Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007375.1 Hibiscus syriacus cultivar Beakdansim tig00019793_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: 56412
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:4095 original size:15 final size:15
Alignment explanation
Indices: 4077--4105 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4067 TTTTTAAAAA
4077 TAATTTGATTTGATT
1 TAATTTGATTTGATT
4092 TAATTTGATTTGAT
1 TAATTTGATTTGAT
4106 CAGATCGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (15 bp):
TAATTTGATTTGATT
Found at i:4257 original size:21 final size:18
Alignment explanation
Indices: 4241--4277 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4231 ATATCATTAT
4241 ATTATTATTTTTAATCAA
1 ATTATTATTTTTAATCAA
4259 ATTATTATTTTTAAT-AA
1 ATTATTATTTTTAATCAA
4276 AT
1 AT
4278 AAAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATTATTTTTAATCAA
Found at i:11790 original size:3 final size:3
Alignment explanation
Indices: 11782--11811 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
11772 TGAACCCTTG
11782 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
11812 ATCCTTGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
GCT
Found at i:12015 original size:41 final size:43
Alignment explanation
Indices: 11931--12017 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 43
11921 ATTACTTAAG
* *
11931 ATTATTTAATTGTTTGGGTAAATTACTAATTTAGCAATTGAACT
1 ATTATTTAATTATTTGGATAAATTAC-AATTTAGCAATTGAACT
* *
11975 ATTATTTAATTATTTGGATATA-TA-AATTTAGTAATTGAACT
1 ATTATTTAATTATTTGGATAAATTACAATTTAGCAATTGAACT
12016 AT
1 AT
12018 CTTCTTTCTC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
41 18 0.46
43 2 0.05
44 19 0.49
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (43 bp):
ATTATTTAATTATTTGGATAAATTACAATTTAGCAATTGAACT
Found at i:12699 original size:35 final size:35
Alignment explanation
Indices: 12660--12730 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
12650 ACTTTGGGAG
12660 TCTTTTGTGATACACTAAGTTTTGGTGTATATATA
1 TCTTTTGTGATACACTAAGTTTTGGTGTATATATA
*
12695 TCTTTTGTGATATACTAAGTTTTGGTGTATATATA
1 TCTTTTGTGATACACTAAGTTTTGGTGTATATATA
12730 T
1 T
12731 TAAGCAGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.25, C:0.07, G:0.17, T:0.51
Consensus pattern (35 bp):
TCTTTTGTGATACACTAAGTTTTGGTGTATATATA
Found at i:13278 original size:42 final size:43
Alignment explanation
Indices: 13219--13317 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 43
13209 AACATGTTTG
* *
13219 ATATTTAGCGGCGTTTGTGGTTACAAATGC-CCAATATATTAA
1 ATATTTAGCGGCGTTTGTAGTCACAAATGCTCCAATATATTAA
* * * **
13261 ATATTTAGCTGCGTTTGTAGTCAGAAATGCTGCAATATATTTG
1 ATATTTAGCGGCGTTTGTAGTCACAAATGCTCCAATATATTAA
*
13304 ATATGTAGCGGCGT
1 ATATTTAGCGGCGT
13318 GTCTGGCAGA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 26 0.55
43 21 0.45
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.36
Consensus pattern (43 bp):
ATATTTAGCGGCGTTTGTAGTCACAAATGCTCCAATATATTAA
Found at i:14709 original size:45 final size:44
Alignment explanation
Indices: 14654--14758 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 44
14644 GCACCAATCC
*
14654 ATGCATCGATGCACCATTGAATAAATT-GAACATCGAATGCATTTT
1 ATGCATCGATGCACCA--GAATAAATTAAAACATCGAATGCATTTT
** **
14699 ATGCATCGATGCACTCAGGCTATTTTAAAACATCGAATGCATTTT
1 ATGCATCGATGCAC-CAGAATAAATTAAAACATCGAATGCATTTT
14744 ATGCATCGATGCACC
1 ATGCATCGATGCACC
14759 CTTAGTGCAC
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
44 6 0.11
45 45 0.85
46 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (44 bp):
ATGCATCGATGCACCAGAATAAATTAAAACATCGAATGCATTTT
Found at i:23686 original size:64 final size:65
Alignment explanation
Indices: 23570--23695 Score: 202
Period size: 64 Copynumber: 1.9 Consensus size: 65
23560 TGCATCAATC
*
23570 CATGCATCGATGCACTCAGGTTTTTATGAAAAACATCGAATGCATTTGATGCATCGATGCACAAG
1 CATGCATCGATGCACTCAGGTATTTAT-AAAAACATCGAATGCATTTGATGCATCGATGCACAAG
23635 A
65 A
*
23636 CATGCATCGATGCACTCAGGCTATTT-T-AAAACATCGAATGCATTTTATGCATCGATGCAC
1 CATGCATCGATGCACTCAGG-TATTTATAAAAACATCGAATGCATTTGATGCATCGATGCAC
23696 CCTTAGTGCA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
64 32 0.56
66 21 0.37
67 4 0.07
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (65 bp):
CATGCATCGATGCACTCAGGTATTTATAAAAACATCGAATGCATTTGATGCATCGATGCACAAGA
Found at i:28736 original size:15 final size:14
Alignment explanation
Indices: 28712--28741 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
28702 ATGGATATGA
28712 GAAAAAGGAAAAGG
1 GAAAAAGGAAAAGG
28726 GAAAAAGGGAAAAGG
