Multiple sequence alignment - TraesCS5D01G236100

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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 TraesCS5D01G236100 chr5D 100.000 3545 0 0 1 3545 344697344 344693800 0.000000e+00 6547.0
1 TraesCS5D01G236100 chr5D 85.350 157 16 6 288 440 404252458 404252305 4.740000e-34 156.0
2 TraesCS5D01G236100 chr5A 97.198 2962 68 12 595 3545 447365141 447368098 0.000000e+00 4996.0
3 TraesCS5D01G236100 chr5A 91.051 257 18 2 347 603 447364771 447365022 3.390000e-90 342.0
4 TraesCS5D01G236100 chr5B 96.386 2822 79 11 734 3545 407123424 407126232 0.000000e+00 4625.0
5 TraesCS5D01G236100 chr5B 82.113 710 75 33 9 702 407122537 407123210 8.590000e-156 560.0
6 TraesCS5D01G236100 chr1D 75.591 381 63 23 97 454 401562622 401562995 1.020000e-35 161.0
7 TraesCS5D01G236100 chr1D 80.741 135 22 4 289 419 462119077 462119211 6.260000e-18 102.0
8 TraesCS5D01G236100 chr7A 76.177 361 47 27 258 602 706034529 706034866 1.700000e-33 154.0
9 TraesCS5D01G236100 chr1A 76.923 312 45 20 166 454 497492540 497492847 6.130000e-33 152.0
10 TraesCS5D01G236100 chr1A 100.000 29 0 0 229 257 46305651 46305623 2.000000e-03 54.7
11 TraesCS5D01G236100 chr6B 80.612 196 21 8 3309 3497 720704871 720704686 6.170000e-28 135.0
12 TraesCS5D01G236100 chr2A 77.731 238 41 8 1697 1927 775615481 775615249 6.170000e-28 135.0
13 TraesCS5D01G236100 chr2A 78.049 205 33 10 429 630 691703759 691703564 6.220000e-23 119.0
14 TraesCS5D01G236100 chr2B 84.000 125 17 3 298 420 656378758 656378881 2.240000e-22 117.0
15 TraesCS5D01G236100 chr2D 84.404 109 15 1 313 419 189291310 189291418 4.840000e-19 106.0
16 TraesCS5D01G236100 chr2D 76.847 203 35 11 429 628 548710350 548710157 1.740000e-18 104.0


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 TraesCS5D01G236100 chr5D 344693800 344697344 3544 True 6547.0 6547 100.0000 1 3545 1 chr5D.!!$R1 3544
1 TraesCS5D01G236100 chr5A 447364771 447368098 3327 False 2669.0 4996 94.1245 347 3545 2 chr5A.!!$F1 3198
2 TraesCS5D01G236100 chr5B 407122537 407126232 3695 False 2592.5 4625 89.2495 9 3545 2 chr5B.!!$F1 3536

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
767 1091 0.330604 ACATGCTGTCATTCAGGGCT 59.669 50.0 0.0 0.0 43.78 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2560 2893 0.179207 GCCTAACCTAAAACGCACGC 60.179 55.0 0.0 0.0 0.0 5.34 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
47 48 6.850752 AGAAACAGAAAAGAACAAAAGGGA 57.149 33.333 0.00 0.00 0.00 4.20
51 52 5.208121 ACAGAAAAGAACAAAAGGGATGGA 58.792 37.500 0.00 0.00 0.00 3.41
52 53 5.302823 ACAGAAAAGAACAAAAGGGATGGAG 59.697 40.000 0.00 0.00 0.00 3.86
