Multiple sequence alignment - TraesCS5A01G216300

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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 TraesCS5A01G216300 chr5A 100.000 2201 0 0 1 2201 433008341 433010541 0.000000e+00 4065.0
1 TraesCS5A01G216300 chr5A 93.185 1893 109 13 306 2197 432991195 432993068 0.000000e+00 2763.0
2 TraesCS5A01G216300 chr2A 91.506 1966 150 5 232 2197 365070247 365072195 0.000000e+00 2689.0
3 TraesCS5A01G216300 chr2A 91.975 1894 125 8 305 2197 365062028 365063895 0.000000e+00 2630.0
4 TraesCS5A01G216300 chr2A 76.190 357 72 11 1584 1935 642963916 642964264 2.250000e-40 176.0
5 TraesCS5A01G216300 chr6A 90.570 1018 88 8 306 1321 119033772 119034783 0.000000e+00 1341.0
6 TraesCS5A01G216300 chr6A 90.164 976 87 8 488 1458 119090948 119091919 0.000000e+00 1262.0
7 TraesCS5A01G216300 chr6A 90.678 236 21 1 872 1106 277221355 277221590 1.640000e-81 313.0
8 TraesCS5A01G216300 chr6A 88.034 234 26 2 879 1110 277234393 277234626 2.150000e-70 276.0
9 TraesCS5A01G216300 chr1D 80.658 760 110 33 1 739 229595967 229595224 2.470000e-154 555.0
10 TraesCS5A01G216300 chr1D 93.548 341 19 2 1 339 134587959 134588298 2.520000e-139 505.0
11 TraesCS5A01G216300 chr1D 84.314 153 20 4 1086 1235 200593426 200593577 1.760000e-31 147.0
12 TraesCS5A01G216300 chr4D 85.857 502 57 12 1 493 159021824 159022320 2.500000e-144 521.0
13 TraesCS5A01G216300 chr4D 89.286 280 29 1 1918 2197 139569654 139569376 1.250000e-92 350.0
14 TraesCS5A01G216300 chr4D 88.095 210 21 3 544 750 382924070 382924278 1.690000e-61 246.0
15 TraesCS5A01G216300 chr2D 89.526 401 32 6 1 397 255323961 255324355 1.170000e-137 499.0
16 TraesCS5A01G216300 chr2D 77.120 507 89 20 266 757 566487910 566487416 3.600000e-68 268.0
17 TraesCS5A01G216300 chr2D 85.771 253 31 5 1674 1924 301779616 301779367 1.680000e-66 263.0
18 TraesCS5A01G216300 chr2D 81.787 291 44 7 451 738 566514405 566514121 3.650000e-58 235.0
19 TraesCS5A01G216300 chr2D 82.500 80 10 4 838 915 519173128 519173205 1.410000e-07 67.6
20 TraesCS5A01G216300 chr3A 85.193 493 54 16 1 482 221449343 221448859 2.540000e-134 488.0
21 TraesCS5A01G216300 chr3A 84.980 253 33 5 1674 1924 152626000 152626249 3.630000e-63 252.0
22 TraesCS5A01G216300 chr1A 86.977 430 47 7 1 426 224050158 224049734 1.980000e-130 475.0
23 TraesCS5A01G216300 chr1A 82.766 470 67 7 1482 1945 157416366 157415905 7.320000e-110 407.0
24 TraesCS5A01G216300 chr1A 83.799 179 23 5 788 964 305541772 305541946 4.860000e-37 165.0
25 TraesCS5A01G216300 chr1A 94.000 50 3 0 1448 1497 157416415 157416366 2.340000e-10 76.8
26 TraesCS5A01G216300 chr4A 83.943 492 60 17 1 482 207134272 207134754 9.270000e-124 453.0
27 TraesCS5A01G216300 chr7B 83.265 490 68 12 1 482 581770514 581770997 2.590000e-119 438.0
28 TraesCS5A01G216300 chr7B 82.653 490 71 12 1 482 581667179 581667662 2.610000e-114 422.0
