Multiple sequence alignment - TraesCS4A01G214300

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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 TraesCS4A01G214300 chr4A 100.000 3044 0 0 1 3044 512537021 512540064 0.000000e+00 5622
1 TraesCS4A01G214300 chr4B 93.322 3040 127 39 60 3044 107459470 107456452 0.000000e+00 4420
2 TraesCS4A01G214300 chr4B 98.413 63 1 0 1 63 107461008 107460946 8.920000e-21 111
3 TraesCS4A01G214300 chr4D 92.565 3107 151 38 1 3044 75053811 75050722 0.000000e+00 4385
4 TraesCS4A01G214300 chr7A 83.810 210 33 1 570 778 516799186 516798977 6.660000e-47 198
5 TraesCS4A01G214300 chr7A 83.412 211 35 0 564 774 670247298 670247508 2.390000e-46 196
6 TraesCS4A01G214300 chr2D 83.333 210 33 2 565 774 574569408 574569615 3.100000e-45 193
7 TraesCS4A01G214300 chr6D 83.663 202 33 0 563 764 816251 816050 1.110000e-44 191
8 TraesCS4A01G214300 chr7B 81.776 214 39 0 564 777 729593317 729593104 2.410000e-41 180
9 TraesCS4A01G214300 chr6B 81.860 215 37 2 564 777 627545490 627545703 2.410000e-41 180
10 TraesCS4A01G214300 chr5D 81.776 214 39 0 564 777 199738917 199738704 2.410000e-41 180


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 TraesCS4A01G214300 chr4A 512537021 512540064 3043 False 5622.0 5622 100.0000 1 3044 1 chr4A.!!$F1 3043
1 TraesCS4A01G214300 chr4B 107456452 107461008 4556 True 2265.5 4420 95.8675 1 3044 2 chr4B.!!$R1 3043
2 TraesCS4A01G214300 chr4D 75050722 75053811 3089 True 4385.0 4385 92.5650 1 3044 1 chr4D.!!$R1 3043

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
354 1836 0.038526 GGTAGGTGTGACCGTGTGAG 60.039 60.0 0.0 0.0 44.9 3.51 F
943 2447 0.178891 TCTTCCCTGCTCCTCCAAGT 60.179 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 3383 0.249657 GCTCCACATGATCCTCGGAC 60.250 60.0 0.0 0.0 0.0 4.79 R
2602 4148 0.111061 TGGCTGCACATGAACTCCTT 59.889 50.0 0.0 0.0 0.0 3.36 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
235 1717 9.079833 CCTTGCAAGTCAATCAATAACTTAATG 57.920 33.333 24.35 0.00 33.57 1.90
315 1797 3.857157 TGGACCAAGCTACTGAAACTT 57.143 42.857 0.00 0.00 0.00 2.66
318 1800 2.226674 GACCAAGCTACTGAAACTTGCC 59.773 50.000 0.00 0.00 39.55 4.52
323 1805 1.807142 GCTACTGAAACTTGCCAGGAC 59.193 52.381 0.00 0.00 34.85 3.85
346 1828 1.595357 CCCCTTCGGTAGGTGTGAC 59.405 63.158 0.00 0.00 43.07 3.67
347 1829 1.595357 CCCTTCGGTAGGTGTGACC 59.405 63.158 0.00 0.00 43.07 4.02
352 1834 4.667420 GGTAGGTGTGACCGTGTG 57.333 61.111 0.00 0.00 44.90 3.82
353 1835 2.043625 GGTAGGTGTGACCGTGTGA 58.956 57.895 0.00 0.00 44.90 3.58
