Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168090.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_337, 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: 33931
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Found at i:1285 original size:11 final size:11
Alignment explanation
Indices: 1267--1309 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
1257 AATTTTTATT
1267 TATTATTTTTA
1 TATTATTTTTA
*
1278 TGTTATTTATT-
1 TATTATTT-TTA
1289 TATTATTTTTA
1 TATTATTTTTA
1300 TCATTATTTT
1 T-ATTATTTT
1310 CATTTACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 2 0.07
11 15 0.56
12 10 0.37
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:1768 original size:26 final size:24
Alignment explanation
Indices: 1713--1769 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
1703 AATTTGTATT
*
1713 GAAATTATTATTTATTATTTTAAA
1 GAAAATATTATTTATTATTTTAAA
*
1737 -ATAAATATTATTTTTTAATTTTTAAA
1 GA-AAATATTATTTATT-A-TTTTAAA
1763 GAAAATA
1 GAAAATA
1770 AAAAAATCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 1 0.04
24 12 0.44
25 1 0.04
26 12 0.44
27 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
GAAAATATTATTTATTATTTTAAA
Found at i:1828 original size:17 final size:17
Alignment explanation
Indices: 1808--1851 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
1798 AAGACAATCA
*
1808 AAAATAAAAA-AAGAAAG
1 AAAAGAAAAAGAA-AAAG
1825 AAAAGAAAAAGAAAAAG
1 AAAAGAAAAAGAAAAAG
1842 AAAAGGAAAA
1 AAAA-GAAAA
1852 TTTACCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAAGAAAAAG
Found at i:2741 original size:24 final size:24
Alignment explanation
Indices: 2702--2764 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
2692 GATTTTATGG
* *
2702 GAAAATAGAAAAAAAT-ACTAAAAA
1 GAAAATA-AAATAAATAAATAAAAA
2726 GAAGAATAAAATAAATAAATAAAAA
1 GAA-AATAAAATAAATAAATAAAAA
*
2751 TAAAATAAACATAA
1 GAAAATAAA-ATAA
2765 TTATATTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (24 bp):
GAAAATAAAATAAATAAATAAAAA
Found at i:3427 original size:36 final size:36
Alignment explanation
Indices: 3342--3449 Score: 103
Period size: 36 Copynumber: 3.0 Consensus size: 36
3332 AATGATATTT
* * *
3342 AAAAAACTTCTCTAACCAAAGACAAT-AATACTTGAAA
1 AAAAAACTCCTCTAACCAAAGGCAATGGA-ACTT-AAA
* * *
3379 AAGAAA-TGCCTCTAACCAAAGGCCATGGCACTTAAA
1 AAAAAACT-CCTCTAACCAAAGGCAATGGAACTTAAA
* *
3415 AAAAAACTCCTCTAACTAAAGGCTATGGAACTTAA
1 AAAAAACTCCTCTAACCAAAGGCAATGGAACTTAA
3450 GATTAAACAA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
36 33 0.57
37 25 0.43
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.20
Consensus pattern (36 bp):
AAAAAACTCCTCTAACCAAAGGCAATGGAACTTAAA
Found at i:4161 original size:33 final size:34
Alignment explanation
Indices: 4112--4184 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 34
4102 TTCTTTTTCC
*
4112 TTTTTCCTTTTATTGTTTTTTTCTTTACAAACTT
1 TTTTTCCTTTTATTGTTTTTTTCTTGACAAACTT
4146 TTTTTCCTTTT-TTGTTTTTTTCTTGACAAACTT
1 TTTTTCCTTTTATTGTTTTTTTCTTGACAAACTT
4179 TTTTTC
1 TTTTTC
4185 TTAATAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 27 0.71
34 11 0.29
ACGTcount: A:0.12, C:0.15, G:0.04, T:0.68
Consensus pattern (34 bp):
TTTTTCCTTTTATTGTTTTTTTCTTGACAAACTT
Found at i:4197 original size:17 final size:17
