Multiple sequence alignment - TraesCS1D01G195300

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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 TraesCS1D01G195300 chr1D 100.000 2795 0 0 1 2795 274253604 274256398 0.000000e+00 5162
1 TraesCS1D01G195300 chr1B 91.137 2753 152 43 1 2691 373627346 373630068 0.000000e+00 3648
2 TraesCS1D01G195300 chr1B 78.879 232 45 2 426 653 17409921 17410152 1.340000e-33 154
3 TraesCS1D01G195300 chr1B 78.879 232 45 2 426 653 17418447 17418678 1.340000e-33 154
4 TraesCS1D01G195300 chr1B 93.103 87 6 0 2709 2795 373630053 373630139 8.130000e-26 128
5 TraesCS1D01G195300 chr1A 94.343 2139 78 27 687 2795 346681261 346683386 0.000000e+00 3240
6 TraesCS1D01G195300 chr1A 86.332 717 82 13 1 705 346680537 346681249 0.000000e+00 767
7 TraesCS1D01G195300 chr3D 81.366 322 46 12 1291 1605 132275352 132275666 1.660000e-62 250
8 TraesCS1D01G195300 chr3A 81.115 323 45 12 1291 1605 145667466 145667780 7.730000e-61 244
9 TraesCS1D01G195300 chr3A 81.726 197 32 4 401 593 651646554 651646750 8.010000e-36 161
10 TraesCS1D01G195300 chr3B 80.864 324 44 12 1291 1605 188877448 188877762 3.600000e-59 239


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 TraesCS1D01G195300 chr1D 274253604 274256398 2794 False 5162.0 5162 100.0000 1 2795 1 chr1D.!!$F1 2794
1 TraesCS1D01G195300 chr1B 373627346 373630139 2793 False 1888.0 3648 92.1200 1 2795 2 chr1B.!!$F3 2794
2 TraesCS1D01G195300 chr1A 346680537 346683386 2849 False 2003.5 3240 90.3375 1 2795 2 chr1A.!!$F1 2794

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
352 364 0.109723 TGGGGTGAGTACTTGTTGCC 59.89 55.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 2325 2.18483 CATGCATCCCGGAGCACAG 61.185 63.158 16.54 9.86 44.49 3.66 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
38 39 1.027357 GCCAGAATTGACGCATCCAT 58.973 50.000 0.00 0.00 0.00 3.41
44 49 0.255604 ATTGACGCATCCATCCACCA 59.744 50.000 0.00 0.00 0.00 4.17
51 56 4.731853 TCCATCCACCAGCCCCGA 62.732 66.667 0.00 0.00 0.00 5.14
137 146 3.306364 CGGTATGGCCTCCTTCTCTAATG 60.306 52.174 3.32 0.00 34.25 1.90
138 147 2.947127 ATGGCCTCCTTCTCTAATGC 57.053 50.000 3.32 0.00 0.00 3.56
139 148 1.885049 TGGCCTCCTTCTCTAATGCT 58.115 50.000 3.32 0.00 0.00 3.79
140 149 1.765314 TGGCCTCCTTCTCTAATGCTC 59.235 52.381 3.32 0.00 0.00 4.26
143 153 1.342819 CCTCCTTCTCTAATGCTCGGG 59.657 57.143 0.00 0.00 0.00 5.14
176 186 4.722700 GGCCACCGTCACAGCCAT 62.723 66.667 0.00 0.00 45.07 4.40
181 191 4.720902 CCGTCACAGCCATGCCCA 62.721 66.667 0.00 0.00 0.00 5.36
