Multiple sequence alignment - TraesCS4A01G049000

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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 TraesCS4A01G049000 chr4A 100.000 3096 0 0 1 3096 39830275 39833370 0.000000e+00 5718
1 TraesCS4A01G049000 chr4A 82.796 372 58 5 1878 2247 40201186 40201553 8.280000e-86 327
2 TraesCS4A01G049000 chr4B 94.849 2951 147 5 1 2947 520524420 520521471 0.000000e+00 4602
3 TraesCS4A01G049000 chr4B 77.985 2253 395 61 893 3096 520425832 520423632 0.000000e+00 1319
4 TraesCS4A01G049000 chr4B 94.675 169 7 2 2930 3096 520521457 520521289 8.520000e-66 261
5 TraesCS4A01G049000 chr4D 93.370 3107 183 13 1 3096 424609441 424606347 0.000000e+00 4575
6 TraesCS4A01G049000 chr4D 77.136 2563 462 79 594 3096 424599348 424596850 0.000000e+00 1373


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 TraesCS4A01G049000 chr4A 39830275 39833370 3095 False 5718.0 5718 100.000 1 3096 1 chr4A.!!$F1 3095
1 TraesCS4A01G049000 chr4B 520521289 520524420 3131 True 2431.5 4602 94.762 1 3096 2 chr4B.!!$R2 3095
2 TraesCS4A01G049000 chr4B 520423632 520425832 2200 True 1319.0 1319 77.985 893 3096 1 chr4B.!!$R1 2203
3 TraesCS4A01G049000 chr4D 424606347 424609441 3094 True 4575.0 4575 93.370 1 3096 1 chr4D.!!$R2 3095
4 TraesCS4A01G049000 chr4D 424596850 424599348 2498 True 1373.0 1373 77.136 594 3096 1 chr4D.!!$R1 2502

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
752 759 4.7007 CCTCAGATGTCATATGCACAAGA 58.299 43.478 2.4 8.82 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2747 2801 1.173913 GGCAGGACATAAGGCGTTTT 58.826 50.0 0.0 0.0 0.0 2.43 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
149 150 7.841729 TGTGTGGGGGTTGTATATCATTTATTT 59.158 33.333 0.00 0.00 0.00 1.40
166 167 9.679661 TCATTTATTTCTCTATTGCAGGTTGTA 57.320 29.630 0.00 0.00 0.00 2.41
272 273 8.303780 TCAAGATGTCTCATCTTCATCTAGTT 57.696 34.615 18.28 0.00 44.70 2.24
286 287 8.299570 TCTTCATCTAGTTTTGGAAATCTTTGC 58.700 33.333 0.00 0.00 0.00 3.68
457 460 4.862902 TGTTTATGTGTTTGGATGTGGG 57.137 40.909 0.00 0.00 0.00 4.61
528 531 6.431234 CCTGCTTTCCTATAACCATCCATTAC 59.569 42.308 0.00 0.00 0.00 1.89
637 641 9.142014 TCCTTTTTGTCTTGAAGGAAAATATGA 57.858 29.630 1.78 0.00 44.33 2.15
752 759 4.700700 CCTCAGATGTCATATGCACAAGA 58.299 43.478 2.40 8.82 0.00 3.02
770 778 7.384660 TGCACAAGATTTACCATCAAAAATGAC 59.615 33.333 0.00 0.00 0.00 3.06
1270 1285 3.916761 TCGCGTACTCACCTTTTTACAT 58.083 40.909 5.77 0.00 0.00 2.29
1284 1299 7.116233 CACCTTTTTACATTTTGGACAGTATGC 59.884 37.037 0.00 0.00 42.53 3.14
1392 1412 9.793259 TGAAGGTAACATGATTTTAGAGAACTT 57.207 29.630 0.00 0.00 41.41 2.66
1502 1522 7.924940 TGCGTAAATGCTTGACAATGATAATA 58.075 30.769 0.00 0.00 35.36 0.98
1536 1556 5.361427 GGGAAACTCAAAGATAGAGGTAGC 58.639 45.833 0.00 0.00 37.43 3.58
1633 1657 9.757227 GACTAGATATTAGACAATATGGGATGC 57.243 37.037 0.00 0.00 37.44 3.91
1757 1781 7.346698 CCCATATCTCCTGGTGATATCATAAGT 59.653 40.741 22.23 4.69 35.61 2.24
1782 1806 5.012148 CCTGTCTCCGGTATCAATAGGAAAT 59.988 44.000 0.00 0.00 31.67 2.17