Alignment explanation
Indices: 4160--4199 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
4150 TCCTTTTTTG
* *
4160 TTTTTTTCTTGACAAAC
1 TTTTTTTCTTAACAAAA
*
4177 TTTTTTTCTTAATAAAA
1 TTTTTTTCTTAACAAAA
4194 TTTTTT
1 TTTTTT
4200 CTTTTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTTTTCTTAACAAAA
Found at i:6196 original size:18 final size:18
Alignment explanation
Indices: 6173--6208 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6163 CACTCCATCA
6173 TTTTATTCTTTTATTTTT
1 TTTTATTCTTTTATTTTT
*
6191 TTTTATTGTTTTATTTTT
1 TTTTATTCTTTTATTTTT
6209 ACTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.83
Consensus pattern (18 bp):
TTTTATTCTTTTATTTTT
Found at i:10313 original size:9 final size:8
Alignment explanation
Indices: 10284--10314 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
10274 AATTTTCATC
10284 TATTTTTA
1 TATTTTTA
10292 TATTTTTA
1 TATTTTTA
10300 TATTTTTA
1 TATTTTTA
10308 TAATTTT
1 T-ATTTT
10315 GTTGTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TATTTTTA
Found at i:11210 original size:54 final size:54
Alignment explanation
Indices: 11126--11232 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
11116 AAGCTAACTA
*
11126 AGATTTTTGTCCAGAAGGCTCAATCGTTGATTTGAAGAAAATTACAAAGTCACT
1 AGATTTTTGTCCAGAAGGCTCAATCATTGATTTGAAGAAAATTACAAAGTCACT
11180 AGATTTTTGTCCAGAAGGCTCAATCATTGATTTGAAGAAAATTACAAAGTCAC
1 AGATTTTTGTCCAGAAGGCTCAATCATTGATTTGAAGAAAATTACAAAGTCAC
11233 CACCAATCTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (54 bp):
AGATTTTTGTCCAGAAGGCTCAATCATTGATTTGAAGAAAATTACAAAGTCACT
Found at i:11860 original size:23 final size:23
Alignment explanation
Indices: 11813--11897 Score: 61
Period size: 23 Copynumber: 3.7 Consensus size: 23
11803 CTTAATTAAT
*
11813 TTTATTTATTA--ATTTTTATGCTA
1 TTTATTTATTATTATTATTAT--TA
11836 TTTATTTATTATTATTATTATTA
1 TTTATTTATTATTATTATTATTA
* *
11859 -TTATTTCTTCATCATTATT-TTAA
1 TTTATTTATT-ATTATTATTATT-A
* *
11882 TTTCTTTTTTATTATT
1 TTTATTTATTATTATT
11898 TAAAATATAC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
22 10 0.20
23 27 0.53
24 7 0.14
25 7 0.14
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (23 bp):
TTTATTTATTATTATTATTATTA
Found at i:11895 original size:20 final size:19
Alignment explanation
Indices: 11849--11898 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
11839 ATTTATTATT
11849 ATTATTATTATTATTTCTTC
1 ATTATTATT-TTATTTCTTC
* *
11869 ATCATTATTTTAATTTCTTT
1 ATTATTATTTT-ATTTCTTC
*
11889 TTTATTATTT
1 ATTATTATTT
11899 AAAATATACC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTATTATTTTATTTCTTC
Found at i:12360 original size:21 final size:21
Alignment explanation
Indices: 12333--12379 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
12323 AATTAATTTT
*
12333 TAAAAAATAAAA-ACAAAAAA
1 TAAAAAATAAAAGAAAAAAAA
12353 TGAAAAAATAAAAGAAAAAAAA
1 T-AAAAAATAAAAGAAAAAAAA
12375 TAAAA
1 TAAAA
12380 CTTGAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 15 0.62
22 8 0.33
ACGTcount: A:0.83, C:0.02, G:0.04, T:0.11
Consensus pattern (21 bp):
TAAAAAATAAAAGAAAAAAAA
Found at i:15805 original size:18 final size:18
Alignment explanation
Indices: 15782--15816 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15772 ATATCTATAG
