Multiple sequence alignment - TraesCS5D01G252300

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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 TraesCS5D01G252300 chr5D 100.000 2707 0 0 1 2707 358009268 358011974 0.000000e+00 5000.0
1 TraesCS5D01G252300 chr5B 92.714 1798 98 17 938 2707 423225195 423226987 0.000000e+00 2564.0
2 TraesCS5D01G252300 chr5B 88.621 457 17 16 1 427 423216258 423216709 8.590000e-145 523.0
3 TraesCS5D01G252300 chr5B 88.462 442 9 6 506 943 423224541 423224944 1.870000e-136 496.0
4 TraesCS5D01G252300 chr5B 100.000 29 0 0 474 502 423216730 423216758 1.000000e-03 54.7
5 TraesCS5D01G252300 chr5A 88.267 1662 84 45 497 2101 458966301 458967908 0.000000e+00 1886.0
6 TraesCS5D01G252300 chr5A 93.002 543 35 3 2168 2707 458968003 458968545 0.000000e+00 789.0
7 TraesCS5D01G252300 chr5A 87.347 245 9 7 1 245 458965907 458966129 7.430000e-66 261.0
8 TraesCS5D01G252300 chr5A 98.246 57 1 0 374 430 458966225 458966281 1.720000e-17 100.0
9 TraesCS5D01G252300 chr7A 85.714 266 26 3 1278 1543 12963649 12963396 1.240000e-68 270.0
10 TraesCS5D01G252300 chr7A 85.338 266 27 5 1278 1543 675516159 675515906 5.750000e-67 265.0
11 TraesCS5D01G252300 chr7A 95.918 98 4 0 1095 1192 12963742 12963645 2.790000e-35 159.0
12 TraesCS5D01G252300 chr7A 92.857 98 7 0 1095 1192 675516252 675516155 2.810000e-30 143.0
13 TraesCS5D01G252300 chr6B 84.586 266 29 1 1278 1543 89687123 89686870 1.240000e-63 254.0
14 TraesCS5D01G252300 chr6B 90.816 98 9 0 1095 1192 89687216 89687119 6.080000e-27 132.0
15 TraesCS5D01G252300 chr3A 87.560 209 14 1 1335 1543 187383796 187383600 5.830000e-57 231.0
16 TraesCS5D01G252300 chr3A 92.857 98 7 0 1095 1192 187385471 187385374 2.810000e-30 143.0
17 TraesCS5D01G252300 chr7B 82.576 264 34 1 1278 1541 65911252 65911001 3.510000e-54 222.0
18 TraesCS5D01G252300 chr2A 78.886 341 38 15 1250 1559 713936130 713935793 1.640000e-47 200.0
19 TraesCS5D01G252300 chr2A 91.304 92 8 0 1095 1186 713936335 713936244 2.830000e-25 126.0
20 TraesCS5D01G252300 chr2D 91.304 92 8 0 1095 1186 575770561 575770470 2.830000e-25 126.0
21 TraesCS5D01G252300 chr2B 91.304 92 8 0 1095 1186 691810730 691810639 2.830000e-25 126.0


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 TraesCS5D01G252300 chr5D 358009268 358011974 2706 False 5000.00 5000 100.0000 1 2707 1 chr5D.!!$F1 2706
1 TraesCS5D01G252300 chr5B 423224541 423226987 2446 False 1530.00 2564 90.5880 506 2707 2 chr5B.!!$F2 2201
2 TraesCS5D01G252300 chr5B 423216258 423216758 500 False 288.85 523 94.3105 1 502 2 chr5B.!!$F1 501
3 TraesCS5D01G252300 chr5A 458965907 458968545 2638 False 759.00 1886 91.7155 1 2707 4 chr5A.!!$F1 2706

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
