Multiple sequence alignment - TraesCS3A01G119200

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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 TraesCS3A01G119200 chr3A 100.000 2942 0 0 1 2942 91286641 91283700 0.000000e+00 5433
1 TraesCS3A01G119200 chr3A 90.206 970 74 19 1 956 486063798 486064760 0.000000e+00 1245
2 TraesCS3A01G119200 chr3D 93.536 2011 104 11 957 2942 78096977 78098986 0.000000e+00 2970
3 TraesCS3A01G119200 chr3D 93.333 2010 108 9 957 2942 77999284 78001291 0.000000e+00 2946
4 TraesCS3A01G119200 chr3B 89.254 2010 155 21 957 2942 124120370 124118398 0.000000e+00 2459
5 TraesCS3A01G119200 chr7D 93.450 1313 84 2 957 2268 177169162 177170473 0.000000e+00 1947
6 TraesCS3A01G119200 chr7D 90.244 164 6 4 2779 2942 177170465 177170618 3.840000e-49 206
7 TraesCS3A01G119200 chr7A 93.069 1313 89 2 957 2268 181169033 181170344 0.000000e+00 1919
8 TraesCS3A01G119200 chr7A 92.536 1313 96 2 957 2268 181014954 181016265 0.000000e+00 1881
9 TraesCS3A01G119200 chr7A 92.542 1314 95 3 957 2268 181050516 181051828 0.000000e+00 1881
10 TraesCS3A01G119200 chr7A 92.232 1313 93 5 957 2268 180843900 180845204 0.000000e+00 1851
11 TraesCS3A01G119200 chr7A 92.079 1313 102 2 957 2268 180984931 180986242 0.000000e+00 1847
12 TraesCS3A01G119200 chr7A 94.161 959 37 14 1 956 190626035 190625093 0.000000e+00 1443
13 TraesCS3A01G119200 chr7A 95.732 164 7 0 2779 2942 180845196 180845359 6.250000e-67 265
14 TraesCS3A01G119200 chr7A 95.732 164 7 0 2779 2942 180986234 180986397 6.250000e-67 265
15 TraesCS3A01G119200 chr7A 95.122 164 8 0 2779 2942 181016257 181016420 2.910000e-65 259
16 TraesCS3A01G119200 chr7A 93.902 164 10 0 2779 2942 181051820 181051983 6.300000e-62 248
17 TraesCS3A01G119200 chr7A 93.902 164 10 0 2779 2942 181170336 181170499 6.300000e-62 248
18 TraesCS3A01G119200 chr4D 90.334 1438 120 9 957 2389 388250866 388249443 0.000000e+00 1868
19 TraesCS3A01G119200 chr4A 94.387 962 41 10 1 957 535526241 535525288 0.000000e+00 1465
20 TraesCS3A01G119200 chr5A 94.375 960 40 11 1 956 171062572 171061623 0.000000e+00 1461
21 TraesCS3A01G119200 chr5A 93.672 964 43 11 1 956 301444954 301445907 0.000000e+00 1426
22 TraesCS3A01G119200 chr1A 93.582 966 47 9 1 956 74137544 74136584 0.000000e+00 1426
23 TraesCS3A01G119200 chr1A 93.111 958 50 8 1 956 294618879 294617936 0.000000e+00 1389
24 TraesCS3A01G119200 chr1A 92.761 967 52 12 1 954 74130168 74129207 0.000000e+00 1382
25 TraesCS3A01G119200 chr2A 93.354 963 52 10 1 957 659930790 659929834 0.000000e+00 1413


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 TraesCS3A01G119200 chr3A 91283700 91286641 2941 True 5433.0 5433 100.0000 1 2942 1 chr3A.!!$R1 2941
