Multiple sequence alignment - TraesCS1D01G043100

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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 TraesCS1D01G043100 chr1D 100.000 3063 0 0 1 3063 22167116 22170178 0.000000e+00 5657.0
1 TraesCS1D01G043100 chr1D 87.373 491 51 6 1 482 374638453 374637965 1.240000e-153 553.0
2 TraesCS1D01G043100 chr6A 95.427 3083 110 14 1 3063 90084749 90087820 0.000000e+00 4883.0
3 TraesCS1D01G043100 chr6A 95.742 2325 68 11 759 3063 10051206 10048893 0.000000e+00 3716.0
4 TraesCS1D01G043100 chr6A 84.071 226 26 6 7 228 58006196 58005977 3.090000e-50 209.0
5 TraesCS1D01G043100 chr1A 95.656 2325 79 8 759 3063 336239220 336236898 0.000000e+00 3714.0
6 TraesCS1D01G043100 chr1A 94.948 2019 72 10 1064 3063 320272196 320270189 0.000000e+00 3136.0
7 TraesCS1D01G043100 chr1A 96.825 315 8 2 759 1073 320287147 320286835 2.710000e-145 525.0
8 TraesCS1D01G043100 chr1A 87.166 187 20 4 7 189 320288162 320287976 3.090000e-50 209.0
9 TraesCS1D01G043100 chr7A 92.283 2216 141 13 873 3063 148015683 148013473 0.000000e+00 3118.0
10 TraesCS1D01G043100 chr7A 95.643 1446 41 10 759 2183 6709548 6710992 0.000000e+00 2302.0
11 TraesCS1D01G043100 chr7A 97.169 883 24 1 2181 3063 6745808 6746689 0.000000e+00 1491.0
12 TraesCS1D01G043100 chr7A 87.166 187 20 3 7 189 518745899 518745713 3.090000e-50 209.0
13 TraesCS1D01G043100 chr4D 91.939 2233 135 17 873 3063 278206176 278203947 0.000000e+00 3085.0
14 TraesCS1D01G043100 chr4D 93.451 1588 76 9 874 2434 150016582 150018168 0.000000e+00 2331.0
15 TraesCS1D01G043100 chr4D 93.280 997 60 2 874 1864 43327274 43328269 0.000000e+00 1463.0
16 TraesCS1D01G043100 chr4D 96.167 600 23 0 2464 3063 150018166 150018765 0.000000e+00 981.0
17 TraesCS1D01G043100 chr5B 89.793 1499 107 20 752 2225 607045082 607046559 0.000000e+00 1879.0
18 TraesCS1D01G043100 chr5B 89.148 1502 114 21 752 2225 607101917 607103397 0.000000e+00 1825.0
19 TraesCS1D01G043100 chr5B 84.375 224 26 4 8 228 607044227 607044444 8.600000e-51 211.0
20 TraesCS1D01G043100 chr5A 92.180 1330 78 8 874 2177 605326668 605325339 0.000000e+00 1857.0
21 TraesCS1D01G043100 chr5A 95.695 604 21 1 2465 3063 605325110 605324507 0.000000e+00 966.0
22 TraesCS1D01G043100 chr3B 82.888 1198 161 30 1513 2689 32012666 32013840 0.000000e+00 1037.0
23 TraesCS1D01G043100 chr3B 88.290 538 53 6 1 529 812652131 812651595 1.200000e-178 636.0
24 TraesCS1D01G043100 chr3B 83.036 224 29 4 8 228 802579930 802580147 8.670000e-46 195.0
25 TraesCS1D01G043100 chr6D 87.050 888 91 17 2180 3063 341372435 341373302 0.000000e+00 981.0
26 TraesCS1D01G043100 chr3D 90.056 714 41 12 9 719 554337529 554336843 0.000000e+00 898.0
27 TraesCS1D01G043100 chr4B 94.286 35 2 0 595 629 508075534 508075568 2.000000e-03 54.7


