Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168486.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_84, 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: 108167
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Warning! 1000 characters in sequence are not A, C, G, or T
Found at i:1223 original size:30 final size:30
Alignment explanation
Indices: 1189--1247 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
1179 GCCAATCTTG
*
1189 ATCGAGGTATGTGCCTACACCAAAGGCCAA
1 ATCGAGGTATGTACCTACACCAAAGGCCAA
* *
1219 ATCGAGGTATGTACCTACACTAAGGGCCA
1 ATCGAGGTATGTACCTACACCAAAGGCCA
1248 GCATGTGTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (30 bp):
ATCGAGGTATGTACCTACACCAAAGGCCAA
Found at i:3804 original size:17 final size:17
Alignment explanation
Indices: 3782--3814 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3772 GATGGTGGTC
3782 GAAGCATGTGTCAAGAT
1 GAAGCATGTGTCAAGAT
3799 GAAGCATGTGTCAAGA
1 GAAGCATGTGTCAAGA
3815 CCAAGGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.21
Consensus pattern (17 bp):
GAAGCATGTGTCAAGAT
Found at i:5046 original size:9 final size:9
Alignment explanation
Indices: 5032--5061 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5022 GATATTTTAT
5032 TAATTAAAA
1 TAATTAAAA
5041 TAATTAAAA
1 TAATTAAAA
5050 TATATTAAAA
1 TA-ATTAAAA
5060 TA
1 TA
5062 TAAAAGATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:5058 original size:10 final size:10
Alignment explanation
Indices: 5034--5063 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5024 TATTTTATTA
5034 ATTAAAATA-
1 ATTAAAATAT
5043 ATTAAAATAT
1 ATTAAAATAT
5053 ATTAAAATAT
1 ATTAAAATAT
5063 A
1 A
5064 AAAGATCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:22699 original size:20 final size:20
Alignment explanation
Indices: 22676--22715 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
22666 CCTCTTTTAT
22676 ACATCATCTTACACTTTTGC
1 ACATCATCTTACACTTTTGC
22696 ACATCATCTTACACTTTTGC
1 ACATCATCTTACACTTTTGC
22716 TTTAGTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.40
Consensus pattern (20 bp):
ACATCATCTTACACTTTTGC
Found at i:26205 original size:17 final size:16
Alignment explanation
Indices: 26166--26199 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
26156 TATGATGTTA
26166 TACCAAGAACCATCATG
1 TACCAAGAACCAT-ATG
26183 TACCAAGAACCAT-TG
1 TACCAAGAACCATATG
26198 TA
1 TA
26200 TGCCAAAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
17 13 0.76
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21
Consensus pattern (16 bp):
TACCAAGAACCATATG
Found at i:31039 original size:17 final size:17
Alignment explanation
Indices: 31017--31049 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31007 GATGGTGTTC
31017 GAAGCATGTGTCAAGAT
1 GAAGCATGTGTCAAGAT
31034 GAAGCATGTGTCAAGA
1 GAAGCATGTGTCAAGA
31050 CCAAGGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.21
Consensus pattern (17 bp):
GAAGCATGTGTCAAGAT
Found at i:32122 original size:36 final size:37
Alignment explanation
Indices: 32057--32127 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
32047 CTTGAGCTTA
* *
32057 AGCTTGACTCAAAATTCAAAGTTCAAAACTTGATTCG
1 AGCTTGACTCAAAATTCAAAGCTCAAAACTCGATTCG
* **
32094 AGCTTGACTCAAATTTTGAAGCTC-AAACTCGATT
1 AGCTTGACTCAAAATTCAAAGCTCAAAACTCGATT
32128 GAGTTTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 9 0.31
37 20 0.69
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (37 bp):
AGCTTGACTCAAAATTCAAAGCTCAAAACTCGATTCG
Found at i:32281 original size:9 final size:9
Alignment explanation
