Multiple sequence alignment - TraesCS3B01G387700

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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 TraesCS3B01G387700 chr3B 100.000 3092 0 0 1 3092 610492436 610495527 0 5710
1 TraesCS3B01G387700 chr3A 96.404 3115 82 17 1 3091 602681041 602684149 0 5105
2 TraesCS3B01G387700 chr3D 95.893 3117 101 13 1 3091 460413468 460416583 0 5022


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 TraesCS3B01G387700 chr3B 610492436 610495527 3091 False 5710 5710 100.000 1 3092 1 chr3B.!!$F1 3091
1 TraesCS3B01G387700 chr3A 602681041 602684149 3108 False 5105 5105 96.404 1 3091 1 chr3A.!!$F1 3090
2 TraesCS3B01G387700 chr3D 460413468 460416583 3115 False 5022 5022 95.893 1 3091 1 chr3D.!!$F1 3090

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
260 261 2.177888 GGCCTTCCCCCTCTGAATTTAT 59.822 50.0 0.00 0.0 0.00 1.40 F
1206 1208 0.548926 TTGACCACTGGGAGCCCATA 60.549 55.0 9.03 0.0 46.15 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1212 1214 0.178533 AGAAGAGCTCATCTGCTGGC 59.821 55.0 20.17 0.00 42.99 4.85 R
2348 2353 0.034756 TGGACTTGCTACATGTGCGT 59.965 50.0 9.11 4.76 33.84 5.24 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
208 209 8.915654 GTTGACATGGAGATGAAATAAACAAAC 58.084 33.333 0.00 0.00 33.36 2.93
210 211 8.637099 TGACATGGAGATGAAATAAACAAACAA 58.363 29.630 0.00 0.00 33.36 2.83
224 225 3.561143 ACAAACAACAGGTTGCTCCATA 58.439 40.909 11.84 0.00 44.03 2.74
260 261 2.177888 GGCCTTCCCCCTCTGAATTTAT 59.822 50.000 0.00 0.00 0.00 1.40
445 447 6.427853 TGAATCTGAACACATTCCTACACTTG 59.572 38.462 0.00 0.00 33.49 3.16
470 472 4.552355 TGCTCGAAAGAATACGAAACTCA 58.448 39.130 0.00 0.00 41.32 3.41
817 819 2.333069 CAAGAGGCAGATCATAGGGGA 58.667 52.381 0.00 0.00 0.00 4.81
820 822 2.978278 AGAGGCAGATCATAGGGGAAAG 59.022 50.000 0.00 0.00 0.00 2.62
824 826 2.979678 GCAGATCATAGGGGAAAGGGTA 59.020 50.000 0.00 0.00 0.00 3.69
844 846 4.141688 GGTAGGTCCCTCAAAAGGAGTATG 60.142 50.000 0.00 0.00 46.67 2.39
856 858 6.945435 TCAAAAGGAGTATGAGCCAATTTACA 59.055 34.615 0.00 0.00 0.00 2.41
961 963 2.880167 GCCAAAACCAAACCAAACCCAA 60.880 45.455 0.00 0.00 0.00 4.12
1041 1043 0.692476 TCCATGACCAACCACTCCAG 59.308 55.000 0.00 0.00 0.00 3.86
1206 1208 0.548926 TTGACCACTGGGAGCCCATA 60.549 55.000 9.03 0.00 46.15 2.74
1212 1214 1.004080 CTGGGAGCCCATAGCATCG 60.004 63.158 9.03 0.00 46.15 3.84
1570 1572 5.125417 GCTTACCTCAAGACAATATTTGCCA 59.875 40.000 0.00 0.00 36.22 4.92
1755 1757 3.833732 AGAAGATGAGTACGGCCATAGA 58.166 45.455 2.24 0.00 0.00 1.98
1857 1859 6.064060 GTCAAATTCATCATCCTACATCCCA 58.936 40.000 0.00 0.00 0.00 4.37
2103 2105 6.666417 CAGACAACGGTAGTATAGATGGTAC 58.334 44.000 0.00 0.00 0.00 3.34
2206 2208 7.683437 AAACTTGGCTATGTAAGTAACTTCC 57.317 36.000 0.00 0.00 36.19 3.46
2207 2209 6.622427 ACTTGGCTATGTAAGTAACTTCCT 57.378 37.500 0.00 0.00 35.50 3.36
2212 2214 7.779073 TGGCTATGTAAGTAACTTCCTTCTAC 58.221 38.462 0.00 0.00 0.00 2.59
2228 2230 5.926542 TCCTTCTACGAATGAACAGTTTCAG 59.073 40.000 0.00 0.00 45.07 3.02
