Multiple sequence alignment - TraesCS4D01G264800

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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 TraesCS4D01G264800 chr4D 100.000 2477 0 0 1 2477 435102730 435100254 0.000000e+00 4575.0
1 TraesCS4D01G264800 chr4D 94.643 168 9 0 2304 2471 435101718 435101551 6.790000e-66 261.0
2 TraesCS4D01G264800 chr3B 94.652 2431 127 3 48 2477 710715326 710717754 0.000000e+00 3766.0
3 TraesCS4D01G264800 chr3B 74.672 229 37 18 1759 1979 754019134 754018919 5.680000e-12 82.4
4 TraesCS4D01G264800 chr5A 94.189 2461 115 18 21 2477 512718484 512720920 0.000000e+00 3727.0
5 TraesCS4D01G264800 chr5A 89.741 926 84 8 21 942 144653620 144654538 0.000000e+00 1173.0
6 TraesCS4D01G264800 chr5A 93.491 169 11 0 2303 2471 512719455 512719623 4.090000e-63 252.0
7 TraesCS4D01G264800 chr1D 95.696 1673 69 3 21 1691 54464811 54466482 0.000000e+00 2687.0
8 TraesCS4D01G264800 chr1D 94.178 876 40 8 21 893 308928769 308929636 0.000000e+00 1325.0
9 TraesCS4D01G264800 chr1D 94.048 168 10 0 2304 2471 54465804 54465971 3.160000e-64 255.0
10 TraesCS4D01G264800 chr7D 89.935 1391 105 19 937 2307 42809930 42811305 0.000000e+00 1760.0
11 TraesCS4D01G264800 chr7D 97.619 168 4 0 2304 2471 42810007 42810174 3.120000e-74 289.0
12 TraesCS4D01G264800 chr7A 92.781 1219 61 5 21 1236 601864742 601863548 0.000000e+00 1738.0
13 TraesCS4D01G264800 chr7A 87.380 1149 85 28 937 2045 42497647 42498775 0.000000e+00 1264.0
14 TraesCS4D01G264800 chr7A 91.776 608 28 14 886 1492 79797806 79798392 0.000000e+00 826.0
15 TraesCS4D01G264800 chr7A 91.776 608 28 14 886 1492 669447037 669446451 0.000000e+00 826.0
16 TraesCS4D01G264800 chr7A 91.279 172 12 1 2135 2303 42498785 42498956 5.330000e-57 231.0
17 TraesCS4D01G264800 chr7A 91.071 168 15 0 2304 2471 601863772 601863605 6.890000e-56 228.0
18 TraesCS4D01G264800 chr4A 92.308 1222 64 11 21 1236 418429592 418428395 0.000000e+00 1709.0
19 TraesCS4D01G264800 chr4A 93.165 673 24 9 937 1596 650367936 650368599 0.000000e+00 968.0
20 TraesCS4D01G264800 chr7B 92.429 1202 74 11 23 1210 725211134 725212332 0.000000e+00 1700.0
21 TraesCS4D01G264800 chr7B 92.857 168 12 0 2304 2471 725212135 725212302 6.840000e-61 244.0
22 TraesCS4D01G264800 chr2D 85.543 1418 129 37 937 2307 21142989 21141601 0.000000e+00 1413.0
23 TraesCS4D01G264800 chr6A 89.860 927 85 8 21 942 24637876 24638798 0.000000e+00 1182.0
24 TraesCS4D01G264800 chr6A 91.776 608 28 14 886 1492 357869881 357870467 0.000000e+00 826.0
25 TraesCS4D01G264800 chr3A 89.145 608 43 15 886 1492 704176037 704175452 0.000000e+00 736.0
26 TraesCS4D01G264800 chr3A 92.754 483 23 1 2001 2471 401132196 401132678 0.000000e+00 688.0
27 TraesCS4D01G264800 chr6B 88.024 167 18 2 1651 1816 35452820 35452655 1.940000e-46 196.0
28 TraesCS4D01G264800 chr2B 78.205 312 51 13 1651 1957 588847725 588848024 1.510000e-42 183.0
29 TraesCS4D01G264800 chr2A 92.241 116 6 3 2354 2468 40751440 40751553 7.090000e-36 161.0
30 TraesCS4D01G264800 chr5B 91.379 58 5 0 1759 1816 45134413 45134356 2.040000e-11 80.5


