Multiple sequence alignment - TraesCS2B01G552700

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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 TraesCS2B01G552700 chr2B 100.000 2126 0 0 1 2126 748699757 748701882 0.000000e+00 3927
1 TraesCS2B01G552700 chr2A 92.817 2144 114 22 1 2126 744978649 744980770 0.000000e+00 3070
2 TraesCS2B01G552700 chr2D 88.200 1322 105 23 1 1286 613321088 613322394 0.000000e+00 1530
3 TraesCS2B01G552700 chr2D 92.849 839 60 0 1288 2126 613322459 613323297 0.000000e+00 1218
4 TraesCS2B01G552700 chr2D 97.710 131 3 0 1 131 19723836 19723966 2.120000e-55 226
5 TraesCS2B01G552700 chr2D 96.947 131 4 0 1 131 19747689 19747819 9.880000e-54 220
6 TraesCS2B01G552700 chr5D 98.473 131 2 0 1 131 473056996 473056866 4.560000e-57 231
7 TraesCS2B01G552700 chr1B 98.473 131 2 0 1 131 34337429 34337559 4.560000e-57 231
8 TraesCS2B01G552700 chr5B 97.710 131 3 0 1 131 617340120 617339990 2.120000e-55 226
9 TraesCS2B01G552700 chr4D 97.710 131 3 0 1 131 446596798 446596668 2.120000e-55 226
10 TraesCS2B01G552700 chr4B 96.947 131 4 0 1 131 381141553 381141423 9.880000e-54 220


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 TraesCS2B01G552700 chr2B 748699757 748701882 2125 False 3927 3927 100.0000 1 2126 1 chr2B.!!$F1 2125
1 TraesCS2B01G552700 chr2A 744978649 744980770 2121 False 3070 3070 92.8170 1 2126 1 chr2A.!!$F1 2125
2 TraesCS2B01G552700 chr2D 613321088 613323297 2209 False 1374 1530 90.5245 1 2126 2 chr2D.!!$F3 2125

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
135 138 0.323451 TGCCTCTAGAGTCGGCTGAA 60.323 55.0 18.42 0.0 44.09 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1147 1207 0.244994 ACTAGAGCGCTGTCAAGTGG 59.755 55.0 18.48 0.18 34.3 4.0 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 47 4.081309 AGTTTGGCATGGATTTGGATCAAG 60.081 41.667 0.00 0.00 33.77 3.02
109 111 1.469703 TGCTGTACACATGATGCTTGC 59.530 47.619 0.00 0.00 0.00 4.01
135 138 0.323451 TGCCTCTAGAGTCGGCTGAA 60.323 55.000 18.42 0.00 44.09 3.02
136 139 0.818296 GCCTCTAGAGTCGGCTGAAA 59.182 55.000 18.42 0.00 40.62 2.69
137 140 1.204941 GCCTCTAGAGTCGGCTGAAAA 59.795 52.381 18.42 0.00 40.62 2.29
138 141 2.882324 CCTCTAGAGTCGGCTGAAAAC 58.118 52.381 18.42 0.00 0.00 2.43
139 142 2.231478 CCTCTAGAGTCGGCTGAAAACA 59.769 50.000 18.42 0.00 0.00 2.83
