Multiple sequence alignment - TraesCS4D01G072300

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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 TraesCS4D01G072300 chr4D 100.000 3790 0 0 1 3790 47437815 47441604 0.000000e+00 6999.0
1 TraesCS4D01G072300 chr4B 96.196 3207 64 19 1 3152 69162024 69165227 0.000000e+00 5193.0
2 TraesCS4D01G072300 chr4B 90.667 450 34 7 3344 3790 69165469 69165913 3.260000e-165 592.0
3 TraesCS4D01G072300 chr4A 96.837 1897 44 3 2 1897 550958572 550956691 0.000000e+00 3157.0
4 TraesCS4D01G072300 chr4A 91.991 924 48 10 2866 3788 550956687 550955789 0.000000e+00 1273.0
5 TraesCS4D01G072300 chr7A 72.251 573 124 31 3213 3764 645841146 645840588 1.100000e-30 145.0
6 TraesCS4D01G072300 chr3D 72.189 507 118 19 3168 3660 277734584 277735081 2.380000e-27 134.0
7 TraesCS4D01G072300 chr7B 95.000 40 1 1 2160 2198 7013134 7013173 1.140000e-05 62.1
8 TraesCS4D01G072300 chr3A 89.583 48 3 2 2163 2208 326044558 326044511 4.090000e-05 60.2
9 TraesCS4D01G072300 chr1A 88.235 51 5 1 2167 2216 76730394 76730344 4.090000e-05 60.2
10 TraesCS4D01G072300 chr1A 87.037 54 3 4 3272 3323 216493605 216493656 1.470000e-04 58.4
11 TraesCS4D01G072300 chr3B 92.683 41 2 1 2160 2199 739599601 739599641 1.470000e-04 58.4
12 TraesCS4D01G072300 chr2A 90.698 43 3 1 2167 2208 181465263 181465305 5.290000e-04 56.5


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 TraesCS4D01G072300 chr4D 47437815 47441604 3789 False 6999.0 6999 100.0000 1 3790 1 chr4D.!!$F1 3789
1 TraesCS4D01G072300 chr4B 69162024 69165913 3889 False 2892.5 5193 93.4315 1 3790 2 chr4B.!!$F1 3789
2 TraesCS4D01G072300 chr4A 550955789 550958572 2783 True 2215.0 3157 94.4140 2 3788 2 chr4A.!!$R1 3786

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
684 687 1.059098 AGAGAATGTGTGACAGGGCA 58.941 50.0 0.0 0.0 0.00 5.36 F
1143 1146 0.463474 GGTCTGAGCTCAAGCCATCC 60.463 60.0 23.7 13.9 43.38 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2661 2689 0.111253 AAGTTTGCTCTCCACCCTGG 59.889 55.000 0.0 0.0 39.43 4.45 R
2821 2872 2.165437 GGCAAACTCACACCAGAAACAA 59.835 45.455 0.0 0.0 0.00 2.83 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
684 687 1.059098 AGAGAATGTGTGACAGGGCA 58.941 50.000 0.00 0.00 0.00 5.36
685 688 1.421268 AGAGAATGTGTGACAGGGCAA 59.579 47.619 0.00 0.00 0.00 4.52
906 909 4.625607 ATAAATAGCCCCCTTCTCTTCG 57.374 45.455 0.00 0.00 0.00 3.79
1119 1122 1.581934 TCAACAACAAGGAGCTGACG 58.418 50.000 0.00 0.00 0.00 4.35
1143 1146 0.463474 GGTCTGAGCTCAAGCCATCC 60.463 60.000 23.70 13.90 43.38 3.51
1316 1319 1.688627 GGACTGGTCCTAGGTAGTGGG 60.689 61.905 16.90 4.83 46.16 4.61
1333 1336 4.521146 AGTGGGTGATATGCTTTTCTCAG 58.479 43.478 0.00 0.00 0.00 3.35
