Multiple sequence alignment - TraesCS7B01G496400

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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 TraesCS7B01G496400 chr7B 100.000 8347 0 0 1 8347 747269975 747278321 0.000000e+00 15415.0
1 TraesCS7B01G496400 chr7B 80.972 720 126 9 2428 3143 748649277 748648565 2.030000e-155 560.0
2 TraesCS7B01G496400 chr7B 83.444 604 86 8 5769 6366 748644779 748644184 4.400000e-152 549.0
3 TraesCS7B01G496400 chr7B 85.714 371 22 11 7281 7640 619071466 619071116 6.160000e-96 363.0
4 TraesCS7B01G496400 chr7B 74.455 963 188 43 1205 2143 746994608 746993680 6.160000e-96 363.0
5 TraesCS7B01G496400 chr7B 73.832 963 188 50 1205 2143 744921269 744920347 2.910000e-84 324.0
6 TraesCS7B01G496400 chr7B 90.717 237 20 2 7760 7994 619070925 619070689 1.750000e-81 315.0
7 TraesCS7B01G496400 chr7B 70.891 1010 204 56 5095 6071 744915075 744914123 4.030000e-33 154.0
8 TraesCS7B01G496400 chr7B 70.933 1008 200 58 5095 6071 746990457 746989512 1.450000e-32 152.0
9 TraesCS7B01G496400 chr7B 80.597 134 15 5 6745 6875 747398978 747399103 8.920000e-15 93.5
10 TraesCS7B01G496400 chr7D 77.128 1727 302 61 1819 3497 632812589 632810908 0.000000e+00 915.0
11 TraesCS7B01G496400 chr7D 74.490 980 184 36 4282 5217 632808330 632807373 1.710000e-96 364.0
12 TraesCS7B01G496400 chr7D 78.997 319 55 11 5776 6088 632804730 632804418 3.050000e-49 207.0
13 TraesCS7B01G496400 chr7D 86.010 193 22 4 1204 1392 632814774 632814583 1.420000e-47 202.0
14 TraesCS7B01G496400 chr7D 85.143 175 25 1 58 232 156184813 156184986 2.390000e-40 178.0
15 TraesCS7B01G496400 chr7D 81.818 143 14 7 6743 6879 632802085 632801949 8.860000e-20 110.0
16 TraesCS7B01G496400 chrUn 79.092 947 156 26 2419 3350 369060882 369059963 1.540000e-171 614.0
17 TraesCS7B01G496400 chrUn 78.986 947 156 27 2419 3350 369093819 369092901 2.580000e-169 606.0
18 TraesCS7B01G496400 chrUn 85.743 491 69 1 2419 2908 469995247 469994757 1.240000e-142 518.0
19 TraesCS7B01G496400 chrUn 88.764 89 4 5 7649 7737 295154399 295154481 4.120000e-18 104.0
20 TraesCS7B01G496400 chrUn 88.764 89 4 5 7649 7737 473591125 473591207 4.120000e-18 104.0
21 TraesCS7B01G496400 chr3A 90.476 378 17 10 7277 7642 708070629 708070259 1.630000e-131 481.0
22 TraesCS7B01G496400 chr3A 90.821 207 15 3 7635 7837 708070224 708070018 2.970000e-69 274.0
23 TraesCS7B01G496400 chr3A 94.186 172 10 0 7822 7993 708069973 708069802 6.430000e-66 263.0
24 TraesCS7B01G496400 chr3A 76.271 236 43 8 1 232 585571914 585572140 6.850000e-21 113.0
25 TraesCS7B01G496400 chr2A 90.186 377 19 6 7278 7642 34870294 34870664 7.580000e-130 475.0
26 TraesCS7B01G496400 chr2A 86.089 381 26 11 7276 7642 21921477 21921110 1.310000e-102 385.0
27 TraesCS7B01G496400 chr2A 94.350 177 10 0 7816 7992 21920992 21920816 1.070000e-68 272.0
28 TraesCS7B01G496400 chr2A 94.767 172 9 0 7822 7993 34870988 34871159 1.380000e-67 268.0
29 TraesCS7B01G496400 chr2A 91.304 161 10 2 7635 7791 34870698 34870858 5.070000e-52 217.0
30 TraesCS7B01G496400 chr2A 94.048 84 3 2 7635 7716 21921069 21920986 8.800000e-25 126.0
31 TraesCS7B01G496400 chr2A 92.308 39 1 1 7753 7791 34870782 34870818 4.000000e-03 54.7
32 TraesCS7B01G496400 chr7A 93.416 243 13 1 7754 7993 501316940 501316698 2.870000e-94 357.0
33 TraesCS7B01G496400 chr7A 85.000 380 23 9 7277 7642 501317410 501317051 1.030000e-93 355.0
34 TraesCS7B01G496400 chr7A 78.043 460 71 17 6178 6622 721073575 721074019 6.430000e-66 263.0
35 TraesCS7B01G496400 chr7A 73.028 786 141 44 4915 5671 734356871 734356128 2.360000e-50 211.0
36 TraesCS7B01G496400 chr7A 89.256 121 12 1 7635 7754 501317020 501316900 5.220000e-32 150.0
37 TraesCS7B01G496400 chr2D 85.673 349 34 11 7273 7608 16252397 16252742 3.710000e-93 353.0
38 TraesCS7B01G496400 chr6D 92.793 222 12 3 7423 7642 19089226 19089007 1.350000e-82 318.0
39 TraesCS7B01G496400 chr6D 88.199 161 5 5 7273 7420 19092794 19092635 6.660000e-41 180.0
40 TraesCS7B01G496400 chr6B 79.321 324 52 14 5766 6082 38213965 38214280 6.560000e-51 213.0
41 TraesCS7B01G496400 chr1B 80.952 273 36 10 62 318 396143739 396143467 1.420000e-47 202.0
42 TraesCS7B01G496400 chr1B 80.124 161 29 3 47 205 588643330 588643489 5.290000e-22 117.0
43 TraesCS7B01G496400 chr1B 88.636 88 9 1 133 220 426781701 426781787 1.150000e-18 106.0
44 TraesCS7B01G496400 chr5A 90.667 150 12 2 7845 7993 662003998 662003850 1.840000e-46 198.0
45 TraesCS7B01G496400 chr1D 78.451 297 42 17 48 326 294462910 294462618 3.100000e-39 174.0
46 TraesCS7B01G496400 chr2B 77.489 231 41 8 55 277 20355196 20354969 2.450000e-25 128.0
47 TraesCS7B01G496400 chr1A 89.000 100 10 1 7310 7408 186481400 186481301 1.140000e-23 122.0
48 TraesCS7B01G496400 chr1A 83.846 130 12 7 133 258 395468939 395469063 1.900000e-21 115.0
49 TraesCS7B01G496400 chr3D 92.208 77 5 1 7310 7385 598047640 598047564 3.190000e-19 108.0
50 TraesCS7B01G496400 chr5D 89.024 82 8 1 137 218 345945967 345946047 5.330000e-17 100.0
51 TraesCS7B01G496400 chr4B 91.667 48 2 2 940 985 95075203 95075156 1.940000e-06 65.8


