Multiple sequence alignment - TraesCS1B01G036400

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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 TraesCS1B01G036400 chr1B 100.000 6817 0 0 1 6817 17358093 17351277 0.000000e+00 12589.0
1 TraesCS1B01G036400 chr1B 95.138 2674 79 23 1634 4266 16922342 16919679 0.000000e+00 4170.0
2 TraesCS1B01G036400 chr1B 96.233 1858 55 7 4965 6817 16851515 16849668 0.000000e+00 3029.0
3 TraesCS1B01G036400 chr1B 90.799 1576 79 28 5292 6808 16914927 16913359 0.000000e+00 2047.0
4 TraesCS1B01G036400 chr1B 93.381 423 17 4 4877 5296 16919487 16919073 3.490000e-172 616.0
5 TraesCS1B01G036400 chr1B 90.705 312 23 5 6161 6467 16742470 16742160 1.770000e-110 411.0
6 TraesCS1B01G036400 chr1B 94.286 210 11 1 4347 4556 16919683 16919475 3.070000e-83 320.0
7 TraesCS1B01G036400 chr1B 97.727 176 3 1 4553 4728 449828212 449828386 1.110000e-77 302.0
8 TraesCS1B01G036400 chr1B 98.630 146 1 1 4735 4880 565662597 565662741 2.440000e-64 257.0
9 TraesCS1B01G036400 chr1A 88.745 2319 152 43 1 2260 13675848 13673580 0.000000e+00 2736.0
10 TraesCS1B01G036400 chr1A 95.159 1570 48 11 4877 6441 13671382 13669836 0.000000e+00 2453.0
11 TraesCS1B01G036400 chr1A 84.412 1251 119 43 3322 4556 13672560 13671370 0.000000e+00 1160.0
12 TraesCS1B01G036400 chr1A 92.371 485 26 7 2598 3071 13673048 13672564 0.000000e+00 680.0
13 TraesCS1B01G036400 chr1A 90.064 312 25 5 6161 6467 13420451 13420141 3.830000e-107 399.0
14 TraesCS1B01G036400 chr1A 86.667 300 22 3 2261 2546 13673338 13673043 3.970000e-82 316.0
15 TraesCS1B01G036400 chr1A 98.830 171 2 0 4550 4720 208903961 208903791 8.590000e-79 305.0
16 TraesCS1B01G036400 chr1A 78.065 155 32 2 4399 4553 490778264 490778112 5.630000e-16 97.1
17 TraesCS1B01G036400 chr1D 88.939 1989 110 40 4877 6815 11545431 11543503 0.000000e+00 2353.0
18 TraesCS1B01G036400 chr1D 91.267 1649 100 24 633 2246 11549594 11547955 0.000000e+00 2207.0
19 TraesCS1B01G036400 chr1D 91.412 850 66 4 3711 4556 11546266 11545420 0.000000e+00 1158.0
20 TraesCS1B01G036400 chr1D 90.270 555 38 12 2531 3071 11547346 11546794 0.000000e+00 712.0
21 TraesCS1B01G036400 chr1D 88.400 500 37 7 1 497 11550152 11549671 3.540000e-162 582.0
22 TraesCS1B01G036400 chr1D 78.710 155 31 2 4399 4553 276797528 276797376 1.210000e-17 102.0
23 TraesCS1B01G036400 chr1D 77.419 155 33 2 4399 4553 225401965 225402117 2.620000e-14 91.6
24 TraesCS1B01G036400 chr1D 80.328 122 20 4 4399 4518 250211940 250212059 9.420000e-14 89.8
25 TraesCS1B01G036400 chr3A 88.912 478 38 12 5881 6351 750729541 750729072 5.930000e-160 575.0
26 TraesCS1B01G036400 chr3A 78.736 348 66 8 2723 3065 740353103 740352759 6.880000e-55 226.0
27 TraesCS1B01G036400 chr3A 90.076 131 10 3 5732 5862 750730107 750729980 4.230000e-37 167.0
28 TraesCS1B01G036400 chr3A 80.255 157 27 4 4399 4553 561333726 561333880 1.550000e-21 115.0
29 TraesCS1B01G036400 chr3A 97.059 34 1 0 4363 4396 497947285 497947252 2.660000e-04 58.4
30 TraesCS1B01G036400 chr3A 92.105 38 3 0 5620 5657 750730244 750730207 3.000000e-03 54.7
31 TraesCS1B01G036400 chr3D 80.294 477 64 24 3730 4201 608068168 608067717 3.940000e-87 333.0
32 TraesCS1B01G036400 chr3D 78.917 351 60 8 2723 3065 608069134 608068790 6.880000e-55 226.0
33 TraesCS1B01G036400 chr3B 80.086 467 63 23 3730 4191 817823902 817823461 3.070000e-83 320.0
34 TraesCS1B01G036400 chr3B 96.703 182 5 1 4553 4734 168268209 168268389 1.110000e-77 302.0
