Multiple sequence alignment - TraesCS4A01G194200

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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 TraesCS4A01G194200 chr4A 100.000 2561 0 0 1 2561 476067397 476064837 0.000000e+00 4730.0
1 TraesCS4A01G194200 chr4D 94.542 2565 115 13 1 2558 100482098 100484644 0.000000e+00 3938.0
2 TraesCS4A01G194200 chr4B 93.435 2559 137 18 1 2550 142696676 142699212 0.000000e+00 3766.0
3 TraesCS4A01G194200 chr5A 78.431 153 21 12 2256 2402 47139563 47139417 3.510000e-14 89.8


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 TraesCS4A01G194200 chr4A 476064837 476067397 2560 True 4730 4730 100.000 1 2561 1 chr4A.!!$R1 2560
1 TraesCS4A01G194200 chr4D 100482098 100484644 2546 False 3938 3938 94.542 1 2558 1 chr4D.!!$F1 2557
2 TraesCS4A01G194200 chr4B 142696676 142699212 2536 False 3766 3766 93.435 1 2550 1 chr4B.!!$F1 2549

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
400 402 0.110295 CTGGGTGATTGGACCACACA 59.89 55.0 15.12 6.62 44.75 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2237 2253 0.252696 AGGCCTATCAGTGGTGACCA 60.253 55.0 1.29 0.0 34.75 4.02 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
23 24 2.679837 CAAAATGATGCTCGGTACAGCT 59.320 45.455 6.73 0.00 40.39 4.24
41 42 8.186163 GGTACAGCTAAATTATGTGGGTAAAAC 58.814 37.037 0.00 0.00 0.00 2.43
63 64 6.893958 ACGATAAGTGCTCAATTTCACTAG 57.106 37.500 5.50 0.00 42.19 2.57
68 69 8.798859 ATAAGTGCTCAATTTCACTAGTCAAT 57.201 30.769 0.00 0.00 42.19 2.57
74 75 7.013178 TGCTCAATTTCACTAGTCAATTGAACA 59.987 33.333 25.93 24.93 43.15 3.18
120 121 3.371034 TCGGATGGTTAGGATCTTGTGA 58.629 45.455 0.00 0.00 0.00 3.58
122 123 3.118775 CGGATGGTTAGGATCTTGTGACA 60.119 47.826 0.00 0.00 0.00 3.58
166 168 1.595382 GGCTTGACACTGTGCTCGT 60.595 57.895 7.90 0.00 0.00 4.18
230 232 8.743085 ATTTAGTGACAGATGACATTATTGCT 57.257 30.769 0.00 0.00 0.00 3.91
233 235 5.583854 AGTGACAGATGACATTATTGCTGAC 59.416 40.000 7.80 3.31 0.00 3.51
240 242 9.702494 CAGATGACATTATTGCTGACTATAAGA 57.298 33.333 0.00 0.00 29.09 2.10
249 251 9.817809 TTATTGCTGACTATAAGACCTTTGTAG 57.182 33.333 0.00 0.00 0.00 2.74
379 381 5.796935 CCAAGTTGTTTCACGATGATCAATC 59.203 40.000 0.00 0.00 0.00 2.67
400 402 0.110295 CTGGGTGATTGGACCACACA 59.890 55.000 15.12 6.62 44.75 3.72
401 403 0.179004 TGGGTGATTGGACCACACAC 60.179 55.000 15.12 16.19 42.40 3.82
441 443 1.004440 GGGCTTTCGCTCTCTGTGT 60.004 57.895 0.00 0.00 32.44 3.72
442 444 1.294659 GGGCTTTCGCTCTCTGTGTG 61.295 60.000 0.00 0.00 32.44 3.82
443 445 1.495069 GCTTTCGCTCTCTGTGTGC 59.505 57.895 0.00 0.00 0.00 4.57
444 446 1.905922 GCTTTCGCTCTCTGTGTGCC 61.906 60.000 0.00 0.00 32.04 5.01
