Multiple sequence alignment - TraesCS4A01G443600

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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 TraesCS4A01G443600 chr4A 100.000 3434 0 0 1 3434 712114069 712110636 0.000000e+00 6342.0
1 TraesCS4A01G443600 chr4A 99.140 2673 18 2 2 2673 712444643 712447311 0.000000e+00 4804.0
2 TraesCS4A01G443600 chr4A 96.993 765 23 0 2670 3434 712450614 712451378 0.000000e+00 1286.0
3 TraesCS4A01G443600 chr4A 95.144 659 32 0 2776 3434 724779414 724778756 0.000000e+00 1040.0
4 TraesCS4A01G443600 chr7D 90.685 2190 139 37 622 2774 21773374 21775535 0.000000e+00 2854.0
5 TraesCS4A01G443600 chr7D 85.185 81 12 0 324 404 191468877 191468797 2.200000e-12 84.2
6 TraesCS4A01G443600 chr7A 93.450 1832 100 13 959 2770 22197956 22199787 0.000000e+00 2700.0
7 TraesCS4A01G443600 chr7A 87.603 242 18 5 672 904 22197513 22197751 1.570000e-68 270.0
8 TraesCS4A01G443600 chr2B 94.872 663 34 0 2772 3434 67171473 67170811 0.000000e+00 1037.0
9 TraesCS4A01G443600 chr2B 94.872 663 33 1 2772 3434 18927671 18928332 0.000000e+00 1035.0
10 TraesCS4A01G443600 chr2B 79.603 755 124 21 1690 2436 5780828 5780096 6.570000e-142 514.0
11 TraesCS4A01G443600 chr2B 74.964 687 131 29 1757 2430 17149773 17150431 9.390000e-71 278.0
12 TraesCS4A01G443600 chr2B 73.414 331 76 10 41 366 39792215 39792538 2.800000e-21 113.0
13 TraesCS4A01G443600 chr2B 85.227 88 9 3 632 717 5725094 5725179 1.700000e-13 87.9
14 TraesCS4A01G443600 chr4B 94.713 662 35 0 2773 3434 644378062 644378723 0.000000e+00 1029.0
15 TraesCS4A01G443600 chr1B 94.570 663 35 1 2773 3434 40370933 40370271 0.000000e+00 1024.0
16 TraesCS4A01G443600 chr1B 94.428 664 36 1 2771 3434 547984547 547983885 0.000000e+00 1020.0
17 TraesCS4A01G443600 chrUn 94.562 662 34 2 2774 3434 83958287 83957627 0.000000e+00 1022.0
18 TraesCS4A01G443600 chrUn 82.119 302 44 5 2128 2426 32344723 32345017 2.050000e-62 250.0
19 TraesCS4A01G443600 chr7B 93.825 664 40 1 2771 3434 15133405 15134067 0.000000e+00 998.0
20 TraesCS4A01G443600 chr7B 73.569 367 94 3 40 404 714556262 714556627 1.660000e-28 137.0
21 TraesCS4A01G443600 chr7B 78.261 115 22 3 40 152 675422040 675421927 1.710000e-08 71.3
22 TraesCS4A01G443600 chr5A 78.840 293 57 5 4 293 687161441 687161731 3.500000e-45 193.0
23 TraesCS4A01G443600 chr6B 76.486 370 76 10 41 404 628883579 628883215 1.260000e-44 191.0
24 TraesCS4A01G443600 chr1A 75.824 364 78 10 40 398 578250448 578250806 3.520000e-40 176.0
25 TraesCS4A01G443600 chr1A 80.435 92 17 1 314 404 572334240 572334149 6.150000e-08 69.4
26 TraesCS4A01G443600 chr1D 77.700 287 59 5 4 288 307786312 307786595 1.640000e-38 171.0
27 TraesCS4A01G443600 chr3D 76.786 224 46 5 42 259 522200830 522200607 1.670000e-23 121.0
28 TraesCS4A01G443600 chr3D 94.286 35 2 0 305 339 8417446 8417480 2.000000e-03 54.7
29 TraesCS4A01G443600 chr2A 74.182 275 64 5 4 276 562727682 562727951 1.300000e-19 108.0
30 TraesCS4A01G443600 chr3A 83.810 105 15 2 302 404 123284404 123284300 7.840000e-17 99.0


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 TraesCS4A01G443600 chr4A 712110636 712114069 3433 True 6342 6342 100.0000 1 3434 1 chr4A.!!$R1 3433
1 TraesCS4A01G443600 chr4A 712444643 712451378 6735 False 3045 4804 98.0665 2 3434 2 chr4A.!!$F1 3432
2 TraesCS4A01G443600 chr4A 724778756 724779414 658 True 1040 1040 95.1440 2776 3434 1 chr4A.!!$R2 658
3 TraesCS4A01G443600 chr7D 21773374 21775535 2161 False 2854 2854 90.6850 622 2774 1 chr7D.!!$F1 2152
4 TraesCS4A01G443600 chr7A 22197513 22199787 2274 False 1485 2700 90.5265 672 2770 2 chr7A.!!$F1 2098
5 TraesCS4A01G443600 chr2B 67170811 67171473 662 True 1037 1037 94.8720 2772 3434 1 chr2B.!!$R2 662
6 TraesCS4A01G443600 chr2B 18927671 18928332 661 False 1035 1035 94.8720 2772 3434 1 chr2B.!!$F3 662
7 TraesCS4A01G443600 chr2B 5780096 5780828 732 True 514 514 79.6030 1690 2436 1 chr2B.!!$R1 746
8 TraesCS4A01G443600 chr2B 17149773 17150431 658 False 278 278 74.9640 1757 2430 1 chr2B.!!$F2 673
9 TraesCS4A01G443600 chr4B 644378062 644378723 661 False 1029 1029 94.7130 2773 3434 1 chr4B.!!$F1 661
10 TraesCS4A01G443600 chr1B 40370271 40370933 662 True 1024 1024 94.5700 2773 3434 1 chr1B.!!$R1 661
11 TraesCS4A01G443600 chr1B 547983885 547984547 662 True 1020 1020 94.4280 2771 3434 1 chr1B.!!$R2 663
12 TraesCS4A01G443600 chrUn 83957627 83958287 660 True 1022 1022 94.5620 2774 3434 1 chrUn.!!$R1 660
13 TraesCS4A01G443600 chr7B 15133405 15134067 662 False 998 998 93.8250 2771 3434 1 chr7B.!!$F1 663

