Multiple sequence alignment - TraesCS5D01G185100

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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 TraesCS5D01G185100 chr5D 100.000 2660 0 0 1 2660 287428550 287431209 0.000000e+00 4913
1 TraesCS5D01G185100 chr5A 90.086 2663 160 49 1 2633 379342508 379345096 0.000000e+00 3360
2 TraesCS5D01G185100 chr5B 92.247 1780 96 22 528 2300 326506875 326508619 0.000000e+00 2484
3 TraesCS5D01G185100 chr5B 90.802 424 24 13 86 507 326506480 326506890 1.080000e-153 553
4 TraesCS5D01G185100 chr5B 94.100 339 18 2 2295 2633 326511053 326511389 5.080000e-142 514


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 TraesCS5D01G185100 chr5D 287428550 287431209 2659 False 4913.000000 4913 100.000 1 2660 1 chr5D.!!$F1 2659
1 TraesCS5D01G185100 chr5A 379342508 379345096 2588 False 3360.000000 3360 90.086 1 2633 1 chr5A.!!$F1 2632
2 TraesCS5D01G185100 chr5B 326506480 326511389 4909 False 1183.666667 2484 92.383 86 2633 3 chr5B.!!$F1 2547

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
949 965 0.098376 ACGAGATAACGTGCGAGGTC 59.902 55.0 0.0 0.0 44.84 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 1869 0.46362 GCAGGAGCCGATCTTCTTCT 59.536 55.0 0.0 0.0 33.58 2.85 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 7.912250 ACAAATATAAGAGCAATTCTTCAAGCG 59.088 33.333 0.00 0.00 42.54 4.68
73 74 4.908601 AACATACACCATCTCACCTTGA 57.091 40.909 0.00 0.00 0.00 3.02
134 136 1.923227 GCTTGCTTACCGCTCCCAAC 61.923 60.000 0.00 0.00 40.11 3.77
442 445 1.611419 CCTGGCCCACATGTCAGAT 59.389 57.895 12.56 0.00 0.00 2.90
446 449 1.524621 GCCCACATGTCAGATCCCG 60.525 63.158 0.00 0.00 0.00 5.14
449 452 1.884464 CACATGTCAGATCCCGGCG 60.884 63.158 0.00 0.00 0.00 6.46
517 521 1.405821 CCATCTCGGTGACAGTACCTC 59.594 57.143 0.00 0.00 38.62 3.85
586 596 1.292992 CTTCACCGCGTATTAACCCC 58.707 55.000 4.92 0.00 0.00 4.95
587 597 0.107752 TTCACCGCGTATTAACCCCC 60.108 55.000 4.92 0.00 0.00 5.40
588 598 1.884004 CACCGCGTATTAACCCCCG 60.884 63.158 4.92 0.00 0.00 5.73
593 603 2.592574 GTATTAACCCCCGCGCCC 60.593 66.667 0.00 0.00 0.00 6.13
807 817 0.531311 CCGTTAGGCCCGACCAATAC 60.531 60.000 0.00 0.00 43.14 1.89
809 819 0.176449 GTTAGGCCCGACCAATACGT 59.824 55.000 0.00 0.00 43.14 3.57
874 884 1.030488 CGTCTCCTCCTCGCCACTTA 61.030 60.000 0.00 0.00 0.00 2.24
879 889 1.284198 TCCTCCTCGCCACTTACTACT 59.716 52.381 0.00 0.00 0.00 2.57
887 897 2.099427 CGCCACTTACTACTTCCTCTCC 59.901 54.545 0.00 0.00 0.00 3.71
890 900 3.955551 CCACTTACTACTTCCTCTCCCTC 59.044 52.174 0.00 0.00 0.00 4.30
891 901 4.325501 CCACTTACTACTTCCTCTCCCTCT 60.326 50.000 0.00 0.00 0.00 3.69
