Multiple sequence alignment - TraesCS4B01G129200

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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 TraesCS4B01G129200 chr4B 100.000 4390 0 0 1 4390 168997719 168993330 0.000000e+00 8107.0
1 TraesCS4B01G129200 chr4D 96.479 3522 100 14 886 4390 107690565 107694079 0.000000e+00 5795.0
2 TraesCS4B01G129200 chr4A 96.387 2519 61 9 887 3400 468629158 468626665 0.000000e+00 4120.0
3 TraesCS4B01G129200 chr4A 94.481 906 40 8 3489 4390 468623871 468622972 0.000000e+00 1387.0
4 TraesCS4B01G129200 chr4A 100.000 36 0 0 3431 3466 468623902 468623867 2.830000e-07 67.6
5 TraesCS4B01G129200 chr5D 86.952 1870 187 22 1069 2929 238546546 238548367 0.000000e+00 2049.0
6 TraesCS4B01G129200 chr5D 88.422 881 92 3 10 888 409567658 409566786 0.000000e+00 1053.0
7 TraesCS4B01G129200 chr5A 86.877 1867 188 23 1078 2935 316096352 316094534 0.000000e+00 2037.0
8 TraesCS4B01G129200 chr5B 86.610 1867 193 23 1078 2935 266519143 266517325 0.000000e+00 2010.0
9 TraesCS4B01G129200 chr2B 93.037 876 54 1 3 878 208289515 208288647 0.000000e+00 1273.0
10 TraesCS4B01G129200 chr2A 91.695 879 65 2 1 879 719693544 719694414 0.000000e+00 1212.0
11 TraesCS4B01G129200 chr3B 91.149 870 68 3 10 878 222265439 222264578 0.000000e+00 1171.0
12 TraesCS4B01G129200 chr7B 83.967 842 135 0 1 842 187209296 187210137 0.000000e+00 808.0
13 TraesCS4B01G129200 chr3D 85.399 589 84 2 2309 2896 456924811 456925398 1.040000e-170 610.0
14 TraesCS4B01G129200 chr6B 84.727 550 82 2 2344 2892 642929630 642930178 2.310000e-152 549.0
15 TraesCS4B01G129200 chr6B 76.738 374 72 13 511 880 43510284 43510646 1.250000e-45 195.0
16 TraesCS4B01G129200 chr6B 75.556 270 60 6 511 777 46688683 46688949 1.280000e-25 128.0
17 TraesCS4B01G129200 chr6A 78.765 810 164 4 70 879 555821549 555820748 1.800000e-148 536.0
18 TraesCS4B01G129200 chr1B 78.007 873 169 16 10 877 180526915 180526061 1.080000e-145 527.0
19 TraesCS4B01G129200 chr1D 88.430 363 34 2 518 880 343182998 343182644 8.720000e-117 431.0


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 TraesCS4B01G129200 chr4B 168993330 168997719 4389 True 8107.0 8107 100.000 1 4390 1 chr4B.!!$R1 4389
1 TraesCS4B01G129200 chr4D 107690565 107694079 3514 False 5795.0 5795 96.479 886 4390 1 chr4D.!!$F1 3504
2 TraesCS4B01G129200 chr4A 468622972 468629158 6186 True 1858.2 4120 96.956 887 4390 3 chr4A.!!$R1 3503
