Multiple sequence alignment - TraesCS1D01G063800

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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 TraesCS1D01G063800 chr1D 100.000 2407 0 0 1 2407 44309500 44311906 0.000000e+00 4446
1 TraesCS1D01G063800 chr1D 97.299 1481 38 1 1 1479 44274300 44275780 0.000000e+00 2512
2 TraesCS1D01G063800 chr1D 95.684 1483 56 4 1 1476 43822383 43823864 0.000000e+00 2377
3 TraesCS1D01G063800 chr1D 96.878 929 29 0 1479 2407 240639861 240638933 0.000000e+00 1555
4 TraesCS1D01G063800 chr1D 96.667 930 28 2 1478 2407 130917085 130916159 0.000000e+00 1543
5 TraesCS1D01G063800 chr1D 96.563 931 30 2 1478 2407 494720566 494721495 0.000000e+00 1541
6 TraesCS1D01G063800 chr1D 96.452 930 29 3 1478 2407 171832802 171833727 0.000000e+00 1531
7 TraesCS1D01G063800 chr1D 97.578 702 17 0 778 1479 44628962 44629663 0.000000e+00 1203
8 TraesCS1D01G063800 chr1D 90.377 769 59 7 722 1477 43305828 43306594 0.000000e+00 996
9 TraesCS1D01G063800 chr1D 94.077 439 20 3 1 433 44158658 44159096 0.000000e+00 662
10 TraesCS1D01G063800 chr1D 96.000 200 6 2 78 275 44628763 44628962 8.300000e-85 324
11 TraesCS1D01G063800 chr3D 96.774 930 30 0 1478 2407 421528037 421527108 0.000000e+00 1552
12 TraesCS1D01G063800 chr3D 96.241 931 33 2 1478 2407 421540658 421539729 0.000000e+00 1524
13 TraesCS1D01G063800 chr3D 94.792 288 12 1 433 717 111181233 111181520 1.700000e-121 446
14 TraesCS1D01G063800 chr3D 92.384 302 21 2 417 717 382108036 382108336 1.710000e-116 429
15 TraesCS1D01G063800 chr3D 95.614 114 4 1 304 417 589199574 589199462 5.290000e-42 182
16 TraesCS1D01G063800 chr5D 96.771 929 29 1 1479 2407 535233744 535232817 0.000000e+00 1548
17 TraesCS1D01G063800 chr5D 96.452 930 32 1 1478 2407 535222743 535221815 0.000000e+00 1533
18 TraesCS1D01G063800 chr6D 96.448 929 33 0 1479 2407 231424867 231425795 0.000000e+00 1533
19 TraesCS1D01G063800 chr6D 94.198 293 15 2 425 717 24480127 24479837 1.700000e-121 446
20 TraesCS1D01G063800 chr1B 94.286 770 43 1 711 1479 63888935 63889704 0.000000e+00 1177
21 TraesCS1D01G063800 chr1B 93.669 774 47 2 711 1483 63479635 63480407 0.000000e+00 1157
22 TraesCS1D01G063800 chr1B 92.894 774 53 2 711 1483 63468403 63469175 0.000000e+00 1123
23 TraesCS1D01G063800 chr1B 93.185 763 52 0 717 1479 63759037 63759799 0.000000e+00 1122
24 TraesCS1D01G063800 chr1B 88.929 280 30 1 32 311 63468117 63468395 6.370000e-91 344
25 TraesCS1D01G063800 chr1B 88.929 280 30 1 32 311 63479349 63479627 6.370000e-91 344
26 TraesCS1D01G063800 chr1B 87.943 282 30 4 32 311 63888648 63888927 1.780000e-86 329
27 TraesCS1D01G063800 chr1A 94.195 758 44 0 722 1479 43271785 43271028 0.000000e+00 1157
28 TraesCS1D01G063800 chr1A 94.048 756 43 1 722 1477 43392401 43391648 0.000000e+00 1146
29 TraesCS1D01G063800 chr1A 89.896 772 63 8 718 1476 42670374 42671143 0.000000e+00 979
30 TraesCS1D01G063800 chr1A 91.144 271 22 2 42 311 43392690 43392421 1.360000e-97 366
31 TraesCS1D01G063800 chr1A 89.630 270 27 1 42 311 43272073 43271805 2.290000e-90 342
32 TraesCS1D01G063800 chr2D 95.502 289 13 0 431 719 371841091 371841379 1.690000e-126 462
33 TraesCS1D01G063800 chr2D 90.226 133 11 2 309 441 460725345 460725215 3.180000e-39 172
34 TraesCS1D01G063800 chr7D 95.406 283 12 1 436 717 550980000 550979718 1.310000e-122 449
35 TraesCS1D01G063800 chr6B 94.737 285 15 0 433 717 481797089 481797373 6.110000e-121 444
36 TraesCS1D01G063800 chr4D 94.737 285 15 0 433 717 329463329 329463613 6.110000e-121 444
37 TraesCS1D01G063800 chr5B 87.755 196 21 3 308 503 167283425 167283617 2.410000e-55 226
38 TraesCS1D01G063800 chr7B 95.833 120 5 0 296 415 420072677 420072796 6.790000e-46 195
39 TraesCS1D01G063800 chr7B 91.729 133 6 4 295 423 58655882 58656013 1.900000e-41 180
40 TraesCS1D01G063800 chr4B 95.690 116 5 0 300 415 60204678 60204563 1.140000e-43 187


