Multiple sequence alignment - TraesCS1B01G391900

Loading Multiple Alignment...

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 TraesCS1B01G391900 chr1B 100.000 2496 0 0 738 3233 624885297 624887792 0.000000e+00 4610
1 TraesCS1B01G391900 chr1B 100.000 287 0 0 1 287 624884560 624884846 6.140000e-147 531
2 TraesCS1B01G391900 chr1D 92.400 2513 115 33 738 3233 454565050 454562597 0.000000e+00 3513
3 TraesCS1B01G391900 chr1D 94.318 264 9 2 24 287 454565356 454565099 1.810000e-107 399
4 TraesCS1B01G391900 chr1A 95.196 1790 72 10 745 2525 548674290 548676074 0.000000e+00 2817
5 TraesCS1B01G391900 chr1A 87.621 1858 130 43 1401 3233 548682956 548684738 0.000000e+00 2065
6 TraesCS1B01G391900 chr1A 83.849 291 20 13 1 287 548673991 548674258 5.350000e-63 252
7 TraesCS1B01G391900 chr3A 83.774 1436 228 4 801 2235 482060613 482062044 0.000000e+00 1356
8 TraesCS1B01G391900 chr3B 83.426 1436 233 4 801 2235 471475071 471476502 0.000000e+00 1328
9 TraesCS1B01G391900 chr3D 83.148 1436 237 4 801 2235 361737361 361738792 0.000000e+00 1306


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 TraesCS1B01G391900 chr1B 624884560 624887792 3232 False 2570.5 4610 100.0000 1 3233 2 chr1B.!!$F1 3232
1 TraesCS1B01G391900 chr1D 454562597 454565356 2759 True 1956.0 3513 93.3590 24 3233 2 chr1D.!!$R1 3209
2 TraesCS1B01G391900 chr1A 548682956 548684738 1782 False 2065.0 2065 87.6210 1401 3233 1 chr1A.!!$F1 1832
3 TraesCS1B01G391900 chr1A 548673991 548676074 2083 False 1534.5 2817 89.5225 1 2525 2 chr1A.!!$F2 2524
4 TraesCS1B01G391900 chr3A 482060613 482062044 1431 False 1356.0 1356 83.7740 801 2235 1 chr3A.!!$F1 1434
5 TraesCS1B01G391900 chr3B 471475071 471476502 1431 False 1328.0 1328 83.4260 801 2235 1 chr3B.!!$F1 1434
6 TraesCS1B01G391900 chr3D 361737361 361738792 1431 False 1306.0 1306 83.1480 801 2235 1 chr3D.!!$F1 1434

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
69 70 0.174845 CCCGTCAGATGTCGGCTAAA 59.825 55.0 12.19 0.0 43.57 1.85 F
1821 1829 0.883833 GGACACAATTCCAGCCACAG 59.116 55.0 0.00 0.0 35.49 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 1841 0.179200 GAATCGCCGACGCAAATGTT 60.179 50.0 0.0 0.0 39.84 2.71 R
2806 2837 0.618458 ATGTTGGGTCGTGCTGGTAT 59.382 50.0 0.0 0.0 0.00 2.73 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
37 38 4.390264 CATCAGCTGGATGTGATCTGATT 58.610 43.478 15.13 0.00 46.81 2.57
51 52 0.798776 CTGATTGAACAGACGGTGCC 59.201 55.000 0.00 0.00 39.94 5.01
66 67 4.148825 GCCCGTCAGATGTCGGCT 62.149 66.667 12.19 0.00 43.57 5.52
