Multiple sequence alignment - TraesCS2B01G468800

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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 TraesCS2B01G468800 chr2B 100.000 2790 0 0 1 2790 664414913 664412124 0.000000e+00 5153.0
1 TraesCS2B01G468800 chr2B 93.333 150 10 0 1097 1246 196347306 196347455 3.620000e-54 222.0
2 TraesCS2B01G468800 chr2B 97.674 43 1 0 1115 1157 682194268 682194226 1.070000e-09 75.0
3 TraesCS2B01G468800 chr2B 95.556 45 2 0 1096 1140 682194736 682194692 3.850000e-09 73.1
4 TraesCS2B01G468800 chr2D 88.626 2110 120 54 730 2788 557173788 557171748 0.000000e+00 2457.0
5 TraesCS2B01G468800 chr2A 89.474 1140 53 21 791 1906 697094863 697093767 0.000000e+00 1378.0
6 TraesCS2B01G468800 chr2A 91.036 357 20 4 1961 2310 697093753 697093402 3.250000e-129 472.0
7 TraesCS2B01G468800 chr2A 85.539 408 21 8 2396 2788 697093370 697092986 2.610000e-105 392.0
8 TraesCS2B01G468800 chr6B 95.304 724 31 1 1 724 210779794 210780514 0.000000e+00 1146.0
9 TraesCS2B01G468800 chr5D 91.783 718 53 6 7 723 480156426 480155714 0.000000e+00 994.0
10 TraesCS2B01G468800 chr3B 91.168 736 57 2 1 736 169264329 169265056 0.000000e+00 992.0
11 TraesCS2B01G468800 chr3A 91.713 724 45 4 1 724 41224222 41223514 0.000000e+00 990.0
12 TraesCS2B01G468800 chr1A 91.540 721 51 4 1 721 477119881 477120591 0.000000e+00 985.0
13 TraesCS2B01G468800 chr3D 92.640 625 45 1 7 630 66901939 66901315 0.000000e+00 898.0
14 TraesCS2B01G468800 chr3D 94.792 96 4 1 628 723 66900935 66900841 6.230000e-32 148.0
15 TraesCS2B01G468800 chr5B 92.623 610 45 0 115 724 231735395 231734786 0.000000e+00 878.0
16 TraesCS2B01G468800 chr4B 94.483 145 8 0 1377 1521 216840015 216840159 1.010000e-54 224.0


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 TraesCS2B01G468800 chr2B 664412124 664414913 2789 True 5153.000000 5153 100.000 1 2790 1 chr2B.!!$R1 2789
1 TraesCS2B01G468800 chr2D 557171748 557173788 2040 True 2457.000000 2457 88.626 730 2788 1 chr2D.!!$R1 2058
2 TraesCS2B01G468800 chr2A 697092986 697094863 1877 True 747.333333 1378 88.683 791 2788 3 chr2A.!!$R1 1997
3 TraesCS2B01G468800 chr6B 210779794 210780514 720 False 1146.000000 1146 95.304 1 724 1 chr6B.!!$F1 723
4 TraesCS2B01G468800 chr5D 480155714 480156426 712 True 994.000000 994 91.783 7 723 1 chr5D.!!$R1 716
5 TraesCS2B01G468800 chr3B 169264329 169265056 727 False 992.000000 992 91.168 1 736 1 chr3B.!!$F1 735
6 TraesCS2B01G468800 chr3A 41223514 41224222 708 True 990.000000 990 91.713 1 724 1 chr3A.!!$R1 723
7 TraesCS2B01G468800 chr1A 477119881 477120591 710 False 985.000000 985 91.540 1 721 1 chr1A.!!$F1 720
8 TraesCS2B01G468800 chr3D 66900841 66901939 1098 True 523.000000 898 93.716 7 723 2 chr3D.!!$R1 716