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 TraesCS4D01G264800 chr4D 435100254 435102730 2476 True 2418.0 4575 97.3215 1 2477 2 chr4D.!!$R1 2476
1 TraesCS4D01G264800 chr3B 710715326 710717754 2428 False 3766.0 3766 94.6520 48 2477 1 chr3B.!!$F1 2429
2 TraesCS4D01G264800 chr5A 512718484 512720920 2436 False 1989.5 3727 93.8400 21 2477 2 chr5A.!!$F2 2456
3 TraesCS4D01G264800 chr5A 144653620 144654538 918 False 1173.0 1173 89.7410 21 942 1 chr5A.!!$F1 921
4 TraesCS4D01G264800 chr1D 54464811 54466482 1671 False 1471.0 2687 94.8720 21 2471 2 chr1D.!!$F2 2450
5 TraesCS4D01G264800 chr1D 308928769 308929636 867 False 1325.0 1325 94.1780 21 893 1 chr1D.!!$F1 872
6 TraesCS4D01G264800 chr7D 42809930 42811305 1375 False 1024.5 1760 93.7770 937 2471 2 chr7D.!!$F1 1534
7 TraesCS4D01G264800 chr7A 601863548 601864742 1194 True 983.0 1738 91.9260 21 2471 2 chr7A.!!$R2 2450
8 TraesCS4D01G264800 chr7A 79797806 79798392 586 False 826.0 826 91.7760 886 1492 1 chr7A.!!$F1 606
9 TraesCS4D01G264800 chr7A 669446451 669447037 586 True 826.0 826 91.7760 886 1492 1 chr7A.!!$R1 606
10 TraesCS4D01G264800 chr7A 42497647 42498956 1309 False 747.5 1264 89.3295 937 2303 2 chr7A.!!$F2 1366
11 TraesCS4D01G264800 chr4A 418428395 418429592 1197 True 1709.0 1709 92.3080 21 1236 1 chr4A.!!$R1 1215
12 TraesCS4D01G264800 chr4A 650367936 650368599 663 False 968.0 968 93.1650 937 1596 1 chr4A.!!$F1 659
13 TraesCS4D01G264800 chr7B 725211134 725212332 1198 False 972.0 1700 92.6430 23 2471 2 chr7B.!!$F1 2448
14 TraesCS4D01G264800 chr2D 21141601 21142989 1388 True 1413.0 1413 85.5430 937 2307 1 chr2D.!!$R1 1370
15 TraesCS4D01G264800 chr6A 24637876 24638798 922 False 1182.0 1182 89.8600 21 942 1 chr6A.!!$F1 921
16 TraesCS4D01G264800 chr6A 357869881 357870467 586 False 826.0 826 91.7760 886 1492 1 chr6A.!!$F2 606
17 TraesCS4D01G264800 chr3A 704175452 704176037 585 True 736.0 736 89.1450 886 1492 1 chr3A.!!$R1 606

