Multiple sequence alignment - TraesCS2A01G264100

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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 TraesCS2A01G264100 chr2A 100.000 6513 0 0 1 6513 419026563 419033075 0.000000e+00 12028.0
1 TraesCS2A01G264100 chr2A 84.661 339 23 9 4061 4394 522519019 522518705 1.760000e-80 311.0
2 TraesCS2A01G264100 chr2A 83.918 342 27 11 4061 4398 235331122 235331439 1.060000e-77 302.0
3 TraesCS2A01G264100 chr2A 82.808 349 31 13 4061 4405 486504317 486504640 1.070000e-72 285.0
4 TraesCS2A01G264100 chr2A 82.787 122 20 1 419 540 725554542 725554422 2.480000e-19 108.0
5 TraesCS2A01G264100 chr2A 100.000 29 0 0 5349 5377 419031747 419031775 3.000000e-03 54.7
6 TraesCS2A01G264100 chr2A 100.000 29 0 0 5185 5213 419031911 419031939 3.000000e-03 54.7
7 TraesCS2A01G264100 chr2A 100.000 28 0 0 5350 5377 419031793 419031820 1.200000e-02 52.8
8 TraesCS2A01G264100 chr2A 100.000 28 0 0 5231 5258 419031912 419031939 1.200000e-02 52.8
9 TraesCS2A01G264100 chr2B 94.900 1745 46 13 1001 2744 384039736 384038034 0.000000e+00 2689.0
10 TraesCS2A01G264100 chr2B 92.197 1602 48 19 3636 5218 384036947 384035404 0.000000e+00 2194.0
11 TraesCS2A01G264100 chr2B 97.521 726 14 1 2842 3563 384037671 384036946 0.000000e+00 1238.0
12 TraesCS2A01G264100 chr2B 91.615 811 55 4 5713 6513 760109736 760110543 0.000000e+00 1109.0
13 TraesCS2A01G264100 chr2B 87.653 818 87 8 5707 6513 138534892 138534078 0.000000e+00 939.0
14 TraesCS2A01G264100 chr2B 92.754 414 18 4 560 973 384043779 384043378 7.270000e-164 588.0
15 TraesCS2A01G264100 chr2B 91.798 317 12 5 5374 5690 384035402 384035100 4.670000e-116 429.0
16 TraesCS2A01G264100 chr2B 84.548 343 26 7 4060 4398 201466183 201465864 1.360000e-81 315.0
17 TraesCS2A01G264100 chr2B 83.465 254 14 9 1 245 384045366 384045132 1.840000e-50 211.0
18 TraesCS2A01G264100 chr2B 82.667 150 23 3 393 541 764873793 764873940 5.300000e-26 130.0
19 TraesCS2A01G264100 chr2B 90.110 91 4 3 3552 3638 675337145 675337234 5.340000e-21 113.0
20 TraesCS2A01G264100 chr2B 87.755 98 8 2 3553 3646 6027274 6027177 1.920000e-20 111.0
21 TraesCS2A01G264100 chr2D 94.514 1604 43 16 3636 5218 316123769 316122190 0.000000e+00 2433.0
22 TraesCS2A01G264100 chr2D 88.812 1877 99 46 1 1840 316127622 316125820 0.000000e+00 2200.0
23 TraesCS2A01G264100 chr2D 95.341 923 33 5 1823 2744 316125810 316124897 0.000000e+00 1458.0
24 TraesCS2A01G264100 chr2D 98.087 732 14 0 2832 3563 316124499 316123768 0.000000e+00 1275.0
25 TraesCS2A01G264100 chr2D 92.848 825 47 3 5701 6513 82667255 82666431 0.000000e+00 1186.0
26 TraesCS2A01G264100 chr2D 91.477 352 8 4 5349 5690 316122223 316121884 1.280000e-126 464.0
27 TraesCS2A01G264100 chr2D 85.207 338 23 6 4061 4394 386504205 386503891 8.150000e-84 322.0
28 TraesCS2A01G264100 chr2D 84.840 343 24 11 4061 4398 239711352 239711033 2.930000e-83 320.0
29 TraesCS2A01G264100 chr2D 91.860 86 3 3 3555 3637 407254405 407254489 4.130000e-22 117.0