177 182 5.188948 GCCCCTTCATTAGTATTTTTGGGTT 59.811 40.000 0.00 0.00 0.00 4.11
217 222 4.517285 AGAAGAACGCATGTGGACATAAT 58.483 39.130 11.65 0.00 34.26 1.28
224 229 4.887071 ACGCATGTGGACATAATTACCAAT 59.113 37.500 11.65 0.00 35.40 3.16
274 284 7.961326 AGTTTCTCAATTTAACCCAGCATAT 57.039 32.000 0.00 0.00 0.00 1.78
359 380 3.317993 ACAATTTTCTTCCACTTGTCCCG 59.682 43.478 0.00 0.00 0.00 5.14
395 416 7.626452 GCCAGGAAGTTTTAACATGTATGACTC 60.626 40.741 0.00 0.00 0.00 3.36
420 441 9.880157 TCCAACTCAAATTTACAGTATAGGTAC 57.120 33.333 3.07 0.00 0.00 3.34
445 466 8.679288 CTGAAATCAGCTGTATTGGTTTTAAG 57.321 34.615 14.67 3.18 37.15 1.85
446 467 7.090173 TGAAATCAGCTGTATTGGTTTTAAGC 58.910 34.615 14.67 0.00 29.44 3.09
447 468 6.588719 AATCAGCTGTATTGGTTTTAAGCA 57.411 33.333 14.67 0.00 33.08 3.91
461 496 1.091537 TAAGCAAACACCATAGCGCC 58.908 50.000 2.29 0.00 0.00 6.53
475 510 2.572191 AGCGCCAATTCATGTTCATG 57.428 45.000 2.29 6.46 0.00 3.07
494 529 1.535028 TGTCAAGCAAACACCATAGCG 59.465 47.619 0.00 0.00 0.00 4.26
541 587 8.685427 CCATTTCCTCATGTACATTAATGAACA 58.315 33.333 22.16 3.97 32.60 3.18
610 656 4.226761 GTTAGCATTTTTGTCCAAGGTCG 58.773 43.478 0.00 0.00 0.00 4.79
639 685 9.599866 TGAACTGGTACTTGTTAATCTCATATG 57.400 33.333 0.00 0.00 0.00 1.78
653 699 9.565090 TTAATCTCATATGTCTGGATTTCCTTG 57.435 33.333 1.90 0.00 36.82 3.61
658 704 3.507162 TGTCTGGATTTCCTTGCAAGA 57.493 42.857 28.05 8.51 36.82 3.02
664 710 4.897140 TGGATTTCCTTGCAAGATTTTGG 58.103 39.130 28.05 10.96 36.82 3.28
688 734 9.967451 TGGATCACTTTATTATTTTCACCTGTA 57.033 29.630 0.00 0.00 0.00 2.74
740 786 2.359900 GTTGTGGATGAGTAGGCTTGG 58.640 52.381 0.00 0.00 0.00 3.61
811 858 7.250569 TCTGTCAGTTGTTTTCTTTTGATCAC 58.749 34.615 0.00 0.00 0.00 3.06
882 929 6.541641 GCAGATCTCAGAGGACATTTAATTGT 59.458 38.462 2.71 2.71 0.00 2.71
887 934 6.650807 TCTCAGAGGACATTTAATTGTGTGAC 59.349 38.462 7.69 0.00 0.00 3.67
910 957 5.240183 ACATGAAGTCTGTTTGTGGATTCTG 59.760 40.000 0.00 0.00 0.00 3.02
922 969 8.028354 TGTTTGTGGATTCTGTTTTATGCATAG 58.972 33.333 6.50 0.00 0.00 2.23
965 1012 1.372582 CCGTAGTGCTGCAACATCAT 58.627 50.000 2.77 0.00 0.00 2.45
977 1024 3.120683 TGCAACATCATCGTTTCTCGTTC 60.121 43.478 0.00 0.00 40.80 3.95
994 1041 1.761198 GTTCGGGACCAGTAAGCCTAT 59.239 52.381 0.00 0.00 0.00 2.57
