Multiple sequence alignment - TraesCS2B01G161100

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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 TraesCS2B01G161100 chr2B 100.000 2929 0 0 1 2929 134340627 134343555 0.000000e+00 5409
1 TraesCS2B01G161100 chr4D 95.385 2925 98 18 24 2929 85853476 85850570 0.000000e+00 4619
2 TraesCS2B01G161100 chr6D 96.080 2245 63 12 470 2697 440673101 440675337 0.000000e+00 3635
3 TraesCS2B01G161100 chr6D 92.993 1313 78 11 1624 2929 450189339 450188034 0.000000e+00 1903
4 TraesCS2B01G161100 chr6D 92.559 766 41 8 32 793 137153310 137152557 0.000000e+00 1085
5 TraesCS2B01G161100 chr6D 93.488 430 13 6 1 426 440672679 440673097 2.480000e-175 625
6 TraesCS2B01G161100 chr5D 95.477 2277 63 19 1 2275 27280088 27282326 0.000000e+00 3598
7 TraesCS2B01G161100 chr5D 95.821 1388 44 7 1071 2450 431973345 431974726 0.000000e+00 2230
8 TraesCS2B01G161100 chr5D 92.965 1322 79 11 1615 2929 127940012 127938698 0.000000e+00 1914
9 TraesCS2B01G161100 chr5D 93.809 743 37 6 22 762 431972612 431973347 0.000000e+00 1109
10 TraesCS2B01G161100 chr4A 94.022 1723 72 9 188 1900 658380915 658382616 0.000000e+00 2582
11 TraesCS2B01G161100 chr4A 92.417 211 10 4 2 208 658380799 658381007 2.210000e-76 296
12 TraesCS2B01G161100 chr2D 95.613 1550 49 8 470 2006 606091670 606090127 0.000000e+00 2468
13 TraesCS2B01G161100 chr2D 96.967 1220 30 5 1713 2929 29096343 29095128 0.000000e+00 2041
14 TraesCS2B01G161100 chr2D 94.322 1092 50 7 21 1110 29097426 29096345 0.000000e+00 1663
15 TraesCS2B01G161100 chr7D 93.090 1317 79 9 1615 2925 530740951 530739641 0.000000e+00 1917
16 TraesCS2B01G161100 chr7D 92.646 1319 83 11 1615 2926 340173622 340174933 0.000000e+00 1886
17 TraesCS2B01G161100 chr6A 95.299 1170 43 4 696 1857 163168206 163167041 0.000000e+00 1845
18 TraesCS2B01G161100 chr6A 91.840 625 40 4 25 647 163168820 163168205 0.000000e+00 861
19 TraesCS2B01G161100 chr7B 93.674 1154 43 14 1 1137 228799927 228801067 0.000000e+00 1700
20 TraesCS2B01G161100 chr7B 97.419 930 23 1 1176 2105 228801064 228801992 0.000000e+00 1583
21 TraesCS2B01G161100 chr7A 90.217 828 59 13 811 1626 41464795 41463978 0.000000e+00 1061
22 TraesCS2B01G161100 chr7A 89.806 824 58 14 811 1623 617598489 617599297 0.000000e+00 1033
23 TraesCS2B01G161100 chr2A 89.684 824 59 13 811 1623 756524456 756525264 0.000000e+00 1027
24 TraesCS2B01G161100 chr3D 94.839 465 15 4 784 1239 614089797 614089333 0.000000e+00 717


