Multiple sequence alignment - TraesCS1A01G368200

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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 TraesCS1A01G368200 chr1A 100.000 3187 0 0 1 3187 546232832 546229646 0.000000e+00 5886
1 TraesCS1A01G368200 chr1A 90.423 1065 81 14 918 1971 546225108 546224054 0.000000e+00 1382
2 TraesCS1A01G368200 chr1D 94.668 2307 81 8 883 3187 451782202 451779936 0.000000e+00 3541
3 TraesCS1A01G368200 chr1D 91.168 985 66 4 993 1971 451637087 451636118 0.000000e+00 1317
4 TraesCS1A01G368200 chr1D 95.200 125 6 0 735 859 451789752 451789628 6.970000e-47 198
5 TraesCS1A01G368200 chr1B 92.171 1571 80 12 736 2298 621409841 621408306 0.000000e+00 2180
6 TraesCS1A01G368200 chr1B 90.850 1071 73 8 918 1971 621260741 621261803 0.000000e+00 1411
7 TraesCS1A01G368200 chr1B 90.921 738 62 3 1 737 408553253 408552520 0.000000e+00 987
8 TraesCS1A01G368200 chr1B 89.159 535 44 7 2328 2851 621408186 621407655 0.000000e+00 654
9 TraesCS1A01G368200 chr7B 98.212 727 13 0 1 727 257653188 257652462 0.000000e+00 1271
10 TraesCS1A01G368200 chr7A 97.687 735 15 2 1 733 299312662 299313396 0.000000e+00 1262
11 TraesCS1A01G368200 chr7A 83.573 347 35 8 1280 1625 675441685 675441360 3.990000e-79 305
12 TraesCS1A01G368200 chr5A 98.305 708 12 0 1 708 484831426 484830719 0.000000e+00 1242
13 TraesCS1A01G368200 chr5A 98.827 682 5 1 1193 1871 11311054 11310373 0.000000e+00 1212
14 TraesCS1A01G368200 chr5B 97.775 719 16 0 1 719 47322407 47323125 0.000000e+00 1240
15 TraesCS1A01G368200 chr2A 97.249 727 20 0 1 727 166817617 166818343 0.000000e+00 1232
16 TraesCS1A01G368200 chr2A 98.510 671 7 1 1204 1871 770129778 770129108 0.000000e+00 1181
17 TraesCS1A01G368200 chr2A 92.329 730 50 4 1 725 395710013 395710741 0.000000e+00 1033
18 TraesCS1A01G368200 chr6B 92.627 746 45 6 1 736 246984092 246983347 0.000000e+00 1064
19 TraesCS1A01G368200 chr6B 92.039 716 50 5 1 714 420862899 420862189 0.000000e+00 1000
20 TraesCS1A01G368200 chr2B 85.023 868 115 7 2326 3183 716044849 716043987 0.000000e+00 869
21 TraesCS1A01G368200 chr2B 91.346 104 9 0 2218 2321 716045016 716044913 3.310000e-30 143
22 TraesCS1A01G368200 chr2D 74.765 638 110 30 1300 1932 439972017 439972608 4.110000e-59 239
23 TraesCS1A01G368200 chr2D 87.000 100 13 0 1448 1547 181192240 181192339 2.600000e-21 113


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 TraesCS1A01G368200 chr1A 546229646 546232832 3186 True 5886 5886 100.0000 1 3187 1 chr1A.!!$R2 3186
1 TraesCS1A01G368200 chr1A 546224054 546225108 1054 True 1382 1382 90.4230 918 1971 1 chr1A.!!$R1 1053
2 TraesCS1A01G368200 chr1D 451779936 451782202 2266 True 3541 3541 94.6680 883 3187 1 chr1D.!!$R2 2304
3 TraesCS1A01G368200 chr1D 451636118 451637087 969 True 1317 1317 91.1680 993 1971 1 chr1D.!!$R1 978
