Multiple sequence alignment - TraesCS4B01G120300

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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 TraesCS4B01G120300 chr4B 100.000 2243 0 0 1 2243 141079228 141081470 0.000000e+00 4143
1 TraesCS4B01G120300 chr4B 87.202 672 85 1 1 672 103764319 103764989 0.000000e+00 763
2 TraesCS4B01G120300 chr4B 94.693 358 17 2 1888 2243 621660522 621660879 2.520000e-154 555
3 TraesCS4B01G120300 chr7B 95.752 1483 60 3 764 2243 253264585 253263103 0.000000e+00 2386
4 TraesCS4B01G120300 chr7B 88.996 727 50 12 838 1535 663107679 663108404 0.000000e+00 872
5 TraesCS4B01G120300 chr2B 92.558 1478 103 4 769 2243 311334446 311335919 0.000000e+00 2113
6 TraesCS4B01G120300 chr2B 94.488 127 6 1 664 790 311334285 311334410 6.320000e-46 195
7 TraesCS4B01G120300 chr7D 91.300 1023 67 7 664 1667 354527225 354528244 0.000000e+00 1376
8 TraesCS4B01G120300 chr7D 92.097 911 66 4 761 1667 195395556 195396464 0.000000e+00 1279
9 TraesCS4B01G120300 chr7D 91.458 878 52 7 664 1540 346185138 346184283 0.000000e+00 1184
10 TraesCS4B01G120300 chr7D 88.966 716 50 14 841 1535 588678986 588678279 0.000000e+00 857
11 TraesCS4B01G120300 chr7D 93.715 541 28 4 1707 2243 195396464 195397002 0.000000e+00 806
12 TraesCS4B01G120300 chr7D 93.103 551 30 6 1699 2243 346184185 346183637 0.000000e+00 800
13 TraesCS4B01G120300 chr7D 92.545 550 32 7 1699 2243 354528244 354528789 0.000000e+00 780
14 TraesCS4B01G120300 chr7D 92.308 91 7 0 1445 1535 588841202 588841292 1.810000e-26 130
15 TraesCS4B01G120300 chr1B 88.756 667 71 3 1 664 339425043 339425708 0.000000e+00 813
16 TraesCS4B01G120300 chr1B 87.538 658 75 5 2 655 157634012 157634666 0.000000e+00 754
17 TraesCS4B01G120300 chr1B 94.972 358 16 2 1888 2243 30060643 30061000 5.410000e-156 560
18 TraesCS4B01G120300 chr1B 87.307 323 34 2 1540 1855 280435876 280436198 1.640000e-96 363
19 TraesCS4B01G120300 chr1B 94.444 126 6 1 682 807 127418134 127418258 2.270000e-45 193
20 TraesCS4B01G120300 chr6B 88.244 672 73 4 1 672 201698068 201697403 0.000000e+00 798
21 TraesCS4B01G120300 chr6B 87.801 664 79 2 1 664 175777029 175777690 0.000000e+00 776
22 TraesCS4B01G120300 chr2D 88.271 665 76 2 1 664 629489900 629489237 0.000000e+00 795
23 TraesCS4B01G120300 chr2D 93.846 130 8 0 664 793 274709717 274709588 1.760000e-46 196
24 TraesCS4B01G120300 chr3B 88.550 655 74 1 1 655 534647870 534647217 0.000000e+00 793
25 TraesCS4B01G120300 chr3B 87.801 664 79 2 1 664 637303381 637304042 0.000000e+00 776
26 TraesCS4B01G120300 chr3B 94.413 358 18 2 1888 2243 658959599 658959956 1.170000e-152 549
27 TraesCS4B01G120300 chr3B 93.872 359 18 4 1888 2243 383919956 383920313 2.530000e-149 538
28 TraesCS4B01G120300 chr3B 95.833 144 5 1 664 807 556456611 556456753 4.820000e-57 231
29 TraesCS4B01G120300 chr5B 87.519 657 79 3 1 655 608965281 608964626 0.000000e+00 756
