Multiple sequence alignment - TraesCS7B01G169300

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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 TraesCS7B01G169300 chr7B 100.000 3062 0 0 1 3062 240024000 240020939 0.000000e+00 5655.0
1 TraesCS7B01G169300 chr7B 82.474 97 15 2 1424 1519 626183465 626183370 1.960000e-12 84.2
2 TraesCS7B01G169300 chr7D 95.634 1397 41 5 900 2277 260726060 260724665 0.000000e+00 2224.0
3 TraesCS7B01G169300 chr7D 94.613 724 25 6 184 903 260729427 260728714 0.000000e+00 1109.0
4 TraesCS7B01G169300 chr7D 94.530 457 23 2 2608 3062 260023569 260023113 0.000000e+00 704.0
5 TraesCS7B01G169300 chr7D 92.754 345 20 4 2276 2616 260024275 260023932 7.630000e-136 494.0
6 TraesCS7B01G169300 chr7D 85.135 74 9 2 1424 1496 570653193 570653121 1.180000e-09 75.0
7 TraesCS7B01G169300 chr7A 96.664 1289 42 1 990 2278 284112728 284111441 0.000000e+00 2141.0
8 TraesCS7B01G169300 chr7A 88.256 860 47 20 7 842 284114221 284113392 0.000000e+00 979.0
9 TraesCS7B01G169300 chr7A 92.732 399 25 4 2667 3062 283155301 283154904 9.520000e-160 573.0
10 TraesCS7B01G169300 chr7A 90.751 346 20 5 2276 2616 283155649 283155311 4.660000e-123 451.0
11 TraesCS7B01G169300 chr7A 89.933 149 15 0 841 989 284113077 284112929 3.120000e-45 193.0
12 TraesCS7B01G169300 chr3A 77.256 277 49 10 2593 2865 699747971 699748237 1.900000e-32 150.0
13 TraesCS7B01G169300 chr4D 81.065 169 26 5 1331 1496 379574580 379574745 2.480000e-26 130.0
14 TraesCS7B01G169300 chr4A 80.114 176 29 5 1331 1503 84897364 84897192 3.210000e-25 126.0
15 TraesCS7B01G169300 chr1D 81.529 157 25 4 2569 2722 427180321 427180166 3.210000e-25 126.0
16 TraesCS7B01G169300 chr3D 83.969 131 13 6 2723 2851 280997539 280997663 5.360000e-23 119.0
17 TraesCS7B01G169300 chr4B 78.916 166 29 5 1331 1493 466786733 466786895 1.160000e-19 108.0
18 TraesCS7B01G169300 chr4B 79.661 118 21 3 2753 2868 659384899 659384783 7.040000e-12 82.4
19 TraesCS7B01G169300 chr4B 79.661 118 21 3 2753 2868 659400195 659400079 7.040000e-12 82.4
20 TraesCS7B01G169300 chr1B 84.058 69 9 2 2790 2856 198640291 198640223 7.090000e-07 65.8


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 TraesCS7B01G169300 chr7B 240020939 240024000 3061 True 5655.000000 5655 100.000000 1 3062 1 chr7B.!!$R1 3061