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 TraesCS1D01G043100 chr1D 22167116 22170178 3062 False 5657.0 5657 100.0000 1 3063 1 chr1D.!!$F1 3062
1 TraesCS1D01G043100 chr6A 90084749 90087820 3071 False 4883.0 4883 95.4270 1 3063 1 chr6A.!!$F1 3062
2 TraesCS1D01G043100 chr6A 10048893 10051206 2313 True 3716.0 3716 95.7420 759 3063 1 chr6A.!!$R1 2304
3 TraesCS1D01G043100 chr1A 336236898 336239220 2322 True 3714.0 3714 95.6560 759 3063 1 chr1A.!!$R2 2304
4 TraesCS1D01G043100 chr1A 320270189 320272196 2007 True 3136.0 3136 94.9480 1064 3063 1 chr1A.!!$R1 1999
5 TraesCS1D01G043100 chr1A 320286835 320288162 1327 True 367.0 525 91.9955 7 1073 2 chr1A.!!$R3 1066
6 TraesCS1D01G043100 chr7A 148013473 148015683 2210 True 3118.0 3118 92.2830 873 3063 1 chr7A.!!$R1 2190
7 TraesCS1D01G043100 chr7A 6709548 6710992 1444 False 2302.0 2302 95.6430 759 2183 1 chr7A.!!$F1 1424
8 TraesCS1D01G043100 chr7A 6745808 6746689 881 False 1491.0 1491 97.1690 2181 3063 1 chr7A.!!$F2 882
9 TraesCS1D01G043100 chr4D 278203947 278206176 2229 True 3085.0 3085 91.9390 873 3063 1 chr4D.!!$R1 2190
10 TraesCS1D01G043100 chr4D 150016582 150018765 2183 False 1656.0 2331 94.8090 874 3063 2 chr4D.!!$F2 2189
11 TraesCS1D01G043100 chr4D 43327274 43328269 995 False 1463.0 1463 93.2800 874 1864 1 chr4D.!!$F1 990
12 TraesCS1D01G043100 chr5B 607101917 607103397 1480 False 1825.0 1825 89.1480 752 2225 1 chr5B.!!$F1 1473
13 TraesCS1D01G043100 chr5B 607044227 607046559 2332 False 1045.0 1879 87.0840 8 2225 2 chr5B.!!$F2 2217
14 TraesCS1D01G043100 chr5A 605324507 605326668 2161 True 1411.5 1857 93.9375 874 3063 2 chr5A.!!$R1 2189
15 TraesCS1D01G043100 chr3B 32012666 32013840 1174 False 1037.0 1037 82.8880 1513 2689 1 chr3B.!!$F1 1176
16 TraesCS1D01G043100 chr3B 812651595 812652131 536 True 636.0 636 88.2900 1 529 1 chr3B.!!$R1 528
17 TraesCS1D01G043100 chr6D 341372435 341373302 867 False 981.0 981 87.0500 2180 3063 1 chr6D.!!$F1 883
18 TraesCS1D01G043100 chr3D 554336843 554337529 686 True 898.0 898 90.0560 9 719 1 chr3D.!!$R1 710

