Multiple sequence alignment - TraesCS6A01G054800

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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 TraesCS6A01G054800 chr6A 100.000 2460 0 0 1 2460 28429207 28431666 0.000000e+00 4543.0
1 TraesCS6A01G054800 chr6B 91.438 2476 167 22 8 2458 49416168 49413713 0.000000e+00 3356.0
2 TraesCS6A01G054800 chr6B 91.523 1628 120 10 26 1646 49761972 49763588 0.000000e+00 2226.0
3 TraesCS6A01G054800 chr6B 86.486 703 50 17 1772 2460 49763592 49764263 0.000000e+00 730.0
4 TraesCS6A01G054800 chr6B 82.331 815 122 12 991 1790 49878531 49879338 0.000000e+00 688.0
5 TraesCS6A01G054800 chr6B 84.211 684 88 10 991 1659 49664241 49664919 0.000000e+00 647.0
6 TraesCS6A01G054800 chr6D 91.476 1924 126 15 1 1903 27117912 27119818 0.000000e+00 2610.0
7 TraesCS6A01G054800 chr6D 82.173 819 118 14 991 1790 27201940 27202749 0.000000e+00 678.0
8 TraesCS6A01G054800 chr6D 89.873 395 14 11 2071 2458 27120610 27120985 3.680000e-133 484.0
9 TraesCS6A01G054800 chr5A 89.274 317 31 2 221 536 6377686 6378000 6.380000e-106 394.0
10 TraesCS6A01G054800 chrUn 85.897 78 10 1 2311 2387 112248631 112248708 5.640000e-12 82.4


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 TraesCS6A01G054800 chr6A 28429207 28431666 2459 False 4543 4543 100.0000 1 2460 1 chr6A.!!$F1 2459
1 TraesCS6A01G054800 chr6B 49413713 49416168 2455 True 3356 3356 91.4380 8 2458 1 chr6B.!!$R1 2450
2 TraesCS6A01G054800 chr6B 49761972 49764263 2291 False 1478 2226 89.0045 26 2460 2 chr6B.!!$F3 2434
3 TraesCS6A01G054800 chr6B 49878531 49879338 807 False 688 688 82.3310 991 1790 1 chr6B.!!$F2 799
4 TraesCS6A01G054800 chr6B 49664241 49664919 678 False 647 647 84.2110 991 1659 1 chr6B.!!$F1 668
5 TraesCS6A01G054800 chr6D 27117912 27120985 3073 False 1547 2610 90.6745 1 2458 2 chr6D.!!$F2 2457
6 TraesCS6A01G054800 chr6D 27201940 27202749 809 False 678 678 82.1730 991 1790 1 chr6D.!!$F1 799

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
566 578 0.460109 TCCAGTTGTCATCGATGCGG 60.46 55.0 20.81 12.64 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1589 1632 0.179103 GCAGGTATTTGCCACATGCC 60.179 55.0 0.94 0.0 45.37 4.4 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
98 99 1.745489 GGGGAAGCGCAGTCGATTT 60.745 57.895 11.47 0.00 45.01 2.17
235 243 2.117156 CGGATGCTTTCCAGGCAGG 61.117 63.158 7.00 0.00 45.78 4.85
340 348 6.926272 GCCATTTTGTTGTACATAGGTGAAAA 59.074 34.615 0.00 0.00 0.00 2.29
354 362 9.620259 ACATAGGTGAAAATAAATCCTCTTCTC 57.380 33.333 0.00 0.00 0.00 2.87
355 363 9.844257 CATAGGTGAAAATAAATCCTCTTCTCT 57.156 33.333 0.00 0.00 0.00 3.10
366 374 6.806668 AATCCTCTTCTCTTCCTTTCTAGG 57.193 41.667 0.00 0.00 43.46 3.02
422 430 4.320494 CCCTACAATATTTTCATGCTCGGC 60.320 45.833 0.00 0.00 0.00 5.54
