Multiple sequence alignment - TraesCS5D01G267700

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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 TraesCS5D01G267700 chr5D 100.000 3107 0 0 1 3107 371267080 371270186 0.000000e+00 5738
1 TraesCS5D01G267700 chr5D 92.074 1615 117 9 906 2511 371023184 371021572 0.000000e+00 2263
2 TraesCS5D01G267700 chr5B 94.863 3134 113 21 1 3106 440513533 440516646 0.000000e+00 4852
3 TraesCS5D01G267700 chr5B 94.490 3140 116 24 1 3106 440533198 440536314 0.000000e+00 4787
4 TraesCS5D01G267700 chr5B 90.805 435 16 11 879 1293 441124340 441123910 7.520000e-156 560
5 TraesCS5D01G267700 chr5A 93.865 2673 133 9 231 2878 474062033 474059367 0.000000e+00 3999
6 TraesCS5D01G267700 chr5A 93.512 2682 134 11 231 2878 474327513 474324838 0.000000e+00 3952
7 TraesCS5D01G267700 chr5A 93.473 2681 136 10 231 2878 474195568 474192894 0.000000e+00 3945
8 TraesCS5D01G267700 chr5A 92.116 241 9 3 2866 3106 474185500 474185270 6.420000e-87 331
9 TraesCS5D01G267700 chr5A 91.701 241 10 3 2866 3106 474052024 474051794 2.990000e-85 326
10 TraesCS5D01G267700 chr5A 91.701 241 10 3 2866 3106 474317446 474317216 2.990000e-85 326
11 TraesCS5D01G267700 chr5A 86.164 159 13 4 712 868 382336308 382336459 2.480000e-36 163
12 TraesCS5D01G267700 chrUn 97.464 1183 21 3 1 1177 371166039 371167218 0.000000e+00 2010
13 TraesCS5D01G267700 chrUn 90.313 1311 78 22 1824 3106 272196413 272195124 0.000000e+00 1672
14 TraesCS5D01G267700 chrUn 91.067 806 50 8 1824 2619 465607524 465606731 0.000000e+00 1070
15 TraesCS5D01G267700 chrUn 95.500 200 2 2 2907 3106 281140476 281140284 2.330000e-81 313
16 TraesCS5D01G267700 chr7D 91.027 691 54 6 2 688 184517282 184517968 0.000000e+00 926
17 TraesCS5D01G267700 chr3D 90.870 690 57 4 1 688 375235290 375235975 0.000000e+00 920
18 TraesCS5D01G267700 chr3D 90.607 692 59 4 7 696 363070237 363069550 0.000000e+00 913
19 TraesCS5D01G267700 chr6D 84.906 159 15 4 712 868 73497393 73497242 5.370000e-33 152
20 TraesCS5D01G267700 chr7A 81.646 158 22 4 712 868 539543828 539543677 1.170000e-24 124


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 TraesCS5D01G267700 chr5D 371267080 371270186 3106 False 5738 5738 100.000 1 3107 1 chr5D.!!$F1 3106
1 TraesCS5D01G267700 chr5D 371021572 371023184 1612 True 2263 2263 92.074 906 2511 1 chr5D.!!$R1 1605
2 TraesCS5D01G267700 chr5B 440513533 440516646 3113 False 4852 4852 94.863 1 3106 1 chr5B.!!$F1 3105