Indices: 32267--32296 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
32257 GATATTTTAT
32267 TAATTAAAA
1 TAATTAAAA
32276 TAATTAAAA
1 TAATTAAAA
32285 TATATTAAAA
1 TA-ATTAAAA
32295 TA
1 TA
32297 TAAAAGATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:32293 original size:10 final size:10
Alignment explanation
Indices: 32269--32298 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
32259 TATTTTATTA
32269 ATTAAAATA-
1 ATTAAAATAT
32278 ATTAAAATAT
1 ATTAAAATAT
32288 ATTAAAATAT
1 ATTAAAATAT
32298 A
1 A
32299 AAAGATCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:46714 original size:21 final size:21
Alignment explanation
Indices: 46688--46734 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
46678 ACACTAGGTA
46688 TGGGCATTGAGTGAAAATGCT
1 TGGGCATTGAGTGAAAATGCT
46709 TGGGCATTGAGTGAAAATGCT
1 TGGGCATTGAGTGAAAATGCT
46730 TGGGC
1 TGGGC
46735 TTTTCCAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.11, G:0.36, T:0.28
Consensus pattern (21 bp):
TGGGCATTGAGTGAAAATGCT
Found at i:47772 original size:45 final size:45
Alignment explanation
Indices: 47640--47773 Score: 110
Period size: 45 Copynumber: 3.0 Consensus size: 45
47630 ATTGAGGTAT
* ** * * *
47640 GTGCCCACACCAAAGGCTAAAATATGCCAATGATGGTCAAGGCAA
1 GTGCCCATACCAAAGGCTAACTTATGCTAATGATGTTCGAGGCAA
* ** * * * *
47685 GTGCCCATACCTATTGCTAGCTTGTG-TCGATGGTGGTT-GAGGCAA
1 GTGCCCATACCAAAGGCTAACTTATGCT-AATGAT-GTTCGAGGCAA
*
47730 GTGCCCATACCGAAGGCTAACTTATGCTAATGATGTTCGAGGCA
1 GTGCCCATACCAAAGGCTAACTTATGCTAATGATGTTCGAGGCA
47774 TGTACCCACA
Statistics
Matches: 65, Mismatches: 20, Indels: 8
0.70 0.22 0.09
Matches are distributed among these distances:
44 3 0.05
45 59 0.91
46 3 0.05
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (45 bp):
GTGCCCATACCAAAGGCTAACTTATGCTAATGATGTTCGAGGCAA
Found at i:49926 original size:20 final size:20
Alignment explanation
Indices: 49903--49942 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
49893 CCTCTTTTAT
49903 ACATCATCTTACACTTTTGC
1 ACATCATCTTACACTTTTGC
49923 ACATCATCTTACACTTTTGC
1 ACATCATCTTACACTTTTGC
49943 TTTAGTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.40
Consensus pattern (20 bp):
ACATCATCTTACACTTTTGC
Found at i:63589 original size:22 final size:22
Alignment explanation
Indices: 63564--63611 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
63554 ATTACTTTAA
*
63564 AACCACT-CCTTATCTTAGTGAG
1 AACCACTCCCTT-TCTCAGTGAG
**
63586 AACCGTTCCCTTTCTCAGTGAG
1 AACCACTCCCTTTCTCAGTGAG
63608 AACC
1 AACC
63612 TCTGGGCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (22 bp):
AACCACTCCCTTTCTCAGTGAG
Found at i:76450 original size:45 final size:45
Alignment explanation
Indices: 76401--76500 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
76391 AATGCTGATC
* * *
76401 GAGGCATGTGCCTACACCAAGGGCTAGCATGTGCTAATGGTGGTT
1 GAGGCAAGTGCCTACACCAAAGGCTAGCATGTGCCAATGGTGGTT
*
76446 GAGGCAAGTGCCTATACCAAAGGCTAGCATGTGCCAATGGTGGTT
1 GAGGCAAGTGCCTACACCAAAGGCTAGCATGTGCCAATGGTGGTT
* *
76491 AAGGTAAGTG
1 GAGGCAAGTG
76501 ACCTTGATGA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (45 bp):
GAGGCAAGTGCCTACACCAAAGGCTAGCATGTGCCAATGGTGGTT
Found at i:78961 original size:19 final size:19
Alignment explanation
Indices: 78937--78981 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
78927 CACTCATTCT
78937 AGCAATGCCTTCATTGCTA
1 AGCAATGCCTTCATTGCTA
78956 AGCAATGCCTTCATTGCTA
1 AGCAATGCCTTCATTGCTA
*
78975 GGCAATG
1 AGCAATG
78982 ATGCACCCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (19 bp):
AGCAATGCCTTCATTGCTA
Found at i:79142 original size:28 final size:28
Alignment explanation