560 572 4.475944 GAACCAATTTCCAGTTGTCATCG 58.524 43.478 0.00 0.00 0.00 3.84
566 578 0.460109 TCCAGTTGTCATCGATGCGG 60.460 55.000 20.81 12.64 0.00 5.69
583 595 1.800286 GCGGATTCTTGAATTGGCTGC 60.800 52.381 10.31 0.00 0.00 5.25
601 613 3.501445 GCTGCTTGATCAACTTCTTCTGT 59.499 43.478 3.38 0.00 0.00 3.41
662 674 3.738830 AACAGCATTGCATGAAACTGT 57.261 38.095 11.91 4.23 36.88 3.55
781 795 2.887152 AGGACACTGAACCTGAAATTGC 59.113 45.455 0.00 0.00 34.99 3.56
840 854 5.984233 TGCTCGGCTACAATACAAATTAG 57.016 39.130 0.00 0.00 0.00 1.73
973 987 5.279206 CCACAGCAGTTCTCTTTCTCTTCTA 60.279 44.000 0.00 0.00 0.00 2.10
988 1007 3.813443 TCTTCTATTCTCATTGCCTGCC 58.187 45.455 0.00 0.00 0.00 4.85
989 1008 3.200605 TCTTCTATTCTCATTGCCTGCCA 59.799 43.478 0.00 0.00 0.00 4.92
1234 1253 2.623915 GCCTGCTGCACCAACTCTG 61.624 63.158 0.00 0.00 40.77 3.35
1239 1258 0.533755 GCTGCACCAACTCTGTCTGT 60.534 55.000 0.00 0.00 0.00 3.41
1290 1325 4.035814 GGACCTACCACCCTACTTTATGT 58.964 47.826 0.00 0.00 38.79 2.29
1300 1335 2.190981 CTACTTTATGTGTCCGTCCGC 58.809 52.381 0.00 0.00 0.00 5.54
1328 1363 2.682856 ACGTTGATGGAATATGTGTGCC 59.317 45.455 0.00 0.00 0.00 5.01
1446 1481 4.447342 GGGTGGCCATGGTCCCAG 62.447 72.222 25.99 0.00 39.68 4.45
1458 1493 0.696501 GGTCCCAGCAAGGAACCTTA 59.303 55.000 5.75 0.00 37.70 2.69
1464 1499 3.445096 CCCAGCAAGGAACCTTAAAGATG 59.555 47.826 5.75 3.68 41.22 2.90
1475 1511 5.437191 ACCTTAAAGATGGAAGATCGGTT 57.563 39.130 0.00 0.00 0.00 4.44
1500 1536 4.886579 TCATGGGATCATACGATGTTGAG 58.113 43.478 0.00 0.00 31.33 3.02
1510 1546 2.281692 ATGTTGAGCGGCTGCACA 60.282 55.556 21.93 17.91 46.23 4.57
1589 1632 8.594881 ATCTTATAACAAAGCCAGTTATCGAG 57.405 34.615 8.71 8.73 41.17 4.04
1710 1760 5.678583 AGGAAGTGACATATGAGGTTCATG 58.321 41.667 10.38 0.00 37.70 3.07
1753 1803 2.574006 TGAGCAAAGTCATCCAAGCT 57.426 45.000 0.00 0.00 34.61 3.74
1823 1873 6.547141 TCAGAACAGAACCAGACAAATTCATT 59.453 34.615 0.00 0.00 0.00 2.57
1832 1882 4.763793 CCAGACAAATTCATTGGTCAGACT 59.236 41.667 9.32 0.00 43.66 3.24
1841 1891 8.408043 AATTCATTGGTCAGACTCACAAAATA 57.592 30.769 0.00 0.00 0.00 1.40
1863 1914 5.091261 AGGACATAAGCAGAAATTCGACT 57.909 39.130 0.00 0.00 0.00 4.18
1919 2120 8.495148 ACACAATCAAAAGAAAACAGTGAAAAC 58.505 29.630 0.00 0.00 0.00 2.43
1924 2125 3.319238 AGAAAACAGTGAAAACGAGCG 57.681 42.857 0.00 0.00 0.00 5.03
1927 2128 0.944386 AACAGTGAAAACGAGCGCAT 59.056 45.000 11.47 0.00 0.00 4.73
1943 2148 2.159986 GCGCATGCAAAATACAACACAC 60.160 45.455 19.57 0.00 42.15 3.82
1945 2150 2.408032 GCATGCAAAATACAACACACCG 59.592 45.455 14.21 0.00 0.00 4.94
2000 2205 3.745799 ACGATAATCACACACACCCAAA 58.254 40.909 0.00 0.00 0.00 3.28
2016 2221 2.529151 CCAAAACACTGAAGCACACAC 58.471 47.619 0.00 0.00 0.00 3.82
