Multiple sequence alignment - TraesCS5D01G545600

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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 TraesCS5D01G545600 chr5D 100.000 3373 0 0 1 3373 554506492 554509864 0.000000e+00 6229
1 TraesCS5D01G545600 chr4A 93.862 2558 126 8 2 2556 614027937 614025408 0.000000e+00 3825
2 TraesCS5D01G545600 chr4A 96.859 764 22 2 2611 3373 614025411 614024649 0.000000e+00 1277
3 TraesCS5D01G545600 chr4A 98.611 72 1 0 3300 3371 614024692 614024621 9.820000e-26 128
4 TraesCS5D01G545600 chr5B 93.152 2468 131 15 1 2454 696176740 696174297 0.000000e+00 3587
5 TraesCS5D01G545600 chr5B 93.939 429 25 1 2945 3372 696173635 696173207 0.000000e+00 647
6 TraesCS5D01G545600 chr5B 88.034 468 32 12 2448 2911 696174248 696173801 1.780000e-147 532


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 TraesCS5D01G545600 chr5D 554506492 554509864 3372 False 6229.000000 6229 100.000000 1 3373 1 chr5D.!!$F1 3372
1 TraesCS5D01G545600 chr4A 614024621 614027937 3316 True 1743.333333 3825 96.444000 2 3373 3 chr4A.!!$R1 3371
2 TraesCS5D01G545600 chr5B 696173207 696176740 3533 True 1588.666667 3587 91.708333 1 3372 3 chr5B.!!$R1 3371

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
829 833 1.545582 TGCCTTGCTGCTATTCCAAAC 59.454 47.619 0.0 0.0 0.0 2.93 F
1664 1672 0.036952 CACCACGCCACTCTCATTCT 60.037 55.000 0.0 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2136 2144 0.817229 TGCTGTCGTGCCAATCACAA 60.817 50.000 0.0 0.0 45.92 3.33 R
2509 2580 1.202687 CCAGGTCTCAAGTCAAGTGCA 60.203 52.381 0.0 0.0 0.00 4.57 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
55 56 7.441890 GCTATACTGAGCATCTCAAGTAGTA 57.558 40.000 0.00 0.00 40.18 1.82
63 65 9.593134 CTGAGCATCTCAAGTAGTATAACTTTT 57.407 33.333 0.00 0.00 40.18 2.27
87 89 8.707796 TTTATGGTCCCTTTATGTTGTAACAA 57.292 30.769 1.10 0.00 43.03 2.83
92 94 6.349860 GGTCCCTTTATGTTGTAACAATGGTC 60.350 42.308 1.10 0.00 43.03 4.02
179 181 7.281774 CAGACAGTCCAATTCAGCATAATTAGT 59.718 37.037 0.00 0.00 0.00 2.24
181 183 7.765307 ACAGTCCAATTCAGCATAATTAGTTG 58.235 34.615 0.00 0.00 0.00 3.16
226 228 5.908341 ACCGCTGATTTTGGTAAAAAGAAA 58.092 33.333 0.00 0.00 38.62 2.52
419 422 6.318900 GGTTTGGAAAGGTTAGATTGATCGAT 59.681 38.462 0.00 0.00 0.00 3.59
470 473 4.275936 GGATTTTGCTGTCGCCTTGTATAT 59.724 41.667 0.00 0.00 34.43 0.86
551 554 6.259638 ACAATGTAAGTTTGTAACAACCACG 58.740 36.000 0.00 0.00 35.61 4.94
586 589 8.299570 ACTTGCAAAATCTTCGATAAATGTCTT 58.700 29.630 0.00 0.00 0.00 3.01
