Multiple sequence alignment - TraesCS2B01G484400

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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 TraesCS2B01G484400 chr2B 100.000 4239 0 0 1 4239 681740861 681736623 0.000000e+00 7829
1 TraesCS2B01G484400 chr2B 89.474 228 23 1 4013 4239 708303488 708303715 1.930000e-73 287
2 TraesCS2B01G484400 chr2D 96.998 3098 70 3 3 3096 569137785 569134707 0.000000e+00 5184
3 TraesCS2B01G484400 chr2D 95.809 2744 99 8 1266 3999 569097554 569094817 0.000000e+00 4416
4 TraesCS2B01G484400 chr2D 96.006 1277 38 4 3 1272 569107358 569106088 0.000000e+00 2063
5 TraesCS2B01G484400 chr2D 97.179 1099 26 4 3143 4239 569134708 569133613 0.000000e+00 1853
6 TraesCS2B01G484400 chr2D 90.351 228 21 1 4013 4239 596575605 596575832 8.910000e-77 298
7 TraesCS2B01G484400 chr1B 90.213 235 22 1 4006 4239 645331169 645331403 5.320000e-79 305
8 TraesCS2B01G484400 chr7D 90.435 230 19 3 4013 4239 120304610 120304381 2.480000e-77 300
9 TraesCS2B01G484400 chr7D 89.427 227 23 1 4014 4239 610839256 610839482 6.940000e-73 285
10 TraesCS2B01G484400 chr1D 89.474 228 24 0 4012 4239 106292444 106292671 5.360000e-74 289
11 TraesCS2B01G484400 chr4B 89.177 231 24 1 4010 4239 500108502 500108732 1.930000e-73 287
12 TraesCS2B01G484400 chr4D 89.427 227 23 1 4014 4239 447333531 447333757 6.940000e-73 285


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 TraesCS2B01G484400 chr2B 681736623 681740861 4238 True 7829.0 7829 100.0000 1 4239 1 chr2B.!!$R1 4238
1 TraesCS2B01G484400 chr2D 569094817 569097554 2737 True 4416.0 4416 95.8090 1266 3999 1 chr2D.!!$R1 2733
2 TraesCS2B01G484400 chr2D 569133613 569137785 4172 True 3518.5 5184 97.0885 3 4239 2 chr2D.!!$R3 4236
3 TraesCS2B01G484400 chr2D 569106088 569107358 1270 True 2063.0 2063 96.0060 3 1272 1 chr2D.!!$R2 1269

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
863 871 0.618458 GGTGACTATGTTGAGGGCCA 59.382 55.0 6.18 0.0 0.00 5.36 F
1458 1466 0.323360 ATTTTAGCCCTCGCAAGCCA 60.323 50.0 0.00 0.0 37.52 4.75 F
2187 2199 1.474330 AAGGAAATTGGGTGGATCGC 58.526 50.0 0.00 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2187 2199 2.783828 AGCAATCTCCGTCATACGAG 57.216 50.000 0.15 0.00 46.05 4.18 R
3096 3108 1.971357 ACAAGACACCACTAGTCAGGG 59.029 52.381 4.40 0.47 38.46 4.45 R
