Multiple sequence alignment - TraesCS5B01G243800

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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 TraesCS5B01G243800 chr5B 100.000 2894 0 0 1 2894 425092605 425095498 0.000000e+00 5345.0
1 TraesCS5B01G243800 chr5D 94.347 2459 82 22 456 2894 359474267 359476688 0.000000e+00 3718.0
2 TraesCS5B01G243800 chr5D 89.956 458 23 7 1 450 359473659 359474101 1.160000e-158 569.0
3 TraesCS5B01G243800 chr5A 89.151 3014 123 86 1 2894 459777356 459774427 0.000000e+00 3567.0
4 TraesCS5B01G243800 chr6B 81.250 208 28 9 1664 1864 539195275 539195072 1.070000e-34 158.0
5 TraesCS5B01G243800 chr6D 82.065 184 24 7 1686 1864 357592095 357591916 6.460000e-32 148.0
6 TraesCS5B01G243800 chr6A 81.579 190 26 7 1680 1864 499955472 499955657 6.460000e-32 148.0
7 TraesCS5B01G243800 chr1B 78.788 132 22 4 1736 1864 185184929 185184801 1.850000e-12 84.2
8 TraesCS5B01G243800 chr2D 80.508 118 14 6 1763 1877 578306522 578306633 6.650000e-12 82.4


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 TraesCS5B01G243800 chr5B 425092605 425095498 2893 False 5345.0 5345 100.0000 1 2894 1 chr5B.!!$F1 2893
1 TraesCS5B01G243800 chr5D 359473659 359476688 3029 False 2143.5 3718 92.1515 1 2894 2 chr5D.!!$F1 2893
2 TraesCS5B01G243800 chr5A 459774427 459777356 2929 True 3567.0 3567 89.1510 1 2894 1 chr5A.!!$R1 2893

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
163 190 0.453793 CATCCTCGACGTCTTCTGCT 59.546 55.000 14.7 0.0 0.0 4.24 F
242 277 1.000717 GGGTTTTGTATGCTTGCGTGT 60.001 47.619 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1212 1450 2.034879 CGCGTGGTTCTTGAGGCAT 61.035 57.895 0.0 0.0 0.0 4.40 R
2217 2487 2.316119 AGAACGAAATCAGCAAACGC 57.684 45.000 0.0 0.0 0.0 4.84 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
38 39 1.813753 ATTTCGCCATGGACGGACG 60.814 57.895 18.40 9.35 0.00 4.79
75 76 3.067833 GTCCTGCTTCAGTACTTGGTTC 58.932 50.000 0.00 0.00 0.00 3.62
102 119 5.767670 TGGAGCTAGTTTATGGTAGTCTCT 58.232 41.667 0.00 0.00 0.00 3.10
156 183 0.864797 GCGTTACCATCCTCGACGTC 60.865 60.000 5.18 5.18 36.22 4.34
161 188 0.811915 ACCATCCTCGACGTCTTCTG 59.188 55.000 14.70 4.00 0.00 3.02
163 190 0.453793 CATCCTCGACGTCTTCTGCT 59.546 55.000 14.70 0.00 0.00 4.24
242 277 1.000717 GGGTTTTGTATGCTTGCGTGT 60.001 47.619 0.00 0.00 0.00 4.49
312 347 1.208052 CTTCGATGCTCTGGGGAAAGA 59.792 52.381 0.00 0.00 0.00 2.52
367 405 4.337274 CGGAAAACAGTTTTGGGTTAGAGT 59.663 41.667 16.21 0.00 31.94 3.24
390 428 2.346099 TAAATTTGCTTGACGCTGCC 57.654 45.000 0.00 0.00 40.11 4.85
