Multiple sequence alignment - TraesCS4A01G150400

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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 TraesCS4A01G150400 chr4A 100.000 2255 0 0 1 2255 295272577 295274831 0 4165
1 TraesCS4A01G150400 chr1D 95.743 2255 84 9 2 2255 141314941 141312698 0 3622
2 TraesCS4A01G150400 chr7B 95.654 2255 88 8 2 2255 644465637 644467882 0 3613
3 TraesCS4A01G150400 chr3A 95.432 2255 92 8 2 2255 633109448 633111692 0 3583
4 TraesCS4A01G150400 chr6B 95.211 2255 97 8 2 2255 306997796 306995552 0 3555
5 TraesCS4A01G150400 chr1B 95.124 2256 97 10 2 2255 638702472 638700228 0 3544
6 TraesCS4A01G150400 chr1B 95.122 2255 99 8 2 2255 672477355 672479599 0 3544
7 TraesCS4A01G150400 chr4B 95.078 2255 99 8 2 2255 209079323 209077080 0 3539
8 TraesCS4A01G150400 chr7A 94.634 2255 109 9 2 2255 46399052 46396809 0 3483
9 TraesCS4A01G150400 chr1A 94.324 2255 116 8 2 2255 415654237 415656480 0 3445


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 TraesCS4A01G150400 chr4A 295272577 295274831 2254 False 4165 4165 100.000 1 2255 1 chr4A.!!$F1 2254
1 TraesCS4A01G150400 chr1D 141312698 141314941 2243 True 3622 3622 95.743 2 2255 1 chr1D.!!$R1 2253
2 TraesCS4A01G150400 chr7B 644465637 644467882 2245 False 3613 3613 95.654 2 2255 1 chr7B.!!$F1 2253
3 TraesCS4A01G150400 chr3A 633109448 633111692 2244 False 3583 3583 95.432 2 2255 1 chr3A.!!$F1 2253
4 TraesCS4A01G150400 chr6B 306995552 306997796 2244 True 3555 3555 95.211 2 2255 1 chr6B.!!$R1 2253
5 TraesCS4A01G150400 chr1B 638700228 638702472 2244 True 3544 3544 95.124 2 2255 1 chr1B.!!$R1 2253
6 TraesCS4A01G150400 chr1B 672477355 672479599 2244 False 3544 3544 95.122 2 2255 1 chr1B.!!$F1 2253
7 TraesCS4A01G150400 chr4B 209077080 209079323 2243 True 3539 3539 95.078 2 2255 1 chr4B.!!$R1 2253
8 TraesCS4A01G150400 chr7A 46396809 46399052 2243 True 3483 3483 94.634 2 2255 1 chr7A.!!$R1 2253
9 TraesCS4A01G150400 chr1A 415654237 415656480 2243 False 3445 3445 94.324 2 2255 1 chr1A.!!$F1 2253

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
462 463 0.8364 ACGGGTGGATTGGTCAGAGT 60.836 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 1772 0.108138 ATGGCTCGCTTAGTTCGCTT 60.108 50.0 0.0 0.0 0.0 4.68 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
