Multiple sequence alignment - TraesCS3A01G347000

Loading Multiple Alignment...

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 TraesCS3A01G347000 chr3A 100.000 2845 0 0 1 2845 596361349 596364193 0.000000e+00 5254.0
1 TraesCS3A01G347000 chr3D 92.070 2913 143 43 1 2845 454230069 454232961 0.000000e+00 4019.0
2 TraesCS3A01G347000 chr3D 84.015 269 38 5 1 267 556176525 556176260 1.310000e-63 254.0
3 TraesCS3A01G347000 chr3D 80.576 278 48 6 1 275 397917040 397916766 2.870000e-50 209.0
4 TraesCS3A01G347000 chr3B 90.443 2867 188 40 1 2845 596856049 596858851 0.000000e+00 3698.0
5 TraesCS3A01G347000 chr6D 85.895 553 41 14 2299 2827 373342297 373342836 3.200000e-154 555.0
6 TraesCS3A01G347000 chr6D 87.267 322 39 2 1998 2318 373341842 373342162 1.610000e-97 366.0
7 TraesCS3A01G347000 chr6D 80.114 176 31 4 13 185 412007374 412007200 8.270000e-26 128.0
8 TraesCS3A01G347000 chr2B 82.616 627 61 17 2248 2845 331237626 331238233 7.030000e-141 510.0
9 TraesCS3A01G347000 chr5A 82.288 271 43 5 1 268 400487661 400487929 2.200000e-56 230.0
10 TraesCS3A01G347000 chr4D 81.685 273 45 4 1 268 454453370 454453098 3.690000e-54 222.0
11 TraesCS3A01G347000 chr1D 77.528 267 50 8 4 266 199417379 199417639 4.910000e-33 152.0
12 TraesCS3A01G347000 chr4A 77.186 263 43 10 4 253 338741776 338742034 1.370000e-28 137.0
13 TraesCS3A01G347000 chr6A 89.583 48 5 0 235 282 105009513 105009466 8.510000e-06 62.1


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 TraesCS3A01G347000 chr3A 596361349 596364193 2844 False 5254.0 5254 100.000 1 2845 1 chr3A.!!$F1 2844
1 TraesCS3A01G347000 chr3D 454230069 454232961 2892 False 4019.0 4019 92.070 1 2845 1 chr3D.!!$F1 2844
2 TraesCS3A01G347000 chr3B 596856049 596858851 2802 False 3698.0 3698 90.443 1 2845 1 chr3B.!!$F1 2844
3 TraesCS3A01G347000 chr6D 373341842 373342836 994 False 460.5 555 86.581 1998 2827 2 chr6D.!!$F1 829
4 TraesCS3A01G347000 chr2B 331237626 331238233 607 False 510.0 510 82.616 2248 2845 1 chr2B.!!$F1 597

