Multiple sequence alignment - TraesCS2B01G438700

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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 TraesCS2B01G438700 chr2B 100.000 3679 0 0 1 3679 631108901 631112579 0 6794
1 TraesCS2B01G438700 chr2B 94.985 3310 134 12 1 3301 143951156 143947870 0 5164
2 TraesCS2B01G438700 chr2B 92.435 965 47 5 2351 3292 245759998 245760959 0 1354
3 TraesCS2B01G438700 chr2B 94.118 867 36 5 2445 3301 56028544 56027683 0 1304
4 TraesCS2B01G438700 chr5B 94.894 3310 160 4 1 3301 379360930 379357621 0 5168
5 TraesCS2B01G438700 chr5B 92.462 849 43 10 2445 3292 579533337 579534165 0 1194
6 TraesCS2B01G438700 chr3B 96.000 2900 109 4 1 2898 678016329 678013435 0 4706
7 TraesCS2B01G438700 chr3B 95.877 2886 110 4 1 2879 708112608 708109725 0 4662
8 TraesCS2B01G438700 chr7B 95.598 2885 121 1 1 2879 400951596 400948712 0 4619
9 TraesCS2B01G438700 chr7B 96.817 2702 86 0 1 2702 468863748 468861047 0 4514
10 TraesCS2B01G438700 chr7B 93.425 2905 165 12 1 2888 687966962 687969857 0 4283
11 TraesCS2B01G438700 chr7B 92.308 858 48 11 2445 3301 580866655 580865815 0 1203
12 TraesCS2B01G438700 chr7B 92.191 858 49 8 2445 3301 248271517 248270677 0 1197
13 TraesCS2B01G438700 chr7B 97.716 394 9 0 3286 3679 546887941 546888334 0 678
14 TraesCS2B01G438700 chr7B 97.716 394 9 0 3286 3679 580865666 580865273 0 678
15 TraesCS2B01G438700 chr7B 97.716 394 9 0 3286 3679 708524678 708524285 0 678
16 TraesCS2B01G438700 chr1B 95.788 2754 106 5 1 2747 115288960 115291710 0 4434
17 TraesCS2B01G438700 chr6A 91.968 2988 206 17 2 2969 157442763 157445736 0 4157
18 TraesCS2B01G438700 chr2A 93.273 550 31 2 2753 3301 608888952 608888408 0 806
19 TraesCS2B01G438700 chr2A 97.716 394 9 0 3286 3679 738426798 738427191 0 678
20 TraesCS2B01G438700 chr4A 97.716 394 9 0 3286 3679 446476038 446476431 0 678
21 TraesCS2B01G438700 chrUn 97.704 392 9 0 3286 3677 304155391 304155000 0 675
22 TraesCS2B01G438700 chrUn 97.462 394 10 0 3286 3679 297867688 297868081 0 673
23 TraesCS2B01G438700 chr3A 97.704 392 9 0 3286 3677 489210619 489210228 0 675
24 TraesCS2B01G438700 chr7A 97.462 394 10 0 3286 3679 105260012 105259619 0 673


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 TraesCS2B01G438700 chr2B 631108901 631112579 3678 False 6794.0 6794 100.000 1 3679 1 chr2B.!!$F2 3678
1 TraesCS2B01G438700 chr2B 143947870 143951156 3286 True 5164.0 5164 94.985 1 3301 1 chr2B.!!$R2 3300
2 TraesCS2B01G438700 chr2B 245759998 245760959 961 False 1354.0 1354 92.435 2351 3292 1 chr2B.!!$F1 941
3 TraesCS2B01G438700 chr2B 56027683 56028544 861 True 1304.0 1304 94.118 2445 3301 1 chr2B.!!$R1 856
4 TraesCS2B01G438700 chr5B 379357621 379360930 3309 True 5168.0 5168 94.894 1 3301 1 chr5B.!!$R1 3300
5 TraesCS2B01G438700 chr5B 579533337 579534165 828 False 1194.0 1194 92.462 2445 3292 1 chr5B.!!$F1 847
6 TraesCS2B01G438700 chr3B 678013435 678016329 2894 True 4706.0 4706 96.000 1 2898 1 chr3B.!!$R1 2897
7 TraesCS2B01G438700 chr3B 708109725 708112608 2883 True 4662.0 4662 95.877 1 2879 1 chr3B.!!$R2 2878
8 TraesCS2B01G438700 chr7B 400948712 400951596 2884 True 4619.0 4619 95.598 1 2879 1 chr7B.!!$R2 2878
9 TraesCS2B01G438700 chr7B 468861047 468863748 2701 True 4514.0 4514 96.817 1 2702 1 chr7B.!!$R3 2701
10 TraesCS2B01G438700 chr7B 687966962 687969857 2895 False 4283.0 4283 93.425 1 2888 1 chr7B.!!$F2 2887
11 TraesCS2B01G438700 chr7B 248270677 248271517 840 True 1197.0 1197 92.191 2445 3301 1 chr7B.!!$R1 856
12 TraesCS2B01G438700 chr7B 580865273 580866655 1382 True 940.5 1203 95.012 2445 3679 2 chr7B.!!$R5 1234
13 TraesCS2B01G438700 chr1B 115288960 115291710 2750 False 4434.0 4434 95.788 1 2747 1 chr1B.!!$F1 2746
14 TraesCS2B01G438700 chr6A 157442763 157445736 2973 False 4157.0 4157 91.968 2 2969 1 chr6A.!!$F1 2967
15 TraesCS2B01G438700 chr2A 608888408 608888952 544 True 806.0 806 93.273 2753 3301 1 chr2A.!!$R1 548

