Multiple sequence alignment - TraesCS6A01G016300

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 TraesCS6A01G016300 chr6A 100.000 3363 0 0 1 3363 8011833 8008471 0.000000e+00 6211.0
1 TraesCS6A01G016300 chr6A 87.861 692 47 14 1089 1762 8165695 8166367 0.000000e+00 778.0
2 TraesCS6A01G016300 chr6A 86.842 228 26 3 876 1102 8163946 8164170 5.570000e-63 252.0
3 TraesCS6A01G016300 chr6A 87.000 200 9 4 681 880 8149431 8149613 3.400000e-50 209.0
4 TraesCS6A01G016300 chr6A 93.519 108 7 0 2114 2221 8002595 8002702 9.660000e-36 161.0
5 TraesCS6A01G016300 chr6A 92.754 69 5 0 611 679 15368121 15368189 2.140000e-17 100.0
6 TraesCS6A01G016300 chr6D 95.511 2673 57 13 1 2618 7748867 7746203 0.000000e+00 4213.0
7 TraesCS6A01G016300 chr6D 87.948 1087 92 14 681 1762 7867361 7868413 0.000000e+00 1245.0
8 TraesCS6A01G016300 chr6D 95.899 756 21 2 2618 3363 7745789 7745034 0.000000e+00 1216.0
9 TraesCS6A01G016300 chr6D 88.562 306 22 7 2226 2524 461526207 461526506 3.190000e-95 359.0
10 TraesCS6A01G016300 chr6D 93.519 108 7 0 2114 2221 7740286 7740393 9.660000e-36 161.0
11 TraesCS6A01G016300 chr6D 96.610 59 2 0 621 679 61766590 61766532 7.680000e-17 99.0
12 TraesCS6A01G016300 chr6B 93.703 1461 51 14 386 1820 14462303 14460858 0.000000e+00 2150.0
13 TraesCS6A01G016300 chr6B 90.020 1022 78 14 753 1761 14411941 14410931 0.000000e+00 1301.0
14 TraesCS6A01G016300 chr6B 85.789 767 80 14 2619 3363 14515530 14516289 0.000000e+00 785.0
15 TraesCS6A01G016300 chr6B 91.729 399 17 6 1834 2224 14460874 14460484 1.060000e-149 540.0
16 TraesCS6A01G016300 chr6B 86.179 369 48 2 878 1245 14457043 14456677 2.430000e-106 396.0
17 TraesCS6A01G016300 chr6B 84.127 378 45 7 1298 1662 14456685 14456310 5.340000e-93 351.0
18 TraesCS6A01G016300 chr6B 91.453 117 10 0 9 125 3754488 3754372 9.660000e-36 161.0
19 TraesCS6A01G016300 chr1A 86.410 390 37 9 2920 3295 449552139 449551752 2.410000e-111 412.0
20 TraesCS6A01G016300 chr1A 76.912 680 123 24 940 1613 110160439 110159788 4.130000e-94 355.0
21 TraesCS6A01G016300 chr1A 81.894 359 56 6 1763 2113 12684068 12683711 9.130000e-76 294.0
22 TraesCS6A01G016300 chr1A 80.811 370 46 12 2930 3296 104431426 104431773 1.990000e-67 267.0
23 TraesCS6A01G016300 chr1A 96.000 50 2 0 3314 3363 449550488 449550439 7.730000e-12 82.4
24 TraesCS6A01G016300 chr5A 86.555 357 38 8 1762 2113 688280385 688280034 5.260000e-103 385.0
25 TraesCS6A01G016300 chr5A 85.950 363 39 10 1758 2113 675524911 675525268 8.810000e-101 377.0
26 TraesCS6A01G016300 chr5A 83.333 276 41 5 934 1206 423030289 423030562 2.000000e-62 250.0
27 TraesCS6A01G016300 chr5A 80.586 273 35 12 2226 2490 607947741 607947479 9.520000e-46 195.0
28 TraesCS6A01G016300 chr7D 84.551 356 49 6 1762 2113 3848207 3848560 6.910000e-92 348.0
29 TraesCS6A01G016300 chr7D 80.930 215 24 5 3163 3363 600897604 600897815 1.620000e-33 154.0
