Multiple sequence alignment - TraesCS5B01G172400

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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 TraesCS5B01G172400 chr5B 100.000 2240 0 0 1 2240 316625042 316622803 0.000000e+00 4137
1 TraesCS5B01G172400 chr5B 86.700 797 93 8 4 799 707354555 707355339 0.000000e+00 872
2 TraesCS5B01G172400 chr5B 86.375 800 104 5 1 799 707312585 707313380 0.000000e+00 869
3 TraesCS5B01G172400 chr5D 95.081 1423 47 11 826 2240 278468395 278466988 0.000000e+00 2218
4 TraesCS5B01G172400 chr5A 94.635 1342 47 7 899 2240 370096463 370097779 0.000000e+00 2056
5 TraesCS5B01G172400 chr5A 93.689 919 48 2 901 1819 370043312 370042404 0.000000e+00 1367
6 TraesCS5B01G172400 chr5A 90.049 412 25 6 1829 2240 370037019 370036624 9.170000e-144 520
7 TraesCS5B01G172400 chr3B 90.411 803 76 1 1 803 814145283 814146084 0.000000e+00 1055
8 TraesCS5B01G172400 chr4B 88.529 802 89 3 2 803 613828164 613827366 0.000000e+00 968
9 TraesCS5B01G172400 chr4B 86.912 787 98 3 14 799 637457695 637458477 0.000000e+00 878
10 TraesCS5B01G172400 chr2D 82.025 790 140 2 7 795 427980530 427979742 0.000000e+00 671
11 TraesCS5B01G172400 chr2D 80.637 754 144 2 43 795 572019846 572019094 1.150000e-162 582
12 TraesCS5B01G172400 chr7D 82.075 742 129 4 55 794 107012890 107012151 4.060000e-177 630
13 TraesCS5B01G172400 chr6D 80.657 791 149 4 7 795 70648560 70649348 5.290000e-171 610
14 TraesCS5B01G172400 chr6D 78.390 236 43 7 1421 1655 369661723 369661951 1.790000e-31 147
15 TraesCS5B01G172400 chr6A 79.661 236 40 7 1421 1655 510865537 510865765 1.780000e-36 163
16 TraesCS5B01G172400 chr6B 77.119 236 46 6 1421 1655 555293863 555294091 1.810000e-26 130


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 TraesCS5B01G172400 chr5B 316622803 316625042 2239 True 4137 4137 100.000 1 2240 1 chr5B.!!$R1 2239
1 TraesCS5B01G172400 chr5B 707354555 707355339 784 False 872 872 86.700 4 799 1 chr5B.!!$F2 795
2 TraesCS5B01G172400 chr5B 707312585 707313380 795 False 869 869 86.375 1 799 1 chr5B.!!$F1 798
3 TraesCS5B01G172400 chr5D 278466988 278468395 1407 True 2218 2218 95.081 826 2240 1 chr5D.!!$R1 1414
4 TraesCS5B01G172400 chr5A 370096463 370097779 1316 False 2056 2056 94.635 899 2240 1 chr5A.!!$F1 1341
5 TraesCS5B01G172400 chr5A 370042404 370043312 908 True 1367 1367 93.689 901 1819 1 chr5A.!!$R2 918
6 TraesCS5B01G172400 chr3B 814145283 814146084 801 False 1055 1055 90.411 1 803 1 chr3B.!!$F1 802
7 TraesCS5B01G172400 chr4B 613827366 613828164 798 True 968 968 88.529 2 803 1 chr4B.!!$R1 801
8 TraesCS5B01G172400 chr4B 637457695 637458477 782 False 878 878 86.912 14 799 1 chr4B.!!$F1 785
9 TraesCS5B01G172400 chr2D 427979742 427980530 788 True 671 671 82.025 7 795 1 chr2D.!!$R1 788
10 TraesCS5B01G172400 chr2D 572019094 572019846 752 True 582 582 80.637 43 795 1 chr2D.!!$R2 752
