Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003708.1 Hibiscus syriacus cultivar Beakdansim tig00007934_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: 97812
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:19162 original size:79 final size:79
Alignment explanation
Indices: 19074--19226 Score: 216
Period size: 79 Copynumber: 1.9 Consensus size: 79
19064 AGGTGTTTAC
* * * * *
19074 AAATTAAGCTCACAAAAACAATCTATGTACAAGAGAAAAGAAATAACAAAGAATTAAAAGTTTTT
1 AAATAAAGCTCACAAAAACAATATATGTACAAGAGAAAAGAAAGAACAAAGAATGAAAAGCTTTT
19139 CTCGTGATCCTATT
66 CTCGTGATCCTATT
* * * *
19153 AAATAAAGCTTACAAAAACACTATATGTATAAGAGAAAAGAAAGAACGAAGAATGAAAAGCTTTT
1 AAATAAAGCTCACAAAAACAATATATGTACAAGAGAAAAGAAAGAACAAAGAATGAAAAGCTTTT
*
19218 CTCTTGATC
66 CTCGTGATC
19227 ATTGTTGCTT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 64 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (79 bp):
AAATAAAGCTCACAAAAACAATATATGTACAAGAGAAAAGAAAGAACAAAGAATGAAAAGCTTTT
CTCGTGATCCTATT
Found at i:21043 original size:33 final size:32
Alignment explanation
Indices: 20974--21052 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 32
20964 AAAGTTAACT
* * *
20974 GGTTTAATATATTTGTCTAGAATTTATAAACC
1 GGTTTAATATCTTTGCCAAGAATTTATAAACC
*
21006 GGTTTAATATCTTTGCCAAGAATTTGTAAAACC
1 GGTTTAATATCTTTGCCAAGAATTTAT-AAACC
21039 GGTTTAATATCTTT
1 GGTTTAATATCTTT
21053 TGACTTTCGA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 23 0.55
33 19 0.45
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (32 bp):
GGTTTAATATCTTTGCCAAGAATTTATAAACC
Found at i:21086 original size:27 final size:27
Alignment explanation
Indices: 21044--21099 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
21034 AAACCGGTTT
21044 AATATCTTTTGACTTTCGATTAAATTG
1 AATATCTTTTGACTTTCGATTAAATTG
* *
21071 AATATCTTTTGGCTTTCGATTAGATTG
1 AATATCTTTTGACTTTCGATTAAATTG
21098 AA
1 AA
21100 GTTGTGGACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (27 bp):
AATATCTTTTGACTTTCGATTAAATTG
Found at i:22623 original size:18 final size:17
Alignment explanation
Indices: 22600--22643 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
22590 CGTTTCTGAG
22600 GGAATTGAAATATGTGAA
1 GGAATTGAAATATGT-AA
* * *
22618 GGAATTGGAATCTGTCA
1 GGAATTGAAATATGTAA
22635 GGAATTGAA
1 GGAATTGAA
22644 TCCAATTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.39, C:0.05, G:0.30, T:0.27
Consensus pattern (17 bp):
GGAATTGAAATATGTAA
Found at i:23305 original size:261 final size:251
Alignment explanation
Indices: 23033--23594 Score: 745
Period size: 261 Copynumber: 2.2 Consensus size: 251
23023 AGTTTCACCC
* *
23033 AACCTGACCCGAAATAATAAAAAAAATTGTTTTATTCAATAAAAATAGTGACTTAATTGGAAAAA
1 AACCCGACCCGAAATAATAAAAAAAATT-TTTTATTCAATAAAAACAGTGACTTAATT-GAAAAA
* *
23098 AA-ATATATAGAGTAGTTTTATTGTAATTATTCCTAAAA-ATATAAGGTAAAATTATATATATTT
64 AATATATATAGAGGAGTATTATTGTAATTATTCC-AAAATATATAAGGTAAAATTATATATA-TT
* * *
23161 TGGGTCGGGTCTGGTCGGGTATTTTTCACCCTACACCCGAACCCGACCCGACCCGAAAATCACAC
127 T---TCAGG--T--T-GAGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAAAATCACAC
* *
23226 TTAAAAAAATTGACCTGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATT
184 TTAAAAAAACTGACCCGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATT
23291 AGAA
249 AG-A
*
23295 ATCCGACCCGACCCGACCCGA-AATAAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAAT
