Multiple sequence alignment - TraesCS3A01G478900

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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 TraesCS3A01G478900 chr3A 100.000 3318 0 0 1 3318 710836017 710839334 0.000000e+00 6128
1 TraesCS3A01G478900 chr3A 86.177 2344 280 20 1001 3318 711056723 711059048 0.000000e+00 2494
2 TraesCS3A01G478900 chr3A 85.216 1434 181 13 1909 3318 710937207 710938633 0.000000e+00 1445
3 TraesCS3A01G478900 chr3A 86.491 1103 119 15 2243 3318 710948358 710949457 0.000000e+00 1184
4 TraesCS3A01G478900 chr3A 84.078 1231 171 18 699 1917 710935303 710936520 0.000000e+00 1164
5 TraesCS3A01G478900 chr3A 81.915 376 31 18 1 355 644630290 644629931 1.950000e-72 283
6 TraesCS3A01G478900 chr3D 97.326 2580 63 3 740 3318 574783114 574780540 0.000000e+00 4377
7 TraesCS3A01G478900 chr3D 88.040 1112 115 7 2224 3318 575479921 575481031 0.000000e+00 1301
8 TraesCS3A01G478900 chr3D 84.781 1163 155 10 2175 3318 575527340 575528499 0.000000e+00 1147
9 TraesCS3A01G478900 chr3D 94.087 761 27 8 1 755 574785606 574784858 0.000000e+00 1140
10 TraesCS3A01G478900 chr3D 83.201 1137 169 13 2201 3318 575546577 575547710 0.000000e+00 1022
11 TraesCS3A01G478900 chr3D 83.934 971 142 10 987 1949 575545389 575546353 0.000000e+00 917
12 TraesCS3A01G478900 chr3D 83.424 368 41 12 1 357 548716511 548716153 1.150000e-84 324
13 TraesCS3A01G478900 chr3D 83.750 320 40 9 2 318 360579764 360579454 3.240000e-75 292
14 TraesCS3A01G478900 chr3B 95.145 1730 72 4 380 2108 765547306 765549024 0.000000e+00 2719
15 TraesCS3A01G478900 chr3B 93.596 1218 66 7 2110 3318 765549080 765550294 0.000000e+00 1807
16 TraesCS3A01G478900 chr3B 85.425 1434 175 15 1909 3318 765669983 765671406 0.000000e+00 1459
17 TraesCS3A01G478900 chr3B 84.685 1430 188 16 1909 3318 765623269 765624687 0.000000e+00 1399
18 TraesCS3A01G478900 chr3B 84.288 1432 177 24 1909 3318 765658031 765659436 0.000000e+00 1354
19 TraesCS3A01G478900 chr3B 84.259 1404 164 29 558 1918 765667735 765669124 0.000000e+00 1315
20 TraesCS3A01G478900 chr3B 87.263 1107 123 13 816 1911 765621768 765622867 0.000000e+00 1247
21 TraesCS3A01G478900 chr3B 88.727 958 103 5 889 1844 765656634 765657588 0.000000e+00 1166
22 TraesCS3A01G478900 chr3B 82.968 1139 169 16 2201 3318 765928465 765929599 0.000000e+00 1005
23 TraesCS3A01G478900 chr3B 80.762 1076 184 18 1000 2063 765853700 765854764 0.000000e+00 819
24 TraesCS3A01G478900 chr3B 94.663 356 14 5 1 354 765546956 765547308 6.260000e-152 547
25 TraesCS3A01G478900 chr6D 83.880 366 43 12 1 356 456737272 456737631 5.300000e-88 335
26 TraesCS3A01G478900 chr1B 88.339 283 22 9 1 276 263981630 263981352 2.470000e-86 329
27 TraesCS3A01G478900 chr1D 82.933 375 41 12 1 357 58567750 58568119 1.920000e-82 316
