Multiple sequence alignment - TraesCS3D01G005600

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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 TraesCS3D01G005600 chr3D 100.000 2516 0 0 1 2516 2152273 2149758 0.000000e+00 4647.0
1 TraesCS3D01G005600 chr3D 88.710 62 5 2 299 359 452490576 452490516 9.650000e-10 75.0
2 TraesCS3D01G005600 chr3D 100.000 29 0 0 737 765 2151460 2151432 1.000000e-03 54.7
3 TraesCS3D01G005600 chr3D 100.000 29 0 0 814 842 2151537 2151509 1.000000e-03 54.7
4 TraesCS3D01G005600 chr3A 90.549 984 44 21 1569 2516 1919290 1920260 0.000000e+00 1256.0
5 TraesCS3D01G005600 chr3A 89.164 646 37 10 1 620 1904224 1904862 0.000000e+00 774.0
6 TraesCS3D01G005600 chr3A 90.722 291 24 1 1281 1568 1918739 1919029 3.930000e-103 385.0
7 TraesCS3D01G005600 chr3A 91.603 262 21 1 1019 1279 1909434 1909695 6.620000e-96 361.0
8 TraesCS3D01G005600 chr3A 92.727 110 7 1 616 725 1904888 1904996 9.320000e-35 158.0
9 TraesCS3D01G005600 chr3A 86.525 141 14 2 2341 2481 95843325 95843190 1.560000e-32 150.0
10 TraesCS3D01G005600 chr3B 86.165 1142 71 44 1440 2512 4332192 4331069 0.000000e+00 1153.0
11 TraesCS3D01G005600 chr3B 92.295 623 38 9 1 620 4334384 4333769 0.000000e+00 876.0
12 TraesCS3D01G005600 chr3B 90.728 604 48 2 765 1362 4332803 4332202 0.000000e+00 798.0
13 TraesCS3D01G005600 chr3B 91.484 411 28 6 4 413 4406791 4406387 2.190000e-155 558.0
14 TraesCS3D01G005600 chr2A 79.495 634 69 28 1745 2346 20809281 20809885 6.520000e-106 394.0
15 TraesCS3D01G005600 chr5B 87.671 292 30 6 1729 2017 670366538 670366250 4.010000e-88 335.0
16 TraesCS3D01G005600 chrUn 96.000 200 8 0 1 200 351353410 351353211 2.410000e-85 326.0
17 TraesCS3D01G005600 chrUn 90.574 244 18 4 378 620 351355343 351355104 4.040000e-83 318.0
18 TraesCS3D01G005600 chrUn 77.856 569 62 28 1740 2285 306110406 306110933 6.810000e-76 294.0
19 TraesCS3D01G005600 chrUn 93.458 107 6 1 619 725 351355075 351354970 9.320000e-35 158.0
20 TraesCS3D01G005600 chr2B 78.207 569 61 28 1740 2285 31678209 31677681 3.140000e-79 305.0
21 TraesCS3D01G005600 chr2B 77.719 570 61 30 1740 2285 31656948 31656421 3.170000e-74 289.0
22 TraesCS3D01G005600 chr5D 87.429 175 21 1 2106 2280 12872122 12871949 1.530000e-47 200.0
23 TraesCS3D01G005600 chr5D 88.276 145 10 4 2336 2478 227771908 227772047 1.550000e-37 167.0
