Multiple sequence alignment - TraesCS7B01G332000

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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 TraesCS7B01G332000 chr7B 100.000 3655 0 0 1 3655 587266106 587269760 0.000000e+00 6750.0
1 TraesCS7B01G332000 chr7B 98.636 3667 35 5 1 3655 587100889 587104552 0.000000e+00 6481.0
2 TraesCS7B01G332000 chr7B 93.442 2211 91 16 1 2160 587478792 587480999 0.000000e+00 3230.0
3 TraesCS7B01G332000 chr7B 92.833 2065 84 26 1 2019 587518051 587520097 0.000000e+00 2935.0
4 TraesCS7B01G332000 chr7B 95.616 1095 37 3 2209 3302 587520088 587521172 0.000000e+00 1746.0
5 TraesCS7B01G332000 chr7B 94.558 1121 24 7 870 1953 587440662 587441782 0.000000e+00 1698.0
6 TraesCS7B01G332000 chr7B 97.622 883 17 3 1 880 587438246 587439127 0.000000e+00 1511.0
7 TraesCS7B01G332000 chr7B 96.189 866 32 1 2790 3655 587442620 587443484 0.000000e+00 1415.0
8 TraesCS7B01G332000 chr7B 95.843 866 32 4 2790 3655 587481947 587482808 0.000000e+00 1397.0
9 TraesCS7B01G332000 chr7B 92.943 836 32 7 1511 2334 587620573 587621393 0.000000e+00 1192.0
10 TraesCS7B01G332000 chr7B 93.226 620 17 12 2178 2792 587441940 587442539 0.000000e+00 889.0
11 TraesCS7B01G332000 chr7B 93.160 614 19 5 928 1518 587615264 587615877 0.000000e+00 880.0
12 TraesCS7B01G332000 chr7B 91.276 619 32 6 228 846 587614631 587615227 0.000000e+00 824.0
13 TraesCS7B01G332000 chr7B 98.365 367 6 0 3289 3655 587522619 587522985 0.000000e+00 645.0
14 TraesCS7B01G332000 chr7B 96.721 305 6 3 2178 2479 587480986 587481289 4.210000e-139 505.0
15 TraesCS7B01G332000 chr7B 96.861 223 7 0 1 223 587600125 587600347 1.240000e-99 374.0
16 TraesCS7B01G332000 chr7B 88.379 327 12 11 2472 2792 587481560 587481866 1.600000e-98 370.0
17 TraesCS7B01G332000 chr7B 94.667 150 3 1 1988 2132 587441782 587441931 1.020000e-55 228.0
18 TraesCS7B01G332000 chr7B 83.398 259 27 6 2799 3043 587653122 587653378 3.670000e-55 226.0
19 TraesCS7B01G332000 chr7B 83.616 177 27 2 534 709 639285740 639285565 8.120000e-37 165.0
20 TraesCS7B01G332000 chr7B 85.714 154 12 2 2395 2539 587635764 587635916 1.760000e-33 154.0
21 TraesCS7B01G332000 chr7B 95.556 90 4 0 2317 2406 587635354 587635443 1.060000e-30 145.0
22 TraesCS7B01G332000 chr7B 77.193 228 18 5 3060 3255 587654479 587654704 6.460000e-18 102.0
23 TraesCS7B01G332000 chr7B 87.097 62 4 3 2347 2406 587635687 587635746 2.360000e-07 67.6
24 TraesCS7B01G332000 chr6B 96.814 2982 52 15 711 3655 694681056 694684031 0.000000e+00 4940.0
25 TraesCS7B01G332000 chr6B 84.692 503 60 12 3 493 617126804 617127301 1.530000e-133 486.0
26 TraesCS7B01G332000 chr7D 89.919 1359 65 30 706 2031 543731495 543732814 0.000000e+00 1685.0
27 TraesCS7B01G332000 chr7D 86.288 299 19 5 2896 3194 543733522 543733798 4.590000e-79 305.0
28 TraesCS7B01G332000 chr7D 85.121 289 26 9 2127 2406 543732833 543733113 2.780000e-71 279.0
29 TraesCS7B01G332000 chr7D 85.827 254 21 8 2395 2639 543733131 543733378 4.680000e-64 255.0
30 TraesCS7B01G332000 chr7D 92.857 126 7 1 2775 2900 543733374 543733497 8.060000e-42 182.0
31 TraesCS7B01G332000 chr7A 89.487 1170 84 21 706 1841 625642256 625643420 0.000000e+00 1443.0
32 TraesCS7B01G332000 chr7A 88.786 1186 76 25 706 1841 625675038 625676216 0.000000e+00 1400.0
33 TraesCS7B01G332000 chr1D 85.601 882 63 23 706 1531 110905255 110906128 0.000000e+00 867.0
34 TraesCS7B01G332000 chr3B 83.357 715 94 19 3 706 762402190 762402890 3.980000e-179 638.0
35 TraesCS7B01G332000 chr3B 94.118 323 19 0 3333 3655 187547164 187546842 3.280000e-135 492.0
36 TraesCS7B01G332000 chr5D 82.627 708 108 9 3 702 72198332 72197632 2.410000e-171 612.0
37 TraesCS7B01G332000 chr5D 85.000 180 24 3 533 709 559603428 559603607 2.900000e-41 180.0
38 TraesCS7B01G332000 chr4A 81.466 723 109 17 3 706 732795043 732795759 1.470000e-158 569.0
39 TraesCS7B01G332000 chr6D 95.666 323 12 1 3333 3655 388547382 388547702 5.410000e-143 518.0
40 TraesCS7B01G332000 chr2D 95.356 323 15 0 3333 3655 102820227 102819905 7.000000e-142 514.0
41 TraesCS7B01G332000 chr2D 85.465 172 24 1 530 700 501552961 501552790 1.040000e-40 178.0
42 TraesCS7B01G332000 chr5B 94.704 321 16 1 3333 3653 467381311 467380992 7.050000e-137 497.0


