Multiple sequence alignment - TraesCS5D01G539700

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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 TraesCS5D01G539700 chr5D 100.000 3261 0 0 1 3261 551072787 551076047 0.000000e+00 6023.0
1 TraesCS5D01G539700 chr5D 88.124 421 41 8 237 654 324595264 324595678 2.920000e-135 492.0
2 TraesCS5D01G539700 chr5D 88.221 416 40 8 239 650 434423570 434423980 3.780000e-134 488.0
3 TraesCS5D01G539700 chr5D 77.903 620 92 27 991 1583 552422865 552422264 8.660000e-91 344.0
4 TraesCS5D01G539700 chr5D 78.717 343 62 9 1020 1358 543536886 543536551 5.480000e-53 219.0
5 TraesCS5D01G539700 chr5D 100.000 33 0 0 2664 2696 551075352 551075384 9.770000e-06 62.1
6 TraesCS5D01G539700 chr5D 100.000 33 0 0 2566 2598 551075450 551075482 9.770000e-06 62.1
7 TraesCS5D01G539700 chr4A 93.339 2297 71 23 1001 3261 616886030 616883780 0.000000e+00 3319.0
8 TraesCS5D01G539700 chr4A 100.000 33 0 0 2664 2696 616884477 616884445 9.770000e-06 62.1
9 TraesCS5D01G539700 chr4A 100.000 32 0 0 2566 2597 616884379 616884348 3.510000e-05 60.2
10 TraesCS5D01G539700 chr5B 94.524 1680 70 12 926 2598 703488334 703489998 0.000000e+00 2573.0
11 TraesCS5D01G539700 chr5B 93.738 1517 52 12 993 2490 699353985 699355477 0.000000e+00 2235.0
12 TraesCS5D01G539700 chr5B 89.825 973 46 20 1 955 699353047 699353984 0.000000e+00 1199.0
13 TraesCS5D01G539700 chr5B 97.997 599 11 1 2664 3261 703489966 703490564 0.000000e+00 1038.0
14 TraesCS5D01G539700 chr5B 96.675 421 14 0 2522 2942 699355478 699355898 0.000000e+00 701.0
15 TraesCS5D01G539700 chr5B 94.562 331 11 3 2937 3261 699357484 699357813 3.750000e-139 505.0
16 TraesCS5D01G539700 chr5B 95.652 184 8 0 701 884 703488077 703488260 2.460000e-76 296.0
17 TraesCS5D01G539700 chr5B 75.490 612 104 27 997 1585 698256494 698257082 1.160000e-64 257.0
18 TraesCS5D01G539700 chr5B 81.731 312 47 10 1054 1359 703716172 703716479 5.400000e-63 252.0
19 TraesCS5D01G539700 chr5B 80.968 310 51 8 1054 1358 685422922 685422616 4.210000e-59 239.0
20 TraesCS5D01G539700 chr5B 83.871 248 34 6 1019 1265 699430580 699430822 7.040000e-57 231.0
21 TraesCS5D01G539700 chr5B 84.615 234 28 6 1030 1261 703529332 703529559 3.270000e-55 226.0
22 TraesCS5D01G539700 chr5B 100.000 33 0 0 2566 2598 699355620 699355652 9.770000e-06 62.1
23 TraesCS5D01G539700 chr3D 88.942 416 41 4 242 653 25967187 25967601 2.900000e-140 508.0
