Multiple sequence alignment - TraesCS7D01G093700

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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 TraesCS7D01G093700 chr7D 100.000 5704 0 0 1 5704 56073457 56067754 0.000000e+00 10534
1 TraesCS7D01G093700 chr7D 98.694 3139 34 4 2567 5704 56055074 56051942 0.000000e+00 5563
2 TraesCS7D01G093700 chr7D 98.337 2586 20 5 1 2565 56057819 56055236 0.000000e+00 4516
3 TraesCS7D01G093700 chr7D 84.233 1167 117 42 2165 3305 56100821 56099696 0.000000e+00 1074
4 TraesCS7D01G093700 chr7A 94.243 4447 201 27 600 5014 60404279 60399856 0.000000e+00 6743
5 TraesCS7D01G093700 chr7A 94.173 4445 203 26 600 5014 60372757 60368339 0.000000e+00 6722
6 TraesCS7D01G093700 chr7A 94.024 4451 210 26 599 5014 60082865 60078436 0.000000e+00 6695
7 TraesCS7D01G093700 chr7A 94.029 3668 141 37 241 3863 60513845 60510211 0.000000e+00 5489
8 TraesCS7D01G093700 chr7A 94.411 3149 131 18 1895 5014 59956324 59953192 0.000000e+00 4798
9 TraesCS7D01G093700 chr7A 94.070 2091 88 14 1675 3748 60062594 60060523 0.000000e+00 3142
10 TraesCS7D01G093700 chr7A 93.926 2091 91 14 1675 3748 59937800 59935729 0.000000e+00 3125
11 TraesCS7D01G093700 chr7A 93.092 1853 78 15 3740 5576 59934170 59932352 0.000000e+00 2667
12 TraesCS7D01G093700 chr7A 92.930 1853 82 13 3740 5576 60058698 60056879 0.000000e+00 2651
13 TraesCS7D01G093700 chr7A 94.136 1296 49 7 1287 2561 59805227 59803938 0.000000e+00 1947
14 TraesCS7D01G093700 chr7A 93.309 1091 62 6 599 1686 59939390 59938308 0.000000e+00 1600
15 TraesCS7D01G093700 chr7A 92.942 1091 65 7 599 1686 60064182 60063101 0.000000e+00 1578
16 TraesCS7D01G093700 chr7A 96.078 357 10 3 241 593 59939825 59939469 3.830000e-161 579
17 TraesCS7D01G093700 chr7A 95.798 357 11 3 241 593 60064617 60064261 1.780000e-159 573
18 TraesCS7D01G093700 chr7A 81.380 768 84 32 2559 3305 59931723 59930994 6.410000e-159 571
19 TraesCS7D01G093700 chr7A 93.636 220 14 0 2 221 60514153 60513934 4.260000e-86 329
20 TraesCS7D01G093700 chr7A 93.119 218 15 0 2 219 59816694 59816477 2.560000e-83 320
21 TraesCS7D01G093700 chr7A 90.783 217 20 0 5 221 60386912 60386696 2.010000e-74 291
22 TraesCS7D01G093700 chr7A 87.273 220 13 4 2 221 59940118 59939914 2.660000e-58 237
23 TraesCS7D01G093700 chr7A 87.273 220 13 4 2 221 60064910 60064706 2.660000e-58 237
24 TraesCS7D01G093700 chr4A 93.158 2324 111 21 599 2889 672797508 672795200 0.000000e+00 3367
25 TraesCS7D01G093700 chr4A 93.115 2324 112 21 599 2889 672679278 672676970 0.000000e+00 3362
26 TraesCS7D01G093700 chr4A 93.112 2323 113 17 599 2889 672776244 672773937 0.000000e+00 3360
