Multiple sequence alignment - TraesCS2A01G349500

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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 TraesCS2A01G349500 chr2A 100.000 2399 0 0 1 2399 588979354 588981752 0.000000e+00 4431
1 TraesCS2A01G349500 chr2A 83.406 458 66 7 732 1187 592371649 592371200 1.330000e-112 416
2 TraesCS2A01G349500 chr2D 93.363 1778 104 7 1 1776 446045736 446047501 0.000000e+00 2617
3 TraesCS2A01G349500 chr2D 80.952 1176 175 27 985 2147 447554900 447553761 0.000000e+00 885
4 TraesCS2A01G349500 chr2D 91.770 243 16 3 1906 2147 446047940 446048179 3.820000e-88 335
5 TraesCS2A01G349500 chr2B 92.404 1685 104 12 718 2399 525071672 525073335 0.000000e+00 2381
6 TraesCS2A01G349500 chr2B 88.398 1155 127 7 1 1152 524786070 524787220 0.000000e+00 1384
7 TraesCS2A01G349500 chr2B 79.694 458 79 10 732 1187 527305524 527305079 3.850000e-83 318
8 TraesCS2A01G349500 chr2B 88.142 253 26 3 467 717 525071384 525071634 5.010000e-77 298
9 TraesCS2A01G349500 chr3B 82.740 730 92 22 1104 1818 780542827 780542117 9.420000e-174 619


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 TraesCS2A01G349500 chr2A 588979354 588981752 2398 False 4431.0 4431 100.0000 1 2399 1 chr2A.!!$F1 2398
1 TraesCS2A01G349500 chr2D 446045736 446048179 2443 False 1476.0 2617 92.5665 1 2147 2 chr2D.!!$F1 2146
2 TraesCS2A01G349500 chr2D 447553761 447554900 1139 True 885.0 885 80.9520 985 2147 1 chr2D.!!$R1 1162
3 TraesCS2A01G349500 chr2B 524786070 524787220 1150 False 1384.0 1384 88.3980 1 1152 1 chr2B.!!$F1 1151
4 TraesCS2A01G349500 chr2B 525071384 525073335 1951 False 1339.5 2381 90.2730 467 2399 2 chr2B.!!$F2 1932
5 TraesCS2A01G349500 chr3B 780542117 780542827 710 True 619.0 619 82.7400 1104 1818 1 chr3B.!!$R1 714

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
464 468 0.10852 TGCTCCCCGACGTATCAAAC 60.109 55.0 0.0 0.0 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 2815 0.529992 CCGCTCAGGACGTAAATCCC 60.53 60.0 0.0 0.0 45.0 3.85 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
72 73 9.965824 CCTAATAATTTAATTGGAACGAGCAAT 57.034 29.630 0.00 0.0 0.00 3.56
187 189 0.733150 GCTTACTCGGTCAAATGGCC 59.267 55.000 0.00 0.0 36.18 5.36
215 217 5.421056 AGGATTGTTGGACTCACTAACGATA 59.579 40.000 0.00 0.0 41.82 2.92
256 258 1.270839 ACTTGTAGCATGGAAGCACGT 60.271 47.619 0.00 0.0 36.85 4.49
259 261 1.156736 GTAGCATGGAAGCACGTGTT 58.843 50.000 18.38 8.6 36.85 3.32
311 314 0.185901 AGCCAAGTTTGCTGGGAAGA 59.814 50.000 0.00 0.0 38.10 2.87
