Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167942.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_203, 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: 51904
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Found at i:5779 original size:45 final size:45
Alignment explanation
Indices: 5755--5847 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
5745 CCTTGACTAT
*
5755 CATCGACACAAGCTGGCCTTTGGTATGAGCACTTGCATCAACCAC
1 CATCGACACAAGCTGGCCTTTGGTATGGGCACTTGCATCAACCAC
* *
5800 CATCGACACAAGCTGGCCTTTGGTATGGGCACTTGCCTCGACCAC
1 CATCGACACAAGCTGGCCTTTGGTATGGGCACTTGCATCAACCAC
5845 CAT
1 CAT
5848 TGGCACATGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.23
Consensus pattern (45 bp):
CATCGACACAAGCTGGCCTTTGGTATGGGCACTTGCATCAACCAC
Found at i:5868 original size:45 final size:45
Alignment explanation
Indices: 5755--5876 Score: 145
Period size: 45 Copynumber: 2.7 Consensus size: 45
5745 CCTTGACTAT
* *
5755 CATCGACACAAGCTGGCCTTTGGTATGAGCACTTGCATCAACCAC
1 CATCGACACAAGCTAGCCCTTGGTATGAGCACTTGCATCAACCAC
* * * * *
5800 CATCGACACAAGCTGGCCTTTGGTATGGGCACTTGCCTCGACCAC
1 CATCGACACAAGCTAGCCCTTGGTATGAGCACTTGCATCAACCAC
* * * *
5845 CATTGGCACATGCTAGCCCTTGGTGTGAGCAC
1 CATCGACACAAGCTAGCCCTTGGTATGAGCAC
5877 ATGCCAACCC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.23
Consensus pattern (45 bp):
CATCGACACAAGCTAGCCCTTGGTATGAGCACTTGCATCAACCAC
Found at i:5898 original size:23 final size:23
Alignment explanation
Indices: 5850--5904 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
5840 ACCACCATTG
* * **
5850 GCACATGCTAGCCCTTGGTGTGA
1 GCACATGCCAACCCTTGGTGCAA
5873 GCACATGCCAACCCTTGGTGCAA
1 GCACATGCCAACCCTTGGTGCAA
*
5896 GCATATGCC
1 GCACATGCC
5905 TCAATTAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.31, G:0.25, T:0.22
Consensus pattern (23 bp):
GCACATGCCAACCCTTGGTGCAA
Found at i:7411 original size:398 final size:396
Alignment explanation
Indices: 6676--7469 Score: 1214
Period size: 398 Copynumber: 2.0 Consensus size: 396
6666 ATTGAGGGTA
*
6676 TATGCCACTGTTGCCTATTGGATGGCAGGGGTAGTCTCATGGACATTGCTTGTGTTTCTCCCATG
1 TATGCCACTGTTGCCTATTGGATGGCAGGGGCAGTCTCATGGACATTGCTTGTGTTTCTCCCATG
* * * *
6741 CCAAGCAGTTGTGGCATGGCCTCACACATTGTTTCATCTACTAGCTTATTGAATAATTGATTGGG
66 CCAAGCAGTTGTGGCATGGCCTCACACATTATTTCATCTACTAGCTCATCGAATAATCGATTGGG
6806 TGTTATAGACCAGTGTGTGTGGATGCTACCACTTGTAGTAATAAGCATAGGAGTGGTGCTACAAT
131 TGTTATAGACCAGTGTGTGTGGATGCTACCACTTGTAGTAATAAGCATAGGAGTGGTGCTACAAT
* * * *
6871 TTTGCATGTTAGTAGGCTCTAAGCTTGATGCATCAAACTATTGACCTATCATCCATTTCAATCTA
196 TGTGCATGTTAGCAGGCTCCAAGCTTGATGCATCAAACTATTGACCCATCATCCATTTCAATCTA
* **
6936 CCCCTATGTGGTCATCATACCTTGAGGGTGCAATTAGGATCCTATGCCGCATGTCGAAATCAATG
261 CCCCTATGTGGTCATCATACCTTGAGGGTGCAATTAGGATCCGATGCCGCATACCGAAATCAATG
* * * *
7001 GAAATTGGATGTCTTACTAT-CTCTCATCAATCTTATGTCCTTAG-GGACTACGAGTCAGACCTC
326 GAAATCGGATGTCTTACCATAC-CTCATCAATCTTATGTCCTTAGAGG-CTACGAGTCAAAACTC
7064 AATCATGC
389 AATCATGC
* * * *
7072 TATGCCATTGTTGCCTATTGGATGGTAGGGGCAGTCTCGTGGACATTGCTTGTGTTTTTCCCATG
