Multiple sequence alignment - TraesCS1B01G266600

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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 TraesCS1B01G266600 chr1B 100.000 3884 0 0 1 3884 469162676 469158793 0.000000e+00 7173.0
1 TraesCS1B01G266600 chr1B 84.422 199 28 2 3141 3338 242744399 242744595 3.960000e-45 193.0
2 TraesCS1B01G266600 chr1D 97.644 2801 44 13 437 3225 347787450 347784660 0.000000e+00 4787.0
3 TraesCS1B01G266600 chr1D 96.837 411 12 1 1 411 347787932 347787523 0.000000e+00 686.0
4 TraesCS1B01G266600 chr1D 89.211 380 22 7 3498 3859 347784407 347784029 1.270000e-124 457.0
5 TraesCS1B01G266600 chr1A 97.176 2550 58 6 922 3466 448629313 448626773 0.000000e+00 4298.0
6 TraesCS1B01G266600 chr1A 93.034 890 29 5 1 859 448630201 448629314 0.000000e+00 1269.0
7 TraesCS1B01G266600 chr1A 88.021 384 23 10 3499 3862 448626683 448626303 2.140000e-117 433.0
8 TraesCS1B01G266600 chr1A 80.976 205 32 7 3137 3338 251339806 251339606 5.200000e-34 156.0
9 TraesCS1B01G266600 chr7B 85.859 198 26 1 3141 3338 576660241 576660046 3.930000e-50 209.0
10 TraesCS1B01G266600 chr3B 85.128 195 21 7 3145 3337 592335054 592334866 3.960000e-45 193.0
11 TraesCS1B01G266600 chr4B 82.915 199 31 2 3141 3338 347061689 347061885 3.990000e-40 176.0
12 TraesCS1B01G266600 chr6B 82.266 203 32 3 3137 3338 286910790 286910989 5.160000e-39 172.0
13 TraesCS1B01G266600 chr6D 81.910 199 33 2 3141 3338 454270591 454270787 8.630000e-37 165.0
14 TraesCS1B01G266600 chr7A 80.000 130 24 2 3214 3342 122039615 122039743 1.150000e-15 95.3


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 TraesCS1B01G266600 chr1B 469158793 469162676 3883 True 7173.000000 7173 100.000000 1 3884 1 chr1B.!!$R1 3883
1 TraesCS1B01G266600 chr1D 347784029 347787932 3903 True 1976.666667 4787 94.564000 1 3859 3 chr1D.!!$R1 3858
2 TraesCS1B01G266600 chr1A 448626303 448630201 3898 True 2000.000000 4298 92.743667 1 3862 3 chr1A.!!$R2 3861

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
209 210 1.550976 GACTGGGGTAGGTGAACAGAG 59.449 57.143 0.00 0.0 33.57 3.35 F
682 730 1.911357 TCAGCATGTCAAGGTGAGGAT 59.089 47.619 5.88 0.0 38.45 3.24 F
2226 2281 0.172578 TGCGAGATCCGGTAGTTGTG 59.827 55.000 0.00 0.0 39.04 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1816 0.178891 TCTGGGTCTTCAAGGCCTCT 60.179 55.0 5.23 0.0 40.65 3.69 R
2470 2525 0.039618 CCACCCCAACCATTAGCAGT 59.960 55.0 0.00 0.0 0.00 4.40 R
3168 3226 0.324285 AGTTGAGGAGAGGCAGCTTG 59.676 55.0 0.00 0.0 0.00 4.01 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
