Multiple sequence alignment - TraesCS5D01G092800

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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 TraesCS5D01G092800 chr5D 100.000 4274 0 0 1 4274 101697438 101701711 0.000000e+00 7893
1 TraesCS5D01G092800 chr5D 78.868 265 46 6 958 1213 101460633 101460370 2.040000e-38 171
2 TraesCS5D01G092800 chr5A 97.289 3431 63 19 1 3427 98454550 98451146 0.000000e+00 5794
3 TraesCS5D01G092800 chr5A 98.971 486 5 0 3419 3904 98449191 98448706 0.000000e+00 870
4 TraesCS5D01G092800 chr5A 99.110 337 3 0 3938 4274 98448706 98448370 1.310000e-169 606
5 TraesCS5D01G092800 chr5A 78.868 265 46 6 958 1213 98978640 98978903 2.040000e-38 171
6 TraesCS5D01G092800 chr5B 97.324 3176 58 12 354 3524 110112949 110116102 0.000000e+00 5369
7 TraesCS5D01G092800 chr5B 97.753 356 8 0 1 356 110112481 110112836 7.850000e-172 614
8 TraesCS5D01G092800 chr5B 90.184 163 12 1 4112 4274 110116479 110116637 4.330000e-50 209
9 TraesCS5D01G092800 chr5B 78.113 265 48 6 958 1213 109889050 109888787 4.420000e-35 159


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 TraesCS5D01G092800 chr5D 101697438 101701711 4273 False 7893.000000 7893 100.000000 1 4274 1 chr5D.!!$F1 4273
1 TraesCS5D01G092800 chr5A 98448370 98454550 6180 True 2423.333333 5794 98.456667 1 4274 3 chr5A.!!$R1 4273
2 TraesCS5D01G092800 chr5B 110112481 110116637 4156 False 2064.000000 5369 95.087000 1 4274 3 chr5B.!!$F1 4273

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
558 674 2.242926 GGGAAAGCCTCTCTTTTGCTT 58.757 47.619 0.00 0.00 44.58 3.91 F
1021 1140 0.179078 GGCTGAGACAGGAGATGCAG 60.179 60.000 0.00 0.00 31.21 4.41 F
1561 1680 0.327259 ATGAAGAGCTGGCAGCAGAA 59.673 50.000 38.09 20.23 45.56 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 2184 1.947456 GGGTGCATAAAGATTCGTCCC 59.053 52.381 0.0 0.0 0.00 4.46 R
2296 2417 2.806244 GCCTCGAGCTCAGTGTTTAAAA 59.194 45.455 15.4 0.0 38.99 1.52 R
3285 3409 1.600636 ATCCTGTTGCACCACCACG 60.601 57.895 0.0 0.0 0.00 4.94 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
337 338 6.821388 AGAGAGTACTTTGACTTCACACATT 58.179 36.000 0.00 0.00 0.00 2.71
344 345 6.215845 ACTTTGACTTCACACATTATTTGGC 58.784 36.000 0.00 0.00 0.00 4.52
511 627 5.241949 GGATCGATGTAAGTCAGTCTGGTAT 59.758 44.000 0.54 0.00 0.00 2.73
