Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008249.1 Hibiscus syriacus cultivar Beakdansim tig00110901_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: 175145
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:169556 original size:12 final size:11
Alignment explanation
Indices: 169452--169713 Score: 74
Period size: 11 Copynumber: 23.3 Consensus size: 11
169442 TAACCTATAG
169452 TATATAATTTA
1 TATATAATTTA
*
169463 TAAACTATAGTTTA
1 T--A-TATAATTTA
*
169477 TAT-TAATGTA
1 TATATAATTTA
*
169487 CTATATAGTTTA
1 -TATATAATTTA
169499 TAT-TAATGTTA
1 TATATAAT-TTA
169510 -AT-T-ATCTTA
1 TATATAAT-TTA
169519 -ACTATAATTTA
1 TA-TATAATTTA
*
169530 TAT-TAATATA
1 TATATAATTTA
169540 GTATATAATTTA
1 -TATATAATTTA
169552 CTATATAATTTA
1 -TATATAATTTA
* *
169564 AATAT-AGTTA
1 TATATAATTTA
169574 TAT-TAATATTA
1 TATATAAT-TTA
169585 -ATATTAATTTA
1 TATA-TAATTTA
*
169596 TAGACTATATTTA
1 TATA-TA-ATTTA
169609 TAT-TAATATTA
1 TATATAAT-TTA
* *
169620 -ATTACAAATTA
1 TA-TATAATTTA
*
169631 TAAACT-ATATTA
1 TATA-TAAT-TTA
*
169643 TAT-TAATATA
1 TATATAATTTA
*
169653 AAT-TAATATTA
1 TATATAAT-TTA
169664 -ATAATAATTATA
1 TAT-ATAATT-TA
169676 TTAATATTAA-TTA
1 -T-ATA-TAATTTA
169689 TAATATAA-TTA
1 T-ATATAATTTA
169700 TATATAATTTA
1 TATATAATTTA
169711 TAT
1 TAT
169714 TAAGGGCGGG
Statistics
Matches: 191, Mismatches: 26, Indels: 68
0.67 0.09 0.24
Matches are distributed among these distances:
9 7 0.04
10 47 0.25
11 58 0.30
12 53 0.28
13 10 0.05
14 11 0.06
15 5 0.03
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (11 bp):
TATATAATTTA
Found at i:169582 original size:6 final size:6
Alignment explanation
Indices: 169573--169686 Score: 62
Period size: 6 Copynumber: 19.3 Consensus size: 6
169563 AAATATAGTT
* * *
169573 ATATTA ATATTA ATATTA AT-TTA TAGACT- ATATTT ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA -ATATTA ATATTA ATATTA ATATTA
** * * *
169620 ATTACAA ATTATAA ACTATATT ATATTA ATA-TA A-ATTA ATATTA ATAAT-
1 A-TATTA A-TATTA A-TAT-TA ATATTA ATATTA ATATTA ATATTA ATATTA
169669 A-ATT- ATATTA ATATTA AT
1 ATATTA ATATTA ATATTA AT
169687 TATAATATAA
Statistics
Matches: 85, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
4 4 0.05
5 16 0.19
6 47 0.55
7 17 0.20
8 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (6 bp):
ATATTA
Found at i:169612 original size:35 final size:33
Alignment explanation
Indices: 169536--169686 Score: 131
Period size: 35 Copynumber: 4.6 Consensus size: 33
169526 TTTATATTAA
* *
169536 TATAGTATA-TAAT-TTACTATATAATTTA-AA-
1 TATATTATATTAATATTAATAT-TAATTTATAAC
169566 TATAGTTATATTAATATTAATATTAATTTATAGAC
1 TATA-TTATATTAATATTAATATTAATTTATA-AC
* *
169601 TATATTTATATTAATATTAAT-TACAAATTATAAAC
1 TATA-TTATATTAATATTAATAT-TAATTTAT-AAC
169636 TATATTATATTAATA-TAA-ATTAATATTAATAA-
1 TATATTATATTAATATTAATATTAAT-TT-ATAAC
169668 TA-ATTATATTAATATTAAT
1 TATATTATATTAATATTAAT
169687 TATAATATAA
Statistics
Matches: 101, Mismatches: 7, Indels: 23
0.77 0.05 0.18
Matches are distributed among these distances:
30 4 0.04
31 16 0.16
32 18 0.18
33 15 0.15
34 15 0.15
35 32 0.32
36 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (33 bp):
TATATTATATTAATATTAATATTAATTTATAAC
Found at i:169691 original size:21 final size:21
Alignment explanation
Indices: 169516--169708 Score: 83
Period size: 21 Copynumber: 9.3 Consensus size: 21
169506 GTTAATTATC
*
169516 TTAACTATAATTTATATTAATA
1 TTAATTATAA-TTATATTAATA
*
169538 -TAGTATATAATTTACTATATAAT-
1 TTAAT-TATAA-TTA-TAT-TAATA
* *
169561 TTAAATATAGTTATATTAATA
1 TTAATTATAATTATATTAATA
169582 TTAA-TATTAATT-TA-TAGACTA
1 TTAATTA-TAATTATATTA-A-TA
*
169603 -TATTTAT-ATTAATATTAATTA
1 TTAATTATAATT-ATATTAA-TA
