Multiple sequence alignment - TraesCS1B01G385700

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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 TraesCS1B01G385700 chr1B 100.000 2192 0 0 1 2192 619195330 619193139 0.000000e+00 4048.0
1 TraesCS1B01G385700 chr3A 98.176 2193 39 1 1 2192 495104759 495102567 0.000000e+00 3827.0
2 TraesCS1B01G385700 chr3A 88.664 494 46 6 352 837 21284878 21284387 5.210000e-166 593.0
3 TraesCS1B01G385700 chr3A 98.294 293 4 1 1598 1889 482776520 482776228 1.500000e-141 512.0
4 TraesCS1B01G385700 chr3A 92.000 275 21 1 1 274 21285152 21284878 3.410000e-103 385.0
5 TraesCS1B01G385700 chr3A 98.077 52 1 0 1328 1379 737346036 737346087 8.330000e-15 91.6
6 TraesCS1B01G385700 chr2B 98.085 2193 41 1 1 2192 234541159 234538967 0.000000e+00 3816.0
7 TraesCS1B01G385700 chr1A 97.994 2193 42 2 1 2192 278521195 278523386 0.000000e+00 3805.0
8 TraesCS1B01G385700 chrUn 97.948 2193 43 2 1 2192 217907669 217909860 0.000000e+00 3799.0
9 TraesCS1B01G385700 chr3B 97.948 2193 43 2 1 2192 6010765 6008574 0.000000e+00 3799.0
10 TraesCS1B01G385700 chr3B 97.904 2195 40 4 1 2192 92296731 92294540 0.000000e+00 3794.0
11 TraesCS1B01G385700 chr3B 92.896 929 62 4 491 1418 342687462 342688387 0.000000e+00 1347.0
12 TraesCS1B01G385700 chr3B 87.717 920 95 12 1 909 22162928 22163840 0.000000e+00 1057.0
13 TraesCS1B01G385700 chr3B 90.947 486 43 1 1414 1898 342695924 342696409 0.000000e+00 652.0
14 TraesCS1B01G385700 chr3B 90.970 299 27 0 1894 2192 342697320 342697618 9.420000e-109 403.0
15 TraesCS1B01G385700 chr3B 89.316 234 24 1 1897 2130 505898801 505899033 2.130000e-75 292.0
16 TraesCS1B01G385700 chr3B 100.000 47 0 0 1283 1329 21186282 21186328 1.080000e-13 87.9
17 TraesCS1B01G385700 chr4A 97.583 2193 52 1 1 2192 67519499 67521691 0.000000e+00 3755.0


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 TraesCS1B01G385700 chr1B 619193139 619195330 2191 True 4048.0 4048 100.0000 1 2192 1 chr1B.!!$R1 2191
1 TraesCS1B01G385700 chr3A 495102567 495104759 2192 True 3827.0 3827 98.1760 1 2192 1 chr3A.!!$R2 2191
2 TraesCS1B01G385700 chr3A 21284387 21285152 765 True 489.0 593 90.3320 1 837 2 chr3A.!!$R3 836
3 TraesCS1B01G385700 chr2B 234538967 234541159 2192 True 3816.0 3816 98.0850 1 2192 1 chr2B.!!$R1 2191
4 TraesCS1B01G385700 chr1A 278521195 278523386 2191 False 3805.0 3805 97.9940 1 2192 1 chr1A.!!$F1 2191
5 TraesCS1B01G385700 chrUn 217907669 217909860 2191 False 3799.0 3799 97.9480 1 2192 1 chrUn.!!$F1 2191
6 TraesCS1B01G385700 chr3B 6008574 6010765 2191 True 3799.0 3799 97.9480 1 2192 1 chr3B.!!$R1 2191
7 TraesCS1B01G385700 chr3B 92294540 92296731 2191 True 3794.0 3794 97.9040 1 2192 1 chr3B.!!$R2 2191
8 TraesCS1B01G385700 chr3B 342687462 342688387 925 False 1347.0 1347 92.8960 491 1418 1 chr3B.!!$F3 927
9 TraesCS1B01G385700 chr3B 22162928 22163840 912 False 1057.0 1057 87.7170 1 909 1 chr3B.!!$F2 908
10 TraesCS1B01G385700 chr3B 342695924 342697618 1694 False 527.5 652 90.9585 1414 2192 2 chr3B.!!$F5 778
11 TraesCS1B01G385700 chr4A 67519499 67521691 2192 False 3755.0 3755 97.5830 1 2192 1 chr4A.!!$F1 2191

