Multiple sequence alignment - TraesCS4D01G106900

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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 TraesCS4D01G106900 chr4D 100.000 5150 0 0 1 5150 85176559 85171410 0.000000e+00 9511
1 TraesCS4D01G106900 chr4D 94.509 4061 206 11 119 4171 85263725 85259674 0.000000e+00 6248
2 TraesCS4D01G106900 chr4D 95.039 766 33 4 4385 5148 396428901 396428139 0.000000e+00 1199
3 TraesCS4D01G106900 chr4D 92.135 178 11 3 4193 4370 85259685 85259511 1.110000e-61 248
4 TraesCS4D01G106900 chr4B 96.765 4173 127 7 7 4173 122301278 122297108 0.000000e+00 6951
5 TraesCS4D01G106900 chr4B 96.703 182 4 1 4191 4370 122297123 122296942 8.380000e-78 302
6 TraesCS4D01G106900 chr4A 96.715 4171 123 9 4 4171 498989768 498985609 0.000000e+00 6931
7 TraesCS4D01G106900 chr4A 95.028 181 8 1 4191 4370 498985622 498985442 3.040000e-72 283
8 TraesCS4D01G106900 chr7B 95.924 785 25 3 4373 5150 585534271 585533487 0.000000e+00 1266
9 TraesCS4D01G106900 chr7B 94.615 780 40 2 4371 5148 561071781 561071002 0.000000e+00 1206
10 TraesCS4D01G106900 chrUn 75.541 2633 580 53 1079 3682 75441564 75444161 0.000000e+00 1236
11 TraesCS4D01G106900 chr2D 95.703 768 31 2 4385 5150 476984927 476985694 0.000000e+00 1234
12 TraesCS4D01G106900 chr2D 93.821 793 39 10 4364 5150 194695219 194696007 0.000000e+00 1184
13 TraesCS4D01G106900 chr6D 94.898 784 36 4 4368 5148 309989261 309988479 0.000000e+00 1223
14 TraesCS4D01G106900 chr6D 82.035 1091 168 19 3040 4108 473271844 473270760 0.000000e+00 904
15 TraesCS4D01G106900 chr2B 94.750 781 36 4 4370 5148 79649538 79648761 0.000000e+00 1210
16 TraesCS4D01G106900 chr5D 94.125 783 43 3 4368 5148 250594781 250594000 0.000000e+00 1188
17 TraesCS4D01G106900 chr3A 75.237 2641 576 71 1080 3683 36246497 36249096 0.000000e+00 1182
18 TraesCS4D01G106900 chr3A 75.009 2637 588 61 1080 3682 36300277 36302876 0.000000e+00 1153
19 TraesCS4D01G106900 chr1D 93.484 798 46 6 4354 5148 19406806 19406012 0.000000e+00 1181
20 TraesCS4D01G106900 chr3D 75.079 2544 565 57 1080 3585 26300877 26303389 0.000000e+00 1122
21 TraesCS4D01G106900 chr3D 78.976 1270 245 18 2330 3588 26282540 26283798 0.000000e+00 846


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 TraesCS4D01G106900 chr4D 85171410 85176559 5149 True 9511.0 9511 100.0000 1 5150 1 chr4D.!!$R1 5149
1 TraesCS4D01G106900 chr4D 85259511 85263725 4214 True 3248.0 6248 93.3220 119 4370 2 chr4D.!!$R3 4251
2 TraesCS4D01G106900 chr4D 396428139 396428901 762 True 1199.0 1199 95.0390 4385 5148 1 chr4D.!!$R2 763
3 TraesCS4D01G106900 chr4B 122296942 122301278 4336 True 3626.5 6951 96.7340 7 4370 2 chr4B.!!$R1 4363
