Multiple sequence alignment - TraesCS5B01G104000

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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 TraesCS5B01G104000 chr5B 100.000 2345 0 0 1 2345 139001625 139003969 0.000000e+00 4331.0
1 TraesCS5B01G104000 chr3A 91.623 2316 169 14 47 2345 134617281 134619588 0.000000e+00 3179.0
2 TraesCS5B01G104000 chr3A 91.038 2254 164 18 125 2345 134612497 134614745 0.000000e+00 3009.0
3 TraesCS5B01G104000 chr6A 91.692 2323 141 19 47 2345 204306988 204304694 0.000000e+00 3173.0
4 TraesCS5B01G104000 chr6A 91.435 2265 148 14 100 2345 328875926 328878163 0.000000e+00 3066.0
5 TraesCS5B01G104000 chr6A 91.272 2257 155 18 102 2345 213994225 213991998 0.000000e+00 3038.0
6 TraesCS5B01G104000 chr6A 91.166 2264 153 18 102 2345 136164320 136162084 0.000000e+00 3029.0
7 TraesCS5B01G104000 chr6A 91.082 2265 151 21 102 2345 518075637 518073403 0.000000e+00 3016.0
8 TraesCS5B01G104000 chr6A 91.700 2012 123 14 350 2345 473515390 473517373 0.000000e+00 2750.0
9 TraesCS5B01G104000 chr5A 92.087 2262 130 17 102 2345 109667611 109669841 0.000000e+00 3140.0
10 TraesCS5B01G104000 chr5A 92.002 2263 135 16 102 2345 268344307 268346542 0.000000e+00 3134.0
11 TraesCS5B01G104000 chr2A 91.442 2267 146 17 100 2345 616456352 616454113 0.000000e+00 3068.0
12 TraesCS5B01G104000 chr2A 90.937 2273 149 17 92 2345 154894747 154892513 0.000000e+00 3003.0
13 TraesCS5B01G104000 chr3B 92.174 1955 142 11 45 1990 243090674 243088722 0.000000e+00 2752.0
14 TraesCS5B01G104000 chr3B 89.937 159 11 4 10 167 716930379 716930533 1.420000e-47 200.0
15 TraesCS5B01G104000 chr1A 91.309 1864 118 17 497 2345 465251795 465253629 0.000000e+00 2505.0
16 TraesCS5B01G104000 chr2D 90.702 1054 81 8 581 1624 628411726 628412772 0.000000e+00 1387.0
17 TraesCS5B01G104000 chr2B 95.833 48 2 0 4 51 558925576 558925623 6.950000e-11 78.7


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 TraesCS5B01G104000 chr5B 139001625 139003969 2344 False 4331 4331 100.0000 1 2345 1 chr5B.!!$F1 2344
1 TraesCS5B01G104000 chr3A 134612497 134619588 7091 False 3094 3179 91.3305 47 2345 2 chr3A.!!$F1 2298
2 TraesCS5B01G104000 chr6A 204304694 204306988 2294 True 3173 3173 91.6920 47 2345 1 chr6A.!!$R2 2298
3 TraesCS5B01G104000 chr6A 328875926 328878163 2237 False 3066 3066 91.4350 100 2345 1 chr6A.!!$F1 2245
4 TraesCS5B01G104000 chr6A 213991998 213994225 2227 True 3038 3038 91.2720 102 2345 1 chr6A.!!$R3 2243
5 TraesCS5B01G104000 chr6A 136162084 136164320 2236 True 3029 3029 91.1660 102 2345 1 chr6A.!!$R1 2243
