Multiple sequence alignment - TraesCS5A01G319200

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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 TraesCS5A01G319200 chr5A 100.000 2253 0 0 850 3102 530302850 530300598 0.000000e+00 4161
1 TraesCS5A01G319200 chr5A 100.000 426 0 0 1 426 530303699 530303274 0.000000e+00 787
2 TraesCS5A01G319200 chr5D 96.201 2264 55 15 850 3102 417041307 417039064 0.000000e+00 3675
3 TraesCS5A01G319200 chr5D 91.355 428 11 7 1 426 417041805 417041402 2.090000e-156 562
4 TraesCS5A01G319200 chr5B 95.697 2254 64 14 852 3102 504307542 504305319 0.000000e+00 3594
5 TraesCS5A01G319200 chr5B 86.517 445 10 8 1 426 504308053 504307640 7.890000e-121 444
6 TraesCS5A01G319200 chr7A 86.628 172 23 0 1675 1846 282368854 282368683 1.140000e-44 191
7 TraesCS5A01G319200 chr7A 86.577 149 20 0 1300 1448 282369255 282369107 6.880000e-37 165
8 TraesCS5A01G319200 chr7B 86.047 172 24 0 1675 1846 239363366 239363537 5.280000e-43 185
9 TraesCS5A01G319200 chr7B 86.577 149 20 0 1300 1448 239362965 239363113 6.880000e-37 165
10 TraesCS5A01G319200 chr3B 88.514 148 15 2 1297 1443 786970547 786970401 8.840000e-41 178
11 TraesCS5A01G319200 chr3D 87.838 148 16 2 1297 1443 588489275 588489129 4.110000e-39 172
12 TraesCS5A01G319200 chr7D 87.248 149 19 0 1300 1448 259840844 259840696 1.480000e-38 171
13 TraesCS5A01G319200 chr3A 87.162 148 17 2 1297 1443 718836820 718836674 1.910000e-37 167


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 TraesCS5A01G319200 chr5A 530300598 530303699 3101 True 2474.0 4161 100.000 1 3102 2 chr5A.!!$R1 3101
1 TraesCS5A01G319200 chr5D 417039064 417041805 2741 True 2118.5 3675 93.778 1 3102 2 chr5D.!!$R1 3101
2 TraesCS5A01G319200 chr5B 504305319 504308053 2734 True 2019.0 3594 91.107 1 3102 2 chr5B.!!$R1 3101

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
326 355 0.105709 GAGAGAGAGAAGGGGAGGGG 60.106 65.0 0.00 0.0 0.00 4.79 F
918 951 0.585357 ATAGCGCGTACTCCTACACG 59.415 55.0 8.43 0.0 41.04 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1688 0.812014 CCCTACACACGCACACACAA 60.812 55.0 0.00 0.0 0.0 3.33 R
2790 2832 0.911769 ATCGGTCAGCTCCCAATCAA 59.088 50.0 0.15 0.0 0.0 2.57 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
111 123 0.818040 GTGGTACATTCCATCCGGGC 60.818 60.000 0.00 0.00 44.52 6.13
175 198 1.733402 TTGTGCTGTGCCCTTTTCCG 61.733 55.000 0.00 0.00 0.00 4.30
288 317 1.866880 GCTTGTGCTGCAAACTCCAAG 60.867 52.381 19.64 19.64 36.53 3.61
296 325 3.524541 CTGCAAACTCCAAGCTTGTTTT 58.475 40.909 24.35 16.59 32.42 2.43
305 334 4.384056 TCCAAGCTTGTTTTGAGAGAGAG 58.616 43.478 24.35 5.06 0.00 3.20
