Multiple sequence alignment - TraesCS6B01G113300

Loading Multiple Alignment...

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 TraesCS6B01G113300 chr6B 100.000 3846 0 0 1 3846 95511439 95515284 0.000000e+00 7103
1 TraesCS6B01G113300 chr6B 95.226 3142 123 7 5 3124 95553292 95556428 0.000000e+00 4946
2 TraesCS6B01G113300 chr6B 93.204 721 36 5 3124 3835 95556460 95557176 0.000000e+00 1048
3 TraesCS6B01G113300 chr6A 91.878 3189 144 31 2 3124 52290259 52287120 0.000000e+00 4348
4 TraesCS6B01G113300 chr6A 89.100 3211 231 40 1 3124 74148255 74151433 0.000000e+00 3880
5 TraesCS6B01G113300 chr6A 94.070 2226 92 9 919 3124 52184910 52182705 0.000000e+00 3343
6 TraesCS6B01G113300 chr6A 93.056 720 40 4 3124 3835 52182673 52181956 0.000000e+00 1044
7 TraesCS6B01G113300 chr6A 86.961 928 60 27 3 887 52185821 52184912 0.000000e+00 987
8 TraesCS6B01G113300 chr6A 86.471 717 76 7 3124 3834 555445296 555445997 0.000000e+00 767
9 TraesCS6B01G113300 chr6D 93.611 2927 115 11 250 3124 41624288 41621382 0.000000e+00 4303
10 TraesCS6B01G113300 chr6D 93.897 721 33 6 3124 3835 41621350 41620632 0.000000e+00 1077
11 TraesCS6B01G113300 chr6D 87.981 208 18 5 5 208 41624501 41624297 4.970000e-59 239
12 TraesCS6B01G113300 chr7D 90.134 3203 206 38 2 3124 562196597 562199769 0.000000e+00 4063
13 TraesCS6B01G113300 chr7D 89.416 3203 231 37 2 3124 524311416 524314590 0.000000e+00 3938
14 TraesCS6B01G113300 chr7D 89.400 3198 230 39 2 3124 524303771 524306934 0.000000e+00 3927
15 TraesCS6B01G113300 chr7D 89.350 3202 231 40 1 3124 524249037 524252206 0.000000e+00 3923
16 TraesCS6B01G113300 chr7D 90.622 3007 163 32 169 3098 523547137 523550101 0.000000e+00 3880
17 TraesCS6B01G113300 chr7D 88.381 2668 205 37 2 2596 524256879 524259514 0.000000e+00 3112
18 TraesCS6B01G113300 chr7D 87.727 717 71 7 3124 3834 562199800 562200505 0.000000e+00 821
19 TraesCS6B01G113300 chr7D 86.890 717 71 9 3124 3834 524306965 524307664 0.000000e+00 782
20 TraesCS6B01G113300 chr7A 88.587 3198 263 37 2 3124 604249905 604253075 0.000000e+00 3790
21 TraesCS6B01G113300 chr7A 88.438 3200 265 39 2 3124 604260684 604263855 0.000000e+00 3762
22 TraesCS6B01G113300 chr7A 88.204 3196 276 38 2 3124 604255308 604258475 0.000000e+00 3720
23 TraesCS6B01G113300 chr7A 88.528 2990 233 40 206 3124 604221838 604224788 0.000000e+00 3520
24 TraesCS6B01G113300 chr7A 86.315 1688 154 32 2 1636 604289903 604291566 0.000000e+00 1766
25 TraesCS6B01G113300 chr7A 87.448 717 71 8 3124 3834 604263886 604264589 0.000000e+00 808
26 TraesCS6B01G113300 chr7A 86.053 717 81 8 3124 3834 604224819 604225522 0.000000e+00 752
27 TraesCS6B01G113300 chr7A 85.774 717 81 10 3124 3834 604305355 604306056 0.000000e+00 739
28 TraesCS6B01G113300 chr7B 89.969 2871 179 40 339 3124 560501435 560504281 0.000000e+00 3605
