Multiple sequence alignment - TraesCS4A01G418000

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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 TraesCS4A01G418000 chr4A 100.000 3819 0 0 1 3819 687891533 687895351 0.000000e+00 7053.0
1 TraesCS4A01G418000 chr4A 96.935 3621 71 13 1 3597 687830030 687833634 0.000000e+00 6035.0
2 TraesCS4A01G418000 chr4A 97.406 2891 52 8 932 3819 687813421 687816291 0.000000e+00 4902.0
3 TraesCS4A01G418000 chr4A 98.353 2550 28 7 1 2544 687918346 687920887 0.000000e+00 4464.0
4 TraesCS4A01G418000 chr4A 90.557 1938 174 4 1000 2931 688327782 688325848 0.000000e+00 2556.0
5 TraesCS4A01G418000 chr4A 90.557 1938 174 4 1000 2931 688375385 688373451 0.000000e+00 2556.0
6 TraesCS4A01G418000 chr4A 98.882 1252 13 1 2568 3819 687920883 687922133 0.000000e+00 2233.0
7 TraesCS4A01G418000 chr4A 94.061 1448 63 8 2190 3616 687866393 687867838 0.000000e+00 2176.0
8 TraesCS4A01G418000 chr4A 90.929 893 33 11 1 882 687881336 687882191 0.000000e+00 1157.0
9 TraesCS4A01G418000 chr4A 93.895 344 21 0 941 1284 687928551 687928894 1.570000e-143 520.0
10 TraesCS4A01G418000 chr7D 94.408 2271 109 7 932 3187 36045217 36042950 0.000000e+00 3474.0
11 TraesCS4A01G418000 chr7D 90.187 1284 111 8 1728 3002 35552400 35553677 0.000000e+00 1659.0
12 TraesCS4A01G418000 chr7D 95.499 1022 43 1 1818 2839 35798298 35797280 0.000000e+00 1629.0
13 TraesCS4A01G418000 chr7D 93.362 708 42 2 933 1640 35799163 35798461 0.000000e+00 1042.0
14 TraesCS4A01G418000 chr7D 88.646 229 22 4 3190 3417 36042785 36042560 3.760000e-70 276.0
15 TraesCS4A01G418000 chr7D 84.783 276 33 9 3548 3819 36042605 36042335 6.290000e-68 268.0
16 TraesCS4A01G418000 chr7D 81.013 79 12 3 507 583 511925886 511925963 4.120000e-05 60.2
17 TraesCS4A01G418000 chr7A 94.848 2174 102 5 932 3098 35696531 35698701 0.000000e+00 3386.0
18 TraesCS4A01G418000 chr7A 91.377 835 54 6 886 1720 35746280 35747096 0.000000e+00 1127.0
19 TraesCS4A01G418000 chr7A 88.259 247 23 5 3157 3403 35706911 35707151 1.340000e-74 291.0
20 TraesCS4A01G418000 chr7A 84.112 107 3 8 787 883 35746147 35746249 1.460000e-14 91.6
21 TraesCS4A01G418000 chr1A 97.761 134 3 0 3412 3545 94684039 94684172 8.250000e-57 231.0
22 TraesCS4A01G418000 chr1A 97.059 136 4 0 3412 3547 94560215 94560080 2.970000e-56 230.0
23 TraesCS4A01G418000 chr6A 97.015 134 4 0 3412 3545 537593487 537593354 3.840000e-55 226.0
24 TraesCS4A01G418000 chr3A 97.015 134 4 0 3412 3545 633092390 633092523 3.840000e-55 226.0