24 TraesCS5D01G539700 chr3D 88.293 410 41 6 246 653 548731057 548731461 4.890000e-133 484.0
25 TraesCS5D01G539700 chr2D 88.647 414 36 10 244 654 344348247 344347842 8.130000e-136 494.0
26 TraesCS5D01G539700 chr2D 88.136 413 37 9 246 654 9577292 9577696 6.330000e-132 481.0
27 TraesCS5D01G539700 chr2D 87.715 407 43 6 246 650 622932541 622932942 4.930000e-128 468.0
28 TraesCS5D01G539700 chr7D 87.990 408 44 4 246 651 16320957 16321361 8.190000e-131 477.0
29 TraesCS5D01G539700 chr1D 81.646 316 47 9 1092 1405 22968923 22968617 5.400000e-63 252.0
30 TraesCS5D01G539700 chr1B 92.208 77 6 0 1492 1568 115749426 115749502 3.440000e-20 110.0


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 TraesCS5D01G539700 chr5D 551072787 551076047 3260 False 2049.066667 6023 100.000000 1 3261 3 chr5D.!!$F3 3260
1 TraesCS5D01G539700 chr5D 552422264 552422865 601 True 344.000000 344 77.903000 991 1583 1 chr5D.!!$R2 592
2 TraesCS5D01G539700 chr4A 616883780 616886030 2250 True 1147.100000 3319 97.779667 1001 3261 3 chr4A.!!$R1 2260
3 TraesCS5D01G539700 chr5B 703488077 703490564 2487 False 1302.333333 2573 96.057667 701 3261 3 chr5B.!!$F6 2560
4 TraesCS5D01G539700 chr5B 699353047 699357813 4766 False 940.420000 2235 94.960000 1 3261 5 chr5B.!!$F5 3260
5 TraesCS5D01G539700 chr5B 698256494 698257082 588 False 257.000000 257 75.490000 997 1585 1 chr5B.!!$F1 588


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
939 980 0.035534 TACCAGCCTACCACGACGTA 60.036 55.0 0.0 0.0 0.0 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2735 2932 0.801251 AGCTGACGCTGCAAGAAATC 59.199 50.0 0.0 0.0 46.86 2.17 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
177 179 5.773176 GGAACTAGGGAAACATTTGAAGGAA 59.227 40.000 0.00 0.00 0.00 3.36
278 280 2.580815 CGAGCTCATCTGCACCCA 59.419 61.111 15.40 0.00 34.99 4.51
279 281 1.145598 CGAGCTCATCTGCACCCAT 59.854 57.895 15.40 0.00 34.99 4.00
364 366 5.293324 GTGTGGTAGATAATTTGATGCGTGA 59.707 40.000 0.00 0.00 0.00 4.35
368 370 5.177696 GGTAGATAATTTGATGCGTGAGGTC 59.822 44.000 0.00 0.00 0.00 3.85
381 383 3.551551 CGTGAGGTCCGTTCAAAATTTC 58.448 45.455 0.00 0.00 0.00 2.17
392 394 8.690840 GTCCGTTCAAAATTTCAACTCATTTAG 58.309 33.333 9.93 0.00 0.00 1.85
402 404 6.974932 TTCAACTCATTTAGACATCTGAGC 57.025 37.500 0.00 0.00 38.94 4.26
449 453 6.999705 TTCAGGGTCTGTAAAGGTTTACTA 57.000 37.500 12.61 0.68 42.61 1.82
