Multiple sequence alignment - TraesCS1B01G039300

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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 TraesCS1B01G039300 chr1B 100.000 5202 0 0 1 5202 19016819 19022020 0.000000e+00 9607.0
1 TraesCS1B01G039300 chr1B 93.043 1308 61 9 2717 4001 602341449 602342749 0.000000e+00 1884.0
2 TraesCS1B01G039300 chr1B 96.170 731 22 4 912 1641 602339777 602340502 0.000000e+00 1190.0
3 TraesCS1B01G039300 chr1B 96.983 232 3 4 1861 2091 602340510 602340738 2.270000e-103 387.0
4 TraesCS1B01G039300 chr1B 90.909 220 9 3 1 209 602338436 602338655 8.530000e-73 285.0
5 TraesCS1B01G039300 chr1B 94.340 106 6 0 5097 5202 14603738 14603843 4.170000e-36 163.0
6 TraesCS1B01G039300 chr1B 93.878 49 3 0 4903 4951 684201696 684201744 2.010000e-09 75.0
7 TraesCS1B01G039300 chr1B 100.000 31 0 0 2687 2717 19019417 19019447 2.020000e-04 58.4
8 TraesCS1B01G039300 chr7D 96.517 1292 32 5 2717 4001 553874606 553875891 0.000000e+00 2124.0
9 TraesCS1B01G039300 chr7D 97.468 790 18 2 1861 2650 553873697 553874484 0.000000e+00 1347.0
10 TraesCS1B01G039300 chr7D 96.986 730 18 1 912 1641 553872964 553873689 0.000000e+00 1223.0
11 TraesCS1B01G039300 chr7D 90.323 217 10 1 1 206 553871630 553871846 1.850000e-69 274.0
12 TraesCS1B01G039300 chr7D 90.164 61 3 3 4892 4951 311185682 311185740 5.590000e-10 76.8
13 TraesCS1B01G039300 chr7D 100.000 31 0 0 2687 2717 328007910 328007940 2.020000e-04 58.4
14 TraesCS1B01G039300 chr4D 96.101 1308 24 6 2717 4001 447219674 447218371 0.000000e+00 2108.0
15 TraesCS1B01G039300 chr4D 98.228 790 12 1 1861 2650 447220583 447219796 0.000000e+00 1380.0
16 TraesCS1B01G039300 chr4D 97.811 731 10 3 912 1641 447221316 447220591 0.000000e+00 1256.0
17 TraesCS1B01G039300 chr4D 95.918 147 6 0 63 209 447222571 447222425 6.730000e-59 239.0
18 TraesCS1B01G039300 chr4D 100.000 31 0 0 2687 2717 447219847 447219817 2.020000e-04 58.4
19 TraesCS1B01G039300 chr3D 96.024 1308 27 7 2717 4001 250987961 250989266 0.000000e+00 2104.0
20 TraesCS1B01G039300 chr3D 93.854 1025 38 5 3000 4001 577327979 577329001 0.000000e+00 1520.0
21 TraesCS1B01G039300 chr3D 97.470 830 15 4 1821 2650 250987016 250987839 0.000000e+00 1411.0
22 TraesCS1B01G039300 chr3D 97.229 830 19 3 1821 2650 10523958 10523133 0.000000e+00 1402.0
23 TraesCS1B01G039300 chr3D 98.358 731 7 3 912 1641 250986307 250987033 0.000000e+00 1279.0
24 TraesCS1B01G039300 chr3D 97.541 732 11 4 912 1641 10524667 10523941 0.000000e+00 1245.0
25 TraesCS1B01G039300 chr3D 95.599 409 11 2 3517 3919 9496301 9495894 0.000000e+00 649.0
26 TraesCS1B01G039300 chr3D 91.284 218 8 1 1 207 250972601 250972818 2.370000e-73 287.0
27 TraesCS1B01G039300 chr3D 95.858 169 7 0 41 209 10525950 10525782 1.850000e-69 274.0
28 TraesCS1B01G039300 chr3D 82.979 94 16 0 4296 4389 596060204 596060111 9.280000e-13 86.1
29 TraesCS1B01G039300 chr3D 91.111 45 2 2 8 52 10525992 10525950 5.630000e-05 60.2
30 TraesCS1B01G039300 chr3D 100.000 31 0 0 2687 2717 10523184 10523154 2.020000e-04 58.4
