Multiple sequence alignment - TraesCS1A01G276700

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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 TraesCS1A01G276700 chr1A 100.000 2327 0 0 1 2327 471705692 471708018 0 4298
1 TraesCS1A01G276700 chr1A 87.174 1497 181 8 833 2327 168565871 168567358 0 1690
2 TraesCS1A01G276700 chr1A 87.888 1354 152 11 979 2327 554076594 554077940 0 1581
3 TraesCS1A01G276700 chr5D 96.608 2329 74 5 1 2327 223873451 223871126 0 3858
4 TraesCS1A01G276700 chr5D 85.792 1295 178 6 1 1292 277275601 277276892 0 1367
5 TraesCS1A01G276700 chr7D 92.532 2330 154 10 1 2327 498246951 498244639 0 3321
6 TraesCS1A01G276700 chr7D 88.435 1591 183 1 1 1591 3204784 3203195 0 1917
7 TraesCS1A01G276700 chr1D 92.275 2330 160 11 1 2327 486056414 486058726 0 3288
8 TraesCS1A01G276700 chr2D 88.269 2259 248 13 1 2251 417973311 417975560 0 2687
9 TraesCS1A01G276700 chr3B 86.809 2335 275 26 1 2327 733085042 733082733 0 2575
10 TraesCS1A01G276700 chr3B 86.591 2282 288 12 1 2275 9911370 9909100 0 2503
11 TraesCS1A01G276700 chr3B 83.901 2230 334 13 1 2224 54862634 54864844 0 2106
12 TraesCS1A01G276700 chr5A 86.027 2333 307 18 4 2327 241748586 241746264 0 2484


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 TraesCS1A01G276700 chr1A 471705692 471708018 2326 False 4298 4298 100.000 1 2327 1 chr1A.!!$F2 2326
1 TraesCS1A01G276700 chr1A 168565871 168567358 1487 False 1690 1690 87.174 833 2327 1 chr1A.!!$F1 1494
2 TraesCS1A01G276700 chr1A 554076594 554077940 1346 False 1581 1581 87.888 979 2327 1 chr1A.!!$F3 1348
3 TraesCS1A01G276700 chr5D 223871126 223873451 2325 True 3858 3858 96.608 1 2327 1 chr5D.!!$R1 2326
4 TraesCS1A01G276700 chr5D 277275601 277276892 1291 False 1367 1367 85.792 1 1292 1 chr5D.!!$F1 1291
5 TraesCS1A01G276700 chr7D 498244639 498246951 2312 True 3321 3321 92.532 1 2327 1 chr7D.!!$R2 2326
6 TraesCS1A01G276700 chr7D 3203195 3204784 1589 True 1917 1917 88.435 1 1591 1 chr7D.!!$R1 1590
7 TraesCS1A01G276700 chr1D 486056414 486058726 2312 False 3288 3288 92.275 1 2327 1 chr1D.!!$F1 2326
8 TraesCS1A01G276700 chr2D 417973311 417975560 2249 False 2687 2687 88.269 1 2251 1 chr2D.!!$F1 2250
9 TraesCS1A01G276700 chr3B 733082733 733085042 2309 True 2575 2575 86.809 1 2327 1 chr3B.!!$R2 2326
10 TraesCS1A01G276700 chr3B 9909100 9911370 2270 True 2503 2503 86.591 1 2275 1 chr3B.!!$R1 2274
11 TraesCS1A01G276700 chr3B 54862634 54864844 2210 False 2106 2106 83.901 1 2224 1 chr3B.!!$F1 2223
12 TraesCS1A01G276700 chr5A 241746264 241748586 2322 True 2484 2484 86.027 4 2327 1 chr5A.!!$R1 2323

