Multiple sequence alignment - TraesCS7D01G178700

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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 TraesCS7D01G178700 chr7D 100.000 2264 0 0 1 2264 131689395 131691658 0.000000e+00 4181.0
1 TraesCS7D01G178700 chr7D 94.470 2152 115 4 1 2149 528561188 528563338 0.000000e+00 3312.0
2 TraesCS7D01G178700 chrUn 96.015 2158 78 5 1 2153 10399174 10401328 0.000000e+00 3502.0
3 TraesCS7D01G178700 chr4D 93.319 2260 138 12 1 2249 470196637 470194380 0.000000e+00 3325.0
4 TraesCS7D01G178700 chr2D 94.347 2158 112 9 1 2152 619853632 619855785 0.000000e+00 3301.0
5 TraesCS7D01G178700 chr2D 80.899 89 16 1 2162 2249 619855785 619855697 4.040000e-08 69.4
6 TraesCS7D01G178700 chr6D 96.513 1950 66 2 1 1948 377212206 377214155 0.000000e+00 3223.0
7 TraesCS7D01G178700 chr4B 91.981 2257 157 15 1 2253 551060038 551062274 0.000000e+00 3144.0
8 TraesCS7D01G178700 chr2B 92.192 2203 156 15 1 2192 549352846 549355043 0.000000e+00 3101.0
9 TraesCS7D01G178700 chr6B 92.670 2142 152 5 1 2139 181111563 181109424 0.000000e+00 3081.0
10 TraesCS7D01G178700 chr5B 92.115 2194 153 13 1 2186 506965544 506967725 0.000000e+00 3075.0
11 TraesCS7D01G178700 chr3B 86.343 1545 147 33 741 2264 103209534 103211035 0.000000e+00 1626.0
12 TraesCS7D01G178700 chr3B 81.933 238 41 2 2029 2264 103211056 103210819 1.370000e-47 200.0
13 TraesCS7D01G178700 chr3B 80.631 222 33 7 2034 2253 420919100 420918887 1.800000e-36 163.0


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 TraesCS7D01G178700 chr7D 131689395 131691658 2263 False 4181 4181 100.000 1 2264 1 chr7D.!!$F1 2263
1 TraesCS7D01G178700 chr7D 528561188 528563338 2150 False 3312 3312 94.470 1 2149 1 chr7D.!!$F2 2148
2 TraesCS7D01G178700 chrUn 10399174 10401328 2154 False 3502 3502 96.015 1 2153 1 chrUn.!!$F1 2152
3 TraesCS7D01G178700 chr4D 470194380 470196637 2257 True 3325 3325 93.319 1 2249 1 chr4D.!!$R1 2248
4 TraesCS7D01G178700 chr2D 619853632 619855785 2153 False 3301 3301 94.347 1 2152 1 chr2D.!!$F1 2151
5 TraesCS7D01G178700 chr6D 377212206 377214155 1949 False 3223 3223 96.513 1 1948 1 chr6D.!!$F1 1947
6 TraesCS7D01G178700 chr4B 551060038 551062274 2236 False 3144 3144 91.981 1 2253 1 chr4B.!!$F1 2252
7 TraesCS7D01G178700 chr2B 549352846 549355043 2197 False 3101 3101 92.192 1 2192 1 chr2B.!!$F1 2191
8 TraesCS7D01G178700 chr6B 181109424 181111563 2139 True 3081 3081 92.670 1 2139 1 chr6B.!!$R1 2138
9 TraesCS7D01G178700 chr5B 506965544 506967725 2181 False 3075 3075 92.115 1 2186 1 chr5B.!!$F1 2185
