Multiple sequence alignment - TraesCS5D01G094300

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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 TraesCS5D01G094300 chr5D 100.000 2584 0 0 1 2584 103986674 103984091 0.000000e+00 4772.0
1 TraesCS5D01G094300 chr5D 80.040 501 83 7 1061 1560 104113148 104112664 3.160000e-94 355.0
2 TraesCS5D01G094300 chr5D 78.685 502 91 6 1058 1559 104142959 104142474 1.150000e-83 320.0
3 TraesCS5D01G094300 chr5B 94.131 1721 58 19 887 2584 113087184 113085484 0.000000e+00 2579.0
4 TraesCS5D01G094300 chr5B 93.345 571 26 10 330 896 113087778 113087216 0.000000e+00 833.0
5 TraesCS5D01G094300 chr5B 86.957 345 19 4 1 332 113089465 113089134 5.250000e-97 364.0
6 TraesCS5D01G094300 chr5B 82.412 398 70 0 1163 1560 113327888 113327491 5.290000e-92 348.0
7 TraesCS5D01G094300 chr5A 93.246 1066 54 10 887 1948 94689854 94690905 0.000000e+00 1554.0
8 TraesCS5D01G094300 chr5A 90.487 452 26 10 2145 2584 94691291 94691737 4.790000e-162 580.0
9 TraesCS5D01G094300 chr5A 79.880 502 82 8 1061 1560 94310799 94311283 1.470000e-92 350.0
10 TraesCS5D01G094300 chr5A 94.118 34 2 0 132 165 627013852 627013885 5.000000e-03 52.8
11 TraesCS5D01G094300 chr6D 78.723 517 85 17 1050 1557 9147163 9147663 3.210000e-84 322.0
12 TraesCS5D01G094300 chr6B 78.571 504 88 13 1063 1562 16970593 16971080 5.370000e-82 315.0
13 TraesCS5D01G094300 chr6A 80.435 414 72 7 1152 1562 10138034 10137627 8.980000e-80 307.0
14 TraesCS5D01G094300 chr7A 83.838 99 12 2 61 158 138181575 138181670 9.850000e-15 91.6
15 TraesCS5D01G094300 chr3A 76.730 159 32 3 1 159 741740448 741740601 1.650000e-12 84.2
16 TraesCS5D01G094300 chr7B 75.862 174 28 9 1 170 719642511 719642348 2.760000e-10 76.8


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 TraesCS5D01G094300 chr5D 103984091 103986674 2583 True 4772.000000 4772 100.000000 1 2584 1 chr5D.!!$R1 2583
1 TraesCS5D01G094300 chr5B 113085484 113089465 3981 True 1258.666667 2579 91.477667 1 2584 3 chr5B.!!$R2 2583
2 TraesCS5D01G094300 chr5A 94689854 94691737 1883 False 1067.000000 1554 91.866500 887 2584 2 chr5A.!!$F3 1697
3 TraesCS5D01G094300 chr6D 9147163 9147663 500 False 322.000000 322 78.723000 1050 1557 1 chr6D.!!$F1 507

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
188 201 0.108898 ACAGCTGAGACTCGTCATGC 60.109 55.0 23.35 1.14 0.0 4.06 F
372 1744 0.398522 ACATATCCACCCGCTCTCCA 60.399 55.0 0.00 0.00 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1047 2463 0.037975 GCCATTGGCTGTTTGGAGTG 60.038 55.0 20.66 0.0 46.69 3.51 R
