Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004783.1 Hibiscus syriacus cultivar Beakdansim tig00010786_pilon, 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: 15208
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:9195 original size:2 final size:2
Alignment explanation
Indices: 9188--9216 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9178 AATAATTTAT
9188 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9217 TTATTTAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10794 original size:18 final size:18
Alignment explanation
Indices: 10771--10811 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
10761 AATTATGAAT
*
10771 AAATATTAATTTTTTTAA-
1 AAATATT-ATTATTTTAAC
10789 AAATA-TATTATTTTAAC
1 AAATATTATTATTTTAAC
10806 AAATAT
1 AAATAT
10812 AATAACTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 9 0.45
17 6 0.30
18 5 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATATTATTATTTTAAC
Found at i:11359 original size:8 final size:7
Alignment explanation
Indices: 11329--11358 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
11319 AATTTAAAAA
11329 TAAAGTTT
1 TAAA-TTT
11337 TAAATTT
1 TAAATTT
11344 TAAATTT
1 TAAATTT
11351 TAAATTT
1 TAAATTT
11358 T
1 T
11359 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (7 bp):
TAAATTT
Found at i:14294 original size:40 final size:38
Alignment explanation
Indices: 14250--14465 Score: 121
Period size: 40 Copynumber: 5.4 Consensus size: 38
14240 GTTTCTGCAA
*
14250 TCGCAACGCGAATTTCTTTCTCGCAACGCGATTTTCAAAT
1 TCGCAACAC-AATTTCTTT-TCGCAACGCGATTTTCAAAT
* * ** *
14290 TCGCAACGCTATTTCCAAATTCGCAACATG-GAATTTCAAAT
1 TCGCAACACAATTT-C-TTTTCGCAAC--GCGATTTTCAAAT
* * * * ***
14331 TCGCAACTCAATTTCTGAATTCGCAAAGCGAATTTCTTTT
1 TCGCAACACAATTTCT--TTTCGCAACGCGATTTTCAAAT
**
14371 TCGCAACACAAGTTTCATTTTCGCAACAAGATTTTCTAAA-
1 TCGCAACACAA-TTTC-TTTTCGCAACGCGATTTTC-AAAT
* * * *
14411 TCGCAACATGAATTTTGTTTTCGCAACTCGATTTTCGAAT
1 TCGCAACA-CAA-TTTCTTTTCGCAACGCGATTTTCAAAT
14451 TCGCAACACGAATTT
1 TCGCAACAC-AATTT
14466 TAATTTCACA
Statistics
Matches: 136, Mismatches: 27, Indels: 27
0.72 0.14 0.14
Matches are distributed among these distances:
39 10 0.07
40 84 0.62
41 40 0.29
42 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (38 bp):
TCGCAACACAATTTCTTTTCGCAACGCGATTTTCAAAT
Found at i:14353 original size:20 final size:20
Alignment explanation
Indices: 14186--14367 Score: 97
Period size: 20 Copynumber: 9.0 Consensus size: 20
14176 AATGACCAAC
*
14186 AAATTCGCAACGCAAACTT-T
1 AAATTCGCAACGC-AATTTCT
* ** * *
14206 AATTTCGCAACATAGTTTCC
1 AAATTCGCAACGCAATTTCT
* *
14226 AAATTCGCAACTCAGTTTCT
1 AAATTCGCAACGCAATTTCT
*
14246 GCAA-TCGCAACGCGAATTTCT
1 -AAATTCGCAACGC-AATTTCT
* *
14267 --TTCTCGCAACGCGATTT-T
1 AAAT-TCGCAACGCAATTTCT
* *
14285 CAAATTCGCAACGCTATTTCC
1 -AAATTCGCAACGCAATTTCT
*
14306 AAATTCGCAACATGGAATTTC-
1 AAATTCGCAAC--GCAATTTCT
*
14327 AAATTCGCAACTCAATTTCT
1 AAATTCGCAACGCAATTTCT
* *
14347 GAATTCGCAAAGCGAATTTCT
1 AAATTCGCAACGC-AATTTCT
14368 TTTTCGCAAC
Statistics
Matches: 124, Mismatches: 25, Indels: 25
0.71 0.14 0.14
Matches are distributed among these distances:
18 1 0.01
19 13 0.10
20 77 0.62
21 27 0.22
22 6 0.05
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (20 bp):
AAATTCGCAACGCAATTTCT
Found at i:14466 original size:40 final size:40
Alignment explanation
Indices: 14370--14478 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 40
14360 GAATTTCTTT
* *
14370 TTCGCAACAC-AAGTTTCATTTTCGCAACAAGATTTTCTAA
1 TTCGCAACACGAA-TTTTATTTTCGCAACAAGATTTTCGAA
* * * **
14410 ATCGCAACATGAATTTTGTTTTCGCAACTCGATTTTCGAA
1 TTCGCAACACGAATTTTATTTTCGCAACAAGATTTTCGAA
* *
14450 TTCGCAACACGAATTTTAATTTCACAACA
1 TTCGCAACACGAATTTTATTTTCGCAACA
14479 GCTTTTATTT
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
40 53 0.96
41 2 0.04
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (40 bp):
TTCGCAACACGAATTTTATTTTCGCAACAAGATTTTCGAA
Done.