Multiple sequence alignment - TraesCS1A01G319500

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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 TraesCS1A01G319500 chr1A 100.000 2309 0 0 1 2309 510374620 510372312 0.000000e+00 4265.0
1 TraesCS1A01G319500 chr1B 87.599 2137 145 38 2 2082 557923156 557921084 0.000000e+00 2368.0
2 TraesCS1A01G319500 chr1B 88.106 227 13 5 2097 2309 557920705 557920479 8.190000e-65 257.0
3 TraesCS1A01G319500 chr1D 92.301 1195 71 12 920 2095 413416225 413415033 0.000000e+00 1677.0
4 TraesCS1A01G319500 chr1D 86.042 480 59 8 205 681 413417235 413416761 2.050000e-140 508.0
5 TraesCS1A01G319500 chr1D 92.019 213 13 1 2 210 413572468 413572256 1.730000e-76 296.0
6 TraesCS1A01G319500 chr1D 84.716 229 18 9 2097 2309 413414751 413414524 1.800000e-51 213.0
7 TraesCS1A01G319500 chr2D 75.691 543 96 24 394 916 430508219 430508745 2.960000e-59 239.0
8 TraesCS1A01G319500 chr2D 80.068 296 39 5 392 686 277681565 277681289 3.890000e-48 202.0
9 TraesCS1A01G319500 chr2A 79.795 292 41 5 392 683 293935153 293935426 1.810000e-46 196.0
10 TraesCS1A01G319500 chr2A 94.286 35 2 0 230 264 37098767 37098733 1.000000e-03 54.7


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 TraesCS1A01G319500 chr1A 510372312 510374620 2308 True 4265.000000 4265 100.000000 1 2309 1 chr1A.!!$R1 2308
1 TraesCS1A01G319500 chr1B 557920479 557923156 2677 True 1312.500000 2368 87.852500 2 2309 2 chr1B.!!$R1 2307
2 TraesCS1A01G319500 chr1D 413414524 413417235 2711 True 799.333333 1677 87.686333 205 2309 3 chr1D.!!$R2 2104
3 TraesCS1A01G319500 chr2D 430508219 430508745 526 False 239.000000 239 75.691000 394 916 1 chr2D.!!$F1 522

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
755 802 0.669318 TGTTCGAGTTCGTCCATGCC 60.669 55.0 1.07 0.0 40.8 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 2111 0.24746 GCAATTCAAGCCCAGGTTCC 59.753 55.0 0.0 0.0 0.0 3.62 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
32 33 1.229529 GGACCCCTCCTCCACTCAA 60.230 63.158 0.00 0.00 33.07 3.02
47 48 4.777366 TCCACTCAACTCTCCAATGACATA 59.223 41.667 0.00 0.00 0.00 2.29
49 50 5.939883 CCACTCAACTCTCCAATGACATAAA 59.060 40.000 0.00 0.00 0.00 1.40
142 147 2.169352 TCTGAGGCTGAGCAATCTTACC 59.831 50.000 6.82 0.00 0.00 2.85
160 165 5.197189 TCTTACCCCCTCTCTACTTAATCCA 59.803 44.000 0.00 0.00 0.00 3.41
161 166 4.578149 ACCCCCTCTCTACTTAATCCAT 57.422 45.455 0.00 0.00 0.00 3.41
174 179 5.883661 ACTTAATCCATGCTTTTGATGTCG 58.116 37.500 0.00 0.00 0.00 4.35
198 203 2.357075 TGCTTGTGTACGTCACCAAAA 58.643 42.857 13.24 1.69 45.61 2.44
227 232 6.513033 CACCCCTATAAACTATCTCCCCTAT 58.487 44.000 0.00 0.00 0.00 2.57
