Multiple sequence alignment - TraesCS1A01G313000

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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 TraesCS1A01G313000 chr1A 100.000 2216 0 0 1 2216 504739305 504741520 0.000000e+00 4093.0
1 TraesCS1A01G313000 chr1A 97.075 2222 57 4 1 2216 504998635 505000854 0.000000e+00 3736.0
2 TraesCS1A01G313000 chr1A 92.849 881 42 6 712 1591 577834774 577833914 0.000000e+00 1258.0
3 TraesCS1A01G313000 chr1A 89.412 340 31 3 1880 2216 97855166 97855503 7.310000e-115 424.0
4 TraesCS1A01G313000 chr3A 95.041 1593 67 6 1 1592 170479960 170478379 0.000000e+00 2494.0
5 TraesCS1A01G313000 chr3A 88.993 1599 151 14 1 1586 709153716 709155302 0.000000e+00 1954.0
6 TraesCS1A01G313000 chr3A 96.590 1085 35 2 1 1084 57173910 57174993 0.000000e+00 1797.0
7 TraesCS1A01G313000 chr3A 90.058 342 30 2 1878 2216 521310025 521309685 7.260000e-120 440.0
8 TraesCS1A01G313000 chr3A 89.181 342 33 2 1879 2216 695518083 695518424 7.310000e-115 424.0
9 TraesCS1A01G313000 chr3A 96.618 207 7 0 1381 1587 383085524 383085318 5.860000e-91 344.0
10 TraesCS1A01G313000 chr7A 88.136 1593 173 11 1 1587 78561579 78563161 0.000000e+00 1881.0
11 TraesCS1A01G313000 chr7A 84.005 1588 228 20 9 1587 42712198 42710628 0.000000e+00 1502.0
12 TraesCS1A01G313000 chr7A 81.341 343 62 2 6 346 317146089 317146431 6.030000e-71 278.0
13 TraesCS1A01G313000 chr5B 87.875 1600 174 11 1 1589 415646445 415648035 0.000000e+00 1862.0
14 TraesCS1A01G313000 chr4B 83.566 1144 169 14 453 1584 515049931 515048795 0.000000e+00 1053.0
15 TraesCS1A01G313000 chr7D 86.291 817 100 7 769 1584 12421473 12422278 0.000000e+00 878.0
16 TraesCS1A01G313000 chr7D 86.417 773 97 8 6 774 12417676 12418444 0.000000e+00 839.0
17 TraesCS1A01G313000 chr1D 94.702 302 15 1 1584 1884 408871330 408871631 3.330000e-128 468.0
18 TraesCS1A01G313000 chr1D 75.538 650 145 12 578 1222 18964259 18964899 7.690000e-80 307.0
19 TraesCS1A01G313000 chr6A 91.471 340 25 3 1879 2216 564981500 564981163 4.310000e-127 464.0
20 TraesCS1A01G313000 chr6A 92.735 234 16 1 1357 1589 555108594 555108361 9.800000e-89 337.0
21 TraesCS1A01G313000 chr6A 79.861 144 28 1 84 226 452095531 452095388 1.080000e-18 104.0
22 TraesCS1A01G313000 chr6A 77.778 144 30 2 84 226 452093495 452093353 1.090000e-13 87.9
23 TraesCS1A01G313000 chr1B 94.040 302 17 1 1584 1884 550370240 550370541 7.210000e-125 457.0
24 TraesCS1A01G313000 chr5A 90.294 340 29 3 1881 2216 547816142 547815803 2.020000e-120 442.0
25 TraesCS1A01G313000 chr5A 90.029 341 28 2 1879 2216 509986263 509986600 9.400000e-119 436.0
