Multiple sequence alignment - TraesCS7B01G176300

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 TraesCS7B01G176300 chr7B 100.000 2357 0 0 1 2357 248269143 248271499 0.000000e+00 4353
1 TraesCS7B01G176300 chr7B 98.519 2364 28 2 1 2357 580864274 580866637 0.000000e+00 4165
2 TraesCS7B01G176300 chr7B 93.648 2204 108 11 170 2357 708523477 708525664 0.000000e+00 3265
3 TraesCS7B01G176300 chr1B 98.337 2105 31 2 254 2357 500915458 500913357 0.000000e+00 3690
4 TraesCS7B01G176300 chr1B 91.376 487 35 2 1 480 612198236 612198722 0.000000e+00 660
5 TraesCS7B01G176300 chr4B 98.213 1959 34 1 400 2357 468279768 468281726 0.000000e+00 3422
6 TraesCS7B01G176300 chr7A 96.589 2052 46 5 329 2357 222655910 222653860 0.000000e+00 3380
7 TraesCS7B01G176300 chr7A 96.074 484 13 1 1 478 121050680 121050197 0.000000e+00 784
8 TraesCS7B01G176300 chr3B 94.624 2102 96 8 270 2357 532656706 532658804 0.000000e+00 3240
9 TraesCS7B01G176300 chr3B 92.881 2065 110 28 321 2357 259903039 259905094 0.000000e+00 2964
10 TraesCS7B01G176300 chr3B 95.519 424 12 2 1 417 85113214 85113637 0.000000e+00 671
11 TraesCS7B01G176300 chr5A 98.967 1742 17 1 617 2357 549968008 549966267 0.000000e+00 3116
12 TraesCS7B01G176300 chr5A 96.171 444 17 0 1914 2357 22286573 22287016 0.000000e+00 726
13 TraesCS7B01G176300 chr5A 99.187 246 1 1 2112 2357 488268536 488268292 2.150000e-120 442
14 TraesCS7B01G176300 chr5B 97.928 1689 27 3 674 2357 579535040 579533355 0.000000e+00 2918
15 TraesCS7B01G176300 chr3A 97.603 1627 16 2 732 2357 604314348 604312744 0.000000e+00 2767
16 TraesCS7B01G176300 chr2B 95.833 456 13 1 1 450 689371889 689372344 0.000000e+00 732
17 TraesCS7B01G176300 chr2B 95.641 390 11 1 1 384 39430533 39430144 2.570000e-174 621
18 TraesCS7B01G176300 chr2A 96.226 424 10 1 1 418 86283385 86283808 0.000000e+00 689
19 TraesCS7B01G176300 chr4A 95.822 359 9 1 1 353 152585333 152584975 2.030000e-160 575
20 TraesCS7B01G176300 chr4A 94.415 376 15 1 1 370 377598250 377597875 7.310000e-160 573


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 TraesCS7B01G176300 chr7B 248269143 248271499 2356 False 4353 4353 100.000 1 2357 1 chr7B.!!$F1 2356
1 TraesCS7B01G176300 chr7B 580864274 580866637 2363 False 4165 4165 98.519 1 2357 1 chr7B.!!$F2 2356
2 TraesCS7B01G176300 chr7B 708523477 708525664 2187 False 3265 3265 93.648 170 2357 1 chr7B.!!$F3 2187
3 TraesCS7B01G176300 chr1B 500913357 500915458 2101 True 3690 3690 98.337 254 2357 1 chr1B.!!$R1 2103
4 TraesCS7B01G176300 chr4B 468279768 468281726 1958 False 3422 3422 98.213 400 2357 1 chr4B.!!$F1 1957
5 TraesCS7B01G176300 chr7A 222653860 222655910 2050 True 3380 3380 96.589 329 2357 1 chr7A.!!$R2 2028
6 TraesCS7B01G176300 chr3B 532656706 532658804 2098 False 3240 3240 94.624 270 2357 1 chr3B.!!$F3 2087
7 TraesCS7B01G176300 chr3B 259903039 259905094 2055 False 2964 2964 92.881 321 2357 1 chr3B.!!$F2 2036
8 TraesCS7B01G176300 chr5A 549966267 549968008 1741 True 3116 3116 98.967 617 2357 1 chr5A.!!$R2 1740
9 TraesCS7B01G176300 chr5B 579533355 579535040 1685 True 2918 2918 97.928 674 2357 1 chr5B.!!$R1 1683
10 TraesCS7B01G176300 chr3A 604312744 604314348 1604 True 2767 2767 97.603 732 2357 1 chr3A.!!$R1 1625