192 202 4.015406 ATGCCCAGCGACCGTTGA 62.015 61.111 7.80 0.00 0.00 3.18
210 220 2.804828 GAACGGGCTTGGCACTAGCT 62.805 60.000 10.74 0.00 41.70 3.32
211 221 2.821366 CGGGCTTGGCACTAGCTG 60.821 66.667 10.74 1.18 41.70 4.24
293 304 2.607892 GCCAAGTTTCGAGCACGCT 61.608 57.895 0.00 0.00 39.58 5.07
302 313 1.808799 CGAGCACGCTGAAGCATCT 60.809 57.895 0.00 0.00 42.21 2.90
343 355 3.256704 AGTGAAAAGGATGGGGTGAGTA 58.743 45.455 0.00 0.00 0.00 2.59
352 364 0.109723 TGGGGTGAGTACTTGTTGCC 59.890 55.000 0.00 0.00 0.00 4.52
369 381 1.208259 GCCACGGTTTGCTCAAAAAG 58.792 50.000 0.00 0.00 31.33 2.27
371 383 2.223618 GCCACGGTTTGCTCAAAAAGTA 60.224 45.455 0.00 0.00 31.33 2.24
373 385 3.980775 CCACGGTTTGCTCAAAAAGTATG 59.019 43.478 0.00 0.00 31.33 2.39
376 388 5.851177 CACGGTTTGCTCAAAAAGTATGTAG 59.149 40.000 0.00 0.00 31.33 2.74
381 393 7.094377 GGTTTGCTCAAAAAGTATGTAGGATGA 60.094 37.037 0.00 0.00 31.33 2.92
388 400 9.396022 TCAAAAAGTATGTAGGATGAGATTTCC 57.604 33.333 0.00 0.00 0.00 3.13
392 404 8.915057 AAGTATGTAGGATGAGATTTCCATTG 57.085 34.615 0.00 0.00 35.59 2.82
397 409 8.089625 TGTAGGATGAGATTTCCATTGAAGTA 57.910 34.615 0.00 0.00 35.59 2.24
434 447 8.985805 GTTCTAGTTTTTCGATTGGTTCTCTTA 58.014 33.333 0.00 0.00 0.00 2.10
452 465 6.173339 TCTCTTAGCGAAGAATTGGTGAATT 58.827 36.000 10.62 0.00 41.23 2.17
457 470 6.515272 AGCGAAGAATTGGTGAATTATGTT 57.485 33.333 0.00 0.00 31.58 2.71
460 473 6.470235 GCGAAGAATTGGTGAATTATGTTCTG 59.530 38.462 0.00 0.00 31.58 3.02
461 474 7.530010 CGAAGAATTGGTGAATTATGTTCTGT 58.470 34.615 0.00 0.00 31.58 3.41
469 482 6.149633 GGTGAATTATGTTCTGTGGTGTTTC 58.850 40.000 0.00 0.00 0.00 2.78
483 496 3.942115 TGGTGTTTCAAGATGACGTTCAA 59.058 39.130 0.00 0.00 0.00 2.69
529 542 2.517650 TTCGGTGGCCAAAAATGAAC 57.482 45.000 7.24 0.00 0.00 3.18
637 651 1.916000 CTTTACTCGGCGGTTTACTCG 59.084 52.381 7.21 0.00 0.00 4.18
647 661 4.491441 CGGCGGTTTACTCGTCTATTTTTC 60.491 45.833 0.00 0.00 0.00 2.29
676 696 8.878769 GGAGATGCTCTTAGTTTAGAAAAAGAG 58.121 37.037 10.26 10.26 45.00 2.85
760 830 9.593134 GTAAATCCGAAGAGAGAATATGCATAT 57.407 33.333 13.63 13.63 0.00 1.78
762 832 9.593134 AAATCCGAAGAGAGAATATGCATATAC 57.407 33.333 19.39 13.34 0.00 1.47
763 833 7.101652 TCCGAAGAGAGAATATGCATATACC 57.898 40.000 19.39 13.83 0.00 2.73
765 835 6.754209 CCGAAGAGAGAATATGCATATACCAC 59.246 42.308 19.39 12.46 0.00 4.16
766 836 7.315890 CGAAGAGAGAATATGCATATACCACA 58.684 38.462 19.39 0.00 0.00 4.17
768 838 9.149225 GAAGAGAGAATATGCATATACCACAAG 57.851 37.037 19.39 0.00 0.00 3.16
769 839 7.102346 AGAGAGAATATGCATATACCACAAGC 58.898 38.462 19.39 5.39 0.00 4.01
