Multiple sequence alignment - TraesCS5B01G428800

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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 TraesCS5B01G428800 chr5B 100.000 3095 0 0 1 3095 604178412 604181506 0.000000e+00 5716
1 TraesCS5B01G428800 chr5A 93.426 3103 179 21 3 3093 611655600 611658689 0.000000e+00 4577
2 TraesCS5B01G428800 chr5D 92.809 2823 158 25 289 3093 490046283 490049078 0.000000e+00 4047
3 TraesCS5B01G428800 chr5D 95.092 163 5 1 7 169 490046128 490046287 1.420000e-63 254


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 TraesCS5B01G428800 chr5B 604178412 604181506 3094 False 5716.0 5716 100.0000 1 3095 1 chr5B.!!$F1 3094
1 TraesCS5B01G428800 chr5A 611655600 611658689 3089 False 4577.0 4577 93.4260 3 3093 1 chr5A.!!$F1 3090
2 TraesCS5B01G428800 chr5D 490046128 490049078 2950 False 2150.5 4047 93.9505 7 3093 2 chr5D.!!$F1 3086

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
119 120 1.103803 TGTCTACTCCCTAAGCTGCG 58.896 55.0 0.00 0.0 0.00 5.18 F
1047 1057 0.121197 ACCCTGGGATCCTGGAGAAA 59.879 55.0 22.23 0.0 44.09 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 1755 0.108615 GAGTCGTCCACCACCATCAG 60.109 60.0 0.0 0.0 0.0 2.90 R
2811 2833 0.037232 CTTCGGGGTCTCTGTTGGAC 60.037 60.0 0.0 0.0 0.0 4.02 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
28 29 7.595819 AAGTAAATGAAGAAAATGTGGTGGA 57.404 32.000 0.00 0.00 0.00 4.02
59 60 2.766828 ACCTACCGAATCTGAAGGAAGG 59.233 50.000 4.56 0.00 0.00 3.46
119 120 1.103803 TGTCTACTCCCTAAGCTGCG 58.896 55.000 0.00 0.00 0.00 5.18
220 222 6.986904 ATCTTGAAGGAATTTAGACGGTTC 57.013 37.500 0.00 0.00 0.00 3.62
237 239 2.547855 GGTTCATTCCCCAAACTTGCAC 60.548 50.000 0.00 0.00 0.00 4.57
261 263 7.775093 CACCTCCAATATCAAAGTGGATAGAAA 59.225 37.037 0.00 0.00 40.61 2.52
329 331 3.646736 ATTTTAGTTTCGCCCTAGCCT 57.353 42.857 0.00 0.00 34.57 4.58
332 334 1.112113 TAGTTTCGCCCTAGCCTCTG 58.888 55.000 0.00 0.00 34.57 3.35
501 505 8.725148 CAATCTGCTCAGGTATCCAATAAATAC 58.275 37.037 0.00 0.00 0.00 1.89
514 518 5.712917 TCCAATAAATACACCACTTGAACCC 59.287 40.000 0.00 0.00 0.00 4.11
534 538 2.311841 CCAACCCTAAACCATCTCCCTT 59.688 50.000 0.00 0.00 0.00 3.95
540 544 3.181439 CCTAAACCATCTCCCTTCCATCC 60.181 52.174 0.00 0.00 0.00 3.51
572 576 2.419297 GCATTCCTCACATCGTCCTCTT 60.419 50.000 0.00 0.00 0.00 2.85
695 699 1.741706 CCAGACAATGAGTGGTGATGC 59.258 52.381 0.00 0.00 0.00 3.91
699 703 3.457380 AGACAATGAGTGGTGATGCCTAT 59.543 43.478 0.00 0.00 38.35 2.57
