Multiple sequence alignment - TraesCS4A01G433100

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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 TraesCS4A01G433100 chr4A 100.000 3611 0 0 1 3611 703706254 703709864 0.000000e+00 6669.0
1 TraesCS4A01G433100 chr4A 97.681 3622 42 9 1 3611 703604457 703608047 0.000000e+00 6185.0
2 TraesCS4A01G433100 chr4A 97.308 2006 53 1 913 2917 703651596 703653601 0.000000e+00 3404.0
3 TraesCS4A01G433100 chr4A 96.406 779 10 8 6 784 703650278 703651038 0.000000e+00 1267.0
4 TraesCS4A01G433100 chr4A 86.176 557 68 3 1000 1556 710284833 710284286 8.630000e-166 593.0
5 TraesCS4A01G433100 chr4A 83.971 549 78 7 999 1539 710677393 710676847 5.340000e-143 518.0
6 TraesCS4A01G433100 chr4A 99.273 275 2 0 2940 3214 703612502 703612776 6.960000e-137 497.0
7 TraesCS4A01G433100 chr4A 97.473 277 5 1 2940 3214 703714316 703714592 4.220000e-129 472.0
8 TraesCS4A01G433100 chr4A 83.457 405 59 4 3207 3611 518985676 518986072 1.580000e-98 370.0
9 TraesCS4A01G433100 chr4A 84.259 108 12 4 25 127 93977285 93977178 2.290000e-17 100.0
10 TraesCS4A01G433100 chr4A 84.762 105 10 5 23 122 612373856 612373959 2.290000e-17 100.0
11 TraesCS4A01G433100 chr7A 90.835 1833 120 26 872 2692 27604502 27606298 0.000000e+00 2410.0
12 TraesCS4A01G433100 chr7A 86.432 995 127 7 1646 2635 26823235 26822244 0.000000e+00 1083.0
13 TraesCS4A01G433100 chr7A 85.986 999 131 4 1651 2644 26977641 26976647 0.000000e+00 1061.0
14 TraesCS4A01G433100 chr7A 85.877 963 132 3 1651 2611 27032265 27031305 0.000000e+00 1022.0
15 TraesCS4A01G433100 chr7A 93.642 692 22 1 2942 3611 80592270 80591579 0.000000e+00 1014.0
16 TraesCS4A01G433100 chr7A 88.654 520 42 13 278 792 27603916 27604423 5.120000e-173 617.0
17 TraesCS4A01G433100 chr7A 87.313 536 59 3 1021 1556 27032933 27032407 3.990000e-169 604.0
18 TraesCS4A01G433100 chr7A 84.452 566 78 7 999 1556 26978402 26977839 1.900000e-152 549.0
19 TraesCS4A01G433100 chr7A 98.175 274 5 0 2940 3213 80587184 80586911 2.520000e-131 479.0
20 TraesCS4A01G433100 chr7A 81.752 274 41 9 2664 2935 27606305 27606571 1.690000e-53 220.0
21 TraesCS4A01G433100 chr7A 82.609 115 15 4 13 123 506963912 506964025 2.970000e-16 97.1
22 TraesCS4A01G433100 chr7D 91.562 1268 83 15 1548 2801 27243965 27245222 0.000000e+00 1727.0
23 TraesCS4A01G433100 chr7D 86.556 967 128 2 1646 2611 25898025 25897060 0.000000e+00 1064.0
24 TraesCS4A01G433100 chr7D 85.285 999 138 4 1651 2644 26559472 26558478 0.000000e+00 1022.0
25 TraesCS4A01G433100 chr7D 91.728 677 46 4 874 1549 27243266 27243933 0.000000e+00 931.0
26 TraesCS4A01G433100 chr7D 83.569 566 83 6 999 1556 26560223 26559660 4.130000e-144 521.0