1 TraesCS3A01G119200 chr3A 486063798 486064760 962 False 1245.0 1245 90.2060 1 956 1 chr3A.!!$F1 955
2 TraesCS3A01G119200 chr3D 78096977 78098986 2009 False 2970.0 2970 93.5360 957 2942 1 chr3D.!!$F2 1985
3 TraesCS3A01G119200 chr3D 77999284 78001291 2007 False 2946.0 2946 93.3330 957 2942 1 chr3D.!!$F1 1985
4 TraesCS3A01G119200 chr3B 124118398 124120370 1972 True 2459.0 2459 89.2540 957 2942 1 chr3B.!!$R1 1985
5 TraesCS3A01G119200 chr7D 177169162 177170618 1456 False 1076.5 1947 91.8470 957 2942 2 chr7D.!!$F1 1985
6 TraesCS3A01G119200 chr7A 190625093 190626035 942 True 1443.0 1443 94.1610 1 956 1 chr7A.!!$R1 955
7 TraesCS3A01G119200 chr7A 181169033 181170499 1466 False 1083.5 1919 93.4855 957 2942 2 chr7A.!!$F5 1985
8 TraesCS3A01G119200 chr7A 181014954 181016420 1466 False 1070.0 1881 93.8290 957 2942 2 chr7A.!!$F3 1985
9 TraesCS3A01G119200 chr7A 181050516 181051983 1467 False 1064.5 1881 93.2220 957 2942 2 chr7A.!!$F4 1985
10 TraesCS3A01G119200 chr7A 180843900 180845359 1459 False 1058.0 1851 93.9820 957 2942 2 chr7A.!!$F1 1985
11 TraesCS3A01G119200 chr7A 180984931 180986397 1466 False 1056.0 1847 93.9055 957 2942 2 chr7A.!!$F2 1985
12 TraesCS3A01G119200 chr4D 388249443 388250866 1423 True 1868.0 1868 90.3340 957 2389 1 chr4D.!!$R1 1432
13 TraesCS3A01G119200 chr4A 535525288 535526241 953 True 1465.0 1465 94.3870 1 957 1 chr4A.!!$R1 956
14 TraesCS3A01G119200 chr5A 171061623 171062572 949 True 1461.0 1461 94.3750 1 956 1 chr5A.!!$R1 955
15 TraesCS3A01G119200 chr5A 301444954 301445907 953 False 1426.0 1426 93.6720 1 956 1 chr5A.!!$F1 955
16 TraesCS3A01G119200 chr1A 74136584 74137544 960 True 1426.0 1426 93.5820 1 956 1 chr1A.!!$R2 955
17 TraesCS3A01G119200 chr1A 294617936 294618879 943 True 1389.0 1389 93.1110 1 956 1 chr1A.!!$R3 955
18 TraesCS3A01G119200 chr1A 74129207 74130168 961 True 1382.0 1382 92.7610 1 954 1 chr1A.!!$R1 953
19 TraesCS3A01G119200 chr2A 659929834 659930790 956 True 1413.0 1413 93.3540 1 957 1 chr2A.!!$R1 956

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
423 473 0.89972 CTATATAAAGGCGCCCCCGA 59.1 55.0 26.15 6.6 39.21 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 2066 1.134788 TCGCTAGCTAAGGAACCAAGC 60.135 52.381 13.93 9.26 36.48 4.01 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
66 67 3.446310 TTTGGAAAAAGGGTTTCGAGC 57.554 42.857 0.00 0.00 0.00 5.03
201 202 5.391060 AAAAAGAGAAACGACGAACAGAG 57.609 39.130 0.00 0.00 0.00 3.35
423 473 0.899720 CTATATAAAGGCGCCCCCGA 59.100 55.000 26.15 6.60 39.21 5.14
457 507 3.625745 GGTACGGCCCATAATCAGG 57.374 57.895 0.00 0.00 0.00 3.86
969 1023 5.046520 GGGATGTTACATCTACATAGGGGAC 60.047 48.000 22.48 3.79 36.41 4.46
