Multiple sequence alignment - TraesCS2A01G016900

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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 TraesCS2A01G016900 chr2A 100.000 3925 0 0 1 3925 7785140 7789064 0.000000e+00 7249.0
1 TraesCS2A01G016900 chr2A 81.614 1599 253 22 1361 2935 8630958 8632539 0.000000e+00 1286.0
2 TraesCS2A01G016900 chr2A 80.483 1491 249 23 1361 2830 9094484 9093015 0.000000e+00 1103.0
3 TraesCS2A01G016900 chr2A 80.728 1292 225 14 1587 2866 8683201 8684480 0.000000e+00 985.0
4 TraesCS2A01G016900 chr2A 82.164 998 108 36 2921 3877 8150992 8151960 0.000000e+00 793.0
5 TraesCS2A01G016900 chr2A 75.769 553 82 25 3389 3900 7515888 7515347 8.480000e-57 231.0
6 TraesCS2A01G016900 chr2D 96.212 3933 124 21 1 3916 8682014 8685938 0.000000e+00 6414.0
7 TraesCS2A01G016900 chr2D 80.674 1573 256 25 1318 2856 9588241 9589799 0.000000e+00 1177.0
8 TraesCS2A01G016900 chr2D 81.607 946 103 31 3004 3893 8838998 8838068 0.000000e+00 717.0
9 TraesCS2A01G016900 chr2D 81.604 935 102 34 3010 3893 8959045 8958130 0.000000e+00 710.0
10 TraesCS2A01G016900 chr2D 79.206 529 53 27 3381 3895 8668974 8669459 8.190000e-82 315.0
11 TraesCS2A01G016900 chr2D 80.000 115 14 7 3789 3898 8480681 8480571 4.210000e-10 76.8
12 TraesCS2A01G016900 chr2B 94.426 3678 138 38 1 3630 11399266 11402924 0.000000e+00 5594.0
13 TraesCS2A01G016900 chr2B 82.131 1539 223 30 1360 2882 138998312 138996810 0.000000e+00 1271.0
14 TraesCS2A01G016900 chr2B 81.385 1574 229 30 1323 2856 13058812 13057263 0.000000e+00 1225.0
15 TraesCS2A01G016900 chr2B 79.801 1510 239 29 1313 2780 11454279 11452794 0.000000e+00 1038.0
16 TraesCS2A01G016900 chr2B 81.845 1030 107 37 2921 3893 11993846 11994852 0.000000e+00 793.0
17 TraesCS2A01G016900 chr2B 85.670 321 16 12 3623 3916 11405041 11405358 1.060000e-80 311.0
18 TraesCS2A01G016900 chr2B 75.285 526 83 28 2874 3374 212577465 212577968 1.430000e-49 207.0
19 TraesCS2A01G016900 chr2B 80.625 160 19 5 3214 3373 138995132 138995279 3.210000e-21 113.0
20 TraesCS2A01G016900 chr2B 94.444 72 3 1 3306 3376 11995424 11995495 4.150000e-20 110.0
21 TraesCS2A01G016900 chr2B 78.333 180 29 9 3726 3898 11228510 11228334 1.490000e-19 108.0
22 TraesCS2A01G016900 chr4A 80.850 1483 252 19 1363 2822 647100333 647098860 0.000000e+00 1136.0
23 TraesCS2A01G016900 chr4A 81.172 1434 244 21 1363 2780 647998941 648000364 0.000000e+00 1129.0
24 TraesCS2A01G016900 chrUn 99.814 539 1 0 3387 3925 337298459 337297921 0.000000e+00 990.0
25 TraesCS2A01G016900 chr3D 82.690 1011 112 35 2921 3893 564001488 564000503 0.000000e+00 839.0