4 TraesCS4D01G106900 chr4A 498985442 498989768 4326 True 3607.0 6931 95.8715 4 4370 2 chr4A.!!$R1 4366
5 TraesCS4D01G106900 chr7B 585533487 585534271 784 True 1266.0 1266 95.9240 4373 5150 1 chr7B.!!$R2 777
6 TraesCS4D01G106900 chr7B 561071002 561071781 779 True 1206.0 1206 94.6150 4371 5148 1 chr7B.!!$R1 777
7 TraesCS4D01G106900 chrUn 75441564 75444161 2597 False 1236.0 1236 75.5410 1079 3682 1 chrUn.!!$F1 2603
8 TraesCS4D01G106900 chr2D 476984927 476985694 767 False 1234.0 1234 95.7030 4385 5150 1 chr2D.!!$F2 765
9 TraesCS4D01G106900 chr2D 194695219 194696007 788 False 1184.0 1184 93.8210 4364 5150 1 chr2D.!!$F1 786
10 TraesCS4D01G106900 chr6D 309988479 309989261 782 True 1223.0 1223 94.8980 4368 5148 1 chr6D.!!$R1 780
11 TraesCS4D01G106900 chr6D 473270760 473271844 1084 True 904.0 904 82.0350 3040 4108 1 chr6D.!!$R2 1068
12 TraesCS4D01G106900 chr2B 79648761 79649538 777 True 1210.0 1210 94.7500 4370 5148 1 chr2B.!!$R1 778
13 TraesCS4D01G106900 chr5D 250594000 250594781 781 True 1188.0 1188 94.1250 4368 5148 1 chr5D.!!$R1 780
14 TraesCS4D01G106900 chr3A 36246497 36249096 2599 False 1182.0 1182 75.2370 1080 3683 1 chr3A.!!$F1 2603
15 TraesCS4D01G106900 chr3A 36300277 36302876 2599 False 1153.0 1153 75.0090 1080 3682 1 chr3A.!!$F2 2602
16 TraesCS4D01G106900 chr1D 19406012 19406806 794 True 1181.0 1181 93.4840 4354 5148 1 chr1D.!!$R1 794
17 TraesCS4D01G106900 chr3D 26300877 26303389 2512 False 1122.0 1122 75.0790 1080 3585 1 chr3D.!!$F2 2505
18 TraesCS4D01G106900 chr3D 26282540 26283798 1258 False 846.0 846 78.9760 2330 3588 1 chr3D.!!$F1 1258

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
859 867 0.610687 ACAGTAGGCAAGTCCTGAGC 59.389 55.0 0.00 0.0 46.98 4.26 F
1650 1666 1.028905 TTGCAAAGTTACCTGCGCTT 58.971 45.0 9.73 0.0 41.63 4.68 F
2979 2998 0.167470 CTTGCATGGTCTCACTTGCG 59.833 55.0 0.00 0.0 42.48 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 2338 5.563867 CGAGTCTAGAAGGAGATATGCCAAC 60.564 48.0 0.00 0.0 0.0 3.77 R
3357 3379 2.234661 CAGTAGTCCATGCAAGTCTCCA 59.765 50.0 0.00 0.0 0.0 3.86 R
4197 4238 0.105964 ACTGCAGCACCGAACACTAA 59.894 50.0 15.27 0.0 0.0 2.24 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
76 77 8.043113 TGAAGTAGATATTGCCATGCCTATAAG 58.957 37.037 0.00 0.00 0.00 1.73
78 79 7.922382 AGTAGATATTGCCATGCCTATAAGTT 58.078 34.615 0.00 0.00 0.00 2.66
170 171 0.951558 GGATGTTTGTGCAACCGTCT 59.048 50.000 0.00 0.00 33.97 4.18
176 177 1.210870 TTGTGCAACCGTCTAACGAC 58.789 50.000 0.24 0.00 42.28 4.34
234 235 6.954297 GTGCGTTAATCTCTACTAACTTTTGC 59.046 38.462 0.00 0.00 0.00 3.68
267 270 6.679327 ACAGTCTTGTTTTTAGAGTTCCAC 57.321 37.500 0.00 0.00 32.28 4.02
338 341 9.853555 CATGGTGCTTGTTAGTTGATTTAAATA 57.146 29.630 0.00 0.00 0.00 1.40
