Multiple sequence alignment - TraesCS3A01G505900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G505900 chr3A 100.000 5957 0 0 1 5957 727563861 727569817 0.000000e+00 11001.0
1 TraesCS3A01G505900 chr3A 95.949 5184 184 13 793 5957 446315145 446309969 0.000000e+00 8386.0
2 TraesCS3A01G505900 chr3A 96.038 4796 156 8 1168 5957 178138442 178143209 0.000000e+00 7773.0
3 TraesCS3A01G505900 chr3A 94.969 795 39 1 1 794 408153377 408152583 0.000000e+00 1245.0
4 TraesCS3A01G505900 chr3A 94.228 797 44 2 1 795 522507570 522506774 0.000000e+00 1216.0
5 TraesCS3A01G505900 chr3A 94.095 796 46 1 1 795 322601018 322601813 0.000000e+00 1208.0
6 TraesCS3A01G505900 chr6A 95.845 5198 182 9 793 5957 60187611 60182415 0.000000e+00 8371.0
7 TraesCS3A01G505900 chr6A 95.801 643 26 1 155 796 200284479 200285121 0.000000e+00 1037.0
8 TraesCS3A01G505900 chr6A 92.605 595 35 9 207 796 253642831 253642241 0.000000e+00 846.0
9 TraesCS3A01G505900 chr6A 93.543 573 30 7 226 794 253662656 253662087 0.000000e+00 846.0
10 TraesCS3A01G505900 chr6A 92.079 606 41 7 193 794 343603439 343604041 0.000000e+00 846.0
11 TraesCS3A01G505900 chr6A 92.967 583 35 6 214 794 95611035 95610457 0.000000e+00 845.0
12 TraesCS3A01G505900 chr6A 91.680 613 38 12 190 794 39613536 39612929 0.000000e+00 837.0
13 TraesCS3A01G505900 chr6A 92.637 584 36 7 214 795 95603516 95602938 0.000000e+00 833.0
14 TraesCS3A01G505900 chr6A 88.336 703 62 19 102 794 245249266 245249958 0.000000e+00 826.0
15 TraesCS3A01G505900 chr6A 85.894 716 76 16 87 794 33429229 33429927 0.000000e+00 739.0
16 TraesCS3A01G505900 chr6A 88.350 103 1 2 43 144 384352156 384352064 4.880000e-21 113.0
17 TraesCS3A01G505900 chr6A 87.379 103 2 2 43 144 457648608 457648516 2.270000e-19 108.0
18 TraesCS3A01G505900 chr6A 85.437 103 4 2 43 144 457641046 457640954 4.910000e-16 97.1
19 TraesCS3A01G505900 chr5A 95.783 5193 187 17 793 5957 538776511 538781699 0.000000e+00 8347.0
20 TraesCS3A01G505900 chr5A 94.855 5170 207 11 793 5957 555585185 555580070 0.000000e+00 8019.0
21 TraesCS3A01G505900 chr5A 95.171 4514 195 13 793 5292 34675868 34680372 0.000000e+00 7107.0
22 TraesCS3A01G505900 chr5A 93.421 608 35 5 190 794 332147180 332146575 0.000000e+00 896.0
23 TraesCS3A01G505900 chr5A 93.279 610 36 5 190 796 332139924 332139317 0.000000e+00 894.0
24 TraesCS3A01G505900 chr7A 95.268 5199 210 11 793 5957 484188218 484193414 0.000000e+00 8205.0
25 TraesCS3A01G505900 chr7A 94.088 795 46 1 1 794 479358625 479359419 0.000000e+00 1206.0
26 TraesCS3A01G505900 chr7A 94.051 790 38 2 1 789 479351479 479352260 0.000000e+00 1190.0
27 TraesCS3A01G505900 chr7A 93.601 797 47 4 1 794 534207780 534208575 0.000000e+00 1186.0
28 TraesCS3A01G505900 chr7A 92.965 796 50 3 1 794 534215090 534215881 0.000000e+00 1155.0
29 TraesCS3A01G505900 chr3B 95.194 5181 215 10 794 5957 706223319 706228482 0.000000e+00 8157.0
30 TraesCS3A01G505900 chr3B 91.362 3751 295 22 1545 5288 178572434 178568706 0.000000e+00 5105.0
31 TraesCS3A01G505900 chr3B 93.693 761 46 2 793 1553 751841724 751840966 0.000000e+00 1138.0
32 TraesCS3A01G505900 chr4B 95.170 5197 192 13 793 5957 665839119 665833950 0.000000e+00 8152.0
