Multiple sequence alignment - TraesCS5D01G464900

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 TraesCS5D01G464900 chr5D 100.000 2801 0 0 1 2801 507836895 507834095 0.000000e+00 5173.0
1 TraesCS5D01G464900 chr5D 92.504 1334 90 7 475 1801 507772888 507771558 0.000000e+00 1901.0
2 TraesCS5D01G464900 chr5D 86.327 1236 118 26 659 1874 507776099 507774895 0.000000e+00 1299.0
3 TraesCS5D01G464900 chr5D 96.215 687 20 2 2115 2801 507789280 507788600 0.000000e+00 1120.0
4 TraesCS5D01G464900 chr5D 100.000 35 0 0 2064 2098 507789301 507789267 6.480000e-07 65.8
5 TraesCS5D01G464900 chr5B 94.543 1521 71 8 589 2098 638398237 638396718 0.000000e+00 2338.0
6 TraesCS5D01G464900 chr5B 85.509 1463 151 33 454 1878 638354058 638352619 0.000000e+00 1471.0
7 TraesCS5D01G464900 chr5B 86.933 1301 126 22 593 1875 638345614 638344340 0.000000e+00 1421.0
8 TraesCS5D01G464900 chr5B 88.201 1212 114 19 593 1801 638337320 638336135 0.000000e+00 1419.0
9 TraesCS5D01G464900 chr5B 88.855 987 91 8 906 1878 638364032 638363051 0.000000e+00 1195.0
10 TraesCS5D01G464900 chr5B 91.496 341 21 5 244 582 638398797 638398463 1.970000e-126 462.0
11 TraesCS5D01G464900 chr5B 87.774 319 21 8 2176 2493 638371579 638371278 9.540000e-95 357.0
12 TraesCS5D01G464900 chr5B 98.462 65 1 0 2115 2179 638396731 638396667 6.340000e-22 115.0
13 TraesCS5D01G464900 chr5B 97.059 34 1 0 1845 1878 638336105 638336072 1.080000e-04 58.4
14 TraesCS5D01G464900 chr5A 88.665 1288 128 8 593 1878 635409181 635407910 0.000000e+00 1554.0
15 TraesCS5D01G464900 chr5A 88.372 1204 101 13 819 2009 635415647 635414470 0.000000e+00 1411.0
16 TraesCS5D01G464900 chr5A 85.043 1277 135 31 627 1874 635411854 635410605 0.000000e+00 1249.0
17 TraesCS5D01G464900 chr5A 90.578 796 35 9 2 761 635416439 635415648 0.000000e+00 1018.0
18 TraesCS5D01G464900 chr7B 84.555 887 132 5 1000 1883 118891414 118892298 0.000000e+00 874.0
19 TraesCS5D01G464900 chr1D 96.429 308 10 1 2495 2801 285217463 285217770 8.950000e-140 507.0
20 TraesCS5D01G464900 chr3D 94.921 315 15 1 2488 2801 579435856 579436170 2.510000e-135 492.0
21 TraesCS5D01G464900 chr7D 95.114 307 15 0 2495 2801 293827068 293827374 4.190000e-133 484.0
22 TraesCS5D01G464900 chr7D 94.805 308 15 1 2495 2801 17382017 17382324 1.950000e-131 479.0
23 TraesCS5D01G464900 chr6D 95.130 308 14 1 2495 2801 456816618 456816311 4.190000e-133 484.0
24 TraesCS5D01G464900 chr4D 94.788 307 16 0 2495 2801 73244809 73244503 1.950000e-131 479.0
25 TraesCS5D01G464900 chr4D 94.788 307 16 0 2495 2801 327018973 327019279 1.950000e-131 479.0
