Multiple sequence alignment - TraesCS4B01G261200

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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 TraesCS4B01G261200 chr4B 100.000 3164 0 0 1 3164 529852654 529849491 0.000000e+00 5843
1 TraesCS4B01G261200 chr4A 92.252 2878 108 54 210 3013 32678232 32675396 0.000000e+00 3973
2 TraesCS4B01G261200 chr4A 92.537 134 7 1 3031 3164 32675409 32675279 4.170000e-44 189
3 TraesCS4B01G261200 chr4A 86.000 150 11 4 1 141 32678558 32678410 5.470000e-33 152
4 TraesCS4B01G261200 chr4D 92.745 2812 102 43 1 2776 431418560 431415815 0.000000e+00 3969
5 TraesCS4B01G261200 chr4D 84.302 344 35 4 2821 3164 431415814 431415490 5.090000e-83 318


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 TraesCS4B01G261200 chr4B 529849491 529852654 3163 True 5843.0 5843 100.0000 1 3164 1 chr4B.!!$R1 3163
1 TraesCS4B01G261200 chr4A 32675279 32678558 3279 True 1438.0 3973 90.2630 1 3164 3 chr4A.!!$R1 3163
2 TraesCS4B01G261200 chr4D 431415490 431418560 3070 True 2143.5 3969 88.5235 1 3164 2 chr4D.!!$R1 3163

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
330 464 0.535780 CCTTTCTGCTGCTGTGGTGA 60.536 55.000 0.00 0.00 0.00 4.02 F
333 467 0.607217 TTCTGCTGCTGTGGTGATGG 60.607 55.000 0.00 0.00 0.00 3.51 F
937 1130 1.134521 TGATTCCTCGAAATCCGGTGG 60.135 52.381 0.00 0.00 39.14 4.61 F
1983 2176 0.969149 TCAGCTCAATGGTCGACTGT 59.031 50.000 16.46 1.11 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 2114 0.478072 AGCACCCTGATGTTGTCCAA 59.522 50.000 0.0 0.0 0.00 3.53 R
1975 2168 1.276145 GCGAAGTCCACACAGTCGAC 61.276 60.000 7.7 7.7 35.41 4.20 R
2018 2211 1.687297 GATCTCCTCCACCCCGAACC 61.687 65.000 0.0 0.0 0.00 3.62 R
3027 3241 2.159324 TGTGCGAACATCACAAAAAGCA 60.159 40.909 0.0 0.0 41.01 3.91 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
45 46 1.136336 GCATTTCGTCGACAAGTGGAC 60.136 52.381 17.16 5.42 35.38 4.02
50 61 2.070861 GTCGACAAGTGGACGATGC 58.929 57.895 11.55 0.00 38.27 3.91
58 69 2.280457 TGGACGATGCGCACACAA 60.280 55.556 14.90 0.00 0.00 3.33
59 70 2.173382 GGACGATGCGCACACAAC 59.827 61.111 14.90 3.31 0.00 3.32
98 109 1.202486 AGAGTGACGACGGCTTTCAAA 60.202 47.619 0.65 0.00 0.00 2.69
154 184 9.852091 AAAGTGTACAGTACTAGTAATAACAGC 57.148 33.333 14.50 10.91 0.00 4.40
155 185 8.571461 AGTGTACAGTACTAGTAATAACAGCA 57.429 34.615 14.50 4.07 0.00 4.41
156 186 8.675504 AGTGTACAGTACTAGTAATAACAGCAG 58.324 37.037 14.50 0.55 0.00 4.24
157 187 8.671921 GTGTACAGTACTAGTAATAACAGCAGA 58.328 37.037 14.50 0.00 0.00 4.26