369 372 4.990426 GGATGATTCCCACAAACAACTTTG 59.010 41.667 0.00 0.00 38.40 2.77
388 391 4.411256 TTGTATGGGTCGTATTTCTCCC 57.589 45.455 0.00 0.00 40.26 4.30
407 410 3.140144 TCCCTCCACCTTTTTCAACATCT 59.860 43.478 0.00 0.00 0.00 2.90
529 534 2.092753 GGATGGATCTGAAGAAGGTGCA 60.093 50.000 0.00 0.00 42.19 4.57
555 560 9.975218 ATGTTTTGTATCTCCTTATAACAGGTT 57.025 29.630 0.00 0.00 35.15 3.50
859 867 0.610687 ACAGTAGGCAAGTCCTGAGC 59.389 55.000 0.00 0.00 46.98 4.26
997 1009 3.423539 TCAACAAAGACAGCTAGCCAT 57.576 42.857 12.13 0.00 0.00 4.40
1178 1190 2.093447 CCTGGAATGACAGTACCCACTC 60.093 54.545 0.00 0.00 36.75 3.51
1522 1538 1.678101 ACCTTCAAGTGCTGCAACTTC 59.322 47.619 2.77 0.00 38.34 3.01
1650 1666 1.028905 TTGCAAAGTTACCTGCGCTT 58.971 45.000 9.73 0.00 41.63 4.68
1816 1832 2.487762 CTCCAAAACTTCGCATTAGCCA 59.512 45.455 0.00 0.00 37.52 4.75
2070 2086 2.039613 GGGGAATCATCTAGAAGGCCAG 59.960 54.545 5.01 0.00 0.00 4.85
2176 2195 2.004583 CATAGCGAACCTTCCGAACA 57.995 50.000 0.00 0.00 0.00 3.18
2239 2258 1.681229 TCCCCAATGGTTAGGAGCTT 58.319 50.000 0.00 0.00 34.77 3.74
2271 2290 7.938140 TTTGCAAATACTAGGTTTAGCTGAT 57.062 32.000 8.05 0.00 0.00 2.90
2319 2338 6.006275 TCCTCCCTTTCCAATTTATCTCAG 57.994 41.667 0.00 0.00 0.00 3.35
2544 2563 4.506288 GGTAATGCCAAACAACTCACAAAC 59.494 41.667 0.00 0.00 37.17 2.93
2557 2576 6.550108 ACAACTCACAAACCTAGAACTCTCTA 59.450 38.462 0.00 0.00 32.70 2.43
2703 2722 5.770162 CCTAAAAGTTCTCAGTGTTTCCCAT 59.230 40.000 0.00 0.00 0.00 4.00
2979 2998 0.167470 CTTGCATGGTCTCACTTGCG 59.833 55.000 0.00 0.00 42.48 4.85
2986 3005 1.078759 GGTCTCACTTGCGATGGTCG 61.079 60.000 0.00 0.00 43.89 4.79
3056 3075 4.505922 GTCTTCGCCATCACTTGATAGAAG 59.494 45.833 16.91 16.91 38.97 2.85
3282 3304 1.594331 GGCATCGTAATCTGGTTCCC 58.406 55.000 0.00 0.00 0.00 3.97
3357 3379 6.004574 TCTAGTATATGAGTTCATGCCTCGT 58.995 40.000 4.90 10.56 37.15 4.18
3616 3642 7.946655 GTTGATTCAACGGTATCATCATCTA 57.053 36.000 13.42 0.00 34.63 1.98
4066 4107 2.980233 GGCTTCGCTGCACCAAGT 60.980 61.111 0.00 0.00 34.04 3.16
4176 4217 9.758651 GGTAATCACCATTTTTAGTGTTCTTTT 57.241 29.630 0.00 0.00 45.04 2.27
4222 4263 1.135972 GTTCGGTGCTGCAGTGTTATG 60.136 52.381 16.64 1.09 0.00 1.90
4259 4300 9.131791 ACAAGGTTTTATCACTCACTACATTTT 57.868 29.630 0.00 0.00 0.00 1.82
4938 4990 1.514228 GACAGCGAGCGTCGATCAA 60.514 57.895 11.52 0.00 43.74 2.57
5067 5120 4.043561 ACGGAGGAGATGACTATAGTGGAT 59.956 45.833 10.90 1.74 0.00 3.41
5113 5167 3.052566 ACTCAGGATGTGGACAGGATAGA 60.053 47.826 0.00 0.00 37.40 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.484959 GCCTTTTAACATCCAATACTTTTCGAG 59.515 37.037 0.00 0.00 0.00 4.04
