Multiple sequence alignment - TraesCS3B01G305100

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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 TraesCS3B01G305100 chr3B 100.000 3016 0 0 1 3016 489982338 489979323 0.000000e+00 5570.0
1 TraesCS3B01G305100 chr3B 89.062 64 6 1 336 399 818902050 818901988 8.960000e-11 78.7
2 TraesCS3B01G305100 chr3A 94.790 3052 106 20 2 3015 500528316 500525280 0.000000e+00 4706.0
3 TraesCS3B01G305100 chr3A 87.692 65 6 2 330 393 670825827 670825890 1.160000e-09 75.0
4 TraesCS3B01G305100 chr3D 93.058 3054 91 33 1 3016 375724288 375721318 0.000000e+00 4353.0
5 TraesCS3B01G305100 chr1B 86.982 338 44 0 1012 1349 643567684 643567347 6.100000e-102 381.0
6 TraesCS3B01G305100 chr1D 85.556 360 51 1 990 1349 467002349 467002707 2.840000e-100 375.0
7 TraesCS3B01G305100 chr1A 85.591 347 50 0 1003 1349 558954615 558954961 6.140000e-97 364.0
8 TraesCS3B01G305100 chr1A 89.831 59 4 2 334 391 111531901 111531958 1.160000e-09 75.0
9 TraesCS3B01G305100 chr1A 88.525 61 5 2 334 393 537981325 537981384 4.170000e-09 73.1
10 TraesCS3B01G305100 chr6A 76.966 178 20 11 225 393 116327813 116327978 6.930000e-12 82.4
11 TraesCS3B01G305100 chr4B 86.765 68 6 3 334 399 537375460 537375526 4.170000e-09 73.1
12 TraesCS3B01G305100 chr5A 86.885 61 7 1 332 392 52617959 52617900 1.940000e-07 67.6


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 TraesCS3B01G305100 chr3B 489979323 489982338 3015 True 5570 5570 100.000 1 3016 1 chr3B.!!$R1 3015
1 TraesCS3B01G305100 chr3A 500525280 500528316 3036 True 4706 4706 94.790 2 3015 1 chr3A.!!$R1 3013
2 TraesCS3B01G305100 chr3D 375721318 375724288 2970 True 4353 4353 93.058 1 3016 1 chr3D.!!$R1 3015

