Multiple sequence alignment - TraesCS2A01G207700

Loading Multiple Alignment...

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 TraesCS2A01G207700 chr2A 100.000 4422 0 0 1 4422 187940074 187944495 0.000000e+00 8167.0
1 TraesCS2A01G207700 chr2A 92.889 225 14 1 1977 2199 547265807 547265583 4.270000e-85 326.0
2 TraesCS2A01G207700 chr2A 92.889 225 14 1 1977 2199 642933963 642933739 4.270000e-85 326.0
3 TraesCS2A01G207700 chr2A 83.794 253 30 6 4078 4323 125129469 125129717 3.440000e-56 230.0
4 TraesCS2A01G207700 chr2A 88.525 122 14 0 4218 4339 12623264 12623385 9.910000e-32 148.0
5 TraesCS2A01G207700 chr5A 97.342 3800 66 5 23 3796 680337685 680341475 0.000000e+00 6425.0
6 TraesCS2A01G207700 chr5A 97.356 416 6 1 4012 4422 680341773 680342188 0.000000e+00 702.0
7 TraesCS2A01G207700 chr1A 98.222 2474 37 3 1 2474 535433353 535430887 0.000000e+00 4318.0
8 TraesCS2A01G207700 chr1A 98.443 1349 21 0 2467 3815 535430862 535429514 0.000000e+00 2375.0
9 TraesCS2A01G207700 chr1A 93.833 1054 38 15 932 1976 551511832 551512867 0.000000e+00 1561.0
10 TraesCS2A01G207700 chr1A 97.249 618 10 3 3811 4422 535429467 535428851 0.000000e+00 1040.0
11 TraesCS2A01G207700 chr1A 88.707 611 57 8 1594 2199 592318248 592317645 0.000000e+00 736.0
12 TraesCS2A01G207700 chr1A 94.149 376 17 5 569 940 551510917 551511291 6.420000e-158 568.0
13 TraesCS2A01G207700 chr1A 94.975 199 8 2 2002 2199 551512854 551513051 1.190000e-80 311.0
14 TraesCS2A01G207700 chr1B 87.566 1327 117 28 886 2186 687073847 687072543 0.000000e+00 1493.0
15 TraesCS2A01G207700 chr1B 90.000 700 43 12 2197 2870 58449893 58449195 0.000000e+00 880.0
16 TraesCS2A01G207700 chr1B 92.991 428 26 4 570 995 602227749 602228174 4.860000e-174 621.0
17 TraesCS2A01G207700 chr1B 95.111 225 10 1 553 777 650490007 650489784 1.960000e-93 353.0
18 TraesCS2A01G207700 chr1D 84.361 1298 141 34 900 2186 493937415 493936169 0.000000e+00 1216.0
19 TraesCS2A01G207700 chr1D 94.412 340 17 2 2572 2910 99655519 99655181 5.070000e-144 521.0
20 TraesCS2A01G207700 chr1D 94.030 335 18 2 2577 2910 465937980 465937647 1.420000e-139 507.0
21 TraesCS2A01G207700 chr1D 96.000 275 10 1 2906 3180 465937510 465937237 3.140000e-121 446.0
22 TraesCS2A01G207700 chr1D 95.238 273 13 0 120 392 423889617 423889345 2.440000e-117 433.0
23 TraesCS2A01G207700 chr1D 93.907 279 12 2 2906 3180 99655044 99654767 2.460000e-112 416.0
24 TraesCS2A01G207700 chr1D 93.496 123 6 2 1 121 4551862 4551740 9.770000e-42 182.0
25 TraesCS2A01G207700 chr1D 98.305 59 1 0 4364 4422 465937092 465937034 2.180000e-18 104.0
26 TraesCS2A01G207700 chr1D 96.610 59 2 0 4364 4422 99654622 99654564 1.010000e-16 99.0
27 TraesCS2A01G207700 chr1D 92.308 52 4 0 2148 2199 493936252 493936201 1.710000e-09 75.0
28 TraesCS2A01G207700 chrUn 94.177 395 20 2 2516 2910 41122129 41122520 2.280000e-167 599.0
