Multiple sequence alignment - TraesCS7A01G310600

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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 TraesCS7A01G310600 chr7A 100.000 3877 0 0 768 4644 439625976 439629852 0.000000e+00 7160.0
1 TraesCS7A01G310600 chr7A 100.000 350 0 0 1 350 439625209 439625558 0.000000e+00 647.0
2 TraesCS7A01G310600 chr7D 95.801 3906 106 13 768 4632 388989726 388993614 0.000000e+00 6252.0
3 TraesCS7A01G310600 chr7D 91.860 258 15 3 97 350 388989394 388989649 5.720000e-94 355.0
4 TraesCS7A01G310600 chr7D 92.771 83 6 0 1 83 388985088 388985170 2.270000e-23 121.0
5 TraesCS7A01G310600 chr7B 95.764 3423 94 11 768 4171 384187205 384190595 0.000000e+00 5470.0
6 TraesCS7A01G310600 chr7B 96.796 437 11 2 4208 4644 384190593 384191026 0.000000e+00 726.0
7 TraesCS7A01G310600 chr7B 85.449 323 22 8 50 350 384186809 384187128 3.490000e-81 313.0
8 TraesCS7A01G310600 chr7B 95.000 40 1 1 202 240 384186914 384186953 1.400000e-05 62.1


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 TraesCS7A01G310600 chr7A 439625209 439629852 4643 False 3903.500 7160 100.00000 1 4644 2 chr7A.!!$F1 4643
1 TraesCS7A01G310600 chr7D 388989394 388993614 4220 False 3303.500 6252 93.83050 97 4632 2 chr7D.!!$F2 4535
2 TraesCS7A01G310600 chr7B 384186809 384191026 4217 False 1642.775 5470 93.25225 50 4644 4 chr7B.!!$F1 4594

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
280 307 2.098770 GGTCCTAGACGTGCGACTAATT 59.901 50.000 0.0 0.0 32.65 1.40 F
287 314 3.380637 AGACGTGCGACTAATTACCATCT 59.619 43.478 0.0 0.0 0.00 2.90 F
288 315 3.703420 ACGTGCGACTAATTACCATCTC 58.297 45.455 0.0 0.0 0.00 2.75 F
2425 2486 0.809636 CGATGAATGCAGTGGCGGTA 60.810 55.000 0.0 0.0 45.35 4.02 F
2426 2487 1.597742 GATGAATGCAGTGGCGGTAT 58.402 50.000 0.0 0.0 45.35 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 1206 2.047560 GCGTCCATATACCGCCCC 60.048 66.667 0.0 0.0 41.50 5.80 R
1200 1227 2.577593 GACGTAGGCAGGTCCCAC 59.422 66.667 0.0 0.0 34.22 4.61 R
2785 2846 2.167075 GTGCATTTTGGGGAATCTCCTG 59.833 50.000 0.0 0.0 36.57 3.86 R
3427 3488 0.106918 TTGCGGGGTTCTTGTTCTGT 60.107 50.000 0.0 0.0 0.00 3.41 R
3668 3729 1.808411 TGCTAACTAACTGCTGCACC 58.192 50.000 0.0 0.0 0.00 5.01 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
62 63 8.202745 AGAAATTTTATCTTGACTCGGTCATC 57.797 34.615 7.43 0.17 42.40 2.92
67 68 7.640597 TTTATCTTGACTCGGTCATCTTAGA 57.359 36.000 7.43 7.71 42.40 2.10
70 71 4.765339 TCTTGACTCGGTCATCTTAGAACA 59.235 41.667 7.43 0.00 42.40 3.18
72 73 5.661056 TGACTCGGTCATCTTAGAACAAT 57.339 39.130 3.02 0.00 37.67 2.71
