Multiple sequence alignment - TraesCS1A01G419300

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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 TraesCS1A01G419300 chr1A 100.000 2370 0 0 1 2370 576204543 576202174 0.000000e+00 4377
1 TraesCS1A01G419300 chr1A 88.797 1696 92 37 25 1653 576140157 576138493 0.000000e+00 1989
2 TraesCS1A01G419300 chr1A 90.469 682 49 8 1690 2370 576138494 576137828 0.000000e+00 885
3 TraesCS1A01G419300 chr1A 79.499 639 67 34 1028 1655 576078221 576077636 1.710000e-106 396
4 TraesCS1A01G419300 chr1A 79.487 312 44 13 462 759 576078752 576078447 1.110000e-48 204
5 TraesCS1A01G419300 chr1D 88.521 2413 171 47 1 2370 479751799 479749450 0.000000e+00 2824
6 TraesCS1A01G419300 chr1D 91.287 1779 111 23 1 1752 479760393 479758632 0.000000e+00 2386
7 TraesCS1A01G419300 chr1D 89.590 634 55 3 1738 2370 479758615 479757992 0.000000e+00 795
8 TraesCS1A01G419300 chr1D 92.722 316 17 2 2056 2370 479722102 479721792 3.590000e-123 451
9 TraesCS1A01G419300 chr1D 87.324 284 28 4 1027 1305 479737843 479737563 3.800000e-83 318
10 TraesCS1A01G419300 chr1D 74.934 762 106 48 219 916 479738683 479737943 1.080000e-68 270
11 TraesCS1A01G419300 chr1D 92.414 145 11 0 1881 2025 479722323 479722179 8.590000e-50 207
12 TraesCS1A01G419300 chr1B 90.516 1434 87 13 966 2370 667975792 667974379 0.000000e+00 1849
13 TraesCS1A01G419300 chr1B 89.067 1308 70 25 532 1796 667930469 667931746 0.000000e+00 1555
14 TraesCS1A01G419300 chr1B 88.437 934 73 18 1 930 668031999 668031097 0.000000e+00 1094
15 TraesCS1A01G419300 chr1B 90.932 805 32 16 984 1752 667997262 667996463 0.000000e+00 1044
16 TraesCS1A01G419300 chr1B 89.559 862 33 13 986 1807 668031093 668030249 0.000000e+00 1040
17 TraesCS1A01G419300 chr1B 91.471 680 39 7 1 670 667976849 667976179 0.000000e+00 917
18 TraesCS1A01G419300 chr1B 89.643 560 47 5 1814 2370 668029994 668029443 0.000000e+00 702
19 TraesCS1A01G419300 chr1B 87.857 560 47 7 1808 2356 667932020 667932569 2.570000e-179 638
20 TraesCS1A01G419300 chr1B 85.393 623 53 21 312 930 667997850 667997262 1.560000e-171 612
21 TraesCS1A01G419300 chr1B 88.618 492 32 11 1 470 667929975 667930464 5.680000e-161 577
22 TraesCS1A01G419300 chr1B 90.115 435 37 3 1802 2235 667996255 667995826 5.720000e-156 560
23 TraesCS1A01G419300 chr1B 93.231 325 20 2 1 325 667998690 667998368 5.930000e-131 477
24 TraesCS1A01G419300 chr1B 77.361 932 128 47 581 1478 667965301 667966183 2.130000e-130 475


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 TraesCS1A01G419300 chr1A 576202174 576204543 2369 True 4377.000000 4377 100.00000 1 2370 1 chr1A.!!$R1 2369
1 TraesCS1A01G419300 chr1A 576137828 576140157 2329 True 1437.000000 1989 89.63300 25 2370 2 chr1A.!!$R3 2345
