Multiple sequence alignment - TraesCS3B01G156200

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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 TraesCS3B01G156200 chr3B 100.000 5351 0 0 1 5351 148661750 148656400 0.000000e+00 9882.0
1 TraesCS3B01G156200 chr3B 99.113 3833 27 7 1 3831 148548011 148544184 0.000000e+00 6883.0
2 TraesCS3B01G156200 chr3B 99.113 3833 27 7 1 3831 148584460 148580633 0.000000e+00 6883.0
3 TraesCS3B01G156200 chr3B 99.113 3833 27 7 1 3831 148625797 148621970 0.000000e+00 6883.0
4 TraesCS3B01G156200 chr3B 99.145 1520 12 1 3833 5351 148543747 148542228 0.000000e+00 2734.0
5 TraesCS3B01G156200 chr3B 98.443 578 8 1 4775 5351 148580134 148579557 0.000000e+00 1016.0
6 TraesCS3B01G156200 chr3B 98.443 578 8 1 4775 5351 148621421 148620844 0.000000e+00 1016.0
7 TraesCS3B01G156200 chr3B 96.804 219 7 0 158 376 148682019 148681801 3.050000e-97 366.0
8 TraesCS3B01G156200 chr3B 95.305 213 9 1 158 370 341400434 341400223 2.390000e-88 337.0
9 TraesCS3B01G156200 chr3B 94.521 219 10 2 158 376 341415436 341415220 2.390000e-88 337.0
10 TraesCS3B01G156200 chr3D 95.340 3326 137 12 1457 4771 98149897 98146579 0.000000e+00 5267.0
11 TraesCS3B01G156200 chr3D 89.915 823 52 13 648 1465 98150718 98149922 0.000000e+00 1031.0
12 TraesCS3B01G156200 chr3D 85.517 580 52 11 4801 5351 98146044 98145468 1.290000e-160 577.0
13 TraesCS3B01G156200 chr3D 94.346 283 13 3 371 652 98151689 98151409 1.060000e-116 431.0
14 TraesCS3B01G156200 chr3D 83.654 104 16 1 4834 4936 191861051 191861154 4.410000e-16 97.1
15 TraesCS3B01G156200 chr3A 85.595 2749 262 64 789 3496 115843093 115840438 0.000000e+00 2760.0
16 TraesCS3B01G156200 chr3A 90.754 1644 117 17 789 2410 115393481 115391851 0.000000e+00 2161.0
17 TraesCS3B01G156200 chr3A 90.450 1644 122 17 789 2410 115614943 115613313 0.000000e+00 2134.0
18 TraesCS3B01G156200 chr3A 82.713 1799 253 33 2801 4559 116075556 116073776 0.000000e+00 1546.0
19 TraesCS3B01G156200 chr3A 89.478 1188 90 17 792 1957 115166989 115165815 0.000000e+00 1469.0
20 TraesCS3B01G156200 chr3A 86.076 1185 149 10 3519 4700 115390769 115389598 0.000000e+00 1260.0
21 TraesCS3B01G156200 chr3A 86.064 1184 151 8 3519 4700 115840381 115839210 0.000000e+00 1260.0
22 TraesCS3B01G156200 chr3A 83.415 1429 165 39 1115 2494 116077263 116075858 0.000000e+00 1260.0
23 TraesCS3B01G156200 chr3A 85.895 1184 151 9 3519 4700 115612232 115611063 0.000000e+00 1247.0
24 TraesCS3B01G156200 chr3A 85.000 1180 161 10 3524 4700 115163022 115161856 0.000000e+00 1184.0
25 TraesCS3B01G156200 chr3A 93.191 470 31 1 1942 2410 115164580 115164111 0.000000e+00 689.0
26 TraesCS3B01G156200 chr3A 90.746 389 20 7 371 747 115843481 115843097 6.190000e-139 505.0
27 TraesCS3B01G156200 chr3A 90.674 386 24 6 371 747 115615329 115614947 2.220000e-138 503.0
28 TraesCS3B01G156200 chr3A 90.415 386 25 6 371 747 115167378 115166996 1.030000e-136 497.0
