Multiple sequence alignment - TraesCS4D01G113300

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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 TraesCS4D01G113300 chr4D 100.000 2642 0 0 1 2642 93840197 93842838 0.000000e+00 4879.0
1 TraesCS4D01G113300 chr4B 91.253 1932 71 44 746 2642 132331296 132333164 0.000000e+00 2542.0
2 TraesCS4D01G113300 chr4A 90.700 1914 84 42 746 2616 487869268 487867406 0.000000e+00 2462.0
3 TraesCS4D01G113300 chr4A 84.703 438 23 15 2000 2432 742542800 742542402 5.300000e-107 398.0
4 TraesCS4D01G113300 chr4A 84.354 441 27 10 1997 2432 701625819 701626222 6.850000e-106 394.0
5 TraesCS4D01G113300 chr4A 95.000 40 2 0 2603 2642 487867391 487867352 2.200000e-06 63.9
6 TraesCS4D01G113300 chr6D 96.529 749 23 2 1 746 162802307 162801559 0.000000e+00 1236.0
7 TraesCS4D01G113300 chr2A 96.405 751 24 2 1 748 686609623 686608873 0.000000e+00 1234.0
8 TraesCS4D01G113300 chr2A 95.473 751 31 2 1 748 170071299 170070549 0.000000e+00 1195.0
9 TraesCS4D01G113300 chr5D 92.297 753 52 5 1 748 203056623 203057374 0.000000e+00 1064.0
10 TraesCS4D01G113300 chr5D 84.308 650 77 15 998 1642 213129205 213129834 1.740000e-171 612.0
11 TraesCS4D01G113300 chr5D 81.510 649 97 10 998 1642 212627253 212627882 1.810000e-141 512.0
12 TraesCS4D01G113300 chr6B 90.426 752 68 3 1 748 501071354 501070603 0.000000e+00 987.0
13 TraesCS4D01G113300 chr3D 86.019 751 99 5 1 747 380838759 380838011 0.000000e+00 800.0
14 TraesCS4D01G113300 chr3B 85.904 752 100 5 1 748 384313759 384313010 0.000000e+00 797.0
15 TraesCS4D01G113300 chr3B 85.160 438 23 10 2000 2432 805032060 805031660 6.810000e-111 411.0
16 TraesCS4D01G113300 chr1B 85.867 750 102 3 2 748 167114403 167113655 0.000000e+00 795.0
17 TraesCS4D01G113300 chr1B 94.595 37 1 1 1658 1693 614430304 614430268 3.670000e-04 56.5
18 TraesCS4D01G113300 chr7D 85.658 760 102 6 1 756 191501391 191502147 0.000000e+00 793.0
19 TraesCS4D01G113300 chr5B 84.284 649 79 13 998 1642 227120977 227121606 1.740000e-171 612.0
20 TraesCS4D01G113300 chr5B 79.784 648 110 13 998 1642 226759281 226759910 4.010000e-123 451.0
21 TraesCS4D01G113300 chr5B 84.979 466 25 15 2000 2460 696669722 696669297 5.220000e-117 431.0
22 TraesCS4D01G113300 chr5B 74.930 359 70 17 1228 1575 664998552 664998203 2.120000e-31 147.0
23 TraesCS4D01G113300 chr5A 83.975 649 81 13 998 1642 276980834 276980205 3.760000e-168 601.0
24 TraesCS4D01G113300 chr5A 82.406 557 75 13 998 1550 276111785 276112322 5.150000e-127 464.0