2 TraesCS1A01G419300 chr1A 576077636 576078752 1116 True 300.000000 396 79.49300 462 1655 2 chr1A.!!$R2 1193
3 TraesCS1A01G419300 chr1D 479749450 479751799 2349 True 2824.000000 2824 88.52100 1 2370 1 chr1D.!!$R1 2369
4 TraesCS1A01G419300 chr1D 479757992 479760393 2401 True 1590.500000 2386 90.43850 1 2370 2 chr1D.!!$R4 2369
5 TraesCS1A01G419300 chr1D 479721792 479722323 531 True 329.000000 451 92.56800 1881 2370 2 chr1D.!!$R2 489
6 TraesCS1A01G419300 chr1D 479737563 479738683 1120 True 294.000000 318 81.12900 219 1305 2 chr1D.!!$R3 1086
7 TraesCS1A01G419300 chr1B 667974379 667976849 2470 True 1383.000000 1849 90.99350 1 2370 2 chr1B.!!$R1 2369
8 TraesCS1A01G419300 chr1B 668029443 668031999 2556 True 945.333333 1094 89.21300 1 2370 3 chr1B.!!$R3 2369
9 TraesCS1A01G419300 chr1B 667929975 667932569 2594 False 923.333333 1555 88.51400 1 2356 3 chr1B.!!$F2 2355
10 TraesCS1A01G419300 chr1B 667995826 667998690 2864 True 673.250000 1044 89.91775 1 2235 4 chr1B.!!$R2 2234
11 TraesCS1A01G419300 chr1B 667965301 667966183 882 False 475.000000 475 77.36100 581 1478 1 chr1B.!!$F1 897

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
310 354 1.556911 AGAACCAAGATCATCACGCCT 59.443 47.619 0.00 0.0 0.0 5.52 F
830 1643 2.375146 TCGATCGTCCATCTTCTTCCA 58.625 47.619 15.94 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1272 2173 0.108585 AAACACAGTGATGGCGGTCT 59.891 50.0 7.81 0.0 0.0 3.85 R
2161 3598 0.307760 CACAACAACCTGAAGCGGAC 59.692 55.0 0.00 0.0 0.0 4.79 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
280 324 4.219725 ACCCAACATTACTGCACCAAATAC 59.780 41.667 0.00 0.00 0.00 1.89
310 354 1.556911 AGAACCAAGATCATCACGCCT 59.443 47.619 0.00 0.00 0.00 5.52
378 954 7.452630 TTTTTCGCTATTTTGTGGTGTAAAC 57.547 32.000 0.00 0.00 0.00 2.01
423 999 8.960591 ACATGCACACTTTAAAGCTAATAGAAT 58.039 29.630 15.24 0.00 0.00 2.40
559 1184 8.531982 TCTCAACTTTAACTAGAGCATACATGT 58.468 33.333 2.69 2.69 0.00 3.21
560 1185 9.803315 CTCAACTTTAACTAGAGCATACATGTA 57.197 33.333 8.27 8.27 0.00 2.29
787 1450 7.138736 TGCTTCAAAATTCCTCTAGTTTTTCG 58.861 34.615 0.00 0.00 0.00 3.46
813 1626 2.543653 CCACTCGTATGCACATCATCGA 60.544 50.000 0.00 0.00 36.63 3.59
814 1627 3.311966 CACTCGTATGCACATCATCGAT 58.688 45.455 0.00 0.00 35.67 3.59
815 1628 3.363128 CACTCGTATGCACATCATCGATC 59.637 47.826 0.00 0.00 35.67 3.69
816 1629 2.584791 TCGTATGCACATCATCGATCG 58.415 47.619 9.36 9.36 36.63 3.69
827 1640 4.038522 ACATCATCGATCGTCCATCTTCTT 59.961 41.667 15.94 0.00 0.00 2.52
829 1642 3.004839 TCATCGATCGTCCATCTTCTTCC 59.995 47.826 15.94 0.00 0.00 3.46
830 1643 2.375146 TCGATCGTCCATCTTCTTCCA 58.625 47.619 15.94 0.00 0.00 3.53
