Multiple sequence alignment - TraesCS5B01G267000

Loading Multiple Alignment...

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 TraesCS5B01G267000 chr5B 100.000 2564 0 0 1 2564 451532970 451530407 0.000000e+00 4735
1 TraesCS5B01G267000 chr5B 94.157 753 43 1 840 1591 642595460 642594708 0.000000e+00 1146
2 TraesCS5B01G267000 chr5B 79.853 680 86 24 1690 2337 453673871 453673211 1.400000e-122 449
3 TraesCS5B01G267000 chr5B 77.909 679 92 25 1691 2337 453723512 453722860 1.120000e-98 370
4 TraesCS5B01G267000 chr5D 97.800 1727 34 3 840 2564 378151215 378152939 0.000000e+00 2976
5 TraesCS5B01G267000 chr5D 95.131 842 39 2 1 841 455192763 455191923 0.000000e+00 1327
6 TraesCS5B01G267000 chr5D 95.012 842 40 2 1 841 454948594 454947754 0.000000e+00 1321
7 TraesCS5B01G267000 chr5D 95.012 842 40 2 1 841 455021134 455020294 0.000000e+00 1321
8 TraesCS5B01G267000 chr5D 94.774 842 42 2 1 841 455091879 455091039 0.000000e+00 1310
9 TraesCS5B01G267000 chr5D 82.362 669 82 23 1690 2337 378122412 378123065 1.340000e-152 549
10 TraesCS5B01G267000 chr3B 95.006 841 41 1 1 841 578534391 578533552 0.000000e+00 1319
11 TraesCS5B01G267000 chrUn 94.887 841 41 2 1 841 86095482 86094644 0.000000e+00 1314
12 TraesCS5B01G267000 chrUn 80.117 684 88 23 1690 2338 171237422 171238092 1.390000e-127 466
13 TraesCS5B01G267000 chrUn 79.971 684 89 23 1690 2338 67042055 67041385 6.460000e-126 460
14 TraesCS5B01G267000 chrUn 81.579 570 70 15 1791 2338 342519087 342518531 3.030000e-119 438
15 TraesCS5B01G267000 chr7B 94.887 841 41 2 1 841 339707876 339708714 0.000000e+00 1314
16 TraesCS5B01G267000 chr7B 94.768 841 43 1 1 841 244553396 244554235 0.000000e+00 1308
17 TraesCS5B01G267000 chr7B 94.814 752 39 0 840 1591 407387030 407387781 0.000000e+00 1173
18 TraesCS5B01G267000 chr1D 94.887 841 42 1 1 841 118044699 118043860 0.000000e+00 1314
19 TraesCS5B01G267000 chr1D 94.674 751 39 1 840 1590 142663470 142664219 0.000000e+00 1164
20 TraesCS5B01G267000 chr2B 95.346 752 34 1 840 1591 310898340 310899090 0.000000e+00 1194
21 TraesCS5B01G267000 chr1B 94.364 763 39 3 840 1601 57111078 57110319 0.000000e+00 1168
22 TraesCS5B01G267000 chr2A 94.555 753 39 2 840 1591 550182365 550183116 0.000000e+00 1162
23 TraesCS5B01G267000 chr2A 94.422 753 40 2 840 1591 348050520 348051271 0.000000e+00 1157
24 TraesCS5B01G267000 chr6A 94.541 751 40 1 840 1590 155746775 155746026 0.000000e+00 1158
25 TraesCS5B01G267000 chr5A 86.399 772 78 15 1590 2337 478892602 478893370 0.000000e+00 819
26 TraesCS5B01G267000 chr5A 83.699 638 82 16 1625 2248 478895110 478895739 1.320000e-162 582
27 TraesCS5B01G267000 chr5A 80.535 673 81 25 1690 2338 478858982 478859628 2.990000e-129 472