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
814 850 0.249322 GCGCGCCTTTCCATCTACTA 60.249 55.0 23.24 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2404 2628 1.216678 TGTTGGTCCATTTCCCTGTGT 59.783 47.619 0.0 0.0 0.0 3.72 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
42 43 4.164030 ACTTTTGGCCCAAGAAAAAGTCAT 59.836 37.500 19.82 3.90 46.09 3.06
84 85 7.837863 TGTATTTAGTTTTGGAGATCTCGTCT 58.162 34.615 16.46 11.45 40.81 4.18
185 187 5.865552 CCAAAAAGATTTCGCTGATGTCATT 59.134 36.000 0.00 0.00 0.00 2.57
190 193 6.741992 AGATTTCGCTGATGTCATTTGTTA 57.258 33.333 0.00 0.00 0.00 2.41
290 293 8.322828 TGGGCTAATTAATATACGAGGCAAATA 58.677 33.333 0.00 0.00 0.00 1.40
305 308 6.183360 CGAGGCAAATATTTTGTGTCCATTTG 60.183 38.462 0.00 0.00 38.83 2.32
318 324 8.839310 TTGTGTCCATTTGAAAAAGAAAGAAA 57.161 26.923 0.00 0.00 0.00 2.52
429 435 1.271379 GCCTCACATGTAAGTGGGTGT 60.271 52.381 0.00 0.00 38.34 4.16
451 457 1.000060 TCGTAGGTGCAGCGTTTTAGT 60.000 47.619 10.78 0.00 0.00 2.24
497 503 4.283722 AGTCGTAACCCAGTCTCATCTTTT 59.716 41.667 0.00 0.00 0.00 2.27
501 507 3.228188 ACCCAGTCTCATCTTTTTGCA 57.772 42.857 0.00 0.00 0.00 4.08
504 510 3.152341 CCAGTCTCATCTTTTTGCACCT 58.848 45.455 0.00 0.00 0.00 4.00
508 514 6.044682 CAGTCTCATCTTTTTGCACCTTTTT 58.955 36.000 0.00 0.00 0.00 1.94
560 594 1.620819 AGCATCTATAGCCGAACCTGG 59.379 52.381 0.00 0.00 0.00 4.45
572 606 1.243902 GAACCTGGCAAATTCGACCA 58.756 50.000 0.00 0.00 0.00 4.02
584 618 2.886862 TTCGACCACTTAAACGTCCA 57.113 45.000 0.00 0.00 0.00 4.02
594 628 2.963548 TAAACGTCCACGGATGCATA 57.036 45.000 0.00 0.00 44.95 3.14
595 629 1.651987 AAACGTCCACGGATGCATAG 58.348 50.000 0.00 0.00 44.95 2.23
607 641 3.057526 CGGATGCATAGGACGTGATCTTA 60.058 47.826 0.00 0.00 0.00 2.10
633 667 0.472471 GATGGACGGCCCCTCAAATA 59.528 55.000 3.83 0.00 30.81 1.40
668 702 2.038557 TCACACTCCTTAACCCTCAAGC 59.961 50.000 0.00 0.00 0.00 4.01
698 732 8.888716 TGTACGTTGATCATATAGTGCAAATTT 58.111 29.630 0.00 0.00 0.00 1.82
812 848 1.090052 AAGCGCGCCTTTCCATCTAC 61.090 55.000 30.33 0.00 0.00 2.59
813 849 1.521681 GCGCGCCTTTCCATCTACT 60.522 57.895 23.24 0.00 0.00 2.57
814 850 0.249322 GCGCGCCTTTCCATCTACTA 60.249 55.000 23.24 0.00 0.00 1.82
815 851 1.772182 CGCGCCTTTCCATCTACTAG 58.228 55.000 0.00 0.00 0.00 2.57
816 852 1.067212 CGCGCCTTTCCATCTACTAGT 59.933 52.381 0.00 0.00 0.00 2.57
857 893 1.706287 CGTCTCTCGTCGGCTCATCA 61.706 60.000 0.00 0.00 34.52 3.07
858 894 0.665835 GTCTCTCGTCGGCTCATCAT 59.334 55.000 0.00 0.00 0.00 2.45
907 943 2.194271 GACGGAAAGCGAAGATGTAGG 58.806 52.381 0.00 0.00 0.00 3.18
927 963 1.587547 GAAATGCGTCCCCATCTCTC 58.412 55.000 0.00 0.00 0.00 3.20
1388 1430 1.868251 GAGCACTTCTACCGTCGCG 60.868 63.158 0.00 0.00 0.00 5.87
1661 1703 3.838317 AGCCATTCTCTGTTACCAGTGTA 59.162 43.478 0.00 0.00 39.82 2.90
1793 1837 1.493854 AACTGGGCCGGATTGTACCA 61.494 55.000 21.81 1.64 0.00 3.25
1819 1864 6.203723 GCAATAATATTCTTGGCTCGAGTTCT 59.796 38.462 15.13 0.00 0.00 3.01
2118 2180 3.826729 TCTCCTCGTCAAGTTCATCTTCA 59.173 43.478 0.00 0.00 33.63 3.02
2126 2188 5.119279 CGTCAAGTTCATCTTCACCTGTAAG 59.881 44.000 0.00 0.00 33.63 2.34
2311 2528 5.582665 CACTACCTTTACTTGCAGGAAGATC 59.417 44.000 8.96 0.00 35.42 2.75
2404 2628 2.156098 GGCAACGAACACCTAATTCCA 58.844 47.619 0.00 0.00 0.00 3.53
2637 2880 6.627243 CAGAAATGGAGAATCTTTCATGCAA 58.373 36.000 0.00 0.00 32.55 4.08