1 TraesCS7B01G169300 chr7D 260724665 260729427 4762 True 1666.500000 2224 95.123500 184 2277 2 chr7D.!!$R3 2093
2 TraesCS7B01G169300 chr7D 260023113 260024275 1162 True 599.000000 704 93.642000 2276 3062 2 chr7D.!!$R2 786
3 TraesCS7B01G169300 chr7A 284111441 284114221 2780 True 1104.333333 2141 91.617667 7 2278 3 chr7A.!!$R2 2271
4 TraesCS7B01G169300 chr7A 283154904 283155649 745 True 512.000000 573 91.741500 2276 3062 2 chr7A.!!$R1 786

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
113 114 0.105142 GGTGAGCCCTACCTATCCCA 60.105 60.0 0.0 0.0 35.3 4.37 F
532 559 0.165295 TTGTCGCTCGTACAGTCTCG 59.835 55.0 0.0 0.0 0.0 4.04 F
1006 4214 0.934901 CACTATCCGTCGCATGTCCG 60.935 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1258 4466 1.045407 TACGTGCCAAGAGAGGTGTT 58.955 50.000 0.0 0.0 0.0 3.32 R
1997 5205 1.118838 CATCTCCTCGGCCTTCTCTT 58.881 55.000 0.0 0.0 0.0 2.85 R
2206 5433 1.212935 AGGCCCAAGTGTGATCCATAC 59.787 52.381 0.0 0.0 0.0 2.39 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
36 37 1.354031 TGCTCCAACCTATTCAGCCAA 59.646 47.619 0.00 0.00 0.00 4.52
80 81 2.534042 TGGGAAAGTGTTTGGTTGGA 57.466 45.000 0.00 0.00 0.00 3.53
81 82 3.039252 TGGGAAAGTGTTTGGTTGGAT 57.961 42.857 0.00 0.00 0.00 3.41
82 83 4.186077 TGGGAAAGTGTTTGGTTGGATA 57.814 40.909 0.00 0.00 0.00 2.59
113 114 0.105142 GGTGAGCCCTACCTATCCCA 60.105 60.000 0.00 0.00 35.30 4.37
114 115 1.485210 GGTGAGCCCTACCTATCCCAT 60.485 57.143 0.00 0.00 35.30 4.00
115 116 1.903183 GTGAGCCCTACCTATCCCATC 59.097 57.143 0.00 0.00 0.00 3.51
116 117 1.203313 TGAGCCCTACCTATCCCATCC 60.203 57.143 0.00 0.00 0.00 3.51
117 118 1.079658 GAGCCCTACCTATCCCATCCT 59.920 57.143 0.00 0.00 0.00 3.24
118 119 1.514442 AGCCCTACCTATCCCATCCTT 59.486 52.381 0.00 0.00 0.00 3.36
119 120 1.909986 GCCCTACCTATCCCATCCTTC 59.090 57.143 0.00 0.00 0.00 3.46
120 121 2.552367 CCCTACCTATCCCATCCTTCC 58.448 57.143 0.00 0.00 0.00 3.46
121 122 2.552367 CCTACCTATCCCATCCTTCCC 58.448 57.143 0.00 0.00 0.00 3.97
122 123 2.158004 CCTACCTATCCCATCCTTCCCA 60.158 54.545 0.00 0.00 0.00 4.37
123 124 2.843909 ACCTATCCCATCCTTCCCAT 57.156 50.000 0.00 0.00 0.00 4.00
124 125 3.095299 ACCTATCCCATCCTTCCCATT 57.905 47.619 0.00 0.00 0.00 3.16
125 126 3.417010 ACCTATCCCATCCTTCCCATTT 58.583 45.455 0.00 0.00 0.00 2.32
126 127 3.399305 ACCTATCCCATCCTTCCCATTTC 59.601 47.826 0.00 0.00 0.00 2.17