30 TraesCS4B01G120300 chr5B 86.704 361 34 7 1543 1891 308024175 308023817 2.700000e-104 388
31 TraesCS4B01G120300 chr5B 86.420 324 36 3 1540 1855 570010439 570010762 4.580000e-92 348
32 TraesCS4B01G120300 chr7A 85.596 722 57 21 850 1535 680406664 680407374 0.000000e+00 713
33 TraesCS4B01G120300 chr7A 86.207 319 41 1 1542 1857 238546879 238547197 2.130000e-90 342
34 TraesCS4B01G120300 chr7A 95.714 140 6 0 664 803 173066999 173066860 2.240000e-55 226
35 TraesCS4B01G120300 chr6A 85.172 290 32 9 1540 1821 247135975 247136261 1.010000e-73 287
36 TraesCS4B01G120300 chr6A 96.429 140 5 0 664 803 468509473 468509612 4.820000e-57 231
37 TraesCS4B01G120300 chr4A 91.477 176 14 1 664 839 462308946 462309120 8.000000e-60 241
38 TraesCS4B01G120300 chr1A 94.245 139 8 0 665 803 499323908 499323770 1.740000e-51 213
39 TraesCS4B01G120300 chr4D 93.701 127 7 1 664 790 310939803 310939678 2.940000e-44 189


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 TraesCS4B01G120300 chr4B 141079228 141081470 2242 False 4143.0 4143 100.0000 1 2243 1 chr4B.!!$F2 2242
1 TraesCS4B01G120300 chr4B 103764319 103764989 670 False 763.0 763 87.2020 1 672 1 chr4B.!!$F1 671
2 TraesCS4B01G120300 chr7B 253263103 253264585 1482 True 2386.0 2386 95.7520 764 2243 1 chr7B.!!$R1 1479
3 TraesCS4B01G120300 chr7B 663107679 663108404 725 False 872.0 872 88.9960 838 1535 1 chr7B.!!$F1 697
4 TraesCS4B01G120300 chr2B 311334285 311335919 1634 False 1154.0 2113 93.5230 664 2243 2 chr2B.!!$F1 1579
5 TraesCS4B01G120300 chr7D 354527225 354528789 1564 False 1078.0 1376 91.9225 664 2243 2 chr7D.!!$F3 1579
6 TraesCS4B01G120300 chr7D 195395556 195397002 1446 False 1042.5 1279 92.9060 761 2243 2 chr7D.!!$F2 1482
7 TraesCS4B01G120300 chr7D 346183637 346185138 1501 True 992.0 1184 92.2805 664 2243 2 chr7D.!!$R2 1579
8 TraesCS4B01G120300 chr7D 588678279 588678986 707 True 857.0 857 88.9660 841 1535 1 chr7D.!!$R1 694
9 TraesCS4B01G120300 chr1B 339425043 339425708 665 False 813.0 813 88.7560 1 664 1 chr1B.!!$F5 663
10 TraesCS4B01G120300 chr1B 157634012 157634666 654 False 754.0 754 87.5380 2 655 1 chr1B.!!$F3 653
11 TraesCS4B01G120300 chr6B 201697403 201698068 665 True 798.0 798 88.2440 1 672 1 chr6B.!!$R1 671
12 TraesCS4B01G120300 chr6B 175777029 175777690 661 False 776.0 776 87.8010 1 664 1 chr6B.!!$F1 663
13 TraesCS4B01G120300 chr2D 629489237 629489900 663 True 795.0 795 88.2710 1 664 1 chr2D.!!$R2 663
14 TraesCS4B01G120300 chr3B 534647217 534647870 653 True 793.0 793 88.5500 1 655 1 chr3B.!!$R1 654
15 TraesCS4B01G120300 chr3B 637303381 637304042 661 False 776.0 776 87.8010 1 664 1 chr3B.!!$F3 663
16 TraesCS4B01G120300 chr5B 608964626 608965281 655 True 756.0 756 87.5190 1 655 1 chr5B.!!$R2 654
17 TraesCS4B01G120300 chr7A 680406664 680407374 710 False 713.0 713 85.5960 850 1535 1 chr7A.!!$F2 685

