Multiple sequence alignment - TraesCS6D01G241200

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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 TraesCS6D01G241200 chr6D 100.000 2619 0 0 1 2619 343559668 343557050 0.000000e+00 4837
1 TraesCS6D01G241200 chr6A 91.309 2071 69 31 601 2619 483901672 483899661 0.000000e+00 2724
2 TraesCS6D01G241200 chr6A 90.783 575 39 3 4 564 483903600 483903026 0.000000e+00 756
3 TraesCS6D01G241200 chr6B 92.845 1216 33 22 427 1620 518393227 518392044 0.000000e+00 1714
4 TraesCS6D01G241200 chr6B 94.694 735 29 9 1892 2619 518391661 518390930 0.000000e+00 1133
5 TraesCS6D01G241200 chr6B 95.393 369 14 3 4 370 518395028 518394661 3.760000e-163 584
6 TraesCS6D01G241200 chr7A 81.446 415 47 17 2030 2429 581044937 581045336 1.960000e-81 313
7 TraesCS6D01G241200 chr2B 85.276 163 17 6 1333 1490 585936421 585936581 7.500000e-36 161
8 TraesCS6D01G241200 chr2A 86.184 152 16 4 1333 1480 643493110 643493260 2.700000e-35 159
9 TraesCS6D01G241200 chr2D 84.663 163 18 6 1333 1490 498805526 498805686 3.490000e-34 156


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 TraesCS6D01G241200 chr6D 343557050 343559668 2618 True 4837.000000 4837 100.000000 1 2619 1 chr6D.!!$R1 2618
1 TraesCS6D01G241200 chr6A 483899661 483903600 3939 True 1740.000000 2724 91.046000 4 2619 2 chr6A.!!$R1 2615
2 TraesCS6D01G241200 chr6B 518390930 518395028 4098 True 1143.666667 1714 94.310667 4 2619 3 chr6B.!!$R1 2615

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
445 1826 0.036858 GTCCCAGAGCAAGTGGACTC 60.037 60.0 7.9 0.0 43.16 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 5058 1.125093 TTCGGAGGACAAGAAGGGCA 61.125 55.0 0.0 0.0 0.0 5.36 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
30 32 4.646492 ACTAAATCCCATCTTTGCCATCAC 59.354 41.667 0.00 0.00 0.00 3.06
39 41 2.957680 TCTTTGCCATCACTGCTTCAAA 59.042 40.909 0.00 0.00 0.00 2.69
60 62 5.853572 AAAAAGTTCCACTCCACCCTATA 57.146 39.130 0.00 0.00 0.00 1.31
152 154 3.121944 GTGCGAGATTTCATATGCTACCG 59.878 47.826 0.00 0.00 0.00 4.02
186 188 8.858003 TCTAGTCAGCTTTAGAAAATGATACG 57.142 34.615 0.00 0.00 0.00 3.06
202 204 8.742554 AAATGATACGCTTTCTTTAAAACAGG 57.257 30.769 0.00 0.00 0.00 4.00
223 225 2.385013 ATTGAGCCGGCAATTTTTCC 57.615 45.000 31.54 7.15 35.01 3.13
350 354 1.533625 CCAGGTCATTCGAAAAGGCA 58.466 50.000 0.00 0.00 0.00 4.75
371 375 2.043349 TCCTACTGGCCGCTAGCA 60.043 61.111 16.45 0.00 46.50 3.49