29 TraesCS5A01G216300 chr7B 88.412 233 25 2 880 1110 490568281 490568049 1.660000e-71 279.0
30 TraesCS5A01G216300 chr1B 91.429 280 23 1 1918 2197 237591914 237591636 1.230000e-102 383.0
31 TraesCS5A01G216300 chr1B 91.071 280 23 2 1918 2197 237598330 237598053 5.740000e-101 377.0
32 TraesCS5A01G216300 chr5D 90.000 280 26 2 1918 2197 288639928 288640205 5.780000e-96 361.0
33 TraesCS5A01G216300 chr5D 81.879 149 23 4 1090 1235 13367042 13367189 2.970000e-24 122.0
34 TraesCS5A01G216300 chr6B 89.007 282 27 3 1918 2197 96872864 96873143 1.620000e-91 346.0
35 TraesCS5A01G216300 chr6B 88.194 288 32 2 1913 2198 317998182 317997895 2.090000e-90 342.0
36 TraesCS5A01G216300 chr5B 78.462 520 81 23 247 751 442111296 442111799 5.900000e-81 311.0
37 TraesCS5A01G216300 chr2B 86.268 284 38 1 1086 1369 474361680 474361398 7.630000e-80 307.0
38 TraesCS5A01G216300 chr2B 84.783 276 41 1 1097 1372 765204717 765204991 2.150000e-70 276.0
39 TraesCS5A01G216300 chr2B 84.980 253 33 5 1674 1924 561405763 561405514 3.630000e-63 252.0
40 TraesCS5A01G216300 chr7D 86.071 280 37 1 1585 1862 247851041 247851320 1.280000e-77 300.0
41 TraesCS5A01G216300 chr7D 77.602 442 83 14 305 738 366658195 366657762 1.010000e-63 254.0
42 TraesCS5A01G216300 chr7D 80.081 246 47 2 1643 1887 209392049 209391805 4.830000e-42 182.0
43 TraesCS5A01G216300 chr7D 78.400 250 48 4 1641 1887 209431932 209431686 8.140000e-35 158.0
44 TraesCS5A01G216300 chr7A 85.425 247 26 9 879 1119 339270640 339270398 4.690000e-62 248.0
45 TraesCS5A01G216300 chr7A 78.309 272 53 3 1595 1863 101835889 101836157 1.040000e-38 171.0
46 TraesCS5A01G216300 chr7A 81.928 83 12 3 809 889 385896985 385896904 1.410000e-07 67.6
47 TraesCS5A01G216300 chr4B 82.979 282 35 11 1674 1947 554842754 554843030 2.180000e-60 243.0


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 TraesCS5A01G216300 chr5A 433008341 433010541 2200 False 4065.0 4065 100.000 1 2201 1 chr5A.!!$F2 2200
1 TraesCS5A01G216300 chr5A 432991195 432993068 1873 False 2763.0 2763 93.185 306 2197 1 chr5A.!!$F1 1891
2 TraesCS5A01G216300 chr2A 365070247 365072195 1948 False 2689.0 2689 91.506 232 2197 1 chr2A.!!$F2 1965
3 TraesCS5A01G216300 chr2A 365062028 365063895 1867 False 2630.0 2630 91.975 305 2197 1 chr2A.!!$F1 1892
4 TraesCS5A01G216300 chr6A 119033772 119034783 1011 False 1341.0 1341 90.570 306 1321 1 chr6A.!!$F1 1015
5 TraesCS5A01G216300 chr6A 119090948 119091919 971 False 1262.0 1262 90.164 488 1458 1 chr6A.!!$F2 970
6 TraesCS5A01G216300 chr1D 229595224 229595967 743 True 555.0 555 80.658 1 739 1 chr1D.!!$R1 738
7 TraesCS5A01G216300 chr1A 157415905 157416415 510 True 241.9 407 88.383 1448 1945 2 chr1A.!!$R2 497
8 TraesCS5A01G216300 chr5B 442111296 442111799 503 False 311.0 311 78.462 247 751 1 chr5B.!!$F1 504

