Multiple sequence alignment - TraesCS2A01G257500

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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 TraesCS2A01G257500 chr2A 100.000 2396 0 0 1 2396 395711460 395709065 0 4425
1 TraesCS2A01G257500 chr2A 98.499 2398 15 5 1 2396 405469135 405471513 0 4209
2 TraesCS2A01G257500 chr2A 93.847 1739 75 12 672 2396 166818378 166816658 0 2590
3 TraesCS2A01G257500 chr6B 97.106 1693 33 4 719 2396 246983361 246985052 0 2841
4 TraesCS2A01G257500 chr6B 98.305 708 12 0 1 708 168772768 168773475 0 1242
5 TraesCS2A01G257500 chr7B 94.768 1701 68 8 710 2396 257652454 257654147 0 2628
6 TraesCS2A01G257500 chr7B 99.435 708 4 0 1 708 49029234 49028527 0 1286
7 TraesCS2A01G257500 chr5B 94.665 1687 70 7 727 2396 47328170 47326487 0 2599
8 TraesCS2A01G257500 chr5B 94.027 1691 74 8 727 2396 47323125 47321441 0 2538
9 TraesCS2A01G257500 chr7A 94.559 1691 71 8 720 2396 299313386 299311703 0 2593
10 TraesCS2A01G257500 chr5A 94.756 1678 67 8 733 2396 484830714 484832384 0 2591
11 TraesCS2A01G257500 chr1A 94.382 1691 74 8 720 2396 546232108 546233791 0 2577
12 TraesCS2A01G257500 chr1A 91.620 716 46 10 1 708 520856242 520856951 0 977
13 TraesCS2A01G257500 chr1B 93.672 1691 72 13 720 2396 526807651 526809320 0 2497
14 TraesCS2A01G257500 chr2D 93.735 1692 60 11 720 2396 646477307 646475647 0 2495
15 TraesCS2A01G257500 chr3A 99.011 708 7 0 1 708 699163810 699164517 0 1269
16 TraesCS2A01G257500 chr3A 91.213 717 48 10 1 708 703928421 703927711 0 961
17 TraesCS2A01G257500 chr2B 98.202 723 13 0 1 723 57157665 57156943 0 1264
18 TraesCS2A01G257500 chr2B 92.190 717 48 5 1 711 609285800 609285086 0 1007
19 TraesCS2A01G257500 chr3B 97.881 708 15 0 1 708 795068259 795068966 0 1225


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 TraesCS2A01G257500 chr2A 395709065 395711460 2395 True 4425.0 4425 100.000 1 2396 1 chr2A.!!$R2 2395
1 TraesCS2A01G257500 chr2A 405469135 405471513 2378 False 4209.0 4209 98.499 1 2396 1 chr2A.!!$F1 2395
2 TraesCS2A01G257500 chr2A 166816658 166818378 1720 True 2590.0 2590 93.847 672 2396 1 chr2A.!!$R1 1724
3 TraesCS2A01G257500 chr6B 246983361 246985052 1691 False 2841.0 2841 97.106 719 2396 1 chr6B.!!$F2 1677
4 TraesCS2A01G257500 chr6B 168772768 168773475 707 False 1242.0 1242 98.305 1 708 1 chr6B.!!$F1 707
5 TraesCS2A01G257500 chr7B 257652454 257654147 1693 False 2628.0 2628 94.768 710 2396 1 chr7B.!!$F1 1686
6 TraesCS2A01G257500 chr7B 49028527 49029234 707 True 1286.0 1286 99.435 1 708 1 chr7B.!!$R1 707
7 TraesCS2A01G257500 chr5B 47321441 47328170 6729 True 2568.5 2599 94.346 727 2396 2 chr5B.!!$R1 1669
8 TraesCS2A01G257500 chr7A 299311703 299313386 1683 True 2593.0 2593 94.559 720 2396 1 chr7A.!!$R1 1676
9 TraesCS2A01G257500 chr5A 484830714 484832384 1670 False 2591.0 2591 94.756 733 2396 1 chr5A.!!$F1 1663
10 TraesCS2A01G257500 chr1A 546232108 546233791 1683 False 2577.0 2577 94.382 720 2396 1 chr1A.!!$F2 1676
11 TraesCS2A01G257500 chr1A 520856242 520856951 709 False 977.0 977 91.620 1 708 1 chr1A.!!$F1 707
12 TraesCS2A01G257500 chr1B 526807651 526809320 1669 False 2497.0 2497 93.672 720 2396 1 chr1B.!!$F1 1676
13 TraesCS2A01G257500 chr2D 646475647 646477307 1660 True 2495.0 2495 93.735 720 2396 1 chr2D.!!$R1 1676
14 TraesCS2A01G257500 chr3A 699163810 699164517 707 False 1269.0 1269 99.011 1 708 1 chr3A.!!$F1 707
15 TraesCS2A01G257500 chr3A 703927711 703928421 710 True 961.0 961 91.213 1 708 1 chr3A.!!$R1 707
16 TraesCS2A01G257500 chr2B 57156943 57157665 722 True 1264.0 1264 98.202 1 723 1 chr2B.!!$R1 722
17 TraesCS2A01G257500 chr2B 609285086 609285800 714 True 1007.0 1007 92.190 1 711 1 chr2B.!!$R2 710
18 TraesCS2A01G257500 chr3B 795068259 795068966 707 False 1225.0 1225 97.881 1 708 1 chr3B.!!$F1 707

