Multiple sequence alignment - TraesCS7A01G108000

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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 TraesCS7A01G108000 chr7A 100.000 3443 0 0 1 3443 65440837 65444279 0.000000e+00 6359
1 TraesCS7A01G108000 chr7A 82.119 1331 227 10 1085 2409 65154700 65153375 0.000000e+00 1129
2 TraesCS7A01G108000 chr7D 96.874 2911 75 8 1 2902 62120999 62123902 0.000000e+00 4857
3 TraesCS7A01G108000 chr7D 94.800 2981 140 10 106 3078 62279191 62282164 0.000000e+00 4632
4 TraesCS7A01G108000 chr7D 80.241 1579 277 23 1124 2697 62260560 62259012 0.000000e+00 1155
5 TraesCS7A01G108000 chr7D 81.682 1332 231 11 1085 2409 61228788 61227463 0.000000e+00 1096
6 TraesCS7A01G108000 chr7D 81.490 1329 246 0 1081 2409 60705444 60704116 0.000000e+00 1092
7 TraesCS7A01G108000 chr7D 93.704 540 25 1 2899 3438 62124324 62124854 0.000000e+00 800
8 TraesCS7A01G108000 chr7D 93.443 366 23 1 3074 3438 62337495 62337860 3.020000e-150 542
9 TraesCS7A01G108000 chr7D 93.578 109 7 0 1 109 62278022 62278130 2.750000e-36 163
10 TraesCS7A01G108000 chr2A 80.206 1359 263 5 1089 2446 734654200 734652847 0.000000e+00 1014
11 TraesCS7A01G108000 chr2D 81.075 1247 233 3 1201 2446 601263799 601262555 0.000000e+00 992
12 TraesCS7A01G108000 chr2B 80.298 1208 224 11 1196 2396 731536509 731535309 0.000000e+00 900
13 TraesCS7A01G108000 chr3D 88.492 252 26 2 3189 3438 15873366 15873616 5.580000e-78 302
14 TraesCS7A01G108000 chr3D 91.121 214 19 0 2738 2951 15873054 15873267 1.210000e-74 291


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 TraesCS7A01G108000 chr7A 65440837 65444279 3442 False 6359.0 6359 100.0000 1 3443 1 chr7A.!!$F1 3442
1 TraesCS7A01G108000 chr7A 65153375 65154700 1325 True 1129.0 1129 82.1190 1085 2409 1 chr7A.!!$R1 1324
2 TraesCS7A01G108000 chr7D 62120999 62124854 3855 False 2828.5 4857 95.2890 1 3438 2 chr7D.!!$F2 3437
3 TraesCS7A01G108000 chr7D 62278022 62282164 4142 False 2397.5 4632 94.1890 1 3078 2 chr7D.!!$F3 3077
4 TraesCS7A01G108000 chr7D 62259012 62260560 1548 True 1155.0 1155 80.2410 1124 2697 1 chr7D.!!$R3 1573
5 TraesCS7A01G108000 chr7D 61227463 61228788 1325 True 1096.0 1096 81.6820 1085 2409 1 chr7D.!!$R2 1324
6 TraesCS7A01G108000 chr7D 60704116 60705444 1328 True 1092.0 1092 81.4900 1081 2409 1 chr7D.!!$R1 1328
7 TraesCS7A01G108000 chr2A 734652847 734654200 1353 True 1014.0 1014 80.2060 1089 2446 1 chr2A.!!$R1 1357
8 TraesCS7A01G108000 chr2D 601262555 601263799 1244 True 992.0 992 81.0750 1201 2446 1 chr2D.!!$R1 1245
9 TraesCS7A01G108000 chr2B 731535309 731536509 1200 True 900.0 900 80.2980 1196 2396 1 chr2B.!!$R1 1200
10 TraesCS7A01G108000 chr3D 15873054 15873616 562 False 296.5 302 89.8065 2738 3438 2 chr3D.!!$F1 700

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
603 1671 0.734889 ATTGAAGATTTGCCGGCTCG 59.265 50.0 29.7 0.0 0.00 5.03 F
2148 3216 0.035439 CAGGTGGTCCGGCAGTTATT 60.035 55.0 0.0 0.0 39.05 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2223 3291 1.338200 ACCGATGAGCTCAACTGGTTC 60.338 52.381 22.5 11.56 0.00 3.62 R
