Multiple sequence alignment - TraesCS5A01G000200

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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 TraesCS5A01G000200 chr5A 100.000 4738 0 0 1 4738 20018 24755 0.000000e+00 8750.0
1 TraesCS5A01G000200 chr5A 97.959 98 2 0 872 969 557663738 557663835 2.270000e-38 171.0
2 TraesCS5A01G000200 chr5A 91.176 102 3 2 3978 4073 619456725 619456624 2.970000e-27 134.0
3 TraesCS5A01G000200 chr5A 84.106 151 8 5 526 661 540932509 540932658 1.070000e-26 132.0
4 TraesCS5A01G000200 chr5A 86.029 136 4 4 526 646 557663257 557663392 1.070000e-26 132.0
5 TraesCS5A01G000200 chr5A 90.722 97 4 1 3977 4068 607575768 607575672 1.790000e-24 124.0
6 TraesCS5A01G000200 chr5B 99.439 2495 14 0 1 2495 1748685 1751179 0.000000e+00 4530.0
7 TraesCS5A01G000200 chr5B 98.537 2255 22 3 2484 4738 1751344 1753587 0.000000e+00 3971.0
8 TraesCS5A01G000200 chr5D 91.156 2024 113 26 2153 4126 556934 554927 0.000000e+00 2686.0
9 TraesCS5A01G000200 chr5D 95.380 1342 41 10 790 2114 558260 556923 0.000000e+00 2115.0
10 TraesCS5A01G000200 chr5D 77.632 456 60 24 212 657 558758 558335 6.130000e-59 239.0
11 TraesCS5A01G000200 chr5D 90.000 100 4 3 3978 4071 319101180 319101279 1.790000e-24 124.0
12 TraesCS5A01G000200 chr1B 98.361 427 5 2 4314 4738 143613514 143613940 0.000000e+00 749.0
13 TraesCS5A01G000200 chr1B 96.135 207 7 1 4339 4544 14466246 14466452 2.110000e-88 337.0
14 TraesCS5A01G000200 chr1B 91.346 104 4 1 4640 4738 14466614 14466717 2.300000e-28 137.0
15 TraesCS5A01G000200 chr1B 88.571 105 5 3 3977 4074 610973268 610973164 2.320000e-23 121.0
16 TraesCS5A01G000200 chr1A 85.560 464 29 19 4302 4738 203148868 203149320 7.230000e-123 451.0
17 TraesCS5A01G000200 chr1A 92.683 246 5 6 4302 4547 203141022 203141254 4.540000e-90 342.0
18 TraesCS5A01G000200 chr1A 95.767 189 8 0 4550 4738 203141286 203141474 5.960000e-79 305.0
19 TraesCS5A01G000200 chr1A 93.717 191 12 0 4548 4738 109419388 109419198 2.160000e-73 287.0
20 TraesCS5A01G000200 chr1A 95.789 95 4 0 4548 4642 111991570 111991476 2.280000e-33 154.0
21 TraesCS5A01G000200 chr3B 90.909 297 14 6 682 969 185526452 185526744 2.070000e-103 387.0
22 TraesCS5A01G000200 chr3B 90.909 297 14 7 682 969 826121035 826121327 2.070000e-103 387.0
23 TraesCS5A01G000200 chr3B 95.714 210 8 1 4339 4547 41797340 41797131 2.110000e-88 337.0
24 TraesCS5A01G000200 chr3B 94.836 213 8 2 4338 4547 86133487 86133275 3.530000e-86 329.0
25 TraesCS5A01G000200 chr3B 91.584 202 6 6 779 969 172152526 172152325 7.820000e-68 268.0
26 TraesCS5A01G000200 chr3B 81.424 323 26 11 659 959 550395387 550395077 2.850000e-57 233.0
27 TraesCS5A01G000200 chr3B 83.173 208 14 5 394 592 172152888 172152693 2.270000e-38 171.0
