Multiple sequence alignment - TraesCS5A01G042000

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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 TraesCS5A01G042000 chr5A 100.000 3125 0 0 1 3125 37934223 37937347 0.000000e+00 5771.0
1 TraesCS5A01G042000 chr5D 95.874 2157 84 4 970 3125 47531139 47533291 0.000000e+00 3485.0
2 TraesCS5A01G042000 chr5D 91.688 397 27 5 364 756 47527817 47528211 2.120000e-151 545.0
3 TraesCS5A01G042000 chr5D 93.681 364 19 2 130 489 47527266 47527629 2.740000e-150 542.0
4 TraesCS5A01G042000 chr5D 93.333 135 6 3 362 493 47527634 47527768 2.460000e-46 196.0
5 TraesCS5A01G042000 chr5D 92.593 135 9 1 2 135 47526777 47526911 3.180000e-45 193.0
6 TraesCS5A01G042000 chr5D 89.552 134 10 3 364 493 47527726 47527859 1.930000e-37 167.0
7 TraesCS5A01G042000 chr5D 79.079 239 43 4 1467 1699 438177569 438177806 1.160000e-34 158.0
8 TraesCS5A01G042000 chr5D 91.379 58 5 0 913 970 47531058 47531115 2.580000e-11 80.5
9 TraesCS5A01G042000 chr7A 90.083 1563 115 23 1141 2675 674140351 674138801 0.000000e+00 1991.0
10 TraesCS5A01G042000 chr7A 97.222 36 1 0 772 807 694044215 694044250 9.360000e-06 62.1
11 TraesCS5A01G042000 chr7B 89.184 1544 114 26 784 2277 661724642 661723102 0.000000e+00 1877.0
12 TraesCS5A01G042000 chr7B 90.989 1254 94 7 1177 2414 661720294 661719044 0.000000e+00 1672.0
13 TraesCS5A01G042000 chr7B 88.546 227 22 2 2875 3098 661718568 661718343 3.970000e-69 272.0
14 TraesCS5A01G042000 chr7B 86.145 166 23 0 970 1135 661720456 661720291 2.480000e-41 180.0
15 TraesCS5A01G042000 chr7B 71.941 752 165 27 979 1713 620679018 620678296 8.910000e-41 178.0
16 TraesCS5A01G042000 chrUn 76.243 1267 212 52 1067 2303 225550838 225552045 9.650000e-165 590.0
17 TraesCS5A01G042000 chrUn 76.164 1267 213 52 1067 2303 285617446 285618653 4.490000e-163 584.0
18 TraesCS5A01G042000 chrUn 76.028 1264 214 52 1067 2300 221377713 221378917 9.720000e-160 573.0
19 TraesCS5A01G042000 chrUn 78.547 578 109 12 1821 2390 87051870 87051300 1.770000e-97 366.0
20 TraesCS5A01G042000 chrUn 95.000 40 2 0 416 455 42338381 42338342 2.600000e-06 63.9
21 TraesCS5A01G042000 chrUn 95.000 40 2 0 416 455 42530568 42530607 2.600000e-06 63.9
22 TraesCS5A01G042000 chrUn 95.000 40 2 0 416 455 474064221 474064260 2.600000e-06 63.9
23 TraesCS5A01G042000 chr6A 81.078 761 111 16 973 1713 17947296 17946549 7.520000e-161 577.0
24 TraesCS5A01G042000 chr6A 77.778 504 84 16 1212 1707 616890729 616890246 5.100000e-73 285.0
