Multiple sequence alignment - TraesCS5A01G495200

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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 TraesCS5A01G495200 chr5A 100.000 3524 0 0 1 3524 663335661 663339184 0.000000e+00 6508.0
1 TraesCS5A01G495200 chr5A 95.434 3526 110 14 1 3524 495729768 495726292 0.000000e+00 5572.0
2 TraesCS5A01G495200 chr5A 94.573 2377 114 5 290 2656 495820554 495818183 0.000000e+00 3661.0
3 TraesCS5A01G495200 chr5A 89.076 1840 147 18 923 2709 495397518 495395680 0.000000e+00 2235.0
4 TraesCS5A01G495200 chr5A 96.782 1212 31 8 1 1208 495589085 495587878 0.000000e+00 2015.0
5 TraesCS5A01G495200 chr5A 97.393 1074 20 4 2452 3524 495586964 495585898 0.000000e+00 1821.0
6 TraesCS5A01G495200 chr5A 96.614 886 30 0 1476 2361 495587857 495586972 0.000000e+00 1471.0
7 TraesCS5A01G495200 chr5A 85.965 627 78 8 211 835 495588996 495588378 0.000000e+00 662.0
8 TraesCS5A01G495200 chr5A 87.223 587 66 7 1 583 495820584 495820003 0.000000e+00 660.0
9 TraesCS5A01G495200 chr5A 85.486 627 82 7 88 709 495588873 495588251 0.000000e+00 645.0
10 TraesCS5A01G495200 chr5A 86.216 370 45 4 87 451 663336122 663336490 2.550000e-106 396.0
11 TraesCS5A01G495200 chr5A 85.372 376 47 6 84 454 495729344 495728972 1.980000e-102 383.0
12 TraesCS5A01G495200 chr5D 93.451 2718 136 11 1 2713 393740102 393737422 0.000000e+00 3995.0
13 TraesCS5A01G495200 chr5D 89.730 1850 137 19 912 2709 393619554 393617706 0.000000e+00 2314.0
14 TraesCS5A01G495200 chr5D 86.742 1501 195 4 1019 2517 549324009 549325507 0.000000e+00 1666.0
15 TraesCS5A01G495200 chr5D 87.685 674 75 8 166 836 393740073 393739405 0.000000e+00 778.0
16 TraesCS5A01G495200 chr5D 91.956 547 43 1 290 836 393740076 393739531 0.000000e+00 765.0
17 TraesCS5A01G495200 chr5D 85.569 686 80 7 29 709 393739950 393739279 0.000000e+00 701.0
18 TraesCS5A01G495200 chr5D 93.103 58 4 0 2656 2713 393737005 393736948 6.270000e-13 86.1
19 TraesCS5A01G495200 chr5B 93.418 1808 99 5 920 2713 473610438 473608637 0.000000e+00 2662.0
20 TraesCS5A01G495200 chr5B 89.320 1854 146 17 912 2713 473520260 473518407 0.000000e+00 2279.0
21 TraesCS5A01G495200 chr5B 88.307 821 39 14 2731 3524 673462517 673461727 0.000000e+00 931.0
22 TraesCS5A01G495200 chr7B 81.978 627 107 6 1894 2517 124743609 124742986 8.660000e-146 527.0
23 TraesCS5A01G495200 chr7A 74.734 847 105 45 2731 3507 257360397 257361204 9.630000e-71 278.0


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 TraesCS5A01G495200 chr5A 663335661 663339184 3523 False 3452.00 6508 93.1080 1 3524 2 chr5A.!!$F1 3523
1 TraesCS5A01G495200 chr5A 495726292 495729768 3476 True 2977.50 5572 90.4030 1 3524 2 chr5A.!!$R3 3523
