Multiple sequence alignment - TraesCS2A01G362900

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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 TraesCS2A01G362900 chr2A 100.000 3570 0 0 1 3570 607482902 607486471 0.000000e+00 6593
1 TraesCS2A01G362900 chr2A 92.959 2244 81 26 44 2252 610116440 610118641 0.000000e+00 3197
2 TraesCS2A01G362900 chr2A 97.817 962 18 2 2243 3202 610118818 610119778 0.000000e+00 1657
3 TraesCS2A01G362900 chr2A 96.212 396 12 1 3178 3570 610119779 610120174 0.000000e+00 645
4 TraesCS2A01G362900 chr2B 94.320 2641 83 15 861 3456 544990254 544992872 0.000000e+00 3984
5 TraesCS2A01G362900 chr2B 93.111 479 30 3 4 481 544987070 544987546 0.000000e+00 699
6 TraesCS2A01G362900 chr2B 90.331 362 13 12 506 850 544987540 544987896 4.200000e-124 455
7 TraesCS2A01G362900 chr2B 94.068 118 3 2 3453 3567 544993008 544993124 3.660000e-40 176
8 TraesCS2A01G362900 chr2B 94.048 84 3 1 3378 3459 544992994 544992911 3.740000e-25 126
9 TraesCS2A01G362900 chr2D 96.558 2121 46 11 1470 3570 462204766 462206879 0.000000e+00 3487
10 TraesCS2A01G362900 chr2D 92.736 1418 59 24 1 1393 462203360 462204758 0.000000e+00 2008


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 TraesCS2A01G362900 chr2A 607482902 607486471 3569 False 6593.0 6593 100.000000 1 3570 1 chr2A.!!$F1 3569
1 TraesCS2A01G362900 chr2A 610116440 610120174 3734 False 1833.0 3197 95.662667 44 3570 3 chr2A.!!$F2 3526
2 TraesCS2A01G362900 chr2B 544987070 544993124 6054 False 1328.5 3984 92.957500 4 3567 4 chr2B.!!$F1 3563
3 TraesCS2A01G362900 chr2D 462203360 462206879 3519 False 2747.5 3487 94.647000 1 3570 2 chr2D.!!$F1 3569

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
637 682 1.078214 CAATGCAGCGGAAGGAGGA 60.078 57.895 0.00 0.0 0.00 3.71 F
1489 3915 0.889306 ACTAGCACGACCAGGTTCTC 59.111 55.000 0.00 0.0 0.00 2.87 F
2193 4627 0.620556 GCTCAGAACCCATTGGAGGA 59.379 55.000 3.62 0.0 34.81 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 4514 0.106708 AGCAACCGAAAGAGCAGTCA 59.893 50.000 0.00 0.00 0.00 3.41 R
2333 4953 1.268625 CATGCATGCAGCCAATACGAT 59.731 47.619 26.69 1.43 44.83 3.73 R
3115 5735 3.255642 ACCCAACACCTCAAATTTCATCG 59.744 43.478 0.00 0.00 0.00 3.84 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
82 94 2.857186 TATCCTCACAAAGCTGCACA 57.143 45.000 1.02 0.00 0.00 4.57
98 110 1.804151 GCACAATAGCAGGAACGTCAA 59.196 47.619 0.00 0.00 0.00 3.18
262 274 2.643551 ACATAAGATTGCCAACTCCCG 58.356 47.619 0.00 0.00 0.00 5.14
303 315 3.711704 TCTGAAGTTCTGAACCCTGAAGT 59.288 43.478 16.48 0.00 36.04 3.01
481 522 7.173907 CCAGTTGTCTTCTGAATTCACATTACT 59.826 37.037 3.38 0.00 35.20 2.24
482 523 9.208022 CAGTTGTCTTCTGAATTCACATTACTA 57.792 33.333 3.38 0.00 35.20 1.82
483 524 9.209175 AGTTGTCTTCTGAATTCACATTACTAC 57.791 33.333 3.38 8.05 0.00 2.73
484 525 9.209175 GTTGTCTTCTGAATTCACATTACTACT 57.791 33.333 3.38 0.00 0.00 2.57
