Multiple sequence alignment - TraesCS6A01G137500

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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 TraesCS6A01G137500 chr6A 100.000 3217 0 0 1 3217 108218312 108215096 0.000000e+00 5941.0
1 TraesCS6A01G137500 chr6A 85.471 1294 143 31 1027 2305 108652982 108651719 0.000000e+00 1306.0
2 TraesCS6A01G137500 chr6A 93.076 621 41 1 1688 2308 108332002 108331384 0.000000e+00 907.0
3 TraesCS6A01G137500 chr6A 82.494 794 95 21 849 1613 108332808 108332030 0.000000e+00 656.0
4 TraesCS6A01G137500 chr6A 94.872 39 1 1 2370 2408 470957837 470957874 3.470000e-05 60.2
5 TraesCS6A01G137500 chr6D 92.330 2425 99 53 6 2370 90346552 90348949 0.000000e+00 3367.0
6 TraesCS6A01G137500 chr6D 85.946 1295 144 25 1022 2305 90193902 90195169 0.000000e+00 1349.0
7 TraesCS6A01G137500 chr6B 93.002 2315 92 25 41 2299 172370182 172367882 0.000000e+00 3314.0
8 TraesCS6A01G137500 chr6B 85.649 1533 161 30 808 2308 172466102 172464597 0.000000e+00 1557.0
9 TraesCS6A01G137500 chr6B 99.295 851 5 1 2368 3217 136335879 136336729 0.000000e+00 1537.0
10 TraesCS6A01G137500 chr6B 85.693 1335 150 27 988 2308 172575894 172574587 0.000000e+00 1369.0
11 TraesCS6A01G137500 chr6B 100.000 33 0 0 2370 2402 6296964 6296932 9.640000e-06 62.1
12 TraesCS6A01G137500 chr7B 92.281 855 48 15 2369 3217 363071432 363070590 0.000000e+00 1197.0
13 TraesCS6A01G137500 chr2B 94.588 425 19 2 2397 2817 765037635 765037211 0.000000e+00 654.0
14 TraesCS6A01G137500 chr3B 93.412 425 23 3 2397 2817 39531221 39530798 2.720000e-175 625.0
15 TraesCS6A01G137500 chr3B 92.727 55 3 1 2366 2420 39531277 39531224 9.570000e-11 78.7
16 TraesCS6A01G137500 chr7D 94.375 160 6 1 2450 2606 580605288 580605129 3.210000e-60 243.0
17 TraesCS6A01G137500 chr7D 92.784 97 6 1 2369 2465 580608894 580608799 4.330000e-29 139.0
18 TraesCS6A01G137500 chr7D 93.103 58 3 1 2662 2718 580604943 580604886 2.060000e-12 84.2
19 TraesCS6A01G137500 chr7A 82.143 84 13 2 1810 1892 622372570 622372488 1.600000e-08 71.3
20 TraesCS6A01G137500 chr7A 97.222 36 1 0 2370 2405 14404447 14404482 9.640000e-06 62.1
21 TraesCS6A01G137500 chr5D 93.182 44 1 2 2359 2401 470247781 470247823 2.680000e-06 63.9
22 TraesCS6A01G137500 chr3D 97.059 34 1 0 2370 2403 141497197 141497164 1.250000e-04 58.4
23 TraesCS6A01G137500 chr3A 91.892 37 3 0 1219 1255 120166310 120166346 6.000000e-03 52.8


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 TraesCS6A01G137500 chr6A 108215096 108218312 3216 True 5941.0 5941 100.000 1 3217 1 chr6A.!!$R1 3216
1 TraesCS6A01G137500 chr6A 108651719 108652982 1263 True 1306.0 1306 85.471 1027 2305 1 chr6A.!!$R2 1278
2 TraesCS6A01G137500 chr6A 108331384 108332808 1424 True 781.5 907 87.785 849 2308 2 chr6A.!!$R3 1459
3 TraesCS6A01G137500 chr6D 90346552 90348949 2397 False 3367.0 3367 92.330 6 2370 1 chr6D.!!$F2 2364
4 TraesCS6A01G137500 chr6D 90193902 90195169 1267 False 1349.0 1349 85.946 1022 2305 1 chr6D.!!$F1 1283
5 TraesCS6A01G137500 chr6B 172367882 172370182 2300 True 3314.0 3314 93.002 41 2299 1 chr6B.!!$R2 2258
6 TraesCS6A01G137500 chr6B 172464597 172466102 1505 True 1557.0 1557 85.649 808 2308 1 chr6B.!!$R3 1500
7 TraesCS6A01G137500 chr6B 136335879 136336729 850 False 1537.0 1537 99.295 2368 3217 1 chr6B.!!$F1 849
8 TraesCS6A01G137500 chr6B 172574587 172575894 1307 True 1369.0 1369 85.693 988 2308 1 chr6B.!!$R4 1320
9 TraesCS6A01G137500 chr7B 363070590 363071432 842 True 1197.0 1197 92.281 2369 3217 1 chr7B.!!$R1 848

