Multiple sequence alignment - TraesCS3D01G269500

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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 TraesCS3D01G269500 chr3D 100.000 2702 0 0 1 2702 374070476 374067775 0.000000e+00 4990.0
1 TraesCS3D01G269500 chr3B 95.415 1374 27 12 613 1976 487883902 487882555 0.000000e+00 2156.0
2 TraesCS3D01G269500 chr3B 91.410 617 42 3 2094 2702 487879776 487879163 0.000000e+00 835.0
3 TraesCS3D01G269500 chr3B 100.000 41 0 0 1986 2026 487882561 487882521 2.880000e-10 76.8
4 TraesCS3D01G269500 chr3A 95.413 1199 36 7 809 2004 496637502 496636320 0.000000e+00 1892.0
5 TraesCS3D01G269500 chr3A 88.537 820 47 25 1 777 496638737 496637922 0.000000e+00 950.0
6 TraesCS3D01G269500 chr3A 91.406 256 20 2 2447 2702 496597758 496597505 1.540000e-92 350.0
7 TraesCS3D01G269500 chr3A 89.091 165 14 1 2286 2450 496598405 496598245 4.560000e-48 202.0
8 TraesCS3D01G269500 chr3A 93.694 111 6 1 2094 2203 496635669 496635559 5.980000e-37 165.0
9 TraesCS3D01G269500 chr1D 78.443 167 27 9 377 538 314763275 314763437 1.710000e-17 100.0


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 TraesCS3D01G269500 chr3D 374067775 374070476 2701 True 4990.000000 4990 100.000000 1 2702 1 chr3D.!!$R1 2701
1 TraesCS3D01G269500 chr3B 487879163 487883902 4739 True 1022.600000 2156 95.608333 613 2702 3 chr3B.!!$R1 2089
2 TraesCS3D01G269500 chr3A 496635559 496638737 3178 True 1002.333333 1892 92.548000 1 2203 3 chr3A.!!$R2 2202
3 TraesCS3D01G269500 chr3A 496597505 496598405 900 True 276.000000 350 90.248500 2286 2702 2 chr3A.!!$R1 416

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
19 20 0.248498 TTGAACGCTAGATCGGCTCG 60.248 55.0 10.9 5.45 0.00 5.03 F
1155 1590 0.177604 CTGCCCAGCAAGAGGTAGAG 59.822 60.0 0.0 0.00 38.04 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1157 1592 0.178990 GGGTTCTTGCTCCTGGTTGT 60.179 55.0 0.00 0.0 0.00 3.32 R
2256 5678 0.250338 AGACCTTCTCGGCGCTTTTT 60.250 50.0 7.64 0.0 35.61 1.94 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
19 20 0.248498 TTGAACGCTAGATCGGCTCG 60.248 55.000 10.90 5.45 0.00 5.03
24 25 2.958576 CTAGATCGGCTCGGGCTC 59.041 66.667 7.48 0.00 38.73 4.70
49 50 2.035193 TGATTGCTAGACCGATCTGCTC 59.965 50.000 0.00 0.00 36.29 4.26
118 119 0.313987 GGAAAACAGGCTTCCCGTTG 59.686 55.000 0.00 0.00 37.03 4.10
122 123 2.351706 AACAGGCTTCCCGTTGTTTA 57.648 45.000 0.00 0.00 35.76 2.01
