Multiple sequence alignment - TraesCS1B01G305600

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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 TraesCS1B01G305600 chr1B 100.000 2970 0 0 1 2970 528399093 528396124 0.000000e+00 5485.0
1 TraesCS1B01G305600 chr1D 93.299 2955 128 33 1 2946 393928204 393931097 0.000000e+00 4296.0
2 TraesCS1B01G305600 chr1A 92.605 2042 90 20 1 2004 491313013 491310995 0.000000e+00 2878.0
3 TraesCS1B01G305600 chr1A 88.432 925 54 22 2041 2945 491310991 491310100 0.000000e+00 1066.0
4 TraesCS1B01G305600 chr3A 86.957 69 7 2 2889 2955 476298068 476298000 3.170000e-10 76.8
5 TraesCS1B01G305600 chr3A 84.810 79 7 4 2889 2966 476296541 476296467 1.140000e-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 TraesCS1B01G305600 chr1B 528396124 528399093 2969 True 5485 5485 100.0000 1 2970 1 chr1B.!!$R1 2969
1 TraesCS1B01G305600 chr1D 393928204 393931097 2893 False 4296 4296 93.2990 1 2946 1 chr1D.!!$F1 2945
2 TraesCS1B01G305600 chr1A 491310100 491313013 2913 True 1972 2878 90.5185 1 2945 2 chr1A.!!$R1 2944

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
719 742 0.106149 GGTTATCGAAGCGGGGATGT 59.894 55.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 2278 0.101219 GAAGCCCGTGCCATTGATTC 59.899 55.0 0.0 0.0 38.69 2.52 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
66 67 9.178427 GAAAACTCAATTCACAGATCAAGAAAG 57.822 33.333 0.00 0.00 0.00 2.62
166 171 2.036217 CTCTGCTTCCATTGCAACCAAA 59.964 45.455 0.00 0.00 40.13 3.28
286 291 1.611491 GAAACCAATCCAAAGTCCGCA 59.389 47.619 0.00 0.00 0.00 5.69
287 292 1.698506 AACCAATCCAAAGTCCGCAA 58.301 45.000 0.00 0.00 0.00 4.85
288 293 1.698506 ACCAATCCAAAGTCCGCAAA 58.301 45.000 0.00 0.00 0.00 3.68
306 311 1.256812 AAATTGAAGTCCAAGCCCCG 58.743 50.000 0.00 0.00 38.31 5.73
313 318 3.003173 TCCAAGCCCCGGACAGAG 61.003 66.667 0.73 0.00 0.00 3.35
568 591 3.693578 TCTTTATGCGCATCCAAATGTGA 59.306 39.130 29.11 13.16 44.56 3.58
620 643 7.867921 AGATAGTGGGTACATTTTAATGGTGA 58.132 34.615 7.33 0.00 40.70 4.02
719 742 0.106149 GGTTATCGAAGCGGGGATGT 59.894 55.000 0.00 0.00 0.00 3.06
723 746 0.251916 ATCGAAGCGGGGATGTTTGA 59.748 50.000 0.00 0.00 0.00 2.69
725 748 0.673644 CGAAGCGGGGATGTTTGACT 60.674 55.000 0.00 0.00 0.00 3.41
