Multiple sequence alignment - TraesCS1D01G070200

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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 TraesCS1D01G070200 chr1D 100.000 2747 0 0 586 3332 50967458 50970204 0.000000e+00 5073.0
1 TraesCS1D01G070200 chr1D 98.476 1050 16 0 1158 2207 51002253 51003302 0.000000e+00 1851.0
2 TraesCS1D01G070200 chr1D 97.227 577 16 0 586 1162 51000337 51000913 0.000000e+00 977.0
3 TraesCS1D01G070200 chr1D 100.000 388 0 0 1 388 50966873 50967260 0.000000e+00 717.0
4 TraesCS1D01G070200 chr1D 96.784 342 9 2 1 341 50999991 51000331 1.340000e-158 569.0
5 TraesCS1D01G070200 chr1D 97.396 192 4 1 6 196 50971073 50970882 3.210000e-85 326.0
6 TraesCS1D01G070200 chr2A 97.318 1678 42 3 604 2280 102023725 102022050 0.000000e+00 2846.0
7 TraesCS1D01G070200 chr2A 98.009 1055 20 1 2279 3332 102021830 102020776 0.000000e+00 1831.0
8 TraesCS1D01G070200 chr2A 97.015 335 6 3 6 336 102024416 102024082 8.070000e-156 560.0
9 TraesCS1D01G070200 chr1A 96.751 1693 54 1 586 2277 299540177 299541869 0.000000e+00 2820.0
10 TraesCS1D01G070200 chr1A 96.774 1054 22 3 2279 3332 299542092 299543133 0.000000e+00 1748.0
11 TraesCS1D01G070200 chr1A 97.362 872 21 2 2461 3332 97423109 97422240 0.000000e+00 1482.0
12 TraesCS1D01G070200 chr1A 94.746 590 30 1 586 1174 97423689 97423100 0.000000e+00 917.0
13 TraesCS1D01G070200 chr1A 94.086 372 14 6 6 369 97424056 97423685 2.900000e-155 558.0
14 TraesCS1D01G070200 chr1A 96.375 331 9 3 2 329 299539488 299539818 2.920000e-150 542.0
15 TraesCS1D01G070200 chr1A 95.876 194 7 1 4 196 299544002 299543809 2.500000e-81 313.0
16 TraesCS1D01G070200 chr1A 95.855 193 7 1 5 196 97421371 97421563 8.980000e-81 311.0
17 TraesCS1D01G070200 chr1A 94.231 52 3 0 604 655 299540162 299540213 2.760000e-11 80.5
18 TraesCS1D01G070200 chr3B 94.816 1331 64 3 840 2165 448751276 448752606 0.000000e+00 2071.0
19 TraesCS1D01G070200 chr3B 93.264 193 11 1 6 196 448753047 448752855 1.960000e-72 283.0
20 TraesCS1D01G070200 chr3B 88.321 137 10 1 628 764 448751135 448751265 3.440000e-35 159.0
21 TraesCS1D01G070200 chr4D 91.489 188 15 1 4 191 76028818 76028632 1.190000e-64 257.0
22 TraesCS1D01G070200 chr7A 83.182 220 12 13 132 339 533036357 533036563 9.500000e-41 178.0
23 TraesCS1D01G070200 chr5B 93.617 47 3 0 2334 2380 260237153 260237107 1.660000e-08 71.3
24 TraesCS1D01G070200 chr2B 93.617 47 3 0 2322 2368 697521724 697521770 1.660000e-08 71.3
25 TraesCS1D01G070200 chr2B 84.375 64 10 0 2315 2378 801009263 801009200 2.780000e-06 63.9
26 TraesCS1D01G070200 chr7D 91.489 47 4 0 2322 2368 552506640 552506686 7.720000e-07 65.8
27 TraesCS1D01G070200 chr6D 86.207 58 7 1 2315 2372 452314409 452314353 9.980000e-06 62.1


