Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006514.1 Hibiscus syriacus cultivar Beakdansim tig00015868_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: 64089
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:705 original size:21 final size:22
Alignment explanation
Indices: 663--705 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
653 CCACAGTGAT
* *
663 GGCGATCGATGCGGTGGTCGAC
1 GGCGACCGATGCGGTGGCCGAC
685 GGCGACCGATGC-GTGGCCGAC
1 GGCGACCGATGCGGTGGCCGAC
706 AATGGAGCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (22 bp):
GGCGACCGATGCGGTGGCCGAC
Found at i:4128 original size:19 final size:19
Alignment explanation
Indices: 4078--4133 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
4068 AATTATATGA
*
4078 TATGAGATAAG-TGAATG-
1 TATGAGATAAGATAAATGT
* *
4095 TATGCATATATGATAAATGT
1 TATG-AGATAAGATAAATGT
*
4115 TATGAGATAAGATATATGT
1 TATGAGATAAGATAAATGT
4134 GGTTACATGA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 4 0.13
18 5 0.17
19 17 0.57
20 4 0.13
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (19 bp):
TATGAGATAAGATAAATGT
Found at i:4553 original size:21 final size:21
Alignment explanation
Indices: 4513--4561 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
4503 GTGGTCCTTT
* * *
4513 GGGACATCTATGTGGTCATTC
1 GGGACATATATATGGGCATTC
4534 GGGACATATATATGGGCATTC
1 GGGACATATATATGGGCATTC
4555 GGGACAT
1 GGGACAT
4562 TTCTACGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (21 bp):
GGGACATATATATGGGCATTC
Found at i:4580 original size:22 final size:22
Alignment explanation
Indices: 4550--4604 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
4540 TATATATGGG
*
4550 CATTCGGGACATTTCTACGCAT
1 CATTTGGGACATTTCTACGCAT
4572 CATTTGGGACATTTCTACGCAT
1 CATTTGGGACATTTCTACGCAT
4594 CATTTGGGACA
1 CATTTGGGACA
4605 AATTCTATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (22 bp):
CATTTGGGACATTTCTACGCAT
Found at i:13595 original size:60 final size:60
Alignment explanation
Indices: 13525--13667 Score: 173
Period size: 60 Copynumber: 2.4 Consensus size: 60
13515 GTCTTTCAAT
* * * **
13525 TTTTGAATATTCTAATTTCATCCCTAAACTACGATTC-TCATTCTAAATTAATCCTGAAAC
1 TTTTAAATATTCTAATTTCATCCCTAAACTA-GATCCTTCATTCTAAACTAATCCCCAAAC
* * * *
13585 TTTTAAATATTTTAATTTCATCCCTAAACTATATCCTTCTTTCTAAACTAGTCCCCAAAC
1 TTTTAAATATTCTAATTTCATCCCTAAACTAGATCCTTCATTCTAAACTAATCCCCAAAC
*
13645 -TTTAAATATTCCAATTTCATCCC
1 TTTTAAATATTCTAATTTCATCCC
13668 CGAATTCATC
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
59 24 0.34
60 47 0.66
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (60 bp):
TTTTAAATATTCTAATTTCATCCCTAAACTAGATCCTTCATTCTAAACTAATCCCCAAAC
Found at i:14584 original size:2 final size:2
Alignment explanation
Indices: 14577--14616 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
14567 ATACCTCATA
14577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14617 TTCTATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22981 original size:21 final size:21
Alignment explanation
Indices: 22956--23003 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
22946 CCTAATATTG
22956 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
22977 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
22998 TAATGT
1 CAATGT
23004 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:27631 original size:21 final size:21
Alignment explanation
Indices: 27606--27653 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
27596 CCTAATATTG
27606 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
27627 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
27648 TAATGT
1 CAATGT
27654 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:31073 original size:19 final size:19
Alignment explanation
Indices: 31049--31086 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31039 AATCTCTTTT
