Multiple sequence alignment - TraesCS3B01G529200

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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 TraesCS3B01G529200 chr3B 100.000 2538 0 0 1 2538 770965677 770963140 0.000000e+00 4687.0
1 TraesCS3B01G529200 chr3B 93.208 1811 100 3 1 1807 771241041 771242832 0.000000e+00 2641.0
2 TraesCS3B01G529200 chr3B 90.383 1643 91 23 1 1626 771177507 771179099 0.000000e+00 2097.0
3 TraesCS3B01G529200 chr3B 89.788 754 53 14 1808 2538 771242865 771243617 0.000000e+00 944.0
4 TraesCS3B01G529200 chr3B 88.712 753 50 17 1808 2538 771179396 771180135 0.000000e+00 887.0
5 TraesCS3B01G529200 chr3B 78.856 402 74 6 1855 2248 372190877 372190479 6.960000e-66 261.0
6 TraesCS3B01G529200 chr3D 91.736 2541 157 22 19 2538 578040126 578042634 0.000000e+00 3480.0
7 TraesCS3B01G529200 chr3D 86.257 2474 248 47 47 2485 577780535 577778119 0.000000e+00 2601.0
8 TraesCS3B01G529200 chr3D 92.954 1107 56 8 704 1807 577668970 577667883 0.000000e+00 1592.0
9 TraesCS3B01G529200 chr3D 84.490 1657 179 37 704 2337 577753004 577751403 0.000000e+00 1565.0
10 TraesCS3B01G529200 chr3D 90.521 749 46 9 1813 2538 577667844 577667098 0.000000e+00 966.0
11 TraesCS3B01G529200 chr3D 78.205 390 80 4 1855 2240 24569600 24569212 7.010000e-61 244.0
12 TraesCS3B01G529200 chr3D 92.000 100 8 0 181 280 577780265 577780166 9.470000e-30 141.0
13 TraesCS3B01G529200 chr3A 90.812 1121 77 17 698 1804 713308513 713307405 0.000000e+00 1476.0
14 TraesCS3B01G529200 chr3A 89.157 913 85 12 904 1807 713342779 713341872 0.000000e+00 1125.0
15 TraesCS3B01G529200 chr3A 92.180 665 46 3 650 1311 713418432 713417771 0.000000e+00 935.0
16 TraesCS3B01G529200 chr3A 84.913 749 80 23 1813 2537 713307365 713306626 0.000000e+00 726.0
17 TraesCS3B01G529200 chr3A 82.713 752 99 18 1808 2538 713341838 713341097 7.660000e-180 640.0
18 TraesCS3B01G529200 chr3A 87.500 464 52 3 1341 1802 713417774 713417315 4.810000e-147 531.0
19 TraesCS3B01G529200 chr3A 95.098 102 5 0 701 802 713343477 713343376 7.270000e-36 161.0
20 TraesCS3B01G529200 chr1D 78.663 389 77 5 1855 2239 466407015 466406629 1.170000e-63 254.0
21 TraesCS3B01G529200 chr6D 93.431 137 9 0 284 420 377566427 377566291 1.190000e-48 204.0
22 TraesCS3B01G529200 chr6D 87.500 160 19 1 553 711 28413923 28413764 1.550000e-42 183.0
23 TraesCS3B01G529200 chr6D 91.892 111 7 2 179 289 377566396 377566288 1.220000e-33 154.0
24 TraesCS3B01G529200 chr4D 88.623 167 18 1 545 710 386984671 386984837 4.280000e-48 202.0
25 TraesCS3B01G529200 chr2A 88.820 161 18 0 545 705 367649318 367649158 5.540000e-47 198.0
26 TraesCS3B01G529200 chr2A 90.299 134 13 0 288 421 34657937 34658070 2.600000e-40 176.0
27 TraesCS3B01G529200 chr2A 82.474 194 31 3 518 708 12003247 12003440 1.560000e-37 167.0
28 TraesCS3B01G529200 chr2A 90.090 111 9 2 180 289 34657965 34658074 2.630000e-30 143.0
