Multiple sequence alignment - TraesCS5A01G285100

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 TraesCS5A01G285100 chr5A 100.000 2544 0 0 1 2544 493196380 493193837 0.000000e+00 4698.0
1 TraesCS5A01G285100 chr5D 92.683 1230 45 15 1320 2544 390023459 390022270 0.000000e+00 1731.0
2 TraesCS5A01G285100 chr5D 91.236 696 49 5 1 687 390025489 390024797 0.000000e+00 937.0
3 TraesCS5A01G285100 chr5D 93.602 422 15 6 882 1292 390023877 390023457 1.000000e-173 619.0
4 TraesCS5A01G285100 chr5D 82.353 85 13 2 765 849 354033889 354033807 3.510000e-09 73.1
5 TraesCS5A01G285100 chr5B 85.589 1138 83 35 900 1984 470035107 470033998 0.000000e+00 1118.0
6 TraesCS5A01G285100 chr5B 93.739 559 31 4 1982 2538 470033962 470033406 0.000000e+00 835.0
7 TraesCS5A01G285100 chr5B 79.460 667 104 22 4 650 470055899 470055246 2.320000e-120 442.0
8 TraesCS5A01G285100 chr3D 86.087 115 16 0 743 857 272380455 272380569 9.560000e-25 124.0
9 TraesCS5A01G285100 chr3D 80.606 165 26 2 717 881 9765408 9765566 3.440000e-24 122.0
10 TraesCS5A01G285100 chr3B 86.207 116 15 1 742 857 364594140 364594254 9.560000e-25 124.0
11 TraesCS5A01G285100 chr3B 91.549 71 4 2 792 861 439676928 439676997 2.080000e-16 97.1
12 TraesCS5A01G285100 chr3B 90.141 71 5 2 792 861 439744568 439744637 9.690000e-15 91.6
13 TraesCS5A01G285100 chr1B 80.137 146 21 5 717 861 661629034 661629172 4.480000e-18 102.0
14 TraesCS5A01G285100 chr7A 79.054 148 27 4 715 861 652284120 652284264 5.790000e-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 TraesCS5A01G285100 chr5A 493193837 493196380 2543 True 4698.000000 4698 100.000 1 2544 1 chr5A.!!$R1 2543
1 TraesCS5A01G285100 chr5D 390022270 390025489 3219 True 1095.666667 1731 92.507 1 2544 3 chr5D.!!$R2 2543
2 TraesCS5A01G285100 chr5B 470033406 470035107 1701 True 976.500000 1118 89.664 900 2538 2 chr5B.!!$R2 1638
3 TraesCS5A01G285100 chr5B 470055246 470055899 653 True 442.000000 442 79.460 4 650 1 chr5B.!!$R1 646

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
801 860 0.107848 AGTGGATTTTAGGCCCGACG 60.108 55.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 2484 0.314935 GTTCCAATGGCACCACACAG 59.685 55.0 0.0 0.0 0.0 3.66 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
34 35 4.513318 TCGTTGAACTTGTATGCAACATCA 59.487 37.500 0.00 0.00 40.32 3.07
51 52 6.346040 GCAACATCAAGTCAAAAGTATGCAAC 60.346 38.462 0.00 0.00 0.00 4.17
59 60 5.804979 AGTCAAAAGTATGCAACAACAACAC 59.195 36.000 0.00 0.00 0.00 3.32
60 61 5.574830 GTCAAAAGTATGCAACAACAACACA 59.425 36.000 0.00 0.00 0.00 3.72
62 63 6.646653 TCAAAAGTATGCAACAACAACACAAA 59.353 30.769 0.00 0.00 0.00 2.83
