Multiple sequence alignment - TraesCS5D01G054100

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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 TraesCS5D01G054100 chr5D 100.000 2240 0 0 1 2240 51638780 51636541 0.000000e+00 4137
1 TraesCS5D01G054100 chr5D 87.108 861 61 27 792 1620 51852768 51851926 0.000000e+00 929
2 TraesCS5D01G054100 chr5D 86.652 884 64 33 756 1620 51861501 51860653 0.000000e+00 929
3 TraesCS5D01G054100 chr5D 89.212 723 40 16 914 1620 51698679 51697979 0.000000e+00 869
4 TraesCS5D01G054100 chr5D 87.027 740 50 29 914 1620 51675644 51674918 0.000000e+00 793
5 TraesCS5D01G054100 chr5D 81.713 607 99 11 1638 2240 6911037 6910439 1.550000e-136 496
6 TraesCS5D01G054100 chr5B 89.344 1586 115 25 698 2240 54509263 54507689 0.000000e+00 1943
7 TraesCS5D01G054100 chr5B 91.994 712 34 8 914 1620 54710635 54709942 0.000000e+00 977
8 TraesCS5D01G054100 chr5B 87.027 740 49 29 914 1620 54549846 54549121 0.000000e+00 791
9 TraesCS5D01G054100 chr5B 90.141 426 27 7 792 1216 54850652 54850241 7.040000e-150 540
10 TraesCS5D01G054100 chr5B 84.615 117 10 6 69 180 54509389 54509276 2.350000e-20 110
11 TraesCS5D01G054100 chr5A 87.085 1417 124 32 866 2240 40629403 40628004 0.000000e+00 1548
12 TraesCS5D01G054100 chr5A 92.636 679 28 6 947 1619 40813608 40812946 0.000000e+00 957
13 TraesCS5D01G054100 chr5A 86.152 881 71 30 756 1620 40935291 40934446 0.000000e+00 904
14 TraesCS5D01G054100 chr5A 86.152 881 71 30 756 1620 40969174 40968329 0.000000e+00 904
15 TraesCS5D01G054100 chr5A 86.152 881 71 30 756 1620 41006056 41005211 0.000000e+00 904
16 TraesCS5D01G054100 chr5A 85.012 854 80 28 792 1634 40925845 40925029 0.000000e+00 824
17 TraesCS5D01G054100 chr5A 84.570 849 80 22 4 819 40630230 40629400 0.000000e+00 795
18 TraesCS5D01G054100 chr5A 85.695 734 57 32 925 1620 40685057 40684334 0.000000e+00 730
19 TraesCS5D01G054100 chr4D 83.221 596 97 3 1635 2228 745742 745148 5.440000e-151 544
20 TraesCS5D01G054100 chr2D 82.166 628 106 6 1615 2240 604074418 604075041 3.270000e-148 534
21 TraesCS5D01G054100 chr2D 82.353 595 94 9 1639 2228 625355779 625356367 7.140000e-140 507
22 TraesCS5D01G054100 chr2D 81.788 604 102 7 1635 2235 429081681 429082279 1.190000e-137 499
23 TraesCS5D01G054100 chr2B 81.760 625 102 9 1620 2240 5474889 5475505 1.530000e-141 512
24 TraesCS5D01G054100 chr7A 81.169 616 105 10 1634 2240 30088597 30089210 3.340000e-133 484
25 TraesCS5D01G054100 chr3B 80.921 608 111 5 1635 2240 740098882 740099486 2.010000e-130 475


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 TraesCS5D01G054100 chr5D 51636541 51638780 2239 True 4137.0 4137 100.0000 1 2240 1 chr5D.!!$R2 2239
1 TraesCS5D01G054100 chr5D 51851926 51852768 842 True 929.0 929 87.1080 792 1620 1 chr5D.!!$R5 828
