Multiple sequence alignment - TraesCS7A01G369400

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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 TraesCS7A01G369400 chr7A 100.000 7519 0 0 1 7519 542967303 542974821 0.000000e+00 13886.0
1 TraesCS7A01G369400 chr7A 86.196 2137 203 61 4257 6340 542817332 542819429 0.000000e+00 2228.0
2 TraesCS7A01G369400 chr7A 86.408 515 47 15 40 547 542938500 542938998 6.640000e-150 542.0
3 TraesCS7A01G369400 chr7A 85.656 244 11 7 989 1229 542812007 542812229 1.260000e-57 235.0
4 TraesCS7A01G369400 chr7A 95.276 127 5 1 791 916 542939024 542939150 4.600000e-47 200.0
5 TraesCS7A01G369400 chr7A 77.903 267 49 8 6908 7170 531106200 531105940 2.810000e-34 158.0
6 TraesCS7A01G369400 chr7A 77.387 199 34 10 6908 7100 530938801 530938994 2.870000e-19 108.0
7 TraesCS7A01G369400 chr7A 95.652 46 1 1 6581 6626 33027378 33027422 1.050000e-08 73.1
8 TraesCS7A01G369400 chr7B 84.350 2147 237 62 4257 6363 479646714 479644627 0.000000e+00 2012.0
9 TraesCS7A01G369400 chr7B 88.242 859 66 18 4292 5118 479621235 479620380 0.000000e+00 994.0
10 TraesCS7A01G369400 chr7B 82.831 862 88 34 5186 6041 479620398 479619591 0.000000e+00 717.0
11 TraesCS7A01G369400 chr7B 94.595 333 14 4 6042 6372 479619561 479619231 5.200000e-141 512.0
12 TraesCS7A01G369400 chr7B 82.450 547 42 33 815 1345 479623550 479623042 5.390000e-116 429.0
13 TraesCS7A01G369400 chr7B 86.275 255 14 6 988 1236 479652911 479652672 2.690000e-64 257.0
14 TraesCS7A01G369400 chr7B 80.682 176 14 5 1444 1599 479623027 479622852 1.330000e-22 119.0
15 TraesCS7A01G369400 chr7B 81.560 141 9 8 2436 2576 479621893 479621770 4.800000e-17 100.0
16 TraesCS7A01G369400 chr7B 95.122 41 2 0 2527 2567 479651574 479651534 1.750000e-06 65.8
17 TraesCS7A01G369400 chr7B 96.970 33 1 0 6442 6474 479619173 479619141 1.000000e-03 56.5
18 TraesCS7A01G369400 chr7D 84.141 2188 227 66 4257 6370 457597535 457595394 0.000000e+00 2008.0
19 TraesCS7A01G369400 chr7D 89.005 955 70 18 5426 6372 457226453 457225526 0.000000e+00 1149.0
20 TraesCS7A01G369400 chr7D 89.057 859 67 14 4285 5118 457227712 457226856 0.000000e+00 1040.0
21 TraesCS7A01G369400 chr7D 84.615 559 41 23 815 1345 457230811 457230270 1.450000e-141 514.0
22 TraesCS7A01G369400 chr7D 85.459 392 53 4 1 389 264477651 264478041 9.080000e-109 405.0
23 TraesCS7A01G369400 chr7D 90.455 220 19 2 3583 3800 63379823 63380042 9.550000e-74 289.0
24 TraesCS7A01G369400 chr7D 87.712 236 26 2 5186 5421 457226874 457226642 9.610000e-69 272.0
25 TraesCS7A01G369400 chr7D 86.747 249 12 8 988 1230 457603097 457602864 2.690000e-64 257.0
26 TraesCS7A01G369400 chr7D 83.684 190 15 9 2389 2576 457229315 457229140 1.680000e-36 165.0
27 TraesCS7A01G369400 chr7D 93.182 44 3 0 492 535 127223071 127223028 1.750000e-06 65.8
