Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002483.1 Hibiscus syriacus cultivar Beakdansim tig00005069_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: 65560
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1394 original size:19 final size:19
Alignment explanation
Indices: 1367--1403 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1357 GCTGGCATTG
* *
1367 CAGTTCACGGTGCTGACAA
1 CAGTCCACGGTACTGACAA
1386 CAGTCCACGGTACTGACA
1 CAGTCCACGGTACTGACA
1404 TGACTGTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (19 bp):
CAGTCCACGGTACTGACAA
Found at i:4898 original size:18 final size:18
Alignment explanation
Indices: 4861--4909 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
4851 TTAAGGAGTA
* * *
4861 GTCCTTCGAGAGATAGTG
1 GTCCTTCGGGACATAATG
4879 GTCCTTCGGGACATAATG
1 GTCCTTCGGGACATAATG
* *
4897 GTCATTCAGGACA
1 GTCCTTCGGGACA
4910 AACCTTCAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (18 bp):
GTCCTTCGGGACATAATG
Found at i:9390 original size:17 final size:18
Alignment explanation
Indices: 9358--9391 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9348 AATTTATCAG
*
9358 TTCTTTTGAGTTTTTTTT
1 TTCTTTTCAGTTTTTTTT
9376 TTCTTTTCA-TTTTTTT
1 TTCTTTTCAGTTTTTTT
9392 CTTTTTTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (18 bp):
TTCTTTTCAGTTTTTTTT
Found at i:11369 original size:6 final size:6
Alignment explanation
Indices: 11358--11390 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
11348 ATATGATTTT
11358 ATTATA ATTATA ATTATA ATTATA ATTATA ATT
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATT
11391 TTATATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTATA
Found at i:12591 original size:7 final size:7
Alignment explanation
Indices: 12581--12612 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
12571 TTAAGCTTTG
12581 GCCTTCA
1 GCCTTCA
12588 GCCTTCA
1 GCCTTCA
12595 GCCTTCA
1 GCCTTCA
12602 GCCTTCA
1 GCCTTCA
12609 GCCT
1 GCCT
12613 CCAACCGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.44, G:0.16, T:0.28
Consensus pattern (7 bp):
GCCTTCA
Found at i:19891 original size:14 final size:14
Alignment explanation
Indices: 19855--19892 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
19845 GTAGTTACAC
19855 TTTTAAAAATAAAA
1 TTTTAAAAATAAAA
*
19869 TTTAAAAAATAAAA
1 TTTTAAAAATAAAA
*
19883 TTTTTAAAAT
1 TTTTAAAAAT
19893 TATATAATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTTTAAAAATAAAA
Found at i:24184 original size:137 final size:136
Alignment explanation
Indices: 23824--24265 Score: 565
Period size: 140 Copynumber: 3.2 Consensus size: 136
23814 CAGAGGACGC
* *
23824 GCCTTCCCTTTTTTTGTCAGAGAATAGGTTATAATTG-CCTATTATGTGTCATGTCCCCCGACGG
1 GCCTTCCC-TTTTTTGTTAGAAAATAGGTTATAATTGCCCTATTATGTGTCATGTCCCCCGACGG
* * * * *
23888 GGCACTATTTATATCAGTACTTATAATGTTTGAGGGGACGTAACAATATGGTTAAATC-TCATTT
65 GGCACTATTCATGTCAGTACCTATAATGTTTGAGGGGACGTAACAATGTGGTTAAAGCGT-ATTT
23952 CAGGGGGTGT
129 CA-GGGG-GT
* * * **
23962 GCCTTCCCTTTTTTTTATCAGATAATTGGTTATAATTGCCCTATTATGTGTCATGTCCCCCGGTG
1 GCCTTCCCTTTTTTGT-T-AGAAAATAGGTTATAATTGCCCTATTATGTGTCATGTCCCCCGACG
* *
24027 GGACACTATTCATGTCAGTACCTATAATGTTTGAGGAGACGTAACAATGTGGTTAAAGCGTATTT
64 GGGCACTATTCATGTCAGTACCTATAATGTTTGAGGGGACGTAACAATGTGGTTAAAGCGTATTT
24092 CAGGGGGT
129 CAGGGGGT
*
24100 GCCTTTCCTTTTCTTGTTAGAAAATAGGTTATAATTGCCCTATTATGTGTCATGTCCCCCGACGG