67 68 2.782222 GCCCGTCAGATGTCGGCTA 61.782 63.158 12.19 0.00 43.57 3.93
68 69 1.813859 CCCGTCAGATGTCGGCTAA 59.186 57.895 12.19 0.00 43.57 3.09
69 70 0.174845 CCCGTCAGATGTCGGCTAAA 59.825 55.000 12.19 0.00 43.57 1.85
70 71 1.202533 CCCGTCAGATGTCGGCTAAAT 60.203 52.381 12.19 0.00 43.57 1.40
71 72 2.128035 CCGTCAGATGTCGGCTAAATC 58.872 52.381 5.61 0.00 39.56 2.17
72 73 2.223829 CCGTCAGATGTCGGCTAAATCT 60.224 50.000 5.61 0.00 39.56 2.40
117 118 3.186613 CAGTTTCTACCGCTTTCCAGTTC 59.813 47.826 0.00 0.00 0.00 3.01
170 175 2.657237 GTCCACCTCCACAGTCCG 59.343 66.667 0.00 0.00 0.00 4.79
1806 1814 2.097110 ACTACAAGTCAGGGTGGACA 57.903 50.000 0.00 0.00 40.29 4.02
1821 1829 0.883833 GGACACAATTCCAGCCACAG 59.116 55.000 0.00 0.00 35.49 3.66
1962 1970 0.322366 TGAATGCAATGTCCCTCGCA 60.322 50.000 0.00 0.00 39.01 5.10
2242 2253 1.133790 GTAAGCTTTGAGCATGCCCTG 59.866 52.381 15.66 1.66 45.56 4.45
2407 2424 0.810031 CGTCTGCGGGGAATGGTTAG 60.810 60.000 0.00 0.00 0.00 2.34
2427 2444 0.179001 GGGGGTGGGGTTGATTATCG 60.179 60.000 0.00 0.00 0.00 2.92
2470 2487 9.887629 TTCTATGGATAATAAACGGTTGTGTTA 57.112 29.630 0.00 0.00 0.00 2.41
2527 2544 0.178995 TTGCTCCATGTTGCACTGGA 60.179 50.000 9.02 10.54 39.05 3.86
2573 2590 8.226819 TCTATGGACTGTCACTAGTATTTGAG 57.773 38.462 10.38 0.00 0.00 3.02
2602 2619 5.718649 TTCTTCTGAAGTTGTCTTTGACG 57.281 39.130 16.43 0.00 34.95 4.35
2608 2625 4.693283 TGAAGTTGTCTTTGACGAGTGAT 58.307 39.130 0.00 0.00 34.95 3.06
2644 2664 7.373617 TGAAGTTGGATTCAGGTGCTATATA 57.626 36.000 0.00 0.00 34.31 0.86
2645 2665 7.217200 TGAAGTTGGATTCAGGTGCTATATAC 58.783 38.462 0.00 0.00 34.31 1.47
2646 2666 7.071196 TGAAGTTGGATTCAGGTGCTATATACT 59.929 37.037 0.00 0.00 34.31 2.12
2647 2667 8.492415 AAGTTGGATTCAGGTGCTATATACTA 57.508 34.615 0.00 0.00 0.00 1.82
2648 2668 7.897864 AGTTGGATTCAGGTGCTATATACTAC 58.102 38.462 0.00 0.00 0.00 2.73
2649 2669 6.510879 TGGATTCAGGTGCTATATACTACG 57.489 41.667 0.00 0.00 0.00 3.51
2650 2670 5.105877 TGGATTCAGGTGCTATATACTACGC 60.106 44.000 0.00 0.00 0.00 4.42
2651 2671 4.778534 TTCAGGTGCTATATACTACGCC 57.221 45.455 0.00 0.00 0.00 5.68
2652 2672 4.030314 TCAGGTGCTATATACTACGCCT 57.970 45.455 0.00 0.00 43.67 5.52
2653 2673 5.169992 TCAGGTGCTATATACTACGCCTA 57.830 43.478 7.22 0.00 40.99 3.93
2654 2674 4.940046 TCAGGTGCTATATACTACGCCTAC 59.060 45.833 7.22 0.00 40.99 3.18
2655 2675 4.698780 CAGGTGCTATATACTACGCCTACA 59.301 45.833 7.22 0.00 40.99 2.74
2694 2715 4.386049 CCAGTTTACATGAGTCTTGTCGAC 59.614 45.833 14.44 9.11 43.17 4.20
