Multiple sequence alignment - TraesCS5B01G152700

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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 TraesCS5B01G152700 chr5B 100.000 3539 0 0 1500 5038 281843608 281840070 0.000000e+00 6536
1 TraesCS5B01G152700 chr5B 100.000 1269 0 0 1 1269 281845107 281843839 0.000000e+00 2344
2 TraesCS5B01G152700 chr5D 97.134 3524 62 4 1500 5022 247617165 247613680 0.000000e+00 5912
3 TraesCS5B01G152700 chr5D 94.113 1274 65 6 1 1269 247618735 247617467 0.000000e+00 1929
4 TraesCS5B01G152700 chr5A 96.168 1644 43 8 3393 5022 331404586 331402949 0.000000e+00 2669
5 TraesCS5B01G152700 chr5A 92.308 1105 51 16 2261 3339 331405676 331404580 0.000000e+00 1539
6 TraesCS5B01G152700 chr5A 91.857 921 55 9 319 1234 331407786 331406881 0.000000e+00 1267
7 TraesCS5B01G152700 chr5A 97.432 701 15 2 1569 2269 331406416 331405719 0.000000e+00 1192
8 TraesCS5B01G152700 chr5A 90.030 331 30 2 1 330 331408286 331407958 4.660000e-115 425


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 TraesCS5B01G152700 chr5B 281840070 281845107 5037 True 4440.0 6536 100.0000 1 5038 2 chr5B.!!$R1 5037
1 TraesCS5B01G152700 chr5D 247613680 247618735 5055 True 3920.5 5912 95.6235 1 5022 2 chr5D.!!$R1 5021
2 TraesCS5B01G152700 chr5A 331402949 331408286 5337 True 1418.4 2669 93.5590 1 5022 5 chr5A.!!$R1 5021

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
290 292 0.392461 TAGAAGTTGCGGTCATGCCC 60.392 55.0 0.0 0.0 0.0 5.36 F
959 1151 0.627986 CTTCTTCCTGCTTCCCCCAT 59.372 55.0 0.0 0.0 0.0 4.00 F
2303 2675 2.288186 GCTCTAAAGTTCTAATGCCGCC 59.712 50.0 0.0 0.0 0.0 6.13 F
2497 2869 0.750182 ACAAGTCCGGTGGTTTGGTG 60.750 55.0 0.0 0.0 0.0 4.17 F
3419 3818 0.240945 CTCGTCCGCAAAGCCATTTT 59.759 50.0 0.0 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 2165 0.674581 CGCTGATCTTCCAGTTGGCA 60.675 55.000 0.00 0.0 36.57 4.92 R
2347 2719 0.962356 ACAGCTAACCATGCACAGGC 60.962 55.000 6.93 0.0 41.68 4.85 R
3372 3771 1.224592 CAAAGCGGGCCTAGTGGAT 59.775 57.895 0.84 0.0 34.57 3.41 R
3575 3977 1.473965 CGATGAGGCAGCCACAATACT 60.474 52.381 16.23 0.0 0.00 2.12 R
4662 5075 9.786224 CAACAAAACTTACTTTTAACACAACAC 57.214 29.630 0.00 0.0 30.39 3.32 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
142 144 9.782028 CATTATCACATGCAAATTTAATAACGC 57.218 29.630 0.00 0.00 0.00 4.84
163 165 1.530323 ATTGGTAACCTTGTGGCGAC 58.470 50.000 0.00 0.00 36.63 5.19
167 169 2.303600 TGGTAACCTTGTGGCGACTTAT 59.696 45.455 0.00 0.00 36.63 1.73