26 TraesCS2A01G016900 chr3A 73.339 1264 265 52 1361 2585 20771736 20772966 6.110000e-108 401.0
27 TraesCS2A01G016900 chr4B 84.118 170 24 2 3726 3894 580355586 580355753 1.130000e-35 161.0


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 TraesCS2A01G016900 chr2A 7785140 7789064 3924 False 7249.0 7249 100.0000 1 3925 1 chr2A.!!$F1 3924
1 TraesCS2A01G016900 chr2A 8630958 8632539 1581 False 1286.0 1286 81.6140 1361 2935 1 chr2A.!!$F3 1574
2 TraesCS2A01G016900 chr2A 9093015 9094484 1469 True 1103.0 1103 80.4830 1361 2830 1 chr2A.!!$R2 1469
3 TraesCS2A01G016900 chr2A 8683201 8684480 1279 False 985.0 985 80.7280 1587 2866 1 chr2A.!!$F4 1279
4 TraesCS2A01G016900 chr2A 8150992 8151960 968 False 793.0 793 82.1640 2921 3877 1 chr2A.!!$F2 956
5 TraesCS2A01G016900 chr2A 7515347 7515888 541 True 231.0 231 75.7690 3389 3900 1 chr2A.!!$R1 511
6 TraesCS2A01G016900 chr2D 8682014 8685938 3924 False 6414.0 6414 96.2120 1 3916 1 chr2D.!!$F2 3915
7 TraesCS2A01G016900 chr2D 9588241 9589799 1558 False 1177.0 1177 80.6740 1318 2856 1 chr2D.!!$F3 1538
8 TraesCS2A01G016900 chr2D 8838068 8838998 930 True 717.0 717 81.6070 3004 3893 1 chr2D.!!$R2 889
9 TraesCS2A01G016900 chr2D 8958130 8959045 915 True 710.0 710 81.6040 3010 3893 1 chr2D.!!$R3 883
10 TraesCS2A01G016900 chr2B 11399266 11405358 6092 False 2952.5 5594 90.0480 1 3916 2 chr2B.!!$F3 3915
11 TraesCS2A01G016900 chr2B 138996810 138998312 1502 True 1271.0 1271 82.1310 1360 2882 1 chr2B.!!$R4 1522
12 TraesCS2A01G016900 chr2B 13057263 13058812 1549 True 1225.0 1225 81.3850 1323 2856 1 chr2B.!!$R3 1533
13 TraesCS2A01G016900 chr2B 11452794 11454279 1485 True 1038.0 1038 79.8010 1313 2780 1 chr2B.!!$R2 1467
14 TraesCS2A01G016900 chr2B 11993846 11995495 1649 False 451.5 793 88.1445 2921 3893 2 chr2B.!!$F4 972
15 TraesCS2A01G016900 chr2B 212577465 212577968 503 False 207.0 207 75.2850 2874 3374 1 chr2B.!!$F2 500
16 TraesCS2A01G016900 chr4A 647098860 647100333 1473 True 1136.0 1136 80.8500 1363 2822 1 chr4A.!!$R1 1459
17 TraesCS2A01G016900 chr4A 647998941 648000364 1423 False 1129.0 1129 81.1720 1363 2780 1 chr4A.!!$F1 1417
18 TraesCS2A01G016900 chrUn 337297921 337298459 538 True 990.0 990 99.8140 3387 3925 1 chrUn.!!$R1 538
19 TraesCS2A01G016900 chr3D 564000503 564001488 985 True 839.0 839 82.6900 2921 3893 1 chr3D.!!$R1 972
20 TraesCS2A01G016900 chr3A 20771736 20772966 1230 False 401.0 401 73.3390 1361 2585 1 chr3A.!!$F1 1224

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
78 79 1.375523 GCCATGTCCGTTCGAGGTT 60.376 57.895 0.0 0.0 0.0 3.50 F
