Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167941.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_202, 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: 51944
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:1313 original size:22 final size:22
Alignment explanation
Indices: 1276--1336 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
1266 TCGATTAGAC
*
1276 TTAAAATTAATAAAATATTATTTT
1 TTAAAA-T-ATAAAATATTATATT
*
1300 TTAAAATATAAAATA-AATATT
1 TTAAAATATAAAATATTATATT
1321 TTAAAATAT-AAATATT
1 TTAAAATATAAAATATT
1337 TTAAATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 5 0.15
21 13 0.39
22 8 0.24
23 1 0.03
24 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAAAATATAAAATATTATATT
Found at i:1333 original size:16 final size:17
Alignment explanation
Indices: 1312--1369 Score: 73
Period size: 16 Copynumber: 3.4 Consensus size: 17
1302 AAAATATAAA
1312 ATAAATATTTTAAA-AT
1 ATAAATATTTTAAATAT
1328 ATAAATATTTTAAATAT
1 ATAAATATTTTAAATAT
* * *
1345 ATAATTATATAAATATAT
1 ATAAATATTTTAA-ATAT
1363 ATAAATA
1 ATAAATA
1370 AAAAATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
16 14 0.39
17 12 0.33
18 10 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAAATATTTTAAATAT
Found at i:1344 original size:15 final size:15
Alignment explanation
Indices: 1308--1345 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
1298 TTTTAAAATA
1308 TAAA-ATAAATATTT
1 TAAATATAAATATTT
1322 TAAAATATAAATATTT
1 T-AAATATAAATATTT
1338 TAAATATA
1 TAAATATA
1346 TAATTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 10 0.45
16 11 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAATATAAATATTT
Found at i:1355 original size:8 final size:8
Alignment explanation
Indices: 1312--1363 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
1302 AAAATATAAA
1312 ATAAATATT
1 ATAAATA-T
*
1321 TTAAA-AT
1 ATAAATAT
1328 ATAAATATT
1 ATAAATA-T
*
1337 TTAAATAT
1 ATAAATAT
*
1345 ATAATTAT
1 ATAAATAT
1353 ATAAATAT
1 ATAAATAT
1361 ATA
1 ATA
1364 TAAATAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
7 5 0.14
8 19 0.54
9 11 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
ATAAATAT
Found at i:8784 original size:2 final size:2
Alignment explanation
Indices: 8777--8808 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8767 TTCTTTTGTA
8777 AT AT AT AT AT 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 AT
8809 TACTTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11684 original size:21 final size:21
Alignment explanation
Indices: 11660--11699 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11650 AAACAATATG
*
11660 ATAAGAATTTCAATGTAGCTT
1 ATAAGAATTTCAAGGTAGCTT
**
11681 ATAATCATTTCAAGGTAGC
1 ATAAGAATTTCAAGGTAGC
11700 AAAACACTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (21 bp):
ATAAGAATTTCAAGGTAGCTT
Found at i:12329 original size:21 final size:21
Alignment explanation
Indices: 12303--12344 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
12293 ATTATAAGAT
12303 ATCCTACTTAGCTACAACAGA
1 ATCCTACTTAGCTACAACAGA
12324 ATCCTACTTAGCTACAACAGA
1 ATCCTACTTAGCTACAACAGA
12345 GACATTACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.24
Consensus pattern (21 bp):
ATCCTACTTAGCTACAACAGA
Found at i:13941 original size:16 final size:16
Alignment explanation
Indices: 13920--13962 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
13910 ATCCAGGGTG
*
13920 TATTTGTTGAGTCACT
1 TATTTGGTGAGTCACT
13936 TATTTGGTGAGTCACT
1 TATTTGGTGAGTCACT
13952 TATTTGGTGAG
1 TATTTGGTGAG
13963 ATTTCTCCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.19, C:0.09, G:0.26, T:0.47
Consensus pattern (16 bp):
TATTTGGTGAGTCACT
Found at i:19081 original size:15 final size:15