443 500 0.031585 GACACGCAGTATATCCCGCA 59.968 55.0 0.0 0.0 41.61 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 2099 0.664166 GTGAAGCAAACATGGTGGCG 60.664 55.0 3.97 0.0 0.0 5.69 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
124 125 2.260434 CGATGAACCCGACGGTGT 59.740 61.111 13.94 7.67 43.71 4.16
195 196 0.959553 GAGAACCACGAGTCCTCACA 59.040 55.000 0.00 0.00 0.00 3.58
283 291 1.300266 TTGTAACCTAAAGCGGCGGC 61.300 55.000 9.78 8.43 40.37 6.53
342 387 0.249073 CATCATCTGTCCGTCCGTCC 60.249 60.000 0.00 0.00 0.00 4.79
344 389 3.138798 ATCTGTCCGTCCGTCCCG 61.139 66.667 0.00 0.00 0.00 5.14
345 390 3.933048 ATCTGTCCGTCCGTCCCGT 62.933 63.158 0.00 0.00 0.00 5.28
357 414 1.971695 GTCCCGTCCCTTTTGCTGG 60.972 63.158 0.00 0.00 0.00 4.85
358 415 2.150719 TCCCGTCCCTTTTGCTGGA 61.151 57.895 0.00 0.00 0.00 3.86
359 416 1.971695 CCCGTCCCTTTTGCTGGAC 60.972 63.158 0.00 0.00 46.15 4.02
361 418 4.475527 GTCCCTTTTGCTGGACGT 57.524 55.556 0.00 0.00 41.48 4.34
362 419 2.715536 GTCCCTTTTGCTGGACGTT 58.284 52.632 0.00 0.00 41.48 3.99
363 420 1.029681 GTCCCTTTTGCTGGACGTTT 58.970 50.000 0.00 0.00 41.48 3.60
364 421 1.407618 GTCCCTTTTGCTGGACGTTTT 59.592 47.619 0.00 0.00 41.48 2.43
365 422 2.104170 TCCCTTTTGCTGGACGTTTTT 58.896 42.857 0.00 0.00 0.00 1.94
366 423 3.067040 GTCCCTTTTGCTGGACGTTTTTA 59.933 43.478 0.00 0.00 41.48 1.52
367 424 3.067040 TCCCTTTTGCTGGACGTTTTTAC 59.933 43.478 0.00 0.00 0.00 2.01
368 425 3.377439 CCTTTTGCTGGACGTTTTTACC 58.623 45.455 0.00 0.00 0.00 2.85
369 426 2.759538 TTTGCTGGACGTTTTTACCG 57.240 45.000 0.00 0.00 0.00 4.02
370 427 0.945813 TTGCTGGACGTTTTTACCGG 59.054 50.000 0.00 0.00 0.00 5.28
371 428 0.885596 TGCTGGACGTTTTTACCGGG 60.886 55.000 6.32 0.00 0.00 5.73
372 429 0.603439 GCTGGACGTTTTTACCGGGA 60.603 55.000 6.32 0.00 0.00 5.14
430 487 4.077184 TGTCCATCCCCGACACGC 62.077 66.667 0.00 0.00 35.35 5.34
432 489 3.770040 TCCATCCCCGACACGCAG 61.770 66.667 0.00 0.00 0.00 5.18
434 491 2.717044 CCATCCCCGACACGCAGTA 61.717 63.158 0.00 0.00 41.61 2.74
435 492 1.441729 CATCCCCGACACGCAGTAT 59.558 57.895 0.00 0.00 41.61 2.12
437 494 1.272490 CATCCCCGACACGCAGTATAT 59.728 52.381 0.00 0.00 41.61 0.86
438 495 0.956633 TCCCCGACACGCAGTATATC 59.043 55.000 0.00 0.00 41.61 1.63
439 496 0.038526 CCCCGACACGCAGTATATCC 60.039 60.000 0.00 0.00 41.61 2.59
440 497 0.038526 CCCGACACGCAGTATATCCC 60.039 60.000 0.00 0.00 41.61 3.85
441 498 0.386858 CCGACACGCAGTATATCCCG 60.387 60.000 0.00 0.00 41.61 5.14
442 499 1.002250 CGACACGCAGTATATCCCGC 61.002 60.000 0.00 0.00 41.61 6.13
443 500 0.031585 GACACGCAGTATATCCCGCA 59.968 55.000 0.00 0.00 41.61 5.69
444 501 0.032130 ACACGCAGTATATCCCGCAG 59.968 55.000 0.00 0.00 41.61 5.18
470 527 3.799755 GGCCAATCGGTCACGCAC 61.800 66.667 0.00 0.00 36.65 5.34
471 528 3.047280 GCCAATCGGTCACGCACA 61.047 61.111 0.00 0.00 40.69 4.57