24 TraesCS3D01G005600 chr6A 87.500 144 11 4 2336 2477 31918676 31918814 2.590000e-35 159.0
25 TraesCS3D01G005600 chr6A 93.103 58 3 1 299 355 613904904 613904961 1.600000e-12 84.2
26 TraesCS3D01G005600 chr6B 86.957 138 13 2 2344 2481 22055636 22055504 1.560000e-32 150.0
27 TraesCS3D01G005600 chr1A 86.861 137 13 2 2341 2477 80620369 80620238 5.610000e-32 148.0
28 TraesCS3D01G005600 chr4B 85.417 144 14 4 2336 2477 584687386 584687524 2.610000e-30 143.0
29 TraesCS3D01G005600 chr4A 84.459 148 17 6 2336 2478 602083668 602083814 9.380000e-30 141.0
30 TraesCS3D01G005600 chr4A 90.323 62 4 2 299 359 551127079 551127019 2.070000e-11 80.5
31 TraesCS3D01G005600 chr4D 93.939 66 3 1 2220 2285 244327047 244326983 5.730000e-17 99.0
32 TraesCS3D01G005600 chr4D 90.164 61 4 2 299 357 47343951 47344011 7.460000e-11 78.7
33 TraesCS3D01G005600 chr7B 90.625 64 5 1 299 361 708439152 708439089 1.600000e-12 84.2
34 TraesCS3D01G005600 chr1D 91.379 58 4 1 299 355 352938291 352938348 7.460000e-11 78.7


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 TraesCS3D01G005600 chr3D 2149758 2152273 2515 True 1585.466667 4647 100.000000 1 2516 3 chr3D.!!$R2 2515
1 TraesCS3D01G005600 chr3A 1918739 1920260 1521 False 820.500000 1256 90.635500 1281 2516 2 chr3A.!!$F3 1235
2 TraesCS3D01G005600 chr3A 1904224 1904996 772 False 466.000000 774 90.945500 1 725 2 chr3A.!!$F2 724
3 TraesCS3D01G005600 chr3B 4331069 4334384 3315 True 942.333333 1153 89.729333 1 2512 3 chr3B.!!$R2 2511
4 TraesCS3D01G005600 chr2A 20809281 20809885 604 False 394.000000 394 79.495000 1745 2346 1 chr2A.!!$F1 601
5 TraesCS3D01G005600 chrUn 306110406 306110933 527 False 294.000000 294 77.856000 1740 2285 1 chrUn.!!$F1 545
6 TraesCS3D01G005600 chrUn 351353211 351355343 2132 True 267.333333 326 93.344000 1 725 3 chrUn.!!$R1 724
7 TraesCS3D01G005600 chr2B 31677681 31678209 528 True 305.000000 305 78.207000 1740 2285 1 chr2B.!!$R2 545
8 TraesCS3D01G005600 chr2B 31656421 31656948 527 True 289.000000 289 77.719000 1740 2285 1 chr2B.!!$R1 545


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
945 2192 2.026014 GCACCAACACAGCAACGG 59.974 61.111 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2495 4084 0.036388 CTGGCTCCACCGAAAGCTAA 60.036 55.0 0.0 0.0 43.94 3.09 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
93 94 3.037431 GCAGGAGATACATGCGAGAAT 57.963 47.619 0.00 0.00 45.84 2.40