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 TraesCS2B01G161100 chr2B 134340627 134343555 2928 False 5409.0 5409 100.0000 1 2929 1 chr2B.!!$F1 2928
1 TraesCS2B01G161100 chr4D 85850570 85853476 2906 True 4619.0 4619 95.3850 24 2929 1 chr4D.!!$R1 2905
2 TraesCS2B01G161100 chr6D 440672679 440675337 2658 False 2130.0 3635 94.7840 1 2697 2 chr6D.!!$F1 2696
3 TraesCS2B01G161100 chr6D 450188034 450189339 1305 True 1903.0 1903 92.9930 1624 2929 1 chr6D.!!$R2 1305
4 TraesCS2B01G161100 chr6D 137152557 137153310 753 True 1085.0 1085 92.5590 32 793 1 chr6D.!!$R1 761
5 TraesCS2B01G161100 chr5D 27280088 27282326 2238 False 3598.0 3598 95.4770 1 2275 1 chr5D.!!$F1 2274
6 TraesCS2B01G161100 chr5D 127938698 127940012 1314 True 1914.0 1914 92.9650 1615 2929 1 chr5D.!!$R1 1314
7 TraesCS2B01G161100 chr5D 431972612 431974726 2114 False 1669.5 2230 94.8150 22 2450 2 chr5D.!!$F2 2428
8 TraesCS2B01G161100 chr4A 658380799 658382616 1817 False 1439.0 2582 93.2195 2 1900 2 chr4A.!!$F1 1898
9 TraesCS2B01G161100 chr2D 606090127 606091670 1543 True 2468.0 2468 95.6130 470 2006 1 chr2D.!!$R1 1536
10 TraesCS2B01G161100 chr2D 29095128 29097426 2298 True 1852.0 2041 95.6445 21 2929 2 chr2D.!!$R2 2908
11 TraesCS2B01G161100 chr7D 530739641 530740951 1310 True 1917.0 1917 93.0900 1615 2925 1 chr7D.!!$R1 1310
12 TraesCS2B01G161100 chr7D 340173622 340174933 1311 False 1886.0 1886 92.6460 1615 2926 1 chr7D.!!$F1 1311
13 TraesCS2B01G161100 chr6A 163167041 163168820 1779 True 1353.0 1845 93.5695 25 1857 2 chr6A.!!$R1 1832
14 TraesCS2B01G161100 chr7B 228799927 228801992 2065 False 1641.5 1700 95.5465 1 2105 2 chr7B.!!$F1 2104
15 TraesCS2B01G161100 chr7A 41463978 41464795 817 True 1061.0 1061 90.2170 811 1626 1 chr7A.!!$R1 815
16 TraesCS2B01G161100 chr7A 617598489 617599297 808 False 1033.0 1033 89.8060 811 1623 1 chr7A.!!$F1 812
17 TraesCS2B01G161100 chr2A 756524456 756525264 808 False 1027.0 1027 89.6840 811 1623 1 chr2A.!!$F1 812