25 TraesCS4D01G113300 chr7B 84.368 467 30 15 2000 2460 655427485 655427056 4.070000e-113 418.0
26 TraesCS4D01G113300 chr7B 88.476 269 16 6 2000 2263 655434004 655433746 7.100000e-81 311.0
27 TraesCS4D01G113300 chr7B 97.143 35 0 1 2494 2528 655427039 655427006 1.020000e-04 58.4
28 TraesCS4D01G113300 chr2B 84.368 435 24 18 1997 2426 714391732 714392127 1.150000e-103 387.0
29 TraesCS4D01G113300 chr2B 87.692 195 13 6 2268 2460 103687640 103687825 1.590000e-52 217.0


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 TraesCS4D01G113300 chr4D 93840197 93842838 2641 False 4879.00 4879 100.000 1 2642 1 chr4D.!!$F1 2641
1 TraesCS4D01G113300 chr4B 132331296 132333164 1868 False 2542.00 2542 91.253 746 2642 1 chr4B.!!$F1 1896
2 TraesCS4D01G113300 chr4A 487867352 487869268 1916 True 1262.95 2462 92.850 746 2642 2 chr4A.!!$R2 1896
3 TraesCS4D01G113300 chr6D 162801559 162802307 748 True 1236.00 1236 96.529 1 746 1 chr6D.!!$R1 745
4 TraesCS4D01G113300 chr2A 686608873 686609623 750 True 1234.00 1234 96.405 1 748 1 chr2A.!!$R2 747
5 TraesCS4D01G113300 chr2A 170070549 170071299 750 True 1195.00 1195 95.473 1 748 1 chr2A.!!$R1 747
6 TraesCS4D01G113300 chr5D 203056623 203057374 751 False 1064.00 1064 92.297 1 748 1 chr5D.!!$F1 747
7 TraesCS4D01G113300 chr5D 213129205 213129834 629 False 612.00 612 84.308 998 1642 1 chr5D.!!$F3 644
8 TraesCS4D01G113300 chr5D 212627253 212627882 629 False 512.00 512 81.510 998 1642 1 chr5D.!!$F2 644
9 TraesCS4D01G113300 chr6B 501070603 501071354 751 True 987.00 987 90.426 1 748 1 chr6B.!!$R1 747
10 TraesCS4D01G113300 chr3D 380838011 380838759 748 True 800.00 800 86.019 1 747 1 chr3D.!!$R1 746
11 TraesCS4D01G113300 chr3B 384313010 384313759 749 True 797.00 797 85.904 1 748 1 chr3B.!!$R1 747
12 TraesCS4D01G113300 chr1B 167113655 167114403 748 True 795.00 795 85.867 2 748 1 chr1B.!!$R1 746
13 TraesCS4D01G113300 chr7D 191501391 191502147 756 False 793.00 793 85.658 1 756 1 chr7D.!!$F1 755
14 TraesCS4D01G113300 chr5B 227120977 227121606 629 False 612.00 612 84.284 998 1642 1 chr5B.!!$F2 644
15 TraesCS4D01G113300 chr5B 226759281 226759910 629 False 451.00 451 79.784 998 1642 1 chr5B.!!$F1 644
16 TraesCS4D01G113300 chr5A 276980205 276980834 629 True 601.00 601 83.975 998 1642 1 chr5A.!!$R1 644
17 TraesCS4D01G113300 chr5A 276111785 276112322 537 False 464.00 464 82.406 998 1550 1 chr5A.!!$F1 552

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