28 TraesCS7A01G369400 chr7D 95.122 41 1 1 2527 2566 457601678 457601638 6.300000e-06 63.9
29 TraesCS7A01G369400 chr6B 86.364 396 50 4 4 396 163947260 163946866 5.390000e-116 429.0
30 TraesCS7A01G369400 chr3B 85.784 408 51 7 1 403 112905316 112905721 6.970000e-115 425.0
31 TraesCS7A01G369400 chr3B 85.644 404 53 5 4 404 422314822 422314421 3.240000e-113 420.0
32 TraesCS7A01G369400 chr3B 86.478 318 31 7 7190 7503 103727440 103727749 9.350000e-89 339.0
33 TraesCS7A01G369400 chr3B 81.776 214 37 2 4686 4898 693075504 693075716 2.160000e-40 178.0
34 TraesCS7A01G369400 chr5D 84.577 402 58 4 1 399 464405379 464405779 5.470000e-106 396.0
35 TraesCS7A01G369400 chr5D 87.850 321 26 5 7187 7503 71910331 71910020 1.540000e-96 364.0
36 TraesCS7A01G369400 chr5D 90.625 256 16 6 7267 7518 429964134 429964385 4.350000e-87 333.0
37 TraesCS7A01G369400 chr5D 81.481 162 19 10 438 594 539985542 539985697 1.020000e-23 122.0
38 TraesCS7A01G369400 chr5D 87.143 70 5 3 7078 7143 30610455 30610386 8.090000e-10 76.8
39 TraesCS7A01G369400 chr1A 84.521 407 55 7 4 404 562118620 562118216 5.470000e-106 396.0
40 TraesCS7A01G369400 chr1A 95.431 197 9 0 538 734 14796905 14796709 1.570000e-81 315.0
41 TraesCS7A01G369400 chr1A 82.315 311 37 10 437 740 41071980 41071681 3.480000e-63 254.0
42 TraesCS7A01G369400 chr3A 84.577 402 54 8 4 399 472765329 472764930 7.070000e-105 392.0
43 TraesCS7A01G369400 chr3A 94.792 192 10 0 543 734 401557373 401557564 4.410000e-77 300.0
44 TraesCS7A01G369400 chr3A 93.434 198 11 2 539 735 425145325 425145521 7.380000e-75 292.0
45 TraesCS7A01G369400 chr3A 80.128 312 41 14 7187 7486 575334902 575335204 5.910000e-51 213.0
46 TraesCS7A01G369400 chr3A 80.800 250 42 6 4686 4932 659527989 659528235 2.770000e-44 191.0
47 TraesCS7A01G369400 chr3A 93.548 62 4 0 3819 3880 641172693 641172754 8.030000e-15 93.5
48 TraesCS7A01G369400 chr3A 83.673 98 9 5 7078 7170 724135434 724135529 1.340000e-12 86.1
49 TraesCS7A01G369400 chr3A 95.833 48 1 1 6581 6628 10266662 10266708 8.090000e-10 76.8
50 TraesCS7A01G369400 chr1D 84.236 406 58 6 4 406 361102167 361101765 2.540000e-104 390.0
51 TraesCS7A01G369400 chr1D 88.040 301 24 3 7209 7505 463164005 463163713 5.580000e-91 346.0
52 TraesCS7A01G369400 chr1D 93.607 219 11 3 3584 3800 17161485 17161268 2.620000e-84 324.0
53 TraesCS7A01G369400 chr1D 91.031 223 17 3 3580 3800 401204569 401204790 1.590000e-76 298.0
54 TraesCS7A01G369400 chr1D 90.323 62 6 0 3819 3880 17161284 17161223 1.740000e-11 82.4
55 TraesCS7A01G369400 chr2D 84.275 407 54 8 4 403 468165893 468165490 9.150000e-104 388.0
56 TraesCS7A01G369400 chr2D 90.179 224 20 2 3579 3800 643797411 643797634 2.650000e-74 291.0
57 TraesCS7A01G369400 chr4B 87.539 321 30 6 7187 7503 627441926 627442240 5.550000e-96 363.0