29 TraesCS2A01G207700 chrUn 95.395 304 12 1 2906 3207 41122665 41122968 2.390000e-132 483.0
30 TraesCS2A01G207700 chrUn 94.958 238 9 3 2196 2432 41121687 41121922 1.940000e-98 370.0
31 TraesCS2A01G207700 chrUn 97.222 72 2 0 3209 3280 41122946 41123017 6.010000e-24 122.0
32 TraesCS2A01G207700 chrUn 92.424 66 3 1 4356 4419 28206678 28206743 4.710000e-15 93.5
33 TraesCS2A01G207700 chr7D 94.072 388 21 2 2524 2910 531995020 531995406 4.930000e-164 588.0
34 TraesCS2A01G207700 chr7D 95.636 275 11 1 2906 3180 531995543 531995816 1.460000e-119 440.0
35 TraesCS2A01G207700 chr7D 88.889 342 18 10 2197 2523 531994582 531994918 1.920000e-108 403.0
36 TraesCS2A01G207700 chr7D 85.000 220 22 4 4114 4326 47263099 47262884 3.460000e-51 213.0
37 TraesCS2A01G207700 chr7D 98.214 56 1 0 4364 4419 531995961 531996016 1.010000e-16 99.0
38 TraesCS2A01G207700 chr4D 95.273 275 13 0 120 394 28441361 28441087 1.890000e-118 436.0
39 TraesCS2A01G207700 chr4D 88.679 53 3 2 4372 4422 213723031 213722980 1.330000e-05 62.1
40 TraesCS2A01G207700 chr3B 95.273 275 13 0 120 394 792140268 792139994 1.890000e-118 436.0
41 TraesCS2A01G207700 chr3B 92.359 301 21 1 2197 2495 31459167 31458867 1.140000e-115 427.0
42 TraesCS2A01G207700 chr3B 94.545 275 15 0 120 394 792102834 792102560 4.090000e-115 425.0
43 TraesCS2A01G207700 chr3B 93.182 264 15 2 2516 2779 31458713 31458453 6.940000e-103 385.0
44 TraesCS2A01G207700 chr3B 90.816 196 13 5 4040 4234 813797349 813797158 1.580000e-64 257.0
45 TraesCS2A01G207700 chr3B 97.260 146 4 0 395 540 351293196 351293341 9.500000e-62 248.0
46 TraesCS2A01G207700 chr3B 96.575 146 5 0 395 540 792177996 792177851 4.420000e-60 243.0
47 TraesCS2A01G207700 chr3B 95.890 146 6 0 395 540 792139962 792139817 2.060000e-58 237.0
48 TraesCS2A01G207700 chr3B 95.205 146 7 0 395 540 792102528 792102383 9.570000e-57 231.0
49 TraesCS2A01G207700 chr3B 88.525 122 8 6 4040 4160 10681489 10681605 4.610000e-30 143.0
50 TraesCS2A01G207700 chr3B 93.443 61 4 0 3150 3210 751095574 751095514 1.690000e-14 91.6
51 TraesCS2A01G207700 chr2B 94.964 278 14 0 117 394 741450635 741450912 1.890000e-118 436.0
52 TraesCS2A01G207700 chr2B 93.772 289 13 2 2197 2483 429138409 429138694 3.160000e-116 429.0
53 TraesCS2A01G207700 chr2B 87.640 356 18 6 2516 2870 429138864 429139194 1.490000e-104 390.0
54 TraesCS2A01G207700 chr2B 95.909 220 9 0 558 777 190231373 190231154 1.510000e-94 357.0
55 TraesCS2A01G207700 chr2B 82.310 277 39 5 4053 4323 174344207 174344479 9.570000e-57 231.0
56 TraesCS2A01G207700 chr2B 92.063 126 5 2 1 121 381372906 381373031 5.880000e-39 172.0
57 TraesCS2A01G207700 chr2B 88.889 135 8 7 4040 4173 249193436 249193564 4.580000e-35 159.0
58 TraesCS2A01G207700 chr5D 94.604 278 14 1 117 394 469798072 469798348 3.160000e-116 429.0
