Multiple sequence alignment - TraesCS5B01G048200

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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 TraesCS5B01G048200 chr5B 100.000 6821 0 0 1 6821 54384968 54391788 0.000000e+00 12597.0
1 TraesCS5B01G048200 chr5B 98.338 782 10 2 1 782 430675499 430674721 0.000000e+00 1369.0
2 TraesCS5B01G048200 chr5B 94.972 179 9 0 4528 4706 54389319 54389497 1.450000e-71 281.0
3 TraesCS5B01G048200 chr5B 94.972 179 9 0 4352 4530 54389495 54389673 1.450000e-71 281.0
4 TraesCS5B01G048200 chr5B 77.288 295 32 14 1834 2127 411785573 411785313 2.560000e-29 141.0
5 TraesCS5B01G048200 chr5B 97.826 46 1 0 873 918 54385876 54385921 5.670000e-11 80.5
6 TraesCS5B01G048200 chr5D 97.240 2246 47 8 4588 6821 51137241 51139483 0.000000e+00 3790.0
7 TraesCS5B01G048200 chr5D 97.240 2246 47 8 4588 6821 51157177 51159419 0.000000e+00 3790.0
8 TraesCS5B01G048200 chr5D 97.018 2247 49 11 4588 6821 51119759 51122000 0.000000e+00 3762.0
9 TraesCS5B01G048200 chr5D 96.928 2246 54 8 4588 6821 51177681 51179923 0.000000e+00 3751.0
10 TraesCS5B01G048200 chr5D 96.619 2248 45 7 4585 6821 51196623 51198850 0.000000e+00 3701.0
11 TraesCS5B01G048200 chr5D 97.721 1755 20 7 909 2656 51131095 51132836 0.000000e+00 3001.0
12 TraesCS5B01G048200 chr5D 97.721 1755 20 7 909 2656 51170937 51172678 0.000000e+00 3001.0
13 TraesCS5B01G048200 chr5D 97.434 1754 29 5 909 2656 51190551 51192294 0.000000e+00 2976.0
14 TraesCS5B01G048200 chr5D 97.322 1755 27 7 909 2656 51113643 51115384 0.000000e+00 2963.0
15 TraesCS5B01G048200 chr5D 97.749 1555 27 6 3030 4580 51193816 51195366 0.000000e+00 2671.0
16 TraesCS5B01G048200 chr5D 97.680 1552 28 5 3030 4580 51174824 51176368 0.000000e+00 2660.0
17 TraesCS5B01G048200 chr5D 97.424 1553 31 6 3030 4580 51116906 51118451 0.000000e+00 2638.0
18 TraesCS5B01G048200 chr5D 98.036 1069 19 2 3513 4580 51154803 51155870 0.000000e+00 1857.0
19 TraesCS5B01G048200 chr5D 97.794 952 15 3 3030 3981 51134357 51135302 0.000000e+00 1637.0
20 TraesCS5B01G048200 chr5D 98.454 388 0 1 909 1290 51151330 51151717 0.000000e+00 678.0
21 TraesCS5B01G048200 chr5D 98.454 388 0 1 909 1290 51188647 51189034 0.000000e+00 678.0
22 TraesCS5B01G048200 chr5D 96.000 200 7 1 2778 2977 51115381 51115579 2.370000e-84 324.0
23 TraesCS5B01G048200 chr5D 96.000 200 7 1 2778 2977 51132833 51133031 2.370000e-84 324.0
24 TraesCS5B01G048200 chr5D 96.000 200 7 1 2778 2977 51172675 51172873 2.370000e-84 324.0
25 TraesCS5B01G048200 chr5D 95.500 200 8 1 2778 2977 51192291 51192489 1.100000e-82 318.0