30 TraesCS6A01G016300 chr4A 84.091 352 50 5 1765 2111 741183007 741182657 5.380000e-88 335.0
31 TraesCS6A01G016300 chr4A 94.118 68 3 1 619 685 7123658 7123725 5.940000e-18 102.0
32 TraesCS6A01G016300 chr1D 80.086 467 41 21 2920 3363 349095264 349094827 1.960000e-77 300.0
33 TraesCS6A01G016300 chr1D 79.339 363 52 14 2936 3296 100909120 100908779 2.020000e-57 233.0
34 TraesCS6A01G016300 chr1D 91.250 80 6 1 608 686 466009061 466009140 1.280000e-19 108.0
35 TraesCS6A01G016300 chr7B 81.894 359 56 6 1763 2113 192783589 192783232 9.130000e-76 294.0
36 TraesCS6A01G016300 chr7B 91.429 70 6 0 613 682 746618738 746618669 2.760000e-16 97.1
37 TraesCS6A01G016300 chr2B 81.894 359 56 6 1763 2113 47186695 47187052 9.130000e-76 294.0
38 TraesCS6A01G016300 chr2B 82.584 178 13 8 3198 3360 772117436 772117610 1.260000e-29 141.0
39 TraesCS6A01G016300 chr2B 97.674 43 1 0 3138 3180 772117394 772117436 1.290000e-09 75.0
40 TraesCS6A01G016300 chr1B 81.370 365 44 15 2936 3296 150774891 150775235 3.310000e-70 276.0
41 TraesCS6A01G016300 chr1B 85.000 100 12 3 587 685 4640666 4640569 7.680000e-17 99.0
42 TraesCS6A01G016300 chr7A 81.982 222 25 4 3156 3363 692893561 692893781 1.240000e-39 174.0
43 TraesCS6A01G016300 chr7A 85.047 107 14 1 2265 2369 238833995 238833889 1.280000e-19 108.0
44 TraesCS6A01G016300 chr2D 75.802 405 39 26 2976 3357 629078818 629078450 2.090000e-32 150.0
45 TraesCS6A01G016300 chr2D 90.476 63 5 1 2302 2363 642396659 642396721 7.730000e-12 82.4
46 TraesCS6A01G016300 chr2A 90.000 70 7 0 615 684 76367581 76367512 1.280000e-14 91.6
47 TraesCS6A01G016300 chr2A 92.063 63 4 1 2302 2363 767552204 767552266 1.660000e-13 87.9


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 TraesCS6A01G016300 chr6A 8008471 8011833 3362 True 6211.00 6211 100.0000 1 3363 1 chr6A.!!$R1 3362
1 TraesCS6A01G016300 chr6A 8163946 8166367 2421 False 515.00 778 87.3515 876 1762 2 chr6A.!!$F4 886
2 TraesCS6A01G016300 chr6D 7745034 7748867 3833 True 2714.50 4213 95.7050 1 3363 2 chr6D.!!$R2 3362
3 TraesCS6A01G016300 chr6D 7867361 7868413 1052 False 1245.00 1245 87.9480 681 1762 1 chr6D.!!$F2 1081
4 TraesCS6A01G016300 chr6B 14410931 14411941 1010 True 1301.00 1301 90.0200 753 1761 1 chr6B.!!$R2 1008
5 TraesCS6A01G016300 chr6B 14456310 14462303 5993 True 859.25 2150 88.9345 386 2224 4 chr6B.!!$R3 1838
6 TraesCS6A01G016300 chr6B 14515530 14516289 759 False 785.00 785 85.7890 2619 3363 1 chr6B.!!$F1 744
7 TraesCS6A01G016300 chr1A 110159788 110160439 651 True 355.00 355 76.9120 940 1613 1 chr1A.!!$R2 673
8 TraesCS6A01G016300 chr1A 449550439 449552139 1700 True 247.20 412 91.2050 2920 3363 2 chr1A.!!$R3 443

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
253 254 1.542547 CCCAGTAACAACACGAAGGCT 60.543 52.381 0.00 0.0 0.00 4.58 F