9 TraesCS2B01G468800 chr5B 231734786 231735395 609 True 878.000000 878 92.623 115 724 1 chr5B.!!$R1 609

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
586 598 0.108138 ATCAAGTAGCGCACACCCTC 60.108 55.0 11.47 0.0 0.00 4.30 F
817 1216 1.619654 TGGTTGTTGGCAAGATGGAG 58.380 50.0 0.00 0.0 34.94 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1417 1839 0.322456 CAACTCCATTCCCTTGCCGA 60.322 55.0 0.00 0.0 0.0 5.54 R
1926 2371 0.385723 CCCGCGCGTATCTCTTCTAC 60.386 60.0 29.95 0.0 0.0 2.59 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
184 188 1.202533 ACGAATTATGGGCTGACTCCG 60.203 52.381 0.00 0.00 0.00 4.63
355 367 0.613260 TGCTGAACCCGCTACATTCT 59.387 50.000 0.00 0.00 0.00 2.40
415 427 0.779997 ACTTGGGAATGGGCAGAGTT 59.220 50.000 0.00 0.00 0.00 3.01
509 521 5.448904 GGTGTTGTAGCTGACCGTTTAAAAA 60.449 40.000 0.00 0.00 0.00 1.94
586 598 0.108138 ATCAAGTAGCGCACACCCTC 60.108 55.000 11.47 0.00 0.00 4.30
756 1150 6.819146 TCACCATTTTACATAGCACGACAATA 59.181 34.615 0.00 0.00 0.00 1.90
796 1195 1.947678 GCATCATCTTATCCCCCTGCG 60.948 57.143 0.00 0.00 0.00 5.18
817 1216 1.619654 TGGTTGTTGGCAAGATGGAG 58.380 50.000 0.00 0.00 34.94 3.86
824 1223 2.821969 GTTGGCAAGATGGAGAACACAT 59.178 45.455 0.00 0.00 0.00 3.21
902 1305 4.658786 AGGAAGTCCGTGGGCCCT 62.659 66.667 25.70 0.00 42.08 5.19
1001 1408 4.410400 CCGCAACTCCCTCCACCC 62.410 72.222 0.00 0.00 0.00 4.61
1003 1410 4.048470 GCAACTCCCTCCACCCCC 62.048 72.222 0.00 0.00 0.00 5.40
1060 1478 4.996434 CGGGATCCATCGCAGCCC 62.996 72.222 15.23 0.00 39.45 5.19
1412 1834 4.083862 GCCTCGTTCCGGAAGCCT 62.084 66.667 19.50 0.00 0.00 4.58
1800 2237 7.161404 AGTTGTGAATAGAATGTGTTAGCTGA 58.839 34.615 0.00 0.00 0.00 4.26
1802 2239 7.776933 TGTGAATAGAATGTGTTAGCTGATC 57.223 36.000 0.00 0.00 0.00 2.92
1815 2254 1.146566 AGCTGATCCCAATCCCATTCC 59.853 52.381 0.00 0.00 0.00 3.01
1816 2255 1.824842 GCTGATCCCAATCCCATTCCC 60.825 57.143 0.00 0.00 0.00 3.97
1872 2317 1.202879 TCTTTCTGGTTCGGCAATGGT 60.203 47.619 0.00 0.00 0.00 3.55
1878 2323 1.714899 GGTTCGGCAATGGTGATCGG 61.715 60.000 0.00 0.00 0.00 4.18
1885 2330 1.062587 GCAATGGTGATCGGTTTCTCG 59.937 52.381 0.00 0.00 0.00 4.04
1911 2356 2.661504 TTGTGCGACGTTTCAATCTG 57.338 45.000 0.00 0.00 0.00 2.90
1919 2364 4.755388 CGACGTTTCAATCTGCATAGATG 58.245 43.478 0.00 0.00 42.80 2.90
1924 2369 6.425114 ACGTTTCAATCTGCATAGATGTATCC 59.575 38.462 0.00 0.00 42.80 2.59
1926 2371 7.359849 CGTTTCAATCTGCATAGATGTATCCTG 60.360 40.741 0.00 0.00 42.80 3.86
1927 2372 6.676990 TCAATCTGCATAGATGTATCCTGT 57.323 37.500 0.00 0.00 42.80 4.00
1928 2373 7.781324 TCAATCTGCATAGATGTATCCTGTA 57.219 36.000 0.00 0.00 42.80 2.74
1929 2374 7.834803 TCAATCTGCATAGATGTATCCTGTAG 58.165 38.462 0.00 0.00 42.80 2.74
1930 2375 7.671398 TCAATCTGCATAGATGTATCCTGTAGA 59.329 37.037 12.03 12.03 42.80 2.59
