Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003513.1 Hibiscus syriacus cultivar Beakdansim tig00007425_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: 61946
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:5789 original size:15 final size:15
Alignment explanation
Indices: 5769--5871 Score: 50
Period size: 18 Copynumber: 6.5 Consensus size: 15
5759 TGGCTGTGGC
*
5769 TTCTTCTCCTCTTCT
1 TTCTTCTCCCCTTCT
5784 TTC-T-T-CCCTTCT
1 TTCTTCTCCCCTTCT
* * *
5796 TCCTTCTTGCCTTCTTCC
1 TTCTTC-T-CC-CCTTCT
5814 TTCTTCTCTCCCCCTTCT
1 TTCTT--CTC-CCCTTCT
5832 TTCTTCTCTCCCCCTTCT
1 TTC-T-TCT-CCCCTTCT
*
5850 TTATTCTCCCCTTCT
1 TTCTTCTCCCCTTCT
*
5865 TCCTTCT
1 TTCTTCT
5872 TTTCTCCCTC
Statistics
Matches: 66, Mismatches: 10, Indels: 24
0.66 0.10 0.24
Matches are distributed among these distances:
12 8 0.12
13 2 0.03
14 1 0.02
15 17 0.26
16 3 0.05
17 2 0.03
18 27 0.41
19 4 0.06
20 2 0.03
ACGTcount: A:0.01, C:0.45, G:0.01, T:0.53
Consensus pattern (15 bp):
TTCTTCTCCCCTTCT
Found at i:5838 original size:7 final size:7
Alignment explanation
Indices: 5768--5819 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
5758 CTGGCTGTGG
5768 CTTCTTC
1 CTTCTTC
*
5775 TCCTCTTC
1 -CTTCTTC
*
5783 TTTCTTCC
1 CTTCTT-C
5791 CTTCTTC
1 CTTCTTC
5798 CTTCTTGC
1 CTTCTT-C
5806 CTTCTTC
1 CTTCTTC
5813 CTTCTTC
1 CTTCTTC
5820 TCTCCCCCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
7 19 0.50
8 19 0.50
ACGTcount: A:0.00, C:0.42, G:0.02, T:0.56
Consensus pattern (7 bp):
CTTCTTC
Found at i:5883 original size:18 final size:18
Alignment explanation
Indices: 5808--5916 Score: 86
Period size: 18 Copynumber: 6.2 Consensus size: 18
5798 CTTCTTGCCT
*
5808 TCTTCCTTCTTCTCTCCC
1 TCTTCCTTCTTTTCTCCC
* * *
5826 CCTTCTTTCTTCTCTCCC
1 TCTTCCTTCTTTTCTCCC
* *
5844 CCTT-CTT-TATTCTCCCC
1 TCTTCCTTCTTTTCT-CCC
5861 TTCTTCCTTCTTTTCTCCC
1 -TCTTCCTTCTTTTCTCCC
*
5880 TC-T--TTCTTTTC-CACT
1 TCTTCCTTCTTTTCTC-CC
5895 TCTTCCTTCTTTTCTCCC
1 TCTTCCTTCTTTTCTCCC
5913 TCTT
1 TCTT
5917 TCTTTTCCCC
Statistics
Matches: 73, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
14 1 0.01
15 11 0.15
16 5 0.07
17 6 0.08
18 38 0.52
19 7 0.10
20 5 0.07
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTCCTTCTTTTCTCCC
Found at i:5884 original size:33 final size:33
Alignment explanation
Indices: 5772--5957 Score: 152
Period size: 33 Copynumber: 5.6 Consensus size: 33
5762 CTGTGGCTTC
*
5772 TTCT-CCTC-TTCTTTCTTCCCTTCTTCCTTCTT
1 TTCTCCCTCTTTC-TTCTCCCCTTCTTCCTTCTT
* *
5804 GCCTTCTTCCT-TCTTC-TCTCCCCCTTCTTTCTTC-T
1 ---TTCTCCCTCT-TTCTTCT-CCCCTTCTTCCTTCTT
* * *
5839 CTCCCCCTTCTTTATTCTCCCCTTCTTCCTTCTT
1 TTCTCCC-TCTTTCTTCTCCCCTTCTTCCTTCTT
* *
5873 TTCTCCCTCTTTCTTTTCCACTTCTTCCTTCTT
1 TTCTCCCTCTTTCTTCTCCCCTTCTTCCTTCTT
* *
5906 TTCTCCCTCTTTCTTTTCCCCTTTTTCCTT-TT
1 TTCTCCCTCTTTCTTCTCCCCTTCTTCCTTCTT
5938 TTGC-CTCCTCTTTCTTCTCC
1 TT-CTC-CCTCTTTCTTCTCC
5958 GGTTCCTTTG
Statistics
Matches: 126, Mismatches: 15, Indels: 22
0.77 0.09 0.13
Matches are distributed among these distances:
32 9 0.07
33 81 0.64
34 10 0.08
35 8 0.06
36 15 0.12
37 3 0.02
ACGTcount: A:0.01, C:0.42, G:0.01, T:0.55
Consensus pattern (33 bp):
TTCTCCCTCTTTCTTCTCCCCTTCTTCCTTCTT
Found at i:5886 original size:15 final size:14
Alignment explanation
Indices: 5868--5937 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 14
5858 CCCTTCTTCC
5868 TTCTTTTCTCCCTCT
1 TTCTTTTC-CCCTCT
