Multiple sequence alignment - TraesCS7A01G182700

Loading Multiple Alignment...

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 TraesCS7A01G182700 chr7A 100.000 3149 0 0 1 3149 137801245 137798097 0.000000e+00 5816.0
1 TraesCS7A01G182700 chr7D 95.523 2725 92 15 438 3149 137790651 137787944 0.000000e+00 4329.0
2 TraesCS7A01G182700 chr7D 96.840 443 14 0 1 443 137792976 137792534 0.000000e+00 741.0
3 TraesCS7A01G182700 chr7D 89.267 382 34 3 2618 2995 137605560 137605182 3.680000e-129 472.0
4 TraesCS7A01G182700 chr7D 89.005 382 34 4 2618 2995 137716020 137715643 1.710000e-127 466.0
5 TraesCS7A01G182700 chr7D 83.158 95 9 4 563 657 5173711 5173624 2.600000e-11 80.5
6 TraesCS7A01G182700 chr7B 94.048 2369 99 22 793 3149 103080260 103077922 0.000000e+00 3555.0
7 TraesCS7A01G182700 chr7B 87.175 577 52 17 184 748 103080813 103080247 1.230000e-178 636.0
8 TraesCS7A01G182700 chr7B 88.482 382 37 4 2618 2995 102647243 102646865 3.700000e-124 455.0
9 TraesCS7A01G182700 chr7B 86.331 278 31 4 2723 2995 102805708 102805433 2.370000e-76 296.0
10 TraesCS7A01G182700 chrUn 88.482 382 36 4 2618 2995 330791215 330791592 3.700000e-124 455.0
11 TraesCS7A01G182700 chr4B 87.097 124 13 3 493 615 559158625 559158504 1.520000e-28 137.0
12 TraesCS7A01G182700 chr1B 76.923 169 26 8 489 654 470550982 470551140 2.010000e-12 84.2
13 TraesCS7A01G182700 chr1A 80.000 95 12 4 563 657 17015134 17015221 2.620000e-06 63.9


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 TraesCS7A01G182700 chr7A 137798097 137801245 3148 True 5816.0 5816 100.0000 1 3149 1 chr7A.!!$R1 3148
1 TraesCS7A01G182700 chr7D 137787944 137792976 5032 True 2535.0 4329 96.1815 1 3149 2 chr7D.!!$R4 3148
2 TraesCS7A01G182700 chr7B 103077922 103080813 2891 True 2095.5 3555 90.6115 184 3149 2 chr7B.!!$R3 2965

