Multiple sequence alignment - TraesCS6A01G251300

Loading Multiple Alignment...

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 TraesCS6A01G251300 chr6A 100.000 2189 0 0 1 2189 465933099 465935287 0 4043
1 TraesCS6A01G251300 chr6D 94.788 2053 59 11 151 2189 327205224 327207242 0 3155
2 TraesCS6A01G251300 chr6B 91.565 2217 127 22 2 2189 494428884 494426699 0 3003


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 TraesCS6A01G251300 chr6A 465933099 465935287 2188 False 4043 4043 100.000 1 2189 1 chr6A.!!$F1 2188
1 TraesCS6A01G251300 chr6D 327205224 327207242 2018 False 3155 3155 94.788 151 2189 1 chr6D.!!$F1 2038
2 TraesCS6A01G251300 chr6B 494426699 494428884 2185 True 3003 3003 91.565 2 2189 1 chr6B.!!$R1 2187

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
119 121 0.394352 CCTTAATGGAGCCAGCCGTT 60.394 55.0 0.0 0.0 40.22 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1212 1231 1.464997 GTGTTTCGAACATCTCCAGCC 59.535 52.381 0.0 0.0 44.35 4.85 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
41 42 4.156922 CCACCAGTTTGCACGGATAATTTA 59.843 41.667 0.00 0.00 0.00 1.40
45 46 7.971168 CACCAGTTTGCACGGATAATTTAATTA 59.029 33.333 0.00 0.00 0.00 1.40
47 48 9.528018 CCAGTTTGCACGGATAATTTAATTAAT 57.472 29.630 1.28 0.00 0.00 1.40
81 82 9.042008 ACAATAATTAAGAGCATATTCGTCGTT 57.958 29.630 0.00 0.00 0.00 3.85
104 105 2.314647 GCGTGCACTGCGTTCCTTA 61.315 57.895 16.19 0.00 0.00 2.69
107 108 1.464023 CGTGCACTGCGTTCCTTAATG 60.464 52.381 16.19 0.00 0.00 1.90
119 121 0.394352 CCTTAATGGAGCCAGCCGTT 60.394 55.000 0.00 0.00 40.22 4.44
136 138 1.790623 CGTTGACCTACCGACAAACAG 59.209 52.381 0.00 0.00 0.00 3.16
144 146 2.424302 CGACAAACAGGGGACGGT 59.576 61.111 0.00 0.00 41.96 4.83
264 276 6.483307 TCAAGCAACGGATATCCAAGAAATAG 59.517 38.462 21.70 5.12 35.14 1.73
273 285 6.073003 GGATATCCAAGAAATAGAAGCAACGG 60.073 42.308 17.34 0.00 35.64 4.44
294 306 3.181448 GGCGTTAATAGATGGGGAAAGGA 60.181 47.826 0.00 0.00 0.00 3.36
326 338 1.081242 CGGTTGAACCATGCACAGC 60.081 57.895 15.58 0.00 38.47 4.40
327 339 1.518056 CGGTTGAACCATGCACAGCT 61.518 55.000 15.58 0.00 38.47 4.24
328 340 1.533625 GGTTGAACCATGCACAGCTA 58.466 50.000 9.98 0.00 38.42 3.32
329 341 1.200020 GGTTGAACCATGCACAGCTAC 59.800 52.381 9.98 0.00 38.42 3.58
330 342 1.879380 GTTGAACCATGCACAGCTACA 59.121 47.619 0.00 0.00 0.00 2.74
331 343 2.489329 GTTGAACCATGCACAGCTACAT 59.511 45.455 0.00 0.00 0.00 2.29
332 344 2.358957 TGAACCATGCACAGCTACATC 58.641 47.619 0.00 0.00 0.00 3.06
549 563 4.445879 GCCACTAGTATAAAGGGAAAGGGG 60.446 50.000 0.00 0.00 0.00 4.79
557 571 1.991121 AAGGGAAAGGGGAAAACGTC 58.009 50.000 0.00 0.00 0.00 4.34
595 610 9.855021 GATGATAATAATTAAACCGGGAAATGG 57.145 33.333 6.32 0.00 0.00 3.16
615 630 1.206371 GCAGAATCTTTGCAGGCCAAT 59.794 47.619 5.01 0.00 41.17 3.16
618 633 3.132289 CAGAATCTTTGCAGGCCAATGAT 59.868 43.478 5.01 0.94 45.17 2.45
726 742 2.010582 GCCAACGGTCACAAAAGGCA 62.011 55.000 0.00 0.00 40.29 4.75
818 834 8.703604 ATAAATATAGTAATAGTGCACCGCAG 57.296 34.615 14.63 0.00 40.08 5.18
