Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005570.1 Hibiscus syriacus cultivar Beakdansim tig00012921_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: 51591
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:7776 original size:56 final size:56
Alignment explanation
Indices: 7635--7762 Score: 179
Period size: 56 Copynumber: 2.3 Consensus size: 56
7625 CCTATTTTCT
* * ** * *
7635 AGATAGATTCGATTTCAGAA-CTTTATTTTTATGCTTATTAATAGCAATAACTGAT
1 AGATATATTCGATTTCGGAACCCCTATTTTTATGCTTATTAATAGCAACAACTGAA
*
7690 AGATATATTCGATTTCGGAACCCCTATTTTTATGCTTATTAATGGCAACAACTGAA
1 AGATATATTCGATTTCGGAACCCCTATTTTTATGCTTATTAATAGCAACAACTGAA
7746 AGATATA-TCGATTTCGG
1 AGATATATTCGATTTCGG
7763 GGCCCCTGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 28 0.43
56 37 0.57
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (56 bp):
AGATATATTCGATTTCGGAACCCCTATTTTTATGCTTATTAATAGCAACAACTGAA
Found at i:13050 original size:651 final size:643
Alignment explanation
Indices: 11816--13109 Score: 2471
Period size: 651 Copynumber: 2.0 Consensus size: 643
11806 TGAGCACGGG
11816 TCTTCGTAATTCTACAAGTATGACAACAATGTAGAAAAGCCAAACACATACGTGATTAGAGAAAA
1 TCTTCGTAATTCTACAAGTATGACAACAATGTAGAAAAGCCAAACACATACGTGATTAGAGAAAA
11881 AGTAAGACAGACCAAAGAGATGATCAAACCAGAGTAAGTCTCACAAAAAATCAACATATTTCATG
66 AGTAAGACAGACCAAAGAGATGATCAAACCAGAGTAAGTCTCACAAAAAATCAACATATTTCATG
*
11946 CCAGTTTTGATCTTGGAGGCATAGAGACTATAAATATCAATATCCGTATCACCATAACCATAAAG
131 CCAGTTTTGATCTTGGAGGCATAGAGACCATAAATATCAATATCCGTATCACCATAACCATAAAG
12011 CTTCTTAAGTTCCATATTGCAACCCACCTAAAATTTTCTTGAAAAACTGCAAGGCACTATGATAT
196 CTTCTTAAGTTCCATATTGCAACCCACCTAAAATTTTCTTGAAAAACTGCAAGGCACTATGATAT
12076 ATGTCTCTGCTTTTTAACAACTCCTAGTCTCCTATCTTATATCCATGAAAAGTGTACCTTGCAAC
261 ATGTCTCTGCTTTTTAACAACTCCTAGTCTCCTATCTTATATCCATGAAAAGTGTACCTTGCAAC
*
12141 TAACTGTCCCATTGTACTACTAAAAAGTTCAACTTAAACTCCTTGGGAGATTTCCCAACATGCAA
326 TAAATGTCCCATTGTACTACTAAAAAGTTCAACTTAAACTCCTTGGGAGATTTCCCAACATGCAA
12206 TCTAAGAATAATAAAATATTCTCCTAGACTTGCCAACTGTTAAGGTGAAACATGTATTGTAGAAA
391 TCTAAGAATAATAAAATATTCTCCTAGACTTGCCAACTGTTAAGGTGAAACATGTATTGTAGAAA
*
12271 TTCATTCTACATAAAGCTAATAAAGAAAGCAAAAACAAATTTTTACGAAAACATTTCATGAAAAA
456 TCCATTCTACATAAAGCTAATAAAGAAAGCAAAAACAAATTTTTACGAAAACATTTCATGAAAAA
12336 ATCCAGAATTTCATGATACTCGGTTTCAATTGTATAAGACTTTCGTTAATTAAATGTGCAGAAGA
521 ATCCAGAATTTCATGATACTCGGTTTCAATTGTATAAGACTTTCGTTAATTAAATGTGCAGAAGA
12401 TACATAAGCACTCTGCCTAACATCTCAAGATTTTCTGTATTTATTGATATATCCCTGC
586 TACATAAGCACTCTGCCTAACATCTCAAGATTTTCTGTATTTATTGATATATCCCTGC
12459 TCTTCGTAATTCTACAAGTATGACAACAATGTAGAAAAGCCAAACACATACGTGATTAGAGAAAA
1 TCTTCGTAATTCTACAAGTATGACAACAATGTAGAAAAGCCAAACACATACGTGATTAGAGAAAA
12524 AGTAAGACAGACCAAAGAGATGATCAAACCAGAGTAAGTCTCCACAAAAAATCAACATATTTCAT
66 AGTAAGACAGACCAAAGAGATGATCAAACCAGAGTAAGTCT-CACAAAAAATCAACATATTTCAT
*
12589 GCCAGTTTTGATCCATAATCTTGGAGGCATGGAGACCATAAATATCAATATCCGTATCACCATAA
130 GCCAGTTTTG-------ATCTTGGAGGCATAGAGACCATAAATATCAATATCCGTATCACCATAA
