Multiple sequence alignment - TraesCS2B01G548300

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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 TraesCS2B01G548300 chr2B 100.000 5185 0 0 1 5185 744376430 744371246 0.000000e+00 9575.0
1 TraesCS2B01G548300 chr2B 96.746 1844 36 5 802 2629 774767826 774769661 0.000000e+00 3051.0
2 TraesCS2B01G548300 chr2B 94.842 1609 30 22 2662 4258 774769662 774771229 0.000000e+00 2462.0
3 TraesCS2B01G548300 chr2B 97.289 922 22 3 4265 5185 774771542 774772461 0.000000e+00 1561.0
4 TraesCS2B01G548300 chr2B 87.389 1015 46 32 1672 2637 88853525 88854506 0.000000e+00 1090.0
5 TraesCS2B01G548300 chr2B 88.227 688 39 18 1 667 774767075 774767741 0.000000e+00 784.0
6 TraesCS2B01G548300 chr1D 90.792 2335 74 37 90 2336 432639007 432636726 0.000000e+00 2990.0
7 TraesCS2B01G548300 chr1D 92.688 1559 52 17 2684 4233 432636481 432634976 0.000000e+00 2191.0
8 TraesCS2B01G548300 chr1D 86.404 912 102 11 4265 5171 432632581 432631687 0.000000e+00 977.0
9 TraesCS2B01G548300 chr1D 84.291 261 12 11 2383 2639 432636729 432636494 1.450000e-55 228.0
10 TraesCS2B01G548300 chr1D 98.438 64 1 0 1 64 432639057 432638994 4.240000e-21 113.0
11 TraesCS2B01G548300 chr2D 94.883 1583 53 16 2684 4258 631286320 631287882 0.000000e+00 2449.0
12 TraesCS2B01G548300 chr2D 90.058 1207 27 12 890 2037 631284993 631286165 0.000000e+00 1478.0
13 TraesCS2B01G548300 chr2D 91.542 934 61 8 4265 5185 631288195 631289123 0.000000e+00 1271.0
14 TraesCS2B01G548300 chr2D 90.609 575 28 9 3 555 631284421 631284991 0.000000e+00 739.0
15 TraesCS2B01G548300 chr2D 80.113 709 110 17 3199 3879 648058525 648057820 2.790000e-137 499.0
16 TraesCS2B01G548300 chr2D 85.043 234 31 2 2858 3091 648059816 648059587 8.680000e-58 235.0
17 TraesCS2B01G548300 chr2D 92.308 39 3 0 370 408 600969622 600969660 7.250000e-04 56.5
18 TraesCS2B01G548300 chr3B 87.426 1018 43 35 1672 2637 491825600 491824616 0.000000e+00 1092.0
19 TraesCS2B01G548300 chr4B 87.303 1016 43 34 1672 2634 475801596 475800614 0.000000e+00 1083.0
20 TraesCS2B01G548300 chr7A 86.845 1011 46 33 1672 2637 576087380 576088348 0.000000e+00 1050.0
21 TraesCS2B01G548300 chr7A 85.251 1017 48 41 1672 2637 39479886 39480851 0.000000e+00 953.0
22 TraesCS2B01G548300 chr3A 86.292 1014 40 42 1672 2637 35093652 35092690 0.000000e+00 1011.0
23 TraesCS2B01G548300 chr3A 87.926 323 13 12 2316 2637 35150392 35150095 1.780000e-94 357.0
