Multiple sequence alignment - TraesCS3B01G524100

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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 TraesCS3B01G524100 chr3B 100.000 2959 0 0 1 2959 766342004 766344962 0.000000e+00 5465
1 TraesCS3B01G524100 chr3B 76.444 225 30 13 2743 2958 512391487 512391697 1.880000e-17 100
2 TraesCS3B01G524100 chr7B 98.453 2263 31 1 1 2263 73168038 73170296 0.000000e+00 3982
3 TraesCS3B01G524100 chr7B 94.956 1923 80 3 1 1923 517902595 517904500 0.000000e+00 2998
4 TraesCS3B01G524100 chr7B 97.147 701 14 4 2264 2959 73170335 73171034 0.000000e+00 1179
5 TraesCS3B01G524100 chr2B 95.143 2265 101 6 1 2263 419938626 419940883 0.000000e+00 3565
6 TraesCS3B01G524100 chr2B 93.957 2267 126 8 3 2261 528809433 528807170 0.000000e+00 3417
7 TraesCS3B01G524100 chr2B 93.848 699 32 7 2264 2959 419940922 419941612 0.000000e+00 1042
8 TraesCS3B01G524100 chr2B 90.727 399 19 6 2278 2673 528797549 528797166 1.570000e-142 516
9 TraesCS3B01G524100 chr6B 95.219 2238 99 5 27 2261 617031452 617033684 0.000000e+00 3533
10 TraesCS3B01G524100 chr6B 94.440 1331 71 2 932 2261 676703236 676704564 0.000000e+00 2045
11 TraesCS3B01G524100 chr6B 95.740 939 38 2 1 938 676683728 676684665 0.000000e+00 1511
12 TraesCS3B01G524100 chr6B 94.101 695 32 5 2264 2956 617033725 617034412 0.000000e+00 1048
13 TraesCS3B01G524100 chr6B 93.139 583 31 5 2376 2956 676708372 676708947 0.000000e+00 846
14 TraesCS3B01G524100 chr6B 90.909 396 16 9 2264 2657 138658705 138659082 5.660000e-142 514
15 TraesCS3B01G524100 chr6B 94.624 279 12 2 1984 2260 138658386 138658663 2.110000e-116 429
16 TraesCS3B01G524100 chr6B 91.034 290 20 2 2652 2940 138633788 138634072 1.290000e-103 387
17 TraesCS3B01G524100 chr1B 93.711 2226 113 10 41 2261 344040425 344042628 0.000000e+00 3310
18 TraesCS3B01G524100 chr1B 92.823 418 27 2 2264 2678 344042669 344043086 1.170000e-168 603
19 TraesCS3B01G524100 chr4B 94.548 1339 68 4 926 2261 43564379 43563043 0.000000e+00 2063
20 TraesCS3B01G524100 chr4B 94.952 931 46 1 1 931 43573722 43572793 0.000000e+00 1458
21 TraesCS3B01G524100 chr4B 95.344 494 21 2 925 1418 43578259 43577768 0.000000e+00 784
22 TraesCS3B01G524100 chr4B 91.867 332 22 3 2345 2673 43562945 43562616 2.690000e-125 459
23 TraesCS3B01G524100 chr7D 97.389 1149 30 0 1 1149 83759036 83760184 0.000000e+00 1956
24 TraesCS3B01G524100 chr7D 96.106 719 28 0 1256 1974 83760186 83760904 0.000000e+00 1173
25 TraesCS3B01G524100 chr7D 95.639 665 20 5 2297 2959 83761286 83761943 0.000000e+00 1059
26 TraesCS3B01G524100 chr7D 93.846 390 15 5 2572 2959 366437204 366436822 1.980000e-161 579
27 TraesCS3B01G524100 chr2D 96.245 719 27 0 1256 1974 238091179 238090461 0.000000e+00 1179
