Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004770.1 Hibiscus syriacus cultivar Beakdansim tig00010753_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: 65776
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1076 original size:2 final size:2
Alignment explanation
Indices: 1069--1118 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1059 TTGTGGACAC
1069 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1111 TA TA TA TA
1 TA TA TA TA
1119 ATTCAAAATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2405 original size:14 final size:14
Alignment explanation
Indices: 2368--2408 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2358 GAAATCTACT
*
2368 TTAACAGTTAATGG
1 TTAACAGTTAACGG
**
2382 TTAATGGTTAACGG
1 TTAACAGTTAACGG
2396 TTAACAGTTAACG
1 TTAACAGTTAACG
2409 TGCATTTAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (14 bp):
TTAACAGTTAACGG
Found at i:13685 original size:18 final size:19
Alignment explanation
Indices: 13662--13699 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
13652 GTTTTACAGA
*
13662 ATCAAATT-CAATTTTATC
1 ATCAAATTAAAATTTTATC
13680 ATCAAATTAAAATTTTATC
1 ATCAAATTAAAATTTTATC
13699 A
1 A
13700 ATTGATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (19 bp):
ATCAAATTAAAATTTTATC
Found at i:14053 original size:76 final size:75
Alignment explanation
Indices: 13883--14038 Score: 199
Period size: 76 Copynumber: 2.1 Consensus size: 75
13873 CCTCTCGATT
* * * *
13883 CTCAACTTGATATTAATTTAAGGATAATTTATCATTCAACTCGAATTTTAGAGTTAAAATTCATC
1 CTCAACTTAATATTAATTTAAGGATAAATTATCACTCAACTCGAATTTTAGAGTT-AAATTCACC
*
13948 CAGAACCTTAT
65 CAGAACCTTAA
*
13959 CTCAACTTGATATTAATTTAAGGATACTAATTAGTCACTCAACTCGAATTTTAGAGTT-AATTCA
1 CTCAACTTAATATTAATTTAAGGATA--AATTA-TCACTCAACTCGAATTTTAGAGTTAAATTCA
*
14023 CCCATAACC-TAA
63 CCCAGAACCTTAA
14035 CTCA
1 CTCA
14039 GTATTAATAT
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
76 32 0.44
77 13 0.18
78 4 0.06
79 23 0.32
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.36
Consensus pattern (75 bp):
CTCAACTTAATATTAATTTAAGGATAAATTATCACTCAACTCGAATTTTAGAGTTAAATTCACCC
AGAACCTTAA
Found at i:15395 original size:188 final size:186
Alignment explanation
Indices: 15048--15441 Score: 657
Period size: 188 Copynumber: 2.1 Consensus size: 186
15038 TTTTCTAATT
* * * *
15048 TATATAA-AAATTAAATATTTTATAATTCAAAAAAACAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAATTTACAATTAATTTAAATAATATATA
15112 ATTATAAAATAAAAATTGTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTGTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
* *
15177 TTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTGAGCCCATATGTTA
131 TTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
*
15233 TATATAATATATTTAATATTTTTTAATT-AAAAAAACAATTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAATTTACAATTAATTTAAATAATATATA
* *
15297 ATTATAAAATATAAATTTTATATAAATTTTTAATTAATTAATTAATATTGATTTAGGTTTAAAAG
66 ATTATAAAATAAAAATTGTATATAAA-TTTT--TTAATTAATTAATATTGATTTAGGTTTAAAAG
*
15362 TTATTGGATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
128 TTATTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
15421 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
15442 AAAATTTTAA
Statistics
Matches: 195, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
185 65 0.33
186 21 0.11
188 109 0.56
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTATAATTCAAAAAAACAATTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTGTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
TTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:15462 original size:9 final size:9
Alignment explanation
Indices: 15448--15480 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
15438 ATTTAAAATT
15448 TTAATTCGG
1 TTAATTCGG
15457 TTAATTCGG
1 TTAATTCGG
15466 TTAATTCGG
1 TTAATTCGG
15475 TTAATT
1 TTAATT
15481 AACCAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.48
Consensus pattern (9 bp):
TTAATTCGG
Found at i:22714 original size:60 final size:59
Alignment explanation
Indices: 22589--22717 Score: 161
Period size: 60 Copynumber: 2.2 Consensus size: 59
22579 CTTCACAGAA
* * * * * *
22589 AGTTGAGTGGCCAAATTGATAGCACAATTTTTAAATGGACATATTATTTGGTAGGGTGT
1 AGTTGAGTGGCCAAATTGATAGCAAAATTATTAAATGGACACATTATTTGATAGAGTAT
* *
22648 -GATTGAGTGGCCAATTTGATAGACAAAATTATTAAATGGGCACATTATTTGATAGAGTAT
1 AG-TTGAGTGGCCAAATTGATAG-CAAAATTATTAAATGGACACATTATTTGATAGAGTAT
22708 AGTTGAGTGG
1 AGTTGAGTGG
22718 TGAAAGTGGT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
