Multiple sequence alignment - TraesCS4A01G450500

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 TraesCS4A01G450500 chr4A 100.000 2612 0 0 1 2612 715946512 715943901 0.000000e+00 4824.0
1 TraesCS4A01G450500 chr4A 96.452 1973 53 6 1 1959 715557808 715559777 0.000000e+00 3240.0
2 TraesCS4A01G450500 chr4A 80.137 1314 196 27 362 1655 716299732 716301000 0.000000e+00 920.0
3 TraesCS4A01G450500 chr4A 91.681 601 42 7 2012 2609 715559885 715560480 0.000000e+00 826.0
4 TraesCS4A01G450500 chr4A 74.672 533 109 21 902 1412 715954942 715955470 2.040000e-51 213.0
5 TraesCS4A01G450500 chr4A 75.346 361 84 4 1098 1454 715931729 715931370 4.470000e-38 169.0
6 TraesCS4A01G450500 chr7D 76.488 1327 248 39 372 1655 17665371 17664066 0.000000e+00 664.0
7 TraesCS4A01G450500 chr7D 76.368 402 84 9 1017 1411 12070401 12070798 3.410000e-49 206.0
8 TraesCS4A01G450500 chr7D 75.881 369 84 5 1053 1417 49270817 49270450 1.600000e-42 183.0
9 TraesCS4A01G450500 chr7D 72.987 385 86 13 824 1193 12312729 12312348 4.570000e-23 119.0
10 TraesCS4A01G450500 chr7A 76.194 1319 256 34 372 1647 17162517 17161214 0.000000e+00 643.0
11 TraesCS4A01G450500 chr7A 73.247 385 82 17 825 1193 11761901 11761522 1.270000e-23 121.0
12 TraesCS4A01G450500 chr7A 79.605 152 29 2 1303 1454 11869520 11869371 9.880000e-20 108.0
13 TraesCS4A01G450500 chr5A 87.500 88 8 3 265 350 508332895 508332981 5.950000e-17 99.0
14 TraesCS4A01G450500 chr5A 86.250 80 9 2 273 351 508533621 508533543 4.630000e-13 86.1
15 TraesCS4A01G450500 chr5A 82.609 92 14 2 273 363 508557150 508557060 2.150000e-11 80.5


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 TraesCS4A01G450500 chr4A 715943901 715946512 2611 True 4824 4824 100.0000 1 2612 1 chr4A.!!$R2 2611
1 TraesCS4A01G450500 chr4A 715557808 715560480 2672 False 2033 3240 94.0665 1 2609 2 chr4A.!!$F3 2608
2 TraesCS4A01G450500 chr4A 716299732 716301000 1268 False 920 920 80.1370 362 1655 1 chr4A.!!$F2 1293
3 TraesCS4A01G450500 chr4A 715954942 715955470 528 False 213 213 74.6720 902 1412 1 chr4A.!!$F1 510
4 TraesCS4A01G450500 chr7D 17664066 17665371 1305 True 664 664 76.4880 372 1655 1 chr7D.!!$R2 1283
5 TraesCS4A01G450500 chr7A 17161214 17162517 1303 True 643 643 76.1940 372 1647 1 chr7A.!!$R3 1275

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
