Multiple sequence alignment - TraesCS7B01G031600

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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 TraesCS7B01G031600 chr7B 100.000 5268 0 0 1 5268 32024734 32019467 0.000000e+00 9729.0
1 TraesCS7B01G031600 chr7B 99.053 1056 10 0 1040 2095 32024969 32026024 0.000000e+00 1895.0
2 TraesCS7B01G031600 chr2A 98.652 5269 66 5 1 5268 337858595 337863859 0.000000e+00 9332.0
3 TraesCS7B01G031600 chr2A 98.330 5268 72 5 1 5268 337718802 337724053 0.000000e+00 9226.0
4 TraesCS7B01G031600 chr2A 97.337 2103 53 2 1 2101 337856869 337854768 0.000000e+00 3570.0
5 TraesCS7B01G031600 chr2A 97.147 2103 52 2 1 2101 337717084 337714988 0.000000e+00 3544.0
6 TraesCS7B01G031600 chr3B 93.739 4105 169 34 448 4490 580029557 580033635 0.000000e+00 6076.0
7 TraesCS7B01G031600 chr3B 90.526 285 19 4 11 295 580029269 580029545 2.320000e-98 370.0
8 TraesCS7B01G031600 chr3B 97.849 93 2 0 293 385 69267352 69267260 1.520000e-35 161.0
9 TraesCS7B01G031600 chr3B 94.737 95 5 0 4818 4912 64303429 64303523 1.180000e-31 148.0
10 TraesCS7B01G031600 chr3B 90.826 109 7 3 4818 4924 580034220 580034327 5.500000e-30 143.0
11 TraesCS7B01G031600 chr3B 89.744 78 5 2 4972 5046 693335986 693335909 4.340000e-16 97.1
12 TraesCS7B01G031600 chr3B 86.275 51 5 2 383 433 507388985 507388937 3.000000e-03 54.7
13 TraesCS7B01G031600 chr3A 92.012 2003 106 20 2321 4299 583698392 583700364 0.000000e+00 2763.0
14 TraesCS7B01G031600 chr3A 89.748 1151 75 20 440 1565 583696500 583697632 0.000000e+00 1432.0
15 TraesCS7B01G031600 chr3A 93.875 702 39 3 1590 2291 583697625 583698322 0.000000e+00 1055.0
16 TraesCS7B01G031600 chr3A 94.792 192 10 0 22 213 583696135 583696326 3.080000e-77 300.0
17 TraesCS7B01G031600 chr3A 92.793 111 7 1 4380 4490 583700411 583700520 5.460000e-35 159.0
18 TraesCS7B01G031600 chr3A 92.233 103 8 0 4830 4932 583703907 583704009 4.250000e-31 147.0
19 TraesCS7B01G031600 chr3A 79.339 121 18 6 4618 4733 583703354 583703472 1.570000e-10 78.7
20 TraesCS7B01G031600 chr3D 91.313 2003 126 20 2321 4298 442392806 442394785 0.000000e+00 2691.0
21 TraesCS7B01G031600 chr3D 94.215 1210 56 5 1122 2321 442391551 442392756 0.000000e+00 1834.0
22 TraesCS7B01G031600 chr3D 89.813 697 44 7 434 1124 442390820 442391495 0.000000e+00 869.0
23 TraesCS7B01G031600 chr3D 86.111 288 12 6 11 297 442390558 442390818 8.630000e-73 285.0
24 TraesCS7B01G031600 chr3D 92.661 109 7 1 4380 4488 442394833 442394940 7.060000e-34 156.0
25 TraesCS7B01G031600 chr3D 81.667 120 16 5 4623 4737 442498852 442498970 1.560000e-15 95.3
26 TraesCS7B01G031600 chr3D 100.000 28 0 0 383 410 113802451 113802478 1.000000e-02 52.8
27 TraesCS7B01G031600 chr6B 97.849 93 2 0 293 385 582025939 582025847 1.520000e-35 161.0
28 TraesCS7B01G031600 chr6B 87.313 134 12 4 22 153 663532774 663532644 1.180000e-31 148.0
29 TraesCS7B01G031600 chr4D 97.849 93 2 0 293 385 24988485 24988393 1.520000e-35 161.0
30 TraesCS7B01G031600 chr4D 93.269 104 7 0 286 389 26898035 26897932 2.540000e-33 154.0
