Multiple sequence alignment - TraesCS7D01G134700

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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 TraesCS7D01G134700 chr7D 100.000 3199 0 0 1 3199 86071937 86068739 0.000000e+00 5908
1 TraesCS7D01G134700 chr2B 88.502 3244 300 41 1 3198 259687107 259690323 0.000000e+00 3856
2 TraesCS7D01G134700 chr7A 95.463 2160 86 7 1049 3198 675496841 675498998 0.000000e+00 3435
3 TraesCS7D01G134700 chr7A 83.109 3268 455 65 6 3198 102056526 102059771 0.000000e+00 2887
4 TraesCS7D01G134700 chr7A 97.101 1035 28 1 1 1033 675495501 675496535 0.000000e+00 1744
5 TraesCS7D01G134700 chr5B 89.738 1374 109 8 1 1371 126444821 126446165 0.000000e+00 1727
6 TraesCS7D01G134700 chr5B 88.434 830 73 15 1394 2203 126446494 126447320 0.000000e+00 979
7 TraesCS7D01G134700 chr3B 75.768 586 113 15 2562 3121 232568397 232568979 5.260000e-68 268
8 TraesCS7D01G134700 chr3B 78.365 208 43 2 1619 1825 648183351 648183145 2.000000e-27 134
9 TraesCS7D01G134700 chr4A 78.846 208 42 2 1619 1825 28970638 28970432 4.300000e-29 139
10 TraesCS7D01G134700 chr2D 94.737 76 2 2 1 76 431391132 431391059 2.020000e-22 117


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 TraesCS7D01G134700 chr7D 86068739 86071937 3198 True 5908.0 5908 100.000 1 3199 1 chr7D.!!$R1 3198
1 TraesCS7D01G134700 chr2B 259687107 259690323 3216 False 3856.0 3856 88.502 1 3198 1 chr2B.!!$F1 3197
2 TraesCS7D01G134700 chr7A 102056526 102059771 3245 False 2887.0 2887 83.109 6 3198 1 chr7A.!!$F1 3192
3 TraesCS7D01G134700 chr7A 675495501 675498998 3497 False 2589.5 3435 96.282 1 3198 2 chr7A.!!$F2 3197
4 TraesCS7D01G134700 chr5B 126444821 126447320 2499 False 1353.0 1727 89.086 1 2203 2 chr5B.!!$F1 2202
5 TraesCS7D01G134700 chr3B 232568397 232568979 582 False 268.0 268 75.768 2562 3121 1 chr3B.!!$F1 559

