Multiple sequence alignment - TraesCS4B01G271200

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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 TraesCS4B01G271200 chr4B 100.000 2851 0 0 1 2851 547203905 547206755 0.000000e+00 5265.0
1 TraesCS4B01G271200 chr4D 94.460 2852 96 26 1 2811 441130974 441133804 0.000000e+00 4335.0
2 TraesCS4B01G271200 chr4D 88.991 327 32 4 1133 1456 442222765 442222440 4.420000e-108 401.0
3 TraesCS4B01G271200 chr4A 91.906 2545 120 27 145 2619 26414813 26412285 0.000000e+00 3480.0
4 TraesCS4B01G271200 chr4A 89.408 321 34 0 1130 1450 624733537 624733857 3.420000e-109 405.0
5 TraesCS4B01G271200 chr4A 88.685 327 33 4 1133 1456 24919195 24918870 2.060000e-106 396.0
6 TraesCS4B01G271200 chr5D 90.654 321 30 0 1130 1450 544799364 544799684 7.300000e-116 427.0
7 TraesCS4B01G271200 chr5D 89.097 321 35 0 1130 1450 544817287 544817607 1.590000e-107 399.0
8 TraesCS4B01G271200 chr5D 92.683 41 3 0 1091 1131 544799213 544799253 3.070000e-05 60.2
9 TraesCS4B01G271200 chr5B 89.720 321 32 1 1130 1450 687213003 687213322 2.640000e-110 409.0
10 TraesCS4B01G271200 chr1A 89.308 318 34 0 1133 1450 569355558 569355241 1.590000e-107 399.0


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 TraesCS4B01G271200 chr4B 547203905 547206755 2850 False 5265 5265 100.000 1 2851 1 chr4B.!!$F1 2850
1 TraesCS4B01G271200 chr4D 441130974 441133804 2830 False 4335 4335 94.460 1 2811 1 chr4D.!!$F1 2810
2 TraesCS4B01G271200 chr4A 26412285 26414813 2528 True 3480 3480 91.906 145 2619 1 chr4A.!!$R2 2474

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
370 380 0.029035 ACGTACGCGGTGAGATGATC 59.971 55.0 16.72 0.0 43.45 2.92 F
943 971 0.462047 AACACCATCGATTCCGCCTC 60.462 55.0 0.00 0.0 35.37 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 1734 1.531365 CTGCCAGTTTGCTCCCCAA 60.531 57.895 0.0 0.0 0.0 4.12 R
2572 2671 2.882137 GTCCCGAAGAAAATGTTGACCA 59.118 45.455 0.0 0.0 0.0 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
32 33 5.070446 TCAGTCTGGAGTACTCAACAACAAT 59.930 40.000 23.91 0.99 0.00 2.71
60 64 1.073199 AACGGAAAGAGGGGCTGTG 59.927 57.895 0.00 0.00 0.00 3.66
93 97 0.249741 ACGGCACAAGGTCAGTACAC 60.250 55.000 0.00 0.00 0.00 2.90
106 115 3.631227 GTCAGTACACTAGAGGCCGTAAT 59.369 47.826 0.00 0.00 0.00 1.89
241 251 2.605338 GCGTAGTGTGAACGACTTGGTA 60.605 50.000 0.00 0.00 42.90 3.25
257 267 6.496338 ACTTGGTAAGCTCTTTAATTTCCG 57.504 37.500 0.00 0.00 0.00 4.30
335 345 3.188048 GCCAGATTGAGAATGATTAGGCG 59.812 47.826 0.00 0.00 0.00 5.52
370 380 0.029035 ACGTACGCGGTGAGATGATC 59.971 55.000 16.72 0.00 43.45 2.92
385 395 7.334056 TGAGATGATCAGCACGTACTTCGTT 62.334 44.000 14.38 0.00 41.18 3.85
