Multiple sequence alignment - TraesCS2A01G306800

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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 TraesCS2A01G306800 chr2A 100.000 3030 0 0 1 3030 527700258 527703287 0.000000e+00 5596
1 TraesCS2A01G306800 chr2D 95.764 3045 86 15 1 3030 391112443 391115459 0.000000e+00 4868
2 TraesCS2A01G306800 chr2B 96.398 2887 77 16 159 3030 462300170 462303044 0.000000e+00 4730
3 TraesCS2A01G306800 chr2B 86.232 138 14 4 3 139 462300044 462300177 8.760000e-31 145
4 TraesCS2A01G306800 chr3A 83.764 1121 125 28 1518 2626 57225902 57224827 0.000000e+00 1009
5 TraesCS2A01G306800 chr3A 85.465 172 21 4 2714 2882 57220352 57220182 3.100000e-40 176
6 TraesCS2A01G306800 chr3B 85.023 868 109 12 1530 2390 71327899 71327046 0.000000e+00 863
7 TraesCS2A01G306800 chr3B 86.127 519 41 14 2392 2906 71325241 71324750 5.750000e-147 531
8 TraesCS2A01G306800 chrUn 97.429 389 10 0 1407 1795 479687363 479687751 0.000000e+00 664


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 TraesCS2A01G306800 chr2A 527700258 527703287 3029 False 5596.0 5596 100.000 1 3030 1 chr2A.!!$F1 3029
1 TraesCS2A01G306800 chr2D 391112443 391115459 3016 False 4868.0 4868 95.764 1 3030 1 chr2D.!!$F1 3029
2 TraesCS2A01G306800 chr2B 462300044 462303044 3000 False 2437.5 4730 91.315 3 3030 2 chr2B.!!$F1 3027
3 TraesCS2A01G306800 chr3A 57224827 57225902 1075 True 1009.0 1009 83.764 1518 2626 1 chr3A.!!$R2 1108
4 TraesCS2A01G306800 chr3B 71324750 71327899 3149 True 697.0 863 85.575 1530 2906 2 chr3B.!!$R1 1376

