Multiple sequence alignment - TraesCS7B01G125600

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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 TraesCS7B01G125600 chr7B 100.000 2411 0 0 489 2899 147533871 147536281 0.000000e+00 4453.0
1 TraesCS7B01G125600 chr7B 100.000 363 0 0 1 363 147533383 147533745 0.000000e+00 671.0
2 TraesCS7B01G125600 chr4A 98.469 2416 31 3 489 2899 152579233 152581647 0.000000e+00 4252.0
3 TraesCS7B01G125600 chr4A 93.709 2416 141 7 489 2899 362823886 362826295 0.000000e+00 3609.0
4 TraesCS7B01G125600 chr4A 91.708 2436 144 32 489 2899 740136675 740139077 0.000000e+00 3326.0
5 TraesCS7B01G125600 chr4A 93.364 1507 72 7 489 1967 428100962 428102468 0.000000e+00 2204.0
6 TraesCS7B01G125600 chr4A 97.521 363 9 0 1 363 152578969 152579331 3.170000e-174 621.0
7 TraesCS7B01G125600 chr4A 96.986 365 9 2 1 363 362823621 362823985 1.910000e-171 612.0
8 TraesCS7B01G125600 chr4A 93.077 130 9 0 489 618 589057384 589057255 1.060000e-44 191.0
9 TraesCS7B01G125600 chr4A 100.000 28 0 0 601 628 589057321 589057294 5.000000e-03 52.8
10 TraesCS7B01G125600 chr2A 98.542 2263 33 0 637 2899 738201528 738199266 0.000000e+00 3997.0
11 TraesCS7B01G125600 chr2A 94.405 2413 128 6 489 2899 202055750 202058157 0.000000e+00 3701.0
12 TraesCS7B01G125600 chr2A 97.802 364 7 1 1 363 738202151 738201788 6.820000e-176 627.0
13 TraesCS7B01G125600 chr1A 98.789 2230 27 0 670 2899 552374504 552376733 0.000000e+00 3969.0
14 TraesCS7B01G125600 chr1A 94.693 2412 121 6 489 2899 23398974 23401379 0.000000e+00 3738.0
15 TraesCS7B01G125600 chr1A 96.970 363 10 1 2 363 498221597 498221235 2.470000e-170 608.0
16 TraesCS7B01G125600 chr1A 96.429 364 11 2 1 363 42472986 42472624 1.490000e-167 599.0
17 TraesCS7B01G125600 chr5A 98.949 2189 23 0 711 2899 403293273 403295461 0.000000e+00 3916.0
18 TraesCS7B01G125600 chr5A 98.077 364 6 1 1 363 403292439 403292802 1.470000e-177 632.0
19 TraesCS7B01G125600 chr6A 94.113 2412 133 8 489 2899 559144620 559147023 0.000000e+00 3659.0
20 TraesCS7B01G125600 chr6A 93.499 2415 147 7 489 2899 608727089 608729497 0.000000e+00 3581.0
21 TraesCS7B01G125600 chr6A 96.703 364 10 2 1 363 608726826 608727188 3.200000e-169 604.0
22 TraesCS7B01G125600 chr3B 97.521 363 7 1 1 363 421092270 421091910 1.140000e-173 619.0
23 TraesCS7B01G125600 chr2B 96.970 363 10 1 1 363 113844509 113844870 2.470000e-170 608.0


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 TraesCS7B01G125600 chr7B 147533383 147536281 2898 False 2562.0 4453 100.0000 1 2899 2 chr7B.!!$F1 2898
1 TraesCS7B01G125600 chr4A 740136675 740139077 2402 False 3326.0 3326 91.7080 489 2899 1 chr4A.!!$F2 2410
2 TraesCS7B01G125600 chr4A 152578969 152581647 2678 False 2436.5 4252 97.9950 1 2899 2 chr4A.!!$F3 2898
