Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001841.1 Hibiscus syriacus cultivar Beakdansim tig00003726_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: 75031
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:16478 original size:17 final size:18
Alignment explanation
Indices: 16445--16478 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16435 CCGCTACTAG
16445 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
16463 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
16479 GACTGGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:23335 original size:22 final size:23
Alignment explanation
Indices: 23294--23336 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
23284 ACGATAAATT
*
23294 TATAAAATTTTAAGACAGATATC
1 TATAAAATTTAAAGACAGATATC
23317 TATAAAATTTAAAGA-AGATA
1 TATAAAATTTAAAGACAGATA
23337 AAAATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (23 bp):
TATAAAATTTAAAGACAGATATC
Found at i:23343 original size:22 final size:23
Alignment explanation
Indices: 23295--23343 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
23285 CGATAAATTT
* ***
23295 ATAAAATTTTAAGACAGATATCT
1 ATAAAATTTAAAGACAGATAAAA
23318 ATAAAATTTAAAGA-AGATAAAA
1 ATAAAATTTAAAGACAGATAAAA
23340 ATAA
1 ATAA
23344 TTTTTTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (23 bp):
ATAAAATTTAAAGACAGATAAAA
Found at i:23380 original size:9 final size:9
Alignment explanation
Indices: 23348--23397 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
23338 AAATAATTTT
*
23348 TTTAAAAAA
1 TTTAAAATA
* *
23357 ATTAAAAAA
1 TTTAAAATA
*
23366 TCTAAAATA
1 TTTAAAATA
23375 TTTAAAAT-
1 TTTAAAATA
23383 TTTAAAAT-
1 TTTAAAATA
23391 TTTAAAA
1 TTTAAAA
23398 GAGACGACCG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
8 15 0.42
9 21 0.58
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (9 bp):
TTTAAAATA
Found at i:23386 original size:8 final size:8
Alignment explanation
Indices: 23368--23397 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
23358 TTAAAAAATC
23368 TAAAATATT
1 TAAAAT-TT
23377 TAAAATTT
1 TAAAATTT
23385 TAAAATTT
1 TAAAATTT
23393 TAAAA
1 TAAAA
23398 GAGACGACCG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TAAAATTT
Found at i:24075 original size:2 final size:2
Alignment explanation
Indices: 24068--24093 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24058 TCTAACAATA
24068 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
24094 TCTTTTCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24277 original size:21 final size:21
Alignment explanation
Indices: 24253--24294 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
24243 TCGTAAACAA
*
24253 TTGTAGTTAAAAGACTAAATT
1 TTGTAGTCAAAAGACTAAATT
24274 TTGTAGTCAAAAGACTAAATT
1 TTGTAGTCAAAAGACTAAATT
24295 GAGTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (21 bp):
TTGTAGTCAAAAGACTAAATT
Found at i:33665 original size:2 final size:2
Alignment explanation
Indices: 33658--33730 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
33648 AGTCTTAGTC
33658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33700 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33731 ATCAAAGGTC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33792 original size:6 final size:6
Alignment explanation
Indices: 33781--33818 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
33771 AAGTGTGTAC
33781 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GA
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GA
33819 GCCATTGTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:36537 original size:2 final size:2
Alignment explanation
Indices: 36530--36557 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36520 AAAGATCTTA
36530 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36558 TGTTATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48188 original size:2 final size:2
Alignment explanation
Indices: 48181--48240 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
48171 AAATAAAGTC
*
48181 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48223 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
48241 TATTTGTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58380 original size:2 final size:2
Alignment explanation
Indices: 58373--58412 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
58363 AGTCTTAGTC
58373 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58413 CAAAGGTCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58472 original size:6 final size:6
Alignment explanation
Indices: 58461--58486 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
58451 AAGTGTGTAC
58461 GAAGGA GAAGGA GAAGGA GAAGGA GA
1 GAAGGA GAAGGA GAAGGA GAAGGA GA
58487 GCCATTGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:61196 original size:2 final size:2
Alignment explanation
Indices: 61189--61216 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
61179 AAAGATCTTA
61189 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61217 TGTACGAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67173 original size:4 final size:4
Alignment explanation
Indices: 67164--67223 Score: 70
Period size: 4 Copynumber: 15.0 Consensus size: 4
67154 CATAACGCAG
*
67164 GTAT GTAT GTAT GTAT GTAT -TCAT GTAT TTAT -TGAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GT-AT GTAT GTAT GT-AT GTAT GTAT GTAT
*
67212 GCAT GTAT GTAT
1 GTAT GTAT GTAT
67224 CATGACATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
3 2 0.04
4 45 0.92
5 2 0.04
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.50
Consensus pattern (4 bp):
GTAT
Done.