Multiple sequence alignment - TraesCS1B01G239000

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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 TraesCS1B01G239000 chr1B 100.000 4013 0 0 1 4013 427216869 427212857 0.000 7411.0
1 TraesCS1B01G239000 chr1D 95.915 3305 114 13 713 4013 315536333 315539620 0.000 5336.0
2 TraesCS1B01G239000 chr1D 93.033 732 35 4 1 726 315528625 315529346 0.000 1055.0
3 TraesCS1B01G239000 chr1D 94.286 35 1 1 1504 1538 36959395 36959362 0.007 52.8
4 TraesCS1B01G239000 chr1A 94.828 2494 115 9 619 3106 396100171 396102656 0.000 3879.0
5 TraesCS1B01G239000 chr1A 94.002 917 38 4 3103 4013 396102709 396103614 0.000 1373.0


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 TraesCS1B01G239000 chr1B 427212857 427216869 4012 True 7411 7411 100.000 1 4013 1 chr1B.!!$R1 4012
1 TraesCS1B01G239000 chr1D 315536333 315539620 3287 False 5336 5336 95.915 713 4013 1 chr1D.!!$F2 3300
2 TraesCS1B01G239000 chr1D 315528625 315529346 721 False 1055 1055 93.033 1 726 1 chr1D.!!$F1 725
3 TraesCS1B01G239000 chr1A 396100171 396103614 3443 False 2626 3879 94.415 619 4013 2 chr1A.!!$F1 3394

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
138 145 0.519961 GGCGGGTACAAACACATGAC 59.48 55.0 0.0 0.0 0.0 3.06 F
1983 1998 0.039618 ACGGCTTTGATGATGGGGTT 59.96 50.0 0.0 0.0 0.0 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2107 2122 0.174845 CTTCCATTGCACCATGCCAG 59.825 55.0 0.0 0.00 44.23 4.85 R
3240 3311 0.743097 GGCCACTACGGTACCTACAG 59.257 60.0 10.9 6.53 36.97 2.74 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
24 25 1.139455 GGCAAAGGTAATGGCATGCAT 59.861 47.619 21.36 8.40 42.45 3.96
134 141 2.973600 GCGGCGGGTACAAACACA 60.974 61.111 9.78 0.00 0.00 3.72
138 145 0.519961 GGCGGGTACAAACACATGAC 59.480 55.000 0.00 0.00 0.00 3.06
140 147 1.504359 CGGGTACAAACACATGACGT 58.496 50.000 0.00 0.00 0.00 4.34
161 168 1.515521 AACTGCTTAGCACGTTGGGC 61.516 55.000 16.77 0.00 33.79 5.36
163 170 4.460873 GCTTAGCACGTTGGGCGC 62.461 66.667 0.00 0.00 46.11 6.53
183 190 1.113517 TGGGGGCTACGATGAGCTAC 61.114 60.000 8.26 3.30 42.43 3.58
184 191 1.113517 GGGGGCTACGATGAGCTACA 61.114 60.000 8.26 0.00 42.43 2.74
185 192 0.969894 GGGGCTACGATGAGCTACAT 59.030 55.000 8.26 0.00 42.43 2.29
186 193 1.344763 GGGGCTACGATGAGCTACATT 59.655 52.381 8.26 0.00 42.43 2.71
187 194 2.224305 GGGGCTACGATGAGCTACATTT 60.224 50.000 8.26 0.00 42.43 2.32
188 195 3.060602 GGGCTACGATGAGCTACATTTC 58.939 50.000 8.26 0.00 42.43 2.17
189 196 3.243907 GGGCTACGATGAGCTACATTTCT 60.244 47.826 8.26 0.00 42.43 2.52
190 197 4.372656 GGCTACGATGAGCTACATTTCTT 58.627 43.478 8.26 0.00 42.43 2.52
