Multiple sequence alignment - TraesCS2A01G210200

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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 TraesCS2A01G210200 chr2A 100.000 2736 0 0 1 2736 194305238 194307973 0.000000e+00 5053.0
1 TraesCS2A01G210200 chr2A 95.455 1254 56 1 1483 2736 561597363 561598615 0.000000e+00 1999.0
2 TraesCS2A01G210200 chr2A 92.954 738 46 4 956 1691 554027679 554028412 0.000000e+00 1070.0
3 TraesCS2A01G210200 chr2A 95.251 358 14 2 93 450 500977727 500978081 5.110000e-157 564.0
4 TraesCS2A01G210200 chr2A 95.058 344 15 2 2394 2736 493955213 493954871 8.620000e-150 540.0
5 TraesCS2A01G210200 chr2A 82.698 341 41 16 1 331 261625783 261625451 1.240000e-73 287.0
6 TraesCS2A01G210200 chr2A 81.416 339 44 14 1 331 261617896 261617569 2.700000e-65 259.0
7 TraesCS2A01G210200 chr2A 81.373 306 43 14 1 298 449676725 449677024 1.270000e-58 237.0
8 TraesCS2A01G210200 chr3A 95.443 2743 115 6 1 2736 360420133 360422872 0.000000e+00 4364.0
9 TraesCS2A01G210200 chr3A 92.808 2753 166 23 1 2735 127846358 127849096 0.000000e+00 3958.0
10 TraesCS2A01G210200 chr3A 94.183 1255 71 2 1483 2736 644250826 644252079 0.000000e+00 1912.0
11 TraesCS2A01G210200 chr3A 89.640 695 64 3 768 1455 657902527 657901834 0.000000e+00 878.0
12 TraesCS2A01G210200 chr3A 84.241 698 93 13 768 1457 304550767 304551455 0.000000e+00 664.0
13 TraesCS2A01G210200 chr3A 84.075 697 80 14 786 1454 304543057 304543750 0.000000e+00 643.0
14 TraesCS2A01G210200 chr3A 92.727 110 6 2 512 619 420263693 420263802 1.010000e-34 158.0
15 TraesCS2A01G210200 chr6A 89.635 1341 120 17 1404 2736 537553818 537555147 0.000000e+00 1688.0
16 TraesCS2A01G210200 chr6A 89.635 1341 120 17 1404 2736 537572539 537571210 0.000000e+00 1688.0
17 TraesCS2A01G210200 chr6A 92.112 748 53 5 946 1691 302787183 302786440 0.000000e+00 1050.0
18 TraesCS2A01G210200 chr6A 83.929 728 75 16 768 1455 244969044 244969769 0.000000e+00 658.0
19 TraesCS2A01G210200 chr6A 95.251 358 13 3 93 450 511353825 511353472 5.110000e-157 564.0
20 TraesCS2A01G210200 chr7A 91.134 1252 99 12 1490 2736 264359921 264358677 0.000000e+00 1687.0
21 TraesCS2A01G210200 chr7A 89.688 1251 118 11 1490 2735 264367912 264366668 0.000000e+00 1585.0
22 TraesCS2A01G210200 chr7A 89.038 447 36 10 1 444 445560183 445559747 2.400000e-150 542.0
23 TraesCS2A01G210200 chr7A 88.143 447 40 10 1 444 445552163 445551727 1.120000e-143 520.0
24 TraesCS2A01G210200 chr7A 89.369 301 19 4 487 776 71491499 71491201 1.550000e-97 366.0
25 TraesCS2A01G210200 chr7A 89.003 291 15 11 516 793 71447707 71447421 7.250000e-91 344.0
