Multiple sequence alignment - TraesCS6A01G368300

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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 TraesCS6A01G368300 chr6A 100.000 4881 0 0 1 4881 594640968 594645848 0 9014
1 TraesCS6A01G368300 chr6A 86.711 3597 412 47 613 4167 156166028 156162456 0 3934
2 TraesCS6A01G368300 chr2A 96.073 4915 151 13 1 4881 38551586 38556492 0 7969
3 TraesCS6A01G368300 chr2A 95.712 4921 165 12 2 4881 720324671 720319756 0 7877
4 TraesCS6A01G368300 chr2A 92.235 3709 247 19 1 3688 773698035 773694347 0 5216
5 TraesCS6A01G368300 chr2A 95.977 2908 102 6 1 2897 720513262 720510359 0 4708
6 TraesCS6A01G368300 chr2A 90.319 3419 263 38 294 3685 765908494 765911871 0 4418
7 TraesCS6A01G368300 chr2A 96.137 2045 56 3 2860 4881 758378031 758380075 0 3317
8 TraesCS6A01G368300 chr5A 95.587 4917 162 24 1 4881 312552102 312556999 0 7827
9 TraesCS6A01G368300 chr7A 96.101 3411 109 10 292 3685 62575234 62578637 0 5541
10 TraesCS6A01G368300 chr7A 95.234 1154 54 1 3728 4881 62578635 62579787 0 1825
11 TraesCS6A01G368300 chr4A 92.026 3712 251 22 1 3688 673171624 673167934 0 5173
12 TraesCS6A01G368300 chr2B 92.024 3711 250 19 1 3688 785301107 785297420 0 5171
13 TraesCS6A01G368300 chr1B 92.024 3711 248 20 1 3688 676864741 676861056 0 5169
14 TraesCS6A01G368300 chr7D 88.790 4255 386 53 1 4189 618908519 618904290 0 5131
15 TraesCS6A01G368300 chr7D 89.058 3354 312 33 875 4189 557982843 557979506 0 4109
16 TraesCS6A01G368300 chr7D 84.767 2790 381 32 489 3256 36644235 36647002 0 2758
17 TraesCS6A01G368300 chr3B 91.667 3708 261 18 1 3685 667632847 667636529 0 5092
18 TraesCS6A01G368300 chr7B 91.316 3708 269 19 1 3688 750160610 750156936 0 5014
19 TraesCS6A01G368300 chr5D 86.985 4249 445 67 1 4189 84255008 84250808 0 4684
20 TraesCS6A01G368300 chr3D 90.306 3167 255 31 1061 4189 480140685 480137533 0 4100
21 TraesCS6A01G368300 chr4B 85.919 3281 378 50 1 3248 25629493 25626264 0 3422
22 TraesCS6A01G368300 chr5B 86.539 2667 328 24 1038 3685 408182139 408184793 0 2907
23 TraesCS6A01G368300 chr1A 95.848 1156 45 2 3728 4881 541079815 541078661 0 1866
24 TraesCS6A01G368300 chr1A 95.152 1155 55 1 3728 4881 558456511 558455357 0 1821
25 TraesCS6A01G368300 chr3A 95.581 1154 51 0 3728 4881 30124684 30123531 0 1849
26 TraesCS6A01G368300 chr3A 95.321 1154 54 0 3728 4881 30110742 30109589 0 1832


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 TraesCS6A01G368300 chr6A 594640968 594645848 4880 False 9014 9014 100.0000 1 4881 1 chr6A.!!$F1 4880
1 TraesCS6A01G368300 chr6A 156162456 156166028 3572 True 3934 3934 86.7110 613 4167 1 chr6A.!!$R1 3554
2 TraesCS6A01G368300 chr2A 38551586 38556492 4906 False 7969 7969 96.0730 1 4881 1 chr2A.!!$F1 4880
3 TraesCS6A01G368300 chr2A 720319756 720324671 4915 True 7877 7877 95.7120 2 4881 1 chr2A.!!$R1 4879
4 TraesCS6A01G368300 chr2A 773694347 773698035 3688 True 5216 5216 92.2350 1 3688 1 chr2A.!!$R3 3687
