Multiple sequence alignment - TraesCS3A01G238800

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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 TraesCS3A01G238800 chr3A 100.000 5523 0 0 1 5523 447269734 447275256 0.000000e+00 10200.0
1 TraesCS3A01G238800 chr3A 99.260 2836 15 2 2130 4964 408942744 408945574 0.000000e+00 5116.0
2 TraesCS3A01G238800 chr3A 98.368 2144 15 4 1 2143 408940595 408942719 0.000000e+00 3747.0
3 TraesCS3A01G238800 chr3A 99.023 512 1 2 5012 5523 408946780 408947287 0.000000e+00 915.0
4 TraesCS3A01G238800 chr3A 87.805 205 22 3 401 603 408941149 408941352 2.570000e-58 237.0
5 TraesCS3A01G238800 chr3A 87.805 205 22 3 571 774 447270134 447270336 2.570000e-58 237.0
6 TraesCS3A01G238800 chr3A 87.805 205 22 3 401 603 447270304 447270507 2.570000e-58 237.0
7 TraesCS3A01G238800 chr3A 85.106 188 21 3 587 774 408941001 408941181 9.450000e-43 185.0
8 TraesCS3A01G238800 chr3D 97.062 4935 97 18 5 4922 317559120 317554217 0.000000e+00 8266.0
9 TraesCS3A01G238800 chr3D 96.599 294 7 1 5230 5523 317553433 317553143 8.320000e-133 484.0
10 TraesCS3A01G238800 chr3D 87.745 204 22 3 571 773 317558735 317558534 9.250000e-58 235.0
11 TraesCS3A01G238800 chr3D 88.587 184 19 2 421 603 317558553 317558371 7.200000e-54 222.0
12 TraesCS3A01G238800 chr3D 97.674 129 1 2 5012 5139 317553557 317553430 2.590000e-53 220.0
13 TraesCS3A01G238800 chr3D 97.826 46 1 0 4919 4964 601028885 601028840 4.590000e-11 80.5
14 TraesCS3A01G238800 chr3B 96.429 4957 111 17 5 4922 401405009 401409938 0.000000e+00 8113.0
15 TraesCS3A01G238800 chr3B 98.485 198 3 0 5230 5427 401410846 401411043 3.170000e-92 350.0
16 TraesCS3A01G238800 chr3B 87.317 205 23 3 571 774 401405389 401405591 1.200000e-56 231.0
17 TraesCS3A01G238800 chr3B 96.875 128 3 1 5012 5139 401410723 401410849 4.330000e-51 213.0
18 TraesCS3A01G238800 chr3B 94.340 106 4 2 5129 5233 12406666 12406770 1.590000e-35 161.0
19 TraesCS3A01G238800 chr3B 93.519 108 5 2 5132 5238 220754839 220754733 5.730000e-35 159.0
20 TraesCS3A01G238800 chr3B 92.593 108 6 2 5132 5238 219440341 219440235 2.660000e-33 154.0
21 TraesCS3A01G238800 chr3B 93.137 102 4 1 5422 5523 401411153 401411251 4.460000e-31 147.0
22 TraesCS3A01G238800 chr3B 90.909 55 4 1 4907 4960 662488825 662488879 7.670000e-09 73.1
23 TraesCS3A01G238800 chr6A 85.151 1091 116 16 2625 3707 1464766 1463714 0.000000e+00 1075.0
24 TraesCS3A01G238800 chr6A 85.996 1014 115 13 3807 4816 1463712 1462722 0.000000e+00 1061.0
25 TraesCS3A01G238800 chr6A 83.803 142 22 1 3642 3783 452630057 452630197 3.470000e-27 134.0
26 TraesCS3A01G238800 chr6A 97.619 42 1 0 4920 4961 19780437 19780396 7.670000e-09 73.1
27 TraesCS3A01G238800 chr6D 88.170 448 53 0 3035 3482 465354321 465353874 8.140000e-148 534.0
28 TraesCS3A01G238800 chr6D 87.443 438 55 0 3045 3482 465352790 465352353 6.390000e-139 505.0
29 TraesCS3A01G238800 chr4B 85.129 464 54 5 3426 3888 669916317 669915868 1.400000e-125 460.0
30 TraesCS3A01G238800 chr4B 83.408 446 60 4 3444 3888 669914427 669913995 8.620000e-108 401.0
31 TraesCS3A01G238800 chr4B 83.803 426 52 10 3242 3666 669912450 669912041 6.710000e-104 388.0
32 TraesCS3A01G238800 chr4B 83.693 417 52 6 3248 3663 669910747 669911148 4.040000e-101 379.0
33 TraesCS3A01G238800 chr4B 85.065 308 43 1 3843 4147 669916485 669916792 1.490000e-80 311.0
34 TraesCS3A01G238800 chr4B 82.274 299 39 5 3334 3631 669912041 669911756 4.270000e-61 246.0
35 TraesCS3A01G238800 chr4B 88.235 170 20 0 3978 4147 669912817 669912986 2.610000e-48 204.0
36 TraesCS3A01G238800 chr4B 90.909 99 9 0 4048 4146 669913970 669913872 3.470000e-27 134.0
37 TraesCS3A01G238800 chr4B 86.555 119 16 0 4029 4147 669915862 669915744 1.250000e-26 132.0
38 TraesCS3A01G238800 chr1D 95.098 102 4 1 5134 5234 12070196 12070095 5.730000e-35 159.0
39 TraesCS3A01G238800 chr6B 95.050 101 4 1 5132 5231 633054014 633054114 2.060000e-34 158.0
40 TraesCS3A01G238800 chr6B 94.175 103 5 1 5131 5232 475446854 475446752 7.410000e-34 156.0
41 TraesCS3A01G238800 chr2B 93.458 107 5 2 5132 5237 683270965 683271070 2.060000e-34 158.0
42 TraesCS3A01G238800 chr2B 86.614 127 16 1 4083 4208 114043405 114043531 7.460000e-29 139.0
43 TraesCS3A01G238800 chr2B 100.000 44 0 0 4917 4960 781088286 781088329 1.280000e-11 82.4
44 TraesCS3A01G238800 chr4D 94.175 103 5 1 5133 5234 213702857 213702959 7.410000e-34 156.0
45 TraesCS3A01G238800 chr1A 97.959 49 1 0 4916 4964 12309109 12309157 9.860000e-13 86.1
46 TraesCS3A01G238800 chr5A 91.667 60 3 2 4907 4964 81350284 81350343 1.280000e-11 82.4
47 TraesCS3A01G238800 chr7A 97.826 46 1 0 4919 4964 145459382 145459337 4.590000e-11 80.5
48 TraesCS3A01G238800 chr7A 94.231 52 2 1 4910 4960 97020406 97020457 1.650000e-10 78.7