33 TraesCS3A01G505900 chr4B 90.593 3253 241 21 793 4015 427281176 427284393 0.000000e+00 4252.0
34 TraesCS3A01G505900 chr4B 91.153 746 51 5 793 1527 161605540 161606281 0.000000e+00 998.0
35 TraesCS3A01G505900 chr4B 91.897 580 42 5 218 794 17638921 17638344 0.000000e+00 806.0
36 TraesCS3A01G505900 chr4B 91.207 580 46 5 218 794 17646356 17645779 0.000000e+00 784.0
37 TraesCS3A01G505900 chr4B 92.871 533 29 7 268 794 652195162 652195691 0.000000e+00 765.0
38 TraesCS3A01G505900 chr4B 90.361 581 48 8 218 794 61089602 61089026 0.000000e+00 756.0
39 TraesCS3A01G505900 chr4B 89.673 581 52 8 218 794 61096651 61096075 0.000000e+00 734.0
40 TraesCS3A01G505900 chr4B 89.744 546 50 5 793 1338 554211536 554210997 0.000000e+00 693.0
41 TraesCS3A01G505900 chr1A 94.846 5180 225 14 793 5957 423678075 423683227 0.000000e+00 8048.0
42 TraesCS3A01G505900 chr1A 95.335 3494 134 11 793 4257 494793573 494790080 0.000000e+00 5522.0
43 TraesCS3A01G505900 chr1A 95.127 2832 109 9 793 3596 472432561 472435391 0.000000e+00 4438.0
44 TraesCS3A01G505900 chr1A 91.656 755 47 9 43 794 513341387 513340646 0.000000e+00 1031.0
45 TraesCS3A01G505900 chr1A 90.993 755 52 9 43 794 513333971 513333230 0.000000e+00 1003.0
46 TraesCS3A01G505900 chr1A 94.881 547 26 2 249 794 74621379 74620834 0.000000e+00 854.0
47 TraesCS3A01G505900 chr1A 92.217 591 40 6 206 794 497133501 497132915 0.000000e+00 832.0
48 TraesCS3A01G505900 chr1A 92.982 570 34 6 225 792 191793957 191794522 0.000000e+00 826.0
49 TraesCS3A01G505900 chr1A 92.150 586 39 7 212 794 472097556 472096975 0.000000e+00 821.0
50 TraesCS3A01G505900 chr1A 92.110 583 41 5 214 794 329273128 329273707 0.000000e+00 817.0
51 TraesCS3A01G505900 chr1A 92.361 576 38 6 219 792 497125920 497125349 0.000000e+00 815.0
52 TraesCS3A01G505900 chr1A 91.104 607 44 10 193 794 275577978 275578579 0.000000e+00 813.0
53 TraesCS3A01G505900 chr1A 91.104 607 45 9 193 794 275585576 275586178 0.000000e+00 813.0
54 TraesCS3A01G505900 chr1A 90.554 614 43 14 190 794 370754067 370753460 0.000000e+00 798.0
55 TraesCS3A01G505900 chr2A 94.852 5186 186 29 793 5946 701035897 701041033 0.000000e+00 8022.0
56 TraesCS3A01G505900 chr2A 94.717 795 41 1 1 794 183748066 183748860 0.000000e+00 1234.0
57 TraesCS3A01G505900 chr2A 94.214 795 45 1 1 794 183740671 183741465 0.000000e+00 1212.0
58 TraesCS3A01G505900 chr5B 94.696 4487 198 17 793 5249 130896876 130901352 0.000000e+00 6931.0
59 TraesCS3A01G505900 chr5B 92.335 3692 257 21 1545 5232 194193967 194197636 0.000000e+00 5227.0
60 TraesCS3A01G505900 chr5B 92.785 596 31 11 206 794 246663946 246664536 0.000000e+00 852.0
61 TraesCS3A01G505900 chr5B 91.993 612 37 11 190 794 237152572 237151966 0.000000e+00 848.0
62 TraesCS3A01G505900 chr5B 91.220 615 40 13 190 796 237145150 237144542 0.000000e+00 824.0
63 TraesCS3A01G505900 chr7B 91.020 4432 353 33 1545 5957 697885351 697880946 0.000000e+00 5938.0
64 TraesCS3A01G505900 chr4A 95.369 799 36 1 1 798 467363918 467363120 0.000000e+00 1269.0
65 TraesCS3A01G505900 chr4A 95.472 795 35 1 1 794 467371018 467370224 0.000000e+00 1267.0
66 TraesCS3A01G505900 chr4A 93.586 608 35 4 190 794 507139260 507139866 0.000000e+00 904.0
67 TraesCS3A01G505900 chr4A 92.007 613 39 10 187 794 248914224 248913617 0.000000e+00 852.0