*
5883 TTCTTTTCCACTTCTTCC
1 TTCTTTTCC-C--C-TCT
5901 TTCTTTTCTCCCTCT
1 TTCTTTTC-CCCTCT
*
5916 TTCTTTTCCCCTTT
1 TTCTTTTCCCCTCT
5930 TTCCTTTT
1 TT-CTTTT
5938 TTGCCTCCTC
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
14 8 0.17
15 24 0.52
16 1 0.02
17 1 0.02
18 11 0.24
19 1 0.02
ACGTcount: A:0.01, C:0.37, G:0.00, T:0.61
Consensus pattern (14 bp):
TTCTTTTCCCCTCT
Found at i:7089 original size:18 final size:18
Alignment explanation
Indices: 7066--7113 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
7056 AAATTATTCT
* *
7066 TATTATATATTTGTATAA
1 TATTATATATTTATAAAA
*
7084 TATTATA-AATTATAAAA
1 TATTATATATTTATAAAA
7101 TATTTATATATTT
1 TA-TTATATATTT
7114 TATTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.38
18 12 0.50
19 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TATTATATATTTATAAAA
Found at i:7203 original size:22 final size:21
Alignment explanation
Indices: 7164--7204 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
7154 ACAAAATTAA
**
7164 AAATATAAAAAATGTTTAATG
1 AAATATAAAAAAAATTTAATG
7185 AAATGATAAAAAAAATTTAA
1 AAAT-ATAAAAAAAATTTAA
7205 CCCCTGAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (21 bp):
AAATATAAAAAAAATTTAATG
Found at i:9728 original size:16 final size:17
Alignment explanation
Indices: 9695--9728 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
9685 TTTAATTCAT
9695 TTATATTCAAAATCAAA
1 TTATATTCAAAATCAAA
*
9712 TTATATT-AAACTCAAA
1 TTATATTCAAAATCAAA
9728 T
1 T
9729 GATGATAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (17 bp):
TTATATTCAAAATCAAA
Found at i:15580 original size:14 final size:14
Alignment explanation
Indices: 15561--15592 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
15551 TTTTCTATGA
15561 ATTTTTATATAAAT
1 ATTTTTATATAAAT
*
15575 ATTTTTATTTAAAT
1 ATTTTTATATAAAT
15589 ATTT
1 ATTT
15593 GGAATTCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTTTATATAAAT
Found at i:16732 original size:7 final size:7
Alignment explanation
Indices: 16667--16741 Score: 52
Period size: 7 Copynumber: 10.7 Consensus size: 7
16657 AAGAGGTTTT
16667 ATATTTA
1 ATATTTA
16674 AT-TTT-
1 ATATTTA
16679 ATATTATA
1 ATATT-TA
16687 GATA-TTA
1 -ATATTTA
16694 AT-TTTA
1 ATATTTA
16700 ATA-TTA
1 ATATTTA
*
16706 ATTTTTAA
1 ATATTT-A
*
16714 ATAAATTAA
1 AT--ATTTA
16723 ATATTTA
1 ATATTTA
16730 ATATTTA
1 ATATTTA
16737 ATATT
1 ATATT
16742 ATGTTATAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
5 2 0.04
6 17 0.31
7 23 0.43
8 4 0.07
9 6 0.11
10 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (7 bp):
ATATTTA
Found at i:16801 original size:62 final size:63
Alignment explanation
Indices: 16667--16825 Score: 259
Period size: 63 Copynumber: 2.5 Consensus size: 63
16657 AAGAGGTTTT
*
16667 ATATTTAATTTTATATTATAGATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTTA
1 ATATTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTTA
*
16730 ATATTTAATATTATGTTATAGATATTAATTTTAATATT-ATTTTTAAATAAATTAAATA-TTA
1 ATATTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTTA
*
16791 ATTTTTTAATATTATATTATAGATATTTAATTTTA
1 A-TATTTAATATTATATTATAGATA-TTAATTTTA
16826 TATCATATAA
Statistics
Matches: 90, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
61 4 0.04
62 41 0.46
63 45 0.50
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (63 bp):
ATATTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTTA
Found at i:16817 original size:83 final size:83
