Multiple sequence alignment - TraesCS7A01G324900

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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 TraesCS7A01G324900 chr7A 100.000 3257 0 0 1 3257 472566195 472569451 0.000000e+00 6015
1 TraesCS7A01G324900 chr7D 94.912 3282 114 24 1 3256 411603517 411606771 0.000000e+00 5086
2 TraesCS7A01G324900 chr7B 93.738 2683 85 30 1 2632 426100642 426103292 0.000000e+00 3947
3 TraesCS7A01G324900 chr7B 92.483 439 28 5 2808 3243 426110612 426111048 9.920000e-175 623
4 TraesCS7A01G324900 chr7B 97.638 127 3 0 2626 2752 426110487 426110613 5.470000e-53 219


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 TraesCS7A01G324900 chr7A 472566195 472569451 3256 False 6015 6015 100.0000 1 3257 1 chr7A.!!$F1 3256
1 TraesCS7A01G324900 chr7D 411603517 411606771 3254 False 5086 5086 94.9120 1 3256 1 chr7D.!!$F1 3255
2 TraesCS7A01G324900 chr7B 426100642 426103292 2650 False 3947 3947 93.7380 1 2632 1 chr7B.!!$F1 2631
3 TraesCS7A01G324900 chr7B 426110487 426111048 561 False 421 623 95.0605 2626 3243 2 chr7B.!!$F2 617

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
183 193 0.177836 CCAGTCACACCACACAGACA 59.822 55.0 0.0 0.0 33.56 3.41 F
706 730 0.257039 AGTGGAGTGGGATTCATGGC 59.743 55.0 0.0 0.0 0.00 4.40 F
1065 1106 0.248458 CCGTTCCAGCAAACACACAC 60.248 55.0 0.0 0.0 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1065 1106 0.042188 CCGACTCAAGTTTGTGCGTG 60.042 55.000 0.00 0.0 0.00 5.34 R
1655 1719 0.868406 CGTTGAGCTTGAACTCCACC 59.132 55.000 7.68 0.0 35.72 4.61 R
2383 2447 1.302832 GCCACTACCACTTGCTGCT 60.303 57.895 0.00 0.0 0.00 4.24 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
174 184 1.677552 CTACCCACCCAGTCACACC 59.322 63.158 0.00 0.00 0.00 4.16
183 193 0.177836 CCAGTCACACCACACAGACA 59.822 55.000 0.00 0.00 33.56 3.41
184 194 1.406751 CCAGTCACACCACACAGACAA 60.407 52.381 0.00 0.00 33.56 3.18
185 195 2.355197 CAGTCACACCACACAGACAAA 58.645 47.619 0.00 0.00 33.56 2.83
186 196 2.746904 CAGTCACACCACACAGACAAAA 59.253 45.455 0.00 0.00 33.56 2.44
187 197 3.009723 AGTCACACCACACAGACAAAAG 58.990 45.455 0.00 0.00 33.56 2.27
257 273 0.595095 GGCTGCAACTGCCATATAGC 59.405 55.000 10.43 0.97 45.75 2.97
272 288 8.267620 TGCCATATAGCATATGTCACATTAAC 57.732 34.615 0.00 0.00 38.00 2.01
274 290 8.607459 GCCATATAGCATATGTCACATTAACTC 58.393 37.037 0.00 0.00 0.00 3.01
