Multiple sequence alignment - TraesCS1A01G311900

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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 TraesCS1A01G311900 chr1A 100.000 2684 0 0 1 2684 503378164 503375481 0.000000e+00 4957.0
1 TraesCS1A01G311900 chr1B 88.398 2784 159 70 1 2684 548542373 548539654 0.000000e+00 3201.0
2 TraesCS1A01G311900 chr1D 93.541 1378 62 12 965 2326 407878619 407877253 0.000000e+00 2026.0
3 TraesCS1A01G311900 chr1D 91.024 947 51 14 1 934 407879543 407878618 0.000000e+00 1247.0
4 TraesCS1A01G311900 chr6B 89.084 742 45 13 1382 2103 116214974 116215699 0.000000e+00 889.0
5 TraesCS1A01G311900 chr6B 88.322 745 59 10 1382 2106 160516949 160516213 0.000000e+00 869.0
6 TraesCS1A01G311900 chr7B 88.814 742 48 14 1382 2103 639551495 639552221 0.000000e+00 878.0
7 TraesCS1A01G311900 chr7B 88.322 745 58 13 1382 2106 682603433 682602698 0.000000e+00 867.0
8 TraesCS1A01G311900 chr7B 88.322 745 51 10 1383 2106 66447167 66446438 0.000000e+00 861.0
9 TraesCS1A01G311900 chr7B 87.805 82 10 0 1223 1304 711000857 711000938 2.200000e-16 97.1
10 TraesCS1A01G311900 chr4A 87.337 766 54 14 1382 2112 657047674 657048431 0.000000e+00 837.0
11 TraesCS1A01G311900 chr5A 87.938 257 21 7 862 1111 219924490 219924743 7.270000e-76 294.0
12 TraesCS1A01G311900 chr5D 87.448 239 23 4 871 1103 35590552 35590789 4.400000e-68 268.0
13 TraesCS1A01G311900 chr7D 77.033 209 44 4 1223 1429 616908430 616908636 1.690000e-22 117.0


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 TraesCS1A01G311900 chr1A 503375481 503378164 2683 True 4957.0 4957 100.0000 1 2684 1 chr1A.!!$R1 2683
1 TraesCS1A01G311900 chr1B 548539654 548542373 2719 True 3201.0 3201 88.3980 1 2684 1 chr1B.!!$R1 2683
2 TraesCS1A01G311900 chr1D 407877253 407879543 2290 True 1636.5 2026 92.2825 1 2326 2 chr1D.!!$R1 2325
3 TraesCS1A01G311900 chr6B 116214974 116215699 725 False 889.0 889 89.0840 1382 2103 1 chr6B.!!$F1 721
4 TraesCS1A01G311900 chr6B 160516213 160516949 736 True 869.0 869 88.3220 1382 2106 1 chr6B.!!$R1 724
5 TraesCS1A01G311900 chr7B 639551495 639552221 726 False 878.0 878 88.8140 1382 2103 1 chr7B.!!$F1 721
6 TraesCS1A01G311900 chr7B 682602698 682603433 735 True 867.0 867 88.3220 1382 2106 1 chr7B.!!$R2 724
7 TraesCS1A01G311900 chr7B 66446438 66447167 729 True 861.0 861 88.3220 1383 2106 1 chr7B.!!$R1 723
