Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168386.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_603, 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: 21702
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Found at i:1050 original size:16 final size:16
Alignment explanation
Indices: 1025--1055 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1015 TATCAAATAT
1025 AAAATATATATTTTTA
1 AAAATATATATTTTTA
*
1041 AAAATTTATATTTTT
1 AAAATATATATTTTT
1056 TATTAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAAATATATATTTTTA
Found at i:1056 original size:18 final size:19
Alignment explanation
Indices: 1029--1067 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1019 AAATATAAAA
1029 TATATATTTT-TAAAAATT
1 TATATATTTTATAAAAATT
* *
1047 TATATTTTTTATTAAAATT
1 TATATATTTTATAAAAATT
1066 TA
1 TA
1068 AATTATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATATTTTATAAAAATT
Found at i:1438 original size:28 final size:28
Alignment explanation
Indices: 1394--1448 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
1384 TTTGATTGAC
*
1394 TTTTTTTTTTTGCTTTTTATTTTTTAACA
1 TTTTTTTTTTT-CTTTTTAGTTTTTAACA
*
1423 TTTTTTTTCTTT-TTTTTGGTTTTTAA
1 TTTTTTTT-TTTCTTTTTAGTTTTTAA
1449 GTAATAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 12 0.52
29 8 0.35
30 3 0.13
ACGTcount: A:0.11, C:0.05, G:0.05, T:0.78
Consensus pattern (28 bp):
TTTTTTTTTTTCTTTTTAGTTTTTAACA
Found at i:2346 original size:9 final size:8
Alignment explanation
Indices: 2289--2350 Score: 54
Period size: 9 Copynumber: 7.2 Consensus size: 8
2279 TTGTGAGCTC
2289 TTTTTATTA
1 TTTTT-TTA
*
2298 TTTTTGTTGT
1 TTTTT-TT-A
2308 TTTTCTTTA
1 TTTT-TTTA
2317 TTTTTTTA
1 TTTTTTTA
2325 TTTTTTT-
1 TTTTTTTA
*
2332 TGTTTTTA
1 TTTTTTTA
2340 TCTTTTTTA
1 T-TTTTTTA
2349 TT
1 TT
2351 AGATCAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
7 6 0.14
8 13 0.30
9 18 0.41
10 6 0.14
11 1 0.02
ACGTcount: A:0.10, C:0.03, G:0.05, T:0.82
Consensus pattern (8 bp):
TTTTTTTA
Found at i:2347 original size:27 final size:26
Alignment explanation
Indices: 2289--2351 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
2279 TTGTGAGCTC
*
2289 TTTTTATTATTTTTGTTGTTTTTCTT
1 TTTTTATTATTTTTGTTGTTTTTATT
* *
2315 TATTTTTTTATTTTTTTTGTTTTTATCT
1 T-TTTTATTATTTTTGTTGTTTTTAT-T
2343 TTTTTATTA
1 TTTTTATTA
2352 GATCAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 1 0.03
27 28 0.90
28 2 0.06
ACGTcount: A:0.11, C:0.03, G:0.05, T:0.81
Consensus pattern (26 bp):
TTTTTATTATTTTTGTTGTTTTTATT
Found at i:2839 original size:21 final size:20
Alignment explanation
Indices: 2811--2852 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2801 AAACAAAAAT
*
2811 ATTGTATTATAAAATTTTAA
1 ATTGTATTACAAAATTTTAA
*
2831 ATTGATATTACAACATTTTAA
1 ATTG-TATTACAAAATTTTAA
2852 A
1 A
2853 AGTAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTGTATTACAAAATTTTAA
Found at i:16933 original size:40 final size:44
Alignment explanation
Indices: 16853--16935 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
16843 TTTTGATTCG
* *
16853 TTTTTAGATATATATAAAAATATATATTATATTATTTATTTTAT
1 TTTTTAAATATATATAAAAATATATATTATATTATATATTTTAT
16897 TTTTTAAATATAT-TAATAAA-AT-TATTAT-TTA-ATATTTTA
1 TTTTTAAATATATATAA-AAATATATATTATATTATATATTTTA
16936 ATTTAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
40 7 0.19
41 3 0.08
42 6 0.17
43 5 0.14
44 15 0.42
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (44 bp):
TTTTTAAATATATATAAAAATATATATTATATTATATATTTTAT
Found at i:18585 original size:3 final size:3
Alignment explanation
Indices: 18577--18604 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
18567 AAGGCTTGGT
18577 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
18605 ATGTATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Done.