Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002725.1 Hibiscus syriacus cultivar Beakdansim tig00005622_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: 57351
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:7903 original size:27 final size:27
Alignment explanation
Indices: 7872--7936 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
7862 TTGCAGGTTT
7872 CAACTTCTATTGCTTGCAAGGATGAGG
1 CAACTTCTATTGCTTGCAAGGATGAGG
7899 CAACTTCTATTGCTTGCAAGGATGAGG
1 CAACTTCTATTGCTTGCAAGGATGAGG
7926 CAACTTCTATT
1 CAACTTCTATT
7937 ACAATTGACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (27 bp):
CAACTTCTATTGCTTGCAAGGATGAGG
Found at i:35748 original size:13 final size:13
Alignment explanation
Indices: 35726--35762 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
35716 GACCGGTCAC
35726 GACCCGACCCGTT
1 GACCCGACCCGTT
*
35739 GACCCAACCCGTT
1 GACCCGACCCGTT
35752 GACCCGACCCG
1 GACCCGACCCG
35763 ATCTTTGACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.19, C:0.49, G:0.22, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:35856 original size:29 final size:29
Alignment explanation
Indices: 35780--35856 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 29
35770 ACCGTTGACC
* ** *
35780 GGTGCTATTCTGGTAAATAATTCGATTTT
1 GGTGCTATTCTGGTAATTAATTCGAAATG
35809 GGTGCTATTCTGGTAATTAATTCGAAATG
1 GGTGCTATTCTGGTAATTAATTCGAAATG
* *
35838 GGTGCTATTTTGGTGATTA
1 GGTGCTATTCTGGTAATTA
35857 TTTTAAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (29 bp):
GGTGCTATTCTGGTAATTAATTCGAAATG
Found at i:43112 original size:13 final size:13
Alignment explanation
Indices: 43094--43130 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
43084 GACCGGTCAC
43094 GACCGGACCCGTT
1 GACCGGACCCGTT
43107 GACCGGACCCGTT
1 GACCGGACCCGTT
*
43120 GACCCGACCCG
1 GACCGGACCCG
43131 ATCGTTGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.16, C:0.43, G:0.30, T:0.11
Consensus pattern (13 bp):
GACCGGACCCGTT
Found at i:43209 original size:29 final size:28
Alignment explanation
Indices: 43177--43250 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
43167 ATTAAATTTT
*
43177 GGTGCTATTATGGTAATTAATTCT-AAATG
1 GGTGCTATT-TGGTAATT-ATTCTAAAAAG
* *
43206 GGTGCTAGTTTGGTGATTATTTTAAAAAG
1 GGTGCTA-TTTGGTAATTATTCTAAAAAG
43235 GGTGCTATTTGTGTAA
1 GGTGCTATTTG-GTAA
43251 AATGTTCAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 8 0.21
29 28 0.74
30 2 0.05
ACGTcount: A:0.27, C:0.05, G:0.26, T:0.42
Consensus pattern (28 bp):
GGTGCTATTTGGTAATTATTCTAAAAAG
Found at i:44806 original size:11 final size:11
Alignment explanation
Indices: 44790--44825 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
44780 GTTACAATAA
*
44790 TAATAATAAGT
1 TAATAATAAAT
44801 TAATAATAAAT
1 TAATAATAAAT
44812 TAATAATAAAT
1 TAATAATAAAT
44823 TAA
1 TAA
44826 AACTTGGGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
TAATAATAAAT
Found at i:47233 original size:21 final size:22
Alignment explanation
Indices: 47207--47248 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
47197 CAAAATTATC
47207 ATATATATTTTTT-TA-AAAATT
1 ATATAT-TTTTTTATAGAAAATT
47228 ATATATTTTTTTATAGAAAAT
1 ATATATTTTTTTATAGAAAAT
47249 ATGTTTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATATATTTTTTTATAGAAAATT
Found at i:50361 original size:35 final size:35
Alignment explanation
Indices: 50322--50391 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
50312 TGTTGAAAGT
*
50322 TCAATTTCGTAGTTTGCTAGTTGTTAATTGTTTTA
1 TCAATTTCGTAGTTTGCTAGTTATTAATTGTTTTA
50357 TCAATTTCGTAGTTTGCTAGTTATTAATTGTTTTA
1 TCAATTTCGTAGTTTGCTAGTTATTAATTGTTTTA
50392 AGTGTTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.21, C:0.09, G:0.16, T:0.54
Consensus pattern (35 bp):
TCAATTTCGTAGTTTGCTAGTTATTAATTGTTTTA
Found at i:52130 original size:21 final size:21
Alignment explanation
Indices: 52057--52178 Score: 69
Period size: 21 Copynumber: 6.1 Consensus size: 21
52047 CACCACTGCT
*
52057 CCTCCACCCTCAACAGCAACC-