770 840 6.772605 AGAGAATATGCATATACCACAAGCA 58.227 36.000 19.39 0.00 39.79 3.91
771 841 6.652481 AGAGAATATGCATATACCACAAGCAC 59.348 38.462 19.39 3.57 38.12 4.40
772 842 6.298361 AGAATATGCATATACCACAAGCACA 58.702 36.000 19.39 0.00 38.12 4.57
773 843 5.947228 ATATGCATATACCACAAGCACAC 57.053 39.130 17.72 0.00 38.12 3.82
774 844 3.064900 TGCATATACCACAAGCACACA 57.935 42.857 0.00 0.00 0.00 3.72
775 845 2.746904 TGCATATACCACAAGCACACAC 59.253 45.455 0.00 0.00 0.00 3.82
776 846 2.746904 GCATATACCACAAGCACACACA 59.253 45.455 0.00 0.00 0.00 3.72
777 847 3.190327 GCATATACCACAAGCACACACAA 59.810 43.478 0.00 0.00 0.00 3.33
778 848 4.142403 GCATATACCACAAGCACACACAAT 60.142 41.667 0.00 0.00 0.00 2.71
779 849 5.622007 GCATATACCACAAGCACACACAATT 60.622 40.000 0.00 0.00 0.00 2.32
780 850 6.404184 GCATATACCACAAGCACACACAATTA 60.404 38.462 0.00 0.00 0.00 1.40
781 851 7.534282 CATATACCACAAGCACACACAATTAA 58.466 34.615 0.00 0.00 0.00 1.40
782 852 4.727507 ACCACAAGCACACACAATTAAA 57.272 36.364 0.00 0.00 0.00 1.52
783 853 5.078411 ACCACAAGCACACACAATTAAAA 57.922 34.783 0.00 0.00 0.00 1.52
784 854 5.482908 ACCACAAGCACACACAATTAAAAA 58.517 33.333 0.00 0.00 0.00 1.94
895 969 3.626977 CTTCAGCGTCTACTGCTAGATG 58.373 50.000 0.00 0.00 41.72 2.90
973 1047 1.221293 CCTGCTCCAAGCCTCTCTG 59.779 63.158 0.00 0.00 41.51 3.35
1169 1256 3.004951 CCAGGCCAATGCTCCTCT 58.995 61.111 5.01 0.00 37.74 3.69
1740 1830 1.304381 AATTGACGCATGCAGGGGT 60.304 52.632 21.58 21.58 36.57 4.95
1901 1991 3.188667 CCGTGATTCATAGCTCGCTACTA 59.811 47.826 0.00 0.00 0.00 1.82
1923 2014 7.961351 ACTACTAGATGATCAAGCAGCTTATT 58.039 34.615 7.52 0.00 35.84 1.40
1998 2129 8.803235 CCCTTGTTGATCAATAATGATGATGAT 58.197 33.333 16.75 0.00 46.30 2.45
2072 2206 5.457140 TGCATGATTTAGTGGAAACGAAAC 58.543 37.500 0.00 0.00 0.00 2.78
2080 2214 4.783959 AGTGGAAACGAAACGAAACTAC 57.216 40.909 0.00 0.00 0.00 2.73
2105 2239 3.193691 GTGCTCTAAACTGTAGAGGCTGA 59.806 47.826 11.36 0.00 40.92 4.26
2106 2240 3.445450 TGCTCTAAACTGTAGAGGCTGAG 59.555 47.826 11.36 0.00 40.92 3.35
2112 2246 3.562343 ACTGTAGAGGCTGAGACGATA 57.438 47.619 0.00 0.00 0.00 2.92
2122 2256 4.645136 AGGCTGAGACGATATTACTGTGAA 59.355 41.667 0.00 0.00 0.00 3.18
2191 2325 4.681744 TCTTGTCATGTTTTTCTGTTGCC 58.318 39.130 0.00 0.00 0.00 4.52
2273 2407 1.865865 TCGACACTTGTTGCTTCTCC 58.134 50.000 0.00 0.00 0.00 3.71
2274 2408 0.508641 CGACACTTGTTGCTTCTCCG 59.491 55.000 0.00 0.00 0.00 4.63
2314 2448 2.965147 CAACACTTCCATTTTCCCAGGT 59.035 45.455 0.00 0.00 0.00 4.00
2341 2476 8.011106 CACACTGCAAAATTTGGTGAATTTATC 58.989 33.333 17.62 0.00 44.98 1.75