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 TraesCS5B01G267000 chr5B 451530407 451532970 2563 True 4735.0 4735 100.000 1 2564 1 chr5B.!!$R1 2563
1 TraesCS5B01G267000 chr5B 642594708 642595460 752 True 1146.0 1146 94.157 840 1591 1 chr5B.!!$R4 751
2 TraesCS5B01G267000 chr5B 453673211 453673871 660 True 449.0 449 79.853 1690 2337 1 chr5B.!!$R2 647
3 TraesCS5B01G267000 chr5B 453722860 453723512 652 True 370.0 370 77.909 1691 2337 1 chr5B.!!$R3 646
4 TraesCS5B01G267000 chr5D 378151215 378152939 1724 False 2976.0 2976 97.800 840 2564 1 chr5D.!!$F2 1724
5 TraesCS5B01G267000 chr5D 455191923 455192763 840 True 1327.0 1327 95.131 1 841 1 chr5D.!!$R4 840
6 TraesCS5B01G267000 chr5D 454947754 454948594 840 True 1321.0 1321 95.012 1 841 1 chr5D.!!$R1 840
7 TraesCS5B01G267000 chr5D 455020294 455021134 840 True 1321.0 1321 95.012 1 841 1 chr5D.!!$R2 840
8 TraesCS5B01G267000 chr5D 455091039 455091879 840 True 1310.0 1310 94.774 1 841 1 chr5D.!!$R3 840
9 TraesCS5B01G267000 chr5D 378122412 378123065 653 False 549.0 549 82.362 1690 2337 1 chr5D.!!$F1 647
10 TraesCS5B01G267000 chr3B 578533552 578534391 839 True 1319.0 1319 95.006 1 841 1 chr3B.!!$R1 840
11 TraesCS5B01G267000 chrUn 86094644 86095482 838 True 1314.0 1314 94.887 1 841 1 chrUn.!!$R2 840
12 TraesCS5B01G267000 chrUn 171237422 171238092 670 False 466.0 466 80.117 1690 2338 1 chrUn.!!$F1 648
13 TraesCS5B01G267000 chrUn 67041385 67042055 670 True 460.0 460 79.971 1690 2338 1 chrUn.!!$R1 648
14 TraesCS5B01G267000 chrUn 342518531 342519087 556 True 438.0 438 81.579 1791 2338 1 chrUn.!!$R3 547
15 TraesCS5B01G267000 chr7B 339707876 339708714 838 False 1314.0 1314 94.887 1 841 1 chr7B.!!$F2 840
16 TraesCS5B01G267000 chr7B 244553396 244554235 839 False 1308.0 1308 94.768 1 841 1 chr7B.!!$F1 840
17 TraesCS5B01G267000 chr7B 407387030 407387781 751 False 1173.0 1173 94.814 840 1591 1 chr7B.!!$F3 751
18 TraesCS5B01G267000 chr1D 118043860 118044699 839 True 1314.0 1314 94.887 1 841 1 chr1D.!!$R1 840
19 TraesCS5B01G267000 chr1D 142663470 142664219 749 False 1164.0 1164 94.674 840 1590 1 chr1D.!!$F1 750
20 TraesCS5B01G267000 chr2B 310898340 310899090 750 False 1194.0 1194 95.346 840 1591 1 chr2B.!!$F1 751
21 TraesCS5B01G267000 chr1B 57110319 57111078 759 True 1168.0 1168 94.364 840 1601 1 chr1B.!!$R1 761
22 TraesCS5B01G267000 chr2A 550182365 550183116 751 False 1162.0 1162 94.555 840 1591 1 chr2A.!!$F2 751
23 TraesCS5B01G267000 chr2A 348050520 348051271 751 False 1157.0 1157 94.422 840 1591 1 chr2A.!!$F1 751
24 TraesCS5B01G267000 chr6A 155746026 155746775 749 True 1158.0 1158 94.541 840 1590 1 chr6A.!!$R1 750
25 TraesCS5B01G267000 chr5A 478892602 478895739 3137 False 700.5 819 85.049 1590 2337 2 chr5A.!!$F2 747
26 TraesCS5B01G267000 chr5A 478858982 478859628 646 False 472.0 472 80.535 1690 2338 1 chr5A.!!$F1 648

