Multiple sequence alignment - TraesCS7B01G492400

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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 TraesCS7B01G492400 chr7B 100.000 4267 0 0 1 4267 744492491 744496757 0.000000e+00 7880.0
1 TraesCS7B01G492400 chr7B 98.272 2199 35 2 2070 4267 744506153 744508349 0.000000e+00 3847.0
2 TraesCS7B01G492400 chr7B 96.977 2216 48 6 2070 4267 744483654 744485868 0.000000e+00 3703.0
3 TraesCS7B01G492400 chr7B 96.815 2198 48 4 2070 4267 744461930 744464105 0.000000e+00 3651.0
4 TraesCS7B01G492400 chr7B 97.426 2059 52 1 1 2058 744442842 744444900 0.000000e+00 3507.0
5 TraesCS7B01G492400 chr7B 97.280 2059 54 2 1 2058 744503749 744505806 0.000000e+00 3491.0
6 TraesCS7B01G492400 chr7B 96.702 2062 64 3 1 2058 744481246 744483307 0.000000e+00 3428.0
7 TraesCS7B01G492400 chr7B 95.921 1569 38 5 2714 4267 744445677 744447234 0.000000e+00 2519.0
8 TraesCS7B01G492400 chr7B 98.101 1106 19 2 954 2058 744460479 744461583 0.000000e+00 1925.0
9 TraesCS7B01G492400 chr7B 97.867 422 9 0 2070 2491 744445247 744445668 0.000000e+00 730.0
10 TraesCS7B01G492400 chr7B 95.274 402 19 0 1 402 744526061 744526462 4.650000e-179 638.0
11 TraesCS7B01G492400 chr7A 94.444 2070 101 7 1 2058 735360683 735358616 0.000000e+00 3173.0
12 TraesCS7B01G492400 chr7A 94.348 2070 103 7 1 2058 735396976 735394909 0.000000e+00 3162.0
13 TraesCS7B01G492400 chr7A 94.251 2070 105 7 1 2058 735378909 735376842 0.000000e+00 3151.0
14 TraesCS7B01G492400 chr7A 96.371 1543 40 4 2741 4267 735375889 735374347 0.000000e+00 2525.0
15 TraesCS7B01G492400 chr7A 96.301 1541 43 3 2741 4267 735393956 735392416 0.000000e+00 2518.0
16 TraesCS7B01G492400 chr7A 95.360 1401 50 4 2881 4267 735343035 735341636 0.000000e+00 2213.0
17 TraesCS7B01G492400 chr7A 97.364 607 16 0 2070 2676 735376495 735375889 0.000000e+00 1033.0
18 TraesCS7B01G492400 chr7A 97.364 607 16 0 2070 2676 735394562 735393956 0.000000e+00 1033.0
19 TraesCS7B01G492400 chr7A 98.046 563 11 0 2070 2632 735358269 735357707 0.000000e+00 979.0
20 TraesCS7B01G492400 chr7A 98.611 144 2 0 2741 2884 735357645 735357502 5.480000e-64 255.0
21 TraesCS7B01G492400 chr7A 82.126 207 36 1 1117 1322 151328100 151327894 4.390000e-40 176.0
22 TraesCS7B01G492400 chr7A 82.955 88 13 2 588 673 534298910 534298997 1.270000e-10 78.7
23 TraesCS7B01G492400 chr7A 100.000 40 0 0 2637 2676 735357684 735357645 1.650000e-09 75.0
24 TraesCS7B01G492400 chr7D 93.484 1642 96 7 2070 3708 632353807 632355440 0.000000e+00 2429.0
25 TraesCS7B01G492400 chr7D 93.196 1646 95 9 2071 3708 632362194 632363830 0.000000e+00 2403.0
