Multiple sequence alignment - TraesCS6B01G230000

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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 TraesCS6B01G230000 chr6B 100.000 3251 0 0 1 3251 369528637 369525387 0 6004
1 TraesCS6B01G230000 chr6B 95.858 676 27 1 2577 3251 305957624 305958299 0 1092
2 TraesCS6B01G230000 chr6D 97.543 1750 28 4 831 2576 232743596 232745334 0 2979
3 TraesCS6B01G230000 chr6A 97.480 1746 32 8 834 2576 306766140 306764404 0 2970
4 TraesCS6B01G230000 chr4A 93.602 844 42 9 1 838 697745242 697744405 0 1249
5 TraesCS6B01G230000 chr5B 93.878 833 41 6 1 828 427656752 427657579 0 1247
6 TraesCS6B01G230000 chr5B 93.397 833 46 6 1 828 511450046 511449218 0 1225
7 TraesCS6B01G230000 chr5B 92.909 832 51 6 1 828 419840606 419841433 0 1203
8 TraesCS6B01G230000 chr5B 91.837 833 58 7 1 828 529273056 529273883 0 1153
9 TraesCS6B01G230000 chr5B 95.252 674 30 2 2580 3251 410545138 410544465 0 1066
10 TraesCS6B01G230000 chr5B 94.575 682 30 5 2575 3251 60086235 60085556 0 1048
11 TraesCS6B01G230000 chr4B 93.637 833 43 7 1 828 457047358 457048185 0 1236
12 TraesCS6B01G230000 chr4B 92.797 833 52 6 1 828 609385156 609385985 0 1199
13 TraesCS6B01G230000 chr4B 92.548 832 55 6 1 828 68858936 68858108 0 1186
14 TraesCS6B01G230000 chr2B 93.277 833 47 7 1 828 215483145 215482317 0 1219
15 TraesCS6B01G230000 chr7B 96.476 681 22 2 2573 3251 578788600 578787920 0 1123
16 TraesCS6B01G230000 chrUn 96.029 680 24 3 2573 3251 344735194 344734517 0 1103
17 TraesCS6B01G230000 chr3A 95.882 680 25 3 2573 3251 738491974 738492651 0 1098
18 TraesCS6B01G230000 chr3A 95.735 680 27 2 2573 3251 738664674 738665352 0 1094
19 TraesCS6B01G230000 chr3A 95.588 680 26 4 2573 3251 738564516 738565192 0 1086
20 TraesCS6B01G230000 chr3A 95.441 680 28 3 2573 3251 738586182 738586859 0 1081


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 TraesCS6B01G230000 chr6B 369525387 369528637 3250 True 6004 6004 100.000 1 3251 1 chr6B.!!$R1 3250
1 TraesCS6B01G230000 chr6B 305957624 305958299 675 False 1092 1092 95.858 2577 3251 1 chr6B.!!$F1 674
2 TraesCS6B01G230000 chr6D 232743596 232745334 1738 False 2979 2979 97.543 831 2576 1 chr6D.!!$F1 1745
3 TraesCS6B01G230000 chr6A 306764404 306766140 1736 True 2970 2970 97.480 834 2576 1 chr6A.!!$R1 1742
4 TraesCS6B01G230000 chr4A 697744405 697745242 837 True 1249 1249 93.602 1 838 1 chr4A.!!$R1 837
5 TraesCS6B01G230000 chr5B 427656752 427657579 827 False 1247 1247 93.878 1 828 1 chr5B.!!$F2 827
6 TraesCS6B01G230000 chr5B 511449218 511450046 828 True 1225 1225 93.397 1 828 1 chr5B.!!$R3 827
7 TraesCS6B01G230000 chr5B 419840606 419841433 827 False 1203 1203 92.909 1 828 1 chr5B.!!$F1 827
8 TraesCS6B01G230000 chr5B 529273056 529273883 827 False 1153 1153 91.837 1 828 1 chr5B.!!$F3 827
9 TraesCS6B01G230000 chr5B 410544465 410545138 673 True 1066 1066 95.252 2580 3251 1 chr5B.!!$R2 671
10 TraesCS6B01G230000 chr5B 60085556 60086235 679 True 1048 1048 94.575 2575 3251 1 chr5B.!!$R1 676
11 TraesCS6B01G230000 chr4B 457047358 457048185 827 False 1236 1236 93.637 1 828 1 chr4B.!!$F1 827
12 TraesCS6B01G230000 chr4B 609385156 609385985 829 False 1199 1199 92.797 1 828 1 chr4B.!!$F2 827
13 TraesCS6B01G230000 chr4B 68858108 68858936 828 True 1186 1186 92.548 1 828 1 chr4B.!!$R1 827
14 TraesCS6B01G230000 chr2B 215482317 215483145 828 True 1219 1219 93.277 1 828 1 chr2B.!!$R1 827
15 TraesCS6B01G230000 chr7B 578787920 578788600 680 True 1123 1123 96.476 2573 3251 1 chr7B.!!$R1 678
16 TraesCS6B01G230000 chrUn 344734517 344735194 677 True 1103 1103 96.029 2573 3251 1 chrUn.!!$R1 678
17 TraesCS6B01G230000 chr3A 738491974 738492651 677 False 1098 1098 95.882 2573 3251 1 chr3A.!!$F1 678
18 TraesCS6B01G230000 chr3A 738664674 738665352 678 False 1094 1094 95.735 2573 3251 1 chr3A.!!$F4 678
19 TraesCS6B01G230000 chr3A 738564516 738565192 676 False 1086 1086 95.588 2573 3251 1 chr3A.!!$F2 678
20 TraesCS6B01G230000 chr3A 738586182 738586859 677 False 1081 1081 95.441 2573 3251 1 chr3A.!!$F3 678