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 TraesCS1D01G063800 chr1D 44309500 44311906 2406 False 4446.0 4446 100.0000 1 2407 1 chr1D.!!$F5 2406
1 TraesCS1D01G063800 chr1D 44274300 44275780 1480 False 2512.0 2512 97.2990 1 1479 1 chr1D.!!$F4 1478
2 TraesCS1D01G063800 chr1D 43822383 43823864 1481 False 2377.0 2377 95.6840 1 1476 1 chr1D.!!$F2 1475
3 TraesCS1D01G063800 chr1D 240638933 240639861 928 True 1555.0 1555 96.8780 1479 2407 1 chr1D.!!$R2 928
4 TraesCS1D01G063800 chr1D 130916159 130917085 926 True 1543.0 1543 96.6670 1478 2407 1 chr1D.!!$R1 929
5 TraesCS1D01G063800 chr1D 494720566 494721495 929 False 1541.0 1541 96.5630 1478 2407 1 chr1D.!!$F7 929
6 TraesCS1D01G063800 chr1D 171832802 171833727 925 False 1531.0 1531 96.4520 1478 2407 1 chr1D.!!$F6 929
7 TraesCS1D01G063800 chr1D 43305828 43306594 766 False 996.0 996 90.3770 722 1477 1 chr1D.!!$F1 755
8 TraesCS1D01G063800 chr1D 44628763 44629663 900 False 763.5 1203 96.7890 78 1479 2 chr1D.!!$F8 1401
9 TraesCS1D01G063800 chr3D 421527108 421528037 929 True 1552.0 1552 96.7740 1478 2407 1 chr3D.!!$R1 929
10 TraesCS1D01G063800 chr3D 421539729 421540658 929 True 1524.0 1524 96.2410 1478 2407 1 chr3D.!!$R2 929
11 TraesCS1D01G063800 chr5D 535232817 535233744 927 True 1548.0 1548 96.7710 1479 2407 1 chr5D.!!$R2 928
12 TraesCS1D01G063800 chr5D 535221815 535222743 928 True 1533.0 1533 96.4520 1478 2407 1 chr5D.!!$R1 929
13 TraesCS1D01G063800 chr6D 231424867 231425795 928 False 1533.0 1533 96.4480 1479 2407 1 chr6D.!!$F1 928
14 TraesCS1D01G063800 chr1B 63759037 63759799 762 False 1122.0 1122 93.1850 717 1479 1 chr1B.!!$F1 762
15 TraesCS1D01G063800 chr1B 63888648 63889704 1056 False 753.0 1177 91.1145 32 1479 2 chr1B.!!$F4 1447
16 TraesCS1D01G063800 chr1B 63479349 63480407 1058 False 750.5 1157 91.2990 32 1483 2 chr1B.!!$F3 1451
17 TraesCS1D01G063800 chr1B 63468117 63469175 1058 False 733.5 1123 90.9115 32 1483 2 chr1B.!!$F2 1451
18 TraesCS1D01G063800 chr1A 42670374 42671143 769 False 979.0 979 89.8960 718 1476 1 chr1A.!!$F1 758
19 TraesCS1D01G063800 chr1A 43391648 43392690 1042 True 756.0 1146 92.5960 42 1477 2 chr1A.!!$R2 1435
20 TraesCS1D01G063800 chr1A 43271028 43272073 1045 True 749.5 1157 91.9125 42 1479 2 chr1A.!!$R1 1437

