Multiple sequence alignment - TraesCS7A01G059800

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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 TraesCS7A01G059800 chr7A 100.000 3919 0 0 1 3919 29108357 29112275 0.000000e+00 7238
1 TraesCS7A01G059800 chr7A 85.856 3033 342 52 1 2982 29031041 29034037 0.000000e+00 3144
2 TraesCS7A01G059800 chr7A 88.816 304 23 6 188 483 29034025 29034325 2.880000e-96 363
3 TraesCS7A01G059800 chr7D 96.430 2913 76 11 933 3823 28695546 28698452 0.000000e+00 4778
4 TraesCS7A01G059800 chr7D 87.020 2866 300 39 917 3740 28673554 28676389 0.000000e+00 3166
5 TraesCS7A01G059800 chr7D 94.639 914 34 6 1 901 28694403 28695314 0.000000e+00 1402
6 TraesCS7A01G059800 chr7D 84.226 672 73 18 237 895 28672553 28673204 1.200000e-174 623
7 TraesCS7A01G059800 chr7D 85.799 169 22 2 146 313 28683736 28683903 1.120000e-40 178
8 TraesCS7A01G059800 chr7D 97.917 96 1 1 3823 3917 28698514 28698609 8.710000e-37 165
9 TraesCS7A01G059800 chr4A 93.753 2417 96 19 1452 3823 701313074 701310668 0.000000e+00 3576
10 TraesCS7A01G059800 chr4A 84.822 2161 260 33 1670 3782 702398791 702400931 0.000000e+00 2111
11 TraesCS7A01G059800 chr4A 85.723 1590 182 28 603 2182 702379402 702380956 0.000000e+00 1637
12 TraesCS7A01G059800 chr4A 84.373 1363 151 28 2176 3506 702381010 702382342 0.000000e+00 1280
13 TraesCS7A01G059800 chr4A 83.672 1280 132 36 1 1247 702397569 702398804 0.000000e+00 1134
14 TraesCS7A01G059800 chr4A 82.655 1326 175 37 745 2032 702503744 702505052 0.000000e+00 1123
15 TraesCS7A01G059800 chr4A 85.089 1120 141 13 2217 3321 702339890 702340998 0.000000e+00 1120
16 TraesCS7A01G059800 chr4A 84.970 845 115 5 2217 3051 702505158 702506000 0.000000e+00 846
17 TraesCS7A01G059800 chr4A 88.344 652 67 5 1 646 702337609 702338257 0.000000e+00 774
18 TraesCS7A01G059800 chr4A 92.609 460 33 1 926 1384 701313533 701313074 0.000000e+00 660
19 TraesCS7A01G059800 chr4A 87.589 564 65 3 1 560 702383527 702384089 0.000000e+00 649
20 TraesCS7A01G059800 chr4A 88.994 527 27 5 388 905 701314422 701313918 1.200000e-174 623
21 TraesCS7A01G059800 chr4A 81.405 726 88 15 3041 3740 702508020 702508724 2.060000e-152 549
22 TraesCS7A01G059800 chr4A 83.871 372 45 7 237 602 702378995 702379357 1.350000e-89 340
23 TraesCS7A01G059800 chr4A 95.146 206 9 1 184 389 701314942 701314738 1.360000e-84 324
24 TraesCS7A01G059800 chr4A 96.407 167 6 0 1 167 701315094 701314928 3.860000e-70 276
25 TraesCS7A01G059800 chr4A 83.750 160 14 7 741 889 702338281 702338439 1.470000e-29 141
26 TraesCS7A01G059800 chr4A 93.151 73 4 1 3823 3894 701310606 701310534 5.360000e-19 106