26 TraesCS5D01G464900 chr4A 93.210 324 18 4 2482 2801 162361632 162361309 9.080000e-130 473.0


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 TraesCS5D01G464900 chr5D 507834095 507836895 2800 True 5173.000000 5173 100.000000 1 2801 1 chr5D.!!$R1 2800
1 TraesCS5D01G464900 chr5D 507771558 507776099 4541 True 1600.000000 1901 89.415500 475 1874 2 chr5D.!!$R2 1399
2 TraesCS5D01G464900 chr5D 507788600 507789301 701 True 592.900000 1120 98.107500 2064 2801 2 chr5D.!!$R3 737
3 TraesCS5D01G464900 chr5B 638352619 638354058 1439 True 1471.000000 1471 85.509000 454 1878 1 chr5B.!!$R2 1424
4 TraesCS5D01G464900 chr5B 638344340 638345614 1274 True 1421.000000 1421 86.933000 593 1875 1 chr5B.!!$R1 1282
5 TraesCS5D01G464900 chr5B 638363051 638364032 981 True 1195.000000 1195 88.855000 906 1878 1 chr5B.!!$R3 972
6 TraesCS5D01G464900 chr5B 638396667 638398797 2130 True 971.666667 2338 94.833667 244 2179 3 chr5B.!!$R6 1935
7 TraesCS5D01G464900 chr5B 638336072 638337320 1248 True 738.700000 1419 92.630000 593 1878 2 chr5B.!!$R5 1285
8 TraesCS5D01G464900 chr5A 635407910 635416439 8529 True 1308.000000 1554 88.164500 2 2009 4 chr5A.!!$R1 2007
9 TraesCS5D01G464900 chr7B 118891414 118892298 884 False 874.000000 874 84.555000 1000 1883 1 chr7B.!!$F1 883

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
162 163 0.583438 CATACAAGGAATCGCGCTGG 59.417 55.000 5.56 0.00 0.00 4.85 F
241 242 1.490574 CCAAGTGGGTTTGGTTCCAA 58.509 50.000 0.00 0.00 42.16 3.53 F
242 243 1.834263 CCAAGTGGGTTTGGTTCCAAA 59.166 47.619 12.29 12.29 42.16 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1003 4039 0.473755 AGTGACATGGTGGTTGCAGA 59.526 50.000 0.00 0.0 0.0 4.26 R
1266 11000 1.813862 CGGTTCTTGGCAAAGGTCTCA 60.814 52.381 0.00 0.0 33.9 3.27 R
1962 11711 1.846007 AAATAAATGTGAGCCCGGCA 58.154 45.000 13.15 0.0 0.0 5.69 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
28 29 2.039216 TCCCCTCAAAACGCATGAGTTA 59.961 45.455 15.48 0.00 42.19 2.24
29 30 2.161609 CCCCTCAAAACGCATGAGTTAC 59.838 50.000 15.48 0.00 42.19 2.50
159 160 1.867233 ACATCATACAAGGAATCGCGC 59.133 47.619 0.00 0.00 0.00 6.86
160 161 2.138320 CATCATACAAGGAATCGCGCT 58.862 47.619 5.56 0.00 0.00 5.92
162 163 0.583438 CATACAAGGAATCGCGCTGG 59.417 55.000 5.56 0.00 0.00 4.85
241 242 1.490574 CCAAGTGGGTTTGGTTCCAA 58.509 50.000 0.00 0.00 42.16 3.53
242 243 1.834263 CCAAGTGGGTTTGGTTCCAAA 59.166 47.619 12.29 12.29 42.16 3.28
764 3790 8.146053 TCACAGTTATCTAAAGAGATTCCCAA 57.854 34.615 0.00 0.00 39.56 4.12