31 TraesCS1B01G039300 chr3D 100.000 31 0 0 2687 2717 250987788 250987818 2.020000e-04 58.4
32 TraesCS1B01G039300 chr6A 95.336 1308 33 5 2717 4001 211315652 211316954 0.000000e+00 2052.0
33 TraesCS1B01G039300 chr6A 93.437 1158 26 11 1 1120 211313289 211314434 0.000000e+00 1672.0
34 TraesCS1B01G039300 chr6A 98.108 793 10 2 1861 2650 211314740 211315530 0.000000e+00 1376.0
35 TraesCS1B01G039300 chr6A 85.126 437 24 11 485 887 4627299 4626870 4.850000e-110 409.0
36 TraesCS1B01G039300 chr6A 99.444 180 1 0 1641 1820 605361584 605361405 1.400000e-85 327.0
37 TraesCS1B01G039300 chr6A 94.839 155 7 1 222 375 4627566 4627412 1.870000e-59 241.0
38 TraesCS1B01G039300 chr6A 95.098 102 5 0 5101 5202 35325937 35325836 1.500000e-35 161.0
39 TraesCS1B01G039300 chr6A 93.443 61 3 1 4904 4963 346590685 346590625 7.170000e-14 89.8
40 TraesCS1B01G039300 chr6A 88.710 62 6 1 263 323 4531361 4531422 2.010000e-09 75.0
41 TraesCS1B01G039300 chr5D 95.336 1308 34 6 2717 4001 557863577 557862274 0.000000e+00 2052.0
42 TraesCS1B01G039300 chr5D 95.183 1308 36 6 2717 4001 398036810 398038113 0.000000e+00 2041.0
43 TraesCS1B01G039300 chr5D 95.872 969 33 4 2717 3684 16573349 16572387 0.000000e+00 1561.0
44 TraesCS1B01G039300 chr5D 97.714 831 16 3 1821 2650 557864527 557863699 0.000000e+00 1426.0
45 TraesCS1B01G039300 chr5D 97.349 830 20 1 1821 2650 398035861 398036688 0.000000e+00 1410.0
46 TraesCS1B01G039300 chr5D 96.986 730 17 2 912 1641 398035154 398035878 0.000000e+00 1221.0
47 TraesCS1B01G039300 chr5D 96.311 732 19 5 912 1641 16575021 16574296 0.000000e+00 1195.0
48 TraesCS1B01G039300 chr5D 93.057 821 23 4 1861 2650 16574288 16573471 0.000000e+00 1170.0
49 TraesCS1B01G039300 chr5D 92.273 220 6 2 1 209 557875331 557875112 8.470000e-78 302.0
50 TraesCS1B01G039300 chr5D 89.545 220 12 3 1 209 16576369 16576150 8.590000e-68 268.0
51 TraesCS1B01G039300 chr5D 96.000 150 5 1 63 212 398033892 398034040 5.200000e-60 243.0
52 TraesCS1B01G039300 chr5D 97.826 46 0 1 3 48 398033851 398033895 1.550000e-10 78.7
53 TraesCS1B01G039300 chr5D 100.000 32 0 0 2686 2717 16573523 16573492 5.630000e-05 60.2
54 TraesCS1B01G039300 chr5D 100.000 31 0 0 2687 2717 557863750 557863720 2.020000e-04 58.4
55 TraesCS1B01G039300 chr2D 94.439 1025 32 5 3000 4001 415156336 415157358 0.000000e+00 1554.0
56 TraesCS1B01G039300 chr2D 94.789 806 34 5 2717 3518 420721524 420722325 0.000000e+00 1249.0
57 TraesCS1B01G039300 chr2D 100.000 31 0 0 2687 2717 420721351 420721381 2.020000e-04 58.4
58 TraesCS1B01G039300 chr7A 97.115 728 15 3 915 1641 151593893 151593171 0.000000e+00 1223.0
59 TraesCS1B01G039300 chr7A 92.717 865 27 9 1821 2650 151593188 151592325 0.000000e+00 1216.0
60 TraesCS1B01G039300 chr7A 88.636 220 14 7 1 209 151595244 151595025 1.860000e-64 257.0
61 TraesCS1B01G039300 chr7A 93.103 58 4 0 4893 4950 493700531 493700474 9.280000e-13 86.1
62 TraesCS1B01G039300 chr2A 94.254 731 37 2 912 1641 315961309 315962035 0.000000e+00 1112.0
63 TraesCS1B01G039300 chr2A 92.593 108 8 0 5095 5202 650241308 650241201 6.970000e-34 156.0