4018 4087 0.329596 CTTGGAGGGGAGACAAAGGG 59.670 60.000 0.00 0.00 0.00 3.95 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
141 142 5.426509 TGGATGTAGGAGTGTCATGATCTTT 59.573 40.000 0.00 0.00 0.00 2.52
142 143 5.988561 GGATGTAGGAGTGTCATGATCTTTC 59.011 44.000 0.00 0.00 0.00 2.62
145 146 2.234661 AGGAGTGTCATGATCTTTCGCA 59.765 45.455 0.00 0.00 0.00 5.10
168 169 7.273381 CGCAAAAATTTCAGAACCGATTCTTAT 59.727 33.333 0.00 0.00 42.91 1.73
213 214 6.282199 AGTTCTAATATATAGGGGTGCACG 57.718 41.667 11.45 0.00 0.00 5.34
272 273 3.958147 TCTGTGGTTAGACTGTCTCAACA 59.042 43.478 14.62 9.79 0.00 3.33
469 470 3.560896 GGTGTGTATTGGTGTTTGTACGT 59.439 43.478 0.00 0.00 0.00 3.57
696 704 9.515226 TGTAATGGGATTATTTGCTTATAGACC 57.485 33.333 0.00 0.00 0.00 3.85
863 871 0.618458 GGTGACTATGTTGAGGGCCA 59.382 55.000 6.18 0.00 0.00 5.36
1158 1166 6.126863 AGGTACTGGATCAGAGAGATAGAG 57.873 45.833 1.59 0.00 37.18 2.43
1230 1238 1.857965 AGCTGCAGATCTGGACACTA 58.142 50.000 23.89 0.00 0.00 2.74
1274 1282 5.957771 TGGAGCCAGAAGTACAATATTCT 57.042 39.130 0.00 0.00 36.19 2.40
1305 1313 2.116827 ACATCGCGGGTCCAAATTTA 57.883 45.000 6.13 0.00 0.00 1.40
1458 1466 0.323360 ATTTTAGCCCTCGCAAGCCA 60.323 50.000 0.00 0.00 37.52 4.75
1509 1517 4.486090 AGTCACTTGTACGCTTAGATGTG 58.514 43.478 6.95 6.95 31.37 3.21
1632 1640 4.255833 GTGGAGCCACATTCATCAAAAA 57.744 40.909 14.53 0.00 45.53 1.94
2105 2117 6.308371 AGTGTGTTTACTTTTATTGGACGG 57.692 37.500 0.00 0.00 0.00 4.79
2187 2199 1.474330 AAGGAAATTGGGTGGATCGC 58.526 50.000 0.00 0.00 0.00 4.58
2304 2316 8.255905 GCTTGTTACCACTTTCCTAATCTACTA 58.744 37.037 0.00 0.00 0.00 1.82
2483 2495 6.434028 TGCAAGTTGCCTAGATATTGAGTTTT 59.566 34.615 24.59 0.00 44.23 2.43
2760 2772 4.498009 CGGTTTGCTTTGTGAAAGATGACT 60.498 41.667 0.16 0.00 41.02 3.41
2986 2998 9.657121 CTCTTCTTTTCTTAGTTTGACATGTTC 57.343 33.333 0.00 0.00 0.00 3.18
3107 3119 5.690997 GAAAAGGTTTTCCCTGACTAGTG 57.309 43.478 0.00 0.00 45.47 2.74
3108 3120 3.790089 AAGGTTTTCCCTGACTAGTGG 57.210 47.619 0.00 0.00 45.47 4.00
3109 3121 2.702748 AGGTTTTCCCTGACTAGTGGT 58.297 47.619 0.00 0.00 44.08 4.16
3110 3122 2.372172 AGGTTTTCCCTGACTAGTGGTG 59.628 50.000 0.00 0.00 44.08 4.17
3111 3123 2.105993 GGTTTTCCCTGACTAGTGGTGT 59.894 50.000 0.00 0.00 0.00 4.16
3112 3124 3.400255 GTTTTCCCTGACTAGTGGTGTC 58.600 50.000 0.00 0.00 35.21 3.67
3113 3125 2.696526 TTCCCTGACTAGTGGTGTCT 57.303 50.000 0.00 0.00 35.63 3.41