499 509 1.071699 TGCTGCTAATCGGTTATCCCC 59.928 52.381 0.00 0.00 0.00 4.81
528 538 5.915758 CGAGAGAGACGACCATAATTTAAGG 59.084 44.000 0.00 0.00 0.00 2.69
547 557 1.202222 GGCATGCGAGTTCATTCCAAG 60.202 52.381 12.44 0.00 31.38 3.61
608 618 1.490693 CGATCGTCCAATTGGCTCCG 61.491 60.000 20.33 19.51 34.44 4.63
624 634 4.421479 CGTCTCAAGCCGGCGAGT 62.421 66.667 24.88 12.15 0.00 4.18
627 637 2.202756 CTCAAGCCGGCGAGTACC 60.203 66.667 23.20 0.00 0.00 3.34
701 728 4.557205 GTCAGGAGAGACGTACAAAATGT 58.443 43.478 0.00 0.00 0.00 2.71
867 894 3.509442 TGCCATTCCCTGACAAATTCTT 58.491 40.909 0.00 0.00 0.00 2.52
891 919 6.019748 TCTTCCCTGCTCCTCTTATATAAGG 58.980 44.000 19.98 8.19 34.14 2.69
903 931 5.597806 TCTTATATAAGGCACTCCACGTTG 58.402 41.667 19.98 0.00 38.49 4.10
925 953 3.255642 GTCTGCAAATCCACCAAGCTTAA 59.744 43.478 0.00 0.00 0.00 1.85
932 960 2.790433 TCCACCAAGCTTAACACCATC 58.210 47.619 0.00 0.00 0.00 3.51
943 971 0.462047 AACACCATCGATTCCGCCTC 60.462 55.000 0.00 0.00 35.37 4.70
1030 1061 0.943673 CATGTTGGCACTGTTCGTCA 59.056 50.000 0.00 0.00 0.00 4.35
1036 1067 1.621317 TGGCACTGTTCGTCATCCTAA 59.379 47.619 0.00 0.00 0.00 2.69
1038 1069 2.353803 GGCACTGTTCGTCATCCTAACT 60.354 50.000 0.00 0.00 0.00 2.24
1320 1351 1.455849 CACCAACTTCTGCCCTCCA 59.544 57.895 0.00 0.00 0.00 3.86
1464 1495 2.548707 CCAGCAGTAAGTGAAGAGTGCA 60.549 50.000 4.66 0.00 43.21 4.57
1466 1497 1.801178 GCAGTAAGTGAAGAGTGCACC 59.199 52.381 14.63 5.12 40.93 5.01
1471 1502 0.767375 AGTGAAGAGTGCACCCACAT 59.233 50.000 22.49 4.00 44.53 3.21
1472 1503 1.977854 AGTGAAGAGTGCACCCACATA 59.022 47.619 22.49 3.44 44.53 2.29
1473 1504 2.371841 AGTGAAGAGTGCACCCACATAA 59.628 45.455 22.49 1.37 44.53 1.90
1487 1519 5.182001 CACCCACATAACTTCTTCTTCCTTG 59.818 44.000 0.00 0.00 0.00 3.61
1490 1522 5.335191 CCACATAACTTCTTCTTCCTTGCAC 60.335 44.000 0.00 0.00 0.00 4.57
1492 1524 5.471456 ACATAACTTCTTCTTCCTTGCACTG 59.529 40.000 0.00 0.00 0.00 3.66
1495 1527 2.154854 TCTTCTTCCTTGCACTGTCG 57.845 50.000 0.00 0.00 0.00 4.35
1503 1537 5.416639 TCTTCCTTGCACTGTCGTATAAGTA 59.583 40.000 0.00 0.00 0.00 2.24
1510 1545 9.504710 CTTGCACTGTCGTATAAGTATATATCC 57.495 37.037 0.00 0.00 0.00 2.59
1691 1734 1.449353 GATCCAGCTGAGCCGGAAT 59.551 57.895 14.18 2.51 31.18 3.01
1862 1905 6.204882 AGTTCGGCTATTAATTAATCACCTGC 59.795 38.462 13.95 11.18 0.00 4.85
1904 1956 1.929806 CTACCTCGCACGTACTGCCA 61.930 60.000 10.44 0.00 43.84 4.92
1968 2022 0.872881 GGGATTGCGCGTGTACGTAT 60.873 55.000 8.43 0.00 42.22 3.06
1978 2032 3.302434 CGCGTGTACGTATCTTGATTTGT 59.698 43.478 0.00 0.00 42.22 2.83
1999 2053 3.126858 GTCTGCCATTTATTCGTCTGCAA 59.873 43.478 0.00 0.00 0.00 4.08
2344 2442 6.312180 CCACCAAAAATAAGTCTAGACGTACC 59.688 42.308 18.95 0.00 36.20 3.34