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
984 1008 1.451927 GCCCATGAAGTCATCGCCA 60.452 57.895 0.0 0.0 33.61 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 2374 0.179067 TATTTTCTGCCCGCCGGTAG 60.179 55.0 1.9 2.8 42.97 3.18 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
180 188 5.163302 TGTTAATGTTTTCAGTGACCACG 57.837 39.130 0.00 0.00 34.33 4.94
984 1008 1.451927 GCCCATGAAGTCATCGCCA 60.452 57.895 0.00 0.00 33.61 5.69
1208 1232 0.543749 CCTTCCTTCTTGGCCGAGAT 59.456 55.000 23.85 0.00 35.26 2.75
1209 1233 1.065126 CCTTCCTTCTTGGCCGAGATT 60.065 52.381 23.85 0.00 35.26 2.40
1210 1234 2.284190 CTTCCTTCTTGGCCGAGATTC 58.716 52.381 23.85 0.00 35.26 2.52
1211 1235 0.175760 TCCTTCTTGGCCGAGATTCG 59.824 55.000 23.85 14.22 35.41 3.34
1212 1236 1.432270 CCTTCTTGGCCGAGATTCGC 61.432 60.000 23.85 0.00 38.82 4.70
1213 1237 0.460987 CTTCTTGGCCGAGATTCGCT 60.461 55.000 23.85 0.00 38.82 4.93
1214 1238 0.740868 TTCTTGGCCGAGATTCGCTG 60.741 55.000 23.85 0.00 38.82 5.18
1215 1239 2.817423 CTTGGCCGAGATTCGCTGC 61.817 63.158 15.76 0.00 38.82 5.25
1216 1240 4.838152 TGGCCGAGATTCGCTGCC 62.838 66.667 14.41 14.41 44.06 4.85
1219 1243 3.854669 CCGAGATTCGCTGCCCCT 61.855 66.667 0.00 0.00 38.82 4.79
1220 1244 2.498941 CCGAGATTCGCTGCCCCTA 61.499 63.158 0.00 0.00 38.82 3.53
1221 1245 1.300233 CGAGATTCGCTGCCCCTAC 60.300 63.158 0.00 0.00 31.14 3.18
1222 1246 1.823295 GAGATTCGCTGCCCCTACA 59.177 57.895 0.00 0.00 0.00 2.74
1223 1247 0.530870 GAGATTCGCTGCCCCTACAC 60.531 60.000 0.00 0.00 0.00 2.90
1224 1248 1.523938 GATTCGCTGCCCCTACACC 60.524 63.158 0.00 0.00 0.00 4.16
2304 2373 9.745880 AACATTTGATGATCTTGCTTGATAATC 57.254 29.630 8.85 8.85 35.72 1.75
2305 2374 8.358148 ACATTTGATGATCTTGCTTGATAATCC 58.642 33.333 11.68 0.36 34.75 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
662 678 2.504367 CAACGGGAGAAACAATCCACT 58.496 47.619 0.0 0.00 38.70 4.00
790 806 4.142049 ACTGCGGGTTGATTTCAAAGAAAA 60.142 37.500 0.0 0.00 37.63 2.29
1208 1232 2.606519 AGGTGTAGGGGCAGCGAA 60.607 61.111 0.0 0.00 41.28 4.70
1209 1233 3.075005 GAGGTGTAGGGGCAGCGA 61.075 66.667 0.0 0.00 41.28 4.93
1210 1234 4.514577 CGAGGTGTAGGGGCAGCG 62.515 72.222 0.0 0.00 41.28 5.18
1211 1235 4.840005 GCGAGGTGTAGGGGCAGC 62.840 72.222 0.0 0.00 37.16 5.25
1212 1236 4.162690 GGCGAGGTGTAGGGGCAG 62.163 72.222 0.0 0.00 0.00 4.85
1213 1237 4.715130 AGGCGAGGTGTAGGGGCA 62.715 66.667 0.0 0.00 0.00 5.36
1214 1238 3.387225 GAAGGCGAGGTGTAGGGGC 62.387 68.421 0.0 0.00 0.00 5.80
1215 1239 1.677637 GAGAAGGCGAGGTGTAGGGG 61.678 65.000 0.0 0.00 0.00 4.79
1216 1240 0.684805 AGAGAAGGCGAGGTGTAGGG 60.685 60.000 0.0 0.00 0.00 3.53
1217 1241 1.135333 GAAGAGAAGGCGAGGTGTAGG 59.865 57.143 0.0 0.00 0.00 3.18
1218 1242 1.819288 TGAAGAGAAGGCGAGGTGTAG 59.181 52.381 0.0 0.00 0.00 2.74
1219 1243 1.919240 TGAAGAGAAGGCGAGGTGTA 58.081 50.000 0.0 0.00 0.00 2.90
1220 1244 1.048601 TTGAAGAGAAGGCGAGGTGT 58.951 50.000 0.0 0.00 0.00 4.16
1221 1245 2.169832 TTTGAAGAGAAGGCGAGGTG 57.830 50.000 0.0 0.00 0.00 4.00
1222 1246 2.355209 GGATTTGAAGAGAAGGCGAGGT 60.355 50.000 0.0 0.00 0.00 3.85
1223 1247 2.093235 AGGATTTGAAGAGAAGGCGAGG 60.093 50.000 0.0 0.00 0.00 4.63
1224 1248 3.118811 AGAGGATTTGAAGAGAAGGCGAG 60.119 47.826 0.0 0.00 0.00 5.03
2304 2373 2.886730 ATTTTCTGCCCGCCGGTAGG 62.887 60.000 1.9 7.28 41.95 3.18
2305 2374 0.179067 TATTTTCTGCCCGCCGGTAG 60.179 55.000 1.9 2.80 42.97 3.18


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

AutoCloner maintained by Alex Coulton.