1 GCCTTCCCTTTT-TTGTTAGAAAATAGGTTATAATTGCCCTATTATGTGTCATGTCCCCCGACGG
* *
24165 GGCACTATTCATGTCAGTACC--T-ATGTTTGAGGGGATGCAACAATGTGGTTAAAGTGCGT-TT
65 GGCACTATTCATGTCAGTACCTATAATGTTTGAGGGGACGTAACAATGTGGTTAAA--GCGTATT
*
24226 T-AGGGGGC
128 TCAGGGGGT
*
24234 GCATATTCCCTTTTTTGTTAGAAAATAGGTTA
1 GC--CTTCCCTTTTTTGTTAGAAAATAGGTTA
24266 CATGCCCAAC
Statistics
Matches: 269, Mismatches: 26, Indels: 21
0.85 0.08 0.07
Matches are distributed among these distances:
134 36 0.13
135 22 0.08
136 12 0.04
137 70 0.26
138 22 0.08
139 24 0.09
140 82 0.30
141 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (136 bp):
GCCTTCCCTTTTTTGTTAGAAAATAGGTTATAATTGCCCTATTATGTGTCATGTCCCCCGACGGG
GCACTATTCATGTCAGTACCTATAATGTTTGAGGGGACGTAACAATGTGGTTAAAGCGTATTTCA
GGGGGT
Found at i:24647 original size:140 final size:139
Alignment explanation
Indices: 24376--24728 Score: 514
Period size: 140 Copynumber: 2.6 Consensus size: 139
24366 ACGTAACAAT
*
24376 GTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTATTTTCTGAC--AAAAAAGG
1 GTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGG
** * * * * * *
24439 GTAGGTGCCTCCCTGAAATGCGCTTTAACCATATTGTTGCGTCCTCTCAAACATTATAGGTACTG
66 AAAGATGCCCCCCTAAAATGCGCTTTAACCACATTATTGCGTCCCCTCAAACATTATAGGTACTG
24504 ACATGAATA
131 ACATGAATA
* * *
24513 GTTCCCCGCCGGGGGACATGACACATAATAAGGTAATTATAACCTATTCTCTGACAAAAAAAAGG
1 GTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGG
24578 AAAGATGCTCCCCCTAAAATGCGCTTTAACCACATTATTGCGTCCCCTCAAACATTATAGGTACT
66 AAAGATGC-CCCCCTAAAATGCGCTTTAACCACATTATTGCGTCCCCTCAAACATTATAGGTACT
24643 GACATGAATA
130 GACATGAATA
* * * * *
24653 GTGCCCCACCGAGGGACATAACACATAATAGGGCAATTATAACCTATTCTCTGACAAGAAAAGGG
1 GTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGG
*
24718 AATG-TGCCCCC
66 AAAGATGCCCCC
24729 TGAAACGTGC
Statistics
Matches: 192, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
137 51 0.27
138 4 0.02
139 16 0.08
140 121 0.63
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (139 bp):
GTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGG
AAAGATGCCCCCCTAAAATGCGCTTTAACCACATTATTGCGTCCCCTCAAACATTATAGGTACTG
ACATGAATA
Found at i:31706 original size:12 final size:12
Alignment explanation
Indices: 31689--31713 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31679 TTTAGAAAAA
31689 AAAATTTGTTAT
1 AAAATTTGTTAT
31701 AAAATTTGTTAT
1 AAAATTTGTTAT
31713 A
1 A
31714 TTATAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
AAAATTTGTTAT
Found at i:37153 original size:18 final size:18
Alignment explanation
Indices: 37132--37166 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37122 AGAAGACGTG
* *
37132 GATGACGACGAAGATGAA
1 GATGAAGACCAAGATGAA
37150 GATGAAGACCAAGATGA
1 GATGAAGACCAAGATGA
37167 GACGGAACTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.11, G:0.31, T:0.11
Consensus pattern (18 bp):
GATGAAGACCAAGATGAA
Found at i:38761 original size:2 final size:2
Alignment explanation
Indices: 38754--38780 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38744 AAACATCAAT
38754 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 T
38781 GATTTAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39392 original size:22 final size:22
Alignment explanation
Indices: 39362--39421 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
39352 TAACCATTTT
