Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, 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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 138 of 138
Found at i:19845420 original size:26 final size:26
Alignment explanation
Indices: 19845391--19845443 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
19845381 CCGGTCCGAT
19845391 CTTAGAC-TAGGAATGAACTCCGTATG
1 CTTAGACAT-GGAATGAACTCCGTATG
19845417 CTTAGACATGGAATGAACTCCGTATG
1 CTTAGACATGGAATGAACTCCGTATG
19845443 C
1 C
19845444 CTAAGCCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (26 bp):
CTTAGACATGGAATGAACTCCGTATG
Found at i:19845719 original size:159 final size:159
Alignment explanation
Indices: 19845426--19845919 Score: 523
Period size: 159 Copynumber: 3.1 Consensus size: 159
19845416 GCTTAGACAT
* *
19845426 GGAATGAACTCCGTATGCCTAAGCCAACCCATGAAATGAGCGTGCGGGCACTCAGCCGGTCGGAG
1 GGAATGAACTCCGTATGCCTAAGCCAACCCACGAAATGAGCGTGCGGGCACTCAGCCGGCCGGAG
* * * * * * **
19845491 AGACAGAATGCACAAACCGGGGATCGACCCGAT-CCCCTCGTGCATGCTGTTGATCCTACTATCA
66 AGGCAGAATGCGCAAGCCGGGGATCGACCCGATCCCCCTC-TGCGTGCTGTCGATCCTGCTGCCA
* *
19845555 TAACCCTCGGTCCGATCCAATCTCAAAATG
130 CAACCCTCGGTCCGATCCAATCTTAAAATG
* * * * *
19845585 GGAATGAACTCTGTATGCCTAAGTCAACCCACGAAATTAGCGTGCGGGCATTGAGCCGGCCTGG-
1 GGAATGAACTCCGTATGCCTAAGCCAACCCACGAAATGAGCGTGCGGGCACTCAGCCGGCC-GGA
* *
19845649 GAGGCATAATGCGCAAGCCGGGGATCGACCCGATCCCCCTCTGCGTACTGTCGATCCTGCTGCCA
65 GAGGCAGAATGCGCAAGCCGGGGATCGACCCGATCCCCCTCTGCGTGCTGTCGATCCTGCTGCCA
** **** *
19845714 CAACCCTCGGTTTGA-CTGGGGCTTAGACAT-
130 CAACCCTCGGTCCGATC-CAATCTTA-AAATG
* * * * * *
19845744 GGAATGAGCTCCCTATGCCTAAGCCGACCCACAAAACGGGCGTGCGGGCACTCAGCCGGCCGGAG
1 GGAATGAACTCCGTATGCCTAAGCCAACCCACGAAATGAGCGTGCGGGCACTCAGCCGGCCGGAG
* ** * * * *
19845809 AGGCGGAATGCGCAAGCTAGGGATCGACCTGGTCCCCC-CTGTGTGCTG-CTGATCCTGCTGCCG
66 AGGCAGAATGCGCAAGCCGGGGATCGACCCGATCCCCCTCTGCGTGCTGTC-GATCCTGCTGCCA
* * *
19845872 CAACCCTCAGTCCGATCCAATCTTAGACTG
130 CAACCCTCGGTCCGATCCAATCTTAAAATG
19845902 GGAATGAACTCCGTATGC
1 GGAATGAACTCCGTATGC
19845920 TTAGACTGAG
Statistics
Matches: 269, Mismatches: 58, Indels: 17
0.78 0.17 0.05
Matches are distributed among these distances:
157 2 0.01
158 55 0.20
159 201 0.75
160 11 0.04
ACGTcount: A:0.23, C:0.31, G:0.27, T:0.19
