Multiple sequence alignment - TraesCS3B01G282200

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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 TraesCS3B01G282200 chr3B 100.000 4513 0 0 1 4513 452699897 452695385 0.000000e+00 8335.0
1 TraesCS3B01G282200 chr3B 90.763 498 39 4 2684 3176 452564234 452563739 0.000000e+00 658.0
2 TraesCS3B01G282200 chr4B 94.929 2406 69 13 277 2642 24766777 24769169 0.000000e+00 3718.0
3 TraesCS3B01G282200 chr4B 98.356 1034 13 3 2689 3722 24769306 24770335 0.000000e+00 1812.0
4 TraesCS3B01G282200 chr4B 89.833 1141 73 19 3095 4221 25385363 25384252 0.000000e+00 1424.0
5 TraesCS3B01G282200 chr4B 86.887 1243 100 29 301 1509 25388213 25387000 0.000000e+00 1334.0
6 TraesCS3B01G282200 chr4B 91.251 903 63 7 1550 2442 25386995 25386099 0.000000e+00 1216.0
7 TraesCS3B01G282200 chr4B 98.428 636 10 0 3878 4513 24770938 24771573 0.000000e+00 1120.0
8 TraesCS3B01G282200 chr4B 89.308 636 39 7 2467 3097 25386038 25385427 0.000000e+00 771.0
9 TraesCS3B01G282200 chr4B 86.415 714 60 19 2684 3387 24832635 24833321 0.000000e+00 747.0
10 TraesCS3B01G282200 chr4B 99.130 345 3 0 1 345 24766462 24766806 4.960000e-174 621.0
11 TraesCS3B01G282200 chr4B 88.333 420 24 12 2971 3388 25351965 25351569 8.780000e-132 481.0
12 TraesCS3B01G282200 chr4B 95.276 127 4 2 3766 3891 24770308 24770433 2.750000e-47 200.0
13 TraesCS3B01G282200 chr4B 91.912 136 10 1 4 139 25388656 25388522 5.960000e-44 189.0
14 TraesCS3B01G282200 chr4B 100.000 31 0 0 3766 3796 39247066 39247096 1.750000e-04 58.4
15 TraesCS3B01G282200 chr4D 90.728 2556 128 35 895 3388 14401427 14398919 0.000000e+00 3306.0
16 TraesCS3B01G282200 chr4D 93.891 1768 56 10 1421 3158 14926928 14928673 0.000000e+00 2619.0
17 TraesCS3B01G282200 chr4D 86.953 1326 111 27 303 1576 15153679 15152364 0.000000e+00 1434.0
18 TraesCS3B01G282200 chr4D 88.927 876 82 10 1583 2445 15151055 15150182 0.000000e+00 1066.0
19 TraesCS3B01G282200 chr4D 97.814 183 4 0 3203 3385 14928783 14928965 2.620000e-82 316.0
20 TraesCS3B01G282200 chr4D 90.526 190 13 3 3387 3575 15149141 15148956 3.490000e-61 246.0
21 TraesCS3B01G282200 chr4D 91.724 145 10 1 137 281 14402033 14401891 2.750000e-47 200.0
22 TraesCS3B01G282200 chr4D 92.701 137 9 1 4 139 15154056 15153920 3.560000e-46 196.0
23 TraesCS3B01G282200 chr4D 90.000 90 9 0 3860 3949 15148181 15148092 2.850000e-22 117.0
24 TraesCS3B01G282200 chr5A 86.482 2197 209 51 301 2442 40874793 40876956 0.000000e+00 2331.0
25 TraesCS3B01G282200 chr5A 89.961 518 37 7 2666 3173 40877326 40877838 0.000000e+00 654.0
26 TraesCS3B01G282200 chr5A 83.523 176 24 4 2467 2639 40877015 40877188 4.670000e-35 159.0
27 TraesCS3B01G282200 chr4A 89.151 1862 119 35 1344 3158 586674708 586672883 0.000000e+00 2242.0
28 TraesCS3B01G282200 chr4A 89.086 1860 119 39 1346 3158 456401010 456399188 0.000000e+00 2233.0
29 TraesCS3B01G282200 chr4A 93.107 1059 54 10 301 1346 456402186 456401134 0.000000e+00 1533.0
