Multiple sequence alignment - TraesCS4A01G476100

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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 TraesCS4A01G476100 chr4A 100.000 6158 0 0 1 6158 734729401 734735558 0.000000e+00 11372.0
1 TraesCS4A01G476100 chr4A 98.265 5246 59 11 920 6158 736570392 736575612 0.000000e+00 9154.0
2 TraesCS4A01G476100 chr4A 84.594 4005 553 38 1301 5265 735562666 735558686 0.000000e+00 3919.0
3 TraesCS4A01G476100 chr4A 84.968 3905 531 39 1301 5176 735316354 735320231 0.000000e+00 3908.0
4 TraesCS4A01G476100 chr4A 83.664 4187 593 49 1270 5414 736883975 736888112 0.000000e+00 3858.0
5 TraesCS4A01G476100 chr4A 83.273 4149 611 58 1160 5269 736756218 736760322 0.000000e+00 3740.0
6 TraesCS4A01G476100 chr4A 83.281 4115 605 48 1301 5374 734385222 734389294 0.000000e+00 3711.0
7 TraesCS4A01G476100 chr4A 83.309 4080 595 56 1381 5411 736470575 736466533 0.000000e+00 3683.0
8 TraesCS4A01G476100 chr4A 82.778 4198 628 65 1169 5312 734585034 734589190 0.000000e+00 3659.0
9 TraesCS4A01G476100 chr4A 83.139 4039 627 45 1304 5312 735747182 735751196 0.000000e+00 3637.0
10 TraesCS4A01G476100 chr4A 83.417 3799 544 42 1301 5055 736896812 736900568 0.000000e+00 3446.0
11 TraesCS4A01G476100 chr4A 82.805 3536 550 43 1708 5213 735689506 735693013 0.000000e+00 3109.0
12 TraesCS4A01G476100 chr4A 81.562 3547 564 58 1750 5267 735662557 735659072 0.000000e+00 2844.0
13 TraesCS4A01G476100 chr4A 85.318 2629 333 26 1271 3862 735767122 735769734 0.000000e+00 2667.0
14 TraesCS4A01G476100 chr4A 96.897 838 13 4 1 830 736569562 736570394 0.000000e+00 1391.0
15 TraesCS4A01G476100 chr4A 77.989 527 88 17 428 930 736755421 736755943 7.750000e-79 305.0
16 TraesCS4A01G476100 chr4A 77.342 459 81 19 577 1026 734996246 734996690 3.690000e-62 250.0
17 TraesCS4A01G476100 chr4A 79.310 348 56 10 5004 5343 736900568 736900907 4.800000e-56 230.0
18 TraesCS4A01G476100 chr4A 74.050 605 98 38 417 990 736471547 736470971 6.300000e-45 193.0
19 TraesCS4A01G476100 chr7D 96.781 4566 136 6 1594 6158 5486535 5481980 0.000000e+00 7607.0
20 TraesCS4A01G476100 chr7D 83.166 4194 615 64 1169 5312 5649485 5645333 0.000000e+00 3749.0
21 TraesCS4A01G476100 chr7D 95.754 1366 37 8 246 1601 5488048 5486694 0.000000e+00 2182.0
22 TraesCS4A01G476100 chr7D 74.355 620 99 39 417 1003 5449778 5449186 6.250000e-50 209.0
23 TraesCS4A01G476100 chr7D 96.703 91 2 1 101 190 5488135 5488045 3.850000e-32 150.0
24 TraesCS4A01G476100 chr7D 97.531 81 2 0 1 81 5492497 5492417 8.320000e-29 139.0
25 TraesCS4A01G476100 chr7A 83.103 4060 596 56 1301 5312 7045456 7041439 0.000000e+00 3615.0
26 TraesCS4A01G476100 chr7A 75.234 642 110 43 417 1034 6929311 6928695 6.120000e-65 259.0
27 TraesCS4A01G476100 chr2A 95.000 40 2 0 5988 6027 460090937 460090898 5.150000e-06 63.9


