Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002068.1 Hibiscus syriacus cultivar Beakdansim tig00004220_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: 75261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2571 original size:40 final size:43
Alignment explanation
Indices: 2516--2605 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
2506 TGATTTATCA
2516 TATTAATGGACTCAGTAGG-AAATC-AAA-AAAATTGCATGATT
1 TATT-ATGGACTCAGTAGGCAAATCAAAATAAAATTGCATGATT
** *
2557 TATTATGGACTCAGTAGGCATTTCAAAATAAAATTGCATGCTT
1 TATTATGGACTCAGTAGGCAAATCAAAATAAAATTGCATGATT
2600 TATTAT
1 TATTAT
2606 AATGGACAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 14 0.33
41 7 0.16
42 3 0.07
43 19 0.44
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (43 bp):
TATTATGGACTCAGTAGGCAAATCAAAATAAAATTGCATGATT
Found at i:5771 original size:22 final size:23
Alignment explanation
Indices: 5730--5772 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5720 TTATTTTAAA
* *
5730 AAAATCTTAATTTTTTAATTCTG
1 AAAATCCTAATTTTTAAATTCTG
5753 AAAATCCTAA-TTTTAAATTC
1 AAAATCCTAATTTTTAAATTC
5773 CATTACTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATCCTAATTTTTAAATTCTG
Found at i:6115 original size:2 final size:2
Alignment explanation
Indices: 6110--6138 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6100 TGTGAATAAT
6110 TA TA 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 TA TA T
6139 TGTAGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6739 original size:15 final size:15
Alignment explanation
Indices: 6719--6749 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6709 CATGGCAACT
6719 TTCTTAATCATCTTC
1 TTCTTAATCATCTTC
*
6734 TTCTTAATCGTCTTC
1 TTCTTAATCATCTTC
6749 T
1 T
6750 CGATACGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.26, G:0.03, T:0.55
Consensus pattern (15 bp):
TTCTTAATCATCTTC
Found at i:30087 original size:37 final size:36
Alignment explanation
Indices: 30041--30112 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 36
30031 TACATCACCT
30041 ATAAATATTTATCTCGTTAAACTATAAATATCTTATA
1 ATAAATATTTATCTCGTTAAACTATAAATAT-TTATA
*
30078 ATAAATATTTATCTCGTTAACCTATAAATATTTAT
1 ATAAATATTTATCTCGTTAAACTATAAATATTTAT
30113 CATCACCTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 4 0.12
37 30 0.88
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (36 bp):
ATAAATATTTATCTCGTTAAACTATAAATATTTATA
Found at i:30690 original size:17 final size:17
Alignment explanation
Indices: 30668--30708 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
30658 AACCGTTAAC
*
30668 TGACCGAATTAATT-TGG
1 TGACCGAACTAATTCT-G
30685 TGACCGAACTAATTCTG
1 TGACCGAACTAATTCTG
30702 TGACCGA
1 TGACCGA
30709 CTGAATTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (17 bp):
TGACCGAACTAATTCTG
Found at i:41870 original size:15 final size:16
Alignment explanation
Indices: 41833--41864 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41823 TATTCAATAA
41833 TAAATAAACTTTTTTT
1 TAAATAAACTTTTTTT
41849 TAAATAAACTTTTTTT
1 TAAATAAACTTTTTTT
41865 GGATAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAATAAACTTTTTTT
Found at i:46753 original size:24 final size:24
Alignment explanation
Indices: 46716--46768 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
46706 CATTAAAATG
*
46716 ATAAACGAACACAAGCGAACGAAC
1 ATAAACGAACACAAACGAACGAAC
* * *
46740 GTAAATGAATACAAACGAACGAAC
1 ATAAACGAACACAAACGAACGAAC
46764 ATAAA
1 ATAAA
46769 ATTAATTGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.19, G:0.15, T:0.09
Consensus pattern (24 bp):
ATAAACGAACACAAACGAACGAAC
Found at i:47787 original size:16 final size:19
Alignment explanation
Indices: 47758--47797 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 19
47748 ATTGGTGTTA
47758 TTAT-TTTATATTGT-C-T
1 TTATGTTTATATTGTACTT
47774 TTATGTTTAT-TTGTACTT
1 TTATGTTTATATTGTACTT
47792 TTATGT
1 TTATGT
47798 AGACTAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 8 0.38
17 6 0.29
18 7 0.33
ACGTcount: A:0.17, C:0.05, G:0.10, T:0.68
Consensus pattern (19 bp):
TTATGTTTATATTGTACTT
Found at i:48108 original size:13 final size:13
Alignment explanation
Indices: 48090--48114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48080 ATAAATTTAT
48090 TTCCTTGCTCTAC
1 TTCCTTGCTCTAC
48103 TTCCTTGCTCTA
1 TTCCTTGCTCTA
48115 GAAAACTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.36, G:0.08, T:0.48
Consensus pattern (13 bp):
TTCCTTGCTCTAC
Found at i:48837 original size:49 final size:49
Alignment explanation
Indices: 48780--48907 Score: 213
Period size: 49 Copynumber: 2.6 Consensus size: 49
48770 GCTCTTAGTG
* *
48780 CAGTCGTTAGTATTCTAACGATGTTCCATTACGCTCGACATGTTTTTAC
1 CAGTCGTTAGTATTCTAACGATGTTCCATTACGATCGAAATGTTTTTAC
*
48829 CAGTCGTTAGTATTCTAACGATGTTCCATTACGATCGAAATGTTTTTGC
1 CAGTCGTTAGTATTCTAACGATGTTCCATTACGATCGAAATGTTTTTAC
*
48878 CAGTCGTTAATATTCTAAC-ATGTTCCATTA
1 CAGTCGTTAGTATTCTAACGATGTTCCATTA
48908 TGTTTGGCAT
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
48 11 0.15
49 64 0.85
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (49 bp):
CAGTCGTTAGTATTCTAACGATGTTCCATTACGATCGAAATGTTTTTAC
Found at i:67982 original size:27 final size:26
Alignment explanation
Indices: 67947--67997 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
67937 TAAATATGAA
* * *
67947 TGATTAAATTTATTGAATATCAAATCC
1 TGATAAAATTGATAGAATAT-AAATCC
67974 TGATAAAATTGATAGAATATAAAT
1 TGATAAAATTGATAGAATATAAAT
67998 TTTGGAGACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (26 bp):
TGATAAAATTGATAGAATATAAATCC
Found at i:68612 original size:31 final size:31
Alignment explanation
Indices: 68545--68604 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
68535 CAATTTAAGG
*
68545 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
68576 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
68605 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:68828 original size:21 final size:21
Alignment explanation
Indices: 68802--68842 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
68792 ATTTGAATAT
*
68802 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTAGCGATTCCC
68823 TATGAAGGGGTAGCGATTCC
1 TATGAAGGGGTAGCGATTCC
68843 TCCCATTCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTAGCGATTCCC
Found at i:68905 original size:21 final size:21
Alignment explanation
Indices: 68872--68911 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
68862 TTTTTGCAGA
*
68872 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
68894 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
68912 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:69165 original size:34 final size:32
Alignment explanation
Indices: 69126--69195 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
69116 TTTTGTAAAG
*
69126 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
69160 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
69192 GGGA
1 GGGA
69196 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Done.