757 780 4.582459 GATCTCACAAAATCTAAGCACGC 58.418 43.478 0.00 0.00 0.00 5.34
758 781 3.664107 TCTCACAAAATCTAAGCACGCT 58.336 40.909 0.00 0.00 0.00 5.07
759 782 4.065088 TCTCACAAAATCTAAGCACGCTT 58.935 39.130 9.57 9.57 39.83 4.68
779 802 6.819649 ACGCTTGCCTATTTTGTGTTATAGTA 59.180 34.615 0.00 0.00 0.00 1.82
919 942 7.714500 TCCCTAAAATTCTTGGAAAATCCCTA 58.286 34.615 0.00 0.00 35.03 3.53
920 943 7.839200 TCCCTAAAATTCTTGGAAAATCCCTAG 59.161 37.037 0.00 0.00 35.03 3.02
971 994 3.132111 GGTTTTCAAATCACGCCCCATAT 59.868 43.478 0.00 0.00 0.00 1.78
974 997 6.462347 GGTTTTCAAATCACGCCCCATATAAT 60.462 38.462 0.00 0.00 0.00 1.28
1037 1067 3.837570 AAACCCCACCGCTTCCGTC 62.838 63.158 0.00 0.00 0.00 4.79
1598 1631 2.809601 GCTCAACCGCATCGTCGT 60.810 61.111 0.00 0.00 0.00 4.34
1698 1734 2.124942 GGGAGCCGGAAGAAGCAG 60.125 66.667 5.05 0.00 0.00 4.24
1875 1914 2.275318 CTCTTTACTACTGGCAGCAGC 58.725 52.381 15.89 0.00 41.10 5.25
1877 1916 1.734465 CTTTACTACTGGCAGCAGCAC 59.266 52.381 15.89 0.00 44.61 4.40
1992 2032 1.067060 AGTTCAAACTTCAAAGCCGGC 59.933 47.619 21.89 21.89 35.21 6.13
2011 2051 1.943340 GCTACACCATTGGCTTAGCTC 59.057 52.381 21.17 0.00 0.00 4.09
2020 2060 2.501610 GCTTAGCTCGGGTCTGGG 59.498 66.667 0.00 0.00 0.00 4.45
2029 2069 2.671682 GGGTCTGGGCAGGAGTTC 59.328 66.667 0.00 0.00 0.00 3.01
2073 2116 1.641577 AGCTTCGGCATTACGACTTC 58.358 50.000 0.00 0.00 43.37 3.01
2150 2194 8.370493 ACCAGACGAGAATCATAATACAATTG 57.630 34.615 3.24 3.24 33.17 2.32
2177 2221 8.851541 ACTACTACTACTGCTATACTTGATCC 57.148 38.462 0.00 0.00 0.00 3.36
2178 2222 7.884354 ACTACTACTACTGCTATACTTGATCCC 59.116 40.741 0.00 0.00 0.00 3.85
2179 2223 6.854578 ACTACTACTGCTATACTTGATCCCT 58.145 40.000 0.00 0.00 0.00 4.20
2180 2224 6.943718 ACTACTACTGCTATACTTGATCCCTC 59.056 42.308 0.00 0.00 0.00 4.30
2200 2244 1.340248 CTGGTTGGTCTCTGTACGTGT 59.660 52.381 0.00 0.00 0.00 4.49
2201 2245 1.338973 TGGTTGGTCTCTGTACGTGTC 59.661 52.381 0.00 0.00 0.00 3.67
2202 2246 1.336609 GGTTGGTCTCTGTACGTGTCC 60.337 57.143 0.00 0.00 0.00 4.02
2207 2251 2.430465 GTCTCTGTACGTGTCCCTGTA 58.570 52.381 0.00 0.00 0.00 2.74
2234 2278 7.731302 CGTGCGTTTCAAATCTTTTTAATTCTG 59.269 33.333 0.00 0.00 0.00 3.02
2318 2362 4.583254 TGTTTGCGCACGCGACAC 62.583 61.111 15.93 8.25 45.51 3.67