1931 2376 8.309656 CAATCTGCATAGATGTATCCTGTAGAA 58.690 37.037 13.01 3.13 42.80 2.10
1932 2377 7.459795 TCTGCATAGATGTATCCTGTAGAAG 57.540 40.000 9.04 0.00 32.73 2.85
1933 2378 7.234355 TCTGCATAGATGTATCCTGTAGAAGA 58.766 38.462 9.04 0.00 32.73 2.87
1934 2379 7.392953 TCTGCATAGATGTATCCTGTAGAAGAG 59.607 40.741 9.04 0.00 32.73 2.85
1935 2380 7.234355 TGCATAGATGTATCCTGTAGAAGAGA 58.766 38.462 0.00 0.00 0.00 3.10
1940 2402 5.943706 TGTATCCTGTAGAAGAGATACGC 57.056 43.478 0.00 0.00 39.49 4.42
1941 2403 4.451435 TGTATCCTGTAGAAGAGATACGCG 59.549 45.833 3.53 3.53 39.49 6.01
1943 2405 1.660614 CCTGTAGAAGAGATACGCGCG 60.661 57.143 30.96 30.96 0.00 6.86
2121 2599 4.367023 CGCTTGGGACGGGTCGAA 62.367 66.667 0.00 0.00 0.00 3.71
2146 2624 4.794241 GCCGAATGTGCGTGCGTC 62.794 66.667 0.00 0.00 0.00 5.19
2324 2804 1.148157 CGGTGCACGGTGATCTGATC 61.148 60.000 13.29 10.72 39.42 2.92
2330 2810 1.408340 CACGGTGATCTGATCTCTGCT 59.592 52.381 22.11 11.08 33.58 4.24
2331 2811 1.408340 ACGGTGATCTGATCTCTGCTG 59.592 52.381 22.11 14.74 33.58 4.41
2332 2812 1.269673 CGGTGATCTGATCTCTGCTGG 60.270 57.143 17.82 1.58 0.00 4.85
2333 2813 1.540797 GGTGATCTGATCTCTGCTGGC 60.541 57.143 17.82 0.00 0.00 4.85
2334 2814 0.388294 TGATCTGATCTCTGCTGGCG 59.612 55.000 17.82 0.00 0.00 5.69
2339 2819 3.670637 GATCTCTGCTGGCGTGGCA 62.671 63.158 0.00 0.00 38.10 4.92
2374 2854 0.437678 TCGAAGACGACGAAGAGACG 59.562 55.000 0.00 0.00 43.81 4.18
2379 2859 4.044024 CGACGAAGAGACGTGAGC 57.956 61.111 0.00 0.00 46.52 4.26
2380 2860 1.206831 CGACGAAGAGACGTGAGCA 59.793 57.895 0.00 0.00 46.52 4.26
2381 2861 0.791238 CGACGAAGAGACGTGAGCAG 60.791 60.000 0.00 0.00 46.52 4.24
2382 2862 1.068287 GACGAAGAGACGTGAGCAGC 61.068 60.000 0.00 0.00 46.52 5.25
2383 2863 2.148982 CGAAGAGACGTGAGCAGCG 61.149 63.158 0.00 0.00 0.00 5.18
2384 2864 2.431601 AAGAGACGTGAGCAGCGC 60.432 61.111 0.00 0.00 0.00 5.92
2421 2901 1.794151 TTCGACCGCTTCCGTGTGTA 61.794 55.000 0.00 0.00 0.00 2.90
2424 2904 1.693083 GACCGCTTCCGTGTGTATGC 61.693 60.000 0.00 0.00 0.00 3.14
2427 2907 2.100631 GCTTCCGTGTGTATGCGCT 61.101 57.895 9.73 0.00 0.00 5.92
2579 3067 4.700365 CACGTCGTGAGCAGGCGA 62.700 66.667 20.75 0.00 35.23 5.54
2580 3068 4.406173 ACGTCGTGAGCAGGCGAG 62.406 66.667 0.00 0.00 37.82 5.03
2604 3092 0.886938 CACCCCACACGCATGTACAA 60.887 55.000 0.00 0.00 36.72 2.41
2606 3094 1.173043 CCCCACACGCATGTACAATT 58.827 50.000 0.00 0.00 36.72 2.32
2662 3150 2.098934 TCAGCGTGTGAAAACAAGCAAT 59.901 40.909 16.86 0.00 45.20 3.56
2682 3170 4.819761 TGCTGCATCGGTCGAGCC 62.820 66.667 9.39 1.35 0.00 4.70
2767 3267 1.450312 CTGAATGCGTCCCCTGTCC 60.450 63.158 0.00 0.00 0.00 4.02
2788 3288 1.015085 AATTGGCGCGCGTACAGTAA 61.015 50.000 32.35 15.76 0.00 2.24