325 328 1.835531 GGGAAGACGGAACCTAATCCA 59.164 52.381 0.00 0.0 39.61 3.41
332 335 2.236395 ACGGAACCTAATCCAGTTGAGG 59.764 50.000 0.00 0.0 39.61 3.86
385 388 0.247736 CTAGGAGCTCGGCAAGTGTT 59.752 55.000 7.83 0.0 0.00 3.32
464 468 0.108520 TGCTCCCCGACGTATCAAAC 60.109 55.000 0.00 0.0 0.00 2.93
525 529 4.481368 AAGGTACGTGAATTGGATGCTA 57.519 40.909 0.00 0.0 0.00 3.49
575 580 8.964476 TTCTGACCAAACAAGAGGATATATTC 57.036 34.615 0.00 0.0 0.00 1.75
579 584 7.069455 TGACCAAACAAGAGGATATATTCGAGA 59.931 37.037 0.00 0.0 0.00 4.04
630 637 9.743057 TTTATGTGATCTAGGTGTTTGTTTTTG 57.257 29.630 0.00 0.0 0.00 2.44
684 691 7.170320 TCTCAATCTTGGTTCGTTTGTTACTAC 59.830 37.037 0.00 0.0 0.00 2.73
828 872 7.571080 AACCTACCATTAACGTTTTTGAAGA 57.429 32.000 5.91 0.0 0.00 2.87
932 976 8.522542 AGGAAATCGTATAACTCTAAGTGTCT 57.477 34.615 0.00 0.0 0.00 3.41
956 1000 2.915659 TTGGCGTCGAGGTGGACT 60.916 61.111 7.01 0.0 34.75 3.85
1075 1155 1.138859 GTGATGATGGTGGTGGATCGA 59.861 52.381 0.00 0.0 0.00 3.59
1153 1236 3.014538 ATGATGGTGGTGGCCCGA 61.015 61.111 0.00 0.0 0.00 5.14
1191 1274 1.072332 TGATGTTGGTGGTGTCCCG 59.928 57.895 0.00 0.0 0.00 5.14
1273 1356 1.219773 AGATGGCCATGATGGTGAGT 58.780 50.000 26.56 0.0 40.46 3.41
1364 1447 1.376086 CACCAGAGCCATCACCACA 59.624 57.895 0.00 0.0 0.00 4.17
1365 1448 0.675837 CACCAGAGCCATCACCACAG 60.676 60.000 0.00 0.0 0.00 3.66
1429 1512 1.248101 GGTGGTGGTGGTGGTATTGC 61.248 60.000 0.00 0.0 0.00 3.56
1431 1514 1.003812 GTGGTGGTGGTGGTATTGCTA 59.996 52.381 0.00 0.0 0.00 3.49
1445 1534 0.323302 TTGCTATTGTGGCAGTCGGA 59.677 50.000 0.00 0.0 40.90 4.55
1488 1577 4.340894 TGAGCATGCGTATTTGAAAGAC 57.659 40.909 13.01 0.0 0.00 3.01
1519 1623 6.208644 GGGTCGTCGTATTTACTATAGCAAA 58.791 40.000 0.00 0.0 0.00 3.68
1633 1740 6.707440 AATTGGTGCCATTTATTCGTATCA 57.293 33.333 0.00 0.0 0.00 2.15
1634 1741 5.493133 TTGGTGCCATTTATTCGTATCAC 57.507 39.130 0.00 0.0 0.00 3.06
1889 2008 2.596904 AGGGGTTGTATGATTCGTCG 57.403 50.000 0.00 0.0 0.00 5.12
1895 2014 3.508762 GTTGTATGATTCGTCGAGGTGT 58.491 45.455 4.85 0.0 0.00 4.16
1926 2402 2.029470 CCAACCCAAATGTATTGCACGT 60.029 45.455 0.00 0.0 0.00 4.49
2119 2596 1.676746 GAAAGCCGGAACCTAATCCC 58.323 55.000 5.05 0.0 36.00 3.85
2158 2635 4.011698 CAATGGATGTGAGTCATTGGACA 58.988 43.478 0.00 0.0 46.80 4.02
2159 2636 3.786368 TGGATGTGAGTCATTGGACAA 57.214 42.857 0.00 0.0 46.80 3.18
2160 2637 4.305539 TGGATGTGAGTCATTGGACAAT 57.694 40.909 0.00 0.0 46.80 2.71
2161 2638 4.264253 TGGATGTGAGTCATTGGACAATC 58.736 43.478 0.00 0.0 46.80 2.67