27 TraesCS7D01G093700 chr4A 93.069 2323 113 18 599 2889 672597922 672595616 0.000000e+00 3354
28 TraesCS7D01G093700 chr4A 92.506 2322 109 23 599 2889 672925979 672923692 0.000000e+00 3264
29 TraesCS7D01G093700 chr4A 92.337 2323 114 21 599 2889 672736204 672733914 0.000000e+00 3245
30 TraesCS7D01G093700 chr4A 92.988 1697 82 5 4015 5704 672633895 672632229 0.000000e+00 2440
31 TraesCS7D01G093700 chr4A 92.929 1697 83 5 4015 5704 672655486 672653820 0.000000e+00 2435
32 TraesCS7D01G093700 chr4A 92.874 1698 80 15 4015 5704 672922766 672921102 0.000000e+00 2427
33 TraesCS7D01G093700 chr4A 92.815 1698 82 14 4015 5704 672733001 672731336 0.000000e+00 2423
34 TraesCS7D01G093700 chr4A 92.815 1698 81 15 4015 5704 672773004 672771340 0.000000e+00 2422
35 TraesCS7D01G093700 chr4A 92.697 1698 85 7 4015 5704 672794259 672792593 0.000000e+00 2412
36 TraesCS7D01G093700 chr4A 92.344 1698 87 10 4015 5704 672594675 672593013 0.000000e+00 2375
37 TraesCS7D01G093700 chr4A 92.344 1698 87 10 4015 5704 672676031 672674369 0.000000e+00 2375
38 TraesCS7D01G093700 chr4A 91.035 1227 79 15 599 1807 672658507 672657294 0.000000e+00 1628
39 TraesCS7D01G093700 chr4A 96.100 359 8 3 241 593 672736641 672736283 1.070000e-161 580
40 TraesCS7D01G093700 chr4A 96.100 359 8 3 241 593 672947403 672947045 1.070000e-161 580
41 TraesCS7D01G093700 chr4A 95.822 359 9 3 241 593 672881961 672881603 4.960000e-160 575
42 TraesCS7D01G093700 chr4A 95.543 359 10 3 241 593 672598359 672598001 2.310000e-158 569
43 TraesCS7D01G093700 chr4A 95.543 359 10 3 241 593 672658943 672658585 2.310000e-158 569
44 TraesCS7D01G093700 chrUn 91.756 934 46 11 2915 3843 372313560 372314467 0.000000e+00 1269
45 TraesCS7D01G093700 chrUn 95.543 359 10 3 241 593 348562322 348562680 2.310000e-158 569


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 TraesCS7D01G093700 chr7D 56067754 56073457 5703 True 10534.000000 10534 100.000000 1 5704 1 chr7D.!!$R1 5703
1 TraesCS7D01G093700 chr7D 56051942 56057819 5877 True 5039.500000 5563 98.515500 1 5704 2 chr7D.!!$R3 5703
2 TraesCS7D01G093700 chr7D 56099696 56100821 1125 True 1074.000000 1074 84.233000 2165 3305 1 chr7D.!!$R2 1140
3 TraesCS7D01G093700 chr7A 60399856 60404279 4423 True 6743.000000 6743 94.243000 600 5014 1 chr7A.!!$R7 4414
4 TraesCS7D01G093700 chr7A 60368339 60372757 4418 True 6722.000000 6722 94.173000 600 5014 1 chr7A.!!$R5 4414
5 TraesCS7D01G093700 chr7A 60078436 60082865 4429 True 6695.000000 6695 94.024000 599 5014 1 chr7A.!!$R4 4415
6 TraesCS7D01G093700 chr7A 59953192 59956324 3132 True 4798.000000 4798 94.411000 1895 5014 1 chr7A.!!$R3 3119