445 447 1.621301 CTTTCGCTCTCTGTGTGCCG 61.621 60.000 0.00 0.00 32.04 5.69
446 448 2.082629 TTTCGCTCTCTGTGTGCCGA 62.083 55.000 0.00 0.00 32.04 5.54
469 471 3.801114 TGTAGACATCATCAAGGTCCG 57.199 47.619 0.00 0.00 31.99 4.79
486 488 2.166664 GTCCGAATAGCTGTTGGACTCT 59.833 50.000 24.31 0.00 44.47 3.24
512 514 1.621992 TCAGCCGAGATATGAGACCC 58.378 55.000 0.00 0.00 0.00 4.46
516 518 1.319541 CCGAGATATGAGACCCACGT 58.680 55.000 0.00 0.00 0.00 4.49
730 734 5.347620 TTCCTAAATTTGCCGACTAGCTA 57.652 39.130 0.00 0.00 0.00 3.32
820 824 1.398451 GCACACACGAATACACACAGC 60.398 52.381 0.00 0.00 0.00 4.40
821 825 2.135139 CACACACGAATACACACAGCT 58.865 47.619 0.00 0.00 0.00 4.24
822 826 2.543848 CACACACGAATACACACAGCTT 59.456 45.455 0.00 0.00 0.00 3.74
823 827 3.002246 CACACACGAATACACACAGCTTT 59.998 43.478 0.00 0.00 0.00 3.51
824 828 3.247648 ACACACGAATACACACAGCTTTC 59.752 43.478 0.00 0.00 0.00 2.62
825 829 2.475111 ACACGAATACACACAGCTTTCG 59.525 45.455 11.75 11.75 43.43 3.46
921 931 3.059868 CGATCATATCCCGAACCAAAACG 60.060 47.826 0.00 0.00 0.00 3.60
939 949 2.979240 ACGCTCTCTTGATTTCTTCCC 58.021 47.619 0.00 0.00 0.00 3.97
1137 1149 1.679680 GCCAACATGGTGATCATCCTG 59.320 52.381 13.74 9.46 40.46 3.86
1170 1182 0.452784 GCGTTCTCATTTTCGCGCTT 60.453 50.000 5.56 0.00 41.37 4.68
1338 1350 3.376078 GTGGAGGTGTACGGCGGA 61.376 66.667 13.24 0.00 0.00 5.54
1422 1434 3.818787 GCCGACGGCGAGAAGGTA 61.819 66.667 25.24 0.00 39.62 3.08
1596 1608 6.875726 GGTACGGGTTTGTAATTTCTTCTAGT 59.124 38.462 0.00 0.00 0.00 2.57
1624 1638 2.031191 ACTAAAGTGAAACGTTGCACCG 59.969 45.455 31.40 20.53 45.86 4.94
1989 2004 6.477033 CGTTGCTGAACAGATATTAGTAGCTT 59.523 38.462 5.97 0.00 31.78 3.74
1990 2005 7.010552 CGTTGCTGAACAGATATTAGTAGCTTT 59.989 37.037 5.97 0.00 31.78 3.51
1991 2006 9.314321 GTTGCTGAACAGATATTAGTAGCTTTA 57.686 33.333 5.97 0.00 31.78 1.85
2147 2163 7.517614 TGTGTTCAAAGCATGGTATTTCTAA 57.482 32.000 0.00 0.00 0.00 2.10
2152 2168 7.624360 TCAAAGCATGGTATTTCTAACGAAT 57.376 32.000 0.00 0.00 0.00 3.34
2211 2227 5.134661 AGTATACCTTCTCTAGCTGGTCAC 58.865 45.833 0.00 0.00 34.33 3.67
2234 2250 7.668469 TCACCGCCAATAAGTATATCTTCTCTA 59.332 37.037 0.00 0.00 37.56 2.43
2237 2253 7.147983 CCGCCAATAAGTATATCTTCTCTAGCT 60.148 40.741 0.00 0.00 37.56 3.32
2262 2278 2.103263 CACCACTGATAGGCCTTAGACC 59.897 54.545 12.58 0.00 0.00 3.85
2279 2295 6.070767 CCTTAGACCAACTCCAACAGATCTTA 60.071 42.308 0.00 0.00 0.00 2.10
2311 2327 6.930722 CCTTTTCATAAAAGTGCTTTCATGGT 59.069 34.615 7.68 0.00 44.96 3.55
2316 2332 8.523915 TCATAAAAGTGCTTTCATGGTATGAT 57.476 30.769 7.68 0.00 39.39 2.45
2318 2334 5.490139 AAAGTGCTTTCATGGTATGATCG 57.510 39.130 0.00 0.00 39.39 3.69
2342 2358 5.649557 CATAATTTGCCGGAATTGTCAGAA 58.350 37.500 5.05 0.00 31.96 3.02
