Multiple sequence alignment - TraesCS1D01G060300

Loading Multiple Alignment...

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 TraesCS1D01G060300 chr1D 100.000 3064 0 0 1 3064 40243293 40246356 0.000000e+00 5659
1 TraesCS1D01G060300 chr1D 98.013 3070 43 6 1 3064 40379644 40382701 0.000000e+00 5315
2 TraesCS1D01G060300 chr1D 97.383 3095 47 7 1 3064 40324606 40327697 0.000000e+00 5236
3 TraesCS1D01G060300 chr1D 86.418 1583 100 51 766 2297 40488888 40490406 0.000000e+00 1626
4 TraesCS1D01G060300 chr1D 88.023 1386 100 37 834 2195 40201972 40203315 0.000000e+00 1580
5 TraesCS1D01G060300 chr1D 90.244 943 50 23 1270 2195 40315788 40316705 0.000000e+00 1194
6 TraesCS1D01G060300 chr1D 74.762 420 69 16 287 702 132864783 132864397 1.470000e-33 154
7 TraesCS1D01G060300 chrUn 90.639 1346 71 19 865 2195 335951176 335949871 0.000000e+00 1736
8 TraesCS1D01G060300 chrUn 82.451 661 65 32 1 660 414595753 414595143 5.820000e-147 531
9 TraesCS1D01G060300 chr1B 87.450 1506 111 44 746 2195 59912435 59913918 0.000000e+00 1663
10 TraesCS1D01G060300 chr1B 87.251 1506 114 47 746 2195 59854966 59856449 0.000000e+00 1646
11 TraesCS1D01G060300 chr1B 85.449 1615 99 66 755 2289 60534856 60533298 0.000000e+00 1555
12 TraesCS1D01G060300 chr1B 89.479 960 70 13 1259 2195 59918450 59919401 0.000000e+00 1184
13 TraesCS1D01G060300 chr1B 82.930 703 69 32 1 702 60016593 60017245 1.220000e-163 586
14 TraesCS1D01G060300 chr1B 73.761 545 90 29 168 702 439441416 439440915 6.800000e-37 165
15 TraesCS1D01G060300 chr1B 78.261 230 27 13 768 983 59961001 59961221 3.210000e-25 126
16 TraesCS1D01G060300 chr1B 87.069 116 7 6 2188 2297 59962488 59962601 1.150000e-24 124
17 TraesCS1D01G060300 chr1B 87.069 116 7 6 2188 2297 60048924 60049037 1.150000e-24 124
18 TraesCS1D01G060300 chr1A 88.937 1157 71 31 1178 2296 39832218 39833355 0.000000e+00 1375
19 TraesCS1D01G060300 chr1A 91.348 890 68 4 1075 1961 39821920 39822803 0.000000e+00 1208
20 TraesCS1D01G060300 chr1A 82.167 600 59 34 863 1459 31909125 31909679 3.580000e-129 472
21 TraesCS1D01G060300 chr1A 82.540 252 30 11 778 1025 31945446 31945687 3.100000e-50 209
22 TraesCS1D01G060300 chr6D 94.494 672 35 2 2391 3062 53679047 53679716 0.000000e+00 1035
23 TraesCS1D01G060300 chr6D 93.185 675 45 1 2388 3062 27996869 27996196 0.000000e+00 990
24 TraesCS1D01G060300 chr6D 91.837 98 8 0 2296 2393 68329651 68329748 1.480000e-28 137
25 TraesCS1D01G060300 chr6D 90.816 98 9 0 2296 2393 432816272 432816369 6.890000e-27 132
26 TraesCS1D01G060300 chr7A 93.145 671 45 1 2392 3062 92459396 92460065 0.000000e+00 983
