Multiple sequence alignment - TraesCS2A01G264600

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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 TraesCS2A01G264600 chr2A 100.000 9910 0 0 1 9910 419655040 419645131 0.000000e+00 18301.0
1 TraesCS2A01G264600 chr2A 99.772 438 1 0 2265 2702 727917964 727918401 0.000000e+00 804.0
2 TraesCS2A01G264600 chr2A 84.779 565 71 10 1 560 34383205 34383759 4.040000e-153 553.0
3 TraesCS2A01G264600 chr2A 96.330 109 4 0 657 765 419659620 419659512 7.910000e-41 180.0
4 TraesCS2A01G264600 chr2A 85.124 121 13 4 9495 9614 60247642 60247758 1.750000e-22 119.0
5 TraesCS2A01G264600 chr2A 94.872 39 1 1 5899 5937 43502298 43502335 1.070000e-04 60.2
6 TraesCS2A01G264600 chr2D 97.029 4376 93 13 3094 7463 315415470 315419814 0.000000e+00 7326.0
7 TraesCS2A01G264600 chr2D 97.583 786 17 2 813 1596 315414403 315415188 0.000000e+00 1345.0
8 TraesCS2A01G264600 chr2D 98.792 745 9 0 7464 8208 315419867 315420611 0.000000e+00 1327.0
9 TraesCS2A01G264600 chr2D 94.838 833 33 7 8194 9019 315420627 315421456 0.000000e+00 1291.0
10 TraesCS2A01G264600 chr2D 95.076 264 7 2 1593 1850 315415215 315415478 2.580000e-110 411.0
11 TraesCS2A01G264600 chr2D 94.619 223 11 1 9015 9236 315422536 315422758 2.650000e-90 344.0
12 TraesCS2A01G264600 chr2D 89.333 225 24 0 9368 9592 585117026 585117250 5.860000e-72 283.0
13 TraesCS2A01G264600 chr2D 95.192 104 4 1 558 661 593274241 593274343 7.960000e-36 163.0
14 TraesCS2A01G264600 chr2D 84.615 156 23 1 9450 9604 294620866 294620711 4.790000e-33 154.0
15 TraesCS2A01G264600 chr2D 86.154 130 17 1 9476 9604 287185026 287184897 1.340000e-28 139.0
16 TraesCS2A01G264600 chr2D 93.750 80 5 0 9238 9317 315422810 315422889 4.860000e-23 121.0
17 TraesCS2A01G264600 chr2D 96.296 54 1 1 9313 9365 521565051 521564998 4.930000e-13 87.9
18 TraesCS2A01G264600 chr2B 96.732 4376 103 15 3096 7464 383274650 383278992 0.000000e+00 7252.0
19 TraesCS2A01G264600 chr2B 94.835 1665 47 14 7464 9098 383279044 383280699 0.000000e+00 2562.0
20 TraesCS2A01G264600 chr2B 97.919 769 13 1 828 1596 383273605 383274370 0.000000e+00 1328.0
21 TraesCS2A01G264600 chr2B 94.601 426 23 0 2277 2702 719293670 719294095 0.000000e+00 660.0
22 TraesCS2A01G264600 chr2B 96.250 400 13 2 1848 2246 571767630 571768028 0.000000e+00 654.0
23 TraesCS2A01G264600 chr2B 95.223 314 10 5 1851 2163 573127904 573128213 8.940000e-135 492.0
24 TraesCS2A01G264600 chr2B 97.561 287 5 2 1847 2132 573128867 573128582 3.220000e-134 490.0
25 TraesCS2A01G264600 chr2B 98.479 263 4 0 2831 3093 573128600 573128862 1.950000e-126 464.0
26 TraesCS2A01G264600 chr2B 93.411 258 14 1 1593 1847 383274397 383274654 7.260000e-101 379.0
27 TraesCS2A01G264600 chr2B 85.766 274 34 2 9319 9591 32966661 32966392 1.630000e-72 285.0
28 TraesCS2A01G264600 chr2B 95.968 124 4 1 9094 9217 383291214 383291336 6.070000e-47 200.0
29 TraesCS2A01G264600 chr2B 84.848 198 28 2 9396 9591 519387209 519387406 2.180000e-46 198.0