587 590 8.673626 TTGCAAAATCTTCGATAAATGTCTTC 57.326 30.769 0.00 0.00 0.00 2.87
631 634 6.982141 AGATATGTTGCTATGCCAAAAACATG 59.018 34.615 12.87 0.00 40.62 3.21
751 755 2.093764 AGAGGCAGTGATACTCAAGTGC 60.094 50.000 11.04 4.80 37.69 4.40
815 819 4.326826 TGAAGTCACTAATTCCTGCCTTG 58.673 43.478 0.00 0.00 0.00 3.61
829 833 1.545582 TGCCTTGCTGCTATTCCAAAC 59.454 47.619 0.00 0.00 0.00 2.93
831 835 2.167075 GCCTTGCTGCTATTCCAAACAT 59.833 45.455 0.00 0.00 0.00 2.71
834 838 4.439700 CCTTGCTGCTATTCCAAACATCTG 60.440 45.833 0.00 0.00 0.00 2.90
1081 1088 3.135712 TCAAGTTACTTGCAGTTCTCCCA 59.864 43.478 19.24 0.00 40.84 4.37
1085 1092 0.839946 ACTTGCAGTTCTCCCAGTGT 59.160 50.000 0.00 0.00 0.00 3.55
1106 1113 5.807011 GTGTTCTTCTTGAGTTTTGCAATGT 59.193 36.000 0.00 0.00 0.00 2.71
1183 1190 2.577593 GTACCTGACTGGGACGCC 59.422 66.667 0.00 0.00 40.38 5.68
1208 1215 2.202756 GCTCTTCCTACACCGCCG 60.203 66.667 0.00 0.00 0.00 6.46
1267 1274 2.603247 GCATGGCGTGTTCGTGTCA 61.603 57.895 8.75 0.00 39.49 3.58
1275 1282 0.796312 GTGTTCGTGTCAATCGGCAT 59.204 50.000 0.00 0.00 0.00 4.40
1316 1323 3.611674 TCCTTGCGCTCGACACCA 61.612 61.111 9.73 0.00 0.00 4.17
1317 1324 2.664851 CCTTGCGCTCGACACCAA 60.665 61.111 9.73 0.00 0.00 3.67
1353 1361 0.599991 GTGATGTGTGAGCCGTGTCA 60.600 55.000 0.00 0.00 0.00 3.58
1354 1362 0.599991 TGATGTGTGAGCCGTGTCAC 60.600 55.000 7.31 7.31 46.08 3.67
1360 1368 3.936203 GAGCCGTGTCACCCACCA 61.936 66.667 0.00 0.00 41.26 4.17
1483 1491 3.056328 GCCAACGGGTGCTCCTTC 61.056 66.667 4.53 0.00 36.17 3.46
1585 1593 2.766400 CGGTGTGGCGTTTGGTTGT 61.766 57.895 0.00 0.00 0.00 3.32
1649 1657 2.203832 TGCTCTCCCTCAGCACCA 60.204 61.111 0.00 0.00 42.09 4.17
1660 1668 3.233980 AGCACCACGCCACTCTCA 61.234 61.111 0.00 0.00 44.04 3.27
1664 1672 0.036952 CACCACGCCACTCTCATTCT 60.037 55.000 0.00 0.00 0.00 2.40
1669 1677 1.620819 ACGCCACTCTCATTCTTGACT 59.379 47.619 0.00 0.00 0.00 3.41
1876 1884 0.602638 ACAAGCGCCTTGACATCGAA 60.603 50.000 21.19 0.00 43.42 3.71
1977 1985 3.386237 GGCGAGAGAGCTGGTGGT 61.386 66.667 0.00 0.00 37.29 4.16
2058 2066 1.200020 CAACAAGATTTCCAGGACGGC 59.800 52.381 0.00 0.00 33.14 5.68
2136 2144 2.034221 GGCGGGGAAGCTGTTTCT 59.966 61.111 4.26 0.00 36.03 2.52
2137 2145 1.603739 GGCGGGGAAGCTGTTTCTT 60.604 57.895 4.26 0.00 36.03 2.52
2179 2187 2.933287 TTGGTCGAGGGCCATGGT 60.933 61.111 14.67 0.00 35.71 3.55
2302 2310 0.458543 ATGCAGCGTAGGTCTGTTCG 60.459 55.000 0.00 0.00 33.74 3.95