31049 ATCTCATTTACAAGCCTAA
1 ATCTCATTTACAAGCCTAA
31068 ATCTCATTTACAAGCCTAA
1 ATCTCATTTACAAGCCTAA
31087 TTCTGCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (19 bp):
ATCTCATTTACAAGCCTAA
Found at i:37018 original size:16 final size:16
Alignment explanation
Indices: 36980--37021 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
36970 ATTTAATTTC
*
36980 TATTTTTAATATTTAA
1 TATTTTAAATATTTAA
*
36996 T-TCTTTAAATATTTTA
1 TAT-TTTAAATATTTAA
37012 TATTTTAAAT
1 TATTTTAAAT
37022 TTGAAGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTTAAATATTTAA
Found at i:41231 original size:22 final size:22
Alignment explanation
Indices: 41183--41236 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
41173 TTCAACTGTT
* *
41183 ATAACTCCTGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
* * *
41205 GTAACCCCTGGAATTAAATCAA
1 ATAACTCCTGAAATTAAATCAA
41227 ATAACTCCTG
1 ATAACTCCTG
41237 TAACTCCTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Found at i:48108 original size:30 final size:31
Alignment explanation
Indices: 48063--48141 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 31
48053 ACTCACTGGG
48063 TAACTCGTTGACTTTGACCGAGTCAACCCGT
1 TAACTCGTTGACTTTGACCGAGTCAACCCGT
* *
48094 TAAC-CGTTGGCTTTGACCGGGTCAACCCGT
1 TAACTCGTTGACTTTGACCGAGTCAACCCGT
* * *
48124 TGAC-CTTTGAATTTGACC
1 TAACTCGTTGACTTTGACC
48142 AATAGTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 38 0.90
31 4 0.10
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (31 bp):
TAACTCGTTGACTTTGACCGAGTCAACCCGT
Found at i:49445 original size:26 final size:26
Alignment explanation
Indices: 49415--49467 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
49405 TGACCCAAGA
* *
49415 ATATCACT-AAGCTCTGGAATGATTGG
1 ATATC-CTCAAGCTCTGAAATGAATGG
*
49441 ATATCCTCGAGCTCTGAAATGAATGG
1 ATATCCTCAAGCTCTGAAATGAATGG
49467 A
1 A
49468 ATAAAACCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (26 bp):
ATATCCTCAAGCTCTGAAATGAATGG
Found at i:50442 original size:12 final size:12
Alignment explanation
Indices: 50422--50490 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
50412 TATACATGAC
50422 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
50434 CTGATTTCTGAT
1 CTGAATTCTGTT
* *
50446 CTGGATTCGGTT
1 CTGAATTCTGTT
*
50458 CTG-ATATCT-AT
1 CTGAAT-TCTGTT
50469 CTGAATTCTGTT
1 CTGAATTCTGTT
*
50481 TTGAATTCTG
1 CTGAATTCTG
50491 ATATCTCCGT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
11 9 0.20
12 35 0.80
ACGTcount: A:0.17, C:0.16, G:0.19, T:0.48
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:50453 original size:24 final size:24
Alignment explanation
Indices: 50385--50492 Score: 98
Period size: 24 Copynumber: 4.5 Consensus size: 24
50375 AAATATTTTA
50385 TCTGATTTCTGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* *
50409 TC-G-TATACATGACCTGAATTCTGT
1 TCTGAT-TTC-TGATCTGAATTCTGT
* *
50433 TCTGATTTCTGATCTGGATTCGGT
1 TCTGATTTCTGATCTGAATTCTGT
*
50457 TCTGATATCT-ATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
50480 TTTGAATTCTGAT
1 TCTGATTTCTGAT
50493 ATCTCCGTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
22 1 0.01
23 21 0.31
24 40 0.60
25 4 0.06
26 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:51836 original size:24 final size:24
Alignment explanation
Indices: 51804--51858 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
51794 CCTTCAAAAA
51804 TCCTAAAAACAAGGAAAATATAAT
1 TCCTAAAAACAAGGAAAATATAAT
*
51828 TCCTAAAAACAAGGAAGATATAAT
1 TCCTAAAAACAAGGAAAATATAAT
51852 TCCTAAA
1 TCCTAAA
51859 GATAATTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.22
Consensus pattern (24 bp):
TCCTAAAAACAAGGAAAATATAAT
Found at i:51927 original size:46 final size:46
Alignment explanation
Indices: 51856--51943 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
51846 TATAATTCCT