3 TraesCS5D01G267700 chr5B 440533198 440536314 3116 False 4787 4787 94.490 1 3106 1 chr5B.!!$F2 3105
4 TraesCS5D01G267700 chr5A 474059367 474062033 2666 True 3999 3999 93.865 231 2878 1 chr5A.!!$R2 2647
5 TraesCS5D01G267700 chr5A 474324838 474327513 2675 True 3952 3952 93.512 231 2878 1 chr5A.!!$R6 2647
6 TraesCS5D01G267700 chr5A 474192894 474195568 2674 True 3945 3945 93.473 231 2878 1 chr5A.!!$R4 2647
7 TraesCS5D01G267700 chrUn 371166039 371167218 1179 False 2010 2010 97.464 1 1177 1 chrUn.!!$F1 1176
8 TraesCS5D01G267700 chrUn 272195124 272196413 1289 True 1672 1672 90.313 1824 3106 1 chrUn.!!$R1 1282
9 TraesCS5D01G267700 chrUn 465606731 465607524 793 True 1070 1070 91.067 1824 2619 1 chrUn.!!$R3 795
10 TraesCS5D01G267700 chr7D 184517282 184517968 686 False 926 926 91.027 2 688 1 chr7D.!!$F1 686
11 TraesCS5D01G267700 chr3D 375235290 375235975 685 False 920 920 90.870 1 688 1 chr3D.!!$F1 687
12 TraesCS5D01G267700 chr3D 363069550 363070237 687 True 913 913 90.607 7 696 1 chr3D.!!$R1 689

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
980 1006 3.458189 AGCCACGATATTCAACTACTGC 58.542 45.455 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2629 2690 0.251916 CATCAAAGCAGGTCCGGGTA 59.748 55.0 0.0 0.0 0.0 3.69 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
176 182 6.590068 AGAGGGTATTCTTCAATGTCATCAG 58.410 40.000 0.00 0.00 0.00 2.90
577 602 7.344352 TGATATATTTCCCCCTTTTGTCTTTGG 59.656 37.037 0.00 0.00 0.00 3.28
709 735 4.447138 ACCAAACACACCCTTGATCTTA 57.553 40.909 0.00 0.00 0.00 2.10
864 890 8.798859 ATTGAGTCACTTAGATTTGCAGTAAT 57.201 30.769 0.00 0.00 0.00 1.89
980 1006 3.458189 AGCCACGATATTCAACTACTGC 58.542 45.455 0.00 0.00 0.00 4.40
1284 1310 2.447714 GGGGGAGGGCTCTGTCATC 61.448 68.421 0.00 0.00 0.00 2.92
1580 1606 4.283403 TGGCGGCAACAGCAAAGC 62.283 61.111 10.22 0.00 37.75 3.51
1732 1758 1.435925 CACGGTGCGGCAGAGTATA 59.564 57.895 1.18 0.00 0.00 1.47
1809 1835 0.249031 GCCTGCGTGCTTTTGACTTT 60.249 50.000 0.00 0.00 0.00 2.66
1827 1853 0.776810 TTGATTCCTCCAGGCAACCA 59.223 50.000 0.00 0.00 34.44 3.67
1857 1883 2.763448 GCACTCCTGGAACTATCTCAGT 59.237 50.000 0.00 0.00 40.05 3.41
1949 1975 2.675348 CCACCAGCTTTCGAAATCTCTC 59.325 50.000 11.70 0.00 0.00 3.20
2029 2055 3.071837 TGGAGGTGGTGCGCGATA 61.072 61.111 12.10 0.00 0.00 2.92
2121 2147 5.517054 CGTGCTCTGAGGAAAACTTATCTAC 59.483 44.000 6.83 0.00 0.00 2.59
2126 2152 7.627939 GCTCTGAGGAAAACTTATCTACGTGTA 60.628 40.741 6.83 0.00 0.00 2.90