2369 2385 6.148976 GCTACTTTTCTCAGTTCCCGTAAAAT 59.851 38.462 0.00 0.00 0.00 1.82
2375 2391 6.796705 TCTCAGTTCCCGTAAAATTTCTTC 57.203 37.500 0.00 0.00 0.00 2.87
2399 2415 7.732025 TCCCCTAAAATCTTGTTTTCCTTTTC 58.268 34.615 0.00 0.00 0.00 2.29
2529 2547 3.133014 CGGCCATCTCGATGAGGT 58.867 61.111 2.24 0.00 41.20 3.85
2543 2561 3.330720 AGGTGGGGAAGCGAAGGG 61.331 66.667 0.00 0.00 0.00 3.95
2559 2577 4.256180 GGGGGCATCCTAGCGGTG 62.256 72.222 0.00 0.00 35.33 4.94
2560 2578 4.256180 GGGGCATCCTAGCGGTGG 62.256 72.222 0.00 0.00 34.64 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.868906 TTTACCCACATAATTTAGCTGTACC 57.131 36.000 0.00 0.00 0.00 3.34
17 18 7.823310 TCGTTTTACCCACATAATTTAGCTGTA 59.177 33.333 0.00 0.00 0.00 2.74
41 42 6.531594 TGACTAGTGAAATTGAGCACTTATCG 59.468 38.462 0.00 4.68 42.33 2.92
85 86 1.938577 CATCCGAGCTGAGGTCAATTG 59.061 52.381 12.54 0.00 0.00 2.32
94 95 1.964223 GATCCTAACCATCCGAGCTGA 59.036 52.381 0.00 0.00 0.00 4.26
95 96 1.967066 AGATCCTAACCATCCGAGCTG 59.033 52.381 0.00 0.00 0.00 4.24
120 121 2.496470 GTGAACCCTAGGTCGATTCTGT 59.504 50.000 8.29 0.00 33.12 3.41
122 123 1.749634 CGTGAACCCTAGGTCGATTCT 59.250 52.381 8.29 0.00 33.12 2.40
149 150 1.391485 CATACGAGCACAGTGTCAAGC 59.609 52.381 1.61 0.00 0.00 4.01
214 216 9.702494 TCTTATAGTCAGCAATAATGTCATCTG 57.298 33.333 0.00 0.00 0.00 2.90
226 228 7.039293 TCACTACAAAGGTCTTATAGTCAGCAA 60.039 37.037 5.22 0.00 0.00 3.91
228 230 6.752815 GTCACTACAAAGGTCTTATAGTCAGC 59.247 42.308 5.22 0.00 0.00 4.26
230 232 8.418597 AAGTCACTACAAAGGTCTTATAGTCA 57.581 34.615 5.22 0.00 0.00 3.41
233 235 9.877178 AATGAAGTCACTACAAAGGTCTTATAG 57.123 33.333 0.00 0.00 0.00 1.31
240 242 7.690256 AGGATTAATGAAGTCACTACAAAGGT 58.310 34.615 0.00 0.00 0.00 3.50
359 361 5.791974 CAGTGATTGATCATCGTGAAACAAC 59.208 40.000 0.00 0.00 39.30 3.32
379 381 0.110295 TGTGGTCCAATCACCCAGTG 59.890 55.000 0.00 0.00 35.26 3.66
400 402 5.280882 CCTCATTCATATAGGGGCTTGATGT 60.281 44.000 0.00 0.00 0.00 3.06
401 403 5.191426 CCTCATTCATATAGGGGCTTGATG 58.809 45.833 0.00 0.00 0.00 3.07
426 428 1.621301 CGGCACACAGAGAGCGAAAG 61.621 60.000 0.00 0.00 34.34 2.62
441 443 4.135747 TGATGATGTCTACATTTCGGCA 57.864 40.909 0.00 0.00 36.57 5.69
442 444 4.024556 CCTTGATGATGTCTACATTTCGGC 60.025 45.833 0.00 0.00 36.57 5.54
443 445 5.118990 ACCTTGATGATGTCTACATTTCGG 58.881 41.667 0.00 0.08 36.57 4.30
444 446 5.235186 GGACCTTGATGATGTCTACATTTCG 59.765 44.000 0.00 0.00 36.57 3.46
445 447 5.235186 CGGACCTTGATGATGTCTACATTTC 59.765 44.000 0.00 0.00 36.57 2.17
446 448 5.104941 TCGGACCTTGATGATGTCTACATTT 60.105 40.000 0.00 0.00 36.57 2.32
469 471 3.129638 ACGAGAGAGTCCAACAGCTATTC 59.870 47.826 0.00 0.00 0.00 1.75