869 888 1.369091 CCCGGAATCCAGACAAAGCG 61.369 60.000 0.73 0.00 0.00 4.68
874 893 2.003301 GAATCCAGACAAAGCGAGTCC 58.997 52.381 0.00 0.00 36.68 3.85
939 958 2.788750 GCAACACAAAGCAAAGCAAAGC 60.789 45.455 0.00 0.00 0.00 3.51
940 959 2.383368 ACACAAAGCAAAGCAAAGCA 57.617 40.000 0.00 0.00 0.00 3.91
941 960 2.697654 ACACAAAGCAAAGCAAAGCAA 58.302 38.095 0.00 0.00 0.00 3.91
942 961 3.072944 ACACAAAGCAAAGCAAAGCAAA 58.927 36.364 0.00 0.00 0.00 3.68
943 962 3.125658 ACACAAAGCAAAGCAAAGCAAAG 59.874 39.130 0.00 0.00 0.00 2.77
977 996 7.967303 GTGAAGAAAAGCCATAGAATTTCAGAG 59.033 37.037 0.00 0.00 34.91 3.35
985 1004 1.457346 AGAATTTCAGAGGCCAAGCG 58.543 50.000 5.01 0.00 0.00 4.68
993 1012 1.227497 GAGGCCAAGCGGAGATCAG 60.227 63.158 5.01 0.00 0.00 2.90
1014 1033 2.813754 GCCAACAATGCTGACACTTCTA 59.186 45.455 0.00 0.00 0.00 2.10
1267 1286 2.512515 CGGCCCTTGCTAGCAGTC 60.513 66.667 18.45 7.27 37.74 3.51
1348 1367 4.082733 GCCTTCTCTGGAAACCAAATGTAC 60.083 45.833 0.00 0.00 30.80 2.90
1521 1541 3.462483 TCCAGACTGTGCTCGTTTTAA 57.538 42.857 0.93 0.00 0.00 1.52
1531 1551 4.035441 TGTGCTCGTTTTAACCCTTGTAAC 59.965 41.667 0.00 0.00 0.00 2.50
1549 1569 7.041098 CCTTGTAACATACTTTTTGCAGTCTCT 60.041 37.037 0.00 0.00 0.00 3.10
1572 1592 8.514136 TCTTTTTCCTGCAAATATTAAACACG 57.486 30.769 0.00 0.00 0.00 4.49
1727 1755 0.951558 ACAAACTAAAGCGGGTGCAG 59.048 50.000 0.00 0.00 46.23 4.41
1801 1829 7.552687 TGATCCTTCGTTAACTCATTTGCTAAT 59.447 33.333 3.71 0.00 0.00 1.73
1836 1864 8.676401 CAAGATTTCACCATTTTGTTTCCTTTT 58.324 29.630 0.00 0.00 0.00 2.27
1880 1910 3.983344 GGCTGAAGCAAAGTGTACAAATG 59.017 43.478 0.00 0.00 44.36 2.32
2151 2181 3.323115 CAGCCCTCTCATAGCACTTGATA 59.677 47.826 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.517453 TGGTGGTCGTAAAGAAGAATTTGG 59.483 41.667 0.00 0.00 0.00 3.28
57 58 9.042008 ACAACGACGAATATGCTCTTAATTATT 57.958 29.630 0.00 0.00 0.00 1.40
81 82 2.911439 GAACGCAGTGCACGCAAACA 62.911 55.000 25.50 0.00 45.00 2.83
104 105 1.675641 GTCAACGGCTGGCTCCATT 60.676 57.895 0.00 0.00 0.00 3.16
107 108 2.656069 TAGGTCAACGGCTGGCTCC 61.656 63.158 0.00 0.00 0.00 4.70
115 117 1.142474 GTTTGTCGGTAGGTCAACGG 58.858 55.000 0.00 0.00 0.00 4.44
119 121 0.682852 CCCTGTTTGTCGGTAGGTCA 59.317 55.000 0.00 0.00 0.00 4.02
136 138 1.744320 AAGCAAAAGCAACCGTCCCC 61.744 55.000 0.00 0.00 0.00 4.81
144 146 1.363443 CCGAGGCAAGCAAAAGCAA 59.637 52.632 0.00 0.00 0.00 3.91
145 147 3.041701 CCGAGGCAAGCAAAAGCA 58.958 55.556 0.00 0.00 0.00 3.91
146 148 2.431430 GCCGAGGCAAGCAAAAGC 60.431 61.111 9.58 0.00 41.49 3.51
147 149 1.211190 GAGCCGAGGCAAGCAAAAG 59.789 57.895 17.18 0.00 44.88 2.27
148 150 2.616330 CGAGCCGAGGCAAGCAAAA 61.616 57.895 17.18 0.00 44.88 2.44
149 151 3.049674 CGAGCCGAGGCAAGCAAA 61.050 61.111 17.18 0.00 44.88 3.68
264 276 3.303132 CCATCTATTAACGCCGTTGCTTC 60.303 47.826 13.65 0.00 34.43 3.86
273 285 4.081322 TCCTTTCCCCATCTATTAACGC 57.919 45.455 0.00 0.00 0.00 4.84
275 287 8.533569 TGATTTTCCTTTCCCCATCTATTAAC 57.466 34.615 0.00 0.00 0.00 2.01