68 TraesCS3A01G505900 chr4A 88.201 695 63 19 110 794 595515975 595515290 0.000000e+00 811.0
69 TraesCS3A01G505900 chr4A 86.236 712 77 13 89 794 187622664 187621968 0.000000e+00 752.0
70 TraesCS3A01G505900 chrUn 89.134 681 50 22 126 794 321964162 321964830 0.000000e+00 826.0
71 TraesCS3A01G505900 chrUn 92.670 573 37 5 226 795 252486225 252486795 0.000000e+00 821.0
72 TraesCS3A01G505900 chrUn 91.581 582 40 8 218 794 295086558 295085981 0.000000e+00 795.0
73 TraesCS3A01G505900 chrUn 91.581 582 40 8 218 794 467179572 467178995 0.000000e+00 795.0
74 TraesCS3A01G505900 chrUn 91.207 580 45 6 219 794 237536950 237536373 0.000000e+00 784.0
75 TraesCS3A01G505900 chrUn 92.969 512 35 1 284 794 438628187 438628698 0.000000e+00 745.0
76 TraesCS3A01G505900 chrUn 92.395 526 32 8 274 794 392121524 392121002 0.000000e+00 743.0
77 TraesCS3A01G505900 chrUn 89.775 577 54 5 220 794 461773696 461773123 0.000000e+00 734.0
78 TraesCS3A01G505900 chrUn 93.648 488 29 2 308 794 292213190 292213676 0.000000e+00 728.0
79 TraesCS3A01G505900 chrUn 91.908 519 37 5 279 794 451301954 451301438 0.000000e+00 721.0
80 TraesCS3A01G505900 chrUn 92.246 374 24 4 793 1165 378659339 378659708 5.290000e-145 525.0
81 TraesCS3A01G505900 chrUn 85.476 420 53 6 793 1211 76664467 76664879 1.190000e-116 431.0
82 TraesCS3A01G505900 chrUn 84.524 420 56 8 793 1211 9432386 9432797 2.000000e-109 407.0
83 TraesCS3A01G505900 chrUn 82.775 418 63 8 793 1209 9397002 9396593 1.220000e-96 364.0
84 TraesCS3A01G505900 chrUn 84.350 377 38 21 89 454 371592428 371592794 3.420000e-92 350.0
85 TraesCS3A01G505900 chrUn 80.769 442 65 13 102 536 475969583 475969155 1.600000e-85 327.0
86 TraesCS3A01G505900 chr6D 76.190 630 123 26 104 723 54520358 54520970 2.090000e-79 307.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G505900 chr3A 727563861 727569817 5956 False 11001 11001 100.000 1 5957 1 chr3A.!!$F3 5956
1 TraesCS3A01G505900 chr3A 446309969 446315145 5176 True 8386 8386 95.949 793 5957 1 chr3A.!!$R2 5164
2 TraesCS3A01G505900 chr3A 178138442 178143209 4767 False 7773 7773 96.038 1168 5957 1 chr3A.!!$F1 4789
3 TraesCS3A01G505900 chr3A 408152583 408153377 794 True 1245 1245 94.969 1 794 1 chr3A.!!$R1 793
4 TraesCS3A01G505900 chr3A 522506774 522507570 796 True 1216 1216 94.228 1 795 1 chr3A.!!$R3 794
5 TraesCS3A01G505900 chr3A 322601018 322601813 795 False 1208 1208 94.095 1 795 1 chr3A.!!$F2 794
6 TraesCS3A01G505900 chr6A 60182415 60187611 5196 True 8371 8371 95.845 793 5957 1 chr6A.!!$R2 5164
7 TraesCS3A01G505900 chr6A 200284479 200285121 642 False 1037 1037 95.801 155 796 1 chr6A.!!$F2 641
8 TraesCS3A01G505900 chr6A 253642241 253642831 590 True 846 846 92.605 207 796 1 chr6A.!!$R5 589
9 TraesCS3A01G505900 chr6A 253662087 253662656 569 True 846 846 93.543 226 794 1 chr6A.!!$R6 568
10 TraesCS3A01G505900 chr6A 343603439 343604041 602 False 846 846 92.079 193 794 1 chr6A.!!$F4 601
11 TraesCS3A01G505900 chr6A 95610457 95611035 578 True 845 845 92.967 214 794 1 chr6A.!!$R4 580
12 TraesCS3A01G505900 chr6A 39612929 39613536 607 True 837 837 91.680 190 794 1 chr6A.!!$R1 604