512 514 0.723414 CCATACTCAGCTGCAACGTG 59.277 55.000 9.47 4.02 0.00 4.49
516 518 0.393402 CTGCCCATACTCAGCTGCAA 60.393 55.000 9.47 0.00 0.00 4.08
567 569 1.135731 CGTGCGTGTTGTTGTGGTT 59.864 52.632 0.00 0.00 0.00 3.67
654 656 6.793505 TTTCTCTAGAAACATAGAGGACCC 57.206 41.667 10.10 0.00 45.93 4.46
779 783 3.367607 CATCCTCGCGAGTCTCTTTTAG 58.632 50.000 32.41 15.18 0.00 1.85
820 824 4.434588 CGAAAGTGAAAGTGAAAGCGAAAG 59.565 41.667 0.00 0.00 0.00 2.62
821 825 4.339429 CGAAAGTGAAAGTGAAAGCGAAA 58.661 39.130 0.00 0.00 0.00 3.46
822 826 3.787476 GCGAAAGTGAAAGTGAAAGCGAA 60.787 43.478 0.00 0.00 0.00 4.70
823 827 2.286184 GCGAAAGTGAAAGTGAAAGCGA 60.286 45.455 0.00 0.00 0.00 4.93
824 828 2.036933 GCGAAAGTGAAAGTGAAAGCG 58.963 47.619 0.00 0.00 0.00 4.68
825 829 3.038710 CTGCGAAAGTGAAAGTGAAAGC 58.961 45.455 0.00 0.00 0.00 3.51
921 931 3.252974 TCGGGAAGAAATCAAGAGAGC 57.747 47.619 0.00 0.00 0.00 4.09
939 949 1.350319 CGTGTGTGTGGTGGTTTCG 59.650 57.895 0.00 0.00 0.00 3.46
974 986 1.518133 CTGCGTACCAGCTGAGCTC 60.518 63.158 17.39 6.82 36.40 4.09
1596 1608 5.007921 GCAACGTTTCACTTTAGTTCCCTAA 59.992 40.000 0.00 0.00 0.00 2.69
1624 1638 1.736681 CTAGTGAGGAAGCAAAGCAGC 59.263 52.381 0.00 0.00 0.00 5.25
1941 1956 8.142994 ACGTGCAGATAGTAAATAGGAAAATG 57.857 34.615 0.00 0.00 0.00 2.32
2147 2163 8.968242 GTTCTTTGCTTATTTTCTTTCATTCGT 58.032 29.630 0.00 0.00 0.00 3.85
2152 2168 9.950680 CTACTGTTCTTTGCTTATTTTCTTTCA 57.049 29.630 0.00 0.00 0.00 2.69
2211 2227 6.975772 GCTAGAGAAGATATACTTATTGGCGG 59.024 42.308 0.00 0.00 39.13 6.13
2234 2250 1.198713 CCTATCAGTGGTGACCAGCT 58.801 55.000 3.58 2.35 34.75 4.24
2237 2253 0.252696 AGGCCTATCAGTGGTGACCA 60.253 55.000 1.29 0.00 34.75 4.02
2262 2278 9.014297 AGGTTTTTATAAGATCTGTTGGAGTTG 57.986 33.333 0.00 0.00 0.00 3.16
2291 2307 7.936496 TCATACCATGAAAGCACTTTTATGA 57.064 32.000 22.46 15.54 44.41 2.15
2293 2309 7.642669 CGATCATACCATGAAAGCACTTTTAT 58.357 34.615 0.00 0.00 43.50 1.40
2342 2358 3.071167 ACGGGAACTGAGAAAAGTAGCTT 59.929 43.478 0.00 0.00 38.67 3.74
2369 2385 7.567250 AGGAAAACAAGATTTTAGGGGAAGAAA 59.433 33.333 0.00 0.00 0.00 2.52
2375 2391 6.934645 GGAAAAGGAAAACAAGATTTTAGGGG 59.065 38.462 0.00 0.00 0.00 4.79
2399 2415 1.459450 CCAACGATGTTTAGTGGGGG 58.541 55.000 0.00 0.00 0.00 5.40
2436 2454 1.588082 CCACACTTCCCAATGCTGC 59.412 57.895 0.00 0.00 0.00 5.25
2441 2459 1.331214 CTGTTGCCACACTTCCCAAT 58.669 50.000 0.00 0.00 0.00 3.16
2517 2535 1.418334 CTTCCCCACCTCATCGAGAT 58.582 55.000 0.00 0.00 0.00 2.75
2543 2561 4.256180 CCACCGCTAGGATGCCCC 62.256 72.222 0.00 0.00 41.02 5.80


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

AutoCloner maintained by Alex Coulton.