Multiple sequence alignment - TraesCS4B01G183600

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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 TraesCS4B01G183600 chr4B 100.000 4228 0 0 1 4228 402989480 402985253 0.000000e+00 7808
1 TraesCS4B01G183600 chr4B 98.336 721 10 2 1 719 402996183 402995463 0.000000e+00 1264
2 TraesCS4B01G183600 chr4B 97.493 718 16 2 3 719 596038713 596037997 0.000000e+00 1225
3 TraesCS4B01G183600 chr7B 98.778 3518 34 6 720 4228 113100422 113096905 0.000000e+00 6250
4 TraesCS4B01G183600 chr7D 89.846 3368 237 49 914 4228 150938798 150935483 0.000000e+00 4228
5 TraesCS4B01G183600 chr7A 94.213 1106 54 5 2473 3577 150883538 150882442 0.000000e+00 1679
6 TraesCS4B01G183600 chr7A 87.628 978 85 20 1497 2463 150890816 150889864 0.000000e+00 1103
7 TraesCS4B01G183600 chr7A 92.334 587 39 2 899 1479 150891390 150890804 0.000000e+00 830
8 TraesCS4B01G183600 chr7A 87.680 625 47 13 3616 4228 150882442 150881836 0.000000e+00 701
9 TraesCS4B01G183600 chr4A 97.920 721 14 1 3 722 630848970 630848250 0.000000e+00 1247
10 TraesCS4B01G183600 chr4A 97.911 718 14 1 3 719 209845364 209846081 0.000000e+00 1242
11 TraesCS4B01G183600 chr4A 97.636 719 12 3 3 720 630855495 630856209 0.000000e+00 1229
12 TraesCS4B01G183600 chr4A 97.214 718 19 1 3 719 209838044 209838761 0.000000e+00 1214
13 TraesCS4B01G183600 chr5B 97.087 721 15 6 3 719 413321360 413320642 0.000000e+00 1210
14 TraesCS4B01G183600 chr5B 97.079 719 17 4 3 719 573059871 573059155 0.000000e+00 1208
15 TraesCS4B01G183600 chr5B 96.944 720 17 5 3 719 573052374 573051657 0.000000e+00 1203
16 TraesCS4B01G183600 chrUn 100.000 425 0 0 2467 2891 476593914 476593490 0.000000e+00 785
17 TraesCS4B01G183600 chr6B 91.247 377 30 3 2598 2973 516562843 516563217 1.050000e-140 510
18 TraesCS4B01G183600 chr6B 93.578 109 6 1 2958 3066 516563771 516563878 1.220000e-35 161


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 TraesCS4B01G183600 chr4B 402985253 402989480 4227 True 7808.0 7808 100.0000 1 4228 1 chr4B.!!$R1 4227
1 TraesCS4B01G183600 chr4B 402995463 402996183 720 True 1264.0 1264 98.3360 1 719 1 chr4B.!!$R2 718
2 TraesCS4B01G183600 chr4B 596037997 596038713 716 True 1225.0 1225 97.4930 3 719 1 chr4B.!!$R3 716
3 TraesCS4B01G183600 chr7B 113096905 113100422 3517 True 6250.0 6250 98.7780 720 4228 1 chr7B.!!$R1 3508
4 TraesCS4B01G183600 chr7D 150935483 150938798 3315 True 4228.0 4228 89.8460 914 4228 1 chr7D.!!$R1 3314
