Multiple sequence alignment - TraesCS7A01G289400

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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 TraesCS7A01G289400 chr7A 100.000 2414 0 0 1 2414 352183563 352181150 0 4458
1 TraesCS7A01G289400 chrUn 93.821 2460 103 16 1 2414 93411386 93408930 0 3655
2 TraesCS7A01G289400 chrUn 93.658 2381 105 13 79 2414 216520280 216517901 0 3518
3 TraesCS7A01G289400 chrUn 91.954 1044 43 6 1411 2414 346596834 346595792 0 1424
4 TraesCS7A01G289400 chrUn 92.767 954 47 9 1482 2414 389444786 389445738 0 1360
5 TraesCS7A01G289400 chr5D 93.737 2459 108 13 1 2414 503216463 503218920 0 3646
6 TraesCS7A01G289400 chr5D 93.398 2151 97 9 308 2414 503279673 503277524 0 3144
7 TraesCS7A01G289400 chr5D 93.169 2152 101 11 308 2414 6187492 6189642 0 3118
8 TraesCS7A01G289400 chr3B 93.615 2459 111 13 1 2414 201525269 201527726 0 3629
9 TraesCS7A01G289400 chr2D 93.618 2460 110 14 1 2414 272795649 272793191 0 3629
10 TraesCS7A01G289400 chr3A 93.255 2461 117 15 1 2414 672911764 672909306 0 3579
11 TraesCS7A01G289400 chr6A 93.046 2459 124 14 1 2414 260118035 260115579 0 3550
12 TraesCS7A01G289400 chr6D 93.703 2382 103 14 79 2414 168253248 168255628 0 3524
13 TraesCS7A01G289400 chr6D 93.450 2000 84 13 1 1956 168249785 168251781 0 2924
14 TraesCS7A01G289400 chr5A 92.483 2461 135 14 1 2414 619264615 619267072 0 3474
15 TraesCS7A01G289400 chr3D 93.401 2152 93 11 308 2414 589280989 589278842 0 3142
16 TraesCS7A01G289400 chr1A 93.126 2153 93 11 308 2414 554510807 554512950 0 3105
17 TraesCS7A01G289400 chr4A 93.424 1247 39 11 951 2156 73813309 73812065 0 1808


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 TraesCS7A01G289400 chr7A 352181150 352183563 2413 True 4458 4458 100.0000 1 2414 1 chr7A.!!$R1 2413
1 TraesCS7A01G289400 chrUn 93408930 93411386 2456 True 3655 3655 93.8210 1 2414 1 chrUn.!!$R1 2413
2 TraesCS7A01G289400 chrUn 216517901 216520280 2379 True 3518 3518 93.6580 79 2414 1 chrUn.!!$R2 2335
3 TraesCS7A01G289400 chrUn 346595792 346596834 1042 True 1424 1424 91.9540 1411 2414 1 chrUn.!!$R3 1003
4 TraesCS7A01G289400 chrUn 389444786 389445738 952 False 1360 1360 92.7670 1482 2414 1 chrUn.!!$F1 932
5 TraesCS7A01G289400 chr5D 503216463 503218920 2457 False 3646 3646 93.7370 1 2414 1 chr5D.!!$F2 2413
6 TraesCS7A01G289400 chr5D 503277524 503279673 2149 True 3144 3144 93.3980 308 2414 1 chr5D.!!$R1 2106