2336 4044 0.179004 TGCTTCTTCCTTCCGGCAAA 60.179 50.0 0.00 0.0 0.00 3.68 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
59 72 9.350357 CATCATTTGAAAGAGGTGATGTAAAAG 57.650 33.333 9.81 0.00 40.58 2.27
91 104 5.988287 TCTACATCATGTATTGGAGCAACA 58.012 37.500 0.00 0.00 31.66 3.33
115 128 2.198287 GGGCCTCGGCGTAGATGTA 61.198 63.158 6.85 0.00 43.06 2.29
185 198 2.077627 GTAGACAGCTGAGACTCGTCA 58.922 52.381 23.35 0.00 0.00 4.35
188 201 0.108898 ACAGCTGAGACTCGTCATGC 60.109 55.000 23.35 1.14 0.00 4.06
193 206 2.159310 GCTGAGACTCGTCATGCTAGTT 60.159 50.000 0.00 0.00 0.00 2.24
203 216 3.997021 CGTCATGCTAGTTCCAAAAGACT 59.003 43.478 0.00 0.00 0.00 3.24
232 245 5.518487 CACTAAAACAACAACATCCACCAAC 59.482 40.000 0.00 0.00 0.00 3.77
241 255 1.338200 ACATCCACCAACGAGAGAAGC 60.338 52.381 0.00 0.00 0.00 3.86
253 267 6.202937 CAACGAGAGAAGCGTAGATAGAAAT 58.797 40.000 0.00 0.00 41.75 2.17
254 268 5.753744 ACGAGAGAAGCGTAGATAGAAATG 58.246 41.667 0.00 0.00 40.65 2.32
255 269 5.527951 ACGAGAGAAGCGTAGATAGAAATGA 59.472 40.000 0.00 0.00 40.65 2.57
256 270 6.205853 ACGAGAGAAGCGTAGATAGAAATGAT 59.794 38.462 0.00 0.00 40.65 2.45
257 271 6.740905 CGAGAGAAGCGTAGATAGAAATGATC 59.259 42.308 0.00 0.00 0.00 2.92
258 272 6.919721 AGAGAAGCGTAGATAGAAATGATCC 58.080 40.000 0.00 0.00 0.00 3.36
259 273 6.491745 AGAGAAGCGTAGATAGAAATGATCCA 59.508 38.462 0.00 0.00 0.00 3.41
260 274 7.014711 AGAGAAGCGTAGATAGAAATGATCCAA 59.985 37.037 0.00 0.00 0.00 3.53
261 275 7.675062 AGAAGCGTAGATAGAAATGATCCAAT 58.325 34.615 0.00 0.00 0.00 3.16
262 276 7.816995 AGAAGCGTAGATAGAAATGATCCAATC 59.183 37.037 0.00 0.00 0.00 2.67
263 277 7.238486 AGCGTAGATAGAAATGATCCAATCT 57.762 36.000 0.00 0.00 36.09 2.40
264 278 7.675062 AGCGTAGATAGAAATGATCCAATCTT 58.325 34.615 0.00 0.00 34.66 2.40
282 296 7.658167 TCCAATCTTTAGACACATGAACGTAAA 59.342 33.333 0.00 0.00 0.00 2.01
287 301 9.047371 TCTTTAGACACATGAACGTAAATGAAA 57.953 29.630 15.22 5.96 0.00 2.69
297 311 5.697178 TGAACGTAAATGAAATGAAGACCGA 59.303 36.000 0.00 0.00 0.00 4.69
309 323 2.567169 TGAAGACCGAATCCACACAGAT 59.433 45.455 0.00 0.00 0.00 2.90
354 1726 0.661780 CCGCGAGATCCATCGAAGAC 60.662 60.000 8.23 0.00 45.56 3.01
372 1744 0.398522 ACATATCCACCCGCTCTCCA 60.399 55.000 0.00 0.00 0.00 3.86
379 1751 1.227853 ACCCGCTCTCCAACACAAC 60.228 57.895 0.00 0.00 0.00 3.32
424 1796 3.230976 AGGGAACTTTTGGTCAATGGTC 58.769 45.455 0.00 0.00 37.44 4.02
515 1887 9.533831 AAAATAGACTTGACCTTCCATTGTATT 57.466 29.630 0.00 0.00 0.00 1.89
522 1894 7.507616 ACTTGACCTTCCATTGTATTGGTAAAA 59.492 33.333 0.00 0.00 38.01 1.52
632 2006 8.773645 AGCAAATAGTTTTTGTATTCTTTTGGC 58.226 29.630 7.71 0.00 0.00 4.52
