Multiple sequence alignment - TraesCS7A01G146100

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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 TraesCS7A01G146100 chr7A 100.000 2765 0 0 1 2765 97874865 97872101 0 5107
1 TraesCS7A01G146100 chr7A 91.993 612 48 1 1 611 84709524 84710135 0 857
2 TraesCS7A01G146100 chr7B 90.072 2236 94 58 612 2765 48455797 48453608 0 2782
3 TraesCS7A01G146100 chr7D 90.398 2135 83 45 715 2765 94435017 94432921 0 2695
4 TraesCS7A01G146100 chr7D 91.228 627 40 5 1 613 400187623 400188248 0 839
5 TraesCS7A01G146100 chr3A 92.182 614 41 5 1 613 127968295 127968902 0 861
6 TraesCS7A01G146100 chr3A 90.747 616 52 4 1 614 630759169 630758557 0 817
7 TraesCS7A01G146100 chr2D 91.143 621 44 7 1 613 591573960 591573343 0 832
8 TraesCS7A01G146100 chr5A 90.407 615 57 2 1 613 305963179 305962565 0 808
9 TraesCS7A01G146100 chr3D 90.499 621 46 9 1 611 188364106 188363489 0 808
10 TraesCS7A01G146100 chrUn 90.507 611 55 3 1 609 74747057 74746448 0 804
11 TraesCS7A01G146100 chr6D 90.307 619 48 7 1 611 100902198 100901584 0 800


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 TraesCS7A01G146100 chr7A 97872101 97874865 2764 True 5107 5107 100.000 1 2765 1 chr7A.!!$R1 2764
1 TraesCS7A01G146100 chr7A 84709524 84710135 611 False 857 857 91.993 1 611 1 chr7A.!!$F1 610
2 TraesCS7A01G146100 chr7B 48453608 48455797 2189 True 2782 2782 90.072 612 2765 1 chr7B.!!$R1 2153
3 TraesCS7A01G146100 chr7D 94432921 94435017 2096 True 2695 2695 90.398 715 2765 1 chr7D.!!$R1 2050
4 TraesCS7A01G146100 chr7D 400187623 400188248 625 False 839 839 91.228 1 613 1 chr7D.!!$F1 612
5 TraesCS7A01G146100 chr3A 127968295 127968902 607 False 861 861 92.182 1 613 1 chr3A.!!$F1 612
6 TraesCS7A01G146100 chr3A 630758557 630759169 612 True 817 817 90.747 1 614 1 chr3A.!!$R1 613
7 TraesCS7A01G146100 chr2D 591573343 591573960 617 True 832 832 91.143 1 613 1 chr2D.!!$R1 612
8 TraesCS7A01G146100 chr5A 305962565 305963179 614 True 808 808 90.407 1 613 1 chr5A.!!$R1 612
9 TraesCS7A01G146100 chr3D 188363489 188364106 617 True 808 808 90.499 1 611 1 chr3D.!!$R1 610
10 TraesCS7A01G146100 chrUn 74746448 74747057 609 True 804 804 90.507 1 609 1 chrUn.!!$R1 608
11 TraesCS7A01G146100 chr6D 100901584 100902198 614 True 800 800 90.307 1 611 1 chr6D.!!$R1 610

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
962 992 0.450184 GTGTCTGCGTCTCTCTCTCC 59.55 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 2417 0.320771 AACGGCAGTGATGACAGGTC 60.321 55.0 0.0 0.0 0.0 3.85 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 2.997315 CTCCGCCTGGTCCACTGA 60.997 66.667 0.00 0.00 36.30 3.41
95 96 1.942223 CACTGACACGTTCACGCGA 60.942 57.895 15.93 0.00 44.43 5.87
