Multiple sequence alignment - TraesCS1B01G136200

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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 TraesCS1B01G136200 chr1B 100.000 7345 0 0 1 7345 173978777 173971433 0.000000e+00 13564.0
1 TraesCS1B01G136200 chr1D 96.541 5349 112 23 1589 6918 113876039 113870745 0.000000e+00 8785.0
2 TraesCS1B01G136200 chr1D 92.450 1245 50 15 363 1592 113877321 113876106 0.000000e+00 1738.0
3 TraesCS1B01G136200 chr1D 91.160 181 14 2 200 378 121437330 121437150 2.050000e-60 244.0
4 TraesCS1B01G136200 chr1D 91.018 167 14 1 1 166 323071303 323071137 2.670000e-54 224.0
5 TraesCS1B01G136200 chr1D 98.113 53 1 0 6916 6968 113870777 113870725 7.850000e-15 93.5
6 TraesCS1B01G136200 chr1A 96.543 5004 129 20 1589 6577 121745217 121740243 0.000000e+00 8242.0
7 TraesCS1B01G136200 chr1A 90.885 746 39 15 366 1099 121746511 121745783 0.000000e+00 974.0
8 TraesCS1B01G136200 chr1A 95.732 328 11 3 1128 1453 121745788 121745462 6.530000e-145 525.0
9 TraesCS1B01G136200 chr1A 92.373 354 15 8 6576 6918 121740160 121739808 1.840000e-135 494.0
10 TraesCS1B01G136200 chr6B 94.180 3969 179 17 1589 5544 84125000 84128929 0.000000e+00 6002.0
11 TraesCS1B01G136200 chr6B 84.102 1258 106 46 5655 6857 84128962 84130180 0.000000e+00 1129.0
12 TraesCS1B01G136200 chr6B 80.930 645 64 32 779 1396 84124213 84124825 8.690000e-124 455.0
13 TraesCS1B01G136200 chr6B 86.058 208 12 3 552 742 84120029 84120236 2.690000e-49 207.0
14 TraesCS1B01G136200 chr6B 84.211 133 14 3 443 569 84119864 84119995 1.000000e-23 122.0
15 TraesCS1B01G136200 chr6A 93.720 3981 192 24 1589 5544 47898357 47902304 0.000000e+00 5914.0
16 TraesCS1B01G136200 chr6A 88.058 829 65 14 5651 6467 47902334 47903140 0.000000e+00 952.0
17 TraesCS1B01G136200 chr6A 81.067 581 55 32 845 1396 47897625 47898179 5.300000e-111 412.0
18 TraesCS1B01G136200 chr6A 87.273 165 20 1 1 164 109066204 109066040 3.500000e-43 187.0
19 TraesCS1B01G136200 chr6A 87.273 165 20 1 1 164 109092998 109092834 3.500000e-43 187.0
20 TraesCS1B01G136200 chr6A 82.791 215 13 10 552 742 47893471 47893685 3.520000e-38 171.0
21 TraesCS1B01G136200 chr6A 82.297 209 15 13 6479 6677 47903187 47903383 2.120000e-35 161.0
22 TraesCS1B01G136200 chr6A 79.365 252 30 15 6641 6872 47903386 47903635 2.740000e-34 158.0
23 TraesCS1B01G136200 chr6A 82.877 146 13 6 435 569 47893302 47893446 3.600000e-23 121.0
24 TraesCS1B01G136200 chrUn 94.338 3197 148 10 1589 4773 143899029 143902204 0.000000e+00 4870.0
25 TraesCS1B01G136200 chrUn 93.694 777 35 9 4778 5550 143902244 143903010 0.000000e+00 1151.0
26 TraesCS1B01G136200 chrUn 90.231 737 52 10 5745 6465 143903089 143903821 0.000000e+00 944.0
27 TraesCS1B01G136200 chrUn 80.995 663 69 30 779 1399 143898214 143898861 2.400000e-129 473.0
28 TraesCS1B01G136200 chrUn 79.230 727 96 32 1628 2305 75223049 75223769 8.690000e-124 455.0
29 TraesCS1B01G136200 chrUn 86.242 298 27 9 7041 7329 50799244 50798952 1.990000e-80 311.0
