Multiple sequence alignment - TraesCS1B01G065300

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 TraesCS1B01G065300 chr1B 100.000 3155 0 0 1 3155 49787123 49783969 0 5827
1 TraesCS1B01G065300 chr1B 96.777 3165 81 8 1 3155 583548107 583551260 0 5260
2 TraesCS1B01G065300 chr1B 96.531 3171 90 9 1 3155 49815632 49818798 0 5228
3 TraesCS1B01G065300 chr7B 97.126 3166 70 8 1 3155 716798042 716794887 0 5323
4 TraesCS1B01G065300 chr7B 96.712 3163 73 13 3 3155 742935290 742938431 0 5236
5 TraesCS1B01G065300 chr7B 95.839 3172 114 10 1 3155 47217234 47220404 0 5110
6 TraesCS1B01G065300 chr7B 95.515 3166 110 10 1 3155 139621806 139618662 0 5031
7 TraesCS1B01G065300 chr6B 97.093 3165 67 8 1 3155 128892181 128889032 0 5312
8 TraesCS1B01G065300 chr5B 96.997 3164 75 7 1 3155 713115164 713112012 0 5299
9 TraesCS1B01G065300 chr5B 96.747 3166 80 10 1 3155 713093563 713096716 0 5254
10 TraesCS1B01G065300 chr5B 96.656 2273 55 7 1 2264 127821197 127818937 0 3757
11 TraesCS1B01G065300 chr7A 96.723 2258 53 10 908 3155 60097493 60095247 0 3740


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 TraesCS1B01G065300 chr1B 49783969 49787123 3154 True 5827 5827 100.000 1 3155 1 chr1B.!!$R1 3154
1 TraesCS1B01G065300 chr1B 583548107 583551260 3153 False 5260 5260 96.777 1 3155 1 chr1B.!!$F2 3154
2 TraesCS1B01G065300 chr1B 49815632 49818798 3166 False 5228 5228 96.531 1 3155 1 chr1B.!!$F1 3154
3 TraesCS1B01G065300 chr7B 716794887 716798042 3155 True 5323 5323 97.126 1 3155 1 chr7B.!!$R2 3154
4 TraesCS1B01G065300 chr7B 742935290 742938431 3141 False 5236 5236 96.712 3 3155 1 chr7B.!!$F2 3152
5 TraesCS1B01G065300 chr7B 47217234 47220404 3170 False 5110 5110 95.839 1 3155 1 chr7B.!!$F1 3154
6 TraesCS1B01G065300 chr7B 139618662 139621806 3144 True 5031 5031 95.515 1 3155 1 chr7B.!!$R1 3154
7 TraesCS1B01G065300 chr6B 128889032 128892181 3149 True 5312 5312 97.093 1 3155 1 chr6B.!!$R1 3154
8 TraesCS1B01G065300 chr5B 713112012 713115164 3152 True 5299 5299 96.997 1 3155 1 chr5B.!!$R2 3154
9 TraesCS1B01G065300 chr5B 713093563 713096716 3153 False 5254 5254 96.747 1 3155 1 chr5B.!!$F1 3154
10 TraesCS1B01G065300 chr5B 127818937 127821197 2260 True 3757 3757 96.656 1 2264 1 chr5B.!!$R1 2263
11 TraesCS1B01G065300 chr7A 60095247 60097493 2246 True 3740 3740 96.723 908 3155 1 chr7A.!!$R1 2247

