Multiple sequence alignment - TraesCS7D01G280500

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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 TraesCS7D01G280500 chr7D 100.000 2273 0 0 1 2273 273856378 273854106 0.000000e+00 4198.0
1 TraesCS7D01G280500 chr7D 81.116 233 36 8 52 278 237547181 237546951 1.790000e-41 180.0
2 TraesCS7D01G280500 chr2B 89.037 1505 74 34 821 2273 567577885 567579350 0.000000e+00 1781.0
3 TraesCS7D01G280500 chr2B 90.404 792 57 9 2 785 567072207 567072987 0.000000e+00 1024.0
4 TraesCS7D01G280500 chr2B 91.263 744 18 15 821 1552 567576431 567577139 0.000000e+00 970.0
5 TraesCS7D01G280500 chr7A 94.145 871 25 10 793 1654 307378407 307377554 0.000000e+00 1303.0
6 TraesCS7D01G280500 chr7A 95.425 612 26 2 1662 2273 307377513 307376904 0.000000e+00 974.0
7 TraesCS7D01G280500 chr7A 88.228 807 62 12 2 798 307380322 307379539 0.000000e+00 933.0
8 TraesCS7D01G280500 chr7B 94.897 823 26 8 840 1651 264005184 264006001 0.000000e+00 1273.0
9 TraesCS7D01G280500 chr7B 90.980 510 41 3 10 519 263946428 263946932 0.000000e+00 682.0
10 TraesCS7D01G280500 chr7B 94.514 401 16 3 1662 2060 264006045 264006441 4.150000e-172 614.0
11 TraesCS7D01G280500 chr7B 83.465 254 31 8 515 761 264003733 264003982 2.270000e-55 226.0
12 TraesCS7D01G280500 chr7B 92.143 140 11 0 2133 2272 264006441 264006580 4.950000e-47 198.0
13 TraesCS7D01G280500 chr2D 91.479 845 28 23 821 1651 483066982 483067796 0.000000e+00 1122.0
14 TraesCS7D01G280500 chr2D 91.206 796 52 7 2 789 482804684 482805469 0.000000e+00 1066.0
15 TraesCS7D01G280500 chr2D 86.783 628 25 17 1662 2264 483067840 483068434 0.000000e+00 647.0
16 TraesCS7D01G280500 chr2D 89.796 49 5 0 1882 1930 174242459 174242411 1.880000e-06 63.9
17 TraesCS7D01G280500 chr2A 91.138 835 39 16 821 1651 625564814 625565617 0.000000e+00 1099.0
18 TraesCS7D01G280500 chr2A 89.848 788 61 8 2 785 625292538 625293310 0.000000e+00 994.0
19 TraesCS7D01G280500 chr2A 88.590 631 23 12 1662 2273 625565661 625566261 0.000000e+00 721.0
20 TraesCS7D01G280500 chr4A 80.851 235 37 8 52 280 196773254 196773486 6.450000e-41 178.0
21 TraesCS7D01G280500 chr4A 85.470 117 17 0 1088 1204 615164054 615163938 3.070000e-24 122.0
22 TraesCS7D01G280500 chr6A 79.060 234 43 6 52 280 36009760 36009528 3.020000e-34 156.0
23 TraesCS7D01G280500 chr5D 79.060 234 43 6 52 280 84790444 84790676 3.020000e-34 156.0