2207 2233 7.645058 TTTCTTAGCTTTTATCTCCATTGGG 57.355 36.000 2.09 0.00 0.00 4.12
2219 2262 4.217510 TCTCCATTGGGAAATAGGCAATG 58.782 43.478 2.09 0.00 44.38 2.82
2240 2283 5.920193 TGGATGGCTTAAAGAAGAAATGG 57.080 39.130 0.00 0.00 34.25 3.16
2389 2435 3.127030 GCGCTTGAGCCAACTAGTAAAAT 59.873 43.478 0.00 0.00 37.91 1.82
2451 2500 1.153765 CTCGAGTGGAGAATGCGCA 60.154 57.895 14.96 14.96 46.23 6.09
2475 2524 3.267233 TTGGCCCCAGCAGACCAT 61.267 61.111 0.00 0.00 42.56 3.55
2493 2547 2.006888 CATACCCGCGATTCTTTGTGT 58.993 47.619 8.23 0.00 0.00 3.72
2536 2590 1.514811 CGCTGCTTCGAAGAGTATTCG 59.485 52.381 28.95 13.59 42.74 3.34
2608 2662 3.988379 TCATGCTCAAAGTTTGACACC 57.012 42.857 14.35 6.70 35.46 4.16
2621 2682 2.932184 TGACACCATAGTACAGGGGA 57.068 50.000 8.10 0.00 29.99 4.81
2629 2690 5.544176 CACCATAGTACAGGGGACTCAATAT 59.456 44.000 0.00 0.00 40.21 1.28
2959 3040 7.512992 CCCAGAGTGATAATTTACAGGAATCT 58.487 38.462 0.00 0.00 0.00 2.40
2960 3041 7.659390 CCCAGAGTGATAATTTACAGGAATCTC 59.341 40.741 0.00 0.00 0.00 2.75
2961 3042 8.206867 CCAGAGTGATAATTTACAGGAATCTCA 58.793 37.037 0.00 0.00 0.00 3.27
2962 3043 9.258826 CAGAGTGATAATTTACAGGAATCTCAG 57.741 37.037 0.00 0.00 0.00 3.35
2963 3044 8.428063 AGAGTGATAATTTACAGGAATCTCAGG 58.572 37.037 0.00 0.00 0.00 3.86
2964 3045 8.324191 AGTGATAATTTACAGGAATCTCAGGA 57.676 34.615 0.00 0.00 0.00 3.86
2965 3046 8.428063 AGTGATAATTTACAGGAATCTCAGGAG 58.572 37.037 0.00 0.00 0.00 3.69
2966 3047 8.207545 GTGATAATTTACAGGAATCTCAGGAGT 58.792 37.037 0.00 0.00 0.00 3.85
3006 3087 6.822667 TCATTCTGCAGACAATTTACATGT 57.177 33.333 18.03 2.69 0.00 3.21
3106 3187 6.726490 AAGATATAAGTAGAAGGACGGCAA 57.274 37.500 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
577 602 3.426963 CGTGCTACTTCTCTCTTCCAGAC 60.427 52.174 0.00 0.00 0.00 3.51
864 890 6.688073 AGAAAGATCAAAGGGTCTGTCTAA 57.312 37.500 0.00 0.00 37.30 2.10
917 943 6.755206 AGTACAGTAGCATTAACACTTGTCA 58.245 36.000 0.00 0.00 0.00 3.58
980 1006 4.862574 TCATCCTCGAGAATTTAACACACG 59.137 41.667 15.71 0.00 0.00 4.49
1284 1310 0.458025 GGACGTTAGGGCTGACGAAG 60.458 60.000 13.00 0.00 43.95 3.79
1580 1606 0.725686 CGCTGAAGATGGAGCACAAG 59.274 55.000 0.00 0.00 34.69 3.16
1590 1616 0.670546 CCAACACGACCGCTGAAGAT 60.671 55.000 0.00 0.00 0.00 2.40
1594 1620 1.374125 CATCCAACACGACCGCTGA 60.374 57.895 0.00 0.00 0.00 4.26
1732 1758 0.622665 CAGAGGCCAAACTCAGGGAT 59.377 55.000 5.01 0.00 39.97 3.85