209 210 1.550976 GACTGGGGTAGGTGAACAGAG 59.449 57.143 0.00 0.00 33.57 3.35
223 224 3.447229 TGAACAGAGTCTGTCACTTCACA 59.553 43.478 25.64 13.57 44.62 3.58
233 234 7.952671 AGTCTGTCACTTCACAGTTTATCTAA 58.047 34.615 0.74 0.00 43.80 2.10
344 345 9.971922 GATATGCCTAATGAAAAATAAGCAACT 57.028 29.630 0.00 0.00 31.99 3.16
502 550 2.938956 AGAGGCACTTAGTTGCAACT 57.061 45.000 32.97 32.97 44.94 3.16
609 657 3.942829 TGGGTCAGCTGAATACTTTCTG 58.057 45.455 20.19 0.00 34.79 3.02
614 662 2.030213 CAGCTGAATACTTTCTGAGCGC 59.970 50.000 8.42 0.00 36.49 5.92
682 730 1.911357 TCAGCATGTCAAGGTGAGGAT 59.089 47.619 5.88 0.00 38.45 3.24
835 885 9.750125 GACAACTTCTTAAACAATTTTCTGGAT 57.250 29.630 0.00 0.00 0.00 3.41
897 947 6.515512 AAGGTGTGCTTAGATGGGTATATT 57.484 37.500 0.00 0.00 0.00 1.28
1167 1222 2.220313 GAGCCATCATCCTCTTTGCTC 58.780 52.381 0.00 0.00 37.24 4.26
1761 1816 3.846588 AGGGTGATCTAGAAAAGGCTGAA 59.153 43.478 0.00 0.00 0.00 3.02
1776 1831 1.948144 GCTGAAGAGGCCTTGAAGACC 60.948 57.143 6.77 0.00 31.62 3.85
1912 1967 1.952621 TGGGTTCTCTTCAGTAGGGG 58.047 55.000 0.00 0.00 0.00 4.79
1947 2002 3.457749 GGAGAGATGAGAAGGACCCAAAT 59.542 47.826 0.00 0.00 0.00 2.32
1962 2017 6.553476 AGGACCCAAATTACAAGCTTTTAGTT 59.447 34.615 0.00 0.00 0.00 2.24
2226 2281 0.172578 TGCGAGATCCGGTAGTTGTG 59.827 55.000 0.00 0.00 39.04 3.33
2237 2292 1.673033 GGTAGTTGTGATGCAGCGTCT 60.673 52.381 15.79 0.00 33.27 4.18
2470 2525 3.087343 TCCAATCCTGTGGAGCTGA 57.913 52.632 0.00 0.00 42.97 4.26
2727 2785 1.146774 TGGTCAACCATGTTCATGGGT 59.853 47.619 28.20 22.69 45.84 4.51
2775 2833 2.521465 CTTGGCCTTGGTGGTGCA 60.521 61.111 3.32 0.00 38.35 4.57
3182 3240 2.371658 AAAAACAAGCTGCCTCTCCT 57.628 45.000 0.00 0.00 0.00 3.69
3185 3243 0.767375 AACAAGCTGCCTCTCCTCAA 59.233 50.000 0.00 0.00 0.00 3.02
3193 3251 4.013050 GCTGCCTCTCCTCAACTTAAAAT 58.987 43.478 0.00 0.00 0.00 1.82
3263 3321 5.355596 CCATAACTAGTTCAGAAGCCTCAG 58.644 45.833 12.39 0.00 0.00 3.35
3277 3335 3.185455 AGCCTCAGTGAATAAAGGAGGT 58.815 45.455 7.72 0.00 45.46 3.85
3291 3349 2.482494 AGGAGGTGACTTATGGGGAAG 58.518 52.381 0.00 0.00 44.43 3.46
3292 3350 1.134068 GGAGGTGACTTATGGGGAAGC 60.134 57.143 0.00 0.00 44.43 3.86
3294 3352 1.561542 AGGTGACTTATGGGGAAGCTG 59.438 52.381 0.00 0.00 37.44 4.24
3296 3354 0.918983 TGACTTATGGGGAAGCTGGG 59.081 55.000 0.00 0.00 0.00 4.45
3297 3355 1.213296 GACTTATGGGGAAGCTGGGA 58.787 55.000 0.00 0.00 0.00 4.37
3312 3371 1.071642 GGGAAGGAGGCGGCTTATC 59.928 63.158 14.76 11.78 0.00 1.75
3316 3375 1.943340 GAAGGAGGCGGCTTATCTTTG 59.057 52.381 14.76 0.00 0.00 2.77