12654 CCATAAAGCTTCTTAAGTTCCATATTGCAACCCACCTAAAATTTTCTTGAAAAACTGCAAGGCAC
188 CCATAAAGCTTCTTAAGTTCCATATTGCAACCCACCTAAAATTTTCTTGAAAAACTGCAAGGCAC
12719 TATGATATATGTCTCTGCTTTTTAACAACTCCTAGTCTCCTATCTTATATCCATGAAAAGTGTAC
253 TATGATATATGTCTCTGCTTTTTAACAACTCCTAGTCTCCTATCTTATATCCATGAAAAGTGTAC
12784 CTTGCAACTAAATGTCCCATTGTACTACTAAAAAGTTCAACTTAAACTCCTTGGGAGATTTCCCA
318 CTTGCAACTAAATGTCCCATTGTACTACTAAAAAGTTCAACTTAAACTCCTTGGGAGATTTCCCA
12849 ACATGCAATCTAAGAATAATAAAATATTCTCCTAGACTTGCCAACTGTTAAGGTGAAACATGTAT
383 ACATGCAATCTAAGAATAATAAAATATTCTCCTAGACTTGCCAACTGTTAAGGTGAAACATGTAT
12914 TGTAGAAATCCATTCTACATAAAGCTAATAAAGAAAGCAAAAACAAATTTTTACGAAAACATTTC
448 TGTAGAAATCCATTCTACATAAAGCTAATAAAGAAAGCAAAAACAAATTTTTACGAAAACATTTC
*
12979 ATGAAAAAATCCAGAATTTCATGATACTCGGTTTCAATTGTATAAGACTTTTGTTAATTAAATGT
513 ATGAAAAAATCCAGAATTTCATGATACTCGGTTTCAATTGTATAAGACTTTCGTTAATTAAATGT
13044 GCAGAAGATACATAAGCACTCTGCCTAACATCTCAAGATTTTCTGTATTTATTGATATATCCCTG
578 GCAGAAGATACATAAGCACTCTGCCTAACATCTCAAGATTTTCTGTATTTATTGATATATCCCTG
13109 C
643 C
13110 AAAACAGAAA
Statistics
Matches: 638, Mismatches: 5, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
643 106 0.17
644 33 0.05
651 499 0.78
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.30
Consensus pattern (643 bp):
TCTTCGTAATTCTACAAGTATGACAACAATGTAGAAAAGCCAAACACATACGTGATTAGAGAAAA
AGTAAGACAGACCAAAGAGATGATCAAACCAGAGTAAGTCTCACAAAAAATCAACATATTTCATG
CCAGTTTTGATCTTGGAGGCATAGAGACCATAAATATCAATATCCGTATCACCATAACCATAAAG
CTTCTTAAGTTCCATATTGCAACCCACCTAAAATTTTCTTGAAAAACTGCAAGGCACTATGATAT
ATGTCTCTGCTTTTTAACAACTCCTAGTCTCCTATCTTATATCCATGAAAAGTGTACCTTGCAAC
TAAATGTCCCATTGTACTACTAAAAAGTTCAACTTAAACTCCTTGGGAGATTTCCCAACATGCAA
TCTAAGAATAATAAAATATTCTCCTAGACTTGCCAACTGTTAAGGTGAAACATGTATTGTAGAAA
TCCATTCTACATAAAGCTAATAAAGAAAGCAAAAACAAATTTTTACGAAAACATTTCATGAAAAA
ATCCAGAATTTCATGATACTCGGTTTCAATTGTATAAGACTTTCGTTAATTAAATGTGCAGAAGA
TACATAAGCACTCTGCCTAACATCTCAAGATTTTCTGTATTTATTGATATATCCCTGC
Found at i:21172 original size:29 final size:28
Alignment explanation
Indices: 21114--21172 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
21104 TTAAGTTAGG
*
21114 GGTAAATTTAAATTATAAAATTTCAGAA
1 GGTAAATTTAAATTATAAAATTTCAAAA
* *
21142 GGTAAATTTGAACTTATAAAATTTTAAAA
1 GGTAAATTT-AAATTATAAAATTTCAAAA
21171 GG
1 GG
21173 GGCGAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (28 bp):
GGTAAATTTAAATTATAAAATTTCAAAA
Found at i:21613 original size:36 final size:37
Alignment explanation
Indices: 21569--21642 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 37
21559 TATATATTTT
21569 TTTAAATAAAATATTATT-AAAAATAGTAAAAAAATA
1 TTTAAATAAAATATTATTAAAAAATAGTAAAAAAATA
* * *
21605 TTTAAATAAAATGTTATTAAAAAATATTAAAAATATA
1 TTTAAATAAAATATTATTAAAAAATAGTAAAAAAATA
21642 T
1 T
21643 GGACTTGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 17 0.50
37 17 0.50
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (37 bp):
TTTAAATAAAATATTATTAAAAAATAGTAAAAAAATA
Found at i:21637 original size:11 final size:11