5 TraesCS6A01G368300 chr2A 720510359 720513262 2903 True 4708 4708 95.9770 1 2897 1 chr2A.!!$R2 2896
6 TraesCS6A01G368300 chr2A 765908494 765911871 3377 False 4418 4418 90.3190 294 3685 1 chr2A.!!$F3 3391
7 TraesCS6A01G368300 chr2A 758378031 758380075 2044 False 3317 3317 96.1370 2860 4881 1 chr2A.!!$F2 2021
8 TraesCS6A01G368300 chr5A 312552102 312556999 4897 False 7827 7827 95.5870 1 4881 1 chr5A.!!$F1 4880
9 TraesCS6A01G368300 chr7A 62575234 62579787 4553 False 3683 5541 95.6675 292 4881 2 chr7A.!!$F1 4589
10 TraesCS6A01G368300 chr4A 673167934 673171624 3690 True 5173 5173 92.0260 1 3688 1 chr4A.!!$R1 3687
11 TraesCS6A01G368300 chr2B 785297420 785301107 3687 True 5171 5171 92.0240 1 3688 1 chr2B.!!$R1 3687
12 TraesCS6A01G368300 chr1B 676861056 676864741 3685 True 5169 5169 92.0240 1 3688 1 chr1B.!!$R1 3687
13 TraesCS6A01G368300 chr7D 618904290 618908519 4229 True 5131 5131 88.7900 1 4189 1 chr7D.!!$R2 4188
14 TraesCS6A01G368300 chr7D 557979506 557982843 3337 True 4109 4109 89.0580 875 4189 1 chr7D.!!$R1 3314
15 TraesCS6A01G368300 chr7D 36644235 36647002 2767 False 2758 2758 84.7670 489 3256 1 chr7D.!!$F1 2767
16 TraesCS6A01G368300 chr3B 667632847 667636529 3682 False 5092 5092 91.6670 1 3685 1 chr3B.!!$F1 3684
17 TraesCS6A01G368300 chr7B 750156936 750160610 3674 True 5014 5014 91.3160 1 3688 1 chr7B.!!$R1 3687
18 TraesCS6A01G368300 chr5D 84250808 84255008 4200 True 4684 4684 86.9850 1 4189 1 chr5D.!!$R1 4188
19 TraesCS6A01G368300 chr3D 480137533 480140685 3152 True 4100 4100 90.3060 1061 4189 1 chr3D.!!$R1 3128
20 TraesCS6A01G368300 chr4B 25626264 25629493 3229 True 3422 3422 85.9190 1 3248 1 chr4B.!!$R1 3247
21 TraesCS6A01G368300 chr5B 408182139 408184793 2654 False 2907 2907 86.5390 1038 3685 1 chr5B.!!$F1 2647
22 TraesCS6A01G368300 chr1A 541078661 541079815 1154 True 1866 1866 95.8480 3728 4881 1 chr1A.!!$R1 1153
23 TraesCS6A01G368300 chr1A 558455357 558456511 1154 True 1821 1821 95.1520 3728 4881 1 chr1A.!!$R2 1153
24 TraesCS6A01G368300 chr3A 30123531 30124684 1153 True 1849 1849 95.5810 3728 4881 1 chr3A.!!$R2 1153
25 TraesCS6A01G368300 chr3A 30109589 30110742 1153 True 1832 1832 95.3210 3728 4881 1 chr3A.!!$R1 1153

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
806 888 1.078072 TGACGGCGGCCATACAATT 60.078 52.632 20.71 0.0 0.00 2.32 F
1507 1601 0.323957 GAGAAGGGCCGTACTGGTTT 59.676 55.000 0.00 0.0 41.21 3.27 F
2432 2547 0.912486 GGGGCCAGTACAAGTCATCT 59.088 55.000 4.39 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2221 0.320374 TTTCTACTCCTGCCACCACG 59.680 55.000 0.0 0.0 0.00 4.94 R
2693 2811 2.940410 GTCTTCGGACTTTGTTGGTGAA 59.060 45.455 0.0 0.0 41.44 3.18 R
4204 4426 0.468226 TCTATCCCAATGCCACGTCC 59.532 55.000 0.0 0.0 0.00 4.79 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
44 45 2.743752 CGAGGTGGCATGCACGAAG 61.744 63.158 21.36 1.85 0.00 3.79
