Multiple sequence alignment - TraesCS3D01G231600

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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 TraesCS3D01G231600 chr3D 100.000 4339 0 0 1 4339 317197816 317202154 0.000000e+00 8013.0
1 TraesCS3D01G231600 chr3D 100.000 3831 0 0 4727 8557 317202542 317206372 0.000000e+00 7075.0
2 TraesCS3D01G231600 chr3D 93.564 202 13 0 5580 5781 586958967 586959168 1.400000e-77 302.0
3 TraesCS3D01G231600 chr3D 96.648 179 4 2 7887 8065 563837750 563837574 6.490000e-76 296.0
4 TraesCS3D01G231600 chr3A 94.032 3770 139 28 603 4335 410114985 410111265 0.000000e+00 5637.0
5 TraesCS3D01G231600 chr3A 92.951 2128 78 27 5782 7870 410110139 410108045 0.000000e+00 3033.0
6 TraesCS3D01G231600 chr3A 97.552 858 20 1 4727 5583 410111237 410110380 0.000000e+00 1467.0
7 TraesCS3D01G231600 chr3A 91.991 462 19 6 8055 8505 410108032 410107578 4.360000e-177 632.0
8 TraesCS3D01G231600 chr3A 81.879 447 72 8 66 508 526856582 526857023 1.360000e-97 368.0
9 TraesCS3D01G231600 chr3A 82.567 413 65 6 53 462 444285391 444285799 2.940000e-94 357.0
10 TraesCS3D01G231600 chr3B 94.238 2204 85 10 620 2807 401810359 401808182 0.000000e+00 3328.0
11 TraesCS3D01G231600 chr3B 93.551 1349 55 12 3002 4337 401808178 401806849 0.000000e+00 1980.0
12 TraesCS3D01G231600 chr3B 95.223 1256 38 10 5782 7020 401805739 401804489 0.000000e+00 1967.0
13 TraesCS3D01G231600 chr3B 97.322 859 21 1 4727 5583 401806838 401805980 0.000000e+00 1458.0
14 TraesCS3D01G231600 chr3B 96.038 530 16 2 7074 7603 401804490 401803966 0.000000e+00 857.0
15 TraesCS3D01G231600 chr3B 79.428 909 156 26 1325 2223 406649934 406650821 1.580000e-171 614.0
16 TraesCS3D01G231600 chr3B 90.909 462 19 6 8055 8505 401803747 401803298 4.420000e-167 599.0
17 TraesCS3D01G231600 chr3B 85.398 226 11 8 7648 7870 401803966 401803760 1.870000e-51 215.0
18 TraesCS3D01G231600 chr4D 79.621 3008 369 142 714 3597 96912259 96909372 0.000000e+00 1934.0
19 TraesCS3D01G231600 chr4D 90.371 862 76 6 4737 5592 96908425 96907565 0.000000e+00 1125.0
20 TraesCS3D01G231600 chr4D 79.315 701 99 30 3641 4313 96909379 96908697 4.710000e-122 449.0
21 TraesCS3D01G231600 chr4D 96.517 201 7 0 5579 5779 258893655 258893455 4.950000e-87 333.0
22 TraesCS3D01G231600 chr4D 97.191 178 3 2 7879 8055 113186974 113187150 5.020000e-77 300.0
23 TraesCS3D01G231600 chr4D 95.238 189 5 4 7878 8065 420144051 420143866 6.490000e-76 296.0
24 TraesCS3D01G231600 chr4D 94.709 189 7 3 7865 8052 509818854 509819040 3.020000e-74 291.0
25 TraesCS3D01G231600 chr4A 81.337 2438 298 90 1247 3591 479412044 479414417 0.000000e+00 1836.0
26 TraesCS3D01G231600 chr4A 90.743 821 69 6 4769 5583 479416367 479417186 0.000000e+00 1088.0