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
560 561 0.596577 TCTCTCTCGTTTCCACCACG 59.403 55.0 0.00 0.00 39.08 4.94 F
858 874 2.148916 TAGCATTATGGAGGAACGCG 57.851 50.0 3.53 3.53 0.00 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 2061 3.560025 GCTTTTTCTGGATCTCCTGGTCA 60.560 47.826 3.61 0.0 35.87 4.02 R
2866 6400 3.130693 GCCTATATATCCTGTCGTGGGTC 59.869 52.174 0.00 0.0 0.00 4.46 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
113 114 3.391382 ACCCCTTCTTCGCCGGAG 61.391 66.667 5.05 0.00 0.00 4.63
144 145 7.493320 ACAAAACTTGTTACAGTAGACAATCGA 59.507 33.333 0.00 0.00 42.22 3.59
372 373 1.153549 CTAGAAGCGCCACCAGGAC 60.154 63.158 2.29 0.00 36.89 3.85
560 561 0.596577 TCTCTCTCGTTTCCACCACG 59.403 55.000 0.00 0.00 39.08 4.94
858 874 2.148916 TAGCATTATGGAGGAACGCG 57.851 50.000 3.53 3.53 0.00 6.01
868 885 4.395959 TGGAGGAACGCGAAGTTATTAT 57.604 40.909 15.93 0.00 44.35 1.28
1869 2061 1.607612 CCTCGCCCACCTGGTAAAT 59.392 57.895 0.00 0.00 36.04 1.40
2866 6400 3.572539 ACCGCAACACACGCACAG 61.573 61.111 0.00 0.00 0.00 3.66
2872 6406 1.817941 AACACACGCACAGACCCAC 60.818 57.895 0.00 0.00 0.00 4.61
3204 6739 0.250234 CCCACACGACCATGATGACT 59.750 55.000 0.00 0.00 0.00 3.41
3210 6745 0.392863 CGACCATGATGACTGGGCAA 60.393 55.000 0.00 0.00 42.39 4.52
3380 6916 2.429930 CACCCCCAGCGTCAAGAA 59.570 61.111 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.982516 AGGTGGTCTGCAGATCTTACTA 58.017 45.455 26.71 6.50 0.00 1.82
28 29 3.491792 GCTAGGTGGTCTGCAGATCTTAC 60.492 52.174 26.71 17.37 0.00 2.34
30 31 1.484240 GCTAGGTGGTCTGCAGATCTT 59.516 52.381 26.71 14.89 0.00 2.40
68 69 3.861263 CGCGTTTTCGGCTAGCCC 61.861 66.667 28.09 12.41 44.29 5.19
113 114 4.632538 ACTGTAACAAGTTTTGTCTGGC 57.367 40.909 0.00 0.00 44.59 4.85
144 145 3.372025 GGGGCATTAACATGGAGACTTCT 60.372 47.826 0.00 0.00 0.00 2.85
341 342 1.615883 GCTTCTAGCATCATCGGAGGA 59.384 52.381 0.00 0.00 41.89 3.71
372 373 1.690219 ATTCTCCCTGCCTAGCACCG 61.690 60.000 0.00 0.00 33.79 4.94
560 561 5.059710 GCAATGTTGTTCGAAGCTTCATAAC 59.940 40.000 25.47 24.94 0.00 1.89
858 874 9.185680 ACCCACTATGTCCAAAATAATAACTTC 57.814 33.333 0.00 0.00 0.00 3.01
868 885 3.137544 AGACACACCCACTATGTCCAAAA 59.862 43.478 0.15 0.00 43.10 2.44
1869 2061 3.560025 GCTTTTTCTGGATCTCCTGGTCA 60.560 47.826 3.61 0.00 35.87 4.02
2866 6400 3.130693 GCCTATATATCCTGTCGTGGGTC 59.869 52.174 0.00 0.00 0.00 4.46
2872 6406 2.683362 TCAGCGCCTATATATCCTGTCG 59.317 50.000 2.29 0.00 0.00 4.35
2975 6509 1.334243 CGGAGTCGTATCCTTCCTGAC 59.666 57.143 7.01 0.00 37.20 3.51
3204 6739 2.837291 GTGCCTTGGTGTTGCCCA 60.837 61.111 0.00 0.00 36.04 5.36
3210 6745 4.643387 GAGCCCGTGCCTTGGTGT 62.643 66.667 0.00 0.00 38.69 4.16
3394 6930 0.535335 GTCGGTGGATGCCAGTTCTA 59.465 55.000 0.00 0.00 32.34 2.10


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

AutoCloner maintained by Alex Coulton.