3 TraesCS4B01G129200 chr5D 238546546 238548367 1821 False 2049.0 2049 86.952 1069 2929 1 chr5D.!!$F1 1860
4 TraesCS4B01G129200 chr5D 409566786 409567658 872 True 1053.0 1053 88.422 10 888 1 chr5D.!!$R1 878
5 TraesCS4B01G129200 chr5A 316094534 316096352 1818 True 2037.0 2037 86.877 1078 2935 1 chr5A.!!$R1 1857
6 TraesCS4B01G129200 chr5B 266517325 266519143 1818 True 2010.0 2010 86.610 1078 2935 1 chr5B.!!$R1 1857
7 TraesCS4B01G129200 chr2B 208288647 208289515 868 True 1273.0 1273 93.037 3 878 1 chr2B.!!$R1 875
8 TraesCS4B01G129200 chr2A 719693544 719694414 870 False 1212.0 1212 91.695 1 879 1 chr2A.!!$F1 878
9 TraesCS4B01G129200 chr3B 222264578 222265439 861 True 1171.0 1171 91.149 10 878 1 chr3B.!!$R1 868
10 TraesCS4B01G129200 chr7B 187209296 187210137 841 False 808.0 808 83.967 1 842 1 chr7B.!!$F1 841
11 TraesCS4B01G129200 chr3D 456924811 456925398 587 False 610.0 610 85.399 2309 2896 1 chr3D.!!$F1 587
12 TraesCS4B01G129200 chr6B 642929630 642930178 548 False 549.0 549 84.727 2344 2892 1 chr6B.!!$F3 548
13 TraesCS4B01G129200 chr6A 555820748 555821549 801 True 536.0 536 78.765 70 879 1 chr6A.!!$R1 809
14 TraesCS4B01G129200 chr1B 180526061 180526915 854 True 527.0 527 78.007 10 877 1 chr1B.!!$R1 867

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
438 439 0.108585 AACAAAGCGAGGAGGAGCAA 59.891 50.000 0.0 0.0 35.48 3.91 F
907 908 0.906066 TCGAACCGATCCCCAAATCA 59.094 50.000 0.0 0.0 0.00 2.57 F
1883 1891 1.152419 TCCCTCACCGACCAGTTCA 60.152 57.895 0.0 0.0 0.00 3.18 F
2474 2482 0.390340 GCTGTCTCCGAGCAATGTGA 60.390 55.000 0.0 0.0 36.40 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 1891 0.107066 TTGGTGATGCGCTCATGGAT 60.107 50.0 9.73 0.0 35.97 3.41 R
1933 1941 0.745845 ATCCGTTGATGTGCTGCTCC 60.746 55.0 0.00 0.0 0.00 4.70 R
3272 3281 0.934496 TGGCACAAAAAGAGACGACG 59.066 50.0 0.00 0.0 31.92 5.12 R
4221 6975 0.321298 GGCTACGTCAGGAAAGGCAA 60.321 55.0 0.00 0.0 34.84 4.52 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
53 54 2.652313 TGCCCTTGTTGCATGTACC 58.348 52.632 0.00 0.00 32.85 3.34
86 87 2.189594 TTTGGGCACTGTCAGATGAG 57.810 50.000 6.91 0.00 0.00 2.90
302 303 1.530323 ACATTGCGGAGTTGGGTAAC 58.470 50.000 0.00 0.00 37.06 2.50
342 343 3.428999 GCATGCAATCACAAGATCAAGCT 60.429 43.478 14.21 0.00 31.90 3.74
438 439 0.108585 AACAAAGCGAGGAGGAGCAA 59.891 50.000 0.00 0.00 35.48 3.91
591 592 6.324770 TCTTGTGGAGCAGAAGATATATGTGA 59.675 38.462 0.00 0.00 38.53 3.58
