Multiple sequence alignment - TraesCS5B01G048500

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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 TraesCS5B01G048500 chr5B 100.000 2913 0 0 1 2913 54701270 54704182 0.000000e+00 5380
1 TraesCS5B01G048500 chr5A 93.384 2252 120 13 248 2490 40719126 40721357 0.000000e+00 3306
2 TraesCS5B01G048500 chr5A 87.324 284 34 2 2631 2913 40788988 40789270 1.010000e-84 324
3 TraesCS5B01G048500 chr5A 93.478 184 10 2 1 182 40718653 40718836 3.700000e-69 272
4 TraesCS5B01G048500 chr5D 95.255 1728 58 8 248 1961 51685298 51687015 0.000000e+00 2715
5 TraesCS5B01G048500 chr5D 95.429 722 29 1 2196 2913 51690991 51691712 0.000000e+00 1147
6 TraesCS5B01G048500 chr5D 97.608 209 5 0 1992 2200 51687012 51687220 2.760000e-95 359
7 TraesCS5B01G048500 chr5D 94.022 184 9 2 1 182 51684822 51685005 7.950000e-71 278
8 TraesCS5B01G048500 chr7A 87.772 597 70 3 1322 1916 562303564 562302969 0.000000e+00 695
9 TraesCS5B01G048500 chr7D 88.165 583 68 1 1335 1916 497046201 497045619 0.000000e+00 693
10 TraesCS5B01G048500 chr7D 79.104 335 46 10 801 1126 497046695 497046376 2.940000e-50 209
11 TraesCS5B01G048500 chr7B 87.500 592 70 4 1327 1916 525026161 525025572 0.000000e+00 680
12 TraesCS5B01G048500 chr7B 76.240 484 77 20 741 1203 525026976 525026510 3.780000e-54 222
13 TraesCS5B01G048500 chr3B 87.413 572 69 3 1347 1916 46469335 46468765 0.000000e+00 654
14 TraesCS5B01G048500 chr3B 87.238 572 70 3 1347 1916 46613471 46612901 0.000000e+00 649
15 TraesCS5B01G048500 chrUn 89.216 102 11 0 1023 1124 187693338 187693237 8.470000e-26 128
16 TraesCS5B01G048500 chrUn 89.216 102 11 0 1023 1124 254192281 254192180 8.470000e-26 128
17 TraesCS5B01G048500 chrUn 88.235 102 12 0 1023 1124 110300720 110300619 3.940000e-24 122


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 TraesCS5B01G048500 chr5B 54701270 54704182 2912 False 5380.00 5380 100.0000 1 2913 1 chr5B.!!$F1 2912
1 TraesCS5B01G048500 chr5A 40718653 40721357 2704 False 1789.00 3306 93.4310 1 2490 2 chr5A.!!$F2 2489
2 TraesCS5B01G048500 chr5D 51684822 51691712 6890 False 1124.75 2715 95.5785 1 2913 4 chr5D.!!$F1 2912
3 TraesCS5B01G048500 chr7A 562302969 562303564 595 True 695.00 695 87.7720 1322 1916 1 chr7A.!!$R1 594
4 TraesCS5B01G048500 chr7D 497045619 497046695 1076 True 451.00 693 83.6345 801 1916 2 chr7D.!!$R1 1115