1362 1365 7.095183 ACATATATTGGTTGACCCAGATCAT 57.905 36.000 0.00 0.00 46.31 2.45
1395 1398 3.172229 AGCGTCTCTAATTCTGCCTTC 57.828 47.619 0.00 0.00 0.00 3.46
1511 1514 8.476447 GGGTAGCTCTTTCTTAGTACTATTTGT 58.524 37.037 2.79 0.00 0.00 2.83
1549 1552 3.035942 GCGTTTGAAGCACAACTAAGTG 58.964 45.455 0.00 0.00 42.37 3.16
1897 1901 3.190118 GCTTTATATGCATGCCCTCTGAC 59.810 47.826 16.68 0.00 0.00 3.51
1974 1978 7.365840 ACTAATCACTCAATTTCGACTTTCC 57.634 36.000 0.00 0.00 0.00 3.13
2042 2046 6.039616 TGCAAGTTTTGGTAAGTGATTTGAC 58.960 36.000 0.00 0.00 0.00 3.18
2127 2131 3.259425 CTTGCACTGCCACGGCTTC 62.259 63.158 9.92 0.00 42.51 3.86
2159 2163 8.134202 ACATTTGTCCAGATACGGATATATCA 57.866 34.615 14.60 0.00 37.41 2.15
2160 2164 8.035394 ACATTTGTCCAGATACGGATATATCAC 58.965 37.037 14.60 3.51 37.41 3.06
2161 2165 7.533289 TTTGTCCAGATACGGATATATCACA 57.467 36.000 14.60 4.18 37.41 3.58
2162 2166 7.718334 TTGTCCAGATACGGATATATCACAT 57.282 36.000 14.60 4.18 37.41 3.21
2164 2168 6.321435 TGTCCAGATACGGATATATCACATCC 59.679 42.308 14.60 0.00 37.41 3.51
2184 2211 8.303156 CACATCCGATCTAGACAAATCTAAGAT 58.697 37.037 0.00 0.00 36.98 2.40
2286 2314 9.550811 CTTCAATAAAACGTGGGTTTATTAGAC 57.449 33.333 13.40 0.00 45.35 2.59
2287 2315 8.618702 TCAATAAAACGTGGGTTTATTAGACA 57.381 30.769 13.40 0.82 45.35 3.41
2292 2320 8.806177 AAAACGTGGGTTTATTAGACATTTTC 57.194 30.769 0.00 0.00 45.35 2.29
2423 2451 6.039047 AGCCAGTTGTTATCATAGAAATGCTG 59.961 38.462 0.00 0.00 32.76 4.41
2600 2628 3.825160 GAGCCCACGTCCAACTGCA 62.825 63.158 0.00 0.00 0.00 4.41
2661 2689 1.089920 CAGGCAGACCACTTATGCAC 58.910 55.000 0.00 0.00 41.78 4.57
2756 2784 4.380531 TGTACTTCAACTGCCAAAGAGAG 58.619 43.478 0.00 0.00 0.00 3.20
2818 2869 6.062258 AGTTGGGCGCAACCTTATATATAT 57.938 37.500 34.89 15.52 39.10 0.86
2821 2872 6.801718 TGGGCGCAACCTTATATATATAGT 57.198 37.500 10.83 0.00 39.10 2.12
2864 2915 6.157645 TGCCTCTCTGAAGGAAAGATAGAAAT 59.842 38.462 9.23 0.00 38.87 2.17
2889 2940 4.119862 GGAGATAAGTACGCATGAAGCAA 58.880 43.478 0.00 0.00 46.13 3.91
2925 2976 2.128821 GTGTGCGTGTGTATGTGTGTA 58.871 47.619 0.00 0.00 0.00 2.90
2933 2984 4.918583 CGTGTGTATGTGTGTATGTGTGTA 59.081 41.667 0.00 0.00 0.00 2.90
2943 2994 7.210873 TGTGTGTATGTGTGTATGTTTGTCTA 58.789 34.615 0.00 0.00 0.00 2.59
3152 3210 3.066203 CCAAGTTTTACGACCAGTTGCTT 59.934 43.478 0.00 0.00 0.00 3.91
3155 3213 3.311596 AGTTTTACGACCAGTTGCTTGTC 59.688 43.478 0.00 0.00 0.00 3.18
3195 3253 2.118404 CCCCGTGTGTGCACAGTTT 61.118 57.895 22.40 0.00 45.50 2.66
3203 3261 3.551485 GTGTGTGCACAGTTTGAATTTCC 59.449 43.478 22.40 4.12 44.64 3.13
3229 3287 1.745653 GATTGTCTAAGTGGGGCTTGC 59.254 52.381 0.00 0.00 38.05 4.01
3237 3295 2.256117 AGTGGGGCTTGCGATATAAC 57.744 50.000 0.00 0.00 0.00 1.89
3238 3296 0.865769 GTGGGGCTTGCGATATAACG 59.134 55.000 0.00 0.00 0.00 3.18