4 TraesCS1A01G368200 chr1B 621407655 621409841 2186 True 1417 2180 90.6650 736 2851 2 chr1B.!!$R2 2115
5 TraesCS1A01G368200 chr1B 621260741 621261803 1062 False 1411 1411 90.8500 918 1971 1 chr1B.!!$F1 1053
6 TraesCS1A01G368200 chr1B 408552520 408553253 733 True 987 987 90.9210 1 737 1 chr1B.!!$R1 736
7 TraesCS1A01G368200 chr7B 257652462 257653188 726 True 1271 1271 98.2120 1 727 1 chr7B.!!$R1 726
8 TraesCS1A01G368200 chr7A 299312662 299313396 734 False 1262 1262 97.6870 1 733 1 chr7A.!!$F1 732
9 TraesCS1A01G368200 chr5A 484830719 484831426 707 True 1242 1242 98.3050 1 708 1 chr5A.!!$R2 707
10 TraesCS1A01G368200 chr5A 11310373 11311054 681 True 1212 1212 98.8270 1193 1871 1 chr5A.!!$R1 678
11 TraesCS1A01G368200 chr5B 47322407 47323125 718 False 1240 1240 97.7750 1 719 1 chr5B.!!$F1 718
12 TraesCS1A01G368200 chr2A 166817617 166818343 726 False 1232 1232 97.2490 1 727 1 chr2A.!!$F1 726
13 TraesCS1A01G368200 chr2A 770129108 770129778 670 True 1181 1181 98.5100 1204 1871 1 chr2A.!!$R1 667
14 TraesCS1A01G368200 chr2A 395710013 395710741 728 False 1033 1033 92.3290 1 725 1 chr2A.!!$F2 724
15 TraesCS1A01G368200 chr6B 246983347 246984092 745 True 1064 1064 92.6270 1 736 1 chr6B.!!$R1 735
16 TraesCS1A01G368200 chr6B 420862189 420862899 710 True 1000 1000 92.0390 1 714 1 chr6B.!!$R2 713
17 TraesCS1A01G368200 chr2B 716043987 716045016 1029 True 506 869 88.1845 2218 3183 2 chr2B.!!$R1 965
18 TraesCS1A01G368200 chr2D 439972017 439972608 591 False 239 239 74.7650 1300 1932 1 chr2D.!!$F2 632

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
873 884 0.179032 TGATGCAACCCACTGTCGTT 60.179 50.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2573 2746 0.034089 CATCGGGGGAGCCTCTTTTT 60.034 55.0 0.0 0.0 0.0 1.94 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
150 151 0.400213 AGAATCCCTTGACAACGGCA 59.600 50.000 0.00 0.00 0.00 5.69
201 202 1.302285 CCCAACTGCATCTCCAGCT 59.698 57.895 0.00 0.00 36.29 4.24
289 290 3.300765 GGACCACCGGAGACACGT 61.301 66.667 9.46 0.00 0.00 4.49
610 619 5.957910 ACGCAAAAATGAATCGTTTTTCA 57.042 30.435 19.55 0.37 39.55 2.69
694 705 4.093952 ACCAGCGACGTACGACCG 62.094 66.667 24.41 23.46 45.77 4.79
708 719 3.982372 GACCGGAAGCGATGCGTGA 62.982 63.158 9.46 0.00 41.91 4.35
743 754 5.697633 GGTAGAGAGGTAGAGATACAAGTCG 59.302 48.000 0.00 0.00 0.00 4.18
811 822 3.064408 AGACCGTTTTCGTGTTTTCCTTC 59.936 43.478 0.00 0.00 42.35 3.46
814 825 4.635324 ACCGTTTTCGTGTTTTCCTTCTTA 59.365 37.500 0.00 0.00 42.35 2.10
824 835 8.463607 TCGTGTTTTCCTTCTTAAATCAAGTTT 58.536 29.630 0.00 0.00 35.58 2.66
827 838 9.581099 TGTTTTCCTTCTTAAATCAAGTTTCAC 57.419 29.630 0.00 0.00 35.58 3.18
852 863 3.575256 TCTCATTTTGCCAGCATTCAACT 59.425 39.130 0.00 0.00 0.00 3.16
873 884 0.179032 TGATGCAACCCACTGTCGTT 60.179 50.000 0.00 0.00 0.00 3.85
874 885 0.238289 GATGCAACCCACTGTCGTTG 59.762 55.000 11.21 11.21 41.84 4.10
