Multiple sequence alignment - TraesCS5A01G010300

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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 TraesCS5A01G010300 chr5A 100.000 3312 0 0 1 3312 6726654 6723343 0.000000e+00 6117
1 TraesCS5A01G010300 chr5A 99.776 892 2 0 2421 3312 653383076 653382185 0.000000e+00 1637
2 TraesCS5A01G010300 chr5A 89.729 701 59 9 961 1656 6675832 6675140 0.000000e+00 883
3 TraesCS5A01G010300 chr5A 91.036 357 26 6 1961 2312 6669797 6669442 8.320000e-131 477
4 TraesCS5A01G010300 chr5A 99.526 211 1 0 2423 2633 653377899 653377689 5.180000e-103 385
5 TraesCS5A01G010300 chr5A 99.519 208 1 0 2423 2630 6719058 6718851 2.410000e-101 379
6 TraesCS5A01G010300 chr5D 92.560 2258 95 23 212 2422 8548370 8546139 0.000000e+00 3171
7 TraesCS5A01G010300 chr5D 90.843 1376 115 9 948 2312 8497077 8495702 0.000000e+00 1832
8 TraesCS5A01G010300 chr5B 91.939 1650 99 17 786 2418 8935077 8933445 0.000000e+00 2279
9 TraesCS5A01G010300 chr5B 91.329 692 59 1 2622 3312 139349178 139348487 0.000000e+00 944
10 TraesCS5A01G010300 chr5B 81.852 799 61 42 1 741 260672449 260671677 2.200000e-166 595
11 TraesCS5A01G010300 chr5B 91.506 259 21 1 2160 2418 8902626 8902369 4.070000e-94 355
12 TraesCS5A01G010300 chr5B 92.032 251 17 2 2062 2312 8900277 8900030 1.890000e-92 350
13 TraesCS5A01G010300 chr1B 98.423 888 14 0 2425 3312 588526297 588525410 0.000000e+00 1563
14 TraesCS5A01G010300 chr1B 98.104 211 4 0 2425 2635 588518156 588517946 5.220000e-98 368
15 TraesCS5A01G010300 chr2B 99.399 832 4 1 2482 3312 134555610 134556441 0.000000e+00 1507
16 TraesCS5A01G010300 chr2B 99.454 183 1 0 2425 2607 134568137 134568319 1.900000e-87 333
17 TraesCS5A01G010300 chr4A 91.474 692 58 1 2622 3312 609810481 609811172 0.000000e+00 950
18 TraesCS5A01G010300 chr4A 91.474 692 58 1 2622 3312 618666150 618666841 0.000000e+00 950
19 TraesCS5A01G010300 chr4A 91.329 692 59 1 2622 3312 585673037 585672346 0.000000e+00 944
20 TraesCS5A01G010300 chr6B 91.329 692 59 1 2622 3312 296791976 296791285 0.000000e+00 944
21 TraesCS5A01G010300 chr6B 91.185 692 60 1 2622 3312 159157140 159157831 0.000000e+00 939
22 TraesCS5A01G010300 chr1A 78.631 482 59 31 984 1456 257566241 257565795 2.520000e-71 279
23 TraesCS5A01G010300 chr1D 81.818 319 39 13 988 1302 203311325 203311022 1.970000e-62 250


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 TraesCS5A01G010300 chr5A 6723343 6726654 3311 True 6117.0 6117 100.000 1 3312 1 chr5A.!!$R4 3311