678 721 0.179156 CAAACTGGGCATCGATGTGC 60.179 55.0 25.47 14.64 44.31 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 2236 0.026285 GCGCATCACGTACATCCAAC 59.974 55.0 0.3 0.0 46.11 3.77 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
19 20 2.813908 GCAACGGCGGGTACTCAG 60.814 66.667 13.24 0.00 0.00 3.35
49 50 3.272581 GTTAAAGTTACTATGGCGGGCA 58.727 45.455 6.74 6.74 0.00 5.36
50 51 2.038387 AAAGTTACTATGGCGGGCAG 57.962 50.000 10.83 0.00 0.00 4.85
84 85 4.092968 CCGCCAGTTCTAACTTGTGAATAC 59.907 45.833 8.58 0.00 37.08 1.89
126 127 1.866925 GCGTAGATAATTGCCCGCC 59.133 57.895 0.00 0.00 35.45 6.13
132 133 1.379710 ATAATTGCCCGCCACTGCA 60.380 52.632 0.00 0.00 37.32 4.41
149 163 3.381136 AACGGCGGGCGTAGGTAA 61.381 61.111 29.80 0.00 0.00 2.85
296 310 6.088616 GCACTGCTACTTTTTGAAATTAGCTG 59.911 38.462 18.78 18.78 39.38 4.24
299 313 7.013274 ACTGCTACTTTTTGAAATTAGCTGTGA 59.987 33.333 22.19 7.12 42.71 3.58
347 361 4.229582 TCATTTGGGTTCACCTATAAGCCT 59.770 41.667 5.73 0.00 43.42 4.58
351 365 5.005628 TGGGTTCACCTATAAGCCTTTTT 57.994 39.130 5.73 0.00 43.42 1.94
425 439 3.134458 AGTCTTCAAAACCTTGCTCTCG 58.866 45.455 0.00 0.00 32.14 4.04
672 715 1.402968 CAAGATCCAAACTGGGCATCG 59.597 52.381 0.00 0.00 38.32 3.84
678 721 0.179156 CAAACTGGGCATCGATGTGC 60.179 55.000 25.47 14.64 44.31 4.57
735 831 7.384439 TCCAAAACGAGCATCAATGTATTTA 57.616 32.000 0.00 0.00 33.17 1.40
795 891 2.958355 AGCATTAACATATGTGGCCACC 59.042 45.455 32.62 15.42 0.00 4.61
1090 1219 1.555075 CTGGTAGTGGCAAGCCTAAGA 59.445 52.381 12.96 0.00 36.94 2.10
1207 1339 2.034879 AATCGGAGCACCAACGCTG 61.035 57.895 0.00 0.00 44.01 5.18
1361 1493 2.415512 GCGAGGTGGACTATGAACAAAC 59.584 50.000 0.00 0.00 0.00 2.93
1413 1545 6.013032 CCATGATCAAGGACTACCAAGGATAT 60.013 42.308 11.68 0.00 38.94 1.63
1694 1826 0.744414 ATGCTGTGTACATCCGGTGC 60.744 55.000 0.00 0.00 0.00 5.01
1729 1861 9.525826 AAATCTGATCCTTTTCACAGAATAAGT 57.474 29.630 0.00 0.00 41.57 2.24
1780 1912 6.379133 ACTCATTTTACTACTCCCGTCATACA 59.621 38.462 0.00 0.00 0.00 2.29
1821 1953 5.721480 TGGTAGGATAGCAGTATACATGCAT 59.279 40.000 21.50 15.16 45.27 3.96
1844 1976 3.560278 CCGCCACGTACATTCGGC 61.560 66.667 2.35 2.35 41.30 5.54
1845 1977 2.508439 CGCCACGTACATTCGGCT 60.508 61.111 10.23 0.00 42.59 5.52
1846 1978 2.798501 CGCCACGTACATTCGGCTG 61.799 63.158 10.23 1.36 42.59 4.85
