Multiple sequence alignment - TraesCS4B01G095800

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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 TraesCS4B01G095800 chr4B 100.000 2711 0 0 1 2711 99429002 99426292 0.000000e+00 5007
1 TraesCS4B01G095800 chr4B 94.816 2334 107 9 383 2706 553948354 553946025 0.000000e+00 3627
2 TraesCS4B01G095800 chr7B 94.146 2716 138 12 1 2707 556728915 556726212 0.000000e+00 4115
3 TraesCS4B01G095800 chr3B 91.725 2707 191 22 30 2711 657695671 657692973 0.000000e+00 3727
4 TraesCS4B01G095800 chr3B 91.002 2734 213 29 4 2711 694806899 694804173 0.000000e+00 3655
5 TraesCS4B01G095800 chr3B 94.178 2336 108 12 385 2711 13988761 13986445 0.000000e+00 3535
6 TraesCS4B01G095800 chr3B 93.678 2341 125 15 383 2706 797909564 797911898 0.000000e+00 3482
7 TraesCS4B01G095800 chr3B 91.484 364 29 2 1 364 797909050 797909411 1.450000e-137 499
8 TraesCS4B01G095800 chr2B 89.945 2735 231 32 3 2711 67269421 67266705 0.000000e+00 3487
9 TraesCS4B01G095800 chr2B 88.315 368 39 4 1 366 747121915 747121550 3.200000e-119 438
10 TraesCS4B01G095800 chr2B 86.141 368 47 4 1 366 652827025 652827390 7.040000e-106 394
11 TraesCS4B01G095800 chr2B 83.880 366 54 5 1 363 626152454 626152091 7.190000e-91 344
12 TraesCS4B01G095800 chr2B 83.287 359 55 5 3 358 652826941 652827297 2.600000e-85 326
13 TraesCS4B01G095800 chr2B 83.094 278 39 8 4 277 747121738 747121465 2.080000e-61 246
14 TraesCS4B01G095800 chr2B 82.166 157 23 5 210 362 67269563 67269408 2.190000e-26 130
15 TraesCS4B01G095800 chr1B 93.368 2337 135 14 385 2711 50150842 50148516 0.000000e+00 3439
16 TraesCS4B01G095800 chr6B 93.333 2340 135 16 384 2711 420671212 420673542 0.000000e+00 3437
17 TraesCS4B01G095800 chr7D 94.427 2189 112 6 386 2567 631326898 631329083 0.000000e+00 3358


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 TraesCS4B01G095800 chr4B 99426292 99429002 2710 True 5007.0 5007 100.0000 1 2711 1 chr4B.!!$R1 2710
1 TraesCS4B01G095800 chr4B 553946025 553948354 2329 True 3627.0 3627 94.8160 383 2706 1 chr4B.!!$R2 2323
2 TraesCS4B01G095800 chr7B 556726212 556728915 2703 True 4115.0 4115 94.1460 1 2707 1 chr7B.!!$R1 2706
3 TraesCS4B01G095800 chr3B 657692973 657695671 2698 True 3727.0 3727 91.7250 30 2711 1 chr3B.!!$R2 2681
4 TraesCS4B01G095800 chr3B 694804173 694806899 2726 True 3655.0 3655 91.0020 4 2711 1 chr3B.!!$R3 2707
5 TraesCS4B01G095800 chr3B 13986445 13988761 2316 True 3535.0 3535 94.1780 385 2711 1 chr3B.!!$R1 2326
6 TraesCS4B01G095800 chr3B 797909050 797911898 2848 False 1990.5 3482 92.5810 1 2706 2 chr3B.!!$F1 2705
7 TraesCS4B01G095800 chr2B 67266705 67269563 2858 True 1808.5 3487 86.0555 3 2711 2 chr2B.!!$R2 2708
8 TraesCS4B01G095800 chr1B 50148516 50150842 2326 True 3439.0 3439 93.3680 385 2711 1 chr1B.!!$R1 2326
9 TraesCS4B01G095800 chr6B 420671212 420673542 2330 False 3437.0 3437 93.3330 384 2711 1 chr6B.!!$F1 2327
10 TraesCS4B01G095800 chr7D 631326898 631329083 2185 False 3358.0 3358 94.4270 386 2567 1 chr7D.!!$F1 2181