723 727 5.248020 TGGTGCATCCCACAAAAAGATAATT 59.752 36.000 0.00 0.00 46.50 1.40
794 798 1.538075 CCGCCACCGTAAAATCACTTT 59.462 47.619 0.00 0.00 0.00 2.66
797 801 3.549221 CGCCACCGTAAAATCACTTTGTT 60.549 43.478 0.00 0.00 0.00 2.83
846 850 2.019984 CCTTTGGCACATCCTCTTAGC 58.980 52.381 0.00 0.00 39.30 3.09
866 870 2.138320 CGATGGCGCTAATGAGTTGAT 58.862 47.619 7.64 0.00 0.00 2.57
869 873 3.266510 TGGCGCTAATGAGTTGATTCT 57.733 42.857 7.64 0.00 0.00 2.40
886 890 6.443934 TGATTCTTTTGGTTGACGAAGAAA 57.556 33.333 0.00 0.00 40.34 2.52
1045 1055 1.003442 CACCCTGGGATCCTGGAGA 59.997 63.158 22.23 0.00 44.09 3.71
1047 1057 0.121197 ACCCTGGGATCCTGGAGAAA 59.879 55.000 22.23 0.00 44.09 2.52
1061 1071 1.340114 GGAGAAAATCCCGCCAAGTCT 60.340 52.381 0.00 0.00 43.01 3.24
1106 1116 2.870119 TTTGCAAAGCATGGCGCCT 61.870 52.632 29.70 10.60 44.04 5.52
1115 1125 1.097547 GCATGGCGCCTCATAGTGTT 61.098 55.000 29.70 0.00 32.94 3.32
1173 1183 2.005606 TTGCACCAGTGGTCATGGGT 62.006 55.000 13.31 0.00 42.48 4.51
1191 1201 3.028130 GGGTTTCTTCCACAACTCCAAA 58.972 45.455 0.00 0.00 0.00 3.28
1243 1253 3.381908 CGACACCACTAGCTTATCCTTCT 59.618 47.826 0.00 0.00 0.00 2.85
1255 1265 9.620259 CTAGCTTATCCTTCTGTTTTCCTAATT 57.380 33.333 0.00 0.00 0.00 1.40
1287 1297 3.273434 CTCATGGACGTTCATGGATTGT 58.727 45.455 31.61 0.00 43.33 2.71
1288 1298 3.684908 TCATGGACGTTCATGGATTGTT 58.315 40.909 31.61 0.00 43.33 2.83
1350 1360 3.253061 TGGCACCCAATGACCGGA 61.253 61.111 9.46 0.00 34.05 5.14
1416 1426 0.449388 CCGAGAAGAACAGCAATGCC 59.551 55.000 0.00 0.00 0.00 4.40
1473 1483 0.901124 AAGTTTGCTGCCAACAACCA 59.099 45.000 17.44 0.00 0.00 3.67
1491 1501 3.020984 ACCAACAAGTCCATTTCGTGTT 58.979 40.909 0.00 0.00 37.82 3.32
1530 1540 3.487202 CGGGGTCGTGTTCATGCG 61.487 66.667 0.00 0.00 0.00 4.73
1568 1578 2.848679 TGGTCAGTGGAGCCTGCA 60.849 61.111 0.00 0.00 40.83 4.41
1572 1582 4.031129 CAGTGGAGCCTGCAGCCT 62.031 66.667 8.66 0.94 45.47 4.58
1744 1754 3.199946 AGGAAATGCCCGTCTAATGAAGA 59.800 43.478 0.00 0.00 37.37 2.87
1795 1805 0.321671 CGTGGAGGACCTCACATTGT 59.678 55.000 23.06 0.00 37.04 2.71
1923 1933 1.675310 CTTCCTGGTGATGCCGCAA 60.675 57.895 0.00 0.00 41.21 4.85
1935 1945 1.825090 TGCCGCAAGTGAAGATCATT 58.175 45.000 0.00 0.00 0.00 2.57
1990 2000 2.297880 TGGACCATGGTCGGTATATTCG 59.702 50.000 33.24 0.00 45.41 3.34
2034 2044 0.694771 TCAAGAAGGTGCATGAGGCT 59.305 50.000 0.00 0.00 45.15 4.58
2096 2106 0.995024 ACTCCTGCCAGCTGGTAATT 59.005 50.000 32.81 10.64 37.57 1.40
2097 2107 2.092968 CACTCCTGCCAGCTGGTAATTA 60.093 50.000 32.81 15.61 37.57 1.40