10 TraesCS7D01G178700 chr3B 103209534 103211035 1501 False 1626 1626 86.343 741 2264 1 chr3B.!!$F1 1523

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
793 795 0.039911 ACGTGGAGGAAGGACTAGCT 59.96 55.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2160 0.815615 GGCGGTAGGCTTTGATCCTG 60.816 60.0 0.0 0.0 42.94 3.86 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
66 67 3.945285 GGATTGGCGAAAAGATGGACTAA 59.055 43.478 0.00 0.00 0.00 2.24
254 255 1.498865 CGTTGGTGCCAGTGTGAGAC 61.499 60.000 0.00 0.00 0.00 3.36
468 469 0.752658 CAGATCCCGCACTCATGGTA 59.247 55.000 0.00 0.00 0.00 3.25
651 652 3.630312 GCAAGAAACCTAGAACCAACACA 59.370 43.478 0.00 0.00 0.00 3.72
677 678 0.391597 AGTCAAACACGTGGACGGAT 59.608 50.000 21.57 0.00 44.95 4.18
751 752 2.352805 GTGGCTGTGGAGGAAGGG 59.647 66.667 0.00 0.00 0.00 3.95
774 776 3.636231 CTTGGAGGTGGCCGTGGA 61.636 66.667 0.00 0.00 0.00 4.02
793 795 0.039911 ACGTGGAGGAAGGACTAGCT 59.960 55.000 0.00 0.00 0.00 3.32
804 806 0.914902 GGACTAGCTTTGGAGGGGGT 60.915 60.000 0.00 0.00 0.00 4.95
959 961 9.884465 GATATATTTGCCTCTTTACATGTCAAC 57.116 33.333 0.00 0.00 0.00 3.18
1081 1085 1.072331 AGTGGAAGGACGCATCTTTGT 59.928 47.619 0.00 0.00 0.00 2.83
1245 1249 3.467803 GCTTCCAACTAACGCCTATGAT 58.532 45.455 0.00 0.00 0.00 2.45
1357 1361 4.760530 TGCAAGTACTTCAGCTGGATAT 57.239 40.909 15.13 0.00 0.00 1.63
1511 1515 2.363018 CGAGGAGGAGAGGGCACA 60.363 66.667 0.00 0.00 0.00 4.57
1611 1615 3.593442 TGTGACAAGAAGGGGAAATGT 57.407 42.857 0.00 0.00 0.00 2.71
1747 1768 6.196353 CGTGAACTTGTCGTGAATGAATTTTT 59.804 34.615 0.00 0.00 0.00 1.94
1830 1852 6.128200 TGTCAGCATATTCTGTGATTTGTCAC 60.128 38.462 2.21 1.76 40.78 3.67
1909 1933 6.587608 AGAGTGCTCTGTTTTCAAAGTTTTTG 59.412 34.615 0.28 0.00 38.75 2.44
2027 2170 0.383231 GAATGGCGGCAGGATCAAAG 59.617 55.000 19.29 0.00 0.00 2.77
2072 2215 1.883084 GTTGCAGGATCCTACCGCG 60.883 63.158 15.67 0.00 34.24 6.46
2110 2257 1.327303 GGGGCAAACATTCTGTGACA 58.673 50.000 0.00 0.00 0.00 3.58
2124 2271 2.295349 CTGTGACAAGGAAAGCAAGCAT 59.705 45.455 0.00 0.00 0.00 3.79
2153 2301 2.995547 GGTTGACCCTACCGCCAT 59.004 61.111 0.00 0.00 0.00 4.40
2154 2302 1.301954 GGTTGACCCTACCGCCATT 59.698 57.895 0.00 0.00 0.00 3.16
2202 2353 0.320374 CCAGGGTGCTCGTGTTTCTA 59.680 55.000 0.00 0.00 0.00 2.10
2211 2362 3.255888 TGCTCGTGTTTCTAGTCACAGAT 59.744 43.478 12.78 0.00 34.66 2.90
2213 2364 4.799678 CTCGTGTTTCTAGTCACAGATGT 58.200 43.478 12.78 0.00 34.66 3.06
2216 2367 5.462068 TCGTGTTTCTAGTCACAGATGTTTG 59.538 40.000 12.78 0.00 34.66 2.93