167 197 9.994432 CTAGTAATAACAGCAGATTTTTCAAGG 57.006 33.333 0.00 0.00 0.00 3.61
168 198 8.635765 AGTAATAACAGCAGATTTTTCAAGGA 57.364 30.769 0.00 0.00 0.00 3.36
169 199 9.247861 AGTAATAACAGCAGATTTTTCAAGGAT 57.752 29.630 0.00 0.00 0.00 3.24
170 200 9.294030 GTAATAACAGCAGATTTTTCAAGGATG 57.706 33.333 0.00 0.00 0.00 3.51
171 201 4.184079 ACAGCAGATTTTTCAAGGATGC 57.816 40.909 0.00 0.00 0.00 3.91
173 203 4.222145 ACAGCAGATTTTTCAAGGATGCAT 59.778 37.500 0.00 0.00 34.71 3.96
184 214 3.646787 GGATGCATCCATGGAGAGG 57.353 57.895 35.93 13.05 46.38 3.69
190 220 2.042842 TGCATCCATGGAGAGGGAAAAA 59.957 45.455 21.33 0.00 35.14 1.94
230 359 7.701539 ACTAAATGCAATTAATCACACCAGA 57.298 32.000 0.00 0.00 33.67 3.86
231 360 8.297470 ACTAAATGCAATTAATCACACCAGAT 57.703 30.769 0.00 0.00 33.67 2.90
232 361 9.407380 ACTAAATGCAATTAATCACACCAGATA 57.593 29.630 0.00 0.00 33.67 1.98
243 372 5.039920 TCACACCAGATAATAATGCAGCT 57.960 39.130 0.00 0.00 0.00 4.24
316 450 2.806745 GCACTTTGGCCTTTTCCCTTTC 60.807 50.000 3.32 0.00 0.00 2.62
325 459 1.959282 CTTTTCCCTTTCTGCTGCTGT 59.041 47.619 0.00 0.00 0.00 4.40
330 464 0.535780 CCTTTCTGCTGCTGTGGTGA 60.536 55.000 0.00 0.00 0.00 4.02
331 465 1.531423 CTTTCTGCTGCTGTGGTGAT 58.469 50.000 0.00 0.00 0.00 3.06
333 467 0.607217 TTCTGCTGCTGTGGTGATGG 60.607 55.000 0.00 0.00 0.00 3.51
335 469 3.446570 GCTGCTGTGGTGATGGGC 61.447 66.667 0.00 0.00 0.00 5.36
339 473 2.353958 CTGTGGTGATGGGCTGCT 59.646 61.111 0.00 0.00 0.00 4.24
372 513 4.975631 TCCCCGAGACAAAAACTAATCAA 58.024 39.130 0.00 0.00 0.00 2.57
410 565 2.902705 AGCTCGTGTGTTTACTCCAA 57.097 45.000 0.00 0.00 0.00 3.53
652 830 1.152368 CCCCCTCCCTGCATTCATC 59.848 63.158 0.00 0.00 0.00 2.92
674 852 4.898265 TCCTCATTCATCTTCGATCTCCTT 59.102 41.667 0.00 0.00 0.00 3.36
679 857 3.790091 TCATCTTCGATCTCCTTGCTTG 58.210 45.455 0.00 0.00 0.00 4.01
680 858 2.015736 TCTTCGATCTCCTTGCTTGC 57.984 50.000 0.00 0.00 0.00 4.01
681 859 1.552337 TCTTCGATCTCCTTGCTTGCT 59.448 47.619 0.00 0.00 0.00 3.91
682 860 2.760650 TCTTCGATCTCCTTGCTTGCTA 59.239 45.455 0.00 0.00 0.00 3.49
769 952 2.186384 CGCAGCTTCTCCCTCTGG 59.814 66.667 0.00 0.00 0.00 3.86
816 1009 2.332654 CCGGGTTTTCTTGCGAGGG 61.333 63.158 0.00 0.00 0.00 4.30
937 1130 1.134521 TGATTCCTCGAAATCCGGTGG 60.135 52.381 0.00 0.00 39.14 4.61
1341 1534 4.461784 GAGCTGTTCGACCTCGTC 57.538 61.111 0.00 0.00 40.80 4.20
1443 1636 3.827898 CTCCTCCTCCACGTCGCC 61.828 72.222 0.00 0.00 0.00 5.54
1476 1669 1.791283 CGACGAGGACGACAACGAC 60.791 63.158 9.27 3.57 42.66 4.34
1477 1670 1.791283 GACGAGGACGACAACGACG 60.791 63.158 9.27 0.00 42.66 5.12