275 291 9.102757 CCATATAGCATATGTCACATTAACTCC 57.897 37.037 0.00 0.00 0.00 3.85
281 297 1.084289 GTCACATTAACTCCGTGGCC 58.916 55.000 0.00 0.00 28.95 5.36
314 330 2.354109 AGTGATGCACTCTGTACGTG 57.646 50.000 0.00 0.00 41.21 4.49
324 340 4.499865 GCACTCTGTACGTGGTGATATGAT 60.500 45.833 13.52 0.00 33.10 2.45
375 391 2.292292 CGTGGGTTTCCAGAAAAACGAT 59.708 45.455 14.31 0.00 45.05 3.73
404 420 2.206900 TTGAGGGGCAGACAGGGA 59.793 61.111 0.00 0.00 0.00 4.20
515 531 1.269102 GCTTGGCTGCTGCAGAATATG 60.269 52.381 32.30 18.18 41.91 1.78
522 540 3.490419 GCTGCTGCAGAATATGGGAAAAG 60.490 47.826 32.30 2.57 39.41 2.27
546 564 4.143333 CAATGCCAGCTGCCAGCC 62.143 66.667 14.25 0.00 43.77 4.85
653 672 0.908198 CCCCTTGAGTCTGGAAGGAG 59.092 60.000 8.90 0.00 41.26 3.69
654 673 0.908198 CCCTTGAGTCTGGAAGGAGG 59.092 60.000 8.90 0.00 41.26 4.30
655 674 1.553417 CCCTTGAGTCTGGAAGGAGGA 60.553 57.143 8.90 0.00 41.26 3.71
696 720 4.135153 CGGAGCGGAGTGGAGTGG 62.135 72.222 0.00 0.00 0.00 4.00
706 730 0.257039 AGTGGAGTGGGATTCATGGC 59.743 55.000 0.00 0.00 0.00 4.40
737 761 1.373059 GCTGGGTAGCTGATAGGCC 59.627 63.158 0.00 0.00 46.57 5.19
774 802 2.556144 TTCCCATGCATGCTAGCTAG 57.444 50.000 21.69 16.84 34.99 3.42
775 803 1.427809 TCCCATGCATGCTAGCTAGT 58.572 50.000 21.69 0.00 34.99 2.57
776 804 2.608623 TCCCATGCATGCTAGCTAGTA 58.391 47.619 21.69 18.12 34.99 1.82
777 805 2.300152 TCCCATGCATGCTAGCTAGTAC 59.700 50.000 21.69 7.49 34.99 2.73
778 806 2.301296 CCCATGCATGCTAGCTAGTACT 59.699 50.000 21.69 0.00 34.99 2.73
779 807 3.511540 CCCATGCATGCTAGCTAGTACTA 59.488 47.826 21.69 1.89 34.99 1.82
1010 1051 2.583520 CTCCAGCTCAGCCTCCAC 59.416 66.667 0.00 0.00 0.00 4.02
1064 1105 0.678366 ACCGTTCCAGCAAACACACA 60.678 50.000 0.00 0.00 0.00 3.72
1065 1106 0.248458 CCGTTCCAGCAAACACACAC 60.248 55.000 0.00 0.00 0.00 3.82
1066 1107 0.449786 CGTTCCAGCAAACACACACA 59.550 50.000 0.00 0.00 0.00 3.72
1067 1108 1.793714 CGTTCCAGCAAACACACACAC 60.794 52.381 0.00 0.00 0.00 3.82
1206 1252 4.479993 CCCTTCCTCCAGCAGGCG 62.480 72.222 0.00 0.00 43.08 5.52
1459 1505 1.388065 CCAGGTACGCTCCTCTCCTG 61.388 65.000 0.00 0.00 43.46 3.86
1468 1514 0.617249 CTCCTCTCCTGTCCTGCCTT 60.617 60.000 0.00 0.00 0.00 4.35
1805 1869 2.350895 CACCCATTCCGCACCTCA 59.649 61.111 0.00 0.00 0.00 3.86
1832 1896 1.749334 GCTACGTCTCCTCCATGGGG 61.749 65.000 13.02 8.75 37.77 4.96