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 TraesCS1D01G070200 chr1D 50966873 50970204 3331 False 2895.000000 5073 100.000000 1 3332 2 chr1D.!!$F1 3331
1 TraesCS1D01G070200 chr1D 50999991 51003302 3311 False 1132.333333 1851 97.495667 1 2207 3 chr1D.!!$F2 2206
2 TraesCS1D01G070200 chr2A 102020776 102024416 3640 True 1745.666667 2846 97.447333 6 3332 3 chr2A.!!$R1 3326
3 TraesCS1D01G070200 chr1A 299539488 299543133 3645 False 1297.625000 2820 96.032750 2 3332 4 chr1A.!!$F2 3330
4 TraesCS1D01G070200 chr1A 97422240 97424056 1816 True 985.666667 1482 95.398000 6 3332 3 chr1A.!!$R2 3326
5 TraesCS1D01G070200 chr3B 448751135 448752606 1471 False 1115.000000 2071 91.568500 628 2165 2 chr3B.!!$F1 1537

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
90 91 0.320374 CCGTCTAAGTTGCACCCTCA 59.680 55.000 0.0 0.0 0.0 3.86 F
702 1137 2.184322 GCCGATCTGACGCTTCCA 59.816 61.111 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 3250 1.270199 GCATCTGCCTCATCGTCATCT 60.270 52.381 0.0 0.0 34.31 2.90 R
2626 4645 3.552604 TGCTGCCTAATTGTTTCGAAC 57.447 42.857 0.0 0.0 0.00 3.95 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
90 91 0.320374 CCGTCTAAGTTGCACCCTCA 59.680 55.000 0.00 0.00 0.00 3.86
310 316 3.551407 GCCCCGATCTCTCCCCAC 61.551 72.222 0.00 0.00 0.00 4.61
311 317 2.844839 CCCCGATCTCTCCCCACC 60.845 72.222 0.00 0.00 0.00 4.61
312 318 3.227276 CCCGATCTCTCCCCACCG 61.227 72.222 0.00 0.00 0.00 4.94
313 319 3.917760 CCGATCTCTCCCCACCGC 61.918 72.222 0.00 0.00 0.00 5.68
314 320 3.917760 CGATCTCTCCCCACCGCC 61.918 72.222 0.00 0.00 0.00 6.13
315 321 3.917760 GATCTCTCCCCACCGCCG 61.918 72.222 0.00 0.00 0.00 6.46
387 756 4.530857 CACCGCCACCCCGATCTC 62.531 72.222 0.00 0.00 0.00 2.75
702 1137 2.184322 GCCGATCTGACGCTTCCA 59.816 61.111 0.00 0.00 0.00 3.53
807 1242 3.022914 GAAGTATCGTCGCCGCCG 61.023 66.667 0.00 0.00 0.00 6.46
1074 1515 3.322541 TCAATGACGGGAAGACAGTACAA 59.677 43.478 0.00 0.00 0.00 2.41
1118 1560 6.678900 GCAATGTCCTTTTTAGATCGAGCAAT 60.679 38.462 2.38 0.00 0.00 3.56
1464 3250 2.161855 GTGCCACCAGATTGTTCATCA 58.838 47.619 0.00 0.00 33.75 3.07
1991 3777 5.917447 GGATTGCAGAAAAGTTTGAGAGTTC 59.083 40.000 0.00 0.00 0.00 3.01
2542 4549 1.813178 GCTTGGTTCAGGTTAGGAAGC 59.187 52.381 0.00 0.00 41.75 3.86
2631 4650 9.996554 ATTATATCCTGTGATAACAATGTTCGA 57.003 29.630 0.22 0.00 37.04 3.71
2632 4651 9.825109 TTATATCCTGTGATAACAATGTTCGAA 57.175 29.630 0.22 0.00 37.04 3.71
2633 4652 8.731275 ATATCCTGTGATAACAATGTTCGAAA 57.269 30.769 0.22 0.00 37.04 3.46
2634 4653 6.236017 TCCTGTGATAACAATGTTCGAAAC 57.764 37.500 0.22 0.00 0.00 2.78
2635 4654 5.760743 TCCTGTGATAACAATGTTCGAAACA 59.239 36.000 0.22 0.73 46.94 2.83
