Multiple sequence alignment - TraesCS4D01G137000

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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 TraesCS4D01G137000 chr4D 100.000 2869 0 0 1 2869 123142350 123139482 0.000000e+00 5299.0
1 TraesCS4D01G137000 chr4D 91.403 884 60 7 2000 2869 414385816 414384935 0.000000e+00 1197.0
2 TraesCS4D01G137000 chr4B 93.918 1825 68 23 199 1993 187727921 187726110 0.000000e+00 2715.0
3 TraesCS4D01G137000 chr4B 94.059 101 6 0 67 167 187728110 187728010 1.380000e-33 154.0
4 TraesCS4D01G137000 chr4B 100.000 56 0 0 160 215 187727991 187727936 1.410000e-18 104.0
5 TraesCS4D01G137000 chr4B 92.727 55 4 0 1 55 187728211 187728157 2.370000e-11 80.5
6 TraesCS4D01G137000 chr4A 90.950 2011 99 35 1 1970 446613024 446614992 0.000000e+00 2628.0
7 TraesCS4D01G137000 chr1B 90.762 1797 71 34 253 1993 173123390 173121633 0.000000e+00 2311.0
8 TraesCS4D01G137000 chr1B 91.353 266 17 4 1 262 173123728 173123465 2.720000e-95 359.0
9 TraesCS4D01G137000 chr1A 93.232 1049 31 15 961 1993 121130073 121129049 0.000000e+00 1507.0
10 TraesCS4D01G137000 chr1A 92.823 836 44 10 1 823 121131010 121130178 0.000000e+00 1197.0
11 TraesCS4D01G137000 chr5D 94.032 888 38 6 1994 2869 565736093 565736977 0.000000e+00 1332.0
12 TraesCS4D01G137000 chr5D 93.182 44 3 0 851 894 386942553 386942596 6.640000e-07 65.8
13 TraesCS4D01G137000 chr7D 94.032 888 36 5 1996 2869 17453478 17452594 0.000000e+00 1330.0
14 TraesCS4D01G137000 chr7D 91.246 891 58 8 1995 2869 80798506 80799392 0.000000e+00 1195.0
15 TraesCS4D01G137000 chr7D 91.021 891 64 12 1994 2869 69080924 69081813 0.000000e+00 1188.0
16 TraesCS4D01G137000 chrUn 92.063 882 57 4 2000 2869 108229857 108230737 0.000000e+00 1229.0
17 TraesCS4D01G137000 chrUn 91.377 893 58 7 1992 2869 29759004 29758116 0.000000e+00 1205.0
18 TraesCS4D01G137000 chr1D 91.798 890 56 7 1994 2869 192583495 192582609 0.000000e+00 1223.0
19 TraesCS4D01G137000 chr1D 88.767 365 21 7 1996 2347 232144095 232144452 2.040000e-116 429.0
20 TraesCS4D01G137000 chr1D 95.000 40 2 0 855 894 481182879 481182918 2.390000e-06 63.9
21 TraesCS4D01G137000 chr1D 95.000 40 2 0 855 894 481320538 481320577 2.390000e-06 63.9
22 TraesCS4D01G137000 chr5B 91.874 886 53 8 2000 2869 684070144 684071026 0.000000e+00 1219.0
23 TraesCS4D01G137000 chr5B 79.012 243 31 18 1994 2225 599309637 599309870 6.400000e-32 148.0
24 TraesCS4D01G137000 chr3D 90.503 895 64 16 1995 2869 565957986 565958879 0.000000e+00 1162.0
25 TraesCS4D01G137000 chr3B 89.698 893 75 6 1991 2868 186085933 186085043 0.000000e+00 1123.0
26 TraesCS4D01G137000 chr6B 80.204 884 147 21 1995 2864 21940211 21939342 3.120000e-179 638.0
27 TraesCS4D01G137000 chr6B 97.619 42 1 0 853 894 625324110 625324151 3.970000e-09 73.1
28 TraesCS4D01G137000 chr2A 84.585 253 25 12 1994 2235 90028754 90029003 3.690000e-59 239.0
29 TraesCS4D01G137000 chr7B 76.233 223 33 16 1993 2205 509577355 509577567 1.820000e-17 100.0
30 TraesCS4D01G137000 chr7A 97.500 40 1 0 855 894 671401078 671401117 5.130000e-08 69.4


