Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008780.1 Hibiscus syriacus cultivar Beakdansim tig00111905_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: 57994
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4209 original size:102 final size:103
Alignment explanation
Indices: 4053--4239 Score: 317
Period size: 102 Copynumber: 1.8 Consensus size: 103
4043 ATTAAGACAG
4053 AAGTACTTATGCATAAACTACTTAACAACAATACATTATAATTTAGAAACATTAAAGTACTTATG
1 AAGTACTTATGCATAAACTACTT-ACAACAATACATTATAATTTAGAAACATTAAAGTACTTATG
4118 CATAAACAGTCTTCACCATACATATATTTAGAAACATTA
65 CATAAACAGTCTTCACCATACATATATTTAGAAACATTA
*
4157 AAGTACTTATGCATAAAC-AGTCTT-CAAC-ATACATTATAATTTAGAAATATTAAAGTACTTAT
1 AAGTACTTATGCATAAACTA--CTTACAACAATACATTATAATTTAGAAACATTAAAGTACTTAT
4219 GCATAAACAGTCTTCACCATA
64 GCATAAACAGTCTTCACCATA
4240 TTGTTCAGTA
Statistics
Matches: 80, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
102 54 0.68
103 5 0.06
104 18 0.22
105 3 0.04
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (103 bp):
AAGTACTTATGCATAAACTACTTACAACAATACATTATAATTTAGAAACATTAAAGTACTTATGC
ATAAACAGTCTTCACCATACATATATTTAGAAACATTA
Found at i:4221 original size:52 final size:52
Alignment explanation
Indices: 4053--4239 Score: 283
Period size: 52 Copynumber: 3.6 Consensus size: 52
4043 ATTAAGACAG
4053 AAGTACTTATGCATAAAC--TACTTAACAACAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAACAGT-CTT--CAAC-ATACATTATAATTTAGAAACATTA
*
4107 AAGTACTTATGCATAAACAGTCTTCACCATACA-TAT-ATTTAGAAACATTA
1 AAGTACTTATGCATAAACAGTCTTCAACATACATTATAATTTAGAAACATTA
*
4157 AAGTACTTATGCATAAACAGTCTTCAACATACATTATAATTTAGAAATATTA
1 AAGTACTTATGCATAAACAGTCTTCAACATACATTATAATTTAGAAACATTA
*
4209 AAGTACTTATGCATAAACAGTCTTCACCATA
1 AAGTACTTATGCATAAACAGTCTTCAACATA
4240 TTGTTCAGTA
Statistics
Matches: 125, Mismatches: 4, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
50 46 0.37
51 6 0.05
52 48 0.38
53 3 0.02
54 18 0.14
55 3 0.02
56 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (52 bp):
AAGTACTTATGCATAAACAGTCTTCAACATACATTATAATTTAGAAACATTA
Found at i:7676 original size:15 final size:15
Alignment explanation
Indices: 7656--7689 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
7646 TAAAGATGTC
7656 ACATCAACTTTACAA
1 ACATCAACTTTACAA
7671 ACATCAACTTTACAA
1 ACATCAACTTTACAA
7686 ACAT
1 ACAT
7690 TCACTGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
ACATCAACTTTACAA
Found at i:8445 original size:24 final size:25
Alignment explanation
Indices: 8399--8453 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
8389 CAGAATTTTC
* *
8399 TTAT-TTTATTCTCATTTTCCATTT
1 TTATATTTATTCACATATTCCATTT
8423 TTATATTTATTCACATATT-CATTT
1 TTATATTTATTCACATATTCCATTT
*
8447 TCATATT
1 TTATATT
8454 CCATGTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.62
Consensus pattern (25 bp):
TTATATTTATTCACATATTCCATTT
Found at i:8590 original size:19 final size:19
Alignment explanation
Indices: 8507--8602 Score: 111
Period size: 19 Copynumber: 5.1 Consensus size: 19
8497 AGAATCGGAA
* *
8507 CTTATTTCCAGATTCATAA
1 CTTATTTTCAGATTCATAG
* *
8526 CTTATTTCCAGACTCATAG
1 CTTATTTTCAGATTCATAG
* *
8545 CTTACTGTCAGATTCATAG
1 CTTATTTTCAGATTCATAG
*
8564 CTTATTTTCAAATTCATAG
1 CTTATTTTCAGATTCATAG
* *
8583 CTTATTTTTAAATTCATAG
1 CTTATTTTCAGATTCATAG
8602 C
1 C
8603 CCAATGCATA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (19 bp):
