Multiple sequence alignment - TraesCS5D01G076200

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 TraesCS5D01G076200 chr5D 100.000 2366 0 0 1 2366 75420304 75417939 0.000000e+00 4370
1 TraesCS5D01G076200 chr5D 81.169 154 21 5 360 507 496276584 496276433 1.490000e-22 117
2 TraesCS5D01G076200 chr5B 95.381 1862 37 15 516 2366 83906372 83904549 0.000000e+00 2916
3 TraesCS5D01G076200 chr5B 86.719 512 62 4 1 507 83928778 83928268 4.410000e-157 564
4 TraesCS5D01G076200 chr5B 86.719 512 62 4 1 507 83934924 83934414 4.410000e-157 564
5 TraesCS5D01G076200 chr5A 96.184 1284 35 6 516 1796 70677000 70675728 0.000000e+00 2087
6 TraesCS5D01G076200 chr5A 87.821 468 21 13 1799 2250 70665454 70665007 1.250000e-142 516
7 TraesCS5D01G076200 chr5A 83.688 141 22 1 360 499 281137520 281137660 5.310000e-27 132
8 TraesCS5D01G076200 chr1A 79.775 178 33 3 330 507 449691807 449691633 2.470000e-25 126
9 TraesCS5D01G076200 chr7B 82.394 142 22 3 360 499 629046054 629046194 1.150000e-23 121
10 TraesCS5D01G076200 chr6B 82.270 141 24 1 360 499 68112066 68111926 1.150000e-23 121
11 TraesCS5D01G076200 chr2D 82.270 141 24 1 360 499 33961945 33961805 1.150000e-23 121
12 TraesCS5D01G076200 chr2A 79.433 141 28 1 360 499 68322236 68322376 5.380000e-17 99


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 TraesCS5D01G076200 chr5D 75417939 75420304 2365 True 4370 4370 100.000 1 2366 1 chr5D.!!$R1 2365
1 TraesCS5D01G076200 chr5B 83904549 83906372 1823 True 2916 2916 95.381 516 2366 1 chr5B.!!$R1 1850
2 TraesCS5D01G076200 chr5B 83928268 83928778 510 True 564 564 86.719 1 507 1 chr5B.!!$R2 506
3 TraesCS5D01G076200 chr5B 83934414 83934924 510 True 564 564 86.719 1 507 1 chr5B.!!$R3 506
4 TraesCS5D01G076200 chr5A 70675728 70677000 1272 True 2087 2087 96.184 516 1796 1 chr5A.!!$R2 1280

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
41 42 0.734889 CCCAGGAGCATGTAAAAGCG 59.265 55.0 0.0 0.0 35.48 4.68 F
220 224 0.974383 AAGTGGATCCCGAAAGACGT 59.026 50.0 9.9 0.0 40.78 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1146 1157 2.280797 GCTGTGTCGAAGGTGCCA 60.281 61.111 0.0 0.0 0.0 4.92 R
2145 2164 1.398692 GGGTCAGCAACAACTTTCCA 58.601 50.000 0.0 0.0 0.0 3.53 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
41 42 0.734889 CCCAGGAGCATGTAAAAGCG 59.265 55.000 0.00 0.00 35.48 4.68
71 72 2.398252 AGTCGTCGATGTAGACCAGA 57.602 50.000 4.21 0.00 37.85 3.86
73 74 3.079578 AGTCGTCGATGTAGACCAGAAA 58.920 45.455 4.21 0.00 37.85 2.52
76 77 3.253921 TCGTCGATGTAGACCAGAAAACA 59.746 43.478 4.21 0.00 37.85 2.83
78 79 4.265556 CGTCGATGTAGACCAGAAAACATC 59.734 45.833 0.00 4.59 43.00 3.06
79 80 5.168569 GTCGATGTAGACCAGAAAACATCA 58.831 41.667 13.05 0.66 45.44 3.07