24 TraesCS7D01G280500 chr5B 85.470 117 17 0 1088 1204 697499833 697499717 3.070000e-24 122.0
25 TraesCS7D01G280500 chr3D 89.655 58 5 1 1951 2008 241398086 241398030 3.130000e-09 73.1
26 TraesCS7D01G280500 chr6B 79.612 103 14 4 1830 1925 80968320 80968422 1.460000e-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 TraesCS7D01G280500 chr7D 273854106 273856378 2272 True 4198.00 4198 100.000000 1 2273 1 chr7D.!!$R2 2272
1 TraesCS7D01G280500 chr2B 567576431 567579350 2919 False 1375.50 1781 90.150000 821 2273 2 chr2B.!!$F2 1452
2 TraesCS7D01G280500 chr2B 567072207 567072987 780 False 1024.00 1024 90.404000 2 785 1 chr2B.!!$F1 783
3 TraesCS7D01G280500 chr7A 307376904 307380322 3418 True 1070.00 1303 92.599333 2 2273 3 chr7A.!!$R1 2271
4 TraesCS7D01G280500 chr7B 263946428 263946932 504 False 682.00 682 90.980000 10 519 1 chr7B.!!$F1 509
5 TraesCS7D01G280500 chr7B 264003733 264006580 2847 False 577.75 1273 91.254750 515 2272 4 chr7B.!!$F2 1757
6 TraesCS7D01G280500 chr2D 482804684 482805469 785 False 1066.00 1066 91.206000 2 789 1 chr2D.!!$F1 787
7 TraesCS7D01G280500 chr2D 483066982 483068434 1452 False 884.50 1122 89.131000 821 2264 2 chr2D.!!$F2 1443
8 TraesCS7D01G280500 chr2A 625292538 625293310 772 False 994.00 994 89.848000 2 785 1 chr2A.!!$F1 783
9 TraesCS7D01G280500 chr2A 625564814 625566261 1447 False 910.00 1099 89.864000 821 2273 2 chr2A.!!$F2 1452

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
455 466 0.179056 CGGGTGGATAAGAACCGCAT 60.179 55.0 0.0 0.0 39.38 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2227 6122 0.400525 TAAGGATGGCAGGAGGGAGG 60.401 60.0 0.0 0.0 0.0 4.3 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
80 81 0.899019 TACATGACGGCTAGTGGCAA 59.101 50.000 0.00 0.00 44.01 4.52
148 149 1.604947 CGGTAGCTCTCGTCCTCGATA 60.605 57.143 0.00 0.00 45.21 2.92
182 186 3.402628 TGTCAAAGAGGTTGTAGAGGC 57.597 47.619 0.00 0.00 38.47 4.70
234 238 4.195334 GCCGAGATGCCCCATGGT 62.195 66.667 11.73 0.00 0.00 3.55
287 291 3.580895 GGAAACCATGGCCTTCCTTTAAA 59.419 43.478 27.85 0.00 36.48 1.52
298 302 3.119137 CCTTCCTTTAAAGAAATGCCCCG 60.119 47.826 16.98 0.00 0.00 5.73
321 325 2.485426 TGCTATTTGTGCTGCAGAGAAC 59.515 45.455 20.43 12.62 0.00 3.01
342 346 9.571810 GAGAACATGTGTATTTGCATTATCAAA 57.428 29.630 0.00 0.00 39.87 2.69
343 347 9.357652 AGAACATGTGTATTTGCATTATCAAAC 57.642 29.630 0.00 0.00 38.58 2.93
