Multiple sequence alignment - TraesCS3D01G049800

Loading Multiple Alignment...

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 TraesCS3D01G049800 chr3D 100.000 2375 0 0 1 2375 19042526 19040152 0.000000e+00 4386
1 TraesCS3D01G049800 chr3D 90.237 338 27 5 1483 1814 97679857 97680194 1.010000e-118 436
2 TraesCS3D01G049800 chr3D 85.642 397 52 4 4 396 601004408 601004013 1.700000e-111 412
3 TraesCS3D01G049800 chr3D 84.962 399 56 3 4 398 582908286 582907888 3.680000e-108 401
4 TraesCS3D01G049800 chr3D 84.962 399 56 3 4 398 582919433 582919035 3.680000e-108 401
5 TraesCS3D01G049800 chr3A 94.823 1719 65 10 672 2375 26526758 26525049 0.000000e+00 2660
6 TraesCS3D01G049800 chr3A 90.104 768 71 3 708 1474 26721808 26721045 0.000000e+00 992
7 TraesCS3D01G049800 chr3A 94.505 637 34 1 8 643 26527395 26526759 0.000000e+00 981
8 TraesCS3D01G049800 chr3A 88.000 425 35 7 1812 2223 26720796 26720375 2.740000e-134 488
9 TraesCS3D01G049800 chr3A 87.295 244 31 0 465 708 95892264 95892507 1.800000e-71 279
10 TraesCS3D01G049800 chr3B 90.989 1476 106 9 9 1482 30795330 30793880 0.000000e+00 1964
11 TraesCS3D01G049800 chr3B 90.617 778 66 5 708 1482 30771839 30771066 0.000000e+00 1026
12 TraesCS3D01G049800 chr3B 89.323 768 61 5 717 1482 30832535 30831787 0.000000e+00 944
13 TraesCS3D01G049800 chr3B 89.193 768 62 9 717 1482 30834379 30833631 0.000000e+00 939
14 TraesCS3D01G049800 chr3B 89.062 768 63 5 717 1482 30830691 30829943 0.000000e+00 933
15 TraesCS3D01G049800 chr3B 87.929 787 73 6 698 1482 30874793 30874027 0.000000e+00 907
16 TraesCS3D01G049800 chr3B 88.281 768 69 9 717 1482 30881781 30881033 0.000000e+00 900
17 TraesCS3D01G049800 chr3B 88.136 767 72 3 717 1482 30883562 30882814 0.000000e+00 894
18 TraesCS3D01G049800 chr3B 88.139 489 22 10 1812 2287 30740208 30739743 1.240000e-152 549
19 TraesCS3D01G049800 chr5D 91.124 338 24 4 1483 1814 541436158 541435821 1.000000e-123 453
20 TraesCS3D01G049800 chr5D 90.149 335 29 4 1483 1814 153950475 153950142 1.300000e-117 433
21 TraesCS3D01G049800 chr2D 90.179 336 28 4 1483 1814 365452275 365451941 1.300000e-117 433
22 TraesCS3D01G049800 chr1D 89.941 338 28 4 1483 1814 316941046 316941383 4.690000e-117 431
23 TraesCS3D01G049800 chr1D 84.975 406 51 8 4 401 463333392 463332989 1.020000e-108 403
24 TraesCS3D01G049800 chr4D 89.911 337 29 4 1483 1814 386696255 386695919 1.690000e-116 429
25 TraesCS3D01G049800 chr6D 89.676 339 29 4 1483 1815 258096716 258097054 6.070000e-116 427
26 TraesCS3D01G049800 chr6D 89.645 338 28 5 1483 1814 410361524 410361860 7.850000e-115 424
27 TraesCS3D01G049800 chr6A 85.323 402 54 4 4 400 592431821 592431420 6.110000e-111 411
28 TraesCS3D01G049800 chrUn 84.962 399 56 3 4 398 370989883 370989485 3.680000e-108 401
29 TraesCS3D01G049800 chrUn 84.962 399 56 3 4 398 384981160 384981558 3.680000e-108 401


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 TraesCS3D01G049800 chr3D 19040152 19042526 2374 True 4386.000000 4386 100.000000 1 2375 1 chr3D.!!$R1 2374
1 TraesCS3D01G049800 chr3A 26525049 26527395 2346 True 1820.500000 2660 94.664000 8 2375 2 chr3A.!!$R1 2367
2 TraesCS3D01G049800 chr3A 26720375 26721808 1433 True 740.000000 992 89.052000 708 2223 2 chr3A.!!$R2 1515
3 TraesCS3D01G049800 chr3B 30793880 30795330 1450 True 1964.000000 1964 90.989000 9 1482 1 chr3B.!!$R3 1473
4 TraesCS3D01G049800 chr3B 30771066 30771839 773 True 1026.000000 1026 90.617000 708 1482 1 chr3B.!!$R2 774
5 TraesCS3D01G049800 chr3B 30829943 30834379 4436 True 938.666667 944 89.192667 717 1482 3 chr3B.!!$R5 765
6 TraesCS3D01G049800 chr3B 30874027 30874793 766 True 907.000000 907 87.929000 698 1482 1 chr3B.!!$R4 784
7 TraesCS3D01G049800 chr3B 30881033 30883562 2529 True 897.000000 900 88.208500 717 1482 2 chr3B.!!$R6 765