84 85 4.458989 TGTAGACCAGAAAACATCAATGGC 59.541 41.667 0.00 0.00 34.24 4.40
86 87 4.922206 AGACCAGAAAACATCAATGGCTA 58.078 39.130 0.00 0.00 34.24 3.93
87 88 4.702131 AGACCAGAAAACATCAATGGCTAC 59.298 41.667 0.00 0.00 34.24 3.58
88 89 4.406456 ACCAGAAAACATCAATGGCTACA 58.594 39.130 0.00 0.00 34.24 2.74
94 95 4.644103 AACATCAATGGCTACAATCTGC 57.356 40.909 0.00 0.00 0.00 4.26
127 128 2.076863 CGTCCCGAAAAAGAGAATGCT 58.923 47.619 0.00 0.00 0.00 3.79
135 136 5.220931 CCGAAAAAGAGAATGCTGATAAGGG 60.221 44.000 0.00 0.00 0.00 3.95
163 167 5.572126 GCAGAAACTCAAAGATCATGAAAGC 59.428 40.000 0.00 0.00 0.00 3.51
164 168 6.091437 CAGAAACTCAAAGATCATGAAAGCC 58.909 40.000 0.00 0.00 0.00 4.35
165 169 5.771666 AGAAACTCAAAGATCATGAAAGCCA 59.228 36.000 0.00 0.00 0.00 4.75
170 174 2.054232 AGATCATGAAAGCCAGCCAG 57.946 50.000 0.00 0.00 0.00 4.85
188 192 2.648059 CAGATCCAAACAGATCCACCC 58.352 52.381 0.00 0.00 43.14 4.61
201 205 5.073965 ACAGATCCACCCTAAACTTAAACCA 59.926 40.000 0.00 0.00 0.00 3.67
218 222 1.003233 ACCAAGTGGATCCCGAAAGAC 59.997 52.381 9.90 0.00 38.94 3.01
220 224 0.974383 AAGTGGATCCCGAAAGACGT 59.026 50.000 9.90 0.00 40.78 4.34
222 226 1.079405 TGGATCCCGAAAGACGTGC 60.079 57.895 9.90 0.00 40.78 5.34
229 233 2.087009 CGAAAGACGTGCCGGAGAC 61.087 63.158 5.05 0.00 37.22 3.36
231 235 1.282930 GAAAGACGTGCCGGAGACAC 61.283 60.000 5.05 2.46 34.62 3.67
235 239 1.828331 GACGTGCCGGAGACACAAAC 61.828 60.000 5.05 0.00 37.93 2.93
242 247 1.593196 CGGAGACACAAACCACACAT 58.407 50.000 0.00 0.00 0.00 3.21
247 252 2.439507 AGACACAAACCACACATCCTCT 59.560 45.455 0.00 0.00 0.00 3.69
275 280 1.961277 GAGCACACCAACGGGACAG 60.961 63.158 0.00 0.00 38.05 3.51
277 282 2.281484 CACACCAACGGGACAGGG 60.281 66.667 0.00 0.00 38.05 4.45
283 288 1.696097 CCAACGGGACAGGGATAGGG 61.696 65.000 0.00 0.00 35.59 3.53
312 317 8.917415 GGAAGACATACTTTCCAATTGATTTC 57.083 34.615 7.12 0.00 39.13 2.17
358 363 4.928020 CACAATATAGTCGCAGATGCTCAT 59.072 41.667 2.95 0.00 40.67 2.90
368 373 3.672397 CGCAGATGCTCATATACACTCAC 59.328 47.826 2.95 0.00 39.32 3.51
370 375 4.564041 CAGATGCTCATATACACTCACCC 58.436 47.826 0.00 0.00 0.00 4.61
371 376 3.580458 AGATGCTCATATACACTCACCCC 59.420 47.826 0.00 0.00 0.00 4.95
390 395 1.678728 CCTATGAACCCACACACGCAT 60.679 52.381 0.00 0.00 0.00 4.73
406 412 1.203523 CGCATCCCTACTCCTATGAGC 59.796 57.143 0.00 0.00 42.74 4.26
407 413 1.203523 GCATCCCTACTCCTATGAGCG 59.796 57.143 0.00 0.00 42.74 5.03
419 425 1.131504 CTATGAGCGCCTCCGAGATAC 59.868 57.143 2.29 0.00 36.29 2.24
426 432 1.109920 GCCTCCGAGATACTGAGCCA 61.110 60.000 0.00 0.00 0.00 4.75
433 439 3.056250 CCGAGATACTGAGCCAGCATAAT 60.056 47.826 2.50 0.00 34.37 1.28
448 454 6.429078 GCCAGCATAATATCTTGAGATTGACA 59.571 38.462 0.00 0.00 36.05 3.58