26 TraesCS5B01G048200 chr5D 86.735 294 28 10 4705 4989 132472632 132472923 3.970000e-82 316.0
27 TraesCS5B01G048200 chr5D 94.413 179 10 0 4528 4706 51176140 51176318 6.740000e-70 276.0
28 TraesCS5B01G048200 chr5D 93.855 179 11 0 4528 4706 51118222 51118400 3.140000e-68 270.0
29 TraesCS5B01G048200 chr5D 95.031 161 7 1 775 934 51130996 51131156 1.140000e-62 252.0
30 TraesCS5B01G048200 chr5D 95.031 161 7 1 775 934 51151231 51151391 1.140000e-62 252.0
31 TraesCS5B01G048200 chr5D 95.031 161 7 1 775 934 51170838 51170998 1.140000e-62 252.0
32 TraesCS5B01G048200 chr5D 95.031 161 7 1 775 934 51188548 51188708 1.140000e-62 252.0
33 TraesCS5B01G048200 chr5D 97.931 145 2 1 775 918 51113544 51113688 4.080000e-62 250.0
34 TraesCS5B01G048200 chr5D 94.444 162 7 2 775 934 51190451 51190612 1.470000e-61 248.0
35 TraesCS5B01G048200 chr5D 95.798 119 5 0 4412 4530 51119759 51119877 6.980000e-45 193.0
36 TraesCS5B01G048200 chr5D 95.122 123 5 1 4409 4530 51196623 51196745 6.980000e-45 193.0
37 TraesCS5B01G048200 chrUn 97.427 1749 41 4 5074 6821 280931969 280933714 0.000000e+00 2977.0
38 TraesCS5B01G048200 chrUn 98.331 599 8 2 3983 4580 415624850 415625447 0.000000e+00 1050.0
39 TraesCS5B01G048200 chrUn 94.413 179 10 0 4528 4706 415625219 415625397 6.740000e-70 276.0
40 TraesCS5B01G048200 chr5A 96.756 1048 28 5 3248 4292 40613910 40614954 0.000000e+00 1742.0
41 TraesCS5B01G048200 chr5A 96.257 935 9 5 909 1834 40611709 40612626 0.000000e+00 1509.0
42 TraesCS5B01G048200 chr5A 96.601 912 21 4 5063 5972 40617067 40617970 0.000000e+00 1504.0
43 TraesCS5B01G048200 chr5A 91.321 530 32 7 2134 2656 40612618 40613140 0.000000e+00 712.0
44 TraesCS5B01G048200 chr5A 89.837 492 43 4 6330 6821 40618041 40618525 5.810000e-175 625.0
45 TraesCS5B01G048200 chr5A 87.474 479 33 10 2778 3252 40613137 40613592 1.680000e-145 527.0
46 TraesCS5B01G048200 chr5A 94.688 320 17 0 4661 4980 40615704 40616023 1.320000e-136 497.0
47 TraesCS5B01G048200 chr5A 93.863 277 16 1 4704 4980 40616308 40616583 3.810000e-112 416.0
48 TraesCS5B01G048200 chr5A 84.492 374 42 9 4705 5062 40616582 40616955 8.410000e-94 355.0
49 TraesCS5B01G048200 chr5A 90.909 198 11 3 4292 4485 40615209 40615403 6.790000e-65 259.0
50 TraesCS5B01G048200 chr5A 99.275 138 1 0 781 918 40611617 40611754 4.080000e-62 250.0
51 TraesCS5B01G048200 chr5A 97.015 67 2 0 5956 6022 40617988 40618054 5.590000e-21 113.0
52 TraesCS5B01G048200 chr1A 98.465 782 9 2 1 782 366259657 366260435 0.000000e+00 1375.0
53 TraesCS5B01G048200 chr1A 82.119 302 41 6 1834 2134 21000354 21000643 5.280000e-61 246.0
