Multiple sequence alignment - TraesCS3B01G358800

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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 TraesCS3B01G358800 chr3B 100.000 3176 0 0 1 3176 571299249 571302424 0.000000e+00 5866.0
1 TraesCS3B01G358800 chr3A 93.899 3114 137 23 1 3102 574012405 574015477 0.000000e+00 4649.0
2 TraesCS3B01G358800 chr3A 97.368 76 2 0 3101 3176 574015829 574015904 2.570000e-26 130.0
3 TraesCS3B01G358800 chr3A 89.855 69 7 0 288 356 514834 514766 4.360000e-14 89.8
4 TraesCS3B01G358800 chr3D 94.583 2289 98 6 894 3176 435295477 435297745 0.000000e+00 3517.0
5 TraesCS3B01G358800 chr3D 95.273 825 27 4 1 824 435294101 435294914 0.000000e+00 1297.0
6 TraesCS3B01G358800 chr3D 100.000 29 0 0 840 868 435294912 435294940 2.000000e-03 54.7
7 TraesCS3B01G358800 chr4A 84.211 95 15 0 263 357 630842857 630842763 3.370000e-15 93.5
8 TraesCS3B01G358800 chr5D 83.158 95 16 0 263 357 538672925 538673019 1.570000e-13 87.9
9 TraesCS3B01G358800 chr5B 80.808 99 15 3 263 357 679690691 679690789 1.220000e-09 75.0


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 TraesCS3B01G358800 chr3B 571299249 571302424 3175 False 5866.0 5866 100.000000 1 3176 1 chr3B.!!$F1 3175
1 TraesCS3B01G358800 chr3A 574012405 574015904 3499 False 2389.5 4649 95.633500 1 3176 2 chr3A.!!$F1 3175
2 TraesCS3B01G358800 chr3D 435294101 435297745 3644 False 1622.9 3517 96.618667 1 3176 3 chr3D.!!$F1 3175

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
634 636 0.250901 GCTTCCCATGGAGTGTGTGT 60.251 55.0 15.22 0.00 31.21 3.72 F
1167 1681 0.733150 TCCGAGAGTGCATGTACGAG 59.267 55.0 8.36 1.76 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 2376 0.035458 ACCTCTCTCTTTGGGCAACG 59.965 55.0 0.0 0.0 37.6 4.10 R
2542 3062 0.610174 TCAGTCTCCCTCACACATGC 59.390 55.0 0.0 0.0 0.0 4.06 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
36 37 2.685017 AGCGCCCATGTCCTCTCA 60.685 61.111 2.29 0.00 0.00 3.27
90 91 1.006281 ACGGCCGGGTATAGGATATCA 59.994 52.381 31.76 0.00 0.00 2.15
151 152 5.002464 GGCAACCTGTTATAACGAGTAGA 57.998 43.478 10.92 0.00 0.00 2.59
152 153 5.413499 GGCAACCTGTTATAACGAGTAGAA 58.587 41.667 10.92 0.00 0.00 2.10
153 154 5.290400 GGCAACCTGTTATAACGAGTAGAAC 59.710 44.000 10.92 0.00 34.97 3.01