1835 1899 3.866582 GTCTCCTCCATGGGGCGG 61.867 72.222 13.02 10.46 40.66 6.13
1973 2037 2.264794 GACAGGGTCGTCGCCATT 59.735 61.111 7.78 0.00 0.00 3.16
2048 2112 2.914289 GGGATGCTGAGGTCAGGG 59.086 66.667 9.03 0.00 43.94 4.45
2051 2115 3.746949 GATGCTGAGGTCAGGGGCG 62.747 68.421 9.03 0.00 43.94 6.13
2084 2148 0.667792 GCGAGCTGGACGACTTCTTT 60.668 55.000 0.00 0.00 0.00 2.52
2234 2298 7.341445 ACAACAAGGCTAACAAATTAGAACA 57.659 32.000 0.00 0.00 40.38 3.18
2235 2299 7.777095 ACAACAAGGCTAACAAATTAGAACAA 58.223 30.769 0.00 0.00 40.38 2.83
2383 2447 4.711846 TGTATTCTTCCTAAGCAGAGCAGA 59.288 41.667 0.00 0.00 0.00 4.26
2390 2454 0.322648 TAAGCAGAGCAGAGCAGCAA 59.677 50.000 0.00 0.00 36.85 3.91
2530 2595 7.020827 AGTTGATGGTGAAAGGAAGAATCTA 57.979 36.000 0.00 0.00 0.00 1.98
2637 2702 6.174049 ACAAAAAGAGAGTTCTATAGGGTGC 58.826 40.000 0.00 0.00 31.96 5.01
2794 2859 3.111838 CTCACGATGGAGAAGATGAACG 58.888 50.000 0.00 0.00 37.05 3.95
2800 2865 1.205655 TGGAGAAGATGAACGAGGCAG 59.794 52.381 0.00 0.00 0.00 4.85
2911 2976 3.596214 GAACTTAAGAGGCATCGGTTCA 58.404 45.455 10.09 0.00 33.91 3.18
2947 3012 3.119990 GCAGCTGCAATGCAAAATTGATT 60.120 39.130 33.36 0.00 43.31 2.57
2951 3016 5.064707 AGCTGCAATGCAAAATTGATTGATC 59.935 36.000 9.92 0.00 38.41 2.92
2986 3053 7.195374 TGCAGGGTTATACAGTAGAGAAATT 57.805 36.000 0.00 0.00 0.00 1.82
3064 3131 7.526608 TGAATCAACCAAATCGAATCACTTAC 58.473 34.615 0.00 0.00 0.00 2.34
3110 3177 4.465632 TTTCGCTAAAGTAGGATCTGCA 57.534 40.909 0.00 0.00 0.00 4.41
3191 3259 2.910199 TGATTCACCATCAGCTGCTAC 58.090 47.619 9.47 0.00 36.94 3.58
3199 3267 2.479049 CCATCAGCTGCTACACAAATGC 60.479 50.000 9.47 0.00 0.00 3.56
3218 3286 6.985188 AATGCATGTGTTTACGTTCTCTAT 57.015 33.333 0.00 0.00 0.00 1.98
3231 3299 5.928153 ACGTTCTCTATAAAAAGCAAGTGC 58.072 37.500 0.00 0.00 42.49 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 110 1.613317 TAGTACGCCTGGCATGCACT 61.613 55.000 21.36 14.44 0.00 4.40
146 156 1.132657 TGGGTGGGTAGGAGTTGAAGA 60.133 52.381 0.00 0.00 0.00 2.87
174 184 8.519492 TTCTTTTCTTTTCTTTTGTCTGTGTG 57.481 30.769 0.00 0.00 0.00 3.82
214 224 9.550406 GCCAAATGTATTTACTACCAGTATGTA 57.450 33.333 0.00 0.00 29.64 2.29
216 226 8.559536 CAGCCAAATGTATTTACTACCAGTATG 58.440 37.037 0.00 0.00 29.64 2.39
222 238 5.828299 TGCAGCCAAATGTATTTACTACC 57.172 39.130 0.00 0.00 0.00 3.18
