Multiple sequence alignment - TraesCS2A01G068800

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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 TraesCS2A01G068800 chr2A 100.000 5229 0 0 1 5229 30273079 30267851 0.000000e+00 9657.0
1 TraesCS2A01G068800 chr2A 98.129 5078 82 6 1 5075 30257430 30252363 0.000000e+00 8839.0
2 TraesCS2A01G068800 chr2A 98.423 4312 64 4 806 5116 30247025 30242717 0.000000e+00 7583.0
3 TraesCS2A01G068800 chr2A 85.737 3716 478 35 835 4511 30300825 30304527 0.000000e+00 3879.0
4 TraesCS2A01G068800 chr2A 84.620 3329 472 20 997 4298 30164886 30161571 0.000000e+00 3275.0
5 TraesCS2A01G068800 chr2A 88.652 423 24 6 310 708 30196105 30195683 1.310000e-135 494.0
6 TraesCS2A01G068800 chr2A 97.368 38 1 0 688 725 30247059 30247022 1.220000e-06 65.8
7 TraesCS2A01G068800 chr2A 92.683 41 2 1 731 771 30300749 30300788 2.030000e-04 58.4
8 TraesCS2A01G068800 chr7D 90.558 3241 230 28 608 3808 302743215 302746419 0.000000e+00 4220.0
9 TraesCS2A01G068800 chr7D 95.745 94 4 0 4774 4867 302746411 302746504 9.070000e-33 152.0
10 TraesCS2A01G068800 chr2D 95.771 2388 77 9 2196 4569 28417358 28414981 0.000000e+00 3829.0
11 TraesCS2A01G068800 chr2D 84.350 3310 487 15 1011 4295 28001720 27998417 0.000000e+00 3214.0
12 TraesCS2A01G068800 chr2D 84.055 3324 499 17 997 4295 27956831 27960148 0.000000e+00 3173.0
13 TraesCS2A01G068800 chr2D 87.418 1073 82 26 537 1585 28418426 28417383 0.000000e+00 1184.0
14 TraesCS2A01G068800 chr2D 84.176 455 47 14 4636 5080 28414831 28414392 8.100000e-113 418.0
15 TraesCS2A01G068800 chr2D 84.940 166 17 8 7 169 28420261 28420101 1.510000e-35 161.0
16 TraesCS2A01G068800 chr2D 94.595 74 4 0 4777 4850 28059737 28059664 1.190000e-21 115.0
17 TraesCS2A01G068800 chr2B 84.083 3311 493 16 1011 4295 44754691 44751389 0.000000e+00 3164.0
18 TraesCS2A01G068800 chr2B 91.323 2132 145 14 2950 5065 45617055 45614948 0.000000e+00 2876.0
19 TraesCS2A01G068800 chr2B 85.614 2426 279 31 544 2960 44924081 44926445 0.000000e+00 2483.0
20 TraesCS2A01G068800 chr2B 92.823 1672 108 3 2950 4609 44926462 44928133 0.000000e+00 2412.0
21 TraesCS2A01G068800 chr2B 92.189 1626 116 9 2950 4567 45625116 45626738 0.000000e+00 2289.0
22 TraesCS2A01G068800 chr2B 88.785 535 30 10 4533 5065 45626760 45627266 3.440000e-176 628.0
23 TraesCS2A01G068800 chr2B 89.605 481 27 6 4587 5065 44928311 44928770 1.620000e-164 590.0
24 TraesCS2A01G068800 chr2B 83.000 200 27 5 7 203 44923409 44923604 1.940000e-39 174.0