424 428 2.030562 AGTCGTCGCAAACCCCAG 59.969 61.111 0.00 0.00 0.00 4.45
425 429 2.029964 GTCGTCGCAAACCCCAGA 59.970 61.111 0.00 0.00 0.00 3.86
445 1826 0.036858 GTCCCAGAGCAAGTGGACTC 60.037 60.000 7.90 0.00 43.16 3.36
542 1935 1.642037 CGCAGGCACAGTCATCCAAG 61.642 60.000 0.00 0.00 0.00 3.61
619 3329 1.052617 GCCTTATCCTCTCCCACTCC 58.947 60.000 0.00 0.00 0.00 3.85
706 3416 1.638529 AGGGAGGAGATAATGCCGAG 58.361 55.000 0.00 0.00 31.11 4.63
721 3432 1.944676 CGAGTCTACCAATCGGCGC 60.945 63.158 0.00 0.00 34.57 6.53
772 3483 0.104304 TTTTATCTCCTCCGCTCGCC 59.896 55.000 0.00 0.00 0.00 5.54
773 3484 1.745320 TTTATCTCCTCCGCTCGCCC 61.745 60.000 0.00 0.00 0.00 6.13
845 3557 3.051803 TCCTTATCCTCCCAGTGACTCAT 60.052 47.826 0.00 0.00 0.00 2.90
847 3559 2.557555 ATCCTCCCAGTGACTCATCA 57.442 50.000 0.00 0.00 0.00 3.07
855 3567 4.480480 TGACTCATCACCCTCCCC 57.520 61.111 0.00 0.00 0.00 4.81
856 3568 1.790541 TGACTCATCACCCTCCCCT 59.209 57.895 0.00 0.00 0.00 4.79
857 3569 0.325671 TGACTCATCACCCTCCCCTC 60.326 60.000 0.00 0.00 0.00 4.30
858 3570 1.003573 ACTCATCACCCTCCCCTCC 59.996 63.158 0.00 0.00 0.00 4.30
859 3571 1.316266 CTCATCACCCTCCCCTCCT 59.684 63.158 0.00 0.00 0.00 3.69
860 3572 0.762461 CTCATCACCCTCCCCTCCTC 60.762 65.000 0.00 0.00 0.00 3.71
861 3573 1.768077 CATCACCCTCCCCTCCTCC 60.768 68.421 0.00 0.00 0.00 4.30
862 3574 1.949449 ATCACCCTCCCCTCCTCCT 60.949 63.158 0.00 0.00 0.00 3.69
863 3575 1.967343 ATCACCCTCCCCTCCTCCTC 61.967 65.000 0.00 0.00 0.00 3.71
875 3587 0.047176 TCCTCCTCCTCCTCCTCTCT 59.953 60.000 0.00 0.00 0.00 3.10
895 3607 2.607892 CCTTTATAGCCGCTGCGCC 61.608 63.158 18.00 5.47 44.33 6.53
950 3662 1.959985 ACCGATCGCTGATCTCAGATT 59.040 47.619 10.32 0.00 46.59 2.40
971 3683 0.459934 CCTGCTGCTTCTCTCCTTCG 60.460 60.000 0.00 0.00 0.00 3.79
1176 3902 4.500116 GACGCCAGCTCCTCGTCC 62.500 72.222 16.62 4.18 44.62 4.79
1268 3994 1.416049 CGAATGCGAGTGTTGACGG 59.584 57.895 0.00 0.00 40.82 4.79
1269 3995 1.282248 CGAATGCGAGTGTTGACGGT 61.282 55.000 0.00 0.00 40.82 4.83
1270 3996 0.865769 GAATGCGAGTGTTGACGGTT 59.134 50.000 0.00 0.00 0.00 4.44
1296 4023 8.195436 TGTTTACGTTCCTGATCTATTCTAAGG 58.805 37.037 0.00 0.00 0.00 2.69
1303 4030 7.640577 TCCTGATCTATTCTAAGGAGAGAGA 57.359 40.000 0.00 0.00 32.07 3.10
1609 4338 2.825836 GCCGCCAACTCCCTCATG 60.826 66.667 0.00 0.00 0.00 3.07
1626 4379 5.128827 CCCTCATGTTTAGCTAGGTTCTGTA 59.871 44.000 0.00 0.00 0.00 2.74
1673 4428 6.390048 TCGTAGAGGGAGATGTATTAGGAT 57.610 41.667 0.00 0.00 0.00 3.24
