Multiple sequence alignment - TraesCS6D01G205500

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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 TraesCS6D01G205500 chr6D 100.000 4025 0 0 1 4025 291249345 291245321 0.000000e+00 7433
1 TraesCS6D01G205500 chr6A 96.497 3654 82 10 1 3639 432241985 432245607 0.000000e+00 5997
2 TraesCS6D01G205500 chr6A 93.253 415 10 2 3629 4025 432245852 432246266 2.680000e-166 595
3 TraesCS6D01G205500 chr6B 96.847 3552 77 10 1 3540 452191851 452188323 0.000000e+00 5906
4 TraesCS6D01G205500 chr6B 91.633 502 15 3 3542 4025 452188162 452187670 0.000000e+00 669
5 TraesCS6D01G205500 chr2D 77.326 516 97 17 1232 1732 460207265 460206755 1.830000e-73 287
6 TraesCS6D01G205500 chr2D 88.068 176 14 2 968 1142 460208120 460207951 6.820000e-48 202
7 TraesCS6D01G205500 chr2A 77.326 516 97 15 1232 1732 603085361 603084851 1.830000e-73 287
8 TraesCS6D01G205500 chr2A 88.636 176 13 2 968 1142 603086227 603086058 1.470000e-49 207
9 TraesCS6D01G205500 chr2B 77.087 515 100 14 1232 1732 541203134 541202624 8.520000e-72 281
10 TraesCS6D01G205500 chr2B 94.074 135 8 0 1008 1142 541203970 541203836 5.270000e-49 206


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 TraesCS6D01G205500 chr6D 291245321 291249345 4024 True 7433.0 7433 100.0000 1 4025 1 chr6D.!!$R1 4024
1 TraesCS6D01G205500 chr6A 432241985 432246266 4281 False 3296.0 5997 94.8750 1 4025 2 chr6A.!!$F1 4024
2 TraesCS6D01G205500 chr6B 452187670 452191851 4181 True 3287.5 5906 94.2400 1 4025 2 chr6B.!!$R1 4024
3 TraesCS6D01G205500 chr2D 460206755 460208120 1365 True 244.5 287 82.6970 968 1732 2 chr2D.!!$R1 764
4 TraesCS6D01G205500 chr2A 603084851 603086227 1376 True 247.0 287 82.9810 968 1732 2 chr2A.!!$R1 764
5 TraesCS6D01G205500 chr2B 541202624 541203970 1346 True 243.5 281 85.5805 1008 1732 2 chr2B.!!$R1 724

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
58 59 1.066143 GCCACCTCGAAGGAATTCTGA 60.066 52.381 5.23 0.0 37.67 3.27 F
276 278 1.303643 GGTTCAACTGAGCCCCCAG 60.304 63.158 1.30 0.0 39.22 4.45 F
494 496 1.755179 ATCGTCTTGAATTGGCCTGG 58.245 50.000 3.32 0.0 0.00 4.45 F
1162 1466 3.206150 ACAATGCTCAGACGTTCAACTT 58.794 40.909 0.00 0.0 0.00 2.66 F
2605 3237 3.243602 GGGACACATGGTTTGGTTTGTAC 60.244 47.826 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 2325 0.390472 GTAGTGCAGTGCTCCAGACC 60.390 60.000 17.60 0.00 0.00 3.85 R
2044 2673 6.815089 AGGACTAGATAAGTTTCTGATGCAG 58.185 40.000 0.00 0.00 39.07 4.41 R
2410 3041 4.494091 AGCAGCTCCTGTATTGTAATGT 57.506 40.909 0.00 0.00 33.43 2.71 R
2811 3443 1.106944 AAAAACCCAGGGTCAGCACG 61.107 55.000 13.17 0.00 33.12 5.34 R