2353 2488 4.702131 GGTGAATTTATCTCCAGCTTGTGT 59.298 41.667 0.00 0.00 40.69 3.72
2476 2611 4.727507 TTGCCAAGCAAGTTTTTACTCA 57.272 36.364 0.00 0.00 43.99 3.41
2477 2612 4.935352 TGCCAAGCAAGTTTTTACTCAT 57.065 36.364 0.00 0.00 34.76 2.90
2508 2644 7.566760 TTTACGATCAATCCATTGCTATTGT 57.433 32.000 0.00 0.00 37.68 2.71
2777 2960 0.253044 TAGGTGCTCCACTTGCCATC 59.747 55.000 7.70 0.00 34.40 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.408821 TCAATTCTGGCGCCGGCT 62.409 61.111 31.15 17.19 39.81 5.52
25 26 0.255604 TGGTGGATGGATGCGTCAAT 59.744 50.000 8.47 0.82 0.00 2.57
74 79 0.317479 GGCTATGCGGTTCGATACCT 59.683 55.000 12.80 0.76 45.40 3.08
137 146 2.486042 GACGAGTGAGACCCGAGC 59.514 66.667 0.00 0.00 0.00 5.03
138 147 1.740664 TCGACGAGTGAGACCCGAG 60.741 63.158 0.00 0.00 0.00 4.63
139 148 2.031516 GTCGACGAGTGAGACCCGA 61.032 63.158 0.00 0.00 0.00 5.14
140 149 2.033755 AGTCGACGAGTGAGACCCG 61.034 63.158 10.46 0.00 35.65 5.28
143 153 1.154188 GCCAGTCGACGAGTGAGAC 60.154 63.158 29.69 16.64 35.20 3.36
176 186 4.243008 TTCAACGGTCGCTGGGCA 62.243 61.111 0.00 0.00 0.00 5.36
192 202 2.359975 GCTAGTGCCAAGCCCGTT 60.360 61.111 0.00 0.00 33.73 4.44
229 240 1.449601 ACTTGATAACCGGCAGCGG 60.450 57.895 0.00 0.00 0.00 5.52
235 246 2.073816 GTGGTCACACTTGATAACCGG 58.926 52.381 0.00 0.00 44.29 5.28
293 304 0.108186 CACCCACGCTAGATGCTTCA 60.108 55.000 2.07 0.00 40.11 3.02
302 313 1.689813 TCTTGAAGAACACCCACGCTA 59.310 47.619 0.00 0.00 0.00 4.26
352 364 4.606961 ACATACTTTTTGAGCAAACCGTG 58.393 39.130 0.00 0.00 0.00 4.94
369 381 8.908786 TTCAATGGAAATCTCATCCTACATAC 57.091 34.615 0.00 0.00 37.85 2.39
371 383 7.580910 ACTTCAATGGAAATCTCATCCTACAT 58.419 34.615 0.00 0.00 37.85 2.29
420 432 3.770666 TCTTCGCTAAGAGAACCAATCG 58.229 45.455 0.00 0.00 36.80 3.34
421 433 6.457528 CCAATTCTTCGCTAAGAGAACCAATC 60.458 42.308 0.55 0.00 42.60 2.67
424 437 4.253685 CCAATTCTTCGCTAAGAGAACCA 58.746 43.478 0.55 0.00 42.60 3.67
434 447 6.375455 AGAACATAATTCACCAATTCTTCGCT 59.625 34.615 0.00 0.00 33.95 4.93
452 465 6.204688 GTCATCTTGAAACACCACAGAACATA 59.795 38.462 0.00 0.00 0.00 2.29
457 470 3.130633 CGTCATCTTGAAACACCACAGA 58.869 45.455 0.00 0.00 0.00 3.41
460 473 3.311322 TGAACGTCATCTTGAAACACCAC 59.689 43.478 0.00 0.00 0.00 4.16
461 474 3.536570 TGAACGTCATCTTGAAACACCA 58.463 40.909 0.00 0.00 0.00 4.17
496 509 4.638865 GGCCACCGAAATAAACTTCACTAT 59.361 41.667 0.00 0.00 0.00 2.12
505 518 5.215252 TCATTTTTGGCCACCGAAATAAA 57.785 34.783 3.88 0.00 36.84 1.40
572 586 8.760980 TCCATTAAATTTTGATCGGACCTAAT 57.239 30.769 0.00 0.00 0.00 1.73