2141 2151 6.500400 TGCCTAAGCACTTATGATATTCCCTA 59.500 38.462 0.00 0.00 46.52 3.53
2148 2158 6.656693 GCACTTATGATATTCCCTATGTTGCT 59.343 38.462 0.00 0.00 0.00 3.91
2154 2164 2.961526 TTCCCTATGTTGCTCGAGAC 57.038 50.000 18.75 7.00 0.00 3.36
2156 2166 0.824109 CCCTATGTTGCTCGAGACCA 59.176 55.000 18.75 9.11 0.00 4.02
2199 2211 1.327303 TTTTGGCCAGTACTTGCAGG 58.673 50.000 19.57 6.92 0.00 4.85
2260 2272 5.869888 AGTAGCAAGTTTACTATCAGTGCAC 59.130 40.000 9.40 9.40 32.98 4.57
2262 2274 3.181520 GCAAGTTTACTATCAGTGCACCG 60.182 47.826 14.63 2.63 0.00 4.94
2556 2570 9.643693 TTAGCATAGCTTACGGTATATAAAACC 57.356 33.333 0.00 0.00 40.44 3.27
2561 2575 9.759473 ATAGCTTACGGTATATAAAACCCTCTA 57.241 33.333 0.00 0.00 32.36 2.43
2640 2654 2.851195 AGCCTTATTTGTATGGAGCCG 58.149 47.619 0.00 0.00 0.00 5.52
2732 2754 9.273016 ACATTCAAACATCGTAATATCCCTTAG 57.727 33.333 0.00 0.00 0.00 2.18
2739 2761 2.352814 CGTAATATCCCTTAGCTGCGCT 60.353 50.000 9.73 8.09 43.41 5.92
2741 2763 2.464157 ATATCCCTTAGCTGCGCTTC 57.536 50.000 9.73 0.00 40.44 3.86
2774 2796 2.906388 ACGCAGCCACACATGCAA 60.906 55.556 0.00 0.00 42.68 4.08
2775 2797 2.126618 CGCAGCCACACATGCAAG 60.127 61.111 0.00 0.00 42.68 4.01
2776 2798 2.911484 CGCAGCCACACATGCAAGT 61.911 57.895 0.00 0.00 42.68 3.16
2777 2799 1.576451 CGCAGCCACACATGCAAGTA 61.576 55.000 0.00 0.00 42.68 2.24
2778 2800 0.169672 GCAGCCACACATGCAAGTAG 59.830 55.000 0.00 0.00 42.11 2.57
2780 2802 0.962356 AGCCACACATGCAAGTAGCC 60.962 55.000 0.00 0.00 44.83 3.93
2781 2803 1.243342 GCCACACATGCAAGTAGCCA 61.243 55.000 0.00 0.00 44.83 4.75
2947 2969 0.317160 CAGGACAGTGTAGCAACCGA 59.683 55.000 0.00 0.00 0.00 4.69
3007 3029 8.702163 ACGAACAAGTTTTGAAATTTCTCAAT 57.298 26.923 18.64 0.02 35.31 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.308000 TCCACCACATTTTCTTCATTTACTTAT 57.692 29.630 0.00 0.00 0.00 1.73
3 4 8.698973 TCCACCACATTTTCTTCATTTACTTA 57.301 30.769 0.00 0.00 0.00 2.24
4 5 7.595819 TCCACCACATTTTCTTCATTTACTT 57.404 32.000 0.00 0.00 0.00 2.24
59 60 5.907197 ATGCAACTATGTACAGTATTCGC 57.093 39.130 0.33 0.43 0.00 4.70
185 187 8.767478 AATTCCTTCAAGATAATGCTTTTGTG 57.233 30.769 0.00 0.00 0.00 3.33
215 217 1.336795 GCAAGTTTGGGGAATGAACCG 60.337 52.381 0.00 0.00 0.00 4.44
220 222 1.273327 GAGGTGCAAGTTTGGGGAATG 59.727 52.381 0.00 0.00 0.00 2.67
237 239 8.752005 TTTTCTATCCACTTTGATATTGGAGG 57.248 34.615 0.00 0.00 42.72 4.30
332 334 1.153147 GGGCCGGTCCTGAGATTTC 60.153 63.158 20.78 0.00 34.39 2.17
372 374 1.278985 CCATTGAGGCAGACTGTACCA 59.721 52.381 3.99 0.00 0.00 3.25