25 TraesCS5A01G042000 chr6A 82.075 106 3 7 786 875 616809559 616809664 3.340000e-10 76.8
26 TraesCS5A01G042000 chr7D 73.948 1639 315 72 979 2564 566520016 566521595 2.720000e-155 558.0
27 TraesCS5A01G042000 chr7D 76.471 748 138 26 1795 2528 602287615 602288338 3.810000e-99 372.0
28 TraesCS5A01G042000 chr6B 73.960 1563 311 67 979 2493 718597786 718596272 7.620000e-151 544.0
29 TraesCS5A01G042000 chr6B 74.759 725 152 18 979 1695 716425808 716426509 2.360000e-76 296.0
30 TraesCS5A01G042000 chr6B 79.259 405 64 10 1310 1707 718253060 718253451 6.650000e-67 265.0
31 TraesCS5A01G042000 chr6B 85.106 94 2 3 769 850 103288669 103288762 5.550000e-13 86.1
32 TraesCS5A01G042000 chr6D 80.606 330 39 17 811 1121 473104326 473104003 6.740000e-57 231.0
33 TraesCS5A01G042000 chr6D 88.136 177 11 2 1153 1328 473104007 473103840 5.280000e-48 202.0
34 TraesCS5A01G042000 chr6D 85.294 136 20 0 979 1114 472925118 472925253 1.170000e-29 141.0
35 TraesCS5A01G042000 chr5B 80.870 230 38 2 1463 1686 532768340 532768569 3.200000e-40 176.0
36 TraesCS5A01G042000 chr4B 86.170 94 1 3 769 850 139799181 139799088 1.190000e-14 91.6
37 TraesCS5A01G042000 chr4B 85.106 94 2 3 769 850 139809083 139809176 5.550000e-13 86.1
38 TraesCS5A01G042000 chr4B 82.353 85 7 5 769 851 645443953 645443875 2.010000e-07 67.6
39 TraesCS5A01G042000 chr3D 79.845 129 19 6 1481 1605 579599526 579599651 1.540000e-13 87.9
40 TraesCS5A01G042000 chr3D 97.500 40 1 0 415 454 611163086 611163125 5.590000e-08 69.4
41 TraesCS5A01G042000 chr1A 84.043 94 3 3 769 850 65242463 65242370 2.580000e-11 80.5
42 TraesCS5A01G042000 chr1A 81.915 94 5 3 769 850 65254456 65254549 5.590000e-08 69.4
43 TraesCS5A01G042000 chr3B 83.158 95 4 3 769 851 467380103 467380009 3.340000e-10 76.8
44 TraesCS5A01G042000 chr3B 97.500 40 1 0 415 454 828917458 828917497 5.590000e-08 69.4
45 TraesCS5A01G042000 chr4A 96.970 33 1 0 479 511 429541110 429541142 4.350000e-04 56.5


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 TraesCS5A01G042000 chr5A 37934223 37937347 3124 False 5771.000000 5771 100.000000 1 3125 1 chr5A.!!$F1 3124
1 TraesCS5A01G042000 chr5D 47526777 47533291 6514 False 744.071429 3485 92.585714 2 3125 7 chr5D.!!$F2 3123
2 TraesCS5A01G042000 chr7A 674138801 674140351 1550 True 1991.000000 1991 90.083000 1141 2675 1 chr7A.!!$R1 1534
3 TraesCS5A01G042000 chr7B 661718343 661724642 6299 True 1000.250000 1877 88.716000 784 3098 4 chr7B.!!$R2 2314