3939 5022 0.394192 TCAGGACTCTGCAGTGTTGG 59.606 55.000 21.45 13.97 40.69 3.77 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
31 32 2.933287 ACCGGCATCCTTCCACCA 60.933 61.111 0.00 0.00 0.00 4.17
58 59 1.066143 GCCACCTCGAAGGAATTCTGA 60.066 52.381 5.23 0.00 37.67 3.27
87 88 3.020237 GCCGTTCTCCACCTCTCCC 62.020 68.421 0.00 0.00 0.00 4.30
88 89 1.305381 CCGTTCTCCACCTCTCCCT 60.305 63.158 0.00 0.00 0.00 4.20
276 278 1.303643 GGTTCAACTGAGCCCCCAG 60.304 63.158 1.30 0.00 39.22 4.45
347 349 4.399978 CGACCTGTTAAACTTAAATGCCG 58.600 43.478 0.00 0.00 0.00 5.69
440 442 3.311596 CGCATGAATTTGATCAGCTCTGA 59.688 43.478 0.00 1.67 44.59 3.27
456 458 5.294306 CAGCTCTGATGCCGAAAAAGTATAA 59.706 40.000 0.00 0.00 0.00 0.98
494 496 1.755179 ATCGTCTTGAATTGGCCTGG 58.245 50.000 3.32 0.00 0.00 4.45
1162 1466 3.206150 ACAATGCTCAGACGTTCAACTT 58.794 40.909 0.00 0.00 0.00 2.66
1163 1467 3.627577 ACAATGCTCAGACGTTCAACTTT 59.372 39.130 0.00 0.00 0.00 2.66
1604 2232 8.882415 AAGTTCGTTACTCAAGAGATACAAAA 57.118 30.769 3.73 0.00 35.54 2.44
1697 2325 4.142816 GGGTTGATAGCTGCAATAATAGCG 60.143 45.833 1.02 0.00 44.43 4.26
1811 2440 3.320826 TGGGATGTGTGATGTATCTACCG 59.679 47.826 0.00 0.00 0.00 4.02
2093 2722 6.423905 TCGCCAGTTCTTGTAGCATTATAATC 59.576 38.462 0.00 0.00 0.00 1.75
2319 2948 8.251750 TCCTCTTGATTATTGTGAAGTAAACG 57.748 34.615 0.00 0.00 0.00 3.60
2329 2958 7.972832 ATTGTGAAGTAAACGGATCTTACAA 57.027 32.000 6.23 0.00 32.66 2.41
2410 3041 6.529829 GCCGTTTGAAATGCTAAAATATGTCA 59.470 34.615 0.00 0.00 0.00 3.58
2411 3042 7.462724 GCCGTTTGAAATGCTAAAATATGTCAC 60.463 37.037 0.00 0.00 0.00 3.67
2476 3107 5.675538 AGGTCAAGTATGCCTGATTTAGAC 58.324 41.667 0.00 0.00 33.56 2.59
2587 3219 5.690464 ATTCTAGGATATGAGCATGGGAC 57.310 43.478 0.00 0.00 0.00 4.46
2605 3237 3.243602 GGGACACATGGTTTGGTTTGTAC 60.244 47.826 0.00 0.00 0.00 2.90
2811 3443 4.414337 AGGCCACATGAAGACTATTCTC 57.586 45.455 5.01 0.00 0.00 2.87
2871 3503 3.119495 GCCTTAATTTCCATGTCGCACTT 60.119 43.478 0.00 0.00 0.00 3.16
3216 3848 4.734398 ACTTTTCTGGCAAATGTCACAA 57.266 36.364 0.00 0.00 0.00 3.33
3341 3973 6.039941 GCACACTACATAGAGAGGTGACTTAT 59.960 42.308 0.00 0.00 44.43 1.73
3342 3974 7.416890 GCACACTACATAGAGAGGTGACTTATT 60.417 40.741 0.00 0.00 44.43 1.40
3343 3975 9.121658 CACACTACATAGAGAGGTGACTTATTA 57.878 37.037 0.00 0.00 44.43 0.98
3551 4350 8.775220 TTCAAAACAACTACAACAACATATCG 57.225 30.769 0.00 0.00 0.00 2.92
3563 4362 1.300931 CATATCGGGGCCTGTGTCG 60.301 63.158 13.14 2.01 0.00 4.35
3995 5078 3.325870 ACCCGTGATGATTGCATATACG 58.674 45.455 0.00 0.00 41.22 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.069765 CGCGCTATGGTGGAAGGAT 59.930 57.895 5.56 0.00 0.00 3.24
