Multiple sequence alignment - TraesCS7B01G361100

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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 TraesCS7B01G361100 chr7B 100.000 2390 0 0 1 2390 623271718 623269329 0.000000e+00 4414.0
1 TraesCS7B01G361100 chr7B 94.576 1899 85 12 177 2070 623485940 623484055 0.000000e+00 2920.0
2 TraesCS7B01G361100 chr7B 92.357 2041 126 17 167 2198 623059946 623057927 0.000000e+00 2878.0
3 TraesCS7B01G361100 chr7B 92.308 1963 114 11 237 2198 623102632 623100706 0.000000e+00 2754.0
4 TraesCS7B01G361100 chr7B 93.846 1170 56 8 231 1388 623373593 623372428 0.000000e+00 1748.0
5 TraesCS7B01G361100 chr7B 94.832 1103 51 4 1101 2198 586929659 586930760 0.000000e+00 1716.0
6 TraesCS7B01G361100 chr7B 93.134 1005 63 4 269 1267 623537885 623536881 0.000000e+00 1469.0
7 TraesCS7B01G361100 chr7B 92.654 1021 69 3 249 1267 623523444 623522428 0.000000e+00 1465.0
8 TraesCS7B01G361100 chr7B 95.005 921 43 2 1281 2198 623522372 623521452 0.000000e+00 1443.0
9 TraesCS7B01G361100 chr7B 94.886 919 46 1 1281 2198 623504495 623503577 0.000000e+00 1435.0
10 TraesCS7B01G361100 chr7B 94.565 920 48 2 1281 2198 623536811 623535892 0.000000e+00 1421.0
11 TraesCS7B01G361100 chr7B 91.546 970 48 11 1441 2389 623372415 623371459 0.000000e+00 1306.0
12 TraesCS7B01G361100 chr7B 91.892 777 58 3 249 1025 623540120 623539349 0.000000e+00 1081.0
13 TraesCS7B01G361100 chr7B 91.938 769 58 2 249 1017 623508332 623507568 0.000000e+00 1074.0
14 TraesCS7B01G361100 chr7B 85.373 335 37 7 1 333 623486006 623485682 1.060000e-88 337.0
15 TraesCS7B01G361100 chr7B 86.321 212 8 13 2199 2390 623521490 623521280 6.690000e-51 211.0
16 TraesCS7B01G361100 chr7B 85.849 212 9 13 2199 2390 623503615 623503405 3.110000e-49 206.0
17 TraesCS7B01G361100 chr7B 86.124 209 8 13 2202 2390 623535927 623535720 3.110000e-49 206.0
18 TraesCS7B01G361100 chr7B 84.906 212 11 2 2199 2390 586930722 586930932 6.740000e-46 195.0
19 TraesCS7B01G361100 chr7B 83.568 213 13 3 2199 2390 623057965 623057754 1.890000e-41 180.0
20 TraesCS7B01G361100 chr7D 92.853 1861 104 17 351 2198 568236268 568234424 0.000000e+00 2673.0
21 TraesCS7B01G361100 chr7D 83.159 1342 191 21 455 1771 568185804 568184473 0.000000e+00 1194.0
22 TraesCS7B01G361100 chr7D 83.333 210 14 2 2201 2390 568234460 568234252 8.780000e-40 174.0
23 TraesCS7B01G361100 chr2B 83.962 106 17 0 2199 2304 524517363 524517468 4.200000e-18 102.0
24 TraesCS7B01G361100 chr1B 81.818 110 14 5 2199 2304 553802603 553802710 1.180000e-13 87.9
25 TraesCS7B01G361100 chr4A 100.000 32 0 0 2264 2295 191794166 191794197 2.570000e-05 60.2