374 376 2.770164 ACCATTGAGGCAGACTGTAC 57.230 50.000 3.99 0.00 43.14 2.90
375 377 2.500098 GGTACCATTGAGGCAGACTGTA 59.500 50.000 7.15 0.00 43.14 2.74
501 505 0.106217 AGGGTTGGGTTCAAGTGGTG 60.106 55.000 0.00 0.00 32.92 4.17
514 518 3.621558 GAAGGGAGATGGTTTAGGGTTG 58.378 50.000 0.00 0.00 0.00 3.77
572 576 6.581388 AAAAAGATAGATGAGGGTGGATGA 57.419 37.500 0.00 0.00 0.00 2.92
664 668 0.904649 ATTGTCTGGAGGCGACATCA 59.095 50.000 0.00 0.00 40.70 3.07
695 699 2.142356 TTTGTGGGATGCACCATAGG 57.858 50.000 0.00 0.00 43.59 2.57
699 703 2.079170 TCTTTTTGTGGGATGCACCA 57.921 45.000 7.49 0.00 41.20 4.17
794 798 0.318441 CAAGAGAGAGACCGCCAACA 59.682 55.000 0.00 0.00 0.00 3.33
797 801 0.318441 CAACAAGAGAGAGACCGCCA 59.682 55.000 0.00 0.00 0.00 5.69
846 850 1.570813 TCAACTCATTAGCGCCATCG 58.429 50.000 2.29 0.00 39.07 3.84
857 861 5.530915 TCGTCAACCAAAAGAATCAACTCAT 59.469 36.000 0.00 0.00 0.00 2.90
858 862 4.878971 TCGTCAACCAAAAGAATCAACTCA 59.121 37.500 0.00 0.00 0.00 3.41
980 987 6.299141 ACCATAACTGCACTATTGGATTAGG 58.701 40.000 7.74 0.00 0.00 2.69
1017 1027 3.501019 GGATCCCAGGGTGCAATTCATAT 60.501 47.826 5.01 0.00 0.00 1.78
1045 1055 0.539438 TGCAGACTTGGCGGGATTTT 60.539 50.000 0.00 0.00 0.00 1.82
1047 1057 1.377725 CTGCAGACTTGGCGGGATT 60.378 57.895 8.42 0.00 33.98 3.01
1061 1071 2.918345 GCGTGGGCAATTGTCTGCA 61.918 57.895 10.38 0.00 44.52 4.41
1106 1116 3.788227 AACCAGGAGCAAACACTATGA 57.212 42.857 0.00 0.00 0.00 2.15
1115 1125 0.110486 GTGGAGGAAACCAGGAGCAA 59.890 55.000 0.00 0.00 40.85 3.91
1173 1183 4.770010 AGTGTTTTGGAGTTGTGGAAGAAA 59.230 37.500 0.00 0.00 0.00 2.52
1191 1201 1.304134 GAATGGGCGGGGAAGTGTT 60.304 57.895 0.00 0.00 0.00 3.32
1243 1253 9.249053 TGAGTAATTGCCATAATTAGGAAAACA 57.751 29.630 0.00 0.00 0.00 2.83
1255 1265 4.415881 ACGTCCATGAGTAATTGCCATA 57.584 40.909 0.00 0.00 0.00 2.74
1330 1340 2.334946 CGGTCATTGGGTGCCACAG 61.335 63.158 0.00 0.00 30.78 3.66
1350 1360 2.561569 GCATTGATTAGGCGGTAGTGT 58.438 47.619 0.00 0.00 0.00 3.55
1416 1426 1.226547 AACCACACAAAGCAACGCG 60.227 52.632 3.53 3.53 0.00 6.01
1450 1460 2.741517 GTTGTTGGCAGCAAACTTGTTT 59.258 40.909 18.52 0.00 0.00 2.83
1452 1462 1.405391 GGTTGTTGGCAGCAAACTTGT 60.405 47.619 22.75 0.00 31.36 3.16
1473 1483 2.223711 GGCAACACGAAATGGACTTGTT 60.224 45.455 0.00 0.00 31.69 2.83
1491 1501 2.170166 GAATCATTGTGGACAAGGGCA 58.830 47.619 4.48 0.00 39.47 5.36
1530 1540 1.404748 GTAAGTGAGGAGTAGACGCCC 59.595 57.143 0.00 0.00 36.39 6.13
1568 1578 1.076923 AGATCCACCGACGTAGGCT 60.077 57.895 15.29 0.03 33.69 4.58
