Multiple sequence alignment - TraesCS5B01G420900

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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 TraesCS5B01G420900 chr5B 100.000 3842 0 0 1 3842 596824625 596820784 0.000000e+00 7095
1 TraesCS5B01G420900 chr5B 97.376 3849 61 8 1 3842 596224023 596227838 0.000000e+00 6512
2 TraesCS5B01G420900 chr5B 93.522 3674 192 20 1 3659 596393731 596397373 0.000000e+00 5424
3 TraesCS5B01G420900 chr5B 79.938 1944 363 20 97 2030 280605596 280603670 0.000000e+00 1404
4 TraesCS5B01G420900 chr5B 78.418 1960 393 22 97 2043 280650159 280648217 0.000000e+00 1249
5 TraesCS5B01G420900 chr5B 83.500 600 94 5 1442 2039 85946172 85945576 4.340000e-154 555
6 TraesCS5B01G420900 chr5B 80.285 421 66 7 2447 2863 280603534 280603127 6.240000e-78 302
7 TraesCS5B01G420900 chr5B 79.036 415 76 7 2451 2863 280647693 280647288 1.360000e-69 274
8 TraesCS5B01G420900 chr5D 96.039 2247 68 7 1 2246 485060182 485057956 0.000000e+00 3637
9 TraesCS5B01G420900 chr5D 92.420 1438 79 13 2245 3662 485057866 485056439 0.000000e+00 2025
10 TraesCS5B01G420900 chr5D 78.135 1962 387 30 133 2081 246012369 246010437 0.000000e+00 1208
11 TraesCS5B01G420900 chr5D 80.940 1149 189 21 904 2043 77017252 77016125 0.000000e+00 881
12 TraesCS5B01G420900 chr5D 80.108 372 61 9 2451 2818 246010013 246009651 8.180000e-67 265
13 TraesCS5B01G420900 chr5A 95.839 2235 78 6 5 2237 606353001 606350780 0.000000e+00 3598
14 TraesCS5B01G420900 chr5A 78.186 1962 393 28 97 2043 329994849 329992908 0.000000e+00 1219
15 TraesCS5B01G420900 chr5A 92.297 740 52 3 2234 2972 606350677 606349942 0.000000e+00 1046
16 TraesCS5B01G420900 chr5A 86.364 726 49 24 2971 3662 606349838 606349129 0.000000e+00 747
17 TraesCS5B01G420900 chr5A 80.055 366 61 8 2456 2818 329992459 329992103 1.060000e-65 261
18 TraesCS5B01G420900 chr5A 93.605 172 10 1 3658 3828 382566636 382566807 4.930000e-64 255
19 TraesCS5B01G420900 chr7A 79.345 1985 368 34 67 2034 2958981 2957022 0.000000e+00 1356
20 TraesCS5B01G420900 chr4A 78.269 2034 415 21 7 2030 741160110 741162126 0.000000e+00 1282
21 TraesCS5B01G420900 chr4A 79.381 388 73 5 2455 2838 713503219 713502835 2.280000e-67 267
22 TraesCS5B01G420900 chr4A 93.605 172 10 1 3656 3826 582529973 582530144 4.930000e-64 255
23 TraesCS5B01G420900 chr4B 95.181 166 7 1 3659 3823 565737177 565737012 1.060000e-65 261
24 TraesCS5B01G420900 chr4B 93.605 172 10 1 3653 3823 113961110 113961281 4.930000e-64 255
25 TraesCS5B01G420900 chr2A 93.678 174 9 2 3656 3827 746757159 746756986 3.810000e-65 259
26 TraesCS5B01G420900 chr7D 93.182 176 11 1 3651 3825 39001276 39001451 1.370000e-64 257
27 TraesCS5B01G420900 chr2D 94.048 168 9 1 3660 3826 516708476 516708309 1.770000e-63 254
28 TraesCS5B01G420900 chr2D 90.860 186 11 5 3640 3823 576955567 576955386 1.070000e-60 244