1 TATGCCACTGTTGCCTATTGGATGGCAGGGGCAGTCTCATGGACATTGCTTGTGTTTCTCCCATG
* ** * * *
7137 CCAAGCAGTTGTGGCATGGCCTCACACATTATTTCATTTGTTTGCTCGTCGAATACTCGATTGGG
66 CCAAGCAGTTGTGGCATGGCCTCACACATTATTTCATCTACTAGCTCATCGAATAATCGATTGGG
* * **
7202 TGGGTTATAGACCAGTGTGTGTGGATGCTATCACTTGTAGTAATAGGCATAGGAGTGGTGCTATG
131 T--GTTATAGACCAGTGTGTGTGGATGCTACCACTTGTAGTAATAAGCATAGGAGTGGTGCTACA
* *
7267 GTTGTGCATGTTGGCAGGCTCCAAGCTTGATGCATCAAACTATTGACCCATCATCCATTTCAATC
194 ATTGTGCATGTTAGCAGGCTCCAAGCTTGATGCATCAAACTATTGACCCATCATCCATTTCAATC
* *
7332 TACCCCTATGTGGTCATCATACCTTTAGGGTGCAATTAGGATCCGATGCTGCATACCGAAATCAA
259 TACCCCTATGTGGTCATCATACCTTGAGGGTGCAATTAGGATCCGATGCCGCATACCGAAATCAA
* *
7397 TGGAAATCGGATGTCTTGCCATACCTCATCAATCTTATGTCCTTAGAGGCTATGAGTCAAAACTC
324 TGGAAATCGGATGTCTTACCATACCTCATCAATCTTATGTCCTTAGAGGCTACGAGTCAAAACTC
7462 AATCATGC
389 AATCATGC
7470 CTTGAAATCA
Statistics
Matches: 358, Mismatches: 36, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
396 116 0.32
398 239 0.67
399 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (396 bp):
TATGCCACTGTTGCCTATTGGATGGCAGGGGCAGTCTCATGGACATTGCTTGTGTTTCTCCCATG
CCAAGCAGTTGTGGCATGGCCTCACACATTATTTCATCTACTAGCTCATCGAATAATCGATTGGG
TGTTATAGACCAGTGTGTGTGGATGCTACCACTTGTAGTAATAAGCATAGGAGTGGTGCTACAAT
TGTGCATGTTAGCAGGCTCCAAGCTTGATGCATCAAACTATTGACCCATCATCCATTTCAATCTA
CCCCTATGTGGTCATCATACCTTGAGGGTGCAATTAGGATCCGATGCCGCATACCGAAATCAATG
GAAATCGGATGTCTTACCATACCTCATCAATCTTATGTCCTTAGAGGCTACGAGTCAAAACTCAA
TCATGC
Found at i:14381 original size:14 final size:14
Alignment explanation
Indices: 14362--14392 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
14352 TATGCTAGTT
14362 CCTCGTGACCTAGG
1 CCTCGTGACCTAGG
14376 CCTCGTGACCTAGG
1 CCTCGTGACCTAGG
14390 CCT
1 CCT
14393 TAAGGCTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.39, G:0.26, T:0.23
Consensus pattern (14 bp):
CCTCGTGACCTAGG
Found at i:25366 original size:45 final size:45
Alignment explanation
Indices: 25296--25399 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 45
25286 ACCAAGGACT
* *
25296 TACCATCAATGGCATATGTTAGTGCATGGTGCAGGCACATGCCTC
1 TACCATCATTGGCACATGTTAGTGCATGGTGCAGGCACATGCCTC
* * * * *
25341 TACCATCATTGGCACGTGTTGGTGCATGGTTCGGGCACATGTCTC
1 TACCATCATTGGCACATGTTAGTGCATGGTGCAGGCACATGCCTC
*
25386 GACCATCATTGGCA
1 TACCATCATTGGCA
25400 TAAGCTACTT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (45 bp):
TACCATCATTGGCACATGTTAGTGCATGGTGCAGGCACATGCCTC
Found at i:40865 original size:45 final size:45
Alignment explanation
Indices: 40780--40877 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 45
40770 TAGCACAAGT
* * ** *
40780 TGGCCTTTGGTATGGACACTTGGCTTGACCATCATCGGCATAAGC
1 TGGCCCTTGGTATGGACACTTGCCTCAACCAACATCGGCATAAGC
* * * * *
40825 TGGCCCTTGGTATGGGCATTTGCCTCAACCAACATTGGCATATGT
1 TGGCCCTTGGTATGGACACTTGCCTCAACCAACATCGGCATAAGC
40870 TGGCCCTT
1 TGGCCCTT
40878 TGTGCAAGCA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (45 bp):
TGGCCCTTGGTATGGACACTTGCCTCAACCAACATCGGCATAAGC
Done.