1478 1671 2.501222 CGAGGACGACAACGACGG 60.501 66.667 0.00 0.00 42.66 4.79
1479 1672 2.804090 GAGGACGACAACGACGGC 60.804 66.667 0.00 0.00 42.66 5.68
1480 1673 4.695231 AGGACGACAACGACGGCG 62.695 66.667 10.39 10.39 42.66 6.46
1481 1674 4.688419 GGACGACAACGACGGCGA 62.688 66.667 22.49 0.00 42.66 5.54
1626 1819 1.679977 GCTGGCCATGCTGGAGAAA 60.680 57.895 5.51 0.00 40.96 2.52
1659 1852 1.896660 GCACCGGCTGGACAAGAAA 60.897 57.895 21.41 0.00 39.21 2.52
1921 2114 1.942657 CGTTCATCGCCATCAAGGATT 59.057 47.619 0.00 0.00 41.22 3.01
1975 2168 3.773418 AGATGGAGATCAGCTCAATGG 57.227 47.619 0.00 0.00 45.81 3.16
1983 2176 0.969149 TCAGCTCAATGGTCGACTGT 59.031 50.000 16.46 1.11 0.00 3.55
2018 2211 3.827898 GGACGAGGAGGCGGTCAG 61.828 72.222 0.00 0.00 35.12 3.51
2169 2362 1.452833 GCATCCCAACTGAGAGGCC 60.453 63.158 0.00 0.00 33.85 5.19
2213 2413 7.556844 AGGTATGGAATGATAAGTTATAGCCG 58.443 38.462 0.00 0.00 0.00 5.52
2337 2537 3.874383 TTCTTCTGTTTCATGACCCCA 57.126 42.857 0.00 0.00 0.00 4.96
2395 2597 8.385898 TGAAATTTCTCCGTATGTTAAGTTGT 57.614 30.769 18.64 0.00 0.00 3.32
2489 2698 6.404708 CATGACTATATGATCCAGACCAAGG 58.595 44.000 0.00 0.00 0.00 3.61
2494 2703 1.452833 GATCCAGACCAAGGCAGGC 60.453 63.158 0.00 0.00 0.00 4.85
2496 2705 3.970410 CCAGACCAAGGCAGGCCA 61.970 66.667 13.63 0.00 38.92 5.36
2497 2706 2.357836 CAGACCAAGGCAGGCCAT 59.642 61.111 13.63 0.00 38.92 4.40
2549 2758 0.887933 AGCTTAACCGCCCACATTTG 59.112 50.000 0.00 0.00 0.00 2.32
2550 2759 0.108851 GCTTAACCGCCCACATTTGG 60.109 55.000 0.00 0.00 43.50 3.28
2567 2776 2.951229 TGGGAGGTCCAAGTTTTCTC 57.049 50.000 0.00 0.00 43.84 2.87
2857 3068 3.003275 CGCGGCATGTACTTTTTGGATAT 59.997 43.478 0.00 0.00 0.00 1.63
2858 3069 4.497340 CGCGGCATGTACTTTTTGGATATT 60.497 41.667 0.00 0.00 0.00 1.28
2863 3076 7.201513 CGGCATGTACTTTTTGGATATTTTTGG 60.202 37.037 0.00 0.00 0.00 3.28
2936 3149 9.886337 TGTACCCTCCTAAGTATGTCAAATATA 57.114 33.333 0.00 0.00 0.00 0.86
2966 3180 8.746922 TTTTGATCTGCATCATGTTTCTTTAC 57.253 30.769 0.00 0.00 38.89 2.01
2978 3192 8.868522 TCATGTTTCTTTACCAGAATGATCTT 57.131 30.769 0.00 0.00 41.42 2.40
3078 3292 5.860941 TCTGCTATTTCCTCTCGAATCTT 57.139 39.130 0.00 0.00 0.00 2.40
3114 3328 6.660521 TCTGGATTCTATGTTCTTGCATTTGT 59.339 34.615 0.00 0.00 0.00 2.83
3121 3335 8.334263 TCTATGTTCTTGCATTTGTATGTGAA 57.666 30.769 0.00 0.00 34.12 3.18
3122 3336 8.236586 TCTATGTTCTTGCATTTGTATGTGAAC 58.763 33.333 0.00 0.00 38.09 3.18
3123 3337 6.389830 TGTTCTTGCATTTGTATGTGAACT 57.610 33.333 0.00 0.00 38.23 3.01
