Multiple sequence alignment - TraesCS1B01G300300

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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 TraesCS1B01G300300 chr1B 100.000 3099 0 0 1 3099 520896684 520893586 0 5723
1 TraesCS1B01G300300 chr1D 94.429 3141 107 26 1 3099 387550715 387547601 0 4769
2 TraesCS1B01G300300 chr1A 91.627 3177 144 39 1 3099 487310256 487307124 0 4281


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 TraesCS1B01G300300 chr1B 520893586 520896684 3098 True 5723 5723 100.000 1 3099 1 chr1B.!!$R1 3098
1 TraesCS1B01G300300 chr1D 387547601 387550715 3114 True 4769 4769 94.429 1 3099 1 chr1D.!!$R1 3098
2 TraesCS1B01G300300 chr1A 487307124 487310256 3132 True 4281 4281 91.627 1 3099 1 chr1A.!!$R1 3098

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
895 916 0.960286 CTAGCCGCCCTACTACCTTC 59.04 60.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2113 2141 0.037303 ACCAGACAGCACCAATCAGG 59.963 55.0 0.0 0.0 45.67 3.86 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
49 50 3.806521 CACATCAGTTATCCAGCTACAGC 59.193 47.826 0.00 0.00 42.49 4.40
86 87 3.274288 CACCTTTCTATTCCTGCTCCAC 58.726 50.000 0.00 0.00 0.00 4.02
114 115 6.267014 TGCTAGTTACTAGTCCTGTTGTCTTT 59.733 38.462 19.12 0.00 36.53 2.52
227 228 5.195940 TGGCAAATCCAAAACCAAATTCAA 58.804 33.333 0.00 0.00 43.21 2.69
316 325 8.868103 TCTCTAGTACTATTATCTTCTCGTGGA 58.132 37.037 2.33 0.00 0.00 4.02
339 348 8.802267 TGGATTTCTTAAGAAAATGTTAGGTGG 58.198 33.333 29.22 0.00 45.81 4.61
361 370 4.142038 GTCCTTAACCTGGTTGTGATGTT 58.858 43.478 22.04 0.00 0.00 2.71
362 371 5.310451 GTCCTTAACCTGGTTGTGATGTTA 58.690 41.667 22.04 0.00 0.00 2.41
364 373 7.107542 GTCCTTAACCTGGTTGTGATGTTATA 58.892 38.462 22.04 0.00 0.00 0.98
525 546 6.638096 TTTCTTCATTTCTGTGCAGAATGA 57.362 33.333 14.43 15.34 45.78 2.57
593 614 4.778213 TGGAGCATATTCCTTAACAGCT 57.222 40.909 0.00 0.00 38.12 4.24
618 639 2.028876 TGACACCTGTTCGTCTTCTGA 58.971 47.619 0.00 0.00 33.18 3.27
670 691 6.065976 TCTATCAAAGGAAGGCAGATTTCA 57.934 37.500 0.00 0.00 0.00 2.69
855 876 8.146412 GCTGGCATATCAATTAGGAAATTTCTT 58.854 33.333 17.42 12.81 32.87 2.52
895 916 0.960286 CTAGCCGCCCTACTACCTTC 59.040 60.000 0.00 0.00 0.00 3.46
909 930 8.270744 CCCTACTACCTTCGGTATATAGTGTAT 58.729 40.741 0.00 0.00 37.56 2.29
1024 1046 0.253044 CAATCCTTCTTCCTCGCCCA 59.747 55.000 0.00 0.00 0.00 5.36
1026 1048 0.909610 ATCCTTCTTCCTCGCCCACA 60.910 55.000 0.00 0.00 0.00 4.17
1035 1057 2.285069 TCGCCCACACCCACCTAT 60.285 61.111 0.00 0.00 0.00 2.57
1078 1100 2.941720 GCATGGAACTTCTCTGGTGATC 59.058 50.000 0.00 0.00 0.00 2.92
1113 1135 2.100631 CGAAATTCCTCGCGGCACT 61.101 57.895 6.13 0.00 31.04 4.40
1125 1147 1.949257 CGGCACTGGTTTCTTCCAC 59.051 57.895 0.00 0.00 33.55 4.02
