Multiple sequence alignment - TraesCS6A01G345900

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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 TraesCS6A01G345900 chr6A 100.000 3111 0 0 1 3111 579144034 579140924 0.000000e+00 5746.0
1 TraesCS6A01G345900 chr6A 89.283 1577 148 9 808 2375 579125017 579123453 0.000000e+00 1956.0
2 TraesCS6A01G345900 chr6D 94.735 3115 144 11 1 3111 433281562 433278464 0.000000e+00 4826.0
3 TraesCS6A01G345900 chr6D 93.190 2379 133 15 3 2375 433156216 433153861 0.000000e+00 3469.0
4 TraesCS6A01G345900 chr6D 93.333 2280 131 13 102 2375 432932315 432930051 0.000000e+00 3349.0
5 TraesCS6A01G345900 chr6D 84.812 2390 270 53 2 2375 432915293 432912981 0.000000e+00 2316.0
6 TraesCS6A01G345900 chr6D 89.682 1667 153 9 699 2360 433259321 433257669 0.000000e+00 2108.0
7 TraesCS6A01G345900 chr6D 86.897 580 75 1 2533 3111 433153866 433153287 0.000000e+00 649.0
8 TraesCS6A01G345900 chr6D 87.193 367 46 1 2533 2898 432930056 432929690 1.730000e-112 416.0
9 TraesCS6A01G345900 chr6B 93.902 3116 167 11 1 3111 653873534 653870437 0.000000e+00 4680.0
10 TraesCS6A01G345900 chr6B 88.322 1687 173 10 699 2375 653715843 653714171 0.000000e+00 2002.0
11 TraesCS6A01G345900 chr6B 88.671 1580 158 9 808 2375 653856640 653855070 0.000000e+00 1906.0
12 TraesCS6A01G345900 chr6B 88.897 1396 111 9 1 1395 653699923 653698571 0.000000e+00 1679.0
13 TraesCS6A01G345900 chr6B 84.274 585 80 8 2533 3111 653697624 653697046 7.530000e-156 560.0
14 TraesCS6A01G345900 chr6B 86.667 165 21 1 2369 2533 708939714 708939551 6.850000e-42 182.0
15 TraesCS6A01G345900 chr6B 78.333 180 30 7 2365 2542 547722481 547722653 1.180000e-19 108.0
16 TraesCS6A01G345900 chr6B 90.909 66 3 1 2259 2321 654918815 654918880 5.530000e-13 86.1
17 TraesCS6A01G345900 chr7A 82.153 353 54 9 2762 3111 30868695 30869041 8.440000e-76 294.0
18 TraesCS6A01G345900 chr1D 80.780 359 62 7 2758 3111 30225998 30226354 1.100000e-69 274.0
19 TraesCS6A01G345900 chr2D 80.791 354 63 4 2760 3111 429082295 429081945 3.950000e-69 272.0
20 TraesCS6A01G345900 chr4B 80.466 343 63 4 2771 3110 377932449 377932790 3.080000e-65 259.0
21 TraesCS6A01G345900 chr4B 82.278 158 20 8 2366 2521 24732631 24732782 2.520000e-26 130.0
22 TraesCS6A01G345900 chr2A 79.775 356 63 9 2761 3111 527370122 527370473 1.850000e-62 250.0
23 TraesCS6A01G345900 chr5A 80.745 161 27 3 2374 2533 482121526 482121683 4.210000e-24 122.0
24 TraesCS6A01G345900 chr5A 79.114 158 30 2 2374 2531 539090221 539090375 4.240000e-19 106.0
25 TraesCS6A01G345900 chr5B 79.878 164 28 4 2371 2533 711486543 711486384 7.050000e-22 115.0
26 TraesCS6A01G345900 chr3D 77.714 175 31 7 2371 2542 505787202 505787033 1.970000e-17 100.0


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 TraesCS6A01G345900 chr6A 579140924 579144034 3110 True 5746.0 5746 100.0000 1 3111 1 chr6A.!!$R2 3110