58 1 0.02
59 19 0.32
60 38 0.64
61 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.34
Consensus pattern (59 bp):
AGTTGAGTGGCCAAATTGATAGCAAAATTATTAAATGGACACATTATTTGATAGAGTAT
Found at i:23622 original size:106 final size:106
Alignment explanation
Indices: 23494--23688 Score: 293
Period size: 107 Copynumber: 1.8 Consensus size: 106
23484 GGATTAATTT
*
23494 GCTTAACAGTTTGAGTGGAGTTCTATTTTTAAAATCCTCTGGT-GAAACTGGAATTCGAAATTTT
1 GCTTAACAGTTTGAGTGGAGTTCTATTTTTAAAATCCTCTGGTGGAAACCGGAATTCGAAATTTT
*
23558 AAATCTTGGCCATGGAAAGCTTAGTGGGAGAAGCATAACTA
66 AAATCTTGACCATGGAAAGCTTAGTGGGAGAAGCATAACTA
* * * *
23599 GCTTAAGAGTTTTGAGTGTAGTTCTATTTTTTAAATCTTCTGGTGGAAACCGGAATTCGAAATTT
1 GCTTAACAG-TTTGAGTGGAGTTCTATTTTTAAAATCCTCTGGTGGAAACCGGAATTCGAAATTT
* **
23664 TGAATCTTGACCATTTAAAGCTTAG
65 TAAATCTTGACCATGGAAAGCTTAG
23689 CGAGTATATA
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
105 8 0.10
106 31 0.39
107 40 0.51
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.36
Consensus pattern (106 bp):
GCTTAACAGTTTGAGTGGAGTTCTATTTTTAAAATCCTCTGGTGGAAACCGGAATTCGAAATTTT
AAATCTTGACCATGGAAAGCTTAGTGGGAGAAGCATAACTA
Found at i:32514 original size:94 final size:95
Alignment explanation
Indices: 32403--32583 Score: 319
Period size: 94 Copynumber: 1.9 Consensus size: 95
32393 TAAAGTTTAG
32403 AAATCAATTAAATATTATTTATTAAAAACAATTAATATCCATTTTCTTGTGTCATTTTTATTTTA
1 AAATCAATTAAATATTATTTATTAAAAACAATTAATATCCATTTTCTTGTGTCATTTTTATTTTA
*
32468 AAATAC-AAAATTTATGTATTTATTTAAAA
66 AAATACAAAAAATTATGTATTTATTTAAAA
* * *
32497 AAATCAATTAAATATTATTTATTAAAAATAATTAATATCTATTTTCTTTTGTCATTTTTATTTTA
1 AAATCAATTAAATATTATTTATTAAAAACAATTAATATCCATTTTCTTGTGTCATTTTTATTTTA
32562 AAATACAAAAAATTATGTATTT
66 AAATACAAAAAATTATGTATTT
32584 TTCCTTCTTT
Statistics
Matches: 82, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
94 68 0.83
95 14 0.17
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.48
Consensus pattern (95 bp):
AAATCAATTAAATATTATTTATTAAAAACAATTAATATCCATTTTCTTGTGTCATTTTTATTTTA
AAATACAAAAAATTATGTATTTATTTAAAA
Found at i:32523 original size:24 final size:23
Alignment explanation
Indices: 32487--32540 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
32477 ATTTATGTAT
32487 TTATTT-AAAAAAATCAATTAAATA
1 TTATTTAAAAAAAAT-AATT-AATA
**
32511 TTATTTATTAAAAATAATTAATA
1 TTATTTAAAAAAAATAATTAATA
32534 TCTATTT
1 T-TATTT
32541 TCTTTTGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 5 0.19
24 15 0.58
25 6 0.23
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TTATTTAAAAAAAATAATTAATA
Found at i:32643 original size:22 final size:22
Alignment explanation
Indices: 32618--32660 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
32608 TTAAAGTTGA
32618 TGACTTCAATAAAATTATAAAG
1 TGACTTCAATAAAATTATAAAG
*
32640 TGACTTTAATAAAATTATAAA
1 TGACTTCAATAAAATTATAAA
32661 ATGTTTCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (22 bp):
TGACTTCAATAAAATTATAAAG
Found at i:34805 original size:39 final size:39
Alignment explanation
Indices: 34748--34853 Score: 124
Period size: 39 Copynumber: 2.7 Consensus size: 39
34738 CATAATTTTC
* * * *
34748 AAATTAATTT-ACCCTAACATTATAAATTCTCAATCTGTT
1 AAATT-ATTTCACCATAACATTCTAAATTCTAAATCTCTT
* *
34787 AAATTATTTCACCATAACATTCTAAATTTTAAATTTCTT
1 AAATTATTTCACCATAACATTCTAAATTCTAAATCTCTT
* *
34826 AAATTATTTCATCATAAGATTCTAAATT
1 AAATTATTTCACCATAACATTCTAAATT
34854 GTTTCTCAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 4 0.07
39 54 0.93
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.43
Consensus pattern (39 bp):
AAATTATTTCACCATAACATTCTAAATTCTAAATCTCTT
Found at i:41163 original size:6 final size:6
Alignment explanation
Indices: 41152--41176 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41142 AACTACTCCC
41152 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
41177 TAAATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:52406 original size:2 final size:2
Alignment explanation
Indices: 52399--52423 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52389 CTAATATTCT
52399 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
52424 TTGTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60449 original size:14 final size:14
Alignment explanation
Indices: 60423--60456 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
60413 TGTAATAGTA
60423 AATTTAGACTGTTT
1 AATTTAGACTGTTT
60437 AATTT-GACTTGTTT
1 AATTTAGAC-TGTTT
60451 AATTTA
1 AATTTA
60457 TCAGTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (14 bp):
AATTTAGACTGTTT
Done.