Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167973.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_231, 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: 46201
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:1321 original size:26 final size:26
Alignment explanation
Indices: 1283--1340 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
1273 GATTGATGAA
*
1283 ATGGATTACATTATGGGAAACAATGC
1 ATGGATTACATTATGGGAAACAATAC
*
1309 ATGGATTATATTATGGGAAACAATAC
1 ATGGATTACATTATGGGAAACAATAC
1335 ATGGAT
1 ATGGAT
1341 CTTAGTTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (26 bp):
ATGGATTACATTATGGGAAACAATAC
Found at i:12517 original size:27 final size:27
Alignment explanation
Indices: 12487--12543 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
12477 AACTTAATTG
*
12487 AATGTGGGCAAACATCATTTAATACTA
1 AATGTGCGCAAACATCATTTAATACTA
*
12514 AATGTGCGCTAACATCATTTAATACTA
1 AATGTGCGCAAACATCATTTAATACTA
12541 AAT
1 AAT
12544 ACCTTGATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (27 bp):
AATGTGCGCAAACATCATTTAATACTA
Found at i:16872 original size:23 final size:24
Alignment explanation
Indices: 16846--16911 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 24
16836 TGTTTTGACT
*
16846 TTATTTTTCTTATTTTATTTA-TG
1 TTATTTTTCTTATTTTATTTACTC
16869 TTATTTTGT-TTATTTTTATTTACTC
1 TTATTTT-TCTTA-TTTTATTTACTC
16894 TTATTATTTCTTATTTTA
1 TTATT-TTTCTTATTTTA
16912 AATTGAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 10 0.27
24 10 0.27
25 12 0.32
26 5 0.14
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (24 bp):
TTATTTTTCTTATTTTATTTACTC
Found at i:20395 original size:2 final size:2
Alignment explanation
Indices: 20388--20419 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
20378 TTACTTTATC
*
20388 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20420 GAAAAAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21304 original size:20 final size:20
Alignment explanation
Indices: 21281--21323 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
21271 GAAACTTTTT
21281 CAAA-AATTAAAAATAAAATA
1 CAAAGAATTAAAAA-AAAATA
* *
21301 CAAAGATTTAAAAAACAATA
1 CAAAGAATTAAAAAAAAATA
21321 CAA
1 CAA
21324 TTTTGCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.19
Consensus pattern (20 bp):
CAAAGAATTAAAAAAAAATA
Found at i:23825 original size:22 final size:22
Alignment explanation
Indices: 23791--23854 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 22
23781 GAAATATATT
23791 AATTTTA-ATTTATCTAAAATAA
1 AATTTTATA-TTATCTAAAATAA
*
23813 AATTTTATATTAT-T-TAATAA
1 AATTTTATATTATCTAAAATAA
*
23833 AAATTTAT-TTA-CTAAATATAA
1 AATTTTATATTATCTAAA-ATAA
23854 A
1 A
23855 TATAAGATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
19 4 0.11
20 13 0.37
21 6 0.17
22 11 0.31
23 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTTTATATTATCTAAAATAA
Found at i:24359 original size:6 final size:7
Alignment explanation
Indices: 24338--24362 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
24328 TTTACTATTT
24338 AATTAAA
1 AATTAAA
24345 AATTAAA
1 AATTAAA
24352 AATTAAA
1 AATTAAA
24359 AATT
1 AATT
24363 TATCCTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:28590 original size:32 final size:32
Alignment explanation
Indices: 28554--28618 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
28544 AAGTTTAACC
28554 AAGTAATAACCTAACTTGCATAACAAGAAATA
1 AAGTAATAACCTAACTTGCATAACAAGAAATA
28586 AAGTAATAACCTAACTTGCATAACAAGAAATA
1 AAGTAATAACCTAACTTGCATAACAAGAAATA
28618 A
1 A
28619 TTTAGCTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.54, C:0.15, G:0.09, T:0.22
Consensus pattern (32 bp):
AAGTAATAACCTAACTTGCATAACAAGAAATA
Found at i:30859 original size:52 final size:51
Alignment explanation
Indices: 30802--30931 Score: 129
Period size: 50 Copynumber: 2.5 Consensus size: 51
30792 TTTTTTAGAA
**
30802 TTAATTCCAGAATCAATTGGCATTAAAAATGAT-GTGGAGAGATTGTCGAAAT
1 TTAATTCCAGAATCAATTCACATTAAAAATGATAG-GGAGAGATT-TCGAAAT