29 TraesCS3B01G156200 chr3A 89.896 386 26 7 371 747 115393866 115393485 8.060000e-133 484.0
30 TraesCS3B01G156200 chr7A 74.092 1459 298 60 2949 4352 76356495 76355062 1.320000e-145 527.0
31 TraesCS3B01G156200 chr7A 74.087 1451 294 63 2949 4343 76420702 76419278 6.140000e-144 521.0
32 TraesCS3B01G156200 chr7A 74.018 1451 294 64 2949 4343 76394006 76392583 1.030000e-141 514.0
33 TraesCS3B01G156200 chr7A 75.379 1056 216 34 3319 4343 76453786 76452744 2.260000e-128 470.0
34 TraesCS3B01G156200 chr7A 73.370 1104 231 43 1334 2412 76422133 76421068 8.530000e-93 351.0
35 TraesCS3B01G156200 chr7A 73.279 1104 232 43 1334 2412 76395437 76394372 3.970000e-91 346.0
36 TraesCS3B01G156200 chr7A 89.815 108 8 3 4802 4907 98503933 98504039 9.350000e-28 135.0
37 TraesCS3B01G156200 chr7D 75.573 1048 214 33 3343 4358 69782281 69781244 3.750000e-131 479.0
38 TraesCS3B01G156200 chr7D 75.596 1049 212 35 3343 4358 69805976 69804939 3.750000e-131 479.0
39 TraesCS3B01G156200 chr7D 75.028 909 192 27 1514 2410 69720452 69719567 6.500000e-104 388.0
40 TraesCS3B01G156200 chr7D 74.753 911 203 22 1514 2414 69813435 69812542 3.020000e-102 383.0
41 TraesCS3B01G156200 chr7D 76.443 433 83 17 3549 3967 69718254 69717827 3.250000e-52 217.0
42 TraesCS3B01G156200 chr7D 83.186 113 19 0 4801 4913 572760001 572759889 2.640000e-18 104.0
43 TraesCS3B01G156200 chr6A 74.071 1292 259 51 1161 2416 106734882 106736133 1.360000e-125 460.0
44 TraesCS3B01G156200 chr6A 76.885 809 166 20 3549 4343 106737133 106737934 6.360000e-119 438.0
45 TraesCS3B01G156200 chr6A 89.189 111 12 0 1164 1274 185249012 185248902 7.230000e-29 139.0
46 TraesCS3B01G156200 chr1B 95.775 213 9 0 158 370 173331325 173331537 1.430000e-90 344.0
47 TraesCS3B01G156200 chr1B 92.169 166 13 0 1 166 372548160 372547995 8.960000e-58 235.0
48 TraesCS3B01G156200 chr7B 94.118 221 11 1 158 376 205289708 205289488 8.590000e-88 335.0
49 TraesCS3B01G156200 chrUn 94.470 217 10 2 158 373 55579914 55579699 3.090000e-87 333.0
50 TraesCS3B01G156200 chrUn 92.169 166 13 0 1 166 238891310 238891145 8.960000e-58 235.0
51 TraesCS3B01G156200 chrUn 92.638 163 12 0 1 163 291460610 291460772 8.960000e-58 235.0
52 TraesCS3B01G156200 chr6D 73.667 919 200 32 1516 2409 140648682 140647781 8.650000e-83 318.0
53 TraesCS3B01G156200 chr6D 83.333 138 21 2 4802 4939 412017369 412017234 5.630000e-25 126.0
54 TraesCS3B01G156200 chr4B 93.373 166 10 1 1 165 627936463 627936628 1.490000e-60 244.0
55 TraesCS3B01G156200 chr6B 94.839 155 8 0 4 158 449596888 449597042 5.350000e-60 243.0
56 TraesCS3B01G156200 chr6B 93.210 162 10 1 1 161 179132009 179132170 2.490000e-58 237.0
57 TraesCS3B01G156200 chr2D 87.770 139 15 2 4802 4939 165470961 165470824 1.540000e-35 161.0
58 TraesCS3B01G156200 chr5A 87.050 139 13 5 4801 4937 6665510 6665645 9.280000e-33 152.0
59 TraesCS3B01G156200 chr5D 78.974 195 34 7 1506 1695 447620337 447620145 5.630000e-25 126.0