67 68 4.305769 CGTCATCAAATTTTTGGAGGCAA 58.694 39.130 3.38 0.00 38.66 4.52
114 115 1.454276 GCAAGATTTGAACGACGTCGA 59.546 47.619 41.52 21.39 43.02 4.20
265 267 2.159226 CGTGTGCAAAAAGTTTGGGGTA 60.159 45.455 0.00 0.00 0.00 3.69
455 489 3.618690 ATAGAGTCCCACAAACTGAGC 57.381 47.619 0.00 0.00 0.00 4.26
543 593 7.865385 TGTGGTATTAAACTGAAATGTTGAAGC 59.135 33.333 0.00 0.00 0.00 3.86
806 888 1.078072 TGACGGCGGCCATACAATT 60.078 52.632 20.71 0.00 0.00 2.32
1279 1371 7.604927 AGCGATTTATTATTCGGCCAAATACTA 59.395 33.333 2.24 0.00 35.93 1.82
1309 1401 6.486253 TCAGTGTGCTTAATGAAGATGTTC 57.514 37.500 0.00 0.00 34.25 3.18
1440 1534 3.007290 CAGGCCTAATCCTCATCGATGAA 59.993 47.826 27.09 15.24 36.18 2.57
1507 1601 0.323957 GAGAAGGGCCGTACTGGTTT 59.676 55.000 0.00 0.00 41.21 3.27
1683 1779 9.875691 GATCTTGAAAAATTTAAGTGGCCTATT 57.124 29.630 3.32 0.55 0.00 1.73
1706 1802 2.039084 GGAACTTGGCTCTTCTTCAGGA 59.961 50.000 0.00 0.00 0.00 3.86
1920 2017 2.258755 CGACTATGACAACATGCACGA 58.741 47.619 0.00 0.00 37.87 4.35
1922 2019 2.604914 GACTATGACAACATGCACGAGG 59.395 50.000 0.00 0.00 37.87 4.63
2087 2191 1.616865 CACGTGAAGGGACTGTCCTAA 59.383 52.381 25.01 6.95 40.86 2.69
2117 2221 7.423199 AGAAATGAAGAAACCTAAACGGAAAC 58.577 34.615 0.00 0.00 36.31 2.78
2207 2312 5.291858 CGTGTGATGACATACATAAAGCTGT 59.708 40.000 0.00 0.00 39.56 4.40
2209 2314 7.182761 GTGTGATGACATACATAAAGCTGTTC 58.817 38.462 0.00 0.00 39.56 3.18
2282 2387 9.912634 AGAAGTTGTATTGAACATGGTTTAATG 57.087 29.630 8.75 0.00 38.10 1.90
2410 2516 7.519008 CGAATTTGATAATGTAGGTGAAGGAGC 60.519 40.741 0.00 0.00 0.00 4.70
2432 2547 0.912486 GGGGCCAGTACAAGTCATCT 59.088 55.000 4.39 0.00 0.00 2.90
2693 2811 4.225942 TCTGGTGAGTCTATGGATGCTTTT 59.774 41.667 0.00 0.00 0.00 2.27
2734 2852 0.466963 ACGTTTGAGAGTTTCCCGGT 59.533 50.000 0.00 0.00 0.00 5.28
2978 3104 5.334802 CGTCACCACATTCAATTCTAGCAAA 60.335 40.000 0.00 0.00 0.00 3.68
2983 3109 7.816031 CACCACATTCAATTCTAGCAAATTCTT 59.184 33.333 0.00 0.00 0.00 2.52
3173 3300 5.382303 CGCTGTAAGTATGAGTTTGGTTTG 58.618 41.667 0.00 0.00 35.30 2.93
3502 3636 6.658849 ACATCATTTGGTTACTATGTAGGCA 58.341 36.000 0.00 0.00 0.00 4.75
3902 4123 9.933723 GGTAAGTTAAATGAGTACAAGGAAGTA 57.066 33.333 0.00 0.00 0.00 2.24
3997 4218 1.516365 ATACTGGGACGGAGATCGCG 61.516 60.000 0.00 0.00 43.89 5.87
4204 4426 9.520204 GTTGGATACTTTGAATGATTGTAATGG 57.480 33.333 0.00 0.00 37.61 3.16
4208 4430 6.194796 ACTTTGAATGATTGTAATGGGACG 57.805 37.500 0.00 0.00 0.00 4.79
4288 4510 7.041712 TGAGACTAAACATTTAAATGCGTGTGA 60.042 33.333 24.82 9.49 40.04 3.58
4333 4555 1.014352 AATGTATCGGTTTGCGGCTC 58.986 50.000 0.00 0.00 0.00 4.70
4348 4570 3.179830 GCGGCTCCGATGTTATATGTAG 58.820 50.000 13.11 0.00 42.83 2.74
4436 4659 1.541147 CGATGTGGACAAAACCTGCAT 59.459 47.619 0.00 0.00 0.00 3.96
4645 4868 2.997315 CCGGTGGCAGAGGTCTCA 60.997 66.667 0.00 0.00 0.00 3.27
4699 4923 0.391661 CGAGGGGGAATATGGCGATG 60.392 60.000 0.00 0.00 0.00 3.84