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
852 860 0.390860 ATGCTGAGATACGTCCAGCC 59.609 55.0 21.28 10.10 42.78 4.85 F
1673 2280 1.133809 TTAGACCCAGCAGTTGGCCT 61.134 55.0 3.32 0.02 46.32 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 2323 0.109597 CGGCATGGAGTTTGTTGCTC 60.110 55.000 0.0 0.0 35.46 4.26 R
2990 3708 1.513586 GACTACGAACCAGCGACGG 60.514 63.158 0.0 0.0 34.83 4.79 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
301 303 3.270877 AGCGTTCCAGTCCAATATGTTC 58.729 45.455 0.00 0.00 0.00 3.18
450 454 5.475909 ACAGATCAAACTCAATTCAGCATGT 59.524 36.000 0.00 0.00 37.40 3.21
561 566 7.391275 TGAATGCATATACACGATGATCCAATT 59.609 33.333 0.00 0.00 0.00 2.32
581 586 6.550854 CCAATTTGACACTACCCATTATCCAT 59.449 38.462 0.00 0.00 0.00 3.41
582 587 7.069826 CCAATTTGACACTACCCATTATCCATT 59.930 37.037 0.00 0.00 0.00 3.16
777 784 3.760684 AGGATGCAACTGTCAAGGAAATC 59.239 43.478 0.00 0.00 0.00 2.17
831 838 6.177610 CCTTACAGCCATCTTGGTTACTTAA 58.822 40.000 0.00 0.00 40.46 1.85
852 860 0.390860 ATGCTGAGATACGTCCAGCC 59.609 55.000 21.28 10.10 42.78 4.85
1042 1051 4.941609 TTGAGAGGCAAGATCGGC 57.058 55.556 4.06 4.06 31.55 5.54
1346 1645 3.639099 CTGTGAGTGTTCCCAGCAT 57.361 52.632 0.00 0.00 0.00 3.79
1390 1690 4.494091 TTTTGCTTTGATGAAAACCCCA 57.506 36.364 0.00 0.00 0.00 4.96
1392 1692 1.691434 TGCTTTGATGAAAACCCCACC 59.309 47.619 0.00 0.00 0.00 4.61
1443 2048 3.185299 AACGCCGACCCAATGACCA 62.185 57.895 0.00 0.00 0.00 4.02
1607 2213 2.105306 TCCCGACGATACTACCTGATGA 59.895 50.000 0.00 0.00 0.00 2.92
1673 2280 1.133809 TTAGACCCAGCAGTTGGCCT 61.134 55.000 3.32 0.02 46.32 5.19
1716 2323 3.845178 AGTCAGCATGCATGAATTTGTG 58.155 40.909 30.64 15.17 34.76 3.33
1880 2488 3.084070 TCGACCATCGATCACATTGAG 57.916 47.619 0.00 0.00 44.82 3.02
1881 2489 2.687935 TCGACCATCGATCACATTGAGA 59.312 45.455 0.00 0.00 44.82 3.27
1883 2491 3.488678 CGACCATCGATCACATTGAGAAG 59.511 47.826 0.00 0.00 43.74 2.85
1884 2492 4.437239 GACCATCGATCACATTGAGAAGT 58.563 43.478 0.00 0.00 0.00 3.01
2161 2796 1.594293 CTCCAGTGGCAAACGACGT 60.594 57.895 3.51 0.00 0.00 4.34
2184 2819 1.730064 TTGAAGCGGTCAAAGTATCGC 59.270 47.619 3.67 0.00 43.43 4.58
2204 2839 4.399618 TCGCTCACTGCTCTTTAGAATACT 59.600 41.667 0.00 0.00 40.11 2.12
2218 2886 9.453572 TCTTTAGAATACTGTTCTAACTACCGA 57.546 33.333 7.34 0.00 39.79 4.69
2370 3040 7.011389 TCTGATAGAAACCAAAGTTCATATGCG 59.989 37.037 0.00 0.00 34.19 4.73
2463 3138 1.901591 ACTCAACAACAGCTGATGGG 58.098 50.000 25.57 17.58 34.50 4.00
2676 3378 1.004918 GGTAGAGCGGTGTTGTGCT 60.005 57.895 0.00 0.00 45.90 4.40
2737 3439 0.386476 TAAGTGACGCACCTTGTCGT 59.614 50.000 6.39 0.00 42.09 4.34
2874 3576 6.829849 TGTATGAATCATAGATCAGCCAACA 58.170 36.000 2.74 0.00 0.00 3.33
2983 3701 0.689623 CTTGGGTCTCTCCTTGCACT 59.310 55.000 0.00 0.00 36.25 4.40
3028 3746 1.210478 CAAGAGGACCCACCCTGTATG 59.790 57.143 0.00 0.00 40.05 2.39