Consensus pattern (159 bp):
GGAATGAACTCCGTATGCCTAAGCCAACCCACGAAATGAGCGTGCGGGCACTCAGCCGGCCGGAG
AGGCAGAATGCGCAAGCCGGGGATCGACCCGATCCCCCTCTGCGTGCTGTCGATCCTGCTGCCAC
AACCCTCGGTCCGATCCAATCTTAAAATG
Found at i:19845922 original size:26 final size:26
Alignment explanation
Indices: 19845893--19845945 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
19845883 CCGATCCAAT
19845893 CTTAGACTG-GGAATGAACTCCGTATG
1 CTTAGACTGAGG-ATGAACTCCGTATG
19845919 CTTAGACTGAGGATGAACTCCGTATG
1 CTTAGACTGAGGATGAACTCCGTATG
19845945 C
1 C
19845946 CTAAATCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (26 bp):
CTTAGACTGAGGATGAACTCCGTATG
Found at i:19846655 original size:26 final size:26
Alignment explanation
Indices: 19846617--19846669 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
19846607 GGCTCAAAAT
*
19846617 CTTAGACTGGGAATGAACTCTGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
19846643 CTTAGACAT-GGAATGAACTCCGTATG
1 CTTAGAC-TGGGAATGAACTCCGTATG
19846669 C
1 C
19846670 CTAAGCCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (26 bp):
CTTAGACTGGGAATGAACTCCGTATG
Found at i:19847439 original size:278 final size:279
Alignment explanation
Indices: 19846933--19847448 Score: 653
Period size: 278 Copynumber: 1.9 Consensus size: 279
19846923 GCCGGTCCCA
* * * * *
19846933 CTGCCACAACCCTCGGTTCGGCTGGGGCTTAGACATTGAATGAACTCCCTATGCCTAAGCTAACC
1 CTGCCACAACCCTCGATCCAGCTGGGGCTTAGACATGGAATGAACTCCCTATGCCTAAGCCAACC
** * * * * * *
19846998 CATGAAATGGGCGTGCGAGCACTCAGCTGACCGGAGAGGTAGAATGCGCAAGCCGGGGATCGACC
66 CACAAAACGGGCGTGCGAGCACTCAACCGACCAGAGAGGCAGAATGCACAAGCCGGGGATCGACC
** *** * ** * *
19847063 TGATCCCTTCTGTGTGCTGCCAATCCTGCTACCGCAACCCTCGATTTGATTCGGTCTTAGACTGG
131 TGATCCCCCCTACATGCTACCAATCCTGCTACCGCAACCCTCGATCCGATCCGATCTTAGACTGG
*
19847128 GAATGAACTCCGTATGCTTAGACTAGAGATGAACTTCGTATGCTGAAGCCTTGAAATGGGTCCGA
196 GAATGAACTCCGTATGCTCAGACTAGAGATGAACTTCGTATGCTGAAGCCTTGAAATGGGTCCGA
19847193 TTCAGAAAAAAGGGTATCG
261 TTCAGAAAAAAGGGTATCG
* *
19847212 CTGCCACAACCCTTGATCCAGCTGGGGCTTAGACATGGAATGAACTCCCTATTCCTAAGCCAACC
1 CTGCCACAACCCTCGATCCAGCTGGGGCTTAGACATGGAATGAACTCCCTATGCCTAAGCCAACC
* * **
19847277 CACAAAACGGGCGTGC-AGGCGCTCAACCGGCCAGA-AGGCAGAATGCACAAGTTGGGGATC-AG
66 CACAAAACGGGCGTGCGA-GCACTCAACCGACCAGAGAGGCAGAATGCACAAGCCGGGGATCGA-