1126 1148 0.535102 CGGCACTGGTTTCTTCCACT 60.535 55.000 0.00 0.00 33.55 4.00
1197 1219 1.704007 CCTGCATCTCTCCCCTTCCC 61.704 65.000 0.00 0.00 0.00 3.97
1239 1261 1.299976 CAGCTCACACCCCTTACCC 59.700 63.158 0.00 0.00 0.00 3.69
1392 1414 2.029666 AGCTCCGATACCATGCGC 59.970 61.111 0.00 0.00 0.00 6.09
1401 1423 2.252072 ATACCATGCGCCGTGTCCTT 62.252 55.000 4.18 0.00 0.00 3.36
1482 1504 1.226746 AAACAGCTGCTAACCACGTC 58.773 50.000 15.27 0.00 0.00 4.34
1601 1623 1.889170 CCTTTTTCAGAGAAGGTGGGC 59.111 52.381 6.52 0.00 38.07 5.36
1692 1714 5.056480 TCCACAAGAAGATAACTGTGTGTG 58.944 41.667 9.44 0.00 34.45 3.82
1872 1894 2.711922 GCGACATGGAGACGGAGGT 61.712 63.158 0.00 0.00 35.94 3.85
2002 2024 3.425014 AAGTGGTGGTGGGGCACA 61.425 61.111 0.00 0.00 35.86 4.57
2030 2052 4.052229 CCAACAGGCAGCAGCAGC 62.052 66.667 2.65 0.00 44.61 5.25
2031 2053 3.292159 CAACAGGCAGCAGCAGCA 61.292 61.111 12.41 0.00 45.49 4.41
2032 2054 2.984155 AACAGGCAGCAGCAGCAG 60.984 61.111 12.41 6.04 45.49 4.24
2113 2141 3.565910 CTAGCTCCGGCGCCTGATC 62.566 68.421 26.68 19.37 44.37 2.92
2116 2144 4.598894 CTCCGGCGCCTGATCCTG 62.599 72.222 26.68 7.70 0.00 3.86
2118 2146 3.933722 CCGGCGCCTGATCCTGAT 61.934 66.667 26.68 0.00 0.00 2.90
2203 2237 0.744771 CGCTGACCTTCTTAAGCCCC 60.745 60.000 0.00 0.00 31.84 5.80
2408 2466 1.980772 ATGGCCCTGCTGTTGCTTC 60.981 57.895 0.00 0.00 40.48 3.86
2417 2475 1.584380 GCTGTTGCTTCCTGCTCCTG 61.584 60.000 0.00 0.00 43.37 3.86
2454 2512 5.712152 AAATCGAAACAAATCTCCTTGCT 57.288 34.783 0.00 0.00 0.00 3.91
2469 2527 3.131396 CCTTGCTGTAACTTTCGTGTCT 58.869 45.455 0.00 0.00 0.00 3.41
2474 2532 3.244579 GCTGTAACTTTCGTGTCTCGTTT 59.755 43.478 0.00 0.00 40.80 3.60
2521 2579 1.878775 GAATGTCAGTGCTGGTGCC 59.121 57.895 0.00 0.00 38.71 5.01
2610 2685 3.978193 TTCCGGCATGCCCCTTGT 61.978 61.111 30.79 0.00 0.00 3.16
2730 2826 1.303236 TGCGGGCTTTGCACTATGT 60.303 52.632 0.00 0.00 37.44 2.29
2731 2827 1.137404 GCGGGCTTTGCACTATGTG 59.863 57.895 0.00 0.00 36.51 3.21
2740 2836 3.737559 TTGCACTATGTGATTTCCCCT 57.262 42.857 1.52 0.00 35.23 4.79
2846 2943 2.217393 GCTTGACGCTATCATTGTCTCG 59.783 50.000 0.00 0.00 37.11 4.04
2857 2954 7.508965 GCTATCATTGTCTCGAGAATCATTTC 58.491 38.462 18.55 3.14 33.17 2.17
2877 2974 2.361610 GTGTGGGGATGGTGCAGG 60.362 66.667 0.00 0.00 0.00 4.85
2882 2979 2.693871 GGGGATGGTGCAGGGATGT 61.694 63.158 0.00 0.00 0.00 3.06
2892 2989 3.142174 GTGCAGGGATGTAGGCTATTTC 58.858 50.000 0.00 0.00 0.00 2.17
2938 3035 6.267471 TCAGAATGTTGGTGGAATAGCTTTTT 59.733 34.615 0.00 0.00 37.40 1.94
2997 3100 3.213206 ACTGCTTTCTCCAACATCACA 57.787 42.857 0.00 0.00 0.00 3.58
3000 3103 4.202357 ACTGCTTTCTCCAACATCACACTA 60.202 41.667 0.00 0.00 0.00 2.74
3009 3112 3.055530 CCAACATCACACTAGAAGGAGCT 60.056 47.826 0.00 0.00 0.00 4.09
