Multiple sequence alignment - TraesCS4B01G332100

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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 TraesCS4B01G332100 chr4B 100.000 2222 0 0 1 2222 622489846 622487625 0.000000e+00 4104.0
1 TraesCS4B01G332100 chr3B 96.000 1550 41 6 1 1538 12308423 12309963 0.000000e+00 2499.0
2 TraesCS4B01G332100 chr3B 91.975 1433 92 12 114 1539 452906815 452908231 0.000000e+00 1988.0
3 TraesCS4B01G332100 chr3B 91.301 1437 105 7 114 1540 77702026 77703452 0.000000e+00 1943.0
4 TraesCS4B01G332100 chr3B 94.562 662 31 2 1537 2194 10030214 10029554 0.000000e+00 1018.0
5 TraesCS4B01G332100 chr3B 95.798 119 5 0 1 119 753818090 753817972 2.250000e-45 193.0
6 TraesCS4B01G332100 chr3B 95.000 120 6 0 1 120 791761806 791761687 2.910000e-44 189.0
7 TraesCS4B01G332100 chr7B 92.243 1431 89 11 117 1540 290955046 290953631 0.000000e+00 2008.0
8 TraesCS4B01G332100 chr7B 90.111 1436 118 10 114 1539 692826492 692827913 0.000000e+00 1844.0
9 TraesCS4B01G332100 chr7B 90.497 1168 87 10 114 1270 692793780 692794934 0.000000e+00 1520.0
10 TraesCS4B01G332100 chr7B 92.509 881 63 3 665 1542 226424060 226424940 0.000000e+00 1258.0
11 TraesCS4B01G332100 chr7B 86.736 671 69 16 1537 2194 316355444 316354781 0.000000e+00 728.0
12 TraesCS4B01G332100 chr7B 93.774 257 16 0 1938 2194 36423339 36423083 9.620000e-104 387.0
13 TraesCS4B01G332100 chr7B 96.552 116 4 0 1 116 692792582 692792697 2.250000e-45 193.0
14 TraesCS4B01G332100 chr5A 90.847 1453 110 10 98 1537 33169969 33171411 0.000000e+00 1925.0
15 TraesCS4B01G332100 chrUn 89.713 1254 109 7 117 1361 278600336 278599094 0.000000e+00 1583.0
16 TraesCS4B01G332100 chr6A 89.427 1135 85 11 411 1535 49138649 49139758 0.000000e+00 1399.0
17 TraesCS4B01G332100 chr6A 89.339 1135 86 11 411 1535 49137276 49138385 0.000000e+00 1393.0
18 TraesCS4B01G332100 chr7A 90.551 1016 76 7 532 1537 709417192 709418197 0.000000e+00 1327.0
19 TraesCS4B01G332100 chr7A 91.620 895 66 6 652 1538 709547055 709546162 0.000000e+00 1229.0
20 TraesCS4B01G332100 chr7A 95.798 119 5 0 1 119 644039184 644039066 2.250000e-45 193.0
21 TraesCS4B01G332100 chr3A 92.584 863 62 2 679 1539 675317128 675316266 0.000000e+00 1238.0
22 TraesCS4B01G332100 chr3A 94.286 455 25 1 117 570 675317578 675317124 0.000000e+00 695.0
23 TraesCS4B01G332100 chr3A 97.368 114 3 0 6 119 675318767 675318654 6.260000e-46 195.0
24 TraesCS4B01G332100 chr6B 96.505 658 17 2 1537 2194 717734518 717735169 0.000000e+00 1083.0
25 TraesCS4B01G332100 chr6B 100.000 41 0 0 2182 2222 717735178 717735218 2.370000e-10 76.8
26 TraesCS4B01G332100 chr2B 95.137 658 29 2 1537 2194 225321978 225321324 0.000000e+00 1035.0
27 TraesCS4B01G332100 chr2B 92.184 435 31 3 1537 1971 664326415 664325984 1.460000e-171 612.0
28 TraesCS4B01G332100 chr2B 95.798 119 5 0 1 119 140782831 140782713 2.250000e-45 193.0
29 TraesCS4B01G332100 chr2B 97.561 41 1 0 2182 2222 225321315 225321275 1.100000e-08 71.3
30 TraesCS4B01G332100 chr1B 94.833 658 26 2 1537 2194 359216888 359216239 0.000000e+00 1020.0
31 TraesCS4B01G332100 chr1B 95.798 119 5 0 1 119 679687819 679687701 2.250000e-45 193.0
32 TraesCS4B01G332100 chr1B 100.000 41 0 0 2182 2222 359216230 359216190 2.370000e-10 76.8
33 TraesCS4B01G332100 chr5B 92.042 666 44 5 1537 2194 529283588 529284252 0.000000e+00 928.0
