Multiple sequence alignment - TraesCS5B01G178500

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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 TraesCS5B01G178500 chr5B 100.000 2546 0 0 1 2546 326570391 326572936 0.000000e+00 4702
1 TraesCS5B01G178500 chr5A 88.108 2548 147 61 62 2546 379351663 379354117 0.000000e+00 2883
2 TraesCS5B01G178500 chr5D 92.773 1785 67 24 1 1775 287439173 287440905 0.000000e+00 2525
3 TraesCS5B01G178500 chr5D 90.526 760 57 12 1796 2546 287441062 287441815 0.000000e+00 990
4 TraesCS5B01G178500 chrUn 90.196 102 6 3 890 988 103504829 103504929 2.060000e-26 130


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 TraesCS5B01G178500 chr5B 326570391 326572936 2545 False 4702.0 4702 100.0000 1 2546 1 chr5B.!!$F1 2545
1 TraesCS5B01G178500 chr5A 379351663 379354117 2454 False 2883.0 2883 88.1080 62 2546 1 chr5A.!!$F1 2484
2 TraesCS5B01G178500 chr5D 287439173 287441815 2642 False 1757.5 2525 91.6495 1 2546 2 chr5D.!!$F1 2545

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
940 958 1.006922 GCTCCAAAGCCAACACAGC 60.007 57.895 0.0 0.0 43.1 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2118 0.036732 TGAGGCTGCGTTTTCATCCT 59.963 50.0 0.0 0.0 35.47 3.24 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
37 38 6.615088 TCTTAGAGCAGTGCAATTTGAAATC 58.385 36.000 19.20 2.29 0.00 2.17
245 246 5.525378 AGAATTAGCCTGCGATTGTTCTTAG 59.475 40.000 0.00 0.00 0.00 2.18
430 444 6.757897 ATCGCTCACAAAATTTCAGGAATA 57.242 33.333 0.00 0.00 0.00 1.75
431 445 6.757897 TCGCTCACAAAATTTCAGGAATAT 57.242 33.333 0.00 0.00 0.00 1.28
467 483 4.271696 TGACTCAGACCAAAACGATCAT 57.728 40.909 0.00 0.00 0.00 2.45
468 484 4.641396 TGACTCAGACCAAAACGATCATT 58.359 39.130 0.00 0.00 0.00 2.57
547 563 1.107114 AGAGCCCGTCAGTGTATCAG 58.893 55.000 0.00 0.00 0.00 2.90
548 564 1.103803 GAGCCCGTCAGTGTATCAGA 58.896 55.000 0.00 0.00 0.00 3.27
549 565 1.683917 GAGCCCGTCAGTGTATCAGAT 59.316 52.381 0.00 0.00 0.00 2.90
550 566 1.410517 AGCCCGTCAGTGTATCAGATG 59.589 52.381 0.00 0.00 0.00 2.90
551 567 1.137086 GCCCGTCAGTGTATCAGATGT 59.863 52.381 0.00 0.00 0.00 3.06
552 568 2.361119 GCCCGTCAGTGTATCAGATGTA 59.639 50.000 0.00 0.00 0.00 2.29
553 569 3.181479 GCCCGTCAGTGTATCAGATGTAA 60.181 47.826 0.00 0.00 0.00 2.41
554 570 4.360563 CCCGTCAGTGTATCAGATGTAAC 58.639 47.826 0.00 0.00 0.00 2.50
555 571 4.098044 CCCGTCAGTGTATCAGATGTAACT 59.902 45.833 0.00 0.00 0.00 2.24
556 572 5.274718 CCGTCAGTGTATCAGATGTAACTC 58.725 45.833 0.00 0.00 0.00 3.01
557 573 5.163652 CCGTCAGTGTATCAGATGTAACTCA 60.164 44.000 0.00 0.00 0.00 3.41
601 617 2.224499 TGTTTGTGCTATGACTCAGCCA 60.224 45.455 0.00 0.00 38.29 4.75
653 669 4.216902 TCAGTCTCATGTCCTGCAAAAATG 59.783 41.667 0.00 0.00 0.00 2.32