278 290 7.070322 CACATGATTTTCCTTTCCCCATCTATT 59.930 37.037 0.00 0.00 0.00 1.73
284 296 3.855668 ACACATGATTTTCCTTTCCCCA 58.144 40.909 0.00 0.00 0.00 4.96
294 306 5.067936 TGGTTCAACCGTAACACATGATTTT 59.932 36.000 1.02 0.00 42.58 1.82
326 338 4.202357 TGCTTTGCCCTATGTAGGATGTAG 60.202 45.833 7.66 1.89 46.63 2.74
327 339 3.714280 TGCTTTGCCCTATGTAGGATGTA 59.286 43.478 7.66 0.00 46.63 2.29
328 340 2.509548 TGCTTTGCCCTATGTAGGATGT 59.490 45.455 7.66 0.00 46.63 3.06
329 341 3.213206 TGCTTTGCCCTATGTAGGATG 57.787 47.619 7.66 0.00 46.63 3.51
330 342 3.557898 CGATGCTTTGCCCTATGTAGGAT 60.558 47.826 7.66 0.00 46.63 3.24
331 343 2.224281 CGATGCTTTGCCCTATGTAGGA 60.224 50.000 7.66 0.00 46.63 2.94
332 344 2.146342 CGATGCTTTGCCCTATGTAGG 58.854 52.381 0.00 0.00 43.25 3.18
499 512 9.997482 TGTGATGTTACTAGTTTTCTTTTGTTC 57.003 29.630 0.00 0.00 0.00 3.18
549 563 1.204312 GAGTGGCGCTGACGTTTTC 59.796 57.895 4.71 0.00 42.83 2.29
557 571 2.229675 TTATCATCTGAGTGGCGCTG 57.770 50.000 4.71 0.00 0.00 5.18
595 610 0.604578 TTGGCCTGCAAAGATTCTGC 59.395 50.000 3.32 0.00 40.35 4.26
615 630 5.046529 ACTAATGCGTGCAAAAACAAATCA 58.953 33.333 0.00 0.00 0.00 2.57
618 633 5.583495 AGTACTAATGCGTGCAAAAACAAA 58.417 33.333 0.00 0.00 0.00 2.83
726 742 1.349688 TGTTGATGTTTCGTAGGCCCT 59.650 47.619 0.00 0.00 0.00 5.19
869 888 0.752054 CAGGCATCTCTGGAGGACTC 59.248 60.000 0.00 0.00 39.89 3.36
939 958 4.604976 CTTTTCTTCACTGGACTGCTTTG 58.395 43.478 0.00 0.00 0.00 2.77
940 959 3.067320 GCTTTTCTTCACTGGACTGCTTT 59.933 43.478 0.00 0.00 0.00 3.51
941 960 2.620585 GCTTTTCTTCACTGGACTGCTT 59.379 45.455 0.00 0.00 0.00 3.91
942 961 2.225467 GCTTTTCTTCACTGGACTGCT 58.775 47.619 0.00 0.00 0.00 4.24
943 962 1.268079 GGCTTTTCTTCACTGGACTGC 59.732 52.381 0.00 0.00 0.00 4.40
977 996 2.899339 GCTGATCTCCGCTTGGCC 60.899 66.667 0.00 0.00 0.00 5.36
985 1004 1.760192 AGCATTGTTGGCTGATCTCC 58.240 50.000 0.00 0.00 40.80 3.71
993 1012 1.610522 AGAAGTGTCAGCATTGTTGGC 59.389 47.619 0.00 0.00 0.00 4.52
1212 1231 1.464997 GTGTTTCGAACATCTCCAGCC 59.535 52.381 0.00 0.00 44.35 4.85
1265 1284 2.936032 ACTCCAGGGGCAAGGGAC 60.936 66.667 0.00 0.00 0.00 4.46
1267 1286 4.052518 CCACTCCAGGGGCAAGGG 62.053 72.222 0.00 0.00 0.00 3.95
1334 1353 3.756963 GAGGGACAGTACATTTGGTTTCC 59.243 47.826 0.00 0.00 0.00 3.13
1348 1367 2.762887 TCTTACATGCAGAGAGGGACAG 59.237 50.000 0.00 0.00 0.00 3.51
1521 1541 5.596772 ACTGCAAAAAGTATGTTACAAGGGT 59.403 36.000 0.00 0.00 0.00 4.34
1531 1551 7.380602 CAGGAAAAAGAGACTGCAAAAAGTATG 59.619 37.037 0.00 0.00 0.00 2.39
1719 1747 3.006672 CCTAATTAGGCTGCACCCG 57.993 57.895 18.52 0.00 40.58 5.28
1727 1755 6.015772 TGAAACCAACTTCAACCTAATTAGGC 60.016 38.462 28.19 9.63 37.40 3.93
1801 1829 2.027285 TGGTGAAATCTTGAGATCGGCA 60.027 45.455 0.00 0.00 32.75 5.69
1836 1864 9.912634 CAGCCTAATTGAAAAGAAAAACAGATA 57.087 29.630 0.00 0.00 0.00 1.98
1880 1910 3.532542 GATTACACTGGCCCAGTAAGTC 58.467 50.000 17.77 10.30 43.43 3.01


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

AutoCloner maintained by Alex Coulton.