Multiple sequence alignment - TraesCS2D01G446200

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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 TraesCS2D01G446200 chr2D 100.000 3020 0 0 1 3020 556371728 556374747 0.000000e+00 5578
1 TraesCS2D01G446200 chr2D 97.053 1561 29 7 623 2181 46907919 46906374 0.000000e+00 2612
2 TraesCS2D01G446200 chr2D 99.046 629 6 0 2392 3020 46905375 46904747 0.000000e+00 1129
3 TraesCS2D01G446200 chr2D 96.488 541 16 1 1 541 46908480 46907943 0.000000e+00 891
4 TraesCS2D01G446200 chr2D 98.047 512 6 4 1 512 599594957 599595464 0.000000e+00 887
5 TraesCS2D01G446200 chr2D 98.588 425 6 0 2392 2816 599599788 599600212 0.000000e+00 752
6 TraesCS2D01G446200 chr2D 91.584 202 10 6 2823 3020 385381940 385382138 3.840000e-69 272
7 TraesCS2D01G446200 chr7D 96.606 1915 30 12 512 2395 66522156 66520246 0.000000e+00 3144
8 TraesCS2D01G446200 chr1D 92.181 2187 80 16 576 2742 33570189 33568074 0.000000e+00 3007
9 TraesCS2D01G446200 chr1D 95.698 1534 37 9 623 2145 21343600 21345115 0.000000e+00 2440
10 TraesCS2D01G446200 chr1D 92.789 1567 39 13 442 1961 404205012 404206551 0.000000e+00 2200
11 TraesCS2D01G446200 chr1D 97.575 1031 25 0 1990 3020 404206550 404207580 0.000000e+00 1766
12 TraesCS2D01G446200 chr1D 98.092 629 10 2 2392 3020 21345898 21346524 0.000000e+00 1094
13 TraesCS2D01G446200 chr1D 98.353 425 7 0 2392 2816 492588871 492588447 0.000000e+00 747
14 TraesCS2D01G446200 chr1D 95.618 251 11 0 2770 3020 33568088 33567838 1.300000e-108 403
15 TraesCS2D01G446200 chr3D 91.724 2187 92 30 576 2742 584752182 584750065 0.000000e+00 2953
16 TraesCS2D01G446200 chr3D 93.571 1602 33 11 623 2179 551375785 551374209 0.000000e+00 2324
17 TraesCS2D01G446200 chr3D 98.242 512 6 1 1 512 32366727 32367235 0.000000e+00 893
18 TraesCS2D01G446200 chr3D 98.588 425 6 0 2392 2816 551373304 551372880 0.000000e+00 752
19 TraesCS2D01G446200 chr3D 98.353 425 7 0 2392 2816 580704711 580704287 0.000000e+00 747
20 TraesCS2D01G446200 chr3D 95.219 251 12 0 2770 3020 584750079 584749829 6.070000e-107 398
21 TraesCS2D01G446200 chr5D 92.440 1918 76 27 863 2742 520987259 520985373 0.000000e+00 2675
22 TraesCS2D01G446200 chr5D 98.047 512 7 1 1 512 348506035 348506543 0.000000e+00 887
23 TraesCS2D01G446200 chr5D 97.461 512 7 2 1 512 435226991 435227496 0.000000e+00 869
24 TraesCS2D01G446200 chr5D 98.824 425 5 0 2392 2816 348510869 348511293 0.000000e+00 758
25 TraesCS2D01G446200 chr5D 93.789 322 10 1 576 897 520987495 520987184 2.720000e-130 475
26 TraesCS2D01G446200 chr5D 96.813 251 8 0 2770 3020 520985387 520985137 1.290000e-113 420
27 TraesCS2D01G446200 chr5D 91.089 202 11 6 2823 3020 489241439 489241637 1.780000e-67 267
28 TraesCS2D01G446200 chr3B 86.962 1465 86 52 708 2110 557701815 557703236 0.000000e+00 1550
29 TraesCS2D01G446200 chr3B 95.597 159 4 1 513 668 557701600 557701758 5.000000e-63 252
30 TraesCS2D01G446200 chr2B 88.126 918 49 32 513 1396 796940076 796940967 0.000000e+00 1037
31 TraesCS2D01G446200 chr2B 84.363 1068 86 52 513 1536 750605346 750606376 0.000000e+00 972
32 TraesCS2D01G446200 chr2B 88.827 716 40 21 696 1396 87173415 87172725 0.000000e+00 843
33 TraesCS2D01G446200 chr4A 90.274 730 42 17 1392 2110 404426514 404425803 0.000000e+00 928
34 TraesCS2D01G446200 chr4B 89.771 743 38 21 1381 2110 8025019 8024302 0.000000e+00 917
35 TraesCS2D01G446200 chr4B 88.624 712 40 18 883 1572 8025613 8024921 0.000000e+00 828