641 2015 4.479158 TGTATTCTTTTGGCCCTGAAGTT 58.521 39.130 0.00 0.00 0.00 2.66
644 2018 3.243359 TCTTTTGGCCCTGAAGTTGAT 57.757 42.857 0.00 0.00 0.00 2.57
786 2162 7.950124 CCTATATACACCCAAAAATCAAGGGAT 59.050 37.037 3.32 0.00 45.80 3.85
894 2310 9.981114 TGTTAGCTTGAATATCATATCTCGAAA 57.019 29.630 0.00 0.00 0.00 3.46
986 2402 0.912486 ATACCCTTCACAGTGAGCCC 59.088 55.000 2.82 0.00 0.00 5.19
1013 2429 0.673437 CAACTCAAACCACCGGCATT 59.327 50.000 0.00 0.00 0.00 3.56
1033 2449 2.685106 AGTCACTCCTCTTCACTCCA 57.315 50.000 0.00 0.00 0.00 3.86
1045 2461 1.334160 TCACTCCAAACCAGCGAGTA 58.666 50.000 0.00 0.00 35.12 2.59
1046 2462 1.689813 TCACTCCAAACCAGCGAGTAA 59.310 47.619 0.00 0.00 35.12 2.24
1047 2463 1.798813 CACTCCAAACCAGCGAGTAAC 59.201 52.381 0.00 0.00 35.12 2.50
1048 2464 1.414919 ACTCCAAACCAGCGAGTAACA 59.585 47.619 0.00 0.00 35.12 2.41
1049 2465 1.798813 CTCCAAACCAGCGAGTAACAC 59.201 52.381 0.00 0.00 0.00 3.32
1050 2466 1.414919 TCCAAACCAGCGAGTAACACT 59.585 47.619 0.00 0.00 0.00 3.55
1051 2467 1.798813 CCAAACCAGCGAGTAACACTC 59.201 52.381 0.00 0.00 41.71 3.51
1052 2468 1.798813 CAAACCAGCGAGTAACACTCC 59.201 52.381 0.89 0.00 42.12 3.85
1053 2469 1.045407 AACCAGCGAGTAACACTCCA 58.955 50.000 0.89 0.00 42.12 3.86
1394 2822 2.048127 GTGAGCACCGACCAGTCC 60.048 66.667 0.00 0.00 0.00 3.85
1624 3052 1.855360 GTCGTATTGCAGCTGCTAGTC 59.145 52.381 36.61 23.75 42.66 2.59
1628 3056 1.735386 ATTGCAGCTGCTAGTCAGTG 58.265 50.000 36.61 0.00 44.66 3.66
1629 3057 0.681175 TTGCAGCTGCTAGTCAGTGA 59.319 50.000 36.61 12.87 44.66 3.41
1676 3111 2.309693 GTGTCGTGTCGTGTCGATTTA 58.690 47.619 0.00 0.00 38.42 1.40
1727 3162 5.675684 TGTGTGGCTAGAGATGTTTCATA 57.324 39.130 0.00 0.00 0.00 2.15
1840 3275 3.195661 GGGTCACCGAACTGATGTTATC 58.804 50.000 0.00 0.00 36.39 1.75
1920 3367 3.896133 CATGGCCGCACATGCTCC 61.896 66.667 0.00 3.91 41.43 4.70
1936 3383 3.299190 CCCCCTCTCCTCGCGATC 61.299 72.222 10.36 0.00 0.00 3.69
1948 3395 2.911723 CCTCGCGATCGATGAATCTAAC 59.088 50.000 21.57 0.00 44.56 2.34
1961 3408 3.128764 TGAATCTAACGTCTGCGAGACAT 59.871 43.478 14.09 6.86 45.30 3.06
2108 3615 3.303395 CGAAGATTAATTTCTCCGGCAGC 60.303 47.826 0.00 0.00 0.00 5.25
2140 3648 1.081892 CAAGACAGAATCACAGCCGG 58.918 55.000 0.00 0.00 0.00 6.13
2335 4043 1.371389 GCCGTTCGTCGTTGTCTCT 60.371 57.895 0.00 0.00 37.94 3.10
2336 4044 0.938168 GCCGTTCGTCGTTGTCTCTT 60.938 55.000 0.00 0.00 37.94 2.85
2573 4281 3.484547 CGTGCCCGGTTAACGCTC 61.485 66.667 0.00 0.00 42.52 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 72 9.710900 TCCAATACATGATGTAGATGTATGAAC 57.289 33.333 11.32 0.00 43.26 3.18