1847 1979 3.089784 CCACGTACATTCGGCTGC 58.910 61.111 0.00 0.00 34.94 5.25
1848 1980 2.461110 CCACGTACATTCGGCTGCC 61.461 63.158 9.11 9.11 34.94 4.85
1849 1981 1.739929 CACGTACATTCGGCTGCCA 60.740 57.895 20.29 0.00 34.94 4.92
1850 1982 1.740296 ACGTACATTCGGCTGCCAC 60.740 57.895 20.29 7.00 34.94 5.01
1886 2018 1.869774 CTGTAGACAAGCAGCACACA 58.130 50.000 0.00 0.00 0.00 3.72
1887 2019 1.528586 CTGTAGACAAGCAGCACACAC 59.471 52.381 0.00 0.00 0.00 3.82
1911 2043 1.106285 GGATCAGCCCATCAACAACC 58.894 55.000 0.00 0.00 0.00 3.77
1929 2061 1.206578 CAACACGGACGCATCCAAC 59.793 57.895 0.00 0.00 46.67 3.77
1937 2069 2.511600 CGCATCCAACCCCTCGTC 60.512 66.667 0.00 0.00 0.00 4.20
1998 2168 7.148507 TGCAAATTTTCCATATTCGCGAAAAAT 60.149 29.630 27.23 21.05 38.56 1.82
2006 2176 8.786826 TCCATATTCGCGAAAAATATAGGAAT 57.213 30.769 27.23 7.03 31.17 3.01
2008 2178 8.122952 CCATATTCGCGAAAAATATAGGAATCC 58.877 37.037 27.23 0.00 30.13 3.01
2046 2233 5.815233 AGCTTGGTAGTATGCAGATGTAT 57.185 39.130 0.00 0.00 0.00 2.29
2047 2234 6.918067 AGCTTGGTAGTATGCAGATGTATA 57.082 37.500 0.00 0.00 0.00 1.47
2048 2235 6.692486 AGCTTGGTAGTATGCAGATGTATAC 58.308 40.000 11.71 11.71 41.81 1.47
2049 2236 5.573282 GCTTGGTAGTATGCAGATGTATACG 59.427 44.000 13.21 2.64 44.70 3.06
2050 2237 6.644248 TTGGTAGTATGCAGATGTATACGT 57.356 37.500 13.21 0.00 44.70 3.57
2051 2238 6.644248 TGGTAGTATGCAGATGTATACGTT 57.356 37.500 13.21 2.91 44.70 3.99
2052 2239 6.443792 TGGTAGTATGCAGATGTATACGTTG 58.556 40.000 13.21 1.69 44.70 4.10
2053 2240 5.862323 GGTAGTATGCAGATGTATACGTTGG 59.138 44.000 13.21 0.00 44.70 3.77
2054 2241 5.784578 AGTATGCAGATGTATACGTTGGA 57.215 39.130 13.21 2.13 44.70 3.53
2055 2242 6.346477 AGTATGCAGATGTATACGTTGGAT 57.654 37.500 13.21 14.09 44.70 3.41
2056 2243 6.159293 AGTATGCAGATGTATACGTTGGATG 58.841 40.000 13.21 8.97 44.70 3.51
2057 2244 4.400529 TGCAGATGTATACGTTGGATGT 57.599 40.909 0.00 0.00 0.00 3.06
2070 2257 1.081556 TGGATGTACGTGATGCGCAC 61.082 55.000 14.90 7.75 46.11 5.34
2084 2271 1.003851 GCGCACGCCAACTAGAAATA 58.996 50.000 0.30 0.00 34.56 1.40
2096 2283 8.826710 CGCCAACTAGAAATACATAATCAGAAA 58.173 33.333 0.00 0.00 0.00 2.52
2122 2309 3.317711 CCATATCAGCGTCTCTTGTCTCT 59.682 47.826 0.00 0.00 0.00 3.10
2154 2341 0.179121 ATAATTCTGCGACGACGGCA 60.179 50.000 9.67 6.81 40.15 5.69
2164 2351 3.179265 CGACGGCAACCTACAGCG 61.179 66.667 0.00 0.00 0.00 5.18
