Multiple sequence alignment - TraesCS7D01G414800

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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 TraesCS7D01G414800 chr7D 100.000 2567 0 0 1 2567 533429063 533431629 0.000000e+00 4741
1 TraesCS7D01G414800 chr7D 92.543 523 33 3 925 1442 532898200 532898721 0.000000e+00 745
2 TraesCS7D01G414800 chr7D 90.251 359 19 7 1440 1796 532898774 532899118 3.010000e-124 455
3 TraesCS7D01G414800 chr7D 90.683 322 21 7 1 321 227381255 227381568 1.100000e-113 420
4 TraesCS7D01G414800 chr1D 96.636 773 24 1 1795 2567 269356164 269355394 0.000000e+00 1282
5 TraesCS7D01G414800 chr4D 96.244 772 28 1 1796 2567 55272044 55272814 0.000000e+00 1264
6 TraesCS7D01G414800 chr3B 95.850 771 30 2 1797 2567 312168494 312167726 0.000000e+00 1245
7 TraesCS7D01G414800 chr5D 95.437 767 34 1 1801 2567 51643496 51642731 0.000000e+00 1221
8 TraesCS7D01G414800 chr2D 95.306 767 36 0 1801 2567 582815305 582814539 0.000000e+00 1218
9 TraesCS7D01G414800 chr2D 90.483 704 41 14 235 918 89219686 89220383 0.000000e+00 905
10 TraesCS7D01G414800 chr2D 90.222 675 38 17 264 918 104872902 104872236 0.000000e+00 856
11 TraesCS7D01G414800 chr2D 83.226 465 61 17 1 458 89219416 89219870 6.610000e-111 411
12 TraesCS7D01G414800 chr2D 82.366 465 63 18 1 458 104873200 104872748 1.110000e-103 387
13 TraesCS7D01G414800 chr5B 94.955 773 39 0 1795 2567 711254569 711253797 0.000000e+00 1212
14 TraesCS7D01G414800 chr5B 90.506 632 41 12 264 879 421455850 421455222 0.000000e+00 817
15 TraesCS7D01G414800 chr5B 87.623 711 55 19 235 920 373034872 373035574 0.000000e+00 795
16 TraesCS7D01G414800 chr5B 92.744 317 17 6 1 315 373034603 373034915 1.080000e-123 453
17 TraesCS7D01G414800 chr5B 88.644 317 30 6 1 315 411376392 411376080 5.180000e-102 381
18 TraesCS7D01G414800 chr3D 94.915 767 35 2 1801 2567 532758119 532757357 0.000000e+00 1197
19 TraesCS7D01G414800 chr3D 88.619 905 59 18 13 894 183589597 183588714 0.000000e+00 1061
20 TraesCS7D01G414800 chr3D 89.435 672 36 11 264 917 379088205 379088859 0.000000e+00 815
21 TraesCS7D01G414800 chr3D 88.994 318 28 6 1 315 379087906 379088219 1.110000e-103 387
22 TraesCS7D01G414800 chr4A 94.675 770 35 3 1801 2567 722418930 722419696 0.000000e+00 1190
23 TraesCS7D01G414800 chr2B 94.301 772 43 1 1796 2567 728230450 728231220 0.000000e+00 1181
24 TraesCS7D01G414800 chr2B 87.612 670 51 14 264 918 90712521 90713173 0.000000e+00 749
25 TraesCS7D01G414800 chr2B 88.384 396 26 12 504 879 23105174 23105569 2.330000e-125 459
26 TraesCS7D01G414800 chr3A 90.653 674 35 14 264 919 360175077 360175740 0.000000e+00 870
27 TraesCS7D01G414800 chr3A 88.095 672 58 9 264 918 746591871 746592537 0.000000e+00 778
28 TraesCS7D01G414800 chr7B 88.952 706 53 14 235 921 727667593 727666894 0.000000e+00 848
29 TraesCS7D01G414800 chr7B 93.499 523 26 4 924 1442 573259529 573260047 0.000000e+00 771
