Multiple sequence alignment - TraesCS3A01G532100

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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 TraesCS3A01G532100 chr3A 100.000 6088 0 0 1 6088 745084611 745078524 0.000000e+00 11243.0
1 TraesCS3A01G532100 chr3A 99.228 6089 44 3 1 6088 745197814 745191728 0.000000e+00 10981.0
2 TraesCS3A01G532100 chr3A 99.151 3532 25 4 2560 6088 745015244 745011715 0.000000e+00 6351.0
3 TraesCS3A01G532100 chr3A 98.426 2923 40 5 2560 5478 744942317 744939397 0.000000e+00 5138.0
4 TraesCS3A01G532100 chr3A 98.283 2562 43 1 1 2562 744944904 744942344 0.000000e+00 4486.0
5 TraesCS3A01G532100 chr3A 97.972 2564 49 2 1 2562 745017833 745015271 0.000000e+00 4444.0
6 TraesCS3A01G532100 chr3A 83.254 2299 327 31 3819 6081 745298950 745296674 0.000000e+00 2060.0
7 TraesCS3A01G532100 chr3A 91.386 1068 74 13 895 1959 744978218 744977166 0.000000e+00 1447.0
8 TraesCS3A01G532100 chr3A 91.292 1068 75 13 895 1959 745064495 745063443 0.000000e+00 1441.0
9 TraesCS3A01G532100 chr3A 90.513 896 79 4 1 895 744979143 744978253 0.000000e+00 1179.0
10 TraesCS3A01G532100 chr3A 90.402 896 80 4 1 895 745065420 745064530 0.000000e+00 1173.0
11 TraesCS3A01G532100 chr3A 90.290 896 81 4 1 895 744912922 744912032 0.000000e+00 1168.0
12 TraesCS3A01G532100 chr3A 93.548 403 22 4 1558 1959 744911840 744911441 1.130000e-166 597.0
13 TraesCS3A01G532100 chr3A 89.286 448 42 4 1 447 744986945 744986503 1.920000e-154 556.0
14 TraesCS3A01G532100 chr3A 93.519 216 13 1 3294 3508 745299444 745299229 2.740000e-83 320.0
15 TraesCS3A01G532100 chr3A 91.083 157 12 1 895 1049 744911997 744911841 1.720000e-50 211.0
16 TraesCS3A01G532100 chr3D 84.837 2295 241 62 1272 3505 610631482 610629234 0.000000e+00 2211.0
17 TraesCS3A01G532100 chr3D 86.934 1944 231 18 4158 6087 610628384 610626450 0.000000e+00 2161.0
18 TraesCS3A01G532100 chr3D 81.048 1488 235 26 3908 5380 610668064 610666609 0.000000e+00 1142.0
19 TraesCS3A01G532100 chr3D 82.509 869 137 11 4472 5333 610685057 610684197 0.000000e+00 749.0
20 TraesCS3A01G532100 chr3D 83.788 623 81 16 2668 3282 610686816 610686206 1.900000e-159 573.0
21 TraesCS3A01G532100 chr3D 84.906 530 72 7 2674 3195 610561562 610561033 4.180000e-146 529.0
22 TraesCS3A01G532100 chr3D 83.130 575 80 13 3610 4169 610629026 610628454 5.440000e-140 508.0
23 TraesCS3A01G532100 chr3D 81.331 616 88 10 1548 2144 610689677 610689070 5.520000e-130 475.0
24 TraesCS3A01G532100 chr3D 80.296 609 104 8 3828 4427 610685653 610685052 4.330000e-121 446.0
25 TraesCS3A01G532100 chr3D 89.200 250 23 2 3281 3526 610686169 610685920 5.930000e-80 309.0
26 TraesCS3A01G532100 chr3D 84.588 279 35 8 2288 2562 610602346 610602072 2.800000e-68 270.0
27 TraesCS3A01G532100 chr3D 93.478 92 5 1 3520 3610 610629176 610629085 1.060000e-27 135.0
28 TraesCS3A01G532100 chr3B 87.139 1524 186 6 3804 5325 828254311 828252796 0.000000e+00 1720.0
29 TraesCS3A01G532100 chr3B 82.554 1519 214 20 3825 5323 828293470 828291983 0.000000e+00 1290.0
30 TraesCS3A01G532100 chr3B 87.486 895 69 22 2647 3508 828256818 828255934 0.000000e+00 992.0
31 TraesCS3A01G532100 chr3B 80.678 1180 188 17 3825 4989 828332453 828331299 0.000000e+00 880.0
32 TraesCS3A01G532100 chr3B 84.307 873 91 27 2681 3508 828294554 828293683 0.000000e+00 811.0
33 TraesCS3A01G532100 chr3B 86.074 596 70 10 2692 3278 828333538 828332947 4.010000e-176 628.0
34 TraesCS3A01G532100 chr3B 83.923 622 77 17 5464 6068 828330983 828330368 1.900000e-159 573.0
35 TraesCS3A01G532100 chr3B 83.412 633 87 12 5468 6086 828287155 828286527 6.850000e-159 571.0
36 TraesCS3A01G532100 chr3B 84.602 591 71 13 1259 1842 828258609 828258032 2.460000e-158 569.0
37 TraesCS3A01G532100 chr3B 90.046 432 29 8 1828 2246 828166935 828166505 1.150000e-151 547.0
38 TraesCS3A01G532100 chr3B 84.956 565 56 16 1898 2443 828258013 828257459 4.150000e-151 545.0
39 TraesCS3A01G532100 chr3B 92.095 253 13 3 3281 3526 828332905 828332653 3.490000e-92 350.0
40 TraesCS3A01G532100 chr3B 93.617 94 5 1 2469 2562 828257188 828257096 8.230000e-29 139.0
41 TraesCS3A01G532100 chr3B 80.000 105 16 3 991 1092 549843521 549843419 8.460000e-09 73.1
42 TraesCS3A01G532100 chrUn 98.795 415 5 0 1535 1949 477225523 477225109 0.000000e+00 739.0
43 TraesCS3A01G532100 chrUn 81.250 160 22 5 1213 1365 331996743 331996901 8.290000e-24 122.0
44 TraesCS3A01G532100 chr1B 76.898 303 50 13 600 884 82555789 82556089 2.940000e-33 154.0
45 TraesCS3A01G532100 chr2D 75.850 294 47 18 613 887 4008067 4008355 1.780000e-25 128.0
46 TraesCS3A01G532100 chr5A 79.781 183 27 7 1198 1372 275654947 275655127 2.300000e-24 124.0
47 TraesCS3A01G532100 chr5A 80.702 171 20 5 1204 1365 546412456 546412622 2.980000e-23 121.0
48 TraesCS3A01G532100 chr4A 82.301 113 14 3 985 1094 359447942 359448051 6.500000e-15 93.5
49 TraesCS3A01G532100 chr7B 86.486 74 9 1 989 1061 71655624 71655697 5.060000e-11 80.5
50 TraesCS3A01G532100 chr7D 91.837 49 3 1 3734 3781 19418740 19418692 3.940000e-07 67.6
51 TraesCS3A01G532100 chr5B 82.278 79 13 1 613 691 547079136 547079059 3.940000e-07 67.6
52 TraesCS3A01G532100 chr5B 100.000 30 0 0 1154 1183 6961355 6961384 8.520000e-04 56.5
53 TraesCS3A01G532100 chr1D 100.000 28 0 0 4221 4248 146195502 146195529 1.100000e-02 52.8


