Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004738.1 Hibiscus syriacus cultivar Beakdansim tig00010698_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: 62702
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:2129 original size:23 final size:23
Alignment explanation
Indices: 2084--2129 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2074 TTATACCTAT
*
2084 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
2107 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
2130 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:3390 original size:12 final size:12
Alignment explanation
Indices: 3373--3416 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
3363 CATCTTCATT
*
3373 TCATCAACAACA
1 TCATCAACACCA
*
3385 TCATCAACATCCT
1 TCATCAACA-CCA
*
3398 TCATCAAGACCA
1 TCATCAACACCA
3410 TCATCAA
1 TCATCAA
3417 TCCCATAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 18 0.67
13 9 0.33
ACGTcount: A:0.41, C:0.34, G:0.02, T:0.23
Consensus pattern (12 bp):
TCATCAACACCA
Found at i:7229 original size:31 final size:31
Alignment explanation
Indices: 7191--7313 Score: 219
Period size: 31 Copynumber: 4.0 Consensus size: 31
7181 ATTACCATTT
* *
7191 ACCAAGACACCTAACCCTTATCATCTTCCAA
1 ACCAAGACACATAACCGTTATCATCTTCCAA
*
7222 ACCAAGACACATAGCCGTTATCATCTTCCAA
1 ACCAAGACACATAACCGTTATCATCTTCCAA
7253 ACCAAGACACATAACCGTTATCATCTTCCAA
1 ACCAAGACACATAACCGTTATCATCTTCCAA
7284 ACCAAGACACATAACCGTTATCATCTTCCA
1 ACCAAGACACATAACCGTTATCATCTTCCA
7314 TAAGTCAAAG
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 88 1.00
ACGTcount: A:0.37, C:0.34, G:0.07, T:0.23
Consensus pattern (31 bp):
ACCAAGACACATAACCGTTATCATCTTCCAA
Found at i:14276 original size:31 final size:31
Alignment explanation
Indices: 14238--14300 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
14228 AATTACCATT
14238 AAACCAAGACACCTAACCCTTATCATCTTCC
1 AAACCAAGACACCTAACCCTTATCATCTTCC
14269 AAACCAAGACACCTAACCCTTATCATCTTCC
1 AAACCAAGACACCTAACCCTTATCATCTTCC
14300 A
1 A
14301 TAAGTCAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.38, G:0.03, T:0.22
Consensus pattern (31 bp):
AAACCAAGACACCTAACCCTTATCATCTTCC
Found at i:15467 original size:22 final size:22
Alignment explanation
Indices: 15427--15477 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
15417 TTCACTGTTT
* *
15427 TTATTTTTATTATTGTTATTTA
1 TTATTTTAATTATTGTTATTAA
15449 TTATTTTAATTA-TGTTTATTAA
1 TTATTTTAATTATTG-TTATTAA
*
15471 TTGTTTT
1 TTATTTT
15478 GATATTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (22 bp):
TTATTTTAATTATTGTTATTAA
Found at i:17245 original size:22 final size:21
Alignment explanation
Indices: 17211--17257 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
17201 TTACATCCGT
17211 TTCTTTAAATTTT-TGCTAATTA
1 TTCTTTAAATTTTATG--AATTA
* *
17233 TTCTTTTATTTTTATGAATTA
1 TTCTTTAAATTTTATGAATTA
17254 TTCT
1 TTCT
17258 AATGTTACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 9 0.41
22 11 0.50
23 2 0.09
ACGTcount: A:0.23, C:0.09, G:0.04, T:0.64
Consensus pattern (21 bp):
TTCTTTAAATTTTATGAATTA
Found at i:17798 original size:19 final size:19
Alignment explanation
Indices: 17774--17811 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17764 CCTTTACACC
17774 AAGGCAATCCGACCTAAAG
1 AAGGCAATCCGACCTAAAG
17793 AAGGCAATCCGACCTAAAG
1 AAGGCAATCCGACCTAAAG
17812 GGTTCACAAC
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:0.42, C:0.26, G:0.21, T:0.11
Consensus pattern (19 bp):
AAGGCAATCCGACCTAAAG
Found at i:22205 original size:12 final size:11
Alignment explanation
Indices: 22190--22234 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 11
22180 TAAAACTCTT
22190 AAGAAATAAAAA
1 AAGAAA-AAAAA
*
22202 AAG-AGAAAAA
1 AAGAAAAAAAA
22212 AAGAGAAAAAAA
1 AAGA-AAAAAAA
22224 AAGAAAAAAAA
1 AAGAAAAAAAA
22235 GAAAAGGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 8 0.28
11 8 0.28
12 13 0.45
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.02
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:22212 original size:10 final size:10
Alignment explanation
Indices: 22197--22239 Score: 70
Period size: 10 Copynumber: 4.4 Consensus size: 10
22187 CTTAAGAAAT
22197 AAAAAAAGAG
1 AAAAAAAGAG
22207 AAAAAAAGAG
1 AAAAAAAGAG
*
22217 AAAAAAAAAG
1 AAAAAAAGAG
22227 AAAAAAA-AG
1 AAAAAAAGAG
22236 AAAA
1 AAAA
22240 GGAGAGGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
9 6 0.19
10 26 0.81
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:23362 original size:59 final size:59