28 TraesCS3A01G478900 chr4A 81.694 366 52 10 2 357 596787441 596787801 1.160000e-74 291


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 TraesCS3A01G478900 chr3A 710836017 710839334 3317 False 6128.0 6128 100.0000 1 3318 1 chr3A.!!$F1 3317
1 TraesCS3A01G478900 chr3A 711056723 711059048 2325 False 2494.0 2494 86.1770 1001 3318 1 chr3A.!!$F3 2317
2 TraesCS3A01G478900 chr3A 710935303 710938633 3330 False 1304.5 1445 84.6470 699 3318 2 chr3A.!!$F4 2619
3 TraesCS3A01G478900 chr3A 710948358 710949457 1099 False 1184.0 1184 86.4910 2243 3318 1 chr3A.!!$F2 1075
4 TraesCS3A01G478900 chr3D 574780540 574785606 5066 True 2758.5 4377 95.7065 1 3318 2 chr3D.!!$R3 3317
5 TraesCS3A01G478900 chr3D 575479921 575481031 1110 False 1301.0 1301 88.0400 2224 3318 1 chr3D.!!$F1 1094
6 TraesCS3A01G478900 chr3D 575527340 575528499 1159 False 1147.0 1147 84.7810 2175 3318 1 chr3D.!!$F2 1143
7 TraesCS3A01G478900 chr3D 575545389 575547710 2321 False 969.5 1022 83.5675 987 3318 2 chr3D.!!$F3 2331
8 TraesCS3A01G478900 chr3B 765546956 765550294 3338 False 1691.0 2719 94.4680 1 3318 3 chr3B.!!$F3 3317
9 TraesCS3A01G478900 chr3B 765667735 765671406 3671 False 1387.0 1459 84.8420 558 3318 2 chr3B.!!$F6 2760
10 TraesCS3A01G478900 chr3B 765621768 765624687 2919 False 1323.0 1399 85.9740 816 3318 2 chr3B.!!$F4 2502
11 TraesCS3A01G478900 chr3B 765656634 765659436 2802 False 1260.0 1354 86.5075 889 3318 2 chr3B.!!$F5 2429
12 TraesCS3A01G478900 chr3B 765928465 765929599 1134 False 1005.0 1005 82.9680 2201 3318 1 chr3B.!!$F2 1117
13 TraesCS3A01G478900 chr3B 765853700 765854764 1064 False 819.0 819 80.7620 1000 2063 1 chr3B.!!$F1 1063

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
970 2782 2.186384 CGCTTCCAGCCCTCTGAG 59.814 66.667 0.0 0.0 42.95 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2486 5580 3.652869 TCTTGAGGACACCCTTTCTCATT 59.347 43.478 0.0 0.0 44.53 2.57 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
125 136 5.271598 TGAAATACATTGGAATGAGGGCTT 58.728 37.500 6.37 0.00 39.67 4.35
195 207 3.085952 TCCCCAGACCATGAATTTGTC 57.914 47.619 0.00 0.00 0.00 3.18
276 288 6.147821 CCTCACATCCTTGTTTACTTGTACAG 59.852 42.308 0.00 0.00 32.34 2.74
373 385 4.436242 AACGCTTCTCTCGAGTTATTGA 57.564 40.909 13.13 1.92 0.00 2.57
429 441 4.863491 CAGGTTCAAATCTGTCCTTTGTG 58.137 43.478 0.00 0.00 35.56 3.33
743 785 2.841442 AGCCTTGTCAGAGTAACACC 57.159 50.000 0.00 0.00 0.00 4.16
825 2627 2.611292 GCAGCCAGACTATGAACATGAC 59.389 50.000 0.00 0.00 0.00 3.06
970 2782 2.186384 CGCTTCCAGCCCTCTGAG 59.814 66.667 0.00 0.00 42.95 3.35
1111 2925 1.039068 AGGCATCGAGTCTCTCATGG 58.961 55.000 9.55 0.00 0.00 3.66
1112 2926 0.749649 GGCATCGAGTCTCTCATGGT 59.250 55.000 9.55 0.00 0.00 3.55
