Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167990.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_247, 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: 43584
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Found at i:6542 original size:19 final size:20
Alignment explanation
Indices: 6520--6561 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
6510 AAAATATCAA
*
6520 TTATTATTAATTT-CATTTT
1 TTATTATTAATTTACATTGT
*
6539 TTATTATTATTTTACATTGT
1 TTATTATTAATTTACATTGT
6559 TTA
1 TTA
6562 AATCAATCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATTATTAATTTACATTGT
Found at i:7023 original size:6 final size:6
Alignment explanation
Indices: 6946--7035 Score: 56
Period size: 6 Copynumber: 14.3 Consensus size: 6
6936 TACCAGTAAT
* * *
6946 AATATAA AATAAC AATAATA AA-AAA ACATAAA AATCAA CATAAA ATATAAA
1 AATA-AA AATAAA AATAA-A AATAAA A-ATAAA AATAAA AATAAA A-ATAAA
* * * * *
6997 AATCAA AATCAA AATGGAA AATAAA AAGAAA AAGAAA AA
1 AATAAA AATAAA AAT-AAA AATAAA AATAAA AATAAA AA
7036 CCTATGAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
5 2 0.03
6 45 0.66
7 21 0.31
ACGTcount: A:0.73, C:0.07, G:0.04, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:7029 original size:25 final size:25
Alignment explanation
Indices: 6975--7029 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
6965 AAAAAAACAT
* *
6975 AAAAATCAACATAAAATATAAAAAT
1 AAAAATCAAAATAAAATATAAAAAG
* *
7000 CAAAATCAAAATGGAAA-ATAAAAAG
1 AAAAATCAAAAT-AAAATATAAAAAG
7025 AAAAA
1 AAAAA
7030 GAAAAACCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.15
Consensus pattern (25 bp):
AAAAATCAAAATAAAATATAAAAAG
Found at i:7881 original size:3 final size:3
Alignment explanation
Indices: 7875--7953 Score: 78
Period size: 3 Copynumber: 27.7 Consensus size: 3
7865 TTTTGTTTTA
*
7875 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- ACAT AAT TAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* * *
7919 AAT AAT AA- AAA AAT AAC AA- AAT TAT -AT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
7954 AAAAAAGAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
2 9 0.14
3 56 0.85
4 1 0.02
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:7957 original size:27 final size:28
Alignment explanation
Indices: 7888--7958 Score: 108
Period size: 27 Copynumber: 2.5 Consensus size: 28
7878 AATAATAATA
* *
7888 ATAATAATAATAATAATAAACATAATTAT
1 ATAATAATAA-AAAAATAAACAAAATTAT
7917 ATAATAATAAAAAAAT-AACAAAATTAT
1 ATAATAATAAAAAAATAAACAAAATTAT
7944 ATAATAATAAAAAAA
1 ATAATAATAAAAAAA
7959 AGAAGAACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 25 0.62
28 5 0.12
29 10 0.25
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (28 bp):
ATAATAATAAAAAAATAAACAAAATTAT
Found at i:18297 original size:45 final size:45
Alignment explanation
Indices: 18214--18300 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
18204 CTATCATCAG
* * *
18214 CACAAGCTGGCCTTTGGTACGAGTACTTGCATCAACCACCATCGA
1 CACAAGCTGGCCTTTGGTAAGAGCACTTACATCAACCACCATCGA
* *
18259 CACAAGCTGGCCTTTGGTATAG-GCACTTACCTCGACCACCAT
1 CACAAGCTGGCCTTTGGTA-AGAGCACTTACATCAACCACCAT
18301 TGTCACATGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 35 0.97
46 1 0.03
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (45 bp):
