Multiple sequence alignment - TraesCS4D01G146700

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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 TraesCS4D01G146700 chr4D 100.000 5274 0 0 1 5274 136188603 136183330 0.000000e+00 9740.0
1 TraesCS4D01G146700 chr4A 95.284 3435 107 23 1834 5260 423155893 423159280 0.000000e+00 5395.0
2 TraesCS4D01G146700 chr4A 94.885 1310 26 4 401 1702 423154622 423155898 0.000000e+00 2010.0
3 TraesCS4D01G146700 chr4A 93.720 207 13 0 160 366 423154417 423154623 1.430000e-80 311.0
4 TraesCS4D01G146700 chr4A 93.210 162 10 1 3 164 423154232 423154392 2.460000e-58 237.0
5 TraesCS4D01G146700 chr4B 97.181 2164 41 5 971 3132 195464792 195462647 0.000000e+00 3640.0
6 TraesCS4D01G146700 chr4B 96.004 2152 65 12 3132 5274 195462567 195460428 0.000000e+00 3478.0
7 TraesCS4D01G146700 chr4B 89.918 486 43 3 160 644 195465565 195465085 5.800000e-174 621.0
8 TraesCS4D01G146700 chr4B 93.976 166 6 3 1 164 195465753 195465590 1.130000e-61 248.0
9 TraesCS4D01G146700 chr4B 97.872 47 1 0 887 933 195464846 195464800 1.220000e-11 82.4
10 TraesCS4D01G146700 chr4B 97.436 39 1 0 827 865 195464885 195464847 3.410000e-07 67.6
11 TraesCS4D01G146700 chr5D 83.628 226 37 0 1476 1701 116174511 116174286 4.140000e-51 213.0
12 TraesCS4D01G146700 chr5D 83.621 116 19 0 2506 2621 116173373 116173258 5.580000e-20 110.0
13 TraesCS4D01G146700 chr5D 100.000 29 0 0 5223 5251 471052448 471052420 3.000000e-03 54.7
14 TraesCS4D01G146700 chr5B 83.628 226 37 0 1476 1701 128218645 128218420 4.140000e-51 213.0
15 TraesCS4D01G146700 chr5B 83.621 116 19 0 2506 2621 128217501 128217386 5.580000e-20 110.0
16 TraesCS4D01G146700 chr5A 83.945 218 35 0 1476 1693 123712419 123712202 5.350000e-50 209.0
17 TraesCS4D01G146700 chr5A 74.177 395 79 16 2506 2885 123711289 123710903 5.510000e-30 143.0
18 TraesCS4D01G146700 chr5A 100.000 29 0 0 5223 5251 591324424 591324396 3.000000e-03 54.7
19 TraesCS4D01G146700 chr7D 86.441 59 4 3 465 521 449416171 449416115 1.590000e-05 62.1


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 TraesCS4D01G146700 chr4D 136183330 136188603 5273 True 9740.000000 9740 100.000000 1 5274 1 chr4D.!!$R1 5273
1 TraesCS4D01G146700 chr4A 423154232 423159280 5048 False 1988.250000 5395 94.274750 3 5260 4 chr4A.!!$F1 5257
2 TraesCS4D01G146700 chr4B 195460428 195465753 5325 True 1356.166667 3640 95.397833 1 5274 6 chr4B.!!$R1 5273