7 TraesCS7D01G093700 chr7A 60510211 60514153 3942 True 2909.000000 5489 93.832500 2 3863 2 chr7A.!!$R10 3861
8 TraesCS7D01G093700 chr7A 59803938 59805227 1289 True 1947.000000 1947 94.136000 1287 2561 1 chr7A.!!$R1 1274
9 TraesCS7D01G093700 chr7A 60056879 60064910 8031 True 1636.200000 3142 92.602600 2 5576 5 chr7A.!!$R9 5574
10 TraesCS7D01G093700 chr7A 59930994 59940118 9124 True 1463.166667 3125 90.843000 2 5576 6 chr7A.!!$R8 5574
11 TraesCS7D01G093700 chr4A 672771340 672776244 4904 True 2891.000000 3360 92.963500 599 5704 2 chr4A.!!$R8 5105
12 TraesCS7D01G093700 chr4A 672792593 672797508 4915 True 2889.500000 3367 92.927500 599 5704 2 chr4A.!!$R9 5105
13 TraesCS7D01G093700 chr4A 672674369 672679278 4909 True 2868.500000 3362 92.729500 599 5704 2 chr4A.!!$R6 5105
14 TraesCS7D01G093700 chr4A 672921102 672925979 4877 True 2845.500000 3264 92.690000 599 5704 2 chr4A.!!$R10 5105
15 TraesCS7D01G093700 chr4A 672632229 672633895 1666 True 2440.000000 2440 92.988000 4015 5704 1 chr4A.!!$R1 1689
16 TraesCS7D01G093700 chr4A 672593013 672598359 5346 True 2099.333333 3354 93.652000 241 5704 3 chr4A.!!$R4 5463
17 TraesCS7D01G093700 chr4A 672731336 672736641 5305 True 2082.666667 3245 93.750667 241 5704 3 chr4A.!!$R7 5463
18 TraesCS7D01G093700 chr4A 672653820 672658943 5123 True 1544.000000 2435 93.169000 241 5704 3 chr4A.!!$R5 5463
19 TraesCS7D01G093700 chrUn 372313560 372314467 907 False 1269.000000 1269 91.756000 2915 3843 1 chrUn.!!$F2 928

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
873 1029 1.912043 CCAGTCTTCCACCCTCTTGAT 59.088 52.381 0.00 0.0 0.00 2.57 F
1657 1840 5.240891 TCTGACATGAAAGTTCAGATCCAC 58.759 41.667 8.48 0.0 41.08 4.02 F
2667 3786 6.884836 ACAAAACCTTCAACTGTTTCTAGACT 59.115 34.615 0.00 0.0 33.76 3.24 F
3156 4321 2.025981 TGCAGCCAGTGATATGAACCTT 60.026 45.455 0.00 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 2514 8.019656 ACTAATATAAACACCGGATCTGAAGT 57.980 34.615 9.46 0.00 0.00 3.01 R
3156 4321 2.174424 TGTATATGGCTTGGTGATGGCA 59.826 45.455 0.00 0.00 42.73 4.92 R
3736 4905 0.175302 AGTAGTAGCAGCAGCAGCAG 59.825 55.000 12.92 0.00 45.49 4.24 R
5001 8062 0.388520 GCGTGGTGGAATTCAAAGGC 60.389 55.000 7.93 3.22 0.00 4.35 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
782 936 3.906846 TGGCCAAAAACATGGTAGGAAAT 59.093 39.130 0.61 0.0 42.75 2.17
873 1029 1.912043 CCAGTCTTCCACCCTCTTGAT 59.088 52.381 0.00 0.0 0.00 2.57
1657 1840 5.240891 TCTGACATGAAAGTTCAGATCCAC 58.759 41.667 8.48 0.0 41.08 4.02
2667 3786 6.884836 ACAAAACCTTCAACTGTTTCTAGACT 59.115 34.615 0.00 0.0 33.76 3.24
