Multiple sequence alignment - TraesCS2A01G257700

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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 TraesCS2A01G257700 chr2A 100.000 2563 0 0 1 2563 398508437 398505875 0.000000e+00 4734.0
1 TraesCS2A01G257700 chr2A 99.298 2564 17 1 1 2563 398767368 398764805 0.000000e+00 4634.0
2 TraesCS2A01G257700 chr2A 93.944 1189 66 3 1180 2365 447942413 447943598 0.000000e+00 1792.0
3 TraesCS2A01G257700 chr2A 95.538 493 20 2 1875 2365 166633093 166632601 0.000000e+00 787.0
4 TraesCS2A01G257700 chr2A 88.824 340 35 3 2024 2361 197562011 197562349 5.100000e-112 414.0
5 TraesCS2A01G257700 chr2A 93.939 231 12 1 1672 1900 166633346 166633116 5.250000e-92 348.0
6 TraesCS2A01G257700 chr2A 94.839 155 6 1 880 1032 447940915 447941069 9.160000e-60 241.0
7 TraesCS2A01G257700 chr2A 88.235 170 19 1 1672 1840 197561826 197561995 4.320000e-48 202.0
8 TraesCS2A01G257700 chr2A 98.276 58 1 0 230 287 447940827 447940884 4.510000e-18 102.0
9 TraesCS2A01G257700 chr2D 91.828 722 30 13 1672 2365 156712694 156711974 0.000000e+00 979.0
10 TraesCS2A01G257700 chr2D 87.689 528 52 8 1810 2331 182571621 182572141 1.010000e-168 603.0
11 TraesCS2A01G257700 chr2D 94.737 57 3 0 230 286 30736663 30736607 3.510000e-14 89.8
12 TraesCS2A01G257700 chr2B 90.985 721 28 14 1673 2365 214318134 214317423 0.000000e+00 937.0
13 TraesCS2A01G257700 chr2B 84.615 416 39 4 1210 1624 765085445 765085054 8.600000e-105 390.0
14 TraesCS2A01G257700 chr1A 94.779 498 25 1 1537 2034 512490947 512491443 0.000000e+00 774.0
15 TraesCS2A01G257700 chr1A 84.497 587 63 15 305 866 14462670 14462087 2.880000e-154 555.0
16 TraesCS2A01G257700 chr3A 82.799 593 69 17 305 866 726386551 726385961 1.370000e-137 499.0
17 TraesCS2A01G257700 chr1D 97.034 236 3 2 1 233 105752773 105753007 6.650000e-106 394.0
18 TraesCS2A01G257700 chr1D 96.610 236 4 2 1 233 106170508 106170742 3.090000e-104 388.0
19 TraesCS2A01G257700 chrUn 84.652 417 39 4 1209 1624 371328289 371327897 2.390000e-105 392.0
20 TraesCS2A01G257700 chr7D 97.021 235 4 2 1 233 230542003 230541770 2.390000e-105 392.0
21 TraesCS2A01G257700 chr5A 84.652 417 39 4 1209 1624 589363612 589363220 2.390000e-105 392.0
22 TraesCS2A01G257700 chr5A 89.831 236 24 0 982 1217 508868649 508868414 1.150000e-78 303.0
23 TraesCS2A01G257700 chr5A 94.444 54 3 0 234 287 613926596 613926649 1.630000e-12 84.2
24 TraesCS2A01G257700 chr6A 96.610 236 4 3 1 233 415249354 415249588 3.090000e-104 388.0
25 TraesCS2A01G257700 chr6A 92.708 192 13 1 2370 2561 21658744 21658554 2.510000e-70 276.0
26 TraesCS2A01G257700 chr5D 96.610 236 4 3 1 233 170069882 170069648 3.090000e-104 388.0
27 TraesCS2A01G257700 chr5D 96.610 236 4 2 1 233 416693730 416693964 3.090000e-104 388.0
28 TraesCS2A01G257700 chr5D 96.186 236 5 3 1 233 240346185 240346419 1.440000e-102 383.0
29 TraesCS2A01G257700 chr3D 96.186 236 5 2 1 233 417045947 417046181 1.440000e-102 383.0
30 TraesCS2A01G257700 chr3D 94.262 122 7 0 2367 2488 575921718 575921597 1.210000e-43 187.0
31 TraesCS2A01G257700 chr6D 92.386 197 14 1 2367 2563 306003792 306003987 1.940000e-71 279.0
32 TraesCS2A01G257700 chr6B 87.347 245 30 1 982 1225 513357915 513358159 1.940000e-71 279.0
33 TraesCS2A01G257700 chr6B 88.832 197 19 1 2367 2563 11708764 11708571 3.300000e-59 239.0
34 TraesCS2A01G257700 chr6B 91.803 122 10 0 2367 2488 148829778 148829899 1.220000e-38 171.0
35 TraesCS2A01G257700 chr5B 92.268 194 14 1 2370 2563 140951188 140950996 9.030000e-70 274.0
36 TraesCS2A01G257700 chr4A 90.698 86 8 0 1027 1112 102386888 102386803 5.790000e-22 115.0
37 TraesCS2A01G257700 chr7A 96.667 60 2 0 231 290 628831489 628831430 1.620000e-17 100.0