115 116 2.733227 GCATTCAAGGCGATCCACAAAG 60.733 50.000 0.00 0.00 33.74 2.77
116 117 2.270352 TTCAAGGCGATCCACAAAGT 57.730 45.000 0.00 0.00 33.74 2.66
134 135 3.998672 GTCTCCCGTGGCCGACAA 61.999 66.667 0.00 0.00 35.63 3.18
206 207 4.125703 CTGCTCCTCACCAAATGATCTAC 58.874 47.826 0.00 0.00 36.48 2.59
250 251 7.575414 TGTCTGTTCCTCTCAGTAATAGATC 57.425 40.000 0.00 0.00 34.86 2.75
251 252 6.261158 TGTCTGTTCCTCTCAGTAATAGATCG 59.739 42.308 0.00 0.00 34.86 3.69
253 254 6.261158 TCTGTTCCTCTCAGTAATAGATCGTG 59.739 42.308 0.00 0.00 34.86 4.35
258 259 7.258441 TCCTCTCAGTAATAGATCGTGTTTTG 58.742 38.462 0.00 0.00 0.00 2.44
260 261 7.221067 CCTCTCAGTAATAGATCGTGTTTTGTC 59.779 40.741 0.00 0.00 0.00 3.18
261 262 7.827701 TCTCAGTAATAGATCGTGTTTTGTCT 58.172 34.615 0.00 0.00 0.00 3.41
262 263 7.755373 TCTCAGTAATAGATCGTGTTTTGTCTG 59.245 37.037 0.00 0.00 0.00 3.51
263 264 7.375834 TCAGTAATAGATCGTGTTTTGTCTGT 58.624 34.615 0.00 0.00 0.00 3.41
264 265 7.541091 TCAGTAATAGATCGTGTTTTGTCTGTC 59.459 37.037 0.00 0.00 0.00 3.51
267 269 3.309388 AGATCGTGTTTTGTCTGTCGAG 58.691 45.455 0.00 0.00 0.00 4.04
486 511 4.838486 GGTCCAGTCTCGCGCTCG 62.838 72.222 5.56 0.00 0.00 5.03
531 556 3.624305 GCACGAAGCGAGACATAGA 57.376 52.632 0.00 0.00 0.00 1.98
561 586 6.213600 CCCTAGGGCATACAAGACATATTACT 59.786 42.308 16.90 0.00 0.00 2.24
576 601 8.107095 AGACATATTACTGTTTGGTACCACATT 58.893 33.333 16.04 7.34 0.00 2.71
615 640 5.504665 CCCAGAAGCAAATCATAACTTAGCG 60.505 44.000 0.00 0.00 0.00 4.26
645 700 2.094494 TCTTTCCTAGCAAGCTGTCGAG 60.094 50.000 4.53 0.00 0.00 4.04
928 2175 6.971602 AGATATGTAGAGTCACCGTGTATTG 58.028 40.000 0.00 0.00 0.00 1.90
945 2192 2.026014 GCACCAACACAGCAACGG 59.974 61.111 0.00 0.00 0.00 4.44
1014 2261 3.364062 CTTAGCTATGGTTCTCGTCGTG 58.636 50.000 0.00 0.00 0.00 4.35
1041 2288 0.419459 CCCTATCCTATGGCCTCCCT 59.581 60.000 3.32 0.00 0.00 4.20
1125 2372 1.592669 CGTGGCTATGCTAAGCGCT 60.593 57.895 2.64 2.64 43.74 5.92
1173 2420 3.190849 CATGACCTCGCCAGCGTG 61.191 66.667 12.32 9.56 40.74 5.34
1216 2463 2.736995 CCAAGAAGAACGCCGCGA 60.737 61.111 21.79 0.00 0.00 5.87
1224 2471 3.215606 GAACGCCGCGATCATCTGC 62.216 63.158 21.79 0.00 0.00 4.26
1302 2549 2.577644 GCACATGTCATTGCCGCG 60.578 61.111 0.00 0.00 32.21 6.46
1476 2723 3.774959 GACGATGGAGCGATGCGGT 62.775 63.158 0.00 0.00 41.33 5.68
1504 2751 3.781770 GACCTCATCGGCCTGCTCG 62.782 68.421 0.00 0.00 35.61 5.03