168 169 4.523083 AGTAGAACACAAGACAAGGCAAA 58.477 39.130 0.00 0.00 0.00 3.68
378 380 4.321966 TGGATGCGGTGGTTGCGA 62.322 61.111 0.00 0.00 34.24 5.10
383 385 1.647545 ATGCGGTGGTTGCGATTGAG 61.648 55.000 0.00 0.00 34.24 3.02
404 406 3.545481 CGACTGTGCATCGTCGCC 61.545 66.667 21.96 0.00 45.08 5.54
617 619 1.344763 GTTCCACACAGTGAGTAGGCT 59.655 52.381 7.81 0.00 35.23 4.58
634 636 0.250901 GCTTCCCATGGAGTGTGTGT 60.251 55.000 15.22 0.00 31.21 3.72
643 645 1.207593 GAGTGTGTGTTCATGCCGC 59.792 57.895 0.00 0.00 0.00 6.53
695 697 1.280133 CTGGCACTTCTCCAGGATCAA 59.720 52.381 0.00 0.00 45.62 2.57
805 808 1.389106 GACATGTACGCGTCTTGGAAC 59.611 52.381 18.63 8.04 0.00 3.62
821 824 3.360867 TGGAACAAGAAACAAGAGCCAA 58.639 40.909 0.00 0.00 31.92 4.52
822 825 3.766591 TGGAACAAGAAACAAGAGCCAAA 59.233 39.130 0.00 0.00 31.92 3.28
823 826 4.142182 TGGAACAAGAAACAAGAGCCAAAG 60.142 41.667 0.00 0.00 31.92 2.77
1167 1681 0.733150 TCCGAGAGTGCATGTACGAG 59.267 55.000 8.36 1.76 0.00 4.18
1202 1716 3.740397 GCAGTGCCGCATGCTCAA 61.740 61.111 17.13 0.00 42.00 3.02
1216 1730 1.883021 CTCAACAACCGGCCAATCC 59.117 57.895 0.00 0.00 0.00 3.01
1242 1756 1.994507 CTGCTGCTTCTCCCCCTCT 60.995 63.158 0.00 0.00 0.00 3.69
1248 1762 2.689073 CTTCTCCCCCTCTGAAGCA 58.311 57.895 0.00 0.00 32.22 3.91
1314 1828 1.632409 AGAGTCCTGCAATGTGTCCAT 59.368 47.619 0.00 0.00 0.00 3.41
1320 1834 2.945008 CCTGCAATGTGTCCATAACGAT 59.055 45.455 0.00 0.00 0.00 3.73
1368 1882 1.903877 CGGAGGAGAATGCCACCACT 61.904 60.000 0.00 0.00 38.45 4.00
1380 1894 1.149174 CACCACTGCTGGGTTCAGT 59.851 57.895 0.00 0.00 44.87 3.41
1462 1976 1.605058 GCTAGAGTCCAGGGCGTTCA 61.605 60.000 0.00 0.00 0.00 3.18
1470 1984 2.203788 AGGGCGTTCAGGGACAGA 60.204 61.111 0.00 0.00 0.00 3.41
1558 2072 2.954753 CTCGTGTTCAACAGCCCGC 61.955 63.158 0.00 0.00 0.00 6.13
1711 2225 1.770658 CCATTGATAGCCTGGGAGACA 59.229 52.381 0.00 0.00 0.00 3.41
1862 2376 1.010419 CAAAATGGCCTTGTGCTCGC 61.010 55.000 3.32 0.00 40.92 5.03
1885 2399 0.693049 GCCCAAAGAGAGAGGTGGAA 59.307 55.000 0.00 0.00 32.54 3.53
1891 2405 4.505566 CCAAAGAGAGAGGTGGAATTGTGA 60.506 45.833 0.00 0.00 32.54 3.58
1905 2419 0.319083 TTGTGATCGTTACCAGCCGT 59.681 50.000 0.00 0.00 0.00 5.68
1908 2422 0.604073 TGATCGTTACCAGCCGTCAA 59.396 50.000 0.00 0.00 0.00 3.18
1957 2471 0.961019 GGGTAGTGTGTACCGTGTGA 59.039 55.000 0.00 0.00 38.46 3.58
