Multiple sequence alignment - TraesCS4B01G206500

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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 TraesCS4B01G206500 chr4B 100.000 3454 0 0 1 3454 439195295 439198748 0.000000e+00 6379.0
1 TraesCS4B01G206500 chr4A 99.083 3273 27 2 183 3454 548526247 548522977 0.000000e+00 5875.0
2 TraesCS4B01G206500 chr4A 94.086 186 9 2 1 185 109443575 109443391 7.300000e-72 281.0
3 TraesCS4B01G206500 chr6A 98.961 3273 33 1 183 3454 466092189 466095461 0.000000e+00 5854.0
4 TraesCS4B01G206500 chr5A 98.595 3274 20 4 182 3454 422075409 422072161 0.000000e+00 5768.0
5 TraesCS4B01G206500 chr6B 97.863 3276 63 5 183 3454 698114883 698118155 0.000000e+00 5655.0
6 TraesCS4B01G206500 chr6B 96.868 3289 85 6 170 3454 458495670 458498944 0.000000e+00 5487.0
7 TraesCS4B01G206500 chr6B 98.971 2527 24 2 929 3454 325035064 325037589 0.000000e+00 4521.0
8 TraesCS4B01G206500 chr1A 99.218 2559 19 1 897 3454 80308210 80305652 0.000000e+00 4614.0
9 TraesCS4B01G206500 chr7A 99.367 2527 15 1 929 3454 176257263 176259789 0.000000e+00 4577.0
10 TraesCS4B01G206500 chr7A 98.034 763 14 1 178 940 176256557 176257318 0.000000e+00 1325.0
11 TraesCS4B01G206500 chr7A 88.889 99 11 0 36 134 613179623 613179525 4.680000e-24 122.0
12 TraesCS4B01G206500 chr7A 83.077 65 10 1 64 127 613179725 613179789 1.340000e-04 58.4
13 TraesCS4B01G206500 chr2A 99.129 2527 21 1 929 3454 642923998 642921472 0.000000e+00 4543.0
14 TraesCS4B01G206500 chr2A 97.120 764 19 3 181 943 642924701 642923940 0.000000e+00 1286.0
15 TraesCS4B01G206500 chr2B 99.050 2527 22 2 929 3454 669227501 669230026 0.000000e+00 4532.0
16 TraesCS4B01G206500 chr5B 98.419 759 11 1 182 940 161074845 161075602 0.000000e+00 1334.0
17 TraesCS4B01G206500 chr5B 90.625 64 6 0 61 124 577244731 577244668 6.140000e-13 86.1
18 TraesCS4B01G206500 chr7D 91.345 751 40 18 183 924 264763322 264764056 0.000000e+00 1003.0
19 TraesCS4B01G206500 chr2D 90.559 752 45 21 179 924 33017489 33018220 0.000000e+00 972.0
20 TraesCS4B01G206500 chr4D 97.268 183 5 0 1 183 355710984 355711166 9.310000e-81 311.0
21 TraesCS4B01G206500 chr3D 85.915 71 9 1 65 134 170240313 170240243 1.330000e-09 75.0
22 TraesCS4B01G206500 chr3A 82.222 90 11 4 44 130 207847102 207847015 4.780000e-09 73.1
23 TraesCS4B01G206500 chr3B 82.558 86 10 4 48 130 245514300 245514217 1.720000e-08 71.3


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 TraesCS4B01G206500 chr4B 439195295 439198748 3453 False 6379.0 6379 100.0000 1 3454 1 chr4B.!!$F1 3453