1041 1088 1.271379 GGCTTTCTTGGTAGTGGCTCA 60.271 52.381 0.00 0.00 0.00 4.26
1064 1111 2.753989 TGCAAGAACATTGACGTGTG 57.246 45.000 0.00 0.00 31.49 3.82
1135 1195 0.676736 GGGGTTTTGATTGTTCGGCA 59.323 50.000 0.00 0.00 0.00 5.69
1136 1196 1.336795 GGGGTTTTGATTGTTCGGCAG 60.337 52.381 0.00 0.00 0.00 4.85
1137 1197 1.611491 GGGTTTTGATTGTTCGGCAGA 59.389 47.619 0.00 0.00 0.00 4.26
1138 1198 2.035321 GGGTTTTGATTGTTCGGCAGAA 59.965 45.455 0.00 0.00 0.00 3.02
1139 1199 3.308530 GGTTTTGATTGTTCGGCAGAAG 58.691 45.455 0.00 0.00 36.99 2.85
1140 1200 2.704725 TTTGATTGTTCGGCAGAAGC 57.295 45.000 0.00 0.00 36.99 3.86
1141 1201 1.896220 TTGATTGTTCGGCAGAAGCT 58.104 45.000 0.00 0.00 41.70 3.74
1142 1202 2.760634 TGATTGTTCGGCAGAAGCTA 57.239 45.000 0.00 0.00 41.70 3.32
1143 1203 3.266510 TGATTGTTCGGCAGAAGCTAT 57.733 42.857 0.00 0.00 41.70 2.97
1144 1204 3.609853 TGATTGTTCGGCAGAAGCTATT 58.390 40.909 0.00 0.00 41.70 1.73
1145 1205 3.374988 TGATTGTTCGGCAGAAGCTATTG 59.625 43.478 0.00 0.00 41.70 1.90
1146 1206 1.737838 TGTTCGGCAGAAGCTATTGG 58.262 50.000 0.00 0.00 41.70 3.16
1147 1207 0.378610 GTTCGGCAGAAGCTATTGGC 59.621 55.000 12.32 12.32 41.70 4.52
1152 1212 1.467920 GCAGAAGCTATTGGCCACTT 58.532 50.000 3.88 5.24 43.05 3.16
1196 1256 8.679725 TCTCTGTCCTAATCCTACCTTATACAT 58.320 37.037 0.00 0.00 0.00 2.29
1383 1506 0.397254 GCAGGCTGGTCCTAGGACTA 60.397 60.000 35.12 30.19 45.52 2.59
1496 1619 1.702401 TGCAAGTGATCCTGGGTTACA 59.298 47.619 4.56 0.00 0.00 2.41
1530 1653 5.316167 TCAAGAGGCAGCTCAAGAAATTTA 58.684 37.500 0.00 0.00 0.00 1.40
1633 1756 2.362077 TCAACTTCAGCCAAAAGGAAGC 59.638 45.455 0.00 0.00 41.26 3.86
1679 1802 3.349927 TGTTTGCTCCAAGATCAGATGG 58.650 45.455 0.00 0.32 38.09 3.51
1767 1890 5.350914 GGCCGATCATGATTTATCTCTTGAG 59.649 44.000 10.14 0.00 34.13 3.02
1775 1898 3.592898 TTTATCTCTTGAGCAGCACGA 57.407 42.857 0.00 0.00 0.00 4.35
1840 1963 1.725641 TGCCGCAACTTCAGATACAG 58.274 50.000 0.00 0.00 0.00 2.74
1848 1971 6.238786 CCGCAACTTCAGATACAGTAGATAGT 60.239 42.308 0.00 0.00 0.00 2.12
1896 2019 1.023513 AGCGCCATCTCAAGAAGTGC 61.024 55.000 2.29 9.66 37.84 4.40
1938 2061 3.732849 GGAAGGGGTGCCTCAGGG 61.733 72.222 0.00 0.00 0.00 4.45
2049 2172 2.747855 GGAGGAAAGCGGTGCCAG 60.748 66.667 9.14 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 47 6.259550 ACAAACCTATCTCAGAATGCAAAC 57.740 37.500 0.00 0.00 34.76 2.93