2703 2724 3.181494 TGAGTCTTGTCGACACTTTTCGA 60.181 43.478 19.90 0.00 45.62 3.71
2743 2774 0.107831 TTTAGACAACGGGCAGCACT 59.892 50.000 0.00 0.00 0.00 4.40
2795 2826 4.927267 AACAATGGTCCTGTCCTGATAA 57.073 40.909 0.00 0.00 0.00 1.75
2799 2830 3.981071 TGGTCCTGTCCTGATAACTTG 57.019 47.619 0.00 0.00 0.00 3.16
2806 2837 4.020218 CCTGTCCTGATAACTTGAGGTTCA 60.020 45.833 0.00 0.00 39.17 3.18
2879 2916 4.558178 TGCCTCATTGCTACAACATTTTG 58.442 39.130 0.00 0.00 38.83 2.44
2937 2977 8.802267 AGGCTCTATTCTTGATATCTTAGACAC 58.198 37.037 3.98 0.00 0.00 3.67
2940 2981 9.624697 CTCTATTCTTGATATCTTAGACACTGC 57.375 37.037 3.98 0.00 0.00 4.40
2947 2988 0.815734 TCTTAGACACTGCCGCCTAC 59.184 55.000 0.00 0.00 0.00 3.18
3030 3072 3.885901 GGGAAAATATCAGGTGCTTCCTC 59.114 47.826 0.00 0.00 46.24 3.71
3031 3073 4.385754 GGGAAAATATCAGGTGCTTCCTCT 60.386 45.833 0.00 0.00 46.24 3.69
3032 3074 4.578105 GGAAAATATCAGGTGCTTCCTCTG 59.422 45.833 0.00 0.00 46.24 3.35
3033 3075 5.431765 GAAAATATCAGGTGCTTCCTCTGA 58.568 41.667 0.00 0.00 46.24 3.27
3034 3076 5.441718 AAATATCAGGTGCTTCCTCTGAA 57.558 39.130 0.00 0.00 46.24 3.02
3035 3077 5.441718 AATATCAGGTGCTTCCTCTGAAA 57.558 39.130 0.00 0.00 46.24 2.69
3036 3078 3.795688 ATCAGGTGCTTCCTCTGAAAA 57.204 42.857 0.00 0.00 46.24 2.29
3037 3079 2.851195 TCAGGTGCTTCCTCTGAAAAC 58.149 47.619 0.00 0.00 46.24 2.43
3038 3080 2.439507 TCAGGTGCTTCCTCTGAAAACT 59.560 45.455 0.00 0.00 46.24 2.66
3039 3081 2.810852 CAGGTGCTTCCTCTGAAAACTC 59.189 50.000 0.00 0.00 46.24 3.01
3040 3082 2.708325 AGGTGCTTCCTCTGAAAACTCT 59.292 45.455 0.00 0.00 44.42 3.24
3044 3086 4.759183 GTGCTTCCTCTGAAAACTCTGAAT 59.241 41.667 0.00 0.00 0.00 2.57
3059 3101 5.136105 ACTCTGAATTGCCTCTGAAAACTT 58.864 37.500 0.00 0.00 0.00 2.66
3097 3142 2.727123 TGAAAACCTGAACTCCTGCA 57.273 45.000 0.00 0.00 0.00 4.41
3101 3146 4.142182 TGAAAACCTGAACTCCTGCAAAAG 60.142 41.667 0.00 0.00 0.00 2.27
3102 3147 3.297134 AACCTGAACTCCTGCAAAAGA 57.703 42.857 2.18 0.00 0.00 2.52
3109 3155 1.001406 ACTCCTGCAAAAGACGAGAGG 59.999 52.381 2.18 0.00 0.00 3.69
3134 3180 0.179073 GCGATGCTAGGGCTTTCAGA 60.179 55.000 0.00 0.00 39.59 3.27
3162 3208 4.229353 TCTGGGATTCCAACATGGTGAATA 59.771 41.667 13.74 0.00 43.51 1.75
3166 3212 4.202050 GGATTCCAACATGGTGAATAGCAC 60.202 45.833 13.74 0.00 46.98 4.40
3178 3224 0.180406 AATAGCACCCCGATTCGCTT 59.820 50.000 0.00 0.00 35.93 4.68
3200 3248 1.805943 CTGCACATCCATGAACAACGA 59.194 47.619 0.00 0.00 0.00 3.85