1 TraesCS4B01G206500 chr4A 548522977 548526247 3270 True 5875.0 5875 99.0830 183 3454 1 chr4A.!!$R2 3271
2 TraesCS4B01G206500 chr6A 466092189 466095461 3272 False 5854.0 5854 98.9610 183 3454 1 chr6A.!!$F1 3271
3 TraesCS4B01G206500 chr5A 422072161 422075409 3248 True 5768.0 5768 98.5950 182 3454 1 chr5A.!!$R1 3272
4 TraesCS4B01G206500 chr6B 698114883 698118155 3272 False 5655.0 5655 97.8630 183 3454 1 chr6B.!!$F3 3271
5 TraesCS4B01G206500 chr6B 458495670 458498944 3274 False 5487.0 5487 96.8680 170 3454 1 chr6B.!!$F2 3284
6 TraesCS4B01G206500 chr6B 325035064 325037589 2525 False 4521.0 4521 98.9710 929 3454 1 chr6B.!!$F1 2525
7 TraesCS4B01G206500 chr1A 80305652 80308210 2558 True 4614.0 4614 99.2180 897 3454 1 chr1A.!!$R1 2557
8 TraesCS4B01G206500 chr7A 176256557 176259789 3232 False 2951.0 4577 98.7005 178 3454 2 chr7A.!!$F2 3276
9 TraesCS4B01G206500 chr2A 642921472 642924701 3229 True 2914.5 4543 98.1245 181 3454 2 chr2A.!!$R1 3273
10 TraesCS4B01G206500 chr2B 669227501 669230026 2525 False 4532.0 4532 99.0500 929 3454 1 chr2B.!!$F1 2525
11 TraesCS4B01G206500 chr5B 161074845 161075602 757 False 1334.0 1334 98.4190 182 940 1 chr5B.!!$F1 758
12 TraesCS4B01G206500 chr7D 264763322 264764056 734 False 1003.0 1003 91.3450 183 924 1 chr7D.!!$F1 741
13 TraesCS4B01G206500 chr2D 33017489 33018220 731 False 972.0 972 90.5590 179 924 1 chr2D.!!$F1 745

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
131 132 0.326238 ATTTAGGGACGGAGGCAGGA 60.326 55.0 0.0 0.0 0.0 3.86 F
133 134 0.559205 TTAGGGACGGAGGCAGGATA 59.441 55.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1015 1121 1.302832 CCAAAGCCTCGGCAAGACT 60.303 57.895 11.02 0.0 44.88 3.24 R
2628 2734 5.388408 TTGCATATTCACAAGCATCACAA 57.612 34.783 0.00 0.0 36.80 3.33 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
40 41 9.868277 TTTTTCAGAATGTGTTTATTCAGTTGT 57.132 25.926 0.00 0.00 39.08 3.32
41 42 9.868277 TTTTCAGAATGTGTTTATTCAGTTGTT 57.132 25.926 0.00 0.00 39.08 2.83
71 72 9.574516 AGTTTCTTCTATGTATTTGGTCAAACT 57.425 29.630 0.00 0.00 32.51 2.66
86 87 8.974060 TTGGTCAAACTTAGAAATAGTTGACT 57.026 30.769 12.51 0.00 36.06 3.41
87 88 8.974060 TGGTCAAACTTAGAAATAGTTGACTT 57.026 30.769 12.51 0.00 36.06 3.01
88 89 9.052759 TGGTCAAACTTAGAAATAGTTGACTTC 57.947 33.333 12.51 0.71 36.06 3.01
89 90 9.274206 GGTCAAACTTAGAAATAGTTGACTTCT 57.726 33.333 12.51 0.00 36.06 2.85
122 123 8.964476 ATTTATATGCCATCTATTTAGGGACG 57.036 34.615 0.00 0.00 0.00 4.79
