Multiple sequence alignment - TraesCS1D01G289500

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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 TraesCS1D01G289500 chr1D 100.000 3093 0 0 1 3093 387550706 387547614 0 5712
1 TraesCS1D01G289500 chr1B 94.421 3119 106 26 1 3093 520896675 520893599 0 4734
2 TraesCS1D01G289500 chr1A 92.868 3155 119 36 1 3093 487310247 487307137 0 4482


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 TraesCS1D01G289500 chr1D 387547614 387550706 3092 True 5712 5712 100.000 1 3093 1 chr1D.!!$R1 3092
1 TraesCS1D01G289500 chr1B 520893599 520896675 3076 True 4734 4734 94.421 1 3093 1 chr1B.!!$R1 3092
2 TraesCS1D01G289500 chr1A 487307137 487310247 3110 True 4482 4482 92.868 1 3093 1 chr1A.!!$R1 3092

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
240 241 3.393089 ACTGCAGTGGAGAAGTTAGTG 57.607 47.619 20.97 0.0 0.0 2.74 F
1026 1039 1.040339 ATCCTTCTTCCTCGCTCGCT 61.040 55.000 0.00 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1260 1273 0.035439 CAGCATTACCGTTGAGGGGT 60.035 55.0 0.0 0.0 46.96 4.95 R
2720 2792 0.607762 TCATAGTGCAAAGCCCGCAA 60.608 50.0 0.0 0.0 41.97 4.85 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
154 155 9.916397 CGTAGATGGAACTATACATTTGTTTTC 57.084 33.333 0.00 0.00 0.00 2.29
198 199 8.147058 ACTGCATTTGTAAATGTGTTTATTGGA 58.853 29.630 16.21 0.00 45.77 3.53
240 241 3.393089 ACTGCAGTGGAGAAGTTAGTG 57.607 47.619 20.97 0.00 0.00 2.74
338 339 6.866770 GGGTTTCTTAAGAAAATGTTAGGTGC 59.133 38.462 27.81 13.67 44.58 5.01
347 348 6.543735 AGAAAATGTTAGGTGCTCCTTAACT 58.456 36.000 13.50 0.68 42.12 2.24
376 377 9.691362 GTTGTGATGTGGTTATATTTTCTTGTT 57.309 29.630 0.00 0.00 0.00 2.83
569 581 8.275015 TCCCCGTGTTTATTAATGCATATATG 57.725 34.615 8.45 8.45 0.00 1.78
587 599 7.415989 GCATATATGGTTGGAGCATATTCCTTG 60.416 40.741 14.51 10.52 44.24 3.61
1022 1035 2.303022 TGTTCAATCCTTCTTCCTCGCT 59.697 45.455 0.00 0.00 0.00 4.93
1026 1039 1.040339 ATCCTTCTTCCTCGCTCGCT 61.040 55.000 0.00 0.00 0.00 4.93
1217 1230 4.899457 TCCTCCCTACAATATCAACACGAT 59.101 41.667 0.00 0.00 38.21 3.73
1253 1266 3.610911 CCTTACCATTTCACCTCCAGTC 58.389 50.000 0.00 0.00 0.00 3.51
1260 1273 4.505566 CCATTTCACCTCCAGTCTCTTGAA 60.506 45.833 0.00 0.00 0.00 2.69
1298 1311 1.153745 CCTTCTCTTGCCCGTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
1326 1339 2.440147 CAGTTGCATCCACCCCCA 59.560 61.111 0.00 0.00 0.00 4.96
1410 1423 3.991051 CGTGTCCTCAGCACCGGT 61.991 66.667 0.00 0.00 33.61 5.28
1574 1587 1.602888 CAACTGCAGCCAGGAAGCT 60.603 57.895 15.27 0.00 46.45 3.74
1946 1959 4.694233 ACAGCCAGAGCCAGTGCG 62.694 66.667 0.00 0.00 44.33 5.34
2098 2117 1.150567 CTGACATGTGCTAGCTCCGC 61.151 60.000 17.23 4.37 0.00 5.54
2100 2119 2.187685 CATGTGCTAGCTCCGCCA 59.812 61.111 17.23 5.27 0.00 5.69
2131 2156 2.740055 GTCTGGTCTGCTGGTGCG 60.740 66.667 0.00 0.00 43.34 5.34
2327 2364 2.906388 TCCGTGTGTTCCGTCCGA 60.906 61.111 0.00 0.00 0.00 4.55