31 32 3.774959 CTTCGAGGTGGCGCGCTAT 62.775 63.158 32.29 11.39 0.00 2.97
58 59 0.741221 GAGAACGGCGGCTTTGAGAT 60.741 55.000 13.24 0.00 0.00 2.75
87 88 1.513158 CTCCACGCCTGTCCAGTAG 59.487 63.158 0.00 0.00 0.00 2.57
88 89 2.646175 GCTCCACGCCTGTCCAGTA 61.646 63.158 0.00 0.00 0.00 2.74
324 326 4.670735 CGGCATTTAAGTTTAACAGGTCGG 60.671 45.833 0.00 0.00 0.00 4.79
418 420 3.311596 TCAGAGCTGATCAAATTCATGCG 59.688 43.478 0.00 0.00 34.14 4.73
456 458 9.823647 AAGACGATAGATGACTCAATACAAAAT 57.176 29.630 0.00 0.00 41.38 1.82
494 496 5.565439 GCAACATATGGATTATTGCTCCCAC 60.565 44.000 16.59 0.00 41.88 4.61
855 859 5.510690 CCACAAAAATCTTAAGGTCCCAACC 60.511 44.000 1.85 0.00 46.87 3.77
924 928 4.860907 CCTTCAGTAGCAATTGCAATCAAC 59.139 41.667 30.89 19.07 45.16 3.18
1604 2232 7.268586 CAACTAGGACAAGCATTATACTGAGT 58.731 38.462 0.00 0.00 0.00 3.41
1697 2325 0.390472 GTAGTGCAGTGCTCCAGACC 60.390 60.000 17.60 0.00 0.00 3.85
1795 2424 6.963049 AAAAGAACGGTAGATACATCACAC 57.037 37.500 0.00 0.00 0.00 3.82
1905 2534 7.513371 AAAGGACCAAATATTAACAACGACA 57.487 32.000 0.00 0.00 0.00 4.35
2044 2673 6.815089 AGGACTAGATAAGTTTCTGATGCAG 58.185 40.000 0.00 0.00 39.07 4.41
2319 2948 7.544566 TCTGTACGATCTGTTTTTGTAAGATCC 59.455 37.037 6.37 0.00 42.14 3.36
2410 3041 4.494091 AGCAGCTCCTGTATTGTAATGT 57.506 40.909 0.00 0.00 33.43 2.71
2411 3042 4.877823 TGAAGCAGCTCCTGTATTGTAATG 59.122 41.667 0.00 0.00 33.43 1.90
2476 3107 6.745159 TGACAGTAGAACTTCACTAGCTAG 57.255 41.667 19.44 19.44 0.00 3.42
2605 3237 3.611766 ACTATCAACCAAGAGAACGGG 57.388 47.619 0.00 0.00 0.00 5.28
2811 3443 1.106944 AAAAACCCAGGGTCAGCACG 61.107 55.000 13.17 0.00 33.12 5.34
3307 3939 8.414003 CCTCTCTATGTAGTGTGCTATAACAAA 58.586 37.037 0.00 0.00 0.00 2.83
3310 3942 7.228906 TCACCTCTCTATGTAGTGTGCTATAAC 59.771 40.741 0.00 0.00 0.00 1.89
3314 3946 4.882427 GTCACCTCTCTATGTAGTGTGCTA 59.118 45.833 0.00 0.00 0.00 3.49
3341 3973 4.908601 ATCCACCACACATGAAGTCTAA 57.091 40.909 0.00 0.00 0.00 2.10
3342 3974 4.908601 AATCCACCACACATGAAGTCTA 57.091 40.909 0.00 0.00 0.00 2.59
3343 3975 3.795688 AATCCACCACACATGAAGTCT 57.204 42.857 0.00 0.00 0.00 3.24
3551 4350 4.947147 TTGCACGACACAGGCCCC 62.947 66.667 0.00 0.00 0.00 5.80
3563 4362 4.088496 CGCAGCTAATACAAGTTTTTGCAC 59.912 41.667 10.86 3.95 37.85 4.57
3603 4413 3.517602 CTTATTTTGCCGCCCCTTAAAC 58.482 45.455 0.00 0.00 0.00 2.01
3639 4449 6.859112 AGTGTAATCAGTAGAGGTGAATGT 57.141 37.500 0.00 0.00 0.00 2.71
3640 4450 7.278868 GGAAAGTGTAATCAGTAGAGGTGAATG 59.721 40.741 0.00 0.00 0.00 2.67
3939 5022 0.394192 TCAGGACTCTGCAGTGTTGG 59.606 55.000 21.45 13.97 40.69 3.77
3995 5078 2.576615 GGACATAAGAAGGGGATGCAC 58.423 52.381 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.