892 902 5.265989 CACTTACTACTTCCTCTCCCTCTT 58.734 45.833 0.00 0.00 0.00 2.85
893 903 5.358725 CACTTACTACTTCCTCTCCCTCTTC 59.641 48.000 0.00 0.00 0.00 2.87
916 926 0.614979 CCTTCGTCTTCCTCCTCCCA 60.615 60.000 0.00 0.00 0.00 4.37
943 959 3.613145 GTACACAACGAGATAACGTGC 57.387 47.619 0.00 0.00 45.83 5.34
949 965 0.098376 ACGAGATAACGTGCGAGGTC 59.902 55.000 0.00 0.00 44.84 3.85
953 969 1.671845 AGATAACGTGCGAGGTCTCTC 59.328 52.381 0.00 0.00 36.69 3.20
968 984 1.645704 CTCTCGTTCTTCTCCGCCGA 61.646 60.000 0.00 0.00 0.00 5.54
1197 1213 0.038159 GCGGGAAGGAGGTCATATCG 60.038 60.000 0.00 0.00 0.00 2.92
1317 1336 3.673597 TCCGGTGAGGAGGAGGCT 61.674 66.667 0.00 0.00 45.98 4.58
1410 1429 4.436998 CGGACGTGGCAGGACCTC 62.437 72.222 22.37 7.31 40.22 3.85
1479 1498 3.640407 GGAGGAGGTGTGCAGGCA 61.640 66.667 0.00 0.00 0.00 4.75
1494 1513 3.958860 GCAGTGAGGCTGTGGGGT 61.959 66.667 0.00 0.00 46.64 4.95
1736 1756 1.443407 CGGAGATGCTGATTCCCGT 59.557 57.895 0.00 0.00 33.02 5.28
1785 1805 1.692173 GCGGGTGATTGCTAGGGGTA 61.692 60.000 0.00 0.00 0.00 3.69
1792 1812 3.965347 GTGATTGCTAGGGGTAGTTAGGA 59.035 47.826 0.00 0.00 0.00 2.94
1794 1814 4.078805 TGATTGCTAGGGGTAGTTAGGAGA 60.079 45.833 0.00 0.00 0.00 3.71
1795 1815 3.596940 TGCTAGGGGTAGTTAGGAGAG 57.403 52.381 0.00 0.00 0.00 3.20
1799 1819 1.214923 AGGGGTAGTTAGGAGAGACGG 59.785 57.143 0.00 0.00 0.00 4.79
1800 1820 1.064091 GGGGTAGTTAGGAGAGACGGT 60.064 57.143 0.00 0.00 0.00 4.83
1801 1821 2.022934 GGGTAGTTAGGAGAGACGGTG 58.977 57.143 0.00 0.00 0.00 4.94
1802 1822 2.620108 GGGTAGTTAGGAGAGACGGTGT 60.620 54.545 0.00 0.00 0.00 4.16
1803 1823 3.087781 GGTAGTTAGGAGAGACGGTGTT 58.912 50.000 0.00 0.00 0.00 3.32
1804 1824 3.119566 GGTAGTTAGGAGAGACGGTGTTG 60.120 52.174 0.00 0.00 0.00 3.33
1805 1825 2.872732 AGTTAGGAGAGACGGTGTTGA 58.127 47.619 0.00 0.00 0.00 3.18
1806 1826 3.432378 AGTTAGGAGAGACGGTGTTGAT 58.568 45.455 0.00 0.00 0.00 2.57
1807 1827 3.193691 AGTTAGGAGAGACGGTGTTGATG 59.806 47.826 0.00 0.00 0.00 3.07
1808 1828 1.924731 AGGAGAGACGGTGTTGATGA 58.075 50.000 0.00 0.00 0.00 2.92
1809 1829 2.461695 AGGAGAGACGGTGTTGATGAT 58.538 47.619 0.00 0.00 0.00 2.45
1810 1830 2.167281 AGGAGAGACGGTGTTGATGATG 59.833 50.000 0.00 0.00 0.00 3.07
1811 1831 2.166459 GGAGAGACGGTGTTGATGATGA 59.834 50.000 0.00 0.00 0.00 2.92
1849 1869 3.347216 GCTTATCTGGAAAGCAAGACCA 58.653 45.455 3.07 0.00 46.85 4.02
1855 1875 3.576078 TGGAAAGCAAGACCAGAAGAA 57.424 42.857 0.00 0.00 0.00 2.52
1932 1952 1.429021 GGAAATGCTCGATTGCGCA 59.571 52.632 5.66 5.66 40.64 6.09
1948 1968 0.596083 CGCATCGATCGCTCCTTCTT 60.596 55.000 11.09 0.00 0.00 2.52
1979 1999 3.314080 TCCAATGTCGTGGAAAGTTGTTC 59.686 43.478 0.00 0.00 44.91 3.18