29 TraesCS6B01G113300 chr7B 89.057 1846 107 30 169 1957 559632527 559634334 0.000000e+00 2202
30 TraesCS6B01G113300 chrUn 88.717 1551 102 23 489 1981 77011484 77009949 0.000000e+00 1827
31 TraesCS6B01G113300 chrUn 88.395 1551 107 24 489 1981 76991850 76990315 0.000000e+00 1799
32 TraesCS6B01G113300 chrUn 93.252 1141 65 6 1992 3124 76990222 76989086 0.000000e+00 1670


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 TraesCS6B01G113300 chr6B 95511439 95515284 3845 False 7103.000000 7103 100.000000 1 3846 1 chr6B.!!$F1 3845
1 TraesCS6B01G113300 chr6B 95553292 95557176 3884 False 2997.000000 4946 94.215000 5 3835 2 chr6B.!!$F2 3830
2 TraesCS6B01G113300 chr6A 52287120 52290259 3139 True 4348.000000 4348 91.878000 2 3124 1 chr6A.!!$R1 3122
3 TraesCS6B01G113300 chr6A 74148255 74151433 3178 False 3880.000000 3880 89.100000 1 3124 1 chr6A.!!$F1 3123
4 TraesCS6B01G113300 chr6A 52181956 52185821 3865 True 1791.333333 3343 91.362333 3 3835 3 chr6A.!!$R2 3832
5 TraesCS6B01G113300 chr6A 555445296 555445997 701 False 767.000000 767 86.471000 3124 3834 1 chr6A.!!$F2 710
6 TraesCS6B01G113300 chr6D 41620632 41624501 3869 True 1873.000000 4303 91.829667 5 3835 3 chr6D.!!$R1 3830
7 TraesCS6B01G113300 chr7D 524249037 524252206 3169 False 3923.000000 3923 89.350000 1 3124 1 chr7D.!!$F2 3123
8 TraesCS6B01G113300 chr7D 523547137 523550101 2964 False 3880.000000 3880 90.622000 169 3098 1 chr7D.!!$F1 2929
9 TraesCS6B01G113300 chr7D 524256879 524259514 2635 False 3112.000000 3112 88.381000 2 2596 1 chr7D.!!$F3 2594
10 TraesCS6B01G113300 chr7D 524303771 524314590 10819 False 2882.333333 3938 88.568667 2 3834 3 chr7D.!!$F4 3832
11 TraesCS6B01G113300 chr7D 562196597 562200505 3908 False 2442.000000 4063 88.930500 2 3834 2 chr7D.!!$F5 3832
12 TraesCS6B01G113300 chr7A 604249905 604264589 14684 False 3020.000000 3790 88.169250 2 3834 4 chr7A.!!$F4 3832
13 TraesCS6B01G113300 chr7A 604221838 604225522 3684 False 2136.000000 3520 87.290500 206 3834 2 chr7A.!!$F3 3628
14 TraesCS6B01G113300 chr7A 604289903 604291566 1663 False 1766.000000 1766 86.315000 2 1636 1 chr7A.!!$F1 1634
15 TraesCS6B01G113300 chr7A 604305355 604306056 701 False 739.000000 739 85.774000 3124 3834 1 chr7A.!!$F2 710
16 TraesCS6B01G113300 chr7B 560501435 560504281 2846 False 3605.000000 3605 89.969000 339 3124 1 chr7B.!!$F2 2785
17 TraesCS6B01G113300 chr7B 559632527 559634334 1807 False 2202.000000 2202 89.057000 169 1957 1 chr7B.!!$F1 1788
18 TraesCS6B01G113300 chrUn 77009949 77011484 1535 True 1827.000000 1827 88.717000 489 1981 1 chrUn.!!$R1 1492
19 TraesCS6B01G113300 chrUn 76989086 76991850 2764 True 1734.500000 1799 90.823500 489 3124 2 chrUn.!!$R2 2635

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
