Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002747.1 Hibiscus syriacus cultivar Beakdansim tig00005658_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: 70968
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2496 original size:18 final size:16
Alignment explanation
Indices: 2468--2501 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
2458 CTCAAGCCTT
2468 TAAAATAACATATAACA
1 TAAAATAACATA-AACA
2485 TAAAAGTAACATAAACA
1 TAAAA-TAACATAAACA
2502 CCATGAGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.65, C:0.12, G:0.03, T:0.21
Consensus pattern (16 bp):
TAAAATAACATAAACA
Found at i:6899 original size:116 final size:117
Alignment explanation
Indices: 6694--6910 Score: 276
Period size: 116 Copynumber: 1.9 Consensus size: 117
6684 GTATTCTTTT
* * * *
6694 GAAAGCTAAAATAGACTTGGAAAATCAAAATGAAATGTTGAAAAAGGAGTTAGAGCTTTCAAAAA
1 GAAAGCTAAAATAGACTTGGAAAATCAAAATGAAATATTGAAAAAGGAGTTACAACTCTCAAAAA
* * *
6759 CGAAATCTGAATACTTTGATAAAGAAATTTTGAATTAAACAAACTTCTTCTA
66 CGAAATCTGAATACTTTGAAAAAGAAAATTTCAATTAAACAAACTTCTTCTA
* * * * *
6811 GAAA-CTAAAATGGATTTTGAAAATCAAAATGAAATATTGAAGAAGGATTTACAACTCTCAAAAA
1 GAAAGCTAAAATAGACTTGGAAAATCAAAATGAAATATTGAAAAAGGAGTTACAACTCTCAAAAA
* * *
6875 TGAAATTTGAA-AGTATTGAAAAAGAAAATTTCAATT
66 CGAAATCTGAATACT-TTGAAAAAGAAAATTTCAATT
6911 TGAAAGTTAA
Statistics
Matches: 84, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
115 2 0.02
116 78 0.93
117 4 0.05
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.28
Consensus pattern (117 bp):
GAAAGCTAAAATAGACTTGGAAAATCAAAATGAAATATTGAAAAAGGAGTTACAACTCTCAAAAA
CGAAATCTGAATACTTTGAAAAAGAAAATTTCAATTAAACAAACTTCTTCTA
Found at i:10799 original size:21 final size:22
Alignment explanation
Indices: 10767--10829 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 22
10757 ATCCATACCC
*
10767 CCTTG-ATATGTATCGATACA-
1 CCTTGAATGTGTATCGATACAT
* *
10787 CCTTGAATGTGTACCTATACATT
1 CCTTGAATGTGTATCGATACA-T
* *
10810 CCTTTAATGTGTATTGATAC
1 CCTTGAATGTGTATCGATAC
10830 CCCCCAAGGG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 5 0.15
21 12 0.36
23 16 0.48
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (22 bp):
CCTTGAATGTGTATCGATACAT
Found at i:11442 original size:2 final size:2
Alignment explanation
Indices: 11437--11474 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
11427 TTTTTTTAAA
11437 AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11475 ATCCGGGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15542 original size:2 final size:2
Alignment explanation
Indices: 15535--15578 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
15525 TTACTATTTG
15535 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
15578 A
1 A
15579 GTGTCACTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26472 original size:504 final size:503
Alignment explanation
Indices: 25518--26529 Score: 1805