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
183 185 0.955428 GGACCATCGCAGCAGAACAA 60.955 55.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 5400 0.034574 TGCATTGATACGTTGCCCCT 60.035 50.0 6.7 0.0 35.51 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
130 132 7.174253 CAGAGCCGGGCAAATTTAATATAGTAA 59.826 37.037 23.09 0.00 0.00 2.24
183 185 0.955428 GGACCATCGCAGCAGAACAA 60.955 55.000 0.00 0.00 0.00 2.83
277 279 2.098117 CGACCAGATCCAAGCAAATTCC 59.902 50.000 0.00 0.00 0.00 3.01
279 281 2.043526 ACCAGATCCAAGCAAATTCCCT 59.956 45.455 0.00 0.00 0.00 4.20
384 386 4.790790 ACCTTATTCCATCTTCAGGGAACT 59.209 41.667 0.00 0.00 45.35 3.01
428 430 3.988517 GGAAGTTCTTTCTCGTCGAACAT 59.011 43.478 2.25 0.00 39.48 2.71
450 452 2.376518 TGCTTCCCCTTCTTCTTGATGT 59.623 45.455 0.00 0.00 0.00 3.06
597 600 3.689161 CGTTCCTGAAATATTGTGCCTCA 59.311 43.478 0.00 0.00 0.00 3.86
786 789 4.770010 TCATAATTTCGTTTCCTTGCCCTT 59.230 37.500 0.00 0.00 0.00 3.95
1088 4716 9.010029 GTTTAATCAGTTCCTCCAAGAATGTTA 57.990 33.333 0.00 0.00 0.00 2.41
1512 5177 1.618640 GCACCGCTTCTCTTCGTGAC 61.619 60.000 0.00 0.00 0.00 3.67
1556 5221 1.636988 ACGTTCGCCACAATAGTAGC 58.363 50.000 0.00 0.00 0.00 3.58
1628 5294 6.409524 TTTTTAGAAGTTCTGACGGTAGGA 57.590 37.500 15.90 0.00 0.00 2.94
1652 5318 5.118286 TGTGAAGAGCATATATGTGTGTGG 58.882 41.667 14.14 0.00 0.00 4.17
1713 5379 3.384014 GAGTCGCGACTCGTGAGGG 62.384 68.421 43.07 0.00 46.84 4.30
1734 5400 1.282875 CGTGTGTGCGTGAGAGAGA 59.717 57.895 0.00 0.00 0.00 3.10
1739 5405 3.071206 TGCGTGAGAGAGAGGGGC 61.071 66.667 0.00 0.00 0.00 5.80
1807 5475 2.644992 GCCACAAGCCGTTTCCTG 59.355 61.111 0.00 0.00 34.35 3.86
1862 5531 2.355756 CACGGTTGATATTGGCTGGAAG 59.644 50.000 0.00 0.00 0.00 3.46
1872 5541 6.493115 TGATATTGGCTGGAAGAAAAACTGAA 59.507 34.615 0.00 0.00 34.07 3.02
2104 5784 3.834813 AGATCGATTTATGGAGCCTAGCA 59.165 43.478 0.00 0.00 0.00 3.49
2191 5872 4.398988 GCATGGTGGAACTCATCAACATAA 59.601 41.667 0.00 0.00 40.31 1.90
2227 5908 4.202461 ACCTCATGACTTAAAAGTGGCAGA 60.202 41.667 0.00 0.00 39.88 4.26
2231 5912 3.740115 TGACTTAAAAGTGGCAGAGTCC 58.260 45.455 0.00 0.00 39.88 3.85
2235 5916 2.922740 AAAAGTGGCAGAGTCCGTTA 57.077 45.000 0.00 0.00 0.00 3.18
2240 5921 3.894759 AGTGGCAGAGTCCGTTAGTATA 58.105 45.455 0.00 0.00 0.00 1.47
2290 5971 3.146066 GGCATGTCCAACACTGACTAAA 58.854 45.455 0.00 0.00 33.83 1.85
2318 6074 1.380246 GGGGCCATGCATGTGAAGA 60.380 57.895 24.58 0.00 0.00 2.87
2319 6075 1.389609 GGGGCCATGCATGTGAAGAG 61.390 60.000 24.58 9.73 0.00 2.85
2320 6076 0.394762 GGGCCATGCATGTGAAGAGA 60.395 55.000 24.58 0.00 0.00 3.10
2346 6102 3.470709 GACCATGATGTGATCCGTGAAT 58.529 45.455 0.00 0.00 0.00 2.57
2353 6109 6.726258 TGATGTGATCCGTGAATATTATGC 57.274 37.500 0.00 0.00 0.00 3.14
2354 6110 5.643348 TGATGTGATCCGTGAATATTATGCC 59.357 40.000 0.00 0.00 0.00 4.40