1984 2004 2.287103 GTCGTGGAAAGTTGTTCCTGTC 59.713 50.000 6.67 0.00 39.31 3.51
2035 2056 9.705290 AAGTTAATAAAACCATGTTGTCCATTC 57.295 29.630 0.00 0.00 0.00 2.67
2071 2092 7.444558 TTTACATTTCTCTTTTGTTTGCGAC 57.555 32.000 0.00 0.00 0.00 5.19
2106 2131 8.995906 GTACAACGAAAATGAATAGTACATTGC 58.004 33.333 0.00 0.00 37.89 3.56
2152 2178 1.132643 GTGTTGATAGACGCTCGAGGT 59.867 52.381 15.58 10.42 0.00 3.85
2200 2226 2.674033 ACCACCCACGTCGATCGA 60.674 61.111 15.15 15.15 42.86 3.59
2235 2261 4.782691 TGTCACCCAAATCCTCTTCATAGA 59.217 41.667 0.00 0.00 0.00 1.98
2244 2270 7.255173 CCAAATCCTCTTCATAGATCAAGCTTG 60.255 40.741 20.81 20.81 0.00 4.01
2262 2288 4.756084 CTTGGTTTCCTAGCAGTTTCTG 57.244 45.455 0.00 0.00 35.32 3.02
2273 2299 0.954452 CAGTTTCTGCAGGACCCAAC 59.046 55.000 15.13 9.31 0.00 3.77
2395 4860 3.527533 TCGACGATTTAACCTTGGATGG 58.472 45.455 0.00 0.00 0.00 3.51
2416 4881 3.016736 GTCGATTGGGTTCATTGACCAT 58.983 45.455 0.00 0.00 41.65 3.55
2432 4916 6.959639 TTGACCATATTAAGCCTGAATTCC 57.040 37.500 2.27 0.00 0.00 3.01
2511 4995 3.693085 AGCTGTCAATGTTCATCCATCAC 59.307 43.478 0.00 0.00 0.00 3.06
2527 5011 3.224324 ACGGGCACACACGAGACT 61.224 61.111 0.00 0.00 0.00 3.24
2528 5012 2.734723 CGGGCACACACGAGACTG 60.735 66.667 0.00 0.00 0.00 3.51
2538 5022 3.374402 CGAGACTGGGACACGCCT 61.374 66.667 0.00 0.00 36.66 5.52
2539 5023 2.262915 GAGACTGGGACACGCCTG 59.737 66.667 0.00 0.00 36.66 4.85
2559 5044 1.666888 GCAAACAAATCCCTGTCAGCG 60.667 52.381 0.00 0.00 0.00 5.18
2612 5097 1.078759 CGAGAGCATCCGTCGCTTTT 61.079 55.000 0.00 0.00 40.63 2.27
2633 5118 6.957920 TTTCAATCAACTCTGTCCATCAAA 57.042 33.333 0.00 0.00 0.00 2.69
2634 5119 5.947228 TCAATCAACTCTGTCCATCAAAC 57.053 39.130 0.00 0.00 0.00 2.93
2635 5120 5.624159 TCAATCAACTCTGTCCATCAAACT 58.376 37.500 0.00 0.00 0.00 2.66
2636 5121 5.471116 TCAATCAACTCTGTCCATCAAACTG 59.529 40.000 0.00 0.00 0.00 3.16
2637 5122 3.743521 TCAACTCTGTCCATCAAACTGG 58.256 45.455 0.00 0.00 37.66 4.00
2638 5123 2.191128 ACTCTGTCCATCAAACTGGC 57.809 50.000 0.00 0.00 36.16 4.85
2639 5124 1.701847 ACTCTGTCCATCAAACTGGCT 59.298 47.619 0.00 0.00 36.16 4.75
2640 5125 2.107204 ACTCTGTCCATCAAACTGGCTT 59.893 45.455 0.00 0.00 36.16 4.35
2641 5126 2.746362 CTCTGTCCATCAAACTGGCTTC 59.254 50.000 0.00 0.00 36.16 3.86
2642 5127 2.373169 TCTGTCCATCAAACTGGCTTCT 59.627 45.455 0.00 0.00 36.16 2.85
2643 5128 2.746362 CTGTCCATCAAACTGGCTTCTC 59.254 50.000 0.00 0.00 36.16 2.87
2644 5129 2.373169 TGTCCATCAAACTGGCTTCTCT 59.627 45.455 0.00 0.00 36.16 3.10
2645 5130 3.181440 TGTCCATCAAACTGGCTTCTCTT 60.181 43.478 0.00 0.00 36.16 2.85
2646 5131 4.041567 TGTCCATCAAACTGGCTTCTCTTA 59.958 41.667 0.00 0.00 36.16 2.10