64 TraesCS1B01G039300 chr2A 96.078 51 2 0 4901 4951 57447057 57447107 3.340000e-12 84.2
65 TraesCS1B01G039300 chr2A 91.525 59 5 0 4904 4962 569588171 569588113 1.200000e-11 82.4
66 TraesCS1B01G039300 chr1A 87.486 919 87 10 4004 4905 14600699 14599792 0.000000e+00 1035.0
67 TraesCS1B01G039300 chr1A 86.400 125 4 1 4960 5071 14599794 14599670 1.970000e-24 124.0
68 TraesCS1B01G039300 chr1A 92.308 52 4 0 4900 4951 335543460 335543409 2.010000e-09 75.0
69 TraesCS1B01G039300 chr6B 92.421 409 23 3 3517 3919 483725296 483724890 1.260000e-160 577.0
70 TraesCS1B01G039300 chr6B 91.198 409 26 5 3517 3919 152441170 152440766 9.850000e-152 547.0
71 TraesCS1B01G039300 chr6B 79.208 202 26 7 399 595 9380060 9380250 5.470000e-25 126.0
72 TraesCS1B01G039300 chr3B 91.198 409 26 5 3517 3919 286476899 286477303 9.850000e-152 547.0
73 TraesCS1B01G039300 chr3B 97.059 102 3 0 5101 5202 436561652 436561753 6.930000e-39 172.0
74 TraesCS1B01G039300 chr3B 93.578 109 5 2 5094 5202 786783979 786784085 1.500000e-35 161.0
75 TraesCS1B01G039300 chr1D 83.610 482 46 15 4398 4874 13355765 13355312 6.230000e-114 422.0
76 TraesCS1B01G039300 chr1D 88.991 109 10 2 4999 5105 13355204 13355096 3.270000e-27 134.0
77 TraesCS1B01G039300 chr1D 94.231 52 3 0 4900 4951 475911948 475911897 4.320000e-11 80.5
78 TraesCS1B01G039300 chr1D 92.593 54 4 0 4903 4956 142966610 142966663 1.550000e-10 78.7
79 TraesCS1B01G039300 chr7B 99.448 181 1 0 1640 1820 46028673 46028493 3.880000e-86 329.0
80 TraesCS1B01G039300 chr7B 97.884 189 3 1 1639 1827 198551069 198551256 5.020000e-85 326.0
81 TraesCS1B01G039300 chr7B 98.387 186 2 1 1638 1823 252794450 252794266 5.020000e-85 326.0
82 TraesCS1B01G039300 chr7B 97.030 101 3 0 5102 5202 603591627 603591727 2.490000e-38 171.0
83 TraesCS1B01G039300 chr5B 99.444 180 1 0 1642 1821 284367523 284367702 1.400000e-85 327.0
84 TraesCS1B01G039300 chr5A 98.907 183 2 0 1639 1821 463712165 463712347 1.400000e-85 327.0
85 TraesCS1B01G039300 chr5A 94.444 108 5 1 5096 5202 611639848 611639955 1.160000e-36 165.0
86 TraesCS1B01G039300 chr4A 98.907 183 2 0 1639 1821 662286867 662287049 1.400000e-85 327.0
87 TraesCS1B01G039300 chr4B 99.441 179 1 0 1642 1820 128540849 128540671 5.020000e-85 326.0
88 TraesCS1B01G039300 chr4B 98.901 182 2 0 1642 1823 588430996 588430815 5.020000e-85 326.0
89 TraesCS1B01G039300 chr4B 95.146 103 3 1 5100 5202 95717029 95717129 1.500000e-35 161.0
90 TraesCS1B01G039300 chr4B 100.000 38 0 0 3964 4001 160257975 160258012 2.600000e-08 71.3
91 TraesCS1B01G039300 chr4B 100.000 31 0 0 2687 2717 236163731 236163701 2.020000e-04 58.4
92 TraesCS1B01G039300 chr3A 96.970 99 3 0 5104 5202 580564995 580565093 3.220000e-37 167.0
93 TraesCS1B01G039300 chr6D 100.000 30 0 0 4716 4745 453996308 453996279 7.280000e-04 56.5


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 TraesCS1B01G039300 chr1B 19016819 19022020 5201 False 4832.700000 9607 100.000000 1 5202 2 chr1B.!!$F3 5201