3127 3341 8.717821 GTTCTTGCATTTGTATGTGAACTACTA 58.282 33.333 0.00 0.00 36.65 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 0.111045 TAAACGTTGTGTGCGCATCG 60.111 50.000 15.91 15.80 37.52 3.84
50 61 0.384230 CCAGCTAAACGTTGTGTGCG 60.384 55.000 0.00 1.64 0.00 5.34
58 69 0.037046 CCGTTACCCCAGCTAAACGT 60.037 55.000 13.04 0.00 42.25 3.99
59 70 0.247185 TCCGTTACCCCAGCTAAACG 59.753 55.000 9.26 9.26 43.15 3.60
98 109 2.215451 AATTCAGCTGGCGGATGGGT 62.215 55.000 15.13 0.00 31.38 4.51
121 132 9.565090 TTACTAGTACTGTACACTTTCTCTTGA 57.435 33.333 19.27 0.00 0.00 3.02
131 161 8.671921 TCTGCTGTTATTACTAGTACTGTACAC 58.328 37.037 19.27 7.18 0.00 2.90
148 178 5.243507 TGCATCCTTGAAAAATCTGCTGTTA 59.756 36.000 0.00 0.00 0.00 2.41
151 181 4.182693 TGCATCCTTGAAAAATCTGCTG 57.817 40.909 0.00 0.00 0.00 4.41
153 183 4.117685 GGATGCATCCTTGAAAAATCTGC 58.882 43.478 34.20 6.30 43.73 4.26
167 197 1.062364 TCCCTCTCCATGGATGCATC 58.938 55.000 16.63 18.81 0.00 3.91
168 198 1.526315 TTCCCTCTCCATGGATGCAT 58.474 50.000 16.63 0.00 0.00 3.96
169 199 1.297968 TTTCCCTCTCCATGGATGCA 58.702 50.000 16.63 1.18 0.00 3.96
170 200 2.442236 TTTTCCCTCTCCATGGATGC 57.558 50.000 16.63 0.00 0.00 3.91
201 231 9.632807 GGTGTGATTAATTGCATTTAGTAACAA 57.367 29.630 12.92 0.00 0.00 2.83
202 232 8.797438 TGGTGTGATTAATTGCATTTAGTAACA 58.203 29.630 9.01 9.01 0.00 2.41
206 236 7.701539 TCTGGTGTGATTAATTGCATTTAGT 57.298 32.000 1.68 0.00 0.00 2.24
230 359 5.474876 GCCCACTTTCTAGCTGCATTATTAT 59.525 40.000 1.02 0.00 0.00 1.28
231 360 4.821805 GCCCACTTTCTAGCTGCATTATTA 59.178 41.667 1.02 0.00 0.00 0.98
232 361 3.633986 GCCCACTTTCTAGCTGCATTATT 59.366 43.478 1.02 0.00 0.00 1.40
243 372 1.176527 GCAGCATTGCCCACTTTCTA 58.823 50.000 4.70 0.00 44.74 2.10
262 391 8.285776 AGTAATTTGCAAACTGATTTCTTTCG 57.714 30.769 15.41 0.00 0.00 3.46
316 450 2.044555 CCCATCACCACAGCAGCAG 61.045 63.158 0.00 0.00 0.00 4.24
325 459 1.818959 GCAAAAGCAGCCCATCACCA 61.819 55.000 0.00 0.00 0.00 4.17
330 464 1.004200 GCAAGCAAAAGCAGCCCAT 60.004 52.632 0.00 0.00 0.00 4.00
331 465 1.688269 AAGCAAGCAAAAGCAGCCCA 61.688 50.000 0.00 0.00 0.00 5.36
333 467 0.947660 GGAAGCAAGCAAAAGCAGCC 60.948 55.000 0.00 0.00 0.00 4.85
335 469 0.320160 GGGGAAGCAAGCAAAAGCAG 60.320 55.000 0.00 0.00 0.00 4.24
339 473 0.179004 TCTCGGGGAAGCAAGCAAAA 60.179 50.000 0.00 0.00 0.00 2.44
391 546 2.159014 TGTTGGAGTAAACACACGAGCT 60.159 45.455 0.00 0.00 35.16 4.09
410 565 1.810755 CAGCAGCAGTGTGATGATTGT 59.189 47.619 0.00 0.00 35.45 2.71
448 608 4.451150 TGCGGCGGATGTGGTCTC 62.451 66.667 9.78 0.00 0.00 3.36
471 637 2.692557 TGCTTCTCACTCCATCTCTAGC 59.307 50.000 0.00 0.00 0.00 3.42
