Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000514.1 Hibiscus syriacus cultivar Beakdansim tig00000980_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: 55613
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1535 original size:24 final size:26
Alignment explanation
Indices: 1499--1547 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
1489 TGTTTTCAAA
*
1499 TTTTTATTAAATA-TTTTCAAAATTC
1 TTTTAATTAAATATTTTTCAAAATTC
1524 TTTTAATT-AATATTTTTCAAAATT
1 TTTTAATTAAATATTTTTCAAAATT
1548 TTGAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTTAATTAAATATTTTTCAAAATTC
Found at i:4256 original size:83 final size:83
Alignment explanation
Indices: 4102--4282 Score: 251
Period size: 83 Copynumber: 2.2 Consensus size: 83
4092 ATAGCTAGAT
* * *
4102 TTCCTC-A-ACGAAGGAACAATGTCGTCAACCGATCATATCTTCTCAACACGAAGGAGCAGTGTC
1 TTCCTCAACACGAAGGAACAATGTCGTAAACCGACCATATCTCCTCAACACGAAGGAGCAGTGTC
* *
4165 ATCTTCAGACAATCAGAC
66 ATCCTCAGACAACCAGAC
* *
4183 TTCCTCAACACGAAGGAACAATGTTGTAAACCGACCATATCTCCTCAATACGAAGGAGCAGT-TC
1 TTCCTCAACACGAAGGAACAATGTCGTAAACCGACCATATCTCCTCAACACGAAGGAGCAGTGT-
*
4247 CATCCTCAGACAACCATAC
65 CATCCTCAGACAACCAGAC
*
4266 TTCCTCAACAAGAAGGA
1 TTCCTCAACACGAAGGA
4283 GTAATGTCAT
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
81 6 0.07
82 2 0.02
83 80 0.91
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (83 bp):
TTCCTCAACACGAAGGAACAATGTCGTAAACCGACCATATCTCCTCAACACGAAGGAGCAGTGTC
ATCCTCAGACAACCAGAC
Found at i:5839 original size:28 final size:30
Alignment explanation
Indices: 5775--5849 Score: 91
Period size: 28 Copynumber: 2.5 Consensus size: 30
5765 AGTCACTAGC
* *
5775 TTACTAACATTCTAACTTTTATTATTTGTTC
1 TTACTAACATACTAAC-TTTATTATTTGTTA
* *
5806 CTACTAACATACTAAC-TTGTT-TTTGTTA
1 TTACTAACATACTAACTTTATTATTTGTTA
5834 TTACTAACATACTAAC
1 TTACTAACATACTAAC
5850 ACTTTATTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 21 0.54
29 4 0.10
31 14 0.36
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.47
Consensus pattern (30 bp):
TTACTAACATACTAACTTTATTATTTGTTA
Found at i:6588 original size:21 final size:21
Alignment explanation
Indices: 6572--6613 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6562 CCATTTTGTT
6572 TTATTATATTATTATTTTATC
1 TTATTATATTATTATTTTATC
* *
6593 TTGTTATATTTTTATTATTAT
1 TTATTATATTATTATT-TTAT
6614 ATTTATCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (21 bp):
TTATTATATTATTATTTTATC
Found at i:7074 original size:23 final size:23
Alignment explanation
Indices: 7013--7101 Score: 106
Period size: 23 Copynumber: 3.7 Consensus size: 23
7003 AAAGTTGTTT
7013 ATTTATTCTATAAAAAATAAATTAA
1 ATTTATTCTAT--AAAATAAATTAA
* *
7038 ATATATATTTTATAGAATAAATTAA
1 AT-T-TATTCTATAAAATAAATTAA
* *
7063 ATTTATTCTATAAAATATATTTA
1 ATTTATTCTATAAAATAAATTAA
7086 ATTTATTCTATAAAAT
1 ATTTATTCTATAAAAT
7102 GGTGTTTTAC
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
23 32 0.57
24 1 0.02
25 15 0.27
26 1 0.02
27 7 0.12
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (23 bp):
ATTTATTCTATAAAATAAATTAA
Found at i:7359 original size:21 final size:23
Alignment explanation
Indices: 7329--7378 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
7319 GAAGAGCCCA
*
7329 AAAATGTATA-TT-TTATTCTAT
1 AAAATATATATTTATTATTCTAT
7350 AAAATATATATTTAATTATTCTAT
1 AAAATATATATTT-ATTATTCTAT
7374 AAAAT
1 AAAAT