30 TraesCS2A01G264100 chr2D 92.593 81 2 2 3561 3641 621608983 621609059 5.340000e-21 113.0
31 TraesCS2A01G264100 chr2D 80.328 122 18 4 424 541 418766360 418766479 3.240000e-13 87.9
32 TraesCS2A01G264100 chr2D 87.097 62 8 0 481 542 178617500 178617561 3.260000e-08 71.3
33 TraesCS2A01G264100 chr2D 86.441 59 8 0 2324 2382 298290238 298290296 1.520000e-06 65.8
34 TraesCS2A01G264100 chr2D 100.000 28 0 0 5231 5258 316122222 316122195 1.200000e-02 52.8
35 TraesCS2A01G264100 chr5A 93.317 823 43 3 5701 6511 666343584 666344406 0.000000e+00 1205.0
36 TraesCS2A01G264100 chr5A 92.727 165 11 1 4236 4399 141878705 141878869 3.040000e-58 237.0
37 TraesCS2A01G264100 chr5A 81.818 143 23 2 402 541 700311842 700311700 4.130000e-22 117.0
38 TraesCS2A01G264100 chr5A 80.451 133 20 5 412 541 613573481 613573610 5.380000e-16 97.1
39 TraesCS2A01G264100 chr5B 91.515 825 55 5 5701 6513 103331844 103332665 0.000000e+00 1122.0
40 TraesCS2A01G264100 chr5B 85.380 342 22 7 4061 4398 394973746 394973429 4.870000e-86 329.0
41 TraesCS2A01G264100 chr5B 92.857 84 3 3 3556 3637 462131189 462131271 1.150000e-22 119.0
42 TraesCS2A01G264100 chr5B 78.571 140 29 1 402 541 549671743 549671881 2.500000e-14 91.6
43 TraesCS2A01G264100 chr5B 90.000 60 5 1 2324 2382 462745552 462745493 7.000000e-10 76.8
44 TraesCS2A01G264100 chr5B 87.879 66 6 2 2324 2389 462745656 462745593 7.000000e-10 76.8
45 TraesCS2A01G264100 chr3B 89.841 817 69 5 5707 6513 814390471 814389659 0.000000e+00 1037.0
46 TraesCS2A01G264100 chr3B 87.638 817 89 4 5707 6513 672534248 672533434 0.000000e+00 939.0
47 TraesCS2A01G264100 chr3B 83.217 143 16 6 402 541 593937488 593937625 2.470000e-24 124.0
48 TraesCS2A01G264100 chr4A 92.493 706 50 2 5742 6446 28561421 28560718 0.000000e+00 1007.0
49 TraesCS2A01G264100 chr4A 86.246 349 45 3 6168 6513 691269586 691269238 6.170000e-100 375.0
50 TraesCS2A01G264100 chr4A 84.795 342 25 9 4061 4398 458238309 458238627 1.050000e-82 318.0
51 TraesCS2A01G264100 chr4A 78.723 141 24 5 401 541 183617236 183617370 8.990000e-14 89.8
52 TraesCS2A01G264100 chr4A 89.831 59 6 0 2324 2382 185435368 185435426 7.000000e-10 76.8
53 TraesCS2A01G264100 chr4D 90.182 713 68 2 5802 6513 478268564 478269275 0.000000e+00 928.0
54 TraesCS2A01G264100 chr4D 85.337 341 21 13 4061 4395 479956937 479957254 6.300000e-85 326.0
55 TraesCS2A01G264100 chr4D 80.714 140 27 0 402 541 425705159 425705020 6.900000e-20 110.0
56 TraesCS2A01G264100 chr4D 80.556 144 20 6 402 541 44636735 44636874 3.210000e-18 104.0
57 TraesCS2A01G264100 chr4D 92.000 50 4 0 485 534 82573614 82573663 3.260000e-08 71.3
58 TraesCS2A01G264100 chr4D 90.000 50 5 0 2332 2381 177475788 177475739 1.520000e-06 65.8
59 TraesCS2A01G264100 chr4B 88.359 713 72 4 5802 6513 604880930 604881632 0.000000e+00 846.0
60 TraesCS2A01G264100 chr4B 89.831 59 6 0 2324 2382 193676416 193676474 7.000000e-10 76.8