170 172 3.688694 AACCTTGTGGCGACTTATACA 57.311 42.857 0.00 0.00 36.63 2.29
174 176 2.293677 TGTGGCGACTTATACAGCAG 57.706 50.000 0.00 0.00 0.00 4.24
191 193 1.892329 GCAGAAAGGAAGGCCATCCAA 60.892 52.381 28.12 0.00 42.27 3.53
210 212 6.713762 TCCAAGAAGAAAATTTTCAGAGCA 57.286 33.333 28.00 7.16 39.61 4.26
221 223 1.725641 TTCAGAGCACTATGCCAACG 58.274 50.000 0.00 0.00 46.52 4.10
234 236 3.784701 TGCCAACGTACATGTTTGTTT 57.215 38.095 2.30 0.00 37.28 2.83
237 239 5.833082 TGCCAACGTACATGTTTGTTTAAT 58.167 33.333 2.30 0.00 37.28 1.40
277 279 4.104102 TGACAACATGAAACCCCTAGAAGT 59.896 41.667 0.00 0.00 0.00 3.01
290 292 0.392461 TAGAAGTTGCGGTCATGCCC 60.392 55.000 0.00 0.00 0.00 5.36
332 334 4.576463 CCATCTATAACTGTTGGAAGCCAC 59.424 45.833 2.69 0.00 30.78 5.01
343 528 3.607370 GAAGCCACCCCCAGTCGAC 62.607 68.421 7.70 7.70 0.00 4.20
385 570 1.497161 GTAGTCTAGCCCATGGTGGT 58.503 55.000 11.73 10.37 35.17 4.16
393 578 1.925285 GCCCATGGTGGTGATGGAGA 61.925 60.000 11.73 0.00 42.81 3.71
398 583 3.073503 CCATGGTGGTGATGGAGATGTAT 59.926 47.826 2.57 0.00 42.81 2.29
457 642 4.206477 TGGATCATCGACAATTGTCTGT 57.794 40.909 30.45 18.65 42.66 3.41
472 657 2.028112 TGTCTGTCCTGGCATGAAGTAC 60.028 50.000 0.00 0.00 0.00 2.73
484 669 3.181479 GCATGAAGTACCCGACATCACTA 60.181 47.826 0.00 0.00 38.53 2.74
572 757 2.410517 GCATGTGATTGCAAGCAAAACG 60.411 45.455 20.56 10.93 42.31 3.60
638 824 9.853177 CCATCATAAGGAGTTTATTCTTAGGTT 57.147 33.333 0.00 0.00 29.37 3.50
670 856 3.181453 TGATAGTTGTTCGGTTGGGTTCA 60.181 43.478 0.00 0.00 0.00 3.18
704 890 6.560253 TTCAAGTTTTGAAGCTCATAGTCC 57.440 37.500 0.36 0.00 44.21 3.85
716 902 4.019860 AGCTCATAGTCCTGTCAAACATGT 60.020 41.667 0.00 0.00 0.00 3.21
724 910 2.033299 CCTGTCAAACATGTCGCTTTGT 59.967 45.455 0.00 0.00 0.00 2.83
726 912 3.690422 TGTCAAACATGTCGCTTTGTTC 58.310 40.909 0.00 0.00 35.09 3.18
733 919 4.242475 ACATGTCGCTTTGTTCGATTAGA 58.758 39.130 0.00 0.00 38.29 2.10
763 950 3.213206 TGTGGCTTGCTAATCCTATGG 57.787 47.619 0.00 0.00 0.00 2.74
938 1130 3.018149 GTCCTCGTACATCTCAGAACCT 58.982 50.000 0.00 0.00 0.00 3.50
939 1131 3.444388 GTCCTCGTACATCTCAGAACCTT 59.556 47.826 0.00 0.00 0.00 3.50
940 1132 3.695060 TCCTCGTACATCTCAGAACCTTC 59.305 47.826 0.00 0.00 0.00 3.46
959 1151 0.627986 CTTCTTCCTGCTTCCCCCAT 59.372 55.000 0.00 0.00 0.00 4.00
2063 2385 7.837863 TCATATATTTATCAGTTCGGAGGGTC 58.162 38.462 0.00 0.00 0.00 4.46
2111 2433 5.622914 GCATTCACACTAAATTGCAGGATGT 60.623 40.000 0.00 0.00 39.31 3.06