344 348 9.138062 GAACATGTGTATTTGCATTATCAAACA 57.862 29.630 0.00 0.00 38.58 2.83
345 349 9.486497 AACATGTGTATTTGCATTATCAAACAA 57.514 25.926 0.00 0.00 38.58 2.83
358 362 7.464444 GCATTATCAAACAATCAATCAAACCCG 60.464 37.037 0.00 0.00 0.00 5.28
359 363 4.927978 TCAAACAATCAATCAAACCCGT 57.072 36.364 0.00 0.00 0.00 5.28
360 364 6.582677 ATCAAACAATCAATCAAACCCGTA 57.417 33.333 0.00 0.00 0.00 4.02
361 365 6.392625 TCAAACAATCAATCAAACCCGTAA 57.607 33.333 0.00 0.00 0.00 3.18
428 439 0.625849 GGAGGAAAGAGGAATGCCCA 59.374 55.000 0.00 0.00 37.41 5.36
455 466 0.179056 CGGGTGGATAAGAACCGCAT 60.179 55.000 0.00 0.00 39.38 4.73
532 543 3.760151 ACGTCATACAACCAGCAGTAGTA 59.240 43.478 0.00 0.00 0.00 1.82
533 544 4.219070 ACGTCATACAACCAGCAGTAGTAA 59.781 41.667 0.00 0.00 0.00 2.24
549 561 4.544968 AGTAGTAAGAGAGGGAGGAAAGGA 59.455 45.833 0.00 0.00 0.00 3.36
553 565 3.569135 AGAGAGGGAGGAAAGGAGAAA 57.431 47.619 0.00 0.00 0.00 2.52
603 618 2.792749 AGAAAACGAAACTTTGGTGCG 58.207 42.857 0.00 0.00 0.00 5.34
610 625 2.410730 CGAAACTTTGGTGCGTACTAGG 59.589 50.000 3.01 0.00 0.00 3.02
622 637 2.557490 GCGTACTAGGGAGGATCGATTT 59.443 50.000 0.00 0.00 34.37 2.17
668 684 2.529389 AGCGGGTCAGGGGTTCTT 60.529 61.111 0.00 0.00 0.00 2.52
669 685 2.046217 GCGGGTCAGGGGTTCTTC 60.046 66.667 0.00 0.00 0.00 2.87
670 686 2.593956 GCGGGTCAGGGGTTCTTCT 61.594 63.158 0.00 0.00 0.00 2.85
710 726 1.379044 CGAGGCTGGCTGGGATTTT 60.379 57.895 9.06 0.00 0.00 1.82
755 779 2.660064 GCCAAGGAAGGCGAGGAGA 61.660 63.158 0.00 0.00 46.12 3.71
774 1965 3.849953 GACGCGACCGCAATGACC 61.850 66.667 15.93 0.00 42.06 4.02
785 1976 2.437359 AATGACCGCTGCCTGCTC 60.437 61.111 0.00 0.00 40.11 4.26
829 3157 2.419297 GCTGCCTGCTGACTAACACTAT 60.419 50.000 0.00 0.00 38.95 2.12
917 3251 2.537401 GTCCGTCCAGTCCGATAAAAG 58.463 52.381 0.00 0.00 0.00 2.27
1422 5223 1.463553 TTGTGACTGCTCCTGCTCGA 61.464 55.000 0.00 0.00 40.48 4.04
1455 5280 2.100087 TCGCAATATCACCGACTTGCTA 59.900 45.455 4.81 0.00 41.33 3.49
1459 5284 5.047847 GCAATATCACCGACTTGCTAAGTA 58.952 41.667 2.17 0.00 43.03 2.24
1504 5329 6.591001 TGCTTGTGATGCCTATTTAGATACA 58.409 36.000 0.00 0.00 0.00 2.29
1505 5330 7.226441 TGCTTGTGATGCCTATTTAGATACAT 58.774 34.615 0.00 0.00 0.00 2.29
1506 5331 8.374743 TGCTTGTGATGCCTATTTAGATACATA 58.625 33.333 0.00 0.00 0.00 2.29
1651 5484 5.902681 TGTACTGATCCTCGAAATAACCAG 58.097 41.667 0.00 0.00 0.00 4.00