54 TraesCS5B01G048200 chr7A 98.342 784 10 2 1 784 542101253 542102033 0.000000e+00 1373.0
55 TraesCS5B01G048200 chr7A 98.338 782 10 2 1 782 495576840 495576062 0.000000e+00 1369.0
56 TraesCS5B01G048200 chr7A 95.745 47 2 0 2084 2130 488502244 488502290 7.340000e-10 76.8
57 TraesCS5B01G048200 chr4A 98.342 784 9 3 1 784 686576946 686577725 0.000000e+00 1373.0
58 TraesCS5B01G048200 chr4A 84.362 243 34 4 1855 2095 39605884 39606124 1.140000e-57 235.0
59 TraesCS5B01G048200 chr2B 98.464 781 8 3 1 781 325907369 325906593 0.000000e+00 1373.0
60 TraesCS5B01G048200 chr2B 94.697 132 6 1 2655 2785 685272734 685272603 3.230000e-48 204.0
61 TraesCS5B01G048200 chr2A 98.464 781 9 2 1 781 238721800 238721023 0.000000e+00 1373.0
62 TraesCS5B01G048200 chr2A 90.000 170 16 1 6365 6534 161772884 161773052 1.150000e-52 219.0
63 TraesCS5B01G048200 chr4B 98.219 786 11 2 1 786 75187296 75188078 0.000000e+00 1371.0
64 TraesCS5B01G048200 chr4B 91.667 144 11 1 2638 2781 55925889 55926031 1.500000e-46 198.0
65 TraesCS5B01G048200 chr4B 89.308 159 13 4 2622 2780 17256304 17256458 5.400000e-46 196.0
66 TraesCS5B01G048200 chr1B 98.338 782 9 3 1 781 673416664 673415886 0.000000e+00 1369.0
67 TraesCS5B01G048200 chr1D 91.586 309 23 3 6020 6326 318585616 318585923 2.270000e-114 424.0
68 TraesCS5B01G048200 chr4D 91.503 306 25 1 6027 6331 226384948 226385253 2.940000e-113 420.0
69 TraesCS5B01G048200 chr4D 82.353 85 12 3 2565 2648 294346447 294346365 3.410000e-08 71.3
70 TraesCS5B01G048200 chr6B 90.584 308 29 0 6025 6332 692450221 692449914 6.370000e-110 409.0
71 TraesCS5B01G048200 chr3A 86.288 299 32 6 4693 4984 12613142 12612846 3.970000e-82 316.0
72 TraesCS5B01G048200 chr3A 85.185 243 32 4 1855 2095 105028048 105028288 5.280000e-61 246.0
73 TraesCS5B01G048200 chr3A 94.074 135 7 1 2651 2785 55506936 55506803 3.230000e-48 204.0
74 TraesCS5B01G048200 chr3A 79.310 116 22 1 2541 2656 335471217 335471104 5.670000e-11 80.5
75 TraesCS5B01G048200 chr7D 84.818 303 37 5 1834 2135 51735396 51735690 5.170000e-76 296.0
76 TraesCS5B01G048200 chr7D 92.308 143 9 2 2648 2790 40443827 40443967 1.160000e-47 202.0
77 TraesCS5B01G048200 chr3B 82.909 275 38 6 1862 2134 371037236 371037503 8.840000e-59 239.0
78 TraesCS5B01G048200 chr3B 89.759 166 16 1 6369 6534 183594431 183594267 1.930000e-50 211.0
79 TraesCS5B01G048200 chr3B 94.574 129 5 2 2655 2782 436445334 436445207 1.500000e-46 198.0
80 TraesCS5B01G048200 chr3B 91.429 140 10 2 2643 2781 784067264 784067402 2.510000e-44 191.0
81 TraesCS5B01G048200 chr3B 80.531 113 20 1 2541 2653 305534519 305534629 1.220000e-12 86.1