74 75 4.506886 ACAACACAAAAACGACTTGGAA 57.493 36.364 0.00 0.00 0.00 3.53
221 223 1.933021 TCGTCTAGGTCCATGGTTGT 58.067 50.000 12.58 0.00 0.00 3.32
259 261 6.240549 AGATAGTTCCGACAATGATTTCCT 57.759 37.500 0.00 0.00 0.00 3.36
269 272 5.126061 CGACAATGATTTCCTCCCTTTTGAT 59.874 40.000 0.00 0.00 0.00 2.57
313 316 2.342648 GAACCCCTCAGAACGCGT 59.657 61.111 5.58 5.58 0.00 6.01
319 322 3.414700 CTCAGAACGCGTGGTGGC 61.415 66.667 14.98 0.00 0.00 5.01
388 393 0.407918 TAAAGGTGGGGGCTTTGAGG 59.592 55.000 0.00 0.00 0.00 3.86
392 397 2.451493 TGGGGGCTTTGAGGGACA 60.451 61.111 0.00 0.00 0.00 4.02
401 406 2.173519 CTTTGAGGGACAATGGTGCAT 58.826 47.619 0.00 0.00 38.36 3.96
444 452 1.913262 ACGACCATGCCCTGAGACA 60.913 57.895 0.00 0.00 0.00 3.41
452 460 1.191489 TGCCCTGAGACACGATCCAA 61.191 55.000 0.00 0.00 0.00 3.53
492 501 1.615124 TCCCTTGATTGGCCTCCGA 60.615 57.895 3.32 0.00 0.00 4.55
498 507 0.911769 TGATTGGCCTCCGATGTCTT 59.088 50.000 3.32 0.00 0.00 3.01
506 515 2.931320 GCCTCCGATGTCTTTCTTCGTT 60.931 50.000 0.00 0.00 40.53 3.85
507 516 2.924290 CCTCCGATGTCTTTCTTCGTTC 59.076 50.000 0.00 0.00 40.53 3.95
527 536 6.917477 TCGTTCTGATGTGAAAATTCCAAAAG 59.083 34.615 0.00 0.00 0.00 2.27
579 589 1.469308 CGTCACGAGTAAGCTCCTTCT 59.531 52.381 0.00 0.00 38.49 2.85
581 591 2.488545 GTCACGAGTAAGCTCCTTCTCA 59.511 50.000 0.00 0.00 38.49 3.27
589 599 1.582389 AGCTCCTTCTCAAGATGGCT 58.418 50.000 7.00 0.50 38.74 4.75
592 602 3.134442 AGCTCCTTCTCAAGATGGCTTAG 59.866 47.826 7.00 2.22 38.74 2.18
648 670 0.886490 GCGGGCATCAAGATACCTGG 60.886 60.000 9.61 0.00 32.33 4.45
730 777 0.916086 TCTGGGCCCGTCATATTTGT 59.084 50.000 19.37 0.00 0.00 2.83
746 793 9.455847 GTCATATTTGTGATTTATTGAAGAGGC 57.544 33.333 0.00 0.00 0.00 4.70
750 797 3.054728 TGTGATTTATTGAAGAGGCCCGA 60.055 43.478 0.00 0.00 0.00 5.14
752 799 3.054728 TGATTTATTGAAGAGGCCCGACA 60.055 43.478 0.00 0.00 0.00 4.35
764 823 1.597027 CCCGACAGGCTTTCACGTT 60.597 57.895 1.08 0.00 35.76 3.99
767 826 0.232303 CGACAGGCTTTCACGTTGAC 59.768 55.000 1.08 0.00 0.00 3.18
771 830 2.251371 GCTTTCACGTTGACGGGC 59.749 61.111 8.52 1.18 43.59 6.13
796 855 2.379005 CTTGGGAGTGGATTTTAGGCC 58.621 52.381 0.00 0.00 0.00 5.19
800 859 1.664873 GAGTGGATTTTAGGCCCGAC 58.335 55.000 0.00 0.00 0.00 4.79
801 860 0.107848 AGTGGATTTTAGGCCCGACG 60.108 55.000 0.00 0.00 0.00 5.12
802 861 1.093496 GTGGATTTTAGGCCCGACGG 61.093 60.000 6.99 6.99 0.00 4.79
840 899 1.609841 CGGGCCTAGGTTTTCTTCGTT 60.610 52.381 11.31 0.00 0.00 3.85
850 909 3.113322 GTTTTCTTCGTTGGGCTTTGTC 58.887 45.455 0.00 0.00 0.00 3.18
851 910 2.341846 TTCTTCGTTGGGCTTTGTCT 57.658 45.000 0.00 0.00 0.00 3.41
852 911 1.593196 TCTTCGTTGGGCTTTGTCTG 58.407 50.000 0.00 0.00 0.00 3.51
