Multiple sequence alignment - TraesCS7D01G411100

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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 TraesCS7D01G411100 chr7D 100.000 2411 0 0 1 2411 529957538 529955128 0.000000e+00 4453.0
1 TraesCS7D01G411100 chr7B 92.516 1844 74 25 596 2411 568107916 568106109 0.000000e+00 2582.0
2 TraesCS7D01G411100 chr7B 97.778 45 1 0 44 88 568107965 568107921 7.150000e-11 78.7
3 TraesCS7D01G411100 chr7A 94.494 1126 30 13 614 1724 609431978 609430870 0.000000e+00 1707.0
4 TraesCS7D01G411100 chr7A 94.463 596 28 2 1817 2411 609430805 609430214 0.000000e+00 913.0
5 TraesCS7D01G411100 chr7A 90.446 628 57 3 1 627 609432619 609431994 0.000000e+00 824.0
6 TraesCS7D01G411100 chr1D 79.656 639 73 29 1101 1709 14986304 14985693 8.020000e-110 407.0
7 TraesCS7D01G411100 chr6A 81.972 355 50 11 997 1347 85586837 85586493 3.030000e-74 289.0
8 TraesCS7D01G411100 chr6B 81.356 354 51 10 997 1347 143200178 143199837 8.490000e-70 274.0
9 TraesCS7D01G411100 chr2D 83.412 211 32 3 1123 1331 539895943 539895734 2.450000e-45 193.0
10 TraesCS7D01G411100 chr5D 80.392 204 33 6 1123 1322 330078606 330078806 5.370000e-32 148.0
11 TraesCS7D01G411100 chr5D 81.646 158 21 5 441 593 321613835 321613681 9.050000e-25 124.0
12 TraesCS7D01G411100 chr5D 89.157 83 7 2 441 523 384139459 384139379 4.240000e-18 102.0
13 TraesCS7D01G411100 chr5D 80.000 130 21 4 441 566 467427558 467427686 9.180000e-15 91.6
14 TraesCS7D01G411100 chr5B 79.512 205 33 8 1123 1322 383036031 383036231 1.160000e-28 137.0
15 TraesCS7D01G411100 chr5A 78.873 213 38 6 1123 1331 426730439 426730230 1.160000e-28 137.0
16 TraesCS7D01G411100 chr5A 82.667 150 17 8 441 587 51793064 51793207 9.050000e-25 124.0
17 TraesCS7D01G411100 chr1A 82.394 142 16 6 444 580 532486743 532486880 5.450000e-22 115.0
18 TraesCS7D01G411100 chr1A 80.690 145 22 5 444 585 589856196 589856337 9.110000e-20 108.0
19 TraesCS7D01G411100 chrUn 80.851 141 21 4 441 581 88060745 88060611 3.280000e-19 106.0
20 TraesCS7D01G411100 chr6D 83.908 87 9 5 456 538 389647761 389647676 7.150000e-11 78.7


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 TraesCS7D01G411100 chr7D 529955128 529957538 2410 True 4453.00 4453 100.000000 1 2411 1 chr7D.!!$R1 2410
1 TraesCS7D01G411100 chr7B 568106109 568107965 1856 True 1330.35 2582 95.147000 44 2411 2 chr7B.!!$R1 2367
2 TraesCS7D01G411100 chr7A 609430214 609432619 2405 True 1148.00 1707 93.134333 1 2411 3 chr7A.!!$R1 2410
3 TraesCS7D01G411100 chr1D 14985693 14986304 611 True 407.00 407 79.656000 1101 1709 1 chr1D.!!$R1 608

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