82 TraesCS5B01G048200 chr7B 94.697 132 6 1 2653 2784 91727768 91727898 3.230000e-48 204.0
83 TraesCS5B01G048200 chr6A 93.798 129 8 0 2653 2781 551982237 551982109 1.940000e-45 195.0
84 TraesCS5B01G048200 chr6D 85.526 76 11 0 6699 6774 54522531 54522606 5.670000e-11 80.5
85 TraesCS5B01G048200 chr3D 79.439 107 20 1 2541 2647 254109868 254109972 2.640000e-09 75.0


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 TraesCS5B01G048200 chr5B 54384968 54391788 6820 False 12597.000000 12597 100.000000 1 6821 1 chr5B.!!$F1 6820
1 TraesCS5B01G048200 chr5B 430674721 430675499 778 True 1369.000000 1369 98.338000 1 782 1 chr5B.!!$R2 781
2 TraesCS5B01G048200 chr5B 54385876 54389673 3797 False 214.166667 281 95.923333 873 4706 3 chr5B.!!$F2 3833
3 TraesCS5B01G048200 chr5D 51130996 51139483 8487 False 1800.800000 3790 96.757200 775 6821 5 chr5D.!!$F3 6046
4 TraesCS5B01G048200 chr5D 51170838 51179923 9085 False 1710.666667 3751 96.295500 775 6821 6 chr5D.!!$F5 6046
5 TraesCS5B01G048200 chr5D 51151231 51159419 8188 False 1644.250000 3790 97.190250 775 6821 4 chr5D.!!$F4 6046
6 TraesCS5B01G048200 chr5D 51113544 51122000 8456 False 1485.714286 3762 96.478286 775 6821 7 chr5D.!!$F2 6046
7 TraesCS5B01G048200 chr5D 51188548 51198850 10302 False 1379.625000 3701 96.294125 775 6821 8 chr5D.!!$F6 6046
8 TraesCS5B01G048200 chrUn 280931969 280933714 1745 False 2977.000000 2977 97.427000 5074 6821 1 chrUn.!!$F1 1747
9 TraesCS5B01G048200 chrUn 415624850 415625447 597 False 663.000000 1050 96.372000 3983 4706 2 chrUn.!!$F2 723
10 TraesCS5B01G048200 chr5A 40611617 40618525 6908 False 709.083333 1742 93.207333 781 6821 12 chr5A.!!$F1 6040
11 TraesCS5B01G048200 chr1A 366259657 366260435 778 False 1375.000000 1375 98.465000 1 782 1 chr1A.!!$F2 781
12 TraesCS5B01G048200 chr7A 542101253 542102033 780 False 1373.000000 1373 98.342000 1 784 1 chr7A.!!$F2 783
13 TraesCS5B01G048200 chr7A 495576062 495576840 778 True 1369.000000 1369 98.338000 1 782 1 chr7A.!!$R1 781
14 TraesCS5B01G048200 chr4A 686576946 686577725 779 False 1373.000000 1373 98.342000 1 784 1 chr4A.!!$F2 783
15 TraesCS5B01G048200 chr2B 325906593 325907369 776 True 1373.000000 1373 98.464000 1 781 1 chr2B.!!$R1 780
16 TraesCS5B01G048200 chr2A 238721023 238721800 777 True 1373.000000 1373 98.464000 1 781 1 chr2A.!!$R1 780
17 TraesCS5B01G048200 chr4B 75187296 75188078 782 False 1371.000000 1371 98.219000 1 786 1 chr4B.!!$F3 785
18 TraesCS5B01G048200 chr1B 673415886 673416664 778 True 1369.000000 1369 98.338000 1 781 1 chr1B.!!$R1 780

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