91 104 2.311688 CTACGCCGAGGCCCAAGAAT 62.312 60.000 8.72 0.00 37.98 2.40
115 128 8.109705 TGCAGATGTGTAAATAACTGATGTTT 57.890 30.769 0.00 0.00 37.59 2.83
131 144 7.674471 ATCTTCAATAGATGATGCAGATGTG 57.326 36.000 0.00 0.00 42.11 3.21
150 163 7.923344 TCAGCTGTCTACTATAAAAGCATCTTC 59.077 37.037 14.67 0.00 33.08 2.87
159 172 6.114089 ACGAGTCTCAGCTGTCTACTATAAA 58.886 40.000 14.67 0.00 0.00 1.40
172 185 1.403679 ACTAGCATGACGAGTCTCAGC 59.596 52.381 0.00 6.02 25.90 4.26
185 198 7.038941 AGTGTACTAGTCTTTTGGAACTAGCAT 60.039 37.037 0.00 0.00 36.55 3.79
193 206 9.101655 GTTGTTTTAGTGTACTAGTCTTTTGGA 57.898 33.333 0.00 0.00 0.00 3.53
203 216 7.227116 GGTGGATGTTGTTGTTTTAGTGTACTA 59.773 37.037 0.00 0.00 0.00 1.82
232 245 5.991568 TCATTTCTATCTACGCTTCTCTCG 58.008 41.667 0.00 0.00 0.00 4.04
253 267 6.313658 CGTTCATGTGTCTAAAGATTGGATCA 59.686 38.462 0.00 0.00 0.00 2.92
254 268 6.313905 ACGTTCATGTGTCTAAAGATTGGATC 59.686 38.462 0.00 0.00 0.00 3.36
255 269 6.173339 ACGTTCATGTGTCTAAAGATTGGAT 58.827 36.000 0.00 0.00 0.00 3.41
256 270 5.547465 ACGTTCATGTGTCTAAAGATTGGA 58.453 37.500 0.00 0.00 0.00 3.53
257 271 5.862924 ACGTTCATGTGTCTAAAGATTGG 57.137 39.130 0.00 0.00 0.00 3.16
258 272 9.265938 CATTTACGTTCATGTGTCTAAAGATTG 57.734 33.333 0.00 0.00 0.00 2.67
259 273 9.214957 TCATTTACGTTCATGTGTCTAAAGATT 57.785 29.630 0.00 0.00 0.00 2.40
260 274 8.771920 TCATTTACGTTCATGTGTCTAAAGAT 57.228 30.769 0.00 0.00 0.00 2.40
261 275 8.596271 TTCATTTACGTTCATGTGTCTAAAGA 57.404 30.769 0.00 0.00 0.00 2.52
262 276 9.825972 ATTTCATTTACGTTCATGTGTCTAAAG 57.174 29.630 0.00 0.00 0.00 1.85
263 277 9.605955 CATTTCATTTACGTTCATGTGTCTAAA 57.394 29.630 0.00 0.00 0.00 1.85
264 278 8.994170 TCATTTCATTTACGTTCATGTGTCTAA 58.006 29.630 0.00 0.00 0.00 2.10
282 296 4.396166 GTGTGGATTCGGTCTTCATTTCAT 59.604 41.667 0.00 0.00 0.00 2.57
287 301 2.567169 TCTGTGTGGATTCGGTCTTCAT 59.433 45.455 0.00 0.00 0.00 2.57
297 311 4.946157 GTCTTTGATGGATCTGTGTGGATT 59.054 41.667 0.00 0.00 0.00 3.01
354 1726 0.758734 TTGGAGAGCGGGTGGATATG 59.241 55.000 0.00 0.00 0.00 1.78
493 1865 6.012858 ACCAATACAATGGAAGGTCAAGTCTA 60.013 38.462 0.00 0.00 43.54 2.59
494 1866 5.222130 ACCAATACAATGGAAGGTCAAGTCT 60.222 40.000 0.00 0.00 43.54 3.24
495 1867 5.010282 ACCAATACAATGGAAGGTCAAGTC 58.990 41.667 0.00 0.00 43.54 3.01
497 1869 7.461182 TTTACCAATACAATGGAAGGTCAAG 57.539 36.000 0.00 0.00 43.54 3.02
632 2006 1.915141 AACCAGCATCAACTTCAGGG 58.085 50.000 0.00 0.00 0.00 4.45
753 2129 7.454553 TTTTTGGGTGTATATAGGCCTCTTA 57.545 36.000 9.68 2.49 0.00 2.10