25 TraesCS4A01G418000 chr1B 97.015 134 4 0 3412 3545 619205266 619205399 3.840000e-55 226.0
26 TraesCS4A01G418000 chr7B 100.000 28 0 0 552 579 5932399 5932372 7.000000e-03 52.8
27 TraesCS4A01G418000 chr6D 100.000 28 0 0 559 586 446232159 446232186 7.000000e-03 52.8
28 TraesCS4A01G418000 chr4B 100.000 28 0 0 558 585 139375799 139375826 7.000000e-03 52.8
29 TraesCS4A01G418000 chr2D 100.000 28 0 0 473 500 193084780 193084807 7.000000e-03 52.8


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 TraesCS4A01G418000 chr4A 687891533 687895351 3818 False 7053.000000 7053 100.0000 1 3819 1 chr4A.!!$F5 3818
1 TraesCS4A01G418000 chr4A 687830030 687833634 3604 False 6035.000000 6035 96.9350 1 3597 1 chr4A.!!$F2 3596
2 TraesCS4A01G418000 chr4A 687813421 687816291 2870 False 4902.000000 4902 97.4060 932 3819 1 chr4A.!!$F1 2887
3 TraesCS4A01G418000 chr4A 687918346 687922133 3787 False 3348.500000 4464 98.6175 1 3819 2 chr4A.!!$F7 3818
4 TraesCS4A01G418000 chr4A 688325848 688327782 1934 True 2556.000000 2556 90.5570 1000 2931 1 chr4A.!!$R1 1931
5 TraesCS4A01G418000 chr4A 688373451 688375385 1934 True 2556.000000 2556 90.5570 1000 2931 1 chr4A.!!$R2 1931
6 TraesCS4A01G418000 chr4A 687866393 687867838 1445 False 2176.000000 2176 94.0610 2190 3616 1 chr4A.!!$F3 1426
7 TraesCS4A01G418000 chr4A 687881336 687882191 855 False 1157.000000 1157 90.9290 1 882 1 chr4A.!!$F4 881
8 TraesCS4A01G418000 chr7D 35552400 35553677 1277 False 1659.000000 1659 90.1870 1728 3002 1 chr7D.!!$F1 1274
9 TraesCS4A01G418000 chr7D 36042335 36045217 2882 True 1339.333333 3474 89.2790 932 3819 3 chr7D.!!$R2 2887
10 TraesCS4A01G418000 chr7D 35797280 35799163 1883 True 1335.500000 1629 94.4305 933 2839 2 chr7D.!!$R1 1906
11 TraesCS4A01G418000 chr7A 35696531 35698701 2170 False 3386.000000 3386 94.8480 932 3098 1 chr7A.!!$F1 2166
12 TraesCS4A01G418000 chr7A 35746147 35747096 949 False 609.300000 1127 87.7445 787 1720 2 chr7A.!!$F3 933

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
795 807 3.817084 GCGTAAGGGTTAAGGAACAACTT 59.183 43.478 0.00 0.0 37.74 2.66 F
2086 2203 1.192146 AGCAGGACGAGTTTGGCCTA 61.192 55.000 3.32 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2543 2688 0.804544 ATACCGTTGCATGTCGACCG 60.805 55.000 14.12 7.89 0.00 4.79 R
3253 3584 4.320456 CACTGCAGTGTCCCGCCT 62.320 66.667 34.04 0.00 40.96 5.52 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
795 807 3.817084 GCGTAAGGGTTAAGGAACAACTT 59.183 43.478 0.00 0.00 37.74 2.66