8 TraesCS1A01G311900 chr4A 657047674 657048431 757 False 837.0 837 87.3370 1382 2112 1 chr4A.!!$F1 730

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
557 595 0.038251 GGCGAAAAGGGAAAGCCAAG 60.038 55.0 0.0 0.0 46.48 3.61 F
558 596 0.667487 GCGAAAAGGGAAAGCCAAGC 60.667 55.0 0.0 0.0 35.15 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 1631 0.389948 GCCGTCTTCATCGAACCTGT 60.390 55.0 0.0 0.0 0.00 4.00 R
2086 2255 0.667993 TCCGTTTTGCTTGAGGCTTG 59.332 50.0 0.0 0.0 42.39 4.01 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
23 24 2.181975 CTTTCATGGGTGCCATCCTTT 58.818 47.619 0.00 0.00 43.15 3.11
28 29 3.461458 TCATGGGTGCCATCCTTTACATA 59.539 43.478 0.00 0.00 43.15 2.29
58 59 4.024387 TGTCCGACAAGAAATTACAGCAAC 60.024 41.667 0.00 0.00 0.00 4.17
62 63 4.464112 GACAAGAAATTACAGCAACGACC 58.536 43.478 0.00 0.00 0.00 4.79
160 167 5.067273 ACTGAATTGTTTATCCACCGTCAA 58.933 37.500 0.00 0.00 0.00 3.18
286 293 3.003480 GTCCAACTAGATGACACAAGCC 58.997 50.000 0.79 0.00 0.00 4.35
371 378 0.040425 CGCAAACGAAAACCTCCCAG 60.040 55.000 0.00 0.00 43.93 4.45
441 451 1.635487 TCCTTTCCCACTCCAATCCAG 59.365 52.381 0.00 0.00 0.00 3.86
449 459 0.243907 ACTCCAATCCAGTCACGTCG 59.756 55.000 0.00 0.00 0.00 5.12
451 461 2.444624 CCAATCCAGTCACGTCGCG 61.445 63.158 0.00 0.00 0.00 5.87
525 563 4.244802 GCGGCGAGACGAGAGAGG 62.245 72.222 12.98 0.00 35.47 3.69
537 575 4.491409 GAGAGGGAAAGGCCGGCC 62.491 72.222 39.29 39.29 37.63 6.13
551 589 2.986979 GGCCGGCGAAAAGGGAAA 60.987 61.111 22.54 0.00 0.00 3.13
552 590 2.566529 GCCGGCGAAAAGGGAAAG 59.433 61.111 12.58 0.00 0.00 2.62
553 591 2.566529 CCGGCGAAAAGGGAAAGC 59.433 61.111 9.30 0.00 0.00 3.51
554 592 2.566529 CGGCGAAAAGGGAAAGCC 59.433 61.111 0.00 0.00 44.00 4.35
555 593 3.771978 GGCGAAAAGGGAAAGCCA 58.228 55.556 0.00 0.00 46.48 4.75
556 594 2.046108 GGCGAAAAGGGAAAGCCAA 58.954 52.632 0.00 0.00 46.48 4.52
557 595 0.038251 GGCGAAAAGGGAAAGCCAAG 60.038 55.000 0.00 0.00 46.48 3.61
558 596 0.667487 GCGAAAAGGGAAAGCCAAGC 60.667 55.000 0.00 0.00 35.15 4.01
609 647 4.824515 AGAGGAGAGGCCGGTCCG 62.825 72.222 17.93 3.60 43.43 4.79
676 714 1.341209 GGGATTTTGATGCCGGATTCC 59.659 52.381 5.05 0.00 0.00 3.01
697 736 3.462021 CTCCCGCTTTCTTTATCTCCAG 58.538 50.000 0.00 0.00 0.00 3.86
