Multiple sequence alignment - TraesCS2D01G387500

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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 TraesCS2D01G387500 chr2D 100.000 2609 0 0 1 2609 492899447 492902055 0.000000e+00 4819
1 TraesCS2D01G387500 chr2B 92.393 2537 115 28 69 2589 579523887 579526361 0.000000e+00 3544
2 TraesCS2D01G387500 chr2A 91.941 1973 79 29 1 1939 640863718 640861792 0.000000e+00 2689
3 TraesCS2D01G387500 chr2A 89.443 682 40 11 1930 2609 640861695 640861044 0.000000e+00 832
4 TraesCS2D01G387500 chrUn 87.037 108 13 1 2040 2146 86621860 86621753 1.270000e-23 121
5 TraesCS2D01G387500 chr7B 83.051 118 17 3 2033 2148 234910226 234910110 1.280000e-18 104
6 TraesCS2D01G387500 chr7B 85.294 102 14 1 2040 2140 327855978 327855877 1.280000e-18 104
7 TraesCS2D01G387500 chr3A 83.784 111 16 2 2032 2140 7458942 7458832 1.280000e-18 104
8 TraesCS2D01G387500 chr3D 83.636 110 17 1 2032 2140 595701489 595701380 4.590000e-18 102
9 TraesCS2D01G387500 chr6A 84.314 102 15 1 2040 2140 22197557 22197456 5.940000e-17 99
10 TraesCS2D01G387500 chr4B 83.333 108 17 1 2034 2140 45409057 45409164 5.940000e-17 99


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 TraesCS2D01G387500 chr2D 492899447 492902055 2608 False 4819.0 4819 100.000 1 2609 1 chr2D.!!$F1 2608
1 TraesCS2D01G387500 chr2B 579523887 579526361 2474 False 3544.0 3544 92.393 69 2589 1 chr2B.!!$F1 2520
2 TraesCS2D01G387500 chr2A 640861044 640863718 2674 True 1760.5 2689 90.692 1 2609 2 chr2A.!!$R1 2608

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
33 34 0.252197 ACATCCGGCCAAAGTAGGAC 59.748 55.0 2.24 0.00 35.36 3.85 F
516 535 0.382515 TTTGTTAACTGTGTGGCCGC 59.617 50.0 10.11 10.11 0.00 6.53 F
546 565 0.885879 TCGGTTGCTGTATCGACTGT 59.114 50.0 0.00 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1497 0.313043 TGAGTTCGTCGTCCTCCAAC 59.687 55.0 10.09 0.0 0.0 3.77 R
1448 1499 0.526211 CATGAGTTCGTCGTCCTCCA 59.474 55.0 10.09 0.0 0.0 3.86 R
2436 2600 0.820226 TCTGAGCATCCTTCCAGTCG 59.180 55.0 0.00 0.0 0.0 4.18 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
33 34 0.252197 ACATCCGGCCAAAGTAGGAC 59.748 55.000 2.24 0.00 35.36 3.85
66 70 4.395959 TTCTTGTGGAACGTCAGTAACT 57.604 40.909 0.00 0.00 42.39 2.24
75 79 5.818336 TGGAACGTCAGTAACTTTTCATCAA 59.182 36.000 0.00 0.00 0.00 2.57
119 125 2.813908 GACGGCACAGCGTTAGGG 60.814 66.667 0.00 0.00 0.00 3.53
155 161 5.655586 GTACTTACGTACGCACTTAACTG 57.344 43.478 16.72 0.00 36.93 3.16
236 254 4.701437 ACCCCTGGCCCAGACCAT 62.701 66.667 13.74 0.00 39.54 3.55
240 258 0.972471 CCCTGGCCCAGACCATTTTC 60.972 60.000 13.74 0.00 39.54 2.29
401 420 1.108776 TGTAGACATGGACGTAGCCC 58.891 55.000 0.00 0.00 0.00 5.19
509 528 8.331022 CGATCCTCTATCATTTTGTTAACTGTG 58.669 37.037 7.22 1.07 33.87 3.66