1 CCTCCTCCCTCAACAGC-ACCA
**
52078 CCTCCTCCCTCAACTTCACCA
1 CCTCCTCCCTCAACAGCACCA
* * *
52099 CC-CC-CGC-CAACGGCAGCA
1 CCTCCTCCCTCAACAGCACCA
**
52117 CCTCCTCCCTCAACTTCACCA
1 CCTCCTCCCTCAACAGCACCA
* *
52138 CCTACT---TCAACAGCAGCA
1 CCTCCTCCCTCAACAGCACCA
* **
52156 CCTCCACCCTCAACTTCACCA
1 CCTCCTCCCTCAACAGCACCA
52177 CC
1 CC
52179 CCCTTCAACA
Statistics
Matches: 74, Mismatches: 20, Indels: 14
0.69 0.19 0.13
Matches are distributed among these distances:
18 23 0.31
19 4 0.05
20 7 0.09
21 40 0.54
ACGTcount: A:0.24, C:0.55, G:0.06, T:0.16
Consensus pattern (21 bp):
CCTCCTCCCTCAACAGCACCA
Found at i:52199 original size:39 final size:39
Alignment explanation
Indices: 52066--52199 Score: 178
Period size: 39 Copynumber: 3.4 Consensus size: 39
52056 TCCTCCACCC
* *
52066 TCAACAGCAACCCCTCCTCCCTCAACTTCACCACCCCCG
1 TCAACAGCAACACCTCCTCCCTCAACTTCACCACCCCCT
* * * **
52105 CCAACGGCAGCACCTCCTCCCTCAACTTCACCACCTACT
1 TCAACAGCAACACCTCCTCCCTCAACTTCACCACCCCCT
* *
52144 TCAACAGCAGCACCTCCACCCTCAACTTCACCACCCCCT
1 TCAACAGCAACACCTCCTCCCTCAACTTCACCACCCCCT
*
52183 TCAACAGCAACGCCTCC
1 TCAACAGCAACACCTCC
52200 GCATACCACC
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.25, C:0.53, G:0.07, T:0.16
Consensus pattern (39 bp):
TCAACAGCAACACCTCCTCCCTCAACTTCACCACCCCCT
Found at i:53193 original size:20 final size:20
Alignment explanation
Indices: 53170--53224 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
53160 GCAATGCGAA
53170 TTCCAATTTCGCAACACAGT
1 TTCCAATTTCGCAACACAGT
* *
53190 TTCCAATTTCACAACCCAGT
1 TTCCAATTTCGCAACACAGT
53210 TTCCAATTTCGCAAC
1 TTCCAATTTCGCAAC
53225 GTGAATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.33, G:0.07, T:0.31
Consensus pattern (20 bp):
TTCCAATTTCGCAACACAGT
Found at i:54089 original size:12 final size:12
Alignment explanation
Indices: 54068--54101 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54058 ACCACATTTC
*
54068 CAATACCAAACA
1 CAATATCAAACA
54080 CAATATCAAACA
1 CAATATCAAACA
*
54092 CAATCTCAAA
1 CAATATCAAA
54102 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:54280 original size:24 final size:24
Alignment explanation
Indices: 54222--54268 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
54212 AGTCAGTATT
*
54222 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
54246 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
54269 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:54474 original size:14 final size:14
Alignment explanation
Indices: 54455--54481 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54445 ATATAACCCT
54455 GAAGAAGAAAAAGA
1 GAAGAAGAAAAAGA
54469 GAAGAAGAAAAAG
1 GAAGAAGAAAAAG
54482 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (14 bp):
GAAGAAGAAAAAGA
Found at i:56426 original size:18 final size:18
Alignment explanation
Indices: 56403--56443 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
56393 AAGCAAAAGG
*
56403 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
56421 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
*
56439 CAATC
1 AAATC
56444 GGCTTCACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.27, G:0.02, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:56907 original size:25 final size:25
Alignment explanation
Indices: 56869--56920 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
56859 AAATCAATTA
*
56869 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
56894 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
56919 AA
1 AA
56921 AATAATGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:57320 original size:24 final size:24
Alignment explanation
Indices: 57293--57339 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
57283 ATATGTATTG
*
57293 GAGTTTGAATTTAAATTTCAATTT
1 GAGTTTGAATTTAAATATCAATTT
*
57317 GAGTTTGAATTTTAATATCAATT
1 GAGTTTGAATTTAAATATCAATT
57340 AACCTTGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (24 bp):
GAGTTTGAATTTAAATATCAATTT
Done.