306 335 4.101585 TCCAAGCTTGTTTTGAGAGAGAGA 59.898 41.667 24.35 7.33 0.00 3.10
307 336 4.451774 CCAAGCTTGTTTTGAGAGAGAGAG 59.548 45.833 24.35 0.00 0.00 3.20
308 337 5.295950 CAAGCTTGTTTTGAGAGAGAGAGA 58.704 41.667 18.65 0.00 0.00 3.10
309 338 5.138125 AGCTTGTTTTGAGAGAGAGAGAG 57.862 43.478 0.00 0.00 0.00 3.20
310 339 4.832266 AGCTTGTTTTGAGAGAGAGAGAGA 59.168 41.667 0.00 0.00 0.00 3.10
311 340 5.047802 AGCTTGTTTTGAGAGAGAGAGAGAG 60.048 44.000 0.00 0.00 0.00 3.20
312 341 5.048083 GCTTGTTTTGAGAGAGAGAGAGAGA 60.048 44.000 0.00 0.00 0.00 3.10
313 342 6.573664 TTGTTTTGAGAGAGAGAGAGAGAG 57.426 41.667 0.00 0.00 0.00 3.20
314 343 5.875224 TGTTTTGAGAGAGAGAGAGAGAGA 58.125 41.667 0.00 0.00 0.00 3.10
315 344 5.939883 TGTTTTGAGAGAGAGAGAGAGAGAG 59.060 44.000 0.00 0.00 0.00 3.20
316 345 6.173339 GTTTTGAGAGAGAGAGAGAGAGAGA 58.827 44.000 0.00 0.00 0.00 3.10
317 346 6.373005 TTTGAGAGAGAGAGAGAGAGAGAA 57.627 41.667 0.00 0.00 0.00 2.87
318 347 5.604758 TGAGAGAGAGAGAGAGAGAGAAG 57.395 47.826 0.00 0.00 0.00 2.85
319 348 4.406972 TGAGAGAGAGAGAGAGAGAGAAGG 59.593 50.000 0.00 0.00 0.00 3.46
320 349 3.713764 AGAGAGAGAGAGAGAGAGAAGGG 59.286 52.174 0.00 0.00 0.00 3.95
321 350 2.780010 AGAGAGAGAGAGAGAGAAGGGG 59.220 54.545 0.00 0.00 0.00 4.79
322 351 2.777692 GAGAGAGAGAGAGAGAAGGGGA 59.222 54.545 0.00 0.00 0.00 4.81
323 352 2.780010 AGAGAGAGAGAGAGAAGGGGAG 59.220 54.545 0.00 0.00 0.00 4.30
324 353 1.852965 AGAGAGAGAGAGAAGGGGAGG 59.147 57.143 0.00 0.00 0.00 4.30
325 354 0.933700 AGAGAGAGAGAAGGGGAGGG 59.066 60.000 0.00 0.00 0.00 4.30
326 355 0.105709 GAGAGAGAGAAGGGGAGGGG 60.106 65.000 0.00 0.00 0.00 4.79
867 900 4.147449 CCATCGACGAGGCCAGCA 62.147 66.667 5.01 0.00 0.00 4.41
918 951 0.585357 ATAGCGCGTACTCCTACACG 59.415 55.000 8.43 0.00 41.04 4.49
951 984 1.680522 CCAGGGCAGCGACTGTAGAT 61.681 60.000 13.02 0.00 33.43 1.98
952 985 1.032794 CAGGGCAGCGACTGTAGATA 58.967 55.000 7.41 0.00 33.43 1.98
953 986 1.000827 CAGGGCAGCGACTGTAGATAG 60.001 57.143 7.41 0.00 33.43 2.08
954 987 1.133761 AGGGCAGCGACTGTAGATAGA 60.134 52.381 8.32 0.00 33.43 1.98
1023 1056 1.995626 GGGCTTCCCTCTAGGCACA 60.996 63.158 0.00 0.00 41.34 4.57
1254 1287 2.693017 GCCTCCTCCTCCTCCTCA 59.307 66.667 0.00 0.00 0.00 3.86
1645 1680 2.902705 TCTGACGCTAAAACCTGTGT 57.097 45.000 0.00 0.00 0.00 3.72
2246 2281 4.873259 GCTATAGCTTAGCTTAATGAGGCC 59.127 45.833 13.44 0.00 40.44 5.19
2265 2300 3.371273 GGCCCCGTAATTTAGACCTTTCT 60.371 47.826 0.00 0.00 35.66 2.52
2294 2329 1.340399 TGGGAGCATCTGAGGCGATT 61.340 55.000 8.79 0.00 36.08 3.34
2444 2480 7.867403 TGTTCTTAACAATCTTGATTTTCCTGC 59.133 33.333 0.00 0.00 38.72 4.85
