Multiple sequence alignment - TraesCS6A01G347700

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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 TraesCS6A01G347700 chr6A 100.000 2540 0 0 1 2540 580185887 580188426 0.000000e+00 4691.0
1 TraesCS6A01G347700 chr6A 97.854 699 13 2 1 698 333829274 333829971 0.000000e+00 1206.0
2 TraesCS6A01G347700 chr1B 94.048 1613 71 19 945 2540 15689924 15691528 0.000000e+00 2423.0
3 TraesCS6A01G347700 chr1B 87.687 268 24 6 696 958 546257175 546256912 1.140000e-78 303.0
4 TraesCS6A01G347700 chr1B 85.656 244 27 5 695 934 15689594 15689833 1.510000e-62 250.0
5 TraesCS6A01G347700 chr1B 88.525 61 7 0 696 756 446619051 446619111 9.750000e-10 75.0
6 TraesCS6A01G347700 chr6B 96.549 1188 38 2 1196 2382 679365017 679366202 0.000000e+00 1964.0
7 TraesCS6A01G347700 chr6B 95.652 161 5 2 2381 2540 679376198 679376357 9.020000e-65 257.0
8 TraesCS6A01G347700 chr7A 96.609 1032 28 6 697 1724 64596057 64595029 0.000000e+00 1705.0
9 TraesCS6A01G347700 chr7A 99.339 757 4 1 1785 2540 64595019 64594263 0.000000e+00 1369.0
10 TraesCS6A01G347700 chr7A 95.286 700 31 2 1 698 684490650 684489951 0.000000e+00 1109.0
11 TraesCS6A01G347700 chr3B 95.986 847 32 2 1201 2047 467068591 467067747 0.000000e+00 1375.0
12 TraesCS6A01G347700 chr3B 96.286 700 24 2 1 698 758333907 758334606 0.000000e+00 1147.0
13 TraesCS6A01G347700 chr3B 96.215 502 15 3 2042 2540 467062283 467061783 0.000000e+00 819.0
14 TraesCS6A01G347700 chr7B 96.350 274 6 3 2270 2540 42784308 42784580 4.980000e-122 448.0
15 TraesCS6A01G347700 chr7B 94.891 274 6 4 2270 2540 747442876 747442608 3.020000e-114 422.0
16 TraesCS6A01G347700 chr7B 93.609 266 16 1 694 958 506764147 506764412 1.830000e-106 396.0
17 TraesCS6A01G347700 chr2B 96.350 274 6 3 2270 2540 184672693 184672965 4.980000e-122 448.0
18 TraesCS6A01G347700 chr2B 86.707 331 42 2 1234 1562 166612230 166611900 1.440000e-97 366.0
19 TraesCS6A01G347700 chr2B 80.645 186 27 7 2028 2204 225247437 225247622 4.410000e-28 135.0
20 TraesCS6A01G347700 chr2B 76.879 173 23 14 697 860 30990259 30990423 5.820000e-12 82.4
21 TraesCS6A01G347700 chr2B 90.164 61 6 0 697 757 95092827 95092767 2.090000e-11 80.5
22 TraesCS6A01G347700 chr2A 84.422 398 58 4 1234 1629 117403713 117403318 3.060000e-104 388.0
23 TraesCS6A01G347700 chr2A 81.967 183 27 4 2028 2204 176866863 176867045 1.570000e-32 150.0
24 TraesCS6A01G347700 chr3A 93.774 257 12 3 696 949 712649511 712649256 1.430000e-102 383.0
25 TraesCS6A01G347700 chr3A 76.000 175 34 5 690 860 437862182 437862012 1.620000e-12 84.2
26 TraesCS6A01G347700 chr5B 90.034 291 28 1 1 290 473176928 473177218 2.390000e-100 375.0
27 TraesCS6A01G347700 chr5B 96.444 225 7 1 697 921 60593789 60593566 1.110000e-98 370.0
28 TraesCS6A01G347700 chr5D 89.691 291 29 1 1 290 393457113 393457403 1.110000e-98 370.0
29 TraesCS6A01G347700 chr5D 91.935 62 5 0 696 757 57107652 57107713 1.250000e-13 87.9
30 TraesCS6A01G347700 chr2D 86.970 330 41 2 1234 1561 115959081 115958752 1.110000e-98 370.0
31 TraesCS6A01G347700 chr5A 88.889 297 30 3 1 295 495320969 495321264 1.860000e-96 363.0
32 TraesCS6A01G347700 chr5A 81.019 216 29 10 2112 2324 19539307 19539513 7.270000e-36 161.0
33 TraesCS6A01G347700 chr5A 74.112 197 42 9 697 888 624717524 624717716 3.510000e-09 73.1