3156 4321 2.025981 TGCAGCCAGTGATATGAACCTT 60.026 45.455 0.00 0.0 0.00 3.50
3421 4590 6.377080 TCATATGGTGCCCCAAATTACAATA 58.623 36.000 2.13 0.0 46.04 1.90
3728 4897 3.135994 CAACCAAAGGTACGTTACTGCT 58.864 45.455 0.43 0.0 33.12 4.24
3729 4898 4.309099 CAACCAAAGGTACGTTACTGCTA 58.691 43.478 0.43 0.0 33.12 3.49
3730 4899 3.917988 ACCAAAGGTACGTTACTGCTAC 58.082 45.455 0.43 0.0 32.11 3.58
3731 4900 3.575687 ACCAAAGGTACGTTACTGCTACT 59.424 43.478 0.43 0.0 32.11 2.57
3732 4901 3.924686 CCAAAGGTACGTTACTGCTACTG 59.075 47.826 0.43 0.0 0.00 2.74
3733 4902 2.935481 AGGTACGTTACTGCTACTGC 57.065 50.000 0.00 0.0 40.20 4.40
3734 4903 2.444421 AGGTACGTTACTGCTACTGCT 58.556 47.619 0.00 0.0 40.48 4.24
3735 4904 2.163815 AGGTACGTTACTGCTACTGCTG 59.836 50.000 0.00 0.0 42.70 4.41
3736 4905 1.918609 GTACGTTACTGCTACTGCTGC 59.081 52.381 0.00 0.0 41.07 5.25
4988 8049 0.611618 ATGATTTCCAGCAACCGCCA 60.612 50.000 0.00 0.0 39.83 5.69
4997 8058 2.978010 CAACCGCCACCACACTCC 60.978 66.667 0.00 0.0 0.00 3.85
4998 8059 3.168528 AACCGCCACCACACTCCT 61.169 61.111 0.00 0.0 0.00 3.69
4999 8060 1.839747 AACCGCCACCACACTCCTA 60.840 57.895 0.00 0.0 0.00 2.94
5000 8061 1.198759 AACCGCCACCACACTCCTAT 61.199 55.000 0.00 0.0 0.00 2.57
5001 8062 1.153369 CCGCCACCACACTCCTATG 60.153 63.158 0.00 0.0 0.00 2.23
5002 8063 1.815421 CGCCACCACACTCCTATGC 60.815 63.158 0.00 0.0 0.00 3.14
5003 8064 1.452108 GCCACCACACTCCTATGCC 60.452 63.158 0.00 0.0 0.00 4.40
5004 8065 1.915078 GCCACCACACTCCTATGCCT 61.915 60.000 0.00 0.0 0.00 4.75
5005 8066 0.620556 CCACCACACTCCTATGCCTT 59.379 55.000 0.00 0.0 0.00 4.35
5006 8067 1.004745 CCACCACACTCCTATGCCTTT 59.995 52.381 0.00 0.0 0.00 3.11
5007 8068 2.086869 CACCACACTCCTATGCCTTTG 58.913 52.381 0.00 0.0 0.00 2.77
5008 8069 1.985159 ACCACACTCCTATGCCTTTGA 59.015 47.619 0.00 0.0 0.00 2.69
5009 8070 2.375174 ACCACACTCCTATGCCTTTGAA 59.625 45.455 0.00 0.0 0.00 2.69
5010 8071 3.010584 ACCACACTCCTATGCCTTTGAAT 59.989 43.478 0.00 0.0 0.00 2.57
5011 8072 4.019174 CCACACTCCTATGCCTTTGAATT 58.981 43.478 0.00 0.0 0.00 2.17
5012 8073 4.096984 CCACACTCCTATGCCTTTGAATTC 59.903 45.833 0.00 0.0 0.00 2.17
5013 8074 4.096984 CACACTCCTATGCCTTTGAATTCC 59.903 45.833 2.27 0.0 0.00 3.01
5014 8075 4.263905 ACACTCCTATGCCTTTGAATTCCA 60.264 41.667 2.27 0.0 0.00 3.53
5015 8076 4.096984 CACTCCTATGCCTTTGAATTCCAC 59.903 45.833 2.27 0.0 0.00 4.02
5016 8077 3.631250 TCCTATGCCTTTGAATTCCACC 58.369 45.455 2.27 0.0 0.00 4.61
5017 8078 3.011144 TCCTATGCCTTTGAATTCCACCA 59.989 43.478 2.27 0.0 0.00 4.17
5018 8079 3.131046 CCTATGCCTTTGAATTCCACCAC 59.869 47.826 2.27 0.0 0.00 4.16
5019 8080 0.958091 TGCCTTTGAATTCCACCACG 59.042 50.000 2.27 0.0 0.00 4.94