1507 2754 4.193334 TCATCGGCCTGCTCGTCG 62.193 66.667 0.00 0.00 0.00 5.12
1537 2784 7.926555 AGTGACCGATAATAAATCATTTCTCGT 59.073 33.333 0.00 0.00 32.71 4.18
1688 3200 2.034999 GGCATTCCGTTGTCCCCA 59.965 61.111 0.00 0.00 0.00 4.96
1689 3201 1.379843 GGCATTCCGTTGTCCCCAT 60.380 57.895 0.00 0.00 0.00 4.00
1690 3202 0.970427 GGCATTCCGTTGTCCCCATT 60.970 55.000 0.00 0.00 0.00 3.16
1692 3204 1.955208 GCATTCCGTTGTCCCCATTCT 60.955 52.381 0.00 0.00 0.00 2.40
1693 3205 2.682563 GCATTCCGTTGTCCCCATTCTA 60.683 50.000 0.00 0.00 0.00 2.10
1694 3206 3.616219 CATTCCGTTGTCCCCATTCTAA 58.384 45.455 0.00 0.00 0.00 2.10
1695 3207 2.773993 TCCGTTGTCCCCATTCTAAC 57.226 50.000 0.00 0.00 0.00 2.34
1698 3210 1.066716 CGTTGTCCCCATTCTAACCGA 60.067 52.381 0.00 0.00 0.00 4.69
1699 3211 2.419574 CGTTGTCCCCATTCTAACCGAT 60.420 50.000 0.00 0.00 0.00 4.18
1700 3212 3.203716 GTTGTCCCCATTCTAACCGATC 58.796 50.000 0.00 0.00 0.00 3.69
1701 3213 2.473070 TGTCCCCATTCTAACCGATCA 58.527 47.619 0.00 0.00 0.00 2.92
1702 3214 2.434336 TGTCCCCATTCTAACCGATCAG 59.566 50.000 0.00 0.00 0.00 2.90
1703 3215 2.698797 GTCCCCATTCTAACCGATCAGA 59.301 50.000 0.00 0.00 0.00 3.27
1736 3274 3.827898 CTGCCGTCCCCGTCTCTC 61.828 72.222 0.00 0.00 0.00 3.20
1737 3275 4.361971 TGCCGTCCCCGTCTCTCT 62.362 66.667 0.00 0.00 0.00 3.10
1740 3278 1.820481 CCGTCCCCGTCTCTCTCTC 60.820 68.421 0.00 0.00 0.00 3.20
1741 3279 1.222387 CGTCCCCGTCTCTCTCTCT 59.778 63.158 0.00 0.00 0.00 3.10
1742 3280 0.812412 CGTCCCCGTCTCTCTCTCTC 60.812 65.000 0.00 0.00 0.00 3.20
1743 3281 0.544697 GTCCCCGTCTCTCTCTCTCT 59.455 60.000 0.00 0.00 0.00 3.10
2090 3669 2.088674 CTCCGCCCTCTTACATCCGG 62.089 65.000 0.00 0.00 37.21 5.14
2266 3845 2.803133 CGTCAACAAAGTCTGCTCCTCA 60.803 50.000 0.00 0.00 0.00 3.86
2289 3876 3.652869 GGGATGAAGGGTAATCCATCTCA 59.347 47.826 4.22 0.00 43.63 3.27
2290 3877 4.505742 GGGATGAAGGGTAATCCATCTCAC 60.506 50.000 4.22 0.00 43.63 3.51
2298 3885 3.243771 GGTAATCCATCTCACCACCTACG 60.244 52.174 0.00 0.00 0.00 3.51
2337 3926 3.111098 GTCACTGCTGCTCAAAAACTTG 58.889 45.455 0.00 0.00 0.00 3.16
2356 3945 1.109323 GTGTTGTTGGCCTGCTCCTT 61.109 55.000 3.32 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 0.322366 TGTGGATCGCCTTGAATGCA 60.322 50.000 0.00 0.00 34.31 3.96
115 116 4.736896 GTCGGCCACGGGAGACAC 62.737 72.222 2.24 0.00 41.39 3.67