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 TraesCS7A01G059800 chr7A 29108357 29112275 3918 False 7238.000000 7238 100.000000 1 3919 1 chr7A.!!$F1 3918
1 TraesCS7A01G059800 chr7A 29031041 29034325 3284 False 1753.500000 3144 87.336000 1 2982 2 chr7A.!!$F2 2981
2 TraesCS7A01G059800 chr7D 28694403 28698609 4206 False 2115.000000 4778 96.328667 1 3917 3 chr7D.!!$F3 3916
3 TraesCS7A01G059800 chr7D 28672553 28676389 3836 False 1894.500000 3166 85.623000 237 3740 2 chr7D.!!$F2 3503
4 TraesCS7A01G059800 chr4A 702397569 702400931 3362 False 1622.500000 2111 84.247000 1 3782 2 chr4A.!!$F3 3781
5 TraesCS7A01G059800 chr4A 702378995 702384089 5094 False 976.500000 1637 85.389000 1 3506 4 chr4A.!!$F2 3505
6 TraesCS7A01G059800 chr4A 701310534 701315094 4560 True 927.500000 3576 93.343333 1 3894 6 chr4A.!!$R1 3893
7 TraesCS7A01G059800 chr4A 702503744 702508724 4980 False 839.333333 1123 83.010000 745 3740 3 chr4A.!!$F4 2995
8 TraesCS7A01G059800 chr4A 702337609 702340998 3389 False 678.333333 1120 85.727667 1 3321 3 chr4A.!!$F1 3320

