Multiple sequence alignment - TraesCS3B01G130800

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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 TraesCS3B01G130800 chr3B 100.000 2264 0 0 1 2264 112909786 112912049 0.000000e+00 4181
1 TraesCS3B01G130800 chr3B 95.244 1703 62 10 1 1702 179362653 179360969 0.000000e+00 2678
2 TraesCS3B01G130800 chr3B 87.500 512 39 4 1768 2264 803582994 803582493 3.260000e-158 568
3 TraesCS3B01G130800 chr3B 95.455 330 14 1 1936 2264 28618989 28619318 1.990000e-145 525
4 TraesCS3B01G130800 chr3B 94.242 330 18 1 1936 2264 16122385 16122056 9.330000e-139 503
5 TraesCS3B01G130800 chr2B 93.002 2172 105 17 1 2166 798600957 798603087 0.000000e+00 3125
6 TraesCS3B01G130800 chr7B 92.449 2172 108 19 1 2166 707572945 707570824 0.000000e+00 3051
7 TraesCS3B01G130800 chr7B 92.208 1861 123 16 1 1851 34282300 34280452 0.000000e+00 2614
8 TraesCS3B01G130800 chr7B 93.636 330 20 1 1936 2264 95039914 95039585 2.020000e-135 492
9 TraesCS3B01G130800 chr3A 96.350 1781 55 6 1 1780 44774218 44772447 0.000000e+00 2920
10 TraesCS3B01G130800 chr5D 93.184 1878 103 11 1 1875 387840675 387838820 0.000000e+00 2736
11 TraesCS3B01G130800 chr5B 92.766 1880 116 13 1 1875 578837544 578835680 0.000000e+00 2700
12 TraesCS3B01G130800 chr2A 93.711 1781 100 7 1 1780 372742770 372744539 0.000000e+00 2658
13 TraesCS3B01G130800 chr4A 92.287 1880 126 9 1 1875 737660737 737662602 0.000000e+00 2651
14 TraesCS3B01G130800 chr6B 95.825 1006 30 6 1271 2264 694764793 694765798 0.000000e+00 1615
15 TraesCS3B01G130800 chr4B 94.637 317 16 1 1949 2264 402771990 402771674 7.270000e-135 490
16 TraesCS3B01G130800 chr4B 93.155 336 16 3 1936 2264 74253895 74254230 9.400000e-134 486
17 TraesCS3B01G130800 chr1B 84.553 246 25 8 1733 1967 302770659 302770416 4.860000e-57 231


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 TraesCS3B01G130800 chr3B 112909786 112912049 2263 False 4181 4181 100.000 1 2264 1 chr3B.!!$F2 2263
1 TraesCS3B01G130800 chr3B 179360969 179362653 1684 True 2678 2678 95.244 1 1702 1 chr3B.!!$R2 1701
2 TraesCS3B01G130800 chr3B 803582493 803582994 501 True 568 568 87.500 1768 2264 1 chr3B.!!$R3 496
3 TraesCS3B01G130800 chr2B 798600957 798603087 2130 False 3125 3125 93.002 1 2166 1 chr2B.!!$F1 2165
4 TraesCS3B01G130800 chr7B 707570824 707572945 2121 True 3051 3051 92.449 1 2166 1 chr7B.!!$R3 2165
5 TraesCS3B01G130800 chr7B 34280452 34282300 1848 True 2614 2614 92.208 1 1851 1 chr7B.!!$R1 1850
6 TraesCS3B01G130800 chr3A 44772447 44774218 1771 True 2920 2920 96.350 1 1780 1 chr3A.!!$R1 1779
7 TraesCS3B01G130800 chr5D 387838820 387840675 1855 True 2736 2736 93.184 1 1875 1 chr5D.!!$R1 1874
8 TraesCS3B01G130800 chr5B 578835680 578837544 1864 True 2700 2700 92.766 1 1875 1 chr5B.!!$R1 1874
9 TraesCS3B01G130800 chr2A 372742770 372744539 1769 False 2658 2658 93.711 1 1780 1 chr2A.!!$F1 1779
10 TraesCS3B01G130800 chr4A 737660737 737662602 1865 False 2651 2651 92.287 1 1875 1 chr4A.!!$F1 1874
11 TraesCS3B01G130800 chr6B 694764793 694765798 1005 False 1615 1615 95.825 1271 2264 1 chr6B.!!$F1 993