24 TraesCS2B01G548300 chr3A 97.516 161 4 0 1672 1832 35151782 35151622 5.110000e-70 276.0
25 TraesCS2B01G548300 chr5A 86.997 869 28 31 1672 2485 637187690 637186852 0.000000e+00 900.0
26 TraesCS2B01G548300 chrUn 87.363 641 27 21 1842 2458 472255659 472256269 0.000000e+00 686.0
27 TraesCS2B01G548300 chrUn 87.926 323 13 10 2316 2637 309098550 309098847 1.780000e-94 357.0
28 TraesCS2B01G548300 chrUn 87.926 323 13 10 2316 2637 309114647 309114350 1.780000e-94 357.0
29 TraesCS2B01G548300 chrUn 85.115 262 32 4 2832 3089 76852278 76852536 1.430000e-65 261.0
30 TraesCS2B01G548300 chrUn 79.114 158 33 0 3214 3371 76852679 76852836 5.490000e-20 110.0
31 TraesCS2B01G548300 chr6D 75.391 703 137 21 3214 3888 31641347 31642041 1.810000e-79 307.0
32 TraesCS2B01G548300 chr6D 86.538 260 28 4 2834 3089 31640956 31641212 3.950000e-71 279.0
33 TraesCS2B01G548300 chr6D 93.182 44 3 0 5018 5061 472136670 472136627 1.210000e-06 65.8
34 TraesCS2B01G548300 chr6A 74.716 704 140 23 3214 3888 31594158 31594852 3.950000e-71 279.0
35 TraesCS2B01G548300 chr6A 84.364 275 33 8 2834 3103 31593766 31594035 1.430000e-65 261.0
36 TraesCS2B01G548300 chr2A 91.489 47 2 2 376 420 244297513 244297559 4.330000e-06 63.9
37 TraesCS2B01G548300 chr3D 85.246 61 6 2 374 432 283308939 283308998 5.610000e-05 60.2


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 TraesCS2B01G548300 chr2B 744371246 744376430 5184 True 9575.00 9575 100.0000 1 5185 1 chr2B.!!$R1 5184
1 TraesCS2B01G548300 chr2B 774767075 774772461 5386 False 1964.50 3051 94.2760 1 5185 4 chr2B.!!$F2 5184
2 TraesCS2B01G548300 chr2B 88853525 88854506 981 False 1090.00 1090 87.3890 1672 2637 1 chr2B.!!$F1 965
3 TraesCS2B01G548300 chr1D 432631687 432639057 7370 True 1299.80 2990 90.5226 1 5171 5 chr1D.!!$R1 5170
4 TraesCS2B01G548300 chr2D 631284421 631289123 4702 False 1484.25 2449 91.7730 3 5185 4 chr2D.!!$F2 5182
5 TraesCS2B01G548300 chr2D 648057820 648059816 1996 True 367.00 499 82.5780 2858 3879 2 chr2D.!!$R1 1021
6 TraesCS2B01G548300 chr3B 491824616 491825600 984 True 1092.00 1092 87.4260 1672 2637 1 chr3B.!!$R1 965
7 TraesCS2B01G548300 chr4B 475800614 475801596 982 True 1083.00 1083 87.3030 1672 2634 1 chr4B.!!$R1 962
8 TraesCS2B01G548300 chr7A 576087380 576088348 968 False 1050.00 1050 86.8450 1672 2637 1 chr7A.!!$F2 965
9 TraesCS2B01G548300 chr7A 39479886 39480851 965 False 953.00 953 85.2510 1672 2637 1 chr7A.!!$F1 965