1726 4561 5.706916 CACATTTGAATCTGAGAAGTTGGG 58.293 41.667 0.00 0.00 0.00 4.12
1736 4571 5.200483 TCTGAGAAGTTGGGTTTTCAACAT 58.800 37.500 9.85 0.00 46.74 2.71
1762 4597 5.930837 TCAAAGGCCAAAGTATAAATGGG 57.069 39.130 5.01 0.00 34.71 4.00
1790 4625 6.604795 CCATGGATCCATTCTTAAGAAACAGT 59.395 38.462 25.20 8.77 37.61 3.55
1791 4626 7.201767 CCATGGATCCATTCTTAAGAAACAGTC 60.202 40.741 25.20 15.75 37.61 3.51
1809 4697 3.828451 CAGTCAAACAGGGATGGAAATGT 59.172 43.478 0.00 0.00 0.00 2.71
1869 4757 0.934436 CGGCAACAAGTGAAAAGGCG 60.934 55.000 0.00 0.00 38.61 5.52
1885 4774 4.764336 CGGCGCTGGTGCACATTG 62.764 66.667 20.43 8.83 39.64 2.82
1887 4776 2.644418 GCGCTGGTGCACATTGAA 59.356 55.556 20.43 0.00 39.64 2.69
1888 4777 1.730547 GCGCTGGTGCACATTGAAC 60.731 57.895 20.43 0.00 39.64 3.18
1890 4779 0.030504 CGCTGGTGCACATTGAACAA 59.969 50.000 20.43 0.00 39.64 2.83
1927 4828 6.841443 AAATCATTCGATCTTGACTAGCAG 57.159 37.500 0.00 0.00 0.00 4.24
2030 4932 2.032965 TCCCCCTACTACAGCAACAA 57.967 50.000 0.00 0.00 0.00 2.83
2031 4933 1.626825 TCCCCCTACTACAGCAACAAC 59.373 52.381 0.00 0.00 0.00 3.32
2032 4934 1.628846 CCCCCTACTACAGCAACAACT 59.371 52.381 0.00 0.00 0.00 3.16
2033 4935 2.835764 CCCCCTACTACAGCAACAACTA 59.164 50.000 0.00 0.00 0.00 2.24
2035 4937 4.251268 CCCCTACTACAGCAACAACTAAC 58.749 47.826 0.00 0.00 0.00 2.34
2084 4986 4.105486 GAGCGCTTAATTTTCCATTCACC 58.895 43.478 13.26 0.00 0.00 4.02
2115 5017 7.603404 TGATGCTTCCAACAATTGAAAAATAGG 59.397 33.333 13.59 3.20 0.00 2.57
2123 5025 8.096414 CCAACAATTGAAAAATAGGGAGATTGT 58.904 33.333 13.59 0.00 37.89 2.71
2128 5030 7.961325 TTGAAAAATAGGGAGATTGTTTTGC 57.039 32.000 0.00 0.00 0.00 3.68
2129 5031 7.060383 TGAAAAATAGGGAGATTGTTTTGCA 57.940 32.000 0.00 0.00 0.00 4.08
2171 5075 0.035056 ATTGCCCTTCTTGTCCTCCG 60.035 55.000 0.00 0.00 0.00 4.63
2205 5109 2.164219 TGGAAAATGATTTCTCGCCAGC 59.836 45.455 0.00 0.00 43.65 4.85
2211 5115 1.552348 GATTTCTCGCCAGCGGATCG 61.552 60.000 12.71 0.00 40.25 3.69
2277 5184 1.322442 GGCAGCTCCAAACTTCACTT 58.678 50.000 0.00 0.00 34.01 3.16
2326 5233 0.764890 CCTTCACCCCAACAGACTGA 59.235 55.000 10.08 0.00 0.00 3.41
2348 5255 4.631131 ACGATTTGAGAGACATCACACAA 58.369 39.130 0.00 0.00 0.00 3.33
2550 5457 3.861276 TCAGCCATTGAATGAGCTTTG 57.139 42.857 15.35 8.94 35.54 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.480954 AGATGGGATTTAGTCACGCGT 59.519 47.619 5.58 5.58 30.69 6.01
1 2 2.225068 AGATGGGATTTAGTCACGCG 57.775 50.000 3.53 3.53 30.69 6.01