109 111 2.939103 CCGACTCTAGAGGCAAAAATGG 59.061 50.000 25.31 13.00 35.77 3.16
177 182 8.622157 CGTTCTTCTCATACTAGGATTTACTCA 58.378 37.037 0.00 0.00 0.00 3.41
344 365 1.344065 TTAGCGGGACAAGTGGAAGA 58.656 50.000 0.00 0.00 0.00 2.87
395 416 9.886132 AGTACCTATACTGTAAATTTGAGTTGG 57.114 33.333 0.00 8.37 40.32 3.77
420 441 7.274250 GCTTAAAACCAATACAGCTGATTTCAG 59.726 37.037 23.35 6.79 46.40 3.02
445 466 0.173255 ATTGGCGCTATGGTGTTTGC 59.827 50.000 7.64 0.00 0.00 3.68
446 467 2.094803 TGAATTGGCGCTATGGTGTTTG 60.095 45.455 7.64 0.00 0.00 2.93
447 468 2.166829 TGAATTGGCGCTATGGTGTTT 58.833 42.857 7.64 0.00 0.00 2.83
449 470 1.677576 CATGAATTGGCGCTATGGTGT 59.322 47.619 7.64 0.00 0.00 4.16
453 474 3.696281 TGAACATGAATTGGCGCTATG 57.304 42.857 7.64 0.00 0.00 2.23
461 496 6.201234 TGTTTGCTTGACATGAACATGAATTG 59.799 34.615 19.56 9.09 41.20 2.32
475 510 1.729149 GCGCTATGGTGTTTGCTTGAC 60.729 52.381 0.00 0.00 0.00 3.18
494 529 8.882415 AATGGTGAATCATGATTAGAATTTGC 57.118 30.769 20.75 6.72 0.00 3.68
541 587 1.745087 CAGCCGGTGCATGTATTTTCT 59.255 47.619 1.90 0.00 41.13 2.52
610 656 8.997621 TGAGATTAACAAGTACCAGTTCATAC 57.002 34.615 4.03 0.38 0.00 2.39
638 684 3.507162 TCTTGCAAGGAAATCCAGACA 57.493 42.857 25.73 0.00 38.89 3.41
639 685 5.397142 AAATCTTGCAAGGAAATCCAGAC 57.603 39.130 25.73 0.00 38.89 3.51
740 786 8.142551 TGAAGGAGAACTCAAAAGACTAAGTAC 58.857 37.037 4.23 0.00 0.00 2.73
887 934 5.240183 ACAGAATCCACAAACAGACTTCATG 59.760 40.000 0.00 0.00 0.00 3.07
922 969 2.953466 AAATCATGTGCACTGCATCC 57.047 45.000 19.41 0.00 41.91 3.51
965 1012 1.286880 GGTCCCGAACGAGAAACGA 59.713 57.895 0.00 0.00 45.77 3.85
977 1024 1.810412 GCAATAGGCTTACTGGTCCCG 60.810 57.143 0.00 0.00 40.25 5.14
1029 1076 0.399833 TGCAATGTGAGCCACTACCA 59.600 50.000 6.83 0.00 35.11 3.25
1041 1088 3.066621 ACACGTCAATGTTCTTGCAATGT 59.933 39.130 0.00 0.00 0.00 2.71
1135 1195 2.040278 TGTCAAGTGGCCAATAGCTTCT 59.960 45.455 7.24 0.00 43.05 2.85
1136 1196 2.421424 CTGTCAAGTGGCCAATAGCTTC 59.579 50.000 7.24 0.00 43.05 3.86
1137 1197 2.440409 CTGTCAAGTGGCCAATAGCTT 58.560 47.619 7.24 3.14 43.05 3.74
1138 1198 1.952367 GCTGTCAAGTGGCCAATAGCT 60.952 52.381 16.46 3.13 43.05 3.32
1139 1199 0.453390 GCTGTCAAGTGGCCAATAGC 59.547 55.000 7.24 8.79 42.60 2.97