27 TraesCS3D01G231600 chr4A 86.986 876 87 12 4730 5592 497815650 497814789 0.000000e+00 961.0
28 TraesCS3D01G231600 chr4A 83.455 550 79 6 55 603 200056288 200055750 1.280000e-137 501.0
29 TraesCS3D01G231600 chr4A 79.571 700 98 27 3641 4310 479414416 479415100 7.830000e-125 459.0
30 TraesCS3D01G231600 chr4A 92.883 281 20 0 53 333 516586135 516585855 8.000000e-110 409.0
31 TraesCS3D01G231600 chr4A 77.312 692 107 35 2923 3597 497819876 497819218 6.310000e-96 363.0
32 TraesCS3D01G231600 chr4A 80.255 471 66 13 3641 4090 497819216 497818752 6.400000e-86 329.0
33 TraesCS3D01G231600 chr4A 85.217 115 16 1 3477 3591 479415141 479415254 5.430000e-22 117.0
34 TraesCS3D01G231600 chr4A 94.000 50 3 0 6959 7008 497814516 497814467 9.210000e-10 76.8
35 TraesCS3D01G231600 chr4A 85.938 64 7 2 8483 8546 101515665 101515604 5.540000e-07 67.6
36 TraesCS3D01G231600 chr4B 79.225 1704 233 71 1971 3597 138305553 138303894 0.000000e+00 1074.0
37 TraesCS3D01G231600 chr4B 90.363 799 70 6 4800 5592 138302844 138302047 0.000000e+00 1042.0
38 TraesCS3D01G231600 chr4B 79.919 1240 141 65 714 1908 138306744 138305568 0.000000e+00 811.0
39 TraesCS3D01G231600 chr4B 79.627 1232 170 51 6407 7588 138301117 138299917 0.000000e+00 809.0
40 TraesCS3D01G231600 chr4B 84.142 618 76 17 1235 1840 119858920 119859527 5.760000e-161 579.0
41 TraesCS3D01G231600 chr4B 91.228 57 4 1 8500 8556 581066330 581066385 9.210000e-10 76.8
42 TraesCS3D01G231600 chr7B 85.814 860 111 10 4731 5583 665542936 665542081 0.000000e+00 902.0
43 TraesCS3D01G231600 chr7B 91.176 272 23 1 333 603 107926339 107926068 1.360000e-97 368.0
44 TraesCS3D01G231600 chr7B 94.340 53 3 0 8504 8556 488352249 488352301 1.980000e-11 82.4
45 TraesCS3D01G231600 chr7B 89.286 56 6 0 8501 8556 83536237 83536292 4.290000e-08 71.3
46 TraesCS3D01G231600 chr5B 84.890 867 112 14 4728 5583 93459332 93460190 0.000000e+00 857.0
47 TraesCS3D01G231600 chr2A 84.755 551 83 1 54 603 693643025 693642475 1.260000e-152 551.0
48 TraesCS3D01G231600 chr5A 84.139 517 71 7 4739 5245 684629502 684628987 2.780000e-134 490.0
49 TraesCS3D01G231600 chr5A 93.659 205 12 1 5576 5779 688698211 688698415 1.080000e-78 305.0
50 TraesCS3D01G231600 chr5A 94.444 198 10 1 5583 5779 357050962 357050765 3.880000e-78 303.0
51 TraesCS3D01G231600 chr6A 81.555 553 84 12 55 603 421221864 421221326 2.840000e-119 440.0
52 TraesCS3D01G231600 chr6A 95.122 41 2 0 2092 2132 549539526 549539486 1.990000e-06 65.8
53 TraesCS3D01G231600 chr2D 82.724 492 74 10 54 539 339196798 339196312 2.210000e-115 427.0
54 TraesCS3D01G231600 chr2D 94.554 202 11 0 5578 5779 647674604 647674805 6.450000e-81 313.0