58 TraesCS7A01G369400 chr4B 86.646 322 30 7 7187 7503 597303864 597303551 2.010000e-90 344.0
59 TraesCS7A01G369400 chr4B 84.472 322 37 9 7187 7503 285531580 285531893 9.480000e-79 305.0
60 TraesCS7A01G369400 chr4B 83.200 125 18 3 423 547 427278682 427278561 2.220000e-20 111.0
61 TraesCS7A01G369400 chr5A 86.350 337 28 10 7187 7518 679127374 679127051 1.200000e-92 351.0
62 TraesCS7A01G369400 chr5A 96.277 188 7 0 545 732 475465608 475465421 7.330000e-80 309.0
63 TraesCS7A01G369400 chr5A 96.196 184 6 1 544 727 569174134 569174316 4.410000e-77 300.0
64 TraesCS7A01G369400 chr5A 92.929 198 13 1 538 734 244431527 244431724 3.430000e-73 287.0
65 TraesCS7A01G369400 chr5A 92.537 201 14 1 536 735 643571220 643571020 3.430000e-73 287.0
66 TraesCS7A01G369400 chr5A 93.651 63 4 0 3819 3881 632556675 632556737 2.230000e-15 95.3
67 TraesCS7A01G369400 chr5A 97.674 43 0 1 6584 6626 694522261 694522220 1.050000e-08 73.1
68 TraesCS7A01G369400 chr5A 95.238 42 1 1 6584 6625 694543992 694543952 1.750000e-06 65.8
69 TraesCS7A01G369400 chr4A 85.799 338 29 8 7189 7518 632977393 632977719 2.600000e-89 340.0
70 TraesCS7A01G369400 chr4A 90.909 55 5 0 7176 7230 208256433 208256379 2.910000e-09 75.0
71 TraesCS7A01G369400 chr6D 85.714 322 34 6 7187 7503 440650642 440650956 5.620000e-86 329.0
72 TraesCS7A01G369400 chr6A 91.597 238 13 4 7272 7503 604838846 604839082 9.410000e-84 322.0
73 TraesCS7A01G369400 chr6A 96.216 185 6 1 543 727 234189571 234189754 1.230000e-77 302.0
74 TraesCS7A01G369400 chr6A 91.935 62 3 2 3819 3880 601962579 601962520 1.340000e-12 86.1
75 TraesCS7A01G369400 chr3D 93.659 205 13 0 3593 3797 603709272 603709068 2.640000e-79 307.0
76 TraesCS7A01G369400 chr3D 80.800 250 42 6 4686 4932 525334682 525334928 2.770000e-44 191.0
77 TraesCS7A01G369400 chr1B 91.818 220 15 3 3574 3790 190292825 190293044 3.410000e-78 303.0
78 TraesCS7A01G369400 chr1B 97.727 44 0 1 6584 6627 567366985 567366943 2.910000e-09 75.0
79 TraesCS7A01G369400 chr2A 93.069 202 11 3 538 738 749623834 749623635 7.380000e-75 292.0
80 TraesCS7A01G369400 chr2A 90.411 219 19 2 3584 3800 575349283 575349065 3.430000e-73 287.0
81 TraesCS7A01G369400 chr2A 84.507 142 11 7 7176 7315 656245735 656245867 6.120000e-26 130.0
82 TraesCS7A01G369400 chr2A 100.000 41 0 0 6581 6621 166057621 166057581 8.090000e-10 76.8
83 TraesCS7A01G369400 chrUn 89.427 227 21 3 3576 3800 310932870 310933095 4.440000e-72 283.0
84 TraesCS7A01G369400 chrUn 89.427 227 21 3 3576 3800 320954078 320953853 4.440000e-72 283.0
85 TraesCS7A01G369400 chrUn 95.455 44 1 1 6584 6627 87948394 87948352 1.350000e-07 69.4
86 TraesCS7A01G369400 chr5B 95.652 46 1 1 6581 6626 319327202 319327246 1.050000e-08 73.1
