Multiple sequence alignment - TraesCS5A01G264300

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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 TraesCS5A01G264300 chr5A 100.000 2360 0 0 1 2360 476667577 476665218 0.000000e+00 4359
1 TraesCS5A01G264300 chr5D 91.482 1714 106 28 648 2344 375309501 375307811 0.000000e+00 2320
2 TraesCS5A01G264300 chr5D 84.220 583 58 19 1 574 375310082 375309525 9.600000e-149 536
3 TraesCS5A01G264300 chr5B 92.568 1184 60 12 742 1901 448129599 448128420 0.000000e+00 1674
4 TraesCS5A01G264300 chr5B 90.344 756 54 10 1 744 448130395 448129647 0.000000e+00 974
5 TraesCS5A01G264300 chr5B 84.539 401 40 10 1962 2358 448128420 448128038 6.160000e-101 377
6 TraesCS5A01G264300 chr7A 91.566 166 12 2 1160 1325 222360989 222361152 6.560000e-56 228
7 TraesCS5A01G264300 chr7B 88.333 180 16 4 1176 1351 191904434 191904256 6.610000e-51 211


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 TraesCS5A01G264300 chr5A 476665218 476667577 2359 True 4359.000000 4359 100.000000 1 2360 1 chr5A.!!$R1 2359
1 TraesCS5A01G264300 chr5D 375307811 375310082 2271 True 1428.000000 2320 87.851000 1 2344 2 chr5D.!!$R1 2343
2 TraesCS5A01G264300 chr5B 448128038 448130395 2357 True 1008.333333 1674 89.150333 1 2358 3 chr5B.!!$R1 2357

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
885 958 0.038251 TTACACCACTCTCTGCAGCG 60.038 55.0 9.47 2.08 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 1879 1.840635 GAGACAATACCCAAGCCCTCT 59.159 52.381 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
22 23 2.601240 TCCAATCCCAAACAGCATGA 57.399 45.000 0.00 0.00 39.69 3.07
61 62 6.092396 GCTGTCTGCATATATGAAGGAGATTG 59.908 42.308 18.99 6.74 42.31 2.67
82 83 1.521450 CTGGCTTGGCTGTGTTCTGG 61.521 60.000 0.00 0.00 0.00 3.86
112 115 4.362932 TCAAGACTGTAGAGCTGATTCG 57.637 45.455 0.00 0.00 0.00 3.34
142 145 4.688879 CCGATTTGCACTTGTCAGTACTTA 59.311 41.667 0.00 0.00 0.00 2.24
236 243 5.806654 ATGGCTTGTGTTTTGTCCTATTT 57.193 34.783 0.00 0.00 0.00 1.40
237 244 5.606348 TGGCTTGTGTTTTGTCCTATTTT 57.394 34.783 0.00 0.00 0.00 1.82
301 308 4.346418 CCAGGTCAAGTAGATGGAGCTATT 59.654 45.833 0.00 0.00 37.29 1.73
416 427 8.627487 AACACATGTTGTACAATAGTTTTGTG 57.373 30.769 23.87 23.87 37.51 3.33
445 457 8.806146 AGAAATATGCCGGCTTTATTAAATCAT 58.194 29.630 29.70 13.59 0.00 2.45
