Multiple sequence alignment - TraesCS6A01G328300

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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 TraesCS6A01G328300 chr6A 100.000 3054 0 0 1 3054 561605168 561602115 0.000000e+00 5640.0
1 TraesCS6A01G328300 chr6A 97.971 3055 60 2 1 3054 561448726 561451779 0.000000e+00 5297.0
2 TraesCS6A01G328300 chr6A 98.157 2496 44 2 560 3054 561591353 561588859 0.000000e+00 4353.0
3 TraesCS6A01G328300 chr2D 94.133 2983 118 11 101 3054 564467534 564470488 0.000000e+00 4486.0
4 TraesCS6A01G328300 chr2D 90.844 1813 138 14 101 1895 556220801 556222603 0.000000e+00 2403.0
5 TraesCS6A01G328300 chr2D 90.310 516 26 3 1895 2386 556223391 556223906 0.000000e+00 654.0
6 TraesCS6A01G328300 chr3D 94.828 1740 77 7 965 2699 482837248 482835517 0.000000e+00 2702.0
7 TraesCS6A01G328300 chr3D 93.174 835 42 3 101 932 482838072 482837250 0.000000e+00 1212.0
8 TraesCS6A01G328300 chr3D 93.333 105 4 3 2375 2477 135533997 135534100 5.270000e-33 152.0
9 TraesCS6A01G328300 chr4A 92.626 1763 95 5 963 2699 30775799 30777552 0.000000e+00 2503.0
10 TraesCS6A01G328300 chr4A 90.048 834 63 2 101 934 30774988 30775801 0.000000e+00 1062.0
11 TraesCS6A01G328300 chr2A 90.349 1803 152 14 101 1895 695816590 695818378 0.000000e+00 2346.0
12 TraesCS6A01G328300 chr2A 89.854 1577 131 16 101 1660 695973989 695975553 0.000000e+00 1999.0
13 TraesCS6A01G328300 chr2A 90.310 516 26 3 1895 2386 695977128 695977643 0.000000e+00 654.0
14 TraesCS6A01G328300 chr2A 90.116 516 27 5 1895 2386 695819148 695819663 0.000000e+00 649.0
15 TraesCS6A01G328300 chr2A 83.058 242 24 5 1654 1895 695976132 695976356 1.440000e-48 204.0
16 TraesCS6A01G328300 chr2A 93.939 99 5 1 2379 2476 407739177 407739275 6.820000e-32 148.0
17 TraesCS6A01G328300 chr2A 89.899 99 8 2 3 100 16228071 16227974 3.200000e-25 126.0
18 TraesCS6A01G328300 chr2B 90.027 1825 156 15 103 1915 663336556 663334746 0.000000e+00 2338.0
19 TraesCS6A01G328300 chr2B 90.588 1700 119 9 244 1936 601729757 601731422 0.000000e+00 2215.0
20 TraesCS6A01G328300 chr2B 95.765 850 31 2 2080 2925 601732563 601733411 0.000000e+00 1365.0
21 TraesCS6A01G328300 chr2B 87.016 516 29 7 1895 2386 663333944 663333443 5.760000e-152 547.0
22 TraesCS6A01G328300 chr2B 97.260 146 4 0 2909 3054 601733533 601733678 6.540000e-62 248.0
23 TraesCS6A01G328300 chr2B 93.333 150 10 0 101 250 601720973 601721122 3.960000e-54 222.0
24 TraesCS6A01G328300 chr2B 97.802 91 2 0 2962 3052 675713750 675713840 1.130000e-34 158.0
25 TraesCS6A01G328300 chr4B 88.191 669 61 11 2211 2863 22448065 22447399 0.000000e+00 782.0
26 TraesCS6A01G328300 chr4B 100.000 82 0 0 2973 3054 22447592 22447511 5.270000e-33 152.0
27 TraesCS6A01G328300 chr6D 90.385 104 9 1 1 103 322588930 322588827 5.310000e-28 135.0
28 TraesCS6A01G328300 chr6B 91.837 98 7 1 1 97 500892105 500892202 5.310000e-28 135.0
29 TraesCS6A01G328300 chr5B 89.109 101 10 1 1 100 550223215 550223315 1.150000e-24 124.0
30 TraesCS6A01G328300 chr5B 87.379 103 12 1 1 102 92194095 92193993 1.920000e-22 117.0
31 TraesCS6A01G328300 chr1B 87.129 101 12 1 1 100 53247068 53247168 2.490000e-21 113.0
32 TraesCS6A01G328300 chr1B 80.392 102 17 3 1 100 686827517 686827617 1.170000e-09 75.0
33 TraesCS6A01G328300 chrUn 85.870 92 8 4 16 104 119256012 119255923 3.240000e-15 93.5