453 457 7.236019 TCAGGGTCTGTAAAGGTTTACTATTCA 59.764 37.037 12.61 0.00 42.61 2.57
463 467 4.689345 AGGTTTACTATTCACGCACTGTTC 59.311 41.667 0.00 0.00 0.00 3.18
501 505 3.859414 GCCGAGGGCTGCTCAGAT 61.859 66.667 0.74 0.00 46.69 2.90
506 510 1.614525 AGGGCTGCTCAGATGTCCA 60.615 57.895 0.74 0.00 0.00 4.02
530 534 5.452078 AATGAGTTGAAATTTGAAGCGGA 57.548 34.783 0.00 0.00 0.00 5.54
562 566 7.166307 CGCATCAAATTATCTACCACACAATTG 59.834 37.037 3.24 3.24 0.00 2.32
632 639 2.108566 CGGGAGCAGATGAGCCTG 59.891 66.667 0.00 0.00 37.23 4.85
633 640 2.509916 GGGAGCAGATGAGCCTGG 59.490 66.667 0.00 0.00 34.82 4.45
634 641 2.509916 GGAGCAGATGAGCCTGGG 59.490 66.667 0.00 0.00 34.82 4.45
635 642 2.203181 GAGCAGATGAGCCTGGGC 60.203 66.667 3.00 3.00 42.33 5.36
636 643 3.013327 AGCAGATGAGCCTGGGCA 61.013 61.111 14.39 0.00 44.88 5.36
637 644 2.827642 GCAGATGAGCCTGGGCAC 60.828 66.667 14.39 8.23 44.88 5.01
652 659 0.243636 GGCACCAAGTTGGATTTCCG 59.756 55.000 28.80 9.79 40.96 4.30
657 664 2.632512 ACCAAGTTGGATTTCCGCAATT 59.367 40.909 28.80 0.00 40.96 2.32
669 676 6.593770 GGATTTCCGCAATTTTGTTTTCCTAT 59.406 34.615 0.00 0.00 0.00 2.57
673 680 7.793927 TCCGCAATTTTGTTTTCCTATTTTT 57.206 28.000 0.00 0.00 0.00 1.94
872 881 4.020039 TCTCATGCCTTGGCAAATGATTTT 60.020 37.500 18.76 0.00 0.00 1.82
887 896 2.562298 TGATTTTAGGTTGCAAGCAGGG 59.438 45.455 28.75 0.00 0.00 4.45
889 898 1.616159 TTTAGGTTGCAAGCAGGGTC 58.384 50.000 28.75 1.76 0.00 4.46
939 980 0.035534 TACCAGCCTACCACGACGTA 60.036 55.000 0.00 0.00 0.00 3.57
970 1011 1.114627 GCCCAAAGCCCAAATAGAGG 58.885 55.000 0.00 0.00 34.35 3.69
1559 1637 1.229951 TGTCATGAGGGCCCCTTCT 60.230 57.895 21.43 0.00 31.76 2.85
1792 1878 6.713903 AGGATTATCGTCGTGTAGGAATTCTA 59.286 38.462 5.23 0.00 0.00 2.10
1805 1891 8.475639 GTGTAGGAATTCTAAAGTATGACCTGA 58.524 37.037 5.23 0.00 0.00 3.86
1806 1892 9.042450 TGTAGGAATTCTAAAGTATGACCTGAA 57.958 33.333 5.23 0.00 0.00 3.02
1958 2051 3.055819 GTCAAGGCAGATAGGTTCTCACA 60.056 47.826 0.00 0.00 29.93 3.58
1996 2089 0.380733 AGCGTGCAATCGTCGATCTA 59.619 50.000 8.45 0.00 0.00 1.98
2023 2116 3.077391 ACCTTCTCCCCATTCAAAATCCA 59.923 43.478 0.00 0.00 0.00 3.41
2024 2117 4.095946 CCTTCTCCCCATTCAAAATCCAA 58.904 43.478 0.00 0.00 0.00 3.53
2048 2141 4.074970 GGAAGATCTTGAACTGCTTGGAA 58.925 43.478 14.00 0.00 0.00 3.53
2167 2260 3.319122 ACAAGTTCTGTGCTTTGATTCCC 59.681 43.478 0.00 0.00 36.69 3.97
2342 2441 7.370383 TCTGAAATGCATCCTAACAAACTTTC 58.630 34.615 0.00 0.00 0.00 2.62
