Multiple sequence alignment - TraesCS2B01G497100

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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 TraesCS2B01G497100 chr2B 100.000 2855 0 0 1 2855 693492018 693494872 0 5273
1 TraesCS2B01G497100 chr2B 93.203 2854 163 20 1 2853 694895837 694898660 0 4167
2 TraesCS2B01G497100 chr3D 95.666 2861 115 9 1 2855 64822306 64819449 0 4588
3 TraesCS2B01G497100 chr3D 95.278 2859 126 9 1 2855 613553202 613556055 0 4523
4 TraesCS2B01G497100 chr3D 93.305 2823 181 7 38 2855 175422134 175419315 0 4159
5 TraesCS2B01G497100 chr4B 95.061 2855 138 3 1 2855 200734668 200731817 0 4488
6 TraesCS2B01G497100 chr6D 95.501 2712 116 6 1 2711 419840842 419843548 0 4327
7 TraesCS2B01G497100 chr7B 94.017 2858 148 15 1 2855 92647857 92650694 0 4309
8 TraesCS2B01G497100 chr1D 93.073 2844 183 13 20 2855 58485447 58482610 0 4148
9 TraesCS2B01G497100 chr7D 92.902 2846 186 15 20 2855 30312874 30315713 0 4122


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 TraesCS2B01G497100 chr2B 693492018 693494872 2854 False 5273 5273 100.000 1 2855 1 chr2B.!!$F1 2854
1 TraesCS2B01G497100 chr2B 694895837 694898660 2823 False 4167 4167 93.203 1 2853 1 chr2B.!!$F2 2852
2 TraesCS2B01G497100 chr3D 64819449 64822306 2857 True 4588 4588 95.666 1 2855 1 chr3D.!!$R1 2854
3 TraesCS2B01G497100 chr3D 613553202 613556055 2853 False 4523 4523 95.278 1 2855 1 chr3D.!!$F1 2854
4 TraesCS2B01G497100 chr3D 175419315 175422134 2819 True 4159 4159 93.305 38 2855 1 chr3D.!!$R2 2817
5 TraesCS2B01G497100 chr4B 200731817 200734668 2851 True 4488 4488 95.061 1 2855 1 chr4B.!!$R1 2854
6 TraesCS2B01G497100 chr6D 419840842 419843548 2706 False 4327 4327 95.501 1 2711 1 chr6D.!!$F1 2710
7 TraesCS2B01G497100 chr7B 92647857 92650694 2837 False 4309 4309 94.017 1 2855 1 chr7B.!!$F1 2854
8 TraesCS2B01G497100 chr1D 58482610 58485447 2837 True 4148 4148 93.073 20 2855 1 chr1D.!!$R1 2835
9 TraesCS2B01G497100 chr7D 30312874 30315713 2839 False 4122 4122 92.902 20 2855 1 chr7D.!!$F1 2835