14 15 7.589958 TCAAACTTTAGCCTTTTAACATCCA 57.410 32.000 0.00 0.00 0.00 3.41
15 16 9.569167 GTATCAAACTTTAGCCTTTTAACATCC 57.431 33.333 0.00 0.00 0.00 3.51
16 17 9.569167 GGTATCAAACTTTAGCCTTTTAACATC 57.431 33.333 0.00 0.00 0.00 3.06
76 77 1.816835 GCTGCTTGGTTACCCCTTAAC 59.183 52.381 0.00 0.00 39.66 2.01
78 79 1.368374 AGCTGCTTGGTTACCCCTTA 58.632 50.000 0.00 0.00 0.00 2.69
98 99 5.657302 ACTGCCATAGCTACAAGTAACTAGT 59.343 40.000 0.00 0.00 40.80 2.57
170 171 0.104120 CCATCATCCTGCCGTCGTTA 59.896 55.000 0.00 0.00 0.00 3.18
176 177 1.820906 CACCACCATCATCCTGCCG 60.821 63.158 0.00 0.00 0.00 5.69
267 270 8.085909 ACCTAAAAACACTTGGATAAAATTCGG 58.914 33.333 0.00 0.00 0.00 4.30
338 341 3.843422 TGTGGGAATCATCCTTGTTGTT 58.157 40.909 0.00 0.00 45.77 2.83
369 372 3.006644 GGAGGGAGAAATACGACCCATAC 59.993 52.174 0.00 0.00 40.38 2.39
388 391 4.829492 AGGAAGATGTTGAAAAAGGTGGAG 59.171 41.667 0.00 0.00 0.00 3.86
407 410 5.193124 TCATACTACAGGTAGGAGTGAGGAA 59.807 44.000 10.91 0.00 36.46 3.36
529 534 9.975218 AACCTGTTATAAGGAGATACAAAACAT 57.025 29.630 0.00 0.00 40.02 2.71
618 623 4.688879 CGCATATGGACCAATATGTTACGT 59.311 41.667 17.79 0.00 40.95 3.57
859 867 7.387948 CCTAACCAATTATACTTCAATCCCTCG 59.612 40.741 0.00 0.00 0.00 4.63
960 972 8.733458 TCTTTGTTGAAGATCTTGATTACATGG 58.267 33.333 14.00 3.50 39.44 3.66
997 1009 9.264719 CTGCATGATTGTAGTAATCTTCATGTA 57.735 33.333 0.00 6.87 41.42 2.29
1178 1190 1.338020 GAACACCTTCCCAACTGCAAG 59.662 52.381 0.00 0.00 42.29 4.01
1650 1666 3.449377 TGCTACCCACGTTCAGAATATGA 59.551 43.478 0.00 0.00 35.62 2.15
1816 1832 8.879227 TGGGATTTTTCCATGAAAGAAGTTATT 58.121 29.630 0.00 0.00 32.93 1.40
2070 2086 7.881775 AAGGTTGGATAATGAACTTGGTATC 57.118 36.000 0.00 0.00 0.00 2.24
2271 2290 9.403583 GATGGAATAAACCCTGTAAAGATGTTA 57.596 33.333 0.00 0.00 0.00 2.41
2319 2338 5.563867 CGAGTCTAGAAGGAGATATGCCAAC 60.564 48.000 0.00 0.00 0.00 3.77
2979 2998 7.221067 CAGAACAATAAGAGAAGTACGACCATC 59.779 40.741 0.00 0.00 0.00 3.51
2986 3005 6.342111 CCCTCCAGAACAATAAGAGAAGTAC 58.658 44.000 0.00 0.00 0.00 2.73
3056 3075 5.357032 TCACTGAAAGAAACTTTGGGAAGAC 59.643 40.000 1.41 0.00 37.43 3.01
3282 3304 4.206698 GCTTGAGCATGCAGTTAGTATG 57.793 45.455 21.98 1.06 42.51 2.39
3357 3379 2.234661 CAGTAGTCCATGCAAGTCTCCA 59.765 50.000 0.00 0.00 0.00 3.86
3418 3443 8.088981 GCTTAGCCTTTGAGCTACTGTAATATA 58.911 37.037 0.00 0.00 44.86 0.86
3616 3642 6.244552 TGAAGAGGCTGAGTATGAATCATT 57.755 37.500 0.00 0.00 0.00 2.57
4066 4107 2.103538 GCGCTCGTTCGGGTATGA 59.896 61.111 0.00 0.00 0.00 2.15
4122 4163 4.884961 ACCCTCTGAGATAAGCTTCCTTA 58.115 43.478 0.00 0.00 37.90 2.69
4175 4216 3.828875 AATGGTTTCCCGCAAGAAAAA 57.171 38.095 0.03 0.00 37.49 1.94
4176 4217 3.828875 AAATGGTTTCCCGCAAGAAAA 57.171 38.095 0.03 0.00 37.49 2.29