634 635 4.504858 GTGAACGACATAAACAGAGGGAT 58.495 43.478 0.00 0.00 0.00 3.85
709 710 6.311200 AGTTTTGTGTCTTGCTCATTTGTTTC 59.689 34.615 0.00 0.00 0.00 2.78
748 749 8.506168 TTTAATTTCGAGGCTCATAATCTTGT 57.494 30.769 15.95 1.35 0.00 3.16
793 794 5.013704 ACATAGGTAGACATGTTTGGTTGGA 59.986 40.000 0.00 0.00 31.32 3.53
803 804 2.959707 TGTTTGGTTGGATTACCCACAC 59.040 45.455 0.00 0.00 46.62 3.82
842 843 9.125026 GTACCTATGACAATTCCTTTGAATGAT 57.875 33.333 0.00 0.00 40.34 2.45
843 844 8.004087 ACCTATGACAATTCCTTTGAATGATG 57.996 34.615 0.00 0.00 40.34 3.07
844 845 7.835682 ACCTATGACAATTCCTTTGAATGATGA 59.164 33.333 0.00 0.00 40.34 2.92
845 846 8.689061 CCTATGACAATTCCTTTGAATGATGAA 58.311 33.333 0.00 0.00 40.34 2.57
847 848 8.942338 ATGACAATTCCTTTGAATGATGAATG 57.058 30.769 0.00 0.00 40.34 2.67
848 849 8.124808 TGACAATTCCTTTGAATGATGAATGA 57.875 30.769 0.00 0.00 40.34 2.57
907 908 0.906066 TCGAACCGATCCCCAAATCA 59.094 50.000 0.00 0.00 0.00 2.57
1345 1347 4.371417 ACCGCGTCCTCACCCCTA 62.371 66.667 4.92 0.00 0.00 3.53
1512 1514 2.050351 CGTCGTGCTCTTCACCGT 60.050 61.111 0.00 0.00 42.69 4.83
1883 1891 1.152419 TCCCTCACCGACCAGTTCA 60.152 57.895 0.00 0.00 0.00 3.18
1888 1896 1.208052 CTCACCGACCAGTTCATCCAT 59.792 52.381 0.00 0.00 0.00 3.41
1933 1941 3.200593 GACGCAGGCATGGAGCTG 61.201 66.667 0.00 0.00 44.79 4.24
2474 2482 0.390340 GCTGTCTCCGAGCAATGTGA 60.390 55.000 0.00 0.00 36.40 3.58
2542 2550 0.839946 TATTGAGGCAAGGGAGCTCC 59.160 55.000 25.59 25.59 34.17 4.70
3096 3105 4.522722 TTCATGATCATGTTTTGCAGCA 57.477 36.364 30.01 9.34 39.72 4.41
3106 3115 2.760092 TGTTTTGCAGCAAGAAAGGAGT 59.240 40.909 8.12 0.00 0.00 3.85
3225 3234 4.436242 ACTGTTGACCTGATAGTGTACG 57.564 45.455 0.00 0.00 0.00 3.67
3272 3281 5.294552 ACGTGCCTTCTGATTATAGAAAAGC 59.705 40.000 0.00 0.00 36.34 3.51
3304 3316 6.826741 TCTTTTTGTGCCACTAGAGTTACTTT 59.173 34.615 0.00 0.00 0.00 2.66
3329 3341 8.958119 TGAAGTTCTTGAAGTGTGTAAACTAT 57.042 30.769 4.17 0.00 0.00 2.12
3482 6227 8.731275 TGTATAATACTTCTGGTGGTTGATTG 57.269 34.615 0.00 0.00 0.00 2.67
3483 6228 6.699575 ATAATACTTCTGGTGGTTGATTGC 57.300 37.500 0.00 0.00 0.00 3.56
3517 6262 4.455877 CCTTCCACAAATTCAGTAGGTCAC 59.544 45.833 0.00 0.00 0.00 3.67
3662 6407 8.620416 TCCACAAAGATATAATCAATTCGTTGG 58.380 33.333 0.00 0.00 33.65 3.77
3687 6432 4.751600 TGCTCTCACTCAAATGTGTTAGTG 59.248 41.667 0.00 0.00 40.54 2.74
3806 6552 2.609459 CTGCGCTAACCAAGTTCCATAG 59.391 50.000 9.73 0.00 0.00 2.23