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
95 98 0.394762 TGGATGGATCTGCAGCAACC 60.395 55.0 9.47 10.32 0.00 3.77 F
746 832 0.610232 AGCCCAAGGTGCTTTGCTAG 60.610 55.0 0.00 0.00 34.87 3.42 F
2279 2375 0.179043 CATGCTGCTCTGATGCTCCT 60.179 55.0 0.00 0.00 0.00 3.69 F
2736 2833 1.048601 GACTTATCGATGGCCAGGGA 58.951 55.0 13.05 11.63 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1355 1450 0.388134 CTGCCATGAACACAGCAAGC 60.388 55.000 0.00 0.0 34.26 4.01 R
2736 2833 2.138542 AGCCAATCCCACCATACTGAT 58.861 47.619 0.00 0.0 0.00 2.90 R
4126 4316 2.520549 AGACCAGGGAGTAGAATAGGCT 59.479 50.000 0.00 0.0 0.00 4.58 R
4546 4741 2.714259 TTGTGCACACAAGCCCTAC 58.286 52.632 21.56 0.0 45.42 3.18 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
68 70 2.612251 CCCAACCAAACACCCCCT 59.388 61.111 0.00 0.00 0.00 4.79
81 84 0.981277 ACCCCCTAAGTCGGTGGATG 60.981 60.000 0.00 0.00 0.00 3.51
95 98 0.394762 TGGATGGATCTGCAGCAACC 60.395 55.000 9.47 10.32 0.00 3.77
172 204 8.028938 GCACCTTCTTTCTTGCAATATCTAAAA 58.971 33.333 0.00 0.00 34.97 1.52
174 206 9.914131 ACCTTCTTTCTTGCAATATCTAAAAAC 57.086 29.630 0.00 0.00 0.00 2.43
177 209 8.948853 TCTTTCTTGCAATATCTAAAAACGTG 57.051 30.769 0.00 0.00 0.00 4.49
195 227 2.279741 GTGTCGCTATCCTTGCAATGA 58.720 47.619 6.89 6.89 0.00 2.57
382 415 4.883006 TCGTAGTTAAAATAATGCCACCCC 59.117 41.667 0.00 0.00 0.00 4.95
400 433 4.221262 CACCCCTTTTATGGCATCATATGG 59.779 45.833 1.65 1.68 35.94 2.74
432 465 1.153353 GCGTACTGCAGTTTGGCTAA 58.847 50.000 27.06 0.99 45.45 3.09
436 469 4.181578 CGTACTGCAGTTTGGCTAAGTAT 58.818 43.478 27.06 0.00 31.99 2.12
438 471 5.808540 CGTACTGCAGTTTGGCTAAGTATAA 59.191 40.000 27.06 0.00 31.99 0.98
485 518 2.418976 TCGTCTTCGGTCATGTGTCTAG 59.581 50.000 0.00 0.00 37.69 2.43
545 578 2.666994 GGTTCGCTCTAGTGTTTGTAGC 59.333 50.000 0.00 0.00 0.00 3.58
564 597 1.800315 CGTCGCTAGTTGGTCCACG 60.800 63.158 0.00 0.00 0.00 4.94
600 633 9.814899 GTCTAATATTCTCTATACTGCATGCAT 57.185 33.333 22.97 13.83 0.00 3.96
714 800 3.055094 GGAGATACAAAGACTTGGCCAGA 60.055 47.826 5.11 0.00 36.82 3.86
746 832 0.610232 AGCCCAAGGTGCTTTGCTAG 60.610 55.000 0.00 0.00 34.87 3.42
857 944 1.139853 GCTCTCCTGAATCCCAACGAT 59.860 52.381 0.00 0.00 0.00 3.73
1355 1450 8.863049 GTTTTGATGTGTAAGGAATGCTAATTG 58.137 33.333 0.00 0.00 0.00 2.32
1701 1796 2.910479 ATCATCGGCGCGGAGGTA 60.910 61.111 25.47 14.71 0.00 3.08
1703 1798 2.694829 ATCATCGGCGCGGAGGTAAC 62.695 60.000 25.47 0.00 0.00 2.50