459 471 9.773328 TTTATTAAATCATGACTCGCAAAAGAG 57.227 29.630 0.00 0.00 43.56 2.85
484 497 2.165845 CCGTAGTACCAAGGTGAAGAGG 59.834 54.545 1.07 0.00 0.00 3.69
501 514 2.432510 AGAGGCGACCAAAATCTAGGAG 59.567 50.000 0.00 0.00 0.00 3.69
508 521 6.486993 GGCGACCAAAATCTAGGAGATAATTT 59.513 38.462 0.00 0.00 32.89 1.82
612 625 6.526056 TTGGAGAGGGTAGAGCTATAGTAA 57.474 41.667 0.84 0.00 0.00 2.24
615 628 6.791466 TGGAGAGGGTAGAGCTATAGTAACTA 59.209 42.308 0.84 0.86 0.00 2.24
630 643 4.625028 AGTAACTAAGTGAACAACCCGAC 58.375 43.478 0.00 0.00 0.00 4.79
651 664 7.437267 CCCGACTAAATGTACTGTAGTAAATGG 59.563 40.741 0.00 0.98 29.32 3.16
722 737 6.829985 TCATTTGGAGAGGGAATTCTCATA 57.170 37.500 8.33 0.00 44.34 2.15
746 783 2.450609 TTTCGGCAGTCCTTAGTGAC 57.549 50.000 0.00 0.00 35.43 3.67
792 856 9.464714 AGAATAGTGACAATATTACTTGCTACG 57.535 33.333 8.07 0.00 0.00 3.51
793 857 8.589335 AATAGTGACAATATTACTTGCTACGG 57.411 34.615 6.37 0.00 0.00 4.02
835 906 6.380079 AAAGATCACCCACTTCTTCATAGT 57.620 37.500 0.00 0.00 0.00 2.12
883 956 2.611473 CCACTTACACCACTCTCTGCAG 60.611 54.545 7.63 7.63 0.00 4.41
884 957 1.001406 ACTTACACCACTCTCTGCAGC 59.999 52.381 9.47 0.00 0.00 5.25
885 958 0.038251 TTACACCACTCTCTGCAGCG 60.038 55.000 9.47 2.08 0.00 5.18
982 1065 1.480212 AATCCTCCACCTCGCACACA 61.480 55.000 0.00 0.00 0.00 3.72
1389 1472 4.148825 CGCCCCAGGTCTTCCTCG 62.149 72.222 0.00 0.00 43.07 4.63
1418 1501 4.016444 AGGTTGCTTCTGTTCTGTTTTGA 58.984 39.130 0.00 0.00 0.00 2.69
1486 1569 1.217057 ATGGGACCTGGGCTGAACAT 61.217 55.000 0.00 0.00 0.00 2.71
1490 1573 2.301346 GGACCTGGGCTGAACATTATG 58.699 52.381 0.00 0.00 0.00 1.90
1567 1650 2.678471 CATTTCCAAATGCCCTGTCC 57.322 50.000 0.00 0.00 39.29 4.02
1568 1651 1.207811 CATTTCCAAATGCCCTGTCCC 59.792 52.381 0.00 0.00 39.29 4.46
1569 1652 0.486879 TTTCCAAATGCCCTGTCCCT 59.513 50.000 0.00 0.00 0.00 4.20
1570 1653 1.377690 TTCCAAATGCCCTGTCCCTA 58.622 50.000 0.00 0.00 0.00 3.53
1574 1661 3.106827 CCAAATGCCCTGTCCCTAAAAT 58.893 45.455 0.00 0.00 0.00 1.82
1609 1696 4.511454 TCTCGGCATTGTATTATCTTGTGC 59.489 41.667 0.00 0.00 0.00 4.57
1610 1697 3.247411 TCGGCATTGTATTATCTTGTGCG 59.753 43.478 0.00 0.00 32.23 5.34
1617 1704 4.839121 TGTATTATCTTGTGCGTCCCTTT 58.161 39.130 0.00 0.00 0.00 3.11
1697 1784 1.110442 CCTGTCTCTCTTCGCCTGAT 58.890 55.000 0.00 0.00 0.00 2.90
1717 1804 6.750501 CCTGATATGACTTGTTGCAGAAAATG 59.249 38.462 0.00 0.00 0.00 2.32