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
458 471 1.226974 CACCTCTACGCACCCATCG 60.227 63.158 0.0 0.0 0.0 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2256 2299 1.657162 TCTAGGATTTCCAGGGGGTCT 59.343 52.381 0.0 0.0 38.89 3.85 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
30 31 1.580994 GGAAAGGGCCTGTATGGGGT 61.581 60.000 6.92 0.00 36.00 4.95
109 110 2.607282 GGATTGATCGCTCGTACCGAAT 60.607 50.000 0.00 0.00 38.31 3.34
130 131 2.203669 TCGTTCGGTCTGGGGGAA 60.204 61.111 0.00 0.00 0.00 3.97
150 151 3.594603 ACTCCAGAACGAACATGTAGG 57.405 47.619 0.00 0.00 0.00 3.18
151 152 2.897969 ACTCCAGAACGAACATGTAGGT 59.102 45.455 0.00 0.00 0.00 3.08
156 157 7.069578 ACTCCAGAACGAACATGTAGGTATTAT 59.930 37.037 0.00 0.00 0.00 1.28
157 158 7.431249 TCCAGAACGAACATGTAGGTATTATC 58.569 38.462 0.00 0.00 0.00 1.75
158 159 7.287005 TCCAGAACGAACATGTAGGTATTATCT 59.713 37.037 0.00 0.00 0.00 1.98
163 164 5.690409 CGAACATGTAGGTATTATCTGCGTT 59.310 40.000 0.00 0.00 0.00 4.84
165 166 6.406692 ACATGTAGGTATTATCTGCGTTCT 57.593 37.500 0.00 0.00 0.00 3.01
207 208 4.392619 TTTGTTTAGTCCGCACATTACG 57.607 40.909 0.00 0.00 0.00 3.18
328 333 7.492352 AAATCTAGCGGTATTGATTTGGTAC 57.508 36.000 16.51 0.00 37.62 3.34
329 334 4.613944 TCTAGCGGTATTGATTTGGTACG 58.386 43.478 0.00 0.00 0.00 3.67
330 335 1.937899 AGCGGTATTGATTTGGTACGC 59.062 47.619 0.00 0.00 45.36 4.42
401 414 4.043037 ACGAAAGCTAATACGAGGAAGG 57.957 45.455 8.31 0.00 0.00 3.46
402 415 2.795470 CGAAAGCTAATACGAGGAAGGC 59.205 50.000 0.00 0.00 0.00 4.35
409 422 1.765230 ATACGAGGAAGGCGAAGAGT 58.235 50.000 0.00 0.00 0.00 3.24
458 471 1.226974 CACCTCTACGCACCCATCG 60.227 63.158 0.00 0.00 0.00 3.84
1298 1334 3.721706 CTCGCCCTGGCCCTTCTT 61.722 66.667 0.00 0.00 37.98 2.52
1556 1595 2.691526 ACTCGGACGATGGCTACAATAA 59.308 45.455 0.00 0.00 0.00 1.40
1557 1596 3.050619 CTCGGACGATGGCTACAATAAC 58.949 50.000 0.00 0.00 0.00 1.89
1558 1597 2.427812 TCGGACGATGGCTACAATAACA 59.572 45.455 0.00 0.00 0.00 2.41
1827 1866 3.909995 TCAAGTTCCTCAAGGATCTGGAA 59.090 43.478 10.56 0.00 44.98 3.53
2030 2069 6.838090 AGGTTACTGTAATAGACTTAGGGGAC 59.162 42.308 3.23 0.00 0.00 4.46
2042 2081 3.846588 ACTTAGGGGACTGATGATGTGTT 59.153 43.478 0.00 0.00 43.88 3.32
2139 2180 6.318913 ACATGTAACCAGAGATCTAGGCTAT 58.681 40.000 12.46 3.86 0.00 2.97
2288 2334 9.007901 CCTGGAAATCCTAGATAATGAATGTTC 57.992 37.037 0.44 0.00 36.82 3.18
2291 2337 9.566432 GGAAATCCTAGATAATGAATGTTCTGT 57.434 33.333 0.00 0.00 0.00 3.41
2334 2380 1.212751 CATCTGCGTCGTCTGGTCA 59.787 57.895 0.00 0.00 0.00 4.02
2388 2434 6.183360 TGCGTATAGGCGAATGGTTTAATTTT 60.183 34.615 12.43 0.00 35.06 1.82
2439 2485 7.042335 CGGTCAAATTCTTAGTTATCAGGTCT 58.958 38.462 0.00 0.00 0.00 3.85
2482 2528 3.232213 TCTAATGGTCGACTCTTGTGC 57.768 47.619 16.46 0.00 0.00 4.57
2505 2551 4.846779 TGCCAGTTTAGAATTTGTGGTC 57.153 40.909 0.00 0.00 0.00 4.02
2584 2637 7.376615 AGGAAATGCTCAAAATCTTTTCTCTG 58.623 34.615 0.00 0.00 31.24 3.35
2597 2650 4.997395 TCTTTTCTCTGGTGTTATGCTGAC 59.003 41.667 0.00 0.00 0.00 3.51
2603 2656 4.910195 TCTGGTGTTATGCTGACTTGATT 58.090 39.130 0.00 0.00 0.00 2.57
2615 2668 7.769272 TGCTGACTTGATTTTAAGTTTTTGG 57.231 32.000 0.00 0.00 40.78 3.28
2616 2669 7.327214 TGCTGACTTGATTTTAAGTTTTTGGT 58.673 30.769 0.00 0.00 40.78 3.67
2617 2670 7.821846 TGCTGACTTGATTTTAAGTTTTTGGTT 59.178 29.630 0.00 0.00 40.78 3.67
2618 2671 9.308318 GCTGACTTGATTTTAAGTTTTTGGTTA 57.692 29.630 0.00 0.00 40.78 2.85
2664 2717 5.003804 TGAAGATCTTCTTTTGTACTGGGC 58.996 41.667 30.45 5.69 36.73 5.36
2684 2737 5.357878 TGGGCTTTCATGCTTAGATTAGTTG 59.642 40.000 0.00 0.00 0.00 3.16
2708 2761 4.880120 AGCTGGTGATGAATGAGTATTGTG 59.120 41.667 0.00 0.00 0.00 3.33
2734 2787 3.393687 TGGTAGATTATGGAGTGGGCTT 58.606 45.455 0.00 0.00 0.00 4.35