3114 3126 2.696526 TCCCTGACTAGTGGTGTCTT 57.303 50.000 0.00 0.00 35.63 3.01
3115 3127 2.248248 TCCCTGACTAGTGGTGTCTTG 58.752 52.381 0.00 0.00 35.63 3.02
3116 3128 1.971357 CCCTGACTAGTGGTGTCTTGT 59.029 52.381 0.00 0.00 35.63 3.16
3117 3129 2.368875 CCCTGACTAGTGGTGTCTTGTT 59.631 50.000 0.00 0.00 35.63 2.83
3118 3130 3.576982 CCCTGACTAGTGGTGTCTTGTTA 59.423 47.826 0.00 0.00 35.63 2.41
3119 3131 4.223032 CCCTGACTAGTGGTGTCTTGTTAT 59.777 45.833 0.00 0.00 35.63 1.89
3120 3132 5.171476 CCTGACTAGTGGTGTCTTGTTATG 58.829 45.833 0.00 0.00 35.63 1.90
3121 3133 5.147330 TGACTAGTGGTGTCTTGTTATGG 57.853 43.478 0.00 0.00 35.63 2.74
3122 3134 4.836175 TGACTAGTGGTGTCTTGTTATGGA 59.164 41.667 0.00 0.00 35.63 3.41
3123 3135 5.305902 TGACTAGTGGTGTCTTGTTATGGAA 59.694 40.000 0.00 0.00 35.63 3.53
3124 3136 6.182507 ACTAGTGGTGTCTTGTTATGGAAA 57.817 37.500 0.00 0.00 0.00 3.13
3125 3137 6.779860 ACTAGTGGTGTCTTGTTATGGAAAT 58.220 36.000 0.00 0.00 0.00 2.17
3126 3138 7.913789 ACTAGTGGTGTCTTGTTATGGAAATA 58.086 34.615 0.00 0.00 0.00 1.40
3127 3139 8.548877 ACTAGTGGTGTCTTGTTATGGAAATAT 58.451 33.333 0.00 0.00 0.00 1.28
3128 3140 7.865706 AGTGGTGTCTTGTTATGGAAATATC 57.134 36.000 0.00 0.00 0.00 1.63
3129 3141 7.402054 AGTGGTGTCTTGTTATGGAAATATCA 58.598 34.615 0.00 0.00 0.00 2.15
3130 3142 7.554118 AGTGGTGTCTTGTTATGGAAATATCAG 59.446 37.037 0.00 0.00 0.00 2.90
3131 3143 7.336931 GTGGTGTCTTGTTATGGAAATATCAGT 59.663 37.037 0.00 0.00 0.00 3.41
3132 3144 7.336679 TGGTGTCTTGTTATGGAAATATCAGTG 59.663 37.037 0.00 0.00 0.00 3.66
3133 3145 7.189512 GTGTCTTGTTATGGAAATATCAGTGC 58.810 38.462 0.00 0.00 0.00 4.40
3134 3146 6.318648 TGTCTTGTTATGGAAATATCAGTGCC 59.681 38.462 0.00 0.00 0.00 5.01
3135 3147 6.543831 GTCTTGTTATGGAAATATCAGTGCCT 59.456 38.462 0.00 0.00 0.00 4.75
3136 3148 7.067494 GTCTTGTTATGGAAATATCAGTGCCTT 59.933 37.037 0.00 0.00 0.00 4.35
3137 3149 6.698008 TGTTATGGAAATATCAGTGCCTTG 57.302 37.500 0.00 0.00 0.00 3.61
3138 3150 6.186957 TGTTATGGAAATATCAGTGCCTTGT 58.813 36.000 0.00 0.00 0.00 3.16
3141 3153 5.172687 TGGAAATATCAGTGCCTTGTGTA 57.827 39.130 0.00 0.00 0.00 2.90
3418 3483 5.484173 CACATGTTTAGTGTGTGTGAACT 57.516 39.130 0.00 0.00 41.93 3.01
3538 3603 7.202016 TCGATAGAAATTCTGCAAAAGTTGT 57.798 32.000 5.64 0.00 46.15 3.32
3895 3964 9.862371 ATCTACACTCTGTAATAGAACAGTTTG 57.138 33.333 4.11 5.36 45.78 2.93