27 TraesCS4A01G433100 chr7D 87.871 371 30 10 427 792 27242827 27243187 4.310000e-114 422.0
28 TraesCS4A01G433100 chr7D 79.365 126 19 6 408 529 31634771 31634893 8.310000e-12 82.4
29 TraesCS4A01G433100 chr7D 84.146 82 7 6 2839 2920 27245225 27245300 1.390000e-09 75.0
30 TraesCS4A01G433100 chr6B 97.463 670 17 0 2942 3611 142092565 142093234 0.000000e+00 1144.0
31 TraesCS4A01G433100 chr6B 94.161 274 3 7 2940 3213 142097654 142097914 4.340000e-109 405.0
32 TraesCS4A01G433100 chr6B 94.667 75 3 1 18 91 39369570 39369644 8.190000e-22 115.0
33 TraesCS4A01G433100 chr5B 96.418 670 17 2 2942 3611 461861036 461860374 0.000000e+00 1098.0
34 TraesCS4A01G433100 chr5B 99.273 275 2 0 2940 3214 461832114 461831840 6.960000e-137 497.0
35 TraesCS4A01G433100 chr5B 80.292 411 69 7 3203 3611 611725299 611724899 2.110000e-77 300.0
36 TraesCS4A01G433100 chr2D 90.667 675 50 7 2940 3611 649033358 649032694 0.000000e+00 885.0
37 TraesCS4A01G433100 chr2A 86.642 539 61 5 1001 1538 448294893 448294365 1.440000e-163 586.0
38 TraesCS4A01G433100 chr7B 81.433 684 94 24 2942 3611 66168618 66167954 2.470000e-146 529.0
39 TraesCS4A01G433100 chr2B 82.944 557 84 6 1000 1556 800172498 800171953 3.240000e-135 492.0
40 TraesCS4A01G433100 chr2B 82.727 110 16 3 22 128 43427134 43427243 1.070000e-15 95.3
41 TraesCS4A01G433100 chr3D 82.734 417 60 6 3197 3611 260979731 260979325 9.530000e-96 361.0
42 TraesCS4A01G433100 chr1B 82.469 405 65 4 3207 3609 478255049 478254649 2.060000e-92 350.0
43 TraesCS4A01G433100 chr5D 95.522 67 2 1 24 89 559346440 559346506 4.930000e-19 106.0
44 TraesCS4A01G433100 chr4D 82.456 114 16 3 14 123 62231212 62231325 2.970000e-16 97.1


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 TraesCS4A01G433100 chr4A 703706254 703709864 3610 False 6669.000000 6669 100.000000 1 3611 1 chr4A.!!$F5 3610
1 TraesCS4A01G433100 chr4A 703604457 703608047 3590 False 6185.000000 6185 97.681000 1 3611 1 chr4A.!!$F3 3610
2 TraesCS4A01G433100 chr4A 703650278 703653601 3323 False 2335.500000 3404 96.857000 6 2917 2 chr4A.!!$F7 2911
3 TraesCS4A01G433100 chr4A 710284286 710284833 547 True 593.000000 593 86.176000 1000 1556 1 chr4A.!!$R2 556
4 TraesCS4A01G433100 chr4A 710676847 710677393 546 True 518.000000 518 83.971000 999 1539 1 chr4A.!!$R3 540
5 TraesCS4A01G433100 chr7A 26822244 26823235 991 True 1083.000000 1083 86.432000 1646 2635 1 chr7A.!!$R1 989
6 TraesCS4A01G433100 chr7A 27603916 27606571 2655 False 1082.333333 2410 87.080333 278 2935 3 chr7A.!!$F2 2657
7 TraesCS4A01G433100 chr7A 80591579 80592270 691 True 1014.000000 1014 93.642000 2942 3611 1 chr7A.!!$R3 669