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
457 464 2.381725 GCCACAGTGGGTAGTAACTC 57.618 55.0 21.77 0.0 38.19 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 2130 0.543646 GCCCCCTTATAGTCGGCCTA 60.544 60.0 0.0 0.0 33.3 3.93 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
56 57 7.811117 TGTAATTAATGTAATGGTGTAGCCC 57.189 36.000 0.00 0.00 36.04 5.19
74 75 7.119262 GTGTAGCCCGTAGATATGCAATTAATT 59.881 37.037 0.00 0.00 0.00 1.40
249 254 7.118825 GTCATATTGTAGCATGTAGATGTGCAT 59.881 37.037 1.37 0.00 43.63 3.96
457 464 2.381725 GCCACAGTGGGTAGTAACTC 57.618 55.000 21.77 0.00 38.19 3.01
636 643 6.398918 TGTTACTACATGCCTCTCTTTCTTC 58.601 40.000 0.00 0.00 0.00 2.87
649 656 7.362401 GCCTCTCTTTCTTCATTAATTGCTTGA 60.362 37.037 0.00 0.00 0.00 3.02
733 740 7.101652 AGTAGTCTAACATGTCGATGTGAAT 57.898 36.000 0.00 0.00 42.30 2.57
767 778 8.632679 ACACACTCATTGTTTGATGTTATTTCT 58.367 29.630 0.00 0.00 35.67 2.52
1298 1323 2.202395 ATGCCTTTGCGCTGGTGTT 61.202 52.632 9.73 0.00 41.78 3.32
1436 1461 5.700832 GGAGTTATGATGATCGGTATTGCAA 59.299 40.000 0.00 0.00 0.00 4.08
1443 1468 2.223226 TGATCGGTATTGCAAACATGCG 60.223 45.455 1.71 3.36 37.69 4.73
1613 1638 2.685380 CCAGGTTCGGGGCTCTCT 60.685 66.667 0.00 0.00 0.00 3.10
1992 2019 1.858091 CTGAGGTAAGCATGGCTACG 58.142 55.000 0.00 0.00 38.25 3.51
2114 2141 1.822457 GCTACACCCTAGGCCGACTAT 60.822 57.143 2.05 0.00 0.00 2.12
2159 2186 1.382420 CTCTCTGGCTGTAGGGGCT 60.382 63.158 0.00 0.00 0.00 5.19
2190 2217 1.301165 GCCGTACTGACAACCCGTT 60.301 57.895 0.00 0.00 0.00 4.44
2328 2356 2.738521 CACGCCCGGTCTTGTCAG 60.739 66.667 0.00 0.00 0.00 3.51
2374 2402 2.998279 GCAATCTTGGCCGCTTGCT 61.998 57.895 18.60 0.00 40.55 3.91
2377 2405 2.803155 AATCTTGGCCGCTTGCTCGA 62.803 55.000 0.00 0.00 40.92 4.04
2395 2423 2.814280 GAAGTCGGTCTTCTTGTGGA 57.186 50.000 7.59 0.00 46.36 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.484308 ACGGGCTACACCATTACATTAATTAC 59.516 38.462 0.00 0.00 42.05 1.89
312 319 2.564062 ACAAGTAATTCCGAACGGAGGA 59.436 45.455 15.34 3.20 46.06 3.71
375 382 6.292168 CGAATTACTTGTCGCGGAAATAGATT 60.292 38.462 6.13 0.00 0.00 2.40
385 392 1.266211 CGTTCCGAATTACTTGTCGCG 60.266 52.381 0.00 0.00 35.93 5.87
733 740 7.851387 TCAAACAATGAGTGTGTACAGTAAA 57.149 32.000 0.00 0.00 40.60 2.01
865 876 5.102953 ACATTAATTGCACTCTAGAGGCA 57.897 39.130 23.79 23.79 34.44 4.75
1415 1440 6.724263 TGTTTGCAATACCGATCATCATAAC 58.276 36.000 0.00 0.00 0.00 1.89
1436 1461 8.770438 AATAACAAATATCAAAACCGCATGTT 57.230 26.923 0.00 0.00 39.43 2.71
1613 1638 3.371965 GACTAGGGGTGTTATCTCCACA 58.628 50.000 0.00 0.00 33.49 4.17
1828 1855 2.708861 TCCAGCCGGATTACCATTGTAT 59.291 45.455 5.05 0.00 35.91 2.29
2009 2036 3.764972 GAGGTAAGGCTACAGTGAGAGTT 59.235 47.826 0.00 0.00 0.00 3.01
2103 2130 0.543646 GCCCCCTTATAGTCGGCCTA 60.544 60.000 0.00 0.00 33.30 3.93
2190 2217 3.545124 GACCATGACGCCACCCACA 62.545 63.158 0.00 0.00 0.00 4.17
2328 2356 1.644786 GGACAGCACCCACATAACGC 61.645 60.000 0.00 0.00 0.00 4.84
2377 2405 1.269621 CGTCCACAAGAAGACCGACTT 60.270 52.381 0.00 0.00 42.03 3.01


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

AutoCloner maintained by Alex Coulton.