Period size: 504 Copynumber: 2.0 Consensus size: 503
25508 AGCTCTAAAG
25518 ATGCTTGTTTCGAATCTTACCTTTACAAGACTGAACTAGATATGAAGGATAACAAAGCTTCTACC
1 ATGCTTGTTTCGAATCTTACCTTTACAAGACTGAACTAGATATGAAGGATAACAAAGCTTCTACC
* *
25583 TTTTCTCAAGATACTAGGAAGATGAGAGGAAGTTTGAATGAAGGAGAAAATGACAAGGGAGCGGG
66 TTTTCTCAAGATACTAGGAAGAGGAGAGGAAGTTTGAATGAAGGAGAAAATGACAAAGGAGCGGG
*
25648 GAGAAAAATAGAGAAACATATGACCTCACCCAATATTAAAGAATTCAACATATCTAACATAAAAG
131 GAGAAAAATAGAGAAACATACGACCTCACCCAATATTAAAGAATTCAACATATCTAACATAAAAG
*
25713 GGGTAAATTGTTTCCTTGGTCCTTCAATTTTTAGTCACAATTCAAATATACCCATTTTATCATCC
196 GGGTAAATTGTTTCCTTGGTCCTTCAATTTTTAGTCACAATTCAAAGATACCCATTTTATCATCC
25778 ATTGGGCCCAAAGCAAGCCCAAACTAAAGGTCATTTGGTCCAAGTTTAATGGCCTTATCTAAACC
261 ATT-GG-----AG--AGCCCAAACTAAAGGTCATTTGGTCCAAGTTTAATGGCCTTATCTAAACC
*
25843 CTCTCGGGTTAACCCGAAATTTCTAATCTAGGATTTGGAGAGTTACATGGATCATCAAAAGATGA
318 CTCTCGGGTTAACCCAAAATTTCTAATCTAGGATTTGGAGAGTTACATGGATCATCAAAAGATGA
25908 CAACTTGTGTTATTGTATTGGGAGCTAGGAACTCAAATATGAAATTGGTAAGATATGTAGTTTAT
383 CAACTTGTGTTATTGTATTGGGAGCTAGGAACTCAAATATGAAATTGGTAAGATATGTAGTTTAT
* *
25973 AAGCGTCCATTGTTACTTTGTATGAGTTTTTTTTAGATTTCGGTTTTGTTAGTCAT
448 AAGCGTCCATTGTTACTTTGTATGAGTATTGTTTAGATTTCGGTTTTGTTAGTCAT
26029 ATGCTTGTTTCGAATCTTACCTTTACAAGACTGAACTAGATATGAAGGATAACAAAGCTTCTACC
1 ATGCTTGTTTCGAATCTTACCTTTACAAGACTGAACTAGATATGAAGGATAACAAAGCTTCTACC
26094 TTTTCTCAAGATACTAGGAAGAGGAGAGGAAGTTTGAATGAAGGAGAAAATGACAAAGGAGCGGG
66 TTTTCTCAAGATACTAGGAAGAGGAGAGGAAGTTTGAATGAAGGAGAAAATGACAAAGGAGCGGG
*
26159 GAGAAAAATAGAGAAGTCAGCATACGACCTCACCCAGTATTAAAGAATTCAACATATCTAACATA
131 GAGAAAAATAGAGAA---A-CATACGACCTCACCCAATATTAAAGAATTCAACATATCTAACATA
*
26224 AAAGGGGTAAATTGTTTCCTTGGTCCTTCAATTTTTTGTCACAATTCAAAGATACCCATTTTATC
192 AAAGGGGTAAATTGTTTCCTTGGTCCTTCAATTTTTAGTCACAATTCAAAGATACCCATTTTATC
26289 ATCCATT-G-G-GCCCAAACTAAAGGTCATTTGGTCCAAGTTTAATGGCCTTATCTAAACCCTCT
257 ATCCATTGGAGAGCCCAAACTAAAGGTCATTTGGTCCAAGTTTAATGGCCTTATCTAAACCCTCT
26351 CGGGTTAACCCAAAATTTCTAATCTAGGATTTGGAGAGTTACATGGATCATCAAAAGATGACAAC
322 CGGGTTAACCCAAAATTTCTAATCTAGGATTTGGAGAGTTACATGGATCATCAAAAGATGACAAC
*
26416 TTGTGTTATTGTATTGGGAGCTAGTAACTCAAATATGAAATTGGTAAGATATGTAGTTTATAAGC
387 TTGTGTTATTGTATTGGGAGCTAGGAACTCAAATATGAAATTGGTAAGATATGTAGTTTATAAGC
26481 GTCCATTGTTACTTTGTATGAGTATTGTTTAGATTTCGGTTTTGTTAGT
452 GTCCATTGTTACTTTGTATGAGTATTGTTTAGATTTCGGTTTTGTTAGT
26530 GATAGAGGGA
Statistics
Matches: 487, Mismatches: 10, Indels: 15
0.95 0.02 0.03
Matches are distributed among these distances:
504 228 0.47
507 1 0.00
511 143 0.29
513 1 0.00
514 1 0.00
515 113 0.23
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (503 bp):
ATGCTTGTTTCGAATCTTACCTTTACAAGACTGAACTAGATATGAAGGATAACAAAGCTTCTACC
TTTTCTCAAGATACTAGGAAGAGGAGAGGAAGTTTGAATGAAGGAGAAAATGACAAAGGAGCGGG
GAGAAAAATAGAGAAACATACGACCTCACCCAATATTAAAGAATTCAACATATCTAACATAAAAG