4 TraesCS5A01G042000 chrUn 225550838 225552045 1207 False 590.000000 590 76.243000 1067 2303 1 chrUn.!!$F3 1236
5 TraesCS5A01G042000 chrUn 285617446 285618653 1207 False 584.000000 584 76.164000 1067 2303 1 chrUn.!!$F4 1236
6 TraesCS5A01G042000 chrUn 221377713 221378917 1204 False 573.000000 573 76.028000 1067 2300 1 chrUn.!!$F2 1233
7 TraesCS5A01G042000 chrUn 87051300 87051870 570 True 366.000000 366 78.547000 1821 2390 1 chrUn.!!$R2 569
8 TraesCS5A01G042000 chr6A 17946549 17947296 747 True 577.000000 577 81.078000 973 1713 1 chr6A.!!$R1 740
9 TraesCS5A01G042000 chr7D 566520016 566521595 1579 False 558.000000 558 73.948000 979 2564 1 chr7D.!!$F1 1585
10 TraesCS5A01G042000 chr7D 602287615 602288338 723 False 372.000000 372 76.471000 1795 2528 1 chr7D.!!$F2 733
11 TraesCS5A01G042000 chr6B 718596272 718597786 1514 True 544.000000 544 73.960000 979 2493 1 chr6B.!!$R1 1514
12 TraesCS5A01G042000 chr6B 716425808 716426509 701 False 296.000000 296 74.759000 979 1695 1 chr6B.!!$F2 716

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
335 698 0.175989 GGGCTGAGTCTCCCTTAACG 59.824 60.0 12.18 0.0 39.46 3.18 F
342 705 0.389426 GTCTCCCTTAACGCTCGCAA 60.389 55.0 0.00 0.0 0.00 4.85 F
1008 4428 0.700564 ACCACCTGCTCATGGTCAAT 59.299 50.0 0.00 0.0 46.62 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 9195 0.039618 TTCCCCATCTTGTCCTTGGC 59.960 55.0 0.0 0.0 0.00 4.52 R
2036 9504 1.288508 ATGCCCCCAGCCATTACTCA 61.289 55.0 0.0 0.0 42.71 3.41 R
2652 10167 0.108089 GCTCCGACCTTTTCTCTCCC 60.108 60.0 0.0 0.0 0.00 4.30 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
29 30 7.395772 TCCATCACATGCTAAAATGTTTTCCTA 59.604 33.333 0.00 0.00 38.75 2.94
30 31 8.199449 CCATCACATGCTAAAATGTTTTCCTAT 58.801 33.333 0.00 0.00 38.75 2.57
135 137 7.953493 AGTAAAAGGAAATAGGGGAACATGAAA 59.047 33.333 0.00 0.00 0.00 2.69
138 140 7.813087 AAGGAAATAGGGGAACATGAAAAAT 57.187 32.000 0.00 0.00 0.00 1.82
274 637 6.016192 CGCTAGGTTTCTCATAGAGGACATAA 60.016 42.308 0.00 0.00 32.86 1.90
287 650 1.394917 GGACATAACGCTCAAGCACTG 59.605 52.381 2.50 0.00 42.21 3.66
288 651 0.798776 ACATAACGCTCAAGCACTGC 59.201 50.000 2.50 0.00 42.21 4.40
292 655 3.429141 CGCTCAAGCACTGCTGGG 61.429 66.667 3.73 0.26 39.62 4.45
311 674 2.439701 ATGGCTCATGCAAGCGCT 60.440 55.556 2.64 2.64 43.45 5.92
327 690 1.145819 GCTCCATGGGCTGAGTCTC 59.854 63.158 13.02 0.00 0.00 3.36