2 TraesCS5D01G054100 chr5D 51860653 51861501 848 True 929.0 929 86.6520 756 1620 1 chr5D.!!$R6 864
3 TraesCS5D01G054100 chr5D 51697979 51698679 700 True 869.0 869 89.2120 914 1620 1 chr5D.!!$R4 706
4 TraesCS5D01G054100 chr5D 51674918 51675644 726 True 793.0 793 87.0270 914 1620 1 chr5D.!!$R3 706
5 TraesCS5D01G054100 chr5D 6910439 6911037 598 True 496.0 496 81.7130 1638 2240 1 chr5D.!!$R1 602
6 TraesCS5D01G054100 chr5B 54507689 54509389 1700 True 1026.5 1943 86.9795 69 2240 2 chr5B.!!$R4 2171
7 TraesCS5D01G054100 chr5B 54709942 54710635 693 True 977.0 977 91.9940 914 1620 1 chr5B.!!$R2 706
8 TraesCS5D01G054100 chr5B 54549121 54549846 725 True 791.0 791 87.0270 914 1620 1 chr5B.!!$R1 706
9 TraesCS5D01G054100 chr5A 40628004 40630230 2226 True 1171.5 1548 85.8275 4 2240 2 chr5A.!!$R7 2236
10 TraesCS5D01G054100 chr5A 40812946 40813608 662 True 957.0 957 92.6360 947 1619 1 chr5A.!!$R2 672
11 TraesCS5D01G054100 chr5A 40934446 40935291 845 True 904.0 904 86.1520 756 1620 1 chr5A.!!$R4 864
12 TraesCS5D01G054100 chr5A 40968329 40969174 845 True 904.0 904 86.1520 756 1620 1 chr5A.!!$R5 864
13 TraesCS5D01G054100 chr5A 41005211 41006056 845 True 904.0 904 86.1520 756 1620 1 chr5A.!!$R6 864
14 TraesCS5D01G054100 chr5A 40925029 40925845 816 True 824.0 824 85.0120 792 1634 1 chr5A.!!$R3 842
15 TraesCS5D01G054100 chr5A 40684334 40685057 723 True 730.0 730 85.6950 925 1620 1 chr5A.!!$R1 695
16 TraesCS5D01G054100 chr4D 745148 745742 594 True 544.0 544 83.2210 1635 2228 1 chr4D.!!$R1 593
17 TraesCS5D01G054100 chr2D 604074418 604075041 623 False 534.0 534 82.1660 1615 2240 1 chr2D.!!$F2 625
18 TraesCS5D01G054100 chr2D 625355779 625356367 588 False 507.0 507 82.3530 1639 2228 1 chr2D.!!$F3 589
19 TraesCS5D01G054100 chr2D 429081681 429082279 598 False 499.0 499 81.7880 1635 2235 1 chr2D.!!$F1 600
20 TraesCS5D01G054100 chr2B 5474889 5475505 616 False 512.0 512 81.7600 1620 2240 1 chr2B.!!$F1 620
21 TraesCS5D01G054100 chr7A 30088597 30089210 613 False 484.0 484 81.1690 1634 2240 1 chr7A.!!$F1 606
22 TraesCS5D01G054100 chr3B 740098882 740099486 604 False 475.0 475 80.9210 1635 2240 1 chr3B.!!$F1 605

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
254 258 0.036765 TACGTGAGGGGTCATTGTGC 60.037 55.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2121 2244 0.411848 GGGGAGGGGATTTTTGGTGA 59.588 55.0 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
105 106 7.727331 TTTGAAAATTTGTGGCCATTCTAAG 57.273 32.000 9.72 0.00 0.00 2.18
111 112 7.967890 AATTTGTGGCCATTCTAAGAAAAAG 57.032 32.000 9.72 0.00 0.00 2.27
112 113 5.467035 TTGTGGCCATTCTAAGAAAAAGG 57.533 39.130 9.72 0.00 0.00 3.11
113 114 3.258123 TGTGGCCATTCTAAGAAAAAGGC 59.742 43.478 9.72 0.00 39.86 4.35
114 115 3.511540 GTGGCCATTCTAAGAAAAAGGCT 59.488 43.478 9.72 0.00 40.40 4.58