463 469 5.396484 AGATTGACAAAATCATCACAAGCG 58.604 37.500 0.00 0.00 37.11 4.68
497 503 2.493675 CGAGAACATCTTCTCCCACTGA 59.506 50.000 5.28 0.00 46.98 3.41
507 513 1.275291 TCTCCCACTGAACGAACATCC 59.725 52.381 0.00 0.00 0.00 3.51
508 514 1.001974 CTCCCACTGAACGAACATCCA 59.998 52.381 0.00 0.00 0.00 3.41
509 515 1.001974 TCCCACTGAACGAACATCCAG 59.998 52.381 0.00 0.00 0.00 3.86
510 516 1.442769 CCACTGAACGAACATCCAGG 58.557 55.000 0.00 0.00 0.00 4.45
511 517 1.270839 CCACTGAACGAACATCCAGGT 60.271 52.381 0.00 0.00 0.00 4.00
512 518 2.028476 CCACTGAACGAACATCCAGGTA 60.028 50.000 0.00 0.00 0.00 3.08
513 519 3.369471 CCACTGAACGAACATCCAGGTAT 60.369 47.826 0.00 0.00 0.00 2.73
514 520 4.142026 CCACTGAACGAACATCCAGGTATA 60.142 45.833 0.00 0.00 0.00 1.47
518 524 7.872993 CACTGAACGAACATCCAGGTATAATAT 59.127 37.037 0.00 0.00 0.00 1.28
565 572 8.784043 AGACAACTAATTAGTCAAAATCACACC 58.216 33.333 18.28 0.00 34.99 4.16
688 695 8.753175 CGATACTAGTCTAATTAACAACTTGCC 58.247 37.037 0.00 0.00 0.00 4.52
902 909 1.372997 GTCGTCGACACAGCCACAT 60.373 57.895 20.28 0.00 32.09 3.21
1146 1157 2.672996 AGCGTCCGCAAATGGCTT 60.673 55.556 14.70 0.00 44.88 4.35
1316 1327 0.879400 CTCGAGTGCCTGGATGATGC 60.879 60.000 3.62 0.00 0.00 3.91
1547 1558 8.783093 CAGTATTCTTAGGTGTTCAATGAAACA 58.217 33.333 0.00 0.00 36.82 2.83
1665 1683 3.192422 TGGGTTGCTTGTTGGATTAATCG 59.808 43.478 9.32 0.00 0.00 3.34
1824 1842 9.688592 ACGAGTTTACCATAAACTAGCATATAC 57.311 33.333 16.65 3.37 40.27 1.47
1825 1843 9.909644 CGAGTTTACCATAAACTAGCATATACT 57.090 33.333 12.70 0.00 40.27 2.12
1869 1887 4.837896 TGCCAACGAAATTACAACATCA 57.162 36.364 0.00 0.00 0.00 3.07
1871 1889 4.277174 TGCCAACGAAATTACAACATCAGT 59.723 37.500 0.00 0.00 0.00 3.41
1905 1923 3.407698 TGATTGGTTCGTATGCACACTT 58.592 40.909 0.00 0.00 0.00 3.16
1981 1999 5.509501 CCAAGGTACAAATGCTCAAATGTGT 60.510 40.000 0.00 0.00 32.62 3.72
1982 2000 6.294453 CCAAGGTACAAATGCTCAAATGTGTA 60.294 38.462 0.00 0.00 30.48 2.90
1983 2001 6.254281 AGGTACAAATGCTCAAATGTGTAC 57.746 37.500 8.52 8.52 45.06 2.90
1984 2002 5.767665 AGGTACAAATGCTCAAATGTGTACA 59.232 36.000 15.84 0.00 46.54 2.90
2039 2058 8.125448 GCCAGCAAAAATTGTTTTACAAATGTA 58.875 29.630 0.00 0.00 41.96 2.29
2067 2086 2.485266 TACGTACCGATGCATGAGTG 57.515 50.000 2.46 0.00 0.00 3.51
2115 2134 4.494855 CGTGCTAGAAAGAATTTAGCTGCC 60.495 45.833 0.00 0.00 39.70 4.85
2144 2163 7.510685 ACCTGAACTAAAGAGCATCCTCATATA 59.489 37.037 0.00 0.00 40.68 0.86
2145 2164 8.538701 CCTGAACTAAAGAGCATCCTCATATAT 58.461 37.037 0.00 0.00 40.68 0.86
2160 2179 6.543465 TCCTCATATATGGAAAGTTGTTGCTG 59.457 38.462 12.78 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.062525 CGCCGCTTTTACATGCTCC 59.937 57.895 0.00 0.00 0.00 4.70