56 57 1.357761 GAACAAAAGGGATGGAGGGGA 59.642 52.381 0.00 0.00 0.00 4.81
62 63 2.009302 GGGATGGAGGGGAAGGCTT 61.009 63.158 0.00 0.00 0.00 4.35
71 72 2.281484 GGAAGGCTTGGTCGCACA 60.281 61.111 3.46 0.00 0.00 4.57
73 74 2.281761 AAGGCTTGGTCGCACAGG 60.282 61.111 0.00 0.00 0.00 4.00
74 75 3.850098 AAGGCTTGGTCGCACAGGG 62.850 63.158 0.00 0.00 0.00 4.45
81 82 2.359850 GTCGCACAGGGAATGGCA 60.360 61.111 0.00 0.00 0.00 4.92
83 84 1.451927 TCGCACAGGGAATGGCATC 60.452 57.895 0.00 0.00 0.00 3.91
88 89 0.706433 ACAGGGAATGGCATCAACCT 59.294 50.000 0.00 6.09 0.00 3.50
115 116 4.035112 AGGAACTGACCGACCCAAATATA 58.965 43.478 0.00 0.00 37.18 0.86
122 123 2.175931 ACCGACCCAAATATATGGCCAA 59.824 45.455 10.96 0.00 39.26 4.52
124 125 3.443681 CCGACCCAAATATATGGCCAATC 59.556 47.826 10.96 0.00 39.26 2.67
156 159 6.859112 ACAGCCTAAAATAACTCAGAGAGA 57.141 37.500 3.79 0.00 33.32 3.10
170 173 5.389859 TCAGAGAGAGAGAGCAGAAAAAG 57.610 43.478 0.00 0.00 0.00 2.27
171 174 4.220382 TCAGAGAGAGAGAGCAGAAAAAGG 59.780 45.833 0.00 0.00 0.00 3.11
172 175 4.220382 CAGAGAGAGAGAGCAGAAAAAGGA 59.780 45.833 0.00 0.00 0.00 3.36
173 176 4.463891 AGAGAGAGAGAGCAGAAAAAGGAG 59.536 45.833 0.00 0.00 0.00 3.69
174 177 3.055891 AGAGAGAGAGCAGAAAAAGGAGC 60.056 47.826 0.00 0.00 0.00 4.70
175 178 2.636893 AGAGAGAGCAGAAAAAGGAGCA 59.363 45.455 0.00 0.00 0.00 4.26
176 179 2.741517 GAGAGAGCAGAAAAAGGAGCAC 59.258 50.000 0.00 0.00 0.00 4.40
177 180 1.462670 GAGAGCAGAAAAAGGAGCACG 59.537 52.381 0.00 0.00 0.00 5.34
180 188 2.485814 GAGCAGAAAAAGGAGCACGAAT 59.514 45.455 0.00 0.00 0.00 3.34
196 204 4.318332 GCACGAATCTTAAAGCAAAAGTCG 59.682 41.667 0.00 0.00 32.08 4.18
200 208 4.663636 ATCTTAAAGCAAAAGTCGACGG 57.336 40.909 10.46 2.58 0.00 4.79
235 244 4.674281 TGGGCGAAAAACAATTTTAGGT 57.326 36.364 0.00 0.00 38.83 3.08
241 250 7.385478 GGGCGAAAAACAATTTTAGGTGATTTA 59.615 33.333 0.00 0.00 38.83 1.40
270 280 6.442513 AGCTAAAGTGATGCAAGAAATACC 57.557 37.500 0.00 0.00 0.00 2.73
271 281 5.358160 AGCTAAAGTGATGCAAGAAATACCC 59.642 40.000 0.00 0.00 0.00 3.69
272 282 5.125417 GCTAAAGTGATGCAAGAAATACCCA 59.875 40.000 0.00 0.00 0.00 4.51
273 283 6.350110 GCTAAAGTGATGCAAGAAATACCCAA 60.350 38.462 0.00 0.00 0.00 4.12
274 284 5.649782 AAGTGATGCAAGAAATACCCAAG 57.350 39.130 0.00 0.00 0.00 3.61
275 285 4.666512 AGTGATGCAAGAAATACCCAAGT 58.333 39.130 0.00 0.00 0.00 3.16
276 286 5.815581 AGTGATGCAAGAAATACCCAAGTA 58.184 37.500 0.00 0.00 0.00 2.24
277 287 6.245408 AGTGATGCAAGAAATACCCAAGTAA 58.755 36.000 0.00 0.00 30.59 2.24
278 288 6.891908 AGTGATGCAAGAAATACCCAAGTAAT 59.108 34.615 0.00 0.00 30.59 1.89