1572 1582 4.247781 GGGAGATCCACCGACGTA 57.752 61.111 0.47 0.00 37.91 3.57
1744 1754 0.832135 AGTCGTCCACCACCATCAGT 60.832 55.000 0.00 0.00 0.00 3.41
1745 1755 0.108615 GAGTCGTCCACCACCATCAG 60.109 60.000 0.00 0.00 0.00 2.90
1774 1784 0.836400 AATGTGAGGTCCTCCACGGT 60.836 55.000 16.60 5.23 35.89 4.83
1795 1805 2.039787 TCCCCGAGCCCACATACA 59.960 61.111 0.00 0.00 0.00 2.29
1923 1933 1.745141 GCGCTCCCAATGATCTTCACT 60.745 52.381 0.00 0.00 0.00 3.41
1990 2000 9.315525 GAACTCCATAGTTTTAGGACATAGAAC 57.684 37.037 0.00 0.00 46.09 3.01
2034 2044 3.245229 ACACAATCTCCATGCCCTTAACA 60.245 43.478 0.00 0.00 0.00 2.41
2141 2151 1.673477 TGCTGGTCTCGAGCAACAT 59.327 52.632 7.81 0.00 43.47 2.71
2148 2158 2.233676 ACACATTACATGCTGGTCTCGA 59.766 45.455 0.00 0.00 0.00 4.04
2154 2164 3.651206 TGCAAAACACATTACATGCTGG 58.349 40.909 0.00 0.00 34.97 4.85
2156 2166 3.742369 GCTTGCAAAACACATTACATGCT 59.258 39.130 0.00 0.00 34.97 3.79
2199 2211 5.121142 TGAGTACCAGCTACGCAATAAAAAC 59.879 40.000 0.00 0.00 32.71 2.43
2228 2240 9.185680 TGATAGTAAACTTGCTACTCATACTCA 57.814 33.333 0.00 0.00 31.98 3.41
2260 2272 8.973378 CAGATAGAAAATAAAAGACTAGCTCGG 58.027 37.037 0.00 0.00 29.37 4.63
2510 2524 5.293079 GCTAAGAAGGAAGTCTTATGCACAG 59.707 44.000 0.00 0.00 38.96 3.66
2556 2570 9.941664 CAACTAGCATGATTACAAAATTAGAGG 57.058 33.333 0.00 0.00 0.00 3.69
2685 2707 6.811253 TGTAGATTCAACGGCTACAAAAAT 57.189 33.333 0.00 0.00 40.88 1.82
2739 2761 2.344981 TGCTACCGTGCGCCTAGAA 61.345 57.895 4.18 0.00 35.36 2.10
2741 2763 2.582498 GTGCTACCGTGCGCCTAG 60.582 66.667 4.18 0.00 37.48 3.02
2762 2784 1.243342 TGGCTACTTGCATGTGTGGC 61.243 55.000 15.08 17.59 45.15 5.01
2774 2796 5.485708 ACATAGGACTTCTCTTTTGGCTACT 59.514 40.000 0.00 0.00 0.00 2.57
2775 2797 5.582665 CACATAGGACTTCTCTTTTGGCTAC 59.417 44.000 0.00 0.00 0.00 3.58
2776 2798 5.483937 TCACATAGGACTTCTCTTTTGGCTA 59.516 40.000 0.00 0.00 0.00 3.93
2777 2799 4.287067 TCACATAGGACTTCTCTTTTGGCT 59.713 41.667 0.00 0.00 0.00 4.75
2778 2800 4.393371 GTCACATAGGACTTCTCTTTTGGC 59.607 45.833 0.00 0.00 34.92 4.52
2780 2802 4.092091 GCGTCACATAGGACTTCTCTTTTG 59.908 45.833 0.00 0.00 35.63 2.44
2781 2803 4.021016 AGCGTCACATAGGACTTCTCTTTT 60.021 41.667 0.00 0.00 35.63 2.27
2811 2833 0.037232 CTTCGGGGTCTCTGTTGGAC 60.037 60.000 0.00 0.00 0.00 4.02
2817 2839 0.951040 GTTGTGCTTCGGGGTCTCTG 60.951 60.000 0.00 0.00 0.00 3.35
2895 2917 0.526096 GGCCGCTACAACGAATCGTA 60.526 55.000 9.30 0.00 39.99 3.43
3032 3055 7.858052 ATTTCAAAAACAAATCGCAGTCTAG 57.142 32.000 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.