2741 3000 1.069049 ACAACTGCTGGAACATTTGGC 59.931 47.619 0.00 0.00 38.20 4.52
2754 3013 7.402054 TGGAACATTTGGCTAAGAGATAAGAA 58.598 34.615 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 147 9.586435 AATCTTTTTGGTTTTTCAGACTTACAG 57.414 29.630 0.00 0.00 0.00 2.74
215 218 7.063662 GCACAAAGCAATATGATTCAAACATCA 59.936 33.333 0.00 0.00 44.79 3.07
218 221 6.709145 GCACAAAGCAATATGATTCAAACA 57.291 33.333 0.00 0.00 44.79 2.83
290 293 9.447157 TCTTTCTTTTTCAAATGGACACAAAAT 57.553 25.926 0.00 0.00 0.00 1.82
297 300 8.716646 TCCTTTTCTTTCTTTTTCAAATGGAC 57.283 30.769 0.00 0.00 29.74 4.02
312 315 7.284034 AGCATGTCATCGAATATCCTTTTCTTT 59.716 33.333 0.00 0.00 0.00 2.52
318 324 6.596309 TCTAGCATGTCATCGAATATCCTT 57.404 37.500 0.00 0.00 0.00 3.36
325 331 6.207417 TCATGACTATCTAGCATGTCATCGAA 59.793 38.462 16.08 7.25 45.01 3.71
412 418 2.029380 CGAGACACCCACTTACATGTGA 60.029 50.000 9.11 0.00 40.12 3.58
429 435 0.032952 AAAACGCTGCACCTACGAGA 59.967 50.000 0.00 0.00 0.00 4.04
451 457 1.065199 CAGAATTGGCTGCTAGTGGGA 60.065 52.381 0.00 0.00 0.00 4.37
472 478 4.200874 AGATGAGACTGGGTTACGACTAG 58.799 47.826 0.00 0.00 0.00 2.57
474 480 3.088789 AGATGAGACTGGGTTACGACT 57.911 47.619 0.00 0.00 0.00 4.18
508 514 6.018262 CAGATTGAGTAGGAACACAACGAAAA 60.018 38.462 0.00 0.00 38.71 2.29
511 517 4.556233 CAGATTGAGTAGGAACACAACGA 58.444 43.478 0.00 0.00 38.71 3.85
560 594 3.880610 ACGTTTAAGTGGTCGAATTTGC 58.119 40.909 0.00 0.00 0.00 3.68
572 606 1.270412 TGCATCCGTGGACGTTTAAGT 60.270 47.619 0.00 0.00 37.74 2.24
584 618 1.000163 GATCACGTCCTATGCATCCGT 60.000 52.381 0.19 5.09 0.00 4.69
594 628 1.402259 CGCTGTCTAAGATCACGTCCT 59.598 52.381 0.00 0.00 0.00 3.85
595 629 1.400846 TCGCTGTCTAAGATCACGTCC 59.599 52.381 0.00 0.00 0.00 4.79
607 641 4.148825 GGCCGTCCATCGCTGTCT 62.149 66.667 0.00 0.00 38.35 3.41
633 667 6.319048 AGGAGTGTGATTGTTCAATAGGAT 57.681 37.500 0.00 0.00 32.48 3.24
668 702 6.863126 TGCACTATATGATCAACGTACATGAG 59.137 38.462 0.00 0.00 0.00 2.90
698 732 9.438228 TCGTTTTGTATGGACTTAATTGTGATA 57.562 29.630 0.00 0.00 0.00 2.15
857 893 1.148310 CTCCGCACACGAACTCAAAT 58.852 50.000 0.00 0.00 43.93 2.32
858 894 1.495584 GCTCCGCACACGAACTCAAA 61.496 55.000 0.00 0.00 43.93 2.69
870 906 0.103755 GTCAGATGAGATGCTCCGCA 59.896 55.000 0.00 0.00 44.86 5.69
907 943 0.181350 AGAGATGGGGACGCATTTCC 59.819 55.000 13.74 0.00 34.52 3.13
1388 1430 2.130073 GAACCTTGCTCGTGGTTGCC 62.130 60.000 1.88 0.00 45.48 4.52
1556 1598 1.292242 TCCCTCTACTTGGATGAGGCT 59.708 52.381 0.00 0.00 44.32 4.58
1793 1837 5.615289 ACTCGAGCCAAGAATATTATTGCT 58.385 37.500 13.61 15.41 0.00 3.91
2149 2212 1.258445 AACCACCACAAAAACCCGCA 61.258 50.000 0.00 0.00 0.00 5.69
2153 2216 3.118956 TGATGTCAACCACCACAAAAACC 60.119 43.478 0.00 0.00 0.00 3.27
2311 2528 5.924475 AGAATTGTTGAAACTACTCCACG 57.076 39.130 0.00 0.00 0.00 4.94
2348 2565 6.062095 GCCTCCTGGTATTATTGAAGCTTTA 58.938 40.000 0.00 0.00 35.27 1.85
2404 2628 1.216678 TGTTGGTCCATTTCCCTGTGT 59.783 47.619 0.00 0.00 0.00 3.72
2735 2994 9.466497 TTGAACATTCTTATCTCTTAGCCAAAT 57.534 29.630 0.00 0.00 0.00 2.32
2741 3000 9.868277 ACTGTCTTGAACATTCTTATCTCTTAG 57.132 33.333 0.00 0.00 37.23 2.18
2806 3087 1.372683 GAGTGTGCAAGAGCTCCCA 59.627 57.895 10.93 2.39 42.74 4.37


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

AutoCloner maintained by Alex Coulton.