Multiple sequence alignment - TraesCS1A01G154100

Loading Multiple Alignment...

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 TraesCS1A01G154100 chr1A 100.000 3514 0 0 1 3514 268124732 268121219 0 6490
1 TraesCS1A01G154100 chr1B 95.123 3527 122 23 2 3514 304381476 304384966 0 5515
2 TraesCS1A01G154100 chr1B 94.762 3303 112 29 1 3280 303223223 303226487 0 5084
3 TraesCS1A01G154100 chr1D 96.274 3113 70 11 406 3514 212080279 212077209 0 5064


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 TraesCS1A01G154100 chr1A 268121219 268124732 3513 True 6490 6490 100.000 1 3514 1 chr1A.!!$R1 3513
1 TraesCS1A01G154100 chr1B 304381476 304384966 3490 False 5515 5515 95.123 2 3514 1 chr1B.!!$F2 3512
2 TraesCS1A01G154100 chr1B 303223223 303226487 3264 False 5084 5084 94.762 1 3280 1 chr1B.!!$F1 3279
3 TraesCS1A01G154100 chr1D 212077209 212080279 3070 True 5064 5064 96.274 406 3514 1 chr1D.!!$R1 3108

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
796 823 0.324943 ACTGCGGACCTTTGCTGTAT 59.675 50.000 0.00 0.00 40.77 2.29 F
799 826 1.026718 GCGGACCTTTGCTGTATGCT 61.027 55.000 0.00 0.00 43.37 3.79 F
1098 1127 1.227350 CTCGATGATGCGCCCTTCA 60.227 57.895 4.18 6.05 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 1907 0.392998 CTTCCATGGCACGCTTAGGT 60.393 55.00 6.96 0.0 0.00 3.08 R
2259 2288 4.917385 TGGCATTTAGGAGTGTGTTGTAT 58.083 39.13 0.00 0.0 0.00 2.29 R
3062 3096 4.870636 ACTCCAATCCAAGGAATGCATAA 58.129 39.13 0.00 0.0 34.08 1.90 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
73 81 7.756272 TCGGTTTAGGTTTTCTTCAAGTTTTTC 59.244 33.333 0.00 0.00 0.00 2.29
80 97 7.390440 AGGTTTTCTTCAAGTTTTTCCCTTTTG 59.610 33.333 0.00 0.00 0.00 2.44
81 98 7.389330 GGTTTTCTTCAAGTTTTTCCCTTTTGA 59.611 33.333 0.00 0.00 0.00 2.69
82 99 8.946085 GTTTTCTTCAAGTTTTTCCCTTTTGAT 58.054 29.630 0.00 0.00 0.00 2.57
83 100 9.513906 TTTTCTTCAAGTTTTTCCCTTTTGATT 57.486 25.926 0.00 0.00 0.00 2.57
84 101 9.513906 TTTCTTCAAGTTTTTCCCTTTTGATTT 57.486 25.926 0.00 0.00 0.00 2.17
85 102 9.513906 TTCTTCAAGTTTTTCCCTTTTGATTTT 57.486 25.926 0.00 0.00 0.00 1.82
86 103 9.161629 TCTTCAAGTTTTTCCCTTTTGATTTTC 57.838 29.630 0.00 0.00 0.00 2.29
87 104 9.166173 CTTCAAGTTTTTCCCTTTTGATTTTCT 57.834 29.630 0.00 0.00 0.00 2.52
88 105 9.513906 TTCAAGTTTTTCCCTTTTGATTTTCTT 57.486 25.926 0.00 0.00 0.00 2.52
89 106 9.513906 TCAAGTTTTTCCCTTTTGATTTTCTTT 57.486 25.926 0.00 0.00 0.00 2.52
213 234 9.068008 ACGTGATAAACTTTTTGTTAAACACAG 57.932 29.630 0.00 0.00 38.03 3.66
304 325 4.399004 TTGTTTTTCACAAGGTGGATGG 57.601 40.909 0.00 0.00 40.71 3.51
378 401 9.495754 GTCTGAACAGTAATATTTTCTGAATGC 57.504 33.333 19.91 10.54 33.93 3.56
544 571 2.518973 CTTCTCTCCTGCTGCCGCTT 62.519 60.000 0.70 0.00 36.97 4.68
658 685 3.519930 GCTCGGGACCTCGACTCC 61.520 72.222 0.00 0.00 35.18 3.85
796 823 0.324943 ACTGCGGACCTTTGCTGTAT 59.675 50.000 0.00 0.00 40.77 2.29
799 826 1.026718 GCGGACCTTTGCTGTATGCT 61.027 55.000 0.00 0.00 43.37 3.79
939 968 6.732862 TGATTCAAAATTTCCCCTTCCCAATA 59.267 34.615 0.00 0.00 0.00 1.90
1078 1107 2.944094 GCCCCAATTATCGTTGTCACCT 60.944 50.000 0.00 0.00 0.00 4.00