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
720 724 4.754322 TGACTTGCTTTGAAAACCTTTCC 58.246 39.13 0.0 0.0 0.0 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2248 2292 1.228124 CCAACGCCAGGAGAAACCA 60.228 57.895 0.0 0.0 42.04 3.67 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
255 256 6.538381 GGTTCATTTTGGAAAGTGTTGTGATT 59.462 34.615 0.00 0.00 0.00 2.57
332 333 7.554118 TCTTAAGTTGGATTATGAGAAGGCTTG 59.446 37.037 3.46 0.00 0.00 4.01
355 356 5.825679 TGTGATAGGGTTAATTGGGATTTCG 59.174 40.000 0.00 0.00 0.00 3.46
429 431 8.442374 TGGGTTTTTAGTACTCTTTATCAAGGT 58.558 33.333 0.00 0.00 0.00 3.50
553 557 5.781210 TGCTGATGTGTTTACCAAAATGA 57.219 34.783 0.00 0.00 0.00 2.57
720 724 4.754322 TGACTTGCTTTGAAAACCTTTCC 58.246 39.130 0.00 0.00 0.00 3.13
847 870 5.205517 TCCATTCAAATATCTTGGGGTGT 57.794 39.130 0.00 0.00 0.00 4.16
1070 1097 4.141390 ACAGATGTCTCACTTCTTTTGGGT 60.141 41.667 0.00 0.00 31.20 4.51
1102 1130 6.772716 GGGTGACAATCATAAATACCATCTGT 59.227 38.462 0.00 0.00 0.00 3.41
1225 1266 7.304054 AGATTCTATGATGGGAGGGATAGTA 57.696 40.000 0.00 0.00 0.00 1.82
1228 1269 5.590818 TCTATGATGGGAGGGATAGTAACC 58.409 45.833 0.00 0.00 0.00 2.85
1325 1366 4.106663 TCCCTTTTGGAAAAGCCTAACCTA 59.893 41.667 6.37 0.00 43.07 3.08
1372 1413 5.694995 TCATTAGTTGGATCCCTGGAAATC 58.305 41.667 9.90 0.00 0.00 2.17
1451 1492 3.960102 AGATTTTGGGAGCTGTTTGACAA 59.040 39.130 0.00 0.00 0.00 3.18
1517 1558 7.230510 TGGCAATACTTTACAGTTGACTTTCAT 59.769 33.333 0.00 0.00 34.06 2.57
1724 1766 2.721906 TCTGGAAAATCAAAGTCCCCCT 59.278 45.455 0.00 0.00 0.00 4.79
1745 1787 7.663493 CCCCCTTAATATTCATGTCTTTCTCTC 59.337 40.741 0.00 0.00 0.00 3.20
1784 1826 9.202273 CAATAAGTGCTTGACTAGAGATAATCC 57.798 37.037 0.00 0.00 33.09 3.01
1817 1859 5.144159 AGACATGTGGAAGATCCTACCTA 57.856 43.478 1.15 0.00 37.46 3.08
1827 1870 7.927092 GTGGAAGATCCTACCTATGTTTTCTAC 59.073 40.741 0.00 0.00 37.46 2.59
2029 2073 0.524180 GCTTATGGCTTCTGCGCAAC 60.524 55.000 13.05 0.59 40.82 4.17
2148 2192 3.483587 GGGTGCACCTCTTCTCCA 58.516 61.111 33.91 0.00 35.85 3.86
2248 2292 4.334481 CAGAACTTTAGTCCACCGTGTTTT 59.666 41.667 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
210 211 1.005215 CTCCCCTTGATGAAGGCAGTT 59.995 52.381 5.26 0.00 46.89 3.16
332 333 5.826208 ACGAAATCCCAATTAACCCTATCAC 59.174 40.000 0.00 0.00 0.00 3.06
553 557 1.885163 GCTCTGGCAGCTTTGGCAAT 61.885 55.000 10.34 0.00 45.83 3.56
847 870 9.838339 CCTCCTAAGCTTTTTATAATGAAGAGA 57.162 33.333 3.20 0.00 0.00 3.10
912 938 3.449746 TTACCTAACCAGCCAGCAATT 57.550 42.857 0.00 0.00 0.00 2.32
1070 1097 7.068103 GGTATTTATGATTGTCACCCACATTGA 59.932 37.037 0.00 0.00 33.90 2.57
1102 1130 0.539986 GCAATCGACCCCCAACTAGA 59.460 55.000 0.00 0.00 0.00 2.43
1372 1413 1.466167 CCAGAAGGCAATGTTCTCACG 59.534 52.381 0.00 0.00 31.64 4.35
1451 1492 2.297033 GTGGCATCCTGTTGTTGACAAT 59.703 45.455 0.00 0.00 37.93 2.71
1517 1558 5.876651 AATGCTATCATCTACACACCTCA 57.123 39.130 0.00 0.00 31.27 3.86
1724 1766 9.684448 CTAGCGAGAGAAAGACATGAATATTAA 57.316 33.333 0.00 0.00 0.00 1.40
1745 1787 5.230942 AGCACTTATTGTTATAGGCTAGCG 58.769 41.667 9.00 0.00 0.00 4.26
1784 1826 2.082231 CCACATGTCTTCTCTTGGCTG 58.918 52.381 0.00 0.00 0.00 4.85
1817 1859 6.404293 CGATTCATTTTCCCCGTAGAAAACAT 60.404 38.462 10.86 5.48 45.72 2.71
1827 1870 6.142817 GTGATTAATCGATTCATTTTCCCCG 58.857 40.000 15.25 0.00 0.00 5.73
1988 2032 1.742761 CACAAGGTAGCAGATGTGGG 58.257 55.000 14.18 0.00 39.51 4.61
2029 2073 1.665735 CGCCCCTGAAACACAAATTCG 60.666 52.381 0.00 0.00 0.00 3.34
2137 2181 2.569404 CCTTAAGCACTGGAGAAGAGGT 59.431 50.000 0.00 0.00 0.00 3.85
2248 2292 1.228124 CCAACGCCAGGAGAAACCA 60.228 57.895 0.00 0.00 42.04 3.67


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

AutoCloner maintained by Alex Coulton.