Multiple sequence alignment - TraesCS7D01G455600

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 TraesCS7D01G455600 chr7D 100.000 2348 0 0 1 2348 574721142 574723489 0 4337
1 TraesCS7D01G455600 chr7D 96.913 907 22 5 1443 2348 113995923 113995022 0 1515
2 TraesCS7D01G455600 chr5D 97.095 2375 42 11 1 2348 336342354 336344728 0 3978
3 TraesCS7D01G455600 chr5D 96.509 2349 45 5 1 2348 213965274 213962962 0 3849
4 TraesCS7D01G455600 chr5D 96.424 2349 47 5 1 2348 559988282 559990594 0 3838
5 TraesCS7D01G455600 chr5D 96.343 1832 42 8 1 1808 482324764 482326594 0 2988
6 TraesCS7D01G455600 chr6D 96.797 2373 49 4 1 2348 109969253 109966883 0 3936
7 TraesCS7D01G455600 chr6D 96.514 2352 45 4 1 2348 52515771 52518089 0 3855
8 TraesCS7D01G455600 chr6D 96.214 2351 42 5 1 2348 277561450 277563756 0 3805
9 TraesCS7D01G455600 chr2D 96.674 2375 50 4 1 2348 547205943 547208315 0 3921
10 TraesCS7D01G455600 chr2D 96.346 2381 47 6 1 2348 435218591 435216218 0 3879
11 TraesCS7D01G455600 chr2D 96.207 2373 61 5 1 2348 299997995 299995627 0 3856
12 TraesCS7D01G455600 chr2D 96.128 2350 50 6 1 2348 498465676 498467986 0 3797
13 TraesCS7D01G455600 chrUn 95.597 2385 64 16 1 2348 93720440 93722820 0 3784
14 TraesCS7D01G455600 chr2A 95.447 2350 67 10 1 2348 50268185 50270496 0 3711
15 TraesCS7D01G455600 chr2B 95.396 2346 72 4 6 2348 757368695 757366383 0 3701
16 TraesCS7D01G455600 chr3D 95.928 1940 38 7 1 1906 475112748 475110816 0 3107
17 TraesCS7D01G455600 chr7B 95.861 1788 68 2 1 1783 223460029 223461815 0 2887
18 TraesCS7D01G455600 chr3A 95.634 962 35 5 1390 2348 120658453 120657496 0 1537


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 TraesCS7D01G455600 chr7D 574721142 574723489 2347 False 4337 4337 100.000 1 2348 1 chr7D.!!$F1 2347
1 TraesCS7D01G455600 chr7D 113995022 113995923 901 True 1515 1515 96.913 1443 2348 1 chr7D.!!$R1 905
2 TraesCS7D01G455600 chr5D 336342354 336344728 2374 False 3978 3978 97.095 1 2348 1 chr5D.!!$F1 2347
3 TraesCS7D01G455600 chr5D 213962962 213965274 2312 True 3849 3849 96.509 1 2348 1 chr5D.!!$R1 2347
4 TraesCS7D01G455600 chr5D 559988282 559990594 2312 False 3838 3838 96.424 1 2348 1 chr5D.!!$F3 2347
5 TraesCS7D01G455600 chr5D 482324764 482326594 1830 False 2988 2988 96.343 1 1808 1 chr5D.!!$F2 1807
6 TraesCS7D01G455600 chr6D 109966883 109969253 2370 True 3936 3936 96.797 1 2348 1 chr6D.!!$R1 2347
7 TraesCS7D01G455600 chr6D 52515771 52518089 2318 False 3855 3855 96.514 1 2348 1 chr6D.!!$F1 2347
8 TraesCS7D01G455600 chr6D 277561450 277563756 2306 False 3805 3805 96.214 1 2348 1 chr6D.!!$F2 2347
9 TraesCS7D01G455600 chr2D 547205943 547208315 2372 False 3921 3921 96.674 1 2348 1 chr2D.!!$F2 2347
10 TraesCS7D01G455600 chr2D 435216218 435218591 2373 True 3879 3879 96.346 1 2348 1 chr2D.!!$R2 2347
11 TraesCS7D01G455600 chr2D 299995627 299997995 2368 True 3856 3856 96.207 1 2348 1 chr2D.!!$R1 2347
12 TraesCS7D01G455600 chr2D 498465676 498467986 2310 False 3797 3797 96.128 1 2348 1 chr2D.!!$F1 2347
13 TraesCS7D01G455600 chrUn 93720440 93722820 2380 False 3784 3784 95.597 1 2348 1 chrUn.!!$F1 2347
14 TraesCS7D01G455600 chr2A 50268185 50270496 2311 False 3711 3711 95.447 1 2348 1 chr2A.!!$F1 2347
15 TraesCS7D01G455600 chr2B 757366383 757368695 2312 True 3701 3701 95.396 6 2348 1 chr2B.!!$R1 2342
16 TraesCS7D01G455600 chr3D 475110816 475112748 1932 True 3107 3107 95.928 1 1906 1 chr3D.!!$R1 1905
17 TraesCS7D01G455600 chr7B 223460029 223461815 1786 False 2887 2887 95.861 1 1783 1 chr7B.!!$F1 1782
18 TraesCS7D01G455600 chr3A 120657496 120658453 957 True 1537 1537 95.634 1390 2348 1 chr3A.!!$R1 958