30 TraesCS3B01G282200 chr4A 92.373 1062 62 9 301 1346 586675888 586674830 0.000000e+00 1495.0
31 TraesCS3B01G282200 chr4A 85.150 1367 127 28 195 1509 585690179 585691521 0.000000e+00 1330.0
32 TraesCS3B01G282200 chr4A 88.078 1082 81 21 360 1406 538490078 538489010 0.000000e+00 1240.0
33 TraesCS3B01G282200 chr4A 87.748 1110 73 22 2576 3669 585692837 585693899 0.000000e+00 1238.0
34 TraesCS3B01G282200 chr4A 90.104 869 76 4 1582 2442 586089515 586090381 0.000000e+00 1120.0
35 TraesCS3B01G282200 chr4A 90.545 550 39 6 3662 4200 585694867 585695414 0.000000e+00 715.0
36 TraesCS3B01G282200 chr4A 89.041 292 24 7 4202 4490 585697866 585698152 5.550000e-94 355.0
37 TraesCS3B01G282200 chr4A 98.387 186 3 0 3203 3388 456399067 456398882 1.210000e-85 327.0
38 TraesCS3B01G282200 chr4A 97.312 186 5 0 3203 3388 586672776 586672591 2.620000e-82 316.0
39 TraesCS3B01G282200 chr4A 86.260 262 25 5 2190 2442 585692325 585692584 1.600000e-69 274.0
40 TraesCS3B01G282200 chr4A 92.350 183 13 1 3393 3575 538487493 538487312 4.480000e-65 259.0
41 TraesCS3B01G282200 chr4A 90.000 190 14 3 3387 3575 586091489 586091674 1.620000e-59 241.0
42 TraesCS3B01G282200 chr4A 94.483 145 8 0 137 281 586676087 586675943 1.630000e-54 224.0
43 TraesCS3B01G282200 chr4A 82.463 268 29 13 3587 3848 456398327 456398072 7.600000e-53 219.0
44 TraesCS3B01G282200 chr4A 81.955 266 33 10 3587 3848 586672036 586671782 1.270000e-50 211.0
45 TraesCS3B01G282200 chr4A 93.617 141 7 1 1 139 586676271 586676131 4.570000e-50 209.0
46 TraesCS3B01G282200 chr4A 92.414 145 11 0 137 281 456402385 456402241 1.650000e-49 207.0
47 TraesCS3B01G282200 chr4A 93.571 140 8 1 1 139 456402568 456402429 1.650000e-49 207.0
48 TraesCS3B01G282200 chr4A 88.889 90 10 0 3860 3949 586092460 586092549 1.330000e-20 111.0
49 TraesCS3B01G282200 chr5D 86.437 1423 129 28 301 1687 51842654 51844048 0.000000e+00 1500.0
50 TraesCS3B01G282200 chr5D 84.671 972 110 26 1678 2641 51844193 51845133 0.000000e+00 933.0
51 TraesCS3B01G282200 chr5D 85.946 185 21 1 3387 3566 51846063 51846247 4.610000e-45 193.0
52 TraesCS3B01G282200 chr5B 87.027 1241 130 18 1222 2442 54826896 54828125 0.000000e+00 1371.0
53 TraesCS3B01G282200 chr5B 86.332 578 50 9 301 852 54825832 54826406 1.800000e-168 603.0
54 TraesCS3B01G282200 chr5B 90.370 135 13 0 4 138 54825458 54825592 1.290000e-40 178.0
55 TraesCS3B01G282200 chr2A 84.919 1366 131 25 195 1509 195821290 195822631 0.000000e+00 1312.0
56 TraesCS3B01G282200 chr2A 88.018 1110 70 22 2576 3669 195823947 195825009 0.000000e+00 1254.0
57 TraesCS3B01G282200 chr2A 88.241 1080 83 17 360 1406 196121697 196122765 0.000000e+00 1251.0
58 TraesCS3B01G282200 chr2A 90.545 550 38 7 3662 4200 195825972 195826518 0.000000e+00 715.0
59 TraesCS3B01G282200 chr2A 90.613 522 38 6 2645 3158 196125181 196125699 0.000000e+00 682.0
60 TraesCS3B01G282200 chr2A 90.411 292 21 7 4202 4490 195829208 195829495 1.190000e-100 377.0
61 TraesCS3B01G282200 chr2A 99.429 175 1 0 3203 3377 196345009 196344835 7.290000e-83 318.0