1 TraesCS6A01G345900 chr6A 579123453 579125017 1564 True 1956.0 1956 89.2830 808 2375 1 chr6A.!!$R1 1567
2 TraesCS6A01G345900 chr6D 433278464 433281562 3098 True 4826.0 4826 94.7350 1 3111 1 chr6D.!!$R3 3110
3 TraesCS6A01G345900 chr6D 432912981 432915293 2312 True 2316.0 2316 84.8120 2 2375 1 chr6D.!!$R1 2373
4 TraesCS6A01G345900 chr6D 433257669 433259321 1652 True 2108.0 2108 89.6820 699 2360 1 chr6D.!!$R2 1661
5 TraesCS6A01G345900 chr6D 433153287 433156216 2929 True 2059.0 3469 90.0435 3 3111 2 chr6D.!!$R5 3108
6 TraesCS6A01G345900 chr6D 432929690 432932315 2625 True 1882.5 3349 90.2630 102 2898 2 chr6D.!!$R4 2796
7 TraesCS6A01G345900 chr6B 653870437 653873534 3097 True 4680.0 4680 93.9020 1 3111 1 chr6B.!!$R3 3110
8 TraesCS6A01G345900 chr6B 653714171 653715843 1672 True 2002.0 2002 88.3220 699 2375 1 chr6B.!!$R1 1676
9 TraesCS6A01G345900 chr6B 653855070 653856640 1570 True 1906.0 1906 88.6710 808 2375 1 chr6B.!!$R2 1567
10 TraesCS6A01G345900 chr6B 653697046 653699923 2877 True 1119.5 1679 86.5855 1 3111 2 chr6B.!!$R5 3110

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
100 101 0.970640 TGTCTACTTTGCAGGGCGTA 59.029 50.0 0.00 0.00 0.00 4.42 F
1068 1102 1.091771 TCTACGGTTCGGTCCTAGCG 61.092 60.0 9.94 9.94 40.97 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 2107 0.747644 CCATCGCAAGGCCACACATA 60.748 55.0 5.01 0.0 38.47 2.29 R
2741 2789 1.127343 AAGCTATCTCTGGTCTGGCC 58.873 55.0 0.00 0.0 37.90 5.36 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
31 32 2.782341 CAAATCAAGGGGAGGAGGAGAT 59.218 50.000 0.00 0.00 0.00 2.75
100 101 0.970640 TGTCTACTTTGCAGGGCGTA 59.029 50.000 0.00 0.00 0.00 4.42
116 117 3.510719 GGCGTAACATACTACCGTTCAA 58.489 45.455 0.00 0.00 0.00 2.69
142 143 2.911509 TGCAATGCCGCACAACCT 60.912 55.556 1.53 0.00 36.86 3.50
220 221 4.099573 CAGGGAATGTGAGATACGGTACTT 59.900 45.833 0.00 0.00 0.00 2.24
221 222 4.341520 AGGGAATGTGAGATACGGTACTTC 59.658 45.833 0.00 0.00 0.00 3.01
222 223 4.341520 GGGAATGTGAGATACGGTACTTCT 59.658 45.833 0.00 0.00 0.00 2.85
223 224 5.533903 GGGAATGTGAGATACGGTACTTCTA 59.466 44.000 0.00 0.00 0.00 2.10
224 225 6.208994 GGGAATGTGAGATACGGTACTTCTAT 59.791 42.308 0.00 0.00 0.00 1.98
225 226 7.085116 GGAATGTGAGATACGGTACTTCTATG 58.915 42.308 0.00 0.00 0.00 2.23
226 227 7.040617 GGAATGTGAGATACGGTACTTCTATGA 60.041 40.741 0.00 0.00 0.00 2.15
227 228 7.818997 ATGTGAGATACGGTACTTCTATGAA 57.181 36.000 0.00 0.00 0.00 2.57
228 229 7.634671 TGTGAGATACGGTACTTCTATGAAA 57.365 36.000 0.00 0.00 0.00 2.69
273 274 2.031919 ATCTGCGTGGCCGTGAAA 59.968 55.556 0.00 0.00 36.15 2.69
481 484 5.242434 TCAACTTATTATGTCCGTGTTGCT 58.758 37.500 0.00 0.00 34.95 3.91
572 577 9.220906 TGTATTCTCTGTAGGTACCCATAATTT 57.779 33.333 8.74 0.00 0.00 1.82
580 585 6.948886 TGTAGGTACCCATAATTTTTCTTGCA 59.051 34.615 8.74 0.00 0.00 4.08
653 677 7.088589 ACACTCCAAATTCTTATACATGCAC 57.911 36.000 0.00 0.00 0.00 4.57
