Multiple sequence alignment - TraesCS5B01G162200

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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 TraesCS5B01G162200 chr5B 100.000 3439 0 0 1 3439 299228719 299225281 0 6351
1 TraesCS5B01G162200 chr5B 95.797 3450 128 10 1 3439 197387107 197390550 0 5552
2 TraesCS5B01G162200 chr4B 96.059 3451 119 9 1 3439 407695548 407692103 0 5603
3 TraesCS5B01G162200 chr4B 95.709 3449 132 9 1 3439 213397338 213400780 0 5535
4 TraesCS5B01G162200 chr2B 96.013 3436 116 16 17 3439 506424421 506420994 0 5566
5 TraesCS5B01G162200 chr2B 95.687 3455 127 15 1 3439 300243649 300240201 0 5535
6 TraesCS5B01G162200 chr2B 95.569 3453 134 15 1 3439 259485623 259482176 0 5511
7 TraesCS5B01G162200 chr7B 95.827 3451 126 12 1 3439 381026456 381023012 0 5559
8 TraesCS5B01G162200 chr7B 95.419 3449 144 11 1 3439 406726490 406729934 0 5481
9 TraesCS5B01G162200 chr1B 95.314 3457 140 19 1 3439 330756297 330759749 0 5467


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 TraesCS5B01G162200 chr5B 299225281 299228719 3438 True 6351 6351 100.000 1 3439 1 chr5B.!!$R1 3438
1 TraesCS5B01G162200 chr5B 197387107 197390550 3443 False 5552 5552 95.797 1 3439 1 chr5B.!!$F1 3438
2 TraesCS5B01G162200 chr4B 407692103 407695548 3445 True 5603 5603 96.059 1 3439 1 chr4B.!!$R1 3438
3 TraesCS5B01G162200 chr4B 213397338 213400780 3442 False 5535 5535 95.709 1 3439 1 chr4B.!!$F1 3438
4 TraesCS5B01G162200 chr2B 506420994 506424421 3427 True 5566 5566 96.013 17 3439 1 chr2B.!!$R3 3422
5 TraesCS5B01G162200 chr2B 300240201 300243649 3448 True 5535 5535 95.687 1 3439 1 chr2B.!!$R2 3438
6 TraesCS5B01G162200 chr2B 259482176 259485623 3447 True 5511 5511 95.569 1 3439 1 chr2B.!!$R1 3438
7 TraesCS5B01G162200 chr7B 381023012 381026456 3444 True 5559 5559 95.827 1 3439 1 chr7B.!!$R1 3438
8 TraesCS5B01G162200 chr7B 406726490 406729934 3444 False 5481 5481 95.419 1 3439 1 chr7B.!!$F1 3438
9 TraesCS5B01G162200 chr1B 330756297 330759749 3452 False 5467 5467 95.314 1 3439 1 chr1B.!!$F1 3438

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
560 569 0.320374 GACCTCCATCAACACCGACA 59.680 55.000 0.0 0.0 0.00 4.35 F
1083 1101 1.216178 CGACATTAACGTCCCCGGT 59.784 57.895 0.0 0.0 38.78 5.28 F
2230 2256 0.872388 CACCCGTTCTACAAAGGCAC 59.128 55.000 0.0 0.0 30.07 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 2050 0.325602 TGTCATGCTGCACCATCTCA 59.674 50.0 3.57 0.0 0.00 3.27 R
2398 2424 0.532115 GGGGCGGTCGTAGAAGTTTA 59.468 55.0 0.00 0.0 39.69 2.01 R
3161 3212 0.459934 CGCTTGCCCTCTCTCTTGAG 60.460 60.0 0.00 0.0 41.51 3.02 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
310 317 4.463891 GTCCCAATTCAGAAACACCATCAT 59.536 41.667 0.00 0.00 0.00 2.45
