Multiple sequence alignment - TraesCS1B01G378200

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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 TraesCS1B01G378200 chr1B 100.000 4558 0 0 1 4558 610377545 610382102 0 8418
1 TraesCS1B01G378200 chr6A 98.941 3967 37 2 595 4557 570351810 570355775 0 7088
2 TraesCS1B01G378200 chr6A 97.621 3994 58 6 596 4558 584409024 584413011 0 6815
3 TraesCS1B01G378200 chr6A 98.732 2130 21 2 594 2718 570360086 570362214 0 3779
4 TraesCS1B01G378200 chr4A 98.741 3971 43 2 594 4558 611653958 611657927 0 7049
5 TraesCS1B01G378200 chr4A 99.155 3552 30 0 1007 4558 739024530 739020979 0 6394
6 TraesCS1B01G378200 chr4A 98.873 2129 18 1 594 2716 739016669 739014541 0 3794
7 TraesCS1B01G378200 chr7B 98.022 3994 46 6 596 4558 535640812 535644803 0 6907
8 TraesCS1B01G378200 chr6B 92.832 4018 185 36 596 4558 47738934 47734965 0 5729
9 TraesCS1B01G378200 chr6B 92.415 4021 187 42 594 4558 47659872 47655914 0 5627
10 TraesCS1B01G378200 chr6B 92.212 4019 188 42 595 4558 47699823 47695875 0 5572
11 TraesCS1B01G378200 chr2B 99.127 2291 20 0 2268 4558 626032645 626034935 0 4120
12 TraesCS1B01G378200 chr2B 98.967 2130 15 2 594 2717 626039245 626041373 0 3805
13 TraesCS1B01G378200 chr1A 98.778 2128 20 1 596 2717 533310366 533312493 0 3781
14 TraesCS1B01G378200 chr7D 94.949 594 30 0 1 594 476837227 476836634 0 931
15 TraesCS1B01G378200 chr5D 94.781 594 31 0 1 594 45090084 45090677 0 926
16 TraesCS1B01G378200 chr5D 94.444 594 33 0 1 594 441033794 441033201 0 915
17 TraesCS1B01G378200 chr5D 94.276 594 34 0 1 594 230980525 230979932 0 909
18 TraesCS1B01G378200 chr5D 94.276 594 34 0 1 594 377216510 377217103 0 909
19 TraesCS1B01G378200 chr6D 94.444 594 32 1 1 594 275401298 275400706 0 913
20 TraesCS1B01G378200 chrUn 94.276 594 34 0 1 594 94168258 94168851 0 909
21 TraesCS1B01G378200 chr4D 94.276 594 34 0 1 594 109405239 109405832 0 909
22 TraesCS1B01G378200 chr1D 94.276 594 34 0 1 594 403408249 403407656 0 909


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 TraesCS1B01G378200 chr1B 610377545 610382102 4557 False 8418 8418 100.000 1 4558 1 chr1B.!!$F1 4557
1 TraesCS1B01G378200 chr6A 570351810 570355775 3965 False 7088 7088 98.941 595 4557 1 chr6A.!!$F1 3962
2 TraesCS1B01G378200 chr6A 584409024 584413011 3987 False 6815 6815 97.621 596 4558 1 chr6A.!!$F3 3962
3 TraesCS1B01G378200 chr6A 570360086 570362214 2128 False 3779 3779 98.732 594 2718 1 chr6A.!!$F2 2124
4 TraesCS1B01G378200 chr4A 611653958 611657927 3969 False 7049 7049 98.741 594 4558 1 chr4A.!!$F1 3964
5 TraesCS1B01G378200 chr4A 739020979 739024530 3551 True 6394 6394 99.155 1007 4558 1 chr4A.!!$R2 3551
6 TraesCS1B01G378200 chr4A 739014541 739016669 2128 True 3794 3794 98.873 594 2716 1 chr4A.!!$R1 2122
7 TraesCS1B01G378200 chr7B 535640812 535644803 3991 False 6907 6907 98.022 596 4558 1 chr7B.!!$F1 3962