516 535 0.382515 TTTGTTAACTGTGTGGCCGC 59.617 50.000 10.11 10.11 0.00 6.53
517 536 1.448922 TTGTTAACTGTGTGGCCGCC 61.449 55.000 15.15 1.04 0.00 6.13
518 537 2.666862 TTAACTGTGTGGCCGCCG 60.667 61.111 15.15 4.76 0.00 6.46
520 539 2.457743 TTAACTGTGTGGCCGCCGAT 62.458 55.000 15.15 0.00 0.00 4.18
540 559 0.989890 GACGTGTCGGTTGCTGTATC 59.010 55.000 0.00 0.00 0.00 2.24
545 564 1.269166 GTCGGTTGCTGTATCGACTG 58.731 55.000 11.01 0.00 45.61 3.51
546 565 0.885879 TCGGTTGCTGTATCGACTGT 59.114 50.000 0.00 0.00 0.00 3.55
547 566 2.086094 TCGGTTGCTGTATCGACTGTA 58.914 47.619 0.00 0.00 0.00 2.74
548 567 2.686405 TCGGTTGCTGTATCGACTGTAT 59.314 45.455 0.00 0.00 0.00 2.29
549 568 3.878699 TCGGTTGCTGTATCGACTGTATA 59.121 43.478 0.00 0.00 0.00 1.47
673 693 2.463589 AATCTCCGGTTTCAGGCGCA 62.464 55.000 10.83 0.00 0.00 6.09
886 933 2.978018 GCCAATAATAGGGGCGCGC 61.978 63.158 25.94 25.94 38.04 6.86
917 964 1.524621 AGCGCTGAAACACACTGCT 60.525 52.632 10.39 0.00 0.00 4.24
1062 1113 2.109126 GCGCTTCCTCGGCTTCATT 61.109 57.895 0.00 0.00 0.00 2.57
1443 1494 3.760035 GCCGCTGACGAGGAGGAA 61.760 66.667 0.00 0.00 43.93 3.36
1446 1497 1.431440 CGCTGACGAGGAGGAAGAG 59.569 63.158 0.00 0.00 43.93 2.85
1447 1498 1.309499 CGCTGACGAGGAGGAAGAGT 61.309 60.000 0.00 0.00 43.93 3.24
1448 1499 0.892063 GCTGACGAGGAGGAAGAGTT 59.108 55.000 0.00 0.00 0.00 3.01
1452 1503 1.474879 GACGAGGAGGAAGAGTTGGAG 59.525 57.143 0.00 0.00 0.00 3.86
1701 1752 5.706916 CAGAAAATGTGGATCTTCTGTTGG 58.293 41.667 10.49 0.00 39.83 3.77
1720 1771 3.175594 TGGTACGTTTGGGATTCTAGGT 58.824 45.455 0.00 0.00 0.00 3.08
1807 1862 4.284123 TGCTGATCACGGAGCAAC 57.716 55.556 4.98 0.00 42.22 4.17
1888 1943 8.507249 GGATACAATTGCTTTATGATCTGTACC 58.493 37.037 5.05 0.00 0.00 3.34
1925 1980 4.202245 TGATACTTCCTTCGTCCCAAAG 57.798 45.455 0.00 0.00 0.00 2.77
1928 1983 1.766496 ACTTCCTTCGTCCCAAAGTGA 59.234 47.619 0.00 0.00 0.00 3.41
1929 1984 2.171870 ACTTCCTTCGTCCCAAAGTGAA 59.828 45.455 0.00 0.00 0.00 3.18
1930 1985 2.543777 TCCTTCGTCCCAAAGTGAAG 57.456 50.000 0.00 0.00 38.01 3.02
2092 2255 2.234661 TCAGACAGCCCACAGAATAGTG 59.765 50.000 0.00 0.00 39.21 2.74
2202 2365 4.146443 CAGTCGTACGTGTATATGTGCATG 59.854 45.833 16.05 0.00 33.70 4.06
2207 2370 5.176774 CGTACGTGTATATGTGCATGGATTT 59.823 40.000 7.22 0.00 31.99 2.17
2210 2373 5.356751 ACGTGTATATGTGCATGGATTTTGT 59.643 36.000 4.87 0.00 31.99 2.83
2217 2380 3.451540 TGTGCATGGATTTTGTATGCCAT 59.548 39.130 0.00 0.00 44.91 4.40
2260 2423 9.803315 CTTTTATCTGATGTTGCACTAGTACTA 57.197 33.333 1.89 1.89 0.00 1.82
2275 2438 6.012333 CACTAGTACTATATCCAGGGTCTCCT 60.012 46.154 2.33 0.00 46.26 3.69
2355 2518 5.694816 TGGTTTACAATAACGTTGATGCTG 58.305 37.500 11.99 3.42 0.00 4.41
2370 2534 6.454795 GTTGATGCTGGTTTGATCCTTTTAA 58.545 36.000 0.00 0.00 0.00 1.52
2371 2535 6.024552 TGATGCTGGTTTGATCCTTTTAAC 57.975 37.500 0.00 0.00 0.00 2.01