4018 4087 7.593875 AATATACATACGTACGTCTCTCCTC 57.406 40.000 26.53 0.00 0.00 3.71
4057 4126 3.538387 AGAAAAGGGGCTAGGGTTTCTA 58.462 45.455 0.00 0.00 36.90 2.10
4066 4135 2.030371 CTAGGGTTTCTACCTCCCGTC 58.970 57.143 0.00 0.00 45.27 4.79
4094 4163 1.090625 CGTCGATCTCCCACGTCTCT 61.091 60.000 0.00 0.00 0.00 3.10
4117 4186 1.571773 GGCCTTAGGGTCATGGGTGT 61.572 60.000 0.00 0.00 37.14 4.16
4139 4208 3.338250 TGGATCCCGGCCTTTGCT 61.338 61.111 9.90 0.00 37.74 3.91
4165 4234 1.813178 GAGGGCTCTGTTTTTAGGTGC 59.187 52.381 0.00 0.00 0.00 5.01
4207 4276 8.073467 AGGGTTTGTGTTCTATTCAAAAAGAA 57.927 30.769 0.00 0.00 41.28 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 142 3.972950 TCGGTTCTGAAATTTTTGCGA 57.027 38.095 0.00 0.00 0.00 5.10
142 143 4.917415 AGAATCGGTTCTGAAATTTTTGCG 59.083 37.500 10.88 0.00 42.97 4.85
469 470 1.885887 CCGGATCAAGTTTTTCCAGCA 59.114 47.619 0.00 0.00 0.00 4.41
693 701 4.245660 TCTTGATTGTCGATGTCTTGGTC 58.754 43.478 0.00 0.00 0.00 4.02
696 704 5.752472 AGCTATCTTGATTGTCGATGTCTTG 59.248 40.000 0.00 0.00 0.00 3.02
742 750 8.862325 TTCTTTATAGGTTTCTCAAGATGCAA 57.138 30.769 0.00 0.00 0.00 4.08
863 871 3.833559 ATTTGTCTCCATTCTTGGGGT 57.166 42.857 0.00 0.00 44.67 4.95
1005 1013 7.807977 AGTTGCCATATCATTAGTTAACCAG 57.192 36.000 0.88 0.00 0.00 4.00
1158 1166 6.013842 GCAGTTGCTATACATATTTTCCCC 57.986 41.667 0.00 0.00 38.21 4.81
1230 1238 2.213499 CTTTGCTCGACCTTGTTGTCT 58.787 47.619 0.00 0.00 32.97 3.41
1274 1282 1.635844 CGCGATGTAACCTGCTGTAA 58.364 50.000 0.00 0.00 0.00 2.41
1305 1313 8.393259 TGCATCAATAACTTATCCCCATAAGAT 58.607 33.333 8.43 0.37 43.07 2.40
1430 1438 5.736813 TGCGAGGGCTAAAATCTAAAACTA 58.263 37.500 0.00 0.00 40.82 2.24
1632 1640 6.409704 ACAACATACAGTTATGTCATGCTCT 58.590 36.000 0.00 0.00 46.45 4.09
2187 2199 2.783828 AGCAATCTCCGTCATACGAG 57.216 50.000 0.15 0.00 46.05 4.18
2432 2444 9.031360 ACATGTAGCATAAAGAACATAAGTACG 57.969 33.333 0.00 0.00 31.55 3.67
2697 2709 7.365741 AGAAGTGCAGAAAGAACATGTTATTG 58.634 34.615 18.53 8.87 0.00 1.90
2728 2740 3.728718 CACAAAGCAAACCGACAATGTAC 59.271 43.478 0.00 0.00 0.00 2.90
2737 2749 3.730715 GTCATCTTTCACAAAGCAAACCG 59.269 43.478 0.00 0.00 38.39 4.44
2910 2922 9.567848 GGTATCAATGACGTTTACAATCAATTT 57.432 29.630 0.00 0.00 0.00 1.82
2914 2926 7.857734 ATGGTATCAATGACGTTTACAATCA 57.142 32.000 0.00 0.00 0.00 2.57
