Multiple sequence alignment - TraesCS5B01G553300

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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 TraesCS5B01G553300 chr5B 100.000 2363 0 0 1 2363 703496529 703498891 0.000000e+00 4364.0
1 TraesCS5B01G553300 chr5B 92.101 633 46 3 705 1336 699384292 699384921 0.000000e+00 889.0
2 TraesCS5B01G553300 chr5B 91.498 494 36 4 164 654 699383691 699384181 0.000000e+00 675.0
3 TraesCS5B01G553300 chr5B 87.102 566 41 18 1647 2192 685501155 685501708 1.550000e-171 612.0
4 TraesCS5B01G553300 chr5B 86.166 506 56 6 149 654 685499428 685499919 3.460000e-148 534.0
5 TraesCS5B01G553300 chr5B 89.735 302 29 1 1401 1700 685417625 685417324 3.680000e-103 385.0
6 TraesCS5B01G553300 chr5B 89.542 306 28 4 1349 1651 685500692 685500996 3.680000e-103 385.0
7 TraesCS5B01G553300 chr5B 87.868 272 23 5 1349 1618 699386154 699386417 6.340000e-81 311.0
8 TraesCS5B01G553300 chr5B 76.201 437 87 10 215 646 699415113 699415537 5.120000e-52 215.0
9 TraesCS5B01G553300 chr5B 87.662 154 15 3 1 154 699382291 699382440 2.410000e-40 176.0
10 TraesCS5B01G553300 chr5B 100.000 34 0 0 657 690 703497149 703497182 1.960000e-06 63.9
11 TraesCS5B01G553300 chr4A 90.414 1377 101 18 1014 2363 616871180 616869808 0.000000e+00 1783.0
12 TraesCS5B01G553300 chr4A 85.327 627 81 5 705 1331 616876242 616875627 2.560000e-179 638.0
13 TraesCS5B01G553300 chr4A 85.928 469 40 14 165 630 616876816 616876371 5.910000e-131 477.0
14 TraesCS5B01G553300 chr4A 85.246 427 46 10 232 657 616871852 616871442 7.810000e-115 424.0
15 TraesCS5B01G553300 chr4A 84.322 236 27 6 149 381 471841863 471841635 3.060000e-54 222.0
16 TraesCS5B01G553300 chr4B 93.501 1031 48 4 1352 2363 581072326 581071296 0.000000e+00 1515.0
17 TraesCS5B01G553300 chr4B 96.672 631 19 1 705 1335 581073000 581072372 0.000000e+00 1048.0
18 TraesCS5B01G553300 chr4B 95.341 558 13 8 149 706 581073641 581073097 0.000000e+00 874.0
19 TraesCS5B01G553300 chr4B 100.000 34 0 0 621 654 581073144 581073111 1.960000e-06 63.9
20 TraesCS5B01G553300 chr4B 100.000 34 0 0 657 690 581073180 581073147 1.960000e-06 63.9
21 TraesCS5B01G553300 chr5D 85.463 626 83 7 714 1339 543508233 543507616 0.000000e+00 645.0
22 TraesCS5B01G553300 chr5D 85.200 500 64 6 154 650 543508852 543508360 2.710000e-139 505.0
23 TraesCS5B01G553300 chr5D 81.092 513 70 17 158 654 552422854 552422353 3.680000e-103 385.0
24 TraesCS5B01G553300 chr5D 90.244 287 15 8 165 447 551081060 551081337 1.730000e-96 363.0
25 TraesCS5B01G553300 chr5D 85.714 112 16 0 543 654 551081943 551082054 4.130000e-23 119.0
26 TraesCS5B01G553300 chr5D 80.220 182 12 8 2087 2266 543506528 543506369 5.340000e-22 115.0
27 TraesCS5B01G553300 chr7B 81.693 508 55 24 162 654 854276 854760 2.850000e-104 388.0
28 TraesCS5B01G553300 chr1B 76.890 463 76 19 169 615 115748942 115749389 1.410000e-57 233.0
