Multiple sequence alignment - TraesCS4B01G318400

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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 TraesCS4B01G318400 chr4B 100.000 5773 0 0 1 5773 608965689 608971461 0.000000e+00 10661.0
1 TraesCS4B01G318400 chr4B 92.398 171 12 1 5222 5391 61314274 61314104 5.780000e-60 243.0
2 TraesCS4B01G318400 chr4B 99.153 118 1 0 2939 3056 545037295 545037178 4.530000e-51 213.0
3 TraesCS4B01G318400 chr4B 94.737 133 6 1 3463 3594 20719388 20719256 7.580000e-49 206.0
4 TraesCS4B01G318400 chr4B 93.182 132 9 0 5260 5391 522286018 522285887 1.640000e-45 195.0
5 TraesCS4B01G318400 chr4B 90.909 143 11 2 3468 3609 300811321 300811462 2.120000e-44 191.0
6 TraesCS4B01G318400 chr4B 90.541 148 8 6 3463 3608 425296292 425296149 2.120000e-44 191.0
7 TraesCS4B01G318400 chr4B 90.972 144 7 6 3469 3611 132331055 132331193 7.640000e-44 189.0
8 TraesCS4B01G318400 chr4D 89.851 2020 109 48 1 1982 480878248 480880209 0.000000e+00 2507.0
9 TraesCS4B01G318400 chr4D 93.349 1308 62 13 3593 4891 480881389 480882680 0.000000e+00 1910.0
10 TraesCS4B01G318400 chr4D 93.408 622 32 7 2028 2647 480880197 480880811 0.000000e+00 913.0
11 TraesCS4B01G318400 chr4D 91.697 277 10 3 2678 2941 480880815 480881091 7.060000e-99 372.0
12 TraesCS4B01G318400 chr4D 97.895 190 4 0 3283 3472 480881200 480881389 4.310000e-86 329.0
13 TraesCS4B01G318400 chr4D 80.531 339 21 26 5467 5773 480883323 480883648 9.740000e-53 219.0
14 TraesCS4B01G318400 chr4D 94.643 112 6 0 3055 3166 480881090 480881201 2.140000e-39 174.0
15 TraesCS4B01G318400 chr4D 93.617 47 3 0 5163 5209 480883212 480883258 2.890000e-08 71.3
16 TraesCS4B01G318400 chr5A 88.280 1988 139 57 3 1938 662532394 662530449 0.000000e+00 2294.0
17 TraesCS4B01G318400 chr5A 91.703 1627 92 17 3591 5209 662529164 662527573 0.000000e+00 2217.0
18 TraesCS4B01G318400 chr5A 87.661 932 80 14 2040 2941 662530381 662529455 0.000000e+00 1051.0
19 TraesCS4B01G318400 chr5A 95.789 190 6 1 3281 3470 662529348 662529161 7.270000e-79 305.0
20 TraesCS4B01G318400 chr5A 94.815 135 5 2 3469 3601 652657840 652657706 5.860000e-50 209.0
21 TraesCS4B01G318400 chr5A 90.476 147 10 4 3467 3611 708307783 708307639 2.120000e-44 191.0
22 TraesCS4B01G318400 chr5A 95.327 107 5 0 3055 3161 662529456 662529350 2.770000e-38 171.0
23 TraesCS4B01G318400 chr5A 78.138 247 39 10 1 240 320058493 320058731 6.030000e-30 143.0
24 TraesCS4B01G318400 chr5A 83.117 154 10 6 5489 5641 662527500 662527362 6.070000e-25 126.0
25 TraesCS4B01G318400 chr5A 93.103 58 0 3 5402 5459 662527563 662527510 1.330000e-11 82.4
26 TraesCS4B01G318400 chr3B 89.860 286 12 7 4951 5233 717561137 717560866 9.200000e-93 351.0
27 TraesCS4B01G318400 chr3B 94.340 159 8 1 5236 5393 815182903 815183061 5.780000e-60 243.0
28 TraesCS4B01G318400 chr3B 98.361 122 2 0 2940 3061 667390119 667389998 1.260000e-51 215.0
29 TraesCS4B01G318400 chr3B 82.018 228 19 15 5392 5605 717560871 717560652 2.140000e-39 174.0