2427 2525 9.822727 AAAGATAAATCAAGGGGTAAAAGAGAA 57.177 29.630 0.00 0.00 0.00 2.87
2433 2532 9.559732 AAATCAAGGGGTAAAAGAGAATTTTTG 57.440 29.630 0.00 0.00 32.79 2.44
2467 2566 5.723672 TTACAGTCTAAGTTCAGTCCCTG 57.276 43.478 0.00 0.00 0.00 4.45
2490 2589 8.239998 CCTGAATCAATTCCAAAAGTTCTAGAC 58.760 37.037 0.00 0.00 35.97 2.59
2572 2671 4.796110 ATGGTTCATACAATGCCTACCT 57.204 40.909 0.00 0.00 31.54 3.08
2584 2684 3.237268 TGCCTACCTGGTCAACATTTT 57.763 42.857 0.63 0.00 38.35 1.82
2665 2765 7.890655 AGCAGATAATTAAAGAGGGAAGTTTGT 59.109 33.333 0.00 0.00 0.00 2.83
2667 2767 9.014297 CAGATAATTAAAGAGGGAAGTTTGTGT 57.986 33.333 0.00 0.00 0.00 3.72
2803 2903 7.847096 AGTTTGCATTAGGTAAAAATAAGGGG 58.153 34.615 0.00 0.00 32.72 4.79
2804 2904 7.676468 AGTTTGCATTAGGTAAAAATAAGGGGA 59.324 33.333 0.00 0.00 32.72 4.81
2805 2905 7.654022 TTGCATTAGGTAAAAATAAGGGGAG 57.346 36.000 0.00 0.00 0.00 4.30
2807 2907 7.186268 TGCATTAGGTAAAAATAAGGGGAGTT 58.814 34.615 0.00 0.00 0.00 3.01
2808 2908 8.337739 TGCATTAGGTAAAAATAAGGGGAGTTA 58.662 33.333 0.00 0.00 0.00 2.24
2809 2909 9.363401 GCATTAGGTAAAAATAAGGGGAGTTAT 57.637 33.333 0.00 0.00 0.00 1.89
2821 2921 8.838649 ATAAGGGGAGTTATAAAAATGCAAGT 57.161 30.769 0.00 0.00 0.00 3.16
2822 2922 9.930158 ATAAGGGGAGTTATAAAAATGCAAGTA 57.070 29.630 0.00 0.00 0.00 2.24
2823 2923 8.658840 AAGGGGAGTTATAAAAATGCAAGTAA 57.341 30.769 0.00 0.00 0.00 2.24
2824 2924 8.658840 AGGGGAGTTATAAAAATGCAAGTAAA 57.341 30.769 0.00 0.00 0.00 2.01
2825 2925 9.267071 AGGGGAGTTATAAAAATGCAAGTAAAT 57.733 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.824196 TGTTGTTATTGTTGTTGAGTACTCCA 59.176 34.615 20.11 6.48 0.00 3.86
32 33 3.628487 CCCTCTTTCCGTTGTTGTTGTTA 59.372 43.478 0.00 0.00 0.00 2.41
78 82 3.367498 GCCTCTAGTGTACTGACCTTGTG 60.367 52.174 0.00 0.00 0.00 3.33
93 97 1.289380 GCGGGATTACGGCCTCTAG 59.711 63.158 0.00 0.00 39.31 2.43
106 115 2.322081 GCAGTTAAGCGTTGCGGGA 61.322 57.895 0.00 0.00 0.00 5.14
241 251 6.569179 TGTTTAGCGGAAATTAAAGAGCTT 57.431 33.333 0.00 0.00 36.30 3.74
257 267 2.989422 AGTTGACGGCATTGTTTAGC 57.011 45.000 0.00 0.00 0.00 3.09
335 345 2.422276 ACGTACGTTGGTTGGTAGAC 57.578 50.000 16.72 0.00 0.00 2.59
385 395 2.508300 GCCCTGGAGGTGGATAAACTAA 59.492 50.000 0.00 0.00 38.26 2.24
499 509 1.235281 TGGTCGTCTCTCTCGTGTGG 61.235 60.000 0.00 0.00 0.00 4.17
528 538 1.739466 TCTTGGAATGAACTCGCATGC 59.261 47.619 7.91 7.91 0.00 4.06
547 557 5.341727 GCATACGCCGTTAAACTAGAGTATC 59.658 44.000 0.00 0.00 0.00 2.24
575 585 4.097437 TGGACGATCGACAGCTTAATAACT 59.903 41.667 24.34 0.00 0.00 2.24
577 587 4.642445 TGGACGATCGACAGCTTAATAA 57.358 40.909 24.34 0.00 0.00 1.40
580 590 3.520290 ATTGGACGATCGACAGCTTAA 57.480 42.857 24.34 7.41 0.00 1.85
