Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008403.1 Hibiscus syriacus cultivar Beakdansim tig00111172_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: 60244
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1184 original size:12 final size:13
Alignment explanation
Indices: 1161--1185 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1151 TAACCCCCTA
1161 CCAAACCTTTTTG
1 CCAAACCTTTTTG
1174 CCAAACCTTTTT
1 CCAAACCTTTTT
1186 ATTCCAATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.32, G:0.04, T:0.40
Consensus pattern (13 bp):
CCAAACCTTTTTG
Found at i:11362 original size:2 final size:2
Alignment explanation
Indices: 11355--11396 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
11345 TCCCTAGTTT
11355 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11397 GAAAGATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13145 original size:41 final size:40
Alignment explanation
Indices: 13050--13145 Score: 93
Period size: 41 Copynumber: 2.3 Consensus size: 40
13040 GAATTTTGAA
* * * * *
13050 TTTATATAAAAATTAAATATTTTTTAATAATAAAAAAACAG
1 TTTATAT-AAATTTAAATAATATATAATAATAAAAAAAAAG
* * *
13091 TTTATAATTAATTTAAATAATATATAATTATAAAATAAAAAT
1 TTTAT-ATAAATTTAAATAATATATAATAATAAAA-AAAAAG
13133 TTTATATAAATTT
1 TTTATATAAATTT
13146 TTTAATTAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
41 33 0.75
42 11 0.25
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (40 bp):
TTTATATAAATTTAAATAATATATAATAATAAAAAAAAAG
Found at i:13541 original size:20 final size:20
Alignment explanation
Indices: 13518--13555 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
13508 TTAACCGTTA
13518 ACCGACCGAATTAATTCGTG
1 ACCGACCGAATTAATTCGTG
13538 ACCGACCGAATTAATTCG
1 ACCGACCGAATTAATTCG
13556 ATTAATTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ACCGACCGAATTAATTCGTG
Found at i:17079 original size:13 final size:15
Alignment explanation
Indices: 17051--17080 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17041 GCTTCAATCG
17051 TTAGTCCAATATATA
1 TTAGTCCAATATATA
17066 TTAGTCCAATATATA
1 TTAGTCCAATATATA
17081 CCGCTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
TTAGTCCAATATATA
Found at i:18304 original size:44 final size:44
Alignment explanation
Indices: 18241--18341 Score: 184
Period size: 44 Copynumber: 2.3 Consensus size: 44
18231 AGAAACTATC
*
18241 CACCTATAATAGTACAAAATACAATAAATTTTGTAATTATAATT
1 CACCTATAATAGTACAAAATACAATAAAATTTGTAATTATAATT
18285 CACCTATAATAGTACAAAATACAATAAAATTTGTAATTATAATT
1 CACCTATAATAGTACAAAATACAATAAAATTTGTAATTATAATT
*
18329 CATCTATAATAGT
1 CACCTATAATAGT
18342 TACATATAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.36
Consensus pattern (44 bp):
CACCTATAATAGTACAAAATACAATAAAATTTGTAATTATAATT
Found at i:20141 original size:2 final size:2
Alignment explanation
Indices: 20136--20166 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20126 TGCGTGTGTG
*
20136 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20167 TAAAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:24612 original size:18 final size:18
Alignment explanation
Indices: 24585--24702 Score: 98
Period size: 18 Copynumber: 6.4 Consensus size: 18
24575 ATAAGAAAAA
24585 GAAG-AGAAGAAAGGAAG
1 GAAGAAGAAGAAAGGAAG
24602 GAAGAAGAAGAAAGAAAAGAAG
1 GAAGAAGAAGAAAG----GAAG
* *
24624 GAAGAAGAAGAAAGAAAA
1 GAAGAAGAAGAAAGGAAG
*
24642 GAAGAAGGAAGAAAGTAA-
1 GAAGAA-GAAGAAAGGAAG
* *
24660 GAAGAAGGAGAAAAGAA-
1 GAAGAAGAAGAAAGGAAG
* **
24677 AAAGAAGAAGAAATAAAG
1 GAAGAAGAAGAAAGGAAG
24695 GAAGAAGA
1 GAAGAAGA
24703 GAAGGAAACA
Statistics
Matches: 83, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
17 25 0.30
18 30 0.36
19 10 0.12
22 18 0.22
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (18 bp):
GAAGAAGAAGAAAGGAAG
Found at i:24623 original size:22 final size:22
Alignment explanation
Indices: 24583--24688 Score: 121
Period size: 22 Copynumber: 4.8 Consensus size: 22
24573 AAATAAGAAA
*
24583 AAGAAGAGAAGAAAGGAAGGAAG
1 AAGAAGA-AAGAAAAGAAGGAAG
24606 AAGAAGAAAGAAAAGAAGGAAG
1 AAGAAGAAAGAAAAGAAGGAAG
24628 AAGAAGAAAGAAAAGAA-GAAG
1 AAGAAGAAAGAAAAGAAGGAAG
*
24649 --GAAGAAAGTAAGAAGAAGGAGAA
1 AAGAAGAAAG-AA-AAGAAGGA-AG
24672 AAGAA-AAAGAAGAAGAA
1 AAGAAGAAAGAA-AAGAA
24689 ATAAAGGAAG
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
19 8 0.11
20 2 0.03
21 9 0.12
22 33 0.44
23 16 0.21
24 4 0.05
25 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (22 bp):
AAGAAGAAAGAAAAGAAGGAAG
Found at i:24702 original size:3 final size:3
Alignment explanation
Indices: 24577--24688 Score: 90
Period size: 3 Copynumber: 36.7 Consensus size: 3
24567 GAGATAAAAT
* *
24577 AAG AAA AAG AAG -AG AAG AA- AGG AAGG AAG AAG AAG AAAG AA- AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG -AAG AAG AAG