1809 1835 0.329261 CTGGTTGCCTGGAGGAATCA 59.671 55.000 0.00 0.00 37.39 2.57
1857 1883 4.147449 CACTCATCCGGCAGGCGA 62.147 66.667 19.71 4.35 37.47 5.54
1927 1953 2.039084 AGAGATTTCGAAAGCTGGTGGT 59.961 45.455 31.42 8.22 34.31 4.16
1982 2008 1.899814 AGACGGTAAGCTCATTGACCA 59.100 47.619 0.00 0.00 31.89 4.02
2029 2055 5.068723 GCTTGATGATCTGGAAACCATTGAT 59.931 40.000 0.00 0.00 30.82 2.57
2121 2147 5.236478 GGATCCATCCAATAACAGTTACACG 59.764 44.000 6.95 0.00 46.38 4.49
2185 2211 6.575244 TCCCAATGGAGATAAAAGCTAAGA 57.425 37.500 0.00 0.00 35.03 2.10
2204 2230 2.961510 CCATCCATTGCCTATTTCCCA 58.038 47.619 0.00 0.00 0.00 4.37
2206 2232 2.601905 AGCCATCCATTGCCTATTTCC 58.398 47.619 0.00 0.00 0.00 3.13
2207 2233 5.789643 TTAAGCCATCCATTGCCTATTTC 57.210 39.130 0.00 0.00 0.00 2.17
2219 2262 6.530019 TTCCATTTCTTCTTTAAGCCATCC 57.470 37.500 0.00 0.00 32.36 3.51
2227 2270 6.153170 TGCATGATGCTTCCATTTCTTCTTTA 59.847 34.615 19.19 0.00 45.31 1.85
2228 2271 5.046878 TGCATGATGCTTCCATTTCTTCTTT 60.047 36.000 19.19 0.00 45.31 2.52
2389 2435 5.165961 ACGGAGAAATCCTCAAGATGAAA 57.834 39.130 0.00 0.00 43.76 2.69
2475 2524 1.001068 TGACACAAAGAATCGCGGGTA 59.999 47.619 6.13 0.00 0.00 3.69
2493 2547 4.460263 AGCATACCAAAACAGTTCACTGA 58.540 39.130 14.00 0.00 46.59 3.41
2536 2590 8.028938 AGTTTAAGTCACAAAATCATATGGTGC 58.971 33.333 2.13 0.31 0.00 5.01
2589 2643 3.713858 TGGTGTCAAACTTTGAGCATG 57.286 42.857 4.36 0.00 41.01 4.06
2608 2662 6.154706 GGGTATATTGAGTCCCCTGTACTATG 59.845 46.154 0.00 0.00 34.32 2.23
2621 2682 1.692519 GCAGGTCCGGGTATATTGAGT 59.307 52.381 0.00 0.00 0.00 3.41
2629 2690 0.251916 CATCAAAGCAGGTCCGGGTA 59.748 55.000 0.00 0.00 0.00 3.69
2959 3040 4.475381 AGACTATAGTGTCCTGACTCCTGA 59.525 45.833 10.90 0.00 37.66 3.86
2960 3041 4.787551 AGACTATAGTGTCCTGACTCCTG 58.212 47.826 10.90 0.00 37.66 3.86
2961 3042 5.044772 TGAAGACTATAGTGTCCTGACTCCT 60.045 44.000 10.90 0.00 37.66 3.69
2962 3043 5.194432 TGAAGACTATAGTGTCCTGACTCC 58.806 45.833 10.90 0.00 37.66 3.85
2963 3044 6.952773 ATGAAGACTATAGTGTCCTGACTC 57.047 41.667 10.90 0.16 37.66 3.36
2964 3045 7.068103 CAGAATGAAGACTATAGTGTCCTGACT 59.932 40.741 10.90 2.14 39.69 3.41
2965 3046 7.199766 CAGAATGAAGACTATAGTGTCCTGAC 58.800 42.308 10.90 0.00 39.69 3.51
2966 3047 6.183360 GCAGAATGAAGACTATAGTGTCCTGA 60.183 42.308 10.90 0.00 39.69 3.86
3006 3087 3.251509 TCAGCAAGAGGCCCTGCA 61.252 61.111 20.66 2.17 46.50 4.41


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

AutoCloner maintained by Alex Coulton.