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
85 86 0.106015 TCATCCTCCCTCATCGCTCA 60.106 55.0 0.0 0.0 0.00 4.26 F
510 829 0.107831 TGATGGCCCGTATGTTAGCC 59.892 55.0 0.0 0.0 45.96 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1133 1506 1.067565 CACTCTTCAACCGCTGCTCTA 60.068 52.381 0.00 0.0 0.00 2.43 R
2248 2667 1.239347 GAAAGGAACTGGAGTGCCAC 58.761 55.000 6.58 0.0 46.68 5.01 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
85 86 0.106015 TCATCCTCCCTCATCGCTCA 60.106 55.000 0.00 0.00 0.00 4.26
163 168 1.524621 GCATGCCGCTGGTATCTGT 60.525 57.895 6.36 0.00 37.77 3.41
171 176 1.897423 CTGGTATCTGTGGACGGCA 59.103 57.895 0.00 0.00 0.00 5.69
459 742 3.989817 GCGATTTTGCTGTTTTCCATTCT 59.010 39.130 0.00 0.00 0.00 2.40
510 829 0.107831 TGATGGCCCGTATGTTAGCC 59.892 55.000 0.00 0.00 45.96 3.93
578 897 0.546747 AGGAGACGGGGATGGTTTGA 60.547 55.000 0.00 0.00 0.00 2.69
676 1005 0.742281 CCCTGTGCTGATTCTGGTCG 60.742 60.000 0.00 0.00 0.00 4.79
683 1012 1.539929 GCTGATTCTGGTCGGATCCTG 60.540 57.143 10.75 3.62 0.00 3.86
937 1310 2.888594 CTGATGCATTTTGCTTCCCAG 58.111 47.619 0.00 0.00 44.13 4.45
1152 1525 1.257743 TAGAGCAGCGGTTGAAGAGT 58.742 50.000 0.00 0.00 0.00 3.24
1289 1677 4.917906 AGTGGAGATACAAAGCTTTCCT 57.082 40.909 9.23 4.26 0.00 3.36
1303 1691 7.121315 ACAAAGCTTTCCTTTACTATGATGACC 59.879 37.037 9.23 0.00 41.75 4.02
1393 1783 9.595823 GCTTGTAGTTTACAATGTATTCCTCTA 57.404 33.333 0.00 0.00 46.51 2.43
1428 1818 1.905512 CGGAGGGGAAGGGTTGTAG 59.094 63.158 0.00 0.00 0.00 2.74
1437 1827 2.576648 GGAAGGGTTGTAGGAGGACAAT 59.423 50.000 0.00 0.00 41.21 2.71
1579 1969 6.260936 CAGGCTTTGAAGGTCATAATTACGAT 59.739 38.462 0.00 0.00 0.00 3.73
1604 1994 4.284490 GGACTGAAGGCATATATGGTGAGA 59.716 45.833 14.51 0.00 0.00 3.27
1605 1995 5.477510 GACTGAAGGCATATATGGTGAGAG 58.522 45.833 14.51 0.00 0.00 3.20
1951 2361 4.652421 TCTCTCAGCAAGTGATCATCTC 57.348 45.455 0.00 0.00 33.51 2.75
2248 2667 8.567948 TGTCTCAGCTCTAAACTTTTATTTTGG 58.432 33.333 0.00 0.00 0.00 3.28
2450 2872 4.214332 TGACGCACTAATATTTGTTGCACA 59.786 37.500 17.27 14.44 0.00 4.57
2647 3074 6.153680 CCTGGAGATACTCACAGTAGTCTTTT 59.846 42.308 0.00 0.00 33.66 2.27
2769 3196 8.939932 TGGAATATCAACTATATGTGTTGGGTA 58.060 33.333 17.51 13.09 43.36 3.69
2806 3233 0.386731 GGTCAAACCATTGTTCGCCG 60.387 55.000 0.00 0.00 38.42 6.46
2867 3294 6.484643 ACATGCTATGACAATATCAGGTTGAC 59.515 38.462 0.00 0.00 41.91 3.18
2873 3300 6.990341 TGACAATATCAGGTTGACATTCAG 57.010 37.500 0.00 0.00 31.91 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.757355 CCTTTCCCATGGCCGCCA 62.757 66.667 16.17 16.17 38.19 5.69
18 19 2.162681 CCATTGCCGTCTCTTTCCTTT 58.837 47.619 0.00 0.00 0.00 3.11
171 176 2.202703 GAGGTTATGCGTCGCGGT 60.203 61.111 13.38 6.45 0.00 5.68
304 309 0.604578 GCCAGTGCCAATTGTGATGT 59.395 50.000 4.43 0.00 0.00 3.06
400 410 0.099968 CAGACAAATCATGCGGGCTG 59.900 55.000 0.00 0.00 0.00 4.85
547 866 3.442977 CCCCGTCTCCTAGTTATAATCCG 59.557 52.174 0.00 0.00 0.00 4.18
937 1310 4.201950 TGCTCTCTTTTTCTTGTCTGCAAC 60.202 41.667 0.00 0.00 0.00 4.17
1021 1394 6.566079 TCCATTCTGACCATGAAATCTAGT 57.434 37.500 0.00 0.00 0.00 2.57
1031 1404 2.118679 TCGTCCATCCATTCTGACCAT 58.881 47.619 0.00 0.00 0.00 3.55
1133 1506 1.067565 CACTCTTCAACCGCTGCTCTA 60.068 52.381 0.00 0.00 0.00 2.43
1289 1677 4.779696 TGCATGCAGGTCATCATAGTAAA 58.220 39.130 18.46 0.00 31.79 2.01
1303 1691 4.913345 CGTACCATCATAAATTGCATGCAG 59.087 41.667 21.50 8.30 0.00 4.41
1393 1783 1.910671 TCCGCTGTTTTACCTGGGTAT 59.089 47.619 0.00 0.00 0.00 2.73
1428 1818 3.420893 TCAACCACATCAATTGTCCTCC 58.579 45.455 5.13 0.00 36.00 4.30
1437 1827 4.141505 TGGACTTCTCTTCAACCACATCAA 60.142 41.667 0.00 0.00 0.00 2.57
1579 1969 4.411869 TCACCATATATGCCTTCAGTCCAA 59.588 41.667 7.24 0.00 0.00 3.53
1604 1994 6.597562 TGTTACCAGGAAATACTTCAACACT 58.402 36.000 0.00 0.00 32.75 3.55
1605 1995 6.870971 TGTTACCAGGAAATACTTCAACAC 57.129 37.500 0.00 0.00 32.75 3.32
1879 2275 5.759273 GCAATTGGCAATGCAATAAGGATTA 59.241 36.000 14.47 0.00 43.97 1.75
1880 2276 4.577283 GCAATTGGCAATGCAATAAGGATT 59.423 37.500 14.47 0.00 43.97 3.01
1951 2361 6.640499 GTCCTTTCAGATACTCGATCATCTTG 59.360 42.308 6.25 3.97 36.98 3.02
2248 2667 1.239347 GAAAGGAACTGGAGTGCCAC 58.761 55.000 6.58 0.00 46.68 5.01
2769 3196 1.341080 CCAGGTTGGCTCCAATGTTT 58.659 50.000 4.47 0.00 38.28 2.83
2772 3199 0.251297 TGACCAGGTTGGCTCCAATG 60.251 55.000 4.47 0.30 42.67 2.82
2806 3233 1.295792 TTATTCGCAATCACGAGGGC 58.704 50.000 0.00 0.00 44.00 5.19
2867 3294 4.218200 TGCTTCACATTACCCAACTGAATG 59.782 41.667 0.00 0.00 36.77 2.67
2873 3300 2.884639 AGTGTGCTTCACATTACCCAAC 59.115 45.455 13.23 0.00 46.32 3.77


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

AutoCloner maintained by Alex Coulton.