Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007368.1 Hibiscus syriacus cultivar Beakdansim tig00019762_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: 423757
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:393110 original size:21 final size:21
Alignment explanation
Indices: 393086--393125 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
393076 AAAACCTTAC
393086 TATTTCTAAAATTTTGTAAAA
1 TATTTCTAAAATTTTGTAAAA
*
393107 TATTTCTTAAATTTTGTAA
1 TATTTCTAAAATTTTGTAA
393126 CCCCCTAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (21 bp):
TATTTCTAAAATTTTGTAAAA
Found at i:399266 original size:9 final size:9
Alignment explanation
Indices: 399233--399306 Score: 58
Period size: 10 Copynumber: 7.7 Consensus size: 9
399223 GTCGGGTTAG
399233 ACCGGTCAA
1 ACCGGTCAA
* *
399242 ACCAGTTCAG
1 ACC-GGTCAA
399252 ACCGGTCAA
1 ACCGGTCAA
*
399261 ACCGGTTCGA
1 ACCGG-TCAA
399271 ACCGGTCAGA
1 ACCGGTCA-A
*
399281 ACCGGTTGAAA
1 ACCGG-T-CAA
399292 ACCGGTCAA
1 ACCGGTCAA
*
399301 ATCGGT
1 ACCGGT
399307 TTCCAGCCCT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
9 21 0.41
10 22 0.43
11 7 0.14
12 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:399306 original size:20 final size:19
Alignment explanation
Indices: 399233--399307 Score: 82
Period size: 19 Copynumber: 3.8 Consensus size: 19
399223 GTCGGGTTAG
*
399233 ACCGGTCAAACCAGTTC-A
1 ACCGGTCAAACCGGTTCGA
399251 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
399271 ACCGGTCAGAACCGGTT-GAAA
1 ACCGGTCA-AACCGGTTCG--A
*
399292 ACCGGTCAAATCGGTT
1 ACCGGTCAAACCGGTT
399308 TCCAGCCCTC
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
19 25 0.50
20 16 0.32
21 9 0.18
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.17
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:401186 original size:24 final size:24
Alignment explanation
Indices: 401176--401290 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
401166 CATAATTCAC
* * *
401176 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
401200 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
401224 GTCAAGTATTAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
401248 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
401272 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
401291 ATCAAATCGA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 2 0.02
24 79 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:403745 original size:7 final size:7
Alignment explanation
Indices: 403733--403772 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
403723 TGGTCAACGC
403733 CGGTCAA
1 CGGTCAA
403740 CGGTCAA
1 CGGTCAA
*
403747 TGGGTCAA
1 -CGGTCAA
403755 CGGTCAA
1 CGGTCAA
403762 CGGGTCAA
1 C-GGTCAA
403770 CGG
1 CGG
403773 GTCGGGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 16 0.55
8 13 0.45
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:403754 original size:15 final size:15
Alignment explanation
Indices: 403724--403772 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
403714 AGTCAACAGT
403724 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
*
403741 GGTCAATGGGTCAAC
1 GGTCAACGGGTCAAC
403756 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
403771 GG
1 GG
403773 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 23 0.77
17 7 0.23
ACGTcount: A:0.24, C:0.27, G:0.35, T:0.14
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:403780 original size:13 final size:13
Alignment explanation
Indices: 403762--403816 Score: 80
Period size: 13 Copynumber: 4.5 Consensus size: 13
403752 CAACGGTCAA
403762 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
403775 CGGGTCAATGGGT
1 CGGGTCAACGGGT
403788 CGGGT---CGGGT
1 CGGGTCAACGGGT
403798 CGGGTCAACGGGT
1 CGGGTCAACGGGT
403811 CGGGTC
1 CGGGTC
403817 GGGTTGTGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
10 9 0.24
13 28 0.76
ACGTcount: A:0.11, C:0.22, G:0.49, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:403796 original size:23 final size:23
Alignment explanation
Indices: 403770--403820 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
403760 AACGGGTCAA
*
403770 CGGGTCGGGTCAATGGGTCGGGT
1 CGGGTCGGGTCAACGGGTCGGGT
403793 CGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCGGGTCAACGGGTCGGGT
403816 CGGGT
1 CGGGT
403821 TGTGACCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.08, C:0.20, G:0.53, T:0.20
Consensus pattern (23 bp):
CGGGTCGGGTCAACGGGTCGGGT
Found at i:423668 original size:30 final size:30
Alignment explanation
Indices: 423606--423668 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
423596 TGTTAGTTAT
* *
423606 TATGTCTCCCAAATGCTCCACCAAGTTGTA
1 TATGTCTCCCAAATGCTCCACCAAGCTATA
* *
423636 TATGTCTTCCAAATGCTCCACTAAGCTATA
1 TATGTCTCCCAAATGCTCCACCAAGCTATA
423666 TAT
1 TAT
423669 TTATGATTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (30 bp):
TATGTCTCCCAAATGCTCCACCAAGCTATA
Done.