2371 6127 1.134401 TGCCGGAGAGAATCATCCAAC 60.134 52.381 5.05 0.00 37.82 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.620115 CGCTAGGTGGTTTACGGATCTA 59.380 50.000 0.00 0.00 0.00 1.98
34 35 0.807496 GTAGTCGTCGCTAGGTGGTT 59.193 55.000 0.00 0.00 0.00 3.67
130 132 2.936498 CCACGACAACTTCTCAACTGTT 59.064 45.455 0.00 0.00 0.00 3.16
183 185 4.690719 TTCATCGGCGGCGGTTGT 62.691 61.111 31.73 12.34 0.00 3.32
228 230 8.656849 AGTTCATCTACGTTCATGTATTTTCAC 58.343 33.333 0.00 0.00 0.00 3.18
277 279 2.101582 CTCCGGTGGATCTGTCTTTAGG 59.898 54.545 0.00 0.00 0.00 2.69
279 281 2.758979 GTCTCCGGTGGATCTGTCTTTA 59.241 50.000 0.00 0.00 0.00 1.85
428 430 3.181429 ACATCAAGAAGAAGGGGAAGCAA 60.181 43.478 0.00 0.00 0.00 3.91
450 452 6.597672 ACATTAATTAAGATCACCACGAGCAA 59.402 34.615 3.94 0.00 30.15 3.91
597 600 3.840078 CCCAATTTCCCACTCCAAGAAAT 59.160 43.478 0.00 0.00 40.92 2.17
940 4568 2.224402 ACTTGTGAGCCTTGAGGAAGAC 60.224 50.000 0.06 0.00 37.39 3.01
1088 4716 6.355747 ACAATTTTGTTGATTGGGTTGATGT 58.644 32.000 0.00 0.00 38.47 3.06
1611 5277 3.192844 TCACATCCTACCGTCAGAACTTC 59.807 47.826 0.00 0.00 0.00 3.01
1617 5283 2.480416 GCTCTTCACATCCTACCGTCAG 60.480 54.545 0.00 0.00 0.00 3.51
1618 5284 1.476891 GCTCTTCACATCCTACCGTCA 59.523 52.381 0.00 0.00 0.00 4.35
1622 5288 6.815641 CACATATATGCTCTTCACATCCTACC 59.184 42.308 12.79 0.00 0.00 3.18
1628 5294 5.761726 CCACACACATATATGCTCTTCACAT 59.238 40.000 12.79 0.00 0.00 3.21
1652 5318 4.073549 ACCATCTATCTGTAGGTAGACGC 58.926 47.826 4.10 0.00 30.35 5.19
1713 5379 2.932083 CTCTCACGCACACACGCAC 61.932 63.158 0.00 0.00 36.19 5.34
1734 5400 0.034574 TGCATTGATACGTTGCCCCT 60.035 50.000 6.70 0.00 35.51 4.79
1766 5434 7.345192 GCGAACGTTTGTCAGATATGATTTAT 58.655 34.615 16.75 0.00 0.00 1.40
1913 5593 8.993121 AGATTACAAATCAGAAGTATTATGCGG 58.007 33.333 2.74 0.00 37.20 5.69
2087 5767 4.039730 TCTCAGTGCTAGGCTCCATAAATC 59.960 45.833 0.00 0.00 0.00 2.17
2104 5784 2.306805 TGGAAGCAACATCCATCTCAGT 59.693 45.455 0.00 0.00 41.98 3.41
2128 5808 0.756294 TTGTCAGAGTCGGAGGCAAA 59.244 50.000 0.00 0.00 0.00 3.68
2191 5872 3.684788 GTCATGAGGTGTATTTTGAGCGT 59.315 43.478 0.00 0.00 0.00 5.07
2254 5935 3.531538 ACATGCCCTTACTTGTCATACG 58.468 45.455 0.00 0.00 0.00 3.06
2290 5971 1.348775 GCATGGCCCCCTCTACTCTT 61.349 60.000 0.00 0.00 0.00 2.85
2318 6074 2.557555 TCACATCATGGTCCTCCTCT 57.442 50.000 0.00 0.00 34.23 3.69
2319 6075 3.399440 GATCACATCATGGTCCTCCTC 57.601 52.381 0.00 0.00 31.49 3.71
2346 6102 4.777366 TGGATGATTCTCTCCGGCATAATA 59.223 41.667 0.00 0.00 34.05 0.98
2353 6109 2.169352 AGTGTTGGATGATTCTCTCCGG 59.831 50.000 0.00 0.00 34.05 5.14
2354 6110 3.533606 AGTGTTGGATGATTCTCTCCG 57.466 47.619 2.68 0.00 34.05 4.63


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

AutoCloner maintained by Alex Coulton.