Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000871.1 Hibiscus syriacus cultivar Beakdansim tig00001684_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: 58737
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1044 original size:17 final size:17
Alignment explanation
Indices: 1018--1053 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1008 ACAAGGAATG
*
1018 AAAGTTCTTGTGGAGCA
1 AAAGTCCTTGTGGAGCA
1035 AAAGTCCTTGTGGAGCA
1 AAAGTCCTTGTGGAGCA
1052 AA
1 AA
1054 GCTACTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (17 bp):
AAAGTCCTTGTGGAGCA
Found at i:8073 original size:57 final size:57
Alignment explanation
Indices: 7979--8089 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
7969 GTTTTGTAAC
* * *
7979 TTATAATTCTCAAGTGAAACAATGATGTAAAGTCTTATAAATAAATAGACTTGTCAT
1 TTATAATTCTCAAGTAAAACAATGAAGTAAAGGCTTATAAATAAATAGACTTGTCAT
* * * *
8036 TTATGATTCTCAAGTAAAACAATGAAGTAGAGGCTTATAAATTAATAGATTTGT
1 TTATAATTCTCAAGTAAAACAATGAAGTAAAGGCTTATAAATAAATAGACTTGT
8090 AAAACGGATG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (57 bp):
TTATAATTCTCAAGTAAAACAATGAAGTAAAGGCTTATAAATAAATAGACTTGTCAT
Found at i:14369 original size:23 final size:23
Alignment explanation
Indices: 14338--14400 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
14328 CTGAATGATT
*
14338 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGAATGATTCAGCAAAA
*
14361 TAGTGCTGAATGATTCAGCAAAA
1 CAGTGCTGAATGATTCAGCAAAA
*
14384 CAGTGTTGAATGATTCA
1 CAGTGCTGAATGATTCA
14401 TTCAGTGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (23 bp):
CAGTGCTGAATGATTCAGCAAAA
Found at i:14412 original size:19 final size:19
Alignment explanation
Indices: 14384--14434 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 19
14374 TTCAGCAAAA
*
14384 CAGTGTTGAATGATTCATT
1 CAGTGCTGAATGATTCATT
14403 CAGTGCTGAATG----ATT
1 CAGTGCTGAATGATTCATT
14418 CAGTGCTGAATGATTCA
1 CAGTGCTGAATGATTCA
14435 GCAAAACAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
15 15 0.56
19 12 0.44
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (19 bp):
CAGTGCTGAATGATTCATT
Found at i:14420 original size:15 final size:15
Alignment explanation
Indices: 14400--14435 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
14390 TGAATGATTC
14400 ATTCAGTGCTGAATG
1 ATTCAGTGCTGAATG
14415 ATTCAGTGCTGAATG
1 ATTCAGTGCTGAATG
14430 ATTCAG
1 ATTCAG
14436 CAAAACAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (15 bp):
ATTCAGTGCTGAATG
Found at i:14558 original size:16 final size:15
Alignment explanation
Indices: 14539--14639 Score: 85
Period size: 16 Copynumber: 6.5 Consensus size: 15
14529 AGAGCATCTC
14539 AATCATTCAGCATTT
1 AATCATTCAGCATTT
* **
14554 GAATCATTCAACGCTT
1 -AATCATTCAGCATTT
14570 AATCATTCAGCATTT
1 AATCATTCAGCATTT
* **
14585 AAATCATTCAACGCTT
1 -AATCATTCAGCATTT
*
14601 AATCATTCAGTATTT
1 AATCATTCAGCATTT
* **
14616 GAATCATTCAACGCTT
1 -AATCATTCAGCATTT
14632 AATCATTC
1 AATCATTC
14640 TTAAGTAAAC
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
15 31 0.47
16 35 0.53
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.37
Consensus pattern (15 bp):
AATCATTCAGCATTT
Found at i:14575 original size:15 final size:15
Alignment explanation
Indices: 14555--14639 Score: 89
Period size: 15 Copynumber: 5.5 Consensus size: 15
14545 TCAGCATTTG
14555 AATCATTCAACGCTT
1 AATCATTCAACGCTT
* **
14570 AATCATTCAGCATTT
1 AATCATTCAACGCTT
14585 AAATCATTCAACGCTT
1 -AATCATTCAACGCTT
****
14601 AATCATTCAGTATTT
1 AATCATTCAACGCTT
14616 GAATCATTCAACGCTT
1 -AATCATTCAACGCTT
14632 AATCATTC
1 AATCATTC
14640 TTAAGTAAAC
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
15 31 0.57
16 23 0.43
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.36
Consensus pattern (15 bp):
AATCATTCAACGCTT