889 8716 0.321021 CAAGCAGCAGTCTCCACTCT 59.679 55.000 0.00 0.0 0.0 3.24 F
890 8717 0.607620 AAGCAGCAGTCTCCACTCTC 59.392 55.000 0.00 0.0 0.0 3.20 F
1724 9594 1.065491 AGTGGACAGACTGCACAACAA 60.065 47.619 13.57 0.0 43.6 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2239 10216 0.606401 CCCACTCCACTGCGTTTGAT 60.606 55.000 0.0 0.0 0.00 2.57 R
2338 10315 2.029844 GTCCGACTCTTGCACCAGC 61.030 63.158 0.0 0.0 42.57 4.85 R
3480 22310 0.187117 TTCACTGGTTCCATTGGCCA 59.813 50.000 0.0 0.0 0.00 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
133 146 3.764466 CTCCCTCGTTCGCTGGCT 61.764 66.667 0.00 0.00 0.00 4.75
157 170 2.108168 ACAGCGCTAAATAGGAGGTCA 58.892 47.619 10.99 0.00 0.00 4.02
167 184 0.622136 TAGGAGGTCACGAGCAGGTA 59.378 55.000 0.00 0.00 0.00 3.08
183 200 3.149196 CAGGTAATTGAATCCCGGATGG 58.851 50.000 0.73 0.00 0.00 3.51
230 273 4.469657 GAAAGTTGCCCATATGGTCCATA 58.530 43.478 20.46 14.08 36.04 2.74
238 281 3.593328 CCCATATGGTCCATAATCCTGGT 59.407 47.826 20.46 1.90 37.57 4.00
246 296 4.192317 GTCCATAATCCTGGTGTCTGAAC 58.808 47.826 0.00 0.00 37.57 3.18
248 298 4.536090 TCCATAATCCTGGTGTCTGAACTT 59.464 41.667 0.00 0.00 37.57 2.66
300 350 6.183360 GGTTAGTTTTTGGATAAGTACGCTCC 60.183 42.308 4.90 4.90 0.00 4.70
792 8612 4.649845 CATGCACTCATGGGCAGA 57.350 55.556 12.00 0.00 44.84 4.26
793 8613 2.405143 CATGCACTCATGGGCAGAG 58.595 57.895 12.00 0.00 44.84 3.35
886 8713 3.261933 GCAAGCAGCAGTCTCCAC 58.738 61.111 0.00 0.00 44.79 4.02
887 8714 1.302351 GCAAGCAGCAGTCTCCACT 60.302 57.895 0.00 0.00 44.79 4.00
888 8715 1.297456 GCAAGCAGCAGTCTCCACTC 61.297 60.000 0.00 0.00 44.79 3.51
889 8716 0.321021 CAAGCAGCAGTCTCCACTCT 59.679 55.000 0.00 0.00 0.00 3.24
890 8717 0.607620 AAGCAGCAGTCTCCACTCTC 59.392 55.000 0.00 0.00 0.00 3.20
891 8718 1.217779 GCAGCAGTCTCCACTCTCC 59.782 63.158 0.00 0.00 0.00 3.71
892 8719 1.539560 GCAGCAGTCTCCACTCTCCA 61.540 60.000 0.00 0.00 0.00 3.86
955 8791 8.198778 TCATTGTAATAACGCTCATACACCTTA 58.801 33.333 0.00 0.00 0.00 2.69
956 8792 8.822855 CATTGTAATAACGCTCATACACCTTAA 58.177 33.333 0.00 0.00 0.00 1.85
1632 9501 1.543802 CTCTTCTCCTTCTGCGTCAGT 59.456 52.381 6.72 0.00 32.61 3.41
1724 9594 1.065491 AGTGGACAGACTGCACAACAA 60.065 47.619 13.57 0.00 43.60 2.83
2239 10216 2.018355 TAGCGGCCATAGATAACCCA 57.982 50.000 2.24 0.00 0.00 4.51
2894 21671 6.183360 CGATAAGGCGAGTATGCTATTTTCTG 60.183 42.308 0.00 0.00 34.52 3.02
3010 21800 4.446385 GCTATTTTGGTTTTGTCCGTTTCC 59.554 41.667 0.00 0.00 0.00 3.13
3011 21801 3.955650 TTTTGGTTTTGTCCGTTTCCA 57.044 38.095 0.00 0.00 0.00 3.53
3112 21903 4.007659 CCAAACAACCACCCATCTACTAC 58.992 47.826 0.00 0.00 0.00 2.73
3168 21991 0.763035 AAGTGGGTCGGCCATATACC 59.237 55.000 9.07 4.11 36.17 2.73
3202 22025 3.065371 CGTTTGAGTTGTTTCTTCCAGCT 59.935 43.478 0.00 0.00 0.00 4.24
