Multiple sequence alignment - TraesCS5D01G427000

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 TraesCS5D01G427000 chr5D 100.000 2609 0 0 1 2609 485293483 485296091 0.000000e+00 4819.0
1 TraesCS5D01G427000 chr5D 92.025 978 58 10 858 1826 485268063 485269029 0.000000e+00 1356.0
2 TraesCS5D01G427000 chr5D 96.433 785 27 1 1826 2609 311803330 311802546 0.000000e+00 1293.0
3 TraesCS5D01G427000 chr5D 91.730 786 60 4 1825 2607 472397586 472396803 0.000000e+00 1086.0
4 TraesCS5D01G427000 chr5D 89.186 786 84 1 1825 2609 426472973 426473758 0.000000e+00 979.0
5 TraesCS5D01G427000 chr5D 90.882 680 50 5 737 1406 485266990 485267667 0.000000e+00 902.0
6 TraesCS5D01G427000 chr5A 94.138 1177 57 7 658 1826 606525957 606527129 0.000000e+00 1781.0
7 TraesCS5D01G427000 chr5A 86.280 984 57 29 864 1823 606460719 606461648 0.000000e+00 998.0
8 TraesCS5D01G427000 chr5A 87.371 871 74 8 1 861 606487340 606488184 0.000000e+00 966.0
9 TraesCS5D01G427000 chr5A 76.683 609 97 19 994 1569 606306986 606307582 1.960000e-76 296.0
10 TraesCS5D01G427000 chr5A 87.143 140 9 4 1475 1614 606307629 606307759 1.620000e-32 150.0
11 TraesCS5D01G427000 chr5B 89.878 1067 59 18 674 1718 596903969 596905008 0.000000e+00 1327.0
12 TraesCS5D01G427000 chr5B 91.118 304 27 0 436 739 596898428 596898731 1.870000e-111 412.0
13 TraesCS5D01G427000 chr5B 88.365 318 31 1 42 359 596898105 596898416 6.820000e-101 377.0
14 TraesCS5D01G427000 chr5B 77.482 564 73 24 1000 1527 596439068 596438523 3.290000e-74 289.0
15 TraesCS5D01G427000 chr5B 91.406 128 6 3 1699 1823 596905021 596905146 1.240000e-38 171.0
16 TraesCS5D01G427000 chr4D 96.943 785 23 1 1826 2609 120093484 120092700 0.000000e+00 1315.0
17 TraesCS5D01G427000 chr2D 96.547 782 25 2 1829 2609 405178984 405178204 0.000000e+00 1293.0
18 TraesCS5D01G427000 chr2D 96.183 786 29 1 1825 2609 552117488 552118273 0.000000e+00 1284.0
19 TraesCS5D01G427000 chr4A 91.293 781 64 4 1830 2607 590357609 590358388 0.000000e+00 1062.0
20 TraesCS5D01G427000 chr4A 90.434 784 72 3 1827 2609 659824937 659824156 0.000000e+00 1029.0
21 TraesCS5D01G427000 chr2B 87.883 784 90 5 1827 2609 648368922 648368143 0.000000e+00 917.0
22 TraesCS5D01G427000 chr6A 91.071 56 4 1 509 563 573133882 573133827 1.000000e-09 75.0
23 TraesCS5D01G427000 chr3D 91.667 48 4 0 32 79 82758094 82758141 1.680000e-07 67.6


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 TraesCS5D01G427000 chr5D 485293483 485296091 2608 False 4819.0 4819 100.0000 1 2609 1 chr5D.!!$F2 2608
1 TraesCS5D01G427000 chr5D 311802546 311803330 784 True 1293.0 1293 96.4330 1826 2609 1 chr5D.!!$R1 783
2 TraesCS5D01G427000 chr5D 485266990 485269029 2039 False 1129.0 1356 91.4535 737 1826 2 chr5D.!!$F3 1089
3 TraesCS5D01G427000 chr5D 472396803 472397586 783 True 1086.0 1086 91.7300 1825 2607 1 chr5D.!!$R2 782
4 TraesCS5D01G427000 chr5D 426472973 426473758 785 False 979.0 979 89.1860 1825 2609 1 chr5D.!!$F1 784