1 A----ACCCGACCCGA---AATAATAAAAAAAA-T-TTTTTATTCAATAAAAACAGTGACTTAAT
*
23359 TGAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCAAAATATATAAGGTAAAATTATA
57 TGAAAAAAA-TATATATAGAGGAGTATTATTGTAATTATTCCAAAATATATAAGGTAAAATTATA
* * *
23424 TATATTTTCAGGTTGAGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACATTT
121 TATATTTTCAGGTTGAGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAAAATCACACTT
*
23489 AAAAAAACTGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAG
186 AAAAAAACTGACCCGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAG
23554 A
251 A
23555 AACCCGACCCGAAATAA-AAAAAAAATATTTTTATTCAATA
1 AACCCGACCCGAAATAATAAAAAAAAT-TTTTTATTCAATA
23595 TATGAATTAG
Statistics
Matches: 271, Mismatches: 16, Indels: 36
0.84 0.05 0.11
Matches are distributed among these distances:
252 15 0.06
253 9 0.03
254 2 0.01
256 11 0.04
260 2 0.01
261 108 0.40
262 2 0.01
264 1 0.00
266 14 0.05
268 19 0.07
269 37 0.14
270 51 0.19
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (251 bp):
AACCCGACCCGAAATAATAAAAAAAATTTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
TATATATAGAGGAGTATTATTGTAATTATTCCAAAATATATAAGGTAAAATTATATATATTTTCA
GGTTGAGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAAAATCACACTTAAAAAAACTG
ACCCGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGA
Found at i:24785 original size:31 final size:31
Alignment explanation
Indices: 24750--24811 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
24740 TAACACATGA
24750 TTGAAGCTAGCACAAAAAGAATTACATCAAT
1 TTGAAGCTAGCACAAAAAGAATTACATCAAT
* * * *
24781 TTGAAGCTCGCTCATAAAGAATTACGTCAAT
1 TTGAAGCTAGCACAAAAAGAATTACATCAAT
24812 AGGTTTCGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26
Consensus pattern (31 bp):
TTGAAGCTAGCACAAAAAGAATTACATCAAT
Found at i:25059 original size:20 final size:20
Alignment explanation
Indices: 25034--25093 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
25024 AAGTGAGAAT
25034 CCTTACCACTACACGATAAC
1 CCTTACCACTACACGATAAC
*
25054 CCTTACCATTACACGATAAC
1 CCTTACCACTACACGATAAC
*
25074 CCTTACCACTACACTATAAC
1 CCTTACCACTACACGATAAC
25094 GACTTGATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.35, C:0.38, G:0.03, T:0.23
Consensus pattern (20 bp):
CCTTACCACTACACGATAAC
Found at i:45635 original size:484 final size:488
Alignment explanation
Indices: 44719--45693 Score: 1808
Period size: 484 Copynumber: 2.0 Consensus size: 488
44709 GCCATACCAA
44719 AAGAGTTCCTTAAAAATGCTCAAGTCAACTGATAAAAGGAAATGCTGATTATACTCGTATACTAA
1 AAGAGTTCCTTAAAAATGCTCAAGTCAACTGATAAAAGGAAATGCTGATTATACTCGTATACTAA
44784 CCCTCTACTCTAGGGTAGACATCATGGTGTGGCTGAGGGATTTTTGTTTCTCGGAGCTCACACAC
66 CCCTCTACTCTAGGGTAGACATCATGGTGTGGCTGAGGGATTTTTGTTTCTCGGAGCT-ACACAC
44849 ACTGTAGTCTAACGAGGATAAGACCAAATCTCTACATGGGACACAACACCCGACTAACCCACCCT
130 ACTGTAGTCTAACGAGGATAAGACCAAATCTCTACATGGGACACAACACCCGACTAACCCACCCT
44914 TGCGAGTATCAGACCTTGGGACCTAGTTAGTCTGTTTAAAGTTTCTTATGCACTACCTAAGGATA
195 TGCGAGTATCAGACCTTGGGACCTAGTTAGTCTGTTTAAAGTTTCTTATGCACTACCTAAGGATA
44979 TTCAGATTGATTCTAAACTTCATCAACTTTTCTTTACTAAAGAAAATTTGAGTGTCCTAGTCGTT
260 TTCAGATTGATTCTAAACTTCATCAACTTTTCTTTACTAAAGAAAATTTGAGTGTCCTAGTCGTT
45044 CCCGAGCATCAATCAACGCTAGTTTATTTCACCCTAATTGATCATGTTTCTAAATGTAATTAAAC
325 CCCGAGCATCAATCAACGCTAGTTTATTTCACCCTAATTGATCATGTTTCTAAATGTAATTAAAC
