Multiple sequence alignment - TraesCS7D01G316200

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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 TraesCS7D01G316200 chr7D 100.000 4022 0 0 1 4022 402148505 402152526 0 7428
1 TraesCS7D01G316200 chr7A 96.230 4032 94 23 1 4019 460116263 460120249 0 6551
2 TraesCS7D01G316200 chr7B 96.027 4027 97 24 1 4019 411748798 411752769 0 6492


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 TraesCS7D01G316200 chr7D 402148505 402152526 4021 False 7428 7428 100.000 1 4022 1 chr7D.!!$F1 4021
1 TraesCS7D01G316200 chr7A 460116263 460120249 3986 False 6551 6551 96.230 1 4019 1 chr7A.!!$F1 4018
2 TraesCS7D01G316200 chr7B 411748798 411752769 3971 False 6492 6492 96.027 1 4019 1 chr7B.!!$F1 4018

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
293 294 0.988832 AGAGAGACCAGTCGGAGTCT 59.011 55.000 0.00 0.0 45.9 3.24 F
1173 1198 1.006043 TCGTCCATTCTCCTCTCCTGT 59.994 52.381 0.00 0.0 0.0 4.00 F
1740 1765 1.257750 GGGTTCCTGGGGCAAACATC 61.258 60.000 0.00 0.0 0.0 3.06 F
2556 2581 0.600782 CTGTGTTTGGCATTGCACCC 60.601 55.000 11.39 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 1765 0.110688 CAACTGCATTCCACGTCACG 60.111 55.000 0.00 0.0 0.00 4.35 R
2547 2572 1.310933 GCTCCACTCTGGGTGCAATG 61.311 60.000 1.04 0.0 44.70 2.82 R
2938 2963 2.036604 TGCGGTCAGACAAGTCACAATA 59.963 45.455 2.17 0.0 0.00 1.90 R
3460 3486 2.548904 GCAATCATCTTGCTCAGCTAGG 59.451 50.000 8.34 0.0 41.87 3.02 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
293 294 0.988832 AGAGAGACCAGTCGGAGTCT 59.011 55.000 0.00 0.00 45.90 3.24
302 303 2.571212 CAGTCGGAGTCTCTGCTCTAT 58.429 52.381 3.55 0.00 35.89 1.98
931 941 1.699257 CCTCCCCCTACCATTAGCCTT 60.699 57.143 0.00 0.00 0.00 4.35
947 966 3.249189 TTTCGCTCCCCACCAGCT 61.249 61.111 0.00 0.00 34.45 4.24
948 967 2.754664 CTTTCGCTCCCCACCAGCTT 62.755 60.000 0.00 0.00 34.45 3.74
949 968 2.748058 TTTCGCTCCCCACCAGCTTC 62.748 60.000 0.00 0.00 34.45 3.86
952 971 4.785453 CTCCCCACCAGCTTCGCC 62.785 72.222 0.00 0.00 0.00 5.54
1021 1040 3.256960 GCCCTTCTCCCACCACCA 61.257 66.667 0.00 0.00 0.00 4.17
1155 1180 3.430497 TCCCCCTCCTCCCTCTCG 61.430 72.222 0.00 0.00 0.00 4.04
1165 1190 1.036707 CTCCCTCTCGTCCATTCTCC 58.963 60.000 0.00 0.00 0.00 3.71
1173 1198 1.006043 TCGTCCATTCTCCTCTCCTGT 59.994 52.381 0.00 0.00 0.00 4.00
1740 1765 1.257750 GGGTTCCTGGGGCAAACATC 61.258 60.000 0.00 0.00 0.00 3.06
1944 1969 4.927425 GTGGCTGTTCGTCTATACTTTGAA 59.073 41.667 0.00 0.00 0.00 2.69
2115 2140 3.825328 TGAGGAAGCTTCTTTGCTCTTT 58.175 40.909 25.05 1.39 43.47 2.52