29 TraesCS5B01G553300 chr1A 77.612 201 38 5 1821 2014 519418021 519417821 5.340000e-22 115.0
30 TraesCS5B01G553300 chr3B 100.000 36 0 0 2168 2203 809422901 809422936 1.520000e-07 67.6


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 TraesCS5B01G553300 chr5B 703496529 703498891 2362 False 2213.950000 4364 100.000000 1 2363 2 chr5B.!!$F4 2362
1 TraesCS5B01G553300 chr5B 699382291 699386417 4126 False 512.750000 889 89.782250 1 1618 4 chr5B.!!$F3 1617
2 TraesCS5B01G553300 chr5B 685499428 685501708 2280 False 510.333333 612 87.603333 149 2192 3 chr5B.!!$F2 2043
3 TraesCS5B01G553300 chr4A 616869808 616876816 7008 True 830.500000 1783 86.728750 165 2363 4 chr4A.!!$R2 2198
4 TraesCS5B01G553300 chr4B 581071296 581073641 2345 True 712.960000 1515 97.102800 149 2363 5 chr4B.!!$R1 2214
5 TraesCS5B01G553300 chr5D 543506369 543508852 2483 True 421.666667 645 83.627667 154 2266 3 chr5D.!!$R2 2112
6 TraesCS5B01G553300 chr5D 552422353 552422854 501 True 385.000000 385 81.092000 158 654 1 chr5D.!!$R1 496
7 TraesCS5B01G553300 chr5D 551081060 551082054 994 False 241.000000 363 87.979000 165 654 2 chr5D.!!$F1 489

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
96 97 0.698818 GGAGTCCAACATTGTCCCCT 59.301 55.0 3.6 0.0 0.0 4.79 F
213 1467 0.815213 CGCATCCATCCACCGACAAT 60.815 55.0 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 2937 0.033796 AGATGTCAAGGCCCATGGTG 60.034 55.000 11.73 1.95 0.0 4.17 R
1651 8607 1.067283 CACCACTGCACAAAACCAACA 60.067 47.619 0.00 0.00 0.0 3.33 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
28 29 3.695060 GGTGCTGCTCTAGTAGTACTTGA 59.305 47.826 8.40 11.04 41.48 3.02
35 36 7.009723 GCTGCTCTAGTAGTACTTGAAAATGTC 59.990 40.741 8.40 0.00 30.15 3.06
52 53 9.835389 TGAAAATGTCTCTTCAAAATGGAAAAT 57.165 25.926 0.00 0.00 0.00 1.82
65 66 8.435982 TCAAAATGGAAAATTATTTGTGGTCCT 58.564 29.630 7.41 0.00 33.76 3.85
75 76 6.509418 TTATTTGTGGTCCTTGACTATTGC 57.491 37.500 0.00 0.00 32.47 3.56
87 88 2.637382 TGACTATTGCTGGAGTCCAACA 59.363 45.455 14.17 12.69 41.22 3.33
94 95 1.826385 CTGGAGTCCAACATTGTCCC 58.174 55.000 14.17 0.00 30.80 4.46
96 97 0.698818 GGAGTCCAACATTGTCCCCT 59.301 55.000 3.60 0.00 0.00 4.79
98 99 1.351017 GAGTCCAACATTGTCCCCTCA 59.649 52.381 0.00 0.00 0.00 3.86
100 101 2.379907 AGTCCAACATTGTCCCCTCAAT 59.620 45.455 0.00 0.00 38.38 2.57
102 103 3.193479 GTCCAACATTGTCCCCTCAATTC 59.807 47.826 0.00 0.00 36.10 2.17
103 104 3.075882 TCCAACATTGTCCCCTCAATTCT 59.924 43.478 0.00 0.00 36.10 2.40
104 105 4.290985 TCCAACATTGTCCCCTCAATTCTA 59.709 41.667 0.00 0.00 36.10 2.10
135 136 3.214328 GGATATTCATCGCTTGGGTGTT 58.786 45.455 0.00 0.00 31.33 3.32
140 141 1.801771 TCATCGCTTGGGTGTTAAACG 59.198 47.619 0.00 0.00 0.00 3.60
150 151 2.413634 GGGTGTTAAACGCATACAGCAC 60.414 50.000 0.00 0.00 46.13 4.40
151 152 2.482721 GGTGTTAAACGCATACAGCACT 59.517 45.455 0.00 0.00 46.13 4.40