5 TraesCS5B01G048500 chr7B 525025572 525026976 1404 True 451.00 680 81.8700 741 1916 2 chr7B.!!$R1 1175
6 TraesCS5B01G048500 chr3B 46468765 46469335 570 True 654.00 654 87.4130 1347 1916 1 chr3B.!!$R1 569
7 TraesCS5B01G048500 chr3B 46612901 46613471 570 True 649.00 649 87.2380 1347 1916 1 chr3B.!!$R2 569

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
285 551 0.179124 GGCGGTTGTGACAAGCAAAA 60.179 50.0 24.74 0.0 34.13 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2641 0.324091 TACGAGGGAAGAGGACACCC 60.324 60.0 0.0 0.0 43.55 4.61 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
26 27 5.799435 CACGTAGCTGCATAGAGATATGAAG 59.201 44.000 1.02 0.00 36.41 3.02
40 41 0.615331 ATGAAGCATGTCACCGACCT 59.385 50.000 0.00 0.00 0.00 3.85
67 69 8.394971 ACTTTAATGATCTCATGTTTGTCACA 57.605 30.769 0.00 0.00 40.71 3.58
71 73 4.459330 TGATCTCATGTTTGTCACAACCA 58.541 39.130 0.00 0.00 39.50 3.67
86 88 3.631686 CACAACCACTGACTTTTCCATCA 59.368 43.478 0.00 0.00 0.00 3.07
93 95 5.009911 CCACTGACTTTTCCATCATTGAACA 59.990 40.000 0.00 0.00 29.44 3.18
182 185 6.743575 ATTGTCTAGTGCAACCTTAATGTC 57.256 37.500 0.00 0.00 37.80 3.06
183 186 4.575885 TGTCTAGTGCAACCTTAATGTCC 58.424 43.478 0.00 0.00 37.80 4.02
184 187 4.041075 TGTCTAGTGCAACCTTAATGTCCA 59.959 41.667 0.00 0.00 37.80 4.02
185 188 4.392138 GTCTAGTGCAACCTTAATGTCCAC 59.608 45.833 0.00 6.55 37.80 4.02
186 189 2.514803 AGTGCAACCTTAATGTCCACC 58.485 47.619 0.00 0.00 37.80 4.61
188 191 0.808755 GCAACCTTAATGTCCACCCG 59.191 55.000 0.00 0.00 0.00 5.28
189 192 0.808755 CAACCTTAATGTCCACCCGC 59.191 55.000 0.00 0.00 0.00 6.13
190 193 0.402504 AACCTTAATGTCCACCCGCA 59.597 50.000 0.00 0.00 0.00 5.69
191 194 0.402504 ACCTTAATGTCCACCCGCAA 59.597 50.000 0.00 0.00 0.00 4.85
192 195 1.202952 ACCTTAATGTCCACCCGCAAA 60.203 47.619 0.00 0.00 0.00 3.68
193 196 1.889829 CCTTAATGTCCACCCGCAAAA 59.110 47.619 0.00 0.00 0.00 2.44
194 197 2.297597 CCTTAATGTCCACCCGCAAAAA 59.702 45.455 0.00 0.00 0.00 1.94
195 198 3.574614 CTTAATGTCCACCCGCAAAAAG 58.425 45.455 0.00 0.00 0.00 2.27
196 199 1.698506 AATGTCCACCCGCAAAAAGA 58.301 45.000 0.00 0.00 0.00 2.52
197 200 1.698506 ATGTCCACCCGCAAAAAGAA 58.301 45.000 0.00 0.00 0.00 2.52
198 201 1.475403 TGTCCACCCGCAAAAAGAAA 58.525 45.000 0.00 0.00 0.00 2.52
199 202 1.825474 TGTCCACCCGCAAAAAGAAAA 59.175 42.857 0.00 0.00 0.00 2.29