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 TraesCS3A01G238800 chr3A 447269734 447275256 5522 False 10200.000000 10200 100.000000 1 5523 1 chr3A.!!$F1 5522
1 TraesCS3A01G238800 chr3A 408940595 408947287 6692 False 2040.000000 5116 93.912400 1 5523 5 chr3A.!!$F2 5522
2 TraesCS3A01G238800 chr3D 317553143 317559120 5977 True 1885.400000 8266 93.533400 5 5523 5 chr3D.!!$R2 5518
3 TraesCS3A01G238800 chr3B 401405009 401409938 4929 False 8113.000000 8113 96.429000 5 4922 1 chr3B.!!$F2 4917
4 TraesCS3A01G238800 chr3B 401410723 401411251 528 False 236.666667 350 96.165667 5012 5523 3 chr3B.!!$F5 511
5 TraesCS3A01G238800 chr6A 1462722 1464766 2044 True 1068.000000 1075 85.573500 2625 4816 2 chr6A.!!$R2 2191
6 TraesCS3A01G238800 chr6D 465352353 465354321 1968 True 519.500000 534 87.806500 3035 3482 2 chr6D.!!$R1 447
7 TraesCS3A01G238800 chr4B 669910747 669916792 6045 False 298.000000 379 85.664333 3248 4147 3 chr4B.!!$F1 899
8 TraesCS3A01G238800 chr4B 669911756 669916317 4561 True 293.500000 460 85.346333 3242 4147 6 chr4B.!!$R1 905