2329 2374 4.620437 GCGACACGGCGATATACA 57.380 55.556 16.62 0.00 0.00 2.29
2390 2435 3.160047 AGAGCATCCTCTGGCCGG 61.160 66.667 4.71 4.71 46.51 6.13
2525 2586 2.194212 GCGAGCCGAGAGATGGGTA 61.194 63.158 0.00 0.00 37.33 3.69
2552 2613 3.629035 TTCGAGGGGTAGGGTGGGG 62.629 68.421 0.00 0.00 0.00 4.96
2579 2640 0.892063 AATTTAACGGCGCCCACATT 59.108 45.000 23.46 12.84 0.00 2.71
2627 2690 3.109547 CGCGTGTATGCCGTGTGT 61.110 61.111 0.00 0.00 0.00 3.72
2628 2691 2.474266 GCGTGTATGCCGTGTGTG 59.526 61.111 0.00 0.00 0.00 3.82
2629 2692 2.314647 GCGTGTATGCCGTGTGTGT 61.315 57.895 0.00 0.00 0.00 3.72
2630 2693 1.009903 GCGTGTATGCCGTGTGTGTA 61.010 55.000 0.00 0.00 0.00 2.90
2773 2836 2.169789 CAGCGGTGATCGGCTCTTG 61.170 63.158 9.50 0.00 45.97 3.02
2825 2888 2.917227 TGACAGCACCGAGAGCCA 60.917 61.111 0.00 0.00 0.00 4.75
2905 2968 2.582498 GCGCGCCACAGTACTAGG 60.582 66.667 23.24 8.77 0.00 3.02
2946 3009 2.896801 CGTGCTTGCTTCGCTGGTT 61.897 57.895 0.00 0.00 0.00 3.67
2947 3010 1.370900 GTGCTTGCTTCGCTGGTTG 60.371 57.895 0.00 0.00 0.00 3.77
2948 3011 1.823470 TGCTTGCTTCGCTGGTTGT 60.823 52.632 0.00 0.00 0.00 3.32
2949 3012 1.360192 GCTTGCTTCGCTGGTTGTT 59.640 52.632 0.00 0.00 0.00 2.83
2950 3013 0.661483 GCTTGCTTCGCTGGTTGTTC 60.661 55.000 0.00 0.00 0.00 3.18
2951 3014 0.384725 CTTGCTTCGCTGGTTGTTCG 60.385 55.000 0.00 0.00 0.00 3.95
2952 3015 2.127232 GCTTCGCTGGTTGTTCGC 60.127 61.111 0.00 0.00 0.00 4.70
2953 3016 2.607892 GCTTCGCTGGTTGTTCGCT 61.608 57.895 0.00 0.00 0.00 4.93
2954 3017 1.941812 CTTCGCTGGTTGTTCGCTT 59.058 52.632 0.00 0.00 0.00 4.68
2955 3018 0.110644 CTTCGCTGGTTGTTCGCTTC 60.111 55.000 0.00 0.00 0.00 3.86
2956 3019 1.827315 TTCGCTGGTTGTTCGCTTCG 61.827 55.000 0.00 0.00 0.00 3.79
2957 3020 2.556287 GCTGGTTGTTCGCTTCGG 59.444 61.111 0.00 0.00 0.00 4.30
2958 3021 1.959226 GCTGGTTGTTCGCTTCGGA 60.959 57.895 0.00 0.00 0.00 4.55
2959 3022 1.298859 GCTGGTTGTTCGCTTCGGAT 61.299 55.000 0.00 0.00 0.00 4.18
2960 3023 0.721718 CTGGTTGTTCGCTTCGGATC 59.278 55.000 0.00 0.00 0.00 3.36
2961 3024 0.320374 TGGTTGTTCGCTTCGGATCT 59.680 50.000 0.00 0.00 0.00 2.75
2962 3025 1.000145 GGTTGTTCGCTTCGGATCTC 59.000 55.000 0.00 0.00 0.00 2.75
2963 3026 1.404315 GGTTGTTCGCTTCGGATCTCT 60.404 52.381 0.00 0.00 0.00 3.10
