Multiple sequence alignment - TraesCS3A01G457000

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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 TraesCS3A01G457000 chr3A 100.000 2519 0 0 1 2519 694516309 694513791 0.000000e+00 4652.0
1 TraesCS3A01G457000 chr3D 93.744 2270 99 19 268 2517 558283158 558280912 0.000000e+00 3365.0
2 TraesCS3A01G457000 chrUn 96.085 894 33 2 598 1490 461575821 461576713 0.000000e+00 1456.0
3 TraesCS3A01G457000 chrUn 97.013 636 18 1 1831 2465 443899946 443900581 0.000000e+00 1068.0
4 TraesCS3A01G457000 chrUn 89.280 597 41 10 1 593 343438617 343439194 0.000000e+00 726.0
5 TraesCS3A01G457000 chrUn 90.058 342 25 5 1492 1832 443899514 443899847 3.850000e-118 435.0
6 TraesCS3A01G457000 chrUn 100.000 43 0 0 2467 2509 407446194 407446236 2.080000e-11 80.5


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 TraesCS3A01G457000 chr3A 694513791 694516309 2518 True 4652.0 4652 100.0000 1 2519 1 chr3A.!!$R1 2518
1 TraesCS3A01G457000 chr3D 558280912 558283158 2246 True 3365.0 3365 93.7440 268 2517 1 chr3D.!!$R1 2249
2 TraesCS3A01G457000 chrUn 461575821 461576713 892 False 1456.0 1456 96.0850 598 1490 1 chrUn.!!$F3 892
3 TraesCS3A01G457000 chrUn 443899514 443900581 1067 False 751.5 1068 93.5355 1492 2465 2 chrUn.!!$F4 973
4 TraesCS3A01G457000 chrUn 343438617 343439194 577 False 726.0 726 89.2800 1 593 1 chrUn.!!$F1 592

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
49 52 0.464554 GATAACCCCAGCCTCTGCAC 60.465 60.0 0.0 0.0 41.13 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1694 1705 0.89832 TTCTCAGGTACAGCAGGAGC 59.102 55.0 0.0 0.0 42.56 4.7 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
39 42 3.040655 TCGAGAATGAGGATAACCCCA 57.959 47.619 0.00 0.00 36.73 4.96
49 52 0.464554 GATAACCCCAGCCTCTGCAC 60.465 60.000 0.00 0.00 41.13 4.57
66 69 1.676635 ACCAAGCGATGCATGCAGT 60.677 52.632 26.69 13.42 33.85 4.40
149 153 4.258543 GACAATCTTTCGGTGGTCCATTA 58.741 43.478 0.00 0.00 0.00 1.90
179 183 8.182227 TCAAACTCGATATACACAAGTACTCTG 58.818 37.037 0.00 0.00 31.96 3.35
201 205 6.094742 TCTGCACTTGTACTTCAAAATGTTCA 59.905 34.615 0.00 0.00 35.48 3.18
218 222 4.322567 TGTTCAAAGCAAGCCTTTTGTTT 58.677 34.783 6.65 0.00 41.75 2.83
219 223 5.482908 TGTTCAAAGCAAGCCTTTTGTTTA 58.517 33.333 6.65 0.00 41.75 2.01
220 224 6.112058 TGTTCAAAGCAAGCCTTTTGTTTAT 58.888 32.000 6.65 0.00 41.75 1.40
221 225 6.036953 TGTTCAAAGCAAGCCTTTTGTTTATG 59.963 34.615 6.65 0.00 41.75 1.90
222 226 4.511082 TCAAAGCAAGCCTTTTGTTTATGC 59.489 37.500 6.65 0.00 41.75 3.14
224 228 4.070630 AGCAAGCCTTTTGTTTATGCAA 57.929 36.364 0.00 0.00 34.89 4.08
225 229 3.809279 AGCAAGCCTTTTGTTTATGCAAC 59.191 39.130 0.00 0.00 34.89 4.17
226 230 3.362888 GCAAGCCTTTTGTTTATGCAACG 60.363 43.478 0.00 0.00 38.36 4.10
227 231 4.047822 CAAGCCTTTTGTTTATGCAACGA 58.952 39.130 0.00 0.00 38.36 3.85