31 TraesCS7B01G031600 chr7D 94.231 104 3 2 284 385 609026656 609026758 7.060000e-34 156.0
32 TraesCS7B01G031600 chr7D 95.604 91 4 0 4825 4915 582461012 582460922 4.250000e-31 147.0
33 TraesCS7B01G031600 chr5D 94.792 96 3 2 4818 4913 113879304 113879397 1.180000e-31 148.0
34 TraesCS7B01G031600 chr5D 87.179 78 8 2 5107 5182 209319184 209319107 2.610000e-13 87.9
35 TraesCS7B01G031600 chr5D 94.118 34 2 0 5235 5268 209319075 209319042 1.000000e-02 52.8
36 TraesCS7B01G031600 chr5D 100.000 28 0 0 383 410 264635042 264635015 1.000000e-02 52.8
37 TraesCS7B01G031600 chr5B 94.792 96 4 1 4818 4913 689115708 689115802 1.180000e-31 148.0
38 TraesCS7B01G031600 chr5B 88.158 76 7 2 5107 5180 222378382 222378307 7.270000e-14 89.8
39 TraesCS7B01G031600 chr5A 94.792 96 4 1 4816 4911 561124545 561124639 1.180000e-31 148.0
40 TraesCS7B01G031600 chr5A 90.909 55 4 1 4972 5025 439568074 439568020 7.320000e-09 73.1
41 TraesCS7B01G031600 chr5A 100.000 28 0 0 383 410 450473654 450473627 1.000000e-02 52.8
42 TraesCS7B01G031600 chr6A 100.000 28 0 0 383 410 602749949 602749922 1.000000e-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 TraesCS7B01G031600 chr7B 32019467 32024734 5267 True 9729.000000 9729 100.000000 1 5268 1 chr7B.!!$R1 5267
1 TraesCS7B01G031600 chr7B 32024969 32026024 1055 False 1895.000000 1895 99.053000 1040 2095 1 chr7B.!!$F1 1055
2 TraesCS7B01G031600 chr2A 337858595 337863859 5264 False 9332.000000 9332 98.652000 1 5268 1 chr2A.!!$F2 5267
3 TraesCS7B01G031600 chr2A 337718802 337724053 5251 False 9226.000000 9226 98.330000 1 5268 1 chr2A.!!$F1 5267
4 TraesCS7B01G031600 chr2A 337854768 337856869 2101 True 3570.000000 3570 97.337000 1 2101 1 chr2A.!!$R2 2100
5 TraesCS7B01G031600 chr2A 337714988 337717084 2096 True 3544.000000 3544 97.147000 1 2101 1 chr2A.!!$R1 2100
6 TraesCS7B01G031600 chr3B 580029269 580034327 5058 False 2196.333333 6076 91.697000 11 4924 3 chr3B.!!$F2 4913
7 TraesCS7B01G031600 chr3A 583696135 583704009 7874 False 847.814286 2763 90.684571 22 4932 7 chr3A.!!$F1 4910
8 TraesCS7B01G031600 chr3D 442390558 442394940 4382 False 1167.000000 2691 90.822600 11 4488 5 chr3D.!!$F3 4477

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
603 693 0.107945 GGCTCCGATGAAGCTGACTT 60.108 55.0 0.0 0.0 39.43 3.01 F
1036 1143 0.252103 AGTACATCAGGTGTCCCCGT 60.252 55.0 0.0 0.0 42.29 5.28 F
1711 1882 0.963962 CAGCATGTGTTCCCTTGCTT 59.036 50.0 0.0 0.0 42.09 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1863 0.963962 AAGCAAGGGAACACATGCTG 59.036 50.0 7.53 0.0 43.34 4.41 R
1989 2164 5.605488 GGGGGAATCACTAGACCTATTAACA 59.395 44.0 0.00 0.0 0.00 2.41 R
4699 8146 0.250124 TTAGCGTGGGGTGTCACTTG 60.250 55.0 2.35 0.0 35.63 3.16 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
44 45 2.104859 CAGCCACATCAGTCTGCCG 61.105 63.158 0.00 0.00 0.00 5.69
412 496 5.865552 TGTACCGAAATACTTGTAGTTGAGC 59.134 40.000 0.00 0.00 0.00 4.26
418 502 7.360861 CCGAAATACTTGTAGTTGAGCATTTCA 60.361 37.037 0.00 0.00 33.03 2.69