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
281 285 0.536460 TGGAAACTTCGGCCCACTTC 60.536 55.0 0.0 0.0 0.0 3.01 F
1612 3550 0.037232 AAGCTTGTACTCCTGTCGGC 60.037 55.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1866 3804 0.179097 GCAGACCGACCTCCTTCATC 60.179 60.0 0.0 0.0 0.0 2.92 R
2920 4866 2.091852 AAGAAGCAGCAGTGACTAGC 57.908 50.0 0.0 0.0 0.0 3.42 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
223 226 3.819337 CGGGTAGCTATAGTGCTAAGTCA 59.181 47.826 0.00 0.00 45.64 3.41
251 255 6.705825 CGACCATTTTTCCCTTTTGAGAAAAT 59.294 34.615 0.00 0.00 40.58 1.82
281 285 0.536460 TGGAAACTTCGGCCCACTTC 60.536 55.000 0.00 0.00 0.00 3.01
561 2455 9.421806 CCAGTTTTCAAAATGCACATTTATAGA 57.578 29.630 8.92 5.63 39.88 1.98
615 2513 5.550290 TGTTCACATCACATGAGTGTACAT 58.450 37.500 0.00 0.00 46.01 2.29
616 2514 6.093082 ATGTTCACATCACATGAGTGTACATG 59.907 38.462 22.40 0.00 45.85 3.21
737 2635 5.331876 TCCACAAATGTTTTCGGAGTTTT 57.668 34.783 0.00 0.00 0.00 2.43
746 2644 5.774630 TGTTTTCGGAGTTTTTGAACACTT 58.225 33.333 0.00 0.00 0.00 3.16
747 2645 6.910995 TGTTTTCGGAGTTTTTGAACACTTA 58.089 32.000 0.00 0.00 0.00 2.24
833 2732 7.498239 TGTGATTTTTGAAAATTTGGAGCATGA 59.502 29.630 0.00 0.00 38.64 3.07
893 2792 3.140814 GGCCGGCCTTTGATCCAC 61.141 66.667 38.76 7.31 0.00 4.02
894 2793 3.140814 GCCGGCCTTTGATCCACC 61.141 66.667 18.11 0.00 0.00 4.61
979 2917 2.922950 TACGTTTCCGCTGACCGCT 61.923 57.895 0.00 0.00 37.70 5.52
1030 2968 4.651008 TCCGAACGCGCGTCCTTT 62.651 61.111 37.77 21.66 35.83 3.11
1182 3120 2.031012 CTCACCCGAGCACAAGCA 59.969 61.111 0.00 0.00 45.49 3.91
1281 3219 3.782443 GTCCCCCGCTCCGACATT 61.782 66.667 0.00 0.00 0.00 2.71
1361 3299 3.255379 CCGCTTCGCCGAGCTTAC 61.255 66.667 6.90 0.00 40.52 2.34
1612 3550 0.037232 AAGCTTGTACTCCTGTCGGC 60.037 55.000 0.00 0.00 0.00 5.54
1671 3609 2.050934 GCGGGTCGAGGAGTTAGGT 61.051 63.158 0.00 0.00 0.00 3.08
1698 3636 1.740380 CGAAGCTCATGGATGTTCCGT 60.740 52.381 0.00 0.00 40.17 4.69
1724 3662 2.816958 CGCTGCACTCGCCTTCAT 60.817 61.111 0.00 0.00 37.32 2.57
1726 3664 2.789917 CTGCACTCGCCTTCATGC 59.210 61.111 0.00 0.00 37.32 4.06
1727 3665 2.032376 TGCACTCGCCTTCATGCA 59.968 55.556 0.00 0.00 45.45 3.96
1740 3678 2.254546 TCATGCACAAGGACGTTCTT 57.745 45.000 2.29 2.29 0.00 2.52
1765 3703 9.566432 TTGCCAGGAAAATACAATTTTTACATT 57.434 25.926 0.00 0.00 32.76 2.71
1866 3804 1.998315 CAGCGATCTGTGGAGTTCTTG 59.002 52.381 0.00 0.00 35.61 3.02
1875 3813 4.020751 TCTGTGGAGTTCTTGATGAAGGAG 60.021 45.833 0.00 0.00 35.01 3.69
2205 4143 7.996098 TTTTGAGATTATCCGAGGAGTTTTT 57.004 32.000 0.00 0.00 0.00 1.94
2393 4331 7.667043 TTTACTCATTAATTGCTCGTTCTGT 57.333 32.000 0.00 0.00 0.00 3.41
2668 4610 5.150683 TCCGATTGCTACAAAAACAATTCG 58.849 37.500 0.00 0.00 34.28 3.34
2669 4611 4.915085 CCGATTGCTACAAAAACAATTCGT 59.085 37.500 0.00 0.00 34.28 3.85
2670 4612 5.164196 CCGATTGCTACAAAAACAATTCGTG 60.164 40.000 0.00 0.00 34.28 4.35
2671 4613 5.398122 CGATTGCTACAAAAACAATTCGTGT 59.602 36.000 0.00 0.00 44.64 4.49
2820 4762 7.391148 TCAAGGTTATGCTTTAGTTGGAATC 57.609 36.000 0.00 0.00 0.00 2.52
2831 4773 8.908903 TGCTTTAGTTGGAATCTTCTTTTACAA 58.091 29.630 0.00 0.00 0.00 2.41
2887 4833 5.984926 CCTCTTTTCTCTCATCTGCTCATAC 59.015 44.000 0.00 0.00 0.00 2.39
2920 4866 4.556233 TCGACTGAAGTTTACATCACTGG 58.444 43.478 0.00 0.00 0.00 4.00
