Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168357.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_578, 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: 22529
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:12816 original size:47 final size:47
Alignment explanation
Indices: 12643--12970 Score: 338
Period size: 47 Copynumber: 7.0 Consensus size: 47
12633 CTCGGTTTCG
* * * *
12643 TTAAAGTTGTTGAA-CCTTTATTTAGATGAGCTTTTTCAAGATAAAAATT
1 TTAAAGTTGTT-AAGCCTCTGTTTAGAGGAGCTTTTTCAAGAT--GAATT
* * *
12692 TTAAAATTGTTAAGCCTCTATTTAGAGGAGCTTTTTCAAGATGAATG
1 TTAAAGTTGTTAAGCCTCTGTTTAGAGGAGCTTTTTCAAGATGAATT
*
12739 TTAAAGTT-TTAAGCCTTTGTTTAGAGGAGCTTTTTCAAGATGAATT
1 TTAAAGTTGTTAAGCCTCTGTTTAGAGGAGCTTTTTCAAGATGAATT
* * * * *
12785 TTAAAGTTATTAAGCCTCTGCTTAGAGGAGCTTTTTTAAGATAAAGT
1 TTAAAGTTGTTAAGCCTCTGTTTAGAGGAGCTTTTTCAAGATGAATT
* * *
12832 TTAAAGTTGTTAAGCCTTTGATTA-AGAAGCTTTTTCAAGATGAATTT
1 TTAAAGTTGTTAAGCCTCTGTTTAGAGGAGCTTTTTCAAGATGAA-TT
* ** * * * * *
12879 TTTAAGTCATTGAGCCTTTGCTTAGAGGAGCTTTTCCAAGATGAAAT
1 TTAAAGTTGTTAAGCCTCTGTTTAGAGGAGCTTTTTCAAGATGAATT
* * * * *
12926 TTAAAGTCGTTGAGTCTCTGTTTATAAGAGCTTTTTCAAGATGAA
1 TTAAAGTTGTTAAGCCTCTGTTTAGAGGAGCTTTTTCAAGATGAA
12971 GTACTTAGAG
Statistics
Matches: 238, Mismatches: 37, Indels: 10
0.84 0.13 0.04
Matches are distributed among these distances:
46 60 0.25
47 122 0.51
48 20 0.08
49 36 0.15
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (47 bp):
TTAAAGTTGTTAAGCCTCTGTTTAGAGGAGCTTTTTCAAGATGAATT
Found at i:12911 original size:94 final size:91
Alignment explanation
Indices: 12643--12970 Score: 331
Period size: 93 Copynumber: 3.5 Consensus size: 91
12633 CTCGGTTTCG
* * **
12643 TTAAAGTTGTTGAA-CCTTT-ATTTAGATGAGCTTTTTCAAGATAAAAATTTTAAAATTGTTAAG
1 TTAAAGTTGTT-AAGCCTTTGA-TTA-A-GAGCTTTTTCAAGAT--GAATTTTAAAGTCATTAAG
** *
12706 CCTCTATTTAGAGGAGCTTTTTCAAGATGAAT
60 CCTCTGCTTAGAGGAGCTTTTTCAAGATAAAT
* *
12738 GTTAAAGTT-TTAAGCCTTTGTTTAGAGGAGCTTTTTCAAGATGAATTTTAAAGTTATTAAGCCT
1 -TTAAAGTTGTTAAGCCTTTGATTA-A-GAGCTTTTTCAAGATGAATTTTAAAGTCATTAAGCCT
*
12802 CTGCTTAGAGGAGCTTTTTTAAGATAAAGT
63 CTGCTTAGAGGAGCTTTTTCAAGATAAA-T
* * *
12832 TTAAAGTTGTTAAGCCTTTGATTAAGAAGCTTTTTCAAGATGAATTTTTTAAGTCATTGAGCCTT
1 TTAAAGTTGTTAAGCCTTTGATTAAG-AGCTTTTTCAAGATGAA-TTTTAAAGTCATTAAGCCTC
*
12897 TGCTTAGAGGAGCTTTTCCAAGATGAAAT
64 TGCTTAGAGGAGCTTTTTCAAGAT-AAAT
* * *
12926 TTAAAGTCGTTGAGTCTCTGTTTA-TAAGAGCTTTTTCAAGATGAA
1 TTAAAGTTGTTAAG-C-CT-TTGATTAAGAGCTTTTTCAAGATGAA
12971 GTACTTAGAG
Statistics
Matches: 203, Mismatches: 19, Indels: 21
0.84 0.08 0.09
Matches are distributed among these distances:
92 1 0.00
93 69 0.34
94 68 0.33
95 48 0.24
96 14 0.07
97 3 0.01
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (91 bp):
TTAAAGTTGTTAAGCCTTTGATTAAGAGCTTTTTCAAGATGAATTTTAAAGTCATTAAGCCTCTG
CTTAGAGGAGCTTTTTCAAGATAAAT
Found at i:13059 original size:48 final size:47
Alignment explanation
Indices: 12974--13124 Score: 187
Period size: 48 Copynumber: 3.2 Consensus size: 47
12964 AGATGAAGTA
* *
12974 CTTAGAGAAGATTTTTTCAA-ATGAAGTTTAAAGTTGTTGAGCCTTTG
1 CTTAGAGGAGA-TTTTTCAAGATGAATTTTAAAGTTGTTGAGCCTTTG
* * * * *