266 272 9.218440 TGATACACATCATTGCATATTCGTAAT 57.782 29.630 0.00 0.00 36.22 1.89
352 359 6.871492 TGACAAGCGTTGTGATAGATAAAAGA 59.129 34.615 7.89 0.00 45.52 2.52
390 398 1.670971 ATACGTCAACTCGTTGCGCG 61.671 55.000 18.98 18.41 43.80 6.86
485 496 8.044309 TCATCCCGAATAGATCTTGTAAAACAA 58.956 33.333 0.00 0.00 36.54 2.83
527 538 1.623811 GCAGGCTCCCCTATATTCGAA 59.376 52.381 0.00 0.00 40.33 3.71
542 553 3.328382 TTCGAACCCCAGTCTGTTATG 57.672 47.619 0.00 0.00 0.00 1.90
544 555 2.635915 TCGAACCCCAGTCTGTTATGTT 59.364 45.455 0.00 0.00 0.00 2.71
590 601 2.007608 GATCCTGTAAAGCCGGTCAAC 58.992 52.381 1.90 0.00 0.00 3.18
623 634 4.700365 CTCTCGACGCCGTGCACA 62.700 66.667 18.64 0.00 37.05 4.57
644 655 3.311110 AGCGAACAGGCGGAGGAA 61.311 61.111 0.00 0.00 38.18 3.36
645 656 2.125106 GCGAACAGGCGGAGGAAT 60.125 61.111 0.00 0.00 0.00 3.01
657 668 1.153549 GAGGAATTCGCCGACAGCT 60.154 57.895 0.00 0.00 40.39 4.24
709 731 1.666872 GCGCGTCACCAAAGTAGGT 60.667 57.895 8.43 0.00 44.48 3.08
734 756 0.817013 GCCAAATCAGGCGGAAATCA 59.183 50.000 0.00 0.00 46.12 2.57
735 757 1.204467 GCCAAATCAGGCGGAAATCAA 59.796 47.619 0.00 0.00 46.12 2.57
736 758 2.159057 GCCAAATCAGGCGGAAATCAAT 60.159 45.455 0.00 0.00 46.12 2.57
755 802 0.669318 TGTTCGAGTTCGTCCATGCC 60.669 55.000 1.07 0.00 40.80 4.40
758 805 1.079819 CGAGTTCGTCCATGCCTGT 60.080 57.895 0.00 0.00 34.11 4.00
814 875 6.777213 AATGTTTACTGTGTGGGTTTACAA 57.223 33.333 0.00 0.00 31.36 2.41
818 879 7.612677 TGTTTACTGTGTGGGTTTACAAAATT 58.387 30.769 0.00 0.00 31.36 1.82
826 887 5.105473 TGTGGGTTTACAAAATTTGTTCCGA 60.105 36.000 16.99 11.18 42.22 4.55
828 889 5.127356 TGGGTTTACAAAATTTGTTCCGACT 59.873 36.000 16.99 0.00 42.22 4.18
829 890 5.460748 GGGTTTACAAAATTTGTTCCGACTG 59.539 40.000 16.99 0.00 42.22 3.51
830 891 6.267070 GGTTTACAAAATTTGTTCCGACTGA 58.733 36.000 16.99 0.00 42.22 3.41
831 892 6.197655 GGTTTACAAAATTTGTTCCGACTGAC 59.802 38.462 16.99 4.85 42.22 3.51
891 1215 5.697633 CGTATAGTGTTTTTACAGGTGGTGT 59.302 40.000 0.00 0.00 43.86 4.16
894 1218 9.054922 GTATAGTGTTTTTACAGGTGGTGTTTA 57.945 33.333 0.00 0.00 40.94 2.01
895 1219 8.700439 ATAGTGTTTTTACAGGTGGTGTTTAT 57.300 30.769 0.00 0.00 40.94 1.40
898 1224 5.069251 TGTTTTTACAGGTGGTGTTTATGGG 59.931 40.000 0.00 0.00 40.94 4.00
899 1225 4.726035 TTTACAGGTGGTGTTTATGGGA 57.274 40.909 0.00 0.00 40.94 4.37
900 1226 4.938575 TTACAGGTGGTGTTTATGGGAT 57.061 40.909 0.00 0.00 40.94 3.85
917 1243 3.181457 TGGGATTGCTAGAGATGCTCTTG 60.181 47.826 1.88 2.09 41.50 3.02
928 1254 2.281484 GCTCTTGCACCGAACCCA 60.281 61.111 0.00 0.00 39.41 4.51
1330 1662 1.049289 ACGAGGAGATAAGCACCCCC 61.049 60.000 0.00 0.00 0.00 5.40
1366 1698 2.802816 GCTATCTATCTTGGGTGTTGCG 59.197 50.000 0.00 0.00 0.00 4.85