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
403 412 0.322456 TGGCAAGAGATGGGGTTTCG 60.322 55.0 0.0 0.0 0.0 3.46 F
1314 1340 0.464036 TCGTCATCCATTTCCTCCGG 59.536 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1359 1385 0.101399 CGTAGCGATTCTGAGGCAGT 59.899 55.000 0.0 0.0 32.61 4.40 R
2366 2401 1.304134 CTAACCCCCACAAGCCACC 60.304 63.158 0.0 0.0 0.00 4.61 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
26 27 6.053650 AGTAGTTCACTTCAGGTAAAACACC 58.946 40.000 0.00 0.00 40.49 4.16
57 58 3.374220 TGAACCGACACGAGTAATGTT 57.626 42.857 0.00 0.00 0.00 2.71
108 111 2.851263 TGAAACGTCTGGTATTGCCT 57.149 45.000 0.00 0.00 38.35 4.75
111 114 1.722011 AACGTCTGGTATTGCCTTCG 58.278 50.000 0.00 0.00 38.35 3.79
123 126 7.332557 TGGTATTGCCTTCGAAAATAGAAGTA 58.667 34.615 0.00 0.00 42.48 2.24
189 192 2.249743 TGAAATATTGGGGCTGGGGAAT 59.750 45.455 0.00 0.00 0.00 3.01
196 204 2.627933 TGGGGCTGGGGAATATAGTAC 58.372 52.381 0.00 0.00 0.00 2.73
392 401 7.259882 TCAGCACAATAATTTAATGGCAAGAG 58.740 34.615 0.00 0.00 0.00 2.85
393 402 7.122501 TCAGCACAATAATTTAATGGCAAGAGA 59.877 33.333 0.00 0.00 0.00 3.10
394 403 7.924412 CAGCACAATAATTTAATGGCAAGAGAT 59.076 33.333 0.00 0.00 0.00 2.75
397 406 7.654520 CACAATAATTTAATGGCAAGAGATGGG 59.345 37.037 0.00 0.00 0.00 4.00
398 407 6.923199 ATAATTTAATGGCAAGAGATGGGG 57.077 37.500 0.00 0.00 0.00 4.96
400 409 3.756082 TTAATGGCAAGAGATGGGGTT 57.244 42.857 0.00 0.00 0.00 4.11
401 410 2.629017 AATGGCAAGAGATGGGGTTT 57.371 45.000 0.00 0.00 0.00 3.27
403 412 0.322456 TGGCAAGAGATGGGGTTTCG 60.322 55.000 0.00 0.00 0.00 3.46
404 413 1.657751 GGCAAGAGATGGGGTTTCGC 61.658 60.000 0.00 0.00 0.00 4.70
439 458 8.491152 GGTATCAGATAATTGTTGATTCTGTCG 58.509 37.037 6.51 0.00 33.81 4.35
442 461 6.535150 TCAGATAATTGTTGATTCTGTCGTCC 59.465 38.462 0.00 0.00 0.00 4.79
499 518 1.521764 TGGATGGGCATATGTGAGGT 58.478 50.000 4.29 0.00 0.00 3.85
664 683 6.487668 TGGATGAGATGGTTATGCAATGTAAG 59.512 38.462 0.00 0.00 0.00 2.34
853 875 6.048732 TGCATTGATGGACTCTGTTAGTTA 57.951 37.500 0.00 0.00 39.07 2.24
862 884 7.458409 TGGACTCTGTTAGTTAGTAACGATT 57.542 36.000 7.38 1.51 43.68 3.34
879 901 9.616156 AGTAACGATTCATCTAAGAAGTAGAGA 57.384 33.333 0.00 0.00 42.23 3.10
1003 1029 1.457346 GTGAGGACAAGGAAGCATGG 58.543 55.000 0.00 0.00 0.00 3.66
1094 1120 1.251527 TTGCACGTCTCTCCCTCTCC 61.252 60.000 0.00 0.00 0.00 3.71
1109 1135 2.023888 CCTCTCCCTCCCTTTCTCTACA 60.024 54.545 0.00 0.00 0.00 2.74
1133 1159 4.778904 ACAAATACACACACGCATACAAC 58.221 39.130 0.00 0.00 0.00 3.32
1314 1340 0.464036 TCGTCATCCATTTCCTCCGG 59.536 55.000 0.00 0.00 0.00 5.14
1359 1385 1.471119 GACCTGACATCGTCCCTACA 58.529 55.000 0.00 0.00 0.00 2.74
1538 1564 1.813513 CCAAGCAACACAGAGTAGGG 58.186 55.000 0.00 0.00 0.00 3.53
1565 1591 0.684153 AAATGGGTGCTGGAATCCCG 60.684 55.000 0.00 0.00 43.75 5.14
1597 1623 1.814169 GGCAGTAAGTAGTGGCGGC 60.814 63.158 0.00 0.00 41.41 6.53
1704 1730 2.370849 ACCACTTACTTGACGGGAATGT 59.629 45.455 0.00 0.00 0.00 2.71
1709 1741 0.250727 ACTTGACGGGAATGTGGGTG 60.251 55.000 0.00 0.00 0.00 4.61
1759 1791 3.214328 GTCTCACAAGAAGAAAGGCCAA 58.786 45.455 5.01 0.00 31.93 4.52
1795 1827 3.792956 GTGCTGCATACATGTTATTGCAC 59.207 43.478 20.37 19.99 39.98 4.57
1821 1853 9.696917 CCTAACATTTTCTTAAACTCTGCATTT 57.303 29.630 0.00 0.00 0.00 2.32
1850 1882 7.173047 AGCATTATCATATACGCATGACAAACA 59.827 33.333 0.00 0.00 37.74 2.83
1876 1908 3.572255 CCAACATGCATGGATGATCATCA 59.428 43.478 31.07 20.08 40.56 3.07
1993 2028 1.409427 GACGAGGTGTTCCTATCCCTG 59.591 57.143 0.00 0.00 45.24 4.45
2201 2236 3.710209 ATTCTCCTCCAAGAAGGTGTG 57.290 47.619 0.00 0.00 38.60 3.82
2283 2318 5.183140 GGCCACTCTTTCAACTAGCAATTAA 59.817 40.000 0.00 0.00 0.00 1.40
2366 2401 0.671472 TCAACAGTGAGCGCCATGAG 60.671 55.000 2.29 0.00 0.00 2.90
2390 4225 1.886655 GCTTGTGGGGGTTAGGACTTG 60.887 57.143 0.00 0.00 0.00 3.16
