Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002661.1 Hibiscus syriacus cultivar Beakdansim tig00005461_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: 51337
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:796 original size:19 final size:19
Alignment explanation
Indices: 772--809 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
762 ACAAATTTTG
772 AAAATACATATAGCACCAT
1 AAAATACATATAGCACCAT
791 AAAATACATATAGCACCAT
1 AAAATACATATAGCACCAT
810 CCCTGGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.21, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAATACATATAGCACCAT
Found at i:1370 original size:2 final size:2
Alignment explanation
Indices: 1363--1427 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
1353 ACCTAGTTCA
*
1363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1405 AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1428 GACATAGAGA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23014 original size:3 final size:3
Alignment explanation
Indices: 23008--23048 Score: 64
Period size: 3 Copynumber: 13.0 Consensus size: 3
22998 TTTTTTTAAA
23008 AAT AAT ACAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
23049 TTATTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 31 0.86
4 4 0.11
5 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:25397 original size:12 final size:12
Alignment explanation
Indices: 25382--25408 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
25372 TATATATATA
25382 TATATTTAAATT
1 TATATTTAAATT
25394 TATATTTAAATT
1 TATATTTAAATT
25406 TAT
1 TAT
25409 TAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATATTTAAATT
Found at i:37212 original size:22 final size:22
Alignment explanation
Indices: 37187--37237 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
37177 AATTACCAAA
*
37187 AAAAGAGAAACAAAAATAACAG
1 AAAAGAGAAACAAAAAAAACAG
* **
37209 AAAATAGATCCAAAAAAAACAG
1 AAAAGAGAAACAAAAAAAACAG
37231 AAGAAGA
1 AA-AAGA
37238 AAAAGCCTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.71, C:0.10, G:0.14, T:0.06
Consensus pattern (22 bp):
AAAAGAGAAACAAAAAAAACAG
Found at i:41382 original size:24 final size:24
Alignment explanation
Indices: 41355--41412 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
41345 TGGGCAAAGT
41355 TTTGAAAAACTATTGAAAATAATG
1 TTTGAAAAACTATTGAAAATAATG
41379 TTTGAAAAACTATTGAAAATAATG
1 TTTGAAAAACTATTGAAAATAATG
41403 TTTGAAAAAC
1 TTTGAAAAAC
41413 CATAGTATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (24 bp):
TTTGAAAAACTATTGAAAATAATG
Found at i:41385 original size:13 final size:13
Alignment explanation
Indices: 41367--41410 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
41357 TGAAAAACTA
41367 TTGAAAATAATGT
1 TTGAAAATAATGT
* *
41380 TTGAAAA-ACT-A
1 TTGAAAATAATGT
41391 TTGAAAATAATGT
1 TTGAAAATAATGT
41404 TTGAAAA
1 TTGAAAA
41411 ACCATAGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 7 0.28
12 4 0.16
13 14 0.56
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (13 bp):
TTGAAAATAATGT
Found at i:47016 original size:31 final size:31
Alignment explanation
Indices: 46978--47131 Score: 274
Period size: 31 Copynumber: 5.0 Consensus size: 31
46968 CCCGAAGGAC
* *
46978 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
47009 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
47040 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
47071 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
47102 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
47132 CCCTCGACCC
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:47833 original size:21 final size:21
Alignment explanation
Indices: 47803--47847 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
47793 ATTCTGTCGT
* *
47803 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
47824 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
47845 TTG
1 TTG
47848 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Done.