34 TraesCS4B01G332100 chr5B 90.991 666 50 4 1537 2194 649897394 649898057 0.000000e+00 889.0
35 TraesCS4B01G332100 chr5B 89.501 381 24 7 1832 2196 574967444 574967064 3.340000e-128 468.0
36 TraesCS4B01G332100 chr5B 97.368 114 3 0 3 116 9038790 9038903 6.260000e-46 195.0
37 TraesCS4B01G332100 chr5D 89.681 659 55 6 1537 2194 387245806 387246452 0.000000e+00 828.0
38 TraesCS4B01G332100 chr5D 86.018 329 40 4 1866 2194 478199535 478199213 4.540000e-92 348.0


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 TraesCS4B01G332100 chr4B 622487625 622489846 2221 True 4104.000000 4104 100.0000 1 2222 1 chr4B.!!$R1 2221
1 TraesCS4B01G332100 chr3B 12308423 12309963 1540 False 2499.000000 2499 96.0000 1 1538 1 chr3B.!!$F1 1537
2 TraesCS4B01G332100 chr3B 452906815 452908231 1416 False 1988.000000 1988 91.9750 114 1539 1 chr3B.!!$F3 1425
3 TraesCS4B01G332100 chr3B 77702026 77703452 1426 False 1943.000000 1943 91.3010 114 1540 1 chr3B.!!$F2 1426
4 TraesCS4B01G332100 chr3B 10029554 10030214 660 True 1018.000000 1018 94.5620 1537 2194 1 chr3B.!!$R1 657
5 TraesCS4B01G332100 chr7B 290953631 290955046 1415 True 2008.000000 2008 92.2430 117 1540 1 chr7B.!!$R2 1423
6 TraesCS4B01G332100 chr7B 692826492 692827913 1421 False 1844.000000 1844 90.1110 114 1539 1 chr7B.!!$F2 1425
7 TraesCS4B01G332100 chr7B 226424060 226424940 880 False 1258.000000 1258 92.5090 665 1542 1 chr7B.!!$F1 877
8 TraesCS4B01G332100 chr7B 692792582 692794934 2352 False 856.500000 1520 93.5245 1 1270 2 chr7B.!!$F3 1269
9 TraesCS4B01G332100 chr7B 316354781 316355444 663 True 728.000000 728 86.7360 1537 2194 1 chr7B.!!$R3 657
10 TraesCS4B01G332100 chr5A 33169969 33171411 1442 False 1925.000000 1925 90.8470 98 1537 1 chr5A.!!$F1 1439
11 TraesCS4B01G332100 chrUn 278599094 278600336 1242 True 1583.000000 1583 89.7130 117 1361 1 chrUn.!!$R1 1244
12 TraesCS4B01G332100 chr6A 49137276 49139758 2482 False 1396.000000 1399 89.3830 411 1535 2 chr6A.!!$F1 1124
13 TraesCS4B01G332100 chr7A 709417192 709418197 1005 False 1327.000000 1327 90.5510 532 1537 1 chr7A.!!$F1 1005
14 TraesCS4B01G332100 chr7A 709546162 709547055 893 True 1229.000000 1229 91.6200 652 1538 1 chr7A.!!$R2 886
15 TraesCS4B01G332100 chr3A 675316266 675318767 2501 True 709.333333 1238 94.7460 6 1539 3 chr3A.!!$R1 1533
16 TraesCS4B01G332100 chr6B 717734518 717735218 700 False 579.900000 1083 98.2525 1537 2222 2 chr6B.!!$F1 685
17 TraesCS4B01G332100 chr2B 225321275 225321978 703 True 553.150000 1035 96.3490 1537 2222 2 chr2B.!!$R3 685
18 TraesCS4B01G332100 chr1B 359216190 359216888 698 True 548.400000 1020 97.4165 1537 2222 2 chr1B.!!$R2 685
19 TraesCS4B01G332100 chr5B 529283588 529284252 664 False 928.000000 928 92.0420 1537 2194 1 chr5B.!!$F2 657
20 TraesCS4B01G332100 chr5B 649897394 649898057 663 False 889.000000 889 90.9910 1537 2194 1 chr5B.!!$F3 657
21 TraesCS4B01G332100 chr5D 387245806 387246452 646 False 828.000000 828 89.6810 1537 2194 1 chr5D.!!$F1 657

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
894 1991 4.077184 CTACGCCACGGCCCAGAA 62.077 66.667 1.63 0.0 37.98 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 3065 0.395586 TTTTGCTGCTGTGGTGAGGT 60.396 50.0 0.0 0.0 0.0 3.85 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