2929 2941 8.961634 TGTAAATTTTCGGATGAATGGTATCAA 58.038 29.630 0.00 0.00 33.20 2.57
3000 3012 6.021596 GCACACAACTAGGATTATTTTGTCG 58.978 40.000 0.00 0.00 0.00 4.35
3091 3103 3.071167 AGACACCACTAGTCAGGGAAAAC 59.929 47.826 4.80 0.00 38.46 2.43
3092 3104 3.314693 AGACACCACTAGTCAGGGAAAA 58.685 45.455 4.80 0.00 38.46 2.29
3093 3105 2.972348 AGACACCACTAGTCAGGGAAA 58.028 47.619 4.80 0.00 38.46 3.13
3094 3106 2.632996 CAAGACACCACTAGTCAGGGAA 59.367 50.000 4.80 0.00 38.46 3.97
3095 3107 2.248248 CAAGACACCACTAGTCAGGGA 58.752 52.381 4.80 0.00 38.46 4.20
3096 3108 1.971357 ACAAGACACCACTAGTCAGGG 59.029 52.381 4.40 0.47 38.46 4.45
3097 3109 3.753294 AACAAGACACCACTAGTCAGG 57.247 47.619 0.00 0.00 38.46 3.86
3098 3110 5.047306 TCCATAACAAGACACCACTAGTCAG 60.047 44.000 0.00 0.00 38.46 3.51
3099 3111 4.836175 TCCATAACAAGACACCACTAGTCA 59.164 41.667 0.00 0.00 38.46 3.41
3100 3112 5.401531 TCCATAACAAGACACCACTAGTC 57.598 43.478 0.00 0.00 36.26 2.59
3101 3113 5.818678 TTCCATAACAAGACACCACTAGT 57.181 39.130 0.00 0.00 0.00 2.57
3102 3114 8.964476 ATATTTCCATAACAAGACACCACTAG 57.036 34.615 0.00 0.00 0.00 2.57
3103 3115 8.544622 TGATATTTCCATAACAAGACACCACTA 58.455 33.333 0.00 0.00 0.00 2.74
3104 3116 7.402054 TGATATTTCCATAACAAGACACCACT 58.598 34.615 0.00 0.00 0.00 4.00
3105 3117 7.336931 ACTGATATTTCCATAACAAGACACCAC 59.663 37.037 0.00 0.00 0.00 4.16
3106 3118 7.336679 CACTGATATTTCCATAACAAGACACCA 59.663 37.037 0.00 0.00 0.00 4.17
3107 3119 7.679638 GCACTGATATTTCCATAACAAGACACC 60.680 40.741 0.00 0.00 0.00 4.16
3108 3120 7.189512 GCACTGATATTTCCATAACAAGACAC 58.810 38.462 0.00 0.00 0.00 3.67
3109 3121 6.318648 GGCACTGATATTTCCATAACAAGACA 59.681 38.462 0.00 0.00 0.00 3.41
3110 3122 6.543831 AGGCACTGATATTTCCATAACAAGAC 59.456 38.462 0.00 0.00 37.18 3.01
3111 3123 6.662755 AGGCACTGATATTTCCATAACAAGA 58.337 36.000 0.00 0.00 37.18 3.02
3112 3124 6.949352 AGGCACTGATATTTCCATAACAAG 57.051 37.500 0.00 0.00 37.18 3.16
3113 3125 6.663093 ACAAGGCACTGATATTTCCATAACAA 59.337 34.615 0.00 0.00 40.86 2.83
3114 3126 6.095300 CACAAGGCACTGATATTTCCATAACA 59.905 38.462 0.00 0.00 40.86 2.41
3115 3127 6.095440 ACACAAGGCACTGATATTTCCATAAC 59.905 38.462 0.00 0.00 40.86 1.89
3116 3128 6.186957 ACACAAGGCACTGATATTTCCATAA 58.813 36.000 0.00 0.00 40.86 1.90
3117 3129 5.754782 ACACAAGGCACTGATATTTCCATA 58.245 37.500 0.00 0.00 40.86 2.74