164 165 7.979444 TTCAAATCTGTAGGAAAACGAAGAT 57.021 32.000 0.00 0.00 0.00 2.40
182 205 7.155328 ACGAAGATGATACTTCAGTCTTTTGT 58.845 34.615 0.00 0.00 44.28 2.83
280 307 2.098770 GGTCCTAGACGTGCGACTAATT 59.901 50.000 0.00 0.00 32.65 1.40
282 309 4.278058 GTCCTAGACGTGCGACTAATTAC 58.722 47.826 0.00 0.00 0.00 1.89
287 314 3.380637 AGACGTGCGACTAATTACCATCT 59.619 43.478 0.00 0.00 0.00 2.90
288 315 3.703420 ACGTGCGACTAATTACCATCTC 58.297 45.455 0.00 0.00 0.00 2.75
290 317 4.109766 CGTGCGACTAATTACCATCTCAA 58.890 43.478 0.00 0.00 0.00 3.02
294 321 7.472543 GTGCGACTAATTACCATCTCAATTTT 58.527 34.615 0.00 0.00 0.00 1.82
295 322 7.640240 GTGCGACTAATTACCATCTCAATTTTC 59.360 37.037 0.00 0.00 0.00 2.29
904 931 3.703420 CAATTTACGACTAGGACCTCGG 58.297 50.000 0.00 0.00 34.07 4.63
1200 1227 2.803670 CGGTATATGGACGCGCCG 60.804 66.667 5.73 4.23 40.66 6.46
1219 1246 3.834799 GGGACCTGCCTACGTCGG 61.835 72.222 0.79 0.79 36.66 4.79
1882 1909 1.541588 GGTTGCTTTCTTGGCTGGTAG 59.458 52.381 0.00 0.00 0.00 3.18
1982 2028 6.769341 TGATACTAACTTCATGTCTACGCCTA 59.231 38.462 0.00 0.00 0.00 3.93
2017 2063 9.630098 GTGATGACAAATTCTTGTTGTATGAAT 57.370 29.630 0.00 0.00 45.98 2.57
2021 2067 9.605955 TGACAAATTCTTGTTGTATGAATAACG 57.394 29.630 0.00 0.00 45.98 3.18
2099 2146 1.229496 AAGGAAATGGGGGTTGGGC 60.229 57.895 0.00 0.00 0.00 5.36
2113 2160 2.482142 GGTTGGGCGTCAAATTTGTTGA 60.482 45.455 17.47 0.00 37.08 3.18
2114 2161 3.190874 GTTGGGCGTCAAATTTGTTGAA 58.809 40.909 17.47 0.00 37.08 2.69
2172 2219 1.410004 TCTGGAAGGTCAACACGAGT 58.590 50.000 0.00 0.00 0.00 4.18
2181 2228 2.290641 GGTCAACACGAGTTTGCTGATT 59.709 45.455 0.00 0.00 35.28 2.57
2269 2316 6.041296 AGCTGATTCTCAAATGGTGTTTTTCT 59.959 34.615 0.00 0.00 0.00 2.52
2307 2354 4.325119 CCTGATAGATTGAAGATGCCCTG 58.675 47.826 0.00 0.00 0.00 4.45
2423 2484 2.711311 CGATGAATGCAGTGGCGG 59.289 61.111 0.00 0.00 45.35 6.13
2424 2485 2.108514 CGATGAATGCAGTGGCGGT 61.109 57.895 0.00 0.00 45.35 5.68
2425 2486 0.809636 CGATGAATGCAGTGGCGGTA 60.810 55.000 0.00 0.00 45.35 4.02
2426 2487 1.597742 GATGAATGCAGTGGCGGTAT 58.402 50.000 0.00 0.00 45.35 2.73
2427 2488 2.766313 GATGAATGCAGTGGCGGTATA 58.234 47.619 0.00 0.00 45.35 1.47
2428 2489 2.928801 TGAATGCAGTGGCGGTATAT 57.071 45.000 0.00 0.00 45.35 0.86
2429 2490 4.503910 GATGAATGCAGTGGCGGTATATA 58.496 43.478 0.00 0.00 45.35 0.86
2430 2491 4.551702 TGAATGCAGTGGCGGTATATAT 57.448 40.909 0.00 0.00 45.35 0.86
2431 2492 4.905429 TGAATGCAGTGGCGGTATATATT 58.095 39.130 0.00 0.00 45.35 1.28
2432 2493 5.312895 TGAATGCAGTGGCGGTATATATTT 58.687 37.500 0.00 0.00 45.35 1.40
