Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_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: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 26
Found at i:5076364 original size:3 final size:3
Alignment explanation
Indices: 5076358--5076399 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
5076348 TAAGCAAAGG
5076358 AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
5076400 ATGACCTACG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5076385 original size:19 final size:19
Alignment explanation
Indices: 5076361--5076401 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
5076351 GCAAAGGAAT
5076361 AATAATAATAATAATAATA
1 AATAATAATAATAATAATA
5076380 AATAATAATAATAATAATA
1 AATAATAATAATAATAATA
5076399 AAT
1 AAT
5076402 GACCTACGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAATAATAATAATAATA
Found at i:5077109 original size:41 final size:41
Alignment explanation
Indices: 5077058--5077168 Score: 141
Period size: 41 Copynumber: 2.7 Consensus size: 41
5077048 TAAATATATC
* * *
5077058 GTGGAGTTTTTAGATAAACGTCGCTAAATCCTAGTACTTTA
1 GTGGCGTTTTTTGACAAACGTCGCTAAATCCTAGTACTTTA
** * * *
5077099 GTGGTTTTTTTTGACAAACATCGCTAAAACCTATTACTTTA
1 GTGGCGTTTTTTGACAAACGTCGCTAAATCCTAGTACTTTA
*
5077140 GTGGCGTTTTTTGACAAACGCCGCTAAAT
1 GTGGCGTTTTTTGACAAACGTCGCTAAAT
5077169 ACTCACACAT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (41 bp):
GTGGCGTTTTTTGACAAACGTCGCTAAATCCTAGTACTTTA
Found at i:5077578 original size:22 final size:22
Alignment explanation
Indices: 5077550--5077598 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
5077540 GGTGCCGCCT
5077550 CCGCCCAAACGGAAGCCATGGA
1 CCGCCCAAACGGAAGCCATGGA
5077572 CCGCCCAAACGGAAGCCATGGA
1 CCGCCCAAACGGAAGCCATGGA
5077594 CCGCC
1 CCGCC
5077599 GTGAGCGGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.29, C:0.41, G:0.27, T:0.04
Consensus pattern (22 bp):
CCGCCCAAACGGAAGCCATGGA
Found at i:5080524 original size:43 final size:43
Alignment explanation
Indices: 5080475--5080672 Score: 177
Period size: 43 Copynumber: 4.6 Consensus size: 43
5080465 ACATTTTACT
* *
5080475 GCGTTTGTGGGAAAAATGCCGCTAAACATCATCACCTTCTGCG
1 GCGTTTGTGGGAAAAACGCCGCTAAACATCAACACCTTCTGCG
* * *
5080518 GCGTTTGTGGGAAAAACGCCGCAAAATATCAAAACCTTCTGCG
1 GCGTTTGTGGGAAAAACGCCGCTAAACATCAACACCTTCTGCG
** * * * *
5080561 GCGTTTGTAAGTAAAATGCCGCTAAATC-TCAACACCTACCGCG
1 GCGTTTGTGGGAAAAACGCCGCTAAA-CATCAACACCTTCTGCG
* * *
5080604 ACGCTTGTAGGG-AAAACGCCGCTAAACATTAACACCTAT-TGCG
1 GCGTTTGT-GGGAAAAACGCCGCTAAACATCAACACCT-TCTGCG
* * ** *
5080647 GCATTTTTCTGACAAACGCCGCTAAA
1 GCGTTTGTGGGAAAAACGCCGCTAAA
5080673 TAACAAACCC
Statistics
Matches: 121, Mismatches: 29, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
42 2 0.02
43 118 0.98
44 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (43 bp):
GCGTTTGTGGGAAAAACGCCGCTAAACATCAACACCTTCTGCG
Found at i:5083312 original size:27 final size:27
Alignment explanation
Indices: 5083281--5083337 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
5083271 AAGTAAGACA
5083281 TTATTAACACATACATCATCAAGATGG
1 TTATTAACACATACATCATCAAGATGG
* * * * *
5083308 TTATTTATACATATATTATTAAGATGG
1 TTATTAACACATACATCATCAAGATGG
5083335 TTA
1 TTA
5083338 GAAATCACCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.40
Consensus pattern (27 bp):
TTATTAACACATACATCATCAAGATGG
Found at i:5085079 original size:25 final size:26
Alignment explanation
Indices: 5085038--5085087 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
5085028 TTAAAAGAAA
*
5085038 TAAGAATATTAACATAGGA-AAAAATT
1 TAAGAATATTAAAATA-GATAAAAATT
5085064 TAAGAA-ATTAAAATAGATAAAAAT
1 TAAGAATATTAAAATAGATAAAAAT
5085088 AAATTTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 2 0.09
25 14 0.64
26 6 0.27
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (26 bp):
TAAGAATATTAAAATAGATAAAAATT
Found at i:5086107 original size:48 final size:50
Alignment explanation
Indices: 5086013--5086108 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 50
5086003 CATCCTTAAA
5086013 AATTATATTTTAAAAATTATTTAAAAAATAAAAAAAAAACTCATCTCTTC
1 AATTATATTTTAAAAATTATTTAAAAAATAAAAAAAAAACTCATCTCTTC
5086063 AATTA-ATTTTAAAAATTATTTAAAAAA-AATAAAAAAAA-TCATCTCT
1 AATTATATTTTAAAAATTATTTAAAAAATAA-AAAAAAAACTCATCTCT
5086109 AATTTGAAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
48 10 0.22
49 30 0.67
50 5 0.11
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.35
Consensus pattern (50 bp):
