Multiple sequence alignment - TraesCS7A01G289700

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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 TraesCS7A01G289700 chr7A 100.000 2720 0 0 1 2720 352182787 352185506 0 5024
1 TraesCS7A01G289700 chrUn 95.142 2738 112 13 1 2720 93410605 93413339 0 4300
2 TraesCS7A01G289700 chr5D 94.920 2736 119 13 1 2720 503217243 503214512 0 4265
3 TraesCS7A01G289700 chr5D 94.113 2735 139 18 1 2720 329121081 329123808 0 4139
4 TraesCS7A01G289700 chr2D 94.846 2736 119 19 1 2720 272794868 272797597 0 4252
5 TraesCS7A01G289700 chr6D 94.599 2740 121 18 1 2720 168250565 168247833 0 4215
6 TraesCS7A01G289700 chr3A 94.081 2737 139 17 1 2720 672910983 672913713 0 4135
7 TraesCS7A01G289700 chr3B 94.004 2752 127 17 1 2720 201526049 201523304 0 4133
8 TraesCS7A01G289700 chr6A 93.939 2739 141 17 1 2720 260117255 260119987 0 4115
9 TraesCS7A01G289700 chr6A 94.238 2100 106 10 633 2720 271188163 271186067 0 3193
10 TraesCS7A01G289700 chr4D 94.515 2042 89 18 695 2720 19927126 19925092 0 3129
11 TraesCS7A01G289700 chr7D 95.021 1205 50 7 1 1195 231547618 231546414 0 1884


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 TraesCS7A01G289700 chr7A 352182787 352185506 2719 False 5024 5024 100.000 1 2720 1 chr7A.!!$F1 2719
1 TraesCS7A01G289700 chrUn 93410605 93413339 2734 False 4300 4300 95.142 1 2720 1 chrUn.!!$F1 2719
2 TraesCS7A01G289700 chr5D 503214512 503217243 2731 True 4265 4265 94.920 1 2720 1 chr5D.!!$R1 2719
3 TraesCS7A01G289700 chr5D 329121081 329123808 2727 False 4139 4139 94.113 1 2720 1 chr5D.!!$F1 2719
4 TraesCS7A01G289700 chr2D 272794868 272797597 2729 False 4252 4252 94.846 1 2720 1 chr2D.!!$F1 2719
5 TraesCS7A01G289700 chr6D 168247833 168250565 2732 True 4215 4215 94.599 1 2720 1 chr6D.!!$R1 2719
6 TraesCS7A01G289700 chr3A 672910983 672913713 2730 False 4135 4135 94.081 1 2720 1 chr3A.!!$F1 2719
7 TraesCS7A01G289700 chr3B 201523304 201526049 2745 True 4133 4133 94.004 1 2720 1 chr3B.!!$R1 2719
8 TraesCS7A01G289700 chr6A 260117255 260119987 2732 False 4115 4115 93.939 1 2720 1 chr6A.!!$F1 2719
9 TraesCS7A01G289700 chr6A 271186067 271188163 2096 True 3193 3193 94.238 633 2720 1 chr6A.!!$R1 2087
10 TraesCS7A01G289700 chr4D 19925092 19927126 2034 True 3129 3129 94.515 695 2720 1 chr4D.!!$R1 2025
11 TraesCS7A01G289700 chr7D 231546414 231547618 1204 True 1884 1884 95.021 1 1195 1 chr7D.!!$R1 1194

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
24 25 0.769873 ATCTGCCCCTTATCCAGCTG 59.230 55.0 6.78 6.78 0.0 4.24 F
1170 1210 0.817654 GGAAAAAGGGCTCGAATGGG 59.182 55.0 0.00 0.00 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1586 1630 1.538075 CCTTTTTAATGGTGTCGGCGT 59.462 47.619 6.85 0.0 0.0 5.68 R