7379 GAATTTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 9 0.36
22 2 0.08
24 14 0.56
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (23 bp):
AAAATATATATTTATTATTCTAT
Found at i:16217 original size:20 final size:20
Alignment explanation
Indices: 16171--16211 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
16161 TACCAGAAGT
* *
16171 GATTCTTCACCAAGGGTCGTG
1 GATT-TTCACCAAAGGTCATG
16192 GATTTTCACCAAAGGTCATG
1 GATTTTCACCAAAGGTCATG
16212 ACTTTTTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
GATTTTCACCAAAGGTCATG
Found at i:22000 original size:44 final size:44
Alignment explanation
Indices: 21944--22164 Score: 354
Period size: 44 Copynumber: 5.0 Consensus size: 44
21934 ATACCATAAG
*
21944 TGGCACTTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* ** *
21988 TGACATTTTTCTGCCAATAATGCACCGTTATGTATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
22032 TGGCACATTTCTGCCAATAATGCACCGTTATGTATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
22076 TGGCACATTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
22120 TGGCACCTTTCTGCCAATAATGCACCGTTATGCAGTTTT-ATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCA-TTTTCATTTA
22164 T
1 T
22165 TTCGGTAATA
Statistics
Matches: 166, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
44 162 0.98
45 4 0.02
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.41
Consensus pattern (44 bp):
TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:22212 original size:4 final size:4
Alignment explanation
Indices: 22203--22250 Score: 96
Period size: 4 Copynumber: 12.0 Consensus size: 4
22193 CATTAACATC
22203 CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT
1 CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT
22251 TTAGAGCAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
CATT
Found at i:25540 original size:19 final size:19
Alignment explanation
Indices: 25512--25563 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
25502 TGTTACTATT
25512 CTTT-TTGACATTTCAAAA
1 CTTTCTTGACATTTCAAAA
25530 CTTTCTTGACATTTCAAAA
1 CTTTCTTGACATTTCAAAA
*
25549 CTTTCTTGGCATTTC
1 CTTTCTTGACATTTC
25564 TCCATCCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 4 0.12
19 28 0.88
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (19 bp):
CTTTCTTGACATTTCAAAA
Found at i:28888 original size:44 final size:42
Alignment explanation
Indices: 28832--29134 Score: 311
Period size: 44 Copynumber: 6.9 Consensus size: 42
28822 TGAGTGGTAC
*
28832 CTTTCTTCCAATAATGCACCGTTATGTATTTTCATTTATGGCA
1 CTTTCTT-CAATAATGCACCGTTATGCATTTTCATTTATGGCA
* * * * *
28875 TCTTTCTATCAATAATTCACCATTTTTCATTTTCATTTATGACA
1 -CTTTCT-TCAATAATGCACCGTTATGCATTTTCATTTATGGCA
* * *
28919 CATTTCTGCCAATAATG-ACTGTTATGCATTTTCATTTATGACA
1 C-TTTCT-TCAATAATGCACCGTTATGCATTTTCATTTATGGCA
* * *
28962 CCTTTCTACCAATAATGCACCATTATGCATTTTTTATTTATGGCA
1 -CTTTCT-TCAATAATGCACCGTTATGCA-TTTTCATTTATGGCA
* *
29007 CATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGAA
1 C-TTTCT-TCAATAATGCACCGTTATGCATTTTCATTTATGGCA
*
29051 CCTTTCTTCCAATAATGCACCGTTATGAATTTTCATTTATGGCA
1 -CTTTCTT-CAATAATGCACCGTTATGCATTTTCATTTATGGCA
* * *
29095 CATTTCTTCCAATAATGCACCATTATGTATTTTTATTTAT
1 C-TTTCTT-CAATAATGCACCGTTATGCATTTTCATTTAT
29135 TTCGGTAACA
Statistics
Matches: 222, Mismatches: 28, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
43 38 0.17
44 144 0.65
45 40 0.18
