Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168008.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_263, 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: 41214
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:3001 original size:20 final size:20
Alignment explanation
Indices: 2976--3013 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2966 AAATCTTAAA
*
2976 TTATATCATTTTCATATTTT
1 TTATATAATTTTCATATTTT
*
2996 TTATATAATTTTTATATT
1 TTATATAATTTTCATATT
3014 ATATCAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATATAATTTTCATATTTT
Found at i:3088 original size:23 final size:23
Alignment explanation
Indices: 3043--3088 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3033 AAAATTATCA
* * *
3043 AATTTAATTGAAATTTTTTTAAT
1 AATTTAATAGAAATGTTTGTAAT
*
3066 AATTTAATAGATATGTTTGTAAT
1 AATTTAATAGAAATGTTTGTAAT
3089 TCATTTATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (23 bp):
AATTTAATAGAAATGTTTGTAAT
Found at i:9113 original size:25 final size:24
Alignment explanation
Indices: 9079--9140 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 24
9069 ACTTTTATTT
*
9079 TTAGGCCTTCATTGCCGAACCCTG
1 TTAGGCCTTCATTGCCAAACCCTG
9103 CTTAGGCCTTCATTGCCAAACCCTG
1 -TTAGGCCTTCATTGCCAAACCCTG
*
9128 TTAAAGCCTTCAT
1 TT-AGGCCTTCAT
9141 AACCATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 2 0.06
25 32 0.94
ACGTcount: A:0.21, C:0.32, G:0.16, T:0.31
Consensus pattern (24 bp):
TTAGGCCTTCATTGCCAAACCCTG
Found at i:16117 original size:73 final size:73
Alignment explanation
Indices: 15998--16144 Score: 267
Period size: 73 Copynumber: 2.0 Consensus size: 73
15988 CCAGTGAATA
* *
15998 CAAGAGCATTTCCAGAATTCTGTCTTCTTGTCTTGTTTTTCTTTAACTTGCGTAATCAACCATTC
1 CAAGAGCATTTCCAGAATTCTGTCTTCTTGTCCTGTTTTTCTTTAACTTGCGTAATCAACAATTC
16063 CCATTGTT
66 CCATTGTT
*
16071 CAAGAGCATTTCCAGAATTCTGTCTTCTTGTCCTGTTTTTCTTTAACTTGCGTAATCAGCAATTC
1 CAAGAGCATTTCCAGAATTCTGTCTTCTTGTCCTGTTTTTCTTTAACTTGCGTAATCAACAATTC
16136 CCATTGTT
66 CCATTGTT
16144 C
1 C
16145 TAGTGCCCGC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (73 bp):
CAAGAGCATTTCCAGAATTCTGTCTTCTTGTCCTGTTTTTCTTTAACTTGCGTAATCAACAATTC
CCATTGTT
Found at i:16368 original size:180 final size:180
Alignment explanation
Indices: 16066--16425 Score: 675
Period size: 180 Copynumber: 2.0 Consensus size: 180
16056 ACCATTCCCA
16066 TTGTTCAAGAGCATTTCCAGAATTCTGTCTTCTTGTCCTGTTTTTCTTTAACTTGCGTAATCAGC
1 TTGTTCAAGAGCATTTCCAGAATTCTGTCTTCTTGTCCTGTTTTTCTTTAACTTGCGTAATCAGC
16131 AATTCCCATTGTTCTAGTGCCCGCACGCTTGTGTTTTAGGCTGACTTAGGCATAAAGGAGGAGAT
66 AATTCCCATTGTTCTAGTGCCCGCACGCTTGTGTTTTAGGCTGACTTAGGCATAAAGGAGGAGAT
16196 TCCAAGCCTAAGGCCGCACGGATTCTGAGTCTAAGGTCGGAGCCCGTGAC
131 TCCAAGCCTAAGGCCGCACGGATTCTGAGTCTAAGGTCGGAGCCCGTGAC
* * *
16246 TTGTTCAAGAGCATTTCCAGAATTCTGTCTTTTTGTCCTGTTTTTCTTTAACTTGTGTAGTCAGC
1 TTGTTCAAGAGCATTTCCAGAATTCTGTCTTCTTGTCCTGTTTTTCTTTAACTTGCGTAATCAGC
*
16311 CATTCCCATTGTTCTAGTGCCCGCACGCTTGTGTTTTAGGCTGACTTAGGCATAAAGGAGGAGAT
66 AATTCCCATTGTTCTAGTGCCCGCACGCTTGTGTTTTAGGCTGACTTAGGCATAAAGGAGGAGAT
*
16376 TCCAAGCCTAAGGCCGCACGGATTTTGAGTCTAAGGTCGGAGCCCGTGAC
131 TCCAAGCCTAAGGCCGCACGGATTCTGAGTCTAAGGTCGGAGCCCGTGAC
16426 AGTTGGTGTC
Statistics
Matches: 175, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
180 175 1.00
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.33
Consensus pattern (180 bp):
TTGTTCAAGAGCATTTCCAGAATTCTGTCTTCTTGTCCTGTTTTTCTTTAACTTGCGTAATCAGC
AATTCCCATTGTTCTAGTGCCCGCACGCTTGTGTTTTAGGCTGACTTAGGCATAAAGGAGGAGAT
TCCAAGCCTAAGGCCGCACGGATTCTGAGTCTAAGGTCGGAGCCCGTGAC
Found at i:24235 original size:22 final size:22
Alignment explanation
Indices: 24209--24250 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
24199 TATATTAATT
*
24209 TTTGTATCTCTAGAATTAAGTA
1 TTTGTATCCCTAGAATTAAGTA
24231 TTTGTATCCCTAGAATTAAG
1 TTTGTATCCCTAGAATTAAG
24251 GATAATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (22 bp):
TTTGTATCCCTAGAATTAAGTA
Found at i:30166 original size:22 final size:22
Alignment explanation
Indices: 30151--30193 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
30141 ATATTTTTTA
30151 TTTT-TTAAAATTATATATTAT
1 TTTTATTAAAATTATATATTAT
* *
30172 TTTTATTAAAATTTTAAATTAT
1 TTTTATTAAAATTATATATTAT
30194 ATTATATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTATTAAAATTATATATTAT
Found at i:30633 original size:14 final size:14
Alignment explanation
Indices: 30614--30646 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
30604 GTTCAACGCT
30614 AATTTTAAAATTCA
1 AATTTTAAAATTCA
*
30628 AATTTTCAAATTCA
1 AATTTTAAAATTCA
30642 AATTT
1 AATTT
30647 CAATAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTTTAAAATTCA
Found at i:40839 original size:14 final size:15
Alignment explanation
Indices: 40820--40848 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40810 CCTAGAATTC
40820 TATTTCTA-ATAATA
1 TATTTCTATATAATA
40834 TATTTCTATATAATA
1 TATTTCTATATAATA
40849 AAAAAGGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTCTATATAATA
Found at i:40926 original size:26 final size:26
Alignment explanation
Indices: 40881--40939 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
40871 TGTCTTAGTG
*
40881 AATCAAAT-ATTTTATATTATTAATA
1 AATCAAATAATATTATATTATTAATA
*
40906 AATCAAATAATATTATATTATTAATT
1 AATCAAATAATATTATATTATTAATA
40932 AAT-AAATA
1 AATCAAATA
40940 TTAATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 13 0.42
26 18 0.58
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (26 bp):
AATCAAATAATATTATATTATTAATA
Done.