28 TraesCS3B01G524100 chr2D 95.188 665 23 5 2297 2959 238090079 238089422 0.000000e+00 1042
29 TraesCS3B01G524100 chrUn 91.162 396 15 9 2264 2657 194984585 194984208 1.220000e-143 520
30 TraesCS3B01G524100 chrUn 94.982 279 11 2 1984 2260 194984904 194984627 4.530000e-118 435
31 TraesCS3B01G524100 chrUn 91.349 289 18 2 2652 2940 194970926 194970645 3.580000e-104 388


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 TraesCS3B01G524100 chr3B 766342004 766344962 2958 False 5465.0 5465 100.0000 1 2959 1 chr3B.!!$F2 2958
1 TraesCS3B01G524100 chr7B 517902595 517904500 1905 False 2998.0 2998 94.9560 1 1923 1 chr7B.!!$F1 1922
2 TraesCS3B01G524100 chr7B 73168038 73171034 2996 False 2580.5 3982 97.8000 1 2959 2 chr7B.!!$F2 2958
3 TraesCS3B01G524100 chr2B 528807170 528809433 2263 True 3417.0 3417 93.9570 3 2261 1 chr2B.!!$R2 2258
4 TraesCS3B01G524100 chr2B 419938626 419941612 2986 False 2303.5 3565 94.4955 1 2959 2 chr2B.!!$F1 2958
5 TraesCS3B01G524100 chr6B 617031452 617034412 2960 False 2290.5 3533 94.6600 27 2956 2 chr6B.!!$F4 2929
6 TraesCS3B01G524100 chr6B 676683728 676684665 937 False 1511.0 1511 95.7400 1 938 1 chr6B.!!$F2 937
7 TraesCS3B01G524100 chr6B 676703236 676708947 5711 False 1445.5 2045 93.7895 932 2956 2 chr6B.!!$F5 2024
8 TraesCS3B01G524100 chr6B 138658386 138659082 696 False 471.5 514 92.7665 1984 2657 2 chr6B.!!$F3 673
9 TraesCS3B01G524100 chr1B 344040425 344043086 2661 False 1956.5 3310 93.2670 41 2678 2 chr1B.!!$F1 2637
10 TraesCS3B01G524100 chr4B 43572793 43573722 929 True 1458.0 1458 94.9520 1 931 1 chr4B.!!$R1 930
11 TraesCS3B01G524100 chr4B 43562616 43564379 1763 True 1261.0 2063 93.2075 926 2673 2 chr4B.!!$R3 1747
12 TraesCS3B01G524100 chr7D 83759036 83761943 2907 False 1396.0 1956 96.3780 1 2959 3 chr7D.!!$F1 2958
13 TraesCS3B01G524100 chr2D 238089422 238091179 1757 True 1110.5 1179 95.7165 1256 2959 2 chr2D.!!$R1 1703
14 TraesCS3B01G524100 chrUn 194984208 194984904 696 True 477.5 520 93.0720 1984 2657 2 chrUn.!!$R2 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
404 408 0.387929 TGTCTGTCGACCCACTTGAC 59.612 55.0 14.12 11.47 39.47 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2366 2633 0.322816 TCTGCCAATGAGGAGCCAAC 60.323 55.0 0.0 0.0 41.22 3.77 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
404 408 0.387929 TGTCTGTCGACCCACTTGAC 59.612 55.000 14.12 11.47 39.47 3.18
411 415 1.414550 TCGACCCACTTGACATCAACA 59.585 47.619 0.00 0.00 0.00 3.33
421 425 5.630680 CACTTGACATCAACAAGCCAATAAC 59.369 40.000 0.00 0.00 45.66 1.89
581 585 5.065474 GGCGCATTGAGGTATAAGTTGTTTA 59.935 40.000 10.83 0.00 0.00 2.01
682 688 5.095691 TCTCGTTTGCATTTGTTCTCTTC 57.904 39.130 0.00 0.00 0.00 2.87