4717 4941 0.250793 TGTGTCGGCCCATAAACGAT 59.749 50.000 0.00 0.00 38.99 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.667969 GCCTCCAAAAATTTGATGACGC 59.332 45.455 7.44 0.44 40.55 5.19
50 51 3.810033 GCCCATTGCCTCCAAAAATTTGA 60.810 43.478 7.44 0.00 40.55 2.69
114 115 1.515304 GCAACGTGCGTTTGGTGTT 60.515 52.632 7.27 0.00 36.00 3.32
455 489 4.431809 TCTTTTGGTCAATGCACAAACAG 58.568 39.130 0.00 0.00 34.21 3.16
543 593 9.776158 ATGCATTTATTAAAAACATGCATTGTG 57.224 25.926 16.63 0.00 42.18 3.33
639 718 2.049894 ATGCACGCACGTACGACA 60.050 55.556 24.41 12.76 36.70 4.35
723 805 3.551407 GATCGGGGAGGGGTGAGC 61.551 72.222 0.00 0.00 0.00 4.26
922 1012 3.691342 TTAGTCGTGGCAGCCGCT 61.691 61.111 22.79 12.32 38.60 5.52
1309 1401 7.088272 TCGTTACTTATCCCGAATATGTCATG 58.912 38.462 0.00 0.00 32.24 3.07
1327 1419 3.096852 TGACATCATCACCCTCGTTACT 58.903 45.455 0.00 0.00 29.99 2.24
1507 1601 4.532916 TGGTGCTAAGACTGTACCCATAAA 59.467 41.667 0.00 0.00 39.04 1.40
1645 1740 5.779806 TTTTCAAGATCTTCGACCGATTC 57.220 39.130 4.57 0.00 0.00 2.52
1683 1779 1.774254 TGAAGAAGAGCCAAGTTCCCA 59.226 47.619 0.00 0.00 0.00 4.37
1922 2019 1.933115 CTTACATTGCCGGTGCCACC 61.933 60.000 2.98 2.98 36.33 4.61
2087 2191 7.255486 CCGTTTAGGTTTCTTCATTTCTTCCTT 60.255 37.037 0.00 0.00 34.51 3.36
2117 2221 0.320374 TTTCTACTCCTGCCACCACG 59.680 55.000 0.00 0.00 0.00 4.94
2207 2312 5.779241 ATATTGAGAACCTCCTTGTGGAA 57.221 39.130 0.00 0.00 42.66 3.53
2209 2314 5.368989 GGTATATTGAGAACCTCCTTGTGG 58.631 45.833 0.00 0.00 0.00 4.17
2282 2387 6.774354 TGAAACACGATAAGTAGTTGAACC 57.226 37.500 0.00 0.00 0.00 3.62
2352 2458 4.698780 GTCCCTCTTATTGGGTTTGTACAC 59.301 45.833 0.00 0.00 44.84 2.90
2664 2782 6.939163 GCATCCATAGACTCACCAGAAATATT 59.061 38.462 0.00 0.00 0.00 1.28
2693 2811 2.940410 GTCTTCGGACTTTGTTGGTGAA 59.060 45.455 0.00 0.00 41.44 3.18
2734 2852 5.897250 TCACCATTACCTATGTTGCTCTCTA 59.103 40.000 0.00 0.00 31.99 2.43
3173 3300 9.371136 TGTGAAGTACAAATGAGAGATATGTTC 57.629 33.333 0.00 0.00 36.06 3.18
3530 3664 6.710295 GTGTGCATCACTATGGTTATCCAATA 59.290 38.462 10.87 0.00 43.93 1.90
3902 4123 6.212187 TGTGATCAGCTTAGGATATAGCATGT 59.788 38.462 0.00 0.00 39.85 3.21
3997 4218 2.493278 CCTGGTCAAATTCATGTGTCCC 59.507 50.000 0.00 0.00 0.00 4.46
4074 4296 8.924511 TCATCTTGACCTTCTCTAATTTGTTT 57.075 30.769 0.00 0.00 0.00 2.83
4122 4344 5.657302 CCCTACCGATGCTAATACCTATTCT 59.343 44.000 0.00 0.00 0.00 2.40
4204 4426 0.468226 TCTATCCCAATGCCACGTCC 59.532 55.000 0.00 0.00 0.00 4.79
4208 4430 3.251004 GTCGAAATCTATCCCAATGCCAC 59.749 47.826 0.00 0.00 0.00 5.01
4436 4659 2.417239 GCACAATCGACGTGGGAAATTA 59.583 45.455 16.25 0.00 34.85 1.40
4468 4691 1.452953 TATTCGTCGGATCCAGCGCT 61.453 55.000 13.41 2.64 0.00 5.92
4699 4923 0.655733 CATCGTTTATGGGCCGACAC 59.344 55.000 0.00 0.00 32.86 3.67
4736 4960 0.108615 CCGCACAAGAAGAGGATCGT 60.109 55.000 0.00 0.00 42.67 3.73


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

AutoCloner maintained by Alex Coulton.