701 740 4.142600 CCCGCTTTCTTTATCTCCAGTTTG 60.143 45.833 0.00 0.00 0.00 2.93
741 783 2.851045 TGGGGTTTCCAGCTTCCC 59.149 61.111 0.00 0.00 41.46 3.97
805 852 1.150567 CCGCCTCTTCAATCTCGCAG 61.151 60.000 0.00 0.00 0.00 5.18
841 892 2.930682 GTTAGCTGTGTTCCTCCGATTC 59.069 50.000 0.00 0.00 0.00 2.52
922 979 6.922957 TGTTCTTGATTCCAATTTCTTTTCCG 59.077 34.615 0.00 0.00 0.00 4.30
954 1011 2.028043 GCTGTGCAACTTGCCCAC 59.972 61.111 11.29 4.46 44.23 4.61
1041 1098 0.811616 CGAGCCAATTCCTCTTCCCG 60.812 60.000 2.24 0.00 0.00 5.14
1309 1369 1.621672 CCTGGAGGAGGAGGTCAAGC 61.622 65.000 0.00 0.00 46.33 4.01
1587 1647 3.797256 CGGATTACAGGTTCGATGAAGAC 59.203 47.826 0.00 0.00 0.00 3.01
1670 1736 0.997932 GATGTCGTTGAGCTCTGCTG 59.002 55.000 16.19 2.42 39.88 4.41
1671 1737 1.018226 ATGTCGTTGAGCTCTGCTGC 61.018 55.000 16.19 3.41 39.88 5.25
1697 1763 5.840693 TCCCTAGCTGAATCTATGAATGTGA 59.159 40.000 0.00 0.00 0.00 3.58
1754 1847 9.536558 GAGTTGTTTTACATTTTTGGTGAAAAC 57.463 29.630 0.00 0.00 39.87 2.43
1864 1960 4.143986 AGCAATAGAAGGAGGTTACAGC 57.856 45.455 0.00 0.00 0.00 4.40
1925 2057 4.039124 TGCCAATATACGCTTGATCTCTGA 59.961 41.667 0.00 0.00 0.00 3.27
1926 2058 4.991056 GCCAATATACGCTTGATCTCTGAA 59.009 41.667 0.00 0.00 0.00 3.02
1927 2059 5.107298 GCCAATATACGCTTGATCTCTGAAC 60.107 44.000 0.00 0.00 0.00 3.18
1928 2060 5.406780 CCAATATACGCTTGATCTCTGAACC 59.593 44.000 0.00 0.00 0.00 3.62
1929 2061 6.219473 CAATATACGCTTGATCTCTGAACCT 58.781 40.000 0.00 0.00 0.00 3.50
1930 2062 2.663826 ACGCTTGATCTCTGAACCTC 57.336 50.000 0.00 0.00 0.00 3.85
1931 2063 1.205893 ACGCTTGATCTCTGAACCTCC 59.794 52.381 0.00 0.00 0.00 4.30
1932 2064 1.800655 CGCTTGATCTCTGAACCTCCG 60.801 57.143 0.00 0.00 0.00 4.63
2019 2152 2.476821 TCGGTTCTTTCTCGTTGTTCC 58.523 47.619 0.00 0.00 0.00 3.62
2086 2255 6.582636 TCTTCCACACATAACCTGATGATAC 58.417 40.000 0.00 0.00 0.00 2.24
2152 2321 3.223674 TCGTATCTCCTGGTGCAGATA 57.776 47.619 0.00 0.00 32.44 1.98
2153 2322 3.149981 TCGTATCTCCTGGTGCAGATAG 58.850 50.000 4.34 0.00 33.21 2.08
2154 2323 3.149981 CGTATCTCCTGGTGCAGATAGA 58.850 50.000 4.34 0.00 33.21 1.98
2155 2324 3.190327 CGTATCTCCTGGTGCAGATAGAG 59.810 52.174 4.34 0.00 33.21 2.43
2156 2325 3.609256 ATCTCCTGGTGCAGATAGAGA 57.391 47.619 8.42 8.42 33.40 3.10
2157 2326 3.609256 TCTCCTGGTGCAGATAGAGAT 57.391 47.619 0.00 0.00 32.44 2.75
