Multiple sequence alignment - TraesCS1D01G358100

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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 TraesCS1D01G358100 chr1D 100.000 2318 0 0 1 2318 441739534 441741851 0.000000e+00 4281.0
1 TraesCS1D01G358100 chr1D 91.557 1374 80 27 962 2315 441644236 441645593 0.000000e+00 1862.0
2 TraesCS1D01G358100 chr1D 93.767 754 11 6 34 782 441631940 441632662 0.000000e+00 1099.0
3 TraesCS1D01G358100 chr1D 90.871 241 21 1 36 276 441577892 441578131 2.870000e-84 322.0
4 TraesCS1D01G358100 chr1D 96.000 150 3 2 820 969 441632658 441632804 8.280000e-60 241.0
5 TraesCS1D01G358100 chr1D 95.556 45 1 1 1 44 441631867 441631911 1.150000e-08 71.3
6 TraesCS1D01G358100 chr1D 84.722 72 7 3 2048 2117 413959509 413959578 4.130000e-08 69.4
7 TraesCS1D01G358100 chr1B 92.218 1889 103 20 34 1908 599764816 599766674 0.000000e+00 2634.0
8 TraesCS1D01G358100 chr1B 93.193 1807 81 20 34 1827 599635646 599637423 0.000000e+00 2617.0
9 TraesCS1D01G358100 chr1B 92.640 1807 91 20 34 1827 599706854 599708631 0.000000e+00 2562.0
10 TraesCS1D01G358100 chr1B 92.597 1810 86 20 31 1827 599836358 599838132 0.000000e+00 2556.0
11 TraesCS1D01G358100 chr1B 92.330 1395 68 19 445 1827 599925579 599926946 0.000000e+00 1947.0
12 TraesCS1D01G358100 chr1B 92.115 1395 73 18 445 1827 599982767 599984136 0.000000e+00 1932.0
13 TraesCS1D01G358100 chr1B 90.863 1182 68 21 658 1827 599577664 599578817 0.000000e+00 1548.0
14 TraesCS1D01G358100 chr1B 95.533 403 18 0 34 436 599982215 599982617 0.000000e+00 645.0
15 TraesCS1D01G358100 chr1B 90.323 465 34 7 1856 2318 599578816 599579271 1.190000e-167 599.0
16 TraesCS1D01G358100 chr1B 90.302 464 36 6 1856 2318 599708630 599709085 1.190000e-167 599.0
17 TraesCS1D01G358100 chr1B 90.065 463 35 7 1856 2318 599838131 599838582 7.130000e-165 590.0
18 TraesCS1D01G358100 chr1B 94.947 376 19 0 34 409 599924899 599925274 7.130000e-165 590.0
19 TraesCS1D01G358100 chr1B 96.122 361 10 4 34 393 599577316 599577673 9.230000e-164 586.0
20 TraesCS1D01G358100 chr1B 89.655 464 38 6 1856 2318 599926945 599927399 1.190000e-162 582.0
21 TraesCS1D01G358100 chr1B 89.677 465 37 7 1856 2318 599984135 599984590 1.190000e-162 582.0
22 TraesCS1D01G358100 chr1B 89.462 465 39 6 1856 2318 599637422 599637878 1.540000e-161 579.0
23 TraesCS1D01G358100 chr1B 90.338 414 33 6 1907 2318 599766789 599767197 9.430000e-149 536.0
24 TraesCS1D01G358100 chr1B 95.556 45 1 1 1 44 599635573 599635617 1.150000e-08 71.3
25 TraesCS1D01G358100 chr1B 95.556 45 1 1 1 44 599706781 599706825 1.150000e-08 71.3
26 TraesCS1D01G358100 chr1B 95.556 45 1 1 1 44 599764743 599764787 1.150000e-08 71.3
27 TraesCS1D01G358100 chr1B 95.556 45 1 1 1 44 599836288 599836332 1.150000e-08 71.3
28 TraesCS1D01G358100 chr1B 95.556 45 1 1 1 44 599982142 599982186 1.150000e-08 71.3
29 TraesCS1D01G358100 chr1B 93.333 45 2 1 1 44 599924827 599924871 5.350000e-07 65.8
30 TraesCS1D01G358100 chr1A 85.496 1241 111 29 996 2223 536629864 536628680 0.000000e+00 1230.0
31 TraesCS1D01G358100 chr5D 82.286 175 26 5 213 384 330312250 330312078 1.860000e-31 147.0


