Multiple sequence alignment - TraesCS7D01G275000

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 TraesCS7D01G275000 chr7D 100.000 2330 0 0 1 2330 264328217 264325888 0.000000e+00 4303
1 TraesCS7D01G275000 chr7D 92.512 1843 109 25 491 2316 264362567 264360737 0.000000e+00 2612
2 TraesCS7D01G275000 chr7D 92.452 1603 101 17 652 2246 264340339 264338749 0.000000e+00 2272
3 TraesCS7D01G275000 chr7D 93.040 1523 80 22 809 2318 264372117 264370608 0.000000e+00 2202
4 TraesCS7D01G275000 chr7D 85.201 473 44 10 4 462 264344830 264344370 1.630000e-126 462
5 TraesCS7D01G275000 chr7A 95.290 1656 58 7 652 2288 287891134 287889480 0.000000e+00 2608
6 TraesCS7D01G275000 chr7A 95.755 1013 42 1 492 1504 287863660 287862649 0.000000e+00 1631
7 TraesCS7D01G275000 chr7A 93.874 506 21 4 1 498 287864193 287863690 0.000000e+00 754
8 TraesCS7D01G275000 chr7A 85.169 472 46 10 4 462 287895602 287895142 1.630000e-126 462
9 TraesCS7D01G275000 chr7B 92.237 1842 113 27 493 2318 244646770 244644943 0.000000e+00 2582
10 TraesCS7D01G275000 chr7B 92.355 1622 96 23 702 2316 244694347 244692747 0.000000e+00 2283
11 TraesCS7D01G275000 chr7B 95.726 1357 58 0 652 2008 244652999 244651643 0.000000e+00 2185
12 TraesCS7D01G275000 chr7B 92.895 1520 83 21 809 2316 244717727 244716221 0.000000e+00 2185
13 TraesCS7D01G275000 chr7B 84.402 468 47 9 4 462 244657430 244656980 9.890000e-119 436
14 TraesCS7D01G275000 chr7B 93.651 252 15 1 2070 2321 244651644 244651394 2.190000e-100 375
15 TraesCS7D01G275000 chr7B 88.824 170 14 2 6 172 244654850 244654683 1.090000e-48 204


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 TraesCS7D01G275000 chr7D 264325888 264328217 2329 True 4303.0 4303 100.00000 1 2330 1 chr7D.!!$R1 2329
1 TraesCS7D01G275000 chr7D 264360737 264362567 1830 True 2612.0 2612 92.51200 491 2316 1 chr7D.!!$R4 1825
2 TraesCS7D01G275000 chr7D 264338749 264340339 1590 True 2272.0 2272 92.45200 652 2246 1 chr7D.!!$R2 1594
3 TraesCS7D01G275000 chr7D 264370608 264372117 1509 True 2202.0 2202 93.04000 809 2318 1 chr7D.!!$R5 1509
4 TraesCS7D01G275000 chr7A 287889480 287891134 1654 True 2608.0 2608 95.29000 652 2288 1 chr7A.!!$R1 1636
5 TraesCS7D01G275000 chr7A 287862649 287864193 1544 True 1192.5 1631 94.81450 1 1504 2 chr7A.!!$R3 1503
6 TraesCS7D01G275000 chr7B 244644943 244646770 1827 True 2582.0 2582 92.23700 493 2318 1 chr7B.!!$R1 1825
7 TraesCS7D01G275000 chr7B 244692747 244694347 1600 True 2283.0 2283 92.35500 702 2316 1 chr7B.!!$R2 1614
8 TraesCS7D01G275000 chr7B 244716221 244717727 1506 True 2185.0 2185 92.89500 809 2316 1 chr7B.!!$R3 1507
9 TraesCS7D01G275000 chr7B 244651394 244657430 6036 True 800.0 2185 90.65075 4 2321 4 chr7B.!!$R4 2317