Alignment explanation
Indices: 19061--19102 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
19051 AAATAGATTA
19061 TAAATATTTAATTTT
1 TAAATATTTAATTTT
19076 TAAATATTT--TTATT
1 TAAATATTTAATT-TT
19090 TAAATA-TTAATTT
1 TAAATATTTAATTT
19103 AAATTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 4 0.17
14 9 0.38
15 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TAAATATTTAATTTT
Found at i:19230 original size:19 final size:19
Alignment explanation
Indices: 19203--19251 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
19193 TATTTGAGTA
*
19203 ATTAATTGTATCTAATTAT
1 ATTAATTGTATATAATTAT
*
19222 ATTATTTGTATATAATTAT
1 ATTAATTGTATATAATTAT
* *
19241 GTTAATCGTAT
1 ATTAATTGTAT
19252 TGTATAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (19 bp):
ATTAATTGTATATAATTAT
Found at i:19300 original size:38 final size:37
Alignment explanation
Indices: 19215--19300 Score: 86
Period size: 38 Copynumber: 2.3 Consensus size: 37
19205 TAATTGTATC
*
19215 TAATTATATTATTTGTATATAATTATGTTAATCGTAT
1 TAATTATATTATTTGTATATAATTATGTTAATCATAT
* * *
19252 TGTATAATATTATTT-TGATATAAATTAATTTTAAT-ATAT
1 T-AATTATATTATTTGT-ATAT-AATT-ATGTTAATCATAT
19291 TAATTATATT
1 TAATTATATT
19301 GTATTACATA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
37 2 0.05
38 22 0.56
39 8 0.21
40 7 0.18
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (37 bp):
TAATTATATTATTTGTATATAATTATGTTAATCATAT
Found at i:19359 original size:9 final size:9
Alignment explanation
Indices: 19327--19377 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
19317 GTATAATAAA
19327 TATATTATAT
1 TATATTAT-T
19337 T-TA-TATT
1 TATATTATT
*
19344 TAAATTATT
1 TATATTATT
*
19353 TGTATTATT
1 TATATTATT
19362 TATA-TATT
1 TATATTATT
19370 TATATTAT
1 TATATTAT
19378 ATTTAAAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
7 2 0.06
8 12 0.35
9 19 0.56
10 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TATATTATT
Found at i:19801 original size:22 final size:21
Alignment explanation
Indices: 19751--19807 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
19741 ATTACAAACA
*
19751 AAATTTTAATAAT-TTTTTTT
1 AAATTTTATTAATCTTTTTTT
* *
19771 ACATATTATTAATCTTTTTATT
1 AAATTTTATTAATCTTTTT-TT
*
19793 AAATTTTATAAATCT
1 AAATTTTATTAATCT
19808 ATTAATTTGG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 10 0.34
21 5 0.17
22 14 0.48
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (21 bp):
AAATTTTATTAATCTTTTTTT
Found at i:19978 original size:32 final size:32
Alignment explanation
Indices: 19942--20009 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
19932 AGTGAAATCC
* * *
19942 TCAACTTAATATAATTAAATTAAAATTAAAAA
1 TCAACTAAAAATAATAAAATTAAAATTAAAAA
19974 TCAACTAAAAATAATAAAATTAAAATTAAAAA
1 TCAACTAAAAATAATAAAATTAAAATTAAAAA
20006 TCAA
1 TCAA
20010 AACCTCCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (32 bp):
TCAACTAAAAATAATAAAATTAAAATTAAAAA
Found at i:29157 original size:15 final size:15
Alignment explanation
Indices: 29133--29162 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29123 ATTGTGTAAG
*
29133 TTGATCACTTTAAAC
1 TTGATAACTTTAAAC
29148 TTGATAACTTTAAAC
1 TTGATAACTTTAAAC
29163 AATTTTCAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.40
Consensus pattern (15 bp):
TTGATAACTTTAAAC
Found at i:30353 original size:2 final size:2
Alignment explanation
Indices: 30346--30394 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
30336 GATCCTTTAC
* * *
30346 AT AT AT AT AT GT AT AT GT GT 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 AT AT AT AT AT AT
*
30388 AT GT AT A
1 AT AT AT A
30395 AACACATGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30673 original size:30 final size:30
Alignment explanation