* * *
19847339 CCTGATCCCCCCTACATGCTACCAATCTTGCTACCGTAACCCTCAGA-CCGATCCGATCTTAGGC
129 CCTGATCCCCCCTACATGCTACCAATCCTGCTACCGCAACCCTC-GATCCGATCCGATCTTAGAC
* * *
19847403 TGGGAATGAACTCCGTCTGCTCAGACTGGGGATGAACTTCGTATGC
193 TGGGAATGAACTCCGTATGCTCAGACTAGAGATGAACTTCGTATGC
19847449 CTAAACCAAC
Statistics
Matches: 198, Mismatches: 36, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
277 1 0.01
278 112 0.57
279 85 0.43
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (279 bp):
CTGCCACAACCCTCGATCCAGCTGGGGCTTAGACATGGAATGAACTCCCTATGCCTAAGCCAACC
CACAAAACGGGCGTGCGAGCACTCAACCGACCAGAGAGGCAGAATGCACAAGCCGGGGATCGACC
TGATCCCCCCTACATGCTACCAATCCTGCTACCGCAACCCTCGATCCGATCCGATCTTAGACTGG
GAATGAACTCCGTATGCTCAGACTAGAGATGAACTTCGTATGCTGAAGCCTTGAAATGGGTCCGA
TTCAGAAAAAAGGGTATCG
Found at i:19847596 original size:184 final size:180
Alignment explanation
Indices: 19847242--19847791 Score: 611
Period size: 184 Copynumber: 3.0 Consensus size: 180
19847232 GCTGGGGCTT
* * * *
19847242 AGACATGGAATGAACTCCCTATTCCTAAGCCAACCCACAAAACGGGCGTGCAGGCGCTCAACCGG
1 AGACATGGAATGAACTCCGTATGCCTAAGCCAACCCACAAAACGAGCGTGCGGGCGCTCAACC-G
* * * * * * *
19847307 CCAGAAGGCAGAATGCACAAGTTGGGGATCAGCCTGATCCCCCCTACATGCTACCAATCTTGCTA
65 CCAG-AGGCAGAATGCGCAAGCTGAGGATCAGCCTGATCCCCCCTGCGTGCTACCGATCCTGCTA
* *
19847372 CCGTAACCCTCAGA-CCGATCCGATCTTAGGCTGGGAATGAACTCCGTCTGCTC
129 CCGTAACCCTC-GATCCGATCCGATC-TAGACTGGGAATGAACTCCGTATGCTC
* * * *
19847425 AGAC-TGGGGATGAACTTCGTATGCCTAAACCAACCCACAAAACGAGCATGCGGGCGCTCAACCA
1 AGACAT-GGAATGAACTCCGTATGCCTAAGCCAACCCACAAAACGAGCGTGCGGGCGCTCAACC-
* * * * *
19847489 GCCTAAGAGGCAAAATGCGCAAGCTGAGGATCGGCTTGGTCCCCACTGCGTGCTACCGATCCTGC
64 GCC--AGAGGCAGAATGCGCAAGCTGAGGATCAGCCTGATCCCCCCTGCGTGCTACCGATCCTGC
* * *
19847554 TACCGCAACCCTCGATCCGATCTGATCTGAGACTGGGAATGAACTCCGTATGCTT
127 TACCGTAACCCTCGATCCGATCCGATCT-AGACTGGGAATGAACTCCGTATGCTC
* * *
19847609 AGACATGGAATGAACTCCGTATGCCTAAGCCAACCCATAAAACTAGCGTGCGGGTGCTCAACCGA
1 AGACATGGAATGAACTCCGTATGCCTAAGCCAACCCACAAAACGAGCGTGCGGGCGCTCAACCG-
* * * * **
19847674 TCGGAGAGGCAGAATGCGCAAGCCGAGGA-CTAGCCCGATCCCCTCCTGTGTGCTGTCGATCCTG
65 -C-CAGAGGCAGAATGCGCAAGCTGAGGATC-AGCCTGATCCCC-CCTGCGTGCTACCGATCCTG
* * *
19847738 CTGCTGTAACCCTCGATCCAATCCGATCCTAGACTGGGAATGAACTCCGTATGC