1962 2476 1.070105 TGTGTACCGTGTGAAGCCC 59.930 57.895 0.00 0.00 0.00 5.19
2025 2539 1.532868 CTGAACAAGGAAAGACAGCCG 59.467 52.381 0.00 0.00 0.00 5.52
2103 2617 3.814268 CCGTCAATGGCCAAGGCG 61.814 66.667 23.80 23.80 43.06 5.52
2187 2701 8.911918 TTAAGCTTGAGTAGTGGAAATGTAAA 57.088 30.769 9.86 0.00 0.00 2.01
2189 2703 6.534634 AGCTTGAGTAGTGGAAATGTAAAGT 58.465 36.000 0.00 0.00 0.00 2.66
2190 2704 7.676947 AGCTTGAGTAGTGGAAATGTAAAGTA 58.323 34.615 0.00 0.00 0.00 2.24
2191 2705 7.819900 AGCTTGAGTAGTGGAAATGTAAAGTAG 59.180 37.037 0.00 0.00 0.00 2.57
2208 2722 8.920174 TGTAAAGTAGAGTAAGCAATATGCCTA 58.080 33.333 0.00 0.00 46.52 3.93
2213 2727 9.480861 AGTAGAGTAAGCAATATGCCTATCATA 57.519 33.333 0.00 0.00 46.52 2.15
2228 2742 5.297029 GCCTATCATAGACCAAAAAGACACC 59.703 44.000 0.00 0.00 0.00 4.16
2238 2752 4.588528 ACCAAAAAGACACCACATAGCAAT 59.411 37.500 0.00 0.00 0.00 3.56
2313 2827 4.259356 TGAATGGCTGTGAGAAGAAGATG 58.741 43.478 0.00 0.00 0.00 2.90
2314 2828 2.775911 TGGCTGTGAGAAGAAGATGG 57.224 50.000 0.00 0.00 0.00 3.51
2315 2829 1.339438 TGGCTGTGAGAAGAAGATGGC 60.339 52.381 0.00 0.00 0.00 4.40
2316 2830 1.339438 GGCTGTGAGAAGAAGATGGCA 60.339 52.381 0.00 0.00 0.00 4.92
2317 2831 2.641305 GCTGTGAGAAGAAGATGGCAT 58.359 47.619 0.00 0.00 0.00 4.40
2319 2833 3.607741 CTGTGAGAAGAAGATGGCATGT 58.392 45.455 3.81 0.00 0.00 3.21
2320 2834 4.763073 CTGTGAGAAGAAGATGGCATGTA 58.237 43.478 3.81 0.00 0.00 2.29
2321 2835 5.363562 TGTGAGAAGAAGATGGCATGTAT 57.636 39.130 3.81 0.00 0.00 2.29
2337 2856 4.404640 CATGTATCCATTTCTCCCTGCAT 58.595 43.478 0.00 0.00 0.00 3.96
2356 2875 3.129638 GCATAATAAGTTTGAACCCCGCA 59.870 43.478 0.00 0.00 0.00 5.69
2370 2889 2.951642 ACCCCGCATAGAATTGAATGTG 59.048 45.455 4.04 4.04 34.19 3.21
2404 2923 5.689961 CGGTTTCCTCATAAACAAAAAGTGG 59.310 40.000 0.00 0.00 40.42 4.00
2406 2925 6.700081 GGTTTCCTCATAAACAAAAAGTGGAC 59.300 38.462 0.00 0.00 40.42 4.02
2413 2932 4.506886 AAACAAAAAGTGGACGTGTCAA 57.493 36.364 0.00 0.00 0.00 3.18
2530 3050 3.119849 GCCGTAACAAACTTCTGCATGAT 60.120 43.478 0.00 0.00 0.00 2.45
2533 3053 4.378770 CGTAACAAACTTCTGCATGATGCT 60.379 41.667 19.19 0.00 45.31 3.79
2534 3054 4.595762 AACAAACTTCTGCATGATGCTT 57.404 36.364 19.19 0.68 45.31 3.91
2542 3062 6.561614 ACTTCTGCATGATGCTTTGAAATAG 58.438 36.000 19.19 4.92 45.31 1.73