886 1717 3.951775 AAGTAGCACCTCTTCTCACAG 57.048 47.619 0.00 0.00 0.00 3.66
977 1812 4.933330 AGCAGCTTAATTATCGTTCGAGA 58.067 39.130 0.00 0.00 0.00 4.04
1272 2173 1.660560 GCTACGAGGCCGACAGGTAA 61.661 60.000 0.00 0.00 40.50 2.85
1552 2512 6.148315 TGCATGCATGTTGATAATACTCTAGC 59.852 38.462 26.79 7.58 0.00 3.42
1622 2584 6.106673 ACTCACATGGGTTTAACTTATCTCG 58.893 40.000 0.00 0.00 0.00 4.04
1623 2585 6.045072 TCACATGGGTTTAACTTATCTCGT 57.955 37.500 0.00 0.00 0.00 4.18
1624 2586 7.093640 ACTCACATGGGTTTAACTTATCTCGTA 60.094 37.037 0.00 0.00 0.00 3.43
1625 2587 7.788026 TCACATGGGTTTAACTTATCTCGTAT 58.212 34.615 0.00 0.00 0.00 3.06
1695 2659 3.625313 TGCACATTGTAACCATATGTCCG 59.375 43.478 1.24 0.00 30.45 4.79
1715 2679 7.154656 TGTCCGTATCAATGGAGAGATAAATG 58.845 38.462 0.00 0.00 41.64 2.32
1745 2751 4.411993 TGCCAAATATGTTACACACACG 57.588 40.909 0.00 0.00 38.61 4.49
1752 2758 7.201461 CCAAATATGTTACACACACGTACTACC 60.201 40.741 0.00 0.00 38.61 3.18
1780 2786 1.400494 AGACAAAACAACTGCGGTGTC 59.600 47.619 0.00 0.72 36.48 3.67
1938 3318 3.527533 CACCAATTGATCAAATGGCAGG 58.472 45.455 33.22 22.37 43.46 4.85
1949 3329 2.424842 AATGGCAGGGCAGAACCGAA 62.425 55.000 1.13 0.00 40.62 4.30
1950 3330 2.044946 GGCAGGGCAGAACCGAAT 60.045 61.111 0.00 0.00 40.62 3.34
1956 3336 2.161609 CAGGGCAGAACCGAATACAAAC 59.838 50.000 0.00 0.00 40.62 2.93
2003 3383 1.007238 TGCTAGGGTTGCTACCTCTCT 59.993 52.381 17.03 8.36 44.38 3.10
2015 3425 3.307762 GCTACCTCTCTTCACATGGGTTT 60.308 47.826 0.00 0.00 0.00 3.27
2027 3437 4.214545 TCACATGGGTTTATCGTTGTTGTC 59.785 41.667 0.00 0.00 0.00 3.18
2104 3541 2.637872 TCCCCTTCCACTAGTTGAAGTG 59.362 50.000 26.49 19.22 45.33 3.16
2158 3595 2.696707 CAACATCCCCTTTGATGATGGG 59.303 50.000 7.93 0.00 43.94 4.00
2241 3678 2.224793 GCAAGGGTTTCCAGAGGTAAGT 60.225 50.000 0.00 0.00 34.83 2.24
2243 3680 4.072839 CAAGGGTTTCCAGAGGTAAGTTC 58.927 47.826 0.00 0.00 34.83 3.01
2244 3681 2.643304 AGGGTTTCCAGAGGTAAGTTCC 59.357 50.000 0.00 0.00 34.83 3.62
2245 3682 2.290768 GGGTTTCCAGAGGTAAGTTCCC 60.291 54.545 0.00 0.00 0.00 3.97
2246 3683 2.290768 GGTTTCCAGAGGTAAGTTCCCC 60.291 54.545 0.00 0.00 0.00 4.81
2247 3684 1.665137 TTCCAGAGGTAAGTTCCCCC 58.335 55.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
220 264 8.842358 TGAGTGTACCTTAAAAATCTCGATTT 57.158 30.769 0.00 0.00 42.35 2.17
378 954 5.448225 GCATGTACATCCATGTTGACTCTTG 60.448 44.000 5.07 0.00 43.33 3.02
423 999 8.125448 GCATTTTGTTACACCAAATTAAGCAAA 58.875 29.630 0.00 0.00 34.50 3.68
447 1023 4.458989 GTCCATGGTTAGTGAATCAAAGCA 59.541 41.667 12.58 2.59 35.35 3.91
597 1253 4.330250 CTCCCTCTCAAAGATTCAAAGCA 58.670 43.478 0.00 0.00 0.00 3.91
598 1254 3.693578 CCTCCCTCTCAAAGATTCAAAGC 59.306 47.826 0.00 0.00 0.00 3.51