62 TraesCS3B01G282200 chr2A 98.857 175 2 0 3203 3377 196348843 196348669 3.390000e-81 313.0
63 TraesCS3B01G282200 chr2A 86.260 262 25 5 2190 2442 195823435 195823694 1.600000e-69 274.0
64 TraesCS3B01G282200 chr2A 82.772 267 28 13 3587 3848 196314556 196314303 5.880000e-54 222.0
65 TraesCS3B01G282200 chr2A 92.763 152 10 1 3424 3575 196126050 196126200 7.600000e-53 219.0
66 TraesCS3B01G282200 chr2A 88.889 153 13 4 2467 2616 196124381 196124532 7.710000e-43 185.0
67 TraesCS3B01G282200 chr2A 94.444 54 3 0 2389 2442 196124197 196124250 2.890000e-12 84.2
68 TraesCS3B01G282200 chr1D 85.949 975 101 14 305 1248 320387545 320388514 0.000000e+00 1009.0
69 TraesCS3B01G282200 chr1D 86.339 732 71 15 2666 3392 320390396 320391103 0.000000e+00 771.0
70 TraesCS3B01G282200 chr1D 88.034 117 14 0 22 138 320387185 320387301 6.090000e-29 139.0
71 TraesCS3B01G282200 chr1B 85.920 973 99 20 305 1248 433424591 433425554 0.000000e+00 1003.0
72 TraesCS3B01G282200 chr1B 87.395 119 11 3 22 138 433424228 433424344 2.830000e-27 134.0


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 TraesCS3B01G282200 chr3B 452695385 452699897 4512 True 8335.000000 8335 100.000000 1 4513 1 chr3B.!!$R2 4512
1 TraesCS3B01G282200 chr4B 24766462 24771573 5111 False 1494.200000 3718 97.223800 1 4513 5 chr4B.!!$F3 4512
2 TraesCS3B01G282200 chr4B 25384252 25388656 4404 True 986.800000 1424 89.838200 4 4221 5 chr4B.!!$R2 4217
3 TraesCS3B01G282200 chr4B 24832635 24833321 686 False 747.000000 747 86.415000 2684 3387 1 chr4B.!!$F1 703
4 TraesCS3B01G282200 chr4D 14398919 14402033 3114 True 1753.000000 3306 91.226000 137 3388 2 chr4D.!!$R1 3251
5 TraesCS3B01G282200 chr4D 14926928 14928965 2037 False 1467.500000 2619 95.852500 1421 3385 2 chr4D.!!$F1 1964
6 TraesCS3B01G282200 chr4D 15148092 15154056 5964 True 611.800000 1434 89.821400 4 3949 5 chr4D.!!$R2 3945
7 TraesCS3B01G282200 chr5A 40874793 40877838 3045 False 1048.000000 2331 86.655333 301 3173 3 chr5A.!!$F1 2872
8 TraesCS3B01G282200 chr4A 456398072 456402568 4496 True 787.666667 2233 91.504667 1 3848 6 chr4A.!!$R1 3847
9 TraesCS3B01G282200 chr4A 586671782 586676271 4489 True 782.833333 2242 91.481833 1 3848 6 chr4A.!!$R3 3847
10 TraesCS3B01G282200 chr4A 585690179 585698152 7973 False 782.400000 1330 87.748800 195 4490 5 chr4A.!!$F1 4295
11 TraesCS3B01G282200 chr4A 538487312 538490078 2766 True 749.500000 1240 90.214000 360 3575 2 chr4A.!!$R2 3215
12 TraesCS3B01G282200 chr4A 586089515 586092549 3034 False 490.666667 1120 89.664333 1582 3949 3 chr4A.!!$F2 2367
13 TraesCS3B01G282200 chr5D 51842654 51846247 3593 False 875.333333 1500 85.684667 301 3566 3 chr5D.!!$F1 3265
14 TraesCS3B01G282200 chr5B 54825458 54828125 2667 False 717.333333 1371 87.909667 4 2442 3 chr5B.!!$F1 2438
15 TraesCS3B01G282200 chr2A 195821290 195829495 8205 False 786.400000 1312 88.030600 195 4490 5 chr2A.!!$F1 4295
16 TraesCS3B01G282200 chr2A 196121697 196126200 4503 False 484.240000 1251 90.990000 360 3575 5 chr2A.!!$F2 3215