637 682 1.078214 CAATGCAGCGGAAGGAGGA 60.078 57.895 0.00 0.00 0.00 3.71
881 3289 6.952358 AGGTTAGTATGACTAGGTTTGACTGA 59.048 38.462 0.00 0.00 31.47 3.41
884 3292 6.227298 AGTATGACTAGGTTTGACTGATGG 57.773 41.667 0.00 0.00 0.00 3.51
909 3317 1.228675 ACTCTTTTGCCCCTGCCTG 60.229 57.895 0.00 0.00 36.33 4.85
1218 3633 4.767255 CTCCGGCTGCTCCACACC 62.767 72.222 0.00 0.00 34.01 4.16
1257 3672 0.904865 TCGACATGAAGTGGAGCCCT 60.905 55.000 0.00 0.00 30.91 5.19
1369 3787 5.451242 GCTTGCTACTGCTGTTACTATCTCT 60.451 44.000 0.09 0.00 40.48 3.10
1373 3791 6.261158 TGCTACTGCTGTTACTATCTCTGTAG 59.739 42.308 0.09 0.00 40.48 2.74
1425 3851 2.373836 ACAGGGCCATGTGTTAACTGTA 59.626 45.455 24.62 0.00 36.09 2.74
1477 3903 5.005490 GGCTACGTTTCATTAGAACTAGCAC 59.995 44.000 0.00 0.00 32.39 4.40
1487 3913 1.272769 AGAACTAGCACGACCAGGTTC 59.727 52.381 0.00 0.00 34.95 3.62
1489 3915 0.889306 ACTAGCACGACCAGGTTCTC 59.111 55.000 0.00 0.00 0.00 2.87
1649 4077 1.406205 GGGTTGCTCTGCTAGTCTTCC 60.406 57.143 0.00 0.00 0.00 3.46
1706 4134 6.854381 CGTTGTTCGATTAAAAAGTTAGCCTT 59.146 34.615 0.00 0.00 42.86 4.35
1717 4145 5.453567 AAAGTTAGCCTTGTGAATTCCAC 57.546 39.130 2.27 2.27 45.88 4.02
1740 4168 1.768275 TGATGCCGGGAACTGATGTAT 59.232 47.619 0.00 0.00 36.31 2.29
1741 4169 2.969262 TGATGCCGGGAACTGATGTATA 59.031 45.455 0.00 0.00 36.31 1.47
1742 4170 3.006859 TGATGCCGGGAACTGATGTATAG 59.993 47.826 0.00 0.00 36.31 1.31
1743 4171 2.394632 TGCCGGGAACTGATGTATAGT 58.605 47.619 2.18 0.00 36.31 2.12
1930 4364 1.937191 ACCAAAATGCCGATTCCCTT 58.063 45.000 0.00 0.00 0.00 3.95
2080 4514 3.260884 ACTTGTTGTACAGTGGATCGGAT 59.739 43.478 0.00 0.00 0.00 4.18
2164 4598 9.656323 AATAAGAAGACTCATACTATGGGTGTA 57.344 33.333 6.28 0.00 45.85 2.90
2193 4627 0.620556 GCTCAGAACCCATTGGAGGA 59.379 55.000 3.62 0.00 34.81 3.71
2267 4887 4.945543 TGAGATCAATGATGAAACCTGTGG 59.054 41.667 0.00 0.00 39.49 4.17
2480 5100 1.442769 AGCAGCGGAACATAACACAG 58.557 50.000 0.00 0.00 0.00 3.66
2741 5361 6.566197 AATTTATAGCTAGGCATTCACAGC 57.434 37.500 0.00 0.00 0.00 4.40
2893 5513 1.359474 ACCTGGAAGAGCCTCTGACTA 59.641 52.381 0.00 0.00 37.63 2.59
3115 5735 8.424274 AAAGTGTTGGATCATTGTTTTTCTTC 57.576 30.769 0.00 0.00 0.00 2.87
3279 5928 2.480845 ACTCAAACCACGCTTCAGTAC 58.519 47.619 0.00 0.00 0.00 2.73
3373 6022 1.220206 CAGAAGGCAGGACGCAGAT 59.780 57.895 0.00 0.00 45.17 2.90
3456 6107 8.795513 AGACATGAATCAATTTTGACATGTACA 58.204 29.630 20.52 0.00 46.22 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 6.116711 TCAGGCTAACAACTTATGTGGTTA 57.883 37.500 8.13 8.13 42.99 2.85
19 20 5.185454 TGATCAGGCTAACAACTTATGTGG 58.815 41.667 0.00 0.00 42.99 4.17
82 94 4.157840 GGGAATTTTGACGTTCCTGCTATT 59.842 41.667 1.96 0.00 42.76 1.73
94 106 3.569701 TGTGAGAGCTTGGGAATTTTGAC 59.430 43.478 0.00 0.00 0.00 3.18
98 110 3.512724 CCAATGTGAGAGCTTGGGAATTT 59.487 43.478 0.00 0.00 36.58 1.82