2175 2362 1.088306 CCTACAGCGTCTCTCGTCTT 58.912 55.000 0.00 0.00 42.13 3.01
2179 2366 3.637998 ACAGCGTCTCTCGTCTTAAAA 57.362 42.857 0.00 0.00 42.13 1.52
2229 2416 3.633525 TGGATGGTTGATAATTCTGCAGC 59.366 43.478 9.47 0.00 0.00 5.25
2240 2427 1.782201 TTCTGCAGCCCCATGTGACT 61.782 55.000 9.47 0.00 0.00 3.41
2242 2429 2.352422 GCAGCCCCATGTGACTGA 59.648 61.111 9.55 0.00 31.67 3.41
2282 2469 6.889198 TCAGCCTATTATATCCAAGCCATAC 58.111 40.000 0.00 0.00 0.00 2.39
2318 2505 6.295011 CCATGACTGTCATCCTCCTACTATTC 60.295 46.154 19.89 0.00 34.28 1.75
2333 2520 7.809665 TCCTACTATTCGTTTTAACTTTTGGC 58.190 34.615 0.00 0.00 0.00 4.52
2357 2544 1.059913 CCTCTTCTCCACACAACCCT 58.940 55.000 0.00 0.00 0.00 4.34
2381 2568 1.754803 CCTTACATACAGCCGACCAGA 59.245 52.381 0.00 0.00 0.00 3.86
2413 2600 1.082038 CTATCTACGGACCGCAGCG 60.082 63.158 15.39 8.18 0.00 5.18
2437 2624 4.025401 GTTCCCGCGTGTGGCTTG 62.025 66.667 4.92 0.00 40.44 4.01
2441 2628 4.688419 CCGCGTGTGGCTTGCAAG 62.688 66.667 22.44 22.44 40.44 4.01
2464 2651 3.453353 CCCACCCTTCTAAACCTTATCGA 59.547 47.826 0.00 0.00 0.00 3.59
2475 2662 7.391620 TCTAAACCTTATCGACCACAAGATTT 58.608 34.615 0.00 0.00 0.00 2.17
2479 2666 5.875359 ACCTTATCGACCACAAGATTTTCTC 59.125 40.000 0.00 0.00 0.00 2.87
2488 2675 1.740025 CAAGATTTTCTCGGTGAGCCC 59.260 52.381 0.00 0.00 0.00 5.19
2503 2690 4.143333 CCCGCGTCCTACCACCTG 62.143 72.222 4.92 0.00 0.00 4.00
2540 2727 3.367395 GGCCCAAGAATTTAAGACTGTGC 60.367 47.826 0.00 0.00 0.00 4.57
2603 2792 7.101652 TCTTTTTGGCGCATATAACCAATTA 57.898 32.000 10.83 0.00 42.77 1.40
2609 2798 5.353956 TGGCGCATATAACCAATTATAGCAG 59.646 40.000 10.83 0.00 36.83 4.24
2610 2799 5.266242 GCGCATATAACCAATTATAGCAGC 58.734 41.667 0.30 0.00 36.83 5.25
2611 2800 5.163764 GCGCATATAACCAATTATAGCAGCA 60.164 40.000 0.30 0.00 36.83 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.161943 AGTAACTTTAACCCTACTGGCTG 57.838 43.478 0.00 0.00 37.83 4.85
19 20 6.053650 CCATAGTAACTTTAACCCTACTGGC 58.946 44.000 0.00 0.00 37.83 4.85
49 50 3.612247 CTGGCGGGTGCTAAGTGCT 62.612 63.158 0.00 0.00 43.37 4.40
50 51 3.127533 CTGGCGGGTGCTAAGTGC 61.128 66.667 0.00 0.00 42.25 4.40
84 85 7.478322 GCCAGCCACAAGATCATATATTTATG 58.522 38.462 0.00 0.00 37.19 1.90
149 163 4.307032 AAAGTGATTAGTGGCAGGTCAT 57.693 40.909 0.00 0.00 0.00 3.06
319 333 2.863809 AGGTGAACCCAAATGAGTGAC 58.136 47.619 0.00 0.00 36.42 3.67