249 1336 5.350504 TCAAATTTCTCAACCAGGCAAAA 57.649 34.783 0.00 0.00 0.00 2.44
528 1617 6.837471 AACGGAGGGAGTATATATGAGAAC 57.163 41.667 0.00 0.00 0.00 3.01
643 1740 9.896645 TTTCTAGAATGCATCTCAAGAATTACT 57.103 29.630 5.89 0.00 39.71 2.24
644 1741 9.896645 TTCTAGAATGCATCTCAAGAATTACTT 57.103 29.630 0.00 0.00 39.71 2.24
894 1991 4.077184 CTACGCCACGGCCCAGAA 62.077 66.667 1.63 0.00 37.98 3.02
1058 2162 0.317479 GGAGTTGTCGCAGTAGTGGT 59.683 55.000 0.00 0.00 0.00 4.16
1150 2256 4.161295 CTCGCGCTTCCCCCATCA 62.161 66.667 5.56 0.00 0.00 3.07
1177 2283 4.429522 TGCATGATGGCGGCAGGT 62.430 61.111 19.29 0.00 36.28 4.00
1228 2334 4.807304 GGATGCGTCCGAGATAAGTTTTTA 59.193 41.667 9.75 0.00 34.13 1.52
1258 2364 7.555554 AGGATGGATTTGTCTGAGATTAGTTTG 59.444 37.037 0.00 0.00 0.00 2.93
1375 2482 1.531365 TCCACGGTGGAGTACGGTT 60.531 57.895 25.53 0.00 42.67 4.44
1658 2769 4.942852 TGATGTGATTCCAACCAACAAAC 58.057 39.130 0.00 0.00 0.00 2.93
1666 2777 2.093394 TCCAACCAACAAACGTGAGAGA 60.093 45.455 0.00 0.00 0.00 3.10
1941 3065 0.469331 CTATGGCGGTAGGGTCCTGA 60.469 60.000 0.00 0.00 0.00 3.86
1988 3114 7.773690 ACACCTATAAACTTCAGTTTTCACAGT 59.226 33.333 10.15 0.89 45.07 3.55
2049 3187 8.510243 TTCACAGCAGTTCATCATATGTAATT 57.490 30.769 1.90 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
528 1617 3.624410 TGTGATCTGGAGCATGAAAATCG 59.376 43.478 0.00 0.00 0.00 3.34
635 1732 4.323417 TCAACCATCGCACAAGTAATTCT 58.677 39.130 0.00 0.00 0.00 2.40
639 1736 5.079689 TCTATCAACCATCGCACAAGTAA 57.920 39.130 0.00 0.00 0.00 2.24
640 1737 4.729227 TCTATCAACCATCGCACAAGTA 57.271 40.909 0.00 0.00 0.00 2.24
641 1738 3.610040 TCTATCAACCATCGCACAAGT 57.390 42.857 0.00 0.00 0.00 3.16
642 1739 4.122046 TCATCTATCAACCATCGCACAAG 58.878 43.478 0.00 0.00 0.00 3.16
643 1740 4.135747 TCATCTATCAACCATCGCACAA 57.864 40.909 0.00 0.00 0.00 3.33
644 1741 3.817709 TCATCTATCAACCATCGCACA 57.182 42.857 0.00 0.00 0.00 4.57
645 1742 5.679734 ATTTCATCTATCAACCATCGCAC 57.320 39.130 0.00 0.00 0.00 5.34
646 1743 5.506151 GCAATTTCATCTATCAACCATCGCA 60.506 40.000 0.00 0.00 0.00 5.10
647 1744 4.913924 GCAATTTCATCTATCAACCATCGC 59.086 41.667 0.00 0.00 0.00 4.58
648 1745 6.017687 TCTGCAATTTCATCTATCAACCATCG 60.018 38.462 0.00 0.00 0.00 3.84
649 1746 7.268199 TCTGCAATTTCATCTATCAACCATC 57.732 36.000 0.00 0.00 0.00 3.51
650 1747 7.504574 TGATCTGCAATTTCATCTATCAACCAT 59.495 33.333 0.00 0.00 0.00 3.55
890 1987 1.079127 CTAGGGTGGCACCGTTCTG 60.079 63.158 33.90 20.80 39.83 3.02
894 1991 4.326227 TCCCTAGGGTGGCACCGT 62.326 66.667 31.84 31.84 39.83 4.83
1058 2162 2.364317 AGGCCAGGCGCTCTTCTA 60.364 61.111 7.64 0.00 37.74 2.10
1150 2256 1.311859 CCATCATGCACGCTAACCAT 58.688 50.000 0.00 0.00 0.00 3.55
1177 2283 1.227263 GGAAGCTAATCGCGAGCCA 60.227 57.895 16.66 0.37 45.59 4.75
1228 2334 9.790344 CTAATCTCAGACAAATCCATCCTATTT 57.210 33.333 0.00 0.00 0.00 1.40
1258 2364 2.072298 GAGTGCATCCATCCTATTCGC 58.928 52.381 0.00 0.00 0.00 4.70
1658 2769 4.693566 GGTATCTCTATCACCTCTCTCACG 59.306 50.000 0.00 0.00 0.00 4.35
1666 2777 7.786943 TCATCTTTGAAGGTATCTCTATCACCT 59.213 37.037 0.00 0.00 44.66 4.00
1741 2852 1.230281 TCCCCATTGAAGCCCTCCT 60.230 57.895 0.00 0.00 0.00 3.69
1893 3017 3.602104 TAGGGCTGCGTAACCTACT 57.398 52.632 0.00 0.00 35.84 2.57
1941 3065 0.395586 TTTTGCTGCTGTGGTGAGGT 60.396 50.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.