Multiple sequence alignment - TraesCS3A01G444200

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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 TraesCS3A01G444200 chr3A 100.000 2743 0 0 1 2743 685955193 685957935 0 5066
1 TraesCS3A01G444200 chr3A 95.435 2125 53 6 1 2109 7292220 7290124 0 3347
2 TraesCS3A01G444200 chr3A 95.256 2129 68 7 1 2101 57977973 57980096 0 3341
3 TraesCS3A01G444200 chr3A 80.201 1293 203 28 2 1270 691598191 691599454 0 920
4 TraesCS3A01G444200 chr3A 79.907 1284 207 21 4 1260 38028779 38027520 0 894
5 TraesCS3A01G444200 chr4D 95.783 2134 61 5 1 2106 387335396 387337528 0 3415
6 TraesCS3A01G444200 chr4D 95.781 640 21 5 2107 2743 415426675 415426039 0 1027
7 TraesCS3A01G444200 chr4D 95.476 641 25 4 2107 2743 396078666 396079306 0 1020
8 TraesCS3A01G444200 chr4D 95.469 640 26 3 2107 2743 467697976 467697337 0 1018
9 TraesCS3A01G444200 chr5D 95.640 2133 64 5 1 2106 554882995 554880865 0 3397
10 TraesCS3A01G444200 chr5D 95.033 2134 68 7 1 2107 8002437 8004559 0 3319
11 TraesCS3A01G444200 chr6D 96.118 2061 64 2 1 2045 273676763 273678823 0 3349
12 TraesCS3A01G444200 chr2A 95.878 2062 68 3 1 2045 668463531 668461470 0 3321
13 TraesCS3A01G444200 chr3D 94.905 1904 68 5 230 2106 461880916 461879015 0 2952
14 TraesCS3A01G444200 chr3D 95.614 1254 41 4 866 2106 578964895 578963643 0 1999
15 TraesCS3A01G444200 chr3D 95.476 641 24 4 2107 2743 561672308 561671669 0 1018
16 TraesCS3A01G444200 chr7D 95.632 641 24 4 2107 2743 549482197 549482837 0 1026
17 TraesCS3A01G444200 chr7D 95.483 642 24 4 2107 2743 552215426 552214785 0 1020
18 TraesCS3A01G444200 chr2D 95.625 640 24 4 2107 2743 430489494 430490132 0 1024
19 TraesCS3A01G444200 chr2D 95.483 642 23 6 2107 2743 572757110 572756470 0 1020
20 TraesCS3A01G444200 chr2D 95.469 640 25 4 2107 2743 35874774 35874136 0 1018
21 TraesCS3A01G444200 chr7B 80.015 1291 210 25 2 1270 728282574 728283838 0 911


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 TraesCS3A01G444200 chr3A 685955193 685957935 2742 False 5066 5066 100.000 1 2743 1 chr3A.!!$F2 2742
1 TraesCS3A01G444200 chr3A 7290124 7292220 2096 True 3347 3347 95.435 1 2109 1 chr3A.!!$R1 2108
2 TraesCS3A01G444200 chr3A 57977973 57980096 2123 False 3341 3341 95.256 1 2101 1 chr3A.!!$F1 2100
3 TraesCS3A01G444200 chr3A 691598191 691599454 1263 False 920 920 80.201 2 1270 1 chr3A.!!$F3 1268
4 TraesCS3A01G444200 chr3A 38027520 38028779 1259 True 894 894 79.907 4 1260 1 chr3A.!!$R2 1256
5 TraesCS3A01G444200 chr4D 387335396 387337528 2132 False 3415 3415 95.783 1 2106 1 chr4D.!!$F1 2105
6 TraesCS3A01G444200 chr4D 415426039 415426675 636 True 1027 1027 95.781 2107 2743 1 chr4D.!!$R1 636
7 TraesCS3A01G444200 chr4D 396078666 396079306 640 False 1020 1020 95.476 2107 2743 1 chr4D.!!$F2 636
8 TraesCS3A01G444200 chr4D 467697337 467697976 639 True 1018 1018 95.469 2107 2743 1 chr4D.!!$R2 636
9 TraesCS3A01G444200 chr5D 554880865 554882995 2130 True 3397 3397 95.640 1 2106 1 chr5D.!!$R1 2105
10 TraesCS3A01G444200 chr5D 8002437 8004559 2122 False 3319 3319 95.033 1 2107 1 chr5D.!!$F1 2106
