Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168072.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_320, 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: 35058
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:11064 original size:15 final size:15
Alignment explanation
Indices: 11044--11072 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11034 TTGCAAGAAT
11044 ATATCATCTATAATC
1 ATATCATCTATAATC
11059 ATATCATCTATAAT
1 ATATCATCTATAAT
11073 AATTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATCATCTATAATC
Found at i:13478 original size:15 final size:16
Alignment explanation
Indices: 13443--13479 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
13433 TTAAAAAGGT
*
13443 ATATGATACAATAAAC
1 ATATAATACAATAAAC
13459 A-ATAATACAATAAA-
1 ATATAATACAATAAAC
13473 ATATAAT
1 ATATAAT
13480 CATATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 1 0.05
15 17 0.89
16 1 0.05
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (16 bp):
ATATAATACAATAAAC
Found at i:14555 original size:8 final size:8
Alignment explanation
Indices: 14508--14537 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
14498 CTAATTTAGT
14508 TTTTAA-A
1 TTTTAATA
14515 TTTTAATA
1 TTTTAATA
14523 TTTTAATA
1 TTTTAATA
14531 TTTTAAT
1 TTTTAAT
14538 TAAAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTTAATA
Found at i:18130 original size:37 final size:37
Alignment explanation
Indices: 18089--18199 Score: 94
Period size: 37 Copynumber: 3.2 Consensus size: 37
18079 GTCATTTTAT
18089 TTTATATTTTATGTGTGTAAGGATTAAAATGAGATAA
1 TTTATATTTTATGTGTGTAAGGATTAAAATGAGATAA
* * * ** *
18126 TTTATATATTA---GT-TAA--A-TAATATTATCTTAG
1 TTTATATTTTATGTGTGTAAGGATTAAAATGA-GATAA
*
18157 TTTATA-TTTGTGTGTGTAAGGATTAAAATGAGATAA
1 TTTATATTTTATGTGTGTAAGGATTAAAATGAGATAA
18193 TTTATAT
1 TTTATAT
18200 ATTGGTTAAA
Statistics
Matches: 52, Mismatches: 13, Indels: 18
0.63 0.16 0.22
Matches are distributed among these distances:
30 8 0.15
31 9 0.17
33 5 0.10
34 5 0.10
36 9 0.17
37 16 0.31
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.47
Consensus pattern (37 bp):
TTTATATTTTATGTGTGTAAGGATTAAAATGAGATAA
Found at i:18188 original size:67 final size:67
Alignment explanation
Indices: 18065--18217 Score: 227
Period size: 67 Copynumber: 2.3 Consensus size: 67
18055 TATAGATAGA
* * * *
18065 ATTAGCTAAATAATGTCATTTTATTTTATATTTTATGTGTGTAAGGATTAAAATGAGATAATTTA
1 ATTAGTTAAATAAT-TTATCTTAGTTTATATTTTATGTGTGTAAGGATTAAAATGAGATAATTTA
18130 TAT
65 TAT
*
18133 ATTAGTTAAATAATATTATCTTAGTTTATA-TTTGTGTGTGTAAGGATTAAAATGAGATAATTTA
1 ATTAGTTAAATAAT-TTATCTTAGTTTATATTTTATGTGTGTAAGGATTAAAATGAGATAATTTA
18197 TAT
65 TAT
*
18200 ATTGGTTAAATAATTTAT
1 ATTAGTTAAATAATTTAT
18218 ATATTGATTA
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
66 4 0.05
67 49 0.63
68 25 0.32
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (67 bp):
ATTAGTTAAATAATTTATCTTAGTTTATATTTTATGTGTGTAAGGATTAAAATGAGATAATTTAT
AT
Found at i:18214 original size:20 final size:20
Alignment explanation
