Multiple sequence alignment - TraesCS4D01G334900

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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 TraesCS4D01G334900 chr4D 100.000 5043 0 0 1 5043 492815610 492810568 0.000000e+00 9313.0
1 TraesCS4D01G334900 chr4D 85.388 1225 128 34 635 1827 491949929 491948724 0.000000e+00 1223.0
2 TraesCS4D01G334900 chr4D 85.166 1173 131 28 679 1827 493757338 493758491 0.000000e+00 1162.0
3 TraesCS4D01G334900 chr4D 84.802 658 65 22 1 635 491952499 491951854 3.310000e-176 628.0
4 TraesCS4D01G334900 chr4D 86.881 404 40 8 243 635 493738585 493738986 1.670000e-119 440.0
5 TraesCS4D01G334900 chr4D 84.483 232 24 12 2182 2405 238760936 238761163 8.500000e-53 219.0
6 TraesCS4D01G334900 chr5A 97.693 5072 62 19 1 5043 672510416 672505371 0.000000e+00 8667.0
7 TraesCS4D01G334900 chr5A 88.235 680 69 11 679 1354 672823767 672823095 0.000000e+00 802.0
8 TraesCS4D01G334900 chr5A 80.805 646 73 34 11 635 672827199 672826584 4.600000e-125 459.0
9 TraesCS4D01G334900 chr5A 86.957 230 26 4 3654 3880 533267823 533268051 6.480000e-64 255.0
10 TraesCS4D01G334900 chr4B 97.515 3260 53 13 231 3471 631070503 631073753 0.000000e+00 5546.0
11 TraesCS4D01G334900 chr4B 90.737 1004 38 18 3557 4558 631073752 631074702 0.000000e+00 1288.0
12 TraesCS4D01G334900 chr4B 84.352 1227 142 35 635 1827 631529170 631527960 0.000000e+00 1157.0
13 TraesCS4D01G334900 chr4B 86.420 405 40 10 243 635 631531301 631530900 3.610000e-116 429.0
14 TraesCS4D01G334900 chr4B 100.000 70 0 0 1 70 631070405 631070474 4.100000e-26 130.0
15 TraesCS4D01G334900 chrUn 93.846 195 7 3 4737 4926 76650981 76650787 6.390000e-74 289.0
16 TraesCS4D01G334900 chrUn 94.565 92 4 1 4952 5043 76650801 76650711 1.890000e-29 141.0
17 TraesCS4D01G334900 chr7A 88.415 164 18 1 3664 3827 689390611 689390773 3.980000e-46 196.0
18 TraesCS4D01G334900 chr2A 79.153 307 46 16 2116 2410 209848868 209848568 3.980000e-46 196.0
19 TraesCS4D01G334900 chr2A 79.085 306 42 17 2116 2407 513641080 513641377 1.850000e-44 191.0
20 TraesCS4D01G334900 chr1A 79.016 305 48 14 2116 2409 155490912 155490613 1.430000e-45 195.0
21 TraesCS4D01G334900 chr1A 79.016 305 47 15 2114 2409 194634502 194634798 5.150000e-45 193.0
22 TraesCS4D01G334900 chr3A 78.758 306 48 15 2116 2410 219503715 219504014 6.670000e-44 189.0
23 TraesCS4D01G334900 chr3A 80.488 164 20 11 1545 1702 42366546 42366389 1.150000e-21 115.0
24 TraesCS4D01G334900 chr6B 78.878 303 44 18 2116 2405 663997726 663997431 2.400000e-43 187.0
25 TraesCS4D01G334900 chr1B 80.973 226 26 11 3655 3878 35473652 35473862 4.040000e-36 163.0
26 TraesCS4D01G334900 chr3D 82.550 149 12 12 1545 1687 30429280 30429420 8.870000e-23 119.0
27 TraesCS4D01G334900 chr3D 80.488 164 19 10 1545 1702 30675091 30674935 4.130000e-21 113.0
28 TraesCS4D01G334900 chr3B 80.488 164 20 11 1545 1702 53354856 53354699 1.150000e-21 115.0
29 TraesCS4D01G334900 chr3B 81.879 149 14 12 1545 1687 53217722 53217581 4.130000e-21 113.0
30 TraesCS4D01G334900 chr5D 74.265 272 55 14 779 1039 437808996 437808729 3.210000e-17 100.0
31 TraesCS4D01G334900 chr5D 73.381 278 59 13 778 1044 437696064 437696337 6.950000e-14 89.8
