Multiple sequence alignment - TraesCS4D01G211200

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 TraesCS4D01G211200 chr4D 100.000 4953 0 0 1 4953 363675579 363680531 0.000000e+00 9147
1 TraesCS4D01G211200 chr4D 90.419 167 10 4 1811 1976 100229655 100229494 1.080000e-51 215
2 TraesCS4D01G211200 chr4B 94.079 2297 102 17 2003 4282 449123676 449125955 0.000000e+00 3458
3 TraesCS4D01G211200 chr4B 91.647 1724 60 22 341 2005 449121875 449123573 0.000000e+00 2309
4 TraesCS4D01G211200 chr4B 88.933 506 40 13 4277 4775 449127401 449127897 1.180000e-170 610
5 TraesCS4D01G211200 chr4B 93.906 361 16 3 1 355 449101476 449101836 1.570000e-149 540
6 TraesCS4D01G211200 chr4B 93.838 357 17 2 1 352 449104105 449104461 2.620000e-147 532
7 TraesCS4D01G211200 chr4B 95.161 186 9 0 4763 4948 449128662 449128847 1.350000e-75 294
8 TraesCS4D01G211200 chr4B 78.613 173 27 8 2 171 49113015 49113180 6.780000e-19 106
9 TraesCS4D01G211200 chr4A 97.684 1986 43 2 2003 3986 101750118 101748134 0.000000e+00 3410
10 TraesCS4D01G211200 chr4A 92.941 2040 83 16 1 2005 101752296 101750283 0.000000e+00 2913
11 TraesCS4D01G211200 chr4A 92.593 567 23 5 4076 4635 101747695 101747141 0.000000e+00 797
12 TraesCS4D01G211200 chr4A 87.296 307 12 16 4651 4953 101747080 101746797 4.780000e-85 326
13 TraesCS4D01G211200 chr4A 91.124 169 10 4 1808 1975 150653310 150653474 1.790000e-54 224
14 TraesCS4D01G211200 chr3B 90.058 171 12 2 1809 1978 519860082 519860248 3.000000e-52 217
15 TraesCS4D01G211200 chr5D 89.595 173 10 6 1808 1977 461072598 461072765 3.880000e-51 213
16 TraesCS4D01G211200 chr5D 89.017 173 12 3 1808 1978 241274683 241274850 1.810000e-49 207
17 TraesCS4D01G211200 chr2D 89.535 172 13 2 1807 1977 336511299 336511132 3.880000e-51 213
18 TraesCS4D01G211200 chr7A 89.474 171 13 5 1809 1978 498937204 498937370 1.400000e-50 211
19 TraesCS4D01G211200 chr6A 78.049 246 43 10 2 244 39459097 39459334 1.440000e-30 145
20 TraesCS4D01G211200 chr7D 76.654 257 50 9 2 254 623708797 623708547 3.110000e-27 134
21 TraesCS4D01G211200 chr3A 76.562 256 51 9 2 254 21333318 21333069 1.120000e-26 132
22 TraesCS4D01G211200 chrUn 79.487 156 29 3 17 172 75994389 75994237 1.890000e-19 108
23 TraesCS4D01G211200 chrUn 79.487 156 29 3 17 172 231198092 231197940 1.890000e-19 108


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 TraesCS4D01G211200 chr4D 363675579 363680531 4952 False 9147.00 9147 100.0000 1 4953 1 chr4D.!!$F1 4952
1 TraesCS4D01G211200 chr4B 449121875 449128847 6972 False 1667.75 3458 92.4550 341 4948 4 chr4B.!!$F3 4607
2 TraesCS4D01G211200 chr4B 449101476 449104461 2985 False 536.00 540 93.8720 1 355 2 chr4B.!!$F2 354
3 TraesCS4D01G211200 chr4A 101746797 101752296 5499 True 1861.50 3410 92.6285 1 4953 4 chr4A.!!$R1 4952