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
705 905 1.323271 TTGCCAACGGAAAACCTGCA 61.323 50.0 0.00 0.0 0.0 4.41 F
1288 1506 0.606944 AACCGCGGCAAATGTTCCTA 60.607 50.0 28.58 0.0 0.0 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1540 1761 1.030457 CCTCCATCATCAGCTTTGGC 58.970 55.0 0.0 0.0 39.06 4.52 R
2178 2413 1.480789 TCCGGCTGCACAGTAATAGA 58.519 50.0 0.5 0.0 0.00 1.98 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
83 137 6.498303 ACTGATATATGCATCCTGACCAACTA 59.502 38.462 0.19 0.0 0.00 2.24
139 194 3.070476 TGCAACAGAACATGCATCCTA 57.930 42.857 0.00 0.0 46.87 2.94
311 458 7.643569 TGATTGTCCAACTAAATATGCATGT 57.356 32.000 10.16 0.0 0.00 3.21
629 827 5.569355 TCTTTCACCTGGATTTTGCATCTA 58.431 37.500 0.00 0.0 0.00 1.98
705 905 1.323271 TTGCCAACGGAAAACCTGCA 61.323 50.000 0.00 0.0 0.00 4.41
745 946 8.575649 AAACAGAGGAAAAAGTCAGAAAACTA 57.424 30.769 0.00 0.0 0.00 2.24
896 1109 9.638239 TTTGGAACTAAGATTGTCATAAAATGC 57.362 29.630 0.00 0.0 0.00 3.56
897 1110 8.347004 TGGAACTAAGATTGTCATAAAATGCA 57.653 30.769 0.00 0.0 0.00 3.96
962 1176 8.691661 ACACTCTTTTCTATGGTTAACAATGT 57.308 30.769 8.10 0.0 0.00 2.71
1014 1229 0.911053 TGAGTATGTGGCAGCATCCA 59.089 50.000 5.95 0.0 0.00 3.41
1075 1293 3.134262 TCCTGATCTCAATGAGCTTCCTG 59.866 47.826 5.18 1.9 31.32 3.86
1137 1355 1.004161 TGGACAGAAAATGGGCGATCA 59.996 47.619 0.00 0.0 0.00 2.92
1288 1506 0.606944 AACCGCGGCAAATGTTCCTA 60.607 50.000 28.58 0.0 0.00 2.94
1480 1701 4.416516 TGTCAAGATGAACACCTCTAGGA 58.583 43.478 2.23 0.0 38.94 2.94
1540 1761 2.099592 TGCTGCAACAAGTTCAAGAAGG 59.900 45.455 0.00 0.0 0.00 3.46
1592 1813 1.651770 TCCTGTCCTGGACCCTATTCT 59.348 52.381 23.42 0.0 0.00 2.40
1611 1832 9.401058 CCTATTCTAGATCCAAAAACTGTTGAT 57.599 33.333 0.00 0.0 0.00 2.57
1621 1842 7.223584 TCCAAAAACTGTTGATAGTGATGAGA 58.776 34.615 0.00 0.0 0.00 3.27
1768 1995 3.458163 GGCGATGGGAGGTGACGA 61.458 66.667 0.00 0.0 0.00 4.20
1864 2091 4.036144 GCATCTCACCTAATGAAAAGGAGC 59.964 45.833 0.00 0.0 36.69 4.70
1906 2133 2.093181 TGCAACTTGACTACAGGTGTGT 60.093 45.455 0.00 0.0 41.06 3.72
1979 2208 6.015265 TGTGCAACTGTTATGGTACTACTGTA 60.015 38.462 0.00 0.0 38.04 2.74
2107 2340 9.394767 ACTACACAATATCATGTATGCAAAAGA 57.605 29.630 0.00 0.0 31.10 2.52
2194 2429 3.941483 ACATGTTCTATTACTGTGCAGCC 59.059 43.478 0.00 0.0 0.00 4.85
2363 2599 4.989168 AGTTTCCGTAGAGATGACACAAAC 59.011 41.667 0.00 0.0 0.00 2.93
2531 2768 3.133901 AGGTGTACCACGATTGCATATCA 59.866 43.478 3.56 0.0 38.89 2.15