2964 3027 2.338500 GTTGTTCGCTTCGGATCTCTT 58.662 47.619 0.00 0.00 0.00 2.85
2965 3028 2.737252 GTTGTTCGCTTCGGATCTCTTT 59.263 45.455 0.00 0.00 0.00 2.52
2966 3029 2.337583 TGTTCGCTTCGGATCTCTTTG 58.662 47.619 0.00 0.00 0.00 2.77
2967 3030 1.061276 GTTCGCTTCGGATCTCTTTGC 59.939 52.381 0.00 0.00 0.00 3.68
2968 3031 0.460284 TCGCTTCGGATCTCTTTGCC 60.460 55.000 0.00 0.00 0.00 4.52
2969 3032 0.460987 CGCTTCGGATCTCTTTGCCT 60.461 55.000 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.539173 TGAGTTTTCCTTAGTTATGGCTTGA 58.461 36.000 0.00 0.00 0.00 3.02
66 67 3.439129 GGTTGTTGCATGTACTTCCCTAC 59.561 47.826 0.00 0.00 0.00 3.18
133 138 0.257039 AAGCAGAGGAATTGGGCGAT 59.743 50.000 0.00 0.00 0.00 4.58
147 152 2.529780 TTTGGTTGCAATGGAAGCAG 57.470 45.000 17.88 0.00 43.75 4.24
166 171 5.478679 TCCGAGACTCTTCTTCTTTCATCTT 59.521 40.000 0.03 0.00 29.47 2.40
286 291 1.618343 CGGGGCTTGGACTTCAATTTT 59.382 47.619 0.00 0.00 34.45 1.82
287 292 1.256812 CGGGGCTTGGACTTCAATTT 58.743 50.000 0.00 0.00 34.45 1.82
288 293 0.611896 CCGGGGCTTGGACTTCAATT 60.612 55.000 0.00 0.00 34.45 2.32
306 311 1.981256 TTTGTGGGCTTTCTCTGTCC 58.019 50.000 0.00 0.00 0.00 4.02
313 318 1.404035 ACGTGTCTTTTGTGGGCTTTC 59.596 47.619 0.00 0.00 0.00 2.62
431 436 3.755905 TGCACCACATGATTATCGTGTTT 59.244 39.130 16.49 5.18 43.56 2.83
486 509 6.726764 AGTCAAGAGTCATTACCTTCCTTAGT 59.273 38.462 0.00 0.00 0.00 2.24
568 591 0.107897 TGGAGCGTTAATGCGGTGAT 60.108 50.000 13.84 0.00 42.89 3.06
719 742 2.923655 GAGATCGCGATGACAAGTCAAA 59.076 45.455 29.09 0.00 43.58 2.69
723 746 1.202348 TGTGAGATCGCGATGACAAGT 59.798 47.619 29.09 0.00 0.00 3.16
725 748 2.362169 TTGTGAGATCGCGATGACAA 57.638 45.000 29.09 25.66 0.00 3.18
831 854 9.931210 GTACCATAACAAAAGAATTCGATAAGG 57.069 33.333 0.00 0.00 0.00 2.69
872 895 4.178956 ACACCACCTCACAAACCTTAAT 57.821 40.909 0.00 0.00 0.00 1.40
874 897 3.547746 GAACACCACCTCACAAACCTTA 58.452 45.455 0.00 0.00 0.00 2.69
877 900 1.029681 GGAACACCACCTCACAAACC 58.970 55.000 0.00 0.00 0.00 3.27
971 994 1.347050 TCGTTCGTTTGGGGTGGATTA 59.653 47.619 0.00 0.00 0.00 1.75
974 997 1.070105 CTCGTTCGTTTGGGGTGGA 59.930 57.895 0.00 0.00 0.00 4.02
1011 1041 2.561037 CGGTGGGGTTTTGTCTGCC 61.561 63.158 0.00 0.00 0.00 4.85
