Multiple sequence alignment - TraesCS2A01G257100

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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 TraesCS2A01G257100 chr2A 100.000 2279 0 0 1 2279 394048746 394051024 0 4209
1 TraesCS2A01G257100 chr2A 96.963 1844 36 5 1 1831 543187640 543189476 0 3077
2 TraesCS2A01G257100 chr7B 96.909 1844 37 5 1 1831 662732893 662734729 0 3072
3 TraesCS2A01G257100 chr7B 96.816 1633 32 5 1 1620 622431989 622430364 0 2710
4 TraesCS2A01G257100 chr7B 97.130 453 10 3 1828 2279 662734766 662735216 0 761
5 TraesCS2A01G257100 chr1D 96.799 1843 40 4 1 1831 254531577 254533412 0 3059
6 TraesCS2A01G257100 chr1B 96.584 1844 42 6 1 1831 633733491 633731656 0 3037
7 TraesCS2A01G257100 chr3B 96.529 1844 44 5 1 1831 201565402 201563566 0 3033
8 TraesCS2A01G257100 chr3B 96.691 1632 35 5 1 1620 201549281 201550905 0 2697
9 TraesCS2A01G257100 chr3A 96.419 1843 46 5 1 1831 672883049 672881215 0 3020
10 TraesCS2A01G257100 chr3A 97.130 453 12 1 1828 2279 672881178 672880726 0 763
11 TraesCS2A01G257100 chr2D 96.204 1844 40 7 1 1831 272806269 272804443 0 2990
12 TraesCS2A01G257100 chr2D 97.164 1622 36 4 1 1620 591991653 591993266 0 2732
13 TraesCS2A01G257100 chr2D 97.351 453 10 2 1828 2279 630266479 630266930 0 769
14 TraesCS2A01G257100 chr2D 97.130 453 11 2 1828 2279 272804406 272803955 0 763
15 TraesCS2A01G257100 chr5B 94.973 1830 70 8 1 1825 432872128 432873940 0 2850
16 TraesCS2A01G257100 chr6B 96.934 1631 32 5 1 1620 515380592 515378969 0 2719
17 TraesCS2A01G257100 chr6B 97.345 452 12 0 1828 2279 615599749 615599298 0 769
18 TraesCS2A01G257100 chrUn 95.924 1006 22 4 836 1829 351215174 351214176 0 1613
19 TraesCS2A01G257100 chrUn 96.909 453 12 2 1828 2279 351214135 351213684 0 758
20 TraesCS2A01G257100 chr4B 95.221 837 21 4 1007 1831 151526835 151527664 0 1306
21 TraesCS2A01G257100 chr4B 97.130 453 11 2 1828 2279 151527701 151528152 0 763
22 TraesCS2A01G257100 chr5D 97.351 453 11 1 1828 2279 432295457 432295005 0 769
23 TraesCS2A01G257100 chr5D 97.351 453 10 2 1828 2279 449150215 449150666 0 769


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 TraesCS2A01G257100 chr2A 394048746 394051024 2278 False 4209.0 4209 100.0000 1 2279 1 chr2A.!!$F1 2278
1 TraesCS2A01G257100 chr2A 543187640 543189476 1836 False 3077.0 3077 96.9630 1 1831 1 chr2A.!!$F2 1830
2 TraesCS2A01G257100 chr7B 622430364 622431989 1625 True 2710.0 2710 96.8160 1 1620 1 chr7B.!!$R1 1619