1 TraesCS5A01G010300 chr5A 653382185 653383076 891 True 1637.0 1637 99.776 2421 3312 1 chr5A.!!$R6 891
2 TraesCS5A01G010300 chr5A 6675140 6675832 692 True 883.0 883 89.729 961 1656 1 chr5A.!!$R2 695
3 TraesCS5A01G010300 chr5D 8546139 8548370 2231 True 3171.0 3171 92.560 212 2422 1 chr5D.!!$R2 2210
4 TraesCS5A01G010300 chr5D 8495702 8497077 1375 True 1832.0 1832 90.843 948 2312 1 chr5D.!!$R1 1364
5 TraesCS5A01G010300 chr5B 8933445 8935077 1632 True 2279.0 2279 91.939 786 2418 1 chr5B.!!$R1 1632
6 TraesCS5A01G010300 chr5B 139348487 139349178 691 True 944.0 944 91.329 2622 3312 1 chr5B.!!$R2 690
7 TraesCS5A01G010300 chr5B 260671677 260672449 772 True 595.0 595 81.852 1 741 1 chr5B.!!$R3 740
8 TraesCS5A01G010300 chr5B 8900030 8902626 2596 True 352.5 355 91.769 2062 2418 2 chr5B.!!$R4 356
9 TraesCS5A01G010300 chr1B 588525410 588526297 887 True 1563.0 1563 98.423 2425 3312 1 chr1B.!!$R2 887
10 TraesCS5A01G010300 chr2B 134555610 134556441 831 False 1507.0 1507 99.399 2482 3312 1 chr2B.!!$F1 830
11 TraesCS5A01G010300 chr4A 609810481 609811172 691 False 950.0 950 91.474 2622 3312 1 chr4A.!!$F1 690
12 TraesCS5A01G010300 chr4A 618666150 618666841 691 False 950.0 950 91.474 2622 3312 1 chr4A.!!$F2 690
13 TraesCS5A01G010300 chr4A 585672346 585673037 691 True 944.0 944 91.329 2622 3312 1 chr4A.!!$R1 690
14 TraesCS5A01G010300 chr6B 296791285 296791976 691 True 944.0 944 91.329 2622 3312 1 chr6B.!!$R1 690
15 TraesCS5A01G010300 chr6B 159157140 159157831 691 False 939.0 939 91.185 2622 3312 1 chr6B.!!$F1 690

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
467 513 0.036388 TAAACCGGGAGCTCTGCTTG 60.036 55.000 14.64 0.89 39.88 4.01 F
670 723 0.397941 TCCTGCCAACTCTGGTTCAG 59.602 55.000 0.00 0.00 45.53 3.02 F
738 812 1.066430 TGACCGAATGTTCAGGCCTAC 60.066 52.381 3.98 0.46 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 2016 1.451651 GCGGTTTTGAACAATCTTGCG 59.548 47.619 0.00 0.0 0.00 4.85 R
2173 2462 2.444624 CGAGTCCATGTTGGCGTCG 61.445 63.158 0.00 0.0 37.47 5.12 R
2418 2710 4.479158 ACCAAAAGGCCAGACAAAAGATA 58.521 39.130 5.01 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
46 47 0.527565 CGCTTGCTAATTTGGCCTGT 59.472 50.000 3.32 0.00 0.00 4.00
58 59 1.078143 GGCCTGTCTTCTGCGGATT 60.078 57.895 0.00 0.00 0.00 3.01
80 81 2.897326 GTGTGGAGTTTTTAGGGGCATT 59.103 45.455 0.00 0.00 0.00 3.56
84 85 4.082190 GTGGAGTTTTTAGGGGCATTTCTC 60.082 45.833 0.00 0.00 0.00 2.87
94 95 3.093278 CATTTCTCGACCTGCGGC 58.907 61.111 0.00 0.00 41.33 6.53
110 111 1.671328 GCGGCTAATCTTTCAGGAACC 59.329 52.381 0.00 0.00 0.00 3.62