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
869 3536 0.097674 GCGTGAGTCACATTGCATCC 59.902 55.000 22.66 0.0 33.40 3.51 F
1321 3989 1.406069 CGGAGCAAGAAGGCTATGTGT 60.406 52.381 0.00 0.0 45.99 3.72 F
3198 6083 0.537188 GGCAGTGGAGAAGATTCGGA 59.463 55.000 0.00 0.0 0.00 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1867 4573 4.021894 AGTGTAGATTCACTCGTTTGCTCT 60.022 41.667 0.0 0.0 44.07 4.09 R
3253 6138 2.470983 TTGAATCTGCATGGTCACGA 57.529 45.000 0.0 0.0 0.00 4.35 R
4064 6949 0.107654 GCCTGTCAAGCGGTAATCCT 60.108 55.000 0.0 0.0 0.00 3.24 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
181 183 1.957177 TGTCTATCCGAGCACCTGATC 59.043 52.381 0.00 0.00 0.00 2.92
224 226 2.220479 GGCTTAAACTCGCCGATACT 57.780 50.000 0.00 0.00 36.45 2.12
240 242 5.277828 GCCGATACTTCACAAAAGTTTCTGT 60.278 40.000 0.00 0.00 0.00 3.41
251 253 5.163519 ACAAAAGTTTCTGTCTCACCCATTG 60.164 40.000 0.00 0.00 0.00 2.82
256 258 1.839994 TCTGTCTCACCCATTGATCCC 59.160 52.381 0.00 0.00 32.17 3.85
258 260 1.991813 TGTCTCACCCATTGATCCCAA 59.008 47.619 0.00 0.00 36.61 4.12
259 261 2.025981 TGTCTCACCCATTGATCCCAAG 60.026 50.000 0.00 0.00 35.48 3.61
534 3178 3.735029 GCCGACGAGACGACAGGT 61.735 66.667 0.00 0.00 35.09 4.00
566 3210 0.478789 ATACCCCCACAGTCCCCAAA 60.479 55.000 0.00 0.00 0.00 3.28
676 3321 2.045885 ACAGGTAATCCTTCCTCCTCCA 59.954 50.000 0.00 0.00 43.07 3.86
696 3350 1.386550 CCCCAATTCCCCTCCGTTT 59.613 57.895 0.00 0.00 0.00 3.60
701 3355 2.764637 AATTCCCCTCCGTTTGCGCT 62.765 55.000 9.73 0.00 36.67 5.92
712 3366 1.007011 CGTTTGCGCTTCGTCTCATAG 60.007 52.381 9.73 0.00 0.00 2.23
742 3396 2.869256 GCTCGCAGCTTGCTCGATC 61.869 63.158 13.97 8.92 42.25 3.69
771 3425 2.020720 AGAGCTCAGATCGAACGATGT 58.979 47.619 17.77 7.71 34.60 3.06
780 3434 3.312973 AGATCGAACGATGTAGTCTGGTC 59.687 47.826 14.33 0.00 34.60 4.02
781 3435 2.429478 TCGAACGATGTAGTCTGGTCA 58.571 47.619 0.00 0.00 0.00 4.02
783 3437 3.064958 TCGAACGATGTAGTCTGGTCATC 59.935 47.826 0.00 0.00 35.87 2.92
791 3445 2.593346 AGTCTGGTCATCTTCATCGC 57.407 50.000 0.00 0.00 0.00 4.58
800 3454 1.271934 CATCTTCATCGCCGGATCTCT 59.728 52.381 5.05 0.00 0.00 3.10
826 3480 1.539124 AGTTCCTGGGTGGGGTCTC 60.539 63.158 0.00 0.00 36.20 3.36
827 3481 2.204090 TTCCTGGGTGGGGTCTCC 60.204 66.667 0.00 0.00 36.20 3.71
828 3482 4.715130 TCCTGGGTGGGGTCTCCG 62.715 72.222 0.00 0.00 38.76 4.63
829 3483 4.715130 CCTGGGTGGGGTCTCCGA 62.715 72.222 0.00 0.00 38.76 4.55
830 3484 3.391382 CTGGGTGGGGTCTCCGAC 61.391 72.222 0.00 0.00 40.52 4.79
836 3490 4.828296 GGGGTCTCCGACGGGCTA 62.828 72.222 15.25 0.00 32.65 3.93
837 3491 2.521224 GGGTCTCCGACGGGCTAT 60.521 66.667 15.25 0.00 32.65 2.97
838 3492 2.728817 GGTCTCCGACGGGCTATG 59.271 66.667 15.25 0.00 32.65 2.23