7 TraesCS7A01G289400 chr5D 6187492 6189642 2150 False 3118 3118 93.1690 308 2414 1 chr5D.!!$F1 2106
8 TraesCS7A01G289400 chr3B 201525269 201527726 2457 False 3629 3629 93.6150 1 2414 1 chr3B.!!$F1 2413
9 TraesCS7A01G289400 chr2D 272793191 272795649 2458 True 3629 3629 93.6180 1 2414 1 chr2D.!!$R1 2413
10 TraesCS7A01G289400 chr3A 672909306 672911764 2458 True 3579 3579 93.2550 1 2414 1 chr3A.!!$R1 2413
11 TraesCS7A01G289400 chr6A 260115579 260118035 2456 True 3550 3550 93.0460 1 2414 1 chr6A.!!$R1 2413
12 TraesCS7A01G289400 chr6D 168249785 168255628 5843 False 3224 3524 93.5765 1 2414 2 chr6D.!!$F1 2413
13 TraesCS7A01G289400 chr5A 619264615 619267072 2457 False 3474 3474 92.4830 1 2414 1 chr5A.!!$F1 2413
14 TraesCS7A01G289400 chr3D 589278842 589280989 2147 True 3142 3142 93.4010 308 2414 1 chr3D.!!$R1 2106
15 TraesCS7A01G289400 chr1A 554510807 554512950 2143 False 3105 3105 93.1260 308 2414 1 chr1A.!!$F1 2106
16 TraesCS7A01G289400 chr4A 73812065 73813309 1244 True 1808 1808 93.4240 951 2156 1 chr4A.!!$R1 1205

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
510 3899 0.58873 CGCGATTGTATGGCCAAACG 60.589 55.0 10.96 4.74 41.68 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 5628 2.03187 GGAATCATTACCCCAAGGCAC 58.968 52.381 0.0 0.0 36.11 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
77 78 5.311649 AGGGCATGAGGTTCAGTATCATAAT 59.688 40.000 0.00 0.00 32.51 1.28
108 109 2.472695 AGTAACGCCAGCAAATCTCA 57.527 45.000 0.00 0.00 0.00 3.27
113 114 2.372264 ACGCCAGCAAATCTCATCAAT 58.628 42.857 0.00 0.00 0.00 2.57
149 150 6.374333 GCTTTGAAAACAGACATAGGGATACA 59.626 38.462 0.00 0.00 39.74 2.29
188 189 7.507733 AAACTCTCTCGAACTTAAGTAGACA 57.492 36.000 8.92 0.00 0.00 3.41
191 192 8.113173 ACTCTCTCGAACTTAAGTAGACAATT 57.887 34.615 8.92 0.00 0.00 2.32
225 226 0.672401 TTGCGAGTTTCCTTAGCCCG 60.672 55.000 0.00 0.00 0.00 6.13
296 297 8.566109 ACTTGTCATAAATAAGGTTATTCCCCT 58.434 33.333 0.00 0.00 36.75 4.79
310 311 6.409005 GGTTATTCCCCTCCTACCTTTACTTC 60.409 46.154 0.00 0.00 0.00 3.01
385 3774 8.311836 ACAACGAGATTTAGTATCCTTTCTTGA 58.688 33.333 0.00 0.00 0.00 3.02
426 3815 0.870307 CCGAGTAGGCACGAATTCCG 60.870 60.000 0.00 0.00 45.44 4.30
435 3824 1.668628 GCACGAATTCCGCCAATTTGT 60.669 47.619 0.00 5.51 46.36 2.83
438 3827 2.491693 ACGAATTCCGCCAATTTGTGAT 59.508 40.909 9.17 0.00 44.49 3.06
508 3897 1.674359 ATCGCGATTGTATGGCCAAA 58.326 45.000 17.62 0.00 0.00 3.28
510 3899 0.588730 CGCGATTGTATGGCCAAACG 60.589 55.000 10.96 4.74 41.68 3.60
