Multiple sequence alignment - TraesCS4A01G468400

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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 TraesCS4A01G468400 chr4A 100.000 3564 0 0 1 3564 730278800 730282363 0.000000e+00 6582.0
1 TraesCS4A01G468400 chr4A 96.168 2636 95 6 568 3199 730886252 730888885 0.000000e+00 4303.0
2 TraesCS4A01G468400 chr4A 91.892 2183 142 18 905 3075 730787010 730784851 0.000000e+00 3018.0
3 TraesCS4A01G468400 chr4A 91.549 2130 144 16 1444 3564 730193841 730191739 0.000000e+00 2904.0
4 TraesCS4A01G468400 chr4A 91.454 1217 90 6 1560 2764 728851006 728852220 0.000000e+00 1659.0
5 TraesCS4A01G468400 chr4A 98.783 575 5 2 1 575 730885172 730885744 0.000000e+00 1022.0
6 TraesCS4A01G468400 chr4A 88.056 787 74 10 1 776 728847574 728848351 0.000000e+00 915.0
7 TraesCS4A01G468400 chr4A 87.783 794 75 11 1 782 730791480 730790697 0.000000e+00 909.0
8 TraesCS4A01G468400 chr4A 87.531 794 77 12 1 782 730203556 730202773 0.000000e+00 898.0
9 TraesCS4A01G468400 chr4A 94.118 544 26 3 905 1444 730199164 730198623 0.000000e+00 822.0
10 TraesCS4A01G468400 chr4A 92.754 69 5 0 905 973 728850406 728850474 2.260000e-17 100.0
11 TraesCS4A01G468400 chr4A 85.507 69 9 1 834 902 584037903 584037970 1.780000e-08 71.3
12 TraesCS4A01G468400 chr7A 90.305 2620 209 15 957 3564 9411275 9413861 0.000000e+00 3389.0
13 TraesCS4A01G468400 chr7D 90.165 2115 175 19 1456 3562 8982152 8984241 0.000000e+00 2723.0
14 TraesCS4A01G468400 chr7D 90.046 1959 153 21 1617 3562 9378349 9380278 0.000000e+00 2499.0
15 TraesCS4A01G468400 chr7D 90.046 1949 157 16 1624 3564 8988517 8990436 0.000000e+00 2490.0
16 TraesCS4A01G468400 chr7D 93.638 613 30 4 957 1562 9377737 9378347 0.000000e+00 907.0
17 TraesCS4A01G468400 chr7D 93.011 558 39 0 904 1461 8981105 8981662 0.000000e+00 815.0
18 TraesCS4A01G468400 chr7D 91.577 463 34 4 1119 1581 8985509 8985966 5.020000e-178 634.0
19 TraesCS4A01G468400 chr7D 77.909 679 87 33 2892 3537 618719397 618720045 7.270000e-97 364.0
20 TraesCS4A01G468400 chr5D 86.943 965 124 1 1615 2577 445719892 445718928 0.000000e+00 1083.0
21 TraesCS4A01G468400 chr5D 88.929 551 51 5 902 1445 445720742 445720195 0.000000e+00 671.0
22 TraesCS4A01G468400 chr5D 81.301 123 10 8 2986 3100 560872084 560872201 1.760000e-13 87.9
23 TraesCS4A01G468400 chr6A 86.415 795 89 6 2767 3559 604452116 604452893 0.000000e+00 852.0
24 TraesCS4A01G468400 chrUn 100.000 442 0 0 712 1153 475916668 475917109 0.000000e+00 817.0
25 TraesCS4A01G468400 chr5A 90.000 480 42 3 971 1444 563376435 563375956 1.820000e-172 616.0
26 TraesCS4A01G468400 chr5A 93.878 49 3 0 853 901 485616166 485616214 1.370000e-09 75.0
27 TraesCS4A01G468400 chr6D 93.056 72 5 0 836 907 12259963 12260034 4.870000e-19 106.0
28 TraesCS4A01G468400 chr6D 90.769 65 6 0 836 900 318993723 318993787 1.760000e-13 87.9
29 TraesCS4A01G468400 chr3D 81.905 105 13 4 804 902 84474027 84474131 2.280000e-12 84.2
30 TraesCS4A01G468400 chr3D 100.000 29 0 0 2956 2984 587568472 587568500 2.000000e-03 54.7
31 TraesCS4A01G468400 chr4D 94.000 50 3 0 853 902 16454777 16454728 3.820000e-10 76.8
32 TraesCS4A01G468400 chr2D 84.416 77 12 0 2858 2934 620315384 620315460 3.820000e-10 76.8
33 TraesCS4A01G468400 chr7B 100.000 36 0 0 858 893 703998132 703998097 2.300000e-07 67.6