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.44
Consensus pattern (42 bp):
CTTTCTTCAATAATGCACCGTTATGCATTTTCATTTATGGCA
Found at i:29021 original size:88 final size:88
Alignment explanation
Indices: 28833--29134 Score: 410
Period size: 88 Copynumber: 3.4 Consensus size: 88
28823 GAGTGGTACC
* * * * * *
28833 TTTCTTCCAATAATGCACCGTTATGTATTTTCATTTATGGCATCTTTCTATCAATAATTCACCAT
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGACACCTTTCTACCAATAATGCACCAT
* * *
28898 TTTTCATTTTCATTTATGACACA
66 TATGCATTTTCATTTATGGCACA
*
28921 TTTCTGCCAATAATG-ACTGTTATGCATTTTCATTTATGACACCTTTCTACCAATAATGCACCAT
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGACACCTTTCTACCAATAATGCACCAT
*
28985 TATGCATTTTTTATTTATGGCACA
66 TATGCA-TTTTCATTTATGGCACA
* *
29009 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGA-ACCTTTCTTCCAATAATGCACCG
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT-GACACCTTTCTACCAATAATGCACCA
*
29073 TTATGAATTTTCATTTATGGCACA
65 TTATGCATTTTCATTTATGGCACA
* * * *
29097 TTTCTTCCAATAATGCACCATTATGTATTTTTATTTAT
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
29135 TTCGGTAACA
Statistics
Matches: 191, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
87 47 0.25
88 94 0.49
89 48 0.25
90 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.44
Consensus pattern (88 bp):
TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGACACCTTTCTACCAATAATGCACCAT
TATGCATTTTCATTTATGGCACA
Found at i:38316 original size:31 final size:31
Alignment explanation
Indices: 38278--38433 Score: 269
Period size: 31 Copynumber: 5.0 Consensus size: 31
38268 CCCGAAGGAC
* * *
38278 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
38309 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
38340 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
38371 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
38402 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
38433 C
1 C
38434 CCTCGACCCT
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 120 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:42851 original size:31 final size:31
Alignment explanation
Indices: 42813--42968 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
42803 CCCGAAGGAC
* * *
42813 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
42844 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
42875 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
42906 TAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
42937 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
42968 C
1 C
42969 CCTCGACTCT
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:47295 original size:11 final size:12
Alignment explanation
Indices: 47279--47308 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
47269 TAGTGACCTA
47279 TTTTTTTTA-CC
1 TTTTTTTTACCC
47290 TTTTTTTTACCC
1 TTTTTTTTACCC
47302 TTTTTTT
1 TTTTTTT
47309 GTATTCCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTTTACCC
Found at i:48411 original size:24 final size:25
Alignment explanation
Indices: 48363--48411 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
48353 TGTCAGAAGA
* * *
48363 AAATGTTTTCCCATGATTTGTTTTT
1 AAATGTATTCCCATGAGTTGATTTT
48388 AAATGTATT-CCATGAGTTGATTTT
1 AAATGTATTCCCATGAGTTGATTTT
48412 GGGTATTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.51
Consensus pattern (25 bp):
AAATGTATTCCCATGAGTTGATTTT