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
871 876 0.386838 GCAATGGCAGATAACTGGGC 59.613 55.0 1.85 0.0 43.62 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 2249 8.585018 AGTTAGGTTTGACCAGAATTTAAATGG 58.415 33.333 0.39 3.08 41.95 3.16 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
27 28 3.368948 GGGTTTTTGTCTGTTTTGAGGCA 60.369 43.478 0.00 0.00 0.00 4.75
42 43 3.810896 GCATGTCGCCGGGGTTTC 61.811 66.667 19.13 10.71 32.94 2.78
215 217 5.146010 TGGACTTGGTTTTTGCATAATCC 57.854 39.130 9.37 9.37 0.00 3.01
350 352 2.796593 GTCACCTTGCTGCAAATTTCAC 59.203 45.455 16.74 6.04 0.00 3.18
475 478 5.705609 TCCCAAAGTGAAAGAATACTTGC 57.294 39.130 0.00 0.00 37.23 4.01
592 595 5.009210 TCAACGATCCAAAAACTAAAGGGTG 59.991 40.000 0.00 0.00 0.00 4.61
715 720 2.198827 ACCTGCCGTGATGAATGAAA 57.801 45.000 0.00 0.00 0.00 2.69
871 876 0.386838 GCAATGGCAGATAACTGGGC 59.613 55.000 1.85 0.00 43.62 5.36
1154 1159 1.194772 GAAGCGTAAGTGCACAAGGTC 59.805 52.381 21.04 4.97 41.68 3.85
1290 1295 6.694877 ACAGATGATGAAAATGATGGTCAG 57.305 37.500 0.00 0.00 0.00 3.51
1294 1299 4.338012 TGATGAAAATGATGGTCAGCAGT 58.662 39.130 0.00 0.00 33.06 4.40
1441 1479 4.414337 AGTGAGGCTCCAAATAGTGATC 57.586 45.455 12.86 0.00 0.00 2.92
1468 1506 2.205022 TCCAAGTGAGGCTCCAAATG 57.795 50.000 12.86 5.93 0.00 2.32
1469 1507 1.180029 CCAAGTGAGGCTCCAAATGG 58.820 55.000 12.86 11.21 0.00 3.16
1470 1508 1.548582 CCAAGTGAGGCTCCAAATGGT 60.549 52.381 12.86 0.00 36.34 3.55
1471 1509 1.542915 CAAGTGAGGCTCCAAATGGTG 59.457 52.381 12.86 0.00 36.34 4.17
1472 1510 1.067295 AGTGAGGCTCCAAATGGTGA 58.933 50.000 12.86 0.00 36.34 4.02
1473 1511 1.637553 AGTGAGGCTCCAAATGGTGAT 59.362 47.619 12.86 0.00 36.34 3.06
1554 1820 6.414732 TGCTAGGTATGTAAATCTTGCAAGT 58.585 36.000 25.19 9.72 35.72 3.16
2230 2528 2.226437 AGACTATGTGCGCTGGTTTTTG 59.774 45.455 9.73 0.00 0.00 2.44
2285 2591 9.807649 GCTCATTTGAATTATGGTCAAACTTAT 57.192 29.630 1.94 0.00 45.19 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.368948 GCCTCAAAACAGACAAAAACCCA 60.369 43.478 0.00 0.00 0.00 4.51
27 28 1.674322 CAAGAAACCCCGGCGACAT 60.674 57.895 9.30 0.00 0.00 3.06
350 352 5.831997 ACACCTTTCCTTTGAATTTCTTCG 58.168 37.500 0.00 0.00 33.86 3.79
475 478 4.858935 CATAACTTGGAGTGGTGTGTTTG 58.141 43.478 0.00 0.00 0.00 2.93
592 595 5.105797 TGTCAAGCAAATCCACCACATAATC 60.106 40.000 0.00 0.00 0.00 1.75
715 720 2.157738 GCCTGTTGTCTTCTGCTTCAT 58.842 47.619 0.00 0.00 0.00 2.57
1154 1159 1.826385 GAAATGACCAGACCCACCAG 58.174 55.000 0.00 0.00 0.00 4.00
1198 1203 0.457851 CTCTCTCCGAACGCTGGATT 59.542 55.000 0.00 0.00 34.32 3.01
1290 1295 0.376152 CATCTGATGCAACCGACTGC 59.624 55.000 4.47 2.09 42.95 4.40
1294 1299 1.194218 TCCTCATCTGATGCAACCGA 58.806 50.000 12.78 0.00 0.00 4.69
1441 1479 1.064906 AGCCTCACTTGGATCACCATG 60.065 52.381 0.00 0.00 46.34 3.66
1472 1510 2.422519 GCCTCACTTGGATCACCATGAT 60.423 50.000 0.00 0.00 46.34 2.45
1473 1511 1.065199 GCCTCACTTGGATCACCATGA 60.065 52.381 0.00 0.00 46.34 3.07
1584 1850 7.496529 AACATAAACGGTAATGAGATCATGG 57.503 36.000 9.60 0.00 36.56 3.66
1954 2249 8.585018 AGTTAGGTTTGACCAGAATTTAAATGG 58.415 33.333 0.39 3.08 41.95 3.16



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

AutoCloner maintained by Alex Coulton.