279 289 8.052748 AGTGATGCAAGAAATACCCAAGTAATA 58.947 33.333 0.00 0.00 30.59 0.98
280 290 8.682710 GTGATGCAAGAAATACCCAAGTAATAA 58.317 33.333 0.00 0.00 30.59 1.40
281 291 9.249053 TGATGCAAGAAATACCCAAGTAATAAA 57.751 29.630 0.00 0.00 30.59 1.40
411 422 5.056480 ACAAGGGCAAGTCAAAAATTTAGC 58.944 37.500 0.00 0.00 0.00 3.09
480 492 8.316214 TCCAACCTACGAAATAATTGACTTACT 58.684 33.333 0.00 0.00 0.00 2.24
528 541 4.261994 GCCTAAGAAGCCATGAAACAACAA 60.262 41.667 0.00 0.00 0.00 2.83
530 543 6.279882 CCTAAGAAGCCATGAAACAACAAAA 58.720 36.000 0.00 0.00 0.00 2.44
532 545 5.596836 AGAAGCCATGAAACAACAAAAGA 57.403 34.783 0.00 0.00 0.00 2.52
533 546 5.976458 AGAAGCCATGAAACAACAAAAGAA 58.024 33.333 0.00 0.00 0.00 2.52
534 547 6.405538 AGAAGCCATGAAACAACAAAAGAAA 58.594 32.000 0.00 0.00 0.00 2.52
766 1090 2.042686 TACATGCTGTCATTCAGGGC 57.957 50.000 0.00 0.00 43.78 5.19
767 1091 0.330604 ACATGCTGTCATTCAGGGCT 59.669 50.000 0.00 0.00 43.78 5.19
1542 1875 4.569180 AGGCTGCACACCAACGCT 62.569 61.111 0.50 0.00 0.00 5.07
1860 2193 1.759445 CTCCTCATCCAGACGACCAAT 59.241 52.381 0.00 0.00 0.00 3.16
2034 2367 2.711922 CGGGAAGGTGACCCTCTCG 61.712 68.421 8.27 8.27 41.56 4.04
2560 2893 1.674441 TGTAGCTCCGATTACGTCTGG 59.326 52.381 0.00 0.00 37.88 3.86
2688 3022 1.527311 GAGCAATATTCGAACCTCGCC 59.473 52.381 0.00 0.00 40.21 5.54
2734 3068 3.217231 CCGGACAGGACGGCTTAT 58.783 61.111 0.00 0.00 45.34 1.73
2735 3069 2.422303 CCGGACAGGACGGCTTATA 58.578 57.895 0.00 0.00 45.34 0.98
2736 3070 0.031721 CCGGACAGGACGGCTTATAC 59.968 60.000 0.00 0.00 45.34 1.47
2737 3071 0.742505 CGGACAGGACGGCTTATACA 59.257 55.000 0.00 0.00 0.00 2.29
2738 3072 1.269102 CGGACAGGACGGCTTATACAG 60.269 57.143 0.00 0.00 0.00 2.74
2796 3140 1.849097 GTATACTTGAACCTCGCCCG 58.151 55.000 0.00 0.00 0.00 6.13
2958 3302 6.551975 TCGAAATATCACTGGGAATACTGGTA 59.448 38.462 0.00 0.00 0.00 3.25
2977 3321 4.010349 GGTAATCTTCAAGAACCTGTGGG 58.990 47.826 1.42 0.00 38.88 4.61
2989 3333 2.030862 TGTGGGTTCGGTTACGGC 59.969 61.111 0.00 0.00 41.39 5.68
3123 3467 1.754234 GGGGACAATGAGCGGCAAT 60.754 57.895 1.45 0.00 0.00 3.56
3400 3744 3.251509 TGCTCAAGGAGGCCTGCA 61.252 61.111 27.56 18.00 32.13 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 8.879342 TGTTCTTTTCTGTTTCTTTGTTTTCA 57.121 26.923 0.00 0.00 0.00 2.69
21 22 7.602265 TCCCTTTTGTTCTTTTCTGTTTCTTTG 59.398 33.333 0.00 0.00 0.00 2.77
23 24 7.239763 TCCCTTTTGTTCTTTTCTGTTTCTT 57.760 32.000 0.00 0.00 0.00 2.52
47 48 1.544917 ACCAAGCCTTCCCCTCCAT 60.545 57.895 0.00 0.00 0.00 3.41
51 52 4.035102 GCGACCAAGCCTTCCCCT 62.035 66.667 0.00 0.00 0.00 4.79
52 53 4.344865 TGCGACCAAGCCTTCCCC 62.345 66.667 0.00 0.00 36.02 4.81
