Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000975.1 Hibiscus syriacus cultivar Beakdansim tig00001951_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: 58564
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2370 original size:26 final size:26
Alignment explanation
Indices: 2347--2401 Score: 65
Period size: 31 Copynumber: 1.9 Consensus size: 26
2337 TTAAGCTCGC
2347 GAGTTTTCGAGTCGAGTCGAGCTCCATTTAA
1 GAGTTTTCGAGTCGAGTCGAGCTCC-----A
2378 GAGTTTTCGAGTCGAGTCGAGCTC
1 GAGTTTTCGAGTCGAGTCGAGCTC
2402 AGCAATACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (26 bp):
GAGTTTTCGAGTCGAGTCGAGCTCCA
Found at i:6002 original size:45 final size:45
Alignment explanation
Indices: 5953--6167 Score: 245
Period size: 45 Copynumber: 4.8 Consensus size: 45
5943 AGGATGCCAG
* *
5953 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATATTAT
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
* * * *
5998 AGTTGAAATGCATATGGATGTATTATCAACAGAAAAGTATGCTAG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
* * * *
6043 AGTTGAAATGTATATGGGTACATTCTCAACAGAAAAGTATATTAT
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
* * * * * * * *
6088 GGTTGAGATG--TATAGTTACATCATCAACATAAAAGTATACAAT
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
*
6131 AGTTGAAATACATATGGGTGCATTATCAACAGAAAAG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
6168 ATGTTATAGT
Statistics
Matches: 137, Mismatches: 31, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
43 33 0.24
45 104 0.76
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (45 bp):
AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
Found at i:6072 original size:90 final size:88
Alignment explanation
Indices: 5941--6201 Score: 274
Period size: 90 Copynumber: 2.9 Consensus size: 88
5931 TAGTGGCATG
* *
5941 AAAGGATGCCAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATATTATAGTTGAAA
1 AAAGTATGCAAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATATTATAGTTGAAA
6006 TGCATATGGATGTATTATCAACAGA
66 TG-ATAT-GATGTATTATCAACAGA
* * * * * * *
6031 AAAGTATGCTAGAGTTGAAATGTATATGGGTACATTCTCAACAGAAAAGTATATTATGGTTGAGA
1 AAAGTATGCAAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATATTATAGTTGAAA
* ** * *
6096 TG-TATAGTTACATCATCAACATA
66 TGATAT-GATGTATTATCAACAGA
* * * * * *
6119 AAAGTATACAATAGTTGAAATACATATGGGTGCATTATCAACAG-AAAAGATGTTATAGTTTAAA
1 AAAGTATGCAAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATATTATAG-TTGAA
6183 ATGTATAATGATGTATTAT
65 ATG-AT-ATGATGTATTAT
6202 AAATATATCG
Statistics
Matches: 136, Mismatches: 31, Indels: 8
0.78 0.18 0.05
Matches are distributed among these distances:
87 10 0.07
88 58 0.43
90 66 0.49
91 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (88 bp):
AAAGTATGCAAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATATTATAGTTGAAA
TGATATGATGTATTATCAACAGA
Found at i:6149 original size:88 final size:89
Alignment explanation
Indices: 5951--6178 Score: 280
Period size: 88 Copynumber: 2.6 Consensus size: 89
5941 AAAGGATGCC
* *
5951 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATATTATAGTTGAAATGCATATGGA
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATATTATAGTTGAAATG-ATATAGA
** * * *
6016 TGTATTATCAACAGAAAAGTATGCT
65 TACATCATCAACAGAAAAGTATACA
* * * * * *
6041 AGAGTTGAAATGTATATGGGTACATTCTCAACAGAAAAGTATATTATGGTTGAGATG-TATAGTT
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATATTATAGTTGAAATGATATAGAT
*
6105 ACATCATCAACATAAAAGTATACA
66 ACATCATCAACAGAAAAGTATACA
* * *
6129 ATAGTTGAAATACATATGGGTGCATTATCAACAGAAAAG-ATGTTATAGTT
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATATTATAGTT
6179 TAAAATGTAT
Statistics
Matches: 117, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
87 9 0.08
88 57 0.49
90 51 0.44
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (89 bp):
AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATATTATAGTTGAAATGATATAGAT
ACATCATCAACAGAAAAGTATACA
Found at i:12248 original size:79 final size:79
Alignment explanation
Indices: 12106--12269 Score: 231
Period size: 79 Copynumber: 2.1 Consensus size: 79
12096 AGAACAAATT
* * **
12106 GAAAAGAAAAATGCATATGGGTGCATTATCGACATGAAAGGATGCCATAGTTGTAATGTATATGG
1 GAAAAGAAAAATGCATATGGGTGCATTATCGACATGAAAGGATGCCAGAGTTGAAATACATATGG
*
12171 GTACATTGTCAACA
66 GTACATTATCAACA
* * *
12185 TAAAAGAATAATGCATATGGGTGCATTAAT-GGCATGAAAGGATGCCAGAGTTGAAATACATATG
1 GAAAAGAAAAATGCATATGGGTGCATT-ATCGACATGAAAGGATGCCAGAGTTGAAATACATATG
*
12249 GGTGCATTATCAACA
65 GGTACATTATCAACA
12264 GAAAAG
1 GAAAAG
12270 TATACTAGAG
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
79 72 0.97
80 2 0.03
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (79 bp):
GAAAAGAAAAATGCATATGGGTGCATTATCGACATGAAAGGATGCCAGAGTTGAAATACATATGG
GTACATTATCAACA
Found at i:12280 original size:45 final size:45
Alignment explanation
Indices: 12231--12449 Score: 260
Period size: 45 Copynumber: 4.9 Consensus size: 45
12221 AAAGGATGCC
*
12231 AGAGTTGAAATACATATGGGTGCATTATCAACAGAAAAGTATACT
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT
* * * *
12276 AGAGTTTAAATGCATATGGGTGTATTTTCAACAGAAAAGTATGCT
