Multiple sequence alignment - TraesCS2D01G087100

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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 TraesCS2D01G087100 chr2D 100.000 2210 0 0 1 2210 37489490 37491699 0.000000e+00 4082.0
1 TraesCS2D01G087100 chr2D 84.549 233 25 5 1535 1766 187732168 187732390 1.030000e-53 220.0
2 TraesCS2D01G087100 chr2A 95.701 1419 31 6 818 2210 42365577 42366991 0.000000e+00 2255.0
3 TraesCS2D01G087100 chr2A 97.887 852 11 2 1 850 42363996 42364842 0.000000e+00 1467.0
4 TraesCS2D01G087100 chr2A 84.918 305 45 1 1858 2161 409197769 409197465 7.660000e-80 307.0
5 TraesCS2D01G087100 chr2A 83.934 305 45 2 1858 2158 625412049 625412353 2.780000e-74 289.0
6 TraesCS2D01G087100 chr2A 94.444 72 4 0 761 832 42364841 42364912 6.450000e-21 111.0
7 TraesCS2D01G087100 chr7D 87.921 356 35 6 1858 2210 158722500 158722850 1.580000e-111 412.0
8 TraesCS2D01G087100 chr7D 84.914 232 22 7 1535 1765 48465002 48464783 2.860000e-54 222.0
9 TraesCS2D01G087100 chr7A 85.794 359 41 6 1858 2210 60721768 60721414 2.680000e-99 372.0
10 TraesCS2D01G087100 chr7A 86.520 319 29 6 1883 2201 690819045 690819349 2.720000e-89 339.0
11 TraesCS2D01G087100 chr7A 89.773 88 8 1 1769 1856 76936842 76936756 6.450000e-21 111.0
12 TraesCS2D01G087100 chr7A 93.750 48 3 0 541 588 466945228 466945181 3.040000e-09 73.1
13 TraesCS2D01G087100 chr5A 88.235 272 31 1 1860 2131 119068762 119068492 7.610000e-85 324.0
14 TraesCS2D01G087100 chr5A 93.478 46 3 0 542 587 17366596 17366551 3.940000e-08 69.4
15 TraesCS2D01G087100 chr1A 87.132 272 34 1 1860 2131 96743443 96743713 7.660000e-80 307.0
16 TraesCS2D01G087100 chr1A 84.444 90 12 2 1769 1856 579205151 579205240 1.090000e-13 87.9
17 TraesCS2D01G087100 chr1A 89.831 59 4 2 541 598 247796303 247796246 8.460000e-10 75.0
18 TraesCS2D01G087100 chr1A 95.652 46 2 0 541 586 248034679 248034724 8.460000e-10 75.0
19 TraesCS2D01G087100 chr1A 97.619 42 1 0 545 586 282696299 282696258 3.040000e-09 73.1
20 TraesCS2D01G087100 chr4A 87.500 272 23 8 1860 2125 374642275 374642009 9.920000e-79 303.0
21 TraesCS2D01G087100 chr3D 84.549 233 22 8 1535 1765 211945352 211945132 3.690000e-53 219.0
22 TraesCS2D01G087100 chr3D 79.310 174 30 3 142 311 585000797 585000626 1.390000e-22 117.0
23 TraesCS2D01G087100 chr5B 82.645 242 34 5 1535 1775 186088178 186087944 8.000000e-50 207.0
24 TraesCS2D01G087100 chr5B 90.625 96 9 0 1559 1654 592248503 592248598 6.400000e-26 128.0
25 TraesCS2D01G087100 chr1D 89.773 88 9 0 1769 1856 202281913 202282000 1.790000e-21 113.0
26 TraesCS2D01G087100 chr1D 95.652 46 2 0 541 586 283042079 283042034 8.460000e-10 75.0
27 TraesCS2D01G087100 chr6B 88.889 81 6 2 1770 1849 31110545 31110623 1.810000e-16 97.1
28 TraesCS2D01G087100 chr6B 88.889 81 6 2 1770 1849 31130332 31130410 1.810000e-16 97.1
