Multiple sequence alignment - TraesCS5A01G180800

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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 TraesCS5A01G180800 chr5A 100.000 2933 0 0 1 2933 379355845 379352913 0.000000e+00 5417
1 TraesCS5A01G180800 chr5B 92.556 2969 139 40 1 2933 326574658 326571736 0.000000e+00 4183
2 TraesCS5A01G180800 chr5D 93.489 2534 111 22 1 2511 287443527 287441025 0.000000e+00 3716
3 TraesCS5A01G180800 chr5D 90.596 436 20 7 2513 2933 287440905 287440476 2.550000e-155 558


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 TraesCS5A01G180800 chr5A 379352913 379355845 2932 True 5417 5417 100.0000 1 2933 1 chr5A.!!$R1 2932
1 TraesCS5A01G180800 chr5B 326571736 326574658 2922 True 4183 4183 92.5560 1 2933 1 chr5B.!!$R1 2932
2 TraesCS5A01G180800 chr5D 287440476 287443527 3051 True 2137 3716 92.0425 1 2933 2 chr5D.!!$R1 2932

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
415 416 0.162933 CGTGCACGCGAAGTAACAAT 59.837 50.000 28.16 0.0 0.0 2.71 F
1143 1158 1.271926 CCAATGAAAACCTCCGGACCT 60.272 52.381 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 1946 0.036010 CCTCAATGTTGTCGAGGCCT 60.036 55.0 3.86 3.86 39.95 5.19 R
1963 1979 1.270907 ACTCACCCTGACATCTGTCC 58.729 55.0 7.81 0.00 44.15 4.02 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 1.919918 GCCACAGCGCATAACAAAATC 59.080 47.619 11.47 0.00 0.00 2.17
56 57 2.415893 GCCACAGCGCATAACAAAATCT 60.416 45.455 11.47 0.00 0.00 2.40
148 149 5.409826 CCGGTCATCTTAATTATTGCTCCTC 59.590 44.000 0.00 0.00 0.00 3.71
333 334 2.039480 TGATGAGCTGTGCTTTCCTTCT 59.961 45.455 0.00 0.00 39.88 2.85
334 335 2.645838 TGAGCTGTGCTTTCCTTCTT 57.354 45.000 0.00 0.00 39.88 2.52
335 336 2.224606 TGAGCTGTGCTTTCCTTCTTG 58.775 47.619 0.00 0.00 39.88 3.02
415 416 0.162933 CGTGCACGCGAAGTAACAAT 59.837 50.000 28.16 0.00 0.00 2.71
416 417 1.591248 GTGCACGCGAAGTAACAATG 58.409 50.000 15.93 0.00 0.00 2.82
704 711 9.280174 TCACAGAAAAATAATAACTCCGTCTTT 57.720 29.630 0.00 0.00 0.00 2.52
762 769 5.302568 AGTTTCTGATTTTGGAGATTGTGCA 59.697 36.000 0.00 0.00 0.00 4.57
768 775 1.527034 TTGGAGATTGTGCACTCAGC 58.473 50.000 19.41 7.59 45.96 4.26
834 843 4.811024 CGGTATGTGCACATCTTATGTTCT 59.189 41.667 34.54 11.48 42.70 3.01
836 845 6.510157 CGGTATGTGCACATCTTATGTTCTTC 60.510 42.308 34.54 6.71 42.70 2.87
986 1001 5.568620 TGGATCTTAAGATTAAGGGGCTC 57.431 43.478 18.88 4.12 40.35 4.70