3 TraesCS7B01G125600 chr4A 428100962 428102468 1506 False 2204.0 2204 93.3640 489 1967 1 chr4A.!!$F1 1478
4 TraesCS7B01G125600 chr4A 362823621 362826295 2674 False 2110.5 3609 95.3475 1 2899 2 chr4A.!!$F4 2898
5 TraesCS7B01G125600 chr2A 202055750 202058157 2407 False 3701.0 3701 94.4050 489 2899 1 chr2A.!!$F1 2410
6 TraesCS7B01G125600 chr2A 738199266 738202151 2885 True 2312.0 3997 98.1720 1 2899 2 chr2A.!!$R1 2898
7 TraesCS7B01G125600 chr1A 552374504 552376733 2229 False 3969.0 3969 98.7890 670 2899 1 chr1A.!!$F2 2229
8 TraesCS7B01G125600 chr1A 23398974 23401379 2405 False 3738.0 3738 94.6930 489 2899 1 chr1A.!!$F1 2410
9 TraesCS7B01G125600 chr5A 403292439 403295461 3022 False 2274.0 3916 98.5130 1 2899 2 chr5A.!!$F1 2898
10 TraesCS7B01G125600 chr6A 559144620 559147023 2403 False 3659.0 3659 94.1130 489 2899 1 chr6A.!!$F1 2410
11 TraesCS7B01G125600 chr6A 608726826 608729497 2671 False 2092.5 3581 95.1010 1 2899 2 chr6A.!!$F2 2898

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
185 186 0.109272 CTGTTTACAGAGAGCGGCGA 60.109 55.0 12.98 0.0 46.59 5.54 F
253 255 1.124780 TTTGAGGCCCGGATTCGATA 58.875 50.0 0.73 0.0 39.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 1546 1.22184 CGTAAGGCATGGCAGGACT 59.778 57.895 22.64 0.0 0.00 3.85 R
2192 2558 1.46852 CACCTATGAAACAGGGCAACG 59.531 52.381 0.00 0.0 37.51 4.10 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
35 36 4.196778 TTGCGGCCCCACAGACAA 62.197 61.111 0.00 0.00 0.00 3.18
121 122 2.415893 GCACATTGACTTAAGCCGCATT 60.416 45.455 1.29 0.00 0.00 3.56
185 186 0.109272 CTGTTTACAGAGAGCGGCGA 60.109 55.000 12.98 0.00 46.59 5.54
253 255 1.124780 TTTGAGGCCCGGATTCGATA 58.875 50.000 0.73 0.00 39.00 2.92
285 287 5.340194 CCTCCTACTAGGTAAACTCCTCTGT 60.340 48.000 1.83 0.00 38.86 3.41
286 288 6.150034 TCCTACTAGGTAAACTCCTCTGTT 57.850 41.667 1.83 0.00 38.86 3.16
287 289 6.186234 TCCTACTAGGTAAACTCCTCTGTTC 58.814 44.000 1.83 0.00 38.86 3.18
288 290 5.360429 CCTACTAGGTAAACTCCTCTGTTCC 59.640 48.000 0.00 0.00 38.86 3.62
289 291 4.095211 ACTAGGTAAACTCCTCTGTTCCC 58.905 47.826 0.00 0.00 38.86 3.97
290 292 3.277416 AGGTAAACTCCTCTGTTCCCT 57.723 47.619 0.00 0.00 31.32 4.20
291 293 3.599348 AGGTAAACTCCTCTGTTCCCTT 58.401 45.455 0.00 0.00 31.41 3.95
292 294 3.981375 AGGTAAACTCCTCTGTTCCCTTT 59.019 43.478 0.00 0.00 31.41 3.11
293 295 4.415846 AGGTAAACTCCTCTGTTCCCTTTT 59.584 41.667 0.00 0.00 31.41 2.27
294 296 5.103643 AGGTAAACTCCTCTGTTCCCTTTTT 60.104 40.000 0.00 0.00 31.41 1.94
314 316 2.604969 TTTCTCCGTAAATGCGTTGC 57.395 45.000 0.00 0.00 0.00 4.17
315 317 1.514003 TTCTCCGTAAATGCGTTGCA 58.486 45.000 0.00 0.00 44.86 4.08
316 318 1.514003 TCTCCGTAAATGCGTTGCAA 58.486 45.000 0.00 0.00 43.62 4.08