244 248 6.346096 TGCAACGAGCTAGTAGGATATTTTT 58.654 36.000 0.00 0.00 45.94 1.94
273 277 7.810766 TGCTTCACCATTTTATCGAAATTTC 57.189 32.000 8.20 8.20 35.79 2.17
297 301 1.068541 GGTTGACAATCTTTCGGTGGC 60.069 52.381 0.00 0.00 0.00 5.01
309 313 1.973281 CGGTGGCCAGTTTGCTCAT 60.973 57.895 5.11 0.00 0.00 2.90
319 323 3.693085 CCAGTTTGCTCATAAGACATGCT 59.307 43.478 0.00 0.00 0.00 3.79
396 400 8.147642 AGTTAAATAAGCTAGCTAGTTGCATG 57.852 34.615 19.70 0.00 45.94 4.06
405 409 6.599244 AGCTAGCTAGTTGCATGTTTTTGATA 59.401 34.615 17.69 0.00 45.94 2.15
469 473 1.994779 CGATGGCCATTTTGCTCAAAC 59.005 47.619 21.84 1.30 0.00 2.93
504 508 9.477484 CAAGTACTCTACACTTGTAGTTCAAAT 57.523 33.333 14.61 0.00 45.06 2.32
584 589 5.050227 CGATGCACCATTGTTGAAAATTTGT 60.050 36.000 0.00 0.00 0.00 2.83
587 592 9.149225 GATGCACCATTGTTGAAAATTTGTATA 57.851 29.630 0.00 0.00 0.00 1.47
649 654 2.611518 CAGGTACTCAGCACTTGTAGC 58.388 52.381 0.00 0.00 34.60 3.58
667 672 9.515226 ACTTGTAGCTAAAAATGTTCAGGATAA 57.485 29.630 0.00 0.00 0.00 1.75
710 716 8.352942 CCACAAGCTAGTTGGATATTTTAATCC 58.647 37.037 2.58 0.00 44.96 3.01
747 753 8.585189 AAATGTAACGGGCGTAATTTTTAAAA 57.415 26.923 0.00 0.00 0.00 1.52
885 891 6.870965 CACAGCTCTCAGTGTATAAAAAGAGT 59.129 38.462 5.08 0.00 34.20 3.24
919 925 3.118775 AGCACTCGCAATATGAGTACCAA 60.119 43.478 0.00 0.00 44.60 3.67
942 948 0.714439 GAAGACTACTTTCGGCGTGC 59.286 55.000 6.85 0.00 36.39 5.34
1591 1598 2.098443 TCTTTTGTGTTTGCGGTCTTCC 59.902 45.455 0.00 0.00 0.00 3.46
1623 1634 5.586243 TCTTGCTTATTCAGTGCTATGTTCC 59.414 40.000 0.00 0.00 0.00 3.62
1652 1663 5.232610 ACAAAAATTGCACCAACATTGTG 57.767 34.783 0.00 0.00 30.93 3.33
1653 1664 4.096081 ACAAAAATTGCACCAACATTGTGG 59.904 37.500 0.00 0.00 44.92 4.17
1694 1705 7.812669 TGTACTAATGCAATCGATATGTACCTG 59.187 37.037 0.00 0.00 0.00 4.00
1695 1706 5.639506 ACTAATGCAATCGATATGTACCTGC 59.360 40.000 8.66 8.66 0.00 4.85
1696 1707 3.751479 TGCAATCGATATGTACCTGCT 57.249 42.857 14.94 0.00 0.00 4.24
1697 1708 3.653344 TGCAATCGATATGTACCTGCTC 58.347 45.455 14.94 0.00 0.00 4.26
1698 1709 2.996621 GCAATCGATATGTACCTGCTCC 59.003 50.000 0.00 0.00 0.00 4.70
1699 1710 3.306364 GCAATCGATATGTACCTGCTCCT 60.306 47.826 0.00 0.00 0.00 3.69
1711 1722 0.175302 CTGCTCCTGCTGTACCTGAG 59.825 60.000 0.00 0.00 40.48 3.35
1713 1724 0.898320 GCTCCTGCTGTACCTGAGAA 59.102 55.000 0.00 0.00 36.03 2.87
1720 1731 5.425217 TCCTGCTGTACCTGAGAATATTTCA 59.575 40.000 0.00 0.00 0.00 2.69
1725 1736 8.318412 TGCTGTACCTGAGAATATTTCAACTTA 58.682 33.333 0.00 0.00 0.00 2.24
1769 1780 8.468720 TGCATGTCATGTTTAGAATGATTTTG 57.531 30.769 14.26 0.00 36.49 2.44
1821 1832 6.594284 TGCTGTCAGAATAATCTCGAATTG 57.406 37.500 3.32 0.00 32.03 2.32
2091 2203 6.393990 TGTATTAAATTCATGTGCACCCAAC 58.606 36.000 15.69 0.00 0.00 3.77
2280 2392 6.276611 TCACGCGTGGTTGTTATATATTTC 57.723 37.500 36.41 0.00 0.00 2.17