230 246 2.660189 GCAGTTGCAGCCAAATGTAT 57.340 45.000 0.00 0.00 45.88 2.29
257 273 4.024893 GCCACGGAGTTAATGTGACATATG 60.025 45.833 0.00 0.00 41.61 1.78
281 297 3.803082 CACTCGCCATTGCACCCG 61.803 66.667 0.00 0.00 37.32 5.28
314 330 5.643777 GCCCACATTACACTATCATATCACC 59.356 44.000 0.00 0.00 0.00 4.02
324 340 3.583526 TGTTAGGTGCCCACATTACACTA 59.416 43.478 1.45 0.00 31.17 2.74
346 362 4.829872 TCTGGAAACCCACGTTATGTAT 57.170 40.909 0.00 0.00 0.00 2.29
347 363 4.620589 TTCTGGAAACCCACGTTATGTA 57.379 40.909 0.00 0.00 0.00 2.29
375 391 3.003173 CCTCAACGGAGCCCCTCA 61.003 66.667 0.00 0.00 39.96 3.86
404 420 2.123897 AAACACACGCTGCCCCTT 60.124 55.556 0.00 0.00 0.00 3.95
515 531 0.108472 GCATTGCTGCCTCTTTTCCC 60.108 55.000 0.16 0.00 42.88 3.97
546 564 0.322975 AGCAGTACTCAGCACTTGGG 59.677 55.000 7.83 0.00 0.00 4.12
653 672 4.474113 CTGTCTTGAGTTGTACGTACTCC 58.526 47.826 25.12 15.47 41.02 3.85
654 673 4.474113 CCTGTCTTGAGTTGTACGTACTC 58.526 47.826 25.12 17.21 41.86 2.59
655 674 3.255149 CCCTGTCTTGAGTTGTACGTACT 59.745 47.826 25.12 8.29 0.00 2.73
696 720 1.551883 AGCCAGTTTTGCCATGAATCC 59.448 47.619 0.00 0.00 0.00 3.01
706 730 1.368579 CCCAGCCAAGCCAGTTTTG 59.631 57.895 0.00 0.00 0.00 2.44
737 761 3.125316 GGGAAAACGTATTCAGTCAGCTG 59.875 47.826 7.63 7.63 43.87 4.24
748 772 2.378038 AGCATGCATGGGAAAACGTAT 58.622 42.857 27.34 0.00 0.00 3.06
775 803 7.228507 CACGAGAGAGGAGTACTACTAGTAGTA 59.771 44.444 30.50 30.50 43.98 1.82
776 804 8.819303 CCACGAGAGAGGAGTACTACTAGTAGT 61.819 48.148 32.39 32.39 45.46 2.73
777 805 6.441274 CACGAGAGAGGAGTACTACTAGTAG 58.559 48.000 25.30 25.30 39.04 2.57
778 806 5.301551 CCACGAGAGAGGAGTACTACTAGTA 59.698 48.000 7.87 1.89 45.46 1.82
779 807 4.099881 CCACGAGAGAGGAGTACTACTAGT 59.900 50.000 7.87 0.00 45.46 2.57
809 837 2.125350 CCACTCTGCCTTCGCCTC 60.125 66.667 0.00 0.00 0.00 4.70
811 839 2.743928 CACCACTCTGCCTTCGCC 60.744 66.667 0.00 0.00 0.00 5.54
813 841 1.374758 GACCACCACTCTGCCTTCG 60.375 63.158 0.00 0.00 0.00 3.79
816 844 1.892819 CGATGACCACCACTCTGCCT 61.893 60.000 0.00 0.00 0.00 4.75
1010 1051 2.361610 GTGGTGGTGCATGGGAGG 60.362 66.667 0.00 0.00 0.00 4.30
1064 1105 0.650512 CGACTCAAGTTTGTGCGTGT 59.349 50.000 0.00 0.00 0.00 4.49
1065 1106 0.042188 CCGACTCAAGTTTGTGCGTG 60.042 55.000 0.00 0.00 0.00 5.34
1066 1107 1.772063 GCCGACTCAAGTTTGTGCGT 61.772 55.000 0.00 0.00 0.00 5.24