354 1836 0.038526 GGTAGGTGTGACCGTGTGAG 60.039 60.000 0.00 0.00 44.90 3.51
592 2074 2.203070 GGTGCGCTGGTCCTATGG 60.203 66.667 9.73 0.00 0.00 2.74
621 2103 0.888285 ACGACGACTTCCCGACTCTT 60.888 55.000 0.00 0.00 0.00 2.85
641 2123 3.648339 TTACTACGACGAGTTTTGCCT 57.352 42.857 0.00 0.00 0.00 4.75
648 2130 2.335712 CGAGTTTTGCCTGGCTCCC 61.336 63.158 21.03 5.22 0.00 4.30
649 2131 1.228552 GAGTTTTGCCTGGCTCCCA 60.229 57.895 21.03 0.00 0.00 4.37
650 2132 1.527433 GAGTTTTGCCTGGCTCCCAC 61.527 60.000 21.03 11.02 0.00 4.61
704 2186 2.160417 GCTCGCTTCAATGCTTGTAGTT 59.840 45.455 0.00 0.00 31.53 2.24
714 2196 2.409975 TGCTTGTAGTTGTCGTTAGGC 58.590 47.619 0.00 0.00 0.00 3.93
808 2308 3.432262 AAAAAGAACCGGTCCCAGG 57.568 52.632 8.04 0.00 0.00 4.45
849 2352 2.930682 GCGGAGAGGTTAAGCAAAGTAG 59.069 50.000 7.52 0.00 0.00 2.57
850 2353 3.368116 GCGGAGAGGTTAAGCAAAGTAGA 60.368 47.826 7.52 0.00 0.00 2.59
899 2402 2.301583 GTTCTCTTGCTTCACTCCTCCT 59.698 50.000 0.00 0.00 0.00 3.69
914 2418 1.555765 CCTCCTCTTCCCTCCCTTTGA 60.556 57.143 0.00 0.00 0.00 2.69
943 2447 0.178891 TCTTCCCTGCTCCTCCAAGT 60.179 55.000 0.00 0.00 0.00 3.16
978 2482 4.437239 CAAATACGCAGGTCATCTCTCTT 58.563 43.478 0.00 0.00 0.00 2.85
982 2486 1.802136 CGCAGGTCATCTCTCTTGCTC 60.802 57.143 0.00 0.00 0.00 4.26
991 2502 4.715792 TCATCTCTCTTGCTCCATCTTCTT 59.284 41.667 0.00 0.00 0.00 2.52
1134 2648 1.227380 GCTGTCCGCCGAAGATGAT 60.227 57.895 0.00 0.00 0.00 2.45
1143 2657 1.226974 CGAAGATGATGACGGCGGT 60.227 57.895 13.24 0.00 0.00 5.68
1562 3076 3.465871 GAAAGATCATCTCCAGCTCCAC 58.534 50.000 0.00 0.00 0.00 4.02
1566 3080 2.060383 CATCTCCAGCTCCACCGGA 61.060 63.158 9.46 0.00 0.00 5.14
1869 3383 2.815647 GGCGGCAAGACGGAAGAG 60.816 66.667 3.07 0.00 0.00 2.85
1872 3386 1.446272 CGGCAAGACGGAAGAGTCC 60.446 63.158 0.00 0.00 41.83 3.85
1953 3467 4.051237 TGTTCGACTGTGTTCTTGATCAG 58.949 43.478 0.00 0.00 0.00 2.90
2020 3534 2.677914 TCAGAGACAAGGTCCTCACAA 58.322 47.619 0.00 0.00 32.18 3.33
2109 3624 9.520204 GTTTGTAATGTTGGATTTGATATCCTG 57.480 33.333 0.00 0.00 38.95 3.86
2142 3659 5.729974 TCATCGATCAGCTGAAATTTCTG 57.270 39.130 22.50 18.29 0.00 3.02
2208 3732 3.241784 CGTGTGGTTTTATGTGTTTGCAC 59.758 43.478 0.00 0.00 45.44 4.57
2211 3735 5.350091 GTGTGGTTTTATGTGTTTGCACTTT 59.650 36.000 0.00 0.00 45.44 2.66
2326 3852 1.239968 CCTGAACCAGCAAGAGCACC 61.240 60.000 0.00 0.00 45.49 5.01
2365 3894 7.150640 TGTGAAGCAACATATTGTTTATTGCA 58.849 30.769 9.65 0.00 46.38 4.08
2379 3908 7.231705 TGTTTATTGCACATTCAACACAAAG 57.768 32.000 0.00 0.00 0.00 2.77
