Multiple sequence alignment - TraesCS7D01G385500

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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 TraesCS7D01G385500 chr7D 100.000 4191 0 0 1 4191 499971055 499975245 0.000000e+00 7740
1 TraesCS7D01G385500 chr7D 78.605 1921 314 65 476 2358 500098177 500100038 0.000000e+00 1181
2 TraesCS7D01G385500 chr7D 81.818 638 101 11 2629 3256 500100359 500100991 4.800000e-144 521
3 TraesCS7D01G385500 chr7B 97.442 4183 86 8 7 4188 527961294 527965456 0.000000e+00 7112
4 TraesCS7D01G385500 chr7B 78.063 1910 342 58 476 2357 527979145 527981005 0.000000e+00 1134
5 TraesCS7D01G385500 chr7B 81.818 638 101 11 2629 3256 527981327 527981959 4.800000e-144 521
6 TraesCS7D01G385500 chr7A 96.004 4004 134 14 3 3994 566007174 566011163 0.000000e+00 6484
7 TraesCS7D01G385500 chr7A 80.240 1498 256 32 870 2357 566017725 566019192 0.000000e+00 1090
8 TraesCS7D01G385500 chr7A 81.975 638 100 10 2629 3256 566019514 566020146 1.030000e-145 527
9 TraesCS7D01G385500 chr7A 94.089 203 12 0 3989 4191 566011187 566011389 4.070000e-80 309
10 TraesCS7D01G385500 chr2B 93.407 364 19 5 3 363 769913351 769912990 6.170000e-148 534
11 TraesCS7D01G385500 chr2B 92.837 363 21 5 3 362 769908056 769907696 4.800000e-144 521
12 TraesCS7D01G385500 chr5A 93.407 364 17 7 3 362 519675308 519675668 2.220000e-147 532
13 TraesCS7D01G385500 chr3A 93.370 362 20 4 3 362 193998969 193999328 2.220000e-147 532
14 TraesCS7D01G385500 chr5B 93.113 363 20 5 3 362 608860510 608860150 1.030000e-145 527
15 TraesCS7D01G385500 chr4B 92.837 363 20 6 3 362 42535210 42535569 4.800000e-144 521
16 TraesCS7D01G385500 chr1B 92.562 363 23 4 3 362 511375255 511375616 6.210000e-143 518


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 TraesCS7D01G385500 chr7D 499971055 499975245 4190 False 7740.0 7740 100.0000 1 4191 1 chr7D.!!$F1 4190
1 TraesCS7D01G385500 chr7D 500098177 500100991 2814 False 851.0 1181 80.2115 476 3256 2 chr7D.!!$F2 2780
2 TraesCS7D01G385500 chr7B 527961294 527965456 4162 False 7112.0 7112 97.4420 7 4188 1 chr7B.!!$F1 4181
3 TraesCS7D01G385500 chr7B 527979145 527981959 2814 False 827.5 1134 79.9405 476 3256 2 chr7B.!!$F2 2780
4 TraesCS7D01G385500 chr7A 566007174 566011389 4215 False 3396.5 6484 95.0465 3 4191 2 chr7A.!!$F1 4188
5 TraesCS7D01G385500 chr7A 566017725 566020146 2421 False 808.5 1090 81.1075 870 3256 2 chr7A.!!$F2 2386