2592 2691 5.359576 TGCCATTATTTAGTAGCTGGTTTGG 59.640 40.000 0.00 0.00 0.00 3.28
2661 2760 1.678598 TTGACAGTTCCCCGTGTCGT 61.679 55.000 0.00 0.00 45.13 4.34
2731 2928 9.853555 GTGATTGGATTATGTTTGTAATGAACA 57.146 29.630 0.00 0.00 40.86 3.18
2777 2974 4.241590 TGTGGCTTCTTGTAATTTGCTG 57.758 40.909 0.00 0.00 0.00 4.41
2838 3036 3.963383 AAAACCTGTACAGTTTGCTCG 57.037 42.857 21.18 6.79 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.363167 TTCTTCCAGATTCCATTGCATTTT 57.637 33.333 0.00 0.00 0.00 1.82
11 12 8.884124 TGTTTCTTATTCTTCCAGATTCCATT 57.116 30.769 0.00 0.00 0.00 3.16
103 104 5.745227 TCCTTGGAAATTTAGTCTGCCTAG 58.255 41.667 0.00 0.00 0.00 3.02
120 121 6.269077 ACCCTGGTTTAAATTTTACTCCTTGG 59.731 38.462 0.00 1.42 0.00 3.61
177 179 6.239289 CCATTCATGTTTTGTGTTTCCCTAGT 60.239 38.462 0.00 0.00 0.00 2.57
237 239 0.234884 CAGAAACTCCGCGTCCAAAC 59.765 55.000 4.92 0.00 0.00 2.93
238 240 1.503818 GCAGAAACTCCGCGTCCAAA 61.504 55.000 4.92 0.00 0.00 3.28
241 243 2.048127 AGCAGAAACTCCGCGTCC 60.048 61.111 4.92 0.00 0.00 4.79
242 244 2.095252 GGAGCAGAAACTCCGCGTC 61.095 63.158 4.92 0.00 46.52 5.19
243 245 2.048127 GGAGCAGAAACTCCGCGT 60.048 61.111 4.92 0.00 46.52 6.01
278 280 8.436046 TTTGTTTTGCTTATTTTTCTGAGCAT 57.564 26.923 0.00 0.00 43.83 3.79
279 281 7.840342 TTTGTTTTGCTTATTTTTCTGAGCA 57.160 28.000 0.00 0.00 42.84 4.26
324 326 7.560368 TCTACCACACAAAAACAATTTGGATT 58.440 30.769 0.78 0.00 33.92 3.01
325 327 7.118496 TCTACCACACAAAAACAATTTGGAT 57.882 32.000 0.78 0.00 33.92 3.41
326 328 6.531503 TCTACCACACAAAAACAATTTGGA 57.468 33.333 0.78 0.00 33.92 3.53
327 329 8.879342 TTATCTACCACACAAAAACAATTTGG 57.121 30.769 0.78 0.00 33.92 3.28
364 366 4.642885 TGAGTTGAAATTTTGAACGGACCT 59.357 37.500 5.94 0.00 0.00 3.85
368 370 8.690840 GTCTAAATGAGTTGAAATTTTGAACGG 58.309 33.333 5.94 0.00 32.17 4.44
381 383 5.220624 GCTGCTCAGATGTCTAAATGAGTTG 60.221 44.000 0.29 0.00 41.00 3.16
428 430 7.333672 GTGAATAGTAAACCTTTACAGACCCTG 59.666 40.741 9.95 0.00 44.14 4.45
430 432 6.312180 CGTGAATAGTAAACCTTTACAGACCC 59.688 42.308 9.95 0.00 44.14 4.46
449 453 1.151668 GCTCAGAACAGTGCGTGAAT 58.848 50.000 0.00 0.00 0.00 2.57
453 457 2.159819 ATCGGCTCAGAACAGTGCGT 62.160 55.000 0.00 0.00 0.00 5.24
490 494 1.538047 TTTTGGACATCTGAGCAGCC 58.462 50.000 0.00 0.00 0.00 4.85
498 502 8.423349 TCAAATTTCAACTCATTTTGGACATCT 58.577 29.630 0.00 0.00 0.00 2.90