608 618 1.516603 GTACTCGCCGGCTTGAGAC 60.517 63.158 30.61 21.22 36.11 3.36
627 637 3.364889 TGTTCCATAATCCGTAGCTCG 57.635 47.619 0.00 0.00 39.52 5.03
733 760 6.406042 CGCGTTAATTAAATTGGACGACTTAC 59.594 38.462 8.83 0.00 36.14 2.34
811 838 1.609072 GATCGATCGACATCCCAGTGA 59.391 52.381 22.06 0.00 0.00 3.41
867 894 6.019748 CCTTATATAAGAGGAGCAGGGAAGA 58.980 44.000 21.75 0.00 35.33 2.87
891 919 1.436195 TTGCAGACAACGTGGAGTGC 61.436 55.000 12.58 12.58 0.00 4.40
903 931 1.251251 AGCTTGGTGGATTTGCAGAC 58.749 50.000 0.00 0.00 0.00 3.51
925 953 1.144057 GAGGCGGAATCGATGGTGT 59.856 57.895 0.00 0.00 39.00 4.16
932 960 2.731374 GAGGGAGAGGCGGAATCG 59.269 66.667 0.00 0.00 39.81 3.34
943 971 2.627699 GAGCTACAAGAGATGGAGGGAG 59.372 54.545 0.00 0.00 40.71 4.30
1030 1061 4.547367 GCCGGCCGCAGTTAGGAT 62.547 66.667 22.85 0.00 37.47 3.24
1227 1258 1.552337 CAGGTGATGAGGTAGCACTGT 59.448 52.381 0.00 0.00 44.90 3.55
1265 1296 4.349503 TGCCGGGCTTGCACATCT 62.350 61.111 21.46 0.00 32.85 2.90
1464 1495 5.316987 CAAGGAAGAAGAAGTTATGTGGGT 58.683 41.667 0.00 0.00 0.00 4.51
1466 1497 4.761739 TGCAAGGAAGAAGAAGTTATGTGG 59.238 41.667 0.00 0.00 0.00 4.17
1471 1502 5.036117 ACAGTGCAAGGAAGAAGAAGTTA 57.964 39.130 0.00 0.00 0.00 2.24
1472 1503 3.879892 GACAGTGCAAGGAAGAAGAAGTT 59.120 43.478 0.00 0.00 0.00 2.66
1473 1504 3.471680 GACAGTGCAAGGAAGAAGAAGT 58.528 45.455 0.00 0.00 0.00 3.01
1503 1537 6.041423 TCACGACATGCTCATTGGATATAT 57.959 37.500 0.00 0.00 0.00 0.86
1510 1545 2.011947 ACCATCACGACATGCTCATTG 58.988 47.619 0.00 0.00 0.00 2.82
1691 1734 1.531365 CTGCCAGTTTGCTCCCCAA 60.531 57.895 0.00 0.00 0.00 4.12
1968 2022 6.150976 ACGAATAAATGGCAGACAAATCAAGA 59.849 34.615 0.00 0.00 0.00 3.02
1978 2032 2.984562 TGCAGACGAATAAATGGCAGA 58.015 42.857 0.00 0.00 0.00 4.26
1999 2053 6.120905 CCCAACTTCAGATCAGAATTCAGAT 58.879 40.000 12.70 12.70 0.00 2.90
2192 2272 8.934023 AGGTATAGTATCCTTCTTCTTCAGAG 57.066 38.462 0.00 0.00 31.12 3.35
2211 2291 6.987403 TCAGTAACATGCATGGTAGGTATA 57.013 37.500 29.41 4.99 29.10 1.47
2212 2292 5.887214 TCAGTAACATGCATGGTAGGTAT 57.113 39.130 29.41 11.55 29.10 2.73
2272 2364 4.877823 TGTTCATCTCACAGGATAATGCAC 59.122 41.667 0.00 0.00 0.00 4.57
2317 2413 5.699458 ACGTCTAGACTTATTTTTGGTGGTG 59.301 40.000 20.34 1.97 0.00 4.17
2344 2442 5.611374 TCTGGAGTAAAGTTGAAGTTGAGG 58.389 41.667 0.00 0.00 0.00 3.86
2467 2566 7.394641 AGGGTCTAGAACTTTTGGAATTGATTC 59.605 37.037 7.92 0.00 36.08 2.52
2490 2589 4.036734 CCATTTGTTATCGACAATGGAGGG 59.963 45.833 13.21 0.00 46.99 4.30
2572 2671 2.882137 GTCCCGAAGAAAATGTTGACCA 59.118 45.455 0.00 0.00 0.00 4.02
2584 2684 3.835978 TCAGAAATTACCAGTCCCGAAGA 59.164 43.478 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.