6 TraesCS5B01G104000 chr6A 518073403 518075637 2234 True 3016 3016 91.0820 102 2345 1 chr6A.!!$R4 2243
7 TraesCS5B01G104000 chr6A 473515390 473517373 1983 False 2750 2750 91.7000 350 2345 1 chr6A.!!$F2 1995
8 TraesCS5B01G104000 chr5A 109667611 109669841 2230 False 3140 3140 92.0870 102 2345 1 chr5A.!!$F1 2243
9 TraesCS5B01G104000 chr5A 268344307 268346542 2235 False 3134 3134 92.0020 102 2345 1 chr5A.!!$F2 2243
10 TraesCS5B01G104000 chr2A 616454113 616456352 2239 True 3068 3068 91.4420 100 2345 1 chr2A.!!$R2 2245
11 TraesCS5B01G104000 chr2A 154892513 154894747 2234 True 3003 3003 90.9370 92 2345 1 chr2A.!!$R1 2253
12 TraesCS5B01G104000 chr3B 243088722 243090674 1952 True 2752 2752 92.1740 45 1990 1 chr3B.!!$R1 1945
13 TraesCS5B01G104000 chr1A 465251795 465253629 1834 False 2505 2505 91.3090 497 2345 1 chr1A.!!$F1 1848
14 TraesCS5B01G104000 chr2D 628411726 628412772 1046 False 1387 1387 90.7020 581 1624 1 chr2D.!!$F1 1043

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
902 5678 0.032952 ACGCTACGACAACATGTGGT 59.967 50.0 5.28 5.28 42.02 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 6973 1.139095 GTGCTCCGTCGAGTTAGGG 59.861 63.158 0.0 0.0 38.49 3.53 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
26 27 7.124147 AGTTTTTCAATTTCCTCAGTCTTTCCA 59.876 33.333 0.00 0.00 0.00 3.53
27 28 7.601705 TTTTCAATTTCCTCAGTCTTTCCAT 57.398 32.000 0.00 0.00 0.00 3.41
28 29 6.824305 TTCAATTTCCTCAGTCTTTCCATC 57.176 37.500 0.00 0.00 0.00 3.51
29 30 4.937620 TCAATTTCCTCAGTCTTTCCATCG 59.062 41.667 0.00 0.00 0.00 3.84
30 31 4.559862 ATTTCCTCAGTCTTTCCATCGT 57.440 40.909 0.00 0.00 0.00 3.73
31 32 4.351874 TTTCCTCAGTCTTTCCATCGTT 57.648 40.909 0.00 0.00 0.00 3.85
32 33 3.319137 TCCTCAGTCTTTCCATCGTTG 57.681 47.619 0.00 0.00 0.00 4.10
33 34 2.632996 TCCTCAGTCTTTCCATCGTTGT 59.367 45.455 0.00 0.00 0.00 3.32
35 36 3.433615 CCTCAGTCTTTCCATCGTTGTTC 59.566 47.826 0.00 0.00 0.00 3.18
37 38 4.703897 TCAGTCTTTCCATCGTTGTTCTT 58.296 39.130 0.00 0.00 0.00 2.52
38 39 4.750098 TCAGTCTTTCCATCGTTGTTCTTC 59.250 41.667 0.00 0.00 0.00 2.87
39 40 4.511454 CAGTCTTTCCATCGTTGTTCTTCA 59.489 41.667 0.00 0.00 0.00 3.02
40 41 5.180117 CAGTCTTTCCATCGTTGTTCTTCAT 59.820 40.000 0.00 0.00 0.00 2.57
41 42 5.765182 AGTCTTTCCATCGTTGTTCTTCATT 59.235 36.000 0.00 0.00 0.00 2.57
42 43 5.853282 GTCTTTCCATCGTTGTTCTTCATTG 59.147 40.000 0.00 0.00 0.00 2.82
44 45 3.411446 TCCATCGTTGTTCTTCATTGCT 58.589 40.909 0.00 0.00 0.00 3.91