1461 1498 2.161855 CCTTAAGCCATGCACACTCAA 58.838 47.619 0.0 0.0 0.0 3.02 F
2024 2086 0.249699 ATGTGTGTGGCGACGAAAGA 60.250 50.000 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1670 0.036875 CCACTGTCTTGGAGGGTTCC 59.963 60.000 0.00 0.0 44.31 3.62 R
2731 2815 2.468532 AACAAAACGAGCAAACGAGG 57.531 45.000 5.12 0.0 37.03 4.63 R
2965 3053 3.890147 GGGTCGTTGGATCTGATAGTACT 59.110 47.826 0.00 0.0 0.00 2.73 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
78 79 1.375523 GCCATGTCCGTTCGAGGTT 60.376 57.895 0.00 0.00 0.00 3.50
302 312 5.362430 GGAGATCAGTATCAGGTCAAGACTT 59.638 44.000 0.00 0.00 34.28 3.01
486 496 3.440173 CGTTCCTTACCAATGAGTTGCAT 59.560 43.478 0.00 0.00 39.43 3.96
686 703 5.048083 GTCCAATACCTGCAACAATCTGAAA 60.048 40.000 0.00 0.00 0.00 2.69
906 926 6.465149 TGTTTCACGTACAATTGTTAAACACG 59.535 34.615 22.70 22.70 32.40 4.49
932 952 7.360438 GCCTTACATTTTGTTACAGAGAGAGTG 60.360 40.741 0.00 0.00 0.00 3.51
968 989 5.840715 ACAAATGCAACATAACATCACACA 58.159 33.333 0.00 0.00 0.00 3.72
1041 1064 6.303054 TGTAAAATGTGAAAGGATGGAGTCA 58.697 36.000 0.00 0.00 0.00 3.41
1242 1265 4.499399 CGTAGTTGATGTTGTAGTCATCGG 59.501 45.833 0.00 0.00 42.96 4.18
1461 1498 2.161855 CCTTAAGCCATGCACACTCAA 58.838 47.619 0.00 0.00 0.00 3.02
1820 1882 2.109126 GCTTCTGGGTGGATGCGAC 61.109 63.158 0.00 0.00 0.00 5.19
1842 1904 1.068588 GCATGTCTCGTAGGCCATACA 59.931 52.381 5.01 0.00 33.65 2.29
2024 2086 0.249699 ATGTGTGTGGCGACGAAAGA 60.250 50.000 0.00 0.00 0.00 2.52
2133 2198 3.253921 GGTGCTGGTGGTTATTACGTTTT 59.746 43.478 0.00 0.00 0.00 2.43
2289 2354 3.839293 ACTGTTCTGTCTTATGACGAGC 58.161 45.455 4.48 7.18 45.70 5.03
2690 2774 5.950549 TCCTAGTGTTAGACCGAAAGAAGAT 59.049 40.000 0.00 0.00 0.00 2.40
2731 2815 4.019231 GGAATCAAGGATACCCCCTCATAC 60.019 50.000 0.00 0.00 34.95 2.39
2857 2941 6.584185 AATGTAACCCATGTTGTACTTTCC 57.416 37.500 0.00 0.00 35.87 3.13
2958 3042 7.621428 ATGTGTTGGAGATCTCAATTGTAAG 57.379 36.000 23.85 0.00 0.00 2.34
2965 3053 9.567776 TTGGAGATCTCAATTGTAAGTAAAACA 57.432 29.630 23.85 4.28 0.00 2.83
2989 3077 2.039418 CTATCAGATCCAACGACCCCA 58.961 52.381 0.00 0.00 0.00 4.96
3074 3163 9.482175 GAATCTAATCCATATAGGTAGGTGAGT 57.518 37.037 0.00 0.00 39.02 3.41
3128 3226 7.874940 TCAAATGTTGTCTATTTGAAGGACTG 58.125 34.615 9.86 0.00 46.04 3.51
3138 3236 7.226720 GTCTATTTGAAGGACTGTGAAACTTCA 59.773 37.037 0.00 0.00 45.24 3.02
3139 3237 6.966534 ATTTGAAGGACTGTGAAACTTCAT 57.033 33.333 6.77 0.00 45.91 2.57
3152 3250 8.450578 TGTGAAACTTCATAACATTCAGAACT 57.549 30.769 0.00 0.00 39.73 3.01
3210 3326 0.108186 TCATTGCTTCGCCTCGTCAT 60.108 50.000 0.00 0.00 0.00 3.06
