Multiple sequence alignment - TraesCS4A01G407400

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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 TraesCS4A01G407400 chr4A 100.000 2348 0 0 1 2348 680344238 680341891 0.000000e+00 4337
1 TraesCS4A01G407400 chr4A 97.615 2348 55 1 1 2348 680334030 680331684 0.000000e+00 4024
2 TraesCS4A01G407400 chr7A 96.469 1926 67 1 423 2348 652172971 652171047 0.000000e+00 3179
3 TraesCS4A01G407400 chr5D 95.176 1928 72 1 421 2348 363187067 363185161 0.000000e+00 3025
4 TraesCS4A01G407400 chr6D 95.073 1928 74 1 421 2348 72037763 72035857 0.000000e+00 3014
5 TraesCS4A01G407400 chr7D 94.658 1928 82 1 421 2348 95072194 95074100 0.000000e+00 2970
6 TraesCS4A01G407400 chr2A 97.654 1577 36 1 772 2348 642732543 642734118 0.000000e+00 2706
7 TraesCS4A01G407400 chr1D 90.989 1709 127 12 664 2348 454864593 454862888 0.000000e+00 2278
8 TraesCS4A01G407400 chr1D 93.959 1225 53 1 421 1645 107600652 107601855 0.000000e+00 1832
9 TraesCS4A01G407400 chr1D 96.751 708 22 1 1641 2348 107610492 107611198 0.000000e+00 1179
10 TraesCS4A01G407400 chr1D 92.000 250 19 1 1 249 394187489 394187240 1.340000e-92 350
11 TraesCS4A01G407400 chr6B 94.127 1311 60 7 1038 2348 413740005 413738712 0.000000e+00 1978
12 TraesCS4A01G407400 chr6B 96.429 252 8 1 1 251 215740216 215739965 4.670000e-112 414
13 TraesCS4A01G407400 chr6B 96.429 252 8 1 1 251 558776216 558776467 4.670000e-112 414
14 TraesCS4A01G407400 chr6B 96.429 252 8 1 1 251 558858954 558859205 4.670000e-112 414
15 TraesCS4A01G407400 chr6B 96.032 252 9 1 1 251 558693356 558693607 2.170000e-110 409
16 TraesCS4A01G407400 chr6B 97.076 171 5 0 248 418 558693656 558693826 2.950000e-74 289
17 TraesCS4A01G407400 chr6B 96.491 171 6 0 248 418 558776516 558776686 1.370000e-72 283
18 TraesCS4A01G407400 chr6B 95.906 171 7 0 248 418 558859254 558859424 6.390000e-71 278
19 TraesCS4A01G407400 chr6B 95.322 171 8 0 248 418 215739916 215739746 2.970000e-69 272
20 TraesCS4A01G407400 chr4B 94.489 1252 66 3 421 1670 246309804 246311054 0.000000e+00 1927
21 TraesCS4A01G407400 chr7B 83.158 1900 289 22 469 2348 220295956 220294068 0.000000e+00 1707
22 TraesCS4A01G407400 chr5A 98.008 251 5 0 1 251 416176492 416176742 9.960000e-119 436
23 TraesCS4A01G407400 chr5A 97.661 171 4 0 248 418 416176791 416176961 6.350000e-76 294
24 TraesCS4A01G407400 chr6A 96.032 252 9 1 1 251 453566215 453566466 2.170000e-110 409
25 TraesCS4A01G407400 chr6A 95.238 168 8 0 248 415 453566515 453566682 1.380000e-67 267
26 TraesCS4A01G407400 chr5B 95.635 252 10 1 1 251 339995175 339995426 1.010000e-108 403
27 TraesCS4A01G407400 chr5B 95.906 171 7 0 248 418 339995475 339995645 6.390000e-71 278
28 TraesCS4A01G407400 chr3D 92.265 181 13 1 238 418 110745802 110745981 2.990000e-64 255


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 TraesCS4A01G407400 chr4A 680341891 680344238 2347 True 4337 4337 100.000 1 2348 1 chr4A.!!$R2 2347
1 TraesCS4A01G407400 chr4A 680331684 680334030 2346 True 4024 4024 97.615 1 2348 1 chr4A.!!$R1 2347
2 TraesCS4A01G407400 chr7A 652171047 652172971 1924 True 3179 3179 96.469 423 2348 1 chr7A.!!$R1 1925
3 TraesCS4A01G407400 chr5D 363185161 363187067 1906 True 3025 3025 95.176 421 2348 1 chr5D.!!$R1 1927
4 TraesCS4A01G407400 chr6D 72035857 72037763 1906 True 3014 3014 95.073 421 2348 1 chr6D.!!$R1 1927
5 TraesCS4A01G407400 chr7D 95072194 95074100 1906 False 2970 2970 94.658 421 2348 1 chr7D.!!$F1 1927
6 TraesCS4A01G407400 chr2A 642732543 642734118 1575 False 2706 2706 97.654 772 2348 1 chr2A.!!$F1 1576
7 TraesCS4A01G407400 chr1D 454862888 454864593 1705 True 2278 2278 90.989 664 2348 1 chr1D.!!$R2 1684
8 TraesCS4A01G407400 chr1D 107600652 107601855 1203 False 1832 1832 93.959 421 1645 1 chr1D.!!$F1 1224
9 TraesCS4A01G407400 chr1D 107610492 107611198 706 False 1179 1179 96.751 1641 2348 1 chr1D.!!$F2 707
10 TraesCS4A01G407400 chr6B 413738712 413740005 1293 True 1978 1978 94.127 1038 2348 1 chr6B.!!$R1 1310
11 TraesCS4A01G407400 chr4B 246309804 246311054 1250 False 1927 1927 94.489 421 1670 1 chr4B.!!$F1 1249
12 TraesCS4A01G407400 chr7B 220294068 220295956 1888 True 1707 1707 83.158 469 2348 1 chr7B.!!$R1 1879