* * * * *
30854 TTAATTCTATAATCAATTCACATT-AAATTGATAGGGAGAGATTTTGGAAT
1 TTAATTCCAGAATCAATTCACATTAAAAATGATAGGGAGAGATTTCGAAAT
* * **
30904 TTGATTTCAGAATCAATTTTCATTAAAA
1 TTAATTCCAGAATCAATTCACATTAAAA
30932 CGAAAATAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
50 23 0.37
51 19 0.30
52 21 0.33
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (51 bp):
TTAATTCCAGAATCAATTCACATTAAAAATGATAGGGAGAGATTTCGAAAT
Found at i:31453 original size:23 final size:24
Alignment explanation
Indices: 31427--31492 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 24
31417 TGTTTTGATT
*
31427 TTATTTTTCTTATTTTATTTA-TG
1 TTATTTTTCTTATTTTATTTACTC
31450 TTATTTTGT-TTATTTTTATTTACTC
1 TTATTTT-TCTTA-TTTTATTTACTC
31475 TTATTATTTCTTATTTTA
1 TTATT-TTTCTTATTTTA
31493 AATTGAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 10 0.27
24 10 0.27
25 12 0.32
26 5 0.14
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (24 bp):
TTATTTTTCTTATTTTATTTACTC
Found at i:37969 original size:42 final size:41
Alignment explanation
Indices: 37907--37990 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 41
37897 AACACAGTAT
* * *
37907 TTTCAATTGGAACTGTTCTTTCTCGTATAATAGTGTTTATA
1 TTTCAATCGGAACCGTTCTTTCTCATATAATAGTGTTTATA
37948 TTTCAATCGGAACCGTTTCTTTCTCATATAATAGTGTTTATA
1 TTTCAATCGGAACCG-TTCTTTCTCATATAATAGTGTTTATA
37990 T
1 T
37991 AAAGAAGCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 13 0.33
42 26 0.67
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (41 bp):
TTTCAATCGGAACCGTTCTTTCTCATATAATAGTGTTTATA
Found at i:38391 original size:22 final size:22
Alignment explanation
Indices: 38357--38420 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 22
38347 GAAATATATT
38357 AATTTTA-ATTTATCTAAAATAA
1 AATTTTATA-TTATCTAAAATAA
*
38379 AATTTTATATTAT-T-TAATAA
1 AATTTTATATTATCTAAAATAA
*
38399 AAATTTAT-TTA-CTAAATATAA
1 AATTTTATATTATCTAAA-ATAA
38420 A
1 A
38421 TATAAGATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
19 4 0.11
20 13 0.37
21 6 0.17
22 11 0.31
23 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTTTATATTATCTAAAATAA
Found at i:40471 original size:9 final size:9
Alignment explanation
Indices: 40451--40488 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
40441 TCTTAATTAT
40451 TTTTATCT-
1 TTTTATCTC
40459 TTTTATCTC
1 TTTTATCTC
40468 TTTTTAGTCTC
1 -TTTTA-TCTC
40479 TTTTATCTC
1 TTTTATCTC
40488 T
1 T
40489 CTTTTCACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.30
9 5 0.19
10 10 0.37
11 4 0.15
ACGTcount: A:0.11, C:0.18, G:0.03, T:0.68
Consensus pattern (9 bp):
TTTTATCTC
Found at i:40478 original size:11 final size:10
Alignment explanation
Indices: 40456--40493 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
40446 ATTATTTTTA
40456 TCTTTTTATC
1 TCTTTTTATC
40466 TCTTTTTAGTC
1 TCTTTTTA-TC
40477 TC-TTTTATC
1 TCTTTTTATC
40486 TCTCTTTT
1 TCT-TTTT
40494 CACCCTCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.16
10 13 0.52
11 8 0.32
ACGTcount: A:0.08, C:0.21, G:0.03, T:0.68
Consensus pattern (10 bp):
TCTTTTTATC
Found at i:40484 original size:20 final size:18
Alignment explanation
Indices: 40450--40493 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
40440 TTCTTAATTA
40450 TTTTTATCTTTTTATCTC
1 TTTTTATCTTTTTATCTC
40468 TTTTTAGTCTCTTTTATCTC
1 TTTTTA-TCT-TTTTATCTC
40488 TCTTTT
1 T-TTTT
40494 CACCCTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.26
19 3 0.13
20 10 0.43
21 4 0.17
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTTATCTTTTTATCTC
Found at i:41483 original size:30 final size:30
Alignment explanation
Indices: 41447--41505 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
41437 GTTTAGATAT
41447 AAACCAAATATGATATAAAATGATTATTAC
1 AAACCAAATATGATATAAAATGATTATTAC
41477 AAACCAAATATGATATAAAATGATTATTA
1 AAACCAAATATGATATAAAATGATTATTA
41506 TCCTATCCTC
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:0.54, C:0.08, G:0.07, T:0.31
Consensus pattern (30 bp):
AAACCAAATATGATATAAAATGATTATTAC
Done.