351 365 4.431416 TTTCCTTTAGTGCACTCCTGAA 57.569 40.909 25.56 18.08 0.00 3.02
352 366 4.431416 TTTTCCTTTAGTGCACTCCTGA 57.569 40.909 25.56 13.08 0.00 3.86
356 370 6.420903 GGAACAATTTTTCCTTTAGTGCACTC 59.579 38.462 25.56 2.19 41.80 3.51
425 439 4.113354 CCCGTGTTGCTACTCTTCTATTC 58.887 47.826 0.00 0.00 0.00 1.75
497 519 0.181114 TGATGTGCCCTAGACATGCC 59.819 55.000 0.54 0.00 34.10 4.40
672 715 7.019774 TGCTCTTTATATTCACAAGCACATC 57.980 36.000 0.00 0.00 33.67 3.06
735 831 6.014647 TGGTATTAGTGCCCTCTATATTCGT 58.985 40.000 0.00 0.00 0.00 3.85
795 891 9.864034 GATACAAGTATGGTTTATGTCAAATCG 57.136 33.333 0.00 0.00 0.00 3.34
1361 1493 0.249447 TATGTTGAGGATGCTCGCCG 60.249 55.000 9.88 0.00 0.00 6.46
1413 1545 2.792947 GGACCGCATCTCGCCCTTA 61.793 63.158 0.00 0.00 37.30 2.69
1660 1792 9.394767 TGTACACAGCATCTCAAACATAATAAT 57.605 29.630 0.00 0.00 0.00 1.28
1792 1924 5.472478 TGTATACTGCTATCCTACCAAGACG 59.528 44.000 4.17 0.00 0.00 4.18
1815 1947 1.429021 GTGGCGGTGTGTATGCATG 59.571 57.895 10.16 0.00 0.00 4.06
1821 1953 0.317799 AATGTACGTGGCGGTGTGTA 59.682 50.000 0.00 0.00 0.00 2.90
1856 1988 2.688666 TCTACAGCCTGCAGGGGG 60.689 66.667 33.46 10.79 35.18 5.40
1886 2018 1.040893 TGATGGGCTGATCCGTACGT 61.041 55.000 15.21 0.00 34.94 3.57
1887 2019 0.104120 TTGATGGGCTGATCCGTACG 59.896 55.000 8.69 8.69 34.94 3.67
1929 2061 2.158740 TGAGACTATGAGAGACGAGGGG 60.159 54.545 0.00 0.00 0.00 4.79
1937 2069 8.620116 TTGATAGACAGATGAGACTATGAGAG 57.380 38.462 0.00 0.00 0.00 3.20
1969 2139 5.912396 TCGCGAATATGGAAAATTTGCATAC 59.088 36.000 19.52 9.21 44.89 2.39
1972 2142 4.362932 TCGCGAATATGGAAAATTTGCA 57.637 36.364 6.20 1.73 41.79 4.08
1982 2152 8.122952 GGATTCCTATATTTTTCGCGAATATGG 58.877 37.037 24.05 17.91 33.16 2.74
1987 2157 5.617252 AGGGATTCCTATATTTTTCGCGAA 58.383 37.500 19.38 19.38 42.75 4.70
1998 2168 5.548056 GGGAAGATGTGAAGGGATTCCTATA 59.452 44.000 0.00 0.00 44.07 1.31
2000 2170 3.716872 GGGAAGATGTGAAGGGATTCCTA 59.283 47.826 0.00 0.00 44.07 2.94
2006 2176 2.119495 GCTAGGGAAGATGTGAAGGGA 58.881 52.381 0.00 0.00 0.00 4.20
2008 2178 3.539604 CAAGCTAGGGAAGATGTGAAGG 58.460 50.000 0.00 0.00 0.00 3.46
2048 2235 0.297525 CGCATCACGTACATCCAACG 59.702 55.000 0.00 0.00 45.64 4.10
2049 2236 0.026285 GCGCATCACGTACATCCAAC 59.974 55.000 0.30 0.00 46.11 3.77