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 TraesCS6A01G347700 chr6A 580185887 580188426 2539 False 4691.0 4691 100.000 1 2540 1 chr6A.!!$F2 2539
1 TraesCS6A01G347700 chr6A 333829274 333829971 697 False 1206.0 1206 97.854 1 698 1 chr6A.!!$F1 697
2 TraesCS6A01G347700 chr1B 15689594 15691528 1934 False 1336.5 2423 89.852 695 2540 2 chr1B.!!$F2 1845
3 TraesCS6A01G347700 chr6B 679365017 679366202 1185 False 1964.0 1964 96.549 1196 2382 1 chr6B.!!$F1 1186
4 TraesCS6A01G347700 chr7A 64594263 64596057 1794 True 1537.0 1705 97.974 697 2540 2 chr7A.!!$R2 1843
5 TraesCS6A01G347700 chr7A 684489951 684490650 699 True 1109.0 1109 95.286 1 698 1 chr7A.!!$R1 697
6 TraesCS6A01G347700 chr3B 467067747 467068591 844 True 1375.0 1375 95.986 1201 2047 1 chr3B.!!$R2 846
7 TraesCS6A01G347700 chr3B 758333907 758334606 699 False 1147.0 1147 96.286 1 698 1 chr3B.!!$F1 697
8 TraesCS6A01G347700 chr3B 467061783 467062283 500 True 819.0 819 96.215 2042 2540 1 chr3B.!!$R1 498