59 TraesCS2A01G207700 chr5D 90.260 154 7 1 395 540 370304095 370303942 1.250000e-45 195.0
60 TraesCS2A01G207700 chr3D 94.545 275 10 1 120 394 19412982 19412713 1.900000e-113 420.0
61 TraesCS2A01G207700 chr3D 91.503 153 6 1 395 540 19412681 19412529 2.090000e-48 204.0
62 TraesCS2A01G207700 chr3D 92.500 80 6 0 2906 2985 545247738 545247817 1.010000e-21 115.0
63 TraesCS2A01G207700 chr6B 96.774 217 7 0 558 774 422698728 422698944 3.250000e-96 363.0
64 TraesCS2A01G207700 chr6B 96.532 173 5 1 569 741 332443851 332443680 7.240000e-73 285.0
65 TraesCS2A01G207700 chr6B 96.341 164 5 1 2208 2370 101217626 101217789 7.290000e-68 268.0
66 TraesCS2A01G207700 chr6B 95.041 121 5 1 1 121 710292132 710292013 5.840000e-44 189.0
67 TraesCS2A01G207700 chr5B 95.954 173 6 1 569 741 497373831 497373660 3.370000e-71 279.0
68 TraesCS2A01G207700 chr5B 88.514 148 12 5 1 145 588640763 588640618 1.630000e-39 174.0
69 TraesCS2A01G207700 chr5B 97.222 72 2 0 3209 3280 533439398 533439327 6.010000e-24 122.0
70 TraesCS2A01G207700 chr4B 94.220 173 9 1 2197 2369 605511903 605512074 3.390000e-66 263.0
71 TraesCS2A01G207700 chr2D 82.818 291 38 10 4040 4323 120972169 120972454 2.640000e-62 250.0
72 TraesCS2A01G207700 chr7A 90.789 152 8 1 395 540 619255243 619255092 9.700000e-47 198.0
73 TraesCS2A01G207700 chr7A 92.562 121 9 0 1 121 686264760 686264880 1.630000e-39 174.0
74 TraesCS2A01G207700 chr7A 91.200 125 6 3 1 121 34221184 34221307 9.840000e-37 165.0
75 TraesCS2A01G207700 chr3A 92.742 124 6 1 1 121 11848326 11848449 4.550000e-40 176.0
76 TraesCS2A01G207700 chr7B 90.517 116 9 1 4213 4326 713856232 713856117 7.660000e-33 152.0
77 TraesCS2A01G207700 chr6D 90.351 114 11 0 4213 4326 69409779 69409666 2.760000e-32 150.0


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 TraesCS2A01G207700 chr2A 187940074 187944495 4421 False 8167.000000 8167 100.000000 1 4422 1 chr2A.!!$F3 4421
1 TraesCS2A01G207700 chr5A 680337685 680342188 4503 False 3563.500000 6425 97.349000 23 4422 2 chr5A.!!$F1 4399
2 TraesCS2A01G207700 chr1A 535428851 535433353 4502 True 2577.666667 4318 97.971333 1 4422 3 chr1A.!!$R2 4421
3 TraesCS2A01G207700 chr1A 551510917 551513051 2134 False 813.333333 1561 94.319000 569 2199 3 chr1A.!!$F1 1630
4 TraesCS2A01G207700 chr1A 592317645 592318248 603 True 736.000000 736 88.707000 1594 2199 1 chr1A.!!$R1 605
5 TraesCS2A01G207700 chr1B 687072543 687073847 1304 True 1493.000000 1493 87.566000 886 2186 1 chr1B.!!$R3 1300
6 TraesCS2A01G207700 chr1B 58449195 58449893 698 True 880.000000 880 90.000000 2197 2870 1 chr1B.!!$R1 673
7 TraesCS2A01G207700 chr1D 493936169 493937415 1246 True 645.500000 1216 88.334500 900 2199 2 chr1D.!!$R5 1299
8 TraesCS2A01G207700 chr1D 465937034 465937980 946 True 352.333333 507 96.111667 2577 4422 3 chr1D.!!$R4 1845
9 TraesCS2A01G207700 chr1D 99654564 99655519 955 True 345.333333 521 94.976333 2572 4422 3 chr1D.!!$R3 1850