1776 1863 5.673337 TGCTTGCTTGTTAGAACTTACAG 57.327 39.130 0.00 0.00 0.00 2.74
1792 1879 5.070001 ACTTACAGGTGATGCTTGCTTTTA 58.930 37.500 0.00 0.00 0.00 1.52
1816 1904 2.239907 GGGCTTGGGTATTGTCTCTCTT 59.760 50.000 0.00 0.00 0.00 2.85
1845 1933 4.761739 TCTTTTCCAATGATGAGTGGACAC 59.238 41.667 0.00 0.00 45.99 3.67
1872 1960 5.633830 TCGATAGAAGAAAGGTTACACGT 57.366 39.130 0.00 0.00 46.15 4.49
1900 1988 6.985188 TGTTACTTCAGTAAATGATCAGGC 57.015 37.500 0.09 0.00 41.58 4.85
1913 2001 9.959721 GTAAATGATCAGGCCCTATCTTTATAA 57.040 33.333 14.31 3.98 0.00 0.98
1918 2006 8.894592 TGATCAGGCCCTATCTTTATAAAAGAT 58.105 33.333 16.64 16.64 39.97 2.40
1923 2011 8.606830 AGGCCCTATCTTTATAAAAGATACAGG 58.393 37.037 17.16 17.16 38.00 4.00
2081 2173 7.731882 TTGTTGCAAATTGTGATGAATCATT 57.268 28.000 0.00 0.00 39.30 2.57
2093 2185 8.164058 TGTGATGAATCATTTTGTGTAACTCA 57.836 30.769 0.00 0.00 39.30 3.41
2094 2186 8.628280 TGTGATGAATCATTTTGTGTAACTCAA 58.372 29.630 0.00 0.00 39.30 3.02
2241 2333 4.716794 AGTAGCTAGTTAGGCGTGATAGT 58.283 43.478 0.00 0.00 34.52 2.12
2245 2337 6.074544 AGCTAGTTAGGCGTGATAGTAAAG 57.925 41.667 0.00 0.00 34.52 1.85
2246 2338 5.593502 AGCTAGTTAGGCGTGATAGTAAAGT 59.406 40.000 0.00 0.00 34.52 2.66
2247 2339 5.914074 GCTAGTTAGGCGTGATAGTAAAGTC 59.086 44.000 0.00 0.00 0.00 3.01
2248 2340 5.909621 AGTTAGGCGTGATAGTAAAGTCA 57.090 39.130 0.00 0.00 0.00 3.41
2250 2342 3.166489 AGGCGTGATAGTAAAGTCAGC 57.834 47.619 0.00 0.00 0.00 4.26
2251 2343 2.496070 AGGCGTGATAGTAAAGTCAGCA 59.504 45.455 0.00 0.00 0.00 4.41
2252 2344 2.860735 GGCGTGATAGTAAAGTCAGCAG 59.139 50.000 0.00 0.00 0.00 4.24
2270 2362 5.355071 TCAGCAGGAATAACTTTGCACTATG 59.645 40.000 0.00 0.00 38.97 2.23
2277 2369 8.978472 AGGAATAACTTTGCACTATGTCTACTA 58.022 33.333 0.00 0.00 0.00 1.82
2278 2370 9.765795 GGAATAACTTTGCACTATGTCTACTAT 57.234 33.333 0.00 0.00 0.00 2.12
2346 2438 6.421501 TGCATTGATTTGTTTCATGTCAACTC 59.578 34.615 10.55 9.94 32.30 3.01
2348 2440 5.107109 TGATTTGTTTCATGTCAACTCGG 57.893 39.130 10.55 0.00 0.00 4.63
2358 2450 4.571984 TCATGTCAACTCGGCTATCAATTG 59.428 41.667 0.00 0.00 0.00 2.32
2359 2451 3.937814 TGTCAACTCGGCTATCAATTGT 58.062 40.909 5.13 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.937706 GCAGACAGCAGAAATGAGTACAT 59.062 43.478 0.00 0.00 44.79 2.29
52 53 0.324091 CCAAGCCAGGCAATCTCCTT 60.324 55.000 15.80 0.00 33.25 3.36