1374 1706 0.106918 TTGGGTGTTGCGAGGTTTCT 60.107 50.000 0.00 0.00 0.00 2.52
1418 1750 1.398390 GCTGTATACTGGTGCTTGTGC 59.602 52.381 11.26 0.00 40.20 4.57
1434 1766 4.327087 GCTTGTGCATTTCCCGAAATAAAG 59.673 41.667 2.45 6.19 38.84 1.85
1478 1810 2.033801 GTGGATGATAACATGTGCTGGC 59.966 50.000 0.00 0.00 36.82 4.85
1481 1813 2.785540 TGATAACATGTGCTGGCTGA 57.214 45.000 0.00 0.00 0.00 4.26
1485 1817 4.463539 TGATAACATGTGCTGGCTGAAATT 59.536 37.500 0.00 0.00 0.00 1.82
1543 1876 5.273944 CCAATTTCGGCAGCTCTTTATAAC 58.726 41.667 0.00 0.00 0.00 1.89
1548 1882 4.679662 TCGGCAGCTCTTTATAACACTAC 58.320 43.478 0.00 0.00 0.00 2.73
1567 1914 7.394816 ACACTACCAAATTAGATTGCTGTACT 58.605 34.615 0.00 0.00 0.00 2.73
1657 2006 8.442660 ACTAAATCTTCATAGGGATTAGGGAG 57.557 38.462 0.00 0.00 32.65 4.30
1746 2096 4.650734 TGCATTGTTAGACATGAGTCCAA 58.349 39.130 0.00 0.00 46.15 3.53
1761 2111 7.121759 ACATGAGTCCAAAAGATATCAAACAGG 59.878 37.037 5.32 0.51 29.80 4.00
1764 2114 6.552008 AGTCCAAAAGATATCAAACAGGGAA 58.448 36.000 5.32 0.00 0.00 3.97
1784 2134 0.324091 CCTGGGCTTGAATTGCTCCT 60.324 55.000 0.00 0.00 0.00 3.69
1805 2155 4.398319 CTTGACCAATGGTAAGGACAAGT 58.602 43.478 17.61 0.00 45.86 3.16
1811 2161 4.700213 CCAATGGTAAGGACAAGTACCTTG 59.300 45.833 9.13 2.54 45.74 3.61
1904 2257 4.598373 TGTACCTTACCTTTGGGCTTAGAA 59.402 41.667 0.00 0.00 35.63 2.10
1907 2260 5.651303 ACCTTACCTTTGGGCTTAGAATTT 58.349 37.500 0.00 0.00 35.63 1.82
1910 2263 7.396339 ACCTTACCTTTGGGCTTAGAATTTTAG 59.604 37.037 0.00 0.00 35.63 1.85
1942 2295 6.017605 GCACATACATGAAGATCCCAAACTAG 60.018 42.308 0.00 0.00 0.00 2.57
1971 2324 6.224665 TCATGCCAATTGGAAGAAATTAGG 57.775 37.500 29.02 4.98 37.39 2.69
1996 2349 7.819415 GGTTTTGGCTTTCAAATTAGCTTATCT 59.181 33.333 0.00 0.00 43.95 1.98
2044 2398 4.148079 TGGTATGCACTGAAATTTGTGGA 58.852 39.130 9.85 7.77 38.76 4.02
2095 2532 5.652452 GGTGCAAACTAAATCTTCATAGGGT 59.348 40.000 0.00 0.00 0.00 4.34
2137 2855 7.068593 TGCTTCACTATTATTTGATGGAAAGGG 59.931 37.037 0.00 0.00 0.00 3.95
2141 2859 9.713684 TCACTATTATTTGATGGAAAGGGATTT 57.286 29.630 0.00 0.00 0.00 2.17
2193 2911 2.288395 CCCTGAACTCGCTTGCAATTTT 60.288 45.455 0.00 0.00 0.00 1.82
2241 2960 6.857777 ACTAGCTCACAATTTATGATGCTC 57.142 37.500 12.65 0.00 34.53 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.431415 AGGGGTCCATTAGAAAGTTTGC 58.569 45.455 0.00 0.00 0.00 3.68
11 12 0.621862 GAGTGGAGGAGGGGTCCATT 60.622 60.000 0.00 0.00 45.91 3.16
142 147 3.906846 AGCATGGATTAAGTAGAGAGGGG 59.093 47.826 0.00 0.00 0.00 4.79
174 179 2.539003 TGACGTACACAAGCATGGC 58.461 52.632 0.00 0.00 0.00 4.40
198 203 6.017830 GGAGATAGTTTATAGGGGTGCTACT 58.982 44.000 0.00 0.00 0.00 2.57