61 TraesCS2A01G264100 chr4B 86.567 67 7 2 2324 2390 659159244 659159180 9.060000e-09 73.1
62 TraesCS2A01G264100 chr4B 89.362 47 5 0 547 593 413876610 413876564 7.050000e-05 60.2
63 TraesCS2A01G264100 chr3A 89.869 533 47 3 5982 6513 453652744 453652218 0.000000e+00 678.0
64 TraesCS2A01G264100 chr3A 82.584 356 60 2 5843 6197 36947404 36947758 4.900000e-81 313.0
65 TraesCS2A01G264100 chr3A 89.516 248 16 2 5707 5945 453652991 453652745 8.200000e-79 305.0
66 TraesCS2A01G264100 chr3A 94.231 52 3 0 6027 6078 114542050 114541999 5.410000e-11 80.5
67 TraesCS2A01G264100 chr7D 86.765 476 50 7 6039 6513 156033196 156033659 9.680000e-143 518.0
68 TraesCS2A01G264100 chr7D 89.542 306 26 3 5741 6046 156031219 156031518 3.680000e-102 383.0
69 TraesCS2A01G264100 chr1A 87.135 342 23 10 4061 4398 292774086 292773762 1.030000e-97 368.0
70 TraesCS2A01G264100 chr1A 88.136 59 5 2 2332 2390 350014361 350014305 1.170000e-07 69.4
71 TraesCS2A01G264100 chr5D 84.884 344 23 10 4060 4398 256469525 256469844 2.930000e-83 320.0
72 TraesCS2A01G264100 chr5D 80.142 141 26 2 402 541 316112133 316111994 3.210000e-18 104.0
73 TraesCS2A01G264100 chr5D 83.529 85 14 0 457 541 264373835 264373919 5.410000e-11 80.5
74 TraesCS2A01G264100 chr5D 88.136 59 7 0 2324 2382 162425242 162425300 3.260000e-08 71.3
75 TraesCS2A01G264100 chr5D 89.362 47 5 0 2335 2381 336451977 336451931 7.050000e-05 60.2
76 TraesCS2A01G264100 chr7B 84.503 342 26 10 4061 4398 446166208 446166526 4.900000e-81 313.0
77 TraesCS2A01G264100 chr7B 82.114 369 33 21 4060 4398 511302076 511301711 1.070000e-72 285.0
78 TraesCS2A01G264100 chr1D 88.571 175 15 4 4061 4231 225405049 225405222 2.380000e-49 207.0
79 TraesCS2A01G264100 chr1D 81.690 142 21 4 403 541 483526073 483526212 5.340000e-21 113.0
80 TraesCS2A01G264100 chr1D 86.957 69 7 2 2324 2392 438324180 438324114 7.000000e-10 76.8
81 TraesCS2A01G264100 chr1D 90.741 54 5 0 2324 2377 211684874 211684927 9.060000e-09 73.1
82 TraesCS2A01G264100 chr1D 90.909 55 4 1 2324 2377 221932834 221932888 9.060000e-09 73.1
83 TraesCS2A01G264100 chr1D 86.567 67 7 2 2324 2390 277359787 277359723 9.060000e-09 73.1
84 TraesCS2A01G264100 chr7A 79.535 215 32 9 401 606 182020999 182020788 6.810000e-30 143.0
85 TraesCS2A01G264100 chrUn 91.860 86 6 1 3552 3637 110687494 110687410 1.150000e-22 119.0
86 TraesCS2A01G264100 chr6D 91.011 89 2 4 3555 3637 363881652 363881740 1.480000e-21 115.0
87 TraesCS2A01G264100 chr6B 90.110 91 3 2 3554 3638 713473818 713473728 5.340000e-21 113.0
88 TraesCS2A01G264100 chr6B 83.838 99 14 2 433 531 30554093 30554189 6.950000e-15 93.5
89 TraesCS2A01G264100 chr1B 88.421 95 10 1 3551 3645 584135346 584135439 5.340000e-21 113.0
90 TraesCS2A01G264100 chr1B 85.135 74 8 3 2324 2396 402109901 402109830 9.060000e-09 73.1
91 TraesCS2A01G264100 chr6A 82.203 118 20 1 424 541 32228154 32228038 4.160000e-17 100.0
92 TraesCS2A01G264100 chr6A 90.909 55 4 1 2324 2377 481235309 481235363 9.060000e-09 73.1
