Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005997.1 Hibiscus syriacus cultivar Beakdansim tig00014132_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: 61434
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:134 original size:21 final size:20
Alignment explanation
Indices: 91--131 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
81 GGTAAAGCGC
91 TACCGGTTTTGTTATTTTTT
1 TACCGGTTTTGTTATTTTTT
111 TACCGGTTTTGTTATTTTTT
1 TACCGGTTTTGTTATTTTTT
131 T
1 T
132 TACATGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.10, G:0.15, T:0.66
Consensus pattern (20 bp):
TACCGGTTTTGTTATTTTTT
Found at i:203 original size:113 final size:109
Alignment explanation
Indices: 8--243 Score: 391
Period size: 113 Copynumber: 2.1 Consensus size: 109
1 AAACTGG
* * *
8 TTTGTCATTTTTTTTACTGTTATATTAAAGTATCTATCCTTTTTATAAAAGGATCGATACTTTCA
1 TTTGTTATTTTTTTTACTGTTATATTAAAGTATCGATCCTTTTTATAAAAGAATCGATACTTTCA
73 ATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTACCGGT
66 ATATATCAGGTAAAGCGCTACCGGTTTTGTTA-TTTTTTACCGGT
*
118 TTTGTTATTTTTTTTACATGTTATATTGTAAAGTATCGATTCTTTTTATAAAAGAATCGATACTT
1 TTTGTTATTTTTTTTAC-TGTTATA-T-TAAAGTATCGATCCTTTTTATAAAAGAATCGATACTT
*
183 TCAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTATCGGT
63 TCAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTACCGGT
230 TTTGTTATTTTTTT
1 TTTGTTATTTTTTT
244 ACCGGTTTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
110 16 0.14
111 7 0.06
112 26 0.22
113 69 0.58
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (109 bp):
TTTGTTATTTTTTTTACTGTTATATTAAAGTATCGATCCTTTTTATAAAAGAATCGATACTTTCA
ATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTACCGGT
Found at i:231 original size:19 final size:20
Alignment explanation
Indices: 204--252 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
194 GGTAAAGCGC
204 TACCGGTTTTGTTA-TTTTT
1 TACCGGTTTTGTTATTTTTT
*
223 TATCGGTTTTGTTATTTTTT
1 TACCGGTTTTGTTATTTTTT
243 TACCGGTTTT
1 TACCGGTTTT
253 ACCAAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.10, C:0.10, G:0.16, T:0.63
Consensus pattern (20 bp):
TACCGGTTTTGTTATTTTTT
Found at i:311 original size:19 final size:19
Alignment explanation
Indices: 279--326 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
269 AACATTGATG
*
279 TTTTAGGTAAAAATAATAA
1 TTTTAAGTAAAAATAATAA
*
298 TTTTAAGTAGAAATAATAA
1 TTTTAAGTAAAAATAATAA
*
317 TTTTAGGTAA
1 TTTTAAGTAA
327 TTTTTACCGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (19 bp):
TTTTAAGTAAAAATAATAA
Found at i:652 original size:197 final size:197
Alignment explanation
Indices: 317--707 Score: 764
Period size: 197 Copynumber: 2.0 Consensus size: 197
307 GAAATAATAA
317 TTTTAGGTAATTTTTACCGGTTTTGTTATGCCCAACAATAACAAAACCGATAAAAATAGACTTTT
1 TTTTAGGTAATTTTTACCGGTTTTGTTATGCCCAACAATAACAAAACCGATAAAAATAGACTTTT
382 TAATAATAAAATTAGTAAACACAAATTATACAAATTGTTAAATTTAAATTCTAAATAATATTTTA
66 TAATAATAAAATTAGTAAACACAAATTATACAAATTGTTAAATTTAAATTCTAAATAATATTTTA
*
447 TAAAATATCAAAATAATTAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTA
131 TAAAATATCAAAATAATTAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATCGTAGGTA
512 AT
196 AT
*
514 TTTTAGGTAATTTTTACCGGTTTTGTTATGCCCAACAATAACAAAACCGGTAAAAATAGACTTTT
1 TTTTAGGTAATTTTTACCGGTTTTGTTATGCCCAACAATAACAAAACCGATAAAAATAGACTTTT
579 TAATAATAAAATTAGTAAACACAAATTATACAAATTGTTAAATTTAAATTCTAAATAATATTTTA
66 TAATAATAAAATTAGTAAACACAAATTATACAAATTGTTAAATTTAAATTCTAAATAATATTTTA
644 TAAAATATCAAAATAATTAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATCGTAGGT
131 TAAAATATCAAAATAATTAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATCGTAGGT
708 GGAAAACATG
Statistics
Matches: 192, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
197 192 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (197 bp):
TTTTAGGTAATTTTTACCGGTTTTGTTATGCCCAACAATAACAAAACCGATAAAAATAGACTTTT
TAATAATAAAATTAGTAAACACAAATTATACAAATTGTTAAATTTAAATTCTAAATAATATTTTA
TAAAATATCAAAATAATTAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATCGTAGGTA
AT
Found at i:1120 original size:92 final size:92
Alignment explanation
Indices: 768--1119 Score: 521
Period size: 92 Copynumber: 3.8 Consensus size: 92
758 TTCAAAAAAT
* * * * * *** *
768 TATCGATCATTTTTACAAAAAGTATCTATACTTTCAACATATCAGGTAAA-TATTATCGGTTTTG
1 TATCGATCTTTTTTA-TAAAAGGATCGATACTTTCAATATATCAGGTAAAGCGCTACCGGTTTTG
*
832 TCA-TTTTTTACCTGTTATATTGTAAAG
65 TTATTTTTTTACCTGTTATATTGTAAAG
** * *
859 TATTTATCCTTTTTATAAAAGGATCGATACTTTCAATATATCAGGTAAAGCGCTACCGATTTTGT
1 TATCGATCTTTTTTATAAAAGGATCGATACTTTCAATATATCAGGTAAAGCGCTACCGGTTTTGT
*
924 TATTTTTTTACCTGTTATATTGCAAAG
66 TATTTTTTTACCTGTTATATTGTAAAG
951 TATCGATCTTTTTTATAAAAGGATCGATACTTTCAATATATCAGGTAAAGCGCTACCGGTTTTGT
1 TATCGATCTTTTTTATAAAAGGATCGATACTTTCAATATATCAGGTAAAGCGCTACCGGTTTTGT
1016 TATTTTTTTACC-GATTATATTGTAAAG
66 TATTTTTTTACCTG-TTATATTGTAAAG
*
1043 TATCGATCTTTTTTATAAAAGGATCGATACTTTCAATATATCAAGTAAAGCGCTACCGGTTTTGT
1 TATCGATCTTTTTTATAAAAGGATCGATACTTTCAATATATCAGGTAAAGCGCTACCGGTTTTGT
1108 TATTTTTTTACC
66 TATTTTTTTACC
1120 GGTTTTACCG
Statistics
Matches: 238, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
90 30 0.13
91 24 0.10
92 184 0.77
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (92 bp):
TATCGATCTTTTTTATAAAAGGATCGATACTTTCAATATATCAGGTAAAGCGCTACCGGTTTTGT
TATTTTTTTACCTGTTATATTGTAAAG
Found at i:1583 original size:28 final size:28
Alignment explanation
Indices: 1548--1620 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
1538 TATTTATGTC
1548 AATATTATTATTAAAATATTAT-ATCTAT
1 AATATTATTATTAAAATATTATGAT-TAT
* * * *
1576 AATTTTATAAATAAAAAATTATGATTAT
1 AATATTATTATTAAAATATTATGATTAT
*
1604 TATATT-TTATTAAAATA
1 AATATTATTATTAAAATA
1621 AATTTGCAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
27 8 0.23
28 25 0.71
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
AATATTATTATTAAAATATTATGATTAT
Found at i:1788 original size:87 final size:88
Alignment explanation
Indices: 1673--1907 Score: 343
Period size: 87 Copynumber: 2.7 Consensus size: 88
1663 GAATAGATCA
* * *
1673 ATATAAGCGTTACCTATTACATTTTATAAGCAG-TACCTAATATGTTATTGTACTTAATAATGTT
1 ATATAAGCGCTACCTATTACATTATATAAGCAGCTACCTAATATGTTATTGTACTTGATAATGTT
1737 TACAGTAATTAACCTATTTTATT
66 TACAGTAATTAACCTATTTTATT
* * *
1760 ATATAAGCGCTACATATTACATTATATAA--ATGTTACCTAATATGTTATTGTGCTTGATAATGT
1 ATATAAGCGCTACCTATTACATTATATAAGCA-GCTACCTAATATGTTATTGTACTTGATAATGT
1823 TTACAGTAATTAACCTATTTTATT
65 TTACAGTAATTAACCTATTTTATT
* * * *
1847 ATATAAACGCTACCTAGTACATTATATAAGC-GCTACCTAATTTGTTATTTTACTTGATAAT
1 ATATAAGCGCTACCTATTACATTATATAAGCAGCTACCTAATATGTTATTGTACTTGATAAT
1908 ATTTTCGGTT
Statistics
Matches: 132, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
85 1 0.01
86 1 0.01
87 130 0.98
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (88 bp):
ATATAAGCGCTACCTATTACATTATATAAGCAGCTACCTAATATGTTATTGTACTTGATAATGTT
TACAGTAATTAACCTATTTTATT
Found at i:1894 original size:23 final size:23
Alignment explanation
Indices: 1835--1894 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1825 ACAGTAATTA
*
1835 ACCTATTTTATTATATAAACGCT
1 ACCTAATTTATTATATAAACGCT
* ** *
1858 ACCTAGTACATTATATAAGCGCT
1 ACCTAATTTATTATATAAACGCT
*
1881 ACCTAATTTGTTAT
1 ACCTAATTTATTAT
1895 TTTACTTGAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (23 bp):
ACCTAATTTATTATATAAACGCT
Found at i:11605 original size:22 final size:23
Alignment explanation
Indices: 11570--11616 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
11560 AACCCTAAAT
11570 AAGCCCAAAAATCGTATCTGCTA
1 AAGCCCAAAAATCGTATCTGCTA
*
11593 AAGCCC-AAAATCGTATCTTCTA
1 AAGCCCAAAAATCGTATCTGCTA
11615 AA
1 AA
11617 CTCGCGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (23 bp):
AAGCCCAAAAATCGTATCTGCTA
Found at i:13430 original size:15 final size:15
Alignment explanation
Indices: 13393--13445 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