266 272 5.385198 AGGTTGAATCTGGTGAAGCTTTAA 58.615 37.500 0.00 0.00 0.00 1.52
352 359 6.134787 CGTATTAAACGTGCAATTTGCTTT 57.865 33.333 21.19 15.34 46.72 3.51
384 391 0.173481 AGAGATGCTCTAACGCGCAA 59.827 50.000 5.73 0.00 39.28 4.85
390 398 6.428771 ACGGAATCTACTAGAGATGCTCTAAC 59.571 42.308 0.00 0.00 44.68 2.34
462 471 7.162761 TGTTGTTTTACAAGATCTATTCGGGA 58.837 34.615 0.00 0.00 39.00 5.14
500 511 2.621556 TAGGGGAGCCTGCAATTTTT 57.378 45.000 0.00 0.00 0.00 1.94
501 512 2.854736 ATAGGGGAGCCTGCAATTTT 57.145 45.000 0.00 0.00 0.00 1.82
527 538 4.225267 CCTCTAAACATAACAGACTGGGGT 59.775 45.833 7.51 0.00 0.00 4.95
542 553 2.019948 ACGGCCGAAATCCTCTAAAC 57.980 50.000 35.90 0.00 0.00 2.01
544 555 2.773993 AAACGGCCGAAATCCTCTAA 57.226 45.000 35.90 0.00 0.00 2.10
623 634 4.314440 TCCGCCTGTTCGCTGCTT 62.314 61.111 0.00 0.00 0.00 3.91
632 643 2.125106 GCGAATTCCTCCGCCTGT 60.125 61.111 0.00 0.00 45.06 4.00
652 663 4.479993 GATGCTCCGGCCAGCTGT 62.480 66.667 13.81 5.15 40.39 4.40
692 714 1.625616 CTACCTACTTTGGTGACGCG 58.374 55.000 3.53 3.53 41.05 6.01
709 731 2.124320 GCCTGATTTGGCCCGCTA 60.124 61.111 0.00 0.00 46.82 4.26
729 751 4.062293 TGGACGAACTCGAACATTGATTT 58.938 39.130 6.05 0.00 43.02 2.17
732 754 2.804697 TGGACGAACTCGAACATTGA 57.195 45.000 6.05 0.00 43.02 2.57
734 756 1.732259 GCATGGACGAACTCGAACATT 59.268 47.619 6.05 0.00 43.02 2.71
735 757 1.359848 GCATGGACGAACTCGAACAT 58.640 50.000 6.05 6.77 43.02 2.71
736 758 0.669318 GGCATGGACGAACTCGAACA 60.669 55.000 6.05 4.69 43.02 3.18
758 805 0.693049 GCTTCTTCTTCCCTGGGACA 59.307 55.000 16.85 1.53 0.00 4.02
814 875 1.265905 GGCGTCAGTCGGAACAAATTT 59.734 47.619 0.00 0.00 40.26 1.82
818 879 1.006571 GAGGCGTCAGTCGGAACAA 60.007 57.895 0.52 0.00 40.26 2.83
826 887 1.433879 GATACAGCGAGGCGTCAGT 59.566 57.895 7.26 4.50 0.00 3.41
828 889 1.091197 TACGATACAGCGAGGCGTCA 61.091 55.000 7.26 0.00 36.51 4.35
829 890 0.028505 TTACGATACAGCGAGGCGTC 59.971 55.000 0.00 0.00 36.51 5.19
830 891 0.452987 TTTACGATACAGCGAGGCGT 59.547 50.000 0.00 0.00 38.81 5.68
831 892 1.767289 ATTTACGATACAGCGAGGCG 58.233 50.000 0.00 0.00 34.83 5.52
839 902 6.638610 TCCCCTAAAACGAATTTACGATACA 58.361 36.000 0.00 0.00 37.03 2.29
873 936 5.980715 CCATAAACACCACCTGTAAAAACAC 59.019 40.000 0.00 0.00 30.51 3.32
875 938 5.302313 TCCCATAAACACCACCTGTAAAAAC 59.698 40.000 0.00 0.00 30.51 2.43
891 1215 5.555017 GAGCATCTCTAGCAATCCCATAAA 58.445 41.667 0.00 0.00 0.00 1.40
894 1218 3.699411 GAGCATCTCTAGCAATCCCAT 57.301 47.619 0.00 0.00 0.00 4.00
917 1243 1.445582 CTAGACGTGGGTTCGGTGC 60.446 63.158 0.00 0.00 34.94 5.01
922 1248 3.259902 GGAACAATCTAGACGTGGGTTC 58.740 50.000 0.00 5.09 34.08 3.62
928 1254 1.553704 GGTGGGGAACAATCTAGACGT 59.446 52.381 0.00 0.00 0.00 4.34