2278 2335 0.883370 CCCGGGCGGCTCTTTATTAC 60.883 60.000 8.08 0.0 0.0 1.89 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
24 25 0.769873 ATCTGCCCCTTATCCAGCTG 59.230 55.000 6.78 6.78 0.00 4.24
83 85 9.729281 TTCTATTTATTCCAACCTTCGTACTTT 57.271 29.630 0.00 0.00 0.00 2.66
103 105 9.862371 GTACTTTGATCGAGATATTGGACATAT 57.138 33.333 3.20 0.00 0.00 1.78
114 116 7.341805 AGATATTGGACATATAATGCCACTCC 58.658 38.462 0.00 0.00 36.60 3.85
217 226 5.379706 AAAGGTCAATATGAAGGAGGAGG 57.620 43.478 0.00 0.00 0.00 4.30
240 249 5.930569 GGAAGAAACAATAGTAACGTGGTCT 59.069 40.000 0.00 0.00 0.00 3.85
243 252 4.771590 AACAATAGTAACGTGGTCTCGA 57.228 40.909 0.00 0.00 34.70 4.04
244 253 4.771590 ACAATAGTAACGTGGTCTCGAA 57.228 40.909 0.00 0.00 34.70 3.71
266 275 4.770795 ACATCTAGCATTCTACCCACAAC 58.229 43.478 0.00 0.00 0.00 3.32
268 277 2.829720 TCTAGCATTCTACCCACAACGT 59.170 45.455 0.00 0.00 0.00 3.99
350 359 5.376625 TCCTATGGTAGATCACAAATTGGC 58.623 41.667 0.00 0.00 0.00 4.52
391 400 7.151308 TCGGCATTTCACAAGTTATGAAAATT 58.849 30.769 13.00 0.00 46.26 1.82
480 491 9.807921 AAGATTCAAAATGAAGTAAAGGTAGGA 57.192 29.630 0.00 0.00 40.05 2.94
551 562 7.339482 TCCCTAGGATAAAGAAGAAGAAAAGC 58.661 38.462 11.48 0.00 0.00 3.51
621 632 5.059833 AGTTCGAGAGAGTTTTCAAAGCAT 58.940 37.500 0.00 0.00 43.69 3.79
627 638 8.567948 TCGAGAGAGTTTTCAAAGCATAAAAAT 58.432 29.630 0.00 0.00 34.84 1.82
663 674 7.027161 GTCTGTTTTCAAAGCACAAAGAGTTA 58.973 34.615 0.00 0.00 0.00 2.24
668 679 9.034544 GTTTTCAAAGCACAAAGAGTTATTGAT 57.965 29.630 0.00 0.00 0.00 2.57
675 686 8.345724 AGCACAAAGAGTTATTGATGAGATTT 57.654 30.769 0.00 0.00 0.00 2.17
1070 1108 2.661718 ACACCATTCCTTTTGGTTCGT 58.338 42.857 0.00 0.00 45.19 3.85
1071 1109 2.360801 ACACCATTCCTTTTGGTTCGTG 59.639 45.455 0.00 0.00 45.19 4.35
1168 1208 4.884164 AGAATAGGAAAAAGGGCTCGAATG 59.116 41.667 0.00 0.00 0.00 2.67
1170 1210 0.817654 GGAAAAAGGGCTCGAATGGG 59.182 55.000 0.00 0.00 0.00 4.00
1288 1328 7.555914 TCCAAAAAGAAATCGATATGATCCACA 59.444 33.333 0.00 0.00 35.84 4.17
1464 1506 8.613060 TTCTTGCAGAATATATAGCTTTCCAG 57.387 34.615 0.00 0.00 0.00 3.86
1586 1630 3.218453 TCGGAGGAAAAGAAATTGCACA 58.782 40.909 0.00 0.00 0.00 4.57
1593 1637 0.040425 AAGAAATTGCACACGCCGAC 60.040 50.000 0.00 0.00 37.32 4.79
1594 1638 1.163420 AGAAATTGCACACGCCGACA 61.163 50.000 0.00 0.00 37.32 4.35
1610 1654 3.697542 GCCGACACCATTAAAAAGGGTAT 59.302 43.478 0.00 0.00 32.55 2.73
1735 1779 9.706691 ACGAAGAATAAGTAATCTTGTCTTCAA 57.293 29.630 21.56 0.00 44.82 2.69
1802 1850 4.465305 CCTGAAATCCCTGCAAAAGAAGAT 59.535 41.667 0.00 0.00 0.00 2.40