123 124 3.703001 ATGCCATCTATTTAGGGACGG 57.297 47.619 0.00 0.00 0.00 4.79
124 125 2.684943 TGCCATCTATTTAGGGACGGA 58.315 47.619 0.00 0.00 0.00 4.69
125 126 2.632996 TGCCATCTATTTAGGGACGGAG 59.367 50.000 0.00 0.00 0.00 4.63
126 127 2.028020 GCCATCTATTTAGGGACGGAGG 60.028 54.545 0.00 0.00 0.00 4.30
127 128 2.028020 CCATCTATTTAGGGACGGAGGC 60.028 54.545 0.00 0.00 0.00 4.70
128 129 2.464796 TCTATTTAGGGACGGAGGCA 57.535 50.000 0.00 0.00 0.00 4.75
129 130 2.317040 TCTATTTAGGGACGGAGGCAG 58.683 52.381 0.00 0.00 0.00 4.85
130 131 1.344763 CTATTTAGGGACGGAGGCAGG 59.655 57.143 0.00 0.00 0.00 4.85
131 132 0.326238 ATTTAGGGACGGAGGCAGGA 60.326 55.000 0.00 0.00 0.00 3.86
132 133 0.326238 TTTAGGGACGGAGGCAGGAT 60.326 55.000 0.00 0.00 0.00 3.24
133 134 0.559205 TTAGGGACGGAGGCAGGATA 59.441 55.000 0.00 0.00 0.00 2.59
134 135 0.784495 TAGGGACGGAGGCAGGATAT 59.216 55.000 0.00 0.00 0.00 1.63
135 136 0.833834 AGGGACGGAGGCAGGATATG 60.834 60.000 0.00 0.00 0.00 1.78
162 163 5.713792 TTTTCTCCGAGAGCTAGGATATG 57.286 43.478 5.63 0.00 33.89 1.78
163 164 2.717390 TCTCCGAGAGCTAGGATATGC 58.283 52.381 5.63 0.00 33.89 3.14
164 165 1.748493 CTCCGAGAGCTAGGATATGCC 59.252 57.143 5.63 0.00 33.89 4.40
177 178 1.742831 GATATGCCTTTGTCGTGCCAA 59.257 47.619 0.00 0.00 0.00 4.52
611 619 1.521616 CAGAGGAAGAGGAGCTGCC 59.478 63.158 0.00 0.00 43.55 4.85
1055 1161 1.335496 GAAGCTCGCTAAGATCCTCGT 59.665 52.381 0.00 0.00 0.00 4.18
2628 2734 0.401738 TAGGCAAAGGCAAGCTGACT 59.598 50.000 0.00 0.00 37.28 3.41
3042 3153 3.961480 ATCGTCATGTTCTTGAGGTCA 57.039 42.857 0.00 0.00 34.10 4.02
3368 3479 7.662669 AGGTTTGTAAGTATGGACGTTACATTT 59.337 33.333 11.21 4.73 36.73 2.32
3402 3513 2.628178 CCATTCTATGGTGAGCCGACTA 59.372 50.000 0.00 0.00 45.54 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.868277 ACAACTGAATAAACACATTCTGAAAAA 57.132 25.926 8.97 0.00 37.33 1.94
15 16 9.868277 AACAACTGAATAAACACATTCTGAAAA 57.132 25.926 8.97 0.00 37.33 2.29
45 46 9.574516 AGTTTGACCAAATACATAGAAGAAACT 57.425 29.630 0.00 0.00 32.36 2.66
60 61 9.403583 AGTCAACTATTTCTAAGTTTGACCAAA 57.596 29.630 8.30 0.00 36.60 3.28
61 62 8.974060 AGTCAACTATTTCTAAGTTTGACCAA 57.026 30.769 8.30 0.00 36.60 3.67
62 63 8.974060 AAGTCAACTATTTCTAAGTTTGACCA 57.026 30.769 8.30 0.00 36.60 4.02
63 64 9.274206 AGAAGTCAACTATTTCTAAGTTTGACC 57.726 33.333 8.30 0.00 36.60 4.02
96 97 9.396022 CGTCCCTAAATAGATGGCATATAAATT 57.604 33.333 5.85 7.24 0.00 1.82
97 98 7.993183 CCGTCCCTAAATAGATGGCATATAAAT 59.007 37.037 5.85 1.02 32.60 1.40