102 103 3.554692 CGTTCACGCGATGCCTCC 61.555 66.667 15.93 0.00 0.00 4.30
278 303 2.029964 TGGACGGCGAGTTTGGAC 59.970 61.111 16.62 0.00 0.00 4.02
279 304 2.029964 GGACGGCGAGTTTGGACA 59.970 61.111 16.62 0.00 0.00 4.02
321 347 1.154197 GGCTTAAAAAGGACGAGCGT 58.846 50.000 0.00 0.00 0.00 5.07
416 445 2.589442 GGAACACGGCGGACAACA 60.589 61.111 13.24 0.00 0.00 3.33
477 506 0.689623 ATTTGGGGCGCAAATTTGGA 59.310 45.000 29.96 11.06 0.00 3.53
537 567 3.641986 GTTTGGGTCGCGCGTTGA 61.642 61.111 30.98 7.84 0.00 3.18
588 618 2.472059 GCGCAGGCGGATGAAATGA 61.472 57.895 16.06 0.00 40.19 2.57
593 623 0.824109 AGGCGGATGAAATGAGTCGA 59.176 50.000 0.00 0.00 0.00 4.20
638 668 3.788227 TGTTCAAGTGGGAGCTGTAAT 57.212 42.857 0.00 0.00 0.00 1.89
640 670 4.469657 TGTTCAAGTGGGAGCTGTAATTT 58.530 39.130 0.00 0.00 0.00 1.82
676 706 8.696374 TCGGAAATTATATTAAACCAATGGCAA 58.304 29.630 0.00 0.00 0.00 4.52
697 727 7.821846 TGGCAATGACCAAAATAAGATTTTACC 59.178 33.333 0.00 0.00 36.55 2.85
698 728 7.821846 GGCAATGACCAAAATAAGATTTTACCA 59.178 33.333 0.00 0.00 0.00 3.25
699 729 8.872845 GCAATGACCAAAATAAGATTTTACCAG 58.127 33.333 0.00 0.00 0.00 4.00
962 992 0.450184 GTGTCTGCGTCTCTCTCTCC 59.550 60.000 0.00 0.00 0.00 3.71
1041 1108 3.453679 GCCTCCGCCTCGTCTTCT 61.454 66.667 0.00 0.00 0.00 2.85
1054 1121 1.645710 GTCTTCTTCCTCCACCTCCA 58.354 55.000 0.00 0.00 0.00 3.86
1164 1240 2.126734 GTGTACGACGTGACCCCG 60.127 66.667 11.56 0.00 0.00 5.73
1802 1899 2.605837 TTCGTTTACAGCTCACACCA 57.394 45.000 0.00 0.00 0.00 4.17
1850 1947 8.665685 GTTACCTGAATTTTGTCCATAGTACTG 58.334 37.037 5.39 0.00 0.00 2.74
1851 1948 6.779860 ACCTGAATTTTGTCCATAGTACTGT 58.220 36.000 5.39 0.00 0.00 3.55
1885 1988 6.538021 AGATTAAGATTTGTGCTCTGCTAGTG 59.462 38.462 0.00 0.00 0.00 2.74
1906 2009 2.353889 GCTGCACTGTCACCATGATTAG 59.646 50.000 0.00 0.00 0.00 1.73
1940 2043 8.159344 ACTGCAGTTCATTAGGCTATTAATTC 57.841 34.615 15.25 0.00 0.00 2.17
1945 2048 7.607991 CAGTTCATTAGGCTATTAATTCCCGAT 59.392 37.037 0.00 0.00 0.00 4.18
1969 2075 5.656213 TTGTCTGGCTTTACTACCTAGAC 57.344 43.478 0.00 0.00 35.97 2.59
2100 2220 2.816204 TTTGTTGTGTGGCATGGATG 57.184 45.000 0.00 0.00 0.00 3.51
2177 2297 5.212194 CGTTCTTTGGAGTAAACAACCATG 58.788 41.667 0.00 0.00 33.56 3.66
2208 2333 6.670695 AGCCTTGTTTGGATTTTCAACTAT 57.329 33.333 0.00 0.00 0.00 2.12
2209 2334 7.775053 AGCCTTGTTTGGATTTTCAACTATA 57.225 32.000 0.00 0.00 0.00 1.31
2227 2352 9.803315 TCAACTATAGATAAAAGCTACACACAG 57.197 33.333 6.78 0.00 0.00 3.66
2232 2357 6.240549 AGATAAAAGCTACACACAGGCTAT 57.759 37.500 0.00 0.00 35.06 2.97
2240 2365 0.462581 CACACAGGCTATGCACCGAT 60.463 55.000 0.00 0.00 0.00 4.18
2243 2368 1.665916 CAGGCTATGCACCGATCGG 60.666 63.158 32.20 32.20 42.03 4.18
2288 2414 0.324943 AATTCCCCGTGTCTGGACAG 59.675 55.000 3.47 0.00 42.74 3.51