1788 1884 6.228258 ACAGATTCTGCTTTGCATTGAATTT 58.772 32.000 13.64 1.94 38.13 1.82
2114 2210 6.983890 AGTTGGCTGGTATTTTTAGTTGTTTG 59.016 34.615 0.00 0.00 0.00 2.93
2279 2375 0.179043 CATGCTGCTCTGATGCTCCT 60.179 55.000 0.00 0.00 0.00 3.69
2333 2429 3.741830 TTCCTTGTGTGCCACGCGA 62.742 57.895 15.93 0.48 37.14 5.87
2342 2438 2.158058 GTGTGCCACGCGACTATTTTTA 59.842 45.455 15.93 0.00 0.00 1.52
2640 2736 9.646336 CTGGTAATTTTCTTGTTATATGTACGC 57.354 33.333 0.00 0.00 0.00 4.42
2641 2737 9.163899 TGGTAATTTTCTTGTTATATGTACGCA 57.836 29.630 0.00 0.00 0.00 5.24
2736 2833 1.048601 GACTTATCGATGGCCAGGGA 58.951 55.000 13.05 11.63 0.00 4.20
2949 3056 8.626526 TCGTGAGTGTTATTTGAGCATATACTA 58.373 33.333 0.00 0.00 0.00 1.82
2950 3057 9.244799 CGTGAGTGTTATTTGAGCATATACTAA 57.755 33.333 0.00 0.00 0.00 2.24
3822 4012 5.468072 CAGGTATTCATGCTGATCACCTAAC 59.532 44.000 13.74 0.00 38.26 2.34
4130 4320 5.105146 AGTTTCTCGATAACTGATTCAGCCT 60.105 40.000 13.64 4.03 34.68 4.58
4137 4327 7.594714 TCGATAACTGATTCAGCCTATTCTAC 58.405 38.462 13.64 0.00 34.37 2.59
4208 4398 2.100916 GAGCCTTGCTCGGAACTGTATA 59.899 50.000 0.00 0.00 45.85 1.47
4211 4401 3.741388 GCCTTGCTCGGAACTGTATACAT 60.741 47.826 5.91 0.00 0.00 2.29
4705 4900 2.038295 GCCTGGCTATGAATGTAGAGCT 59.962 50.000 12.43 0.00 35.35 4.09
4709 4904 5.421693 CCTGGCTATGAATGTAGAGCTAGAT 59.578 44.000 7.57 0.00 43.51 1.98
4758 4953 8.394971 TGTCAGATGAGTTGTTAATTTGATGT 57.605 30.769 0.00 0.00 0.00 3.06
4809 5004 7.255730 GGGCTCATTCATTATGATTAGCTTGTT 60.256 37.037 17.35 0.00 42.26 2.83
5087 5283 7.594758 GCATTCACAAAAAGTAGCACAAGATTA 59.405 33.333 0.00 0.00 0.00 1.75
5093 5289 8.560374 ACAAAAAGTAGCACAAGATTACTCTTC 58.440 33.333 0.00 0.00 39.78 2.87
5099 5295 5.642686 AGCACAAGATTACTCTTCGTCTAC 58.357 41.667 0.00 0.00 39.78 2.59
5121 5317 3.941483 CGGACTAGTCTTTACCGGAGTTA 59.059 47.826 21.88 0.00 39.92 2.24
5153 5350 5.745312 ACGCTCTTATATCATGGGATGAA 57.255 39.130 0.00 0.00 43.50 2.57
5154 5351 6.114187 ACGCTCTTATATCATGGGATGAAA 57.886 37.500 0.00 0.00 43.50 2.69
5155 5352 6.533730 ACGCTCTTATATCATGGGATGAAAA 58.466 36.000 0.00 0.00 43.50 2.29
5181 5378 8.338072 AGGGAGTATATATTACACTGAACTCG 57.662 38.462 0.00 0.00 34.35 4.18
5223 5420 4.141711 TGTTCATGTGTCCTATTCTAGCCC 60.142 45.833 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 70 1.412710 GCAGATCCATCCACCGACTTA 59.587 52.381 0.00 0.00 0.00 2.24
81 84 1.404391 CATTCTGGTTGCTGCAGATCC 59.596 52.381 20.43 15.82 0.00 3.36