2681 2717 3.064958 GTCCTTCGCCTTAAGTTAATGGC 59.935 47.826 18.64 18.64 41.76 4.40
2699 2735 3.806380 TGGCGTGGTTCTGTTAGTTTTA 58.194 40.909 0.00 0.00 0.00 1.52
2733 2775 7.454225 ACTATATTAGAATTTGGGAGTGAGCC 58.546 38.462 0.00 0.00 0.00 4.70
2790 2832 6.774656 AGAAAGTTTGAGACCAAATGATCAGT 59.225 34.615 0.09 0.00 43.37 3.41
2901 2943 2.391678 GGGAATGATTGATTGGTGGCT 58.608 47.619 0.00 0.00 0.00 4.75
2912 2954 3.054213 TGATTGGTGGCTCATTCATCTCA 60.054 43.478 0.00 0.00 0.00 3.27
2913 2955 3.657398 TTGGTGGCTCATTCATCTCAT 57.343 42.857 0.00 0.00 0.00 2.90
2914 2956 3.657398 TGGTGGCTCATTCATCTCATT 57.343 42.857 0.00 0.00 0.00 2.57
2918 2960 5.107133 GGTGGCTCATTCATCTCATTTTTG 58.893 41.667 0.00 0.00 0.00 2.44
2961 3005 7.357951 TGAACTTGTTGATTTGTTTTTCCAC 57.642 32.000 0.00 0.00 0.00 4.02
3086 3132 9.938280 ATAATTATATCCGTTAGTGCTAGCAAA 57.062 29.630 21.29 8.55 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.764160 CTCCGGAATCCAGCTGCCC 62.764 68.421 8.66 5.44 0.00 5.36
72 84 1.465689 CGAGTAAATGTTTGCCTGCCG 60.466 52.381 0.00 0.00 0.00 5.69
73 85 1.539827 ACGAGTAAATGTTTGCCTGCC 59.460 47.619 0.00 0.00 0.00 4.85
74 86 2.584791 CACGAGTAAATGTTTGCCTGC 58.415 47.619 0.00 0.00 0.00 4.85
75 87 2.552315 ACCACGAGTAAATGTTTGCCTG 59.448 45.455 0.00 0.00 0.00 4.85
76 88 2.858745 ACCACGAGTAAATGTTTGCCT 58.141 42.857 0.00 0.00 0.00 4.75
77 89 3.499157 TGTACCACGAGTAAATGTTTGCC 59.501 43.478 0.00 0.00 31.05 4.52
238 261 0.609406 CCGAGGGAGTGAGTGAGTGA 60.609 60.000 0.00 0.00 0.00 3.41
239 262 1.886585 CCGAGGGAGTGAGTGAGTG 59.113 63.158 0.00 0.00 0.00 3.51
240 263 1.979693 GCCGAGGGAGTGAGTGAGT 60.980 63.158 0.00 0.00 0.00 3.41
288 317 5.048083 TCTCTCTCTCTCTCTCAAAACAAGC 60.048 44.000 0.00 0.00 0.00 4.01
296 325 4.406972 CCTTCTCTCTCTCTCTCTCTCTCA 59.593 50.000 0.00 0.00 0.00 3.27
305 334 1.133482 CCCTCCCCTTCTCTCTCTCTC 60.133 61.905 0.00 0.00 0.00 3.20
306 335 0.933700 CCCTCCCCTTCTCTCTCTCT 59.066 60.000 0.00 0.00 0.00 3.10
307 336 0.105709 CCCCTCCCCTTCTCTCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
308 337 0.556380 TCCCCTCCCCTTCTCTCTCT 60.556 60.000 0.00 0.00 0.00 3.10
309 338 0.105709 CTCCCCTCCCCTTCTCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
310 339 1.598856 CCTCCCCTCCCCTTCTCTCT 61.599 65.000 0.00 0.00 0.00 3.10
311 340 1.074850 CCTCCCCTCCCCTTCTCTC 60.075 68.421 0.00 0.00 0.00 3.20
312 341 2.652113 CCCTCCCCTCCCCTTCTCT 61.652 68.421 0.00 0.00 0.00 3.10
313 342 2.040359 CCCTCCCCTCCCCTTCTC 60.040 72.222 0.00 0.00 0.00 2.87
314 343 2.543637 TCCCTCCCCTCCCCTTCT 60.544 66.667 0.00 0.00 0.00 2.85
315 344 2.040359 CTCCCTCCCCTCCCCTTC 60.040 72.222 0.00 0.00 0.00 3.46