Alignment explanation
Indices: 16699--16853 Score: 190
Period size: 83 Copynumber: 1.8 Consensus size: 83
16689 TATTAATTTT
* * *
16699 AATATTAATTTTTAAATAAATTAAATATTTAATATTTAATATTATGTTATAGATATTAATTTTA-
1 AATATTAATTTTTAAAT-AATT-AATATTTAATATTTAATATTATATCATAGAAATT-ATTTTAT
16763 ATATTATTTTTAAATAAATTA
63 ATATTATTTTTAAATAAATTA
* * *
16784 AATATTAATTTTTTAAT-ATT-ATATTATAGATATTTAATTTTATATCATATAAATTATTTTATA
1 AATATTAATTTTTAAATAATTAATATT-TA-ATATTTAATATTATATCATAGAAATTATTTTATA
16847 TATTATT
64 TATTATT
16854 AAAATTTTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
81 5 0.08
82 8 0.13
83 32 0.52
85 16 0.26
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (83 bp):
AATATTAATTTTTAAATAATTAATATTTAATATTTAATATTATATCATAGAAATTATTTTATATA
TTATTTTTAAATAAATTA
Found at i:16880 original size:20 final size:19
Alignment explanation
Indices: 16820--16881 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
16810 TAGATATTTA
*
16820 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
16839 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
16857 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
16877 ATTTT
1 ATTTT
16882 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:17532 original size:31 final size:31
Alignment explanation
Indices: 17495--17554 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
17485 TAGTTATATG
* *
17495 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
17526 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
17555 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:20912 original size:143 final size:142
Alignment explanation
Indices: 20408--20935 Score: 1029
Period size: 142 Copynumber: 3.7 Consensus size: 142
20398 GCATGCTGAA
20408 TGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTGGGAGAAGTCCGG
1 TGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTGGGAGAAGTCCGG
20473 TCGACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTATTAACTTATCCTTTGTTTCCCCCCTC
66 TCGACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTATTAACTTATCCTTTGTTTCCCCCCTC
20538 TAGTATAGTGAG
131 TAGTATAGTGAG
20550 TGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTGGGAGAAGTCCGG
1 TGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTGGGAGAAGTCCGG
20615 TCGACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTATTAACTTATCCTTTGTTTCCCCCCTC
66 TCGACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTATTAACTTATCCTTTGTTTCCCCCCTC
20680 TAGTATAGTGAG
131 TAGTATAGTGAG
20692 TGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTGGGAGAAGTCCGG
1 TGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTGGGAGAAGTCCGG
20757 TCGACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTATTTAACTTATCCTTTGTTTCCCCCCT
66 TCGACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTA-TTAACTTATCCTTTGTTTCCCCCCT
*
20822 TTAGTATAGTGAG
130 CTAGTATAGTGAG
20835 TGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTGGGAGAAGTCCGG
1 TGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTGGGAGAAGTCCGG
*
20900 TCAACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTA
66 TCGACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTA
20936 CTATGGAGGT
Statistics
Matches: 383, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
142 246 0.64
143 137 0.36
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (142 bp):
TGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTGGGAGAAGTCCGG
TCGACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTATTAACTTATCCTTTGTTTCCCCCCTC
TAGTATAGTGAG
Found at i:20917 original size:285 final size:284
Alignment explanation
Indices: 20408--20935 Score: 1029
Period size: 285 Copynumber: 1.9 Consensus size: 284
20398 GCATGCTGAA
20408 TGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTGGGAGAAGTCCGG
1 TGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTGGGAGAAGTCCGG
20473 TCGACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTATTAACTTATCCTTTGTTTCCCCCCTC
66 TCGACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTATTAACTTATCCTTTGTTTCCCCCCTC
20538 TAGTATAGTGAGTGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTG
131 TAGTATAGTGAGTGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTG
*
20603 GGAGAAGTCCGGTCGACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTATTAACTTATCCTTT
196 GGAGAAGTCCGGTCAACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTATTAACTTATCCTTT
20668 GTTTCCCCCCTCTAGTATAGTGAG
261 GTTTCCCCCCTCTAGTATAGTGAG
20692 TGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTGGGAGAAGTCCGG
1 TGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTGGGAGAAGTCCGG
20757 TCGACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTATTTAACTTATCCTTTGTTTCCCCCCT
66 TCGACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTA-TTAACTTATCCTTTGTTTCCCCCCT
*
20822 TTAGTATAGTGAGTGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCT
130 CTAGTATAGTGAGTGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCT
20887 GGGAGAAGTCCGGTCAACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTA
195 GGGAGAAGTCCGGTCAACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTA
20936 CTATGGAGGT
Statistics
Matches: 241, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
284 104 0.43
285 137 0.57
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (284 bp):
TGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTGGGAGAAGTCCGG
TCGACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTATTAACTTATCCTTTGTTTCCCCCCTC
TAGTATAGTGAGTGAGAAGAGTGATGTCTATAGCTTCGGTATACTTATTATGGAGATTATTTCTG
GGAGAAGTCCGGTCAACTATAGCCGGCCTCAAGGAGAGGTTAGGCTTATTATTAACTTATCCTTT
GTTTCCCCCCTCTAGTATAGTGAG
Found at i:23162 original size:74 final size:75
Alignment explanation
Indices: 23038--23188 Score: 241
Period size: 74 Copynumber: 2.0 Consensus size: 75
23028 TAAAATATGG
* * *
23038 TTTTATCATATCTCAATCGATATGTTAACATCTAGTTTAAACAATTGTTAA-TTTTTTAACAAAA
1 TTTTATCATATCTCAATCCACATGTTAACATCTAGTTTAAACAATCGTTAATTTTTTTAACAAAA
*
23102 AAGTATGAGT
66 AAGTAGGAGT
* *
23112 TTTTATCATATCTCAATCCACATGTTAACATCTAGTTTAGACAATCGTTAATTTTTTTAACAGAA
1 TTTTATCATATCTCAATCCACATGTTAACATCTAGTTTAAACAATCGTTAATTTTTTTAACAAAA
23177 AAGTAGGAGT
66 AAGTAGGAGT
23187 TT
1 TT
23189 AGAATATACG
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
74 47 0.67
75 23 0.33
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (75 bp):
TTTTATCATATCTCAATCCACATGTTAACATCTAGTTTAAACAATCGTTAATTTTTTTAACAAAA
AAGTAGGAGT
Found at i:27097 original size:14 final size:15
Alignment explanation
Indices: 27078--27106 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
27068 TCTTCTAAAC
27078 AACCAAC-AATTTTT
1 AACCAACAAATTTTT
27092 AACCAACAAATTTTT
1 AACCAACAAATTTTT
27107 TTTTATAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (15 bp):
AACCAACAAATTTTT
Done.