Multiple sequence alignment - TraesCS5D01G274600

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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 TraesCS5D01G274600 chr5D 100.000 3128 0 0 1 3128 377486570 377489697 0.000000e+00 5777
1 TraesCS5D01G274600 chr5B 95.215 2299 77 17 282 2562 450773072 450775355 0.000000e+00 3605
2 TraesCS5D01G274600 chr5B 85.199 277 25 7 4 274 450772685 450772951 1.430000e-68 270
3 TraesCS5D01G274600 chr5A 91.507 2602 132 42 3 2573 478017478 478020021 0.000000e+00 3498
4 TraesCS5D01G274600 chr4D 95.118 553 25 1 2576 3128 483619778 483619228 0.000000e+00 870
5 TraesCS5D01G274600 chr2D 95.118 553 25 1 2576 3128 546411557 546412107 0.000000e+00 870
6 TraesCS5D01G274600 chr3A 93.671 553 33 1 2576 3128 703807487 703806937 0.000000e+00 826
7 TraesCS5D01G274600 chr3A 93.309 553 35 1 2576 3128 100864288 100863738 0.000000e+00 815
8 TraesCS5D01G274600 chr3A 93.128 553 36 1 2576 3128 127190219 127190769 0.000000e+00 809
9 TraesCS5D01G274600 chr1A 93.394 545 29 5 2585 3128 556781666 556782204 0.000000e+00 800
10 TraesCS5D01G274600 chr1B 92.754 552 38 1 2576 3127 651902444 651902993 0.000000e+00 797
11 TraesCS5D01G274600 chr2B 92.586 553 39 1 2576 3128 669239677 669239127 0.000000e+00 793
12 TraesCS5D01G274600 chr6B 92.586 553 38 2 2576 3128 682643934 682643385 0.000000e+00 791
13 TraesCS5D01G274600 chr7B 77.047 684 127 24 1457 2128 185390297 185390962 1.770000e-97 366
14 TraesCS5D01G274600 chr7A 76.075 744 139 29 1379 2110 227958262 227958978 4.960000e-93 351


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 TraesCS5D01G274600 chr5D 377486570 377489697 3127 False 5777.0 5777 100.000 1 3128 1 chr5D.!!$F1 3127
1 TraesCS5D01G274600 chr5B 450772685 450775355 2670 False 1937.5 3605 90.207 4 2562 2 chr5B.!!$F1 2558
2 TraesCS5D01G274600 chr5A 478017478 478020021 2543 False 3498.0 3498 91.507 3 2573 1 chr5A.!!$F1 2570
3 TraesCS5D01G274600 chr4D 483619228 483619778 550 True 870.0 870 95.118 2576 3128 1 chr4D.!!$R1 552
4 TraesCS5D01G274600 chr2D 546411557 546412107 550 False 870.0 870 95.118 2576 3128 1 chr2D.!!$F1 552
5 TraesCS5D01G274600 chr3A 703806937 703807487 550 True 826.0 826 93.671 2576 3128 1 chr3A.!!$R2 552
6 TraesCS5D01G274600 chr3A 100863738 100864288 550 True 815.0 815 93.309 2576 3128 1 chr3A.!!$R1 552