25 TraesCS2A01G068800 chr2B 94.186 86 5 0 440 525 45623035 45623120 1.180000e-26 132.0
26 TraesCS2A01G068800 chr2B 94.186 86 5 0 440 525 45700301 45700386 1.180000e-26 132.0


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 TraesCS2A01G068800 chr2A 30267851 30273079 5228 True 9657.000000 9657 100.00000 1 5229 1 chr2A.!!$R4 5228
1 TraesCS2A01G068800 chr2A 30252363 30257430 5067 True 8839.000000 8839 98.12900 1 5075 1 chr2A.!!$R3 5074
2 TraesCS2A01G068800 chr2A 30242717 30247059 4342 True 3824.400000 7583 97.89550 688 5116 2 chr2A.!!$R5 4428
3 TraesCS2A01G068800 chr2A 30161571 30164886 3315 True 3275.000000 3275 84.62000 997 4298 1 chr2A.!!$R1 3301
4 TraesCS2A01G068800 chr2A 30300749 30304527 3778 False 1968.700000 3879 89.21000 731 4511 2 chr2A.!!$F1 3780
5 TraesCS2A01G068800 chr7D 302743215 302746504 3289 False 2186.000000 4220 93.15150 608 4867 2 chr7D.!!$F1 4259
6 TraesCS2A01G068800 chr2D 27998417 28001720 3303 True 3214.000000 3214 84.35000 1011 4295 1 chr2D.!!$R1 3284
7 TraesCS2A01G068800 chr2D 27956831 27960148 3317 False 3173.000000 3173 84.05500 997 4295 1 chr2D.!!$F1 3298
8 TraesCS2A01G068800 chr2D 28414392 28420261 5869 True 1398.000000 3829 88.07625 7 5080 4 chr2D.!!$R3 5073
9 TraesCS2A01G068800 chr2B 44751389 44754691 3302 True 3164.000000 3164 84.08300 1011 4295 1 chr2B.!!$R1 3284
10 TraesCS2A01G068800 chr2B 45614948 45617055 2107 True 2876.000000 2876 91.32300 2950 5065 1 chr2B.!!$R2 2115
11 TraesCS2A01G068800 chr2B 44923409 44928770 5361 False 1414.750000 2483 87.76050 7 5065 4 chr2B.!!$F2 5058
12 TraesCS2A01G068800 chr2B 45623035 45627266 4231 False 1016.333333 2289 91.72000 440 5065 3 chr2B.!!$F3 4625

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
760 2143 2.075566 TCCTCTGCACCCACCACAA 61.076 57.895 0.0 0.0 0.0 3.33 F
1279 2691 0.106569 TCTCGGTGGGCGGTTATCTA 60.107 55.000 0.0 0.0 0.0 1.98 F
2010 3422 0.034670 GCCTGATCCCTGCTTCACTT 60.035 55.000 0.0 0.0 0.0 3.16 F
3057 4530 3.043586 CTCGCTGCTAATTGTACTACCG 58.956 50.000 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 3221 6.767902 TGTTGAAACTTAGATCAAGCTCAAGT 59.232 34.615 15.45 5.68 38.82 3.16 R
2911 4330 2.224744 TGCCATCCAAAACTACTGCAGA 60.225 45.455 23.35 2.95 0.00 4.26 R
3463 4954 4.936891 AGTGCTTTGAACTCATGGTTTTC 58.063 39.130 0.00 0.00 38.41 2.29 R
4773 6648 4.081917 GTCTCTTTAGTGTTCCTCTCCTGG 60.082 50.000 0.00 0.00 0.00 4.45 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
237 1442 4.024984 CCAGTCCCCCTCCCCTCA 62.025 72.222 0.00 0.00 0.00 3.86
586 1923 3.143728 TCATCAAGCATGATAGCGCAAT 58.856 40.909 11.47 0.00 44.53 3.56