1654 5487 6.240549 ACTGATCCTCGAAATAACCAGAAT 57.759 37.500 0.00 0.00 0.00 2.40
1655 5488 6.653989 ACTGATCCTCGAAATAACCAGAATT 58.346 36.000 0.00 0.00 0.00 2.17
1658 5491 6.706270 TGATCCTCGAAATAACCAGAATTAGC 59.294 38.462 0.00 0.00 0.00 3.09
1659 5492 5.984725 TCCTCGAAATAACCAGAATTAGCA 58.015 37.500 0.00 0.00 0.00 3.49
1712 5584 7.101652 TGATCACTAAGGAGACACATTCTAC 57.898 40.000 0.00 0.00 34.93 2.59
1792 5664 8.469309 TTGATTCCAAGGAATTCCATAAGATC 57.531 34.615 26.22 20.50 43.98 2.75
1875 5747 4.281941 AGGAAATCCTCTCAAACCTTTTGC 59.718 41.667 0.00 0.00 44.77 3.68
2080 5957 1.608717 CCAGCCGTAACTCTCCTGCT 61.609 60.000 0.00 0.00 0.00 4.24
2137 6031 5.084818 AGGCAAAGCAAAACAAGTTACTT 57.915 34.783 0.00 0.00 0.00 2.24
2184 6079 5.122512 AGCTTCTGCATCATATTCATTGC 57.877 39.130 0.00 0.00 42.74 3.56
2227 6122 0.753111 ATCAAGGCGCCATTTCCTCC 60.753 55.000 31.54 0.00 0.00 4.30
2245 6140 1.695597 CCTCCCTCCTGCCATCCTT 60.696 63.158 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.814038 AATTACCATCTGATGCTTAGACTTTT 57.186 30.769 12.17 0.00 0.00 2.27
40 41 6.623486 TGTACAAATGCTACGCTACTTTCTA 58.377 36.000 0.00 0.00 0.00 2.10
80 81 3.325716 AGCCAAAAGAATCAACCAATGCT 59.674 39.130 0.00 0.00 0.00 3.79
148 149 2.452600 TTGACAAAAACTGGGAGCCT 57.547 45.000 0.00 0.00 0.00 4.58
224 228 1.829456 CGTATGAGACCATGGGGCA 59.171 57.895 18.09 11.22 37.90 5.36
234 238 2.024176 GGCTCAAAAGGCGTATGAGA 57.976 50.000 20.23 0.02 42.48 3.27
287 291 0.106519 AATAGCAGCGGGGCATTTCT 60.107 50.000 1.12 0.00 35.83 2.52
298 302 3.324170 CTGCAGCACAAATAGCAGC 57.676 52.632 0.00 0.00 46.51 5.25
342 346 5.975693 ATGTTACGGGTTTGATTGATTGT 57.024 34.783 0.00 0.00 0.00 2.71
343 347 7.696453 GTCTTATGTTACGGGTTTGATTGATTG 59.304 37.037 0.00 0.00 0.00 2.67
344 348 7.392113 TGTCTTATGTTACGGGTTTGATTGATT 59.608 33.333 0.00 0.00 0.00 2.57
345 349 6.882140 TGTCTTATGTTACGGGTTTGATTGAT 59.118 34.615 0.00 0.00 0.00 2.57
393 404 7.194050 TCTTTCCTCCTAGGGTTTTATAGACA 58.806 38.462 9.46 0.00 35.59 3.41
396 407 6.844917 TCCTCTTTCCTCCTAGGGTTTTATAG 59.155 42.308 9.46 0.00 35.59 1.31
400 411 3.883135 TCCTCTTTCCTCCTAGGGTTTT 58.117 45.455 9.46 0.00 35.59 2.43
413 424 4.380973 GCTACTTTTGGGCATTCCTCTTTC 60.381 45.833 0.00 0.00 36.20 2.62
428 439 4.259356 GTTCTTATCCACCCGCTACTTTT 58.741 43.478 0.00 0.00 0.00 2.27
532 543 3.569135 TTCTCCTTTCCTCCCTCTCTT 57.431 47.619 0.00 0.00 0.00 2.85