11 TraesCS3A01G444200 chr6D 273676763 273678823 2060 False 3349 3349 96.118 1 2045 1 chr6D.!!$F1 2044
12 TraesCS3A01G444200 chr2A 668461470 668463531 2061 True 3321 3321 95.878 1 2045 1 chr2A.!!$R1 2044
13 TraesCS3A01G444200 chr3D 461879015 461880916 1901 True 2952 2952 94.905 230 2106 1 chr3D.!!$R1 1876
14 TraesCS3A01G444200 chr3D 578963643 578964895 1252 True 1999 1999 95.614 866 2106 1 chr3D.!!$R3 1240
15 TraesCS3A01G444200 chr3D 561671669 561672308 639 True 1018 1018 95.476 2107 2743 1 chr3D.!!$R2 636
16 TraesCS3A01G444200 chr7D 549482197 549482837 640 False 1026 1026 95.632 2107 2743 1 chr7D.!!$F1 636
17 TraesCS3A01G444200 chr7D 552214785 552215426 641 True 1020 1020 95.483 2107 2743 1 chr7D.!!$R1 636
18 TraesCS3A01G444200 chr2D 430489494 430490132 638 False 1024 1024 95.625 2107 2743 1 chr2D.!!$F1 636
19 TraesCS3A01G444200 chr2D 572756470 572757110 640 True 1020 1020 95.483 2107 2743 1 chr2D.!!$R2 636
20 TraesCS3A01G444200 chr2D 35874136 35874774 638 True 1018 1018 95.469 2107 2743 1 chr2D.!!$R1 636
21 TraesCS3A01G444200 chr7B 728282574 728283838 1264 False 911 911 80.015 2 1270 1 chr7B.!!$F1 1268

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
992 1018 0.179012 GGGTCGTTTGGAAGGGACAA 60.179 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2636 2685 0.035036 TTGGCGTATGGTCGGTTTCA 59.965 50.0 0.0 0.0 0.0 2.69 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
84 85 4.406648 TGTAGTTCATAGTGCTCATGGG 57.593 45.455 0.00 0.00 0.00 4.00
260 262 2.049156 GAAAGCAAAGCGCCCCAC 60.049 61.111 2.29 0.00 44.04 4.61
306 308 6.131264 TGCCCATTCTATTGATCTGATGTTT 58.869 36.000 0.00 0.00 0.00 2.83
450 453 2.027192 GGTGAGGTCTGGCATTACAAGA 60.027 50.000 0.00 0.00 0.00 3.02
457 460 4.418392 GTCTGGCATTACAAGATTTGCTG 58.582 43.478 0.00 0.00 35.46 4.41
522 525 3.715495 ACTGCAGAAGCTATTCAGATCG 58.285 45.455 23.35 0.00 42.74 3.69
622 626 2.089980 GGACAGGAGTAGAACGTGCTA 58.910 52.381 0.00 0.00 0.00 3.49
670 674 4.695993 TGCGGCGAATGGACAGCA 62.696 61.111 12.98 0.00 32.16 4.41
749 774 1.860240 TGAGGAGGCTAGTATCCAGGT 59.140 52.381 15.23 0.00 38.12 4.00
903 929 0.248289 GCCTTGTTGCTTGCATGGAT 59.752 50.000 1.34 0.00 34.29 3.41
992 1018 0.179012 GGGTCGTTTGGAAGGGACAA 60.179 55.000 0.00 0.00 0.00 3.18
1001 1027 5.566627 CGTTTGGAAGGGACAATGCTAAAAT 60.567 40.000 0.00 0.00 0.00 1.82
1028 1054 4.024048 GCGGAGAAACAAGAACTTTGATCA 60.024 41.667 0.00 0.00 0.00 2.92
1074 1100 8.862325 ACATTGTTGAAATAAGATGTGTAGGA 57.138 30.769 0.00 0.00 0.00 2.94
1239 1267 4.769688 TCAGCTTGTGAGAGAAACTTCAA 58.230 39.130 0.00 0.00 0.00 2.69
1505 1533 3.959293 TGCAGATGTTGTGGAAGATGAT 58.041 40.909 0.00 0.00 0.00 2.45
1589 1617 4.447138 AGAAGAACCAATACCACAACCA 57.553 40.909 0.00 0.00 0.00 3.67
1651 1679 1.557371 GCCTAGGAAGAAGTTGCTCCT 59.443 52.381 14.75 7.37 35.64 3.69
1868 1898 8.853077 TGTCTGAAATCTGAATGTATGAACTT 57.147 30.769 0.00 0.00 0.00 2.66
1906 1936 4.597075 TGCCTATATCTGGACCATGCTTTA 59.403 41.667 0.00 0.00 0.00 1.85
2055 2096 7.941795 AATAGCACGCTATTTCGTTTATAGT 57.058 32.000 16.70 0.00 44.18 2.12
2133 2175 8.213518 ACATACACAAATTATCTTAGGCACTG 57.786 34.615 0.00 0.00 41.52 3.66