30 TraesCS7D01G414800 chr7B 90.219 593 38 11 343 918 527726137 527725548 0.000000e+00 756
31 TraesCS7D01G414800 chr7B 93.092 304 9 9 1491 1793 573260682 573260974 3.920000e-118 435
32 TraesCS7D01G414800 chr7B 89.623 318 24 8 1 315 741681221 741680910 1.850000e-106 396
33 TraesCS7D01G414800 chr7B 89.457 313 23 8 1 309 562052160 562052466 1.110000e-103 387
34 TraesCS7D01G414800 chr7A 92.952 525 28 6 924 1439 612989898 612990422 0.000000e+00 756
35 TraesCS7D01G414800 chr7A 93.407 364 13 8 1440 1796 612990478 612990837 1.750000e-146 529
36 TraesCS7D01G414800 chr4B 91.071 560 32 9 264 807 97877744 97877187 0.000000e+00 741
37 TraesCS7D01G414800 chr4B 90.433 554 33 11 264 798 97789165 97788613 0.000000e+00 712
38 TraesCS7D01G414800 chr5A 91.360 544 31 7 264 792 414783379 414782837 0.000000e+00 730
39 TraesCS7D01G414800 chr6B 86.060 703 49 16 235 918 230608905 230608233 0.000000e+00 710
40 TraesCS7D01G414800 chr6B 82.112 464 65 15 1 458 9795839 9796290 5.180000e-102 381


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 TraesCS7D01G414800 chr7D 533429063 533431629 2566 False 4741.0 4741 100.0000 1 2567 1 chr7D.!!$F2 2566
1 TraesCS7D01G414800 chr7D 532898200 532899118 918 False 600.0 745 91.3970 925 1796 2 chr7D.!!$F3 871
2 TraesCS7D01G414800 chr1D 269355394 269356164 770 True 1282.0 1282 96.6360 1795 2567 1 chr1D.!!$R1 772
3 TraesCS7D01G414800 chr4D 55272044 55272814 770 False 1264.0 1264 96.2440 1796 2567 1 chr4D.!!$F1 771
4 TraesCS7D01G414800 chr3B 312167726 312168494 768 True 1245.0 1245 95.8500 1797 2567 1 chr3B.!!$R1 770
5 TraesCS7D01G414800 chr5D 51642731 51643496 765 True 1221.0 1221 95.4370 1801 2567 1 chr5D.!!$R1 766
6 TraesCS7D01G414800 chr2D 582814539 582815305 766 True 1218.0 1218 95.3060 1801 2567 1 chr2D.!!$R1 766
7 TraesCS7D01G414800 chr2D 89219416 89220383 967 False 658.0 905 86.8545 1 918 2 chr2D.!!$F1 917
8 TraesCS7D01G414800 chr2D 104872236 104873200 964 True 621.5 856 86.2940 1 918 2 chr2D.!!$R2 917
9 TraesCS7D01G414800 chr5B 711253797 711254569 772 True 1212.0 1212 94.9550 1795 2567 1 chr5B.!!$R3 772
10 TraesCS7D01G414800 chr5B 421455222 421455850 628 True 817.0 817 90.5060 264 879 1 chr5B.!!$R2 615
11 TraesCS7D01G414800 chr5B 373034603 373035574 971 False 624.0 795 90.1835 1 920 2 chr5B.!!$F1 919
12 TraesCS7D01G414800 chr3D 532757357 532758119 762 True 1197.0 1197 94.9150 1801 2567 1 chr3D.!!$R2 766
13 TraesCS7D01G414800 chr3D 183588714 183589597 883 True 1061.0 1061 88.6190 13 894 1 chr3D.!!$R1 881
14 TraesCS7D01G414800 chr3D 379087906 379088859 953 False 601.0 815 89.2145 1 917 2 chr3D.!!$F1 916
15 TraesCS7D01G414800 chr4A 722418930 722419696 766 False 1190.0 1190 94.6750 1801 2567 1 chr4A.!!$F1 766
16 TraesCS7D01G414800 chr2B 728230450 728231220 770 False 1181.0 1181 94.3010 1796 2567 1 chr2B.!!$F3 771
17 TraesCS7D01G414800 chr2B 90712521 90713173 652 False 749.0 749 87.6120 264 918 1 chr2B.!!$F2 654