191 198 4.811557 GGCTACGATGAGCTACATTTCTTT 59.188 41.667 8.26 0.00 42.43 2.52
196 203 7.295952 ACGATGAGCTACATTTCTTTTACAG 57.704 36.000 0.00 0.00 39.56 2.74
218 225 6.183360 ACAGATGGATGTAGACGTTAGAAGTC 60.183 42.308 0.00 0.00 38.81 3.01
233 240 6.088217 CGTTAGAAGTCGGATATTGCTATGTG 59.912 42.308 0.00 0.00 0.00 3.21
248 255 4.766373 TGCTATGTGGAATGCTTTGAAGAA 59.234 37.500 0.00 0.00 0.00 2.52
250 257 5.335897 GCTATGTGGAATGCTTTGAAGAACA 60.336 40.000 0.00 0.00 0.00 3.18
287 294 4.546570 TCCGAACATATAACATGCTCTCG 58.453 43.478 0.00 0.00 0.00 4.04
291 298 6.183360 CCGAACATATAACATGCTCTCGATTC 60.183 42.308 0.00 0.00 0.00 2.52
323 330 0.824759 GGAAGCGATGTACCCAGACT 59.175 55.000 0.00 0.00 0.00 3.24
330 337 3.864921 GCGATGTACCCAGACTTGAAGTT 60.865 47.826 0.00 0.00 0.00 2.66
342 349 9.177608 CCCAGACTTGAAGTTTTCATTATGATA 57.822 33.333 0.00 0.00 39.84 2.15
426 433 5.973899 TGCAGTTTTGTTTGCCATCTATA 57.026 34.783 0.00 0.00 39.54 1.31
472 479 3.003897 GCTCACGAGTATGTAGCTAGCTT 59.996 47.826 24.88 7.70 0.00 3.74
531 538 0.809636 TATGTGTCCTGCCGAATGCG 60.810 55.000 0.00 0.00 45.60 4.73
583 590 4.142182 ACCCACAAACACACTCAAAGAATG 60.142 41.667 0.00 0.00 0.00 2.67
591 598 6.889301 ACACACTCAAAGAATGATCAACAT 57.111 33.333 0.00 0.00 41.45 2.71
636 643 6.380560 AGTGTGTAATCTAAGGAGTAAGGACC 59.619 42.308 0.00 0.00 0.00 4.46
648 655 4.506802 GGAGTAAGGACCCATTTGTGAAGT 60.507 45.833 0.00 0.00 0.00 3.01
670 677 5.120830 AGTTGAAGTGCGTAAAGAATAGCAG 59.879 40.000 0.00 0.00 40.53 4.24
766 775 6.215495 TGACGGGTGAAGAAAAAGAAAAAT 57.785 33.333 0.00 0.00 0.00 1.82
774 783 8.390354 GGTGAAGAAAAAGAAAAATGAAAGTGG 58.610 33.333 0.00 0.00 0.00 4.00
800 809 9.923143 GTTTATAATGGTTAAAAGAAGTTGGCT 57.077 29.630 0.00 0.00 0.00 4.75
804 813 5.975693 TGGTTAAAAGAAGTTGGCTATGG 57.024 39.130 0.00 0.00 0.00 2.74
829 838 6.204301 GTGTCTCATGTGCATAATAAGCATCT 59.796 38.462 0.00 0.00 44.79 2.90
886 895 1.819632 GCACGGGCAATGACCTAGG 60.820 63.158 3.77 7.41 40.72 3.02
928 940 9.534565 TTCTATGACTGATGCTATTTACTCAAC 57.465 33.333 0.00 0.00 0.00 3.18
947 959 4.082625 TCAACGAAGAGCCGTATTTGACTA 60.083 41.667 0.00 0.00 42.54 2.59
1055 1070 3.817238 CAACAAAACCATACTACCACGC 58.183 45.455 0.00 0.00 0.00 5.34
1056 1071 3.128852 ACAAAACCATACTACCACGCA 57.871 42.857 0.00 0.00 0.00 5.24
1089 1104 2.430332 CCAACATTATTCCATGGCCGTT 59.570 45.455 6.96 0.82 0.00 4.44
1254 1269 1.270826 CCTCATCGCCACATCTATCGT 59.729 52.381 0.00 0.00 0.00 3.73
1701 1716 2.125512 ATTGCTGTCCTCGACCGC 60.126 61.111 1.72 1.72 41.82 5.68
1707 1722 0.734253 CTGTCCTCGACCGCTTCAAG 60.734 60.000 0.00 0.00 0.00 3.02
1908 1923 6.294176 CCTTCAAGATTTCCATCAAGTCGTTT 60.294 38.462 0.00 0.00 0.00 3.60
1944 1959 4.910195 AGATCAAGAATGCAGTTGGTGTA 58.090 39.130 0.00 0.00 0.00 2.90