30 TraesCS1B01G136200 chrUn 91.556 225 18 1 1590 1813 104961974 104962198 7.160000e-80 309.0
31 TraesCS1B01G136200 chrUn 80.056 356 25 11 427 738 143894325 143894678 9.590000e-54 222.0
32 TraesCS1B01G136200 chrUn 87.273 165 20 1 1 164 477248543 477248379 3.500000e-43 187.0
33 TraesCS1B01G136200 chr3D 93.839 1331 65 9 1589 2912 7924894 7923574 0.000000e+00 1988.0
34 TraesCS1B01G136200 chr7D 92.544 228 16 1 1590 1816 27866305 27866078 7.110000e-85 326.0
35 TraesCS1B01G136200 chr7D 94.375 160 8 1 201 359 45837348 45837507 2.050000e-60 244.0
36 TraesCS1B01G136200 chr7B 85.526 304 35 3 7041 7341 36601672 36601375 7.160000e-80 309.0
37 TraesCS1B01G136200 chr7B 84.365 307 37 5 7042 7341 28066638 28066336 2.590000e-74 291.0
38 TraesCS1B01G136200 chr6D 84.967 306 37 5 7041 7341 459281413 459281112 1.200000e-77 302.0
39 TraesCS1B01G136200 chr6D 79.134 254 32 12 1628 1869 468945629 468945873 9.870000e-34 156.0
40 TraesCS1B01G136200 chr6D 83.226 155 13 7 2045 2189 468585696 468585545 5.980000e-26 130.0
41 TraesCS1B01G136200 chr6D 89.535 86 6 2 2135 2217 468916504 468916589 1.010000e-18 106.0
42 TraesCS1B01G136200 chr6D 80.000 135 20 4 931 1064 468914789 468914917 7.850000e-15 93.5
43 TraesCS1B01G136200 chr5B 84.918 305 37 5 7041 7341 188021039 188020740 4.310000e-77 300.0
44 TraesCS1B01G136200 chr5B 84.667 300 37 4 7041 7335 636932097 636932392 2.590000e-74 291.0
45 TraesCS1B01G136200 chr5B 84.142 309 37 8 7041 7343 678441921 678441619 9.320000e-74 289.0
46 TraesCS1B01G136200 chr5B 89.778 225 22 1 1590 1813 380783005 380783229 3.350000e-73 287.0
47 TraesCS1B01G136200 chr5B 92.982 171 11 1 200 369 521152509 521152679 1.580000e-61 248.0
48 TraesCS1B01G136200 chr5B 89.820 167 13 4 2 166 106247950 106248114 2.080000e-50 211.0
49 TraesCS1B01G136200 chr7A 84.488 303 38 6 7047 7345 669403132 669403429 2.590000e-74 291.0
50 TraesCS1B01G136200 chr7A 92.529 174 11 2 195 366 6316658 6316831 1.580000e-61 248.0
51 TraesCS1B01G136200 chr5D 84.314 306 39 5 7041 7341 16748996 16748695 2.590000e-74 291.0
52 TraesCS1B01G136200 chr5D 92.045 176 12 2 194 367 274578002 274578177 5.690000e-61 246.0
53 TraesCS1B01G136200 chr4B 92.655 177 12 1 199 374 80990645 80990821 3.400000e-63 254.0
54 TraesCS1B01G136200 chr4B 86.061 165 20 2 1 164 364199752 364199914 2.720000e-39 174.0
55 TraesCS1B01G136200 chr3B 92.135 178 12 2 197 373 571752694 571752518 4.400000e-62 250.0
56 TraesCS1B01G136200 chr3B 87.574 169 16 3 1 164 789543855 789544023 2.700000e-44 191.0
57 TraesCS1B01G136200 chr3B 77.742 310 67 2 3332 3640 525608744 525609052 9.730000e-44 189.0
58 TraesCS1B01G136200 chr2D 92.135 178 12 2 199 375 5663392 5663216 4.400000e-62 250.0
59 TraesCS1B01G136200 chr2D 91.713 181 13 2 200 378 309971416 309971596 4.400000e-62 250.0
60 TraesCS1B01G136200 chr2D 91.617 167 13 1 1 166 556043129 556043295 5.730000e-56 230.0
61 TraesCS1B01G136200 chr5A 87.879 165 19 1 1 164 642507594 642507430 7.520000e-45 193.0