2410 2574 0.946221 CTATCATTCGGGACAGCGCC 60.946 60.000 2.29 0.00 0.00 6.53
2447 2611 1.066143 GCTTGGAATCGACTGGAAGGA 60.066 52.381 0.00 0.00 39.30 3.36
2493 2658 9.719355 TTAAACTGTTATCTTGTTGAGAGCATA 57.281 29.630 0.00 0.00 37.93 3.14
2535 2700 9.981114 ATAACTGTTGCTAAAATTTGCTAGTTT 57.019 25.926 15.89 0.00 34.04 2.66
2591 2756 8.500773 TCCGATTTCATTTAGTAGAAACAACAC 58.499 33.333 0.00 0.00 36.65 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.252197 GTCCTACTTTGGCCGGATGT 59.748 55.000 5.05 0.22 0.00 3.06
33 34 4.433186 TCCACAAGAAAATTATGCGGTG 57.567 40.909 0.00 0.00 0.00 4.94
75 79 9.485206 AGATAATAATCCTATTAAACGTTGCGT 57.515 29.630 0.00 0.00 35.42 5.24
92 96 3.059884 CGCTGTGCCGTCAGATAATAAT 58.940 45.455 5.11 0.00 37.61 1.28
93 97 2.159156 ACGCTGTGCCGTCAGATAATAA 60.159 45.455 5.11 0.00 36.61 1.40
94 98 1.407618 ACGCTGTGCCGTCAGATAATA 59.592 47.619 5.11 0.00 36.61 0.98
119 125 5.480281 CGTAAGTACAATGCTTGTTTTGC 57.520 39.130 6.82 5.82 42.22 3.68
236 254 6.267699 TCTCACAGTCTCACCTGATAAGAAAA 59.732 38.462 0.00 0.00 36.30 2.29
240 258 4.439974 GCTCTCACAGTCTCACCTGATAAG 60.440 50.000 0.00 0.00 36.30 1.73
401 420 7.360607 GGTTTATTTGTTGTATATCCGATCCCG 60.361 40.741 0.00 0.00 0.00 5.14
491 510 5.335269 CGGCCACACAGTTAACAAAATGATA 60.335 40.000 8.61 0.00 0.00 2.15
517 536 1.733041 AGCAACCGACACGTCATCG 60.733 57.895 11.01 11.01 43.34 3.84
518 537 0.944311 ACAGCAACCGACACGTCATC 60.944 55.000 0.00 0.00 0.00 2.92
520 539 0.315886 ATACAGCAACCGACACGTCA 59.684 50.000 0.00 0.00 0.00 4.35
528 547 2.554806 TACAGTCGATACAGCAACCG 57.445 50.000 0.00 0.00 0.00 4.44
545 564 9.517609 GATACGACATTTCCCATCTGTATATAC 57.482 37.037 5.89 5.89 0.00 1.47
546 565 8.692710 GGATACGACATTTCCCATCTGTATATA 58.307 37.037 0.00 0.00 0.00 0.86
547 566 7.400339 AGGATACGACATTTCCCATCTGTATAT 59.600 37.037 0.00 0.00 46.39 0.86
548 567 6.724441 AGGATACGACATTTCCCATCTGTATA 59.276 38.462 0.00 0.00 46.39 1.47
549 568 5.544176 AGGATACGACATTTCCCATCTGTAT 59.456 40.000 0.00 0.00 46.39 2.29
773 806 4.475444 TACGAGGGGGAGGGGCTG 62.475 72.222 0.00 0.00 0.00 4.85
774 807 4.159108 CTACGAGGGGGAGGGGCT 62.159 72.222 0.00 0.00 0.00 5.19
777 810 3.776016 ATGGCTACGAGGGGGAGGG 62.776 68.421 0.00 0.00 0.00 4.30
778 811 2.122813 ATGGCTACGAGGGGGAGG 60.123 66.667 0.00 0.00 0.00 4.30
779 812 0.833834 ATGATGGCTACGAGGGGGAG 60.834 60.000 0.00 0.00 0.00 4.30
780 813 0.832135 GATGATGGCTACGAGGGGGA 60.832 60.000 0.00 0.00 0.00 4.81
781 814 1.121407 TGATGATGGCTACGAGGGGG 61.121 60.000 0.00 0.00 0.00 5.40
917 964 4.314440 GTGGCCACTGACCAGCGA 62.314 66.667 29.12 0.00 38.04 4.93
953 1004 4.373116 ATCGAAGCGTGGGTGCGT 62.373 61.111 0.00 0.00 40.67 5.24
1062 1113 2.202878 GCGTCATCCGGCTGCTTA 60.203 61.111 0.00 0.00 36.94 3.09
1443 1494 0.597072 GTTCGTCGTCCTCCAACTCT 59.403 55.000 0.00 0.00 0.00 3.24