130 131 3.616379 ACCACGAAATTTTGTTGCTGTTG 59.384 39.130 8.42 0.00 0.00 3.33
146 147 4.022155 TGCTGTTGTGCATTACATGAATGT 60.022 37.500 0.00 0.95 45.88 2.71
157 158 6.722301 CATTACATGAATGTGCAGTTCTAGG 58.278 40.000 0.00 5.37 41.89 3.02
173 174 3.484407 TCTAGGTGGATTACGGCTAGTC 58.516 50.000 0.00 0.00 0.00 2.59
188 193 2.810400 GCTAGTCTTCAACAGCCACCAA 60.810 50.000 0.00 0.00 0.00 3.67
205 210 4.157656 CCACCAAGAAACAAGTCTTTGTCA 59.842 41.667 0.00 0.00 46.54 3.58
209 214 5.342433 CAAGAAACAAGTCTTTGTCATGCA 58.658 37.500 0.00 0.00 46.54 3.96
211 216 3.338818 AACAAGTCTTTGTCATGCACG 57.661 42.857 0.00 0.00 46.54 5.34
214 238 0.588252 AGTCTTTGTCATGCACGCAC 59.412 50.000 0.00 0.00 0.00 5.34
252 276 1.484653 AGTTATGCCGCATAGGTCACA 59.515 47.619 12.73 0.00 43.70 3.58
273 297 3.312421 CAGAGAAGCGAAACTGAAAACCA 59.688 43.478 0.00 0.00 32.90 3.67
367 391 2.747460 CGTGCCCTGTGATGTGGG 60.747 66.667 0.00 0.00 46.00 4.61
433 478 1.766069 GTCGCAATTCGCTTGGTTTT 58.234 45.000 0.69 0.00 39.08 2.43
449 494 5.723672 TGGTTTTGTTTCTGTGGTGTTTA 57.276 34.783 0.00 0.00 0.00 2.01
466 512 0.690762 TTAAACCGGGAGCTCTGCTT 59.309 50.000 14.64 3.32 39.88 3.91
467 513 0.036388 TAAACCGGGAGCTCTGCTTG 60.036 55.000 14.64 0.89 39.88 4.01
539 592 3.706594 GAGACCTACTCATCACATGGGAA 59.293 47.826 0.00 0.00 44.36 3.97
565 618 3.053831 TCTCAAGGACCGAAAATCCAC 57.946 47.619 0.00 0.00 38.86 4.02
607 660 6.146837 CGGTATGAAGAATCTTAGCCATCAAG 59.853 42.308 0.00 0.00 32.80 3.02
610 663 9.202273 GTATGAAGAATCTTAGCCATCAAGTAG 57.798 37.037 0.00 0.00 0.00 2.57
611 664 6.586344 TGAAGAATCTTAGCCATCAAGTAGG 58.414 40.000 0.00 0.00 0.00 3.18
623 676 4.154918 CCATCAAGTAGGCAAACAGAGTTC 59.845 45.833 0.00 0.00 0.00 3.01
624 677 4.415881 TCAAGTAGGCAAACAGAGTTCA 57.584 40.909 0.00 0.00 0.00 3.18
625 678 4.776349 TCAAGTAGGCAAACAGAGTTCAA 58.224 39.130 0.00 0.00 0.00 2.69
627 680 5.296780 TCAAGTAGGCAAACAGAGTTCAAAG 59.703 40.000 0.00 0.00 0.00 2.77
629 682 4.576463 AGTAGGCAAACAGAGTTCAAAGTG 59.424 41.667 0.00 0.00 0.00 3.16
642 695 2.023673 TCAAAGTGTTGTTGCCTCAGG 58.976 47.619 0.00 0.00 36.07 3.86
646 699 2.456577 AGTGTTGTTGCCTCAGGTTTT 58.543 42.857 0.00 0.00 0.00 2.43
668 721 2.206576 ATTCCTGCCAACTCTGGTTC 57.793 50.000 0.00 0.00 45.53 3.62
670 723 0.397941 TCCTGCCAACTCTGGTTCAG 59.602 55.000 0.00 0.00 45.53 3.02
688 762 5.805994 GGTTCAGAGAGTATACCGAAACTTG 59.194 44.000 0.00 0.00 0.00 3.16
738 812 1.066430 TGACCGAATGTTCAGGCCTAC 60.066 52.381 3.98 0.46 0.00 3.18
752 826 9.715119 TGTTCAGGCCTACTCATATATATGTAT 57.285 33.333 19.78 12.68 35.26 2.29