1821 1845 4.942761 AGAGTGTCCAAGGTACGTTTTA 57.057 40.909 0.00 0.00 0.00 1.52
1984 2027 4.265073 ACTTCCCAGCATCACTATTTGAC 58.735 43.478 0.00 0.00 36.92 3.18
2023 2066 4.038402 GCCACTCAAATATCAATTGGAGGG 59.962 45.833 5.42 4.12 44.53 4.30
2040 2088 1.683917 AGGGCATGCTCGAAGTACTAG 59.316 52.381 18.92 0.00 0.00 2.57
2078 2126 2.024941 CCTATGGGAAGTGGAGCCTTTT 60.025 50.000 0.00 0.00 33.58 2.27
2093 2141 2.225041 GCCTTTTCCTCTAACCCTGGTT 60.225 50.000 6.81 6.81 41.65 3.67
2097 2145 5.222068 CCTTTTCCTCTAACCCTGGTTAAGT 60.222 44.000 9.88 0.00 39.69 2.24
2218 2266 1.488393 GCTTCACCCATAGGAAGAGCT 59.512 52.381 5.64 0.00 42.39 4.09
2238 2286 3.956848 GCTCAATTCTTTTATGGAGGCCT 59.043 43.478 3.86 3.86 0.00 5.19
2273 2321 1.077828 AGTGAGGTGGATCTGAGGACA 59.922 52.381 0.00 0.00 0.00 4.02
2304 2352 5.838529 TGCAATGCATGAATAAGAGATTGG 58.161 37.500 2.72 0.00 31.71 3.16
2322 2370 9.336171 AGAGATTGGAAGAAAATATGCTAGTTC 57.664 33.333 0.00 0.00 0.00 3.01
2346 2394 2.193536 GTTCCTTGGTTGTGCGGCT 61.194 57.895 0.00 0.00 0.00 5.52
2358 2406 1.488812 TGTGCGGCTATCCTTATTGGT 59.511 47.619 0.00 0.00 37.07 3.67
2359 2407 2.092646 TGTGCGGCTATCCTTATTGGTT 60.093 45.455 0.00 0.00 37.07 3.67
2487 2535 7.781693 AGTAAAGATAGCATTTTGGATGTCCAT 59.218 33.333 1.98 0.00 46.97 3.41
2566 2619 1.490490 CTAAGGCTCTGCACCCCATTA 59.510 52.381 0.00 0.00 0.00 1.90
2583 2636 6.101150 ACCCCATTATGCTTGAATAGACACTA 59.899 38.462 0.00 0.00 0.00 2.74
2621 2674 2.238646 TGTATGCTCGGTCAGGGATTTT 59.761 45.455 0.00 0.00 0.00 1.82
2664 2717 3.245264 CCCTTGTAACTTTGGGATCACCT 60.245 47.826 0.00 0.00 42.11 4.00
2747 2801 1.615124 TTCTGGCTCCCGGATGGAA 60.615 57.895 0.73 0.00 44.57 3.53
2758 2813 2.021457 CCGGATGGAAAAACGCCTTAT 58.979 47.619 0.00 0.00 37.49 1.73
2824 2884 8.739039 CAATGGTGTAGATCTTATCTAGAGAGG 58.261 40.741 0.00 0.00 42.20 3.69
2855 2915 7.495934 GCTTATGAGTCAAATGCCTTAGAAGTA 59.504 37.037 0.00 0.00 0.00 2.24
2869 2929 7.665559 TGCCTTAGAAGTACAATGTTCTTTGAT 59.334 33.333 6.71 0.38 34.76 2.57
2880 2940 4.008074 TGTTCTTTGATGGAGGTCTGTC 57.992 45.455 0.00 0.00 0.00 3.51
2881 2941 3.244561 TGTTCTTTGATGGAGGTCTGTCC 60.245 47.826 0.00 0.00 37.10 4.02
2888 2948 0.322636 TGGAGGTCTGTCCGTCTCTC 60.323 60.000 0.00 0.00 39.81 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.590451 CCAGATATGCAACTTTGATTTGTTTAT 57.410 29.630 0.00 0.00 0.00 1.40
15 16 7.230849 TCCAGATATGCAACTTTGATTTGTT 57.769 32.000 0.00 0.00 0.00 2.83
127 128 8.732854 AGAGAAATAAATGATATACAACCCCCA 58.267 33.333 0.00 0.00 0.00 4.96
149 150 3.428999 GCGACTACAACCTGCAATAGAGA 60.429 47.826 0.00 0.00 0.00 3.10
162 163 4.558178 TCTTAATTTCCACGCGACTACAA 58.442 39.130 15.93 0.00 0.00 2.41
166 167 3.314541 ACTCTTAATTTCCACGCGACT 57.685 42.857 15.93 0.00 0.00 4.18
410 412 4.823442 TGGGAGATTCATTGTACATGATGC 59.177 41.667 0.00 0.00 0.00 3.91
457 460 9.330063 TCCACATGTATGTTGAATCTTCTATTC 57.670 33.333 0.00 0.00 39.39 1.75
752 759 7.754924 GTGTCATCGTCATTTTTGATGGTAAAT 59.245 33.333 2.02 0.00 39.89 1.40