472 529 2.612567 GCCAATCGGTCACGCACAA 61.613 57.895 0.00 0.00 40.69 3.33
728 808 2.092291 GCCGCTGTCGTTTGATCGA 61.092 57.895 0.00 0.00 37.51 3.59
729 809 1.421410 GCCGCTGTCGTTTGATCGAT 61.421 55.000 0.00 0.00 41.78 3.59
730 810 0.572590 CCGCTGTCGTTTGATCGATC 59.427 55.000 18.72 18.72 41.78 3.69
731 811 0.224746 CGCTGTCGTTTGATCGATCG 59.775 55.000 20.03 9.36 41.78 3.69
758 838 5.451662 CGTTCGTTCGTTTTCAATTTTACCA 59.548 36.000 0.00 0.00 0.00 3.25
761 841 4.441744 CGTTCGTTTTCAATTTTACCACCC 59.558 41.667 0.00 0.00 0.00 4.61
792 872 3.445687 GGGGGTAAAAAGGCGCCG 61.446 66.667 23.20 0.00 0.00 6.46
794 874 2.404186 GGGGTAAAAAGGCGCCGAG 61.404 63.158 23.20 0.00 0.00 4.63
798 878 0.672711 GTAAAAAGGCGCCGAGGAGT 60.673 55.000 23.20 8.23 0.00 3.85
843 928 4.012895 CGCGGACGCAGCTTTTGT 62.013 61.111 17.35 0.00 42.06 2.83
844 929 2.427410 GCGGACGCAGCTTTTGTG 60.427 61.111 12.31 0.00 43.06 3.33
845 930 2.427410 CGGACGCAGCTTTTGTGC 60.427 61.111 0.00 0.00 41.06 4.57
846 931 2.050077 GGACGCAGCTTTTGTGCC 60.050 61.111 0.00 0.00 41.06 5.01
847 932 2.427410 GACGCAGCTTTTGTGCCG 60.427 61.111 0.00 0.00 41.06 5.69
848 933 4.629115 ACGCAGCTTTTGTGCCGC 62.629 61.111 0.00 0.00 41.06 6.53
1211 1561 1.804372 GCTACTTCCCATGCTCGTCAG 60.804 57.143 0.00 0.00 0.00 3.51
1220 1570 2.389059 CATGCTCGTCAGAGTTATCGG 58.611 52.381 0.00 0.00 46.03 4.18
1222 1572 2.635714 TGCTCGTCAGAGTTATCGGTA 58.364 47.619 0.00 0.00 46.03 4.02
1223 1573 2.612672 TGCTCGTCAGAGTTATCGGTAG 59.387 50.000 0.00 0.00 46.03 3.18
1225 1575 1.945394 TCGTCAGAGTTATCGGTAGGC 59.055 52.381 0.00 0.00 0.00 3.93
1725 2099 0.649475 GTGACACGATGATGCTCTGC 59.351 55.000 0.00 0.00 0.00 4.26
1730 2104 2.879070 CGATGATGCTCTGCGCCAC 61.879 63.158 4.18 0.00 38.05 5.01
1738 2112 1.210931 CTCTGCGCCACCATGTTTG 59.789 57.895 4.18 0.00 0.00 2.93
1739 2113 2.431260 CTGCGCCACCATGTTTGC 60.431 61.111 4.18 0.00 0.00 3.68
1778 2152 6.437755 TCAACCTGTAGGATTAGTAGGCTTA 58.562 40.000 4.64 0.00 38.94 3.09
1780 2154 8.229605 TCAACCTGTAGGATTAGTAGGCTTATA 58.770 37.037 4.64 0.00 38.94 0.98
1782 2156 8.653036 ACCTGTAGGATTAGTAGGCTTATAAG 57.347 38.462 8.20 8.20 38.94 1.73
1844 2221 2.353406 GCTGGCTTTGCAATCACTGAAT 60.353 45.455 0.00 0.00 0.00 2.57
1875 2255 2.485426 CAGGTTCTGTAATGGCAGTGTG 59.515 50.000 0.00 0.00 37.70 3.82
2069 2452 3.126000 GCAGTACAGAGTCATGAAAAGGC 59.874 47.826 0.00 0.00 0.00 4.35
2111 2494 5.839063 TCAGATAACAGAAACCTCCCGATAT 59.161 40.000 0.00 0.00 0.00 1.63
2152 2535 7.445121 TGGAGATGAGCTACTACAATATTTGG 58.555 38.462 0.00 0.00 34.12 3.28
2161 2544 9.726438 AGCTACTACAATATTTGGGATGTTATC 57.274 33.333 0.00 0.00 34.12 1.75
2234 2661 3.120234 TGCTTATTTGAGTCACACATGCG 60.120 43.478 0.00 0.00 0.00 4.73
2330 2759 5.880054 ATACAGATGTTACAACACAAGGC 57.120 39.130 0.00 0.00 42.51 4.35