2409 2521 3.569277 TCGGGTGATGCAAATAATGATGG 59.431 43.478 0.00 0.00 0.00 3.51
2423 2535 1.226491 GATGGTGTTCGCATGCAGC 60.226 57.895 19.57 8.28 40.87 5.25
2444 2556 3.722289 GCGAGGTTCTTTTTACACAAACG 59.278 43.478 0.00 0.00 0.00 3.60
2448 2560 3.428163 GTTCTTTTTACACAAACGCCGT 58.572 40.909 0.00 0.00 0.00 5.68
2452 2564 1.595466 TTTACACAAACGCCGTCCAT 58.405 45.000 0.00 0.00 0.00 3.41
2460 2572 0.608035 AACGCCGTCCATTCATTGGT 60.608 50.000 0.00 0.00 46.52 3.67
2477 2589 0.326927 GGTGCTTGTAAGGGTGCCTA 59.673 55.000 0.00 0.00 31.13 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.548920 GCTGGGGTTATCCTCATTCTCG 60.549 54.545 0.00 0.00 44.09 4.04
21 22 2.224646 GGCTGGGGTTATCCTCATTCTC 60.225 54.545 0.00 0.00 44.09 2.87
22 23 1.777272 GGCTGGGGTTATCCTCATTCT 59.223 52.381 0.00 0.00 44.09 2.40
23 24 1.777272 AGGCTGGGGTTATCCTCATTC 59.223 52.381 0.00 0.00 44.09 2.67
37 40 3.060615 GCTTGGTGCAGAGGCTGG 61.061 66.667 0.00 0.00 42.31 4.85
39 42 2.964310 ATCGCTTGGTGCAGAGGCT 61.964 57.895 0.00 0.00 43.06 4.58
49 52 1.063649 GACTGCATGCATCGCTTGG 59.936 57.895 22.97 10.18 34.84 3.61
61 64 3.701205 AGTACCATGTTCATGACTGCA 57.299 42.857 13.51 0.00 0.00 4.41
105 108 6.801377 TGTCGCTAAGCAAATTTTTAGTGATG 59.199 34.615 20.63 7.52 43.91 3.07
112 115 7.358352 CGAAAGATTGTCGCTAAGCAAATTTTT 60.358 33.333 0.00 0.00 0.00 1.94
113 116 6.088085 CGAAAGATTGTCGCTAAGCAAATTTT 59.912 34.615 0.00 0.00 0.00 1.82
149 153 4.365899 TGTGTATATCGAGTTTGAGCGT 57.634 40.909 0.00 0.00 0.00 5.07
179 183 7.518731 TTTGAACATTTTGAAGTACAAGTGC 57.481 32.000 0.00 0.00 39.77 4.40
201 205 4.450053 TGCATAAACAAAAGGCTTGCTTT 58.550 34.783 0.00 1.52 0.00 3.51
218 222 6.835819 AATATCCTACTAGCTCGTTGCATA 57.164 37.500 0.00 0.00 45.94 3.14
219 223 5.730296 AATATCCTACTAGCTCGTTGCAT 57.270 39.130 0.00 0.00 45.94 3.96
220 224 5.531122 AAATATCCTACTAGCTCGTTGCA 57.469 39.130 0.00 0.00 45.94 4.08
221 225 6.846325 AAAAATATCCTACTAGCTCGTTGC 57.154 37.500 0.00 0.00 43.29 4.17
266 270 4.798574 AGATTGTCAACCAGCGAAATTTC 58.201 39.130 8.20 8.20 0.00 2.17
267 271 4.853924 AGATTGTCAACCAGCGAAATTT 57.146 36.364 0.00 0.00 0.00 1.82
268 272 4.853924 AAGATTGTCAACCAGCGAAATT 57.146 36.364 0.00 0.00 0.00 1.82
269 273 4.613622 CGAAAGATTGTCAACCAGCGAAAT 60.614 41.667 0.00 0.00 0.00 2.17
270 274 3.303725 CGAAAGATTGTCAACCAGCGAAA 60.304 43.478 0.00 0.00 0.00 3.46
271 275 2.223144 CGAAAGATTGTCAACCAGCGAA 59.777 45.455 0.00 0.00 0.00 4.70
272 276 1.798223 CGAAAGATTGTCAACCAGCGA 59.202 47.619 0.00 0.00 0.00 4.93
273 277 1.135972 CCGAAAGATTGTCAACCAGCG 60.136 52.381 0.00 0.00 0.00 5.18
297 301 3.693085 AGCATGTCTTATGAGCAAACTGG 59.307 43.478 0.00 0.00 0.00 4.00
309 313 4.382040 GCAGAGTACTTGGAGCATGTCTTA 60.382 45.833 0.00 0.00 0.00 2.10
414 418 4.586001 ACAAGCAAATTTCAGTGATGGTCT 59.414 37.500 0.00 0.00 0.00 3.85