95 98 3.748048 TCGAGCTTCTCAAAACCATTCTG 59.252 43.478 0.00 0.00 0.00 3.02
172 204 0.037697 TGCAAGGATAGCGACACGTT 60.038 50.000 0.00 0.00 33.85 3.99
174 206 1.004610 CATTGCAAGGATAGCGACACG 60.005 52.381 4.81 0.00 33.85 4.49
177 209 2.939103 ACTTCATTGCAAGGATAGCGAC 59.061 45.455 15.42 0.00 33.85 5.19
334 367 8.506168 ACGGACATGAATAATACAACATTCTT 57.494 30.769 0.00 0.00 33.26 2.52
382 415 7.361542 GCTCACTACCATATGATGCCATAAAAG 60.362 40.741 3.65 0.00 38.62 2.27
394 427 2.141517 GCTGCTGCTCACTACCATATG 58.858 52.381 8.53 0.00 36.03 1.78
400 433 0.171455 AGTACGCTGCTGCTCACTAC 59.829 55.000 14.03 7.53 36.97 2.73
432 465 4.949856 CACATCAACCAAAGGCCTTATACT 59.050 41.667 20.84 0.00 0.00 2.12
436 469 3.237268 ACACATCAACCAAAGGCCTTA 57.763 42.857 20.84 1.20 0.00 2.69
438 471 2.086610 AACACATCAACCAAAGGCCT 57.913 45.000 0.00 0.00 0.00 5.19
545 578 1.445582 GTGGACCAACTAGCGACGG 60.446 63.158 0.00 0.00 0.00 4.79
722 808 4.830573 AGCACCTTGGGCTTCTTC 57.169 55.556 0.00 0.00 40.61 2.87
728 814 0.895559 ACTAGCAAAGCACCTTGGGC 60.896 55.000 0.00 0.00 0.00 5.36
746 832 3.597255 GAGGAGGTTTTGCTAGTACCAC 58.403 50.000 0.00 0.00 34.32 4.16
857 944 1.320507 AAGCGTTTCCCGGCTAAAAA 58.679 45.000 0.00 0.00 38.88 1.94
1355 1450 0.388134 CTGCCATGAACACAGCAAGC 60.388 55.000 0.00 0.00 34.26 4.01
1593 1688 4.735132 GGGACGTACAGCTGCGCA 62.735 66.667 15.27 10.98 0.00 6.09
1701 1796 4.565022 CAACCCAAATTAAAGCCATCGTT 58.435 39.130 0.00 0.00 0.00 3.85
1703 1798 2.929398 GCAACCCAAATTAAAGCCATCG 59.071 45.455 0.00 0.00 0.00 3.84
1767 1863 6.148150 TCCAAAATTCAATGCAAAGCAGAATC 59.852 34.615 0.00 0.00 43.65 2.52
1788 1884 4.838423 TCATCTAACACACTCCTTCTCCAA 59.162 41.667 0.00 0.00 0.00 3.53
1961 2057 2.565046 TGACCTCACATTGCACATGA 57.435 45.000 13.53 5.05 0.00 3.07
2114 2210 3.311048 GCTGTCTATGGTAAAGCAGAAGC 59.689 47.826 0.00 0.00 42.56 3.86
2342 2438 9.667107 TCTTCCTTCGAATTACATACAAGAAAT 57.333 29.630 0.00 0.00 0.00 2.17
2640 2736 8.633075 AAAAACAAATGTGACATAGTCAAGTG 57.367 30.769 0.00 1.25 44.49 3.16
2641 2737 7.920682 GGAAAAACAAATGTGACATAGTCAAGT 59.079 33.333 0.00 0.00 44.49 3.16
2736 2833 2.138542 AGCCAATCCCACCATACTGAT 58.861 47.619 0.00 0.00 0.00 2.90
2949 3056 9.495572 TGGAAAACAAACAAAACAGTAAGAATT 57.504 25.926 0.00 0.00 0.00 2.17
2950 3057 9.150348 CTGGAAAACAAACAAAACAGTAAGAAT 57.850 29.630 0.00 0.00 0.00 2.40
2951 3058 7.117092 GCTGGAAAACAAACAAAACAGTAAGAA 59.883 33.333 0.00 0.00 0.00 2.52
