Multiple sequence alignment - TraesCS4A01G343900

Loading Multiple Alignment...

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 TraesCS4A01G343900 chr4A 100.000 4219 0 0 1 4219 623953202 623948984 0.000000e+00 7792.0
1 TraesCS4A01G343900 chr4A 82.166 1228 179 27 1178 2386 623988985 623987779 0.000000e+00 1018.0
2 TraesCS4A01G343900 chr4A 85.890 489 63 2 2700 3182 623970792 623970304 2.250000e-142 516.0
3 TraesCS4A01G343900 chr4A 90.870 230 18 2 2700 2927 182239942 182239714 5.300000e-79 305.0
4 TraesCS4A01G343900 chr4A 94.444 144 7 1 1033 1175 623991050 623990907 1.970000e-53 220.0
5 TraesCS4A01G343900 chr1A 98.178 4226 56 4 1 4219 569950701 569946490 0.000000e+00 7358.0
6 TraesCS4A01G343900 chr1A 82.062 1232 182 23 1178 2391 570028866 570027656 0.000000e+00 1014.0
7 TraesCS4A01G343900 chr1A 86.322 329 42 1 2857 3182 570009038 570008710 5.190000e-94 355.0
8 TraesCS4A01G343900 chr1A 89.041 146 8 4 1030 1175 570030385 570030248 1.560000e-39 174.0
9 TraesCS4A01G343900 chr1A 89.041 146 8 4 1030 1175 570081063 570080926 1.560000e-39 174.0
10 TraesCS4A01G343900 chr1A 89.041 146 8 4 1030 1175 570092121 570091984 1.560000e-39 174.0
11 TraesCS4A01G343900 chr5D 93.645 1778 84 11 882 2639 545523444 545525212 0.000000e+00 2630.0
12 TraesCS4A01G343900 chr5D 90.000 780 71 6 112 889 545521444 545522218 0.000000e+00 1002.0
13 TraesCS4A01G343900 chr5D 95.382 498 23 0 2806 3303 545525442 545525939 0.000000e+00 793.0
14 TraesCS4A01G343900 chr5D 81.078 835 118 23 1824 2639 545398750 545399563 7.700000e-177 630.0
15 TraesCS4A01G343900 chr5D 85.745 470 63 2 2712 3177 545401323 545401792 1.050000e-135 494.0
16 TraesCS4A01G343900 chr5D 94.366 142 7 1 3904 4045 360747304 360747444 2.550000e-52 217.0
17 TraesCS4A01G343900 chr5D 92.453 53 4 0 4100 4152 545448415 545448467 4.520000e-10 76.8
18 TraesCS4A01G343900 chr5D 90.566 53 5 0 4100 4152 545410779 545410831 2.100000e-08 71.3
19 TraesCS4A01G343900 chr2D 77.911 1254 226 34 1015 2230 589237710 589238950 0.000000e+00 734.0
20 TraesCS4A01G343900 chr2D 77.869 122 23 3 1518 1635 577536714 577536835 5.850000e-09 73.1
21 TraesCS4A01G343900 chr2D 93.617 47 3 0 1589 1635 577581346 577581300 2.100000e-08 71.3
22 TraesCS4A01G343900 chr2B 77.691 1282 233 36 981 2221 712825166 712826435 0.000000e+00 734.0
23 TraesCS4A01G343900 chr2B 94.340 53 3 0 1584 1636 695508723 695508775 9.720000e-12 82.4
24 TraesCS4A01G343900 chr2B 86.667 60 8 0 1593 1652 695379413 695379354 2.720000e-07 67.6
25 TraesCS4A01G343900 chr2A 84.301 465 56 6 2716 3177 707305414 707304964 5.010000e-119 438.0
26 TraesCS4A01G343900 chr2A 93.617 141 8 1 3904 4044 50059015 50059154 4.270000e-50 209.0
27 TraesCS4A01G343900 chr2A 92.308 52 4 0 1584 1635 715917402 715917351 1.630000e-09 75.0
28 TraesCS4A01G343900 chr2A 93.617 47 3 0 1589 1635 715950644 715950598 2.100000e-08 71.3
29 TraesCS4A01G343900 chr5A 83.153 463 59 7 2716 3177 420345994 420345550 5.080000e-109 405.0
30 TraesCS4A01G343900 chr7D 85.811 296 40 2 2795 3089 61953532 61953238 3.170000e-81 313.0
31 TraesCS4A01G343900 chr4D 79.540 435 87 2 65 499 49306853 49307285 4.100000e-80 309.0
32 TraesCS4A01G343900 chr6D 89.130 230 22 2 2700 2927 374633584 374633812 2.480000e-72 283.0
33 TraesCS4A01G343900 chr3B 95.775 142 5 1 3904 4045 616891562 616891702 1.180000e-55 228.0
34 TraesCS4A01G343900 chr7B 95.745 141 5 1 3904 4044 640260785 640260924 4.240000e-55 226.0
35 TraesCS4A01G343900 chr3A 95.745 141 5 1 3904 4044 41614332 41614471 4.240000e-55 226.0
36 TraesCS4A01G343900 chr3A 91.083 157 12 2 3896 4052 510009046 510009200 1.190000e-50 211.0
37 TraesCS4A01G343900 chr1D 94.366 142 7 1 3904 4045 334233677 334233817 2.550000e-52 217.0
38 TraesCS4A01G343900 chr1B 93.617 141 8 1 3904 4044 27237907 27238046 4.270000e-50 209.0
39 TraesCS4A01G343900 chrUn 89.041 146 8 4 1030 1175 1658554 1658417 1.560000e-39 174.0
40 TraesCS4A01G343900 chr3D 81.884 138 21 4 251 387 485354494 485354628 3.450000e-21 113.0