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 TraesCS4A01G468400 chr4A 730278800 730282363 3563 False 6582.000000 6582 100.000000 1 3564 1 chr4A.!!$F2 3563
1 TraesCS4A01G468400 chr4A 730191739 730193841 2102 True 2904.000000 2904 91.549000 1444 3564 1 chr4A.!!$R1 2120
2 TraesCS4A01G468400 chr4A 730885172 730888885 3713 False 2662.500000 4303 97.475500 1 3199 2 chr4A.!!$F4 3198
3 TraesCS4A01G468400 chr4A 730784851 730791480 6629 True 1963.500000 3018 89.837500 1 3075 2 chr4A.!!$R3 3074
4 TraesCS4A01G468400 chr4A 728847574 728852220 4646 False 891.333333 1659 90.754667 1 2764 3 chr4A.!!$F3 2763
5 TraesCS4A01G468400 chr4A 730198623 730203556 4933 True 860.000000 898 90.824500 1 1444 2 chr4A.!!$R2 1443
6 TraesCS4A01G468400 chr7A 9411275 9413861 2586 False 3389.000000 3389 90.305000 957 3564 1 chr7A.!!$F1 2607
7 TraesCS4A01G468400 chr7D 9377737 9380278 2541 False 1703.000000 2499 91.842000 957 3562 2 chr7D.!!$F3 2605
8 TraesCS4A01G468400 chr7D 8981105 8990436 9331 False 1665.500000 2723 91.199750 904 3564 4 chr7D.!!$F2 2660
9 TraesCS4A01G468400 chr7D 618719397 618720045 648 False 364.000000 364 77.909000 2892 3537 1 chr7D.!!$F1 645
10 TraesCS4A01G468400 chr5D 445718928 445720742 1814 True 877.000000 1083 87.936000 902 2577 2 chr5D.!!$R1 1675
11 TraesCS4A01G468400 chr6A 604452116 604452893 777 False 852.000000 852 86.415000 2767 3559 1 chr6A.!!$F1 792