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 TraesCS4A01G476100 chr4A 734729401 734735558 6157 False 11372.0 11372 100.000000 1 6158 1 chr4A.!!$F3 6157
1 TraesCS4A01G476100 chr4A 736569562 736575612 6050 False 5272.5 9154 97.581000 1 6158 2 chr4A.!!$F10 6157
2 TraesCS4A01G476100 chr4A 735558686 735562666 3980 True 3919.0 3919 84.594000 1301 5265 1 chr4A.!!$R1 3964
3 TraesCS4A01G476100 chr4A 735316354 735320231 3877 False 3908.0 3908 84.968000 1301 5176 1 chr4A.!!$F5 3875
4 TraesCS4A01G476100 chr4A 736883975 736888112 4137 False 3858.0 3858 83.664000 1270 5414 1 chr4A.!!$F9 4144
5 TraesCS4A01G476100 chr4A 734385222 734389294 4072 False 3711.0 3711 83.281000 1301 5374 1 chr4A.!!$F1 4073
6 TraesCS4A01G476100 chr4A 734585034 734589190 4156 False 3659.0 3659 82.778000 1169 5312 1 chr4A.!!$F2 4143
7 TraesCS4A01G476100 chr4A 735747182 735751196 4014 False 3637.0 3637 83.139000 1304 5312 1 chr4A.!!$F7 4008
8 TraesCS4A01G476100 chr4A 735689506 735693013 3507 False 3109.0 3109 82.805000 1708 5213 1 chr4A.!!$F6 3505
9 TraesCS4A01G476100 chr4A 735659072 735662557 3485 True 2844.0 2844 81.562000 1750 5267 1 chr4A.!!$R2 3517
10 TraesCS4A01G476100 chr4A 735767122 735769734 2612 False 2667.0 2667 85.318000 1271 3862 1 chr4A.!!$F8 2591
11 TraesCS4A01G476100 chr4A 736755421 736760322 4901 False 2022.5 3740 80.631000 428 5269 2 chr4A.!!$F11 4841
12 TraesCS4A01G476100 chr4A 736466533 736471547 5014 True 1938.0 3683 78.679500 417 5411 2 chr4A.!!$R3 4994
13 TraesCS4A01G476100 chr4A 736896812 736900907 4095 False 1838.0 3446 81.363500 1301 5343 2 chr4A.!!$F12 4042
14 TraesCS4A01G476100 chr7D 5645333 5649485 4152 True 3749.0 3749 83.166000 1169 5312 1 chr7D.!!$R3 4143
15 TraesCS4A01G476100 chr7D 5481980 5488135 6155 True 3313.0 7607 96.412667 101 6158 3 chr7D.!!$R4 6057
16 TraesCS4A01G476100 chr7D 5449186 5449778 592 True 209.0 209 74.355000 417 1003 1 chr7D.!!$R1 586
17 TraesCS4A01G476100 chr7A 7041439 7045456 4017 True 3615.0 3615 83.103000 1301 5312 1 chr7A.!!$R2 4011
18 TraesCS4A01G476100 chr7A 6928695 6929311 616 True 259.0 259 75.234000 417 1034 1 chr7A.!!$R1 617