3319 3378 1.943340 GGAGGCGGCTTATCTTTGAAG 59.057 52.381 14.76 0.00 0.00 3.02
3320 3379 2.633488 GAGGCGGCTTATCTTTGAAGT 58.367 47.619 14.76 0.00 0.00 3.01
3411 3470 3.316308 GGTTGAGAAAGCGGATGCATATT 59.684 43.478 0.00 0.00 46.23 1.28
3444 3503 3.121738 AGGTAAGTCCTGAACGTTTGG 57.878 47.619 0.46 8.61 46.19 3.28
3447 3506 3.683340 GGTAAGTCCTGAACGTTTGGATC 59.317 47.826 21.34 16.00 32.03 3.36
3469 3544 2.465210 GCTCATGGCAAATCGACTTC 57.535 50.000 0.00 0.00 41.35 3.01
3470 3545 2.012673 GCTCATGGCAAATCGACTTCT 58.987 47.619 0.00 0.00 41.35 2.85
3471 3546 3.198068 GCTCATGGCAAATCGACTTCTA 58.802 45.455 0.00 0.00 41.35 2.10
3486 3561 2.688446 ACTTCTATTGACGCGAGGATGA 59.312 45.455 15.93 0.23 0.00 2.92
3490 3565 2.093306 ATTGACGCGAGGATGACAAA 57.907 45.000 15.93 0.00 0.00 2.83
3544 3672 4.981674 TGCCTCTTTTGCGTCAATAAAAAG 59.018 37.500 0.00 0.00 40.60 2.27
3561 3689 5.754543 AAAAAGTGTTTGATTTGCCATGG 57.245 34.783 7.63 7.63 0.00 3.66
3563 3691 4.895668 AAGTGTTTGATTTGCCATGGAT 57.104 36.364 18.40 0.00 0.00 3.41
3619 3748 7.080099 CGTATTATTTTGGATTGCTGGAGATG 58.920 38.462 0.00 0.00 0.00 2.90
3669 3798 5.467063 TGTGCGATGTGATACTAGTCTAGAG 59.533 44.000 14.02 0.00 0.00 2.43
3709 3838 2.657237 CTCGGCCGAACTTCCTGT 59.343 61.111 30.53 0.00 0.00 4.00
3723 3856 4.659172 CTGTGGCGCCAAAGGGGA 62.659 66.667 35.26 7.60 40.01 4.81
3725 3858 2.274104 GTGGCGCCAAAGGGGATA 59.726 61.111 34.66 0.58 40.01 2.59
3751 3884 2.428171 CCTACCTACGGTGATCGGAAAA 59.572 50.000 0.00 0.00 44.45 2.29
3770 3903 3.528370 GCGGCGCTCTTCCCTAGA 61.528 66.667 26.86 0.00 0.00 2.43
3771 3904 3.077519 GCGGCGCTCTTCCCTAGAA 62.078 63.158 26.86 0.00 30.91 2.10
3773 3906 0.528684 CGGCGCTCTTCCCTAGAAAG 60.529 60.000 7.64 0.00 30.91 2.62
3815 3950 4.804261 GCTCGAGAATAAATGGGCCTACAT 60.804 45.833 18.75 0.00 0.00 2.29
3839 3974 3.612860 CGAACATTCCGTCTTCTCGAAAT 59.387 43.478 0.00 0.00 0.00 2.17
3859 3994 3.502123 TGAAGACATTTCCGTCCCTTT 57.498 42.857 0.00 0.00 36.52 3.11
3860 3995 3.146066 TGAAGACATTTCCGTCCCTTTG 58.854 45.455 0.00 0.00 36.52 2.77
3861 3996 1.534729 AGACATTTCCGTCCCTTTGC 58.465 50.000 0.00 0.00 36.52 3.68
3862 3997 1.202879 AGACATTTCCGTCCCTTTGCA 60.203 47.619 0.00 0.00 36.52 4.08
3863 3998 1.200020 GACATTTCCGTCCCTTTGCAG 59.800 52.381 0.00 0.00 0.00 4.41
3864 3999 0.109132 CATTTCCGTCCCTTTGCAGC 60.109 55.000 0.00 0.00 0.00 5.25
3865 4000 0.539438 ATTTCCGTCCCTTTGCAGCA 60.539 50.000 0.00 0.00 0.00 4.41
3866 4001 1.172180 TTTCCGTCCCTTTGCAGCAG 61.172 55.000 0.00 0.00 0.00 4.24
3867 4002 3.741476 CCGTCCCTTTGCAGCAGC 61.741 66.667 0.00 0.00 42.57 5.25
3868 4003 3.741476 CGTCCCTTTGCAGCAGCC 61.741 66.667 0.00 0.00 41.13 4.85