3237 22060 3.772025 AGGGTAGCATAGCAGCCTATAAG 59.228 47.826 9.36 0.00 41.82 1.73
3243 22066 4.837860 AGCATAGCAGCCTATAAGAGTCTT 59.162 41.667 10.87 10.87 33.01 3.01
3349 22172 1.888512 TGGAAATCAACAAGCAGCCTC 59.111 47.619 0.00 0.00 0.00 4.70
3472 22302 9.167311 AGCAATAAAGACACGATTAAAGATCTT 57.833 29.630 0.88 0.88 0.00 2.40
3523 22358 7.698163 AGACCCAAATAAATATCTGAGAGGT 57.302 36.000 0.00 0.00 0.00 3.85
3576 22411 8.358582 AGATTCAAGATTATTATGGGCCAATC 57.641 34.615 11.89 8.88 0.00 2.67
3579 22414 5.939883 TCAAGATTATTATGGGCCAATCGAG 59.060 40.000 11.89 6.90 33.57 4.04
3603 22438 7.864770 AGGAAATAAAGACCCGATTAAACCTA 58.135 34.615 0.00 0.00 0.00 3.08
3713 22548 1.635817 GGGCAGACCAAGGAGGCATA 61.636 60.000 0.00 0.00 43.14 3.14
3716 22551 2.014068 GCAGACCAAGGAGGCATACAC 61.014 57.143 0.00 0.00 43.14 2.90
3748 22584 2.254546 ACTCGCAATTTCCACACTCA 57.745 45.000 0.00 0.00 0.00 3.41
3808 22644 4.768583 TGAAATCATGGATGATGACACGA 58.231 39.130 2.86 0.00 46.22 4.35
3813 22649 7.806409 AATCATGGATGATGACACGATTAAA 57.194 32.000 2.86 0.00 46.22 1.52
3837 22673 2.203139 CCAATGCCCGTGCCGATA 60.203 61.111 0.00 0.00 36.33 2.92
3838 22674 1.600636 CCAATGCCCGTGCCGATAT 60.601 57.895 0.00 0.00 36.33 1.63
3839 22675 1.577328 CCAATGCCCGTGCCGATATC 61.577 60.000 0.00 0.00 36.33 1.63
3840 22676 1.667830 AATGCCCGTGCCGATATCG 60.668 57.895 18.31 18.31 36.33 2.92
3841 22677 4.961511 TGCCCGTGCCGATATCGC 62.962 66.667 19.78 14.85 38.18 4.58
3842 22678 4.664677 GCCCGTGCCGATATCGCT 62.665 66.667 19.78 0.00 38.18 4.93
3843 22679 2.959372 CCCGTGCCGATATCGCTA 59.041 61.111 19.78 7.48 38.18 4.26
3844 22680 1.443872 CCCGTGCCGATATCGCTAC 60.444 63.158 19.78 17.37 38.18 3.58
3845 22681 1.284715 CCGTGCCGATATCGCTACA 59.715 57.895 19.78 13.64 38.18 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 133 1.868251 GTACGAGCCAGCGAACGAG 60.868 63.158 12.03 0.00 34.83 4.18
157 170 2.741878 CGGGATTCAATTACCTGCTCGT 60.742 50.000 0.00 0.00 0.00 4.18
200 217 3.855689 ATGGGCAACTTTCGATTTGAG 57.144 42.857 6.20 0.00 0.00 3.02
230 273 4.437682 TCAAAGTTCAGACACCAGGATT 57.562 40.909 0.00 0.00 0.00 3.01
238 281 8.287439 TCCAAAAGTATTTCAAAGTTCAGACA 57.713 30.769 0.00 0.00 37.28 3.41
361 423 7.722728 TCTTAGTTTATCCAGATACGAAGGCTA 59.277 37.037 0.00 0.00 0.00 3.93
501 568 8.283291 CGTAGTCAAAACAGAATAGAAAGCTTT 58.717 33.333 12.53 12.53 0.00 3.51
509 581 7.416154 TCCAAACGTAGTCAAAACAGAATAG 57.584 36.000 0.00 0.00 45.00 1.73
687 8490 9.563898 TCTACGTATCTAACACTAAAACATGTG 57.436 33.333 0.00 0.00 39.80 3.21
789 8609 0.867746 TTGCTTTACGTGCTGCTCTG 59.132 50.000 0.00 0.00 0.00 3.35
790 8610 1.532868 CTTTGCTTTACGTGCTGCTCT 59.467 47.619 0.00 0.00 0.00 4.09
791 8611 1.264288 ACTTTGCTTTACGTGCTGCTC 59.736 47.619 0.00 0.00 0.00 4.26
792 8612 1.002468 CACTTTGCTTTACGTGCTGCT 60.002 47.619 0.00 0.00 0.00 4.24