360 363 0.391597 GGGATTGACGGCGGATCTAA 59.608 55.0 13.24 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1806 1.316651 GCCTTGAGCCTTGATGATCC 58.683 55.0 0.0 0.0 34.35 3.36 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
356 359 0.535102 GAATGGGATTGACGGCGGAT 60.535 55.000 13.24 1.54 0.00 4.18
360 363 0.391597 GGGATTGACGGCGGATCTAA 59.608 55.000 13.24 0.00 0.00 2.10
397 400 0.700564 AGATTGGTGCAGTGGTGGAT 59.299 50.000 0.00 0.00 0.00 3.41
592 597 0.460987 CAGGAGCATTCGGAGGTCAC 60.461 60.000 0.00 0.00 35.30 3.67
662 667 0.594602 TAGGGTCGACTTGTGACACG 59.405 55.000 16.46 0.00 44.51 4.49
684 689 6.362551 CACGTAACTAGCGCATATGTAATCTT 59.637 38.462 11.47 0.00 0.00 2.40
796 811 6.512578 GCCCCACACAAACATGAAAATAAAAC 60.513 38.462 0.00 0.00 0.00 2.43
799 814 6.126079 CACACAAACATGAAAATAAAACGCC 58.874 36.000 0.00 0.00 0.00 5.68
858 873 9.549509 TTTATTTTATTTCGGAAATCACGACTG 57.450 29.630 18.59 0.00 40.45 3.51
894 909 1.448985 TTTATTCACGCCACTGGAGC 58.551 50.000 0.00 0.00 0.00 4.70
895 910 0.392461 TTATTCACGCCACTGGAGCC 60.392 55.000 0.00 0.00 0.00 4.70
896 911 2.572095 TATTCACGCCACTGGAGCCG 62.572 60.000 0.00 0.00 0.00 5.52
944 977 2.430610 CCGCCCCTCTTCTCCTCTG 61.431 68.421 0.00 0.00 0.00 3.35
1186 1235 4.385405 GGCAGCTGGACGTGCTCT 62.385 66.667 17.12 2.46 38.92 4.09
1677 1726 3.397482 GTGCTCTGCTTCTTCTTCTTCA 58.603 45.455 0.00 0.00 0.00 3.02
1768 1821 2.848691 CCAAGAGGATCATCAAGGCTC 58.151 52.381 10.44 0.00 37.82 4.70
1803 1856 4.164604 GGGTGGTACATGGTGGTAATAAGA 59.835 45.833 0.00 0.00 44.52 2.10
1804 1857 5.121105 GGTGGTACATGGTGGTAATAAGAC 58.879 45.833 0.00 0.00 44.52 3.01
1867 1921 9.363763 GAATTTAGTGTTGGTTACTCCTACTAC 57.636 37.037 0.00 0.00 41.34 2.73
1868 1922 8.661752 ATTTAGTGTTGGTTACTCCTACTACT 57.338 34.615 0.00 0.00 41.34 2.57
1869 1923 9.759473 ATTTAGTGTTGGTTACTCCTACTACTA 57.241 33.333 0.00 0.00 41.34 1.82
1875 1929 7.820872 TGTTGGTTACTCCTACTACTAAATTGC 59.179 37.037 0.00 0.00 41.34 3.56
1882 1936 6.932960 ACTCCTACTACTAAATTGCGTTTTGT 59.067 34.615 6.68 6.68 38.83 2.83
1903 1957 5.950883 TGTTCGTGTTTAATTGTTGGTGAA 58.049 33.333 0.00 0.00 0.00 3.18
1993 2047 5.198207 GGTTAATGCTGGGGTTACAAGTAT 58.802 41.667 0.00 0.00 0.00 2.12
1994 2048 6.069556 TGGTTAATGCTGGGGTTACAAGTATA 60.070 38.462 0.00 0.00 0.00 1.47
1995 2049 6.261603 GGTTAATGCTGGGGTTACAAGTATAC 59.738 42.308 0.00 0.00 0.00 1.47
2003 2057 7.469732 GCTGGGGTTACAAGTATACTACTAGTG 60.470 44.444 5.65 2.85 38.26 2.74
2186 2254 5.182760 GCAAGTCCAATTCTCTGAACTCATT 59.817 40.000 0.00 0.00 0.00 2.57
2208 2276 1.616994 CCCTGGGAGGATTTGGTGAAC 60.617 57.143 7.01 0.00 37.67 3.18
