Multiple sequence alignment - TraesCS1D01G405000

Loading Multiple Alignment...

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 TraesCS1D01G405000 chr1D 100.000 2675 0 0 1 2675 469805470 469808144 0.000000e+00 4940.0
1 TraesCS1D01G405000 chr1B 91.217 2687 155 22 41 2675 651278215 651280872 0.000000e+00 3579.0
2 TraesCS1D01G405000 chr1A 89.837 2765 166 44 1 2675 562911899 562914638 0.000000e+00 3443.0
3 TraesCS1D01G405000 chr1A 74.206 252 49 10 93 344 562911632 562911867 1.020000e-14 91.6


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 TraesCS1D01G405000 chr1D 469805470 469808144 2674 False 4940.0 4940 100.0000 1 2675 1 chr1D.!!$F1 2674
1 TraesCS1D01G405000 chr1B 651278215 651280872 2657 False 3579.0 3579 91.2170 41 2675 1 chr1B.!!$F1 2634
2 TraesCS1D01G405000 chr1A 562911632 562914638 3006 False 1767.3 3443 82.0215 1 2675 2 chr1A.!!$F1 2674

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
880 1187 0.180642 TTCGCGGGGCCACATTTATA 59.819 50.0 5.46 0.0 0.0 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2646 3037 0.738975 TCTTCATCGTACAGCTCCCG 59.261 55.0 0.0 0.0 0.0 5.14 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
30 298 7.013274 CAGAAAAACTATGAAACAGAGGGTGAA 59.987 37.037 0.00 0.00 0.00 3.18
33 301 8.567285 AAAACTATGAAACAGAGGGTGAATAG 57.433 34.615 0.00 0.00 0.00 1.73
34 302 7.496346 AACTATGAAACAGAGGGTGAATAGA 57.504 36.000 0.00 0.00 0.00 1.98
46 314 4.021016 AGGGTGAATAGAAGGCACGATATC 60.021 45.833 0.00 0.00 33.48 1.63
122 390 4.489810 CAGTCCTAACAAGAGCACAGTAG 58.510 47.826 0.00 0.00 0.00 2.57
201 469 2.032030 GCGCTGCCGTTAACATGAATAT 60.032 45.455 0.00 0.00 36.67 1.28
238 506 7.069455 ACAAAGCATTCCTTACTTTACCAAGTT 59.931 33.333 0.00 0.00 43.45 2.66
239 507 6.819397 AGCATTCCTTACTTTACCAAGTTC 57.181 37.500 0.00 0.00 40.66 3.01
280 548 4.617959 CGTATTTAGAGGAAGGATCGCAA 58.382 43.478 0.00 0.00 0.00 4.85
281 549 5.230942 CGTATTTAGAGGAAGGATCGCAAT 58.769 41.667 0.00 0.00 0.00 3.56
282 550 5.119279 CGTATTTAGAGGAAGGATCGCAATG 59.881 44.000 0.00 0.00 0.00 2.82
283 551 4.753516 TTTAGAGGAAGGATCGCAATGA 57.246 40.909 0.00 0.00 0.00 2.57
284 552 4.963318 TTAGAGGAAGGATCGCAATGAT 57.037 40.909 0.00 0.00 41.06 2.45
300 568 2.620251 TGATCGCCCAATTGACCTAG 57.380 50.000 7.12 0.00 0.00 3.02
501 774 1.293498 GAGCAGGAAGGCGAAGTCA 59.707 57.895 0.00 0.00 39.27 3.41
789 1073 1.385206 GGAGCAGAGGGGAGGGATT 60.385 63.158 0.00 0.00 0.00 3.01