1169 1224 0.030638 GATGCCAACGTTGTTGCTGT 59.969 50.000 25.63 15.22 0.00 4.40
1189 1244 5.817296 GCTGTAGACCATGACAACAATGATA 59.183 40.000 0.00 0.00 0.00 2.15
1198 1253 6.479331 CCATGACAACAATGATAGAGAGACAG 59.521 42.308 0.00 0.00 0.00 3.51
1245 1300 2.816689 CGTGCCATTTATCACCGTCTA 58.183 47.619 0.00 0.00 0.00 2.59
1246 1301 3.390135 CGTGCCATTTATCACCGTCTAT 58.610 45.455 0.00 0.00 0.00 1.98
1294 1349 7.489160 TGAAGCGTACAATACATACTCAATCT 58.511 34.615 0.00 0.00 0.00 2.40
1320 1375 5.181245 TGTTTCTTACCTAGCAAAGATGTGC 59.819 40.000 6.00 0.00 45.28 4.57
1462 1517 3.258228 GGTTCCAAAACAAACACACCTG 58.742 45.455 0.00 0.00 37.10 4.00
1598 1654 5.824624 AGCATTGTTCGTCATTGGATCTTAT 59.175 36.000 0.00 0.00 0.00 1.73
1640 1696 4.139038 CCTCATGAACATGGCATCATACA 58.861 43.478 13.67 0.00 39.24 2.29
1838 1894 2.836636 ACTCAGGATACCTCAGAGCA 57.163 50.000 0.00 0.00 31.71 4.26
1851 1907 2.036475 CTCAGAGCACCAACGCCTATAT 59.964 50.000 0.00 0.00 0.00 0.86
1917 1973 5.187186 TGCCTATCTTAAAGAAGGTCTTCGT 59.813 40.000 5.22 0.00 43.97 3.85
1940 1996 0.473755 AATGGCATGTCGCTCCCATA 59.526 50.000 0.00 0.00 41.91 2.74
2002 2060 5.234329 ACGTTAATCTTCCGCATGAACTATG 59.766 40.000 0.00 0.00 39.88 2.23
2008 2066 4.155826 TCTTCCGCATGAACTATGGTTTTG 59.844 41.667 0.00 0.00 37.26 2.44
2110 2168 1.136305 GGCTCTCATGGTTGCTACGTA 59.864 52.381 0.00 0.00 0.00 3.57
2116 2174 2.764010 TCATGGTTGCTACGTAGGATGT 59.236 45.455 23.47 5.16 0.00 3.06
2202 2260 0.174845 CCGTGAAGCTCGGTCCAATA 59.825 55.000 4.22 0.00 42.62 1.90
2351 2411 2.420022 GTGGTGTGAGTATGCCATTCAC 59.580 50.000 3.10 3.10 42.63 3.18
2419 2479 0.549950 CTTCTGGATCCATGGCTGGT 59.450 55.000 16.63 0.00 43.61 4.00
2483 2565 6.054635 CATAGAGAATGATGAGGGGGATCCT 61.055 48.000 12.58 0.00 42.98 3.24
2498 2580 4.654724 GGGGATCCTAAGCTACAAGTAGTT 59.345 45.833 12.58 0.08 35.65 2.24
2520 2602 3.907474 TCAATACTTGGTGAAGGAGTCCA 59.093 43.478 12.86 0.00 32.95 4.02
2525 2607 1.207488 TGGTGAAGGAGTCCATGGGG 61.207 60.000 13.02 0.00 0.00 4.96
2603 2685 3.822735 ACATGTGAATAAGCAAGTGCAGT 59.177 39.130 6.00 0.00 45.16 4.40
2634 2718 3.245229 TGTCCATGGAGCACAACCTAATT 60.245 43.478 16.81 0.00 0.00 1.40
2735 2819 5.459762 CCAACAACAATGTCAAGAATGTGTC 59.540 40.000 0.00 0.00 39.40 3.67
2797 2881 3.389329 TCAAGAGAGAAAGGCACAAGAGT 59.611 43.478 0.00 0.00 0.00 3.24
2827 2911 2.224475 CGAGATCAAGGCATCCAAGGAT 60.224 50.000 0.00 0.00 34.81 3.24
2908 2992 5.657745 TGTGCTTTGGATGACATATCCATTT 59.342 36.000 9.26 0.00 46.51 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 2.358737 AAGCGCCTGGAGTTTCGG 60.359 61.111 2.29 0.00 0.00 4.30
186 187 3.910767 ACGATTACTCTGTTCGTCGTTTC 59.089 43.478 0.00 0.00 41.93 2.78
704 757 8.339247 TGAGAGAGGGAATAAAATGAATTTCCT 58.661 33.333 0.00 0.00 43.79 3.36