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 TraesCS4D01G137000 chr4D 123139482 123142350 2868 True 5299.000 5299 100.0000 1 2869 1 chr4D.!!$R1 2868
1 TraesCS4D01G137000 chr4D 414384935 414385816 881 True 1197.000 1197 91.4030 2000 2869 1 chr4D.!!$R2 869
2 TraesCS4D01G137000 chr4B 187726110 187728211 2101 True 763.375 2715 95.1760 1 1993 4 chr4B.!!$R1 1992
3 TraesCS4D01G137000 chr4A 446613024 446614992 1968 False 2628.000 2628 90.9500 1 1970 1 chr4A.!!$F1 1969
4 TraesCS4D01G137000 chr1B 173121633 173123728 2095 True 1335.000 2311 91.0575 1 1993 2 chr1B.!!$R1 1992
5 TraesCS4D01G137000 chr1A 121129049 121131010 1961 True 1352.000 1507 93.0275 1 1993 2 chr1A.!!$R1 1992
6 TraesCS4D01G137000 chr5D 565736093 565736977 884 False 1332.000 1332 94.0320 1994 2869 1 chr5D.!!$F2 875
7 TraesCS4D01G137000 chr7D 17452594 17453478 884 True 1330.000 1330 94.0320 1996 2869 1 chr7D.!!$R1 873
8 TraesCS4D01G137000 chr7D 80798506 80799392 886 False 1195.000 1195 91.2460 1995 2869 1 chr7D.!!$F2 874
9 TraesCS4D01G137000 chr7D 69080924 69081813 889 False 1188.000 1188 91.0210 1994 2869 1 chr7D.!!$F1 875
10 TraesCS4D01G137000 chrUn 108229857 108230737 880 False 1229.000 1229 92.0630 2000 2869 1 chrUn.!!$F1 869
11 TraesCS4D01G137000 chrUn 29758116 29759004 888 True 1205.000 1205 91.3770 1992 2869 1 chrUn.!!$R1 877
12 TraesCS4D01G137000 chr1D 192582609 192583495 886 True 1223.000 1223 91.7980 1994 2869 1 chr1D.!!$R1 875
13 TraesCS4D01G137000 chr5B 684070144 684071026 882 False 1219.000 1219 91.8740 2000 2869 1 chr5B.!!$F2 869
14 TraesCS4D01G137000 chr3D 565957986 565958879 893 False 1162.000 1162 90.5030 1995 2869 1 chr3D.!!$F1 874
15 TraesCS4D01G137000 chr3B 186085043 186085933 890 True 1123.000 1123 89.6980 1991 2868 1 chr3B.!!$R1 877
16 TraesCS4D01G137000 chr6B 21939342 21940211 869 True 638.000 638 80.2040 1995 2864 1 chr6B.!!$R1 869