1006 1021 3.663025 TCGTTGCACAAAGAGATGATGA 58.337 40.909 0.00 0.00 0.00 2.92
1050 1065 3.552875 CATTTCCTGCTGTGATCCTGAT 58.447 45.455 0.00 0.00 0.00 2.90
1101 1116 2.159462 GCATGCGAAGAAGGAAAAGAGG 60.159 50.000 0.00 0.00 0.00 3.69
1143 1158 1.271926 CCAATGAAAACCTCCGGACCT 60.272 52.381 0.00 0.00 0.00 3.85
1194 1209 2.004733 GGCAGCAAGAAATCAATTGGC 58.995 47.619 5.42 0.00 0.00 4.52
1287 1302 3.195610 AGATACGTGATCCTGTGAGCAAA 59.804 43.478 0.00 0.00 38.90 3.68
1591 1606 4.384056 AGAAATCCAGGTAGATGCATTCG 58.616 43.478 0.00 0.00 0.00 3.34
1746 1761 6.577103 TGACAAACTCTCACTGGATGATATC 58.423 40.000 0.00 0.00 36.48 1.63
1839 1854 2.673523 GGGCTGGCAGACATCAGT 59.326 61.111 24.18 0.00 33.81 3.41
1870 1885 3.342377 TGCCAATGTTCGAGTTGGATA 57.658 42.857 22.74 12.17 46.15 2.59
1925 1940 3.374367 TCGATGGAACGTGAACTAGAGAG 59.626 47.826 0.00 0.00 34.70 3.20
1931 1946 5.766670 TGGAACGTGAACTAGAGAGACTTTA 59.233 40.000 0.00 0.00 0.00 1.85
1932 1947 6.072618 TGGAACGTGAACTAGAGAGACTTTAG 60.073 42.308 0.00 0.00 0.00 1.85
1934 1949 4.156373 ACGTGAACTAGAGAGACTTTAGGC 59.844 45.833 0.00 0.00 0.00 3.93
1936 1951 4.707934 GTGAACTAGAGAGACTTTAGGCCT 59.292 45.833 11.78 11.78 0.00 5.19
1937 1952 4.951094 TGAACTAGAGAGACTTTAGGCCTC 59.049 45.833 9.68 0.00 0.00 4.70
1938 1953 3.547746 ACTAGAGAGACTTTAGGCCTCG 58.452 50.000 9.68 0.88 32.52 4.63
1940 1955 2.371306 AGAGAGACTTTAGGCCTCGAC 58.629 52.381 9.68 0.00 32.52 4.20
1941 1956 2.093106 GAGAGACTTTAGGCCTCGACA 58.907 52.381 9.68 0.00 32.52 4.35
1963 1979 6.208644 ACAACATTGAGGTTTTCATCTTTCG 58.791 36.000 0.00 0.00 35.27 3.46
1966 1982 5.048713 ACATTGAGGTTTTCATCTTTCGGAC 60.049 40.000 0.00 0.00 35.27 4.79
2034 2051 5.427036 TTTTGTCGGAAATTGTACAGTCC 57.573 39.130 10.74 10.74 0.00 3.85
2035 2052 3.755112 TGTCGGAAATTGTACAGTCCA 57.245 42.857 17.59 6.70 0.00 4.02
2071 2088 7.609532 AGATTAATCTGGTTGAGCCTTATATGC 59.390 37.037 17.26 0.00 35.42 3.14
2300 2324 9.930158 TTGCCATAATTTTTCTATACTAAGGGT 57.070 29.630 0.00 0.00 0.00 4.34
2301 2325 9.930158 TGCCATAATTTTTCTATACTAAGGGTT 57.070 29.630 0.00 0.00 0.00 4.11
2394 2420 7.036996 TGATGTGTTTAGCATCAACAAAGAA 57.963 32.000 5.62 0.00 46.49 2.52
2396 2422 6.449635 TGTGTTTAGCATCAACAAAGAACT 57.550 33.333 0.00 0.00 35.91 3.01
2397 2423 7.561021 TGTGTTTAGCATCAACAAAGAACTA 57.439 32.000 0.00 0.00 35.91 2.24
2401 2431 9.677567 TGTTTAGCATCAACAAAGAACTATTTC 57.322 29.630 0.00 0.00 31.05 2.17