2595 2832 3.192422 CGCACCCTTCATTGGAATAAACA 59.808 43.478 0.00 0.0 31.34 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 137 7.928307 TTCAGCTTGCTAGAATAGATGTTTT 57.072 32.000 0.00 0.00 42.77 2.43
139 194 6.501805 TCCAGGATACATATATCAGTTTGGCT 59.498 38.462 0.00 0.00 39.29 4.75
225 280 4.065088 GGATGCATATAAGAGTTCGCCAA 58.935 43.478 0.00 0.00 0.00 4.52
311 458 5.999600 CAGGATGCATATATCAGTTGGTCAA 59.000 40.000 0.00 0.00 0.00 3.18
597 795 6.641169 AATCCAGGTGAAAGAAGAAAGAAC 57.359 37.500 0.00 0.00 0.00 3.01
629 827 8.538701 TGGGACATAATTTGATGCTATTTTTGT 58.461 29.630 0.00 0.00 0.00 2.83
648 847 5.999205 TTTTCTGCACATAATTGGGACAT 57.001 34.783 0.00 0.00 39.30 3.06
705 905 4.083110 CCTCTGTTTTCGTTGCAATGATCT 60.083 41.667 21.57 0.00 0.00 2.75
718 918 8.029522 AGTTTTCTGACTTTTTCCTCTGTTTTC 58.970 33.333 0.00 0.00 0.00 2.29
765 967 9.014297 AGTTTGCAGTAAATAGTTAGCAAGAAT 57.986 29.630 8.84 0.84 42.11 2.40
897 1110 5.805728 ACTTAGTAAATAGGCAGTTGCACT 58.194 37.500 6.43 2.49 44.36 4.40
1075 1293 3.439476 GGTTGCTGCTGATCCATATCATC 59.561 47.826 0.00 0.00 41.29 2.92
1137 1355 2.224209 ACTTGCCTGCGTGTAGTAAACT 60.224 45.455 0.00 0.00 0.00 2.66
1480 1701 1.360393 ACATTGGTGTGGGGTGTCCT 61.360 55.000 0.00 0.00 37.14 3.85
1540 1761 1.030457 CCTCCATCATCAGCTTTGGC 58.970 55.000 0.00 0.00 39.06 4.52
1592 1813 9.166173 CATCACTATCAACAGTTTTTGGATCTA 57.834 33.333 0.00 0.00 0.00 1.98
1611 1832 7.554118 GGTTCATCTTCCATTTTCTCATCACTA 59.446 37.037 0.00 0.00 0.00 2.74
1708 1935 2.760634 TTCGCCTTGCATTGAGTCTA 57.239 45.000 0.00 0.00 0.00 2.59
1768 1995 3.692101 TGATTGTGGTCACGAACAAAGTT 59.308 39.130 0.00 0.00 39.57 2.66
1864 2091 5.352293 TGCAGTTATACAAGATGTGCAGAAG 59.648 40.000 0.00 0.00 34.65 2.85
1979 2208 5.356751 TGCACAGTTAAGTCATTTCAGTTGT 59.643 36.000 0.00 0.00 0.00 3.32
2106 2339 6.630045 GCATCTTTTCAAAAACACTTTGCATC 59.370 34.615 0.00 0.00 0.00 3.91
2107 2340 6.093771 TGCATCTTTTCAAAAACACTTTGCAT 59.906 30.769 0.00 0.00 30.98 3.96
2122 2357 2.680339 GGACACCTAGCTGCATCTTTTC 59.320 50.000 1.02 0.00 0.00 2.29
2178 2413 1.480789 TCCGGCTGCACAGTAATAGA 58.519 50.000 0.50 0.00 0.00 1.98
2363 2599 2.094026 TGTCTCAATCATGTCACCCTCG 60.094 50.000 0.00 0.00 0.00 4.63
2531 2768 5.755409 TGGTCATGTAGGTAGTGTCAAAT 57.245 39.130 0.00 0.00 0.00 2.32
2595 2832 2.429610 GCATGAAAGATTGGCCATGTCT 59.570 45.455 6.09 11.12 38.78 3.41


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

AutoCloner maintained by Alex Coulton.