26 TraesCS7B01G492400 chr7D 91.681 1695 131 10 369 2058 632360144 632361833 0.000000e+00 2340.0
27 TraesCS7B01G492400 chr7D 91.573 1697 132 10 369 2058 632351754 632353446 0.000000e+00 2331.0
28 TraesCS7B01G492400 chr7D 86.740 543 54 10 3706 4232 398377766 398378306 4.750000e-164 588.0
29 TraesCS7B01G492400 chr7D 90.909 286 26 0 1 286 632340925 632341210 6.690000e-103 385.0
30 TraesCS7B01G492400 chr7D 81.340 209 39 0 1117 1325 151542590 151542382 2.040000e-38 171.0
31 TraesCS7B01G492400 chr7D 98.333 60 1 0 317 376 632341323 632341382 5.840000e-19 106.0
32 TraesCS7B01G492400 chr1D 86.760 574 59 8 3705 4262 225493020 225493592 1.300000e-174 623.0
33 TraesCS7B01G492400 chr2D 86.819 569 58 9 3708 4262 216964907 216964342 1.690000e-173 619.0
34 TraesCS7B01G492400 chr2D 85.468 523 55 10 3761 4267 162995752 162996269 3.780000e-145 525.0
35 TraesCS7B01G492400 chr4A 75.686 547 100 24 2635 3162 732780171 732780703 4.260000e-60 243.0
36 TraesCS7B01G492400 chr2B 78.995 219 27 7 4065 4267 370058560 370058345 9.630000e-27 132.0
37 TraesCS7B01G492400 chr2B 90.566 53 5 0 524 576 98114323 98114375 2.130000e-08 71.3
38 TraesCS7B01G492400 chr5D 87.931 58 7 0 1280 1337 483284375 483284432 7.660000e-08 69.4
39 TraesCS7B01G492400 chr1B 90.196 51 5 0 524 574 381597720 381597670 2.750000e-07 67.6


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 TraesCS7B01G492400 chr7B 744492491 744496757 4266 False 7880.000000 7880 100.000000 1 4267 1 chr7B.!!$F1 4266
1 TraesCS7B01G492400 chr7B 744503749 744508349 4600 False 3669.000000 3847 97.776000 1 4267 2 chr7B.!!$F6 4266
2 TraesCS7B01G492400 chr7B 744481246 744485868 4622 False 3565.500000 3703 96.839500 1 4267 2 chr7B.!!$F5 4266
3 TraesCS7B01G492400 chr7B 744460479 744464105 3626 False 2788.000000 3651 97.458000 954 4267 2 chr7B.!!$F4 3313
4 TraesCS7B01G492400 chr7B 744442842 744447234 4392 False 2252.000000 3507 97.071333 1 4267 3 chr7B.!!$F3 4266
5 TraesCS7B01G492400 chr7A 735392416 735396976 4560 True 2237.666667 3162 96.004333 1 4267 3 chr7A.!!$R5 4266
6 TraesCS7B01G492400 chr7A 735374347 735378909 4562 True 2236.333333 3151 95.995333 1 4267 3 chr7A.!!$R4 4266
7 TraesCS7B01G492400 chr7A 735341636 735343035 1399 True 2213.000000 2213 95.360000 2881 4267 1 chr7A.!!$R2 1386
8 TraesCS7B01G492400 chr7A 735357502 735360683 3181 True 1120.500000 3173 97.775250 1 2884 4 chr7A.!!$R3 2883
9 TraesCS7B01G492400 chr7D 632351754 632355440 3686 False 2380.000000 2429 92.528500 369 3708 2 chr7D.!!$F3 3339