11 TraesCS5B01G172400 chr7D 107012151 107012890 739 True 630 630 82.075 55 794 1 chr7D.!!$R1 739
12 TraesCS5B01G172400 chr6D 70648560 70649348 788 False 610 610 80.657 7 795 1 chr6D.!!$F1 788

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
807 821 0.031178 GCACTTGCACTTGGACTTGG 59.969 55.0 0.0 0.0 41.59 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2094 2112 0.471591 TCCATTTGGGCAGCTGGTTT 60.472 50.0 17.12 0.0 36.21 3.27 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
68 71 1.407437 GCGACATCAGGATCTTTGGGT 60.407 52.381 0.00 0.00 0.00 4.51
131 145 3.365265 CGTTTGGGCAGCACCTCC 61.365 66.667 0.00 0.00 39.10 4.30
133 147 3.185203 TTTGGGCAGCACCTCCCT 61.185 61.111 0.00 0.00 43.04 4.20
134 148 2.777960 TTTGGGCAGCACCTCCCTT 61.778 57.895 0.00 0.00 43.04 3.95
227 241 2.027745 ACACGCAATCTTCATCCTCACT 60.028 45.455 0.00 0.00 0.00 3.41
292 306 1.256812 CCAAGCATTCGGAACCCTTT 58.743 50.000 0.00 0.00 0.00 3.11
332 346 2.507407 TGTGTTTCTTAGGGATGCCC 57.493 50.000 0.00 0.00 45.90 5.36
350 364 4.873810 TGCAGCCGCACACTGGTT 62.874 61.111 0.00 0.00 45.36 3.67
408 422 3.554232 CACGCACAGTGGCAGTAG 58.446 61.111 1.84 0.00 46.77 2.57
420 434 5.178061 CAGTGGCAGTAGTGTCATTGATAA 58.822 41.667 19.78 0.00 46.21 1.75
456 470 0.033504 ACTCGACTTCGCCATGTGTT 59.966 50.000 0.00 0.00 39.60 3.32
680 694 2.290641 CAGACAAAAGAAACCCTCACCG 59.709 50.000 0.00 0.00 0.00 4.94
701 715 2.498167 GAGATCGCACTGCCCATAATT 58.502 47.619 0.00 0.00 0.00 1.40
758 772 1.915769 AGAAGCGTGGCCCTCTTCT 60.916 57.895 19.51 19.51 41.01 2.85
761 775 0.890996 AAGCGTGGCCCTCTTCTTTG 60.891 55.000 0.00 0.00 0.00 2.77
795 809 1.341209 AGGGCTTAAACTTGCACTTGC 59.659 47.619 0.00 0.00 40.41 4.01
806 820 3.557207 GCACTTGCACTTGGACTTG 57.443 52.632 0.00 0.00 41.59 3.16
807 821 0.031178 GCACTTGCACTTGGACTTGG 59.969 55.000 0.00 0.00 41.59 3.61
808 822 1.679139 CACTTGCACTTGGACTTGGA 58.321 50.000 0.00 0.00 0.00 3.53
809 823 1.334869 CACTTGCACTTGGACTTGGAC 59.665 52.381 0.00 0.00 0.00 4.02
810 824 1.064758 ACTTGCACTTGGACTTGGACA 60.065 47.619 0.00 0.00 0.00 4.02
811 825 1.605710 CTTGCACTTGGACTTGGACAG 59.394 52.381 0.00 0.00 0.00 3.51
812 826 0.819259 TGCACTTGGACTTGGACAGC 60.819 55.000 0.00 0.00 0.00 4.40
813 827 0.819259 GCACTTGGACTTGGACAGCA 60.819 55.000 0.00 0.00 0.00 4.41
814 828 0.947244 CACTTGGACTTGGACAGCAC 59.053 55.000 0.00 0.00 0.00 4.40
815 829 0.532862 ACTTGGACTTGGACAGCACG 60.533 55.000 0.00 0.00 0.00 5.34
816 830 1.845809 CTTGGACTTGGACAGCACGC 61.846 60.000 0.00 0.00 0.00 5.34
817 831 2.280797 GGACTTGGACAGCACGCA 60.281 61.111 0.00 0.00 0.00 5.24
818 832 2.320587 GGACTTGGACAGCACGCAG 61.321 63.158 0.00 0.00 0.00 5.18
819 833 1.300931 GACTTGGACAGCACGCAGA 60.301 57.895 0.00 0.00 0.00 4.26
820 834 1.287730 GACTTGGACAGCACGCAGAG 61.288 60.000 0.00 0.00 0.00 3.35
821 835 1.301244 CTTGGACAGCACGCAGAGT 60.301 57.895 0.00 0.00 0.00 3.24