532 3921 4.680708 CGTTGTGGGTAGAATGCTAGATGT 60.681 45.833 0.00 0.00 0.00 3.06
533 3922 5.186198 GTTGTGGGTAGAATGCTAGATGTT 58.814 41.667 0.00 0.00 0.00 2.71
536 3925 3.958147 TGGGTAGAATGCTAGATGTTCGA 59.042 43.478 0.00 0.00 0.00 3.71
559 3948 6.183359 CGAGACCACGTTACTATTGTTTCTTC 60.183 42.308 0.00 0.00 0.00 2.87
617 4006 7.631377 GCCAATAAATGATGAGCTACAAAAGGT 60.631 37.037 0.00 0.00 39.11 3.50
662 4058 7.606839 AGTCGATTACTCCTTTTCCCTTTTAAG 59.393 37.037 0.00 0.00 30.33 1.85
693 4089 7.928167 GGCATTATATGTCCAATATCTCGATCA 59.072 37.037 0.00 0.00 0.00 2.92
701 4097 6.038936 TGTCCAATATCTCGATCAAAGTACGA 59.961 38.462 0.00 0.00 34.90 3.43
706 4102 4.778534 TCTCGATCAAAGTACGAAGGTT 57.221 40.909 0.00 0.00 35.70 3.50
707 4103 4.482386 TCTCGATCAAAGTACGAAGGTTG 58.518 43.478 0.00 0.00 35.70 3.77
891 4288 8.815565 TGCAATTTTCCATATTCCTAGTTACA 57.184 30.769 0.00 0.00 0.00 2.41
1044 4444 4.194497 TGGGGGTGGTCCACAGGA 62.194 66.667 23.48 1.39 45.78 3.86
1069 4469 6.006275 TCATAACTACCCCTCTTACTACGT 57.994 41.667 0.00 0.00 0.00 3.57
1185 4585 3.104519 TGGGATACTAAACGGACCTCA 57.895 47.619 0.00 0.00 0.00 3.86
1290 4690 1.165270 CCCTTCCACGTGTGATTTCC 58.835 55.000 15.65 0.00 0.00 3.13
1558 4977 6.261826 GGCTTATGTTCTTCATGTAGCATTCT 59.738 38.462 13.97 0.00 42.20 2.40
1584 5005 9.762933 TGATCGAATGACTATGAAATTATGTCA 57.237 29.630 0.00 0.00 41.07 3.58
1765 5203 5.586643 TGCGTGCTTCAAACAATACCATATA 59.413 36.000 0.00 0.00 0.00 0.86
1813 5251 8.429641 TGAGGAACTACTAAACTCAATCACTTT 58.570 33.333 0.00 0.00 41.55 2.66
1814 5252 8.608844 AGGAACTACTAAACTCAATCACTTTG 57.391 34.615 0.00 0.00 36.02 2.77
1815 5253 7.173390 AGGAACTACTAAACTCAATCACTTTGC 59.827 37.037 0.00 0.00 36.02 3.68
1817 5255 5.989777 ACTACTAAACTCAATCACTTTGCGT 59.010 36.000 0.00 0.00 34.79 5.24
1818 5256 7.149973 ACTACTAAACTCAATCACTTTGCGTA 58.850 34.615 0.00 0.00 32.18 4.42
1836 5274 6.956299 TGCGTAGTTACTCAATAGTTTTCC 57.044 37.500 0.00 0.00 37.15 3.13
1959 5397 4.638865 AGTTGAAACCACACTCAAAGGTAC 59.361 41.667 0.00 0.00 33.52 3.34
1960 5398 4.223556 TGAAACCACACTCAAAGGTACA 57.776 40.909 0.00 0.00 34.63 2.90
1961 5399 4.590918 TGAAACCACACTCAAAGGTACAA 58.409 39.130 0.00 0.00 34.63 2.41
2106 5546 7.771361 TGCATTTCAATTAGGGTCGTATTCTAA 59.229 33.333 0.00 0.00 0.00 2.10
2112 5552 9.151177 TCAATTAGGGTCGTATTCTAAGGTTAT 57.849 33.333 0.00 0.00 0.00 1.89
2188 5628 0.761802 GCTTATGACCTCCCCCTCTG 59.238 60.000 0.00 0.00 0.00 3.35
