Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167835.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_107, 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: 82982
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Warning! 1000 characters in sequence are not A, C, G, or T
Found at i:6662 original size:17 final size:16
Alignment explanation
Indices: 6623--6659 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
6613 ACTTTTCCTC
**
6623 GAAAATTTATTTTTTT
1 GAAAATTTATTTTTAA
6639 GAAAATTTATTTTTAA
1 GAAAATTTATTTTTAA
6655 GAAAA
1 GAAAA
6660 ATTGATACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (16 bp):
GAAAATTTATTTTTAA
Found at i:6724 original size:59 final size:57
Alignment explanation
Indices: 6537--6988 Score: 591
Period size: 59 Copynumber: 7.7 Consensus size: 57
6527 TCTAGTGCAG
* * *
6537 GGAAAATTGATACTTTCAACTTTTCCCAAAAAATATTCTTTTGAAAATTTAATTTTGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATT-TTTTGAAAATTTATTTTTAA
* *
6595 GGAAAATTGATACTTTCAACTTTTCCTCGAAAATTTATTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCC-CCAAAA-ATA-TTTTTTGAAAATTTATTTTTAA
* **
6655 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTGATTTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAA-TTT-ATTTTTAA
* * *
6714 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACT-TTTTTTAAAAATTAATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTGAAAATTTATTTTTAA
6771 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTGTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TT-TTTTGAAAATTTATTTTTAA
* * * **
6830 GGAAAATTGATAATTTCAACTTTTACCCAAAAATATTTTTTGGAAACTTTGATTTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT-GAAAATTT-ATTTTTAA
* **
6889 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAAGCTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT-GAAAATTTATTTTTAA
* *
6947 GGAAAATTGATACTTTCAAATTTTCCTCAAAAATATATTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAT-TTTTT
6989 TCTTGAAATT
Statistics
Matches: 349, Mismatches: 33, Indels: 23
0.86 0.08 0.06
Matches are distributed among these distances:
56 1 0.00
57 53 0.15
58 83 0.24
59 164 0.47
60 46 0.13
61 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAA
Found at i:6830 original size:175 final size:174
Alignment explanation
Indices: 6537--6989 Score: 680
Period size: 175 Copynumber: 2.6 Consensus size: 174
6527 TCTAGTGCAG
* *
6537 GGAAAATTGATACTTTCAACTTTTCCCAAAAAATATTCTTTTGAAAATTTAA-TTTTGAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATT-TTTTGAAAAATTAATTTTTAAGGAAAA
* *
6601 TTGATACTTTCAACTTTTCCTCGAAAATTTATTTTTTTGAAAATTTATTTTTAAGAAAAATTGAT
64 TTGATACTTTCAACTTTTCC-CCAAAA-ATATTTTTTTGAAAATTTATTTTTAAGAAAAATTGAT
* *
6666 ACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTGATTTTCGA
127 AATTTCAACTTTTACCCAAAAATATTTTTTGAAAACTTTGATTTTCGA
6714 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACT-TTTTTT-AAAAATTAATTTTTAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCC-CAAAAA-TATTTTTTGAAAAATTAATTTTTAAGGAAAA
*
6777 TTGATACTTTCAACTTTTCCCCAAAAATATTTGTTTTGAAAATTTATTTTTAAGGAAAATTGATA
64 TTGATACTTTCAACTTTTCCCCAAAAATATTT-TTTTGAAAATTTATTTTTAAGAAAAATTGATA
*
6842 ATTTCAACTTTTACCCAAAAATATTTTTTGGAAACTTTGATTTTCGA
128 ATTTCAACTTTTACCCAAAAATATTTTTTGAAAACTTTGATTTTCGA
**
6889 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAAGCTT-ATTTTTAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTT-GAAAAATTAATTTTTAAGGAAAA
* *
6953 TTGATACTTTCAAATTTTCCTCAAAAATATATTTTTT
64 TTGATACTTTCAACTTTTCCCCAAAAATAT-TTTTTT
6990 CTTGAAATTA
Statistics
Matches: 255, Mismatches: 12, Indels: 19
0.89 0.04 0.07
Matches are distributed among these distances:
174 7 0.03
175 125 0.49
176 81 0.32
177 40 0.16
178 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (174 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGAAAAATTAATTTTTAAGGAAAATT
GATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGAAAAATTGATAATT
TCAACTTTTACCCAAAAATATTTTTTGAAAACTTTGATTTTCGA
Found at i:7998 original size:21 final size:21
Alignment explanation
Indices: 7969--8009 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7959 TGCCAAGTCA
*
7969 CTTCATCAACATCATCCTCTG
1 CTTCATCAACAGCATCCTCTG
* *
7990 CTTCTTCAATAGCATCCTCT
1 CTTCATCAACAGCATCCTCT
8010 TACATGCCCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.37, G:0.05, T:0.37
Consensus pattern (21 bp):
CTTCATCAACAGCATCCTCTG
Found at i:24143 original size:45 final size:45
Alignment explanation
Indices: 24079--24169 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
24069 AATATAGAAT
24079 AATCTACAGTAATTTATGTGGCAGA-AACTCTATTGCAATTAACTC
1 AATCTACAGTAATTTATGTGGCAGAGAACT-TATTGCAATTAACTC
* * *
24124 AATCTAGAGTAATTTATGTGGTAGAGAACTTATTGCAGTTAACTC
1 AATCTACAGTAATTTATGTGGCAGAGAACTTATTGCAATTAACTC
24169 A
1 A
24170 TAGCGAAGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
45 38 0.90
46 4 0.10
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Consensus pattern (45 bp):
AATCTACAGTAATTTATGTGGCAGAGAACTTATTGCAATTAACTC
Found at i:37853 original size:29 final size:25
Alignment explanation
Indices: 37793--37844 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
37783 ATTTCATGCT
37793 AAATTTTAAGGTACTATATAAATAC
1 AAATTTTAAGGTACTATATAAATAC
37818 AAATTTTAAGGTACTATATAAATAC
1 AAATTTTAAGGTACTATATAAATAC
37843 AA
1 AA
37845 CTTTATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (25 bp):
AAATTTTAAGGTACTATATAAATAC
Found at i:70496 original size:3 final size:3
Alignment explanation
Indices: 70488--70531 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
70478 CTGACTAAAA
*
70488 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
70532 CTACAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:81222 original size:44 final size:45
Alignment explanation
Indices: 81159--81248 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 45
81149 AATATAGGAT
*
81159 AATCTAGAGTAATTTATGTGGCAGA-AACTTATTGCAATTAACTC
1 AATCTAGAGTAATTTATGTGGCAAAGAACTTATTGCAATTAACTC
* *
81203 AATCTAGAGTAATTTATGTGGTAAAGAACTTATTGCAGTTAACTC
1 AATCTAGAGTAATTTATGTGGCAAAGAACTTATTGCAATTAACTC
81248 A
1 A
81249 TAGCGAAGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 23 0.55
45 19 0.45
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (45 bp):
AATCTAGAGTAATTTATGTGGCAAAGAACTTATTGCAATTAACTC
Done.