Multiple sequence alignment - TraesCS5D01G033000

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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 TraesCS5D01G033000 chr5D 100.000 3979 0 0 1 3979 30617434 30621412 0.000000e+00 7348.0
1 TraesCS5D01G033000 chr5D 91.709 796 54 6 3182 3976 439307532 439308316 0.000000e+00 1094.0
2 TraesCS5D01G033000 chr5D 93.151 73 5 0 3365 3437 520295858 520295930 1.510000e-19 108.0
3 TraesCS5D01G033000 chr5A 97.984 2579 35 3 1 2564 23611560 23608984 0.000000e+00 4458.0
4 TraesCS5D01G033000 chr5A 98.361 427 3 1 2564 2990 23606173 23605751 0.000000e+00 747.0
5 TraesCS5D01G033000 chr5A 73.544 412 72 16 374 772 85156739 85157126 5.400000e-24 122.0
6 TraesCS5D01G033000 chr3A 95.970 2407 94 2 1570 3976 692347223 692349626 0.000000e+00 3904.0
7 TraesCS5D01G033000 chr3A 96.602 1589 31 4 1 1573 692345339 692346920 0.000000e+00 2614.0
8 TraesCS5D01G033000 chr3A 89.899 99 9 1 853 950 26493779 26493681 4.170000e-25 126.0
9 TraesCS5D01G033000 chr6D 95.668 1616 47 3 1 1601 98090516 98092123 0.000000e+00 2575.0
10 TraesCS5D01G033000 chr6D 92.938 793 47 4 3184 3976 350110179 350110962 0.000000e+00 1146.0
11 TraesCS5D01G033000 chr1D 82.349 1643 173 42 1602 3184 407296331 407297916 0.000000e+00 1319.0
12 TraesCS5D01G033000 chr1D 95.161 62 3 0 1 62 484189119 484189180 9.100000e-17 99.0
13 TraesCS5D01G033000 chr3B 91.436 794 58 6 3184 3976 685827030 685826246 0.000000e+00 1081.0
14 TraesCS5D01G033000 chr3B 87.929 787 58 8 848 1601 672672706 672671924 0.000000e+00 893.0
15 TraesCS5D01G033000 chr3B 92.706 521 38 0 1672 2192 658558488 658557968 0.000000e+00 752.0
16 TraesCS5D01G033000 chr3B 86.692 263 31 3 372 632 747702963 747703223 5.030000e-74 289.0
17 TraesCS5D01G033000 chr3B 93.229 192 13 0 126 317 756654462 756654271 2.340000e-72 283.0
18 TraesCS5D01G033000 chr3B 90.511 137 13 0 2432 2568 574334428 574334292 8.780000e-42 182.0
19 TraesCS5D01G033000 chr3B 89.610 77 8 0 2992 3068 512424311 512424387 9.100000e-17 99.0
20 TraesCS5D01G033000 chr6B 91.184 794 60 6 3184 3976 597989763 597990547 0.000000e+00 1070.0
21 TraesCS5D01G033000 chr6B 88.959 317 25 8 3229 3545 710288800 710288494 2.240000e-102 383.0
22 TraesCS5D01G033000 chr6B 94.410 161 9 0 3816 3976 42368944 42369104 8.540000e-62 248.0
23 TraesCS5D01G033000 chr6B 93.902 164 10 0 3816 3979 710288502 710288339 8.540000e-62 248.0
24 TraesCS5D01G033000 chr6B 88.889 180 20 0 2320 2499 648198368 648198189 5.180000e-54 222.0
25 TraesCS5D01G033000 chr6B 87.778 180 22 0 2320 2499 563912440 563912261 1.120000e-50 211.0
26 TraesCS5D01G033000 chr6B 81.319 273 20 11 2579 2820 405755013 405754741 4.060000e-45 193.0
27 TraesCS5D01G033000 chr6B 88.435 147 16 1 2840 2985 405800077 405799931 4.090000e-40 176.0
28 TraesCS5D01G033000 chr6B 88.732 142 15 1 2840 2980 405754680 405754539 5.290000e-39 172.0
29 TraesCS5D01G033000 chr6B 90.741 108 10 0 2713 2820 405800245 405800138 1.150000e-30 145.0
30 TraesCS5D01G033000 chr6B 95.349 43 2 0 3365 3407 713129497 713129455 7.140000e-08 69.4