2201 2376 9.088512 GATTAAGAATGCTCGGTATAAGTATGG 57.911 37.037 0.00 0.00 0.00 2.74
2208 2383 4.091509 GCTCGGTATAAGTATGGAAATGCG 59.908 45.833 0.00 0.00 0.00 4.73
2231 2406 5.768164 CGGGGCTTAATATTTTGTGGAGTAT 59.232 40.000 0.00 0.00 0.00 2.12
2262 2437 1.884235 CGCACTTTTCAACCTCTCCT 58.116 50.000 0.00 0.00 0.00 3.69
2266 2441 4.611943 GCACTTTTCAACCTCTCCTTTTC 58.388 43.478 0.00 0.00 0.00 2.29
2281 2456 4.765273 TCCTTTTCCTTTTTCTTGTTGGC 58.235 39.130 0.00 0.00 0.00 4.52
2334 2509 9.732130 ATCTTTCTAGCTTCACTACATTTTTCT 57.268 29.630 0.00 0.00 0.00 2.52
2443 2618 2.511600 GACAATCAGACGGGGCGG 60.512 66.667 0.00 0.00 0.00 6.13
2465 2640 4.438744 GGTGGTACTGATAAAATGCACTGC 60.439 45.833 0.00 0.00 0.00 4.40
2484 2659 1.272704 GCCTCTGGTTCATTTTCCCCT 60.273 52.381 0.00 0.00 0.00 4.79
2528 2703 3.181467 CCCTGCATTTTTCCTGTGAACAA 60.181 43.478 0.00 0.00 0.00 2.83
2538 2713 2.300152 TCCTGTGAACAAGAGCTGGTAG 59.700 50.000 0.00 0.00 0.00 3.18
2593 2768 2.765699 TGGCTGTGATCAGTGCACTATA 59.234 45.455 21.20 11.48 43.05 1.31
2626 2801 3.532232 TCACTACTACTCCCTCCATTCCT 59.468 47.826 0.00 0.00 0.00 3.36
2629 2804 2.946785 ACTACTCCCTCCATTCCTACG 58.053 52.381 0.00 0.00 0.00 3.51
2638 2813 5.078256 CCCTCCATTCCTACGTATAAGTCT 58.922 45.833 0.00 0.00 0.00 3.24
2643 2818 8.712285 TCCATTCCTACGTATAAGTCTTTTTG 57.288 34.615 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.578480 TGTATGTAAAGGATGGCACCCA 59.422 45.455 0.00 0.00 38.19 4.51
12 13 3.063452 CGTGTGTATGTAAAGGATGGCAC 59.937 47.826 0.00 0.00 0.00 5.01
15 16 4.250464 ACACGTGTGTATGTAAAGGATGG 58.750 43.478 22.71 0.00 42.90 3.51
17 18 4.501071 GGACACGTGTGTATGTAAAGGAT 58.499 43.478 28.82 0.00 45.05 3.24
23 24 1.878734 TGTCGGACACGTGTGTATGTA 59.121 47.619 28.82 4.95 45.05 2.29
143 150 7.228906 TGAACTAAATTGACGGTGGATAAACAA 59.771 33.333 0.00 0.00 0.00 2.83
160 167 8.889717 CATAAACTAACGGTGGATGAACTAAAT 58.110 33.333 0.00 0.00 0.00 1.40
371 378 3.365265 CCTGGTTCTTGCCGGTGC 61.365 66.667 1.90 0.00 33.07 5.01
441 451 3.248171 GATGGAGCGCGACGTGAC 61.248 66.667 12.10 5.07 0.00 3.67
449 459 4.959596 GCGGAGGAGATGGAGCGC 62.960 72.222 0.00 0.00 0.00 5.92
451 461 3.934962 GGGCGGAGGAGATGGAGC 61.935 72.222 0.00 0.00 0.00 4.70
537 575 1.801309 TTGGCTTTCCCTTTTCGCCG 61.801 55.000 0.00 0.00 43.54 6.46
538 576 0.038251 CTTGGCTTTCCCTTTTCGCC 60.038 55.000 0.00 0.00 41.06 5.54
