Multiple sequence alignment - TraesCS7A01G075900

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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 TraesCS7A01G075900 chr7A 100.000 2985 0 0 1 2985 41465877 41462893 0.000000e+00 5513.0
1 TraesCS7A01G075900 chr7A 97.969 3003 35 2 1 2983 617597407 617600403 0.000000e+00 5184.0
2 TraesCS7A01G075900 chr2A 97.736 3003 42 2 1 2983 756523374 756526370 0.000000e+00 5145.0
3 TraesCS7A01G075900 chr3D 91.241 1096 51 13 1461 2535 583596393 583597464 0.000000e+00 1450.0
4 TraesCS7A01G075900 chr3D 87.892 446 30 14 1083 1512 614089770 614089333 1.240000e-138 503.0
5 TraesCS7A01G075900 chr3D 96.257 187 7 0 518 704 553215153 553214967 1.040000e-79 307.0
6 TraesCS7A01G075900 chr3D 95.513 156 5 1 860 1013 553214395 553214240 6.390000e-62 248.0
7 TraesCS7A01G075900 chr3D 96.226 106 4 0 705 810 553214933 553214828 1.100000e-39 174.0
8 TraesCS7A01G075900 chr7D 91.158 1097 51 14 1461 2535 449503417 449502345 0.000000e+00 1447.0
9 TraesCS7A01G075900 chr7D 91.158 1097 50 17 1461 2535 621797432 621798503 0.000000e+00 1445.0
10 TraesCS7A01G075900 chr7D 90.537 391 18 1 2612 2983 340192899 340193289 1.600000e-137 499.0
11 TraesCS7A01G075900 chr7D 94.828 58 3 0 2559 2616 340192869 340192926 1.140000e-14 91.6
12 TraesCS7A01G075900 chr7D 95.000 40 2 0 261 300 55126291 55126330 2.480000e-06 63.9
13 TraesCS7A01G075900 chr3A 90.884 1097 55 13 1461 2535 703814313 703815386 0.000000e+00 1430.0
14 TraesCS7A01G075900 chr3A 90.585 393 16 3 2612 2983 703816547 703816939 4.440000e-138 501.0
15 TraesCS7A01G075900 chr3A 84.946 465 26 3 2538 2983 662572023 662571584 5.910000e-117 431.0
16 TraesCS7A01G075900 chr3A 90.759 303 21 4 1010 1309 662597936 662597638 6.000000e-107 398.0
17 TraesCS7A01G075900 chr3A 90.645 310 11 4 705 1013 689496439 689496147 2.160000e-106 396.0
18 TraesCS7A01G075900 chr3A 96.825 189 6 0 516 704 689496661 689496473 1.730000e-82 316.0
19 TraesCS7A01G075900 chr3A 90.196 204 18 2 311 513 662598134 662597932 6.340000e-67 265.0
20 TraesCS7A01G075900 chrUn 90.392 1072 58 13 1461 2510 344422306 344423354 0.000000e+00 1367.0
21 TraesCS7A01G075900 chrUn 90.177 1018 56 12 1539 2535 314367743 314368737 0.000000e+00 1286.0
22 TraesCS7A01G075900 chrUn 90.232 993 53 12 1539 2510 455429912 455430881 0.000000e+00 1256.0
23 TraesCS7A01G075900 chrUn 90.585 393 16 3 2612 2983 314369268 314369660 4.440000e-138 501.0
24 TraesCS7A01G075900 chrUn 85.892 241 33 1 1 240 94308419 94308179 3.820000e-64 255.0
25 TraesCS7A01G075900 chrUn 88.571 210 5 6 2612 2802 476767424 476767633 1.380000e-58 237.0