533 544 3.449918 CTTTCTCCTTTCCTCCCTCTCT 58.550 50.000 0.00 0.00 0.00 3.10
549 561 0.615850 GCTCTAGGTGGGTGCTTTCT 59.384 55.000 0.00 0.00 0.00 2.52
553 565 0.545309 TTCTGCTCTAGGTGGGTGCT 60.545 55.000 0.00 0.00 0.00 4.40
603 618 5.068723 TGTGAAAATCGATCCTCCCTAGTAC 59.931 44.000 0.00 0.00 0.00 2.73
610 625 3.118592 AGGTCTGTGAAAATCGATCCTCC 60.119 47.826 0.00 0.00 0.00 4.30
622 637 2.661537 CGCGTGCAGGTCTGTGAA 60.662 61.111 8.40 0.00 0.00 3.18
668 684 2.125552 CATTCGCACCGCTCCAGA 60.126 61.111 0.00 0.00 0.00 3.86
669 685 3.869272 GCATTCGCACCGCTCCAG 61.869 66.667 0.00 0.00 38.36 3.86
706 722 1.382629 CGGACCCCTCCACCAAAAT 59.617 57.895 0.00 0.00 36.12 1.82
710 726 4.715130 CTCCGGACCCCTCCACCA 62.715 72.222 0.00 0.00 36.12 4.17
755 779 4.710695 TCATTGCGGTCGCGTCGT 62.711 61.111 20.79 4.12 45.51 4.34
829 3157 2.184836 CCGAATGGCGACGGGTAA 59.815 61.111 8.52 0.00 44.59 2.85
1322 3660 7.609760 TGATACTAGCAAAACGAAATGTGAT 57.390 32.000 0.00 0.00 0.00 3.06
1422 5223 9.594478 TCGGTGATATTGCGATAATAATTGTAT 57.406 29.630 0.00 0.00 0.00 2.29
1505 5330 9.154632 ACAATCATGTATGTACTCCCAGTATTA 57.845 33.333 4.66 0.00 38.24 0.98
1506 5331 8.034313 ACAATCATGTATGTACTCCCAGTATT 57.966 34.615 4.66 0.00 38.24 1.89
1512 5337 5.670485 TGTGACAATCATGTATGTACTCCC 58.330 41.667 6.20 0.00 40.74 4.30
1651 5484 4.595986 TCAAACCCCTAACCTGCTAATTC 58.404 43.478 0.00 0.00 0.00 2.17
1654 5487 4.291249 AGAATCAAACCCCTAACCTGCTAA 59.709 41.667 0.00 0.00 0.00 3.09
1655 5488 3.850173 AGAATCAAACCCCTAACCTGCTA 59.150 43.478 0.00 0.00 0.00 3.49
1658 5491 4.524053 GGTAGAATCAAACCCCTAACCTG 58.476 47.826 0.00 0.00 0.00 4.00
1659 5492 3.199289 CGGTAGAATCAAACCCCTAACCT 59.801 47.826 0.11 0.00 31.68 3.50
1712 5584 2.560542 AGCCGACTCAGCCAATATAGAG 59.439 50.000 0.00 0.00 0.00 2.43
1792 5664 7.031226 TCACAAAGATTCAAGTTCTCCAAAG 57.969 36.000 0.00 0.00 0.00 2.77
1826 5698 8.030692 TCCAAAATAGAGTGCAAATGAATCTTG 58.969 33.333 0.00 0.00 0.00 3.02
1875 5747 8.284945 TCATAGGAGAAACAAATGAATTCCAG 57.715 34.615 2.27 0.00 0.00 3.86
2119 5996 7.488150 GCAAGACTAAGTAACTTGTTTTGCTTT 59.512 33.333 18.43 0.00 41.73 3.51
2137 6031 3.800261 GCGCAAGATATGGAGCAAGACTA 60.800 47.826 0.30 0.00 43.02 2.59
2184 6079 4.160642 TCATGGGAGATGATGGTTCAAG 57.839 45.455 0.00 0.00 34.96 3.02
2227 6122 0.400525 TAAGGATGGCAGGAGGGAGG 60.401 60.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.