Multiple sequence alignment - TraesCS4B01G332200

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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 TraesCS4B01G332200 chr4B 100.000 2648 0 0 1 2648 622503280 622500633 0.000000e+00 4891
1 TraesCS4B01G332200 chr6B 96.886 2248 66 4 404 2648 717730829 717733075 0.000000e+00 3760
2 TraesCS4B01G332200 chr6B 95.860 2029 78 5 1 2026 147950687 147948662 0.000000e+00 3277
3 TraesCS4B01G332200 chr6B 90.391 2227 195 18 1 2221 567118187 567115974 0.000000e+00 2909
4 TraesCS4B01G332200 chr3D 91.714 2655 205 14 1 2648 558679303 558681949 0.000000e+00 3670
5 TraesCS4B01G332200 chr2B 91.262 2655 193 25 1 2648 664330484 664327862 0.000000e+00 3581
6 TraesCS4B01G332200 chr2B 94.725 1839 69 3 812 2648 225324993 225323181 0.000000e+00 2833
7 TraesCS4B01G332200 chr5B 91.036 2655 198 29 1 2648 529280456 529283077 0.000000e+00 3548
8 TraesCS4B01G332200 chr5B 96.530 1729 56 2 1 1728 659536140 659537865 0.000000e+00 2857
9 TraesCS4B01G332200 chr5B 92.898 352 22 1 2300 2648 575025523 575025172 2.350000e-140 508
10 TraesCS4B01G332200 chr5D 90.356 2302 160 35 1 2286 387241779 387244034 0.000000e+00 2964
11 TraesCS4B01G332200 chr7B 94.358 1808 89 8 1 1805 36428066 36426269 0.000000e+00 2761
12 TraesCS4B01G332200 chr7B 88.470 2151 224 15 1 2138 636041722 636039583 0.000000e+00 2577
13 TraesCS4B01G332200 chr7B 83.042 914 129 19 1747 2648 316357632 316356733 0.000000e+00 806
14 TraesCS4B01G332200 chr1B 93.395 1847 83 10 812 2648 359219908 359218091 0.000000e+00 2699
15 TraesCS4B01G332200 chr4D 87.440 828 81 14 1836 2648 473876316 473875497 0.000000e+00 931


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 TraesCS4B01G332200 chr4B 622500633 622503280 2647 True 4891 4891 100.000 1 2648 1 chr4B.!!$R1 2647
1 TraesCS4B01G332200 chr6B 717730829 717733075 2246 False 3760 3760 96.886 404 2648 1 chr6B.!!$F1 2244
2 TraesCS4B01G332200 chr6B 147948662 147950687 2025 True 3277 3277 95.860 1 2026 1 chr6B.!!$R1 2025
3 TraesCS4B01G332200 chr6B 567115974 567118187 2213 True 2909 2909 90.391 1 2221 1 chr6B.!!$R2 2220
4 TraesCS4B01G332200 chr3D 558679303 558681949 2646 False 3670 3670 91.714 1 2648 1 chr3D.!!$F1 2647
5 TraesCS4B01G332200 chr2B 664327862 664330484 2622 True 3581 3581 91.262 1 2648 1 chr2B.!!$R2 2647
6 TraesCS4B01G332200 chr2B 225323181 225324993 1812 True 2833 2833 94.725 812 2648 1 chr2B.!!$R1 1836
7 TraesCS4B01G332200 chr5B 529280456 529283077 2621 False 3548 3548 91.036 1 2648 1 chr5B.!!$F1 2647
8 TraesCS4B01G332200 chr5B 659536140 659537865 1725 False 2857 2857 96.530 1 1728 1 chr5B.!!$F2 1727
9 TraesCS4B01G332200 chr5D 387241779 387244034 2255 False 2964 2964 90.356 1 2286 1 chr5D.!!$F1 2285
10 TraesCS4B01G332200 chr7B 36426269 36428066 1797 True 2761 2761 94.358 1 1805 1 chr7B.!!$R1 1804
11 TraesCS4B01G332200 chr7B 636039583 636041722 2139 True 2577 2577 88.470 1 2138 1 chr7B.!!$R3 2137
12 TraesCS4B01G332200 chr7B 316356733 316357632 899 True 806 806 83.042 1747 2648 1 chr7B.!!$R2 901
13 TraesCS4B01G332200 chr1B 359218091 359219908 1817 True 2699 2699 93.395 812 2648 1 chr1B.!!$R1 1836
14 TraesCS4B01G332200 chr4D 473875497 473876316 819 True 931 931 87.440 1836 2648 1 chr4D.!!$R1 812