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 TraesCS5B01G420900 chr5B 596820784 596824625 3841 True 7095.0 7095 100.0000 1 3842 1 chr5B.!!$R2 3841
1 TraesCS5B01G420900 chr5B 596224023 596227838 3815 False 6512.0 6512 97.3760 1 3842 1 chr5B.!!$F1 3841
2 TraesCS5B01G420900 chr5B 596393731 596397373 3642 False 5424.0 5424 93.5220 1 3659 1 chr5B.!!$F2 3658
3 TraesCS5B01G420900 chr5B 280603127 280605596 2469 True 853.0 1404 80.1115 97 2863 2 chr5B.!!$R3 2766
4 TraesCS5B01G420900 chr5B 280647288 280650159 2871 True 761.5 1249 78.7270 97 2863 2 chr5B.!!$R4 2766
5 TraesCS5B01G420900 chr5B 85945576 85946172 596 True 555.0 555 83.5000 1442 2039 1 chr5B.!!$R1 597
6 TraesCS5B01G420900 chr5D 485056439 485060182 3743 True 2831.0 3637 94.2295 1 3662 2 chr5D.!!$R3 3661
7 TraesCS5B01G420900 chr5D 77016125 77017252 1127 True 881.0 881 80.9400 904 2043 1 chr5D.!!$R1 1139
8 TraesCS5B01G420900 chr5D 246009651 246012369 2718 True 736.5 1208 79.1215 133 2818 2 chr5D.!!$R2 2685
9 TraesCS5B01G420900 chr5A 606349129 606353001 3872 True 1797.0 3598 91.5000 5 3662 3 chr5A.!!$R2 3657
10 TraesCS5B01G420900 chr5A 329992103 329994849 2746 True 740.0 1219 79.1205 97 2818 2 chr5A.!!$R1 2721
11 TraesCS5B01G420900 chr7A 2957022 2958981 1959 True 1356.0 1356 79.3450 67 2034 1 chr7A.!!$R1 1967
12 TraesCS5B01G420900 chr4A 741160110 741162126 2016 False 1282.0 1282 78.2690 7 2030 1 chr4A.!!$F2 2023