1067 1108 1.082756 GCCGACTCAAGTTTGTGCG 60.083 57.895 0.00 0.00 0.00 5.34
1398 1444 2.487428 CAGAGCCAGTCGTCGAGG 59.513 66.667 0.00 0.00 0.00 4.63
1459 1505 0.811616 CACGCATAGGAAGGCAGGAC 60.812 60.000 0.00 0.00 31.14 3.85
1468 1514 0.531311 CTGAGCATGCACGCATAGGA 60.531 55.000 21.98 0.00 34.91 2.94
1607 1671 1.454111 CGGGTCGATCCTGGTCTCT 60.454 63.158 14.05 0.00 38.86 3.10
1655 1719 0.868406 CGTTGAGCTTGAACTCCACC 59.132 55.000 7.68 0.00 35.72 4.61
1896 1960 2.460918 CCGGAACTCGTACATCATGAC 58.539 52.381 0.00 0.00 37.11 3.06
2084 2148 2.356432 CCTGCCTTCCACAATCTCATCA 60.356 50.000 0.00 0.00 0.00 3.07
2193 2257 3.389983 TGTTGTACTATCTACCATGCCCC 59.610 47.826 0.00 0.00 0.00 5.80
2383 2447 1.302832 GCCACTACCACTTGCTGCT 60.303 57.895 0.00 0.00 0.00 4.24
2390 2454 1.418908 AACTGCCTGCCACTACCACT 61.419 55.000 0.00 0.00 0.00 4.00
2530 2595 1.541588 GCTGCTTTCCTTTTCCGATGT 59.458 47.619 0.00 0.00 0.00 3.06
2580 2645 1.748122 CTGCCCACATCTCCACAGC 60.748 63.158 0.00 0.00 0.00 4.40
2637 2702 1.398390 GCACAAGGGCTCATTCTAACG 59.602 52.381 0.00 0.00 0.00 3.18
2757 2822 9.878667 TCCATCGTGAGTAAAATAATCAGTTTA 57.121 29.630 0.00 0.00 32.99 2.01
2759 2824 8.258007 TCTCCATCGTGAGTAAAATAATCAGTT 58.742 33.333 0.00 0.00 32.99 3.16
2761 2826 8.648557 TTCTCCATCGTGAGTAAAATAATCAG 57.351 34.615 0.00 0.00 32.99 2.90
2794 2859 6.052405 AGATCATATTGAGAATCCTGCCTC 57.948 41.667 0.00 0.00 0.00 4.70
2800 2865 6.030548 TGTCGGAGATCATATTGAGAATCC 57.969 41.667 0.00 0.00 40.67 3.01
2911 2976 2.651071 GCTGCTGCTCCTTTTCCTT 58.349 52.632 8.53 0.00 36.03 3.36
2947 3012 3.637184 TGCAAAGCAGCTCAGATCA 57.363 47.368 0.00 0.00 33.32 2.92
2986 3053 3.807622 GGTTTACGCTGCTGCTTATCATA 59.192 43.478 14.03 0.00 36.97 2.15
3110 3177 5.127682 ACTGATGTTTTCTTGGTTCTTTGCT 59.872 36.000 0.00 0.00 0.00 3.91
3164 3231 6.774170 AGCAGCTGATGGTGAATCAAATAATA 59.226 34.615 20.43 0.00 44.77 0.98
3167 3234 4.529897 AGCAGCTGATGGTGAATCAAATA 58.470 39.130 20.43 0.00 44.77 1.40
3168 3235 3.362706 AGCAGCTGATGGTGAATCAAAT 58.637 40.909 20.43 0.00 44.77 2.32
3170 3237 2.502142 AGCAGCTGATGGTGAATCAA 57.498 45.000 20.43 0.00 44.77 2.57
3172 3239 2.611292 GTGTAGCAGCTGATGGTGAATC 59.389 50.000 20.43 0.00 43.76 2.52
3184 3252 2.256174 CACATGCATTTGTGTAGCAGC 58.744 47.619 11.53 0.00 42.14 5.25
3199 3267 9.262472 GCTTTTTATAGAGAACGTAAACACATG 57.738 33.333 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.