335 698 0.175989 GGGCTGAGTCTCCCTTAACG 59.824 60.000 12.18 0.00 39.46 3.18
339 702 0.809385 TGAGTCTCCCTTAACGCTCG 59.191 55.000 0.00 0.00 0.00 5.03
342 705 0.389426 GTCTCCCTTAACGCTCGCAA 60.389 55.000 0.00 0.00 0.00 4.85
444 1036 7.928307 AAGCAGCGTCAATTAATATGGATAT 57.072 32.000 0.00 0.00 0.00 1.63
489 1172 4.401519 TGCTACTGCGGAAAATAGTACTCT 59.598 41.667 0.00 0.00 43.34 3.24
493 1176 4.951094 ACTGCGGAAAATAGTACTCTCTCT 59.049 41.667 0.00 0.00 0.00 3.10
494 1177 6.120905 ACTGCGGAAAATAGTACTCTCTCTA 58.879 40.000 0.00 0.00 0.00 2.43
537 1220 5.964887 TTCATTTTCGAAAAGCCAAACAG 57.035 34.783 25.87 9.97 0.00 3.16
670 1353 9.426837 CATTGTGGATGTTGATATTTTGTTTCT 57.573 29.630 0.00 0.00 0.00 2.52
706 1389 8.312564 GTCAAAACAGAGGGAGTATTACTACTT 58.687 37.037 6.03 0.00 38.33 2.24
707 1390 9.537852 TCAAAACAGAGGGAGTATTACTACTTA 57.462 33.333 6.03 0.00 38.33 2.24
708 1391 9.804758 CAAAACAGAGGGAGTATTACTACTTAG 57.195 37.037 6.03 0.00 38.33 2.18
709 1392 7.585579 AACAGAGGGAGTATTACTACTTAGC 57.414 40.000 6.03 0.00 38.33 3.09
713 1396 8.475639 CAGAGGGAGTATTACTACTTAGCAAAA 58.524 37.037 6.03 0.00 38.33 2.44
714 1397 8.697292 AGAGGGAGTATTACTACTTAGCAAAAG 58.303 37.037 6.03 0.00 38.33 2.27
715 1398 7.793036 AGGGAGTATTACTACTTAGCAAAAGG 58.207 38.462 6.03 0.00 38.33 3.11
730 1413 5.327732 AGCAAAAGGAAATGGATTCTCTCA 58.672 37.500 0.00 0.00 38.18 3.27
756 1439 9.625747 AAAGAAAAAGCAAAAGGAAATGGATTA 57.374 25.926 0.00 0.00 0.00 1.75
758 1441 8.432013 AGAAAAAGCAAAAGGAAATGGATTACT 58.568 29.630 0.00 0.00 31.63 2.24
759 1442 9.705290 GAAAAAGCAAAAGGAAATGGATTACTA 57.295 29.630 0.00 0.00 29.54 1.82
764 1447 5.813080 AAAGGAAATGGATTACTACGTGC 57.187 39.130 0.00 0.00 29.54 5.34
765 1448 3.805207 AGGAAATGGATTACTACGTGCC 58.195 45.455 0.00 0.00 27.02 5.01
767 1450 4.080526 AGGAAATGGATTACTACGTGCCTT 60.081 41.667 0.00 0.00 27.02 4.35
769 1452 2.572191 TGGATTACTACGTGCCTTCG 57.428 50.000 0.00 0.00 0.00 3.79
770 1453 1.820519 TGGATTACTACGTGCCTTCGT 59.179 47.619 0.00 4.36 45.97 3.85
842 4219 3.565902 CCCAACTCCAAACTCTGAAACTC 59.434 47.826 0.00 0.00 0.00 3.01
843 4220 4.455606 CCAACTCCAAACTCTGAAACTCT 58.544 43.478 0.00 0.00 0.00 3.24
844 4221 4.884164 CCAACTCCAAACTCTGAAACTCTT 59.116 41.667 0.00 0.00 0.00 2.85
1008 4428 0.700564 ACCACCTGCTCATGGTCAAT 59.299 50.000 0.00 0.00 46.62 2.57
1012 4432 1.389609 CCTGCTCATGGTCAATGGCC 61.390 60.000 0.00 0.00 36.86 5.36
1187 4628 2.215604 CCGATGACGACGACGAAGC 61.216 63.158 15.32 3.69 42.66 3.86
