Multiple sequence alignment - TraesCS7B01G372800

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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 TraesCS7B01G372800 chr7B 100.000 2450 0 0 1 2450 638611652 638609203 0.000000e+00 4525
1 TraesCS7B01G372800 chr7B 96.864 2455 72 2 1 2450 456122105 456124559 0.000000e+00 4102
2 TraesCS7B01G372800 chr3B 95.035 2457 113 6 1 2450 331024950 331027404 0.000000e+00 3853
3 TraesCS7B01G372800 chr3B 90.802 2457 206 15 1 2448 533671479 533669034 0.000000e+00 3267
4 TraesCS7B01G372800 chr3B 85.918 2521 269 52 1 2448 120083002 120080495 0.000000e+00 2610
5 TraesCS7B01G372800 chr3B 85.302 2497 301 47 1 2448 288475206 288477685 0.000000e+00 2518
6 TraesCS7B01G372800 chr3B 89.200 1213 95 25 1270 2448 361554921 361556131 0.000000e+00 1482
7 TraesCS7B01G372800 chr3B 87.829 1216 102 29 1270 2447 284885577 284884370 0.000000e+00 1384
8 TraesCS7B01G372800 chr3B 85.699 958 89 33 1536 2448 115674057 115673103 0.000000e+00 966
9 TraesCS7B01G372800 chr1B 93.156 2484 129 28 1 2448 367658329 367660807 0.000000e+00 3607
10 TraesCS7B01G372800 chr4B 92.044 2476 162 27 1 2447 451467493 451469962 0.000000e+00 3448
11 TraesCS7B01G372800 chr5B 91.453 2492 161 34 1 2448 373340473 373342956 0.000000e+00 3374
12 TraesCS7B01G372800 chr5B 91.372 2492 163 34 1 2448 373348572 373351055 0.000000e+00 3363
13 TraesCS7B01G372800 chr5B 90.179 224 20 2 2227 2448 4634660 4634437 8.570000e-75 291
14 TraesCS7B01G372800 chr2B 90.770 2492 174 38 1 2448 388226096 388228575 0.000000e+00 3277
15 TraesCS7B01G372800 chr2B 90.909 2475 172 39 1 2433 724014234 724011771 0.000000e+00 3275


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 TraesCS7B01G372800 chr7B 638609203 638611652 2449 True 4525 4525 100.000 1 2450 1 chr7B.!!$R1 2449
1 TraesCS7B01G372800 chr7B 456122105 456124559 2454 False 4102 4102 96.864 1 2450 1 chr7B.!!$F1 2449
2 TraesCS7B01G372800 chr3B 331024950 331027404 2454 False 3853 3853 95.035 1 2450 1 chr3B.!!$F2 2449
3 TraesCS7B01G372800 chr3B 533669034 533671479 2445 True 3267 3267 90.802 1 2448 1 chr3B.!!$R4 2447
4 TraesCS7B01G372800 chr3B 120080495 120083002 2507 True 2610 2610 85.918 1 2448 1 chr3B.!!$R2 2447
5 TraesCS7B01G372800 chr3B 288475206 288477685 2479 False 2518 2518 85.302 1 2448 1 chr3B.!!$F1 2447
6 TraesCS7B01G372800 chr3B 361554921 361556131 1210 False 1482 1482 89.200 1270 2448 1 chr3B.!!$F3 1178
7 TraesCS7B01G372800 chr3B 284884370 284885577 1207 True 1384 1384 87.829 1270 2447 1 chr3B.!!$R3 1177
8 TraesCS7B01G372800 chr3B 115673103 115674057 954 True 966 966 85.699 1536 2448 1 chr3B.!!$R1 912
9 TraesCS7B01G372800 chr1B 367658329 367660807 2478 False 3607 3607 93.156 1 2448 1 chr1B.!!$F1 2447
10 TraesCS7B01G372800 chr4B 451467493 451469962 2469 False 3448 3448 92.044 1 2447 1 chr4B.!!$F1 2446
11 TraesCS7B01G372800 chr5B 373340473 373342956 2483 False 3374 3374 91.453 1 2448 1 chr5B.!!$F1 2447
12 TraesCS7B01G372800 chr5B 373348572 373351055 2483 False 3363 3363 91.372 1 2448 1 chr5B.!!$F2 2447
13 TraesCS7B01G372800 chr2B 388226096 388228575 2479 False 3277 3277 90.770 1 2448 1 chr2B.!!$F1 2447
14 TraesCS7B01G372800 chr2B 724011771 724014234 2463 True 3275 3275 90.909 1 2433 1 chr2B.!!$R1 2432

