Multiple sequence alignment - TraesCS7D01G257200

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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 TraesCS7D01G257200 chr7D 100.000 3380 0 0 1 3380 232498017 232501396 0.000000e+00 6242
1 TraesCS7D01G257200 chr7D 77.483 453 87 9 425 868 230993223 230992777 1.200000e-64 257
2 TraesCS7D01G257200 chr7B 94.625 3423 127 22 1 3380 203281889 203285297 0.000000e+00 5249
3 TraesCS7D01G257200 chr7B 77.232 448 70 19 425 854 202506098 202505665 2.030000e-57 233
4 TraesCS7D01G257200 chr7A 96.579 2397 68 5 986 3380 244672582 244674966 0.000000e+00 3960
5 TraesCS7D01G257200 chr7A 89.773 968 64 5 1 937 244671618 244672581 0.000000e+00 1206
6 TraesCS7D01G257200 chr7A 81.386 505 63 14 2828 3326 244673951 244674430 1.900000e-102 383
7 TraesCS7D01G257200 chr7A 78.775 457 70 17 425 868 243852673 243852231 7.140000e-72 281


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 TraesCS7D01G257200 chr7D 232498017 232501396 3379 False 6242.000000 6242 100.000 1 3380 1 chr7D.!!$F1 3379
1 TraesCS7D01G257200 chr7B 203281889 203285297 3408 False 5249.000000 5249 94.625 1 3380 1 chr7B.!!$F1 3379
2 TraesCS7D01G257200 chr7A 244671618 244674966 3348 False 1849.666667 3960 89.246 1 3380 3 chr7A.!!$F1 3379

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
386 420 0.035152 CTACAGCAGGCCATGAACCA 60.035 55.0 5.01 0.0 0.00 3.67 F
939 973 0.107165 ATGGGCCTCCGTTTCTAAGC 60.107 55.0 4.53 0.0 35.24 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2075 0.475906 GGTGGCCATCCTCAATAGCT 59.524 55.0 9.72 0.0 0.0 3.32 R
2751 2788 0.957395 CATGGAGCGCAGAGTTGGTT 60.957 55.0 11.47 0.0 0.0 3.67 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
83 84 7.497249 CCAGCTAAGTGTCTGCTATAATCTTTT 59.503 37.037 0.00 0.00 35.05 2.27
117 118 9.571810 TGTTCATTGATAATTTGATGTACAAGC 57.428 29.630 0.00 0.00 39.77 4.01
118 119 9.571810 GTTCATTGATAATTTGATGTACAAGCA 57.428 29.630 0.00 0.00 39.77 3.91
177 178 7.042051 TCAGTTATCTACTTTGTGCTTGTTCAC 60.042 37.037 0.00 0.00 33.85 3.18
254 272 1.698165 TCGTGCTGAATCAACGACTC 58.302 50.000 6.12 0.00 0.00 3.36
261 279 3.130633 CTGAATCAACGACTCCAACACA 58.869 45.455 0.00 0.00 0.00 3.72
262 280 3.536570 TGAATCAACGACTCCAACACAA 58.463 40.909 0.00 0.00 0.00 3.33
263 281 3.942115 TGAATCAACGACTCCAACACAAA 59.058 39.130 0.00 0.00 0.00 2.83
332 350 2.987149 CAGCGACTACGAATCACAAGTT 59.013 45.455 0.00 0.00 42.66 2.66
386 420 0.035152 CTACAGCAGGCCATGAACCA 60.035 55.000 5.01 0.00 0.00 3.67
391 425 2.034066 AGGCCATGAACCACGGTG 59.966 61.111 5.01 0.00 0.00 4.94
509 543 4.134379 ACATCCACTGCATAGAAGTCTG 57.866 45.455 0.00 0.00 0.00 3.51
512 546 1.065926 CCACTGCATAGAAGTCTGGCA 60.066 52.381 8.58 8.58 36.58 4.92
517 551 1.939255 GCATAGAAGTCTGGCAGAAGC 59.061 52.381 20.62 11.36 41.10 3.86
521 555 1.004440 AAGTCTGGCAGAAGCGGTC 60.004 57.895 20.62 5.54 43.41 4.79