501 505 7.011295 GCTTCAAATTTCAACTCATTTTGGACA 59.989 33.333 0.00 0.00 0.00 4.02
506 510 6.200854 GTCCGCTTCAAATTTCAACTCATTTT 59.799 34.615 0.00 0.00 0.00 1.82
530 534 5.057149 GGTAGATAATTTGATGCGTGAGGT 58.943 41.667 0.00 0.00 0.00 3.85
609 616 2.108566 CATCTGCTCCCGCTCAGG 59.891 66.667 0.00 0.00 40.63 3.86
626 633 2.116125 AACTTGGTGCCCAGGCTC 59.884 61.111 10.58 6.18 42.51 4.70
627 634 2.203538 CAACTTGGTGCCCAGGCT 60.204 61.111 10.58 0.00 42.51 4.58
628 635 3.305516 CCAACTTGGTGCCCAGGC 61.306 66.667 0.38 0.38 33.66 4.85
629 636 0.542702 AATCCAACTTGGTGCCCAGG 60.543 55.000 7.72 2.42 39.03 4.45
630 637 1.273327 GAAATCCAACTTGGTGCCCAG 59.727 52.381 7.72 0.00 39.03 4.45
631 638 1.337118 GAAATCCAACTTGGTGCCCA 58.663 50.000 7.72 0.00 39.03 5.36
632 639 0.608130 GGAAATCCAACTTGGTGCCC 59.392 55.000 7.72 2.41 39.03 5.36
633 640 0.243636 CGGAAATCCAACTTGGTGCC 59.756 55.000 7.72 4.75 39.03 5.01
634 641 0.388520 GCGGAAATCCAACTTGGTGC 60.389 55.000 7.72 1.07 39.03 5.01
635 642 0.958091 TGCGGAAATCCAACTTGGTG 59.042 50.000 7.72 0.00 39.03 4.17
636 643 1.698506 TTGCGGAAATCCAACTTGGT 58.301 45.000 7.72 0.00 39.03 3.67
637 644 3.317603 AATTGCGGAAATCCAACTTGG 57.682 42.857 0.74 0.74 39.43 3.61
638 645 4.511082 ACAAAATTGCGGAAATCCAACTTG 59.489 37.500 0.00 0.00 35.14 3.16
639 646 4.702831 ACAAAATTGCGGAAATCCAACTT 58.297 34.783 0.00 0.00 35.14 2.66
640 647 4.335400 ACAAAATTGCGGAAATCCAACT 57.665 36.364 0.00 0.00 35.14 3.16
641 648 5.416862 AAACAAAATTGCGGAAATCCAAC 57.583 34.783 0.00 0.00 35.14 3.77
642 649 5.008118 GGAAAACAAAATTGCGGAAATCCAA 59.992 36.000 0.00 0.00 35.14 3.53
643 650 4.513318 GGAAAACAAAATTGCGGAAATCCA 59.487 37.500 0.00 0.00 35.14 3.41
644 651 4.754618 AGGAAAACAAAATTGCGGAAATCC 59.245 37.500 0.00 0.00 0.00 3.01
645 652 5.922739 AGGAAAACAAAATTGCGGAAATC 57.077 34.783 0.00 0.00 0.00 2.17
646 653 7.977789 AATAGGAAAACAAAATTGCGGAAAT 57.022 28.000 0.00 0.00 0.00 2.17
647 654 7.793927 AAATAGGAAAACAAAATTGCGGAAA 57.206 28.000 0.00 0.00 0.00 3.13
648 655 7.793927 AAAATAGGAAAACAAAATTGCGGAA 57.206 28.000 0.00 0.00 0.00 4.30
649 656 7.793927 AAAAATAGGAAAACAAAATTGCGGA 57.206 28.000 0.00 0.00 0.00 5.54
673 680 2.785357 AACCTCACAATTTCCCCCAA 57.215 45.000 0.00 0.00 0.00 4.12
754 762 4.622260 TGATGTCTTCCAGTGATCAACA 57.378 40.909 0.00 0.00 0.00 3.33
872 881 0.771127 AAGACCCTGCTTGCAACCTA 59.229 50.000 0.00 0.00 0.00 3.08
939 980 0.901580 CTTTGGGCTTCCAGGCACAT 60.902 55.000 0.00 0.00 45.54 3.21
