Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000539.1 Hibiscus syriacus cultivar Beakdansim tig00001041_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: 66671
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:4378 original size:21 final size:21
Alignment explanation
Indices: 4354--4393 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4344 CTGCGATTGT
4354 GGCCATAGCGAGCACTGTTGC
1 GGCCATAGCGAGCACTGTTGC
* *
4375 GGCCGTAGCGGGCACTGTT
1 GGCCATAGCGAGCACTGTT
4394 ACGACTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.38, T:0.20
Consensus pattern (21 bp):
GGCCATAGCGAGCACTGTTGC
Found at i:5902 original size:19 final size:19
Alignment explanation
Indices: 5878--5927 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
5868 TGTAATTTGG
5878 GTATCGATACCTATGCATT
1 GTATCGATACCTATGCATT
5897 GTATCGATACCTATGCATT
1 GTATCGATACCTATGCATT
5916 GTATCGATACCT
1 GTATCGATACCT
5928 CAGCTAGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (19 bp):
GTATCGATACCTATGCATT
Found at i:16457 original size:12 final size:12
Alignment explanation
Indices: 16448--16472 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16438 ATGAATAAAG
16448 ATAAGAATAATA
1 ATAAGAATAATA
16460 ATAAGAATAATA
1 ATAAGAATAATA
16472 A
1 A
16473 AATGATATGT
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
ATAAGAATAATA
Found at i:31991 original size:18 final size:18
Alignment explanation
Indices: 31968--32002 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31958 AAAACTATAT
*
31968 TATAAAATTATCTTAATA
1 TATAAAATTATATTAATA
31986 TATAAAATTATATTAAT
1 TATAAAATTATATTAAT
32003 GTTGTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TATAAAATTATATTAATA
Found at i:32794 original size:3 final size:3
Alignment explanation
Indices: 32788--32873 Score: 55
Period size: 3 Copynumber: 25.7 Consensus size: 3
32778 TAATATTATT
* * *
32788 TAA TAA TAC TAA TAT TAT TAA TATA TAA TATA TAA TAA TAA CGTATA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA --TA-A
*
32835 TAA TAA AACA TATA TAA TTAA TAA TATA TAA TAA TAA TA
1 TAA TAA TA-A TA-A TAA -TAA TAA TA-A TAA TAA TAA TA
32874 TAAACGGACA
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
3 46 0.68
4 19 0.28
5 2 0.03
6 1 0.01
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:32815 original size:22 final size:19
Alignment explanation
Indices: 32778--32818 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
32768 TGGTATTTTG
32778 TAATATTATTTAATAATAC
1 TAATATTATTTAATAATAC
32797 TAATATTA-TTAAT-ATA-
1 TAATATTATTTAATAATAC
32813 TAATAT
1 TAATAT
32819 ATAATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.27
17 3 0.14
18 5 0.23
19 8 0.36
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATATTATTTAATAATAC
Found at i:32818 original size:7 final size:7
Alignment explanation
Indices: 32806--32875 Score: 67
Period size: 7 Copynumber: 10.0 Consensus size: 7
32796 CTAATATTAT
32806 TAATATA
1 TAATATA
32813 TAATATA
1 TAATATA
32820 TAATA-A
1 TAATATA
32826 TAACGTATA
1 TAA--TATA
32835 TAATA-A
1 TAATATA
*
32841 AACATATA
1 TA-ATATA
32849 TAAT-TAA
1 TAATAT-A
32856 TAATATA
1 TAATATA
32863 TAATA-A
1 TAATATA
32869 TAATATA
1 TAATATA
32876 AACGGACAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
6 13 0.25
7 31 0.58
8 5 0.09
9 4 0.08
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (7 bp):
TAATATA
Found at i:33366 original size:17 final size:17
Alignment explanation
Indices: 33333--33367 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
33323 ACGTGACACC
*
33333 ATTTGATTAAATGAAAA
1 ATTTGATTAAATAAAAA
33350 ATTT-ATTAAATAAAAA
1 ATTTGATTAAATAAAAA
33366 AT
1 AT
33368 ATTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (17 bp):
ATTTGATTAAATAAAAA
Found at i:33574 original size:25 final size:25
Alignment explanation
Indices: 33543--33591 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
33533 GACTTAATTG
* *
33543 ACAAGATTTAAATAGTTAGATAACA
1 ACAAGATTTAAAAACTTAGATAACA
33568 ACAAGATTTAAAAACTTAGATAAC
1 ACAAGATTTAAAAACTTAGATAAC
33592 CTTATCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (25 bp):
ACAAGATTTAAAAACTTAGATAACA
Found at i:35052 original size:2 final size:2
Alignment explanation
Indices: 35040--35071 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
35030 ATATAATAGT
*
35040 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35072 ATAACTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:35101 original size:16 final size:16