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 TraesCS1D01G358100 chr1D 441739534 441741851 2317 False 4281.000000 4281 100.000000 1 2318 1 chr1D.!!$F4 2317
1 TraesCS1D01G358100 chr1D 441644236 441645593 1357 False 1862.000000 1862 91.557000 962 2315 1 chr1D.!!$F3 1353
2 TraesCS1D01G358100 chr1D 441631867 441632804 937 False 470.433333 1099 95.107667 1 969 3 chr1D.!!$F5 968
3 TraesCS1D01G358100 chr1B 599635573 599637878 2305 False 1089.100000 2617 92.737000 1 2318 3 chr1B.!!$F2 2317
4 TraesCS1D01G358100 chr1B 599764743 599767197 2454 False 1080.433333 2634 92.704000 1 2318 3 chr1B.!!$F4 2317
5 TraesCS1D01G358100 chr1B 599706781 599709085 2304 False 1077.433333 2562 92.832667 1 2318 3 chr1B.!!$F3 2317
6 TraesCS1D01G358100 chr1B 599836288 599838582 2294 False 1072.433333 2556 92.739333 1 2318 3 chr1B.!!$F5 2317
7 TraesCS1D01G358100 chr1B 599577316 599579271 1955 False 911.000000 1548 92.436000 34 2318 3 chr1B.!!$F1 2284
8 TraesCS1D01G358100 chr1B 599982142 599984590 2448 False 807.575000 1932 93.220250 1 2318 4 chr1B.!!$F7 2317
9 TraesCS1D01G358100 chr1B 599924827 599927399 2572 False 796.200000 1947 92.566250 1 2318 4 chr1B.!!$F6 2317
10 TraesCS1D01G358100 chr1A 536628680 536629864 1184 True 1230.000000 1230 85.496000 996 2223 1 chr1A.!!$R1 1227