18 TraesCS7D01G414800 chr3A 360175077 360175740 663 False 870.0 870 90.6530 264 919 1 chr3A.!!$F1 655
19 TraesCS7D01G414800 chr3A 746591871 746592537 666 False 778.0 778 88.0950 264 918 1 chr3A.!!$F2 654
20 TraesCS7D01G414800 chr7B 727666894 727667593 699 True 848.0 848 88.9520 235 921 1 chr7B.!!$R2 686
21 TraesCS7D01G414800 chr7B 527725548 527726137 589 True 756.0 756 90.2190 343 918 1 chr7B.!!$R1 575
22 TraesCS7D01G414800 chr7B 573259529 573260974 1445 False 603.0 771 93.2955 924 1793 2 chr7B.!!$F2 869
23 TraesCS7D01G414800 chr7A 612989898 612990837 939 False 642.5 756 93.1795 924 1796 2 chr7A.!!$F1 872
24 TraesCS7D01G414800 chr4B 97877187 97877744 557 True 741.0 741 91.0710 264 807 1 chr4B.!!$R2 543
25 TraesCS7D01G414800 chr4B 97788613 97789165 552 True 712.0 712 90.4330 264 798 1 chr4B.!!$R1 534
26 TraesCS7D01G414800 chr5A 414782837 414783379 542 True 730.0 730 91.3600 264 792 1 chr5A.!!$R1 528
27 TraesCS7D01G414800 chr6B 230608233 230608905 672 True 710.0 710 86.0600 235 918 1 chr6B.!!$R1 683

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
922 1017 0.620556 CACATAGGTGCTCCCCTGTT 59.379 55.0 0.0 0.0 38.37 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2222 2949 0.668535 CGATGTGCGAGGATGGACTA 59.331 55.0 0.0 0.0 44.57 2.59 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
93 98 4.829064 TGAACAAATTTCAGGTTCGAGG 57.171 40.909 12.57 0.00 42.86 4.63
101 107 6.405278 AATTTCAGGTTCGAGGACATTTTT 57.595 33.333 0.00 0.00 0.00 1.94
189 196 7.999322 CGTTTTTCATATTTTGTTTTGGTACGG 59.001 33.333 0.00 0.00 0.00 4.02
315 368 9.657121 TTGAAAAGTGTTCACAAATTCAAAAAC 57.343 25.926 18.60 0.00 34.25 2.43
346 399 6.901357 GCATTTTGTCAAAACTTGTTCATGAC 59.099 34.615 12.86 17.74 40.53 3.06
561 621 8.940952 CCACAACTTCAAAATTGTTCCTTTTTA 58.059 29.630 0.00 0.00 36.92 1.52
703 798 7.283354 TCTGGTGATGTGACTAGTTCTATAGTG 59.717 40.741 0.00 0.00 36.13 2.74
724 819 2.275134 TCGCATTGCCATATCACCAT 57.725 45.000 2.41 0.00 0.00 3.55
748 843 2.205074 CATCAATCAGGCGTAGTGGTC 58.795 52.381 0.00 0.00 0.00 4.02
793 888 2.799917 CGGTCGTGAGATTGATTCCTCC 60.800 54.545 0.00 0.00 45.19 4.30
799 894 4.623886 CGTGAGATTGATTCCTCCCTGAAA 60.624 45.833 0.00 0.00 0.00 2.69
921 1016 2.300996 CACATAGGTGCTCCCCTGT 58.699 57.895 0.00 2.67 38.37 4.00
922 1017 0.620556 CACATAGGTGCTCCCCTGTT 59.379 55.000 0.00 0.00 38.37 3.16
923 1018 1.004745 CACATAGGTGCTCCCCTGTTT 59.995 52.381 0.00 0.00 38.37 2.83
927 1022 1.002011 GGTGCTCCCCTGTTTCCTC 60.002 63.158 0.00 0.00 0.00 3.71
940 1035 3.578968 TTCCTCCCCGCTCGTCTCA 62.579 63.158 0.00 0.00 0.00 3.27
947 1042 2.765356 CCGCTCGTCTCAGCTAGCA 61.765 63.158 18.83 0.00 37.25 3.49
1063 1165 4.201679 CCGCCGCCGACATACTCA 62.202 66.667 0.00 0.00 36.29 3.41
1080 1182 4.664267 AGGGACTGCTCCAGGGCA 62.664 66.667 0.00 0.00 38.52 5.36
1081 1183 3.415087 GGGACTGCTCCAGGGCAT 61.415 66.667 0.00 0.00 41.63 4.40