39362 TTTTGAAAAATAATTAAATATTA
1 TTTT-AAAAATAATTAAATATTA
*
39385 TTTTAAAAGTAATTAAATATTA
1 TTTTAAAAATAATTAAATATTA
39407 TTTTAAAAATAATTA
1 TTTTAAAAATAATTA
39422 TGATTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 31 0.89
23 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (22 bp):
TTTTAAAAATAATTAAATATTA
Found at i:40891 original size:2 final size:2
Alignment explanation
Indices: 40884--40911 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40874 TAATTAAAGA
40884 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
40912 TAGCTACACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47730 original size:2 final size:2
Alignment explanation
Indices: 47725--47756 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47715 ATTAAAGAAG
47725 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
47757 TAGCTACACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50903 original size:3 final size:3
Alignment explanation
Indices: 50895--50958 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
50885 TTACAAAATG
*
50895 TAA TAA TAA TTAA TAA TAA TAA -AA GTAA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
*
50941 TAC TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
50959 AAAGACACAG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 2 0.04
3 47 0.87
4 5 0.09
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54451 original size:23 final size:24
Alignment explanation
Indices: 54419--54468 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
54409 GTAAGCTACA
54419 AAAAGACAGAGAAAAACATGCCAT
1 AAAAGACAGAGAAAAACATGCCAT
* *
54443 AAAA-ACAGAGATAAACATGTCAT
1 AAAAGACAGAGAAAAACATGCCAT
54466 AAA
1 AAA
54469 GTTAGATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.14, T:0.12
Consensus pattern (24 bp):
AAAAGACAGAGAAAAACATGCCAT
Found at i:54481 original size:20 final size:21
Alignment explanation
Indices: 54451--54489 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
54441 ATAAAAACAG
*
54451 AGATAAACATGTCATAAAGTT
1 AGATAAACATGTCACAAAGTT
54472 AGAT-AACATGTCACAAAG
1 AGATAAACATGTCACAAAG
54490 ACATACTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (21 bp):
AGATAAACATGTCACAAAGTT
Found at i:55226 original size:8 final size:8
Alignment explanation
Indices: 55198--55237 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
55188 AATTCAAGAT
55198 TAAAAATA
1 TAAAAATA
*
55206 -AATAAAAA
1 TAA-AAATA
55214 TAAAAATA
1 TAAAAATA
55222 TAAAAATA
1 TAAAAATA
55230 TAAAAATA
1 TAAAAATA
55238 AAGGTGAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 2 0.07
8 24 0.86
9 2 0.07
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
TAAAAATA
Found at i:55226 original size:14 final size:13
Alignment explanation
Indices: 55205--55239 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
55195 GATTAAAAAT
55205 AAATAAAAATAAA
1 AAATAAAAATAAA
55218 AATATAAAAATATAA
1 AA-ATAAAAATA-AA
55233 AAATAAA
1 AAATAAA
55240 GGTGAGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 14 0.70
15 4 0.20
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:55918 original size:6 final size:6
Alignment explanation
Indices: 55907--55933 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
55897 AACATTTTTG
55907 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
55934 CAAAGAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Done.