13383 TTGAGACATT
13393 ACCCGCCCCGCATCC
1 ACCCGCCCCGCATCC
* ** *
13408 GCTTGCCCTGCATCC
1 ACCCGCCCCGCATCC
*
13423 ACCCGCCCCACATCC
1 ACCCGCCCCGCATCC
*
13438 GCCCGCCC
1 ACCCGCCC
13446 AGCTAAATAT
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.11, C:0.62, G:0.15, T:0.11
Consensus pattern (15 bp):
ACCCGCCCCGCATCC
Found at i:31122 original size:14 final size:14
Alignment explanation
Indices: 31105--31132 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31095 ATTATTACAA
31105 AATTATATAACTAT
1 AATTATATAACTAT
31119 AATTATATAACTAT
1 AATTATATAACTAT
31133 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:37442 original size:18 final size:17
Alignment explanation
Indices: 37398--37442 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
37388 ATTTTAGATT
*
37398 ATTAAAAGAATATATTA
1 ATTAAAATAATATATTA
*
37415 ATATATAATAATATATATA
1 AT-TAAAATAATATAT-TA
37434 ATTAAAATA
1 ATTAAAATA
37443 TTCAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 2 0.09
18 17 0.74
19 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
ATTAAAATAATATATTA
Found at i:38664 original size:16 final size:16
Alignment explanation
Indices: 38643--38673 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
38633 AAAAAAAAAT
38643 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
38659 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
38674 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:38883 original size:27 final size:27
Alignment explanation
Indices: 38825--38890 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
38815 TATGCCCTTG
*
38825 TTTTAAAGGAATATTAATATGATTTGT
1 TTTTAAAGGAATATTAATATGATTTCT
* * *
38852 GTTTAAAGGAATATTAATGTGGTTTCT
1 TTTTAAAGGAATATTAATATGATTTCT
38879 TTTTAAAGGAAT
1 TTTTAAAGGAAT
38891 TCAAAAGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.35, C:0.02, G:0.18, T:0.45
Consensus pattern (27 bp):
TTTTAAAGGAATATTAATATGATTTCT
Found at i:39170 original size:18 final size:19
Alignment explanation
Indices: 39134--39174 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
39124 ATATTTTATT
*
39134 TAAAGTTCAGGGATCAAAC
1 TAAAGTTCAGGGATAAAAC
*
39153 TAAAGTTTA-GGATAAAAC
1 TAAAGTTCAGGGATAAAAC
39171 TAAA
1 TAAA
39175 ATTAACTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (19 bp):
TAAAGTTCAGGGATAAAAC
Found at i:41783 original size:84 final size:84
Alignment explanation
Indices: 41642--41834 Score: 370
Period size: 84 Copynumber: 2.3 Consensus size: 84
41632 AGAAAATACC
41642 CAAAATTAAGGTGGGTTTGATAAATAATTAAAAAATCTTTTTTTTATTAAAACAAAATTTTGTAT
1 CAAAATTAAGGTGGGTTTGATAAATAATTAAAAAATCTTTTTTTTATTAAAACAAAATTTTGTAT
41707 GACTTAATTTTTATTAAAA
66 GACTTAATTTTTATTAAAA
41726 CAAAATTAAGGTGGGTTTGATAAATAATTAAAAAAATC-TTTTTTTATTAAAACAAAATTTTGTA
1 CAAAATTAAGGTGGGTTTGATAAATAATT-AAAAAATCTTTTTTTTATTAAAACAAAATTTTGTA
41790 TGACTTAATTTTTATTAAAA
65 TGACTTAATTTTTATTAAAA
41810 CAAAATTAAGGTGGGTTTGATAAAT
1 CAAAATTAAGGTGGGTTTGATAAAT
41835 TTTTACTATG
Statistics
Matches: 108, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
84 100 0.93
85 8 0.07
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (84 bp):
CAAAATTAAGGTGGGTTTGATAAATAATTAAAAAATCTTTTTTTTATTAAAACAAAATTTTGTAT
GACTTAATTTTTATTAAAA
Found at i:44062 original size:18 final size:18
Alignment explanation
Indices: 44039--44073 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
44029 TCTCTTTCCA
44039 TTTTATAAATTTTAAATT
1 TTTTATAAATTTTAAATT
*
44057 TTTTATAATTTTTAAAT
1 TTTTATAAATTTTAAAT
44074 ATATTTCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTATAAATTTTAAATT
Found at i:58734 original size:11 final size:11
Alignment explanation
Indices: 58718--58742 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58708 GTGGATTATT
58718 AAAAAAAATTA
1 AAAAAAAATTA
58729 AAAAAAAATTA
1 AAAAAAAATTA
58740 AAA
1 AAA
58743 GGAAAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAAATTA
Done.