3807 6553 2.235155 TGCGCTAACCAAGTTCCATAGA 59.765 45.455 9.73 0.00 0.00 1.98
4016 6770 5.075493 AGAAAGAAAATGACAGTCCAGCAT 58.925 37.500 0.00 0.00 0.00 3.79
4064 6818 1.348036 AGGACCTTGGGTTCTTCTTCG 59.652 52.381 0.00 0.00 38.65 3.79
4072 6826 1.826096 GGGTTCTTCTTCGCCTAGAGT 59.174 52.381 0.00 0.00 0.00 3.24
4114 6868 0.032540 GTGGGTTTGCCTCTTTGCAG 59.967 55.000 0.00 0.00 43.21 4.41
4221 6975 5.828328 AGCTACAAGTTAACAGAGCCTTTTT 59.172 36.000 8.61 0.00 0.00 1.94
4346 7102 5.291858 TCTTCATTTGTATCATCACGTCAGC 59.708 40.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.407656 AAGAGTCCTCGCACCCACAA 61.408 55.000 0.00 0.00 34.09 3.33
53 54 0.457166 CCCAAATGCAGCGTGACATG 60.457 55.000 0.00 0.00 0.00 3.21
86 87 0.749649 ACATCTGGGAGACGAGCATC 59.250 55.000 0.00 0.00 35.92 3.91
302 303 0.438830 GCTCACTTCCAACGCGTAAG 59.561 55.000 14.46 15.81 43.44 2.34
478 479 5.451937 CCATAGTACACCATCGTTGATGAGT 60.452 44.000 8.32 8.68 42.09 3.41
591 592 0.902516 GCCTCCTGACAGTCTGAGGT 60.903 60.000 27.20 0.00 32.75 3.85
634 635 3.106986 GCTGCATTAGGGCCTCCGA 62.107 63.158 10.74 0.00 38.33 4.55
709 710 5.005971 TCGAAATTAAAATTCCTACGCTCGG 59.994 40.000 0.00 0.00 0.00 4.63
793 794 0.037046 GTTCGGGTCGTGTGGGTAAT 60.037 55.000 0.00 0.00 0.00 1.89
803 804 1.176527 TAGGTACAAGGTTCGGGTCG 58.823 55.000 0.00 0.00 0.00 4.79
842 843 6.534475 AATCTTGCCTGCTTTATTCATTCA 57.466 33.333 0.00 0.00 0.00 2.57
843 844 7.263496 AGAAATCTTGCCTGCTTTATTCATTC 58.737 34.615 0.00 0.00 0.00 2.67
844 845 7.093640 TGAGAAATCTTGCCTGCTTTATTCATT 60.094 33.333 0.00 0.00 0.00 2.57
845 846 6.379133 TGAGAAATCTTGCCTGCTTTATTCAT 59.621 34.615 0.00 0.00 0.00 2.57
846 847 5.711506 TGAGAAATCTTGCCTGCTTTATTCA 59.288 36.000 0.00 0.00 0.00 2.57
847 848 6.199937 TGAGAAATCTTGCCTGCTTTATTC 57.800 37.500 0.00 0.00 0.00 1.75
848 849 6.594788 TTGAGAAATCTTGCCTGCTTTATT 57.405 33.333 0.00 0.00 0.00 1.40
879 880 3.072211 GGGATCGGTTCGAAAAGAGTTT 58.928 45.455 0.00 0.00 39.99 2.66
882 883 1.066430 TGGGGATCGGTTCGAAAAGAG 60.066 52.381 0.00 0.00 39.99 2.85
883 884 0.978151 TGGGGATCGGTTCGAAAAGA 59.022 50.000 0.00 2.48 39.99 2.52
893 894 2.097466 CGTTTTCTGATTTGGGGATCGG 59.903 50.000 0.00 0.00 34.40 4.18
907 908 1.070786 TGAAGGCTCCGCGTTTTCT 59.929 52.632 4.92 0.00 36.76 2.52
1039 1041 6.452757 AAAATGGAAAATTGGAGGAATGGT 57.547 33.333 0.00 0.00 0.00 3.55
1669 1677 1.000486 CCGTCTCTTCCTCCTCCCA 60.000 63.158 0.00 0.00 0.00 4.37