171 172 2.685017 AGCAGGCGGATGAGGTCA 60.685 61.111 0.00 0.00 0.00 4.02
206 207 5.757320 AGACAAGCCGAGAAATGATCTATTG 59.243 40.000 0.00 0.00 38.96 1.90
250 251 3.918258 TTTCTCGACAGACAAAACACG 57.082 42.857 0.00 0.00 0.00 4.49
421 446 2.414161 GCGCTCGCTATTTCTGGTTTTT 60.414 45.455 0.00 0.00 38.26 1.94
422 447 1.130561 GCGCTCGCTATTTCTGGTTTT 59.869 47.619 0.00 0.00 38.26 2.43
486 511 0.174617 AAGCTAGTCTCGCCTGAAGC 59.825 55.000 0.00 0.00 38.52 3.86
487 512 1.748493 AGAAGCTAGTCTCGCCTGAAG 59.252 52.381 0.00 0.00 0.00 3.02
561 586 1.333177 GGGCAATGTGGTACCAAACA 58.667 50.000 18.31 12.24 0.00 2.83
615 640 2.514803 TGCTAGGAAAGAAAAGCCCAC 58.485 47.619 0.00 0.00 33.99 4.61
662 721 4.539726 TGATGATCTGGGAAAATTCAGGG 58.460 43.478 0.00 0.00 0.00 4.45
928 2175 2.026014 CCGTTGCTGTGTTGGTGC 59.974 61.111 0.00 0.00 0.00 5.01
945 2192 7.787725 AGTTTGCACTTTGTATATACCTAGC 57.212 36.000 10.38 7.87 0.00 3.42
1024 2271 0.908198 GCAGGGAGGCCATAGGATAG 59.092 60.000 5.01 0.00 0.00 2.08
1026 2273 3.913107 GCAGGGAGGCCATAGGAT 58.087 61.111 5.01 0.00 0.00 3.24
1125 2372 3.565214 TGGCCGCTCTTTGGGTCA 61.565 61.111 0.00 0.00 35.08 4.02
1152 2399 2.580815 CTGGCGAGGTCATGCTCA 59.419 61.111 0.00 0.00 0.00 4.26
1216 2463 1.043816 CCACCTAGGTCGCAGATGAT 58.956 55.000 12.84 0.00 40.67 2.45
1302 2549 1.810030 GTCGACCATGAGTTCGGCC 60.810 63.158 3.51 0.00 0.00 6.13
1438 2685 2.281070 GCGATCCATGTCGGCCAT 60.281 61.111 2.24 0.00 41.72 4.40
1476 2723 2.994995 ATGAGGTCACCGGCGACA 60.995 61.111 23.31 4.34 37.66 4.35
1504 2751 1.935933 ATTATCGGTCACTTGGCGAC 58.064 50.000 0.00 0.00 0.00 5.19
1507 2754 6.560253 ATGATTTATTATCGGTCACTTGGC 57.440 37.500 0.00 0.00 0.00 4.52
1567 3066 2.802247 GCCAGCATTTTGTTTTCTCCAC 59.198 45.455 0.00 0.00 0.00 4.02
1568 3067 2.699846 AGCCAGCATTTTGTTTTCTCCA 59.300 40.909 0.00 0.00 0.00 3.86
1569 3068 3.391506 AGCCAGCATTTTGTTTTCTCC 57.608 42.857 0.00 0.00 0.00 3.71
1570 3069 5.739752 AAAAGCCAGCATTTTGTTTTCTC 57.260 34.783 0.00 0.00 0.00 2.87
1598 3108 5.237048 GCCCAGCATTTGTTTTATTCTCAA 58.763 37.500 0.00 0.00 0.00 3.02
1599 3109 4.322650 GGCCCAGCATTTGTTTTATTCTCA 60.323 41.667 0.00 0.00 0.00 3.27
1602 3112 3.934579 CTGGCCCAGCATTTGTTTTATTC 59.065 43.478 0.00 0.00 0.00 1.75
1603 3113 3.327464 ACTGGCCCAGCATTTGTTTTATT 59.673 39.130 11.63 0.00 34.37 1.40
1605 3115 2.298729 GACTGGCCCAGCATTTGTTTTA 59.701 45.455 11.63 0.00 34.37 1.52