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
328 329 0.178900 AAAACCCTCGTCCTCTCCCT 60.179 55.000 0.0 0.0 0.0 4.20 F
2799 2881 2.368591 CTGGGGTACGGGAAGACAA 58.631 57.895 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2934 3016 1.630369 TGATTGCTAGCCTGGTCTTGT 59.370 47.619 13.29 0.0 0.00 3.16 R
4577 12822 7.573916 CACCGTTGCATAAAATGTCAATTAA 57.426 32.000 0.00 0.0 32.15 1.40 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
48 49 3.149196 AGTGGTCATTTCAAAGCGATGT 58.851 40.909 0.00 0.00 0.00 3.06
74 75 3.259314 TGGTGGGTGGCATGAGCT 61.259 61.111 0.00 0.00 41.70 4.09
328 329 0.178900 AAAACCCTCGTCCTCTCCCT 60.179 55.000 0.00 0.00 0.00 4.20
2186 2250 8.028354 TGAATTAATTGTCCAATTGTGCTACTG 58.972 33.333 14.02 0.00 40.83 2.74
2799 2881 2.368591 CTGGGGTACGGGAAGACAA 58.631 57.895 0.00 0.00 0.00 3.18
3033 3115 1.143684 CAGGGGTATGCTGGCTACATT 59.856 52.381 0.00 0.00 0.00 2.71
3383 3471 2.800250 ACAAGAAGAGCCTCATTTGGG 58.200 47.619 0.00 0.00 0.00 4.12
4577 12822 6.112058 GGAAGCTTCTGAGATTAGAATGTGT 58.888 40.000 25.05 0.00 36.21 3.72
4964 13395 2.746362 CAAAGAGGCAGATCCAACTGAC 59.254 50.000 0.00 0.00 45.37 3.51
4967 13398 3.233355 GGCAGATCCAACTGACGTT 57.767 52.632 0.00 0.00 39.94 3.99
4968 13399 2.380084 GGCAGATCCAACTGACGTTA 57.620 50.000 0.00 0.00 39.94 3.18
4969 13400 2.271800 GGCAGATCCAACTGACGTTAG 58.728 52.381 5.69 5.69 39.94 2.34
4970 13401 2.353803 GGCAGATCCAACTGACGTTAGT 60.354 50.000 7.24 7.24 39.94 2.24
4971 13402 3.326747 GCAGATCCAACTGACGTTAGTT 58.673 45.455 19.03 19.03 41.37 2.24
4972 13403 3.746492 GCAGATCCAACTGACGTTAGTTT 59.254 43.478 21.77 9.12 38.78 2.66
4973 13404 4.377431 GCAGATCCAACTGACGTTAGTTTG 60.377 45.833 21.77 18.46 38.78 2.93
4974 13405 4.750098 CAGATCCAACTGACGTTAGTTTGT 59.250 41.667 21.77 11.33 38.78 2.83
4976 13407 6.590292 CAGATCCAACTGACGTTAGTTTGTAT 59.410 38.462 21.77 14.98 38.78 2.29
4977 13408 7.117812 CAGATCCAACTGACGTTAGTTTGTATT 59.882 37.037 21.77 9.20 38.78 1.89
4978 13409 8.308931 AGATCCAACTGACGTTAGTTTGTATTA 58.691 33.333 21.77 4.70 38.78 0.98
4979 13410 7.878477 TCCAACTGACGTTAGTTTGTATTAG 57.122 36.000 21.77 9.68 38.78 1.73
4980 13411 7.436118 TCCAACTGACGTTAGTTTGTATTAGT 58.564 34.615 21.77 0.00 38.78 2.24
4981 13412 7.596248 TCCAACTGACGTTAGTTTGTATTAGTC 59.404 37.037 21.77 0.00 38.78 2.59
4982 13413 7.148689 CCAACTGACGTTAGTTTGTATTAGTCC 60.149 40.741 21.77 0.00 38.78 3.85
4983 13414 6.393171 ACTGACGTTAGTTTGTATTAGTCCC 58.607 40.000 7.24 0.00 0.00 4.46
4984 13415 6.210185 ACTGACGTTAGTTTGTATTAGTCCCT 59.790 38.462 7.24 0.00 0.00 4.20
5145 14766 3.995077 ACCTGGTCTATATACTCCCTCCA 59.005 47.826 0.00 0.00 0.00 3.86
5511 15607 7.555554 GGCAGGATAATGCTATCAACAGATTAT 59.444 37.037 0.00 0.00 45.75 1.28
5512 15608 8.954350 GCAGGATAATGCTATCAACAGATTATT 58.046 33.333 0.00 0.00 43.07 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.930019 CACCCACCAGCCCAGAGA 60.930 66.667 0.00 0.00 0.00 3.10
74 75 2.754552 GCATGATCTTGTGGCAAGGTAA 59.245 45.455 10.05 0.00 0.00 2.85
666 676 0.596082 CGGGTTTCGCAACAAATCCT 59.404 50.000 0.00 0.00 34.70 3.24
2934 3016 1.630369 TGATTGCTAGCCTGGTCTTGT 59.370 47.619 13.29 0.00 0.00 3.16
3033 3115 3.307691 CCATTTACTGAACTCCTGCTCCA 60.308 47.826 0.00 0.00 0.00 3.86
3383 3471 1.989430 CTGACCTCTGCGAGAACTTC 58.011 55.000 7.07 0.54 0.00 3.01
4577 12822 7.573916 CACCGTTGCATAAAATGTCAATTAA 57.426 32.000 0.00 0.00 32.15 1.40
4964 13395 8.992835 AACTAAGGGACTAATACAAACTAACG 57.007 34.615 0.00 0.00 38.49 3.18
4980 13411 9.895138 GGACAATAACTAATACAAACTAAGGGA 57.105 33.333 0.00 0.00 0.00 4.20
4981 13412 9.117183 GGGACAATAACTAATACAAACTAAGGG 57.883 37.037 0.00 0.00 0.00 3.95
4982 13413 9.675464 TGGGACAATAACTAATACAAACTAAGG 57.325 33.333 0.00 0.00 31.92 2.69
5145 14766 8.193953 ACAAATTGAGTCACTTATTTTGGGAT 57.806 30.769 16.81 0.00 30.25 3.85


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

AutoCloner maintained by Alex Coulton.