393 431 4.617520 TTGCTTGACGCTGCCGGA 62.618 61.111 5.05 0.00 40.11 5.14
395 433 4.742201 GCTTGACGCTGCCGGAGA 62.742 66.667 5.05 0.00 39.22 3.71
396 434 2.507992 CTTGACGCTGCCGGAGAG 60.508 66.667 5.05 4.19 39.22 3.20
397 435 3.997064 CTTGACGCTGCCGGAGAGG 62.997 68.421 5.05 0.00 44.97 3.69
406 444 2.765807 CCGGAGAGGCCTGTCCAT 60.766 66.667 39.65 10.01 42.66 3.41
407 445 2.503061 CGGAGAGGCCTGTCCATG 59.497 66.667 39.65 25.33 42.66 3.66
450 652 6.247676 TCATGAATTTCATTTCACCTCCTGA 58.752 36.000 9.19 0.00 38.37 3.86
451 653 6.720748 TCATGAATTTCATTTCACCTCCTGAA 59.279 34.615 9.19 0.00 38.37 3.02
487 689 2.033299 CGGGATAATGTGTTGACCATGC 59.967 50.000 0.00 0.00 0.00 4.06
503 709 3.954904 ACCATGCTCTAGACACGAGTAAT 59.045 43.478 0.00 0.00 0.00 1.89
506 712 6.146216 CCATGCTCTAGACACGAGTAATAAG 58.854 44.000 0.00 0.00 0.00 1.73
508 714 6.997239 TGCTCTAGACACGAGTAATAAGAA 57.003 37.500 0.00 0.00 0.00 2.52
533 739 5.380043 AGAAAAGAGATGCAAAGACCAGAA 58.620 37.500 0.00 0.00 0.00 3.02
551 757 5.520288 ACCAGAAGTCACGATCAAATATTCG 59.480 40.000 0.00 0.00 41.04 3.34
556 766 5.661458 AGTCACGATCAAATATTCGGAACT 58.339 37.500 0.00 0.49 39.61 3.01
587 797 1.976474 GCATTGGAGCCAAACCGGA 60.976 57.895 9.46 0.00 39.55 5.14
722 939 2.126812 AAGTGCGCGACTCGAGAC 60.127 61.111 21.68 12.76 41.67 3.36
1083 1318 1.754621 CTCCAGCTACGAGCCTCCA 60.755 63.158 0.00 0.00 43.77 3.86
1089 1324 4.753662 TACGAGCCTCCACCGCCT 62.754 66.667 0.00 0.00 0.00 5.52
1092 1327 4.154347 GAGCCTCCACCGCCTCTG 62.154 72.222 0.00 0.00 0.00 3.35
1161 1399 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
1212 1450 4.382320 GGTGCCAGGTACCGCGAA 62.382 66.667 11.53 0.00 0.00 4.70
1395 1633 3.077556 GGCTCGCCCTTCTCTCCA 61.078 66.667 0.00 0.00 0.00 3.86
2027 2286 2.616510 GGTACCTGCATGTGCTTCTCTT 60.617 50.000 4.06 0.00 42.66 2.85
2217 2487 4.488136 TAGCTGTGGCGCCATGGG 62.488 66.667 35.23 24.78 44.37 4.00
2280 2550 1.743321 GATCAGCTAGCTGGCGAGGT 61.743 60.000 37.60 19.96 43.75 3.85
2341 2611 1.801913 CGTGCGTGCTCCTGAGTAC 60.802 63.158 5.43 5.43 40.08 2.73
2342 2612 1.587054 GTGCGTGCTCCTGAGTACT 59.413 57.895 12.51 0.00 41.09 2.73
2343 2613 0.456995 GTGCGTGCTCCTGAGTACTC 60.457 60.000 16.32 16.32 41.09 2.59
2344 2614 1.139947 GCGTGCTCCTGAGTACTCC 59.860 63.158 20.11 4.85 41.09 3.85
2392 2669 2.889503 CTAGCTGAGCTGCGTGCC 60.890 66.667 18.79 0.00 44.23 5.01
2435 2712 2.108168 TCCAGGTTTGCTAGTCGCTAT 58.892 47.619 0.00 0.00 40.11 2.97
2437 2714 2.866762 CCAGGTTTGCTAGTCGCTATTC 59.133 50.000 0.00 0.00 40.11 1.75
2438 2715 2.866762 CAGGTTTGCTAGTCGCTATTCC 59.133 50.000 0.00 0.00 40.11 3.01
