Multiple sequence alignment - TraesCS2B01G201600

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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 TraesCS2B01G201600 chr2B 100.000 3542 0 0 1 3542 180604684 180608225 0.000000e+00 6541
1 TraesCS2B01G201600 chr2D 94.502 3001 83 25 608 3542 126982750 126985734 0.000000e+00 4553
2 TraesCS2B01G201600 chr2D 89.519 582 42 10 1 575 126982181 126982750 0.000000e+00 719
3 TraesCS2B01G201600 chr2D 84.718 373 45 6 1896 2266 103370613 103370251 2.600000e-96 363
4 TraesCS2B01G201600 chr2D 84.865 370 44 6 1896 2263 104398127 104398486 2.600000e-96 363
5 TraesCS2B01G201600 chr2A 91.817 3214 149 46 1 3147 133684108 133687274 0.000000e+00 4373
6 TraesCS2B01G201600 chr2A 86.290 372 6 5 3187 3542 133687271 133687613 2.600000e-96 363
7 TraesCS2B01G201600 chr2A 80.155 388 48 16 1891 2266 525822929 525822559 2.710000e-66 263
8 TraesCS2B01G201600 chr4D 91.365 718 42 7 997 1713 236934453 236935151 0.000000e+00 965
9 TraesCS2B01G201600 chr4D 93.886 458 28 0 1712 2169 236936017 236936474 0.000000e+00 691
10 TraesCS2B01G201600 chr4D 95.567 203 9 0 2168 2370 236936594 236936796 3.410000e-85 326
11 TraesCS2B01G201600 chr4B 89.086 788 58 12 932 1713 338424341 338425106 0.000000e+00 953
12 TraesCS2B01G201600 chr4B 94.323 458 26 0 1712 2169 338425980 338426437 0.000000e+00 702
13 TraesCS2B01G201600 chr4B 95.567 203 9 0 2168 2370 338426551 338426753 3.410000e-85 326
14 TraesCS2B01G201600 chr4A 89.837 738 54 7 977 1713 282080867 282081584 0.000000e+00 928
15 TraesCS2B01G201600 chr4A 94.541 458 25 0 1712 2169 282082449 282082906 0.000000e+00 708
16 TraesCS2B01G201600 chr4A 95.074 203 10 0 2168 2370 282083027 282083229 1.590000e-83 320
17 TraesCS2B01G201600 chr4A 90.950 221 14 6 2435 2653 282085646 282085862 3.460000e-75 292
18 TraesCS2B01G201600 chr4A 97.590 83 2 0 2365 2447 282083305 282083387 3.690000e-30 143


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 TraesCS2B01G201600 chr2B 180604684 180608225 3541 False 6541.000000 6541 100.0000 1 3542 1 chr2B.!!$F1 3541
1 TraesCS2B01G201600 chr2D 126982181 126985734 3553 False 2636.000000 4553 92.0105 1 3542 2 chr2D.!!$F2 3541
2 TraesCS2B01G201600 chr2A 133684108 133687613 3505 False 2368.000000 4373 89.0535 1 3542 2 chr2A.!!$F1 3541
3 TraesCS2B01G201600 chr4D 236934453 236936796 2343 False 660.666667 965 93.6060 997 2370 3 chr4D.!!$F1 1373
4 TraesCS2B01G201600 chr4B 338424341 338426753 2412 False 660.333333 953 92.9920 932 2370 3 chr4B.!!$F1 1438