2135 2457 8.952278 TGTTTCTAACGATTGCCAAACTATATT 58.048 29.630 0.00 0.00 0.00 1.28
2283 2655 9.250624 CAGTTGTTACTAGATCTTATTAGGTGC 57.749 37.037 0.00 0.00 31.96 5.01
2303 2675 2.288186 GCTCTAAAGTTCTAATGCCGCC 59.712 50.000 0.00 0.00 0.00 6.13
2347 2719 3.323136 GCGTGTCTCTATGCGCGG 61.323 66.667 8.83 0.00 40.46 6.46
2375 2747 7.679783 TGTGCATGGTTAGCTGTATATATCTT 58.320 34.615 0.00 0.00 0.00 2.40
2462 2834 6.755141 TGACGTGCTTTGGTAACTCTATATTC 59.245 38.462 0.00 0.00 37.61 1.75
2497 2869 0.750182 ACAAGTCCGGTGGTTTGGTG 60.750 55.000 0.00 0.00 0.00 4.17
2578 2950 1.201414 GTGTATTTCGGTGGGCAAAGG 59.799 52.381 0.00 0.00 0.00 3.11
2756 3128 9.523168 AGAGTCTAGTGTAGTTTCTTCTGTTAT 57.477 33.333 0.00 0.00 0.00 1.89
2924 3297 3.313012 TGTATGTTGTGACCGAGGAAG 57.687 47.619 0.00 0.00 0.00 3.46
3009 3403 4.457496 CAGGATGCAGGCGGACGT 62.457 66.667 0.00 0.00 0.00 4.34
3011 3405 4.760047 GGATGCAGGCGGACGTGT 62.760 66.667 0.00 0.00 34.13 4.49
3012 3406 3.188786 GATGCAGGCGGACGTGTC 61.189 66.667 0.00 0.00 34.13 3.67
3158 3557 2.364970 CAGCTTGTATCTAGCTCCTGCT 59.635 50.000 0.00 0.00 45.52 4.24
3173 3572 1.406069 CCTGCTGTTAGAGTTGCCGAT 60.406 52.381 0.00 0.00 0.00 4.18
3211 3610 4.491676 TCAAGTAAACATACAGGCTCGTC 58.508 43.478 0.00 0.00 0.00 4.20
3246 3645 5.863935 GGCCCAAAGCGATAATATCATTTTC 59.136 40.000 0.00 0.00 45.17 2.29
3263 3662 4.969196 CGTGTGCTGACGCTGGGT 62.969 66.667 0.00 0.00 36.97 4.51
3302 3701 2.108514 GCAGCGTGCCTGATGCTTA 61.109 57.895 8.11 0.00 45.28 3.09
3372 3771 2.646175 GCAGGCTCCACAGGACGTA 61.646 63.158 0.00 0.00 0.00 3.57
3419 3818 0.240945 CTCGTCCGCAAAGCCATTTT 59.759 50.000 0.00 0.00 0.00 1.82
3430 3829 4.275443 GCAAAGCCATTTTGGTGATTTTGA 59.725 37.500 13.75 0.00 45.09 2.69
3445 3844 4.728102 TGACGGCGCGGACGAAAT 62.728 61.111 22.76 0.00 43.93 2.17
3472 3871 3.818787 GACGTCCGCTTCCGCCTA 61.819 66.667 3.51 0.00 0.00 3.93
3575 3977 4.951715 AGCTGTCATCAGATTTGCCATTTA 59.048 37.500 0.00 0.00 43.76 1.40
3978 4383 0.602905 AAGCTGCGAACCAGTACCAC 60.603 55.000 0.00 0.00 43.71 4.16
4669 5082 1.668628 GGCCTTAATTGCCGTGTTGTG 60.669 52.381 0.00 0.00 39.48 3.33
5013 5426 4.522789 TGGAAGTTGCCAGAAAAGGATTAC 59.477 41.667 0.00 0.00 33.10 1.89
5019 5432 5.309323 TGCCAGAAAAGGATTACAAATCG 57.691 39.130 0.00 0.00 0.00 3.34
5022 5435 5.106317 GCCAGAAAAGGATTACAAATCGTCA 60.106 40.000 0.00 0.00 0.00 4.35
5023 5436 6.404734 GCCAGAAAAGGATTACAAATCGTCAT 60.405 38.462 0.00 0.00 0.00 3.06