980 1021 2.671682 GAGTGGAGTGGGGCTTCC 59.328 66.667 0.00 0.00 0.00 3.46
981 1022 2.190488 CTGGAGTGGAGTGGGGCTTC 62.190 65.000 0.00 0.00 0.00 3.86
982 1023 2.121963 TGGAGTGGAGTGGGGCTT 60.122 61.111 0.00 0.00 0.00 4.35
983 1024 2.608988 CTGGAGTGGAGTGGGGCT 60.609 66.667 0.00 0.00 0.00 5.19
985 1026 3.721706 GGCTGGAGTGGAGTGGGG 61.722 72.222 0.00 0.00 0.00 4.96
986 1027 4.087892 CGGCTGGAGTGGAGTGGG 62.088 72.222 0.00 0.00 0.00 4.61
987 1028 4.767255 GCGGCTGGAGTGGAGTGG 62.767 72.222 0.00 0.00 0.00 4.00
988 1029 3.947132 CTGCGGCTGGAGTGGAGTG 62.947 68.421 5.78 0.00 0.00 3.51
989 1030 3.699894 CTGCGGCTGGAGTGGAGT 61.700 66.667 5.78 0.00 0.00 3.85
1386 1449 4.778143 GGAGAACGCGGCCATGGT 62.778 66.667 14.67 0.00 0.00 3.55
1559 1637 1.616865 CAGGTAGACAAAGACGACCCA 59.383 52.381 0.00 0.00 34.43 4.51
1730 1814 2.224281 TGAAGTGAAGTGCGTCTTGGAT 60.224 45.455 0.00 0.00 36.40 3.41
1767 1853 5.535406 AGAATTCCTACACGACGATAATCCT 59.465 40.000 0.00 0.00 0.00 3.24
1768 1854 5.770417 AGAATTCCTACACGACGATAATCC 58.230 41.667 0.00 0.00 0.00 3.01
1792 1878 6.014156 AGCAGTTAGAGTTCAGGTCATACTTT 60.014 38.462 0.00 0.00 0.00 2.66
1806 1892 9.539825 CATCAATTAGTGATAAGCAGTTAGAGT 57.460 33.333 0.00 0.00 45.69 3.24
2023 2116 4.522022 CCAAGCAGTTCAAGATCTTCCTTT 59.478 41.667 4.57 0.00 0.00 3.11
2024 2117 4.077822 CCAAGCAGTTCAAGATCTTCCTT 58.922 43.478 4.57 0.00 0.00 3.36
2074 2167 2.747022 CCCATGTCCGTGGTCACA 59.253 61.111 4.89 0.00 37.57 3.58
2113 2206 3.119316 ACAGCTTCTTCCATCGTAGTGAG 60.119 47.826 0.00 0.00 0.00 3.51
2167 2260 4.327357 CAGCGGTTGTAGAAACTCATGTAG 59.673 45.833 0.00 0.00 0.00 2.74
2223 2316 8.650490 AGCTTTATTCCCAAATCAGAAGAAAAA 58.350 29.630 0.00 0.00 34.02 1.94
2228 2321 9.578439 CTTTAAGCTTTATTCCCAAATCAGAAG 57.422 33.333 3.20 0.00 0.00 2.85
2318 2417 7.147312 TGAAAGTTTGTTAGGATGCATTTCAG 58.853 34.615 0.00 0.00 32.23 3.02
2342 2441 9.095065 GTAACCTTCTATTGTTACATACCACTG 57.905 37.037 7.46 0.00 43.89 3.66
2592 2691 5.181690 TGATAAAACAAGAACCACTGCAC 57.818 39.130 0.00 0.00 0.00 4.57
2661 2760 7.745717 ACCAGCTACTAAATAATGGCATAAGA 58.254 34.615 0.00 0.00 0.00 2.10
2731 2928 2.676839 CTGACGCTGCAAGAAATCAGAT 59.323 45.455 0.00 0.00 39.58 2.90
2735 2932 0.801251 AGCTGACGCTGCAAGAAATC 59.199 50.000 0.00 0.00 46.86 2.17
2838 3036 3.255149 CAGATATTGGATCAAAGCTGGGC 59.745 47.826 0.00 0.00 0.00 5.36



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

AutoCloner maintained by Alex Coulton.