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
789 811 1.178276 GCGAGAGTCCAGAGGAAGAA 58.822 55.0 0.0 0.0 31.38 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 2302 0.834612 GGAACATACCACCGATCCCA 59.165 55.0 0.0 0.0 0.0 4.37 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
134 135 4.594920 TCCTTATTCTAGAGGCCATCCTTG 59.405 45.833 5.01 0.0 44.46 3.61
373 374 3.118261 GCAGGGATTCAGGTACAATGAGA 60.118 47.826 0.00 0.0 0.00 3.27
428 429 9.775539 TTATTCAGCTCCTATTCATATACCTCT 57.224 33.333 0.00 0.0 0.00 3.69
644 666 3.266636 GAAAGGAGCTAGTGGAAGAAGC 58.733 50.000 0.00 0.0 36.48 3.86
789 811 1.178276 GCGAGAGTCCAGAGGAAGAA 58.822 55.000 0.00 0.0 31.38 2.52
817 839 7.456725 ACTTCAGATCCAAGAAGAAATTCTCA 58.543 34.615 20.58 0.0 42.95 3.27
847 869 2.419713 GCACAAGATGATCCAGAGCTCA 60.420 50.000 17.77 0.0 0.00 4.26
925 947 9.472361 CAAAAGAAGTTGATGTGATTGAAGATT 57.528 29.630 0.00 0.0 0.00 2.40
1168 1191 8.895141 TCCTTATGCTAGTCCTATGCTTAATA 57.105 34.615 0.00 0.0 0.00 0.98
1511 1535 3.249752 AGCAGGCATGAGGATAGAGAAT 58.750 45.455 0.62 0.0 0.00 2.40
1520 1544 6.204495 GCATGAGGATAGAGAATCAAAAGGAC 59.796 42.308 0.00 0.0 37.82 3.85
1662 1701 8.932791 GTTGCTTGAGCTAGTTATTACTTGTTA 58.067 33.333 4.44 0.0 42.66 2.41
2359 2458 3.726557 TGTTCTTGGGATCATGCTCTT 57.273 42.857 0.00 0.0 0.00 2.85
2406 2505 8.514594 GTCATCATTTAAACTTGTTGATCCTCA 58.485 33.333 6.06 0.0 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 0.035056 ATGGCAGGTAGGAGCAACAC 60.035 55.000 0.00 0.00 0.00 3.32
185 186 1.479323 GGGAGTAACCACGCTGACATA 59.521 52.381 0.00 0.00 41.20 2.29
373 374 3.181445 TGTGGAGCATAGTTGTGGTTCTT 60.181 43.478 0.00 0.00 0.00 2.52
644 666 7.303998 GTTGATGTTCTTCTCAATCTTCCTTG 58.696 38.462 0.00 0.00 34.18 3.61
789 811 9.972106 AGAATTTCTTCTTGGATCTGAAGTATT 57.028 29.630 16.84 16.31 38.63 1.89
817 839 1.999648 TCATCTTGTGCCTTGGCTTT 58.000 45.000 13.18 0.00 0.00 3.51
847 869 7.542130 GTCTTCAACTTGATCACTTTGTTGTTT 59.458 33.333 19.98 0.00 39.03 2.83
887 909 7.338800 TCAACTTCTTTTGCTTCTTCAAGAT 57.661 32.000 0.00 0.00 0.00 2.40
925 947 3.305064 GGCAAATGCGTTTCTGGTTCTTA 60.305 43.478 0.00 0.00 43.26 2.10
1168 1191 9.646522 AAGACTAGCATGGGAATAATATGTTTT 57.353 29.630 0.00 0.00 0.00 2.43
1216 1239 3.614150 GCAAGGTCGACACTAACATGAGA 60.614 47.826 18.91 0.00 0.00 3.27
1511 1535 0.473755 TGCAGCTCCTGTCCTTTTGA 59.526 50.000 0.00 0.00 33.43 2.69
1520 1544 0.954449 CTCACCAACTGCAGCTCCTG 60.954 60.000 15.27 6.18 34.12 3.86
2236 2302 0.834612 GGAACATACCACCGATCCCA 59.165 55.000 0.00 0.00 0.00 4.37
2359 2458 3.964031 ACTGTGCCAAATGGTTCCTAAAA 59.036 39.130 0.71 0.00 37.57 1.52


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

AutoCloner maintained by Alex Coulton.