26 TraesCS1A01G313000 chr5A 89.349 338 32 2 1882 2216 485472972 485472636 2.630000e-114 422.0
27 TraesCS1A01G313000 chr2A 90.000 340 28 4 1880 2216 179990492 179990156 3.380000e-118 435.0
28 TraesCS1A01G313000 chr7B 81.308 321 58 2 9 328 251131478 251131159 2.180000e-65 259.0


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 TraesCS1A01G313000 chr1A 504739305 504741520 2215 False 4093.0 4093 100.000 1 2216 1 chr1A.!!$F2 2215
1 TraesCS1A01G313000 chr1A 504998635 505000854 2219 False 3736.0 3736 97.075 1 2216 1 chr1A.!!$F3 2215
2 TraesCS1A01G313000 chr1A 577833914 577834774 860 True 1258.0 1258 92.849 712 1591 1 chr1A.!!$R1 879
3 TraesCS1A01G313000 chr3A 170478379 170479960 1581 True 2494.0 2494 95.041 1 1592 1 chr3A.!!$R1 1591
4 TraesCS1A01G313000 chr3A 709153716 709155302 1586 False 1954.0 1954 88.993 1 1586 1 chr3A.!!$F3 1585
5 TraesCS1A01G313000 chr3A 57173910 57174993 1083 False 1797.0 1797 96.590 1 1084 1 chr3A.!!$F1 1083
6 TraesCS1A01G313000 chr7A 78561579 78563161 1582 False 1881.0 1881 88.136 1 1587 1 chr7A.!!$F1 1586
7 TraesCS1A01G313000 chr7A 42710628 42712198 1570 True 1502.0 1502 84.005 9 1587 1 chr7A.!!$R1 1578
8 TraesCS1A01G313000 chr5B 415646445 415648035 1590 False 1862.0 1862 87.875 1 1589 1 chr5B.!!$F1 1588
9 TraesCS1A01G313000 chr4B 515048795 515049931 1136 True 1053.0 1053 83.566 453 1584 1 chr4B.!!$R1 1131
10 TraesCS1A01G313000 chr7D 12417676 12422278 4602 False 858.5 878 86.354 6 1584 2 chr7D.!!$F1 1578
11 TraesCS1A01G313000 chr1D 18964259 18964899 640 False 307.0 307 75.538 578 1222 1 chr1D.!!$F1 644

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
90 91 1.816074 GGCAGGAAACGTTATCACCA 58.184 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 4994 0.110823 CAGCACCGACGCTACAAAAC 60.111 55.0 0.0 0.0 41.38 2.43 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
90 91 1.816074 GGCAGGAAACGTTATCACCA 58.184 50.000 0.00 0.00 0.00 4.17
215 219 4.141482 ACTTGAGACTCAACAAGGGCTTTA 60.141 41.667 13.99 0.00 45.03 1.85
844 3884 4.249661 GTCTCAACATCTCTTCTTCACCC 58.750 47.826 0.00 0.00 0.00 4.61
1163 4204 3.005554 CGAAGATGCTCAAGACCAACAT 58.994 45.455 0.00 0.00 0.00 2.71
1219 4264 0.179062 ATCAGCGATGGACTGAAGGC 60.179 55.000 0.00 0.00 46.63 4.35
1325 4386 1.144708 TGTGTGGGCTTTTCCTGATGA 59.855 47.619 0.00 0.00 34.39 2.92
1453 4522 0.757512 ATGGTGAGCTGCTCGATGAT 59.242 50.000 23.35 10.57 32.35 2.45
1642 4712 3.746492 AGAGTCGTTGATTTAGTGGCAAC 59.254 43.478 0.00 0.00 38.73 4.17
1666 4736 8.797350 ACAAATGTTGAGAATGAGATACATCA 57.203 30.769 0.00 0.00 38.38 3.07