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
823 864 0.033405 CAGGTCGTCCCCTTCCTCTA 60.033 60.0 0.0 0.0 30.33 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 2127 0.252103 GACCAGTGGGACCTAGGTGA 60.252 60.0 22.1 0.0 38.05 4.02 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
43 44 3.130516 CACGAGCTAACTTCCTCACCATA 59.869 47.826 0.00 0.00 0.00 2.74
51 52 7.500559 AGCTAACTTCCTCACCATATTTCATTC 59.499 37.037 0.00 0.00 0.00 2.67
78 79 6.767902 GGTATCAGAGGCAACATTATTCTTCA 59.232 38.462 0.00 0.00 41.41 3.02
81 82 7.092137 TCAGAGGCAACATTATTCTTCATTG 57.908 36.000 0.00 0.00 41.41 2.82
82 83 5.747197 CAGAGGCAACATTATTCTTCATTGC 59.253 40.000 0.00 0.00 41.29 3.56
103 104 1.630369 TCTGAACCCCTTCATCACCTG 59.370 52.381 0.00 0.00 35.78 4.00
109 110 4.675063 ACCCCTTCATCACCTGTTTTAT 57.325 40.909 0.00 0.00 0.00 1.40
110 111 4.344104 ACCCCTTCATCACCTGTTTTATG 58.656 43.478 0.00 0.00 0.00 1.90
133 136 1.134007 TCAGCTGGATGCCTATGGTTG 60.134 52.381 15.13 0.00 44.23 3.77
137 140 2.760092 GCTGGATGCCTATGGTTGAAAA 59.240 45.455 0.00 0.00 35.15 2.29
139 142 4.141869 GCTGGATGCCTATGGTTGAAAATT 60.142 41.667 0.00 0.00 35.15 1.82
143 146 5.581874 GGATGCCTATGGTTGAAAATTGTTG 59.418 40.000 0.00 0.00 0.00 3.33
146 149 5.988561 TGCCTATGGTTGAAAATTGTTGAAC 59.011 36.000 0.00 0.00 0.00 3.18
149 152 7.216494 CCTATGGTTGAAAATTGTTGAACCTT 58.784 34.615 9.06 5.74 37.54 3.50
150 153 7.384932 CCTATGGTTGAAAATTGTTGAACCTTC 59.615 37.037 9.06 1.13 37.54 3.46
151 154 6.293004 TGGTTGAAAATTGTTGAACCTTCT 57.707 33.333 9.06 0.00 37.54 2.85
168 171 7.448777 TGAACCTTCTTATAGCACTCTCGATAT 59.551 37.037 0.00 0.00 0.00 1.63
170 173 6.717540 ACCTTCTTATAGCACTCTCGATATGT 59.282 38.462 0.00 0.00 0.00 2.29
171 174 7.231722 ACCTTCTTATAGCACTCTCGATATGTT 59.768 37.037 0.00 0.00 0.00 2.71
185 188 3.941483 CGATATGTTTCCTGGTGCTTCTT 59.059 43.478 0.00 0.00 0.00 2.52
192 195 5.833131 TGTTTCCTGGTGCTTCTTAAATCTT 59.167 36.000 0.00 0.00 0.00 2.40
214 217 4.863548 TCTTCCTTGAGATAACTACCGGA 58.136 43.478 9.46 0.00 0.00 5.14
218 221 3.069586 CCTTGAGATAACTACCGGATGCA 59.930 47.826 9.46 0.00 0.00 3.96
222 225 4.218635 TGAGATAACTACCGGATGCAGATC 59.781 45.833 9.46 3.61 0.00 2.75
223 226 4.411927 AGATAACTACCGGATGCAGATCT 58.588 43.478 9.46 6.08 0.00 2.75
262 265 5.254032 CCTTATAGCTTCCCCCTTATTCCAT 59.746 44.000 0.00 0.00 0.00 3.41
320 323 3.439129 GGAGATTTGTAACACCCGGAAAG 59.561 47.826 0.73 0.00 0.00 2.62
336 339 6.155049 ACCCGGAAAGTTAAGCTACAGTAATA 59.845 38.462 0.73 0.00 0.00 0.98
394 400 9.754382 CTATGCTAATTGCCACTTAATTCAAAT 57.246 29.630 0.00 0.00 42.00 2.32
396 402 7.609960 TGCTAATTGCCACTTAATTCAAATCA 58.390 30.769 0.00 0.00 42.00 2.57
398 404 8.382875 GCTAATTGCCACTTAATTCAAATCAAC 58.617 33.333 0.00 0.00 35.15 3.18
400 406 8.538409 AATTGCCACTTAATTCAAATCAACTC 57.462 30.769 0.00 0.00 0.00 3.01
405 411 7.440856 GCCACTTAATTCAAATCAACTCCAAAA 59.559 33.333 0.00 0.00 0.00 2.44