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
831 832 0.396435 TTGATGCTGGACACGACCTT 59.604 50.0 0.0 0.0 0.0 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1720 1.20233 AGCCTTGACAGCTGCTCTAT 58.798 50.0 15.27 0.0 39.69 1.98 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
278 279 5.450137 CGGGACATAGATATCCACGTAATCC 60.450 48.000 0.00 0.00 36.65 3.01
419 420 2.483013 GGATGTAGCCGTCAATGTAGCA 60.483 50.000 0.00 0.00 0.00 3.49
713 714 1.338200 GCGACCTCTTCTGGACATGTT 60.338 52.381 0.00 0.00 0.00 2.71
718 719 0.613260 TCTTCTGGACATGTTCCCGG 59.387 55.000 0.46 3.77 45.17 5.73
831 832 0.396435 TTGATGCTGGACACGACCTT 59.604 50.000 0.00 0.00 0.00 3.50
904 905 1.202639 TCTTCTGCTCAAAACAGCCGA 60.203 47.619 0.00 0.00 38.80 5.54
1168 1180 1.604438 CGACCCTGAATGTGTTCACGA 60.604 52.381 0.00 0.00 39.36 4.35
1227 1239 2.632512 GGCCATGAGGGACTTTTTCAAA 59.367 45.455 0.00 0.00 43.78 2.69
1334 1347 1.992519 GATGGCCAGGGATCACAGCT 61.993 60.000 13.05 0.00 0.00 4.24
1437 1459 5.183228 GGGATTGCACTTGCTACTAGTTTA 58.817 41.667 0.00 0.00 42.66 2.01
1735 1771 4.431416 ACACCACTTGTCATTTGGTCTA 57.569 40.909 3.37 0.00 41.93 2.59
1881 1917 2.859165 TGACAACCTCCTTCATGTCC 57.141 50.000 0.00 0.00 41.08 4.02
1960 1996 4.065789 GACTCCTCCTTCAAAATCACGTT 58.934 43.478 0.00 0.00 0.00 3.99
2085 2122 0.251916 CCAAATCTACCGTGCCAGGA 59.748 55.000 1.23 0.00 34.73 3.86
2242 2279 5.290493 TGCAAACTTGACTCCTTCTTCTA 57.710 39.130 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
278 279 4.183865 TGGTGCTCTTTTGATCTATGTCG 58.816 43.478 0.00 0.00 0.00 4.35
342 343 8.070769 GTCCTTCTCTTTGACTTTGTTACAATC 58.929 37.037 0.00 0.00 0.00 2.67
354 355 2.156343 AGTGCGTCCTTCTCTTTGAC 57.844 50.000 0.00 0.00 0.00 3.18
378 379 1.080093 TAGCAACGAGGAAGTGGCG 60.080 57.895 0.00 0.00 45.39 5.69
419 420 1.539869 ATGGGAGGAGTGCACAGGT 60.540 57.895 21.04 1.49 0.00 4.00
427 428 1.003355 CAACACGCATGGGAGGAGT 60.003 57.895 17.76 6.45 0.00 3.85
679 680 2.891936 TCGCTGCATCATGGTCGC 60.892 61.111 0.00 0.00 0.00 5.19
846 847 2.345244 CAGGGCACAACGAGCTCT 59.655 61.111 12.85 0.00 45.50 4.09
921 922 1.949525 GCTTCAGAAGGTTGCACAGAA 59.050 47.619 12.30 0.00 0.00 3.02
1144 1156 2.367241 TGAACACATTCAGGGTCGAAGA 59.633 45.455 0.00 0.00 40.01 2.87
1168 1180 2.093021 GGAGCTGCTCCTTGAATCTCTT 60.093 50.000 35.51 0.00 46.41 2.85
1227 1239 2.069273 GCAACAGCACTATCGTCAAGT 58.931 47.619 0.00 0.00 0.00 3.16
1684 1720 1.202330 AGCCTTGACAGCTGCTCTAT 58.798 50.000 15.27 0.00 39.69 1.98
1735 1771 3.704061 GCTCAACTTAGTCTCCTGGAGAT 59.296 47.826 27.96 18.56 40.98 2.75
1881 1917 2.184322 CGAGGTGGTGATGTCGGG 59.816 66.667 0.00 0.00 0.00 5.14
1960 1996 3.151710 CGGTGGGGCCATAGACGA 61.152 66.667 4.39 0.00 36.97 4.20
2085 2122 8.063339 CGGTTAACATTCCGTTTGTTTTTATT 57.937 30.769 8.10 0.00 41.58 1.40
2242 2279 3.542676 TGTCCCACTCGGCGTTGT 61.543 61.111 6.85 4.49 0.00 3.32


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

AutoCloner maintained by Alex Coulton.