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
21 22 3.048337 TGCGGTCTCGGTTAAAAGAAT 57.952 42.857 0.0 0.0 36.79 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 2287 0.888619 GGAGCCCCCTTTTCGAAAAG 59.111 55.0 33.84 33.84 43.82 2.27 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
21 22 3.048337 TGCGGTCTCGGTTAAAAGAAT 57.952 42.857 0.00 0.00 36.79 2.40
24 25 5.180271 TGCGGTCTCGGTTAAAAGAATTAT 58.820 37.500 0.00 0.00 36.79 1.28
60 61 7.255491 TGTGATCTAGCATCATCAATGTTTC 57.745 36.000 7.75 0.00 37.71 2.78
163 204 7.083875 TCCTGAAACAGAAAACTGTTACTTG 57.916 36.000 14.45 6.28 45.64 3.16
215 313 5.437060 CAGTACAAGTATACCCCATGCTTT 58.563 41.667 0.00 0.00 37.46 3.51
494 681 3.126831 CGTCTTGCAGTTGAGAAAGTCT 58.873 45.455 0.00 0.00 0.00 3.24
608 806 5.234543 GGAAGTCAACTACGCATTATTCCTC 59.765 44.000 0.00 0.00 32.72 3.71
626 824 3.117701 TCCTCTTGACACAAACCATCCAA 60.118 43.478 0.00 0.00 0.00 3.53
815 1019 5.298276 TGTCTTTGTGCTTAACTTAACCAGG 59.702 40.000 0.00 0.00 0.00 4.45
904 1128 3.698040 GACGGAGGGAGTTACATCTAACA 59.302 47.826 0.00 0.00 35.56 2.41
906 1130 3.700038 CGGAGGGAGTTACATCTAACAGT 59.300 47.826 0.00 0.00 35.56 3.55
989 1217 8.061857 TCGATTTCGAGAAATTGGATTAATTCG 58.938 33.333 19.89 12.51 44.22 3.34
1064 1298 2.914777 CTAGCGTGGCCTCCTCTTGC 62.915 65.000 3.32 0.00 0.00 4.01
1325 1571 1.888512 TGGATGCTTCTCCTTGCAAAC 59.111 47.619 0.00 0.00 42.74 2.93
1366 1625 3.033659 ACTACTTCATCCGGTGATCCT 57.966 47.619 0.00 0.00 36.54 3.24
1375 1634 1.906574 TCCGGTGATCCTTTTAGCTGT 59.093 47.619 0.00 0.00 0.00 4.40
1445 1704 3.292159 GGTTGCCTTCGCCCGTTT 61.292 61.111 0.00 0.00 0.00 3.60
1746 2018 1.672356 TTTGCTTGCTCGCTCTCCC 60.672 57.895 0.00 0.00 0.00 4.30
1784 2059 3.202906 GTCCTTGTGTGTATGTGTGTGT 58.797 45.455 0.00 0.00 0.00 3.72
1815 2090 5.703130 GTCCCTGTAATTGCTTCATCTATCC 59.297 44.000 0.00 0.00 0.00 2.59
1932 2218 3.126000 GCGCATCTTCAGCTATTTATCCC 59.874 47.826 0.30 0.00 0.00 3.85
2105 2411 6.404293 GGTCTTGCAGTCTCAAAACAAGTAAA 60.404 38.462 0.00 0.00 38.99 2.01
2325 2653 1.006832 CAGTGGCCCGAAAGATAACG 58.993 55.000 0.00 0.00 0.00 3.18
2450 2779 5.969423 TGTTTCGAACTCTATCCCGTTAAT 58.031 37.500 0.00 0.00 0.00 1.40
2502 2831 4.178540 TCGGAGGAGTAATGTTAAAAGCG 58.821 43.478 0.00 0.00 0.00 4.68
2525 2854 1.227556 GCACCGTCCGCCATAGAAT 60.228 57.895 0.00 0.00 0.00 2.40
2583 2912 6.018669 GGATAGTTTCATTCCGATCACAGAAC 60.019 42.308 0.00 0.00 0.00 3.01
2856 3192 0.323302 TCACTAAATGGAGCCACGCA 59.677 50.000 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 114 9.149225 GCAATGATCCTTATGAAGACTACTATG 57.851 37.037 0.00 0.00 0.00 2.23
94 134 5.051891 GTATGCATTACCAGCAATGATCC 57.948 43.478 3.54 0.00 46.27 3.36
158 199 4.365514 TTCTCCACTCCAATTGCAAGTA 57.634 40.909 4.94 0.00 0.00 2.24
163 204 4.320608 TTGTTTTCTCCACTCCAATTGC 57.679 40.909 0.00 0.00 0.00 3.56
215 313 7.466185 CGGGCACATAACGAATTAGTATTTTGA 60.466 37.037 0.00 0.00 0.00 2.69
237 335 2.279784 CTCTGGAATCGAGCGGGC 60.280 66.667 0.00 0.00 0.00 6.13
528 715 8.722480 ATTCGACATCATTTTGTATCTTCTCA 57.278 30.769 0.00 0.00 0.00 3.27
608 806 3.885297 AGACTTGGATGGTTTGTGTCAAG 59.115 43.478 0.00 0.00 37.98 3.02
626 824 7.551585 CAGTATACTGTTCCTTGATGAAGACT 58.448 38.462 22.48 0.00 39.09 3.24
758 962 5.240183 TGATCTTTCTGGTTGCTTTCTGAAG 59.760 40.000 0.00 0.00 35.92 3.02
815 1019 2.421073 GTGATAAAAGGGGTTGCGGTAC 59.579 50.000 0.00 0.00 0.00 3.34
1007 1235 1.449423 TTGCGTGGCACGATGCTAT 60.449 52.632 40.94 0.00 46.05 2.97
1078 1312 2.264005 AGCCGAATGGTGTACACAAA 57.736 45.000 26.51 14.93 37.67 2.83
1297 1543 5.163478 GCAAGGAGAAGCATCCATTAATGTT 60.163 40.000 14.25 1.54 42.26 2.71
1366 1625 7.415025 AGGAACTGATGCTTGAACAGCTAAAA 61.415 38.462 0.00 0.00 44.48 1.52
1375 1634 4.202141 CCACAAAAGGAACTGATGCTTGAA 60.202 41.667 0.00 0.00 38.99 2.69
1650 1917 5.654603 ATTCACGTATACTCTCACACCAA 57.345 39.130 0.56 0.00 0.00 3.67
1746 2018 1.379443 ACACCATGGGCAGAGCATG 60.379 57.895 18.09 4.86 0.00 4.06
1784 2059 1.818060 GCAATTACAGGGACACATGCA 59.182 47.619 0.00 0.00 33.00 3.96
1815 2090 2.974794 TCATCACTCCATCCATAGTGGG 59.025 50.000 0.00 0.00 42.72 4.61
1932 2218 5.692204 CCTTCGCTGTATACTTCATGTTAGG 59.308 44.000 4.17 0.00 0.00 2.69
1998 2287 0.888619 GGAGCCCCCTTTTCGAAAAG 59.111 55.000 33.84 33.84 43.82 2.27
2389 2718 5.050972 GCGTAGGAGTATGTGCTTTATTGTC 60.051 44.000 0.00 0.00 0.00 3.18
2502 2831 2.916502 TATGGCGGACGGTGCACATC 62.917 60.000 20.43 15.12 0.00 3.06


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

AutoCloner maintained by Alex Coulton.