30 TraesCS2A01G264600 chr2B 84.946 186 24 3 9407 9591 23230786 23230968 1.700000e-42 185.0
31 TraesCS2A01G264600 chr2B 97.959 98 2 0 559 656 462945967 462945870 4.760000e-38 171.0
32 TraesCS2A01G264600 chr2B 95.000 80 4 0 9238 9317 383321213 383321292 1.040000e-24 126.0
33 TraesCS2A01G264600 chr4B 99.336 1054 3 2 2041 3094 612330139 612329090 0.000000e+00 1905.0
34 TraesCS2A01G264600 chr4B 97.744 266 6 0 2834 3099 301791619 301791354 9.070000e-125 459.0
35 TraesCS2A01G264600 chr4B 98.462 260 4 0 2834 3093 301904578 301904319 9.070000e-125 459.0
36 TraesCS2A01G264600 chr4B 97.368 266 7 0 2834 3099 301737295 301737030 4.220000e-123 453.0
37 TraesCS2A01G264600 chr4B 97.368 266 7 0 2834 3099 301845411 301845146 4.220000e-123 453.0
38 TraesCS2A01G264600 chr4B 97.368 266 7 0 2834 3099 301872551 301872286 4.220000e-123 453.0
39 TraesCS2A01G264600 chr4B 79.640 555 92 16 1 547 77159267 77158726 7.260000e-101 379.0
40 TraesCS2A01G264600 chr4B 91.304 276 16 7 1181 1449 74853015 74852741 4.370000e-98 370.0
41 TraesCS2A01G264600 chr4B 76.751 671 129 25 3950 4608 95673537 95674192 5.700000e-92 350.0
42 TraesCS2A01G264600 chr4B 98.980 98 1 0 559 656 300941616 300941713 1.020000e-39 176.0
43 TraesCS2A01G264600 chr4B 78.571 224 28 16 6051 6262 95703758 95703973 8.080000e-26 130.0
44 TraesCS2A01G264600 chr4B 85.047 107 16 0 5529 5635 95676082 95676188 1.050000e-19 110.0
45 TraesCS2A01G264600 chr1A 92.007 563 42 2 1 560 494354679 494354117 0.000000e+00 787.0
46 TraesCS2A01G264600 chr1A 99.057 106 1 0 2735 2840 527099926 527099821 3.650000e-44 191.0
47 TraesCS2A01G264600 chr1A 96.330 109 3 1 657 765 494354115 494354008 2.840000e-40 178.0
48 TraesCS2A01G264600 chr1A 96.040 101 3 1 657 757 494376196 494376097 7.960000e-36 163.0
49 TraesCS2A01G264600 chr1A 97.059 34 1 0 2700 2733 527098386 527098419 3.870000e-04 58.4
50 TraesCS2A01G264600 chr3B 91.351 555 42 4 1 550 763529920 763530473 0.000000e+00 754.0
51 TraesCS2A01G264600 chr3B 89.636 550 54 2 1 547 381848552 381849101 0.000000e+00 697.0
52 TraesCS2A01G264600 chr3B 96.078 102 3 1 560 661 177503776 177503876 2.210000e-36 165.0
53 TraesCS2A01G264600 chr3B 87.368 95 9 2 658 750 763530485 763530578 1.360000e-18 106.0
54 TraesCS2A01G264600 chr3B 86.458 96 8 4 657 750 381843969 381844061 6.330000e-17 100.0
55 TraesCS2A01G264600 chr3B 86.316 95 10 2 658 750 763525356 763525449 6.330000e-17 100.0
56 TraesCS2A01G264600 chr3B 85.417 96 9 4 657 750 381849117 381849209 2.950000e-15 95.3
57 TraesCS2A01G264600 chr7A 97.229 397 9 2 1851 2246 237508335 237507940 0.000000e+00 671.0
58 TraesCS2A01G264600 chr7A 97.887 284 5 1 1849 2132 237507362 237507644 3.220000e-134 490.0
59 TraesCS2A01G264600 chr7A 98.846 260 3 0 2834 3093 237507623 237507364 1.950000e-126 464.0
60 TraesCS2A01G264600 chr7A 85.379 383 50 4 2326 2702 478502989 478503371 9.330000e-105 392.0
