Multiple sequence alignment - TraesCS2B01G191000

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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 TraesCS2B01G191000 chr2B 100.000 2111 0 0 1 2111 166467468 166465358 0.000000e+00 3899.0
1 TraesCS2B01G191000 chr2B 89.086 394 38 5 800 1191 166407087 166406697 3.150000e-133 484.0
2 TraesCS2B01G191000 chr2B 82.927 164 15 7 1185 1345 166406620 166406467 3.650000e-28 135.0
3 TraesCS2B01G191000 chr2A 94.246 1738 70 10 400 2111 117388660 117386927 0.000000e+00 2628.0
4 TraesCS2B01G191000 chr2A 95.593 295 11 1 1 293 117389052 117388758 2.450000e-129 472.0
5 TraesCS2B01G191000 chr2A 100.000 74 0 0 326 399 117388762 117388689 1.020000e-28 137.0
6 TraesCS2B01G191000 chr2D 91.843 1226 65 8 511 1720 115942968 115941762 0.000000e+00 1677.0
7 TraesCS2B01G191000 chr2D 88.083 386 32 11 966 1345 115929345 115928968 1.490000e-121 446.0
8 TraesCS2B01G191000 chr2D 96.891 193 5 1 1809 2000 115941607 115941415 2.610000e-84 322.0
9 TraesCS2B01G191000 chr2D 87.719 171 20 1 814 983 115929532 115929362 4.590000e-47 198.0
10 TraesCS2B01G191000 chr2D 90.909 110 5 2 1713 1818 115941741 115941633 2.180000e-30 143.0
11 TraesCS2B01G191000 chr2D 85.106 94 4 4 2001 2084 115941210 115941117 1.040000e-13 87.9
12 TraesCS2B01G191000 chr2D 100.000 30 0 0 1805 1834 115941638 115941609 2.930000e-04 56.5
13 TraesCS2B01G191000 chr6D 94.000 150 9 0 511 660 353733072 353732923 5.860000e-56 228.0


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 TraesCS2B01G191000 chr2B 166465358 166467468 2110 True 3899.00 3899 100.0000 1 2111 1 chr2B.!!$R1 2110
1 TraesCS2B01G191000 chr2B 166406467 166407087 620 True 309.50 484 86.0065 800 1345 2 chr2B.!!$R2 545
2 TraesCS2B01G191000 chr2A 117386927 117389052 2125 True 1079.00 2628 96.6130 1 2111 3 chr2A.!!$R1 2110
3 TraesCS2B01G191000 chr2D 115941117 115942968 1851 True 457.28 1677 92.9498 511 2084 5 chr2D.!!$R2 1573
4 TraesCS2B01G191000 chr2D 115928968 115929532 564 True 322.00 446 87.9010 814 1345 2 chr2D.!!$R1 531

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
832 863 0.251341 TGCTTCTTGCCCTCCTTTCC 60.251 55.0 0.0 0.0 42.0 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1726 1924 1.22184 CCCCTTCACGTCCATCCAG 59.778 63.158 0.0 0.0 0.0 3.86 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