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
839 905 0.25589 CCATGGATTCCGGGAACAGT 59.744 55.0 12.53 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 2041 1.302511 CCGTTCACTTCCCCACCTG 60.303 63.158 0.0 0.0 0.0 4.0 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
25 26 4.164988 ACTCTGCATGATAAAGGCCTTACT 59.835 41.667 20.84 9.14 33.58 2.24
68 70 2.598985 ATCTCCTAGCGAGCCCCG 60.599 66.667 0.00 0.00 38.62 5.73
95 97 3.864983 AACCCGGGCCTCCTTCAGA 62.865 63.158 24.08 0.00 0.00 3.27
142 144 3.511477 AGGCCTGTTCTGAACTCTTCTA 58.489 45.455 20.18 0.00 0.00 2.10
248 250 3.468071 TGCTCCACCTCTAACTCCTTA 57.532 47.619 0.00 0.00 0.00 2.69
283 285 2.294078 CCGCCTTCCTCACCTCCTT 61.294 63.158 0.00 0.00 0.00 3.36
299 301 3.264450 CCTCCTTCTCCTTCTTGGCTTTA 59.736 47.826 0.00 0.00 35.26 1.85
332 334 4.361971 AGGGACTCGACCTCGGCA 62.362 66.667 0.00 0.00 40.29 5.69
333 335 3.379445 GGGACTCGACCTCGGCAA 61.379 66.667 0.00 0.00 40.29 4.52
474 478 1.472878 CGGTCGAGTTCCTCATCAGAA 59.527 52.381 0.00 0.00 0.00 3.02
636 646 2.245028 TCTCAGGGGCTACTGTCTACAT 59.755 50.000 9.02 0.00 39.48 2.29
645 655 5.397559 GGGCTACTGTCTACATATGGGTTTT 60.398 44.000 7.80 0.00 0.00 2.43
655 665 1.529226 TATGGGTTTTGCCTCACACG 58.471 50.000 0.00 0.00 37.43 4.49
674 684 6.207810 TCACACGCACACACATATATATAGGA 59.792 38.462 11.22 0.00 0.00 2.94
698 708 5.105853 TGGGACTATTTAGAAACTCCCCTT 58.894 41.667 7.99 0.00 37.17 3.95
833 899 2.113986 GGCTCCATGGATTCCGGG 59.886 66.667 16.63 3.17 0.00 5.73
839 905 0.255890 CCATGGATTCCGGGAACAGT 59.744 55.000 12.53 0.00 0.00 3.55
964 1063 4.491409 GGCGAGGGGAAGAAGGGC 62.491 72.222 0.00 0.00 0.00 5.19
983 1088 1.341383 GCTCAACATGGAGGGGTCATT 60.341 52.381 0.00 0.00 35.41 2.57
1159 1264 1.004080 GTGCTCTGCTTCCTGCTGA 60.004 57.895 0.00 0.00 45.30 4.26
1163 1268 1.411977 GCTCTGCTTCCTGCTGATCTA 59.588 52.381 0.00 0.00 46.07 1.98
1182 1287 0.106708 ACCTCAAGAACAAGCGCAGA 59.893 50.000 11.47 0.00 0.00 4.26
1349 1462 6.599244 TGAAGATTTTCGTTAGATGCCAGATT 59.401 34.615 0.00 0.00 36.04 2.40
1422 1535 4.503910 CCGCGGATCTTGATTTGGATATA 58.496 43.478 24.07 0.00 0.00 0.86
1466 1597 2.573462 TGGCTAGATGTTTCTTGCTCCT 59.427 45.455 8.80 0.00 46.10 3.69
1572 1711 4.630069 GTGTCTTCGCTCCTAGCAATTAAA 59.370 41.667 0.00 0.00 42.58 1.52
1612 1751 3.515602 CCCCAGGCAGATAGCTATTTT 57.484 47.619 7.87 0.00 44.79 1.82
1679 1818 4.623932 AATAGTGTCTTCAGTCTGGCAA 57.376 40.909 0.00 0.00 0.00 4.52
1740 1911 3.916438 TTCAGTCCCGGCAGGCCTA 62.916 63.158 3.98 0.00 35.76 3.93
1760 1933 6.262273 GGCCTAATCTGGTCGAAAAATGAATA 59.738 38.462 0.00 0.00 0.00 1.75
1783 1960 9.987272 AATAAAAGAAAAAGTATTTGCAGCTCT 57.013 25.926 0.00 0.00 39.02 4.09
1864 2041 1.000506 TGTAGCAGTTCGGGAAGTGAC 59.999 52.381 18.00 9.80 42.77 3.67
2005 2183 6.419484 TCTCTCTATCTTTGTGTGTGGAAA 57.581 37.500 0.00 0.00 0.00 3.13