7 TraesCS5D01G274600 chr3A 127190219 127190769 550 False 809.0 809 93.128 2576 3128 1 chr3A.!!$F1 552
8 TraesCS5D01G274600 chr1A 556781666 556782204 538 False 800.0 800 93.394 2585 3128 1 chr1A.!!$F1 543
9 TraesCS5D01G274600 chr1B 651902444 651902993 549 False 797.0 797 92.754 2576 3127 1 chr1B.!!$F1 551
10 TraesCS5D01G274600 chr2B 669239127 669239677 550 True 793.0 793 92.586 2576 3128 1 chr2B.!!$R1 552
11 TraesCS5D01G274600 chr6B 682643385 682643934 549 True 791.0 791 92.586 2576 3128 1 chr6B.!!$R1 552
12 TraesCS5D01G274600 chr7B 185390297 185390962 665 False 366.0 366 77.047 1457 2128 1 chr7B.!!$F1 671
13 TraesCS5D01G274600 chr7A 227958262 227958978 716 False 351.0 351 76.075 1379 2110 1 chr7A.!!$F1 731

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
27 32 0.598065 AATTTGGCAAGCGGTGTCTC 59.402 50.000 0.0 0.0 30.97 3.36 F
149 155 0.966920 GGGTGAAGGAGTGAAGACGA 59.033 55.000 0.0 0.0 0.00 4.20 F
937 1069 1.264288 CGTTTGCTTCCACTCAAGGAC 59.736 52.381 0.0 0.0 37.42 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1131 1265 1.827344 CCTCTGCAAAATCCTTTCCCC 59.173 52.381 0.0 0.0 0.0 4.81 R
2112 2261 2.933287 CCCTAGCCACCACCACCA 60.933 66.667 0.0 0.0 0.0 4.17 R
2477 2639 1.069227 CGCAAAGACAAAGTACTGGCC 60.069 52.381 0.0 0.0 0.0 5.36 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
27 32 0.598065 AATTTGGCAAGCGGTGTCTC 59.402 50.000 0.00 0.00 30.97 3.36
35 40 2.489971 CAAGCGGTGTCTCTTTGGTTA 58.510 47.619 0.00 0.00 0.00 2.85
83 88 3.913089 GGTTGCAACCTCCTGTTTTATG 58.087 45.455 36.26 0.00 45.75 1.90
86 92 1.204704 GCAACCTCCTGTTTTATGGCC 59.795 52.381 0.00 0.00 34.00 5.36
100 106 6.375736 TGTTTTATGGCCAATGAATCTACGAA 59.624 34.615 10.96 0.00 0.00 3.85
101 107 7.068103 TGTTTTATGGCCAATGAATCTACGAAT 59.932 33.333 10.96 0.00 0.00 3.34
114 120 6.801862 TGAATCTACGAATGTGCATATCTACG 59.198 38.462 12.92 12.92 0.00 3.51
132 138 2.504367 ACGGTCAATCTTTGTTCTGGG 58.496 47.619 0.00 0.00 0.00 4.45
137 143 4.022849 GGTCAATCTTTGTTCTGGGTGAAG 60.023 45.833 0.00 0.00 35.01 3.02
147 153 1.971357 TCTGGGTGAAGGAGTGAAGAC 59.029 52.381 0.00 0.00 0.00 3.01
149 155 0.966920 GGGTGAAGGAGTGAAGACGA 59.033 55.000 0.00 0.00 0.00 4.20
150 156 1.343465 GGGTGAAGGAGTGAAGACGAA 59.657 52.381 0.00 0.00 0.00 3.85
153 159 4.065789 GGTGAAGGAGTGAAGACGAAATT 58.934 43.478 0.00 0.00 0.00 1.82
154 160 4.083802 GGTGAAGGAGTGAAGACGAAATTG 60.084 45.833 0.00 0.00 0.00 2.32