760 2143 2.075566 TCCTCTGCACCCACCACAA 61.076 57.895 0.00 0.00 0.00 3.33
999 2404 1.246649 TGTTCTTGCACATCGGCATT 58.753 45.000 0.00 0.00 44.48 3.56
1138 2550 1.348696 TCAAGTCTGGCATCAGCTTCA 59.651 47.619 0.00 0.00 40.69 3.02
1279 2691 0.106569 TCTCGGTGGGCGGTTATCTA 60.107 55.000 0.00 0.00 0.00 1.98
1920 3332 3.243367 GCAGCAATACACTTGTTGGACAA 60.243 43.478 4.39 0.00 36.54 3.18
2010 3422 0.034670 GCCTGATCCCTGCTTCACTT 60.035 55.000 0.00 0.00 0.00 3.16
2911 4330 4.207891 AGTGGTATCTTCACGCATTCTT 57.792 40.909 0.00 0.00 39.86 2.52
3057 4530 3.043586 CTCGCTGCTAATTGTACTACCG 58.956 50.000 0.00 0.00 0.00 4.02
3226 4717 4.769488 AGAAGCTGAAGAGAGTGTCATACA 59.231 41.667 0.00 0.00 0.00 2.29
3836 5327 5.474532 ACCTTTTCCGTTTCCACCTAATTAC 59.525 40.000 0.00 0.00 0.00 1.89
4432 5948 9.185192 CTTTGTTCCAGAGTTGTTGATTATTTC 57.815 33.333 0.00 0.00 0.00 2.17
4899 6775 2.679059 CGCTGGAGATGACACCAAAGAT 60.679 50.000 0.00 0.00 36.43 2.40
5127 7010 7.617533 TTTCTAGCAAAGTTTTCATTAACGC 57.382 32.000 0.00 0.00 33.26 4.84
5128 7011 6.307031 TCTAGCAAAGTTTTCATTAACGCA 57.693 33.333 0.00 0.00 33.26 5.24
5129 7012 6.730175 TCTAGCAAAGTTTTCATTAACGCAA 58.270 32.000 0.00 0.00 33.26 4.85
5131 7014 4.209080 AGCAAAGTTTTCATTAACGCAAGC 59.791 37.500 0.00 0.00 45.62 4.01
5132 7015 4.608222 GCAAAGTTTTCATTAACGCAAGCC 60.608 41.667 0.00 0.00 45.62 4.35
5133 7016 2.928694 AGTTTTCATTAACGCAAGCCG 58.071 42.857 0.00 0.00 45.62 5.52
5134 7017 1.385409 GTTTTCATTAACGCAAGCCGC 59.615 47.619 0.00 0.00 45.62 6.53
5166 7049 3.339253 GGGGGTTGATACTGTACGTTT 57.661 47.619 0.00 0.00 0.00 3.60
5167 7050 4.470334 GGGGGTTGATACTGTACGTTTA 57.530 45.455 0.00 0.00 0.00 2.01
5168 7051 5.027293 GGGGGTTGATACTGTACGTTTAT 57.973 43.478 0.00 0.00 0.00 1.40
5169 7052 5.430886 GGGGGTTGATACTGTACGTTTATT 58.569 41.667 0.00 0.00 0.00 1.40
5170 7053 5.525012 GGGGGTTGATACTGTACGTTTATTC 59.475 44.000 0.00 0.00 0.00 1.75
5171 7054 6.108015 GGGGTTGATACTGTACGTTTATTCA 58.892 40.000 0.00 0.00 0.00 2.57
5172 7055 6.036408 GGGGTTGATACTGTACGTTTATTCAC 59.964 42.308 0.00 0.00 0.00 3.18
5173 7056 6.591062 GGGTTGATACTGTACGTTTATTCACA 59.409 38.462 0.00 0.00 0.00 3.58
5174 7057 7.118101 GGGTTGATACTGTACGTTTATTCACAA 59.882 37.037 0.00 0.00 0.00 3.33
5175 7058 8.497554 GGTTGATACTGTACGTTTATTCACAAA 58.502 33.333 0.00 0.00 0.00 2.83
5176 7059 9.525007 GTTGATACTGTACGTTTATTCACAAAG 57.475 33.333 0.00 0.00 0.00 2.77
5177 7060 7.735500 TGATACTGTACGTTTATTCACAAAGC 58.264 34.615 0.00 0.00 0.00 3.51
5178 7061 7.601130 TGATACTGTACGTTTATTCACAAAGCT 59.399 33.333 0.00 0.00 0.00 3.74