Indices: 79088--79145 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
79078 ACTATTCTCG
* * * *
79088 ATCCTATGTTCCTCAGCATTTTGCTACA
1 ATCCTATATTCCTCAGCACTCTACTACA
79116 ATCCTATATTCCTCAGCACTCTACTACA
1 ATCCTATATTCCTCAGCACTCTACTACA
79144 AT
1 AT
79146 GGACCTTTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.31, G:0.07, T:0.36
Consensus pattern (28 bp):
ATCCTATATTCCTCAGCACTCTACTACA
Found at i:88214 original size:15 final size:15
Alignment explanation
Indices: 88191--88221 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
88181 GATGATGGGT
88191 CAACAATTTGATGCA
1 CAACAATTTGATGCA
*
88206 CAACCATTTGATGCA
1 CAACAATTTGATGCA
88221 C
1 C
88222 CGAGCATAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (15 bp):
CAACAATTTGATGCA
Found at i:95387 original size:43 final size:44
Alignment explanation
Indices: 95339--95459 Score: 145
Period size: 44 Copynumber: 2.8 Consensus size: 44
95329 AAGGGCCATC
*
95339 TTATGCCAATGTTGATCGAGGCATGTGCTCGCAC-AAGTCTAGA
1 TTATGCCAATGTTGATCGAGGCATGTGCTCACACTAAGTCTAGA
* * ** * * *
95382 TTATGCCAATGTTAATCAAGGCATACGCCCACACTAGGTTTAGA
1 TTATGCCAATGTTGATCGAGGCATGTGCTCACACTAAGTCTAGA
* *
95426 TTATGCTAATGCTGATCGAGGCATGTGCTCACAC
1 TTATGCCAATGTTGATCGAGGCATGTGCTCACAC
95460 CAAGGGCCAG
Statistics
Matches: 62, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
43 28 0.45
44 34 0.55
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (44 bp):
TTATGCCAATGTTGATCGAGGCATGTGCTCACACTAAGTCTAGA
Found at i:95548 original size:45 final size:45
Alignment explanation
Indices: 95461--95549 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 45
95451 TGCTCACACC
* ** ** *
95461 AAGGGCCAGCATATGCCAATGTTGGTTGAGGTAAATGTCCATACG
1 AAGGGCCAGCATATGCCAATGATGGTCAAGCCAAATGCCCATACG
* *
95506 AAGGGCCAGCTTATGCCAATGATGGTCAAGCCAAGTGCCCATAC
1 AAGGGCCAGCATATGCCAATGATGGTCAAGCCAAATGCCCATAC
95550 CAAAGGCTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.21
Consensus pattern (45 bp):
AAGGGCCAGCATATGCCAATGATGGTCAAGCCAAATGCCCATACG
Found at i:97325 original size:30 final size:27
Alignment explanation
Indices: 97291--97347 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
97281 AGATACATTC
*
97291 CTAAGCTCTAGAGATTACAATCCCTTAATT
1 CTAAGATCTA-AG-TTACAATCCC-TAATT
*
97321 CTAAGATCTAAGTTATAATCCCTAATT
1 CTAAGATCTAAGTTACAATCCCTAATT
97348 ATAGGGGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 9 0.36
29 2 0.08
30 9 0.36
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (27 bp):
CTAAGATCTAAGTTACAATCCCTAATT
Found at i:98890 original size:126 final size:126
Alignment explanation
Indices: 98665--98919 Score: 510
Period size: 126 Copynumber: 2.0 Consensus size: 126
98655 ACTGCATGAG
98665 CTTTTCCATTGCCTTATTCGAGGATCCCTCAACATCTCTAAACTAATATATTATCTAAATAATGG
1 CTTTTCCATTGCCTTATTCGAGGATCCCTCAACATCTCTAAACTAATATATTATCTAAATAATGG
98730 CCTCCTTACACTTCGCTAATCGAGTGCTTGTTAGCACATATCTTGTTGAAACCTTCCCCTA
66 CCTCCTTACACTTCGCTAATCGAGTGCTTGTTAGCACATATCTTGTTGAAACCTTCCCCTA
98791 CTTTTCCATTGCCTTATTCGAGGATCCCTCAACATCTCTAAACTAATATATTATCTAAATAATGG
1 CTTTTCCATTGCCTTATTCGAGGATCCCTCAACATCTCTAAACTAATATATTATCTAAATAATGG
98856 CCTCCTTACACTTCGCTAATCGAGTGCTTGTTAGCACATATCTTGTTGAAACCTTCCCCTA
66 CCTCCTTACACTTCGCTAATCGAGTGCTTGTTAGCACATATCTTGTTGAAACCTTCCCCTA
98917 CTT
1 CTT
98920 CTTTGTAGGT
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 129 1.00
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.36
Consensus pattern (126 bp):
CTTTTCCATTGCCTTATTCGAGGATCCCTCAACATCTCTAAACTAATATATTATCTAAATAATGG
CCTCCTTACACTTCGCTAATCGAGTGCTTGTTAGCACATATCTTGTTGAAACCTTCCCCTA
Done.