188 4929 2.488087 AAGAGGCGTTCCCGAACTCG 62.488 60.000 6.06 0.00 41.52 4.18
286 5032 0.107800 CCCATCTGCACACTCCTCAG 60.108 60.000 0.00 0.00 0.00 3.35
294 5040 1.610673 ACACTCCTCAGGGCATCGT 60.611 57.895 0.00 0.00 0.00 3.73
319 5065 0.525668 CGTCGATGAACTTCTCCCGG 60.526 60.000 0.00 0.00 0.00 5.73
434 5184 4.803908 CCCTTCTTCCCCAGCGCC 62.804 72.222 2.29 0.00 0.00 6.53
437 5187 3.984193 CTTCTTCCCCAGCGCCCTG 62.984 68.421 2.29 0.00 38.85 4.45
537 5291 0.952497 CAGCTGCAACTCCGACACAT 60.952 55.000 0.00 0.00 0.00 3.21
556 5310 3.233980 CCTCGGATCCGGCCATGA 61.234 66.667 32.79 12.48 40.25 3.07
697 5473 4.680237 CCTGCGACGTGCCCTTCA 62.680 66.667 0.00 0.00 45.60 3.02
703 5479 2.847234 ACGTGCCCTTCACTCCCA 60.847 61.111 0.00 0.00 43.46 4.37
719 5495 2.509336 CATCCGGCGCGAACTTCT 60.509 61.111 12.10 0.00 0.00 2.85
752 5528 1.305887 GACCTTCCCTCCCCTTCGA 60.306 63.158 0.00 0.00 0.00 3.71
893 5669 2.767445 CCCATCGGACGCTACGACA 61.767 63.158 0.00 0.00 43.78 4.35
902 5678 0.032952 ACGCTACGACAACATGTGGT 59.967 50.000 5.28 5.28 42.02 4.16
908 5684 3.525619 GACAACATGTGGTCGGCTA 57.474 52.632 17.49 0.00 0.00 3.93
963 5739 3.565482 ACACGCATCATCTTTGAGTTTGT 59.435 39.130 0.00 0.00 34.73 2.83
977 5753 0.237498 GTTTGTTCCGGCTGTACTGC 59.763 55.000 15.79 15.79 0.00 4.40
1015 5791 3.971245 TGTGTATGTGTGCAGGTGATA 57.029 42.857 0.00 0.00 0.00 2.15
1064 5841 2.072487 GGGCTGCCCTACATCTGGA 61.072 63.158 30.42 0.00 41.34 3.86
1083 5860 2.599578 CAGCAAGGCCAGCAACCT 60.600 61.111 20.51 0.00 40.02 3.50
1085 5862 0.895100 CAGCAAGGCCAGCAACCTAA 60.895 55.000 20.51 0.00 36.14 2.69
1151 5928 2.774234 GACATCATCCCCTTCTTCCAGA 59.226 50.000 0.00 0.00 0.00 3.86
1159 5936 2.436417 CCCTTCTTCCAGATCGCAAAA 58.564 47.619 0.00 0.00 0.00 2.44
1228 6005 0.322975 GCAGGTCAAGGAGAAGCTCA 59.677 55.000 0.00 0.00 31.08 4.26
1281 6058 1.077501 CGCCATGGTCACCTGGATT 60.078 57.895 14.67 0.00 34.24 3.01
1411 6205 2.809706 GGTGAGCCGGCGTATACA 59.190 61.111 23.20 14.39 0.00 2.29
1457 6252 1.264288 GCGTGCATCAGGTATTTAGGC 59.736 52.381 0.00 0.00 0.00 3.93
1494 6289 5.121221 ACTACAAAACATTTGCTACCTGC 57.879 39.130 2.88 0.00 43.25 4.85
1650 6445 3.144506 CAAGAATTGCGGCTGGATAGAT 58.855 45.455 0.00 0.00 40.39 1.98
1651 6446 4.318332 CAAGAATTGCGGCTGGATAGATA 58.682 43.478 0.00 0.00 40.39 1.98
1671 6466 0.248458 GGCAAAACGATGGTATGCCG 60.248 55.000 17.71 0.00 44.38 5.69
1895 6692 2.225467 GCTTCTCCTGCAGAACAAGTT 58.775 47.619 17.39 0.00 36.08 2.66
2018 6815 1.345741 CTTCTCCTGCAGACCAAGTCA 59.654 52.381 17.39 0.00 34.60 3.41
2069 6866 1.929169 CACGAATGCATGTCGATGTCT 59.071 47.619 26.77 10.20 41.02 3.41