822 836 0.882042 CTTGGACAGCACGCAGAGTT 60.882 55.000 0.00 0.00 0.00 3.01
823 837 0.391228 TTGGACAGCACGCAGAGTTA 59.609 50.000 0.00 0.00 0.00 2.24
824 838 0.038251 TGGACAGCACGCAGAGTTAG 60.038 55.000 0.00 0.00 0.00 2.34
831 845 2.071688 CACGCAGAGTTAGTGCTCTT 57.928 50.000 0.00 0.00 42.69 2.85
1092 1110 3.114647 CTCCTCGTCGCCTTCGGAG 62.115 68.421 0.00 0.00 35.75 4.63
1419 1437 1.132643 GACGACACGTAGATGAAGCCT 59.867 52.381 0.00 0.00 41.37 4.58
1985 2003 6.210078 TCCAAAGTTAATTTAAGTTGCACCG 58.790 36.000 9.44 0.00 32.00 4.94
2008 2026 5.228635 CGCAATTTACTTTCATCTCATGTGC 59.771 40.000 0.00 0.00 0.00 4.57
2027 2045 3.862845 GTGCGAATGTTTCACCAAAAGTT 59.137 39.130 0.00 0.00 0.00 2.66
2031 2049 6.419413 TGCGAATGTTTCACCAAAAGTTAATC 59.581 34.615 0.00 0.00 0.00 1.75
2036 2054 6.674066 TGTTTCACCAAAAGTTAATCCGATC 58.326 36.000 0.00 0.00 0.00 3.69
2059 2077 3.813529 AACGCTCAACTATTGAACAGC 57.186 42.857 0.00 0.00 39.58 4.40
2066 2084 5.734498 GCTCAACTATTGAACAGCGTAAATG 59.266 40.000 0.00 0.00 39.58 2.32
2094 2112 6.014242 ACAGAAGAATGTGAGGTGACAGATAA 60.014 38.462 0.00 0.00 30.46 1.75
2120 2138 0.032813 CTGCCCAAATGGACCCAGAT 60.033 55.000 0.00 0.00 37.39 2.90
2128 2146 4.040217 CCAAATGGACCCAGATTTGAACAA 59.960 41.667 14.42 0.00 36.43 2.83
2129 2147 5.232463 CAAATGGACCCAGATTTGAACAAG 58.768 41.667 9.22 0.00 36.43 3.16
2133 2151 5.640147 TGGACCCAGATTTGAACAAGTATT 58.360 37.500 0.00 0.00 0.00 1.89
2199 2220 5.132897 TGCAATGTTGGTATTTGGTTCTC 57.867 39.130 0.00 0.00 0.00 2.87
2224 2245 3.188048 GCCTTCACAAGTGATCTGTCAAG 59.812 47.826 3.43 0.00 39.64 3.02
2226 2247 3.758755 TCACAAGTGATCTGTCAAGCT 57.241 42.857 0.00 0.00 35.80 3.74
2227 2248 3.396560 TCACAAGTGATCTGTCAAGCTG 58.603 45.455 0.00 0.00 35.80 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 117 4.999939 CCAAACGCGGTGGCAAGC 63.000 66.667 16.85 6.18 39.92 4.01
131 145 3.193479 GCTACCAAATCAAGGTGGAAAGG 59.807 47.826 0.00 0.00 39.74 3.11
133 147 3.161866 GGCTACCAAATCAAGGTGGAAA 58.838 45.455 0.00 0.00 39.74 3.13
134 148 2.378547 AGGCTACCAAATCAAGGTGGAA 59.621 45.455 0.00 0.00 39.74 3.53
227 241 3.664769 CTCATCAGGATGGGGCCA 58.335 61.111 4.39 0.00 39.24 5.36
292 306 0.037326 GTGTGAGGACCGCATCAAGA 60.037 55.000 0.00 0.00 36.47 3.02
344 358 1.303317 GGTCATGCCCGAAACCAGT 60.303 57.895 0.00 0.00 0.00 4.00
346 360 0.679640 GATGGTCATGCCCGAAACCA 60.680 55.000 4.34 4.34 45.32 3.67
347 361 1.714899 CGATGGTCATGCCCGAAACC 61.715 60.000 4.07 0.00 36.04 3.27
350 364 2.189257 CCGATGGTCATGCCCGAA 59.811 61.111 4.07 0.00 36.04 4.30
386 400 0.933097 CTGCCACTGTGCGTGATATC 59.067 55.000 1.29 0.00 46.81 1.63
420 434 5.414765 AGTCGAGTGGAAAACTTTTCTTGTT 59.585 36.000 12.88 0.00 40.07 2.83
434 448 1.215382 CATGGCGAAGTCGAGTGGA 59.785 57.895 4.59 0.00 43.02 4.02
456 470 1.757118 CTTCCCTTCTGCGGATCTGTA 59.243 52.381 2.89 0.00 0.00 2.74
618 632 1.003355 CCGAACTGCCAGTGGATGT 60.003 57.895 15.20 7.56 0.00 3.06