2363 2793 2.430956 GCAGCATTACACATCGTTTCG 58.569 47.619 0.00 0.00 0.00 3.46
2397 2827 0.675522 TGCAGTTTTACTAGCCGCCC 60.676 55.000 0.00 0.00 0.00 6.13
2465 2895 0.759959 TTGTCCCGGCAGTTTACAGA 59.240 50.000 0.00 0.00 0.00 3.41
2475 2905 5.333875 CCGGCAGTTTACAGACTTTACTTTC 60.334 44.000 0.00 0.00 0.00 2.62
2579 3009 5.656206 TACCACCTGGAGCAAGTTGCAAT 62.656 47.826 28.65 10.08 41.81 3.56
2654 3084 7.489757 GCAGAGTGAACTTTACCAGAGTATAAG 59.510 40.741 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 179 0.674534 ACTGTGAGGACTCGTGGTTC 59.325 55.000 0.00 0.00 0.00 3.62
324 332 1.392710 GGGACGGACGGACAGATGAT 61.393 60.000 0.00 0.00 0.00 2.45
342 387 3.668386 GTCCAGCAAAAGGGACGG 58.332 61.111 0.00 0.00 43.67 4.79
345 390 1.770294 AAAACGTCCAGCAAAAGGGA 58.230 45.000 0.00 0.00 0.00 4.20
347 392 3.377439 GGTAAAAACGTCCAGCAAAAGG 58.623 45.455 0.00 0.00 0.00 3.11
348 393 3.040099 CGGTAAAAACGTCCAGCAAAAG 58.960 45.455 0.00 0.00 0.00 2.27
441 498 3.721370 ATTGGCCGATGGACCCTGC 62.721 63.158 4.07 0.00 0.00 4.85
442 499 1.526917 GATTGGCCGATGGACCCTG 60.527 63.158 11.28 0.00 0.00 4.45
443 500 2.919043 GATTGGCCGATGGACCCT 59.081 61.111 11.28 0.00 0.00 4.34
444 501 2.591715 CGATTGGCCGATGGACCC 60.592 66.667 11.28 0.00 0.00 4.46
446 503 1.887707 GACCGATTGGCCGATGGAC 60.888 63.158 21.72 14.72 39.70 4.02
447 504 2.363172 TGACCGATTGGCCGATGGA 61.363 57.895 21.72 0.55 39.70 3.41
448 505 2.180204 GTGACCGATTGGCCGATGG 61.180 63.158 11.28 14.35 39.70 3.51
449 506 2.525248 CGTGACCGATTGGCCGATG 61.525 63.158 11.28 0.00 39.70 3.84
450 507 2.202878 CGTGACCGATTGGCCGAT 60.203 61.111 4.69 4.69 39.70 4.18
455 512 1.206578 GTTGTGCGTGACCGATTGG 59.793 57.895 0.00 0.00 42.84 3.16
468 525 3.976306 CAGTACATGTGCATTGTGTTGTG 59.024 43.478 16.62 0.00 0.00 3.33
469 526 3.004629 CCAGTACATGTGCATTGTGTTGT 59.995 43.478 16.62 4.12 0.00 3.32
470 527 3.567530 CCAGTACATGTGCATTGTGTTG 58.432 45.455 16.62 3.63 0.00 3.33
471 528 2.030007 GCCAGTACATGTGCATTGTGTT 60.030 45.455 16.62 0.00 0.00 3.32
472 529 1.541147 GCCAGTACATGTGCATTGTGT 59.459 47.619 16.62 10.22 0.00 3.72
593 663 0.997196 GCGTGGTAATTCTGTCCGAC 59.003 55.000 0.00 0.00 0.00 4.79
596 666 0.719465 CGTGCGTGGTAATTCTGTCC 59.281 55.000 0.00 0.00 0.00 4.02
645 724 3.006940 GCAACTATTTGTGATGGACGGA 58.993 45.455 0.00 0.00 34.90 4.69
728 808 1.123756 GAAAACGAACGAACGAGCGAT 59.876 47.619 16.11 5.77 37.03 4.58
729 809 0.499761 GAAAACGAACGAACGAGCGA 59.500 50.000 16.11 0.00 37.03 4.93
730 810 0.227735 TGAAAACGAACGAACGAGCG 59.772 50.000 11.97 6.58 37.03 5.03
731 811 2.356386 TTGAAAACGAACGAACGAGC 57.644 45.000 11.97 0.00 37.03 5.03
758 838 0.324460 CCCCGTGTTAGAGAGAGGGT 60.324 60.000 0.00 0.00 37.21 4.34
781 861 0.035739 TAACTCCTCGGCGCCTTTTT 59.964 50.000 26.68 10.98 0.00 1.94
