Multiple sequence alignment - TraesCS2B01G460500

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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 TraesCS2B01G460500 chr2B 100.000 2318 0 0 1 2318 654547184 654544867 0.000000e+00 4281
1 TraesCS2B01G460500 chr2B 88.742 1057 89 13 662 1701 654649573 654648530 0.000000e+00 1266
2 TraesCS2B01G460500 chr2B 88.531 1055 95 11 662 1701 654727155 654726112 0.000000e+00 1254
3 TraesCS2B01G460500 chr2B 93.220 826 45 7 3 824 654434465 654433647 0.000000e+00 1205
4 TraesCS2B01G460500 chr2B 85.185 1053 134 15 832 1872 654422413 654421371 0.000000e+00 1061
5 TraesCS2B01G460500 chr2B 89.720 428 41 2 1891 2316 654725558 654725132 5.630000e-151 544
6 TraesCS2B01G460500 chr2B 89.486 428 42 2 1891 2316 654679252 654678826 2.620000e-149 538
7 TraesCS2B01G460500 chr2B 89.252 428 43 2 1891 2316 654647976 654647550 1.220000e-147 532
8 TraesCS2B01G460500 chr2B 90.237 379 34 2 1891 2267 654698100 654697723 2.070000e-135 492
9 TraesCS2B01G460500 chr2B 86.935 199 22 2 1699 1893 654648448 654648250 1.080000e-53 220
10 TraesCS2B01G460500 chr2D 93.065 1240 72 7 662 1892 547791594 547790360 0.000000e+00 1801
11 TraesCS2B01G460500 chr2D 86.600 1403 145 21 505 1892 547775514 547774140 0.000000e+00 1509
12 TraesCS2B01G460500 chr2D 91.788 548 36 2 1355 1893 547899934 547899387 0.000000e+00 754
13 TraesCS2B01G460500 chr2D 96.262 428 16 0 1891 2318 547790090 547789663 0.000000e+00 702
14 TraesCS2B01G460500 chr2D 88.492 504 51 4 1 503 381719879 381720376 9.160000e-169 603
15 TraesCS2B01G460500 chr2D 90.845 426 38 1 1891 2316 547899117 547898693 9.290000e-159 569
16 TraesCS2B01G460500 chr2A 90.716 1271 95 8 640 1893 691139913 691141177 0.000000e+00 1672
17 TraesCS2B01G460500 chr2A 87.294 1393 144 17 505 1872 691168583 691169967 0.000000e+00 1561
18 TraesCS2B01G460500 chr2A 90.198 959 82 7 653 1602 691119616 691120571 0.000000e+00 1240
19 TraesCS2B01G460500 chr2A 84.954 1203 154 19 706 1892 691115812 691117003 0.000000e+00 1194
20 TraesCS2B01G460500 chr2A 94.601 426 17 1 1891 2316 691141454 691141873 0.000000e+00 654
21 TraesCS2B01G460500 chr2A 84.328 536 73 10 1364 1892 691134200 691134731 4.420000e-142 514
22 TraesCS2B01G460500 chr2A 90.190 316 28 2 1580 1893 691120576 691120890 2.140000e-110 409
23 TraesCS2B01G460500 chrUn 88.931 1057 87 13 662 1701 248123008 248121965 0.000000e+00 1277
24 TraesCS2B01G460500 chrUn 89.720 428 41 2 1891 2316 422207141 422206715 5.630000e-151 544
25 TraesCS2B01G460500 chrUn 89.486 428 42 2 1891 2316 422316521 422316095 2.620000e-149 538
26 TraesCS2B01G460500 chr5A 90.316 506 44 3 1 506 245967044 245966544 0.000000e+00 658
27 TraesCS2B01G460500 chr5A 88.802 509 57 0 1 509 41130568 41130060 1.960000e-175 625
28 TraesCS2B01G460500 chr4D 89.662 503 49 3 1 502 442243509 442244009 2.510000e-179 638
29 TraesCS2B01G460500 chr1D 89.744 507 41 5 1 506 338925729 338925233 2.510000e-179 638
30 TraesCS2B01G460500 chr6D 89.600 500 52 0 3 502 417697403 417696904 9.030000e-179 636
31 TraesCS2B01G460500 chr6D 88.270 503 55 2 1 503 391684690 391684192 1.190000e-167 599
32 TraesCS2B01G460500 chr7A 89.484 504 49 4 2 504 5008906 5009406 3.250000e-178 634