654 670 3.057033 AGTCTCATGTCCTGCAAAAATGC 60.057 43.478 0.00 0.00 0.00 3.56
655 671 2.231964 TCTCATGTCCTGCAAAAATGCC 59.768 45.455 0.00 0.00 0.00 4.40
657 673 1.276989 CATGTCCTGCAAAAATGCCCT 59.723 47.619 0.00 0.00 0.00 5.19
743 761 2.702592 AACGAACCTCAGGTCAACAA 57.297 45.000 0.00 0.00 33.12 2.83
757 775 3.065371 GGTCAACAAGGTCAAGTGTCAAG 59.935 47.826 0.00 0.00 0.00 3.02
795 813 7.741027 AGCATGATCAACCTATAAATCACTG 57.259 36.000 0.00 0.00 31.41 3.66
832 850 2.033550 GCAAACCGTAACCATGTCACAA 59.966 45.455 0.00 0.00 0.00 3.33
833 851 3.305064 GCAAACCGTAACCATGTCACAAT 60.305 43.478 0.00 0.00 0.00 2.71
837 855 1.809547 CGTAACCATGTCACAATGCCA 59.190 47.619 0.00 0.00 0.00 4.92
856 874 3.112263 CCATCCTAACCCCTACTGAACA 58.888 50.000 0.00 0.00 0.00 3.18
857 875 3.716872 CCATCCTAACCCCTACTGAACAT 59.283 47.826 0.00 0.00 0.00 2.71
938 956 2.192861 CCGCTCCAAAGCCAACACA 61.193 57.895 0.00 0.00 46.34 3.72
939 957 1.283793 CGCTCCAAAGCCAACACAG 59.716 57.895 0.00 0.00 46.34 3.66
940 958 1.006922 GCTCCAAAGCCAACACAGC 60.007 57.895 0.00 0.00 43.10 4.40
966 984 1.347707 CAGCTGTCAGTAACCAAGGGA 59.652 52.381 5.25 0.00 0.00 4.20
1053 1071 3.844090 GCGGTGCTCCTCCTCCTC 61.844 72.222 2.85 0.00 0.00 3.71
1197 1218 1.578206 GGCCACTTCTTCTCAACGCC 61.578 60.000 0.00 0.00 0.00 5.68
1200 1221 1.270305 CCACTTCTTCTCAACGCCTCA 60.270 52.381 0.00 0.00 0.00 3.86
1371 1398 3.056458 CACCAGCACCACGTAGGA 58.944 61.111 10.46 0.00 41.22 2.94
1500 1527 0.842030 ACTCCATCAAGCTCACCCCA 60.842 55.000 0.00 0.00 0.00 4.96
1551 1578 2.181021 GGCGTCTACTGACCACGG 59.819 66.667 0.00 0.00 39.94 4.94
1552 1579 2.338015 GGCGTCTACTGACCACGGA 61.338 63.158 0.00 0.00 39.94 4.69
1760 1795 2.291209 ATTGGCATTCTCCACACACA 57.709 45.000 0.00 0.00 35.50 3.72
1761 1796 1.317613 TTGGCATTCTCCACACACAC 58.682 50.000 0.00 0.00 35.50 3.82
1783 1932 4.821805 ACTGGTGAAATTTCTGTGGTAGTG 59.178 41.667 18.64 3.24 0.00 2.74
1784 1933 3.568007 TGGTGAAATTTCTGTGGTAGTGC 59.432 43.478 18.64 0.00 0.00 4.40
1796 1945 6.999950 TCTGTGGTAGTGCAAACTTATCTTA 58.000 36.000 0.00 0.00 0.00 2.10
1799 1948 6.993308 TGTGGTAGTGCAAACTTATCTTACAA 59.007 34.615 0.00 0.00 0.00 2.41
1869 2041 7.761249 CCTGGCAATGACCTCTTTTTATAAAAG 59.239 37.037 10.40 5.72 0.00 2.27
1916 2091 9.744468 AACACATCAAAGTTTATAAAACTGTCC 57.256 29.630 5.85 0.00 0.00 4.02
1935 2110 9.965824 AACTGTCCTTTATGAAAACTAAACATG 57.034 29.630 0.00 0.00 0.00 3.21
1936 2111 8.576442 ACTGTCCTTTATGAAAACTAAACATGG 58.424 33.333 0.00 0.00 0.00 3.66
1937 2112 8.472007 TGTCCTTTATGAAAACTAAACATGGT 57.528 30.769 0.00 0.00 0.00 3.55
1969 2144 1.455383 AAACGCAGCCTCAACTTGGG 61.455 55.000 0.00 0.00 0.00 4.12
1978 2153 0.034089 CTCAACTTGGGCCCCTTAGG 60.034 60.000 22.27 3.22 39.47 2.69