155 161 4.511826 GTGAAGGAGTGAAGACGAAATTGT 59.488 41.667 0.00 0.00 0.00 2.71
156 162 5.694910 GTGAAGGAGTGAAGACGAAATTGTA 59.305 40.000 0.00 0.00 0.00 2.41
196 203 5.749109 GTGAATTCAGGATTCTAGTACACCG 59.251 44.000 8.80 0.00 43.74 4.94
223 231 9.811995 AGTTTTAAACCAACTGTTCCTAAAATC 57.188 29.630 4.01 0.00 34.29 2.17
274 282 9.585099 GTCAGACCAATATTTGCATCAATTTTA 57.415 29.630 0.00 0.00 0.00 1.52
396 518 4.210120 GCATCGACTCCTTAAATACTGCAG 59.790 45.833 13.48 13.48 0.00 4.41
401 523 5.921408 CGACTCCTTAAATACTGCAGGTATC 59.079 44.000 19.93 0.31 39.94 2.24
404 526 8.184304 ACTCCTTAAATACTGCAGGTATCTAG 57.816 38.462 19.93 8.25 39.94 2.43
411 533 8.713708 AAATACTGCAGGTATCTAGTGAGTAT 57.286 34.615 19.93 0.00 39.94 2.12
413 535 8.713708 ATACTGCAGGTATCTAGTGAGTATTT 57.286 34.615 19.93 0.00 36.48 1.40
414 536 6.810911 ACTGCAGGTATCTAGTGAGTATTTG 58.189 40.000 19.93 0.00 0.00 2.32
460 582 8.506437 CAAAGAAGCATCTTACTGTGTTGATTA 58.494 33.333 4.34 0.00 45.19 1.75
468 590 7.962964 TCTTACTGTGTTGATTAAAGACTGG 57.037 36.000 0.00 0.00 35.90 4.00
489 611 8.466617 ACTGGTACATATTCTACCTTCTACTG 57.533 38.462 0.00 0.00 38.20 2.74
491 613 9.570468 CTGGTACATATTCTACCTTCTACTGTA 57.430 37.037 0.00 0.00 38.20 2.74
611 741 3.009363 TCCATGATTCCTGCACTTTCTGA 59.991 43.478 0.00 0.00 0.00 3.27
816 947 8.976471 GTTGAAACTTCTACTACTAACAGGAAC 58.024 37.037 0.00 0.00 31.64 3.62
870 1002 5.707242 ATGACATATCCTAACACGACGAT 57.293 39.130 0.00 0.00 0.00 3.73
937 1069 1.264288 CGTTTGCTTCCACTCAAGGAC 59.736 52.381 0.00 0.00 37.42 3.85
972 1104 9.436957 CCTACCAACCTATATTATTAAGCACAG 57.563 37.037 0.00 0.00 0.00 3.66
1131 1265 1.579698 CATGGAGATCAGGCTTCACG 58.420 55.000 0.00 0.00 0.00 4.35
1359 1493 4.314121 CCTTCTTGTCCTCTTCAGACTTG 58.686 47.826 0.00 0.00 35.21 3.16
2112 2261 2.616458 GGAGGCCTTCATGGTGGGT 61.616 63.158 6.77 0.00 38.35 4.51
2333 2493 2.246719 CGGAGGAGGATGAATGGAAC 57.753 55.000 0.00 0.00 0.00 3.62
2439 2600 3.482436 CGTTTTTACCGCTGATTACGTCC 60.482 47.826 0.00 0.00 0.00 4.79
2477 2639 1.553248 TCAGTCAGGTAAATCGGTGGG 59.447 52.381 0.00 0.00 0.00 4.61
2489 2651 1.674322 CGGTGGGGCCAGTACTTTG 60.674 63.158 4.39 0.00 36.97 2.77
2491 2653 0.608308 GGTGGGGCCAGTACTTTGTC 60.608 60.000 4.39 0.00 37.17 3.18
2499 2666 2.096218 GCCAGTACTTTGTCTTTGCGAG 60.096 50.000 0.00 0.00 0.00 5.03
2508 2675 4.383774 TTGTCTTTGCGAGAAATGTACG 57.616 40.909 0.00 0.00 35.79 3.67