GGGTAAATTGTTTCCTTGGTCCTTCAATTTTTAGTCACAATTCAAAGATACCCATTTTATCATCC
ATTGGAGAGCCCAAACTAAAGGTCATTTGGTCCAAGTTTAATGGCCTTATCTAAACCCTCTCGGG
TTAACCCAAAATTTCTAATCTAGGATTTGGAGAGTTACATGGATCATCAAAAGATGACAACTTGT
GTTATTGTATTGGGAGCTAGGAACTCAAATATGAAATTGGTAAGATATGTAGTTTATAAGCGTCC
ATTGTTACTTTGTATGAGTATTGTTTAGATTTCGGTTTTGTTAGTCAT
Found at i:28369 original size:24 final size:25
Alignment explanation
Indices: 28325--28371 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
28315 AAAAATGAGT
*
28325 AAATAAACATACAAGGATTGAATTA
1 AAATAAACATAAAAGGATTGAATTA
28350 AAATAAA-ATAAAATGG-TTGAAT
1 AAATAAACATAAAA-GGATTGAAT
28372 AATAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (25 bp):
AAATAAACATAAAAGGATTGAATTA
Found at i:40648 original size:24 final size:24
Alignment explanation
Indices: 40616--40664 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
40606 AAGTGGGAGA
*
40616 TTGTTAAAAGTCCAAATTGGCAGC
1 TTGTTAAAAGCCCAAATTGGCAGC
40640 TTGTTAAAAGCCCAAATTGGCAGC
1 TTGTTAAAAGCCCAAATTGGCAGC
40664 T
1 T
40665 GCAAATTGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (24 bp):
TTGTTAAAAGCCCAAATTGGCAGC
Found at i:42428 original size:24 final size:24
Alignment explanation
Indices: 42401--42446 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
42391 TGTGACACGT
* *
42401 TTTTCTTTGTTCTTATGGCATGTG
1 TTTTCTCTGCTCTTATGGCATGTG
42425 TTTTCTCTGCTCTTATGGCATG
1 TTTTCTCTGCTCTTATGGCATG
42447 ATCCTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.09, C:0.17, G:0.20, T:0.54
Consensus pattern (24 bp):
TTTTCTCTGCTCTTATGGCATGTG
Found at i:63822 original size:20 final size:20
Alignment explanation
Indices: 63797--63834 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
63787 TAGGTTTGAG
* *
63797 TATCGATATTTGATGAACAA
1 TATCGATACTAGATGAACAA
63817 TATCGATACTAGATGAAC
1 TATCGATACTAGATGAAC
63835 TAGGAAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (20 bp):
TATCGATACTAGATGAACAA
Found at i:64662 original size:19 final size:18
Alignment explanation
Indices: 64622--64657 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
64612 TAAAATTATC
*
64622 ACATGATATTTATATAAA
1 ACATGATATTAATATAAA
64640 ACAT-ATATTAATATAAA
1 ACATGATATTAATATAAA
64657 A
1 A
64658 TACATCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (18 bp):
ACATGATATTAATATAAA
Found at i:66462 original size:20 final size:20
Alignment explanation
Indices: 66437--66477 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
66427 GGTCGTGCGT
66437 CGCCGCCTGAAAATGGTGGC
1 CGCCGCCTGAAAATGGTGGC
66457 CGCCGCCTGAAAATGGTGGC
1 CGCCGCCTGAAAATGGTGGC
66477 C
1 C
66478 ACCACCTCGC
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:0.20, C:0.32, G:0.34, T:0.15
Consensus pattern (20 bp):
CGCCGCCTGAAAATGGTGGC
Found at i:67828 original size:105 final size:106
Alignment explanation
Indices: 67584--68328 Score: 995
Period size: 106 Copynumber: 7.0 Consensus size: 106
67574 TGTACTGTTC
