Multiple sequence alignment - TraesCS4A01G436500

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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 TraesCS4A01G436500 chr4A 100.000 3191 0 0 1 3191 706093938 706097128 0.000000e+00 5893.0
1 TraesCS4A01G436500 chr4A 97.061 3198 58 17 3 3191 705957634 705960804 0.000000e+00 5352.0
2 TraesCS4A01G436500 chr4A 92.126 1270 90 5 888 2152 707478372 707477108 0.000000e+00 1783.0
3 TraesCS4A01G436500 chr4A 97.135 1047 26 2 2149 3191 705906864 705907910 0.000000e+00 1764.0
4 TraesCS4A01G436500 chr4A 90.902 1319 97 7 834 2152 707177682 707178977 0.000000e+00 1749.0
5 TraesCS4A01G436500 chr4A 90.902 1319 97 7 834 2152 707201207 707202502 0.000000e+00 1749.0
6 TraesCS4A01G436500 chr4A 91.734 1234 98 2 904 2137 707402822 707404051 0.000000e+00 1711.0
7 TraesCS4A01G436500 chr4A 91.167 1234 105 3 904 2137 705889350 705890579 0.000000e+00 1672.0
8 TraesCS4A01G436500 chr4A 93.251 1052 54 10 2149 3191 707477045 707476002 0.000000e+00 1533.0
9 TraesCS4A01G436500 chr4A 92.819 376 17 6 2353 2725 707645625 707645257 1.300000e-148 536.0
10 TraesCS4A01G436500 chr4A 93.304 224 15 0 2716 2939 707643443 707643220 6.600000e-87 331.0
11 TraesCS4A01G436500 chr4A 97.895 95 1 1 2259 2352 707645840 707645746 2.550000e-36 163.0
12 TraesCS4A01G436500 chr4A 85.496 131 17 1 670 798 256680461 256680591 5.550000e-28 135.0
13 TraesCS4A01G436500 chr4A 95.385 65 3 0 2261 2325 707179270 707179334 1.570000e-18 104.0
14 TraesCS4A01G436500 chr4A 95.385 65 3 0 2261 2325 707202795 707202859 1.570000e-18 104.0
15 TraesCS4A01G436500 chr4A 84.545 110 10 4 796 900 707484619 707484512 5.630000e-18 102.0
16 TraesCS4A01G436500 chr4A 84.091 88 8 4 2507 2594 707301288 707301369 2.640000e-11 80.5
17 TraesCS4A01G436500 chrUn 98.847 1822 19 2 479 2299 220054487 220056307 0.000000e+00 3247.0
18 TraesCS4A01G436500 chrUn 98.749 1039 11 2 1571 2608 447800388 447801425 0.000000e+00 1845.0
19 TraesCS4A01G436500 chrUn 98.454 582 9 0 2610 3191 343476104 343476685 0.000000e+00 1026.0
20 TraesCS4A01G436500 chrUn 92.105 38 3 0 2596 2633 368050301 368050338 2.000000e-03 54.7
21 TraesCS4A01G436500 chr7D 91.614 1276 92 4 885 2146 24157283 24156009 0.000000e+00 1749.0
22 TraesCS4A01G436500 chr7D 85.990 414 46 6 2443 2846 24155530 24155119 1.760000e-117 433.0
23 TraesCS4A01G436500 chr7D 85.577 208 20 7 2149 2351 24033892 24034094 3.230000e-50 209.0
24 TraesCS4A01G436500 chr7D 92.857 42 3 0 2285 2326 24155771 24155730 9.560000e-06 62.1
25 TraesCS4A01G436500 chr5B 93.205 677 36 6 1 671 142232342 142233014 0.000000e+00 987.0
26 TraesCS4A01G436500 chr1D 93.323 674 35 6 2 669 124564650 124565319 0.000000e+00 987.0
27 TraesCS4A01G436500 chr1D 85.714 133 17 1 670 800 397751173 397751041 4.290000e-29 139.0
28 TraesCS4A01G436500 chr1B 92.931 679 38 6 1 673 109247165 109246491 0.000000e+00 979.0
29 TraesCS4A01G436500 chr1B 92.467 677 39 8 1 671 2351323 2350653 0.000000e+00 957.0