*
15782 TGAAGCTAACCTGTATGA
1 TGAAGCTAACCTATATGA
*
15800 TGAAGCTGACCTATATG
1 TGAAGCTAACCTATATG
15817 GTGGAACATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (18 bp):
TGAAGCTAACCTATATGA
Found at i:17163 original size:27 final size:27
Alignment explanation
Indices: 17133--17187 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
17123 GGAAAAGAAG
*
17133 AATAAAATAGAACAATTTATTTTATTT
1 AATAAAATAGAACAATTTAATTTATTT
*
17160 AATAAAATAGAACAATTTAATTTGTTT
1 AATAAAATAGAACAATTTAATTTATTT
17187 A
1 A
17188 TAACAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (27 bp):
AATAAAATAGAACAATTTAATTTATTT
Found at i:18329 original size:146 final size:144
Alignment explanation
Indices: 18103--18380 Score: 339
Period size: 146 Copynumber: 1.9 Consensus size: 144
18093 CAGCAATACA
* * *
18103 CCAAGAAGTGTGAAATTACCAAAAACCCTTTAAGGGGTATTTTCATAATTTGGCTTTTTCGAGAT
1 CCAAAAAGTGTGAAATTACCAAAAACCCTATAAGGGGTATTTTCATAATTTGCCTTTTTCGAGAT
* * *
18168 TGGAATATCATGAAACTTTCCAAATCTCAA-TTCTATAATATTCCATGATTTTTTATGCATTTAA
66 TGGAATATAACGAAACTTTCCAAATCTCAATTTC-ATAATATTCCATGATTTTTGATGC-TTTAA
18232 AATCACAATAGTACCC
129 AATCACAATAGTACCC
* *
18248 CCAAAAAGTGTGAAATTACTAAAATACCCTA-ATAGGGGTATTTTCGTAATTTAGCCTTTTT-GA
1 CCAAAAAGTGTGAAATTACCAAAA-ACCCTATA-AGGGGTATTTTCATAATTT-GCCTTTTTCGA
* * * * ** *
18311 G-TTCGGATTTTAACGAAACTTTTCAAATCTTAATTTCATAATATTTTATGATTTTTGGTGCTTT
63 GATT-GGAATATAACGAAACTTTCCAAATCTCAATTTCATAATATTCCATGATTTTTGATGCTTT
18375 AAAATC
127 AAAATC
18381 CCAAAAATGA
Statistics
Matches: 113, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
145 34 0.30
146 69 0.61
147 10 0.09
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (144 bp):
CCAAAAAGTGTGAAATTACCAAAAACCCTATAAGGGGTATTTTCATAATTTGCCTTTTTCGAGAT
TGGAATATAACGAAACTTTCCAAATCTCAATTTCATAATATTCCATGATTTTTGATGCTTTAAAA
TCACAATAGTACCC
Found at i:25240 original size:14 final size:14
Alignment explanation
Indices: 25221--25276 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
25211 AATTTAAATT
*
25221 TTATTATAAATAAA
1 TTATTAAAAATAAA
25235 TTATTAAAAAATAAA
1 TTATT-AAAAATAAA
*
25250 CTTATTACAAAT-AA
1 -TTATTAAAAATAAA
25264 TCTATTAAAAATA
1 T-TATTAAAAATA
25277 TTATAAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
13 1 0.03
14 16 0.46
15 13 0.37
16 5 0.14
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (14 bp):
TTATTAAAAATAAA
Found at i:25248 original size:15 final size:15
Alignment explanation
Indices: 25228--25274 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
25218 ATTTTATTAT
25228 AAATAAATTATTAAA
1 AAATAAATTATTAAA
*
25243 AAATAAACTTATT-AC
1 AAATAAA-TTATTAAA
25258 AAAT-AATCTATTAAA
1 AAATAAAT-TATTAAA
25273 AA
1 AA
25275 TATTATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 1 0.04
14 6 0.22
15 15 0.56
16 5 0.19
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAAATTATTAAA
Found at i:25751 original size:13 final size:13
Alignment explanation
Indices: 25717--25761 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
25707 ATTCTCATTC
25717 ACTTTAAAATTTT
1 ACTTTAAAATTTT
*
25730 ATTTTTAAAATTTT
1 A-CTTTAAAATTTT
25744 ACTTTAAAATTTT
1 ACTTTAAAATTTT
25757 ACTTT
1 ACTTT
25762 GTTTTCTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (13 bp):
ACTTTAAAATTTT
Done.