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
176 180 2.070783 CATGCATGTTGGCCAAAACTC 58.929 47.619 22.47 10.87 0.0 3.01 F
1465 1483 1.600413 GCAACAAGTTCAAGAAGCCCG 60.600 52.381 0.00 0.00 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 1587 0.179234 GACCAGCCTCCTCTTTAGCC 59.821 60.0 0.0 0.0 0.0 3.93 R
2492 2519 0.109532 TCCAATGAAGGGTGCGAACA 59.890 50.0 0.0 0.0 0.0 3.18 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
130 133 8.960591 CCAACTGAAACATCTATTCTAACCAAT 58.039 33.333 0.00 0.00 0.00 3.16
151 154 7.153985 CCAATTGAACACATTAACTGTCCAAT 58.846 34.615 7.12 0.00 35.29 3.16
176 180 2.070783 CATGCATGTTGGCCAAAACTC 58.929 47.619 22.47 10.87 0.00 3.01
180 184 3.140623 GCATGTTGGCCAAAACTCAAAT 58.859 40.909 22.47 0.00 0.00 2.32
191 197 5.521372 GCCAAAACTCAAATAATGCATCCTC 59.479 40.000 0.00 0.00 0.00 3.71
214 220 5.359860 TCGCCAACTGAGACATCTATTCTAA 59.640 40.000 0.00 0.00 0.00 2.10
253 259 7.181569 TGACTGTCCAACTGAATATGTATGA 57.818 36.000 5.17 0.00 0.00 2.15
263 269 7.078249 ACTGAATATGTATGATGGCCAACTA 57.922 36.000 10.96 0.00 0.00 2.24
424 430 4.968719 TGTCCCACACATATATTCTGGTCT 59.031 41.667 0.00 0.00 0.00 3.85
560 568 2.076863 CACCTGGATTTTCCGTCTCAC 58.923 52.381 0.00 0.00 40.17 3.51
599 607 5.833406 TGTGCAGAAAAATCTGAAACAGA 57.167 34.783 9.89 3.95 44.99 3.41
613 622 3.703556 TGAAACAGATCCTTGCCAAACAA 59.296 39.130 0.00 0.00 36.62 2.83
616 625 4.961438 ACAGATCCTTGCCAAACAAAAT 57.039 36.364 0.00 0.00 37.96 1.82
739 750 9.973450 AACTAACATAATAAATGTGTGCAAACA 57.027 25.926 13.21 13.21 31.80 2.83
846 859 7.312657 ACCGCCTATTTACTAAGTTTTTAGC 57.687 36.000 0.00 0.00 39.96 3.09
886 899 5.241403 TCCTGTGGTTAACAACTGATGAT 57.759 39.130 18.78 0.00 38.67 2.45
1042 1058 4.021544 GCATACCACAAGGAAATTGGACAA 60.022 41.667 0.00 0.00 43.68 3.18
1167 1183 1.604185 GCGTCTTTGCAGTCAGAGAGT 60.604 52.381 0.00 0.00 34.57 3.24
1282 1299 3.206412 AGAAGAAGGAGAGGATGAGGCTA 59.794 47.826 0.00 0.00 0.00 3.93
1465 1483 1.600413 GCAACAAGTTCAAGAAGCCCG 60.600 52.381 0.00 0.00 0.00 6.13
1569 1587 4.592942 TGGAAGATGAACCTCCAATCTTG 58.407 43.478 2.06 0.00 32.39 3.02
1735 1755 0.234884 GCTCGTGAACAAACCTTCGG 59.765 55.000 0.00 0.00 0.00 4.30
1791 1811 7.287061 TCTCACCTGATGAAAAGGAGTTTTTA 58.713 34.615 0.00 0.00 39.06 1.52
1865 1889 7.888546 TCCCTTAAAGAATTAAGTTTCCCTCTG 59.111 37.037 7.37 0.00 44.29 3.35
2008 2032 0.512952 GCCTTCACTGTGCAACTACG 59.487 55.000 2.12 0.00 38.04 3.51
2074 2101 2.026822 CAGCTAGGTGTCCATTTCCTGT 60.027 50.000 13.89 0.00 33.34 4.00
2086 2113 9.832445 GTGTCCATTTCCTGTAATTATCTTCTA 57.168 33.333 0.00 0.00 0.00 2.10
2269 2296 9.515020 CAATAACAAATGTGTGTACAAGTTTCT 57.485 29.630 0.00 0.00 40.84 2.52
2453 2480 5.326900 TGAGGCATACCATGATTGCATATT 58.673 37.500 13.89 0.70 38.12 1.28
2517 2544 4.277476 TCGCACCCTTCATTGGAATAAAT 58.723 39.130 0.00 0.00 31.34 1.40
2524 2551 8.917088 CACCCTTCATTGGAATAAATAGACATT 58.083 33.333 0.00 0.00 31.34 2.71
2535 2562 9.822185 GGAATAAATAGACATTGCCAATCTTTT 57.178 29.630 0.00 0.00 0.00 2.27
2643 2670 4.373156 ACCTTCTGGCAACTTCATAACT 57.627 40.909 0.00 0.00 36.63 2.24
2701 2728 0.673437 CTTTCCAACCACCGTGCATT 59.327 50.000 0.00 0.00 0.00 3.56
2842 2871 3.751175 CGAGTTTGAACAGAATTGGGCTA 59.249 43.478 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 133 7.340122 TCAATTGGACAGTTAATGTGTTCAA 57.660 32.000 14.02 14.02 45.42 2.69