30 TraesCS4A01G436500 chr6B 92.899 676 38 6 1 670 168071591 168072262 0.000000e+00 974.0
31 TraesCS4A01G436500 chr6B 92.500 680 38 7 3 673 204593162 204593837 0.000000e+00 961.0
32 TraesCS4A01G436500 chr6B 86.260 131 15 2 670 797 503936652 503936782 4.290000e-29 139.0
33 TraesCS4A01G436500 chr6D 92.593 675 39 7 1 669 168298964 168298295 0.000000e+00 959.0
34 TraesCS4A01G436500 chr2D 92.353 680 42 6 1 673 81455197 81455873 0.000000e+00 959.0
35 TraesCS4A01G436500 chr2D 88.696 115 9 2 686 800 531963174 531963064 1.540000e-28 137.0
36 TraesCS4A01G436500 chr2D 94.737 38 2 0 2596 2633 251023839 251023876 3.440000e-05 60.2
37 TraesCS4A01G436500 chr7A 85.926 135 17 1 670 802 431993012 431992878 3.320000e-30 143.0
38 TraesCS4A01G436500 chr4B 85.606 132 17 1 670 799 167583648 167583779 1.540000e-28 137.0
39 TraesCS4A01G436500 chr7B 84.848 132 17 2 669 798 750580143 750580013 2.580000e-26 130.0
40 TraesCS4A01G436500 chr4D 82.418 91 14 2 3084 3173 359843236 359843147 9.490000e-11 78.7
41 TraesCS4A01G436500 chr4D 100.000 29 0 0 2605 2633 20241357 20241329 2.000000e-03 54.7


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 TraesCS4A01G436500 chr4A 706093938 706097128 3190 False 5893.000000 5893 100.000000 1 3191 1 chr4A.!!$F5 3190
1 TraesCS4A01G436500 chr4A 705957634 705960804 3170 False 5352.000000 5352 97.061000 3 3191 1 chr4A.!!$F4 3188
2 TraesCS4A01G436500 chr4A 705906864 705907910 1046 False 1764.000000 1764 97.135000 2149 3191 1 chr4A.!!$F3 1042
3 TraesCS4A01G436500 chr4A 707402822 707404051 1229 False 1711.000000 1711 91.734000 904 2137 1 chr4A.!!$F7 1233
4 TraesCS4A01G436500 chr4A 705889350 705890579 1229 False 1672.000000 1672 91.167000 904 2137 1 chr4A.!!$F2 1233
5 TraesCS4A01G436500 chr4A 707476002 707478372 2370 True 1658.000000 1783 92.688500 888 3191 2 chr4A.!!$R2 2303
6 TraesCS4A01G436500 chr4A 707177682 707179334 1652 False 926.500000 1749 93.143500 834 2325 2 chr4A.!!$F8 1491
7 TraesCS4A01G436500 chr4A 707201207 707202859 1652 False 926.500000 1749 93.143500 834 2325 2 chr4A.!!$F9 1491
8 TraesCS4A01G436500 chr4A 707643220 707645840 2620 True 343.333333 536 94.672667 2259 2939 3 chr4A.!!$R3 680
9 TraesCS4A01G436500 chrUn 220054487 220056307 1820 False 3247.000000 3247 98.847000 479 2299 1 chrUn.!!$F1 1820
10 TraesCS4A01G436500 chrUn 447800388 447801425 1037 False 1845.000000 1845 98.749000 1571 2608 1 chrUn.!!$F4 1037
11 TraesCS4A01G436500 chrUn 343476104 343476685 581 False 1026.000000 1026 98.454000 2610 3191 1 chrUn.!!$F2 581
12 TraesCS4A01G436500 chr7D 24155119 24157283 2164 True 748.033333 1749 90.153667 885 2846 3 chr7D.!!$R1 1961
13 TraesCS4A01G436500 chr5B 142232342 142233014 672 False 987.000000 987 93.205000 1 671 1 chr5B.!!$F1 670
14 TraesCS4A01G436500 chr1D 124564650 124565319 669 False 987.000000 987 93.323000 2 669 1 chr1D.!!$F1 667
15 TraesCS4A01G436500 chr1B 109246491 109247165 674 True 979.000000 979 92.931000 1 673 1 chr1B.!!$R2 672