10 TraesCS2A01G207700 chrUn 41121687 41123017 1330 False 393.500000 599 95.438000 2196 3280 4 chrUn.!!$F2 1084
11 TraesCS2A01G207700 chr7D 531994582 531996016 1434 False 382.500000 588 94.202750 2197 4419 4 chr7D.!!$F1 2222
12 TraesCS2A01G207700 chr3B 31458453 31459167 714 True 406.000000 427 92.770500 2197 2779 2 chr3B.!!$R4 582
13 TraesCS2A01G207700 chr2B 429138409 429139194 785 False 409.500000 429 90.706000 2197 2870 2 chr2B.!!$F5 673

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
268 269 0.179051 GCTTATGCTCTGCCTGCTCT 60.179 55.000 0.00 0.00 36.03 4.09 F
1348 1917 3.657398 TCCAGCAACAAGGATGATGAT 57.343 42.857 0.00 0.00 36.32 2.45 F
1751 2342 2.671130 ACCAGTGCACTTTTGTTTGG 57.329 45.000 18.94 16.78 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 2080 0.039618 ACCCTTTCATCGGCATTGGT 59.960 50.000 0.00 0.0 0.0 3.67 R
3141 4203 7.362056 GCATCTAATTCCTCTTGTTTAACTGCA 60.362 37.037 0.00 0.0 0.0 4.41 R
3482 4544 3.501568 GGTTACCATTCTTTTCCCAGGGT 60.502 47.826 5.01 0.0 0.0 4.34 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
268 269 0.179051 GCTTATGCTCTGCCTGCTCT 60.179 55.000 0.00 0.00 36.03 4.09
347 348 4.410400 CCCCTCCCCTCACGTTGC 62.410 72.222 0.00 0.00 0.00 4.17
519 520 9.941325 CACATCTATCTTATCTAGCCAATTCTT 57.059 33.333 0.00 0.00 0.00 2.52
720 721 4.573201 GTCGGTTAATGGCTTATTGCACTA 59.427 41.667 0.00 0.00 45.15 2.74
730 731 8.839310 ATGGCTTATTGCACTAGTCTTAATAG 57.161 34.615 0.00 0.00 45.15 1.73
757 758 6.265196 AGAATTTCAGCATTGTAAGAACACCA 59.735 34.615 0.00 0.00 34.61 4.17
930 1484 7.423199 TCGCTATCGATATTGTCTTACACTTT 58.577 34.615 5.40 0.00 40.21 2.66
965 1519 8.673711 ACGCTACATTGTATCATTGTTAAACAT 58.326 29.630 0.00 0.00 31.72 2.71
1348 1917 3.657398 TCCAGCAACAAGGATGATGAT 57.343 42.857 0.00 0.00 36.32 2.45
1377 1962 8.885722 GGTTACAATGTTTTCTAACCATATCGA 58.114 33.333 9.45 0.00 38.59 3.59
1491 2080 8.867112 AGTAGAATCATTACGAAGCGAAATTA 57.133 30.769 0.00 0.00 0.00 1.40
1494 2083 6.537301 AGAATCATTACGAAGCGAAATTACCA 59.463 34.615 0.00 0.00 0.00 3.25
1751 2342 2.671130 ACCAGTGCACTTTTGTTTGG 57.329 45.000 18.94 16.78 0.00 3.28
2146 2740 3.761897 CCACCCTGAACCTTAATCACAA 58.238 45.455 0.00 0.00 0.00 3.33
2277 2871 2.736721 CGAGGCGTGAAAAAGAAGATGA 59.263 45.455 0.00 0.00 0.00 2.92
2527 3294 8.918202 TTAGGTACTCACAAACATGAAAGAAT 57.082 30.769 0.00 0.00 41.75 2.40
2566 3333 3.136763 CCTGCTCGTCATGAAGCATATT 58.863 45.455 19.72 0.00 36.65 1.28
3110 4168 7.872483 AGCTAAAACCACCAACAATTAAATCAG 59.128 33.333 0.00 0.00 0.00 2.90
3366 4428 6.040247 CGATGAGTTTAGTGGCTATTGTGTA 58.960 40.000 0.00 0.00 0.00 2.90
3482 4544 0.539438 ATGGCGGAGACCTTTGCAAA 60.539 50.000 12.14 12.14 25.51 3.68
3594 4656 4.551702 TCTCACCTGCAGTGCTTTAATA 57.448 40.909 17.60 0.00 46.81 0.98
3600 4662 7.090173 TCACCTGCAGTGCTTTAATAAATTTC 58.910 34.615 17.60 0.00 46.81 2.17
