Multiple sequence alignment - TraesCS7B01G091600

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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 TraesCS7B01G091600 chr7B 100.000 2111 0 0 1 2111 105256863 105254753 0.000000e+00 3899
1 TraesCS7B01G091600 chr1A 95.630 2128 70 17 1 2107 554458199 554460324 0.000000e+00 3393
2 TraesCS7B01G091600 chr1D 95.611 2119 79 10 1 2107 254416797 254418913 0.000000e+00 3386
3 TraesCS7B01G091600 chr1D 94.499 2127 90 15 4 2107 51878338 51876216 0.000000e+00 3254
4 TraesCS7B01G091600 chr6D 94.974 2129 74 21 4 2107 45511836 45509716 0.000000e+00 3308
5 TraesCS7B01G091600 chr5D 94.717 2139 79 17 1 2107 503287032 503289168 0.000000e+00 3293
6 TraesCS7B01G091600 chr5D 94.283 2134 84 20 4 2111 6181211 6179090 0.000000e+00 3230
7 TraesCS7B01G091600 chr2B 95.720 2056 70 15 64 2107 474900137 474902186 0.000000e+00 3293
8 TraesCS7B01G091600 chr5A 94.747 2113 95 15 4 2107 607200355 607198250 0.000000e+00 3273
9 TraesCS7B01G091600 chr4B 93.599 1531 74 14 589 2107 308683448 308681930 0.000000e+00 2263
10 TraesCS7B01G091600 chr2A 94.592 1054 43 5 4 1045 335830892 335829841 0.000000e+00 1618
11 TraesCS7B01G091600 chr3B 95.750 800 31 3 4 800 101919310 101918511 0.000000e+00 1286
12 TraesCS7B01G091600 chr3B 93.333 165 5 5 484 648 796323883 796323725 2.710000e-59 239


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 TraesCS7B01G091600 chr7B 105254753 105256863 2110 True 3899 3899 100.000 1 2111 1 chr7B.!!$R1 2110
1 TraesCS7B01G091600 chr1A 554458199 554460324 2125 False 3393 3393 95.630 1 2107 1 chr1A.!!$F1 2106
2 TraesCS7B01G091600 chr1D 254416797 254418913 2116 False 3386 3386 95.611 1 2107 1 chr1D.!!$F1 2106
3 TraesCS7B01G091600 chr1D 51876216 51878338 2122 True 3254 3254 94.499 4 2107 1 chr1D.!!$R1 2103
4 TraesCS7B01G091600 chr6D 45509716 45511836 2120 True 3308 3308 94.974 4 2107 1 chr6D.!!$R1 2103
5 TraesCS7B01G091600 chr5D 503287032 503289168 2136 False 3293 3293 94.717 1 2107 1 chr5D.!!$F1 2106
6 TraesCS7B01G091600 chr5D 6179090 6181211 2121 True 3230 3230 94.283 4 2111 1 chr5D.!!$R1 2107
7 TraesCS7B01G091600 chr2B 474900137 474902186 2049 False 3293 3293 95.720 64 2107 1 chr2B.!!$F1 2043
8 TraesCS7B01G091600 chr5A 607198250 607200355 2105 True 3273 3273 94.747 4 2107 1 chr5A.!!$R1 2103
9 TraesCS7B01G091600 chr4B 308681930 308683448 1518 True 2263 2263 93.599 589 2107 1 chr4B.!!$R1 1518
10 TraesCS7B01G091600 chr2A 335829841 335830892 1051 True 1618 1618 94.592 4 1045 1 chr2A.!!$R1 1041
11 TraesCS7B01G091600 chr3B 101918511 101919310 799 True 1286 1286 95.750 4 800 1 chr3B.!!$R1 796

