Multiple sequence alignment - TraesCS2A01G118800

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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 TraesCS2A01G118800 chr2A 100.000 3954 0 0 1 3954 69256101 69260054 0.000000e+00 7302
1 TraesCS2A01G118800 chr2A 99.039 3954 22 1 1 3954 306684911 306680974 0.000000e+00 7077
2 TraesCS2A01G118800 chr2A 84.708 582 65 7 1 568 26027899 26028470 9.600000e-156 560
3 TraesCS2A01G118800 chr2A 81.043 422 59 11 3472 3881 347871778 347872190 2.290000e-82 316
4 TraesCS2A01G118800 chr2A 97.101 69 2 0 3886 3954 704710210 704710278 2.500000e-22 117
5 TraesCS2A01G118800 chr5A 99.039 3954 20 1 1 3954 403897906 403901841 0.000000e+00 7075
6 TraesCS2A01G118800 chr5A 88.995 209 16 6 615 819 688125865 688126070 6.560000e-63 252
7 TraesCS2A01G118800 chr5A 86.667 225 27 2 293 515 688125413 688125636 3.050000e-61 246
8 TraesCS2A01G118800 chr5A 90.370 135 10 3 2706 2838 482027212 482027345 1.460000e-39 174
9 TraesCS2A01G118800 chr3A 99.007 2718 11 3 1238 3954 405833217 405830515 0.000000e+00 4855
10 TraesCS2A01G118800 chr3A 99.034 1242 12 0 1 1242 405843009 405841768 0.000000e+00 2228
11 TraesCS2A01G118800 chr3A 84.746 413 48 4 1 407 644202707 644203110 2.210000e-107 399
12 TraesCS2A01G118800 chr3A 84.298 242 17 15 3658 3890 455227976 455227747 2.390000e-52 217
13 TraesCS2A01G118800 chr3A 89.630 135 10 4 2706 2838 672876261 672876393 6.800000e-38 169
14 TraesCS2A01G118800 chr3A 92.593 108 8 0 2079 2186 42045565 42045458 5.290000e-34 156
15 TraesCS2A01G118800 chr3B 96.948 2490 48 4 1406 3885 561701219 561703690 0.000000e+00 4152
16 TraesCS2A01G118800 chr3B 88.951 2335 157 37 1609 3885 793141591 793143882 0.000000e+00 2789
17 TraesCS2A01G118800 chr3B 97.686 821 17 2 570 1390 561700417 561701235 0.000000e+00 1410
18 TraesCS2A01G118800 chr3B 98.063 568 10 1 1 568 561699692 561700258 0.000000e+00 987
19 TraesCS2A01G118800 chr3B 80.752 904 132 28 2968 3842 412402880 412401990 0.000000e+00 667
20 TraesCS2A01G118800 chr3B 88.189 254 25 5 570 819 70003167 70003419 8.310000e-77 298
21 TraesCS2A01G118800 chr3B 85.185 243 14 15 3658 3890 449164742 449164512 3.070000e-56 230
22 TraesCS2A01G118800 chr3B 89.431 123 8 3 1246 1364 774716298 774716419 2.460000e-32 150
23 TraesCS2A01G118800 chr6A 96.042 1895 53 5 570 2461 602829510 602831385 0.000000e+00 3064
24 TraesCS2A01G118800 chr6A 97.183 568 15 1 1 568 602828785 602829351 0.000000e+00 959
25 TraesCS2A01G118800 chr6A 89.372 207 20 2 615 819 592405923 592406129 3.920000e-65 259
26 TraesCS2A01G118800 chrUn 100.000 1622 0 0 1665 3286 384178460 384180081 0.000000e+00 2996
27 TraesCS2A01G118800 chr5B 81.728 903 124 24 2968 3842 350710553 350709664 0.000000e+00 715
28 TraesCS2A01G118800 chr5B 87.451 255 26 6 570 819 672541152 672540899 5.000000e-74 289
29 TraesCS2A01G118800 chr5B 82.831 332 38 8 3561 3883 415054874 415055195 3.010000e-71 279
30 TraesCS2A01G118800 chr5B 90.686 204 17 2 1374 1575 505360998 505361201 1.810000e-68 270
31 TraesCS2A01G118800 chr5B 80.342 351 41 16 1731 2058 347127649 347127994 1.420000e-59 241
32 TraesCS2A01G118800 chr5B 85.965 228 25 6 1144 1364 533416995 533417222 1.840000e-58 237
33 TraesCS2A01G118800 chr5B 100.000 69 0 0 3886 3954 678454812 678454880 1.150000e-25 128
34 TraesCS2A01G118800 chr7B 82.166 471 69 10 2968 3429 524611207 524611671 1.330000e-104 390
35 TraesCS2A01G118800 chr7B 85.185 243 14 15 3658 3890 353328535 353328765 3.070000e-56 230
36 TraesCS2A01G118800 chr4A 88.073 327 39 0 2075 2401 222106844 222107170 4.790000e-104 388
37 TraesCS2A01G118800 chr7A 84.262 413 41 7 1 407 374542661 374542267 8.020000e-102 381
38 TraesCS2A01G118800 chr7A 92.623 122 8 1 2706 2826 731392157 731392036 1.460000e-39 174
39 TraesCS2A01G118800 chr7A 89.431 123 9 2 1246 1364 121783571 121783693 6.840000e-33 152
40 TraesCS2A01G118800 chr6D 83.649 422 49 11 3472 3884 425060481 425060891 2.880000e-101 379
41 TraesCS2A01G118800 chr6B 87.795 254 27 4 570 819 599819473 599819726 1.070000e-75 294
42 TraesCS2A01G118800 chr6B 84.120 233 24 7 3658 3882 536849880 536849653 3.100000e-51 213
43 TraesCS2A01G118800 chr6B 98.551 69 1 0 3886 3954 176215908 176215840 5.370000e-24 122
44 TraesCS2A01G118800 chr6B 98.551 69 1 0 3886 3954 176240690 176240622 5.370000e-24 122
45 TraesCS2A01G118800 chr6B 97.101 69 2 0 3886 3954 176154602 176154534 2.500000e-22 117
46 TraesCS2A01G118800 chr6B 97.101 69 2 0 3886 3954 176178572 176178504 2.500000e-22 117
47 TraesCS2A01G118800 chr2B 87.795 254 27 4 570 819 183534428 183534175 1.070000e-75 294
48 TraesCS2A01G118800 chr2D 86.347 271 34 2 293 561 117801407 117801676 3.860000e-75 292
49 TraesCS2A01G118800 chr2D 88.942 208 20 3 615 819 117801697 117801904 1.820000e-63 254
50 TraesCS2A01G118800 chr3D 86.400 250 30 4 574 819 550355777 550356026 1.810000e-68 270
51 TraesCS2A01G118800 chr3D 86.096 187 18 7 2987 3172 266665125 266665304 1.120000e-45 195
52 TraesCS2A01G118800 chr4B 83.966 237 23 9 3658 3884 305510803 305510572 3.100000e-51 213
53 TraesCS2A01G118800 chr4B 86.000 200 24 2 369 568 241184998 241185193 1.110000e-50 211
54 TraesCS2A01G118800 chr1B 89.759 166 16 1 1409 1573 562727229 562727064 1.110000e-50 211
55 TraesCS2A01G118800 chr1B 88.710 124 9 3 1246 1364 562727811 562727688 3.180000e-31 147
56 TraesCS2A01G118800 chr1A 86.992 123 12 2 1246 1364 9766932 9767054 6.890000e-28 135