560 569 0.320374 GACCTCCATCAACACCGACA 59.680 55.000 0.00 0.00 0.00 4.35
687 696 5.133221 GGATTTGGCAGGTCATAAGTACAT 58.867 41.667 0.00 0.00 0.00 2.29
726 735 8.962679 AGTCAGTTCAACAGTAAAAACCATTTA 58.037 29.630 0.00 0.00 0.00 1.40
736 745 7.148035 ACAGTAAAAACCATTTAACTTGGACGT 60.148 33.333 10.00 0.00 37.69 4.34
833 849 1.279558 ACAACACCCACTACACACACA 59.720 47.619 0.00 0.00 0.00 3.72
847 863 2.424302 CACACCCCCGAACGAACT 59.576 61.111 0.00 0.00 0.00 3.01
905 923 2.045047 TCCCATTCTCTTCCACCTCTCT 59.955 50.000 0.00 0.00 0.00 3.10
929 947 1.760029 GTTCCCACAAACCACCATTGT 59.240 47.619 0.00 0.00 41.50 2.71
946 964 2.270352 TGTCGCTTCCATTTCCACTT 57.730 45.000 0.00 0.00 0.00 3.16
979 997 3.864789 AAACTTCTCTCTCCAAAGCCA 57.135 42.857 0.00 0.00 0.00 4.75
1083 1101 1.216178 CGACATTAACGTCCCCGGT 59.784 57.895 0.00 0.00 38.78 5.28
1092 1110 3.692406 GTCCCCGGTGAGAAGCGT 61.692 66.667 0.00 0.00 0.00 5.07
1094 1112 4.003788 CCCCGGTGAGAAGCGTGT 62.004 66.667 0.00 0.00 0.00 4.49
1219 1237 3.272364 ATGAAGCTTGGCGGCAGGA 62.272 57.895 25.57 3.92 34.17 3.86
1336 1356 1.736645 GTGTACCACATCGCAGCGT 60.737 57.895 15.93 0.00 34.08 5.07
1574 1594 7.915293 TGCGGAAGATTAAATTCTGAAGTTA 57.085 32.000 13.92 6.23 35.45 2.24
1753 1777 5.009631 TGGTTCTGTGTTATCCCATTTCAG 58.990 41.667 0.00 0.00 0.00 3.02
1802 1826 4.216042 TGCAGAACATACAACATTGACTGG 59.784 41.667 0.00 0.00 0.00 4.00
2031 2057 1.088340 CAAGCGCCTGACTGAGATGG 61.088 60.000 2.29 0.00 0.00 3.51
2185 2211 3.447944 ACCGGAAAAGAGTATGACTCCTC 59.552 47.826 9.46 0.00 46.18 3.71
2230 2256 0.872388 CACCCGTTCTACAAAGGCAC 59.128 55.000 0.00 0.00 30.07 5.01
2476 2503 2.412455 GCCTTCGTTTTACTTCCGCTTC 60.412 50.000 0.00 0.00 0.00 3.86
2523 2550 9.170584 GTTTCAAATTAGTAGTTTGCTCTTGTC 57.829 33.333 12.08 0.00 36.69 3.18
2688 2716 2.622436 AGTAGCTTCTGAATGGAACGC 58.378 47.619 0.00 0.00 0.00 4.84
2772 2800 4.848562 ACAACTCAGTACACTTGATCGA 57.151 40.909 0.00 0.00 0.00 3.59
2905 2937 4.081142 TGACACCAGAAGACACTTGAGAAA 60.081 41.667 0.00 0.00 0.00 2.52
3132 3183 3.654414 GAATCCCTAGTAATCCGCACAG 58.346 50.000 0.00 0.00 0.00 3.66
3143 3194 4.624364 CGCACAGCACAGGACCCA 62.624 66.667 0.00 0.00 0.00 4.51
3176 3227 0.543883 ACAGCTCAAGAGAGAGGGCA 60.544 55.000 0.32 0.00 44.98 5.36
3208 3259 2.256117 AAGCGCTCAGGTAAGTGTTT 57.744 45.000 12.06 0.00 0.00 2.83
3233 3284 0.540830 AGTTCGACTGGTGAGCCTCT 60.541 55.000 0.00 0.00 35.27 3.69
3263 3314 4.908479 TATAAACAGGTCCGGAGCCCCA 62.908 54.545 29.33 11.35 0.00 4.96
3277 3328 1.227674 CCCCATCGACTAGCAAGGC 60.228 63.158 0.00 0.00 0.00 4.35
3287 3338 1.626825 ACTAGCAAGGCGGGACTAAAA 59.373 47.619 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 3.421826 GCGTTTTGCGTCAGATATATCCG 60.422 47.826 9.18 7.23 43.66 4.18
198 203 7.811117 TGTTTTACTATGCCTTTTGTACTGT 57.189 32.000 0.00 0.00 0.00 3.55