27 TraesCS1D01G060300 chr2A 93.006 672 46 1 2391 3062 710350312 710350982 0.000000e+00 979
28 TraesCS1D01G060300 chr2A 90.099 101 10 0 2293 2393 469603278 469603378 6.890000e-27 132
29 TraesCS1D01G060300 chr6B 92.857 672 46 2 2391 3062 30254672 30254003 0.000000e+00 974
30 TraesCS1D01G060300 chr2B 92.285 674 48 2 2389 3062 30452293 30451624 0.000000e+00 953
31 TraesCS1D01G060300 chr7B 92.042 666 53 0 2397 3062 481885895 481885230 0.000000e+00 937
32 TraesCS1D01G060300 chr2D 77.371 464 75 22 241 702 484937206 484936771 6.560000e-62 248
33 TraesCS1D01G060300 chr5B 75.000 484 86 21 223 702 511051458 511051006 1.120000e-44 191
34 TraesCS1D01G060300 chr5B 74.449 454 83 21 251 702 538396541 538396963 6.800000e-37 165
35 TraesCS1D01G060300 chr5D 73.443 546 107 26 162 702 442202783 442203295 1.460000e-38 171
36 TraesCS1D01G060300 chr5D 90.099 101 10 0 2293 2393 17316153 17316253 6.890000e-27 132
37 TraesCS1D01G060300 chr3D 89.796 98 10 0 2296 2393 476440804 476440707 3.210000e-25 126
38 TraesCS1D01G060300 chr3B 89.796 98 9 1 2296 2393 133209844 133209748 1.150000e-24 124
39 TraesCS1D01G060300 chr3A 87.156 109 10 2 2293 2401 338054286 338054390 1.490000e-23 121


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 TraesCS1D01G060300 chr1D 40243293 40246356 3063 False 5659 5659 100.000 1 3064 1 chr1D.!!$F2 3063
1 TraesCS1D01G060300 chr1D 40379644 40382701 3057 False 5315 5315 98.013 1 3064 1 chr1D.!!$F5 3063
2 TraesCS1D01G060300 chr1D 40324606 40327697 3091 False 5236 5236 97.383 1 3064 1 chr1D.!!$F4 3063
3 TraesCS1D01G060300 chr1D 40488888 40490406 1518 False 1626 1626 86.418 766 2297 1 chr1D.!!$F6 1531
4 TraesCS1D01G060300 chr1D 40201972 40203315 1343 False 1580 1580 88.023 834 2195 1 chr1D.!!$F1 1361
5 TraesCS1D01G060300 chr1D 40315788 40316705 917 False 1194 1194 90.244 1270 2195 1 chr1D.!!$F3 925
6 TraesCS1D01G060300 chrUn 335949871 335951176 1305 True 1736 1736 90.639 865 2195 1 chrUn.!!$R1 1330
7 TraesCS1D01G060300 chrUn 414595143 414595753 610 True 531 531 82.451 1 660 1 chrUn.!!$R2 659
8 TraesCS1D01G060300 chr1B 59912435 59913918 1483 False 1663 1663 87.450 746 2195 1 chr1B.!!$F2 1449
9 TraesCS1D01G060300 chr1B 59854966 59856449 1483 False 1646 1646 87.251 746 2195 1 chr1B.!!$F1 1449
10 TraesCS1D01G060300 chr1B 60533298 60534856 1558 True 1555 1555 85.449 755 2289 1 chr1B.!!$R1 1534
11 TraesCS1D01G060300 chr1B 59918450 59919401 951 False 1184 1184 89.479 1259 2195 1 chr1B.!!$F3 936
12 TraesCS1D01G060300 chr1B 60016593 60017245 652 False 586 586 82.930 1 702 1 chr1B.!!$F4 701