29 TraesCS2D01G087100 chr6B 89.157 83 2 5 1770 1849 31140763 31140841 1.810000e-16 97.1
30 TraesCS2D01G087100 chr6B 88.889 81 6 2 1770 1849 31172985 31173063 1.810000e-16 97.1
31 TraesCS2D01G087100 chr6B 86.420 81 8 2 1770 1849 31183418 31183496 3.910000e-13 86.1
32 TraesCS2D01G087100 chr1B 97.619 42 1 0 545 586 314739122 314739081 3.040000e-09 73.1
33 TraesCS2D01G087100 chr3B 95.455 44 2 0 546 589 70272826 70272783 1.090000e-08 71.3


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 TraesCS2D01G087100 chr2D 37489490 37491699 2209 False 4082.000000 4082 100.000000 1 2210 1 chr2D.!!$F1 2209
1 TraesCS2D01G087100 chr2A 42363996 42366991 2995 False 1277.666667 2255 96.010667 1 2210 3 chr2A.!!$F2 2209

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
471 474 0.393808 GGGTCGATTTAGGCTTGGCA 60.394 55.0 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 2581 0.105607 AGAGACCGGGGGTAATCCTC 60.106 60.0 6.32 0.0 35.25 3.71 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
154 155 4.939509 ATTCCGTACACAACTAACATGC 57.060 40.909 0.00 0.00 0.00 4.06
471 474 0.393808 GGGTCGATTTAGGCTTGGCA 60.394 55.000 0.00 0.00 0.00 4.92
472 475 0.733150 GGTCGATTTAGGCTTGGCAC 59.267 55.000 0.00 0.00 0.00 5.01
473 476 1.679032 GGTCGATTTAGGCTTGGCACT 60.679 52.381 0.00 0.00 0.00 4.40
474 477 1.398390 GTCGATTTAGGCTTGGCACTG 59.602 52.381 0.00 0.00 0.00 3.66
475 478 1.277842 TCGATTTAGGCTTGGCACTGA 59.722 47.619 0.00 0.00 0.00 3.41
528 531 3.001330 GCGACAATTAGCCAGTGTGATAC 59.999 47.826 0.00 0.00 0.00 2.24
539 542 4.512944 GCCAGTGTGATACTTATGGATGTG 59.487 45.833 0.00 0.00 37.60 3.21
884 1654 0.527817 CCAGTCGAGGCACCGATTAC 60.528 60.000 5.38 0.00 40.91 1.89
892 1662 3.335579 GAGGCACCGATTACTTCAGTTT 58.664 45.455 0.00 0.00 0.00 2.66
1077 1858 6.238648 TCAGGGTTTTTATCTTCAGGAGTTC 58.761 40.000 0.00 0.00 0.00 3.01
1289 2085 5.378332 TGGGTCTTCATCTAGTAGTCTAGC 58.622 45.833 0.00 0.00 42.28 3.42
1295 2091 7.501225 GTCTTCATCTAGTAGTCTAGCTTCCTT 59.499 40.741 0.00 0.00 42.28 3.36
1296 2092 8.056400 TCTTCATCTAGTAGTCTAGCTTCCTTT 58.944 37.037 0.00 0.00 42.28 3.11
1379 2175 0.029300 ATTGGCAATGTATCGCGTGC 59.971 50.000 12.82 7.37 0.00 5.34
1382 2178 1.060308 GCAATGTATCGCGTGCGTT 59.940 52.632 14.47 8.60 40.74 4.84
1389 2185 2.412429 TGTATCGCGTGCGTTATTGTTT 59.588 40.909 14.47 0.00 40.74 2.83
1497 2293 5.473796 TGTTTGTTTCCGAGAACTTGTAC 57.526 39.130 0.00 0.00 0.00 2.90
1518 2314 5.265350 ACTCTCTTCTCCCTATTTTACGC 57.735 43.478 0.00 0.00 0.00 4.42
1609 2405 4.119442 TCCTCCTACTAAATGAACACGC 57.881 45.455 0.00 0.00 0.00 5.34
1815 2611 1.395045 CCGGTCTCTGCATCTAGGCA 61.395 60.000 0.00 0.00 42.53 4.75
1874 2670 6.223852 ACTTTAGTCATATAAGCATCCACCG 58.776 40.000 0.00 0.00 0.00 4.94
1929 2725 1.071228 ACACTGCAAGCATCAGAGTCA 59.929 47.619 0.00 0.00 37.60 3.41
1967 2763 4.288398 AGGTCCCTCTAGCCTTAAAGTAC 58.712 47.826 0.00 0.00 0.00 2.73