Found at i:51696 original size:17 final size:17
Alignment explanation
Indices: 51676--51711 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
51666 AGTAACTAAT
51676 TAATAAAATAAAAATAA
1 TAATAAAATAAAAATAA
* *
51693 TAATAAACTAAAGATAA
1 TAATAAAATAAAAATAA
51710 TA
1 TA
51712 TTTTCATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (17 bp):
TAATAAAATAAAAATAA
Found at i:51744 original size:52 final size:51
Alignment explanation
Indices: 51686--51795 Score: 175
Period size: 52 Copynumber: 2.1 Consensus size: 51
51676 TAATAAAATA
* *
51686 AAAATAATAATAAACTAAAGATAATATTTTCATTCTATCCTTAATTCCTAAT
1 AAAATAATAATAAACTAAAGATAATATTTTAACTCTAT-CTTAATTCCTAAT
* *
51738 AAAATAATAATAAACTAAGGATGATATTTTAACTCTATCTTAATTCCTAAT
1 AAAATAATAATAAACTAAAGATAATATTTTAACTCTATCTTAATTCCTAAT
51789 AAAATAA
1 AAAATAA
51796 AATTCAATCT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
51 20 0.37
52 34 0.63
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.36
Consensus pattern (51 bp):
AAAATAATAATAAACTAAAGATAATATTTTAACTCTATCTTAATTCCTAAT
Found at i:55485 original size:33 final size:33
Alignment explanation
Indices: 55422--55607 Score: 158
Period size: 32 Copynumber: 5.6 Consensus size: 33
55412 TATCTAGAGT
*
55422 TTTTGAAAATATTTTCG-AAAA-ATATAATATA-
1 TTTTGAAAACATTTT-GAAAAATATATAATATAG
*
55453 TTTTGAAAACGATTTTCAAAAATATATAATATA-
1 TTTTGAAAAC-ATTTTGAAAAATATATAATATAG
*
55486 TAGTTTG-GAA-ATTTTGAAAACAATATATAATATATAG
1 T--TTTGAAAACATTTTG-AAA-AATATAT-A-ATATAG
*
55523 TTTTTG-AAACATTTTTG-AAAATATATTATATAG
1 -TTTTGAAAACA-TTTTGAAAAATATATAATATAG
*
55556 TTTTGAAAACATTTTGAAAAATACAT--TATAG
1 TTTTGAAAACATTTTGAAAAATATATAATATAG
55587 TTTTGAAAACAATTTTGAAAA
1 TTTTGAAAAC-ATTTTGAAAA
55608 CAATTT
Statistics
Matches: 132, Mismatches: 7, Indels: 31
0.78 0.04 0.18
Matches are distributed among these distances:
31 24 0.18
32 34 0.26
33 33 0.25
34 9 0.07
35 12 0.09
36 13 0.10
37 1 0.01
38 6 0.05
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (33 bp):
TTTTGAAAACATTTTGAAAAATATATAATATAG
Found at i:55601 original size:102 final size:101
Alignment explanation
Indices: 55405--55611 Score: 237
Period size: 102 Copynumber: 2.0 Consensus size: 101
55395 TAGTATATAT
*
55405 ATATATATATCTAGAGTTTTTGAAAATATTTTCGAAAAATATAATATATTTTGAAAACGATTTTC
1 ATATATATATATAGAGTTTTTGAAAATATTTTCGAAAAATATAATATATTTTGAAAACGATTTTC
* *
55470 AAAAATATATAATATATAGTTTGGAAATTTTGAAAACA
66 AAAAATACAT-ATATATA-TTTGAAAATTTTGAAAACA
* *
55508 ATATATA-ATATATAGTTTTTGAAACAT-TTTT-GAAAATATATTATATAGTTTTGAAAAC-ATT
1 ATATATATATATAGAGTTTTTGAAA-ATATTTTCGAAAA-ATATAATATA-TTTTGAAAACGATT
*
55569 TTGAAAAATACAT-TATAGT-TTTGAAAACAATTTTGAAAACA
63 TTCAAAAATACATATATA-TATTTG--AA-AATTTTGAAAACA
55610 AT
1 AT
55612 TT
Statistics
Matches: 91, Mismatches: 6, Indels: 15
0.81 0.05 0.13
Matches are distributed among these distances:
99 4 0.04
100 4 0.04
101 7 0.08
102 57 0.63
103 19 0.21
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (101 bp):
ATATATATATATAGAGTTTTTGAAAATATTTTCGAAAAATATAATATATTTTGAAAACGATTTTC
AAAAATACATATATATATTTGAAAATTTTGAAAACA
Found at i:55604 original size:12 final size:12
Alignment explanation
Indices: 55587--55613 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55577 TACATTATAG
55587 TTTTGAAAACAA
1 TTTTGAAAACAA
55599 TTTTGAAAACAA
1 TTTTGAAAACAA
55611 TTT
1 TTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (12 bp):
TTTTGAAAACAA
Done.