AATTATATTTTAAAAATTATTTAAAAAATAAAAAAAAAACTCATCTCTTC
Found at i:5086293 original size:12 final size:13
Alignment explanation
Indices: 5086276--5086304 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5086266 AAGTCTCAAC
5086276 TCCCCAT-CCCCA
1 TCCCCATCCCCCA
5086288 TCCCCATCCCCCA
1 TCCCCATCCCCCA
5086301 TCCC
1 TCCC
5086305 TCAACCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.14, C:0.69, G:0.00, T:0.17
Consensus pattern (13 bp):
TCCCCATCCCCCA
Found at i:5087735 original size:22 final size:21
Alignment explanation
Indices: 5087687--5087736 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
5087677 CTTGGGTTGG
* * *
5087687 TGTTTTTGAATGGTATACTCA
1 TGTTTTGGAAGGGTAAACTCA
*
5087708 TATTTTGGAAGGGTAAACTACA
1 TGTTTTGGAAGGGTAAACT-CA
5087730 TGTTTTG
1 TGTTTTG
5087737 TGTCCAACTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (21 bp):
TGTTTTGGAAGGGTAAACTCA
Found at i:5089832 original size:22 final size:22
Alignment explanation
Indices: 5089807--5089848 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5089797 ATATGCTTTA
5089807 ATGTAT-GAAATGTGAATGCAAC
1 ATGTATCGAAATGT-AATGCAAC
*
5089829 ATGTATCTAAATGTAATGCA
1 ATGTATCGAAATGTAATGCA
5089849 TGATTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (22 bp):
ATGTATCGAAATGTAATGCAAC
Found at i:5091632 original size:11 final size:11
Alignment explanation
Indices: 5091602--5091652 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
5091592 ATTCAATTTC
5091602 TTTTTCTTCTTT
1 TTTTTC-TCTTT
5091614 TCTTTTCTCTTT
1 T-TTTTCTCTTT
5091626 TTTTTCTCTTT
1 TTTTTCTCTTT
5091637 TTTTT-TCTTT
1 TTTTTCTCTTT
5091647 TCTTTT
1 T-TTTT
5091653 TTTCCTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.16
11 19 0.51
12 7 0.19
13 5 0.14
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTCTTT
Found at i:5091635 original size:23 final size:25
Alignment explanation
Indices: 5091602--5091654 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
5091592 ATTCAATTTC
5091602 TTTTTCTTCTTTTCTTTTCTCTT-T
1 TTTTTCTTCTTTTCTTTTCTCTTCT
* *
5091626 TTTTTC-TCTTTTTTTTTCTTTTCT
1 TTTTTCTTCTTTTCTTTTCTCTTCT
5091650 TTTTT
1 TTTTT
5091655 TCCTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (25 bp):
TTTTTCTTCTTTTCTTTTCTCTTCT
Found at i:5091652 original size:10 final size:10
Alignment explanation
Indices: 5091598--5091652 Score: 53
Period size: 10 Copynumber: 5.8 Consensus size: 10
5091588 CTTGATTCAA
5091598 TTTCTTTT-T
1 TTTCTTTTCT
*
5091607 CTTCTTTTCT
1 TTTCTTTTCT
*
5091617 TTTCTCTT-T
1 TTTCTTTTCT
*
5091626 TTT-TTCTCT
1 TTTCTTTTCT
*
5091635 TTTTTTTTCT
1 TTTCTTTTCT
5091645 TTTCTTTT
1 TTTCTTTT
5091653 TTTCCTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
8 2 0.06
9 15 0.42
10 19 0.53
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTCTTTTCT
Found at i:5091664 original size:12 final size:12
Alignment explanation
Indices: 5091602--5091667 Score: 73
Period size: 12 Copynumber: 5.4 Consensus size: 12
5091592 ATTCAATTTC
5091602 TTTTTCTTCTTTT
1 TTTTTC-TCTTTT
*
5091615 CTTTTCTC-TTT
1 TTTTTCTCTTTT
5091626 TTTTTCTCTTTT
1 TTTTTCTCTTTT
*
5091638 TTTTTCTTTTCTT
1 TTTTTCTCTT-TT
5091651 TTTTTC-CTTATT
1 TTTTTCTCTT-TT
5091663 TTTTT
1 TTTTT
5091668 TGATGGATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.22
12 23 0.50
13 13 0.28
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:5091665 original size:13 final size:11
Alignment explanation
Indices: 5091602--5091668 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
5091592 ATTCAATTTC
5091602 TTTTTCTTCTTT
1 TTTTTCTT-TTT
*
5091614 TCTTTTCTCTTT
1 T-TTTTCTTTTT
5091626 TTTTTCTCTTTT
1 TTTTTCT-TTTT
5091638 TTTTTCTTTTCTT
1 TTTTTC-TTT-TT
5091651 TTTTTCCTTATTT
1 TTTTT-CTT-TTT
5091664 TTTTT
1 TTTTT
5091669 GATGGATGAG
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
11 6 0.13
12 16 0.34
13 23 0.49
14 2 0.04
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:5091665 original size:28 final size:28
Alignment explanation
Indices: 5091611--5091668 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
5091601 CTTTTTCTTC
*
5091611 TTTTCTTTTCTCTTTTTTTTCTCTTTTT
1 TTTTCTTTTCTCTTTTTTTTATCTTTTT
5091639 TTTTCTTTTCT-TTTTTTCCTTAT-TTTTT
1 TTTTCTTTTCTCTTTTTT--TTATCTTTTT
5091667 TT
1 TT
5091669 GATGGATGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 6 0.22
28 18 0.67
29 3 0.11
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.83
Consensus pattern (28 bp):
TTTTCTTTTCTCTTTTTTTTATCTTTTT
Done.