330 337 9.065871 GGATGTATTATATTCGCATTTTGCTTC 57.934 33.333 0.00 0.00 42.25 3.86
560 569 1.523711 CCCACTTGCACGTGTCAGT 60.524 57.895 20.52 15.86 33.07 3.41
687 696 6.127451 TGTTGAACTGACTAGTCTTGTCAAGA 60.127 38.462 23.92 21.63 42.85 3.02
726 735 4.573607 GTGGAAGAACTAAACGTCCAAGTT 59.426 41.667 9.19 9.19 44.44 2.66
736 745 1.141254 TGGTGGCGTGGAAGAACTAAA 59.859 47.619 0.00 0.00 0.00 1.85
775 784 0.465460 GCAGTCCCTTGTGTCAACCA 60.465 55.000 0.00 0.00 0.00 3.67
833 849 4.324991 GGCAGTTCGTTCGGGGGT 62.325 66.667 0.00 0.00 0.00 4.95
847 863 2.770130 GGGGATTTGTGGGAGGCA 59.230 61.111 0.00 0.00 0.00 4.75
905 923 0.179040 GGTGGTTTGTGGGAACGAGA 60.179 55.000 0.00 0.00 0.00 4.04
929 947 2.151202 GTGAAGTGGAAATGGAAGCGA 58.849 47.619 0.00 0.00 0.00 4.93
946 964 5.710099 AGAGAGAAGTTTTTGGTTTGTGTGA 59.290 36.000 0.00 0.00 0.00 3.58
979 997 1.674057 CCTTCCTCTGGCGACTGTT 59.326 57.895 0.00 0.00 0.00 3.16
1092 1110 3.351794 TTGAGGGTTGTTGTGTACACA 57.648 42.857 24.62 24.62 36.21 3.72
1094 1112 3.283751 CCTTTGAGGGTTGTTGTGTACA 58.716 45.455 0.00 0.00 34.12 2.90
1219 1237 1.281960 CGCCGACGATCCTACGAAT 59.718 57.895 0.00 0.00 43.93 3.34
1410 1430 6.222389 TGGGAAAGCAAGTGTGATTAATTTG 58.778 36.000 0.00 0.00 30.32 2.32
1574 1594 7.216973 ACTTCAGAAACTACACTAGTCGATT 57.783 36.000 0.00 0.00 38.26 3.34
1753 1777 8.782339 TTGGTACTAGTTTAGTCTATTTTGGC 57.218 34.615 0.00 0.00 40.14 4.52
2024 2050 0.325602 TGTCATGCTGCACCATCTCA 59.674 50.000 3.57 0.00 0.00 3.27
2031 2057 2.223548 TGAACAACTTGTCATGCTGCAC 60.224 45.455 3.57 0.00 0.00 4.57
2185 2211 1.792301 CTGGCTGCAACATCAGTCG 59.208 57.895 0.50 0.00 41.36 4.18
2216 2242 3.558418 TGTTCTTCGTGCCTTTGTAGAAC 59.442 43.478 0.00 0.00 40.96 3.01
2230 2256 2.220824 TGCGTGTTGATCTTGTTCTTCG 59.779 45.455 0.00 0.00 0.00 3.79
2398 2424 0.532115 GGGGCGGTCGTAGAAGTTTA 59.468 55.000 0.00 0.00 39.69 2.01
2476 2503 4.874970 ACAACAAGATAAAAGGCAAGCAG 58.125 39.130 0.00 0.00 0.00 4.24
2523 2550 1.604604 AATCACACTGGTTCAACCCG 58.395 50.000 3.42 0.00 37.50 5.28
2626 2653 6.399743 TGGATTAACAACATACGAAGCTACA 58.600 36.000 0.00 0.00 0.00 2.74
2688 2716 5.940595 ACTAGTACTTTAGAGCAACGACAG 58.059 41.667 0.00 0.00 0.00 3.51
3132 3183 4.699522 GGTCGGTGGGTCCTGTGC 62.700 72.222 0.00 0.00 0.00 4.57
3161 3212 0.459934 CGCTTGCCCTCTCTCTTGAG 60.460 60.000 0.00 0.00 41.51 3.02
3176 3227 3.700961 CGCTTATACACGGCGCTT 58.299 55.556 6.90 0.00 42.28 4.68
3208 3259 2.712709 CTCACCAGTCGAACTCCTCTA 58.287 52.381 0.00 0.00 0.00 2.43
3233 3284 3.343617 GGACCTGTTTATAAGTGCAGCA 58.656 45.455 0.00 0.00 0.00 4.41
3263 3314 1.756950 TCCCGCCTTGCTAGTCGAT 60.757 57.895 0.00 0.00 0.00 3.59
3277 3328 1.359459 GCGCTCTGGTTTTAGTCCCG 61.359 60.000 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.