3312 3396 7.624344 GCGAAATATTCACAGTTTAAGAGCAGT 60.624 37.037 0.00 0.00 0.00 4.40
3479 3591 8.768501 AATTCCCTATGGTTTAAGAGGAATTC 57.231 34.615 8.02 0.00 45.07 2.17
3490 3602 6.582677 TTAAGAGGAATTCGAAAAATGGCA 57.417 33.333 0.00 0.00 0.00 4.92
3555 3667 9.567776 TTTCTAAATGGTTTAACAGAGTGATGA 57.432 29.630 0.00 0.00 0.00 2.92
3608 3720 6.834959 AACGCACTCATATTTCATGTAGAG 57.165 37.500 0.00 0.00 0.00 2.43
3666 3779 2.853235 AGGGGTAGAAGTTTGAACGG 57.147 50.000 0.00 0.00 0.00 4.44
3672 3785 4.999311 GGGTAGAAGTTTGAACGGTATTGT 59.001 41.667 0.00 0.00 0.00 2.71
3675 3788 7.981225 GGGTAGAAGTTTGAACGGTATTGTATA 59.019 37.037 0.00 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
684 687 8.934507 TTCGTTTGTGAATAAATCTTTTGGTT 57.065 26.923 0.00 0.00 0.00 3.67
685 688 8.934507 TTTCGTTTGTGAATAAATCTTTTGGT 57.065 26.923 0.00 0.00 0.00 3.67
906 909 4.094146 GCTGTTCTGGCTTGATTAGAAGTC 59.906 45.833 0.00 0.00 31.66 3.01
1038 1041 2.318519 TATCCCCAACGATGTGGCCG 62.319 60.000 0.00 0.00 37.34 6.13
1119 1122 1.016653 GCTTGAGCTCAGACCCGTTC 61.017 60.000 17.43 0.00 38.21 3.95
1143 1146 2.680841 TCTTGGAACGTTGAACACTTGG 59.319 45.455 5.00 0.00 0.00 3.61
1316 1319 3.549794 AGCCCTGAGAAAAGCATATCAC 58.450 45.455 0.00 0.00 0.00 3.06
1333 1336 4.332828 GGGTCAACCAATATATGTAGCCC 58.667 47.826 0.89 0.00 39.85 5.19
1362 1365 6.525578 TTAGAGACGCTTTAGGAGAAATGA 57.474 37.500 0.00 0.00 0.00 2.57
1511 1514 3.688694 ACGCAACACCTTACCAATAGA 57.311 42.857 0.00 0.00 0.00 1.98
1549 1552 9.274065 CGTGAAAATAATTAGCCAGTAAGTTTC 57.726 33.333 0.00 0.00 0.00 2.78
1676 1679 8.923270 TGTCCTCTTCACCAATTTTAGAAATTT 58.077 29.630 0.00 0.00 0.00 1.82
1696 1700 4.194640 ACATGCATGTGAGTTATGTCCTC 58.805 43.478 30.92 0.00 40.03 3.71
1897 1901 3.349927 TCAACCAGAAAGAGGATGCATG 58.650 45.455 2.46 0.00 0.00 4.06
1974 1978 7.334421 GTCTGTTACCAACCTATATATGCATGG 59.666 40.741 10.16 3.69 0.00 3.66
2042 2046 8.759641 GTAACATTGCAGTTACTGATAGATCAG 58.240 37.037 17.40 16.34 46.41 2.90
2075 2079 7.812669 CCGGCTCTGAAACTTAAAACATTAATT 59.187 33.333 0.00 0.00 0.00 1.40
2076 2080 7.312899 CCGGCTCTGAAACTTAAAACATTAAT 58.687 34.615 0.00 0.00 0.00 1.40
2127 2131 5.926542 CCGTATCTGGACAAATGTACCATAG 59.073 44.000 0.00 0.00 33.08 2.23
2150 2154 7.809546 TGTCTAGATCGGATGTGATATATCC 57.190 40.000 10.25 2.71 40.57 2.59
2159 2163 7.825331 TCTTAGATTTGTCTAGATCGGATGT 57.175 36.000 0.00 0.00 0.00 3.06
2162 2166 9.575868 ACTTATCTTAGATTTGTCTAGATCGGA 57.424 33.333 0.00 0.00 0.00 4.55
2184 2211 9.042450 TCATACTCTTCAGTCCCAAATTACTTA 57.958 33.333 0.00 0.00 33.62 2.24
2195 2222 6.704050 GCCTCTAATTTCATACTCTTCAGTCC 59.296 42.308 0.00 0.00 33.62 3.85
2199 2226 6.540189 GCAAGCCTCTAATTTCATACTCTTCA 59.460 38.462 0.00 0.00 0.00 3.02
2270 2297 7.446013 TGAAGAAAATGTCTAATAAACCCACGT 59.554 33.333 0.00 0.00 34.56 4.49