690 715 7.587757 GCAGCAAACTTATATATTTTGTCCTCG 59.412 37.037 14.38 0.00 33.57 4.63
753 778 6.771076 TCATTGATAGAAAAATCCGTCAACG 58.229 36.000 0.00 0.00 39.44 4.10
793 818 7.553044 ACTTCCAGCTAGGTATGTTTGATTTAC 59.447 37.037 0.00 0.00 39.02 2.01
815 840 2.231380 ACCATCCCCACACCAGACC 61.231 63.158 0.00 0.00 0.00 3.85
862 887 8.007742 ACATCTTCCCACTAGATATACTTCACT 58.992 37.037 0.00 0.00 31.32 3.41
936 961 9.274206 GAACTATATAAGAAACCCAGTTCCATC 57.726 37.037 0.00 0.00 36.17 3.51
1068 1102 1.091771 TCTACGGTTCGGTCCTAGCG 61.092 60.000 9.94 9.94 40.97 4.26
1216 1250 3.582780 GGGTTCATCGAGTCGTTTAACT 58.417 45.455 13.12 0.00 0.00 2.24
1218 1252 4.483311 GGTTCATCGAGTCGTTTAACTCT 58.517 43.478 13.12 0.00 42.90 3.24
1254 1288 6.438425 AGTTCTATTTGGGCATCAATCAGTTT 59.562 34.615 0.00 0.00 34.98 2.66
1612 1651 5.718146 CTTATCTCACTGTCAGAGCAAGAA 58.282 41.667 6.91 0.00 31.81 2.52
1801 1840 4.191544 TCAAAAGCTATGAGGATGTTCCG 58.808 43.478 0.00 0.00 42.75 4.30
2068 2107 1.553704 GACATTACCGACAAGAGGGGT 59.446 52.381 0.00 0.00 37.84 4.95
2249 2288 9.378551 TGTCTTGTATAGTATTTCATGTTCCAC 57.621 33.333 0.00 0.00 0.00 4.02
2356 2403 3.121030 CCGCCTCTTGTGCCTTCG 61.121 66.667 0.00 0.00 0.00 3.79
2375 2422 6.018262 GCCTTCGTGCATACATAATGAACTAA 60.018 38.462 0.00 0.00 41.51 2.24
2383 2430 7.168219 GCATACATAATGAACTAATCCCTCCA 58.832 38.462 0.00 0.00 37.86 3.86
2497 2545 3.750130 GCTCCATATGCAATCTACAGTGG 59.250 47.826 0.00 0.00 0.00 4.00
2508 2556 7.394016 TGCAATCTACAGTGGAATCTCTAAAA 58.606 34.615 0.00 0.00 0.00 1.52
2545 2593 8.857694 TTAGAAACGGAGGAATTATTTGACTT 57.142 30.769 0.00 0.00 0.00 3.01
2741 2789 1.090625 TCGTTCAACCCACAACACCG 61.091 55.000 0.00 0.00 0.00 4.94
2781 2829 0.836400 TCTTTCCCCTCTCGCAAGGT 60.836 55.000 2.74 0.00 34.34 3.50
2889 2942 2.840753 GGAGGGGGTTTCTGGTGCA 61.841 63.158 0.00 0.00 0.00 4.57
2936 2989 1.485294 TTTTAGTCCTCGCAGGGGCA 61.485 55.000 0.00 0.00 41.24 5.36
2983 3036 2.594131 TCTTTGAGTCAGTCTTCCGGA 58.406 47.619 0.00 0.00 0.00 5.14
3004 3057 3.766591 GACTCTGATCCTCCTCAAGTTCA 59.233 47.826 0.00 0.00 0.00 3.18
3036 3089 1.485066 GGATTAGAAGGAACTCCGGCA 59.515 52.381 0.00 0.00 38.49 5.69
3056 3109 3.247173 GCATAGATTCCTGTCAGCTTTCG 59.753 47.826 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.319136 ACCAACGCAGACAACACTTA 57.681 45.000 0.00 0.00 0.00 2.24
100 101 5.217978 TCAAGGTTGAACGGTAGTATGTT 57.782 39.130 0.00 0.00 33.55 2.71
116 117 2.338015 CGGCATTGCAGCTCAAGGT 61.338 57.895 11.39 0.00 38.61 3.50
142 143 1.888172 CGTGTGGTGCGGGTTGTTA 60.888 57.895 0.00 0.00 0.00 2.41
178 179 3.276846 GGTGGTCGTGGTGTGTGC 61.277 66.667 0.00 0.00 0.00 4.57
193 194 1.139058 GTATCTCACATTCCCTGCGGT 59.861 52.381 0.00 0.00 0.00 5.68
203 204 7.818997 TTCATAGAAGTACCGTATCTCACAT 57.181 36.000 0.00 0.00 0.00 3.21
227 228 9.667107 TCCTTTCGACTAACAATTTCATAGATT 57.333 29.630 0.00 0.00 0.00 2.40