652 830 4.870123 AGGAGATCGAAGATGAATGAGG 57.130 45.455 0.00 0.00 45.12 3.86
679 857 1.070615 GGGGAGCAAGCTAGCTAGC 59.929 63.158 33.96 33.96 46.75 3.42
680 858 1.751563 GGGGGAGCAAGCTAGCTAG 59.248 63.158 19.70 16.84 46.75 3.42
681 859 2.134287 CGGGGGAGCAAGCTAGCTA 61.134 63.158 19.70 0.00 46.75 3.32
937 1130 1.141234 GGATGGACGGACGGACTTC 59.859 63.158 0.00 0.00 0.00 3.01
1005 1198 2.853290 GCTGCTGCTGCTGGTGTTT 61.853 57.895 22.10 0.00 40.48 2.83
1341 1534 1.329292 CTGCTCTCGAAGTAGTCCTCG 59.671 57.143 0.00 0.00 33.37 4.63
1443 1636 4.116328 TCGTCGAAGCGCTGGAGG 62.116 66.667 12.58 17.32 0.00 4.30
1659 1852 2.489329 CCACGCTTTGATGGTCTTGATT 59.511 45.455 0.00 0.00 0.00 2.57
1857 2050 2.525629 TCCTTCTGCCCACGGACA 60.526 61.111 0.00 0.00 0.00 4.02
1899 2092 7.914110 CAAATCCTTGATGGCGATGAACGTC 62.914 48.000 0.00 0.00 39.91 4.34
1921 2114 0.478072 AGCACCCTGATGTTGTCCAA 59.522 50.000 0.00 0.00 0.00 3.53
1975 2168 1.276145 GCGAAGTCCACACAGTCGAC 61.276 60.000 7.70 7.70 35.41 4.20
2018 2211 1.687297 GATCTCCTCCACCCCGAACC 61.687 65.000 0.00 0.00 0.00 3.62
2169 2362 7.389884 CCATACCTTACATTCTTCATCATCCTG 59.610 40.741 0.00 0.00 0.00 3.86
2213 2413 5.470098 ACCACAACATGATCAAAGAGTACAC 59.530 40.000 0.00 0.00 0.00 2.90
2319 2519 4.281688 ACAAATGGGGTCATGAAACAGAAG 59.718 41.667 0.00 0.00 33.18 2.85
2337 2537 8.023128 GCAATCTTGTACAGTATTGTGACAAAT 58.977 33.333 22.84 0.00 38.23 2.32
2549 2758 2.951229 TGAGAAAACTTGGACCTCCC 57.049 50.000 0.00 0.00 34.29 4.30
2550 2759 3.815962 GACTTGAGAAAACTTGGACCTCC 59.184 47.826 0.00 0.00 0.00 4.30
2839 3050 8.546597 ACCAAAAATATCCAAAAAGTACATGC 57.453 30.769 0.00 0.00 0.00 4.06
2857 3068 7.199766 CAGAAACTGCATTAGTGTACCAAAAA 58.800 34.615 0.00 0.00 40.26 1.94
2858 3069 6.734137 CAGAAACTGCATTAGTGTACCAAAA 58.266 36.000 0.00 0.00 40.26 2.44
2894 3107 4.076394 GGGTACAATTGCTCCAAAGTACA 58.924 43.478 17.42 0.00 38.95 2.90
2939 3152 8.842358 AAAGAAACATGATGCAGATCAAAAAT 57.158 26.923 0.00 0.00 42.02 1.82
2940 3153 9.195411 GTAAAGAAACATGATGCAGATCAAAAA 57.805 29.630 0.00 0.00 42.02 1.94
3023 3237 4.389992 TGCGAACATCACAAAAAGCAAAAA 59.610 33.333 0.00 0.00 0.00 1.94
3024 3238 3.928992 TGCGAACATCACAAAAAGCAAAA 59.071 34.783 0.00 0.00 0.00 2.44
3025 3239 3.305629 GTGCGAACATCACAAAAAGCAAA 59.694 39.130 0.00 0.00 35.05 3.68
3027 3241 2.159324 TGTGCGAACATCACAAAAAGCA 60.159 40.909 0.00 0.00 41.01 3.91
3028 3242 2.458951 TGTGCGAACATCACAAAAAGC 58.541 42.857 0.00 0.00 41.01 3.51
3078 3292 7.904558 ACATAGAATCCAGATAGTGAAGTCA 57.095 36.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.