317 319 2.080693 TCTCCGTAAATGCGTTGCAAT 58.919 42.857 0.59 0.00 43.62 3.56
318 320 2.486203 TCTCCGTAAATGCGTTGCAATT 59.514 40.909 0.59 0.00 43.62 2.32
319 321 3.057876 TCTCCGTAAATGCGTTGCAATTT 60.058 39.130 0.59 1.29 43.62 1.82
320 322 3.643763 TCCGTAAATGCGTTGCAATTTT 58.356 36.364 0.59 3.84 43.62 1.82
321 323 4.795268 TCCGTAAATGCGTTGCAATTTTA 58.205 34.783 0.59 2.88 43.62 1.52
322 324 4.854291 TCCGTAAATGCGTTGCAATTTTAG 59.146 37.500 0.59 0.00 43.62 1.85
323 325 4.031201 CCGTAAATGCGTTGCAATTTTAGG 59.969 41.667 0.59 10.17 43.62 2.69
324 326 4.031201 CGTAAATGCGTTGCAATTTTAGGG 59.969 41.667 0.59 0.00 43.62 3.53
325 327 3.951775 AATGCGTTGCAATTTTAGGGA 57.048 38.095 0.59 0.00 43.62 4.20
326 328 4.470334 AATGCGTTGCAATTTTAGGGAT 57.530 36.364 0.59 0.00 43.62 3.85
327 329 3.951775 TGCGTTGCAATTTTAGGGATT 57.048 38.095 0.59 0.00 34.76 3.01
328 330 4.264460 TGCGTTGCAATTTTAGGGATTT 57.736 36.364 0.59 0.00 34.76 2.17
329 331 3.993081 TGCGTTGCAATTTTAGGGATTTG 59.007 39.130 0.59 0.00 34.76 2.32
330 332 3.181521 GCGTTGCAATTTTAGGGATTTGC 60.182 43.478 0.59 0.00 0.00 3.68
331 333 3.370672 CGTTGCAATTTTAGGGATTTGCC 59.629 43.478 0.59 0.00 0.00 4.52
344 346 2.695147 GGATTTGCCCAAGATTAGGTGG 59.305 50.000 0.00 0.00 34.44 4.61
345 347 3.627237 GGATTTGCCCAAGATTAGGTGGA 60.627 47.826 0.00 0.00 37.03 4.02
346 348 3.534357 TTTGCCCAAGATTAGGTGGAA 57.466 42.857 0.00 0.00 37.03 3.53
347 349 2.507407 TGCCCAAGATTAGGTGGAAC 57.493 50.000 0.00 0.00 37.03 3.62
362 364 3.392882 GTGGAACCTTTGATTTGCTTGG 58.607 45.455 0.00 0.00 0.00 3.61
1188 1546 0.839277 TCGGTATCACGGGGTCTCTA 59.161 55.000 0.00 0.00 0.00 2.43
1292 1650 2.813908 ACGCCGAATCTGAACGCC 60.814 61.111 0.00 0.00 0.00 5.68
1366 1724 1.062886 TCTTCGGACTGGGGAGATGAT 60.063 52.381 0.00 0.00 0.00 2.45
1555 1919 2.185310 GAAAGGAAGGCAGCCGGAGA 62.185 60.000 5.05 0.00 0.00 3.71
2320 2686 1.153249 GCTTATGCGGTGCCCACTA 60.153 57.895 0.00 0.00 0.00 2.74
2350 2716 2.817258 CTGGGCGGTTGAGTTTCATTTA 59.183 45.455 0.00 0.00 0.00 1.40
2437 2803 6.984474 CGGATAAAGCACTTCATAGGTAAGAA 59.016 38.462 0.00 0.00 0.00 2.52
2562 2928 1.565759 ACTGGGCCAAGCATCATTCTA 59.434 47.619 7.20 0.00 0.00 2.10
2612 2978 3.075998 CAAGCTCGTAGCACTGCG 58.924 61.111 1.42 1.42 45.56 5.18
2613 2979 1.734477 CAAGCTCGTAGCACTGCGT 60.734 57.895 7.99 0.00 45.56 5.24
2879 3245 5.034152 CGTATTACACATGTTTGAATGGCC 58.966 41.667 0.00 0.00 31.46 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
185 186 2.660064 CCTAAGGGAGTGCCGCTGT 61.660 63.158 0.00 0.00 38.16 4.40
253 255 5.698369 TTACCTAGTAGGAGGGATTGGAT 57.302 43.478 23.50 0.00 41.36 3.41
293 295 3.243101 TGCAACGCATTTACGGAGAAAAA 60.243 39.130 0.00 0.00 37.37 1.94
294 296 2.290916 TGCAACGCATTTACGGAGAAAA 59.709 40.909 0.00 0.00 37.37 2.29