1610 3120 1.065199 TCTAGACTGGCCCAGCATTTG 60.065 52.381 11.63 0.00 34.37 2.32
1612 3122 1.211457 CTTCTAGACTGGCCCAGCATT 59.789 52.381 11.63 0.00 34.37 3.56
1686 3198 2.100916 ACGGTCTGATCGGTTAGAATGG 59.899 50.000 15.53 0.00 0.00 3.16
1688 3200 2.361438 GGACGGTCTGATCGGTTAGAAT 59.639 50.000 15.53 0.00 0.00 2.40
1689 3201 1.747355 GGACGGTCTGATCGGTTAGAA 59.253 52.381 15.53 0.00 0.00 2.10
1690 3202 1.386533 GGACGGTCTGATCGGTTAGA 58.613 55.000 15.53 0.00 0.00 2.10
1692 3204 0.033796 AGGGACGGTCTGATCGGTTA 60.034 55.000 15.53 0.00 0.00 2.85
1693 3205 1.305046 AGGGACGGTCTGATCGGTT 60.305 57.895 15.53 0.00 0.00 4.44
1694 3206 1.753463 GAGGGACGGTCTGATCGGT 60.753 63.158 15.53 0.07 0.00 4.69
1695 3207 1.448922 GAGAGGGACGGTCTGATCGG 61.449 65.000 15.53 0.00 0.00 4.18
1698 3210 2.122167 GCGAGAGGGACGGTCTGAT 61.122 63.158 8.23 0.00 0.00 2.90
1699 3211 2.750637 GCGAGAGGGACGGTCTGA 60.751 66.667 8.23 0.00 0.00 3.27
1700 3212 3.827898 GGCGAGAGGGACGGTCTG 61.828 72.222 8.23 0.00 0.00 3.51
1736 3274 2.838736 CCGGAGAGAGAGAAGAGAGAG 58.161 57.143 0.00 0.00 0.00 3.20
1737 3275 1.134220 GCCGGAGAGAGAGAAGAGAGA 60.134 57.143 5.05 0.00 0.00 3.10
1740 3278 0.395036 TGGCCGGAGAGAGAGAAGAG 60.395 60.000 5.05 0.00 0.00 2.85
1741 3279 0.039764 TTGGCCGGAGAGAGAGAAGA 59.960 55.000 5.05 0.00 0.00 2.87
1742 3280 0.898320 TTTGGCCGGAGAGAGAGAAG 59.102 55.000 5.05 0.00 0.00 2.85
1743 3281 1.482593 GATTTGGCCGGAGAGAGAGAA 59.517 52.381 5.05 0.00 0.00 2.87
1788 3331 0.260523 GCTCCTACCCCTCTGTCTCT 59.739 60.000 0.00 0.00 0.00 3.10
1999 3555 2.168728 CGGGGGAGTAAGAAAGAAGAGG 59.831 54.545 0.00 0.00 0.00 3.69
2078 3657 5.359756 TGATCAATCAACCGGATGTAAGAG 58.640 41.667 9.46 0.00 36.02 2.85
2090 3669 1.596727 GAGAGCGCCTGATCAATCAAC 59.403 52.381 2.29 0.00 36.18 3.18
2266 3845 3.913163 GAGATGGATTACCCTTCATCCCT 59.087 47.826 0.00 0.00 40.54 4.20
2290 3877 2.218603 ACAAGCAACTTTCGTAGGTGG 58.781 47.619 7.31 0.00 42.15 4.61
2298 3885 4.098416 GTGACAACTGACAAGCAACTTTC 58.902 43.478 0.00 0.00 0.00 2.62
2337 3926 1.109323 AAGGAGCAGGCCAACAACAC 61.109 55.000 5.01 0.00 0.00 3.32
2356 3945 2.959372 GCAAGCATGACAGCTGCA 59.041 55.556 15.27 13.46 45.89 4.41
2377 3966 0.904865 TCCCCAGCTGAATCGACTGT 60.905 55.000 17.39 0.00 0.00 3.55
2495 4084 0.036388 CTGGCTCCACCGAAAGCTAA 60.036 55.000 0.00 0.00 43.94 3.09



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

AutoCloner maintained by Alex Coulton.