Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002951.1 Hibiscus syriacus cultivar Beakdansim tig00006090_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: 70916
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:5729 original size:21 final size:21
Alignment explanation
Indices: 5704--5768 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
5694 CTATTGTTTT
5704 TTTATTTTTATAATTGAATCC
1 TTTATTTTTATAATTGAATCC
* ** **
5725 TTTATTTTTTTTCAATTTTATTT
1 TTTA-TTTTTAT-AATTGAATCC
5748 TTTATTTTTATAATTGAATCC
1 TTTATTTTTATAATTGAATCC
5769 CCTAATTTTT
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
21 10 0.31
22 12 0.38
23 10 0.31
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTATTTTTATAATTGAATCC
Found at i:5793 original size:44 final size:44
Alignment explanation
Indices: 5701--5849 Score: 128
Period size: 44 Copynumber: 3.5 Consensus size: 44
5691 TTTCTATTGT
** * * **
5701 TTTTTTATTTTTATAATTGAATCCTTTATTTTTTTTCAATTTTA
1 TTTTTTATTTTTATAATTGAATCCCCTAATTTTTATCAATCCTA
*
5745 TTTTTTATTTTTATAATTGAATCCCCTAATTTTTAT-AGTCCTA
1 TTTTTTATTTTTATAATTGAATCCCCTAATTTTTATCAATCCTA
* * * *
5788 CTTTTTATCTTTATAATTGAAGT---TTTATTTTT-TCAATCCTA
1 TTTTTTATTTTTATAATTGAA-TCCCCTAATTTTTATCAATCCTA
**
5829 TTTTTTTACATTTATAATTGA
1 -TTTTTTATTTTTATAATTGA
5850 TTAACCTAAG
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
40 1 0.01
41 13 0.15
42 17 0.20
43 23 0.26
44 33 0.38
ACGTcount: A:0.25, C:0.10, G:0.04, T:0.61
Consensus pattern (44 bp):
TTTTTTATTTTTATAATTGAATCCCCTAATTTTTATCAATCCTA
Found at i:6001 original size:43 final size:42
Alignment explanation
Indices: 5745--6056 Score: 112
Period size: 43 Copynumber: 7.4 Consensus size: 42
5735 TTCAATTTTA
* * *
5745 TTTTTTATTTTTATAATTGAATCCCCTAATTTTT-ATAGTCCTAC
1 TTTTTTA-CTTTATAATTGAAGCCCCTAATTTTTCA-A-TCCCAC
*** * * *
5789 -TTTTTATCTTTATAATTGAAG-TTTTATTTTTTCAATCCTAT
1 TTTTTTA-CTTTATAATTGAAGCCCCTAATTTTTCAATCCCAC
**** * *
5830 TTTTTTACATTTATAATTGATTAACCTAAGTTTGTCAATCTCAC
1 TTTTTTAC-TTTATAATTGAAGCCCCTAA-TTTTTCAATCCCAC
* * * * **
5874 -TTTGTAC-ATATAATTG-AGCTCCTAATTTTTTTAATATCAC
1 TTTTTTACTTTATAATTGAAGCCCCTAA-TTTTTCAATCCCAC
* * * *
5914 TTTATCCTT--TTTATAATTGAAGCTCATAA-TCTT-AATCTCA-
1 TTT-T--TTACTTTATAATTGAAGCCCCTAATTTTTCAATCCCAC
*
5954 TTTTTTATCTTTATAATTGAGGCCCCTAATTTTTCAATCCCAC
1 TTTTTTA-CTTTATAATTGAAGCCCCTAATTTTTCAATCCCAC
* * * *
5997 -TTTTTAC-TTAT-ATTGTTTAGGCCTTAACTTTTTTCAATCCCAT
1 TTTTTTACTTTATAATTG--AAGCCCCTAA--TTTTTCAATCCCAC
*
6040 TTTTTTAATTTATAATT
1 TTTTTTACTTTATAATT
6057 TATGATCCTA
Statistics
Matches: 201, Mismatches: 43, Indels: 46
0.69 0.15 0.16
Matches are distributed among these distances:
37 2 0.01
39 5 0.02
40 40 0.20
41 32 0.16
42 41 0.20
43 49 0.24
44 25 0.12
45 4 0.02
46 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (42 bp):
TTTTTTACTTTATAATTGAAGCCCCTAATTTTTCAATCCCAC
Found at i:7801 original size:36 final size:36
Alignment explanation
Indices: 7737--7878 Score: 241
Period size: 36 Copynumber: 4.0 Consensus size: 36
7727 TTTGTTCTAG
* *