200 203 2.233922 TGTCCACCCGCAAAAAGAAAAA 59.766 40.909 0.00 0.00 0.00 1.94
235 243 8.887036 TGTCGTTGCATTACTATCATAATTCT 57.113 30.769 0.00 0.00 0.00 2.40
251 515 8.958119 TCATAATTCTTAAAATGCTCGGTACT 57.042 30.769 0.00 0.00 0.00 2.73
255 519 5.401531 TCTTAAAATGCTCGGTACTGTCT 57.598 39.130 0.64 0.00 0.00 3.41
262 526 1.800655 GCTCGGTACTGTCTGCAGATG 60.801 57.143 21.47 17.76 45.28 2.90
271 535 0.390860 GTCTGCAGATGATAGGCGGT 59.609 55.000 21.47 0.00 35.45 5.68
277 543 2.205074 CAGATGATAGGCGGTTGTGAC 58.795 52.381 0.00 0.00 0.00 3.67
279 545 2.236146 AGATGATAGGCGGTTGTGACAA 59.764 45.455 0.00 0.00 0.00 3.18
280 546 2.093306 TGATAGGCGGTTGTGACAAG 57.907 50.000 0.00 0.00 0.00 3.16
281 547 0.727398 GATAGGCGGTTGTGACAAGC 59.273 55.000 16.85 16.85 0.00 4.01
284 550 1.034838 AGGCGGTTGTGACAAGCAAA 61.035 50.000 24.74 0.00 34.13 3.68
285 551 0.179124 GGCGGTTGTGACAAGCAAAA 60.179 50.000 24.74 0.00 34.13 2.44
286 552 1.537990 GGCGGTTGTGACAAGCAAAAT 60.538 47.619 24.74 0.00 34.13 1.82
287 553 1.786579 GCGGTTGTGACAAGCAAAATC 59.213 47.619 24.74 6.63 33.15 2.17
288 554 2.043411 CGGTTGTGACAAGCAAAATCG 58.957 47.619 24.74 5.96 41.51 3.34
299 565 4.851558 ACAAGCAAAATCGCGATTCTTTAC 59.148 37.500 32.56 19.15 36.85 2.01
301 567 6.128391 ACAAGCAAAATCGCGATTCTTTACTA 60.128 34.615 32.56 0.00 36.85 1.82
364 636 7.411486 TTCCATTGTAACTCTGAAACCAAAA 57.589 32.000 0.00 0.00 0.00 2.44
367 639 9.137459 TCCATTGTAACTCTGAAACCAAAATAA 57.863 29.630 0.00 0.00 0.00 1.40
414 690 7.108841 TGAGCTAACGTAATACTTGGAGAAT 57.891 36.000 0.00 0.00 0.00 2.40
440 716 6.880942 ACCATTTTTACAAGCATGCAATTT 57.119 29.167 21.98 2.08 0.00 1.82
577 853 1.006832 CTACTCGGTTGAATTGCCCG 58.993 55.000 0.00 0.00 43.03 6.13
676 952 2.704065 AGAACGGAGGAAGAAAACCAGA 59.296 45.455 0.00 0.00 0.00 3.86
724 1000 4.633565 TCAGTCGTGCAAAATATGTATGCA 59.366 37.500 6.30 6.30 46.97 3.96
892 1175 1.065358 GTTTGCTCACATGCATGCAC 58.935 50.000 25.37 9.84 42.96 4.57
898 1181 2.095110 GCTCACATGCATGCACAAGTTA 60.095 45.455 25.37 12.40 0.00 2.24
1017 1301 1.211456 CAATGGCCTCCTCTTCCTCT 58.789 55.000 3.32 0.00 0.00 3.69
1238 1551 4.142708 TGAGTTTTGCATGCTATACGTTGG 60.143 41.667 20.33 0.00 0.00 3.77
1254 1567 5.233957 ACGTTGGTACCAAAACAAAGTAC 57.766 39.130 28.67 12.76 35.60 2.73
1397 1946 1.602323 GACCCAATGGCCGTCAACA 60.602 57.895 0.00 0.00 33.59 3.33
