAAATTCTAATATATCTAATTTTTTAATTAAAATAGT
Done.