596 630 3.430098 CCCTCTTCTTCACGATCTTCCTG 60.430 52.174 0.00 0.00 0.00 3.86
652 686 2.101415 GCAAAACCAGCAGAAGGAGTTT 59.899 45.455 0.00 0.00 32.26 2.66
669 703 2.557056 AGTTTGAATCAGACGACGAGGA 59.443 45.455 0.00 0.00 0.00 3.71
695 729 3.053896 CCCGGGAAAACGAGGTGC 61.054 66.667 18.48 0.00 35.47 5.01
726 760 2.007049 GCGAGCTTGCTTGCTACCTTA 61.007 52.381 23.29 0.00 44.17 2.69
754 788 2.014010 ACGACCCTAACCCTAACACA 57.986 50.000 0.00 0.00 0.00 3.72
755 789 1.897802 ACGACCCTAACCCTAACACAG 59.102 52.381 0.00 0.00 0.00 3.66
763 797 3.261818 AACCCTAACACAGAGAGAGGT 57.738 47.619 0.00 0.00 0.00 3.85
765 799 1.205893 CCCTAACACAGAGAGAGGTGC 59.794 57.143 0.00 0.00 38.57 5.01
939 973 0.107165 ATGGGCCTCCGTTTCTAAGC 60.107 55.000 4.53 0.00 35.24 3.09
961 995 2.494918 CTCCACCGTTAGCTCCCG 59.505 66.667 0.00 0.00 0.00 5.14
1614 1649 2.186903 GGCGCCTACAAGCTGCTA 59.813 61.111 22.15 0.00 34.30 3.49
1992 2027 1.019278 ACAAAGTGATGCTACCGGCG 61.019 55.000 0.00 0.00 45.43 6.46
2026 2061 2.042686 CCGAATTGAGGAGGCATTCA 57.957 50.000 0.00 0.00 0.00 2.57
2040 2075 4.529897 AGGCATTCAGATTGTTCTATGCA 58.470 39.130 11.01 0.00 42.20 3.96
2255 2290 5.620206 TGCAAACTACCTTCTTGAGATGAA 58.380 37.500 0.00 0.00 0.00 2.57
2401 2436 2.329267 TGGATCCGGAAGTAGATGCAT 58.671 47.619 9.01 0.00 36.12 3.96
2405 2440 3.459232 TCCGGAAGTAGATGCATTCTG 57.541 47.619 0.00 0.00 35.79 3.02
2432 2467 1.202177 CGCTGCGAATTGCTTGGTAAT 60.202 47.619 18.66 0.00 46.63 1.89
2450 2485 5.047377 TGGTAATGTTTCTGAATTTCCAGGC 60.047 40.000 0.00 0.00 30.84 4.85
2540 2577 6.135290 TGATATGCTTGGCAAGTGATTTAC 57.865 37.500 26.71 10.06 43.62 2.01
2664 2701 3.971245 AGGCACTAAGTTCAGAGGAAG 57.029 47.619 0.00 0.00 36.02 3.46
2684 2721 4.320608 AGGTAAGTTTTGTGGTTGCATG 57.679 40.909 0.00 0.00 0.00 4.06
2725 2762 3.763360 TCCATGATCCATTGGTGTTTGAC 59.237 43.478 1.86 0.00 0.00 3.18
2762 2799 6.072112 TGTTCAATTTAGAACCAACTCTGC 57.928 37.500 6.28 0.00 45.62 4.26
2774 2811 2.133553 CAACTCTGCGCTCCATGATAG 58.866 52.381 9.73 0.00 0.00 2.08
2813 2853 4.319177 GACCCATGCTACCTTGTATGATC 58.681 47.826 0.00 0.00 32.93 2.92
2858 2898 6.706270 TGTCACTAGAAGGAAACTGAATGAAC 59.294 38.462 0.00 0.00 42.68 3.18
2865 2905 5.003096 AGGAAACTGAATGAACCAGGAAT 57.997 39.130 0.00 0.00 41.13 3.01
2873 2913 4.889409 TGAATGAACCAGGAATTAGATGCC 59.111 41.667 0.00 0.00 0.00 4.40
3025 3065 8.929487 AGTGATTTATTTGTTTTGGGTAGGAAA 58.071 29.630 0.00 0.00 0.00 3.13
3077 3117 7.523052 GCCTCAACTAATGTGGTCAAATTTGTA 60.523 37.037 17.47 2.47 43.29 2.41
3083 3123 8.879759 ACTAATGTGGTCAAATTTGTATAGACG 58.120 33.333 17.47 3.77 0.00 4.18
3084 3124 7.915293 AATGTGGTCAAATTTGTATAGACGA 57.085 32.000 17.47 3.14 0.00 4.20
3085 3125 6.961359 TGTGGTCAAATTTGTATAGACGAG 57.039 37.500 17.47 0.00 0.00 4.18
3086 3126 6.460781 TGTGGTCAAATTTGTATAGACGAGT 58.539 36.000 17.47 0.00 0.00 4.18
