Multiple sequence alignment - TraesCS2A01G235200

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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 TraesCS2A01G235200 chr2A 100.000 2544 0 0 1 2544 291665035 291667578 0.000000e+00 4698.0
1 TraesCS2A01G235200 chr2A 92.642 2188 135 13 376 2544 556948462 556950642 0.000000e+00 3125.0
2 TraesCS2A01G235200 chr1B 93.494 1614 90 8 591 2196 502774236 502775842 0.000000e+00 2385.0
3 TraesCS2A01G235200 chr1B 86.813 91 9 3 27 115 502776983 502776894 5.790000e-17 99.0
4 TraesCS2A01G235200 chr1D 88.736 1811 155 30 28 1818 198826417 198828198 0.000000e+00 2169.0
5 TraesCS2A01G235200 chr2D 88.631 1812 147 37 26 1818 80028978 80030749 0.000000e+00 2150.0
6 TraesCS2A01G235200 chr2D 88.571 105 9 3 28 130 80032519 80032416 9.560000e-25 124.0
7 TraesCS2A01G235200 chr3A 79.609 2555 412 67 28 2542 667165284 667162799 0.000000e+00 1731.0
8 TraesCS2A01G235200 chr5A 92.941 1190 74 8 30 1213 341537354 341536169 0.000000e+00 1724.0
9 TraesCS2A01G235200 chr5A 95.006 821 40 1 1724 2544 341511690 341510871 0.000000e+00 1288.0
10 TraesCS2A01G235200 chr3D 83.190 1749 258 25 801 2542 418712592 418710873 0.000000e+00 1568.0
11 TraesCS2A01G235200 chr7D 83.076 1749 260 27 801 2542 136701352 136699633 0.000000e+00 1557.0
12 TraesCS2A01G235200 chr6A 83.081 1649 252 23 901 2539 563488496 563490127 0.000000e+00 1474.0
13 TraesCS2A01G235200 chr6A 82.374 1651 258 27 901 2544 591517121 591518745 0.000000e+00 1406.0
14 TraesCS2A01G235200 chr4B 82.160 1648 263 26 904 2539 168271015 168269387 0.000000e+00 1386.0
15 TraesCS2A01G235200 chr1A 82.089 1647 262 26 904 2544 8361833 8360214 0.000000e+00 1376.0
16 TraesCS2A01G235200 chr7A 82.209 1349 224 16 904 2241 106410392 106409049 0.000000e+00 1147.0
17 TraesCS2A01G235200 chr5B 91.429 455 34 2 215 667 18641975 18641524 1.000000e-173 619.0
18 TraesCS2A01G235200 chr5B 90.374 187 16 2 32 217 18664033 18663848 7.030000e-61 244.0
19 TraesCS2A01G235200 chr5B 94.340 53 2 1 28 79 18595202 18595254 2.100000e-11 80.5
20 TraesCS2A01G235200 chr5D 81.818 352 52 7 2191 2542 460223212 460223551 4.140000e-73 285.0


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 TraesCS2A01G235200 chr2A 291665035 291667578 2543 False 4698 4698 100.000 1 2544 1 chr2A.!!$F1 2543
1 TraesCS2A01G235200 chr2A 556948462 556950642 2180 False 3125 3125 92.642 376 2544 1 chr2A.!!$F2 2168
2 TraesCS2A01G235200 chr1B 502774236 502775842 1606 False 2385 2385 93.494 591 2196 1 chr1B.!!$F1 1605
3 TraesCS2A01G235200 chr1D 198826417 198828198 1781 False 2169 2169 88.736 28 1818 1 chr1D.!!$F1 1790
4 TraesCS2A01G235200 chr2D 80028978 80030749 1771 False 2150 2150 88.631 26 1818 1 chr2D.!!$F1 1792
5 TraesCS2A01G235200 chr3A 667162799 667165284 2485 True 1731 1731 79.609 28 2542 1 chr3A.!!$R1 2514
6 TraesCS2A01G235200 chr5A 341536169 341537354 1185 True 1724 1724 92.941 30 1213 1 chr5A.!!$R2 1183