13 TraesCS1D01G060300 chr1A 39832218 39833355 1137 False 1375 1375 88.937 1178 2296 1 chr1A.!!$F4 1118
14 TraesCS1D01G060300 chr1A 39821920 39822803 883 False 1208 1208 91.348 1075 1961 1 chr1A.!!$F3 886
15 TraesCS1D01G060300 chr1A 31909125 31909679 554 False 472 472 82.167 863 1459 1 chr1A.!!$F1 596
16 TraesCS1D01G060300 chr6D 53679047 53679716 669 False 1035 1035 94.494 2391 3062 1 chr6D.!!$F1 671
17 TraesCS1D01G060300 chr6D 27996196 27996869 673 True 990 990 93.185 2388 3062 1 chr6D.!!$R1 674
18 TraesCS1D01G060300 chr7A 92459396 92460065 669 False 983 983 93.145 2392 3062 1 chr7A.!!$F1 670
19 TraesCS1D01G060300 chr2A 710350312 710350982 670 False 979 979 93.006 2391 3062 1 chr2A.!!$F2 671
20 TraesCS1D01G060300 chr6B 30254003 30254672 669 True 974 974 92.857 2391 3062 1 chr6B.!!$R1 671
21 TraesCS1D01G060300 chr2B 30451624 30452293 669 True 953 953 92.285 2389 3062 1 chr2B.!!$R1 673
22 TraesCS1D01G060300 chr7B 481885230 481885895 665 True 937 937 92.042 2397 3062 1 chr7B.!!$R1 665

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
237 241 0.476771 ATCCGTTTGGTTGACTGGGT 59.523 50.0 0.0 0.0 36.3 4.51 F
272 276 1.084289 GCCCGCACGAATCTTAAAGT 58.916 50.0 0.0 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 1711 0.86988 CGGCGCTGTATGACGATGAA 60.870 55.0 8.45 0.0 0.0 2.57 R
2225 2474 1.06541 TGGAAGCCTTTGGAGTGGGA 61.065 55.0 0.00 0.0 0.0 4.37 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
23 24 3.387091 CGGGGGTCGACCATGTCA 61.387 66.667 34.40 0.00 42.91 3.58
24 25 2.949909 CGGGGGTCGACCATGTCAA 61.950 63.158 34.40 0.00 42.91 3.18
111 113 4.631234 AGGACATCATAAAGGAGGTGGTA 58.369 43.478 0.00 0.00 31.00 3.25
171 173 4.871993 AGATTGACTTCAATGATGCGTC 57.128 40.909 9.21 0.00 45.72 5.19
237 241 0.476771 ATCCGTTTGGTTGACTGGGT 59.523 50.000 0.00 0.00 36.30 4.51
267 271 2.436646 CTGGCCCGCACGAATCTT 60.437 61.111 0.00 0.00 0.00 2.40
272 276 1.084289 GCCCGCACGAATCTTAAAGT 58.916 50.000 0.00 0.00 0.00 2.66
408 412 2.693591 GGACGTCTCATAACTCCCATCA 59.306 50.000 16.46 0.00 0.00 3.07
423 427 1.468224 CCATCACTCCTTCTCGTCACG 60.468 57.143 0.00 0.00 0.00 4.35
467 503 7.671398 ACATTCTCTTTCTTTCTCTCTCTCTCT 59.329 37.037 0.00 0.00 0.00 3.10
468 504 7.687941 TTCTCTTTCTTTCTCTCTCTCTCTC 57.312 40.000 0.00 0.00 0.00 3.20
469 505 7.020827 TCTCTTTCTTTCTCTCTCTCTCTCT 57.979 40.000 0.00 0.00 0.00 3.10
470 506 7.106239 TCTCTTTCTTTCTCTCTCTCTCTCTC 58.894 42.308 0.00 0.00 0.00 3.20
471 507 5.874810 TCTTTCTTTCTCTCTCTCTCTCTCG 59.125 44.000 0.00 0.00 0.00 4.04
472 508 3.531538 TCTTTCTCTCTCTCTCTCTCGC 58.468 50.000 0.00 0.00 0.00 5.03