60 TraesCS3B01G156200 chr4D 87.671 73 9 0 4793 4865 133607490 133607562 9.550000e-13 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 TraesCS3B01G156200 chr3B 148656400 148661750 5350 True 9882.000000 9882 100.000000 1 5351 1 chr3B.!!$R1 5350
1 TraesCS3B01G156200 chr3B 148542228 148548011 5783 True 4808.500000 6883 99.129000 1 5351 2 chr3B.!!$R5 5350
2 TraesCS3B01G156200 chr3B 148579557 148584460 4903 True 3949.500000 6883 98.778000 1 5351 2 chr3B.!!$R6 5350
3 TraesCS3B01G156200 chr3B 148620844 148625797 4953 True 3949.500000 6883 98.778000 1 5351 2 chr3B.!!$R7 5350
4 TraesCS3B01G156200 chr3D 98145468 98151689 6221 True 1826.500000 5267 91.279500 371 5351 4 chr3D.!!$R1 4980
5 TraesCS3B01G156200 chr3A 115839210 115843481 4271 True 1508.333333 2760 87.468333 371 4700 3 chr3A.!!$R4 4329
6 TraesCS3B01G156200 chr3A 116073776 116077263 3487 True 1403.000000 1546 83.064000 1115 4559 2 chr3A.!!$R5 3444
7 TraesCS3B01G156200 chr3A 115389598 115393866 4268 True 1301.666667 2161 88.908667 371 4700 3 chr3A.!!$R2 4329
8 TraesCS3B01G156200 chr3A 115611063 115615329 4266 True 1294.666667 2134 89.006333 371 4700 3 chr3A.!!$R3 4329
9 TraesCS3B01G156200 chr3A 115161856 115167378 5522 True 959.750000 1469 89.521000 371 4700 4 chr3A.!!$R1 4329
10 TraesCS3B01G156200 chr7A 76355062 76356495 1433 True 527.000000 527 74.092000 2949 4352 1 chr7A.!!$R1 1403
11 TraesCS3B01G156200 chr7A 76452744 76453786 1042 True 470.000000 470 75.379000 3319 4343 1 chr7A.!!$R2 1024
12 TraesCS3B01G156200 chr7A 76419278 76422133 2855 True 436.000000 521 73.728500 1334 4343 2 chr7A.!!$R4 3009
13 TraesCS3B01G156200 chr7A 76392583 76395437 2854 True 430.000000 514 73.648500 1334 4343 2 chr7A.!!$R3 3009
14 TraesCS3B01G156200 chr7D 69781244 69782281 1037 True 479.000000 479 75.573000 3343 4358 1 chr7D.!!$R1 1015
15 TraesCS3B01G156200 chr7D 69804939 69805976 1037 True 479.000000 479 75.596000 3343 4358 1 chr7D.!!$R2 1015
16 TraesCS3B01G156200 chr7D 69812542 69813435 893 True 383.000000 383 74.753000 1514 2414 1 chr7D.!!$R3 900
17 TraesCS3B01G156200 chr7D 69717827 69720452 2625 True 302.500000 388 75.735500 1514 3967 2 chr7D.!!$R5 2453
18 TraesCS3B01G156200 chr6A 106734882 106737934 3052 False 449.000000 460 75.478000 1161 4343 2 chr6A.!!$F1 3182
19 TraesCS3B01G156200 chr6D 140647781 140648682 901 True 318.000000 318 73.667000 1516 2409 1 chr6D.!!$R1 893

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
352 354 0.034059 CATCCGGAGCGCCTTAAGAT 59.966 55.000 11.34 0.0 0.00 2.40 F
734 1447 1.683385 AGCTGCTTGTTTTGGAAGTCC 59.317 47.619 0.00 0.0 0.00 3.85 F
2648 4757 5.277345 GGTTGACATAACACACAGTTGACTC 60.277 44.000 0.00 0.0 41.50 3.36 F
3042 5677 1.565305 GCAAGATCGTCCTGTGCTAG 58.435 55.000 0.00 0.0 32.43 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 2576 0.232816 GCCTGCAACAAAAACATGCG 59.767 50.000 0.00 0.00 42.91 4.73 R
2719 4828 0.813610 CGCCAGTTCAACACCTGACA 60.814 55.000 0.00 0.00 32.21 3.58 R
4208 7463 1.136611 GCTTTGTAGCGAACGACACTG 60.137 52.381 0.00 0.00 37.71 3.66 R