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT
* * *
12321 AGAGTTGAAATGTATATGGGTACATTCTCAACAGAAAAGTATACT
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT
* * * * * **
12366 ATG-GTTGAGATGTATATGGGTACATCATCAACATAAAAGTATAAA
1 A-GAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT
* * *
12411 ATAGTTGAAATACATATGGGTGCATTATTAACAGAAAAG
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
12450 ATGTTATAGT
Statistics
Matches: 147, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
45 146 0.99
46 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.29
Consensus pattern (45 bp):
AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT
Found at i:12489 original size:90 final size:88
Alignment explanation
Indices: 12231--12490 Score: 261
Period size: 90 Copynumber: 2.9 Consensus size: 88
12221 AAAGGATGCC
* *
12231 AGAGTTGAAATACATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTTAAATGCATATGGG
1 AGAGTTGAAATACATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTTAAATGTATAT--G
* * ***
12296 TGTATTTTCAACAGAAAAGTATGCT
64 TGTATTATCAACATAAAAGTATAAA
** * * * * * *
12321 AGAGTTGAAATGTATATGGGTACATTCTCAACAGAAAAGTATACTATGGTTGAGATGTATATGGG
1 AGAGTTGAAATACATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTTAAATGTATATGTG
*
12386 TACATCATCAACATAAAAGTATAAA
66 T--ATTATCAACATAAAAGTATAAA
* * **
12411 ATAGTTGAAATACATATGGGTGCATTATTAACAGAAAAG-ATGTTATAGTTTAAAATGTATAATG
1 AGAGTTGAAATACATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTT-AAATGTAT-ATG
*
12475 ATGTATTATAAACATA
64 -TGTATTATCAACATA
12491 TGGAGATTGC
Statistics
Matches: 135, Mismatches: 30, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
88 3 0.02
89 8 0.06
90 119 0.88
91 3 0.02
92 2 0.01
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.31
Consensus pattern (88 bp):
AGAGTTGAAATACATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTTAAATGTATATGTG
TATTATCAACATAAAAGTATAAA
Found at i:16893 original size:36 final size:35
Alignment explanation
Indices: 16851--16931 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 35
16841 TTATTATGTT
16851 TATAATATTA-ATTATAAATTTTTAATATTTATAAAC
1 TATAATATTATATTATAAATTTTTAATA-TT-TAAAC
*
16887 TATAATATTATTTTTATAAATTTTTAATATTTAAAC
1 TATAATATTA-TATTATAAATTTTTAATATTTAAAC
16923 TAATAATAT
1 T-ATAATAT
16932 CATTAAGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
36 16 0.39
37 9 0.22
38 16 0.39
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (35 bp):
TATAATATTATATTATAAATTTTTAATATTTAAAC
Found at i:20691 original size:15 final size:15
Alignment explanation
Indices: 20671--20700 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20661 ACTCTTTCAT
20671 GGTTTTATAACAACC
1 GGTTTTATAACAACC
20686 GGTTTTATAACAACC
1 GGTTTTATAACAACC
20701 TTACCAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (15 bp):
GGTTTTATAACAACC
Found at i:30181 original size:18 final size:18
Alignment explanation
Indices: 30138--30175 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
30128 GTGAAGTATG
*
30138 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
30156 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
30174 AA
1 AA
30176 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:31024 original size:45 final size:47
Alignment explanation
Indices: 30914--31029 Score: 137
Period size: 49 Copynumber: 2.5 Consensus size: 47
30904 ACCTTTTACC
*
30914 CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCATTTAAAATT
1 CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCAATT--AATT
* ** * *
30963 CCATAAGCTCGTAAGCTTATTTTTTTCAATATACTT-GCAATT-ATT
1 CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCAATTAATT
*
31008 CCGTAAGCTCATAAGCTTATTT
1 CCATAAGCTCATAAGCTTATTT
31030 GCATGGTTAC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 23 0.39
48 4 0.07
49 32 0.54
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.40
Consensus pattern (47 bp):
CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCAATTAATT
Found at i:33571 original size:17 final size:18
Alignment explanation
Indices: 33538--33571 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33528 TCAATTCTGT
*
33538 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
33556 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
33572 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:41337 original size:45 final size:47
Alignment explanation
Indices: 41209--41342 Score: 148
Period size: 49 Copynumber: 2.9 Consensus size: 47
41199 AATATAATAT
* * *
41209 AAATTCTTACC-TTTTATCCCATAAGCTCATAAGCTTATTTTTACCA
1 AAATACTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTACCA
* **
41255 AAATACTTACCATTTAAAATTCCATAAGCTCGTAAGCTTATTTTTTTCA
1 AAATACTTACCATTT--AATTCCATAAGCTCATAAGCTTATTTTTACCA
* * *
41304 ATATACTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 AAATACTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
41343 GCATGGTTAC
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
45 23 0.31
46 10 0.13
47 3 0.04
48 2 0.03
49 37 0.49
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (47 bp):
AAATACTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTACCA
Done.