1114 1216 1.154205 CGGCAAGCCAGAATCCGTAG 61.154 60.000 12.19 0.00 35.75 3.51
1123 1225 2.285818 AATCCGTAGCCCCCACCA 60.286 61.111 0.00 0.00 0.00 4.17
1124 1226 1.917336 GAATCCGTAGCCCCCACCAA 61.917 60.000 0.00 0.00 0.00 3.67
1166 1269 4.103103 CGCTCCGTCTGCTCGACA 62.103 66.667 7.35 0.00 42.98 4.35
1181 1284 0.807667 CGACAGAATGCCTTCCCGAG 60.808 60.000 0.00 0.00 42.53 4.63
1423 1531 0.389948 AAGTTCGACGATGTCCAGGC 60.390 55.000 0.00 0.00 0.00 4.85
1426 1534 1.811645 TTCGACGATGTCCAGGCACA 61.812 55.000 0.00 0.00 0.00 4.57
1430 1538 1.301637 CGATGTCCAGGCACACACA 60.302 57.895 0.00 0.00 0.00 3.72
1444 2161 3.305539 GCACACACACACATTGATCCATT 60.306 43.478 0.00 0.00 0.00 3.16
1494 2212 6.309251 ACAACAAGAAATGTACCGTGTTTTTG 59.691 34.615 0.00 0.00 42.99 2.44
1497 2215 5.570234 AGAAATGTACCGTGTTTTTGTGT 57.430 34.783 0.00 0.00 0.00 3.72
1502 2220 3.501062 TGTACCGTGTTTTTGTGTTGTGA 59.499 39.130 0.00 0.00 0.00 3.58
1503 2221 3.859411 ACCGTGTTTTTGTGTTGTGAT 57.141 38.095 0.00 0.00 0.00 3.06
1504 2222 3.506810 ACCGTGTTTTTGTGTTGTGATG 58.493 40.909 0.00 0.00 0.00 3.07
1505 2223 3.191581 ACCGTGTTTTTGTGTTGTGATGA 59.808 39.130 0.00 0.00 0.00 2.92
1754 2478 7.118971 TGCTTTTGTTTGCTTATTTGTTCAGTT 59.881 29.630 0.00 0.00 0.00 3.16
1796 2520 6.553100 TGAAAATAATCCAACCACTCCAGTTT 59.447 34.615 0.00 0.00 0.00 2.66
1797 2521 6.994421 AAATAATCCAACCACTCCAGTTTT 57.006 33.333 0.00 0.00 0.00 2.43
1798 2522 6.994421 AATAATCCAACCACTCCAGTTTTT 57.006 33.333 0.00 0.00 0.00 1.94
1799 2523 4.937201 AATCCAACCACTCCAGTTTTTC 57.063 40.909 0.00 0.00 0.00 2.29
1842 2566 4.119363 GGCCTCTGCATCTGGGCA 62.119 66.667 17.30 0.00 45.68 5.36
2197 2924 3.676605 ATCGACGCCACCACGACA 61.677 61.111 0.00 0.00 38.79 4.35
2246 2973 0.460109 CATCCTCGCACATCGGACAA 60.460 55.000 0.00 0.00 39.05 3.18
2265 2992 2.789917 GAATCTGCACTGCGCCAG 59.210 61.111 4.18 4.78 41.33 4.85
2346 3073 2.121963 ACTGGTCCCTTGAGCCCA 60.122 61.111 0.00 0.00 38.24 5.36
2362 3089 0.679002 CCCATGCACACCTCCAAGAG 60.679 60.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 107 9.617975 GTGAACAATTTTTGAAACATTCCAAAA 57.382 25.926 5.04 5.04 38.25 2.44
102 108 7.959651 CGTGAACAATTTTTGAAACATTCCAAA 59.040 29.630 0.00 0.00 0.00 3.28
172 179 8.999220 AAAGAAAACCGTACCAAAACAAAATA 57.001 26.923 0.00 0.00 0.00 1.40
315 368 5.062058 ACAAGTTTTGACAAAATGCGAACAG 59.938 36.000 16.03 3.64 32.22 3.16
526 585 9.260002 ACAATTTTGAAGTTGTGGACAAATATC 57.740 29.630 4.15 0.00 37.19 1.63
703 798 1.675483 TGGTGATATGGCAATGCGAAC 59.325 47.619 0.00 0.00 0.00 3.95
724 819 3.457234 CACTACGCCTGATTGATGCTTA 58.543 45.455 0.00 0.00 0.00 3.09
748 843 2.093106 ACTTGTAGAGCGAGGTACCTG 58.907 52.381 22.10 12.88 32.77 4.00
799 894 8.713271 TGTAAAAATGAAAGAAAAACGCAAAGT 58.287 25.926 0.00 0.00 0.00 2.66
921 1016 2.283676 AGACGAGCGGGGAGGAAA 60.284 61.111 0.00 0.00 0.00 3.13
922 1017 2.754658 GAGACGAGCGGGGAGGAA 60.755 66.667 0.00 0.00 0.00 3.36
923 1018 3.997400 CTGAGACGAGCGGGGAGGA 62.997 68.421 0.00 0.00 0.00 3.71
