Multiple sequence alignment - TraesCS6B01G441700

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 TraesCS6B01G441700 chr6B 100.000 3516 0 0 1 3516 705759586 705756071 0.000000e+00 6493
1 TraesCS6B01G441700 chr6B 96.468 2718 53 13 826 3516 705784830 705782129 0.000000e+00 4447
2 TraesCS6B01G441700 chr6B 93.551 2729 121 23 826 3516 706409872 706407161 0.000000e+00 4013
3 TraesCS6B01G441700 chr6B 93.516 2730 120 24 826 3516 706352886 706350175 0.000000e+00 4008
4 TraesCS6B01G441700 chr6B 88.705 1691 155 22 1323 2997 706528982 706527312 0.000000e+00 2032
5 TraesCS6B01G441700 chr6B 88.286 1733 150 27 1272 2990 706443982 706442289 0.000000e+00 2026
6 TraesCS6B01G441700 chr6B 94.037 805 38 5 3 798 547694358 547693555 0.000000e+00 1212
7 TraesCS6B01G441700 chr6B 91.793 463 32 6 3 462 706640340 706639881 1.060000e-179 640
8 TraesCS6B01G441700 chr6B 89.628 376 24 8 855 1224 706112448 706112082 6.870000e-127 464
9 TraesCS6B01G441700 chr6B 89.836 305 16 4 826 1116 706523650 706523347 9.210000e-101 377
10 TraesCS6B01G441700 chr6B 89.069 247 22 3 875 1120 706529796 706529554 5.700000e-78 302
11 TraesCS6B01G441700 chr6D 93.580 2726 129 20 826 3516 463074221 463071507 0.000000e+00 4023
12 TraesCS6B01G441700 chr6D 88.940 1745 148 25 1272 2997 463079999 463078281 0.000000e+00 2111
13 TraesCS6B01G441700 chr6D 92.382 1457 95 13 2066 3516 463069051 463067605 0.000000e+00 2061
14 TraesCS6B01G441700 chr6D 90.588 170 14 1 1109 1278 463091076 463090909 1.270000e-54 224
15 TraesCS6B01G441700 chr6D 89.286 140 10 5 2992 3130 446736199 446736334 1.680000e-38 171
16 TraesCS6B01G441700 chr6A 90.168 2146 156 15 1222 3362 609815278 609813183 0.000000e+00 2743
17 TraesCS6B01G441700 chr6A 88.289 1742 165 18 1272 3000 609821474 609819759 0.000000e+00 2050
18 TraesCS6B01G441700 chr6A 92.550 349 18 4 877 1225 609816247 609815907 8.770000e-136 494
19 TraesCS6B01G441700 chr6A 88.066 243 21 3 875 1116 609821821 609821586 7.430000e-72 281
20 TraesCS6B01G441700 chr5B 95.262 802 28 4 3 795 470626464 470627264 0.000000e+00 1262
21 TraesCS6B01G441700 chr5B 91.797 829 33 12 3 798 664477065 664476239 0.000000e+00 1122
22 TraesCS6B01G441700 chr5B 80.357 336 56 9 3185 3516 322757497 322757168 2.710000e-61 246
23 TraesCS6B01G441700 chr7B 94.396 803 31 6 3 795 124361352 124362150 0.000000e+00 1221
24 TraesCS6B01G441700 chr7B 93.878 196 12 0 603 798 452159208 452159013 2.650000e-76 296
25 TraesCS6B01G441700 chr4B 94.764 783 31 4 26 798 585725891 585725109 0.000000e+00 1210
26 TraesCS6B01G441700 chr4B 77.261 387 65 20 3143 3516 619458850 619459226 4.600000e-49 206
27 TraesCS6B01G441700 chr2A 91.811 806 54 6 3 798 277179300 277178497 0.000000e+00 1112
28 TraesCS6B01G441700 chr2A 88.276 145 11 4 2991 3132 158180049 158180190 6.040000e-38 169
29 TraesCS6B01G441700 chr4A 90.582 807 57 13 3 795 503623804 503624605 0.000000e+00 1051
30 TraesCS6B01G441700 chr3B 86.358 843 64 30 3 798 66627352 66626514 0.000000e+00 872