Alignment explanation
Indices: 35080--35115 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
35070 TAATAACTTT
35080 AAAAAACATTAAAATA
1 AAAAAACATTAAAATA
* *
35096 AAAAAATATTAGAATA
1 AAAAAACATTAAAATA
35112 AAAA
1 AAAA
35116 TAATTAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAAACATTAAAATA
Found at i:36349 original size:2 final size:2
Alignment explanation
Indices: 36337--36373 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
36327 TATTTATACA
*
36337 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36374 GTTCATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:37325 original size:106 final size:106
Alignment explanation
Indices: 37138--37491 Score: 411
Period size: 106 Copynumber: 3.4 Consensus size: 106
37128 GCTCCGAGTT
* * * * * * **
37138 CAATATCCTTCG-TCGTGAAGTTGAAATTAGTTCTGGAACTAGAAAATTGTTTGTTGACAGTCAG
1 CAATATCCTTCGCT-GTGAAGTTGAAATTGGATATGAAATTGGGGAATTGTTTGTTGACAGTCAG
* *
37202 CCACCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTTGGGTC
65 CCGCCCCTTCACCGTGAAGTTGAGCTTGTGTTGTCTTGGGTC
* * *
37244 CAATATCCTTTGCTGTGAAGTTGAAATTGGATATGAAATTGGGGAATTATTTGTTGAGAGTCAGC
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGATATGAAATTGGGGAATTGTTTGTTGACAGTCAGC
* * *
37309 CGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTGAGTC
66 CGCCCCTTCACCGTGAAGTTGAGCTTGTGTTGTCTTGGGTC
* * * *
37350 CAATATCCTTCGTTGTGAAGTTGAAATT-GACTCTGAAA-----G--CTGTTTGTTGACAATCAG
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGA-TATGAAATTGGGGAATTGTTTGTTGACAGTCAG
*
37407 CCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGGGTC
65 CCGCCCCTTCACCGTGAAGTTGAGCTTGTGTTGTCTTGGGTC
* * *
37449 CAATATCCTTCGCTATGAAGTTGAAATTGGTTATGACATTGGG
1 CAATATCCTTCGCTGTGAAGTTGAAATTGGATATGAAATTGGG
37492 AAGCCCCTTC
Statistics
Matches: 208, Mismatches: 32, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
99 83 0.40
100 1 0.00
101 1 0.00
105 2 0.01
106 120 0.58
107 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
CAATATCCTTCGCTGTGAAGTTGAAATTGGATATGAAATTGGGGAATTGTTTGTTGACAGTCAGC
CGCCCCTTCACCGTGAAGTTGAGCTTGTGTTGTCTTGGGTC
Found at i:38170 original size:75 final size:77
Alignment explanation
Indices: 38048--38195 Score: 185
Period size: 75 Copynumber: 1.9 Consensus size: 77
38038 TTCTTTTCTT
* ** * * *
38048 TTTTTTTTTTTTTTTTTTTTTCCCTTTTCCTTTTTTTTTCAATTTAGGGCGCCCTTTCAGGTTTT
1 TTTTTTATTTTTTTCCTTTTTCCCTTTTCCTTTTTTTTTCAACTTAGGACGCCCTCTCAGGTTTT
38113 CACCCTAAATGA
66 CACCCTAAATGA
* *
38125 TTTTTTATTTTTTTCCTTTTT--CTTTTTCTCTTTTTTTT-AACTTAGGACGCCCTCTCGGGTTT
1 TTTTTTATTTTTTTCCTTTTTCCCTTTTCCT-TTTTTTTTCAACTTAGGACGCCCTCTCAGGTTT
*
38187 TCATCCTAA
65 TCACCCTAA
38196 GCGAAGTACT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
75 35 0.57
76 8 0.13
77 18 0.30
ACGTcount: A:0.11, C:0.20, G:0.09, T:0.59
Consensus pattern (77 bp):
TTTTTTATTTTTTTCCTTTTTCCCTTTTCCTTTTTTTTTCAACTTAGGACGCCCTCTCAGGTTTT
CACCCTAAATGA
Found at i:47936 original size:12 final size:13
Alignment explanation
Indices: 47914--47949 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
47904 GAAAAATATG
47914 AAAACATAAAACA
1 AAAACATAAAACA
47927 AAAACA-AAAACA
1 AAAACATAAAACA
*
47939 AATACATAAAA
1 AAAACATAAAA
47950 AAGCGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.78, C:0.14, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAACATAAAACA
Found at i:48372 original size:2 final size:2
Alignment explanation
Indices: 48365--48408 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
48355 AAAATAATTA
48365 AT 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 AT
48407 AT
1 AT
48409 TTAATACGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49525 original size:2 final size:2
Alignment explanation
Indices: 49518--49570 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
49508 TATTTATACA
49518 AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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 AT
*
49559 AT AT AA AT AT AT
1 AT AT AT AT AT AT
49571 GTTCATTTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:62945 original size:10 final size:10
Alignment explanation
Indices: 62930--62964 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
62920 TGCACATCAC
62930 TTTAGTTGTA
1 TTTAGTTGTA
*
62940 TTTAGTTGCA
1 TTTAGTTGTA
*
62950 TTTAGTTTTA
1 TTTAGTTGTA
62960 TTTAG
1 TTTAG
62965 GTTATATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.20, C:0.03, G:0.17, T:0.60
Consensus pattern (10 bp):
TTTAGTTGTA
Done.