Multiple sequence alignment - TraesCS7A01G230700

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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 TraesCS7A01G230700 chr7A 100.000 2432 0 0 1 2432 201367144 201369575 0.000000e+00 4492
1 TraesCS7A01G230700 chrUn 97.375 1600 31 6 841 2432 93418001 93419597 0.000000e+00 2712
2 TraesCS7A01G230700 chrUn 98.588 850 8 2 1 846 327660628 327661477 0.000000e+00 1500
3 TraesCS7A01G230700 chrUn 98.239 852 9 4 1 846 93417096 93417947 0.000000e+00 1485
4 TraesCS7A01G230700 chr1D 97.312 1600 31 7 841 2432 144237051 144235456 0.000000e+00 2706
5 TraesCS7A01G230700 chr1D 97.892 854 10 5 1 846 144237958 144237105 0.000000e+00 1471
6 TraesCS7A01G230700 chr5D 97.250 1600 32 7 841 2432 560878815 560877220 0.000000e+00 2700
7 TraesCS7A01G230700 chr5D 97.188 1600 32 8 841 2432 503212254 503210660 0.000000e+00 2693
8 TraesCS7A01G230700 chr5D 97.070 1331 36 2 1099 2427 329196036 329194707 0.000000e+00 2239
9 TraesCS7A01G230700 chr5D 98.474 852 7 3 1 846 560879720 560878869 0.000000e+00 1496
10 TraesCS7A01G230700 chr5D 97.535 852 10 6 1 846 503213154 503212308 0.000000e+00 1447
11 TraesCS7A01G230700 chr3B 97.188 1600 33 7 841 2432 201521022 201519427 0.000000e+00 2695
12 TraesCS7A01G230700 chr3B 97.186 853 16 6 1 846 201521926 201521075 0.000000e+00 1435
13 TraesCS7A01G230700 chr3B 94.964 139 2 2 891 1024 804586607 804586469 1.890000e-51 213
14 TraesCS7A01G230700 chr6A 96.289 1590 49 5 850 2432 271183789 271182203 0.000000e+00 2601
15 TraesCS7A01G230700 chr6A 95.810 1599 56 6 841 2432 260126433 260128027 0.000000e+00 2571
16 TraesCS7A01G230700 chr6A 98.233 849 12 1 1 846 271184698 271183850 0.000000e+00 1482
17 TraesCS7A01G230700 chr1A 95.812 1600 52 9 841 2432 168444269 168445861 0.000000e+00 2569
18 TraesCS7A01G230700 chr2D 98.588 850 8 2 1 846 272798982 272799831 0.000000e+00 1500
19 TraesCS7A01G230700 chr4A 97.532 851 13 5 1 846 722779640 722780487 0.000000e+00 1448


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 TraesCS7A01G230700 chr7A 201367144 201369575 2431 False 4492.0 4492 100.0000 1 2432 1 chr7A.!!$F1 2431
1 TraesCS7A01G230700 chrUn 93417096 93419597 2501 False 2098.5 2712 97.8070 1 2432 2 chrUn.!!$F2 2431
2 TraesCS7A01G230700 chrUn 327660628 327661477 849 False 1500.0 1500 98.5880 1 846 1 chrUn.!!$F1 845
3 TraesCS7A01G230700 chr1D 144235456 144237958 2502 True 2088.5 2706 97.6020 1 2432 2 chr1D.!!$R1 2431
4 TraesCS7A01G230700 chr5D 329194707 329196036 1329 True 2239.0 2239 97.0700 1099 2427 1 chr5D.!!$R1 1328
5 TraesCS7A01G230700 chr5D 560877220 560879720 2500 True 2098.0 2700 97.8620 1 2432 2 chr5D.!!$R3 2431
6 TraesCS7A01G230700 chr5D 503210660 503213154 2494 True 2070.0 2693 97.3615 1 2432 2 chr5D.!!$R2 2431
7 TraesCS7A01G230700 chr3B 201519427 201521926 2499 True 2065.0 2695 97.1870 1 2432 2 chr3B.!!$R2 2431
8 TraesCS7A01G230700 chr6A 260126433 260128027 1594 False 2571.0 2571 95.8100 841 2432 1 chr6A.!!$F1 1591
9 TraesCS7A01G230700 chr6A 271182203 271184698 2495 True 2041.5 2601 97.2610 1 2432 2 chr6A.!!$R1 2431
10 TraesCS7A01G230700 chr1A 168444269 168445861 1592 False 2569.0 2569 95.8120 841 2432 1 chr1A.!!$F1 1591
11 TraesCS7A01G230700 chr2D 272798982 272799831 849 False 1500.0 1500 98.5880 1 846 1 chr2D.!!$F1 845
12 TraesCS7A01G230700 chr4A 722779640 722780487 847 False 1448.0 1448 97.5320 1 846 1 chr4A.!!$F1 845