31 TraesCS6B01G441700 chr3B 85.207 845 70 31 3 798 767301798 767300960 0.000000e+00 817
32 TraesCS6B01G441700 chr2B 81.627 381 55 13 3143 3516 247365754 247365382 5.700000e-78 302
33 TraesCS6B01G441700 chr2D 81.003 379 60 10 3143 3516 190329173 190328802 1.230000e-74 291
34 TraesCS6B01G441700 chrUn 86.228 167 18 4 495 658 79888445 79888281 3.610000e-40 176
35 TraesCS6B01G441700 chr3D 89.706 136 12 2 3000 3134 49478743 49478609 4.670000e-39 172


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 TraesCS6B01G441700 chr6B 705756071 705759586 3515 True 6493.000000 6493 100.000000 1 3516 1 chr6B.!!$R2 3515
1 TraesCS6B01G441700 chr6B 705782129 705784830 2701 True 4447.000000 4447 96.468000 826 3516 1 chr6B.!!$R3 2690
2 TraesCS6B01G441700 chr6B 706407161 706409872 2711 True 4013.000000 4013 93.551000 826 3516 1 chr6B.!!$R6 2690
3 TraesCS6B01G441700 chr6B 706350175 706352886 2711 True 4008.000000 4008 93.516000 826 3516 1 chr6B.!!$R5 2690
4 TraesCS6B01G441700 chr6B 706442289 706443982 1693 True 2026.000000 2026 88.286000 1272 2990 1 chr6B.!!$R7 1718
5 TraesCS6B01G441700 chr6B 547693555 547694358 803 True 1212.000000 1212 94.037000 3 798 1 chr6B.!!$R1 795
6 TraesCS6B01G441700 chr6B 706523347 706529796 6449 True 903.666667 2032 89.203333 826 2997 3 chr6B.!!$R9 2171
7 TraesCS6B01G441700 chr6D 463067605 463074221 6616 True 3042.000000 4023 92.981000 826 3516 2 chr6D.!!$R3 2690
8 TraesCS6B01G441700 chr6D 463078281 463079999 1718 True 2111.000000 2111 88.940000 1272 2997 1 chr6D.!!$R1 1725
9 TraesCS6B01G441700 chr6A 609813183 609821821 8638 True 1392.000000 2743 89.768250 875 3362 4 chr6A.!!$R1 2487
10 TraesCS6B01G441700 chr5B 470626464 470627264 800 False 1262.000000 1262 95.262000 3 795 1 chr5B.!!$F1 792
11 TraesCS6B01G441700 chr5B 664476239 664477065 826 True 1122.000000 1122 91.797000 3 798 1 chr5B.!!$R2 795
12 TraesCS6B01G441700 chr7B 124361352 124362150 798 False 1221.000000 1221 94.396000 3 795 1 chr7B.!!$F1 792
13 TraesCS6B01G441700 chr4B 585725109 585725891 782 True 1210.000000 1210 94.764000 26 798 1 chr4B.!!$R1 772
14 TraesCS6B01G441700 chr2A 277178497 277179300 803 True 1112.000000 1112 91.811000 3 798 1 chr2A.!!$R1 795
15 TraesCS6B01G441700 chr4A 503623804 503624605 801 False 1051.000000 1051 90.582000 3 795 1 chr4A.!!$F1 792
16 TraesCS6B01G441700 chr3B 66626514 66627352 838 True 872.000000 872 86.358000 3 798 1 chr3B.!!$R1 795
17 TraesCS6B01G441700 chr3B 767300960 767301798 838 True 817.000000 817 85.207000 3 798 1 chr3B.!!$R2 795

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
836 918 0.239082 ACTCGTGTCGTGCGTGATAA 59.761 50.000 0.00 0.0 0.0 1.75 F
1022 1112 2.217038 AAGAGAGGCTGCCGTTCCA 61.217 57.895 13.96 0.0 0.0 3.53 F
1493 1963 2.585330 TGCTGCTCATTTCTTGTGGAA 58.415 42.857 0.00 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 2452 0.034477 GGTGGGATTGTTCCGGTGAT 60.034 55.000 0.00 0.0 43.63 3.06 R
2064 2534 4.042884 ACTTCCCATCTCATCAGGAATGA 58.957 43.478 0.00 0.0 42.21 2.57 R
