Multiple sequence alignment - TraesCS3A01G248200

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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 TraesCS3A01G248200 chr3A 100.000 3525 0 0 1 3525 466113622 466110098 0.000000e+00 6510.0
1 TraesCS3A01G248200 chr3D 95.823 3543 113 16 1 3525 346980101 346976576 0.000000e+00 5690.0
2 TraesCS3A01G248200 chr3B 95.806 3457 106 15 81 3525 447010079 447006650 0.000000e+00 5544.0
3 TraesCS3A01G248200 chr4D 88.430 242 15 6 2835 3073 7831716 7831485 2.680000e-71 279.0
4 TraesCS3A01G248200 chr4A 85.537 242 22 6 2835 3073 595566777 595567008 1.260000e-59 241.0
5 TraesCS3A01G248200 chr4B 85.308 211 18 6 2835 3042 14120969 14121169 4.610000e-49 206.0
6 TraesCS3A01G248200 chr5A 86.486 111 12 3 2966 3073 43689729 43689839 6.180000e-23 119.0
7 TraesCS3A01G248200 chr5A 85.586 111 13 3 2966 3073 43737652 43737762 2.880000e-21 113.0
8 TraesCS3A01G248200 chr5B 83.594 128 18 3 2966 3090 57871848 57871975 2.220000e-22 117.0
9 TraesCS3A01G248200 chr2D 85.227 88 12 1 2938 3024 522750928 522750841 4.850000e-14 89.8
10 TraesCS3A01G248200 chr1D 92.500 40 2 1 2851 2889 176382692 176382731 4.920000e-04 56.5
11 TraesCS3A01G248200 chr1D 100.000 28 0 0 2807 2834 176386072 176386099 6.000000e-03 52.8
12 TraesCS3A01G248200 chr1B 92.500 40 2 1 2851 2889 242736246 242736285 4.920000e-04 56.5
13 TraesCS3A01G248200 chr1B 100.000 28 0 0 2807 2834 242737823 242737850 6.000000e-03 52.8


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 TraesCS3A01G248200 chr3A 466110098 466113622 3524 True 6510 6510 100.000 1 3525 1 chr3A.!!$R1 3524
1 TraesCS3A01G248200 chr3D 346976576 346980101 3525 True 5690 5690 95.823 1 3525 1 chr3D.!!$R1 3524
2 TraesCS3A01G248200 chr3B 447006650 447010079 3429 True 5544 5544 95.806 81 3525 1 chr3B.!!$R1 3444

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
879 884 0.242555 CCGGTATGCACAAACCAACC 59.757 55.0 13.48 2.09 35.35 3.77 F
1674 1697 0.253044 TTCTCCTTTGCCGATCCTGG 59.747 55.0 0.00 0.00 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2312 2335 1.172812 GCTTCTGCCGAGGTTTTGGT 61.173 55.0 0.0 0.0 0.0 3.67 R
3070 3093 0.179018 AAGAGCCACGCCTGAAACTT 60.179 50.0 0.0 0.0 0.0 2.66 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 1.499049 AGCTTCGACGTTTCTTCACC 58.501 50.000 0.00 0.00 0.00 4.02