811 1111 4.219115 TGATTTTTGCAGTTCAACCCCTA 58.781 39.130 0.00 0.00 33.73 3.53
866 1173 4.317839 CGAGGGTTTCTATGTAAATTCGCG 60.318 45.833 0.00 0.00 0.00 5.87
873 1180 1.381165 ATGTAAATTCGCGGGGCCAC 61.381 55.000 6.13 0.00 0.00 5.01
880 1187 0.180642 TTCGCGGGGCCACATTTATA 59.819 50.000 5.46 0.00 0.00 0.98
889 1196 6.404293 GCGGGGCCACATTTATAATTATACAG 60.404 42.308 5.46 1.47 0.00 2.74
918 1225 2.772515 AGGGCCTTTAAGCTTCTACGAT 59.227 45.455 0.00 0.00 0.00 3.73
919 1226 3.200165 AGGGCCTTTAAGCTTCTACGATT 59.800 43.478 0.00 0.00 0.00 3.34
946 1260 0.610509 AGTTCCGCAGAGCAGAGAGA 60.611 55.000 0.00 0.00 0.00 3.10
947 1261 0.244994 GTTCCGCAGAGCAGAGAGAA 59.755 55.000 0.00 0.00 0.00 2.87
949 1263 0.895559 TCCGCAGAGCAGAGAGAACA 60.896 55.000 0.00 0.00 0.00 3.18
950 1264 0.458197 CCGCAGAGCAGAGAGAACAG 60.458 60.000 0.00 0.00 0.00 3.16
1107 1429 1.213013 CACCTCGGTCTGGAACTCG 59.787 63.158 0.00 0.00 0.00 4.18
1110 1432 1.134901 CTCGGTCTGGAACTCGTCG 59.865 63.158 0.00 0.00 0.00 5.12
1623 1945 2.125961 GCACCTCGACCCGGAGTAT 61.126 63.158 0.73 0.00 31.98 2.12
1817 2151 1.484038 TGGCTTCCATGGGTTAATGC 58.516 50.000 13.02 6.20 0.00 3.56
1978 2347 3.736252 CCTAACACTCAACTTCTGTGTCG 59.264 47.826 0.00 0.00 43.11 4.35
2065 2434 7.764901 CCAACTAGGGTAAGAGATTAACTGAAC 59.235 40.741 0.00 0.00 0.00 3.18
2066 2435 8.311836 CAACTAGGGTAAGAGATTAACTGAACA 58.688 37.037 0.00 0.00 0.00 3.18
2214 2583 5.994668 GGAGATAATTGAATGTGACTCCTCC 59.005 44.000 0.00 0.00 39.36 4.30
2238 2607 5.928839 CGGTATGCAAAATCTAGCTGAGTAT 59.071 40.000 0.00 0.00 0.00 2.12
2239 2608 6.128715 CGGTATGCAAAATCTAGCTGAGTATG 60.129 42.308 0.00 0.00 0.00 2.39
2241 2610 3.879295 TGCAAAATCTAGCTGAGTATGCC 59.121 43.478 0.00 0.00 32.65 4.40
2271 2643 5.991328 TTCTGTCATGTCTTCTGTTGTTC 57.009 39.130 0.00 0.00 0.00 3.18
2282 2658 7.195646 TGTCTTCTGTTGTTCAAAGCAAATAG 58.804 34.615 0.00 0.00 0.00 1.73
2315 2691 5.010516 TGTGGTTTTATGAAATGGTGGTGAG 59.989 40.000 0.00 0.00 0.00 3.51
2325 2701 5.044919 TGAAATGGTGGTGAGAACCTGATAT 60.045 40.000 0.00 0.00 38.60 1.63
2438 2815 4.380867 CCATGTAGTTCCTTTTGGCACATC 60.381 45.833 0.00 0.00 38.23 3.06
2439 2816 3.826524 TGTAGTTCCTTTTGGCACATCA 58.173 40.909 0.00 0.00 38.23 3.07
2448 2825 1.107114 TTGGCACATCAAAACCGTGT 58.893 45.000 0.00 0.00 39.30 4.49
2463 2840 0.179140 CGTGTTGTATGCCCATTGCC 60.179 55.000 0.00 0.00 40.16 4.52
2477 2854 1.587522 ATTGCCCCCTTGATGAGGCT 61.588 55.000 1.12 0.00 45.94 4.58
2492 2869 5.304357 TGATGAGGCTAATCGAGTTCCATTA 59.696 40.000 7.36 0.00 0.00 1.90