1983 1998 0.039618 ACGGCTTTGATGATGGGGTT 59.960 50.000 0.00 0.00 0.00 4.11
1989 2004 2.806945 TTGATGATGGGGTTGAGTCC 57.193 50.000 0.00 0.00 0.00 3.85
2022 2037 2.023673 CTATTCGCTTTGGCCCATGAA 58.976 47.619 0.00 0.00 34.44 2.57
2043 2058 4.120755 CTGGGGAAGGAGGCAGCC 62.121 72.222 1.84 1.84 0.00 4.85
2047 2062 3.334054 GGAAGGAGGCAGCCCAGT 61.334 66.667 8.22 0.00 0.00 4.00
2107 2122 1.202222 GCTCATACACAGCCATGTTGC 60.202 52.381 0.00 0.00 37.65 4.17
2193 2208 1.523758 GGATGAAGCCAGACGTTGTT 58.476 50.000 0.00 0.00 0.00 2.83
2259 2274 2.354259 CCTGAGGCTGTGAAGATGTTC 58.646 52.381 0.00 0.00 0.00 3.18
2333 2348 4.200838 TGATTCGAGACCATTGTAAGCA 57.799 40.909 0.00 0.00 0.00 3.91
2465 2480 3.553511 CGAATGGATAGAGTGACTGCAAC 59.446 47.826 0.00 0.00 0.00 4.17
2670 2685 1.322442 GGAGGAACTATGCAATGGGC 58.678 55.000 0.00 0.00 41.55 5.36
2859 2874 2.346766 TTGCTGCAGACTTCTCCAAA 57.653 45.000 20.43 0.00 0.00 3.28
2871 2886 1.075482 CTCCAAAGCTGGGAAGCCA 59.925 57.895 8.58 0.00 43.71 4.75
2976 2991 0.756294 TGAGAAGTCGGGTCAAGCAA 59.244 50.000 0.00 0.00 0.00 3.91
2988 3003 2.552743 GGTCAAGCAAACTGTCCCTAAC 59.447 50.000 0.00 0.00 0.00 2.34
3006 3021 0.409876 ACCAGACTAGGAGCAGGACA 59.590 55.000 0.00 0.00 0.00 4.02
3042 3057 7.301868 AGATGTTTGTAATGGTGTTTGGAAT 57.698 32.000 0.00 0.00 0.00 3.01
3175 3246 5.181811 TGCACCAAGTCATGATTAAGTTCTG 59.818 40.000 0.00 0.00 0.00 3.02
3407 3478 1.271817 ACGGACCCCTAGATCGATACC 60.272 57.143 0.00 0.00 0.00 2.73
3466 3537 4.851639 AGACATTGGAACTAGCTGGAAT 57.148 40.909 3.17 0.00 0.00 3.01
3705 3782 3.438781 GTCATCATGGTGTTTAGCGGAAA 59.561 43.478 5.73 0.00 0.00 3.13
3714 3791 5.163499 TGGTGTTTAGCGGAAATTCTTTGTT 60.163 36.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 141 2.069273 GTGCTAAGCAGTTGACGTCAT 58.931 47.619 20.80 5.63 40.08 3.06
138 145 0.859232 AACGTGCTAAGCAGTTGACG 59.141 50.000 0.00 0.00 40.08 4.35
140 147 1.225855 CCAACGTGCTAAGCAGTTGA 58.774 50.000 19.75 0.00 43.34 3.18
163 170 0.827925 TAGCTCATCGTAGCCCCCAG 60.828 60.000 0.00 0.00 43.86 4.45
174 181 8.341173 CCATCTGTAAAAGAAATGTAGCTCATC 58.659 37.037 0.00 0.00 38.79 2.92
175 182 8.049117 TCCATCTGTAAAAGAAATGTAGCTCAT 58.951 33.333 0.00 0.00 38.79 2.90
183 190 8.331022 CGTCTACATCCATCTGTAAAAGAAATG 58.669 37.037 0.00 0.00 38.79 2.32
184 191 8.041323 ACGTCTACATCCATCTGTAAAAGAAAT 58.959 33.333 0.00 0.00 38.79 2.17
185 192 7.383687 ACGTCTACATCCATCTGTAAAAGAAA 58.616 34.615 0.00 0.00 38.79 2.52
186 193 6.931838 ACGTCTACATCCATCTGTAAAAGAA 58.068 36.000 0.00 0.00 38.79 2.52
187 194 6.525578 ACGTCTACATCCATCTGTAAAAGA 57.474 37.500 0.00 0.00 39.94 2.52
188 195 8.188799 TCTAACGTCTACATCCATCTGTAAAAG 58.811 37.037 0.00 0.00 31.50 2.27
