Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168198.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_434, 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: 26978
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
File 2 of 2
Found at i:25882 original size:15 final size:15
Alignment explanation
Indices: 25859--25922 Score: 60
Period size: 15 Copynumber: 4.2 Consensus size: 15
25849 TATTTAATTA
25859 TTAAAATTAATAAAT
1 TTAAAATTAATAAAT
*
25874 TTAACATTAATAAA-
1 TTAAAATTAATAAAT
*
25888 TTATAATT-ATAAACT
1 TTAAAATTAATAAA-T
*
25903 TATTAAATTGAATAAAT
1 T-TAAAATT-AATAAAT
25920 TTA
1 TTA
25923 TACTTATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
13 5 0.13
14 6 0.16
15 14 0.37
16 6 0.16
17 2 0.05
18 5 0.13
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (15 bp):
TTAAAATTAATAAAT
Found at i:26006 original size:30 final size:30
Alignment explanation
Indices: 25972--26034 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
25962 TAACTAAAAA
* *
25972 TATAATGTATTTAATTAA-AATTATAGTTAG
1 TATAAT-TATTTAACTAATAACTATAGTTAG
*
26002 TATAATTATTTAACTAATAACTATAGTTTG
1 TATAATTATTTAACTAATAACTATAGTTAG
26032 TAT
1 TAT
26035 TACAATAACC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (30 bp):
TATAATTATTTAACTAATAACTATAGTTAG
Found at i:26340 original size:27 final size:26
Alignment explanation
Indices: 26290--26352 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
26280 ATTGTATATT
* * *
26290 TTAATAAATTTATTACAATTAAATTAG
1 TTAATAATTTTATAACAATCAAA-TAG
*
26317 TTAATAATTTTATAATAATCAAATAG
1 TTAATAATTTTATAACAATCAAATAG
26343 TATAATAATT
1 T-TAATAATT
26353 AAATGTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (26 bp):
TTAATAATTTTATAACAATCAAATAG
Found at i:26348 original size:16 final size:15
Alignment explanation
Indices: 26327--26361 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
26317 TTAATAATTT
26327 TATAATAATCAAATAG
1 TATAATAATCAAAT-G
*
26343 TATAATAATTAAATG
1 TATAATAATCAAATG
26358 TATA
1 TATA
26362 TATGAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (15 bp):
TATAATAATCAAATG
Found at i:26503 original size:29 final size:27
Alignment explanation
Indices: 26450--26506 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 27
26440 ATATCGATAA
26450 TTAAATAATAAAATTAAATATTTTAAT
1 TTAAATAATAAAATTAAATATTTTAAT
*
26477 TTAAATATTTAAAACTTAAA-ATTTTTAAT
1 TTAAATA-ATAAAA-TTAAATA-TTTTAAT
26506 T
1 T
26507 ATTAACATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 7 0.27
28 6 0.23
29 13 0.50
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAAATAATAAAATTAAATATTTTAAT
Found at i:26737 original size:18 final size:19
Alignment explanation
Indices: 26714--26749 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
26704 TAATTACATA
26714 TATATTATAATAT-TAATT
1 TATATTATAATATATAATT
*
26732 TATATTTTAATATATAAT
1 TATATTATAATATATAAT
26750 AATTATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATAATATATAATT
Found at i:26834 original size:14 final size:14
Alignment explanation
Indices: 26817--26844 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
26807 AACTATTTTA
26817 TAATATTATATAAT
1 TAATATTATATAAT
26831 TAATATTATATAAT
1 TAATATTATATAAT
26845 ATTATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATTATATAAT
Done.