2501 2778 2.053627 GTTGCATTCCGTTCTTTGCTG 58.946 47.619 0.00 0.00 36.10 4.41
2505 2782 1.808945 CATTCCGTTCTTTGCTGAGCT 59.191 47.619 5.83 0.00 0.00 4.09
2518 2798 1.212935 GCTGAGCTATTTTCCTCCCCA 59.787 52.381 0.00 0.00 0.00 4.96
2595 2883 0.107456 CGTCCCCTCCATTGATCCAG 59.893 60.000 0.00 0.00 0.00 3.86
2597 2885 0.698886 TCCCCTCCATTGATCCAGGG 60.699 60.000 0.00 0.00 44.92 4.45
2602 2890 4.729552 CCTCCATTGATCCAGGGATAAA 57.270 45.455 0.02 0.14 34.60 1.40
2660 2948 0.394192 AGCAGAACTGTAGCAGCACA 59.606 50.000 0.00 0.00 34.37 4.57
2724 3012 0.939419 TCTCGCCATGAATCAATGCG 59.061 50.000 19.19 19.19 0.00 4.73
2762 3050 1.822186 CCCCCGCATTTAACTCCCG 60.822 63.158 0.00 0.00 0.00 5.14
2869 3166 1.144716 CTCGCTTCTGCCCTGCATA 59.855 57.895 0.00 0.00 38.13 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 119 0.108804 CTCGCTCGGCTTCAGGTTTA 60.109 55.000 0.00 0.00 0.00 2.01
138 162 0.731417 AGACGTCGAGGATGGTAACG 59.269 55.000 12.85 0.00 42.51 3.18
156 183 2.792890 CGTCGACCATGTAGAGCAGAAG 60.793 54.545 10.58 0.00 0.00 2.85
161 188 0.248539 GTCCGTCGACCATGTAGAGC 60.249 60.000 10.58 0.00 32.40 4.09
163 190 1.371337 CCGTCCGTCGACCATGTAGA 61.371 60.000 10.58 0.00 42.86 2.59
242 277 5.949952 TGATTAAGTAGTAGTCTCTGCACCA 59.050 40.000 0.00 0.00 0.00 4.17
312 347 2.753452 TGTAAGCAACGCTAGAGCTAGT 59.247 45.455 6.41 0.00 38.25 2.57
331 369 0.682852 TTTTCCGGGTCGAGTGATGT 59.317 50.000 0.00 0.00 0.00 3.06
390 428 2.503061 CATGGACAGGCCTCTCCG 59.497 66.667 20.88 5.15 40.77 4.63
393 431 0.987081 AGATGCATGGACAGGCCTCT 60.987 55.000 2.46 10.22 38.05 3.69
394 432 0.761187 TAGATGCATGGACAGGCCTC 59.239 55.000 2.46 6.33 37.30 4.70
395 433 0.763652 CTAGATGCATGGACAGGCCT 59.236 55.000 2.46 0.00 37.30 5.19
396 434 0.888285 GCTAGATGCATGGACAGGCC 60.888 60.000 2.46 0.00 42.31 5.19
397 435 1.226686 CGCTAGATGCATGGACAGGC 61.227 60.000 2.46 1.48 43.06 4.85
398 436 0.602106 CCGCTAGATGCATGGACAGG 60.602 60.000 2.46 0.00 43.06 4.00
399 437 1.226686 GCCGCTAGATGCATGGACAG 61.227 60.000 2.46 0.00 43.06 3.51
400 438 1.227645 GCCGCTAGATGCATGGACA 60.228 57.895 2.46 0.00 43.06 4.02
401 439 0.604780 ATGCCGCTAGATGCATGGAC 60.605 55.000 15.98 0.00 45.96 4.02
402 440 1.756665 ATGCCGCTAGATGCATGGA 59.243 52.632 15.98 0.00 45.96 3.41
403 441 4.391869 ATGCCGCTAGATGCATGG 57.608 55.556 15.98 0.00 45.96 3.66
406 444 2.592574 GCCATGCCGCTAGATGCA 60.593 61.111 8.78 8.78 43.06 3.96
407 445 3.360340 GGCCATGCCGCTAGATGC 61.360 66.667 0.00 0.00 39.62 3.91
452 654 5.010617 ACATTATCCCGCTTCTTGTGTTTTT 59.989 36.000 0.00 0.00 0.00 1.94
453 655 4.522789 ACATTATCCCGCTTCTTGTGTTTT 59.477 37.500 0.00 0.00 0.00 2.43