13 TraesCS3A01G505900 chr6A 95602938 95603516 578 True 833 833 92.637 214 795 1 chr6A.!!$R3 581
14 TraesCS3A01G505900 chr6A 245249266 245249958 692 False 826 826 88.336 102 794 1 chr6A.!!$F3 692
15 TraesCS3A01G505900 chr6A 33429229 33429927 698 False 739 739 85.894 87 794 1 chr6A.!!$F1 707
16 TraesCS3A01G505900 chr5A 538776511 538781699 5188 False 8347 8347 95.783 793 5957 1 chr5A.!!$F2 5164
17 TraesCS3A01G505900 chr5A 555580070 555585185 5115 True 8019 8019 94.855 793 5957 1 chr5A.!!$R3 5164
18 TraesCS3A01G505900 chr5A 34675868 34680372 4504 False 7107 7107 95.171 793 5292 1 chr5A.!!$F1 4499
19 TraesCS3A01G505900 chr5A 332146575 332147180 605 True 896 896 93.421 190 794 1 chr5A.!!$R2 604
20 TraesCS3A01G505900 chr5A 332139317 332139924 607 True 894 894 93.279 190 796 1 chr5A.!!$R1 606
21 TraesCS3A01G505900 chr7A 484188218 484193414 5196 False 8205 8205 95.268 793 5957 1 chr7A.!!$F3 5164
22 TraesCS3A01G505900 chr7A 479358625 479359419 794 False 1206 1206 94.088 1 794 1 chr7A.!!$F2 793
23 TraesCS3A01G505900 chr7A 479351479 479352260 781 False 1190 1190 94.051 1 789 1 chr7A.!!$F1 788
24 TraesCS3A01G505900 chr7A 534207780 534208575 795 False 1186 1186 93.601 1 794 1 chr7A.!!$F4 793
25 TraesCS3A01G505900 chr7A 534215090 534215881 791 False 1155 1155 92.965 1 794 1 chr7A.!!$F5 793
26 TraesCS3A01G505900 chr3B 706223319 706228482 5163 False 8157 8157 95.194 794 5957 1 chr3B.!!$F1 5163
27 TraesCS3A01G505900 chr3B 178568706 178572434 3728 True 5105 5105 91.362 1545 5288 1 chr3B.!!$R1 3743
28 TraesCS3A01G505900 chr3B 751840966 751841724 758 True 1138 1138 93.693 793 1553 1 chr3B.!!$R2 760
29 TraesCS3A01G505900 chr4B 665833950 665839119 5169 True 8152 8152 95.170 793 5957 1 chr4B.!!$R6 5164
30 TraesCS3A01G505900 chr4B 427281176 427284393 3217 False 4252 4252 90.593 793 4015 1 chr4B.!!$F2 3222
31 TraesCS3A01G505900 chr4B 161605540 161606281 741 False 998 998 91.153 793 1527 1 chr4B.!!$F1 734
32 TraesCS3A01G505900 chr4B 17638344 17638921 577 True 806 806 91.897 218 794 1 chr4B.!!$R1 576
33 TraesCS3A01G505900 chr4B 17645779 17646356 577 True 784 784 91.207 218 794 1 chr4B.!!$R2 576
34 TraesCS3A01G505900 chr4B 652195162 652195691 529 False 765 765 92.871 268 794 1 chr4B.!!$F3 526
35 TraesCS3A01G505900 chr4B 61089026 61089602 576 True 756 756 90.361 218 794 1 chr4B.!!$R3 576
36 TraesCS3A01G505900 chr4B 61096075 61096651 576 True 734 734 89.673 218 794 1 chr4B.!!$R4 576
37 TraesCS3A01G505900 chr4B 554210997 554211536 539 True 693 693 89.744 793 1338 1 chr4B.!!$R5 545
38 TraesCS3A01G505900 chr1A 423678075 423683227 5152 False 8048 8048 94.846 793 5957 1 chr1A.!!$F5 5164
39 TraesCS3A01G505900 chr1A 494790080 494793573 3493 True 5522 5522 95.335 793 4257 1 chr1A.!!$R4 3464
40 TraesCS3A01G505900 chr1A 472432561 472435391 2830 False 4438 4438 95.127 793 3596 1 chr1A.!!$F6 2803
41 TraesCS3A01G505900 chr1A 513340646 513341387 741 True 1031 1031 91.656 43 794 1 chr1A.!!$R8 751
42 TraesCS3A01G505900 chr1A 513333230 513333971 741 True 1003 1003 90.993 43 794 1 chr1A.!!$R7 751
43 TraesCS3A01G505900 chr1A 74620834 74621379 545 True 854 854 94.881 249 794 1 chr1A.!!$R1 545
44 TraesCS3A01G505900 chr1A 497132915 497133501 586 True 832 832 92.217 206 794 1 chr1A.!!$R6 588