Found at i:14576 original size:31 final size:31
Alignment explanation
Indices: 14539--14639 Score: 184
Period size: 31 Copynumber: 3.3 Consensus size: 31
14529 AGAGCATCTC
14539 AATCATTCAGCATTTGAATCATTCAACGCTT
1 AATCATTCAGCATTTGAATCATTCAACGCTT
*
14570 AATCATTCAGCATTTAAATCATTCAACGCTT
1 AATCATTCAGCATTTGAATCATTCAACGCTT
*
14601 AATCATTCAGTATTTGAATCATTCAACGCTT
1 AATCATTCAGCATTTGAATCATTCAACGCTT
14632 AATCATTC
1 AATCATTC
14640 TTAAGTAAAC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.37
Consensus pattern (31 bp):
AATCATTCAGCATTTGAATCATTCAACGCTT
Found at i:22204 original size:17 final size:17
Alignment explanation
Indices: 22172--22211 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
22162 CAATTCACAA
*
22172 TTAATT-TAAATGATAT
1 TTAATTATAAATAATAT
22188 TTAATTATAAATAATAT
1 TTAATTATAAATAATAT
*
22205 CTAATTA
1 TTAATTA
22212 ATTTGATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAATTATAAATAATAT
Found at i:27915 original size:72 final size:72
Alignment explanation
Indices: 27782--27915 Score: 164
Period size: 73 Copynumber: 1.9 Consensus size: 72
27772 CGATTTCGGA
* * *
27782 GCAACAATAGTGGCGTTTTCTTAACAAACGCCGCGATAGACCTATCTATAATGGCGTTTTATCAA
1 GCAACAATAGTGGCGTTTTCTTAAAAAACGCCGCAATAGACCTATCTATAATGGCGATTTATCAA
27847 TAAAGCC
66 TAAAGCC
* * * * *
27854 GCAATAATAGTGGCGTTTTTTTGAAAAAACGTCGCAATATG-TCTATCTATAGTGGC-ATTTAT
1 GCAACAATAGTGGCGTTTTCTT-AAAAAACGCCGCAATA-GACCTATCTATAATGGCGATTTAT
27916 TGGAAAAACG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
72 25 0.48
73 26 0.50
74 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (72 bp):
GCAACAATAGTGGCGTTTTCTTAAAAAACGCCGCAATAGACCTATCTATAATGGCGATTTATCAA
TAAAGCC
Found at i:30860 original size:21 final size:20
Alignment explanation
Indices: 30829--30877 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
30819 ACGGAGAGAA
*
30829 AAGATAGAGAGGGAAAAAGGG
1 AAGATAGAGAGAG-AAAAGGG
30850 AACGATA-AGAGAGAAAAGGG
1 AA-GATAGAGAGAGAAAAGGG
30870 AAGATAGA
1 AAGATAGA
30878 TGGAGAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 10 0.40
21 7 0.28
22 4 0.16
ACGTcount: A:0.55, C:0.02, G:0.37, T:0.06
Consensus pattern (20 bp):
AAGATAGAGAGAGAAAAGGG
Found at i:32324 original size:18 final size:20
Alignment explanation
Indices: 32285--32327 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
32275 ACTAAATGGT
32285 AGTTAGTTTGTTAAACGAGC
1 AGTTAGTTTGTTAAACGAGC
32305 AGTTAGTTTGTT-AA-GAGC
1 AGTTAGTTTGTTAAACGAGC
32323 AGTTA
1 AGTTA
32328 TGTGCTGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 9 0.39
19 2 0.09
20 12 0.52
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (20 bp):
AGTTAGTTTGTTAAACGAGC
Found at i:34998 original size:63 final size:63
Alignment explanation
Indices: 34885--35008 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
34875 CAAGTCAGTT
* * *
34885 ACCAAATACCACCACTGTGCATGAAGAAGATGGTAATGCAGAAGTACATAATGAAGCCGAGTC
1 ACCAAATACCACCACCGTGCATGAAGAAGATGGTAATGCAGAAATACATAATGAAGACGAGTC
* * *
34948 ACCAAATATCATCACCGTGCATGAAGAAG-TGAGTAATGCA-ACAATTCATAATGAAGACGAG
1 ACCAAATACCACCACCGTGCATGAAGAAGATG-GTAATGCAGA-AATACATAATGAAGACGAG
35009 ATGATTAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 3 0.06
63 50 0.94
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (63 bp):
ACCAAATACCACCACCGTGCATGAAGAAGATGGTAATGCAGAAATACATAATGAAGACGAGTC
Found at i:38589 original size:20 final size:21
Alignment explanation
Indices: 38560--38599 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
38550 CGGTAAAGCG
*
38560 TTACCTAAAACATT-ATTTTT
1 TTACCGAAAACATTAATTTTT
*
38580 TTACCGAAAATATTAATTTT
1 TTACCGAAAACATTAATTTT
38600 GCTACCTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (21 bp):
TTACCGAAAACATTAATTTTT
Found at i:39542 original size:21 final size:22
Alignment explanation