35 TraesCS1B01G036400 chr3B 79.429 350 60 9 2723 3065 817824720 817824376 3.180000e-58 237.0
36 TraesCS1B01G036400 chr3B 86.935 199 24 2 5510 5706 817822329 817822131 8.900000e-54 222.0
37 TraesCS1B01G036400 chr7A 98.830 171 2 0 4553 4723 639786703 639786533 8.590000e-79 305.0
38 TraesCS1B01G036400 chr7A 80.645 155 24 6 4401 4553 665742352 665742502 1.550000e-21 115.0
39 TraesCS1B01G036400 chr5A 98.824 170 2 0 4551 4720 439421078 439420909 3.090000e-78 303.0
40 TraesCS1B01G036400 chr5A 97.740 177 2 2 4545 4720 680850638 680850813 3.090000e-78 303.0
41 TraesCS1B01G036400 chr5A 81.013 158 25 5 4399 4553 493816056 493816211 3.340000e-23 121.0
42 TraesCS1B01G036400 chr5A 80.851 141 25 2 2748 2887 484080636 484080497 7.230000e-20 110.0
43 TraesCS1B01G036400 chr5A 97.059 34 1 0 4363 4396 691814720 691814687 2.660000e-04 58.4
44 TraesCS1B01G036400 chr4B 91.228 228 13 4 3853 4076 406211170 406211394 3.090000e-78 303.0
45 TraesCS1B01G036400 chr4B 84.390 205 18 4 3633 3825 406210971 406211173 9.030000e-44 189.0
46 TraesCS1B01G036400 chr6A 98.266 173 2 1 4554 4726 64065217 64065388 1.110000e-77 302.0
47 TraesCS1B01G036400 chr6A 97.727 176 2 2 4545 4720 582491251 582491078 1.110000e-77 302.0
48 TraesCS1B01G036400 chr6A 97.059 34 1 0 4363 4396 77111291 77111258 2.660000e-04 58.4
49 TraesCS1B01G036400 chr4A 96.648 179 4 2 4552 4730 3725996 3725820 5.170000e-76 296.0
50 TraesCS1B01G036400 chr4A 100.000 137 0 0 4735 4871 229501633 229501769 3.160000e-63 254.0
51 TraesCS1B01G036400 chr4A 84.034 119 18 1 4399 4517 286747778 286747661 5.590000e-21 113.0
52 TraesCS1B01G036400 chr4A 77.576 165 33 4 4399 4563 742356810 742356650 5.630000e-16 97.1
53 TraesCS1B01G036400 chr7B 98.013 151 2 1 4735 4884 183306551 183306701 1.890000e-65 261.0
54 TraesCS1B01G036400 chr7B 96.178 157 3 3 4735 4890 624944871 624944717 3.160000e-63 254.0
55 TraesCS1B01G036400 chr2A 99.306 144 0 1 4735 4878 385446466 385446608 6.780000e-65 259.0
56 TraesCS1B01G036400 chr2A 97.143 35 1 0 4362 4396 25078412 25078378 7.380000e-05 60.2
57 TraesCS1B01G036400 chr5B 100.000 139 0 0 4735 4873 128671441 128671579 2.440000e-64 257.0
58 TraesCS1B01G036400 chr5B 94.479 163 6 3 4735 4894 554754512 554754674 1.470000e-61 248.0
59 TraesCS1B01G036400 chr5B 80.142 141 26 2 2748 2887 460267522 460267383 3.360000e-18 104.0
60 TraesCS1B01G036400 chr5B 97.143 35 1 0 4362 4396 562455992 562456026 7.380000e-05 60.2
61 TraesCS1B01G036400 chr2B 97.351 151 1 3 4735 4885 522079021 522079168 3.160000e-63 254.0
62 TraesCS1B01G036400 chr2B 97.931 145 1 2 4739 4881 316008066 316008210 4.080000e-62 250.0
63 TraesCS1B01G036400 chr2B 84.615 156 17 7 4400 4553 740319119 740319269 1.530000e-31 148.0
64 TraesCS1B01G036400 chr2D 81.132 159 25 4 4399 4556 627516638 627516484 9.280000e-24 122.0
65 TraesCS1B01G036400 chr2D 80.255 157 25 5 4399 4553 393585419 393585571 5.590000e-21 113.0
66 TraesCS1B01G036400 chr2D 81.955 133 23 1 4402 4534 16177849 16177718 2.010000e-20 111.0
67 TraesCS1B01G036400 chr2D 79.618 157 28 4 4399 4554 50400568 50400721 7.230000e-20 110.0
68 TraesCS1B01G036400 chr2D 97.143 35 1 0 4362 4396 637738387 637738353 7.380000e-05 60.2
69 TraesCS1B01G036400 chr6D 80.769 156 26 4 4399 4553 123267960 123268112 1.200000e-22 119.0
70 TraesCS1B01G036400 chr6D 81.618 136 22 2 4399 4534 402325126 402325258 7.230000e-20 110.0