189 190 0.172803 AACGGGAAGATCTTCGACGG 59.827 55.0 34.35 24.92 41.55 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1905 0.111253 CCTTGAGCTGAAACCCTGGT 59.889 55.0 0.0 0.0 0.0 4.0 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
59 60 6.759497 AACACTCTAGATATTTTGTTGCCC 57.241 37.500 0.00 0.00 0.00 5.36
116 117 1.025812 CCTGCTAAGTCTCGGTCGAT 58.974 55.000 0.00 0.00 0.00 3.59
118 119 2.455032 CTGCTAAGTCTCGGTCGATTG 58.545 52.381 0.00 0.00 0.00 2.67
166 167 1.864029 GCTTGGTCGCTTTGGAAACAC 60.864 52.381 0.00 0.00 42.67 3.32
167 168 0.741915 TTGGTCGCTTTGGAAACACC 59.258 50.000 0.00 0.00 42.67 4.16
172 173 1.598601 TCGCTTTGGAAACACCGTAAC 59.401 47.619 0.00 0.00 42.67 2.50
187 188 2.448219 CGTAACGGGAAGATCTTCGAC 58.552 52.381 25.40 19.91 40.37 4.20
189 190 0.172803 AACGGGAAGATCTTCGACGG 59.827 55.000 34.35 24.92 41.55 4.79
190 191 1.589196 CGGGAAGATCTTCGACGGC 60.589 63.158 28.96 17.16 40.37 5.68
200 201 3.493830 TTCGACGGCGCACAAGTCT 62.494 57.895 5.31 0.00 37.46 3.24
220 221 1.021390 CCATCGACAACCTGCTGACC 61.021 60.000 0.00 0.00 0.00 4.02
222 223 0.247736 ATCGACAACCTGCTGACCTC 59.752 55.000 0.00 0.00 0.00 3.85
246 247 2.872245 TCAAAGACGAGGCAAGACTTTG 59.128 45.455 21.09 21.09 45.54 2.77
298 299 8.204903 AGAGCATCATTCCTCTAATATGAACT 57.795 34.615 0.00 0.00 36.70 3.01
324 325 2.759795 GGCTGAGCAACCCCTTCT 59.240 61.111 6.82 0.00 0.00 2.85
338 339 1.654317 CCTTCTGATGCTCACTCTGC 58.346 55.000 0.00 0.00 0.00 4.26
344 345 1.339438 TGATGCTCACTCTGCTTTCCC 60.339 52.381 0.00 0.00 0.00 3.97
351 352 1.959282 CACTCTGCTTTCCCTTTTGCT 59.041 47.619 0.00 0.00 0.00 3.91
352 353 1.959282 ACTCTGCTTTCCCTTTTGCTG 59.041 47.619 0.00 0.00 0.00 4.41
399 400 1.483004 GCTCTTCTGTTACTCTCCCCC 59.517 57.143 0.00 0.00 0.00 5.40
416 417 5.433051 TCTCCCCCATCAATGAAAAGATACT 59.567 40.000 0.00 0.00 0.00 2.12
417 418 6.619437 TCTCCCCCATCAATGAAAAGATACTA 59.381 38.462 0.00 0.00 0.00 1.82
425 426 7.496346 TCAATGAAAAGATACTACCCTGAGT 57.504 36.000 0.00 0.00 0.00 3.41
431 432 8.475639 TGAAAAGATACTACCCTGAGTGTATTC 58.524 37.037 0.00 0.00 0.00 1.75
434 435 6.071984 AGATACTACCCTGAGTGTATTCCTG 58.928 44.000 0.00 0.00 0.00 3.86
435 436 4.332683 ACTACCCTGAGTGTATTCCTGA 57.667 45.455 0.00 0.00 0.00 3.86
474 475 7.916450 GCCAATACTATATCCGTGAGATCTTAC 59.084 40.741 7.56 7.56 36.33 2.34
538 540 8.077991 TCTCTTTTGCAAATTATGTCACTTGAG 58.922 33.333 13.65 2.56 0.00 3.02
566 568 7.456684 AACTTGATTAAATCTCGATCGACTG 57.543 36.000 15.15 5.81 0.00 3.51
575 577 1.529438 CTCGATCGACTGAGACCTAGC 59.471 57.143 15.15 0.00 34.04 3.42
593 595 5.071384 ACCTAGCCACACCCATTTACTATAC 59.929 44.000 0.00 0.00 0.00 1.47