454 656 4.079253 ACATTATCCCGCTTCTTGTGTTT 58.921 39.130 0.00 0.00 0.00 2.83
472 674 4.256920 GTCTAGAGCATGGTCAACACATT 58.743 43.478 25.71 6.73 0.00 2.71
473 675 3.261643 TGTCTAGAGCATGGTCAACACAT 59.738 43.478 25.71 7.44 0.00 3.21
503 709 8.352942 GGTCTTTGCATCTCTTTTCTTTTCTTA 58.647 33.333 0.00 0.00 0.00 2.10
506 712 6.507023 TGGTCTTTGCATCTCTTTTCTTTTC 58.493 36.000 0.00 0.00 0.00 2.29
508 714 5.829924 TCTGGTCTTTGCATCTCTTTTCTTT 59.170 36.000 0.00 0.00 0.00 2.52
533 739 5.661458 AGTTCCGAATATTTGATCGTGACT 58.339 37.500 4.10 0.37 37.36 3.41
551 757 6.726258 CAATGCCTTTTAAATTGGAGTTCC 57.274 37.500 10.76 0.00 0.00 3.62
669 882 0.902048 CCTCTCTCTCCCTGTGTGCA 60.902 60.000 0.00 0.00 0.00 4.57
670 883 0.613292 TCCTCTCTCTCCCTGTGTGC 60.613 60.000 0.00 0.00 0.00 4.57
722 939 3.649277 CTCCTGTTCACCGCCTCCG 62.649 68.421 0.00 0.00 0.00 4.63
944 1174 4.337060 GGGTTTGCCGGCGTGTTC 62.337 66.667 23.90 9.97 34.97 3.18
1080 1315 3.311110 GTGGACAGAGGCGGTGGA 61.311 66.667 0.00 0.00 0.00 4.02
1089 1324 2.833227 CCAAACCCCGTGGACAGA 59.167 61.111 0.00 0.00 38.54 3.41
1212 1450 2.034879 CGCGTGGTTCTTGAGGCAT 61.035 57.895 0.00 0.00 0.00 4.40
1234 1472 3.537874 GGCGTGCCCTCCGATACT 61.538 66.667 0.00 0.00 0.00 2.12
1581 1822 3.071206 ATGCCCGACAGCTCGTCT 61.071 61.111 12.45 0.00 42.98 4.18
1928 2169 4.152625 GCCAGACGCATCGTGCAC 62.153 66.667 6.82 6.82 45.36 4.57
2027 2286 4.984785 CGAATGCTATAGCTAAGCTGAACA 59.015 41.667 24.61 1.44 40.10 3.18
2217 2487 2.316119 AGAACGAAATCAGCAAACGC 57.684 45.000 0.00 0.00 0.00 4.84
2219 2489 3.423206 CAGCAAGAACGAAATCAGCAAAC 59.577 43.478 0.00 0.00 0.00 2.93
2280 2550 2.546899 CCCCGATCCCCAGATACAATA 58.453 52.381 0.00 0.00 30.90 1.90
2392 2669 4.772100 ACCCATCAGTAAAATTGTCCCAAG 59.228 41.667 0.00 0.00 0.00 3.61
2409 2686 1.282157 ACTAGCAAACCTGGACCCATC 59.718 52.381 0.00 0.00 0.00 3.51
2501 2778 1.847088 AGGTGGGGAGGAAAATAGCTC 59.153 52.381 0.00 0.00 0.00 4.09
2505 2782 2.844348 GAGTGAGGTGGGGAGGAAAATA 59.156 50.000 0.00 0.00 0.00 1.40
2518 2798 0.773644 ATGCCCAAAGTGAGTGAGGT 59.226 50.000 0.00 0.00 0.00 3.85
2617 2905 3.797225 GATCATCGCGCTGGGCAGA 62.797 63.158 17.13 14.18 43.84 4.26
2629 2917 2.290916 CAGTTCTGCTGCATGGATCATC 59.709 50.000 1.31 0.00 38.52 2.92
2660 2948 1.188219 AGTGGAGCACGTCATGGAGT 61.188 55.000 0.00 0.00 39.64 3.85
2834 3131 2.671396 GCGAGTAAAATCGGCAGAAAGA 59.329 45.455 1.81 0.00 42.94 2.52
2846 3143 1.808411 CAGGGCAGAAGCGAGTAAAA 58.192 50.000 0.00 0.00 43.41 1.52
2869 3166 2.497138 CGGGAGTAAAAACGGAAAGGT 58.503 47.619 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.