Multiple sequence alignment - TraesCS3A01G452400

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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 TraesCS3A01G452400 chr3A 100.000 4136 0 0 1 4136 690783602 690787737 0.000000e+00 7638.0
1 TraesCS3A01G452400 chr3A 93.949 2264 107 10 1414 3672 690857624 690859862 0.000000e+00 3395.0
2 TraesCS3A01G452400 chr3A 91.193 2112 127 31 1241 3334 690896500 690898570 0.000000e+00 2815.0
3 TraesCS3A01G452400 chr3A 92.841 433 28 3 3706 4136 690860178 690860609 3.510000e-175 625.0
4 TraesCS3A01G452400 chr3A 82.114 738 74 19 430 1116 690856861 690857591 2.770000e-161 579.0
5 TraesCS3A01G452400 chr3A 86.508 378 36 6 761 1133 690896098 690896465 6.440000e-108 401.0
6 TraesCS3A01G452400 chr3A 84.444 315 39 9 651 956 690795986 690796299 6.720000e-78 302.0
7 TraesCS3A01G452400 chr3A 87.793 213 17 5 744 956 690752830 690753033 1.490000e-59 241.0
8 TraesCS3A01G452400 chr3A 76.344 465 64 25 300 727 690895580 690896035 1.510000e-49 207.0
9 TraesCS3A01G452400 chr3A 76.970 330 38 23 300 601 690751818 690752137 1.990000e-33 154.0
10 TraesCS3A01G452400 chr3D 95.224 2994 111 14 1156 4136 554216660 554219634 0.000000e+00 4708.0
11 TraesCS3A01G452400 chr3D 93.886 1979 100 13 1375 3334 554328749 554330725 0.000000e+00 2964.0
12 TraesCS3A01G452400 chr3D 96.532 346 10 1 788 1131 554216330 554216675 4.640000e-159 571.0
13 TraesCS3A01G452400 chr3D 80.946 719 55 36 430 1100 554317271 554317955 1.030000e-135 494.0
14 TraesCS3A01G452400 chr3D 92.056 214 15 2 744 956 554170121 554170333 2.420000e-77 300.0
15 TraesCS3A01G452400 chr3D 83.616 177 26 1 425 601 554169596 554169769 3.310000e-36 163.0
16 TraesCS3A01G452400 chr3D 92.188 64 2 1 1424 1487 554318339 554318399 2.050000e-13 87.9
17 TraesCS3A01G452400 chr3B 95.100 3000 121 15 1148 4136 736310747 736313731 0.000000e+00 4702.0
18 TraesCS3A01G452400 chr3B 91.612 2146 118 28 1244 3340 736324828 736326960 0.000000e+00 2909.0
19 TraesCS3A01G452400 chr3B 92.754 1173 46 10 2 1144 736309612 736310775 0.000000e+00 1659.0
20 TraesCS3A01G452400 chr3B 86.198 384 46 6 761 1140 736324409 736324789 3.850000e-110 409.0
21 TraesCS3A01G452400 chr3B 88.837 215 14 6 744 956 736304514 736304720 5.310000e-64 255.0
22 TraesCS3A01G452400 chr3B 83.588 262 24 8 479 727 736324091 736324346 1.160000e-55 228.0
23 TraesCS3A01G452400 chr3B 93.333 75 5 0 1154 1228 736324767 736324841 1.220000e-20 111.0