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
605 609 0.523519 GGCAAGCTGCTGTAGGTTTC 59.476 55.0 1.35 3.24 44.32 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 1751 3.834813 AGAATAGCGGATAGAGGCATCAA 59.165 43.478 0.0 0.0 0.0 2.57 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
42 43 3.447944 AGGATTCGAACCTCTGAGTAACC 59.552 47.826 0.00 0.00 31.43 2.85
114 115 9.469239 GTTTTATGCGACACTAATAAACACTAC 57.531 33.333 0.00 0.00 0.00 2.73
186 187 6.876257 GGAGGGATATTGTCTTGCTAGTATTG 59.124 42.308 0.00 0.00 0.00 1.90
193 194 9.884636 ATATTGTCTTGCTAGTATTGTACACAA 57.115 29.630 0.00 0.00 40.51 3.33
194 195 8.615878 ATTGTCTTGCTAGTATTGTACACAAA 57.384 30.769 0.00 0.00 39.55 2.83
600 604 0.953727 TGTTTGGCAAGCTGCTGTAG 59.046 50.000 15.19 0.00 44.28 2.74
605 609 0.523519 GGCAAGCTGCTGTAGGTTTC 59.476 55.000 1.35 3.24 44.32 2.78
651 655 7.160049 TGTATGCCAAATTGAATGATGTGTTT 58.840 30.769 0.00 0.00 0.00 2.83
655 659 9.887629 ATGCCAAATTGAATGATGTGTTTATTA 57.112 25.926 0.00 0.00 0.00 0.98
691 699 7.571080 AAAATGGGTAAAAGTCGACAAGTTA 57.429 32.000 19.50 9.66 0.00 2.24
782 790 8.592809 ACAACAATAAATTTGGATCAGCCTTTA 58.407 29.630 0.00 0.00 37.63 1.85
852 880 6.605995 ACCACCTAACCCTATTTTTGCTATTC 59.394 38.462 0.00 0.00 0.00 1.75
1054 1091 8.660373 CAGTAGTGATATTCTTTGTTTCACTCC 58.340 37.037 7.11 0.00 44.27 3.85
1118 1155 4.202377 TGGACACGAGGAGTAAAAATTCCA 60.202 41.667 0.00 0.00 35.88 3.53
1149 1190 9.834628 TTCTTATTGGATTTGTTTCGTACATTC 57.165 29.630 0.00 0.00 36.44 2.67
1309 1350 0.803768 CAGCCATCTCTCCACGTTCG 60.804 60.000 0.00 0.00 0.00 3.95
1341 1382 7.792364 AAGGTTTCCGTGATATGATATAGGA 57.208 36.000 1.26 1.26 0.00 2.94
1342 1383 7.979786 AGGTTTCCGTGATATGATATAGGAT 57.020 36.000 5.13 0.00 0.00 3.24
1683 1743 6.223351 AGCATAAAGTAAGTAGACCTGACC 57.777 41.667 0.00 0.00 0.00 4.02
1691 1751 6.269974 AGTAAGTAGACCTGACCCCTTTAAT 58.730 40.000 0.00 0.00 0.00 1.40
1781 1843 8.358582 TCTTTATTTCCTTAGACTTAGACCGT 57.641 34.615 0.00 0.00 0.00 4.83
1808 1870 9.076596 GCAAGACAAGAATTTTTCGCTATTTAT 57.923 29.630 0.00 0.00 34.02 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.960689 CCTTCCGTCCCACATTGTTTT 59.039 47.619 0.00 0.00 0.00 2.43
10 11 0.248289 TTCGAATCCTTCCGTCCCAC 59.752 55.000 0.00 0.00 0.00 4.61
34 35 1.202794 GGGTTTTGGTCCGGTTACTCA 60.203 52.381 0.00 0.00 0.00 3.41
172 173 9.582431 TCTATTTGTGTACAATACTAGCAAGAC 57.418 33.333 0.00 0.00 35.55 3.01
261 262 7.606073 TCAAATGAGAGTGGAATAAATTCGACA 59.394 33.333 16.81 0.46 44.64 4.35
293 294 9.981114 CAAACACAAAATACCTCCTTTTATTCT 57.019 29.630 0.00 0.00 0.00 2.40
299 300 5.212745 TCCCAAACACAAAATACCTCCTTT 58.787 37.500 0.00 0.00 0.00 3.11
600 604 7.764901 AGAGTACTAAAGATTTCATCGGAAACC 59.235 37.037 0.00 0.00 45.22 3.27
605 609 9.186323 CATACAGAGTACTAAAGATTTCATCGG 57.814 37.037 0.00 0.00 0.00 4.18
742 750 7.624360 TTTATTGTTGTAGCTACCCATTCAG 57.376 36.000 21.01 0.00 0.00 3.02
782 790 0.032416 ACGTAGGTGCAGGGGAGTAT 60.032 55.000 0.00 0.00 0.00 2.12
934 969 1.134788 CCTTACCACACGGATCCACTC 60.135 57.143 13.41 0.00 35.59 3.51
1149 1190 3.073062 ACCCCCGGATTTTCTCATAGATG 59.927 47.826 0.73 0.00 0.00 2.90
1267 1308 5.246203 TGAGTGGACTAAAGCAGTAGATTGT 59.754 40.000 1.04 0.00 37.72 2.71
1273 1314 2.233922 GGCTGAGTGGACTAAAGCAGTA 59.766 50.000 13.28 0.00 37.72 2.74
1309 1350 1.600485 TCACGGAAACCTTTCGCTTTC 59.400 47.619 0.00 0.00 38.06 2.62
1515 1572 5.405935 AAATGCCCGCTAAAGAGAAAATT 57.594 34.783 0.00 0.00 0.00 1.82
1683 1743 4.697352 CGGATAGAGGCATCAATTAAAGGG 59.303 45.833 0.00 0.00 0.00 3.95
1691 1751 3.834813 AGAATAGCGGATAGAGGCATCAA 59.165 43.478 0.00 0.00 0.00 2.57
1757 1817 7.010275 GCACGGTCTAAGTCTAAGGAAATAAAG 59.990 40.741 0.00 0.00 0.00 1.85
1781 1843 4.305989 AGCGAAAAATTCTTGTCTTGCA 57.694 36.364 0.00 0.00 0.00 4.08
1841 1903 8.924511 AAGGAGTTGTGATTTCTTCTTATTCA 57.075 30.769 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.