127 128 3.398967 CCTATCCCATCCTTCCCATTTCA 59.601 47.826 0.00 0.00 0.00 2.69
132 133 3.385755 CCCATCCTTCCCATTTCACATTC 59.614 47.826 0.00 0.00 0.00 2.67
134 135 4.098960 CCATCCTTCCCATTTCACATTCAG 59.901 45.833 0.00 0.00 0.00 3.02
169 170 1.244816 GGGGGCTATATTTGGAACGC 58.755 55.000 0.00 0.00 0.00 4.84
170 171 1.477923 GGGGGCTATATTTGGAACGCA 60.478 52.381 0.00 0.00 0.00 5.24
171 172 1.880027 GGGGCTATATTTGGAACGCAG 59.120 52.381 0.00 0.00 0.00 5.18
172 173 2.486548 GGGGCTATATTTGGAACGCAGA 60.487 50.000 0.00 0.00 0.00 4.26
173 174 2.808543 GGGCTATATTTGGAACGCAGAG 59.191 50.000 0.00 0.00 0.00 3.35
175 176 3.495001 GGCTATATTTGGAACGCAGAGTC 59.505 47.826 0.00 0.00 0.00 3.36
176 177 4.119862 GCTATATTTGGAACGCAGAGTCA 58.880 43.478 0.00 0.00 0.00 3.41
179 195 3.904136 ATTTGGAACGCAGAGTCAAAG 57.096 42.857 0.00 0.00 0.00 2.77
182 198 0.884704 GGAACGCAGAGTCAAAGCCA 60.885 55.000 0.00 0.00 0.00 4.75
191 207 1.408702 GAGTCAAAGCCAAAACAGCCA 59.591 47.619 0.00 0.00 0.00 4.75
195 211 3.027412 TCAAAGCCAAAACAGCCACTAA 58.973 40.909 0.00 0.00 0.00 2.24
211 227 4.622220 GCCACTAATAAACCTGGACGAAGA 60.622 45.833 0.00 0.00 0.00 2.87
532 559 0.165295 TTGTCGCTCGTACAGTCTCG 59.835 55.000 0.00 0.00 0.00 4.04
540 567 1.400846 TCGTACAGTCTCGAGGCAATC 59.599 52.381 20.97 5.69 0.00 2.67
700 727 2.499732 CACCTTCGCGCGCTTTTC 60.500 61.111 30.48 0.00 0.00 2.29
740 767 1.859080 GCGAGTTTATTAGACCCTGCG 59.141 52.381 0.00 0.00 0.00 5.18
908 3916 4.176271 GGCTCCATTGCACATTAAAAGAC 58.824 43.478 0.00 0.00 34.04 3.01
933 3941 1.601419 ATGCACTGATGGTTGCTGCC 61.601 55.000 0.00 0.00 0.00 4.85
1006 4214 0.934901 CACTATCCGTCGCATGTCCG 60.935 60.000 0.00 0.00 0.00 4.79
1103 4311 4.147322 CATGGTCGCGGACGTTGC 62.147 66.667 6.13 3.84 41.18 4.17
1293 4501 1.884579 ACGTACATCCGGCTATACCTG 59.115 52.381 0.00 0.00 35.61 4.00
1390 4598 1.669440 GACACCGCCTTCTACCACA 59.331 57.895 0.00 0.00 0.00 4.17
1650 4858 2.522923 ATCGATCTGAGCCCCGCT 60.523 61.111 0.00 0.00 43.88 5.52
2050 5258 1.273455 CGATTTCGTATCCGCCGACC 61.273 60.000 0.00 0.00 33.41 4.79
2052 5267 4.557605 TTCGTATCCGCCGACCGC 62.558 66.667 0.00 0.00 33.41 5.68
2104 5331 1.625511 GATGGGAGGCCATCAATTCC 58.374 55.000 5.01 0.65 44.13 3.01
2127 5354 2.097304 GCATGTGACTGTGTGTTGTGAA 59.903 45.455 0.00 0.00 0.00 3.18