2454 2515 2.733227 GCCCAACATGATCTTTTCTGCG 60.733 50.000 0.00 0.00 0.00 5.18
2488 2549 7.328404 AGTTATTGGGGGAATTTTGTTCATT 57.672 32.000 0.00 0.00 0.00 2.57
2542 2603 6.702723 TCAATGGAATGCAATATAAAGCAAGC 59.297 34.615 6.56 2.80 44.88 4.01
2785 2846 2.489722 GAGGAAACTTCTGTTGGATGGC 59.510 50.000 0.00 0.00 44.43 4.40
2883 2944 6.127101 TGAAGAGATATACGGAGGACTTGAA 58.873 40.000 0.00 0.00 0.00 2.69
3017 3078 5.068636 CCTGATGCTAATATGCTGTTCCTT 58.931 41.667 0.00 0.00 0.00 3.36
3086 3147 1.941812 CGCGAGCAAGAGTTGGTTT 59.058 52.632 0.00 0.00 42.23 3.27
3427 3488 2.033448 GGTGTGCCATGGACCGAA 59.967 61.111 18.40 0.00 34.09 4.30
3668 3729 5.460646 GTGAACATCACAGGTAAAATGGTG 58.539 41.667 5.65 0.00 46.22 4.17
3669 3730 4.522405 TGAACATCACAGGTAAAATGGTGG 59.478 41.667 0.00 0.00 32.29 4.61
3670 3731 4.112634 ACATCACAGGTAAAATGGTGGT 57.887 40.909 0.00 0.00 32.29 4.16
3681 3743 1.538047 AATGGTGGTGCAGCAGTTAG 58.462 50.000 20.85 0.00 45.01 2.34
3704 3766 5.416952 AGTTAGCATGAATGGAACCTTCTTG 59.583 40.000 0.00 0.00 33.33 3.02
3904 3966 2.434702 ACAGAAAACTAGATAGGGGCCG 59.565 50.000 0.00 0.00 0.00 6.13
3959 4021 5.833131 AGGTTTACCACACATCTGTTCATTT 59.167 36.000 1.13 0.00 38.89 2.32
4040 4102 7.450323 ACTGTACCATTATTTTGCCTGTAAACT 59.550 33.333 0.00 0.00 0.00 2.66
4041 4103 7.598278 TGTACCATTATTTTGCCTGTAAACTG 58.402 34.615 0.00 0.00 0.00 3.16
4042 4104 6.664428 ACCATTATTTTGCCTGTAAACTGT 57.336 33.333 0.00 0.00 0.00 3.55
4043 4105 7.768807 ACCATTATTTTGCCTGTAAACTGTA 57.231 32.000 0.00 0.00 0.00 2.74
4044 4106 8.184304 ACCATTATTTTGCCTGTAAACTGTAA 57.816 30.769 0.00 0.00 0.00 2.41
4045 4107 8.085909 ACCATTATTTTGCCTGTAAACTGTAAC 58.914 33.333 0.00 0.00 0.00 2.50
4046 4108 8.085296 CCATTATTTTGCCTGTAAACTGTAACA 58.915 33.333 0.00 0.00 0.00 2.41
4047 4109 9.638239 CATTATTTTGCCTGTAAACTGTAACAT 57.362 29.630 0.00 0.00 0.00 2.71
4150 4220 9.027202 TGATTTTTCTTCAGAATTGGATCATGA 57.973 29.630 0.00 0.00 33.54 3.07
4156 4226 8.048534 TCTTCAGAATTGGATCATGAAAGAAC 57.951 34.615 0.00 0.00 30.10 3.01
4310 4380 6.992063 AAAGCATCTTCAGAATATTCACGT 57.008 33.333 17.56 0.00 0.00 4.49
4400 4470 7.498570 ACAGTTATTCCAAATTTGCACAACATT 59.501 29.630 12.92 2.87 0.00 2.71
4469 4540 2.642807 AGACGGATTCCCCAAGAGAAAA 59.357 45.455 0.00 0.00 34.14 2.29
4513 4584 3.120060 ACATCTGAAGCGCATTTCACTTC 60.120 43.478 11.47 2.87 40.17 3.01
4535 4606 1.071471 CGCCACCAAGGACAAGAGT 59.929 57.895 0.00 0.00 41.22 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 8.034058 ACCGAGTCAAGATAAAATTTCTCTTG 57.966 34.615 24.25 24.25 44.59 3.02
34 35 7.878127 TGACCGAGTCAAGATAAAATTTCTCTT 59.122 33.333 9.17 9.17 39.78 2.85