2017 2222 2.094803 CCAAAACACTGAAGCACACACA 60.095 45.455 0.00 0.00 0.00 3.72
2058 2263 4.646945 TCAAGTTCAAACATTAGCCAACCA 59.353 37.500 0.00 0.00 0.00 3.67
2059 2264 4.584327 AGTTCAAACATTAGCCAACCAC 57.416 40.909 0.00 0.00 0.00 4.16
2081 2287 4.225942 ACTGAAGCCTTCACCATATCTCAA 59.774 41.667 2.24 0.00 35.46 3.02
2082 2288 5.178096 TGAAGCCTTCACCATATCTCAAA 57.822 39.130 2.24 0.00 34.08 2.69
2083 2289 5.569355 TGAAGCCTTCACCATATCTCAAAA 58.431 37.500 2.24 0.00 34.08 2.44
2187 2866 7.766219 ATTGCAAACAATTCATAAGAGATGC 57.234 32.000 1.71 0.00 44.21 3.91
2304 2988 9.454585 CAATAGTTTTTACTGATATGTGCCATG 57.545 33.333 0.00 0.00 0.00 3.66
2305 2989 5.894807 AGTTTTTACTGATATGTGCCATGC 58.105 37.500 0.00 0.00 0.00 4.06
2306 2990 5.418524 AGTTTTTACTGATATGTGCCATGCA 59.581 36.000 0.00 0.00 35.60 3.96
2307 2991 6.097270 AGTTTTTACTGATATGTGCCATGCAT 59.903 34.615 0.00 0.00 41.91 3.96
2339 3023 8.970691 AAACAGTATTGTATGAAAACTGCATC 57.029 30.769 0.00 0.00 40.94 3.91
2438 3122 7.592938 TGCAACTGTCTAATCAGGTTATTTTG 58.407 34.615 0.00 0.00 39.48 2.44
2439 3123 7.029563 GCAACTGTCTAATCAGGTTATTTTGG 58.970 38.462 0.00 0.00 39.48 3.28
2440 3124 6.759497 ACTGTCTAATCAGGTTATTTTGGC 57.241 37.500 0.00 0.00 39.48 4.52
2441 3125 6.245408 ACTGTCTAATCAGGTTATTTTGGCA 58.755 36.000 0.00 0.00 39.48 4.92
2442 3126 6.891908 ACTGTCTAATCAGGTTATTTTGGCAT 59.108 34.615 0.00 0.00 39.48 4.40
2443 3127 7.099266 TGTCTAATCAGGTTATTTTGGCATG 57.901 36.000 0.00 0.00 0.00 4.06
2445 3129 7.395772 TGTCTAATCAGGTTATTTTGGCATGAA 59.604 33.333 0.00 0.00 0.00 2.57
2454 3143 7.553760 AGGTTATTTTGGCATGAAATTCCATTC 59.446 33.333 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 3.073798 TCACCTGGGTAAATTGCTTCAGA 59.926 43.478 0.00 0.00 0.00 3.27
170 171 1.819632 CTCCTATTGTGCCGCCACC 60.820 63.158 0.00 0.00 41.35 4.61
235 243 2.859165 TGTCACTGAATCTTCCACCC 57.141 50.000 0.00 0.00 0.00 4.61
417 425 7.010091 ACAAAACTAAAATTTGTTTCAGCCGAG 59.990 33.333 7.00 0.00 45.97 4.63
475 483 2.734606 TGTTTCGATCGTTCATGTCCAC 59.265 45.455 15.94 1.03 0.00 4.02
560 572 2.360165 AGCCAATTCAAGAATCCGCATC 59.640 45.455 13.29 0.00 31.17 3.91
566 578 4.445452 TCAAGCAGCCAATTCAAGAATC 57.555 40.909 0.00 0.00 0.00 2.52
583 595 7.953158 TCTAACACAGAAGAAGTTGATCAAG 57.047 36.000 8.80 0.00 0.00 3.02
840 854 1.359848 ATCTCGACATTTGACACGGC 58.640 50.000 0.00 0.00 0.00 5.68
973 987 1.409802 CCTCTGGCAGGCAATGAGAAT 60.410 52.381 15.73 0.00 34.56 2.40
988 1007 0.326048 ACCACCATCTCCCTCCTCTG 60.326 60.000 0.00 0.00 0.00 3.35
989 1008 0.326048 CACCACCATCTCCCTCCTCT 60.326 60.000 0.00 0.00 0.00 3.69
1228 1247 1.072159 GCAGGCCACAGACAGAGTT 59.928 57.895 5.01 0.00 0.00 3.01
1300 1335 1.742761 ATTCCATCAACGTGCCTCTG 58.257 50.000 0.00 0.00 0.00 3.35