3032 3135 9.428097 AGCTTGCTTCTAATTAAAAGGAAAATG 57.572 29.630 6.89 0.00 33.30 2.32
3047 3150 8.856153 AAAGGAAAATGGTTTTACAACAAACT 57.144 26.923 0.73 0.00 35.89 2.66
3087 3191 7.039993 ACCTATTTTTACCAAACTGGCAACTAG 60.040 37.037 0.00 0.00 42.67 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 6.398918 ACAACAGGACTAGTAACTAGCATTG 58.601 40.000 0.00 3.82 37.57 2.82
114 115 4.594123 TTGTCAACGAGATCCACTTACA 57.406 40.909 0.00 0.00 0.00 2.41
227 228 4.423625 ACTAACTTCTCCACTGCAGTTT 57.576 40.909 18.94 9.83 31.83 2.66
303 312 9.938280 TTTTCTTAAGAAATCCACGAGAAGATA 57.062 29.630 26.90 8.01 42.83 1.98
312 321 9.626045 CACCTAACATTTTCTTAAGAAATCCAC 57.374 33.333 26.90 0.00 42.83 4.02
316 325 8.803235 GGACCACCTAACATTTTCTTAAGAAAT 58.197 33.333 26.90 16.56 42.83 2.17
339 348 3.751518 ACATCACAACCAGGTTAAGGAC 58.248 45.455 3.89 0.00 0.00 3.85
525 546 1.412074 GGGGAGATTGATGCCATTGGT 60.412 52.381 4.26 0.00 30.95 3.67
568 589 5.008118 GCTGTTAAGGAATATGCTCCAACTC 59.992 44.000 0.00 0.00 38.02 3.01
588 609 3.694364 CAGGTGTCAGACAAGCTGT 57.306 52.632 4.32 0.00 45.14 4.40
593 614 1.754803 AGACGAACAGGTGTCAGACAA 59.245 47.619 4.32 0.00 37.58 3.18
618 639 7.524717 AAAAAGTATGCTGAACATAACACCT 57.475 32.000 0.00 0.00 42.88 4.00
855 876 3.396611 AGGGCCACTACTTTTAACAAGGA 59.603 43.478 6.18 0.00 0.00 3.36
909 930 3.407698 AGAACGTTTGATGTGCATGGTA 58.592 40.909 0.46 0.00 0.00 3.25
1024 1046 1.624391 GGGGTCACTATAGGTGGGTGT 60.624 57.143 4.43 0.00 45.38 4.16
1026 1048 1.024536 AGGGGTCACTATAGGTGGGT 58.975 55.000 4.43 0.00 45.38 4.51
1035 1057 1.271840 GGTGCATGGAGGGGTCACTA 61.272 60.000 0.00 0.00 0.00 2.74
1060 1082 2.027745 GCAGATCACCAGAGAAGTTCCA 60.028 50.000 0.00 0.00 0.00 3.53
1061 1083 2.027745 TGCAGATCACCAGAGAAGTTCC 60.028 50.000 0.00 0.00 0.00 3.62
1066 1088 1.693606 TGTGTGCAGATCACCAGAGAA 59.306 47.619 3.73 0.00 45.03 2.87
1067 1089 1.274447 CTGTGTGCAGATCACCAGAGA 59.726 52.381 3.73 0.00 45.28 3.10
1078 1100 2.740055 GGTCGGAGCTGTGTGCAG 60.740 66.667 0.00 0.00 45.94 4.41
1113 1135 2.176798 ACCATTGGAGTGGAAGAAACCA 59.823 45.455 10.37 0.00 42.02 3.67
1197 1219 3.131396 GCTCGTGTTGATATTGTAGGGG 58.869 50.000 0.00 0.00 0.00 4.79
1225 1247 1.422402 GTGAAAGGGTAAGGGGTGTGA 59.578 52.381 0.00 0.00 0.00 3.58
1239 1261 3.565902 GGTCAAGAAACTGGAGGTGAAAG 59.434 47.826 0.00 0.00 0.00 2.62
1392 1414 2.125673 CCGGTGCTAAGGACACGG 60.126 66.667 0.00 0.00 38.98 4.94
1401 1423 2.361483 TGTAGGTCGCCGGTGCTA 60.361 61.111 11.05 4.03 34.43 3.49
1416 1438 4.085357 TGAGTCTTGTTGCATTACCTGT 57.915 40.909 0.00 0.00 0.00 4.00
1482 1504 2.137523 GTTGCCCTGTTTTGCATCAAG 58.862 47.619 0.00 0.00 37.33 3.02
1601 1623 1.735198 TTCTTCGGCGCTGTAACGG 60.735 57.895 17.37 3.46 0.00 4.44
1692 1714 1.077429 GGCTGTGAGGGGGATCAAC 60.077 63.158 0.00 0.00 0.00 3.18
1872 1894 2.437413 ACTCGTAGCTGATGTCAGACA 58.563 47.619 13.94 5.50 46.59 3.41