1155 1188 0.692419 AGTGGGAGGCGATGGAGAAT 60.692 55.000 0.00 0.00 0.00 2.40
1833 1872 1.334160 TCAGTTACTGGACAGCCGAA 58.666 50.000 12.79 0.00 36.79 4.30
1875 1914 1.268285 CGATGAGGAGTAGCTGTCGTG 60.268 57.143 0.00 0.00 0.00 4.35
1877 1916 1.003331 GTCGATGAGGAGTAGCTGTCG 60.003 57.143 0.00 0.00 0.00 4.35
1958 1998 9.386010 TGAAGTTTGAACTACTTTAACTAGCAA 57.614 29.630 0.00 0.00 38.57 3.91
1966 2006 6.238538 CCGGCTTTGAAGTTTGAACTACTTTA 60.239 38.462 0.00 0.00 38.57 1.85
1992 2032 2.205074 CGAGCTAAGCCAATGGTGTAG 58.795 52.381 0.00 4.16 0.00 2.74
2011 2051 3.316573 GAACTCCTGCCCAGACCCG 62.317 68.421 0.00 0.00 0.00 5.28
2068 2111 3.080319 AGCAGCAAATCTTCTGGAAGTC 58.920 45.455 9.73 0.00 39.38 3.01
2073 2116 4.421948 GAAATGAGCAGCAAATCTTCTGG 58.578 43.478 0.00 0.00 0.00 3.86
2155 2199 6.854578 AGGGATCAAGTATAGCAGTAGTAGT 58.145 40.000 0.00 0.00 0.00 2.73
2161 2205 3.900601 CCAGAGGGATCAAGTATAGCAGT 59.099 47.826 0.00 0.00 35.59 4.40
2162 2206 3.900601 ACCAGAGGGATCAAGTATAGCAG 59.099 47.826 0.00 0.00 38.05 4.24
2163 2207 3.928754 ACCAGAGGGATCAAGTATAGCA 58.071 45.455 0.00 0.00 38.05 3.49
2164 2208 4.503991 CCAACCAGAGGGATCAAGTATAGC 60.504 50.000 0.00 0.00 38.05 2.97
2165 2209 4.656112 ACCAACCAGAGGGATCAAGTATAG 59.344 45.833 0.00 0.00 38.05 1.31
2166 2210 4.631234 ACCAACCAGAGGGATCAAGTATA 58.369 43.478 0.00 0.00 38.05 1.47
2167 2211 3.456277 GACCAACCAGAGGGATCAAGTAT 59.544 47.826 0.00 0.00 38.05 2.12
2168 2212 2.838202 GACCAACCAGAGGGATCAAGTA 59.162 50.000 0.00 0.00 38.05 2.24
2169 2213 1.630878 GACCAACCAGAGGGATCAAGT 59.369 52.381 0.00 0.00 38.05 3.16
2170 2214 1.912043 AGACCAACCAGAGGGATCAAG 59.088 52.381 0.00 0.00 38.05 3.02
2171 2215 1.909302 GAGACCAACCAGAGGGATCAA 59.091 52.381 0.00 0.00 38.05 2.57
2172 2216 1.079490 AGAGACCAACCAGAGGGATCA 59.921 52.381 0.00 0.00 38.05 2.92
2173 2217 1.484240 CAGAGACCAACCAGAGGGATC 59.516 57.143 0.00 0.00 38.05 3.36
2174 2218 1.203364 ACAGAGACCAACCAGAGGGAT 60.203 52.381 0.00 0.00 38.05 3.85
2175 2219 0.191064 ACAGAGACCAACCAGAGGGA 59.809 55.000 0.00 0.00 38.05 4.20
2176 2220 1.550976 GTACAGAGACCAACCAGAGGG 59.449 57.143 0.00 0.00 41.29 4.30
2177 2221 1.202582 CGTACAGAGACCAACCAGAGG 59.797 57.143 0.00 0.00 0.00 3.69
2178 2222 1.887198 ACGTACAGAGACCAACCAGAG 59.113 52.381 0.00 0.00 0.00 3.35