Indices: 18189--18233 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
18179 TTAAAATGAG
*
18189 ATAATTTATATATTGGTTAA
1 ATAATTTATATATTGATTAA
18209 ATAATTTATATATTGATTAA
1 ATAATTTATATATTGATTAA
18229 ATAAT
1 ATAAT
18234 ATCATCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
ATAATTTATATATTGATTAA
Found at i:20967 original size:48 final size:48
Alignment explanation
Indices: 20908--21004 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
20898 AGAACATCTA
20908 TAACTTATAGAAGACTACACTATAAAAGTGAAGCATAACATCAAACTT
1 TAACTTATAGAAGACTACACTATAAAAGTGAAGCATAACATCAAACTT
* * *
20956 TAACTTATAGAAGACTATATTATTAAAGTGAAGCATAACATCAAACTT
1 TAACTTATAGAAGACTACACTATAAAAGTGAAGCATAACATCAAACTT
21004 T
1 T
21005 TAGTCATAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.29
Consensus pattern (48 bp):
TAACTTATAGAAGACTACACTATAAAAGTGAAGCATAACATCAAACTT
Found at i:23164 original size:239 final size:239
Alignment explanation
Indices: 22738--23206 Score: 875
Period size: 239 Copynumber: 2.0 Consensus size: 239
22728 AAAGGAGGCA
*
22738 GGTTCTGCAAATGAATGGAAGACAACCACATTGCAAAGTTGAACTATAATCAGTGCAACCACATT
1 GGTTCTACAAATGAATGGAAGACAACCACATTGCAAAGTTGAACTATAATCAGTGCAACCACATT
*
22803 CCAAAGATTTGTTTGAGGCAAGATTCATTTTGCTTTCTTTGTGCTTGTGCAAGATAGTAGCATTT
66 CCAAAGATTTGTCTGAGGCAAGATTCATTTTGCTTTCTTTGTGCTTGTGCAAGATAGTAGCATTT
*
22868 ACATAGTTTTTCCCTATATTAATTCCCAGACAACAACTTACCCATATGCCCTCACTGAAACTCTA
131 ACATAGTTTTTCCCTAAATTAATTCCCAGACAACAACTTACCCATATGCCCTCACTGAAACTCTA
*
22933 TAACAATATGATATTAAAACTATACACTCTTTTACCCATTTGCT
196 TAAAAATATGATATTAAAACTATACACTCTTTTACCCATTTGCT
*
22977 GGTTCTACAAATGAATGGAAGACAACCACATTGCAAAGTTGAACTATAATCAGTGCAACCGCATT
1 GGTTCTACAAATGAATGGAAGACAACCACATTGCAAAGTTGAACTATAATCAGTGCAACCACATT
23042 CCAAAGATTTGTCTGAGGCAAGATTCATTTTGCTTTCTTTGTGCTTGTGCAAGATAGTAGCATTT
66 CCAAAGATTTGTCTGAGGCAAGATTCATTTTGCTTTCTTTGTGCTTGTGCAAGATAGTAGCATTT
23107 ACATAGTTTTTCCCTAAATTAATTCCCAGACAACAACTTACCCATATGCCCTCACTGAAACTCTA
131 ACATAGTTTTTCCCTAAATTAATTCCCAGACAACAACTTACCCATATGCCCTCACTGAAACTCTA
* *
23172 TAAAAATATGTTATTGAAACTATACACTCTTTTAC
196 TAAAAATATGATATTAAAACTATACACTCTTTTAC
23207 TTGTTTTACA
Statistics
Matches: 223, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
239 223 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (239 bp):
GGTTCTACAAATGAATGGAAGACAACCACATTGCAAAGTTGAACTATAATCAGTGCAACCACATT
CCAAAGATTTGTCTGAGGCAAGATTCATTTTGCTTTCTTTGTGCTTGTGCAAGATAGTAGCATTT
ACATAGTTTTTCCCTAAATTAATTCCCAGACAACAACTTACCCATATGCCCTCACTGAAACTCTA
TAAAAATATGATATTAAAACTATACACTCTTTTACCCATTTGCT
Found at i:28011 original size:22 final size:20
Alignment explanation
Indices: 27980--28033 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
27970 AAAAAACATG
*
27980 CATTACCGATGAAAATATTAA
1 CATTATCGATG-AAATATTAA
* *
28001 TCATTATCGATGGAATTTTAA
1 -CATTATCGATGAAATATTAA
28022 CTATTATCGATG
1 C-ATTATCGATG
28034 GAGTTTTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 17 0.61
22 10 0.36
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (20 bp):
CATTATCGATGAAATATTAA
Done.