26 TraesCS7A01G075900 chr2B 90.303 825 58 13 1083 1897 134341437 134342249 0.000000e+00 1061.0
27 TraesCS7A01G075900 chr2B 84.731 465 29 12 2538 2983 100091188 100090747 7.650000e-116 427.0
28 TraesCS7A01G075900 chr2B 90.429 303 22 4 1010 1309 100101772 100101474 2.790000e-105 392.0
29 TraesCS7A01G075900 chr2B 92.000 200 14 2 308 506 759994051 759994249 2.270000e-71 279.0
30 TraesCS7A01G075900 chr5D 89.806 824 60 13 1083 1897 27280867 27281675 0.000000e+00 1035.0
31 TraesCS7A01G075900 chr5D 91.049 391 16 1 2612 2983 127929097 127928707 7.380000e-141 510.0
32 TraesCS7A01G075900 chr5D 92.053 151 12 0 2385 2535 27284964 27285114 2.330000e-51 213.0
33 TraesCS7A01G075900 chr5D 95.745 47 2 0 1010 1056 27280823 27280869 3.190000e-10 76.8
34 TraesCS7A01G075900 chr1B 92.658 681 37 6 1010 1689 675900497 675901165 0.000000e+00 968.0
35 TraesCS7A01G075900 chr1B 91.626 203 9 6 311 513 675900307 675900501 1.050000e-69 274.0
36 TraesCS7A01G075900 chr1B 81.214 346 30 12 1 311 289692540 289692885 2.300000e-61 246.0
37 TraesCS7A01G075900 chr6D 88.193 830 67 15 1083 1897 440673450 440674263 0.000000e+00 961.0
38 TraesCS7A01G075900 chr6D 91.049 391 16 1 2612 2983 450178314 450177924 7.380000e-141 510.0
39 TraesCS7A01G075900 chr6D 83.237 346 23 11 1 311 13475314 13475659 4.870000e-73 285.0
40 TraesCS7A01G075900 chr6D 91.720 157 13 0 2379 2535 440675727 440675883 5.010000e-53 219.0
41 TraesCS7A01G075900 chr6D 94.828 58 3 0 2559 2616 450178344 450178287 1.140000e-14 91.6
42 TraesCS7A01G075900 chr6A 91.560 391 14 1 2612 2983 163162549 163162159 3.410000e-144 521.0
43 TraesCS7A01G075900 chr6A 82.659 346 25 13 1 311 589344247 589344592 1.050000e-69 274.0
44 TraesCS7A01G075900 chr6A 83.796 216 35 0 3 218 557415724 557415939 3.900000e-49 206.0
45 TraesCS7A01G075900 chr6A 95.745 47 2 0 1010 1056 163168135 163168089 3.190000e-10 76.8
46 TraesCS7A01G075900 chr5A 90.537 391 18 1 2612 2983 3897906 3897516 1.600000e-137 499.0
47 TraesCS7A01G075900 chr5A 89.295 383 22 1 2620 2983 470943296 470943678 2.100000e-126 462.0
48 TraesCS7A01G075900 chr5A 91.000 300 20 4 1010 1306 470930907 470931202 6.000000e-107 398.0
49 TraesCS7A01G075900 chr5A 82.370 346 26 8 1 311 689191941 689191596 4.900000e-68 268.0
50 TraesCS7A01G075900 chr5A 89.048 210 21 2 305 513 470930703 470930911 2.950000e-65 259.0
51 TraesCS7A01G075900 chr5A 81.341 343 30 10 3 311 3949589 3949247 6.390000e-62 248.0
52 TraesCS7A01G075900 chr5A 92.053 151 12 0 2385 2535 689189649 689189499 2.330000e-51 213.0
53 TraesCS7A01G075900 chr1D 90.281 391 19 6 2612 2983 415606542 415606932 7.430000e-136 494.0
54 TraesCS7A01G075900 chr1D 83.526 346 22 11 1 311 62893263 62893608 1.050000e-74 291.0