66 67 4.721776 AGATAGGGGTTTGCTATTCTCACA 59.278 41.667 0.00 0.00 0.00 3.58
114 115 6.820470 TTGAATAGTTTTTGCCTTGTTTCG 57.180 33.333 0.00 0.00 0.00 3.46
148 149 6.698380 TCATCTGAACCTTCCAAGTACTAAC 58.302 40.000 0.00 0.00 0.00 2.34
253 254 5.184671 GGAGCAAAAAGAGTGAAATGAGGAT 59.815 40.000 0.00 0.00 0.00 3.24
254 255 6.375455 GGAGCAAAAAGAGTGAAATGAGGATA 59.625 38.462 0.00 0.00 0.00 2.59
262 263 4.899502 AGTGAAATGAGGATATAAGCCCG 58.100 43.478 0.00 0.00 0.00 6.13
283 284 3.100671 GCTAGGTCTTCCTCTTCCTTCA 58.899 50.000 0.00 0.00 43.94 3.02
340 341 6.525578 AAAAGTATACTGAGTGGTCGATGA 57.474 37.500 6.06 0.00 0.00 2.92
421 422 7.412237 GCAAAAATGGACATACAATCAAAGAGC 60.412 37.037 0.00 0.00 0.00 4.09
462 463 0.836400 ACGGGTGGATTGGTCAGAGT 60.836 55.000 0.00 0.00 0.00 3.24
464 465 1.271379 CGGGTGGATTGGTCAGAGTTT 60.271 52.381 0.00 0.00 0.00 2.66
467 468 3.562176 GGGTGGATTGGTCAGAGTTTCAT 60.562 47.826 0.00 0.00 0.00 2.57
540 541 7.584122 TTCCGATAGAAAGTAAGAGCAGTAT 57.416 36.000 0.00 0.00 39.76 2.12
589 590 7.397192 ACTTGAAATTAGTAGTCCCGGTAGTTA 59.603 37.037 0.00 0.00 0.00 2.24
700 701 3.497640 GCTTCGGGATCAGATCATTCAAG 59.502 47.826 12.66 8.90 0.00 3.02
713 714 5.353678 AGATCATTCAAGTAAAGCTGTCAGC 59.646 40.000 17.48 17.48 42.84 4.26
742 743 1.549950 GCTTTGAGGAACATTGGGGGA 60.550 52.381 0.00 0.00 0.00 4.81
777 778 7.823745 TGTGACTGAGCAGATATGTCTATTA 57.176 36.000 4.21 0.00 32.09 0.98
783 784 5.723405 TGAGCAGATATGTCTATTATGCCCT 59.277 40.000 0.00 0.00 33.82 5.19
784 785 6.214208 TGAGCAGATATGTCTATTATGCCCTT 59.786 38.462 0.00 0.00 33.82 3.95
831 834 2.162408 CCAAAGGCTTTCTCATTCGGAC 59.838 50.000 10.08 0.00 0.00 4.79
834 837 2.704572 AGGCTTTCTCATTCGGACAAG 58.295 47.619 0.00 0.00 0.00 3.16
835 838 1.740025 GGCTTTCTCATTCGGACAAGG 59.260 52.381 0.00 0.00 0.00 3.61
836 839 1.740025 GCTTTCTCATTCGGACAAGGG 59.260 52.381 0.00 0.00 0.00 3.95
837 840 2.615493 GCTTTCTCATTCGGACAAGGGA 60.615 50.000 0.00 0.00 0.00 4.20
838 841 3.674997 CTTTCTCATTCGGACAAGGGAA 58.325 45.455 0.00 0.00 0.00 3.97
839 842 3.780804 TTCTCATTCGGACAAGGGAAA 57.219 42.857 0.00 0.00 0.00 3.13
840 843 4.301072 TTCTCATTCGGACAAGGGAAAT 57.699 40.909 0.00 0.00 0.00 2.17
841 844 5.429681 TTCTCATTCGGACAAGGGAAATA 57.570 39.130 0.00 0.00 0.00 1.40
842 845 5.630415 TCTCATTCGGACAAGGGAAATAT 57.370 39.130 0.00 0.00 0.00 1.28