2206 5433 8.960591 AGTCTTTCCTATAAATTGGTTGATGTG 58.039 33.333 0.00 0.00 0.00 3.21
2366 5593 1.301479 GTTCGGTCTCGGGCTGTTT 60.301 57.895 0.00 0.00 36.95 2.83
2372 5599 0.739813 GTCTCGGGCTGTTTATGCGT 60.740 55.000 0.00 0.00 0.00 5.24
2479 5709 0.890683 ACCTTAATGCCAGTTGCTGC 59.109 50.000 0.00 0.00 42.00 5.25
2501 5732 0.461961 CCAGGGGCGTTTTTGACAAA 59.538 50.000 0.00 0.00 0.00 2.83
2609 5841 7.855904 AGTTACGAAATCAAACAAATGTCACTC 59.144 33.333 0.00 0.00 0.00 3.51
2616 5848 5.328691 TCAAACAAATGTCACTCGTTCAAC 58.671 37.500 0.00 0.00 0.00 3.18
2617 5849 5.123186 TCAAACAAATGTCACTCGTTCAACT 59.877 36.000 0.00 0.00 0.00 3.16
2637 6240 3.898123 ACTGCATCTATCCAACGGTCTAT 59.102 43.478 0.00 0.00 0.00 1.98
2645 6248 6.124340 TCTATCCAACGGTCTATGTAACTCA 58.876 40.000 0.00 0.00 0.00 3.41
2655 6258 7.122353 ACGGTCTATGTAACTCAGATGTTTAGT 59.878 37.037 0.00 0.00 0.00 2.24
2656 6259 8.618677 CGGTCTATGTAACTCAGATGTTTAGTA 58.381 37.037 0.00 0.00 0.00 1.82
2693 6296 7.005062 AGCACTAAATAATTTAGCACTGTCG 57.995 36.000 0.00 0.00 45.05 4.35
2735 6338 9.472995 GCATAATATCAACGTCAATATTAACCG 57.527 33.333 18.76 13.86 35.22 4.44
2902 6505 5.073691 AGAGGGGCATATTTAAGCACACTAT 59.926 40.000 0.00 0.00 35.37 2.12
2923 6526 9.996554 CACTATAGAATTATGGGTACATGTGAA 57.003 33.333 9.11 0.00 37.97 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.424956 GGAGCATCAATCCAAACAGTCC 59.575 50.000 0.00 0.00 36.79 3.85
1 2 3.084039 TGGAGCATCAATCCAAACAGTC 58.916 45.455 0.00 0.00 43.87 3.51
2 3 3.159213 TGGAGCATCAATCCAAACAGT 57.841 42.857 0.00 0.00 43.87 3.55
44 45 1.457346 CCATGAACTCACTCAAGGCC 58.543 55.000 0.00 0.00 28.16 5.19
47 48 4.214971 CACTTTCCCATGAACTCACTCAAG 59.785 45.833 0.00 0.00 0.00 3.02
49 50 3.136443 ACACTTTCCCATGAACTCACTCA 59.864 43.478 0.00 0.00 0.00 3.41
96 97 1.203313 GGATGGGATAGGTAGGGCTCA 60.203 57.143 0.00 0.00 0.00 4.26
104 105 2.843909 ATGGGAAGGATGGGATAGGT 57.156 50.000 0.00 0.00 0.00 3.08
113 114 4.284178 CCTGAATGTGAAATGGGAAGGAT 58.716 43.478 0.00 0.00 0.00 3.24
114 115 3.700538 CCTGAATGTGAAATGGGAAGGA 58.299 45.455 0.00 0.00 0.00 3.36
115 116 2.167075 GCCTGAATGTGAAATGGGAAGG 59.833 50.000 0.00 0.00 0.00 3.46
116 117 2.167075 GGCCTGAATGTGAAATGGGAAG 59.833 50.000 0.00 0.00 0.00 3.46
117 118 2.178580 GGCCTGAATGTGAAATGGGAA 58.821 47.619 0.00 0.00 0.00 3.97
118 119 1.076841 TGGCCTGAATGTGAAATGGGA 59.923 47.619 3.32 0.00 0.00 4.37