1098 1127 1.227350 CTCGATGATGCGCCCTTCA 60.227 57.895 4.18 6.05 0.00 3.02
1220 1249 2.508439 GGACGATTTCGCCGAGCA 60.508 61.111 0.00 0.00 44.43 4.26
1278 1307 1.750193 GAAGAATGCGGGATGGTTCA 58.250 50.000 0.00 0.00 0.00 3.18
1785 1814 2.317609 GCGTATGTATGGCAGGGCG 61.318 63.158 0.00 0.00 0.00 6.13
1809 1838 4.947645 TCACCTTTTGGAAAGAGCAATTG 58.052 39.130 0.00 0.00 44.07 2.32
1878 1907 5.534278 TGATCTTGTATGCAAAAACTGTGGA 59.466 36.000 0.00 0.00 33.73 4.02
2831 2860 4.890581 AGAGCGTGATACCAAGATACTTCT 59.109 41.667 0.00 0.00 0.00 2.85
2832 2861 5.009210 AGAGCGTGATACCAAGATACTTCTC 59.991 44.000 0.00 0.00 0.00 2.87
2834 2863 5.127194 AGCGTGATACCAAGATACTTCTCAA 59.873 40.000 0.00 0.00 0.00 3.02
2932 2965 5.995565 ACAGTACAAGGCTATGTTCACTA 57.004 39.130 7.46 0.00 34.75 2.74
3118 3152 3.254411 TGTTGTGTTCTTTGTTGAGTGCA 59.746 39.130 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 55 6.762702 AAACTTGAAGAAAACCTAAACCGA 57.237 33.333 0.00 0.00 0.00 4.69
73 81 9.773328 GAAGAAAACAAAAGAAAATCAAAAGGG 57.227 29.630 0.00 0.00 0.00 3.95
386 409 9.630098 GCATCTTATTTTCTCTCAAAACAATCA 57.370 29.630 0.00 0.00 0.00 2.57
544 571 2.048784 GAGCTGCGAGACTGTGCA 60.049 61.111 0.00 0.00 39.13 4.57
758 785 4.793353 GCAGTACAGAGTCGGGATTGTATC 60.793 50.000 0.00 0.00 0.00 2.24
796 823 4.121317 CCATTTCAAAAGAACAAGCAGCA 58.879 39.130 0.00 0.00 0.00 4.41
799 826 5.360714 AGAGACCATTTCAAAAGAACAAGCA 59.639 36.000 0.00 0.00 0.00 3.91
939 968 4.722700 GCCACCGTCCCTGCACAT 62.723 66.667 0.00 0.00 0.00 3.21
968 997 1.860326 GCCATGGCAATACGATTTTGC 59.140 47.619 32.08 11.44 46.82 3.68
969 998 2.118683 CGCCATGGCAATACGATTTTG 58.881 47.619 34.93 11.33 42.06 2.44
970 999 1.066908 CCGCCATGGCAATACGATTTT 59.933 47.619 34.93 0.00 42.06 1.82
1078 1107 0.530650 GAAGGGCGCATCATCGAGAA 60.531 55.000 10.83 0.00 0.00 2.87
1098 1127 1.568612 CCGCATGTGCTCTGAAACGT 61.569 55.000 0.00 0.00 39.32 3.99
1201 1230 2.954868 CTCGGCGAAATCGTCCCG 60.955 66.667 12.13 13.41 41.58 5.14
1216 1245 2.024176 TTACCCGCATTCTTCTGCTC 57.976 50.000 0.00 0.00 40.06 4.26
1220 1249 2.026262 ACCACATTACCCGCATTCTTCT 60.026 45.455 0.00 0.00 0.00 2.85
1278 1307 4.101448 GGGGCTGCACGATCCACT 62.101 66.667 0.50 0.00 0.00 4.00
1785 1814 4.853924 TTGCTCTTTCCAAAAGGTGATC 57.146 40.909 0.00 0.00 0.00 2.92
1878 1907 0.392998 CTTCCATGGCACGCTTAGGT 60.393 55.000 6.96 0.00 0.00 3.08
1995 2024 7.254151 GCAATAAGACGAGTTAAGATGGTCTTC 60.254 40.741 16.46 4.71 44.33 2.87
2259 2288 4.917385 TGGCATTTAGGAGTGTGTTGTAT 58.083 39.130 0.00 0.00 0.00 2.29
2818 2847 5.661056 TCACGATTGAGAAGTATCTTGGT 57.339 39.130 0.00 0.00 35.54 3.67
2831 2860 5.294306 GCTGACTTCCATATTTCACGATTGA 59.706 40.000 0.00 0.00 0.00 2.57
2832 2861 5.295292 AGCTGACTTCCATATTTCACGATTG 59.705 40.000 0.00 0.00 0.00 2.67
2834 2863 5.028549 AGCTGACTTCCATATTTCACGAT 57.971 39.130 0.00 0.00 0.00 3.73
2932 2965 8.564509 AATATTTGCAACATAAACAGCCATTT 57.435 26.923 0.00 0.00 0.00 2.32
3062 3096 4.870636 ACTCCAATCCAAGGAATGCATAA 58.129 39.130 0.00 0.00 34.08 1.90
3118 3152 3.243068 GGTCATGCACTTTGAAGAAACGT 60.243 43.478 0.00 0.00 0.00 3.99
3269 3304 4.079253 GTCCTTAAAATTCCCTGACAGCA 58.921 43.478 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.