Multiple sequence alignment - TraesCS1B01G065200

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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 TraesCS1B01G065200 chr1B 100.000 2342 0 0 1 2342 49784720 49782379 0 4325
1 TraesCS1B01G065200 chrUn 97.567 2343 56 1 1 2342 257944316 257946658 0 4010
2 TraesCS1B01G065200 chrUn 97.311 2343 57 2 1 2342 233525064 233522727 0 3973
3 TraesCS1B01G065200 chr1D 97.311 2343 62 1 1 2342 212429073 212431415 0 3976
4 TraesCS1B01G065200 chr7B 97.268 2343 57 3 1 2342 698126729 698124393 0 3965
5 TraesCS1B01G065200 chr7B 97.012 2343 64 2 1 2342 716795634 716793297 0 3934
6 TraesCS1B01G065200 chr7B 96.884 2343 63 4 1 2342 742937686 742940019 0 3914
7 TraesCS1B01G065200 chr2D 97.140 2343 64 3 1 2342 637308501 637306161 0 3952
8 TraesCS1B01G065200 chr7A 97.140 2343 61 2 1 2342 60095994 60093657 0 3951
9 TraesCS1B01G065200 chr6B 96.756 2343 70 2 1 2342 128889779 128887442 0 3901


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 TraesCS1B01G065200 chr1B 49782379 49784720 2341 True 4325 4325 100.000 1 2342 1 chr1B.!!$R1 2341
1 TraesCS1B01G065200 chrUn 257944316 257946658 2342 False 4010 4010 97.567 1 2342 1 chrUn.!!$F1 2341
2 TraesCS1B01G065200 chrUn 233522727 233525064 2337 True 3973 3973 97.311 1 2342 1 chrUn.!!$R1 2341
3 TraesCS1B01G065200 chr1D 212429073 212431415 2342 False 3976 3976 97.311 1 2342 1 chr1D.!!$F1 2341
4 TraesCS1B01G065200 chr7B 698124393 698126729 2336 True 3965 3965 97.268 1 2342 1 chr7B.!!$R1 2341
5 TraesCS1B01G065200 chr7B 716793297 716795634 2337 True 3934 3934 97.012 1 2342 1 chr7B.!!$R2 2341
6 TraesCS1B01G065200 chr7B 742937686 742940019 2333 False 3914 3914 96.884 1 2342 1 chr7B.!!$F1 2341
7 TraesCS1B01G065200 chr2D 637306161 637308501 2340 True 3952 3952 97.140 1 2342 1 chr2D.!!$R1 2341
8 TraesCS1B01G065200 chr7A 60093657 60095994 2337 True 3951 3951 97.140 1 2342 1 chr7A.!!$R1 2341
9 TraesCS1B01G065200 chr6B 128887442 128889779 2337 True 3901 3901 96.756 1 2342 1 chr6B.!!$R1 2341

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
316 317 1.065782 TCCCTTGCTAAAGCGCATACA 60.066 47.619 11.47 0.0 45.83 2.29 F
470 471 1.470632 CCATCTTGGTCTCGCTCACTC 60.471 57.143 0.00 0.0 31.35 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1291 0.107410 TCCAAACGTGCTCACAAGGT 60.107 50.000 0.00 0.0 0.0 3.50 R
2299 2301 1.142667 TGGTTGACAAGCCACTGATCA 59.857 47.619 14.49 0.0 0.0 2.92 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