2291 2417 2.343758 CCCGTGTCTGGACAGTGG 59.656 66.667 3.47 8.88 42.74 4.00
2305 2431 2.090400 CAGTGGACCTGTCATCACTG 57.910 55.000 16.76 16.76 46.94 3.66
2306 2432 0.322975 AGTGGACCTGTCATCACTGC 59.677 55.000 7.97 0.00 38.80 4.40
2374 2507 3.757248 ATGATTGCGTCCGGCCTCC 62.757 63.158 0.00 0.00 42.61 4.30
2399 2532 0.108585 TATCTGGAAATGCGGAGGGC 59.891 55.000 0.00 0.00 43.96 5.19
2622 2775 1.007038 GCACAGTGCACCACATTGG 60.007 57.895 21.22 0.60 44.26 3.16
2691 2846 4.301027 GATCCTTCGGCGGGCGAT 62.301 66.667 27.28 12.63 0.00 4.58
2692 2847 4.301027 ATCCTTCGGCGGGCGATC 62.301 66.667 27.28 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 2.927618 CGCGTGAACGTGTCAGTGG 61.928 63.158 8.19 0.00 44.02 4.00
132 145 3.330720 CGCCACCCCTTTCCTCCT 61.331 66.667 0.00 0.00 0.00 3.69
300 325 1.154197 GCTCGTCCTTTTTAAGCCGT 58.846 50.000 0.00 0.00 0.00 5.68
321 347 1.450134 GCCCACATGTCAGCGATGA 60.450 57.895 0.00 0.00 0.00 2.92
373 402 3.698820 GGCCGTCCAACTACCCGT 61.699 66.667 0.00 0.00 0.00 5.28
401 430 2.590575 CCTGTTGTCCGCCGTGTT 60.591 61.111 0.00 0.00 0.00 3.32
404 433 2.030562 CTTCCTGTTGTCCGCCGT 59.969 61.111 0.00 0.00 0.00 5.68
500 529 1.016627 CCAAATCACATCCGCGTCAT 58.983 50.000 4.92 0.00 0.00 3.06
501 530 1.024046 CCCAAATCACATCCGCGTCA 61.024 55.000 4.92 0.00 0.00 4.35
510 539 1.323412 CGACCCAAACCCAAATCACA 58.677 50.000 0.00 0.00 0.00 3.58
537 567 1.579429 GCGGACAAAAATGACGGCT 59.421 52.632 0.00 0.00 0.00 5.52
542 572 1.961791 TCGGCGCGGACAAAAATGA 60.962 52.632 14.27 0.00 0.00 2.57
570 600 2.025156 CATTTCATCCGCCTGCGC 59.975 61.111 5.91 0.00 38.24 6.09
588 618 0.250338 GCAACTCCAAAGGGTCGACT 60.250 55.000 16.46 0.00 34.93 4.18
593 623 3.756117 CTTAAGAGCAACTCCAAAGGGT 58.244 45.455 0.00 0.00 34.93 4.34
625 655 3.139077 CGGGATAAATTACAGCTCCCAC 58.861 50.000 9.38 0.00 44.93 4.61
658 688 7.904558 TGGTCATTGCCATTGGTTTAATATA 57.095 32.000 4.26 0.00 32.81 0.86
659 689 6.805016 TGGTCATTGCCATTGGTTTAATAT 57.195 33.333 4.26 0.00 32.81 1.28
668 698 7.852971 AATCTTATTTTGGTCATTGCCATTG 57.147 32.000 1.47 0.00 38.48 2.82
697 727 6.198216 CCCATGAACGACTTTTTGTTTTACTG 59.802 38.462 0.00 0.00 28.49 2.74
698 728 6.270064 CCCATGAACGACTTTTTGTTTTACT 58.730 36.000 0.00 0.00 28.49 2.24
699 729 5.051307 GCCCATGAACGACTTTTTGTTTTAC 60.051 40.000 0.00 0.00 28.49 2.01
705 735 2.607771 CCTGCCCATGAACGACTTTTTG 60.608 50.000 0.00 0.00 0.00 2.44
871 901 7.430441 GTTTTTATGTGGGTTTCTTTAGCAGA 58.570 34.615 0.00 0.00 0.00 4.26
1030 1097 0.108567 GTGGAGGAAGAAGACGAGGC 60.109 60.000 0.00 0.00 0.00 4.70
1031 1098 0.533032 GGTGGAGGAAGAAGACGAGG 59.467 60.000 0.00 0.00 0.00 4.63
1032 1099 1.474879 GAGGTGGAGGAAGAAGACGAG 59.525 57.143 0.00 0.00 0.00 4.18
1038 1105 0.193574 AGGTGGAGGTGGAGGAAGAA 59.806 55.000 0.00 0.00 0.00 2.52