783 857 3.019564 ACCAGTTCTGCAATTCATAGGC 58.980 45.455 0.00 0.00 0.00 3.93
784 858 3.285484 CCAGTTCTGCAATTCATAGGCT 58.715 45.455 0.00 0.00 0.00 4.58
821 897 8.504005 TCGTAATTTCTGTTGATCTTTTCCTTC 58.496 33.333 0.00 0.00 0.00 3.46
923 999 8.552034 CCTCTTATGTTTCGAATAATTCCACTC 58.448 37.037 0.00 0.00 0.00 3.51
968 1044 2.464459 CGCTGCATCGAAACCCTCC 61.464 63.158 3.33 0.00 0.00 4.30
1073 1149 1.528824 GCTTCCCATAGCTGGCTCA 59.471 57.895 0.00 0.00 41.64 4.26
1118 1194 4.726416 CTTGTCAACCGATTGATTCTTGG 58.274 43.478 0.00 0.00 46.43 3.61
1662 1744 6.525121 TGTATTATGCTTACGAGATGCAAC 57.475 37.500 0.00 0.00 41.20 4.17
1828 1914 8.912988 TGAAAACTTGAGACAATATGAAAAGGT 58.087 29.630 0.00 0.00 0.00 3.50
1929 2016 5.144100 TCAGAGGAGGTGAATCTCTATTCC 58.856 45.833 0.00 0.00 40.78 3.01
2006 2096 8.934023 TCCTTTAACCTGAGTGTTCAATTTAT 57.066 30.769 0.00 0.00 31.69 1.40
2137 2426 1.209747 GAGTTCATAAAGAGCGGGGGT 59.790 52.381 0.00 0.00 31.99 4.95
2170 2459 3.272847 ATCGGGCCCAAGGGGTTT 61.273 61.111 24.92 0.00 46.51 3.27
2418 2710 8.116026 ACATTTTCCTGGGATAAAGTTAGATGT 58.884 33.333 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.497991 TTAGCAAGCGCCATCGATAC 58.502 50.000 2.29 0.00 39.83 2.24
46 47 0.684535 TCCACACAATCCGCAGAAGA 59.315 50.000 0.00 0.00 0.00 2.87
58 59 1.215673 TGCCCCTAAAAACTCCACACA 59.784 47.619 0.00 0.00 0.00 3.72
84 85 3.618760 CTGAAAGATTAGCCGCAGGTCG 61.619 54.545 0.00 0.00 46.36 4.79
94 95 6.743575 ATTTCGTGGTTCCTGAAAGATTAG 57.256 37.500 12.46 0.00 35.31 1.73
110 111 4.567127 CACAACAGCAACAAAATTTCGTG 58.433 39.130 0.00 0.00 0.00 4.35
146 147 2.167693 CCGTAATCCACCTAGAACTGCA 59.832 50.000 0.00 0.00 0.00 4.41
157 158 3.795623 TGAAGACTAGCCGTAATCCAC 57.204 47.619 0.00 0.00 0.00 4.02
173 174 2.426738 TGTTTCTTGGTGGCTGTTGAAG 59.573 45.455 0.00 0.00 0.00 3.02
188 193 4.496341 CGTGCATGACAAAGACTTGTTTCT 60.496 41.667 0.00 0.00 45.98 2.52
252 276 3.541632 TGGTTTTCAGTTTCGCTTCTCT 58.458 40.909 0.00 0.00 0.00 3.10
273 297 7.439056 GCCTTTTATGCATATAACAGCACAATT 59.561 33.333 7.36 0.00 44.49 2.32
421 466 3.506810 CACAGAAACAAAACCAAGCGAA 58.493 40.909 0.00 0.00 0.00 4.70
433 478 3.128938 CCGGTTTAAACACCACAGAAACA 59.871 43.478 19.57 0.00 36.49 2.83
449 494 1.302832 CAAGCAGAGCTCCCGGTTT 60.303 57.895 10.93 1.91 38.25 3.27
466 512 4.459337 CGATAGAGTACCATGGTGCTATCA 59.541 45.833 34.17 25.26 40.98 2.15
467 513 4.459685 ACGATAGAGTACCATGGTGCTATC 59.540 45.833 32.30 31.23 40.98 2.08
534 587 4.226394 TCGGTCCTTGAGAAATAATTCCCA 59.774 41.667 0.00 0.00 36.12 4.37
535 588 4.777463 TCGGTCCTTGAGAAATAATTCCC 58.223 43.478 0.00 0.00 36.12 3.97