17 TraesCS3B01G282200 chr2A 196344835 196348843 4008 True 315.500000 318 99.143000 3203 3377 2 chr2A.!!$R2 174
18 TraesCS3B01G282200 chr1D 320387185 320391103 3918 False 639.666667 1009 86.774000 22 3392 3 chr1D.!!$F1 3370
19 TraesCS3B01G282200 chr1B 433424228 433425554 1326 False 568.500000 1003 86.657500 22 1248 2 chr1B.!!$F1 1226

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
877 1247 1.136891 GGCTAAAATGGGCATGTCCAC 59.863 52.381 24.12 7.59 39.97 4.02 F
1664 3803 0.918799 TGTAGGTGCCCCATGTGGAT 60.919 55.000 0.00 0.00 37.39 3.41 F
1847 4142 3.272574 TCTTGAAGCCAGCCTTATGAG 57.727 47.619 0.00 0.00 32.78 2.90 F
2888 7503 1.482748 CCAAGGGGGCTTGCACATTT 61.483 55.000 0.00 0.00 33.30 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 4282 1.427819 GCCAATTCCGTAACTGCCG 59.572 57.895 0.0 0.0 0.0 5.69 R
2511 6087 4.041567 TCAGTAGCCAAAGTCCATCAGAAA 59.958 41.667 0.0 0.0 0.0 2.52 R
2976 7599 5.733226 TCCAACAATCATATTACACTGCG 57.267 39.130 0.0 0.0 0.0 5.18 R
4302 18269 1.063764 GTCTCACCGTCAGTATCGTCC 59.936 57.143 0.0 0.0 0.0 4.79 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
349 569 1.995542 ACATCAAATCCCCTGTCTGGT 59.004 47.619 0.00 0.00 0.00 4.00
422 643 6.239036 AGAACACCTTTTGTGCTTTATCTTCC 60.239 38.462 0.00 0.00 42.17 3.46
423 644 5.712152 CACCTTTTGTGCTTTATCTTCCT 57.288 39.130 0.00 0.00 38.34 3.36
877 1247 1.136891 GGCTAAAATGGGCATGTCCAC 59.863 52.381 24.12 7.59 39.97 4.02
1062 1485 2.158608 CCAAGAAACAGGGAGTTGGAGT 60.159 50.000 0.00 0.00 41.19 3.85
1176 1611 5.520376 AGTTTGTCTGAACTTCATTTGGG 57.480 39.130 0.00 0.00 36.49 4.12
1219 1673 2.949644 ACACCTTTCTCTTTGGGAAACG 59.050 45.455 0.00 0.00 0.00 3.60
1275 1755 9.295825 AGTTGGAATTTGAATAACTGTGATGTA 57.704 29.630 0.00 0.00 31.00 2.29
1486 2319 4.764679 TGCGATAACTCTTTTTGCACAT 57.235 36.364 0.00 0.00 0.00 3.21
1577 2414 6.147164 TCGCTGCTTACAATTGGTTATATAGC 59.853 38.462 10.83 9.31 0.00 2.97
1664 3803 0.918799 TGTAGGTGCCCCATGTGGAT 60.919 55.000 0.00 0.00 37.39 3.41
1847 4142 3.272574 TCTTGAAGCCAGCCTTATGAG 57.727 47.619 0.00 0.00 32.78 2.90
1978 4282 8.716646 ATAATAGGGCTTAAAAATGCAAACAC 57.283 30.769 0.00 0.00 0.00 3.32
2072 4383 8.783660 ATCTAGTTTTGGATAGACTGATGGTA 57.216 34.615 0.00 0.00 31.09 3.25
2112 4423 7.894376 ATGATATTGTTGCACCAAAAAGAAG 57.106 32.000 0.00 0.00 0.00 2.85
2139 4450 8.854117 CAAAGCTATAAGAATATCTGCCCTTTT 58.146 33.333 0.00 0.00 0.00 2.27
2461 6021 5.048782 CAGCAAAGTGATGGTTTTAGTGCTA 60.049 40.000 0.00 0.00 28.61 3.49
2462 6022 5.711976 AGCAAAGTGATGGTTTTAGTGCTAT 59.288 36.000 0.00 0.00 0.00 2.97
2511 6087 8.965172 CGTATTTATAGAGTACAAGCATTCGTT 58.035 33.333 0.00 0.00 0.00 3.85
2642 6962 8.341903 TGTTTTCACACACATGTATAGAAACTG 58.658 33.333 0.00 0.00 36.72 3.16
2751 7358 3.519107 TCTCTGCCATCCTAATGTGTTGA 59.481 43.478 0.00 0.00 0.00 3.18
2758 7365 4.577693 CCATCCTAATGTGTTGACCATCAG 59.422 45.833 0.00 0.00 0.00 2.90
2888 7503 1.482748 CCAAGGGGGCTTGCACATTT 61.483 55.000 0.00 0.00 33.30 2.32
2955 7574 6.418057 TCTGAAATTTATTTGGTGCCTGTT 57.582 33.333 0.00 0.00 0.00 3.16