869 3536 0.097674 GCGTGAGTCACATTGCATCC 59.902 55.000 22.66 0.00 33.40 3.51
939 3607 4.711355 ACGAATGAATCAATCCCCAAATGT 59.289 37.500 0.00 0.00 0.00 2.71
1027 3695 5.692204 CGCTATTCTTCGATGTTACTCCATT 59.308 40.000 0.00 0.00 0.00 3.16
1321 3989 1.406069 CGGAGCAAGAAGGCTATGTGT 60.406 52.381 0.00 0.00 45.99 3.72
1370 4038 3.312421 CCGTTGCCGAGATTCAACATAAT 59.688 43.478 6.03 0.00 41.80 1.28
1734 4417 8.630917 CAGTACCTGCAATACTGTAACTAGTAT 58.369 37.037 21.73 0.00 43.03 2.12
1736 4419 9.813446 GTACCTGCAATACTGTAACTAGTATTT 57.187 33.333 8.09 0.00 46.42 1.40
1813 4516 8.697292 AGAAACTGAGAAGTACTGGATAATACC 58.303 37.037 0.00 0.00 0.00 2.73
1875 4581 8.338259 CCAATATGAACTACATACAGAGCAAAC 58.662 37.037 0.00 0.00 43.12 2.93
2044 4918 6.560003 TTGAGCATAGAAATAGTGGGAGAA 57.440 37.500 0.00 0.00 0.00 2.87
2158 5040 2.758423 TCGCATGGCAGACTAGTCTAAA 59.242 45.455 24.75 13.50 37.98 1.85
2553 5435 3.583526 ACCTCCTAAGTTTTCCAGTCTCC 59.416 47.826 0.00 0.00 0.00 3.71
2849 5734 2.012673 ACATGCGCTCCATTTTCTCTC 58.987 47.619 9.73 0.00 29.71 3.20
3198 6083 0.537188 GGCAGTGGAGAAGATTCGGA 59.463 55.000 0.00 0.00 0.00 4.55
3253 6138 3.053842 TGGACGTTAGAGTCTATCCTGGT 60.054 47.826 16.00 4.19 40.76 4.00
3256 6141 3.204526 CGTTAGAGTCTATCCTGGTCGT 58.795 50.000 0.00 0.00 0.00 4.34
3368 6253 1.804372 GCGATGTAGCTGCTAGTGCTT 60.804 52.381 10.13 0.00 41.46 3.91
3384 6269 3.868077 AGTGCTTGTTCGAGCTATTCATC 59.132 43.478 12.44 0.00 43.11 2.92
3724 6609 0.846693 AGAGGTTTGTCAGGGTTGCT 59.153 50.000 0.00 0.00 0.00 3.91
3928 6813 0.466922 AACAGCAGTGCAAGGAGCTT 60.467 50.000 19.20 0.00 45.94 3.74
4064 6949 3.243035 CGGAAACATGTGTGCTCTGAAAA 60.243 43.478 5.94 0.00 0.00 2.29
4074 6959 2.096013 GTGCTCTGAAAAGGATTACCGC 59.904 50.000 0.00 0.00 41.83 5.68
4174 7408 1.278238 GGCGATTGTGAAGTCTACCG 58.722 55.000 0.00 0.00 0.00 4.02
4300 8992 1.274167 CTCCACTACCGTGTAAAGCCA 59.726 52.381 0.00 0.00 39.55 4.75
4402 9096 2.254546 TCCTGTGTGCCACTTGTTAG 57.745 50.000 0.00 0.00 35.11 2.34
4412 9107 2.224548 GCCACTTGTTAGAACCTGGAGT 60.225 50.000 0.00 0.00 0.00 3.85
4413 9108 3.403038 CCACTTGTTAGAACCTGGAGTG 58.597 50.000 0.00 0.48 34.38 3.51
4414 9109 2.808543 CACTTGTTAGAACCTGGAGTGC 59.191 50.000 0.00 0.00 0.00 4.40
4424 9119 1.288127 CTGGAGTGCTGCTTTTGGC 59.712 57.895 0.00 0.00 42.22 4.52
4535 9230 2.278792 CGCTCGACGCATCATCCA 60.279 61.111 7.47 0.00 39.08 3.41
4540 9235 1.007387 CGACGCATCATCCATCCGA 60.007 57.895 0.00 0.00 0.00 4.55
4544 9239 2.862536 GACGCATCATCCATCCGATATG 59.137 50.000 0.00 0.00 0.00 1.78
4553 9248 5.837438 TCATCCATCCGATATGCATATCTCT 59.163 40.000 33.25 20.06 37.57 3.10
4583 9278 2.081462 ACACGATTCCGACCAAATTCC 58.919 47.619 0.00 0.00 39.50 3.01