4946 8718 3.000623 CACATTCCAGACGATGATTGTCG 59.999 47.826 7.15 3.06 46.56 4.35 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
59 60 2.604462 GGAAAACATGCGGATGAAATGC 59.396 45.455 24.66 9.76 33.36 3.56
74 75 3.067601 TGAAATGCAGATGATGACATGGC 59.932 43.478 0.00 0.00 36.82 4.40
249 251 9.508567 GAAATACTTGCTTCTCATACCATTTTC 57.491 33.333 0.00 0.00 0.00 2.29
252 254 6.917533 ACTTGCTTCTCATACCATTTTCTTG 58.082 36.000 0.00 0.00 0.00 3.02
268 270 8.656849 CCATTTTCTTGTGTACTATGTACACTC 58.343 37.037 29.11 13.80 45.77 3.51
352 354 0.034059 CATCCGGAGCGCCTTAAGAT 59.966 55.000 11.34 0.00 0.00 2.40
734 1447 1.683385 AGCTGCTTGTTTTGGAAGTCC 59.317 47.619 0.00 0.00 0.00 3.85
2648 4757 5.277345 GGTTGACATAACACACAGTTGACTC 60.277 44.000 0.00 0.00 41.50 3.36
3042 5677 1.565305 GCAAGATCGTCCTGTGCTAG 58.435 55.000 0.00 0.00 32.43 3.42
3113 5748 2.169769 CCATCAACCGTACTATGGGTGT 59.830 50.000 11.50 0.00 42.61 4.16
3145 5780 1.740025 GCCTCATCTTTGCACAGTACC 59.260 52.381 0.00 0.00 0.00 3.34
3236 5892 5.525378 AGAGAATTGAATCATACTTGGCGAC 59.475 40.000 0.00 0.00 0.00 5.19
3252 5908 2.059541 GCGACCACAGAGTAAGAACAC 58.940 52.381 0.00 0.00 0.00 3.32
3496 6297 8.421784 TCTCACAGAAAAGATAGTTGTACTTGT 58.578 33.333 0.00 0.00 0.00 3.16
4208 7463 3.426695 GGTAGCACAAGCATGACATTCAC 60.427 47.826 0.00 0.00 45.49 3.18
4284 7539 5.434182 TGACATGGTCAGATGGAAATACA 57.566 39.130 0.00 0.00 37.67 2.29
4946 8718 9.289303 GGACAATATATTTCAACAACACACATC 57.711 33.333 0.00 0.00 0.00 3.06
5042 8837 4.101790 GACGCAACGGCATGTGGG 62.102 66.667 5.91 0.00 41.24 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.336293 CCAAAACTTGCATTTGTTTGGGTTT 60.336 36.000 18.34 0.00 40.54 3.27
59 60 3.802139 GCATTTTGCCATGTCATCATCTG 59.198 43.478 0.00 0.00 37.42 2.90
252 254 3.096461 CGTGCGAGTGTACATAGTACAC 58.904 50.000 25.17 25.17 45.89 2.90
268 270 2.896428 GAAAAGTATGCGGGCGTGCG 62.896 60.000 0.00 0.00 37.81 5.34
352 354 5.157781 CCACTTTGTTTGACACGAGAAAAA 58.842 37.500 0.00 0.00 0.00 1.94
512 521 1.956477 GCTTTGCTGGGTCTTTCAGAA 59.044 47.619 0.00 0.00 34.36 3.02
734 1447 8.954950 AGTCTTAATAATGATGACAAGAGGTG 57.045 34.615 0.00 0.00 0.00 4.00
1765 2576 0.232816 GCCTGCAACAAAAACATGCG 59.767 50.000 0.00 0.00 42.91 4.73
2648 4757 7.262772 TGGAGTAAAACTAGACGATTATGGTG 58.737 38.462 0.00 0.00 0.00 4.17
2719 4828 0.813610 CGCCAGTTCAACACCTGACA 60.814 55.000 0.00 0.00 32.21 3.58
3145 5780 4.760047 CGGCAGGAGGTTCGTGGG 62.760 72.222 1.58 0.00 33.25 4.61
3236 5892 2.316792 CGACGTGTTCTTACTCTGTGG 58.683 52.381 0.00 0.00 0.00 4.17
3252 5908 2.170985 CTTTCAGGCAACGCGACG 59.829 61.111 15.93 3.67 46.39 5.12
4208 7463 1.136611 GCTTTGTAGCGAACGACACTG 60.137 52.381 0.00 0.00 37.71 3.66
4830 8601 6.549912 GCCAAAAGCTCTTGAATTCAAAAT 57.450 33.333 20.82 5.49 38.99 1.82
4946 8718 3.000623 CACATTCCAGACGATGATTGTCG 59.999 47.826 7.15 3.06 46.56 4.35
5042 8837 1.632589 AGCCCTTGTTTTGGTCATCC 58.367 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.