Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168166.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_405, 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: 28468
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Found at i:797 original size:11 final size:10
Alignment explanation
Indices: 783--827 Score: 58
Period size: 9 Copynumber: 4.5 Consensus size: 10
773 TTAGAGGGTG
783 AAAAGAGAGAT
1 AAAA-AGAGAT
794 -AAAAGAGAAT
1 AAAAAGAG-AT
804 AAAAAGAGAT
1 AAAAAGAGAT
814 AAAAA-AGAT
1 AAAAAGAGAT
823 AAAAA
1 AAAAA
828 TAAATAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 13 0.41
10 12 0.38
11 7 0.22
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (10 bp):
AAAAAGAGAT
Found at i:813 original size:20 final size:19
Alignment explanation
Indices: 783--827 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
773 TTAGAGGGTG
*
783 AAAAGAGAGATAAAAGAGAAT
1 AAAA-AGAGATAAAAAAG-AT
804 AAAAAGAGATAAAAAAGAT
1 AAAAAGAGATAAAAAAGAT
823 AAAAA
1 AAAAA
828 TAAATAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 12 0.52
21 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (19 bp):
AAAAAGAGATAAAAAAGAT
Found at i:3360 original size:41 final size:41
Alignment explanation
Indices: 3283--3362 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
3273 CTTCTTTATA
* * *
3283 TAAACACGATTATATAGAAAGAACGGTTCCCGATTGAAATC
1 TAAACACGATTATAGAGAAAGAACAGTTCCCAATTGAAATC
*
3324 TAAACACTATTATACGAGAAAGAACAGTT-CCAATTGAAA
1 TAAACACGATTATA-GAGAAAGAACAGTTCCCAATTGAAA
3363 ATACTGTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 22 0.65
42 12 0.35
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (41 bp):
TAAACACGATTATAGAGAAAGAACAGTTCCCAATTGAAATC
Found at i:6293 original size:2 final size:2
Alignment explanation
Indices: 6280--6309 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6270 ATTCTTTTTC
*
6280 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6310 GATAAAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10337 original size:52 final size:51
Alignment explanation
Indices: 10228--10337 Score: 114
Period size: 52 Copynumber: 2.1 Consensus size: 51
10218 ATGAAATTCC
** * * **
10228 AAAATCTCTCCCTATCAGTTTAATGTGAATTGATTGTAGAATTAAATTTCG
1 AAAATCTCTCCCTATCAGTTTAATGCCAATTGATTCTAGAATTAAATCTAA
* * *
10279 ACAATCTCTCCAC-ATCATTTTTAATGCCAATTGATTCTGGAATTAAATCTAA
1 AAAATCTCTCC-CTATCA-GTTTAATGCCAATTGATTCTAGAATTAAATCTAA
10331 AAAATCT
1 AAAATCT
10338 TTCAATTACG
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
51 14 0.30
52 33 0.70
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.37
Consensus pattern (51 bp):
AAAATCTCTCCCTATCAGTTTAATGCCAATTGATTCTAGAATTAAATCTAA
Found at i:14714 original size:27 final size:27
Alignment explanation
Indices: 14676--14732 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
14666 GGATCAAGGT
14676 ATTTAGTATTAAATGATGTTAGCCCAC
1 ATTTAGTATTAAATGATGTTAGCCCAC
*
14703 ATTTAGTATTAAATGATGTTTGCCCAC
1 ATTTAGTATTAAATGATGTTAGCCCAC
14730 ATT
1 ATT
14733 CAATTAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (27 bp):
ATTTAGTATTAAATGATGTTAGCCCAC
Found at i:19968 original size:30 final size:30
Alignment explanation
Indices: 19932--19990 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
19922 GAGGATAGGA
19932 TAATAATCATTTTATATCATATTTGGTTTG
1 TAATAATCATTTTATATCATATTTGGTTTG
19962 TAATAATCATTTTATATCATATTTGGTTT
1 TAATAATCATTTTATATCATATTTGGTTT
19991 ATATCTAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.08, T:0.54
Consensus pattern (30 bp):
TAATAATCATTTTATATCATATTTGGTTTG
Found at i:20957 original size:11 final size:10
Alignment explanation
Indices: 20943--20987 Score: 58
Period size: 9 Copynumber: 4.5 Consensus size: 10
20933 TTAGAGGGTG
20943 AAAAGAGAGAT
1 AAAA-AGAGAT
20954 -AAAAGAGAAT
1 AAAAAGAG-AT
20964 AAAAAGAGAT
1 AAAAAGAGAT
20974 AAAAA-AGAT
1 AAAAAGAGAT
20983 AAAAA
1 AAAAA
20988 TAAATAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 13 0.41
10 12 0.38
11 7 0.22
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (10 bp):
AAAAAGAGAT
Found at i:20973 original size:20 final size:19
Alignment explanation
Indices: 20943--20987 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
20933 TTAGAGGGTG
*
20943 AAAAGAGAGATAAAAGAGAAT
1 AAAA-AGAGATAAAAAAG-AT
20964 AAAAAGAGATAAAAAAGAT
1 AAAAAGAGATAAAAAAGAT
20983 AAAAA
1 AAAAA
20988 TAAATAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 12 0.52
21 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (19 bp):
AAAAAGAGATAAAAAAGAT
Found at i:23043 original size:19 final size:20
Alignment explanation
Indices: 23016--23063 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
23006 CGTATCTTAT
* *
23016 ATTTATATTTAGTAA-ATAA
1 ATTTTTATTTAATAATATAA
23035 ATTTTTA-TTAATAATATAA
1 ATTTTTATTTAATAATATAA
*
23054 AATTTTATTT
1 ATTTTTATTT
23064 TAGATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.25
19 16 0.67
20 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTTTTATTTAATAATATAA
Found at i:23527 original size:42 final size:42
Alignment explanation
Indices: 23440--23523 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
23430 TTGCTTCTTT
* * *
23440 ATATAAACACTATTATATGAGAAAGAAACGGTTCCGATTGAA
1 ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
*
23482 ATATAAACACTATTATACGGGAAAG-AACAGTTCCAATTGAA
1 ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
23523 A
1 A
23524 ATATTGTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
41 15 0.39
42 23 0.61
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.25
Consensus pattern (42 bp):
ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
Done.