1431 1980 1.033746 AATCCAGCCATGCTTGACCG 61.034 55.000 0.22 0.00 36.40 4.79
1672 2221 1.814429 TCTCCAGGGTGGTCAAGAAA 58.186 50.000 0.00 0.00 39.03 2.52
1726 2275 5.178096 TCCACTTCCAAATGAATCTAGCA 57.822 39.130 0.00 0.00 31.06 3.49
2091 2641 7.773149 TGGTTGTTTAATAAATGGAATACCGG 58.227 34.615 0.00 0.00 39.42 5.28
2156 2706 7.719193 TGAAGTTCATGAGAAAACCAATGACTA 59.281 33.333 0.08 0.00 35.08 2.59
2173 2723 5.840243 TGACTATGCTTGCATGCTATTTT 57.160 34.783 23.31 3.82 0.00 1.82
2243 6568 4.107820 GGGGAGAGCTAAGGGATGATTAT 58.892 47.826 0.00 0.00 0.00 1.28
2321 6646 6.600032 AGTTTTTACGGTGCATCATATTACCA 59.400 34.615 0.00 0.00 32.75 3.25
2395 6724 0.701147 TGGGTTATGGTGTGATGGCA 59.299 50.000 0.00 0.00 0.00 4.92
2515 6844 0.609406 GGAAGGGAGGAACTTGTGGC 60.609 60.000 0.00 0.00 41.55 5.01
2527 6856 4.546570 GAACTTGTGGCCAATTTAGTCAC 58.453 43.478 7.24 3.51 0.00 3.67
2547 6876 5.006358 GTCACGTGAGTTGAAGTATGTTGTT 59.994 40.000 20.73 0.00 46.40 2.83
2635 6964 9.975218 AGTTTGACCATCTGTAATTAAGGTAAT 57.025 29.630 0.00 0.00 0.00 1.89
2655 6984 8.528643 AGGTAATACAAAAGCAAGATTTAACCC 58.471 33.333 0.00 0.00 0.00 4.11
2744 7073 7.487822 TTTCCTAATTGTTTTGGATGGCATA 57.512 32.000 0.00 0.00 36.76 3.14
2779 7108 8.087750 TGCATCAAACTAAAAACTAGGGAAATG 58.912 33.333 0.00 0.00 0.00 2.32
2794 7123 5.894807 AGGGAAATGATAAAACATCAAGCG 58.105 37.500 0.00 0.00 0.00 4.68
2819 7148 6.223852 CCATAGTAAATCATTAGGCGTGACT 58.776 40.000 0.00 0.00 0.00 3.41
2823 7152 6.875076 AGTAAATCATTAGGCGTGACTACTT 58.125 36.000 0.00 0.00 29.79 2.24
2838 7167 7.315142 CGTGACTACTTATGGTTGGTAAGTAA 58.685 38.462 7.06 0.00 41.52 2.24
2864 7193 3.902881 AGTAGAGAAGGCAAGACATGG 57.097 47.619 0.00 0.00 0.00 3.66
2890 7219 4.536489 AGGCATTATTAGAGGGGACATACC 59.464 45.833 0.00 0.00 38.08 2.73
2909 7238 7.562135 ACATACCGGTCTAATCTAACATGTTT 58.438 34.615 17.78 0.51 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.094762 AAGTTAGGTCGGTGACATGC 57.905 50.000 0.00 0.00 33.68 4.06
67 69 5.139727 TCAATGATGGAAAAGTCAGTGGTT 58.860 37.500 3.47 0.00 39.95 3.67
71 73 5.242393 CCTGTTCAATGATGGAAAAGTCAGT 59.758 40.000 0.00 0.00 29.29 3.41
149 151 5.422666 TGCACTAGACAATTTGTTGAGTG 57.577 39.130 25.58 25.58 41.93 3.51
201 204 9.769093 GATAGTAATGCAACGACATTAAGTTTT 57.231 29.630 10.36 0.00 42.53 2.43
202 205 8.941977 TGATAGTAATGCAACGACATTAAGTTT 58.058 29.630 10.36 3.17 42.53 2.66