7 TraesCS2A01G235200 chr5A 341510871 341511690 819 True 1288 1288 95.006 1724 2544 1 chr5A.!!$R1 820
8 TraesCS2A01G235200 chr3D 418710873 418712592 1719 True 1568 1568 83.190 801 2542 1 chr3D.!!$R1 1741
9 TraesCS2A01G235200 chr7D 136699633 136701352 1719 True 1557 1557 83.076 801 2542 1 chr7D.!!$R1 1741
10 TraesCS2A01G235200 chr6A 563488496 563490127 1631 False 1474 1474 83.081 901 2539 1 chr6A.!!$F1 1638
11 TraesCS2A01G235200 chr6A 591517121 591518745 1624 False 1406 1406 82.374 901 2544 1 chr6A.!!$F2 1643
12 TraesCS2A01G235200 chr4B 168269387 168271015 1628 True 1386 1386 82.160 904 2539 1 chr4B.!!$R1 1635
13 TraesCS2A01G235200 chr1A 8360214 8361833 1619 True 1376 1376 82.089 904 2544 1 chr1A.!!$R1 1640
14 TraesCS2A01G235200 chr7A 106409049 106410392 1343 True 1147 1147 82.209 904 2241 1 chr7A.!!$R1 1337

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
122 123 0.396811 GTATGGACGCTGGGCCTTAT 59.603 55.0 4.53 0.0 0.0 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 1995 0.462759 CACTTTCCTCATCTCCGGGC 60.463 60.0 0.0 0.0 0.0 6.13 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
20 21 3.757947 TTGATCACAGGACCTCCTAGA 57.242 47.619 0.00 0.00 46.65 2.43
21 22 3.981516 TGATCACAGGACCTCCTAGAT 57.018 47.619 7.76 7.76 46.65 1.98
22 23 5.403558 TTGATCACAGGACCTCCTAGATA 57.596 43.478 0.00 0.00 46.65 1.98
23 24 5.607168 TGATCACAGGACCTCCTAGATAT 57.393 43.478 0.00 0.00 46.65 1.63
24 25 5.328565 TGATCACAGGACCTCCTAGATATG 58.671 45.833 0.00 0.00 46.65 1.78
25 26 4.816048 TCACAGGACCTCCTAGATATGT 57.184 45.455 0.00 0.00 46.65 2.29
26 27 4.474394 TCACAGGACCTCCTAGATATGTG 58.526 47.826 0.00 0.00 46.65 3.21
27 28 3.006323 CACAGGACCTCCTAGATATGTGC 59.994 52.174 0.00 0.00 46.65 4.57
28 29 2.564947 CAGGACCTCCTAGATATGTGCC 59.435 54.545 0.00 0.00 46.65 5.01
122 123 0.396811 GTATGGACGCTGGGCCTTAT 59.603 55.000 4.53 0.00 0.00 1.73
130 131 1.006102 CTGGGCCTTATAGCGTCCG 60.006 63.158 4.53 0.00 0.00 4.79
131 132 1.456145 TGGGCCTTATAGCGTCCGA 60.456 57.895 4.53 0.00 0.00 4.55
133 134 1.289380 GGCCTTATAGCGTCCGAGG 59.711 63.158 0.00 0.00 0.00 4.63
206 207 0.893727 CACAGTTAGGTTGGCCCCAC 60.894 60.000 0.00 0.00 34.57 4.61
208 209 0.609131 CAGTTAGGTTGGCCCCACTG 60.609 60.000 0.00 2.11 38.32 3.66
209 210 1.304134 GTTAGGTTGGCCCCACTGG 60.304 63.158 0.00 0.00 34.57 4.00
297 325 3.787001 CCACCCTCCGCCTCTTCC 61.787 72.222 0.00 0.00 0.00 3.46
331 372 3.670629 CTGACCTCCGCCTCTCCCT 62.671 68.421 0.00 0.00 0.00 4.20
405 446 4.812476 TCATTCCCTCGCGCACCG 62.812 66.667 8.75 0.00 38.61 4.94
467 516 4.504132 CCTGACTAGGTTGCGCTC 57.496 61.111 9.73 1.18 39.39 5.03
468 517 1.517257 CCTGACTAGGTTGCGCTCG 60.517 63.158 9.73 0.00 39.39 5.03
561 612 2.979676 CCAGCAAGCCTCGCAACA 60.980 61.111 0.00 0.00 0.00 3.33
720 777 9.173939 GTTACTTGTCTCTTTTTGTGATTGATG 57.826 33.333 0.00 0.00 0.00 3.07
