Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003970.1 Hibiscus syriacus cultivar Beakdansim tig00008605_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: 88714
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:5570 original size:13 final size:13
Alignment explanation
Indices: 5545--5588 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
5535 AAAATTACAT
5545 ATTGTTATTCAAAC
1 ATTGTT-TTCAAAC
*
5559 ATTGTTTTCAAAA
1 ATTGTTTTCAAAC
**
5572 ATAATTTTCAAAC
1 ATTGTTTTCAAAC
5585 ATTG
1 ATTG
5589 CCCATTAGGA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (13 bp):
ATTGTTTTCAAAC
Found at i:7360 original size:12 final size:14
Alignment explanation
Indices: 7333--7367 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
7323 AGGGGGAGTA
7333 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
7347 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
7359 ATTTTCAAA
1 ATTTTCAAA
7368 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 16 0.80
14 1 0.05
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:15107 original size:24 final size:24
Alignment explanation
Indices: 15075--15122 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
15065 TTATCGCAAT
15075 GGAAACATTTTCCTTCCTTGCTAA
1 GGAAACATTTTCCTTCCTTGCTAA
15099 GGAAACATTTTCCTTCCTTGCTAA
1 GGAAACATTTTCCTTCCTTGCTAA
15123 CTCCCCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (24 bp):
GGAAACATTTTCCTTCCTTGCTAA
Found at i:15806 original size:14 final size:14
Alignment explanation
Indices: 15787--15824 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
15777 CCAATCAAGG
*
15787 AAGTTTATTCCATT
1 AAGTTTATCCCATT
15801 AAGTTTATCCCATT
1 AAGTTTATCCCATT
15815 AAGTTTATCC
1 AAGTTTATCC
15825 TTCTCAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (14 bp):
AAGTTTATCCCATT
Found at i:19472 original size:45 final size:45
Alignment explanation
Indices: 19404--19502 Score: 162
Period size: 45 Copynumber: 2.2 Consensus size: 45
19394 TAGAATGAAT
* *
19404 CCATAAATAAAATGCATAGCGGTGCATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
19449 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
**
19494 TTATAAATG
1 CCATAAATG
19503 TAATACCCCA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.22
Consensus pattern (45 bp):
CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
Found at i:34373 original size:15 final size:15
Alignment explanation
Indices: 34349--34379 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34339 TTTCCACGCC
34349 TCTTCATTTTAGGTA
1 TCTTCATTTTAGGTA
*
34364 TCTTCGTTTTAGGTA
1 TCTTCATTTTAGGTA
34379 T
1 T
34380 TTCTTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.55
Consensus pattern (15 bp):
TCTTCATTTTAGGTA
Found at i:35965 original size:22 final size:22
Alignment explanation
Indices: 35939--35989 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
35929 ACTGAAATGG
*
35939 AGTATCGGTACCATAGTATAGT
1 AGTATCGGTACAATAGTATAGT
35961 AGTATCGGTACAATAGTATAGT
1 AGTATCGGTACAATAGTATAGT
35983 AGTATCG
1 AGTATCG
35990 ATACTAAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (22 bp):
AGTATCGGTACAATAGTATAGT
Found at i:36573 original size:45 final size:45
Alignment explanation
Indices: 36509--36652 Score: 225
Period size: 45 Copynumber: 3.2 Consensus size: 45
36499 TAAAACGAAT
* * *
36509 CCATAAATAAAATGCATAACGGTGCATTAAAGGCATGAAAGGACG
1 CCATAAATGAAATGCATAACGGTACATTAAAGGCATGAAAGGATG
*
36554 CCATAAATGAAATGCATAACAGTACATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTACATTAAAGGCATGAAAGGATG
* *
36599 CCATAAATGAAATGCATAACGGTTCATTAAAGGCATGAAAAGATG
1 CCATAAATGAAATGCATAACGGTACATTAAAGGCATGAAAGGATG
*
36644 TCATAAATG
1 CCATAAATG
36653 TAATACCCCA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 91 1.00
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21
Consensus pattern (45 bp):
CCATAAATGAAATGCATAACGGTACATTAAAGGCATGAAAGGATG
Found at i:39289 original size:21 final size:23
Alignment explanation
Indices: 39263--39308 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
39253 TGATTGTTAC
39263 ATATGAT-GTTATCATGAAC-AT
1 ATATGATAGTTATCATGAACGAT
* *
39284 ATATGATATTTATTATGAACGAT
1 ATATGATAGTTATCATGAACGAT
39307 AT
1 AT
39309 TTTGAGTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 10 0.48
23 4 0.19
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (23 bp):
ATATGATAGTTATCATGAACGAT