8 TraesCS4A01G433100 chr7A 27031305 27032933 1628 True 813.000000 1022 86.595000 1021 2611 2 chr7A.!!$R5 1590
9 TraesCS4A01G433100 chr7A 26976647 26978402 1755 True 805.000000 1061 85.219000 999 2644 2 chr7A.!!$R4 1645
10 TraesCS4A01G433100 chr7D 25897060 25898025 965 True 1064.000000 1064 86.556000 1646 2611 1 chr7D.!!$R1 965
11 TraesCS4A01G433100 chr7D 27242827 27245300 2473 False 788.750000 1727 88.826750 427 2920 4 chr7D.!!$F2 2493
12 TraesCS4A01G433100 chr7D 26558478 26560223 1745 True 771.500000 1022 84.427000 999 2644 2 chr7D.!!$R2 1645
13 TraesCS4A01G433100 chr6B 142092565 142093234 669 False 1144.000000 1144 97.463000 2942 3611 1 chr6B.!!$F2 669
14 TraesCS4A01G433100 chr5B 461860374 461861036 662 True 1098.000000 1098 96.418000 2942 3611 1 chr5B.!!$R2 669
15 TraesCS4A01G433100 chr2D 649032694 649033358 664 True 885.000000 885 90.667000 2940 3611 1 chr2D.!!$R1 671
16 TraesCS4A01G433100 chr2A 448294365 448294893 528 True 586.000000 586 86.642000 1001 1538 1 chr2A.!!$R1 537
17 TraesCS4A01G433100 chr7B 66167954 66168618 664 True 529.000000 529 81.433000 2942 3611 1 chr7B.!!$R1 669
18 TraesCS4A01G433100 chr2B 800171953 800172498 545 True 492.000000 492 82.944000 1000 1556 1 chr2B.!!$R1 556

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
852 901 0.167908 GTGTGGTGTGTGTGTGTGTG 59.832 55.0 0.0 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2723 3464 9.319143 ACATCTTAATAAACTCTTCGGATTCTG 57.681 33.333 0.0 0.0 0.0 3.02 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
205 206 3.763360 TCACACATGCTTCTTTTATGGGG 59.237 43.478 0.00 0.00 29.59 4.96
213 214 6.036577 TGCTTCTTTTATGGGGTTTCAATC 57.963 37.500 0.00 0.00 0.00 2.67
363 364 7.315890 CAGTTTTATCTTTCTGAATGGAACCC 58.684 38.462 3.79 0.00 0.00 4.11
379 384 3.279116 CCCACATACGGGCATGCG 61.279 66.667 12.44 0.62 40.07 4.73
666 688 1.332686 CCACATGATTCATGCTCCACG 59.667 52.381 23.43 7.81 44.80 4.94
751 773 4.703575 TCAAATTAGCATCTTGAGCTGCTT 59.296 37.500 13.76 0.00 44.09 3.91
848 897 3.097672 CCGTGTGGTGTGTGTGTG 58.902 61.111 0.00 0.00 0.00 3.82
849 898 1.743623 CCGTGTGGTGTGTGTGTGT 60.744 57.895 0.00 0.00 0.00 3.72
850 899 1.423450 CGTGTGGTGTGTGTGTGTG 59.577 57.895 0.00 0.00 0.00 3.82
851 900 1.295357 CGTGTGGTGTGTGTGTGTGT 61.295 55.000 0.00 0.00 0.00 3.72
852 901 0.167908 GTGTGGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
853 902 0.250510 TGTGGTGTGTGTGTGTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
854 903 0.167908 GTGGTGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
855 904 0.250510 TGGTGTGTGTGTGTGTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
856 905 1.002087 TGGTGTGTGTGTGTGTGTGTA 59.998 47.619 0.00 0.00 0.00 2.90