45 TraesCS3A01G505900 chr1A 191793957 191794522 565 False 826 826 92.982 225 792 1 chr1A.!!$F1 567
46 TraesCS3A01G505900 chr1A 472096975 472097556 581 True 821 821 92.150 212 794 1 chr1A.!!$R3 582
47 TraesCS3A01G505900 chr1A 329273128 329273707 579 False 817 817 92.110 214 794 1 chr1A.!!$F4 580
48 TraesCS3A01G505900 chr1A 497125349 497125920 571 True 815 815 92.361 219 792 1 chr1A.!!$R5 573
49 TraesCS3A01G505900 chr1A 275577978 275578579 601 False 813 813 91.104 193 794 1 chr1A.!!$F2 601
50 TraesCS3A01G505900 chr1A 275585576 275586178 602 False 813 813 91.104 193 794 1 chr1A.!!$F3 601
51 TraesCS3A01G505900 chr1A 370753460 370754067 607 True 798 798 90.554 190 794 1 chr1A.!!$R2 604
52 TraesCS3A01G505900 chr2A 701035897 701041033 5136 False 8022 8022 94.852 793 5946 1 chr2A.!!$F3 5153
53 TraesCS3A01G505900 chr2A 183748066 183748860 794 False 1234 1234 94.717 1 794 1 chr2A.!!$F2 793
54 TraesCS3A01G505900 chr2A 183740671 183741465 794 False 1212 1212 94.214 1 794 1 chr2A.!!$F1 793
55 TraesCS3A01G505900 chr5B 130896876 130901352 4476 False 6931 6931 94.696 793 5249 1 chr5B.!!$F1 4456
56 TraesCS3A01G505900 chr5B 194193967 194197636 3669 False 5227 5227 92.335 1545 5232 1 chr5B.!!$F2 3687
57 TraesCS3A01G505900 chr5B 246663946 246664536 590 False 852 852 92.785 206 794 1 chr5B.!!$F3 588
58 TraesCS3A01G505900 chr5B 237151966 237152572 606 True 848 848 91.993 190 794 1 chr5B.!!$R2 604
59 TraesCS3A01G505900 chr5B 237144542 237145150 608 True 824 824 91.220 190 796 1 chr5B.!!$R1 606
60 TraesCS3A01G505900 chr7B 697880946 697885351 4405 True 5938 5938 91.020 1545 5957 1 chr7B.!!$R1 4412
61 TraesCS3A01G505900 chr4A 467363120 467363918 798 True 1269 1269 95.369 1 798 1 chr4A.!!$R3 797
62 TraesCS3A01G505900 chr4A 467370224 467371018 794 True 1267 1267 95.472 1 794 1 chr4A.!!$R4 793
63 TraesCS3A01G505900 chr4A 507139260 507139866 606 False 904 904 93.586 190 794 1 chr4A.!!$F1 604
64 TraesCS3A01G505900 chr4A 248913617 248914224 607 True 852 852 92.007 187 794 1 chr4A.!!$R2 607
65 TraesCS3A01G505900 chr4A 595515290 595515975 685 True 811 811 88.201 110 794 1 chr4A.!!$R5 684
66 TraesCS3A01G505900 chr4A 187621968 187622664 696 True 752 752 86.236 89 794 1 chr4A.!!$R1 705
67 TraesCS3A01G505900 chrUn 321964162 321964830 668 False 826 826 89.134 126 794 1 chrUn.!!$F5 668
68 TraesCS3A01G505900 chrUn 252486225 252486795 570 False 821 821 92.670 226 795 1 chrUn.!!$F3 569
69 TraesCS3A01G505900 chrUn 295085981 295086558 577 True 795 795 91.581 218 794 1 chrUn.!!$R3 576
70 TraesCS3A01G505900 chrUn 467178995 467179572 577 True 795 795 91.581 218 794 1 chrUn.!!$R7 576
71 TraesCS3A01G505900 chrUn 237536373 237536950 577 True 784 784 91.207 219 794 1 chrUn.!!$R2 575
72 TraesCS3A01G505900 chrUn 438628187 438628698 511 False 745 745 92.969 284 794 1 chrUn.!!$F8 510
73 TraesCS3A01G505900 chrUn 392121002 392121524 522 True 743 743 92.395 274 794 1 chrUn.!!$R4 520
74 TraesCS3A01G505900 chrUn 461773123 461773696 573 True 734 734 89.775 220 794 1 chrUn.!!$R6 574
75 TraesCS3A01G505900 chrUn 451301438 451301954 516 True 721 721 91.908 279 794 1 chrUn.!!$R5 515
76 TraesCS3A01G505900 chr6D 54520358 54520970 612 False 307 307 76.190 104 723 1 chr6D.!!$F1 619