35 36 7.386851 TGACCGAGTCAAGATAAAATTTCTCT 58.613 34.615 4.51 0.00 39.78 3.10
36 37 7.596749 TGACCGAGTCAAGATAAAATTTCTC 57.403 36.000 4.51 0.00 39.78 2.87
37 38 8.043710 AGATGACCGAGTCAAGATAAAATTTCT 58.956 33.333 10.17 3.33 45.96 2.52
38 39 8.202745 AGATGACCGAGTCAAGATAAAATTTC 57.797 34.615 10.17 1.46 45.96 2.17
39 40 8.567285 AAGATGACCGAGTCAAGATAAAATTT 57.433 30.769 10.17 0.00 45.96 1.82
40 41 9.319143 CTAAGATGACCGAGTCAAGATAAAATT 57.681 33.333 10.17 0.00 45.96 1.82
41 42 8.696374 TCTAAGATGACCGAGTCAAGATAAAAT 58.304 33.333 10.17 0.00 45.96 1.82
42 43 8.063200 TCTAAGATGACCGAGTCAAGATAAAA 57.937 34.615 10.17 0.00 45.96 1.52
43 44 7.640597 TCTAAGATGACCGAGTCAAGATAAA 57.359 36.000 10.17 0.00 45.96 1.40
44 45 7.122204 TGTTCTAAGATGACCGAGTCAAGATAA 59.878 37.037 10.17 0.59 45.96 1.75
45 46 6.602009 TGTTCTAAGATGACCGAGTCAAGATA 59.398 38.462 10.17 4.31 45.96 1.98
46 47 5.419155 TGTTCTAAGATGACCGAGTCAAGAT 59.581 40.000 10.17 3.54 45.96 2.40
47 48 4.765339 TGTTCTAAGATGACCGAGTCAAGA 59.235 41.667 10.17 6.48 45.96 3.02
48 49 5.060662 TGTTCTAAGATGACCGAGTCAAG 57.939 43.478 10.17 4.58 45.96 3.02
153 154 7.820044 AGACTGAAGTATCATCTTCGTTTTC 57.180 36.000 0.00 0.00 44.53 2.29
158 159 7.588143 ACAAAAGACTGAAGTATCATCTTCG 57.412 36.000 0.00 0.00 44.53 3.79
182 205 7.771361 TCCTATTTGACCGCTGAATACATAAAA 59.229 33.333 0.00 0.00 0.00 1.52
294 321 9.679661 TCTGCAGGTGTTATAATAGAATTTTGA 57.320 29.630 15.13 0.00 0.00 2.69
303 330 6.399639 TCACGATCTGCAGGTGTTATAATA 57.600 37.500 15.13 0.00 33.51 0.98
783 810 3.243816 AGGTTGTTACCCGCCCGT 61.244 61.111 0.00 0.00 46.28 5.28
864 891 2.266055 GAAGCAGGGGACGTGGAG 59.734 66.667 0.00 0.00 45.29 3.86
904 931 7.151308 ACTATATCATAGTTTCTCAGCTGTGC 58.849 38.462 14.67 0.00 0.00 4.57
1179 1206 2.047560 GCGTCCATATACCGCCCC 60.048 66.667 0.00 0.00 41.50 5.80
1200 1227 2.577593 GACGTAGGCAGGTCCCAC 59.422 66.667 0.00 0.00 34.22 4.61
1982 2028 4.834496 AGAATTTGTCATCACCAACCACAT 59.166 37.500 0.00 0.00 0.00 3.21
2017 2063 6.976636 TGATGATTAATGCAACTCACGTTA 57.023 33.333 0.00 0.00 0.00 3.18
2021 2067 8.996271 TCTATGATGATGATTAATGCAACTCAC 58.004 33.333 0.00 0.00 0.00 3.51
2099 2146 8.115520 ACATCAACAATTTCAACAAATTTGACG 58.884 29.630 24.64 14.04 39.75 4.35
2113 2160 4.448395 CGTTCCAATGCACATCAACAATTT 59.552 37.500 0.00 0.00 0.00 1.82
2114 2161 3.989167 CGTTCCAATGCACATCAACAATT 59.011 39.130 0.00 0.00 0.00 2.32
2172 2219 7.226325 CACAATTAACCCAAGAAAATCAGCAAA 59.774 33.333 0.00 0.00 0.00 3.68
2181 2228 6.739331 ACAATCCACAATTAACCCAAGAAA 57.261 33.333 0.00 0.00 0.00 2.52
2269 2316 3.923273 TCAGGGAATGGCCTCTAGATA 57.077 47.619 3.32 0.00 36.66 1.98