* *
51856 AAAGATAATTCTTAAGATATATAAACTAAAATCCTAAAAACAAGTA
1 AAAGATAATTCCTAAAATATATAAACTAAAATCCTAAAAACAAGTA
* *
51902 AAAGATAATTCCTAAAATATTTAAACTAAAATTCTAAAAACA
1 AAAGATAATTCCTAAAATATATAAACTAAAATCCTAAAAACA
51944 TGAGTTTAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (46 bp):
AAAGATAATTCCTAAAATATATAAACTAAAATCCTAAAAACAAGTA
Found at i:51941 original size:23 final size:23
Alignment explanation
Indices: 51862--51941 Score: 56
Period size: 23 Copynumber: 3.5 Consensus size: 23
51852 TCCTAAAGAT
* *
51862 AATTCTTAAGATATATAAACTAA
1 AATTCTAAAAATATATAAACTAA
* * ** *
51885 AATCCTAAAAACA-AGTAAAAGAT
1 AATTCTAAAAATATA-TAAACTAA
*
51908 AATTCCT-AAAATATTTAAACTAA
1 AATT-CTAAAAATATATAAACTAA
51931 AATTCTAAAAA
1 AATTCTAAAAA
51942 CATGAGTTTA
Statistics
Matches: 40, Mismatches: 13, Indels: 8
0.66 0.21 0.13
Matches are distributed among these distances:
22 3 0.08
23 35 0.88
24 2 0.05
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (23 bp):
AATTCTAAAAATATATAAACTAA
Found at i:52466 original size:55 final size:55
Alignment explanation
Indices: 52401--52530 Score: 165
Period size: 55 Copynumber: 2.4 Consensus size: 55
52391 AGAGGTCCAT
*
52401 CCAAAAGTCATGTCTCTTTATGAAAAAATGGCA-TT-TCAAAAGTTGTGACTTTTCA
1 CCAAAAGTCATGTCTCTTCAT-AAAAAAT-GCATTTATCAAAAGTTGTGACTTTTCA
* * ** * *
52456 CCAAAAGTCATGTCTCTTCCTAAGAGGTGTATTTATTAAAAGTTGTGACTTTTCA
1 CCAAAAGTCATGTCTCTTCATAAAAAATGCATTTATCAAAAGTTGTGACTTTTCA
52511 CCAAAAGTCATGTCTCTTCA
1 CCAAAAGTCATGTCTCTTCA
52531 CCAAATGACA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
53 2 0.03
54 6 0.09
55 57 0.88
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (55 bp):
CCAAAAGTCATGTCTCTTCATAAAAAATGCATTTATCAAAAGTTGTGACTTTTCA
Found at i:53725 original size:21 final size:22
Alignment explanation
Indices: 53690--53734 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
53680 CACCGAAGTG
*
53690 CCACATAGAATGTCCCGAACGA
1 CCACATAGAATGTCCAGAACGA
*
53712 CCACATAG-ATGTCCAGAAGGA
1 CCACATAGAATGTCCAGAACGA
53733 CC
1 CC
53735 GTGTAGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.36, C:0.31, G:0.20, T:0.13
Consensus pattern (22 bp):
CCACATAGAATGTCCAGAACGA
Found at i:56007 original size:24 final size:25
Alignment explanation
Indices: 55962--56008 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
55952 AAACATAAAT
* *
55962 AAATAAAAATAACATATCAATGTTA
1 AAATAAAAATAAAATATAAATGTTA
*
55987 AAAT-AAAATAAAATGTAAATGT
1 AAATAAAAATAAAATATAAATGT
56009 GACCAGAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (25 bp):
AAATAAAAATAAAATATAAATGTTA
Found at i:57793 original size:15 final size:15
Alignment explanation
Indices: 57769--57799 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
57759 ATTTAATCAT
57769 TGGTACCGATACTAC
1 TGGTACCGATACTAC
*
57784 TGGTATCGATACTAC
1 TGGTACCGATACTAC
57799 T
1 T
57800 ACCTCAGTAT
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:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (15 bp):
TGGTACCGATACTAC
Found at i:61236 original size:20 final size:20
Alignment explanation
Indices: 61211--61249 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61201 TTTAAAATAA
* *
61211 AATAAAAATAATTTGTTTTC
1 AATAAAAACAATTGGTTTTC
61231 AATAAAAACAATTGGTTTT
1 AATAAAAACAATTGGTTTT
61250 ACAAAAACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (20 bp):
AATAAAAACAATTGGTTTTC
Found at i:62101 original size:23 final size:23
Alignment explanation
Indices: 62042--62084 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
62032 TAGATGTCCA
62042 GAAGGA-C-CGTAGAAATATCCC
1 GAAGGACCACGTAGAAATATCCC
*
62063 GAAGGACCACGTAGAATTATCC
1 GAAGGACCACGTAGAAATATCC
62085 TGAATGACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 12 0.63
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.16
Consensus pattern (23 bp):
GAAGGACCACGTAGAAATATCCC
Done.