3685 4747 6.943146 TGTTGGCCACTTAAAAGTATACATGA 59.057 34.615 3.88 0.00 37.08 3.07
3689 4751 7.831690 TGGCCACTTAAAAGTATACATGAATCA 59.168 33.333 0.00 0.00 37.08 2.57
3801 4863 5.644644 GCATACCATCTAAAATATGCAGGC 58.355 41.667 9.58 0.00 45.98 4.85
3831 4944 6.014925 ACACAAAATCAATACAGGTAAACCCC 60.015 38.462 0.00 0.00 36.42 4.95
3855 4968 7.276658 CCCACTCAGATATAATATTTCTCACGC 59.723 40.741 0.00 0.00 0.00 5.34
3894 5007 2.297033 TCGGTAGTAGAAAAACAGCGGT 59.703 45.455 0.00 0.00 0.00 5.68
4103 5252 5.163077 TGTCCTGGTTGTTATTGGGAACTTA 60.163 40.000 0.00 0.00 0.00 2.24
4237 5386 5.163195 ACCAAAGAAGAGAAGAAGGCAGTTA 60.163 40.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
305 306 1.289244 ATTAGGGTTGGAGCAGGGGG 61.289 60.000 0.00 0.0 0.00 5.40
306 307 0.183731 GATTAGGGTTGGAGCAGGGG 59.816 60.000 0.00 0.0 0.00 4.79
347 348 1.370900 GCGTGACCAAAAGCAGCAG 60.371 57.895 0.00 0.0 0.00 4.24
403 404 3.321648 TGCCTCGTCCACCTGCAT 61.322 61.111 0.00 0.0 0.00 3.96
519 520 7.933215 GGTTTTTGGAACCTAGCTAAATCTA 57.067 36.000 0.00 0.0 37.34 1.98
558 559 4.191544 GAGCACATTAGTTGGCAGTGATA 58.808 43.478 6.50 0.0 32.14 2.15
559 560 3.012518 GAGCACATTAGTTGGCAGTGAT 58.987 45.455 6.50 0.0 32.14 3.06
730 731 7.750903 GGTGTTCTTACAATGCTGAAATTCTAC 59.249 37.037 0.00 0.0 35.69 2.59
965 1519 6.763135 CAGGTGCTAGAAGAAATTGCATAGTA 59.237 38.462 0.00 0.0 36.04 1.82
1370 1939 5.410924 TGACAGAAACAGAGGTTCGATATG 58.589 41.667 0.00 0.0 35.82 1.78
1377 1962 5.934625 GTGATACATGACAGAAACAGAGGTT 59.065 40.000 0.00 0.0 39.43 3.50
1491 2080 0.039618 ACCCTTTCATCGGCATTGGT 59.960 50.000 0.00 0.0 0.00 3.67
1494 2083 1.463674 GACACCCTTTCATCGGCATT 58.536 50.000 0.00 0.0 0.00 3.56
1751 2342 0.249868 GAAGCTGTTTTGGGGGCAAC 60.250 55.000 0.00 0.0 0.00 4.17
2128 2722 5.711976 AGTGAATTGTGATTAAGGTTCAGGG 59.288 40.000 0.00 0.0 0.00 4.45
2129 2723 6.824305 AGTGAATTGTGATTAAGGTTCAGG 57.176 37.500 0.00 0.0 0.00 3.86
2146 2740 5.360714 ACAAAGAACACATCACCAAGTGAAT 59.639 36.000 0.91 0.0 45.96 2.57
2277 2871 7.425224 AAACAGCTAGACTATCAACCTATGT 57.575 36.000 0.00 0.0 0.00 2.29
2566 3333 9.739276 CCCTTCTATTTATTAATCCACATGCTA 57.261 33.333 0.00 0.0 0.00 3.49
3141 4203 7.362056 GCATCTAATTCCTCTTGTTTAACTGCA 60.362 37.037 0.00 0.0 0.00 4.41
3207 4269 8.428536 GCATCAACTTGAGTTATATAGTTAGCG 58.571 37.037 0.00 0.0 36.32 4.26
3482 4544 3.501568 GGTTACCATTCTTTTCCCAGGGT 60.502 47.826 5.01 0.0 0.00 4.34
3831 4944 7.462069 GCGCGTGAGAAATATTATATCTGAGTG 60.462 40.741 8.43 0.0 0.00 3.51
3855 4968 2.348666 CCGAGGTAAAAGAAGTGATGCG 59.651 50.000 0.00 0.0 0.00 4.73
3894 5007 6.854496 AAATAAGTGAGAGCGTTGTGTTTA 57.146 33.333 0.00 0.0 0.00 2.01
4328 5477 7.716998 CACCAGCAAGATAACTAATACAGGAAT 59.283 37.037 0.00 0.0 0.00 3.01


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

AutoCloner maintained by Alex Coulton.