36 37 0.249489 ACCTCGAGCATATGTTCGGC 60.249 55.000 32.60 7.90 46.43 5.54
47 48 3.793144 GTTCGGCTTGCTCCAGCG 61.793 66.667 0.00 0.00 45.83 5.18
53 54 2.437180 CTTGCTCCAGCGCATCCA 60.437 61.111 11.47 0.00 45.83 3.41
56 57 4.479993 GCTCCAGCGCATCCAGGT 62.480 66.667 11.47 0.00 0.00 4.00
58 59 3.746949 CTCCAGCGCATCCAGGTCC 62.747 68.421 11.47 0.00 0.00 4.46
73 74 2.749441 TCCGCATGCCGCAATTCA 60.749 55.556 13.15 0.00 42.60 2.57
79 80 1.472026 GCATGCCGCAATTCATTTCCT 60.472 47.619 6.36 0.00 41.79 3.36
152 154 7.099764 TCCAACATTTTTGCAAAGAGTTAACA 58.900 30.769 19.00 8.64 0.00 2.41
164 166 1.208293 GAGTTAACAGGAGGAGCAGGG 59.792 57.143 8.61 0.00 0.00 4.45
187 189 4.320608 AACCAAAATGTTGTAGCACCAG 57.679 40.909 0.00 0.00 32.40 4.00
274 276 8.061304 ACCAGTCCAATATTCTAATGGTCAATT 58.939 33.333 11.19 0.00 34.83 2.32
616 620 1.766069 AACAAAATCGCACCGCTTTC 58.234 45.000 0.00 0.00 0.00 2.62
620 624 0.309612 AAATCGCACCGCTTTCGTTT 59.690 45.000 0.00 0.00 0.00 3.60
621 625 1.149987 AATCGCACCGCTTTCGTTTA 58.850 45.000 0.00 0.00 0.00 2.01
876 881 0.958382 GCTCCGGTATGCACAAACCA 60.958 55.000 13.48 0.00 35.35 3.67
879 884 0.242555 CCGGTATGCACAAACCAACC 59.757 55.000 13.48 2.09 35.35 3.77
1129 1149 5.869344 GGTTCCATGAAATTTAGGTTTCTGC 59.131 40.000 0.00 0.00 38.58 4.26
1186 1206 3.738982 ACTGTCAACAATCGATGAACCA 58.261 40.909 0.00 0.00 0.00 3.67
1187 1207 4.133820 ACTGTCAACAATCGATGAACCAA 58.866 39.130 0.00 0.00 0.00 3.67
1393 1416 4.697828 AGCAGTAAGAAGAAGCTAAAAGGC 59.302 41.667 0.00 0.00 33.06 4.35
1396 1419 4.697828 AGTAAGAAGAAGCTAAAAGGCAGC 59.302 41.667 0.00 0.00 39.41 5.25
1399 1422 2.575805 AGAAGCTAAAAGGCAGCAGT 57.424 45.000 0.00 0.00 41.66 4.40
1441 1464 2.094234 TGCACGCAGATTAGAGCAGTTA 60.094 45.455 0.00 0.00 30.93 2.24
1525 1548 3.874392 ACAAAGCAGCTTGAACAAACT 57.126 38.095 8.88 0.00 0.00 2.66
1568 1591 5.080642 CAAGCTTGAGATAGATTCGCTTG 57.919 43.478 22.31 6.69 44.28 4.01
1642 1665 4.077822 CAGCCAGGAATTTCAGAAGAAGT 58.922 43.478 0.00 0.00 34.71 3.01
1674 1697 0.253044 TTCTCCTTTGCCGATCCTGG 59.747 55.000 0.00 0.00 0.00 4.45
1930 1953 0.990374 AAGAGGCTGCCAGACTGAAT 59.010 50.000 22.65 0.00 30.20 2.57
1938 1961 3.005155 GCTGCCAGACTGAATTTTGAGTT 59.995 43.478 3.32 0.00 0.00 3.01
2026 2049 2.232208 GGGGGAGATGAACAAAGCAAAG 59.768 50.000 0.00 0.00 0.00 2.77
2158 2181 1.965414 TGGAGATTGCCAGGGTAGAA 58.035 50.000 0.00 0.00 33.10 2.10