29 TraesCS3B01G529200 chr4B 85.632 174 22 3 535 707 362845772 362845601 2.010000e-41 180.0
30 TraesCS3B01G529200 chr4B 89.130 138 13 2 283 419 36809713 36809849 1.210000e-38 171.0
31 TraesCS3B01G529200 chr7A 89.630 135 14 0 286 420 565767136 565767002 3.360000e-39 172.0
32 TraesCS3B01G529200 chr7A 89.720 107 11 0 179 285 565767107 565767001 1.220000e-28 137.0
33 TraesCS3B01G529200 chr2D 88.889 144 11 5 284 424 284574944 284574803 3.360000e-39 172.0
34 TraesCS3B01G529200 chr6A 90.291 103 10 0 180 282 196882427 196882325 4.400000e-28 135.0
35 TraesCS3B01G529200 chr5D 88.000 75 7 1 105 177 468644871 468644945 1.250000e-13 87.9


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 TraesCS3B01G529200 chr3B 770963140 770965677 2537 True 4687.0 4687 100.000000 1 2538 1 chr3B.!!$R2 2537
1 TraesCS3B01G529200 chr3B 771241041 771243617 2576 False 1792.5 2641 91.498000 1 2538 2 chr3B.!!$F2 2537
2 TraesCS3B01G529200 chr3B 771177507 771180135 2628 False 1492.0 2097 89.547500 1 2538 2 chr3B.!!$F1 2537
3 TraesCS3B01G529200 chr3D 578040126 578042634 2508 False 3480.0 3480 91.736000 19 2538 1 chr3D.!!$F1 2519
4 TraesCS3B01G529200 chr3D 577751403 577753004 1601 True 1565.0 1565 84.490000 704 2337 1 chr3D.!!$R2 1633
5 TraesCS3B01G529200 chr3D 577778119 577780535 2416 True 1371.0 2601 89.128500 47 2485 2 chr3D.!!$R4 2438
6 TraesCS3B01G529200 chr3D 577667098 577668970 1872 True 1279.0 1592 91.737500 704 2538 2 chr3D.!!$R3 1834
7 TraesCS3B01G529200 chr3A 713306626 713308513 1887 True 1101.0 1476 87.862500 698 2537 2 chr3A.!!$R1 1839
8 TraesCS3B01G529200 chr3A 713417315 713418432 1117 True 733.0 935 89.840000 650 1802 2 chr3A.!!$R3 1152
9 TraesCS3B01G529200 chr3A 713341097 713343477 2380 True 642.0 1125 88.989333 701 2538 3 chr3A.!!$R2 1837

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
308 312 0.034896 AACACTTGATCGGACGGCTT 59.965 50.000 0.0 0.0 0.0 4.35 F
1254 1817 1.687123 GGCCAGTACGACATCCACTAT 59.313 52.381 0.0 0.0 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1359 1922 0.957362 GCCTAAGCTCATTGCCATCC 59.043 55.0 0.00 0.0 44.23 3.51 R
2129 2833 1.600511 TAGCGTCATCGAAGGGCACA 61.601 55.0 7.22 0.0 39.71 4.57 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
100 102 3.371595 GGGCTTCTTAGTGGCCAAATCTA 60.372 47.826 7.24 1.26 46.87 1.98
109 112 1.490490 TGGCCAAATCTAGTGCCTAGG 59.510 52.381 0.61 3.67 44.32 3.02
211 215 1.601903 TGCATCAACGACTGGAACAAC 59.398 47.619 0.00 0.00 38.70 3.32
256 260 2.441750 AGGCAGGAAAAACACCTAGTGA 59.558 45.455 0.96 0.00 36.96 3.41
308 312 0.034896 AACACTTGATCGGACGGCTT 59.965 50.000 0.00 0.00 0.00 4.35
390 394 9.142515 CATGAGAAGACATAGAAATCATCTAGC 57.857 37.037 0.00 0.00 43.75 3.42
447 451 4.807304 GCCTTGCATGATTCAAAAGGTATG 59.193 41.667 19.35 3.44 39.70 2.39