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
724 761 0.31812 TCTGACGAAGCACATGAGCA 59.682 50.0 17.61 0.0 36.85 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2429 2559 0.178953 AGCCCAAGAGCCAACATTGT 60.179 50.0 0.0 0.0 0.0 2.71 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
63 68 2.967201 TCCACTCTTCCCGTAGAAAACA 59.033 45.455 0.00 0.00 32.88 2.83
68 73 5.238650 CACTCTTCCCGTAGAAAACATGTTT 59.761 40.000 18.13 18.13 32.88 2.83
96 101 2.032528 TGTTCGAAGCAGCAGGGG 59.967 61.111 0.00 0.00 0.00 4.79
694 729 6.891388 TCAGTTCTGGTTAGTAGTTGGAAAA 58.109 36.000 0.00 0.00 0.00 2.29
724 761 0.318120 TCTGACGAAGCACATGAGCA 59.682 50.000 17.61 0.00 36.85 4.26
781 818 4.513442 TGCTTCGTTATGCTTAATGGAGT 58.487 39.130 17.07 0.00 33.86 3.85
968 1011 0.813610 CACACAGCCCAACTCGACAA 60.814 55.000 0.00 0.00 0.00 3.18
1093 1163 4.343814 TGCACAGGAATATGAGGAACGATA 59.656 41.667 0.00 0.00 0.00 2.92
1169 1239 5.076182 TGAGAGGGAGTCTATCAAGCATAG 58.924 45.833 0.00 0.00 40.37 2.23
1472 1590 3.256631 CCAAGACCACCTTTTCATTCCTG 59.743 47.826 0.00 0.00 31.42 3.86
1642 1763 6.154363 TGAAACAAGACAGAAGGACCAAAATT 59.846 34.615 0.00 0.00 0.00 1.82
1738 1862 4.693042 TTGTTTAGACGGAGGGAAGAAA 57.307 40.909 0.00 0.00 0.00 2.52
1920 2044 1.299468 GCGACTAGACTGGCCATCG 60.299 63.158 17.71 17.71 0.00 3.84
1935 2059 5.890334 TGGCCATCGAGCTTTAAATTTTAG 58.110 37.500 0.00 0.00 0.00 1.85
2042 2166 5.988561 TCTTTGGTCTTTTGCGCATTTAAAT 59.011 32.000 12.75 0.00 0.00 1.40
2083 2207 7.147312 TGCCAATCTCTTTAATTTTCACACAG 58.853 34.615 0.00 0.00 0.00 3.66
2218 2346 7.016072 CAGTATCTTTCTAATCTCCCACCTCAT 59.984 40.741 0.00 0.00 0.00 2.90
2237 2365 2.208132 TGCGCTGAAATTAAAGGGGA 57.792 45.000 9.73 1.71 0.00 4.81
2429 2559 6.549364 TCTTCTTGCCTTTTTCAGGTATTTGA 59.451 34.615 0.00 0.00 46.07 2.69
2520 2650 0.689623 CAGGGGCTGTGAAGAACTCT 59.310 55.000 0.00 0.00 0.00 3.24
2648 2782 3.950794 GACGTGCTCATCCCGGCAA 62.951 63.158 0.00 0.00 40.26 4.52
2764 2899 3.301274 AGAGTATCCTCCTGGCTGTTAC 58.699 50.000 0.00 0.00 38.58 2.50
2769 2904 3.876309 TCCTCCTGGCTGTTACTTTTT 57.124 42.857 0.00 0.00 0.00 1.94
2881 3016 0.461548 TCATCGAGGCTGCTAACCAG 59.538 55.000 0.00 0.00 44.67 4.00
2891 3026 3.633361 GCTAACCAGCCAACAGACT 57.367 52.632 0.00 0.00 42.37 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 43 1.356738 TCTACGGGAAGAGTGGAGGAA 59.643 52.381 0.00 0.00 0.00 3.36
63 68 3.197766 TCGAACAGATAGGGCTCAAACAT 59.802 43.478 0.00 0.00 0.00 2.71
68 73 1.137086 GCTTCGAACAGATAGGGCTCA 59.863 52.381 0.00 0.00 0.00 4.26
378 387 1.480545 GGTGCTCTTCCTCTTCCTCTC 59.519 57.143 0.00 0.00 0.00 3.20
428 445 1.002011 GCCCTTTCTCTCCGCCTTT 60.002 57.895 0.00 0.00 0.00 3.11
429 446 2.224159 TGCCCTTTCTCTCCGCCTT 61.224 57.895 0.00 0.00 0.00 4.35
694 729 6.163476 TGTGCTTCGTCAGATACTTTTACAT 58.837 36.000 0.00 0.00 0.00 2.29
724 761 2.041620 AGTTACATGGCCACTGTGGAAT 59.958 45.455 30.23 18.64 40.96 3.01
849 886 2.095869 CAGCAACTGCAGAATCAGTCAC 60.096 50.000 23.35 0.00 45.77 3.67
968 1011 1.339438 CCTGTTGACATGGCTAGTGCT 60.339 52.381 0.00 0.00 39.59 4.40
1055 1115 0.179100 GTGCAGCTTGATCTCGCCTA 60.179 55.000 0.00 0.00 0.00 3.93
1093 1163 3.118482 AGCGTCATCTTCATGTTCTCCAT 60.118 43.478 0.00 0.00 0.00 3.41
1169 1239 1.001641 AGCCACAGAAGCATGGACC 60.002 57.895 0.00 0.00 38.34 4.46
1472 1590 7.595130 GTGAAACATAAGAAAACAGGGACATTC 59.405 37.037 0.00 0.00 36.32 2.67
1642 1763 8.803397 TTCTACTTAGTGAGCAAGTGTAGATA 57.197 34.615 0.00 0.00 36.88 1.98
1738 1862 8.850156 GTGCAGAATAAAGGGATATGTTGTATT 58.150 33.333 0.00 0.00 0.00 1.89
1773 1897 1.204941 GTCCTACAACTGCTCCATCGT 59.795 52.381 0.00 0.00 0.00 3.73
1935 2059 8.623903 TCAATTGCAATATCTTGAGATTACACC 58.376 33.333 13.39 0.00 36.05 4.16
2042 2166 3.834489 TGGCAAAATTTTCTCTGGCAA 57.166 38.095 12.82 0.00 40.89 4.52
2083 2207 2.808906 AATGGGGAACACCTTAGCTC 57.191 50.000 0.00 0.00 40.03 4.09
2218 2346 2.208132 TCCCCTTTAATTTCAGCGCA 57.792 45.000 11.47 0.00 0.00 6.09
2237 2365 3.493176 GGTGCTCATTGTTTGCTCCTTTT 60.493 43.478 0.00 0.00 37.38 2.27
2296 2424 6.040504 ACGATGATTACTAGCATTGTGTAGGA 59.959 38.462 0.00 0.00 41.92 2.94
2400 2529 4.363138 CCTGAAAAAGGCAAGAAGACAAC 58.637 43.478 0.00 0.00 39.93 3.32
2429 2559 0.178953 AGCCCAAGAGCCAACATTGT 60.179 50.000 0.00 0.00 0.00 2.71
2511 2641 6.690194 ATGTCAATGCCATTAGAGTTCTTC 57.310 37.500 0.00 0.00 0.00 2.87
2568 2699 2.040442 TCGGAGCCCTTGATCCCA 59.960 61.111 0.00 0.00 44.50 4.37
2820 2955 4.553330 TCAACATTGTCCCTAGGAGAAC 57.447 45.455 11.48 6.16 37.80 3.01
2881 3016 2.435059 GCCTCGGAGTCTGTTGGC 60.435 66.667 18.00 18.00 0.00 4.52



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

AutoCloner maintained by Alex Coulton.