** *
169624 CAAATTATAAACTATATT-ATA
1 TTAATTAT-AATTATATTAATA
169645 TTAA-TAT-A--A-ATTAATA
1 TTAATTATAATTATATTAATA
*
169661 TTAATAATAATTATATTAATA
1 TTAATTATAATTATATTAATA
169682 TTAATTATAA-TATAATT-ATA
1 TTAATTATAATTAT-ATTAATA
169702 TATAATT
1 T-TAATT
169709 TATATTAAGG
Statistics
Matches: 133, Mismatches: 15, Indels: 47
0.68 0.08 0.24
Matches are distributed among these distances:
15 3 0.02
16 8 0.06
17 2 0.02
18 2 0.02
19 5 0.04
20 23 0.17
21 50 0.38
22 20 0.15
23 12 0.09
24 8 0.06
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAATTATAATTATATTAATA
Found at i:169700 original size:69 final size:70
Alignment explanation
Indices: 169553--169716 Score: 177
Period size: 69 Copynumber: 2.4 Consensus size: 70
169543 TATAATTTAC
169553 TATATAATT-TAAATATAGTTATATTAATATTAATATTAATTTATAGACTATATTTATATTAATA
1 TATATAATTATAAATATAGTTATATTAATATTAATATTAATTTATAGACTATATTTATATTAATA
169617 TTAAT
66 TTAAT
*
169622 TACA-AATTATAAACTATA-TTATATTAATA-TAA-ATTAATATTAATA-A-TA-A-TTATATTA
1 TATATAATTATAAA-TATAGTTATATTAATATTAATATTAAT-TT-ATAGACTATATTTATATTA
169679 ATATTAATT
63 ATATTAA-T
* *
169688 ATAATATAATTATATATA-ATTTATATTAA
1 -T-ATATAATTATAAATATAGTTATATTAA
169717 GGGCGGGAAC
Statistics
Matches: 83, Mismatches: 3, Indels: 19
0.79 0.03 0.18
Matches are distributed among these distances:
65 15 0.18
66 2 0.02
67 10 0.12
68 23 0.28
69 29 0.35
70 4 0.05
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (70 bp):
TATATAATTATAAATATAGTTATATTAATATTAATATTAATTTATAGACTATATTTATATTAATA
TTAAT
Found at i:170097 original size:39 final size:39
Alignment explanation
Indices: 170025--170100 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 39
170015 GATTTTATTT
* *
170025 ATTAAATGAACGAACTGAACAAGATTTTGTGTTCGTTTA
1 ATTAAATGAACGAACTGAACAAGAGTCTGTGTTCGTTTA
170064 ATTAAATGAACGAACATGAACATAG-GTCT-TGTTCGTT
1 ATTAAATGAACGAAC-TGAACA-AGAGTCTGTGTTCGTT
170101 ATTACGTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 23 0.70
40 8 0.24
41 2 0.06
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (39 bp):
ATTAAATGAACGAACTGAACAAGAGTCTGTGTTCGTTTA
Found at i:170138 original size:14 final size:13
Alignment explanation
Indices: 170115--170184 Score: 74
Period size: 14 Copynumber: 5.3 Consensus size: 13
170105 CGTTCGTGAA
170115 CGTTCGGTTATGTT
1 CGTTC-GTTATGTT
170129 CGTTCAGTTATGTT
1 CGTTC-GTTATGTT
*
170143 CGTT--TT-CGTT
1 CGTTCGTTATGTT
170153 CGTTCGATTATGTT
1 CGTTCG-TTATGTT
170167 CGTTCGATTATGTT
1 CGTTCG-TTATGTT
170181 CGTT
1 CGTT
170185 TATGTTCATT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
10 7 0.14
11 2 0.04
13 2 0.04
14 38 0.78
ACGTcount: A:0.10, C:0.16, G:0.23, T:0.51
Consensus pattern (13 bp):
CGTTCGTTATGTT
Found at i:170143 original size:24 final size:25
Alignment explanation
Indices: 170116--170168 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
170106 GTTCGTGAAC
170116 GTTCGGTTAT-GTTCGTTC-AGTTAT
1 GTTCGGTTATCGTTCGTTCGA-TTAT
*
170140 GTTC-GTTTTCGTTCGTTCGATTAT
1 GTTCGGTTATCGTTCGTTCGATTAT
170164 GTTCG
1 GTTCG
170169 TTCGATTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 4 0.16
24 20 0.80
25 1 0.04
ACGTcount: A:0.09, C:0.15, G:0.25, T:0.51
Consensus pattern (25 bp):
GTTCGGTTATCGTTCGTTCGATTAT
Found at i:171281 original size:16 final size:16
Alignment explanation
Indices: 171260--171295 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
171250 GGGTCTCCAA
171260 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
171276 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
171292 CGTT
1 CGTT
171296 ATTAAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.06, C:0.14, G:0.25, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Done.