2493 2870 5.808366 TGAGGCTAATCGAGTTCCATTAT 57.192 39.130 0.00 0.00 0.00 1.28
2496 2873 4.841246 AGGCTAATCGAGTTCCATTATCCT 59.159 41.667 0.00 0.00 29.78 3.24
2556 2933 0.407918 TCAAGGGGGTGAATTGTCCC 59.592 55.000 6.10 6.10 42.73 4.46
2581 2958 2.224426 TGGACGTACCATTGAAGCTTGT 60.224 45.455 2.10 0.00 44.64 3.16
2588 2965 3.499338 ACCATTGAAGCTTGTGATTCCA 58.501 40.909 2.10 0.00 37.76 3.53
2638 3029 2.149578 CTGAAGTCTCTTGCTTGGGTG 58.850 52.381 0.00 0.00 0.00 4.61
2646 3037 1.304381 TTGCTTGGGTGATGCCTCC 60.304 57.895 0.00 0.00 37.43 4.30
2658 3049 4.208686 GCCTCCGGGAGCTGTACG 62.209 72.222 18.91 4.99 33.58 3.67
2667 3058 2.025155 GGGAGCTGTACGATGAAGAGA 58.975 52.381 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.846211 CCCTCTGTTTCATAGTTTTTCTGTAAA 58.154 33.333 0.00 0.00 0.00 2.01
2 3 7.444183 CACCCTCTGTTTCATAGTTTTTCTGTA 59.556 37.037 0.00 0.00 0.00 2.74
4 5 6.486657 TCACCCTCTGTTTCATAGTTTTTCTG 59.513 38.462 0.00 0.00 0.00 3.02
46 314 3.242712 GTGCAGTGTTGAAAATTCCAACG 59.757 43.478 14.83 6.17 44.92 4.10
122 390 6.595772 CATCCTCTGCATTTCAGTAGTAAC 57.404 41.667 0.00 0.00 43.32 2.50
201 469 9.255304 GTAAGGAATGCTTTGTTAATTTGTTCA 57.745 29.630 0.00 0.00 0.00 3.18
232 500 6.591834 CCTAGATTTGTAGTGTGAGAACTTGG 59.408 42.308 0.00 0.00 0.00 3.61
238 506 3.762288 ACGCCTAGATTTGTAGTGTGAGA 59.238 43.478 0.00 0.00 0.00 3.27
239 507 4.111375 ACGCCTAGATTTGTAGTGTGAG 57.889 45.455 0.00 0.00 0.00 3.51
280 548 2.224621 CCTAGGTCAATTGGGCGATCAT 60.225 50.000 5.42 0.00 0.00 2.45
281 549 1.140852 CCTAGGTCAATTGGGCGATCA 59.859 52.381 5.42 0.00 0.00 2.92
282 550 1.884235 CCTAGGTCAATTGGGCGATC 58.116 55.000 5.42 0.00 0.00 3.69
283 551 0.179018 GCCTAGGTCAATTGGGCGAT 60.179 55.000 11.31 0.00 33.30 4.58
284 552 1.223487 GCCTAGGTCAATTGGGCGA 59.777 57.895 11.31 0.00 33.30 5.54
285 553 0.466189 ATGCCTAGGTCAATTGGGCG 60.466 55.000 11.31 0.00 45.06 6.13
286 554 1.035139 CATGCCTAGGTCAATTGGGC 58.965 55.000 11.31 13.85 42.73 5.36
287 555 1.063717 ACCATGCCTAGGTCAATTGGG 60.064 52.381 20.60 15.97 32.90 4.12
288 556 2.442236 ACCATGCCTAGGTCAATTGG 57.558 50.000 11.31 15.33 32.90 3.16
308 576 2.284514 GCTTATTCAGTTCGTCGCTTCG 60.285 50.000 0.00 0.00 0.00 3.79
390 663 1.066573 CCATTTGGTGAGCTCTCGACT 60.067 52.381 16.19 0.00 0.00 4.18
392 665 0.250234 CCCATTTGGTGAGCTCTCGA 59.750 55.000 16.19 5.76 0.00 4.04
616 889 4.214327 CGGCGGCTCCTCCTCTTC 62.214 72.222 7.61 0.00 0.00 2.87