316 345 4.439901 GCTCCCTCCCCTCCCCTT 62.440 72.222 0.00 0.00 0.00 3.95
918 951 2.971413 CTGGCCATGCGCTAGCTC 60.971 66.667 5.51 5.25 45.42 4.09
951 984 5.317808 CCGATCTCCCTCTATTTCACTCTA 58.682 45.833 0.00 0.00 0.00 2.43
952 985 4.148838 CCGATCTCCCTCTATTTCACTCT 58.851 47.826 0.00 0.00 0.00 3.24
953 986 3.305744 GCCGATCTCCCTCTATTTCACTC 60.306 52.174 0.00 0.00 0.00 3.51
954 987 2.630580 GCCGATCTCCCTCTATTTCACT 59.369 50.000 0.00 0.00 0.00 3.41
1080 1113 1.255667 TGGCGTAGAGGAAGGTGGAC 61.256 60.000 0.00 0.00 0.00 4.02
1239 1272 2.124693 GCGTGAGGAGGAGGAGGAG 61.125 68.421 0.00 0.00 0.00 3.69
1645 1680 3.426859 CACACGCACACACAAAAAGAAAA 59.573 39.130 0.00 0.00 0.00 2.29
1648 1683 1.537638 ACACACGCACACACAAAAAGA 59.462 42.857 0.00 0.00 0.00 2.52
1649 1684 1.975837 ACACACGCACACACAAAAAG 58.024 45.000 0.00 0.00 0.00 2.27
1653 1688 0.812014 CCCTACACACGCACACACAA 60.812 55.000 0.00 0.00 0.00 3.33
2246 2281 5.915175 AGCTAGAAAGGTCTAAATTACGGG 58.085 41.667 0.00 0.00 35.89 5.28
2522 2558 8.484641 TTGTGCAAGACAGATAAATAGAAGAG 57.515 34.615 0.00 0.00 35.44 2.85
2523 2559 7.550551 CCTTGTGCAAGACAGATAAATAGAAGA 59.449 37.037 12.99 0.00 40.79 2.87
2524 2560 7.335422 ACCTTGTGCAAGACAGATAAATAGAAG 59.665 37.037 12.99 0.00 40.79 2.85
2669 2705 4.391155 ACAGAACCACGCCATTAACTTAA 58.609 39.130 0.00 0.00 0.00 1.85
2681 2717 4.454504 AGCCATAAAACTAACAGAACCACG 59.545 41.667 0.00 0.00 0.00 4.94
2718 2754 2.893424 ACAATGGCTCACTCCCAAATT 58.107 42.857 0.00 0.00 35.67 1.82
2723 2765 1.133976 AGCATACAATGGCTCACTCCC 60.134 52.381 0.00 0.00 34.76 4.30
2733 2775 7.341512 TCCTCTCTCCTATATGAGCATACAATG 59.658 40.741 0.41 0.00 32.22 2.82
2747 2789 5.428131 ACTTTCTTGCATTCCTCTCTCCTAT 59.572 40.000 0.00 0.00 0.00 2.57
2748 2790 4.780021 ACTTTCTTGCATTCCTCTCTCCTA 59.220 41.667 0.00 0.00 0.00 2.94
2749 2791 3.586618 ACTTTCTTGCATTCCTCTCTCCT 59.413 43.478 0.00 0.00 0.00 3.69
2790 2832 0.911769 ATCGGTCAGCTCCCAATCAA 59.088 50.000 0.15 0.00 0.00 2.57
2822 2864 2.754552 CCGAAATCAAGCAAAGGGATCA 59.245 45.455 0.00 0.00 0.00 2.92
2901 2943 8.134261 TGACGAAAACAAAAATGAGATGAATGA 58.866 29.630 0.00 0.00 0.00 2.57
2912 2954 6.686630 TGCCATAGATGACGAAAACAAAAAT 58.313 32.000 0.00 0.00 0.00 1.82
2913 2955 6.078202 TGCCATAGATGACGAAAACAAAAA 57.922 33.333 0.00 0.00 0.00 1.94
2914 2956 5.697473 TGCCATAGATGACGAAAACAAAA 57.303 34.783 0.00 0.00 0.00 2.44
2918 2960 5.065218 AGTTCATGCCATAGATGACGAAAAC 59.935 40.000 0.00 0.00 29.39 2.43
3072 3118 3.319755 TGGTACGTTTGCTAGCACTAAC 58.680 45.455 19.17 18.70 0.00 2.34


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

AutoCloner maintained by Alex Coulton.