202 1456 3.344137 AAACCCTCGCCGCATCCAT 62.344 57.895 0.00 0.00 0.00 3.41
209 1463 4.545706 GCCGCATCCATCCACCGA 62.546 66.667 0.00 0.00 0.00 4.69
210 1464 2.588877 CCGCATCCATCCACCGAC 60.589 66.667 0.00 0.00 0.00 4.79
211 1465 2.186644 CGCATCCATCCACCGACA 59.813 61.111 0.00 0.00 0.00 4.35
212 1466 1.449423 CGCATCCATCCACCGACAA 60.449 57.895 0.00 0.00 0.00 3.18
213 1467 0.815213 CGCATCCATCCACCGACAAT 60.815 55.000 0.00 0.00 0.00 2.71
367 1632 3.338126 CTTCCGTGCTCGCTACCGT 62.338 63.158 1.89 0.00 35.54 4.83
527 1792 2.731571 GGATGGGGCTACACTGCGA 61.732 63.158 0.00 0.00 0.00 5.10
698 2336 4.864334 GCAGCAGCTACGGGGCAT 62.864 66.667 0.00 0.00 37.91 4.40
699 2337 2.898840 CAGCAGCTACGGGGCATG 60.899 66.667 0.00 0.00 34.17 4.06
700 2338 4.864334 AGCAGCTACGGGGCATGC 62.864 66.667 9.90 9.90 36.97 4.06
890 2624 6.965500 ACTTTACGTCAATCTCGTGTACTATG 59.035 38.462 0.00 0.00 41.62 2.23
922 2656 6.845302 TGATCACATTGCAATTCTCAAGTAC 58.155 36.000 9.83 0.45 0.00 2.73
928 2662 3.585862 TGCAATTCTCAAGTACGACCTC 58.414 45.455 0.00 0.00 0.00 3.85
929 2663 3.006430 TGCAATTCTCAAGTACGACCTCA 59.994 43.478 0.00 0.00 0.00 3.86
930 2664 4.184629 GCAATTCTCAAGTACGACCTCAT 58.815 43.478 0.00 0.00 0.00 2.90
943 2677 3.068307 ACGACCTCATGTATCTAACTGCC 59.932 47.826 0.00 0.00 0.00 4.85
1135 2869 9.775854 CTGTCATCAATCTTAATAACCATCTCT 57.224 33.333 0.00 0.00 0.00 3.10
1162 2896 7.118680 CCATTCAAAATCCCAATGAAAGACTTG 59.881 37.037 0.00 0.00 36.72 3.16
1186 2920 1.344803 TGATTGGATCTCTGGAGGGCT 60.345 52.381 0.00 0.00 0.00 5.19
1203 2937 2.354821 GGGCTGTGATACCATTTTCGTC 59.645 50.000 0.00 0.00 0.00 4.20
1310 3044 6.330278 TGATTCCGTACATGAGTTTCTACAG 58.670 40.000 0.00 0.00 0.00 2.74
1366 8290 6.489361 ACGTCCTCTACATATTAGTTAGTGGG 59.511 42.308 0.00 0.00 0.00 4.61
1373 8297 9.263446 TCTACATATTAGTTAGTGGGACAAACT 57.737 33.333 0.00 0.00 44.16 2.66
1387 8311 5.304101 TGGGACAAACTAAACATTGAATGCT 59.696 36.000 4.84 0.00 31.92 3.79
1393 8317 9.423061 ACAAACTAAACATTGAATGCTTAATCC 57.577 29.630 4.84 0.00 0.00 3.01
1425 8349 5.885912 AGTTATATTTGAAATGTGCCCGAGT 59.114 36.000 0.00 0.00 0.00 4.18
1429 8355 3.907894 TTGAAATGTGCCCGAGTAAAC 57.092 42.857 0.00 0.00 0.00 2.01
1435 8361 2.920524 TGTGCCCGAGTAAACTTTGAA 58.079 42.857 0.00 0.00 0.00 2.69
1593 8524 0.323360 TGGTTGAGTATGCTTGGGGC 60.323 55.000 0.00 0.00 42.22 5.80
1646 8602 3.389329 AGGCTACAAGGGTCATCACTATG 59.611 47.826 0.00 0.00 0.00 2.23
1651 8607 6.407074 GCTACAAGGGTCATCACTATGTAGTT 60.407 42.308 10.60 0.00 38.86 2.24
1882 9033 5.121811 AGATTCATCTCAAAGGATGTTCCG 58.878 41.667 0.00 0.00 42.45 4.30
1910 9064 3.831883 CATGAGAACATGCCCGGG 58.168 61.111 19.09 19.09 45.51 5.73
2156 9564 4.883026 CAGCATTTGCACAGAGCC 57.117 55.556 5.20 0.00 44.83 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.966965 TCAAGTACTACTAGAGCAGCAC 57.033 45.455 0.00 0.00 0.00 4.40