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
650 4479 1.202879 TGGCCGTGAAGAAAATCTGGT 60.203 47.619 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 5999 0.168788 CAAGTAGCATGGGTTGTGCG 59.831 55.0 0.0 0.0 46.86 5.34 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
224 3436 5.655090 TCCAAACGATCTTACACATCCTCTA 59.345 40.000 0.00 0.00 0.00 2.43
226 3438 6.405953 CCAAACGATCTTACACATCCTCTACT 60.406 42.308 0.00 0.00 0.00 2.57
234 3446 4.232188 ACACATCCTCTACTAGGTTCGA 57.768 45.455 0.00 0.00 46.62 3.71
263 3475 2.432444 CCACCAATACAACGTGATGGT 58.568 47.619 0.00 0.00 44.95 3.55
307 3519 2.487762 CGCCACATGTCACCACTAAATT 59.512 45.455 0.00 0.00 0.00 1.82
311 3528 4.236935 CACATGTCACCACTAAATTTGGC 58.763 43.478 0.00 0.00 37.69 4.52
384 3601 7.632721 ACAACATTCAAAATCAAAACTGATGC 58.367 30.769 0.00 0.00 0.00 3.91
650 4479 1.202879 TGGCCGTGAAGAAAATCTGGT 60.203 47.619 0.00 0.00 0.00 4.00
744 4573 7.318141 CAAAATCATGAGATTAAGCAGGTGTT 58.682 34.615 0.09 0.00 43.52 3.32
771 4602 5.179368 GCAACGTGGCTACATTGATATACAT 59.821 40.000 13.47 0.00 0.00 2.29
784 4615 8.201464 ACATTGATATACATGGTACGAACAAGA 58.799 33.333 0.00 0.00 0.00 3.02
1263 5096 0.179936 CCATCCTGCAGTCCTCCTTC 59.820 60.000 13.81 0.00 0.00 3.46
1509 5342 2.596346 TGCTGGGAAGAGCAAATTTGA 58.404 42.857 22.31 0.00 46.05 2.69
1794 5627 6.374578 GTTTGATGTGTTTAGCCTTCTTCTC 58.625 40.000 0.00 0.00 0.00 2.87
2054 5889 9.347240 CTCTATTGGTGGATCTTGACATAATTT 57.653 33.333 0.00 0.00 0.00 1.82
2057 5892 5.964758 TGGTGGATCTTGACATAATTTTGC 58.035 37.500 0.00 0.00 0.00 3.68
2065 5917 6.389091 TCTTGACATAATTTTGCATGGTGTC 58.611 36.000 0.00 0.00 36.09 3.67
2141 5999 6.741992 TGATTTGAATAGGTGTGATGTGTC 57.258 37.500 0.00 0.00 0.00 3.67
2167 6025 0.454600 CCCATGCTACTTGCTTGCTG 59.545 55.000 0.00 0.00 43.09 4.41
2288 6148 4.574674 AACATGGCCATCTTGTAGAGAA 57.425 40.909 17.61 0.00 38.06 2.87
2294 6154 4.943705 TGGCCATCTTGTAGAGAAACATTC 59.056 41.667 0.00 0.00 38.06 2.67
2313 6173 4.364415 TTCCAAAACTCGGTTTGAACAG 57.636 40.909 8.90 0.00 40.29 3.16
2321 6181 4.563061 ACTCGGTTTGAACAGTATGGTAC 58.437 43.478 0.00 0.00 33.00 3.34
2322 6182 3.929094 TCGGTTTGAACAGTATGGTACC 58.071 45.455 4.43 4.43 33.00 3.34
2323 6183 3.324268 TCGGTTTGAACAGTATGGTACCA 59.676 43.478 18.99 18.99 33.00 3.25
2324 6184 4.066490 CGGTTTGAACAGTATGGTACCAA 58.934 43.478 20.76 5.65 33.00 3.67