3218 3266 0.458716 GACGCCTAGACCAGCTTGTC 60.459 60.000 9.90 9.90 35.43 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.293814 GTCTGTTCAATCAGATCACATCCAG 59.706 44.000 0.00 0.00 44.59 3.86
66 67 3.456644 TGGACGGCCCTGATTTAGATTTA 59.543 43.478 3.83 0.00 35.38 1.40
67 68 2.241176 TGGACGGCCCTGATTTAGATTT 59.759 45.455 3.83 0.00 35.38 2.17
68 69 1.843851 TGGACGGCCCTGATTTAGATT 59.156 47.619 3.83 0.00 35.38 2.40
69 70 1.507140 TGGACGGCCCTGATTTAGAT 58.493 50.000 3.83 0.00 35.38 1.98
70 71 1.416401 GATGGACGGCCCTGATTTAGA 59.584 52.381 3.83 0.00 35.38 2.10
71 72 1.543429 GGATGGACGGCCCTGATTTAG 60.543 57.143 3.83 0.00 35.38 1.85
72 73 0.472471 GGATGGACGGCCCTGATTTA 59.528 55.000 3.83 0.00 35.38 1.40
186 191 4.603535 GGGATGCGGGGATTGGGG 62.604 72.222 0.00 0.00 0.00 4.96
875 880 1.303888 TCGTACCAGGCGGAGAAGT 60.304 57.895 2.43 0.00 35.59 3.01
1536 1544 1.748879 GTAAATGGGCAGCTCGGCA 60.749 57.895 10.86 0.23 43.60 5.69
1656 1664 1.497309 TTCCAAGATTGCCTCCCGGT 61.497 55.000 0.00 0.00 0.00 5.28
1806 1814 0.540365 CCACCTGTGGCTGGAATTGT 60.540 55.000 2.89 0.00 44.73 2.71
1833 1841 0.179200 GAATCGCCGACGCAAATGTT 60.179 50.000 0.00 0.00 39.84 2.71
2133 2141 0.391661 CGTACTTGCAGGCCATGTCT 60.392 55.000 5.01 0.00 34.15 3.41
2172 2180 3.793144 GCGCCGAAGTCAGCCTTG 61.793 66.667 0.00 0.00 32.03 3.61
2214 2222 2.106511 TGCTCAAAGCTTACCCTTGAGT 59.893 45.455 20.70 0.00 42.97 3.41
2255 2269 4.463879 CGGAGGGGTCAGCAGCAG 62.464 72.222 0.00 0.00 0.00 4.24
2257 2271 3.036429 AATCGGAGGGGTCAGCAGC 62.036 63.158 0.00 0.00 0.00 5.25
2258 2272 1.153289 CAATCGGAGGGGTCAGCAG 60.153 63.158 0.00 0.00 0.00 4.24
2259 2273 2.669133 CCAATCGGAGGGGTCAGCA 61.669 63.158 0.00 0.00 0.00 4.41
2260 2274 2.190578 CCAATCGGAGGGGTCAGC 59.809 66.667 0.00 0.00 0.00 4.26
2341 2355 5.163513 CAAGATTTCAAATCAAGGGTTCGG 58.836 41.667 12.74 0.00 0.00 4.30
2427 2444 1.937899 AGAACACAACACGGTACAAGC 59.062 47.619 0.00 0.00 0.00 4.01
2527 2544 2.895404 AGCAGTGAACATTTCCAGCAAT 59.105 40.909 0.00 0.00 0.00 3.56
2573 2590 6.685527 AGACAACTTCAGAAGAAAGAAACC 57.314 37.500 17.56 0.00 32.35 3.27
2602 2619 3.309961 TCAGCTTGTCAGTCATCACTC 57.690 47.619 0.00 0.00 0.00 3.51
2608 2625 2.170397 TCCAACTTCAGCTTGTCAGTCA 59.830 45.455 0.00 0.00 0.00 3.41
2644 2664 1.677942 GAGTAGGCTGTAGGCGTAGT 58.322 55.000 0.00 0.00 44.50 2.73
2645 2665 0.953003 GGAGTAGGCTGTAGGCGTAG 59.047 60.000 0.00 0.00 46.23 3.51
2646 2666 0.816825 CGGAGTAGGCTGTAGGCGTA 60.817 60.000 0.00 0.00 46.23 4.42
2647 2667 2.119655 CGGAGTAGGCTGTAGGCGT 61.120 63.158 0.00 0.00 46.23 5.68