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 TraesCS7B01G361100 chr7B 623269329 623271718 2389 True 4414.000000 4414 100.000000 1 2390 1 chr7B.!!$R2 2389
1 TraesCS7B01G361100 chr7B 623100706 623102632 1926 True 2754.000000 2754 92.308000 237 2198 1 chr7B.!!$R1 1961
2 TraesCS7B01G361100 chr7B 623484055 623486006 1951 True 1628.500000 2920 89.974500 1 2070 2 chr7B.!!$R5 2069
3 TraesCS7B01G361100 chr7B 623057754 623059946 2192 True 1529.000000 2878 87.962500 167 2390 2 chr7B.!!$R3 2223
4 TraesCS7B01G361100 chr7B 623371459 623373593 2134 True 1527.000000 1748 92.696000 231 2389 2 chr7B.!!$R4 2158
5 TraesCS7B01G361100 chr7B 623535720 623540120 4400 True 1044.250000 1469 91.428750 249 2390 4 chr7B.!!$R8 2141
6 TraesCS7B01G361100 chr7B 623521280 623523444 2164 True 1039.666667 1465 91.326667 249 2390 3 chr7B.!!$R7 2141
7 TraesCS7B01G361100 chr7B 586929659 586930932 1273 False 955.500000 1716 89.869000 1101 2390 2 chr7B.!!$F1 1289
8 TraesCS7B01G361100 chr7B 623503405 623508332 4927 True 905.000000 1435 90.891000 249 2390 3 chr7B.!!$R6 2141
9 TraesCS7B01G361100 chr7D 568234252 568236268 2016 True 1423.500000 2673 88.093000 351 2390 2 chr7D.!!$R2 2039
10 TraesCS7B01G361100 chr7D 568184473 568185804 1331 True 1194.000000 1194 83.159000 455 1771 1 chr7D.!!$R1 1316