2510 2677 4.052608 TGTCTTTGCGAGAAATGTACGAA 58.947 39.130 0.00 0.00 35.79 3.85
2531 2698 0.107993 TCAGTACTGCTCAGCATGGC 60.108 55.000 18.45 0.00 38.13 4.40
2532 2699 0.107800 CAGTACTGCTCAGCATGGCT 60.108 55.000 10.54 0.00 38.13 4.75
2533 2700 0.617413 AGTACTGCTCAGCATGGCTT 59.383 50.000 0.00 0.00 38.13 4.35
2534 2701 0.731417 GTACTGCTCAGCATGGCTTG 59.269 55.000 0.00 0.00 38.13 4.01
2535 2702 0.614812 TACTGCTCAGCATGGCTTGA 59.385 50.000 0.00 0.00 38.13 3.02
2536 2703 0.251033 ACTGCTCAGCATGGCTTGAA 60.251 50.000 0.00 0.00 38.13 2.69
2537 2704 0.885879 CTGCTCAGCATGGCTTGAAA 59.114 50.000 0.00 0.00 38.13 2.69
2572 2739 1.912971 TCGTCCTCGATCTCCTGGA 59.087 57.895 0.00 0.00 41.35 3.86
2574 2741 1.133761 TCGTCCTCGATCTCCTGGAAT 60.134 52.381 0.00 0.00 41.35 3.01
2631 2798 3.894759 ACTGGTTGTCTAGCTATACCGA 58.105 45.455 6.79 0.00 0.00 4.69
2641 2808 6.430308 TGTCTAGCTATACCGACAAAGATAGG 59.570 42.308 10.26 0.00 33.84 2.57
2642 2809 6.654161 GTCTAGCTATACCGACAAAGATAGGA 59.346 42.308 6.09 0.00 30.73 2.94
2686 2853 4.038522 GCTGCTCTCTTGTGGTCTATATGA 59.961 45.833 0.00 0.00 0.00 2.15
2691 2858 8.049117 TGCTCTCTTGTGGTCTATATGAAAAAT 58.951 33.333 0.00 0.00 0.00 1.82
2736 2903 7.863901 AAAGTGTTATGCCTAGAGATCCTAT 57.136 36.000 0.00 0.00 0.00 2.57
2739 2906 6.212388 AGTGTTATGCCTAGAGATCCTATTGG 59.788 42.308 0.00 0.00 0.00 3.16
2775 2942 6.488769 TGTTTGTTCCCTACTTGACTCTTA 57.511 37.500 0.00 0.00 0.00 2.10
2776 2943 6.891388 TGTTTGTTCCCTACTTGACTCTTAA 58.109 36.000 0.00 0.00 0.00 1.85
2956 3124 7.087639 TCGAAGCCTTTATGTTAATTTGGTTG 58.912 34.615 0.00 0.00 0.00 3.77
3058 3226 8.788238 AGCATCCTGATGTGGTGATATATATA 57.212 34.615 8.79 0.00 40.80 0.86
3059 3227 9.389949 AGCATCCTGATGTGGTGATATATATAT 57.610 33.333 4.86 4.86 40.80 0.86
3073 3241 9.755804 GTGATATATATATCAGTGGTGTGATGG 57.244 37.037 28.19 0.00 46.94 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.258123 ACCGCTTGCCAAATTCAAATAGT 59.742 39.130 0.00 0.00 0.00 2.12
1 2 3.613737 CACCGCTTGCCAAATTCAAATAG 59.386 43.478 0.00 0.00 0.00 1.73
11 12 0.465460 AAAGAGACACCGCTTGCCAA 60.465 50.000 0.00 0.00 32.69 4.52
27 32 3.070018 CCTGTCAGTCAGCTAACCAAAG 58.930 50.000 0.00 0.00 42.38 2.77
35 40 2.219875 CCCCACCTGTCAGTCAGCT 61.220 63.158 0.00 0.00 42.38 4.24
81 86 4.276678 CACATTCGTAGATTCATTGGCCAT 59.723 41.667 6.09 0.00 35.04 4.40