Indices: 39518--39575 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
39508 CACCAAAACT
*
39518 ATTTCAGATGGCACCA-TAGCC
1 ATTTCAGATGACACCAGTAGCC
*
39539 ATTTTC-GATGATA-CAGTAGCC
1 A-TTTCAGATGACACCAGTAGCC
*
39560 ATTTCAGATGTCACCA
1 ATTTCAGATGACACCA
39576 CTGCAGGGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 6 0.21
21 17 0.59
22 6 0.21
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (22 bp):
ATTTCAGATGACACCAGTAGCC
Found at i:40010 original size:44 final size:44
Alignment explanation
Indices: 39943--40026 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
39933 GATAAACTTG
* *
39943 TTTTTATTTATTTTTTTTCTTAATGTTTTTATTTAATTATGGAT
1 TTTTTATTTATTTTGTTTATTAATGTTTTTATTTAATTATGGAT
39987 TTTTTATTTATTTTGTTTATTAATGTTTTTATTTAATTAT
1 TTTTTATTTATTTTGTTTATTAATGTTTTTATTTAATTAT
40027 TGGACCCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.21, C:0.01, G:0.06, T:0.71
Consensus pattern (44 bp):
TTTTTATTTATTTTGTTTATTAATGTTTTTATTTAATTATGGAT
Found at i:44432 original size:15 final size:15
Alignment explanation
Indices: 44407--44444 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
44397 ATATTTTGTA
44407 TTAATTATTTTATTAT
1 TTAATT-TTTTATTAT
44423 TTAATTTTTTATTAT
1 TTAATTTTTTATTAT
44438 TTAATTT
1 TTAATTT
44445 AATTATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTAATTTTTTATTAT
Found at i:44449 original size:28 final size:27
Alignment explanation
Indices: 44399--44460 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
44389 ATTTAATCAT
* *
44399 ATTTTGTATTAATTATTTTATTATTTA
1 ATTTTTTATTAATTATTTAATTATTTA
* *
44426 ATTTTTTATTATTTAATTTAATTATTTT
1 ATTTTTTATTAATT-ATTTAATTATTTA
44454 ATTTTTT
1 ATTTTTT
44461 TGCAGTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 12 0.40
28 18 0.60
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (27 bp):
ATTTTTTATTAATTATTTAATTATTTA
Found at i:44731 original size:16 final size:17
Alignment explanation
Indices: 44710--44757 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
44700 TTATAACTGC
*
44710 AAAAAAATAAAATAATA
1 AAAAAAATTAAATAATA
44727 AAAAAAATTAAATAAT-
1 AAAAAAATTAAATAATA
* *
44743 ACAATAATTAAATAA
1 AAAAAAATTAAATAA
44758 AATACTAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAAAATTAAATAATA
Found at i:46118 original size:3 final size:3
Alignment explanation
Indices: 46110--46134 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
46100 TCCACTATTC
46110 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
46135 CTCTGGTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:47013 original size:24 final size:24
Alignment explanation
Indices: 46969--47017 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
46959 ACTGTCTCAA
*
46969 CATCCCCAATAGAAGACTTGGAAC
1 CATCCCCAATACAAGACTTGGAAC
*
46993 CATCTCCCAATACAAG-TTTGGAAC
1 CATC-CCCAATACAAGACTTGGAAC
47017 C
1 C
47018 TTCAATGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.35, C:0.31, G:0.14, T:0.20
Consensus pattern (24 bp):
CATCCCCAATACAAGACTTGGAAC
Found at i:48858 original size:26 final size:26
Alignment explanation
Indices: 48811--48860 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
48801 GGATAAATTC
*
48811 ATAAAATTTTAAGTAGAAAAAAACTT
1 ATAAAATTTTAAGGAGAAAAAAACTT
* *
48837 ATAAAATTTTAAGGATACAAAAAC
1 ATAAAATTTTAAGGAGAAAAAAAC
48861 ATATTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (26 bp):
ATAAAATTTTAAGGAGAAAAAAACTT
Found at i:49678 original size:12 final size:12
Alignment explanation
Indices: 49661--49685 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49651 ACCTTACCTC
49661 ATTATATATGAG
1 ATTATATATGAG
49673 ATTATATATGAG
1 ATTATATATGAG
49685 A
1 A
49686 ACAAGGACAT
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:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
ATTATATATGAG
Done.