2325 6185 4.153475 CGGTTTGAACAGTATGGTACCAAG 59.847 45.833 20.76 11.74 33.00 3.61
2326 6186 5.067954 GGTTTGAACAGTATGGTACCAAGT 58.932 41.667 20.76 12.40 33.00 3.16
2327 6187 5.533528 GGTTTGAACAGTATGGTACCAAGTT 59.466 40.000 20.76 19.72 33.00 2.66
2328 6188 6.040054 GGTTTGAACAGTATGGTACCAAGTTT 59.960 38.462 20.76 4.60 33.00 2.66
2329 6189 7.229106 GGTTTGAACAGTATGGTACCAAGTTTA 59.771 37.037 20.76 14.47 33.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
269 3481 2.919666 GCGTAAGGCATGTTCAACAT 57.080 45.000 0.00 0.00 42.87 2.71
601 4430 1.150827 GCCTGCCATTGCTTTGTTTC 58.849 50.000 0.00 0.00 38.71 2.78
650 4479 4.678574 GCTTGCAAATGGATAACATGCTGA 60.679 41.667 0.00 0.00 40.44 4.26
744 4573 1.276705 TCAATGTAGCCACGTTGCCTA 59.723 47.619 11.81 0.00 46.80 3.93
757 4586 9.471084 CTTGTTCGTACCATGTATATCAATGTA 57.529 33.333 0.00 0.00 0.00 2.29
763 4594 7.208080 ACCTTCTTGTTCGTACCATGTATATC 58.792 38.462 0.00 0.00 0.00 1.63
771 4602 4.942761 AACTACCTTCTTGTTCGTACCA 57.057 40.909 0.00 0.00 0.00 3.25
784 4615 1.134491 GCGCTGGTCCATAACTACCTT 60.134 52.381 0.00 0.00 36.67 3.50
1211 5044 1.519751 CGAGGCTAGGGAGATCACCG 61.520 65.000 2.87 0.00 0.00 4.94
1263 5096 2.854777 CGCGAAGAAGGTTACATCTGAG 59.145 50.000 0.00 0.00 0.00 3.35
1509 5342 1.927487 TCATGTGCCTTCCAAGCAAT 58.073 45.000 0.00 0.00 43.02 3.56
1627 5460 1.063183 AAGGTTGAAGAGGAGCTGCT 58.937 50.000 7.79 7.79 0.00 4.24
1794 5627 6.226787 CAGTTCCTCTGTATAAATAGGCCTG 58.773 44.000 17.99 0.00 39.17 4.85
1836 5669 5.762179 TGATTCCTTGTGTCTACCATTCT 57.238 39.130 0.00 0.00 0.00 2.40
2054 5889 0.687920 TCGGTTAGGACACCATGCAA 59.312 50.000 0.00 0.00 36.49 4.08
2057 5892 3.492656 CCATACTCGGTTAGGACACCATG 60.493 52.174 0.00 0.00 36.49 3.66
2065 5917 1.835531 ACCAACCCATACTCGGTTAGG 59.164 52.381 0.00 0.00 41.78 2.69
2117 5972 6.128309 CGACACATCACACCTATTCAAATCAA 60.128 38.462 0.00 0.00 0.00 2.57
2141 5999 0.168788 CAAGTAGCATGGGTTGTGCG 59.831 55.000 0.00 0.00 46.86 5.34
2167 6025 3.312697 GCCAACTCGAATATCCAAGGTTC 59.687 47.826 0.00 0.00 0.00 3.62
2221 6080 3.255642 GCAACAAGCAAAGGATCCTTGTA 59.744 43.478 27.71 0.00 45.95 2.41
2288 6148 4.993029 TCAAACCGAGTTTTGGAATGTT 57.007 36.364 0.03 0.00 37.13 2.71
2294 6154 3.775661 ACTGTTCAAACCGAGTTTTGG 57.224 42.857 0.03 0.00 37.13 3.28


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

AutoCloner maintained by Alex Coulton.