71 TraesCS1B01G036400 chr6D 78.431 153 31 2 4401 4553 117361953 117362103 1.560000e-16 99.0
72 TraesCS1B01G036400 chr6D 80.672 119 19 4 4399 4515 35257889 35257773 9.420000e-14 89.8
73 TraesCS1B01G036400 chr6D 78.295 129 21 7 4399 4523 35294436 35294311 7.330000e-10 76.8
74 TraesCS1B01G036400 chr6D 88.000 50 4 1 4487 4536 109723171 109723124 2.660000e-04 58.4
75 TraesCS1B01G036400 chr4D 80.519 154 27 2 4399 4552 428482010 428481860 1.550000e-21 115.0
76 TraesCS1B01G036400 chr4D 82.727 110 15 3 4402 4509 316913470 316913363 2.020000e-15 95.3
77 TraesCS1B01G036400 chr4D 78.761 113 20 4 4399 4509 19642523 19642633 9.480000e-09 73.1
78 TraesCS1B01G036400 chr5D 80.851 141 25 2 2748 2887 383778004 383777865 7.230000e-20 110.0
79 TraesCS1B01G036400 chr5D 78.710 155 28 4 4399 4553 38729872 38729723 1.560000e-16 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 TraesCS1B01G036400 chr1B 17351277 17358093 6816 True 12589.000000 12589 100.000000 1 6817 1 chr1B.!!$R4 6816
1 TraesCS1B01G036400 chr1B 16849668 16851515 1847 True 3029.000000 3029 96.233000 4965 6817 1 chr1B.!!$R2 1852
2 TraesCS1B01G036400 chr1B 16913359 16914927 1568 True 2047.000000 2047 90.799000 5292 6808 1 chr1B.!!$R3 1516
3 TraesCS1B01G036400 chr1B 16919073 16922342 3269 True 1702.000000 4170 94.268333 1634 5296 3 chr1B.!!$R5 3662
4 TraesCS1B01G036400 chr1A 13669836 13675848 6012 True 1469.000000 2736 89.470800 1 6441 5 chr1A.!!$R4 6440
5 TraesCS1B01G036400 chr1D 11543503 11550152 6649 True 1402.400000 2353 90.057600 1 6815 5 chr1D.!!$R2 6814
6 TraesCS1B01G036400 chr3A 750729072 750730244 1172 True 265.566667 575 90.364333 5620 6351 3 chr3A.!!$R3 731
7 TraesCS1B01G036400 chr3D 608067717 608069134 1417 True 279.500000 333 79.605500 2723 4201 2 chr3D.!!$R1 1478
8 TraesCS1B01G036400 chr3B 817822131 817824720 2589 True 259.666667 320 82.150000 2723 5706 3 chr3B.!!$R1 2983


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
393 408 0.036765 TTGCGTCGGAGGCATACTTT 60.037 50.000 24.01 0.0 38.88 2.66 F
739 758 0.042708 GCATCTATGCGTCTGTTGCG 60.043 55.000 0.00 0.0 44.67 4.85 F
1386 1446 0.325577 TGGTGGCTGCTCTATCTGGA 60.326 55.000 0.00 0.0 0.00 3.86 F
2001 2070 0.322008 CAAGTCCTGTTCTGCCCTCC 60.322 60.000 0.00 0.0 0.00 4.30 F
2332 2651 2.293399 GCACACGAATCCTCCTTTGTTT 59.707 45.455 0.00 0.0 0.00 2.83 F
3818 4855 1.537202 GTTGCTGAACTGGATGGACAC 59.463 52.381 0.00 0.0 0.00 3.67 F
4260 5317 0.036952 ATGCTGCTTCACTACTGCGT 60.037 50.000 0.00 0.0 33.87 5.24 F
4839 6306 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.0 44.78 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1461 0.394565 GCCCATTACCAGCTCTCGAT 59.605 55.000 0.00 0.00 0.00 3.59 R
1983 2052 0.474660 AGGAGGGCAGAACAGGACTT 60.475 55.000 0.00 0.00 0.00 3.01 R
2613 3029 1.235724 GGTCAGTACCCTGTGCAAAC 58.764 55.000 0.00 0.00 40.21 2.93 R
3818 4855 0.025384 CACGTACACAGCGCATGATG 59.975 55.000 17.51 5.75 37.57 3.07 R
4093 5150 0.676466 TTATCTGCTGCGTTGTGGGG 60.676 55.000 0.00 0.00 0.00 4.96 R
4680 6147 0.036875 GGTGAAGTCCTCCCCACTTG 59.963 60.000 0.00 0.00 34.10 3.16 R
5356 6844 0.942962 CAATCAAGATCTGCCGCTCC 59.057 55.000 0.00 0.00 0.00 4.70 R
6714 8769 3.691118 CACAAGGGTATGGACAGTTCATG 59.309 47.826 4.35 0.00 0.00 3.07 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)



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

AutoCloner maintained by Alex Coulton.