2976 7599 9.528018 CCTGTTAGAAAGATTCTGATAGAAGAC 57.472 37.037 9.27 0.00 40.94 3.01
3590 12962 7.927788 TGCCCCACATGATTTATAGTATATGT 58.072 34.615 0.00 0.00 0.00 2.29
3731 14103 0.679002 GATGCTCACCATGGTGCTGT 60.679 55.000 35.73 22.16 45.04 4.40
3806 14181 3.071479 GCTCACCGACATGGAGTTTTTA 58.929 45.455 0.00 0.00 42.00 1.52
3847 14237 3.668447 ACATGGAGTTGAGTAGTGCTTG 58.332 45.455 0.00 0.00 0.00 4.01
4011 15280 8.463930 TCTACCAAAGTGATTCTGATTTTGTT 57.536 30.769 0.00 0.00 0.00 2.83
4302 18269 1.967066 AGGAAGACACAGGTGAGACAG 59.033 52.381 6.40 0.00 0.00 3.51
4392 18360 3.041211 AGCTCTACCACATGGCAATAGA 58.959 45.455 0.00 0.00 39.32 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
877 1247 0.242825 CAGCTGCCACCACAAGAATG 59.757 55.000 0.00 0.00 0.00 2.67
1062 1485 5.935789 GGCCACAGACAAGTTACTGTAATAA 59.064 40.000 12.44 0.00 44.07 1.40
1176 1611 7.254932 GGTGTCAATTTCTTCAGGCTATATGAC 60.255 40.741 0.00 0.00 35.30 3.06
1460 2293 5.284660 GTGCAAAAAGAGTTATCGCATTCAG 59.715 40.000 0.00 0.00 0.00 3.02
1486 2319 6.154192 TGCAATATGAGTTGGAAGGCAATAAA 59.846 34.615 0.00 0.00 0.00 1.40
1633 3772 3.873910 GGCACCTACATGACATACAAGT 58.126 45.455 0.00 0.00 34.72 3.16
1664 3803 7.884877 AGGATAGATGAAACATGTTGAAAGACA 59.115 33.333 12.82 6.58 0.00 3.41
1847 4142 2.210116 TCTCCGTTTGACTTTCTGCAC 58.790 47.619 0.00 0.00 0.00 4.57
1966 4268 2.307934 AACTGCCGTGTTTGCATTTT 57.692 40.000 0.00 0.00 38.22 1.82
1978 4282 1.427819 GCCAATTCCGTAACTGCCG 59.572 57.895 0.00 0.00 0.00 5.69
2082 4393 7.459795 TTTGGTGCAACAATATCATTACTCA 57.540 32.000 19.74 0.00 39.98 3.41
2102 4413 8.992835 ATTCTTATAGCTTTGCTTCTTTTTGG 57.007 30.769 0.00 0.00 40.44 3.28
2112 4423 5.942826 AGGGCAGATATTCTTATAGCTTTGC 59.057 40.000 0.00 0.00 30.76 3.68
2461 6021 6.073765 CGGCTGAATTCGCTACTACAATTTAT 60.074 38.462 17.53 0.00 0.00 1.40
2462 6022 5.233476 CGGCTGAATTCGCTACTACAATTTA 59.767 40.000 17.53 0.00 0.00 1.40
2511 6087 4.041567 TCAGTAGCCAAAGTCCATCAGAAA 59.958 41.667 0.00 0.00 0.00 2.52
2654 6974 7.613411 AGAGCCAACTCAAAGCTAGAATTTAAT 59.387 33.333 0.00 0.00 46.09 1.40
2655 6975 6.942576 AGAGCCAACTCAAAGCTAGAATTTAA 59.057 34.615 0.00 0.00 46.09 1.52
2955 7574 7.067615 ACTGCGTCTTCTATCAGAATCTTTCTA 59.932 37.037 0.00 0.00 38.11 2.10
2976 7599 5.733226 TCCAACAATCATATTACACTGCG 57.267 39.130 0.00 0.00 0.00 5.18
3731 14103 8.519526 CAAGCTTTAACATGGTAGTTAATGGAA 58.480 33.333 0.00 0.00 41.89 3.53
3806 14181 8.303156 TCCATGTAACAAAATGATCGTCAAAAT 58.697 29.630 0.00 0.00 0.00 1.82
3847 14237 2.238521 TCCTTTGGCTGGTGATTGAAC 58.761 47.619 0.00 0.00 0.00 3.18
4011 15280 3.815809 ACACCAGAACGGAAAGAAATCA 58.184 40.909 0.00 0.00 38.63 2.57
4018 15287 2.614983 GCAAAGTACACCAGAACGGAAA 59.385 45.455 0.00 0.00 38.63 3.13
4302 18269 1.063764 GTCTCACCGTCAGTATCGTCC 59.936 57.143 0.00 0.00 0.00 4.79
4392 18360 9.601217 CTCTACCTGCATTACAGTATTACTTTT 57.399 33.333 0.00 0.00 45.68 2.27


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

AutoCloner maintained by Alex Coulton.