123 124 1.601166 ACAGGCTTCCCGTTGTTTAC 58.399 50.000 0.00 0.00 35.76 2.01
124 125 1.134037 ACAGGCTTCCCGTTGTTTACA 60.134 47.619 0.00 0.00 35.76 2.41
125 126 1.535462 CAGGCTTCCCGTTGTTTACAG 59.465 52.381 0.00 0.00 35.76 2.74
126 127 1.418637 AGGCTTCCCGTTGTTTACAGA 59.581 47.619 0.00 0.00 35.76 3.41
127 128 1.534163 GGCTTCCCGTTGTTTACAGAC 59.466 52.381 0.00 0.00 0.00 3.51
135 138 5.032220 CCCGTTGTTTACAGACTGAAAAAC 58.968 41.667 21.18 21.18 32.00 2.43
192 196 5.744171 AGGTTTGCAGATTTGGAAAAAGTT 58.256 33.333 4.45 0.00 44.62 2.66
194 198 6.316140 AGGTTTGCAGATTTGGAAAAAGTTTC 59.684 34.615 4.45 0.00 44.62 2.78
243 248 7.475771 TTGAAAAAGGAAATTCGTGGATTTG 57.524 32.000 0.00 0.00 29.75 2.32
315 325 7.691463 TGAATTTGAAAAGCGTTCACAAATTTG 59.309 29.630 26.15 16.67 45.02 2.32
317 327 4.748892 TGAAAAGCGTTCACAAATTTGGA 58.251 34.783 21.74 13.03 0.00 3.53
321 331 6.676237 AAAGCGTTCACAAATTTGGAAAAT 57.324 29.167 21.74 8.91 0.00 1.82
322 332 6.676237 AAGCGTTCACAAATTTGGAAAATT 57.324 29.167 21.74 13.06 0.00 1.82
323 333 6.285790 AGCGTTCACAAATTTGGAAAATTC 57.714 33.333 21.74 9.37 0.00 2.17
324 334 5.814705 AGCGTTCACAAATTTGGAAAATTCA 59.185 32.000 21.74 0.00 0.00 2.57
325 335 6.314896 AGCGTTCACAAATTTGGAAAATTCAA 59.685 30.769 21.74 0.80 0.00 2.69
326 336 6.963805 GCGTTCACAAATTTGGAAAATTCAAA 59.036 30.769 21.74 0.00 38.30 2.69
327 337 7.483059 GCGTTCACAAATTTGGAAAATTCAAAA 59.517 29.630 21.74 0.00 37.60 2.44
328 338 9.334693 CGTTCACAAATTTGGAAAATTCAAAAA 57.665 25.926 21.74 0.00 37.60 1.94
415 434 8.995220 CATGAATCTGAAAAATGTTTGTGGATT 58.005 29.630 0.00 0.00 0.00 3.01
716 761 9.567776 TTCTAGAATGTTCACAAAACCAGATTA 57.432 29.630 0.00 0.00 0.00 1.75
820 1255 3.345737 CGCAGCGTAGATTGGAAGA 57.654 52.632 6.65 0.00 0.00 2.87
955 1390 7.276218 TCCAAACCTATCTATCACGTAAAAACG 59.724 37.037 0.00 0.00 39.31 3.60
1053 1488 1.547901 CCCAAACCTTTCCTCTCCACC 60.548 57.143 0.00 0.00 0.00 4.61
1151 1586 4.357279 GCCTGCCCAGCAAGAGGT 62.357 66.667 0.00 0.00 38.41 3.85
1152 1587 2.971598 GCCTGCCCAGCAAGAGGTA 61.972 63.158 0.00 0.00 38.41 3.08
1153 1588 1.222936 CCTGCCCAGCAAGAGGTAG 59.777 63.158 0.00 0.00 38.41 3.18
1154 1589 1.267574 CCTGCCCAGCAAGAGGTAGA 61.268 60.000 0.00 0.00 38.04 2.59
1155 1590 0.177604 CTGCCCAGCAAGAGGTAGAG 59.822 60.000 0.00 0.00 38.04 2.43
1156 1591 1.267574 TGCCCAGCAAGAGGTAGAGG 61.268 60.000 0.00 0.00 34.76 3.69