10 TraesCS7B01G492400 chr7D 632360144 632363830 3686 False 2371.500000 2403 92.438500 369 3708 2 chr7D.!!$F4 3339
11 TraesCS7B01G492400 chr7D 398377766 398378306 540 False 588.000000 588 86.740000 3706 4232 1 chr7D.!!$F1 526
12 TraesCS7B01G492400 chr1D 225493020 225493592 572 False 623.000000 623 86.760000 3705 4262 1 chr1D.!!$F1 557
13 TraesCS7B01G492400 chr2D 216964342 216964907 565 True 619.000000 619 86.819000 3708 4262 1 chr2D.!!$R1 554
14 TraesCS7B01G492400 chr2D 162995752 162996269 517 False 525.000000 525 85.468000 3761 4267 1 chr2D.!!$F1 506
15 TraesCS7B01G492400 chr4A 732780171 732780703 532 False 243.000000 243 75.686000 2635 3162 1 chr4A.!!$F1 527

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
147 148 0.174617 TGCATGGATAGAACGCGTCA 59.825 50.0 14.44 5.13 0.00 4.35 F
1337 1350 1.172180 TCCAAGCAAAGGCCGTTGAG 61.172 55.0 32.08 20.15 42.56 3.02 F
1460 1473 0.250793 TCGACACGGCCACCATATTT 59.749 50.0 2.24 0.00 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1460 1473 1.471829 ATCACACCAGTGCGAGGTCA 61.472 55.000 0.0 0.0 45.49 4.02 R
3129 3619 1.152567 CCCACTGGTTTTCCCTGCA 60.153 57.895 0.0 0.0 39.73 4.41 R
4102 4605 4.058817 GCCCATAATAAGGAGTCACTTCG 58.941 47.826 0.0 0.0 32.02 3.79 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 44 5.182760 ACTCAAATCTTGTCCTGAAATGAGC 59.817 40.000 0.00 0.00 35.49 4.26
136 137 1.305219 CCAAACCGACGTGCATGGAT 61.305 55.000 11.36 0.00 0.00 3.41
147 148 0.174617 TGCATGGATAGAACGCGTCA 59.825 50.000 14.44 5.13 0.00 4.35
325 335 6.590677 GTCAAGAGTACTCCAACATCCTTTAC 59.409 42.308 19.38 3.02 0.00 2.01
494 504 4.188937 TCATAGGGGTGAAGGTATACGT 57.811 45.455 0.00 0.00 0.00 3.57
673 685 9.322773 TGCATGTTTTTGATTTGACAGAAAATA 57.677 25.926 0.00 0.00 29.89 1.40
913 925 9.213799 TGTTTTGTATTATTTGGCTTCATTTCC 57.786 29.630 0.00 0.00 0.00 3.13
947 959 5.448768 CCGTAAGCTACATATCTACCCATCG 60.449 48.000 0.00 0.00 0.00 3.84
982 994 1.202475 CGGCCCAAAATAAATTCCCCG 60.202 52.381 0.00 0.00 0.00 5.73
1032 1044 2.158310 CCCCACCTTTCCTCCTTTCTTT 60.158 50.000 0.00 0.00 0.00 2.52
1095 1107 1.306056 CCCAATTTCCCCACCCCAG 60.306 63.158 0.00 0.00 0.00 4.45
1219 1231 2.291365 CATGGAGTCGCAAATGATCCA 58.709 47.619 0.00 0.00 43.82 3.41
1316 1328 5.207768 GTCATTGAGTACTGCAACAAACAG 58.792 41.667 0.00 0.00 41.08 3.16
1334 1347 2.200337 GGTCCAAGCAAAGGCCGTT 61.200 57.895 0.00 0.00 42.56 4.44
1337 1350 1.172180 TCCAAGCAAAGGCCGTTGAG 61.172 55.000 32.08 20.15 42.56 3.02
1460 1473 0.250793 TCGACACGGCCACCATATTT 59.749 50.000 2.24 0.00 0.00 1.40
2066 2084 8.885693 TGATCTTGTATGCTAGATACCACTAT 57.114 34.615 7.65 0.00 37.33 2.12