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
23 24 1.163420 TCTGCCGCAATCGTGTGTTT 61.163 50.000 0.0 0.0 33.10 2.83 F
205 206 3.356529 AATCACGAGCCTTTCCTTCAT 57.643 42.857 0.0 0.0 0.00 2.57 F
868 888 6.170846 GTATTTATACCTGTACACCAGCCT 57.829 41.667 0.0 0.0 40.06 4.58 F
2544 2627 1.029947 CCAAAGTATGTGGCGACCCC 61.030 60.000 0.0 0.0 36.10 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1518 1.522668 CAAGAAACGCCATCCTGTCA 58.477 50.000 0.00 0.00 0.00 3.58 R
2182 2213 2.185004 ACCCAACAGGATTGAACTCG 57.815 50.000 0.00 0.00 39.89 4.18 R
2627 2729 1.891150 CAAGGCCAACTTCAGCTGAAT 59.109 47.619 28.57 13.14 37.29 2.57 R
4018 4165 1.725164 CTCGCTAAACCAACTTCGGAC 59.275 52.381 0.00 0.00 0.00 4.79 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
23 24 1.163420 TCTGCCGCAATCGTGTGTTT 61.163 50.000 0.00 0.00 33.10 2.83
46 47 4.584325 TGTTGCTGCTGAGGTTAGAAAATT 59.416 37.500 0.00 0.00 0.00 1.82
129 130 8.981647 AGCATAAAACTGAGTTATTTTTGCTTG 58.018 29.630 16.59 3.68 38.05 4.01
189 190 6.540551 TGCCTTTCGTATTTGCATACTAATCA 59.459 34.615 0.00 0.00 34.10 2.57
198 199 4.137116 TGCATACTAATCACGAGCCTTT 57.863 40.909 0.00 0.00 0.00 3.11
205 206 3.356529 AATCACGAGCCTTTCCTTCAT 57.643 42.857 0.00 0.00 0.00 2.57
868 888 6.170846 GTATTTATACCTGTACACCAGCCT 57.829 41.667 0.00 0.00 40.06 4.58
1220 1242 7.665559 AGAGCTCTTATGAATGTACTCCTAGAG 59.334 40.741 11.45 0.00 35.52 2.43
1491 1518 7.683704 GCATAGCTGAATCAAATGTCTGGATTT 60.684 37.037 0.00 0.00 31.77 2.17
2182 2213 4.568760 GCAGCTCACTTTATAGGTCTTCAC 59.431 45.833 0.00 0.00 0.00 3.18
2544 2627 1.029947 CCAAAGTATGTGGCGACCCC 61.030 60.000 0.00 0.00 36.10 4.95
2598 2682 7.301868 TCTTGCAGGTTTTTCCTTTCATAAT 57.698 32.000 0.00 0.00 45.67 1.28
2793 2895 4.027295 GTCGCAGAGTAAGAATCACAATCG 60.027 45.833 0.00 0.00 36.95 3.34
2938 3044 5.695816 GGAAAACATGAAGCATTACAAGCAA 59.304 36.000 0.00 0.00 0.00 3.91
3468 3578 7.995289 TCAAACTTCTGAAGAAAATGCTGTTA 58.005 30.769 23.36 0.00 33.07 2.41
3570 3682 5.102313 GCTTAAAGCTGTTGTGAAAAGTGT 58.898 37.500 0.00 0.00 38.45 3.55
3576 3688 6.935741 AGCTGTTGTGAAAAGTGTATTACA 57.064 33.333 0.00 0.00 0.00 2.41
3788 3906 4.471904 TGATTATGTCCTTCGTTCTGCT 57.528 40.909 0.00 0.00 0.00 4.24
3807 3925 5.831525 TCTGCTCGGTTAGGATTTACTATGA 59.168 40.000 0.00 0.00 0.00 2.15
3828 3946 1.293498 CGCTTGTGTCCCTAGCTGT 59.707 57.895 0.00 0.00 39.43 4.40
3967 4085 2.281692 TTGTGGCTGCGATGCACT 60.282 55.556 7.97 0.00 33.79 4.40
3994 4112 6.934083 TGCATGTGTGGTATACGATAATCAAT 59.066 34.615 0.00 0.00 0.00 2.57
3995 4113 7.095271 TGCATGTGTGGTATACGATAATCAATG 60.095 37.037 0.00 0.00 0.00 2.82
4052 4199 1.220749 GCGAGCAATACCACCCTCA 59.779 57.895 0.00 0.00 0.00 3.86
4143 4290 2.094854 GCTGGATCTGAAGTTTGCAAGG 60.095 50.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.955428 ACACGATTGCGGCAGACATT 60.955 50.000 1.67 0.00 43.17 2.71
1 2 1.375908 ACACGATTGCGGCAGACAT 60.376 52.632 1.67 0.00 43.17 3.06
15 16 0.098552 TCAGCAGCAACAAACACACG 59.901 50.000 0.00 0.00 0.00 4.49
23 24 2.928801 TTCTAACCTCAGCAGCAACA 57.071 45.000 0.00 0.00 0.00 3.33
46 47 5.483811 TGCGGAAGACAAAACTGATGTATA 58.516 37.500 0.00 0.00 0.00 1.47
119 120 4.398988 TGACTGTCTGTGACAAGCAAAAAT 59.601 37.500 9.51 0.00 42.26 1.82
129 130 4.673061 CGAAGTAGGATGACTGTCTGTGAC 60.673 50.000 9.51 1.51 0.00 3.67
131 132 3.191581 ACGAAGTAGGATGACTGTCTGTG 59.808 47.826 9.51 0.00 41.94 3.66
189 190 2.945668 GCATTATGAAGGAAAGGCTCGT 59.054 45.455 0.00 0.00 30.17 4.18
205 206 8.235905 GCCAAAGCAATTCAAAATTTAGCATTA 58.764 29.630 0.00 0.00 39.53 1.90
868 888 1.800586 GAGAACAGTGATGCTTTGCGA 59.199 47.619 0.00 0.00 0.00 5.10
1491 1518 1.522668 CAAGAAACGCCATCCTGTCA 58.477 50.000 0.00 0.00 0.00 3.58
2182 2213 2.185004 ACCCAACAGGATTGAACTCG 57.815 50.000 0.00 0.00 39.89 4.18
2430 2513 2.160417 GCACATTAGGAGTTGTGACTGC 59.840 50.000 7.20 0.00 44.74 4.40
2544 2627 3.287312 ACATCGTGGCAGTCAATTTTG 57.713 42.857 0.00 0.00 0.00 2.44
2627 2729 1.891150 CAAGGCCAACTTCAGCTGAAT 59.109 47.619 28.57 13.14 37.29 2.57
2793 2895 4.224715 ACAAGCGAAAACTTAAGCTTCC 57.775 40.909 0.00 1.36 46.71 3.46
3421 3531 9.519191 TTTGAGATCTTCCAATAATTGTCTGAA 57.481 29.630 0.00 0.00 0.00 3.02
3570 3682 8.458052 CAGTATGATTTGCCAAACAGTGTAATA 58.542 33.333 0.00 0.00 39.69 0.98
3576 3688 5.068987 ACAACAGTATGATTTGCCAAACAGT 59.931 36.000 0.00 0.00 39.69 3.55
3788 3906 5.734220 GCGTGTCATAGTAAATCCTAACCGA 60.734 44.000 0.00 0.00 0.00 4.69
3967 4085 3.535280 ATCGTATACCACACATGCACA 57.465 42.857 0.00 0.00 0.00 4.57
3994 4112 3.380471 AAAATCGGACCAATCATCCCA 57.620 42.857 0.00 0.00 31.99 4.37
4016 4163 1.787012 GCTAAACCAACTTCGGACGA 58.213 50.000 0.00 0.00 0.00 4.20
4018 4165 1.725164 CTCGCTAAACCAACTTCGGAC 59.275 52.381 0.00 0.00 0.00 4.79
4052 4199 4.507512 GGGGAGTGGAGAACAAGAAGATTT 60.508 45.833 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.