2 TraesCS5A01G495200 chr5A 495395680 495397518 1838 True 2235.00 2235 89.0760 923 2709 1 chr5A.!!$R1 1786
3 TraesCS5A01G495200 chr5A 495818183 495820584 2401 True 2160.50 3661 90.8980 1 2656 2 chr5A.!!$R4 2655
4 TraesCS5A01G495200 chr5A 495585898 495589085 3187 True 1322.80 2015 92.4480 1 3524 5 chr5A.!!$R2 3523
5 TraesCS5A01G495200 chr5D 393617706 393619554 1848 True 2314.00 2314 89.7300 912 2709 1 chr5D.!!$R1 1797
6 TraesCS5A01G495200 chr5D 549324009 549325507 1498 False 1666.00 1666 86.7420 1019 2517 1 chr5D.!!$F1 1498
7 TraesCS5A01G495200 chr5D 393736948 393740102 3154 True 1265.02 3995 90.3528 1 2713 5 chr5D.!!$R2 2712
8 TraesCS5A01G495200 chr5B 473608637 473610438 1801 True 2662.00 2662 93.4180 920 2713 1 chr5B.!!$R2 1793
9 TraesCS5A01G495200 chr5B 473518407 473520260 1853 True 2279.00 2279 89.3200 912 2713 1 chr5B.!!$R1 1801
10 TraesCS5A01G495200 chr5B 673461727 673462517 790 True 931.00 931 88.3070 2731 3524 1 chr5B.!!$R3 793
11 TraesCS5A01G495200 chr7B 124742986 124743609 623 True 527.00 527 81.9780 1894 2517 1 chr7B.!!$R1 623
12 TraesCS5A01G495200 chr7A 257360397 257361204 807 False 278.00 278 74.7340 2731 3507 1 chr7A.!!$F1 776

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
336 346 0.918983 CTAATCTCTGCCCCCAACCA 59.081 55.000 0.00 0.0 0.0 3.67 F
990 1261 1.949847 GCGAGCTAGCTGAACCTCCA 61.950 60.000 24.99 0.0 0.0 3.86 F
1284 1567 1.153369 CGACGTCATGAAGGCCCAT 60.153 57.895 17.16 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1567 2.661537 CTGCAACAGTCGGCGTCA 60.662 61.111 6.85 0.0 0.00 4.35 R
2400 2692 1.073722 CAGCTCCCACTCAAAGCCA 59.926 57.895 0.00 0.0 36.69 4.75 R
2631 2961 3.264193 AGAGTGATTCATGTTACCAGCCA 59.736 43.478 0.00 0.0 0.00 4.75 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
69 75 2.480642 AGACTCCTAATCTCCACCCC 57.519 55.000 0.00 0.00 0.00 4.95
71 77 1.027815 ACTCCTAATCTCCACCCCCT 58.972 55.000 0.00 0.00 0.00 4.79
309 319 5.065731 TGTCAATTTTTGGCATCAAACCAAC 59.934 36.000 0.00 0.00 46.66 3.77
329 339 1.899142 CTAGCCTCCTAATCTCTGCCC 59.101 57.143 0.00 0.00 0.00 5.36
336 346 0.918983 CTAATCTCTGCCCCCAACCA 59.081 55.000 0.00 0.00 0.00 3.67
354 364 6.700345 CAACCAGTTGTGTGATTGGCAACA 62.700 45.833 0.00 0.00 43.31 3.33
394 404 8.553459 ACCAATCTCTAGTCAACATTTAACAG 57.447 34.615 0.00 0.00 0.00 3.16
404 414 6.876257 AGTCAACATTTAACAGTTGCCAAAAA 59.124 30.769 12.23 0.00 43.55 1.94
407 417 8.734386 TCAACATTTAACAGTTGCCAAAAATTT 58.266 25.926 12.23 0.00 43.55 1.82
454 464 8.440771 CAAACCTATTACCCTCCTAATCTTCAT 58.559 37.037 0.00 0.00 0.00 2.57
465 475 8.147704 CCCTCCTAATCTTCATCTCTAACTTTC 58.852 40.741 0.00 0.00 0.00 2.62
990 1261 1.949847 GCGAGCTAGCTGAACCTCCA 61.950 60.000 24.99 0.00 0.00 3.86
1051 1334 2.443394 GGCATCCTCATCCCCGTCA 61.443 63.158 0.00 0.00 0.00 4.35