1157 1592 0.978146 GCCCAGCAAGAGGTAGAGGA 60.978 60.000 0.00 0.00 0.00 3.71
1971 2417 1.142748 GTCCACGATCCCTCTGCAG 59.857 63.158 7.63 7.63 0.00 4.41
2057 5435 0.391661 TGCCTCGACATTCAAGCTCC 60.392 55.000 0.00 0.00 0.00 4.70
2070 5448 8.388484 ACATTCAAGCTCCTATATTCATGAAC 57.612 34.615 11.07 0.00 0.00 3.18
2073 5451 6.216569 TCAAGCTCCTATATTCATGAACGAC 58.783 40.000 11.07 0.00 0.00 4.34
2076 5454 6.393990 AGCTCCTATATTCATGAACGACATC 58.606 40.000 11.07 0.00 37.07 3.06
2090 5469 2.028930 ACGACATCACAGAGGGAAAGAC 60.029 50.000 0.00 0.00 0.00 3.01
2091 5470 2.232452 CGACATCACAGAGGGAAAGACT 59.768 50.000 0.00 0.00 0.00 3.24
2092 5471 3.444034 CGACATCACAGAGGGAAAGACTA 59.556 47.826 0.00 0.00 0.00 2.59
2136 5557 3.128415 CGTCCACCACAATATTGCAATCA 59.872 43.478 16.86 3.12 0.00 2.57
2144 5565 4.038763 CACAATATTGCAATCAGAGGCCAT 59.961 41.667 16.86 0.00 0.00 4.40
2165 5586 8.078596 GGCCATGAGAATTCTATGAACATAAAC 58.921 37.037 8.25 0.91 0.00 2.01
2198 5620 1.639280 GCTAGTGCTTCTCTCACTGC 58.361 55.000 5.96 4.45 43.85 4.40
2223 5645 5.659440 TTGCCTCTAAAATTGTTGGATCC 57.341 39.130 4.20 4.20 0.00 3.36
2244 5666 8.362639 GGATCCGTAATACCTCTAAATACACAA 58.637 37.037 0.00 0.00 0.00 3.33
2256 5678 0.538516 ATACACAACAAAGGCGCCCA 60.539 50.000 26.15 0.00 0.00 5.36
2298 5720 4.320456 CACGGCTCCCACTGCACT 62.320 66.667 0.00 0.00 0.00 4.40
2303 5725 0.610232 GGCTCCCACTGCACTGAAAT 60.610 55.000 0.00 0.00 0.00 2.17
2370 5800 2.063979 CAGGAGATGCCACCCGGTA 61.064 63.158 0.00 0.00 40.02 4.02
2381 5811 0.459585 CACCCGGTACATTCGTCTGG 60.460 60.000 0.00 0.00 0.00 3.86
2396 5826 0.539669 TCTGGTTCGAGCTGTCCTGA 60.540 55.000 0.00 0.00 0.00 3.86
2506 6425 1.330306 CTTGTGGATTGCTTTTCGCG 58.670 50.000 0.00 0.00 43.27 5.87
2526 6445 2.805295 CGTAGCGATCCAAATAGCCCAA 60.805 50.000 0.00 0.00 34.35 4.12
2562 6481 6.035435 CCAAACGAATGAACTACTCATGAGAG 59.965 42.308 29.27 21.50 44.43 3.20
2566 6485 6.824196 ACGAATGAACTACTCATGAGAGAGTA 59.176 38.462 29.27 16.02 46.52 2.59
2597 6516 7.148356 CGATCATTGAGAAAATCCAGTTCTTGA 60.148 37.037 0.00 0.00 35.46 3.02
2654 6573 0.683973 CCTCTTGAGATAGCGCCCAT 59.316 55.000 2.29 0.00 0.00 4.00
2666 6585 3.480133 GCCCATACGGACCTGGCT 61.480 66.667 0.00 0.00 39.05 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.288290 CCCGAGCCGATCTAGCGT 61.288 66.667 0.00 0.00 34.64 5.07
19 20 0.179073 TCTAGCAATCAAGCGAGCCC 60.179 55.000 0.00 0.00 37.20 5.19