409 410 0.179040 TGAAACCCTTGACGTCCCAC 60.179 55.000 14.12 0.0 0.00 4.61 F
904 2811 1.977009 GGGGGAAAAGCACCTTCCG 60.977 63.158 5.66 0.0 42.91 4.30 F
908 2815 2.600470 AAAAGCACCTTCCGGGCC 60.600 61.111 0.00 0.0 39.10 5.80 F
5446 12285 2.516930 CCGCCATGACCACCATCC 60.517 66.667 0.00 0.0 31.94 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
5012 11740 3.897239 AGGTGTTGACAACCAGATTTGA 58.103 40.909 15.59 0.00 32.98 2.69 R
5437 12276 0.980754 TACATGAGGCGGATGGTGGT 60.981 55.000 0.00 0.00 0.00 4.16 R
5754 12593 4.111016 TACGGCCAGAGACACGCG 62.111 66.667 3.53 3.53 0.00 6.01 R
6290 13167 3.099905 TGGATGGTTAGAGAGACAGTGG 58.900 50.000 0.00 0.00 0.00 4.00 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
18 19 1.541169 TGATTGGCTGGGTGGTGTT 59.459 52.632 0.00 0.00 0.00 3.32
409 410 0.179040 TGAAACCCTTGACGTCCCAC 60.179 55.000 14.12 0.00 0.00 4.61
563 566 4.388577 AAGGGATAGGCACTTTTCAACT 57.611 40.909 0.00 0.00 36.68 3.16
589 592 5.189928 AGTGCATGACGGACCAAAAATATA 58.810 37.500 0.00 0.00 36.40 0.86
642 645 5.579384 ATTATTCGTTGTTGTTCGTTCGA 57.421 34.783 0.00 0.00 0.00 3.71
903 2810 4.113617 GGGGGAAAAGCACCTTCC 57.886 61.111 3.51 3.51 41.14 3.46
904 2811 1.977009 GGGGGAAAAGCACCTTCCG 60.977 63.158 5.66 0.00 42.91 4.30
905 2812 1.977009 GGGGAAAAGCACCTTCCGG 60.977 63.158 0.00 0.00 42.91 5.14
906 2813 1.977009 GGGAAAAGCACCTTCCGGG 60.977 63.158 0.00 0.00 42.91 5.73
907 2814 2.636412 GGAAAAGCACCTTCCGGGC 61.636 63.158 0.00 0.00 39.10 6.13
908 2815 2.600470 AAAAGCACCTTCCGGGCC 60.600 61.111 0.00 0.00 39.10 5.80
924 2831 4.856801 CCGCCAATGGAGTCGGGG 62.857 72.222 2.05 0.00 38.35 5.73
925 2832 4.856801 CGCCAATGGAGTCGGGGG 62.857 72.222 2.05 0.00 0.00 5.40
4967 11122 9.657419 GAAATGTGAAATGGGAATCTTACATTT 57.343 29.630 10.62 10.62 45.03 2.32
5012 11740 9.623000 AGTTTACAAAGGAAGTAGTTATGTTGT 57.377 29.630 8.95 8.95 32.98 3.32
5437 12276 2.958281 TTGCTCTGCTCCGCCATGA 61.958 57.895 0.00 0.00 0.00 3.07
5446 12285 2.516930 CCGCCATGACCACCATCC 60.517 66.667 0.00 0.00 31.94 3.51
5754 12593 2.577593 GTCCTACGTGGGGTGCTC 59.422 66.667 18.84 0.68 36.20 4.26
6025 12900 6.295236 CCTTCAGGGATGCACATTTCTTTTTA 60.295 38.462 0.00 0.00 37.23 1.52
6026 12901 6.855763 TCAGGGATGCACATTTCTTTTTAT 57.144 33.333 0.00 0.00 0.00 1.40
6067 12942 4.625311 CAGACACAAACGCTCATACATACA 59.375 41.667 0.00 0.00 0.00 2.29
6083 12960 0.037139 TACACGCATACACACACCCC 60.037 55.000 0.00 0.00 0.00 4.95
6094 12971 0.618458 ACACACCCCTATGAACGCAT 59.382 50.000 0.00 0.00 38.54 4.73
6111 12988 1.674817 GCATACACGCACACCTTACCT 60.675 52.381 0.00 0.00 0.00 3.08