891 894 1.117994 TCTCTGCTCGGATGATTGCT 58.882 50.000 0.00 0.00 0.00 3.91
911 914 4.053295 GCTGCTTGTGTGAATTTCATTGT 58.947 39.130 1.78 0.00 0.00 2.71
921 924 4.039124 GTGAATTTCATTGTTGTGGGTCCT 59.961 41.667 1.78 0.00 0.00 3.85
942 945 5.105513 TCCTGTGTGTGCTCGAATAAGATTA 60.106 40.000 0.00 0.00 0.00 1.75
988 991 2.099652 CTTGACTCCACGGTGCTGGA 62.100 60.000 1.68 0.00 38.05 3.86
1010 1013 2.644555 ATCGAGTTTATGGCGCCGCT 62.645 55.000 23.90 14.61 0.00 5.52
1017 1020 2.884997 TTATGGCGCCGCTGACCATT 62.885 55.000 23.90 0.00 41.44 3.16
1087 1090 5.994416 AATAGTGGTCCCTTGGTATTCAT 57.006 39.130 0.00 0.00 0.00 2.57
1091 1094 3.694566 GTGGTCCCTTGGTATTCATGTTC 59.305 47.826 0.00 0.00 0.00 3.18
1127 1130 5.963594 AGGAAAGTCGACTGTTATACCTTC 58.036 41.667 20.85 15.44 0.00 3.46
1166 1169 7.963465 CCTATCTTCTTTAAAAAGCCGAAAGAC 59.037 37.037 6.51 0.00 38.56 3.01
1175 1178 4.937201 AAAGCCGAAAGACAAGGATTTT 57.063 36.364 0.00 0.00 40.24 1.82
1264 1267 3.681593 TCCATTTCCTGAACCTAAACCG 58.318 45.455 0.00 0.00 0.00 4.44
1371 1374 3.195661 CAGGCTTTAGGTACGCTTTAGG 58.804 50.000 0.00 0.00 0.00 2.69
1375 1378 3.999001 GCTTTAGGTACGCTTTAGGTTGT 59.001 43.478 0.00 0.00 0.00 3.32
1380 1383 4.427312 AGGTACGCTTTAGGTTGTAATCG 58.573 43.478 0.00 0.00 0.00 3.34
1393 1396 9.602568 TTAGGTTGTAATCGTTAAAGATATGCA 57.397 29.630 4.25 0.00 0.00 3.96
1636 1639 3.064207 CTGAAAAGCCGTAGTGCTAACA 58.936 45.455 0.00 0.00 41.80 2.41
1709 1712 1.658717 CGAAGCGATCCGTGCTAGG 60.659 63.158 0.00 0.00 43.14 3.02
1716 1719 1.878656 GATCCGTGCTAGGGCGCTAT 61.879 60.000 11.35 0.00 45.75 2.97
1742 1745 5.697473 TCCTTTATGAGCGAGACTCTATG 57.303 43.478 0.03 0.00 46.41 2.23
1769 1772 4.524053 TCTACTGATCTAAGAACTCCGCA 58.476 43.478 0.00 0.00 0.00 5.69
1778 1781 0.601558 AGAACTCCGCAAGCGAACTA 59.398 50.000 16.97 0.00 42.83 2.24
1851 1854 2.567615 GCTCCCTTCCTTCACTGAACTA 59.432 50.000 0.00 0.00 0.00 2.24
1904 1907 9.314321 CTAGCTAATTTTTCCTTTACGAGATCA 57.686 33.333 0.00 0.00 0.00 2.92
1921 1924 0.108804 TCACGGCTCTTCGGAATGAC 60.109 55.000 0.00 0.00 0.00 3.06
1983 1987 3.370104 AGAGTGATGGGACTACTTCCTG 58.630 50.000 0.00 0.00 45.09 3.86
1991 1995 2.835156 GGGACTACTTCCTGAAAGAGCT 59.165 50.000 0.00 0.00 45.09 4.09
1996 2000 5.930135 ACTACTTCCTGAAAGAGCTTTTCA 58.070 37.500 17.41 17.41 38.44 2.69
2007 2011 2.340328 GCTTTTCATTCGGGCCGGT 61.340 57.895 27.98 12.84 0.00 5.28