1979 2154 0.774491 TCAACTTGGGCCCCTTAGGT 60.774 55.000 22.27 10.15 38.26 3.08
1980 2155 0.996583 CAACTTGGGCCCCTTAGGTA 59.003 55.000 22.27 0.00 38.26 3.08
1982 2157 2.781174 CAACTTGGGCCCCTTAGGTATA 59.219 50.000 22.27 0.00 38.26 1.47
1983 2158 2.702748 ACTTGGGCCCCTTAGGTATAG 58.297 52.381 22.27 4.97 38.26 1.31
1994 2170 6.297068 GCCCCTTAGGTATAGAAATTATGGCT 60.297 42.308 0.00 0.00 38.26 4.75
2008 2184 9.771534 AGAAATTATGGCTATCTCTGAACTTAC 57.228 33.333 0.00 0.00 0.00 2.34
2010 2186 9.553064 AAATTATGGCTATCTCTGAACTTACTG 57.447 33.333 0.00 0.00 0.00 2.74
2011 2187 7.898014 TTATGGCTATCTCTGAACTTACTGA 57.102 36.000 0.00 0.00 0.00 3.41
2056 2232 1.681327 GGACTCCAGAGCACGGGTA 60.681 63.158 0.00 0.00 33.25 3.69
2087 2263 9.797642 AAATATGACAGGAGCACATTATATTCA 57.202 29.630 0.00 0.00 0.00 2.57
2090 2266 6.594744 TGACAGGAGCACATTATATTCACAT 58.405 36.000 0.00 0.00 0.00 3.21
2094 2270 9.060347 ACAGGAGCACATTATATTCACATAAAG 57.940 33.333 0.00 0.00 0.00 1.85
2099 2276 7.857389 AGCACATTATATTCACATAAAGCAACG 59.143 33.333 0.00 0.00 0.00 4.10
2130 2307 7.588143 ATTCTGAGACACGAATAACAAGAAG 57.412 36.000 0.00 0.00 0.00 2.85
2131 2308 6.327279 TCTGAGACACGAATAACAAGAAGA 57.673 37.500 0.00 0.00 0.00 2.87
2132 2309 6.150318 TCTGAGACACGAATAACAAGAAGAC 58.850 40.000 0.00 0.00 0.00 3.01
2133 2310 5.838529 TGAGACACGAATAACAAGAAGACA 58.161 37.500 0.00 0.00 0.00 3.41
2134 2311 5.690409 TGAGACACGAATAACAAGAAGACAC 59.310 40.000 0.00 0.00 0.00 3.67
2136 2313 5.462398 AGACACGAATAACAAGAAGACACAC 59.538 40.000 0.00 0.00 0.00 3.82
2140 2317 5.345202 ACGAATAACAAGAAGACACACGATC 59.655 40.000 0.00 0.00 0.00 3.69
2157 2334 4.687948 CACGATCGAGCTTCCATTATGAAT 59.312 41.667 24.34 0.00 0.00 2.57
2161 2338 6.073602 CGATCGAGCTTCCATTATGAATTTCA 60.074 38.462 10.26 0.75 0.00 2.69
2173 2350 9.338291 CCATTATGAATTTCAATAGCAGATTCG 57.662 33.333 2.68 0.00 31.15 3.34
2233 2412 6.814954 AAGGCTCAACCAGATTAATCTAGA 57.185 37.500 17.53 11.83 43.14 2.43
2306 2486 1.800586 CACAAACTCACCCTGACATCG 59.199 52.381 0.00 0.00 0.00 3.84
2360 2541 5.013599 AGGCCTCAAAGTTTCTCTAGTTCAT 59.986 40.000 0.00 0.00 0.00 2.57
2491 2672 2.354188 TCGCCTGTTGTGTCGACG 60.354 61.111 11.62 0.00 0.00 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
245 246 4.712476 ACTTCAGATGATATGGCCAACTC 58.288 43.478 10.96 10.52 0.00 3.01
430 444 4.092279 TGAGTCATAGCAGCAGCCTATAT 58.908 43.478 0.00 0.00 43.56 0.86
431 445 3.500343 TGAGTCATAGCAGCAGCCTATA 58.500 45.455 0.00 0.00 43.56 1.31
506 522 6.441274 TCTGTTGCATCTGAAGATTGTTTTC 58.559 36.000 2.19 0.00 31.21 2.29
601 617 4.503910 GGCCAAAAAGTGACAGTTTCTTT 58.496 39.130 8.69 0.00 33.61 2.52
653 669 1.475682 CTTTGAATCCTCTGCAAGGGC 59.524 52.381 12.99 6.03 46.23 5.19