178 179 2.443387 TCGTTATCGTGGAATTCGTCG 58.557 47.619 12.52 12.52 38.33 5.12
191 192 3.801114 ATTCGTCGTCAAGATGGATCA 57.199 42.857 0.00 0.00 36.53 2.92
225 226 5.220416 GGTCAACGAACTCATACTAATGCAC 60.220 44.000 0.00 0.00 32.76 4.57
226 227 5.347635 GTCAACGAACTCATACTAATGCACA 59.652 40.000 0.00 0.00 32.76 4.57
316 317 1.065782 TCCCTTGCTAAAGCGCATACA 60.066 47.619 11.47 0.00 45.83 2.29
355 356 6.210584 TGGTACTTGTCTGATCAATCACACTA 59.789 38.462 0.00 0.00 32.50 2.74
470 471 1.470632 CCATCTTGGTCTCGCTCACTC 60.471 57.143 0.00 0.00 31.35 3.51
482 484 1.725557 GCTCACTCCGTCGCCTATCA 61.726 60.000 0.00 0.00 0.00 2.15
560 562 4.520179 TCGCTCATGACTGGTAGTAGTTA 58.480 43.478 0.00 0.00 0.00 2.24
735 737 2.554370 ACCTTGCTTGCATTGCATTT 57.446 40.000 12.95 1.60 38.76 2.32
761 763 1.745489 GGTAGCTTCCGCACCCTTG 60.745 63.158 0.00 0.00 39.10 3.61
864 866 7.881142 TCTGTTTTGTCTCTGTTTTCTTTTCA 58.119 30.769 0.00 0.00 0.00 2.69
879 881 8.517878 GTTTTCTTTTCAGATGATGAGGATGAA 58.482 33.333 0.00 0.00 39.68 2.57
881 883 6.955364 TCTTTTCAGATGATGAGGATGAACT 58.045 36.000 0.00 0.00 39.68 3.01
889 891 3.643320 TGATGAGGATGAACTAGCCGATT 59.357 43.478 0.00 0.00 40.72 3.34
951 953 8.206867 TCAAAATCAGATAAAGATGTCTCCGAT 58.793 33.333 0.00 0.00 0.00 4.18
953 955 6.662865 ATCAGATAAAGATGTCTCCGATGT 57.337 37.500 0.00 0.00 0.00 3.06
1050 1052 3.636231 CCCAGCTTCCACGGTCCA 61.636 66.667 0.00 0.00 0.00 4.02
1065 1067 2.108970 GGTCCACTTACCGAGGAAGAT 58.891 52.381 3.23 0.00 33.99 2.40
1112 1114 3.216230 AGTTGGGTTGGGGTATAGAGT 57.784 47.619 0.00 0.00 0.00 3.24
1142 1144 2.300967 TGGGGGTGACAGAGGATGC 61.301 63.158 0.00 0.00 0.00 3.91
1196 1198 1.876416 CGTGGATTGTTGGGAACGTCT 60.876 52.381 0.00 0.00 0.00 4.18
1289 1291 9.330063 CTCTATTGGTCTTATTCTTATTGTGCA 57.670 33.333 0.00 0.00 0.00 4.57
1434 1436 0.323087 GTTTTGGGTCATAGGGCGGT 60.323 55.000 0.00 0.00 0.00 5.68
1835 1837 0.399075 ATTTCGTGAAAGTCCCCGGT 59.601 50.000 0.00 0.00 33.32 5.28
1837 1839 1.269012 TTCGTGAAAGTCCCCGGTAT 58.731 50.000 0.00 0.00 0.00 2.73
1911 1913 1.441729 CTATGGGATCGTGCGTGGT 59.558 57.895 0.00 0.00 0.00 4.16
1913 1915 0.386476 TATGGGATCGTGCGTGGTAC 59.614 55.000 0.00 0.00 0.00 3.34
2012 2014 0.181350 GAAAGGGGGCGACTGATGAT 59.819 55.000 0.00 0.00 0.00 2.45
2024 2026 3.174375 GACTGATGATTGCCTTTTTCGC 58.826 45.455 0.00 0.00 0.00 4.70
2025 2027 2.557924 ACTGATGATTGCCTTTTTCGCA 59.442 40.909 0.00 0.00 0.00 5.10
2103 2105 3.283751 AGAAAGATGAGACGAGACGGAT 58.716 45.455 0.00 0.00 0.00 4.18
2156 2158 3.626924 CCGCCCCCGCTAGCTAAT 61.627 66.667 13.93 0.00 0.00 1.73
