Multiple sequence alignment - TraesCS3D01G216100

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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 TraesCS3D01G216100 chr3D 100.000 2635 0 0 1 2635 292372948 292375582 0.000000e+00 4867
1 TraesCS3D01G216100 chr3A 96.205 1713 45 8 1 1710 385525403 385523708 0.000000e+00 2785
2 TraesCS3D01G216100 chr3A 88.020 793 83 8 1846 2635 385522489 385521706 0.000000e+00 928
3 TraesCS3D01G216100 chr3A 76.695 236 43 9 1860 2089 509854115 509854344 1.280000e-23 121
4 TraesCS3D01G216100 chr3B 92.650 1347 53 18 815 2127 386375765 386374431 0.000000e+00 1897
5 TraesCS3D01G216100 chr3B 95.818 813 30 2 1 812 386376814 386376005 0.000000e+00 1310
6 TraesCS3D01G216100 chr3B 93.190 558 35 3 2079 2635 386374420 386373865 0.000000e+00 817
7 TraesCS3D01G216100 chr3B 81.959 194 22 11 1862 2048 71324527 71324714 4.540000e-33 152
8 TraesCS3D01G216100 chr3B 78.037 214 31 11 1860 2065 257036430 257036225 1.280000e-23 121
9 TraesCS3D01G216100 chr2D 79.079 239 32 16 1860 2089 440185588 440185359 5.880000e-32 148
10 TraesCS3D01G216100 chr6D 79.048 210 34 7 1860 2065 9373259 9373056 4.570000e-28 135
11 TraesCS3D01G216100 chr2B 77.619 210 37 8 1860 2064 231655752 231655548 4.610000e-23 119
12 TraesCS3D01G216100 chr2A 75.610 246 44 11 1855 2093 86378858 86378622 9.970000e-20 108


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 TraesCS3D01G216100 chr3D 292372948 292375582 2634 False 4867.000000 4867 100.0000 1 2635 1 chr3D.!!$F1 2634
1 TraesCS3D01G216100 chr3A 385521706 385525403 3697 True 1856.500000 2785 92.1125 1 2635 2 chr3A.!!$R1 2634
2 TraesCS3D01G216100 chr3B 386373865 386376814 2949 True 1341.333333 1897 93.8860 1 2635 3 chr3B.!!$R2 2634

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
569 570 0.597637 AGACGTGAGCGGTTGTTGAG 60.598 55.0 0.0 0.0 43.45 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 3271 0.308068 CGCGTCTCCATAGTCGACAT 59.692 55.0 19.5 6.5 36.54 3.06 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
24 25 4.037803 TCTTCTCTGCTCTGCATACTCATC 59.962 45.833 0.00 0.00 38.13 2.92
159 160 6.279882 TGTTCTGGCATTTTTGGTTCTTAAG 58.720 36.000 0.00 0.00 0.00 1.85
175 176 9.362151 TGGTTCTTAAGTTTCCAAGATAAATGT 57.638 29.630 1.63 0.00 31.15 2.71
226 227 3.307762 CGAGATGTTCCCCCTTTTCTCTT 60.308 47.826 0.00 0.00 0.00 2.85