2789 3289 1.418342 ATTGGCGCGCGTACAGTAAG 61.418 55.000 32.35 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 156 4.196193 CCATAATTCGTTGGTTCCAGCTA 58.804 43.478 4.37 0.00 0.00 3.32
184 188 1.820906 TGGATTCCATCGCTGCTGC 60.821 57.895 0.00 5.34 0.00 5.25
237 241 3.181500 GCAGTCGTTTGGTTTGAAAGAGT 60.181 43.478 0.00 0.00 0.00 3.24
389 401 0.324943 CCCATTCCCAAGTCTGACGT 59.675 55.000 1.52 0.00 0.00 4.34
415 427 3.254166 GCAGAGCATCAGTTTCCAAGAAA 59.746 43.478 0.00 0.00 37.82 2.52
511 523 9.051027 CACTCAATAAAATTACACACGATGAAC 57.949 33.333 0.00 0.00 0.00 3.18
746 1140 3.059570 GCTATATGCTCGTATTGTCGTGC 59.940 47.826 6.26 6.26 46.00 5.34
756 1150 0.039074 GCTGGACGCTATATGCTCGT 60.039 55.000 0.00 0.00 40.11 4.18
796 1195 2.165030 CTCCATCTTGCCAACAACCATC 59.835 50.000 0.00 0.00 0.00 3.51
817 1216 1.662026 GCACCGGTTTTCGATGTGTTC 60.662 52.381 2.97 0.00 42.43 3.18
887 1290 4.410400 CCAGGGCCCACGGACTTC 62.410 72.222 27.56 0.00 0.00 3.01
911 1318 3.546714 CTTATAAGCGGGGCCGGGG 62.547 68.421 13.45 0.00 40.19 5.73
912 1319 2.032071 CTTATAAGCGGGGCCGGG 59.968 66.667 13.45 0.54 40.19 5.73
913 1320 1.004918 CTCTTATAAGCGGGGCCGG 60.005 63.158 7.67 6.75 40.19 6.13
914 1321 0.038159 CTCTCTTATAAGCGGGGCCG 60.038 60.000 7.67 0.00 43.09 6.13
915 1322 1.001068 GTCTCTCTTATAAGCGGGGCC 59.999 57.143 7.67 0.00 0.00 5.80
916 1323 1.336056 CGTCTCTCTTATAAGCGGGGC 60.336 57.143 7.67 1.99 0.00 5.80
1091 1513 2.819595 ATGTGTGCGCCGATGGAC 60.820 61.111 4.18 0.00 0.00 4.02
1092 1514 2.819154 CATGTGTGCGCCGATGGA 60.819 61.111 4.18 0.00 0.00 3.41
1094 1516 3.879682 CCCATGTGTGCGCCGATG 61.880 66.667 4.18 1.27 0.00 3.84
1417 1839 0.322456 CAACTCCATTCCCTTGCCGA 60.322 55.000 0.00 0.00 0.00 5.54
1427 1849 0.539051 CCTCGCTCTCCAACTCCATT 59.461 55.000 0.00 0.00 0.00 3.16
1667 2100 1.403679 CACAACAGGCACGGAAAGAAA 59.596 47.619 0.00 0.00 0.00 2.52
1782 2219 6.252599 TGGGATCAGCTAACACATTCTATT 57.747 37.500 0.00 0.00 0.00 1.73
1800 2237 2.264709 GGGGGAATGGGATTGGGAT 58.735 57.895 0.00 0.00 0.00 3.85
1815 2254 1.754234 CATTTCCAAGGCTCGGGGG 60.754 63.158 5.44 0.00 0.00 5.40
1816 2255 1.754234 CCATTTCCAAGGCTCGGGG 60.754 63.158 5.44 0.00 0.00 5.73
1820 2259 1.186200 GAACCCCATTTCCAAGGCTC 58.814 55.000 0.00 0.00 0.00 4.70
1878 2323 3.840763 GTCGCACAAATCAATCGAGAAAC 59.159 43.478 0.00 0.00 0.00 2.78
1885 2330 3.550561 TGAAACGTCGCACAAATCAATC 58.449 40.909 0.00 0.00 0.00 2.67
1887 2332 3.406728 TTGAAACGTCGCACAAATCAA 57.593 38.095 0.00 0.00 0.00 2.57
1892 2337 1.333702 GCAGATTGAAACGTCGCACAA 60.334 47.619 0.00 0.00 0.00 3.33
1911 2356 7.695480 TCTCTTCTACAGGATACATCTATGC 57.305 40.000 0.00 0.00 41.41 3.14
1919 2364 4.669708 GCGCGTATCTCTTCTACAGGATAC 60.670 50.000 8.43 0.00 37.93 2.24
1924 2369 1.660614 CCGCGCGTATCTCTTCTACAG 60.661 57.143 29.95 3.54 0.00 2.74