3454 14609 2.024464 TGCAGGTTATTTACAGGGCCAT 60.024 45.455 6.18 0.0 0.00 4.40 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
84 87 5.947228 TCGCAGATTGAAACTTTTCATCT 57.053 34.783 5.26 7.68 45.65 2.90
97 101 7.496529 AACTTTTCATCTTGTCGATTGAAGA 57.503 32.000 6.88 6.88 32.83 2.87
145 151 9.142993 CTTATTTTTAAACGCTTGCAACTTTTC 57.857 29.630 0.00 0.00 0.00 2.29
157 163 2.985139 GCAACTTTTCTCATCTTGCAGC 59.015 45.455 0.00 0.00 37.70 5.25
433 463 1.373246 CTTCCGACGTTGCCGGTTA 60.373 57.895 13.17 3.55 46.53 2.85
450 480 2.037381 GGTTATAGCACTGCCCTAGTCC 59.963 54.545 0.00 0.00 37.60 3.85
546 594 2.436173 GCTTGGAGTAGTAGCAGGGATT 59.564 50.000 0.00 0.00 35.05 3.01
623 672 2.089059 AGAGATAGAGGAGGGGGAGAGA 60.089 54.545 0.00 0.00 0.00 3.10
631 680 1.133009 GGAGGGGGAGAGATCAAGCTA 60.133 57.143 0.00 0.00 0.00 3.32
817 899 4.673298 CGGTGCACCAGCCGTGTA 62.673 66.667 34.16 0.00 44.97 2.90
820 902 2.342279 TGCACCAGCCGTGTACTC 59.658 61.111 3.69 0.00 44.97 2.59
821 903 2.809601 GCACCAGCCGTGTACTCG 60.810 66.667 10.28 10.28 44.97 4.18
822 904 2.649034 CACCAGCCGTGTACTCGT 59.351 61.111 15.43 0.00 37.73 4.18
823 905 1.733041 CACCAGCCGTGTACTCGTG 60.733 63.158 15.43 8.43 37.73 4.35
824 906 2.198287 ACCAGCCGTGTACTCGTGT 61.198 57.895 15.43 5.22 0.00 4.49
834 916 0.453950 GTACTCGTGTCGTGCGTGAT 60.454 55.000 0.00 0.00 0.00 3.06
836 918 0.239082 ACTCGTGTCGTGCGTGATAA 59.761 50.000 0.00 0.00 0.00 1.75
945 1035 2.504367 CGTTCCAACCTCCAACTCAAT 58.496 47.619 0.00 0.00 0.00 2.57
951 1041 3.828451 CCAACCTCCAACTCAATTCACAT 59.172 43.478 0.00 0.00 0.00 3.21
1022 1112 2.217038 AAGAGAGGCTGCCGTTCCA 61.217 57.895 13.96 0.00 0.00 3.53
1102 1201 4.274147 TCCTCCTGATTACTCACTCAGTC 58.726 47.826 0.00 0.00 37.73 3.51
1123 1368 7.539436 CAGTCAGTACTGCTTCTTACATCTTA 58.461 38.462 18.45 0.00 46.28 2.10
1175 1420 9.579610 CAAAAGGCAAAACTAATATTTTTCACG 57.420 29.630 0.00 0.00 29.17 4.35
1198 1443 8.943002 CACGTGGGTTCTACTTCTAATATTTTT 58.057 33.333 7.95 0.00 0.00 1.94
1345 1815 4.647853 AGGCTTGTGTATCAATTGATGCAT 59.352 37.500 32.72 20.51 46.05 3.96
1493 1963 2.585330 TGCTGCTCATTTCTTGTGGAA 58.415 42.857 0.00 0.00 0.00 3.53
2033 2503 5.406780 AGAAACAATAGTCAGCTTGAAGACG 59.593 40.000 0.00 0.00 39.67 4.18
2064 2534 7.885399 GCTTACTGATAATAGGTTCATGGGAAT 59.115 37.037 0.00 0.00 35.05 3.01
3202 14352 3.748048 ACTGATGCATGCGACCATATTAC 59.252 43.478 14.09 0.00 0.00 1.89
3290 14444 8.947055 AAGAGCAAATAAAAGTTGACAACAAT 57.053 26.923 20.08 6.00 38.32 2.71
3324 14478 4.226113 GTCGAGATGACTAAACGCCTAT 57.774 45.455 0.00 0.00 44.58 2.57
3454 14609 0.461163 CCACGTACGGATCCATGCAA 60.461 55.000 21.06 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.509575 TGATAAAAAGCTTCAACCGGCAT 59.490 39.130 0.00 0.00 0.00 4.40
1 2 2.887783 TGATAAAAAGCTTCAACCGGCA 59.112 40.909 0.00 0.00 0.00 5.69
145 151 3.207669 GGGGCGCTGCAAGATGAG 61.208 66.667 7.64 0.00 34.07 2.90
157 163 1.007849 CAAAGTTTCAACCGGGGCG 60.008 57.895 6.32 0.00 0.00 6.13
433 463 1.115930 CGGGACTAGGGCAGTGCTAT 61.116 60.000 16.11 6.46 44.61 2.97