55 TraesCS3D01G231600 chr2D 96.133 181 6 1 7874 8054 252715232 252715053 2.340000e-75 294.0
56 TraesCS3D01G231600 chr2D 96.154 52 0 2 8505 8556 5909192 5909241 5.500000e-12 84.2
57 TraesCS3D01G231600 chr1B 92.908 282 20 0 52 333 558919895 558919614 2.220000e-110 411.0
58 TraesCS3D01G231600 chr1B 92.657 286 20 1 51 336 660674443 660674727 2.220000e-110 411.0
59 TraesCS3D01G231600 chr1B 79.342 547 104 9 57 598 612399941 612400483 8.110000e-100 375.0
60 TraesCS3D01G231600 chr7D 93.382 272 17 1 333 603 583442202 583441931 1.340000e-107 401.0
61 TraesCS3D01G231600 chr7D 92.336 274 20 1 331 603 123368358 123368085 1.040000e-103 388.0
62 TraesCS3D01G231600 chr7D 90.842 273 24 1 329 600 326122829 326123101 1.760000e-96 364.0
63 TraesCS3D01G231600 chr7D 95.918 49 1 1 8505 8553 295151127 295151080 2.560000e-10 78.7
64 TraesCS3D01G231600 chr7D 91.071 56 5 0 8501 8556 340233596 340233651 9.210000e-10 76.8
65 TraesCS3D01G231600 chr6D 91.176 272 23 1 333 603 183017157 183016886 1.360000e-97 368.0
66 TraesCS3D01G231600 chr6D 94.554 202 10 1 5583 5784 181729733 181729533 2.320000e-80 311.0
67 TraesCS3D01G231600 chr6D 96.154 182 5 2 7879 8060 115783102 115782923 6.490000e-76 296.0
68 TraesCS3D01G231600 chr6D 95.122 41 2 0 2092 2132 403066780 403066740 1.990000e-06 65.8
69 TraesCS3D01G231600 chr7A 94.146 205 9 2 5580 5784 504221549 504221348 8.340000e-80 309.0
70 TraesCS3D01G231600 chr7A 95.833 48 2 0 8503 8550 571270589 571270542 2.560000e-10 78.7
71 TraesCS3D01G231600 chr5D 91.593 226 15 4 5568 5791 362579277 362579500 8.340000e-80 309.0
72 TraesCS3D01G231600 chr5D 96.610 177 6 0 7877 8053 466142342 466142518 2.340000e-75 294.0
73 TraesCS3D01G231600 chr5D 96.629 178 4 2 7887 8063 486175133 486175309 2.340000e-75 294.0
74 TraesCS3D01G231600 chr5D 95.604 182 6 2 7871 8052 508629017 508629196 3.020000e-74 291.0
75 TraesCS3D01G231600 chr6B 91.943 211 15 2 5576 5785 347750841 347751050 2.340000e-75 294.0
76 TraesCS3D01G231600 chr6B 85.714 70 6 4 2092 2159 604109806 604109739 4.290000e-08 71.3
77 TraesCS3D01G231600 chrUn 93.103 58 4 0 1 58 314145583 314145526 1.530000e-12 86.1
78 TraesCS3D01G231600 chr2B 97.917 48 1 0 8503 8550 140746874 140746827 5.500000e-12 84.2


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 TraesCS3D01G231600 chr3D 317197816 317206372 8556 False 7544.000000 8013 100.000000 1 8557 2 chr3D.!!$F2 8556
1 TraesCS3D01G231600 chr3A 410107578 410114985 7407 True 2692.250000 5637 94.131500 603 8505 4 chr3A.!!$R1 7902
2 TraesCS3D01G231600 chr3B 401803298 401810359 7061 True 1486.285714 3328 93.239857 620 8505 7 chr3B.!!$R1 7885
3 TraesCS3D01G231600 chr3B 406649934 406650821 887 False 614.000000 614 79.428000 1325 2223 1 chr3B.!!$F1 898