2050 2237 0.390472 TGCGCATCACGTACATCCAA 60.390 50.000 5.66 0.00 46.11 3.53
2051 2238 1.216710 TGCGCATCACGTACATCCA 59.783 52.632 5.66 0.00 46.11 3.41
2052 2239 4.102561 TGCGCATCACGTACATCC 57.897 55.556 5.66 0.00 46.11 3.51
2070 2257 7.946655 TCTGATTATGTATTTCTAGTTGGCG 57.053 36.000 0.00 0.00 0.00 5.69
2096 2283 4.579869 ACAAGAGACGCTGATATGGTTTT 58.420 39.130 0.00 0.00 0.00 2.43
2097 2284 4.081420 AGACAAGAGACGCTGATATGGTTT 60.081 41.667 0.00 0.00 0.00 3.27
2122 2309 6.128391 GTCGCAGAATTATGGAACAGTTGTAA 60.128 38.462 1.67 0.00 40.69 2.41
2154 2341 0.803740 GACGAGAGACGCTGTAGGTT 59.196 55.000 0.00 0.00 46.94 3.50
2282 2469 2.019249 ACAGTCATGGGATTCGCATTG 58.981 47.619 13.07 11.67 34.83 2.82
2318 2505 2.048498 GAGGCGCCAAAAGTTAAAACG 58.952 47.619 31.54 0.00 0.00 3.60
2333 2520 1.216710 GTGTGGAGAAGAGGAGGCG 59.783 63.158 0.00 0.00 0.00 5.52
2357 2544 2.431782 GGTCGGCTGTATGTAAGGGTTA 59.568 50.000 0.00 0.00 0.00 2.85
2393 2580 1.082038 CTGCGGTCCGTAGATAGCG 60.082 63.158 23.49 0.00 41.80 4.26
2419 2606 4.555709 AAGCCACACGCGGGAACA 62.556 61.111 19.19 0.00 44.76 3.18
2437 2624 0.888619 GTTTAGAAGGGTGGGCTTGC 59.111 55.000 0.00 0.00 0.00 4.01
2438 2625 1.075536 AGGTTTAGAAGGGTGGGCTTG 59.924 52.381 0.00 0.00 0.00 4.01
2439 2626 1.456919 AGGTTTAGAAGGGTGGGCTT 58.543 50.000 0.00 0.00 0.00 4.35
2441 2628 3.552875 GATAAGGTTTAGAAGGGTGGGC 58.447 50.000 0.00 0.00 0.00 5.36
2445 2632 4.081254 GTGGTCGATAAGGTTTAGAAGGGT 60.081 45.833 0.00 0.00 0.00 4.34
2464 2651 3.403038 CTCACCGAGAAAATCTTGTGGT 58.597 45.455 9.60 3.74 33.26 4.16
2488 2675 1.445582 GTTCAGGTGGTAGGACGCG 60.446 63.158 3.53 3.53 0.00 6.01
2490 2677 0.246635 CTGGTTCAGGTGGTAGGACG 59.753 60.000 0.00 0.00 0.00 4.79
2491 2678 0.036294 GCTGGTTCAGGTGGTAGGAC 60.036 60.000 0.00 0.00 31.21 3.85
2494 2681 0.036010 CCTGCTGGTTCAGGTGGTAG 60.036 60.000 0.51 0.00 46.59 3.18
2513 2700 0.892063 TTAAATTCTTGGGCCCGCAC 59.108 50.000 19.37 0.00 0.00 5.34
2514 2701 1.181786 CTTAAATTCTTGGGCCCGCA 58.818 50.000 19.37 5.08 0.00 5.69
2524 2711 9.415544 GAATTTGAATGCACAGTCTTAAATTCT 57.584 29.630 19.03 1.39 36.27 2.40
2565 2752 3.696548 CCAAAAAGAAGACCATAGGCTCC 59.303 47.826 0.00 0.00 0.00 4.70
2566 2753 3.129462 GCCAAAAAGAAGACCATAGGCTC 59.871 47.826 0.00 0.00 36.72 4.70
2576 2765 4.702612 TGGTTATATGCGCCAAAAAGAAGA 59.297 37.500 4.18 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.