406 412 9.323985 CCACTTAATTCAAATCAACTCCAAAAA 57.676 29.630 0.00 0.00 0.00 1.94
447 478 8.327429 CAAGTGCGAAAACATTTATTCAAACTT 58.673 29.630 0.00 0.00 34.10 2.66
550 583 6.796785 ATTGGGCTCTAGCATTTAAAACAT 57.203 33.333 4.07 0.00 44.36 2.71
691 727 7.523293 TCCACATTCTAAAAAGAGCAATTGA 57.477 32.000 10.34 0.00 0.00 2.57
823 864 0.033405 CAGGTCGTCCCCTTCCTCTA 60.033 60.000 0.00 0.00 30.33 2.43
845 886 2.276116 ATCGGGCGCTCGTGGATAT 61.276 57.895 31.23 12.84 0.00 1.63
974 1015 0.760572 TTTCCCCTCTCGGTTTCGTT 59.239 50.000 0.00 0.00 37.69 3.85
1065 1106 2.659800 CTCCACCGTCTTCTGGAGT 58.340 57.895 5.65 0.00 46.03 3.85
1134 1175 2.108514 CACCAGCATCGTCGCCAAT 61.109 57.895 0.00 0.00 0.00 3.16
1207 1248 2.683572 TGCGCTCCTAAGCTCCCA 60.684 61.111 9.73 0.00 46.91 4.37
1257 1298 1.772453 TCCTTCGACTCCCCTGTTTTT 59.228 47.619 0.00 0.00 0.00 1.94
1274 1315 2.438800 TTTCCCCCTTTGTTTCGTCA 57.561 45.000 0.00 0.00 0.00 4.35
1414 1455 4.093291 CGCTCCCCTGCTCTGCTT 62.093 66.667 0.00 0.00 0.00 3.91
1731 1793 1.204146 CTAGCCCTCTAAACAGCCCA 58.796 55.000 0.00 0.00 0.00 5.36
1734 1796 2.422746 AGCCCTCTAAACAGCCCATAT 58.577 47.619 0.00 0.00 0.00 1.78
1780 1842 8.458573 AACATGGGTAAAAATTATATGAGCGA 57.541 30.769 0.00 0.00 0.00 4.93
1812 1874 8.013378 AGACGTAACAATCTTTATTTTGTTCCG 58.987 33.333 10.55 10.55 45.09 4.30
1960 2024 1.409521 CCGGCCCCATGTTCAATTAGA 60.410 52.381 0.00 0.00 0.00 2.10
2063 2127 9.287373 AGAAAATGCCAAAATATGTTTGAATGT 57.713 25.926 10.22 0.00 0.00 2.71
2069 2133 7.039434 TGCCAAAATATGTTTGAATGTCACCTA 60.039 33.333 10.22 0.00 0.00 3.08
2085 2149 2.038329 TAGGTCCCACTGGTCCCG 59.962 66.667 0.00 0.00 40.40 5.14
2185 2249 2.560542 CTCAGTTGACTGCTGACTAGGT 59.439 50.000 6.27 0.00 43.46 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.570772 GCTCGTGAATTACATAAGAAGCCA 59.429 41.667 0.00 0.00 0.00 4.75
11 12 7.553334 AGGAAGTTAGCTCGTGAATTACATAA 58.447 34.615 0.00 0.00 0.00 1.90
20 21 1.544691 GGTGAGGAAGTTAGCTCGTGA 59.455 52.381 0.00 0.00 0.00 4.35
43 44 3.136443 TGCCTCTGATACCGGAATGAAAT 59.864 43.478 9.46 0.00 0.00 2.17
51 52 2.332063 AATGTTGCCTCTGATACCGG 57.668 50.000 0.00 0.00 0.00 5.28
78 79 2.309755 TGATGAAGGGGTTCAGAGCAAT 59.690 45.455 0.00 0.00 34.02 3.56
81 82 1.680249 GGTGATGAAGGGGTTCAGAGC 60.680 57.143 0.00 0.00 34.02 4.09
82 83 1.912043 AGGTGATGAAGGGGTTCAGAG 59.088 52.381 0.00 0.00 34.02 3.35
128 129 6.293004 AGAAGGTTCAACAATTTTCAACCA 57.707 33.333 8.19 0.00 39.26 3.67
129 130 8.887036 ATAAGAAGGTTCAACAATTTTCAACC 57.113 30.769 0.00 0.00 37.38 3.77
133 136 9.129209 GTGCTATAAGAAGGTTCAACAATTTTC 57.871 33.333 0.00 0.00 0.00 2.29
137 140 7.398024 AGAGTGCTATAAGAAGGTTCAACAAT 58.602 34.615 0.00 0.00 0.00 2.71
139 142 6.360370 AGAGTGCTATAAGAAGGTTCAACA 57.640 37.500 0.00 0.00 0.00 3.33
143 146 5.502153 TCGAGAGTGCTATAAGAAGGTTC 57.498 43.478 0.00 0.00 0.00 3.62