1041 1108 1.609501 CGAGGTGGAGGTGGAGGAA 60.610 63.158 0.00 0.00 0.00 3.36
1065 1132 4.131088 GAGGTGGACGCGGAGGAC 62.131 72.222 12.47 0.65 0.00 3.85
1365 1441 4.899239 GCGAGGTCGGCCATGAGG 62.899 72.222 9.71 0.00 40.23 3.86
1940 2043 3.081804 AGTAAAGCCAGACAAAATCGGG 58.918 45.455 0.00 0.00 45.03 5.14
1945 2048 6.042322 TGTCTAGGTAGTAAAGCCAGACAAAA 59.958 38.462 3.57 0.00 38.58 2.44
1969 2075 2.981909 CACAGCCAGCCAGGTGTG 60.982 66.667 18.07 18.07 40.47 3.82
2064 2184 7.041916 ACACAACAAAAACAATTGCATGATAGG 60.042 33.333 5.05 0.00 33.52 2.57
2100 2220 1.569479 GGCTCGCCGGATAGAATTGC 61.569 60.000 5.05 0.82 0.00 3.56
2120 2240 4.636206 GGAGCGAATATATTCCCATTGGAC 59.364 45.833 17.83 3.71 41.57 4.02
2127 2247 4.828072 AAGGAGGAGCGAATATATTCCC 57.172 45.455 17.83 13.59 33.28 3.97
2155 2275 5.300792 TCCATGGTTGTTTACTCCAAAGAAC 59.699 40.000 12.58 2.19 45.24 3.01
2177 2297 0.600057 CCAAACAAGGCTTCAGCTCC 59.400 55.000 0.00 0.00 41.70 4.70
2208 2333 5.677319 AGCCTGTGTGTAGCTTTTATCTA 57.323 39.130 0.00 0.00 31.27 1.98
2209 2334 4.559862 AGCCTGTGTGTAGCTTTTATCT 57.440 40.909 0.00 0.00 31.27 1.98
2220 2345 1.375908 CGGTGCATAGCCTGTGTGT 60.376 57.895 0.00 0.00 0.00 3.72
2225 2350 1.665916 CCGATCGGTGCATAGCCTG 60.666 63.158 26.35 0.00 0.00 4.85
2226 2351 2.737180 CCGATCGGTGCATAGCCT 59.263 61.111 26.35 0.00 0.00 4.58
2227 2352 3.044305 GCCGATCGGTGCATAGCC 61.044 66.667 33.33 11.97 37.65 3.93
2232 2357 2.570284 ATATCGGCCGATCGGTGCA 61.570 57.895 42.11 25.20 36.17 4.57
2240 2365 0.463654 AGCAAAAGCATATCGGCCGA 60.464 50.000 33.12 33.12 0.00 5.54
2243 2368 2.658285 CATCAGCAAAAGCATATCGGC 58.342 47.619 0.00 0.00 0.00 5.54
2266 2392 1.003233 GTCCAGACACGGGGAATTCTT 59.997 52.381 5.23 0.00 34.34 2.52
2288 2414 0.674895 GGCAGTGATGACAGGTCCAC 60.675 60.000 0.00 0.00 0.00 4.02
2291 2417 0.320771 AACGGCAGTGATGACAGGTC 60.321 55.000 0.00 0.00 0.00 3.85
2374 2507 0.583438 CGCATTTCCAGATAGGCACG 59.417 55.000 0.00 0.00 37.29 5.34
2399 2532 6.173191 ACAAGTCACGTTAAAATTATCCCG 57.827 37.500 0.00 0.00 0.00 5.14
2543 2693 1.682344 GGTGCCCAATTCTGACCCC 60.682 63.158 0.00 0.00 0.00 4.95
2574 2724 1.069227 GTGTCCTCCACAAATGCGAAC 60.069 52.381 0.00 0.00 43.92 3.95
2575 2725 1.234821 GTGTCCTCCACAAATGCGAA 58.765 50.000 0.00 0.00 43.92 4.70
2599 2752 4.854924 TGGTGCACTGTGCTGCGT 62.855 61.111 30.43 0.00 45.31 5.24
2622 2775 2.202892 GATCGGACGGGTCAAGGC 60.203 66.667 0.75 0.00 0.00 4.35
2649 2802 2.029666 GCCCGTCCATCCTGATCG 59.970 66.667 0.00 0.00 0.00 3.69
2650 2803 2.427753 GGCCCGTCCATCCTGATC 59.572 66.667 0.00 0.00 34.01 2.92
2651 2804 2.366837 TGGCCCGTCCATCCTGAT 60.367 61.111 0.00 0.00 40.72 2.90
2720 2875 4.939368 CCCGTGCACCGAACCCAA 62.939 66.667 12.15 0.00 39.56 4.12


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

AutoCloner maintained by Alex Coulton.