759 2135 6.015434 CCCTTGATTTTTGGGTGTATATAGGC 60.015 42.308 0.00 0.00 36.32 3.93
760 2136 7.294584 TCCCTTGATTTTTGGGTGTATATAGG 58.705 38.462 0.00 0.00 41.58 2.57
925 2341 4.655963 TCCCACTCAATCAAAAGAGGAAG 58.344 43.478 0.00 0.00 36.20 3.46
927 2343 3.560025 GCTCCCACTCAATCAAAAGAGGA 60.560 47.826 0.00 0.00 36.20 3.71
928 2344 2.751806 GCTCCCACTCAATCAAAAGAGG 59.248 50.000 0.00 0.00 36.20 3.69
930 2346 2.376518 AGGCTCCCACTCAATCAAAAGA 59.623 45.455 0.00 0.00 0.00 2.52
931 2347 2.800250 AGGCTCCCACTCAATCAAAAG 58.200 47.619 0.00 0.00 0.00 2.27
932 2348 2.978156 AGGCTCCCACTCAATCAAAA 57.022 45.000 0.00 0.00 0.00 2.44
986 2402 3.250040 CGGTGGTTTGAGTTGAGGTTTAG 59.750 47.826 0.00 0.00 0.00 1.85
1013 2429 3.808834 TGGAGTGAAGAGGAGTGACTA 57.191 47.619 0.00 0.00 0.00 2.59
1033 2449 1.414919 TGGAGTGTTACTCGCTGGTTT 59.585 47.619 3.17 0.00 45.96 3.27
1045 2461 1.688197 CCATTGGCTGTTTGGAGTGTT 59.312 47.619 0.00 0.00 31.94 3.32
1046 2462 1.331214 CCATTGGCTGTTTGGAGTGT 58.669 50.000 0.00 0.00 31.94 3.55
1047 2463 0.037975 GCCATTGGCTGTTTGGAGTG 60.038 55.000 20.66 0.00 46.69 3.51
1048 2464 2.354902 GCCATTGGCTGTTTGGAGT 58.645 52.632 20.66 0.00 46.69 3.85
1343 2771 3.055080 GCCGTCGTACCCGATGTGA 62.055 63.158 1.43 0.00 46.36 3.58
1394 2822 2.045045 ACACGGATGGGCATGTGG 60.045 61.111 0.00 0.00 36.67 4.17
1571 2999 4.549599 CGAGCTGCAAACTTATTAAACACG 59.450 41.667 1.02 0.00 0.00 4.49
1624 3052 2.350804 CGTTGGAGCAGATGATTCACTG 59.649 50.000 10.20 10.20 37.22 3.66
1676 3111 4.451096 CACCGCAACTACTAATTGAACAGT 59.549 41.667 0.00 0.00 0.00 3.55
1727 3162 2.956987 GCAGTTCATTGCACGGCT 59.043 55.556 4.52 0.00 43.53 5.52
1802 3237 3.192422 TGACCCAGCCACATTTTAAATCG 59.808 43.478 0.00 0.00 0.00 3.34
1813 3248 2.668550 GTTCGGTGACCCAGCCAC 60.669 66.667 0.00 0.00 0.00 5.01
1918 3365 3.793957 GATCGCGAGGAGAGGGGGA 62.794 68.421 16.66 0.00 0.00 4.81
1920 3367 3.665226 CGATCGCGAGGAGAGGGG 61.665 72.222 16.66 0.00 40.82 4.79
1936 3383 2.716398 TCGCAGACGTTAGATTCATCG 58.284 47.619 0.00 0.00 41.18 3.84
1961 3408 7.225538 CACATTTTACACCATTTTTGCTACCAA 59.774 33.333 0.00 0.00 0.00 3.67
2042 3490 1.666700 CTCGGGTTTCACGTTGACAAA 59.333 47.619 0.00 0.00 0.00 2.83
2108 3615 3.838120 TCTGTCTTGTGCATAGTTCTCG 58.162 45.455 0.00 0.00 0.00 4.04
2335 4043 0.958822 GCTTCTTCCTTCCGGCAAAA 59.041 50.000 0.00 0.00 0.00 2.44
2336 4044 0.179004 TGCTTCTTCCTTCCGGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
2531 4239 0.535102 GCAGGTACAGGTGCAGTGTT 60.535 55.000 6.94 0.00 39.62 3.32


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

AutoCloner maintained by Alex Coulton.