2215 2238 6.508777 AGAGAATACCTTAAAGAGCATCGTC 58.491 40.000 0.00 0.00 42.67 4.20
2312 2335 3.506067 TGCTATGTTCAGTTCAGAGTCGA 59.494 43.478 0.00 0.00 0.00 4.20
2403 2426 7.522901 CAGCAGATAATATGTACTCTGATGC 57.477 40.000 11.36 4.48 42.84 3.91
2606 2629 9.816354 TTTTTCTTCAAATCCCTTTAACTCAAG 57.184 29.630 0.00 0.00 0.00 3.02
2607 2630 8.760980 TTTCTTCAAATCCCTTTAACTCAAGA 57.239 30.769 0.00 0.00 0.00 3.02
2608 2631 8.940397 TTCTTCAAATCCCTTTAACTCAAGAT 57.060 30.769 0.00 0.00 0.00 2.40
2610 2633 9.672673 TCTTCAAATCCCTTTAACTCAAGATAG 57.327 33.333 0.00 0.00 0.00 2.08
2611 2634 9.454859 CTTCAAATCCCTTTAACTCAAGATAGT 57.545 33.333 0.00 0.00 0.00 2.12
2612 2635 9.807921 TTCAAATCCCTTTAACTCAAGATAGTT 57.192 29.630 0.00 0.00 42.31 2.24
2734 2757 8.836268 AAAACATACAGGTAGTGAAAATACGA 57.164 30.769 0.00 0.00 38.49 3.43
2742 2765 4.690280 GGTAGTGAAAATACGAAACCCGAA 59.310 41.667 0.00 0.00 38.49 4.30
2756 2779 3.555527 ACCCGAAATAGTTTCTAGGGC 57.444 47.619 12.49 0.00 41.40 5.19
2779 2802 1.945394 CTTGACATATGCTGCCTCCAC 59.055 52.381 1.58 0.00 0.00 4.02
2841 2864 4.082679 GGTAGATGATAGGTAGCCAAGACG 60.083 50.000 0.00 0.00 0.00 4.18
2886 2909 2.439880 GGGAGAAACTTGGGGAGGATAG 59.560 54.545 0.00 0.00 0.00 2.08
2991 3014 4.514401 AGGCCGAACTAACAGATTTTAGG 58.486 43.478 0.00 0.00 33.92 2.69
2993 3016 4.331992 GGCCGAACTAACAGATTTTAGGAC 59.668 45.833 0.00 0.00 33.92 3.85
2995 3018 5.163884 GCCGAACTAACAGATTTTAGGACAC 60.164 44.000 0.00 0.00 33.92 3.67
3096 3119 1.377202 GGCGTGGCTCTTTCCATCA 60.377 57.895 0.00 0.00 38.57 3.07
3100 3123 1.396653 GTGGCTCTTTCCATCATGGG 58.603 55.000 3.05 0.00 38.32 4.00
3224 3247 5.064071 GTGCAATTTAGCAGTCCTAGTCTTC 59.936 44.000 0.00 0.00 46.69 2.87
3249 3272 3.838244 AACAGTCTGCAGAACCTGTTA 57.162 42.857 34.23 7.09 44.08 2.41
3254 3277 4.391216 CAGTCTGCAGAACCTGTTAATGAG 59.609 45.833 20.19 0.00 33.43 2.90
3295 3318 6.621316 TTGAACTTGCCTAATCGTTGTTTA 57.379 33.333 0.00 0.00 0.00 2.01
3375 3398 4.072839 CCCAGTTCTAAACTTCCTTGTCC 58.927 47.826 0.00 0.00 40.46 4.02
3384 3407 1.956477 ACTTCCTTGTCCATGTGTTGC 59.044 47.619 0.00 0.00 0.00 4.17
3390 3413 1.674359 TGTCCATGTGTTGCGAGTTT 58.326 45.000 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.524355 CAAGCCGAACATATGCTCGAG 59.476 52.381 25.93 17.56 35.85 4.04
79 80 6.827586 ACGCCATTAATGTCCTTCTTTTTA 57.172 33.333 14.25 0.00 0.00 1.52
152 154 0.178873 TTGGTTACCCTGCTCCTCCT 60.179 55.000 0.00 0.00 0.00 3.69