41 42 2.202453 GACGACTTCTCGACCGCC 60.202 66.667 0.00 0.00 43.06 6.13
63 64 4.922206 AGCCATTGATGTTTTCTGGTCTA 58.078 39.130 0.00 0.00 0.00 2.59
71 72 5.413499 GCAGATTGTAGCCATTGATGTTTT 58.587 37.500 0.00 0.00 0.00 2.43
73 74 3.065786 CGCAGATTGTAGCCATTGATGTT 59.934 43.478 0.00 0.00 0.00 2.71
76 77 3.198409 TCGCAGATTGTAGCCATTGAT 57.802 42.857 0.00 0.00 0.00 2.57
78 79 2.540361 GCTTCGCAGATTGTAGCCATTG 60.540 50.000 0.00 0.00 35.04 2.82
79 80 1.672881 GCTTCGCAGATTGTAGCCATT 59.327 47.619 0.00 0.00 35.04 3.16
84 85 3.740590 CACTTTGCTTCGCAGATTGTAG 58.259 45.455 0.00 0.00 40.61 2.74
86 87 1.335324 GCACTTTGCTTCGCAGATTGT 60.335 47.619 0.00 0.00 40.61 2.71
87 88 1.334054 GCACTTTGCTTCGCAGATTG 58.666 50.000 0.00 0.00 40.61 2.67
88 89 0.242017 GGCACTTTGCTTCGCAGATT 59.758 50.000 0.00 0.00 44.28 2.40
94 95 2.556287 GGACGGCACTTTGCTTCG 59.444 61.111 0.00 0.00 44.28 3.79
109 110 3.417069 TCAGCATTCTCTTTTTCGGGA 57.583 42.857 0.00 0.00 0.00 5.14
110 111 5.220931 CCTTATCAGCATTCTCTTTTTCGGG 60.221 44.000 0.00 0.00 0.00 5.14
127 128 1.635487 AGTTTCTGCAGGCCCTTATCA 59.365 47.619 15.13 0.00 0.00 2.15
135 136 2.816087 TGATCTTTGAGTTTCTGCAGGC 59.184 45.455 15.13 4.80 0.00 4.85
163 167 2.295885 GATCTGTTTGGATCTGGCTGG 58.704 52.381 0.00 0.00 39.06 4.85
164 168 2.295885 GGATCTGTTTGGATCTGGCTG 58.704 52.381 0.00 0.00 41.15 4.85
165 169 1.918262 TGGATCTGTTTGGATCTGGCT 59.082 47.619 0.00 0.00 41.15 4.75
170 174 4.503714 TTAGGGTGGATCTGTTTGGATC 57.496 45.455 0.00 0.00 40.78 3.36
201 205 0.974383 ACGTCTTTCGGGATCCACTT 59.026 50.000 15.23 0.00 44.69 3.16
220 224 1.525077 GTGGTTTGTGTCTCCGGCA 60.525 57.895 0.00 0.00 0.00 5.69
222 226 0.462937 TGTGTGGTTTGTGTCTCCGG 60.463 55.000 0.00 0.00 0.00 5.14
229 233 1.267806 GCAGAGGATGTGTGGTTTGTG 59.732 52.381 0.00 0.00 0.00 3.33
231 235 0.883833 GGCAGAGGATGTGTGGTTTG 59.116 55.000 0.00 0.00 0.00 2.93
235 239 2.124983 CCGGCAGAGGATGTGTGG 60.125 66.667 0.00 0.00 0.00 4.17
242 247 2.725312 GCTCATCACCGGCAGAGGA 61.725 63.158 0.00 6.52 34.73 3.71
247 252 2.358615 GTGTGCTCATCACCGGCA 60.359 61.111 0.00 0.00 45.03 5.69
269 274 3.242291 CCGCCCTATCCCTGTCCC 61.242 72.222 0.00 0.00 0.00 4.46
275 280 2.122547 TCTTCCCCGCCCTATCCC 60.123 66.667 0.00 0.00 0.00 3.85
277 282 1.275573 GTATGTCTTCCCCGCCCTATC 59.724 57.143 0.00 0.00 0.00 2.08
283 288 1.065709 TGGAAAGTATGTCTTCCCCGC 60.066 52.381 0.00 0.00 35.02 6.13
350 355 3.580458 AGGGGTGAGTGTATATGAGCATC 59.420 47.826 0.00 0.00 0.00 3.91
358 363 4.228824 GGGTTCATAGGGGTGAGTGTATA 58.771 47.826 0.00 0.00 0.00 1.47
368 373 0.392461 CGTGTGTGGGTTCATAGGGG 60.392 60.000 0.00 0.00 0.00 4.79
370 375 0.321210 TGCGTGTGTGGGTTCATAGG 60.321 55.000 0.00 0.00 0.00 2.57
371 376 1.665679 GATGCGTGTGTGGGTTCATAG 59.334 52.381 0.00 0.00 0.00 2.23