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 TraesCS7B01G332000 chr7B 587266106 587269760 3654 False 6750.000000 6750 100.000000 1 3655 1 chr7B.!!$F2 3654
1 TraesCS7B01G332000 chr7B 587100889 587104552 3663 False 6481.000000 6481 98.636000 1 3655 1 chr7B.!!$F1 3654
2 TraesCS7B01G332000 chr7B 587518051 587522985 4934 False 1775.333333 2935 95.604667 1 3655 3 chr7B.!!$F7 3654
3 TraesCS7B01G332000 chr7B 587478792 587482808 4016 False 1375.500000 3230 93.596250 1 3655 4 chr7B.!!$F6 3654
4 TraesCS7B01G332000 chr7B 587620573 587621393 820 False 1192.000000 1192 92.943000 1511 2334 1 chr7B.!!$F4 823
5 TraesCS7B01G332000 chr7B 587438246 587443484 5238 False 1148.200000 1698 95.252400 1 3655 5 chr7B.!!$F5 3654
6 TraesCS7B01G332000 chr7B 587614631 587615877 1246 False 852.000000 880 92.218000 228 1518 2 chr7B.!!$F8 1290
7 TraesCS7B01G332000 chr6B 694681056 694684031 2975 False 4940.000000 4940 96.814000 711 3655 1 chr6B.!!$F2 2944
8 TraesCS7B01G332000 chr7D 543731495 543733798 2303 False 541.200000 1685 88.002400 706 3194 5 chr7D.!!$F1 2488
9 TraesCS7B01G332000 chr7A 625642256 625643420 1164 False 1443.000000 1443 89.487000 706 1841 1 chr7A.!!$F1 1135
10 TraesCS7B01G332000 chr7A 625675038 625676216 1178 False 1400.000000 1400 88.786000 706 1841 1 chr7A.!!$F2 1135
11 TraesCS7B01G332000 chr1D 110905255 110906128 873 False 867.000000 867 85.601000 706 1531 1 chr1D.!!$F1 825
12 TraesCS7B01G332000 chr3B 762402190 762402890 700 False 638.000000 638 83.357000 3 706 1 chr3B.!!$F1 703
13 TraesCS7B01G332000 chr5D 72197632 72198332 700 True 612.000000 612 82.627000 3 702 1 chr5D.!!$R1 699
14 TraesCS7B01G332000 chr4A 732795043 732795759 716 False 569.000000 569 81.466000 3 706 1 chr4A.!!$F1 703