5 TraesCS2B01G201600 chr4A 282080867 282085862 4995 False 478.200000 928 93.5984 977 2653 5 chr4A.!!$F1 1676

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
110 116 0.101399 AACTGTCATCTAGCCGCTCG 59.899 55.0 0.0 0.0 0.0 5.03 F
1797 2876 0.168128 GCCATACAGAACGTGCAACC 59.832 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 2999 0.174162 ATGGATGAAAAGCAAGGCGC 59.826 50.0 0.00 0.00 42.91 6.53 R
2981 6539 0.877743 TCGATTCCAAATTGCGCACA 59.122 45.0 11.12 1.31 0.00 4.57 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
65 71 2.762887 TGAAACAAATTGTGGTCAGCCA 59.237 40.909 0.00 0.00 43.73 4.75
110 116 0.101399 AACTGTCATCTAGCCGCTCG 59.899 55.000 0.00 0.00 0.00 5.03
113 119 1.659954 GTCATCTAGCCGCTCGCAG 60.660 63.158 0.00 0.00 41.38 5.18
127 133 0.539986 TCGCAGGAAACATACCTCCC 59.460 55.000 0.00 0.00 35.35 4.30
128 134 0.541863 CGCAGGAAACATACCTCCCT 59.458 55.000 0.00 0.00 35.35 4.20
138 144 2.333695 ATACCTCCCTCCCTGCCTCC 62.334 65.000 0.00 0.00 0.00 4.30
183 189 0.251474 ATAGGGTGGTAGCGCCGATA 60.251 55.000 17.82 13.31 41.21 2.92
190 196 1.354506 GTAGCGCCGATAGTCGTGT 59.645 57.895 2.29 0.00 38.40 4.49
192 198 0.248336 TAGCGCCGATAGTCGTGTTG 60.248 55.000 2.29 0.00 38.40 3.33
241 247 3.214123 CCCATGGCCATGCTCACG 61.214 66.667 36.08 23.00 37.49 4.35
265 272 3.646162 TCTCCTCTACCAAGTTGCTTTCA 59.354 43.478 0.00 0.00 0.00 2.69
267 274 3.391296 TCCTCTACCAAGTTGCTTTCACT 59.609 43.478 0.00 0.00 0.00 3.41
281 288 2.672651 CACTGCCAATGCCACCGA 60.673 61.111 0.00 0.00 36.33 4.69
283 290 2.360350 CTGCCAATGCCACCGACT 60.360 61.111 0.00 0.00 36.33 4.18
284 291 2.672651 TGCCAATGCCACCGACTG 60.673 61.111 0.00 0.00 36.33 3.51
326 333 0.179062 ATCGCTCTTCACTGCATCCC 60.179 55.000 0.00 0.00 0.00 3.85
353 360 4.022603 CTCCCTCTGATCCATATGTCGAT 58.977 47.826 1.24 0.00 0.00 3.59
411 419 1.134220 ACAACACCAATGACCACGAGT 60.134 47.619 0.00 0.00 0.00 4.18
424 432 1.303398 ACGAGTTCGAGCTCCCTCA 60.303 57.895 21.70 0.00 43.02 3.86
445 453 1.741401 CCGCAAGTCGATGGAGCAA 60.741 57.895 0.00 0.00 41.67 3.91
452 460 2.125552 CGATGGAGCAACGCCTCA 60.126 61.111 0.00 0.00 33.47 3.86
498 507 2.493907 AAGAGAGAGCGTCGGGTTGC 62.494 60.000 0.00 0.00 0.00 4.17
500 509 4.373116 GAGAGCGTCGGGTTGCCA 62.373 66.667 0.00 0.00 0.00 4.92
599 608 1.963855 CCCATGCCAAACGACGACA 60.964 57.895 0.00 0.00 0.00 4.35
604 613 1.281353 GCCAAACGACGACATGCAA 59.719 52.632 0.00 0.00 0.00 4.08
636 645 0.238289 CGAAAGGATGCAGCGTTTGT 59.762 50.000 25.41 4.27 0.00 2.83
705 716 4.394712 AAAGAGAGTGGCGCGGGG 62.395 66.667 8.83 0.00 0.00 5.73