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
530 535 0.698818 CCCCTGAACTACCTTTGCCT 59.301 55.000 0.0 0.00 0.00 4.75 F
1198 1207 1.333619 GAATTGCCGGCGTCACAATAT 59.666 47.619 23.9 6.41 33.01 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 1603 5.838531 ATTTGTTCGTTTACCAGGTTCAA 57.161 34.783 0.0 0.0 0.00 2.69 R
2873 2903 0.525668 GCCGATATGATAGGCGACGG 60.526 60.000 0.0 0.0 41.17 4.79 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
63 68 3.983821 CCCCCTCTAGTCAGTACTTTCT 58.016 50.000 0.00 0.00 37.15 2.52
381 386 5.163713 GGAGCTAGCCTTTGTGTTAAGATTG 60.164 44.000 12.13 0.00 0.00 2.67
432 437 3.416156 GGTGATTCCATTGCTCTATCCC 58.584 50.000 0.00 0.00 35.97 3.85
530 535 0.698818 CCCCTGAACTACCTTTGCCT 59.301 55.000 0.00 0.00 0.00 4.75
729 736 2.232452 AGTGTTCAGCGAAGTCTGCTAT 59.768 45.455 0.00 0.00 41.72 2.97
852 859 2.413837 GACAAACGCTCCAGTGTATGT 58.586 47.619 0.00 0.00 37.87 2.29
1129 1138 4.935352 TTTTTCCCAACCAACATCTCTG 57.065 40.909 0.00 0.00 0.00 3.35
1174 1183 1.687660 TGGATATAACGCCAACGCCTA 59.312 47.619 0.00 0.00 45.53 3.93
1198 1207 1.333619 GAATTGCCGGCGTCACAATAT 59.666 47.619 23.90 6.41 33.01 1.28
1400 1415 6.554605 CCTAATACCCCATTGGATCAATTTGT 59.445 38.462 3.62 0.00 38.00 2.83
1434 1449 6.795144 ATAATTGATCTTCATGTGGGCAAA 57.205 33.333 0.00 0.00 0.00 3.68
1491 1506 2.479837 CTGCTCACTGTCGTTTTGGTA 58.520 47.619 0.00 0.00 0.00 3.25
1500 1515 5.963586 CACTGTCGTTTTGGTAGTTTTTCTC 59.036 40.000 0.00 0.00 0.00 2.87
1585 1603 6.018994 GGTCGAGCTTATTTATGATTTCGTGT 60.019 38.462 7.51 0.00 0.00 4.49
1668 1692 5.278266 CCCTCGCATCACTTTTACTTTTTCA 60.278 40.000 0.00 0.00 0.00 2.69
2341 2368 2.023984 TCAGGAGCTAGATCACTTCCCA 60.024 50.000 10.68 0.00 0.00 4.37
2581 2610 2.443387 TCGTTATCGTGGAATTCGTCG 58.557 47.619 12.52 12.52 38.33 5.12
2594 2623 3.801114 ATTCGTCGTCAAGATGGATCA 57.199 42.857 0.00 0.00 36.53 2.92
2628 2657 5.220416 GGTCAACGAACTCATACTAATGCAC 60.220 44.000 0.00 0.00 32.76 4.57
2629 2658 5.347635 GTCAACGAACTCATACTAATGCACA 59.652 40.000 0.00 0.00 32.76 4.57
2719 2748 1.065782 TCCCTTGCTAAAGCGCATACA 60.066 47.619 11.47 0.00 45.83 2.29
2873 2903 1.470632 CCATCTTGGTCTCGCTCACTC 60.471 57.143 0.00 0.00 31.35 3.51
2876 2906 1.867919 CTTGGTCTCGCTCACTCCGT 61.868 60.000 0.00 0.00 0.00 4.69
2885 2916 1.725557 GCTCACTCCGTCGCCTATCA 61.726 60.000 0.00 0.00 0.00 2.15
2930 2961 1.519719 GACAGCTTCCGCCTCTGAT 59.480 57.895 0.00 0.00 36.60 2.90
2963 2994 4.520179 TCGCTCATGACTGGTAGTAGTTA 58.480 43.478 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 68 2.610479 CGAAGAAGCCTTGCACTACTCA 60.610 50.000 0.00 0.00 31.62 3.41
432 437 2.541437 CGATCGAATCTTGCGGCG 59.459 61.111 10.26 0.51 0.00 6.46
530 535 4.079253 GGTGGATTCTACAAGAAAAGGCA 58.921 43.478 2.42 0.00 37.82 4.75
729 736 1.339631 CCTGAACGTAAGGCCAATGGA 60.340 52.381 5.01 0.00 46.39 3.41
852 859 5.782893 AAAATGCTAGTTGCCTTGTAACA 57.217 34.783 0.00 0.00 42.00 2.41
880 887 8.209917 ACAAGAACATTCTTTTACGAACTTCT 57.790 30.769 4.08 0.00 44.70 2.85
890 897 7.600752 TCCAACGAAAAACAAGAACATTCTTTT 59.399 29.630 4.08 0.00 44.70 2.27
1129 1138 6.856895 AGTTTGGCATTATAGCAAAGTTCTC 58.143 36.000 0.00 0.00 35.83 2.87
1174 1183 3.799755 GACGCCGGCAATTCGCTT 61.800 61.111 28.98 0.00 41.91 4.68
1198 1207 8.315482 GCCCAAATACCCTTCTATTTGTAAAAA 58.685 33.333 9.63 0.00 40.39 1.94
1286 1295 2.574450 CCTGCCAAGTTTTGCCATTTT 58.426 42.857 0.00 0.00 0.00 1.82
1294 1303 4.609301 TCTAATATGCCCTGCCAAGTTTT 58.391 39.130 0.00 0.00 0.00 2.43
1585 1603 5.838531 ATTTGTTCGTTTACCAGGTTCAA 57.161 34.783 0.00 0.00 0.00 2.69
1668 1692 6.273730 TCATACCCTGGGGATTACGAAATAAT 59.726 38.462 18.88 0.00 38.96 1.28
2341 2368 6.899393 TGAGGCAATTCTTACTTGTTCATT 57.101 33.333 0.00 0.00 0.00 2.57
2581 2610 3.458189 CGTAAGGGTGATCCATCTTGAC 58.542 50.000 0.00 0.00 38.24 3.18
2649 2678 3.008594 TCGGTAGCCTTCTTTCATTTCCA 59.991 43.478 0.00 0.00 0.00 3.53
2719 2748 5.140454 ACAAGTACCAAGGAGCAAGAAAAT 58.860 37.500 0.00 0.00 0.00 1.82
2873 2903 0.525668 GCCGATATGATAGGCGACGG 60.526 60.000 0.00 0.00 41.17 4.79
2885 2916 1.286260 GACGAAGCCGAGCCGATAT 59.714 57.895 0.00 0.00 39.50 1.63
2930 2961 1.756538 TCATGAGCGATAGTGAAGCCA 59.243 47.619 0.00 0.00 39.35 4.75
2963 2994 6.384305 ACAAAGGCCAACTACTACATAGAGAT 59.616 38.462 5.01 0.00 34.65 2.75
3014 3045 1.630878 AGAAAGAGGCATTCGGGAAGT 59.369 47.619 0.00 0.00 32.04 3.01


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

AutoCloner maintained by Alex Coulton.