112 115 0.593128 AAGTGCAAATCGGCTCACAC 59.407 50.000 0.00 0.00 34.04 3.82
142 145 3.884037 AGGTGGAAGGTTCACTTGAAT 57.116 42.857 0.00 0.00 40.21 2.57
248 255 3.895998 AGGGGAGAAATGATTCTGAAGC 58.104 45.455 0.00 0.00 45.91 3.86
251 258 6.829985 TTGATAGGGGAGAAATGATTCTGA 57.170 37.500 0.00 0.00 45.91 3.27
301 308 5.185454 ACGCTCACATCTGAAAAATGGATA 58.815 37.500 0.00 0.00 0.00 2.59
395 405 8.349245 TCTTCCACAAAACTATTGTACAACATG 58.651 33.333 11.22 6.61 0.00 3.21
396 406 8.458573 TCTTCCACAAAACTATTGTACAACAT 57.541 30.769 11.22 0.00 0.00 2.71
406 416 6.183360 CCGGCATATTTCTTCCACAAAACTAT 60.183 38.462 0.00 0.00 0.00 2.12
416 427 5.453567 AATAAAGCCGGCATATTTCTTCC 57.546 39.130 31.54 0.00 0.00 3.46
445 457 1.230635 GGCTGCTCTTTTGCGAGTCA 61.231 55.000 0.00 0.00 35.36 3.41
459 471 0.739813 CACCTTGGTACTACGGCTGC 60.740 60.000 1.29 0.00 0.00 5.25
484 497 7.497925 AAATTATCTCCTAGATTTTGGTCGC 57.502 36.000 0.00 0.00 36.20 5.19
583 596 5.262455 AGCTCTACCCTCTCCAAATTTTT 57.738 39.130 0.00 0.00 0.00 1.94
584 597 4.936685 AGCTCTACCCTCTCCAAATTTT 57.063 40.909 0.00 0.00 0.00 1.82
585 598 6.847036 ACTATAGCTCTACCCTCTCCAAATTT 59.153 38.462 0.00 0.00 0.00 1.82
586 599 6.386284 ACTATAGCTCTACCCTCTCCAAATT 58.614 40.000 0.00 0.00 0.00 1.82
587 600 5.971493 ACTATAGCTCTACCCTCTCCAAAT 58.029 41.667 0.00 0.00 0.00 2.32
603 616 6.474751 CGGGTTGTTCACTTAGTTACTATAGC 59.525 42.308 0.00 0.00 0.00 2.97
612 625 4.942761 TTAGTCGGGTTGTTCACTTAGT 57.057 40.909 0.00 0.00 0.00 2.24
615 628 4.457466 ACATTTAGTCGGGTTGTTCACTT 58.543 39.130 0.00 0.00 0.00 3.16
630 643 8.388103 GTGTGCCATTTACTACAGTACATTTAG 58.612 37.037 0.00 0.00 0.00 1.85
763 800 9.757227 AGCAAGTAATATTGTCACTATTCTCTC 57.243 33.333 0.00 0.00 32.56 3.20
767 804 8.700644 CCGTAGCAAGTAATATTGTCACTATTC 58.299 37.037 0.00 0.00 32.56 1.75
776 840 5.007332 GGTTGGACCGTAGCAAGTAATATTG 59.993 44.000 0.00 0.00 0.00 1.90
835 906 0.840617 TTGGTCAGTGTTGGGCTACA 59.159 50.000 0.00 0.00 0.00 2.74
885 958 3.883744 CTGGGGTGTGGACGCTCAC 62.884 68.421 2.24 2.24 38.09 3.51
1389 1472 4.214332 CAGAACAGAAGCAACCTAGGTTTC 59.786 45.833 24.99 20.13 36.00 2.78
1486 1569 9.482627 AACAACAAAACAGAAACAGAAACATAA 57.517 25.926 0.00 0.00 0.00 1.90
1513 1596 8.473358 TCTGCCATCATCATCAGATAAATTTT 57.527 30.769 0.00 0.00 31.35 1.82
1547 1630 1.901833 GGACAGGGCATTTGGAAATGT 59.098 47.619 12.51 0.00 45.77 2.71