1 TraesCS1B01G039300 chr1B 602338436 602342749 4313 False 936.500000 1884 94.276250 1 4001 4 chr1B.!!$F4 4000
2 TraesCS1B01G039300 chr7D 553871630 553875891 4261 False 1242.000000 2124 95.323500 1 4001 4 chr7D.!!$F3 4000
3 TraesCS1B01G039300 chr4D 447218371 447222571 4200 True 1008.280000 2108 97.611600 63 4001 5 chr4D.!!$R1 3938
4 TraesCS1B01G039300 chr3D 577327979 577329001 1022 False 1520.000000 1520 93.854000 3000 4001 1 chr3D.!!$F2 1001
5 TraesCS1B01G039300 chr3D 250986307 250989266 2959 False 1213.100000 2104 97.963000 912 4001 4 chr3D.!!$F3 3089
6 TraesCS1B01G039300 chr3D 10523133 10525992 2859 True 607.920000 1402 96.347800 8 2717 5 chr3D.!!$R3 2709
7 TraesCS1B01G039300 chr6A 211313289 211316954 3665 False 1700.000000 2052 95.627000 1 4001 3 chr6A.!!$F2 4000
8 TraesCS1B01G039300 chr6A 4626870 4627566 696 True 325.000000 409 89.982500 222 887 2 chr6A.!!$R4 665
9 TraesCS1B01G039300 chr5D 557862274 557864527 2253 True 1178.800000 2052 97.683333 1821 4001 3 chr5D.!!$R3 2180
10 TraesCS1B01G039300 chr5D 398033851 398038113 4262 False 998.740000 2041 96.668800 3 4001 5 chr5D.!!$F1 3998
11 TraesCS1B01G039300 chr5D 16572387 16576369 3982 True 850.840000 1561 94.957000 1 3684 5 chr5D.!!$R2 3683
12 TraesCS1B01G039300 chr2D 415156336 415157358 1022 False 1554.000000 1554 94.439000 3000 4001 1 chr2D.!!$F1 1001
13 TraesCS1B01G039300 chr2D 420721351 420722325 974 False 653.700000 1249 97.394500 2687 3518 2 chr2D.!!$F2 831
14 TraesCS1B01G039300 chr7A 151592325 151595244 2919 True 898.666667 1223 92.822667 1 2650 3 chr7A.!!$R2 2649
15 TraesCS1B01G039300 chr2A 315961309 315962035 726 False 1112.000000 1112 94.254000 912 1641 1 chr2A.!!$F2 729
16 TraesCS1B01G039300 chr1A 14599670 14600699 1029 True 579.500000 1035 86.943000 4004 5071 2 chr1A.!!$R2 1067
17 TraesCS1B01G039300 chr1D 13355096 13355765 669 True 278.000000 422 86.300500 4398 5105 2 chr1D.!!$R2 707


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
141 153 1.374758 GCAACTCCAGTCACTCCCG 60.375 63.158 0.0 0.0 0.00 5.14 F
1768 2460 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.0 0.0 0.00 4.94 F
1777 2469 0.107831 TTGAACCCGTGACCTCTTGG 59.892 55.000 0.0 0.0 39.83 3.61 F
2097 2822 0.108804 GTCACGAGATCCTTTCCGCA 60.109 55.000 0.0 0.0 0.00 5.69 F
2664 3398 0.109412 GTGAAGCATGAGCCAAGCAC 60.109 55.000 0.0 0.0 43.56 4.40 F
2668 3402 0.323087 AGCATGAGCCAAGCACATCA 60.323 50.000 0.0 0.0 37.73 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 2502 0.100861 CGTACTCTTCGAAGGGGAGC 59.899 60.0 28.03 15.97 32.01 4.70 R
2645 3379 0.109412 GTGCTTGGCTCATGCTTCAC 60.109 55.0 12.12 2.33 39.59 3.18 R
2649 3383 0.323087 TGATGTGCTTGGCTCATGCT 60.323 50.0 11.00 0.00 41.77 3.79 R
3871 4992 0.942962 GATCAGCATCAAGGGCTTCG 59.057 55.0 0.00 0.00 40.23 3.79 R
4138 5261 0.107800 CTCATCAGTGGCAGGGACAG 60.108 60.0 0.00 0.00 0.00 3.51 R
4413 5551 0.637195 TAGGCTGGAAGGTCCTAGCT 59.363 55.0 11.19 0.00 39.23 3.32 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)



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

AutoCloner maintained by Alex Coulton.