Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009101.1 Hibiscus syriacus cultivar Beakdansim tig00112561_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: 62628
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3240 original size:21 final size:21
Alignment explanation
Indices: 3214--3255 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3204 ATTTTAAATT
3214 TTATATAAAATTAAAAAAAAA
1 TTATATAAAATTAAAAAAAAA
***
3235 TTATATATTTTTAAAAAAAAA
1 TTATATAAAATTAAAAAAAAA
3256 ATACAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TTATATAAAATTAAAAAAAAA
Found at i:3265 original size:21 final size:21
Alignment explanation
Indices: 3224--3266 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3214 TTATATAAAA
* * *
3224 TTAAAAAAAAATTATATATTT
1 TTAAAAAAAAAATACAAATTT
3245 TTAAAAAAAAAATACAAATTT
1 TTAAAAAAAAAATACAAATTT
3266 T
1 T
3267 GAAATAACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TTAAAAAAAAAATACAAATTT
Found at i:8773 original size:35 final size:35
Alignment explanation
Indices: 8734--8805 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
8724 CCATAGATGG
8734 AACAATCCAGTGCATGGCCCTACTCCCAATGAATT
1 AACAATCCAGTGCATGGCCCTACTCCCAATGAATT
8769 AACAATCCAGTGCATGGCCCTACTCCCAATGAATT
1 AACAATCCAGTGCATGGCCCTACTCCCAATGAATT
8804 AA
1 AA
8806 ATATTTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (35 bp):
AACAATCCAGTGCATGGCCCTACTCCCAATGAATT
Found at i:8882 original size:28 final size:28
Alignment explanation
Indices: 8850--8919 Score: 140
Period size: 28 Copynumber: 2.5 Consensus size: 28
8840 GTAATTTAGT
8850 CTCTCCTATCTTCTAATCCCAATTCCAC
1 CTCTCCTATCTTCTAATCCCAATTCCAC
8878 CTCTCCTATCTTCTAATCCCAATTCCAC
1 CTCTCCTATCTTCTAATCCCAATTCCAC
8906 CTCTCCTATCTTCT
1 CTCTCCTATCTTCT
8920 TAAATTTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.19, C:0.43, G:0.00, T:0.39
Consensus pattern (28 bp):
CTCTCCTATCTTCTAATCCCAATTCCAC
Found at i:11404 original size:27 final size:27
Alignment explanation
Indices: 11374--11431 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
11364 GTTATTTTTT
* *
11374 AGACATATTTTGTTCTACTTGGTGTTG
1 AGACATACTTTGTTCTACTTGATGTTG
*
11401 AGACATACTTTGTTCTACTTGATTTTG
1 AGACATACTTTGTTCTACTTGATGTTG
11428 AGAC
1 AGAC
11432 TTCTTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (27 bp):
AGACATACTTTGTTCTACTTGATGTTG
Found at i:11557 original size:91 final size:90
Alignment explanation
Indices: 11441--11723 Score: 323
Period size: 92 Copynumber: 3.1 Consensus size: 90
11431 CTTCTTTTTA
* * *
11441 TTTTCATTGTTGTTTTTATAGTAGTTAGTTTAATTATTGGTTTAGATATTTTGCTGTACTTGATT
1 TTTTCATTGTTG-TTTTATAGTAGTT-GTTTGATTATTGGTCTAGATATTTTGTTGTACTTGATT
*
11506 TTTAGACATATTAACTTATTATTATTG
64 TTTAGACATATTAGCTTATTATTATTG
* * * * **
11533 TTTTTATTGTTGTTTTATAATAGTTGATTTGATTATTGGTCTGGATATTTTGTTATACACGATTT
1 TTTTCATTGTTGTTTTATAGTAGTTG-TTTGATTATTGGTCTAGATATTTTGTTGTACTTGATTT
* *
11598 TTAGACATATTGGCTTATTATTATTA
65 TTAGACATATTAGCTTATTATTATTG
* * * * * * * *
11624 TTTTCATTGTTACTTTTATAGCAGTTGGTTTGATTATCGATCTAAAAATTTAGTTGCACTTGATT
1 TTTTCATTGTT-GTTTTATAGTAGTT-GTTTGATTATTGGTCTAGATATTTTGTTGTACTTGATT
**
11689 TTTAGACATATTAGCTTACCATTATTG
64 TTTAGACATATTAGCTTATTATTATTG
11716 TTTTCATT
1 TTTTCATT
11724 ATTTTTTTGA
Statistics
Matches: 158, Mismatches: 30, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
90 1 0.01
91 76 0.48
92 80 0.51
93 1 0.01
ACGTcount: A:0.24, C:0.08, G:0.14, T:0.54
Consensus pattern (90 bp):
TTTTCATTGTTGTTTTATAGTAGTTGTTTGATTATTGGTCTAGATATTTTGTTGTACTTGATTTT
TAGACATATTAGCTTATTATTATTG
Found at i:19074 original size:30 final size:31
Alignment explanation
Indices: 19009--19075 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
18999 ATCATAATTC
* *
19009 AAATGAGTCTTTATGTGAAAAAATATTGATA
1 AAATGAGTCATTATATGAAAAAATATTGATA
* * *
19040 AAATGGGTCATTATATGAAAAATTA-TGATT
1 AAATGAGTCATTATATGAAAAAATATTGATA
19070 AAATGA
1 AAATGA
19076 ACTATTATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.46, C:0.03, G:0.16, T:0.34