2102 2107 5.304871 AGAAAGAAGGGTCGAAGTTTAGACT 59.695 40.000 10.80 0.00 37.52 3.24
2186 2191 5.630415 TCCATTTATGATCCCGAGTTTCT 57.370 39.130 0.00 0.00 0.00 2.52
2226 2231 2.579738 GGTCGAGGCTTCCACTCC 59.420 66.667 0.00 0.00 0.00 3.85
2237 2242 2.997315 CCACTCCGCCCTCAGACA 60.997 66.667 0.00 0.00 0.00 3.41
2239 2244 2.681778 ACTCCGCCCTCAGACAGG 60.682 66.667 0.00 0.00 43.01 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.546476 GGTCCACGAGTTGAGACAGAT 59.454 52.381 0.00 0.00 30.80 2.90
86 87 5.306678 ACAAGGCAAAAACTATTCAATGGGA 59.693 36.000 0.00 0.00 0.00 4.37
114 115 1.683319 GGTTCAGATGAAGGAAGGGCC 60.683 57.143 0.00 0.00 34.27 5.80
335 336 3.853671 CCATTCCTTTTCGCTTTTCATCG 59.146 43.478 0.00 0.00 0.00 3.84
338 339 2.627699 AGCCATTCCTTTTCGCTTTTCA 59.372 40.909 0.00 0.00 0.00 2.69
340 341 3.751479 AAGCCATTCCTTTTCGCTTTT 57.249 38.095 0.00 0.00 36.40 2.27
421 422 4.860907 GTCATTGCAAATAACTGCTCCTTG 59.139 41.667 1.71 0.00 43.07 3.61
462 463 5.627735 GCCATAACTGAGTCTCTCCATGAAA 60.628 44.000 0.65 0.00 0.00 2.69
464 465 3.386078 GCCATAACTGAGTCTCTCCATGA 59.614 47.826 0.65 0.00 0.00 3.07
467 468 1.751351 CGCCATAACTGAGTCTCTCCA 59.249 52.381 0.65 0.00 0.00 3.86
478 479 2.135933 GCTCTTTATCGCGCCATAACT 58.864 47.619 6.98 0.00 0.00 2.24
540 541 8.484214 AGTACAAAGCTCTCCTATGAATATGA 57.516 34.615 0.00 0.00 0.00 2.15
700 701 1.745489 CCCGGGCTGACAGCTTTAC 60.745 63.158 25.92 9.94 41.99 2.01
713 714 1.559065 TTCCTCAAAGCCTACCCGGG 61.559 60.000 22.25 22.25 0.00 5.73
742 743 4.910195 TGCTCAGTCACAACATAAGGAAT 58.090 39.130 0.00 0.00 0.00 3.01
777 778 4.067192 GCAAATCTGTTTTTGAAGGGCAT 58.933 39.130 9.07 0.00 38.58 4.40
783 784 5.976458 ACTCCTTGCAAATCTGTTTTTGAA 58.024 33.333 0.00 0.00 38.58 2.69
784 785 5.596836 ACTCCTTGCAAATCTGTTTTTGA 57.403 34.783 0.00 0.00 38.58 2.69
866 869 1.410517 TCATCCGAGCAGAGAATGGAC 59.589 52.381 0.00 0.00 0.00 4.02
891 894 5.291371 CACAACAATGAAATTCACACAAGCA 59.709 36.000 0.00 0.00 31.22 3.91
911 914 1.453015 GCACACACAGGACCCACAA 60.453 57.895 0.00 0.00 0.00 3.33
921 924 7.609760 AAATAATCTTATTCGAGCACACACA 57.390 32.000 0.00 0.00 32.46 3.72
978 981 1.112113 ACTCGATAATCCAGCACCGT 58.888 50.000 0.00 0.00 0.00 4.83
988 991 2.066262 CGGCGCCATAAACTCGATAAT 58.934 47.619 28.98 0.00 0.00 1.28
1010 1013 6.514947 CCATCTTTGACTTTTTGAATGGTCA 58.485 36.000 0.00 0.00 37.00 4.02