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 TraesCS2A01G257700 chr2A 398505875 398508437 2562 True 4734.000000 4734 100.000000 1 2563 1 chr2A.!!$R1 2562
1 TraesCS2A01G257700 chr2A 398764805 398767368 2563 True 4634.000000 4634 99.298000 1 2563 1 chr2A.!!$R2 2562
2 TraesCS2A01G257700 chr2A 447940827 447943598 2771 False 711.666667 1792 95.686333 230 2365 3 chr2A.!!$F2 2135
3 TraesCS2A01G257700 chr2A 166632601 166633346 745 True 567.500000 787 94.738500 1672 2365 2 chr2A.!!$R3 693
4 TraesCS2A01G257700 chr2A 197561826 197562349 523 False 308.000000 414 88.529500 1672 2361 2 chr2A.!!$F1 689
5 TraesCS2A01G257700 chr2D 156711974 156712694 720 True 979.000000 979 91.828000 1672 2365 1 chr2D.!!$R2 693
6 TraesCS2A01G257700 chr2D 182571621 182572141 520 False 603.000000 603 87.689000 1810 2331 1 chr2D.!!$F1 521
7 TraesCS2A01G257700 chr2B 214317423 214318134 711 True 937.000000 937 90.985000 1673 2365 1 chr2B.!!$R1 692
8 TraesCS2A01G257700 chr1A 14462087 14462670 583 True 555.000000 555 84.497000 305 866 1 chr1A.!!$R1 561
9 TraesCS2A01G257700 chr3A 726385961 726386551 590 True 499.000000 499 82.799000 305 866 1 chr3A.!!$R1 561

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 3.687698 TGCTTAGGACGGCAAAAGAATAC 59.312 43.478 6.05 0.0 35.40 1.89 F
187 188 3.798337 GTGAACTCATGTGGCAAAAACTG 59.202 43.478 0.00 0.0 0.00 3.16 F
1024 1058 4.408821 TTCTGCTCGGGCGCCATT 62.409 61.111 30.85 0.0 42.25 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1024 1058 1.597854 CAACAGCGACCTTCAGGCA 60.598 57.895 0.00 0.0 39.32 4.75 R
1164 1382 2.907236 GCCTCTTCCTCCTCTGGC 59.093 66.667 0.00 0.0 0.00 4.85 R
2207 3495 1.259609 TGTACTCCGGAAATGGTCGT 58.740 50.000 5.23 0.0 0.00 4.34 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
146 147 3.687698 TGCTTAGGACGGCAAAAGAATAC 59.312 43.478 6.05 0.00 35.40 1.89
187 188 3.798337 GTGAACTCATGTGGCAAAAACTG 59.202 43.478 0.00 0.00 0.00 3.16
1024 1058 4.408821 TTCTGCTCGGGCGCCATT 62.409 61.111 30.85 0.00 42.25 3.16
1164 1382 2.969238 GTCTCGCCGCCATGGATG 60.969 66.667 18.40 6.69 42.00 3.51
2207 3495 8.989131 AGGGTCTCTTACATTTATTAGCAGTTA 58.011 33.333 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 169 2.765699 ACCAGTTTTTGCCACATGAGTT 59.234 40.909 0.00 0.0 0.00 3.01
187 188 5.546526 TGTGCATCCAAAATCCTTTAAACC 58.453 37.500 0.00 0.0 0.00 3.27
753 781 5.185828 TCTTTCTTCTCTACATGCTGCACTA 59.814 40.000 3.57 0.0 0.00 2.74
832 863 8.281212 AGCCTTTTGAACTACCAATTACATAG 57.719 34.615 0.00 0.0 0.00 2.23
876 907 8.741841 TCAACAGCAATCATGAAAAGAATATGA 58.258 29.630 0.00 0.0 35.52 2.15
1024 1058 1.597854 CAACAGCGACCTTCAGGCA 60.598 57.895 0.00 0.0 39.32 4.75
1164 1382 2.907236 GCCTCTTCCTCCTCTGGC 59.093 66.667 0.00 0.0 0.00 4.85
2207 3495 1.259609 TGTACTCCGGAAATGGTCGT 58.740 50.000 5.23 0.0 0.00 4.34


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

AutoCloner maintained by Alex Coulton.