3198 3922 2.672996 CAAGGGCTCCCACCAACG 60.673 66.667 7.82 0.00 38.92 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 149 2.494870 AGGGAAAACAAGATGATGCTGC 59.505 45.455 0.00 0.00 0.00 5.25
301 303 6.671190 TGACATAAGCTTGTCTGTGAAATTG 58.329 36.000 17.26 0.00 45.07 2.32
450 454 1.277842 TCCAATCTTGCTGGCTAACGA 59.722 47.619 0.00 0.00 33.63 3.85
561 566 7.578571 GCAAAAATGGATAATGGGTAGTGTCAA 60.579 37.037 0.00 0.00 0.00 3.18
710 717 1.546773 GGTCTTGCCCACATGTTGGTA 60.547 52.381 16.79 10.17 45.25 3.25
852 860 3.561143 TCCAAACAATATGAATCCGGGG 58.439 45.455 0.00 0.00 0.00 5.73
1043 1052 5.891551 AGTAAAAATATTACTGCACAGGGGG 59.108 40.000 2.21 0.00 34.25 5.40
1044 1053 6.601613 TCAGTAAAAATATTACTGCACAGGGG 59.398 38.462 18.79 0.00 46.90 4.79
1090 1389 6.402658 GGAAATGCAGTTACTAAGTGAGAAGC 60.403 42.308 0.82 0.00 33.58 3.86
1390 1690 2.224784 GTCTACAAAAATGCGGTTCGGT 59.775 45.455 0.00 0.00 0.00 4.69
1392 1692 3.529634 TGTCTACAAAAATGCGGTTCG 57.470 42.857 0.00 0.00 0.00 3.95
1443 2048 2.176364 AGCTGGCCCTGATTGATTGTAT 59.824 45.455 0.00 0.00 0.00 2.29
1607 2213 7.776969 ACATATCAAAAGCATAGACAGTCCAAT 59.223 33.333 0.00 0.00 0.00 3.16
1673 2280 1.091537 GCGGTTGCTATAGCCAAACA 58.908 50.000 21.84 0.00 41.18 2.83
1716 2323 0.109597 CGGCATGGAGTTTGTTGCTC 60.110 55.000 0.00 0.00 35.46 4.26
1799 2406 5.104527 TCCCTCATTATGATCGGAAAAGTGT 60.105 40.000 8.24 0.00 0.00 3.55
1866 2474 8.498054 AAAACATACTTCTCAATGTGATCGAT 57.502 30.769 0.00 0.00 36.47 3.59
1872 2480 9.950680 ACAAGTTAAAACATACTTCTCAATGTG 57.049 29.630 0.00 0.00 36.47 3.21
1874 2482 9.612620 GGACAAGTTAAAACATACTTCTCAATG 57.387 33.333 0.00 0.00 32.50 2.82
1876 2484 7.776030 TGGGACAAGTTAAAACATACTTCTCAA 59.224 33.333 0.00 0.00 32.50 3.02
1878 2486 7.739498 TGGGACAAGTTAAAACATACTTCTC 57.261 36.000 0.00 0.00 32.50 2.87
2018 2636 4.623932 TTCCATGGGAGTATGATGCTAC 57.376 45.455 13.02 0.00 31.21 3.58
2161 2796 3.596214 GATACTTTGACCGCTTCAAGGA 58.404 45.455 12.25 0.07 45.22 3.36
2184 2819 7.319646 AGAACAGTATTCTAAAGAGCAGTGAG 58.680 38.462 0.00 0.00 0.00 3.51
2204 2839 7.173735 GGGAAGAAATTTTCGGTAGTTAGAACA 59.826 37.037 3.57 0.00 34.02 3.18
2463 3138 4.120589 GTGATAGTTGTAACCCTAGCAGC 58.879 47.826 0.00 0.00 30.87 5.25
2507 3208 5.182001 AGTGATCTTTTAACTGCATCCACAC 59.818 40.000 0.00 0.00 0.00 3.82
2676 3378 1.593196 GAGCTGCAACAAGTGTGGTA 58.407 50.000 1.02 0.00 0.00 3.25
2687 3389 1.613925 ACTCAGAGTTACGAGCTGCAA 59.386 47.619 1.02 0.00 32.21 4.08
2737 3439 4.916041 AACAACTCCTCATTGATCTCCA 57.084 40.909 0.00 0.00 0.00 3.86
2874 3576 5.640783 GCGGGTATGTGTTCTACTAAAACTT 59.359 40.000 0.00 0.00 0.00 2.66
2983 3701 3.309436 AACCAGCGACGGCATGCTA 62.309 57.895 18.92 0.00 40.03 3.49
2990 3708 1.513586 GACTACGAACCAGCGACGG 60.514 63.158 0.00 0.00 34.83 4.79


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

AutoCloner maintained by Alex Coulton.