4 TraesCS3D01G231600 chr4D 96907565 96912259 4694 True 1169.333333 1934 83.102333 714 5592 3 chr4D.!!$R3 4878
5 TraesCS3D01G231600 chr4A 479412044 479417186 5142 False 875.000000 1836 84.217000 1247 5583 4 chr4A.!!$F1 4336
6 TraesCS3D01G231600 chr4A 200055750 200056288 538 True 501.000000 501 83.455000 55 603 1 chr4A.!!$R2 548
7 TraesCS3D01G231600 chr4A 497814467 497819876 5409 True 432.450000 961 84.638250 2923 7008 4 chr4A.!!$R4 4085
8 TraesCS3D01G231600 chr4B 138299917 138306744 6827 True 934.000000 1074 82.283500 714 7588 4 chr4B.!!$R1 6874
9 TraesCS3D01G231600 chr4B 119858920 119859527 607 False 579.000000 579 84.142000 1235 1840 1 chr4B.!!$F1 605
10 TraesCS3D01G231600 chr7B 665542081 665542936 855 True 902.000000 902 85.814000 4731 5583 1 chr7B.!!$R2 852
11 TraesCS3D01G231600 chr5B 93459332 93460190 858 False 857.000000 857 84.890000 4728 5583 1 chr5B.!!$F1 855
12 TraesCS3D01G231600 chr2A 693642475 693643025 550 True 551.000000 551 84.755000 54 603 1 chr2A.!!$R1 549
13 TraesCS3D01G231600 chr5A 684628987 684629502 515 True 490.000000 490 84.139000 4739 5245 1 chr5A.!!$R2 506
14 TraesCS3D01G231600 chr6A 421221326 421221864 538 True 440.000000 440 81.555000 55 603 1 chr6A.!!$R1 548
15 TraesCS3D01G231600 chr1B 612399941 612400483 542 False 375.000000 375 79.342000 57 598 1 chr1B.!!$F1 541


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
356 357 3.104512 CTGGTCATAGTGGGGAGTAACA 58.895 50.000 0.00 0.00 0.00 2.41 F
1119 1151 4.021981 GCAATTTACTGCCTTTGTTCTCCT 60.022 41.667 0.00 0.00 36.25 3.69 F
2174 2248 0.040157 TTGATGAACTTGCTGTGCGC 60.040 50.000 0.00 0.00 39.77 6.09 F
2492 2595 0.676782 AATGGACGTTACTGGCCAGC 60.677 55.000 33.06 15.65 33.26 4.85 F
4017 4983 1.295792 GTTCCGAGCACTGTTGTCAA 58.704 50.000 0.00 0.00 0.00 3.18 F
5678 9262 0.107831 TTTGTACAGGGCAGACGCTT 59.892 50.000 0.00 0.00 36.86 4.68 F
5679 9263 0.970640 TTGTACAGGGCAGACGCTTA 59.029 50.000 0.00 0.00 36.86 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1448 1498 0.323360 CCTTCTGGGGGCAAAATCGA 60.323 55.000 0.00 0.00 0.00 3.59 R
2478 2581 0.248289 AATACGCTGGCCAGTAACGT 59.752 50.000 30.74 30.74 40.53 3.99 R
3939 4900 0.172578 TCAGAATCCCACACGCGTAG 59.827 55.000 13.44 9.47 0.00 3.51 R
4211 7771 1.266718 TGTTGTCCGAGAGCAAAATGC 59.733 47.619 0.00 0.00 45.46 3.56 R
5746 9330 0.042731 TGCTAGGTGCTTAGGGAGGT 59.957 55.000 0.00 0.00 43.37 3.85 R
6722 10679 2.277084 CACTACTCCACGGGCAAATAC 58.723 52.381 0.00 0.00 0.00 1.89 R
7627 11645 2.309162 TGGATAATCCAACGAAACCCCA 59.691 45.455 0.00 0.00 45.00 4.96 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)



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AutoCloner maintained by Alex Coulton.