1567 1650 6.918022 GCCGAGACATTCCAAAATATTTTAGG 59.082 38.462 12.98 15.35 0.00 2.69
1568 1651 7.479980 TGCCGAGACATTCCAAAATATTTTAG 58.520 34.615 12.98 6.57 0.00 1.85
1569 1652 7.397892 TGCCGAGACATTCCAAAATATTTTA 57.602 32.000 12.98 0.00 0.00 1.52
1570 1653 6.279513 TGCCGAGACATTCCAAAATATTTT 57.720 33.333 7.64 7.64 0.00 1.82
1574 1661 4.704540 ACAATGCCGAGACATTCCAAAATA 59.295 37.500 0.00 0.00 38.19 1.40
1717 1804 6.801377 TGTTCAATGCGACAACTGATTTATTC 59.199 34.615 0.00 0.00 0.00 1.75
1776 1863 2.424956 CCCTCTAAAAGCAAGCATCACC 59.575 50.000 0.00 0.00 0.00 4.02
1792 1879 1.840635 GAGACAATACCCAAGCCCTCT 59.159 52.381 0.00 0.00 0.00 3.69
1816 1904 6.015180 CCACTCATCATTGGAAAAGAAAAGGA 60.015 38.462 0.00 0.00 34.46 3.36
1845 1933 6.748198 GTGTAACCTTTCTTCTATCGACAGAG 59.252 42.308 0.00 0.00 0.00 3.35
1849 1937 5.285607 CACGTGTAACCTTTCTTCTATCGAC 59.714 44.000 7.58 0.00 0.00 4.20
1950 2038 6.926272 ACAGCATATCCTAAGACTCGAATTTC 59.074 38.462 0.00 0.00 0.00 2.17
1956 2044 5.048364 AGCTTACAGCATATCCTAAGACTCG 60.048 44.000 0.00 0.00 45.56 4.18
1966 2054 2.856222 AGGCCAAGCTTACAGCATATC 58.144 47.619 5.01 1.06 45.56 1.63
1968 2056 2.806945 AAGGCCAAGCTTACAGCATA 57.193 45.000 5.01 0.00 45.56 3.14
2017 2108 7.047891 TCTACTTCAATCACACAAACTCAACT 58.952 34.615 0.00 0.00 0.00 3.16
2026 2117 7.335673 TCAAACAAACTCTACTTCAATCACACA 59.664 33.333 0.00 0.00 0.00 3.72
2123 2215 3.676646 GGATCAGCAAAATTCAAGTGTGC 59.323 43.478 0.00 0.00 35.41 4.57
2162 2254 4.599041 TGGTGTCAAGAAATAGAATGGGG 58.401 43.478 0.00 0.00 0.00 4.96
2241 2333 5.767665 TGCAAAGTTATTCCTGCTGACTTTA 59.232 36.000 6.93 0.00 38.19 1.85
2245 2337 3.503748 AGTGCAAAGTTATTCCTGCTGAC 59.496 43.478 0.00 0.00 35.78 3.51
2246 2338 3.754965 AGTGCAAAGTTATTCCTGCTGA 58.245 40.909 0.00 0.00 35.78 4.26
2247 2339 5.124457 ACATAGTGCAAAGTTATTCCTGCTG 59.876 40.000 0.00 0.00 35.78 4.41
2248 2340 5.256474 ACATAGTGCAAAGTTATTCCTGCT 58.744 37.500 0.00 0.00 35.78 4.24
2250 2342 6.992063 AGACATAGTGCAAAGTTATTCCTG 57.008 37.500 0.00 0.00 0.00 3.86
2251 2343 7.852263 AGTAGACATAGTGCAAAGTTATTCCT 58.148 34.615 0.00 0.00 0.00 3.36
2252 2344 9.765795 ATAGTAGACATAGTGCAAAGTTATTCC 57.234 33.333 0.00 0.00 0.00 3.01
2296 2388 9.512588 CATTTATAAGCTCTGGGAAGTATGAAT 57.487 33.333 0.00 0.00 0.00 2.57
2307 2399 7.924412 ACAAATCAATGCATTTATAAGCTCTGG 59.076 33.333 9.83 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.