2136 2161 2.048601 AGAGAGATGATTGGCTCAGGG 58.951 52.381 0.00 0.00 37.28 4.45
2330 2355 5.223382 AGCTTCACGGATAGTATTTGATCG 58.777 41.667 0.00 0.00 0.00 3.69
2547 2572 2.514205 AGATGTTTGCTGTGTTTGGC 57.486 45.000 0.00 0.00 0.00 4.52
2556 2581 0.600782 CTGTGTTTGGCATTGCACCC 60.601 55.000 11.39 0.00 0.00 4.61
2938 2963 3.962063 TGATGGCTTAAATCATGGTGCAT 59.038 39.130 0.00 0.00 0.00 3.96
2983 3008 5.831702 AACGGATACTGATTCGTCTAGTT 57.168 39.130 0.00 0.00 46.99 2.24
3112 3137 8.948631 ACAAACTGATACTACCACATCTTATG 57.051 34.615 0.00 0.00 0.00 1.90
3119 3144 9.807921 TGATACTACCACATCTTATGACATAGA 57.192 33.333 0.00 0.00 0.00 1.98
3174 3200 9.290483 GAACTACTAGCTGGAAATTATTTTTGC 57.710 33.333 3.17 0.00 0.00 3.68
3175 3201 8.348285 ACTACTAGCTGGAAATTATTTTTGCA 57.652 30.769 3.17 0.00 0.00 4.08
3176 3202 8.971073 ACTACTAGCTGGAAATTATTTTTGCAT 58.029 29.630 3.17 0.00 0.00 3.96
3177 3203 9.241317 CTACTAGCTGGAAATTATTTTTGCATG 57.759 33.333 3.17 0.00 0.00 4.06
3178 3204 5.806366 AGCTGGAAATTATTTTTGCATGC 57.194 34.783 11.82 11.82 0.00 4.06
3179 3205 4.637091 AGCTGGAAATTATTTTTGCATGCC 59.363 37.500 16.68 0.00 30.62 4.40
3180 3206 4.494526 GCTGGAAATTATTTTTGCATGCCG 60.495 41.667 16.68 0.00 0.00 5.69
3201 3227 2.652941 ATTAACGCACTGGGCATTTG 57.347 45.000 1.50 0.00 45.17 2.32
3225 3251 3.897239 TCTCTTTTCCCAGCTTGAAACA 58.103 40.909 7.51 0.00 31.78 2.83
3236 3262 4.320494 CCAGCTTGAAACACTACAATGACC 60.320 45.833 0.00 0.00 0.00 4.02
3377 3403 2.299326 ACTTTTTGCCAGAGCCATCT 57.701 45.000 0.00 0.00 38.69 2.90
3449 3475 3.713826 TTCCTTGCTAGAACCGGAATT 57.286 42.857 9.46 0.00 0.00 2.17
3460 3486 6.183360 GCTAGAACCGGAATTTGATATATGCC 60.183 42.308 9.46 0.00 0.00 4.40
3625 3651 6.494842 TCTTAAAGATTTTGCGATGGTATGC 58.505 36.000 0.00 0.00 0.00 3.14
3896 3925 5.411493 TGATGGGTAGGGAGAAGCATAATA 58.589 41.667 0.00 0.00 0.00 0.98
3898 3927 7.196187 TGATGGGTAGGGAGAAGCATAATATA 58.804 38.462 0.00 0.00 0.00 0.86
3903 3932 7.988028 GGGTAGGGAGAAGCATAATATATTGAC 59.012 40.741 8.28 0.00 0.00 3.18
4019 4048 4.779993 AATTTTAGCTGGAGGAGGTAGG 57.220 45.455 0.00 0.00 36.04 3.18
4020 4049 2.176247 TTTAGCTGGAGGAGGTAGGG 57.824 55.000 0.00 0.00 36.04 3.53
4021 4050 0.264955 TTAGCTGGAGGAGGTAGGGG 59.735 60.000 0.00 0.00 36.04 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 3.838903 AGTACTGGATTCGGTTCTTCCTT 59.161 43.478 0.00 0.00 33.86 3.36
293 294 6.622289 CCATTATGGGCAGCATAGAGCAGA 62.622 50.000 2.72 0.00 38.92 4.26
769 779 0.934436 ACAGCACGCAAAATTGTCGC 60.934 50.000 8.97 3.68 33.29 5.19