558 674 2.242926 GGGAAAGCCTCTCTTTTGCTT 58.757 47.619 0.00 0.00 44.58 3.91
674 793 2.471462 ACCTTAGGTGGGACCCAAC 58.529 57.895 22.12 22.12 42.50 3.77
926 1045 2.267192 GACTTCCTAGTTCCAACCCCT 58.733 52.381 0.00 0.00 33.84 4.79
1021 1140 0.179078 GGCTGAGACAGGAGATGCAG 60.179 60.000 0.00 0.00 31.21 4.41
1561 1680 0.327259 ATGAAGAGCTGGCAGCAGAA 59.673 50.000 38.09 20.23 45.56 3.02
1905 2024 6.696441 AGCTCAAATGATCTTGGAAGATTC 57.304 37.500 3.42 0.00 45.39 2.52
1998 2118 9.429359 GACATGGAATCAGTGTATTATCTTAGG 57.571 37.037 0.00 0.00 0.00 2.69
2027 2147 3.897505 CCAGAGTTCAAAATTTCCCACCT 59.102 43.478 0.00 0.00 0.00 4.00
2063 2184 7.860613 TGTATTTTCAGTATCATGTAATGCCG 58.139 34.615 0.00 0.00 46.21 5.69
2296 2417 8.651589 TCCGTTATAGATAATCCTGATCAAGT 57.348 34.615 0.00 0.00 0.00 3.16
2364 2485 4.287067 TCCACTCTAAGCTGATTGAGGTTT 59.713 41.667 0.00 0.00 42.52 3.27
2387 2508 6.114187 TGGTTGTTCTCTGTTGATATCAGT 57.886 37.500 5.39 0.00 34.86 3.41
2400 2522 8.109705 TGTTGATATCAGTTACAGCAAACATT 57.890 30.769 5.39 0.00 0.00 2.71
3099 3221 9.436957 CTTCTGCCTCTTAAAGATTGTTTACTA 57.563 33.333 0.00 0.00 0.00 1.82
3270 3394 0.250038 GGGATCTATGCAGCGCAAGA 60.250 55.000 11.47 4.45 43.62 3.02
3285 3409 2.044123 CAAGATGACCTTGTAGGGGC 57.956 55.000 0.00 0.00 45.52 5.80
3575 5945 4.723309 AGAAAGCAATTCAAGTCCTGAGT 58.277 39.130 5.24 0.00 40.72 3.41
3768 6142 6.426633 GGCAGTTGTTTTGGCTAATTAATTGT 59.573 34.615 11.05 0.00 38.03 2.71
3793 6167 5.446473 CGTGAAGATGCCATAACTTCTGAAC 60.446 44.000 0.00 0.00 40.13 3.18
3892 6266 9.325198 GGTTTTCTTAGTTTTCATCCATTTTGT 57.675 29.630 0.00 0.00 0.00 2.83
3903 6277 2.170166 TCCATTTTGTGCCTTGGCTAG 58.830 47.619 13.18 0.00 0.00 3.42
3913 6287 2.660189 CCTTGGCTAGGCACAAAATG 57.340 50.000 20.09 5.22 37.17 2.32
3914 6288 2.170166 CCTTGGCTAGGCACAAAATGA 58.830 47.619 20.09 1.03 37.17 2.57
3915 6289 2.762327 CCTTGGCTAGGCACAAAATGAT 59.238 45.455 20.09 0.00 37.17 2.45
3916 6290 3.429822 CCTTGGCTAGGCACAAAATGATG 60.430 47.826 20.09 0.00 37.17 3.07
3917 6291 1.477700 TGGCTAGGCACAAAATGATGC 59.522 47.619 16.16 0.00 41.29 3.91
3922 6296 3.446507 GCACAAAATGATGCCTGGG 57.553 52.632 0.00 0.00 35.73 4.45
3923 6297 0.741927 GCACAAAATGATGCCTGGGC 60.742 55.000 4.43 4.43 42.35 5.36
3924 6298 0.899720 CACAAAATGATGCCTGGGCT 59.100 50.000 13.05 0.00 42.51 5.19
3925 6299 2.101783 CACAAAATGATGCCTGGGCTA 58.898 47.619 13.05 0.04 42.51 3.93