CACAAGCTGGCCTTTGGTAAGAGCACTTACATCAACCACCATCGA
Found at i:19912 original size:410 final size:410
Alignment explanation
Indices: 19152--19977 Score: 1195
Period size: 410 Copynumber: 2.0 Consensus size: 410
19142 TGGGGGTGTC
* ** * * *
19152 ATGCCATTGTTGCCTATTAAATGGTAAGGGTAGTCTCATGGACATTGCTTATGTTTCTCCCATGC
1 ATGCCATCGTTGCCTATTAAATGACAAGGGCAGTCACATGGACATTGCTTATGTTTCTCCCATAC
** * * ** * * *
19217 CAAGTAGTTGTGGCATGGCTTCATATGTTGTTTCATCTGTTTGCTCATCAAATTATTGATTGGGT
66 CAACCAGTTGTGGCATGGCCTCATACGTTGTTTCATCTACTTGCTCATCAAATAATAGATTGGAT
*
19282 AGGTTATAGACCAGTATGCGTAGATGCTACCACTTGTAGTAATAGGCATAGGAGTGGTGCTACGG
131 AGGTTATAGACCAGTATGCGTAGATGCTACCACTTGTAGTAATAGGCATAGGAGTGGTGATACGG
* * *
19347 TTGTGCTTGTTGGTAGGCTCTAAGCTTGATGCATCAAACTATTGACCCATCATCCTTTTCAATCT
196 TTGTGCATGTTGATAGGCTCCAAGCTTGATGCATCAAACTATTGACCCATCATCCTTTTCAATCT
* * * * *
19412 ACCCTTATATGGTCATCATACCTTGGGGTGCAATTAGGACCCTATGCCGCATATCGAAATCAATG
261 ACCCCTATATAGTCATCATACCTTGAGGTGCAATTAGGACCCTATGCCGCATACCAAAATCAATG
* * * *
19477 GAAATCAGATGTCTTGCCATCCCTCATCAATCTTATGTCCTTAGGGGCTATGAGTCAGACCTCAA
326 GAAAGCAGATGTCTTGCCATCCCTCATCAATCTTATGTCCTTAGGGGATACGAGTCAGAACTCAA
*
19542 TCATGTCTCGTGACCCAATT
391 TCATGCCTCGTGACCCAATT
* * * * *
19562 ATGCCATCGTTGCCTATTAGATGACAGGGGCAGTCACGTGGACATTGCTTGTGTTTTTCCCATAC
1 ATGCCATCGTTGCCTATTAAATGACAAGGGCAGTCACATGGACATTGCTTATGTTTCTCCCATAC
* * *
19627 CAACCAGTTGTGGCATGGCCTCGTACGTTGTTTCATTTACTTGCTCATCGAATAATAGATTGGAT
66 CAACCAGTTGTGGCATGGCCTCATACGTTGTTTCATCTACTTGCTCATCAAATAATAGATTGGAT
* * * * * *
19692 GGGTTATAGACCAGTGTGTGTGGATGTTACCACTTGTAGTAATAGGCATAGGAGTGGTGATATGG
131 AGGTTATAGACCAGTATGCGTAGATGCTACCACTTGTAGTAATAGGCATAGGAGTGGTGATACGG
*
19757 TTGTGCATGTTGATAGGCTCCAAGCTTGATGCATCAATCTATTGACCCATCAT-CTATTTCAATC
196 TTGTGCATGTTGATAGGCTCCAAGCTTGATGCATCAAACTATTGACCCATCATCCT-TTTCAATC
* * *
19821 TACCCCTATGTAGTCATCATACCTTGAGGTGCAATTAGGATCCTATGTCGCATACCAAAATCAAT
260 TACCCCTATATAGTCATCATACCTTGAGGTGCAATTAGGACCCTATGCCGCATACCAAAATCAAT
19886 GGAAAGCAGATGTCTTGCCATCCCTCATCAATCTTATGTCCTTAGGGGATACGAGTCAGAACTCA
325 GGAAAGCAGATGTCTTGCCATCCCTCATCAATCTTATGTCCTTAGGGGATACGAGTCAGAACTCA
*
19951 ATCATGCCTTGTGACCCAATT
390 ATCATGCCTCGTGACCCAATT
*
19972 CTGCCA
1 ATGCCA
19978 CCCAAACCTC
Statistics
Matches: 366, Mismatches: 49, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
409 2 0.01
410 364 0.99
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (410 bp):
ATGCCATCGTTGCCTATTAAATGACAAGGGCAGTCACATGGACATTGCTTATGTTTCTCCCATAC
CAACCAGTTGTGGCATGGCCTCATACGTTGTTTCATCTACTTGCTCATCAAATAATAGATTGGAT
AGGTTATAGACCAGTATGCGTAGATGCTACCACTTGTAGTAATAGGCATAGGAGTGGTGATACGG
TTGTGCATGTTGATAGGCTCCAAGCTTGATGCATCAAACTATTGACCCATCATCCTTTTCAATCT
ACCCCTATATAGTCATCATACCTTGAGGTGCAATTAGGACCCTATGCCGCATACCAAAATCAATG
GAAAGCAGATGTCTTGCCATCCCTCATCAATCTTATGTCCTTAGGGGATACGAGTCAGAACTCAA
TCATGCCTCGTGACCCAATT
Found at i:38004 original size:23 final size:23
Alignment explanation
Indices: 37969--38023 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
37959 GACCATCAAT
* * *
37969 GGCATATGTTAGTGCATGGTGTG
1 GGCACATGCTAGTGCATGGTGTA
*
37992 GGCACATGCTAGTGCATTGTGTA
1 GGCACATGCTAGTGCATGGTGTA
38015 GGCACATGC
1 GGCACATGC
38024 CTCTACCATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.20, C:0.16, G:0.35, T:0.29
Consensus pattern (23 bp):
GGCACATGCTAGTGCATGGTGTA
Done.