718 729 3.327404 CGGGGTTGTGGCCTAGGT 61.327 66.667 11.31 0.00 0.00 3.08
721 732 0.611062 GGGGTTGTGGCCTAGGTTTC 60.611 60.000 11.31 1.29 0.00 2.78
722 733 0.958876 GGGTTGTGGCCTAGGTTTCG 60.959 60.000 11.31 0.00 0.00 3.46
741 752 1.540363 CGTGTAGTGGCTGTGAGGTTT 60.540 52.381 0.00 0.00 0.00 3.27
771 782 3.408389 TTTTTGTGTGTGTGTGGCG 57.592 47.368 0.00 0.00 0.00 5.69
772 783 0.734253 TTTTTGTGTGTGTGTGGCGC 60.734 50.000 0.00 0.00 0.00 6.53
773 784 2.857380 TTTTGTGTGTGTGTGGCGCG 62.857 55.000 0.00 0.00 0.00 6.86
788 804 1.673009 CGCGGGGGTATGTGTGTTT 60.673 57.895 0.00 0.00 0.00 2.83
803 819 3.291383 TTTTGCGGACGGGCTTGG 61.291 61.111 0.00 0.00 0.00 3.61
874 890 0.461339 GAATAGCGACCGGAAAGGCA 60.461 55.000 9.46 0.00 46.52 4.75
896 913 1.791204 GAAACAGGACCGACTTCGAAC 59.209 52.381 0.00 0.00 43.02 3.95
900 922 2.082231 CAGGACCGACTTCGAACTCTA 58.918 52.381 0.00 0.00 43.02 2.43
904 926 4.104066 GGACCGACTTCGAACTCTATTTC 58.896 47.826 0.00 0.00 43.02 2.17
906 928 3.106672 CCGACTTCGAACTCTATTTCGG 58.893 50.000 0.00 0.00 46.77 4.30
907 929 2.530700 CGACTTCGAACTCTATTTCGGC 59.469 50.000 0.00 0.00 46.77 5.54
908 930 3.508762 GACTTCGAACTCTATTTCGGCA 58.491 45.455 0.00 0.00 46.77 5.69
909 931 3.921677 ACTTCGAACTCTATTTCGGCAA 58.078 40.909 0.00 0.00 46.77 4.52
910 932 4.504858 ACTTCGAACTCTATTTCGGCAAT 58.495 39.130 0.00 0.00 46.77 3.56
992 1024 1.229593 TACCCAAACCCCGGCTAGT 60.230 57.895 0.00 0.00 0.00 2.57
993 1025 1.555477 TACCCAAACCCCGGCTAGTG 61.555 60.000 0.00 0.00 0.00 2.74
1020 1052 3.732849 GAGAACCCCAGGCCCCTG 61.733 72.222 7.36 7.36 43.26 4.45
1614 1664 3.294493 GCCGCCCTTGCTGTGAAA 61.294 61.111 0.00 0.00 34.43 2.69
1797 2876 0.168128 GCCATACAGAACGTGCAACC 59.832 55.000 0.00 0.00 0.00 3.77
1920 2999 1.078759 GTCACCTGGATCGTCTTGCG 61.079 60.000 0.00 0.00 43.01 4.85
2263 3464 3.119352 GGATTTGAGGACCAGACAAATGC 60.119 47.826 20.73 19.75 41.96 3.56
2316 3517 3.567585 TCTCGCATGTGAAATTTGAACCA 59.432 39.130 10.71 0.00 0.00 3.67
2462 6013 2.421424 GTGGAGATGGACAACAGATTGC 59.579 50.000 0.00 0.00 39.66 3.56
2677 6233 7.208064 TGGCCTTTGAAATACTAGATTACCT 57.792 36.000 3.32 0.00 0.00 3.08
2943 6501 7.077050 TCAATTGAAACCCTTGGATGAAAAT 57.923 32.000 5.45 0.00 0.00 1.82
3232 6822 8.934023 TCTTTGGTATTGGAAAATGAAGTAGT 57.066 30.769 0.00 0.00 0.00 2.73
3314 6904 5.640732 GACGATGCCACTAATTGTTCATTT 58.359 37.500 0.00 0.00 0.00 2.32
3320 6910 4.929211 GCCACTAATTGTTCATTTGGTTCC 59.071 41.667 0.00 0.00 28.59 3.62