1446 1497 0.313043 TGAGTTCGTCGTCCTCCAAC 59.687 55.000 10.09 0.00 0.00 3.77
1447 1498 1.067846 CATGAGTTCGTCGTCCTCCAA 60.068 52.381 10.09 0.00 0.00 3.53
1448 1499 0.526211 CATGAGTTCGTCGTCCTCCA 59.474 55.000 10.09 0.00 0.00 3.86
1452 1503 1.352156 GCACCATGAGTTCGTCGTCC 61.352 60.000 0.00 0.00 0.00 4.79
1584 1635 3.691342 TCGAGGAAGCCGGTGGTG 61.691 66.667 1.90 0.00 0.00 4.17
1635 1686 3.858868 GAGTGACGTGGGCAGCGAA 62.859 63.158 0.00 0.00 0.00 4.70
1701 1752 4.460948 TCACCTAGAATCCCAAACGTAC 57.539 45.455 0.00 0.00 0.00 3.67
1807 1862 7.881775 AACCAGCCATTTAGACCTTATTTAG 57.118 36.000 0.00 0.00 0.00 1.85
1896 1951 5.106317 GGACGAAGGAAGTATCATTTTGCAA 60.106 40.000 0.00 0.00 27.88 4.08
1904 1959 3.581332 ACTTTGGGACGAAGGAAGTATCA 59.419 43.478 0.00 0.00 0.00 2.15
1925 1980 5.163632 GCTCAGTAGTAAGTACTCCCTTCAC 60.164 48.000 0.00 0.00 40.27 3.18
1928 1983 5.195848 AGCTCAGTAGTAAGTACTCCCTT 57.804 43.478 0.00 0.00 40.27 3.95
1929 1984 4.866327 AGCTCAGTAGTAAGTACTCCCT 57.134 45.455 0.00 0.00 40.27 4.20
1930 1985 4.948621 TGAAGCTCAGTAGTAAGTACTCCC 59.051 45.833 0.00 0.00 40.27 4.30
1931 1986 6.702716 ATGAAGCTCAGTAGTAAGTACTCC 57.297 41.667 0.00 0.00 40.27 3.85
2059 2222 3.055819 GGGCTGTCTGAATTGTCTAGACA 60.056 47.826 21.74 21.74 46.05 3.41
2092 2255 3.236816 CGTTTTGGACAGATGACATTGC 58.763 45.455 0.00 0.00 0.00 3.56
2163 2326 3.242936 ACGACTGGTAAAATGTGTTGTGC 60.243 43.478 0.00 0.00 0.00 4.57
2202 2365 6.421801 GCTAATCACAATGGCATACAAAATCC 59.578 38.462 0.00 0.00 0.00 3.01
2207 2370 5.192176 TCTGCTAATCACAATGGCATACAA 58.808 37.500 0.00 0.00 32.39 2.41
2210 2373 4.818005 CACTCTGCTAATCACAATGGCATA 59.182 41.667 0.00 0.00 32.39 3.14
2260 2423 4.235372 CTGGTAAAGGAGACCCTGGATAT 58.765 47.826 0.00 0.00 43.48 1.63
2275 2438 1.419762 TCTTCACCTGCAGCTGGTAAA 59.580 47.619 22.64 14.67 33.97 2.01
2345 2508 2.086869 AGGATCAAACCAGCATCAACG 58.913 47.619 0.00 0.00 0.00 4.10
2355 2518 6.750501 GGATTTAGCGTTAAAAGGATCAAACC 59.249 38.462 8.57 0.00 32.80 3.27
2370 2534 2.030274 GCACCAAAACAGGATTTAGCGT 60.030 45.455 0.00 0.00 0.00 5.07
2371 2535 2.228822 AGCACCAAAACAGGATTTAGCG 59.771 45.455 0.00 0.00 0.00 4.26
2436 2600 0.820226 TCTGAGCATCCTTCCAGTCG 59.180 55.000 0.00 0.00 0.00 4.18
2447 2611 1.556911 ACTTCGGTTCCATCTGAGCAT 59.443 47.619 0.00 0.00 0.00 3.79
2493 2658 6.305272 ACAGTTATCTCACAACCATCAGAT 57.695 37.500 0.00 0.00 0.00 2.90
2542 2707 7.334858 GGAGGGAGAGCCATCTTTATATAAAG 58.665 42.308 23.77 23.77 44.30 1.85
2544 2709 5.422331 CGGAGGGAGAGCCATCTTTATATAA 59.578 44.000 0.00 0.00 44.30 0.98
2545 2710 4.956700 CGGAGGGAGAGCCATCTTTATATA 59.043 45.833 0.00 0.00 44.30 0.86
2546 2711 3.772025 CGGAGGGAGAGCCATCTTTATAT 59.228 47.826 0.00 0.00 44.30 0.86


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

AutoCloner maintained by Alex Coulton.