2162 2639 4.019051 TGGATGTGAGTCATTGGACAATCT 60.019 41.667 0.00 0.0 46.80 2.40
2163 2640 4.946157 GGATGTGAGTCATTGGACAATCTT 59.054 41.667 0.00 0.0 46.80 2.40
2164 2641 5.065731 GGATGTGAGTCATTGGACAATCTTC 59.934 44.000 0.00 0.0 46.80 2.87
2165 2642 5.233083 TGTGAGTCATTGGACAATCTTCT 57.767 39.130 0.00 0.0 46.80 2.85
2166 2643 5.624159 TGTGAGTCATTGGACAATCTTCTT 58.376 37.500 0.00 0.0 46.80 2.52
2167 2644 6.064060 TGTGAGTCATTGGACAATCTTCTTT 58.936 36.000 0.00 0.0 46.80 2.52
2204 2681 0.609662 CCCCCACTGCAAGAAAATGG 59.390 55.000 0.00 0.0 37.43 3.16
2231 2708 1.264020 CATGATATTGTGGCCCGAACG 59.736 52.381 0.00 0.0 0.00 3.95
2280 2757 8.671028 TGACACTTTCATGATGATAATTGACAG 58.329 33.333 0.00 0.0 0.00 3.51
2282 2759 8.890718 ACACTTTCATGATGATAATTGACAGAG 58.109 33.333 0.00 0.0 0.00 3.35
2331 2808 4.388378 GTGGACACCTAGTTCTATGACC 57.612 50.000 0.00 0.0 0.00 4.02
2338 2815 7.148239 GGACACCTAGTTCTATGACCAAAAATG 60.148 40.741 0.00 0.0 0.00 2.32
2341 2818 6.011981 ACCTAGTTCTATGACCAAAAATGGGA 60.012 38.462 0.00 0.0 0.00 4.37
2346 2823 8.749354 AGTTCTATGACCAAAAATGGGATTTAC 58.251 33.333 0.00 0.0 0.00 2.01
2352 2829 4.219725 ACCAAAAATGGGATTTACGTCCTG 59.780 41.667 0.00 0.0 38.38 3.86
2353 2830 4.461081 CCAAAAATGGGATTTACGTCCTGA 59.539 41.667 0.00 0.0 38.38 3.86
2359 2836 1.152383 GATTTACGTCCTGAGCGGGC 61.152 60.000 0.00 0.0 0.00 6.13
2383 2860 2.486504 CGCATCTGCATGGCGTTT 59.513 55.556 15.86 0.0 45.27 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.948309 AGGTGCTCCATTATTAATTGGATACC 59.052 38.462 21.56 21.56 37.61 2.73
72 73 6.349243 TCCGTCAAAGAACTTCTATTACCA 57.651 37.500 0.00 0.00 0.00 3.25
187 189 4.392921 AGTGAGTCCAACAATCCTATCG 57.607 45.455 0.00 0.00 0.00 2.92
189 191 5.421056 TCGTTAGTGAGTCCAACAATCCTAT 59.579 40.000 0.00 0.00 0.00 2.57
192 194 3.921677 TCGTTAGTGAGTCCAACAATCC 58.078 45.455 0.00 0.00 0.00 3.01
215 217 6.985188 AGTCATTTATTCTACAACACGCAT 57.015 33.333 0.00 0.00 0.00 4.73
256 258 2.549754 GCTCTCTGCAGTTTTAGCAACA 59.450 45.455 14.67 0.00 42.17 3.33
259 261 1.072173 TGGCTCTCTGCAGTTTTAGCA 59.928 47.619 23.44 13.13 45.15 3.49
311 314 2.236395 CCTCAACTGGATTAGGTTCCGT 59.764 50.000 0.00 0.00 38.74 4.69
325 328 3.584406 TCATCATCTTGACACCCTCAACT 59.416 43.478 0.00 0.00 33.65 3.16
332 335 5.050499 CGCTATTTCTCATCATCTTGACACC 60.050 44.000 0.00 0.00 0.00 4.16
410 414 8.739972 AGAGTCAACATCTTTACAAAGTTTGTT 58.260 29.630 25.35 10.59 42.22 2.83
464 468 1.134226 AGTGTTTTTACGCCTCGTCG 58.866 50.000 0.00 0.00 41.54 5.12
546 550 3.646162 TCCTCTTGTTTGGTCAGAAGCTA 59.354 43.478 0.00 0.00 0.00 3.32