203 206 8.487313 TGATAGTAATGCAACGACATTAAGTT 57.513 30.769 10.36 4.84 42.53 2.66
204 207 8.662781 ATGATAGTAATGCAACGACATTAAGT 57.337 30.769 10.36 5.83 42.53 2.24
209 212 9.494271 AGAATTATGATAGTAATGCAACGACAT 57.506 29.630 0.00 0.00 0.00 3.06
210 213 8.887036 AGAATTATGATAGTAATGCAACGACA 57.113 30.769 0.00 0.00 0.00 4.35
235 243 3.682858 GCAGACAGTACCGAGCATTTTAA 59.317 43.478 0.00 0.00 0.00 1.52
238 246 1.001974 TGCAGACAGTACCGAGCATTT 59.998 47.619 0.00 0.00 0.00 2.32
239 247 0.608130 TGCAGACAGTACCGAGCATT 59.392 50.000 0.00 0.00 0.00 3.56
240 248 0.174389 CTGCAGACAGTACCGAGCAT 59.826 55.000 8.42 0.00 39.22 3.79
241 249 0.893727 TCTGCAGACAGTACCGAGCA 60.894 55.000 13.74 0.00 44.77 4.26
243 251 1.745653 TCATCTGCAGACAGTACCGAG 59.254 52.381 20.97 0.91 44.77 4.63
244 252 1.834188 TCATCTGCAGACAGTACCGA 58.166 50.000 20.97 4.33 44.77 4.69
246 254 3.553922 GCCTATCATCTGCAGACAGTACC 60.554 52.174 20.97 1.33 44.77 3.34
251 515 0.390492 CCGCCTATCATCTGCAGACA 59.610 55.000 20.97 9.32 0.00 3.41
255 519 0.541392 ACAACCGCCTATCATCTGCA 59.459 50.000 0.00 0.00 0.00 4.41
262 526 0.727398 GCTTGTCACAACCGCCTATC 59.273 55.000 0.00 0.00 0.00 2.08
271 535 1.332065 TCGCGATTTTGCTTGTCACAA 59.668 42.857 3.71 0.00 0.00 3.33
277 543 5.088739 AGTAAAGAATCGCGATTTTGCTTG 58.911 37.500 32.89 0.00 0.00 4.01
279 545 4.946784 AGTAAAGAATCGCGATTTTGCT 57.053 36.364 32.89 27.18 0.00 3.91
280 546 5.796813 AGTAGTAAAGAATCGCGATTTTGC 58.203 37.500 32.89 25.63 0.00 3.68
281 547 8.655378 AAAAGTAGTAAAGAATCGCGATTTTG 57.345 30.769 32.89 0.00 0.00 2.44
309 575 9.288576 GGATCATGACAATAATAAATCCTCACA 57.711 33.333 0.00 0.00 0.00 3.58
369 641 8.664079 AGCTCATGTATCTGAACCCTTATTATT 58.336 33.333 0.00 0.00 0.00 1.40
371 643 7.618019 AGCTCATGTATCTGAACCCTTATTA 57.382 36.000 0.00 0.00 0.00 0.98
374 646 6.461092 CGTTAGCTCATGTATCTGAACCCTTA 60.461 42.308 0.00 0.00 0.00 2.69
382 655 8.906693 CAAGTATTACGTTAGCTCATGTATCTG 58.093 37.037 0.00 0.00 0.00 2.90
384 657 8.080417 TCCAAGTATTACGTTAGCTCATGTATC 58.920 37.037 0.00 0.00 0.00 2.24
414 690 6.462500 ATTGCATGCTTGTAAAAATGGTACA 58.538 32.000 20.33 0.00 34.88 2.90
457 733 6.877855 TGCGTCATACTACCTACTCCTATAAG 59.122 42.308 0.00 0.00 0.00 1.73
505 781 6.130298 ACGACAATGACATGAAAACAGAAA 57.870 33.333 0.00 0.00 0.00 2.52
514 790 4.188462 GGTGGATAACGACAATGACATGA 58.812 43.478 0.00 0.00 0.00 3.07
577 853 2.095668 CGTAGAGACCGGAGATATGCAC 60.096 54.545 9.46 0.00 0.00 4.57