1140 1200 0.729116 CGCTGTCAAGTGGCCAATAG 59.271 55.000 7.24 0.49 0.00 1.73
1141 1201 1.305219 GCGCTGTCAAGTGGCCAATA 61.305 55.000 7.24 0.00 34.30 1.90
1142 1202 2.629656 GCGCTGTCAAGTGGCCAAT 61.630 57.895 7.24 1.65 34.30 3.16
1143 1203 3.286751 GCGCTGTCAAGTGGCCAA 61.287 61.111 7.24 0.00 34.30 4.52
1144 1204 4.254709 AGCGCTGTCAAGTGGCCA 62.255 61.111 10.39 0.00 34.30 5.36
1145 1205 2.507110 TAGAGCGCTGTCAAGTGGCC 62.507 60.000 18.48 0.00 34.30 5.36
1146 1206 1.079819 TAGAGCGCTGTCAAGTGGC 60.080 57.895 18.48 0.00 34.30 5.01
1147 1207 0.244994 ACTAGAGCGCTGTCAAGTGG 59.755 55.000 18.48 0.18 34.30 4.00
1152 1212 2.162608 GAGAAAGACTAGAGCGCTGTCA 59.837 50.000 18.48 0.00 33.56 3.58
1196 1256 6.811574 AGGTCCATCCCAGTACACATATATA 58.188 40.000 0.00 0.00 36.75 0.86
1203 1263 4.772886 ATTAAGGTCCATCCCAGTACAC 57.227 45.455 0.00 0.00 36.75 2.90
1205 1265 6.042781 TGTCATATTAAGGTCCATCCCAGTAC 59.957 42.308 0.00 0.00 36.75 2.73
1383 1506 2.610438 ACAGATTTGGCATTGGTCCT 57.390 45.000 0.00 0.00 0.00 3.85
1496 1619 0.398318 GCCTCTTGAAGTGTCCACCT 59.602 55.000 0.00 0.00 0.00 4.00
1502 1625 0.761187 TGAGCTGCCTCTTGAAGTGT 59.239 50.000 0.00 0.00 38.93 3.55
1503 1626 1.805345 CTTGAGCTGCCTCTTGAAGTG 59.195 52.381 0.00 0.00 38.93 3.16
1530 1653 1.915228 AGGCACTGTTGTGGACTGT 59.085 52.632 0.00 0.00 43.97 3.55
1633 1756 3.201290 GTGACAGCTCATAATCACCTGG 58.799 50.000 0.00 0.00 36.31 4.45
1679 1802 7.302524 TGCCGTTGTTCTATCAATAAAAAGAC 58.697 34.615 0.00 0.00 0.00 3.01
1767 1890 0.670546 TAAGCTCAACCTCGTGCTGC 60.671 55.000 0.00 0.00 35.97 5.25
1775 1898 1.612442 TCGGGGCTAAGCTCAACCT 60.612 57.895 0.00 0.00 0.00 3.50
1824 1947 6.730175 ACTATCTACTGTATCTGAAGTTGCG 58.270 40.000 0.00 0.00 0.00 4.85
1840 1963 6.663953 TGCTCCCCATTATCAGTACTATCTAC 59.336 42.308 0.00 0.00 0.00 2.59
1848 1971 5.191722 ACTTTTCTGCTCCCCATTATCAGTA 59.808 40.000 0.00 0.00 0.00 2.74
1896 2019 1.993956 TGGAACACCCATTGAACCTG 58.006 50.000 0.00 0.00 40.82 4.00
1932 2055 1.839994 TGGGAAATACAGAGCCCTGAG 59.160 52.381 0.65 0.00 43.02 3.35
1938 2061 0.947244 CGCCATGGGAAATACAGAGC 59.053 55.000 15.13 0.00 0.00 4.09
1944 2067 2.203280 CCGCCGCCATGGGAAATA 60.203 61.111 15.13 0.00 38.63 1.40
2049 2172 0.609131 TTTTGGTGCAGCCTAGCTCC 60.609 55.000 14.36 7.35 45.82 4.70


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

AutoCloner maintained by Alex Coulton.