770 780 1.044725 GACAGCACGCAAAATTGTCG 58.955 50.000 7.92 7.92 35.13 4.35
771 781 2.046313 CAGACAGCACGCAAAATTGTC 58.954 47.619 1.31 1.31 38.68 3.18
916 926 1.594331 GCGAAAGGCTAATGGTAGGG 58.406 55.000 0.00 0.00 39.11 3.53
931 941 3.249189 AAGCTGGTGGGGAGCGAA 61.249 61.111 0.00 0.00 41.61 4.70
1155 1180 1.134551 GCACAGGAGAGGAGAATGGAC 60.135 57.143 0.00 0.00 0.00 4.02
1740 1765 0.110688 CAACTGCATTCCACGTCACG 60.111 55.000 0.00 0.00 0.00 4.35
1944 1969 1.045407 TTACCACACACTCGAGCCTT 58.955 50.000 13.61 0.00 0.00 4.35
2115 2140 3.237746 CCCTGAGCCAATCATCTCTCTA 58.762 50.000 0.00 0.00 37.28 2.43
2136 2161 5.003804 ACAGTAACATCATTTGGACAGACC 58.996 41.667 0.00 0.00 39.54 3.85
2330 2355 1.936547 GCTTGTCTCGACATTCCATCC 59.063 52.381 0.00 0.00 41.52 3.51
2547 2572 1.310933 GCTCCACTCTGGGTGCAATG 61.311 60.000 1.04 0.00 44.70 2.82
2556 2581 3.005050 TGCAAGAAAAATGCTCCACTCTG 59.995 43.478 0.00 0.00 44.14 3.35
2752 2777 2.489938 TTGTAGTGGCCAGGATTGTC 57.510 50.000 5.11 0.00 0.00 3.18
2763 2788 6.079763 CGTGTTTGAGATCAATTTGTAGTGG 58.920 40.000 0.00 0.00 35.55 4.00
2938 2963 2.036604 TGCGGTCAGACAAGTCACAATA 59.963 45.455 2.17 0.00 0.00 1.90
2983 3008 2.945008 CACTGCTTTTCACTTCCTCACA 59.055 45.455 0.00 0.00 0.00 3.58
3192 3218 4.023291 GGGAAAAGAGATACAAATGCCCA 58.977 43.478 0.00 0.00 0.00 5.36
3196 3222 6.151648 TCAAGCTGGGAAAAGAGATACAAATG 59.848 38.462 0.00 0.00 0.00 2.32
3201 3227 5.473504 TGTTTCAAGCTGGGAAAAGAGATAC 59.526 40.000 13.58 3.72 36.14 2.24
3225 3251 8.974060 AATTCCAAATATACGGTCATTGTAGT 57.026 30.769 0.00 0.00 0.00 2.73
3236 3262 9.931210 GGAGTCAACTAAAATTCCAAATATACG 57.069 33.333 0.00 0.00 0.00 3.06
3449 3475 3.840078 TGCTCAGCTAGGGCATATATCAA 59.160 43.478 6.61 0.00 41.70 2.57
3460 3486 2.548904 GCAATCATCTTGCTCAGCTAGG 59.451 50.000 8.34 0.00 41.87 3.02
3519 3545 7.516557 TCTCTAATAGAGGGATCAGTACCTGTA 59.483 40.741 16.47 0.00 39.48 2.74
3625 3651 4.187694 GTGACTGGAGCCTATGAAGAAAG 58.812 47.826 0.00 0.00 0.00 2.62
3820 3849 5.759273 CAGACCTCTCCAAATCAGAATCATC 59.241 44.000 0.00 0.00 0.00 2.92
3821 3850 5.682659 CAGACCTCTCCAAATCAGAATCAT 58.317 41.667 0.00 0.00 0.00 2.45
3822 3851 4.624843 GCAGACCTCTCCAAATCAGAATCA 60.625 45.833 0.00 0.00 0.00 2.57
3896 3925 8.543774 AGAAAAGACCATCAGTACTGTCAATAT 58.456 33.333 21.99 5.51 0.00 1.28
3898 3927 6.773638 AGAAAAGACCATCAGTACTGTCAAT 58.226 36.000 21.99 6.25 0.00 2.57
3903 3932 8.420222 AGATCATAGAAAAGACCATCAGTACTG 58.580 37.037 17.17 17.17 0.00 2.74


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

AutoCloner maintained by Alex Coulton.