Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168419.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_633, 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: 20998
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Found at i:6386 original size:45 final size:45
Alignment explanation
Indices: 6284--6387 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
6274 AGGTTCGTAG
* * * *
6284 GTGCCAGTGGTGGTCAAGGTATGTACTTGCACCAAGGCCTAGCAT
1 GTGCCAATGGTGTTCAAGGTAAGTACCTGCACCAAGGCCTAGCAT
* * **
6329 GTGCCAAAGGTGTTCAAGGTAAGTGCCTGCTGCAAGGGCC-AGCAT
1 GTGCCAATGGTGTTCAAGGTAAGTACCTGCACCAA-GGCCTAGCAT
6374 GTGCCAATGGTGTT
1 GTGCCAATGGTGTT
6388 TAAGCCAGCT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 45 0.92
46 4 0.08
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (45 bp):
GTGCCAATGGTGTTCAAGGTAAGTACCTGCACCAAGGCCTAGCAT
Found at i:6499 original size:44 final size:44
Alignment explanation
Indices: 6435--6533 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
6425 ATGTTGATCG
* * *
6435 AGGCATGTGCCTACACCAAGGGCTAGCATGTGCTAATGGTGGTTT
1 AGGCAAGTG-CTACACCAAGGGCTAGCATGTGCCAATGGTGGTTA
* *
6480 AGGCAAGTGCTATACCAAGGGCTAGCTTGTGCCAATGGTGGTTA
1 AGGCAAGTGCTACACCAAGGGCTAGCATGTGCCAATGGTGGTTA
*
6524 AGGTAAGTGC
1 AGGCAAGTGC
6534 CCTCGATGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 40 0.83
45 8 0.17
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.25
Consensus pattern (44 bp):
AGGCAAGTGCTACACCAAGGGCTAGCATGTGCCAATGGTGGTTA
Found at i:9128 original size:28 final size:28
Alignment explanation
Indices: 9074--9131 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
9064 GCTATTCTTG
* * *
9074 ATCCTATGTTCCTCAACATTTTGCTACA
1 ATCCTATGTTCCTCAACACTCTACTACA
*
9102 ATCCTATGTTCCTCAATACTCTACTACA
1 ATCCTATGTTCCTCAACACTCTACTACA
9130 AT
1 AT
9132 GGCCCTTTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.29, G:0.05, T:0.38
Consensus pattern (28 bp):
ATCCTATGTTCCTCAACACTCTACTACA
Found at i:16310 original size:17 final size:17
Alignment explanation
Indices: 16284--16325 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
16274 TCTTGTCCCT
*
16284 ATGGTCCTTGGCACATG
1 ATGGTTCTTGGCACATG
**
16301 ATGGTTCTTGTTACATG
1 ATGGTTCTTGGCACATG
16318 ATGGTTCT
1 ATGGTTCT
16326 CGATACACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (17 bp):
ATGGTTCTTGGCACATG
Found at i:16332 original size:17 final size:17
Alignment explanation
Indices: 16296--16332 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16286 GGTCCTTGGC
* *
16296 ACATGATGGTTCTTGTT
1 ACATGATGGTTCTCGAT
16313 ACATGATGGTTCTCGAT
1 ACATGATGGTTCTCGAT
16330 ACA
1 ACA
16333 CCTTCATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (17 bp):
ACATGATGGTTCTCGAT
Found at i:17911 original size:253 final size:253
Alignment explanation
Indices: 17463--17965 Score: 882
Period size: 253 Copynumber: 2.0 Consensus size: 253
17453 TTGTTGATAC
* * **
17463 AACTCAAACCAATATCAAGACTGGTCATAATGAAGGTTTTTATCCCCTTGTTACGAACCTACTTT
1 AACTCAAACCAACATCAACACTGGTCATAACAAAGGTTTTTATCCCCTTGTTACGAACCTACTTT
17528 GATACCAACTGTCATGGGTAGAGAGCTTAAGCCTAGCACCCATGTTACCTTAAGCTGAAAACTAT
66 GATACCAACTGTCATGGGTAGAGAGCTTAAGCCTAGCACCCATGTTACCTTAAGCTGAAAACTAT
17593 CATCCATGTGCCTAAGCCAACCTCTTTTTTGACTCTATGTTGAACACTTATGCTATGCATTCCAT
131 CATCCATGTGCCTAAGCCAACCTCTTTTTTGACTCTATGTTGAACACTTATGCTATGCATTCCAT
*
17658 TGGCTCCCTAAGTGCTTGGAAGAAAGCTAGGAAGGAGAGTTAAAGCAATTGTATTAAT
196 TGGCTCCCTAAGTGCTTGGAAGAAAACTAGGAAGGAGAGTTAAAGCAATTGTATTAAT
* *
17716 AACTCAAACCAACATTAACACTGGTCATAACAAAGGTTTTTATCCCCTTGTTGC-AAGCCTACTT
1 AACTCAAACCAACATCAACACTGGTCATAACAAAGGTTTTTATCCCCTTGTTACGAA-CCTACTT
* * *
17780 TGATACCAACTGTCATGGGTGGAGAGCTTAAGCCTAGCACCCATGTTGCCTTAAGTTGAAAACTA
65 TGATACCAACTGTCATGGGTAGAGAGCTTAAGCCTAGCACCCATGTTACCTTAAGCTGAAAACTA
17845 TCATCCATGTGCCTAAGCCAACCTCTTTTTTGACTCTATGTTGAACACTTATGCTATGCATTCCA
130 TCATCCATGTGCCTAAGCCAACCTCTTTTTTGACTCTATGTTGAACACTTATGCTATGCATTCCA
* *
17910 TTGGCTCCCTAAGTGCTTGGATGAAAACTAGGAGGGAGAGTTAAAGCAATTGTATT
195 TTGGCTCCCTAAGTGCTTGGAAGAAAACTAGGAAGGAGAGTTAAAGCAATTGTATT
17966 TCTATTTATA
Statistics
Matches: 237, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
252 2 0.01
253 235 0.99
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (253 bp):
AACTCAAACCAACATCAACACTGGTCATAACAAAGGTTTTTATCCCCTTGTTACGAACCTACTTT
GATACCAACTGTCATGGGTAGAGAGCTTAAGCCTAGCACCCATGTTACCTTAAGCTGAAAACTAT
CATCCATGTGCCTAAGCCAACCTCTTTTTTGACTCTATGTTGAACACTTATGCTATGCATTCCAT
TGGCTCCCTAAGTGCTTGGAAGAAAACTAGGAAGGAGAGTTAAAGCAATTGTATTAAT
Found at i:18913 original size:17 final size:17
Alignment explanation
Indices: 18893--18926 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18883 CTATGGCACG
* *
18893 TGATGGTTCTTTGTACA
1 TGATGGCTCTTAGTACA
18910 TGATGGCTCTTAGTACA
1 TGATGGCTCTTAGTACA
18927 CCTTAGTAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.41
Consensus pattern (17 bp):
TGATGGCTCTTAGTACA
Done.