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
923 973 2.044946 ATCTGCCAGCGGGTTTCC 60.045 61.111 4.36 0.0 36.17 3.13 F
926 976 2.597217 TGCCAGCGGGTTTCCTTG 60.597 61.111 4.36 0.0 36.17 3.61 F
2733 3320 0.741221 GAGTGTGGAAGATGTCGGGC 60.741 60.000 0.00 0.0 0.00 6.13 F
3545 4189 3.565482 GCAAGGATGACACAAACTCTGAA 59.435 43.478 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2733 3320 0.539051 ATCTCCTTGAAGCAGTCCCG 59.461 55.000 0.00 0.00 0.00 5.14 R
3545 4189 8.928448 TCTAGAATCTCCAAATGTAAGCTATGT 58.072 33.333 0.00 0.00 0.00 2.29 R
4177 4821 5.559148 AAGAGTGAGTTCATGAAGTCCTT 57.441 39.130 31.19 24.88 39.42 3.36 R
5496 6212 1.002468 GCGCCCATGTTGCATAAGTAG 60.002 52.381 0.00 0.00 0.00 2.57 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
243 245 9.040259 CATCTCTCCCAGGTGATAAATAAGATA 57.960 37.037 0.00 0.00 34.74 1.98
244 246 9.621239 ATCTCTCCCAGGTGATAAATAAGATAA 57.379 33.333 0.00 0.00 0.00 1.75
354 363 8.850156 CCTGCTTAGTTTATGCTACCATTTAAT 58.150 33.333 0.00 0.00 32.85 1.40
505 518 8.540507 TCAGTGAGCTAGACCTTAAAAGATAT 57.459 34.615 0.00 0.00 0.00 1.63
761 807 6.043411 ACAGGCTAGTTTATCTCGTGATTTC 58.957 40.000 5.15 0.00 34.32 2.17
849 898 8.352942 GCACTTTTATCCCTCGATTATCATTTT 58.647 33.333 0.00 0.00 0.00 1.82
871 920 2.083774 TCATGTCATTTTCCACGCTCC 58.916 47.619 0.00 0.00 0.00 4.70
923 973 2.044946 ATCTGCCAGCGGGTTTCC 60.045 61.111 4.36 0.00 36.17 3.13
926 976 2.597217 TGCCAGCGGGTTTCCTTG 60.597 61.111 4.36 0.00 36.17 3.61
2733 3320 0.741221 GAGTGTGGAAGATGTCGGGC 60.741 60.000 0.00 0.00 0.00 6.13
3545 4189 3.565482 GCAAGGATGACACAAACTCTGAA 59.435 43.478 0.00 0.00 0.00 3.02
4177 4821 2.935740 CGCTGCTGACTCCACCAGA 61.936 63.158 0.00 0.00 33.65 3.86
4566 5211 8.593679 ACATGGATCGTATTTTCATATCCTACA 58.406 33.333 0.00 0.00 37.57 2.74
5374 6088 3.137533 GTTCCTTATGCTGGCTCATCTC 58.862 50.000 0.00 0.00 0.00 2.75
5422 6137 2.981302 CTGGTGCTGATCGGTCCA 59.019 61.111 15.98 15.98 0.00 4.02
5427 6142 0.535335 GTGCTGATCGGTCCACCTTA 59.465 55.000 2.89 0.00 0.00 2.69
5436 6152 1.182667 GGTCCACCTTATTGGCCAAC 58.817 55.000 23.27 4.90 40.22 3.77
5483 6199 3.271729 GCCTTAAGAGTTGGAAGCTACC 58.728 50.000 3.36 0.00 0.00 3.18
5515 6231 1.002468 GCTACTTATGCAACATGGGCG 60.002 52.381 0.00 0.00 0.00 6.13
5608 6324 8.560374 AGATAACTGTTGTTTAGCTGTTTTCTC 58.440 33.333 2.69 0.00 34.82 2.87
5713 6429 2.027192 AGCGGTACCATGACTGAACAAT 60.027 45.455 13.54 0.00 0.00 2.71
5816 6532 3.070446 TGTCATCCCAGAGTTTGTTACGT 59.930 43.478 0.00 0.00 0.00 3.57
5855 6571 1.564348 GGCCTAATTGGGAGGTTCTCA 59.436 52.381 12.81 0.00 36.37 3.27
5976 6692 6.262601 GCTAAGTTGTGTGTATGTGTTTGTT 58.737 36.000 0.00 0.00 0.00 2.83
5978 6694 7.274686 GCTAAGTTGTGTGTATGTGTTTGTTTT 59.725 33.333 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 168 7.581213 TGACTGGACTTGTGAATAAACAAAT 57.419 32.000 0.00 0.00 39.47 2.32
243 245 0.771755 GACAAGGGAGGTGGGAGTTT 59.228 55.000 0.00 0.00 0.00 2.66
244 246 1.134438 GGACAAGGGAGGTGGGAGTT 61.134 60.000 0.00 0.00 0.00 3.01
320 322 4.832248 CATAAACTAAGCAGGGACAGTGA 58.168 43.478 0.00 0.00 0.00 3.41
505 518 2.083774 GATCCGATCCAACAACTTGCA 58.916 47.619 0.00 0.00 0.00 4.08
761 807 1.318576 GAAAACCTGTGTGAGTGGGG 58.681 55.000 0.00 0.00 0.00 4.96
849 898 3.057596 GGAGCGTGGAAAATGACATGAAA 60.058 43.478 0.00 0.00 0.00 2.69
871 920 8.776376 ATGGCAAAAACCAAGAATACTATTTG 57.224 30.769 0.00 0.00 44.65 2.32
926 976 8.439286 TGCAACAGAGATTAAAACAAAACAAAC 58.561 29.630 0.00 0.00 0.00 2.93
1231 1396 2.148916 TTGCGTATATGCCTTCGGAG 57.851 50.000 14.32 0.00 0.00 4.63
2699 3286 5.010933 TCCACACTCTTGTTTTGGTTGTAA 58.989 37.500 0.00 0.00 31.66 2.41
2733 3320 0.539051 ATCTCCTTGAAGCAGTCCCG 59.461 55.000 0.00 0.00 0.00 5.14
3545 4189 8.928448 TCTAGAATCTCCAAATGTAAGCTATGT 58.072 33.333 0.00 0.00 0.00 2.29
4177 4821 5.559148 AAGAGTGAGTTCATGAAGTCCTT 57.441 39.130 31.19 24.88 39.42 3.36
5374 6088 8.783093 TGAAGTAGGAAACATAGTTCAATTGTG 58.217 33.333 5.13 0.00 38.83 3.33
5436 6152 3.285838 CCTCGTCATCATGAGGCAG 57.714 57.895 1.57 0.00 46.83 4.85
5496 6212 1.002468 GCGCCCATGTTGCATAAGTAG 60.002 52.381 0.00 0.00 0.00 2.57
5499 6215 1.066257 GGCGCCCATGTTGCATAAG 59.934 57.895 18.11 0.00 0.00 1.73
5608 6324 3.553511 CGCTACTTGCCTCTCATACAAAG 59.446 47.826 0.00 0.00 38.78 2.77
5640 6356 1.537202 GGTAGCACCAGCAAAACAGAG 59.463 52.381 1.01 0.00 45.49 3.35
5790 6506 4.013267 ACAAACTCTGGGATGACAAGAG 57.987 45.455 1.12 1.12 0.00 2.85
5816 6532 1.068417 AACAACACGTAGGCAGCGA 59.932 52.632 7.66 0.00 0.00 4.93
5855 6571 9.920946 AACAAGAGAGAAAGAGAGAGATATACT 57.079 33.333 0.00 0.00 0.00 2.12
5978 6694 8.299570 GTCATATGCCTTTTCTCTTGAGAAAAA 58.700 33.333 27.67 18.89 44.15 1.94


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

AutoCloner maintained by Alex Coulton.