853 912 0.593128 CTTCGTTGGGCTTTGTCTGG 59.407 55.000 0.00 0.00 0.00 3.86
854 913 1.452145 TTCGTTGGGCTTTGTCTGGC 61.452 55.000 0.00 0.00 0.00 4.85
898 1665 1.305930 GGCTTAAACGGTCCAGGCAG 61.306 60.000 0.90 0.00 0.00 4.85
1141 1908 3.447025 GACAGGGAAGCCGGATCCG 62.447 68.421 27.65 27.65 37.87 4.18
1260 2057 0.892755 TTCGGTATGTGCTTCTCGGT 59.107 50.000 0.00 0.00 0.00 4.69
1270 2067 0.793250 GCTTCTCGGTTCTTGCTGAC 59.207 55.000 0.00 0.00 0.00 3.51
1329 2126 1.890041 CACTCCACGGCGGTTGAAA 60.890 57.895 13.24 0.00 35.57 2.69
1330 2127 1.890510 ACTCCACGGCGGTTGAAAC 60.891 57.895 13.24 0.00 35.57 2.78
1382 2179 3.149981 TCACCGGCATTGTAAATCAACA 58.850 40.909 0.00 0.00 38.97 3.33
1383 2180 3.190327 TCACCGGCATTGTAAATCAACAG 59.810 43.478 0.00 0.00 38.97 3.16
1384 2181 3.190327 CACCGGCATTGTAAATCAACAGA 59.810 43.478 0.00 0.00 38.97 3.41
1417 2214 2.386661 ATCAAGGTACGGAACTGCTG 57.613 50.000 0.00 0.00 0.00 4.41
1430 2227 5.593095 ACGGAACTGCTGTATATAGAAGTCA 59.407 40.000 10.37 0.00 35.46 3.41
1556 2356 7.659390 GGATGGAGAGGTAGAATACAATGAAAG 59.341 40.741 0.00 0.00 45.43 2.62
1562 2362 8.697292 AGAGGTAGAATACAATGAAAGTAGACC 58.303 37.037 0.00 0.00 45.43 3.85
1575 2375 1.692519 AGTAGACCCGTGTTTCAAGCT 59.307 47.619 0.00 0.00 0.00 3.74
1633 2451 4.024218 GCTGCAAAGGTCATATCTGATGAC 60.024 45.833 8.82 8.82 45.59 3.06
1678 2496 0.321210 CGTATTCCTGTGTGGTGCCA 60.321 55.000 0.00 0.00 37.07 4.92
1690 2508 1.272212 GTGGTGCCATTGGAACGATTT 59.728 47.619 6.95 0.00 30.21 2.17
1696 2514 5.641636 GGTGCCATTGGAACGATTTTTATTT 59.358 36.000 6.95 0.00 30.21 1.40
1697 2515 6.148645 GGTGCCATTGGAACGATTTTTATTTT 59.851 34.615 6.95 0.00 30.21 1.82
1698 2516 7.233689 GTGCCATTGGAACGATTTTTATTTTC 58.766 34.615 6.95 0.00 0.00 2.29
1699 2517 6.370166 TGCCATTGGAACGATTTTTATTTTCC 59.630 34.615 6.95 0.00 36.95 3.13
1712 2530 2.702270 ATTTTCCTTCCTTGCACCCT 57.298 45.000 0.00 0.00 0.00 4.34
1734 2552 4.142609 TCATGTCCAAATCCTAGCTCAC 57.857 45.455 0.00 0.00 0.00 3.51
1755 2573 2.105821 CCCCCTGACTGTTTGTGTTAGA 59.894 50.000 0.00 0.00 0.00 2.10
1756 2574 3.403038 CCCCTGACTGTTTGTGTTAGAG 58.597 50.000 0.00 0.00 0.00 2.43
1757 2575 3.403038 CCCTGACTGTTTGTGTTAGAGG 58.597 50.000 0.00 0.00 0.00 3.69
1758 2576 3.181454 CCCTGACTGTTTGTGTTAGAGGT 60.181 47.826 0.00 0.00 0.00 3.85
1759 2577 4.039973 CCCTGACTGTTTGTGTTAGAGGTA 59.960 45.833 0.00 0.00 0.00 3.08
1760 2578 5.454187 CCCTGACTGTTTGTGTTAGAGGTAA 60.454 44.000 0.00 0.00 0.00 2.85
1761 2579 6.231211 CCTGACTGTTTGTGTTAGAGGTAAT 58.769 40.000 0.00 0.00 0.00 1.89
1762 2580 6.369065 CCTGACTGTTTGTGTTAGAGGTAATC 59.631 42.308 0.00 0.00 0.00 1.75