680 694 0.106708 TTATGGGCAGTGCGATCTCC 59.893 55.000 9.45 4.63 0.00 3.71
758 772 1.356270 CTTCTGCGTGCTGTGCAAA 59.644 52.632 0.00 0.00 42.70 3.68
761 775 3.730761 CCCTTCTGCGTGCTGTGC 61.731 66.667 0.00 0.00 0.00 4.57
795 809 0.947244 GTGCTGTCCAAGTCCAAGTG 59.053 55.000 0.00 0.00 0.00 3.16
799 813 2.280797 GCGTGCTGTCCAAGTCCA 60.281 61.111 0.00 0.00 0.00 4.02
801 815 1.287730 CTCTGCGTGCTGTCCAAGTC 61.288 60.000 0.00 0.00 0.00 3.01
802 816 1.301244 CTCTGCGTGCTGTCCAAGT 60.301 57.895 0.00 0.00 0.00 3.16
803 817 0.882042 AACTCTGCGTGCTGTCCAAG 60.882 55.000 0.00 0.00 0.00 3.61
804 818 0.391228 TAACTCTGCGTGCTGTCCAA 59.609 50.000 0.00 0.00 0.00 3.53
805 819 0.038251 CTAACTCTGCGTGCTGTCCA 60.038 55.000 0.00 0.00 0.00 4.02
806 820 0.038159 ACTAACTCTGCGTGCTGTCC 60.038 55.000 0.00 0.00 0.00 4.02
807 821 1.063806 CACTAACTCTGCGTGCTGTC 58.936 55.000 0.00 0.00 0.00 3.51
808 822 3.201342 CACTAACTCTGCGTGCTGT 57.799 52.632 0.00 0.00 0.00 4.40
811 825 1.937108 AAGAGCACTAACTCTGCGTGC 60.937 52.381 5.55 5.55 46.38 5.34
812 826 2.071688 AAGAGCACTAACTCTGCGTG 57.928 50.000 0.00 0.00 46.38 5.34
813 827 2.416162 GCTAAGAGCACTAACTCTGCGT 60.416 50.000 0.00 0.00 46.38 5.24
814 828 2.189342 GCTAAGAGCACTAACTCTGCG 58.811 52.381 0.00 0.00 46.38 5.18
821 835 7.118390 GAGACAAATCTTTGCTAAGAGCACTAA 59.882 37.037 15.63 0.00 43.14 2.24
822 836 6.591834 GAGACAAATCTTTGCTAAGAGCACTA 59.408 38.462 15.63 0.00 43.14 2.74
823 837 5.411053 GAGACAAATCTTTGCTAAGAGCACT 59.589 40.000 15.63 10.03 43.14 4.40
824 838 5.180117 TGAGACAAATCTTTGCTAAGAGCAC 59.820 40.000 15.63 6.14 43.14 4.40
831 845 5.562696 CGCCTTTTGAGACAAATCTTTGCTA 60.563 40.000 2.63 0.00 41.79 3.49
836 850 3.004734 CACCGCCTTTTGAGACAAATCTT 59.995 43.478 0.00 0.00 34.34 2.40
919 937 2.396160 ACGTCAGTCAGTCGTGTAAC 57.604 50.000 0.00 0.00 40.37 2.50
1092 1110 3.200593 CCGCTGCTCATGCTGTCC 61.201 66.667 0.00 0.00 39.81 4.02
1419 1437 2.363795 ATCAGCCGGACCGAGGAA 60.364 61.111 17.49 0.00 0.00 3.36
1755 1773 2.357034 ACCCGCTACAACACGCTG 60.357 61.111 0.00 0.00 0.00 5.18
1886 1904 2.586357 GGGACTGGAAGATCGCGC 60.586 66.667 0.00 0.00 37.43 6.86
1985 2003 5.228635 CGCACATGAGATGAAAGTAAATTGC 59.771 40.000 0.00 0.00 0.00 3.56
2008 2026 6.087555 CGGATTAACTTTTGGTGAAACATTCG 59.912 38.462 0.00 0.00 39.98 3.34
2027 2045 2.933906 GTTGAGCGTTTGGATCGGATTA 59.066 45.455 0.00 0.00 32.36 1.75
2031 2049 2.004583 TAGTTGAGCGTTTGGATCGG 57.995 50.000 0.00 0.00 32.36 4.18
2036 2054 4.466828 CTGTTCAATAGTTGAGCGTTTGG 58.533 43.478 2.85 0.00 42.91 3.28
2059 2077 6.401474 CCTCACATTCTTCTGTCACATTTACG 60.401 42.308 0.00 0.00 0.00 3.18
2066 2084 3.743396 GTCACCTCACATTCTTCTGTCAC 59.257 47.826 0.00 0.00 0.00 3.67
2094 2112 0.471591 TCCATTTGGGCAGCTGGTTT 60.472 50.000 17.12 0.00 36.21 3.27
2199 2220 2.082231 CAGATCACTTGTGAAGGCCAG 58.918 52.381 5.01 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.