1806 1854 7.549839 TGAAATCCCTGCAAAAGAAGATATTG 58.450 34.615 0.00 0.00 0.00 1.90
1817 1865 6.765915 AAAGAAGATATTGCACCTCTTTCC 57.234 37.500 6.17 0.00 29.64 3.13
1981 2035 7.223260 TGTCGAGATCCTAACTAAGAAACAA 57.777 36.000 0.00 0.00 0.00 2.83
2097 2153 6.861065 TCTAGGTTGTGAAGCAAAACTAAG 57.139 37.500 0.00 0.00 39.03 2.18
2124 2180 3.395607 TGTGGATAAAGGGAGGGATGATG 59.604 47.826 0.00 0.00 0.00 3.07
2137 2193 3.854994 AGGGATGATGGAAAGAAGGAAGT 59.145 43.478 0.00 0.00 0.00 3.01
2177 2233 5.871396 ATGATTCCACTACGTATGGTCTT 57.129 39.130 17.86 9.04 38.47 3.01
2331 2389 8.622948 ACTGAGAAAATTAACTCGGAAAGAAT 57.377 30.769 20.30 2.36 40.67 2.40
2358 2416 2.225343 TGGAAGCTCCATTGTGGGATTT 60.225 45.455 1.25 0.00 42.67 2.17
2383 2441 3.589288 ACCTAACCATTCAAGGAGAAGCT 59.411 43.478 0.00 0.00 40.15 3.74
2395 2453 1.646189 GAGAAGCTGTGGGAACGATC 58.354 55.000 0.00 0.00 0.00 3.69
2401 2459 0.739813 CTGTGGGAACGATCGAACCC 60.740 60.000 31.39 31.39 42.37 4.11
2407 2465 2.135933 GGAACGATCGAACCCATGATC 58.864 52.381 24.34 5.31 38.08 2.92
2409 2467 1.119684 ACGATCGAACCCATGATCCA 58.880 50.000 24.34 0.00 38.17 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.548031 CTTCAGCTGGATAAGGGGCA 59.452 55.000 15.13 0.00 0.00 5.36
69 71 4.482386 TCTCGATCAAAGTACGAAGGTTG 58.518 43.478 0.00 0.00 35.70 3.77
70 72 4.778534 TCTCGATCAAAGTACGAAGGTT 57.221 40.909 0.00 0.00 35.70 3.50
75 77 6.038936 TGTCCAATATCTCGATCAAAGTACGA 59.961 38.462 0.00 0.00 34.90 3.43
83 85 7.928167 GGCATTATATGTCCAATATCTCGATCA 59.072 37.037 0.00 0.00 0.00 2.92
114 116 7.606839 AGTCGATTACTCCTTTTCCCTTTTAAG 59.393 37.037 0.00 0.00 30.33 1.85
155 161 5.551760 ATGATGAGCTACAAAAGGTTTCG 57.448 39.130 0.00 0.00 35.60 3.46
156 162 9.860898 AATAAATGATGAGCTACAAAAGGTTTC 57.139 29.630 0.00 0.00 35.60 2.78
158 164 8.253113 CCAATAAATGATGAGCTACAAAAGGTT 58.747 33.333 0.00 0.00 35.60 3.50
159 165 7.631377 GCCAATAAATGATGAGCTACAAAAGGT 60.631 37.037 0.00 0.00 39.11 3.50
217 226 6.183359 CGAGACCACGTTACTATTGTTTCTTC 60.183 42.308 0.00 0.00 0.00 2.87
240 249 3.958147 TGGGTAGAATGCTAGATGTTCGA 59.042 43.478 0.00 0.00 0.00 3.71
243 252 5.186198 GTTGTGGGTAGAATGCTAGATGTT 58.814 41.667 0.00 0.00 0.00 2.71
244 253 4.680708 CGTTGTGGGTAGAATGCTAGATGT 60.681 45.833 0.00 0.00 0.00 3.06
266 275 0.588730 CGCGATTGTATGGCCAAACG 60.589 55.000 10.96 4.74 41.68 3.60
268 277 1.674359 ATCGCGATTGTATGGCCAAA 58.326 45.000 17.62 0.00 0.00 3.28
338 347 2.491693 ACGAATTCCGCCAATTTGTGAT 59.508 40.909 9.17 0.00 44.49 3.06
341 350 1.668628 GCACGAATTCCGCCAATTTGT 60.669 47.619 0.00 5.51 46.36 2.83
350 359 0.870307 CCGAGTAGGCACGAATTCCG 60.870 60.000 0.00 0.00 45.44 4.30
391 400 8.311836 ACAACGAGATTTAGTATCCTTTCTTGA 58.688 33.333 0.00 0.00 0.00 3.02