119 120 1.559368 TGGCCTGAATGTGAAATGGG 58.441 50.000 3.32 0.00 0.00 4.00
120 121 2.671914 CGTTGGCCTGAATGTGAAATGG 60.672 50.000 3.32 0.00 0.00 3.16
121 122 2.598589 CGTTGGCCTGAATGTGAAATG 58.401 47.619 3.32 0.00 0.00 2.32
122 123 1.545582 CCGTTGGCCTGAATGTGAAAT 59.454 47.619 3.32 0.00 0.00 2.17
123 124 0.958091 CCGTTGGCCTGAATGTGAAA 59.042 50.000 3.32 0.00 0.00 2.69
124 125 0.109532 TCCGTTGGCCTGAATGTGAA 59.890 50.000 3.32 0.00 0.00 3.18
125 126 0.327924 ATCCGTTGGCCTGAATGTGA 59.672 50.000 3.32 0.00 0.00 3.58
126 127 0.452987 CATCCGTTGGCCTGAATGTG 59.547 55.000 3.32 0.00 0.00 3.21
127 128 0.680921 CCATCCGTTGGCCTGAATGT 60.681 55.000 3.32 0.00 39.09 2.71
151 152 1.880027 CTGCGTTCCAAATATAGCCCC 59.120 52.381 0.00 0.00 0.00 5.80
152 153 2.808543 CTCTGCGTTCCAAATATAGCCC 59.191 50.000 0.00 0.00 0.00 5.19
155 156 6.662414 TTTGACTCTGCGTTCCAAATATAG 57.338 37.500 0.00 0.00 0.00 1.31
156 157 5.064707 GCTTTGACTCTGCGTTCCAAATATA 59.935 40.000 0.00 0.00 0.00 0.86
157 158 4.142600 GCTTTGACTCTGCGTTCCAAATAT 60.143 41.667 0.00 0.00 0.00 1.28
158 159 3.188460 GCTTTGACTCTGCGTTCCAAATA 59.812 43.478 0.00 0.00 0.00 1.40
159 160 2.030805 GCTTTGACTCTGCGTTCCAAAT 60.031 45.455 0.00 0.00 0.00 2.32
160 161 1.333619 GCTTTGACTCTGCGTTCCAAA 59.666 47.619 0.00 0.00 0.00 3.28
161 162 0.944386 GCTTTGACTCTGCGTTCCAA 59.056 50.000 0.00 0.00 0.00 3.53
162 163 0.884704 GGCTTTGACTCTGCGTTCCA 60.885 55.000 0.00 0.00 0.00 3.53
163 164 0.884704 TGGCTTTGACTCTGCGTTCC 60.885 55.000 0.00 0.00 0.00 3.62
164 165 0.944386 TTGGCTTTGACTCTGCGTTC 59.056 50.000 0.00 0.00 0.00 3.95
165 166 1.388547 TTTGGCTTTGACTCTGCGTT 58.611 45.000 0.00 0.00 0.00 4.84
166 167 1.065551 GTTTTGGCTTTGACTCTGCGT 59.934 47.619 0.00 0.00 0.00 5.24
167 168 1.065401 TGTTTTGGCTTTGACTCTGCG 59.935 47.619 0.00 0.00 0.00 5.18
168 169 2.735823 CTGTTTTGGCTTTGACTCTGC 58.264 47.619 0.00 0.00 0.00 4.26
169 170 2.544486 GGCTGTTTTGGCTTTGACTCTG 60.544 50.000 0.00 0.00 0.00 3.35
170 171 1.683385 GGCTGTTTTGGCTTTGACTCT 59.317 47.619 0.00 0.00 0.00 3.24
171 172 1.408702 TGGCTGTTTTGGCTTTGACTC 59.591 47.619 0.00 0.00 0.00 3.36
172 173 1.136891 GTGGCTGTTTTGGCTTTGACT 59.863 47.619 0.00 0.00 0.00 3.41
173 174 1.136891 AGTGGCTGTTTTGGCTTTGAC 59.863 47.619 0.00 0.00 0.00 3.18
175 176 3.451141 TTAGTGGCTGTTTTGGCTTTG 57.549 42.857 0.00 0.00 0.00 2.77