164 166 5.189659 TGGTGCTACAACATTTTGGTTAC 57.810 39.130 0.00 0.00 37.00 2.50
176 178 4.968259 ACTTGACATAACTGGTGCTACAA 58.032 39.130 0.00 0.00 0.00 2.41
187 189 8.915871 AATGTGCATTTCATACTTGACATAAC 57.084 30.769 0.00 0.00 0.00 1.89
274 276 1.072391 ATTTATCGTTGCGTGCACGA 58.928 45.000 41.19 23.48 43.02 4.35
455 457 2.504244 GTCCGTCAGACGAAGGCG 60.504 66.667 24.88 7.17 46.05 5.52
561 563 6.994496 TGATGAGATACCTATTCTTTTGCCTG 59.006 38.462 0.00 0.00 0.00 4.85
620 624 9.419297 GACCACAATACAATTCGCTATTCTATA 57.581 33.333 0.00 0.00 0.00 1.31
621 625 8.150945 AGACCACAATACAATTCGCTATTCTAT 58.849 33.333 0.00 0.00 0.00 1.98
876 881 2.457464 AGGTACTGCCCCGAGAGGTT 62.457 60.000 0.00 0.00 46.31 3.50
1129 1149 8.574196 AAGAAATAACAACACAAGAAATTCGG 57.426 30.769 0.00 0.00 0.00 4.30
1186 1206 4.407296 TGAACATAAAACAAAGCCCCTGTT 59.593 37.500 0.00 0.00 38.65 3.16
1187 1207 3.964031 TGAACATAAAACAAAGCCCCTGT 59.036 39.130 0.00 0.00 0.00 4.00
1393 1416 0.529833 ACTGATCGTCTCCACTGCTG 59.470 55.000 0.00 0.00 0.00 4.41
1396 1419 1.546029 TCCAACTGATCGTCTCCACTG 59.454 52.381 0.00 0.00 0.00 3.66
1399 1422 0.895530 GGTCCAACTGATCGTCTCCA 59.104 55.000 0.00 0.00 0.00 3.86
1441 1464 0.324285 CTGCCTCCAGCTCAACTTCT 59.676 55.000 0.00 0.00 44.23 2.85
1525 1548 2.158295 GGCCTCCTCCAGAGATACCTTA 60.158 54.545 0.00 0.00 46.50 2.69
1568 1591 3.694566 ACCAAGGTCTTGTTGTTGTCTTC 59.305 43.478 9.51 0.00 38.85 2.87
1591 1614 2.237392 AGTTGGATTAGAGGACAGTGCC 59.763 50.000 0.00 0.00 0.00 5.01
1642 1665 4.651778 CAAAGGAGAAGGACATTACACCA 58.348 43.478 0.00 0.00 0.00 4.17
1674 1697 3.902881 ATGAGAATGTCTCCACCTCAC 57.097 47.619 2.91 0.00 42.73 3.51
1726 1749 1.462670 GCTTTCTTGCACTTCTCCTCG 59.537 52.381 0.00 0.00 0.00 4.63
1930 1953 3.295093 TGCCAACTCATCCAACTCAAAA 58.705 40.909 0.00 0.00 0.00 2.44
1938 1961 1.676635 GCTGCTGCCAACTCATCCA 60.677 57.895 3.85 0.00 0.00 3.41
1962 1985 4.273480 CGATGAGTCCTCTCTCTTTCTCTC 59.727 50.000 0.00 0.00 40.98 3.20
2026 2049 6.377327 TCAAACAGTTTGTCATTCTCTTCC 57.623 37.500 22.70 0.00 41.36 3.46
2107 2130 6.588719 TTTGCTACATTGGCTTCATTAACT 57.411 33.333 0.00 0.00 0.00 2.24
2158 2181 6.489361 ACATGTCTTCTTGAAGCTGAGAATTT 59.511 34.615 5.56 0.00 31.97 1.82
2215 2238 4.184629 CCTTCAAGGACTCGTATTCTTGG 58.815 47.826 0.00 0.00 37.67 3.61
2268 2291 6.039493 AGCATCAATCATGTCCTTCAATTCTC 59.961 38.462 0.00 0.00 34.56 2.87