2 3 3.487544 GCAAAGATGGGATTTAGTCACGC 60.488 47.826 0.00 0.00 30.69 5.34
60 62 6.054860 AGGCCGATATGAGTAAAGCATATT 57.945 37.500 0.00 0.00 38.64 1.28
91 93 1.740296 CGGCCAAGAGGGTGTTACG 60.740 63.158 2.24 0.00 39.65 3.18
186 188 6.146184 GGCTCAATTCCTGTTTTAAAGAAAGC 59.854 38.462 0.00 0.00 0.00 3.51
202 204 2.672874 GGAAAAATTGCCGGCTCAATTC 59.327 45.455 29.70 22.47 43.56 2.17
223 225 4.092968 GGTGCTACACAAGAAGGAATAACG 59.907 45.833 0.00 0.00 35.86 3.18
350 354 0.824759 CTAGCGGCCAGTAGGACTTT 59.175 55.000 2.24 0.00 42.67 2.66
404 408 3.723348 GGGTTTGCGACGACTGGC 61.723 66.667 0.00 0.00 0.00 4.85
424 428 0.036858 GTCCACTTGCTCTGGGACTC 60.037 60.000 9.85 0.00 44.99 3.36
425 429 2.062070 GTCCACTTGCTCTGGGACT 58.938 57.895 9.85 0.00 44.99 3.85
706 3416 0.814010 AATGGCGCCGATTGGTAGAC 60.814 55.000 23.90 0.00 37.67 2.59
721 3432 4.974368 TTATTCACGCCCAAGTAAATGG 57.026 40.909 0.00 0.00 40.35 3.16
845 3557 2.540910 AGGAGGAGGGGAGGGTGA 60.541 66.667 0.00 0.00 0.00 4.02
847 3559 3.369388 GGAGGAGGAGGGGAGGGT 61.369 72.222 0.00 0.00 0.00 4.34
848 3560 3.039526 AGGAGGAGGAGGGGAGGG 61.040 72.222 0.00 0.00 0.00 4.30
851 3563 2.015726 GAGGAGGAGGAGGAGGGGA 61.016 68.421 0.00 0.00 0.00 4.81
852 3564 2.612251 GAGGAGGAGGAGGAGGGG 59.388 72.222 0.00 0.00 0.00 4.79
853 3565 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
854 3566 0.998945 AGAGGAGGAGGAGGAGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
855 3567 0.478507 GAGAGGAGGAGGAGGAGGAG 59.521 65.000 0.00 0.00 0.00 3.69
856 3568 0.047176 AGAGAGGAGGAGGAGGAGGA 59.953 60.000 0.00 0.00 0.00 3.71
857 3569 0.478507 GAGAGAGGAGGAGGAGGAGG 59.521 65.000 0.00 0.00 0.00 4.30
858 3570 0.478507 GGAGAGAGGAGGAGGAGGAG 59.521 65.000 0.00 0.00 0.00 3.69
859 3571 0.996762 GGGAGAGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
860 3572 0.998945 AGGGAGAGAGGAGGAGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
861 3573 0.933700 AAGGGAGAGAGGAGGAGGAG 59.066 60.000 0.00 0.00 0.00 3.69
862 3574 1.398799 AAAGGGAGAGAGGAGGAGGA 58.601 55.000 0.00 0.00 0.00 3.71
863 3575 3.628832 ATAAAGGGAGAGAGGAGGAGG 57.371 52.381 0.00 0.00 0.00 4.30
875 3587 1.069090 CGCAGCGGCTATAAAGGGA 59.931 57.895 7.00 0.00 38.10 4.20
895 3607 1.927210 CGATGGAGGATCAAACGCG 59.073 57.895 3.53 3.53 36.25 6.01
950 3662 1.827969 GAAGGAGAGAAGCAGCAGGTA 59.172 52.381 0.00 0.00 0.00 3.08
971 3683 1.609072 GAGCAGACCAAACCAAGGAAC 59.391 52.381 0.00 0.00 0.00 3.62
1176 3902 2.837291 CCGGAGCTGGAGGAGGAG 60.837 72.222 0.00 0.00 0.00 3.69