28 TraesCS5A01G000200 chr3A 90.667 300 13 7 681 969 511223073 511223368 7.440000e-103 385.0
29 TraesCS5A01G000200 chr3A 94.330 194 10 1 4545 4738 263962444 263962636 3.590000e-76 296.0
30 TraesCS5A01G000200 chr3A 92.632 95 5 1 3978 4072 163799440 163799348 8.270000e-28 135.0
31 TraesCS5A01G000200 chr3A 84.106 151 8 5 526 661 511222850 511222999 1.070000e-26 132.0
32 TraesCS5A01G000200 chr6B 90.572 297 15 7 682 969 525982271 525981979 9.620000e-102 381.0
33 TraesCS5A01G000200 chr6B 81.618 408 38 18 587 959 115216752 115216347 2.140000e-78 303.0
34 TraesCS5A01G000200 chr4A 89.333 300 17 7 681 969 517572449 517572154 3.490000e-96 363.0
35 TraesCS5A01G000200 chr4A 85.294 136 5 7 526 646 517572672 517572537 4.980000e-25 126.0
36 TraesCS5A01G000200 chr4A 94.286 35 1 1 496 530 700241259 700241292 9.000000e-03 52.8
37 TraesCS5A01G000200 chr6A 97.156 211 6 0 4337 4547 200805063 200805273 1.620000e-94 357.0
38 TraesCS5A01G000200 chr6A 86.012 336 20 10 657 969 49438168 49437837 7.600000e-88 335.0
39 TraesCS5A01G000200 chr6A 94.211 190 11 0 4545 4734 200805302 200805491 1.670000e-74 291.0
40 TraesCS5A01G000200 chr6A 87.838 148 4 7 526 661 49438353 49438208 1.360000e-35 161.0
41 TraesCS5A01G000200 chr7A 88.816 304 15 7 681 969 187794954 187794655 5.830000e-94 355.0
42 TraesCS5A01G000200 chr7A 87.697 317 16 10 666 969 721556686 721556992 9.760000e-92 348.0
43 TraesCS5A01G000200 chr7A 84.106 151 8 5 526 661 721556484 721556633 1.070000e-26 132.0
44 TraesCS5A01G000200 chr7A 82.993 147 10 5 526 657 187795167 187795021 8.330000e-23 119.0
45 TraesCS5A01G000200 chr7A 89.691 97 4 4 3978 4068 441514106 441514010 8.330000e-23 119.0
46 TraesCS5A01G000200 chr7B 96.618 207 7 0 4338 4544 192098343 192098549 1.260000e-90 344.0
47 TraesCS5A01G000200 chr7B 95.146 103 5 0 4185 4287 453316542 453316644 3.790000e-36 163.0
48 TraesCS5A01G000200 chr7B 94.231 104 6 0 4185 4288 42026926 42026823 4.910000e-35 159.0
49 TraesCS5A01G000200 chr7B 90.385 104 5 1 4640 4738 192098709 192098812 1.070000e-26 132.0
50 TraesCS5A01G000200 chr4D 96.135 207 7 1 4338 4544 72667187 72666982 2.110000e-88 337.0
51 TraesCS5A01G000200 chr4D 93.269 104 7 0 4185 4288 392514810 392514707 2.280000e-33 154.0
52 TraesCS5A01G000200 chr2B 82.045 401 41 17 587 959 496456272 496455875 3.560000e-81 313.0
53 TraesCS5A01G000200 chr2B 81.538 260 31 8 260 517 496456761 496456517 1.040000e-46 198.0
54 TraesCS5A01G000200 chr3D 95.146 103 5 0 4185 4287 549062354 549062456 3.790000e-36 163.0
55 TraesCS5A01G000200 chr3D 93.578 109 6 1 4184 4292 614914923 614915030 1.360000e-35 161.0
56 TraesCS5A01G000200 chr3D 94.231 104 5 1 4184 4287 96440116 96440218 1.770000e-34 158.0