98 99 7.181305 TCCGTCCCTAAATAGATGGCATATAAA 59.819 37.037 5.85 0.00 38.78 1.40
99 100 6.670464 TCCGTCCCTAAATAGATGGCATATAA 59.330 38.462 5.85 0.00 38.78 0.98
100 101 6.199376 TCCGTCCCTAAATAGATGGCATATA 58.801 40.000 4.04 4.04 38.78 0.86
101 102 5.030147 TCCGTCCCTAAATAGATGGCATAT 58.970 41.667 0.00 0.00 38.78 1.78
102 103 4.422057 TCCGTCCCTAAATAGATGGCATA 58.578 43.478 0.00 0.00 38.78 3.14
103 104 3.248024 TCCGTCCCTAAATAGATGGCAT 58.752 45.455 0.00 0.00 38.78 4.40
104 105 2.632996 CTCCGTCCCTAAATAGATGGCA 59.367 50.000 0.00 0.00 38.78 4.92
105 106 2.028020 CCTCCGTCCCTAAATAGATGGC 60.028 54.545 0.00 0.00 38.78 4.40
106 107 2.028020 GCCTCCGTCCCTAAATAGATGG 60.028 54.545 0.00 0.00 40.04 3.51
107 108 2.632996 TGCCTCCGTCCCTAAATAGATG 59.367 50.000 0.00 0.00 0.00 2.90
108 109 2.900546 CTGCCTCCGTCCCTAAATAGAT 59.099 50.000 0.00 0.00 0.00 1.98
109 110 2.317040 CTGCCTCCGTCCCTAAATAGA 58.683 52.381 0.00 0.00 0.00 1.98
110 111 1.344763 CCTGCCTCCGTCCCTAAATAG 59.655 57.143 0.00 0.00 0.00 1.73
111 112 1.062734 TCCTGCCTCCGTCCCTAAATA 60.063 52.381 0.00 0.00 0.00 1.40
112 113 0.326238 TCCTGCCTCCGTCCCTAAAT 60.326 55.000 0.00 0.00 0.00 1.40
113 114 0.326238 ATCCTGCCTCCGTCCCTAAA 60.326 55.000 0.00 0.00 0.00 1.85
114 115 0.559205 TATCCTGCCTCCGTCCCTAA 59.441 55.000 0.00 0.00 0.00 2.69
115 116 0.784495 ATATCCTGCCTCCGTCCCTA 59.216 55.000 0.00 0.00 0.00 3.53
116 117 0.833834 CATATCCTGCCTCCGTCCCT 60.834 60.000 0.00 0.00 0.00 4.20
117 118 1.674057 CATATCCTGCCTCCGTCCC 59.326 63.158 0.00 0.00 0.00 4.46
118 119 1.004440 GCATATCCTGCCTCCGTCC 60.004 63.158 0.00 0.00 45.66 4.79
119 120 4.683432 GCATATCCTGCCTCCGTC 57.317 61.111 0.00 0.00 45.66 4.79
139 140 5.509840 GCATATCCTAGCTCTCGGAGAAAAA 60.510 44.000 9.32 0.00 34.09 1.94
140 141 4.021894 GCATATCCTAGCTCTCGGAGAAAA 60.022 45.833 9.32 0.00 34.09 2.29
141 142 3.508012 GCATATCCTAGCTCTCGGAGAAA 59.492 47.826 9.32 0.00 34.09 2.52
142 143 3.085533 GCATATCCTAGCTCTCGGAGAA 58.914 50.000 9.32 0.00 34.09 2.87
143 144 2.619332 GGCATATCCTAGCTCTCGGAGA 60.619 54.545 7.60 7.60 31.82 3.71
144 145 1.748493 GGCATATCCTAGCTCTCGGAG 59.252 57.143 0.00 0.00 31.82 4.63
145 146 1.356059 AGGCATATCCTAGCTCTCGGA 59.644 52.381 0.00 0.00 45.41 4.55
146 147 1.846007 AGGCATATCCTAGCTCTCGG 58.154 55.000 0.00 0.00 45.41 4.63
147 148 3.006323 ACAAAGGCATATCCTAGCTCTCG 59.994 47.826 0.00 0.00 46.94 4.04
148 149 4.565022 GACAAAGGCATATCCTAGCTCTC 58.435 47.826 0.00 0.00 46.94 3.20
149 150 3.006323 CGACAAAGGCATATCCTAGCTCT 59.994 47.826 0.00 0.00 46.94 4.09