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
938 963 1.135575 GGTGAAAATGCAGAGCCTTCG 60.136 52.381 0.00 0.00 0.00 3.79 F
1603 1706 1.339055 GCCATGACTGGACAGCTACAA 60.339 52.381 0.00 0.00 46.37 2.41 F
1990 2096 1.577468 TGAAACTGACGACAACGCAT 58.423 45.000 0.00 0.00 43.96 4.73 F
2864 2976 2.569853 AGACACGGATGGGTACATTTGA 59.430 45.455 0.00 0.00 37.47 2.69 F
4323 4485 0.531200 AGGCGAGTACTACTGCCAAC 59.469 55.000 26.27 7.94 41.60 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 1878 1.898154 GCAGTAGATGTCCCCGTGT 59.102 57.895 0.0 0.0 0.00 4.49 R
3243 3355 1.675310 CATTGAACCCCTCGCTGCA 60.675 57.895 0.0 0.0 0.00 4.41 R
3359 3471 2.357034 GCCGTGGTCGCTTCTTGA 60.357 61.111 0.0 0.0 35.54 3.02 R
4405 4567 0.107410 TCGCCGCCTTATGAAATGGT 60.107 50.000 0.0 0.0 0.00 3.55 R
5858 6159 0.249741 GTGGCGTTACACACCAGACT 60.250 55.000 0.0 0.0 40.99 3.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
294 310 2.776659 CGAAATTTCGGGGAGGGTC 58.223 57.895 28.73 0.00 46.30 4.46
345 363 2.554893 GTCCAAATGAGGTGCGGTTTTA 59.445 45.455 0.00 0.00 0.00 1.52
551 573 2.048222 CCGCTTGGCAAGACTCGA 60.048 61.111 30.45 0.00 0.00 4.04
635 657 1.139520 GAAGCGCCGGAATGCAAAT 59.860 52.632 5.05 0.00 0.00 2.32
817 840 5.422331 AGCCAACTTCAACTAGCTAGTATGA 59.578 40.000 26.29 24.52 34.99 2.15
874 898 3.715628 ACTGCTGTGGACATGAAAAAC 57.284 42.857 0.00 0.00 0.00 2.43
938 963 1.135575 GGTGAAAATGCAGAGCCTTCG 60.136 52.381 0.00 0.00 0.00 3.79
997 1022 2.271821 TCGACGTCATACACATGTGG 57.728 50.000 28.64 12.14 33.57 4.17
1064 1092 6.942576 AGGAGCATAGTTGACAACTACAATTT 59.057 34.615 26.37 10.71 45.99 1.82
1122 1150 4.000928 ACTACACTTCTCATCCCTGGAT 57.999 45.455 0.00 0.00 34.81 3.41
1398 1498 2.327343 GGTAACCCGGCAAACGTCC 61.327 63.158 0.00 0.00 42.24 4.79
1447 1547 4.139786 GGAGCATGTCATTATGGTGTCAT 58.860 43.478 0.00 0.00 38.76 3.06
1603 1706 1.339055 GCCATGACTGGACAGCTACAA 60.339 52.381 0.00 0.00 46.37 2.41
1653 1756 3.505680 ACGGCTTGCTGTTTGAAATGATA 59.494 39.130 0.63 0.00 0.00 2.15
1772 1878 2.882927 ACAACTACACTGAACAGCGA 57.117 45.000 1.46 0.00 0.00 4.93
1792 1898 2.279517 CGGGGACATCTACTGCGC 60.280 66.667 0.00 0.00 0.00 6.09
1984 2090 4.631131 AGTGAATGATGAAACTGACGACA 58.369 39.130 0.00 0.00 0.00 4.35
1990 2096 1.577468 TGAAACTGACGACAACGCAT 58.423 45.000 0.00 0.00 43.96 4.73
2103 2209 7.749666 AGGAATACTACCAGACATATGCAAAT 58.250 34.615 1.58 0.00 0.00 2.32
2208 2315 3.152341 CAAGGCACAGAGGAACAAGAAT 58.848 45.455 0.00 0.00 0.00 2.40
2427 2537 4.593597 CGAAAGGCAATTCGTAAAGCTA 57.406 40.909 14.78 0.00 45.32 3.32
2615 2727 4.333926 GCCTACTTCAATGAGAAAGCGAAT 59.666 41.667 0.00 0.00 35.40 3.34
2864 2976 2.569853 AGACACGGATGGGTACATTTGA 59.430 45.455 0.00 0.00 37.47 2.69
3322 3434 2.586425 ACAGTTTGCCAAGCAGTACAT 58.414 42.857 0.00 0.00 40.61 2.29
3359 3471 5.643421 AAATTCTGGGATCTGAGCTACAT 57.357 39.130 0.00 0.00 0.00 2.29
3384 3496 1.666872 GCGACCACGGCACTAAAGT 60.667 57.895 0.00 0.00 40.15 2.66
3789 3918 6.258287 TGTTTAATAAAATGCATCTGCCATGC 59.742 34.615 0.00 10.18 44.76 4.06
3826 3958 6.892658 ATTGCCATGTTTACTCAACTGTAA 57.107 33.333 0.00 0.00 36.21 2.41
3965 4124 2.699954 AGTGTACTACAGTTGCCATGC 58.300 47.619 0.00 0.00 0.00 4.06