Found at i:47484 original size:45 final size:45
Alignment explanation
Indices: 47435--47851 Score: 586
Period size: 45 Copynumber: 9.3 Consensus size: 45
47425 TAAAACGAAT
* *
47435 CCATAAATGAAATGCGTAACGGCGCATTAAAGGCATGAAATGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
* ** * *
47480 CCATAATTGAAATAAATAACGGTACATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
47525 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAA-GAATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATG-ATG
*
47570 CCATAAATGAAATGCATAGCGGTGCATTAAAGGCATGAAATGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
* * *
47615 CCAGAAATGAAATGCATAAAGGTACATTAAAGGCATGAAATGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
*
47660 CCATAAATGAGATGCATAACGGTGCATTAAAGGCATGAAA-GAATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATG-ATG
* * *
47705 CCATAAATGAAATACATAAAGGTGCATTAAAGGCATGAAGTGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
* * * *
47750 CAATAAATGAAATGCATAACGGTTCATTAAAGGTATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
* * * *
47795 CCATAAATGAAATGTATAACGGTGCATTAAGGGCATAAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
*
47840 CCTTAAATGAAA
1 CCATAAATGAAA
47852 ATAATGAATA
Statistics
Matches: 330, Mismatches: 38, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
44 2 0.01
45 326 0.99
46 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.22
Consensus pattern (45 bp):
CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
Found at i:47639 original size:135 final size:135
Alignment explanation
Indices: 47431--47851 Score: 646
Period size: 135 Copynumber: 3.1 Consensus size: 135
47421 ACTCTAAAAC
* * * **
47431 GAAT-CCATAAATGAAATGCGTAACGGCGCATTAAAGGCATGAAATGATGCCATAATTGAAATAA
1 GAATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGCCATAAATGAAATGC
47495 ATAACGGTACATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCA
66 ATAACGGTACATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCA
47560 TGAAA
131 TGAAA
* *
47565 GAATGCCATAAATGAAATGCATAGCGGTGCATTAAAGGCATGAAATGATGCCAGAAATGAAATGC
1 GAATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGCCATAAATGAAATGC
* * *
47630 ATAAAGGTACATTAAAGGCATGAAATGATGCCATAAATGAGATGCATAACGGTGCATTAAAGGCA
66 ATAACGGTACATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCA
47695 TGAAA
131 TGAAA
* * * *
47700 GAATGCCATAAATGAAATACATAAAGGTGCATTAAAGGCATGAAGTGATGCAATAAATGAAATGC
1 GAATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGCCATAAATGAAATGC
* * * *
47765 ATAACGGTTCATTAAAGGTATGAAAGGATGCCATAAATGAAATGTATAACGGTGCATTAAGGGCA
66 ATAACGGTACATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCA
*
47830 TAAAA
131 TGAAA
* *
47835 GGATGCCTTAAATGAAA
1 GAATGCCATAAATGAAA
47852 ATAATGAATA
Statistics
Matches: 260, Mismatches: 26, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
134 4 0.02
135 256 0.98
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.22
Consensus pattern (135 bp):
GAATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGCCATAAATGAAATGC
ATAACGGTACATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCA
TGAAA
Found at i:49481 original size:20 final size:20
Alignment explanation
Indices: 49456--49558 Score: 125
Period size: 20 Copynumber: 4.8 Consensus size: 20
49446 ATATATATGA
49456 CATCCTTTCATGCATTAATG
1 CATCCTTTCATGCATTAATG
49476 CATCCTTTCATGCATTAATG
1 CATCCTTTCATGCATTAATG
49496 CATCCTTTCATGCATTTTCAATCATGG
1 CATCCTTTCATGCA--TT--A--AT-G
*
49523 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTAATG
*
49543 CATCCTTTTATGCATT
1 CATCCTTTCATGCATT
49559 TTAAATTATG
Statistics
Matches: 73, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
20 49 0.67
21 2 0.03
22 2 0.03
23 1 0.01
24 1 0.01
25 2 0.03
26 2 0.03
27 14 0.19
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.42
Consensus pattern (20 bp):
CATCCTTTCATGCATTAATG
Found at i:49526 original size:47 final size:47
Alignment explanation
Indices: 49475--49569 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
49465 ATGCATTAAT
*
49475 GCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTCAATCATG
1 GCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTAAATCATG
* * *
49522 GCATCCTTTCATGCCTTAATGCATCCTTTTATGCATTTTAAATTATG
1 GCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTAAATCATG
49569 G
1 G