87 TraesCS7A01G369400 chr5B 87.273 55 6 1 492 546 636899190 636899243 2.270000e-05 62.1
88 TraesCS7A01G369400 chr5B 100.000 28 0 0 6584 6611 441075464 441075437 1.400000e-02 52.8


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 TraesCS7A01G369400 chr7A 542967303 542974821 7518 False 13886.000000 13886 100.000000 1 7519 1 chr7A.!!$F5 7518
1 TraesCS7A01G369400 chr7A 542817332 542819429 2097 False 2228.000000 2228 86.196000 4257 6340 1 chr7A.!!$F4 2083
2 TraesCS7A01G369400 chr7A 542938500 542939150 650 False 371.000000 542 90.842000 40 916 2 chr7A.!!$F6 876
3 TraesCS7A01G369400 chr7B 479644627 479646714 2087 True 2012.000000 2012 84.350000 4257 6363 1 chr7B.!!$R1 2106
4 TraesCS7A01G369400 chr7B 479619141 479623550 4409 True 418.214286 994 86.761429 815 6474 7 chr7B.!!$R2 5659
5 TraesCS7A01G369400 chr7D 457595394 457597535 2141 True 2008.000000 2008 84.141000 4257 6370 1 chr7D.!!$R2 2113
6 TraesCS7A01G369400 chr7D 457225526 457230811 5285 True 628.000000 1149 86.814600 815 6372 5 chr7D.!!$R3 5557


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
254 256 0.104934 AGTGGAGGTGTCTCTTGGGT 60.105 55.0 0.00 0.00 39.86 4.51 F
1424 1460 0.099436 GGCGCAATCTACAAGCCAAG 59.901 55.0 10.83 0.00 46.48 3.61 F
2588 3090 0.035739 TGCCGGTAAAGTTCCCAGAC 59.964 55.0 1.90 0.00 0.00 3.51 F
2998 3500 0.028770 TTTCGTGAGCTTTGCAACGG 59.971 50.0 0.00 0.00 39.87 4.44 F
3553 4055 0.035439 CTAAACCACAGCCGGGTCAT 60.035 55.0 1.27 0.00 37.77 3.06 F
3554 4056 0.035820 TAAACCACAGCCGGGTCATC 60.036 55.0 1.27 0.00 37.77 2.92 F
3931 4433 0.036010 AACTCGACCAATGGCTGAGG 60.036 55.0 20.73 7.45 0.00 3.86 F
4309 6034 0.109781 GCACGGCTGTTATGTTGGTG 60.110 55.0 0.00 0.00 0.00 4.17 F
4967 6726 0.171679 ACACGTGAGACACAACGTGA 59.828 50.0 28.56 0.00 46.20 4.35 F
5539 7504 0.321653 AACGCATGGAGAGTTGGGTC 60.322 55.0 0.00 0.00 38.89 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1762 0.037697 TACTCACGTGGATTGCGCTT 60.038 50.0 17.00 0.0 0.00 4.68 R
2979 3481 0.028770 CCGTTGCAAAGCTCACGAAA 59.971 50.0 0.00 0.0 37.86 3.46 R
3534 4036 0.035439 ATGACCCGGCTGTGGTTTAG 60.035 55.0 0.00 0.0 35.85 1.85 R
3912 4414 0.036010 CCTCAGCCATTGGTCGAGTT 60.036 55.0 17.17 0.0 0.00 3.01 R
5173 6954 0.107410 AACTCACCTGCACGGACAAA 60.107 50.0 8.91 0.0 36.31 2.83 R
5182 6963 0.321653 ATCCCGTGAAACTCACCTGC 60.322 55.0 1.34 0.0 44.20 4.85 R
5600 7565 0.248458 CGCACAAACAACAGTGGGTC 60.248 55.0 0.00 0.0 41.89 4.46 R
5784 7771 0.311165 CCGTGGGCTCGATGTAGTAG 59.689 60.0 4.48 0.0 0.00 2.57 R
6405 8446 0.036952 TTCTCTTGCTGCTTCCCTCG 60.037 55.0 0.00 0.0 0.00 4.63 R
7254 9304 0.033208 CCCCACATGGCCACATACTT 60.033 55.0 8.16 0.0 34.99 2.24 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)



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AutoCloner maintained by Alex Coulton.