438 522 3.945921 TCAGTACAGAGGGAGTAATGTCG 59.054 47.826 0.00 0.00 38.35 4.35
445 529 4.398358 CAGAGGGAGTAATGTCGAGTACAA 59.602 45.833 0.00 0.00 42.70 2.41
596 686 1.590932 CAATCCTGGCTCCGATGAAG 58.409 55.000 0.00 0.00 0.00 3.02
603 693 0.107945 GGCTCCGATGAAGCTGACTT 60.108 55.000 0.00 0.00 39.43 3.01
631 721 4.274459 GTGCTCTTGAAGATCTGTGTTTGT 59.726 41.667 0.00 0.00 0.00 2.83
733 834 2.233271 CCAAACAATGTGCTGGAGAGT 58.767 47.619 8.62 0.00 0.00 3.24
835 936 9.770097 AGACGTCTTCAACATATATCATCAAAT 57.230 29.630 13.58 0.00 0.00 2.32
915 1016 7.451255 TGATCAAAGATCCACCAACTTTGTTAT 59.549 33.333 15.16 6.01 45.72 1.89
1036 1143 0.252103 AGTACATCAGGTGTCCCCGT 60.252 55.000 0.00 0.00 42.29 5.28
1054 1161 2.913765 TTGTTGGCGCCAATGTCCG 61.914 57.895 41.80 0.00 38.28 4.79
1692 1863 6.431234 CCCAGCTGATTTTGTAGGATATAACC 59.569 42.308 17.39 0.00 0.00 2.85
1711 1882 0.963962 CAGCATGTGTTCCCTTGCTT 59.036 50.000 0.00 0.00 42.09 3.91
1989 2164 7.072581 CCCTTTCCTAGAATCCCTATTTGTACT 59.927 40.741 0.00 0.00 0.00 2.73
3109 3367 7.730364 AACTCTTTGTAACACTAGGATGTTG 57.270 36.000 8.58 0.00 42.74 3.33
3181 3447 7.654116 GTCTATTTGGCTGAAACTAGTATCTCC 59.346 40.741 0.00 0.00 0.00 3.71
4222 4495 4.382320 TGGGACTTGCGGCCGTAC 62.382 66.667 28.70 11.89 0.00 3.67
4320 4610 3.285484 AGTGCCTGATGGACAATGATTC 58.715 45.455 0.00 0.00 34.57 2.52
4699 8146 1.153329 TCGTCACCCACACAACACC 60.153 57.895 0.00 0.00 0.00 4.16
5147 8678 2.124903 CACCGCTACGAATGGATGTAC 58.875 52.381 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
412 496 6.644347 ACATTACTCCCTCTGTACTGAAATG 58.356 40.000 15.45 15.45 0.00 2.32
418 502 4.200874 CTCGACATTACTCCCTCTGTACT 58.799 47.826 0.00 0.00 0.00 2.73
438 522 7.010552 GTGTTCATCAGGTCATGTATTGTACTC 59.989 40.741 0.00 0.00 0.00 2.59
445 529 6.763135 GTGTATGTGTTCATCAGGTCATGTAT 59.237 38.462 0.00 0.00 35.70 2.29
596 686 0.601311 AAGAGCACGGACAAGTCAGC 60.601 55.000 2.29 3.37 0.00 4.26
603 693 1.895798 AGATCTTCAAGAGCACGGACA 59.104 47.619 5.26 0.00 31.99 4.02
631 721 1.484653 AGCGCACATCCCTATACACAA 59.515 47.619 11.47 0.00 0.00 3.33
661 751 1.226888 GTGGGCATACTCGTCGTCC 60.227 63.158 0.00 0.00 0.00 4.79
733 834 1.847798 ATGCCCTTGTTGGACCGCTA 61.848 55.000 0.00 0.00 38.35 4.26
797 898 8.199176 TGTTGAAGACGTCTTTACAAATACAA 57.801 30.769 29.49 23.37 36.11 2.41
915 1016 6.158520 TCAGGTTGGAGGAATTTGATGATCTA 59.841 38.462 0.00 0.00 0.00 1.98
1036 1143 2.913765 CGGACATTGGCGCCAACAA 61.914 57.895 42.32 23.68 38.88 2.83
1054 1161 4.882396 GCGCCGAGCTTCCTCCTC 62.882 72.222 0.00 0.00 44.04 3.71
1692 1863 0.963962 AAGCAAGGGAACACATGCTG 59.036 50.000 7.53 0.00 43.34 4.41
1711 1882 7.686438 AATCACAACAGAAGTGTATATGCAA 57.314 32.000 0.00 0.00 35.08 4.08
1989 2164 5.605488 GGGGGAATCACTAGACCTATTAACA 59.395 44.000 0.00 0.00 0.00 2.41
4699 8146 0.250124 TTAGCGTGGGGTGTCACTTG 60.250 55.000 2.35 0.00 35.63 3.16
5147 8678 1.399791 GGTTAGAGGTCGGTGTACTCG 59.600 57.143 0.00 0.00 36.40 4.18


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

AutoCloner maintained by Alex Coulton.