4070 4230 4.548991 TTGCCATGTTCAAACAAAATGC 57.451 36.364 0.00 1.88 43.03 3.56
4174 4336 4.280436 TCCAGGAAGAAATAAAGCGTGA 57.720 40.909 0.00 0.00 0.00 4.35
4236 4398 2.159382 AGGTGTGTTCTATTTTGGGCG 58.841 47.619 0.00 0.00 0.00 6.13
4254 4416 2.094182 GGCGTGTCAGATTCAGAACCTA 60.094 50.000 0.00 0.00 0.00 3.08
4262 4424 4.844085 TCAGATTCAGAACCTAAAGACCCA 59.156 41.667 0.00 0.00 0.00 4.51
4323 4485 0.531200 AGGCGAGTACTACTGCCAAC 59.469 55.000 26.27 7.94 41.60 3.77
4405 4567 3.245346 TGTGACACGGATGCCCCA 61.245 61.111 0.22 0.00 34.14 4.96
4446 4608 2.338620 CTTGGGACGCTGACGACA 59.661 61.111 0.00 0.00 43.93 4.35
4502 4665 1.135915 GTGCATGACGAGAGACCTGAT 59.864 52.381 0.00 0.00 0.00 2.90
4560 4723 7.391554 TGACAAAGAACTATGCTGAGCTAATTT 59.608 33.333 5.83 0.00 0.00 1.82
4797 4960 2.290705 CCCCGTTCTATCACAAAGGGTT 60.291 50.000 3.23 0.00 40.07 4.11
4800 4963 3.818773 CCGTTCTATCACAAAGGGTTGTT 59.181 43.478 0.00 0.00 46.01 2.83
4804 4967 6.206498 GTTCTATCACAAAGGGTTGTTCAAC 58.794 40.000 7.09 7.09 46.01 3.18
4822 4985 8.185506 TGTTCAACAGAGATAAGGTACAAGTA 57.814 34.615 0.00 0.00 0.00 2.24
4947 5112 7.685481 TGTTTTGTACCCTAGATGATGAGAAA 58.315 34.615 0.00 0.00 0.00 2.52
5187 5479 6.710744 ACTAAATATGCCATGCTAGTTGTACC 59.289 38.462 0.00 0.00 0.00 3.34
5202 5494 3.080300 TGTACCGGATCTGCCATTTTT 57.920 42.857 9.46 0.00 35.94 1.94
5336 5629 5.277490 CCATGGTATTTGTAATGACTCTGCG 60.277 44.000 2.57 0.00 0.00 5.18
5353 5646 4.397420 TCTGCGTGGCATATATTTCCATT 58.603 39.130 6.72 0.00 38.13 3.16
5360 5653 8.405531 GCGTGGCATATATTTCCATTACAATAT 58.594 33.333 6.72 0.00 31.83 1.28
5479 5775 3.053395 ACATGATCAACCTACCCATGCTT 60.053 43.478 0.00 0.00 38.43 3.91
5634 5931 1.736645 CCGGTGCGAGAAACGATGT 60.737 57.895 0.00 0.00 45.77 3.06
5682 5979 2.423926 ACATATCTGCTCTAACGCCG 57.576 50.000 0.00 0.00 0.00 6.46
5714 6011 6.704493 GGTTCACGTCCACACATATATTACAT 59.296 38.462 0.00 0.00 0.00 2.29
5779 6078 2.173669 CGCGGGGTTGCAGTCATAG 61.174 63.158 0.00 0.00 34.15 2.23
5821 6122 6.921857 AGTTTTCGACGAGAACAAAGAGATAA 59.078 34.615 26.93 0.44 38.83 1.75
5921 6222 3.389329 TGACTTTCTTGACAGCTTCCTCT 59.611 43.478 0.00 0.00 0.00 3.69
5923 6224 5.247110 TGACTTTCTTGACAGCTTCCTCTAT 59.753 40.000 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
345 363 1.146930 AATCATGATCGCGTGGCCT 59.853 52.632 9.06 0.00 0.00 5.19
388 406 0.178947 TGGCCCAAAACCCACCTAAG 60.179 55.000 0.00 0.00 0.00 2.18
572 594 2.024369 ACCTTTCTTTCTTGTGTGGGGT 60.024 45.455 0.00 0.00 0.00 4.95
614 636 4.223964 GCATTCCGGCGCTTCGTC 62.224 66.667 7.64 0.00 0.00 4.20
635 657 1.238625 GCATTTTCCCCGTTGTCCGA 61.239 55.000 0.00 0.00 39.56 4.55
817 840 6.811253 TCGTTTTGCATTACCTTGATTAGT 57.189 33.333 0.00 0.00 0.00 2.24
938 963 4.450122 CGATGCCACGTGCTGCAC 62.450 66.667 22.38 22.38 40.88 4.57
1239 1338 4.465632 AACTGTAGTTGCATCGGTATGA 57.534 40.909 0.00 0.00 36.80 2.15
1329 1429 2.036992 TGGTTGGTCAATTCATGGCAAC 59.963 45.455 0.00 0.00 34.42 4.17
1398 1498 0.314935 ATTTGTGAAGCTTGCCACGG 59.685 50.000 2.10 0.00 36.15 4.94
1603 1706 0.744414 GCGTGGACATGTATGGCAGT 60.744 55.000 0.00 0.00 37.62 4.40
1653 1756 3.877559 TCTTCGAGTGATTTGGCATGAT 58.122 40.909 0.00 0.00 0.00 2.45
1772 1878 1.898154 GCAGTAGATGTCCCCGTGT 59.102 57.895 0.00 0.00 0.00 4.49