797 809 5.561532 GCGTAAGGGTTAAGGAACAACTTTC 60.562 44.000 3.44 0.00 36.39 2.62
798 810 5.333568 CGTAAGGGTTAAGGAACAACTTTCG 60.334 44.000 8.13 8.13 37.88 3.46
799 811 4.160642 AGGGTTAAGGAACAACTTTCGT 57.839 40.909 0.00 0.00 37.29 3.85
800 812 5.294734 AGGGTTAAGGAACAACTTTCGTA 57.705 39.130 0.00 0.00 37.29 3.43
1010 1082 8.790718 AGAGACTACTACTAAAATGTTCACGAA 58.209 33.333 0.00 0.00 0.00 3.85
1720 1834 5.336744 CGCTTCTCTTTTCTCTCGTCTAAT 58.663 41.667 0.00 0.00 0.00 1.73
2069 2186 2.434359 AGGCCGTCGTTAAGCAGC 60.434 61.111 0.00 0.00 0.00 5.25
2070 2187 2.740826 GGCCGTCGTTAAGCAGCA 60.741 61.111 0.00 0.00 0.00 4.41
2071 2188 2.740714 GGCCGTCGTTAAGCAGCAG 61.741 63.158 0.00 0.00 0.00 4.24
2086 2203 1.192146 AGCAGGACGAGTTTGGCCTA 61.192 55.000 3.32 0.00 0.00 3.93
2113 2230 1.967319 TGGAGTTCCTTCACAAGCAC 58.033 50.000 0.00 0.00 36.82 4.40
2271 2388 1.344763 GACCTACAAGATAGCCCGCAT 59.655 52.381 0.00 0.00 0.00 4.73
2356 2473 1.789078 GCATCGGCCGCATCAAGATT 61.789 55.000 23.51 0.00 0.00 2.40
2513 2630 2.418746 CCTAACTCCACCACCTTCATCG 60.419 54.545 0.00 0.00 0.00 3.84
2543 2688 4.884257 TATTCCCGACGCGGCTGC 62.884 66.667 11.76 7.70 46.86 5.25
2556 2701 3.422303 GCTGCGGTCGACATGCAA 61.422 61.111 27.50 15.80 38.30 4.08
2557 2702 2.476051 CTGCGGTCGACATGCAAC 59.524 61.111 27.50 6.66 38.30 4.17
2558 2703 3.353114 CTGCGGTCGACATGCAACG 62.353 63.158 27.50 17.66 38.30 4.10
2559 2704 4.147322 GCGGTCGACATGCAACGG 62.147 66.667 22.46 0.00 0.00 4.44
2560 2705 2.736995 CGGTCGACATGCAACGGT 60.737 61.111 18.91 0.65 0.00 4.83
2561 2706 1.444724 CGGTCGACATGCAACGGTA 60.445 57.895 18.91 0.00 0.00 4.02
2562 2707 0.804544 CGGTCGACATGCAACGGTAT 60.805 55.000 18.91 0.00 0.00 2.73
2563 2708 1.534385 CGGTCGACATGCAACGGTATA 60.534 52.381 18.91 0.00 0.00 1.47
2564 2709 2.750948 GGTCGACATGCAACGGTATAT 58.249 47.619 18.91 0.00 0.00 0.86
2565 2710 2.729882 GGTCGACATGCAACGGTATATC 59.270 50.000 18.91 0.00 0.00 1.63
2566 2711 2.404029 GTCGACATGCAACGGTATATCG 59.596 50.000 11.55 3.25 37.38 2.92
2567 2712 1.719246 CGACATGCAACGGTATATCGG 59.281 52.381 10.69 0.00 33.24 4.18
2568 2713 1.459592 GACATGCAACGGTATATCGGC 59.540 52.381 10.69 5.02 0.00 5.54
2569 2714 1.070134 ACATGCAACGGTATATCGGCT 59.930 47.619 10.69 0.00 0.00 5.52
2570 2715 1.460743 CATGCAACGGTATATCGGCTG 59.539 52.381 10.69 7.78 0.00 4.85
3062 3230 1.526887 CGCTGGTTCAGTACAACTGTG 59.473 52.381 6.93 0.00 46.03 3.66
3253 3584 2.370349 CAAACCACCACTGTACAACCA 58.630 47.619 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