1169 1224 7.561356 TCTCTCTATCATTGTTGTCATGGTCTA 59.439 37.037 0.00 0.00 0.00 2.59
1189 1244 4.164030 TCTCTGCTCACTATCTGTCTCTCT 59.836 45.833 0.00 0.00 0.00 3.10
1198 1253 2.103771 TGGCCATTCTCTGCTCACTATC 59.896 50.000 0.00 0.00 0.00 2.08
1245 1300 4.099881 AGTTGTTGGATTTGTTCACTGCAT 59.900 37.500 0.00 0.00 0.00 3.96
1246 1301 3.446873 AGTTGTTGGATTTGTTCACTGCA 59.553 39.130 0.00 0.00 0.00 4.41
1294 1349 7.065803 GCACATCTTTGCTAGGTAAGAAACATA 59.934 37.037 0.00 0.00 39.59 2.29
1320 1375 9.520204 GGTCATGTTAATGAAAATGGATTAGTG 57.480 33.333 0.00 0.00 44.40 2.74
1462 1517 7.201705 GGAAAAGAATGGTATGTACCTTACTGC 60.202 40.741 10.36 0.00 46.58 4.40
1504 1559 2.300152 ACTGCATATCATAGGTGACCCG 59.700 50.000 0.00 0.00 37.14 5.28
1619 1675 4.820173 AGTGTATGATGCCATGTTCATGAG 59.180 41.667 13.51 5.83 34.52 2.90
1640 1696 7.361457 GCGTCATTTTAATTAGTGGTTACCAGT 60.361 37.037 16.58 16.58 40.67 4.00
1809 1865 6.199376 TGAGGTATCCTGAGTTTGTACCATA 58.801 40.000 0.00 0.00 37.78 2.74
1838 1894 2.867624 TCTCGGTATATAGGCGTTGGT 58.132 47.619 0.00 0.00 0.00 3.67
1851 1907 3.574396 CCTTGAGCCTCATATTCTCGGTA 59.426 47.826 0.00 0.00 0.00 4.02
1940 1996 2.297895 TATGGTCAGTTGCGGCCCT 61.298 57.895 0.00 0.00 0.00 5.19
2002 2060 2.628178 AGCTAAGGAACCAAGCAAAACC 59.372 45.455 16.45 0.00 38.75 3.27
2008 2066 1.134788 TCGCTAGCTAAGGAACCAAGC 60.135 52.381 13.93 9.26 36.48 4.01
2110 2168 2.319844 TGCCATATCTCGTGACATCCT 58.680 47.619 0.00 0.00 0.00 3.24
2116 2174 3.324556 TCCATGATTGCCATATCTCGTGA 59.675 43.478 0.00 0.00 33.31 4.35
2202 2260 2.434702 ACTCAAAGAGACAAAGACGGGT 59.565 45.455 0.31 0.00 33.32 5.28
2351 2411 4.004314 ACATCGATGGTAGAGGTATCTCG 58.996 47.826 28.09 0.00 44.47 4.04
2419 2479 3.062466 CCGAGGAGTGCACGAGGA 61.062 66.667 12.01 0.00 0.00 3.71
2461 2543 3.407540 AGGATCCCCCTCATCATTCTCTA 59.592 47.826 8.55 0.00 43.31 2.43
2466 2548 2.646798 GCTTAGGATCCCCCTCATCATT 59.353 50.000 8.55 0.00 43.31 2.57
2520 2602 2.616458 GGGCACAAGAGGACCCCAT 61.616 63.158 0.00 0.00 36.24 4.00
2525 2607 2.358737 CACCGGGCACAAGAGGAC 60.359 66.667 6.32 0.00 0.00 3.85
2560 2642 3.618150 GTGATGAAATTTCCCATTTGGCG 59.382 43.478 15.48 0.00 0.00 5.69
2603 2685 1.820519 GCTCCATGGACATGAAAAGCA 59.179 47.619 11.44 0.00 41.20 3.91
2634 2718 2.757868 GCTCCTGTCTTTCTGCTCTCTA 59.242 50.000 0.00 0.00 0.00 2.43
2689 2773 3.494924 GCCACCACTATGCACATCATCTA 60.495 47.826 0.00 0.00 36.63 1.98
2735 2819 2.287103 CACATGGTCTTCGCATCATCTG 59.713 50.000 0.00 0.00 0.00 2.90
2797 2881 4.801330 TGCCTTGATCTCGAACTCTTTA 57.199 40.909 0.00 0.00 0.00 1.85
2827 2911 7.043961 TGCAATGTATTAAACAAACTCACCA 57.956 32.000 0.00 0.00 42.70 4.17


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

AutoCloner maintained by Alex Coulton.