Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003261.1 Hibiscus syriacus cultivar Beakdansim tig00006855_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: 59572
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7562 original size:21 final size:23
Alignment explanation
Indices: 7537--7579 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
7527 TTATGCTACA
*
7537 ACAAATCAA-CTA-ACAAAAGAG
1 ACAAAGCAACCTATACAAAAGAG
7558 ACAAAGCAACCTATACAAAAGA
1 ACAAAGCAACCTATACAAAAGA
7580 ACCAAAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.60, C:0.21, G:0.09, T:0.09
Consensus pattern (23 bp):
ACAAAGCAACCTATACAAAAGAG
Found at i:8600 original size:12 final size:12
Alignment explanation
Indices: 8583--8608 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8573 ATTAATTAAT
8583 ACTAATCAAGTA
1 ACTAATCAAGTA
8595 ACTAATCAAGTA
1 ACTAATCAAGTA
8607 AC
1 AC
8609 AATATATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (12 bp):
ACTAATCAAGTA
Found at i:8643 original size:41 final size:43
Alignment explanation
Indices: 8598--8684 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
8588 TCAAGTAACT
*
8598 AATCAAGTAAC-A-ATATATAATATTATTAACAAACAATACCA
1 AATCAAGTAACAATATATATAATATTATTAACAAACAAGACCA
8639 AATCAAGTAACAATATATATAATATTATTAACAAACAAGACCA
1 AATCAAGTAACAATATATATAATATTATTAACAAACAAGACCA
8682 AAT
1 AAT
8685 GATAATTCGG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
41 11 0.26
42 1 0.02
43 31 0.72
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.26
Consensus pattern (43 bp):
AATCAAGTAACAATATATATAATATTATTAACAAACAAGACCA
Found at i:17707 original size:93 final size:92
Alignment explanation
Indices: 17528--18081 Score: 513
Period size: 93 Copynumber: 6.0 Consensus size: 92
17518 AACTCCGTCT
* * * * * *
17528 ATTAATGGATGAAAGCTTGAATAACGTTGACATGTTTTAACTAAACACTTTGATGTTTATGGAC-
1 ATTAATGGATG-AAGTTTGAATAGCGTTGAAATATCTTAACTAAACACTTTGATGTTTATAGACT
* **
17592 ATAAGATGTTATGTTATCCAAGTTGTTAC
65 A-AAGAGGTTAACTTATCCAAGTTGTTAC
* * *
17621 ATTAATGGATGTAAGTTTAAATAGCGTTGAAATATCTTAATTAAACATTTTGATGTTTATAGACT
1 ATTAATGGATG-AAGTTTGAATAGCGTTGAAATATCTTAACTAAACACTTTGATGTTTATAGACT
* *
17686 AAAGAGGTAAACTTATGCAAGTTGTTAC
65 AAAGAGGTTAACTTATCCAAGTTGTTAC
* * * * *
17714 GTTAATAGATAGAAATTTGAATAGCGTTGAAATATCTTAACTAAACACTTTAATGTTTATGGACT
1 ATTAATGGAT-GAAGTTTGAATAGCGTTGAAATATCTTAACTAAACACTTTGATGTTTATAGACT
*
17779 AAAGAGGTTAATTTATCCAAGTTGTTAC
65 AAAGAGGTTAACTTATCCAAGTTGTTAC
* * * ** * * * * *
17807 ATTAATGGATGAAACTTTGAATTGTGTTGATTTTTTTTTAACTAAATACTTTGATTTTTACAGAC
1 ATTAATGGATG-AAGTTTGAATAGCGTTGA-AATATCTTAACTAAACACTTTGATGTTTATAGAC
* * ** *
17872 TAAAGAGGCTAATTTATTTAAGTAGTTAC
64 TAAAGAGGTTAACTTATCCAAGTTGTTAC
* * ** *
17901 ATTAATGGATGAGAGTTTGAATAGCGTTGAAATGTCTTAATTAAGTACTTTGATGTTTACAGACT
1 ATTAATGGATGA-AGTTTGAATAGCGTTGAAATATCTTAACTAAACACTTTGATGTTTATAGACT
* * *
17966 GGAA-ATGTTTACTTATCCAAGTTGTTAC
65 -AAAGAGGTTAACTTATCCAAGTTGTTAC
* ** * * * * * *
17994 ATTAATGGATG--GATTGAATAATGTTAAAATGTCTTAACTAAATAATTTGATGTTTACAAACTA
1 ATTAATGGATGAAGTTTGAATAGCGTTGAAATATCTTAACTAAACACTTTGATGTTTATAGACTA
* * *
18057 AAAAGGTTAACTCATCCAAATTGTT
66 AAGAGGTTAACTTATCCAAGTTGTT
18082 GATGGAAGTT
Statistics
Matches: 379, Mismatches: 75, Indels: 17
0.80 0.16 0.04
Matches are distributed among these distances:
89 2 0.01
90 61 0.16
92 1 0.00
93 236 0.62
94 79 0.21
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.39
Consensus pattern (92 bp):
ATTAATGGATGAAGTTTGAATAGCGTTGAAATATCTTAACTAAACACTTTGATGTTTATAGACTA