57 TraesCS5A01G000200 chr2D 94.231 104 6 0 4185 4288 629474331 629474434 4.910000e-35 159.0
58 TraesCS5A01G000200 chr1D 93.396 106 7 0 4185 4290 334232703 334232598 1.770000e-34 158.0
59 TraesCS5A01G000200 chr2A 94.845 97 5 0 4545 4641 398874306 398874402 8.210000e-33 152.0
60 TraesCS5A01G000200 chrUn 90.000 100 4 2 3975 4068 42259706 42259805 1.790000e-24 124.0


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 TraesCS5A01G000200 chr5A 20018 24755 4737 False 8750.0 8750 100.0000 1 4738 1 chr5A.!!$F1 4737
1 TraesCS5A01G000200 chr5B 1748685 1753587 4902 False 4250.5 4530 98.9880 1 4738 2 chr5B.!!$F1 4737
2 TraesCS5A01G000200 chr5D 554927 558758 3831 True 1680.0 2686 88.0560 212 4126 3 chr5D.!!$R1 3914
3 TraesCS5A01G000200 chr3B 172152325 172152888 563 True 219.5 268 87.3785 394 969 2 chr3B.!!$R4 575
4 TraesCS5A01G000200 chr3A 511222850 511223368 518 False 258.5 385 87.3865 526 969 2 chr3A.!!$F2 443
5 TraesCS5A01G000200 chr4A 517572154 517572672 518 True 244.5 363 87.3135 526 969 2 chr4A.!!$R1 443
6 TraesCS5A01G000200 chr6A 49437837 49438353 516 True 248.0 335 86.9250 526 969 2 chr6A.!!$R1 443
7 TraesCS5A01G000200 chr7A 721556484 721556992 508 False 240.0 348 85.9015 526 969 2 chr7A.!!$F1 443
8 TraesCS5A01G000200 chr7A 187794655 187795167 512 True 237.0 355 85.9045 526 969 2 chr7A.!!$R2 443
9 TraesCS5A01G000200 chr2B 496455875 496456761 886 True 255.5 313 81.7915 260 959 2 chr2B.!!$R1 699

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
209 210 1.028905 GGAGAGATCAGTCGAGTGGG 58.971 60.000 19.86 0.0 0.00 4.61 F
734 1112 1.076332 GGCTGTAACTAGTGGCAACG 58.924 55.000 0.00 0.0 42.51 4.10 F
2151 2562 6.071840 GGACATACATACCAGTCTCATACTCC 60.072 46.154 0.00 0.0 35.76 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2562 9.726232 CAACTAAGTCACAATATCAATTCATGG 57.274 33.333 0.00 0.0 0.00 3.66 R
3135 3727 1.332065 GTCGTGATCAGATCGAGCTCA 59.668 52.381 15.40 0.0 34.33 4.26 R
3914 4527 3.111853 TCACCTGAAACTACTGCTGTG 57.888 47.619 6.48 0.0 0.00 3.66 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
112 113 4.885907 ACTCGAATTCAAATGCATCTGGAT 59.114 37.500 0.00 0.0 0.00 3.41
209 210 1.028905 GGAGAGATCAGTCGAGTGGG 58.971 60.000 19.86 0.0 0.00 4.61
734 1112 1.076332 GGCTGTAACTAGTGGCAACG 58.924 55.000 0.00 0.0 42.51 4.10
2151 2562 6.071840 GGACATACATACCAGTCTCATACTCC 60.072 46.154 0.00 0.0 35.76 3.85
3135 3727 1.003233 GCGCCTTCTTGACCTCCTT 60.003 57.895 0.00 0.0 0.00 3.36
3914 4527 1.670967 CCCGACCGACAGAGTTTTACC 60.671 57.143 0.00 0.0 0.00 2.85
4193 4822 5.303259 TGTATGGCTGCATGGAATTACTA 57.697 39.130 0.50 0.0 0.00 1.82
4199 4828 4.191544 GCTGCATGGAATTACTAGTCACA 58.808 43.478 0.00 0.0 0.00 3.58