13021 TTTATAGGAGCTTTTTCAAGATAGATTTTTAAAATTGTTGAGCCTTTG
1 CTTAGAGGAGATTTTTCAAGAT-GAATTTTAAAGTTGTTGAGCCTTTG
* * *
13069 CTCAGAGCAGATTTTTCAAGATGAATTTTAAAGTTGTTGAGCTTTTG
1 CTTAGAGGAGATTTTTCAAGATGAATTTTAAAGTTGTTGAGCCTTTG
13116 CTTAGAGGA
1 CTTAGAGGA
13125 ACCTTTTTAA
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
46 8 0.09
47 38 0.45
48 39 0.46
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.41
Consensus pattern (47 bp):
CTTAGAGGAGATTTTTCAAGATGAATTTTAAAGTTGTTGAGCCTTTG
Found at i:13260 original size:87 final size:88
Alignment explanation
Indices: 13104--13319 Score: 249
Period size: 87 Copynumber: 2.5 Consensus size: 88
13094 TTTTAAAGTT
* * * * * *
13104 GTTGAGCTTTTGCTTAGAGGAACCTTTTTAAATTTTCAAAATGTTGTTGAGCCTCTGCCTAGATG
1 GTTGAGCTTCTGCTTAGAGGAACC-TTTTAAATTTTTAAAATGTCGTTAAGCCTCTGCCTAAAAG
*
13169 AGCCTCTTTAAATTTTCAAAAATC
65 AGCCTCTTTAAAATTTCAAAAATC
* *
13193 GTTGAG-TCTCTGTTTAGAGGAACCTTTTAAATTTTTAAAA-GTCGTTAAGCCTCTGCTTAAAAG
1 GTTGAGCT-TCTGCTTAGAGGAACCTTTTAAATTTTTAAAATGTCGTTAAGCCTCTGCCTAAAAG
* * *
13256 AGCCTTTTTAAAATTTCAAAAGTT
65 AGCCTCTTTAAAATTTCAAAAATC
** *
13280 GTTGAGCTTCTGCTTA-AATAAGCTTTTTAAATTTTTAAAA
1 GTTGAGCTTCTGCTTAGAGGAA-CCTTTTAAATTTTTAAAA
13320 AAGTTATTGA
Statistics
Matches: 108, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
86 3 0.03
87 68 0.63
88 17 0.16
89 20 0.19
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (88 bp):
GTTGAGCTTCTGCTTAGAGGAACCTTTTAAATTTTTAAAATGTCGTTAAGCCTCTGCCTAAAAGA
GCCTCTTTAAAATTTCAAAAATC
Found at i:13292 original size:44 final size:44
Alignment explanation
Indices: 13098--13319 Score: 209
Period size: 44 Copynumber: 5.1 Consensus size: 44
13088 GATGAATTTT
* * *
13098 AAAGTTGTTGAGCTTTTGCTTAGAGGAACCTTTTTAAATTTTCA
1 AAAGTTGTTGAGCTTCTGCTTAGAAGAGCCTTTTTAAATTTTCA
* * * *
13142 AAATGTTGTTGAGCCTCTGCCTAGATGAGCCTCTTTAAATTTTCA
1 AAA-GTTGTTGAGCTTCTGCTTAGAAGAGCCTTTTTAAATTTTCA
* * * * * *
13187 AAAATCGTTGAG-TCTCTGTTTAGAGGAACC-TTTTAAATTTTTA
1 AAAGTTGTTGAGCT-TCTGCTTAGAAGAGCCTTTTTAAATTTTCA
* * * * *
13230 AAAGTCGTTAAGCCTCTGCTTAAAAGAGCCTTTTTAAAATTTCA
1 AAAGTTGTTGAGCTTCTGCTTAGAAGAGCCTTTTTAAATTTTCA
* *
13274 AAAGTTGTTGAGCTTCTGCTTA-AATAAG-CTTTTTAAATTTTTA
1 AAAGTTGTTGAGCTTCTGCTTAGAA-GAGCCTTTTTAAATTTTCA
13317 AAA
1 AAA
13320 AAGTTATTGA
Statistics
Matches: 143, Mismatches: 30, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
43 51 0.36
44 54 0.38
45 38 0.27
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (44 bp):
AAAGTTGTTGAGCTTCTGCTTAGAAGAGCCTTTTTAAATTTTCA
Found at i:13490 original size:3 final size:3
Alignment explanation
Indices: 13478--13552 Score: 92
Period size: 3 Copynumber: 27.3 Consensus size: 3
13468 TACCATTTTG
13478 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT T-T T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
13522 T-T TTT TAT TAT T-T TAT TAT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
13553 TTTTATTTTT
Statistics
Matches: 65, Mismatches: 1, Indels: 12
0.83 0.01 0.15
Matches are distributed among these distances:
2 14 0.22
3 51 0.78
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:13496 original size:9 final size:9