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
443 492 1.275573 GGAGGCCGACTACAGTTTCTT 59.724 52.381 0.00 0.00 0.0 2.52 F
1072 1124 1.067565 GTGTCATTCCGAGTCAGCTGA 60.068 52.381 13.74 13.74 0.0 4.26 F
1591 1652 2.038952 AGAGCTCAGTTACCAACATGCA 59.961 45.455 17.77 0.00 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2357 2701 0.685097 AAGTAAGAAGGCGTGGCTCA 59.315 50.000 0.0 0.0 0.00 4.26 R
2378 2722 2.119495 AGACTTGTTCCCTGTCACACT 58.881 47.619 0.0 0.0 33.56 3.55 R
3216 3829 1.806542 GAGCATTTCCAAGAGCGTGAA 59.193 47.619 0.0 0.0 0.00 3.18 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
443 492 1.275573 GGAGGCCGACTACAGTTTCTT 59.724 52.381 0.00 0.00 0.00 2.52
954 1006 3.366781 GCTTCACTTCCTGAATTTGAGCC 60.367 47.826 0.00 0.00 38.26 4.70
955 1007 3.507162 TCACTTCCTGAATTTGAGCCA 57.493 42.857 0.00 0.00 0.00 4.75
956 1008 4.038271 TCACTTCCTGAATTTGAGCCAT 57.962 40.909 0.00 0.00 0.00 4.40
957 1009 5.178096 TCACTTCCTGAATTTGAGCCATA 57.822 39.130 0.00 0.00 0.00 2.74
958 1010 5.569355 TCACTTCCTGAATTTGAGCCATAA 58.431 37.500 0.00 0.00 0.00 1.90
959 1011 6.009589 TCACTTCCTGAATTTGAGCCATAAA 58.990 36.000 0.00 0.00 0.00 1.40
960 1012 6.664816 TCACTTCCTGAATTTGAGCCATAAAT 59.335 34.615 0.00 0.00 0.00 1.40
1072 1124 1.067565 GTGTCATTCCGAGTCAGCTGA 60.068 52.381 13.74 13.74 0.00 4.26
1277 1332 3.141398 AGCAATTGTGTGGTGTAGTGAG 58.859 45.455 7.40 0.00 0.00 3.51
1390 1448 6.170506 TCTTTTCTGTTTATCACGGCACTAT 58.829 36.000 0.00 0.00 0.00 2.12
1408 1466 7.201316 CGGCACTATTAACTTTGCAATGTAAAC 60.201 37.037 17.36 3.43 36.66 2.01
1510 1571 6.658816 AGATATGTACAGGCAAATTGTTGACA 59.341 34.615 0.33 6.87 46.22 3.58
1591 1652 2.038952 AGAGCTCAGTTACCAACATGCA 59.961 45.455 17.77 0.00 0.00 3.96
2232 2328 9.705290 ATGAAACCAATTATACAGTCAAAAACC 57.295 29.630 0.00 0.00 0.00 3.27
2357 2701 2.933834 ACTAGCCAGCCCGGGTTT 60.934 61.111 24.63 8.28 45.83 3.27
2378 2722 2.300723 TGAGCCACGCCTTCTTACTTTA 59.699 45.455 0.00 0.00 0.00 1.85
3290 3903 7.244886 TCTTCTAGTGGAATTCAGATTGACA 57.755 36.000 7.93 0.00 33.01 3.58
3291 3904 7.326454 TCTTCTAGTGGAATTCAGATTGACAG 58.674 38.462 7.93 0.00 33.01 3.51
3292 3905 6.857437 TCTAGTGGAATTCAGATTGACAGA 57.143 37.500 7.93 0.00 0.00 3.41
3293 3906 6.634805 TCTAGTGGAATTCAGATTGACAGAC 58.365 40.000 7.93 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
290 339 7.070074 TGGTTGAAATTAAGGTTTAAGAAGGCA 59.930 33.333 0.00 0.00 0.00 4.75
1072 1124 0.035317 TCGAGCATGCTCAAACCACT 59.965 50.000 38.97 9.28 42.86 4.00
1277 1332 1.152830 TCACAAGGGGGCAAACCTC 59.847 57.895 0.00 0.00 41.56 3.85
1390 1448 5.531659 TCCTCCGTTTACATTGCAAAGTTAA 59.468 36.000 13.15 7.40 0.00 2.01
1408 1466 1.303317 CCACCTTGGGTTTCCTCCG 60.303 63.158 0.00 0.00 31.02 4.63
1510 1571 4.578928 AGCGTCACTAAAATTTTCTGTGGT 59.421 37.500 24.30 14.24 0.00 4.16
2166 2262 8.596781 AAGTAATACTCTACTTCCTGACACAT 57.403 34.615 0.00 0.00 37.53 3.21
2357 2701 0.685097 AAGTAAGAAGGCGTGGCTCA 59.315 50.000 0.00 0.00 0.00 4.26
2378 2722 2.119495 AGACTTGTTCCCTGTCACACT 58.881 47.619 0.00 0.00 33.56 3.55
2689 3176 2.434185 GCACCGAACAGCGATGGA 60.434 61.111 5.32 0.00 44.57 3.41
2952 3446 4.808364 CAGCTAGGACTGATCAGCTTAAAC 59.192 45.833 22.83 8.74 42.33 2.01
3216 3829 1.806542 GAGCATTTCCAAGAGCGTGAA 59.193 47.619 0.00 0.00 0.00 3.18
3290 3903 5.067023 GCAATTTGCAGGCTAGATTAAGTCT 59.933 40.000 16.35 0.00 44.26 3.24
3291 3904 5.277047 GCAATTTGCAGGCTAGATTAAGTC 58.723 41.667 16.35 0.00 44.26 3.01
3292 3905 5.254339 GCAATTTGCAGGCTAGATTAAGT 57.746 39.130 16.35 0.00 44.26 2.24


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

AutoCloner maintained by Alex Coulton.