24 TraesCS3A01G452400 chr3B 90.698 43 4 0 559 601 736253604 736253646 1.610000e-04 58.4
25 TraesCS3A01G452400 chr1B 89.628 1880 168 14 1461 3317 121715423 121713548 0.000000e+00 2366.0
26 TraesCS3A01G452400 chr1B 80.515 272 49 4 3 272 660919356 660919087 5.420000e-49 206.0
27 TraesCS3A01G452400 chr1D 91.583 1699 143 0 1461 3159 78066947 78065249 0.000000e+00 2346.0
28 TraesCS3A01G452400 chr1D 80.488 246 41 5 2 244 454899195 454899436 9.130000e-42 182.0
29 TraesCS3A01G452400 chr1A 89.683 1735 165 8 1428 3159 105302948 105304671 0.000000e+00 2200.0
30 TraesCS3A01G452400 chr1A 88.199 1449 169 2 1711 3159 109416571 109415125 0.000000e+00 1727.0
31 TraesCS3A01G452400 chr6D 82.642 265 41 4 6 267 303028848 303028586 3.220000e-56 230.0
32 TraesCS3A01G452400 chr6D 79.323 266 53 2 2 267 6772669 6772406 7.060000e-43 185.0
33 TraesCS3A01G452400 chr6B 81.181 271 50 1 2 271 595230575 595230305 2.500000e-52 217.0
34 TraesCS3A01G452400 chr6B 97.143 35 1 0 3976 4010 714083694 714083728 4.470000e-05 60.2
35 TraesCS3A01G452400 chr7A 81.132 265 46 4 5 267 553237399 553237137 4.190000e-50 209.0
36 TraesCS3A01G452400 chr4D 79.699 266 49 5 3 267 309623155 309622894 1.960000e-43 187.0
37 TraesCS3A01G452400 chr2B 78.652 267 56 1 3 269 770230146 770229881 4.250000e-40 176.0


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 TraesCS3A01G452400 chr3A 690783602 690787737 4135 False 7638.00 7638 100.000000 1 4136 1 chr3A.!!$F1 4135
1 TraesCS3A01G452400 chr3A 690856861 690860609 3748 False 1533.00 3395 89.634667 430 4136 3 chr3A.!!$F4 3706
2 TraesCS3A01G452400 chr3A 690895580 690898570 2990 False 1141.00 2815 84.681667 300 3334 3 chr3A.!!$F5 3034
3 TraesCS3A01G452400 chr3D 554328749 554330725 1976 False 2964.00 2964 93.886000 1375 3334 1 chr3D.!!$F1 1959
4 TraesCS3A01G452400 chr3D 554216330 554219634 3304 False 2639.50 4708 95.878000 788 4136 2 chr3D.!!$F3 3348
5 TraesCS3A01G452400 chr3D 554317271 554318399 1128 False 290.95 494 86.567000 430 1487 2 chr3D.!!$F4 1057
6 TraesCS3A01G452400 chr3D 554169596 554170333 737 False 231.50 300 87.836000 425 956 2 chr3D.!!$F2 531
7 TraesCS3A01G452400 chr3B 736309612 736313731 4119 False 3180.50 4702 93.927000 2 4136 2 chr3B.!!$F3 4134
8 TraesCS3A01G452400 chr3B 736324091 736326960 2869 False 914.25 2909 88.682750 479 3340 4 chr3B.!!$F4 2861