1835 2653 8.971073 CCTTAGGTAATCATTCATGGTTCTTTT 58.029 33.333 0.00 0.00 32.49 2.27
2067 2923 8.488651 TCCCGAAGAGAATTACTTTTTGATAC 57.511 34.615 0.00 0.00 0.00 2.24
2144 3000 9.270640 GCAGATGTATGAAAAATGTAGAGAGAT 57.729 33.333 0.00 0.00 0.00 2.75
2174 3030 7.708322 TGCTACTAATTGAAGAATAGTGCTCAG 59.292 37.037 0.00 0.00 0.00 3.35
2224 3080 3.929002 GCATCTGGCATGCCTTCA 58.071 55.556 35.53 20.22 43.97 3.02
2225 3081 2.426651 GCATCTGGCATGCCTTCAT 58.573 52.632 35.53 21.49 43.97 2.57
2322 3180 1.207089 CTACTCACGGGCATTTCCTGA 59.793 52.381 0.00 0.00 44.37 3.86
2337 3195 3.388552 TCCTGAGAGCAAGATACTCCA 57.611 47.619 0.00 0.00 34.56 3.86
2439 3298 3.706373 GCTGGCGACCCCTTCTCA 61.706 66.667 0.00 0.00 0.00 3.27
2523 3382 5.760253 AGCATACTTGTGGAGATTTAATCCG 59.240 40.000 0.78 0.00 39.91 4.18
2541 3400 4.664150 TCCGTGTATGAACATGCTATCA 57.336 40.909 0.00 0.00 40.67 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 6.310224 GTGTTGTTGTTGCATACTTTTGACTT 59.690 34.615 0.00 0.00 0.00 3.01
51 52 4.230657 TCCAAGTCGTTTTTGTGTTGTTG 58.769 39.130 0.00 0.00 0.00 3.33
59 60 5.332506 GCATTCATGTTCCAAGTCGTTTTTG 60.333 40.000 0.00 0.00 0.00 2.44
60 61 4.744631 GCATTCATGTTCCAAGTCGTTTTT 59.255 37.500 0.00 0.00 0.00 1.94
62 63 3.317711 TGCATTCATGTTCCAAGTCGTTT 59.682 39.130 0.00 0.00 0.00 3.60
74 75 7.495279 AGTTTGTTGTAAATGTTGCATTCATGT 59.505 29.630 5.81 3.66 0.00 3.21
122 123 2.875094 AGCTTGAAGGCTCATGAAGT 57.125 45.000 0.00 0.00 38.24 3.01
131 132 2.821810 GCGGGAGAGCTTGAAGGC 60.822 66.667 0.00 0.00 0.00 4.35
221 223 5.598830 GGAACTATCTCCATCAACCTCACTA 59.401 44.000 0.00 0.00 35.36 2.74
313 316 4.860881 TTTTTGCCCCCGCCACCA 62.861 61.111 0.00 0.00 0.00 4.17
401 406 2.623502 GGACCACTTCTCCCTAGCACTA 60.624 54.545 0.00 0.00 0.00 2.74
492 501 5.541845 TCACATCAGAACGAAGAAAGACAT 58.458 37.500 0.00 0.00 0.00 3.06
498 507 6.262049 TGGAATTTTCACATCAGAACGAAGAA 59.738 34.615 0.00 0.00 0.00 2.52
506 515 6.159299 TGCTTTTGGAATTTTCACATCAGA 57.841 33.333 0.00 0.00 0.00 3.27
507 516 6.619874 GCATGCTTTTGGAATTTTCACATCAG 60.620 38.462 11.37 0.00 0.00 2.90
543 553 1.270625 TGACGCTAACCAGGAAGTTGG 60.271 52.381 0.00 0.00 44.09 3.77
552 562 1.401931 GCTTACTCGTGACGCTAACCA 60.402 52.381 0.00 0.00 0.00 3.67
555 565 1.131883 GGAGCTTACTCGTGACGCTAA 59.868 52.381 0.00 0.00 44.48 3.09
579 589 1.511613 CCTCCCCTAAGCCATCTTGA 58.488 55.000 0.00 0.00 33.85 3.02
581 591 1.356494 GGCCTCCCCTAAGCCATCTT 61.356 60.000 0.00 0.00 46.34 2.40
707 754 0.398522 ATATGACGGGCCCAGACTCA 60.399 55.000 24.92 16.28 0.00 3.41
709 756 1.134098 CAAATATGACGGGCCCAGACT 60.134 52.381 24.92 5.81 0.00 3.24
711 758 0.916086 ACAAATATGACGGGCCCAGA 59.084 50.000 24.92 4.39 0.00 3.86