82 87 3.627123 CACATTCGTAGATTCATTGGCCA 59.373 43.478 0.00 0.00 35.04 5.36
83 88 3.548818 GCACATTCGTAGATTCATTGGCC 60.549 47.826 0.00 0.00 35.04 5.36
86 92 8.026341 AGATATGCACATTCGTAGATTCATTG 57.974 34.615 0.00 0.00 35.04 2.82
100 106 5.474578 AGATTGACCGTAGATATGCACAT 57.525 39.130 0.00 0.00 0.00 3.21
101 107 4.937201 AGATTGACCGTAGATATGCACA 57.063 40.909 0.00 0.00 0.00 4.57
114 120 3.486383 TCACCCAGAACAAAGATTGACC 58.514 45.455 0.00 0.00 0.00 4.02
132 138 4.511826 ACAATTTCGTCTTCACTCCTTCAC 59.488 41.667 0.00 0.00 0.00 3.18
164 170 8.407064 ACTAGAATCCTGAATTCACTACTTACG 58.593 37.037 3.38 0.00 45.34 3.18
176 182 5.202004 ACTCGGTGTACTAGAATCCTGAAT 58.798 41.667 0.00 0.00 0.00 2.57
196 203 9.811995 ATTTTAGGAACAGTTGGTTTAAAACTC 57.188 29.630 4.60 0.00 40.63 3.01
223 231 2.542178 GGCGGCTGGTTTAAAACTTTTG 59.458 45.455 4.60 0.00 0.00 2.44
227 235 0.468400 TGGGCGGCTGGTTTAAAACT 60.468 50.000 9.56 0.00 0.00 2.66
237 245 2.821366 GTCTGACATGGGCGGCTG 60.821 66.667 9.56 2.20 0.00 4.85
294 415 5.749462 CATCCAAAGAGTTCCTCCAGTAAT 58.251 41.667 0.00 0.00 0.00 1.89
396 518 8.983724 GCTTTGATCAAATACTCACTAGATACC 58.016 37.037 20.76 0.00 0.00 2.73
401 523 8.494347 GCTATGCTTTGATCAAATACTCACTAG 58.506 37.037 20.76 14.25 0.00 2.57
404 526 7.019774 TGCTATGCTTTGATCAAATACTCAC 57.980 36.000 20.76 10.47 0.00 3.51
411 533 3.506844 TGTGCTGCTATGCTTTGATCAAA 59.493 39.130 19.45 19.45 0.00 2.69
413 535 2.421073 GTGTGCTGCTATGCTTTGATCA 59.579 45.455 0.00 0.00 0.00 2.92
414 536 2.421073 TGTGTGCTGCTATGCTTTGATC 59.579 45.455 0.00 0.00 0.00 2.92
460 582 8.611051 AGAAGGTAGAATATGTACCAGTCTTT 57.389 34.615 14.26 2.89 42.28 2.52
468 590 9.571816 AGGTACAGTAGAAGGTAGAATATGTAC 57.428 37.037 0.00 0.00 39.63 2.90
530 660 7.604549 TGACTCCGCATATATTAAATTCCGTA 58.395 34.615 0.00 0.00 0.00 4.02
545 675 3.766068 ATGAATGATCTGACTCCGCAT 57.234 42.857 0.00 0.00 0.00 4.73
611 741 1.596603 GCCAACTTTTGCATTTGCCT 58.403 45.000 0.00 0.00 41.18 4.75
816 947 1.775208 CTGCGTTTTCGTCTTTGCAAG 59.225 47.619 0.00 0.00 46.03 4.01
937 1069 0.889186 AGGTTGGTAGGCAGTTTGCG 60.889 55.000 0.00 0.00 46.21 4.85
972 1104 8.557869 CAAGCTCTGCAATTTTACATCTATTC 57.442 34.615 0.00 0.00 0.00 1.75
1131 1265 1.827344 CCTCTGCAAAATCCTTTCCCC 59.173 52.381 0.00 0.00 0.00 4.81
1685 1828 4.379243 ACAAGCTGGCCGACCTCG 62.379 66.667 0.00 0.00 36.63 4.63
2016 2165 4.821589 GGGCTGCCGTTCCTCTCG 62.822 72.222 13.40 0.00 0.00 4.04