1318 4762 0.890683 CTGGGGCAATGACAGGTTTC 59.109 55.000 0.00 0.00 0.00 2.78
1370 4814 5.355596 GGACCTCAAGTATGATTGTCTCAG 58.644 45.833 7.90 0.00 37.38 3.35
1579 5038 3.137484 CGATCCACGGTGTTCATGT 57.863 52.632 7.45 0.00 38.46 3.21
1605 5064 1.009997 TCTTTGGCCCCATGAAGGAT 58.990 50.000 0.00 0.00 41.22 3.24
1778 9195 0.804989 GAAATGTCGGAAGCTGTGGG 59.195 55.000 0.00 0.00 0.00 4.61
1813 9281 1.301677 GGAAGCGGCAGAGGTTGAAG 61.302 60.000 1.45 0.00 31.35 3.02
1857 9325 1.283793 CTTGTTTGTGGCGGCAGAG 59.716 57.895 13.91 0.00 0.00 3.35
2036 9504 2.548057 CGTGTTTGCAGACACTAATGGT 59.452 45.455 30.72 0.00 45.96 3.55
2063 9532 0.178953 GGCTGGGGGCATATTGTCAT 60.179 55.000 0.00 0.00 44.01 3.06
2109 9581 1.476891 CTCATTGCCATGCTTGCTTCT 59.523 47.619 0.00 0.00 0.00 2.85
2424 9934 4.893608 TCTGTGCATAGTGTTGTGTACAT 58.106 39.130 10.52 0.00 39.49 2.29
2652 10167 4.115199 GCTGCCCCACACCCCTAG 62.115 72.222 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.534475 AACATTTTAGCATGTGATGGACAT 57.466 33.333 0.00 0.00 46.98 3.06
103 105 6.999950 TCCCCTATTTCCTTTTACTTTTTGC 58.000 36.000 0.00 0.00 0.00 3.68
108 110 7.475299 TCATGTTCCCCTATTTCCTTTTACTT 58.525 34.615 0.00 0.00 0.00 2.24
215 578 0.852777 CGTATACATGGCGCACTGAC 59.147 55.000 10.83 0.00 0.00 3.51
224 587 3.679980 GGTTGCTATGCTCGTATACATGG 59.320 47.826 3.32 0.00 0.00 3.66
274 637 2.667536 CCAGCAGTGCTTGAGCGT 60.668 61.111 16.89 0.00 45.83 5.07
311 674 1.690633 GGGAGACTCAGCCCATGGA 60.691 63.158 15.22 0.00 44.07 3.41
327 690 1.003866 GCTTATTGCGAGCGTTAAGGG 60.004 52.381 14.41 0.00 0.00 3.95
339 702 4.256090 CGGGGCAGCGCTTATTGC 62.256 66.667 7.50 9.44 39.56 3.56
342 705 4.569180 ATGCGGGGCAGCGCTTAT 62.569 61.111 7.50 0.00 43.65 1.73
444 1036 7.067421 AGCAGTACTATTTATGTACTCCCTCA 58.933 38.462 0.00 0.00 45.93 3.86
460 1143 4.730949 ATTTTCCGCAGTAGCAGTACTA 57.269 40.909 0.00 0.00 37.40 1.82
465 1148 4.683832 AGTACTATTTTCCGCAGTAGCAG 58.316 43.478 0.00 0.00 42.27 4.24
473 1156 7.085746 GGAATAGAGAGAGTACTATTTTCCGC 58.914 42.308 0.00 0.00 38.76 5.54
474 1157 8.167605 TGGAATAGAGAGAGTACTATTTTCCG 57.832 38.462 0.00 0.00 39.89 4.30
489 1172 9.725019 AATATGCACGATATTTTGGAATAGAGA 57.275 29.630 0.00 0.00 34.07 3.10
494 1177 9.985730 AATGAAATATGCACGATATTTTGGAAT 57.014 25.926 5.49 0.00 44.15 3.01
506 1189 6.171006 GCTTTTCGAAAATGAAATATGCACG 58.829 36.000 22.73 8.27 37.66 5.34
507 1190 6.090628 TGGCTTTTCGAAAATGAAATATGCAC 59.909 34.615 22.73 13.51 37.66 4.57