256 257 1.117142 TTACCCTTCTATCCCCCGCG 61.117 60.000 0.00 0.00 0.00 6.46
569 570 0.597637 AGACGTGAGCGGTTGTTGAG 60.598 55.000 0.00 0.00 43.45 3.02
646 647 9.946165 GCTTTTAGTACATTTTGTTAGTGACTT 57.054 29.630 0.00 0.00 0.00 3.01
762 764 4.599041 TCTTTTGGAGTATGTGGGAATGG 58.401 43.478 0.00 0.00 0.00 3.16
875 1114 0.663153 GTTGCCTCAGTCACAACCAC 59.337 55.000 0.00 0.00 38.15 4.16
888 1127 3.449377 TCACAACCACAGTCACTCAACTA 59.551 43.478 0.00 0.00 0.00 2.24
889 1128 4.081365 TCACAACCACAGTCACTCAACTAA 60.081 41.667 0.00 0.00 0.00 2.24
943 1182 2.290323 ACCAGCGACTTTGCTAAGGATT 60.290 45.455 12.54 0.00 45.23 3.01
970 1210 4.223032 TCTCTAGGTTGGTGGTTGATCTTC 59.777 45.833 0.00 0.00 0.00 2.87
971 1211 4.168101 TCTAGGTTGGTGGTTGATCTTCT 58.832 43.478 0.00 0.00 0.00 2.85
972 1212 3.884037 AGGTTGGTGGTTGATCTTCTT 57.116 42.857 0.00 0.00 0.00 2.52
986 1226 8.030106 GGTTGATCTTCTTCGTATCCCTAATAG 58.970 40.741 0.00 0.00 0.00 1.73
1562 1820 1.901464 GGTGACCGTGGTTGGCAAT 60.901 57.895 1.92 0.00 0.00 3.56
1711 1969 4.632153 GATGAGCGCTATCCCTCTTTTTA 58.368 43.478 11.50 0.00 0.00 1.52
1786 2078 3.842925 TTTCAGGAGCCACCCGTGC 62.843 63.158 0.00 0.00 40.05 5.34
1854 3195 0.404040 TTGTGGTGGAATCAGGGTCC 59.596 55.000 0.00 0.00 35.55 4.46
1902 3244 2.743636 TTCAGACTTCCGGTGATGTC 57.256 50.000 0.00 6.09 42.87 3.06
1926 3268 1.005332 TCAGTGGGAGAGAGGAGACAG 59.995 57.143 0.00 0.00 0.00 3.51
1929 3271 2.650322 AGTGGGAGAGAGGAGACAGTTA 59.350 50.000 0.00 0.00 0.00 2.24
1952 3294 1.138883 GACTATGGAGACGCGTGCA 59.861 57.895 20.70 4.46 0.00 4.57
1991 3333 5.185454 TCAAGATGATGTGTCGGCTTTATT 58.815 37.500 0.00 0.00 0.00 1.40
1996 3338 3.616821 TGATGTGTCGGCTTTATTTCTCG 59.383 43.478 0.00 0.00 0.00 4.04
1999 3341 4.059511 TGTGTCGGCTTTATTTCTCGAAA 58.940 39.130 0.00 0.00 34.46 3.46
2049 3391 1.728971 GCGCATAGGATGAGTGTATGC 59.271 52.381 0.30 3.90 43.71 3.14
2128 3471 1.207089 CGTCTTAGGGCATCTCCAACA 59.793 52.381 0.00 0.00 36.21 3.33
2129 3472 2.158900 CGTCTTAGGGCATCTCCAACAT 60.159 50.000 0.00 0.00 36.21 2.71
2143 3544 0.378257 CAACATTGGCCCTCGAATCG 59.622 55.000 0.00 0.00 0.00 3.34
2152 3553 3.026879 CTCGAATCGCGCGCATCT 61.027 61.111 32.61 14.20 40.61 2.90
2237 3639 4.783667 CGGAGGTTCGTTTTCCCA 57.216 55.556 0.00 0.00 0.00 4.37
2291 3693 4.429522 TGGACCGCTGCCATGCAT 62.430 61.111 0.00 0.00 38.13 3.96
2337 3739 4.756642 GTCGATCCCAATCATGATAGCAAA 59.243 41.667 9.04 0.00 31.76 3.68