3087 3127 7.604549 TGTGGTCAAATTTGTATAGACGAGTA 58.395 34.615 17.47 0.00 0.00 2.59
3088 3128 8.255206 TGTGGTCAAATTTGTATAGACGAGTAT 58.745 33.333 17.47 0.00 0.00 2.12
3089 3129 9.740239 GTGGTCAAATTTGTATAGACGAGTATA 57.260 33.333 17.47 0.00 0.00 1.47
3090 3130 9.961265 TGGTCAAATTTGTATAGACGAGTATAG 57.039 33.333 17.47 0.00 0.00 1.31
3120 3160 6.285990 GTTAACAAGAAGAGTAGTGGTGGAA 58.714 40.000 0.00 0.00 0.00 3.53
3137 3177 5.045942 TGGTGGAATATGCAGTAAGTTGAGA 60.046 40.000 0.00 0.00 0.00 3.27
3195 3235 2.513317 TGAAATATCCACTGCCCCATCA 59.487 45.455 0.00 0.00 0.00 3.07
3205 3245 0.478072 TGCCCCATCAGTGTTTGACT 59.522 50.000 0.00 0.00 38.99 3.41
3312 3352 6.811253 TGCTACCTTGTACGATTTGAAATT 57.189 33.333 0.00 0.00 0.00 1.82
3314 3354 6.205853 TGCTACCTTGTACGATTTGAAATTGT 59.794 34.615 14.65 14.65 0.00 2.71
3338 3378 4.790718 TGTAGAGATAGGGCTGACTACA 57.209 45.455 0.00 0.00 38.12 2.74
3343 3383 5.815581 AGAGATAGGGCTGACTACAGATAG 58.184 45.833 0.00 0.00 46.03 2.08
3363 3405 1.953686 GTGTTTGCTAACCTCAAGGCA 59.046 47.619 8.56 0.00 39.32 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.777580 ACCTTGTTGTTTTATTGATGACTCCT 59.222 34.615 0.00 0.00 0.00 3.69
13 14 6.981722 ACCTTGTTGTTTTATTGATGACTCC 58.018 36.000 0.00 0.00 0.00 3.85
14 15 9.959749 TTTACCTTGTTGTTTTATTGATGACTC 57.040 29.630 0.00 0.00 0.00 3.36
102 103 6.815641 TGTTTGTTGTGCTTGTACATCAAATT 59.184 30.769 21.47 0.00 44.92 1.82
145 146 6.311445 AGCACAAAGTAGATAACTGAACGATG 59.689 38.462 0.00 0.00 38.88 3.84
177 178 5.016173 TGAAGGTGGAAACCATTTAGGATG 58.984 41.667 0.00 0.00 41.22 3.51
254 272 4.122143 ACTGTGAAATGGTTTGTGTTGG 57.878 40.909 0.00 0.00 0.00 3.77
261 279 6.010219 AGGCTATGTTACTGTGAAATGGTTT 58.990 36.000 0.00 0.00 0.00 3.27
262 280 5.570320 AGGCTATGTTACTGTGAAATGGTT 58.430 37.500 0.00 0.00 0.00 3.67
263 281 5.179452 AGGCTATGTTACTGTGAAATGGT 57.821 39.130 0.00 0.00 0.00 3.55
343 363 0.106918 TGGAGGTCTGTGGCGTTTTT 60.107 50.000 0.00 0.00 0.00 1.94
414 448 2.158957 AGATCCCGATTGTTACGCATGT 60.159 45.455 0.00 0.00 0.00 3.21
509 543 1.591863 GGTATCGACCGCTTCTGCC 60.592 63.158 0.00 0.00 35.52 4.85
521 555 2.332063 ACATTGGCCTCAAGGTATCG 57.668 50.000 3.32 0.00 44.70 2.92
652 686 4.976224 TTTATCCTCGTCGTCTGATTCA 57.024 40.909 0.00 0.00 0.00 2.57
669 703 3.688235 TCGTTTTCCCGGGTGATTTTAT 58.312 40.909 22.86 0.00 0.00 1.40
754 788 1.550072 GCTCTTCTTGCACCTCTCTCT 59.450 52.381 0.00 0.00 0.00 3.10
755 789 1.735369 CGCTCTTCTTGCACCTCTCTC 60.735 57.143 0.00 0.00 0.00 3.20
785 819 1.135315 CGTCGCCTTGCAATTCCAG 59.865 57.895 0.00 0.00 0.00 3.86
939 973 2.125106 GCTAACGGTGGAGCTGGG 60.125 66.667 0.00 0.00 35.73 4.45
989 1024 0.806492 GGACGACATTTCTCGCCTCC 60.806 60.000 0.00 0.00 37.15 4.30
1761 1796 3.709633 TCGACGAGGAGGTCCCGA 61.710 66.667 12.16 3.13 40.87 5.14
1899 1934 0.744414 CGGCGAATTCCACATCACCT 60.744 55.000 0.00 0.00 0.00 4.00