876 887 3.030652 CAACCCACTGTCGTTGCC 58.969 61.111 4.80 0.00 33.56 4.52
877 888 1.525995 CAACCCACTGTCGTTGCCT 60.526 57.895 4.80 0.00 33.56 4.75
878 889 1.227853 AACCCACTGTCGTTGCCTC 60.228 57.895 0.00 0.00 0.00 4.70
879 890 1.978455 AACCCACTGTCGTTGCCTCA 61.978 55.000 0.00 0.00 0.00 3.86
880 891 1.227823 CCCACTGTCGTTGCCTCAA 60.228 57.895 0.00 0.00 0.00 3.02
909 920 2.292866 CCACGATCAGGGGTGGTTA 58.707 57.895 8.83 0.00 46.79 2.85
910 921 0.837272 CCACGATCAGGGGTGGTTAT 59.163 55.000 8.83 0.00 46.79 1.89
911 922 2.043992 CCACGATCAGGGGTGGTTATA 58.956 52.381 8.83 0.00 46.79 0.98
912 923 2.637872 CCACGATCAGGGGTGGTTATAT 59.362 50.000 8.83 0.00 46.79 0.86
1892 1937 1.000506 GTCTACCTCGTGTGCAGGAAA 59.999 52.381 0.00 0.00 34.75 3.13
1977 2028 3.056821 TCTTCTCCCGGCAATCGTATATG 60.057 47.826 0.00 0.00 37.11 1.78
2007 2059 6.407074 CCCCGTAGTGTCTGAAAATCTATTCT 60.407 42.308 0.00 0.00 0.00 2.40
2139 2191 8.035984 GCTGAGTAGGTATTTAGTTCAGAACTT 58.964 37.037 21.05 6.19 42.81 2.66
2154 2206 5.547465 TCAGAACTTCTATGCGGAGAAAAA 58.453 37.500 2.17 0.00 35.06 1.94
2357 2522 4.000331 GGACATGTCCCATCTATGACAG 58.000 50.000 31.37 0.00 44.07 3.51
2365 2530 4.645136 GTCCCATCTATGACAGTGTAGACA 59.355 45.833 0.00 0.00 30.35 3.41
2461 2626 3.995048 GCTACCACAAGACCAGTTACTTC 59.005 47.826 0.00 0.00 0.00 3.01
2558 2731 5.105554 TGGCGTATTTGGCAATTACAGAATT 60.106 36.000 24.07 0.00 41.96 2.17
2677 2851 4.526438 ACAGAGGAAATCATTAAGGGGG 57.474 45.455 0.00 0.00 0.00 5.40
2703 2877 3.261390 TGCCAATTGCTGATTAGGCTTTT 59.739 39.130 17.95 0.00 40.04 2.27
2794 2972 5.250543 TCAGTATGGATCCTTTTCAGTGGAA 59.749 40.000 14.23 0.00 34.21 3.53
2808 2986 1.756950 TGGAATCTAGCGAGGCGGT 60.757 57.895 0.00 0.00 41.50 5.68
2828 3006 1.747444 AGTGGGAATGGTTCTCAGGT 58.253 50.000 0.00 0.00 41.71 4.00
2844 3022 1.195448 CAGGTGACACAACGAATCTGC 59.805 52.381 8.08 0.00 0.00 4.26
2982 3160 5.680619 TGTACAATTTGACTCAAGTGAGGT 58.319 37.500 12.76 2.08 46.13 3.85
3016 3194 2.433318 GCGGATGGGCTAGATCGC 60.433 66.667 0.00 0.00 36.51 4.58
3049 3227 5.048083 TGGTCATCTTGTGGCTGAAATTAAC 60.048 40.000 0.00 0.00 31.47 2.01
3135 3313 5.105513 TCGATTGTCTGGCAAAGTATAGTCA 60.106 40.000 0.00 0.00 40.91 3.41
3138 3316 7.600375 CGATTGTCTGGCAAAGTATAGTCATAT 59.400 37.037 0.00 0.00 40.91 1.78
3150 3328 7.670009 AGTATAGTCATATCGAGTGTACCAC 57.330 40.000 0.00 0.00 40.67 4.16
3163 3341 2.363038 GTGTACCACGGCTGTATGGATA 59.637 50.000 9.10 0.00 39.46 2.59
3183 3361 5.307196 GGATACACTAAGGACCACCATGTAT 59.693 44.000 9.86 9.86 36.68 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 0.034477 GTTCCCCATCCATCACGGTT 60.034 55.000 0.00 0.00 35.57 4.44
201 202 5.960811 ACCTCACCTTCTCTTCATATTCTCA 59.039 40.000 0.00 0.00 0.00 3.27
610 619 6.231211 CAGTCCTTGTTTAAGTGGTACTCAT 58.769 40.000 0.00 0.00 31.80 2.90