1330 1662 3.824117 TAGCGCGACGGCAGCATAG 62.824 63.158 12.10 0.00 39.84 2.23
1346 1678 4.302455 CTCGCAACACCCAAGATAGATAG 58.698 47.826 0.00 0.00 0.00 2.08
1366 1698 3.568430 CACCTTTGTACCCAAGAAACCTC 59.432 47.826 3.91 0.00 0.00 3.85
1374 1706 4.447138 AAGATCACACCTTTGTACCCAA 57.553 40.909 0.00 0.00 33.30 4.12
1418 1750 6.194796 TCTCAAGCTTTATTTCGGGAAATG 57.805 37.500 15.11 2.20 40.83 2.32
1424 1756 8.777413 TCATCAATATCTCAAGCTTTATTTCGG 58.223 33.333 0.00 0.00 0.00 4.30
1434 1766 4.996122 CCAGGACTCATCAATATCTCAAGC 59.004 45.833 0.00 0.00 0.00 4.01
1478 1810 1.891150 ACAGCAAGCCCAGAATTTCAG 59.109 47.619 0.00 0.00 0.00 3.02
1481 1813 0.883833 CGACAGCAAGCCCAGAATTT 59.116 50.000 0.00 0.00 0.00 1.82
1485 1817 1.148273 AAACGACAGCAAGCCCAGA 59.852 52.632 0.00 0.00 0.00 3.86
1543 1876 7.849804 AGTACAGCAATCTAATTTGGTAGTG 57.150 36.000 0.00 0.00 35.67 2.74
1548 1882 6.311200 GCCAAAAGTACAGCAATCTAATTTGG 59.689 38.462 8.65 8.65 44.33 3.28
1567 1914 4.662468 TCAGTGCATACAAAAGCCAAAA 57.338 36.364 0.00 0.00 0.00 2.44
1657 2006 4.457949 CCACCACAATTTCAAGGTACTACC 59.542 45.833 0.00 0.00 38.49 3.18
1672 2021 3.030291 AGCAAATTGACTTCCACCACAA 58.970 40.909 0.00 0.00 0.00 3.33
1673 2022 2.622942 GAGCAAATTGACTTCCACCACA 59.377 45.455 0.00 0.00 0.00 4.17
1761 2111 0.247460 GCAATTCAAGCCCAGGTTCC 59.753 55.000 0.00 0.00 0.00 3.62
1764 2114 0.613012 GGAGCAATTCAAGCCCAGGT 60.613 55.000 0.00 0.00 0.00 4.00
1770 2120 1.888512 TGGTCAAGGAGCAATTCAAGC 59.111 47.619 0.00 0.00 37.11 4.01
1784 2134 4.447138 ACTTGTCCTTACCATTGGTCAA 57.553 40.909 12.68 9.00 37.09 3.18
1805 2155 1.669440 GGACAGTCGTGGCAAGGTA 59.331 57.895 0.00 0.00 30.34 3.08
1811 2161 3.740818 TATTGCTCGGACAGTCGTGGC 62.741 57.143 0.00 0.00 0.00 5.01
1876 2229 3.671716 CCCAAAGGTAAGGTACAGACAC 58.328 50.000 0.00 0.00 0.00 3.67
1877 2230 2.039348 GCCCAAAGGTAAGGTACAGACA 59.961 50.000 0.00 0.00 34.57 3.41
1878 2231 2.305052 AGCCCAAAGGTAAGGTACAGAC 59.695 50.000 0.00 0.00 34.57 3.51
1907 2260 9.481340 GATCTTCATGTATGTGCTATCAACTAA 57.519 33.333 0.00 0.00 0.00 2.24
1910 2263 6.148480 GGGATCTTCATGTATGTGCTATCAAC 59.852 42.308 0.00 0.00 0.00 3.18
1953 2306 6.149308 GCCAAAACCTAATTTCTTCCAATTGG 59.851 38.462 19.08 19.08 36.41 3.16
1971 2324 8.763049 AGATAAGCTAATTTGAAAGCCAAAAC 57.237 30.769 0.00 0.00 46.64 2.43
1996 2349 5.476599 AGCCAAAAGTACAGCAATACATCAA 59.523 36.000 0.00 0.00 0.00 2.57
2044 2398 6.879993 TGCAAATATTTCAACAAATGGCTGAT 59.120 30.769 0.00 0.00 33.95 2.90
2095 2532 6.819284 AGTGAAGCAAATCATTTTGGAGAAA 58.181 32.000 1.13 0.00 42.09 2.52
2241 2960 6.204688 TGAAAACTAGCGCCATCCAATATAAG 59.795 38.462 2.29 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.