2002 2024 4.954970 CTGTTGGCTGCCACCGGT 62.955 66.667 23.30 0.00 30.78 5.28
2030 2052 1.205064 CGTCGAAACCAAGCTGCTG 59.795 57.895 1.35 0.00 0.00 4.41
2031 2053 1.222115 GACGTCGAAACCAAGCTGCT 61.222 55.000 0.00 0.00 0.00 4.24
2032 2054 1.204312 GACGTCGAAACCAAGCTGC 59.796 57.895 0.00 0.00 0.00 5.25
2113 2141 0.037303 ACCAGACAGCACCAATCAGG 59.963 55.000 0.00 0.00 45.67 3.86
2114 2142 1.002888 AGACCAGACAGCACCAATCAG 59.997 52.381 0.00 0.00 0.00 2.90
2115 2143 1.059098 AGACCAGACAGCACCAATCA 58.941 50.000 0.00 0.00 0.00 2.57
2116 2144 1.446907 CAGACCAGACAGCACCAATC 58.553 55.000 0.00 0.00 0.00 2.67
2117 2145 0.607489 GCAGACCAGACAGCACCAAT 60.607 55.000 0.00 0.00 0.00 3.16
2118 2146 1.227943 GCAGACCAGACAGCACCAA 60.228 57.895 0.00 0.00 0.00 3.67
2265 2310 5.337169 CCTCTTCATCCTCGTCTTTCTTTCT 60.337 44.000 0.00 0.00 0.00 2.52
2417 2475 2.096819 TCGATTTTTCGGGTGCTTATGC 59.903 45.455 0.00 0.00 40.20 3.14
2422 2480 1.950909 TGTTTCGATTTTTCGGGTGCT 59.049 42.857 0.00 0.00 0.00 4.40
2454 2512 4.626604 ACAAAACGAGACACGAAAGTTACA 59.373 37.500 0.00 0.00 46.40 2.41
2469 2527 4.032355 GCGATGAAAAACAGACAAAACGA 58.968 39.130 0.00 0.00 0.00 3.85
2474 2532 3.184379 CGAGAGCGATGAAAAACAGACAA 59.816 43.478 0.00 0.00 40.82 3.18
2584 2657 4.109675 ATGCCGGAACCTTCGGGG 62.110 66.667 5.05 2.50 46.86 5.73
2660 2735 4.319133 GTGATCGGCACCACCATT 57.681 55.556 0.00 0.00 41.78 3.16
2730 2826 7.570982 TGTGGTATCTTTATAGAGGGGAAATCA 59.429 37.037 0.00 0.00 32.92 2.57
2731 2827 7.878644 GTGTGGTATCTTTATAGAGGGGAAATC 59.121 40.741 0.00 0.00 32.92 2.17
2740 2836 8.534954 AACTGCTAGTGTGGTATCTTTATAGA 57.465 34.615 0.00 0.00 34.21 1.98
2846 2943 2.420022 CCCCACACACGAAATGATTCTC 59.580 50.000 0.00 0.00 33.17 2.87
2857 2954 3.055719 GCACCATCCCCACACACG 61.056 66.667 0.00 0.00 0.00 4.49
2877 2974 2.367567 TGACCGGAAATAGCCTACATCC 59.632 50.000 9.46 0.00 0.00 3.51
2882 2979 1.697432 CCCATGACCGGAAATAGCCTA 59.303 52.381 9.46 0.00 0.00 3.93
2938 3035 6.303839 ACCTAAATAGTTCTCAACAAGGCAA 58.696 36.000 0.00 0.00 0.00 4.52
2943 3040 5.929992 CCGTGACCTAAATAGTTCTCAACAA 59.070 40.000 0.00 0.00 0.00 2.83
2944 3041 5.244402 TCCGTGACCTAAATAGTTCTCAACA 59.756 40.000 0.00 0.00 0.00 3.33
2945 3042 5.717119 TCCGTGACCTAAATAGTTCTCAAC 58.283 41.667 0.00 0.00 0.00 3.18
2949 3046 6.154706 ACTGATTCCGTGACCTAAATAGTTCT 59.845 38.462 0.00 0.00 0.00 3.01
2997 3100 5.948742 ATTAGAAGCAAGCTCCTTCTAGT 57.051 39.130 24.28 21.39 46.63 2.57
3060 3163 6.099125 AGTTGCCAGTTTGGTAAAAATAGGTT 59.901 34.615 0.09 0.00 43.61 3.50
3070 3174 1.271707 GCCCTAGTTGCCAGTTTGGTA 60.272 52.381 0.00 0.00 40.46 3.25
3080 3184 2.746277 CGTGTGGGCCCTAGTTGC 60.746 66.667 25.70 6.71 0.00 4.17


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

AutoCloner maintained by Alex Coulton.