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 TraesCS4A01G343900 chr4A 623948984 623953202 4218 True 7792 7792 100.0000 1 4219 1 chr4A.!!$R2 4218
1 TraesCS4A01G343900 chr4A 623987779 623991050 3271 True 619 1018 88.3050 1033 2386 2 chr4A.!!$R4 1353
2 TraesCS4A01G343900 chr1A 569946490 569950701 4211 True 7358 7358 98.1780 1 4219 1 chr1A.!!$R1 4218
3 TraesCS4A01G343900 chr1A 570027656 570030385 2729 True 594 1014 85.5515 1030 2391 2 chr1A.!!$R5 1361
4 TraesCS4A01G343900 chr5D 545521444 545525939 4495 False 1475 2630 93.0090 112 3303 3 chr5D.!!$F5 3191
5 TraesCS4A01G343900 chr5D 545398750 545401792 3042 False 562 630 83.4115 1824 3177 2 chr5D.!!$F4 1353
6 TraesCS4A01G343900 chr2D 589237710 589238950 1240 False 734 734 77.9110 1015 2230 1 chr2D.!!$F2 1215
7 TraesCS4A01G343900 chr2B 712825166 712826435 1269 False 734 734 77.6910 981 2221 1 chr2B.!!$F2 1240

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
184 185 0.546122 GTACATGGGGTCATCCTGCA 59.454 55.0 0.00 0.0 35.33 4.41 F
313 314 1.450531 GGGCATTGAGATCAAGCGGG 61.451 60.0 1.32 0.0 39.47 6.13 F
1804 5077 1.064825 AACCGGAGTTGGGTGAATCT 58.935 50.0 9.46 0.0 37.96 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 4957 0.251916 TCCAGTAAACGAGCCCATGG 59.748 55.000 4.14 4.14 0.00 3.66 R
2994 8085 3.798206 GCGATTCTGCTGATAAGAGAGCA 60.798 47.826 0.00 0.00 42.94 4.26 R
4035 9126 0.179032 TTCGAAGACAAAGGCCAGCA 60.179 50.000 5.01 0.00 34.32 4.41 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 2.027625 GTCTTCGCCTTGGTGGTCG 61.028 63.158 0.00 0.00 38.35 4.79
89 90 2.258726 GGGTGTCTTGGTTGCGACC 61.259 63.158 17.01 17.01 46.71 4.79
162 163 4.408921 ACCATCTCCTCCATGAAATCGTTA 59.591 41.667 0.00 0.00 0.00 3.18
184 185 0.546122 GTACATGGGGTCATCCTGCA 59.454 55.000 0.00 0.00 35.33 4.41
224 225 3.322541 TCAAATAGGATGCGGGTATCGAA 59.677 43.478 0.00 0.00 42.43 3.71
313 314 1.450531 GGGCATTGAGATCAAGCGGG 61.451 60.000 1.32 0.00 39.47 6.13
364 365 1.964373 AATTTCCGCACGAGCCGTT 60.964 52.632 0.00 0.00 38.32 4.44
671 672 2.816087 AGTGCGCATCATCTTTGACTTT 59.184 40.909 15.91 0.00 33.85 2.66
675 676 4.229096 GCGCATCATCTTTGACTTTTTCA 58.771 39.130 0.30 0.00 33.85 2.69
712 713 2.707849 CCACGACTAGGACGGTGGG 61.708 68.421 14.15 9.45 32.67 4.61
799 805 1.646912 TAGTGGGAATGGACGGACAA 58.353 50.000 0.00 0.00 0.00 3.18
1804 5077 1.064825 AACCGGAGTTGGGTGAATCT 58.935 50.000 9.46 0.00 37.96 2.40
3428 8519 3.548745 TGAATGTAGCCATCACTCCAG 57.451 47.619 0.00 0.00 0.00 3.86
3633 8724 4.091365 GCCTGTTGTGTGTTTTTGTTTCTC 59.909 41.667 0.00 0.00 0.00 2.87
3936 9027 1.070445 CCATCCCATCTGCTCCGAC 59.930 63.158 0.00 0.00 0.00 4.79
4001 9092 2.516460 TAGAGGCTCGTCCGCTCC 60.516 66.667 9.22 0.00 41.47 4.70
4019 9110 3.151022 GGAGCGGAGTGGAGGGAG 61.151 72.222 0.00 0.00 0.00 4.30