1926 2371 0.385723 CCCGCGCGTATCTCTTCTAC 60.386 60.000 29.95 0.00 0.00 2.59
1927 2372 1.947013 CCCGCGCGTATCTCTTCTA 59.053 57.895 29.95 0.00 0.00 2.10
1928 2373 2.722487 CCCGCGCGTATCTCTTCT 59.278 61.111 29.95 0.00 0.00 2.85
1929 2374 3.030882 GCCCGCGCGTATCTCTTC 61.031 66.667 29.95 4.16 0.00 2.87
1959 2431 4.814294 GTGACGCCGGCTACAGGG 62.814 72.222 26.68 10.34 0.00 4.45
1993 2465 1.898574 CTGTTGGCAAAGGACGGCT 60.899 57.895 0.00 0.00 0.00 5.52
2127 2605 4.799473 CGCACGCACATTCGGCTG 62.799 66.667 0.00 0.00 0.00 4.85
2146 2624 4.129737 ACGTCTCCATCGCCACGG 62.130 66.667 0.00 0.00 36.56 4.94
2307 2785 1.135915 AGAGATCAGATCACCGTGCAC 59.864 52.381 13.14 6.82 0.00 4.57
2308 2786 1.135721 CAGAGATCAGATCACCGTGCA 59.864 52.381 13.14 0.00 0.00 4.57
2309 2787 1.850377 CAGAGATCAGATCACCGTGC 58.150 55.000 13.14 0.00 0.00 5.34
2310 2788 1.408340 AGCAGAGATCAGATCACCGTG 59.592 52.381 13.14 3.37 0.00 4.94
2311 2789 1.408340 CAGCAGAGATCAGATCACCGT 59.592 52.381 13.14 0.00 0.00 4.83
2312 2790 1.269673 CCAGCAGAGATCAGATCACCG 60.270 57.143 13.14 0.00 0.00 4.94
2313 2791 1.540797 GCCAGCAGAGATCAGATCACC 60.541 57.143 13.14 4.17 0.00 4.02
2330 2810 4.735132 GACGCTACTGCCACGCCA 62.735 66.667 0.00 0.00 35.36 5.69
2332 2812 2.657484 TATCGACGCTACTGCCACGC 62.657 60.000 0.00 0.00 35.45 5.34
2333 2813 0.928908 GTATCGACGCTACTGCCACG 60.929 60.000 1.71 0.00 36.27 4.94
2334 2814 0.928908 CGTATCGACGCTACTGCCAC 60.929 60.000 7.22 0.00 43.21 5.01
2362 2842 0.791238 CTGCTCACGTCTCTTCGTCG 60.791 60.000 0.00 0.00 42.27 5.12
2363 2843 1.068287 GCTGCTCACGTCTCTTCGTC 61.068 60.000 0.00 0.00 42.27 4.20
2364 2844 1.081108 GCTGCTCACGTCTCTTCGT 60.081 57.895 0.00 0.00 45.10 3.85
2365 2845 2.148982 CGCTGCTCACGTCTCTTCG 61.149 63.158 0.00 0.00 0.00 3.79
2366 2846 2.440569 GCGCTGCTCACGTCTCTTC 61.441 63.158 0.00 0.00 0.00 2.87
2367 2847 2.431601 GCGCTGCTCACGTCTCTT 60.432 61.111 0.00 0.00 0.00 2.85
2368 2848 4.767841 CGCGCTGCTCACGTCTCT 62.768 66.667 5.56 0.00 0.00 3.10
2385 2865 2.862347 GAAACAGAGCAGCCGCATGC 62.862 60.000 7.91 7.91 46.88 4.06
2537 3025 3.576356 CGGCCATCACCATGCGTC 61.576 66.667 2.24 0.00 0.00 5.19
2545 3033 2.585247 GGTACGAGCGGCCATCAC 60.585 66.667 2.24 0.00 0.00 3.06
2556 3044 2.178892 CTGCTCACGACGTGGTACGA 62.179 60.000 26.55 7.13 46.05 3.43
2604 3092 0.882927 AACACCGTGTAGCGTGCAAT 60.883 50.000 4.17 0.00 39.32 3.56
2606 3094 1.952133 GAACACCGTGTAGCGTGCA 60.952 57.895 4.17 0.00 39.32 4.57
2662 3150 3.068064 TCGACCGATGCAGCAGGA 61.068 61.111 17.52 0.00 0.00 3.86
2682 3170 2.171701 CACACGCACGCACAGATG 59.828 61.111 0.00 0.00 0.00 2.90
2767 3267 1.863012 CTGTACGCGCGCCAATTTG 60.863 57.895 32.58 13.10 0.00 2.32


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

AutoCloner maintained by Alex Coulton.