466 477 6.409005 GGTTATTCCCCTCCTACCTTTACTTC 60.409 46.154 0.00 0.00 0.00 3.01
480 491 8.566109 ACTTGTCATAAATAAGGTTATTCCCCT 58.434 33.333 0.00 0.00 36.75 4.79
551 562 0.672401 TTGCGAGTTTCCTTAGCCCG 60.672 55.000 0.00 0.00 0.00 6.13
585 596 8.113173 ACTCTCTCGAACTTAAGTAGACAATT 57.887 34.615 8.92 0.00 0.00 2.32
588 599 7.507733 AAACTCTCTCGAACTTAAGTAGACA 57.492 36.000 8.92 0.00 0.00 3.41
627 638 6.374333 GCTTTGAAAACAGACATAGGGATACA 59.626 38.462 0.00 0.00 39.74 2.29
663 674 2.372264 ACGCCAGCAAATCTCATCAAT 58.628 42.857 0.00 0.00 0.00 2.57
668 679 2.472695 AGTAACGCCAGCAAATCTCA 57.527 45.000 0.00 0.00 0.00 3.27
699 710 5.311649 AGGGCATGAGGTTCAGTATCATAAT 59.688 40.000 0.00 0.00 32.51 1.28
1024 1062 5.376756 TGGGTTGTACCAAGTCTAAAACT 57.623 39.130 0.00 0.00 41.02 2.66
1168 1208 7.066404 GGAACTTGAGTCTGATTCTATTTTCCC 59.934 40.741 1.79 0.00 0.00 3.97
1170 1210 7.545965 TCGGAACTTGAGTCTGATTCTATTTTC 59.454 37.037 1.79 1.22 0.00 2.29
1280 1320 7.931046 TCCAATATGGATTATGATGTGGATCA 58.069 34.615 0.00 0.00 42.67 2.92
1539 1583 5.213675 CGACCCGCAATTTTTACTTTTACA 58.786 37.500 0.00 0.00 0.00 2.41
1586 1630 1.538075 CCTTTTTAATGGTGTCGGCGT 59.462 47.619 6.85 0.00 0.00 5.68
1593 1637 7.342769 GGGAAGTATACCCTTTTTAATGGTG 57.657 40.000 0.00 0.00 43.65 4.17
1610 1654 4.510571 GCGAATTGTTAGGAAGGGAAGTA 58.489 43.478 0.00 0.00 0.00 2.24
1618 1662 5.554822 ATTTTAGCGCGAATTGTTAGGAA 57.445 34.783 12.10 0.00 0.00 3.36
1622 1666 9.509855 AATAATCAATTTTAGCGCGAATTGTTA 57.490 25.926 28.83 25.61 41.61 2.41
1707 1751 8.705048 AAGACAAGATTACTTATTCTTCGTCC 57.295 34.615 13.12 0.00 34.97 4.79
1776 1822 4.222336 TCTTTTGCAGGGATTTCAGGAAA 58.778 39.130 0.00 0.00 34.46 3.13
1802 1850 9.693739 TTAAATCTTATGGAAAGAGGTGCAATA 57.306 29.630 0.00 0.00 0.00 1.90
1806 1854 8.225603 TCATTAAATCTTATGGAAAGAGGTGC 57.774 34.615 0.00 0.00 0.00 5.01
2000 2054 7.032580 ACGCATCTACTCATTTATGATAGAGC 58.967 38.462 12.81 13.41 36.02 4.09
2097 2153 1.425448 CCTCCCTTTATCCACATCCCC 59.575 57.143 0.00 0.00 0.00 4.81
2156 2212 5.186215 TCAAAGACCATACGTAGTGGAATCA 59.814 40.000 22.74 6.26 45.73 2.57
2267 2324 6.633234 GCGGCTCTTTATTACTGCTTTAAATC 59.367 38.462 0.00 0.00 0.00 2.17
2278 2335 0.883370 CCCGGGCGGCTCTTTATTAC 60.883 60.000 8.08 0.00 0.00 1.89
2351 2409 6.395780 TTGAATGGTTAGGTCTAAATCCCA 57.604 37.500 2.43 2.43 0.00 4.37
2358 2416 5.104900 GCTTCTCCTTGAATGGTTAGGTCTA 60.105 44.000 0.00 0.00 33.71 2.59
2383 2441 1.294138 GGGTTCGATCGTTCCCACA 59.706 57.895 30.20 6.01 39.68 4.17
2395 2453 3.769739 TCCTATTGGATCATGGGTTCG 57.230 47.619 0.00 0.00 37.46 3.95


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

AutoCloner maintained by Alex Coulton.