32 TraesCS4D01G334900 chr5B 87.879 66 6 2 767 831 342873395 342873459 5.410000e-10 76.8


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 TraesCS4D01G334900 chr4D 492810568 492815610 5042 True 9313.000000 9313 100.000 1 5043 1 chr4D.!!$R1 5042
1 TraesCS4D01G334900 chr4D 493757338 493758491 1153 False 1162.000000 1162 85.166 679 1827 1 chr4D.!!$F3 1148
2 TraesCS4D01G334900 chr4D 491948724 491952499 3775 True 925.500000 1223 85.095 1 1827 2 chr4D.!!$R2 1826
3 TraesCS4D01G334900 chr5A 672505371 672510416 5045 True 8667.000000 8667 97.693 1 5043 1 chr5A.!!$R1 5042
4 TraesCS4D01G334900 chr5A 672823095 672827199 4104 True 630.500000 802 84.520 11 1354 2 chr5A.!!$R2 1343
5 TraesCS4D01G334900 chr4B 631070405 631074702 4297 False 2321.333333 5546 96.084 1 4558 3 chr4B.!!$F1 4557
6 TraesCS4D01G334900 chr4B 631527960 631531301 3341 True 793.000000 1157 85.386 243 1827 2 chr4B.!!$R1 1584

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
43 48 5.772672 TCTCAGCTAGTTTCTCACTCTCTTT 59.227 40.000 0.0 0.0 36.88 2.52 F
1783 4864 4.383850 TGGTTTCTGTTCCAACAACATG 57.616 40.909 0.0 0.0 38.66 3.21 F
2455 5551 5.676811 AGGGGGAGTAATGTTGATAAGGAAT 59.323 40.000 0.0 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 4959 3.413846 AGCTGCAGATCAGAACTTGAA 57.586 42.857 20.43 0.0 45.72 2.69 R
3357 6461 4.202357 CCAGATTGAATTATCGGTGGAGGA 60.202 45.833 0.00 0.0 0.00 3.71 R
4356 7467 0.179051 GAGGGAGATGGCTTCAGCAG 60.179 60.000 0.30 0.0 44.36 4.24 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
43 48 5.772672 TCTCAGCTAGTTTCTCACTCTCTTT 59.227 40.000 0.00 0.00 36.88 2.52
44 49 6.266558 TCTCAGCTAGTTTCTCACTCTCTTTT 59.733 38.462 0.00 0.00 36.88 2.27
1106 4167 6.010219 ACACTGGTTTAACCTTATCATTGCT 58.990 36.000 15.68 0.00 39.58 3.91
1783 4864 4.383850 TGGTTTCTGTTCCAACAACATG 57.616 40.909 0.00 0.00 38.66 3.21
2455 5551 5.676811 AGGGGGAGTAATGTTGATAAGGAAT 59.323 40.000 0.00 0.00 0.00 3.01
3608 6712 5.413309 TTGGACCATTTCTTTGTTTGTGT 57.587 34.783 0.00 0.00 0.00 3.72
3775 6883 6.741992 ACTTTGACGAATTCTGAATATGCA 57.258 33.333 2.85 0.00 0.00 3.96
3915 7025 3.536158 TGTTTCTTAGCACGCATGTTC 57.464 42.857 0.00 0.00 0.00 3.18
3982 7092 2.027653 TGTTCACGAGGGTGCATATGAA 60.028 45.455 6.97 0.00 44.03 2.57
3983 7093 2.602257 TCACGAGGGTGCATATGAAG 57.398 50.000 6.97 0.00 44.03 3.02
4114 7224 1.171308 ATGAGTGTTGTGCCTGCATC 58.829 50.000 0.00 0.00 0.00 3.91
4341 7452 6.513180 TCAAATAGTGTCGAGATGATAACCC 58.487 40.000 0.00 0.00 0.00 4.11
4457 7568 2.969238 GCGCACTGTGAGCTGTGT 60.969 61.111 25.93 0.00 43.60 3.72
4493 7604 2.287977 AGGAACCCCTGCACTTTAAC 57.712 50.000 0.00 0.00 42.42 2.01
4505 7616 5.029650 TGCACTTTAACTAAATGTCGCAG 57.970 39.130 0.00 0.00 0.00 5.18
4509 7620 6.635239 GCACTTTAACTAAATGTCGCAGAAAA 59.365 34.615 0.00 0.00 39.69 2.29
4560 7672 5.048013 GCTAATTCCCCTAATTCCCAAATCG 60.048 44.000 0.00 0.00 38.71 3.34
4581 7693 6.049955 TCGTGAAATGAAATCCCTAACTCT 57.950 37.500 0.00 0.00 0.00 3.24
4596 7708 0.963856 ACTCTATCCACACGACGGCA 60.964 55.000 0.00 0.00 0.00 5.69
4598 7710 0.963856 TCTATCCACACGACGGCAGT 60.964 55.000 0.00 0.00 0.00 4.40
4761 7876 5.637006 TGCAGTTTACTGTTTGAACAAGT 57.363 34.783 11.23 2.14 45.45 3.16