5024 5437 7.201696 GCCAGAAAAGGATTACAAATCGTCATA 60.202 37.037 0.00 0.00 0.00 2.15
5025 5438 8.673711 CCAGAAAAGGATTACAAATCGTCATAA 58.326 33.333 0.00 0.00 0.00 1.90
5026 5439 9.708222 CAGAAAAGGATTACAAATCGTCATAAG 57.292 33.333 0.00 0.00 0.00 1.73
5027 5440 9.667107 AGAAAAGGATTACAAATCGTCATAAGA 57.333 29.630 0.00 0.00 0.00 2.10
5030 5443 8.786826 AAGGATTACAAATCGTCATAAGAACA 57.213 30.769 0.00 0.00 0.00 3.18
5031 5444 8.786826 AGGATTACAAATCGTCATAAGAACAA 57.213 30.769 0.00 0.00 0.00 2.83
5032 5445 9.396022 AGGATTACAAATCGTCATAAGAACAAT 57.604 29.630 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.138304 GCTCATACACACCTTGTTGTCA 58.862 45.455 0.00 0.00 39.91 3.58
13 14 3.403038 AGCTCATACACACCTTGTTGTC 58.597 45.455 0.00 0.00 39.91 3.18
142 144 2.676342 GTCGCCACAAGGTTACCAATAG 59.324 50.000 3.51 0.00 37.19 1.73
163 165 3.879892 GGCCTTCCTTTCTGCTGTATAAG 59.120 47.826 0.00 0.00 0.00 1.73
167 169 1.064003 TGGCCTTCCTTTCTGCTGTA 58.936 50.000 3.32 0.00 0.00 2.74
170 172 0.033699 GGATGGCCTTCCTTTCTGCT 60.034 55.000 26.72 0.00 32.68 4.24
174 176 2.514458 TCTTGGATGGCCTTCCTTTC 57.486 50.000 31.68 11.49 36.68 2.62
191 193 7.311408 GCATAGTGCTCTGAAAATTTTCTTCT 58.689 34.615 26.73 17.72 40.96 2.85
210 212 4.069304 ACAAACATGTACGTTGGCATAGT 58.931 39.130 12.22 0.00 0.00 2.12
234 236 9.677567 GTTGTCAAGCTCAGAAATAAAACATTA 57.322 29.630 0.00 0.00 0.00 1.90
237 239 7.094508 TGTTGTCAAGCTCAGAAATAAAACA 57.905 32.000 0.00 0.00 0.00 2.83
305 307 4.015617 TCCAACAGTTATAGATGGGGGA 57.984 45.455 0.00 0.00 30.61 4.81
332 334 0.616371 TTAACATGGTCGACTGGGGG 59.384 55.000 16.46 3.79 0.00 5.40
368 553 0.252696 TCACCACCATGGGCTAGACT 60.253 55.000 18.09 0.00 43.37 3.24
385 570 0.603065 CCGCCGATACATCTCCATCA 59.397 55.000 0.00 0.00 0.00 3.07
393 578 0.670546 GCATACTGCCGCCGATACAT 60.671 55.000 0.00 0.00 37.42 2.29
398 583 2.796193 ATCTGCATACTGCCGCCGA 61.796 57.895 0.00 0.00 44.23 5.54
457 642 0.616395 TCGGGTACTTCATGCCAGGA 60.616 55.000 0.00 0.00 33.91 3.86
472 657 1.749334 GAGCCCCTAGTGATGTCGGG 61.749 65.000 0.00 0.00 36.78 5.14
484 669 3.710722 CTCCACGCAAGAGCCCCT 61.711 66.667 0.00 0.00 43.62 4.79
553 738 2.796031 CACGTTTTGCTTGCAATCACAT 59.204 40.909 8.93 0.00 0.00 3.21
572 757 5.220854 CGGAACCATCTTTGATATTGTCCAC 60.221 44.000 0.00 0.00 0.00 4.02
638 824 8.447833 CAACCGAACAACTATCAAAATAGCTAA 58.552 33.333 0.00 0.00 38.81 3.09
670 856 5.560966 TCAAAACTTGAAGCTCGACTTTT 57.439 34.783 0.00 0.00 39.29 2.27
701 887 1.512926 AGCGACATGTTTGACAGGAC 58.487 50.000 0.00 0.00 33.56 3.85