2647 5132 4.633565 GTCCATCAAACTGGCTTCTCTTAG 59.366 45.833 0.00 0.00 36.16 2.18
2648 5133 4.532126 TCCATCAAACTGGCTTCTCTTAGA 59.468 41.667 0.00 0.00 36.16 2.10
2649 5134 5.013079 TCCATCAAACTGGCTTCTCTTAGAA 59.987 40.000 0.00 0.00 36.16 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.701651 TCATGGATTGACGCTTGAAGAATT 59.298 37.500 0.00 0.00 0.00 2.17
73 74 8.807948 ATTGCATTATACTACTTCCAAGTGTT 57.192 30.769 2.01 0.00 40.07 3.32
221 224 1.291877 CCACTACTTGCCTGACACGC 61.292 60.000 0.00 0.00 0.00 5.34
335 338 1.735038 CGTGATCTGTGAGTCAGCCTG 60.735 57.143 0.00 0.00 43.32 4.85
421 424 2.044946 GACATGTGGGCCAGGGTC 60.045 66.667 6.40 11.57 0.00 4.46
524 528 0.721718 GACCGAGATGGCGTCTTTTG 59.278 55.000 11.18 5.23 43.94 2.44
525 529 0.736325 CGACCGAGATGGCGTCTTTT 60.736 55.000 11.18 0.00 43.94 2.27
527 531 2.490217 CGACCGAGATGGCGTCTT 59.510 61.111 11.18 0.00 43.94 3.01
586 596 3.879682 CACATGTCATGGGCGCGG 61.880 66.667 17.08 0.00 33.60 6.46
587 597 3.879682 CCACATGTCATGGGCGCG 61.880 66.667 17.08 0.00 33.18 6.86
593 603 0.038021 TGGTGACCCCACATGTCATG 59.962 55.000 11.41 11.41 43.98 3.07
719 729 3.934391 AAGTGGTACTCGCAGCGGC 62.934 63.158 16.42 0.00 0.00 6.53
730 740 0.613853 CGTGGGGGAGAGAAGTGGTA 60.614 60.000 0.00 0.00 0.00 3.25
874 884 2.930405 AGGAAGAGGGAGAGGAAGTAGT 59.070 50.000 0.00 0.00 0.00 2.73
879 889 0.340208 GGGAGGAAGAGGGAGAGGAA 59.660 60.000 0.00 0.00 0.00 3.36
887 897 1.478916 GAAGACGAAGGGAGGAAGAGG 59.521 57.143 0.00 0.00 0.00 3.69
890 900 1.478916 GAGGAAGACGAAGGGAGGAAG 59.521 57.143 0.00 0.00 0.00 3.46
891 901 1.558233 GAGGAAGACGAAGGGAGGAA 58.442 55.000 0.00 0.00 0.00 3.36
892 902 0.324460 GGAGGAAGACGAAGGGAGGA 60.324 60.000 0.00 0.00 0.00 3.71
893 903 0.324830 AGGAGGAAGACGAAGGGAGG 60.325 60.000 0.00 0.00 0.00 4.30
949 965 1.226435 CGGCGGAGAAGAACGAGAG 60.226 63.158 0.00 0.00 0.00 3.20
953 969 0.645868 GAAATCGGCGGAGAAGAACG 59.354 55.000 7.21 0.00 0.00 3.95
968 984 0.980231 AGCTGAGCTCTCCCCGAAAT 60.980 55.000 16.19 0.00 30.62 2.17
1197 1213 0.818296 AGTAGGTGGAGATGTGCGAC 59.182 55.000 0.00 0.00 0.00 5.19
1305 1321 1.305633 CCTCACAGCCTCCTCCTCA 60.306 63.158 0.00 0.00 0.00 3.86
1317 1336 0.629596 AGTACCCGATCCTCCTCACA 59.370 55.000 0.00 0.00 0.00 3.58
1356 1375 3.760035 GGGAAGCAGCCGTCGAGA 61.760 66.667 0.00 0.00 0.00 4.04
1467 1486 2.429058 CTCACTGCCTGCACACCT 59.571 61.111 0.00 0.00 0.00 4.00
1479 1498 3.958860 GCACCCCACAGCCTCACT 61.959 66.667 0.00 0.00 0.00 3.41
1633 1652 4.083862 GGAGGGCAGGACACGGAC 62.084 72.222 0.00 0.00 0.00 4.79
1669 1688 0.108615 CCTACCACTCTCCGTTGCAG 60.109 60.000 0.00 0.00 0.00 4.41