24 25 1.789464 GATCGGTCTAGCAATCAAGCG 59.211 52.381 0.00 0.00 40.15 4.68
49 50 1.614227 TAACAACAAGCGAGCGAGCG 61.614 55.000 0.00 0.00 43.00 5.03
82 83 2.352561 TCCCCCTCAAACCATCACTA 57.647 50.000 0.00 0.00 0.00 2.74
118 119 9.783256 AAAGTATGTGTTTTTCAGTCTGTAAAC 57.217 29.630 18.32 18.32 0.00 2.01
135 138 9.590451 AATCCATGAGCATTTTTAAAGTATGTG 57.410 29.630 0.00 4.94 0.00 3.21
149 152 9.603921 CAAACCTTTTTATTAATCCATGAGCAT 57.396 29.630 0.00 0.00 0.00 3.79
152 155 9.090692 CTGCAAACCTTTTTATTAATCCATGAG 57.909 33.333 0.00 0.00 0.00 2.90
162 165 8.744568 TTTCCAAATCTGCAAACCTTTTTATT 57.255 26.923 0.00 0.00 0.00 1.40
163 166 8.744568 TTTTCCAAATCTGCAAACCTTTTTAT 57.255 26.923 0.00 0.00 0.00 1.40
164 167 8.567285 TTTTTCCAAATCTGCAAACCTTTTTA 57.433 26.923 0.00 0.00 0.00 1.52
169 173 5.357742 ACTTTTTCCAAATCTGCAAACCT 57.642 34.783 0.00 0.00 0.00 3.50
296 306 5.710613 TTCCAAATTTGTGAACGCTTTTC 57.289 34.783 16.73 0.00 0.00 2.29
499 519 8.688747 TCCATGAACATTTTTAAAATTTGCCT 57.311 26.923 0.55 0.00 0.00 4.75
716 761 2.093106 CCAAGCGTACAGTAGACCTCT 58.907 52.381 0.00 0.00 0.00 3.69
805 1240 4.695928 GGAAAAAGTCTTCCAATCTACGCT 59.304 41.667 0.00 0.00 43.84 5.07
806 1241 4.695928 AGGAAAAAGTCTTCCAATCTACGC 59.304 41.667 5.24 0.00 46.38 4.42
807 1242 5.932303 TCAGGAAAAAGTCTTCCAATCTACG 59.068 40.000 5.24 0.00 46.38 3.51
815 1250 8.246871 CAGGATTAAATCAGGAAAAAGTCTTCC 58.753 37.037 0.00 0.00 44.61 3.46
820 1255 7.039011 GGGAACAGGATTAAATCAGGAAAAAGT 60.039 37.037 0.00 0.00 0.00 2.66
850 1285 3.358775 CGAGCTGGATCGAATCGATATC 58.641 50.000 18.75 13.72 47.00 1.63
1053 1488 0.774908 TAGGGACTTGTGGTTTGGGG 59.225 55.000 0.00 0.00 41.75 4.96
1131 1566 1.300963 CTCTTGCTGGGCAGGCTTA 59.699 57.895 0.00 0.00 40.61 3.09
1151 1586 1.902508 CTTGCTCCTGGTTGTCCTCTA 59.097 52.381 0.00 0.00 34.23 2.43
1152 1587 0.689623 CTTGCTCCTGGTTGTCCTCT 59.310 55.000 0.00 0.00 34.23 3.69
1153 1588 0.687354 TCTTGCTCCTGGTTGTCCTC 59.313 55.000 0.00 0.00 34.23 3.71
1154 1589 1.140312 TTCTTGCTCCTGGTTGTCCT 58.860 50.000 0.00 0.00 34.23 3.85
1155 1590 1.239347 GTTCTTGCTCCTGGTTGTCC 58.761 55.000 0.00 0.00 0.00 4.02
1156 1591 1.239347 GGTTCTTGCTCCTGGTTGTC 58.761 55.000 0.00 0.00 0.00 3.18
1157 1592 0.178990 GGGTTCTTGCTCCTGGTTGT 60.179 55.000 0.00 0.00 0.00 3.32
1712 2157 2.229690 TTACACCCGTCCCTAAGCGC 62.230 60.000 0.00 0.00 0.00 5.92
1764 2209 0.960364 ACGTGTTGGATGGATGCACC 60.960 55.000 0.00 0.00 39.54 5.01