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 TraesCS6A01G328300 chr6A 561602115 561605168 3053 True 5640.000000 5640 100.000000 1 3054 1 chr6A.!!$R2 3053
1 TraesCS6A01G328300 chr6A 561448726 561451779 3053 False 5297.000000 5297 97.971000 1 3054 1 chr6A.!!$F1 3053
2 TraesCS6A01G328300 chr6A 561588859 561591353 2494 True 4353.000000 4353 98.157000 560 3054 1 chr6A.!!$R1 2494
3 TraesCS6A01G328300 chr2D 564467534 564470488 2954 False 4486.000000 4486 94.133000 101 3054 1 chr2D.!!$F1 2953
4 TraesCS6A01G328300 chr2D 556220801 556223906 3105 False 1528.500000 2403 90.577000 101 2386 2 chr2D.!!$F2 2285
5 TraesCS6A01G328300 chr3D 482835517 482838072 2555 True 1957.000000 2702 94.001000 101 2699 2 chr3D.!!$R1 2598
6 TraesCS6A01G328300 chr4A 30774988 30777552 2564 False 1782.500000 2503 91.337000 101 2699 2 chr4A.!!$F1 2598
7 TraesCS6A01G328300 chr2A 695816590 695819663 3073 False 1497.500000 2346 90.232500 101 2386 2 chr2A.!!$F2 2285
8 TraesCS6A01G328300 chr2A 695973989 695977643 3654 False 952.333333 1999 87.740667 101 2386 3 chr2A.!!$F3 2285
9 TraesCS6A01G328300 chr2B 663333443 663336556 3113 True 1442.500000 2338 88.521500 103 2386 2 chr2B.!!$R1 2283
10 TraesCS6A01G328300 chr2B 601729757 601733678 3921 False 1276.000000 2215 94.537667 244 3054 3 chr2B.!!$F3 2810
11 TraesCS6A01G328300 chr4B 22447399 22448065 666 True 467.000000 782 94.095500 2211 3054 2 chr4B.!!$R1 843