2068 2086 9.579768 GATCTTGTATGCTAGATACCACTATTG 57.420 37.037 7.65 0.00 37.33 1.90
3039 3529 1.367471 CTGACTTGCCAGACCGTCA 59.633 57.895 0.40 0.00 36.29 4.35
3042 3532 2.377628 GACTTGCCAGACCGTCACCA 62.378 60.000 0.40 0.00 0.00 4.17
3129 3619 1.144913 CCGAGGAGGAGGAGAAGATCT 59.855 57.143 0.00 0.00 45.00 2.75
3227 3717 5.048504 CCATGTCTACATTTCAGTGTGCTTT 60.049 40.000 0.00 0.00 33.61 3.51
3805 4307 1.612199 GCCGTGTCTTCCCAATACCAA 60.612 52.381 0.00 0.00 0.00 3.67
4102 4605 3.383761 CAACAACATCTTTGCTCCCAAC 58.616 45.455 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.441016 GCTTTTTGTCTGCTCGCGG 60.441 57.895 6.13 0.00 0.00 6.46
147 148 0.250901 AAGACCAACTCCAATGCGCT 60.251 50.000 9.73 0.00 0.00 5.92
325 335 3.551890 CGACCATCACCGAATTACTCTTG 59.448 47.826 0.00 0.00 0.00 3.02
494 504 4.643334 ACCGAGCAGAACATAGTACATACA 59.357 41.667 0.00 0.00 0.00 2.29
673 685 0.100503 GGCTTAACGCATGCCGAATT 59.899 50.000 13.15 4.29 41.67 2.17
913 925 2.429610 TGTAGCTTACGGGCCTTAGAAG 59.570 50.000 0.84 2.72 0.00 2.85
947 959 1.469767 GGGCCGATTGAGCAATGTTTC 60.470 52.381 0.00 0.00 0.00 2.78
982 994 0.247460 GCAGGGTTGATTGGGCTTTC 59.753 55.000 0.00 0.00 0.00 2.62
1032 1044 3.695022 GAAACTCTAGCGGCGGCGA 62.695 63.158 36.87 14.73 46.35 5.54
1095 1107 2.737830 GTGGATCGGAGCTAGGGC 59.262 66.667 0.00 0.00 39.06 5.19
1219 1231 2.493547 TCGTCCTCGATCATGTGCT 58.506 52.632 0.00 0.00 41.35 4.40
1316 1328 2.200337 AACGGCCTTTGCTTGGACC 61.200 57.895 0.00 0.00 37.74 4.46
1334 1347 4.566278 CCTCCACCAAAATCAGATGTCTCA 60.566 45.833 0.00 0.00 0.00 3.27
1337 1350 3.944015 CTCCTCCACCAAAATCAGATGTC 59.056 47.826 0.00 0.00 0.00 3.06
1400 1413 2.575532 CAGTTTTTGAGGTCCTCTGCA 58.424 47.619 19.82 1.34 0.00 4.41
1460 1473 1.471829 ATCACACCAGTGCGAGGTCA 61.472 55.000 0.00 0.00 45.49 4.02
1619 1632 3.887621 CCTTGATGAAGGTACGAGGAA 57.112 47.619 2.24 0.00 43.63 3.36
1647 1660 8.192774 TGTAACCTAACCTAATACAATCGAGTG 58.807 37.037 11.98 11.98 0.00 3.51
2059 2077 8.993424 AGTGGTATCTAAAAGATCAATAGTGGT 58.007 33.333 0.00 0.00 36.20 4.16
2239 2623 1.812571 GGAAGTCATGCGTGGTTTCAT 59.187 47.619 18.60 0.00 0.00 2.57
3039 3529 2.039746 TCTTTCCCGTGATCATGTTGGT 59.960 45.455 13.81 0.00 0.00 3.67
3042 3532 2.346803 CGTCTTTCCCGTGATCATGTT 58.653 47.619 13.81 0.00 0.00 2.71
3129 3619 1.152567 CCCACTGGTTTTCCCTGCA 60.153 57.895 0.00 0.00 39.73 4.41
4102 4605 4.058817 GCCCATAATAAGGAGTCACTTCG 58.941 47.826 0.00 0.00 32.02 3.79
4143 4646 2.276116 GCGTCCCAGTGGTCTGAGA 61.276 63.158 8.74 0.00 43.76 3.27
4147 4650 3.626924 GGTGCGTCCCAGTGGTCT 61.627 66.667 8.74 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.