5179 7062 8.991243 ATACTGTACGTTTATTCACAAAGCTA 57.009 30.769 0.00 0.00 0.00 3.32
5180 7063 7.113704 ACTGTACGTTTATTCACAAAGCTAC 57.886 36.000 0.00 0.00 0.00 3.58
5181 7064 6.702723 ACTGTACGTTTATTCACAAAGCTACA 59.297 34.615 0.00 0.00 0.00 2.74
5182 7065 6.879962 TGTACGTTTATTCACAAAGCTACAC 58.120 36.000 0.00 0.00 0.00 2.90
5183 7066 5.994887 ACGTTTATTCACAAAGCTACACA 57.005 34.783 0.00 0.00 0.00 3.72
5184 7067 6.366315 ACGTTTATTCACAAAGCTACACAA 57.634 33.333 0.00 0.00 0.00 3.33
5185 7068 6.787225 ACGTTTATTCACAAAGCTACACAAA 58.213 32.000 0.00 0.00 0.00 2.83
5186 7069 6.689669 ACGTTTATTCACAAAGCTACACAAAC 59.310 34.615 0.00 0.00 0.00 2.93
5187 7070 6.689241 CGTTTATTCACAAAGCTACACAAACA 59.311 34.615 0.00 0.00 0.00 2.83
5188 7071 7.378461 CGTTTATTCACAAAGCTACACAAACAT 59.622 33.333 0.00 0.00 0.00 2.71
5189 7072 9.672086 GTTTATTCACAAAGCTACACAAACATA 57.328 29.630 0.00 0.00 0.00 2.29
5194 7077 7.471721 TCACAAAGCTACACAAACATATATGC 58.528 34.615 12.79 0.00 0.00 3.14
5195 7078 7.120432 TCACAAAGCTACACAAACATATATGCA 59.880 33.333 12.79 0.00 0.00 3.96
5196 7079 7.754475 CACAAAGCTACACAAACATATATGCAA 59.246 33.333 12.79 0.00 0.00 4.08
5197 7080 8.303156 ACAAAGCTACACAAACATATATGCAAA 58.697 29.630 12.79 0.00 0.00 3.68
5198 7081 8.586273 CAAAGCTACACAAACATATATGCAAAC 58.414 33.333 12.79 0.00 0.00 2.93
5199 7082 7.630242 AGCTACACAAACATATATGCAAACT 57.370 32.000 12.79 0.00 0.00 2.66
5200 7083 8.055279 AGCTACACAAACATATATGCAAACTT 57.945 30.769 12.79 0.00 0.00 2.66
5201 7084 7.970061 AGCTACACAAACATATATGCAAACTTG 59.030 33.333 12.79 10.45 0.00 3.16
5202 7085 7.967854 GCTACACAAACATATATGCAAACTTGA 59.032 33.333 12.79 0.00 0.00 3.02
5218 7101 9.995003 TGCAAACTTGATTAGGATAAAACATTT 57.005 25.926 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
586 1923 1.614413 TGCATTGCAATTCAGTCAGCA 59.386 42.857 9.83 11.58 34.76 4.41
760 2143 2.031163 GCGACTGGCAGAACTGGT 59.969 61.111 23.66 0.00 42.87 4.00
999 2404 3.678965 AGAGACAAGAGAGAGGGCATA 57.321 47.619 0.00 0.00 0.00 3.14
1138 2550 2.582636 AGTGTAGGATGCCAAAGGGATT 59.417 45.455 0.00 0.00 32.75 3.01
1279 2691 4.602340 AAGTCAAGTTACCGACACATCT 57.398 40.909 5.52 0.00 34.48 2.90
1809 3221 6.767902 TGTTGAAACTTAGATCAAGCTCAAGT 59.232 34.615 15.45 5.68 38.82 3.16
2010 3422 8.584157 AGTATTTGAAGATTTAACATGTTGGCA 58.416 29.630 21.42 5.05 0.00 4.92
2911 4330 2.224744 TGCCATCCAAAACTACTGCAGA 60.225 45.455 23.35 2.95 0.00 4.26
3226 4717 6.431234 CAGTTGGTAGCTTTAAGAATGTCCTT 59.569 38.462 0.00 0.00 0.00 3.36