115 116 4.705023 GTGGCCATTCTAAGAAAAAGGCTA 59.295 41.667 9.72 5.92 40.40 3.93
117 118 5.777732 TGGCCATTCTAAGAAAAAGGCTAAA 59.222 36.000 0.00 0.73 40.40 1.85
118 119 6.100004 GGCCATTCTAAGAAAAAGGCTAAAC 58.900 40.000 0.00 0.00 40.40 2.01
119 120 6.295067 GGCCATTCTAAGAAAAAGGCTAAACA 60.295 38.462 0.00 0.00 40.40 2.83
163 167 5.221263 CCCGTAGCTAGCTTTTCTTGAGATA 60.221 44.000 24.88 0.00 0.00 1.98
200 204 8.631480 AACTAGAAAAATGAAAGGGTAATCGT 57.369 30.769 0.00 0.00 0.00 3.73
201 205 8.631480 ACTAGAAAAATGAAAGGGTAATCGTT 57.369 30.769 0.00 0.00 0.00 3.85
204 208 6.492087 AGAAAAATGAAAGGGTAATCGTTCCA 59.508 34.615 0.00 0.00 0.00 3.53
217 221 0.248458 CGTTCCATATGCGTTTGCCC 60.248 55.000 0.00 0.00 41.78 5.36
250 254 2.939640 GCAATGTACGTGAGGGGTCATT 60.940 50.000 0.00 0.00 0.00 2.57
254 258 0.036765 TACGTGAGGGGTCATTGTGC 60.037 55.000 0.00 0.00 0.00 4.57
258 262 2.034066 AGGGGTCATTGTGCACGG 59.966 61.111 13.13 4.42 0.00 4.94
264 268 0.387239 GTCATTGTGCACGGAAAGGC 60.387 55.000 13.13 0.00 0.00 4.35
266 270 0.109597 CATTGTGCACGGAAAGGCTC 60.110 55.000 13.13 0.00 0.00 4.70
268 272 1.444119 TTGTGCACGGAAAGGCTCAC 61.444 55.000 13.13 0.00 33.76 3.51
272 276 0.246635 GCACGGAAAGGCTCACTCTA 59.753 55.000 0.00 0.00 0.00 2.43
281 285 0.249238 GGCTCACTCTATGCTGGTCG 60.249 60.000 0.00 0.00 0.00 4.79
285 289 1.043116 CACTCTATGCTGGTCGGGGA 61.043 60.000 0.00 0.00 0.00 4.81
289 293 2.978452 CTATGCTGGTCGGGGAAGCG 62.978 65.000 0.00 0.00 39.88 4.68
333 337 0.321122 CGCTTTTCTGAGGAGCTGGT 60.321 55.000 0.00 0.00 34.33 4.00
387 391 5.697473 TCATTTCCGTGCAAAGTTCATTA 57.303 34.783 0.00 0.00 0.00 1.90
394 398 6.276847 TCCGTGCAAAGTTCATTACAATTTT 58.723 32.000 0.00 0.00 0.00 1.82
396 400 6.019156 CCGTGCAAAGTTCATTACAATTTTGT 60.019 34.615 1.08 1.08 44.86 2.83
489 497 2.781431 AAAGTTCATGTCCCCGCCCC 62.781 60.000 0.00 0.00 0.00 5.80
502 510 1.448922 CCGCCCCGTTTGTTCTCAAA 61.449 55.000 0.00 0.00 40.64 2.69
506 514 2.100087 GCCCCGTTTGTTCTCAAAAGAA 59.900 45.455 7.84 0.00 43.78 2.52
508 516 4.359706 CCCCGTTTGTTCTCAAAAGAAAG 58.640 43.478 7.84 0.00 43.04 2.62
540 571 8.557029 AGTGTTGTCTTAAGTCTAAATTTTCGG 58.443 33.333 1.63 0.00 0.00 4.30
551 582 7.807680 AGTCTAAATTTTCGGAGTTTGATCAC 58.192 34.615 0.00 0.00 0.00 3.06
554 585 2.823924 TTTCGGAGTTTGATCACGGA 57.176 45.000 0.00 0.00 0.00 4.69
644 675 8.258007 TGTTTTCATGTTGTATTTGTTGGGTAA 58.742 29.630 0.00 0.00 0.00 2.85
646 677 9.482627 TTTTCATGTTGTATTTGTTGGGTAATC 57.517 29.630 0.00 0.00 0.00 1.75
649 680 8.865090 TCATGTTGTATTTGTTGGGTAATCTTT 58.135 29.630 0.00 0.00 0.00 2.52
1129 1165 2.687902 CCCCTAGGGTCCTCGTCA 59.312 66.667 26.66 0.00 38.25 4.35
1268 1314 2.307098 ACCTGCTCCATCAAGCTTAGTT 59.693 45.455 0.00 0.00 42.94 2.24
1279 1325 5.584253 TCAAGCTTAGTTCTAGTGCTAGG 57.416 43.478 0.00 0.00 34.06 3.02
