Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005734.1 Hibiscus syriacus cultivar Beakdansim tig00013403_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: 33917
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:2220 original size:587 final size:587
Alignment explanation
Indices: 1179--2349 Score: 1966
Period size: 587 Copynumber: 2.0 Consensus size: 587
1169 GTTGGCTCTA
*
1179 ATTTAAAGGGTGAGGGTTGCTTGGCCGAATGGTGTTGGAAATTCGGTCATTGAAAGCCTTGATTT
1 ATTTAAAGGGTGAGGGCTGCTTGGCCGAATGGTGTTGGAAATTCGGTCATTGAAAGCCTTGATTT
*
1244 AGTCATAATCCGTGACATATTCTAGGATCTGTTTTCTATGTAAATATAGAATGATGTAAATCAAG
66 AGTCATAATCCGTGACATATTCTAGGATATGTTTTCTATGTAAATATAGAATGATGTAAATCAAG
1309 ACAAAGTAGGAAAGTAGAAGCTATCAATATTGACTCTAATTAGTTTCCTTTTTTGTTGTAATTTC
131 ACAAAGTAGGAAAGTAGAAGCTATCAATATTGACTCTAATTAGTTTCCTTTTTTGTTGTAATTTC
*
1374 CCTCTGTATAAAAAGGAAGCCTTGTACTCATTCAAAAAATAGACACGCATTATTTCTTCATTTTT
196 CCTATGTATAAAAAGGAAGCCTTGTACTCATTCAAAAAATAGACACGCATTATTTCTTCATTTTT
* * *
1439 TCTAAGTTGGTATCATAGCTATAATTATGTCTTAACCCTAAAACACAACAGCTCCAAAATCACCG
261 TCTAAGTTGGTATCAGAGCTATAATCATGTCTTAACCATAAAACACAACAGCTCCAAAATCACCG
1504 TAGCCATGTCCGAAGTCGCATCGGAAATCCAATTCAACAAAGAGCAGATTGATCAACTCTTGAAG
326 TAGCCATGTCCGAAGTCGCATCGGAAATCCAATTCAACAAAGAGCAGATTGATCAACTCTTGAAG
*
1569 CTGATAAAATCCAATTCCTCATCCGATATTCCTAGTGTTTATTTGGCACAAACAGGTAGTAATCC
391 CTGATAAAATCCAATTCCTCATCCGATATTCCTAGTGTTTATTTGGCACAAAAAGGTAGTAATCC
*
1634 TAAAGCCCTTTC-TATCCAAATTCCTCTCTGTGAATAATAGATTCCGGAGCCTCAGATTACATG-
456 TAAAGCCCTTTCTTATCCAAATTCCTCTCTGTGAATAATAGATTCCGGAGCCTCAGATCACATGA
1697 AGTTTTTCTC-GTTTATTTAATACCTATTCACCTTACCCTGGAAATGAAAAAATTAGAATTGCCT
521 AGTTTTTCTCAGTTTATTTAATACCTATTCACCTTACCCTGGAAATGAAAAAATTAGAATTGCCT
1761 TG
586 TG
1763 ATTTAAAGGGTGAGGGCTGCTTGGCCGAATGGTGTTGGAAATTCGGTCATTGAAAGCCTTGATTT
1 ATTTAAAGGGTGAGGGCTGCTTGGCCGAATGGTGTTGGAAATTCGGTCATTGAAAGCCTTGATTT
1828 AGTCATAATCCGTGACATATTCTAGGATATG-TTTCTATGTAAATATAGAAACTGGAAGCTGTAA
66 AGTCATAATCCGTGACATATTCTAGGATATGTTTTCTATGTAAATATAG-AA-T-G-A--TGTAA
* *
1892 ATTAAGACAAAGTAGGAAA-TGAGAAGCTGTCAAATATTGACTCTAATTAGTTTCCTTTTTTTGT
125 ATCAAGACAAAGTAGGAAAGT-AGAAGCTATC-AATATTGACTCTAATTAGTTTCC-TTTTTTGT
* *
1956 TGTAATTTCCCTATGTAT-AAAAGGAAGCCTTGTACTCATTCAAGAAATAAGACACGTATTATTT
187 TGTAATTTCCCTATGTATAAAAAGGAAGCCTTGTACTCATTCAAAAAAT-AGACACGCATTATTT
* * *
2020 CTTCATTTTTTCTAAGTTGGTATCAGAGCTATAATCATGTCTTAACCATAAAAC-TAGCAGCTCT
251 CTTCATTTTTTCTAAGTTGGTATCAGAGCTATAATCATGTCTTAACCATAAAACACAACAGCTCC
*
2084 AAAATCACCGTAGCCATGTCCG-A-TCGCTTCGG-AATCCAATTCAACAAAGAGCAGATTGATCA
316 AAAATCACCGTAGCCATGTCCGAAGTCGCATCGGAAATCCAATTCAACAAAGAGCAGATTGATCA
* *
2146 ATTCTTGAAGCTGATAAAATCCAATTCCTCATCTGATATTCCTAGTGTTTATTTGGCACAAAAAG
381 ACTCTTGAAGCTGATAAAATCCAATTCCTCATCCGATATTCCTAGTGTTTATTTGGCACAAAAAG
* *
2211 GTGGTAATCCTAAAGCCCTTTCTTGTCCAAATTCCTCTCTGTGAATAATAGATTCCGGAGCCTCA
446 GTAGTAATCCTAAAGCCCTTTCTTATCCAAATTCCTCTCTGTGAATAATAGATTCCGGAGCCTCA
* *
2276 GATCACATGACTAGTTTTTCTCATTTTATTTAATACCTATTCACCTTACCTTGGAAATGAAAAAA
511 GATCACATGA--AGTTTTTCTCAGTTTATTTAATACCTATTCACCTTACCCTGGAAATGAAAAAA
2341 TTAGAATTG
574 TTAGAATTG
2350 TTAATGGTAA
Statistics
Matches: 550, Mismatches: 22, Indels: 22
0.93 0.04 0.04
Matches are distributed among these distances:
583 17 0.03
584 96 0.17
585 1 0.00
586 1 0.00
587 114 0.21
588 58 0.11
589 33 0.06
590 81 0.15
591 100 0.18
592 49 0.09
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (587 bp):