176 177 5.799827 TTATTAGTGGCTGTTTTGGCTTT 57.200 34.783 0.00 0.00 0.00 3.51
179 195 4.021456 AGGTTTATTAGTGGCTGTTTTGGC 60.021 41.667 0.00 0.00 0.00 4.52
182 198 5.243060 GTCCAGGTTTATTAGTGGCTGTTTT 59.757 40.000 0.00 0.00 0.00 2.43
191 207 7.657023 ACTATCTTCGTCCAGGTTTATTAGT 57.343 36.000 0.00 0.00 0.00 2.24
220 238 8.498358 GCAGCTAAACATTTTTCTAGCAAAAAT 58.502 29.630 4.39 10.74 39.60 1.82
230 251 5.685511 TCGTTTGAGCAGCTAAACATTTTTC 59.314 36.000 19.14 0.00 36.77 2.29
266 290 1.723542 CACTAGTTGACTTGCTCTGCG 59.276 52.381 0.00 0.00 0.00 5.18
532 559 1.298638 GGCGCGATTTGATTGCCTC 60.299 57.895 12.10 0.00 42.44 4.70
700 727 1.203994 CCCTTTGCTCCATGCTTTCTG 59.796 52.381 0.00 0.00 43.37 3.02
908 3916 0.677731 AACCATCAGTGCATCGGTGG 60.678 55.000 14.37 14.37 0.00 4.61
945 3953 0.729140 GTTTTTATGCTGCGCGCTGT 60.729 50.000 33.52 20.47 40.11 4.40
1006 4214 2.361104 TTTGGCGAGTGGGATGGC 60.361 61.111 0.00 0.00 0.00 4.40
1134 4342 3.678252 CGATCTGCATGAAGAGGTTGTCT 60.678 47.826 9.83 0.00 36.94 3.41
1258 4466 1.045407 TACGTGCCAAGAGAGGTGTT 58.955 50.000 0.00 0.00 0.00 3.32
1997 5205 1.118838 CATCTCCTCGGCCTTCTCTT 58.881 55.000 0.00 0.00 0.00 2.85
2104 5331 1.672363 ACAACACACAGTCACATGCTG 59.328 47.619 0.00 0.00 39.67 4.41
2127 5354 2.159572 GCGAACAGTGGCGAATTATTGT 60.160 45.455 11.21 0.00 0.00 2.71
2181 5408 8.739972 ACACATCAACCAATTTATAGGAAAGAC 58.260 33.333 0.00 0.00 0.00 3.01
2191 5418 7.613411 TGTGATCCATACACATCAACCAATTTA 59.387 33.333 0.00 0.00 42.20 1.40
2206 5433 1.212935 AGGCCCAAGTGTGATCCATAC 59.787 52.381 0.00 0.00 0.00 2.39
2579 5810 8.918961 ACATTTGTTTGATTTCGTAACTCAAA 57.081 26.923 8.15 8.15 36.74 2.69
2587 5818 5.204833 CGAGTGACATTTGTTTGATTTCGT 58.795 37.500 0.00 0.00 0.00 3.85
2609 5841 3.242091 CGTTGGATAGATGCAGTTGAACG 60.242 47.826 0.00 0.00 0.00 3.95
2616 5848 2.898729 AGACCGTTGGATAGATGCAG 57.101 50.000 0.00 0.00 0.00 4.41
2617 5849 3.641436 ACATAGACCGTTGGATAGATGCA 59.359 43.478 0.00 0.00 0.00 3.96
2876 6479 3.953612 TGTGCTTAAATATGCCCCTCTTG 59.046 43.478 0.00 0.00 0.00 3.02
2892 6495 8.029782 TGTACCCATAATTCTATAGTGTGCTT 57.970 34.615 0.00 0.00 0.00 3.91
2902 6505 9.958180 CCATATTCACATGTACCCATAATTCTA 57.042 33.333 0.00 0.00 0.00 2.10
2923 6526 6.575244 TGTGTCCCTAACTCAATTCCATAT 57.425 37.500 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.