Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000153.1 Hibiscus syriacus cultivar Beakdansim tig00000272_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: 48544
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:16436 original size:47 final size:47
Alignment explanation
Indices: 16382--16476 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
16372 CAATCCATAA
16382 CCATAGTCTGCTTATAACATAAGACTTAACTACCTAAACACATACTG
1 CCATAGTCTGCTTATAACATAAGACTTAACTACCTAAACACATACTG
16429 CCATAGTCTGCTTATAACATAAGACTTAACTACCTAAACACATACTG
1 CCATAGTCTGCTTATAACATAAGACTTAACTACCTAAACACATACTG
16476 C
1 C
16477 AGCACTAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.38, C:0.26, G:0.08, T:0.27
Consensus pattern (47 bp):
CCATAGTCTGCTTATAACATAAGACTTAACTACCTAAACACATACTG
Found at i:16621 original size:33 final size:33
Alignment explanation
Indices: 16579--16677 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
16569 GAAATGACTT
*
16579 ATATTATGATCAATATATTAAGGCATATGCTGC
1 ATATTATGATCAATATATTAAGGAATATGCTGC
* *
16612 ATATTATGATCGATAAATTAAGGAATATGCTGC
1 ATATTATGATCAATATATTAAGGAATATGCTGC
* * * *
16645 ATGTCATGTTCAATATATTAAGGAATACGCTGC
1 ATATTATGATCAATATATTAAGGAATATGCTGC
16678 TGTATTGATT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (33 bp):
ATATTATGATCAATATATTAAGGAATATGCTGC
Found at i:31071 original size:5 final size:5
Alignment explanation
Indices: 31061--31086 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31051 ATTTATCTCT
31061 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
31087 CTCACATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:31263 original size:14 final size:14
Alignment explanation
Indices: 31237--31282 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
31227 ATATATAGTA
31237 ATTTAAT-TTTTAT
1 ATTTAATATTTTAT
*
31250 TTTTAATATTTTAT
1 ATTTAATATTTTAT
*
31264 ATTCAATATTTCTAT
1 ATTTAATATTT-TAT
31279 ATTT
1 ATTT
31283 GTATAGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 6 0.22
14 15 0.56
15 6 0.22
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTAATATTTTAT
Found at i:43372 original size:6 final size:6
Alignment explanation
Indices: 43361--43386 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
43351 GCTTCTTGTC
43361 CCTGCT CCTGCT CCTGCT CCTGCT CC
1 CCTGCT CCTGCT CCTGCT CCTGCT CC
43387 ATGTCTATTT
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:0.00, C:0.54, G:0.15, T:0.31
Consensus pattern (6 bp):
CCTGCT
Found at i:44786 original size:23 final size:23
Alignment explanation
Indices: 44746--44806 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
44736 ATGAATAATG
*
44746 TTATT-TTTTATTTAATAATTTA
1 TTATTATTTTATTTAATAATATA
44768 TTATTATTTTA-TTACATAATATA
1 TTATTATTTTATTTA-ATAATATA
*
44791 TT-TT-TATTATTTAATA
1 TTATTATTTTATTTAATA
44807 GTAAACTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 7 0.21
22 13 0.38
23 14 0.41
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
TTATTATTTTATTTAATAATATA
Found at i:47788 original size:48 final size:49
Alignment explanation
Indices: 47735--47853 Score: 158
Period size: 48 Copynumber: 2.5 Consensus size: 49
47725 CATAAATCAG
47735 GTCAAGTATCATATCAGAAATT-A-GATCA-AGTAACATATCAGAATCCAA
1 GTCAAGTATCATATCAGAAATTCATG-TCAGA-TAACATATCAGAATCCAA
* * *
47783 GTCAAGTATCAGATCAG-AATTCATGTCAGATATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAAATTCATGTCAGATAACATATCAGAATCCAA
47831 GTCAAGTATCATATCAG-AATTCA
1 GTCAAGTATCATATCAGAAATTCA
47854 AATCGAAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
47 4 0.06
48 58 0.91
49 2 0.03
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (49 bp):
GTCAAGTATCATATCAGAAATTCATGTCAGATAACATATCAGAATCCAA
Found at i:47850 original size:24 final size:24
Alignment explanation
Indices: 47735--47850 Score: 139
Period size: 24 Copynumber: 4.8 Consensus size: 24
47725 CATAAATCAG
*
47735 GTCAAGTATCATATCAGAAAT-TA-
1 GTCAAGTATCATATCAG-AATCCAT
* *
47758 GATCAAGTAACATATCAGAATCCAA
1 G-TCAAGTATCATATCAGAATCCAT
* *
47783 GTCAAGTATCAGATCAGAATTCAT
1 GTCAAGTATCATATCAGAATCCAT
47807 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAT
47831 GTCAAGTATCATATCAGAAT
1 GTCAAGTATCATATCAGAAT
47851 TCAAATCGAA
Statistics
Matches: 80, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
23 6 0.08
24 71 0.89
25 3 0.04
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Done.