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 TraesCS2A01G118800 chr2A 69256101 69260054 3953 False 7302.0 7302 100.000000 1 3954 1 chr2A.!!$F2 3953
1 TraesCS2A01G118800 chr2A 306680974 306684911 3937 True 7077.0 7077 99.039000 1 3954 1 chr2A.!!$R1 3953
2 TraesCS2A01G118800 chr2A 26027899 26028470 571 False 560.0 560 84.708000 1 568 1 chr2A.!!$F1 567
3 TraesCS2A01G118800 chr5A 403897906 403901841 3935 False 7075.0 7075 99.039000 1 3954 1 chr5A.!!$F1 3953
4 TraesCS2A01G118800 chr5A 688125413 688126070 657 False 249.0 252 87.831000 293 819 2 chr5A.!!$F3 526
5 TraesCS2A01G118800 chr3A 405830515 405833217 2702 True 4855.0 4855 99.007000 1238 3954 1 chr3A.!!$R2 2716
6 TraesCS2A01G118800 chr3A 405841768 405843009 1241 True 2228.0 2228 99.034000 1 1242 1 chr3A.!!$R3 1241
7 TraesCS2A01G118800 chr3B 793141591 793143882 2291 False 2789.0 2789 88.951000 1609 3885 1 chr3B.!!$F3 2276
8 TraesCS2A01G118800 chr3B 561699692 561703690 3998 False 2183.0 4152 97.565667 1 3885 3 chr3B.!!$F4 3884
9 TraesCS2A01G118800 chr3B 412401990 412402880 890 True 667.0 667 80.752000 2968 3842 1 chr3B.!!$R1 874
10 TraesCS2A01G118800 chr6A 602828785 602831385 2600 False 2011.5 3064 96.612500 1 2461 2 chr6A.!!$F2 2460
11 TraesCS2A01G118800 chrUn 384178460 384180081 1621 False 2996.0 2996 100.000000 1665 3286 1 chrUn.!!$F1 1621
12 TraesCS2A01G118800 chr5B 350709664 350710553 889 True 715.0 715 81.728000 2968 3842 1 chr5B.!!$R1 874