793 8613 1.398595 CACTTTGCTTTACGTGCTGC 58.601 50.000 0.00 0.00 0.00 5.25
818 8638 3.007074 TGCCTTGTTATCGTTGTGTAGGA 59.993 43.478 0.00 0.00 0.00 2.94
886 8713 0.809385 CAAGCCAGCATTGTGGAGAG 59.191 55.000 8.80 0.00 40.44 3.20
887 8714 1.246056 GCAAGCCAGCATTGTGGAGA 61.246 55.000 8.80 0.00 40.44 3.71
888 8715 1.214589 GCAAGCCAGCATTGTGGAG 59.785 57.895 8.80 1.27 40.44 3.86
889 8716 1.228644 AGCAAGCCAGCATTGTGGA 60.229 52.632 8.80 0.00 40.44 4.02
890 8717 1.080093 CAGCAAGCCAGCATTGTGG 60.080 57.895 0.55 2.10 41.01 4.17
891 8718 1.736645 GCAGCAAGCCAGCATTGTG 60.737 57.895 0.55 0.00 37.23 3.33
892 8719 2.654877 GCAGCAAGCCAGCATTGT 59.345 55.556 0.55 0.00 37.23 2.71
955 8791 2.664402 ACCTTGCTCTTGGTCATGTT 57.336 45.000 0.00 0.00 29.18 2.71
1290 9126 1.078918 CTTCATCCACTGCTCGCCA 60.079 57.895 0.00 0.00 0.00 5.69
1632 9501 1.632409 AGTAGACACGGGAGGTAGTCA 59.368 52.381 0.00 0.00 32.52 3.41
1724 9594 1.347707 TCCAACGCTCTTCAATGACCT 59.652 47.619 0.00 0.00 0.00 3.85
1833 9703 1.478631 TGACCTCATCGATGCTGAGT 58.521 50.000 20.81 13.75 38.77 3.41
2096 10066 9.825972 AATACAGTTTAAGTTGAAATCACATCG 57.174 29.630 0.00 0.00 0.00 3.84
2239 10216 0.606401 CCCACTCCACTGCGTTTGAT 60.606 55.000 0.00 0.00 0.00 2.57
2338 10315 2.029844 GTCCGACTCTTGCACCAGC 61.030 63.158 0.00 0.00 42.57 4.85
3010 21800 0.802494 AAACCGGCTCGCTTGTATTG 59.198 50.000 0.00 0.00 0.00 1.90
3011 21801 1.084289 GAAACCGGCTCGCTTGTATT 58.916 50.000 0.00 0.00 0.00 1.89
3112 21903 7.885297 TGGTGATAAAAAGAGTCCAAAATCAG 58.115 34.615 0.00 0.00 0.00 2.90
3219 22042 5.575157 AGACTCTTATAGGCTGCTATGCTA 58.425 41.667 0.00 0.00 44.33 3.49
3304 22127 5.995282 TGGCAACTTGCTAGCGTATATAAAT 59.005 36.000 13.43 0.00 44.28 1.40
3472 22302 4.099633 TGGTTCCATTGGCCAATAATCAA 58.900 39.130 30.19 16.62 0.00 2.57
3480 22310 0.187117 TTCACTGGTTCCATTGGCCA 59.813 50.000 0.00 0.00 0.00 5.36
3523 22358 5.312895 TCGGGTCTTCATTTCTTTCATTGA 58.687 37.500 0.00 0.00 0.00 2.57
3576 22411 6.238293 GGTTTAATCGGGTCTTTATTTCCTCG 60.238 42.308 0.00 0.00 0.00 4.63
3579 22414 7.553760 TGTAGGTTTAATCGGGTCTTTATTTCC 59.446 37.037 0.00 0.00 0.00 3.13
3603 22438 4.037565 CCATGCATATCAACATGAGCTTGT 59.962 41.667 0.00 0.00 45.23 3.16
3644 22479 8.909923 GTGTAAATTATAATGGTTTAGCCCACT 58.090 33.333 0.00 0.00 37.31 4.00
3713 22548 0.680061 GAGTTCCTCCTTGTCCGTGT 59.320 55.000 0.00 0.00 0.00 4.49
3716 22551 1.446272 GCGAGTTCCTCCTTGTCCG 60.446 63.158 0.00 0.00 0.00 4.79
3748 22584 2.930040 CGACGAGCTGGTCATATGTTTT 59.070 45.455 25.81 0.00 36.73 2.43
3797 22633 4.024893 GCGGACATTTAATCGTGTCATCAT 60.025 41.667 14.33 0.00 44.99 2.45
3808 22644 1.412343 GGGCATTGGCGGACATTTAAT 59.588 47.619 3.93 0.00 42.47 1.40
3813 22649 4.424711 ACGGGCATTGGCGGACAT 62.425 61.111 21.93 0.00 42.47 3.06


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

AutoCloner maintained by Alex Coulton.