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
953 5555 0.250252 TCTTGTTCGCTCCATGCACA 60.25 50.0 0.0 0.0 43.06 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 7302 0.107703 TCATTCCATGGACGAGCACC 60.108 55.0 15.91 0.0 0.0 5.01 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
196 197 9.958125 AGATGGAGATAGAGATAGAGATAGAGA 57.042 37.037 0.00 0.0 0.00 3.10
379 396 8.821686 AGAGATAGAGATAGAGAGAGAGAGAG 57.178 42.308 0.00 0.0 0.00 3.20
383 400 8.821686 ATAGAGATAGAGAGAGAGAGAGAGAG 57.178 42.308 0.00 0.0 0.00 3.20
387 404 6.947733 AGATAGAGAGAGAGAGAGAGAGAGAG 59.052 46.154 0.00 0.0 0.00 3.20
953 5555 0.250252 TCTTGTTCGCTCCATGCACA 60.250 50.000 0.00 0.0 43.06 4.57
1083 5686 3.486841 GCGCATGTTGCAATACAATAAGG 59.513 43.478 0.59 0.0 45.36 2.69
1239 5842 4.752604 TGGTATATTGTCATATTTGCGCGT 59.247 37.500 8.43 0.0 0.00 6.01
1462 6561 6.405508 GCAAAGAATGATGTCAGATGAATGGT 60.406 38.462 0.00 0.0 0.00 3.55
1475 6576 6.316140 TCAGATGAATGGTATTTGCTGTGTAC 59.684 38.462 0.00 0.0 0.00 2.90
1486 6587 4.893424 TTGCTGTGTACTTGACCTTTTC 57.107 40.909 0.00 0.0 0.00 2.29
1497 6598 6.377327 ACTTGACCTTTTCTGTGTGTATTG 57.623 37.500 0.00 0.0 0.00 1.90
1539 6642 3.127721 TCGTCACTTGTTGTTTGCATTGA 59.872 39.130 0.00 0.0 0.00 2.57
1830 6952 4.953579 GCACATAAGGGGAAATAAGGTGAA 59.046 41.667 0.00 0.0 0.00 3.18
1848 6970 3.067601 GTGAAACCGAACACCCAAAGAAT 59.932 43.478 0.00 0.0 0.00 2.40
1992 7118 0.182061 TCCGGCACTACGATCTACCT 59.818 55.000 0.00 0.0 35.47 3.08
2038 7164 2.093447 GGATCAACGTGTGGAGAGGATT 60.093 50.000 0.00 0.0 0.00 3.01
2140 7266 1.217244 GTAGCGGGACACGGATGTT 59.783 57.895 0.00 0.0 44.51 2.71
2176 7302 1.339235 TAAGCGAACGGAAGCGAACG 61.339 55.000 0.00 0.0 38.61 3.95
2210 7336 2.159282 GGAATGAGTAGCGAACGGAAGA 60.159 50.000 0.00 0.0 0.00 2.87
2253 7379 2.024369 TGAGTGACAGGGTAGGATAGCA 60.024 50.000 0.00 0.0 41.82 3.49
2383 7550 1.266175 CGAGGGCATCTACGTTCGTAT 59.734 52.381 5.55 0.0 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 5.698104 TCTGATACTAATAACGGACTCCCA 58.302 41.667 0.00 0.00 0.00 4.37
170 171 9.958125 TCTCTATCTCTATCTCTATCTCCATCT 57.042 37.037 0.00 0.00 0.00 2.90
363 380 6.945435 TCTCTCTCTCTCTCTCTCTCTCTATC 59.055 46.154 0.00 0.00 0.00 2.08
371 388 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
375 392 4.590647 TCCATCTCTCTCTCTCTCTCTCTC 59.409 50.000 0.00 0.00 0.00 3.20
379 396 4.963318 TCTCCATCTCTCTCTCTCTCTC 57.037 50.000 0.00 0.00 0.00 3.20
383 400 6.611613 TCTCTATCTCCATCTCTCTCTCTC 57.388 45.833 0.00 0.00 0.00 3.20
387 404 7.851228 TCACTATCTCTATCTCCATCTCTCTC 58.149 42.308 0.00 0.00 0.00 3.20
618 5212 5.389859 TTGGCAATGGAGTAGTTGATTTG 57.610 39.130 0.00 0.00 0.00 2.32
651 5245 1.202486 GGCAATGGATGTGGATGCAAG 60.202 52.381 0.00 0.00 38.73 4.01
741 5339 8.475331 TCGCTTAATTGGACTCTTTTAACTAG 57.525 34.615 0.00 0.00 0.00 2.57
819 5419 1.131638 AGGACTTCTGTGCCACTCAA 58.868 50.000 0.00 0.00 34.93 3.02
953 5555 6.261826 GCAGTGATCTATATTGTTGGCTTCTT 59.738 38.462 0.00 0.00 0.00 2.52
995 5598 0.036952 CCAACAGTCTCGCATCACCT 60.037 55.000 0.00 0.00 0.00 4.00
1239 5842 2.223805 TGTTTGTGTGTTTGTGTGTGCA 60.224 40.909 0.00 0.00 0.00 4.57
1378 6477 4.422984 ACACTTAAGGCCTAGGTACTTGA 58.577 43.478 23.16 17.01 41.75 3.02
1462 6561 6.770785 AGAAAAGGTCAAGTACACAGCAAATA 59.229 34.615 0.00 0.00 0.00 1.40
1475 6576 6.618287 TCAATACACACAGAAAAGGTCAAG 57.382 37.500 0.00 0.00 0.00 3.02
1830 6952 2.938838 TCATTCTTTGGGTGTTCGGTT 58.061 42.857 0.00 0.00 0.00 4.44
1861 6987 4.093115 TCTCGCGTGTTTTTGTTTAAGTCA 59.907 37.500 5.77 0.00 0.00 3.41
2038 7164 8.875604 AGCTTTGGTGTAGCTCCATTTACACA 62.876 42.308 15.19 0.00 45.52 3.72
2071 7197 0.606401 CCGTCCAGATGCAACCAGTT 60.606 55.000 0.00 0.00 0.00 3.16
2074 7200 2.350895 CCCGTCCAGATGCAACCA 59.649 61.111 0.00 0.00 0.00 3.67
2176 7302 0.107703 TCATTCCATGGACGAGCACC 60.108 55.000 15.91 0.00 0.00 5.01
2188 7314 1.179152 TCCGTTCGCTACTCATTCCA 58.821 50.000 0.00 0.00 0.00 3.53
2220 7346 1.079503 GTCACTCATTTCCTGGACGC 58.920 55.000 0.00 0.00 0.00 5.19
2229 7355 4.101741 GCTATCCTACCCTGTCACTCATTT 59.898 45.833 0.00 0.00 0.00 2.32
2263 7389 2.660802 GCAATGCCAGCAAGCCTT 59.339 55.556 8.70 0.00 0.00 4.35



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

AutoCloner maintained by Alex Coulton.