10 TraesCS2B01G548300 chr3A 35092690 35093652 962 True 1011.00 1011 86.2920 1672 2637 1 chr3A.!!$R1 965
11 TraesCS2B01G548300 chr3A 35150095 35151782 1687 True 316.50 357 92.7210 1672 2637 2 chr3A.!!$R2 965
12 TraesCS2B01G548300 chr5A 637186852 637187690 838 True 900.00 900 86.9970 1672 2485 1 chr5A.!!$R1 813
13 TraesCS2B01G548300 chrUn 472255659 472256269 610 False 686.00 686 87.3630 1842 2458 1 chrUn.!!$F2 616
14 TraesCS2B01G548300 chr6D 31640956 31642041 1085 False 293.00 307 80.9645 2834 3888 2 chr6D.!!$F1 1054
15 TraesCS2B01G548300 chr6A 31593766 31594852 1086 False 270.00 279 79.5400 2834 3888 2 chr6A.!!$F1 1054

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
885 960 0.033504 AGTGACCGACTTGCAATCGT 59.966 50.000 21.46 10.00 37.90 3.73 F
993 1070 1.021390 AAATTCGTCGGCTGCCTCAG 61.021 55.000 17.92 7.43 34.12 3.35 F
2113 2310 1.153369 ATGGCAACGACGCTATGCT 60.153 52.632 16.94 0.37 39.94 3.79 F
2864 3772 2.039624 AGCTGATGTCGGGGGAGT 59.960 61.111 0.00 0.00 0.00 3.85 F
3576 5506 0.393077 CAGATTACTACGCCCCTGGG 59.607 60.000 5.50 5.50 38.57 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2793 3698 0.249676 TAGTGACGGCCGGCAATTAA 59.750 50.000 41.11 21.14 33.39 1.40 R
2864 3772 4.812476 CGTCCATCGCCGCCTTCA 62.812 66.667 0.00 0.00 0.00 3.02 R
3314 5219 0.801251 GCATGTCACCAGCAAGTCTC 59.199 55.000 0.00 0.00 0.00 3.36 R
4112 6063 0.890683 GTGCCAATCAAGTGAAGGGG 59.109 55.000 5.60 0.26 0.00 4.79 R
4623 8949 1.299541 CGCTGGAGCCGAAATACATT 58.700 50.000 0.00 0.00 37.91 2.71 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
50 51 2.703536 TCCCTCAAGTTGCAACTCTGTA 59.296 45.455 31.20 15.84 38.57 2.74
168 170 5.238650 CGCCTATTTGAAACGGGATCTAAAT 59.761 40.000 2.78 0.00 0.00 1.40
329 333 1.473434 GCGCTAGCAAATAGGGACAGT 60.473 52.381 16.45 0.00 45.10 3.55
360 369 2.977772 AATGAAGAGAGGAAGGCGAG 57.022 50.000 0.00 0.00 0.00 5.03
421 430 2.585247 GCCGATCGCTACGCCTTT 60.585 61.111 10.32 0.00 0.00 3.11
428 437 2.032634 CGCTACGCCTTTGCCTTCA 61.033 57.895 0.00 0.00 0.00 3.02
479 509 2.055299 ACGAACCCTGGTGAATCGT 58.945 52.632 8.36 8.36 41.44 3.73
536 566 2.130426 GCGGAGAGAGATGGAGGCA 61.130 63.158 0.00 0.00 0.00 4.75
548 578 1.383803 GGAGGCATGAGAGGGGAGT 60.384 63.158 0.00 0.00 0.00 3.85
555 585 0.622738 ATGAGAGGGGAGTGTGGCAT 60.623 55.000 0.00 0.00 0.00 4.40
570 600 6.114767 AGTGTGGCATGAAATTTGAAACTTT 58.885 32.000 0.00 0.00 0.00 2.66
634 664 2.081787 TGAGGCCCACCACAAAGGA 61.082 57.895 0.00 0.00 41.22 3.36