3463 4954 4.936891 AGTGCTTTGAACTCATGGTTTTC 58.063 39.130 0.00 0.00 38.41 2.29
4773 6648 4.081917 GTCTCTTTAGTGTTCCTCTCCTGG 60.082 50.000 0.00 0.00 0.00 4.45
5116 6999 3.393112 GCGGCTTGCGTTAATGAAA 57.607 47.368 0.00 0.00 0.00 2.69
5146 7029 3.339253 AAACGTACAGTATCAACCCCC 57.661 47.619 0.00 0.00 0.00 5.40
5147 7030 6.036408 GTGAATAAACGTACAGTATCAACCCC 59.964 42.308 0.00 0.00 0.00 4.95
5148 7031 6.591062 TGTGAATAAACGTACAGTATCAACCC 59.409 38.462 0.00 0.00 0.00 4.11
5149 7032 7.585286 TGTGAATAAACGTACAGTATCAACC 57.415 36.000 0.00 0.00 0.00 3.77
5150 7033 9.525007 CTTTGTGAATAAACGTACAGTATCAAC 57.475 33.333 0.00 0.00 0.00 3.18
5151 7034 8.225107 GCTTTGTGAATAAACGTACAGTATCAA 58.775 33.333 0.00 0.00 0.00 2.57
5152 7035 7.601130 AGCTTTGTGAATAAACGTACAGTATCA 59.399 33.333 0.00 0.00 0.00 2.15
5153 7036 7.960793 AGCTTTGTGAATAAACGTACAGTATC 58.039 34.615 0.00 0.00 0.00 2.24
5154 7037 7.900782 AGCTTTGTGAATAAACGTACAGTAT 57.099 32.000 0.00 0.00 0.00 2.12
5155 7038 7.866898 TGTAGCTTTGTGAATAAACGTACAGTA 59.133 33.333 0.00 0.00 0.00 2.74
5156 7039 6.702723 TGTAGCTTTGTGAATAAACGTACAGT 59.297 34.615 0.00 0.00 0.00 3.55
5157 7040 7.007697 GTGTAGCTTTGTGAATAAACGTACAG 58.992 38.462 0.00 0.00 0.00 2.74
5158 7041 6.479331 TGTGTAGCTTTGTGAATAAACGTACA 59.521 34.615 0.00 0.00 0.00 2.90
5159 7042 6.879962 TGTGTAGCTTTGTGAATAAACGTAC 58.120 36.000 0.00 0.00 0.00 3.67
5160 7043 7.479897 TTGTGTAGCTTTGTGAATAAACGTA 57.520 32.000 0.00 0.00 0.00 3.57
5161 7044 5.994887 TGTGTAGCTTTGTGAATAAACGT 57.005 34.783 0.00 0.00 0.00 3.99
5162 7045 6.689241 TGTTTGTGTAGCTTTGTGAATAAACG 59.311 34.615 0.00 0.00 0.00 3.60
5163 7046 7.979115 TGTTTGTGTAGCTTTGTGAATAAAC 57.021 32.000 0.00 0.00 0.00 2.01
5168 7051 7.967854 GCATATATGTTTGTGTAGCTTTGTGAA 59.032 33.333 14.14 0.00 0.00 3.18
5169 7052 7.120432 TGCATATATGTTTGTGTAGCTTTGTGA 59.880 33.333 14.14 0.00 0.00 3.58
5170 7053 7.249858 TGCATATATGTTTGTGTAGCTTTGTG 58.750 34.615 14.14 0.00 0.00 3.33
5171 7054 7.389803 TGCATATATGTTTGTGTAGCTTTGT 57.610 32.000 14.14 0.00 0.00 2.83
5172 7055 8.586273 GTTTGCATATATGTTTGTGTAGCTTTG 58.414 33.333 14.14 0.00 0.00 2.77
5173 7056 8.522830 AGTTTGCATATATGTTTGTGTAGCTTT 58.477 29.630 14.14 0.00 0.00 3.51
5174 7057 8.055279 AGTTTGCATATATGTTTGTGTAGCTT 57.945 30.769 14.14 0.00 0.00 3.74
5175 7058 7.630242 AGTTTGCATATATGTTTGTGTAGCT 57.370 32.000 14.14 0.00 0.00 3.32
5176 7059 7.967854 TCAAGTTTGCATATATGTTTGTGTAGC 59.032 33.333 14.14 0.00 0.00 3.58
5192 7075 9.995003 AAATGTTTTATCCTAATCAAGTTTGCA 57.005 25.926 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.