126 CTACCGTAACCCTCGATCCGATCCGAT-CTAGACTGGGAATGAACTCCGTATGC
19847792 CTAAGTTAAC
Statistics
Matches: 306, Mismatches: 49, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
182 1 0.00
183 61 0.20
184 176 0.58
185 66 0.22
186 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.24, T:0.19
Consensus pattern (180 bp):
AGACATGGAATGAACTCCGTATGCCTAAGCCAACCCACAAAACGAGCGTGCGGGCGCTCAACCGC
CAGAGGCAGAATGCGCAAGCTGAGGATCAGCCTGATCCCCCCTGCGTGCTACCGATCCTGCTACC
GTAACCCTCGATCCGATCCGATCTAGACTGGGAATGAACTCCGTATGCTC
Found at i:19847930 original size:159 final size:158
Alignment explanation
Indices: 19847605--19848053 Score: 370
Period size: 159 Copynumber: 2.8 Consensus size: 158
19847595 AACTCCGTAT
* * * ** * **
19847605 GCTTAGACATGGAATGAACTCCGTATGCCTAAGCCAACCCATAAAAC-TAGCGTGCGGGTGCTCA
1 GCTTAGACATAGAATGAACACCCTATGCCTAAGCCAACCCACGAAACGGA-CGTGCGGGCACTCA
* * ** * * **
19847669 ACCGATCGGAGAGGCAGAATGCGCAAGCCGAGGA-CTAGCCCGATCCCCTCCTGTGTGCTGTCGA
65 GCTGGCCGGAGAGGCAGAATGCGCAAGTCGAGGATC-AGCCCGGTCCCC-CCTGCATGCTGTCGA
* *** * * * * *
19847733 TCCTGCTGCTGTAACCCTCGATCCA-ATCCGA
128 TCTTGCTGCCACAACCCTTGGTCCAGCT-GGG
* * * * * ** * * *
19847764 TCCTAGAC-TGGGAATGAACTCCGTATGCCTAAGTTAACCCACGAAAC-GAGCGTTCGGGCGCTG
1 GCTTAGACAT-AGAATGAACACCCTATGCCTAAGCCAACCCACGAAACGGA-CGTGCGGGCACTC
* * * * * *
19847827 AGTTGGCCGGAGAGGCATAATGTGCAAG-CTGGGGATCGGCCCGGTCCCCCTCTGCATGTTGTCG
64 AGCTGGCCGGAGAGGCAGAATGCGCAAGTC-GAGGATCAGCCCGGTCCCCC-CTGCATGCTGTCG
*
19847891 GTCTTGCTGCCACAACCCTTGGTCCAGCTGGG
127 ATCTTGCTGCCACAACCCTTGGTCCAGCTGGG
*
19847923 GCTTAGACATAGAATGAACACCCTATGCCTAAGCCAACCCATGAAACGGACGTGCGGGCACTCAG
1 GCTTAGACATAGAATGAACACCCTATGCCTAAGCCAACCCACGAAACGGACGTGCGGGCACTCAG
* * *
19847988 CTGGCTGGAGAGGCAGAATGCGCAAGTCGAGGATCAGCTCGGTCCCCCCTGCGTGCTGTCGATCT
66 CTGGCCGGAGAGGCAGAATGCGCAAGTCGAGGATCAGCCCGGTCCCCCCTGCATGCTGTCGATCT
19848053 T
131 T
19848054 ACTGTCG
Statistics
Matches: 228, Mismatches: 54, Indels: 17
0.76 0.18 0.06
Matches are distributed among these distances:
158 18 0.08
159 204 0.89
160 6 0.03
ACGTcount: A:0.22, C:0.29, G:0.28, T:0.20
Consensus pattern (158 bp):
GCTTAGACATAGAATGAACACCCTATGCCTAAGCCAACCCACGAAACGGACGTGCGGGCACTCAG
CTGGCCGGAGAGGCAGAATGCGCAAGTCGAGGATCAGCCCGGTCCCCCCTGCATGCTGTCGATCT
TGCTGCCACAACCCTTGGTCCAGCTGGG
Done.