Consensus pattern (31 bp):
AAATGAGTCATTATATGAAAAAATATTGATA
Found at i:21257 original size:18 final size:18
Alignment explanation
Indices: 21225--21259 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21215 ATTTAAAATT
* *
21225 TAGGGTTAGTTTTTAGAG
1 TAGGGTTAATATTTAGAG
21243 TAGGGTTAATATTTAGA
1 TAGGGTTAATATTTAGA
21260 ATTTAATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (18 bp):
TAGGGTTAATATTTAGAG
Found at i:21616 original size:31 final size:32
Alignment explanation
Indices: 21550--21609 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
21540 TCTAGTTATA
* *
21550 AAAATAATCATTAAAGTTTATAAAATTATTAC
1 AAAATAATCATTAAAATTGATAAAATTATTAC
*
21582 AAAAT-ATCATTAAAATTGATTAAATTAT
1 AAAATAATCATTAAAATTGATAAAATTAT
21610 CTCAAAACGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (32 bp):
AAAATAATCATTAAAATTGATAAAATTATTAC
Found at i:24878 original size:14 final size:14
Alignment explanation
Indices: 24859--24889 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
24849 TTATCTTATG
24859 AATCTCATCAGAAA
1 AATCTCATCAGAAA
24873 AATCTCATCAGAAA
1 AATCTCATCAGAAA
24887 AAT
1 AAT
24890 ACTCGCGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (14 bp):
AATCTCATCAGAAA
Found at i:37091 original size:12 final size:12
Alignment explanation
Indices: 37074--37098 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37064 ACATCACTAT
37074 ATCCTAAGATAA
1 ATCCTAAGATAA
37086 ATCCTAAGATAA
1 ATCCTAAGATAA
37098 A
1 A
37099 CAATTGCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (12 bp):
ATCCTAAGATAA
Found at i:40420 original size:3 final size:3
Alignment explanation
Indices: 40414--40453 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
40404 TTGGAAAAAA
40414 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40454 GGGAATGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40541 original size:6 final size:6
Alignment explanation
Indices: 40530--40560 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
40520 AGTAACAGAG
40530 CAACAT CAACAT CAACAT CAACAT CAACAT C
1 CAACAT CAACAT CAACAT CAACAT CAACAT C
40561 GCACAAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.16
Consensus pattern (6 bp):
CAACAT
Found at i:41944 original size:21 final size:21
Alignment explanation
Indices: 41920--41963 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
41910 AGAGATCTCG
41920 AAATGATTACATCTCTCCAAT
1 AAATGATTACATCTCTCCAAT
*
41941 AAATGATTGCATCTCTCCAAT
1 AAATGATTACATCTCTCCAAT
41962 AA
1 AA
41964 TTCTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.32
Consensus pattern (21 bp):
AAATGATTACATCTCTCCAAT
Found at i:48766 original size:78 final size:77
Alignment explanation
Indices: 48637--48793 Score: 269
Period size: 78 Copynumber: 2.0 Consensus size: 77
48627 TGATAACTCT
* *
48637 TTCGTTTGAAAATCGAATCTGATGTGTGGAATTGAATGCGCTGTTTTAGATTTTTGTTTCTTTAA
1 TTCGTTTGAAAATCGAATCTGAGGTGTGGAACTGAATGCGCTGTTTTAGATTTTT-TTTCTTTAA
48702 TTTGATTCACTTA
65 TTTGATTCACTTA
* *
48715 TTCGTTTGAAGATCGGATCTGAGGTGTGGAACTGAATGCGCTGTTTTAGATTTTTTTTCTTTAAT
1 TTCGTTTGAAAATCGAATCTGAGGTGTGGAACTGAATGCGCTGTTTTAGATTTTTTTTCTTTAAT
48780 TTGATTCACTTA
66 TTGATTCACTTA
48792 TT
1 TT
48794 TTGTTTTGTG
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
77 24 0.32
78 51 0.68
ACGTcount: A:0.22, C:0.11, G:0.20, T:0.47
Consensus pattern (77 bp):
TTCGTTTGAAAATCGAATCTGAGGTGTGGAACTGAATGCGCTGTTTTAGATTTTTTTTCTTTAAT
TTGATTCACTTA
Found at i:49296 original size:56 final size:56
Alignment explanation
Indices: 49235--49344 Score: 211
Period size: 56 Copynumber: 2.0 Consensus size: 56
49225 CTCTTTCTGT
*
49235 GCAGTTTTATAAATGGTTCACAGACCTTGAATCGGCCATGTTGTCGGAGGTTAGAA
1 GCAGTTTTATAAATGGTTCACAGACCTTGAATCGGCCATGTGGTCGGAGGTTAGAA
49291 GCAGTTTTATAAATGGTTCACAGACCTTGAATCGGCCATGTGGTCGGAGGTTAG
1 GCAGTTTTATAAATGGTTCACAGACCTTGAATCGGCCATGTGGTCGGAGGTTAG
49345 TGGTGATATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (56 bp):
GCAGTTTTATAAATGGTTCACAGACCTTGAATCGGCCATGTGGTCGGAGGTTAGAA
Done.