473 509 3.197766 TCTTTCTCTCTCTCTCTCTCGCT 59.802 47.826 0.00 0.00 0.00 4.93
1542 1665 6.231211 ACTCGGACAAGAAATACAACAAGAT 58.769 36.000 0.00 0.00 0.00 2.40
1570 1711 2.178521 GCCGTGTCATCGTCGTCT 59.821 61.111 0.00 0.00 0.00 4.18
1679 1823 0.908198 GTCTCTCCAGCCCACAGATT 59.092 55.000 0.00 0.00 0.00 2.40
1954 2123 8.372459 TGTACAAGTCATTAAGTCCATTACAGT 58.628 33.333 0.00 0.00 0.00 3.55
2167 2377 4.189231 ACTGTAGCGTTCAACTTGAAGTT 58.811 39.130 4.45 4.45 39.39 2.66
2218 2467 2.362397 CGCCTGAACTCCTCTATTGCTA 59.638 50.000 0.00 0.00 0.00 3.49
2225 2474 5.721960 TGAACTCCTCTATTGCTACCTTTCT 59.278 40.000 0.00 0.00 0.00 2.52
2324 2579 6.173339 CCTCTGTCTCATTTTACAAGGCTTA 58.827 40.000 0.00 0.00 0.00 3.09
2341 2596 3.549070 GGCTTACACGTGTATTTAGGTCG 59.451 47.826 27.82 10.63 0.00 4.79
2351 2606 7.896274 CACGTGTATTTAGGTCGTCAATTTAAG 59.104 37.037 7.58 0.00 32.47 1.85
2844 3102 1.079127 ATTGTCTCCGGCCAAGACG 60.079 57.895 23.33 1.95 44.96 4.18
2885 3143 3.864003 GTCGAGCATGAACCCTACTAAAC 59.136 47.826 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
267 271 1.134098 GCCATGCCCAGAGCTACTTTA 60.134 52.381 0.00 0.00 44.23 1.85
272 276 1.383664 AGAGCCATGCCCAGAGCTA 60.384 57.895 0.00 0.00 44.23 3.32
408 412 1.242665 GGGTCGTGACGAGAAGGAGT 61.243 60.000 8.41 0.00 36.23 3.85
423 427 1.134521 TGTGTGTGAACTGTCAGGGTC 60.135 52.381 4.53 1.94 33.27 4.46
467 503 0.468226 GGGAGAGAGAGAGAGCGAGA 59.532 60.000 0.00 0.00 0.00 4.04
468 504 0.469917 AGGGAGAGAGAGAGAGCGAG 59.530 60.000 0.00 0.00 0.00 5.03
469 505 0.468226 GAGGGAGAGAGAGAGAGCGA 59.532 60.000 0.00 0.00 0.00 4.93
470 506 0.180171 TGAGGGAGAGAGAGAGAGCG 59.820 60.000 0.00 0.00 0.00 5.03
471 507 2.508526 GATGAGGGAGAGAGAGAGAGC 58.491 57.143 0.00 0.00 0.00 4.09
472 508 2.771089 CGATGAGGGAGAGAGAGAGAG 58.229 57.143 0.00 0.00 0.00 3.20
473 509 1.202758 GCGATGAGGGAGAGAGAGAGA 60.203 57.143 0.00 0.00 0.00 3.10
547 583 0.178767 ATTGCTGCCAGCGATGACTA 59.821 50.000 18.64 0.00 43.46 2.59
1556 1685 1.840741 CGATGAAGACGACGATGACAC 59.159 52.381 0.00 0.00 0.00 3.67
1570 1711 0.869880 CGGCGCTGTATGACGATGAA 60.870 55.000 8.45 0.00 0.00 2.57
1954 2123 6.837312 TCACAAAGGAAAAGGAACTAGATCA 58.163 36.000 0.00 0.00 38.49 2.92
2167 2377 1.197492 CAAACTGTAATGAGCTGCGCA 59.803 47.619 10.98 10.98 0.00 6.09
2218 2467 1.425448 CCTTTGGAGTGGGAGAAAGGT 59.575 52.381 0.00 0.00 39.69 3.50
2225 2474 1.065410 TGGAAGCCTTTGGAGTGGGA 61.065 55.000 0.00 0.00 0.00 4.37
2324 2579 3.921119 TGACGACCTAAATACACGTGT 57.079 42.857 26.52 26.52 37.32 4.49
2885 3143 1.648720 CGTGGTGTTGGTCTGCTTG 59.351 57.895 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.