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 TraesCS2B01G460500 chr2B 654544867 654547184 2317 True 4281.000000 4281 100.000000 1 2318 1 chr2B.!!$R3 2317
1 TraesCS2B01G460500 chr2B 654433647 654434465 818 True 1205.000000 1205 93.220000 3 824 1 chr2B.!!$R2 821
2 TraesCS2B01G460500 chr2B 654421371 654422413 1042 True 1061.000000 1061 85.185000 832 1872 1 chr2B.!!$R1 1040
3 TraesCS2B01G460500 chr2B 654725132 654727155 2023 True 899.000000 1254 89.125500 662 2316 2 chr2B.!!$R7 1654
4 TraesCS2B01G460500 chr2B 654647550 654649573 2023 True 672.666667 1266 88.309667 662 2316 3 chr2B.!!$R6 1654
5 TraesCS2B01G460500 chr2D 547774140 547775514 1374 True 1509.000000 1509 86.600000 505 1892 1 chr2D.!!$R1 1387
6 TraesCS2B01G460500 chr2D 547789663 547791594 1931 True 1251.500000 1801 94.663500 662 2318 2 chr2D.!!$R2 1656
7 TraesCS2B01G460500 chr2D 547898693 547899934 1241 True 661.500000 754 91.316500 1355 2316 2 chr2D.!!$R3 961
8 TraesCS2B01G460500 chr2A 691168583 691169967 1384 False 1561.000000 1561 87.294000 505 1872 1 chr2A.!!$F2 1367
9 TraesCS2B01G460500 chr2A 691139913 691141873 1960 False 1163.000000 1672 92.658500 640 2316 2 chr2A.!!$F4 1676
10 TraesCS2B01G460500 chr2A 691115812 691120890 5078 False 947.666667 1240 88.447333 653 1893 3 chr2A.!!$F3 1240
11 TraesCS2B01G460500 chr2A 691134200 691134731 531 False 514.000000 514 84.328000 1364 1892 1 chr2A.!!$F1 528
12 TraesCS2B01G460500 chrUn 248121965 248123008 1043 True 1277.000000 1277 88.931000 662 1701 1 chrUn.!!$R1 1039
13 TraesCS2B01G460500 chr5A 245966544 245967044 500 True 658.000000 658 90.316000 1 506 1 chr5A.!!$R2 505
14 TraesCS2B01G460500 chr5A 41130060 41130568 508 True 625.000000 625 88.802000 1 509 1 chr5A.!!$R1 508
15 TraesCS2B01G460500 chr4D 442243509 442244009 500 False 638.000000 638 89.662000 1 502 1 chr4D.!!$F1 501
16 TraesCS2B01G460500 chr7A 5008906 5009406 500 False 634.000000 634 89.484000 2 504 1 chr7A.!!$F1 502