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
286 293 1.882989 GAGAGCACCAGGAGCGTTCT 61.883 60.000 2.85 1.75 37.01 3.01 F
1032 1067 2.220586 TTCCATGACGAGGCCACCA 61.221 57.895 5.01 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1112 1147 0.478072 ATCTCCACACCAACAAGGCA 59.522 50.000 0.00 0.00 43.14 4.75 R
1949 1985 4.873810 ACACTTGGGCGCTGCACA 62.874 61.111 7.64 1.27 41.67 4.57 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
28 29 8.668510 ATGACTATGTGATTTGGACAAGTATC 57.331 34.615 0.00 0.00 0.00 2.24
92 93 2.952978 TGTGTTTTGGACGCCTACATTT 59.047 40.909 0.00 0.00 37.99 2.32
286 293 1.882989 GAGAGCACCAGGAGCGTTCT 61.883 60.000 2.85 1.75 37.01 3.01
604 632 3.632049 TCCCTCCCACCCATCCCA 61.632 66.667 0.00 0.00 0.00 4.37
970 1005 4.400251 GGTTATTGTTAAGTGGGGGTTAGC 59.600 45.833 0.00 0.00 0.00 3.09
1032 1067 2.220586 TTCCATGACGAGGCCACCA 61.221 57.895 5.01 0.00 0.00 4.17
1477 1513 0.448593 CGTCGTCAGAAGGAGAGGAC 59.551 60.000 0.00 0.00 43.64 3.85
1585 1621 1.893919 GAGGCGCAAGAGGAGGACTT 61.894 60.000 10.83 0.00 43.02 3.01
1949 1985 0.469917 ACAGGGCGCTGCACTATATT 59.530 50.000 28.90 5.57 42.13 1.28
2006 2042 1.595093 GCAGCGCCTAAATGTTGGGT 61.595 55.000 2.29 0.00 33.15 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.199719 CACATAGTCATACACACATAGCACAG 59.800 42.308 0.00 0.00 0.00 3.66
92 93 9.758021 AGATGCCACATAATCATATCCAAATTA 57.242 29.630 0.00 0.00 0.00 1.40
261 268 0.979665 CTCCTGGTGCTCTCTGGAAA 59.020 55.000 0.00 0.00 33.00 3.13
454 461 2.281484 GCACCAGGAGCGTTCCAA 60.281 61.111 21.22 0.00 46.64 3.53
554 582 2.159179 AATAAATGTCCAGGGGTGCC 57.841 50.000 0.00 0.00 0.00 5.01
604 632 3.828023 GGTGGGGTGTGTGGGGTT 61.828 66.667 0.00 0.00 0.00 4.11
970 1005 4.939509 AACCGAGAATTATTGGTCAACG 57.060 40.909 12.46 0.00 35.79 4.10
1032 1067 3.441572 GCATGTCTTCTTGGTTAGCACAT 59.558 43.478 0.00 0.00 0.00 3.21
1112 1147 0.478072 ATCTCCACACCAACAAGGCA 59.522 50.000 0.00 0.00 43.14 4.75
1477 1513 0.798771 CTCTCGTTTCTTCCGCTCCG 60.799 60.000 0.00 0.00 0.00 4.63
1585 1621 1.227823 CCCTTCTTGTCACGTGCCA 60.228 57.895 11.67 1.63 0.00 4.92
1949 1985 4.873810 ACACTTGGGCGCTGCACA 62.874 61.111 7.64 1.27 41.67 4.57


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

AutoCloner maintained by Alex Coulton.