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
502 512 0.033504 GTGAAGCCTTGGAGACGACA 59.966 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 2854 1.852895 GGCGTGTCAGCTTAGTTATCG 59.147 52.381 0.0 0.0 37.29 2.92 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
65 66 6.758416 CACTTGCTTCAACTACTCATGCTATA 59.242 38.462 0.00 0.0 0.00 1.31
108 109 1.499007 TCCTTTGGGCTTTTGAGGAGT 59.501 47.619 0.00 0.0 32.91 3.85
430 432 2.610438 AGTTCCCATCAGGCAACAAT 57.390 45.000 0.00 0.0 41.41 2.71
502 512 0.033504 GTGAAGCCTTGGAGACGACA 59.966 55.000 0.00 0.0 0.00 4.35
978 989 7.614192 ACCCTATTTATATGATTTTTAGGGCCG 59.386 37.037 11.18 0.0 45.49 6.13
1011 1022 4.363546 TCCCTCCCTTATGTTTAGGAGT 57.636 45.455 4.34 0.0 43.73 3.85
1052 1063 1.298667 GTGGTGGTACGGAAGGCAT 59.701 57.895 0.00 0.0 0.00 4.40
1168 1179 2.203337 TTCCTTGCTGTTGCGGCT 60.203 55.556 0.00 0.0 43.34 5.52
1221 1232 6.297582 CAGATCATAAGGAAAGATGCCTCTT 58.702 40.000 0.00 0.0 43.71 2.85
1362 1375 0.468029 AAAGTGAAGTGGTGGGCCTG 60.468 55.000 4.53 0.0 35.27 4.85
1625 1638 0.255604 ATCCATGGAATCGTGTGCCA 59.744 50.000 20.67 0.0 35.91 4.92
1656 1669 3.520290 AGATCATCGCCGTTCTTAACA 57.480 42.857 0.00 0.0 0.00 2.41
1925 2854 2.229792 TCAAGGTTGTGGCTTGATGAC 58.770 47.619 0.00 0.0 32.89 3.06
2124 3053 0.249447 CGCTGCCATCTTATCCACGA 60.249 55.000 0.00 0.0 0.00 4.35
2142 3071 2.988493 ACGAAAAACGCGTCAAGCTATA 59.012 40.909 14.44 0.0 46.94 1.31
2143 3072 3.615496 ACGAAAAACGCGTCAAGCTATAT 59.385 39.130 14.44 0.0 46.94 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.706339 GAGTTGATGCTCCCACATCT 57.294 50.000 6.13 0.00 45.51 2.90
108 109 7.181361 TCATAGAATTCCAACAATTTCTCCCA 58.819 34.615 0.65 0.00 0.00 4.37
929 940 6.262273 GGTTGTAGAAAGACCAGTTTCATTCA 59.738 38.462 0.00 0.00 38.66 2.57
978 989 1.427895 GGGAGGGATAGGGGGAAAGC 61.428 65.000 0.00 0.00 0.00 3.51
1221 1232 2.689471 CGAATCATTCTCAAATGCCCCA 59.311 45.455 0.00 0.00 41.76 4.96
1229 1240 2.672961 ACGGCTCGAATCATTCTCAA 57.327 45.000 0.00 0.00 0.00 3.02
1625 1638 3.123804 GGCGATGATCTACGTTTCACAT 58.876 45.455 0.00 0.00 0.00 3.21
1656 1669 2.096248 CGGAGCTTAACCTGAGTCTCT 58.904 52.381 0.65 0.00 0.00 3.10
1925 2854 1.852895 GGCGTGTCAGCTTAGTTATCG 59.147 52.381 0.00 0.00 37.29 2.92
2124 3053 5.500290 CGAAGATATAGCTTGACGCGTTTTT 60.500 40.000 15.53 0.16 45.59 1.94


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

AutoCloner maintained by Alex Coulton.