600 602 7.656948 GCCACACCCATTTACTATACGTAATTA 59.343 37.037 0.00 0.00 37.88 1.40
659 691 6.706270 TGACAGTTGTTCCTAAGTGATCTTTC 59.294 38.462 0.00 0.00 35.47 2.62
668 700 7.609097 TCCTAAGTGATCTTTCATGCTCTAT 57.391 36.000 0.00 0.00 35.36 1.98
669 701 8.027524 TCCTAAGTGATCTTTCATGCTCTATT 57.972 34.615 0.00 0.00 35.36 1.73
670 702 7.930325 TCCTAAGTGATCTTTCATGCTCTATTG 59.070 37.037 0.00 0.00 35.36 1.90
685 717 6.177610 TGCTCTATTGGTATTTTCGAAACCT 58.822 36.000 10.79 3.72 34.23 3.50
697 729 8.974408 GTATTTTCGAAACCTTGCTAAACAAAT 58.026 29.630 10.79 0.00 37.96 2.32
743 776 6.780457 ATAGTGCATAGACCTTTGCAAAAT 57.220 33.333 13.84 4.23 46.07 1.82
815 863 2.821991 ACAAACCGAAGAGACTCAGG 57.178 50.000 5.02 7.59 0.00 3.86
876 924 3.607661 GTCGCCGATCTCCCTCCC 61.608 72.222 0.00 0.00 0.00 4.30
888 936 6.242396 CGATCTCCCTCCCCTATATATACAG 58.758 48.000 0.00 0.00 0.00 2.74
1481 1545 2.397597 GGAGCAGAGATCTCCTTCCTT 58.602 52.381 19.30 0.00 45.13 3.36
1652 1730 0.725784 GTTTGTGCGTGCCATTCTCG 60.726 55.000 0.00 0.00 35.03 4.04
1657 1736 2.480555 CGTGCCATTCTCGGTTGC 59.519 61.111 0.00 0.00 0.00 4.17
1667 1746 3.410631 TTCTCGGTTGCTTACATTCCA 57.589 42.857 0.00 0.00 0.00 3.53
1740 1844 4.574599 AGCCTTCTTTGCTTAACAGTTG 57.425 40.909 0.00 0.00 34.87 3.16
1757 1861 1.028905 TTGAGCAACCGGAACAAAGG 58.971 50.000 9.46 0.00 0.00 3.11
1784 1888 3.291809 TTCACTTCACGCAGACGATAA 57.708 42.857 0.00 0.00 43.93 1.75
1787 1891 2.923655 CACTTCACGCAGACGATAACAT 59.076 45.455 0.00 0.00 43.93 2.71
1793 1897 2.061773 CGCAGACGATAACATCCCATC 58.938 52.381 0.00 0.00 43.93 3.51
1922 2026 1.934589 TGGCATACGCATGTACAGAC 58.065 50.000 0.33 0.00 41.24 3.51
1947 2051 2.104967 CATGCCCACTCCATTGACAAT 58.895 47.619 0.00 0.00 0.00 2.71
1962 2066 9.066892 TCCATTGACAATAGTTGCTTATTATCC 57.933 33.333 0.00 0.00 0.00 2.59
1977 2081 6.016443 GCTTATTATCCACTACTACGTCCAGT 60.016 42.308 0.00 0.00 0.00 4.00
2014 2119 4.335647 ATGGCGGCCGGATGATCC 62.336 66.667 29.38 18.82 0.00 3.36
2019 2124 2.931068 CGGCCGGATGATCCATCGA 61.931 63.158 20.10 0.00 41.35 3.59
2074 2179 2.202756 CGCGGCCCTAACTCACTC 60.203 66.667 0.00 0.00 0.00 3.51
2076 2181 2.656069 GCGGCCCTAACTCACTCCA 61.656 63.158 0.00 0.00 0.00 3.86
2077 2182 1.972660 GCGGCCCTAACTCACTCCAT 61.973 60.000 0.00 0.00 0.00 3.41
2078 2183 0.541863 CGGCCCTAACTCACTCCATT 59.458 55.000 0.00 0.00 0.00 3.16
2079 2184 1.743772 CGGCCCTAACTCACTCCATTG 60.744 57.143 0.00 0.00 0.00 2.82
2080 2185 1.383523 GCCCTAACTCACTCCATTGC 58.616 55.000 0.00 0.00 0.00 3.56
2325 2430 3.360340 GGAGCAGCAGGTGTGTGC 61.360 66.667 0.66 0.00 44.35 4.57
2326 2431 2.592574 GAGCAGCAGGTGTGTGCA 60.593 61.111 0.66 0.00 46.60 4.57