Alignment explanation
Indices: 21570--21642 Score: 56
Period size: 12 Copynumber: 6.1 Consensus size: 11
21560 ATATATTTTT
21570 TTAAATAAAATA
1 TTAAA-AAAATA
*
21582 TTATTAAAAATA
1 TTA-AAAAAATA
*
21594 GTAAAAAAATA
1 TTAAAAAAATA
*
21605 TTTAAATAAAATG
1 -TTAAA-AAAATA
21618 TTATTAAAAAATA
1 TTA--AAAAAATA
*
21631 TTAAAAATATA
1 TTAAAAAAATA
21642 T
1 T
21643 GGACTTGAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
11 15 0.31
12 18 0.37
13 14 0.29
14 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
TTAAAAAAATA
Found at i:26095 original size:35 final size:35
Alignment explanation
Indices: 26049--26207 Score: 201
Period size: 35 Copynumber: 4.5 Consensus size: 35
26039 AAAGTTTGCA
* * *
26049 TCGATTCAAGTCGAATGGAATGAGGCATCACACTT
1 TCGATTCAAGTAGAACGGAAGGAGGCATCACACTT
* *
26084 TCGATTCAAGTCGAACGAAAGGAGGCATCACACTT
1 TCGATTCAAGTAGAACGGAAGGAGGCATCACACTT
* * **
26119 TTGATTCAAGTAGAACGGAAGGAAGCATTGCACTT
1 TCGATTCAAGTAGAACGGAAGGAGGCATCACACTT
* * *
26154 TTGATTCAAGTAGAACCGAAGGAGGCATCGCACTT
1 TCGATTCAAGTAGAACGGAAGGAGGCATCACACTT
*
26189 TCGATTCAACTAGAACGGA
1 TCGATTCAAGTAGAACGGA
26208 TGGTTTACTA
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 109 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.23
Consensus pattern (35 bp):
TCGATTCAAGTAGAACGGAAGGAGGCATCACACTT
Found at i:27255 original size:114 final size:115
Alignment explanation
Indices: 27045--27259 Score: 281
Period size: 114 Copynumber: 1.9 Consensus size: 115
27035 ATCAAAACCA
* * * * * *
27045 AATTTTACCAAAAATCAAAAACCATACTTTTACAACAAATATTGTCTTCTCGATTAATATCTACG
1 AATTTGACCAAAAATCAAAAACCATACTCTTACAACAAATATTGTCTCCTCAATTAATATCAAAG
* * * *
27110 CATAAGAAAGCTTGAGTTTCTTGATCACTTCTGCTATGGACCAGAACAAC
66 CAAAAGAAAACTTCAGTTTATTGATCACTTCTGCTATGGACCAGAACAAC
* * *
27160 AATTTGACC-AAAATCAAATACTATACTCTTATAACAAATATTGTCTCCTCAATT-ATAATCAAA
1 AATTTGACCAAAAATCAAAAACCATACTCTTACAACAAATATTGTCTCCTCAATTAAT-ATCAAA
*
27223 GTAAAAGAAAACTTCAGTTTATTGATCACTTCTGCTA
65 GCAAAAGAAAACTTCAGTTTATTGATCACTTCTGCTA
27260 ACAAAAACTG
Statistics
Matches: 85, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
113 2 0.02
114 75 0.88
115 8 0.09
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (115 bp):
AATTTGACCAAAAATCAAAAACCATACTCTTACAACAAATATTGTCTCCTCAATTAATATCAAAG
CAAAAGAAAACTTCAGTTTATTGATCACTTCTGCTATGGACCAGAACAAC
Found at i:50408 original size:24 final size:24
Alignment explanation
Indices: 50381--50480 Score: 120
Period size: 24 Copynumber: 4.4 Consensus size: 24
50371 ATTTGATTTC
50381 TGATCTGATACTTGACATGGATTA
1 TGATCTGATACTTGACATGGATTA
* *
50405 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTA
*
50429 TGATCTGATACTTGACCTGGATT-
1 TGATCTGATACTTGACATGGATTA
* *
50452 T--T-TGATACTTGACGTGAATTA
1 TGATCTGATACTTGACATGGATTA
50473 TGAT-TGAT
1 TGATCTGAT
50481 TTTTGATATA
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
20 16 0.24
21 2 0.03
23 6 0.09
24 44 0.65
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTA
Done.