1771 2216 5.768317 ACAAAATTTCTACGTGTTGGATGG 58.232 37.500 0.00 0.00 0.00 3.51
1772 2217 8.964420 ATAACAAAATTTCTACGTGTTGGATG 57.036 30.769 13.10 0.00 34.43 3.51
1773 2218 8.788806 TGATAACAAAATTTCTACGTGTTGGAT 58.211 29.630 13.10 2.84 34.43 3.41
1774 2219 8.155821 TGATAACAAAATTTCTACGTGTTGGA 57.844 30.769 13.10 0.00 34.43 3.53
1971 2417 6.586463 TCTCGTCATCTGTAACACAAATCTTC 59.414 38.462 0.00 0.00 0.00 2.87
2057 5435 7.328005 CCTCTGTGATGTCGTTCATGAATATAG 59.672 40.741 12.12 4.32 36.83 1.31
2070 5448 2.232452 AGTCTTTCCCTCTGTGATGTCG 59.768 50.000 0.00 0.00 0.00 4.35
2073 5451 4.574013 GCAATAGTCTTTCCCTCTGTGATG 59.426 45.833 0.00 0.00 0.00 3.07
2076 5454 3.686726 GTGCAATAGTCTTTCCCTCTGTG 59.313 47.826 0.00 0.00 0.00 3.66
2090 5469 4.728882 GCATCAAACGAGGAAGTGCAATAG 60.729 45.833 0.00 0.00 0.00 1.73
2091 5470 3.126858 GCATCAAACGAGGAAGTGCAATA 59.873 43.478 0.00 0.00 0.00 1.90
2092 5471 2.095059 GCATCAAACGAGGAAGTGCAAT 60.095 45.455 0.00 0.00 0.00 3.56
2136 5557 5.131642 TGTTCATAGAATTCTCATGGCCTCT 59.868 40.000 12.24 0.00 0.00 3.69
2198 5620 5.404466 TCCAACAATTTTAGAGGCAATGG 57.596 39.130 0.00 0.00 0.00 3.16
2244 5666 1.227527 GCTTTTTGGGCGCCTTTGT 60.228 52.632 28.56 0.00 0.00 2.83
2256 5678 0.250338 AGACCTTCTCGGCGCTTTTT 60.250 50.000 7.64 0.00 35.61 1.94
2268 5690 2.029844 GCCGTGTGCAGAGACCTTC 61.030 63.158 0.00 0.00 40.77 3.46
2298 5720 4.395854 CCATGTCAAGGAACGATGATTTCA 59.604 41.667 0.00 0.00 32.35 2.69
2303 5725 1.678728 GGCCATGTCAAGGAACGATGA 60.679 52.381 0.00 0.00 0.00 2.92
2370 5800 0.603569 AGCTCGAACCAGACGAATGT 59.396 50.000 0.00 0.00 39.23 2.71
2381 5811 1.634702 GACATCAGGACAGCTCGAAC 58.365 55.000 0.00 0.00 0.00 3.95
2396 5826 3.532155 GCCGGCGAGAGAGGACAT 61.532 66.667 12.58 0.00 33.12 3.06
2506 6425 2.543777 TGGGCTATTTGGATCGCTAC 57.456 50.000 0.00 0.00 0.00 3.58
2526 6445 4.647611 TCATTCGTTTGGTGGTGACTATT 58.352 39.130 0.00 0.00 0.00 1.73
2562 6481 8.707839 GGATTTTCTCAATGATCGAGATTACTC 58.292 37.037 0.00 0.00 39.22 2.59
2566 6485 7.052873 ACTGGATTTTCTCAATGATCGAGATT 58.947 34.615 0.00 0.00 39.22 2.40
2568 6487 5.982356 ACTGGATTTTCTCAATGATCGAGA 58.018 37.500 0.00 0.00 37.74 4.04
2597 6516 5.450818 TGTGCTAAAAGGGATCCTAACAT 57.549 39.130 12.58 0.00 31.13 2.71
2629 6548 2.099921 GCGCTATCTCAAGAGGAGTTGA 59.900 50.000 0.00 0.00 44.40 3.18
2654 6573 5.776208 TGAATGTAATATAGCCAGGTCCGTA 59.224 40.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.