26 TraesCS2A01G210200 chr7A 93.478 138 7 2 487 622 379776541 379776404 1.280000e-48 204.0
27 TraesCS2A01G210200 chr1A 90.960 1261 98 14 1483 2736 509454340 509455591 0.000000e+00 1683.0
28 TraesCS2A01G210200 chr4A 93.585 795 41 10 1 790 70562907 70562118 0.000000e+00 1177.0
29 TraesCS2A01G210200 chr4A 89.481 694 64 4 768 1454 249663545 249664236 0.000000e+00 869.0
30 TraesCS2A01G210200 chr4A 89.322 693 64 5 768 1452 249656400 249657090 0.000000e+00 861.0
31 TraesCS2A01G210200 chr4A 89.162 692 67 4 768 1452 249671456 249672146 0.000000e+00 856.0
32 TraesCS2A01G210200 chr4A 93.186 499 29 4 1 497 70593870 70593375 0.000000e+00 728.0
33 TraesCS2A01G210200 chr4A 91.118 304 21 5 490 790 70592913 70592613 9.120000e-110 407.0
34 TraesCS2A01G210200 chr4A 79.586 338 54 14 1 332 277442183 277441855 7.620000e-56 228.0
35 TraesCS2A01G210200 chr4A 80.479 292 44 13 1 286 604519308 604519024 7.680000e-51 211.0
36 TraesCS2A01G210200 chr4A 85.714 168 19 5 1 166 177088519 177088683 3.620000e-39 172.0
37 TraesCS2A01G210200 chr5A 89.172 628 59 7 934 1559 158407166 158407786 0.000000e+00 774.0
38 TraesCS2A01G210200 chr5A 95.251 358 14 2 93 450 448130092 448130446 5.110000e-157 564.0
39 TraesCS2A01G210200 chr1B 89.286 56 5 1 509 564 593814166 593814220 4.890000e-08 69.4


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 TraesCS2A01G210200 chr2A 194305238 194307973 2735 False 5053.0 5053 100.000 1 2736 1 chr2A.!!$F1 2735
1 TraesCS2A01G210200 chr2A 561597363 561598615 1252 False 1999.0 1999 95.455 1483 2736 1 chr2A.!!$F5 1253
2 TraesCS2A01G210200 chr2A 554027679 554028412 733 False 1070.0 1070 92.954 956 1691 1 chr2A.!!$F4 735
3 TraesCS2A01G210200 chr3A 360420133 360422872 2739 False 4364.0 4364 95.443 1 2736 1 chr3A.!!$F4 2735
4 TraesCS2A01G210200 chr3A 127846358 127849096 2738 False 3958.0 3958 92.808 1 2735 1 chr3A.!!$F1 2734
5 TraesCS2A01G210200 chr3A 644250826 644252079 1253 False 1912.0 1912 94.183 1483 2736 1 chr3A.!!$F6 1253
6 TraesCS2A01G210200 chr3A 657901834 657902527 693 True 878.0 878 89.640 768 1455 1 chr3A.!!$R1 687
7 TraesCS2A01G210200 chr3A 304550767 304551455 688 False 664.0 664 84.241 768 1457 1 chr3A.!!$F3 689
8 TraesCS2A01G210200 chr3A 304543057 304543750 693 False 643.0 643 84.075 786 1454 1 chr3A.!!$F2 668
9 TraesCS2A01G210200 chr6A 537553818 537555147 1329 False 1688.0 1688 89.635 1404 2736 1 chr6A.!!$F2 1332
10 TraesCS2A01G210200 chr6A 537571210 537572539 1329 True 1688.0 1688 89.635 1404 2736 1 chr6A.!!$R3 1332