1218 3032 4.136796 CAGGAAATGTCAAGGAGTTGTCA 58.863 43.478 0.00 0.00 36.37 3.58
1397 3211 1.065854 AGCGGTTCATCAAGCTAAGCT 60.066 47.619 0.00 0.00 42.56 3.74
1770 3584 4.053983 AGTATGCACGCAATCATAGTGAG 58.946 43.478 0.00 0.00 38.06 3.51
1792 3606 5.206587 AGGAATGGGAAGAAAATCATCTGG 58.793 41.667 0.00 0.00 0.00 3.86
1935 4953 7.263100 TGCATCTTGATACCATATTGTTGAC 57.737 36.000 0.00 0.00 0.00 3.18
1941 4959 9.952030 TCTTGATACCATATTGTTGACTTACAA 57.048 29.630 0.00 0.00 41.81 2.41
2115 5201 7.938140 AGTTGCACATAAGTTATGGTATGTT 57.062 32.000 23.49 2.27 38.57 2.71
2317 5408 5.660864 TGACATATGGGATACAGAAGTGTGA 59.339 40.000 7.80 0.00 37.52 3.58
2384 5478 2.102070 AATTACGACAACCCGCATCA 57.898 45.000 0.00 0.00 0.00 3.07
2386 5480 1.647346 TTACGACAACCCGCATCATC 58.353 50.000 0.00 0.00 0.00 2.92
2909 6007 8.773033 AAATAGAAGTATGATCCAGCCAATTT 57.227 30.769 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
195 207 9.925268 ACGTTGAAATACTACTTGTACAAAAAG 57.075 29.630 10.03 11.77 33.45 2.27
311 323 7.659390 ACATGAAGGCCGAATTTTTGAAAAATA 59.341 29.630 15.45 0.00 0.00 1.40
373 385 6.357579 TGAATTGTTGCATCATTTAAGGGT 57.642 33.333 0.00 0.00 0.00 4.34
704 746 6.700352 AGGCTTAGATTAGATCTTGAGATGC 58.300 40.000 0.00 0.00 40.76 3.91
718 760 6.166982 GTGTTACTCTGACAAGGCTTAGATT 58.833 40.000 0.00 0.00 0.00 2.40
743 785 5.505286 CGGTTGTGGTAGTAATAGTAGACG 58.495 45.833 0.00 0.00 0.00 4.18
825 2627 6.072618 ACGATGTATCTGGATTAGTTAGACGG 60.073 42.308 0.00 0.00 0.00 4.79
876 2684 5.615925 CTGGCTAAGGTATAGAAACCAGT 57.384 43.478 0.00 0.00 42.40 4.00
970 2782 0.036875 CTCTGGGAGTGGTTTGGGTC 59.963 60.000 0.00 0.00 0.00 4.46
1111 2925 3.303857 GCATGCATCAATGTGAGCTCTAC 60.304 47.826 14.21 11.83 0.00 2.59
1112 2926 2.876550 GCATGCATCAATGTGAGCTCTA 59.123 45.455 14.21 4.39 0.00 2.43
1218 3032 7.180766 ACATCAACAATTTCCTCCATTTGGTAT 59.819 33.333 0.00 0.00 36.34 2.73
1770 3584 4.958581 ACCAGATGATTTTCTTCCCATTCC 59.041 41.667 0.00 0.00 0.00 3.01
1935 4953 6.704512 ACGCCAAAAGCATAAAATTGTAAG 57.295 33.333 0.00 0.00 44.04 2.34
1941 4959 7.548780 ACATCATTTACGCCAAAAGCATAAAAT 59.451 29.630 0.00 0.00 41.95 1.82
2115 5201 6.627087 ATTCTGAGACCTAGATTTCCACAA 57.373 37.500 0.00 0.00 0.00 3.33
2317 5408 5.863935 GGAGAAAGCGCACTTGATTAATTTT 59.136 36.000 11.47 0.00 35.85 1.82
2384 5478 4.190001 CAGCATGCTTTAGAGACACTGAT 58.810 43.478 19.98 0.00 0.00 2.90
2451 5545 8.846943 TTTATAGAAGAGCATTCTTGACACAA 57.153 30.769 9.20 0.00 43.63 3.33
2486 5580 3.652869 TCTTGAGGACACCCTTTCTCATT 59.347 43.478 0.00 0.00 44.53 2.57
2853 5951 5.472137 TCATTGAAGTAGTTGTTACCAAGCC 59.528 40.000 0.00 0.00 32.37 4.35
2909 6007 9.617523 TTGTTTATCTTCTCTATCATCAATGCA 57.382 29.630 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.