31 TraesCS5D01G033000 chr7A 85.672 677 62 13 953 1601 528294514 528293845 0.000000e+00 680.0
32 TraesCS5D01G033000 chr7A 86.454 502 66 2 2167 2667 711610485 711609985 2.090000e-152 549.0
33 TraesCS5D01G033000 chr7A 84.884 172 17 4 3801 3964 426575334 426575504 8.850000e-37 165.0
34 TraesCS5D01G033000 chr7A 89.109 101 10 1 850 950 528294703 528294604 1.500000e-24 124.0
35 TraesCS5D01G033000 chr1B 96.154 416 16 0 2882 3297 77960013 77959598 0.000000e+00 680.0
36 TraesCS5D01G033000 chr1B 85.202 446 54 7 1040 1476 469173947 469173505 7.840000e-122 448.0
37 TraesCS5D01G033000 chr1B 87.778 180 21 1 2320 2499 550223862 550223684 4.030000e-50 209.0
38 TraesCS5D01G033000 chr1B 90.625 64 4 2 135 196 570305928 570305991 2.550000e-12 84.2
39 TraesCS5D01G033000 chr7B 83.988 687 76 9 2168 2821 712085405 712084720 2.610000e-176 628.0
40 TraesCS5D01G033000 chr7B 84.615 416 45 12 954 1352 608904925 608904512 2.880000e-106 396.0
41 TraesCS5D01G033000 chr7B 87.805 205 23 1 372 574 60366993 60366789 5.140000e-59 239.0
42 TraesCS5D01G033000 chr7B 88.112 143 17 0 2843 2985 712084657 712084515 1.900000e-38 171.0
43 TraesCS5D01G033000 chr7B 88.043 92 9 2 2167 2257 22257656 22257566 1.510000e-19 108.0
44 TraesCS5D01G033000 chr5B 90.870 471 39 4 315 785 562105700 562105234 2.610000e-176 628.0
45 TraesCS5D01G033000 chr5B 88.000 150 17 1 2837 2985 669718999 669719148 4.090000e-40 176.0
46 TraesCS5D01G033000 chr5B 79.487 273 25 16 2579 2820 669718669 669718941 8.850000e-37 165.0
47 TraesCS5D01G033000 chr5B 90.909 99 8 1 853 950 65100978 65101076 8.970000e-27 132.0
48 TraesCS5D01G033000 chr5B 90.000 90 9 0 3680 3769 649869310 649869399 2.510000e-22 117.0
49 TraesCS5D01G033000 chr5B 95.082 61 3 0 792 852 84732015 84731955 3.270000e-16 97.1
50 TraesCS5D01G033000 chr4B 92.272 427 32 1 315 741 527960132 527960557 4.400000e-169 604.0
51 TraesCS5D01G033000 chr4B 86.692 263 32 2 372 632 59873286 59873547 5.030000e-74 289.0
52 TraesCS5D01G033000 chr4B 90.625 192 15 1 126 317 14179412 14179224 6.600000e-63 252.0
53 TraesCS5D01G033000 chr4B 82.051 273 18 6 2579 2820 121556676 121556948 1.870000e-48 204.0
54 TraesCS5D01G033000 chr4B 88.000 150 17 1 2837 2985 121557006 121557155 4.090000e-40 176.0
55 TraesCS5D01G033000 chr4B 89.610 77 8 0 2992 3068 577220270 577220194 9.100000e-17 99.0
56 TraesCS5D01G033000 chr7D 82.066 697 81 22 2167 2821 618033310 618032616 4.490000e-154 555.0
57 TraesCS5D01G033000 chr7D 83.333 570 71 14 950 1498 561004951 561004385 4.590000e-139 505.0
58 TraesCS5D01G033000 chr7D 85.870 184 17 4 3801 3976 378321268 378321450 1.890000e-43 187.0
59 TraesCS5D01G033000 chr7D 91.919 99 7 1 853 950 159081320 159081222 1.930000e-28 137.0
60 TraesCS5D01G033000 chr7D 95.161 62 3 0 1 62 564891349 564891288 9.100000e-17 99.0
61 TraesCS5D01G033000 chr2B 83.029 548 63 17 954 1477 234826355 234826896 1.670000e-128 470.0
62 TraesCS5D01G033000 chr2B 81.685 273 19 6 2579 2820 10447890 10447618 8.720000e-47 198.0
63 TraesCS5D01G033000 chr2B 89.116 147 15 1 2840 2985 10447557 10447411 8.780000e-42 182.0