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
578 586 3.78085 ACTTCCCCATAAGGATTCGAAGT 59.219 43.478 3.35 0.0 38.24 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1598 1675 0.400213 AGCGGGGACAGAATGAAACA 59.6 50.0 0.0 0.0 39.69 2.83 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
144 145 6.183361 GGAATTCCTAAAGTTTTGGGTGGAAA 60.183 38.462 17.73 3.51 39.55 3.13
578 586 3.780850 ACTTCCCCATAAGGATTCGAAGT 59.219 43.478 3.35 0.00 38.24 3.01
619 627 6.268847 AGGATAGCGAAGATTTGAAGGATAGT 59.731 38.462 0.00 0.00 0.00 2.12
848 917 7.011482 GTGGACGAATTAGAGTCATTTGCTAAT 59.989 37.037 9.46 0.00 39.01 1.73
1078 1154 8.276252 ACGTAGGAATGCACATTTTAGTTTAT 57.724 30.769 0.00 0.00 0.00 1.40
1101 1177 4.219944 TGGAAGAGTGCACGTAGAATAACT 59.780 41.667 12.01 0.00 0.00 2.24
1131 1207 7.309805 GGGGTTATTCATGTTCAAGCTAGTTTT 60.310 37.037 0.00 0.00 0.00 2.43
1323 1399 0.179124 GCGCTGGTAGTGGAAGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
1408 1484 1.270785 TGCCGCATAATGGATGTCGAT 60.271 47.619 0.00 0.00 37.29 3.59
1570 1647 4.526970 AGTGGAAGTGTGTTGAATCAAGT 58.473 39.130 0.00 0.00 0.00 3.16
1598 1675 7.450903 AGATAGTAAGCGCCTTTATTATGGTT 58.549 34.615 2.29 0.00 0.00 3.67
1655 1732 0.672401 CACCGTCGGTATTGCCTTGT 60.672 55.000 18.38 0.00 32.11 3.16
1834 1911 4.184629 GAGTTAGAGACGCATCCATTTGT 58.815 43.478 0.00 0.00 0.00 2.83
2002 2079 6.740110 TCAGACAGAACTCAGAAAGAACTAC 58.260 40.000 0.00 0.00 0.00 2.73
2223 2303 0.103390 GAGGAAGAGGGCGCTAGTTC 59.897 60.000 7.64 9.89 0.00 3.01
2256 2336 1.525175 AACAGGTTTACTCCACCCCA 58.475 50.000 0.00 0.00 34.44 4.96
2387 2467 8.862325 TTGTCTATAAAGGGCCAATATACATG 57.138 34.615 6.18 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 145 7.866870 AGAAGTAGAAAGAATAGCAATTCCCT 58.133 34.615 0.00 0.0 42.20 4.20
212 213 9.273137 CCATATATAACATAAGACTTCTCCCCT 57.727 37.037 0.00 0.0 0.00 4.79
415 423 2.094182 GGTGTCATTCTCTAGCCGAACA 60.094 50.000 0.00 0.0 0.00 3.18
619 627 8.884124 AATCTTTGGTATCCTTCAAATCTTCA 57.116 30.769 0.00 0.0 33.19 3.02
1078 1154 4.219944 AGTTATTCTACGTGCACTCTTCCA 59.780 41.667 16.19 0.0 0.00 3.53
1101 1177 6.252995 AGCTTGAACATGAATAACCCCTTTA 58.747 36.000 0.00 0.0 0.00 1.85
1264 1340 3.386486 CTCGTTGCAAACCTACTGTACA 58.614 45.455 0.00 0.0 46.28 2.90
1570 1647 8.033038 CCATAATAAAGGCGCTTACTATCTACA 58.967 37.037 7.64 0.0 0.00 2.74
1598 1675 0.400213 AGCGGGGACAGAATGAAACA 59.600 50.000 0.00 0.0 39.69 2.83
1655 1732 7.907389 TCTATTTCTCCAAGTAAAGCTCTTCA 58.093 34.615 0.00 0.0 0.00 3.02
1834 1911 7.632898 GCAGTTATGTATCTAGGACCTTTGACA 60.633 40.741 0.00 0.0 0.00 3.58
2223 2303 9.177304 GAGTAAACCTGTTTTTATTTTCTTCGG 57.823 33.333 0.00 0.0 34.23 4.30
2369 2449 5.060427 AGTGCATGTATATTGGCCCTTTA 57.940 39.130 0.00 0.0 0.00 1.85
2387 2467 5.938125 TCTTACTCAAAAGGTCCAATAGTGC 59.062 40.000 0.00 0.0 0.00 4.40



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

AutoCloner maintained by Alex Coulton.