1 GAAAAA-GGAAAAGG
28741 G
1 G
28742 TTTCGCACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (14 bp):
GAAAAAGGAAAAGG
Found at i:28954 original size:82 final size:80
Alignment explanation
Indices: 28854--29095 Score: 216
Period size: 82 Copynumber: 2.9 Consensus size: 80
28844 CGAGTTATCG
* *
28854 CGGTGTTTGTATACAAAAAAATCGCTAAAGTACTAATATGTTGCAGCGTTTATTAAAAAACGCCA
1 CGGTGTTTGTAT--AAAAAAA-CGCTAAAGTACTAATCTGTTGCGGCGTTTATTAAAAAACGCCA
28919 CTATAGTTGAACCATATTA
63 CTATAGTT-AACCATATTA
** * * * * * * *
28938 CGGTGTTTGTATAAAAATGCCGCTAAAGTATTAATCTATTACGGCATTTATTGCACAAATGCCAC
1 CGGTGTTTGTATAAAAA-AACGCTAAAGTACTAATCTGTTGCGGCGTTTATT-AAAAAACGCCAC
* *
29003 TATAGGTTAACCCTATTG
64 TATA-GTTAACCATATTA
* * * * * *
29021 TGGCGTTTGTATAAAAACACTGCTAAA-TACTACTCTGTTGCGGCGTTTGTCGAAAAAACGCCAC
1 CGGTGTTTGTATAAAAAAAC-GCTAAAGTACTAATCTGTTGCGGCGTTTAT-TAAAAAACGCCAC
29085 TATAGGTTAAC
64 TATA-GTTAAC
29096 ACTATTGCGG
Statistics
Matches: 126, Mismatches: 27, Indels: 12
0.76 0.16 0.07
Matches are distributed among these distances:
82 69 0.55
83 42 0.33
84 15 0.12
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (80 bp):
CGGTGTTTGTATAAAAAAACGCTAAAGTACTAATCTGTTGCGGCGTTTATTAAAAAACGCCACTA
TAGTTAACCATATTA
Found at i:34888 original size:14 final size:14
Alignment explanation
Indices: 34869--34904 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
34859 AATAGTGATC
34869 GAGAGAGAGAAAGA
1 GAGAGAGAGAAAGA
34883 GAGAGAGAGAAAGA
1 GAGAGAGAGAAAGA
34897 GAGAGAGA
1 GAGAGAGA
34905 AATTAAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (14 bp):
GAGAGAGAGAAAGA
Found at i:34916 original size:2 final size:2
Alignment explanation
Indices: 34869--34904 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
34859 AATAGTGATC
* *
34869 GA GA GA GA GA AA GA GA GA GA GA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34905 AATTAAAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40847 original size:3 final size:3
Alignment explanation
Indices: 40839--40887 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
40829 TATTTTATTT
40839 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40887 A
1 A
40888 CAATTTATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:52933 original size:5 final size:5
Alignment explanation
Indices: 52910--52974 Score: 69
Period size: 5 Copynumber: 13.0 Consensus size: 5
52900 TGTCAATACT
* ** * *
52910 TAAAT TAAAA TAAGG TAAAA TAAAA TAACA TAAAAA TAGAA T-AAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA
52960 TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA
52975 ATATTTCTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
4 3 0.06
5 42 0.86
6 4 0.08
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:53281 original size:9 final size:9
Alignment explanation
Indices: 53267--53291 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53257 ATTCATAAGG
53267 AAATAAATA
1 AAATAAATA
53276 AAATAAATA
1 AAATAAATA
53285 AAATAAA
1 AAATAAA
53292 AATTCATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAATA
Found at i:54894 original size:3 final size:3
Alignment explanation
Indices: 54886--54939 Score: 58
Period size: 3 Copynumber: 17.7 Consensus size: 3
54876 ATTTTATTTT
*
54886 ATA ATA AT- ATA ATTA ATTA ATA ATTA ATA ATA ATA ATA AT- ATA AGA
1 ATA ATA ATA ATA A-TA A-TA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
54932 ATA ATA AT
1 ATA ATA AT
54940 TTATTTTTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
2 4 0.09
3 31 0.69
4 10 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:54908 original size:16 final size:16
Alignment explanation
Indices: 54885--54939 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
54875 TATTTTATTT
54885 TATAATAATATAATTAA
1 TATAATAATATAA-TAA
54902 T-TAATAAT-TAATAA
1 TATAATAATATAATAA
*
54916 TAATAATAATATAAGAA
1 T-ATAATAATATAATAA
54933 TAATAAT
1 T-ATAAT
54940 TTATTTTTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
14 4 0.12
15 3 0.09
16 14 0.41
17 13 0.38
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
TATAATAATATAATAA
Found at i:54929 original size:11 final size:11
Alignment explanation
Indices: 54886--54937 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
54876 ATTTTATTTT
54886 ATAATAATATA
1 ATAATAATATA
54897 AT--TAAT-TA
1 ATAATAATATA
54905 ATAATTAATAATA
1 ATAA-TAAT-ATA
54918 ATAATAATATA
1 ATAATAATATA
*
54929 AGAATAATA
1 ATAATAATA
54938 ATTTATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
8 4 0.11
9 4 0.11
11 17 0.49
12 4 0.11
13 6 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
ATAATAATATA
Done.