1171 1177 4.857679 TGTACCTTGGTTACCTGTTGTTT 58.142 39.130 2.07 0.00 0.00 2.83
1277 1286 7.844779 AGGAGAAAGTAGTACCATTTCTATCCA 59.155 37.037 14.32 0.00 41.95 3.41
1283 1292 8.964476 AGTAGTACCATTTCTATCCATTGTTG 57.036 34.615 0.00 0.00 0.00 3.33
1292 1301 5.186256 TCTATCCATTGTTGTTGCCCTTA 57.814 39.130 0.00 0.00 0.00 2.69
1310 1319 6.015772 TGCCCTTACTATTGAAAACCAACTTC 60.016 38.462 0.00 0.00 37.63 3.01
1701 1714 1.612950 TGGGTGCAATGACAACATCAC 59.387 47.619 0.00 0.00 41.24 3.06
1769 1782 6.685657 ACAGAAATCAAGAGAAAAGGCAATC 58.314 36.000 0.00 0.00 0.00 2.67
1930 1945 5.013391 TGTCCGGTATCCCTTTTTCTAAACT 59.987 40.000 0.00 0.00 0.00 2.66
1931 1946 5.583854 GTCCGGTATCCCTTTTTCTAAACTC 59.416 44.000 0.00 0.00 0.00 3.01
2208 2436 2.459555 CCTTGGGGGTTGATAGCATT 57.540 50.000 0.00 0.00 0.00 3.56
2366 2633 5.344743 TCCTTGTATCTAACTCCTGCTTG 57.655 43.478 0.00 0.00 0.00 4.01
2695 6622 1.975660 TCCCACCTTTTCCTTTGTCG 58.024 50.000 0.00 0.00 0.00 4.35
2826 6757 6.393171 GCAGATGAGAAAATAAGCAAGGTTT 58.607 36.000 0.00 0.00 0.00 3.27
2848 6779 6.959639 TTATTAGAAAATGGGATCAGTGGC 57.040 37.500 0.00 0.00 0.00 5.01
2849 6780 2.905415 AGAAAATGGGATCAGTGGCA 57.095 45.000 0.00 0.00 0.00 4.92
2852 6783 2.832643 AAATGGGATCAGTGGCATGA 57.167 45.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
404 408 5.771469 TCTTGTGTTATTGGCTTGTTGATG 58.229 37.500 0.00 0.00 0.00 3.07
411 415 8.177119 TCTAATGTTTCTTGTGTTATTGGCTT 57.823 30.769 0.00 0.00 0.00 4.35
421 425 7.361542 CCTCCATGTCTTCTAATGTTTCTTGTG 60.362 40.741 0.00 0.00 0.00 3.33
623 629 7.011389 GCTTGCAAATATAATTGAAAGGGAACC 59.989 37.037 18.91 2.87 43.43 3.62
1277 1286 6.909550 TTCAATAGTAAGGGCAACAACAAT 57.090 33.333 0.00 0.00 39.74 2.71
1283 1292 5.715434 TGGTTTTCAATAGTAAGGGCAAC 57.285 39.130 0.00 0.00 0.00 4.17
1292 1301 7.898014 AAGAAGGAAGTTGGTTTTCAATAGT 57.102 32.000 0.00 0.00 37.73 2.12
1701 1714 1.226491 GCGCCATTGCTGCTGTAAG 60.226 57.895 0.00 0.00 35.24 2.34
1769 1782 3.076621 TGCAAGCCTAGACAATTCACTG 58.923 45.455 0.00 0.00 0.00 3.66
1955 1972 4.057432 CGGAAAAACCAAAACTGCATCAT 58.943 39.130 0.00 0.00 38.90 2.45
2343 2610 5.248477 ACAAGCAGGAGTTAGATACAAGGAA 59.752 40.000 0.00 0.00 0.00 3.36
2366 2633 0.322816 TCTGCCAATGAGGAGCCAAC 60.323 55.000 0.00 0.00 41.22 3.77
2695 6622 7.642669 TGATTGTTCTTTCTCATCAACACTTC 58.357 34.615 0.00 0.00 0.00 3.01
2794 6724 7.340232 TGCTTATTTTCTCATCTGCCAATAAGT 59.660 33.333 9.89 0.00 36.90 2.24
2826 6757 6.012337 TGCCACTGATCCCATTTTCTAATA 57.988 37.500 0.00 0.00 0.00 0.98
2848 6779 4.436332 TGATCTTCATCTTCCACGTCATG 58.564 43.478 0.00 0.00 0.00 3.07
2849 6780 4.743057 TGATCTTCATCTTCCACGTCAT 57.257 40.909 0.00 0.00 0.00 3.06
2852 6783 4.080919 TCCATTGATCTTCATCTTCCACGT 60.081 41.667 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.