3476 7066 3.636300 TGCTTTCAGGCTAACACATGTTT 59.364 39.130 1.98 0.00 39.31 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 71 7.069331 TGACTGAAAACAATATTTGGGTCAGTT 59.931 33.333 16.75 2.49 43.69 3.16
110 116 1.134068 GGAGGGAGGTATGTTTCCTGC 60.134 57.143 0.00 0.00 41.63 4.85
113 119 1.490910 CAGGGAGGGAGGTATGTTTCC 59.509 57.143 0.00 0.00 0.00 3.13
140 146 4.493747 GGAAGGAGACGCGGACGG 62.494 72.222 12.47 0.00 46.04 4.79
142 148 4.144703 GGGGAAGGAGACGCGGAC 62.145 72.222 12.47 3.93 0.00 4.79
143 149 3.899545 AAGGGGAAGGAGACGCGGA 62.900 63.158 12.47 0.00 0.00 5.54
144 150 3.372554 GAAGGGGAAGGAGACGCGG 62.373 68.421 12.47 0.00 0.00 6.46
190 196 1.001974 ACAGAGGCTCAATACGTGCAA 59.998 47.619 18.26 0.00 35.77 4.08
192 198 1.394917 CAACAGAGGCTCAATACGTGC 59.605 52.381 18.26 0.00 0.00 5.34
224 230 3.214123 CGTGAGCATGGCCATGGG 61.214 66.667 39.72 21.59 39.16 4.00
241 247 1.903183 AGCAACTTGGTAGAGGAGACC 59.097 52.381 0.00 0.00 37.49 3.85
265 272 2.672996 GTCGGTGGCATTGGCAGT 60.673 61.111 13.88 0.00 43.71 4.40
267 274 2.672651 CAGTCGGTGGCATTGGCA 60.673 61.111 9.11 9.11 43.71 4.92
281 288 2.435693 GGCGATAGGTGGAGGCAGT 61.436 63.158 0.00 0.00 0.00 4.40
283 290 3.161450 GGGCGATAGGTGGAGGCA 61.161 66.667 0.00 0.00 0.00 4.75
284 291 2.742116 TTGGGCGATAGGTGGAGGC 61.742 63.158 0.00 0.00 0.00 4.70
353 360 0.177836 ATCCGAATGATGTGGCGTCA 59.822 50.000 0.00 0.00 33.71 4.35
374 381 4.671590 TCTCCGGCGACCAGGACA 62.672 66.667 9.30 0.00 32.33 4.02
411 419 2.046864 CGGTCTGAGGGAGCTCGAA 61.047 63.158 7.83 0.00 40.01 3.71
424 432 1.513158 CTCCATCGACTTGCGGTCT 59.487 57.895 7.79 0.00 42.44 3.85
461 469 0.037697 TTCTTGTCATGGACGGTCGG 60.038 55.000 1.43 0.00 34.95 4.79
464 473 2.232452 CTCTCTTCTTGTCATGGACGGT 59.768 50.000 0.00 0.00 34.95 4.83
468 477 2.165234 CGCTCTCTCTTCTTGTCATGGA 59.835 50.000 0.00 0.00 0.00 3.41
498 507 1.081892 CGCATTGGTGAAGTCTCTGG 58.918 55.000 0.00 0.00 0.00 3.86
500 509 0.035317 TGCGCATTGGTGAAGTCTCT 59.965 50.000 5.66 0.00 0.00 3.10
531 540 4.899239 GACCAGCGCCCGGATGAG 62.899 72.222 19.66 1.13 32.47 2.90
591 600 1.569493 GCAAGTTGCATGTCGTCGT 59.431 52.632 22.90 0.00 44.26 4.34
604 613 1.528309 CTTTCGGGGGTGTGCAAGT 60.528 57.895 0.00 0.00 0.00 3.16
674 683 5.256474 CACTCTCTTTCCTCTTCTCTCTCT 58.744 45.833 0.00 0.00 0.00 3.10
705 716 0.872388 CACGAAACCTAGGCCACAAC 59.128 55.000 9.30 0.00 0.00 3.32
718 729 1.270094 CCTCACAGCCACTACACGAAA 60.270 52.381 0.00 0.00 0.00 3.46
721 732 0.033504 AACCTCACAGCCACTACACG 59.966 55.000 0.00 0.00 0.00 4.49
722 733 2.256117 AAACCTCACAGCCACTACAC 57.744 50.000 0.00 0.00 0.00 2.90
770 781 1.238625 AAAACACACATACCCCCGCG 61.239 55.000 0.00 0.00 0.00 6.46