2636 4655 6.261158 TCCTGTGATAACAATGTTCGAAACAA 59.739 34.615 0.22 0.00 45.86 2.83
2637 4656 7.040755 TCCTGTGATAACAATGTTCGAAACAAT 60.041 33.333 0.22 0.00 45.86 2.71
2987 5007 8.524870 AAAAACTTATGCTTATTGTCTGCAAG 57.475 30.769 0.00 0.00 40.24 4.01
3146 5166 0.242017 GGTTGGCACAGTGATCAAGC 59.758 55.000 17.50 17.50 42.39 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 5.576447 AATTCGTCTGGTTTTGACAGTTT 57.424 34.783 0.00 0.00 37.25 2.66
314 320 3.917760 GTGGGGAGAGATCGGGCG 61.918 72.222 0.00 0.00 0.00 6.13
315 321 3.551407 GGTGGGGAGAGATCGGGC 61.551 72.222 0.00 0.00 0.00 6.13
316 322 3.227276 CGGTGGGGAGAGATCGGG 61.227 72.222 0.00 0.00 0.00 5.14
317 323 3.917760 GCGGTGGGGAGAGATCGG 61.918 72.222 0.00 0.00 0.00 4.18
318 324 3.917760 GGCGGTGGGGAGAGATCG 61.918 72.222 0.00 0.00 0.00 3.69
319 325 3.917760 CGGCGGTGGGGAGAGATC 61.918 72.222 0.00 0.00 0.00 2.75
370 739 4.530857 GAGATCGGGGTGGCGGTG 62.531 72.222 0.00 0.00 0.00 4.94
607 976 2.123854 TCGGGAGAGATCGGGGTG 60.124 66.667 0.00 0.00 0.00 4.61
702 1137 1.049289 GGATAACTGGAGGAGGCGGT 61.049 60.000 0.00 0.00 0.00 5.68
807 1242 2.485814 CTGGAAGAACTTGGCAAGCTAC 59.514 50.000 26.45 16.99 34.07 3.58
1118 1560 6.524734 TGTTGAATTCTCTGTAAGCTCAAGA 58.475 36.000 7.05 0.00 0.00 3.02
1464 3250 1.270199 GCATCTGCCTCATCGTCATCT 60.270 52.381 0.00 0.00 34.31 2.90
1991 3777 5.118990 ACCATTCTGGACTTGACATTATCG 58.881 41.667 0.00 0.00 40.96 2.92
2277 4063 8.674263 AACAACATTCAATATTCCTTTTTGCA 57.326 26.923 0.00 0.00 0.00 4.08
2542 4549 4.214980 GTTGTCCACAGAATCACAACAG 57.785 45.455 8.54 0.00 45.27 3.16
2626 4645 3.552604 TGCTGCCTAATTGTTTCGAAC 57.447 42.857 0.00 0.00 0.00 3.95
2627 4646 4.576216 TTTGCTGCCTAATTGTTTCGAA 57.424 36.364 0.00 0.00 0.00 3.71
2628 4647 4.782019 ATTTGCTGCCTAATTGTTTCGA 57.218 36.364 0.00 0.00 0.00 3.71
2629 4648 6.751425 TCATAATTTGCTGCCTAATTGTTTCG 59.249 34.615 15.73 3.45 30.84 3.46
2630 4649 8.652810 ATCATAATTTGCTGCCTAATTGTTTC 57.347 30.769 15.73 0.00 30.84 2.78
2631 4650 8.259411 TGATCATAATTTGCTGCCTAATTGTTT 58.741 29.630 15.73 4.25 30.84 2.83
2632 4651 7.784037 TGATCATAATTTGCTGCCTAATTGTT 58.216 30.769 15.73 5.16 30.84 2.83
2633 4652 7.350744 TGATCATAATTTGCTGCCTAATTGT 57.649 32.000 15.73 9.29 30.84 2.71
2634 4653 6.866770 CCTGATCATAATTTGCTGCCTAATTG 59.133 38.462 15.73 5.50 30.84 2.32
2635 4654 6.779049 TCCTGATCATAATTTGCTGCCTAATT 59.221 34.615 12.45 12.45 32.53 1.40
2636 4655 6.309357 TCCTGATCATAATTTGCTGCCTAAT 58.691 36.000 0.00 0.00 0.00 1.73
2637 4656 5.693961 TCCTGATCATAATTTGCTGCCTAA 58.306 37.500 0.00 0.00 0.00 2.69
2828 4847 5.955959 ACCTACAACTACATGTCCTGTCATA 59.044 40.000 0.00 0.00 39.39 2.15
3163 5183 5.704888 CAAGTTGTTTTGTTGTGTCCACTA 58.295 37.500 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.