2380 3909 6.815641 TGTTTATTGCACATTCAACACAAAGT 59.184 30.769 0.00 0.00 0.00 2.66
2406 3938 6.839124 TGTGCTTGGAAATATCAGACAAAT 57.161 33.333 0.00 0.00 0.00 2.32
2415 3947 9.699410 TGGAAATATCAGACAAATTTAGGTCAT 57.301 29.630 10.33 0.99 36.50 3.06
2467 4013 7.503566 TCAAGACTGAAGATTCCAAAAGTTCAT 59.496 33.333 0.00 0.00 0.00 2.57
2470 4016 5.302568 ACTGAAGATTCCAAAAGTTCATGCA 59.697 36.000 0.00 0.00 0.00 3.96
2614 4160 0.036010 CCGGCTCAAGGAGTTCATGT 60.036 55.000 0.00 0.00 31.39 3.21
2633 4179 0.884704 TGCAGCCAGACCGTTTCTTC 60.885 55.000 0.00 0.00 28.96 2.87
2807 4353 4.554036 GCATCGACTCCCTGGCCC 62.554 72.222 0.00 0.00 0.00 5.80
2905 4456 6.854578 TCTCTAAACCCACCCTTTGAAAATA 58.145 36.000 0.00 0.00 0.00 1.40
2981 4532 5.101628 TGAAATAGTTTTGCCATTGATCGC 58.898 37.500 0.00 0.00 0.00 4.58
3031 4583 8.823818 AGGATAACGATTAAACTTAAACGGATG 58.176 33.333 13.97 0.00 41.36 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
235 1717 4.340617 TGGATTTGGATGTAGGAACAACC 58.659 43.478 0.00 0.00 46.17 3.77
303 1785 1.807142 GTCCTGGCAAGTTTCAGTAGC 59.193 52.381 0.00 0.00 0.00 3.58
306 1788 2.427095 GTTTGTCCTGGCAAGTTTCAGT 59.573 45.455 0.00 0.00 0.00 3.41
315 1797 2.366153 GAAGGGGGTTTGTCCTGGCA 62.366 60.000 0.00 0.00 36.25 4.92
318 1800 4.397348 CGAAGGGGGTTTGTCCTG 57.603 61.111 0.00 0.00 36.25 3.86
346 1828 3.119708 GGTAACAGGTAGTACTCACACGG 60.120 52.174 0.00 0.00 0.00 4.94
347 1829 3.503363 TGGTAACAGGTAGTACTCACACG 59.497 47.826 0.00 0.00 46.17 4.49
592 2074 2.488087 AAGTCGTCGTGCTAGTGCCC 62.488 60.000 0.00 0.00 38.71 5.36
621 2103 3.311106 CAGGCAAAACTCGTCGTAGTAA 58.689 45.455 0.00 0.00 0.00 2.24
641 2123 3.003173 CCTTCCTCGTGGGAGCCA 61.003 66.667 6.27 0.00 46.01 4.75
648 2130 2.202932 CATCGCCCCTTCCTCGTG 60.203 66.667 0.00 0.00 0.00 4.35
649 2131 2.363795 TCATCGCCCCTTCCTCGT 60.364 61.111 0.00 0.00 0.00 4.18
650 2132 2.107141 GTCATCGCCCCTTCCTCG 59.893 66.667 0.00 0.00 0.00 4.63
677 2159 1.361668 GCATTGAAGCGAGCCGAAGA 61.362 55.000 0.00 0.00 0.00 2.87
704 2186 2.212576 TTCGTAGACCGCCTAACGACA 61.213 52.381 0.00 0.00 40.31 4.35
714 2196 5.171147 ACTACATTCAGATTCGTAGACCG 57.829 43.478 0.00 0.00 35.86 4.79
751 2233 7.857734 TTAATCATGACGGTACAATGAACAT 57.142 32.000 0.00 0.00 0.00 2.71
757 2239 9.974980 AAAAACTTTTAATCATGACGGTACAAT 57.025 25.926 0.00 0.00 0.00 2.71
793 2293 1.057851 TTGACCTGGGACCGGTTCTT 61.058 55.000 13.96 0.00 34.19 2.52
808 2308 4.676924 CCGCACTTCTTCTTTTGATTTGAC 59.323 41.667 0.00 0.00 0.00 3.18
849 2352 2.604046 ACTATTCCATGCACCTCGTC 57.396 50.000 0.00 0.00 0.00 4.20