2249 2317 3.411454 TGGGAGTTCAGGATCATCTCT 57.589 47.619 0.00 0.00 0.00 3.10
2329 2416 5.196341 TCTATGGAAGCACCTTACATACG 57.804 43.478 5.92 4.08 42.55 3.06
2330 2417 3.906720 ATGGAAGCACCTTACATACGT 57.093 42.857 0.92 0.00 42.55 3.57
2331 2418 5.829391 TCTATGGAAGCACCTTACATACGTA 59.171 40.000 0.00 0.00 42.55 3.57
2394 2481 3.255888 TGACAGAGTAGTGGTGATGTGTC 59.744 47.826 0.00 0.00 34.86 3.67
2395 2482 3.501349 ACAGAGTAGTGGTGATGTGTCT 58.499 45.455 0.00 0.00 0.00 3.41
2401 2488 1.345741 AGTGGTGATGTGTCTGACTGG 59.654 52.381 9.51 0.00 0.00 4.00
2402 2489 1.070758 GTGGTGATGTGTCTGACTGGT 59.929 52.381 9.51 0.00 0.00 4.00
2403 2490 1.070601 TGGTGATGTGTCTGACTGGTG 59.929 52.381 9.51 0.00 0.00 4.17
2404 2491 1.344438 GGTGATGTGTCTGACTGGTGA 59.656 52.381 9.51 0.00 0.00 4.02
2405 2492 2.611473 GGTGATGTGTCTGACTGGTGAG 60.611 54.545 9.51 0.00 0.00 3.51
2406 2493 2.297315 GTGATGTGTCTGACTGGTGAGA 59.703 50.000 9.51 0.00 0.00 3.27
2422 2509 1.611851 AGAGGTGAGGAGTGGCCAG 60.612 63.158 5.11 0.00 40.02 4.85
2428 2515 0.114364 TGAGGAGTGGCCAGTGAGTA 59.886 55.000 20.47 0.00 40.02 2.59
2484 2573 6.483640 GTGCAGGAGAGGAATTATACGAAATT 59.516 38.462 0.00 0.00 0.00 1.82
2533 2622 1.855360 GAACCAATTAGCTCTCTCGCG 59.145 52.381 0.00 0.00 34.40 5.87
2605 2724 0.604780 ATGATATCTGCGGCCTGTGC 60.605 55.000 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
356 359 6.178324 TCTTGAGTCGTTAGATGGACTTAGA 58.822 40.000 0.00 0.33 43.23 2.10
360 363 5.394663 CCAATCTTGAGTCGTTAGATGGACT 60.395 44.000 5.93 0.00 45.71 3.85
397 400 7.934120 GCTTATCTATTCTTTTCCTAGCTTCCA 59.066 37.037 0.00 0.00 0.00 3.53
592 597 9.090692 GCTCTACTCGACTACTCTAATAATAGG 57.909 40.741 0.00 0.00 0.00 2.57
662 667 8.548721 ACAAAAGATTACATATGCGCTAGTTAC 58.451 33.333 9.73 0.00 0.00 2.50
755 760 0.326264 GGGCAGAGATTGTGTGAGGT 59.674 55.000 0.00 0.00 0.00 3.85
796 811 0.893270 TTCTTTGGTGGGTCATGGCG 60.893 55.000 0.00 0.00 0.00 5.69
799 814 1.993956 TGGTTCTTTGGTGGGTCATG 58.006 50.000 0.00 0.00 0.00 3.07
898 913 4.660938 AAAGACTGGGGTGGCCGC 62.661 66.667 8.12 8.12 36.97 6.53
944 977 0.846693 AGAGGAGAGGAGAGGAGAGC 59.153 60.000 0.00 0.00 0.00 4.09
1596 1645 2.224159 GGTCTGGAACCTGAGCCCA 61.224 63.158 15.58 0.00 45.45 5.36
1653 1702 1.458827 GAAGAAGAAGCAGAGCACGTG 59.541 52.381 12.28 12.28 0.00 4.49
1677 1726 1.686052 GACGGAGCAGAGGAAGATGAT 59.314 52.381 0.00 0.00 0.00 2.45
1754 1806 1.316651 GCCTTGAGCCTTGATGATCC 58.683 55.000 0.00 0.00 34.35 3.36
1782 1835 5.985911 AGTCTTATTACCACCATGTACCAC 58.014 41.667 0.00 0.00 0.00 4.16
1803 1856 2.502295 CTATACCCCTCGACGCTAAGT 58.498 52.381 0.00 0.00 0.00 2.24