3212 3338 0.176680 ATTGCTTCGCCTCGTCATCT 59.823 50.000 0.00 0.00 0.00 2.90
3218 3344 0.601057 TCGCCTCGTCATCTGTTCAA 59.399 50.000 0.00 0.00 0.00 2.69
3253 3380 2.325583 TCCAACGGCATGATTCTACC 57.674 50.000 0.00 0.00 0.00 3.18
3352 3480 1.610624 CCAAGTGCCTAATGTGACCGT 60.611 52.381 0.00 0.00 0.00 4.83
3460 3591 0.727398 GGCCACAGTGATAGCGTTTC 59.273 55.000 0.62 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.452114 TCATGATTGTTTTCAGAGTGGACG 59.548 41.667 0.00 0.00 0.00 4.79
78 79 4.380843 TGGCCCAAAATCTAACAGAAGA 57.619 40.909 0.00 0.00 0.00 2.87
225 226 1.940613 GATGCAACCTGGACGATAACC 59.059 52.381 0.00 0.00 0.00 2.85
302 312 4.997395 GCACCTTGTGATTCTTCAGAGTTA 59.003 41.667 0.00 0.00 35.23 2.24
486 496 0.673985 CGGAAGCGACCATCCTGATA 59.326 55.000 0.00 0.00 33.36 2.15
686 703 2.721425 TTGGGAACGGTGAACTTCTT 57.279 45.000 0.00 0.00 0.00 2.52
906 926 6.651225 ACTCTCTCTGTAACAAAATGTAAGGC 59.349 38.462 0.00 0.00 0.00 4.35
953 973 6.942532 AGTTTGACTGTGTGATGTTATGTT 57.057 33.333 0.00 0.00 0.00 2.71
968 989 3.458487 ACCACCTCTAACCAAGTTTGACT 59.542 43.478 0.00 0.00 0.00 3.41
1461 1498 4.927049 TCCATCATCTTCTTTTGCTCCTT 58.073 39.130 0.00 0.00 0.00 3.36
1632 1670 0.036875 CCACTGTCTTGGAGGGTTCC 59.963 60.000 0.00 0.00 44.31 3.62
1820 1882 2.279517 GGCCTACGAGACATGCGG 60.280 66.667 0.00 0.00 0.00 5.69
1842 1904 7.250445 AGTTTTCGGTGTAAAGATAAACGTT 57.750 32.000 0.00 0.00 0.00 3.99
2024 2086 1.271102 GAGGAGAAGCGTGAGTGAACT 59.729 52.381 0.00 0.00 0.00 3.01
2133 2198 7.121907 CCAATCATCGTCTCCTATATCAGAAGA 59.878 40.741 1.04 1.04 32.65 2.87
2289 2354 4.962155 AGTGTCTTGAAAAGGTACCTCAG 58.038 43.478 16.64 6.77 46.24 3.35
2731 2815 2.468532 AACAAAACGAGCAAACGAGG 57.531 45.000 5.12 0.00 37.03 4.63
2857 2941 6.139638 CGAACACATCTTATTTTCATGCATCG 59.860 38.462 0.00 0.00 0.00 3.84
2958 3042 7.972277 TCGTTGGATCTGATAGTACTGTTTTAC 59.028 37.037 5.39 0.00 0.00 2.01
2965 3053 3.890147 GGGTCGTTGGATCTGATAGTACT 59.110 47.826 0.00 0.00 0.00 2.73
3107 3205 6.533730 TCACAGTCCTTCAAATAGACAACAT 58.466 36.000 0.00 0.00 32.82 2.71
3120 3218 6.861065 TGTTATGAAGTTTCACAGTCCTTC 57.139 37.500 0.00 0.00 40.49 3.46
3128 3226 8.559536 TGAGTTCTGAATGTTATGAAGTTTCAC 58.440 33.333 0.00 0.00 40.49 3.18
3152 3250 3.894427 TGGCCAGCTTCAAATTAAAGTGA 59.106 39.130 0.00 0.00 0.00 3.41
3204 3305 4.790765 ATCACTCTTGAACAGATGACGA 57.209 40.909 0.00 0.00 34.61 4.20
3210 3326 9.383519 GGATACATTTAATCACTCTTGAACAGA 57.616 33.333 0.00 0.00 34.61 3.41
3253 3380 5.160641 CAACAAGGAAATGGTAAATGACGG 58.839 41.667 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.