539 592 6.889722 TGGATTTTCGGTCCTTGAGAAATAAT 59.110 34.615 0.00 0.00 36.68 1.28
607 660 4.335594 ACACTTTGAACTCTGTTTGCCTAC 59.664 41.667 0.00 0.00 0.00 3.18
610 663 3.782889 ACACTTTGAACTCTGTTTGCC 57.217 42.857 0.00 0.00 0.00 4.52
611 664 4.485163 ACAACACTTTGAACTCTGTTTGC 58.515 39.130 0.00 0.00 36.48 3.68
620 673 3.438360 CTGAGGCAACAACACTTTGAAC 58.562 45.455 0.00 0.00 36.48 3.18
623 676 1.750778 ACCTGAGGCAACAACACTTTG 59.249 47.619 0.00 0.00 38.83 2.77
624 677 2.143876 ACCTGAGGCAACAACACTTT 57.856 45.000 0.00 0.00 41.41 2.66
625 678 2.143876 AACCTGAGGCAACAACACTT 57.856 45.000 0.00 0.00 41.41 3.16
627 680 2.165437 TCAAAACCTGAGGCAACAACAC 59.835 45.455 0.00 0.00 41.41 3.32
629 682 3.518634 TTCAAAACCTGAGGCAACAAC 57.481 42.857 0.00 0.00 34.81 3.32
642 695 4.301628 CAGAGTTGGCAGGAATTCAAAAC 58.698 43.478 7.93 4.18 0.00 2.43
646 699 2.205022 CCAGAGTTGGCAGGAATTCA 57.795 50.000 7.93 0.00 37.73 2.57
668 721 6.197364 AGTCAAGTTTCGGTATACTCTCTG 57.803 41.667 2.25 0.00 0.00 3.35
670 723 9.583765 AAATAAGTCAAGTTTCGGTATACTCTC 57.416 33.333 2.25 0.00 0.00 3.20
752 826 2.102757 TGCAGAACTGGTTACGGTGTTA 59.897 45.455 3.99 0.00 36.03 2.41
756 830 2.561478 ATTGCAGAACTGGTTACGGT 57.439 45.000 3.99 0.00 37.99 4.83
808 882 9.520515 AGCATAGTAAAAAGAAGGAAAAGATCA 57.479 29.630 0.00 0.00 0.00 2.92
821 897 5.412594 TGCCTGAACTGAGCATAGTAAAAAG 59.587 40.000 0.00 0.00 0.00 2.27
968 1044 3.480470 TGCAGGAAAGGAGAAAAGTGAG 58.520 45.455 0.00 0.00 0.00 3.51
1073 1149 4.161377 GCCAAAGAGAACTGTAGAGAGGAT 59.839 45.833 0.00 0.00 0.00 3.24
1118 1194 6.551385 AATCAACAAGAACAGAGACATCAC 57.449 37.500 0.00 0.00 0.00 3.06
1306 1382 8.364142 CAAGAAATAAATTAAAGGTCACCACCA 58.636 33.333 0.00 0.00 46.68 4.17
1652 1734 1.728971 GGTTGTCTGAGTTGCATCTCG 59.271 52.381 17.72 13.05 37.28 4.04
1662 1744 5.630415 TCCCCATATAAAGGTTGTCTGAG 57.370 43.478 0.00 0.00 0.00 3.35
1929 2016 1.451651 GCGGTTTTGAACAATCTTGCG 59.548 47.619 0.00 0.00 0.00 4.85
2006 2096 5.152623 ACAGAGCTTTGAGCAACAGTATA 57.847 39.130 11.85 0.00 45.56 1.47
2007 2097 3.999663 GACAGAGCTTTGAGCAACAGTAT 59.000 43.478 11.85 0.00 45.56 2.12
2170 2459 4.321966 TCCATGTTGGCGTCGGCA 62.322 61.111 18.58 18.58 42.47 5.69
2173 2462 2.444624 CGAGTCCATGTTGGCGTCG 61.445 63.158 0.00 0.00 37.47 5.12
2380 2669 6.044404 TCCCAGGAAAATGTTTCTTCTACTCT 59.956 38.462 0.00 0.00 0.00 3.24
2381 2670 6.238648 TCCCAGGAAAATGTTTCTTCTACTC 58.761 40.000 0.00 0.00 0.00 2.59
2418 2710 4.479158 ACCAAAAGGCCAGACAAAAGATA 58.521 39.130 5.01 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.