8 9 5.977489 TTTCAAGTACTACTAGAGCAGCA 57.023 39.130 0.00 0.00 0.00 4.41
10 11 8.247562 AGACATTTTCAAGTACTACTAGAGCAG 58.752 37.037 0.00 0.00 0.00 4.24
52 53 6.150976 CAGCAATAGTCAAGGACCACAAATAA 59.849 38.462 0.00 0.00 32.18 1.40
65 66 3.072330 TGTTGGACTCCAGCAATAGTCAA 59.928 43.478 11.96 1.08 41.55 3.18
75 76 1.614317 GGGGACAATGTTGGACTCCAG 60.614 57.143 0.00 0.00 33.81 3.86
87 88 6.160459 ACTGGTATTAGAATTGAGGGGACAAT 59.840 38.462 0.00 0.00 41.43 2.71
94 95 9.799106 AATATCCAACTGGTATTAGAATTGAGG 57.201 33.333 0.00 0.00 36.34 3.86
100 101 7.602644 GCGATGAATATCCAACTGGTATTAGAA 59.397 37.037 0.00 0.00 36.34 2.10
102 103 7.099764 AGCGATGAATATCCAACTGGTATTAG 58.900 38.462 0.00 0.00 36.34 1.73
103 104 7.004555 AGCGATGAATATCCAACTGGTATTA 57.995 36.000 0.00 0.00 36.34 0.98
104 105 5.869579 AGCGATGAATATCCAACTGGTATT 58.130 37.500 0.00 0.37 36.34 1.89
135 136 1.635844 CGGAGTGCTGTATGCGTTTA 58.364 50.000 0.00 0.00 46.63 2.01
367 1632 1.274703 GGGGAGCTCCATGGAAGTCA 61.275 60.000 33.29 0.00 37.91 3.41
698 2336 1.061729 CGCTCACAAAACACACGCA 59.938 52.632 0.00 0.00 0.00 5.24
699 2337 2.285857 GCGCTCACAAAACACACGC 61.286 57.895 0.00 0.00 37.93 5.34
700 2338 0.316937 ATGCGCTCACAAAACACACG 60.317 50.000 9.73 0.00 0.00 4.49
890 2624 4.365899 TTGCAATGTGATCATCTTGCTC 57.634 40.909 29.63 14.16 39.13 4.26
922 2656 3.319405 AGGCAGTTAGATACATGAGGTCG 59.681 47.826 0.00 0.00 0.00 4.79
1135 2869 6.497954 AGTCTTTCATTGGGATTTTGAATGGA 59.502 34.615 0.00 0.00 0.00 3.41
1162 2896 2.368221 CCTCCAGAGATCCAATCAGTCC 59.632 54.545 0.00 0.00 0.00 3.85
1186 2920 4.009370 TGGTGACGAAAATGGTATCACA 57.991 40.909 5.18 0.00 41.18 3.58
1203 2937 0.033796 AGATGTCAAGGCCCATGGTG 60.034 55.000 11.73 1.95 0.00 4.17
1340 3074 7.663081 CCCACTAACTAATATGTAGAGGACGTA 59.337 40.741 0.00 0.00 33.99 3.57
1341 3075 6.489361 CCCACTAACTAATATGTAGAGGACGT 59.511 42.308 0.00 0.00 0.00 4.34
1345 3079 7.834881 TGTCCCACTAACTAATATGTAGAGG 57.165 40.000 0.00 0.00 0.00 3.69
1373 8297 8.681806 TCAATCGGATTAAGCATTCAATGTTTA 58.318 29.630 2.35 2.72 35.31 2.01
1448 8378 7.555914 TGCCAATCAGTAAGCATAATTAGTCAA 59.444 33.333 0.00 0.00 0.00 3.18
1449 8379 7.053498 TGCCAATCAGTAAGCATAATTAGTCA 58.947 34.615 0.00 0.00 0.00 3.41
1450 8380 7.496529 TGCCAATCAGTAAGCATAATTAGTC 57.503 36.000 0.00 0.00 0.00 2.59
1563 8494 5.819379 AGCATACTCAACCATACATTGTCAG 59.181 40.000 0.00 0.00 0.00 3.51
1593 8524 2.723322 TTGATGAGAATGGCCTCCTG 57.277 50.000 3.32 0.00 32.32 3.86
1603 8535 6.268387 AGCCTCCAATTTCTTTTTGATGAGAA 59.732 34.615 0.00 0.00 0.00 2.87
1646 8602 3.857093 CACTGCACAAAACCAACAACTAC 59.143 43.478 0.00 0.00 0.00 2.73
1651 8607 1.067283 CACCACTGCACAAAACCAACA 60.067 47.619 0.00 0.00 0.00 3.33
1910 9064 1.244816 GGGCAACAGAACCACTAACC 58.755 55.000 0.00 0.00 39.74 2.85
2150 9558 2.174360 TCCTATGATCATCCGGCTCTG 58.826 52.381 12.53 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.