64 TraesCS5D01G033000 chr2B 88.889 90 10 0 3680 3769 655603382 655603293 1.170000e-20 111.0
65 TraesCS5D01G033000 chr2B 95.082 61 3 0 792 852 613039671 613039611 3.270000e-16 97.1
66 TraesCS5D01G033000 chr2D 94.366 142 8 0 126 267 582153618 582153477 6.690000e-53 219.0
67 TraesCS5D01G033000 chr2D 90.909 99 8 1 853 950 398665849 398665751 8.970000e-27 132.0
68 TraesCS5D01G033000 chr2A 93.056 144 10 0 126 269 509365173 509365030 1.120000e-50 211.0
69 TraesCS5D01G033000 chr4A 92.361 144 11 0 126 269 435436975 435437118 5.210000e-49 206.0
70 TraesCS5D01G033000 chr3D 87.619 105 12 1 853 956 19018428 19018324 1.940000e-23 121.0
71 TraesCS5D01G033000 chr3D 96.774 62 2 0 1 62 33324817 33324878 1.960000e-18 104.0
72 TraesCS5D01G033000 chr4D 93.056 72 5 0 3365 3436 49872464 49872393 5.440000e-19 106.0
73 TraesCS5D01G033000 chr1A 87.952 83 10 0 2986 3068 490515604 490515686 9.100000e-17 99.0


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 TraesCS5D01G033000 chr5D 30617434 30621412 3978 False 7348.0 7348 100.0000 1 3979 1 chr5D.!!$F1 3978
1 TraesCS5D01G033000 chr5D 439307532 439308316 784 False 1094.0 1094 91.7090 3182 3976 1 chr5D.!!$F2 794
2 TraesCS5D01G033000 chr5A 23605751 23611560 5809 True 2602.5 4458 98.1725 1 2990 2 chr5A.!!$R1 2989
3 TraesCS5D01G033000 chr3A 692345339 692349626 4287 False 3259.0 3904 96.2860 1 3976 2 chr3A.!!$F1 3975
4 TraesCS5D01G033000 chr6D 98090516 98092123 1607 False 2575.0 2575 95.6680 1 1601 1 chr6D.!!$F1 1600
5 TraesCS5D01G033000 chr6D 350110179 350110962 783 False 1146.0 1146 92.9380 3184 3976 1 chr6D.!!$F2 792
6 TraesCS5D01G033000 chr1D 407296331 407297916 1585 False 1319.0 1319 82.3490 1602 3184 1 chr1D.!!$F1 1582
7 TraesCS5D01G033000 chr3B 685826246 685827030 784 True 1081.0 1081 91.4360 3184 3976 1 chr3B.!!$R4 792
8 TraesCS5D01G033000 chr3B 672671924 672672706 782 True 893.0 893 87.9290 848 1601 1 chr3B.!!$R3 753
9 TraesCS5D01G033000 chr3B 658557968 658558488 520 True 752.0 752 92.7060 1672 2192 1 chr3B.!!$R2 520
10 TraesCS5D01G033000 chr6B 597989763 597990547 784 False 1070.0 1070 91.1840 3184 3976 1 chr6B.!!$F2 792
11 TraesCS5D01G033000 chr7A 711609985 711610485 500 True 549.0 549 86.4540 2167 2667 1 chr7A.!!$R1 500
12 TraesCS5D01G033000 chr7A 528293845 528294703 858 True 402.0 680 87.3905 850 1601 2 chr7A.!!$R2 751
13 TraesCS5D01G033000 chr7B 712084515 712085405 890 True 399.5 628 86.0500 2168 2985 2 chr7B.!!$R4 817
14 TraesCS5D01G033000 chr7D 618032616 618033310 694 True 555.0 555 82.0660 2167 2821 1 chr7D.!!$R4 654
15 TraesCS5D01G033000 chr7D 561004385 561004951 566 True 505.0 505 83.3330 950 1498 1 chr7D.!!$R2 548
16 TraesCS5D01G033000 chr2B 234826355 234826896 541 False 470.0 470 83.0290 954 1477 1 chr2B.!!$F1 523

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
649 651 6.551601 TCAAAGGCTTTTGTCCCTGTTATTTA 59.448 34.615 19.42 0.00 43.33 1.40 F
1603 2045 0.833287 CACATCCGGGATCTGGAAGT 59.167 55.000 6.55 9.68 39.39 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 2272 4.206477 ACGACATCAATTGACTGATCCA 57.794 40.909 11.07 0.0 33.66 3.41 R