AAGAGGTTAACTTATCCAAGTTGTTAC
Found at i:17984 original size:187 final size:185
Alignment explanation
Indices: 17528--18068 Score: 529
Period size: 187 Copynumber: 2.9 Consensus size: 185
17518 AACTCCGTCT
* * * * *
17528 ATTAATGGATGAAAGCTTGAATAACGTTGACATGTTTTAACTAAACACTTTGATGTTTATGGACA
1 ATTAATGGATGAGAGTTTGAATAGCGTTGAAATGTCTTAACTAAACACTTTGATGTTTATGGAC-
* * *
17593 TAAGATG-TTATGTTATCCAAGTTGTTACATTAATGGATGTAAGTTTAAATAGCGTTGAAATATC
65 TAAGATGTTTA-CTTATCCAAGTTGTTACATTAATGGATGAAACTTTAAATAGCGTTGAAATATC
* * * *
17657 TTAATTAAACATTTTGATGTTTATAGACTAAAGAGGTAAACTTATGCAAGTTGTTAC
129 TTAACTAAACACTTTGATGTTTACAGACTAAAGAGGTAAACTTATGCAAGTAGTTAC
* * * * *
17714 GTTAATAGAT-AGAAATTTGAATAGCGTTGAAATATCTTAACTAAACACTTTAATGTTTATGGAC
1 ATTAATGGATGAG-AGTTTGAATAGCGTTGAAATGTCTTAACTAAACACTTTGATGTTTATGGAC
* * * * * * ** *
17778 TAAAGAGGTTAATTTATCCAAGTTGTTACATTAATGGATGAAACTTTGAATTGTGTTGATTTTTT
65 T-AAGATGTTTACTTATCCAAGTTGTTACATTAATGGATGAAACTTTAAATAGCGTTGA-AATAT
* * * * **
17843 TTTAACTAAATACTTTGATTTTTACAGACTAAAGAGGCT-AATTTATTTAAGTAGTTAC
128 CTTAACTAAACACTTTGATGTTTACAGACTAAAGAGG-TAAACTTATGCAAGTAGTTAC
* ** **
17901 ATTAATGGATGAGAGTTTGAATAGCGTTGAAATGTCTTAATTAAGTACTTTGATGTTTACAGACT
1 ATTAATGGATGAGAGTTTGAATAGCGTTGAAATGTCTTAACTAAACACTTTGATGTTTATGGACT
* * ** * *
17966 GGAA-ATGTTTACTTATCCAAGTTGTTACATTAATGGATG-GA--TTGAATAATGTTAAAATGTC
66 --AAGATGTTTACTTATCCAAGTTGTTACATTAATGGATGAAACTTTAAATAGCGTTGAAATATC
* * * * *
18027 TTAACTAAATAATTTGATGTTTACAAACTAAAAAGGTTAACT
129 TTAACTAAACACTTTGATGTTTACAGACTAAAGAGGTAAACT
18069 CATCCAAATT
Statistics
Matches: 289, Mismatches: 58, Indels: 19
0.79 0.16 0.05
Matches are distributed among these distances:
182 1 0.00
183 37 0.13
184 11 0.04
185 2 0.01
186 99 0.34
187 134 0.46
188 5 0.02
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.39
Consensus pattern (185 bp):
ATTAATGGATGAGAGTTTGAATAGCGTTGAAATGTCTTAACTAAACACTTTGATGTTTATGGACT
AAGATGTTTACTTATCCAAGTTGTTACATTAATGGATGAAACTTTAAATAGCGTTGAAATATCTT
AACTAAACACTTTGATGTTTACAGACTAAAGAGGTAAACTTATGCAAGTAGTTAC
Found at i:19561 original size:16 final size:17
Alignment explanation
Indices: 19540--19574 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
19530 AACCTACTTA
19540 CAAAGAAAATCAAA-AT
1 CAAAGAAAATCAAAGAT
19556 CAAAGAAAATCAAAGAT
1 CAAAGAAAATCAAAGAT
19573 CA
1 CA
19575 CATATTTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.66, C:0.14, G:0.09, T:0.11
Consensus pattern (17 bp):
CAAAGAAAATCAAAGAT
Found at i:21139 original size:29 final size:29
Alignment explanation
Indices: 21090--21278 Score: 181
Period size: 29 Copynumber: 6.6 Consensus size: 29
21080 TAGAGGATCC
*
21090 CATGCAGAATCAGGACTAGGATATAATCT
1 CATGCAGAATCAGGACGAGGATATAATCT
* * *
21119 CATGTAGAATCAGAACGAGGATATATTCT
1 CATGCAGAATCAGGACGAGGATATAATCT
* * * *
21148 CATGCAAAATTAGGTCGGGGATATAAT-T
1 CATGCAGAATCAGGACGAGGATATAATCT
*
21176 CTATGCAGAATCAGGATGA-GAGTATAATCT
1 C-ATGCAGAATCAGGACGAGGA-TATAATCT
* *
21206 CATGCAGAATCTA-GATGAGAATATAATAC-
1 CATGCAGAATC-AGGACGAGGATATAAT-CT
* *
21235 CATTCAGAATCAGGATG-GGATATAATCT
1 CATGCAGAATCAGGACGAGGATATAATCT
*
21263 CATGCAGAATTAGGAC
1 CATGCAGAATCAGGAC
21279 ATAGATTATG
Statistics
Matches: 130, Mismatches: 22, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
27 1 0.01
28 26 0.20
29 98 0.75
30 5 0.04
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (29 bp):
CATGCAGAATCAGGACGAGGATATAATCT
Found at i:23806 original size:9 final size:11
Alignment explanation
Indices: 23784--23820 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