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
828 863 0.396139 GATGGTGGCCATGGATGTGT 60.396 55.0 18.40 0.0 45.26 3.72 F
1662 3320 0.676466 ATCTTGTCGGCGGCATCAAA 60.676 50.0 17.58 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2570 4777 3.134574 TGCTACACTCCCAAATTTCGT 57.865 42.857 0.00 0.0 0.0 3.85 R
3006 5331 3.805422 CACGCTCAAAGTTTGGTAGTACA 59.195 43.478 15.47 0.0 0.0 2.90 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
456 478 0.474614 TTTTGGTGATCGGGTGTGGA 59.525 50.000 0.00 0.00 0.00 4.02
577 605 2.166664 ACAGAGAGTAATCTTGACGGCC 59.833 50.000 0.00 0.00 0.00 6.13
619 647 3.575297 CGATGCTTGAACTCGCTTG 57.425 52.632 0.00 0.00 0.00 4.01
828 863 0.396139 GATGGTGGCCATGGATGTGT 60.396 55.000 18.40 0.00 45.26 3.72
1049 2666 1.064946 CGCGATCGCTTCTTCCTCT 59.935 57.895 34.69 0.00 39.32 3.69
1662 3320 0.676466 ATCTTGTCGGCGGCATCAAA 60.676 50.000 17.58 0.00 0.00 2.69
2993 5318 5.955961 ATTATGGCAAAATTGTTAGGCCT 57.044 34.783 11.78 11.78 44.85 5.19
3058 5383 9.787532 GTATAAAATTGCAGTTCAGCTCAAATA 57.212 29.630 0.00 0.00 34.99 1.40
3097 5422 8.598916 TGACTCAAAATAGTACAAGTCCCAATA 58.401 33.333 0.00 0.00 33.79 1.90
3397 7182 6.183347 GCATATTGGGTATCTGCCTAAGAAT 58.817 40.000 0.00 0.00 38.79 2.40
3477 7262 6.534793 GCTGTGTTGGAAAGAAAGAAAATTCA 59.465 34.615 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
385 398 3.448934 ACATCACTCCCTGAGTCAATCT 58.551 45.455 0.00 0.0 41.37 2.40
577 605 1.880027 GGAAACCCACTGTAAGCACTG 59.120 52.381 0.00 0.0 37.60 3.66
619 647 4.760878 AGAGAATAAGACGGGAAAGAAGC 58.239 43.478 0.00 0.0 0.00 3.86
1049 2666 1.979155 CGAGCTGTGAGAGGTGGGA 60.979 63.158 0.00 0.0 30.42 4.37
1172 2815 4.134187 CGTCGCGGCACATGTCAC 62.134 66.667 12.89 0.0 0.00 3.67
2570 4777 3.134574 TGCTACACTCCCAAATTTCGT 57.865 42.857 0.00 0.0 0.00 3.85
3006 5331 3.805422 CACGCTCAAAGTTTGGTAGTACA 59.195 43.478 15.47 0.0 0.00 2.90
3089 5414 4.781087 TGGCCTACTGGTATATATTGGGAC 59.219 45.833 3.32 0.0 35.27 4.46
3097 5422 5.606749 TGAGATTTGTGGCCTACTGGTATAT 59.393 40.000 3.32 0.0 35.27 0.86
3397 7182 4.218635 AGTCTCTTACGAGCACATTCAAGA 59.781 41.667 0.00 0.0 37.19 3.02
3477 7262 5.527026 AAGAAGTTCATCCATCTCCCTTT 57.473 39.130 5.50 0.0 0.00 3.11
3609 7396 6.099845 TCCTTCCTAAGAGCCGAAATAGAATT 59.900 38.462 0.00 0.0 0.00 2.17
3610 7397 5.602978 TCCTTCCTAAGAGCCGAAATAGAAT 59.397 40.000 0.00 0.0 0.00 2.40



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

AutoCloner maintained by Alex Coulton.