2299 2301 1.680651 CTCCAGTCCAGTCGCCTCT 60.681 63.158 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 179 3.458189 CGTAAGGGTGATCCATCTTGAC 58.542 50.000 0.00 0.00 38.24 3.18
246 247 3.008594 TCGGTAGCCTTCTTTCATTTCCA 59.991 43.478 0.00 0.00 0.00 3.53
316 317 5.140454 ACAAGTACCAAGGAGCAAGAAAAT 58.860 37.500 0.00 0.00 0.00 1.82
355 356 9.965824 AACGAAAAATCAAGTGAACTAATGAAT 57.034 25.926 0.00 0.00 0.00 2.57
470 471 0.525668 GCCGATATGATAGGCGACGG 60.526 60.000 0.00 0.00 41.17 4.79
482 484 1.286260 GACGAAGCCGAGCCGATAT 59.714 57.895 0.00 0.00 39.50 1.63
560 562 6.384305 ACAAAGGCCAACTACTACATAGAGAT 59.616 38.462 5.01 0.00 34.65 2.75
611 613 1.630878 AGAAAGAGGCATTCGGGAAGT 59.369 47.619 0.00 0.00 32.04 3.01
761 763 1.203994 ACATCAATTGAAGCAGGCAGC 59.796 47.619 13.09 0.00 46.19 5.25
864 866 3.257873 CGGCTAGTTCATCCTCATCATCT 59.742 47.826 0.00 0.00 0.00 2.90
879 881 7.990886 TCCAAAATTATGTTAGAATCGGCTAGT 59.009 33.333 0.00 0.00 0.00 2.57
881 883 7.444183 CCTCCAAAATTATGTTAGAATCGGCTA 59.556 37.037 0.00 0.00 0.00 3.93
889 891 5.123227 CGGCTCCTCCAAAATTATGTTAGA 58.877 41.667 0.00 0.00 34.01 2.10
951 953 1.202964 TCTAGTGGAAGTCCGGTCACA 60.203 52.381 0.00 0.00 39.43 3.58
953 955 2.526888 ATCTAGTGGAAGTCCGGTCA 57.473 50.000 0.00 0.00 39.43 4.02
1050 1052 2.296471 CCGCATATCTTCCTCGGTAAGT 59.704 50.000 0.00 0.00 35.75 2.24
1142 1144 1.844357 CAACTATGAACCGTACGAGCG 59.156 52.381 18.76 2.16 0.00 5.03
1289 1291 0.107410 TCCAAACGTGCTCACAAGGT 60.107 50.000 0.00 0.00 0.00 3.50
1327 1329 1.920351 GTTGGGTTAGGGGAAGATCCA 59.080 52.381 0.00 0.00 38.64 3.41
1835 1837 4.274794 TCACCTACAGCCCTTTCCTATA 57.725 45.455 0.00 0.00 0.00 1.31
1837 1839 2.634639 TCACCTACAGCCCTTTCCTA 57.365 50.000 0.00 0.00 0.00 2.94
1911 1913 7.310671 GCCTTTCATCATCATCTATACCAGGTA 60.311 40.741 0.39 0.39 0.00 3.08
1913 1915 5.879223 GCCTTTCATCATCATCTATACCAGG 59.121 44.000 0.00 0.00 0.00 4.45
2024 2026 6.203338 CACATTCCACCCTTTTTGATTTCTTG 59.797 38.462 0.00 0.00 0.00 3.02
2025 2027 6.290605 CACATTCCACCCTTTTTGATTTCTT 58.709 36.000 0.00 0.00 0.00 2.52
2103 2105 2.049156 CGCTGCGTCCTCTGACAA 60.049 61.111 14.93 0.00 41.85 3.18
2156 2158 7.865706 TGCGCACTGAGAATAGATATCTATA 57.134 36.000 22.69 8.78 38.15 1.31
2173 2175 4.871513 TCTAAATCTCGAATATGCGCACT 58.128 39.130 14.90 4.70 0.00 4.40
2220 2222 1.606313 CCAAGTGGTGGCCCGATTT 60.606 57.895 0.00 0.00 41.72 2.17
2299 2301 1.142667 TGGTTGACAAGCCACTGATCA 59.857 47.619 14.49 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.