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
865 891 0.171903 ATGTATATACGTCCGCCGCC 59.828 55.0 8.33 0.0 41.42 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2636 2750 1.19365 CGGCAAAATCGAAGTCGTCAA 59.806 47.619 0.0 0.0 40.8 3.18 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
88 94 1.790043 CGTCATCGTACAGTTTGCACA 59.210 47.619 0.00 0.00 0.00 4.57
91 97 3.247648 GTCATCGTACAGTTTGCACAACT 59.752 43.478 8.03 8.03 0.00 3.16
112 118 1.544724 GGACCACATGCCAAGCTAAA 58.455 50.000 0.00 0.00 0.00 1.85
130 136 5.982516 AGCTAAATGCAATTTTGTCGTCAAA 59.017 32.000 3.64 3.64 46.10 2.69
137 143 6.927746 TGCAATTTTGTCGTCAAATTTACAC 58.072 32.000 8.61 5.93 42.14 2.90
193 199 8.321353 AGATCATAATTTTGGATATCGGTGCTA 58.679 33.333 0.00 0.00 0.00 3.49
215 221 8.801299 TGCTACAAACAAATAAGATTGATCCAA 58.199 29.630 0.00 0.00 34.38 3.53
273 279 9.736023 GAAGTGCTTTATTTTTCTTTTGAGAGA 57.264 29.630 0.00 0.00 0.00 3.10
395 401 2.315925 AGGTGTCCAAGCACATATCG 57.684 50.000 0.00 0.00 40.89 2.92
756 775 0.391130 ACATGGACGATGGACCAACG 60.391 55.000 21.27 21.27 41.25 4.10
774 793 5.362430 ACCAACGATGCCATAAAAACCATAT 59.638 36.000 0.00 0.00 0.00 1.78
775 794 5.920273 CCAACGATGCCATAAAAACCATATC 59.080 40.000 0.00 0.00 0.00 1.63
863 889 2.477357 CCTCATGTATATACGTCCGCCG 60.477 54.545 4.54 0.00 44.03 6.46
864 890 1.135603 TCATGTATATACGTCCGCCGC 60.136 52.381 4.54 0.00 41.42 6.53
865 891 0.171903 ATGTATATACGTCCGCCGCC 59.828 55.000 8.33 0.00 41.42 6.13
956 987 6.217693 ACCCCATGAAGTTCTATAAAAGGACT 59.782 38.462 4.17 0.00 46.97 3.85
1494 1573 3.920093 GAACCCGCCTTCCACCCTG 62.920 68.421 0.00 0.00 0.00 4.45
1574 1653 7.273598 CGGTGAGTAACATAGTACATGCATATC 59.726 40.741 0.00 0.00 0.00 1.63
1616 1702 2.054687 TGCGTCGTCTATTTCACGTT 57.945 45.000 0.00 0.00 38.45 3.99
1640 1726 4.733887 CGTACGTGTGGTTCAATAGATCTC 59.266 45.833 7.22 0.00 0.00 2.75
1642 1728 3.192844 ACGTGTGGTTCAATAGATCTCGT 59.807 43.478 0.00 0.00 0.00 4.18
1643 1729 3.791887 CGTGTGGTTCAATAGATCTCGTC 59.208 47.826 0.00 0.00 0.00 4.20
1926 2038 3.494336 CGGCCGACTACGACGAGT 61.494 66.667 24.07 0.16 42.66 4.18
1972 2084 0.250295 TTCTCCCAGAAGCACAACCG 60.250 55.000 0.00 0.00 29.50 4.44
2227 2339 1.375908 GCACATGACGGAGAAGGCA 60.376 57.895 0.00 0.00 0.00 4.75
2360 2472 6.093633 TCGATTCGTATAGCTGCAGTATACAT 59.906 38.462 27.40 20.46 34.32 2.29