4177 4218 3.828875 AAAATGGTTTCCCGCAAGAAA 57.171 38.095 0.00 0.00 43.02 2.52
4178 4219 3.828875 AAAAATGGTTTCCCGCAAGAA 57.171 38.095 0.00 0.00 43.02 2.52
4179 4220 3.892588 ACTAAAAATGGTTTCCCGCAAGA 59.107 39.130 0.00 0.00 43.02 3.02
4180 4221 3.987220 CACTAAAAATGGTTTCCCGCAAG 59.013 43.478 0.00 0.00 0.00 4.01
4181 4222 3.385111 ACACTAAAAATGGTTTCCCGCAA 59.615 39.130 0.00 0.00 0.00 4.85
4182 4223 2.959707 ACACTAAAAATGGTTTCCCGCA 59.040 40.909 0.00 0.00 0.00 5.69
4183 4224 3.653539 ACACTAAAAATGGTTTCCCGC 57.346 42.857 0.00 0.00 0.00 6.13
4184 4225 4.223659 CGAACACTAAAAATGGTTTCCCG 58.776 43.478 0.00 0.00 0.00 5.14
4185 4226 4.038282 ACCGAACACTAAAAATGGTTTCCC 59.962 41.667 0.00 0.00 0.00 3.97
4186 4227 4.979815 CACCGAACACTAAAAATGGTTTCC 59.020 41.667 0.00 0.00 0.00 3.13
4187 4228 4.443063 GCACCGAACACTAAAAATGGTTTC 59.557 41.667 0.00 0.00 0.00 2.78
4188 4229 4.098807 AGCACCGAACACTAAAAATGGTTT 59.901 37.500 0.00 0.00 0.00 3.27
4189 4230 3.634910 AGCACCGAACACTAAAAATGGTT 59.365 39.130 0.00 0.00 0.00 3.67
4190 4231 3.004315 CAGCACCGAACACTAAAAATGGT 59.996 43.478 0.00 0.00 0.00 3.55
4191 4232 3.564511 CAGCACCGAACACTAAAAATGG 58.435 45.455 0.00 0.00 0.00 3.16
4192 4233 2.979813 GCAGCACCGAACACTAAAAATG 59.020 45.455 0.00 0.00 0.00 2.32
4193 4234 2.621055 TGCAGCACCGAACACTAAAAAT 59.379 40.909 0.00 0.00 0.00 1.82
4194 4235 2.017782 TGCAGCACCGAACACTAAAAA 58.982 42.857 0.00 0.00 0.00 1.94
4195 4236 1.601903 CTGCAGCACCGAACACTAAAA 59.398 47.619 0.00 0.00 0.00 1.52
4196 4237 1.225855 CTGCAGCACCGAACACTAAA 58.774 50.000 0.00 0.00 0.00 1.85
4197 4238 0.105964 ACTGCAGCACCGAACACTAA 59.894 50.000 15.27 0.00 0.00 2.24
4198 4239 0.599991 CACTGCAGCACCGAACACTA 60.600 55.000 15.27 0.00 0.00 2.74
4199 4240 1.889105 CACTGCAGCACCGAACACT 60.889 57.895 15.27 0.00 0.00 3.55
4200 4241 1.714899 AACACTGCAGCACCGAACAC 61.715 55.000 15.27 0.00 0.00 3.32
4201 4242 0.179070 TAACACTGCAGCACCGAACA 60.179 50.000 15.27 0.00 0.00 3.18
4202 4243 1.135972 CATAACACTGCAGCACCGAAC 60.136 52.381 15.27 0.00 0.00 3.95
4203 4244 1.155889 CATAACACTGCAGCACCGAA 58.844 50.000 15.27 0.00 0.00 4.30
4259 4300 1.539388 CTCCAAAAATACGGTGCTGCA 59.461 47.619 0.00 0.00 0.00 4.41
4938 4990 2.436173 GCTACTTGGGCTAGTGATCCTT 59.564 50.000 3.59 0.00 0.00 3.36
4954 5007 2.315176 CAGGCCTACTCTGATGCTACT 58.685 52.381 3.98 0.00 34.36 2.57
5067 5120 3.010138 AGTTTATTTCAGCCCCACTGCTA 59.990 43.478 0.00 0.00 46.76 3.49
5084 5138 3.901222 TGTCCACATCCTGAGTCAGTTTA 59.099 43.478 18.74 4.60 0.00 2.01
5113 5167 0.388649 GTCACGCGTCCTGACATCTT 60.389 55.000 19.79 0.00 38.36 2.40


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

AutoCloner maintained by Alex Coulton.