763 845 1.517257 CGCGTTCGATGAAGGAGCT 60.517 57.895 0.00 0.00 38.10 4.09
806 888 2.138656 GACACGAGTACACGGCTGGT 62.139 60.000 16.97 9.03 37.61 4.00
807 889 1.443872 GACACGAGTACACGGCTGG 60.444 63.158 16.97 6.11 37.61 4.85
808 890 1.796355 CGACACGAGTACACGGCTG 60.796 63.158 16.97 9.35 37.61 4.85
809 891 2.256591 ACGACACGAGTACACGGCT 61.257 57.895 16.97 1.02 37.61 5.52
810 892 2.078914 CACGACACGAGTACACGGC 61.079 63.158 16.97 5.24 37.61 5.68
811 893 2.078914 GCACGACACGAGTACACGG 61.079 63.158 16.97 8.36 37.61 4.94
812 894 2.415220 CGCACGACACGAGTACACG 61.415 63.158 11.29 11.29 39.31 4.49
813 895 1.369689 ACGCACGACACGAGTACAC 60.370 57.895 0.00 0.00 0.00 2.90
814 896 1.369568 CACGCACGACACGAGTACA 60.370 57.895 0.00 0.00 0.00 2.90
815 897 0.453950 ATCACGCACGACACGAGTAC 60.454 55.000 0.00 0.00 0.00 2.73
816 898 1.077915 TATCACGCACGACACGAGTA 58.922 50.000 0.00 0.00 0.00 2.59
817 899 0.239082 TTATCACGCACGACACGAGT 59.761 50.000 0.00 0.00 0.00 4.18
818 900 1.545759 ATTATCACGCACGACACGAG 58.454 50.000 0.00 0.00 0.00 4.18
819 901 2.828874 TATTATCACGCACGACACGA 57.171 45.000 0.00 0.00 0.00 4.35
820 902 3.729217 AGAATATTATCACGCACGACACG 59.271 43.478 0.00 0.00 0.00 4.49
821 903 5.423717 CAAGAATATTATCACGCACGACAC 58.576 41.667 0.00 0.00 0.00 3.67
822 904 4.026062 GCAAGAATATTATCACGCACGACA 60.026 41.667 0.00 0.00 0.00 4.35
823 905 4.026062 TGCAAGAATATTATCACGCACGAC 60.026 41.667 0.00 0.00 0.00 4.34
824 906 4.116238 TGCAAGAATATTATCACGCACGA 58.884 39.130 0.00 0.00 0.00 4.35
834 916 5.726397 ACGTACACACCTGCAAGAATATTA 58.274 37.500 0.00 0.00 34.07 0.98
836 918 4.202245 ACGTACACACCTGCAAGAATAT 57.798 40.909 0.00 0.00 34.07 1.28
945 1035 0.250252 TCAGCCGTGAAGCATGTGAA 60.250 50.000 0.00 0.00 34.23 3.18
951 1041 1.887242 GTGTGTCAGCCGTGAAGCA 60.887 57.895 0.00 0.00 33.27 3.91
987 1077 3.527775 TTGCATGGTTTTGCCGCCC 62.528 57.895 0.00 0.00 42.06 6.13
1026 1116 0.388907 CACCTTTGCTTGGCCGAATG 60.389 55.000 0.00 0.00 0.00 2.67
1123 1368 8.539674 GCGAGATTTTTGTTTTTGACAGTAAAT 58.460 29.630 0.00 0.00 39.94 1.40
1175 1420 8.900781 GGGAAAAATATTAGAAGTAGAACCCAC 58.099 37.037 0.00 0.00 0.00 4.61
1672 2142 2.364324 TCGTTGTCTGAGGTACAGCTTT 59.636 45.455 0.00 0.00 45.38 3.51
1982 2452 0.034477 GGTGGGATTGTTCCGGTGAT 60.034 55.000 0.00 0.00 43.63 3.06
2033 2503 6.270815 TGAACCTATTATCAGTAAGCACGAC 58.729 40.000 0.00 0.00 0.00 4.34
2064 2534 4.042884 ACTTCCCATCTCATCAGGAATGA 58.957 43.478 0.00 0.00 42.21 2.57
2149 2619 8.807118 AGAGAAGACTGATTGTATTTGTACAGA 58.193 33.333 0.00 0.00 29.25 3.41
2532 3008 7.981142 TCAAGTGAGACGAAACTGTTATTTTT 58.019 30.769 0.00 0.00 0.00 1.94
3202 14352 7.344441 GCAAACATTTTGGTACTTTTGCTTAG 58.656 34.615 9.09 0.00 43.43 2.18
3290 14444 3.118920 TCATCTCGACCTATTTTCGCCAA 60.119 43.478 0.00 0.00 36.40 4.52
3319 14473 5.072741 TGGCAATCCAATAAGAAGATAGGC 58.927 41.667 0.00 0.00 39.99 3.93
3454 14609 2.024464 TGCAGGTTATTTACAGGGCCAT 60.024 45.455 6.18 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.