676 952 2.878406 CACAACTTGGTCGACAATCCTT 59.122 45.455 18.91 0.00 38.65 3.36
724 1000 3.396260 AGTAACCTTACGTGTGCATGT 57.604 42.857 0.00 2.46 38.65 3.21
775 1052 6.262273 GGTTGTTCAACATCTCCTGTTTTCTA 59.738 38.462 15.89 0.00 45.98 2.10
892 1175 4.756642 AGTGTGGTGACATGATGTAACTTG 59.243 41.667 12.58 0.00 46.14 3.16
898 1181 4.156556 GCAAATAGTGTGGTGACATGATGT 59.843 41.667 0.00 0.00 46.14 3.06
1017 1301 1.503818 GCACGGCGAGGAGAAACAAA 61.504 55.000 16.62 0.00 0.00 2.83
1431 1980 3.007074 GCTGTTCTTAGTATCCCTAGGCC 59.993 52.174 2.05 0.00 0.00 5.19
1672 2221 2.774687 GGGAACACAAATACGTCACCT 58.225 47.619 0.00 0.00 0.00 4.00
1726 2275 3.677527 GCTGCTGGCTTGTCATGT 58.322 55.556 0.00 0.00 38.06 3.21
1957 2507 1.452110 GCAGGCACACACATACATGA 58.548 50.000 0.00 0.00 0.00 3.07
2089 2639 2.284699 AGGGAAGAGGACACCCCG 60.285 66.667 0.00 0.00 44.21 5.73
2091 2641 0.324091 TACGAGGGAAGAGGACACCC 60.324 60.000 0.00 0.00 43.55 4.61
2156 2706 3.537580 CCCAAAAATAGCATGCAAGCAT 58.462 40.909 21.98 0.86 36.85 3.79
2173 2723 5.874810 GCATATCTCTAAATATCGTGCCCAA 59.125 40.000 0.00 0.00 0.00 4.12
2243 6568 2.747686 GTGGCAAGGAACTCGGGA 59.252 61.111 0.00 0.00 38.49 5.14
2247 6572 1.172812 GGTGTGGTGGCAAGGAACTC 61.173 60.000 0.00 0.00 38.49 3.01
2354 6679 7.237055 ACCCATAGGAAACTTCTAGTGTTACTT 59.763 37.037 4.79 0.00 43.67 2.24
2515 6844 5.236478 ACTTCAACTCACGTGACTAAATTGG 59.764 40.000 15.76 4.80 0.00 3.16
2527 6856 6.062646 CGTAAACAACATACTTCAACTCACG 58.937 40.000 0.00 0.00 0.00 4.35
2547 6876 2.414559 CGTAAACTCTTCGGGCTCGTAA 60.415 50.000 5.57 0.00 37.69 3.18
2773 7102 4.504097 GGCGCTTGATGTTTTATCATTTCC 59.496 41.667 7.64 0.00 0.00 3.13
2779 7108 5.424121 ACTATGGCGCTTGATGTTTTATC 57.576 39.130 7.64 0.00 0.00 1.75
2794 7123 4.994852 TCACGCCTAATGATTTACTATGGC 59.005 41.667 0.00 0.00 36.14 4.40
2815 7144 9.038072 TCATTACTTACCAACCATAAGTAGTCA 57.962 33.333 5.14 0.00 42.92 3.41
2819 7148 9.661563 CTTGTCATTACTTACCAACCATAAGTA 57.338 33.333 1.42 1.42 41.84 2.24
2823 7152 9.038072 TCTACTTGTCATTACTTACCAACCATA 57.962 33.333 0.00 0.00 0.00 2.74
2838 7167 4.284490 TGTCTTGCCTTCTCTACTTGTCAT 59.716 41.667 0.00 0.00 0.00 3.06
2864 7193 1.623811 TCCCCTCTAATAATGCCTCGC 59.376 52.381 0.00 0.00 0.00 5.03
2868 7197 4.623171 CGGTATGTCCCCTCTAATAATGCC 60.623 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.