3 TraesCS2A01G257100 chr7B 662732893 662735216 2323 False 1916.5 3072 97.0195 1 2279 2 chr7B.!!$F1 2278
4 TraesCS2A01G257100 chr1D 254531577 254533412 1835 False 3059.0 3059 96.7990 1 1831 1 chr1D.!!$F1 1830
5 TraesCS2A01G257100 chr1B 633731656 633733491 1835 True 3037.0 3037 96.5840 1 1831 1 chr1B.!!$R1 1830
6 TraesCS2A01G257100 chr3B 201563566 201565402 1836 True 3033.0 3033 96.5290 1 1831 1 chr3B.!!$R1 1830
7 TraesCS2A01G257100 chr3B 201549281 201550905 1624 False 2697.0 2697 96.6910 1 1620 1 chr3B.!!$F1 1619
8 TraesCS2A01G257100 chr3A 672880726 672883049 2323 True 1891.5 3020 96.7745 1 2279 2 chr3A.!!$R1 2278
9 TraesCS2A01G257100 chr2D 591991653 591993266 1613 False 2732.0 2732 97.1640 1 1620 1 chr2D.!!$F1 1619
10 TraesCS2A01G257100 chr2D 272803955 272806269 2314 True 1876.5 2990 96.6670 1 2279 2 chr2D.!!$R1 2278
11 TraesCS2A01G257100 chr5B 432872128 432873940 1812 False 2850.0 2850 94.9730 1 1825 1 chr5B.!!$F1 1824
12 TraesCS2A01G257100 chr6B 515378969 515380592 1623 True 2719.0 2719 96.9340 1 1620 1 chr6B.!!$R1 1619
13 TraesCS2A01G257100 chrUn 351213684 351215174 1490 True 1185.5 1613 96.4165 836 2279 2 chrUn.!!$R1 1443
14 TraesCS2A01G257100 chr4B 151526835 151528152 1317 False 1034.5 1306 96.1755 1007 2279 2 chr4B.!!$F1 1272

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
491 492 1.922135 TTCGAAATCAGGCCAAGCGC 61.922 55.0 5.01 0.0 0.0 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 1919 0.178998 TAGATCGGCGGCTACTCCTT 60.179 55.0 7.21 0.0 0.0 3.36 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
115 116 4.158949 TCATGGACTCGAAAAACGGATCTA 59.841 41.667 0.00 0.00 42.82 1.98
402 403 7.962964 TTCATGTCTTTCAATTCTCGTACTT 57.037 32.000 0.00 0.00 0.00 2.24
491 492 1.922135 TTCGAAATCAGGCCAAGCGC 61.922 55.000 5.01 0.00 0.00 5.92
1089 1097 7.255801 GGGGTTCTGTTGAATTTCAAGTATTCA 60.256 37.037 12.02 5.79 37.00 2.57
1090 1098 7.809806 GGGTTCTGTTGAATTTCAAGTATTCAG 59.190 37.037 12.02 14.08 41.53 3.02
1091 1099 8.352942 GGTTCTGTTGAATTTCAAGTATTCAGT 58.647 33.333 12.02 0.00 41.53 3.41
1116 1124 9.309516 GTATTCAGTTTCACCAATAAGATACGA 57.690 33.333 0.00 0.00 0.00 3.43
1143 1151 6.815089 ACTTGCTTCACATTTGGAATTACAA 58.185 32.000 0.00 0.00 0.00 2.41
1176 1184 2.022195 TCATCGGAAAGAGGTCTACGG 58.978 52.381 0.00 0.00 31.60 4.02
1352 1374 4.669206 TTTTTCATTTTGCTGAGCCTCA 57.331 36.364 0.23 0.00 0.00 3.86
1566 1588 5.957771 AGGCTATTTACACAGAGGAATGA 57.042 39.130 0.00 0.00 0.00 2.57
1787 1810 2.241176 TGGACCTTTTATGGCGGATCTT 59.759 45.455 0.00 0.00 0.00 2.40