8 TraesCS1B01G378200 chr6B 47734965 47738934 3969 True 5729 5729 92.832 596 4558 1 chr6B.!!$R3 3962
9 TraesCS1B01G378200 chr6B 47655914 47659872 3958 True 5627 5627 92.415 594 4558 1 chr6B.!!$R1 3964
10 TraesCS1B01G378200 chr6B 47695875 47699823 3948 True 5572 5572 92.212 595 4558 1 chr6B.!!$R2 3963
11 TraesCS1B01G378200 chr2B 626032645 626034935 2290 False 4120 4120 99.127 2268 4558 1 chr2B.!!$F1 2290
12 TraesCS1B01G378200 chr2B 626039245 626041373 2128 False 3805 3805 98.967 594 2717 1 chr2B.!!$F2 2123
13 TraesCS1B01G378200 chr1A 533310366 533312493 2127 False 3781 3781 98.778 596 2717 1 chr1A.!!$F1 2121
14 TraesCS1B01G378200 chr7D 476836634 476837227 593 True 931 931 94.949 1 594 1 chr7D.!!$R1 593
15 TraesCS1B01G378200 chr5D 45090084 45090677 593 False 926 926 94.781 1 594 1 chr5D.!!$F1 593
16 TraesCS1B01G378200 chr5D 441033201 441033794 593 True 915 915 94.444 1 594 1 chr5D.!!$R2 593
17 TraesCS1B01G378200 chr5D 230979932 230980525 593 True 909 909 94.276 1 594 1 chr5D.!!$R1 593
18 TraesCS1B01G378200 chr5D 377216510 377217103 593 False 909 909 94.276 1 594 1 chr5D.!!$F2 593
19 TraesCS1B01G378200 chr6D 275400706 275401298 592 True 913 913 94.444 1 594 1 chr6D.!!$R1 593
20 TraesCS1B01G378200 chrUn 94168258 94168851 593 False 909 909 94.276 1 594 1 chrUn.!!$F1 593
21 TraesCS1B01G378200 chr4D 109405239 109405832 593 False 909 909 94.276 1 594 1 chr4D.!!$F1 593
22 TraesCS1B01G378200 chr1D 403407656 403408249 593 True 909 909 94.276 1 594 1 chr1D.!!$R1 593

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
500 501 0.765903 ATGGCGATGATGGACCCTCT 60.766 55.0 0.00 0.00 0.0 3.69 F
1489 1506 0.535780 CAGGACCCATGCATGCGTAT 60.536 55.0 21.69 8.39 0.0 3.06 F
2169 2190 5.587844 ACGACGGTTATTAGTATGTCTCTGT 59.412 40.0 0.00 0.00 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 2190 6.590292 GCGCAAACCTATAGCAATAATCTCTA 59.410 38.462 0.30 0.00 0.00 2.43 R
2818 2888 0.969894 CTAGGCCAGGGTTATCTCCG 59.030 60.000 5.01 0.00 0.00 4.63 R
4170 4293 6.628185 CACCGTAGACAATTAGTAAAGGTCT 58.372 40.000 18.31 18.31 41.37 3.85 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
54 55 4.008074 ACCCACTATAAGCGAATCATGG 57.992 45.455 0.00 0.00 0.00 3.66
73 74 2.237643 TGGACGTATTGCAACACCCTAT 59.762 45.455 0.00 0.00 0.00 2.57
76 77 4.202182 GGACGTATTGCAACACCCTATAGA 60.202 45.833 0.00 0.00 0.00 1.98
104 105 4.075910 CATGCTTGCGCGACACGT 62.076 61.111 12.10 0.00 46.11 4.49
129 130 4.097892 GGGCATAATAGGACAACACCAAAG 59.902 45.833 0.00 0.00 0.00 2.77
182 183 7.065120 TCATCAATCAACCCAAAGACAAAAT 57.935 32.000 0.00 0.00 0.00 1.82
380 381 1.270414 CCTCCTGATGGCACTCTGGT 61.270 60.000 16.42 0.00 36.10 4.00
398 399 1.076727 TGCCACCGAGAGAGAGGAA 59.923 57.895 0.00 0.00 0.00 3.36
461 462 1.912043 CCTGGATGAGGAGTGGTTCTT 59.088 52.381 0.00 0.00 46.33 2.52
474 475 1.978580 TGGTTCTTCCTCTGGTCCTTC 59.021 52.381 0.00 0.00 37.07 3.46
500 501 0.765903 ATGGCGATGATGGACCCTCT 60.766 55.000 0.00 0.00 0.00 3.69