3118 3130 4.603131 ACACAAGGCACTGATATTTCCAT 58.397 39.130 0.00 0.00 40.86 3.41
3119 3131 4.032960 ACACAAGGCACTGATATTTCCA 57.967 40.909 0.00 0.00 40.86 3.53
3120 3132 6.318648 TCAATACACAAGGCACTGATATTTCC 59.681 38.462 0.00 0.00 40.86 3.13
3121 3133 7.320443 TCAATACACAAGGCACTGATATTTC 57.680 36.000 0.00 0.00 40.86 2.17
3122 3134 7.776969 AGATCAATACACAAGGCACTGATATTT 59.223 33.333 0.00 0.00 40.86 1.40
3123 3135 7.285566 AGATCAATACACAAGGCACTGATATT 58.714 34.615 0.00 0.00 40.86 1.28
3124 3136 6.835174 AGATCAATACACAAGGCACTGATAT 58.165 36.000 0.00 0.00 40.86 1.63
3125 3137 6.239217 AGATCAATACACAAGGCACTGATA 57.761 37.500 0.00 0.00 40.86 2.15
3126 3138 5.108187 AGATCAATACACAAGGCACTGAT 57.892 39.130 0.00 0.00 40.86 2.90
3127 3139 4.558226 AGATCAATACACAAGGCACTGA 57.442 40.909 0.00 0.00 40.86 3.41
3128 3140 5.633830 AAAGATCAATACACAAGGCACTG 57.366 39.130 0.00 0.00 40.86 3.66
3130 3142 6.371548 TGAGTAAAGATCAATACACAAGGCAC 59.628 38.462 9.69 0.00 0.00 5.01
3131 3143 6.472016 TGAGTAAAGATCAATACACAAGGCA 58.528 36.000 9.69 0.00 0.00 4.75
3132 3144 6.985188 TGAGTAAAGATCAATACACAAGGC 57.015 37.500 9.69 0.00 0.00 4.35
3133 3145 8.498054 ACATGAGTAAAGATCAATACACAAGG 57.502 34.615 0.00 8.99 0.00 3.61
3141 3153 8.960591 CCACCTAAAACATGAGTAAAGATCAAT 58.039 33.333 0.00 0.00 0.00 2.57
3538 3603 7.896496 ACCATGGATAAAATACACAAGGGTTTA 59.104 33.333 21.47 0.00 0.00 2.01
3756 3822 7.253983 CGAGCTAATAAGAATGTCACGCTAAAA 60.254 37.037 0.00 0.00 0.00 1.52
3885 3951 4.470334 AACAAATGTGGCAAACTGTTCT 57.530 36.364 1.94 0.00 0.00 3.01
3993 4062 7.118971 GGAGGAGAGACGTACGTATGTATATTT 59.881 40.741 21.75 7.49 32.11 1.40
4018 4087 0.329596 CTTGGAGGGGAGACAAAGGG 59.670 60.000 0.00 0.00 0.00 3.95
4077 4146 1.095600 CAAGAGACGTGGGAGATCGA 58.904 55.000 0.00 0.00 0.00 3.59
4086 4155 1.673033 CCTAAGGCCACAAGAGACGTG 60.673 57.143 5.01 0.00 0.00 4.49
4094 4163 0.331278 CCATGACCCTAAGGCCACAA 59.669 55.000 5.01 0.00 36.11 3.33
4143 4212 1.354705 ACCTAAAAACAGAGCCCTCCC 59.645 52.381 0.00 0.00 0.00 4.30
4155 4224 7.382898 ACAAAACTTGAAGAAGCACCTAAAAA 58.617 30.769 0.00 0.00 31.68 1.94
4165 4234 7.275560 CACAAACCCTAACAAAACTTGAAGAAG 59.724 37.037 0.00 0.00 35.07 2.85
4207 4276 4.587189 GAAGCCGCCGCCGTCTAT 62.587 66.667 0.00 0.00 34.57 1.98


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

AutoCloner maintained by Alex Coulton.