189 196 8.058667 TCTAACGTCTACATCCATCTGTAAAA 57.941 34.615 0.00 0.00 31.50 1.52
190 197 7.634671 TCTAACGTCTACATCCATCTGTAAA 57.365 36.000 0.00 0.00 31.50 2.01
191 198 7.338703 ACTTCTAACGTCTACATCCATCTGTAA 59.661 37.037 0.00 0.00 31.50 2.41
196 203 5.206299 CGACTTCTAACGTCTACATCCATC 58.794 45.833 0.00 0.00 0.00 3.51
207 214 4.650754 AGCAATATCCGACTTCTAACGT 57.349 40.909 0.00 0.00 0.00 3.99
218 225 4.005650 AGCATTCCACATAGCAATATCCG 58.994 43.478 0.00 0.00 0.00 4.18
233 240 5.403466 GTCACAATGTTCTTCAAAGCATTCC 59.597 40.000 0.00 0.00 30.17 3.01
248 255 0.601841 GGAACCCGTCGTCACAATGT 60.602 55.000 0.00 0.00 0.00 2.71
250 257 1.373748 CGGAACCCGTCGTCACAAT 60.374 57.895 0.00 0.00 42.73 2.71
311 318 5.690865 TGAAAACTTCAAGTCTGGGTACAT 58.309 37.500 0.00 0.00 36.59 2.29
330 337 8.009513 TGGAACCCATGGATTATCATAATGAAA 58.990 33.333 15.22 0.00 0.00 2.69
342 349 1.358787 TGCTTCTGGAACCCATGGATT 59.641 47.619 15.22 0.00 30.82 3.01
348 355 6.489603 TCTATTTTATTGCTTCTGGAACCCA 58.510 36.000 0.00 0.00 0.00 4.51
426 433 4.980573 TCACAAAAATAGCCACACTACCT 58.019 39.130 0.00 0.00 32.32 3.08
531 538 2.945008 TGCACTAACCTATTGAGCATGC 59.055 45.455 10.51 10.51 0.00 4.06
591 598 9.013229 ACACACTCATGATTATTTTTAAGCTCA 57.987 29.630 0.00 0.00 0.00 4.26
636 643 3.044986 CGCACTTCAACTTCACAAATGG 58.955 45.455 0.00 0.00 0.00 3.16
648 655 4.142902 GCTGCTATTCTTTACGCACTTCAA 60.143 41.667 0.00 0.00 0.00 2.69
716 725 8.234546 TCTTCGCCTTCTCAATAAATAACAAAC 58.765 33.333 0.00 0.00 0.00 2.93
733 742 1.079127 CACCCGTCATCTTCGCCTT 60.079 57.895 0.00 0.00 0.00 4.35
774 783 9.923143 AGCCAACTTCTTTTAACCATTATAAAC 57.077 29.630 0.00 0.00 0.00 2.01
786 795 5.876357 AGACACCATAGCCAACTTCTTTTA 58.124 37.500 0.00 0.00 0.00 1.52
800 809 6.427853 GCTTATTATGCACATGAGACACCATA 59.572 38.462 0.00 0.00 0.00 2.74
804 813 5.739752 TGCTTATTATGCACATGAGACAC 57.260 39.130 0.00 0.00 35.31 3.67
923 935 3.060895 GTCAAATACGGCTCTTCGTTGAG 59.939 47.826 0.00 3.70 43.59 3.02
928 940 5.773239 TTTTAGTCAAATACGGCTCTTCG 57.227 39.130 0.00 0.00 0.00 3.79
1055 1070 0.960364 ATGTTGGGTTAGCGGCACTG 60.960 55.000 1.45 0.00 0.00 3.66
1056 1071 0.251165 AATGTTGGGTTAGCGGCACT 60.251 50.000 1.45 0.00 0.00 4.40
1089 1104 1.904378 GGTTGCGGGTTTGGGCTTA 60.904 57.895 0.00 0.00 0.00 3.09
1189 1204 2.258591 CACAGTAGCACCGTCGCT 59.741 61.111 1.17 1.17 46.26 4.93
1201 1216 3.501911 ACCAGGCAAGGGCACAGT 61.502 61.111 0.00 0.00 43.71 3.55
1276 1291 0.462047 CGACAGGGGAGTGGCAATAC 60.462 60.000 0.00 0.00 0.00 1.89
1593 1608 4.141965 ATGACGTCCGCGATGGCA 62.142 61.111 14.12 8.36 41.16 4.92
1701 1716 0.931662 GCTTGTGTGCGTGCTTGAAG 60.932 55.000 0.00 0.00 0.00 3.02