551 568 5.931294 TGCTAAAATAATATCGTCCCACCA 58.069 37.500 0.00 0.00 0.00 4.17
1052 1612 4.904241 GCAATAGTAGCCATCCTTCTCAT 58.096 43.478 0.00 0.00 0.00 2.90
1254 1817 1.687123 GGCCAGTACGACATCCACTAT 59.313 52.381 0.00 0.00 0.00 2.12
1323 1886 4.919774 TGAAGGCATTAAGGTGAAGGTA 57.080 40.909 0.00 0.00 0.00 3.08
1327 1890 6.723977 TGAAGGCATTAAGGTGAAGGTATTTT 59.276 34.615 0.00 0.00 0.00 1.82
1604 2178 6.546034 ACCAATTAATGTACTCCCATTGTAGC 59.454 38.462 0.00 0.00 35.85 3.58
1718 2380 5.525378 GGACAGTGAATGTGTTATCTGATCC 59.475 44.000 0.00 0.00 44.17 3.36
1749 2412 4.250116 TGATGGTATTGTGGCACAAAAC 57.750 40.909 34.01 25.45 38.99 2.43
1858 2557 6.877236 TCTAGTAATCATGTCATGTCAGCAA 58.123 36.000 12.54 0.00 0.00 3.91
2070 2774 5.447757 TGAACATAGATTGGATCCATGCAA 58.552 37.500 17.06 0.00 42.28 4.08
2077 2781 2.832643 TGGATCCATGCAAATCCACT 57.167 45.000 19.43 0.00 45.05 4.00
2129 2833 3.068881 CCGGAGACACACCACCAT 58.931 61.111 0.00 0.00 0.00 3.55
2227 2934 0.248661 CGTCGCATCGTCTTCCTGAT 60.249 55.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 102 1.341383 CCATCTTTTGGCCTAGGCACT 60.341 52.381 34.09 7.98 44.11 4.40
142 145 3.169355 ACACACCGTTTCGTTCTTACT 57.831 42.857 0.00 0.00 0.00 2.24
211 215 2.432628 GAAGCCACGTCACCCGAG 60.433 66.667 0.00 0.00 40.70 4.63
256 260 9.250246 GTCTTCTATATCTAAATAGAGGCACCT 57.750 37.037 0.00 0.00 39.14 4.00
308 312 6.264518 TGATGCAACATAGATCGGTAGTCTAA 59.735 38.462 0.00 0.00 32.37 2.10
408 412 4.127171 GCAAGGCGACCAATCTTCTATAA 58.873 43.478 0.00 0.00 0.00 0.98
447 451 5.394115 CCATTATTATTTATCTTGGCCCGCC 60.394 44.000 0.00 0.00 0.00 6.13
539 555 3.649843 ACTTAGGAATGGTGGGACGATA 58.350 45.455 0.00 0.00 0.00 2.92
542 558 5.540400 TTATACTTAGGAATGGTGGGACG 57.460 43.478 0.00 0.00 0.00 4.79
864 1410 8.883731 GCAATAAATGTGTATTCAGTACTCACT 58.116 33.333 11.59 0.00 39.00 3.41
1327 1890 2.009051 CTGTATGCTGATCCACGCAAA 58.991 47.619 5.68 0.00 39.89 3.68
1359 1922 0.957362 GCCTAAGCTCATTGCCATCC 59.043 55.000 0.00 0.00 44.23 3.51
1478 2041 1.860641 TCGAAGAGGCAGATTGGGTA 58.139 50.000 0.00 0.00 0.00 3.69
1551 2122 1.039856 ACGGGATTGCAAAACAAGCT 58.960 45.000 1.71 0.00 44.27 3.74
1604 2178 2.704464 TCATTCAGTCTCAGCCCATG 57.296 50.000 0.00 0.00 0.00 3.66
1718 2380 3.249320 CACAATACCATCATGCCTTCTCG 59.751 47.826 0.00 0.00 0.00 4.04
1858 2557 4.567318 GCCTTCGGCTCATTCCAT 57.433 55.556 0.00 0.00 46.69 3.41
2000 2704 8.903723 CGTTGTATCCTTTCGATCTATACTTTC 58.096 37.037 0.00 0.00 31.92 2.62
2070 2774 3.579586 TCGGTGGTAGTGTTTAGTGGATT 59.420 43.478 0.00 0.00 0.00 3.01
2077 2781 4.525487 AGATTCAGTCGGTGGTAGTGTTTA 59.475 41.667 0.00 0.00 0.00 2.01
2129 2833 1.600511 TAGCGTCATCGAAGGGCACA 61.601 55.000 7.22 0.00 39.71 4.57
2227 2934 4.082463 GGGTTTTGTGAGTTTGTGTCTTGA 60.082 41.667 0.00 0.00 0.00 3.02
2496 3227 9.424319 CACCATCAAATATATACAGTACAGACC 57.576 37.037 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.