CTTATTTTCAGATTCATAG
Found at i:11496 original size:3 final size:3
Alignment explanation
Indices: 11480--11529 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
11470 ACATATTAAA
11480 AAT AAT AA- ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11525 AAT AA
1 AAT AA
11530 CATCCGGATG
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 1 0.02
3 43 0.96
4 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11928 original size:20 final size:20
Alignment explanation
Indices: 11905--11967 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
11895 CTTGAGAGAG
11905 AATTGCCTCGAGTGAGGCAA
1 AATTGCCTCGAGTGAGGCAA
* ** *
11925 AATTTTCCT--TTTGAGAG-AG
1 AA-TTGCCTCGAGTGAG-GCAA
11944 AATTGCCTCGAGTGAGGCAA
1 AATTGCCTCGAGTGAGGCAA
11964 AATT
1 AATT
11968 TGTTTAAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
18 5 0.17
19 8 0.27
20 12 0.40
21 5 0.17
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (20 bp):
AATTGCCTCGAGTGAGGCAA
Found at i:11939 original size:39 final size:39
Alignment explanation
Indices: 11884--11968 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
11874 TAAGAGATAA
*
11884 AAAAATTTCCTCTTGAGAGAGAATTGCCTCGAGTGAGGC
1 AAAATTTTCCTCTTGAGAGAGAATTGCCTCGAGTGAGGC
*
11923 AAAATTTTCCTTTTGAGAGAGAATTGCCTCGAGTGAGGC
1 AAAATTTTCCTCTTGAGAGAGAATTGCCTCGAGTGAGGC
11962 AAAATTT
1 AAAATTT
11969 GTTTAAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (39 bp):
AAAATTTTCCTCTTGAGAGAGAATTGCCTCGAGTGAGGC
Found at i:13180 original size:16 final size:16
Alignment explanation
Indices: 13141--13181 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
13131 GATTTGGTTG
*
13141 CAGAAATGA-TGATGA
1 CAGAAATGACTAATGA
*
13156 CA-CAATGACTAATGA
1 CAGAAATGACTAATGA
13171 CAGAAATGACT
1 CAGAAATGACT
13182 TCACCGACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 5 0.24
15 9 0.43
16 7 0.33
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (16 bp):
CAGAAATGACTAATGA
Found at i:14932 original size:30 final size:30
Alignment explanation
Indices: 14888--14953 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
14878 AAAACCAGTA
* *
14888 GAACCGACTGAAAACCGATAAAACCGGGGT
1 GAACCGACTAAAAACCGACAAAACCGGGGT
* **
14918 GAACCGGCTAAAAACCGACAAAACCGGTTT
1 GAACCGACTAAAAACCGACAAAACCGGGGT
14948 GAACCG
1 GAACCG
14954 CCGGTTCACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.26, G:0.24, T:0.11
Consensus pattern (30 bp):
GAACCGACTAAAAACCGACAAAACCGGGGT
Found at i:16314 original size:12 final size:12
Alignment explanation
Indices: 16299--16323 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16289 ATATATCTGA
16299 TAAAATATTATT
1 TAAAATATTATT
16311 TAAAATATTATT
1 TAAAATATTATT
16323 T
1 T
16324 TTTTATCAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:24759 original size:97 final size:97
Alignment explanation
Indices: 24593--24787 Score: 390
Period size: 97 Copynumber: 2.0 Consensus size: 97
24583 TTATTAAAAA
24593 TCTGTCTTTTATTTACTTCAGTTTGACTTAACCAATCTTGATATTGTTAACGGGTTGCTAAATAT
1 TCTGTCTTTTATTTACTTCAGTTTGACTTAACCAATCTTGATATTGTTAACGGGTTGCTAAATAT
24658 TTATTTTTCTTTCCTTCCAGAATTTCTGAATG
66 TTATTTTTCTTTCCTTCCAGAATTTCTGAATG
24690 TCTGTCTTTTATTTACTTCAGTTTGACTTAACCAATCTTGATATTGTTAACGGGTTGCTAAATAT
1 TCTGTCTTTTATTTACTTCAGTTTGACTTAACCAATCTTGATATTGTTAACGGGTTGCTAAATAT
24755 TTATTTTTCTTTCCTTCCAGAATTTCTGAATG