848 923 3.003173 TTGCCCGCCTGTAGAGCT 61.003 61.111 0.00 0.00 0.00 4.09
851 926 2.759973 CCCGCCTGTAGAGCTGGA 60.760 66.667 0.00 0.00 36.79 3.86
885 960 0.033504 AGTGACCGACTTGCAATCGT 59.966 50.000 21.46 10.00 37.90 3.73
993 1070 1.021390 AAATTCGTCGGCTGCCTCAG 61.021 55.000 17.92 7.43 34.12 3.35
1054 1131 1.501582 GCCAAGATACAGGGGTCTCT 58.498 55.000 0.00 0.00 32.36 3.10
1556 1675 3.660111 GGCGCCTTGCTGAACGTT 61.660 61.111 22.15 0.00 45.43 3.99
2113 2310 1.153369 ATGGCAACGACGCTATGCT 60.153 52.632 16.94 0.37 39.94 3.79
2290 2492 8.870116 AGAAATTTACCCTAGAAAAATGTTGCT 58.130 29.630 0.00 0.00 0.00 3.91
2864 3772 2.039624 AGCTGATGTCGGGGGAGT 59.960 61.111 0.00 0.00 0.00 3.85
2958 3884 3.575247 ACCGACATTGGGGCCACA 61.575 61.111 1.54 1.54 0.00 4.17
3448 5363 2.282745 AAGGCTTGGAGCACTGCC 60.283 61.111 0.00 0.00 44.75 4.85
3576 5506 0.393077 CAGATTACTACGCCCCTGGG 59.607 60.000 5.50 5.50 38.57 4.45
4112 6063 2.945447 TTCCTTACATGCATGCAAGC 57.055 45.000 27.58 7.04 31.33 4.01
4157 6110 2.236395 AGGACTAGCGTGGCAGTTTATT 59.764 45.455 0.00 0.00 0.00 1.40
4343 8667 0.179137 CAGAGCTTCGCCATGTACGA 60.179 55.000 4.13 4.13 37.86 3.43
4435 8759 2.589157 CCAAGGGTACACCGGCTCA 61.589 63.158 0.00 0.00 46.96 4.26
4562 8887 0.755686 GATCCTAGCCAGTGGGTCTG 59.244 60.000 19.18 11.97 43.27 3.51
4928 9267 4.450080 GTCGGGAAATTTTACTTGACGACT 59.550 41.667 11.36 0.00 43.18 4.18
4961 9300 4.652421 AGTATATTTACTCCTTGTCGGCCA 59.348 41.667 2.24 0.00 33.18 5.36
5013 9352 3.947612 TGTAGGGGATCGACTAGTTCT 57.052 47.619 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 170 1.889454 GGTCCATGCGATTTTGCCA 59.111 52.632 0.00 0.00 0.00 4.92
257 260 0.673644 AGCGGTTACTGCAGCGAATT 60.674 50.000 18.97 0.00 40.13 2.17
329 333 1.222387 CTTCATTTACCCCCGCGGA 59.778 57.895 30.73 5.29 34.64 5.54
421 430 3.436924 CGCAGCTGCATGAAGGCA 61.437 61.111 36.03 0.00 42.53 4.75
479 509 3.788708 TCTCTCCATTCTCTCTCCCTACA 59.211 47.826 0.00 0.00 0.00 2.74
536 566 0.622738 ATGCCACACTCCCCTCTCAT 60.623 55.000 0.00 0.00 0.00 2.90
548 578 5.233902 CGAAAGTTTCAAATTTCATGCCACA 59.766 36.000 15.67 0.00 41.55 4.17
555 585 4.202172 GGGGGTCGAAAGTTTCAAATTTCA 60.202 41.667 15.67 0.00 41.55 2.69
570 600 0.323178 GACAGAGTAGTGGGGGTCGA 60.323 60.000 0.00 0.00 0.00 4.20
735 765 1.591703 GGACTGCTCGATCACCACA 59.408 57.895 0.00 0.00 0.00 4.17
739 769 1.517257 CCACGGACTGCTCGATCAC 60.517 63.158 0.00 0.00 0.00 3.06
848 923 4.710375 GTCACTACCTAGAAGGAATGTCCA 59.290 45.833 0.00 0.00 39.61 4.02