2107 6906 3.960102 TGACCAAGCAATTCAAAAGGAGT 59.040 39.130 0.00 0.00 0.00 3.85
2174 6973 9.396022 TGATTTTGATTCTCTGTAGTTATTCCC 57.604 33.333 0.00 0.00 0.00 3.97
2185 6984 4.646492 TGTAGTTATTCCCCCTAACTCGAC 59.354 45.833 0.00 0.00 39.50 4.20
2314 7117 4.696455 AGCAACAAGAAGGAAACAATTGG 58.304 39.130 10.83 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.264947 TGGAAAGACTGAGGAAATTGAAAAAC 58.735 34.615 0.00 0.0 0.00 2.43
3 4 7.522073 CGATGGAAAGACTGAGGAAATTGAAAA 60.522 37.037 0.00 0.0 0.00 2.29
5 6 5.412594 CGATGGAAAGACTGAGGAAATTGAA 59.587 40.000 0.00 0.0 0.00 2.69
6 7 4.937620 CGATGGAAAGACTGAGGAAATTGA 59.062 41.667 0.00 0.0 0.00 2.57
7 8 4.697352 ACGATGGAAAGACTGAGGAAATTG 59.303 41.667 0.00 0.0 0.00 2.32
10 11 4.065088 CAACGATGGAAAGACTGAGGAAA 58.935 43.478 0.00 0.0 0.00 3.13
12 13 2.632996 ACAACGATGGAAAGACTGAGGA 59.367 45.455 0.00 0.0 0.00 3.71
13 14 3.045601 ACAACGATGGAAAGACTGAGG 57.954 47.619 0.00 0.0 0.00 3.86
14 15 4.310769 AGAACAACGATGGAAAGACTGAG 58.689 43.478 0.00 0.0 0.00 3.35
16 17 4.511454 TGAAGAACAACGATGGAAAGACTG 59.489 41.667 0.00 0.0 0.00 3.51
17 18 4.703897 TGAAGAACAACGATGGAAAGACT 58.296 39.130 0.00 0.0 0.00 3.24
18 19 5.613358 ATGAAGAACAACGATGGAAAGAC 57.387 39.130 0.00 0.0 0.00 3.01
21 22 4.278170 AGCAATGAAGAACAACGATGGAAA 59.722 37.500 0.00 0.0 0.00 3.13
22 23 3.820467 AGCAATGAAGAACAACGATGGAA 59.180 39.130 0.00 0.0 0.00 3.53
23 24 3.411446 AGCAATGAAGAACAACGATGGA 58.589 40.909 0.00 0.0 0.00 3.41
24 25 3.837213 AGCAATGAAGAACAACGATGG 57.163 42.857 0.00 0.0 0.00 3.51
76 4809 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.0 0.00 3.20
78 4811 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.0 0.00 3.20
80 4813 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.0 0.00 3.20
82 4815 5.278758 GCTACTCTCTCTCTCTCTCTCTCTC 60.279 52.000 0.00 0.0 0.00 3.20
84 4817 4.342378 TGCTACTCTCTCTCTCTCTCTCTC 59.658 50.000 0.00 0.0 0.00 3.20
86 4819 4.100189 AGTGCTACTCTCTCTCTCTCTCTC 59.900 50.000 0.00 0.0 0.00 3.20
88 4821 4.408182 AGTGCTACTCTCTCTCTCTCTC 57.592 50.000 0.00 0.0 0.00 3.20
188 4929 1.302271 GGTCGGGTGGGTTTCTCAC 60.302 63.158 0.00 0.0 34.61 3.51
294 5040 3.583276 AAGTTCATCGACGGCGGCA 62.583 57.895 15.54 0.0 38.28 5.69
302 5048 0.815734 GACCGGGAGAAGTTCATCGA 59.184 55.000 6.32 0.0 0.00 3.59
344 5093 3.818787 GGAGTTAGGCGCGTCGGA 61.819 66.667 5.57 0.0 0.00 4.55
477 5230 2.224159 GGGTTGCAGGAGGAGACCA 61.224 63.158 4.00 0.0 32.00 4.02
689 5465 2.669133 CGGATGGGAGTGAAGGGCA 61.669 63.158 0.00 0.0 0.00 5.36