424 440 1.585297 ACGTAACAACCGGAAAGTGG 58.415 50.000 9.46 0.0 0.00 4.00 F
1069 1109 1.153524 ATGGCACCCAAGAGCAACA 59.846 52.632 0.00 0.0 36.95 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1069 1109 1.958288 ATCACAGCCTTCCTGGTAGT 58.042 50.000 0.00 0.0 46.14 2.73 R
1624 3225 2.104111 TGTGAAGTGACGTCCAAGGAAT 59.896 45.455 14.12 0.0 0.00 3.01 R
2594 4461 1.300542 GAGATGCCCTCGCTACAGC 60.301 63.158 0.00 0.0 35.36 4.40 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
54 55 9.128107 GAGTATGTGGTTTGTAAAATGTTGATG 57.872 33.333 0.00 0.0 0.00 3.07
253 254 1.542547 CCCAGTAACAACACGAAGGCT 60.543 52.381 0.00 0.0 0.00 4.58
270 271 5.802956 CGAAGGCTCAGTTACAAAAACAAAA 59.197 36.000 0.00 0.0 0.00 2.44
289 290 8.902540 AACAAAATAAAATCCAAAGAAGGGAC 57.097 30.769 0.00 0.0 37.23 4.46
290 291 8.028652 ACAAAATAAAATCCAAAGAAGGGACA 57.971 30.769 0.00 0.0 37.23 4.02
292 293 8.773645 CAAAATAAAATCCAAAGAAGGGACAAC 58.226 33.333 0.00 0.0 37.23 3.32
293 294 4.584327 AAAATCCAAAGAAGGGACAACG 57.416 40.909 0.00 0.0 37.23 4.10
350 351 4.255301 TGGTTCGTTGTTTGTGTTAGTCT 58.745 39.130 0.00 0.0 0.00 3.24
424 440 1.585297 ACGTAACAACCGGAAAGTGG 58.415 50.000 9.46 0.0 0.00 4.00
780 818 2.097825 CATTGCCCAGAAAAGGAGGAG 58.902 52.381 0.00 0.0 0.00 3.69
954 992 9.868277 ATTAATTCAACGCCAAAGATTTGATTA 57.132 25.926 6.87 0.0 40.55 1.75
1069 1109 1.153524 ATGGCACCCAAGAGCAACA 59.846 52.632 0.00 0.0 36.95 3.33
1118 2695 4.130118 GTTCTTATGATCGTGGCTTCCAT 58.870 43.478 0.00 0.0 35.28 3.41
1636 3237 6.432783 TGATCACAAATTTATTCCTTGGACGT 59.567 34.615 0.00 0.0 0.00 4.34
1711 3312 3.949113 ACATGTTTTACCTGGTGTTCGTT 59.051 39.130 10.23 0.0 0.00 3.85
2069 3682 4.394712 GAGTGGACCGGTGCCCTG 62.395 72.222 24.47 0.0 0.00 4.45
2171 3784 5.045869 CAGGTCTTACATCTACCTTTTGGGA 60.046 44.000 0.00 0.0 41.75 4.37
2426 4044 1.134965 GGTCCAGAGATCCAACGACAG 60.135 57.143 0.00 0.0 0.00 3.51
2458 4311 2.919043 GATGGGTTCCTGCCGGAT 59.081 61.111 5.05 0.0 39.58 4.18
2540 4393 3.000041 GCACTGGTTCATACGTGATTCA 59.000 45.455 0.00 0.0 33.56 2.57
2612 4479 1.300542 GCTGTAGCGAGGGCATCTC 60.301 63.158 0.00 0.0 43.41 2.75
2632 7198 2.826128 TCGGAGGTATATGAGCACATCC 59.174 50.000 0.00 0.0 41.18 3.51
2647 7213 1.239347 CATCCGAGATACTGAGCCGA 58.761 55.000 0.00 0.0 0.00 5.54
2652 7218 1.335415 CGAGATACTGAGCCGACATGG 60.335 57.143 0.00 0.0 42.50 3.66
2653 7219 1.683917 GAGATACTGAGCCGACATGGT 59.316 52.381 0.00 0.0 41.21 3.55
2690 7256 0.668096 GTAACCACACGGACGCATCA 60.668 55.000 0.00 0.0 35.59 3.07
2723 7289 4.696402 AGAACGTCGATCTCTCACTAAACT 59.304 41.667 0.00 0.0 0.00 2.66
2826 7392 5.650703 AGTTCCACCATAAAAATCCTAACCG 59.349 40.000 0.00 0.0 0.00 4.44
2832 7398 9.122779 CCACCATAAAAATCCTAACCGTATTAA 57.877 33.333 0.00 0.0 0.00 1.40
3054 7646 7.549839 TCCTTATTGCTTAACTACACGTACAT 58.450 34.615 0.00 0.0 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.150827 GCCCAAGCAAAAGCATCAAC 58.849 50.000 0.00 0.00 39.53 3.18