1083 1366 2.661866 GTGACGAACCGCAGCACT 60.662 61.111 0.00 0.00 0.00 4.40
1284 1567 1.153369 CGACGTCATGAAGGCCCAT 60.153 57.895 17.16 0.00 0.00 4.00
1539 1822 2.431942 GTGTTCCGTGTCGCCGAT 60.432 61.111 0.00 0.00 0.00 4.18
1789 2072 2.685017 AGCAGCATCGAGACCCCA 60.685 61.111 0.00 0.00 0.00 4.96
2158 2450 2.441348 TGGAGATCGGCGGCTACA 60.441 61.111 7.21 9.40 0.00 2.74
2400 2692 2.030363 CACGTTGGCCAACATGTTGTAT 60.030 45.455 39.91 16.81 41.20 2.29
2422 2714 2.454832 CTTTGAGTGGGAGCTGCCGA 62.455 60.000 20.39 6.03 37.63 5.54
2588 2914 9.011095 CATCTGGCAAATATATCTTGAGTGAAT 57.989 33.333 10.14 0.00 0.00 2.57
2631 2961 1.081556 TGATACATGCGCGCGTCTTT 61.082 50.000 32.35 15.97 0.00 2.52
2710 3041 3.489785 CGAGTTTATACATCGGGTCTTGC 59.510 47.826 0.00 0.00 32.93 4.01
3087 3480 7.226720 ACAGTGGTACATGAAAACAAAGTAGAG 59.773 37.037 0.00 0.00 44.52 2.43
3089 3482 6.017440 GTGGTACATGAAAACAAAGTAGAGCA 60.017 38.462 0.00 0.00 44.52 4.26
3090 3483 6.017440 TGGTACATGAAAACAAAGTAGAGCAC 60.017 38.462 0.00 0.00 0.00 4.40
3091 3484 6.017440 GGTACATGAAAACAAAGTAGAGCACA 60.017 38.462 0.00 0.00 0.00 4.57
3092 3485 6.449635 ACATGAAAACAAAGTAGAGCACAA 57.550 33.333 0.00 0.00 0.00 3.33
3093 3486 6.265577 ACATGAAAACAAAGTAGAGCACAAC 58.734 36.000 0.00 0.00 0.00 3.32
3094 3487 5.888691 TGAAAACAAAGTAGAGCACAACA 57.111 34.783 0.00 0.00 0.00 3.33
3095 3488 6.260870 TGAAAACAAAGTAGAGCACAACAA 57.739 33.333 0.00 0.00 0.00 2.83
3098 3491 7.653713 TGAAAACAAAGTAGAGCACAACAAAAA 59.346 29.630 0.00 0.00 0.00 1.94
3173 3572 5.389859 AAAACTGCTGCATATTAGCACAA 57.610 34.783 1.31 0.00 45.52 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.699411 TTGATGCCAAAAATTCAGGGG 57.301 42.857 0.00 0.00 0.00 4.79
23 24 3.752747 GGTTTGATGCCAAAAATTCAGGG 59.247 43.478 0.00 0.00 43.18 4.45
71 77 2.981776 AAAAGGTTGGGGGAGGGGGA 62.982 60.000 0.00 0.00 0.00 4.81
170 179 5.379706 AGGAGGCTAATTAGTTTGATGCT 57.620 39.130 13.91 4.12 0.00 3.79
309 319 1.899142 GGGCAGAGATTAGGAGGCTAG 59.101 57.143 0.00 0.00 0.00 3.42
336 346 3.883830 TTTGTTGCCAATCACACAACT 57.116 38.095 6.65 0.00 43.19 3.16
381 391 7.856145 ATTTTTGGCAACTGTTAAATGTTGA 57.144 28.000 19.66 3.72 44.29 3.18
418 428 5.782845 AGGGTAATAGGTTTGATGCCAAAAA 59.217 36.000 0.00 0.00 43.18 1.94
419 429 5.337788 AGGGTAATAGGTTTGATGCCAAAA 58.662 37.500 0.00 0.00 43.18 2.44
420 430 4.941713 AGGGTAATAGGTTTGATGCCAAA 58.058 39.130 0.00 0.00 39.74 3.28
421 431 4.532834 GAGGGTAATAGGTTTGATGCCAA 58.467 43.478 0.00 0.00 0.00 4.52
422 432 3.117663 GGAGGGTAATAGGTTTGATGCCA 60.118 47.826 0.00 0.00 0.00 4.92
423 433 3.138468 AGGAGGGTAATAGGTTTGATGCC 59.862 47.826 0.00 0.00 0.00 4.40
424 434 4.439253 AGGAGGGTAATAGGTTTGATGC 57.561 45.455 0.00 0.00 0.00 3.91
425 435 7.978925 AGATTAGGAGGGTAATAGGTTTGATG 58.021 38.462 0.00 0.00 0.00 3.07
