Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007479.1 Hibiscus syriacus cultivar Beakdansim tig00020584_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: 65823
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3854 original size:18 final size:18
Alignment explanation
Indices: 3831--3866 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3821 TCAACATCAA
*
3831 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
3849 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
3867 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:4670 original size:37 final size:37
Alignment explanation
Indices: 4600--4671 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
4590 TGGAACTAAG
* * * *
4600 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGCCTCCCTTGAGACAGTTTCTCATAAAACAAAA
* *
4637 TTTTGCCTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTTGCCTCCCTTGAGACAGTTTCTCATAAAACAA
4672 CAGATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.39
Consensus pattern (37 bp):
TTTTGCCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:6136 original size:106 final size:106
Alignment explanation
Indices: 5291--6115 Score: 1219
Period size: 106 Copynumber: 7.8 Consensus size: 106
5281 TCTCCACCCG
* *
5291 AGACAACACAAGTTCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAAACAACTT-CCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
*
5355 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* * ** * *
5396 AGACAAAACAAGTTCAACTTCACAACGAAGGGAC-GTTATTTGTCAAAAAACCAATTT-TCAATT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA-CAATTTCCCAATT
*
5459 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* *
5501 AGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
* *
5566 CAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* * *
5607 AGACAAAACAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGTCAACAAAACAATTTCCCAGTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCCCAATT
5672 TCAGAGCCAATTTCAACTTCACAGCGAA-GATTATTGGACTCA
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGA-TATTGGACTCA
* * * * *
5714 AGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTCGTCAACAACCAATTT-TCAGTTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
*
5778 CAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* *
5819 AGACAACCCAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAGCAAACAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
5884 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* *
5925 AGACGACACAAGTTCAAATTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
** *
5990 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTAAACTCG
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* * * * * * * * * *
6031 AGATAACACAAGCTCAACTTCACAGCGAAGGGGCAGCCGGCTGTCAACAAACAATTTCACAGTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
*
6096 CGGAGCCAATTTCAACTTCA
66 CAGAGCCAATTTCAACTTCA
6116 TGACAGAGGA
Statistics
Matches: 650, Mismatches: 63, Indels: 13
0.90 0.09 0.02
Matches are distributed among these distances:
104 12 0.02
105 215 0.33
106 327 0.50
107 96 0.15
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.22
Consensus pattern (106 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
Found at i:7460 original size:2 final size:2
Alignment explanation
Indices: 7455--7493 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
7445 TATATTTTAC
7455 TA TA TA TA TA 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 TA TA TA TA TA T
7494 GTTTCTTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14051 original size:2 final size:2
Alignment explanation
Indices: 14044--14080 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
14034 CCATAATTCC
14044 AT AT AT AT 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 AT AT AT AT A
14081 CCATGTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19171 original size:34 final size:32
Alignment explanation
Indices: 19126--19197 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 32
19116 CCTTTTGTAA
*
19126 AGGGAAAAGGTTCTAGCTTAGCCCGTGTAAAAGCT
1 AGGG-AAAGGTTCTAGCTTAGCCCG-G-AAAAACT
* *
19161 AGGGAAAGGTTCTTGTTTAGCCCGGAAAAACT
1 AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
19193 AGGGA
1 AGGGA
19198 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 18 0.53
35 4 0.12
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (32 bp):
AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
Found at i:22530 original size:34 final size:32
Alignment explanation
Indices: 22491--22560 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
22481 TTTTGTAAAG
* *
22491 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
22525 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
22557 GGGA
1 GGGA
22561 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:25950 original size:2 final size:2
Alignment explanation
Indices: 25943--25984 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
25933 GGATAACGTC
25943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25983 AT
1 AT
25985 TGATCATGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27924 original size:49 final size:49
Alignment explanation
Indices: 27856--28190 Score: 463
Period size: 49 Copynumber: 6.8 Consensus size: 49
27846 ATTAATGAAT
**
27856 GTTAAATGCATAATAGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
1 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
** * *
27905 GTTAAATATATAACGGTGCATTTAGGCTTAAAAGGTGCCACTAATAAAA
1 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
* * * *
27954 GTTAAATGCATAACAGTGCATTGCGACATAAAAGGTGCCAGTAATAAAA
1 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
* * * * *
28003 GTTAAATGCATAATGGTGCATTTCAGCTTAAAAGGTGCCATTAATGAAA
1 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
* * *
28052 GTTAAATGCATAACGGTGCATTTAGGCATAAAAGGTGCTACTAATGAAA