* * * *
67584 TGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACT-GGAAATTTTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
*
67648 ACCAGTCGTCCCTTCGTTGTGAAGTTGAAC-T-TG-TGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
67686 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGATACTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
* *
67751 ACCAGCCGT-CCTTCGTTGTGAATTTTAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
67791 CGAGTCCAATATCATTCGCTGTGAAATTGAAATTGGCTTTGAAACTGGGAAATTGTTTGTTG-GA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
67855 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
67896 TGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
*
67961 ACCAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * * *
68002 TGAGTCCAATATCCTTTACTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTTGTTGAC
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTTGTTGAC
* * * *
68067 GACCAGTCGTTCCTTCATTGTGAAGTTGAAC-TGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
68108 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGG-AATTGTTTTGTTGAC
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTTGTTGAC
* * *
68172 GACCAGCCGTCCCTTCATTGTGAAGTTAAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * ** * *
68214 TAAGTCCAATATCCTTTGCTGTGAAGATGAAATTGGCTCTGAATGAAACT-TAAAAGTGGTTTAT
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC----TGAAACTGGGAAA-TTGTTTGT
* *
68278 TGACAACCAACCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
61 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
68324 CGAGT
1 TGAGT
68329 GGTGCGATAT
Statistics
Matches: 577, Mismatches: 52, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
102 59 0.10
103 26 0.05
104 12 0.02
105 192 0.33
106 194 0.34
107 35 0.06
110 57 0.10
111 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:68644 original size:14 final size:14
Alignment explanation
Indices: 68625--68651 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
68615 CTAAAATCTT
68625 TCTGGAATCTTGAC
1 TCTGGAATCTTGAC
68639 TCTGGAATCTTGA
1 TCTGGAATCTTGA
68652 AGTTTCGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (14 bp):
TCTGGAATCTTGAC
Found at i:69329 original size:57 final size:57
Alignment explanation
Indices: 69267--69378 Score: 138
Period size: 57 Copynumber: 1.9 Consensus size: 57
69257 CTTTTGTTCT
* * *
69267 TTTTTCTCTTTTTC-ATTTTTTCAATTTAGGGTGCCCTTTCGGGTTTTCA-CCTAAACG
1 TTTTTC-CTTTTTCTATTTTTTCAACTTAGGAT-CCCTTTCAGGTTTTCATCCTAAACG
* *
69324 TTTTTCCTTTTTCTTTTTTTTTCGACTTAGGATCCCTTTCAGGTTTTCATCCTAA
1 TTTTTCCTTTTTC-TATTTTTTCAACTTAGGATCCCTTTCAGGTTTTCATCCTAA
69379 GCGAAGTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
56 7 0.15
57 21 0.45
58 19 0.40
ACGTcount: A:0.13, C:0.21, G:0.12, T:0.54
Consensus pattern (57 bp):
TTTTTCCTTTTTCTATTTTTTCAACTTAGGATCCCTTTCAGGTTTTCATCCTAAACG
Done.