1211 1225 9.953565 GATATGGCCAAACCTACATAAGTATAA 57.046 33.333 10.96 0.00 40.22 0.98
1270 1285 4.985538 AGGAAGAAGCATACTGTCCAAAA 58.014 39.130 0.00 0.00 0.00 2.44
1609 1633 8.708378 TGGCATCCCATATTGTCTAATATCTAG 58.292 37.037 0.00 0.00 37.38 2.43
1633 1657 7.864379 GCACTTCCAAACATATCATTTAGATGG 59.136 37.037 0.00 0.00 37.57 3.51
1742 1766 5.540337 GGAGACAGGACTTATGATATCACCA 59.460 44.000 7.78 0.00 0.00 4.17
1757 1781 3.139584 TCCTATTGATACCGGAGACAGGA 59.860 47.826 9.46 7.61 0.00 3.86
1782 1806 6.636705 ACACTCTAATAGTAATCGTTTGGCA 58.363 36.000 0.00 0.00 35.76 4.92
1821 1845 9.991906 CTGCATCCCTAATGAATTAAAATTGAT 57.008 29.630 0.00 0.00 37.59 2.57
1984 2027 4.937620 TGAGTGGCTTTTGTAGATAAGCTG 59.062 41.667 13.36 0.00 44.70 4.24
2023 2066 6.210078 AGTATTTCTAGTACTTCGAGCATGC 58.790 40.000 10.51 10.51 0.00 4.06
2040 2088 7.126733 TCCCATAGGAGGAGCTATAGTATTTC 58.873 42.308 0.84 0.00 37.19 2.17
2078 2126 3.008704 GCAACTTAACCAGGGTTAGAGGA 59.991 47.826 10.56 0.00 40.98 3.71
2093 2141 9.234827 CCAAATATCATGGATAGATGCAACTTA 57.765 33.333 0.30 0.00 40.56 2.24
2097 2145 6.250711 AGCCAAATATCATGGATAGATGCAA 58.749 36.000 10.84 0.00 40.56 4.08
2169 2217 4.938226 AGAGCTTGCCATCTGTAACTTTAC 59.062 41.667 0.00 0.00 0.00 2.01
2218 2266 4.280819 CCAGGCCTCCATAAAAGAATTGA 58.719 43.478 0.00 0.00 0.00 2.57
2238 2286 3.115390 CCTCACTAAGATTTCCCTCCCA 58.885 50.000 0.00 0.00 0.00 4.37
2297 2345 9.113838 TGAACTAGCATATTTTCTTCCAATCTC 57.886 33.333 0.00 0.00 0.00 2.75
2322 2370 3.312421 CCGCACAACCAAGGAACTATATG 59.688 47.826 0.00 0.00 38.49 1.78
2358 2406 9.587772 TCCAAATTTCAACGAACTTTTATCAAA 57.412 25.926 0.00 0.00 0.00 2.69
2359 2407 9.587772 TTCCAAATTTCAACGAACTTTTATCAA 57.412 25.926 0.00 0.00 0.00 2.57
2437 2485 4.161565 AGGTTCCGACAATATGCAAGTCTA 59.838 41.667 0.00 0.00 0.00 2.59
2439 2487 3.270877 AGGTTCCGACAATATGCAAGTC 58.729 45.455 0.00 0.00 0.00 3.01
2532 2585 7.883311 TGCAGAGCCTTAGATACTTTTAAAGTT 59.117 33.333 15.83 4.19 42.81 2.66
2566 2619 6.156949 TCCTTTCCTAGTGTCTATTCAAGCAT 59.843 38.462 0.00 0.00 0.00 3.79
2583 2636 7.604164 CGAGCATACACATATTTATCCTTTCCT 59.396 37.037 0.00 0.00 0.00 3.36
2621 2674 8.642432 CAAGGGACTGTATCTTCTATAACATCA 58.358 37.037 0.00 0.00 40.86 3.07
2664 2717 1.660167 ATCTCGACACGATACGACCA 58.340 50.000 0.00 0.00 34.61 4.02
2747 2801 1.173913 GGCAGGACATAAGGCGTTTT 58.826 50.000 0.00 0.00 0.00 2.43
2758 2813 3.838317 AGTTAATGTCAGTAGGCAGGACA 59.162 43.478 0.00 0.00 44.73 4.02
2824 2884 5.363939 AGGCATTTGACTCATAAGCTAGAC 58.636 41.667 0.00 0.00 0.00 2.59
2855 2915 4.763793 CAGACCTCCATCAAAGAACATTGT 59.236 41.667 0.00 0.00 0.00 2.71
2869 2929 0.322636 GAGAGACGGACAGACCTCCA 60.323 60.000 0.00 0.00 36.31 3.86
2880 2940 6.879276 TTCACCTACTAATATGAGAGACGG 57.121 41.667 0.00 0.00 0.00 4.79
2881 2941 7.877003 ACATTCACCTACTAATATGAGAGACG 58.123 38.462 0.00 0.00 0.00 4.18
2888 2948 9.823098 GTAGTACGACATTCACCTACTAATATG 57.177 37.037 0.73 0.00 0.00 1.78
2978 3081 1.740025 GGTGCACTTAGTCAGGAATGC 59.260 52.381 17.98 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.