704 890 3.338818 ACAAAGCGACATGTTTGACAG 57.661 42.857 13.56 0.81 37.16 3.51
716 902 4.168922 TGACTCTAATCGAACAAAGCGA 57.831 40.909 0.00 0.00 42.48 4.93
724 910 5.294306 GCCACAAATGATGACTCTAATCGAA 59.706 40.000 0.00 0.00 0.00 3.71
726 912 4.813161 AGCCACAAATGATGACTCTAATCG 59.187 41.667 0.00 0.00 0.00 3.34
733 919 2.522185 AGCAAGCCACAAATGATGACT 58.478 42.857 0.00 0.00 0.00 3.41
938 1130 0.698818 GGGGGAAGCAGGAAGAAGAA 59.301 55.000 0.00 0.00 0.00 2.52
939 1131 0.475632 TGGGGGAAGCAGGAAGAAGA 60.476 55.000 0.00 0.00 0.00 2.87
940 1132 0.627986 ATGGGGGAAGCAGGAAGAAG 59.372 55.000 0.00 0.00 0.00 2.85
1567 1830 1.824329 GGAGATGACGCCGGAGAGA 60.824 63.158 13.83 0.00 0.00 3.10
1843 2165 0.674581 CGCTGATCTTCCAGTTGGCA 60.675 55.000 0.00 0.00 36.57 4.92
2016 2338 4.998671 TCTTGTCCAATGCAAGAACAAA 57.001 36.364 5.41 0.00 46.21 2.83
2111 2433 8.332464 CGAATATAGTTTGGCAATCGTTAGAAA 58.668 33.333 0.00 0.00 0.00 2.52
2135 2457 2.697229 AGAATCCATGATCTGAGCACGA 59.303 45.455 0.00 0.00 0.00 4.35
2283 2655 2.540101 CGGCGGCATTAGAACTTTAGAG 59.460 50.000 10.53 0.00 0.00 2.43
2303 2675 2.163818 TGAGTGTGGAGCCTTAAACG 57.836 50.000 0.00 0.00 0.00 3.60
2347 2719 0.962356 ACAGCTAACCATGCACAGGC 60.962 55.000 6.93 0.00 41.68 4.85
2375 2747 4.038042 GTCTCTACATATGTGTGCAGGCTA 59.962 45.833 18.81 0.00 39.39 3.93
2462 2834 7.010738 ACCGGACTTGTATGATTTATAAACACG 59.989 37.037 9.46 0.00 0.00 4.49
2497 2869 4.407945 TGCCCTTGAAGTAGGATAGTAACC 59.592 45.833 0.00 0.00 37.50 2.85
2578 2950 2.489938 TCAACCCATGTGGCTTCTAC 57.510 50.000 0.00 0.00 37.83 2.59
2924 3297 7.335422 TGAGTCAGAGATTAAGCCATTCTTTTC 59.665 37.037 0.00 0.00 36.25 2.29
3158 3557 3.194755 TCAGCTAATCGGCAACTCTAACA 59.805 43.478 0.00 0.00 34.17 2.41
3211 3610 2.565841 GCTTTGGGCCTGTATGTCTAG 58.434 52.381 4.53 0.00 34.27 2.43
3323 3722 2.212869 AGTTCGCTAAACACGACACA 57.787 45.000 0.00 0.00 40.56 3.72
3372 3771 1.224592 CAAAGCGGGCCTAGTGGAT 59.775 57.895 0.84 0.00 34.57 3.41
3419 3818 2.950673 GCGCCGTCAAAATCACCA 59.049 55.556 0.00 0.00 0.00 4.17
3539 3941 3.744238 TGACAGCTGCTAAGTACAACA 57.256 42.857 15.27 0.00 0.00 3.33
3575 3977 1.473965 CGATGAGGCAGCCACAATACT 60.474 52.381 16.23 0.00 0.00 2.12
3978 4383 2.717639 ATAGGTGCACTTTGGCCTAG 57.282 50.000 17.98 3.84 37.07 3.02
4662 5075 9.786224 CAACAAAACTTACTTTTAACACAACAC 57.214 29.630 0.00 0.00 30.39 3.32


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

AutoCloner maintained by Alex Coulton.