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
790 1106 2.900838 GATCGCTGCATGCAGGCT 60.901 61.111 40.59 25.53 43.77 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 2154 0.532573 ACCACTAGCAGTCGTCCATG 59.467 55.0 0.0 0.0 0.0 3.66 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
427 474 4.898861 TCATATAATTTCCCCTTTGGCACC 59.101 41.667 0.00 0.00 0.00 5.01
658 974 6.811954 TGTCAAAATCCATGTACGCTATCTA 58.188 36.000 0.00 0.00 0.00 1.98
790 1106 2.900838 GATCGCTGCATGCAGGCT 60.901 61.111 40.59 25.53 43.77 4.58
938 1256 5.509670 GGTTGTTAGGAAGCAAATCAAAGCT 60.510 40.000 0.00 0.00 44.31 3.74
939 1257 5.125100 TGTTAGGAAGCAAATCAAAGCTG 57.875 39.130 0.00 0.00 41.70 4.24
1008 1326 2.046023 CTCCAAGCCATGTCGCCA 60.046 61.111 0.00 0.00 0.00 5.69
1321 1639 2.978452 GATGTCCGCGCACTAGGCAT 62.978 60.000 8.75 5.81 45.17 4.40
1357 1676 7.526918 AGGGAAATTTTCTTGGTCTTCTTAGA 58.473 34.615 8.93 0.00 0.00 2.10
1474 1807 9.768662 AAGATTCATGTAAGCATTTTCTTTTGT 57.231 25.926 0.00 0.00 31.99 2.83
1475 1808 9.415544 AGATTCATGTAAGCATTTTCTTTTGTC 57.584 29.630 0.00 0.00 31.99 3.18
1476 1809 9.415544 GATTCATGTAAGCATTTTCTTTTGTCT 57.584 29.630 0.00 0.00 31.99 3.41
1477 1810 9.768662 ATTCATGTAAGCATTTTCTTTTGTCTT 57.231 25.926 0.00 0.00 31.99 3.01
1478 1811 9.598517 TTCATGTAAGCATTTTCTTTTGTCTTT 57.401 25.926 0.00 0.00 31.99 2.52
1479 1812 9.598517 TCATGTAAGCATTTTCTTTTGTCTTTT 57.401 25.926 0.00 0.00 31.99 2.27
1556 1889 2.273179 CGGTGACTTGGAGGGTCGA 61.273 63.158 0.00 0.00 36.58 4.20
1720 2059 1.066752 CGTGGTGGTCGACTGTTCA 59.933 57.895 16.46 1.36 0.00 3.18
1743 2082 0.250081 CCTTCGCTCTTGGCTATCCC 60.250 60.000 0.00 0.00 39.13 3.85
1806 2145 3.349006 CTTGGCAGCGTGCGTTCT 61.349 61.111 4.33 0.00 46.21 3.01
1829 2168 2.731571 GGGGCATGGACGACTGCTA 61.732 63.158 0.00 0.00 38.45 3.49
1834 2173 0.532573 CATGGACGACTGCTAGTGGT 59.467 55.000 4.20 4.20 39.92 4.16
1845 2184 1.885163 GCTAGTGGTGTGGTAGCGGT 61.885 60.000 0.00 0.00 30.50 5.68
1867 2206 2.577059 GACCTTGGCGTGGATCGA 59.423 61.111 2.55 0.00 42.86 3.59
1873 2212 0.460109 TTGGCGTGGATCGATCACAG 60.460 55.000 25.93 16.31 42.86 3.66
1874 2213 1.319614 TGGCGTGGATCGATCACAGA 61.320 55.000 25.93 4.78 42.86 3.41
1967 2425 6.255950 AGTAAAGAAAACTCGTGTGCTTTTC 58.744 36.000 14.36 10.28 30.82 2.29
1969 2427 2.031683 AGAAAACTCGTGTGCTTTTCCG 59.968 45.455 8.77 0.00 33.47 4.30
1975 2433 2.482721 CTCGTGTGCTTTTCCGGTTTAT 59.517 45.455 0.00 0.00 0.00 1.40
2295 2765 0.737715 GTAACTGAGCGCCAGAGTGG 60.738 60.000 26.07 6.69 45.78 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
790 1106 1.803453 AATTTCCCTGGCCAGCAGGA 61.803 55.000 28.39 25.25 42.27 3.86
881 1199 4.776322 CTCCGACCAATGCGCCCA 62.776 66.667 4.18 0.00 0.00 5.36
938 1256 8.554011 AGGTAGCCTGGATTTATAAAAGTTACA 58.446 33.333 1.21 0.00 29.57 2.41
939 1257 8.975663 AGGTAGCCTGGATTTATAAAAGTTAC 57.024 34.615 1.21 2.60 29.57 2.50
1008 1326 2.064581 GTCCCTCCCGCTGTATGGT 61.065 63.158 0.00 0.00 0.00 3.55
1321 1639 8.752187 CCAAGAAAATTTCCCTCTCATCAATTA 58.248 33.333 1.57 0.00 0.00 1.40
1357 1676 5.050159 GCCGCTCAACAAATCAGAAAATTTT 60.050 36.000 2.28 2.28 0.00 1.82
1477 1810 8.621286 GTGACTCAATCCAACTAGAAAGAAAAA 58.379 33.333 0.00 0.00 0.00 1.94
1478 1811 7.993183 AGTGACTCAATCCAACTAGAAAGAAAA 59.007 33.333 0.00 0.00 0.00 2.29
1479 1812 7.509546 AGTGACTCAATCCAACTAGAAAGAAA 58.490 34.615 0.00 0.00 0.00 2.52
1480 1813 7.067496 AGTGACTCAATCCAACTAGAAAGAA 57.933 36.000 0.00 0.00 0.00 2.52
1481 1814 6.672266 AGTGACTCAATCCAACTAGAAAGA 57.328 37.500 0.00 0.00 0.00 2.52
1482 1815 8.307483 TCTAAGTGACTCAATCCAACTAGAAAG 58.693 37.037 0.00 0.00 0.00 2.62
1492 1825 3.873952 GGCACATCTAAGTGACTCAATCC 59.126 47.826 0.00 0.00 44.26 3.01
1556 1889 4.438744 GCACAAAGCAAACTACTTCACAGT 60.439 41.667 0.00 0.00 44.79 3.55
1603 1936 2.643232 GGACGACGTAGGGGCAGTT 61.643 63.158 0.00 0.00 0.00 3.16
1604 1937 3.066814 GGACGACGTAGGGGCAGT 61.067 66.667 0.00 0.00 0.00 4.40
1605 1938 3.834799 GGGACGACGTAGGGGCAG 61.835 72.222 0.00 0.00 0.00 4.85
1713 2046 2.175202 AGAGCGAAGGAGATGAACAGT 58.825 47.619 0.00 0.00 0.00 3.55
1743 2082 4.717629 TCCAAGTCGTCCTGCGCG 62.718 66.667 0.00 0.00 41.07 6.86
1815 2154 0.532573 ACCACTAGCAGTCGTCCATG 59.467 55.000 0.00 0.00 0.00 3.66
1816 2155 0.532573 CACCACTAGCAGTCGTCCAT 59.467 55.000 0.00 0.00 0.00 3.41
1829 2168 2.741092 CACCGCTACCACACCACT 59.259 61.111 0.00 0.00 0.00 4.00
1849 2188 2.311688 ATCGATCCACGCCAAGGTCC 62.312 60.000 0.00 0.00 42.26 4.46
1867 2206 1.964223 ACACCGAGTGTCTTCTGTGAT 59.036 47.619 4.13 0.00 43.92 3.06
1942 2400 6.913873 AAAGCACACGAGTTTTCTTTACTA 57.086 33.333 0.00 0.00 0.00 1.82
2273 2743 1.073216 CTCTGGCGCTCAGTTACACG 61.073 60.000 20.54 0.73 43.76 4.49


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

AutoCloner maintained by Alex Coulton.