3869 4004 3.741476 GTCCCTTTGCAGCAGCCG 61.741 66.667 0.00 0.00 41.13 5.52
3870 4005 3.952508 TCCCTTTGCAGCAGCCGA 61.953 61.111 0.00 0.00 41.13 5.54
3871 4006 2.985282 CCCTTTGCAGCAGCCGAA 60.985 61.111 0.00 0.00 41.13 4.30
3872 4007 2.564975 CCTTTGCAGCAGCCGAAG 59.435 61.111 0.00 3.09 41.13 3.79
3873 4008 2.263741 CCTTTGCAGCAGCCGAAGT 61.264 57.895 0.00 0.00 41.13 3.01
3874 4009 1.208614 CTTTGCAGCAGCCGAAGTC 59.791 57.895 0.00 0.00 41.13 3.01
3875 4010 2.192608 CTTTGCAGCAGCCGAAGTCC 62.193 60.000 0.00 0.00 41.13 3.85
3876 4011 2.956799 TTTGCAGCAGCCGAAGTCCA 62.957 55.000 0.00 0.00 41.13 4.02
3877 4012 2.669569 GCAGCAGCCGAAGTCCAA 60.670 61.111 0.00 0.00 33.58 3.53
3878 4013 2.260869 GCAGCAGCCGAAGTCCAAA 61.261 57.895 0.00 0.00 33.58 3.28
3879 4014 1.871772 CAGCAGCCGAAGTCCAAAG 59.128 57.895 0.00 0.00 0.00 2.77
3880 4015 0.603707 CAGCAGCCGAAGTCCAAAGA 60.604 55.000 0.00 0.00 0.00 2.52
3881 4016 0.603975 AGCAGCCGAAGTCCAAAGAC 60.604 55.000 0.00 0.00 43.89 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
209 210 8.764524 ATTAGATAAACTGTGAAGTGACAGAC 57.235 34.615 4.86 0.00 45.39 3.51
223 224 9.384764 GAGCACAAAGTAGGAATTAGATAAACT 57.615 33.333 0.00 0.00 0.00 2.66
233 234 1.628846 ACCGGAGCACAAAGTAGGAAT 59.371 47.619 9.46 0.00 0.00 3.01
280 281 6.903883 TCCATTTTATCTACGAGAGCAAAC 57.096 37.500 0.00 0.00 0.00 2.93
353 354 9.672673 ACTCATATTTACAGTTGCATTACTTCT 57.327 29.630 0.00 0.00 0.00 2.85
502 550 9.352784 CTCAAACAAAGTAGAAACATTCAAACA 57.647 29.630 0.00 0.00 0.00 2.83
614 662 5.355071 TGGATAAGCACAGCTCAATTAGTTG 59.645 40.000 0.00 0.00 38.25 3.16
682 730 4.425180 TTGGCCCAGTATTTATTAGCGA 57.575 40.909 0.00 0.00 0.00 4.93
987 1042 2.556622 AGACGGCATTTCCAAAACGAAT 59.443 40.909 0.00 0.00 34.01 3.34
1167 1222 0.247185 TTTCGTTACCCTGGCTACCG 59.753 55.000 0.00 0.00 0.00 4.02
1531 1586 3.119245 TCAAGACAGCCCTCGTTATGTAC 60.119 47.826 0.00 0.00 0.00 2.90
1761 1816 0.178891 TCTGGGTCTTCAAGGCCTCT 60.179 55.000 5.23 0.00 40.65 3.69
1776 1831 2.555325 TGTTGCTGATTCTTGCTTCTGG 59.445 45.455 4.45 0.00 0.00 3.86
1947 2002 9.005777 CCACTACCATTAACTAAAAGCTTGTAA 57.994 33.333 0.00 0.00 0.00 2.41
1962 2017 4.083565 GTTCTTTTGGGCCACTACCATTA 58.916 43.478 5.23 0.00 37.93 1.90
2133 2188 3.740832 GTGTTTCTGCCTTAATTTGTGGC 59.259 43.478 8.51 8.51 46.26 5.01
2226 2281 0.302890 CGGATTGAAGACGCTGCATC 59.697 55.000 0.00 0.00 0.00 3.91
2237 2292 1.588824 CTTGGCAGCTGCGGATTGAA 61.589 55.000 31.19 15.21 43.26 2.69
2470 2525 0.039618 CCACCCCAACCATTAGCAGT 59.960 55.000 0.00 0.00 0.00 4.40
2727 2785 2.233566 AGGCCTTGTGGATCTGCCA 61.234 57.895 0.00 0.00 46.96 4.92