1731 1739 4.400961 GCAGCCTCCCGAACAGCT 62.401 66.667 0.00 0.00 35.52 4.24
1768 1776 3.172106 TTCCCGTGGAAGGTGCCA 61.172 61.111 1.68 0.00 36.71 4.92
1883 1891 0.107066 TTGGTGATGCGCTCATGGAT 60.107 50.000 9.73 0.00 35.97 3.41
1888 1896 1.737735 CTCGTTGGTGATGCGCTCA 60.738 57.895 9.73 7.24 0.00 4.26
1921 1929 3.013327 TGCTCCAGCTCCATGCCT 61.013 61.111 0.00 0.00 44.23 4.75
1933 1941 0.745845 ATCCGTTGATGTGCTGCTCC 60.746 55.000 0.00 0.00 0.00 4.70
2449 2457 2.568612 CTCGGAGACAGCGCAGAA 59.431 61.111 11.47 0.00 0.00 3.02
2474 2482 3.244284 TGCATTCCTTTTTGCAGCTGATT 60.244 39.130 20.43 0.00 43.54 2.57
2542 2550 3.257561 CCGCTCTTGGTGATCGCG 61.258 66.667 0.00 0.00 38.54 5.87
3162 3171 2.228822 CCATAGTGTGACAAGGTTTGCC 59.771 50.000 0.00 0.00 0.00 4.52
3272 3281 0.934496 TGGCACAAAAAGAGACGACG 59.066 50.000 0.00 0.00 31.92 5.12
3304 3316 8.958119 ATAGTTTACACACTTCAAGAACTTCA 57.042 30.769 0.00 0.00 0.00 3.02
3405 3474 8.686334 AGACAACCAAATGTATCCACATAATTC 58.314 33.333 0.00 0.00 44.83 2.17
3418 3487 4.763793 CCTGATCAAGAGACAACCAAATGT 59.236 41.667 0.00 0.00 35.90 2.71
3482 6227 8.196771 TGAATTTGTGGAAGGATATTAATGTGC 58.803 33.333 0.00 0.00 0.00 4.57
3483 6228 9.740239 CTGAATTTGTGGAAGGATATTAATGTG 57.260 33.333 0.00 0.00 0.00 3.21
3517 6262 8.971073 AGGATTGGGTAAATGAAATTCTTACAG 58.029 33.333 7.23 0.00 33.67 2.74
3662 6407 5.641209 ACTAACACATTTGAGTGAGAGCATC 59.359 40.000 0.57 0.00 42.05 3.91
3687 6432 5.689383 TCAGACTAATCAAGTTTGCAACC 57.311 39.130 0.00 0.00 39.58 3.77
3806 6552 6.319658 TGATTAAGATGCCAAGATTTCCACTC 59.680 38.462 0.00 0.00 0.00 3.51
3807 6553 6.189859 TGATTAAGATGCCAAGATTTCCACT 58.810 36.000 0.00 0.00 0.00 4.00
3846 6594 7.651027 TTTACTGTACTCCTTATGGACCTAC 57.349 40.000 0.00 0.00 37.46 3.18
3996 6746 4.219288 GGAATGCTGGACTGTCATTTTCTT 59.781 41.667 10.38 0.00 31.30 2.52
4003 6753 1.296392 CGGGAATGCTGGACTGTCA 59.704 57.895 10.38 0.00 0.00 3.58
4016 6770 1.629043 ACTCACAAGTCTAGCGGGAA 58.371 50.000 0.00 0.00 0.00 3.97
4064 6818 5.297029 ACTTTGAACAAGAAACACTCTAGGC 59.703 40.000 0.00 0.00 32.46 3.93
4072 6826 7.032580 CACATAACCACTTTGAACAAGAAACA 58.967 34.615 0.00 0.00 0.00 2.83
4114 6868 8.643752 GCAAAATTACATACAAACATGGTGTAC 58.356 33.333 12.24 0.00 34.41 2.90
4221 6975 0.321298 GGCTACGTCAGGAAAGGCAA 60.321 55.000 0.00 0.00 34.84 4.52
4258 7012 9.490379 GGTAAGAAGAGAAACTTACAATTGAGA 57.510 33.333 13.59 0.00 45.62 3.27


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

AutoCloner maintained by Alex Coulton.