426 436 8.582891 AAGATTAGGAGGGTAATAGGTTTGAT 57.417 34.615 0.00 0.00 0.00 2.57
427 437 7.626084 TGAAGATTAGGAGGGTAATAGGTTTGA 59.374 37.037 0.00 0.00 0.00 2.69
428 438 7.802117 TGAAGATTAGGAGGGTAATAGGTTTG 58.198 38.462 0.00 0.00 0.00 2.93
429 439 8.582891 ATGAAGATTAGGAGGGTAATAGGTTT 57.417 34.615 0.00 0.00 0.00 3.27
430 440 8.019652 AGATGAAGATTAGGAGGGTAATAGGTT 58.980 37.037 0.00 0.00 0.00 3.50
431 441 7.549141 AGATGAAGATTAGGAGGGTAATAGGT 58.451 38.462 0.00 0.00 0.00 3.08
432 442 7.898636 AGAGATGAAGATTAGGAGGGTAATAGG 59.101 40.741 0.00 0.00 0.00 2.57
433 443 8.893563 AGAGATGAAGATTAGGAGGGTAATAG 57.106 38.462 0.00 0.00 0.00 1.73
454 464 4.997395 GCCAATCACACAGAAAGTTAGAGA 59.003 41.667 0.00 0.00 0.00 3.10
465 475 2.772568 TTTCGTTGCCAATCACACAG 57.227 45.000 0.00 0.00 0.00 3.66
559 569 3.514309 GGCGGAGATTAGGAGGCTAATTA 59.486 47.826 0.00 0.00 30.47 1.40
945 1215 2.813042 GAGGTGCTGCTGCTCGTC 60.813 66.667 19.55 19.55 39.31 4.20
990 1261 2.088423 GAGATATCCATCGTCTCGGCT 58.912 52.381 0.00 0.00 36.20 5.52
1074 1357 2.435586 CCTTCCTCAGTGCTGCGG 60.436 66.667 2.00 2.00 36.82 5.69
1083 1366 2.927856 TTCAGCCGCCCTTCCTCA 60.928 61.111 0.00 0.00 0.00 3.86
1235 1518 3.299977 CGGACGAGACCACCACCA 61.300 66.667 0.00 0.00 0.00 4.17
1284 1567 2.661537 CTGCAACAGTCGGCGTCA 60.662 61.111 6.85 0.00 0.00 4.35
2400 2692 1.073722 CAGCTCCCACTCAAAGCCA 59.926 57.895 0.00 0.00 36.69 4.75
2422 2714 4.016706 CTCGGCCAACGTCCCCTT 62.017 66.667 2.24 0.00 44.69 3.95
2631 2961 3.264193 AGAGTGATTCATGTTACCAGCCA 59.736 43.478 0.00 0.00 0.00 4.75
2710 3041 3.270027 TCAAGTTCTGGCCATAATGTCG 58.730 45.455 5.51 0.00 0.00 4.35
3087 3480 8.997960 CATTTTTGTTCTACATTTTTGTTGTGC 58.002 29.630 0.00 0.00 0.00 4.57
3089 3482 8.180920 GCCATTTTTGTTCTACATTTTTGTTGT 58.819 29.630 0.00 0.00 0.00 3.32
3090 3483 8.180267 TGCCATTTTTGTTCTACATTTTTGTTG 58.820 29.630 0.00 0.00 0.00 3.33
3091 3484 8.180920 GTGCCATTTTTGTTCTACATTTTTGTT 58.819 29.630 0.00 0.00 0.00 2.83
3092 3485 7.552330 AGTGCCATTTTTGTTCTACATTTTTGT 59.448 29.630 0.00 0.00 0.00 2.83
3093 3486 7.851963 CAGTGCCATTTTTGTTCTACATTTTTG 59.148 33.333 0.00 0.00 0.00 2.44
3094 3487 7.552330 ACAGTGCCATTTTTGTTCTACATTTTT 59.448 29.630 0.00 0.00 0.00 1.94
3095 3488 7.011295 CACAGTGCCATTTTTGTTCTACATTTT 59.989 33.333 0.00 0.00 0.00 1.82
3098 3491 5.301551 TCACAGTGCCATTTTTGTTCTACAT 59.698 36.000 0.00 0.00 0.00 2.29
3365 4033 5.717654 AGTTTTGGGGTTTGTCAAAGTTAGA 59.282 36.000 0.00 0.00 34.83 2.10
3445 4122 7.378461 CAGTTACAACGTATTTTTCAGTGCATT 59.622 33.333 0.00 0.00 0.00 3.56
3446 4123 6.855914 CAGTTACAACGTATTTTTCAGTGCAT 59.144 34.615 0.00 0.00 0.00 3.96
3450 4127 6.427150 CAGCAGTTACAACGTATTTTTCAGT 58.573 36.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.