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
1258 6570 3.157252 GGCGGATGAGGGAGCTCA 61.157 66.667 17.19 0.0 37.79 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3127 15388 0.108138 GTAGCAGAAGCCGTCCATGT 60.108 55.0 0.0 0.0 43.56 3.21 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
1258 6570 3.157252 GGCGGATGAGGGAGCTCA 61.157 66.667 17.19 0.00 37.79 4.26
1287 6599 4.700365 CTCGCCGTCGACTGCACA 62.700 66.667 27.83 14.80 40.21 4.57
1872 14083 2.207590 CGATGATGTGGTGGACATGAG 58.792 52.381 0.00 0.00 45.90 2.90
2065 14276 1.340248 GCCGACGAGGAAATGAGGATA 59.660 52.381 0.00 0.00 45.00 2.59
2317 14530 1.664321 GCACCTACCTCGTGTCGGAT 61.664 60.000 5.64 0.00 33.99 4.18
2401 14614 1.153901 GAATGGCGGAGTCGTCGAA 60.154 57.895 0.00 0.00 45.11 3.71
2448 14661 0.392461 GCTGTAAGGAACGCCATGGA 60.392 55.000 18.40 0.00 36.29 3.41
2699 14921 3.173599 CCAAACGATGTGTGCATGATTC 58.826 45.455 0.00 0.00 35.07 2.52
2704 14926 5.063180 ACGATGTGTGCATGATTCAAATT 57.937 34.783 0.00 0.00 35.07 1.82
2805 15030 6.525578 ACCGGGGAATCTTTTAAAAAGATC 57.474 37.500 6.32 0.83 36.07 2.75
2881 15107 3.068448 TCACTACTGCAACAAAGACCGTA 59.932 43.478 0.00 0.00 0.00 4.02
2908 15134 4.276926 CAGAAGCCTTTGTAACAAAGCTCT 59.723 41.667 0.00 0.00 0.00 4.09
2936 15164 6.862209 TGCAGAAACATTTGTAACAGAGTTT 58.138 32.000 0.00 0.00 32.48 2.66
3071 15332 2.025013 GTTGCCGTCGCCGTTTTT 59.975 55.556 0.00 0.00 0.00 1.94
3078 15339 0.580104 CGTCGCCGTTTTTCAACTCT 59.420 50.000 0.00 0.00 0.00 3.24
3127 15388 2.678580 TCCGCACGTCCTGATGGA 60.679 61.111 0.00 0.00 40.69 3.41
3151 15412 0.179134 GACGGCTTCTGCTACGTGAT 60.179 55.000 0.00 0.00 37.25 3.06
3369 15662 1.221293 CTTCCTGGAGAGCCTGCAG 59.779 63.158 6.78 6.78 46.96 4.41
3396 15689 0.318107 CTTGTTGCGGTCTGCCTTTG 60.318 55.000 0.00 0.00 45.60 2.77
3414 15707 2.738587 TGGAAACTGGTGCCAAGTTA 57.261 45.000 0.00 0.00 0.00 2.24
3423 15716 4.760204 ACTGGTGCCAAGTTACAAGAATAC 59.240 41.667 0.00 0.00 0.00 1.89
3482 15780 4.119363 AGATGTGGCGCATGGGCT 62.119 61.111 30.72 13.95 42.84 5.19
3505 15803 3.401033 TGATGACACGTGGAAGACATT 57.599 42.857 21.57 0.00 0.00 2.71
3506 15804 3.066380 TGATGACACGTGGAAGACATTG 58.934 45.455 21.57 0.00 0.00 2.82
3507 15805 1.877637 TGACACGTGGAAGACATTGG 58.122 50.000 21.57 0.00 0.00 3.16
3508 15806 1.156736 GACACGTGGAAGACATTGGG 58.843 55.000 21.57 0.00 0.00 4.12
3509 15807 0.889186 ACACGTGGAAGACATTGGGC 60.889 55.000 21.57 0.00 0.00 5.36
3510 15808 1.671054 ACGTGGAAGACATTGGGCG 60.671 57.895 0.00 0.00 0.00 6.13
3511 15809 1.671054 CGTGGAAGACATTGGGCGT 60.671 57.895 0.00 0.00 0.00 5.68
3512 15810 1.875963 GTGGAAGACATTGGGCGTG 59.124 57.895 0.00 0.00 0.00 5.34
3513 15811 1.303236 TGGAAGACATTGGGCGTGG 60.303 57.895 0.00 0.00 0.00 4.94
3514 15812 2.700773 GGAAGACATTGGGCGTGGC 61.701 63.158 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 110 3.560025 CCAAGAGTATGCACCTTGACCTT 60.560 47.826 16.67 2.69 36.13 3.50
1176 6488 1.304630 TAGTACAGGCGCAGGGTCA 60.305 57.895 10.83 0.00 0.00 4.02
1246 6558 2.381941 GGCCCTTGAGCTCCCTCAT 61.382 63.158 12.15 0.00 46.84 2.90
2065 14276 2.232941 ACGGATGTTGACGGTACAGATT 59.767 45.455 0.00 0.00 0.00 2.40
2271 14484 2.990967 CAAAGTGTGGCCGCCCAT 60.991 61.111 15.15 0.00 44.51 4.00
2337 14550 1.006102 CAGCCGAAGTCAAGGTCGT 60.006 57.895 0.00 0.00 35.48 4.34
2401 14614 2.186903 CTGCCGACGCCTGGTAAT 59.813 61.111 0.00 0.00 0.00 1.89
2448 14661 1.141053 GGATTGCAATACCCTCCTCGT 59.859 52.381 12.97 0.00 0.00 4.18
2747 14972 9.769677 AGCACAACCCTAGATATATAGTATTCA 57.230 33.333 3.79 0.00 0.00 2.57
2775 15000 4.886121 GATTCCCCGGTCGACGCC 62.886 72.222 9.92 0.00 42.52 5.68
2787 15012 5.105513 TGGGCGGATCTTTTTAAAAGATTCC 60.106 40.000 27.12 25.00 37.14 3.01
2881 15107 4.935352 TTGTTACAAAGGCTTCTGCAAT 57.065 36.364 0.00 0.00 41.91 3.56
2991 15220 6.971726 ATTCTGCAATATCATCCATGTTGT 57.028 33.333 0.00 0.00 36.28 3.32
3078 15339 0.380378 GAGTTTCTGCAACAACGGCA 59.620 50.000 0.00 0.00 37.93 5.69
3118 15379 1.971505 GCCGTCCATGTCCATCAGGA 61.972 60.000 0.00 0.00 43.21 3.86
3124 15385 1.296392 CAGAAGCCGTCCATGTCCA 59.704 57.895 0.00 0.00 0.00 4.02
3127 15388 0.108138 GTAGCAGAAGCCGTCCATGT 60.108 55.000 0.00 0.00 43.56 3.21
3133 15394 0.458543 CATCACGTAGCAGAAGCCGT 60.459 55.000 0.00 0.00 43.56 5.68
3261 15543 4.329545 GTTGGGCCTGAGCGGTCA 62.330 66.667 17.59 17.59 39.98 4.02
3396 15689 2.303175 TGTAACTTGGCACCAGTTTCC 58.697 47.619 9.66 3.05 0.00 3.13
3414 15707 5.360591 GCTAGCCACATACTGTATTCTTGT 58.639 41.667 2.29 0.00 0.00 3.16
3423 15716 2.604914 CTGAAACGCTAGCCACATACTG 59.395 50.000 9.66 0.00 0.00 2.74
3482 15780 2.298729 TGTCTTCCACGTGTCATCATGA 59.701 45.455 15.65 0.00 34.90 3.07
3510 15808 1.155424 TTTTGTCTGACGTCCGCCAC 61.155 55.000 14.12 2.45 0.00 5.01
3511 15809 0.878523 CTTTTGTCTGACGTCCGCCA 60.879 55.000 14.12 0.00 0.00 5.69
3512 15810 0.599204 TCTTTTGTCTGACGTCCGCC 60.599 55.000 14.12 0.00 0.00 6.13
3513 15811 1.390463 GATCTTTTGTCTGACGTCCGC 59.610 52.381 14.12 3.62 0.00 5.54
3514 15812 1.649171 CGATCTTTTGTCTGACGTCCG 59.351 52.381 14.12 6.91 0.00 4.79


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

AutoCloner maintained by Alex Coulton.