2179 2223 1.611977 CACGTACAGAGACCAACCAGA 59.388 52.381 0.00 0.00 0.00 3.86
2180 2224 1.340248 ACACGTACAGAGACCAACCAG 59.660 52.381 0.00 0.00 0.00 4.00
2200 2244 0.104487 TTGAAACGCACGTACAGGGA 59.896 50.000 0.00 0.00 0.00 4.20
2201 2245 0.938713 TTTGAAACGCACGTACAGGG 59.061 50.000 0.00 0.00 0.00 4.45
2202 2246 2.478894 AGATTTGAAACGCACGTACAGG 59.521 45.455 0.00 0.00 0.00 4.00
2207 2251 7.434013 AGAATTAAAAAGATTTGAAACGCACGT 59.566 29.630 0.00 0.00 0.00 4.49
2234 2278 0.101219 GAAGCCCGTGCCATTGATTC 59.899 55.000 0.00 0.00 38.69 2.52
2318 2362 0.439985 GCTGCATGTGTATATCGCCG 59.560 55.000 0.00 0.00 0.00 6.46
2320 2364 2.346847 GCTAGCTGCATGTGTATATCGC 59.653 50.000 7.70 0.00 42.31 4.58
2381 2426 1.190833 ATCATAGGAGCCGGCCAGAG 61.191 60.000 26.15 8.96 0.00 3.35
2389 2434 0.326264 ATCGGGCAATCATAGGAGCC 59.674 55.000 0.00 0.00 46.28 4.70
2390 2435 1.271054 ACATCGGGCAATCATAGGAGC 60.271 52.381 0.00 0.00 0.00 4.70
2552 2613 1.533129 GCGCCGTTAAATTCCCATGAC 60.533 52.381 0.00 0.00 0.00 3.06
2579 2640 0.108520 GGCACGACGAAAGACCCATA 60.109 55.000 0.00 0.00 0.00 2.74
2587 2648 0.944311 GAGCTGAAGGCACGACGAAA 60.944 55.000 0.00 0.00 44.79 3.46
2588 2649 1.372997 GAGCTGAAGGCACGACGAA 60.373 57.895 0.00 0.00 44.79 3.85
2649 2712 0.465278 GCCCTGATCTTGCTCTTCCC 60.465 60.000 0.00 0.00 0.00 3.97
2753 2816 1.888436 AAGAGCCGATCACCGCTGAA 61.888 55.000 3.82 0.00 36.84 3.02
2773 2836 1.787847 CTGCGGTCCATTCGAACAC 59.212 57.895 0.00 0.00 0.00 3.32
2809 2872 1.520342 GATGGCTCTCGGTGCTGTC 60.520 63.158 0.00 0.00 0.00 3.51
2825 2888 0.676466 TTTCGTTCCATGGCGCAGAT 60.676 50.000 10.83 0.00 0.00 2.90
2863 2926 2.516448 TGGGTCGATCCAGGATGAC 58.484 57.895 15.09 13.98 39.69 3.06
2905 2968 4.179579 GCGAACGAATGGGCTGGC 62.180 66.667 0.00 0.00 0.00 4.85
2946 3009 2.337583 CAAAGAGATCCGAAGCGAACA 58.662 47.619 0.00 0.00 0.00 3.18
2947 3010 1.061276 GCAAAGAGATCCGAAGCGAAC 59.939 52.381 0.00 0.00 0.00 3.95
2948 3011 1.359848 GCAAAGAGATCCGAAGCGAA 58.640 50.000 0.00 0.00 0.00 4.70
2949 3012 0.460284 GGCAAAGAGATCCGAAGCGA 60.460 55.000 0.00 0.00 0.00 4.93
2950 3013 0.460987 AGGCAAAGAGATCCGAAGCG 60.461 55.000 0.00 0.00 0.00 4.68
2951 3014 3.467776 AGGCAAAGAGATCCGAAGC 57.532 52.632 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.