9 TraesCS3A01G452400 chr1B 121713548 121715423 1875 True 2366.00 2366 89.628000 1461 3317 1 chr1B.!!$R1 1856
10 TraesCS3A01G452400 chr1D 78065249 78066947 1698 True 2346.00 2346 91.583000 1461 3159 1 chr1D.!!$R1 1698
11 TraesCS3A01G452400 chr1A 105302948 105304671 1723 False 2200.00 2200 89.683000 1428 3159 1 chr1A.!!$F1 1731
12 TraesCS3A01G452400 chr1A 109415125 109416571 1446 True 1727.00 1727 88.199000 1711 3159 1 chr1A.!!$R1 1448

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
236 237 0.315251 CCGCGGATAGATGCAGAAGA 59.685 55.000 24.07 0.00 0.00 2.87 F
263 264 0.770499 TGGGTTGCTGTTGGAGATGA 59.230 50.000 0.00 0.00 0.00 2.92 F
266 267 1.271597 GGTTGCTGTTGGAGATGACCT 60.272 52.381 0.00 0.00 0.00 3.85 F
731 941 1.272037 GCCTCTAGCCGTCCTACCTAT 60.272 57.143 0.00 0.00 34.35 2.57 F
2461 2945 1.870016 GACGAGCGCCTCTTCTTCG 60.870 63.158 2.29 7.72 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1246 1554 1.214367 TCGTCACGACCTTTGAAAGC 58.786 50.000 0.00 0.0 0.00 3.51 R
2025 2501 1.374252 CCGCAGCAGGTACGTCTTT 60.374 57.895 0.00 0.0 0.00 2.52 R
2097 2573 2.125269 GCGCCCACTACCGTGAAT 60.125 61.111 0.00 0.0 43.97 2.57 R
2609 3094 0.603569 CGTGTAGAGGCCACTTGTCT 59.396 55.000 8.39 1.8 0.00 3.41 R
3973 4788 0.036010 AAGAATGTCCGGCCTCTGTG 60.036 55.000 0.00 0.0 0.00 3.66 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
91 92 5.820423 TCCAGTTTGTATGAAATCCGGTATG 59.180 40.000 0.00 0.00 0.00 2.39
110 111 3.916359 TGTTTATATGAAGTCCGGCCA 57.084 42.857 2.24 0.00 0.00 5.36
144 145 8.879342 TGAATTTCATACGGTTTGTTGAAAAT 57.121 26.923 0.00 4.95 39.12 1.82
151 152 8.188799 TCATACGGTTTGTTGAAAATGTGTTTA 58.811 29.630 0.00 0.00 0.00 2.01
157 158 8.793472 GGTTTGTTGAAAATGTGTTTAAAATGC 58.207 29.630 0.00 0.00 0.00 3.56
163 164 7.353497 TGAAAATGTGTTTAAAATGCATGCTG 58.647 30.769 20.33 0.00 0.00 4.41
169 170 4.083057 TGTTTAAAATGCATGCTGCTACGA 60.083 37.500 20.33 0.00 45.31 3.43
171 172 3.344904 AAAATGCATGCTGCTACGATC 57.655 42.857 20.33 0.00 45.31 3.69
209 210 1.125093 TCCATGTCCACGGACTGGTT 61.125 55.000 22.97 5.59 44.80 3.67
224 225 3.782443 GTTCCCCTGTCCGCGGAT 61.782 66.667 33.58 0.00 0.00 4.18
225 226 2.042741 TTCCCCTGTCCGCGGATA 60.043 61.111 33.58 28.44 0.00 2.59
226 227 2.131709 TTCCCCTGTCCGCGGATAG 61.132 63.158 36.82 36.82 33.88 2.08
233 234 1.106944 TGTCCGCGGATAGATGCAGA 61.107 55.000 33.58 0.48 0.00 4.26
236 237 0.315251 CCGCGGATAGATGCAGAAGA 59.685 55.000 24.07 0.00 0.00 2.87