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
293 295 0.248215 GACATGGGCGCAAGATTTCG 60.248 55.0 13.3 0.0 43.02 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1446 0.105453 ATCCCCGTGCATAGGACTCT 60.105 55.0 12.15 0.0 30.97 3.24 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
257 258 0.659957 GCGGATGCAAGAGTTCCATC 59.340 55.000 4.26 0.0 42.15 3.51
293 295 0.248215 GACATGGGCGCAAGATTTCG 60.248 55.000 13.30 0.0 43.02 3.46
704 712 4.147321 AGTGTTCGTAGAGGGAGTACAAA 58.853 43.478 0.00 0.0 38.43 2.83
808 816 1.048601 TCGGAGAGGAAGCACAAGTT 58.951 50.000 0.00 0.0 0.00 2.66
1028 1036 3.382832 CGGTTCCAGGACGAGGCT 61.383 66.667 0.00 0.0 0.00 4.58
1029 1037 2.050350 CGGTTCCAGGACGAGGCTA 61.050 63.158 0.00 0.0 0.00 3.93
1099 1107 2.977808 TGGACAAGGAGAAGGAGAAGT 58.022 47.619 0.00 0.0 0.00 3.01
1114 1122 1.635487 AGAAGTATGTGCCCACACCAT 59.365 47.619 2.82 0.0 46.86 3.55
1159 1167 0.394565 GCTGAAGGTGTCCACTGACT 59.605 55.000 0.00 0.0 42.28 3.41
1223 1231 3.461061 CCAACTATGCACATGATCGTCT 58.539 45.455 0.00 0.0 0.00 4.18
1381 1389 2.501261 TGGATAGATCACGAGGTACCG 58.499 52.381 6.18 0.0 0.00 4.02
1428 1436 0.392461 GATTGGTTACGGAGGCAGCA 60.392 55.000 0.00 0.0 0.00 4.41
1502 1510 2.024319 GCTCGTGAGCGCAAGAAGT 61.024 57.895 11.47 0.0 45.29 3.01
1594 1602 2.037053 CGATGCACGAGAGGAGGAT 58.963 57.895 0.00 0.0 45.77 3.24
1599 1607 0.753479 GCACGAGAGGAGGATGAGGA 60.753 60.000 0.00 0.0 0.00 3.71
1657 1666 2.380064 AGACAAATGGAAAGGCACCA 57.620 45.000 0.00 0.0 41.83 4.17
1696 1705 8.240883 ACTGTCGAGACTTTGTTTAATGTATC 57.759 34.615 4.78 0.0 32.16 2.24
1886 1938 7.647715 GCTTTGTTCATATTTAACAGTGTGTGT 59.352 33.333 0.00 0.0 43.24 3.72
1981 2045 2.095059 GCGTCTGGTTCATTTTGCTCAT 60.095 45.455 0.00 0.0 0.00 2.90
2088 2154 2.611800 ACCCTGGCATCTGGCTCA 60.612 61.111 5.30 0.0 44.01 4.26
2099 2165 0.606130 TCTGGCTCATTTTGCTCGCA 60.606 50.000 0.00 0.0 0.00 5.10
2249 2315 2.285868 GGCCCACCTCTAGCCCTA 59.714 66.667 0.00 0.0 41.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
210 211 6.368516 GGTTTTTCCATCACAAACATGTATGG 59.631 38.462 15.68 15.68 38.76 2.74
257 258 4.437239 CATGTCAACCTAGTAGCTTCCAG 58.563 47.826 0.00 0.00 0.00 3.86
293 295 1.546029 GTGATTGGTCCAAGAAAGGGC 59.454 52.381 10.72 0.00 0.00 5.19
704 712 0.324368 TCGACCACCACCTCTAGCAT 60.324 55.000 0.00 0.00 0.00 3.79
747 755 1.985116 GCTTCCTCTCCGACCACCT 60.985 63.158 0.00 0.00 0.00 4.00
808 816 0.611062 CGACCACCACCACCTCTAGA 60.611 60.000 0.00 0.00 0.00 2.43
860 868 8.537728 TCAACCATCTGGATTAAGCAAATAAT 57.462 30.769 2.55 0.00 38.94 1.28
1099 1107 1.284491 ACATGATGGTGTGGGCACATA 59.716 47.619 0.00 0.00 46.95 2.29
1114 1122 2.275134 ACATCAGCACACCAACATGA 57.725 45.000 0.00 0.00 0.00 3.07
1127 1135 2.295349 ACCTTCAGCTTGCAAACATCAG 59.705 45.455 0.00 0.00 0.00 2.90
1159 1167 2.636647 TCTGTCCATGACTTGTTGCA 57.363 45.000 0.00 0.00 33.15 4.08
1223 1231 4.124238 GTCATATGCGTTAGTTGGCCTTA 58.876 43.478 3.32 0.00 0.00 2.69
1428 1436 4.038162 GTGCATAGGACTCTTCGAATAGGT 59.962 45.833 14.29 6.52 0.00 3.08
1438 1446 0.105453 ATCCCCGTGCATAGGACTCT 60.105 55.000 12.15 0.00 30.97 3.24
1502 1510 1.536073 CGTGCCCTCTCTTCCTCACA 61.536 60.000 0.00 0.00 0.00 3.58
1594 1602 1.070134 CCCTTCTTGTCACGTTCCTCA 59.930 52.381 0.00 0.00 0.00 3.86
1599 1607 2.943033 CACTTTCCCTTCTTGTCACGTT 59.057 45.455 0.00 0.00 0.00 3.99
1657 1666 1.795525 CGACAGTTCATCATCGACGCT 60.796 52.381 0.00 0.00 36.70 5.07
1696 1705 5.236478 ACACAAGGTCTCGAATAACAAGTTG 59.764 40.000 0.00 0.00 0.00 3.16
1981 2045 1.879372 GCATGTGTCTGGTCTTCTGCA 60.879 52.381 0.00 0.00 0.00 4.41
2079 2145 0.737219 GCGAGCAAAATGAGCCAGAT 59.263 50.000 0.00 0.00 0.00 2.90
2088 2154 1.160137 GTCTCCTGTGCGAGCAAAAT 58.840 50.000 0.00 0.00 0.00 1.82
2099 2165 0.833834 CAGGGTGTCTGGTCTCCTGT 60.834 60.000 0.00 0.00 39.90 4.00
2183 2249 4.397481 TCCATCAGACAGATAACTGCAG 57.603 45.455 13.48 13.48 46.95 4.41


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

AutoCloner maintained by Alex Coulton.