742 1400 3.386237 AGGCCAGCACGAGAGGAC 61.386 66.667 5.01 0.00 0.00 3.85
787 1450 1.521681 GTGCATACGAGTGGAGGGC 60.522 63.158 0.00 0.00 0.00 5.19
813 1626 1.486726 GGGTGGAAGAAGATGGACGAT 59.513 52.381 0.00 0.00 0.00 3.73
814 1627 0.902531 GGGTGGAAGAAGATGGACGA 59.097 55.000 0.00 0.00 0.00 4.20
815 1628 0.107654 GGGGTGGAAGAAGATGGACG 60.108 60.000 0.00 0.00 0.00 4.79
816 1629 0.256177 GGGGGTGGAAGAAGATGGAC 59.744 60.000 0.00 0.00 0.00 4.02
849 1663 2.588620 ACTTATAGCAGTCGAGGAGGG 58.411 52.381 0.00 0.00 0.00 4.30
886 1717 1.492176 TGAGATGGATGGGGAAGAAGC 59.508 52.381 0.00 0.00 0.00 3.86
967 1802 2.921754 GACGATTGGTTTCTCGAACGAT 59.078 45.455 0.00 0.00 39.22 3.73
1215 2116 4.185286 GGGCATGGGGGACGGTAC 62.185 72.222 0.00 0.00 0.00 3.34
1251 2152 1.822613 CCTGTCGGCCTCGTAGCTA 60.823 63.158 0.00 0.00 37.69 3.32
1272 2173 0.108585 AAACACAGTGATGGCGGTCT 59.891 50.000 7.81 0.00 0.00 3.85
1329 2240 4.458989 TCAACCTGATCACACAAATTAGCC 59.541 41.667 0.00 0.00 0.00 3.93
1539 2499 4.701171 ACCACTAGCCGCTAGAGTATTATC 59.299 45.833 30.08 0.00 37.49 1.75
1552 2512 5.961396 ACATACTTATAGACCACTAGCCG 57.039 43.478 0.00 0.00 31.78 5.52
1695 2659 9.512588 AACATCCATTTATCTCTCCATTGATAC 57.487 33.333 0.00 0.00 0.00 2.24
1715 2679 8.194104 TGTGTAACATATTTGGCATTAACATCC 58.806 33.333 0.00 0.00 45.67 3.51
1745 2751 9.442033 GTTGTTTTGTCTTTGTATTGGTAGTAC 57.558 33.333 0.00 0.00 0.00 2.73
1752 2758 5.051774 CCGCAGTTGTTTTGTCTTTGTATTG 60.052 40.000 0.00 0.00 0.00 1.90
1938 3318 2.095415 GTGGTTTGTATTCGGTTCTGCC 60.095 50.000 0.00 0.00 0.00 4.85
1949 3329 6.204108 GTGCTTTGTAGTAGTGTGGTTTGTAT 59.796 38.462 0.00 0.00 0.00 2.29
1950 3330 5.524646 GTGCTTTGTAGTAGTGTGGTTTGTA 59.475 40.000 0.00 0.00 0.00 2.41
1956 3336 2.224426 TGGGTGCTTTGTAGTAGTGTGG 60.224 50.000 0.00 0.00 0.00 4.17
2003 3383 4.580995 ACAACAACGATAAACCCATGTGAA 59.419 37.500 0.00 0.00 0.00 3.18
2015 3425 4.732647 GCTCCACTATCGACAACAACGATA 60.733 45.833 0.00 0.00 46.30 2.92
2076 3510 2.873557 TAGTGGAAGGGGAGGAGGCG 62.874 65.000 0.00 0.00 0.00 5.52
2077 3511 1.003051 TAGTGGAAGGGGAGGAGGC 59.997 63.158 0.00 0.00 0.00 4.70
2104 3541 1.343465 TGAGTGGAAGAGGAACCGTTC 59.657 52.381 2.37 2.37 0.00 3.95
2107 3544 0.969894 ACTGAGTGGAAGAGGAACCG 59.030 55.000 0.00 0.00 0.00 4.44
2158 3595 2.359975 CAACCTGAAGCGGACCCC 60.360 66.667 0.00 0.00 0.00 4.95
2161 3598 0.307760 CACAACAACCTGAAGCGGAC 59.692 55.000 0.00 0.00 0.00 4.79
2162 3599 1.444119 GCACAACAACCTGAAGCGGA 61.444 55.000 0.00 0.00 0.00 5.54
2252 3692 3.771577 ACAACAGTTCTCAACTAGGGG 57.228 47.619 0.00 0.00 40.46 4.79
2341 3783 6.093357 TGAAGGGCTTGTTTTTGAATTTTGTC 59.907 34.615 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.