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
315 343 4.019919 CAACAGGTGGAAAATAGATGCG 57.98 45.455 0.0 0.0 0.0 4.73 F
1248 2032 1.089920 GCTCGATGATGTGGTTTGCT 58.91 50.000 0.0 0.0 0.0 3.91 F
2608 3603 1.869767 CCGAGCAGCCATACTTTCATC 59.13 52.381 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1627 2485 2.348472 TGGGAGAAACCTCACAATCCT 58.652 47.619 0.0 0.0 40.85 3.24 R
2742 3750 0.467384 AATCCCATCTCACCTCTGCG 59.533 55.000 0.0 0.0 0.00 5.18 R
3485 6564 1.001633 GTGTTGTCTACGGGTCACCAT 59.998 52.381 0.0 0.0 36.13 3.55 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
118 143 7.429633 AGTTGGAAGATATAGATGTTGAGTCG 58.570 38.462 0.00 0.00 0.00 4.18
235 260 8.145316 TGGTAATAGCATTCCACGTAATTAAC 57.855 34.615 0.00 0.00 0.00 2.01
315 343 4.019919 CAACAGGTGGAAAATAGATGCG 57.980 45.455 0.00 0.00 0.00 4.73
540 893 5.180271 GTTCCCCAACAATAGTTATCGACA 58.820 41.667 0.00 0.00 35.85 4.35
564 917 4.149598 AGTGGGAAAGGTGGTTACAAATC 58.850 43.478 0.00 0.00 0.00 2.17
631 1028 7.800092 AGAGGAACTTAAGTTGAGATATGCAT 58.200 34.615 25.17 3.79 41.55 3.96
796 1198 8.124199 TCAACACAAAATTAACCTTCTCGTAAC 58.876 33.333 0.00 0.00 0.00 2.50
834 1247 4.463879 CCCTGCCTCGCTCCACTG 62.464 72.222 0.00 0.00 0.00 3.66
1075 1859 7.965107 CCATTGAATCTTTGTACAAAGCTAGAC 59.035 37.037 33.93 23.75 45.48 2.59
1165 1949 5.329399 TGTGAATAAGTGCCCAACCTTAAT 58.671 37.500 0.00 0.00 0.00 1.40
1223 2007 4.794169 AGCCGTCAATTTATTGTGTGTTC 58.206 39.130 2.66 0.00 38.84 3.18
1248 2032 1.089920 GCTCGATGATGTGGTTTGCT 58.910 50.000 0.00 0.00 0.00 3.91
1264 2048 6.208007 GTGGTTTGCTTTTTACTACAGGGTAT 59.792 38.462 0.00 0.00 0.00 2.73
1486 2341 5.392767 TTTGTTGGCAGTTTGAGTTAACA 57.607 34.783 8.61 0.00 0.00 2.41
2435 3430 2.112815 GCGAAAAGGGTGCCGCTAT 61.113 57.895 0.00 0.00 43.75 2.97
2608 3603 1.869767 CCGAGCAGCCATACTTTCATC 59.130 52.381 0.00 0.00 0.00 2.92
2815 3823 4.202141 TGTGGAGCAATTGGAAAAACAGAG 60.202 41.667 7.72 0.00 0.00 3.35
3198 6257 7.112528 TGTGAAAGCTACACTGTTTATTACG 57.887 36.000 19.65 0.00 38.81 3.18
3313 6372 7.414098 GGTCCAAGCTGTATATTAACACAACTG 60.414 40.741 0.00 0.00 0.00 3.16
3444 6523 0.037877 ACTTCAGCCAGCTTGCATCT 59.962 50.000 12.92 0.00 0.00 2.90
3917 8064 9.500785 CCATTTTTACACTCCATTTTGGTAATT 57.499 29.630 0.00 0.00 39.03 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 143 6.655003 TCTCGATAATCTGGGATAAATTTGCC 59.345 38.462 0.00 2.16 0.00 4.52
309 337 7.681065 GCCATTGGTAAAATAACTTACGCATCT 60.681 37.037 4.26 0.00 33.36 2.90
540 893 5.327737 TTTGTAACCACCTTTCCCACTAT 57.672 39.130 0.00 0.00 0.00 2.12
834 1247 0.653636 TCACTTTGTCGTGTTTCGGC 59.346 50.000 0.00 0.00 45.13 5.54
972 1749 1.587054 GCTGAGAGCACACCTACGT 59.413 57.895 0.00 0.00 41.89 3.57
1165 1949 9.330063 GCATTGCCAGCTACATAGATTTATATA 57.670 33.333 0.00 0.00 0.00 0.86
1248 2032 8.387813 ACCAAATCTCATACCCTGTAGTAAAAA 58.612 33.333 0.00 0.00 0.00 1.94
1264 2048 4.792068 AGTTCTGAACCAACCAAATCTCA 58.208 39.130 16.48 0.00 0.00 3.27
1486 2341 5.203528 AGCACATACTATTCATTTGCCCTT 58.796 37.500 0.00 0.00 30.96 3.95
1627 2485 2.348472 TGGGAGAAACCTCACAATCCT 58.652 47.619 0.00 0.00 40.85 3.24
1633 2491 3.562182 TCCTTTTTGGGAGAAACCTCAC 58.438 45.455 0.00 0.00 38.98 3.51
1945 2843 8.324306 AGTGGTATTGCTGCATTACATAGATAT 58.676 33.333 26.53 8.64 0.00 1.63
1967 2865 4.144297 TGTTTCCTCTCAAATTCCAGTGG 58.856 43.478 1.40 1.40 0.00 4.00
2408 3403 2.556287 CCTTTTCGCGACTGTGCC 59.444 61.111 9.15 0.00 0.00 5.01
2435 3430 2.363018 CCGGCTCTCTCTGGGTCA 60.363 66.667 0.00 0.00 0.00 4.02
2608 3603 1.886313 CAGCTGCGGCATAGACCAG 60.886 63.158 21.93 0.00 41.70 4.00
2742 3750 0.467384 AATCCCATCTCACCTCTGCG 59.533 55.000 0.00 0.00 0.00 5.18
2815 3823 1.222936 CACCACCTCAGCCTCCATC 59.777 63.158 0.00 0.00 0.00 3.51
3198 6257 7.704899 ACAACTTTTGTTCCATAGTTAGCAAAC 59.295 33.333 0.00 0.00 42.22 2.93
3483 6562 3.101437 TGTTGTCTACGGGTCACCATAT 58.899 45.455 0.00 0.00 36.13 1.78
3485 6564 1.001633 GTGTTGTCTACGGGTCACCAT 59.998 52.381 0.00 0.00 36.13 3.55


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

AutoCloner maintained by Alex Coulton.