851 926 3.700038 CGGTCACTACCTAGAAGGAATGT 59.300 47.826 0.00 0.00 44.35 2.71
885 960 5.358922 GGTAAATACTTGTACGCATGGGTA 58.641 41.667 17.89 17.89 0.00 3.69
951 1028 1.742880 GGTTACGAGCGGGGGTTTC 60.743 63.158 0.00 0.00 0.00 2.78
993 1070 0.529555 GCGAGGTGAATGAGGAGAGC 60.530 60.000 0.00 0.00 0.00 4.09
1054 1131 2.264480 CGATTGTCGGCAGGTCCA 59.736 61.111 0.00 0.00 36.00 4.02
1383 1502 3.792124 GCAAAGAACTGGAAACGAAGGTG 60.792 47.826 0.00 0.00 0.00 4.00
2314 3195 6.498651 AGTTAGCCTATCTAGCAACATACCAT 59.501 38.462 0.00 0.00 31.70 3.55
2639 3529 9.368416 CCCAATAGCTAGCTGTAGGATTATATA 57.632 37.037 27.68 2.16 0.00 0.86
2640 3530 7.846823 ACCCAATAGCTAGCTGTAGGATTATAT 59.153 37.037 27.68 5.47 0.00 0.86
2641 3531 7.124298 CACCCAATAGCTAGCTGTAGGATTATA 59.876 40.741 27.68 2.97 0.00 0.98
2642 3532 6.026186 ACCCAATAGCTAGCTGTAGGATTAT 58.974 40.000 27.68 7.03 0.00 1.28
2657 3547 5.072040 ACACATTTTTAGCACCCAATAGC 57.928 39.130 0.00 0.00 0.00 2.97
2658 3548 7.378181 AGAAACACATTTTTAGCACCCAATAG 58.622 34.615 0.00 0.00 0.00 1.73
2659 3549 7.296628 AGAAACACATTTTTAGCACCCAATA 57.703 32.000 0.00 0.00 0.00 1.90
2660 3550 6.173427 AGAAACACATTTTTAGCACCCAAT 57.827 33.333 0.00 0.00 0.00 3.16
2752 3642 2.766313 TGCACTTGTGCGAAACTCTAT 58.234 42.857 18.99 0.00 37.69 1.98
2793 3698 0.249676 TAGTGACGGCCGGCAATTAA 59.750 50.000 41.11 21.14 33.39 1.40
2864 3772 4.812476 CGTCCATCGCCGCCTTCA 62.812 66.667 0.00 0.00 0.00 3.02
2958 3884 6.214412 AGTCCTTCATCTCAAGAAACCAGTAT 59.786 38.462 0.00 0.00 0.00 2.12
3255 5160 1.302511 GCCGTGCCTCCTCTCAAAA 60.303 57.895 0.00 0.00 0.00 2.44
3314 5219 0.801251 GCATGTCACCAGCAAGTCTC 59.199 55.000 0.00 0.00 0.00 3.36
3448 5363 3.133542 TCCCATGACTTGATCTGTAGCTG 59.866 47.826 0.00 0.00 0.00 4.24
3576 5506 2.087009 GTACACTCGCGTCTGCCAC 61.087 63.158 5.77 1.06 38.08 5.01
4007 5958 2.620115 ACTCAAGACGTACGTTGGAGAA 59.380 45.455 32.65 15.87 0.00 2.87
4112 6063 0.890683 GTGCCAATCAAGTGAAGGGG 59.109 55.000 5.60 0.26 0.00 4.79
4157 6110 8.050778 ACGGTTGCTTGATTAATTTAGAATCA 57.949 30.769 0.00 0.00 40.65 2.57
4343 8667 1.382420 AGGAGCAAGCCGGAGAGAT 60.382 57.895 5.05 0.00 0.00 2.75
4435 8759 1.739667 GGTTGCCTTCTGCCGTTTT 59.260 52.632 0.00 0.00 40.16 2.43
4623 8949 1.299541 CGCTGGAGCCGAAATACATT 58.700 50.000 0.00 0.00 37.91 2.71
4737 9076 4.847516 CGCGATGCTCGGTCGGAA 62.848 66.667 0.00 0.00 40.84 4.30
4961 9300 5.464389 GGTGATTATACATTTTACGCCGAGT 59.536 40.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.