2026 2061 5.996513 CCTCAATAGCTGCATAGAACAATCT 59.003 40.000 1.02 0.00 39.82 2.40
2040 2075 0.475906 GGTGGCCATCCTCAATAGCT 59.524 55.000 9.72 0.00 0.00 3.32
2432 2467 2.892852 CCTGCCTGGAAATTCAGAAACA 59.107 45.455 0.00 0.00 38.35 2.83
2450 2485 5.559148 ACAATTAGAAGATAGGAGCCCTG 57.441 43.478 4.16 0.00 34.61 4.45
2540 2577 6.554334 TTGATTCTTCCTACCGAAAACAAG 57.446 37.500 0.00 0.00 0.00 3.16
2616 2653 4.638421 CACCACTACTTTTCTTGTGAACCA 59.362 41.667 0.00 0.00 32.72 3.67
2664 2701 3.068873 TCCATGCAACCACAAAACTTACC 59.931 43.478 0.00 0.00 0.00 2.85
2725 2762 4.654091 ATTGAACAGTGAAAACACCTGG 57.346 40.909 0.00 0.00 0.00 4.45
2751 2788 0.957395 CATGGAGCGCAGAGTTGGTT 60.957 55.000 11.47 0.00 0.00 3.67
2762 2799 7.371159 TCTTTATACTGAACTATCATGGAGCG 58.629 38.462 0.00 0.00 34.37 5.03
2774 2811 6.238759 GCATGGGTCCAATCTTTATACTGAAC 60.239 42.308 0.00 0.00 0.00 3.18
2793 2830 4.630644 AGATCATACAAGGTAGCATGGG 57.369 45.455 1.89 0.00 0.00 4.00
2813 2853 8.993121 AGTGACATCTCAACAATACACTTTTAG 58.007 33.333 0.00 0.00 34.42 1.85
2858 2898 2.918712 AGACGGCATCTAATTCCTGG 57.081 50.000 0.00 0.00 35.15 4.45
2865 2905 1.342674 ACCCCACTAGACGGCATCTAA 60.343 52.381 0.00 0.00 39.52 2.10
2873 2913 1.079819 CACAGCACCCCACTAGACG 60.080 63.158 0.00 0.00 0.00 4.18
2961 3001 4.144297 ACAGTCCAACAGCATAACATTGT 58.856 39.130 0.00 0.00 0.00 2.71
3077 3117 8.743085 TGTTAACCTTCACTATACTCGTCTAT 57.257 34.615 2.48 0.00 0.00 1.98
3081 3121 7.458409 TCTTGTTAACCTTCACTATACTCGT 57.542 36.000 2.48 0.00 0.00 4.18
3082 3122 8.242053 TCTTCTTGTTAACCTTCACTATACTCG 58.758 37.037 2.48 0.00 0.00 4.18
3083 3123 9.575783 CTCTTCTTGTTAACCTTCACTATACTC 57.424 37.037 2.48 0.00 0.00 2.59
3084 3124 9.091220 ACTCTTCTTGTTAACCTTCACTATACT 57.909 33.333 2.48 0.00 0.00 2.12
3087 3127 9.091220 ACTACTCTTCTTGTTAACCTTCACTAT 57.909 33.333 2.48 0.00 0.00 2.12
3088 3128 8.358148 CACTACTCTTCTTGTTAACCTTCACTA 58.642 37.037 2.48 0.00 0.00 2.74
3089 3129 7.210873 CACTACTCTTCTTGTTAACCTTCACT 58.789 38.462 2.48 0.00 0.00 3.41
3090 3130 6.424207 CCACTACTCTTCTTGTTAACCTTCAC 59.576 42.308 2.48 0.00 0.00 3.18
3120 3160 9.905713 TTAAATTCCTCTCAACTTACTGCATAT 57.094 29.630 0.00 0.00 0.00 1.78
3137 3177 5.983540 TGCAACCACAAAACTTAAATTCCT 58.016 33.333 0.00 0.00 0.00 3.36
3195 3235 2.368875 CTGGTCCACCTAGTCAAACACT 59.631 50.000 0.00 0.00 39.41 3.55
3205 3245 0.690762 GAAAGCACCTGGTCCACCTA 59.309 55.000 0.00 0.00 36.82 3.08
3312 3352 3.447586 GTCAGCCCTATCTCTACAACACA 59.552 47.826 0.00 0.00 0.00 3.72
3314 3354 3.982516 AGTCAGCCCTATCTCTACAACA 58.017 45.455 0.00 0.00 0.00 3.33
3338 3378 5.491982 CCTTGAGGTTAGCAAACACTATCT 58.508 41.667 0.00 0.00 37.34 1.98
3343 3383 1.953686 TGCCTTGAGGTTAGCAAACAC 59.046 47.619 0.00 0.00 37.34 3.32


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

AutoCloner maintained by Alex Coulton.