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
874 887 0.459585 TAAACACCTCTCATCGCCGC 60.46 55.0 0.0 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2819 2835 0.324923 TCCTACCGCCAGAGCCTAAA 60.325 55.0 0.0 0.0 34.57 1.85 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
135 136 3.817959 ACCCTAACCCTAACCATAACCA 58.182 45.455 0.00 0.00 0.00 3.67
156 157 6.563163 ACCATAACCAAAACCATAACCCTAA 58.437 36.000 0.00 0.00 0.00 2.69
186 187 4.290196 ACCTAACCCTAGCACCAACATAAA 59.710 41.667 0.00 0.00 0.00 1.40
266 267 6.942005 ACAAACAAACATCTCACATCTCCATA 59.058 34.615 0.00 0.00 0.00 2.74
344 346 8.131100 AGCAATTTGATAACATTACTTGGATCG 58.869 33.333 0.00 0.00 0.00 3.69
399 402 2.882137 GGGTTTGACTTCGAAATCCACA 59.118 45.455 3.88 0.00 34.22 4.17
439 442 5.191727 TGCAAGATTTGGGAGAGGATTTA 57.808 39.130 0.00 0.00 0.00 1.40
514 520 4.995058 GTGTGGGGGAGTGGGGGA 62.995 72.222 0.00 0.00 0.00 4.81
515 521 4.675303 TGTGGGGGAGTGGGGGAG 62.675 72.222 0.00 0.00 0.00 4.30
615 624 2.658679 TAGGCGCTGCACACTGTGTT 62.659 55.000 11.40 0.00 35.75 3.32
699 709 1.816537 CAACGCCTGCTAGCTAGGA 59.183 57.895 27.37 18.55 37.52 2.94
747 757 2.322081 GCGGGCGCTACACAAAAGA 61.322 57.895 7.64 0.00 38.26 2.52
754 764 2.480419 GCGCTACACAAAAGAGTCATGT 59.520 45.455 0.00 0.00 0.00 3.21
805 815 5.550232 TCTGTGAATTGATTTCGTCCATG 57.450 39.130 0.00 0.00 37.13 3.66
828 838 4.578105 GGGTCAAAATTGTCAAATTTGCCA 59.422 37.500 24.86 5.45 43.63 4.92
829 839 5.505489 GGGTCAAAATTGTCAAATTTGCCAC 60.505 40.000 24.86 17.63 43.63 5.01
830 840 5.065731 GGTCAAAATTGTCAAATTTGCCACA 59.934 36.000 21.86 10.60 43.63 4.17
831 841 5.964751 GTCAAAATTGTCAAATTTGCCACAC 59.035 36.000 17.69 7.02 43.63 3.82
840 850 2.276732 ATTTGCCACACTAGCACACT 57.723 45.000 0.00 0.00 40.69 3.55
870 883 6.727824 AACAAAGATAAACACCTCTCATCG 57.272 37.500 0.00 0.00 0.00 3.84
871 884 4.631813 ACAAAGATAAACACCTCTCATCGC 59.368 41.667 0.00 0.00 0.00 4.58
872 885 3.460857 AGATAAACACCTCTCATCGCC 57.539 47.619 0.00 0.00 0.00 5.54
873 886 2.128035 GATAAACACCTCTCATCGCCG 58.872 52.381 0.00 0.00 0.00 6.46
874 887 0.459585 TAAACACCTCTCATCGCCGC 60.460 55.000 0.00 0.00 0.00 6.53
875 888 3.665675 AACACCTCTCATCGCCGCC 62.666 63.158 0.00 0.00 0.00 6.13
876 889 4.899239 CACCTCTCATCGCCGCCC 62.899 72.222 0.00 0.00 0.00 6.13
1131 1144 2.665603 GCCCTCGCCATCCCTATC 59.334 66.667 0.00 0.00 0.00 2.08
1511 1527 2.925966 AATTCTGGCTCCAATCCCAA 57.074 45.000 0.00 0.00 0.00 4.12
1941 1957 2.031163 GGTGCTCCACTCGCTGTT 59.969 61.111 0.00 0.00 34.40 3.16
2135 2151 0.981183 TCACAACGCCCATCTTACCT 59.019 50.000 0.00 0.00 0.00 3.08