4775 7890 5.229921 TGAACAAGTTGAACAGCTTACAC 57.770 39.130 10.54 0.73 30.55 2.90
4776 7891 4.697828 TGAACAAGTTGAACAGCTTACACA 59.302 37.500 10.54 2.84 30.55 3.72
4777 7892 4.882671 ACAAGTTGAACAGCTTACACAG 57.117 40.909 10.54 0.00 30.55 3.66
4999 8118 6.851330 GCACTACACAACACTCATCTTTTAAC 59.149 38.462 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 48 7.057894 ACATCAAACACCTCAACTAACCTAAA 58.942 34.615 0.00 0.00 0.00 1.85
44 49 6.597562 ACATCAAACACCTCAACTAACCTAA 58.402 36.000 0.00 0.00 0.00 2.69
1783 4864 4.044426 GTGGAAAATTGTGAAGACTGTGC 58.956 43.478 0.00 0.00 0.00 4.57
1876 4959 3.413846 AGCTGCAGATCAGAACTTGAA 57.586 42.857 20.43 0.00 45.72 2.69
2093 5176 6.433093 GCCTTAAATTTCCTAGACTTGTTCCA 59.567 38.462 0.00 0.00 0.00 3.53
3355 6459 4.656112 AGATTGAATTATCGGTGGAGGAGT 59.344 41.667 0.00 0.00 0.00 3.85
3356 6460 4.993584 CAGATTGAATTATCGGTGGAGGAG 59.006 45.833 0.00 0.00 0.00 3.69
3357 6461 4.202357 CCAGATTGAATTATCGGTGGAGGA 60.202 45.833 0.00 0.00 0.00 3.71
3608 6712 5.188434 CAAATAGGGTGCAAGATTCTCTCA 58.812 41.667 0.00 0.00 0.00 3.27
3775 6883 9.715121 ATGTTGTTTCTTCATGAAATTTAGCAT 57.285 25.926 9.88 6.31 45.19 3.79
3915 7025 5.586243 TGAAGACAAACTTTGAGGAGTTCTG 59.414 40.000 8.55 0.00 38.86 3.02
3982 7092 0.468226 TGAAGTTTCTGCACCCGACT 59.532 50.000 0.00 0.00 0.00 4.18
3983 7093 1.197721 CATGAAGTTTCTGCACCCGAC 59.802 52.381 0.00 0.00 0.00 4.79
4114 7224 2.030091 CAGTGCTTGCAGACATGTATCG 59.970 50.000 0.00 0.00 0.00 2.92
4241 7352 5.130975 ACCCTCTTCATACATTAGCATGTCA 59.869 40.000 0.00 0.00 43.06 3.58
4356 7467 0.179051 GAGGGAGATGGCTTCAGCAG 60.179 60.000 0.30 0.00 44.36 4.24
4457 7568 4.097286 GGTTCCTTGTAAAAAGACAGCACA 59.903 41.667 0.00 0.00 0.00 4.57
4493 7604 3.081804 AGGGGTTTTCTGCGACATTTAG 58.918 45.455 0.00 0.00 0.00 1.85
4505 7616 6.329460 AGGGATATACACTTCTAGGGGTTTTC 59.671 42.308 0.00 0.00 0.00 2.29
4509 7620 4.675550 AGAGGGATATACACTTCTAGGGGT 59.324 45.833 0.00 0.00 29.26 4.95
4560 7672 7.993183 TGGATAGAGTTAGGGATTTCATTTCAC 59.007 37.037 0.00 0.00 0.00 3.18
4581 7693 1.214325 CACTGCCGTCGTGTGGATA 59.786 57.895 0.00 0.00 0.00 2.59
4596 7708 4.778143 GATTCCACCGCCGCCACT 62.778 66.667 0.00 0.00 0.00 4.00
4598 7710 3.969250 GAAGATTCCACCGCCGCCA 62.969 63.158 0.00 0.00 0.00 5.69
4604 7716 2.622436 GAACCTGAGAAGATTCCACCG 58.378 52.381 0.00 0.00 0.00 4.94
4605 7717 2.028020 ACGAACCTGAGAAGATTCCACC 60.028 50.000 0.00 0.00 0.00 4.61
4606 7718 3.254892 GACGAACCTGAGAAGATTCCAC 58.745 50.000 0.00 0.00 0.00 4.02
4607 7719 2.094700 CGACGAACCTGAGAAGATTCCA 60.095 50.000 0.00 0.00 0.00 3.53
4608 7720 2.094649 ACGACGAACCTGAGAAGATTCC 60.095 50.000 0.00 0.00 0.00 3.01
4609 7721 3.219052 ACGACGAACCTGAGAAGATTC 57.781 47.619 0.00 0.00 0.00 2.52
4654 7766 1.377333 CCTTTTGGCCTCCTCGTCC 60.377 63.158 3.32 0.00 0.00 4.79
4668 7780 1.862602 GACAAATGACGCCGGCCTTT 61.863 55.000 23.46 12.70 0.00 3.11
4761 7876 2.872245 GCAGTCTGTGTAAGCTGTTCAA 59.128 45.455 0.93 0.00 34.45 2.69
4909 8028 9.692749 CTTTGCATTCTTATATCATTGCATTCT 57.307 29.630 0.00 0.00 39.56 2.40
4910 8029 9.687210 TCTTTGCATTCTTATATCATTGCATTC 57.313 29.630 0.00 0.00 39.56 2.67
4999 8118 3.508793 GCATTCTGATATCATGTTGGGGG 59.491 47.826 5.72 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.