1402 1487 1.005340 CAGGATGAGCTTCGAGCAAC 58.995 55.000 9.09 4.22 45.56 4.17
1608 1723 5.049336 GCTCTGACTTTTTGTAAGTTCTCCC 60.049 44.000 0.00 0.00 0.00 4.30
1682 1801 8.547967 TTCATCAGAAGTACAAAATACCTCAC 57.452 34.615 0.00 0.00 0.00 3.51
1689 1808 9.787435 AGAAGTACAAAATACCTCACACATAAA 57.213 29.630 0.00 0.00 0.00 1.40
1703 1823 7.010183 CCTCACACATAAAAAGATTACGTCGAT 59.990 37.037 0.00 0.00 0.00 3.59
1713 1833 3.574396 AGATTACGTCGATGTCCATGGAT 59.426 43.478 19.62 1.68 0.00 3.41
1735 1855 2.807622 GAATGACCATTGCCGCCC 59.192 61.111 0.00 0.00 0.00 6.13
1841 1961 0.251922 TGTACGTGCCCCTAAGGACT 60.252 55.000 0.00 0.00 38.24 3.85
1857 1977 0.535797 GACTAGCACCCTAAAGCCGT 59.464 55.000 0.00 0.00 0.00 5.68
1871 1991 0.321298 AGCCGTAGTCGTTGCCATTT 60.321 50.000 0.00 0.00 35.01 2.32
1890 2010 8.034215 TGCCATTTAATTCTTGAATCGATTTGT 58.966 29.630 12.81 0.00 0.00 2.83
1900 2020 9.667107 TTCTTGAATCGATTTGTAGAACCTAAT 57.333 29.630 12.81 0.00 0.00 1.73
1918 2038 8.897872 AACCTAATACCAAATATAGTCGTTGG 57.102 34.615 2.18 2.18 46.05 3.77
1945 2065 4.273318 GCATGATGAGAAACCCTAACCTT 58.727 43.478 0.00 0.00 0.00 3.50
2016 2136 1.663739 CCAACGGACGGACTTGAGA 59.336 57.895 0.00 0.00 0.00 3.27
2121 2244 0.763652 TCTACTAGCCGGATCCGAGT 59.236 55.000 35.42 29.38 42.83 4.18
2180 2310 2.660802 GACGGAGGGAAGGCGAAA 59.339 61.111 0.00 0.00 0.00 3.46
2208 2342 0.611062 TCGTTGGTGGAGATCGAGGT 60.611 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 9.528489 AAAGGTTTGGCTATCTTAGAAATGTTA 57.472 29.630 0.00 0.00 0.00 2.41
56 57 8.422577 AAAAGGTTTGGCTATCTTAGAAATGT 57.577 30.769 0.00 0.00 0.00 2.71
91 92 3.258123 GCCTTTTTCTTAGAATGGCCACA 59.742 43.478 8.16 0.00 39.89 4.17
96 97 9.710900 AAATGTTTAGCCTTTTTCTTAGAATGG 57.289 29.630 0.00 0.56 0.00 3.16
163 167 7.447594 TCATTTTTCTAGTTTCCTAGTCGGTT 58.552 34.615 0.00 0.00 41.31 4.44
183 187 7.470009 GCATATGGAACGATTACCCTTTCATTT 60.470 37.037 4.56 0.00 0.00 2.32
192 196 4.523813 CAAACGCATATGGAACGATTACC 58.476 43.478 4.56 0.00 0.00 2.85
200 204 2.102554 CGGGCAAACGCATATGGAA 58.897 52.632 4.56 0.00 0.00 3.53
201 205 3.820590 CGGGCAAACGCATATGGA 58.179 55.556 4.56 0.00 0.00 3.41
224 228 2.091541 CCCTCACGTACATTGCCAATT 58.908 47.619 0.00 0.00 0.00 2.32
238 242 1.577328 CGTGCACAATGACCCCTCAC 61.577 60.000 18.64 0.00 0.00 3.51
250 254 1.891919 GTGAGCCTTTCCGTGCACA 60.892 57.895 18.64 0.00 0.00 4.57
254 258 2.544685 CATAGAGTGAGCCTTTCCGTG 58.455 52.381 0.00 0.00 0.00 4.94
258 262 2.093235 ACCAGCATAGAGTGAGCCTTTC 60.093 50.000 0.00 0.00 0.00 2.62
264 268 0.387202 CCCGACCAGCATAGAGTGAG 59.613 60.000 0.00 0.00 0.00 3.51
266 270 1.043116 TCCCCGACCAGCATAGAGTG 61.043 60.000 0.00 0.00 0.00 3.51
268 272 0.390860 CTTCCCCGACCAGCATAGAG 59.609 60.000 0.00 0.00 0.00 2.43