771 782 0.242555 CAAAACACACATACCCCCGC 59.757 55.000 0.00 0.00 0.00 6.13
772 783 0.242555 GCAAAACACACATACCCCCG 59.757 55.000 0.00 0.00 0.00 5.73
773 784 0.242555 CGCAAAACACACATACCCCC 59.757 55.000 0.00 0.00 0.00 5.40
775 786 1.068816 GTCCGCAAAACACACATACCC 60.069 52.381 0.00 0.00 0.00 3.69
803 819 3.200483 GCATTTGAATTTGGGATCTGGC 58.800 45.455 0.00 0.00 0.00 4.85
874 890 0.317479 CGAAGTCGGTCCTGTTTCCT 59.683 55.000 0.00 0.00 35.37 3.36
896 913 6.751888 CCAAGGTTTTTATTGCCGAAATAGAG 59.248 38.462 0.00 0.00 32.30 2.43
900 922 5.221541 TGACCAAGGTTTTTATTGCCGAAAT 60.222 36.000 0.00 0.00 0.00 2.17
904 926 3.243569 TGTGACCAAGGTTTTTATTGCCG 60.244 43.478 0.00 0.00 0.00 5.69
905 927 4.038642 TCTGTGACCAAGGTTTTTATTGCC 59.961 41.667 0.00 0.00 0.00 4.52
906 928 5.195001 TCTGTGACCAAGGTTTTTATTGC 57.805 39.130 0.00 0.00 0.00 3.56
907 929 6.086222 CGATCTGTGACCAAGGTTTTTATTG 58.914 40.000 0.00 0.00 0.00 1.90
908 930 5.335661 GCGATCTGTGACCAAGGTTTTTATT 60.336 40.000 0.00 0.00 0.00 1.40
909 931 4.156008 GCGATCTGTGACCAAGGTTTTTAT 59.844 41.667 0.00 0.00 0.00 1.40
910 932 3.500680 GCGATCTGTGACCAAGGTTTTTA 59.499 43.478 0.00 0.00 0.00 1.52
992 1024 1.550130 GGGGTTCTCCATGGACGACA 61.550 60.000 11.44 1.95 37.22 4.35
993 1025 1.221021 GGGGTTCTCCATGGACGAC 59.779 63.158 11.44 12.04 37.22 4.34
1543 1593 2.759973 TCGCTTGGCCCTCTCGAT 60.760 61.111 0.00 0.00 0.00 3.59
1607 1657 3.726517 CCGCCGCCTGTTTCACAG 61.727 66.667 0.00 0.00 45.53 3.66
1797 2876 0.745845 CTGGGGAGAAGGCAACATCG 60.746 60.000 0.00 0.00 39.88 3.84
1920 2999 0.174162 ATGGATGAAAAGCAAGGCGC 59.826 50.000 0.00 0.00 42.91 6.53
2100 3179 3.695830 AAATCCCAAACTCGAGCACTA 57.304 42.857 13.61 0.00 0.00 2.74
2316 3517 5.129815 TGTCGCTAAATAATAACCCTCCTGT 59.870 40.000 0.00 0.00 0.00 4.00
2462 6013 4.915667 TCGTTCTATCAAGTGAAACAGTCG 59.084 41.667 0.00 0.00 41.43 4.18
2521 6072 5.371526 TGCTTAATCCAACTCCATCTCATC 58.628 41.667 0.00 0.00 0.00 2.92
2677 6233 6.425114 ACAAATACAAATATTTTGGCGCAACA 59.575 30.769 10.83 0.00 38.67 3.33
2964 6522 8.426881 TTGCGCACACTCAAGTATATATTTTA 57.573 30.769 11.12 0.00 0.00 1.52
2981 6539 0.877743 TCGATTCCAAATTGCGCACA 59.122 45.000 11.12 1.31 0.00 4.57
3232 6822 4.225042 ACATACCACCAGCTGAAGTAATGA 59.775 41.667 17.39 0.00 0.00 2.57
3314 6904 5.373812 AGAACTTTTCTCTTCAGGAACCA 57.626 39.130 0.00 0.00 34.07 3.67
3476 7066 1.608590 GCTGCCAAGTTAGCTGTGAAA 59.391 47.619 0.00 0.00 36.99 2.69


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

AutoCloner maintained by Alex Coulton.