4605 9300 4.154375 CCTAGTCGAGACATATACACGCAT 59.846 45.833 5.99 0.00 0.00 4.73
4629 9324 7.862741 TTAAAACGCGTCTATATACATCTGG 57.137 36.000 14.44 0.00 0.00 3.86
4788 10316 1.231751 ATCAGGGACAGGGAGGGAGA 61.232 60.000 0.00 0.00 0.00 3.71
4948 10476 4.326766 CCCGCAGCAACACCAACG 62.327 66.667 0.00 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 125 6.597280 AGCAGCAAACTTTTGAACCAAAAATA 59.403 30.769 5.87 0.00 41.77 1.40
215 217 3.806316 AACTTTTGTGAAGTATCGGCG 57.194 42.857 0.00 0.00 0.00 6.46
219 221 8.064814 GTGAGACAGAAACTTTTGTGAAGTATC 58.935 37.037 5.90 0.00 35.27 2.24
224 226 4.398044 GGGTGAGACAGAAACTTTTGTGAA 59.602 41.667 5.90 0.00 35.27 3.18
240 242 2.561187 TCTTGGGATCAATGGGTGAGA 58.439 47.619 0.00 0.00 40.43 3.27
251 253 5.934781 ACAAAGACATCCTATCTTGGGATC 58.065 41.667 0.00 0.00 41.17 3.36
256 258 5.006165 GCGAAGACAAAGACATCCTATCTTG 59.994 44.000 0.00 0.00 36.52 3.02
258 260 4.404073 AGCGAAGACAAAGACATCCTATCT 59.596 41.667 0.00 0.00 0.00 1.98
259 261 4.688021 AGCGAAGACAAAGACATCCTATC 58.312 43.478 0.00 0.00 0.00 2.08
534 3178 1.386525 GGGGTATCGACACCGCTGTA 61.387 60.000 21.64 0.00 45.57 2.74
676 3321 1.440362 AACGGAGGGGAATTGGGGTT 61.440 55.000 0.00 0.00 0.00 4.11
696 3350 1.064208 GAGACTATGAGACGAAGCGCA 59.936 52.381 11.47 0.00 0.00 6.09
701 3355 4.882427 CCCTAACTGAGACTATGAGACGAA 59.118 45.833 0.00 0.00 0.00 3.85
712 3366 0.179124 CTGCGAGCCCTAACTGAGAC 60.179 60.000 0.00 0.00 0.00 3.36
742 3396 1.888512 GATCTGAGCTCTAGGCCTCTG 59.111 57.143 9.68 3.39 43.05 3.35
771 3425 2.362397 GGCGATGAAGATGACCAGACTA 59.638 50.000 0.00 0.00 0.00 2.59
780 3434 1.271934 AGAGATCCGGCGATGAAGATG 59.728 52.381 9.30 0.00 0.00 2.90
781 3435 1.543802 GAGAGATCCGGCGATGAAGAT 59.456 52.381 9.30 0.93 0.00 2.40
783 3437 0.038709 GGAGAGATCCGGCGATGAAG 60.039 60.000 9.30 0.00 0.00 3.02
791 3445 1.602323 CTCGAGGGGAGAGATCCGG 60.602 68.421 3.91 0.00 46.23 5.14
800 3454 2.038975 CCCAGGAACTCGAGGGGA 59.961 66.667 18.41 0.00 41.49 4.81
902 3569 3.283751 TCATTCGTGTGGGTCAAAAGTT 58.716 40.909 0.00 0.00 0.00 2.66
939 3607 1.063266 GCCCACTCCATTTCCCCATTA 60.063 52.381 0.00 0.00 0.00 1.90
1321 3989 4.020617 CTCCTCAAGCCACCGCCA 62.021 66.667 0.00 0.00 34.57 5.69
1370 4038 8.174085 TCAAATTTACCTTCCCAGGATAGAAAA 58.826 33.333 0.00 0.00 44.19 2.29
1786 4489 9.738832 GTATTATCCAGTACTTCTCAGTTTCTC 57.261 37.037 0.00 0.00 34.06 2.87
1813 4516 4.565028 GGCTTATATTTAGGAACGGAGGGG 60.565 50.000 0.00 0.00 0.00 4.79
1857 4563 4.923871 CACTCGTTTGCTCTGTATGTAGTT 59.076 41.667 0.00 0.00 0.00 2.24
1867 4573 4.021894 AGTGTAGATTCACTCGTTTGCTCT 60.022 41.667 0.00 0.00 44.07 4.09
2044 4918 9.649316 AAGTACTAAGTCATTAGATAGCTTCCT 57.351 33.333 0.00 0.00 40.86 3.36
2158 5040 5.631096 CGTCGAGAACTGCATATGAACATAT 59.369 40.000 6.97 1.97 34.50 1.78