790 870 0.108138 CCTTGCCACTAACTCCTCGG 60.108 60.000 0.00 0.00 0.00 4.63
792 872 1.623811 TGACCTTGCCACTAACTCCTC 59.376 52.381 0.00 0.00 0.00 3.71
794 874 1.946283 GCTGACCTTGCCACTAACTCC 60.946 57.143 0.00 0.00 0.00 3.85
798 878 0.036732 CCTGCTGACCTTGCCACTAA 59.963 55.000 0.00 0.00 0.00 2.24
830 915 2.427410 CGGCACAAAAGCTGCGTC 60.427 61.111 0.00 0.00 35.31 5.19
837 922 2.202171 CTACGCGCGGCACAAAAG 60.202 61.111 35.22 14.56 0.00 2.27
838 923 4.377661 GCTACGCGCGGCACAAAA 62.378 61.111 35.22 8.87 0.00 2.44
845 930 4.615834 GAGAGGAGCTACGCGCGG 62.616 72.222 35.22 18.64 45.59 6.46
846 931 4.947278 CGAGAGGAGCTACGCGCG 62.947 72.222 30.96 30.96 45.59 6.86
1043 1393 1.371022 CGCTGATCGTCCATCTCCG 60.371 63.158 0.00 0.00 31.92 4.63
1185 1535 0.462759 GCATGGGAAGTAGCGAGCTT 60.463 55.000 1.86 0.00 0.00 3.74
1211 1561 4.489810 CATCATCAGCCTACCGATAACTC 58.510 47.826 0.00 0.00 0.00 3.01
1225 1575 0.879400 GGCTCAGTCGGCATCATCAG 60.879 60.000 0.00 0.00 0.00 2.90
1668 2042 2.202797 GATGAGCGCCGAGAAGCA 60.203 61.111 2.29 0.00 35.48 3.91
1725 2099 0.664166 GTGAAGCAAACATGGTGGCG 60.664 55.000 3.97 0.00 0.00 5.69
1739 2113 3.067106 AGGTTGATACACGCTTGTGAAG 58.933 45.455 6.03 0.00 46.91 3.02
1844 2221 5.491070 CATTACAGAACCTGAAGGACATGA 58.509 41.667 2.62 0.00 38.94 3.07
1875 2255 3.944055 TCTCTCAGTGCCTGTACTTTC 57.056 47.619 0.00 0.00 32.61 2.62
2069 2452 2.473816 TGAGAGCGATATTTCTTGCCG 58.526 47.619 0.00 0.00 0.00 5.69
2111 2494 9.507329 GCTCATCTCCATTCCTATTTATTTGTA 57.493 33.333 0.00 0.00 0.00 2.41
2131 2514 7.880195 ACATCCCAAATATTGTAGTAGCTCATC 59.120 37.037 0.00 0.00 0.00 2.92
2161 2544 5.181811 TCTGTACTGCTTCATTTGTTGGATG 59.818 40.000 0.00 0.00 0.00 3.51
2172 2599 6.654582 TGCTATTTTGAATCTGTACTGCTTCA 59.345 34.615 13.12 13.12 0.00 3.02
2352 2781 4.151689 ACCATAGTCAAACGAAACGATGTG 59.848 41.667 0.00 0.00 29.62 3.21
2357 2787 4.145756 GCAAAACCATAGTCAAACGAAACG 59.854 41.667 0.00 0.00 0.00 3.60
2363 2793 6.902224 AAAACTGCAAAACCATAGTCAAAC 57.098 33.333 0.00 0.00 0.00 2.93
2397 2827 6.517597 CGTTTTCTGTCTAGAATCGTGAAAG 58.482 40.000 0.00 0.00 42.25 2.62
2475 2905 6.701937 ACACAGCGAACAATACATTATTACG 58.298 36.000 0.00 0.00 0.00 3.18
2549 2979 5.103940 ACTTGCTCCAGGTGGTATTGATATT 60.104 40.000 0.00 0.00 36.34 1.28
2552 2982 2.578021 ACTTGCTCCAGGTGGTATTGAT 59.422 45.455 0.00 0.00 36.34 2.57
2560 2990 0.963962 ATTGCAACTTGCTCCAGGTG 59.036 50.000 14.78 0.00 45.31 4.00
2579 3009 2.211806 GCCATTTTGCTGCTGTTTTCA 58.788 42.857 0.00 0.00 0.00 2.69
2583 3013 1.000506 CTCTGCCATTTTGCTGCTGTT 59.999 47.619 0.00 0.00 0.00 3.16
2585 3015 0.601558 ACTCTGCCATTTTGCTGCTG 59.398 50.000 0.00 0.00 0.00 4.41
2654 3084 6.261118 GTCTTGATCAATGAACAGGCATTAC 58.739 40.000 8.96 0.00 36.39 1.89


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

AutoCloner maintained by Alex Coulton.