3036 4982 2.134789 AGGCTTGACTAATGGGCTTG 57.865 50.000 0.00 0.00 0.00 4.01
3068 5014 3.367910 GCAAGAGTCACTACAGAGAAGGG 60.368 52.174 0.00 0.00 0.00 3.95
3118 5064 2.561478 TGGTGTTCTAAGGAGCAACC 57.439 50.000 0.00 0.00 39.21 3.77
3122 5068 3.634910 GGTGTTCTAAGGAGCAACCAAAA 59.365 43.478 2.96 0.00 42.04 2.44
3138 5084 5.823861 ACCAAAATTTCCTGCCTGTTTAT 57.176 34.783 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 8.125728 TCAAAGCTAAAACAATTTTGTAGTGC 57.874 30.769 0.00 0.57 41.31 4.40
91 92 3.366396 TGGTTGCCAACTAAAGAACCAA 58.634 40.909 7.62 0.00 42.37 3.67
223 226 3.707102 TCAAAAGGGAAAAATGGTCGGTT 59.293 39.130 0.00 0.00 0.00 4.44
251 255 4.499019 GCCGAAGTTTCCACAGAAATTGAA 60.499 41.667 0.00 0.00 43.67 2.69
259 263 1.228124 TGGGCCGAAGTTTCCACAG 60.228 57.895 0.00 0.00 0.00 3.66
298 302 7.148289 CCACATGATCTTGTAATGATGCCTATC 60.148 40.741 13.40 0.00 29.94 2.08
397 402 9.083422 CTCAATATTCATGAGGGTAGAAGTAGA 57.917 37.037 0.00 0.00 40.48 2.59
570 2468 8.776376 AACATCCACAATTGTTTTATGGAATC 57.224 30.769 16.17 0.00 42.57 2.52
1030 2968 1.532728 GGTAGCGGAGGAGGAGAGA 59.467 63.158 0.00 0.00 0.00 3.10
1182 3120 2.381445 CCTTCTGGAGGCCTTGAGT 58.619 57.895 6.77 0.00 39.09 3.41
1245 3183 2.671619 CCGCGGCCCAAGAGAAAA 60.672 61.111 14.67 0.00 0.00 2.29
1612 3550 1.333619 CTTGGGTTTCACGGTGAACAG 59.666 52.381 22.33 10.07 35.89 3.16
1671 3609 2.036571 CCATGAGCTTCGCTGCACA 61.037 57.895 0.00 2.81 39.88 4.57
1724 3662 1.444119 GGCAAGAACGTCCTTGTGCA 61.444 55.000 16.30 0.00 43.96 4.57
1726 3664 0.588252 CTGGCAAGAACGTCCTTGTG 59.412 55.000 16.30 3.46 43.96 3.33
1727 3665 0.535102 CCTGGCAAGAACGTCCTTGT 60.535 55.000 16.30 0.00 43.96 3.16
1740 3678 9.213799 GAATGTAAAAATTGTATTTTCCTGGCA 57.786 29.630 0.00 0.00 34.51 4.92
1765 3703 1.228124 CCTGTGAAAACCCCAGCGA 60.228 57.895 0.00 0.00 0.00 4.93
1859 3797 2.234908 CCGACCTCCTTCATCAAGAACT 59.765 50.000 0.00 0.00 31.61 3.01
1866 3804 0.179097 GCAGACCGACCTCCTTCATC 60.179 60.000 0.00 0.00 0.00 2.92
1875 3813 2.435059 GAAGCCTGCAGACCGACC 60.435 66.667 17.39 0.00 0.00 4.79
2114 4052 2.397044 TCCTTTTGGTGCTTTCCCAT 57.603 45.000 0.00 0.00 41.38 4.00
2205 4143 2.435372 AAACTCAGTCTTGTGGCCAA 57.565 45.000 7.24 0.00 0.00 4.52
2207 4145 2.687935 TCAAAAACTCAGTCTTGTGGCC 59.312 45.455 0.00 0.00 0.00 5.36
2347 4285 9.083080 GTAAAAACTAAAGTTGCACAACAATCT 57.917 29.630 15.40 0.23 43.47 2.40
2393 4331 8.786898 CAATGAACTTTGATTTCTTAGTCTCCA 58.213 33.333 0.00 0.00 0.00 3.86
2696 4638 7.278424 CCACATATCCAAAATTTGAACATGGAC 59.722 37.037 10.09 0.00 42.57 4.02
2820 4762 5.009210 TCCGGTGACCATTTTGTAAAAGAAG 59.991 40.000 1.11 0.00 0.00 2.85
2831 4773 3.008594 TGTCAATACTCCGGTGACCATTT 59.991 43.478 16.87 0.00 40.79 2.32
2833 4775 2.168521 CTGTCAATACTCCGGTGACCAT 59.831 50.000 16.87 2.78 40.79 3.55
2887 4833 6.927933 AAACTTCAGTCGAAACAAAAACAG 57.072 33.333 0.00 0.00 0.00 3.16
2920 4866 2.091852 AAGAAGCAGCAGTGACTAGC 57.908 50.000 0.00 0.00 0.00 3.42
3036 4982 4.993029 AGTGACTCTTGCCACTATCTAC 57.007 45.455 0.00 0.00 41.38 2.59
3096 5042 4.042311 TGGTTGCTCCTTAGAACACCAATA 59.958 41.667 0.00 0.00 37.07 1.90
3118 5064 6.930722 AGTTCATAAACAGGCAGGAAATTTTG 59.069 34.615 0.00 0.00 37.88 2.44
3122 5068 7.961326 ATTAGTTCATAAACAGGCAGGAAAT 57.039 32.000 0.00 0.00 37.88 2.17


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

AutoCloner maintained by Alex Coulton.