729 786 9.512435 CTCTTTTTGTGATTGATGGATTGATAC 57.488 33.333 0.00 0.00 0.00 2.24
751 808 6.403866 ACTGATACTGCATCAAACCAAAAA 57.596 33.333 0.00 0.00 43.15 1.94
875 949 4.990543 TGTTTGATAAGCACAAGTCTCG 57.009 40.909 0.00 0.00 0.00 4.04
1019 1099 5.688823 TGAAATGAATACAAGTCAGCGTTG 58.311 37.500 0.00 0.00 0.00 4.10
1389 1472 3.865477 ACGTGAGTTGTTTGTGGGA 57.135 47.368 0.00 0.00 46.40 4.37
1459 1542 6.884472 TGGTCTGGATTAATTGAGAGGTTA 57.116 37.500 0.00 0.00 0.00 2.85
1679 1762 3.859961 CACGGTGTTCACTGATACATCTC 59.140 47.826 17.16 0.00 0.00 2.75
1912 1995 2.593925 AGCCAAAAGAAAGGGAGGAG 57.406 50.000 0.00 0.00 0.00 3.69
1932 2018 0.179000 CCCGGAGATGAGGAAAGTGG 59.821 60.000 0.73 0.00 0.00 4.00
2018 2104 3.118223 TGTTCCACATAATGCGGGTATCA 60.118 43.478 0.00 0.00 0.00 2.15
2052 2139 9.987272 CTCACCTCATCTATTATACATTGTTCA 57.013 33.333 0.00 0.00 0.00 3.18
2491 2581 4.809426 CCCTTTGATGTAGCTAGTTTACCG 59.191 45.833 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.546476 CGGCACATATCTAGGAGGTCC 59.454 57.143 0.00 0.00 0.00 4.46
10 11 2.515854 TCGGCACATATCTAGGAGGTC 58.484 52.381 0.00 0.00 0.00 3.85
11 12 2.677542 TCGGCACATATCTAGGAGGT 57.322 50.000 0.00 0.00 0.00 3.85
12 13 4.543590 AAATCGGCACATATCTAGGAGG 57.456 45.455 0.00 0.00 0.00 4.30
130 131 1.660560 TTGTACTAGCGTCCGCCCTC 61.661 60.000 8.23 0.00 43.17 4.30
131 132 1.041447 ATTGTACTAGCGTCCGCCCT 61.041 55.000 8.23 0.00 43.17 5.19
133 134 0.933509 CGATTGTACTAGCGTCCGCC 60.934 60.000 8.23 0.00 43.17 6.13
181 182 1.001181 GCCAACCTAACTGTGGACGTA 59.999 52.381 0.00 0.00 0.00 3.57
314 342 3.673597 AGGGAGAGGCGGAGGTCA 61.674 66.667 0.00 0.00 0.00 4.02
341 382 1.202879 CGAGAGATGAGGTAGAGGGCT 60.203 57.143 0.00 0.00 0.00 5.19
348 389 1.213182 AGGTGAGCGAGAGATGAGGTA 59.787 52.381 0.00 0.00 0.00 3.08
497 548 0.462225 TGCGGTAGAGAGACGAGAGG 60.462 60.000 0.00 0.00 0.00 3.69
657 712 9.736414 AATGAGATTTGCTAGCATCTATTGTAT 57.264 29.630 20.13 6.90 0.00 2.29
720 777 7.308229 GGTTTGATGCAGTATCAGTATCAATCC 60.308 40.741 14.06 14.06 46.01 3.01
850 920 6.511767 CGAGACTTGTGCTTATCAAACAACTT 60.512 38.462 0.00 0.00 30.93 2.66
1019 1099 4.726416 CGGCATCCATAATAAATCACTGC 58.274 43.478 0.00 0.00 0.00 4.40
1389 1472 3.268334 TGGTTTACCATGGATAGGCAACT 59.732 43.478 21.47 0.00 46.90 3.16
1425 1508 0.549469 TCCAGACCATGCAGCATCAT 59.451 50.000 4.38 0.00 0.00 2.45
1459 1542 7.092444 TGTTGTTCATCTATAGGAATCCCAAGT 60.092 37.037 0.00 0.00 33.88 3.16
1679 1762 0.678395 ATAGCTGGCACTCCATCTCG 59.322 55.000 0.00 0.00 42.51 4.04
1912 1995 0.462759 CACTTTCCTCATCTCCGGGC 60.463 60.000 0.00 0.00 0.00 6.13
1932 2018 8.145122 CAGGGTTATAATCCAAGTCTACTTCTC 58.855 40.741 17.19 0.00 33.11 2.87
2355 2445 4.450757 GCGGTTTCCTTGCAAAATGTTTAT 59.549 37.500 0.00 0.00 0.00 1.40
2369 2459 2.818751 TCCCAATTATGCGGTTTCCT 57.181 45.000 0.00 0.00 0.00 3.36
2491 2581 3.378427 GCTGGAACCAATGTCTGTAATCC 59.622 47.826 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.