Alignment explanation
Indices: 23263--24115 Score: 1177
Period size: 59 Copynumber: 14.4 Consensus size: 59
23253 GACCTATTGA
* * *
23263 TCGATTCACAACACTTCGAATCAGCAATGTCCCACCAGAGGGGTTAACATTTCCTTTTC
1 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGC
* *
23322 TCTATTCACAACACTTCGAATCAGCAACGCCCCACTAGAGGGGTTAACATTTCCTTTGC
1 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGC
*
23381 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTAC
1 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGC
* *
23440 TCGATTCATAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAGCATTTCCTTTGC
1 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGC
* ** *
23499 TCGATTCACAACACTTCGAATCAGGAATACGCCACCAGAGGGGTTAACATTTCCTTTGC
1 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGC
* * * * * * * *
23558 TCAATTCACAACGCTTCGAATCAGCAACACCCAACCAAAGAGATTAACATTTCCTTCGC
1 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGC
* * * *
23617 TCGATTCATAACACTTCGAATCAGCAATGCCCCACCAGAGGAGTTAACATTTCCTTCGC
1 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGC
* * ** *
23676 TCGATTCACAACACTTCGAATCAACAATGCTTCACCAGAGGGGTTAACATTTCCTTTTC
1 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGC
* * * *
23735 TTGATTCACAACACTTTGAATCAACAACGCCCCACCAGAGGGGTTAATATTTCCTATTGC
1 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCT-TTGC
23795 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGC
1 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGC
* * * *
23854 TCGATTCAAAACACTTTGAATCAACAATGCCCCACCA-AGGGGGTTAACATTTCCTATTGC
1 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGA-GGGGTTAACATTTCCT-TTGC
* * * *
23914 TCGATTCATAATACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAAGATTTCTTTTGC
1 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGC
** * * * *
23973 TAAATTCATAACACTTCGAATCAACGACGCCCCACCAGAGGGATTAACATTTCCTTTGC
1 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGC
* * * * *
24032 TCGATTCACAATACTTCGAATCAACAACACCCCACCAGAGGGGTTAATATTTCCTTTGT
1 TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGC
** *
24091 TCGATTCACAATGCTTTGAATCAGC
1 TCGATTCACAACACTTCGAATCAGC
24116 GACATATCAC
Statistics
Matches: 704, Mismatches: 86, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
58 1 0.00
59 598 0.85
60 104 0.15
61 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (59 bp):
TCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCCTTTGC
Found at i:24356 original size:23 final size:22
Alignment explanation
Indices: 24302--24360 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
24292 CAAACTCAGC
* *
24302 TAAACATAACCTAAAACCCTTTA
1 TAAA-ATAACCCAAAACCCCTTA
*
24325 CAAAA-AACCCAAAACCCCCTTA
1 TAAAATAACCCAAAA-CCCCTTA
24347 TAAAATAACCCAAA
1 TAAAATAACCCAAA
24361 TCTAACCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 8 0.27
22 11 0.37
23 11 0.37
ACGTcount: A:0.53, C:0.31, G:0.00, T:0.17
Consensus pattern (22 bp):
TAAAATAACCCAAAACCCCTTA
Found at i:25943 original size:6 final size:7
Alignment explanation
Indices: 25926--25967 Score: 57
Period size: 7 Copynumber: 5.6 Consensus size: 7
25916 GTTTTCACTG
25926 TTTTTTA
1 TTTTTTA
25933 TTTTTTA
1 TTTTTTA
25940 TTTTTTA
1 TTTTTTA
25947 TTATTGTTA
1 TT-TT-TTA
25956 TTTTATTA
1 TTTT-TTA
25964 TTTT
1 TTTT
25968 AATTATGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
7 16 0.50
8 11 0.34
9 5 0.16
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (7 bp):
TTTTTTA
Found at i:25979 original size:23 final size:22
Alignment explanation
Indices: 25928--25980 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
25918 TTTCACTGTT
*
25928 TTTTATTTTTTATTTTTTATTA
1 TTTTATTTTTTATTTTTAATTA
25950 TTGTTATTTTATTA-TTTTAATTA
1 TT-TTATTTT-TTATTTTTAATTA
25973 TGTTTATT
1 T-TTTATT
25981 AATTGTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 2 0.07
23 21 0.78
24 4 0.15
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTTATTTTTTATTTTTAATTA
Found at i:25981 original size:9 final size:8
Alignment explanation
Indices: 25926--25981 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 8
25916 GTTTTCACTG
25926 TTTT-TTA
1 TTTTATTA
25933 TTTT-TTA
1 TTTTATTA
25940 TTTT-TTA
1 TTTTATTA
*
25947 TTATTGTTA
1 TT-TTATTA
25956 TTTTATTA
1 TTTTATTA
25964 TTTTAATTA
1 TTTT-ATTA
25973 TGTTTATTA
1 T-TTTATTA
25982 ATTGTTTTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
7 16 0.36
8 11 0.25
9 14 0.32
10 3 0.07