787 3815 3.784511 AGCCATATCCACAAGATCCAG 57.215 47.619 0.00 0.00 36.33 3.86
817 3845 4.096681 TCTAATCTCCTTGTGGCTCTCAA 58.903 43.478 0.00 0.00 0.00 3.02
891 3921 4.065088 TGTCAGCTTACACCAGTTCAATC 58.935 43.478 0.00 0.00 0.00 2.67
1003 4039 3.708631 AGAACCTCCATCGATCAGAATGT 59.291 43.478 0.00 0.00 37.40 2.71
1131 4167 2.653115 GCAAAGGCCAAGCAGGTC 59.347 61.111 5.01 0.00 44.66 3.85
1667 11401 1.588824 AACGGTCGTCTCGCCATGTA 61.589 55.000 0.00 0.00 0.00 2.29
1801 11535 3.801307 ACTTTGTTCCCGGGAAGTAAT 57.199 42.857 36.45 17.74 34.49 1.89
1807 11556 0.326238 TCCCGGGAAGTAATCTGCCT 60.326 55.000 24.50 0.00 39.36 4.75
1890 11639 8.225603 ACGAGGATTCTATGCAAAAACATTAT 57.774 30.769 0.00 0.00 0.00 1.28
1911 11660 1.481871 AGATTTGCCTGCCTTCCATG 58.518 50.000 0.00 0.00 0.00 3.66
1912 11661 0.179092 GATTTGCCTGCCTTCCATGC 60.179 55.000 0.00 0.00 35.86 4.06
1915 11664 2.443390 GCCTGCCTTCCATGCCAT 60.443 61.111 0.00 0.00 0.00 4.40
1935 11684 1.173913 GGCCCGTATTTGATATGGCC 58.826 55.000 0.00 0.00 43.69 5.36
1997 11747 8.661257 CACATTTATTTACACGTGTCTTCCATA 58.339 33.333 27.16 12.03 0.00 2.74
2015 11765 6.971726 TCCATAGACGGTTGAACATATACT 57.028 37.500 0.00 0.00 0.00 2.12
2084 11834 5.140454 ACAAAAATAGGAAACACTGCTCCT 58.860 37.500 5.75 5.75 44.49 3.69
2085 11835 6.303839 ACAAAAATAGGAAACACTGCTCCTA 58.696 36.000 9.08 9.08 46.03 2.94
2086 11836 6.431234 ACAAAAATAGGAAACACTGCTCCTAG 59.569 38.462 11.41 0.00 45.36 3.02
2087 11837 6.374417 AAAATAGGAAACACTGCTCCTAGA 57.626 37.500 11.41 0.00 45.36 2.43
2088 11838 5.346181 AATAGGAAACACTGCTCCTAGAC 57.654 43.478 11.41 0.00 45.36 2.59
2089 11839 2.609747 AGGAAACACTGCTCCTAGACA 58.390 47.619 0.00 0.00 40.42 3.41
2090 11840 2.300437 AGGAAACACTGCTCCTAGACAC 59.700 50.000 0.00 0.00 40.42 3.67
2091 11841 2.613223 GGAAACACTGCTCCTAGACACC 60.613 54.545 0.00 0.00 0.00 4.16
2092 11842 0.977395 AACACTGCTCCTAGACACCC 59.023 55.000 0.00 0.00 0.00 4.61
2093 11843 0.115349 ACACTGCTCCTAGACACCCT 59.885 55.000 0.00 0.00 0.00 4.34
2094 11844 1.358103 ACACTGCTCCTAGACACCCTA 59.642 52.381 0.00 0.00 0.00 3.53
2095 11845 2.023888 ACACTGCTCCTAGACACCCTAT 60.024 50.000 0.00 0.00 0.00 2.57
2096 11846 3.204606 ACACTGCTCCTAGACACCCTATA 59.795 47.826 0.00 0.00 0.00 1.31
2097 11847 4.140900 ACACTGCTCCTAGACACCCTATAT 60.141 45.833 0.00 0.00 0.00 0.86
2098 11848 4.835615 CACTGCTCCTAGACACCCTATATT 59.164 45.833 0.00 0.00 0.00 1.28
2099 11849 5.305644 CACTGCTCCTAGACACCCTATATTT 59.694 44.000 0.00 0.00 0.00 1.40
2100 11850 5.905913 ACTGCTCCTAGACACCCTATATTTT 59.094 40.000 0.00 0.00 0.00 1.82