2312 2335 1.172812 GCTTCTGCCGAGGTTTTGGT 61.173 55.000 0.00 0.00 0.00 3.67
2357 2380 4.263905 TGCCACATATCTTCCTTTCCTGTT 60.264 41.667 0.00 0.00 0.00 3.16
2360 2383 3.686691 GCTGCCACATATCTTCCTTTCCT 60.687 47.826 0.00 0.00 0.00 3.36
2403 2426 4.023365 CCTTTGAACAAGGAGAGCTTTCAG 60.023 45.833 6.59 0.00 39.81 3.02
2417 2440 6.632672 GCAGGACTCCTAATATCCTTTGAACA 60.633 42.308 0.00 0.00 41.07 3.18
2581 2604 9.196139 TCTTGAGTTAAAGGGATTTGAAGAAAA 57.804 29.630 0.00 0.00 0.00 2.29
2599 2622 9.890629 TGTCAAGCATTATAACTATCTTGAGTT 57.109 29.630 15.13 0.00 40.05 3.01
2600 2623 9.890629 TTGTCAAGCATTATAACTATCTTGAGT 57.109 29.630 15.13 0.00 40.05 3.41
2610 2633 9.793252 ACATCTCATTTTGTCAAGCATTATAAC 57.207 29.630 0.00 0.00 0.00 1.89
2613 2636 7.977853 GGAACATCTCATTTTGTCAAGCATTAT 59.022 33.333 0.00 0.00 0.00 1.28
2708 2731 9.926158 TCGTATTTTCACTACCTGTATGTTTTA 57.074 29.630 0.00 0.00 0.00 1.52
2734 2757 4.018688 AGCCCTAGAAACTATTTCGGGTTT 60.019 41.667 12.89 0.00 44.29 3.27
2742 2765 4.019321 TGTCAAGCAGCCCTAGAAACTATT 60.019 41.667 0.00 0.00 0.00 1.73
2756 2779 1.602851 GAGGCAGCATATGTCAAGCAG 59.397 52.381 4.29 0.00 35.29 4.24
2779 2802 6.677431 GCTTTCAGATGTAGCAGATTGAAAGG 60.677 42.308 20.01 7.77 45.65 3.11
2841 2864 3.259425 CTTGTTGTGCGGCAGCCTC 62.259 63.158 10.54 0.93 44.33 4.70
3070 3093 0.179018 AAGAGCCACGCCTGAAACTT 60.179 50.000 0.00 0.00 0.00 2.66
3100 3123 1.677217 CCTACAGGAGGCACAAGAAGC 60.677 57.143 0.00 0.00 38.96 3.86
3115 3138 5.129815 GTGGGGATAGACATACAAACCTACA 59.870 44.000 0.00 0.00 0.00 2.74
3166 3189 8.296713 GGTTTCTGCATTAGTCTTGAACATAAA 58.703 33.333 0.00 0.00 0.00 1.40
3174 3197 4.937620 TGCTAGGTTTCTGCATTAGTCTTG 59.062 41.667 0.00 0.00 0.00 3.02
3175 3198 5.165961 TGCTAGGTTTCTGCATTAGTCTT 57.834 39.130 0.00 0.00 0.00 3.01
3224 3247 3.931468 CAGGTTCTGCAGACTGTTATGAG 59.069 47.826 18.03 0.00 0.00 2.90
3320 3343 8.513774 GGTATTTATTTTACCTGGTCGTTGAAA 58.486 33.333 0.63 0.54 36.88 2.69
3323 3346 7.619964 AGGTATTTATTTTACCTGGTCGTTG 57.380 36.000 0.63 0.00 46.07 4.10
3366 3389 0.950836 CGCAACACATGGACAAGGAA 59.049 50.000 0.00 0.00 0.00 3.36
3405 3428 5.863935 GGACTGGAATGCAGTTTTATTTGAC 59.136 40.000 9.18 0.00 32.33 3.18
3408 3431 4.618227 GCGGACTGGAATGCAGTTTTATTT 60.618 41.667 9.18 0.00 32.33 1.40
3475 3502 6.611613 TGCTTTGGATATATAGTGGAGAGG 57.388 41.667 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.