3926 6300 2.102578 ACAAAATGATGCCTGGGCTAC 58.897 47.619 13.05 7.30 42.51 3.58
3927 6301 1.410153 CAAAATGATGCCTGGGCTACC 59.590 52.381 13.05 2.89 42.51 3.18
3928 6302 0.929244 AAATGATGCCTGGGCTACCT 59.071 50.000 13.05 0.00 42.51 3.08
3929 6303 0.184451 AATGATGCCTGGGCTACCTG 59.816 55.000 13.05 0.00 42.51 4.00
3930 6304 0.990282 ATGATGCCTGGGCTACCTGT 60.990 55.000 13.05 0.00 42.51 4.00
3931 6305 1.153086 GATGCCTGGGCTACCTGTG 60.153 63.158 13.05 0.00 42.51 3.66
3932 6306 3.350031 ATGCCTGGGCTACCTGTGC 62.350 63.158 13.05 0.00 42.51 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
511 627 4.440802 CCGATTTCACAAAACCAGGTTCAA 60.441 41.667 4.93 0.00 0.00 2.69
674 793 5.110814 TGTGTCCCCATAATAAAGGTCAG 57.889 43.478 0.00 0.00 0.00 3.51
893 1012 7.117956 GGAACTAGGAAGTCAGTGTACAATTTC 59.882 40.741 0.00 0.00 33.75 2.17
926 1045 4.160814 CCAAGATGGCCAAAATCAGAATCA 59.839 41.667 10.96 0.00 0.00 2.57
1021 1140 2.700773 GGGATGTTGGCAAGCGACC 61.701 63.158 0.00 2.12 0.00 4.79
1217 1336 4.404394 TCTGATCTAAACGGGCACTATTCA 59.596 41.667 0.00 0.00 0.00 2.57
1561 1680 4.041444 AGCTGTTCCTTCAGAGATTCAAGT 59.959 41.667 0.00 0.00 37.61 3.16
1905 2024 3.496130 CCAGAGACACTACTGCACAAAAG 59.504 47.826 0.00 0.00 33.40 2.27
1998 2118 6.294564 GGGAAATTTTGAACTCTGGTAAGTCC 60.295 42.308 0.00 0.00 0.00 3.85
2027 2147 9.126151 TGATACTGAAAATACAGACACCAAAAA 57.874 29.630 0.00 0.00 40.63 1.94
2063 2184 1.947456 GGGTGCATAAAGATTCGTCCC 59.053 52.381 0.00 0.00 0.00 4.46
2296 2417 2.806244 GCCTCGAGCTCAGTGTTTAAAA 59.194 45.455 15.40 0.00 38.99 1.52
2364 2485 6.114187 ACTGATATCAACAGAGAACAACCA 57.886 37.500 6.90 0.00 38.55 3.67
2387 2508 4.022416 GTGTGATGGGAATGTTTGCTGTAA 60.022 41.667 0.00 0.00 0.00 2.41
3099 3221 4.768448 TGCTGAAAACATGACTCCAATCAT 59.232 37.500 0.00 0.00 40.03 2.45
3189 3311 6.642540 GCAACTATTATGCATTTAAGAAGGCC 59.357 38.462 3.54 0.00 41.64 5.19
3270 3394 1.602237 CACGCCCCTACAAGGTCAT 59.398 57.895 0.00 0.00 31.93 3.06
3285 3409 1.600636 ATCCTGTTGCACCACCACG 60.601 57.895 0.00 0.00 0.00 4.94
3575 5945 1.186200 AGATTGCGAGCTACCTGTCA 58.814 50.000 0.00 0.00 0.00 3.58
3768 6142 4.081697 TCAGAAGTTATGGCATCTTCACGA 60.082 41.667 23.20 17.76 39.69 4.35
3866 6240 9.325198 ACAAAATGGATGAAAACTAAGAAAACC 57.675 29.630 0.00 0.00 0.00 3.27
3904 6278 0.741927 GCCCAGGCATCATTTTGTGC 60.742 55.000 3.12 0.00 41.49 4.57