2336 2441 1.371183 GTGTGTGCAGGTAGCCAGA 59.629 57.895 0.00 0.00 44.83 3.86
2369 2474 5.394115 GGTTTCATTTGTTTGGTGTCTGAGT 60.394 40.000 0.00 0.00 0.00 3.41
2406 2511 9.372369 GGAATCGGAATAATAATCTCTAGTTGG 57.628 37.037 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 9.555727 GGGCAACAAAATATCTAGAGTGTTATA 57.444 33.333 0.00 0.00 39.74 0.98
91 92 1.133407 CCGAGACTTAGCAGGACTGAC 59.867 57.143 3.00 0.00 0.00 3.51
116 117 2.558359 TGATGAGCGAGTGAAGTCTCAA 59.442 45.455 0.00 0.00 38.81 3.02
118 119 2.929531 TGATGAGCGAGTGAAGTCTC 57.070 50.000 0.00 0.00 0.00 3.36
153 154 1.658094 CGTTACGGTGTTTCCAAAGCG 60.658 52.381 0.00 0.00 42.67 4.68
157 158 0.467384 TCCCGTTACGGTGTTTCCAA 59.533 50.000 22.78 0.00 46.80 3.53
159 160 1.150827 CTTCCCGTTACGGTGTTTCC 58.849 55.000 22.78 0.00 46.80 3.13
166 167 2.793933 GTCGAAGATCTTCCCGTTACGG 60.794 54.545 26.08 17.88 43.49 4.02
167 168 2.448219 GTCGAAGATCTTCCCGTTACG 58.552 52.381 26.08 15.24 40.67 3.18
172 173 1.589196 GCCGTCGAAGATCTTCCCG 60.589 63.158 26.08 25.27 40.67 5.14
181 182 3.000080 GACTTGTGCGCCGTCGAAG 62.000 63.158 4.18 2.10 38.10 3.79
187 188 2.434884 ATGGAGACTTGTGCGCCG 60.435 61.111 4.18 0.00 0.00 6.46
189 190 1.446099 TCGATGGAGACTTGTGCGC 60.446 57.895 0.00 0.00 0.00 6.09
190 191 0.388520 TGTCGATGGAGACTTGTGCG 60.389 55.000 0.00 0.00 41.47 5.34
200 201 0.037326 GTCAGCAGGTTGTCGATGGA 60.037 55.000 0.00 0.00 0.00 3.41
220 221 3.124297 GTCTTGCCTCGTCTTTGATTGAG 59.876 47.826 0.00 0.00 0.00 3.02
222 223 3.070018 AGTCTTGCCTCGTCTTTGATTG 58.930 45.455 0.00 0.00 0.00 2.67
287 288 6.042093 TCAGCCCCTACAGAAGTTCATATTAG 59.958 42.308 5.50 0.16 0.00 1.73
298 299 0.324943 GTTGCTCAGCCCCTACAGAA 59.675 55.000 0.00 0.00 0.00 3.02
338 339 0.320160 GCTGGCAGCAAAAGGGAAAG 60.320 55.000 33.33 0.00 41.89 2.62
361 362 1.740296 CTTGTCCCTTGGCCGTACG 60.740 63.158 8.69 8.69 0.00 3.67
399 400 7.989741 ACTCAGGGTAGTATCTTTTCATTGATG 59.010 37.037 0.00 0.00 0.00 3.07
416 417 6.442541 TTTTTCAGGAATACACTCAGGGTA 57.557 37.500 0.00 0.00 0.00 3.69
417 418 4.993705 TTTTCAGGAATACACTCAGGGT 57.006 40.909 0.00 0.00 0.00 4.34
449 450 8.957466 TGTAAGATCTCACGGATATAGTATTGG 58.043 37.037 0.00 0.00 34.33 3.16
511 512 8.077991 TCAAGTGACATAATTTGCAAAAGAGAG 58.922 33.333 17.19 8.06 0.00 3.20
512 513 7.939782 TCAAGTGACATAATTTGCAAAAGAGA 58.060 30.769 17.19 2.07 0.00 3.10
514 515 7.715657 ACTCAAGTGACATAATTTGCAAAAGA 58.284 30.769 17.19 7.42 0.00 2.52
538 540 7.841758 GTCGATCGAGATTTAATCAAGTTTCAC 59.158 37.037 20.09 0.00 0.00 3.18
555 557 1.529438 GCTAGGTCTCAGTCGATCGAG 59.471 57.143 20.09 8.15 0.00 4.04
558 560 1.335496 GTGGCTAGGTCTCAGTCGATC 59.665 57.143 0.00 0.00 0.00 3.69