654 670 1.475682 GCTTTGAATCCTCTGCAAGGG 59.524 52.381 12.99 6.67 46.23 3.95
657 673 3.225104 ACAAGCTTTGAATCCTCTGCAA 58.775 40.909 0.00 0.00 0.00 4.08
743 761 1.837439 TGACCACTTGACACTTGACCT 59.163 47.619 0.00 0.00 0.00 3.85
757 775 0.520404 CATGCTTGAGCTGTGACCAC 59.480 55.000 4.44 0.00 42.66 4.16
795 813 2.202479 GCGAGGCCGATTTGTTGC 60.202 61.111 0.00 0.00 38.22 4.17
832 850 2.057922 CAGTAGGGGTTAGGATGGCAT 58.942 52.381 0.00 0.00 0.00 4.40
833 851 1.009060 TCAGTAGGGGTTAGGATGGCA 59.991 52.381 0.00 0.00 0.00 4.92
837 855 5.013183 GCATATGTTCAGTAGGGGTTAGGAT 59.987 44.000 4.29 0.00 0.00 3.24
856 874 2.172483 GACGCTGATCCGGGGCATAT 62.172 60.000 0.00 0.00 0.00 1.78
857 875 2.842462 ACGCTGATCCGGGGCATA 60.842 61.111 0.00 0.00 0.00 3.14
950 968 1.071699 GCTGTCCCTTGGTTACTGACA 59.928 52.381 0.00 0.00 34.95 3.58
966 984 4.357279 GCTTCCTGGGCTGGCTGT 62.357 66.667 0.00 0.00 0.00 4.40
977 995 2.977178 CCGCTCTGTCTGCTTCCT 59.023 61.111 0.00 0.00 0.00 3.36
1053 1071 4.208632 GGCATGAGGACGAACAGG 57.791 61.111 0.00 0.00 0.00 4.00
1185 1206 0.888619 ACGATGAGGCGTTGAGAAGA 59.111 50.000 0.00 0.00 42.71 2.87
1188 1209 1.511305 GGACGATGAGGCGTTGAGA 59.489 57.895 0.00 0.00 45.72 3.27
1562 1590 7.595819 TGAGTAAAATGAAATTGTGGGAAGT 57.404 32.000 0.00 0.00 36.10 3.01
1681 1709 6.235231 ACTAATCTGAGAGGGCGAAAAATA 57.765 37.500 0.00 0.00 0.00 1.40
1682 1710 5.104259 ACTAATCTGAGAGGGCGAAAAAT 57.896 39.130 0.00 0.00 0.00 1.82
1689 1718 2.894765 GTCCCTACTAATCTGAGAGGGC 59.105 54.545 0.06 0.00 45.69 5.19
1732 1766 5.125900 TGTGGAGAATGCCAATTCACTATTG 59.874 40.000 1.64 0.00 44.05 1.90
1760 1795 4.821805 CACTACCACAGAAATTTCACCAGT 59.178 41.667 19.99 13.36 0.00 4.00
1761 1796 4.320494 GCACTACCACAGAAATTTCACCAG 60.320 45.833 19.99 9.19 0.00 4.00
1767 1802 5.852282 AGTTTGCACTACCACAGAAATTT 57.148 34.783 0.00 0.00 0.00 1.82
1775 1810 7.429636 TTGTAAGATAAGTTTGCACTACCAC 57.570 36.000 0.00 0.00 30.68 4.16
1776 1811 8.630054 AATTGTAAGATAAGTTTGCACTACCA 57.370 30.769 0.00 0.00 30.68 3.25
1777 1812 9.908152 AAAATTGTAAGATAAGTTTGCACTACC 57.092 29.630 0.00 0.00 30.68 3.18
1840 2011 0.333993 AAGAGGTCATTGCCAGGCAT 59.666 50.000 17.09 0.00 38.76 4.40
1869 2041 6.524586 GTGTTTAGCATCAACAAATAGCACTC 59.475 38.462 0.00 0.00 35.91 3.51
1912 2087 8.472007 ACCATGTTTAGTTTTCATAAAGGACA 57.528 30.769 0.00 0.00 0.00 4.02
1928 2103 9.104965 CGTTTTCATCCTAGAATACCATGTTTA 57.895 33.333 0.00 0.00 0.00 2.01
1929 2104 7.415206 GCGTTTTCATCCTAGAATACCATGTTT 60.415 37.037 0.00 0.00 0.00 2.83
1930 2105 6.038271 GCGTTTTCATCCTAGAATACCATGTT 59.962 38.462 0.00 0.00 0.00 2.71
1931 2106 5.527582 GCGTTTTCATCCTAGAATACCATGT 59.472 40.000 0.00 0.00 0.00 3.21
1932 2107 5.527214 TGCGTTTTCATCCTAGAATACCATG 59.473 40.000 0.00 0.00 0.00 3.66