66 TTATTTTTCTTTCCTTCCAGAATTTCTGAATG
24787 T
1 T
24788 AGATGATGAT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.49
Consensus pattern (97 bp):
TCTGTCTTTTATTTACTTCAGTTTGACTTAACCAATCTTGATATTGTTAACGGGTTGCTAAATAT
TTATTTTTCTTTCCTTCCAGAATTTCTGAATG
Found at i:32636 original size:24 final size:24
Alignment explanation
Indices: 32607--32656 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
32597 TGGTGGTTGA
*
32607 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
32631 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
32655 TT
1 TT
32657 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:34279 original size:19 final size:20
Alignment explanation
Indices: 34257--34300 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
34247 GAGAAAAGGT
34257 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
34276 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
34296 AAAAG
1 AAAAG
34301 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:41180 original size:24 final size:24
Alignment explanation
Indices: 41136--41185 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
41126 ATAAAGAACC
*
41136 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
41160 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
41184 AA
1 AA
41186 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:44224 original size:31 final size:29
Alignment explanation
Indices: 44156--44225 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
44146 AATATTATTT
*
44156 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
44186 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
44219 TTATATT
1 TTATATT
44226 AATTATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:44459 original size:28 final size:25
Alignment explanation
Indices: 44404--44473 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 25
44394 TTGATTATTT
*
44404 TATTATAATATTAAAAATATAATTA
1 TATTATAATATTAATAATATAATTA
*
44429 TATTATAAATATTAATAATATATTTAAA
1 TATTAT-AATATTAATAATATAATT--A
*
44457 TATTTTAATAATTAATA
1 TATTATAAT-ATTAATA
44474 TTTTGATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
25 6 0.16
26 16 0.42
27 3 0.08
28 13 0.34
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TATTATAATATTAATAATATAATTA
Found at i:44468 original size:21 final size:20
Alignment explanation
Indices: 44411--44460 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 20
44401 TTTTATTATA
*
44411 ATATTAAAAATA-TAAT--T
1 ATATTATAAATATTAATAAT
44428 ATATTATAAATATTAATAAT
1 ATATTATAAATATTAATAAT
44448 ATATT-TAAATATT
1 ATATTATAAATATT
44461 TTAATAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 11 0.38
18 4 0.14
19 8 0.28
20 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATTATAAATATTAATAAT
Found at i:44730 original size:42 final size:41
Alignment explanation
Indices: 44671--44760 Score: 137
Period size: 41 Copynumber: 2.2 Consensus size: 41
44661 TTATTTCAAC
*
44671 CAAACACTGAAATACATTTTCCGAAAAGCGAATTACGTGAAA
1 CAAACACAGAAATACATTTT-CGAAAAGCGAATTACGTGAAA
*
44713 CAAACACAAGAAA-ACATTTTCGGAAAGCGAATTACGTGAAA
1 CAAACAC-AGAAATACATTTTCGAAAAGCGAATTACGTGAAA
44754 CAAACAC
1 CAAACAC
44761 GAGATTTTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 27 0.60
42 14 0.31
43 4 0.09
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (41 bp):
CAAACACAGAAATACATTTTCGAAAAGCGAATTACGTGAAA
Done.