24621 AAGG AAG AAG AAG AAAG AA- AAG AAG AAGG AAG AAAG TAAG AAG AAG
1 AA-G AAG AAG AAG -AAG AAG AAG AAG AA-G AAG -AAG -AAG AAG AAG
* *
24667 GAG AA- AAG AAA AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AA
24689 ATAAAGGAAG
Statistics
Matches: 89, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
2 9 0.10
3 59 0.66
4 21 0.24
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:24940 original size:21 final size:22
Alignment explanation
Indices: 24914--24964 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
24904 AGCGATGACT
*
24914 TTATTATTATT-TAATAAAATA
1 TTATTATTATTAGAATAAAATA
*
24935 TTATTATT-TTAGAATAAATTA
1 TTATTATTATTAGAATAAAATA
24956 TTATTATTA
1 TTATTATTA
24965 AATGGTAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTATTATTATTAGAATAAAATA
Found at i:32101 original size:15 final size:16
Alignment explanation
Indices: 32069--32101 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
32059 AAAATCTTTC
32069 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
32085 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
32100 TT
1 TT
32102 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:32875 original size:16 final size:16
Alignment explanation
Indices: 32851--32884 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
32841 TATCGCCGAC
*
32851 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
32867 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
32883 CG
1 CG
32885 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:35384 original size:24 final size:24
Alignment explanation
Indices: 35351--35423 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
35341 TGTAGTTCCC
*
35351 CAGAATTACATCCATAAGGACTTA
1 CAGAACTACATCCATAAGGACTTA
**
35375 CAGAACTACATCCATATTGACTTA
1 CAGAACTACATCCATAAGGACTTA
* *
35399 CATAACTACATCTATAAGGACTTA
1 CAGAACTACATCCATAAGGACTTA
35423 C
1 C
35424 TCTAGACTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (24 bp):
CAGAACTACATCCATAAGGACTTA
Found at i:38557 original size:2 final size:2
Alignment explanation
Indices: 38550--38591 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
38540 GAAACTTCTA
38550 AT AT AT AT AT AT AT AT AT AT AT AT 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
38592 GTTTATGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45827 original size:18 final size:17
Alignment explanation
Indices: 45793--45834 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
45783 AGACTTATTG
45793 AAAAATAAAAAAAAATA
1 AAAAATAAAAAAAAATA
* *
45810 AAAAATAAAATGACAATA
1 AAAAATAAAA-AAAAATA
45828 AAAAATA
1 AAAAATA
45835 CTGACGGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (17 bp):
AAAAATAAAAAAAAATA
Found at i:47502 original size:4 final size:4
Alignment explanation
Indices: 47493--47519 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
47483 CCATAAAGTA
47493 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
47520 CAGCTTCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:55857 original size:22 final size:22
Alignment explanation
Indices: 55832--55895 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
55822 ATTCAATTTA
55832 TTTAATGTTCGCAATATGTTCG
1 TTTAATGTTCGCAATATGTTCG
* * * *
55854 TTTAACGTTTGCGGACATGTTCG
1 TTTAATGTTCGC-AATATGTTCG
*
55877 TTTATATGCTCGCCAATAT
1 TTTA-ATGTTCG-CAATAT
55896 ATTGGAGAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
22 10 0.33
23 12 0.40
24 7 0.23
25 1 0.03
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (22 bp):
TTTAATGTTCGCAATATGTTCG
Found at i:58776 original size:19 final size:20
Alignment explanation
Indices: 58747--58784 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
58737 GAAGTGCCAC
58747 ATAGAATGTCCGAAGGACCA
1 ATAGAATGTCCGAAGGACCA
58767 ATAG-ATGTCCGAAGGACC
1 ATAGAATGTCCGAAGGACC
58785 GCGTAGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (20 bp):
ATAGAATGTCCGAAGGACCA
Found at i:58806 original size:23 final size:23
Alignment explanation
Indices: 58778--58835 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
58768 TAGATGTCCG
* *
58778 AAGGACCGCGTAGAAATGTCCTA
1 AAGGACCACGTAGAAATGTCCCA
* * *
58801 AAGGACTACGTAGAATTGTCCCG
1 AAGGACCACGTAGAAATGTCCCA
58824 AAGGACCACGTA
1 AAGGACCACGTA
58836 AAACCCTCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.17
Consensus pattern (23 bp):
AAGGACCACGTAGAAATGTCCCA
Found at i:58947 original size:15 final size:15
Alignment explanation
Indices: 58927--58965 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
58917 TTTCAATTAT
*
58927 TCACATAGTTCCGTA
1 TCACATAGTTCCATA
*
58942 TCACATAG-ACCATA
1 TCACATAGTTCCATA
58956 TCACATAGTT
1 TCACATAGTT
58966 TATATCATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (15 bp):
TCACATAGTTCCATA
Done.