2553 3073 4.082625 TGCTTTGAAATAGCATGTGTGAGG 60.083 41.667 0.00 0.00 43.30 3.86
2580 3100 4.275936 ACTGACCATAACTTGCACAACTTC 59.724 41.667 0.00 0.00 0.00 3.01
2593 3113 3.439476 GCACAACTTCGGTAGAGACTCTA 59.561 47.826 8.17 8.17 0.00 2.43
2616 3136 9.859427 TCTAATCAAACTTGCTTTCCATTAATG 57.141 29.630 8.58 8.58 0.00 1.90
2663 3183 4.947645 TCACATGAAAAAGCCTGAAAAGG 58.052 39.130 0.00 0.00 0.00 3.11
2665 3185 5.305128 TCACATGAAAAAGCCTGAAAAGGAT 59.695 36.000 0.00 0.00 0.00 3.24
2856 3376 1.078918 CTGGCTTCGTGCATCTCCA 60.079 57.895 0.00 0.00 45.15 3.86
2863 3383 1.750193 TCGTGCATCTCCATTTTCCC 58.250 50.000 0.00 0.00 0.00 3.97
2989 3510 0.764890 CTCTGGTTTCCTGGGTGTCA 59.235 55.000 0.00 0.00 0.00 3.58
2990 3511 0.472471 TCTGGTTTCCTGGGTGTCAC 59.528 55.000 0.00 0.00 0.00 3.67
3040 3561 5.416952 ACAAGGGAAAGATTCTATGTTGCTG 59.583 40.000 0.00 0.00 0.00 4.41
3070 3591 0.615850 CCTCCAGGAAGGTCAGGTTC 59.384 60.000 0.00 0.00 39.02 3.62
3132 4006 5.009010 AGTCATTCAAGAACTTCAAACGCAT 59.991 36.000 0.00 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.206371 AGCGGCATTCTTAAGTACGGT 59.794 47.619 1.45 4.49 0.00 4.83
145 146 3.728845 TGCCTTGTCTTGTGTTCTACTC 58.271 45.455 0.00 0.00 0.00 2.59
146 147 3.838244 TGCCTTGTCTTGTGTTCTACT 57.162 42.857 0.00 0.00 0.00 2.57
147 148 4.789802 GCTTTGCCTTGTCTTGTGTTCTAC 60.790 45.833 0.00 0.00 0.00 2.59
148 149 3.315191 GCTTTGCCTTGTCTTGTGTTCTA 59.685 43.478 0.00 0.00 0.00 2.10
149 150 2.099756 GCTTTGCCTTGTCTTGTGTTCT 59.900 45.455 0.00 0.00 0.00 3.01
150 151 2.099756 AGCTTTGCCTTGTCTTGTGTTC 59.900 45.455 0.00 0.00 0.00 3.18
151 152 2.102578 AGCTTTGCCTTGTCTTGTGTT 58.897 42.857 0.00 0.00 0.00 3.32
152 153 1.767759 AGCTTTGCCTTGTCTTGTGT 58.232 45.000 0.00 0.00 0.00 3.72
153 154 2.466846 CAAGCTTTGCCTTGTCTTGTG 58.533 47.619 0.00 0.00 37.89 3.33
168 169 6.463995 TCACAAACTTGAAATAACCAAGCT 57.536 33.333 0.00 0.00 43.45 3.74
211 213 3.748048 TCTCGAATCTTTTGCACTTCAGG 59.252 43.478 0.00 0.00 0.00 3.86
286 288 3.008330 CTGCCTTCTCCATTGAAGACAG 58.992 50.000 6.27 6.27 43.95 3.51
378 380 2.350522 GATGCACAGTCGTTCCTCAAT 58.649 47.619 0.00 0.00 0.00 2.57
534 536 2.534990 CAGGTGTTCCTCCTCTTCTCT 58.465 52.381 0.00 0.00 43.07 3.10
617 619 1.492599 TGAACACACACTCCATGGGAA 59.507 47.619 13.02 0.00 34.14 3.97
634 636 3.797353 GGAGGGGAGCGGCATGAA 61.797 66.667 1.45 0.00 0.00 2.57