43 44 2.224793 GCAGTAGAAACTTGGGAAGGGT 60.225 50.000 0.00 0.00 31.97 4.34
62 63 6.441088 AGGGTAATGAAGATATGAAGACCC 57.559 41.667 0.00 0.00 43.69 4.46
78 79 0.904394 ACCCATGAATTGGTGCACCC 60.904 55.000 32.62 17.66 44.83 4.61
85 86 0.893727 AATTGGTGCACCCGGAAGAC 60.894 55.000 32.62 5.95 35.15 3.01
129 130 5.465390 TGTATAGCTATCATTGCACGTTTCC 59.535 40.000 10.16 0.00 0.00 3.13
131 132 4.137116 AGCTATCATTGCACGTTTCCTA 57.863 40.909 0.00 0.00 0.00 2.94
155 156 6.882656 ACATGTTCTATTACACTGCAGAGAT 58.117 36.000 23.35 10.50 0.00 2.75
189 190 7.867752 TGTACAGCAGTTAACTAAATTTCACC 58.132 34.615 8.04 0.00 0.00 4.02
190 191 7.717875 TGTACAGCAGTTAACTAAATTTCACCT 59.282 33.333 8.04 0.00 0.00 4.00
191 192 7.582667 ACAGCAGTTAACTAAATTTCACCTT 57.417 32.000 8.04 0.00 0.00 3.50
245 248 9.626045 ATCGAAATTTTGTTTCTGTTATCTTCC 57.374 29.630 5.33 0.00 0.00 3.46
279 282 7.489113 TGTCTTGCTTTCATTTGAAACTTTCTC 59.511 33.333 1.66 0.00 38.94 2.87
293 296 9.601217 TTGAAACTTTCTCTAGATATTGGTAGC 57.399 33.333 0.00 0.00 0.00 3.58
294 297 8.204836 TGAAACTTTCTCTAGATATTGGTAGCC 58.795 37.037 0.00 0.00 0.00 3.93
295 298 6.673839 ACTTTCTCTAGATATTGGTAGCCC 57.326 41.667 0.00 0.00 0.00 5.19
296 299 6.386284 ACTTTCTCTAGATATTGGTAGCCCT 58.614 40.000 0.00 0.00 0.00 5.19
297 300 6.268847 ACTTTCTCTAGATATTGGTAGCCCTG 59.731 42.308 0.00 0.00 0.00 4.45
298 301 5.600669 TCTCTAGATATTGGTAGCCCTGA 57.399 43.478 0.00 0.00 0.00 3.86
299 302 5.965486 TCTCTAGATATTGGTAGCCCTGAA 58.035 41.667 0.00 0.00 0.00 3.02
300 303 6.565974 TCTCTAGATATTGGTAGCCCTGAAT 58.434 40.000 0.00 0.00 0.00 2.57
301 304 7.019388 TCTCTAGATATTGGTAGCCCTGAATT 58.981 38.462 0.00 0.00 0.00 2.17
302 305 8.177456 TCTCTAGATATTGGTAGCCCTGAATTA 58.823 37.037 0.00 0.00 0.00 1.40
303 306 8.917414 TCTAGATATTGGTAGCCCTGAATTAT 57.083 34.615 0.00 0.00 0.00 1.28
304 307 9.338968 TCTAGATATTGGTAGCCCTGAATTATT 57.661 33.333 0.00 0.00 0.00 1.40
307 310 9.338968 AGATATTGGTAGCCCTGAATTATTAGA 57.661 33.333 0.00 0.00 0.00 2.10
311 314 9.660544 ATTGGTAGCCCTGAATTATTAGATTTT 57.339 29.630 0.00 0.00 0.00 1.82
312 315 8.463930 TGGTAGCCCTGAATTATTAGATTTTG 57.536 34.615 0.00 0.00 0.00 2.44
313 316 7.014230 TGGTAGCCCTGAATTATTAGATTTTGC 59.986 37.037 0.00 0.00 0.00 3.68
314 317 7.014230 GGTAGCCCTGAATTATTAGATTTTGCA 59.986 37.037 0.00 0.00 0.00 4.08
315 318 7.047460 AGCCCTGAATTATTAGATTTTGCAG 57.953 36.000 0.00 0.00 0.00 4.41