11 TraesCS2A01G210200 chr6A 302786440 302787183 743 True 1050.0 1050 92.112 946 1691 1 chr6A.!!$R1 745
12 TraesCS2A01G210200 chr6A 244969044 244969769 725 False 658.0 658 83.929 768 1455 1 chr6A.!!$F1 687
13 TraesCS2A01G210200 chr7A 264358677 264359921 1244 True 1687.0 1687 91.134 1490 2736 1 chr7A.!!$R3 1246
14 TraesCS2A01G210200 chr7A 264366668 264367912 1244 True 1585.0 1585 89.688 1490 2735 1 chr7A.!!$R4 1245
15 TraesCS2A01G210200 chr1A 509454340 509455591 1251 False 1683.0 1683 90.960 1483 2736 1 chr1A.!!$F1 1253
16 TraesCS2A01G210200 chr4A 70562118 70562907 789 True 1177.0 1177 93.585 1 790 1 chr4A.!!$R1 789
17 TraesCS2A01G210200 chr4A 249663545 249664236 691 False 869.0 869 89.481 768 1454 1 chr4A.!!$F3 686
18 TraesCS2A01G210200 chr4A 249656400 249657090 690 False 861.0 861 89.322 768 1452 1 chr4A.!!$F2 684
19 TraesCS2A01G210200 chr4A 249671456 249672146 690 False 856.0 856 89.162 768 1452 1 chr4A.!!$F4 684
20 TraesCS2A01G210200 chr4A 70592613 70593870 1257 True 567.5 728 92.152 1 790 2 chr4A.!!$R4 789
21 TraesCS2A01G210200 chr5A 158407166 158407786 620 False 774.0 774 89.172 934 1559 1 chr5A.!!$F1 625

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
703 1180 0.257616 CTTCCTCTCTCCCCTCGTCT 59.742 60.000 0.0 0.0 0.00 4.18 F
1260 1780 1.000938 GGGTTCGTCAAGTCGTGTACT 60.001 52.381 0.0 0.0 41.49 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 2192 0.036952 TCGACGGTAGAGGTTCTCGT 60.037 55.0 0.00 0.0 35.36 4.18 R
2565 3107 1.234821 GGATCCTCACAAACGCAACA 58.765 50.0 3.84 0.0 0.00 3.33 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
44 45 9.889128 CAATAATTTTGGATTCACCCATAAACT 57.111 29.630 0.00 0.00 35.87 2.66
109 112 5.355910 GTCTCCGAACTTTGCCCATAAATTA 59.644 40.000 0.00 0.00 0.00 1.40
333 338 4.081142 CCCTCTCTTTCTTTTCCTCTCTCC 60.081 50.000 0.00 0.00 0.00 3.71
669 1146 4.501229 CCTCGATCTCCTTTCTTCTCCATG 60.501 50.000 0.00 0.00 0.00 3.66
703 1180 0.257616 CTTCCTCTCTCCCCTCGTCT 59.742 60.000 0.00 0.00 0.00 4.18
723 1200 4.129737 TTTCTCGCTAGCGCCGCT 62.130 61.111 31.82 18.67 43.41 5.52
746 1223 2.747855 CTCGCTCAAACCCCCTGC 60.748 66.667 0.00 0.00 0.00 4.85
950 1461 2.889617 CCTATGACCGTGCGACCA 59.110 61.111 0.00 0.00 0.00 4.02
1011 1522 2.597340 CCGACCATGGAGGCCATT 59.403 61.111 21.47 0.00 42.23 3.16
1054 1573 2.672307 GCTGTGCCTTGCTGCTCT 60.672 61.111 0.00 0.00 0.00 4.09
1114 1633 3.691342 CCACCTTCGACCTCGGCA 61.691 66.667 0.00 0.00 40.29 5.69
1260 1780 1.000938 GGGTTCGTCAAGTCGTGTACT 60.001 52.381 0.00 0.00 41.49 2.73
1437 1957 2.048503 GACCACTTCCCACGACGG 60.049 66.667 0.00 0.00 0.00 4.79