2308 5190 9.070179 ACAACACCTATAACTTTACGGAATTTT 57.930 29.630 0.00 0.00 0.00 1.82
2567 5449 7.227049 TGCATCCATGAAGTCGTCTATATAA 57.773 36.000 0.00 0.00 0.00 0.98
2674 5557 5.233988 CAGCCCTAGATAGACAATAACTGC 58.766 45.833 0.00 0.00 0.00 4.40
2834 5719 4.692625 TCTTCAAAGAGAGAAAATGGAGCG 59.307 41.667 0.00 0.00 0.00 5.03
3064 5949 7.301420 TCCCAATATAATATGCACCCTTGAAA 58.699 34.615 0.00 0.00 0.00 2.69
3253 6138 2.470983 TTGAATCTGCATGGTCACGA 57.529 45.000 0.00 0.00 0.00 4.35
3256 6141 6.458615 CGTGAAATATTGAATCTGCATGGTCA 60.459 38.462 0.00 0.00 0.00 4.02
3368 6253 3.198068 GGCAAGATGAATAGCTCGAACA 58.802 45.455 0.00 0.00 0.00 3.18
3384 6269 3.057386 TGACATAATGCACTTGTGGCAAG 60.057 43.478 10.27 7.27 40.64 4.01
3724 6609 2.324330 CGTGGCTGGTGCGATTTCA 61.324 57.895 0.00 0.00 40.82 2.69
4027 6912 3.375922 TGTTTCCGTTTCAGAGTTGGTTC 59.624 43.478 0.00 0.00 0.00 3.62
4031 6916 4.201910 ACACATGTTTCCGTTTCAGAGTTG 60.202 41.667 0.00 0.00 0.00 3.16
4064 6949 0.107654 GCCTGTCAAGCGGTAATCCT 60.108 55.000 0.00 0.00 0.00 3.24
4074 6959 0.316204 CAAAGCAAGGGCCTGTCAAG 59.684 55.000 6.92 0.00 42.56 3.02
4174 7408 2.267324 GAGCACTCCTCACCTGCC 59.733 66.667 0.00 0.00 40.45 4.85
4300 8992 2.869233 ATTGTTGCGAAACACAAGCT 57.131 40.000 8.96 0.00 31.49 3.74
4354 9046 7.495934 GGAGCAACATATACATACAACAAGACT 59.504 37.037 0.00 0.00 0.00 3.24
4360 9052 6.292703 GGAACGGAGCAACATATACATACAAC 60.293 42.308 0.00 0.00 0.00 3.32
4368 9062 3.196901 ACACAGGAACGGAGCAACATATA 59.803 43.478 0.00 0.00 0.00 0.86
4402 9096 1.000938 CAAAAGCAGCACTCCAGGTTC 60.001 52.381 0.00 0.00 0.00 3.62
4412 9107 4.912395 ACCCGGCCAAAAGCAGCA 62.912 61.111 2.24 0.00 46.50 4.41
4413 9108 4.362476 CACCCGGCCAAAAGCAGC 62.362 66.667 2.24 0.00 46.50 5.25
4414 9109 3.683937 CCACCCGGCCAAAAGCAG 61.684 66.667 2.24 0.00 46.50 4.24
4455 9150 2.647297 GCTTGCTGGTTGGTGCTC 59.353 61.111 0.00 0.00 0.00 4.26
4456 9151 3.289834 CGCTTGCTGGTTGGTGCT 61.290 61.111 0.00 0.00 0.00 4.40
4458 9153 1.210931 CATCGCTTGCTGGTTGGTG 59.789 57.895 0.00 0.00 0.00 4.17
4535 9230 4.958581 TGGACAGAGATATGCATATCGGAT 59.041 41.667 31.37 21.80 43.01 4.18
4540 9235 5.046735 GTGAGGTGGACAGAGATATGCATAT 60.047 44.000 19.17 19.17 0.00 1.78
4544 9239 2.432146 TGTGAGGTGGACAGAGATATGC 59.568 50.000 0.00 0.00 0.00 3.14
4553 9248 0.320374 GGAATCGTGTGAGGTGGACA 59.680 55.000 0.00 0.00 0.00 4.02
4583 9278 4.727235 TGCGTGTATATGTCTCGACTAG 57.273 45.455 0.00 0.00 0.00 2.57
4605 9300 7.428020 ACCAGATGTATATAGACGCGTTTTAA 58.572 34.615 15.53 0.00 0.00 1.52
4770 10298 1.862138 TCTCCCTCCCTGTCCCTGA 60.862 63.158 0.00 0.00 0.00 3.86
4788 10316 3.077359 CCCGTCTTTTGCAAGATTCTCT 58.923 45.455 0.00 0.00 41.26 3.10
4807 10335 3.878667 CCCTCGCCAGATTCCCCC 61.879 72.222 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.