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 TraesCS3A01G532100 chr3A 745078524 745084611 6087 True 11243.000000 11243 100.000000 1 6088 1 chr3A.!!$R2 6087
1 TraesCS3A01G532100 chr3A 745191728 745197814 6086 True 10981.000000 10981 99.228000 1 6088 1 chr3A.!!$R3 6087
2 TraesCS3A01G532100 chr3A 745011715 745017833 6118 True 5397.500000 6351 98.561500 1 6088 2 chr3A.!!$R7 6087
3 TraesCS3A01G532100 chr3A 744939397 744944904 5507 True 4812.000000 5138 98.354500 1 5478 2 chr3A.!!$R5 5477
4 TraesCS3A01G532100 chr3A 744977166 744979143 1977 True 1313.000000 1447 90.949500 1 1959 2 chr3A.!!$R6 1958
5 TraesCS3A01G532100 chr3A 745063443 745065420 1977 True 1307.000000 1441 90.847000 1 1959 2 chr3A.!!$R8 1958
6 TraesCS3A01G532100 chr3A 745296674 745299444 2770 True 1190.000000 2060 88.386500 3294 6081 2 chr3A.!!$R9 2787
7 TraesCS3A01G532100 chr3A 744911441 744912922 1481 True 658.666667 1168 91.640333 1 1959 3 chr3A.!!$R4 1958
8 TraesCS3A01G532100 chr3D 610626450 610631482 5032 True 1253.750000 2211 87.094750 1272 6087 4 chr3D.!!$R4 4815
9 TraesCS3A01G532100 chr3D 610666609 610668064 1455 True 1142.000000 1142 81.048000 3908 5380 1 chr3D.!!$R3 1472
10 TraesCS3A01G532100 chr3D 610561033 610561562 529 True 529.000000 529 84.906000 2674 3195 1 chr3D.!!$R1 521
11 TraesCS3A01G532100 chr3D 610684197 610689677 5480 True 510.400000 749 83.424800 1548 5333 5 chr3D.!!$R5 3785
12 TraesCS3A01G532100 chr3B 828291983 828294554 2571 True 1050.500000 1290 83.430500 2681 5323 2 chr3B.!!$R5 2642
13 TraesCS3A01G532100 chr3B 828252796 828258609 5813 True 793.000000 1720 87.560000 1259 5325 5 chr3B.!!$R4 4066
14 TraesCS3A01G532100 chr3B 828330368 828333538 3170 True 607.750000 880 85.692500 2692 6068 4 chr3B.!!$R6 3376
15 TraesCS3A01G532100 chr3B 828286527 828287155 628 True 571.000000 571 83.412000 5468 6086 1 chr3B.!!$R3 618

