Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000746.1 Hibiscus syriacus cultivar Beakdansim tig00001437_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: 54922
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:6148 original size:24 final size:24
Alignment explanation
Indices: 6107--6191 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 24
6097 AAACATAATT
6107 CAGGTCAAG--TCATATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
*
6129 TAGGTCAAGTATCATATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
*
6153 CATGTCAA-TATCATATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
*
6176 CAGGTCAGGTATCATA
1 CAGGTCAAGTATCATA
6192 ACATAATTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
22 8 0.15
23 21 0.38
24 26 0.47
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAGAATC
Found at i:10777 original size:24 final size:24
Alignment explanation
Indices: 10750--10833 Score: 116
Period size: 24 Copynumber: 3.5 Consensus size: 24
10740 CATAATTCAA
10750 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* *
10774 GTCATGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAG
* *
10798 GTCAA-TATCAAATCAGAATCTAG
1 GTCAAGTATCATATCAGAATCCAG
*
10821 GTCAGGTATCATA
1 GTCAAGTATCATA
10834 ATAGAATTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 19 0.37
24 32 0.63
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:18128 original size:29 final size:29
Alignment explanation
Indices: 18063--18128 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
18053 TTAAATCCAT
* *
18063 CGATTATTAAAAGTTAAAAATTGATCTTT
1 CGATTATTAAAAGTTAAAAATTGATCATC
*
18092 CGACTATTAAAAGTTACAAAA-TGATCATC
1 CGATTATTAAAAGTTA-AAAATTGATCATC
18121 CGATTATT
1 CGATTATT
18129 CATTATGTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 28 0.88
30 4 0.12
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (29 bp):
CGATTATTAAAAGTTAAAAATTGATCATC
Found at i:21885 original size:22 final size:21
Alignment explanation
Indices: 21853--21904 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
21843 AAATGGATAT
* *
21853 TTAAACATCAAAATGTTTTAA
1 TTAAATATCAAAATATTTTAA
*
21874 TTAAATTATC-AAATATTTTAG
1 TTAAA-TATCAAAATATTTTAA
21895 TTAAATATCA
1 TTAAATATCA
21905 TTTCATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 4 0.15
21 19 0.73
22 3 0.12
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (21 bp):
TTAAATATCAAAATATTTTAA
Found at i:22401 original size:18 final size:18
Alignment explanation
Indices: 22378--22417 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
22368 TTTCATTAAT
22378 ATTTATGTATGATATGGC
1 ATTTATGTATGATATGGC
*
22396 ATTTATGTATGATGTGGC
1 ATTTATGTATGATATGGC
22414 ATTT
1 ATTT
22418 TTTCTTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.47
Consensus pattern (18 bp):
ATTTATGTATGATATGGC
Found at i:22714 original size:15 final size:17
Alignment explanation
Indices: 22694--22730 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
22684 TTTTAAAATT
22694 TTAATTTAAT-TA-ATA
1 TTAATTTAATATATATA
22709 TTAATTTAATATATATA
1 TTAATTTAATATATATA
22726 TTAAT
1 TTAAT
22731 AAAATAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.50
16 2 0.10
17 8 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAATTTAATATATATA
Found at i:26579 original size:2 final size:2
Alignment explanation
Indices: 26544--26568 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26534 TTTGAAATTA
26544 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 A
26569 AAGAGATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28835 original size:34 final size:34
Alignment explanation
Indices: 28792--28901 Score: 211
Period size: 34 Copynumber: 3.2 Consensus size: 34
28782 TGTGTTCAGT
*
28792 TCGTTTATGTTCACGAACAAGTTCATTTATGAGC
1 TCGTTTATGTTCACGAACAAGCTCATTTATGAGC
28826 TCGTTTATGTTCACGAACAAGCTCATTTATGAGC
1 TCGTTTATGTTCACGAACAAGCTCATTTATGAGC
28860 TCGTTTATGTTCACGAACAAGCTCATTTATGAGC
1 TCGTTTATGTTCACGAACAAGCTCATTTATGAGC
28894 TCGTTTAT
1 TCGTTTAT
28902 CAACTCATTC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 75 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (34 bp):
TCGTTTATGTTCACGAACAAGCTCATTTATGAGC
Found at i:29181 original size:24 final size:24
Alignment explanation
Indices: 29165--29290 Score: 105
Period size: 24 Copynumber: 5.2 Consensus size: 24
29155 ACATGTTCAT
*