2036 2215 2.160205 GAGGCCAACAGTTAGGGAAAC 58.840 52.381 5.01 0.00 38.46 2.78
2088 2267 9.705290 ATATTTGTTGTTTCTATTGGTGTTTCC 57.295 29.630 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 32 0.392193 CAAGAGGCGAGGCAGATTGT 60.392 55.000 0.00 0.00 0.00 2.71
95 97 2.549778 GCTCACCAAAGCTCTTGAGAGT 60.550 50.000 14.70 2.32 43.85 3.24
142 144 2.918712 CAAGTGTGAGTCCTTGGAGT 57.081 50.000 0.00 0.00 35.51 3.85
167 169 2.613977 CGAACAGGAGCTCAAGGATGTT 60.614 50.000 17.19 16.27 33.82 2.71
168 170 1.066573 CGAACAGGAGCTCAAGGATGT 60.067 52.381 17.19 8.80 0.00 3.06
272 274 2.235898 CAAGAAGGAGAAGGAGGTGAGG 59.764 54.545 0.00 0.00 0.00 3.86
283 285 3.560025 CCTTGCTAAAGCCAAGAAGGAGA 60.560 47.826 11.51 0.00 40.75 3.71
355 357 9.712359 GTCGTTTTAAACTGACTAAGATTGTTT 57.288 29.630 18.19 0.00 34.45 2.83
396 399 3.181466 GGCATTAAGGCATACCCAAAAGG 60.181 47.826 14.82 0.00 43.51 3.11
447 451 0.537188 AGGAACTCGACCGCATCAAT 59.463 50.000 0.00 0.00 0.00 2.57
596 606 2.683867 AGACTCTGTCCGGATTAGAACG 59.316 50.000 7.81 6.89 32.18 3.95
636 646 1.529226 CGTGTGAGGCAAAACCCATA 58.471 50.000 0.00 0.00 40.58 2.74
645 655 2.894879 GTGTGTGCGTGTGAGGCA 60.895 61.111 0.00 0.00 36.56 4.75
655 665 6.986817 GTCCCATCCTATATATATGTGTGTGC 59.013 42.308 5.44 0.00 0.00 4.57
674 684 5.297799 AGGGGAGTTTCTAAATAGTCCCAT 58.702 41.667 15.03 6.81 44.87 4.00
819 885 0.546122 CTGTTCCCGGAATCCATGGA 59.454 55.000 18.88 18.88 0.00 3.41
833 899 2.358737 CTGGGCGGTGGACTGTTC 60.359 66.667 0.00 0.00 0.00 3.18
964 1063 2.291153 ACAATGACCCCTCCATGTTGAG 60.291 50.000 0.00 0.00 0.00 3.02
1035 1140 1.898574 CTCCTTGCCGCACACCTTT 60.899 57.895 0.00 0.00 0.00 3.11
1121 1226 2.847234 ACTTGGCCTCCACGTCCA 60.847 61.111 3.32 0.00 29.82 4.02
1159 1264 2.028112 TGCGCTTGTTCTTGAGGTAGAT 60.028 45.455 9.73 0.00 0.00 1.98
1163 1268 0.106708 TCTGCGCTTGTTCTTGAGGT 59.893 50.000 9.73 0.00 0.00 3.85
1207 1312 2.063979 CGGGGTAGGTGATGAGGCA 61.064 63.158 0.00 0.00 0.00 4.75
1349 1462 4.535526 TCAATCGATCTCCAGTTGTTCA 57.464 40.909 0.00 0.00 0.00 3.18
1385 1498 2.978010 CGGGCACGGAAAGCAACT 60.978 61.111 0.00 0.00 36.18 3.16
1422 1535 6.872020 CCAGAATCAAGAAAACAATCAAGCAT 59.128 34.615 0.00 0.00 0.00 3.79
1466 1597 2.866156 CAGACTGAAACTCACGAGCAAA 59.134 45.455 0.00 0.00 0.00 3.68
1572 1711 1.613437 GCTGTGGCAGTTAACACCAAT 59.387 47.619 18.76 0.00 36.80 3.16
1612 1751 1.902556 GAACTAACTGCCGGGCCTA 59.097 57.895 17.97 4.52 0.00 3.93
1711 1882 3.069158 GCCGGGACTGAAATAGCTAACTA 59.931 47.826 2.18 0.00 0.00 2.24
1760 1933 6.703165 CCAGAGCTGCAAATACTTTTTCTTTT 59.297 34.615 1.02 0.00 0.00 2.27
1783 1960 1.974957 TGTTGAGCAAGCTACCTACCA 59.025 47.619 0.00 0.00 0.00 3.25
1864 2041 1.302511 CCGTTCACTTCCCCACCTG 60.303 63.158 0.00 0.00 0.00 4.00
2088 2267 6.047870 TGAATTTTCAAACCCTGTGACAATG 58.952 36.000 0.00 0.00 33.55 2.82


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

AutoCloner maintained by Alex Coulton.