1268 3994 7.829378 AGAATAGATCAGGAACGTAAACAAC 57.171 36.000 0.00 0.00 0.00 3.32
1269 3995 9.582431 CTTAGAATAGATCAGGAACGTAAACAA 57.418 33.333 0.00 0.00 0.00 2.83
1270 3996 8.195436 CCTTAGAATAGATCAGGAACGTAAACA 58.805 37.037 0.00 0.00 0.00 2.83
1296 4023 2.481795 GCAGGTCAGCATCTTCTCTCTC 60.482 54.545 0.00 0.00 0.00 3.20
1303 4030 2.165998 GAAAAGGCAGGTCAGCATCTT 58.834 47.619 0.00 0.00 35.83 2.40
1626 4379 1.483415 ACACGAACACCTAACAGTGGT 59.517 47.619 0.00 0.00 41.46 4.16
1632 4385 3.118542 ACGAAGAACACGAACACCTAAC 58.881 45.455 0.00 0.00 34.70 2.34
1736 4571 7.364585 CCCATTTATACTTTGGCCTTTGAATGA 60.365 37.037 3.32 0.00 0.00 2.57
1762 4597 7.122650 TGTTTCTTAAGAATGGATCCATGGTTC 59.877 37.037 27.97 21.19 36.68 3.62
1790 4625 4.770010 GGTTACATTTCCATCCCTGTTTGA 59.230 41.667 0.00 0.00 0.00 2.69
1791 4626 4.380444 CGGTTACATTTCCATCCCTGTTTG 60.380 45.833 0.00 0.00 0.00 2.93
1884 4773 8.939201 TGATTTTCTTTATTTGCTGTTGTTCA 57.061 26.923 0.00 0.00 0.00 3.18
1887 4776 8.702438 CGAATGATTTTCTTTATTTGCTGTTGT 58.298 29.630 0.00 0.00 0.00 3.32
1888 4777 8.914654 TCGAATGATTTTCTTTATTTGCTGTTG 58.085 29.630 0.00 0.00 0.00 3.33
1890 4779 9.294030 GATCGAATGATTTTCTTTATTTGCTGT 57.706 29.630 0.00 0.00 34.09 4.40
1927 4828 6.089820 TGCACTGTAACTTAATTACGCAGTAC 59.910 38.462 0.00 0.00 45.76 2.73
1938 4839 6.526526 TGGTCATACTTGCACTGTAACTTAA 58.473 36.000 3.30 0.00 0.00 1.85
2030 4932 3.080319 GGTACTCGAGAGGTGTGTTAGT 58.920 50.000 21.68 0.00 0.00 2.24
2031 4933 3.079578 TGGTACTCGAGAGGTGTGTTAG 58.920 50.000 21.68 0.00 0.00 2.34
2032 4934 3.144657 TGGTACTCGAGAGGTGTGTTA 57.855 47.619 21.68 0.00 0.00 2.41
2033 4935 1.991121 TGGTACTCGAGAGGTGTGTT 58.009 50.000 21.68 0.00 0.00 3.32
2035 4937 1.469940 GCATGGTACTCGAGAGGTGTG 60.470 57.143 21.68 12.71 0.00 3.82
2115 5017 6.601741 TGTGATTTTTGCAAAACAATCTCC 57.398 33.333 25.76 19.50 38.31 3.71
2154 5058 1.125093 TTCGGAGGACAAGAAGGGCA 61.125 55.000 0.00 0.00 0.00 5.36
2171 5075 5.937975 TCATTTTCCATTCCCCATCTTTC 57.062 39.130 0.00 0.00 0.00 2.62
2205 5109 1.434555 TGTTTTGGCACTACGATCCG 58.565 50.000 0.00 0.00 0.00 4.18
2211 5115 6.919721 TCAGGAATATTTGTTTTGGCACTAC 58.080 36.000 0.00 0.00 0.00 2.73
2277 5184 6.577103 TGTCATGAACCAAAATGCTTGTTTA 58.423 32.000 0.00 0.00 0.00 2.01
2326 5233 4.257267 TGTGTGATGTCTCTCAAATCGT 57.743 40.909 0.00 0.00 0.00 3.73
2348 5255 3.258372 TGAATACCGAGCTGTCTGAACTT 59.742 43.478 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.