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
718 719 0.492276 AGGAGGTAGGACTGGTGGTT 59.508 55.000 0.0 0.0 0.0 3.67 F
1534 1544 1.302511 GGGCACGCAAAGAGAAGGA 60.303 57.895 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1585 1.351076 TCCTCCTCTTGTGCATCACA 58.649 50.000 0.0 0.0 43.02 3.58 R
2528 2593 1.626825 AGCAGGTTAGGGCGTCTTTTA 59.373 47.619 0.0 0.0 34.54 1.52 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
92 93 5.384336 TGATGATTGGTTGAGGTTTCAAGA 58.616 37.500 0.00 0.00 43.66 3.02
99 100 3.958147 GGTTGAGGTTTCAAGAAGGGAAA 59.042 43.478 0.00 0.00 43.66 3.13
148 149 7.722795 TTCAACGACAAAGAAATGATCTACA 57.277 32.000 0.00 0.00 37.42 2.74
204 205 1.957186 GGCTTACGACGGTGTTGCA 60.957 57.895 0.00 0.00 0.00 4.08
376 377 2.047274 CGAGGTTGACATGGGCGT 60.047 61.111 0.00 0.00 0.00 5.68
473 474 2.311542 TCATGGTGCCTACAAAGGGAAT 59.688 45.455 0.00 0.00 46.04 3.01
659 660 1.536922 CGATGCCAACACGAGCTCTAT 60.537 52.381 12.85 0.00 0.00 1.98
718 719 0.492276 AGGAGGTAGGACTGGTGGTT 59.508 55.000 0.00 0.00 0.00 3.67
1055 1059 1.338011 TGCTGATCGTGAAGACATGCA 60.338 47.619 0.00 0.00 33.49 3.96
1182 1187 1.938585 AGAAGTCATGGACGGAAGGA 58.061 50.000 0.00 0.00 37.67 3.36
1232 1237 1.492176 ACATGATCGGAGGCTTCCAAT 59.508 47.619 16.07 0.70 44.26 3.16
1420 1430 9.753674 AAAGGACCAATATCAAGATTGTCTTAA 57.246 29.630 0.00 0.00 33.78 1.85
1534 1544 1.302511 GGGCACGCAAAGAGAAGGA 60.303 57.895 0.00 0.00 0.00 3.36
1599 1610 1.942776 TGCACAAGAGGAGGATGAGA 58.057 50.000 0.00 0.00 0.00 3.27
1886 1899 6.265577 ACTTGTTGTCTAACATGTTGCTTTC 58.734 36.000 21.42 7.73 46.73 2.62
1891 1904 6.691754 TGTCTAACATGTTGCTTTCTTTCA 57.308 33.333 21.42 4.80 0.00 2.69
2528 2593 0.400093 AGGAGCCCCTAATAAGCCGT 60.400 55.000 0.00 0.00 42.15 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.347062 ATCCATTTGGCGGTGGTTTT 58.653 45.000 3.10 0.00 36.84 2.43
99 100 8.991783 ATCTAATGATTTGTTGATGTGAGGAT 57.008 30.769 0.00 0.00 0.00 3.24
148 149 0.535102 CAACCTGGCTCGTCCACTTT 60.535 55.000 0.00 0.00 40.72 2.66
166 167 1.880796 CACCGTCTCGTGTTGTGCA 60.881 57.895 0.00 0.00 0.00 4.57
233 234 3.147826 TGAGGCCTCTCACACTGAA 57.852 52.632 32.28 6.94 44.39 3.02
303 304 3.459227 TCCTCCCATCAGAAACATGCATA 59.541 43.478 0.00 0.00 0.00 3.14
304 305 2.242965 TCCTCCCATCAGAAACATGCAT 59.757 45.455 0.00 0.00 0.00 3.96
376 377 5.178797 GTCAAGGAAAGGATGAAATCGAGA 58.821 41.667 0.00 0.00 46.86 4.04
473 474 8.368668 CACTCCTAAACCTCTTCTTTCTTCTTA 58.631 37.037 0.00 0.00 0.00 2.10
659 660 5.366768 CCTCCTCTATGAACACCTATTTGGA 59.633 44.000 0.00 0.00 39.71 3.53
698 699 0.492276 ACCACCAGTCCTACCTCCTT 59.508 55.000 0.00 0.00 0.00 3.36
718 719 0.697079 AGACTAGTCCGTCCTCCACA 59.303 55.000 19.38 0.00 34.46 4.17
857 858 2.890945 AGCAAAACGTCAATAGGCCTTT 59.109 40.909 12.58 0.00 0.00 3.11
1055 1059 1.425066 TGGCATTCTCCCACTTGTTCT 59.575 47.619 0.00 0.00 0.00 3.01
1182 1187 5.067805 GTTGGGACACACAAAGAATCTTCTT 59.932 40.000 0.00 0.00 44.40 2.52
1232 1237 2.159254 GGTGGTACGTCATAGGCGTTTA 60.159 50.000 0.86 0.00 42.85 2.01
1315 1324 5.221048 GCGGTGACTGCATAGGATAAATTTT 60.221 40.000 12.26 0.00 0.00 1.82
1316 1325 4.275936 GCGGTGACTGCATAGGATAAATTT 59.724 41.667 12.26 0.00 0.00 1.82
1317 1326 3.815401 GCGGTGACTGCATAGGATAAATT 59.185 43.478 12.26 0.00 0.00 1.82
1318 1327 3.403038 GCGGTGACTGCATAGGATAAAT 58.597 45.455 12.26 0.00 0.00 1.40
1420 1430 2.951475 TTCAAACCGCCGTTGCCTCT 62.951 55.000 0.00 0.00 30.72 3.69
1575 1585 1.351076 TCCTCCTCTTGTGCATCACA 58.649 50.000 0.00 0.00 43.02 3.58
1599 1610 2.335316 TTGCCCTTCTTGTAACGTGT 57.665 45.000 0.00 0.00 0.00 4.49
1891 1904 6.485648 GCGGTAGGGTTCAAATATCTACAAAT 59.514 38.462 0.00 0.00 33.86 2.32
2099 2124 3.026879 CAGGCGCGCGAGTATCAG 61.027 66.667 37.18 11.21 33.17 2.90
2155 2204 2.033602 GCCTGTGGCGGTAAGGTT 59.966 61.111 0.00 0.00 39.62 3.50
2375 2440 5.095490 CGGGTGTTGCTTCTTATTTCATTC 58.905 41.667 0.00 0.00 0.00 2.67
2528 2593 1.626825 AGCAGGTTAGGGCGTCTTTTA 59.373 47.619 0.00 0.00 34.54 1.52


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

AutoCloner maintained by Alex Coulton.