3099 4605 2.806434 TGCATAAGGTTGTGCTTGGAT 58.194 42.857 12.0 0.00 44.38 3.41 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
44 45 5.183140 TGGTTTTAGGATTGTTAGCAGAAGC 59.817 40.000 0.00 0.00 42.56 3.86
45 46 5.183140 GGTTTTAGGATTGTTAGCAGAAGCA 59.817 40.000 0.00 0.00 45.49 3.91
55 56 7.608308 TTGTTAGCAGAAGCAAAAACAAATT 57.392 28.000 10.95 0.00 42.14 1.82
127 1192 2.910688 TAGCACTAGCATACAAGCCC 57.089 50.000 0.00 0.00 45.49 5.19
164 1229 4.878397 CCAACAAAATTAGGTGGCAAAACA 59.122 37.500 2.29 0.00 0.00 2.83
196 1261 7.148239 GGTTGGTAATATGCAATATCTAGTGGC 60.148 40.741 0.00 0.00 38.94 5.01
255 1320 6.312918 GTGGTTGATAATCGACAACATGTACT 59.687 38.462 15.80 0.00 45.27 2.73
455 1521 2.378038 ACTGATTGCTTGTGGTTGTGT 58.622 42.857 0.00 0.00 0.00 3.72
603 1671 0.734889 ATTGAAGATTTGCCGGCTCG 59.265 50.000 29.70 0.00 0.00 5.03
656 1724 7.195374 AGGGTGTATGTGTGTGAGTTTATAT 57.805 36.000 0.00 0.00 0.00 0.86
674 1742 9.472361 AGTTTATATGGATCAATGTACGTACAC 57.528 33.333 29.54 16.44 39.30 2.90
721 1789 6.360618 ACTATTGGGAAGTTCATTGATCTCC 58.639 40.000 5.01 0.29 0.00 3.71
728 1796 6.498651 GGGAAGTTCATTGATCTCCCTAGATA 59.501 42.308 15.91 0.00 42.73 1.98
737 1805 3.238788 TCTCCCTAGATACCGCATGAA 57.761 47.619 0.00 0.00 0.00 2.57
933 2001 6.663734 CATAAAAATCTCCCACCCTTAGAGT 58.336 40.000 0.00 0.00 0.00 3.24
934 2002 7.637301 GCATAAAAATCTCCCACCCTTAGAGTA 60.637 40.741 0.00 0.00 0.00 2.59
935 2003 5.959583 AAAATCTCCCACCCTTAGAGTAG 57.040 43.478 0.00 0.00 0.00 2.57
936 2004 4.901785 AATCTCCCACCCTTAGAGTAGA 57.098 45.455 0.00 0.00 0.00 2.59
937 2005 3.955524 TCTCCCACCCTTAGAGTAGAG 57.044 52.381 0.00 0.00 0.00 2.43
978 2046 2.746359 GTCACCTCTGCAGGCACT 59.254 61.111 15.13 0.00 45.05 4.40
1029 2097 0.106469 AGTCTCATCTCAGGCGCCTA 60.106 55.000 32.30 15.58 0.00 3.93
1494 2562 1.891150 CTTCTGGCCAAGACTTGCATT 59.109 47.619 7.01 0.00 33.46 3.56
1591 2659 6.922247 TTGTGAACAAATACAAGTTACGGA 57.078 33.333 0.00 0.00 33.29 4.69
2148 3216 0.035439 CAGGTGGTCCGGCAGTTATT 60.035 55.000 0.00 0.00 39.05 1.40
2223 3291 2.465860 TGACACTACATCGGTTTGGG 57.534 50.000 0.00 0.00 0.00 4.12
2411 3479 7.158697 TGGGGTAACTGTATCAATCATTATCG 58.841 38.462 0.00 0.00 0.00 2.92
2615 3685 7.138736 CGATGTGGGGCTTTTATAAAGTAATG 58.861 38.462 0.00 0.00 0.00 1.90
2665 3736 4.331168 GTGGTTGTACAGATGAGCATCTTC 59.669 45.833 10.15 5.49 45.31 2.87
2773 3844 4.632153 ACATGTGACTTCTACAACCTGTC 58.368 43.478 0.00 0.00 0.00 3.51
2810 3888 4.101430 GGGTTTGGTATACGTTATGGGAGA 59.899 45.833 0.00 0.00 0.00 3.71
2963 4466 2.865079 TCCAATTTTTGTAGGCCACGA 58.135 42.857 5.01 0.00 0.00 4.35
3068 4574 9.807649 TTCTAATCCGGTAAAATACACTTCTAC 57.192 33.333 0.00 0.00 0.00 2.59
3109 4615 4.910195 AGATTACACTCAATCCAAGCACA 58.090 39.130 0.00 0.00 35.85 4.57
3110 4616 5.316167 AGATTACACTCAATCCAAGCACAA 58.684 37.500 0.00 0.00 35.85 3.33
3173 4679 2.310327 ATATCAGGCTGTTCCGCGCA 62.310 55.000 15.27 0.00 40.77 6.09