2338 3740 5.413833 GTCGATCCCAATCATGATAGCAAAT 59.586 40.000 9.04 0.00 31.76 2.32
2368 3770 4.657824 CGGGTCGCACACCTCGTT 62.658 66.667 1.95 0.00 45.95 3.85
2454 3856 3.814283 GTCGAAGTACTCCGTGGAGATAT 59.186 47.826 22.36 2.90 44.53 1.63
2468 3870 3.564644 TGGAGATATCGACGACTTCCTTC 59.435 47.826 0.00 0.00 0.00 3.46
2482 3884 3.194116 ACTTCCTTCGACTTTACGCCATA 59.806 43.478 0.00 0.00 0.00 2.74
2486 3888 5.904941 TCCTTCGACTTTACGCCATAATAA 58.095 37.500 0.00 0.00 0.00 1.40
2558 3960 7.039853 GCTCCTATATTTACTCCCTACGTTTCT 60.040 40.741 0.00 0.00 0.00 2.52
2573 3975 3.042887 CGTTTCTGCTTGTTTGGCTAAC 58.957 45.455 4.82 4.82 37.26 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.559831 TAAGATGAGCGCATGTCACG 58.440 50.000 11.47 0.00 34.11 4.35
175 176 6.019779 ACGGTGCTTTGCTCAATTAAAATA 57.980 33.333 0.00 0.00 0.00 1.40
183 184 0.465460 AGGAACGGTGCTTTGCTCAA 60.465 50.000 0.00 0.00 0.00 3.02
191 192 1.682684 ATCTCGGAGGAACGGTGCT 60.683 57.895 0.00 0.00 0.00 4.40
226 227 6.296836 GGGATAGAAGGGTAAAGGAGAAAACA 60.297 42.308 0.00 0.00 0.00 2.83
256 257 6.882610 TTACATGATTGGGAGATAATGCAC 57.117 37.500 0.00 0.00 0.00 4.57
569 570 6.825721 ACACAGATCATTATTCAAACCTCTCC 59.174 38.462 0.00 0.00 0.00 3.71
610 611 4.367039 TGTACTAAAAGCCCTTCTTGCT 57.633 40.909 0.00 0.00 41.89 3.91
663 664 9.914834 GGATAGATAGATAGGTACATCAGAGTT 57.085 37.037 0.00 0.00 0.00 3.01
665 666 9.778741 GAGGATAGATAGATAGGTACATCAGAG 57.221 40.741 0.00 0.00 0.00 3.35
762 764 4.990426 CACAAAATTGACAAATCTCACCCC 59.010 41.667 0.00 0.00 0.00 4.95
860 1099 1.138859 TGACTGTGGTTGTGACTGAGG 59.861 52.381 0.00 0.00 0.00 3.86
875 1114 3.238108 AGGCGATTAGTTGAGTGACTG 57.762 47.619 0.00 0.00 0.00 3.51
888 1127 4.569564 GTCCAACTAAACGATTAGGCGATT 59.430 41.667 15.81 0.00 42.39 3.34
889 1128 4.117685 GTCCAACTAAACGATTAGGCGAT 58.882 43.478 15.81 0.00 42.39 4.58
943 1182 5.118729 TCAACCACCAACCTAGAGAAAAA 57.881 39.130 0.00 0.00 0.00 1.94
970 1210 7.331193 GCAACCAATACTATTAGGGATACGAAG 59.669 40.741 0.00 0.00 37.60 3.79
971 1211 7.156673 GCAACCAATACTATTAGGGATACGAA 58.843 38.462 0.00 0.00 37.60 3.85
972 1212 6.295462 GGCAACCAATACTATTAGGGATACGA 60.295 42.308 0.00 0.00 37.60 3.43
1014 1254 8.579863 TGAATGTCACTCACATATATAGAGGTG 58.420 37.037 5.82 5.82 45.77 4.00
1288 1545 3.001330 CACATCTCGAGGTAAATTTCCGC 59.999 47.826 13.56 0.00 0.00 5.54
1289 1546 3.555956 CCACATCTCGAGGTAAATTTCCG 59.444 47.826 13.56 0.00 0.00 4.30