1848 1913 9.851686 AGATAGAATGGTGCATAATTACTTTCA 57.148 29.630 0.00 0.00 0.00 2.69
1854 1919 5.877564 TGGTGCATAATTACTTTCACATCGA 59.122 36.000 0.00 0.00 0.00 3.59
2167 2233 7.531871 CGTTAGCTCGCTATTTAGTACGAATTA 59.468 37.037 11.15 0.00 33.61 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 6.779860 TCTTCCACCTGTTTAGCTAAGAAAT 58.220 36.000 6.24 0.00 0.00 2.17
115 116 6.017400 AGATCGTGCATTTCAGTCAAATTT 57.983 33.333 0.00 0.00 31.79 1.82
275 276 5.961843 CGCGTCTTCGACTTCTATTAGTTTA 59.038 40.000 0.00 0.00 39.71 2.01
402 403 7.610305 GTCTCCTTCCATAACTTTCCAATTACA 59.390 37.037 0.00 0.00 0.00 2.41
847 852 7.699709 TGGATTTGGATAGAAGGGTACATTA 57.300 36.000 0.00 0.00 0.00 1.90
1089 1097 9.314321 CGTATCTTATTGGTGAAACTGAATACT 57.686 33.333 0.00 0.00 36.74 2.12
1090 1098 9.309516 TCGTATCTTATTGGTGAAACTGAATAC 57.690 33.333 0.00 0.00 36.74 1.89
1091 1099 9.878667 TTCGTATCTTATTGGTGAAACTGAATA 57.121 29.630 0.00 0.00 36.74 1.75
1092 1100 8.786826 TTCGTATCTTATTGGTGAAACTGAAT 57.213 30.769 0.00 0.00 36.74 2.57
1093 1101 8.092068 TCTTCGTATCTTATTGGTGAAACTGAA 58.908 33.333 0.00 0.00 36.74 3.02
1094 1102 7.544566 GTCTTCGTATCTTATTGGTGAAACTGA 59.455 37.037 0.00 0.00 36.74 3.41
1095 1103 7.545965 AGTCTTCGTATCTTATTGGTGAAACTG 59.454 37.037 0.00 0.00 36.74 3.16
1116 1124 5.796424 ATTCCAAATGTGAAGCAAGTCTT 57.204 34.783 0.00 0.00 37.83 3.01
1176 1184 2.867975 TCGACGTTTTCCCAAAAGTCTC 59.132 45.455 10.61 0.00 44.63 3.36
1257 1265 7.823745 AAATTACTGCTCCCGAATATTCAAT 57.176 32.000 15.57 1.84 0.00 2.57
1352 1374 8.242729 GGATTATTCCATGAATTCCTCAAAGT 57.757 34.615 2.27 0.00 42.12 2.66
1410 1432 3.957671 TGTAAGCGGTAGACTCGTATG 57.042 47.619 0.00 0.00 0.00 2.39
1414 1436 3.482722 TTCTTGTAAGCGGTAGACTCG 57.517 47.619 0.00 0.00 0.00 4.18
1787 1810 0.465460 AAAAAGGAGTCTGTGCGCCA 60.465 50.000 4.18 0.90 0.00 5.69
1825 1848 8.800370 TGTGAAAGTAATTATGCACCATTCTA 57.200 30.769 0.00 0.00 0.00 2.10
1831 1856 6.358118 TCGATGTGAAAGTAATTATGCACC 57.642 37.500 0.00 0.00 0.00 5.01
1832 1857 6.907212 CCTTCGATGTGAAAGTAATTATGCAC 59.093 38.462 0.00 0.00 35.79 4.57
1837 1902 7.705325 GCTACTCCTTCGATGTGAAAGTAATTA 59.295 37.037 0.00 0.00 35.79 1.40
1848 1913 1.437986 GCGGCTACTCCTTCGATGT 59.562 57.895 0.00 0.00 0.00 3.06
1854 1919 0.178998 TAGATCGGCGGCTACTCCTT 60.179 55.000 7.21 0.00 0.00 3.36
2121 2187 2.352715 CGAATCCCCTTCTTTTTGCCAC 60.353 50.000 0.00 0.00 0.00 5.01
2167 2233 4.868172 TGATGGATTCCCTCATTTCACT 57.132 40.909 6.58 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.