226 238 9.177608 CAATCTTATGTTCCAACCTCTGAAATA 57.822 33.333 0.00 0.00 0.00 1.40
231 243 4.096984 GGCAATCTTATGTTCCAACCTCTG 59.903 45.833 0.00 0.00 0.00 3.35
242 254 2.238646 TCGGGAGTTGGCAATCTTATGT 59.761 45.455 1.92 0.00 0.00 2.29
277 289 6.042638 TCAGGGTTCAGAACTTCAGAATAG 57.957 41.667 13.13 0.00 0.00 1.73
303 315 3.264947 CTCTGCTGAAATGTCGGATTGA 58.735 45.455 0.00 0.00 30.94 2.57
444 456 3.814504 AGACAACTGGTTGATGGGAAT 57.185 42.857 18.63 0.00 42.93 3.01
496 537 5.128827 GTCTCTTGGTCAATGTACATCCCTA 59.871 44.000 9.23 6.06 0.00 3.53
632 677 2.041405 CCCACTCCCCTCTCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
637 682 1.704704 GTACCTCCCACTCCCCTCT 59.295 63.158 0.00 0.00 0.00 3.69
881 3289 1.551883 GGCAAAAGAGTCAATGGCCAT 59.448 47.619 14.09 14.09 39.66 4.40
884 3292 0.247460 GGGGCAAAAGAGTCAATGGC 59.753 55.000 7.56 7.56 37.60 4.40
909 3317 2.151202 TCCCAAATCGTTGAGCTTCAC 58.849 47.619 0.00 0.00 36.83 3.18
968 3380 3.738745 ATTTCCCCCGGGATGCAGC 62.739 63.158 26.32 0.00 44.74 5.25
986 3398 2.041922 CCATCCCCAGACCCTCGA 60.042 66.667 0.00 0.00 0.00 4.04
1314 3729 1.880340 CGAGCCGTCTTCATGCTCC 60.880 63.158 5.26 0.00 46.82 4.70
1369 3787 8.458573 ACAACAGTTTTGTTCCAATATCTACA 57.541 30.769 0.00 0.00 45.53 2.74
1373 3791 9.691362 ACATAACAACAGTTTTGTTCCAATATC 57.309 29.630 10.57 0.00 45.53 1.63
1425 3851 5.877012 CAGCAGATGATACCAGTTACACTTT 59.123 40.000 0.00 0.00 0.00 2.66
1440 3866 1.524002 GTAGCCTGCCAGCAGATGA 59.476 57.895 21.01 2.46 46.30 2.92
1477 3903 2.027625 GGCAACGAGAACCTGGTCG 61.028 63.158 0.00 1.81 42.04 4.79
1487 3913 2.670905 TCGTATGAACATTGGCAACGAG 59.329 45.455 0.00 0.00 42.51 4.18
1489 3915 3.463533 TTCGTATGAACATTGGCAACG 57.536 42.857 0.00 0.00 42.51 4.10
1619 4047 2.226674 GCAGAGCAACCCAACTTTACTC 59.773 50.000 0.00 0.00 0.00 2.59
1649 4077 8.192068 TGAAAAATATGAGCAATGCATTTCAG 57.808 30.769 16.64 5.59 0.00 3.02
1717 4145 0.107508 ATCAGTTCCCGGCATCAGTG 60.108 55.000 0.00 0.00 0.00 3.66
2080 4514 0.106708 AGCAACCGAAAGAGCAGTCA 59.893 50.000 0.00 0.00 0.00 3.41
2164 4598 1.547372 GGGTTCTGAGCAATGCAACAT 59.453 47.619 8.35 0.00 0.00 2.71
2193 4627 4.653341 AGCTTCCAGTGAGTAGCATATTCT 59.347 41.667 11.81 0.00 36.11 2.40
2327 4947 3.044235 TGCAGCCAATACGATATCTGG 57.956 47.619 0.34 2.83 0.00 3.86
2333 4953 1.268625 CATGCATGCAGCCAATACGAT 59.731 47.619 26.69 1.43 44.83 3.73
2480 5100 7.275779 TGAACAAGTAGCGATAACTGAAGAATC 59.724 37.037 0.00 0.00 0.00 2.52
2573 5193 7.658525 TCAACTGGGCATAATGATGTTTTAT 57.341 32.000 0.00 0.00 35.30 1.40
2741 5361 7.538678 GTGGAAGCTTACAACAAATACTGATTG 59.461 37.037 14.43 0.00 0.00 2.67
3115 5735 3.255642 ACCCAACACCTCAAATTTCATCG 59.744 43.478 0.00 0.00 0.00 3.84
3279 5928 8.175069 TGCAAACGATAAAGAATAAAGTAGCTG 58.825 33.333 0.00 0.00 0.00 4.24
3456 6107 6.824958 ACCCATAGTTATTACCACTGTCAT 57.175 37.500 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.