566 568 0.912486 AATGGGTGTGGCTAGGTCTC 59.088 55.000 0.00 0.00 0.00 3.36
593 595 7.009815 TCCGCAAGAACTAAGAACATAATTACG 59.990 37.037 0.00 0.00 43.02 3.18
600 602 6.575162 AAATTCCGCAAGAACTAAGAACAT 57.425 33.333 0.00 0.00 37.29 2.71
607 609 6.090129 GCAATGTTAAATTCCGCAAGAACTA 58.910 36.000 0.00 0.00 37.29 2.24
659 691 6.912591 GGTTTCGAAAATACCAATAGAGCATG 59.087 38.462 13.10 0.00 32.12 4.06
668 700 6.636562 TTAGCAAGGTTTCGAAAATACCAA 57.363 33.333 13.10 0.00 34.32 3.67
669 701 6.039493 TGTTTAGCAAGGTTTCGAAAATACCA 59.961 34.615 13.10 0.00 34.32 3.25
670 702 6.440436 TGTTTAGCAAGGTTTCGAAAATACC 58.560 36.000 13.10 10.85 0.00 2.73
876 924 1.692519 GGCGGGGGCTGTATATATAGG 59.307 57.143 8.41 0.00 0.00 2.57
1652 1730 1.202348 GGCAGTGGAATGTAAGCAACC 59.798 52.381 0.00 0.00 0.00 3.77
1657 1736 2.787473 TGGAGGCAGTGGAATGTAAG 57.213 50.000 0.00 0.00 0.00 2.34
1667 1746 2.957402 TCTGAAACAATGGAGGCAGT 57.043 45.000 0.00 0.00 0.00 4.40
1740 1844 0.822121 ACCCTTTGTTCCGGTTGCTC 60.822 55.000 0.00 0.00 0.00 4.26
1793 1897 0.831288 TGAAACCCTGGTGCCCAATG 60.831 55.000 0.00 0.00 30.80 2.82
1801 1905 0.111253 CCTTGAGCTGAAACCCTGGT 59.889 55.000 0.00 0.00 0.00 4.00
1805 1909 1.527433 GGTGCCTTGAGCTGAAACCC 61.527 60.000 0.00 0.00 44.23 4.11
1922 2026 4.720902 TGGAGTGGGCATGGTGCG 62.721 66.667 0.00 0.00 46.21 5.34
1947 2051 8.455903 ACGTAGTAGTGGATAATAAGCAACTA 57.544 34.615 0.00 0.00 41.94 2.24
2014 2119 1.142965 TACGCACATGGGGTCGATG 59.857 57.895 0.00 0.00 42.41 3.84
2071 2176 5.255687 TGTATTGACAATGAGCAATGGAGT 58.744 37.500 11.05 0.00 36.27 3.85
2072 2177 5.823209 TGTATTGACAATGAGCAATGGAG 57.177 39.130 11.05 0.00 36.27 3.86
2074 2179 5.068067 TCCATGTATTGACAATGAGCAATGG 59.932 40.000 11.05 14.18 39.59 3.16
2076 2181 6.239204 CCATCCATGTATTGACAATGAGCAAT 60.239 38.462 11.05 9.91 39.59 3.56
2077 2182 5.068067 CCATCCATGTATTGACAATGAGCAA 59.932 40.000 11.05 0.00 39.59 3.91
2078 2183 4.581409 CCATCCATGTATTGACAATGAGCA 59.419 41.667 11.05 7.49 39.59 4.26
2079 2184 4.823442 TCCATCCATGTATTGACAATGAGC 59.177 41.667 11.05 2.20 39.59 4.26
2080 2185 6.947644 TTCCATCCATGTATTGACAATGAG 57.052 37.500 11.05 0.00 39.59 2.90
2230 2335 4.925861 GATGCTCCGAGGGCCTGC 62.926 72.222 12.95 9.09 0.00 4.85
2304 2409 0.178981 ACACACCTGCTGCTCCATTT 60.179 50.000 0.00 0.00 0.00 2.32
2325 2430 1.198867 CGATCGATCTCTGGCTACCTG 59.801 57.143 22.43 0.00 0.00 4.00
2326 2431 1.529226 CGATCGATCTCTGGCTACCT 58.471 55.000 22.43 0.00 0.00 3.08
2336 2441 5.391950 CCAAACAAATGAAACCGATCGATCT 60.392 40.000 22.43 4.15 0.00 2.75


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

AutoCloner maintained by Alex Coulton.