857 906 2.285083 GGTGTGTGTGTGTGTGTGTAT 58.715 47.619 0.00 0.00 0.00 2.29
858 907 3.118738 TGGTGTGTGTGTGTGTGTGTATA 60.119 43.478 0.00 0.00 0.00 1.47
859 908 4.062293 GGTGTGTGTGTGTGTGTGTATAT 58.938 43.478 0.00 0.00 0.00 0.86
860 909 5.221461 TGGTGTGTGTGTGTGTGTGTATATA 60.221 40.000 0.00 0.00 0.00 0.86
861 910 5.872617 GGTGTGTGTGTGTGTGTGTATATAT 59.127 40.000 0.00 0.00 0.00 0.86
862 911 7.036829 GGTGTGTGTGTGTGTGTGTATATATA 58.963 38.462 0.00 0.00 0.00 0.86
863 912 7.709182 GGTGTGTGTGTGTGTGTGTATATATAT 59.291 37.037 0.00 0.00 0.00 0.86
864 913 9.738832 GTGTGTGTGTGTGTGTGTATATATATA 57.261 33.333 0.00 0.00 0.00 0.86
1286 1747 2.882777 CGCTGCGCTGTCCTACTG 60.883 66.667 9.88 0.00 0.00 2.74
1831 2529 1.141665 CATGAGACGACCGCCATGA 59.858 57.895 11.71 0.00 38.83 3.07
2494 3194 2.272170 ATGGAGGGGGAGAAGGGGA 61.272 63.158 0.00 0.00 0.00 4.81
3379 4152 2.293399 ACTCTTTCCCGCACAAAATGAC 59.707 45.455 0.00 0.00 0.00 3.06
3386 4159 2.223688 CCCGCACAAAATGACAGTCAAA 60.224 45.455 7.50 0.00 0.00 2.69
3467 4240 2.388310 TTGTCACACCAAAGACACGA 57.612 45.000 0.00 0.00 43.80 4.35
3468 4241 1.934589 TGTCACACCAAAGACACGAG 58.065 50.000 0.00 0.00 39.65 4.18
3514 4287 5.606348 CTCCTTGAGCATAGACTTAACCT 57.394 43.478 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 0.858583 GGCGAAAAATGTGCACCAAC 59.141 50.000 15.69 0.00 0.00 3.77
205 206 5.001267 CGCGTGTCGAAAAATAGATTGAAAC 59.999 40.000 0.00 0.00 41.67 2.78
213 214 2.093638 CATGCGCGTGTCGAAAAATAG 58.906 47.619 21.57 0.00 41.67 1.73
255 256 3.875134 ACGTGTACCAAGGAACAGAAAAG 59.125 43.478 0.00 0.00 0.00 2.27
363 364 1.817520 TTCGCATGCCCGTATGTGG 60.818 57.895 13.15 0.00 38.70 4.17
434 451 1.644786 CGCGACATGTTCCCTTTCCC 61.645 60.000 0.00 0.00 0.00 3.97
666 688 8.887717 TCGGTTCTCTAGTTTATACTACTTGTC 58.112 37.037 0.00 0.00 35.78 3.18
751 773 0.178301 TAAGTCACAACGTGCCCACA 59.822 50.000 0.00 0.00 32.98 4.17
821 870 0.391130 CACCACACGGTATGGGTGAG 60.391 60.000 10.68 0.00 46.94 3.51
1286 1747 0.179108 GAGGCAGGTCGTCATGGTAC 60.179 60.000 0.00 0.00 0.00 3.34
2723 3464 9.319143 ACATCTTAATAAACTCTTCGGATTCTG 57.681 33.333 0.00 0.00 0.00 3.02
3314 4087 2.812011 CGGTTTGTTTCCTCCGAAGATT 59.188 45.455 0.00 0.00 44.86 2.40
3379 4152 7.697691 AGAACTAAACACATTGAGTTTGACTG 58.302 34.615 18.64 10.44 39.36 3.51
3386 4159 8.450578 TCATTCAAGAACTAAACACATTGAGT 57.549 30.769 0.00 0.00 0.00 3.41
3467 4240 4.290942 TGGTATTTTTCCCACACAAACCT 58.709 39.130 0.00 0.00 0.00 3.50
3468 4241 4.674281 TGGTATTTTTCCCACACAAACC 57.326 40.909 0.00 0.00 0.00 3.27
3514 4287 6.698329 GCAAATGCAACAGCAGAAATCATATA 59.302 34.615 0.00 0.00 42.36 0.86


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

AutoCloner maintained by Alex Coulton.