3905 6279 0.899720 AGCCCAGGCATCATTTTGTG 59.100 50.000 12.03 0.00 44.88 3.33
3906 6280 2.102578 GTAGCCCAGGCATCATTTTGT 58.897 47.619 12.03 0.00 44.88 2.83
3907 6281 1.410153 GGTAGCCCAGGCATCATTTTG 59.590 52.381 12.03 0.00 44.88 2.44
3908 6282 1.288932 AGGTAGCCCAGGCATCATTTT 59.711 47.619 12.03 0.00 44.88 1.82
3909 6283 0.929244 AGGTAGCCCAGGCATCATTT 59.071 50.000 12.03 0.00 44.88 2.32
3910 6284 0.184451 CAGGTAGCCCAGGCATCATT 59.816 55.000 12.03 0.00 44.88 2.57
3911 6285 0.990282 ACAGGTAGCCCAGGCATCAT 60.990 55.000 12.03 0.00 44.88 2.45
3912 6286 1.616327 ACAGGTAGCCCAGGCATCA 60.616 57.895 12.03 0.00 44.88 3.07
3913 6287 1.153086 CACAGGTAGCCCAGGCATC 60.153 63.158 12.03 3.05 44.88 3.91
3914 6288 3.001514 CACAGGTAGCCCAGGCAT 58.998 61.111 12.03 0.00 44.88 4.40
3915 6289 4.033776 GCACAGGTAGCCCAGGCA 62.034 66.667 12.03 0.00 44.88 4.75
3916 6290 4.803908 GGCACAGGTAGCCCAGGC 62.804 72.222 0.00 0.00 46.50 4.85
3922 6296 0.035439 TTAGCCAAGGCACAGGTAGC 60.035 55.000 14.40 0.00 44.88 3.58
3923 6297 1.279271 ACTTAGCCAAGGCACAGGTAG 59.721 52.381 14.40 3.67 44.88 3.18
3924 6298 1.003118 CACTTAGCCAAGGCACAGGTA 59.997 52.381 14.40 0.00 44.88 3.08
3925 6299 0.250901 CACTTAGCCAAGGCACAGGT 60.251 55.000 14.40 4.35 44.88 4.00
3926 6300 0.036732 TCACTTAGCCAAGGCACAGG 59.963 55.000 14.40 3.71 44.88 4.00
3927 6301 1.160137 GTCACTTAGCCAAGGCACAG 58.840 55.000 14.40 10.59 44.88 3.66
3928 6302 0.764890 AGTCACTTAGCCAAGGCACA 59.235 50.000 14.40 0.00 44.88 4.57
3929 6303 2.289444 TGTAGTCACTTAGCCAAGGCAC 60.289 50.000 14.40 1.26 44.88 5.01
3930 6304 1.974957 TGTAGTCACTTAGCCAAGGCA 59.025 47.619 14.40 0.00 44.88 4.75
3931 6305 2.762535 TGTAGTCACTTAGCCAAGGC 57.237 50.000 2.02 2.02 42.33 4.35
3932 6306 2.939103 GCATGTAGTCACTTAGCCAAGG 59.061 50.000 0.00 0.00 35.97 3.61
3933 6307 3.866651 AGCATGTAGTCACTTAGCCAAG 58.133 45.455 0.00 0.00 37.81 3.61
3934 6308 3.260632 TGAGCATGTAGTCACTTAGCCAA 59.739 43.478 0.00 0.00 0.00 4.52
3935 6309 2.831526 TGAGCATGTAGTCACTTAGCCA 59.168 45.455 0.00 0.00 0.00 4.75
3936 6310 3.526931 TGAGCATGTAGTCACTTAGCC 57.473 47.619 0.00 0.00 0.00 3.93
4141 6515 6.407187 ATGCACACATTATTAATGGCACATGT 60.407 34.615 18.24 11.08 43.21 3.21
4200 6574 5.510009 GGCATGCCATGATAATCATTTGACA 60.510 40.000 32.08 0.00 34.28 3.58


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

AutoCloner maintained by Alex Coulton.