795 807 3.058708 ACAGAATGAAGACGACGTACGAA 60.059 43.478 24.41 0.00 41.61 3.85
797 809 2.839026 GACAGAATGAAGACGACGTACG 59.161 50.000 15.01 15.01 43.93 3.67
798 810 3.818387 TGACAGAATGAAGACGACGTAC 58.182 45.455 0.00 0.00 39.69 3.67
799 811 4.659088 GATGACAGAATGAAGACGACGTA 58.341 43.478 0.00 0.00 39.69 3.57
800 812 3.502920 GATGACAGAATGAAGACGACGT 58.497 45.455 0.00 0.00 39.69 4.34
2069 2186 2.093447 AGAATAGGCCAAACTCGTCCTG 60.093 50.000 5.01 0.00 0.00 3.86
2070 2187 2.168728 GAGAATAGGCCAAACTCGTCCT 59.831 50.000 5.01 0.00 0.00 3.85
2071 2188 2.552031 GAGAATAGGCCAAACTCGTCC 58.448 52.381 5.01 0.00 0.00 4.79
2086 2203 3.588842 TGTGAAGGAACTCCATGGAGAAT 59.411 43.478 41.91 30.41 44.53 2.40
2271 2388 2.124612 CCACGATGATGGCCTGCA 60.125 61.111 3.32 1.71 31.52 4.41
2356 2473 1.367346 TGGTAAACCCCATGAGCTGA 58.633 50.000 0.00 0.00 34.29 4.26
2513 2630 1.271656 CGGGAATATCTCGGTGGGTAC 59.728 57.143 0.00 0.00 36.56 3.34
2543 2688 0.804544 ATACCGTTGCATGTCGACCG 60.805 55.000 14.12 7.89 0.00 4.79
2544 2689 2.212869 TATACCGTTGCATGTCGACC 57.787 50.000 14.12 0.00 0.00 4.79
2545 2690 2.404029 CGATATACCGTTGCATGTCGAC 59.596 50.000 9.11 9.11 37.81 4.20
2546 2691 2.606065 CCGATATACCGTTGCATGTCGA 60.606 50.000 3.81 0.00 37.81 4.20
2547 2692 1.719246 CCGATATACCGTTGCATGTCG 59.281 52.381 0.00 0.00 36.07 4.35
2548 2693 1.459592 GCCGATATACCGTTGCATGTC 59.540 52.381 0.00 0.00 0.00 3.06
2549 2694 1.070134 AGCCGATATACCGTTGCATGT 59.930 47.619 0.00 0.00 0.00 3.21
2550 2695 1.460743 CAGCCGATATACCGTTGCATG 59.539 52.381 0.00 0.00 0.00 4.06
2551 2696 1.795768 CAGCCGATATACCGTTGCAT 58.204 50.000 0.00 0.00 0.00 3.96
2552 2697 0.878523 GCAGCCGATATACCGTTGCA 60.879 55.000 8.01 0.00 37.81 4.08
2553 2698 1.566018 GGCAGCCGATATACCGTTGC 61.566 60.000 0.00 4.99 37.44 4.17
2554 2699 2.528797 GGCAGCCGATATACCGTTG 58.471 57.895 0.00 0.00 0.00 4.10
2566 2711 4.796495 CACTTACCCCCGGCAGCC 62.796 72.222 0.00 0.00 0.00 4.85
2567 2712 4.029809 ACACTTACCCCCGGCAGC 62.030 66.667 0.00 0.00 0.00 5.25
2568 2713 2.046314 CACACTTACCCCCGGCAG 60.046 66.667 0.00 0.00 0.00 4.85
2569 2714 3.642503 CCACACTTACCCCCGGCA 61.643 66.667 0.00 0.00 0.00 5.69
2570 2715 3.643554 ACCACACTTACCCCCGGC 61.644 66.667 0.00 0.00 0.00 6.13
3062 3230 5.230306 CGCTGCTCTAGTACAATTCTGTAAC 59.770 44.000 0.00 0.00 39.75 2.50
3253 3584 4.320456 CACTGCAGTGTCCCGCCT 62.320 66.667 34.04 0.00 40.96 5.52


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

AutoCloner maintained by Alex Coulton.