45109 AATATTATTGTTCCTCTTGAAGTCTTATTTGAGAGTAATTAGAGTCCTTAGGAACCCCTA-TA-C
390 AATATTATTGTTCCTCTTGAAGTCTTATTTGAGAGTAATTAGAGTCCTTAGGAACCCCTATTACC
45172 CCTTAAAAACTATCGGGTTTAGTGCCCATTACTG
455 CCTTAAAAACTATCGGGTTTAGTGCCCATTACTG
45206 AAGAGTTCCTTAAAAAATGCTCAAGTCAACTGATAAAAGGAAATGCTGATTATAC-CGTATACTA
1 AAGAGTTCCTT-AAAAATGCTCAAGTCAACTGATAAAAGGAAATGCTGATTATACTCGTATACTA
*
45270 ACCCTCTACTCTATGGTAGACATCATGG-GTGGCTG-GGGA-TTTTG-TTCTCGGAGCT-CACAC
65 ACCCTCTACTCTAGGGTAGACATCATGGTGTGGCTGAGGGATTTTTGTTTCTCGGAGCTACACAC
45330 ACTGTAGTCTAACGAGGATAAGACCAAAATCTCTACATGGGACACAACACCCTGACTAACCCACC
130 ACTGTAGTCTAACGAGGATAAGACC-AAATCTCTACATGGGACACAACACCC-GACTAACCCA-C
45395 CCTTGCGAGTATCAGACCTTGGGACCTAGTTAGTCTG-TTAAAGTTTCTTATGCACTACCTAAGG
192 CCTTGCGAGTATCAGACCTTGGGACCTAGTTAGTCTGTTTAAAGTTTCTTATGCACTACCTAAGG
45459 ATATTCAGATTGATTCTAAACTTCATCAACTTTTCTTTACTAAAG-AAATTTGAGTGTCCTAGTC
257 ATATTCAGATTGATTCTAAACTTCATCAACTTTTCTTTACTAAAGAAAATTTGAGTGTCCTAGTC
45523 GTTTCCCGAGCATCAATCAACGCTAGTTTTATTTCACCCTAATTGATCATGTTTCTAAATGTAAT
322 G-TTCCCGAGCATCAATCAACGCTAG-TTTATTTCACCCTAATTGATCATGTTTCTAAATGTAAT
45588 TAAACAATATTATTGTTCCTCTTGAAGTCTTATTTGAGAGTAATTAGAGTCCTTAGGAACCCCTA
385 TAAACAATATTATTGTTCCTCTTGAAGTCTTATTTGAGAGTAATTAGAGTCCTTAGGAACCCCTA
45653 TTACCCCTTAAAAACTATCGGGTTTAGTGCCCATTACTG
450 TTACCCCTTAAAAACTATCGGGTTTAGTGCCCATTACTG
45692 AA
1 AA
45694 CAAGGGTATT
Statistics
Matches: 479, Mismatches: 1, Indels: 17
0.96 0.00 0.03
Matches are distributed among these distances:
481 30 0.06
482 46 0.10
483 117 0.24
484 146 0.30
485 6 0.01
486 44 0.09
487 47 0.10
488 43 0.09
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (488 bp):
AAGAGTTCCTTAAAAATGCTCAAGTCAACTGATAAAAGGAAATGCTGATTATACTCGTATACTAA
CCCTCTACTCTAGGGTAGACATCATGGTGTGGCTGAGGGATTTTTGTTTCTCGGAGCTACACACA
CTGTAGTCTAACGAGGATAAGACCAAATCTCTACATGGGACACAACACCCGACTAACCCACCCTT
GCGAGTATCAGACCTTGGGACCTAGTTAGTCTGTTTAAAGTTTCTTATGCACTACCTAAGGATAT
TCAGATTGATTCTAAACTTCATCAACTTTTCTTTACTAAAGAAAATTTGAGTGTCCTAGTCGTTC
CCGAGCATCAATCAACGCTAGTTTATTTCACCCTAATTGATCATGTTTCTAAATGTAATTAAACA
ATATTATTGTTCCTCTTGAAGTCTTATTTGAGAGTAATTAGAGTCCTTAGGAACCCCTATTACCC
CTTAAAAACTATCGGGTTTAGTGCCCATTACTG
Found at i:48837 original size:27 final size:27
Alignment explanation
Indices: 48799--48851 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
48789 CCTTAAGATC
* *
48799 TATTCAGTGATGATTCTGAATATGATA
1 TATTCAGTGATGAGTCTGAAGATGATA
48826 TATTCAGTGATGAGTCTGAAGATGAT
1 TATTCAGTGATGAGTCTGAAGATGAT
48852 CTATGGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.38
Consensus pattern (27 bp):
TATTCAGTGATGAGTCTGAAGATGATA
Found at i:54479 original size:20 final size:20
Alignment explanation
Indices: 54450--54487 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
54440 ATAAGCTGAC
*
54450 TCTGTTCTATTTTAACCAAA
1 TCTGTCCTATTTTAACCAAA
54470 TCTGTCCTATTTTAACCA
1 TCTGTCCTATTTTAACCA
54488 TGCACGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (20 bp):
TCTGTCCTATTTTAACCAAA
Found at i:57926 original size:19 final size:20
Alignment explanation
Indices: 57881--57928 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
57871 TATACTATGC
* * *
57881 TTGAAATTAATTTTAGAGTG
1 TTGAAATTGATGTTAGAATG
57901 TTGAAATTGATGTTAGAATG
1 TTGAAATTGATGTTAGAATG
57921 -TGAAATTG
1 TTGAAATTG
57929 GGCCACTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (20 bp):