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
117 118 0.747255 AGAAGTGTCTGTGCAGTCGT 59.253 50.000 0.0 0.0 30.83 4.34 F
432 434 1.501741 CGGGAATGTCGGTTTGCAG 59.498 57.895 0.0 0.0 0.00 4.41 F
2200 3766 2.339556 GGTTGCTAACATGCCGGCA 61.340 57.895 34.8 34.8 0.00 5.69 F
2668 4721 0.320508 AGGTCGCTCGGGAGAAAAAC 60.321 55.000 0.0 0.0 39.18 2.43 F
4681 8324 3.114616 CGACAGCCAGTTCAGCGG 61.115 66.667 0.0 0.0 34.64 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1061 1100 2.064014 GACTAACCTCGGTCCAAAACG 58.936 52.381 0.00 0.0 0.00 3.60 R
1519 1562 2.713111 AAACTGGGGAGGGCCAGAGA 62.713 60.000 6.18 0.0 37.48 3.10 R
4681 8324 2.143925 GGTTAGCTGGGTCGAATATGC 58.856 52.381 0.00 0.0 0.00 3.14 R
4811 8454 4.338879 AGCTATTCTGTGCTTCCAACAAT 58.661 39.130 0.00 0.0 35.86 2.71 R
5589 9249 1.349688 TGAAATGGTACCTCAGCCGTT 59.650 47.619 14.36 0.0 35.67 4.44 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
117 118 0.747255 AGAAGTGTCTGTGCAGTCGT 59.253 50.000 0.00 0.0 30.83 4.34
193 195 4.317698 CGTAGAGGATGAAGACGTACGTAC 60.318 50.000 22.87 15.9 0.00 3.67
432 434 1.501741 CGGGAATGTCGGTTTGCAG 59.498 57.895 0.00 0.0 0.00 4.41
2200 3766 2.339556 GGTTGCTAACATGCCGGCA 61.340 57.895 34.80 34.8 0.00 5.69
2668 4721 0.320508 AGGTCGCTCGGGAGAAAAAC 60.321 55.000 0.00 0.0 39.18 2.43
4681 8324 3.114616 CGACAGCCAGTTCAGCGG 61.115 66.667 0.00 0.0 34.64 5.52
4811 8454 1.570857 ATGGGAACGGGATGGAGCAA 61.571 55.000 0.00 0.0 0.00 3.91
5589 9249 2.957006 GCCGGGATTCTACTGTTAGAGA 59.043 50.000 2.18 0.0 35.67 3.10
5808 9477 2.249844 TTTCCCCTTCTTGTCACGTC 57.750 50.000 0.00 0.0 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 6.000219 ACTACTTCGTCTACTCTAACAACCA 59.000 40.000 0.00 0.00 0.00 3.67
432 434 4.097361 GGCCCTCTTCACCGTCCC 62.097 72.222 0.00 0.00 0.00 4.46
1061 1100 2.064014 GACTAACCTCGGTCCAAAACG 58.936 52.381 0.00 0.00 0.00 3.60
1519 1562 2.713111 AAACTGGGGAGGGCCAGAGA 62.713 60.000 6.18 0.00 37.48 3.10
2668 4721 4.944962 TCACAGCGATTTCCAGTATTTG 57.055 40.909 0.00 0.00 0.00 2.32
2947 5007 6.664428 AAATGGTACTAGCAATTTGGTTGT 57.336 33.333 17.27 17.27 40.07 3.32
4681 8324 2.143925 GGTTAGCTGGGTCGAATATGC 58.856 52.381 0.00 0.00 0.00 3.14
4811 8454 4.338879 AGCTATTCTGTGCTTCCAACAAT 58.661 39.130 0.00 0.00 35.86 2.71
5589 9249 1.349688 TGAAATGGTACCTCAGCCGTT 59.650 47.619 14.36 0.00 35.67 4.44
5808 9477 4.394300 CCTTGCACAAGACTAAGATGAAGG 59.606 45.833 11.94 0.00 40.79 3.46


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

AutoCloner maintained by Alex Coulton.