Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009379.1 Hibiscus syriacus cultivar Beakdansim tig00113261_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: 69674
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Found at i:30785 original size:65 final size:65
Alignment explanation
Indices: 30670--30817 Score: 190
Period size: 65 Copynumber: 2.3 Consensus size: 65
30660 GCACACCCAT
* **
30670 TTTTGTGTACCGATGCACAAGCCATGCATCGATGCACTTTTGAATATTTTGAAACATCAAATGCA
1 TTTTGTGTACCGATGCACAAGCCATGCATCAATGCACTCCTGAATATTTTGAAACATCAAATGCA
** * * *
30735 TTTTGTGTACCGATGCACATA-CCATGCATCAATGCACTCCTGGCTTTTTTGAAACATCGAATGT
1 TTTTGTGTACCGATGCACA-AGCCATGCATCAATGCACTCCTGAATATTTTGAAACATCAAATGC
30799 A
65 A
* *
30800 ATTAGTGTACCGATGCAC
1 TTTTGTGTACCGATGCAC
30818 CCCTAGTATA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
65 71 0.99
66 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (65 bp):
TTTTGTGTACCGATGCACAAGCCATGCATCAATGCACTCCTGAATATTTTGAAACATCAAATGCA
Found at i:54330 original size:23 final size:23
Alignment explanation
Indices: 54294--54338 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
54284 TTTCATGAAA
54294 TTTTTAATTAATTTCAAG-TTAAT
1 TTTTTAATTAATTT-AAGCTTAAT
* *
54317 TTTTTATTTTATTTAAGCTTAA
1 TTTTTAATTAATTTAAGCTTAA
54339 ATAAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTTAATTAATTTAAGCTTAAT
Found at i:54736 original size:13 final size:13
Alignment explanation
Indices: 54692--54743 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
54682 GTCATAAATC
*
54692 TATGACACGCATT
1 TATGACGCGCATT
* *
54705 TATGAAGCGTATT
1 TATGACGCGCATT
54718 TATGACGCGCATT
1 TATGACGCGCATT
*
54731 TATGACGCTCATT
1 TATGACGCGCATT
54744 GTGCGTCATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:54797 original size:45 final size:45
Alignment explanation
Indices: 54742--54835 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
54732 ATGACGCTCA
* *
54742 TTGTGCGTCATTGAAG-CCCCATTCATAAATGAAGATGACATACAT
1 TTGTGCGTCATTGAAGCCCCCATT-ATAAATAAAGATGACACACAT
* * * *
54787 TTGTGTGTCATTTAAGCCCCCGTTATAAATAAATATGACACACAT
1 TTGTGCGTCATTGAAGCCCCCATTATAAATAAAGATGACACACAT
54832 TTGT
1 TTGT
54836 ATGACTTACA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 36 0.86
46 6 0.14
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (45 bp):
TTGTGCGTCATTGAAGCCCCCATTATAAATAAAGATGACACACAT
Found at i:60984 original size:13 final size:13
Alignment explanation
Indices: 60966--61006 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
60956 TTAATTAAGA
60966 AAGTTGAAAGTTT
1 AAGTTGAAAGTTT
60979 AAGTTGAAAGTTT
1 AAGTTGAAAGTTT
* *
60992 AAATTGAAAGGTT
1 AAGTTGAAAGTTT
61005 AA
1 AA
61007 ATAACGATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (13 bp):
AAGTTGAAAGTTT
Found at i:61231 original size:30 final size:31
Alignment explanation
Indices: 61173--61237 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
61163 AATAGTAAGT
* *
61173 AAAAAAAAACAAATAATAAAATATATATAA-
1 AAAAAAAAACAAATAAGAAAATAAATATAAC
*
61203 AAAAGAAAAAGAAA-AAGAAAATAAATATAAC
1 AAAA-AAAAACAAATAAGAAAATAAATATAAC
61234 AAAA
1 AAAA
61238 TAATAATAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (31 bp):
AAAAAAAAACAAATAAGAAAATAAATATAAC
Found at i:61547 original size:2 final size:2
Alignment explanation
Indices: 61540--61568 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
61530 CTTGTGTAGA
61540 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61569 ATAATAGTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61817 original size:12 final size:11
Alignment explanation
Indices: 61793--61831 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
61783 TAACAAAATA
61793 AATAATA-AA-
1 AATAATACAAG
61802 AATAATACAAG
1 AATAATACAAG
61813 TAATAATACAAG
1 -AATAATACAAG
61825 AATAATA
1 AATAATA
61832 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
11 7 0.26
12 11 0.41
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (11 bp):
AATAATACAAG
Found at i:62551 original size:37 final size:37
Alignment explanation
Indices: 62510--62614 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
62500 GTGCTTGTGG
* *
62510 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCA
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCA
* * * *
62547 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCA
*
62584 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
62615 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCA
Found at i:63537 original size:106 final size:106
Alignment explanation
Indices: 63345--65031 Score: 2405
Period size: 106 Copynumber: 16.0 Consensus size: 106
63335 GCATTGTTCT