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
1094 1429 2.093181 TGTTGCATACGGAGGCTTACAT 60.093 45.455 5.6 0.0 32.18 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3286 3687 8.032952 ACATACAGTACATGTCACATTCAAAG 57.967 34.615 0.0 0.0 42.7 2.77 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
1094 1429 2.093181 TGTTGCATACGGAGGCTTACAT 60.093 45.455 5.60 0.00 32.18 2.29
1130 1465 2.678934 AGCGAGGGTGGCGTTCTA 60.679 61.111 0.00 0.00 35.00 2.10
1381 1720 2.310349 ACTGGCCAGTTCTAGAGAGAGA 59.690 50.000 33.20 0.00 38.83 3.10
1382 1721 2.951642 CTGGCCAGTTCTAGAGAGAGAG 59.048 54.545 25.53 0.00 31.77 3.20
1383 1722 2.578480 TGGCCAGTTCTAGAGAGAGAGA 59.422 50.000 0.00 0.00 31.77 3.10
1384 1723 3.214328 GGCCAGTTCTAGAGAGAGAGAG 58.786 54.545 0.00 0.00 31.77 3.20
1385 1724 3.118038 GGCCAGTTCTAGAGAGAGAGAGA 60.118 52.174 0.00 0.00 31.77 3.10
1386 1725 4.130118 GCCAGTTCTAGAGAGAGAGAGAG 58.870 52.174 0.00 0.00 31.77 3.20
1387 1726 4.141711 GCCAGTTCTAGAGAGAGAGAGAGA 60.142 50.000 0.00 0.00 31.77 3.10
1388 1727 5.605534 CCAGTTCTAGAGAGAGAGAGAGAG 58.394 50.000 0.00 0.00 31.77 3.20
1389 1728 5.363868 CCAGTTCTAGAGAGAGAGAGAGAGA 59.636 48.000 0.00 0.00 31.77 3.10
1390 1729 6.462207 CCAGTTCTAGAGAGAGAGAGAGAGAG 60.462 50.000 0.00 0.00 31.77 3.20
1391 1730 6.322456 CAGTTCTAGAGAGAGAGAGAGAGAGA 59.678 46.154 0.00 0.00 31.77 3.10
1392 1731 6.549364 AGTTCTAGAGAGAGAGAGAGAGAGAG 59.451 46.154 0.00 0.00 31.77 3.20
1393 1732 6.267492 TCTAGAGAGAGAGAGAGAGAGAGA 57.733 45.833 0.00 0.00 0.00 3.10
1394 1733 6.303054 TCTAGAGAGAGAGAGAGAGAGAGAG 58.697 48.000 0.00 0.00 0.00 3.20
1395 1734 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1396 1735 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1443 1786 9.525826 AGAGATGTATGAGAAACCAAGAAAAAT 57.474 29.630 0.00 0.00 0.00 1.82
3286 3687 8.824159 ATGTGTTATCTGCAGTATATCTCAAC 57.176 34.615 14.67 7.48 0.00 3.18
3861 4287 0.823356 TGGTCTTTGGGCTTGCTCAC 60.823 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
781 1116 5.782893 TTAACAAGCCAAGCAAACAGTAT 57.217 34.783 0.00 0.0 0.00 2.12
1381 1720 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.0 0.00 3.10
1382 1721 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.0 0.00 3.20
1383 1722 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.0 0.00 3.10
1384 1723 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.0 0.00 3.20
1385 1724 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.0 0.00 3.10
1386 1725 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.0 0.00 3.20
1387 1726 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.0 0.00 3.10
1388 1727 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.0 0.00 3.20
1389 1728 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.0 0.00 3.10
1390 1729 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.0 0.00 3.20
1391 1730 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.0 0.00 3.10
1392 1731 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.0 0.00 3.20
1393 1732 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.0 0.00 3.10
1394 1733 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.0 0.00 3.20
1395 1734 5.960811 TCTTTCTCTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.0 0.00 3.10
1396 1735 6.097554 TCTCTTTCTCTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.0 0.00 3.20
1443 1786 7.685481 TCAAGAAAAATGTACATGTCCTCCTA 58.315 34.615 9.63 0.0 0.00 2.94
3286 3687 8.032952 ACATACAGTACATGTCACATTCAAAG 57.967 34.615 0.00 0.0 42.70 2.77
3815 4241 6.416750 GTCAAACCCGAAGTGTTTTGAAATAG 59.583 38.462 0.00 0.0 33.82 1.73


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

AutoCloner maintained by Alex Coulton.