2235 2237 7.259290 ACGAATGAACAGTTTCAGTATGTTT 57.741 32.000 0.00 0.00 45.07 2.83
2237 2239 7.011950 ACGAATGAACAGTTTCAGTATGTTTCA 59.988 33.333 0.00 0.00 45.07 2.69
2238 2240 8.017373 CGAATGAACAGTTTCAGTATGTTTCAT 58.983 33.333 0.00 0.00 45.07 2.57
2336 2341 4.393371 GGCAAACCTTTCTCTGATCAGTAC 59.607 45.833 21.92 0.00 0.00 2.73
2348 2353 7.526918 TCTCTGATCAGTACCCATATTACAGA 58.473 38.462 21.92 9.78 0.00 3.41
2349 2354 7.448777 TCTCTGATCAGTACCCATATTACAGAC 59.551 40.741 21.92 0.00 0.00 3.51
2405 2410 5.900425 TGCAACAGAAACAAGCATCTTAAA 58.100 33.333 0.00 0.00 0.00 1.52
2494 2505 3.782523 TCCCATGCTTGGTTCTTATCTCT 59.217 43.478 16.81 0.00 41.91 3.10
2544 2555 5.298989 TCCTACCTGCTTTCTGTTTGTTA 57.701 39.130 0.00 0.00 0.00 2.41
2584 2596 5.551760 ACTCTCAAAAGTTTGTGTGTCAG 57.448 39.130 3.82 0.00 39.18 3.51
2599 2611 4.623167 GTGTGTCAGATGTGTGTCTATGAC 59.377 45.833 0.00 0.00 0.00 3.06
2603 2615 5.163754 TGTCAGATGTGTGTCTATGACGTAG 60.164 44.000 0.00 0.00 34.95 3.51
2606 2618 3.487563 TGTGTGTCTATGACGTAGCAG 57.512 47.619 0.00 0.00 34.95 4.24
2682 2694 7.339466 AGAAGGCAATACGATGAACCTTTTATT 59.661 33.333 0.00 0.00 37.63 1.40
2704 2716 0.595825 GCAACCTGACTGCAACTTGC 60.596 55.000 6.82 6.82 45.29 4.01
2779 2794 5.659079 ACCCAAAAGACTCCAAAATTGTGTA 59.341 36.000 0.00 0.00 0.00 2.90
2826 2845 9.884465 GTTGCACCTTGATATTATCAGTTAATC 57.116 33.333 6.48 0.00 40.94 1.75
2849 2868 7.928307 TCTGATTTTGGGATTTACTCTTCTG 57.072 36.000 0.00 0.00 0.00 3.02
2855 2874 4.526970 TGGGATTTACTCTTCTGAATGCC 58.473 43.478 0.00 0.00 39.55 4.40
2873 2892 2.288666 GCCGATCCTTGTGCATTTAGA 58.711 47.619 0.00 0.00 0.00 2.10
2908 2927 0.172578 TCATGGCTCTACGTCAACCG 59.827 55.000 0.00 0.00 44.03 4.44
2911 2930 0.607217 TGGCTCTACGTCAACCGAGA 60.607 55.000 0.00 0.00 40.70 4.04
2932 2954 8.230486 CCGAGAAACATTTTCCATATACTATGC 58.770 37.037 0.00 0.00 0.00 3.14
2934 2956 8.099364 AGAAACATTTTCCATATACTATGCCG 57.901 34.615 0.00 0.00 0.00 5.69
2937 2959 3.343941 TTTCCATATACTATGCCGGGC 57.656 47.619 13.32 13.32 0.00 6.13
2996 3023 6.183360 GGCACTTAAAACATGAAAGGCAAAAA 60.183 34.615 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
208 209 5.389859 TGAAAATATGGAGCAACCTGTTG 57.610 39.130 5.66 5.66 43.14 3.33
210 211 4.019174 CCTGAAAATATGGAGCAACCTGT 58.981 43.478 1.91 0.00 39.86 4.00
224 225 2.894919 GCCGCATGCCCTGAAAAT 59.105 55.556 13.15 0.00 0.00 1.82
260 261 1.663173 GCCCAAAGCTTGCGGTTTA 59.337 52.632 0.00 0.00 38.69 2.01
445 447 3.991605 TTCGTATTCTTTCGAGCAAGC 57.008 42.857 0.00 0.00 37.38 4.01
470 472 4.321675 GCGAACTGGGATGGTTTTATTGTT 60.322 41.667 0.00 0.00 0.00 2.83
601 603 4.941263 TGTTTGATGTGTAGGATTACCAGC 59.059 41.667 0.00 0.00 38.94 4.85
784 786 1.403323 GCCTCTTGTTTGCATCCTAGC 59.597 52.381 0.00 0.00 0.00 3.42
824 826 3.777522 CTCATACTCCTTTTGAGGGACCT 59.222 47.826 0.00 0.00 46.01 3.85
844 846 6.084326 TGAAGAGGTTTTGTAAATTGGCTC 57.916 37.500 0.00 0.00 0.00 4.70
856 858 2.106511 TGCCTGTAGCTGAAGAGGTTTT 59.893 45.455 0.00 0.00 44.23 2.43