56 57 2.281761 CCTGTGCGACCAAGCCTT 60.282 61.111 0.00 0.00 36.02 4.35
62 63 2.350895 CCATTCCCTGTGCGACCA 59.649 61.111 0.00 0.00 0.00 4.02
71 72 0.706433 ACAGGTTGATGCCATTCCCT 59.294 50.000 0.00 0.00 0.00 4.20
73 74 3.131046 CCTTAACAGGTTGATGCCATTCC 59.869 47.826 0.00 0.00 35.06 3.01
74 75 4.016444 TCCTTAACAGGTTGATGCCATTC 58.984 43.478 0.00 0.00 41.69 2.67
81 82 4.652822 GGTCAGTTCCTTAACAGGTTGAT 58.347 43.478 0.00 0.00 41.69 2.57
83 84 2.806244 CGGTCAGTTCCTTAACAGGTTG 59.194 50.000 0.00 0.00 41.69 3.77
88 89 1.345415 GGGTCGGTCAGTTCCTTAACA 59.655 52.381 0.00 0.00 38.12 2.41
98 99 3.074412 GCCATATATTTGGGTCGGTCAG 58.926 50.000 13.35 0.00 37.24 3.51
103 104 3.126858 CGATTGGCCATATATTTGGGTCG 59.873 47.826 6.09 0.51 37.24 4.79
105 106 4.380843 TCGATTGGCCATATATTTGGGT 57.619 40.909 6.09 0.00 37.24 4.51
133 136 6.665680 TCTCTCTCTGAGTTATTTTAGGCTGT 59.334 38.462 4.32 0.00 43.13 4.40
134 137 7.068103 TCTCTCTCTCTGAGTTATTTTAGGCTG 59.932 40.741 4.32 0.00 43.13 4.85
139 142 7.831690 TCTGCTCTCTCTCTCTGAGTTATTTTA 59.168 37.037 4.32 0.00 43.13 1.52
144 147 4.835284 TCTGCTCTCTCTCTCTGAGTTA 57.165 45.455 4.32 0.00 43.13 2.24
151 154 4.747810 CTCCTTTTTCTGCTCTCTCTCTC 58.252 47.826 0.00 0.00 0.00 3.20
153 156 3.261580 GCTCCTTTTTCTGCTCTCTCTC 58.738 50.000 0.00 0.00 0.00 3.20
156 159 2.777094 GTGCTCCTTTTTCTGCTCTCT 58.223 47.619 0.00 0.00 0.00 3.10
157 160 1.462670 CGTGCTCCTTTTTCTGCTCTC 59.537 52.381 0.00 0.00 0.00 3.20
170 173 4.419522 TTTGCTTTAAGATTCGTGCTCC 57.580 40.909 0.00 0.00 0.00 4.70
171 174 5.452777 ACTTTTGCTTTAAGATTCGTGCTC 58.547 37.500 0.00 0.00 0.00 4.26
172 175 5.438761 ACTTTTGCTTTAAGATTCGTGCT 57.561 34.783 0.00 0.00 0.00 4.40
173 176 4.318332 CGACTTTTGCTTTAAGATTCGTGC 59.682 41.667 0.00 0.00 0.00 5.34
174 177 5.560378 GTCGACTTTTGCTTTAAGATTCGTG 59.440 40.000 8.70 0.00 0.00 4.35
175 178 5.611844 CGTCGACTTTTGCTTTAAGATTCGT 60.612 40.000 14.70 0.00 0.00 3.85
176 179 4.776532 CGTCGACTTTTGCTTTAAGATTCG 59.223 41.667 14.70 0.00 0.00 3.34
177 180 5.080068 CCGTCGACTTTTGCTTTAAGATTC 58.920 41.667 14.70 0.00 0.00 2.52
180 188 2.222445 GCCGTCGACTTTTGCTTTAAGA 59.778 45.455 14.70 0.00 0.00 2.10
208 216 2.611225 TTGTTTTTCGCCCAATTGCT 57.389 40.000 0.00 0.00 0.00 3.91
217 225 8.756864 TGTAAATCACCTAAAATTGTTTTTCGC 58.243 29.630 0.00 0.00 36.47 4.70
235 244 9.777297 TGCATCACTTTAGCTATATGTAAATCA 57.223 29.630 0.00 0.00 0.00 2.57
241 250 8.737168 TTTCTTGCATCACTTTAGCTATATGT 57.263 30.769 0.00 0.00 0.00 2.29
246 255 6.542370 GGGTATTTCTTGCATCACTTTAGCTA 59.458 38.462 0.00 0.00 0.00 3.32
247 256 5.358160 GGGTATTTCTTGCATCACTTTAGCT 59.642 40.000 0.00 0.00 0.00 3.32
