Multiple sequence alignment - TraesCS7B01G384600

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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 TraesCS7B01G384600 chr7B 100.000 2399 0 0 1 2399 650295684 650293286 0.000000e+00 4431
1 TraesCS7B01G384600 chr7B 96.759 2407 58 7 1 2399 650318609 650316215 0.000000e+00 3995
2 TraesCS7B01G384600 chr7B 96.512 2408 64 9 1 2399 650362879 650360483 0.000000e+00 3964
3 TraesCS7B01G384600 chr7B 96.347 2409 67 9 1 2399 650409864 650407467 0.000000e+00 3941
4 TraesCS7B01G384600 chr7B 95.089 2423 52 14 1 2399 650456585 650454206 0.000000e+00 3753
5 TraesCS7B01G384600 chr7B 97.841 1575 25 5 1 1575 650301822 650300257 0.000000e+00 2712
6 TraesCS7B01G384600 chr7B 94.715 492 23 2 1909 2399 613665011 613664522 0.000000e+00 761
7 TraesCS7B01G384600 chr7B 88.356 146 16 1 206 351 625612104 625612248 8.820000e-40 174
8 TraesCS7B01G384600 chr7D 91.270 1512 83 18 410 1914 582651347 582649878 0.000000e+00 2015
9 TraesCS7B01G384600 chr7D 90.344 1512 80 24 410 1914 582545874 582544422 0.000000e+00 1923
10 TraesCS7B01G384600 chr7D 90.185 1192 86 18 453 1637 582748408 582747241 0.000000e+00 1524
11 TraesCS7B01G384600 chr7D 88.006 1234 94 22 410 1637 582662724 582661539 0.000000e+00 1410
12 TraesCS7B01G384600 chr7D 90.476 882 61 13 762 1637 582557228 582556364 0.000000e+00 1142
13 TraesCS7B01G384600 chr7A 87.305 1410 133 33 413 1802 674506723 674505340 0.000000e+00 1570
14 TraesCS7B01G384600 chr7A 89.857 838 66 11 803 1637 674521292 674520471 0.000000e+00 1059
15 TraesCS7B01G384600 chr7A 91.771 401 26 4 410 810 674522976 674522583 3.490000e-153 551
16 TraesCS7B01G384600 chr7A 91.228 399 27 5 410 808 674527245 674526855 9.760000e-149 536
17 TraesCS7B01G384600 chrUn 95.303 958 39 5 1446 2399 388900209 388901164 0.000000e+00 1515
18 TraesCS7B01G384600 chrUn 95.303 958 39 5 1446 2399 388901873 388902828 0.000000e+00 1515
19 TraesCS7B01G384600 chrUn 94.501 491 23 3 1910 2399 289013299 289013786 0.000000e+00 754
20 TraesCS7B01G384600 chrUn 86.184 152 16 3 251 397 12608204 12608355 2.470000e-35 159
21 TraesCS7B01G384600 chr4A 94.877 488 22 3 1914 2399 731423515 731424001 0.000000e+00 760
22 TraesCS7B01G384600 chr5B 94.501 491 21 5 1911 2399 526265392 526264906 0.000000e+00 752
23 TraesCS7B01G384600 chr1A 87.500 152 15 3 251 401 50680592 50680444 3.170000e-39 172
24 TraesCS7B01G384600 chr2D 83.333 174 23 4 238 409 11981071 11981240 3.190000e-34 156


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 TraesCS7B01G384600 chr7B 650293286 650295684 2398 True 4431.000000 4431 100.000 1 2399 1 chr7B.!!$R2 2398
1 TraesCS7B01G384600 chr7B 650316215 650318609 2394 True 3995.000000 3995 96.759 1 2399 1 chr7B.!!$R4 2398
2 TraesCS7B01G384600 chr7B 650360483 650362879 2396 True 3964.000000 3964 96.512 1 2399 1 chr7B.!!$R5 2398
3 TraesCS7B01G384600 chr7B 650407467 650409864 2397 True 3941.000000 3941 96.347 1 2399 1 chr7B.!!$R6 2398
4 TraesCS7B01G384600 chr7B 650454206 650456585 2379 True 3753.000000 3753 95.089 1 2399 1 chr7B.!!$R7 2398
5 TraesCS7B01G384600 chr7B 650300257 650301822 1565 True 2712.000000 2712 97.841 1 1575 1 chr7B.!!$R3 1574
6 TraesCS7B01G384600 chr7D 582649878 582651347 1469 True 2015.000000 2015 91.270 410 1914 1 chr7D.!!$R3 1504
7 TraesCS7B01G384600 chr7D 582544422 582545874 1452 True 1923.000000 1923 90.344 410 1914 1 chr7D.!!$R1 1504
8 TraesCS7B01G384600 chr7D 582747241 582748408 1167 True 1524.000000 1524 90.185 453 1637 1 chr7D.!!$R5 1184
9 TraesCS7B01G384600 chr7D 582661539 582662724 1185 True 1410.000000 1410 88.006 410 1637 1 chr7D.!!$R4 1227
10 TraesCS7B01G384600 chr7D 582556364 582557228 864 True 1142.000000 1142 90.476 762 1637 1 chr7D.!!$R2 875
11 TraesCS7B01G384600 chr7A 674505340 674506723 1383 True 1570.000000 1570 87.305 413 1802 1 chr7A.!!$R1 1389
12 TraesCS7B01G384600 chr7A 674520471 674527245 6774 True 715.333333 1059 90.952 410 1637 3 chr7A.!!$R2 1227
13 TraesCS7B01G384600 chrUn 388900209 388902828 2619 False 1515.000000 1515 95.303 1446 2399 2 chrUn.!!$F3 953