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
825 3985 0.399833 TACATGTGGGCAGCACTTCA 59.6 50.0 9.11 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 5829 1.573108 TCTGATGGTTCCCAGTCCTC 58.427 55.0 0.0 0.0 36.75 3.71 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
82 83 3.691342 CGGGGTCTCGCTGTTGGA 61.691 66.667 0.00 0.00 0.00 3.53
152 153 1.352404 GCGTCGACGACAGCTAGAT 59.648 57.895 39.74 0.00 43.02 1.98
181 182 2.806244 GTTTGATGTGTCGGTACAGCTT 59.194 45.455 9.05 0.00 37.81 3.74
182 183 2.363788 TGATGTGTCGGTACAGCTTC 57.636 50.000 9.05 0.00 37.81 3.86
256 257 3.175710 GGATGCCCCATACCCGGT 61.176 66.667 0.00 0.00 34.14 5.28
322 324 4.081087 ACTGCGAGGTCTGTTTGGTATTAT 60.081 41.667 0.00 0.00 0.00 1.28
355 362 3.523157 TCAGCATCCCTTTATCAACTGGA 59.477 43.478 0.00 0.00 0.00 3.86
371 378 1.336440 CTGGATGAGAGTAGCGACAGG 59.664 57.143 0.00 0.00 0.00 4.00
529 538 9.829507 AAATCAACTGGTCAATTAAACAATTCA 57.170 25.926 0.00 0.00 0.00 2.57
533 542 9.258826 CAACTGGTCAATTAAACAATTCAATCA 57.741 29.630 0.00 0.00 0.00 2.57
825 3985 0.399833 TACATGTGGGCAGCACTTCA 59.600 50.000 9.11 0.00 0.00 3.02
849 4009 2.744202 CGCCTAAGTTCTTGCTTGATGT 59.256 45.455 0.00 0.00 0.00 3.06
946 4114 9.990868 ACATTCCCAAAGTAAAATCTAGGTAAT 57.009 29.630 0.00 0.00 0.00 1.89
1048 4217 2.443887 ATTGTTGCTTGTCATGGCAC 57.556 45.000 0.00 0.00 38.23 5.01
1055 4224 0.962356 CTTGTCATGGCACTGTCCCC 60.962 60.000 0.00 0.00 0.00 4.81
1109 4278 4.534168 GGCATGTCGAATGATGAATTCAG 58.466 43.478 14.54 0.00 44.34 3.02
1160 4329 2.033755 CGACAGAGAGTCCGTCGGT 61.034 63.158 11.88 2.84 46.59 4.69
1557 4766 7.845037 TGCATGTTGTCCCATGAAATTAATAA 58.155 30.769 5.39 0.00 43.99 1.40
1629 4868 7.739498 ACACCTAAATGTCGATTACAACTTT 57.261 32.000 0.00 0.00 42.70 2.66
1886 5222 5.520288 ACATATAGCACAACAGATCGTTCAC 59.480 40.000 0.00 0.00 34.86 3.18
2049 5666 7.996002 CACACAATGTTTCTATTTAAGTGTGC 58.004 34.615 0.00 0.00 44.87 4.57
2113 5730 4.017808 GACCAAGGAGTAGAGCTTAGTCA 58.982 47.826 10.79 0.00 0.00 3.41
2139 5756 2.463752 AGGTTCATTTCAGCATGCCAT 58.536 42.857 15.66 0.00 34.76 4.40
2146 5763 6.185852 TCATTTCAGCATGCCATATATTCG 57.814 37.500 15.66 0.00 34.76 3.34
2190 5807 4.332268 TGGTTTGAATTGCTTTTTGAGTGC 59.668 37.500 0.00 0.00 0.00 4.40
2212 5829 2.792196 CGTTGAAATCCACATGCATCCG 60.792 50.000 0.00 0.00 0.00 4.18
2294 5911 1.545211 CCAAGATGGCCATGGGGAT 59.455 57.895 26.56 0.00 35.59 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.000429 TGTCGACATGTCAGATGCAG 58.000 50.000 24.93 7.43 0.00 4.41
82 83 0.944311 GCTCGTCCATCAACACACGT 60.944 55.000 0.00 0.00 33.89 4.49
152 153 1.234821 GACACATCAAACTTGCCCGA 58.765 50.000 0.00 0.00 0.00 5.14
181 182 0.617935 TGCCACCAATCCATCTTCGA 59.382 50.000 0.00 0.00 0.00 3.71
182 183 1.019673 CTGCCACCAATCCATCTTCG 58.980 55.000 0.00 0.00 0.00 3.79
241 242 1.846124 CCTACCGGGTATGGGGCAT 60.846 63.158 6.32 0.00 0.00 4.40
256 257 3.176297 CCCCAACCAAGCCACCTA 58.824 61.111 0.00 0.00 0.00 3.08
288 289 2.066262 ACCTCGCAGTCAAACATAACG 58.934 47.619 0.00 0.00 0.00 3.18
322 324 1.630369 GGGATGCTGATAGTATGGGCA 59.370 52.381 8.47 8.47 37.32 5.36
355 362 1.840737 ACACCTGTCGCTACTCTCAT 58.159 50.000 0.00 0.00 0.00 2.90
358 365 0.038159 GCAACACCTGTCGCTACTCT 60.038 55.000 0.00 0.00 0.00 3.24
371 378 4.278956 CCACCGTCTAGGCAACAC 57.721 61.111 0.00 0.00 46.52 3.32
456 464 2.435693 GGCCTCTACATCTGGGCGT 61.436 63.158 0.00 0.00 44.91 5.68
529 538 5.589855 TGGCTCGTGATAACATTTGATGATT 59.410 36.000 0.00 0.00 0.00 2.57
533 542 5.371526 AGATGGCTCGTGATAACATTTGAT 58.628 37.500 0.00 0.00 0.00 2.57
610 635 6.757478 TCAGTCGTTCGCAATGGTATAAATTA 59.243 34.615 0.00 0.00 0.00 1.40
647 672 4.201657 TCCATAATGCAACATGAGGAGTG 58.798 43.478 11.42 0.00 0.00 3.51
825 3985 0.602905 AAGCAAGAACTTAGGCGCGT 60.603 50.000 8.43 8.08 0.00 6.01
849 4009 7.010091 CGCTATGTTCATGAAGTGTGTGTTATA 59.990 37.037 8.80 0.00 0.00 0.98
946 4114 4.444876 GGATGGCTAGCTGAGATTTTGGTA 60.445 45.833 15.72 0.00 0.00 3.25
1048 4217 3.376935 CTAGTGCAGCGGGGGACAG 62.377 68.421 0.00 0.00 0.00 3.51
1055 4224 2.172483 AACACCCTCTAGTGCAGCGG 62.172 60.000 0.00 0.00 41.67 5.52
1557 4766 5.992829 TGACACGAACAACACCAATATAAGT 59.007 36.000 0.00 0.00 0.00 2.24
1629 4868 3.252554 AGGTGTGGCCAATAGGAAAAA 57.747 42.857 7.24 0.00 40.61 1.94
1804 5130 2.814341 CAGAGAGGTGCTGCAGCG 60.814 66.667 32.11 12.67 45.83 5.18
2049 5666 2.854777 CGGATTGTTGCTCTACTCTTCG 59.145 50.000 0.00 0.00 0.00 3.79
2113 5730 4.441079 GCATGCTGAAATGAACCTAGCAAT 60.441 41.667 11.37 0.00 46.11 3.56
2139 5756 9.414295 GTACAATACTTGTGTATGCCGAATATA 57.586 33.333 2.85 0.00 45.03 0.86
2190 5807 2.480073 GGATGCATGTGGATTTCAACGG 60.480 50.000 2.46 0.00 0.00 4.44
2212 5829 1.573108 TCTGATGGTTCCCAGTCCTC 58.427 55.000 0.00 0.00 36.75 3.71


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

AutoCloner maintained by Alex Coulton.