703 5479 2.202756 GAGAAGTTCGCGCCGGAT 60.203 61.111 5.05 0.0 0.00 4.18
893 5669 0.673644 GCACTAGCCGACCACATGTT 60.674 55.000 0.00 0.0 33.58 2.71
902 5678 0.961857 TACCTTGACGCACTAGCCGA 60.962 55.000 9.99 0.0 37.52 5.54
908 5684 5.656213 AGTTATAGTTACCTTGACGCACT 57.344 39.130 0.00 0.0 0.00 4.40
934 5710 6.066054 TCAAAGATGATGCGTGTGTTTTAA 57.934 33.333 0.00 0.0 0.00 1.52
936 5712 4.036734 ACTCAAAGATGATGCGTGTGTTTT 59.963 37.500 0.00 0.0 34.37 2.43
945 5721 4.161333 CGGAACAAACTCAAAGATGATGC 58.839 43.478 0.00 0.0 34.37 3.91
950 5726 2.554032 CAGCCGGAACAAACTCAAAGAT 59.446 45.455 5.05 0.0 0.00 2.40
963 5739 0.107831 AAAGTGCAGTACAGCCGGAA 59.892 50.000 5.05 0.0 0.00 4.30
1015 5791 2.257409 CTAGCCCAAGGTGGTCGCAT 62.257 60.000 0.00 0.0 35.17 4.73
1064 5841 2.501602 GGTTGCTGGCCTTGCTGTT 61.502 57.895 19.10 0.0 0.00 3.16
1083 5860 4.527038 ACTCCTTCTTCAGGTTCACGATTA 59.473 41.667 0.00 0.0 44.37 1.75
1085 5862 2.900546 ACTCCTTCTTCAGGTTCACGAT 59.099 45.455 0.00 0.0 44.37 3.73
1151 5928 3.612479 GCATTCCTTGTCAGTTTTGCGAT 60.612 43.478 0.00 0.0 0.00 4.58
1159 5936 1.512926 GTGTCGCATTCCTTGTCAGT 58.487 50.000 0.00 0.0 0.00 3.41
1228 6005 1.757699 GAAGTAGGGGTCGATCTTGCT 59.242 52.381 0.00 0.0 0.00 3.91
1411 6205 4.100498 TGAACCTACGAACTGAAGAAACCT 59.900 41.667 0.00 0.0 0.00 3.50
1457 6252 3.660501 TGTAGTACACAACAGCCTGAG 57.339 47.619 0.00 0.0 32.95 3.35
1650 6445 2.294074 GGCATACCATCGTTTTGCCTA 58.706 47.619 9.05 0.0 42.53 3.93
1651 6446 1.102978 GGCATACCATCGTTTTGCCT 58.897 50.000 9.05 0.0 42.53 4.75
1671 6466 1.505353 GGTGATGCACTGCTTGAGC 59.495 57.895 1.98 0.0 42.50 4.26
1749 6544 3.444388 GCTGTAGTTGACCTGCTAGTAGT 59.556 47.826 7.10 0.0 0.00 2.73
1930 6727 2.157738 GTCTGCAGGAGAAGCACAAAT 58.842 47.619 15.13 0.0 37.02 2.32
1933 6730 1.372683 GGTCTGCAGGAGAAGCACA 59.627 57.895 15.13 0.0 37.02 4.57
1993 6790 2.047844 TCTGCAGGAGAAGCACGC 60.048 61.111 15.13 0.0 37.02 5.34
2053 6850 3.076621 ACAACAGACATCGACATGCATT 58.923 40.909 0.00 0.0 32.57 3.56
2069 6866 4.157849 TGGTCAACAGGATAACACAACA 57.842 40.909 0.00 0.0 0.00 3.33
2107 6906 3.488778 TTAGGCAAACGAAACCACCTA 57.511 42.857 0.00 0.0 0.00 3.08
2149 6948 8.841300 GGGGAATAACTACAGAGAATCAAAATC 58.159 37.037 0.00 0.0 37.82 2.17
2150 6949 7.780271 GGGGGAATAACTACAGAGAATCAAAAT 59.220 37.037 0.00 0.0 37.82 1.82
2174 6973 1.139095 GTGCTCCGTCGAGTTAGGG 59.861 63.158 0.00 0.0 38.49 3.53
2314 7117 8.871686 AACAATCAAACAAAAGGACATAGTTC 57.128 30.769 0.00 0.0 0.00 3.01


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

AutoCloner maintained by Alex Coulton.