4200 4829 4.272018 GCTGCATGGAATTACTAGTCACAG 59.728 45.833 0.00 0.0 0.00 3.66
4201 4830 5.664457 CTGCATGGAATTACTAGTCACAGA 58.336 41.667 0.00 0.0 0.00 3.41
4202 4831 6.048732 TGCATGGAATTACTAGTCACAGAA 57.951 37.500 0.00 0.0 0.00 3.02
4203 4832 6.472016 TGCATGGAATTACTAGTCACAGAAA 58.528 36.000 0.00 0.0 0.00 2.52
4204 4833 7.112122 TGCATGGAATTACTAGTCACAGAAAT 58.888 34.615 0.00 0.0 0.00 2.17
4205 4834 7.066163 TGCATGGAATTACTAGTCACAGAAATG 59.934 37.037 0.00 0.0 0.00 2.32
4206 4835 7.467811 GCATGGAATTACTAGTCACAGAAATGG 60.468 40.741 0.00 0.0 0.00 3.16
4207 4836 7.252612 TGGAATTACTAGTCACAGAAATGGA 57.747 36.000 0.00 0.0 0.00 3.41
4215 4844 7.495901 ACTAGTCACAGAAATGGATGTATCTG 58.504 38.462 0.00 0.0 43.79 2.90
4276 4905 7.308589 CCACTTTTGAGACGAGTAATTTGGAAT 60.309 37.037 0.00 0.0 0.00 3.01
4299 4928 4.288366 TGGAGGGAGTATGTTTCATGTCAA 59.712 41.667 0.00 0.0 0.00 3.18
4651 5280 3.258872 CCATGTTTCCACACAATGTCCAT 59.741 43.478 0.00 0.0 35.03 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.153369 ATGGACGAGGCAACGGATG 60.153 57.895 8.70 0.00 46.39 3.51
5 6 1.144057 GATGGACGAGGCAACGGAT 59.856 57.895 8.70 0.00 46.39 4.18
86 87 5.163683 CCAGATGCATTTGAATTCGAGTCTT 60.164 40.000 18.32 0.00 0.00 3.01
112 113 1.410517 GGTCTCGGCTGATCAGAATCA 59.589 52.381 27.04 5.48 39.63 2.57
137 138 6.211587 TCTAGAACCGAAATTCCATTACGA 57.788 37.500 0.00 0.00 0.00 3.43
209 210 5.977489 ATTAACCACCTACTCCTTTTTGC 57.023 39.130 0.00 0.00 0.00 3.68
734 1112 3.982576 ACCACAAAGAAAACCATCGTC 57.017 42.857 0.00 0.00 0.00 4.20
2151 2562 9.726232 CAACTAAGTCACAATATCAATTCATGG 57.274 33.333 0.00 0.00 0.00 3.66
3135 3727 1.332065 GTCGTGATCAGATCGAGCTCA 59.668 52.381 15.40 0.00 34.33 4.26
3914 4527 3.111853 TCACCTGAAACTACTGCTGTG 57.888 47.619 6.48 0.00 0.00 3.66
4193 4822 5.426509 TCCAGATACATCCATTTCTGTGACT 59.573 40.000 0.00 0.00 35.01 3.41
4199 4828 9.872684 AAAATACATCCAGATACATCCATTTCT 57.127 29.630 0.00 0.00 0.00 2.52
4204 4833 9.559732 CAACTAAAATACATCCAGATACATCCA 57.440 33.333 0.00 0.00 0.00 3.41
4205 4834 9.561069 ACAACTAAAATACATCCAGATACATCC 57.439 33.333 0.00 0.00 0.00 3.51
4250 4879 5.468746 TCCAAATTACTCGTCTCAAAAGTGG 59.531 40.000 0.00 0.00 0.00 4.00
4253 4882 7.023575 CCATTCCAAATTACTCGTCTCAAAAG 58.976 38.462 0.00 0.00 0.00 2.27
4276 4905 3.843619 TGACATGAAACATACTCCCTCCA 59.156 43.478 0.00 0.00 0.00 3.86
4299 4928 9.257651 CACTTTTGCTAGTAGTAGTACAAAACT 57.742 33.333 10.33 5.75 42.62 2.66
4456 5085 7.613022 TGTTCTTTGCTCTCTTGGATCATTTAT 59.387 33.333 0.00 0.00 0.00 1.40
4465 5094 4.153835 GTCTCATGTTCTTTGCTCTCTTGG 59.846 45.833 0.00 0.00 0.00 3.61
4636 5265 2.947127 TCACATGGACATTGTGTGGA 57.053 45.000 0.00 0.00 42.55 4.02


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

AutoCloner maintained by Alex Coulton.