694 705 3.609103 AATAAATCACGCATCGCTTCC 57.391 42.857 0.00 0.00 0.00 3.46
743 754 8.700644 CCTATCTTTTACATGCATACTTACGTC 58.299 37.037 0.00 0.00 0.00 4.34
767 778 9.722184 GGTCTTCTGAAACTTATAAACTTACCT 57.278 33.333 0.00 0.00 0.00 3.08
814 825 8.553696 GCAAAATGAGAATGTGAAACTTGATTT 58.446 29.630 0.00 0.00 38.04 2.17
824 835 2.892215 TGCTGGCAAAATGAGAATGTGA 59.108 40.909 0.00 0.00 0.00 3.58
827 838 4.500127 TGAATGCTGGCAAAATGAGAATG 58.500 39.130 0.00 0.00 0.00 2.67
852 863 1.277842 ACGACAGTGGGTTGCATCATA 59.722 47.619 0.00 0.00 33.88 2.15
909 920 7.362315 GGCAGTTCCTTTTTGTTACCGTAATAT 60.362 37.037 0.00 0.00 0.00 1.28
910 921 6.072563 GGCAGTTCCTTTTTGTTACCGTAATA 60.073 38.462 0.00 0.00 0.00 0.98
911 922 5.278610 GGCAGTTCCTTTTTGTTACCGTAAT 60.279 40.000 0.00 0.00 0.00 1.89
912 923 4.036616 GGCAGTTCCTTTTTGTTACCGTAA 59.963 41.667 0.00 0.00 0.00 3.18
1977 2028 1.471119 TCAGACACTACGGGGATCAC 58.529 55.000 0.00 0.00 0.00 3.06
2007 2059 0.950836 CGTGGTTGCAATGGACTGAA 59.049 50.000 0.59 0.00 0.00 3.02
2069 2121 9.841295 AGTACAACCTCTGTTTCAAATTACTTA 57.159 29.630 0.00 0.00 39.64 2.24
2180 2232 5.912955 GGAAACGAATCAAAAGATTCACGTT 59.087 36.000 15.89 12.85 40.56 3.99
2206 2258 4.036734 AGTTCATCGTGCACAGAAAACAAT 59.963 37.500 18.64 6.86 0.00 2.71
2357 2522 7.151308 AGCATGATAGCTATCTTTGTCTACAC 58.849 38.462 29.20 14.75 44.50 2.90
2365 2530 6.460676 GCAACCAAAGCATGATAGCTATCTTT 60.461 38.462 29.20 19.75 45.89 2.52
2419 2584 1.276421 CGACCAAACTCTCCTCATGGT 59.724 52.381 0.00 0.00 46.63 3.55
2461 2626 2.028385 ACCACTCCTTACCGCTGTTAAG 60.028 50.000 0.00 0.00 0.00 1.85
2558 2731 8.027524 AGCCTCTTTTTATCATGAGTGAGATA 57.972 34.615 0.09 0.00 37.87 1.98
2573 2746 0.034089 CATCGGGGGAGCCTCTTTTT 60.034 55.000 0.00 0.00 0.00 1.94
2574 2747 0.914417 TCATCGGGGGAGCCTCTTTT 60.914 55.000 0.00 0.00 0.00 2.27
2794 2972 1.173444 CCACTACCGCCTCGCTAGAT 61.173 60.000 0.00 0.00 0.00 1.98
2808 2986 2.571653 CACCTGAGAACCATTCCCACTA 59.428 50.000 0.00 0.00 0.00 2.74
2828 3006 3.660501 ACTAGCAGATTCGTTGTGTCA 57.339 42.857 0.00 0.00 0.00 3.58
2844 3022 9.722056 AAATAAATCGATAAGCAGCAAAACTAG 57.278 29.630 0.00 0.00 0.00 2.57
2888 3066 2.134354 TGCATGTATCCCCATCTCCAA 58.866 47.619 0.00 0.00 0.00 3.53
2919 3097 4.023279 TGTGTTGAATAGCAAGCGTCATTT 60.023 37.500 0.00 0.00 37.12 2.32
2982 3160 5.583061 CCATCCGCTGTTAAACTGTACAATA 59.417 40.000 0.00 0.00 0.00 1.90
3016 3194 4.691175 CCACAAGATGACCATAGACAGAG 58.309 47.826 0.00 0.00 0.00 3.35
3098 3276 6.312918 GCCAGACAATCGACAACTCTATTTTA 59.687 38.462 0.00 0.00 0.00 1.52
3111 3289 5.105513 TGACTATACTTTGCCAGACAATCGA 60.106 40.000 0.00 0.00 38.31 3.59
3150 3328 3.572682 TCCTTAGTGTATCCATACAGCCG 59.427 47.826 0.00 0.00 43.32 5.52
3163 3341 3.199946 CCATACATGGTGGTCCTTAGTGT 59.800 47.826 10.38 0.00 43.05 3.55


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

AutoCloner maintained by Alex Coulton.