523 524 2.881491 ATCCTTCCCCATGGCCTCCA 62.881 60.000 6.09 0.00 38.19 3.86
581 582 3.432326 GGCCTAGATTGATTTCTCGTGGT 60.432 47.826 0.00 0.00 0.00 4.16
813 830 8.049117 AGATAAGTTCAATGTCCTGCAGATTAA 58.951 33.333 17.39 0.00 0.00 1.40
967 984 1.392710 CCACGTAGCCCTTCCTCGAT 61.393 60.000 0.00 0.00 0.00 3.59
1242 1259 5.670818 TCTCCTCTCCTACTACATGTTCCTA 59.329 44.000 2.30 0.00 0.00 2.94
1390 1407 4.397420 TGATCCATGCTTTGTTACACTGT 58.603 39.130 0.00 0.00 0.00 3.55
1489 1506 0.535780 CAGGACCCATGCATGCGTAT 60.536 55.000 21.69 8.39 0.00 3.06
2169 2190 5.587844 ACGACGGTTATTAGTATGTCTCTGT 59.412 40.000 0.00 0.00 0.00 3.41
2808 2878 6.497259 AGTGAGGGTAAAGAGTGTTTATGAGA 59.503 38.462 0.00 0.00 0.00 3.27
2927 2997 4.263994 GCTATGGAGTAGTCCTGGGATAGA 60.264 50.000 17.62 0.00 44.30 1.98
4004 4123 6.741992 ATTGATGTTTCAGTAAATCAGCGA 57.258 33.333 0.00 0.00 32.27 4.93
4170 4293 4.885907 AGTAGGCACGTGCTAGTTTATCTA 59.114 41.667 36.84 23.81 41.70 1.98
4445 4571 2.033407 CAGCAAGAGACTCAACAACGTG 60.033 50.000 5.02 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.143684 AGTGGGTTGCTTGAGTGACAT 59.856 47.619 0.00 0.00 0.00 3.06
54 55 4.940463 TCTATAGGGTGTTGCAATACGTC 58.060 43.478 18.55 13.49 0.00 4.34
104 105 4.041464 TGGTGTTGTCCTATTATGCCCTA 58.959 43.478 0.00 0.00 0.00 3.53
202 203 3.444742 TCCAATGATGTGTTGCCATCTTC 59.555 43.478 0.00 0.00 41.47 2.87
289 290 1.922570 TCCTCATCTCTTTTACGCGC 58.077 50.000 5.73 0.00 0.00 6.86
380 381 0.967887 CTTCCTCTCTCTCGGTGGCA 60.968 60.000 0.00 0.00 0.00 4.92
449 450 1.132689 ACCAGAGGAAGAACCACTCCT 60.133 52.381 0.00 0.00 37.48 3.69
454 455 1.978580 GAAGGACCAGAGGAAGAACCA 59.021 52.381 0.00 0.00 42.04 3.67
461 462 1.229209 AAGGCGAAGGACCAGAGGA 60.229 57.895 0.00 0.00 0.00 3.71
494 495 4.840545 GGAAGGATCCCAGAGGGT 57.159 61.111 8.55 0.00 44.74 4.34
523 524 2.081161 GGAGGGGGCCATCATCACT 61.081 63.158 4.39 0.00 0.00 3.41
581 582 7.195374 AGGTTATTACATCAAGCCTCTGTAA 57.805 36.000 0.00 0.00 39.08 2.41
813 830 3.753294 CAGGTATTCTCCCTGCGTAAT 57.247 47.619 0.00 0.00 42.81 1.89
967 984 5.032846 AGAGGGTTGAAAGGATGACATCTA 58.967 41.667 14.95 0.00 0.00 1.98
1034 1051 0.898326 GGAATTTTCTGGGTGCGGGT 60.898 55.000 0.00 0.00 0.00 5.28
1088 1105 1.809869 CAGCTTCTCCGATCGGTCA 59.190 57.895 32.15 17.85 36.47 4.02
1242 1259 6.209391 AGTGTGGAAATCGATGGAAAGAAAAT 59.791 34.615 0.00 0.00 0.00 1.82
1390 1407 6.751514 TCTTAAGCCAGCGAATAAATTCAA 57.248 33.333 0.00 0.00 36.61 2.69
2169 2190 6.590292 GCGCAAACCTATAGCAATAATCTCTA 59.410 38.462 0.30 0.00 0.00 2.43
2808 2878 5.338137 CCAGGGTTATCTCCGAGTTAGTTTT 60.338 44.000 0.00 0.00 0.00 2.43
2818 2888 0.969894 CTAGGCCAGGGTTATCTCCG 59.030 60.000 5.01 0.00 0.00 4.63
2927 2997 5.304686 AGAGAGACAGCATAGCTACTACT 57.695 43.478 0.00 0.00 36.40 2.57
4170 4293 6.628185 CACCGTAGACAATTAGTAAAGGTCT 58.372 40.000 18.31 18.31 41.37 3.85
4445 4571 2.158449 CGCGCTCCAGAATATCCATTTC 59.842 50.000 5.56 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.