2328 2365 2.430244 CCGTGTGTTCCGTCCGAG 60.430 66.667 0.00 0.00 0.00 4.63
2329 2366 2.333938 CGTGTGTTCCGTCCGAGT 59.666 61.111 0.00 0.00 0.00 4.18
2330 2367 1.728426 CGTGTGTTCCGTCCGAGTC 60.728 63.158 0.00 0.00 0.00 3.36
2411 2457 1.527034 CCTGCTGTTGCTTTCTGCTA 58.473 50.000 0.00 0.00 43.37 3.49
2418 2464 3.754965 TGTTGCTTTCTGCTACTCCATT 58.245 40.909 0.00 0.00 45.30 3.16
2419 2465 3.503363 TGTTGCTTTCTGCTACTCCATTG 59.497 43.478 0.00 0.00 45.30 2.82
2420 2466 3.701205 TGCTTTCTGCTACTCCATTGA 57.299 42.857 0.00 0.00 43.37 2.57
2421 2467 4.226427 TGCTTTCTGCTACTCCATTGAT 57.774 40.909 0.00 0.00 43.37 2.57
2434 2480 5.505780 ACTCCATTGATACCCGAAAAATCA 58.494 37.500 0.00 0.00 0.00 2.57
2571 2617 1.915769 GGGAGGCCACTGACTCACT 60.916 63.158 5.01 0.00 34.33 3.41
2572 2618 1.294780 GGAGGCCACTGACTCACTG 59.705 63.158 5.01 0.00 35.45 3.66
2615 2662 2.584608 CGAAGGTTCCGGCTCCAT 59.415 61.111 15.22 5.07 0.00 3.41
2624 2671 4.113815 CGGCTCCATCCCCTTGCA 62.114 66.667 0.00 0.00 0.00 4.08
2663 2710 2.264794 GGCGACGGTCTCATTGGT 59.735 61.111 6.57 0.00 0.00 3.67
2720 2792 0.815734 CCTGTGTAGATCGACCGGTT 59.184 55.000 9.42 0.00 0.00 4.44
2952 3031 3.507622 GTGGAATAGCTTTTCTGCCTTGT 59.492 43.478 15.27 0.00 0.00 3.16
2953 3032 4.021981 GTGGAATAGCTTTTCTGCCTTGTT 60.022 41.667 15.27 0.00 0.00 2.83
2954 3033 4.022068 TGGAATAGCTTTTCTGCCTTGTTG 60.022 41.667 15.27 0.00 0.00 3.33
2955 3034 4.218417 GGAATAGCTTTTCTGCCTTGTTGA 59.782 41.667 15.27 0.00 0.00 3.18
2956 3035 5.382618 AATAGCTTTTCTGCCTTGTTGAG 57.617 39.130 0.00 0.00 0.00 3.02
2957 3036 2.936202 AGCTTTTCTGCCTTGTTGAGA 58.064 42.857 0.00 0.00 0.00 3.27
2958 3037 3.290710 AGCTTTTCTGCCTTGTTGAGAA 58.709 40.909 0.00 0.00 0.00 2.87
2959 3038 3.067320 AGCTTTTCTGCCTTGTTGAGAAC 59.933 43.478 0.00 0.00 0.00 3.01
2960 3039 3.067320 GCTTTTCTGCCTTGTTGAGAACT 59.933 43.478 0.00 0.00 0.00 3.01
2980 3059 8.757982 AGAACTACTATTTAGGTCACGGAATA 57.242 34.615 0.00 0.00 33.85 1.75
3005 3084 6.893583 AGTATACTGCTTTCTCCAACATCAT 58.106 36.000 4.10 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 155 3.181485 GCAGTAACTAGCAGTGGAGTAGG 60.181 52.174 0.00 0.00 0.00 3.18
198 199 7.467675 GCAGTTCTGAATTTGCTTTTGGATTTT 60.468 33.333 17.31 0.00 33.88 1.82
209 210 2.294233 TCCACTGCAGTTCTGAATTTGC 59.706 45.455 18.94 17.59 37.09 3.68
240 241 7.639113 TTTTGGATTTATACTGGACATGGAC 57.361 36.000 0.00 0.00 0.00 4.02
338 339 4.216257 CCACATCACAACCAAGTTAAGGAG 59.784 45.833 0.00 0.00 0.00 3.69
347 348 8.415950 AGAAAATATAACCACATCACAACCAA 57.584 30.769 0.00 0.00 0.00 3.67
441 442 9.395707 CCAATCACGAGTATGTATAAGTTAGAC 57.604 37.037 0.54 0.54 0.00 2.59
569 581 1.683385 GCCAAGGAATATGCTCCAACC 59.317 52.381 0.00 0.00 38.02 3.77
596 608 1.341531 AGAAGACGAACAGGTGTCAGG 59.658 52.381 0.00 0.00 37.58 3.86
1022 1035 1.076014 TCACTGTAGGTGGGAGCGA 59.924 57.895 0.00 0.00 45.38 4.93
1026 1039 1.229400 GGGGTCACTGTAGGTGGGA 60.229 63.158 0.00 0.00 45.38 4.37