2112 2261 2.933287 CCCTAGCCACCACCACCA 60.933 66.667 0.00 0.00 0.00 4.17
2235 2395 1.153168 CCGAAATGGCGTGATCCCT 60.153 57.895 0.00 0.00 0.00 4.20
2333 2493 1.812571 CCTCCACCCATTTCGTTTCAG 59.187 52.381 0.00 0.00 0.00 3.02
2439 2600 7.650903 CCTGACTGAGAAAGGAAAAGAAAAATG 59.349 37.037 0.00 0.00 32.43 2.32
2477 2639 1.069227 CGCAAAGACAAAGTACTGGCC 60.069 52.381 0.00 0.00 0.00 5.36
2489 2651 4.640805 TTCGTACATTTCTCGCAAAGAC 57.359 40.909 0.00 0.00 32.27 3.01
2491 2653 5.617609 TGATTTCGTACATTTCTCGCAAAG 58.382 37.500 0.00 0.00 0.00 2.77
2499 2666 6.310467 TGAGCAGTACTGATTTCGTACATTTC 59.690 38.462 27.08 4.16 39.66 2.17
2508 2675 3.311871 CCATGCTGAGCAGTACTGATTTC 59.688 47.826 27.08 18.62 43.65 2.17
2510 2677 2.915349 CCATGCTGAGCAGTACTGATT 58.085 47.619 27.08 13.31 43.65 2.57
2531 2698 8.017373 ACGATCAGTTACACATTCAATTTCAAG 58.983 33.333 0.00 0.00 0.00 3.02
2532 2699 7.870826 ACGATCAGTTACACATTCAATTTCAA 58.129 30.769 0.00 0.00 0.00 2.69
2533 2700 7.360861 GGACGATCAGTTACACATTCAATTTCA 60.361 37.037 0.00 0.00 0.00 2.69
2534 2701 6.961554 GGACGATCAGTTACACATTCAATTTC 59.038 38.462 0.00 0.00 0.00 2.17
2535 2702 6.655003 AGGACGATCAGTTACACATTCAATTT 59.345 34.615 0.00 0.00 0.00 1.82
2536 2703 6.173339 AGGACGATCAGTTACACATTCAATT 58.827 36.000 0.00 0.00 0.00 2.32
2537 2704 5.734720 AGGACGATCAGTTACACATTCAAT 58.265 37.500 0.00 0.00 0.00 2.57
2570 2737 3.557228 AGACATTGGAGCTCTCATTCC 57.443 47.619 14.64 0.00 0.00 3.01
2605 2772 6.403878 GGTATAGCTAGACAACCAGTTTTGA 58.596 40.000 19.55 0.00 0.00 2.69
2608 2775 4.708421 TCGGTATAGCTAGACAACCAGTTT 59.292 41.667 19.55 0.00 0.00 2.66
2641 2808 7.472543 CAGCAGTACCCAATAAAACAACTATC 58.527 38.462 0.00 0.00 0.00 2.08
2642 2809 6.127730 GCAGCAGTACCCAATAAAACAACTAT 60.128 38.462 0.00 0.00 0.00 2.12
2736 2903 6.928492 GGAACAAACAAGAAAGATAATGCCAA 59.072 34.615 0.00 0.00 0.00 4.52
2739 2906 6.691508 AGGGAACAAACAAGAAAGATAATGC 58.308 36.000 0.00 0.00 0.00 3.56
2956 3124 2.712057 TCAACGGACTAAAGGACGAC 57.288 50.000 0.00 0.00 0.00 4.34
3058 3226 2.356125 GCCTAACCATCACACCACTGAT 60.356 50.000 0.00 0.00 0.00 2.90
3059 3227 1.003118 GCCTAACCATCACACCACTGA 59.997 52.381 0.00 0.00 0.00 3.41
3073 3241 2.808567 GCTCCAGCCTATCAAGCCTAAC 60.809 54.545 0.00 0.00 34.31 2.34


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

AutoCloner maintained by Alex Coulton.