29165 GAACACGTTTGTGAACATATAAAC
1 GAACACGTTCGTGAACATATAAAC
29189 GAACACGTTCGTGAACAT-TAAAC
1 GAACACGTTCGTGAACATATAAAC
**** * ** *
29212 GAACA--TTAAACAAACATGTGCAT
1 GAACACGTT-CGTGAACATATAAAC
*
29235 GAACACATTCGTGAACATATAAAC
1 GAACACGTTCGTGAACATATAAAC
29259 GAACACGTTCGTGAACATTAAATAAAC
1 GAACACGTTCGTGAACA-T--ATAAAC
29286 GAACA
1 GAACA
29291 TGAACACCTT
Statistics
Matches: 78, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
21 2 0.03
22 5 0.06
23 17 0.22
24 40 0.51
25 3 0.04
27 11 0.14
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.21
Consensus pattern (24 bp):
GAACACGTTCGTGAACATATAAAC
Found at i:29224 original size:70 final size:70
Alignment explanation
Indices: 29148--29280 Score: 239
Period size: 70 Copynumber: 1.9 Consensus size: 70
29138 AAAACAACGC
* * *
29148 TAAACAAACATGTTCATGAACACGTTTGTGAACATATAAACGAACACGTTCGTGAACATTAAACG
1 TAAACAAACATGTGCATGAACACATTCGTGAACATATAAACGAACACGTTCGTGAACATTAAACG
29213 AACAT
66 AACAT
29218 TAAACAAACATGTGCATGAACACATTCGTGAACATATAAACGAACACGTTCGTGAACATTAAA
1 TAAACAAACATGTGCATGAACACATTCGTGAACATATAAACGAACACGTTCGTGAACATTAAA
29281 TAAACGAACA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (70 bp):
TAAACAAACATGTGCATGAACACATTCGTGAACATATAAACGAACACGTTCGTGAACATTAAACG
AACAT
Found at i:33956 original size:2 final size:2
Alignment explanation
Indices: 33949--33973 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33939 CTGTAATTCT
33949 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 T
33974 CTGAATCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35775 original size:36 final size:36
Alignment explanation
Indices: 35735--35807 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
35725 ATATGTGTAA
*
35735 TTAAGTGATAAAAGAATCAGCCATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAGCCATGAATATGTAGAT
35771 TTAAGTGATAAAAGAATCAGCCATGAATATGTAGAT
1 TTAAGTGATAAAAGAATCAGCCATGAATATGTAGAT
35807 T
1 T
35808 ATAATTTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (36 bp):
TTAAGTGATAAAAGAATCAGCCATGAATATGTAGAT
Found at i:37630 original size:12 final size:12
Alignment explanation
Indices: 37615--37678 Score: 67
Period size: 12 Copynumber: 5.3 Consensus size: 12
37605 ATGACTTGAA
37615 TTCTGTTCTGAT
1 TTCTGTTCTGAT
*
37627 TTCTGATCTGGA-
1 TTCTGTTCT-GAT
37639 TTCTGTTCTGAT
1 TTCTGTTCTGAT
* * *
37651 ATATGTTCTGAA
1 TTCTGTTCTGAT
*
37663 TTCTGTTTTGAT
1 TTCTGTTCTGAT
37675 TTCT
1 TTCT
37679 AATATCTCCG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
11 2 0.05
12 37 0.90
13 2 0.05
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.55
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:37641 original size:24 final size:24
Alignment explanation
Indices: 37611--37678 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
37601 ATACATGACT
37611 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATTTCTGATC
* * * *
37635 TGGATTCTGTTCTGATATATGTTC
1 TGAATTCTGTTCTGATTTCTGATC
*
37659 TGAATTCTGTTTTGATTTCT
1 TGAATTCTGTTCTGATTTCT
37679 AATATCTCCG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.16, C:0.13, G:0.18, T:0.53
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATC
Found at i:45396 original size:37 final size:37
Alignment explanation
Indices: 45355--45428 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
45345 TTGACATAAT
*
45355 TTAGCATATATATTATCTAATTTAATAGTTAAAAGTC
1 TTAGCATATATATTATCTAATTTAATAGCTAAAAGTC
*
45392 TTAGCATATATGTTATCTAATTTAATAGCTAAAAGTC
1 TTAGCATATATATTATCTAATTTAATAGCTAAAAGTC
45429 CAAAAAAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (37 bp):
TTAGCATATATATTATCTAATTTAATAGCTAAAAGTC
Found at i:50926 original size:60 final size:59
Alignment explanation
Indices: 50818--50945 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 59
50808 TCAGGTGACT
* * *
50818 ATTTTGTAACTTTTAATAGTCGAGGGACTCAATAAAGCAACGCTCTATAGTTGGAGGACC
1 ATTTTGTAACTTTAAATAGTCGAGGGACTCAATAAAACAACGCTCTATAATTGG-GGACC
* * *
50878 ATTTTGTAACTTTAAATAGTCGAGGGACTTAATAAAATAGTAC-C-CTATAATTGGGTACC
1 ATTTTGTAACTTTAAATAGTCGAGGGACTCAATAAAACA--ACGCTCTATAATTGGGGACC
50937 ATTTGTGTA
1 ATTT-TGTA
50946 TTTTACCCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
59 8 0.14
60 48 0.81
61 1 0.02
62 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.34
Consensus pattern (59 bp):
ATTTTGTAACTTTAAATAGTCGAGGGACTCAATAAAACAACGCTCTATAATTGGGGACC
Done.