55 TraesCS7A01G075900 chr1D 94.828 58 3 0 2559 2616 415606512 415606569 1.140000e-14 91.6
56 TraesCS7A01G075900 chr7B 85.376 465 26 7 2538 2983 593328483 593328042 7.590000e-121 444.0
57 TraesCS7A01G075900 chr7B 88.725 204 21 2 311 513 593348745 593348543 6.390000e-62 248.0
58 TraesCS7A01G075900 chr3B 90.939 309 11 4 705 1013 734429039 734428748 1.670000e-107 399.0
59 TraesCS7A01G075900 chr3B 96.296 189 7 0 516 704 734429261 734429073 8.030000e-81 311.0
60 TraesCS7A01G075900 chr3B 79.511 327 29 15 1 311 775660221 775659917 6.530000e-47 198.0
61 TraesCS7A01G075900 chr3B 97.368 38 1 0 263 300 816273579 816273616 6.910000e-07 65.8
62 TraesCS7A01G075900 chr4A 89.439 303 24 4 1010 1309 742008686 742008389 2.810000e-100 375.0
63 TraesCS7A01G075900 chr4A 93.204 206 14 0 308 513 658381284 658381489 1.340000e-78 303.0
64 TraesCS7A01G075900 chr4A 89.706 204 19 2 311 513 742008884 742008682 2.950000e-65 259.0
65 TraesCS7A01G075900 chr4A 83.146 267 24 7 2249 2496 31395895 31395631 1.080000e-54 224.0
66 TraesCS7A01G075900 chr2D 84.058 345 21 7 1 311 23117260 23116916 4.840000e-78 302.0
67 TraesCS7A01G075900 chr2D 83.188 345 24 8 1 311 517750 518094 4.870000e-73 285.0
68 TraesCS7A01G075900 chr2D 97.222 36 1 0 263 298 245668081 245668046 8.930000e-06 62.1
69 TraesCS7A01G075900 chr4D 92.763 152 9 1 2386 2535 85850332 85850181 5.010000e-53 219.0


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 TraesCS7A01G075900 chr7A 41462893 41465877 2984 True 5513.0 5513 100.000000 1 2985 1 chr7A.!!$R1 2984
1 TraesCS7A01G075900 chr7A 617597407 617600403 2996 False 5184.0 5184 97.969000 1 2983 1 chr7A.!!$F1 2982
2 TraesCS7A01G075900 chr2A 756523374 756526370 2996 False 5145.0 5145 97.736000 1 2983 1 chr2A.!!$F1 2982
3 TraesCS7A01G075900 chr3D 583596393 583597464 1071 False 1450.0 1450 91.241000 1461 2535 1 chr3D.!!$F1 1074
4 TraesCS7A01G075900 chr3D 553214240 553215153 913 True 243.0 307 95.998667 518 1013 3 chr3D.!!$R2 495
5 TraesCS7A01G075900 chr7D 449502345 449503417 1072 True 1447.0 1447 91.158000 1461 2535 1 chr7D.!!$R1 1074
6 TraesCS7A01G075900 chr7D 621797432 621798503 1071 False 1445.0 1445 91.158000 1461 2535 1 chr7D.!!$F2 1074
7 TraesCS7A01G075900 chr3A 703814313 703816939 2626 False 965.5 1430 90.734500 1461 2983 2 chr3A.!!$F1 1522
8 TraesCS7A01G075900 chr3A 689496147 689496661 514 True 356.0 396 93.735000 516 1013 2 chr3A.!!$R3 497
9 TraesCS7A01G075900 chrUn 344422306 344423354 1048 False 1367.0 1367 90.392000 1461 2510 1 chrUn.!!$F1 1049
10 TraesCS7A01G075900 chrUn 455429912 455430881 969 False 1256.0 1256 90.232000 1539 2510 1 chrUn.!!$F2 971