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
501 503 1.213926 TCCTTACCTCCCCTCGTAGTC 59.786 57.143 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 1753 0.040058 ATTGGTGGATGAGCTTGCCA 59.96 50.0 0.0 0.0 0.0 4.92 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
33 34 9.481340 CGACAGAGAAATCATAATCCTTATCAA 57.519 33.333 0.00 0.00 0.00 2.57
104 106 6.060788 AGCATTCAGAGACTTTTCTTTCAGT 58.939 36.000 0.00 0.00 29.47 3.41
162 164 3.372206 GCAAGCAAGAAAATCTCTAGCGA 59.628 43.478 0.00 0.00 32.46 4.93
298 300 3.366374 GCCCTAGCAAGTTGTTCATCAAC 60.366 47.826 4.48 2.97 46.29 3.18
313 315 8.175925 TGTTCATCAACAAATTCACCTAATGA 57.824 30.769 0.00 0.00 39.69 2.57
316 318 7.819644 TCATCAACAAATTCACCTAATGACAG 58.180 34.615 0.00 0.00 36.92 3.51
406 408 9.750882 CAATAACATGCGACATATCAGAATTAG 57.249 33.333 0.00 0.00 0.00 1.73
443 445 3.402628 AGGTGTCGCAAGTTTACTCAT 57.597 42.857 0.00 0.00 39.48 2.90
477 479 2.182827 TCAAGTGCAGAGCTAGATGGT 58.817 47.619 0.00 0.00 0.00 3.55
501 503 1.213926 TCCTTACCTCCCCTCGTAGTC 59.786 57.143 0.00 0.00 0.00 2.59
545 547 4.495422 TCGTCTTTCAAGTTCCTCATAGC 58.505 43.478 0.00 0.00 0.00 2.97
668 670 7.311092 TCATAACAGTTTTCAAGGGTAGAGA 57.689 36.000 0.00 0.00 0.00 3.10
779 781 8.589338 ACCTGGATAACTTAATATCTGCAGTAG 58.411 37.037 14.67 5.54 33.63 2.57
831 833 6.815142 AGTAACGGTAATAGTGGCAAAAGTAG 59.185 38.462 0.00 0.00 0.00 2.57
832 834 5.156608 ACGGTAATAGTGGCAAAAGTAGT 57.843 39.130 0.00 0.00 0.00 2.73
960 962 4.762289 ATGGTGGGATAGAAGTCAACTC 57.238 45.455 0.00 0.00 0.00 3.01
1305 1308 6.597774 TGCAATCGCCTTGTTGTAAACTCG 62.598 45.833 0.00 0.00 42.62 4.18
1383 1386 3.122948 CAGCTGCAGTTTTTGATGATTGC 59.877 43.478 16.64 0.00 0.00 3.56
1629 1634 5.763204 TGTGGACTTCAGAGTGGTATTTTTC 59.237 40.000 0.00 0.00 35.88 2.29
1630 1635 5.998363 GTGGACTTCAGAGTGGTATTTTTCT 59.002 40.000 0.00 0.00 35.88 2.52
1730 1753 7.236432 AGCACCATATTCTGTTCTATCACCTAT 59.764 37.037 0.00 0.00 0.00 2.57
1731 1754 7.332926 GCACCATATTCTGTTCTATCACCTATG 59.667 40.741 0.00 0.00 0.00 2.23
2086 2125 4.783227 AGGGCAAGATAAAGAAGGTCACTA 59.217 41.667 0.00 0.00 0.00 2.74
2262 2313 9.057089 AGTAAAATATGCTCCGGAAAAATAGAG 57.943 33.333 5.23 0.00 0.00 2.43
2541 2979 5.784750 TTGAGCGTTACATTTCATCTCTG 57.215 39.130 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 164 8.281531 TGAGGGTTATGTTATGGATGAAGAAAT 58.718 33.333 0.00 0.0 0.00 2.17
343 345 2.330440 ATGCGTGATGCTTATGGTGA 57.670 45.000 0.00 0.0 46.63 4.02
346 348 2.145536 TGCTATGCGTGATGCTTATGG 58.854 47.619 0.00 0.0 46.63 2.74
406 408 3.003480 CACCTAAACCTGCTTCTGCTAC 58.997 50.000 0.00 0.0 40.48 3.58
443 445 4.713553 TGCACTTGATTCACCTTCTGTTA 58.286 39.130 0.00 0.0 0.00 2.41
477 479 1.642762 ACGAGGGGAGGTAAGGAACTA 59.357 52.381 0.00 0.0 38.49 2.24
501 503 6.147328 ACGAAAGAACTAAGATTTTTCCCTCG 59.853 38.462 0.00 0.0 33.40 4.63
545 547 6.091849 CACTTGGGATTTATATCTGCTGATCG 59.908 42.308 9.62 0.0 34.32 3.69
647 649 8.215050 TGAATTCTCTACCCTTGAAAACTGTTA 58.785 33.333 7.05 0.0 0.00 2.41
692 694 0.555769 TCTTTGGCTCCCCTTGTGTT 59.444 50.000 0.00 0.0 0.00 3.32
960 962 3.684788 CCTGTAACTTTCCTTCATGGACG 59.315 47.826 0.00 0.0 46.14 4.79
1124 1126 4.005650 TGCACCTTGAAGAAGATCATGAC 58.994 43.478 0.00 0.0 0.00 3.06
1305 1308 4.693283 TGTCGATCACTTCCATGTTATCC 58.307 43.478 0.00 0.0 0.00 2.59
1383 1386 6.515832 AGGAAAATCACAAGCCAAAAAGTAG 58.484 36.000 0.00 0.0 0.00 2.57
1433 1436 1.340991 GGGCCACTCTATTTGCTTCCA 60.341 52.381 4.39 0.0 0.00 3.53
1730 1753 0.040058 ATTGGTGGATGAGCTTGCCA 59.960 50.000 0.00 0.0 0.00 4.92
1731 1754 0.743097 GATTGGTGGATGAGCTTGCC 59.257 55.000 0.00 0.0 0.00 4.52
1919 1955 1.328680 CGATGTCGCTCATTGGAAAGG 59.671 52.381 0.00 0.0 36.83 3.11
2086 2125 0.474660 AGCTCCTTGACCTTGACCCT 60.475 55.000 0.00 0.0 0.00 4.34
2262 2313 1.463444 GTGAACATAGTGCCGAACCAC 59.537 52.381 0.00 0.0 35.98 4.16
2490 2769 7.091443 ACTTTTACCTAAGAGTGAGAACATCG 58.909 38.462 0.00 0.0 30.51 3.84


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

AutoCloner maintained by Alex Coulton.