2143 2159 2.277084 GCCCATCTTACCTGTACAACG 58.723 52.381 0.00 0.00 0.00 4.10
2197 2213 1.220749 GGTAGTGGCAGCGATTCCA 59.779 57.895 0.00 0.00 0.00 3.53
2666 2682 2.175715 GGGATCTGACCCTTTTGCCTAT 59.824 50.000 7.74 0.00 45.90 2.57
2781 2797 2.683933 CCTGCCGTCCACCCTACT 60.684 66.667 0.00 0.00 0.00 2.57
2813 2829 1.041437 GGCGGTAGGCTCTGTAATCT 58.959 55.000 0.00 0.00 42.94 2.40
2819 2835 1.853963 AGGCTCTGTAATCTGACCGT 58.146 50.000 0.00 0.00 0.00 4.83
2985 3007 3.027533 CCCCCTCCAATCTCCTTCA 57.972 57.895 0.00 0.00 0.00 3.02
3146 3168 9.747898 TTTGTTTTTATCCTAGGATTGCTTAGA 57.252 29.630 29.06 6.82 36.17 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 136 5.959594 GGGTTAGGGTTATGGTTTTGGTTAT 59.040 40.000 0.00 0.00 0.00 1.89
156 157 2.842496 GTGCTAGGGTTAGGTTTAGGGT 59.158 50.000 0.00 0.00 0.00 4.34
186 187 9.975218 ATGTTAGAGTTATTCTTATGGGTGTTT 57.025 29.630 0.00 0.00 37.36 2.83
241 242 5.132502 TGGAGATGTGAGATGTTTGTTTGT 58.867 37.500 0.00 0.00 0.00 2.83
266 267 9.442047 CTAGTTTTGTTTGGATCTAGAGATTGT 57.558 33.333 0.00 0.00 34.37 2.71
344 346 3.629142 TCTTCTCCGATCCCCTTTTTC 57.371 47.619 0.00 0.00 0.00 2.29
399 402 7.281040 TCTTGCAAATCTGAAGAATTTGTCT 57.719 32.000 0.00 0.00 37.54 3.41
439 442 0.338120 CTCCCACTCTCTCCCCTCTT 59.662 60.000 0.00 0.00 0.00 2.85
559 568 4.024048 ACACATTTAATATGCAGCGCCTAC 60.024 41.667 2.29 0.00 0.00 3.18
805 815 4.578105 TGGCAAATTTGACAATTTTGACCC 59.422 37.500 24.47 21.60 44.72 4.46
896 909 1.576920 CATTTTGTGGCGTGCGGTA 59.423 52.632 0.00 0.00 0.00 4.02
1060 1073 4.547905 GTCGGCGATCGGAAGCGA 62.548 66.667 14.79 0.00 39.77 4.93
1131 1144 0.846015 TGGAGGGACCATGCTTATGG 59.154 55.000 0.00 4.82 44.64 2.74
1614 1630 2.125912 GACGATGCTGACGCCTGT 60.126 61.111 0.00 0.00 34.43 4.00
2121 2137 1.563924 TGTACAGGTAAGATGGGCGT 58.436 50.000 0.00 0.00 0.00 5.68
2197 2213 1.048601 TCCTCGTCTTCCTTGTTGCT 58.951 50.000 0.00 0.00 0.00 3.91
2813 2829 1.295423 GCCAGAGCCTAAACGGTCA 59.705 57.895 0.00 0.00 34.25 4.02
2819 2835 0.324923 TCCTACCGCCAGAGCCTAAA 60.325 55.000 0.00 0.00 34.57 1.85
2947 2964 1.916181 GGAGTGGAGGGGATGAAAGAA 59.084 52.381 0.00 0.00 0.00 2.52
2951 2968 1.307866 GGGGAGTGGAGGGGATGAA 60.308 63.158 0.00 0.00 0.00 2.57
2975 2997 2.225343 TGGTGCCCAAATGAAGGAGATT 60.225 45.455 0.00 0.00 0.00 2.40
2985 3007 1.521580 CGCAAAAATGGTGCCCAAAT 58.478 45.000 0.00 0.00 38.86 2.32
3087 3109 9.030452 AGATAGGTTTGTTTGCACCAAATAATA 57.970 29.630 12.43 7.64 35.20 0.98


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

AutoCloner maintained by Alex Coulton.