2648 2668 2.722487 CGGAGTAGGCTGTAGGCG 59.278 66.667 0.00 0.00 46.23 5.52
2649 2669 3.130227 CCGGAGTAGGCTGTAGGC 58.870 66.667 0.00 0.00 41.43 3.93
2743 2774 9.878667 ATGAAAACATTATGAATGAATGCAAGA 57.121 25.926 6.21 0.00 41.46 3.02
2760 2791 7.656948 CAGGACCATTGTTTGTAATGAAAACAT 59.343 33.333 2.86 0.00 44.57 2.71
2795 2826 2.612972 CGTGCTGGTATGAACCTCAAGT 60.613 50.000 0.00 0.00 46.91 3.16
2799 2830 1.641577 GTCGTGCTGGTATGAACCTC 58.358 55.000 0.00 0.00 46.91 3.85
2806 2837 0.618458 ATGTTGGGTCGTGCTGGTAT 59.382 50.000 0.00 0.00 0.00 2.73
2905 2942 8.204903 AGATATCAAGAATAGAGCCTCAATGT 57.795 34.615 5.32 0.00 0.00 2.71
2909 2946 9.019656 GTCTAAGATATCAAGAATAGAGCCTCA 57.980 37.037 5.32 0.00 0.00 3.86
2916 2953 7.540400 CGGCAGTGTCTAAGATATCAAGAATAG 59.460 40.741 5.32 0.25 0.00 1.73
2932 2972 0.972983 ATCTGTAGGCGGCAGTGTCT 60.973 55.000 13.08 0.00 35.60 3.41
2937 2977 0.678395 AGATCATCTGTAGGCGGCAG 59.322 55.000 13.08 0.00 35.43 4.85
2968 3009 7.177392 GCCTATCTTGGATAAATAAGGTGCAAT 59.823 37.037 0.00 0.00 0.00 3.56
3030 3072 4.758674 TCAGAGGCAATTCAGAGTTTTCAG 59.241 41.667 0.00 0.00 0.00 3.02
3031 3073 4.717877 TCAGAGGCAATTCAGAGTTTTCA 58.282 39.130 0.00 0.00 0.00 2.69
3032 3074 5.695851 TTCAGAGGCAATTCAGAGTTTTC 57.304 39.130 0.00 0.00 0.00 2.29
3033 3075 6.097412 AGTTTTCAGAGGCAATTCAGAGTTTT 59.903 34.615 0.00 0.00 0.00 2.43
3034 3076 5.595952 AGTTTTCAGAGGCAATTCAGAGTTT 59.404 36.000 0.00 0.00 0.00 2.66
3035 3077 5.136105 AGTTTTCAGAGGCAATTCAGAGTT 58.864 37.500 0.00 0.00 0.00 3.01
3036 3078 4.723309 AGTTTTCAGAGGCAATTCAGAGT 58.277 39.130 0.00 0.00 0.00 3.24
3037 3079 5.702349 AAGTTTTCAGAGGCAATTCAGAG 57.298 39.130 0.00 0.00 0.00 3.35
3038 3080 5.593909 TCAAAGTTTTCAGAGGCAATTCAGA 59.406 36.000 0.00 0.00 0.00 3.27
3039 3081 5.835257 TCAAAGTTTTCAGAGGCAATTCAG 58.165 37.500 0.00 0.00 0.00 3.02
3040 3082 5.850557 TCAAAGTTTTCAGAGGCAATTCA 57.149 34.783 0.00 0.00 0.00 2.57
3044 3086 5.650266 TGTAGTTCAAAGTTTTCAGAGGCAA 59.350 36.000 0.00 0.00 0.00 4.52
3097 3142 1.374758 CGCCAGCCTCTCGTCTTTT 60.375 57.895 0.00 0.00 0.00 2.27
3134 3180 3.424703 CATGTTGGAATCCCAGAAGTGT 58.575 45.455 0.00 0.00 44.60 3.55
3162 3208 2.125106 GAAGCGAATCGGGGTGCT 60.125 61.111 4.35 0.00 39.89 4.40
3166 3212 2.897350 GCAGGAAGCGAATCGGGG 60.897 66.667 4.35 0.00 0.00 5.73
3178 3224 2.161855 GTTGTTCATGGATGTGCAGGA 58.838 47.619 0.00 0.00 0.00 3.86
3200 3248 1.592223 GACAAGCTGGTCTAGGCGT 59.408 57.895 14.42 0.00 34.92 5.68


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

AutoCloner maintained by Alex Coulton.