1170 1183 2.899339 GAGATGCAGGAAGGCGGC 60.899 66.667 0.00 0.00 36.28 6.53
1217 1230 1.057275 TAAGGGGTGTGTGCTGGTGA 61.057 55.000 0.00 0.00 0.00 4.02
1253 1266 0.396811 ACCGTTGAGGGGTTCAAGAG 59.603 55.000 0.00 0.00 46.09 2.85
1260 1273 0.035439 CAGCATTACCGTTGAGGGGT 60.035 55.000 0.00 0.00 46.96 4.95
1298 1311 0.523072 ATGCAACTGCCATGTCGAAC 59.477 50.000 0.00 0.00 41.18 3.95
1326 1339 1.286257 GAGGAAGGGGAGGAAGCAAAT 59.714 52.381 0.00 0.00 0.00 2.32
1423 1436 2.223572 CCCAACTTGAGTCTTGTTGCAC 60.224 50.000 17.45 0.00 39.53 4.57
1574 1587 4.104738 ACCTTCTCTGAAAAAGGATCACCA 59.895 41.667 19.80 0.00 44.02 4.17
1616 1629 0.386113 CGATCCTCTCCTTCCGTTCC 59.614 60.000 0.00 0.00 0.00 3.62
1946 1959 1.296056 CCATCACCGACGGTTTCCAC 61.296 60.000 19.02 0.00 31.02 4.02
2258 2295 4.822026 TCTTCATCCTCGTCTTTCTTTCC 58.178 43.478 0.00 0.00 0.00 3.13
2327 2364 4.881019 AATGCTAACTGTCTGACTGACT 57.119 40.909 19.67 9.63 45.54 3.41
2328 2365 5.715070 AGTAATGCTAACTGTCTGACTGAC 58.285 41.667 19.67 5.57 45.54 3.51
2329 2366 5.984695 AGTAATGCTAACTGTCTGACTGA 57.015 39.130 19.67 0.00 0.00 3.41
2330 2367 6.870965 AGAAAGTAATGCTAACTGTCTGACTG 59.129 38.462 12.43 12.43 39.57 3.51
2347 2384 9.754382 AGATTGTAAAACACGAGTAGAAAGTAA 57.246 29.630 0.00 0.00 0.00 2.24
2389 2435 1.152368 AGAAAGCAACAGCAGGGCT 59.848 52.632 0.00 0.00 40.77 5.19
2411 2457 5.505780 TGATTTTTCGGGTATCAATGGAGT 58.494 37.500 0.00 0.00 0.00 3.85
2418 2464 8.364142 AGATTTGTTTTGATTTTTCGGGTATCA 58.636 29.630 0.00 0.00 0.00 2.15
2419 2465 8.757164 AGATTTGTTTTGATTTTTCGGGTATC 57.243 30.769 0.00 0.00 0.00 2.24
2420 2466 7.817478 GGAGATTTGTTTTGATTTTTCGGGTAT 59.183 33.333 0.00 0.00 0.00 2.73
2421 2467 7.014808 AGGAGATTTGTTTTGATTTTTCGGGTA 59.985 33.333 0.00 0.00 0.00 3.69
2434 2480 4.583073 AGTTACGGCAAGGAGATTTGTTTT 59.417 37.500 0.00 0.00 0.00 2.43
2537 2583 2.110967 CCCCGATCAGCAACAGCAG 61.111 63.158 0.00 0.00 0.00 4.24
2624 2671 2.894919 GCCAATTTGCCATCCGCT 59.105 55.556 0.00 0.00 38.78 5.52
2644 2691 2.100631 CCAATGAGACCGTCGCCAC 61.101 63.158 0.00 0.00 0.00 5.01
2720 2792 0.607762 TCATAGTGCAAAGCCCGCAA 60.608 50.000 0.00 0.00 41.97 4.85
2952 3031 6.660521 TCCGTGACCTAAATAGTAGTTCTCAA 59.339 38.462 0.00 0.00 0.00 3.02
2953 3032 6.182627 TCCGTGACCTAAATAGTAGTTCTCA 58.817 40.000 0.00 0.00 0.00 3.27
2954 3033 6.690194 TCCGTGACCTAAATAGTAGTTCTC 57.310 41.667 0.00 0.00 0.00 2.87
2955 3034 7.657023 ATTCCGTGACCTAAATAGTAGTTCT 57.343 36.000 0.00 0.00 0.00 3.01
2956 3035 9.460906 CTTATTCCGTGACCTAAATAGTAGTTC 57.539 37.037 0.00 0.00 0.00 3.01
2957 3036 8.975295 ACTTATTCCGTGACCTAAATAGTAGTT 58.025 33.333 0.00 0.00 0.00 2.24
2958 3037 8.530804 ACTTATTCCGTGACCTAAATAGTAGT 57.469 34.615 0.00 0.00 0.00 2.73
2980 3059 6.711277 TGATGTTGGAGAAAGCAGTATACTT 58.289 36.000 1.56 0.00 0.00 2.24
3005 3084 2.475371 GAAGCAGGCTCCTTCCAGCA 62.475 60.000 6.94 0.00 41.65 4.41


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

AutoCloner maintained by Alex Coulton.