36 TraesCS2D01G446200 chr3A 89.917 724 48 16 1392 2110 153252012 153251309 0.000000e+00 909
37 TraesCS2D01G446200 chr4D 98.633 512 4 1 1 512 388113489 388112981 0.000000e+00 904
38 TraesCS2D01G446200 chr4D 98.047 512 7 1 1 512 434992096 434991588 0.000000e+00 887
39 TraesCS2D01G446200 chr4D 98.824 425 5 0 2392 2816 434988802 434988378 0.000000e+00 758
40 TraesCS2D01G446200 chr4D 89.401 217 4 7 2823 3020 434988449 434988233 3.860000e-64 255
41 TraesCS2D01G446200 chr5A 89.452 730 48 15 1392 2110 596892296 596893007 0.000000e+00 894
42 TraesCS2D01G446200 chr7A 97.461 512 9 2 1 512 63598672 63598165 0.000000e+00 870
43 TraesCS2D01G446200 chr2A 97.461 512 10 1 1 512 696289088 696289596 0.000000e+00 870
44 TraesCS2D01G446200 chr1B 89.489 704 41 11 1427 2110 600349436 600348746 0.000000e+00 859
45 TraesCS2D01G446200 chr5B 96.552 145 2 1 513 654 492523261 492523117 1.400000e-58 237


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 TraesCS2D01G446200 chr2D 556371728 556374747 3019 False 5578.000000 5578 100.000000 1 3020 1 chr2D.!!$F2 3019
1 TraesCS2D01G446200 chr2D 46904747 46908480 3733 True 1544.000000 2612 97.529000 1 3020 3 chr2D.!!$R1 3019
2 TraesCS2D01G446200 chr2D 599594957 599595464 507 False 887.000000 887 98.047000 1 512 1 chr2D.!!$F3 511
3 TraesCS2D01G446200 chr7D 66520246 66522156 1910 True 3144.000000 3144 96.606000 512 2395 1 chr7D.!!$R1 1883
4 TraesCS2D01G446200 chr1D 404205012 404207580 2568 False 1983.000000 2200 95.182000 442 3020 2 chr1D.!!$F2 2578
5 TraesCS2D01G446200 chr1D 21343600 21346524 2924 False 1767.000000 2440 96.895000 623 3020 2 chr1D.!!$F1 2397
6 TraesCS2D01G446200 chr1D 33567838 33570189 2351 True 1705.000000 3007 93.899500 576 3020 2 chr1D.!!$R2 2444
7 TraesCS2D01G446200 chr3D 584749829 584752182 2353 True 1675.500000 2953 93.471500 576 3020 2 chr3D.!!$R3 2444
8 TraesCS2D01G446200 chr3D 551372880 551375785 2905 True 1538.000000 2324 96.079500 623 2816 2 chr3D.!!$R2 2193
9 TraesCS2D01G446200 chr3D 32366727 32367235 508 False 893.000000 893 98.242000 1 512 1 chr3D.!!$F1 511
10 TraesCS2D01G446200 chr5D 520985137 520987495 2358 True 1190.000000 2675 94.347333 576 3020 3 chr5D.!!$R1 2444
11 TraesCS2D01G446200 chr5D 348506035 348506543 508 False 887.000000 887 98.047000 1 512 1 chr5D.!!$F1 511
12 TraesCS2D01G446200 chr5D 435226991 435227496 505 False 869.000000 869 97.461000 1 512 1 chr5D.!!$F3 511
13 TraesCS2D01G446200 chr3B 557701600 557703236 1636 False 901.000000 1550 91.279500 513 2110 2 chr3B.!!$F1 1597
14 TraesCS2D01G446200 chr2B 796940076 796940967 891 False 1037.000000 1037 88.126000 513 1396 1 chr2B.!!$F2 883
15 TraesCS2D01G446200 chr2B 750605346 750606376 1030 False 972.000000 972 84.363000 513 1536 1 chr2B.!!$F1 1023
16 TraesCS2D01G446200 chr2B 87172725 87173415 690 True 843.000000 843 88.827000 696 1396 1 chr2B.!!$R1 700
17 TraesCS2D01G446200 chr4A 404425803 404426514 711 True 928.000000 928 90.274000 1392 2110 1 chr4A.!!$R1 718
18 TraesCS2D01G446200 chr4B 8024302 8025613 1311 True 872.500000 917 89.197500 883 2110 2 chr4B.!!$R1 1227
19 TraesCS2D01G446200 chr3A 153251309 153252012 703 True 909.000000 909 89.917000 1392 2110 1 chr3A.!!$R1 718
20 TraesCS2D01G446200 chr4D 388112981 388113489 508 True 904.000000 904 98.633000 1 512 1 chr4D.!!$R1 511
21 TraesCS2D01G446200 chr4D 434988233 434992096 3863 True 633.333333 887 95.424000 1 3020 3 chr4D.!!$R2 3019