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
807 818 1.604308 CATCCAACCCACTGCAGCA 60.604 57.895 15.27 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2092 2248 2.95566 ACGAAACCTGAAGCATTTCCAA 59.044 40.909 0.0 0.0 32.09 3.53 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
231 234 4.851639 AGCTAGTGGTTGAATCTTGGAT 57.148 40.909 0.00 0.00 0.00 3.41
320 325 5.559148 AGAGCAAACTATAAGGCAGCTAT 57.441 39.130 0.00 0.00 0.00 2.97
387 392 3.319137 TTTTCACGAGAGGTGGATCAG 57.681 47.619 0.00 0.00 46.96 2.90
443 449 9.800572 TGTGCATTAAATATGGCCTAGTATTTA 57.199 29.630 17.23 17.23 33.75 1.40
492 499 8.410673 TGCAACAATTATTTGGTAGGTTCTTA 57.589 30.769 2.66 0.00 37.15 2.10
547 557 4.202131 TGGAAAACGGGTATTTTGTGGAAC 60.202 41.667 0.00 0.00 31.90 3.62
779 790 1.774254 TCCATCCACCCATACATCCAC 59.226 52.381 0.00 0.00 0.00 4.02
807 818 1.604308 CATCCAACCCACTGCAGCA 60.604 57.895 15.27 0.00 0.00 4.41
818 835 2.364647 CCACTGCAGCATATCTCTCTCA 59.635 50.000 15.27 0.00 0.00 3.27
841 858 4.752879 GCGCGTGAACCCTAGCCA 62.753 66.667 8.43 0.00 0.00 4.75
1112 1198 2.824041 GCCATGGCCATCGACGTT 60.824 61.111 27.24 0.00 34.56 3.99
1343 1431 1.218047 CCTCCCTCGAAACGATGCA 59.782 57.895 0.00 0.00 34.61 3.96
1732 1870 7.126421 AGTTCATGGTCAGACCTTATTCAGTAT 59.874 37.037 20.82 0.00 39.58 2.12
2092 2248 7.224297 TGTAGAATGGAAAGTAGCTCAAAAGT 58.776 34.615 0.00 0.00 0.00 2.66
2150 2307 9.167311 GTCTGTAGAATGGACATTTTAATCTGT 57.833 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.891361 TGGAGAAAGCCAAATGATCAATCTTA 59.109 34.615 0.00 0.00 34.31 2.10
1 2 5.718130 TGGAGAAAGCCAAATGATCAATCTT 59.282 36.000 0.00 0.00 34.31 2.40
2 3 5.126707 GTGGAGAAAGCCAAATGATCAATCT 59.873 40.000 0.00 0.00 40.20 2.40
3 4 5.105635 TGTGGAGAAAGCCAAATGATCAATC 60.106 40.000 0.00 0.00 40.20 2.67
4 5 4.773674 TGTGGAGAAAGCCAAATGATCAAT 59.226 37.500 0.00 0.00 40.20 2.57
5 6 4.022068 GTGTGGAGAAAGCCAAATGATCAA 60.022 41.667 0.00 0.00 40.20 2.57
6 7 3.507233 GTGTGGAGAAAGCCAAATGATCA 59.493 43.478 0.00 0.00 40.20 2.92
7 8 3.426695 CGTGTGGAGAAAGCCAAATGATC 60.427 47.826 0.00 0.00 40.20 2.92
8 9 2.489329 CGTGTGGAGAAAGCCAAATGAT 59.511 45.455 0.00 0.00 40.20 2.45
9 10 1.879380 CGTGTGGAGAAAGCCAAATGA 59.121 47.619 0.00 0.00 40.20 2.57
10 11 1.608590 ACGTGTGGAGAAAGCCAAATG 59.391 47.619 0.00 0.00 40.20 2.32
11 12 1.608590 CACGTGTGGAGAAAGCCAAAT 59.391 47.619 7.58 0.00 40.20 2.32
12 13 1.021202 CACGTGTGGAGAAAGCCAAA 58.979 50.000 7.58 0.00 40.20 3.28
13 14 0.179234 TCACGTGTGGAGAAAGCCAA 59.821 50.000 16.51 0.00 40.20 4.52
14 15 0.396435 ATCACGTGTGGAGAAAGCCA 59.604 50.000 16.51 0.00 35.02 4.75
15 16 2.271800 CTATCACGTGTGGAGAAAGCC 58.728 52.381 16.51 0.00 0.00 4.35
16 17 1.661112 GCTATCACGTGTGGAGAAAGC 59.339 52.381 16.51 10.78 0.00 3.51
17 18 3.182967 GAGCTATCACGTGTGGAGAAAG 58.817 50.000 16.51 5.03 0.00 2.62
18 19 2.415491 CGAGCTATCACGTGTGGAGAAA 60.415 50.000 16.51 0.00 0.00 2.52
19 20 1.132453 CGAGCTATCACGTGTGGAGAA 59.868 52.381 16.51 0.00 0.00 2.87
90 91 2.524306 TGTGGCCAAGTTCCCATAAAG 58.476 47.619 7.24 0.00 32.95 1.85
93 94 5.654901 TTATATGTGGCCAAGTTCCCATA 57.345 39.130 7.24 10.68 32.95 2.74
94 95 4.534647 TTATATGTGGCCAAGTTCCCAT 57.465 40.909 7.24 8.42 32.95 4.00
320 325 3.504520 GGAAGCGGGTCAAATTTGAACTA 59.495 43.478 30.02 4.78 44.25 2.24
387 392 6.597262 CAAATGGTTGGGTGTAAAAAGTTC 57.403 37.500 0.00 0.00 0.00 3.01
547 557 4.458989 TGATCTGGGGAGTTTTCATTTTCG 59.541 41.667 0.00 0.00 0.00 3.46
642 653 9.868277 TTTATTTAGGGCAAACATTCAACATAG 57.132 29.630 0.00 0.00 0.00 2.23
698 709 3.002656 CGGATTCCACCAATCAGAATTCG 59.997 47.826 3.09 0.00 42.69 3.34
779 790 1.152963 GGTTGGATGGACGGATGGG 60.153 63.158 0.00 0.00 0.00 4.00
807 818 1.268794 GCGCGTGTGTGAGAGAGATAT 60.269 52.381 8.43 0.00 0.00 1.63
841 858 2.150051 GCGGGGAGGGATCTGGATT 61.150 63.158 0.00 0.00 0.00 3.01
1288 1374 1.137825 GGTCGTTGGAGAGCTCGAG 59.862 63.158 8.45 8.45 35.89 4.04
1474 1582 2.089980 GCTCCTGACGTACTTGGTCTA 58.910 52.381 0.00 0.00 35.45 2.59
1732 1870 6.942976 AGTAGTAACAAATACTAGCAGGCAA 58.057 36.000 0.00 0.00 45.51 4.52
2092 2248 2.955660 ACGAAACCTGAAGCATTTCCAA 59.044 40.909 0.00 0.00 32.09 3.53


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

AutoCloner maintained by Alex Coulton.