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 TraesCS7B01G496400 chr7B 747269975 747278321 8346 False 15415.000000 15415 100.000000 1 8347 1 chr7B.!!$F1 8346
1 TraesCS7B01G496400 chr7B 748644184 748649277 5093 True 554.500000 560 82.208000 2428 6366 2 chr7B.!!$R5 3938
2 TraesCS7B01G496400 chr7B 619070689 619071466 777 True 339.000000 363 88.215500 7281 7994 2 chr7B.!!$R3 713
3 TraesCS7B01G496400 chr7B 744920347 744921269 922 True 324.000000 324 73.832000 1205 2143 1 chr7B.!!$R2 938
4 TraesCS7B01G496400 chr7B 746989512 746994608 5096 True 257.500000 363 72.694000 1205 6071 2 chr7B.!!$R4 4866
5 TraesCS7B01G496400 chr7D 632801949 632814774 12825 True 359.600000 915 79.688600 1204 6879 5 chr7D.!!$R1 5675
6 TraesCS7B01G496400 chrUn 369059963 369060882 919 True 614.000000 614 79.092000 2419 3350 1 chrUn.!!$R1 931
7 TraesCS7B01G496400 chrUn 369092901 369093819 918 True 606.000000 606 78.986000 2419 3350 1 chrUn.!!$R2 931
8 TraesCS7B01G496400 chr3A 708069802 708070629 827 True 339.333333 481 91.827667 7277 7993 3 chr3A.!!$R1 716
9 TraesCS7B01G496400 chr2A 21920816 21921477 661 True 261.000000 385 91.495667 7276 7992 3 chr2A.!!$R1 716
10 TraesCS7B01G496400 chr2A 34870294 34871159 865 False 253.675000 475 92.141250 7278 7993 4 chr2A.!!$F1 715
11 TraesCS7B01G496400 chr7A 501316698 501317410 712 True 287.333333 357 89.224000 7277 7993 3 chr7A.!!$R2 716
12 TraesCS7B01G496400 chr7A 734356128 734356871 743 True 211.000000 211 73.028000 4915 5671 1 chr7A.!!$R1 756
13 TraesCS7B01G496400 chr6D 19089007 19092794 3787 True 249.000000 318 90.496000 7273 7642 2 chr6D.!!$R1 369


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
774 775 0.032912 TCCATCATGCAAGGTGCCAT 60.033 50.0 0.00 0.00 44.23 4.40 F
1856 3459 0.033601 TTGGTTGTGTTGGAGGTGCT 60.034 50.0 0.00 0.00 0.00 4.40 F
3367 7612 0.038166 ACTGTGCACGGGAATGGATT 59.962 50.0 28.65 2.85 0.00 3.01 F
3881 8834 0.038159 GCGCCTGAGTAGACACTTGT 60.038 55.0 0.00 0.00 34.21 3.16 F
4377 10421 0.035152 GTGGAGTGCACCCATGATCA 60.035 55.0 24.13 0.00 35.91 2.92 F
6260 15269 0.036577 CTCCAGTTCTCTGTGCCCTG 60.037 60.0 0.00 0.00 39.82 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2354 4648 0.036164 AGCGATGTAAAGGGTGCACA 59.964 50.0 20.43 0.0 0.00 4.57 R
3787 8739 0.106167 TGGTATCCTCCTCCGAGTGG 60.106 60.0 0.00 0.0 33.93 4.00 R
4262 9346 0.033504 ATCGGCGAACAGAACACACT 59.966 50.0 15.93 0.0 0.00 3.55 R
5560 14208 0.174617 TCTTCACACACGCACAGTCA 59.825 50.0 0.00 0.0 0.00 3.41 R
6376 15385 0.186386 TGGGGTGGGGTTGTAGTTTG 59.814 55.0 0.00 0.0 0.00 2.93 R
8104 22340 0.030773 GATCGATGGCTGTAGACGCA 59.969 55.0 0.54 0.0 0.00 5.24 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.