5 TraesCS4B01G183600 chr7A 150881836 150883538 1702 True 1190.0 1679 90.9465 2473 4228 2 chr7A.!!$R1 1755
6 TraesCS4B01G183600 chr7A 150889864 150891390 1526 True 966.5 1103 89.9810 899 2463 2 chr7A.!!$R2 1564
7 TraesCS4B01G183600 chr4A 630848250 630848970 720 True 1247.0 1247 97.9200 3 722 1 chr4A.!!$R1 719
8 TraesCS4B01G183600 chr4A 209845364 209846081 717 False 1242.0 1242 97.9110 3 719 1 chr4A.!!$F2 716
9 TraesCS4B01G183600 chr4A 630855495 630856209 714 False 1229.0 1229 97.6360 3 720 1 chr4A.!!$F3 717
10 TraesCS4B01G183600 chr4A 209838044 209838761 717 False 1214.0 1214 97.2140 3 719 1 chr4A.!!$F1 716
11 TraesCS4B01G183600 chr5B 413320642 413321360 718 True 1210.0 1210 97.0870 3 719 1 chr5B.!!$R1 716
12 TraesCS4B01G183600 chr5B 573059155 573059871 716 True 1208.0 1208 97.0790 3 719 1 chr5B.!!$R3 716
13 TraesCS4B01G183600 chr5B 573051657 573052374 717 True 1203.0 1203 96.9440 3 719 1 chr5B.!!$R2 716
14 TraesCS4B01G183600 chr6B 516562843 516563878 1035 False 335.5 510 92.4125 2598 3066 2 chr6B.!!$F1 468

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
146 147 1.054978 GTCGCCCTTATCCCTTCCCT 61.055 60.000 0.0 0.0 0.0 4.20 F
1772 1813 1.437160 CAGTGTGTTTGGTGGTGGC 59.563 57.895 0.0 0.0 0.0 5.01 F
1777 1818 0.466555 GTGTTTGGTGGTGGCTGGTA 60.467 55.000 0.0 0.0 0.0 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 1818 0.458543 CTGTGCCTAGCGTCAACGAT 60.459 55.000 6.75 2.03 43.02 3.73 R
3121 3735 1.266178 CAATGGAGTTTTCCCACCCC 58.734 55.000 0.00 0.00 43.33 4.95 R
3469 4083 3.351740 TGAGAACAACCACAGAGCAAAA 58.648 40.909 0.00 0.00 0.00 2.44 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
31 32 2.475371 GATGCGATGGGGAGGGGATG 62.475 65.000 0.00 0.00 0.00 3.51
146 147 1.054978 GTCGCCCTTATCCCTTCCCT 61.055 60.000 0.00 0.00 0.00 4.20
216 217 1.630878 GGTTGGGTGAACAGAGAGGAT 59.369 52.381 0.00 0.00 36.12 3.24
542 549 4.339748 ACCCTTTGCAAAAATGTTGGTTT 58.660 34.783 13.84 0.00 0.00 3.27
775 783 2.478831 ACATGCGCAAATTTTTCGGTT 58.521 38.095 17.11 0.00 0.00 4.44
799 807 7.825331 TTACATGTAGTTTGAAAATGGGTCA 57.175 32.000 5.56 0.00 0.00 4.02
801 809 7.301868 ACATGTAGTTTGAAAATGGGTCAAT 57.698 32.000 0.00 0.00 35.03 2.57
847 855 6.852858 TCATTTGCATCGATATTCGGTTTA 57.147 33.333 0.00 0.00 40.88 2.01
859 867 2.074547 TCGGTTTAGCTTTCTGTCCG 57.925 50.000 0.00 0.00 38.16 4.79
866 874 5.205565 GTTTAGCTTTCTGTCCGTTTTGAG 58.794 41.667 0.00 0.00 0.00 3.02
885 893 3.067106 GAGTCAAACGGATTTCTGCAGA 58.933 45.455 13.74 13.74 0.00 4.26