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
760 763 0.03254 CCCACTTGGTTGAAAGCAGC 59.967 55.0 0.0 0.0 37.74 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 2337 1.27055 GGTTGCCACCATGTTGAAGAG 59.729 52.381 1.17 0.0 43.61 2.85 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
91 92 5.808042 TGACTCTGATAAGCTTGCATTTC 57.192 39.130 9.86 4.91 0.00 2.17
161 162 1.291877 GGCATGACGGCGGATACATC 61.292 60.000 13.24 0.00 33.57 3.06
302 303 1.187087 ACAAGCCTTCTACTCCCTCG 58.813 55.000 0.00 0.00 0.00 4.63
388 390 1.995626 AGGCCAGCCACTCGGTAAT 60.996 57.895 12.03 0.00 38.92 1.89
727 730 3.696548 CCTCTATTCCAGGCAAGGTTTTC 59.303 47.826 0.00 0.00 0.00 2.29
730 733 1.791103 TTCCAGGCAAGGTTTTCGCG 61.791 55.000 0.00 0.00 0.00 5.87
731 734 2.258013 CCAGGCAAGGTTTTCGCGA 61.258 57.895 3.71 3.71 0.00 5.87
737 740 1.201965 GCAAGGTTTTCGCGATGAGAG 60.202 52.381 10.88 0.00 0.00 3.20
741 744 3.251571 AGGTTTTCGCGATGAGAGTTAC 58.748 45.455 10.88 0.00 0.00 2.50
760 763 0.032540 CCCACTTGGTTGAAAGCAGC 59.967 55.000 0.00 0.00 37.74 5.25
761 764 0.032540 CCACTTGGTTGAAAGCAGCC 59.967 55.000 0.00 0.00 44.84 4.85
763 766 1.035139 ACTTGGTTGAAAGCAGCCTG 58.965 50.000 0.00 0.00 44.87 4.85
764 767 0.316204 CTTGGTTGAAAGCAGCCTGG 59.684 55.000 0.00 0.00 44.87 4.45
765 768 1.747325 TTGGTTGAAAGCAGCCTGGC 61.747 55.000 11.65 11.65 44.87 4.85
771 774 1.923227 GAAAGCAGCCTGGCGGTAAC 61.923 60.000 19.80 3.86 39.27 2.50
774 777 2.662596 CAGCCTGGCGGTAACTCA 59.337 61.111 13.96 0.00 0.00 3.41
775 778 1.221840 CAGCCTGGCGGTAACTCAT 59.778 57.895 13.96 0.00 0.00 2.90
776 779 0.392998 CAGCCTGGCGGTAACTCATT 60.393 55.000 13.96 0.00 0.00 2.57
777 780 0.328258 AGCCTGGCGGTAACTCATTT 59.672 50.000 13.96 0.00 0.00 2.32
778 781 0.451783 GCCTGGCGGTAACTCATTTG 59.548 55.000 1.35 0.00 0.00 2.32
779 782 1.948611 GCCTGGCGGTAACTCATTTGA 60.949 52.381 1.35 0.00 0.00 2.69
821 825 0.322098 CCTGGTTGGGTACGAATGCA 60.322 55.000 0.00 0.00 0.00 3.96
1773 1872 3.866883 ACTTTATTTGGGTTGCCATCG 57.133 42.857 0.00 0.00 0.00 3.84
2236 2337 5.297029 GGGATGAATTGGTTAACTACAGAGC 59.703 44.000 5.42 0.00 0.00 4.09
2237 2338 6.116126 GGATGAATTGGTTAACTACAGAGCT 58.884 40.000 5.42 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 162 5.192327 AGTGTGGCAAGATTTCTCAAAAG 57.808 39.130 0.00 0.00 0.00 2.27
388 390 6.648725 GCTTGCCTGGACAACATAAATTTTTA 59.351 34.615 0.00 0.00 0.00 1.52
683 686 5.370880 AGGCTTGGGTATTGTCATATTCTCT 59.629 40.000 0.00 0.00 0.00 3.10
727 730 0.456221 AGTGGGTAACTCTCATCGCG 59.544 55.000 0.00 0.00 31.64 5.87
741 744 0.032540 GCTGCTTTCAACCAAGTGGG 59.967 55.000 1.69 0.00 44.81 4.61
750 753 2.404566 TACCGCCAGGCTGCTTTCAA 62.405 55.000 10.54 0.00 42.76 2.69
756 759 2.820037 GAGTTACCGCCAGGCTGC 60.820 66.667 10.54 3.81 42.76 5.25
757 760 0.392998 AATGAGTTACCGCCAGGCTG 60.393 55.000 10.54 7.75 42.76 4.85
758 761 0.328258 AAATGAGTTACCGCCAGGCT 59.672 50.000 10.54 0.00 42.76 4.58
759 762 0.451783 CAAATGAGTTACCGCCAGGC 59.548 55.000 0.00 0.00 42.76 4.85
760 763 2.107950 TCAAATGAGTTACCGCCAGG 57.892 50.000 0.00 0.00 45.13 4.45
761 764 2.355756 CCATCAAATGAGTTACCGCCAG 59.644 50.000 0.00 0.00 0.00 4.85
763 766 1.065551 GCCATCAAATGAGTTACCGCC 59.934 52.381 0.00 0.00 0.00 6.13
764 767 1.742831 TGCCATCAAATGAGTTACCGC 59.257 47.619 0.00 0.00 0.00 5.68
765 768 2.223021 CGTGCCATCAAATGAGTTACCG 60.223 50.000 0.00 0.00 0.00 4.02
771 774 4.621068 AATACACGTGCCATCAAATGAG 57.379 40.909 17.22 0.00 0.00 2.90
774 777 4.782019 ACAAATACACGTGCCATCAAAT 57.218 36.364 17.22 0.00 0.00 2.32
775 778 4.576216 AACAAATACACGTGCCATCAAA 57.424 36.364 17.22 0.00 0.00 2.69
776 779 4.294232 CAAACAAATACACGTGCCATCAA 58.706 39.130 17.22 0.00 0.00 2.57
777 780 3.304996 CCAAACAAATACACGTGCCATCA 60.305 43.478 17.22 0.00 0.00 3.07
778 781 3.241701 CCAAACAAATACACGTGCCATC 58.758 45.455 17.22 0.00 0.00 3.51
779 782 2.625790 ACCAAACAAATACACGTGCCAT 59.374 40.909 17.22 6.43 0.00 4.40
821 825 0.738389 CGGCAAACCAAAGTCACAGT 59.262 50.000 0.00 0.00 34.57 3.55
1230 1329 4.555709 ACGGCAAGGTGGACGCAA 62.556 61.111 0.00 0.00 45.15 4.85
2236 2337 1.270550 GGTTGCCACCATGTTGAAGAG 59.729 52.381 1.17 0.00 43.61 2.85
2237 2338 1.327303 GGTTGCCACCATGTTGAAGA 58.673 50.000 1.17 0.00 43.61 2.87


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

AutoCloner maintained by Alex Coulton.