Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007750.1 Hibiscus syriacus cultivar Beakdansim tig00110016_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: 41526
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2389 original size:32 final size:32
Alignment explanation
Indices: 2285--2390 Score: 160
Period size: 32 Copynumber: 3.3 Consensus size: 32
2275 TCGTAAACTT
2285 TTTCAATTATCGAACTT-GAAGTTTTTAAGTA
1 TTTCAATTATCGAACTTGGAAGTTTTTAAGTA
*
2316 TTTGAATTTATCGAACTTGGAAGTTTTTAAGTA
1 TTTCAA-TTATCGAACTTGGAAGTTTTTAAGTA
* * *
2349 TTTGAATTATCAAACTTGGAAGTATTTAAGTA
1 TTTCAATTATCGAACTTGGAAGTTTTTAAGTA
2381 TTTCAATTAT
1 TTTCAATTAT
2391 GTTGAGTTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 5 0.07
32 44 0.64
33 20 0.29
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (32 bp):
TTTCAATTATCGAACTTGGAAGTTTTTAAGTA
Found at i:2644 original size:21 final size:21
Alignment explanation
Indices: 2618--2674 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2608 TAGAGCATGG
*
2618 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
2639 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
2660 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
2675 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:16293 original size:10 final size:10
Alignment explanation
Indices: 16264--16295 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
16254 ATAGACATAA
*
16264 ATTTTATATA
1 ATTTTATATT
16274 ATTTTATATT
1 ATTTTATATT
16284 ATTTTATATT
1 ATTTTATATT
16294 AT
1 AT
16296 GTGTACACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTTTATATT
Found at i:17439 original size:15 final size:15
Alignment explanation
Indices: 17419--17447 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17409 TTCGGTTGTA
17419 AGAAGAAAGAAAGGG
1 AGAAGAAAGAAAGGG
17434 AGAAGAAAGAAAGG
1 AGAAGAAAGAAAGG
17448 ATCATAAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (15 bp):
AGAAGAAAGAAAGGG
Found at i:19144 original size:14 final size:13
Alignment explanation
Indices: 19125--19154 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
19115 TAATCAAAAA
19125 TAATAATTTATAAT
1 TAATAATTTAT-AT
19139 TAATAATTTATAT
1 TAATAATTTATAT
19152 TAA
1 TAA
19155 AATAGAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATAATTTATAT
Found at i:21497 original size:26 final size:25
Alignment explanation
Indices: 21441--21497 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
21431 ACTAAGTAGA
* * * *
21441 TTTTTAATTTTTATTATTTTATTTT
1 TTTTTAAATTTAATTATTTGATTAT
21466 TATTTTAAATTTAATTATTTGATTAAT
1 T-TTTTAAATTTAATTATTTGATT-AT
21493 TTTTT
1 TTTTT
21498 GTACTAATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 1 0.04
26 23 0.88
27 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (25 bp):
TTTTTAAATTTAATTATTTGATTAT
Found at i:29997 original size:15 final size:15
Alignment explanation
Indices: 29979--30044 Score: 71
Period size: 15 Copynumber: 4.4 Consensus size: 15
29969 ATGATTTATA
*
29979 TGAATATGTTCTACG
1 TGAAAATGTTCTACG
* **
29994 TG-AAATCATTCTATA
1 TGAAAAT-GTTCTACG
30009 TGAAAATGTTCTACG
1 TGAAAATGTTCTACG
*
30024 TGAAAATGTTCTATG
1 TGAAAATGTTCTACG
30039 TGAAAA
1 TGAAAA
30045 AAGATACTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 3 0.07
15 34 0.83
16 4 0.10
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (15 bp):
TGAAAATGTTCTACG
Found at i:30229 original size:23 final size:24
Alignment explanation
Indices: 30143--30239 Score: 126
Period size: 24 Copynumber: 4.1 Consensus size: 24
30133 TAGTCGAGGG
* * *
30143 TTCTACGTGGTCCTTCGGGATAAA
1 TTCTACGCGGTCCTTTGGGACAAA
30167 TTCTACGCGGTCCTTTGGGACAAA
1 TTCTACGCGGTCCTTTGGGACAAA
30191 TTCTACGCGGTCCTTTGGGACAAA
1 TTCTACGCGGTCCTTTGGGACAAA
* *
30215 -TCTACGTGG-CACTTTGGTACAAA
1 TTCTACGCGGTC-CTTTGGGACAAA
30238 TT
1 TT
30240 ATATGAGCAG
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
22 1 0.02
23 19 0.29
24 46 0.70
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.32
Consensus pattern (24 bp):
TTCTACGCGGTCCTTTGGGACAAA
Found at i:34301 original size:26 final size:26
Alignment explanation
Indices: 34265--34317 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
34255 AAATTTCAAG
*
34265 GAATGGAAAAGGCACTTACTTATAGT
1 GAATGGAAAAGACACTTACTTATAGT
34291 GAATGGAAAAGACACTTACTTATAGT
1 GAATGGAAAAGACACTTACTTATAGT
34317 G
1 G
34318 CTTGGCTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (26 bp):
GAATGGAAAAGACACTTACTTATAGT
Done.