250 251 7.325694 AGATGCAGAAGAAAATTTATGGGTTG 58.674 34.615 0.00 0.00 0.00 3.77
251 252 5.237048 TGCAGAAGAAAATTTATGGGTTGC 58.763 37.500 0.00 0.00 0.00 4.17
252 253 5.011943 TGCAGAAGAAAATTTATGGGTTGCT 59.988 36.000 11.92 0.00 0.00 3.91
263 264 0.770499 TGGGTTGCTGTTGGAGATGA 59.230 50.000 0.00 0.00 0.00 2.92
266 267 1.271597 GGTTGCTGTTGGAGATGACCT 60.272 52.381 0.00 0.00 0.00 3.85
267 268 2.027192 GGTTGCTGTTGGAGATGACCTA 60.027 50.000 0.00 0.00 0.00 3.08
268 269 3.559171 GGTTGCTGTTGGAGATGACCTAA 60.559 47.826 0.00 0.00 0.00 2.69
269 270 4.265073 GTTGCTGTTGGAGATGACCTAAT 58.735 43.478 0.00 0.00 0.00 1.73
461 474 4.561105 GGATAGAGTCCGTGATTTGATCC 58.439 47.826 0.00 0.00 37.23 3.36
494 507 1.785951 GTTCCCGCGTTAACTCAGC 59.214 57.895 4.92 0.00 0.00 4.26
722 932 4.824515 AGCCTCGCCTCTAGCCGT 62.825 66.667 0.00 0.00 38.78 5.68
727 937 1.508808 CTCGCCTCTAGCCGTCCTAC 61.509 65.000 0.00 0.00 38.78 3.18
731 941 1.272037 GCCTCTAGCCGTCCTACCTAT 60.272 57.143 0.00 0.00 34.35 2.57
1127 1401 9.945904 TGTCGTGAGTACAATATCTATCTATCT 57.054 33.333 0.00 0.00 0.00 1.98
1221 1529 7.837863 TGATCACTTCTCGGTAGATTTACTTT 58.162 34.615 0.00 0.00 0.00 2.66
1229 1537 7.673180 TCTCGGTAGATTTACTTTCAAAGGAA 58.327 34.615 1.31 0.00 0.00 3.36
1230 1538 7.601508 TCTCGGTAGATTTACTTTCAAAGGAAC 59.398 37.037 1.31 0.00 28.99 3.62
1232 1540 6.312487 GGTAGATTTACTTTCAAAGGAACGC 58.688 40.000 1.31 0.00 28.99 4.84
1235 1543 5.998363 AGATTTACTTTCAAAGGAACGCTCT 59.002 36.000 1.31 0.00 28.99 4.09
1242 1550 5.432885 TTCAAAGGAACGCTCTAAAAAGG 57.567 39.130 0.00 0.00 0.00 3.11
1246 1554 4.830826 AGGAACGCTCTAAAAAGGTTTG 57.169 40.909 0.00 0.00 0.00 2.93
1285 1622 4.025145 ACGATAATAAACTAGCTTTGCGCC 60.025 41.667 4.18 0.00 40.39 6.53
1331 1679 6.203145 TGGATGTGCATCATGAAAACAAAAAG 59.797 34.615 13.37 0.00 39.54 2.27
1630 2106 4.720902 CCATCCACTGGCACGGCA 62.721 66.667 0.00 0.00 38.47 5.69
1881 2357 4.021925 GGCGAGTGGTGGGAGCTT 62.022 66.667 0.00 0.00 0.00 3.74
2097 2573 2.126596 CAAGGTTGCTGGGCACACA 61.127 57.895 0.00 0.00 38.71 3.72
2280 2764 2.284405 ATCCCGGGGTTCGTGTCT 60.284 61.111 23.50 0.00 37.11 3.41
2461 2945 1.870016 GACGAGCGCCTCTTCTTCG 60.870 63.158 2.29 7.72 0.00 3.79
2609 3094 2.099756 TCGAGAGATACTACGACGGTCA 59.900 50.000 9.10 0.00 33.31 4.02
3227 3729 8.980610 CAAAATAAGAACAAATGAAGATGCACA 58.019 29.630 0.00 0.00 0.00 4.57
3340 3864 1.192428 GTCGGTCCAGTAGGGTTCAT 58.808 55.000 0.00 0.00 38.11 2.57