228 229 9.319143 CTCCTTTCGACTAACAATTTCATAGAT 57.681 33.333 0.00 0.00 0.00 1.98
269 270 6.964741 TTTAATAACACCGAGCGTATTTCA 57.035 33.333 0.00 0.00 0.00 2.69
273 274 7.781548 AGAATTTTAATAACACCGAGCGTAT 57.218 32.000 0.00 0.00 0.00 3.06
278 279 7.305474 AGTGCAAGAATTTTAATAACACCGAG 58.695 34.615 0.00 0.00 0.00 4.63
430 433 8.723942 AAGACAACTTAGCTAACCTTATGATG 57.276 34.615 0.86 0.00 34.28 3.07
437 440 8.549338 GTTGATTAAGACAACTTAGCTAACCT 57.451 34.615 16.12 0.00 42.63 3.50
481 484 1.409802 CCGCTTGTAGGGACTAGGAGA 60.410 57.143 0.00 0.00 44.14 3.71
572 577 2.340731 TGGTACCTACCCTGCAAGAAA 58.659 47.619 14.36 0.00 45.87 2.52
580 585 5.489637 TCACATATTTGTTGGTACCTACCCT 59.510 40.000 21.53 10.03 38.71 4.34
690 715 1.205820 GCGTTTTGGCGTGAGTACC 59.794 57.895 0.00 0.00 0.00 3.34
753 778 1.279840 GAAGTGCTTGCACGGTGAC 59.720 57.895 18.32 3.96 0.00 3.67
793 818 2.035626 GGTGTGGGGATGGTGGTG 59.964 66.667 0.00 0.00 0.00 4.17
852 877 4.945543 TCTCCAACGTAGCAGTGAAGTATA 59.054 41.667 0.00 0.00 0.00 1.47
853 878 3.762288 TCTCCAACGTAGCAGTGAAGTAT 59.238 43.478 0.00 0.00 0.00 2.12
862 887 1.544691 GAGAAGGTCTCCAACGTAGCA 59.455 52.381 0.00 0.00 37.55 3.49
923 948 1.946984 TCTACGGATGGAACTGGGTT 58.053 50.000 0.00 0.00 0.00 4.11
936 961 2.096218 GTGCTCTGCTTTGTTTCTACGG 60.096 50.000 0.00 0.00 0.00 4.02
1068 1102 1.299468 ATCGTTGATCTCGCGAGCC 60.299 57.895 30.97 23.33 38.06 4.70
1216 1250 6.881065 CCCAAATAGAACTTGTGATTCTCAGA 59.119 38.462 0.00 0.00 37.57 3.27
1218 1252 5.415701 GCCCAAATAGAACTTGTGATTCTCA 59.584 40.000 0.00 0.00 37.57 3.27
1520 1559 4.039124 AGAAAATGCCCAACAACAACCTAG 59.961 41.667 0.00 0.00 0.00 3.02
1547 1586 1.406065 ATGCCCTCTGTAGCAGCGAT 61.406 55.000 0.00 0.00 43.38 4.58
1612 1651 3.454719 TGGACATCACAATCCACCAAT 57.545 42.857 0.00 0.00 40.17 3.16
1801 1840 2.409870 CGCTCCCTCATTGTTGGCC 61.410 63.158 0.00 0.00 0.00 5.36
2068 2107 0.747644 CCATCGCAAGGCCACACATA 60.748 55.000 5.01 0.00 38.47 2.29
2356 2403 7.119846 GGAGGGATTAGTTCATTATGTATGCAC 59.880 40.741 0.00 0.00 34.06 4.57
2375 2422 8.061890 AGACTTATATTTGGAAATGGAGGGAT 57.938 34.615 0.00 0.00 0.00 3.85
2524 2572 6.894339 ACAAGTCAAATAATTCCTCCGTTT 57.106 33.333 0.00 0.00 0.00 3.60
2696 2744 4.785376 AGGACAGTAACAATTGGGAGAGAT 59.215 41.667 10.83 0.00 0.00 2.75
2741 2789 1.127343 AAGCTATCTCTGGTCTGGCC 58.873 55.000 0.00 0.00 37.90 5.36
2781 2829 2.180276 GAGACAGGCTTTCCCTAGTCA 58.820 52.381 0.00 0.00 44.09 3.41
2889 2942 1.418334 ATCTGCTAGCCGGAACTGAT 58.582 50.000 13.29 2.77 31.26 2.90
2948 3001 3.390135 TCAAAGAAGAAGCGTCGTCATT 58.610 40.909 16.65 8.97 34.97 2.57
2983 3036 3.784178 TGAACTTGAGGAGGATCAGAGT 58.216 45.455 0.00 0.00 36.25 3.24
3024 3077 1.694696 GGAATCTATGCCGGAGTTCCT 59.305 52.381 5.05 0.00 33.92 3.36
3036 3089 3.181461 CCCGAAAGCTGACAGGAATCTAT 60.181 47.826 4.26 0.00 0.00 1.98
3056 3109 3.846430 CCCTAACCTCGCCGTCCC 61.846 72.222 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.