5 TraesCS5D01G427000 chr5A 606525957 606527129 1172 False 1781.0 1781 94.1380 658 1826 1 chr5A.!!$F3 1168
6 TraesCS5D01G427000 chr5A 606460719 606461648 929 False 998.0 998 86.2800 864 1823 1 chr5A.!!$F1 959
7 TraesCS5D01G427000 chr5A 606487340 606488184 844 False 966.0 966 87.3710 1 861 1 chr5A.!!$F2 860
8 TraesCS5D01G427000 chr5A 606306986 606307759 773 False 223.0 296 81.9130 994 1614 2 chr5A.!!$F4 620
9 TraesCS5D01G427000 chr5B 596903969 596905146 1177 False 749.0 1327 90.6420 674 1823 2 chr5B.!!$F2 1149
10 TraesCS5D01G427000 chr5B 596898105 596898731 626 False 394.5 412 89.7415 42 739 2 chr5B.!!$F1 697
11 TraesCS5D01G427000 chr5B 596438523 596439068 545 True 289.0 289 77.4820 1000 1527 1 chr5B.!!$R1 527
12 TraesCS5D01G427000 chr4D 120092700 120093484 784 True 1315.0 1315 96.9430 1826 2609 1 chr4D.!!$R1 783
13 TraesCS5D01G427000 chr2D 405178204 405178984 780 True 1293.0 1293 96.5470 1829 2609 1 chr2D.!!$R1 780
14 TraesCS5D01G427000 chr2D 552117488 552118273 785 False 1284.0 1284 96.1830 1825 2609 1 chr2D.!!$F1 784
15 TraesCS5D01G427000 chr4A 590357609 590358388 779 False 1062.0 1062 91.2930 1830 2607 1 chr4A.!!$F1 777
16 TraesCS5D01G427000 chr4A 659824156 659824937 781 True 1029.0 1029 90.4340 1827 2609 1 chr4A.!!$R1 782
17 TraesCS5D01G427000 chr2B 648368143 648368922 779 True 917.0 917 87.8830 1827 2609 1 chr2B.!!$R1 782

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
481 486 0.038159 GGGATCCGTTAGAGATGCCG 60.038 60.0 5.45 0.0 41.6 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2303 3567 0.0293 GCTTCTGCACTGCGTTTTCA 59.971 50.0 0.0 0.0 39.41 2.69 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 3.223423 GATACGCATCCATCATCGAGT 57.777 47.619 0.00 0.00 0.00 4.18
26 27 0.318191 ACGCATCCATCATCGAGTCG 60.318 55.000 6.09 6.09 0.00 4.18
29 30 1.269723 GCATCCATCATCGAGTCGGTA 59.730 52.381 13.54 0.00 0.00 4.02
43 44 0.179094 TCGGTATGTGCCCGCTAAAG 60.179 55.000 0.00 0.00 45.09 1.85
49 50 4.010224 TGCCCGCTAAAGCCACGA 62.010 61.111 0.00 0.00 37.91 4.35
57 58 1.739371 GCTAAAGCCACGACGGAGATT 60.739 52.381 0.00 0.00 36.56 2.40
81 82 2.987125 GGCGACACCCAGTACCAT 59.013 61.111 0.00 0.00 0.00 3.55
109 110 0.537188 AGATAACTGCGTGGGACCTG 59.463 55.000 0.00 0.00 0.00 4.00
149 150 1.664333 GCAATGGGTGCGTTTGGTG 60.664 57.895 0.00 0.00 45.10 4.17
157 158 0.663269 GTGCGTTTGGTGGCTAAAGC 60.663 55.000 0.00 0.00 41.14 3.51
165 166 1.376037 GTGGCTAAAGCGCACCTCT 60.376 57.895 11.47 0.00 43.26 3.69
170 171 1.992170 CTAAAGCGCACCTCTACGTT 58.008 50.000 11.47 0.00 0.00 3.99
265 266 4.868734 CCCAAGTTAACATCGAAGGAGTAC 59.131 45.833 8.61 0.00 0.00 2.73
271 272 4.866508 AACATCGAAGGAGTACTTGACA 57.133 40.909 0.00 0.00 40.21 3.58
282 283 2.639839 AGTACTTGACAGGGTGCTTCAT 59.360 45.455 0.00 0.00 0.00 2.57
354 355 3.795639 GTCGCGGAGGAGTATTTTTACTC 59.204 47.826 6.13 4.87 44.23 2.59