850 2353 4.587262 TGTATACTATTCCATGCACCTCGT 59.413 41.667 4.17 0.00 0.00 4.18
922 2426 0.914644 TTGGAGGAGCAGGGAAGATG 59.085 55.000 0.00 0.00 0.00 2.90
931 2435 2.488347 GGTTTGGTTACTTGGAGGAGCA 60.488 50.000 0.00 0.00 0.00 4.26
932 2436 2.160205 GGTTTGGTTACTTGGAGGAGC 58.840 52.381 0.00 0.00 0.00 4.70
934 2438 3.761897 CATGGTTTGGTTACTTGGAGGA 58.238 45.455 0.00 0.00 0.00 3.71
943 2447 3.255888 TGCGTATTTGCATGGTTTGGTTA 59.744 39.130 0.00 0.00 40.62 2.85
978 2482 2.882761 GCATGCATAAGAAGATGGAGCA 59.117 45.455 14.21 0.00 30.02 4.26
982 2486 4.616143 GCTCATGCATGCATAAGAAGATGG 60.616 45.833 31.20 16.91 39.41 3.51
1161 2675 4.451150 TCGGCGCACCACCTCATC 62.451 66.667 10.83 0.00 34.57 2.92
1566 3080 3.984193 GAGGACCATGCTGCCGCTT 62.984 63.158 0.70 0.00 36.97 4.68
1868 3382 1.407936 CTCCACATGATCCTCGGACT 58.592 55.000 0.00 0.00 0.00 3.85
1869 3383 0.249657 GCTCCACATGATCCTCGGAC 60.250 60.000 0.00 0.00 0.00 4.79
1872 3386 0.879400 GCAGCTCCACATGATCCTCG 60.879 60.000 0.00 0.00 0.00 4.63
1881 3395 2.935740 CGTCCTCAGCAGCTCCACA 61.936 63.158 0.00 0.00 0.00 4.17
1953 3467 3.539604 CCTGATCACCTCATCAAAGACC 58.460 50.000 0.00 0.00 32.24 3.85
2020 3534 6.658188 TTAAAATTCACCCCGATTCAGTTT 57.342 33.333 0.00 0.00 0.00 2.66
2109 3624 6.073385 TCAGCTGATCGATGAATTAGCAATTC 60.073 38.462 13.74 12.10 45.86 2.17
2341 3867 7.116090 TGTGCAATAAACAATATGTTGCTTCAC 59.884 33.333 1.57 2.33 40.14 3.18
2365 3894 6.147864 AGCACATTACTTTGTGTTGAATGT 57.852 33.333 6.46 0.00 46.93 2.71
2379 3908 7.320443 TGTCTGATATTTCCAAGCACATTAC 57.680 36.000 0.00 0.00 0.00 1.89
2380 3909 7.936496 TTGTCTGATATTTCCAAGCACATTA 57.064 32.000 0.00 0.00 0.00 1.90
2389 3918 9.699410 ATGACCTAAATTTGTCTGATATTTCCA 57.301 29.630 0.00 0.00 32.67 3.53
2437 3983 8.699130 ACTTTTGGAATCTTCAGTCTTGATTTT 58.301 29.630 0.00 0.00 32.27 1.82
2439 3985 7.830099 ACTTTTGGAATCTTCAGTCTTGATT 57.170 32.000 0.00 0.00 32.27 2.57
2446 3992 5.302568 TGCATGAACTTTTGGAATCTTCAGT 59.697 36.000 0.00 0.00 0.00 3.41
2483 4029 6.780031 TCTGTAATTCTCTCCAGGATAGGAAG 59.220 42.308 2.04 0.00 37.20 3.46
2602 4148 0.111061 TGGCTGCACATGAACTCCTT 59.889 50.000 0.00 0.00 0.00 3.36
2614 4160 0.884704 GAAGAAACGGTCTGGCTGCA 60.885 55.000 0.50 0.00 36.40 4.41
2633 4179 6.037062 GTGAAGTTTTGTTCATTCTTTTGGGG 59.963 38.462 0.00 0.00 38.68 4.96
2807 4353 3.849911 ACCACTGTCAACATCTATGTCG 58.150 45.455 0.00 0.00 40.80 4.35
2905 4456 7.119846 GTGGACAGCTAACAAGATAACAAAGAT 59.880 37.037 0.00 0.00 0.00 2.40
2981 4532 8.844244 CCTATAAATTTTCAGGATTGTGAGAGG 58.156 37.037 10.77 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.