789 1073 3.037549 AGGGGTTGAACTGCAAAAATCA 58.962 40.909 0.00 0.00 38.44 2.57
866 1173 8.417273 AACTGTATAATTATAAATGTGGCCCC 57.583 34.615 6.75 0.00 0.00 5.80
880 1187 4.080526 AGGCCCTCGTGAAACTGTATAATT 60.081 41.667 0.00 0.00 31.75 1.40
889 1196 1.199327 GCTTAAAGGCCCTCGTGAAAC 59.801 52.381 0.00 0.00 0.00 2.78
918 1225 0.756294 TCTGCGGAACTGTCCTGAAA 59.244 50.000 0.00 0.00 42.44 2.69
919 1226 0.318441 CTCTGCGGAACTGTCCTGAA 59.682 55.000 0.00 0.00 42.44 3.02
946 1260 1.704641 GGAAGGGTTTTGCCTCTGTT 58.295 50.000 0.00 0.00 37.43 3.16
947 1261 0.537371 CGGAAGGGTTTTGCCTCTGT 60.537 55.000 0.00 0.00 37.43 3.41
949 1263 0.537371 CACGGAAGGGTTTTGCCTCT 60.537 55.000 0.00 0.00 37.43 3.69
950 1264 1.524008 CCACGGAAGGGTTTTGCCTC 61.524 60.000 0.00 0.00 37.43 4.70
1107 1429 1.512310 CTTGACGAGGACGAGCGAC 60.512 63.158 0.00 0.00 42.66 5.19
1110 1432 1.066114 CGAACTTGACGAGGACGAGC 61.066 60.000 0.00 0.00 42.66 5.03
1623 1945 0.104855 CATCGGATTCCTCGAAGGCA 59.895 55.000 0.30 0.00 40.15 4.75
1817 2151 6.735063 CGGCGAAACTTAACATGTTACTTAAG 59.265 38.462 17.85 15.92 36.45 1.85
1978 2347 7.589221 GTGTCACTCACAAGAAGATTTGATTTC 59.411 37.037 0.00 0.00 45.51 2.17
2102 2471 7.874940 TCACAAAGAAGATTTGATTTCGACAT 58.125 30.769 7.30 0.00 33.83 3.06
2214 2583 4.122776 ACTCAGCTAGATTTTGCATACCG 58.877 43.478 0.00 0.00 0.00 4.02
2238 2607 1.137675 CATGACAGAATCCTCTCGGCA 59.862 52.381 0.00 0.00 0.00 5.69
2239 2608 1.137872 ACATGACAGAATCCTCTCGGC 59.862 52.381 0.00 0.00 0.00 5.54
2241 2610 4.097741 AGAAGACATGACAGAATCCTCTCG 59.902 45.833 0.00 0.00 0.00 4.04
2282 2658 2.295909 TCATAAAACCACAGCAGCAACC 59.704 45.455 0.00 0.00 0.00 3.77
2315 2691 7.192232 GCTCTTTCACAAATCATATCAGGTTC 58.808 38.462 0.00 0.00 0.00 3.62
2325 2701 4.973168 ACTAGTGGCTCTTTCACAAATCA 58.027 39.130 0.00 0.00 37.58 2.57
2438 2815 1.338337 TGGGCATACAACACGGTTTTG 59.662 47.619 5.52 5.52 0.00 2.44
2439 2816 1.693627 TGGGCATACAACACGGTTTT 58.306 45.000 0.00 0.00 0.00 2.43
2463 2840 1.694150 TCGATTAGCCTCATCAAGGGG 59.306 52.381 0.00 0.00 46.32 4.79
2564 2941 4.437390 GGAATCACAAGCTTCAATGGTACG 60.437 45.833 0.00 0.00 0.00 3.67
2567 2944 3.499338 TGGAATCACAAGCTTCAATGGT 58.501 40.909 0.00 0.00 0.00 3.55
2581 2958 1.885233 TGCGCAAATCACTTGGAATCA 59.115 42.857 8.16 0.00 35.38 2.57
2588 2965 1.216178 GCCCATGCGCAAATCACTT 59.784 52.632 17.11 0.00 0.00 3.16
2646 3037 0.738975 TCTTCATCGTACAGCTCCCG 59.261 55.000 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.