7737 TTGAATTGGAAGTG-CGATGCTTCTTTCCGTTCGAT
1 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAT
7772 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAT
1 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAT
*
7808 TTGAATCGGAAGTGACGATGCTTCCTTCCGTTCGAT
1 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAT
*
7844 TTAAATCGGAAGTGCCGATGCTTCCTTCCGTTCGA
1 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGA
7879 CTAGAAACGC
Statistics
Matches: 101, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 13 0.13
36 88 0.87
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.35
Consensus pattern (36 bp):
TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAT
Found at i:13604 original size:24 final size:24
Alignment explanation
Indices: 13570--13617 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
13560 ATCATATTTA
* *
13570 ACGGCCTCGACCACGTCCACGTCC
1 ACGGCCACGACCACGACCACGTCC
*
13594 ACGGCCACGACCCCGACCACGTCC
1 ACGGCCACGACCACGACCACGTCC
13618 CAAAGGCCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.52, G:0.21, T:0.08
Consensus pattern (24 bp):
ACGGCCACGACCACGACCACGTCC
Found at i:22354 original size:22 final size:21
Alignment explanation
Indices: 22319--22359 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
22309 CATAATTATT
22319 TAAAAAATTAAATAAAAATAC
1 TAAAAAATTAAATAAAAATAC
*
22340 TAAAAATATTTAATAAAAAT
1 TAAAAA-ATTAAATAAAAAT
22360 TAATTTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAAATTAAATAAAAATAC
Found at i:28849 original size:2 final size:2
Alignment explanation
Indices: 28842--28876 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28832 ATTGGCAATT
28842 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28877 TCACAGGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30351 original size:13 final size:12
Alignment explanation
Indices: 30327--30360 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
30317 ATAAGGGAAA
30327 GAAGAAAAAGTT
1 GAAGAAAAAGTT
30339 GAAGAAGAAAGTT
1 GAAGAA-AAAGTT
30352 GAGAGAAAA
1 GA-AGAAAA
30361 TAGGGAGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 10 0.50
14 4 0.20
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (12 bp):
GAAGAAAAAGTT
Found at i:52265 original size:18 final size:19
Alignment explanation
Indices: 52227--52265 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
52217 ATTAAAGTTG
* *
52227 TAAAATAATTATTTAATTT
1 TAAAAAAATAATTTAATTT
52246 TAAAAAAATAATTT-ATTT
1 TAAAAAAATAATTTAATTT
52264 TA
1 TA
52266 CTATAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAAAAAATAATTTAATTT
Found at i:52272 original size:23 final size:22
Alignment explanation
Indices: 52228--52272 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
52218 TTAAAGTTGT
* *
52228 AAAATAATTATTTAATTTTAAA
1 AAAATAATTATTTAACTATAAA
*
52250 AAAATAATTTATTTTACTATAAA
1 AAAATAA-TTATTTAACTATAAA
52273 TAAACTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATAATTATTTAACTATAAA
Found at i:53662 original size:2 final size:2
Alignment explanation