2184 2226 7.712639 ACGCATTTCACATCTTTCTACATCTAT 59.287 33.333 0.00 0.00 0.00 1.98
2206 2248 3.588396 TGGGAACCTACGAAAGGGTTAAT 59.412 43.478 12.20 0.00 46.28 1.40
2292 2336 1.867233 ACAATCAACAGCTCACACGTC 59.133 47.619 0.00 0.00 0.00 4.34
2423 2468 3.762779 CGTCGTTTTAGTCGGGATTACT 58.237 45.455 0.00 0.00 0.00 2.24
2429 2474 5.006358 CGTTTTAGTCGGGATTACTGGATTG 59.994 44.000 0.00 0.00 0.00 2.67
2568 2617 0.673644 CCCACACATGTTCGGTCCTC 60.674 60.000 0.00 0.00 0.00 3.71
2636 2685 2.111043 CGTGGGACTGCACTTGGT 59.889 61.111 0.00 0.00 0.00 3.67
2688 2739 2.817834 CGCGCGAAAATCCTCCCA 60.818 61.111 28.94 0.00 0.00 4.37
2700 2751 3.966543 CTCCCACCCCACACCCAC 61.967 72.222 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.865119 TGTCAGTCCATGCATCTGTT 57.135 45.000 12.22 0.00 0.00 3.16
84 85 4.825085 TCCACAGAATTAAGAAACACCACC 59.175 41.667 0.00 0.00 0.00 4.61
306 308 5.714333 TGTTTTAAGCTTGCCAATATCCTCA 59.286 36.000 9.86 0.00 0.00 3.86
420 423 2.290577 GCCAGACCTCACCAGATCTTTT 60.291 50.000 0.00 0.00 0.00 2.27
450 453 3.571401 AGTTCAAGTAAGCTGCAGCAAAT 59.429 39.130 38.24 25.68 45.16 2.32
457 460 4.442403 GCTTTTCAAGTTCAAGTAAGCTGC 59.558 41.667 0.00 0.00 35.04 5.25
522 525 4.109877 ACCCATTTCATCCATCTGATCC 57.890 45.455 0.00 0.00 0.00 3.36
622 626 3.006217 GCCAAAGGCTCAAAGAAGTTGAT 59.994 43.478 0.00 0.00 45.27 2.57
670 674 4.584638 TGAAACCCATAGCTGGTACATT 57.415 40.909 0.00 0.00 41.37 2.71
903 929 8.065627 TCCTTCTTACCATCTCTAACCATCTTA 58.934 37.037 0.00 0.00 0.00 2.10
992 1018 2.042686 TCTCCGCTGCATTTTAGCAT 57.957 45.000 0.00 0.00 44.68 3.79
1001 1027 0.944386 GTTCTTGTTTCTCCGCTGCA 59.056 50.000 0.00 0.00 0.00 4.41
1074 1100 5.968254 TGCAACATCTAATTCACATTGCAT 58.032 33.333 4.73 0.00 44.26 3.96
1164 1192 2.681097 GCCAGTACCCTGAGATTTGGTC 60.681 54.545 0.00 0.00 41.50 4.02
1239 1267 6.655078 ACATTCTTACCTGCTGAAAAACAT 57.345 33.333 0.00 0.00 0.00 2.71
1378 1406 6.466812 TCTCTCATTTTGTCATGAAGTAGCA 58.533 36.000 0.00 0.00 32.63 3.49
1505 1533 3.361786 TCCTGTGATCCACTCGTTATCA 58.638 45.455 0.00 0.00 35.11 2.15
1651 1679 4.093408 GCAGCTCATCATCACGAAAAACTA 59.907 41.667 0.00 0.00 0.00 2.24
1725 1754 5.237561 CAGAAGCTCAATCAGAATCAGATGG 59.762 44.000 0.00 0.00 0.00 3.51
1906 1936 8.253113 CCAAGGCTAAAACATTGTTCAGATAAT 58.747 33.333 1.83 0.00 0.00 1.28
1991 2021 9.574458 TTTCACAAAACGTTATTCAGATTTCAA 57.426 25.926 0.00 0.00 0.00 2.69
2133 2175 4.100707 TGTGTAGTGGACGTACTATTGC 57.899 45.455 0.00 0.00 35.75 3.56
2184 2226 1.437397 AACCCTTTCGTAGGTTCCCA 58.563 50.000 5.78 0.00 42.85 4.37
2206 2248 4.357325 AGGAGAGAGAGAGGCAATTTACA 58.643 43.478 0.00 0.00 0.00 2.41
2423 2468 6.374613 CCATCGATACTACTACTAGCAATCCA 59.625 42.308 0.00 0.00 0.00 3.41
2483 2530 7.985184 CCTTTTTCCTTTTAAACTAGGTGCTTT 59.015 33.333 5.95 0.00 33.15 3.51
2636 2685 0.035036 TTGGCGTATGGTCGGTTTCA 59.965 50.000 0.00 0.00 0.00 2.69
2666 2715 3.122323 GGATTTTCGCGCGGTGGA 61.122 61.111 31.69 14.10 0.00 4.02
2688 2739 0.471022 GGAATTTGTGGGTGTGGGGT 60.471 55.000 0.00 0.00 0.00 4.95
2700 2751 3.450457 TGAATCGGATTTGGGGGAATTTG 59.550 43.478 4.47 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.