2506 2536 7.931275 ACCAAACAGACTGAAAGATAAGTTTC 58.069 34.615 10.08 0.00 37.43 2.78
2557 2707 7.283127 GGAGAATGCCAAGTTCACTATTAATCA 59.717 37.037 0.00 0.00 0.00 2.57
2558 2708 8.757982 AGAATGCCAAGTTCACTATTAATCAT 57.242 30.769 0.00 0.00 0.00 2.45
2559 2709 9.851686 AGAATGCCAAGTTCACTATTAATCATA 57.148 29.630 0.00 0.00 0.00 2.15
2604 2754 5.016173 CCCTACTAATCATGAGAGGGAGAG 58.984 50.000 18.15 8.00 45.65 3.20
2609 2759 7.502060 ACTAATCATGAGAGGGAGAGAAAAA 57.498 36.000 0.09 0.00 0.00 1.94
2613 2763 6.131972 TCATGAGAGGGAGAGAAAAACATT 57.868 37.500 0.00 0.00 0.00 2.71
2624 2774 7.358830 GGAGAGAAAAACATTCAGAACAGAAG 58.641 38.462 0.00 0.00 0.00 2.85
2626 2776 7.701445 AGAGAAAAACATTCAGAACAGAAGTG 58.299 34.615 0.00 0.00 0.00 3.16
2870 3035 0.740868 CGTTGTCGATGCCCATGAGT 60.741 55.000 0.00 0.00 39.71 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 149 8.236084 AGCACACGTACTAACAAATTTAGTAG 57.764 34.615 4.49 3.47 37.93 2.57
162 163 3.257375 TCCAAGATTGTAGCACACGTACT 59.743 43.478 0.00 0.00 0.00 2.73
415 416 5.464588 TGATTTGGGGGATTCTTGTATCA 57.535 39.130 0.00 0.00 0.00 2.15
416 417 6.129179 TCTTGATTTGGGGGATTCTTGTATC 58.871 40.000 0.00 0.00 0.00 2.24
532 533 4.476479 AGATGAGGCCCAATCTTTCTTAGT 59.524 41.667 11.22 0.00 0.00 2.24
704 711 8.746052 TCAAACTTCTGATTAAAACTGGAGAA 57.254 30.769 5.62 0.00 0.00 2.87
738 745 5.302568 TGCACAATCTCCAAAATCAGAAACT 59.697 36.000 0.00 0.00 0.00 2.66
762 769 0.178921 TCCTGGTTGAGAGGCTGAGT 60.179 55.000 0.00 0.00 0.00 3.41
768 775 4.006319 GACAGAAATTCCTGGTTGAGAGG 58.994 47.826 0.00 0.00 38.44 3.69
836 845 9.166126 GGTAGACACTTAAAAATTTCAAAGACG 57.834 33.333 15.63 10.21 0.00 4.18
900 911 2.417924 GGCCAGTGAGTGTGTCAGATAG 60.418 54.545 0.00 0.00 35.13 2.08
986 1001 4.611310 ATCATCATCTCTTTGTGCAACG 57.389 40.909 0.00 0.00 42.39 4.10
1006 1021 3.453559 CCTTCCGCGAACAAGGTAT 57.546 52.632 8.23 0.00 35.34 2.73
1050 1065 0.178767 CATCAGAGGAATCGGTGGCA 59.821 55.000 0.00 0.00 0.00 4.92
1101 1116 5.128827 TGGAACTAGTACCTCCATTGTCATC 59.871 44.000 10.21 0.00 34.26 2.92
1143 1158 2.877866 AGGGTCTTTCGAGACTTGAGA 58.122 47.619 6.53 0.00 38.74 3.27
1178 1193 3.916761 TCTGTGCCAATTGATTTCTTGC 58.083 40.909 7.12 0.00 0.00 4.01
1194 1209 2.291741 GGTTGGTTGCTTCTTCTCTGTG 59.708 50.000 0.00 0.00 0.00 3.66
1287 1302 0.252012 TGCCAATCCATTTCCGGGTT 60.252 50.000 0.00 0.00 0.00 4.11