16 TraesCS4A01G436500 chr1B 2350653 2351323 670 True 957.000000 957 92.467000 1 671 1 chr1B.!!$R1 670
17 TraesCS4A01G436500 chr6B 168071591 168072262 671 False 974.000000 974 92.899000 1 670 1 chr6B.!!$F1 669
18 TraesCS4A01G436500 chr6B 204593162 204593837 675 False 961.000000 961 92.500000 3 673 1 chr6B.!!$F2 670
19 TraesCS4A01G436500 chr6D 168298295 168298964 669 True 959.000000 959 92.593000 1 669 1 chr6D.!!$R1 668
20 TraesCS4A01G436500 chr2D 81455197 81455873 676 False 959.000000 959 92.353000 1 673 1 chr2D.!!$F1 672

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
115 116 1.074248 GGGGGCGTCTTTCTTGGAA 59.926 57.895 0.0 0.0 0.00 3.53 F
180 184 3.282021 GGTGCTTCATCATACACATGGT 58.718 45.455 0.0 0.0 34.69 3.55 F
1542 1592 1.604755 GGCAACATCGTTTACCACACA 59.395 47.619 0.0 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1292 1.619363 AGGTAGCCCATTCCTGCCA 60.619 57.895 0.00 0.00 37.52 4.92 R
1769 1825 2.482664 GCCAGCGATTTGATCTCTGAGA 60.483 50.000 10.23 10.23 43.06 3.27 R
3124 5397 0.902531 TCTCCGGGACCACTTCATTC 59.097 55.000 0.00 0.00 0.00 2.67 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
115 116 1.074248 GGGGGCGTCTTTCTTGGAA 59.926 57.895 0.00 0.00 0.00 3.53
180 184 3.282021 GGTGCTTCATCATACACATGGT 58.718 45.455 0.00 0.00 34.69 3.55
760 770 5.243507 ACATTCACATGGTTAACTTGCATGA 59.756 36.000 22.40 11.24 34.27 3.07
1281 1331 2.490165 CGTCCTCTACGTCCATGGT 58.510 57.895 12.58 0.00 46.72 3.55
1408 1458 1.691337 CCGGAGTTCCCCATACCCA 60.691 63.158 0.00 0.00 0.00 4.51
1542 1592 1.604755 GGCAACATCGTTTACCACACA 59.395 47.619 0.00 0.00 0.00 3.72
1769 1825 2.442272 CCGGATCGACCCTCCAGT 60.442 66.667 0.00 0.00 34.64 4.00
1903 1959 1.113517 ATGGCCTTGGATGATGCAGC 61.114 55.000 3.32 0.00 0.00 5.25
2093 2149 0.316689 CCGTTCAAGGACGTGTTTGC 60.317 55.000 0.00 0.00 41.26 3.68
2580 3024 4.481368 TCACGGTGCTTATTATGTCCTT 57.519 40.909 2.51 0.00 0.00 3.36
2688 3138 6.660949 AGAACAATTCGAATTCAGGGAAATCT 59.339 34.615 20.31 11.38 34.02 2.40
2811 5084 7.389803 TTGATTGGCGAAAGAAATAGATCAA 57.610 32.000 0.00 0.00 0.00 2.57
2909 5182 6.784473 TGATCTGGAGAGCATATTCCTCTTTA 59.216 38.462 4.59 0.00 39.66 1.85
2943 5216 6.150318 TGAACTCAAAAAGCACGTGTTTTTA 58.850 32.000 33.62 22.28 37.44 1.52
3124 5397 5.163550 TGAGGTGTTCGATGACCTAGTAATG 60.164 44.000 14.29 0.00 42.95 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 116 2.045131 GTCCCTCGAGCCGTACACT 61.045 63.158 6.99 0.00 0.00 3.55
134 138 1.001048 CACCAAAGACGTCGTCCACTA 60.001 52.381 21.40 0.00 32.18 2.74
180 184 2.431782 TGCCATCGAGATCTGTCATCAA 59.568 45.455 0.00 0.00 0.00 2.57
1242 1292 1.619363 AGGTAGCCCATTCCTGCCA 60.619 57.895 0.00 0.00 37.52 4.92
1769 1825 2.482664 GCCAGCGATTTGATCTCTGAGA 60.483 50.000 10.23 10.23 43.06 3.27
2909 5182 7.359431 CGTGCTTTTTGAGTTCATGCATAATTT 60.359 33.333 0.00 0.00 0.00 1.82
3124 5397 0.902531 TCTCCGGGACCACTTCATTC 59.097 55.000 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.