1309 1344 3.290710 AGGGCACACATATTCCATCAAC 58.709 45.455 0.00 0.00 0.00 3.18
1328 1363 7.769272 TGAGAACAAAATAACAGCAAAAAGG 57.231 32.000 0.00 0.00 0.00 3.11
1389 1424 1.295792 GATACAATCCGGAGCGCAAA 58.704 50.000 11.34 0.00 0.00 3.68
1445 1480 4.657814 TCCATCTTTAAGGTTCCTTGCT 57.342 40.909 13.64 0.00 0.00 3.91
1446 1481 5.010282 TCTTCCATCTTTAAGGTTCCTTGC 58.990 41.667 13.64 0.00 0.00 4.01
1500 1536 0.458197 TATTGCATTTGTGCAGCCGC 60.458 50.000 3.16 0.00 46.21 6.53
1510 1546 9.507280 CGAAGTGAGATACATTTTATTGCATTT 57.493 29.630 0.00 0.00 0.00 2.32
1573 1616 1.737838 TGCCTCGATAACTGGCTTTG 58.262 50.000 13.16 0.00 46.23 2.77
1589 1632 0.179103 GCAGGTATTTGCCACATGCC 60.179 55.000 0.94 0.00 45.37 4.40
1594 1640 5.719173 TCAAAATTAGCAGGTATTTGCCAC 58.281 37.500 2.13 0.00 45.18 5.01
1675 1722 5.913137 TGTCACTTCCTTGTCACAAAAAT 57.087 34.783 0.00 0.00 0.00 1.82
1685 1732 5.491070 TGAACCTCATATGTCACTTCCTTG 58.509 41.667 1.90 0.00 0.00 3.61
1686 1733 5.762179 TGAACCTCATATGTCACTTCCTT 57.238 39.130 1.90 0.00 0.00 3.36
1753 1803 4.399004 CCTTTGTTGGGATTCACACAAA 57.601 40.909 12.77 12.77 43.93 2.83
1823 1873 4.346709 TGTCCTATTTTGTGAGTCTGACCA 59.653 41.667 3.76 0.00 0.00 4.02
1832 1882 7.994425 TTTCTGCTTATGTCCTATTTTGTGA 57.006 32.000 0.00 0.00 0.00 3.58
1841 1891 5.091261 AGTCGAATTTCTGCTTATGTCCT 57.909 39.130 0.00 0.00 0.00 3.85
1875 1926 5.491323 TGTGTCCCATGTTGTATGAGTAA 57.509 39.130 0.00 0.00 0.00 2.24
1919 2120 1.578915 GTTGTATTTTGCATGCGCTCG 59.421 47.619 14.09 0.00 39.64 5.03
1924 2125 2.408032 CGGTGTGTTGTATTTTGCATGC 59.592 45.455 11.82 11.82 0.00 4.06
1927 2128 2.423892 ACACGGTGTGTTGTATTTTGCA 59.576 40.909 13.92 0.00 45.08 4.08
1943 2148 0.321210 TGTACAATGCAGGGACACGG 60.321 55.000 2.21 0.00 0.00 4.94
1945 2150 3.871594 GTCTATGTACAATGCAGGGACAC 59.128 47.826 8.27 0.46 0.00 3.67
1977 2182 2.300437 TGGGTGTGTGTGATTATCGTCA 59.700 45.455 0.00 0.00 0.00 4.35
2000 2205 1.094785 GGTGTGTGTGCTTCAGTGTT 58.905 50.000 0.00 0.00 0.00 3.32
2016 2221 5.181245 ACTTGAATTCTTTCATACACGGGTG 59.819 40.000 0.00 0.00 41.38 4.61
2017 2222 5.313712 ACTTGAATTCTTTCATACACGGGT 58.686 37.500 7.05 0.00 41.38 5.28
2058 2263 3.776969 TGAGATATGGTGAAGGCTTCAGT 59.223 43.478 29.22 19.61 41.01 3.41
2059 2264 4.412796 TGAGATATGGTGAAGGCTTCAG 57.587 45.455 29.22 0.00 41.01 3.02
2109 2779 9.889128 TTGCATATATTCAGTAGCATAGCAATA 57.111 29.630 0.00 0.00 32.87 1.90
2163 2842 6.759827 GGCATCTCTTATGAATTGTTTGCAAT 59.240 34.615 0.00 0.00 46.38 3.56
2187 2866 4.201657 TGTGAAGTATCTGCATGGAATGG 58.798 43.478 0.00 0.00 46.86 3.16
2339 3023 3.751175 TGCTGATGTAGAAAGAAAACCGG 59.249 43.478 0.00 0.00 0.00 5.28
2438 3122 4.376340 AACTCGAATGGAATTTCATGCC 57.624 40.909 0.00 0.00 36.07 4.40


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

AutoCloner maintained by Alex Coulton.