730 777 3.054728 TGTCGGGCCTCTTCAATAAATCA 60.055 43.478 0.84 0.00 0.00 2.57
746 793 1.597027 AACGTGAAAGCCTGTCGGG 60.597 57.895 0.00 0.00 38.36 5.14
750 797 1.157870 CCGTCAACGTGAAAGCCTGT 61.158 55.000 1.48 0.00 37.74 4.00
752 799 1.597027 CCCGTCAACGTGAAAGCCT 60.597 57.895 1.48 0.00 37.74 4.58
771 830 2.499303 AAATCCACTCCCAAGCCCGG 62.499 60.000 0.00 0.00 0.00 5.73
782 841 0.107848 CGTCGGGCCTAAAATCCACT 60.108 55.000 0.84 0.00 0.00 4.00
783 842 1.093496 CCGTCGGGCCTAAAATCCAC 61.093 60.000 2.34 0.00 0.00 4.02
819 878 0.248289 CGAAGAAAACCTAGGCCCGA 59.752 55.000 9.30 0.00 0.00 5.14
820 879 0.036671 ACGAAGAAAACCTAGGCCCG 60.037 55.000 9.30 4.71 0.00 6.13
876 935 0.036306 CCTGGACCGTTTAAGCCTGT 59.964 55.000 0.00 0.00 0.00 4.00
954 1721 0.540365 CCAGAAAGGGAAGCTGCCAA 60.540 55.000 14.44 0.00 0.00 4.52
1169 1936 4.570663 GATGGTCGTCCGCCTCCG 62.571 72.222 0.00 0.00 36.30 4.63
1172 1939 3.461773 CCTGATGGTCGTCCGCCT 61.462 66.667 0.00 0.00 36.30 5.52
1260 2057 2.048222 CGGCGGAGTCAGCAAGAA 60.048 61.111 17.21 0.00 36.08 2.52
1329 2126 1.608717 GCCGTGGTCTCTCTCATGGT 61.609 60.000 0.00 0.00 41.00 3.55
1330 2127 1.142748 GCCGTGGTCTCTCTCATGG 59.857 63.158 0.00 0.00 41.64 3.66
1382 2179 5.885465 ACCTTGATTCCTTGAAGTTGATCT 58.115 37.500 0.00 0.00 0.00 2.75
1383 2180 6.183360 CGTACCTTGATTCCTTGAAGTTGATC 60.183 42.308 0.00 0.00 0.00 2.92
1384 2181 5.643777 CGTACCTTGATTCCTTGAAGTTGAT 59.356 40.000 0.00 0.00 0.00 2.57
1556 2356 2.067013 GAGCTTGAAACACGGGTCTAC 58.933 52.381 0.00 0.00 0.00 2.59
1562 2362 1.689959 GCAATGAGCTTGAAACACGG 58.310 50.000 0.00 0.00 41.15 4.94
1666 2484 0.314935 GTTCCAATGGCACCACACAG 59.685 55.000 0.00 0.00 0.00 3.66
1690 2508 4.488770 AGGGTGCAAGGAAGGAAAATAAA 58.511 39.130 0.00 0.00 0.00 1.40
1696 2514 0.850100 TGAAGGGTGCAAGGAAGGAA 59.150 50.000 0.00 0.00 0.00 3.36
1697 2515 1.075601 ATGAAGGGTGCAAGGAAGGA 58.924 50.000 0.00 0.00 0.00 3.36
1698 2516 1.180029 CATGAAGGGTGCAAGGAAGG 58.820 55.000 0.00 0.00 0.00 3.46
1699 2517 1.815003 GACATGAAGGGTGCAAGGAAG 59.185 52.381 0.00 0.00 0.00 3.46
1712 2530 4.517285 GTGAGCTAGGATTTGGACATGAA 58.483 43.478 0.00 0.00 0.00 2.57
1734 2552 2.105821 TCTAACACAAACAGTCAGGGGG 59.894 50.000 0.00 0.00 0.00 5.40
1861 2679 6.714356 CCAAACAATTGTTGAACCCCAATAAT 59.286 34.615 23.93 1.14 44.87 1.28
2144 3000 9.261180 GCACTATTCTTCAATTAGTAGCATGTA 57.739 33.333 0.00 0.00 0.00 2.29
2232 3090 2.795117 CTCGCGTAGAGGAAGGTTAAC 58.205 52.381 5.77 0.00 43.20 2.01
2322 3180 6.191315 TCTTAGACTTGGAGTATCTTGCTCT 58.809 40.000 0.00 0.00 33.73 4.09
2337 3195 3.259625 GCCTGACCTCACTTCTTAGACTT 59.740 47.826 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.