2196 5636 2.935481 TCCCCCTCTGTGCCTTGG 60.935 66.667 0.00 0.00 0.00 3.61
2305 5745 1.005867 TACGGTTCCCTTGCGTGTC 60.006 57.895 0.00 0.00 0.00 3.67
2311 5751 4.003788 CCCTTGCGTGTCCTCGGT 62.004 66.667 0.00 0.00 0.00 4.69
2339 5779 8.012957 AGGTGTTTTGTATAAATGTTTCACCA 57.987 30.769 16.92 0.00 42.43 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 8.345724 AGCACAAAGAGTTATTGATGAGATTT 57.654 30.769 0.00 0.00 0.00 2.17
108 109 9.034544 GTTTTCAAAGCACAAAGAGTTATTGAT 57.965 29.630 0.00 0.00 0.00 2.57
113 114 7.027161 GTCTGTTTTCAAAGCACAAAGAGTTA 58.973 34.615 0.00 0.00 0.00 2.24
149 150 8.567948 TCGAGAGAGTTTTCAAAGCATAAAAAT 58.432 29.630 0.00 0.00 34.84 1.82
155 156 5.059833 AGTTCGAGAGAGTTTTCAAAGCAT 58.940 37.500 0.00 0.00 43.69 3.79
225 226 7.339482 TCCCTAGGATAAAGAAGAAGAAAAGC 58.661 38.462 11.48 0.00 0.00 3.51
296 297 9.807921 AAGATTCAAAATGAAGTAAAGGTAGGA 57.192 29.630 0.00 0.00 40.05 2.94
385 3774 7.151308 TCGGCATTTCACAAGTTATGAAAATT 58.849 30.769 13.00 0.00 46.26 1.82
426 3815 5.376625 TCCTATGGTAGATCACAAATTGGC 58.623 41.667 0.00 0.00 0.00 4.52
508 3897 2.829720 TCTAGCATTCTACCCACAACGT 59.170 45.455 0.00 0.00 0.00 3.99
510 3899 4.770795 ACATCTAGCATTCTACCCACAAC 58.229 43.478 0.00 0.00 0.00 3.32
532 3921 4.771590 ACAATAGTAACGTGGTCTCGAA 57.228 40.909 0.00 0.00 34.70 3.71
533 3922 4.771590 AACAATAGTAACGTGGTCTCGA 57.228 40.909 0.00 0.00 34.70 4.04
536 3925 5.930569 GGAAGAAACAATAGTAACGTGGTCT 59.069 40.000 0.00 0.00 0.00 3.85
559 3948 5.379706 AAAGGTCAATATGAAGGAGGAGG 57.620 43.478 0.00 0.00 0.00 4.30
638 4030 6.882678 CCTTAAAAGGGAAAAGGAGTAATCGA 59.117 38.462 0.42 0.00 42.01 3.59
639 4031 6.882678 TCCTTAAAAGGGAAAAGGAGTAATCG 59.117 38.462 8.87 0.00 46.47 3.34
655 4051 7.502226 TGGACATATAATGCCACTCCTTAAAAG 59.498 37.037 0.00 0.00 33.56 2.27
662 4058 7.341805 AGATATTGGACATATAATGCCACTCC 58.658 38.462 0.00 0.00 36.60 3.85
673 4069 9.862371 GTACTTTGATCGAGATATTGGACATAT 57.138 33.333 3.20 0.00 0.00 1.78
693 4089 9.729281 TTCTATTTATTCCAACCTTCGTACTTT 57.271 29.630 0.00 0.00 0.00 2.66
752 4149 0.769873 ATCTGCCCCTTATCCAGCTG 59.230 55.000 6.78 6.78 0.00 4.24
811 4208 2.631580 GGGAATTGAACCCGCGCAA 61.632 57.895 8.75 0.00 37.85 4.85
891 4288 5.779529 TCTTCGTCGCCCTAAGTAAATAT 57.220 39.130 0.00 0.00 0.00 1.28
902 4299 4.085210 CGATAGTTTTATTCTTCGTCGCCC 60.085 45.833 0.00 0.00 0.00 6.13
1044 4444 7.014038 CACGTAGTAAGAGGGGTAGTTATGAAT 59.986 40.741 0.00 0.00 41.61 2.57