22 TraesCS2D01G446200 chr5A 596892296 596893007 711 False 894.000000 894 89.452000 1392 2110 1 chr5A.!!$F1 718
23 TraesCS2D01G446200 chr7A 63598165 63598672 507 True 870.000000 870 97.461000 1 512 1 chr7A.!!$R1 511
24 TraesCS2D01G446200 chr2A 696289088 696289596 508 False 870.000000 870 97.461000 1 512 1 chr2A.!!$F1 511
25 TraesCS2D01G446200 chr1B 600348746 600349436 690 True 859.000000 859 89.489000 1427 2110 1 chr1B.!!$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
853 1704 0.399806 ATCTTCCTCCCTCTGCCTCC 60.4 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2623 5032 1.881973 TGCAGGAAGCTGTCAATTGTC 59.118 47.619 5.13 0.0 45.94 3.18 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
74 75 5.070580 GCCCTACTACTAGGACACATTCAAT 59.929 44.000 0.00 0.00 42.34 2.57
852 1703 0.758123 CATCTTCCTCCCTCTGCCTC 59.242 60.000 0.00 0.00 0.00 4.70
853 1704 0.399806 ATCTTCCTCCCTCTGCCTCC 60.400 60.000 0.00 0.00 0.00 4.30
854 1705 2.041265 TTCCTCCCTCTGCCTCCC 59.959 66.667 0.00 0.00 0.00 4.30
855 1706 2.543978 CTTCCTCCCTCTGCCTCCCT 62.544 65.000 0.00 0.00 0.00 4.20
856 1707 2.445654 CCTCCCTCTGCCTCCCTC 60.446 72.222 0.00 0.00 0.00 4.30
857 1708 2.695597 CTCCCTCTGCCTCCCTCT 59.304 66.667 0.00 0.00 0.00 3.69
858 1709 1.761667 CTCCCTCTGCCTCCCTCTG 60.762 68.421 0.00 0.00 0.00 3.35
859 1710 3.478274 CCCTCTGCCTCCCTCTGC 61.478 72.222 0.00 0.00 0.00 4.26
860 1711 3.478274 CCTCTGCCTCCCTCTGCC 61.478 72.222 0.00 0.00 0.00 4.85
861 1712 2.365370 CTCTGCCTCCCTCTGCCT 60.365 66.667 0.00 0.00 0.00 4.75
1044 1925 2.743928 CCTCCGTCTGCCAAGCAC 60.744 66.667 0.00 0.00 33.79 4.40
2267 3474 6.618287 TCAAACCAGTCAAGTATCAAACAG 57.382 37.500 0.00 0.00 0.00 3.16
2411 4816 1.747444 AATCCAACACCCTGTCCTCT 58.253 50.000 0.00 0.00 0.00 3.69
2451 4860 6.768483 TGATGGACATCTTCAACTAGTTTGA 58.232 36.000 5.07 5.36 38.99 2.69
2623 5032 1.028905 TCAACCCAAGCAAGGAAACG 58.971 50.000 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 0.257328 TTGCACCTCCTCCAACACAA 59.743 50.000 0.00 0.0 0.00 3.33
466 467 0.322277 CAAGTGTGCTCCAGCCTCAT 60.322 55.000 0.00 0.0 41.18 2.90
467 468 1.071987 CAAGTGTGCTCCAGCCTCA 59.928 57.895 0.00 0.0 41.18 3.86
468 469 3.978272 CAAGTGTGCTCCAGCCTC 58.022 61.111 0.00 0.0 41.18 4.70
655 1459 1.377333 CCGGCCTTCTCCTGTTTCC 60.377 63.158 0.00 0.0 0.00 3.13
852 1703 2.445654 GAGGAGGGAGGCAGAGGG 60.446 72.222 0.00 0.0 0.00 4.30
853 1704 0.693767 AATGAGGAGGGAGGCAGAGG 60.694 60.000 0.00 0.0 0.00 3.69
854 1705 0.758123 GAATGAGGAGGGAGGCAGAG 59.242 60.000 0.00 0.0 0.00 3.35
855 1706 0.692419 GGAATGAGGAGGGAGGCAGA 60.692 60.000 0.00 0.0 0.00 4.26
856 1707 0.984961 TGGAATGAGGAGGGAGGCAG 60.985 60.000 0.00 0.0 0.00 4.85
857 1708 0.327867 ATGGAATGAGGAGGGAGGCA 60.328 55.000 0.00 0.0 0.00 4.75
858 1709 0.849417 AATGGAATGAGGAGGGAGGC 59.151 55.000 0.00 0.0 0.00 4.70
859 1710 1.478288 GCAATGGAATGAGGAGGGAGG 60.478 57.143 0.00 0.0 0.00 4.30
860 1711 1.478288 GGCAATGGAATGAGGAGGGAG 60.478 57.143 0.00 0.0 0.00 4.30
861 1712 0.552848 GGCAATGGAATGAGGAGGGA 59.447 55.000 0.00 0.0 0.00 4.20
1105 1986 1.903183 GGTGTAGTCCAGCTTCTTCCT 59.097 52.381 0.00 0.0 38.55 3.36
2411 4816 2.827322 CCATCAACTTCTCAATGCCCAA 59.173 45.455 0.00 0.0 0.00 4.12
2451 4860 3.461085 AGGAATCTGGATGCCAACTATGT 59.539 43.478 10.00 0.0 39.11 2.29
2623 5032 1.881973 TGCAGGAAGCTGTCAATTGTC 59.118 47.619 5.13 0.0 45.94 3.18


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

AutoCloner maintained by Alex Coulton.