ATTTAAAGGGTGAGGGCTGCTTGGCCGAATGGTGTTGGAAATTCGGTCATTGAAAGCCTTGATTT
AGTCATAATCCGTGACATATTCTAGGATATGTTTTCTATGTAAATATAGAATGATGTAAATCAAG
ACAAAGTAGGAAAGTAGAAGCTATCAATATTGACTCTAATTAGTTTCCTTTTTTGTTGTAATTTC
CCTATGTATAAAAAGGAAGCCTTGTACTCATTCAAAAAATAGACACGCATTATTTCTTCATTTTT
TCTAAGTTGGTATCAGAGCTATAATCATGTCTTAACCATAAAACACAACAGCTCCAAAATCACCG
TAGCCATGTCCGAAGTCGCATCGGAAATCCAATTCAACAAAGAGCAGATTGATCAACTCTTGAAG
CTGATAAAATCCAATTCCTCATCCGATATTCCTAGTGTTTATTTGGCACAAAAAGGTAGTAATCC
TAAAGCCCTTTCTTATCCAAATTCCTCTCTGTGAATAATAGATTCCGGAGCCTCAGATCACATGA
AGTTTTTCTCAGTTTATTTAATACCTATTCACCTTACCCTGGAAATGAAAAAATTAGAATTGCCT
TG
Found at i:3035 original size:88 final size:89
Alignment explanation
Indices: 2876--3048 Score: 278
Period size: 88 Copynumber: 2.0 Consensus size: 89
2866 CCTAACACAC
* *
2876 CCTTTTATATTCAAGTTACCCTAATCATATTAGGGTTTTCATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTCATTATTTCAAATTAATTAAATCTAT
*
2941 AATTAATTAATTAGAATTTAATAAT
66 AATTAATTAATT-GAAATTAATAAT
*
2966 CCTTTTATGTCCAAGTTACCCTAATCATA-TAGGGATTT-ATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTCATTATTTCAAATTAATTAAATCTAT
*
3029 ATTTAATTAATTGAAATTAA
66 AATTAATTAATTGAAATTAA
3049 ATATTCGAGA
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
87 7 0.09
88 36 0.46
89 8 0.10
90 27 0.35
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.45
Consensus pattern (89 bp):
CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTCATTATTTCAAATTAATTAAATCTAT
AATTAATTAATTGAAATTAATAAT
Found at i:9035 original size:90 final size:90
Alignment explanation
Indices: 8882--9059 Score: 313
Period size: 90 Copynumber: 2.0 Consensus size: 90
8872 CCTAACACAC
8882 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGTTTTCATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGTTTTCATTATTTCAAATTAATTAAATCTAT
* *
8947 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
8972 CCTTTTATCTCCAAGTTACCCTAATCATATTAGGGATTTT-ATTATTTCAAATTAATTAAATCTA
1 CCTTTTATATCCAAGTTACCCTAATCATATTAGGG-TTTTCATTATTTCAAATTAATTAAATCTA
9036 TATTTAATTAATTGAAATTAAATA
65 TATTTAATTAATTGAAATTAAATA
9060 TTTGGGATTA
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
90 80 0.95
91 4 0.05
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (90 bp):
CCTTTTATATCCAAGTTACCCTAATCATATTAGGGTTTTCATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:24866 original size:45 final size:46
Alignment explanation
Indices: 24765--24867 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 46
24755 CCATTAAACA
* * * *
24765 GGTACCGATACCCTCTTAAATGAAAAGAATCACAGAATATAGTGAG
1 GGTACCGATACCCTCTTAAACGAAAAGAATAACAGAATACAGTAAG
* * *
24811 AGTACTGATACCCTCTTGAACGAAAA-AATAACAGAATACAGTAAG
1 GGTACCGATACCCTCTTAAACGAAAAGAATAACAGAATACAGTAAG
24856 GGTACCGATACC
1 GGTACCGATACC
24868 TCAAGGGGTG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
45 26 0.54
46 22 0.46
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.20
Consensus pattern (46 bp):
GGTACCGATACCCTCTTAAACGAAAAGAATAACAGAATACAGTAAG
Found at i:25524 original size:23 final size:23
Alignment explanation
Indices: 25491--25553 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
25481 CATCTTATAT
* *
25491 GGCACTACGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACAC
* *
25514 GGCACTTCGGTGCAATTCTACAT
1 GGCACTTCGGTGCATTTCTACAC
25537 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
25554 ATATGAGTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACAC
Done.