30 TraesCS4B01G318400 chr3B 85.057 87 8 3 3198 3284 713874113 713874032 3.710000e-12 84.2
31 TraesCS4B01G318400 chr5B 88.811 286 15 8 4951 5233 42874090 42873819 9.270000e-88 335.0
32 TraesCS4B01G318400 chr5B 99.153 118 1 0 2940 3057 711156068 711155951 4.530000e-51 213.0
33 TraesCS4B01G318400 chr5B 91.837 147 8 4 3468 3611 18077089 18076944 9.810000e-48 202.0
34 TraesCS4B01G318400 chr5B 84.000 225 18 12 5392 5606 42873824 42873608 3.530000e-47 200.0
35 TraesCS4B01G318400 chr5B 92.254 142 9 2 3460 3600 118525764 118525904 3.530000e-47 200.0
36 TraesCS4B01G318400 chr6B 93.567 171 10 1 5224 5393 561695754 561695924 2.670000e-63 254.0
37 TraesCS4B01G318400 chr6B 94.776 134 6 1 2939 3072 164883035 164882903 2.110000e-49 207.0
38 TraesCS4B01G318400 chr6B 93.478 138 7 2 2940 3075 658678568 658678705 2.730000e-48 204.0
39 TraesCS4B01G318400 chr1B 96.129 155 5 1 5236 5389 301635740 301635894 9.600000e-63 252.0
40 TraesCS4B01G318400 chr1B 95.385 130 4 2 3469 3597 50989950 50990078 7.580000e-49 206.0
41 TraesCS4B01G318400 chr1B 82.645 121 21 0 1594 1714 491040849 491040729 2.200000e-19 108.0
42 TraesCS4B01G318400 chr1B 97.436 39 1 0 3165 3203 320588132 320588094 3.730000e-07 67.6
43 TraesCS4B01G318400 chr6A 95.484 155 5 2 5236 5389 531408681 531408834 4.470000e-61 246.0
44 TraesCS4B01G318400 chr6A 92.308 169 10 3 5229 5395 58764721 58764554 2.690000e-58 237.0
45 TraesCS4B01G318400 chr6A 97.561 123 3 0 2937 3059 601207222 601207344 1.630000e-50 211.0
46 TraesCS4B01G318400 chr6A 85.185 81 9 1 3205 3282 607680091 607680171 4.800000e-11 80.5
47 TraesCS4B01G318400 chr3A 95.484 155 6 1 5236 5389 163792625 163792471 4.470000e-61 246.0
48 TraesCS4B01G318400 chr3A 90.476 147 10 4 3467 3611 405828114 405827970 2.120000e-44 191.0
49 TraesCS4B01G318400 chr4A 94.839 155 7 1 5236 5389 710670511 710670665 2.080000e-59 241.0
50 TraesCS4B01G318400 chr4A 92.222 90 7 0 3200 3289 738372227 738372316 1.690000e-25 128.0
51 TraesCS4B01G318400 chr4A 84.524 84 4 6 3202 3285 5817676 5817750 2.230000e-09 75.0
52 TraesCS4B01G318400 chr2B 93.750 160 9 1 5236 5394 504194992 504195151 7.480000e-59 239.0
53 TraesCS4B01G318400 chr2B 95.489 133 3 2 3469 3598 19447944 19447812 5.860000e-50 209.0
54 TraesCS4B01G318400 chr5D 99.167 120 1 0 2939 3058 47283883 47284002 3.500000e-52 217.0
55 TraesCS4B01G318400 chr5D 97.561 123 3 0 2934 3056 462793848 462793970 1.630000e-50 211.0
56 TraesCS4B01G318400 chr3D 94.245 139 4 2 2939 3077 66262961 66262827 5.860000e-50 209.0
57 TraesCS4B01G318400 chr3D 84.783 92 5 2 3200 3282 94644848 94644757 3.710000e-12 84.2
58 TraesCS4B01G318400 chr3D 100.000 28 0 0 212 239 574723828 574723855 1.000000e-02 52.8
59 TraesCS4B01G318400 chr7B 95.420 131 5 1 3466 3595 736367488 736367618 2.110000e-49 207.0
60 TraesCS4B01G318400 chr7B 92.308 143 8 3 3463 3604 227053654 227053794 3.530000e-47 200.0
61 TraesCS4B01G318400 chr7B 90.476 147 12 2 3462 3607 141907369 141907224 5.900000e-45 193.0
62 TraesCS4B01G318400 chr7B 85.542 83 6 4 3200 3282 168752754 168752678 1.330000e-11 82.4