927 1022 2.829003 TAGCTGAGACGAGCGGGG 60.829 66.667 0.00 0.00 44.24 5.73
1059 1161 1.611851 CCTGGAGCAGTCCCTGAGT 60.612 63.158 0.00 0.00 43.15 3.41
1063 1165 4.664267 TGCCCTGGAGCAGTCCCT 62.664 66.667 5.85 0.00 43.15 4.20
1080 1182 1.302033 GCCGATGATCCTGGCGAAT 60.302 57.895 4.45 0.00 39.30 3.34
1081 1183 2.108976 GCCGATGATCCTGGCGAA 59.891 61.111 4.45 0.00 39.30 4.70
1114 1216 1.608336 GGGTTTAGTTGGTGGGGGC 60.608 63.158 0.00 0.00 0.00 5.80
1123 1225 0.551871 GGGGAGGGAGGGGTTTAGTT 60.552 60.000 0.00 0.00 0.00 2.24
1124 1226 1.084273 GGGGAGGGAGGGGTTTAGT 59.916 63.158 0.00 0.00 0.00 2.24
1166 1269 0.539051 CTGACTCGGGAAGGCATTCT 59.461 55.000 11.37 0.00 44.01 2.40
1181 1284 1.856012 GTCAGCAACGCAGTCTGAC 59.144 57.895 3.32 0.00 45.00 3.51
1289 1397 0.322975 CGATGGACATGATCTCCCCC 59.677 60.000 0.00 0.00 0.00 5.40
1423 1531 4.231439 CAATGGATCAATGTGTGTGTGTG 58.769 43.478 0.00 0.00 0.00 3.82
1426 1534 2.827322 CCCAATGGATCAATGTGTGTGT 59.173 45.455 0.00 0.00 0.00 3.72
1430 1538 3.744940 ACTCCCAATGGATCAATGTGT 57.255 42.857 0.00 0.00 40.80 3.72
1444 2161 6.722590 TCAACTACAGTACAGATTTACTCCCA 59.277 38.462 0.00 0.00 29.30 4.37
1494 2212 2.751259 AGGCACATCATCATCACAACAC 59.249 45.455 0.00 0.00 0.00 3.32
1497 2215 2.282407 CGAGGCACATCATCATCACAA 58.718 47.619 0.00 0.00 0.00 3.33
1502 2220 2.159338 GCAAAACGAGGCACATCATCAT 60.159 45.455 0.00 0.00 0.00 2.45
1503 2221 1.199789 GCAAAACGAGGCACATCATCA 59.800 47.619 0.00 0.00 0.00 3.07
1504 2222 1.900237 GCAAAACGAGGCACATCATC 58.100 50.000 0.00 0.00 0.00 2.92
1685 2409 9.570488 GACTTAAAATCACAGTACCAGTAGTAG 57.430 37.037 0.00 0.00 0.00 2.57
1686 2410 9.081204 TGACTTAAAATCACAGTACCAGTAGTA 57.919 33.333 0.00 0.00 0.00 1.82
1687 2411 7.959175 TGACTTAAAATCACAGTACCAGTAGT 58.041 34.615 0.00 0.00 0.00 2.73
1688 2412 8.709646 GTTGACTTAAAATCACAGTACCAGTAG 58.290 37.037 0.00 0.00 0.00 2.57
1777 2501 5.701224 AGAAAAACTGGAGTGGTTGGATTA 58.299 37.500 0.00 0.00 0.00 1.75
1796 2520 7.232737 GGGTCATCCTCCTTTTCTAAAAAGAAA 59.767 37.037 12.53 0.00 36.17 2.52
1797 2521 6.719829 GGGTCATCCTCCTTTTCTAAAAAGAA 59.280 38.462 12.53 0.00 0.00 2.52
1798 2522 6.246163 GGGTCATCCTCCTTTTCTAAAAAGA 58.754 40.000 12.53 0.00 0.00 2.52
1799 2523 5.419155 GGGGTCATCCTCCTTTTCTAAAAAG 59.581 44.000 5.40 5.40 35.33 2.27
1842 2566 1.113788 ATAAAGTGGCCGCATGCATT 58.886 45.000 20.59 7.71 43.89 3.56
2197 2924 2.597805 AGGACGACGCTGTCTGGT 60.598 61.111 7.46 0.00 38.91 4.00
2222 2949 0.668535 CGATGTGCGAGGATGGACTA 59.331 55.000 0.00 0.00 44.57 2.59
2265 2992 2.049985 CGACGGATCTCGATGGCC 60.050 66.667 10.05 0.00 42.43 5.36
2269 2996 1.172812 TGATGGCGACGGATCTCGAT 61.173 55.000 8.43 0.00 42.43 3.59
2346 3073 1.376424 CGCTCTTGGAGGTGTGCAT 60.376 57.895 0.00 0.00 0.00 3.96
2394 3121 4.508128 GATCGGAAGACGGCGGCA 62.508 66.667 18.30 0.00 46.97 5.69


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

AutoCloner maintained by Alex Coulton.