643 645 0.693767 AAGGCAGAGATGGAGGGGAG 60.694 60.000 0.00 0.00 0.00 4.30
695 697 2.303022 CCCCACGAGCATTAGGATATGT 59.697 50.000 0.00 0.00 0.00 2.29
805 808 4.114794 CCAACTTTGGCTCTTGTTTCTTG 58.885 43.478 0.00 0.00 42.21 3.02
821 824 4.038763 GCCCTTAACTTTTAGTGCCAACTT 59.961 41.667 0.00 0.00 37.88 2.66
822 825 3.572682 GCCCTTAACTTTTAGTGCCAACT 59.427 43.478 0.00 0.00 40.67 3.16
823 826 3.305813 GGCCCTTAACTTTTAGTGCCAAC 60.306 47.826 0.00 0.00 33.82 3.77
833 836 1.142262 ACAGTGACGGCCCTTAACTTT 59.858 47.619 0.00 0.00 0.00 2.66
892 897 7.739825 TCACAGGATAATGAAGGGATAAAGAG 58.260 38.462 0.00 0.00 0.00 2.85
905 1419 7.754851 TGATTGATGGATTCACAGGATAATG 57.245 36.000 0.00 0.00 32.84 1.90
999 1513 4.594854 TGCACCACCACGGCCATT 62.595 61.111 2.24 0.00 39.03 3.16
1248 1762 2.380064 TGACCTTGTTGGAAAGCCAT 57.620 45.000 0.00 0.00 45.46 4.40
1285 1799 4.928398 CAGGACTCTGCGCTTCAT 57.072 55.556 9.73 0.00 33.86 2.57
1314 1828 1.078988 GCCGTTGGGGTCATCGTTA 60.079 57.895 0.00 0.00 38.44 3.18
1368 1882 2.425592 CACCGACTGAACCCAGCA 59.574 61.111 0.00 0.00 44.16 4.41
1380 1894 1.263356 CCCAAGAAGTACTCCACCGA 58.737 55.000 0.00 0.00 0.00 4.69
1470 1984 1.885163 CTGTAAGTCGTCCGGGGCTT 61.885 60.000 0.00 1.49 0.00 4.35
1711 2225 2.158842 GCTCATGGACAGCTAACTCCAT 60.159 50.000 12.12 12.12 46.48 3.41
1862 2376 0.035458 ACCTCTCTCTTTGGGCAACG 59.965 55.000 0.00 0.00 37.60 4.10
1885 2399 1.066430 ACGGCTGGTAACGATCACAAT 60.066 47.619 0.00 0.00 42.51 2.71
1891 2405 0.892755 TCTTGACGGCTGGTAACGAT 59.107 50.000 0.00 0.00 42.51 3.73
1905 2419 1.190178 TCTCTGCTGCCTGCTCTTGA 61.190 55.000 0.00 0.00 43.37 3.02
1908 2422 0.976590 TCATCTCTGCTGCCTGCTCT 60.977 55.000 0.00 0.00 43.37 4.09
1962 2476 3.074999 GCTCTCTCTGTCGGCCAGG 62.075 68.421 2.24 0.00 41.83 4.45
2025 2539 4.476862 TGTTAATAGCTGCGAGATCGATC 58.523 43.478 17.91 17.91 43.02 3.69
2187 2701 7.782897 TGATAGGCATATTGCTTACTCTACT 57.217 36.000 0.00 0.00 44.28 2.57
2189 2703 9.700831 TCTATGATAGGCATATTGCTTACTCTA 57.299 33.333 0.00 0.00 44.28 2.43
2190 2704 8.474025 GTCTATGATAGGCATATTGCTTACTCT 58.526 37.037 0.00 0.00 44.28 3.24
2191 2705 7.708752 GGTCTATGATAGGCATATTGCTTACTC 59.291 40.741 6.39 0.00 44.28 2.59
2196 2710 6.378661 TTGGTCTATGATAGGCATATTGCT 57.621 37.500 6.39 0.00 44.28 3.91