2775 2833 0.685458 GCAACCCATTCATGCCTCCT 60.685 55.000 0.00 0.00 34.03 3.69
3168 3226 0.324285 AGTTGAGGAGAGGCAGCTTG 59.676 55.000 0.00 0.00 0.00 4.01
3201 3259 7.386025 AGAAGCCTCAACAAATTTAAAGAATGC 59.614 33.333 0.00 0.00 0.00 3.56
3206 3264 9.750125 AGTTTAGAAGCCTCAACAAATTTAAAG 57.250 29.630 0.00 0.00 30.82 1.85
3263 3321 5.823045 CCCATAAGTCACCTCCTTTATTCAC 59.177 44.000 0.00 0.00 0.00 3.18
3277 3335 0.918983 CCCAGCTTCCCCATAAGTCA 59.081 55.000 0.00 0.00 0.00 3.41
3292 3350 1.700042 ATAAGCCGCCTCCTTCCCAG 61.700 60.000 0.00 0.00 0.00 4.45
3294 3352 1.071642 GATAAGCCGCCTCCTTCCC 59.928 63.158 0.00 0.00 0.00 3.97
3296 3354 1.943340 CAAAGATAAGCCGCCTCCTTC 59.057 52.381 0.00 0.00 0.00 3.46
3297 3355 1.559682 TCAAAGATAAGCCGCCTCCTT 59.440 47.619 0.00 0.00 0.00 3.36
3312 3371 4.037690 CAGTTCTTTTGGCGACTTCAAAG 58.962 43.478 0.00 0.00 35.81 2.77
3316 3375 2.688364 CCAGTTCTTTTGGCGACTTC 57.312 50.000 0.00 0.00 0.00 3.01
3343 3402 3.830755 ACTGGAAACCTCGAGTAAGCTAA 59.169 43.478 12.31 0.00 38.71 3.09
3438 3497 1.202222 GCCATGAGCAAGATCCAAACG 60.202 52.381 0.00 0.00 42.97 3.60
3464 3539 2.846039 TCCTCGCGTCAATAGAAGTC 57.154 50.000 5.77 0.00 0.00 3.01
3469 3544 2.492019 TGTCATCCTCGCGTCAATAG 57.508 50.000 5.77 0.00 0.00 1.73
3470 3545 2.951457 TTGTCATCCTCGCGTCAATA 57.049 45.000 5.77 0.00 0.00 1.90
3471 3546 2.093306 TTTGTCATCCTCGCGTCAAT 57.907 45.000 5.77 0.00 0.00 2.57
3544 3672 6.402442 GCTTTTATCCATGGCAAATCAAACAC 60.402 38.462 6.96 0.00 0.00 3.32
3669 3798 1.063174 GGTCACTCATTCAGCGATTGC 59.937 52.381 0.00 0.00 43.24 3.56
3709 3838 2.274104 GTATCCCCTTTGGCGCCA 59.726 61.111 29.03 29.03 0.00 5.69
3751 3884 3.154473 TAGGGAAGAGCGCCGCAT 61.154 61.111 13.36 0.00 0.00 4.73
3815 3950 1.710013 GAGAAGACGGAATGTTCGCA 58.290 50.000 0.00 0.00 35.71 5.10
3839 3974 3.146066 CAAAGGGACGGAAATGTCTTCA 58.854 45.455 0.00 0.00 38.91 3.02
3859 3994 2.956799 TTTGGACTTCGGCTGCTGCA 62.957 55.000 17.89 0.88 41.91 4.41
3860 3995 2.192608 CTTTGGACTTCGGCTGCTGC 62.193 60.000 7.10 7.10 38.76 5.25
3861 3996 0.603707 TCTTTGGACTTCGGCTGCTG 60.604 55.000 0.95 0.95 0.00 4.41
3862 3997 0.603975 GTCTTTGGACTTCGGCTGCT 60.604 55.000 0.00 0.00 39.24 4.24
3863 3998 1.869690 GTCTTTGGACTTCGGCTGC 59.130 57.895 0.00 0.00 39.24 5.25
3864 3999 0.600255 ACGTCTTTGGACTTCGGCTG 60.600 55.000 0.00 0.00 40.10 4.85
3865 4000 1.746517 ACGTCTTTGGACTTCGGCT 59.253 52.632 0.00 0.00 40.10 5.52
3866 4001 4.355925 ACGTCTTTGGACTTCGGC 57.644 55.556 0.00 0.00 40.10 5.54


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

AutoCloner maintained by Alex Coulton.