TTGAAATTGATGTTAGAATG
Found at i:59743 original size:20 final size:20
Alignment explanation
Indices: 59718--59755 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
59708 ATAAGCTGAC
59718 TCTGTTCTATTTTAACCAAA
1 TCTGTTCTATTTTAACCAAA
59738 TCTGTTCTATTTTAACCA
1 TCTGTTCTATTTTAACCA
59756 TGAACGCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.47
Consensus pattern (20 bp):
TCTGTTCTATTTTAACCAAA
Found at i:61230 original size:23 final size:20
Alignment explanation
Indices: 61184--61253 Score: 95
Period size: 20 Copynumber: 3.4 Consensus size: 20
61174 TACCAATTTG
*
61184 TAATATTTATGAACCAATTA
1 TAATATTTATGAATCAATTA
61204 TAATATTTATGAATCTAATATTA
1 TAATATTTATGAATC--A-ATTA
*
61227 TAATAATTATGAATCAATTA
1 TAATATTTATGAATCAATTA
61247 TAATATT
1 TAATATT
61254 ATATATATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
20 24 0.55
21 1 0.02
22 1 0.02
23 18 0.41
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (20 bp):
TAATATTTATGAATCAATTA
Found at i:67480 original size:15 final size:15
Alignment explanation
Indices: 67460--67490 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
67450 ACATGGCCTT
67460 AGTTTGGACTCATTC
1 AGTTTGGACTCATTC
67475 AGTTTGGACTCATTC
1 AGTTTGGACTCATTC
67490 A
1 A
67491 TAGTCCGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (15 bp):
AGTTTGGACTCATTC
Found at i:71056 original size:20 final size:21
Alignment explanation
Indices: 71028--71067 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
71018 TAATGTACCA
71028 TGTTGGAAATTAATGTTAGAG
1 TGTTGGAAATTAATGTTAGAG
*
71049 TGTT-GAAATTGATGTTAGA
1 TGTTGGAAATTAATGTTAGA
71068 ATATGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.40
Consensus pattern (21 bp):
TGTTGGAAATTAATGTTAGAG
Found at i:71076 original size:19 final size:20
Alignment explanation
Indices: 71033--71078 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
71023 TACCATGTTG
* * *
71033 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGAT
71053 GAAATTGATGTTAGAAT-AT
1 GAAATTGATGTTAGAATGAT
71072 GAAATTG
1 GAAATTG
71079 GCCCACATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGAT
Found at i:76908 original size:13 final size:13
Alignment explanation
Indices: 76875--76902 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
76865 AATAATTAAG
76875 CTAATTTATAAAA
1 CTAATTTATAAAA
76888 CTAATTTATAAAA
1 CTAATTTATAAAA
76901 CT
1 CT
76903 GGTTTAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (13 bp):
CTAATTTATAAAA
Found at i:82299 original size:20 final size:20
Alignment explanation
Indices: 82274--82357 Score: 96
Period size: 20 Copynumber: 4.2 Consensus size: 20
82264 TGAATGACTG
*
82274 ACAAATGACCCAAAGGATTT
1 ACAAATGACCCAAAGGCTTT
* ** *
82294 ACAAATTATGCAAAGGTTTT
1 ACAAATGACCCAAAGGCTTT
* *
82314 ACAAATAACCTAAAGGCTTT
1 ACAAATGACCCAAAGGCTTT
*
82334 ACAAATGACCCGAAGGCTTT
1 ACAAATGACCCAAAGGCTTT
82354 ACAA
1 ACAA
82358 TAATTTCATT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (20 bp):
ACAAATGACCCAAAGGCTTT
Found at i:90694 original size:13 final size:13
Alignment explanation
Indices: 90672--90704 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
90662 GGGCCTTATA
90672 AATA-ATAATATT
1 AATATATAATATT
90684 AATATATAATATT
1 AATATATAATATT
*
90697 ATTATATA
1 AATATATA
90705 TATAACAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATATATAATATT
Done.