1 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
** * * *
28101 GTTAAATGCATAACATTGCATTTAGGCATAAAATGTGCCACTAATGAAA
1 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
28150 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
1 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
28191 CCATGGTATT
Statistics
Matches: 250, Mismatches: 36, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 250 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (49 bp):
GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
Found at i:34871 original size:49 final size:49
Alignment explanation
Indices: 34809--35150 Score: 481
Period size: 49 Copynumber: 7.0 Consensus size: 49
34799 TAAAATGAAT
* *
34809 TAATGAAAGTTAAATGCATAATGGTGCATTTCGGCATAAAAGGTGACAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* * * *
34858 TAATAAAAGTTAAATGCATATCGGTGTATTTCGGCATAAAAGGTGTCAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* * * * *
34907 TGATAAAAGTTAAAAGCATGACGGTGCATTTTGGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* * * *
34956 TAATAAAAGTTAAATGCATAACGATGCATTTCGGCATAATAGGTGCCAT
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* * *
35005 TAATGAAAGTTAAATGCACAACAGTGCATTTAGGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
*
35054 TAATGAAAGTTAAATGTATAACGGTGCATTTCGGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
*
35103 GAATGAAAGTTAAATGCATAACGGT--ATTTTCGGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGGTGCA-TTTCGGCATAAAAGGTGCCAC
35151 CCATGGTATT
Statistics
Matches: 260, Mismatches: 32, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
47 1 0.00
48 21 0.08
49 238 0.92
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (49 bp):
TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
Found at i:39713 original size:50 final size:50
Alignment explanation
Indices: 39647--39741 Score: 145
Period size: 50 Copynumber: 1.9 Consensus size: 50
39637 TTATTTGTAT
* * * *
39647 TTTTTATATTTTATTATAGTTTAAATTGATATAATTCATATATAATAATA
1 TTTTTAAAATTTATTATAGTTTAAACTAATATAATTCATATATAATAATA
*
39697 TTTTTAAAATTTATTATAGTTTAAACTAATATGATTCATATATAA
1 TTTTTAAAATTTATTATAGTTTAAACTAATATAATTCATATATAA
39742 GTGTAAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (50 bp):
TTTTTAAAATTTATTATAGTTTAAACTAATATAATTCATATATAATAATA
Found at i:39872 original size:26 final size:25
Alignment explanation
Indices: 39841--39895 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
39831 AACAGTTAAA
* * *
39841 TTTTAAACTGCTCTTTTGTACAACAT
1 TTTTAAA-AGCTCATTTCTACAACAT
*
39867 TTTTAAAAGTTCATTTCTACAACAT
1 TTTTAAAAGCTCATTTCTACAACAT
39892 TTTT
1 TTTT
39896 TTAAAGTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.49
Consensus pattern (25 bp):
TTTTAAAAGCTCATTTCTACAACAT
Found at i:40190 original size:16 final size:16
Alignment explanation
Indices: 40169--40202 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
40159 AAATACAAAC
40169 AAAATATAATTATAAT
1 AAAATATAATTATAAT
*
40185 AAAATATATTTATAAT
1 AAAATATAATTATAAT
40201 AA
1 AA
40203 CTCACTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATATAATTATAAT
Found at i:42847 original size:15 final size:16
Alignment explanation
Indices: 42824--42859 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
42814 AATACTTTCA
*
42824 TATTTTATTAA-ATTT
1 TATTATATTAACATTT
42839 TATTATATTAACATTT
1 TATTATATTAACATTT
42855 TATTA
1 TATTA
42860 ATTTTTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTATATTAACATTT
Found at i:44923 original size:3 final size:3
Alignment explanation
Indices: 44910--44954 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
44900 TATCTTCTTC
* *
44910 TGA TGA CGA TGA TGA TGA TGGA T-A TGA TAA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA T-GA TGA TGA TGA TGA TGA TGA TGA TGA
44955 GTGAGAGTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.36, C:0.02, G:0.31, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:45182 original size:26 final size:26
Alignment explanation
Indices: 45113--45182 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
45103 AATTATTGAC
*
45113 TTTTTATTTATTTTGTT-TCTTAATTT
1 TTTTTA-TTATTTTGTTGTCTTAATTG
* **
45139 TTTTTATTACTTAATTGT-TTGAATTG
1 TTTTTATTATTTTGTTGTCTT-AATTG
45165 TTTTTATTATTTTGTTGT
1 TTTTTATTATTTTGTTGT
45183 ATCATTTTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
25 9 0.26
26 26 0.74
ACGTcount: A:0.17, C:0.03, G:0.09, T:0.71
Consensus pattern (26 bp):
TTTTTATTATTTTGTTGTCTTAATTG
Found at i:47547 original size:60 final size:60
Alignment explanation
Indices: 47447--47563 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
47437 CATGATGTTT
* * * * * *
47447 ACATTTAGGTCGAACAAGCTGGTAGTTGCATGCATTCCCTTTGAACTTGAAGGCATCTCG
1 ACATTAAGGTCGAACAAGCTCGCAGTTGAATGCATTCCCTTGGAACTTGAAGACATCTCG
* * *
47507 ACATTAAGGTTGAAGAAGCTCGCAGTTGAATGC-TTCCCCTTGGAGCTTGAAGACATC
1 ACATTAAGGTCGAACAAGCTCGCAGTTGAATGCATT-CCCTTGGAACTTGAAGACATC
47564 ATGTCAAATG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (60 bp):
ACATTAAGGTCGAACAAGCTCGCAGTTGAATGCATTCCCTTGGAACTTGAAGACATCTCG
Found at i:49745 original size:45 final size:46
Alignment explanation
Indices: 49660--49747 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
49650 AAATAGCCCG
* *
49660 AGTGCATCGATGCATGGTCTTGTGCATCGATGCATTAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
*
49706 AGTGCATCGATTCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
49748 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.56
46 17 0.44
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:65583 original size:25 final size:25
Alignment explanation
Indices: 65549--65596 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
65539 CCAAGGCGGT
*
65549 AGAGAACCCTAATATCGAGTAGAAA
1 AGAGAACCCTAATACCGAGTAGAAA
*
65574 AGAGAACCCTAATACCGGGTAGA
1 AGAGAACCCTAATACCGAGTAGA
65597 TTATTTAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (25 bp):
AGAGAACCCTAATACCGAGTAGAAA
Done.