2101 11851 6.387220 ACTGCTCCTAGACACCCTATATTTTT 59.613 38.462 0.00 0.00 0.00 1.94
2503 12253 7.335924 GTGGCAATAAAAACATCCACTACTAGA 59.664 37.037 0.00 0.00 40.42 2.43
2504 12254 7.885922 TGGCAATAAAAACATCCACTACTAGAA 59.114 33.333 0.00 0.00 0.00 2.10
2601 12351 1.457346 ACTGTTAGTAGTAGCGCGGT 58.543 50.000 17.70 17.70 0.00 5.68
2603 12353 1.669779 CTGTTAGTAGTAGCGCGGTCT 59.330 52.381 16.92 14.55 0.00 3.85
2605 12355 1.399791 GTTAGTAGTAGCGCGGTCTGT 59.600 52.381 16.92 2.69 0.00 3.41
2606 12356 2.602257 TAGTAGTAGCGCGGTCTGTA 57.398 50.000 16.92 1.55 0.00 2.74
2607 12357 1.012841 AGTAGTAGCGCGGTCTGTAC 58.987 55.000 16.92 14.79 0.00 2.90
2608 12358 0.028637 GTAGTAGCGCGGTCTGTACC 59.971 60.000 16.92 0.00 42.95 3.34
2609 12359 1.097547 TAGTAGCGCGGTCTGTACCC 61.098 60.000 16.92 0.00 43.54 3.69
2610 12360 2.361483 TAGCGCGGTCTGTACCCA 60.361 61.111 16.92 0.00 43.54 4.51
2611 12361 1.755395 TAGCGCGGTCTGTACCCAT 60.755 57.895 16.92 0.00 43.54 4.00
2638 12388 8.740906 GCTACTACTATGGACTATATCAGCAAA 58.259 37.037 0.00 0.00 0.00 3.68
2651 12401 1.064357 TCAGCAAAACGTTTCCGGAAC 59.936 47.619 18.64 11.37 38.78 3.62
2652 12402 1.096416 AGCAAAACGTTTCCGGAACA 58.904 45.000 18.64 5.64 38.18 3.18
2675 12425 6.862090 ACACGCTACTATTAATTAGCTGTAGC 59.138 38.462 22.22 22.22 45.19 3.58
2760 12510 7.642071 TTTCAGCTTCAATAAACTGCAATTC 57.358 32.000 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.159707 CGTAACTCATGCGTTTTGAGGG 60.160 50.000 6.36 0.00 43.95 4.30
28 29 4.836125 AGCATTTTCACTTGAATGACGT 57.164 36.364 0.00 0.00 35.74 4.34
29 30 9.507280 AATATAAGCATTTTCACTTGAATGACG 57.493 29.630 0.62 0.00 35.74 4.35
75 76 7.276658 TGCGTTTACATTGTGTTTCTCAAAAAT 59.723 29.630 0.00 0.00 0.00 1.82
80 81 4.572795 TCTGCGTTTACATTGTGTTTCTCA 59.427 37.500 0.00 0.00 0.00 3.27
81 82 5.090652 TCTGCGTTTACATTGTGTTTCTC 57.909 39.130 0.00 0.00 0.00 2.87
99 100 1.302752 TGGTGTGGTGAGCATCTGC 60.303 57.895 0.00 0.00 42.49 4.26
156 157 6.466308 AATTTATTTCAAGTTTTCCAGCGC 57.534 33.333 0.00 0.00 0.00 5.92
233 234 6.014499 TGGTTAGTTTCTTTGTTTTGGAACCA 60.014 34.615 0.00 0.00 40.08 3.67
235 236 7.547722 ACATGGTTAGTTTCTTTGTTTTGGAAC 59.452 33.333 0.00 0.00 36.29 3.62
237 238 7.176589 ACATGGTTAGTTTCTTTGTTTTGGA 57.823 32.000 0.00 0.00 0.00 3.53
724 3750 0.036022 TGTGATTGGATGACACGCCA 59.964 50.000 0.00 0.00 37.35 5.69
764 3790 4.234550 TGGATCTTGTGGATATGGCTAGT 58.765 43.478 0.00 0.00 34.33 2.57
787 3815 7.902087 AGCCACAAGGAGATTAGATATACTTC 58.098 38.462 0.00 0.00 36.89 3.01
798 3826 3.522750 AGATTGAGAGCCACAAGGAGATT 59.477 43.478 0.00 0.00 36.89 2.40