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 TraesCS1B01G136200 chr1B 173971433 173978777 7344 True 13564.000000 13564 100.000000 1 7345 1 chr1B.!!$R1 7344
1 TraesCS1B01G136200 chr1D 113870725 113877321 6596 True 3538.833333 8785 95.701333 363 6968 3 chr1D.!!$R3 6605
2 TraesCS1B01G136200 chr1A 121739808 121746511 6703 True 2558.750000 8242 93.883250 366 6918 4 chr1A.!!$R1 6552
3 TraesCS1B01G136200 chr6B 84119864 84130180 10316 False 1583.000000 6002 85.896200 443 6857 5 chr6B.!!$F1 6414
4 TraesCS1B01G136200 chr6A 47893302 47903635 10333 False 1127.000000 5914 84.310714 435 6872 7 chr6A.!!$F1 6437
5 TraesCS1B01G136200 chrUn 143894325 143903821 9496 False 1532.000000 4870 87.862800 427 6465 5 chrUn.!!$F3 6038
6 TraesCS1B01G136200 chrUn 75223049 75223769 720 False 455.000000 455 79.230000 1628 2305 1 chrUn.!!$F1 677
7 TraesCS1B01G136200 chr3D 7923574 7924894 1320 True 1988.000000 1988 93.839000 1589 2912 1 chr3D.!!$R1 1323


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
26 27 0.032515 TCTAGAAGGATGCCACCCGA 60.033 55.000 0.00 0.00 0.00 5.14 F
103 104 0.036952 ATGTTCGAGCTCCCAGTGTG 60.037 55.000 8.47 0.00 0.00 3.82 F
807 5095 0.106217 GAGTGGAGGAGGAGGAGGAG 60.106 65.000 0.00 0.00 0.00 3.69 F
1157 5482 1.154225 GTCGGCGCCATTTCTGTTG 60.154 57.895 28.98 6.54 0.00 3.33 F
1513 5920 1.280457 ATCTGTTCCAGACCTCACCC 58.720 55.000 0.00 0.00 43.63 4.61 F
2580 7213 1.351017 GTGAGGATTGTGGACCCTTCA 59.649 52.381 0.00 0.00 0.00 3.02 F
2985 7623 1.999648 TTCCTGCAAACCAGCTCAAT 58.000 45.000 0.00 0.00 40.36 2.57 F
3195 7833 2.012673 GACAGGCTTGCATTGAGGTAG 58.987 52.381 0.00 0.00 0.00 3.18 F
4089 8745 2.093973 ACTGGTATGCGTTCTCTTCTGG 60.094 50.000 0.00 0.00 0.00 3.86 F
4404 9060 2.434336 TGTAAGTCTGGTGCTGTCTGTT 59.566 45.455 0.00 0.00 0.00 3.16 F
6266 10960 1.045350 TCGCCTCCATCTTCTCCCTG 61.045 60.000 0.00 0.00 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1214 5539 1.280142 CTAGATCCACCGACTCGCG 59.720 63.158 0.00 0.00 40.47 5.87 R
1264 5606 1.691976 AGATTCATGCGTAATCGGGGA 59.308 47.619 0.00 0.00 38.20 4.81 R
2583 7216 2.839228 AGCCCATAGGAGTTCAAGTCT 58.161 47.619 0.00 0.00 33.47 3.24 R
2905 7542 4.215109 ACCCTGCAAAGACAAAAGTACAT 58.785 39.130 0.00 0.00 0.00 2.29 R
3195 7833 3.929094 TGTAGACCCATTTGTCGTAACC 58.071 45.455 0.00 0.00 40.26 2.85 R
4404 9060 3.044235 AGTGCTGTCGTCATGATGAAA 57.956 42.857 19.12 13.25 0.00 2.69 R
4420 9076 4.453819 AGCATGTAAGAGACAAGAAAGTGC 59.546 41.667 0.00 0.00 42.78 4.40 R
4866 9558 6.371595 AACCTGATGAGATTCAGAAAGAGT 57.628 37.500 3.10 0.00 44.88 3.24 R
5864 10557 4.226761 CAATAACCCAAAACTGCTCGTTC 58.773 43.478 0.00 0.00 33.90 3.95 R
6329 11023 0.671472 CAGATCAGCAGTTGACGCCA 60.671 55.000 0.00 0.00 38.99 5.69 R
7322 12260 0.687354 AGAATGGAAGTCACGGTGCT 59.313 50.000 2.51 1.17 30.01 4.40 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)



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AutoCloner maintained by Alex Coulton.