575 580 4.442375 ACCTAGATCACTTGTTGTCTCG 57.558 45.455 0.00 0.00 0.00 4.04
579 584 5.300752 CACTGAACCTAGATCACTTGTTGT 58.699 41.667 0.00 0.00 0.00 3.32
630 637 6.527423 TCATAAACGGATTTGGGGATAGTAC 58.473 40.000 0.00 0.00 0.00 2.73
710 717 8.641498 AGATGGCAATCATTAATTTAGGTAGG 57.359 34.615 3.34 0.00 35.97 3.18
828 872 6.599244 TGACGGAAGCTCAAATCTCATATTTT 59.401 34.615 0.00 0.00 0.00 1.82
844 888 1.534729 AAGGACCATTTGACGGAAGC 58.465 50.000 0.00 0.00 0.00 3.86
858 902 5.106038 CCGGGGAAGTGTTTAATAAAAGGAC 60.106 44.000 0.00 0.00 0.00 3.85
911 955 8.680039 AGCTAGACACTTAGAGTTATACGATT 57.320 34.615 0.00 0.00 0.00 3.34
932 976 2.415608 CCTCGACGCCAAGGAGCTA 61.416 63.158 0.00 0.00 34.35 3.32
1075 1155 0.467384 CCAAGCTCCGTCTCCATCAT 59.533 55.000 0.00 0.00 0.00 2.45
1348 1431 1.748122 GCTGTGGTGATGGCTCTGG 60.748 63.158 0.00 0.00 0.00 3.86
1364 1447 2.771763 CTTCTCTGTCGCCAACCGCT 62.772 60.000 0.00 0.00 36.73 5.52
1365 1448 2.357034 TTCTCTGTCGCCAACCGC 60.357 61.111 0.00 0.00 36.73 5.68
1394 1477 4.878397 CCACCACCACTCTCAAATCTTATC 59.122 45.833 0.00 0.00 0.00 1.75
1396 1479 3.650942 ACCACCACCACTCTCAAATCTTA 59.349 43.478 0.00 0.00 0.00 2.10
1429 1512 1.804372 GCTCTCCGACTGCCACAATAG 60.804 57.143 0.00 0.00 0.00 1.73
1431 1514 1.078848 GCTCTCCGACTGCCACAAT 60.079 57.895 0.00 0.00 0.00 2.71
1445 1534 3.455327 TCGCTATATATAGACGCGCTCT 58.545 45.455 21.65 11.28 43.14 4.09
1483 1572 4.065281 CGACCCGCTCCCGTCTTT 62.065 66.667 0.00 0.00 0.00 2.52
1591 1696 7.393234 CACCAATTTATTTCCTTCCTGTGTAGA 59.607 37.037 0.00 0.00 0.00 2.59
1633 1740 3.912496 TCATACTGTAATGCTGCCAGT 57.088 42.857 12.65 12.65 41.93 4.00
1634 1741 4.445453 TCTTCATACTGTAATGCTGCCAG 58.555 43.478 0.00 0.00 0.00 4.85
1926 2402 0.911769 AGAGCCATCGGTTGATCCAA 59.088 50.000 0.00 0.00 35.57 3.53
2068 2545 5.664294 TGGCTAGAATCAATGTTTGCAAT 57.336 34.783 0.00 0.00 0.00 3.56
2119 2596 2.509052 TTGTCTGGACACTCTCAACG 57.491 50.000 2.65 0.00 41.67 4.10
2204 2681 2.029649 GGCCACAATATCATGGATGTGC 60.030 50.000 0.00 9.41 41.33 4.57
2331 2808 5.637006 TCAGGACGTAAATCCCATTTTTG 57.363 39.130 0.00 0.00 39.91 2.44
2338 2815 0.529992 CCGCTCAGGACGTAAATCCC 60.530 60.000 0.00 0.00 45.00 3.85
2341 2818 1.153429 GCCCGCTCAGGACGTAAAT 60.153 57.895 0.00 0.00 45.00 1.40
2359 2836 2.203167 ATGCAGATGCGCCTCTGG 60.203 61.111 34.04 20.67 45.83 3.86
2362 2839 3.962421 GCCATGCAGATGCGCCTC 61.962 66.667 4.18 4.25 45.83 4.70


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

AutoCloner maintained by Alex Coulton.