3355 3879 5.321927 AGGGTTCATTGTCGGAAATAAGTT 58.678 37.500 0.00 0.00 0.00 2.66
3415 3939 4.517285 ACGAACTGGCTGATATCACAAAT 58.483 39.130 0.00 0.00 0.00 2.32
3480 4004 0.328258 AACTCAAACCTCCCCGGATG 59.672 55.000 0.73 0.00 36.31 3.51
3561 4088 4.693283 TGACAGGTGTTGTAGAAGAAGTG 58.307 43.478 0.00 0.00 41.05 3.16
3679 4206 2.279741 GTGCCTCATAACGATGCAGAA 58.720 47.619 0.00 0.00 44.64 3.02
3695 4222 3.966543 AAGCCAGGGGGTTCCACG 61.967 66.667 0.00 0.00 39.37 4.94
3905 4720 1.667236 CATTGCATAGCCCTCGTCAA 58.333 50.000 0.00 0.00 0.00 3.18
3926 4741 7.375017 CGTCAAAACTCTGTAATTGGTTTGTAC 59.625 37.037 0.00 0.00 33.09 2.90
3932 4747 5.882040 TCTGTAATTGGTTTGTACATGGGA 58.118 37.500 0.00 0.00 0.00 4.37
3973 4788 4.574828 ACAAGTGGGATCGCATTATGTAAC 59.425 41.667 16.24 0.24 0.00 2.50
3995 4810 0.984230 AGAGGCCGGACATTCTTTCA 59.016 50.000 11.69 0.00 0.00 2.69
4128 4945 6.683974 ATGTTAGTGTTGGTTATCTGCATC 57.316 37.500 0.00 0.00 0.00 3.91
4129 4946 4.629634 TGTTAGTGTTGGTTATCTGCATCG 59.370 41.667 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.932799 AGCATAAAACTATGTGCACGTACA 59.067 37.500 14.85 0.00 39.94 2.90
54 55 8.928733 TCATACAAACTGGACGAAAATACTTAC 58.071 33.333 0.00 0.00 0.00 2.34
91 92 4.134563 ACATGGCCGGACTTCATATAAAC 58.865 43.478 9.82 0.00 0.00 2.01
110 111 5.964758 ACCGTATGAAATTCATGCAAACAT 58.035 33.333 20.71 2.00 39.07 2.71
123 124 7.036220 ACACATTTTCAACAAACCGTATGAAA 58.964 30.769 0.00 0.00 39.33 2.69
129 130 7.653767 TTTAAACACATTTTCAACAAACCGT 57.346 28.000 0.00 0.00 0.00 4.83
157 158 1.066136 CATCCGATCGTAGCAGCATG 58.934 55.000 15.09 0.00 40.87 4.06
163 164 0.038251 TGCCATCATCCGATCGTAGC 60.038 55.000 15.09 6.34 0.00 3.58
171 172 8.807153 ACATGGATATGAGATGCCATCATCCG 62.807 46.154 7.56 2.15 42.14 4.18
224 225 8.469200 CAACCCATAAATTTTCTTCTGCATCTA 58.531 33.333 0.00 0.00 0.00 1.98
225 226 7.325694 CAACCCATAAATTTTCTTCTGCATCT 58.674 34.615 0.00 0.00 0.00 2.90
226 227 6.036408 GCAACCCATAAATTTTCTTCTGCATC 59.964 38.462 0.00 0.00 0.00 3.91
233 234 5.997129 CCAACAGCAACCCATAAATTTTCTT 59.003 36.000 0.00 0.00 0.00 2.52
236 237 5.306678 TCTCCAACAGCAACCCATAAATTTT 59.693 36.000 0.00 0.00 0.00 1.82
250 251 6.116126 ACTTAATTAGGTCATCTCCAACAGC 58.884 40.000 0.00 0.00 0.00 4.40
251 252 7.331026 TGACTTAATTAGGTCATCTCCAACAG 58.669 38.462 22.50 0.00 37.38 3.16
252 253 7.252612 TGACTTAATTAGGTCATCTCCAACA 57.747 36.000 22.50 1.91 37.38 3.33
340 341 9.935682 ACACGAGCAAATACAAATCATATTTAG 57.064 29.630 0.00 0.00 32.27 1.85