2286 2314 6.132056 CGATAATCGAAGCCTGAAGAAAATG 58.868 40.000 0.00 0.00 43.74 2.32
2287 2315 5.277538 GCGATAATCGAAGCCTGAAGAAAAT 60.278 40.000 0.00 0.00 43.74 1.82
2292 2320 1.795286 GGCGATAATCGAAGCCTGAAG 59.205 52.381 10.56 0.00 43.74 3.02
2423 2451 7.699812 GGCTTCTATGTTGATCAGATGTTTTTC 59.300 37.037 0.00 0.00 0.00 2.29
2434 2462 8.677300 TGATAAAAAGTGGCTTCTATGTTGATC 58.323 33.333 0.00 0.00 0.00 2.92
2600 2628 4.069304 TGAAAACGAAACGATGGATTCCT 58.931 39.130 3.95 0.00 0.00 3.36
2661 2689 0.111253 AAGTTTGCTCTCCACCCTGG 59.889 55.000 0.00 0.00 39.43 4.45
2756 2784 2.359900 CTTCTACCACCACAGCCATTC 58.640 52.381 0.00 0.00 0.00 2.67
2818 2869 4.095782 GCAAACTCACACCAGAAACAACTA 59.904 41.667 0.00 0.00 0.00 2.24
2821 2872 2.165437 GGCAAACTCACACCAGAAACAA 59.835 45.455 0.00 0.00 0.00 2.83
2864 2915 2.578786 TCATGCGTACTTATCTCCCGA 58.421 47.619 0.00 0.00 0.00 5.14
2889 2940 3.132925 GCACACATCCAAGCATTTGTTT 58.867 40.909 0.00 0.00 32.21 2.83
2925 2976 7.308529 CCACACAATAGACAAACATACACACAT 60.309 37.037 0.00 0.00 0.00 3.21
2933 2984 3.495331 TGCCCACACAATAGACAAACAT 58.505 40.909 0.00 0.00 0.00 2.71
2943 2994 3.844911 CATGCAATGCCCACACAAT 57.155 47.368 1.53 0.00 37.62 2.71
3152 3210 6.677187 GCAGTTCATGTACTACTATGACGACA 60.677 42.308 4.51 0.00 33.36 4.35
3155 3213 4.976731 GGCAGTTCATGTACTACTATGACG 59.023 45.833 4.51 0.00 33.36 4.35
3195 3253 1.130373 GACAATCTGCGCGGAAATTCA 59.870 47.619 25.06 0.00 0.00 2.57
3203 3261 0.647410 CCACTTAGACAATCTGCGCG 59.353 55.000 0.00 0.00 0.00 6.86
3229 3287 7.378728 TGTCTAGAGCATTTCAACGTTATATCG 59.621 37.037 0.00 1.67 0.00 2.92
3237 3295 3.181516 GCCTTGTCTAGAGCATTTCAACG 60.182 47.826 0.00 0.00 0.00 4.10
3238 3296 3.181516 CGCCTTGTCTAGAGCATTTCAAC 60.182 47.826 0.00 0.00 0.00 3.18
3395 3507 3.009723 AGCAACTTTCCATGTCATACCG 58.990 45.455 0.00 0.00 0.00 4.02
3445 3557 9.785982 CTTAAACCATAGGGAATTTTGGAAAAA 57.214 29.630 0.00 0.00 38.05 1.94
3446 3558 9.160412 TCTTAAACCATAGGGAATTTTGGAAAA 57.840 29.630 0.00 0.00 38.05 2.29
3452 3564 9.560860 AATTCCTCTTAAACCATAGGGAATTTT 57.439 29.630 0.00 0.00 44.50 1.82
3555 3667 6.699575 AACTTTCCAGCGCTATATCATTTT 57.300 33.333 10.99 0.00 0.00 1.82
3644 3757 3.072211 CGTTCAAACTTCTACCCCTTCC 58.928 50.000 0.00 0.00 0.00 3.46
3645 3758 3.072211 CCGTTCAAACTTCTACCCCTTC 58.928 50.000 0.00 0.00 0.00 3.46
3648 3761 2.556144 ACCGTTCAAACTTCTACCCC 57.444 50.000 0.00 0.00 0.00 4.95
3691 3804 5.601583 TGCTACATTCCGACTAACCATTA 57.398 39.130 0.00 0.00 0.00 1.90
3747 3860 9.416284 AGGAAAGTTCTATACCAAAAAGTTTCA 57.584 29.630 13.29 0.00 40.41 2.69
3748 3861 9.894783 GAGGAAAGTTCTATACCAAAAAGTTTC 57.105 33.333 0.00 0.00 39.02 2.78


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

AutoCloner maintained by Alex Coulton.