23774 AACAGAAATT
23784 TATAAATAATA
1 TATAAATAATA
23795 TATAAATAATA
1 TATAAATAATA
*
23806 TATAAATATTA
1 TATAAATAATA
23817 TATA
1 TATA
23821 TTTAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TATAAATAATA
Found at i:23826 original size:22 final size:22
Alignment explanation
Indices: 23784--23838 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
23774 AACAGAAATT
*
23784 TATAAATAATATATAAATAATA
1 TATAAATATTATATAAATAATA
**
23806 TATAAATATTATATATTTAATA
1 TATAAATATTATATAAATAATA
*
23828 T-TTAATATTAT
1 TATAAATATTAT
23839 CAGTTAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATAAATATTATATAAATAATA
Found at i:24202 original size:19 final size:19
Alignment explanation
Indices: 24180--24222 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
24170 ATATTAAAAC
24180 TAAAACAA-AATATAATCTA
1 TAAAACAATAATATAATC-A
* *
24199 TAAAATAATAATTTAATCA
1 TAAAACAATAATATAATCA
24218 TAAAA
1 TAAAA
24223 ATAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAAACAATAATATAATCA
Found at i:37454 original size:2 final size:2
Alignment explanation
Indices: 37449--37482 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
37439 TGTGTGTGTG
*
37449 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37483 CACACACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:43451 original size:22 final size:22
Alignment explanation
Indices: 43408--43451 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
43398 AAAAGCCGAT
**
43408 AAACCGAACCGAACCGTTAAAA
1 AAACCGAACCGAACCGAAAAAA
*
43430 AAACCGAACTGAACCGAAAAAA
1 AAACCGAACCGAACCGAAAAAA
43452 CTAGTTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.25, G:0.14, T:0.07
Consensus pattern (22 bp):
AAACCGAACCGAACCGAAAAAA
Found at i:44123 original size:15 final size:17
Alignment explanation
Indices: 44087--44122 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
44077 ACAATCAAAC
44087 TTTTATTTGATAATATT
1 TTTTATTTGATAATATT
*
44104 TTTTATTTTA-AATATT
1 TTTTATTTGATAATATT
44120 TTT
1 TTT
44123 AAACTTCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTATTTGATAATATT
Found at i:49010 original size:6 final size:6
Alignment explanation
Indices: 48999--49037 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
48989 ATACTACTAC
48999 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAG
1 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAG
49038 CAAAAGCCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:49043 original size:18 final size:18
Alignment explanation
Indices: 49004--49043 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
48994 ACTACAAGGG
**
49004 AAAGGGAAAGGGAAAGGG
1 AAAGGGAAAGGGAAAGCA
49022 AAAGGGAAAGGGAAAGCA
1 AAAGGGAAAGGGAAAGCA
49040 AAAG
1 AAAG
49044 CCAAAGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.03, G:0.42, T:0.00
Consensus pattern (18 bp):
AAAGGGAAAGGGAAAGCA
Found at i:54828 original size:3 final size:3
Alignment explanation
Indices: 54813--54844 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
54803 ATGATTGGAG
*
54813 TGA TGA AGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
54845 CACCACCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:56840 original size:12 final size:11
Alignment explanation
Indices: 56818--56851 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
56808 ACTCGATGAA
56818 AAATAAAAAAT
1 AAATAAAAAAT
*
56829 AACATGAAAAAT
1 AA-ATAAAAAAT
56841 AAATAAAAAAT
1 AAATAAAAAAT
56852 CATATCCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (11 bp):
AAATAAAAAAT
Done.