61 TraesCS2A01G264600 chr7A 92.913 254 16 2 9651 9903 624921665 624921413 1.570000e-97 368.0
62 TraesCS2A01G264600 chr7A 83.065 124 20 1 9482 9604 295953389 295953266 2.930000e-20 111.0
63 TraesCS2A01G264600 chr4A 96.725 397 11 2 1851 2246 737844760 737844365 0.000000e+00 660.0
64 TraesCS2A01G264600 chr4A 81.967 488 74 10 67 547 379028311 379027831 1.550000e-107 401.0
65 TraesCS2A01G264600 chr4A 93.976 249 14 1 9656 9903 107925535 107925783 9.400000e-100 375.0
66 TraesCS2A01G264600 chr4A 97.938 97 2 0 560 656 639988787 639988883 1.710000e-37 169.0
67 TraesCS2A01G264600 chr7B 94.569 313 13 4 1852 2163 713751501 713751810 1.940000e-131 481.0
68 TraesCS2A01G264600 chr7B 80.986 426 54 13 2298 2698 431663199 431663622 7.470000e-81 313.0
69 TraesCS2A01G264600 chr7B 89.381 226 21 3 9367 9591 674235125 674235348 2.110000e-71 281.0
70 TraesCS2A01G264600 chr7B 86.441 236 32 0 9367 9602 194699730 194699495 9.870000e-65 259.0
71 TraesCS2A01G264600 chr7B 96.970 99 3 0 559 657 217312360 217312262 6.160000e-37 167.0
72 TraesCS2A01G264600 chr7B 96.117 103 3 1 555 657 244219407 244219306 6.160000e-37 167.0
73 TraesCS2A01G264600 chr7B 94.737 57 1 2 9311 9365 410646892 410646948 4.930000e-13 87.9
74 TraesCS2A01G264600 chr7B 97.500 40 1 0 2207 2246 59311777 59311738 1.790000e-07 69.4
75 TraesCS2A01G264600 chr3A 97.183 284 7 1 1849 2132 49472548 49472830 6.960000e-131 479.0
76 TraesCS2A01G264600 chr3A 94.422 251 13 1 9657 9907 548974834 548974585 1.560000e-102 385.0
77 TraesCS2A01G264600 chr3A 93.281 253 17 0 9658 9910 16496339 16496087 3.380000e-99 374.0
78 TraesCS2A01G264600 chr3A 93.600 250 16 0 9656 9905 390588080 390588329 3.380000e-99 374.0
79 TraesCS2A01G264600 chr3A 92.913 254 17 1 9658 9910 16590288 16590035 1.570000e-97 368.0
80 TraesCS2A01G264600 chr3A 88.987 227 24 1 9367 9592 700035527 700035301 7.580000e-71 279.0
81 TraesCS2A01G264600 chr3A 85.714 203 18 5 9392 9591 108475992 108475798 4.690000e-48 204.0
82 TraesCS2A01G264600 chr1B 94.702 302 12 3 1838 2137 13254922 13255221 5.420000e-127 466.0
83 TraesCS2A01G264600 chr1B 82.210 534 83 11 1 527 174711532 174712060 5.460000e-122 449.0
84 TraesCS2A01G264600 chr1B 97.727 88 2 0 2735 2822 580621009 580620922 1.720000e-32 152.0
85 TraesCS2A01G264600 chr6A 97.719 263 6 0 2831 3093 435591919 435592181 4.220000e-123 453.0
86 TraesCS2A01G264600 chr6A 94.715 246 13 0 9658 9903 202984468 202984713 5.620000e-102 383.0
87 TraesCS2A01G264600 chr6A 88.764 89 5 3 2161 2246 584911792 584911878 4.900000e-18 104.0
88 TraesCS2A01G264600 chr6D 80.755 556 81 21 1 544 210781304 210780763 2.580000e-110 411.0
89 TraesCS2A01G264600 chr6D 89.778 225 22 1 9367 9591 11913423 11913200 4.530000e-73 287.0
90 TraesCS2A01G264600 chr6D 87.356 87 7 4 2161 2246 436716634 436716717 8.190000e-16 97.1
91 TraesCS2A01G264600 chr7D 84.337 415 54 8 2297 2702 416238052 416238464 7.210000e-106 396.0
92 TraesCS2A01G264600 chr7D 94.286 105 6 0 553 657 30953106 30953210 2.860000e-35 161.0