2356 2371 8.620116 TCACATTCATAGAGTCAATGAAAACA 57.380 30.769 7.67 0.00 44.25 2.83
2367 2382 6.108687 AGTCAATGAAAACAGCATCTATCGA 58.891 36.000 0.00 0.00 0.00 3.59
2409 2424 5.272283 CAAAATTGGATGAGAAGGGATGG 57.728 43.478 0.00 0.00 0.00 3.51
2504 2575 3.253230 GCATCCTGCCATACAAACAAAC 58.747 45.455 0.00 0.00 37.42 2.93
2509 2580 4.343526 TCCTGCCATACAAACAAACATGTT 59.656 37.500 4.92 4.92 0.00 2.71
2563 2635 0.806868 ATGACGAATGCTGCCTGTTG 59.193 50.000 0.00 0.00 0.00 3.33
2583 2655 4.672587 TGCCTTTCAGCGTATAGATCTT 57.327 40.909 0.00 0.00 34.65 2.40
2587 2659 6.183360 TGCCTTTCAGCGTATAGATCTTAACT 60.183 38.462 0.00 0.00 34.65 2.24
2647 2719 3.960102 GGCATTAACCTCCATGGAAATCA 59.040 43.478 17.00 0.00 39.71 2.57
2711 2783 5.063880 AGCTTTTACTGGAACGATTGTCTT 58.936 37.500 0.00 0.00 0.00 3.01
2741 2813 9.826574 AAACCTGAAATGAAATCCATGATAATG 57.173 29.630 0.00 0.00 35.24 1.90
2801 2874 6.948309 ACCACTTCTTGCATTAGTTTTCCTAT 59.052 34.615 0.00 0.00 0.00 2.57
3290 3497 6.478016 CGCTTGTATATGATGTGCTATATGCT 59.522 38.462 0.00 0.00 43.37 3.79
3372 3609 3.301794 AATATGATCCTGTTGCCTGCA 57.698 42.857 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 65 8.744652 CATTGTTACAACATAAAGGGACCATAA 58.255 33.333 0.00 0.00 38.95 1.90
76 78 4.112634 ACCAGGACCATTGTTACAACAT 57.887 40.909 0.00 0.00 38.95 2.71
87 89 1.203050 CCAGGAAACAACCAGGACCAT 60.203 52.381 0.00 0.00 38.63 3.55
92 94 2.230660 GTTCTCCAGGAAACAACCAGG 58.769 52.381 8.75 0.00 37.85 4.45
181 183 7.428472 GCGGTATGCTGTTCTAAGAAATAAAAC 59.572 37.037 0.00 0.00 41.73 2.43
226 228 4.082125 CTGAGATGCCCCACTTAGTTTTT 58.918 43.478 0.00 0.00 0.00 1.94
470 473 8.146412 CAGATTGGTGATACTTCATGAGATACA 58.854 37.037 0.00 0.00 33.56 2.29
538 541 4.652421 TCTCTGTACGTGGTTGTTACAA 57.348 40.909 0.00 0.00 0.00 2.41
551 554 6.073765 TCGAAGATTTTGCAAGTTCTCTGTAC 60.074 38.462 12.11 0.00 0.00 2.90
631 634 5.508994 CCTTCTGGTGGTCCAAACATTTAAC 60.509 44.000 0.00 0.00 43.81 2.01
648 651 9.007901 CATTTATAAAGCTAGAATCCCTTCTGG 57.992 37.037 3.94 0.00 41.83 3.86
751 755 3.584406 TCCAAACAATAAATGCCGGTG 57.416 42.857 1.90 0.00 0.00 4.94
815 819 4.708726 AACAGATGTTTGGAATAGCAGC 57.291 40.909 0.00 0.00 33.93 5.25
829 833 4.533919 TGGCCCAAACATTTAACAGATG 57.466 40.909 0.00 0.00 0.00 2.90
831 835 3.706594 TGTTGGCCCAAACATTTAACAGA 59.293 39.130 0.00 0.00 35.16 3.41
834 838 4.329462 TCTGTTGGCCCAAACATTTAAC 57.671 40.909 8.95 0.00 39.25 2.01
1029 1036 5.532406 GTGGCTCAGGAATTCAAGCATATAA 59.468 40.000 21.15 5.64 36.47 0.98