3274 4803 9.578576 TTTTCAGAGCATTATATTAGCTGGATT 57.421 29.630 0.00 0.00 39.02 3.01
3438 4967 5.473504 GGTTCATGTGTCAAGGAGTTGTAAT 59.526 40.000 0.00 0.00 34.98 1.89
3439 4968 6.653320 GGTTCATGTGTCAAGGAGTTGTAATA 59.347 38.462 0.00 0.00 34.98 0.98
3440 4969 7.336931 GGTTCATGTGTCAAGGAGTTGTAATAT 59.663 37.037 0.00 0.00 34.98 1.28
3441 4970 9.378551 GTTCATGTGTCAAGGAGTTGTAATATA 57.621 33.333 0.00 0.00 34.98 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 4.631234 AGGTCCACAAGAGATAATGGGTA 58.369 43.478 0.00 0.00 32.73 3.69
110 1175 2.158957 TGTAGGGCTTGTATGCTAGTGC 60.159 50.000 0.00 0.00 40.20 4.40
127 1192 1.698506 TGTTGGGCCCAAAAGTGTAG 58.301 50.000 38.70 0.00 37.70 2.74
164 1229 9.200817 AGATATTGCATATTACCAACCAACTTT 57.799 29.630 0.00 0.00 0.00 2.66
196 1261 4.326766 CACCCTTTGCGCGGTGTG 62.327 66.667 20.22 13.15 43.84 3.82
455 1521 1.386155 CCCCATGGGCTGGTTACAA 59.614 57.895 26.87 0.00 44.30 2.41
553 1621 2.430248 TCATAGGCACCTCGTAGTCA 57.570 50.000 0.00 0.00 0.00 3.41
674 1742 5.845985 AAATGAGCCATGATAATACGACG 57.154 39.130 0.00 0.00 0.00 5.12
681 1749 7.754624 TCCCAATAGTAAATGAGCCATGATAA 58.245 34.615 0.00 0.00 0.00 1.75
721 1789 3.753294 AAGGTTCATGCGGTATCTAGG 57.247 47.619 0.00 0.00 0.00 3.02
728 1796 0.534203 ACGTCAAAGGTTCATGCGGT 60.534 50.000 0.00 0.00 0.00 5.68
737 1805 7.439381 TGAGAGAAATACTTAACGTCAAAGGT 58.561 34.615 13.38 1.59 0.00 3.50
936 2004 8.546230 CCGACGAGGATATATAGGAGGGAACT 62.546 50.000 0.00 0.00 44.75 3.01
937 2005 4.575645 CGACGAGGATATATAGGAGGGAAC 59.424 50.000 0.00 0.00 0.00 3.62
978 2046 8.563123 TCATATTGTTTGGTGGTATCGTTTAA 57.437 30.769 0.00 0.00 0.00 1.52
1436 2504 1.620819 AGACGACCAACTCTGCTTCAT 59.379 47.619 0.00 0.00 0.00 2.57
1494 2562 1.735018 CCACCGATTGCATCACGTTTA 59.265 47.619 0.00 0.00 0.00 2.01
1591 2659 5.127845 AGAGGTTCATGACACGAATATCACT 59.872 40.000 0.00 0.00 0.00 3.41
2148 3216 2.168521 GAGGCCATGTTGTACTGAGCTA 59.831 50.000 5.01 0.00 0.00 3.32
2223 3291 1.338200 ACCGATGAGCTCAACTGGTTC 60.338 52.381 22.50 11.56 0.00 3.62
2469 3537 4.133526 TCATATTACTCCCTCCTCCTGG 57.866 50.000 0.00 0.00 0.00 4.45
2532 3600 2.831607 ATCCCCCATCTCTTCATCCT 57.168 50.000 0.00 0.00 0.00 3.24
2773 3844 3.267031 ACCAAACCCTATCTCCCAAGAAG 59.733 47.826 0.00 0.00 34.49 2.85
2810 3888 4.219725 GTCCTCTCTGAGTTTAGTCTGCTT 59.780 45.833 4.32 0.00 0.00 3.91
2848 3926 0.386731 CGAACACCCGCAAACAATCC 60.387 55.000 0.00 0.00 0.00 3.01
2963 4466 6.414732 TCTGAAGGAAACACGATAATCCAAT 58.585 36.000 0.00 0.00 34.30 3.16
3099 4605 2.806434 TGCATAAGGTTGTGCTTGGAT 58.194 42.857 12.00 0.00 44.38 3.41
3109 4615 6.302269 CCTCTAGATTTCCATGCATAAGGTT 58.698 40.000 0.00 0.00 0.00 3.50
3110 4616 5.747248 GCCTCTAGATTTCCATGCATAAGGT 60.747 44.000 0.00 0.00 0.00 3.50
3173 4679 6.319658 CCAGTATGAACCAGCTGTTATCATTT 59.680 38.462 23.02 13.72 39.69 2.32
3339 4868 3.564345 CTTCAGCACCAGCCTGCCT 62.564 63.158 0.00 0.00 43.56 4.75
3400 4929 5.833131 ACACATGAACCAGATAACAACCTTT 59.167 36.000 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.