93 TraesCS2A01G264600 chr7D 91.743 109 8 1 657 765 603744845 603744952 6.200000e-32 150.0
94 TraesCS2A01G264600 chr7D 96.154 52 2 0 9314 9365 49806899 49806848 1.770000e-12 86.1
95 TraesCS2A01G264600 chr7D 97.500 40 1 0 2207 2246 101806970 101806931 1.790000e-07 69.4
96 TraesCS2A01G264600 chr5A 92.885 253 18 0 9658 9910 527269276 527269024 1.570000e-97 368.0
97 TraesCS2A01G264600 chr5A 93.200 250 15 2 9658 9907 96520193 96520440 5.660000e-97 366.0
98 TraesCS2A01G264600 chr5A 84.138 290 27 10 9319 9591 688148855 688149142 7.630000e-66 263.0
99 TraesCS2A01G264600 chr5A 72.343 734 161 35 3733 4449 594143762 594143054 1.020000e-44 193.0
100 TraesCS2A01G264600 chr5B 89.085 284 25 5 212 491 94983808 94983527 2.050000e-91 348.0
101 TraesCS2A01G264600 chr5B 72.109 735 161 35 3733 4449 582165323 582164615 2.200000e-41 182.0
102 TraesCS2A01G264600 chr4D 77.595 607 104 28 4017 4608 65124467 65125056 1.230000e-88 339.0
103 TraesCS2A01G264600 chr4D 87.054 224 26 2 6827 7047 65145950 65146173 5.940000e-62 250.0
104 TraesCS2A01G264600 chr4D 84.615 130 19 1 9472 9601 65531103 65530975 2.910000e-25 128.0
105 TraesCS2A01G264600 chr4D 83.846 130 20 1 9476 9604 262706730 262706601 1.350000e-23 122.0
106 TraesCS2A01G264600 chr4D 85.981 107 15 0 5529 5635 65126859 65126965 2.260000e-21 115.0
107 TraesCS2A01G264600 chrUn 85.766 274 34 2 9319 9591 215699668 215699399 1.630000e-72 285.0
108 TraesCS2A01G264600 chrUn 85.766 274 34 2 9319 9591 215705982 215705713 1.630000e-72 285.0
109 TraesCS2A01G264600 chr5D 89.333 225 24 0 9367 9591 305850179 305850403 5.860000e-72 283.0
110 TraesCS2A01G264600 chr5D 72.093 731 168 31 3733 4449 475013842 475013134 4.730000e-43 187.0
111 TraesCS2A01G264600 chr5D 85.185 135 17 3 9472 9604 116996730 116996863 1.740000e-27 135.0
112 TraesCS2A01G264600 chr1D 89.333 225 24 0 9367 9591 10673150 10673374 5.860000e-72 283.0
113 TraesCS2A01G264600 chr1D 93.396 106 7 0 2735 2840 429598211 429598106 3.710000e-34 158.0
114 TraesCS2A01G264600 chr3D 94.495 109 4 2 551 658 527004853 527004746 6.160000e-37 167.0
115 TraesCS2A01G264600 chr6B 95.238 63 3 0 2184 2246 659936317 659936379 6.330000e-17 100.0


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 TraesCS2A01G264600 chr2A 419645131 419655040 9909 True 18301.000000 18301 100.000000 1 9910 1 chr2A.!!$R1 9909
1 TraesCS2A01G264600 chr2A 34383205 34383759 554 False 553.000000 553 84.779000 1 560 1 chr2A.!!$F1 559
2 TraesCS2A01G264600 chr2D 315414403 315422889 8486 False 1737.857143 7326 95.955286 813 9317 7 chr2D.!!$F3 8504
3 TraesCS2A01G264600 chr2B 383273605 383280699 7094 False 2880.250000 7252 95.724250 828 9098 4 chr2B.!!$F7 8270
4 TraesCS2A01G264600 chr2B 573127904 573128862 958 False 478.000000 492 96.851000 1851 3093 2 chr2B.!!$F8 1242
5 TraesCS2A01G264600 chr4B 612329090 612330139 1049 True 1905.000000 1905 99.336000 2041 3094 1 chr4B.!!$R8 1053