360 361 3.778618 AGGAGTATTTTTACTCGTCCGC 58.221 45.455 6.98 0.00 45.51 5.54
362 363 3.795639 GGAGTATTTTTACTCGTCCGCTC 59.204 47.826 6.98 0.00 45.51 5.03
363 364 4.418392 GAGTATTTTTACTCGTCCGCTCA 58.582 43.478 0.00 0.00 37.35 4.26
365 366 2.074547 TTTTTACTCGTCCGCTCAGG 57.925 50.000 0.00 0.00 42.97 3.86
367 368 0.609957 TTTACTCGTCCGCTCAGGGA 60.610 55.000 0.00 0.00 41.52 4.20
368 369 1.030488 TTACTCGTCCGCTCAGGGAG 61.030 60.000 0.00 0.00 41.52 4.30
369 370 2.194388 TACTCGTCCGCTCAGGGAGT 62.194 60.000 0.00 0.00 42.02 3.85
370 371 1.451567 CTCGTCCGCTCAGGGAGTA 60.452 63.158 0.00 0.00 41.52 2.59
371 372 1.001764 TCGTCCGCTCAGGGAGTAA 60.002 57.895 0.00 0.00 41.52 2.24
406 411 4.888239 TCTCTAACCGGTTTAGGAGATCAG 59.112 45.833 27.64 13.33 38.24 2.90
410 415 3.577919 ACCGGTTTAGGAGATCAGCTAT 58.422 45.455 0.00 0.00 34.73 2.97
433 438 4.259356 GTGCCGGTTAGAGGAGTAAAATT 58.741 43.478 1.90 0.00 0.00 1.82
434 439 5.046448 TGTGCCGGTTAGAGGAGTAAAATTA 60.046 40.000 1.90 0.00 0.00 1.40
435 440 5.876460 GTGCCGGTTAGAGGAGTAAAATTAA 59.124 40.000 1.90 0.00 0.00 1.40
436 441 6.372381 GTGCCGGTTAGAGGAGTAAAATTAAA 59.628 38.462 1.90 0.00 0.00 1.52
437 442 6.941436 TGCCGGTTAGAGGAGTAAAATTAAAA 59.059 34.615 1.90 0.00 0.00 1.52
438 443 7.447853 TGCCGGTTAGAGGAGTAAAATTAAAAA 59.552 33.333 1.90 0.00 0.00 1.94
468 473 5.780793 TCCTCTGTAGCTATTTAAGGGATCC 59.219 44.000 1.92 1.92 0.00 3.36
470 475 5.145564 TCTGTAGCTATTTAAGGGATCCGT 58.854 41.667 5.45 2.61 0.00 4.69
480 485 3.917072 GGGATCCGTTAGAGATGCC 57.083 57.895 5.45 0.00 43.78 4.40
481 486 0.038159 GGGATCCGTTAGAGATGCCG 60.038 60.000 5.45 0.00 41.60 5.69
513 520 9.847224 AGAAAAATTTCTCAAGGAAGTACTACA 57.153 29.630 0.00 0.00 43.72 2.74
603 610 7.299246 ACGGAGTAATACTATTTGCCTACAT 57.701 36.000 0.00 0.00 41.94 2.29
710 721 2.278854 CATGCATACCACACATCGTCA 58.721 47.619 0.00 0.00 0.00 4.35
756 768 1.447838 CTTACGCGGCCATGTGACT 60.448 57.895 12.47 0.00 0.00 3.41
793 805 1.648467 GCCAACAACCGATGCTCTCC 61.648 60.000 0.00 0.00 0.00 3.71
809 821 0.606604 CTCCTGCAAAATGCCAAGCT 59.393 50.000 0.00 0.00 44.23 3.74
967 984 2.101750 GGTTCCAAGAGAGCTACTAGGC 59.898 54.545 0.00 0.00 0.00 3.93
1219 2295 2.527123 TTCCCACCGTACCAGGCA 60.527 61.111 0.00 0.00 33.69 4.75
1455 2588 4.373116 ACGTTGCCGATGCCGTCT 62.373 61.111 0.00 0.00 31.07 4.18
1880 3142 9.883293 TGTATCATCTATTAAGAGAAGAAGGGA 57.117 33.333 8.90 0.00 34.49 4.20
1960 3224 0.893447 AACTCTACCCGGCACACTAC 59.107 55.000 0.00 0.00 0.00 2.73
2303 3567 0.243907 CGAGTCCACACTTGTCGGAT 59.756 55.000 4.52 0.00 30.63 4.18
2341 3605 2.812011 AGCAGGTGGTTTATCGTTTCAC 59.188 45.455 0.00 0.00 0.00 3.18
2456 3721 4.363991 AGAAAAGAACCTGCATCTGAGT 57.636 40.909 0.00 0.00 0.00 3.41
2479 3744 2.035155 TCGCGAGTCCCAGGAGAA 59.965 61.111 3.71 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.057245 CACATACCGACTCGATGATGGAT 60.057 47.826 0.00 0.00 0.00 3.41