248 257 5.125417 TGGGTATTTCTTGCATCACTTTAGC 59.875 40.000 0.00 0.00 0.00 3.09
249 258 6.757897 TGGGTATTTCTTGCATCACTTTAG 57.242 37.500 0.00 0.00 0.00 1.85
305 315 7.922505 TGTTTGTATGTGTTTTTGTCTATGC 57.077 32.000 0.00 0.00 0.00 3.14
338 349 0.878416 GAAGCCCGTTACACATTGCA 59.122 50.000 0.00 0.00 0.00 4.08
369 380 6.270064 CCTTGTTTGTGGTAAGTCGATTTTT 58.730 36.000 0.00 0.00 0.00 1.94
411 422 7.533289 TGGGGTAAATTGACTTTTTCTTAGG 57.467 36.000 0.00 0.00 0.00 2.69
444 455 5.934935 TTCGTAGGTTGGATTTTGACTTC 57.065 39.130 0.00 0.00 0.00 3.01
480 492 5.549742 ATTTTGATTTGCTCCTGTTTGGA 57.450 34.783 0.00 0.00 43.86 3.53
564 577 5.230942 AGTCAATTTTCAGATCGTCGAGTT 58.769 37.500 0.00 0.00 0.00 3.01
568 581 6.255670 TGGATAAGTCAATTTTCAGATCGTCG 59.744 38.462 0.00 0.00 0.00 5.12
604 617 7.067421 ACTTTAGCTATATGTAGGTCACCTGA 58.933 38.462 6.61 0.00 39.30 3.86
774 1102 4.219725 AGGTGTGCACTGTTACAAAAACTT 59.780 37.500 19.41 0.00 0.00 2.66
778 1106 4.792521 AAAGGTGTGCACTGTTACAAAA 57.207 36.364 19.41 0.00 0.00 2.44
783 1111 3.568007 GGATCAAAAGGTGTGCACTGTTA 59.432 43.478 19.41 0.00 0.00 2.41
947 1279 2.358369 TGCTGCTGCTCTGCTCAC 60.358 61.111 17.00 0.00 39.95 3.51
1740 2073 1.424493 CGATCAGCGAAGACTTGCCC 61.424 60.000 0.00 0.00 44.57 5.36
1860 2193 0.867329 CGATGACAATGAGCGAGCGA 60.867 55.000 0.00 0.00 0.00 4.93
2034 2367 1.973812 GGTGAAGTTGAGCAGCCCC 60.974 63.158 0.00 0.00 0.00 5.80
2307 2640 0.673022 CTCTGTTCCTCAGCAGCACC 60.673 60.000 0.00 0.00 43.32 5.01
2560 2893 0.179207 GCCTAACCTAAAACGCACGC 60.179 55.000 0.00 0.00 0.00 5.34
2723 3057 6.737899 GCAAGTATAACTGTATAAGCCGTCCT 60.738 42.308 0.00 0.00 0.00 3.85
2731 3065 4.101274 TGCCGGGCAAGTATAACTGTATAA 59.899 41.667 21.55 0.00 34.76 0.98
2732 3066 3.642377 TGCCGGGCAAGTATAACTGTATA 59.358 43.478 21.55 0.00 34.76 1.47
2733 3067 2.436542 TGCCGGGCAAGTATAACTGTAT 59.563 45.455 21.55 0.00 34.76 2.29
2734 3068 1.832366 TGCCGGGCAAGTATAACTGTA 59.168 47.619 21.55 0.00 34.76 2.74
2735 3069 0.616371 TGCCGGGCAAGTATAACTGT 59.384 50.000 21.55 0.00 34.76 3.55
2736 3070 1.014352 GTGCCGGGCAAGTATAACTG 58.986 55.000 25.70 0.00 41.47 3.16
2737 3071 0.461339 CGTGCCGGGCAAGTATAACT 60.461 55.000 25.70 0.00 41.47 2.24
2738 3072 0.460635 TCGTGCCGGGCAAGTATAAC 60.461 55.000 29.47 13.23 41.47 1.89
2796 3140 2.159268 GGCTACGTGAGAAGGAAGGTAC 60.159 54.545 0.00 0.00 0.00 3.34
2840 3184 3.133464 CGCCGGTCATGGTGCAAT 61.133 61.111 1.90 0.00 31.81 3.56
2977 3321 2.357760 TGCCAGCCGTAACCGAAC 60.358 61.111 0.00 0.00 35.63 3.95
3123 3467 0.249447 CGCATATTGCCTCGACCAGA 60.249 55.000 0.00 0.00 41.12 3.86
3381 3725 2.438075 CAGGCCTCCTTGAGCAGC 60.438 66.667 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.