93 TraesCS2A01G264100 chr3D 81.905 105 15 3 437 541 108420024 108419924 1.160000e-12 86.1


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 TraesCS2A01G264100 chr2A 419026563 419033075 6512 False 2448.600000 12028 100.000000 1 6513 5 chr2A.!!$F3 6512
1 TraesCS2A01G264100 chr2B 384035100 384045366 10266 True 1224.833333 2689 92.105833 1 5690 6 chr2B.!!$R4 5689
2 TraesCS2A01G264100 chr2B 760109736 760110543 807 False 1109.000000 1109 91.615000 5713 6513 1 chr2B.!!$F2 800
3 TraesCS2A01G264100 chr2B 138534078 138534892 814 True 939.000000 939 87.653000 5707 6513 1 chr2B.!!$R2 806
4 TraesCS2A01G264100 chr2D 316121884 316127622 5738 True 1313.800000 2433 94.705167 1 5690 6 chr2D.!!$R4 5689
5 TraesCS2A01G264100 chr2D 82666431 82667255 824 True 1186.000000 1186 92.848000 5701 6513 1 chr2D.!!$R1 812
6 TraesCS2A01G264100 chr5A 666343584 666344406 822 False 1205.000000 1205 93.317000 5701 6511 1 chr5A.!!$F3 810
7 TraesCS2A01G264100 chr5B 103331844 103332665 821 False 1122.000000 1122 91.515000 5701 6513 1 chr5B.!!$F1 812
8 TraesCS2A01G264100 chr3B 814389659 814390471 812 True 1037.000000 1037 89.841000 5707 6513 1 chr3B.!!$R2 806
9 TraesCS2A01G264100 chr3B 672533434 672534248 814 True 939.000000 939 87.638000 5707 6513 1 chr3B.!!$R1 806
10 TraesCS2A01G264100 chr4A 28560718 28561421 703 True 1007.000000 1007 92.493000 5742 6446 1 chr4A.!!$R1 704
11 TraesCS2A01G264100 chr4D 478268564 478269275 711 False 928.000000 928 90.182000 5802 6513 1 chr4D.!!$F3 711
12 TraesCS2A01G264100 chr4B 604880930 604881632 702 False 846.000000 846 88.359000 5802 6513 1 chr4B.!!$F2 711
13 TraesCS2A01G264100 chr3A 453652218 453652991 773 True 491.500000 678 89.692500 5707 6513 2 chr3A.!!$R2 806
14 TraesCS2A01G264100 chr7D 156031219 156033659 2440 False 450.500000 518 88.153500 5741 6513 2 chr7D.!!$F1 772

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
513 1578 0.243907 CCTTCGAGAAACTGAGCCGA 59.756 55.000 0.00 0.00 0.00 5.54 F
963 2048 1.376037 CACCCGCTTCTTCCTCACC 60.376 63.158 0.00 0.00 0.00 4.02 F
2810 7638 0.461693 GTCCTCACATGCTCAGAGGC 60.462 60.000 15.49 9.49 46.71 4.70 F
4133 9199 0.097674 CGTTGGCTAGTGCATGAAGC 59.902 55.000 0.00 8.84 45.96 3.86 F
4245 9311 0.849094 ATAGGGGCCCTTTGTCCACA 60.849 55.000 33.98 10.72 34.61 4.17 F
5271 10348 0.033894 ATGGATGCATGGTGTGAGCA 60.034 50.000 2.46 0.00 43.14 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 6668 0.541998 TGCGAGGTGGGAAAGAGAGA 60.542 55.0 0.00 0.00 0.00 3.10 R
2814 7642 0.396556 ATCTTGGGCTCATGCATGCA 60.397 50.0 25.04 25.04 41.91 3.96 R
4226 9292 0.849094 TGTGGACAAAGGGCCCCTAT 60.849 55.0 21.43 1.24 31.13 2.57 R
5252 10329 0.033894 TGCTCACACCATGCATCCAT 60.034 50.0 0.00 0.00 0.00 3.41 R
5338 10415 0.038599 TGCTCACACCTGCATCCATT 59.961 50.0 0.00 0.00 33.94 3.16 R
6313 13087 0.179004 AGAAACCACGTGCCCAATGA 60.179 50.0 10.91 0.00 0.00 2.57 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.