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
648 651 0.392998 GAACGCTCCATGGATGTGGT 60.393 55.0 16.63 14.5 40.27 4.16 F
1462 1466 0.677731 CCACGCAGGTTGGACATGAT 60.678 55.0 0.00 0.0 30.30 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 2067 0.620556 ATTCAGGATCACGGCAACCT 59.379 50.0 0.00 0.0 0.0 3.50 R
2830 2874 0.320374 TACAGTGCAGCGCCTAACTT 59.680 50.0 2.29 0.0 0.0 2.66 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
133 135 2.683768 GTATCATGGGGTCTCTGGTCT 58.316 52.381 0.00 0.00 0.00 3.85
234 237 1.374252 ACGCCGAATCTGAACGCTT 60.374 52.632 0.00 0.00 0.00 4.68
281 284 1.377202 GAGGCCGGAAATGCACAGA 60.377 57.895 5.05 0.00 0.00 3.41
300 303 1.762957 GATTCCATCTTCGGACTGGGA 59.237 52.381 1.80 0.00 33.75 4.37
431 434 4.337145 CTCTTATCGGTATGGCTCCTACT 58.663 47.826 0.00 0.00 0.00 2.57
487 490 5.371176 AGAAGAAGAAGAGGGAAAGGAAAGT 59.629 40.000 0.00 0.00 0.00 2.66
648 651 0.392998 GAACGCTCCATGGATGTGGT 60.393 55.000 16.63 14.50 40.27 4.16
663 666 1.098712 GTGGTTGAAGGCGTTGACCA 61.099 55.000 16.03 16.03 38.01 4.02
1224 1228 2.109126 GCCTCAACCCGATGTGCTC 61.109 63.158 0.00 0.00 0.00 4.26
1462 1466 0.677731 CCACGCAGGTTGGACATGAT 60.678 55.000 0.00 0.00 30.30 2.45
1743 1747 1.995626 GGGCAAGGAGTCCCTGCTA 60.996 63.158 27.83 0.00 43.48 3.49
1761 1765 6.070995 CCCTGCTATTCCGGTGATTAACTATA 60.071 42.308 0.00 0.00 0.00 1.31
1808 1812 1.994779 CCCGTTGACCGTATTACACAC 59.005 52.381 0.00 0.00 33.66 3.82
1818 1822 4.989797 ACCGTATTACACACGTTTGAATGA 59.010 37.500 9.03 0.00 37.71 2.57
1843 1847 6.820656 ACTAACGCATTCATTCTTTCTCATCT 59.179 34.615 0.00 0.00 0.00 2.90
2127 2132 0.178888 TGGTACACCATCAGACCCCA 60.179 55.000 0.00 0.00 42.01 4.96
2393 2398 4.439057 GCCCAACGACTATGACAATAGAA 58.561 43.478 0.00 0.00 38.49 2.10
2838 2882 2.571757 GGCGCCCAAAAGTTAGGC 59.428 61.111 18.11 2.16 43.53 3.93
2842 2886 1.212751 GCCCAAAAGTTAGGCGCTG 59.787 57.895 7.64 0.00 36.84 5.18
2886 2965 0.669318 GTTAGGCGCTGCACTGTACA 60.669 55.000 7.64 0.00 0.00 2.90
2915 3029 1.001641 CTGCCCTTAGGTGCTGCTT 60.002 57.895 11.78 0.00 34.57 3.91
2933 3048 2.146342 CTTAACTGCCATGGCTATCCG 58.854 52.381 35.53 20.33 42.51 4.18
3291 3571 1.523934 CGAGCCTTTGCAAGCTTTTTG 59.476 47.619 13.77 2.72 40.11 2.44
3301 3581 6.389830 TTGCAAGCTTTTTGACATCTTCTA 57.610 33.333 0.00 0.00 0.00 2.10
3322 3602 5.893824 TCTAGCACTTCAAGATCTATCCACA 59.106 40.000 0.00 0.00 0.00 4.17
3351 3631 0.760567 TGCATAGAGGAGGCGGTGAT 60.761 55.000 0.00 0.00 37.80 3.06
3394 3674 4.880886 TGTTGACACACATTTGAGAGTG 57.119 40.909 0.00 0.00 41.40 3.51
3419 3699 4.771590 TTTTACTTCTCGAGCTTACCGA 57.228 40.909 7.81 0.00 34.61 4.69