316 319 5.693555 GCCCTGAATTATTAGATTTTGCAGC 59.306 40.000 0.00 0.00 0.00 5.25
317 320 6.683610 GCCCTGAATTATTAGATTTTGCAGCA 60.684 38.462 0.00 0.00 0.00 4.41
318 321 7.439381 CCCTGAATTATTAGATTTTGCAGCAT 58.561 34.615 0.00 0.00 0.00 3.79
319 322 7.384115 CCCTGAATTATTAGATTTTGCAGCATG 59.616 37.037 0.00 0.00 40.87 4.06
437 468 7.302184 AGTTTATCTAGCTAGTCTCCCATCTT 58.698 38.462 20.10 0.00 0.00 2.40
468 499 3.116096 TCCCTGAACTACAGTAGGCAT 57.884 47.619 12.42 0.00 44.40 4.40
485 516 1.477558 GCATAGGACACCCTTCCCATG 60.478 57.143 0.00 0.00 40.78 3.66
488 519 0.475632 AGGACACCCTTCCCATGTCA 60.476 55.000 6.00 0.00 43.73 3.58
592 623 7.973944 CACTTAACCCCAGTTTATTTGCTATTC 59.026 37.037 0.00 0.00 37.42 1.75
745 776 8.403732 CCATATGATGGTTAAGCAGGGCTTTG 62.404 46.154 13.51 6.44 45.03 2.77
780 811 3.699779 TGCTGCGTTTTGTATTGACAA 57.300 38.095 0.00 0.00 43.94 3.18
832 863 0.251341 TGCTTCTTGCCCTCCTTTCC 60.251 55.000 0.00 0.00 42.00 3.13
843 874 1.616865 CCTCCTTTCCGACACTACACA 59.383 52.381 0.00 0.00 0.00 3.72
848 879 2.963548 TTCCGACACTACACACACAA 57.036 45.000 0.00 0.00 0.00 3.33
929 960 2.146342 CTGACAAGTGGCAACCAGTAG 58.854 52.381 0.00 0.00 35.94 2.57
1385 1539 5.878406 ATTCTCGTATCTGGGACTTGAAT 57.122 39.130 0.00 0.00 0.00 2.57
1516 1677 2.095567 CCTTGTCGATGAAGCAGGTTTG 60.096 50.000 0.00 0.00 0.00 2.93
1523 1684 3.499918 CGATGAAGCAGGTTTGTCTTCTT 59.500 43.478 0.00 0.00 37.84 2.52
1525 1686 3.884895 TGAAGCAGGTTTGTCTTCTTCA 58.115 40.909 3.56 3.56 37.84 3.02
1543 1704 2.243810 TCACCTTGTTTTACCCATGCC 58.756 47.619 0.00 0.00 0.00 4.40
1623 1793 5.441718 TTCCTGCCATTTATCAGTCTTCT 57.558 39.130 0.00 0.00 0.00 2.85
1688 1858 4.257267 AGCAAACCTTTTTCTATGGTGC 57.743 40.909 0.00 0.00 34.67 5.01
1692 1862 5.183140 GCAAACCTTTTTCTATGGTGCTAGA 59.817 40.000 0.00 0.00 34.67 2.43
1726 1924 1.351017 TCAATTGTCCTGGGGTCTGTC 59.649 52.381 5.13 0.00 0.00 3.51
1738 1936 0.108615 GGTCTGTCTGGATGGACGTG 60.109 60.000 0.00 0.00 38.91 4.49
1909 2147 8.715088 AGCAAAATTTATCTCAATTCTTGCAAC 58.285 29.630 17.95 0.00 39.21 4.17
2057 2508 9.978044 CCCGCTACTAAGAAATACTATTTAGTT 57.022 33.333 0.00 0.00 37.49 2.24
2102 2553 8.247562 TGCAAACTAACAACTTCAAATACTTGT 58.752 29.630 0.00 0.00 33.94 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 0.964860 TCCGGGTGCACCAATTCATG 60.965 55.000 35.78 15.58 40.22 3.07
85 86 3.807622 ACAGAGAAACACACATAACACGG 59.192 43.478 0.00 0.00 0.00 4.94