2457 4296 4.008074 TCTCCTCCAACTCATTGTGTTC 57.992 45.455 1.25 0.00 33.60 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.597742 GTTCATGTCACTGCAGGTGT 58.402 50.000 19.93 0.00 45.50 4.16
26 27 0.792640 GTCGGTTCATGTCACTGCAG 59.207 55.000 13.48 13.48 0.00 4.41
31 32 1.060713 CTCGTGTCGGTTCATGTCAC 58.939 55.000 0.00 0.00 0.00 3.67
95 98 4.965119 ATTTTCGAAGGCAATACCAGAC 57.035 40.909 0.00 0.00 43.14 3.51
189 192 6.427853 TCTTTATAGCCGAAGTGCGTACTATA 59.572 38.462 6.58 6.47 38.04 1.31
196 204 3.182572 GTGATCTTTATAGCCGAAGTGCG 59.817 47.826 0.00 0.00 40.47 5.34
392 401 2.678336 CAGAAGTAAGCGAAACCCCATC 59.322 50.000 0.00 0.00 0.00 3.51
393 402 2.618045 CCAGAAGTAAGCGAAACCCCAT 60.618 50.000 0.00 0.00 0.00 4.00
394 403 1.271163 CCAGAAGTAAGCGAAACCCCA 60.271 52.381 0.00 0.00 0.00 4.96
397 406 4.501071 TGATACCAGAAGTAAGCGAAACC 58.499 43.478 0.00 0.00 33.70 3.27
398 407 5.408356 TCTGATACCAGAAGTAAGCGAAAC 58.592 41.667 0.00 0.00 45.74 2.78
439 458 0.824759 AATGACGAGCTAGGTGGGAC 59.175 55.000 8.85 3.19 0.00 4.46
442 461 1.478510 AGTGAATGACGAGCTAGGTGG 59.521 52.381 0.00 0.00 0.00 4.61
514 533 9.353999 TGTCAATATAGCGTAATATCATGTGAC 57.646 33.333 0.00 11.10 31.96 3.67
664 683 2.128035 CGTTGACTCCGCTTGGATATC 58.872 52.381 0.00 0.00 42.17 1.63
769 788 2.026822 ACAAAGCCGGAGATCAAGACAT 60.027 45.455 5.05 0.00 0.00 3.06
777 796 8.691661 ACATATTTTATAACAAAGCCGGAGAT 57.308 30.769 5.05 0.00 0.00 2.75
837 859 7.642082 ATCGTTACTAACTAACAGAGTCCAT 57.358 36.000 0.00 0.00 37.44 3.41
838 860 7.175467 TGAATCGTTACTAACTAACAGAGTCCA 59.825 37.037 0.00 0.00 37.44 4.02
839 861 7.533426 TGAATCGTTACTAACTAACAGAGTCC 58.467 38.462 0.00 0.00 37.44 3.85
840 862 9.224058 GATGAATCGTTACTAACTAACAGAGTC 57.776 37.037 0.00 0.00 37.44 3.36
841 863 8.958506 AGATGAATCGTTACTAACTAACAGAGT 58.041 33.333 0.00 0.00 41.56 3.24
853 875 9.616156 TCTCTACTTCTTAGATGAATCGTTACT 57.384 33.333 2.03 0.00 36.17 2.24
862 884 9.376075 CTGCAAATTTCTCTACTTCTTAGATGA 57.624 33.333 2.03 0.00 36.17 2.92
870 892 8.439286 CAGAGTTACTGCAAATTTCTCTACTTC 58.561 37.037 0.00 0.00 39.86 3.01
871 893 8.150945 TCAGAGTTACTGCAAATTTCTCTACTT 58.849 33.333 0.00 0.00 45.38 2.24
879 901 7.275888 TGATGTTCAGAGTTACTGCAAATTT 57.724 32.000 0.00 0.00 45.38 1.82
981 1007 1.067295 TGCTTCCTTGTCCTCACCAT 58.933 50.000 0.00 0.00 0.00 3.55
991 1017 2.821969 ACTTAAGTGCCATGCTTCCTTG 59.178 45.455 7.48 0.00 0.00 3.61
1003 1029 0.961753 AAGCCTGCCAACTTAAGTGC 59.038 50.000 9.34 9.88 0.00 4.40
1049 1075 5.125417 TCAAGGAGTGTTGAAAGGTTTTGAG 59.875 40.000 0.00 0.00 33.41 3.02
1094 1120 7.711339 GTGTATTTGTATGTAGAGAAAGGGAGG 59.289 40.741 0.00 0.00 0.00 4.30
1109 1135 6.402766 GGTTGTATGCGTGTGTGTATTTGTAT 60.403 38.462 0.00 0.00 0.00 2.29
1133 1159 9.993454 GTGGTTTCTTAGTAGTATTTATAGGGG 57.007 37.037 0.00 0.00 0.00 4.79
1359 1385 0.101399 CGTAGCGATTCTGAGGCAGT 59.899 55.000 0.00 0.00 32.61 4.40
1432 1458 7.383572 CAGGACTAGACATTACTTGTGATATGC 59.616 40.741 0.00 0.00 39.18 3.14
1538 1564 1.675641 AGCACCCATTTCGTGAGGC 60.676 57.895 0.00 0.00 32.77 4.70
1597 1623 0.820226 TCTTCAGGCCGACATGAGAG 59.180 55.000 0.00 0.00 0.00 3.20
1709 1741 1.270839 TGAACTACCTGAAGTGCTGGC 60.271 52.381 0.00 0.00 39.08 4.85
1759 1791 1.959042 CAGCACTCACTTTGTCTGGT 58.041 50.000 0.00 0.00 0.00 4.00
1795 1827 9.696917 AAATGCAGAGTTTAAGAAAATGTTAGG 57.303 29.630 0.00 0.00 0.00 2.69
1822 1854 8.947055 TTGTCATGCGTATATGATAATGCTAT 57.053 30.769 0.00 0.00 39.13 2.97
1850 1882 3.021177 TCATCCATGCATGTTGGACAT 57.979 42.857 24.58 0.55 45.71 3.06
1876 1908 0.899720 CCCAATTGCTGCATTCCTGT 59.100 50.000 1.84 0.00 0.00 4.00
2366 2401 1.304134 CTAACCCCCACAAGCCACC 60.304 63.158 0.00 0.00 0.00 4.61
2390 4225 2.280628 CATCGCTCCAAAACTAGTCCC 58.719 52.381 0.00 0.00 0.00 4.46
2457 4296 8.081633 ACAATAACATTGTTCACAACACATAGG 58.918 33.333 5.07 0.00 41.97 2.57


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

AutoCloner maintained by Alex Coulton.