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
124 127 2.200337 GGTTGGCGCCTTCAAGGTT 61.200 57.895 29.7 0.0 37.80 3.50 F
1021 1059 0.518636 GAAGCTGCGAAGATGCAACA 59.481 50.000 0.0 0.0 45.74 3.33 F
1596 1644 1.358152 CTCCACTTGTAACCCCCTCA 58.642 55.000 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1342 1389 0.035881 CTGAAGCCAGCCAAGTCTCA 59.964 55.000 0.0 0.0 33.07 3.27 R
1844 2489 1.440938 CGCAAAAGACCAACACGGGA 61.441 55.000 0.0 0.0 40.22 5.14 R
2525 5070 4.260139 TGGCCATGCAGCAAATAATATG 57.740 40.909 0.0 0.0 0.00 1.78 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
124 127 2.200337 GGTTGGCGCCTTCAAGGTT 61.200 57.895 29.70 0.0 37.80 3.50
899 937 4.526970 GCCATCTCCCTATCTTTTGACAA 58.473 43.478 0.00 0.0 0.00 3.18
968 1006 6.835488 TCCTATGGCTAGCAAGAAATGATTTT 59.165 34.615 18.24 0.0 0.00 1.82
1018 1056 0.730840 CATGAAGCTGCGAAGATGCA 59.269 50.000 0.00 0.0 43.95 3.96
1021 1059 0.518636 GAAGCTGCGAAGATGCAACA 59.481 50.000 0.00 0.0 45.74 3.33
1327 1374 1.691976 CAATATACCGAGGGTGGCTCA 59.308 52.381 0.00 0.0 36.19 4.26
1489 1536 7.698163 AAAGTCAGTTAGGATCCCTATCAAT 57.302 36.000 8.55 0.0 35.87 2.57
1596 1644 1.358152 CTCCACTTGTAACCCCCTCA 58.642 55.000 0.00 0.0 0.00 3.86
1844 2489 6.271391 TCGGTCCATTATATGTACCCTTGATT 59.729 38.462 0.00 0.0 36.02 2.57
1859 2504 2.649531 TGATTCCCGTGTTGGTCTTT 57.350 45.000 0.00 0.0 35.15 2.52
1948 3990 3.740115 GAGTCAGGTTAGTGCCTTTTCA 58.260 45.455 0.00 0.0 36.58 2.69
1960 4002 2.828520 TGCCTTTTCAGTGGTTTGTTCA 59.171 40.909 0.00 0.0 0.00 3.18
2047 4115 0.778083 GGGGGTTTGAGGAAGGTCTT 59.222 55.000 0.00 0.0 0.00 3.01
2251 4772 4.574892 TCTGTTCACGGCTGATTTGATTA 58.425 39.130 0.00 0.0 0.00 1.75
2275 4796 7.556733 AGTTACGGTCAACTGTTATTTTCAA 57.443 32.000 0.00 0.0 37.37 2.69
2365 4887 8.428063 GGATGATATAATCCCTTCTCGATTCAT 58.572 37.037 7.84 0.0 40.36 2.57
2525 5070 5.126779 GGTGGTTCTCCAGAAATTAGGATC 58.873 45.833 0.00 0.0 45.24 3.36
2661 5222 6.521162 TGAGAAGTGTTAGTTTCATGCTACA 58.479 36.000 0.00 0.0 0.00 2.74
2891 5452 2.057137 ACTCTTTGCTGCTTGACCAA 57.943 45.000 0.00 0.0 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.800993 CCACTAGCAGTTAATTGAGAGTCG 59.199 45.833 1.56 0.0 0.00 4.18
18 19 5.876357 TCCTTTGACCACTAGCAGTTAATT 58.124 37.500 0.00 0.0 0.00 1.40
124 127 3.144657 AGAATGGCAATGATATCCGCA 57.855 42.857 0.00 0.0 0.00 5.69
662 685 1.218196 CTACTGCTTCTCCCTCCCCTA 59.782 57.143 0.00 0.0 0.00 3.53
899 937 2.420547 CCTTGTCACATCCCGTCATCAT 60.421 50.000 0.00 0.0 0.00 2.45
968 1006 2.303022 CCTCTGGTGGCAAGTCTTCTTA 59.697 50.000 0.00 0.0 32.07 2.10
1018 1056 3.925630 CTGCATGGCCTCCGGTGTT 62.926 63.158 3.32 0.0 0.00 3.32
1327 1374 0.909610 TCTCAAGCTTCCCGGTGGAT 60.910 55.000 0.00 0.0 41.40 3.41
1342 1389 0.035881 CTGAAGCCAGCCAAGTCTCA 59.964 55.000 0.00 0.0 33.07 3.27
1489 1536 2.877154 AAAGGGGATGAGAGCTAGGA 57.123 50.000 0.00 0.0 0.00 2.94
1596 1644 1.229209 ATGTGGGAGGACCTCGTGT 60.229 57.895 15.46 0.0 41.11 4.49
1844 2489 1.440938 CGCAAAAGACCAACACGGGA 61.441 55.000 0.00 0.0 40.22 5.14
1948 3990 6.405538 ACACAAATGAATTGAACAAACCACT 58.594 32.000 0.00 0.0 41.85 4.00
1960 4002 2.971330 TGGAGGCCAACACAAATGAATT 59.029 40.909 5.01 0.0 0.00 2.17
2047 4115 8.812513 AATGATGGAACTCATGAACTCAAATA 57.187 30.769 0.00 0.0 36.03 1.40
2251 4772 7.556733 TTGAAAATAACAGTTGACCGTAACT 57.443 32.000 0.00 0.0 41.37 2.24
2275 4796 5.114780 CACATTCGAGAAGATCTGACCAAT 58.885 41.667 0.00 0.0 0.00 3.16
2365 4887 5.880332 GGGAGTACTGTGCAAATGAATAAGA 59.120 40.000 0.00 0.0 0.00 2.10
2525 5070 4.260139 TGGCCATGCAGCAAATAATATG 57.740 40.909 0.00 0.0 0.00 1.78
2579 5125 7.281100 GTGAAATTTGTTCACCCAATAACCAAA 59.719 33.333 7.80 0.0 42.07 3.28
2656 5217 9.780186 ATTATCTAAACCAAATAGGACTGTAGC 57.220 33.333 0.00 0.0 41.22 3.58
2726 5287 9.571810 CATAATATTTGCTAGCTTTGAACACAA 57.428 29.630 17.23 0.0 0.00 3.33


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

AutoCloner maintained by Alex Coulton.