6 TraesCS2A01G264600 chr4B 77158726 77159267 541 True 379.000000 379 79.640000 1 547 1 chr4B.!!$R2 546
7 TraesCS2A01G264600 chr4B 95673537 95676188 2651 False 230.000000 350 80.899000 3950 5635 2 chr4B.!!$F3 1685
8 TraesCS2A01G264600 chr1A 494354008 494354679 671 True 482.500000 787 94.168500 1 765 2 chr1A.!!$R3 764
9 TraesCS2A01G264600 chr3B 763529920 763530578 658 False 430.000000 754 89.359500 1 750 2 chr3B.!!$F5 749
10 TraesCS2A01G264600 chr3B 381848552 381849209 657 False 396.150000 697 87.526500 1 750 2 chr3B.!!$F4 749
11 TraesCS2A01G264600 chr7A 237507364 237508335 971 True 567.500000 671 98.037500 1851 3093 2 chr7A.!!$R3 1242
12 TraesCS2A01G264600 chr1B 174711532 174712060 528 False 449.000000 449 82.210000 1 527 1 chr1B.!!$F2 526
13 TraesCS2A01G264600 chr6D 210780763 210781304 541 True 411.000000 411 80.755000 1 544 1 chr6D.!!$R2 543
14 TraesCS2A01G264600 chr4D 65124467 65126965 2498 False 227.000000 339 81.788000 4017 5635 2 chr4D.!!$F2 1618

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
34 35 0.680921 CCATTCTGGAACGCATGGGT 60.681 55.000 10.03 10.03 40.96 4.51 F
1077 1098 0.814812 CGTCTCCGTCTACCTCCTCC 60.815 65.000 0.00 0.00 0.00 4.30 F
1717 1801 0.448861 CGTCGTGTGATTGAACGTGC 60.449 55.000 0.00 0.00 40.61 5.34 F
3251 3530 0.183492 TTTGGCCACTGCTTGTCTCT 59.817 50.000 3.88 0.00 37.74 3.10 F
3252 3531 0.535780 TTGGCCACTGCTTGTCTCTG 60.536 55.000 3.88 0.00 37.74 3.35 F
3253 3532 1.072159 GGCCACTGCTTGTCTCTGT 59.928 57.895 0.00 0.00 37.74 3.41 F
3713 3993 1.754555 CGGCCTACCTCTAGTCACCAT 60.755 57.143 0.00 0.00 0.00 3.55 F
3821 4101 2.065799 ACCAGTGGATTTTCCAGTCCT 58.934 47.619 18.40 0.00 46.94 3.85 F
5425 6637 0.032117 TGGTGGAGGACTCGGATGAT 60.032 55.000 0.00 0.00 0.00 2.45 F
6333 7695 0.508641 CGTGGTTCTTCAAGCTCACG 59.491 55.000 10.83 10.83 41.09 4.35 F
7731 9146 1.277557 GTCTGTCTCTTCCTGCATGGT 59.722 52.381 0.00 0.00 37.07 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 1801 1.075425 CGTTTCCTCAGCTCAGCGAG 61.075 60.000 10.50 10.50 0.00 5.03 R
2029 2116 1.480137 CCCGATTGCATTTTTAGCCCA 59.520 47.619 0.00 0.00 0.00 5.36 R
3493 3773 0.032416 TAGAGAGGGAAAGGACCGGG 60.032 60.000 6.32 0.00 0.00 5.73 R
5079 5642 1.259609 TGTCGGGTGAAGTTACGGAT 58.740 50.000 0.00 0.00 0.00 4.18 R
5121 5684 3.128349 GCATAATCTTTTGGCCATGCAG 58.872 45.455 16.77 9.02 38.84 4.41 R
5281 5844 2.859165 AAGTCGTGGATGGTTGATGT 57.141 45.000 0.00 0.00 0.00 3.06 R
5292 5858 1.343465 ACAGACAAGGGTAAGTCGTGG 59.657 52.381 0.00 0.00 39.67 4.94 R
5808 7170 1.339610 AGCAGACGAGAGATATGCACC 59.660 52.381 0.00 0.00 38.88 5.01 R
6351 7713 0.593263 GCAAGCAGGCAATCGTATGC 60.593 55.000 6.64 6.64 45.67 3.14 R
8055 9470 0.032912 AAACCAAACGGTTGAGGGGT 60.033 50.000 16.49 0.00 46.41 4.95 R
9535 12128 0.035317 ACGCACACACACTCATCCAT 59.965 50.000 0.00 0.00 0.00 3.41 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)


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

AutoCloner maintained by Alex Coulton.