5020 8081 0.388520 GCCTTTGAATTCCACCACGC 60.389 55.000 2.27 0.0 0.00 5.34
5021 8082 1.247567 CCTTTGAATTCCACCACGCT 58.752 50.000 2.27 0.0 0.00 5.07
5320 8411 2.009774 ACATTCGCAGAAGTATGCCAC 58.990 47.619 0.00 0.0 45.90 5.01
5325 8416 1.432270 GCAGAAGTATGCCACCGAGC 61.432 60.000 0.00 0.0 40.43 5.03
5344 8435 2.151202 GCAATCGTCCCAACAAAGAGA 58.849 47.619 0.00 0.0 0.00 3.10
5527 8621 4.557895 GCATTTGTGGCCGTAGTTTTTAGT 60.558 41.667 0.00 0.0 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
782 936 5.465935 GCGGGATGTATTTGTTTTCTTTCA 58.534 37.500 0.00 0.00 0.00 2.69
873 1029 2.288666 CTGCTTTATAAAGAGCCGGCA 58.711 47.619 31.54 15.96 38.28 5.69
1018 1174 3.787001 GGGGTTGGAGGAGGAGCG 61.787 72.222 0.00 0.00 0.00 5.03
1811 2514 8.019656 ACTAATATAAACACCGGATCTGAAGT 57.980 34.615 9.46 0.00 0.00 3.01
3156 4321 2.174424 TGTATATGGCTTGGTGATGGCA 59.826 45.455 0.00 0.00 42.73 4.92
3421 4590 6.706270 CACACCTCGCCATCTTATATTTACTT 59.294 38.462 0.00 0.00 0.00 2.24
3736 4905 0.175302 AGTAGTAGCAGCAGCAGCAG 59.825 55.000 12.92 0.00 45.49 4.24
4988 8049 1.985159 TCAAAGGCATAGGAGTGTGGT 59.015 47.619 0.00 0.00 0.00 4.16
4997 8058 3.181497 CGTGGTGGAATTCAAAGGCATAG 60.181 47.826 7.93 0.00 0.00 2.23
4998 8059 2.752354 CGTGGTGGAATTCAAAGGCATA 59.248 45.455 7.93 0.00 0.00 3.14
4999 8060 1.545582 CGTGGTGGAATTCAAAGGCAT 59.454 47.619 7.93 0.00 0.00 4.40
5000 8061 0.958091 CGTGGTGGAATTCAAAGGCA 59.042 50.000 7.93 0.00 0.00 4.75
5001 8062 0.388520 GCGTGGTGGAATTCAAAGGC 60.389 55.000 7.93 3.22 0.00 4.35
5002 8063 1.200020 GAGCGTGGTGGAATTCAAAGG 59.800 52.381 7.93 0.00 0.00 3.11
5003 8064 2.154462 AGAGCGTGGTGGAATTCAAAG 58.846 47.619 7.93 0.00 0.00 2.77
5004 8065 2.270352 AGAGCGTGGTGGAATTCAAA 57.730 45.000 7.93 0.00 0.00 2.69
5005 8066 3.270027 CATAGAGCGTGGTGGAATTCAA 58.730 45.455 7.93 0.00 0.00 2.69
5006 8067 2.905075 CATAGAGCGTGGTGGAATTCA 58.095 47.619 7.93 0.00 0.00 2.57
5007 8068 1.599542 GCATAGAGCGTGGTGGAATTC 59.400 52.381 0.00 0.00 0.00 2.17
5008 8069 1.668419 GCATAGAGCGTGGTGGAATT 58.332 50.000 0.00 0.00 0.00 2.17
5009 8070 3.386543 GCATAGAGCGTGGTGGAAT 57.613 52.632 0.00 0.00 0.00 3.01
5010 8071 4.932789 GCATAGAGCGTGGTGGAA 57.067 55.556 0.00 0.00 0.00 3.53
5019 8080 3.137533 GTGGAATTCAGAGGCATAGAGC 58.862 50.000 7.93 0.00 44.65 4.09
5020 8081 3.135348 TGGTGGAATTCAGAGGCATAGAG 59.865 47.826 7.93 0.00 0.00 2.43
5021 8082 3.114606 TGGTGGAATTCAGAGGCATAGA 58.885 45.455 7.93 0.00 0.00 1.98
5325 8416 2.744202 CCTCTCTTTGTTGGGACGATTG 59.256 50.000 0.00 0.00 0.00 2.67
5344 8435 7.682787 ACACATCCATAAATACTCTTCTCCT 57.317 36.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.