11 TraesCS7A01G075900 chrUn 314367743 314369660 1917 False 893.5 1286 90.381000 1539 2983 2 chrUn.!!$F4 1444
12 TraesCS7A01G075900 chr2B 134341437 134342249 812 False 1061.0 1061 90.303000 1083 1897 1 chr2B.!!$F1 814
13 TraesCS7A01G075900 chr5D 27280823 27285114 4291 False 441.6 1035 92.534667 1010 2535 3 chr5D.!!$F1 1525
14 TraesCS7A01G075900 chr1B 675900307 675901165 858 False 621.0 968 92.142000 311 1689 2 chr1B.!!$F2 1378
15 TraesCS7A01G075900 chr6D 440673450 440675883 2433 False 590.0 961 89.956500 1083 2535 2 chr6D.!!$F2 1452
16 TraesCS7A01G075900 chr5A 689189499 689191941 2442 True 240.5 268 87.211500 1 2535 2 chr5A.!!$R3 2534
17 TraesCS7A01G075900 chr3B 734428748 734429261 513 True 355.0 399 93.617500 516 1013 2 chr3B.!!$R2 497

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
539 831 3.857309 GAGCCCAAGCAGCACCAGT 62.857 63.158 0.0 0.0 43.56 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 4788 0.770499 TGGATGTCAGGAACTTGCCA 59.23 50.0 0.0 0.0 34.6 4.92 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
393 429 4.103311 ACTCTACCTTCTTCCTTGCAAAGT 59.897 41.667 0.00 0.0 44.25 2.66
514 806 6.741992 TTCTGAATGTTGCTTCGTTATGAT 57.258 33.333 0.00 0.0 0.00 2.45
539 831 3.857309 GAGCCCAAGCAGCACCAGT 62.857 63.158 0.00 0.0 43.56 4.00
1109 1837 7.781056 TGCAAGTGTGTGATATCTGTATTCTA 58.219 34.615 3.98 0.0 0.00 2.10
1149 1877 1.882912 TCTGCAGTTGCTGATTCGTT 58.117 45.000 14.67 0.0 42.71 3.85
1245 2209 2.425592 CCCAACTCGACAGGCACA 59.574 61.111 0.00 0.0 0.00 4.57
2086 4788 3.152341 CCAGAAATTCACTGCAAGGAGT 58.848 45.455 0.00 0.0 39.30 3.85
2669 7616 0.106868 TATCGGCGAGAGGGACTTGA 60.107 55.000 17.22 0.0 41.55 3.02
2833 7799 8.977505 CATTATTTTCGAACCAACAATCACTTT 58.022 29.630 0.00 0.0 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
185 207 1.329256 CGTGGAGATATCTTCCCCGT 58.671 55.000 8.62 0.00 0.00 5.28
191 213 1.472662 CGGGCCCGTGGAGATATCTT 61.473 60.000 36.64 0.00 34.35 2.40
349 385 7.995663 AGAGTAAGAGATATGGACCTGTAGAT 58.004 38.462 0.00 0.00 0.00 1.98
393 429 2.224843 TGAAGAGCAATGGAAGCCTTGA 60.225 45.455 0.00 0.00 0.00 3.02
514 806 3.315142 CTGCTTGGGCTCCTACGCA 62.315 63.158 3.64 3.64 39.59 5.24
1109 1837 7.123098 TGCAGAATCAATCATGACCTGTTTTAT 59.877 33.333 0.00 0.00 39.70 1.40
1245 2209 0.109086 CTCGACTGTCGACATGGCTT 60.109 55.000 27.26 0.92 44.82 4.35
1652 2629 4.499183 CAACAGTGAGGTTCAGATCTACC 58.501 47.826 6.57 6.57 34.54 3.18
2086 4788 0.770499 TGGATGTCAGGAACTTGCCA 59.230 50.000 0.00 0.00 34.60 4.92
2833 7799 9.591792 CATAGTCTCACAATTGTCTCTTCAATA 57.408 33.333 8.48 0.00 37.09 1.90


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

AutoCloner maintained by Alex Coulton.