26 27 1.444917 GGCTTTAGCGGGCACATACC 61.445 60.000 0.00 0.00 43.26 2.73
29 30 2.354729 TGGCTTTAGCGGGCACAT 59.645 55.556 0.00 0.00 43.26 3.21
43 44 1.588139 CGGTAATCTCCGTCGTGGC 60.588 63.158 0.00 0.00 44.77 5.01
94 95 4.643387 GCCAGGTCCCACGCAGTT 62.643 66.667 0.00 0.00 41.61 3.16
144 145 3.350377 GTGCGCTTTAGCCACCAA 58.650 55.556 9.73 0.00 36.73 3.67
149 150 1.146358 CGTAGAGGTGCGCTTTAGCC 61.146 60.000 9.73 3.11 37.91 3.93
157 158 1.073216 CTGCTCAACGTAGAGGTGCG 61.073 60.000 0.00 0.00 37.50 5.34
237 238 1.353022 TCGATGTTAACTTGGGGCCTT 59.647 47.619 0.84 0.00 0.00 4.35
239 240 1.743394 CTTCGATGTTAACTTGGGGCC 59.257 52.381 7.22 0.00 0.00 5.80
240 241 1.743394 CCTTCGATGTTAACTTGGGGC 59.257 52.381 7.22 0.00 0.00 5.80
241 242 3.270877 CTCCTTCGATGTTAACTTGGGG 58.729 50.000 7.22 0.57 0.00 4.96
242 243 3.939066 ACTCCTTCGATGTTAACTTGGG 58.061 45.455 7.22 1.48 0.00 4.12
243 244 5.721232 AGTACTCCTTCGATGTTAACTTGG 58.279 41.667 7.22 2.14 0.00 3.61
244 245 6.866770 TCAAGTACTCCTTCGATGTTAACTTG 59.133 38.462 7.22 17.53 41.50 3.16
265 266 0.524862 GCATGAAGCACCCTGTCAAG 59.475 55.000 0.00 0.00 44.79 3.02
354 355 0.460311 AATTACTCCCTGAGCGGACG 59.540 55.000 0.00 0.00 32.04 4.79
406 411 0.750850 TCCTCTAACCGGCACATAGC 59.249 55.000 0.00 0.00 44.65 2.97
410 415 1.927487 TTACTCCTCTAACCGGCACA 58.073 50.000 0.00 0.00 0.00 4.57
438 443 8.652290 CCCTTAAATAGCTACAGAGGAGTAATT 58.348 37.037 13.19 0.00 0.00 1.40
439 444 8.011290 TCCCTTAAATAGCTACAGAGGAGTAAT 58.989 37.037 13.19 0.00 0.00 1.89
450 455 7.176340 TCTCTAACGGATCCCTTAAATAGCTAC 59.824 40.741 6.06 0.00 0.00 3.58
468 473 2.617308 TCTCCTTACGGCATCTCTAACG 59.383 50.000 0.00 0.00 0.00 3.18
470 475 5.670792 TTTTCTCCTTACGGCATCTCTAA 57.329 39.130 0.00 0.00 0.00 2.10
496 501 9.031537 TGTTATGAATGTAGTACTTCCTTGAGA 57.968 33.333 0.00 0.00 0.00 3.27
534 541 6.688637 AAAGTTAGTTTAGCCGACAAAAGT 57.311 33.333 0.00 0.00 0.00 2.66
603 610 9.077885 GTCCAGAGGCCATTAAATATGAAATTA 57.922 33.333 5.01 0.00 0.00 1.40
669 676 2.275134 ATGCAATATGGTCGGCATGA 57.725 45.000 0.00 0.00 44.64 3.07
756 768 2.093394 TGGCCACGCAAAGCTAGTATAA 60.093 45.455 0.00 0.00 0.00 0.98
967 984 1.297451 GACCGCTAGTCGCTACGTG 60.297 63.158 0.00 0.00 35.30 4.49
1854 3116 9.883293 TCCCTTCTTCTCTTAATAGATGATACA 57.117 33.333 7.12 0.00 31.82 2.29
1880 3142 8.208224 CCTGTAAACTATTTTGGGGTTCTTTTT 58.792 33.333 0.00 0.00 0.00 1.94
1960 3224 2.202623 GCAGGGCGAGTAGTCACG 60.203 66.667 0.00 0.00 0.00 4.35
2303 3567 0.029300 GCTTCTGCACTGCGTTTTCA 59.971 50.000 0.00 0.00 39.41 2.69
2394 3659 3.450115 CTGGACCTCGGACCGACC 61.450 72.222 13.88 13.78 32.78 4.79
2435 3700 4.070716 CACTCAGATGCAGGTTCTTTTCT 58.929 43.478 0.00 0.00 0.00 2.52
2479 3744 0.893727 GGTTTCACCCATGGCTTCGT 60.894 55.000 6.09 0.00 30.04 3.85
2548 3813 4.811364 GGGCCTGGAGCAAGGAGC 62.811 72.222 0.84 0.00 46.50 4.70


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

AutoCloner maintained by Alex Coulton.