Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006798.1 Hibiscus syriacus cultivar Beakdansim tig00017247_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: 27971
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Found at i:2837 original size:4 final size:4
Alignment explanation
Indices: 2828--2860 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
2818 AAATGATGAC
2828 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
2861 ATGGTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:3068 original size:31 final size:30
Alignment explanation
Indices: 3030--3125 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
3020 GTCAAAGAAC
3030 TACCTATG-TCTTTCGAGACATATGGACAGT
1 TACCTATGTTCTTT-GAGACATATGGACAGT
** *
3060 ATACCTATGTTCTAAG-GAACATATGGATAGTT
1 -TACCTATGTTCTTTGAG-ACATATGGACAG-T
* * *
3092 TACCTAGGTTCTTTGGGACCTATGGACAGT
1 TACCTATGTTCTTTGAGACATATGGACAGT
3122 TACC
1 TACC
3126 GAGGATCTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
30 6 0.11
31 42 0.79
32 5 0.09
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (30 bp):
TACCTATGTTCTTTGAGACATATGGACAGT
Found at i:3135 original size:30 final size:30
Alignment explanation
Indices: 3081--3210 Score: 179
Period size: 30 Copynumber: 4.3 Consensus size: 30
3071 CTAAGGAACA
* * **
3081 TATGGATAGTTTACCTAGGTTCTTTGGGACC
1 TATGGATAG-TTACCGAGGATCTTTATGACC
*
3112 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
* *
3142 TCTGGATAGTTACTGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
*
3172 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
3202 TATGGATAG
1 TATGGATAG
3211 GTCCTTCGGA
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 81 0.91
31 8 0.09
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.35
Consensus pattern (30 bp):
TATGGATAGTTACCGAGGATCTTTATGACC
Found at i:6607 original size:64 final size:63
Alignment explanation
Indices: 6475--6635 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
6465 AATTGTTCAG
* * * * *
6475 TGTGTATCGATGCACAGGAAGTGCATCGATGCACCTATTAAAATGGAAACATCGAATGCAATT
1 TGTGCATCGATGCAAAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATT
* * **
6538 GGTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTTATT
1 TGTGCATCGATGCA-AAGGAAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATT
** * *
6602 TGTGCATCGATGCACGGGTACTGCATCGATGCAC
1 TGTGCATCGATGCAAAGGAAGTGCATCGATGCAC
6636 ATGCTAAAGA
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 29 0.35
64 53 0.65
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (63 bp):
TGTGCATCGATGCAAAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATT
Found at i:6669 original size:20 final size:20
Alignment explanation
Indices: 6604--6680 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
6594 AGGTTATTTG
* * *
6604 TGCATCGATGCACGGGT-AC
1 TGCATCGATGCACTGTTGAA
*
6623 TGCATCGATGCACATGCTAAAGAA
1 TGCATCGATGCAC-TG-T--TGAA
6647 TGCATCGATGCACTGTTGAA
1 TGCATCGATGCACTGTTGAA
*
6667 TGCATGGATGCACT
1 TGCATCGATGCACT
6681 TCAAGAGAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
19 13 0.28
20 17 0.36
22 1 0.02
23 2 0.04
24 14 0.30
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (20 bp):
TGCATCGATGCACTGTTGAA
Found at i:7745 original size:31 final size:30
Alignment explanation
Indices: 7707--7802 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 30
7697 GTCAAAGAAC
7707 TACCTATGTCTTTCGAGACATATGGACAGT
1 TACCTATGTCTTTCGAGACATATGGACAGT
*** *
7737 ATACCTATGTTCTAAGGA-ACATATGGATAGTT
1 -TACCTATG-TCTTTCGAGACATATGGACAG-T
* * *
7769 TACCTAGGT-TCTTCGGGACCTATGGACAGT
1 TACCTATGTCT-TTCGAGACATATGGACAGT
7799 TACC
1 TACC
7803 GAGGATCTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
29 1 0.02
30 7 0.14
31 36 0.72
32 6 0.12
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (30 bp):
TACCTATGTCTTTCGAGACATATGGACAGT
Found at i:7830 original size:30 final size:30
Alignment explanation
Indices: 7785--7887 Score: 161
Period size: 30 Copynumber: 3.4 Consensus size: 30
7775 GGTTCTTCGG
* *
7785 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
7815 GTCCTCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
7845 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
7875 GACCTTTGGATAG
1 GACCTCTGGATAG
7888 GTCCTTCGGA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:10943 original size:19 final size:19
Alignment explanation
Indices: 10919--10955 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
10909 CTCCTCGATG
10919 CTTGACAATACTTCATCTA
1 CTTGACAATACTTCATCTA
10938 CTTGACAATACTTCATCT
1 CTTGACAATACTTCATCT
10956 GCTAATGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.38
Consensus pattern (19 bp):
CTTGACAATACTTCATCTA
Found at i:18460 original size:18 final size:18
Alignment explanation
Indices: 18437--18489 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
18427 GCTCTTAAGG
18437 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
18455 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
18473 AGTGGTCTTTCGGGACA
1 AGTGGTCCTTCGGGACA
18490 AATATACAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.21, G:0.34, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:18917 original size:21 final size:21
Alignment explanation
Indices: 18891--18930 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18881 AATTGAGGAA
18891 AAAAGG-TATATAAATAAGTAT
1 AAAAGGATAT-TAAATAAGTAT
*
18912 AAAAGGATATTAGATAAGT
1 AAAAGGATATTAAATAAGT
18931 TGTGTAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAAGGATATTAAATAAGTAT
Found at i:23041 original size:2 final size:2
Alignment explanation
Indices: 23034--23109 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
23024 ATTTTTAAAG
23034 AT AT AT AT AT AT AT AT AT AT AT -T 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
23075 AT AT 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 AT AT A
23110 ATAATAATTA
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 72 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23652 original size:20 final size:21
Alignment explanation
Indices: 23627--23676 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
23617 GCCATGGGTC
23627 GCTTATTCTCATTCAAC-AAA
1 GCTTATTCTCATTCAACAAAA
23647 GCTTATTCTCATTCAACAAAA
1 GCTTATTCTCATTCAACAAAA
*
23668 GTTTATTCT
1 GCTTATTCT
23677 AGAACTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (21 bp):
GCTTATTCTCATTCAACAAAA
Found at i:24934 original size:16 final size:16
Alignment explanation
Indices: 24913--24944 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24903 TGAACATTTC
24913 TTTTTATCAATAATAT
1 TTTTTATCAATAATAT
*
24929 TTTTTATCACTAATAT
1 TTTTTATCAATAATAT
24945 CATTGTGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTTATCAATAATAT
Done.