1205 4605 1.749063 CAAAAGAGGGTAAATCGGCCC 59.251 52.381 0.00 0.00 45.16 5.80
1321 4721 9.267084 GAGAAAAGAAGAATCTACTTCAACTGT 57.733 33.333 0.00 0.00 45.83 3.55
1394 4794 8.630054 AGATCGTCATATACTTCTAGAAAGCT 57.370 34.615 6.63 0.00 0.00 3.74
1405 4805 7.768582 CCATCTGTCTAGAGATCGTCATATACT 59.231 40.741 0.00 0.00 36.14 2.12
1558 4977 9.762933 TGACATAATTTCATAGTCATTCGATCA 57.237 29.630 0.00 0.00 34.59 2.92
1591 5012 6.959954 TCTCCTATGCTACCCATAATATGTGT 59.040 38.462 0.00 0.00 36.04 3.72
1607 5028 4.323868 GGGAAATAGGGATGTCTCCTATGC 60.324 50.000 3.71 0.69 44.38 3.14
1609 5030 4.439860 GGGGAAATAGGGATGTCTCCTAT 58.560 47.826 0.00 0.00 46.39 2.57
1765 5203 9.956640 CCTCATAGAAAATTATTGGCTCTAGAT 57.043 33.333 0.00 0.00 0.00 1.98
1813 5251 5.574055 CGGAAAACTATTGAGTAACTACGCA 59.426 40.000 0.00 0.00 33.58 5.24
1814 5252 5.574443 ACGGAAAACTATTGAGTAACTACGC 59.426 40.000 0.00 0.00 33.58 4.42
1815 5253 7.326789 TCAACGGAAAACTATTGAGTAACTACG 59.673 37.037 0.00 0.00 33.58 3.51
1817 5255 7.816031 CCTCAACGGAAAACTATTGAGTAACTA 59.184 37.037 10.89 0.00 44.28 2.24
1818 5256 6.649557 CCTCAACGGAAAACTATTGAGTAACT 59.350 38.462 10.89 0.00 44.28 2.24
1836 5274 2.548904 CTCTACGGGATAGACCTCAACG 59.451 54.545 0.00 0.00 34.80 4.10
1940 5378 4.396790 TGTTGTACCTTTGAGTGTGGTTTC 59.603 41.667 0.00 0.00 35.48 2.78
1946 5384 4.583073 GGGAAATGTTGTACCTTTGAGTGT 59.417 41.667 0.00 0.00 0.00 3.55
2030 5470 8.926710 GGATGGTGAGAACAGATATATTTTACG 58.073 37.037 0.00 0.00 0.00 3.18
2044 5484 2.505819 ACACTATGGGGATGGTGAGAAC 59.494 50.000 5.65 0.00 36.65 3.01
2088 5528 9.151177 TCATAACCTTAGAATACGACCCTAATT 57.849 33.333 0.00 0.00 0.00 1.40
2106 5546 8.964533 AGACATATCTGGTAGAATCATAACCT 57.035 34.615 0.00 0.00 32.29 3.50
2188 5628 2.031870 GGAATCATTACCCCAAGGCAC 58.968 52.381 0.00 0.00 36.11 5.01
2241 5681 6.710295 TCCACGAAATAATTTGATCCATCGAT 59.290 34.615 0.00 0.00 33.61 3.59
2244 5684 7.596248 CCAATCCACGAAATAATTTGATCCATC 59.404 37.037 0.00 0.00 0.00 3.51
2305 5745 8.770828 CATTTATACAAAACACCTATACCGAGG 58.229 37.037 0.00 0.00 42.89 4.63
2382 5823 5.527582 CCTTCAACCGGGTTATTCTATCTTG 59.472 44.000 12.95 0.00 0.00 3.02
2383 5824 5.397559 CCCTTCAACCGGGTTATTCTATCTT 60.398 44.000 12.95 0.00 36.91 2.40
2384 5825 4.102681 CCCTTCAACCGGGTTATTCTATCT 59.897 45.833 12.95 0.00 36.91 1.98
2385 5826 4.386711 CCCTTCAACCGGGTTATTCTATC 58.613 47.826 12.95 0.00 36.91 2.08


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

AutoCloner maintained by Alex Coulton.