1672 2192 1.450848 ACTACCGTCGCCGAGATCA 60.451 57.895 0.00 0.00 35.63 2.92
2081 2606 2.488347 GCACCCCTTTCTTTCTACCACA 60.488 50.000 0.00 0.00 0.00 4.17
2174 2700 9.615295 TCATTCGCATCATGATAATAACATTTG 57.385 29.630 8.15 0.00 0.00 2.32
2235 2762 4.163458 GCATATGGGGATCTACCGGAATTA 59.837 45.833 9.46 0.00 40.11 1.40
2380 2910 4.451096 AGTCATGTGGTGTTTCGTCAATAC 59.549 41.667 0.00 0.00 0.00 1.89
2664 3206 1.490490 GGCAAGATGACCATACCCTCA 59.510 52.381 0.00 0.00 0.00 3.86
2698 3240 1.532868 CTTTGCTTGCTAGTTGCTCGT 59.467 47.619 0.00 0.00 43.37 4.18
2704 3246 3.665585 GCTTGCTAGTTGCTCGTTCTTTC 60.666 47.826 0.00 0.00 43.37 2.62
2718 3260 2.169832 TCTTTCGCTATGCCTATGCC 57.830 50.000 0.00 0.00 36.33 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.694628 GGCATGGGATATTTGCAAGTGA 59.305 45.455 4.47 0.00 38.12 3.41
109 112 3.127030 GGAGCTCCGAAAAATGACGAAAT 59.873 43.478 19.06 0.00 0.00 2.17
457 462 0.108585 GCTGTGGGAACAGGAGACAA 59.891 55.000 7.89 0.00 44.46 3.18
669 1146 1.443828 GAAGATGGGGACGAGAGGC 59.556 63.158 0.00 0.00 39.70 4.70
703 1180 1.063649 CGGCGCTAGCGAGAAACTA 59.936 57.895 39.52 0.00 46.35 2.24
723 1200 2.347490 GGTTTGAGCGAGGCCTGA 59.653 61.111 12.00 0.00 0.00 3.86
743 1220 4.880537 CTGTAGAGGCCGCGGCAG 62.881 72.222 46.88 32.04 44.11 4.85
794 1279 1.366435 AGGGGAAGGTAGAGATGGTGT 59.634 52.381 0.00 0.00 0.00 4.16
1054 1573 4.395080 CGCTATCGGACGAAGCAA 57.605 55.556 20.23 1.44 35.98 3.91
1260 1780 2.285069 TTCCGGCTTGGGCTCCTA 60.285 61.111 0.00 0.00 38.76 2.94
1437 1957 1.001181 TCAACGGTAGTGGTACAAGGC 59.999 52.381 0.00 0.00 44.16 4.35
1646 2166 1.024271 GGCGACGGTAGTGGTACATA 58.976 55.000 0.00 0.00 44.52 2.29
1672 2192 0.036952 TCGACGGTAGAGGTTCTCGT 60.037 55.000 0.00 0.00 35.36 4.18
1727 2247 1.403780 GGAAGTAGTGGTTCACGCGAT 60.404 52.381 15.93 0.00 39.64 4.58
1946 2466 2.142292 AAAAGATGGTGGGGCGCTCT 62.142 55.000 7.48 0.00 0.00 4.09
2081 2606 7.009815 CGAGCATTTTATGAAGCATTTGTCATT 59.990 33.333 0.00 0.00 36.00 2.57
2174 2700 8.017946 TGGTGCAACAACAATTTTTAAAACTTC 58.982 29.630 0.00 0.00 39.98 3.01
2235 2762 1.339929 GAGGCCGGAACAACAAACAAT 59.660 47.619 5.05 0.00 0.00 2.71
2386 2916 3.199508 AGTGGAGCTCAATATGCAACTCT 59.800 43.478 17.19 0.00 0.00 3.24
2565 3107 1.234821 GGATCCTCACAAACGCAACA 58.765 50.000 3.84 0.00 0.00 3.33
2664 3206 7.224522 AGCAAGCAAAGATAGAAGTGATTTT 57.775 32.000 0.00 0.00 0.00 1.82
2698 3240 2.494059 GGCATAGGCATAGCGAAAGAA 58.506 47.619 0.15 0.00 43.71 2.52
2704 3246 3.481903 CGCGGCATAGGCATAGCG 61.482 66.667 18.16 18.16 46.82 4.26


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

AutoCloner maintained by Alex Coulton.