518 1201 6.089249 AGATCTGTTTGGCTTTTCGAAAAT 57.911 33.333 22.73 4.85 0.00 1.82
662 1345 9.326413 TGTTTTGACCAAGTTTAAAGAAACAAA 57.674 25.926 3.60 0.00 46.30 2.83
670 1353 5.952947 TCCCTCTGTTTTGACCAAGTTTAAA 59.047 36.000 0.00 0.00 0.00 1.52
687 1370 7.584122 TTGCTAAGTAGTAATACTCCCTCTG 57.416 40.000 2.87 0.00 0.00 3.35
706 1389 6.484288 TGAGAGAATCCATTTCCTTTTGCTA 58.516 36.000 0.00 0.00 34.67 3.49
707 1390 5.327732 TGAGAGAATCCATTTCCTTTTGCT 58.672 37.500 0.00 0.00 34.67 3.91
708 1391 5.649782 TGAGAGAATCCATTTCCTTTTGC 57.350 39.130 0.00 0.00 34.67 3.68
709 1392 7.889469 TCTTTGAGAGAATCCATTTCCTTTTG 58.111 34.615 0.00 0.00 34.67 2.44
713 1396 8.482852 TTTTTCTTTGAGAGAATCCATTTCCT 57.517 30.769 0.00 0.00 43.65 3.36
714 1397 7.330454 GCTTTTTCTTTGAGAGAATCCATTTCC 59.670 37.037 0.00 0.00 43.65 3.13
715 1398 7.869429 TGCTTTTTCTTTGAGAGAATCCATTTC 59.131 33.333 0.00 0.00 43.65 2.17
730 1413 8.523915 AATCCATTTCCTTTTGCTTTTTCTTT 57.476 26.923 0.00 0.00 0.00 2.52
756 1439 2.564975 CCGACGAAGGCACGTAGT 59.435 61.111 9.43 0.00 46.52 2.73
793 4163 4.043200 GCGAACCTGGGCTTGCAC 62.043 66.667 0.00 0.00 0.00 4.57
856 4238 5.794894 TCACCATTCCTAACTTTCAGAGTC 58.205 41.667 0.00 0.00 37.72 3.36
862 4244 5.710099 TCACCATTCACCATTCCTAACTTTC 59.290 40.000 0.00 0.00 0.00 2.62
871 4253 3.679389 ACTCAGTCACCATTCACCATTC 58.321 45.455 0.00 0.00 0.00 2.67
1012 4432 3.114616 CTCCTTGGTGCGCGAGTG 61.115 66.667 12.10 0.00 0.00 3.51
1126 4546 2.020016 CGAAATGAAGTCGGCGCG 59.980 61.111 0.00 0.00 34.85 6.86
1318 4762 0.891373 TCAAGGGCGTCTCTTCTGAG 59.109 55.000 0.00 0.00 41.51 3.35
1579 5038 2.282180 GGGGCCAAAGAGTTGCGA 60.282 61.111 4.39 0.00 33.01 5.10
1605 5064 1.069358 TGTATGACACTGTTGGACGCA 59.931 47.619 0.00 0.00 0.00 5.24
1778 9195 0.039618 TTCCCCATCTTGTCCTTGGC 59.960 55.000 0.00 0.00 0.00 4.52
1808 9276 2.598394 GCAGCAGCCCCACTTCAA 60.598 61.111 0.00 0.00 33.58 2.69
1813 9281 3.766691 CCATTGCAGCAGCCCCAC 61.767 66.667 0.00 0.00 41.13 4.61
1857 9325 2.353607 CGCTGGAGATCGTACCGC 60.354 66.667 0.00 1.22 0.00 5.68
2036 9504 1.288508 ATGCCCCCAGCCATTACTCA 61.289 55.000 0.00 0.00 42.71 3.41
2063 9532 4.562757 CGTTCAAAACAGAGGGATAGGTCA 60.563 45.833 0.00 0.00 0.00 4.02
2109 9581 5.723672 CAGAGTGTTACTTCCTCTGGTTA 57.276 43.478 14.73 0.00 45.39 2.85
2424 9934 3.010027 TGACAGGGAAGGCATGACATTAA 59.990 43.478 0.00 0.00 0.00 1.40
2652 10167 0.108089 GCTCCGACCTTTTCTCTCCC 60.108 60.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.