4020 9111 3.844090 GAGCGGAGTGGAGGGAGC 61.844 72.222 0.00 0.00 0.00 4.70
4024 9115 3.151022 GGAGTGGAGGGAGCGGAG 61.151 72.222 0.00 0.00 0.00 4.63
4115 9206 8.462589 TGCAATAGAATGCTATATTTGGACAA 57.537 30.769 0.00 0.00 46.54 3.18
4154 9245 1.399791 GGATTTGGAGCAAAGAGAGCG 59.600 52.381 0.00 0.00 36.76 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 0.600255 CCCACGACCAAGACACTCAC 60.600 60.000 0.00 0.00 0.00 3.51
89 90 3.849145 CGACGAGACTCAAAGCTAAGAAG 59.151 47.826 2.82 0.00 0.00 2.85
162 163 2.639839 GCAGGATGACCCCATGTACTAT 59.360 50.000 0.00 0.00 39.69 2.12
184 185 0.687354 GATGGTATGCCGACCCTGAT 59.313 55.000 0.00 0.00 38.89 2.90
224 225 3.224007 ATCCCCACGGCCAGCTTTT 62.224 57.895 2.24 0.00 0.00 2.27
313 314 1.292541 GGTCGTCTCTGTGGTTCCC 59.707 63.158 0.00 0.00 0.00 3.97
352 353 3.777925 CTTGGAACGGCTCGTGCG 61.778 66.667 3.02 1.83 39.99 5.34
364 365 1.887956 GCTTCTCCATGTTGCCTTGGA 60.888 52.381 0.00 0.00 41.31 3.53
397 398 1.143073 GGAACCTTCCTGGACACAACT 59.857 52.381 0.00 0.00 44.11 3.16
603 604 1.971357 TCGGAGAAAGAAGAAGCCACT 59.029 47.619 0.00 0.00 0.00 4.00
712 713 2.810403 GTCGACCATACCCGACCC 59.190 66.667 3.51 0.00 46.54 4.46
799 805 5.163457 GCTCTAATGTTGTCCTCTTCTAGCT 60.163 44.000 0.00 0.00 0.00 3.32
1545 4809 2.007113 TACACGCACACAGACCACGT 62.007 55.000 0.00 0.00 37.47 4.49
1684 4957 0.251916 TCCAGTAAACGAGCCCATGG 59.748 55.000 4.14 4.14 0.00 3.66
2994 8085 3.798206 GCGATTCTGCTGATAAGAGAGCA 60.798 47.826 0.00 0.00 42.94 4.26
3312 8403 6.741992 TGAAGTATCAACCATTGCTAACTG 57.258 37.500 0.00 0.00 30.99 3.16
3428 8519 4.644103 ATTGACCAACTATTCATGCTGC 57.356 40.909 0.00 0.00 0.00 5.25
3633 8724 8.553459 AAAACATAAGTACCATCAGAGTGAAG 57.447 34.615 0.00 0.00 0.00 3.02
3852 8943 5.125417 ACCACGTAAAAATTGCTATGCTGAT 59.875 36.000 0.00 0.00 0.00 2.90
3936 9027 2.125912 CTCCACAACTCCGCGGAG 60.126 66.667 45.26 45.26 46.91 4.63
4011 9102 3.347590 TCCTCTCCGCTCCCTCCA 61.348 66.667 0.00 0.00 0.00 3.86
4012 9103 2.520741 CTCCTCTCCGCTCCCTCC 60.521 72.222 0.00 0.00 0.00 4.30
4013 9104 3.223589 GCTCCTCTCCGCTCCCTC 61.224 72.222 0.00 0.00 0.00 4.30
4014 9105 4.851214 GGCTCCTCTCCGCTCCCT 62.851 72.222 0.00 0.00 0.00 4.20
4017 9108 2.494530 ATTCGGCTCCTCTCCGCTC 61.495 63.158 0.00 0.00 46.05 5.03
4018 9109 2.443016 ATTCGGCTCCTCTCCGCT 60.443 61.111 0.00 0.00 46.05 5.52
4019 9110 2.279784 CATTCGGCTCCTCTCCGC 60.280 66.667 0.00 0.00 46.05 5.54
4035 9126 0.179032 TTCGAAGACAAAGGCCAGCA 60.179 50.000 5.01 0.00 34.32 4.41
4038 9129 4.253685 CTCTATTTCGAAGACAAAGGCCA 58.746 43.478 5.01 0.00 34.32 5.36
4131 9222 3.871463 GCTCTCTTTGCTCCAAATCCTCA 60.871 47.826 0.00 0.00 32.70 3.86


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

AutoCloner maintained by Alex Coulton.