150 151 3.243907 ACGACAAAGGCATATCCTAGCTC 60.244 47.826 0.00 0.00 46.94 4.09
151 152 2.700897 ACGACAAAGGCATATCCTAGCT 59.299 45.455 0.00 0.00 46.94 3.32
152 153 2.802816 CACGACAAAGGCATATCCTAGC 59.197 50.000 0.00 0.00 46.94 3.42
153 154 2.802816 GCACGACAAAGGCATATCCTAG 59.197 50.000 0.00 0.00 46.94 3.02
154 155 2.484770 GGCACGACAAAGGCATATCCTA 60.485 50.000 0.00 0.00 46.94 2.94
156 157 0.663153 GGCACGACAAAGGCATATCC 59.337 55.000 0.00 0.00 0.00 2.59
157 158 1.378531 TGGCACGACAAAGGCATATC 58.621 50.000 0.00 0.00 35.21 1.63
158 159 1.832883 TTGGCACGACAAAGGCATAT 58.167 45.000 0.00 0.00 40.17 1.78
159 160 1.832883 ATTGGCACGACAAAGGCATA 58.167 45.000 0.00 0.00 40.17 3.14
160 161 0.968405 AATTGGCACGACAAAGGCAT 59.032 45.000 0.00 0.00 40.17 4.40
161 162 0.749649 AAATTGGCACGACAAAGGCA 59.250 45.000 0.00 0.00 38.64 4.75
162 163 1.000274 AGAAATTGGCACGACAAAGGC 60.000 47.619 0.00 0.00 33.48 4.35
163 164 2.034558 ACAGAAATTGGCACGACAAAGG 59.965 45.455 0.00 0.00 33.48 3.11
164 165 3.354089 ACAGAAATTGGCACGACAAAG 57.646 42.857 0.00 0.00 33.48 2.77
165 166 3.129462 TCAACAGAAATTGGCACGACAAA 59.871 39.130 0.00 0.00 33.48 2.83
166 167 2.685388 TCAACAGAAATTGGCACGACAA 59.315 40.909 0.00 0.00 34.41 3.18
167 168 2.293170 TCAACAGAAATTGGCACGACA 58.707 42.857 0.00 0.00 0.00 4.35
168 169 3.042887 GTTCAACAGAAATTGGCACGAC 58.957 45.455 0.00 0.00 0.00 4.34
169 170 2.034053 GGTTCAACAGAAATTGGCACGA 59.966 45.455 0.00 0.00 0.00 4.35
170 171 2.393764 GGTTCAACAGAAATTGGCACG 58.606 47.619 0.00 0.00 0.00 5.34
171 172 2.393764 CGGTTCAACAGAAATTGGCAC 58.606 47.619 0.00 0.00 0.00 5.01
172 173 1.339610 CCGGTTCAACAGAAATTGGCA 59.660 47.619 0.00 0.00 0.00 4.92
173 174 1.339929 ACCGGTTCAACAGAAATTGGC 59.660 47.619 0.00 0.00 0.00 4.52
174 175 4.380444 CCATACCGGTTCAACAGAAATTGG 60.380 45.833 15.04 0.00 0.00 3.16
177 178 3.352648 CCCATACCGGTTCAACAGAAAT 58.647 45.455 15.04 0.00 0.00 2.17
474 479 2.729491 CGTCTCTCGTGCGTGCAA 60.729 61.111 0.00 0.00 34.52 4.08
1015 1121 1.302832 CCAAAGCCTCGGCAAGACT 60.303 57.895 11.02 0.00 44.88 3.24
2628 2734 5.388408 TTGCATATTCACAAGCATCACAA 57.612 34.783 0.00 0.00 36.80 3.33
3042 3153 2.036217 TGGTAAACATCAACGACCGAGT 59.964 45.455 0.00 0.00 32.55 4.18
3214 3325 3.684788 GTGATCACGAACAAAGCAGGTAT 59.315 43.478 10.69 0.00 0.00 2.73
3368 3479 2.856760 AGAATGGCTCAGACTCCCTA 57.143 50.000 0.00 0.00 0.00 3.53
3402 3513 5.353678 GCTCTGCAAACAATAGACTGAGATT 59.646 40.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.