1081 1088 5.643379 TTGCAAAACTCAAGAAGAACACT 57.357 34.783 0.00 0.00 0.00 3.55
1085 1092 6.206395 TGACATTGCAAAACTCAAGAAGAA 57.794 33.333 1.71 0.00 0.00 2.52
1183 1190 0.107703 TGTAGGAAGAGCCATTGCCG 60.108 55.000 0.00 0.00 40.02 5.69
1208 1215 2.825836 CAATGGGCGCAGGTCCTC 60.826 66.667 10.83 0.00 39.29 3.71
1232 1239 1.227263 GCACATAGTCGGACGGCAT 60.227 57.895 1.89 0.00 0.00 4.40
1233 1240 1.955495 ATGCACATAGTCGGACGGCA 61.955 55.000 13.56 13.56 0.00 5.69
1267 1274 1.819632 GCCTTGTCCGATGCCGATT 60.820 57.895 0.00 0.00 38.22 3.34
1316 1323 3.049674 CCATGACGTGCTGGCGTT 61.050 61.111 0.00 0.00 45.79 4.84
1353 1361 0.185901 AACTTGATGCAGTGGTGGGT 59.814 50.000 0.00 0.00 0.00 4.51
1354 1362 0.599558 CAACTTGATGCAGTGGTGGG 59.400 55.000 0.00 0.00 0.00 4.61
1649 1657 1.620819 AGTCAAGAATGAGAGTGGCGT 59.379 47.619 0.00 0.00 35.88 5.68
1660 1668 3.251004 GCGAACCAAACTGAGTCAAGAAT 59.749 43.478 0.00 0.00 0.00 2.40
1664 1672 0.934496 CGCGAACCAAACTGAGTCAA 59.066 50.000 0.00 0.00 0.00 3.18
1669 1677 4.007940 GCGCGCGAACCAAACTGA 62.008 61.111 37.18 0.00 0.00 3.41
1977 1985 3.644738 TGATCCTAGCTCATTCATCTGCA 59.355 43.478 0.00 0.00 0.00 4.41
2136 2144 0.817229 TGCTGTCGTGCCAATCACAA 60.817 50.000 0.00 0.00 45.92 3.33
2137 2145 1.227793 TGCTGTCGTGCCAATCACA 60.228 52.632 0.00 0.00 45.92 3.58
2218 2226 1.041726 CGTTGAAAATGAACCGTGCG 58.958 50.000 0.00 0.00 33.73 5.34
2230 2238 3.342627 CCCGCAGCGACGTTGAAA 61.343 61.111 18.75 0.00 0.00 2.69
2302 2310 7.816995 TGGCAATTATTTTCCAGAATACAACAC 59.183 33.333 0.00 0.00 0.00 3.32
2409 2424 2.428530 GTGGGGAGCATTTTGGAAGATC 59.571 50.000 0.00 0.00 0.00 2.75
2504 2575 3.304257 GGTCTCAAGTCAAGTGCAACATG 60.304 47.826 0.00 0.00 41.43 3.21
2509 2580 1.202687 CCAGGTCTCAAGTCAAGTGCA 60.203 52.381 0.00 0.00 0.00 4.57
2556 2628 1.234615 TACGCTGAAAGGCAACAGGC 61.235 55.000 0.00 0.00 43.74 4.85
2563 2635 6.217294 AGTTAAGATCTATACGCTGAAAGGC 58.783 40.000 0.00 0.00 0.00 4.35
2647 2719 6.131972 TCTCCAGTGGAAGAGATGAAAAAT 57.868 37.500 14.17 0.00 34.23 1.82
2711 2783 6.720748 TCATGGATTTCATTTCAGGTTTCAGA 59.279 34.615 0.00 0.00 32.92 3.27
2741 2813 2.548057 TCGAGGTTCAATGACAGCAAAC 59.452 45.455 0.00 0.00 0.00 2.93
2815 2888 4.093408 CCACACACCAGACGAAATCAATAG 59.907 45.833 0.00 0.00 0.00 1.73
2842 2915 2.586079 CAGCACGCCGGTATCAGG 60.586 66.667 1.90 0.00 0.00 3.86
3183 3390 8.816144 TGAAATTGCAGTTACTTGTGAAAAATC 58.184 29.630 0.00 0.00 0.00 2.17
3290 3497 3.384146 TGCAAGCAACAGGAGAAAATTCA 59.616 39.130 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.