693 713 7.881775 AAACTAGAGGAACAACACTTTGATT 57.118 32.000 0.00 0.00 36.48 2.57
760 830 5.836821 TTTAATTGTGTGTGCTTGTGGTA 57.163 34.783 0.00 0.00 0.00 3.25
781 851 8.923270 TCACTCTAGGGAATCAAAAATGTTTTT 58.077 29.630 0.00 0.00 40.75 1.94
782 852 8.477419 TCACTCTAGGGAATCAAAAATGTTTT 57.523 30.769 0.00 0.00 0.00 2.43
783 853 8.477419 TTCACTCTAGGGAATCAAAAATGTTT 57.523 30.769 0.00 0.00 0.00 2.83
784 854 7.177392 CCTTCACTCTAGGGAATCAAAAATGTT 59.823 37.037 0.00 0.00 0.00 2.71
785 855 6.660949 CCTTCACTCTAGGGAATCAAAAATGT 59.339 38.462 0.00 0.00 0.00 2.71
786 856 7.093322 CCTTCACTCTAGGGAATCAAAAATG 57.907 40.000 0.00 0.00 0.00 2.32
895 969 7.813627 GCCTGCTAGTACATTTAATACTACTCC 59.186 40.741 0.00 0.00 34.66 3.85
1055 1142 3.525545 GGTACCTCCGGCTCCGTC 61.526 72.222 4.06 0.00 37.81 4.79
1169 1256 3.751401 GATACGCTGCGCCACGAGA 62.751 63.158 23.51 12.26 0.00 4.04
1740 1830 5.414789 TCAGGAATCACACCTATTCGAAA 57.585 39.130 0.00 0.00 35.84 3.46
1901 1991 7.961351 AGTAATAAGCTGCTTGATCATCTAGT 58.039 34.615 24.35 4.06 0.00 2.57
1998 2129 5.359860 TCGATCAGCAGGTACTAATTCTTCA 59.640 40.000 0.00 0.00 36.02 3.02
2072 2206 4.321217 CAGTTTAGAGCACTCGTAGTTTCG 59.679 45.833 0.00 0.00 34.09 3.46
2080 2214 3.732471 GCCTCTACAGTTTAGAGCACTCG 60.732 52.174 7.69 0.00 39.66 4.18
2105 2239 8.417106 AGACAATCATTCACAGTAATATCGTCT 58.583 33.333 0.00 0.00 0.00 4.18
2106 2240 8.581057 AGACAATCATTCACAGTAATATCGTC 57.419 34.615 0.00 0.00 0.00 4.20
2112 2246 8.890718 CATCTCAAGACAATCATTCACAGTAAT 58.109 33.333 0.00 0.00 0.00 1.89
2122 2256 6.585695 AAACAAGCATCTCAAGACAATCAT 57.414 33.333 0.00 0.00 0.00 2.45
2191 2325 2.184830 CATGCATCCCGGAGCACAG 61.185 63.158 16.54 9.86 44.49 3.66
2314 2448 4.462508 TTCACCAAATTTTGCAGTGTGA 57.537 36.364 12.18 12.18 0.00 3.58
2341 2476 8.093307 ACATATTCAGATATACACAAGCTGGAG 58.907 37.037 0.00 0.00 0.00 3.86
2486 2621 8.720562 CATAACAATAGCAATGGATTGATCGTA 58.279 33.333 3.47 0.00 40.14 3.43
2488 2623 7.587629 ACATAACAATAGCAATGGATTGATCG 58.412 34.615 3.47 0.00 40.14 3.69
2508 2644 7.446931 TGTCTGAATCTTTAAGCACCAACATAA 59.553 33.333 0.00 0.00 0.00 1.90
2714 2864 1.335872 CGGCCTGCATCTTTCGTTTTT 60.336 47.619 0.00 0.00 0.00 1.94
2715 2865 0.240945 CGGCCTGCATCTTTCGTTTT 59.759 50.000 0.00 0.00 0.00 2.43
2716 2866 1.875963 CGGCCTGCATCTTTCGTTT 59.124 52.632 0.00 0.00 0.00 3.60
2717 2867 2.690778 GCGGCCTGCATCTTTCGTT 61.691 57.895 13.61 0.00 45.45 3.85
2718 2868 3.127533 GCGGCCTGCATCTTTCGT 61.128 61.111 13.61 0.00 45.45 3.85


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

AutoCloner maintained by Alex Coulton.