2208 2722 5.630121 TGTGGTGTCTTTTTGGTCTATGAT 58.370 37.500 0.00 0.00 0.00 2.45
2213 2727 3.821033 GCTATGTGGTGTCTTTTTGGTCT 59.179 43.478 0.00 0.00 0.00 3.85
2262 2776 4.517952 TTGTGCCATAACTTTCATGTGG 57.482 40.909 0.00 0.00 0.00 4.17
2281 2795 7.092137 TCTCACAGCCATTCATAAGAATTTG 57.908 36.000 0.00 0.00 42.46 2.32
2319 2833 7.988937 ACTTATTATGCAGGGAGAAATGGATA 58.011 34.615 0.00 0.00 0.00 2.59
2320 2834 6.856757 ACTTATTATGCAGGGAGAAATGGAT 58.143 36.000 0.00 0.00 0.00 3.41
2321 2835 6.266131 ACTTATTATGCAGGGAGAAATGGA 57.734 37.500 0.00 0.00 0.00 3.41
2337 2856 5.991861 TCTATGCGGGGTTCAAACTTATTA 58.008 37.500 0.00 0.00 0.00 0.98
2356 2875 5.163581 GGAAGCACTGCACATTCAATTCTAT 60.164 40.000 3.30 0.00 0.00 1.98
2370 2889 1.578206 GAGGAAACCGGAAGCACTGC 61.578 60.000 9.46 0.00 0.00 4.40
2404 2923 2.812011 AGCCATAAAGGTTTGACACGTC 59.188 45.455 0.00 0.00 40.61 4.34
2406 2925 3.915437 AAGCCATAAAGGTTTGACACG 57.085 42.857 0.00 0.00 39.62 4.49
2533 3053 4.661222 TCCCTCACACATGCTATTTCAAA 58.339 39.130 0.00 0.00 0.00 2.69
2534 3054 4.019411 TCTCCCTCACACATGCTATTTCAA 60.019 41.667 0.00 0.00 0.00 2.69
2542 3062 0.610174 TCAGTCTCCCTCACACATGC 59.390 55.000 0.00 0.00 0.00 4.06
2553 3073 3.003480 GTGCAAGTTATGGTCAGTCTCC 58.997 50.000 0.00 0.00 0.00 3.71
2580 3100 5.517054 GCAAGTTTGATTAGAGTCTCTACCG 59.483 44.000 9.20 0.00 0.00 4.02
2616 3136 4.367450 GCATTGTCAGGAGAGAGTGATAC 58.633 47.826 0.00 0.00 27.74 2.24
2663 3183 5.601662 TCACTGATTTCCCGAGTCATTATC 58.398 41.667 0.00 0.00 0.00 1.75
2665 3185 5.414789 TTCACTGATTTCCCGAGTCATTA 57.585 39.130 0.00 0.00 0.00 1.90
2721 3241 4.269183 TGTGGCCTATGGTTATGAACTTG 58.731 43.478 3.32 0.00 0.00 3.16
2900 3421 7.500892 ACATATGTAATAAGTCAATTTCCGCCA 59.499 33.333 6.56 0.00 29.06 5.69
2930 3451 9.739276 ACCAAATCAAGTGAGTTCTCATTATTA 57.261 29.630 5.80 0.00 29.00 0.98
2931 3452 8.517878 CACCAAATCAAGTGAGTTCTCATTATT 58.482 33.333 5.80 0.00 36.01 1.40
2932 3453 7.362401 GCACCAAATCAAGTGAGTTCTCATTAT 60.362 37.037 5.80 0.00 36.01 1.28
2989 3510 2.026822 GGATGGAGTGTGGATGAACTGT 60.027 50.000 0.00 0.00 0.00 3.55
2990 3511 2.238144 AGGATGGAGTGTGGATGAACTG 59.762 50.000 0.00 0.00 0.00 3.16
3040 3561 3.495806 CCTTCCTGGAGGTATTCAGATGC 60.496 52.174 5.02 0.00 38.35 3.91
3070 3591 2.679837 CCAGGTGAATGAGATGTTTCCG 59.320 50.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.