3084 6464 0.891373 AGACAGACCACCATCGACAG 59.109 55.000 0.00 0.0 0.00 3.51 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
649 651 6.551601 TCAAAGGCTTTTGTCCCTGTTATTTA 59.448 34.615 19.42 0.00 43.33 1.40
1025 1115 2.029623 GACATGCATCAGGAAGCCAAT 58.970 47.619 0.00 0.00 0.00 3.16
1603 2045 0.833287 CACATCCGGGATCTGGAAGT 59.167 55.000 6.55 9.68 39.39 3.01
1824 2272 1.569072 ACCAGTTTGGGACTTGGAACT 59.431 47.619 0.00 0.00 43.37 3.01
2534 3007 5.843673 TGTGGTCAAGCAAACTTATTCAA 57.156 34.783 0.00 0.00 33.74 2.69
2987 6367 3.670625 TCCTTGTGCTTAATTACACGCT 58.329 40.909 2.77 0.00 39.71 5.07
3084 6464 3.181500 CGGGTTTAAGTATCTTTGCTGGC 60.181 47.826 0.00 0.00 0.00 4.85
3098 6478 1.448540 CTGGCTGTCGATGGTGGTC 60.449 63.158 0.00 0.00 0.00 4.02
3138 6518 6.602406 TCTCTGTATGTAGTTCCAGTAGTTCC 59.398 42.308 0.00 0.00 0.00 3.62
3347 6729 3.633525 TGTTCCTCCAATAGCATTGCATC 59.366 43.478 11.91 0.00 0.00 3.91
3467 6849 8.441312 AGTTAAACTTAGATTTTTGTGGTCGA 57.559 30.769 0.00 0.00 0.00 4.20
3476 6858 2.023414 TTTGTGGTCGACGTCCTGCT 62.023 55.000 10.58 0.00 0.00 4.24
3481 6863 4.717629 TCGACGTCCTGCTTGGCG 62.718 66.667 10.58 0.00 39.83 5.69
3630 7013 3.625897 AGTGGCGCTGCACCTACA 61.626 61.111 7.64 0.00 0.00 2.74
3685 7068 3.811083 CCAGCGGGTTGTAAATACCATA 58.189 45.455 0.00 0.00 37.40 2.74
3713 7096 4.584325 AGTTGCACATATGTCTTTGGTTGT 59.416 37.500 5.07 0.00 0.00 3.32
3722 7105 7.446931 ACATATGTCTTTGGTTGTATCAACACA 59.553 33.333 1.41 9.19 34.61 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
795 797 2.158971 GGTTCAACACCCAAAGCAATGT 60.159 45.455 0.00 0.00 40.19 2.71
872 875 3.825328 ACAGTCAGCTCTCCAAAAACAT 58.175 40.909 0.00 0.00 0.00 2.71
1824 2272 4.206477 ACGACATCAATTGACTGATCCA 57.794 40.909 11.07 0.00 33.66 3.41
2534 3007 6.734502 TGATTTATGCATCACAAATCCCAT 57.265 33.333 22.09 0.00 37.70 4.00
2987 6367 4.617520 TTCTTGGTCGCCGCTGCA 62.618 61.111 0.00 0.00 37.32 4.41
3084 6464 0.891373 AGACAGACCACCATCGACAG 59.109 55.000 0.00 0.00 0.00 3.51
3098 6478 7.445121 ACATACAGAGAGAGATAGAGAGACAG 58.555 42.308 0.00 0.00 0.00 3.51
3467 6849 2.244117 ATCATCGCCAAGCAGGACGT 62.244 55.000 0.00 0.00 41.22 4.34
3476 6858 2.358957 CTCTGTTTCCATCATCGCCAA 58.641 47.619 0.00 0.00 0.00 4.52
3481 6863 2.019984 GCCACCTCTGTTTCCATCATC 58.980 52.381 0.00 0.00 0.00 2.92
3578 6961 1.911269 TGCAGACAACCCGCCTAGA 60.911 57.895 0.00 0.00 0.00 2.43
3599 6982 1.174712 GCCACTGACCACTGCAACAT 61.175 55.000 0.00 0.00 0.00 2.71
3620 7003 4.341366 TCCATACATGATGTAGGTGCAG 57.659 45.455 15.06 1.49 36.14 4.41
3630 7013 9.236006 GCCTAGTTTTATTGATCCATACATGAT 57.764 33.333 0.00 0.00 0.00 2.45
3685 7068 6.015180 ACCAAAGACATATGTGCAACTGAATT 60.015 34.615 14.43 0.00 38.04 2.17
3713 7096 8.387354 CACTAAGTAAAATGCGATGTGTTGATA 58.613 33.333 0.00 0.00 0.00 2.15
3722 7105 7.148474 ACGACAAATCACTAAGTAAAATGCGAT 60.148 33.333 0.00 0.00 0.00 4.58
3839 7222 7.494625 CAGAAGATATTAAAGCGTTCAGGGTAA 59.505 37.037 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.