2176 2972 8.630037 ACAAACCAGTAGTTAAGAAAGAATTGG 58.370 33.333 0.00 0.00 37.88 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.224753 CACACTTTTACTCTCTTCAAAGTAGCA 59.775 37.037 0.00 0.00 37.36 3.49
92 93 6.880942 TGATCATGTCTGATGTCACAAAAA 57.119 33.333 0.00 0.00 42.27 1.94
154 155 2.169832 TTTTGGTTGAGAGCTCCTCG 57.830 50.000 10.93 0.00 44.92 4.63
471 474 6.128117 GCATGATCCATTTTTGCATTTTCAGT 60.128 34.615 0.00 0.00 33.58 3.41
472 475 6.128145 TGCATGATCCATTTTTGCATTTTCAG 60.128 34.615 0.00 0.00 38.32 3.02
473 476 5.705905 TGCATGATCCATTTTTGCATTTTCA 59.294 32.000 0.00 0.00 38.32 2.69
474 477 6.025280 GTGCATGATCCATTTTTGCATTTTC 58.975 36.000 0.00 0.00 44.27 2.29
475 478 5.708230 AGTGCATGATCCATTTTTGCATTTT 59.292 32.000 0.00 0.00 44.27 1.82
528 531 5.779529 AGGCTAAAATGCACATCCATAAG 57.220 39.130 0.00 0.00 34.04 1.73
539 542 9.971922 ATAAGATGTTTTGATAGGCTAAAATGC 57.028 29.630 0.00 0.00 0.00 3.56
576 579 8.305317 GTTCACAATATACCATCTACTACCTCC 58.695 40.741 0.00 0.00 0.00 4.30
884 1654 7.988737 TGCAAATATCATGTAGGAAACTGAAG 58.011 34.615 0.00 0.00 43.88 3.02
892 1662 4.665451 CCCCATGCAAATATCATGTAGGA 58.335 43.478 0.00 0.00 39.60 2.94
927 1697 1.525077 GAACGGGTGTGACAAGCCA 60.525 57.895 0.00 0.00 37.59 4.75
986 1766 1.550524 TGTCCATACTGAGCTCACACC 59.449 52.381 13.74 0.00 0.00 4.16
1077 1858 2.133553 CTAGCAAGATGAGCCGTGATG 58.866 52.381 0.00 0.00 0.00 3.07
1289 2085 3.791353 GCAAACGACAGAACAAAAGGAAG 59.209 43.478 0.00 0.00 0.00 3.46
1295 2091 3.305629 GCATTTGCAAACGACAGAACAAA 59.694 39.130 15.41 0.00 41.59 2.83
1296 2092 2.857152 GCATTTGCAAACGACAGAACAA 59.143 40.909 15.41 0.00 41.59 2.83
1379 2175 8.574196 AAGACCAAGAAAATGAAACAATAACG 57.426 30.769 0.00 0.00 0.00 3.18
1389 2185 6.708949 ACGCTAACTAAAGACCAAGAAAATGA 59.291 34.615 0.00 0.00 0.00 2.57
1497 2293 5.523438 AGCGTAAAATAGGGAGAAGAGAG 57.477 43.478 0.00 0.00 0.00 3.20
1548 2344 7.095607 GGATAATAGTTTTTCACTCGATGCGAT 60.096 37.037 0.00 0.00 36.88 4.58
1609 2405 4.787598 CCCGATTCTTGAGTTTTGAACAG 58.212 43.478 0.00 0.00 0.00 3.16
1695 2491 5.541845 AGCCTCAATTGCCTTTTAAAAGTC 58.458 37.500 23.04 13.73 34.20 3.01
1785 2581 0.105607 AGAGACCGGGGGTAATCCTC 60.106 60.000 6.32 0.00 35.25 3.71
1793 2589 1.457643 TAGATGCAGAGACCGGGGG 60.458 63.158 6.32 0.00 0.00 5.40
1794 2590 1.467678 CCTAGATGCAGAGACCGGGG 61.468 65.000 6.32 0.00 0.00 5.73
1868 2664 3.071892 AGACCAAAAATGACTACGGTGGA 59.928 43.478 0.00 0.00 0.00 4.02
1874 2670 8.736244 TGCCTTTATAAGACCAAAAATGACTAC 58.264 33.333 0.00 0.00 0.00 2.73
1967 2763 7.922505 TTAATTTGTTCATTTGTTGGAGACG 57.077 32.000 0.00 0.00 0.00 4.18
2016 2812 1.270839 ACATCACCAGCTACAACGCTT 60.271 47.619 0.00 0.00 38.41 4.68
2151 2947 8.846211 TCCAATTCTTTCTTAACTACTGGTTTG 58.154 33.333 0.00 0.00 39.17 2.93
2176 2972 7.027778 AGACGAACCCTTAATTGCATTATTC 57.972 36.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.