1707 1722 2.126734 GATGGCTTGTGTGCGTGC 60.127 61.111 0.00 0.00 0.00 5.34
1773 1788 1.079127 CTTGCAGTAGGTGACGGGG 60.079 63.158 0.00 0.00 0.00 5.73
1803 1818 3.907260 CTGCCTCGCCTTGCCAAGA 62.907 63.158 5.89 0.00 0.00 3.02
1944 1959 1.764723 TGCACCCTCATCATCTCGAAT 59.235 47.619 0.00 0.00 0.00 3.34
1983 1998 2.867624 AGCAAGCAATTGAAGGACTCA 58.132 42.857 10.34 0.00 0.00 3.41
2043 2058 1.610038 TGCATTCTGCTGAACAACTGG 59.390 47.619 8.32 0.00 45.31 4.00
2047 2062 2.229543 GGTCATGCATTCTGCTGAACAA 59.770 45.455 8.32 0.00 45.31 2.83
2083 2098 0.812811 ATGGCTGTGTATGAGCGCAG 60.813 55.000 11.47 0.00 46.43 5.18
2107 2122 0.174845 CTTCCATTGCACCATGCCAG 59.825 55.000 0.00 0.00 44.23 4.85
2126 2141 2.352805 CAGCCTCCACCAGGTTCC 59.647 66.667 0.00 0.00 45.61 3.62
2149 2164 4.515028 TCTCCAGCATCTCATTCCAAAT 57.485 40.909 0.00 0.00 0.00 2.32
2259 2274 0.731417 CCTTTGCCTTCATCAGCTCG 59.269 55.000 0.00 0.00 0.00 5.03
2333 2348 1.002069 TGCCATGTCCATCTTTCCCT 58.998 50.000 0.00 0.00 0.00 4.20
2394 2409 3.637229 AGCACGTATAGGTAGCAACATCT 59.363 43.478 16.66 0.00 0.00 2.90
2465 2480 0.523072 CTGTGCCATTTCCTCCAACG 59.477 55.000 0.00 0.00 0.00 4.10
2506 2521 0.108377 ATCAGCGCATTGTACGTCCA 60.108 50.000 11.47 0.00 0.00 4.02
2508 2523 3.841372 GCTTAATCAGCGCATTGTACGTC 60.841 47.826 11.47 0.00 39.29 4.34
2537 2552 7.052248 TGCATCATCTGGCATATTCCTATTAG 58.948 38.462 0.00 0.00 34.58 1.73
2538 2553 6.961042 TGCATCATCTGGCATATTCCTATTA 58.039 36.000 0.00 0.00 34.58 0.98
2607 2622 9.577222 TTCATCATCATGTTGTATGTATGGATT 57.423 29.630 3.76 0.00 0.00 3.01
2670 2685 2.046988 TCATCCCACACTGCGCAG 60.047 61.111 34.89 34.89 0.00 5.18
2871 2886 9.453572 TTCTGAGCTAATTCAAACAATATGTCT 57.546 29.630 0.00 0.00 0.00 3.41
2976 2991 3.077088 TCCTAGTCTGGTTAGGGACAGTT 59.923 47.826 0.00 0.00 38.57 3.16
2988 3003 1.786937 ATGTCCTGCTCCTAGTCTGG 58.213 55.000 0.00 0.00 0.00 3.86
3042 3057 7.466746 AAATAGCAGGAGCACATTCTAAAAA 57.533 32.000 0.00 0.00 45.49 1.94
3175 3246 3.541632 TCACCTGAGTTTCACAGAAACC 58.458 45.455 16.49 10.21 37.54 3.27
3240 3311 0.743097 GGCCACTACGGTACCTACAG 59.257 60.000 10.90 6.53 36.97 2.74
3407 3478 5.755375 AGCATCACATTGTTAAGGAGTATCG 59.245 40.000 0.00 0.00 34.37 2.92
3422 3493 4.904895 AGCCTACATATCAGCATCACAT 57.095 40.909 0.00 0.00 0.00 3.21
3466 3537 2.722094 CAGGTGCATGTAGCCCTTAAA 58.278 47.619 9.50 0.00 44.83 1.52
3674 3751 4.640771 ACACCATGATGACACCTTAAGT 57.359 40.909 0.00 0.00 0.00 2.24
3705 3782 7.466455 CGCTACAAGATAGCATCAACAAAGAAT 60.466 37.037 6.73 0.00 40.39 2.40
3714 3791 7.378181 TCATATTTCGCTACAAGATAGCATCA 58.622 34.615 6.73 0.00 40.39 3.07


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

AutoCloner maintained by Alex Coulton.