176 180 3.067180 AGTTGGCGAGGATGCATTATTTG 59.933 43.478 0.00 0.00 36.28 2.32
180 184 1.209261 TCAGTTGGCGAGGATGCATTA 59.791 47.619 0.00 0.00 36.28 1.90
191 197 4.052159 AGAATAGATGTCTCAGTTGGCG 57.948 45.455 0.00 0.00 0.00 5.69
214 220 4.578928 GGACAGTCAATGTGTTTAGTTGGT 59.421 41.667 2.17 0.00 44.17 3.67
424 430 5.817296 CACTATAGCTTTGCAATAGGTGTGA 59.183 40.000 17.76 4.74 0.00 3.58
520 527 8.579863 CCAGGTGAAAGAAGAAATAAGAATTGT 58.420 33.333 0.00 0.00 0.00 2.71
529 536 6.294731 CGGAAAATCCAGGTGAAAGAAGAAAT 60.295 38.462 0.00 0.00 35.91 2.17
560 568 8.914328 TTCTGCACATAATTTGATGTTACATG 57.086 30.769 1.24 0.00 37.99 3.21
599 607 4.563374 GCAGGTATTTTGTTTGGCAAGGAT 60.563 41.667 0.00 0.00 38.47 3.24
668 679 5.350633 TGGCAAGAACATGACTTCTTTTTG 58.649 37.500 8.24 1.42 38.24 2.44
824 837 8.448615 ACAAGCTAAAAACTTAGTAAATAGGCG 58.551 33.333 0.00 0.00 0.00 5.52
846 859 7.141363 CCACAGGAAAGAGTATTTCAAACAAG 58.859 38.462 12.06 0.00 0.00 3.16
857 870 6.053005 CAGTTGTTAACCACAGGAAAGAGTA 58.947 40.000 11.97 0.00 36.48 2.59
865 878 6.823182 TGATATCATCAGTTGTTAACCACAGG 59.177 38.462 11.97 4.31 33.35 4.00
940 955 9.570488 CTCATTGAGATCAAGAATTTCTTTTCC 57.430 33.333 8.00 1.96 39.47 3.13
1042 1058 5.708230 TGTAGTAAACAGATCGCCCATTTTT 59.292 36.000 0.00 0.00 33.01 1.94
1093 1109 1.892338 CCACATTGTCATGGCCCAC 59.108 57.895 0.00 0.00 34.27 4.61
1148 1164 2.287849 TGACTCTCTGACTGCAAAGACG 60.288 50.000 0.00 0.00 0.00 4.18
1167 1183 3.361786 TCCCGTGTCATCAAGAGTATGA 58.638 45.455 0.00 0.00 0.00 2.15
1238 1255 1.400142 CTTGCACAACTCCGTCAACAA 59.600 47.619 0.00 0.00 0.00 2.83
1282 1299 3.532102 AGGGTTCCATAGGTTGAGAACT 58.468 45.455 0.00 0.00 36.53 3.01
1465 1483 1.767681 AGCTCCTCCATCATCACCTTC 59.232 52.381 0.00 0.00 0.00 3.46
1469 1487 1.070445 CCTCAGCTCCTCCATCATCAC 59.930 57.143 0.00 0.00 0.00 3.06
1501 1519 2.408565 TGGATCTGGAATAGGGTCCAC 58.591 52.381 0.00 0.00 42.97 4.02
1569 1587 0.179234 GACCAGCCTCCTCTTTAGCC 59.821 60.000 0.00 0.00 0.00 3.93
1573 1591 1.079658 ACTAGGACCAGCCTCCTCTTT 59.920 52.381 0.00 0.00 46.97 2.52
1735 1755 4.636206 GTGGGATCTCAAGTATTTGGACAC 59.364 45.833 0.00 0.00 34.97 3.67
1791 1811 4.253685 AGTTGCAGTTATACAAGATGCGT 58.746 39.130 0.00 0.00 39.74 5.24
1865 1889 2.203337 TTGCACACTGGACTGCCC 60.203 61.111 0.00 0.00 31.97 5.36
2008 2032 4.386652 CACTTTTTGCATACAGGACATTGC 59.613 41.667 0.00 0.00 35.67 3.56
2041 2067 3.821033 ACACCTAGCTGCACCTTTTTAAG 59.179 43.478 1.02 0.00 0.00 1.85
2074 2101 8.978874 ACATGTGTTGGCATAGAAGATAATTA 57.021 30.769 0.00 0.00 0.00 1.40
2086 2113 5.945784 ACAGTAATAGAACATGTGTTGGCAT 59.054 36.000 0.00 0.00 38.56 4.40
2269 2296 3.515502 CCCTCCTTTGTGTCATCTCTACA 59.484 47.826 0.00 0.00 0.00 2.74
2453 2480 4.345547 TGGTCATGTAGGTAGTGTCAAACA 59.654 41.667 0.00 0.00 0.00 2.83
2492 2519 0.109532 TCCAATGAAGGGTGCGAACA 59.890 50.000 0.00 0.00 0.00 3.18
2517 2544 6.238456 CGAGCATAAAAGATTGGCAATGTCTA 60.238 38.462 19.07 9.26 0.00 2.59
2524 2551 2.722094 ACCGAGCATAAAAGATTGGCA 58.278 42.857 0.00 0.00 31.43 4.92
2535 2562 2.030401 AAACGCGCAACCGAGCATA 61.030 52.632 5.73 0.00 37.91 3.14
2626 2653 5.164620 TGATCAGTTATGAAGTTGCCAGA 57.835 39.130 0.00 0.00 39.39 3.86
2643 2670 3.686405 GCCTCATTGGACCATCTTGATCA 60.686 47.826 0.00 0.00 38.35 2.92
2701 2728 2.009051 GATGTGCCATCGACAACATCA 58.991 47.619 19.04 7.15 35.43 3.07


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

AutoCloner maintained by Alex Coulton.