2307 2354 8.682936 TCCTCTTTTATCTTTATTCCAGCATC 57.317 34.615 0.00 0.00 0.00 3.91
2425 2486 9.151177 AGAAAAGATCATGTTGGGCAAATATAT 57.849 29.630 0.00 0.00 0.00 0.86
2426 2487 8.415553 CAGAAAAGATCATGTTGGGCAAATATA 58.584 33.333 0.00 0.00 0.00 0.86
2427 2488 7.270047 CAGAAAAGATCATGTTGGGCAAATAT 58.730 34.615 0.00 0.00 0.00 1.28
2428 2489 6.632909 CAGAAAAGATCATGTTGGGCAAATA 58.367 36.000 0.00 0.00 0.00 1.40
2429 2490 5.484715 CAGAAAAGATCATGTTGGGCAAAT 58.515 37.500 0.00 0.00 0.00 2.32
2430 2491 4.800249 GCAGAAAAGATCATGTTGGGCAAA 60.800 41.667 0.00 0.00 0.00 3.68
2431 2492 3.306225 GCAGAAAAGATCATGTTGGGCAA 60.306 43.478 0.00 0.00 0.00 4.52
2432 2493 2.231964 GCAGAAAAGATCATGTTGGGCA 59.768 45.455 0.00 0.00 0.00 5.36
2454 2515 0.947244 CCCAATAACTCGCAGATGGC 59.053 55.000 0.00 0.00 33.89 4.40
2488 2549 7.989947 AACCTGTCTAGAACCCAAGATATTA 57.010 36.000 0.00 0.00 0.00 0.98
2658 2719 6.186957 ACATTTGCCATCTGATACCTTGTAA 58.813 36.000 0.00 0.00 0.00 2.41
2785 2846 2.167075 GTGCATTTTGGGGAATCTCCTG 59.833 50.000 0.00 0.00 36.57 3.86
3017 3078 1.070786 GCCGTGAGAAACCACCTGA 59.929 57.895 0.00 0.00 33.67 3.86
3427 3488 0.106918 TTGCGGGGTTCTTGTTCTGT 60.107 50.000 0.00 0.00 0.00 3.41
3565 3626 1.915769 GGAGCCACTCCTGGTCAGT 60.916 63.158 6.38 0.00 46.41 3.41
3668 3729 1.808411 TGCTAACTAACTGCTGCACC 58.192 50.000 0.00 0.00 0.00 5.01
3669 3730 3.002791 TCATGCTAACTAACTGCTGCAC 58.997 45.455 0.00 0.00 33.16 4.57
3670 3731 3.333029 TCATGCTAACTAACTGCTGCA 57.667 42.857 0.88 0.88 34.88 4.41
3681 3743 5.183904 ACAAGAAGGTTCCATTCATGCTAAC 59.816 40.000 0.00 0.00 30.49 2.34
3704 3766 5.238214 GGATTTCAAGGAGATGAGCATACAC 59.762 44.000 0.00 0.00 0.00 2.90
3904 3966 3.691498 GTTGTGAACCAAAGCTGTACAC 58.309 45.455 0.00 0.00 34.07 2.90
4150 4220 6.648192 TGATTTGAAACATGTTGGGTTCTTT 58.352 32.000 12.82 0.00 0.00 2.52
4156 4226 6.864360 ACAAATGATTTGAAACATGTTGGG 57.136 33.333 23.37 0.00 43.26 4.12
4231 4301 5.136828 TCTTGGTCTAAACAATGAAGCCAA 58.863 37.500 0.00 0.00 34.19 4.52
4232 4302 4.724399 TCTTGGTCTAAACAATGAAGCCA 58.276 39.130 0.00 0.00 0.00 4.75
4281 4351 7.613022 TGAATATTCTGAAGATGCTTTTGGACT 59.387 33.333 16.24 0.00 0.00 3.85
4310 4380 3.586470 TGTTGGCTGGTAGGAAGAAAA 57.414 42.857 0.00 0.00 0.00 2.29
4469 4540 3.700538 ACCAATTGCACTCATGTACCAT 58.299 40.909 0.00 0.00 0.00 3.55
4513 4584 3.783362 TTGTCCTTGGTGGCGTGGG 62.783 63.158 0.00 0.00 35.26 4.61
4535 4606 5.699458 GGATTAGTTCTTCGGTCTGAACAAA 59.301 40.000 8.28 0.00 43.38 2.83


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

AutoCloner maintained by Alex Coulton.