2217 2368 5.234329 CGTGTTTCTAGTCACAGATGTTTGT 59.766 40.000 12.78 0.00 34.66 2.83
2254 2407 2.842936 CCGGGCGGTAGGATCCTT 60.843 66.667 22.03 4.11 0.00 3.36
2255 2408 2.440817 CCGGGCGGTAGGATCCTTT 61.441 63.158 22.03 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.436704 CCGTGCTTTCAGAATGCTTTAGA 59.563 43.478 18.99 0.00 34.76 2.10
169 170 2.824880 CCCTTGTTGTCCCACCCGA 61.825 63.158 0.00 0.00 0.00 5.14
254 255 1.202177 GCCAATGATACTTGTGTGGCG 60.202 52.381 0.00 0.00 41.87 5.69
318 319 0.461163 CCGTTGTGCCATCGGATACA 60.461 55.000 15.50 0.00 46.01 2.29
468 469 4.354208 TCTTCTTCTTCCCCTCATAGGT 57.646 45.455 0.00 0.00 31.93 3.08
651 652 1.540363 CCACGTGTTTGACTAGTGCCT 60.540 52.381 15.65 0.00 0.00 4.75
677 678 2.683916 CCACCTCCAAGGCTAGTCA 58.316 57.895 0.00 0.00 39.63 3.41
739 740 1.995626 GGCTAGCCCTTCCTCCACA 60.996 63.158 24.19 0.00 0.00 4.17
774 776 0.039911 AGCTAGTCCTTCCTCCACGT 59.960 55.000 0.00 0.00 0.00 4.49
793 795 2.448931 ACCACGACCCCCTCCAAA 60.449 61.111 0.00 0.00 0.00 3.28
804 806 3.445687 CCGGATCCACGACCACGA 61.446 66.667 13.41 0.00 42.66 4.35
959 961 9.825972 AAGATGTTAAGTCAAAATATGAACACG 57.174 29.630 0.00 0.00 40.50 4.49
1081 1085 5.306937 TCACATCTTTCTCCTTCACCTTGTA 59.693 40.000 0.00 0.00 0.00 2.41
1245 1249 2.092049 TCTCTAGCATACCGGTGGAAGA 60.092 50.000 19.93 13.86 31.64 2.87
1357 1361 7.289310 TGGATATCTTTTGGCACTTCATGATA 58.711 34.615 2.05 0.00 0.00 2.15
1564 1568 1.073722 CCTCCTCTTGTGCCTTGCA 59.926 57.895 0.00 0.00 35.60 4.08
1611 1615 2.429610 GCTTTACTGAGTCATACGGGGA 59.570 50.000 0.00 0.00 0.00 4.81
1747 1768 8.202811 TCTTCACACCAAATTCAATTCAAATGA 58.797 29.630 0.00 0.00 0.00 2.57
1830 1852 7.379529 AGCACAACAGTTTTTCAATAAGAATCG 59.620 33.333 0.00 0.00 35.83 3.34
1901 1925 1.133730 TGGCGGTAGGGTCAAAAACTT 60.134 47.619 0.00 0.00 0.00 2.66
1909 1933 4.468689 GCCTGTGGCGGTAGGGTC 62.469 72.222 4.07 0.00 39.62 4.46
1936 2077 2.822399 GGTAGGGTCCAGCATCCG 59.178 66.667 0.00 0.00 0.00 4.18
2017 2160 0.815615 GGCGGTAGGCTTTGATCCTG 60.816 60.000 0.00 0.00 42.94 3.86
2027 2170 4.840005 GAGGCTGTGGCGGTAGGC 62.840 72.222 0.00 0.00 44.11 3.93
2110 2257 1.553706 CCAGGATGCTTGCTTTCCTT 58.446 50.000 12.62 0.71 37.80 3.36
2124 2271 2.120940 TCAACCCTACCGCCAGGA 59.879 61.111 0.00 0.00 41.02 3.86
2153 2301 1.691337 ACCCTACCGCCATAGCCAA 60.691 57.895 0.00 0.00 34.57 4.52
2154 2302 2.041301 ACCCTACCGCCATAGCCA 60.041 61.111 0.00 0.00 34.57 4.75
2202 2353 1.073923 GGGGGACAAACATCTGTGACT 59.926 52.381 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.