539 577 0.667487 GCTTGGCTTTCCCTTTTCGC 60.667 55.000 0.00 0.00 0.00 4.70
540 578 0.673437 TGCTTGGCTTTCCCTTTTCG 59.327 50.000 0.00 0.00 0.00 3.46
541 579 1.270305 GGTGCTTGGCTTTCCCTTTTC 60.270 52.381 0.00 0.00 0.00 2.29
542 580 0.758734 GGTGCTTGGCTTTCCCTTTT 59.241 50.000 0.00 0.00 0.00 2.27
543 581 1.121407 GGGTGCTTGGCTTTCCCTTT 61.121 55.000 0.00 0.00 34.22 3.11
544 582 1.533994 GGGTGCTTGGCTTTCCCTT 60.534 57.895 0.00 0.00 34.22 3.95
545 583 2.118294 GGGTGCTTGGCTTTCCCT 59.882 61.111 0.00 0.00 34.22 4.20
546 584 2.118294 AGGGTGCTTGGCTTTCCC 59.882 61.111 0.00 0.00 35.95 3.97
547 585 2.935740 GCAGGGTGCTTGGCTTTCC 61.936 63.158 0.00 0.00 40.96 3.13
548 586 1.747325 TTGCAGGGTGCTTGGCTTTC 61.747 55.000 0.00 0.00 45.31 2.62
549 587 1.751349 CTTGCAGGGTGCTTGGCTTT 61.751 55.000 0.00 0.00 45.31 3.51
550 588 2.123338 TTGCAGGGTGCTTGGCTT 60.123 55.556 0.00 0.00 45.31 4.35
551 589 2.599578 CTTGCAGGGTGCTTGGCT 60.600 61.111 0.00 0.00 45.31 4.75
552 590 3.688159 CCTTGCAGGGTGCTTGGC 61.688 66.667 6.72 0.00 45.31 4.52
553 591 3.688159 GCCTTGCAGGGTGCTTGG 61.688 66.667 17.25 3.79 45.31 3.61
554 592 4.047059 CGCCTTGCAGGGTGCTTG 62.047 66.667 16.13 0.00 45.31 4.01
676 714 3.118592 ACTGGAGATAAAGAAAGCGGGAG 60.119 47.826 0.00 0.00 0.00 4.30
697 736 6.122964 AGGGATATAGCAAGAAGAACCAAAC 58.877 40.000 0.00 0.00 0.00 2.93
701 740 4.039366 ACGAGGGATATAGCAAGAAGAACC 59.961 45.833 0.00 0.00 0.00 3.62
741 783 5.404946 TCTATAACGACGAAAAGTTCAGGG 58.595 41.667 0.00 0.00 0.00 4.45
818 865 0.736325 CGGAGGAACACAGCTAACGG 60.736 60.000 0.00 0.00 0.00 4.44
819 866 0.242825 TCGGAGGAACACAGCTAACG 59.757 55.000 0.00 0.00 0.00 3.18
841 892 1.310933 AAAATGGCGAGCTGCTCTGG 61.311 55.000 25.59 13.33 45.43 3.86
954 1011 3.065786 ACAATCACTTTGTGTGCAGTCAG 59.934 43.478 0.00 0.00 46.80 3.51
972 1029 5.046448 TGCCAGAATTATGCCAAGAAACAAT 60.046 36.000 0.00 0.00 0.00 2.71
976 1033 3.831333 TGTGCCAGAATTATGCCAAGAAA 59.169 39.130 0.00 0.00 0.00 2.52
1060 1117 2.125350 CAGGAGGTCGCTGAAGGC 60.125 66.667 0.00 0.00 37.64 4.35
1571 1631 0.389948 GCCGTCTTCATCGAACCTGT 60.390 55.000 0.00 0.00 0.00 4.00
1587 1647 4.876828 CCGCCATTGCCATTGCCG 62.877 66.667 0.00 0.00 36.33 5.69
1671 1737 6.649973 CACATTCATAGATTCAGCTAGGGAAG 59.350 42.308 0.00 0.00 0.00 3.46
1672 1738 6.327365 TCACATTCATAGATTCAGCTAGGGAA 59.673 38.462 0.00 0.00 0.00 3.97