556 560 4.354071 TTCAACAATGGTGCATCGTATG 57.646 40.909 0.00 0.00 0.00 2.39
593 598 5.130292 AGCAAAATGTCCACTCAAAGATG 57.870 39.130 0.00 0.00 0.00 2.90
649 654 8.743714 AGAAAGGCTTATCCTGAACATTTTTAG 58.256 33.333 0.00 0.00 46.94 1.85
710 716 2.285950 CGTTACATTTATTCGCCCACGG 60.286 50.000 0.00 0.00 40.63 4.94
747 753 7.359765 CGCGGGTAAATGATTCGTCTTTATTAT 60.360 37.037 0.00 0.00 0.00 1.28
863 869 6.326375 CGACTCTTTTTATACACTGAGAGCT 58.674 40.000 0.00 0.00 35.26 4.09
885 891 3.633094 GAGTGCTGAAGAGCCGCGA 62.633 63.158 8.23 0.00 45.57 5.87
903 909 2.799978 TCGCATTGGTACTCATATTGCG 59.200 45.455 19.07 19.07 44.02 4.85
919 925 1.641577 GCCGAAAGTAGTCTTCGCAT 58.358 50.000 0.00 0.00 32.90 4.73
942 948 6.084925 GTCACAACGAGATATATAGTTCGGG 58.915 44.000 17.71 13.21 37.38 5.14
1062 1068 1.271840 TTGATGGCGCCCTAGGAAGT 61.272 55.000 26.77 0.00 0.00 3.01
1443 1449 1.005804 CGATCTGGATCATGCCGTCG 61.006 60.000 10.62 0.00 37.69 5.12
1609 1620 1.899814 AGGAACGGAACATAGCACTGA 59.100 47.619 0.00 0.00 0.00 3.41
1623 1634 3.971150 TGGTGCAATTTTTGTAGGAACG 58.029 40.909 0.00 0.00 0.00 3.95
1694 1705 0.898320 TTCTCAGGTACAGCAGGAGC 59.102 55.000 0.00 0.00 42.56 4.70
1695 1706 5.543507 AATATTCTCAGGTACAGCAGGAG 57.456 43.478 0.00 0.00 0.00 3.69
1696 1707 5.425217 TGAAATATTCTCAGGTACAGCAGGA 59.575 40.000 0.00 0.00 0.00 3.86
1697 1708 5.674525 TGAAATATTCTCAGGTACAGCAGG 58.325 41.667 0.00 0.00 0.00 4.85
1698 1709 6.820656 AGTTGAAATATTCTCAGGTACAGCAG 59.179 38.462 0.00 0.00 0.00 4.24
1699 1710 6.711277 AGTTGAAATATTCTCAGGTACAGCA 58.289 36.000 0.00 0.00 0.00 4.41
1720 1731 9.893305 GCATGCTAAAACCGATTAATATAAGTT 57.107 29.630 11.37 0.00 0.00 2.66
1725 1736 7.885297 ACATGCATGCTAAAACCGATTAATAT 58.115 30.769 26.53 0.00 0.00 1.28
1733 1744 2.917701 TGACATGCATGCTAAAACCG 57.082 45.000 26.53 0.00 0.00 4.44
1781 1792 4.901868 ACAGCATCCAAAAATTGCTCAAT 58.098 34.783 0.00 0.00 44.54 2.57
1790 1801 7.414429 CGAGATTATTCTGACAGCATCCAAAAA 60.414 37.037 0.00 0.00 30.30 1.94
1796 1807 7.042187 ACAATTCGAGATTATTCTGACAGCATC 60.042 37.037 0.00 0.00 30.30 3.91
1797 1808 6.765036 ACAATTCGAGATTATTCTGACAGCAT 59.235 34.615 0.00 0.00 30.30 3.79
1842 1953 6.755141 GTGTGCTAATCATTCTGCATTTCAAT 59.245 34.615 1.93 0.00 37.76 2.57
2091 2203 2.917933 TCCAACCATCTTCTTATGCCG 58.082 47.619 0.00 0.00 0.00 5.69
2264 2376 5.533154 CCGGGCAAGAAATATATAACAACCA 59.467 40.000 0.00 0.00 0.00 3.67
2280 2392 1.595093 AAATCGCTTTCCCGGGCAAG 61.595 55.000 26.64 26.64 0.00 4.01
2305 2417 2.422597 TGTTGTCGAACAGCCTTATGG 58.577 47.619 0.00 0.00 37.15 2.74
2423 2535 3.722289 GCGTTTGTGTAAAAAGAACCTCG 59.278 43.478 0.00 0.00 0.00 4.63
2452 2564 2.890311 CACCCTTACAAGCACCAATGAA 59.110 45.455 0.00 0.00 0.00 2.57
2460 2572 1.060729 TGTAGGCACCCTTACAAGCA 58.939 50.000 0.00 0.00 34.61 3.91


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

AutoCloner maintained by Alex Coulton.