2952 3059 6.588373 GCTGGAAAACAAACAAAACAGTAAGA 59.412 34.615 0.00 0.00 0.00 2.10
2953 3060 6.367422 TGCTGGAAAACAAACAAAACAGTAAG 59.633 34.615 0.00 0.00 0.00 2.34
2954 3061 6.223852 TGCTGGAAAACAAACAAAACAGTAA 58.776 32.000 0.00 0.00 0.00 2.24
2955 3062 5.784177 TGCTGGAAAACAAACAAAACAGTA 58.216 33.333 0.00 0.00 0.00 2.74
2956 3063 4.636249 TGCTGGAAAACAAACAAAACAGT 58.364 34.783 0.00 0.00 0.00 3.55
2957 3064 5.604010 TTGCTGGAAAACAAACAAAACAG 57.396 34.783 0.00 0.00 0.00 3.16
2958 3065 5.471456 ACATTGCTGGAAAACAAACAAAACA 59.529 32.000 0.00 0.00 31.40 2.83
3474 3664 7.482113 GTCATGTCTATCGAAATCTACATACGG 59.518 40.741 0.00 0.00 0.00 4.02
3715 3905 4.652881 TCCACTCTGCTGATATGAATGTCT 59.347 41.667 6.58 0.00 0.00 3.41
3822 4012 5.611374 ACCCTTTATCAGAACCATGTATCG 58.389 41.667 0.00 0.00 0.00 2.92
4126 4316 2.520549 AGACCAGGGAGTAGAATAGGCT 59.479 50.000 0.00 0.00 0.00 4.58
4130 4320 4.715297 GGAACAAGACCAGGGAGTAGAATA 59.285 45.833 0.00 0.00 0.00 1.75
4286 4476 3.679389 AGCGAAGGATGAACACAAGATT 58.321 40.909 0.00 0.00 0.00 2.40
4287 4477 3.340814 AGCGAAGGATGAACACAAGAT 57.659 42.857 0.00 0.00 0.00 2.40
4546 4741 2.714259 TTGTGCACACAAGCCCTAC 58.286 52.632 21.56 0.00 45.42 3.18
4628 4823 9.220767 GTTTAGTGGATTTACTGATTCTCACTT 57.779 33.333 0.00 0.00 36.00 3.16
4705 4900 9.627123 CAAATTATTTAACCAGGGAGACATCTA 57.373 33.333 0.00 0.00 0.00 1.98
4709 4904 6.152661 CAGCAAATTATTTAACCAGGGAGACA 59.847 38.462 0.00 0.00 0.00 3.41
4758 4953 2.309755 AGAGGACAAATGGAGCCATCAA 59.690 45.455 1.88 0.00 35.31 2.57
4809 5004 0.325933 AGTACAGCATGGCAGCAAGA 59.674 50.000 10.71 0.00 43.62 3.02
5099 5295 2.363683 ACTCCGGTAAAGACTAGTCCG 58.636 52.381 19.38 15.27 40.72 4.79
5121 5317 9.809096 CCATGATATAAGAGCGTACAGAATATT 57.191 33.333 0.00 0.00 0.00 1.28
5155 5352 8.794553 CGAGTTCAGTGTAATATATACTCCCTT 58.205 37.037 0.00 0.00 0.00 3.95
5176 5373 8.537858 ACAAAATAAGGGTATCTAGTTCGAGTT 58.462 33.333 0.00 0.00 0.00 3.01
5177 5374 8.075761 ACAAAATAAGGGTATCTAGTTCGAGT 57.924 34.615 0.00 0.00 0.00 4.18
5178 5375 8.943909 AACAAAATAAGGGTATCTAGTTCGAG 57.056 34.615 0.00 0.00 0.00 4.04
5179 5376 8.533657 TGAACAAAATAAGGGTATCTAGTTCGA 58.466 33.333 0.00 0.00 35.63 3.71
5180 5377 8.712285 TGAACAAAATAAGGGTATCTAGTTCG 57.288 34.615 0.00 0.00 35.63 3.95
5223 5420 1.656652 CGTTGGAGATGCCCTTAGTG 58.343 55.000 0.00 0.00 34.97 2.74


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

AutoCloner maintained by Alex Coulton.