2735 2788 4.562767 TGGTAGATTATGGAGTGGGCTTA 58.437 43.478 0.00 0.00 0.00 3.09
2737 2790 4.593634 GGTAGATTATGGAGTGGGCTTAGT 59.406 45.833 0.00 0.00 0.00 2.24
2740 2798 5.685728 AGATTATGGAGTGGGCTTAGTTTC 58.314 41.667 0.00 0.00 0.00 2.78
2759 2818 1.051812 CCCATTAGATCCTGGTCGCT 58.948 55.000 0.00 0.00 0.00 4.93
2810 2869 6.043327 TGAAGTACAATCGCCAATATTTCG 57.957 37.500 0.00 1.53 0.00 3.46
2991 3050 9.846248 GTTTATTAACTGTTAGAGTCCGTTAGA 57.154 33.333 0.00 0.00 31.73 2.10
2994 3053 5.625921 AACTGTTAGAGTCCGTTAGAGAC 57.374 43.478 0.00 0.00 31.73 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.269174 CCCGAATGCACACACAAATCA 59.731 47.619 0.00 0.00 0.00 2.57
73 74 2.080693 CAATCCCACCGAACGATTTCA 58.919 47.619 0.00 0.00 0.00 2.69
109 110 2.273179 CCCCAGACCGAACGAGACA 61.273 63.158 0.00 0.00 0.00 3.41
130 131 2.897969 ACCTACATGTTCGTTCTGGAGT 59.102 45.455 2.30 0.00 0.00 3.85
156 157 5.410439 GGGAGTAAAAATGTTAGAACGCAGA 59.590 40.000 0.00 0.00 0.00 4.26
157 158 5.411669 AGGGAGTAAAAATGTTAGAACGCAG 59.588 40.000 0.00 0.00 0.00 5.18
158 159 5.310451 AGGGAGTAAAAATGTTAGAACGCA 58.690 37.500 0.00 0.00 0.00 5.24
163 164 8.347035 CAAAACGAAGGGAGTAAAAATGTTAGA 58.653 33.333 0.00 0.00 0.00 2.10
165 166 7.998580 ACAAAACGAAGGGAGTAAAAATGTTA 58.001 30.769 0.00 0.00 0.00 2.41
304 309 6.202188 CGTACCAAATCAATACCGCTAGATTT 59.798 38.462 0.00 0.00 40.29 2.17
312 317 5.917541 ATTAGCGTACCAAATCAATACCG 57.082 39.130 0.00 0.00 0.00 4.02
377 390 4.548991 TCCTCGTATTAGCTTTCGTCTC 57.451 45.455 0.00 0.00 0.00 3.36
382 395 2.795470 CGCCTTCCTCGTATTAGCTTTC 59.205 50.000 0.00 0.00 0.00 2.62
458 471 0.764890 TTCGGGGATGGATGGTCATC 59.235 55.000 2.52 2.52 41.93 2.92
534 554 1.406205 GGGCCGAAAAGGAGAGAGAAG 60.406 57.143 0.00 0.00 45.00 2.85
1284 1320 4.803908 CGGAAGAAGGGCCAGGGC 62.804 72.222 6.18 3.77 41.06 5.19
1494 1533 2.594592 GCGGCGGCCTTATGGAAT 60.595 61.111 18.34 0.00 34.57 3.01
1556 1595 3.488310 GTCGTCGTCATAGTTGTTGTTGT 59.512 43.478 0.00 0.00 0.00 3.32
1557 1596 3.420035 CGTCGTCGTCATAGTTGTTGTTG 60.420 47.826 0.00 0.00 0.00 3.33
1558 1597 2.722629 CGTCGTCGTCATAGTTGTTGTT 59.277 45.455 0.00 0.00 0.00 2.83
1725 1764 3.638627 ACATCTCAGCGAATGTCTCCATA 59.361 43.478 0.00 0.00 0.00 2.74
1827 1866 2.437359 GCCTGCATCCGCTTGAGT 60.437 61.111 0.00 0.00 39.64 3.41
2042 2081 8.575589 CCACATAAGGCAATATAGCATACAAAA 58.424 33.333 0.00 0.00 35.83 2.44
2139 2180 4.885413 AGCATTGCTTTGCACAAATAAGA 58.115 34.783 5.03 0.00 45.23 2.10
2256 2299 1.657162 TCTAGGATTTCCAGGGGGTCT 59.343 52.381 0.00 0.00 38.89 3.85
2257 2300 2.191981 TCTAGGATTTCCAGGGGGTC 57.808 55.000 0.00 0.00 38.89 4.46
2288 2334 1.964223 ACACTGGGAGACTACACACAG 59.036 52.381 0.00 0.00 42.32 3.66
2291 2337 2.082140 ACACACTGGGAGACTACACA 57.918 50.000 0.00 0.00 0.00 3.72
2482 2528 5.138125 ACCACAAATTCTAAACTGGCATG 57.862 39.130 0.00 0.00 0.00 4.06
2584 2637 7.593825 ACTTAAAATCAAGTCAGCATAACACC 58.406 34.615 0.00 0.00 33.41 4.16
2664 2717 7.408123 CAGCTCAACTAATCTAAGCATGAAAG 58.592 38.462 0.00 0.00 35.42 2.62
2684 2737 5.007430 CACAATACTCATTCATCACCAGCTC 59.993 44.000 0.00 0.00 0.00 4.09
2708 2761 4.503991 CCCACTCCATAATCTACCAAGCTC 60.504 50.000 0.00 0.00 0.00 4.09
2734 2787 4.344102 CGACCAGGATCTAATGGGAAACTA 59.656 45.833 14.10 0.00 41.13 2.24
2735 2788 3.134804 CGACCAGGATCTAATGGGAAACT 59.865 47.826 14.10 0.00 41.13 2.66
2737 2790 2.158813 GCGACCAGGATCTAATGGGAAA 60.159 50.000 14.10 0.00 41.13 3.13
2740 2798 1.051812 AGCGACCAGGATCTAATGGG 58.948 55.000 14.10 3.12 41.13 4.00
2759 2818 1.523758 GCGAAAGAAGAAGGAAGGCA 58.476 50.000 0.00 0.00 0.00 4.75
2798 2857 6.943981 TCTCAGAATTTACGAAATATTGGCG 58.056 36.000 8.83 8.83 0.00 5.69


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

AutoCloner maintained by Alex Coulton.