1934 2109 5.092554 TGCGTTTTCATCCTAGAATACCA 57.907 39.130 0.00 0.00 0.00 3.25
1935 2110 4.024809 GCTGCGTTTTCATCCTAGAATACC 60.025 45.833 0.00 0.00 0.00 2.73
1936 2111 4.024809 GGCTGCGTTTTCATCCTAGAATAC 60.025 45.833 0.00 0.00 0.00 1.89
1937 2112 4.127171 GGCTGCGTTTTCATCCTAGAATA 58.873 43.478 0.00 0.00 0.00 1.75
1940 2115 1.555075 AGGCTGCGTTTTCATCCTAGA 59.445 47.619 0.00 0.00 31.36 2.43
1943 2118 0.036732 TGAGGCTGCGTTTTCATCCT 59.963 50.000 0.00 0.00 35.47 3.24
1949 2124 0.385390 CCAAGTTGAGGCTGCGTTTT 59.615 50.000 3.87 0.00 0.00 2.43
1961 2136 0.996583 TACCTAAGGGGCCCAAGTTG 59.003 55.000 27.72 11.38 39.10 3.16
1969 2144 5.886474 GCCATAATTTCTATACCTAAGGGGC 59.114 44.000 0.00 0.00 39.10 5.80
1982 2157 9.771534 GTAAGTTCAGAGATAGCCATAATTTCT 57.228 33.333 0.00 0.00 0.00 2.52
1983 2158 9.771534 AGTAAGTTCAGAGATAGCCATAATTTC 57.228 33.333 0.00 0.00 0.00 2.17
2052 2228 4.816925 GCTCCTGTCATATTTCAGTTACCC 59.183 45.833 4.04 0.00 0.00 3.69
2056 2232 4.910195 TGTGCTCCTGTCATATTTCAGTT 58.090 39.130 4.04 0.00 0.00 3.16
2074 2250 7.357532 GCGTTGCTTTATGTGAATATAATGTGC 60.358 37.037 0.00 0.00 0.00 4.57
2113 2290 5.609696 CGTGTGTCTTCTTGTTATTCGTGTC 60.610 44.000 0.00 0.00 0.00 3.67
2118 2295 5.571741 TCGATCGTGTGTCTTCTTGTTATTC 59.428 40.000 15.94 0.00 0.00 1.75
2125 2302 1.542030 AGCTCGATCGTGTGTCTTCTT 59.458 47.619 15.94 0.00 0.00 2.52
2127 2304 1.914700 GAAGCTCGATCGTGTGTCTTC 59.085 52.381 15.94 15.55 0.00 2.87
2130 2307 0.109272 TGGAAGCTCGATCGTGTGTC 60.109 55.000 15.94 13.14 0.00 3.67
2131 2308 0.532573 ATGGAAGCTCGATCGTGTGT 59.467 50.000 15.94 4.76 0.00 3.72
2132 2309 1.645034 AATGGAAGCTCGATCGTGTG 58.355 50.000 15.94 7.98 0.00 3.82
2133 2310 3.068165 TCATAATGGAAGCTCGATCGTGT 59.932 43.478 15.94 0.00 0.00 4.49
2134 2311 3.642705 TCATAATGGAAGCTCGATCGTG 58.357 45.455 15.94 14.19 0.00 4.35
2136 2313 5.852738 AATTCATAATGGAAGCTCGATCG 57.147 39.130 9.36 9.36 0.00 3.69
2140 2317 7.536622 GCTATTGAAATTCATAATGGAAGCTCG 59.463 37.037 0.00 0.00 0.00 5.03
2157 2334 9.546428 TCATCTAATTCGAATCTGCTATTGAAA 57.454 29.630 11.83 0.00 0.00 2.69
2161 2338 9.887629 ATGATCATCTAATTCGAATCTGCTATT 57.112 29.630 11.83 0.00 0.00 1.73
2233 2412 3.307480 CGGAAATTGTACAGTCTTCCCCT 60.307 47.826 19.27 0.00 33.40 4.79
2306 2486 5.695851 TTGAGGTTTTCATCTTTCTGAGC 57.304 39.130 0.00 0.00 35.27 4.26
2360 2541 2.547007 TCGACTTTGCTTCGATGGAACA 60.547 45.455 4.71 0.00 40.51 3.18
2383 2564 2.825532 TGCAGAACTTAATTGGGAAGGC 59.174 45.455 0.00 0.00 0.00 4.35
2476 2657 0.874607 ACTTCGTCGACACAACAGGC 60.875 55.000 17.16 0.00 0.00 4.85
2491 2672 7.678218 GCAGATATGTTTCCTGTCAATGACTTC 60.678 40.741 14.97 0.17 33.15 3.01


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

AutoCloner maintained by Alex Coulton.