390 395 0.539901 GGCGCTCATAGGAGTAGGGA 60.540 60.000 7.64 0.00 43.37 4.20
406 412 1.284408 GCTCAGTATCTCGGAGGCG 59.716 63.158 4.96 0.00 38.48 5.52
419 425 5.791666 TCTCAAGATATTATGCTGGCTCAG 58.208 41.667 0.00 0.00 34.12 3.35
433 439 9.452287 TGTGATGATTTTGTCAATCTCAAGATA 57.548 29.630 0.00 0.00 40.97 1.98
448 454 2.950433 CAAGGCGCTTGTGATGATTTT 58.050 42.857 7.64 0.00 36.79 1.82
463 469 2.750948 TGTTCTCGTTGACTACAAGGC 58.249 47.619 0.00 0.00 40.36 4.35
497 503 6.426937 GCACATATTATACCTGGATGTTCGTT 59.573 38.462 0.00 0.00 0.00 3.85
507 513 3.055819 AGCCTCGGCACATATTATACCTG 60.056 47.826 11.02 0.00 44.88 4.00
508 514 3.055819 CAGCCTCGGCACATATTATACCT 60.056 47.826 11.02 0.00 44.88 3.08
509 515 3.056107 TCAGCCTCGGCACATATTATACC 60.056 47.826 11.02 0.00 44.88 2.73
510 516 4.188247 TCAGCCTCGGCACATATTATAC 57.812 45.455 11.02 0.00 44.88 1.47
511 517 5.420725 AATCAGCCTCGGCACATATTATA 57.579 39.130 11.02 0.00 44.88 0.98
512 518 3.988976 ATCAGCCTCGGCACATATTAT 57.011 42.857 11.02 0.00 44.88 1.28
513 519 3.769739 AATCAGCCTCGGCACATATTA 57.230 42.857 11.02 0.00 44.88 0.98
514 520 2.645838 AATCAGCCTCGGCACATATT 57.354 45.000 11.02 1.57 44.88 1.28
518 524 3.034924 AAAAATCAGCCTCGGCACA 57.965 47.368 11.02 0.00 44.88 4.57
565 572 7.528481 TTATTTTTCAATAAGCTGCATGCAG 57.472 32.000 37.81 37.81 45.94 4.41
688 695 9.717844 CGTTACAATTTAAGAAACACTACTACG 57.282 33.333 0.00 0.00 0.00 3.51
859 866 0.935898 CGATGTGAATGGCAGAGAGC 59.064 55.000 0.00 0.00 44.65 4.09
902 909 2.875933 GTTAGGCTTTGTGTGTGTGCTA 59.124 45.455 0.00 0.00 0.00 3.49
1146 1157 2.280797 GCTGTGTCGAAGGTGCCA 60.281 61.111 0.00 0.00 0.00 4.92
1665 1683 3.383505 GGACTAAGAGAGGAGAAGAAGGC 59.616 52.174 0.00 0.00 0.00 4.35
1785 1803 5.533154 TGGTAAACTCGTGACCAATCAATTT 59.467 36.000 2.53 0.00 40.29 1.82
1869 1887 6.569035 CGAACCAATCATATATTGCATGCACT 60.569 38.462 22.58 18.59 0.00 4.40
1871 1889 5.241285 ACGAACCAATCATATATTGCATGCA 59.759 36.000 18.46 18.46 0.00 3.96
1905 1923 7.576403 TGGATGATCTCATTTTATGTTCCAGA 58.424 34.615 0.00 0.00 36.57 3.86
1981 1999 6.379988 TCTGCCACTACTGATTACTCATTGTA 59.620 38.462 0.00 0.00 0.00 2.41
1982 2000 5.187772 TCTGCCACTACTGATTACTCATTGT 59.812 40.000 0.00 0.00 0.00 2.71
1983 2001 5.664457 TCTGCCACTACTGATTACTCATTG 58.336 41.667 0.00 0.00 0.00 2.82
1984 2002 5.939764 TCTGCCACTACTGATTACTCATT 57.060 39.130 0.00 0.00 0.00 2.57
2067 2086 4.091424 CCGTCAAAAGCAATTCTTCGATC 58.909 43.478 0.00 0.00 32.88 3.69
2115 2134 4.081198 AGGATGCTCTTTAGTTCAGGTCAG 60.081 45.833 0.00 0.00 0.00 3.51
2144 2163 1.963515 GGGTCAGCAACAACTTTCCAT 59.036 47.619 0.00 0.00 0.00 3.41
2145 2164 1.398692 GGGTCAGCAACAACTTTCCA 58.601 50.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.