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (8 bp):
TTTTATTA
Found at i:29260 original size:17 final size:18
Alignment explanation
Indices: 29240--29273 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29230 ATATTATTTT
29240 TTATTATT-TATTTTAAA
1 TTATTATTATATTTTAAA
*
29257 TTATTGTTATATTTTAA
1 TTATTATTATATTTTAA
29274 TAATAATAAA
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:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTATTATTATATTTTAAA
Found at i:38206 original size:15 final size:15
Alignment explanation
Indices: 38188--38221 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38178 GATGTTAAAT
38188 ATTTAT-ATATTTAA
1 ATTTATAATATTTAA
38202 CATTTATAATATTTAA
1 -ATTTATAATATTTAA
38218 ATTT
1 ATTT
38222 CAGACTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTATAATATTTAA
Found at i:39706 original size:16 final size:17
Alignment explanation
Indices: 39687--39724 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
39677 TCTGAAAATA
39687 CGGATATCCGAA-ATTT
1 CGGATATCCGAATATTT
*
39703 CGGATATCCGAATTTTT
1 CGGATATCCGAATATTT
39720 CGGAT
1 CGGAT
39725 CGGAAACGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (17 bp):
CGGATATCCGAATATTT
Found at i:39908 original size:20 final size:20
Alignment explanation
Indices: 39883--39939 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
39873 ATGATTGAGC
39883 CAAGGATGGGTCGAGTCGAG
1 CAAGGATGGGTCGAGTCGAG
39903 CAAGGATGGGTCGAGTCGAG
1 CAAGGATGGGTCGAGTCGAG
*
39923 CAAGGATGGATCGAGTC
1 CAAGGATGGGTCGAGTC
39940 TTGTTTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.26, C:0.16, G:0.42, T:0.16
Consensus pattern (20 bp):
CAAGGATGGGTCGAGTCGAG
Found at i:40501 original size:14 final size:16
Alignment explanation
Indices: 40462--40495 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
40452 TAAAATTTAT
40462 ATATATTTTATTAATA
1 ATATATTTTATTAATA
40478 ATATACTTTTATTAATA
1 ATATA-TTTTATTAATA
40495 A
1 A
40496 AATTTTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATTTTATTAATA
Found at i:42805 original size:21 final size:21
Alignment explanation
Indices: 42779--42831 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
42769 AAGCTTTAAT
42779 AATAGCCTTTTCAACATCTGC
1 AATAGCCTTTTCAACATCTGC
42800 AATAGCCTTTTCAACATCTGC
1 AATAGCCTTTTCAACATCTGC
42821 AATAGCCTTTT
1 AATAGCCTTTT
42832 TACAGCCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.36
Consensus pattern (21 bp):
AATAGCCTTTTCAACATCTGC
Found at i:51712 original size:2 final size:2
Alignment explanation
Indices: 51705--51729 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
51695 GCTCTTAATA
51705 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
51730 GCCTTTTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:55083 original size:14 final size:15
Alignment explanation
Indices: 55048--55091 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 15
55038 TTTGATACCA
55048 TGTAGAAAACAGACTG
1 TGTAGAAAACAGAC-G
*
55064 TGTAGAAAACATAC-
1 TGTAGAAAACAGACG
55078 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
55092 AAGTCTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 13 0.50
16 13 0.50
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (15 bp):
TGTAGAAAACAGACG
Found at i:59196 original size:14 final size:13
Alignment explanation
Indices: 59162--59197 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
59152 TTTTAATTTC
59162 TAAAAAATAGAAA
1 TAAAAAATAGAAA
59175 TAAAAAATAGAAA
1 TAAAAAATAGAAA
59188 TAAATAAATA
1 TAAA-AAATA
59198 ACTGTTTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (13 bp):
TAAAAAATAGAAA
Found at i:60283 original size:20 final size:20
Alignment explanation
Indices: 60260--60327 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
60250 GAATATGTAA
*
60260 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTATGACT
*
60280 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTATGACT
* *
60300 GTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTATGACT
*
60320 GTCGCAAC
1 ATCGCAAC
60328 ATTGAATTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTATGACT
Found at i:61377 original size:14 final size:13
Alignment explanation
Indices: 61358--61393 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
61348 AGAAAAAGAA
61358 GAAGAAGAATCCCC
1 GAAGAA-AATCCCC
*
61372 GAAGAAAGTCCCC
1 GAAGAAAATCCCC
61385 GAAGAAAAT
1 GAAGAAAAT
61394 GCACGGGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.08
Consensus pattern (13 bp):
GAAGAAAATCCCC
Done.