* * * * * * *
63345 GAGTACAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * *
63410 CTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* **
63451 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTTTGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
63516 CCAGCGGTTCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
63557 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
63622 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
63663 GAGTCCAATATCCTTCGTTGTGAAGATGAAATTGGCTCTGAATTTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
63728 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * *
63769 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
63834 CCAGCAGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
63875 GAGTCCAATATCTTTCGCTATGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** * * * *
63940 CCAGCCATCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
63981 GAGTCCAATATCCTTTGTTGTGAAATTGAAATTGGCTCTGAAATTTGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
64046 CCAGTGGTTCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
64087 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
64152 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTCCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
64193 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTGTGAAAATGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
64258 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
64299 GAGTCCAATATCCTTCGCTGTGAAGTTGAAA-----T-T---A---GGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
64352 CCAGCAGTTCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
64393 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGATAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
64458 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTCCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
64499 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
64564 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTCCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
64605 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTATTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
64670 CCAGCGGT-CCTTCGT-GATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCG-TGAAGTTGAACTTGCGTTGTCTG
* * * * *
64710 GAGTCCAATATCCTTCGCTGTGAAGTTGAAAGTGGCTCTGAAATTGGGAAATTGTTTATTGAAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
64775 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
64816 GAGTCCAATATCCTTCATTGTGAAGTTGATATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
64881 CTAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
64922 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
64987 CCAATC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CC-AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65028 GAGT
1 GAGT
65032 GGCACGATAT
Statistics
Matches: 1427, Mismatches: 138, Indels: 32
0.89 0.09 0.02
Matches are distributed among these distances:
94 84 0.06
97 1 0.00
99 1 0.00
100 2 0.00
101 1 0.00
103 1 0.00
104 1 0.00
105 96 0.07
106 1237 0.87
107 3 0.00
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:64328 original size:43 final size:41
Alignment explanation
Indices: 64267--64427 Score: 108
Period size: 43 Copynumber: 3.6 Consensus size: 41
64257 ACCAGCGGTC
*
64267 CCTTCGTCATGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
1 CCTTCGT-GTGAAGTTGAACTTG-GTTGTCTTGAGTCCAATAT
* * **
64310 CCTTCGCTGTGAAGTTGAAATTAGGAAATTGTTTATTGACAACCAGCAGT-T
1 CCTTCG-TGTGAAGTTGAACTT-GG---TTG--TCTTGA-GTCCA--A-TAT
*
64361 CCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATAT
1 CCTTCGT-GTGAAGTTGAACTTG-GTTGTCTTGAGTCCAATAT
*
64404 CCTTCGTTGTGAAGTTGAAATTGG
1 CCTTCG-TGTGAAGTTGAACTTGG
64428 CTCTGAAATT
Statistics
Matches: 92, Mismatches: 11, Indels: 31
0.69 0.08 0.23
Matches are distributed among these distances:
42 2 0.02
43 41 0.45
44 3 0.03
45 3 0.03
46 7 0.08
48 8 0.09
49 3 0.03
50 2 0.02
51 22 0.24
52 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (41 bp):
CCTTCGTGTGAAGTTGAACTTGGTTGTCTTGAGTCCAATAT
Found at i:66645 original size:16 final size:15
Alignment explanation
Indices: 66614--66655 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
66604 ATTTAGGTTT
66614 TTTTTTGTTTTCTTC
1 TTTTTTGTTTTCTTC
66629 TTTTTTGCTTCTT-TTC
1 TTTTTTG-TT-TTCTTC
*
66645 TTTTTTATTTT
1 TTTTTTGTTTT
66656 TGCCCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 2 0.08
15 9 0.38
16 11 0.46
17 2 0.08
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (15 bp):
TTTTTTGTTTTCTTC
Done.