1581 1617 1.891150 TCTTAACGCCGGAAGAAGAGT 59.109 47.619 5.05 0.00 0.00 3.24
1637 1673 7.698130 GTCACCAAAATATCATCAGTTAAGTGC 59.302 37.037 5.35 0.00 0.00 4.40
1663 1699 8.169268 CGTTTCACTATCTTACTGTCCATTTTC 58.831 37.037 0.00 0.00 0.00 2.29
1772 1813 1.437160 CAGTGTGTTTGGTGGTGGC 59.563 57.895 0.00 0.00 0.00 5.01
1777 1818 0.466555 GTGTTTGGTGGTGGCTGGTA 60.467 55.000 0.00 0.00 0.00 3.25
3121 3735 9.613957 TGTTTGGATTTATGTTTACACATTACG 57.386 29.630 0.00 0.00 41.16 3.18
3159 3773 1.559682 TGGACCTGAGCCTATGTTTCC 59.440 52.381 0.00 0.00 0.00 3.13
3359 3973 1.945394 CTCCTTTGCATCCGGATTCTG 59.055 52.381 16.19 6.71 0.00 3.02
3469 4083 4.503643 CCATGCAACTTGGAACTTGGAAAT 60.504 41.667 0.00 0.00 36.26 2.17
3983 4633 4.508492 GCATCATCTGAGAGTGAACTCATG 59.492 45.833 12.76 7.51 44.32 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.775654 CTCTCCCTCGCACCCCAC 61.776 72.222 0.00 0.00 0.00 4.61
199 200 1.203300 TCCATCCTCTCTGTTCACCCA 60.203 52.381 0.00 0.00 0.00 4.51
258 263 1.380380 CCCTGGGCCTTTGTCATCC 60.380 63.158 4.53 0.00 0.00 3.51
289 295 7.265647 AGAGCAGAGGTAAAAGAAAAAGAAC 57.734 36.000 0.00 0.00 0.00 3.01
775 783 7.825331 TGACCCATTTTCAAACTACATGTAA 57.175 32.000 7.06 0.00 0.00 2.41
799 807 4.100189 TGGTTGTTCGTTTTTCATCCCATT 59.900 37.500 0.00 0.00 0.00 3.16
801 809 3.024547 TGGTTGTTCGTTTTTCATCCCA 58.975 40.909 0.00 0.00 0.00 4.37
847 855 2.872858 GACTCAAAACGGACAGAAAGCT 59.127 45.455 0.00 0.00 0.00 3.74
859 867 4.441087 GCAGAAATCCGTTTGACTCAAAAC 59.559 41.667 5.76 0.97 35.03 2.43
866 874 2.095718 GGTCTGCAGAAATCCGTTTGAC 60.096 50.000 20.19 1.55 0.00 3.18
1082 1105 1.749634 GACGGTAGTGAGGTAGTGCAT 59.250 52.381 0.00 0.00 0.00 3.96
1509 1543 4.247258 CGGCACAATAAGGTGTACAGTTA 58.753 43.478 0.00 0.00 40.89 2.24
1581 1617 6.239261 GCTGTCTCATTCTGATCCAAGATAGA 60.239 42.308 0.00 0.00 0.00 1.98
1637 1673 7.596749 AAATGGACAGTAAGATAGTGAAACG 57.403 36.000 0.00 0.00 45.86 3.60
1772 1813 1.864435 GCCTAGCGTCAACGATACCAG 60.864 57.143 6.75 0.00 43.02 4.00
1777 1818 0.458543 CTGTGCCTAGCGTCAACGAT 60.459 55.000 6.75 2.03 43.02 3.73
2465 2510 0.250597 AAGGGCCAACGTACAGGAAC 60.251 55.000 6.18 0.00 0.00 3.62
3121 3735 1.266178 CAATGGAGTTTTCCCACCCC 58.734 55.000 0.00 0.00 43.33 4.95
3159 3773 6.933521 AGATCATATGAGTTGAAATCCCTTCG 59.066 38.462 11.78 0.00 36.78 3.79
3359 3973 5.036117 TGGTTCCATCTACATAAGCTTCC 57.964 43.478 0.00 0.00 0.00 3.46
3469 4083 3.351740 TGAGAACAACCACAGAGCAAAA 58.648 40.909 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.