1290 1547 3.312697 GCCACATCTCGAGGTAAATTTCC 59.687 47.826 13.56 0.00 0.00 3.13
1291 1548 3.312697 GGCCACATCTCGAGGTAAATTTC 59.687 47.826 13.56 0.00 0.00 2.17
1292 1549 3.279434 GGCCACATCTCGAGGTAAATTT 58.721 45.455 13.56 0.00 0.00 1.82
1293 1550 2.741878 CGGCCACATCTCGAGGTAAATT 60.742 50.000 13.56 0.00 0.00 1.82
1562 1820 1.074775 GACTTGCATGGGGGTCACA 59.925 57.895 4.44 0.00 0.00 3.58
1667 1925 4.732923 TCGTTTTCATCAAAGAAAAGTGCG 59.267 37.500 2.43 3.95 45.21 5.34
1711 1969 3.265791 CAGATTGAGCGCTAAAAGGAGT 58.734 45.455 11.50 0.00 0.00 3.85
1786 2078 4.748144 GTTGCCAGGAGCCCAGGG 62.748 72.222 0.00 0.00 42.71 4.45
1854 3195 2.216940 CAGAAAAATGCAAGCACACGTG 59.783 45.455 15.48 15.48 0.00 4.49
1857 3198 5.662211 AATTCAGAAAAATGCAAGCACAC 57.338 34.783 0.00 0.00 0.00 3.82
1902 3244 1.824230 CTCCTCTCTCCCACTGAACAG 59.176 57.143 0.00 0.00 0.00 3.16
1926 3268 3.298317 GCGTCTCCATAGTCGACATAAC 58.702 50.000 19.50 4.92 36.54 1.89
1929 3271 0.308068 CGCGTCTCCATAGTCGACAT 59.692 55.000 19.50 6.50 36.54 3.06
1991 3333 2.168521 CCCCTATGAGCACTTTCGAGAA 59.831 50.000 0.00 0.00 0.00 2.87
1996 3338 2.104963 CCCTACCCCTATGAGCACTTTC 59.895 54.545 0.00 0.00 0.00 2.62
1999 3341 0.764752 GCCCTACCCCTATGAGCACT 60.765 60.000 0.00 0.00 0.00 4.40
2049 3391 5.425577 ACATAGGCGCTCATATATACGAG 57.574 43.478 7.64 1.36 0.00 4.18
2128 3471 2.588877 CGCGATTCGAGGGCCAAT 60.589 61.111 10.88 0.00 41.67 3.16
2143 3544 3.558411 GTCCAGACAGATGCGCGC 61.558 66.667 27.26 27.26 0.00 6.86
2174 3575 1.269174 CCGTGTTGGATGTCAAATGCA 59.731 47.619 0.00 0.00 42.00 3.96
2227 3629 2.294074 CTCTGGTTTGTGGGAAAACGA 58.706 47.619 0.00 0.00 40.29 3.85
2237 3639 1.035139 CTGCTTTGCCTCTGGTTTGT 58.965 50.000 0.00 0.00 0.00 2.83
2291 3693 1.440938 CCGTCCGAGTTTTTGGTGCA 61.441 55.000 0.00 0.00 0.00 4.57
2294 3696 0.533531 GTCCCGTCCGAGTTTTTGGT 60.534 55.000 0.00 0.00 0.00 3.67
2317 3719 7.114754 TCCTATTTGCTATCATGATTGGGATC 58.885 38.462 14.65 0.00 0.00 3.36
2468 3870 5.591643 ATGCTTATTATGGCGTAAAGTCG 57.408 39.130 2.82 0.00 0.00 4.18
2482 3884 5.477984 ACACAAGTGGACATCAATGCTTATT 59.522 36.000 5.08 0.00 34.19 1.40
2486 3888 2.816087 GACACAAGTGGACATCAATGCT 59.184 45.455 5.08 0.00 34.19 3.79
2558 3960 1.103987 TGCCGTTAGCCAAACAAGCA 61.104 50.000 9.08 9.08 41.95 3.91


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

AutoCloner maintained by Alex Coulton.