129 130 7.484140 TCTCTGCAGTGTAATAGAACATGTAG 58.516 38.462 14.67 0.00 0.00 2.74
131 132 6.286240 TCTCTGCAGTGTAATAGAACATGT 57.714 37.500 14.67 0.00 0.00 3.21
155 156 5.010719 AGTTAACTGCTGTACAAGAGCACTA 59.989 40.000 7.48 0.00 41.56 2.74
189 190 3.253921 TCCAGTGCAACACATGAATGAAG 59.746 43.478 0.00 0.00 41.43 3.02
190 191 3.220940 TCCAGTGCAACACATGAATGAA 58.779 40.909 0.00 0.00 41.43 2.57
191 192 2.861274 TCCAGTGCAACACATGAATGA 58.139 42.857 0.00 0.00 41.43 2.57
245 248 7.143340 TCAAATGAAAGCAAGACAGAAAGATG 58.857 34.615 0.00 0.00 0.00 2.90
288 291 7.014230 TGCAAAATCTAATAATTCAGGGCTACC 59.986 37.037 0.00 0.00 0.00 3.18
289 292 7.940850 TGCAAAATCTAATAATTCAGGGCTAC 58.059 34.615 0.00 0.00 0.00 3.58
290 293 7.255590 GCTGCAAAATCTAATAATTCAGGGCTA 60.256 37.037 0.00 0.00 0.00 3.93
291 294 6.462067 GCTGCAAAATCTAATAATTCAGGGCT 60.462 38.462 0.00 0.00 0.00 5.19
292 295 5.693555 GCTGCAAAATCTAATAATTCAGGGC 59.306 40.000 0.00 0.00 0.00 5.19
293 296 6.808829 TGCTGCAAAATCTAATAATTCAGGG 58.191 36.000 0.00 0.00 0.00 4.45
294 297 7.095774 GCATGCTGCAAAATCTAATAATTCAGG 60.096 37.037 11.37 0.00 44.26 3.86
295 298 7.784176 GCATGCTGCAAAATCTAATAATTCAG 58.216 34.615 11.37 0.00 44.26 3.02
296 299 7.703298 GCATGCTGCAAAATCTAATAATTCA 57.297 32.000 11.37 0.00 44.26 2.57
312 315 1.377725 ACTACTGTGGGCATGCTGC 60.378 57.895 18.92 8.59 44.08 5.25
313 316 1.651240 GCACTACTGTGGGCATGCTG 61.651 60.000 18.92 5.51 43.97 4.41
314 317 1.377725 GCACTACTGTGGGCATGCT 60.378 57.895 18.92 0.00 43.97 3.79
315 318 1.651240 CTGCACTACTGTGGGCATGC 61.651 60.000 9.90 9.90 43.97 4.06
316 319 1.028330 CCTGCACTACTGTGGGCATG 61.028 60.000 7.44 2.58 43.97 4.06
317 320 1.300963 CCTGCACTACTGTGGGCAT 59.699 57.895 7.44 0.00 43.97 4.40
318 321 1.705002 AACCTGCACTACTGTGGGCA 61.705 55.000 6.91 6.91 43.97 5.36
319 322 0.955919 GAACCTGCACTACTGTGGGC 60.956 60.000 0.00 0.00 43.97 5.36
320 323 0.396435 TGAACCTGCACTACTGTGGG 59.604 55.000 0.00 0.00 43.97 4.61
321 324 1.070758 ACTGAACCTGCACTACTGTGG 59.929 52.381 0.00 0.00 43.97 4.17
322 325 2.408050 GACTGAACCTGCACTACTGTG 58.592 52.381 0.00 0.00 46.37 3.66
323 326 1.000163 CGACTGAACCTGCACTACTGT 60.000 52.381 0.00 0.00 0.00 3.55
324 327 1.702886 CGACTGAACCTGCACTACTG 58.297 55.000 0.00 0.00 0.00 2.74
437 468 0.895530 GTTCAGGGATGAGTCGTGGA 59.104 55.000 0.00 0.00 0.00 4.02
468 499 1.203376 TGACATGGGAAGGGTGTCCTA 60.203 52.381 0.00 0.00 44.07 2.94