907 909 4.037565 GGTTGTGTTTTAGGAAGGAAGTGG 59.962 45.833 0.00 0.00 0.00 4.00
961 963 3.279434 GTGTTTCTGGTGAGTTGGTCTT 58.721 45.455 0.00 0.00 0.00 3.01
1041 1043 5.141182 TCCATGTCTATGTAGTCCTCTTCC 58.859 45.833 0.00 0.00 32.21 3.46
1206 1208 1.227586 CTCATCTGCTGGCGATGCT 60.228 57.895 16.38 0.00 38.47 3.79
1212 1214 0.178533 AGAAGAGCTCATCTGCTGGC 59.821 55.000 20.17 0.00 42.99 4.85
1570 1572 2.270434 TCTGGATCCCCTGCTTTAGT 57.730 50.000 9.90 0.00 0.00 2.24
1638 1640 3.593942 TGGGTTCTTCCTCCAACTCTTA 58.406 45.455 0.00 0.00 36.25 2.10
1755 1757 7.470702 CGGATAATGACACTAGAGAATGACCTT 60.471 40.741 0.00 0.00 0.00 3.50
1857 1859 3.571401 CCAAACCAGAGTCATTTGAGCTT 59.429 43.478 13.28 0.00 35.73 3.74
2103 2105 7.733402 AAATCATCAGGGTGTTGAAATTTTG 57.267 32.000 0.00 0.00 30.83 2.44
2147 2149 7.559590 AGCATGTCTTTAGGAAACATATGAC 57.440 36.000 10.38 0.45 32.54 3.06
2206 2208 6.771188 ACTGAAACTGTTCATTCGTAGAAG 57.229 37.500 0.00 0.00 42.85 2.85
2207 2209 7.870954 ACATACTGAAACTGTTCATTCGTAGAA 59.129 33.333 0.00 0.00 42.85 2.10
2212 2214 7.351981 TGAAACATACTGAAACTGTTCATTCG 58.648 34.615 0.00 0.00 42.85 3.34
2235 2237 8.882736 CATGTCAAGTGCTAAAATACTACATGA 58.117 33.333 0.00 0.00 41.71 3.07
2237 2239 7.829211 ACCATGTCAAGTGCTAAAATACTACAT 59.171 33.333 0.00 0.00 30.28 2.29
2238 2240 7.165485 ACCATGTCAAGTGCTAAAATACTACA 58.835 34.615 0.00 0.00 0.00 2.74
2336 2341 3.466836 ACATGTGCGTCTGTAATATGGG 58.533 45.455 0.00 0.00 0.00 4.00
2348 2353 0.034756 TGGACTTGCTACATGTGCGT 59.965 50.000 9.11 4.76 33.84 5.24
2349 2354 1.372582 ATGGACTTGCTACATGTGCG 58.627 50.000 9.11 0.16 33.84 5.34
2405 2410 3.828921 ACTATGGCTCATTGCATGTGAT 58.171 40.909 3.13 0.00 45.15 3.06
2573 2585 3.872696 AGACACACATCTGACACACAAA 58.127 40.909 0.00 0.00 0.00 2.83
2584 2596 4.028852 TGCTACGTCATAGACACACATC 57.971 45.455 0.00 0.00 31.83 3.06
2599 2611 4.734108 GCTTAGTTCCTTACCTCTGCTACG 60.734 50.000 0.00 0.00 0.00 3.51
2603 2615 3.611766 TGCTTAGTTCCTTACCTCTGC 57.388 47.619 0.00 0.00 0.00 4.26
2665 2677 7.554835 AGGTTGCATAATAAAAGGTTCATCGTA 59.445 33.333 0.00 0.00 0.00 3.43
2704 2716 3.266510 AGTGTGGTGCCATGTAGTATG 57.733 47.619 0.00 0.00 0.00 2.39
2779 2794 7.877097 TGCAACTTGCCAGAATTACATTTTAAT 59.123 29.630 11.29 0.00 44.23 1.40
2788 2803 2.875296 AGGTGCAACTTGCCAGAATTA 58.125 42.857 11.29 0.00 44.23 1.40
2826 2845 7.928307 TCAGAAGAGTAAATCCCAAAATCAG 57.072 36.000 0.00 0.00 0.00 2.90
2849 2868 1.027357 ATGCACAAGGATCGGCATTC 58.973 50.000 0.00 0.00 43.97 2.67
2855 2874 3.535561 ACCTCTAAATGCACAAGGATCG 58.464 45.455 8.24 0.00 0.00 3.69
2873 2892 3.552875 CCATGAGAATGCATTCAGACCT 58.447 45.455 34.59 18.21 39.23 3.85
2908 2927 8.230486 CGGCATAGTATATGGAAAATGTTTCTC 58.770 37.037 1.11 0.00 0.00 2.87
2911 2930 6.208599 CCCGGCATAGTATATGGAAAATGTTT 59.791 38.462 0.00 0.00 0.00 2.83
2932 2954 2.046314 CCTACACAAGGTGCCCGG 60.046 66.667 0.00 0.00 40.94 5.73
2934 2956 2.215942 ATTTCCTACACAAGGTGCCC 57.784 50.000 0.00 0.00 46.62 5.36
2945 2967 4.935808 CCACCAGTGACTTGTATTTCCTAC 59.064 45.833 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.