272 276 4.473520 CGCTTCCCCGACCAGCAT 62.474 66.667 0.00 0.00 32.71 3.79
298 302 2.125147 CGTGTGGATGCCCGACAT 60.125 61.111 0.00 0.00 43.54 3.06
302 306 2.527547 GAAAAGCGTGTGGATGCCCG 62.528 60.000 0.00 0.00 34.26 6.13
307 311 1.347707 TCCTCAGAAAAGCGTGTGGAT 59.652 47.619 0.00 0.00 32.64 3.41
308 312 0.756294 TCCTCAGAAAAGCGTGTGGA 59.244 50.000 0.00 0.00 34.67 4.02
355 359 8.465999 ACTTTGCACGGAAATGAAATAATATGA 58.534 29.630 0.00 0.00 0.00 2.15
372 376 6.932051 ACAAAATTGTAATGAACTTTGCACG 58.068 32.000 0.00 0.00 40.16 5.34
463 467 5.234752 GCGGGGACATGAACTTTAATTTTT 58.765 37.500 0.00 0.00 0.00 1.94
464 468 4.322424 GGCGGGGACATGAACTTTAATTTT 60.322 41.667 0.00 0.00 0.00 1.82
465 469 3.194755 GGCGGGGACATGAACTTTAATTT 59.805 43.478 0.00 0.00 0.00 1.82
481 489 4.653888 AGAACAAACGGGGCGGGG 62.654 66.667 0.00 0.00 0.00 5.73
516 547 8.665643 TCCGAAAATTTAGACTTAAGACAACA 57.334 30.769 10.09 0.00 0.00 3.33
534 565 3.114668 TCCGTGATCAAACTCCGAAAA 57.885 42.857 0.00 0.00 0.00 2.29
538 569 3.116300 CTGTATCCGTGATCAAACTCCG 58.884 50.000 0.00 0.00 0.00 4.63
540 571 6.721571 TTTTCTGTATCCGTGATCAAACTC 57.278 37.500 0.00 0.00 0.00 3.01
734 765 8.899771 GTGTTAAGCACCATAATTATTAGTGGT 58.100 33.333 18.06 18.06 45.41 4.16
1129 1165 1.378762 CCCGATGGTGGTGGAACTT 59.621 57.895 0.00 0.00 36.74 2.66
1268 1314 2.750135 GCTCACTAGCCCTAGCACTAGA 60.750 54.545 18.89 3.06 43.40 2.43
1402 1487 0.958822 CACCTTTTTCCCGGGTCAAG 59.041 55.000 22.86 19.39 0.00 3.02
1627 1742 1.047002 AGATCTGATCCTTCCCGCAG 58.953 55.000 13.83 0.00 0.00 5.18
1682 1801 7.117454 GGACATCGACGTAATCTTTTTATGTG 58.883 38.462 0.00 0.00 0.00 3.21
1689 1808 4.119862 CCATGGACATCGACGTAATCTTT 58.880 43.478 5.56 0.00 0.00 2.52
1692 1811 3.364889 TCCATGGACATCGACGTAATC 57.635 47.619 11.44 0.00 0.00 1.75
1703 1823 1.836802 TCATTCGGTGATCCATGGACA 59.163 47.619 18.99 14.43 0.00 4.02
1713 1833 1.024046 CGGCAATGGTCATTCGGTGA 61.024 55.000 0.00 0.00 0.00 4.02
1759 1879 2.782222 TATGGGAGCGACGACAGCC 61.782 63.158 0.00 0.00 34.64 4.85
1841 1961 1.753073 GACTACGGCTTTAGGGTGCTA 59.247 52.381 0.00 0.00 0.00 3.49
1857 1977 7.441890 TTCAAGAATTAAATGGCAACGACTA 57.558 32.000 0.00 0.00 42.51 2.59
1871 1991 9.667107 AGGTTCTACAAATCGATTCAAGAATTA 57.333 29.630 22.26 7.57 0.00 1.40
1918 2038 1.940613 GGGTTTCTCATCATGCGTACC 59.059 52.381 0.00 0.00 0.00 3.34
2016 2136 0.991920 TCTTTCGGGCTCCAATCCTT 59.008 50.000 0.00 0.00 0.00 3.36
2121 2244 0.411848 GGGGAGGGGATTTTTGGTGA 59.588 55.000 0.00 0.00 0.00 4.02
2172 2302 1.586154 CGAGCCCATGTTTTCGCCTT 61.586 55.000 0.00 0.00 0.00 4.35
2180 2310 1.603455 CCACCAACGAGCCCATGTT 60.603 57.895 0.00 0.00 0.00 2.71
2208 2342 3.864921 GCGACTAGGAAAAGCTTTCCTCA 60.865 47.826 24.51 14.62 45.32 3.86


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

AutoCloner maintained by Alex Coulton.