146 149 7.151999 ACATATCGAGAGTGCTATAAGAAGG 57.848 40.000 0.00 0.00 0.00 3.46
149 152 7.448777 AGGAAACATATCGAGAGTGCTATAAGA 59.551 37.037 0.00 0.00 0.00 2.10
150 153 7.540400 CAGGAAACATATCGAGAGTGCTATAAG 59.460 40.741 0.00 0.00 0.00 1.73
151 154 7.371159 CAGGAAACATATCGAGAGTGCTATAA 58.629 38.462 0.00 0.00 0.00 0.98
168 171 5.385198 AGATTTAAGAAGCACCAGGAAACA 58.615 37.500 0.00 0.00 0.00 2.83
170 173 6.306987 AGAAGATTTAAGAAGCACCAGGAAA 58.693 36.000 0.00 0.00 0.00 3.13
171 174 5.880901 AGAAGATTTAAGAAGCACCAGGAA 58.119 37.500 0.00 0.00 0.00 3.36
192 195 4.863548 TCCGGTAGTTATCTCAAGGAAGA 58.136 43.478 0.00 0.00 0.00 2.87
214 217 4.851843 TGGATGTCTGAAAAGATCTGCAT 58.148 39.130 0.00 0.00 31.53 3.96
218 221 5.972327 AGGATGGATGTCTGAAAAGATCT 57.028 39.130 0.00 0.00 0.00 2.75
222 225 7.222872 AGCTATAAGGATGGATGTCTGAAAAG 58.777 38.462 0.00 0.00 0.00 2.27
223 226 7.141758 AGCTATAAGGATGGATGTCTGAAAA 57.858 36.000 0.00 0.00 0.00 2.29
262 265 1.187974 TCGTCCCGAGATTTAAGGCA 58.812 50.000 0.00 0.00 0.00 4.75
336 339 6.183360 CGATGACTTGGCATTAAACAAGAGAT 60.183 38.462 18.81 12.06 45.22 2.75
394 400 8.991026 CAATTTGCATTAGATTTTTGGAGTTGA 58.009 29.630 0.00 0.00 0.00 3.18
396 402 7.809665 GCAATTTGCATTAGATTTTTGGAGTT 58.190 30.769 16.35 0.00 44.26 3.01
447 478 9.413048 GTAACCCATCGAACATTTTTATTTGAA 57.587 29.630 0.00 0.00 0.00 2.69
513 544 5.583932 AGAGCCCAATTAAGAAATCAGGTT 58.416 37.500 0.00 0.00 0.00 3.50
691 727 4.022416 TCTGTTTGCAATATTTTGAGCCGT 60.022 37.500 0.00 0.00 34.60 5.68
823 864 2.586079 CACGAGCGCCCGATGAAT 60.586 61.111 21.03 0.00 0.00 2.57
974 1015 3.003173 CGGGTCTGCAAGGGGAGA 61.003 66.667 0.00 0.00 39.39 3.71
1065 1106 4.354939 TAAACGGACGCGGCGGAA 62.355 61.111 27.58 8.18 0.00 4.30
1134 1175 4.315803 GTGATCCAAGGAAGAAGACGAAA 58.684 43.478 0.00 0.00 0.00 3.46
1257 1298 0.179012 GGTGACGAAACAAAGGGGGA 60.179 55.000 0.00 0.00 0.00 4.81
1274 1315 3.204418 GGCTACGGCGACTTAGGT 58.796 61.111 16.62 0.00 39.81 3.08
1414 1455 1.735386 GCATCAGCAGCAAGAGAAGA 58.265 50.000 0.00 0.00 41.58 2.87
1633 1692 0.602638 ATTCAGCCGAGCAACAACGA 60.603 50.000 0.00 0.00 0.00 3.85
1731 1793 4.822026 GGACTTGCCTTATCGCTGTATAT 58.178 43.478 0.00 0.00 0.00 0.86
1734 1796 2.596904 GGACTTGCCTTATCGCTGTA 57.403 50.000 0.00 0.00 0.00 2.74
1812 1874 6.012658 TGCATTATCTGAAGTTGGTTCAAC 57.987 37.500 2.85 2.85 44.83 3.18
1878 1941 7.773690 TGCTAGGGGTAAATTCTGTTTTCTATC 59.226 37.037 0.00 0.00 0.00 2.08
2046 2110 8.522830 ACCTAGGTGACATTCAAACATATTTTG 58.477 33.333 15.42 4.81 0.00 2.44
2063 2127 0.252103 GACCAGTGGGACCTAGGTGA 60.252 60.000 22.10 0.00 38.05 4.02
2069 2133 3.786866 AACGGGACCAGTGGGACCT 62.787 63.158 21.45 8.40 46.72 3.85
2160 2224 1.069204 GTCAGCAGTCAACTGAGACCA 59.931 52.381 14.20 0.00 44.51 4.02


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

AutoCloner maintained by Alex Coulton.