49570 ATTCGATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (47 bp):
GCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTAAATCATG
Found at i:50121 original size:95 final size:95
Alignment explanation
Indices: 49978--50157 Score: 254
Period size: 95 Copynumber: 1.9 Consensus size: 95
49968 TCCTACCCTA
* * * ** *
49978 GTATCGATACTTCTATACTATGGTACGGATACCCTCTTCTAGTATCGATACTGAAATTAGCTTCG
1 GTATCGATACTACTATACTATAGTACCGATACCCTCTTCTAGTATCGATACCAAAATTAGATTCG
*
50043 ATGTTGCCTGGTATCGATACCCTTACCATG
66 ATGTTGACTGGTATCGATACCCTTACCATG
* *
50073 GTATCGATACTACTATACTATAGTACCGATA-CCTCTTTCTGGTATCGATACCAAAATTATATTC
1 GTATCGATACTACTATACTATAGTACCGATACCCTC-TTCTAGTATCGATACCAAAATTAGATTC
*
50137 GATGTTTACTGGTATCGATAC
65 GATGTTGACTGGTATCGATAC
50158 TAAGTCCTCG
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
94 4 0.05
95 70 0.95
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (95 bp):
GTATCGATACTACTATACTATAGTACCGATACCCTCTTCTAGTATCGATACCAAAATTAGATTCG
ATGTTGACTGGTATCGATACCCTTACCATG
Found at i:55793 original size:21 final size:21
Alignment explanation
Indices: 55764--55812 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
55754 GCAGGAAATT
*
55764 ATGGCCTCGATGAAAGATTTC
1 ATGGCCTCGATAAAAGATTTC
*
55785 ATGGTCTCGATAAAAGATTTC
1 ATGGCCTCGATAAAAGATTTC
55806 ATGGCCT
1 ATGGCCT
55813 GCACTAAGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (21 bp):
ATGGCCTCGATAAAAGATTTC
Found at i:63784 original size:64 final size:64
Alignment explanation
Indices: 63710--63864 Score: 170
Period size: 65 Copynumber: 2.4 Consensus size: 64
63700 ACACCCTATT
* * *
63710 TCGAATGCATTTTGTGTACCAATGCACAG-CCATGCATCGATGAACTCTTG-ATTTTATTGAAAC
1 TCGAATGCATTTTGT-TACCGATGCACAGACCATGCATCGATGAACTCCTGTA-TATATTGAAAC
63773 A
64 A
* * * * * *
63774 TCGAATGCATTTTATATACTGATGCACAGACCATGCATTGATGCACTCCTGTATATGTTGCAACA
1 TCGAATGCATTTTGT-TACCGATGCACAGACCATGCATCGATGAACTCCTGTATATATTGAAACA
* *
63839 TCGAATGCAATTAGTTACCGATGCAC
1 TCGAATGCATTTTGTTACCGATGCAC
63865 CCCAAGTGTA
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
64 35 0.47
65 39 0.52
66 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (64 bp):
TCGAATGCATTTTGTTACCGATGCACAGACCATGCATCGATGAACTCCTGTATATATTGAAACA
Found at i:70108 original size:13 final size:13
Alignment explanation
Indices: 70083--70126 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
70073 AAAATTACAT
70083 ATTGTTATTCAAAC
1 ATTGTT-TTCAAAC
*
70097 ATTGTTTTCAAAA
1 ATTGTTTTCAAAC
**
70110 ATAATTTTCAAAC
1 ATTGTTTTCAAAC
70123 ATTG
1 ATTG
70127 CCCATTAGGA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (13 bp):
ATTGTTTTCAAAC
Found at i:71899 original size:12 final size:14
Alignment explanation
Indices: 71872--71906 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
71862 AGGGGGAGTA
71872 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
71886 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
71898 ATTTTCAAA
1 ATTTTCAAA
71907 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 16 0.80
14 1 0.05
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:79730 original size:24 final size:24
Alignment explanation
Indices: 79703--79750 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
79693 TTATCGCAAT
79703 GGAAACATTTTCCTTACTTGCTAA
1 GGAAACATTTTCCTTACTTGCTAA
*
79727 GGAAACATTTTCCTTCCTTGCTAA
1 GGAAACATTTTCCTTACTTGCTAA
79751 CTCCCCCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (24 bp):
GGAAACATTTTCCTTACTTGCTAA
Found at i:80435 original size:14 final size:14
Alignment explanation
Indices: 80416--80451 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
80406 CCAGTCAAGG
80416 AAGTTTATTCCATT
1 AAGTTTATTCCATT
80430 AAGTTTATTCCATT
1 AAGTTTATTCCATT
80444 AAGTTTAT
1 AAGTTTAT
80452 CCTTCTCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (14 bp):
AAGTTTATTCCATT
Found at i:84094 original size:45 final size:45
Alignment explanation
Indices: 84030--84128 Score: 162
Period size: 45 Copynumber: 2.2 Consensus size: 45
84020 TAGAACGAAT
* *
84030 CCATAAATAAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTACATTAAAGGCATGAAAGGATG
84075 CCATAAATGAAATGCATAACGGTACATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTACATTAAAGGCATGAAAGGATG
**
84120 TTATAAATG
1 CCATAAATG
84129 TAATACCCCA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAATGAAATGCATAACGGTACATTAAAGGCATGAAAGGATG
Done.