1017 1020 3.629855 TGACGCCATCTTTGACTTTTTGA 59.370 39.130 0.00 0.00 0.00 2.69
1087 1090 7.764443 CGACTTTCCTATCAGGATTTTAGAACA 59.236 37.037 0.00 0.00 45.34 3.18
1091 1094 7.436673 CAGTCGACTTTCCTATCAGGATTTTAG 59.563 40.741 17.26 0.00 45.34 1.85
1166 1169 4.729564 CGCAAAAGTTTTGCAAAATCCTTG 59.270 37.500 38.44 24.95 45.14 3.61
1175 1178 0.820871 AGGACCGCAAAAGTTTTGCA 59.179 45.000 38.44 0.00 45.14 4.08
1371 1374 7.578024 GTCGTGCATATCTTTAACGATTACAAC 59.422 37.037 0.00 0.00 44.14 3.32
1375 1378 6.509656 AGGTCGTGCATATCTTTAACGATTA 58.490 36.000 0.00 0.00 44.14 1.75
1380 1383 6.604735 AATGAGGTCGTGCATATCTTTAAC 57.395 37.500 0.00 0.00 0.00 2.01
1393 1396 3.199946 ACCATGGACATAAATGAGGTCGT 59.800 43.478 21.47 0.00 39.86 4.34
1636 1639 4.392940 AGCTTCAAAACTACAGAGCATGT 58.607 39.130 0.00 0.02 46.45 3.21
1639 1642 6.935741 TTTTAGCTTCAAAACTACAGAGCA 57.064 33.333 0.00 0.00 0.00 4.26
1642 1645 8.500753 TGTCTTTTTAGCTTCAAAACTACAGA 57.499 30.769 0.00 0.00 0.00 3.41
1699 1702 2.083835 GAATAGCGCCCTAGCACGGA 62.084 60.000 2.29 0.00 39.83 4.69
1703 1706 0.393077 GGAAGAATAGCGCCCTAGCA 59.607 55.000 2.29 0.00 39.83 3.49
1709 1712 3.187432 GCTCATAAAGGAAGAATAGCGCC 59.813 47.826 2.29 0.00 0.00 6.53
1716 1719 4.707448 AGAGTCTCGCTCATAAAGGAAGAA 59.293 41.667 0.00 0.00 46.47 2.52
1769 1772 0.108138 ATGGCTCGCTTAGTTCGCTT 60.108 50.000 0.00 0.00 0.00 4.68
1851 1854 2.009681 GGTTTGGACCTGGGTGAATT 57.990 50.000 0.00 0.00 42.99 2.17
1904 1907 0.108615 CAGTCATTCCGAAGAGCCGT 60.109 55.000 0.00 0.00 0.00 5.68
1960 1963 3.366396 GGAAGTAGTCCCATCACTCTCA 58.634 50.000 0.00 0.00 41.10 3.27
1983 1987 2.416027 GGCCCGAATGAAAAGCTCTTTC 60.416 50.000 11.93 11.93 35.71 2.62
1991 1995 0.393267 CCTACCGGCCCGAATGAAAA 60.393 55.000 3.71 0.00 0.00 2.29
1996 2000 2.842936 CCTCCTACCGGCCCGAAT 60.843 66.667 3.71 0.00 0.00 3.34
2007 2011 1.362932 GATAGATCAGGGCCCCTCCTA 59.637 57.143 21.43 15.30 34.92 2.94
2068 2073 6.765403 TCGACCCTTCTTTCTTTCTTCATTA 58.235 36.000 0.00 0.00 0.00 1.90
2118 2123 6.016443 CCTCTTTCATGATCTTTTCTATGGGC 60.016 42.308 0.00 0.00 0.00 5.36
2172 2177 3.427573 TGTGTCTAGAAACTCGGGATCA 58.572 45.455 14.23 0.00 0.00 2.92
2186 2191 0.457853 GCGGAAGTGCGATGTGTCTA 60.458 55.000 0.00 0.00 0.00 2.59
2219 2224 2.680352 GTCTGAGGGCGGAGTGGA 60.680 66.667 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.