485 516 0.839946 AGGCCATCCATGTACCTGAC 59.160 55.000 5.01 0.00 32.94 3.51
488 519 4.079212 ACAAATTAGGCCATCCATGTACCT 60.079 41.667 5.01 4.32 36.67 3.08
592 623 6.092259 CCACTTTCTCCAAAAAGATACGTAGG 59.908 42.308 0.08 0.00 38.30 3.18
745 776 1.774639 CAGCAAGTCAAACATGTGGC 58.225 50.000 0.00 0.00 0.00 5.01
780 811 8.570470 AGCTACTATAGGATTATGGTGATAGGT 58.430 37.037 4.43 0.00 33.58 3.08
832 863 1.779157 CGAGTTGTGTGTGTAGTGTCG 59.221 52.381 0.00 0.00 0.00 4.35
843 874 5.850614 ACAGAGGTTATAAACGAGTTGTGT 58.149 37.500 0.00 0.00 0.00 3.72
848 879 8.092687 ACATACAAACAGAGGTTATAAACGAGT 58.907 33.333 0.00 0.00 35.82 4.18
899 930 4.191544 TGCCACTTGTCAGAAGTATATGC 58.808 43.478 0.00 0.00 0.00 3.14
929 960 7.759886 CAGGCAATCCATGATGATAATCAAATC 59.240 37.037 0.00 0.00 33.83 2.17
1385 1539 3.456380 AGCAAAAATGAAGCTAGGGGA 57.544 42.857 0.00 0.00 36.73 4.81
1434 1588 2.487762 TCCGGCAAGCTTTGTTGATTAG 59.512 45.455 0.00 0.00 0.00 1.73
1436 1590 1.327303 TCCGGCAAGCTTTGTTGATT 58.673 45.000 0.00 0.00 0.00 2.57
1437 1591 1.203052 CATCCGGCAAGCTTTGTTGAT 59.797 47.619 0.00 0.00 0.00 2.57
1438 1592 0.597568 CATCCGGCAAGCTTTGTTGA 59.402 50.000 0.00 0.00 0.00 3.18
1439 1593 0.388907 CCATCCGGCAAGCTTTGTTG 60.389 55.000 0.00 0.00 0.00 3.33
1440 1594 1.966762 CCATCCGGCAAGCTTTGTT 59.033 52.632 0.00 0.00 0.00 2.83
1441 1595 3.685435 CCATCCGGCAAGCTTTGT 58.315 55.556 0.00 0.00 0.00 2.83
1483 1643 1.621317 TCGACAAGGTTCCAGTGCATA 59.379 47.619 0.00 0.00 0.00 3.14
1516 1677 4.885325 TGGGTAAAACAAGGTGAAGAAGAC 59.115 41.667 0.00 0.00 0.00 3.01
1523 1684 2.243810 GGCATGGGTAAAACAAGGTGA 58.756 47.619 0.00 0.00 0.00 4.02
1525 1686 2.390225 TGGCATGGGTAAAACAAGGT 57.610 45.000 0.00 0.00 0.00 3.50
1599 1769 6.151648 CAGAAGACTGATAAATGGCAGGAAAA 59.848 38.462 0.00 0.00 46.03 2.29
1623 1793 9.219603 CTTAACAACTTCCATTCTCTGAATACA 57.780 33.333 0.00 0.00 0.00 2.29
1711 1881 1.536418 CCAGACAGACCCCAGGACA 60.536 63.158 0.00 0.00 0.00 4.02
1726 1924 1.221840 CCCCTTCACGTCCATCCAG 59.778 63.158 0.00 0.00 0.00 3.86
1738 1936 2.284515 ATTCCACGGATGCCCCCTTC 62.285 60.000 0.00 0.00 0.00 3.46
2011 2453 5.410067 CGGGTTTGCAGAACAATTCATTAT 58.590 37.500 11.93 0.00 38.31 1.28
2078 2529 9.781834 TCACAAGTATTTGAAGTTGTTAGTTTG 57.218 29.630 4.81 0.00 40.27 2.93


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

AutoCloner maintained by Alex Coulton.