Alignment explanation
Indices: 13478--13552 Score: 92
Period size: 8 Copynumber: 9.1 Consensus size: 9
13468 TACCATTTTG
13478 TATT-TTAT
1 TATTATTAT
13486 TATTATTAT
1 TATTATTAT
13495 TATTATTAT
1 TATTATTAT
13504 TATTATTA-
1 TATTATTAT
13512 TATT-TT-T
1 TATTATTAT
*
13519 TATT-TTTT
1 TATTATTAT
13527 TATTATT-T
1 TATTATTAT
13535 TATTATTAT
1 TATTATTAT
13544 T-TTATTAT
1 TATTATTAT
13552 T
1 T
13553 TTTTATTTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
7 8 0.13
8 29 0.47
9 25 0.40
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TATTATTAT
Found at i:13560 original size:15 final size:15
Alignment explanation
Indices: 13472--13566 Score: 79
Period size: 15 Copynumber: 6.1 Consensus size: 15
13462 TATAAATACC
*
13472 ATTTTGTATTTTATT
1 ATTTTTTATTTTATT
13487 ATTATTATTATTATTATT
1 ATT-TT-TTATT-TTATT
*
13505 ATTATTATATTTT-TT
1 ATT-TTTTATTTTATT
13520 ATTTTTTTATTATT-TT
1 A-TTTTTTATT-TTATT
*
13536 A-TTATTATTTTATT
1 ATTTTTTATTTTATT
*
13550 ATTTTTTATTTTTTT
1 ATTTTTTATTTTATT
13565 AT
1 AT
13567 CTTTCTTTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
13 2 0.03
14 10 0.15
15 25 0.37
16 11 0.16
17 8 0.12
18 11 0.16
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.75
Consensus pattern (15 bp):
ATTTTTTATTTTATT
Found at i:13563 original size:9 final size:9
Alignment explanation
Indices: 13480--13564 Score: 57
Period size: 9 Copynumber: 9.3 Consensus size: 9
13470 CCATTTTGTA
*
13480 TTTTATTAT
1 TTTTATTTT
* *
13489 TATTATTAT
1 TTTTATTTT
* *
13498 TATTATTAT
1 TTTTATTTT
* *
13507 TATTATATT
1 TTTTATTTT
13516 TTTTA-TTT
1 TTTTATTTT
13524 TTTTATTATT
1 TTTTATT-TT
*
13534 TTATTA-TTA
1 TT-TTATTTT
13543 TTTTATTATT
1 TTTTATT-TT
13553 TTTTATTTT
1 TTTTATTTT
13562 TTT
1 TTT
13565 ATCTTTCTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
8 10 0.16
9 38 0.59
10 13 0.20
11 3 0.05
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTATTTT
Found at i:13564 original size:18 final size:18
Alignment explanation
Indices: 13472--13566 Score: 100
Period size: 18 Copynumber: 4.9 Consensus size: 18
13462 TATAAATACC
* *
13472 ATTTTGTATTTTATTATT
1 ATTTTTTATTTTTTTATT
*
13490 ATTATTATTATTATTATTATTAT
1 ATT-TT-TTATT-TTTTTA-T-T
13513 ATTTTTTATTTTTTTATT
1 ATTTTTTATTTTTTTATT
*
13531 ATTTTATTATTATTTTATT
1 ATTTT-TTATTTTTTTATT
13550 ATTTTTTATTTTTTTAT
1 ATTTTTTATTTTTTTAT
13567 CTTTCTTTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
18 20 0.30
19 20 0.30
20 9 0.13
21 11 0.16
22 3 0.04
23 4 0.06
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.75
Consensus pattern (18 bp):
ATTTTTTATTTTTTTATT
Found at i:19719 original size:2 final size:2
Alignment explanation
Indices: 19712--19751 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
19702 TTCTATATTC
19712 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19752 CTGGAAAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20072 original size:2 final size:2
Alignment explanation
Indices: 20065--20091 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20055 CAAATGAGGA
20065 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20092 ATAGTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.