Indices: 30611--30687 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 30
30601 TCGAAGGCTT
* * *
30611 AATTGAATGAAAATAAATGTATAAAGATTC
1 AATTGATTAAAAATAAATGTATAAAGACTC
* * *
30641 AATTAGA-TAAAAATAAATGTTTAATGGCTC
1 AATT-GATTAAAAATAAATGTATAAAGACTC
*
30671 AATTGATTTAAAATAAA
1 AATTGATTAAAAATAAA
30688 AAATTTAGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 2 0.05
30 35 0.90
31 2 0.05
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.32
Consensus pattern (30 bp):
AATTGATTAAAAATAAATGTATAAAGACTC
Found at i:32115 original size:22 final size:22
Alignment explanation
Indices: 32087--32156 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 22
32077 ATATCATTGG
32087 AAATTTAATTTAATTTTATATT
1 AAATTTAATTTAATTTTATATT
*
32109 AAATTT-ATTT-GTTTTA-ATT
1 AAATTTAATTTAATTTTATATT
* *
32128 TAA-TTAA-TTAATTTTTTATAT
1 AAATTTAATTTAATTTTATAT-T
*
32149 AAAATTAA
1 AAATTTAA
32157 GGTCTTTCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
18 4 0.11
19 10 0.26
20 7 0.18
21 7 0.18
22 10 0.26
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (22 bp):
AAATTTAATTTAATTTTATATT
Found at i:32258 original size:24 final size:25
Alignment explanation
Indices: 32226--32286 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
32216 AAGTCATAAT
32226 TATAAAATTTTAATGAAATT-ACAA
1 TATAAAATTTTAATGAAATTCACAA
**
32250 TATAAAATTAAAAT-AAATTCACAA
1 TATAAAATTTTAATGAAATTCACAA
32274 -A-AAAATTTTAATG
1 TATAAAATTTTAATG
32287 CCTCCTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 9 0.29
23 6 0.19
24 16 0.52
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.34
Consensus pattern (25 bp):
TATAAAATTTTAATGAAATTCACAA
Found at i:32666 original size:20 final size:20
Alignment explanation
Indices: 32617--32670 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
32607 ATATATATAA
*
32617 ATAATTTTTTTAATTATTTAT
1 ATAA-TTTTATAATTATTTAT
*
32638 TTAATTTTATAATTATTTAT
1 ATAATTTTATAATTATTTAT
32658 ATATATTTATATA
1 ATA-ATTT-TATA
32671 TATAATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 17 0.61
21 7 0.25
22 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATAATTTTATAATTATTTAT
Found at i:32682 original size:12 final size:12
Alignment explanation
Indices: 32639--32683 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
32629 ATTATTTATT
32639 TAATTTTATA-A
1 TAATTTTATATA
*
32650 TTA-TTTATATA
1 TAATTTTATATA
32661 T-ATTTATATATA
1 TAATTT-TATATA
32673 TAATTTTATAT
1 TAATTTTATAT
32684 TTATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 7 0.24
11 6 0.21
12 12 0.41
13 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAATTTTATATA
Found at i:32688 original size:14 final size:16
Alignment explanation
Indices: 32651--32689 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
32641 ATTTTATAAT
32651 TATTTATATATATTTA
1 TATTTATATATATTTA
*
32667 TATATATA-AT-TTTA
1 TATTTATATATATTTA
32681 TATTTATAT
1 TATTTATAT
32690 TAAAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 11 0.55
15 2 0.10
16 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTATATATATTTA
Found at i:33017 original size:20 final size:19
Alignment explanation
Indices: 32992--33035 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
32982 TAATTTTTAA
32992 TTTTATAAAATTAATCTTAT
1 TTTTAT-AAATTAATCTTAT
*
33012 TTTTATACATTAATCTTAT
1 TTTTATAAATTAATCTTAT
33031 TTTTA
1 TTTTA
33036 ACTTATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTATAAATTAATCTTAT
Found at i:39226 original size:13 final size:13
Alignment explanation
Indices: 39210--39234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39200 TTGTTTAGTT
39210 TTTTTTTTTATTA
1 TTTTTTTTTATTA
39223 TTTTTTTTTATT
1 TTTTTTTTTATT
39235 TTTATAGAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTATTA
Done.