Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006749.1 Hibiscus syriacus cultivar Beakdansim tig00016976_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: 57833
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:8507 original size:21 final size:20
Alignment explanation
Indices: 8469--8507 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
8459 TAATAAAAAG
* *
8469 AAAATAAAAAAGAGAAGTGC
1 AAAAAAAAAAACAGAAGTGC
8489 AAAAAAAAAAACAGCAAGT
1 AAAAAAAAAAACAG-AAGT
8508 TAATCCCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAAAAAAAAACAGAAGTGC
Found at i:12386 original size:27 final size:23
Alignment explanation
Indices: 12334--12381 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
12324 ATCAGAAAAT
12334 AAGCACTCAAAAAGAAGAAATGA
1 AAGCACTCAAAAAGAAGAAATGA
12357 AAGCACTCAAAGAAGAA-AAA-GA
1 AAGCACTCAAA-AAGAAGAAATGA
12379 AAG
1 AAG
12382 AAAAGTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 5 0.21
23 14 0.58
24 5 0.21
ACGTcount: A:0.62, C:0.12, G:0.19, T:0.06
Consensus pattern (23 bp):
AAGCACTCAAAAAGAAGAAATGA
Found at i:13560 original size:35 final size:37
Alignment explanation
Indices: 13509--13588 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
13499 TTTGAGAATT
* *
13509 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATACAGGCGTGATAATGGAAGATGGACTA
*
13544 TGGTGATGATACAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATACAGGCGTGATAATGGAAGATGGACTA
*
13581 TGGGGATG
1 TGGTGATG
13589 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.05, G:0.39, T:0.29
Consensus pattern (37 bp):
TGGTGATGATACAGGCGTGATAATGGAAGATGGACTA
Found at i:13972 original size:19 final size:20
Alignment explanation
Indices: 13926--13975 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
13916 AAATCCCTTA
**
13926 GAAAATACATGATTTTTGAT
1 GAAAATACATGATTTTAAAT
13946 GAAAATACATGA-TTTAAAT
1 GAAAATACATGATTTTAAAT
*
13965 GAAGATACATG
1 GAAAATACATG
13976 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (20 bp):
GAAAATACATGATTTTAAAT
Found at i:24077 original size:10 final size:10
Alignment explanation
Indices: 24064--24120 Score: 62
Period size: 10 Copynumber: 5.5 Consensus size: 10
24054 TTTTTGGCTC
24064 TTTTTTTGTT
1 TTTTTTTGTT
24074 TTTTTTTGCCTT
1 TTTTTTTG--TT
*
24086 TTTTTTT-TGC
1 TTTTTTTGT-T
*
24096 CTTTTTTGTT
1 TTTTTTTGTT
24106 TTTTTTTGTT
1 TTTTTTTGTT
24116 TTTTT
1 TTTTT
24121 GAAAAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 1 0.03
10 28 0.72
11 1 0.03
12 9 0.23
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:24089 original size:14 final size:13
Alignment explanation
Indices: 24072--24107 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
24062 TCTTTTTTTG
24072 TTTTTTTTTGCCT
1 TTTTTTTTTGCCT
24085 TTTTTTTTTGCCT
1 TTTTTTTTTGCCT
24098 TTTTTGTTTT
1 TTTTT-TTTT
24108 TTTTTGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTGCCT
Found at i:37134 original size:24 final size:24
Alignment explanation
Indices: 37107--37158 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
37097 GACATGTCCT
* * *
37107 TTGACGTTCCAACAGTTATGCCAC
1 TTGACGTTCAAAAAGCTATGCCAC
* *
37131 TTGATGTTCAAAAAGCTGTGCCAC
1 TTGACGTTCAAAAAGCTATGCCAC
37155 TTGA
1 TTGA
37159 AGTGCCAAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (24 bp):
TTGACGTTCAAAAAGCTATGCCAC
Found at i:41526 original size:12 final size:11
Alignment explanation
Indices: 41497--41523 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41487 ATTGGAGTGC
41497 AAAAAGAAAAT
1 AAAAAGAAAAT
41508 AAAAAGAAAAT
1 AAAAAGAAAAT
41519 AAAAA
1 AAAAA
41524 AGAGAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAAGAAAAT
Found at i:46268 original size:22 final size:24
Alignment explanation
Indices: 46219--46269 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
46209 TCTTTCTTTT
**
46219 TTTTTGAGTGCTTTCAATTTCTTC
1 TTTTTGAGTGCTTTCAATTTCTGA
*
46243 TTTTTGAGTGC-TTC-TTTTCTGA
1 TTTTTGAGTGCTTTCAATTTCTGA
46265 TTTTT
1 TTTTT
46270 TTCTTGCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 10 0.42
23 3 0.12
24 11 0.46
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.63
Consensus pattern (24 bp):
TTTTTGAGTGCTTTCAATTTCTGA
Done.