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
473 484 4.32175 CCAGTATGACAAACCAGAGTACGT 60.322 45.833 0.0 0.0 39.69 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 7576 0.251354 GAACCGGGACTAAAGACCCC 59.749 60.0 6.32 6.96 45.35 4.95 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
246 247 9.565090 TTCATTCATCGATTTCTAGGATTGATT 57.435 29.630 0.00 0.00 0.00 2.57
473 484 4.321750 CCAGTATGACAAACCAGAGTACGT 60.322 45.833 0.00 0.00 39.69 3.57
1102 6684 2.362120 CAGTCGTCCCTACCCCGT 60.362 66.667 0.00 0.00 0.00 5.28
1526 7125 6.606796 TCCGGTACTATATGTTAGGTGTTTGA 59.393 38.462 0.00 0.00 0.00 2.69
1617 7216 8.255394 TCGTTATGGTATCTAAATGCATGATG 57.745 34.615 0.00 0.00 0.00 3.07
1706 7325 4.265904 CCCGCAAAAGAAAAGGGTTAAT 57.734 40.909 0.00 0.00 37.36 1.40
1726 7352 1.745232 TTGACCCGTGATATGCCAAC 58.255 50.000 0.00 0.00 0.00 3.77
1729 7355 0.180406 ACCCGTGATATGCCAACCTC 59.820 55.000 0.00 0.00 0.00 3.85
1950 7576 1.597663 GGCATTTGTCCCGATTCGTAG 59.402 52.381 5.20 0.00 0.00 3.51
1976 7625 3.644738 TCTTTAGTCCCGGTTCTTGAACT 59.355 43.478 12.44 0.00 0.00 3.01
2030 7681 4.161754 CCCTTTAGTCCCGATTCTTACACT 59.838 45.833 0.00 0.00 0.00 3.55
2372 8027 9.445878 AAGTCCTACTAATCATGCATCATTATG 57.554 33.333 3.28 1.66 36.09 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 4.292186 AGGTATGTGCTATATGGGCAAG 57.708 45.455 6.74 0.00 41.54 4.01
246 247 6.310764 TGGGTCCAAATTATTACGGTCTAA 57.689 37.500 0.00 0.00 0.00 2.10
1526 7125 3.854669 CGAGCGAGGGAGCCCATT 61.855 66.667 8.53 0.00 38.92 3.16
1617 7216 9.801873 ACATACAATCCTTTTACAAATACATGC 57.198 29.630 0.00 0.00 0.00 4.06
1706 7325 2.088423 GTTGGCATATCACGGGTCAAA 58.912 47.619 0.00 0.00 0.00 2.69
1726 7352 7.346208 TGTACGATAAATATGCATTTCGAGG 57.654 36.000 3.54 0.00 35.88 4.63
1729 7355 7.014702 TGCATGTACGATAAATATGCATTTCG 58.985 34.615 3.54 9.07 46.31 3.46
1919 7545 3.769300 GGGACAAATGCCCTGTTTTCTAT 59.231 43.478 0.00 0.00 42.56 1.98
1950 7576 0.251354 GAACCGGGACTAAAGACCCC 59.749 60.000 6.32 6.96 45.35 4.95
1954 7580 3.644738 AGTTCAAGAACCGGGACTAAAGA 59.355 43.478 6.32 1.48 42.06 2.52
1976 7625 6.239120 GCATTAGTAACGACCTATTAGTCCCA 60.239 42.308 0.00 0.00 32.91 4.37
2020 7671 4.091549 TCTGTCCCGGTTAGTGTAAGAAT 58.908 43.478 0.00 0.00 0.00 2.40
2030 7681 0.986019 ATGCCCATCTGTCCCGGTTA 60.986 55.000 0.00 0.00 0.00 2.85
2164 7819 9.529823 AAAACCCCTAAACCAACAATTTAAAAA 57.470 25.926 0.00 0.00 0.00 1.94
2165 7820 8.957466 CAAAACCCCTAAACCAACAATTTAAAA 58.043 29.630 0.00 0.00 0.00 1.52
2166 7821 7.556635 CCAAAACCCCTAAACCAACAATTTAAA 59.443 33.333 0.00 0.00 0.00 1.52
2173 7828 2.399580 CCCAAAACCCCTAAACCAACA 58.600 47.619 0.00 0.00 0.00 3.33
2175 7830 1.414685 CCCCCAAAACCCCTAAACCAA 60.415 52.381 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.