362 363 7.129109 AGAATAAACTACCAACAATGACACG 57.871 36.000 0.00 0.00 0.00 4.49
517 530 3.119096 GACTTCCAAGCCGGCGTC 61.119 66.667 23.20 17.32 33.14 5.19
722 932 8.902806 CATTTCATGCAAAAGTAATAGGTAGGA 58.097 33.333 0.00 0.00 0.00 2.94
727 937 8.190122 TGCTACATTTCATGCAAAAGTAATAGG 58.810 33.333 0.00 0.00 29.86 2.57
731 941 7.040478 ACTCTGCTACATTTCATGCAAAAGTAA 60.040 33.333 0.00 0.00 33.05 2.24
862 1117 1.359459 GATGGACAAGGCGTCGGAAC 61.359 60.000 0.00 0.00 46.42 3.62
1221 1529 4.457466 ACCTTTTTAGAGCGTTCCTTTGA 58.543 39.130 0.00 0.00 0.00 2.69
1229 1537 4.097286 TGAAAGCAAACCTTTTTAGAGCGT 59.903 37.500 0.00 0.00 43.64 5.07
1230 1538 4.606961 TGAAAGCAAACCTTTTTAGAGCG 58.393 39.130 0.00 0.00 43.64 5.03
1232 1540 7.041721 ACCTTTGAAAGCAAACCTTTTTAGAG 58.958 34.615 0.00 0.00 43.64 2.43
1235 1543 5.808030 CGACCTTTGAAAGCAAACCTTTTTA 59.192 36.000 0.00 0.00 43.64 1.52
1242 1550 3.105937 GTCACGACCTTTGAAAGCAAAC 58.894 45.455 0.00 0.00 38.99 2.93
1246 1554 1.214367 TCGTCACGACCTTTGAAAGC 58.786 50.000 0.00 0.00 0.00 3.51
1285 1622 5.006386 CCAGCCTAAGATTTTAGCCCATAG 58.994 45.833 0.00 0.00 35.88 2.23
1630 2106 1.459158 AGCTCCTCATCTGCCGGAT 60.459 57.895 5.05 0.00 34.51 4.18
1944 2420 1.613255 CCCAGCTTACCGTTGATGGTT 60.613 52.381 0.00 0.00 43.56 3.67
2025 2501 1.374252 CCGCAGCAGGTACGTCTTT 60.374 57.895 0.00 0.00 0.00 2.52
2097 2573 2.125269 GCGCCCACTACCGTGAAT 60.125 61.111 0.00 0.00 43.97 2.57
2609 3094 0.603569 CGTGTAGAGGCCACTTGTCT 59.396 55.000 8.39 1.80 0.00 3.41
3227 3729 8.352137 TCCTCAATACAATGAACAATGAATGT 57.648 30.769 0.00 0.00 46.82 2.71
3480 4004 6.661805 TGGGACAGTTGGATTTAGATTAAACC 59.338 38.462 0.00 0.00 0.00 3.27
3561 4088 5.354842 AGTAAACACATAGGGCTAAGTCC 57.645 43.478 0.00 0.00 0.00 3.85
3733 4542 7.792374 TGCATCTAGATTCCACATTTACTTC 57.208 36.000 1.33 0.00 0.00 3.01
3821 4635 4.451652 GCAGCCGAGAAAGTGCGC 62.452 66.667 0.00 0.00 0.00 6.09
3905 4720 7.255801 CCCATGTACAAACCAATTACAGAGTTT 60.256 37.037 0.00 0.00 32.84 2.66
3926 4741 8.210946 TGTAGAGGTATATCACTTTTTCCCATG 58.789 37.037 0.00 0.00 0.00 3.66
3932 4747 8.047310 CCCACTTGTAGAGGTATATCACTTTTT 58.953 37.037 0.00 0.00 0.00 1.94
3973 4788 0.036010 AAGAATGTCCGGCCTCTGTG 60.036 55.000 0.00 0.00 0.00 3.66
3995 4810 8.613060 ACTTATCAAGATGATACAATCGCATT 57.387 30.769 0.00 0.00 38.92 3.56


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

AutoCloner maintained by Alex Coulton.