2636 2750 5.359194 AGTATCACCCATCACTTTCGATT 57.641 39.130 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.393062 GGAATGACGAGATTGAAAGCTTCA 59.607 41.667 0.00 0.00 38.04 3.02
12 13 3.362581 GGCGGAATGACGAGATTGA 57.637 52.632 0.00 0.00 35.47 2.57
21 22 0.034198 TGTTCAAGTCGGCGGAATGA 59.966 50.000 7.21 6.18 0.00 2.57
88 94 0.540365 CTTGGCATGTGGTCCCAGTT 60.540 55.000 0.00 0.00 0.00 3.16
91 97 1.496444 TAGCTTGGCATGTGGTCCCA 61.496 55.000 0.00 0.00 0.00 4.37
112 118 7.437862 AGTGTAAATTTGACGACAAAATTGCAT 59.562 29.630 24.87 15.69 45.43 3.96
172 178 8.349983 GTTTGTAGCACCGATATCCAAAATTAT 58.650 33.333 0.00 0.00 0.00 1.28
229 235 7.945134 AGCACTTCACTTATTTCACAATCTTT 58.055 30.769 0.00 0.00 0.00 2.52
273 279 6.832384 TCCTCTAATTCCACTATACGACAGTT 59.168 38.462 0.00 0.00 0.00 3.16
470 476 9.734620 TCTATCTTCCAAATAAAAATTGCATCG 57.265 29.630 0.00 0.00 0.00 3.84
504 510 7.646446 AAAGTTATTTATCAAACCGGCAAAC 57.354 32.000 0.00 0.00 0.00 2.93
548 554 8.454106 CCAAGACAAGTGGTGATTAAGATTTAG 58.546 37.037 0.00 0.00 0.00 1.85
756 775 8.401490 AGAAGAGATATGGTTTTTATGGCATC 57.599 34.615 1.65 0.00 0.00 3.91
836 862 6.387465 CGGACGTATATACATGAGGTGAATT 58.613 40.000 13.22 0.00 0.00 2.17
847 873 0.890542 AGGCGGCGGACGTATATACA 60.891 55.000 9.78 0.00 46.52 2.29
863 889 7.809806 GTGCATCAATTAAGGATTATGTAAGGC 59.190 37.037 0.00 0.00 0.00 4.35
864 890 8.849168 TGTGCATCAATTAAGGATTATGTAAGG 58.151 33.333 0.00 0.00 0.00 2.69
960 991 5.858049 ACGTGTACTACATCGAATCGAAAAA 59.142 36.000 10.12 0.00 39.99 1.94
962 993 4.973396 ACGTGTACTACATCGAATCGAAA 58.027 39.130 10.12 0.00 39.99 3.46
965 996 3.002042 AGGACGTGTACTACATCGAATCG 59.998 47.826 14.25 0.00 0.00 3.34
966 997 4.548991 AGGACGTGTACTACATCGAATC 57.451 45.455 14.25 6.04 0.00 2.52
967 998 4.397103 TCAAGGACGTGTACTACATCGAAT 59.603 41.667 14.25 0.00 0.00 3.34
1365 1444 4.247380 GCCTCCTCCGGGATGCTG 62.247 72.222 0.00 0.00 45.65 4.41
1616 1702 4.397103 AGATCTATTGAACCACACGTACGA 59.603 41.667 24.41 0.00 0.00 3.43
1640 1726 1.571460 GACTGCAAGGCACAAGACG 59.429 57.895 0.00 0.00 46.27 4.18
1878 1990 3.391382 GTGGGCGCTCAGGTAGGT 61.391 66.667 12.15 0.00 0.00 3.08
1880 1992 3.376935 CTGGTGGGCGCTCAGGTAG 62.377 68.421 12.15 5.45 0.00 3.18
2636 2750 1.193650 CGGCAAAATCGAAGTCGTCAA 59.806 47.619 0.00 0.00 40.80 3.18


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

AutoCloner maintained by Alex Coulton.