1792 1898 2.951745 CGTGCGCTTAGAGCTCCG 60.952 66.667 10.93 7.98 39.60 4.63
1984 2090 4.141620 ACCATCTTCATCCTCTTATGCGTT 60.142 41.667 0.00 0.00 0.00 4.84
1990 2096 2.439507 GCCCACCATCTTCATCCTCTTA 59.560 50.000 0.00 0.00 0.00 2.10
2103 2209 1.916506 TGACCGCAAATCCATGGAAA 58.083 45.000 20.67 0.00 0.00 3.13
2208 2315 2.909965 GGCGCAACACCTTTCCCA 60.910 61.111 10.83 0.00 0.00 4.37
2427 2537 4.418392 GACCGACGTTACAATCATGTAGT 58.582 43.478 0.00 0.00 42.72 2.73
2465 2576 6.737720 TTGCTGTGGATGAGAGATAGTATT 57.262 37.500 0.00 0.00 0.00 1.89
3243 3355 1.675310 CATTGAACCCCTCGCTGCA 60.675 57.895 0.00 0.00 0.00 4.41
3359 3471 2.357034 GCCGTGGTCGCTTCTTGA 60.357 61.111 0.00 0.00 35.54 3.02
3384 3496 7.474190 GGTAAATACGTTAGCAATTTTGGCTA 58.526 34.615 0.00 0.00 42.62 3.93
3547 3675 4.700213 AGTAAGCATGGCGAACAGTATTTT 59.300 37.500 0.00 0.00 0.00 1.82
3789 3918 4.214545 ACATGGCAATTGCATTTCAACAAG 59.785 37.500 30.32 16.33 44.36 3.16
3826 3958 6.479884 TGCCCTTTTATTTAAACATGGCATT 58.520 32.000 0.00 0.00 37.90 3.56
3965 4124 2.710377 TGGCAAATGCAGTACACTAGG 58.290 47.619 7.80 0.00 44.36 3.02
4110 4272 4.359971 TCTGTTAAACTATCGTGCGCTA 57.640 40.909 9.73 0.00 0.00 4.26
4174 4336 0.593128 GAAAGCCGTGAACATGCTGT 59.407 50.000 0.00 0.00 35.08 4.40
4236 4398 5.639931 GGTCTTTAGGTTCTGAATCTGACAC 59.360 44.000 13.34 4.66 0.00 3.67
4254 4416 2.783510 TCCTTCCTTTGTCTGGGTCTTT 59.216 45.455 0.00 0.00 0.00 2.52
4262 4424 4.344390 ACGAAGTAGTTCCTTCCTTTGTCT 59.656 41.667 4.70 0.00 41.94 3.41
4323 4485 2.170985 CCGTTCGAACTTGCAGCG 59.829 61.111 24.80 10.56 0.00 5.18
4405 4567 0.107410 TCGCCGCCTTATGAAATGGT 60.107 50.000 0.00 0.00 0.00 3.55
4502 4665 0.109532 TCACGGCTTCCATGGTTGAA 59.890 50.000 12.58 0.00 0.00 2.69
4560 4723 2.741759 TCACTCTTGCACGCTTCATA 57.258 45.000 0.00 0.00 0.00 2.15
4797 4960 7.062749 ACTTGTACCTTATCTCTGTTGAACA 57.937 36.000 0.00 0.00 0.00 3.18
4800 4963 6.380274 CCCTACTTGTACCTTATCTCTGTTGA 59.620 42.308 0.00 0.00 0.00 3.18
4804 4967 7.437748 CAATCCCTACTTGTACCTTATCTCTG 58.562 42.308 0.00 0.00 0.00 3.35
5187 5479 3.302365 ACAACAAAAATGGCAGATCCG 57.698 42.857 0.00 0.00 37.80 4.18
5353 5646 5.163632 TGTCTCTAAACCGCGTCATATTGTA 60.164 40.000 4.92 0.00 0.00 2.41
5360 5653 0.669619 TGTGTCTCTAAACCGCGTCA 59.330 50.000 4.92 0.00 0.00 4.35
5494 5790 6.478016 GCTGTTTTGCTTCTTCTTTTTCATCT 59.522 34.615 0.00 0.00 0.00 2.90
5593 5889 5.191059 GTTTGCTATTTCGAATGCGTCTAG 58.809 41.667 0.00 0.00 38.98 2.43
5674 5971 3.241868 CGTGAACCTATTTTCGGCGTTAG 60.242 47.826 6.85 4.53 0.00 2.34
5682 5979 3.810941 TGTGTGGACGTGAACCTATTTTC 59.189 43.478 0.00 0.00 0.00 2.29
5714 6011 4.697828 TGTGAGCGGCATTTGAATAGTTTA 59.302 37.500 1.45 0.00 0.00 2.01
5729 6026 2.094757 TAGTGGTGGTGTGTGAGCGG 62.095 60.000 0.00 0.00 0.00 5.52
5779 6078 5.283717 CGAAAACTATGTTTGTGTGCTATGC 59.716 40.000 0.00 0.00 0.00 3.14
5821 6122 3.199071 TGTTGCCGAGGAATGTAAGGTAT 59.801 43.478 0.00 0.00 0.00 2.73
5858 6159 0.249741 GTGGCGTTACACACCAGACT 60.250 55.000 0.00 0.00 40.99 3.24
5921 6222 1.226575 CGGAGCACGCGAGTTCATA 60.227 57.895 20.36 0.00 46.40 2.15
5923 6224 4.717629 CCGGAGCACGCGAGTTCA 62.718 66.667 20.36 0.00 46.40 3.18


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.