1671 4741 8.484641 TGTTGAGAATGAGATACATCAGAAAC 57.515 34.615 0.00 0.00 38.38 2.78
1691 4761 2.549754 ACGTGTGGCAGAGAAAATTCTG 59.450 45.455 0.00 0.00 45.85 3.02
1748 4818 2.483188 CCCGGTCTAATCAAGTACCAGC 60.483 54.545 0.00 0.00 32.04 4.85
1869 4939 2.039085 GCTGCAATGTCGATTTATGCG 58.961 47.619 0.00 0.00 39.81 4.73
1950 5023 0.454452 GTCGGTGCTGAAAAATCGGC 60.454 55.000 2.72 2.72 42.08 5.54
1952 5025 1.586154 CGGTGCTGAAAAATCGGCCT 61.586 55.000 0.00 0.00 41.09 5.19
2080 5153 1.662122 ACGTTTTGACGCGAAAGAGTT 59.338 42.857 15.93 0.00 46.65 3.01
2091 5164 4.699522 AAGAGTTGCGGGACCGGC 62.700 66.667 16.76 16.76 40.19 6.13
2156 5229 1.110442 CTGCGGGGAATAAATGCCAA 58.890 50.000 0.00 0.00 42.44 4.52
2164 5237 0.461135 AATAAATGCCAAGGCTGCCG 59.539 50.000 13.96 0.00 42.51 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 1.112315 TGCCGTTGGTTTCTTGCCAT 61.112 50.000 0.00 0.00 35.71 4.40
90 91 3.267812 ACAGATCCTGGTCCATTTGACAT 59.732 43.478 0.00 0.00 46.38 3.06
215 219 1.486310 TGGCTCGGATAACATCTTGCT 59.514 47.619 0.00 0.00 0.00 3.91
818 3858 5.117897 GTGAAGAAGAGATGTTGAGACGTTC 59.882 44.000 0.00 0.00 0.00 3.95
844 3884 2.260869 CCACCCTTGCAACTGGACG 61.261 63.158 15.48 7.17 0.00 4.79
1163 4204 0.554305 AATCCTCATCATGGCAGCCA 59.446 50.000 18.99 18.99 38.19 4.75
1219 4264 1.135915 AGGCATAGACGACAGCTTCAG 59.864 52.381 0.00 0.00 0.00 3.02
1325 4386 0.321653 GGGAACGGCTCACAAGTGAT 60.322 55.000 3.01 0.00 39.13 3.06
1453 4522 0.395586 AAACCCACTGCAAGCACTCA 60.396 50.000 0.00 0.00 37.60 3.41
1595 4665 0.465705 TCATCAGCGATCAACCCCTC 59.534 55.000 0.00 0.00 0.00 4.30
1642 4712 9.106070 TCTGATGTATCTCATTCTCAACATTTG 57.894 33.333 0.00 0.00 36.83 2.32
1666 4736 2.325583 TTTCTCTGCCACACGTTTCT 57.674 45.000 0.00 0.00 0.00 2.52
1671 4741 2.807967 TCAGAATTTTCTCTGCCACACG 59.192 45.455 0.00 0.00 42.25 4.49
1691 4761 6.997942 ATCTATTTGGGTAGGTAGTCCTTC 57.002 41.667 0.00 0.00 42.12 3.46
1748 4818 4.290711 TGGTGCTCATACATGATATGGG 57.709 45.455 0.00 5.31 36.02 4.00
1838 4908 0.323178 CATTGCAGCTCCAACCTCCT 60.323 55.000 0.00 0.00 0.00 3.69
1869 4939 0.179100 TGCTCTTAGATCACGCAGCC 60.179 55.000 0.00 0.00 0.00 4.85
1921 4994 0.110823 CAGCACCGACGCTACAAAAC 60.111 55.000 0.00 0.00 41.38 2.43
1939 5012 1.365699 GCGACTAGGCCGATTTTTCA 58.634 50.000 10.39 0.00 0.00 2.69
1950 5023 4.530857 CTTGGGGGCGCGACTAGG 62.531 72.222 13.91 0.00 0.00 3.02
1952 5025 3.458163 CTCTTGGGGGCGCGACTA 61.458 66.667 13.91 0.00 0.00 2.59
2094 5167 3.609703 AGCCTTCGTCTCGCTGAT 58.390 55.556 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.