1332 1347 1.809271 CGTTCTGCCTCATATGCTGCT 60.809 52.381 14.70 0.00 0.00 4.24
1562 1577 5.529060 GCATCTACCTGGATTTCTTTACCTG 59.471 44.000 0.00 0.00 0.00 4.00
1591 1606 1.173043 TCAACATTCATCCGGCCAAC 58.827 50.000 2.24 0.00 0.00 3.77
1746 1761 2.634815 ACATATCTGCCAGCCTTGAG 57.365 50.000 0.00 0.00 0.00 3.02
1870 1885 5.240844 CGAAACCTTCCCAATTAAGTTCTGT 59.759 40.000 0.00 0.00 0.00 3.41
1925 1940 2.450609 TGTTGTCGAGGCCTAAAGTC 57.549 50.000 4.42 0.00 0.00 3.01
1931 1946 0.036010 CCTCAATGTTGTCGAGGCCT 60.036 55.000 3.86 3.86 39.95 5.19
1932 1947 2.471255 CCTCAATGTTGTCGAGGCC 58.529 57.895 0.00 0.00 39.95 5.19
1936 1951 5.063204 AGATGAAAACCTCAATGTTGTCGA 58.937 37.500 0.00 0.00 35.59 4.20
1937 1952 5.362556 AGATGAAAACCTCAATGTTGTCG 57.637 39.130 0.00 0.00 35.59 4.35
1938 1953 6.360681 CGAAAGATGAAAACCTCAATGTTGTC 59.639 38.462 0.00 0.00 37.67 3.18
1940 1955 5.630680 CCGAAAGATGAAAACCTCAATGTTG 59.369 40.000 0.00 0.00 37.67 3.33
1941 1956 5.534654 TCCGAAAGATGAAAACCTCAATGTT 59.465 36.000 0.00 0.00 37.67 2.71
1963 1979 1.270907 ACTCACCCTGACATCTGTCC 58.729 55.000 7.81 0.00 44.15 4.02
1966 1982 2.810274 CACAAACTCACCCTGACATCTG 59.190 50.000 0.00 0.00 0.00 2.90
2071 2088 7.814587 AGATGATCATGTACATATTACACGGTG 59.185 37.037 14.30 6.58 0.00 4.94
2300 2324 1.975660 AACGCAGCCTTAACTTGGAA 58.024 45.000 0.00 0.00 0.00 3.53
2301 2325 1.606668 CAAACGCAGCCTTAACTTGGA 59.393 47.619 0.00 0.00 0.00 3.53
2394 2420 8.914011 GCAATGACCCCTTTTTATAGAAATAGT 58.086 33.333 0.66 0.00 0.00 2.12
2396 2422 7.289084 GGGCAATGACCCCTTTTTATAGAAATA 59.711 37.037 0.00 0.00 45.00 1.40
2397 2423 6.099701 GGGCAATGACCCCTTTTTATAGAAAT 59.900 38.462 0.00 0.00 45.00 2.17
2401 2431 4.937201 GGGCAATGACCCCTTTTTATAG 57.063 45.455 0.00 0.00 45.00 1.31
2463 2493 7.103641 TGTTTGGTTTGGCAGTACAATTTTTA 58.896 30.769 0.00 0.00 0.00 1.52
2468 2498 3.957497 TCTGTTTGGTTTGGCAGTACAAT 59.043 39.130 0.00 0.00 0.00 2.71
2558 2708 9.684702 AGGGAACTCCTTTTTCCACTATATATA 57.315 33.333 3.64 0.00 45.47 0.86
2559 2709 8.582891 AGGGAACTCCTTTTTCCACTATATAT 57.417 34.615 3.64 0.00 45.47 0.86
2560 2710 8.931568 GTAGGGAACTCCTTTTTCCACTATATA 58.068 37.037 3.64 0.00 45.47 0.86
2575 2725 5.245075 CCTCTCATGATTAGTAGGGAACTCC 59.755 48.000 0.00 0.00 43.67 3.85
2576 2726 5.245075 CCCTCTCATGATTAGTAGGGAACTC 59.755 48.000 16.54 0.00 45.53 3.01


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

AutoCloner maintained by Alex Coulton.