1697 1763 2.795329 ACTGCCGAAACAATCCTTGAT 58.205 42.857 0.00 0.00 0.00 2.57
1754 1847 3.693085 CCCTTTCATTCCATGAGAGTGTG 59.307 47.826 0.00 0.00 39.22 3.82
1864 1960 5.010516 CCAGAACACATCCTCCTGAGTATAG 59.989 48.000 0.00 0.00 0.00 1.31
1911 2021 1.205893 GGAGGTTCAGAGATCAAGCGT 59.794 52.381 0.00 0.00 0.00 5.07
1928 2060 1.270465 ACTAACGAACCCAAACCGGAG 60.270 52.381 9.46 0.00 36.56 4.63
1929 2061 0.758123 ACTAACGAACCCAAACCGGA 59.242 50.000 9.46 0.00 36.56 5.14
1930 2062 2.453983 TACTAACGAACCCAAACCGG 57.546 50.000 0.00 0.00 0.00 5.28
1931 2063 3.995705 TGAATACTAACGAACCCAAACCG 59.004 43.478 0.00 0.00 0.00 4.44
1932 2064 4.393990 CCTGAATACTAACGAACCCAAACC 59.606 45.833 0.00 0.00 0.00 3.27
2042 2201 5.344743 AGAACTTTTCTGGATCGATGCTA 57.655 39.130 18.23 3.51 38.91 3.49
2052 2211 6.438763 GTTATGTGTGGAAGAACTTTTCTGG 58.561 40.000 0.00 0.00 40.59 3.86
2086 2255 0.667993 TCCGTTTTGCTTGAGGCTTG 59.332 50.000 0.00 0.00 42.39 4.01
2152 2321 7.878621 TCCCATTGGTTAGATCATTATCTCT 57.121 36.000 1.20 0.00 41.71 3.10
2201 2376 5.234116 CACAAAATATTAAGCCCCGCATTTC 59.766 40.000 0.00 0.00 0.00 2.17
2208 2383 8.700439 TTATACTCCACAAAATATTAAGCCCC 57.300 34.615 0.00 0.00 0.00 5.80
2231 2406 3.818210 TGAAAAGTGCGCCTCTTGAATTA 59.182 39.130 4.18 0.00 0.00 1.40
2262 2437 8.744568 ATATTTGCCAACAAGAAAAAGGAAAA 57.255 26.923 0.00 0.00 37.04 2.29
2266 2441 8.600449 TGTTATATTTGCCAACAAGAAAAAGG 57.400 30.769 0.00 0.00 37.04 3.11
2281 2456 8.773645 TCAGATGCTATTCCGTTGTTATATTTG 58.226 33.333 0.00 0.00 0.00 2.32
2443 2618 4.438744 GGCAGTGCATTTTATCAGTACCAC 60.439 45.833 18.61 0.00 0.00 4.16
2465 2640 2.907458 AGGGGAAAATGAACCAGAGG 57.093 50.000 0.00 0.00 0.00 3.69
2484 2659 5.532779 GGGAGCTCTCTTTCAGAAAAAGAAA 59.467 40.000 14.64 0.00 36.01 2.52
2528 2703 3.494048 GCATCATTAGCACTACCAGCTCT 60.494 47.826 0.00 0.00 42.32 4.09
2538 2713 5.290158 CCAAACATTTCTGCATCATTAGCAC 59.710 40.000 0.00 0.00 37.02 4.40
2593 2768 4.499183 GAGTAGTAGTGAACAGCAAGCAT 58.501 43.478 0.00 0.00 0.00 3.79
2606 2781 4.446023 CGTAGGAATGGAGGGAGTAGTAGT 60.446 50.000 0.00 0.00 0.00 2.73
2626 2801 9.932207 TCAAATCTCCAAAAAGACTTATACGTA 57.068 29.630 0.00 0.00 0.00 3.57
2643 2818 8.499162 CCGAATGTAGTTCATATTCAAATCTCC 58.501 37.037 0.00 0.00 35.15 3.71


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

AutoCloner maintained by Alex Coulton.