1804 1857 1.811359 CCTATACCCCTCGACGCTAAG 59.189 57.143 0.00 0.00 0.00 2.18
1867 1921 5.613964 AACACGAACAAAACGCAATTTAG 57.386 34.783 0.00 0.00 0.00 1.85
1868 1922 7.502177 TTAAACACGAACAAAACGCAATTTA 57.498 28.000 0.00 0.00 0.00 1.40
1869 1923 4.912528 AAACACGAACAAAACGCAATTT 57.087 31.818 0.00 0.00 0.00 1.82
1875 1929 6.172364 CCAACAATTAAACACGAACAAAACG 58.828 36.000 0.00 0.00 0.00 3.60
1882 1936 6.197364 ACTTCACCAACAATTAAACACGAA 57.803 33.333 0.00 0.00 0.00 3.85
1937 1991 5.526010 AATTCCATCGTAACGACAAGTTC 57.474 39.130 0.00 0.00 43.06 3.01
1941 1995 6.645827 TCACTTTAATTCCATCGTAACGACAA 59.354 34.615 0.00 0.00 39.18 3.18
1945 1999 7.428183 CCATTTCACTTTAATTCCATCGTAACG 59.572 37.037 0.00 0.00 0.00 3.18
1993 2047 7.611079 ACAAAAACAAAACCACCACTAGTAGTA 59.389 33.333 1.57 0.00 0.00 1.82
1994 2048 6.434965 ACAAAAACAAAACCACCACTAGTAGT 59.565 34.615 0.00 0.00 0.00 2.73
1995 2049 6.859017 ACAAAAACAAAACCACCACTAGTAG 58.141 36.000 0.00 0.00 0.00 2.57
2003 2057 2.159639 CCGCAACAAAAACAAAACCACC 60.160 45.455 0.00 0.00 0.00 4.61
2186 2254 1.856873 ACCAAATCCTCCCAGGGCA 60.857 57.895 0.00 0.00 35.59 5.36
2208 2276 2.295885 AGTCCAATCCGTACCTACTCG 58.704 52.381 0.00 0.00 0.00 4.18
2249 2317 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2360 2447 6.238621 CCACTACTCTGTCACTTGCTATAGAG 60.239 46.154 3.21 0.00 38.06 2.43
2394 2481 0.894141 CCTCACCTCTCACCAGTCAG 59.106 60.000 0.00 0.00 0.00 3.51
2395 2482 0.482887 TCCTCACCTCTCACCAGTCA 59.517 55.000 0.00 0.00 0.00 3.41
2401 2488 1.594310 GCCACTCCTCACCTCTCAC 59.406 63.158 0.00 0.00 0.00 3.51
2402 2489 1.610673 GGCCACTCCTCACCTCTCA 60.611 63.158 0.00 0.00 0.00 3.27
2403 2490 1.610673 TGGCCACTCCTCACCTCTC 60.611 63.158 0.00 0.00 35.26 3.20
2404 2491 1.611851 CTGGCCACTCCTCACCTCT 60.612 63.158 0.00 0.00 35.26 3.69
2405 2492 1.915769 ACTGGCCACTCCTCACCTC 60.916 63.158 0.00 0.00 35.26 3.85
2406 2493 2.205462 ACTGGCCACTCCTCACCT 59.795 61.111 0.00 0.00 35.26 4.00
2435 2522 0.736053 TTCCGTGCCAACAGAACAAC 59.264 50.000 0.00 0.00 0.00 3.32
2436 2523 1.686355 ATTCCGTGCCAACAGAACAA 58.314 45.000 0.00 0.00 0.00 2.83
2438 2527 1.606668 TCAATTCCGTGCCAACAGAAC 59.393 47.619 0.00 0.00 0.00 3.01
2488 2577 1.144691 TGGAAGTTCCATGGGACACA 58.855 50.000 25.54 17.14 42.67 3.72
2542 2631 1.699634 AGACCTTGCACCTGAGCTAAA 59.300 47.619 0.00 0.00 34.99 1.85
2605 2724 1.588674 TTATAACGCAATCTGGGCCG 58.411 50.000 0.00 0.00 33.10 6.13


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

AutoCloner maintained by Alex Coulton.