3449 3729 3.259876 TCATAGGCGTTAGTTGGAAGTGT 59.740 43.478 0.00 0.00 0.00 3.55
3513 3793 1.001520 TCCGTCCATGCTTTCTTTCGA 59.998 47.619 0.00 0.00 0.00 3.71
3555 3835 2.297033 GCAAACATCTCCACACCAACAT 59.703 45.455 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 6.723977 AGGGCATGTAAATTTCAACTAAAGGA 59.276 34.615 0.00 0.00 0.00 3.36
133 135 1.667236 CTCATCGTAAGGCATGGCAA 58.333 50.000 22.64 6.11 38.47 4.52
234 237 1.367471 CAAGAGCGGACACCAGTGA 59.633 57.895 4.48 0.00 0.00 3.41
281 284 1.879575 TCCCAGTCCGAAGATGGAAT 58.120 50.000 0.00 0.00 40.44 3.01
431 434 1.117994 CTACATCAGCCTCAGCCTCA 58.882 55.000 0.00 0.00 41.25 3.86
487 490 0.669318 CGTGAAAGCAACTCCGGCTA 60.669 55.000 0.00 0.00 41.66 3.93
580 583 2.912967 CTCGACACAACGTACCACATAC 59.087 50.000 0.00 0.00 34.70 2.39
648 651 2.151202 GAAGATGGTCAACGCCTTCAA 58.849 47.619 0.00 0.00 35.76 2.69
663 666 4.063689 CAGCTCCATTTGCTATCGAAGAT 58.936 43.478 0.00 0.00 39.34 2.40
1224 1228 0.244994 CCAGAGATCCTTATCCCGCG 59.755 60.000 0.00 0.00 31.98 6.46
1459 1463 4.380531 CTTTATCTTCCGCTGCCTTATCA 58.619 43.478 0.00 0.00 0.00 2.15
1462 1466 2.769663 TCCTTTATCTTCCGCTGCCTTA 59.230 45.455 0.00 0.00 0.00 2.69
1743 1747 9.720769 CTTTACCATATAGTTAATCACCGGAAT 57.279 33.333 9.46 0.00 0.00 3.01
1818 1822 6.820656 AGATGAGAAAGAATGAATGCGTTAGT 59.179 34.615 0.00 0.00 0.00 2.24
1843 1847 3.525268 TCTTGATCTTGATGCGCTACA 57.475 42.857 9.73 5.92 0.00 2.74
1902 1906 1.080569 CATTGCCAGTTCCAACCGC 60.081 57.895 0.00 0.00 0.00 5.68
2063 2067 0.620556 ATTCAGGATCACGGCAACCT 59.379 50.000 0.00 0.00 0.00 3.50
2830 2874 0.320374 TACAGTGCAGCGCCTAACTT 59.680 50.000 2.29 0.00 0.00 2.66
2838 2882 1.560004 CCACACAGTACAGTGCAGCG 61.560 60.000 17.43 4.86 43.23 5.18
2842 2886 2.954753 GCGCCACACAGTACAGTGC 61.955 63.158 17.43 3.94 43.23 4.40
2915 3029 0.396435 CCGGATAGCCATGGCAGTTA 59.604 55.000 37.18 21.91 44.88 2.24
3105 3220 4.406003 GGTGAACTATCTTCTAGGGCAAGA 59.594 45.833 0.00 0.00 34.37 3.02
3291 3571 6.572519 AGATCTTGAAGTGCTAGAAGATGTC 58.427 40.000 6.79 0.00 35.71 3.06
3301 3581 5.129980 TCATGTGGATAGATCTTGAAGTGCT 59.870 40.000 0.00 0.00 0.00 4.40
3322 3602 4.202305 GCCTCCTCTATGCAAGTACTTCAT 60.202 45.833 18.35 18.35 0.00 2.57
3351 3631 9.979270 CAACACTAACAACAAATTTTTATGCAA 57.021 25.926 0.00 0.00 0.00 4.08
3394 3674 5.004535 CGGTAAGCTCGAGAAGTAAAATGTC 59.995 44.000 18.75 0.00 0.00 3.06
3419 3699 2.504175 ACTAACGCCTATGACCAACCAT 59.496 45.455 0.00 0.00 0.00 3.55
3449 3729 4.617530 GCCCGAACTATGCTTATGATCGTA 60.618 45.833 0.00 0.00 0.00 3.43
3555 3835 4.635769 GATGTCAACATCCCGCCA 57.364 55.556 11.31 0.00 45.24 5.69


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

AutoCloner maintained by Alex Coulton.