Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003056.1 Hibiscus syriacus cultivar Beakdansim tig00006372_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: 58407
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2033 original size:13 final size:13
Alignment explanation
Indices: 2015--2042 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2005 TTCAAAGGTT
2015 TCAAAGAAGCAAG
1 TCAAAGAAGCAAG
2028 TCAAAGAAGCAAG
1 TCAAAGAAGCAAG
2041 TC
1 TC
2043 CTAGAGTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.18, G:0.21, T:0.11
Consensus pattern (13 bp):
TCAAAGAAGCAAG
Found at i:9839 original size:20 final size:20
Alignment explanation
Indices: 9802--9840 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9792 ATTCCACCAC
*
9802 ATGCAACTATACGCTCCTAA
1 ATGCAACTATACGATCCTAA
* *
9822 ATGCATCTATATGATCCTA
1 ATGCAACTATACGATCCTA
9841 TATGAGCTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (20 bp):
ATGCAACTATACGATCCTAA
Found at i:16810 original size:40 final size:40
Alignment explanation
Indices: 16750--16859 Score: 184
Period size: 40 Copynumber: 2.8 Consensus size: 40
16740 ACTGTAGTGC
16750 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
* *
16790 TACACATAAGGTTGTTCCCACCATATACAACGAAGTGTAT
1 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
* *
16830 TACACATAAGGTCGTGCCCACCATGTACAC
1 TACACATAAGGTTGTGCCCACCATATACAC
16860 TTAGTGTCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
Found at i:19043 original size:11 final size:11
Alignment explanation
Indices: 19024--19057 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
19014 ATTTATATAA
*
19024 ATTATTATTTT
1 ATTAATATTTT
19035 ATTAATATTTTT
1 ATTAATA-TTTT
19047 ATTAATATTTT
1 ATTAATATTTT
19058 TGCACTCCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTAATATTTT
Found at i:19046 original size:12 final size:12
Alignment explanation
Indices: 19031--19058 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19021 TAAATTATTA
19031 TTTTATTAATAT
1 TTTTATTAATAT
19043 TTTTATTAATAT
1 TTTTATTAATAT
19055 TTTT
1 TTTT
19059 GCACTCCACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTATTAATAT
Found at i:22037 original size:15 final size:15
Alignment explanation
Indices: 22017--22056 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
22007 GGGGGTGCAT
22017 TTGCAAAATCAATAA
1 TTGCAAAATCAATAA
22032 TTGCAAAATCAATAA
1 TTGCAAAATCAATAA
22047 TTGCAAAATC
1 TTGCAAAATC
22057 TGATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (15 bp):
TTGCAAAATCAATAA
Found at i:30055 original size:7 final size:6
Alignment explanation
Indices: 30028--30052 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30018 TAATTTTAAA
30028 TAATTT TAATTT TAATTT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT T
30053 TAAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TAATTT
Found at i:35886 original size:8 final size:8
Alignment explanation
Indices: 35873--35911 Score: 71
Period size: 8 Copynumber: 5.0 Consensus size: 8
35863 TTGCGTGAGG
35873 AGAGGAGA
1 AGAGGAGA
35881 AGAGGAGA
1 AGAGGAGA
35889 AGAGGAGA
1 AGAGGAGA
35897 AGAGGAG-
1 AGAGGAGA
35904 AGAGGAGA
1 AGAGGAGA
35912 GGATACAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 7 0.23
8 23 0.77
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (8 bp):
AGAGGAGA
Found at i:46075 original size:35 final size:33
Alignment explanation
Indices: 46000--46076 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 33
45990 GTCTAAACCC
*
46000 TAAATTAAATTATTTAGAATTTGGGGTTTAAAA
1 TAAATTGAATTATTTAGAATTTGGGGTTTAAAA
* *
46033 TATAATTGAATTATTTTAGATTTTGGGGTTTAGAA
1 TA-AATTGAATTA-TTTAGAATTTGGGGTTTAAAA
46068 TGAAATTGA
1 T-AAATTGA
46077 GGATTGTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 2 0.05
34 9 0.24
35 26 0.68
36 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (33 bp):
TAAATTGAATTATTTAGAATTTGGGGTTTAAAA
Found at i:51447 original size:3 final size:3
Alignment explanation
Indices: 51433--51476 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
51423 CTCGCTGTCA
* * * *
51433 TCG TCA TCG TCG TCG TCA TCG TCA TTG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
51477 CTGAGCATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.07, C:0.32, G:0.25, T:0.36
Consensus pattern (3 bp):
TCG
Found at i:51452 original size:18 final size:18
Alignment explanation
Indices: 51429--51473 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
51419 ACTCCTCGCT
51429 GTCATCGTCATCGTCGTC
1 GTCATCGTCATCGTCGTC
*
51447 GTCATCGTCATTGTCGTC
1 GTCATCGTCATCGTCGTC
*
51465 GTCGTCGTC
1 GTCATCGTC
51474 GTCCTGAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.09, C:0.31, G:0.24, T:0.36
Consensus pattern (18 bp):
GTCATCGTCATCGTCGTC
Found at i:51842 original size:18 final size:18
Alignment explanation
Indices: 51819--51855 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
51809 AAAGGCGATG
*
51819 GCGGCATCATATATGGTT
1 GCGGCATCATAAATGGTT
51837 GCGGCATCATAAATGGTT
1 GCGGCATCATAAATGGTT
51855 G
1 G
51856 TGGTGGCTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (18 bp):
GCGGCATCATAAATGGTT
Found at i:53551 original size:17 final size:18
Alignment explanation
Indices: 53531--53571 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
53521 GAATTATATT
53531 AGTAAAAT-ATTAAATAA
1 AGTAAAATAATTAAATAA
53548 AGTAAAATAATTAAATAA
1 AGTAAAATAATTAAATAA
*
53566 ATTAAA
1 AGTAAA
53572 TACATAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATAATTAAATAA
Found at i:53648 original size:10 final size:10
Alignment explanation
Indices: 53617--53651 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
53607 CAAAGATATT
53617 ATTTGAGAGA
1 ATTTGAGAGA
* *
53627 AATTAAGAGA
1 ATTTGAGAGA
53637 ATTTGAGAGA
1 ATTTGAGAGA
53647 ATTTG
1 ATTTG
53652 GTGTGATGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (10 bp):
ATTTGAGAGA
Found at i:54916 original size:29 final size:29
Alignment explanation
Indices: 54874--54973 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
54864 TCCTAAAATC
54874 ATTCAAAAGTTTGGGGATAAAATTGGAAT
1 ATTCAAAAGTTTGGGGATAAAATTGGAAT
* * *
54903 ATTCAAAAGTTTGGCGGTTAATA-TAGAAT
1 ATTCAAAAGTTTGG-GGATAAAATTGGAAT
* * *
54932 GAGTGTCATAA-TTTAGGGACAAAATTGGAAT
1 -A-T-TCAAAAGTTTGGGGATAAAATTGGAAT
54963 ATTC-AAAGTTT
1 ATTCAAAAGTTT
54974 AAAGGCCAGT
Statistics
Matches: 55, Mismatches: 10, Indels: 13
0.71 0.13 0.17
Matches are distributed among these distances:
27 2 0.04
28 5 0.09
29 20 0.36
30 13 0.24
31 10 0.18
32 5 0.09
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (29 bp):
ATTCAAAAGTTTGGGGATAAAATTGGAAT
Found at i:56979 original size:2 final size:2
Alignment explanation
Indices: 56974--57022 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
56964 ATATAAGACC
56974 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
57016 AG AG AG A
1 AG AG AG A
57023 TGTATGTGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.