295 297 1.874231 TGCAACGCATTTACGGAGAAA 59.126 42.857 0.00 0.00 37.37 2.52
296 298 1.514003 TGCAACGCATTTACGGAGAA 58.486 45.000 0.00 0.00 37.37 2.87
297 299 1.514003 TTGCAACGCATTTACGGAGA 58.486 45.000 0.00 0.00 38.76 3.71
298 300 2.542766 ATTGCAACGCATTTACGGAG 57.457 45.000 0.00 0.00 38.76 4.63
299 301 2.999507 AATTGCAACGCATTTACGGA 57.000 40.000 0.00 0.00 38.76 4.69
300 302 4.031201 CCTAAAATTGCAACGCATTTACGG 59.969 41.667 0.00 5.85 38.76 4.02
301 303 4.031201 CCCTAAAATTGCAACGCATTTACG 59.969 41.667 0.00 0.62 38.76 3.18
302 304 5.164954 TCCCTAAAATTGCAACGCATTTAC 58.835 37.500 0.00 0.00 38.76 2.01
303 305 5.392767 TCCCTAAAATTGCAACGCATTTA 57.607 34.783 0.00 4.99 38.76 1.40
304 306 4.264460 TCCCTAAAATTGCAACGCATTT 57.736 36.364 0.00 4.01 38.76 2.32
305 307 3.951775 TCCCTAAAATTGCAACGCATT 57.048 38.095 0.00 0.00 38.76 3.56
306 308 4.470334 AATCCCTAAAATTGCAACGCAT 57.530 36.364 0.00 0.00 38.76 4.73
307 309 3.951775 AATCCCTAAAATTGCAACGCA 57.048 38.095 0.00 0.00 36.47 5.24
308 310 3.181521 GCAAATCCCTAAAATTGCAACGC 60.182 43.478 0.00 0.00 45.61 4.84
309 311 4.582441 GCAAATCCCTAAAATTGCAACG 57.418 40.909 0.00 0.00 45.61 4.10
323 325 2.695147 CCACCTAATCTTGGGCAAATCC 59.305 50.000 0.00 0.00 30.94 3.01
324 326 3.631250 TCCACCTAATCTTGGGCAAATC 58.369 45.455 0.00 0.00 33.25 2.17
325 327 3.756082 TCCACCTAATCTTGGGCAAAT 57.244 42.857 0.00 0.00 33.25 2.32
326 328 3.161866 GTTCCACCTAATCTTGGGCAAA 58.838 45.455 0.00 0.00 33.25 3.68
327 329 2.556559 GGTTCCACCTAATCTTGGGCAA 60.557 50.000 0.00 0.00 34.73 4.52
328 330 1.005450 GGTTCCACCTAATCTTGGGCA 59.995 52.381 0.00 0.00 34.73 5.36
329 331 1.763968 GGTTCCACCTAATCTTGGGC 58.236 55.000 0.00 0.00 34.73 5.36
340 342 3.392882 CAAGCAAATCAAAGGTTCCACC 58.607 45.455 0.00 0.00 38.99 4.61
341 343 3.392882 CCAAGCAAATCAAAGGTTCCAC 58.607 45.455 0.00 0.00 0.00 4.02
342 344 3.749665 CCAAGCAAATCAAAGGTTCCA 57.250 42.857 0.00 0.00 0.00 3.53
1151 1509 7.393234 TGATACCGAATCTTCAAAGGTTCAAAT 59.607 33.333 14.37 5.69 44.52 2.32
1152 1510 6.712998 TGATACCGAATCTTCAAAGGTTCAAA 59.287 34.615 14.37 1.71 44.52 2.69
1188 1546 1.221840 CGTAAGGCATGGCAGGACT 59.778 57.895 22.64 0.00 0.00 3.85
1292 1650 2.883828 AAGAGCGGACACCAGTGGG 61.884 63.158 15.21 5.06 41.29 4.61
1366 1724 1.978712 GACATCCTCGAGCGTCACGA 61.979 60.000 17.82 6.22 38.11 4.35
1555 1919 4.582701 TTTTGAATCCACGTGAAAGCAT 57.417 36.364 19.30 0.00 0.00 3.79
2192 2558 1.468520 CACCTATGAAACAGGGCAACG 59.531 52.381 0.00 0.00 37.51 4.10
2320 2686 0.817013 CAACCGCCCAGTTGCATATT 59.183 50.000 0.00 0.00 40.60 1.28
2350 2716 4.395080 CGATACACGTGATGCGGT 57.605 55.556 25.01 0.00 46.52 5.68
2562 2928 0.896923 TGGAAGCGGGTAACATACGT 59.103 50.000 0.00 0.00 39.74 3.57


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

AutoCloner maintained by Alex Coulton.