817 3845 2.812836 TGGATGTCATTGGTGCAGAT 57.187 45.000 0.00 0.00 0.00 2.90
891 3921 2.681778 AGTGGACGGGCAGAGGAG 60.682 66.667 0.00 0.00 0.00 3.69
1003 4039 0.473755 AGTGACATGGTGGTTGCAGA 59.526 50.000 0.00 0.00 0.00 4.26
1266 11000 1.813862 CGGTTCTTGGCAAAGGTCTCA 60.814 52.381 0.00 0.00 33.90 3.27
1374 11108 2.086610 ACCAAACAGCCTCACCAAAT 57.913 45.000 0.00 0.00 0.00 2.32
1623 11357 2.317371 TCTCCTTGACCTTGAGCTCT 57.683 50.000 16.19 0.00 0.00 4.09
1667 11401 4.680440 GCACAAAGAAACCAAACATGGAGT 60.680 41.667 1.10 0.00 0.00 3.85
1801 11535 2.979676 CACCGCAAGCAAGGCAGA 60.980 61.111 0.00 0.00 0.00 4.26
1807 11556 2.186160 CACACCTCACCGCAAGCAA 61.186 57.895 0.00 0.00 0.00 3.91
1890 11639 2.897271 TGGAAGGCAGGCAAATCTTA 57.103 45.000 0.00 0.00 0.00 2.10
1911 11660 1.904287 TATCAAATACGGGCCATGGC 58.096 50.000 29.47 29.47 41.06 4.40
1912 11661 2.754552 CCATATCAAATACGGGCCATGG 59.245 50.000 7.63 7.63 0.00 3.66
1915 11664 1.904287 GCCATATCAAATACGGGCCA 58.096 50.000 4.39 0.00 34.28 5.36
1917 11666 1.904287 TGGCCATATCAAATACGGGC 58.096 50.000 0.00 0.00 43.13 6.13
1960 11709 2.949177 ATAAATGTGAGCCCGGCATA 57.051 45.000 13.15 0.00 0.00 3.14
1961 11710 2.071778 AATAAATGTGAGCCCGGCAT 57.928 45.000 13.15 0.00 0.00 4.40
1962 11711 1.846007 AAATAAATGTGAGCCCGGCA 58.154 45.000 13.15 0.00 0.00 5.69
1997 11747 7.544566 CACTTTGTAGTATATGTTCAACCGTCT 59.455 37.037 0.00 0.00 31.96 4.18
2301 12051 7.064490 CACTTAATTTGCCGGCTTATTTTCATT 59.936 33.333 29.70 14.82 0.00 2.57
2356 12106 9.703892 TTTTTCATCGGTTGATATTTGTTCAAT 57.296 25.926 0.00 0.00 35.68 2.57
2429 12179 8.572185 TGCTTTATTGTGTAAAGATGCTTGTAA 58.428 29.630 10.76 0.00 36.84 2.41
2504 12254 2.417787 CCGCGCTACTACTAGGGTTTTT 60.418 50.000 5.56 0.00 35.73 1.94
2601 12351 5.077564 CCATAGTAGTAGCATGGGTACAGA 58.922 45.833 8.13 0.00 38.76 3.41
2603 12353 4.831155 GTCCATAGTAGTAGCATGGGTACA 59.169 45.833 8.13 0.00 39.79 2.90
2605 12355 5.335028 AGTCCATAGTAGTAGCATGGGTA 57.665 43.478 9.19 0.00 39.79 3.69
2606 12356 4.200447 AGTCCATAGTAGTAGCATGGGT 57.800 45.455 9.19 0.00 39.79 4.51
2607 12357 7.780271 TGATATAGTCCATAGTAGTAGCATGGG 59.220 40.741 9.19 0.00 39.79 4.00
2608 12358 8.753497 TGATATAGTCCATAGTAGTAGCATGG 57.247 38.462 0.00 4.23 40.55 3.66
2609 12359 8.349245 GCTGATATAGTCCATAGTAGTAGCATG 58.651 40.741 0.00 0.00 0.00 4.06
2610 12360 8.055790 TGCTGATATAGTCCATAGTAGTAGCAT 58.944 37.037 0.00 0.00 30.92 3.79
2611 12361 7.402862 TGCTGATATAGTCCATAGTAGTAGCA 58.597 38.462 0.00 0.00 33.15 3.49
2699 12449 6.426587 CCGGGGGAAATGATGAAAGATATAT 58.573 40.000 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.