63 TraesCS4B01G318400 chr7B 83.721 86 13 1 1 85 88859967 88859882 4.800000e-11 80.5
64 TraesCS4B01G318400 chr2A 92.857 140 8 2 3463 3600 70030628 70030767 9.810000e-48 202.0
65 TraesCS4B01G318400 chr1D 89.865 148 12 3 3466 3611 384835328 384835474 2.750000e-43 187.0
66 TraesCS4B01G318400 chr1D 86.792 106 13 1 29 134 363057792 363057896 3.650000e-22 117.0
67 TraesCS4B01G318400 chr1D 83.065 124 21 0 1591 1714 366723826 366723949 4.730000e-21 113.0
68 TraesCS4B01G318400 chr1D 88.235 85 9 1 3200 3284 310858581 310858498 3.680000e-17 100.0
69 TraesCS4B01G318400 chr2D 88.816 152 13 4 3461 3611 619720539 619720687 3.550000e-42 183.0
70 TraesCS4B01G318400 chr2D 87.640 89 6 1 3159 3242 584666822 584666910 1.320000e-16 99.0
71 TraesCS4B01G318400 chr1A 83.333 120 20 0 1595 1714 465454634 465454515 1.700000e-20 111.0
72 TraesCS4B01G318400 chr1A 92.308 39 3 0 3162 3200 172566506 172566544 8.080000e-04 56.5
73 TraesCS4B01G318400 chr7D 82.609 115 17 3 19 132 1248611 1248723 1.320000e-16 99.0
74 TraesCS4B01G318400 chr6D 83.146 89 10 5 3200 3287 7460256 7460172 6.200000e-10 76.8


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 TraesCS4B01G318400 chr4B 608965689 608971461 5772 False 10661.000000 10661 100.000000 1 5773 1 chr4B.!!$F3 5772
1 TraesCS4B01G318400 chr4D 480878248 480883648 5400 False 811.912500 2507 91.873875 1 5773 8 chr4D.!!$F1 5772
2 TraesCS4B01G318400 chr5A 662527362 662532394 5032 True 892.342857 2294 90.711429 3 5641 7 chr5A.!!$R3 5638


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
667 702 0.035317 GATACATCTCATGGCGCCCA 59.965 55.0 26.77 12.96 38.19 5.36 F
757 799 0.109342 CTGCTTCTGGGTCCACAGTT 59.891 55.0 0.00 0.00 39.48 3.16 F
785 827 0.163788 CCACGTGTCATTGAACGAGC 59.836 55.0 15.65 0.00 42.32 5.03 F
791 833 0.234625 GTCATTGAACGAGCGCAACA 59.765 50.0 11.47 0.00 0.00 3.33 F
1996 2074 0.247814 GCATCGTGCGAGTTTGATGG 60.248 55.0 0.00 0.00 38.85 3.51 F
2958 3081 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.00 44.66 2.17 F
2961 3084 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.00 44.66 2.12 F
4612 4747 0.110688 CACTCACATTGTCAACCGCG 60.111 55.0 0.00 0.00 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 2480 0.034059 CTGACGAGGTTCTTGTGCCT 59.966 55.000 0.00 0.0 37.91 4.75 R
2414 2518 0.968901 TGTACCTGTAGGCACCCTCG 60.969 60.000 0.00 0.0 39.32 4.63 R
2665 2770 1.256812 ATAGCACTTGGCAAACCCAC 58.743 50.000 0.00 0.0 45.34 4.61 R
2779 2899 8.394121 GTCTTCTAAGAACTAAAATGCTCATGG 58.606 37.037 0.00 0.0 36.68 3.66 R
2939 3062 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.0 46.06 2.59 R
4593 4728 0.110688 CGCGGTTGACAATGTGAGTG 60.111 55.000 0.00 0.0 0.00 3.51 R
4717 4852 1.538512 GTGCCATTCCCATCATCATCG 59.461 52.381 0.00 0.0 0.00 3.84 R
5523 5972 0.036590 ACCAAACCAATGGCAATGGC 59.963 50.000 21.40 0.0 44.75 4.40 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)



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AutoCloner maintained by Alex Coulton.