6186 13063 1.432251 CCGTAGGCGTCTCGTCATT 59.568 57.895 0.00 0.00 46.14 2.57
6191 13068 2.506217 GCGTCTCGTCATTGGCGA 60.506 61.111 13.37 13.37 36.85 5.54
6263 13140 1.486310 AGGAATTATGCGAGCACCAGA 59.514 47.619 0.00 0.00 0.00 3.86
6271 13148 0.235926 GCGAGCACCAGAACTTGAAC 59.764 55.000 0.00 0.00 0.00 3.18
6290 13167 2.757124 CCTGGTGGGCTGGGGATAC 61.757 68.421 0.00 0.00 0.00 2.24
6473 13350 6.888632 AGAGTATGGATTCACTCATTTTGCTT 59.111 34.615 4.70 0.00 42.99 3.91
6553 13431 9.690913 GGGGTATTACTTTCATAGGTTTAGTTT 57.309 33.333 0.00 0.00 0.00 2.66
6801 13680 1.178276 GTCCACTCGTCAGGTCTGAT 58.822 55.000 3.84 0.00 42.18 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.376466 GTCTCTTCCCAAGGCAGCA 59.624 57.895 0.00 0.00 0.00 4.41
56 57 2.036475 CGGAAGAATCATCGGATCCTGT 59.964 50.000 10.75 0.00 31.88 4.00
310 311 2.647297 GCTTGCACTGTCCTTGCC 59.353 61.111 0.00 0.00 39.39 4.52
409 410 6.038050 GCTCTTCCACTTCCATTGATAAAGAG 59.962 42.308 0.00 0.00 39.93 2.85
563 566 0.107643 TTGGTCCGTCATGCACTTCA 59.892 50.000 0.00 0.00 0.00 3.02
765 768 5.964958 TGTGTATACTAGTATAACGCCCC 57.035 43.478 21.51 10.53 30.60 5.80
766 769 8.498054 TCTATGTGTATACTAGTATAACGCCC 57.502 38.462 21.51 11.14 30.60 6.13
907 2814 4.856801 CCCCGACTCCATTGGCGG 62.857 72.222 11.92 11.92 43.20 6.13
908 2815 4.856801 CCCCCGACTCCATTGGCG 62.857 72.222 0.00 0.00 0.00 5.69
922 2829 1.977009 CGGAAGGTGCTTTTCCCCC 60.977 63.158 8.29 0.00 40.83 5.40
923 2830 3.681473 CGGAAGGTGCTTTTCCCC 58.319 61.111 8.29 0.00 40.83 4.81
5012 11740 3.897239 AGGTGTTGACAACCAGATTTGA 58.103 40.909 15.59 0.00 32.98 2.69
5437 12276 0.980754 TACATGAGGCGGATGGTGGT 60.981 55.000 0.00 0.00 0.00 4.16
5754 12593 4.111016 TACGGCCAGAGACACGCG 62.111 66.667 3.53 3.53 0.00 6.01
6053 12928 2.509052 ATGCGTGTATGTATGAGCGT 57.491 45.000 0.00 0.00 0.00 5.07
6067 12942 1.134521 CATAGGGGTGTGTGTATGCGT 60.135 52.381 0.00 0.00 0.00 5.24
6083 12960 1.923864 TGTGCGTGTATGCGTTCATAG 59.076 47.619 0.00 0.00 35.96 2.23
6094 12971 2.914695 AAAGGTAAGGTGTGCGTGTA 57.085 45.000 0.00 0.00 0.00 2.90
6111 12988 3.260884 AGTCTTTCGGAGGTGCTCATAAA 59.739 43.478 0.00 0.00 31.08 1.40
6184 13061 0.173708 GAGGAGACGTTCTCGCCAAT 59.826 55.000 0.00 0.00 44.28 3.16
6186 13063 1.303398 AGAGGAGACGTTCTCGCCA 60.303 57.895 0.00 0.00 44.28 5.69
6191 13068 2.570415 TCAGTGAGAGGAGACGTTCT 57.430 50.000 0.00 0.00 0.00 3.01
6290 13167 3.099905 TGGATGGTTAGAGAGACAGTGG 58.900 50.000 0.00 0.00 0.00 4.00
6453 13330 6.105397 ACAAAGCAAAATGAGTGAATCCAT 57.895 33.333 0.00 0.00 0.00 3.41
6553 13431 6.072175 GCAGGAAACAATTACAACCACTCATA 60.072 38.462 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.