1671 1690 0.389948 CACCTACCACTCTCCGTTGC 60.390 60.000 0.00 0.00 0.00 4.17
1672 1691 0.966920 ACACCTACCACTCTCCGTTG 59.033 55.000 0.00 0.00 0.00 4.10
1785 1805 2.872732 TCAACACCGTCTCTCCTAACT 58.127 47.619 0.00 0.00 0.00 2.24
1792 1812 4.478206 AATCATCATCAACACCGTCTCT 57.522 40.909 0.00 0.00 0.00 3.10
1794 1814 5.344743 AGTAATCATCATCAACACCGTCT 57.655 39.130 0.00 0.00 0.00 4.18
1795 1815 7.438160 TGAATAGTAATCATCATCAACACCGTC 59.562 37.037 0.00 0.00 0.00 4.79
1849 1869 0.463620 GCAGGAGCCGATCTTCTTCT 59.536 55.000 0.00 0.00 33.58 2.85
1853 1873 0.809241 CACTGCAGGAGCCGATCTTC 60.809 60.000 19.93 0.00 41.13 2.87
1854 1874 1.220206 CACTGCAGGAGCCGATCTT 59.780 57.895 19.93 0.00 41.13 2.40
1855 1875 2.898738 CACTGCAGGAGCCGATCT 59.101 61.111 19.93 0.00 41.13 2.75
1881 1901 6.986817 AGAATAGTGGTACAAATGAAGATCGG 59.013 38.462 0.00 0.00 44.16 4.18
1932 1952 1.403814 TGGAAGAAGGAGCGATCGAT 58.596 50.000 21.57 14.21 0.00 3.59
1948 1968 3.891977 TCCACGACATTGGAAATTTTGGA 59.108 39.130 0.00 0.00 43.04 3.53
1979 1999 1.004918 ACCGAAAAGGAGCGACAGG 60.005 57.895 0.00 0.00 45.00 4.00
1984 2004 2.018542 TAATCCACCGAAAAGGAGCG 57.981 50.000 0.00 0.00 45.00 5.03
2035 2056 8.430801 AAGAGAAATGTAAAAGGAGATCGATG 57.569 34.615 0.54 0.00 0.00 3.84
2066 2087 2.025589 TTGTACACAACCAAGTCGCA 57.974 45.000 0.00 0.00 0.00 5.10
2086 2107 7.162546 CGAACTGCAATGTACTATTCATTTTCG 59.837 37.037 0.00 0.00 36.47 3.46
2097 2118 4.334203 TGTTTTGACGAACTGCAATGTACT 59.666 37.500 0.00 0.00 0.00 2.73
2098 2119 4.436523 GTGTTTTGACGAACTGCAATGTAC 59.563 41.667 0.00 0.00 0.00 2.90
2099 2120 4.334203 AGTGTTTTGACGAACTGCAATGTA 59.666 37.500 0.00 0.00 0.00 2.29
2100 2121 3.128589 AGTGTTTTGACGAACTGCAATGT 59.871 39.130 0.00 0.00 0.00 2.71
2106 2131 3.757745 ACCAAGTGTTTTGACGAACTG 57.242 42.857 0.00 0.00 0.00 3.16
2200 2226 6.989759 GGATTTGGGTGACAATTTTGTTTAGT 59.010 34.615 0.00 0.00 42.43 2.24
2235 2261 3.245052 ACTGCTAGGAAACCAAGCTTGAT 60.245 43.478 28.05 8.09 39.82 2.57
2262 2288 4.329545 TGAGGCGTTGGGTCCTGC 62.330 66.667 0.00 0.00 31.71 4.85
2395 4860 2.432444 TGGTCAATGAACCCAATCGAC 58.568 47.619 0.00 0.00 38.65 4.20
2432 4916 1.866601 TCTCACGCGGCAATAATGATG 59.133 47.619 12.47 0.00 0.00 3.07
2511 4995 2.734723 CAGTCTCGTGTGTGCCCG 60.735 66.667 0.00 0.00 0.00 6.13
2527 5011 2.904866 GTTTGCAGGCGTGTCCCA 60.905 61.111 8.40 0.00 34.51 4.37
2528 5012 2.010582 TTTGTTTGCAGGCGTGTCCC 62.011 55.000 8.40 0.00 34.51 4.46
2538 5022 1.340889 GCTGACAGGGATTTGTTTGCA 59.659 47.619 4.26 0.00 33.14 4.08
2539 5023 1.666888 CGCTGACAGGGATTTGTTTGC 60.667 52.381 14.07 0.00 0.00 3.68
2612 5097 5.471116 CAGTTTGATGGACAGAGTTGATTGA 59.529 40.000 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.