54 55 0.104671 TTGTCAGCCCAAGCAAAAGC 59.895 50.000 0.00 0.00 43.56 3.51
236 237 2.102588 ACTGAGCCTTCGTGTTGTTACT 59.897 45.455 0.00 0.00 0.00 2.24
270 271 5.773176 ACGTTGTCCCTTCTTTGGATTTTAT 59.227 36.000 0.00 0.00 33.65 1.40
303 304 2.640826 ACATCGTTCCTTACCCCTCAAA 59.359 45.455 0.00 0.00 0.00 2.69
304 305 2.262637 ACATCGTTCCTTACCCCTCAA 58.737 47.619 0.00 0.00 0.00 3.02
350 351 4.042809 TCTTTCTTTACTGCCCATCTTCCA 59.957 41.667 0.00 0.00 0.00 3.53
424 440 5.379757 TTCTACACTTTCGTTTGTTCGAC 57.620 39.130 0.00 0.00 39.58 4.20
452 476 4.226427 TCCATGCAAGATCTTTGCTAGT 57.774 40.909 22.12 11.36 45.13 2.57
686 724 3.643199 TGAGGCATGCTTGGTATTACA 57.357 42.857 18.92 0.00 0.00 2.41
687 725 4.981806 TTTGAGGCATGCTTGGTATTAC 57.018 40.909 18.92 0.00 0.00 1.89
767 805 5.885449 AGATGTATCCTCCTCCTTTTCTG 57.115 43.478 0.00 0.00 0.00 3.02
954 992 8.251721 GCATAGTCGTTTATATAGAGGGACAAT 58.748 37.037 6.99 0.00 0.00 2.71
1036 1076 3.002791 GTGCCATGACGAAGAGATCAAA 58.997 45.455 0.00 0.00 0.00 2.69
1069 1109 1.958288 ATCACAGCCTTCCTGGTAGT 58.042 50.000 0.00 0.00 46.14 2.73
1118 2695 4.083271 CGTAGCAAGACGATGATGATAGGA 60.083 45.833 0.00 0.00 45.82 2.94
1624 3225 2.104111 TGTGAAGTGACGTCCAAGGAAT 59.896 45.455 14.12 0.00 0.00 3.01
1880 3484 4.345859 TTGTCAAACAGGTCTAATCGGT 57.654 40.909 0.00 0.00 0.00 4.69
1913 3519 3.138283 GTCATCATTTATGGAGGGACCCA 59.862 47.826 14.60 0.00 41.05 4.51
2069 3682 4.554036 GCTGGGATGACGAGGGCC 62.554 72.222 0.00 0.00 0.00 5.80
2426 4044 4.602340 ACCCATCGACTATGTACAATCC 57.398 45.455 0.00 0.00 33.34 3.01
2458 4311 5.047377 GTGATTTCCTCAGCCAAAAATACCA 60.047 40.000 0.00 0.00 33.51 3.25
2594 4461 1.300542 GAGATGCCCTCGCTACAGC 60.301 63.158 0.00 0.00 35.36 4.40
2603 4470 2.043115 TCATATACCTCCGAGATGCCCT 59.957 50.000 0.00 0.00 0.00 5.19
2612 4479 2.416027 CGGATGTGCTCATATACCTCCG 60.416 54.545 10.70 10.70 44.41 4.63
2632 7198 1.335415 CCATGTCGGCTCAGTATCTCG 60.335 57.143 0.00 0.00 0.00 4.04
2647 7213 6.043938 ACCCCGTCAATATTAAGATACCATGT 59.956 38.462 0.00 0.00 0.00 3.21
2652 7218 7.386025 GTGGTTACCCCGTCAATATTAAGATAC 59.614 40.741 0.00 0.00 35.15 2.24
2653 7219 7.070946 TGTGGTTACCCCGTCAATATTAAGATA 59.929 37.037 0.00 0.00 35.15 1.98
2690 7256 3.564644 AGATCGACGTTCTCATCGGTTAT 59.435 43.478 2.56 0.00 38.86 1.89
2714 7280 6.365247 GCTTTCTGACGATGTTAGTTTAGTGA 59.635 38.462 0.00 0.00 0.00 3.41
2723 7289 4.320202 GCTTTTGGCTTTCTGACGATGTTA 60.320 41.667 0.00 0.00 38.06 2.41
2826 7392 8.798748 ATATGTGAACTGAGCGTAGTTAATAC 57.201 34.615 8.34 8.71 40.78 1.89
2832 7398 5.720202 TGAAATATGTGAACTGAGCGTAGT 58.280 37.500 0.00 0.00 0.00 2.73
2983 7575 9.524106 AATTGATTAAATCACATACACATGCAG 57.476 29.630 0.00 0.00 39.39 4.41


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

AutoCloner maintained by Alex Coulton.