Indices: 53655--53680 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53645 CTTCTGTCAA
53655 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
53681 TATTTTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57881 original size:46 final size:47
Alignment explanation
Indices: 57813--57923 Score: 188
Period size: 46 Copynumber: 2.4 Consensus size: 47
57803 GAAGATTGCT
* *
57813 TGAAGACGCCGAAAAATTGATAAATCCTGAAGTCTTCCTGATTGGCC
1 TGAAGACGCCGAGAAATCGATAAATCCTGAAGTCTTCCTGATTGGCC
*
57860 TGAA-ACGCCGAGAAATCGATAAATCCTGAAGTCTTCCTGGTTGGCC
1 TGAAGACGCCGAGAAATCGATAAATCCTGAAGTCTTCCTGATTGGCC
57906 TGAAGACGCCGAGAAATC
1 TGAAGACGCCGAGAAATC
57924 TTGGAGTCTT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
46 43 0.72
47 17 0.28
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (47 bp):
TGAAGACGCCGAGAAATCGATAAATCCTGAAGTCTTCCTGATTGGCC
Found at i:60159 original size:30 final size:30
Alignment explanation
Indices: 60123--60225 Score: 107
Period size: 30 Copynumber: 3.3 Consensus size: 30
60113 GTTCATGAAC
* *
60123 AATAAATAAACGAACATGAATACCTTCAAA
1 AATAAATAAACGAACATGAACATCTTCAAA
* * * *
60153 AATAAATAAATGAATACGAACATGTTCATGAA
1 AATAAATAAACGAACATGAACATCTTCA--AA
* *
60185 CAATAAATAAACAAACATAAACATCTTCAAA
1 -AATAAATAAACGAACATGAACATCTTCAAA
60216 AATAAATAAA
1 AATAAATAAA
60226 TAAATAAATA
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
30 32 0.55
31 2 0.03
32 2 0.03
33 22 0.38
ACGTcount: A:0.59, C:0.14, G:0.06, T:0.21
Consensus pattern (30 bp):
AATAAATAAACGAACATGAACATCTTCAAA
Found at i:60243 original size:67 final size:63
Alignment explanation
Indices: 60106--60231 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 63
60096 GAGCATTAAG
* * * *
60106 CGAACATGTTCATGAACAATAAATAAACGAACATGAATACCTTCAAAAATAAATAAATGAATA
1 CGAACATGTTCATGAACAATAAATAAACAAACATAAACACCTTCAAAAATAAATAAATAAATA
*
60169 CGAACATGTTCATGAACAATAAATAAACAAACATAAACATCTTCAAAAATAAATAAATAAATA
1 CGAACATGTTCATGAACAATAAATAAACAAACATAAACACCTTCAAAAATAAATAAATAAATA
60232 AATACGAACA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.56, C:0.14, G:0.07, T:0.22
Consensus pattern (63 bp):
CGAACATGTTCATGAACAATAAATAAACAAACATAAACACCTTCAAAAATAAATAAATAAATA
Found at i:61702 original size:12 final size:12
Alignment explanation
Indices: 61687--61715 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
61677 CTTTACTCAC
61687 CTCCGATGGCCG
1 CTCCGATGGCCG
61699 CTCCGATGGCCG
1 CTCCGATGGCCG
61711 CTCCG
1 CTCCG
61716 GTGCCGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.45, G:0.31, T:0.17
Consensus pattern (12 bp):
CTCCGATGGCCG
Found at i:68023 original size:34 final size:34
Alignment explanation
Indices: 67985--68050 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
67975 GTTCTAAAAT
*
67985 CTTTTAATTATTTGACAATAAACGCTTAAATAAA
1 CTTTTAATTATTTGACAATAAACGCTCAAATAAA
*
68019 CTTTTAATTATTTGATAATAAACGCTCAAATA
1 CTTTTAATTATTTGACAATAAACGCTCAAATA
68051 TTTAACAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (34 bp):
CTTTTAATTATTTGACAATAAACGCTCAAATAAA
Done.