Multiple sequence alignment - TraesCS5D01G126200

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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 TraesCS5D01G126200 chr5D 100.000 2654 0 0 1 2654 193136321 193138974 0.000000e+00 4902
1 TraesCS5D01G126200 chr5D 80.254 1023 176 19 560 1560 482800387 482801405 0.000000e+00 747
2 TraesCS5D01G126200 chr6D 93.914 2251 85 16 1 2221 425836991 425839219 0.000000e+00 3350
3 TraesCS5D01G126200 chr6D 79.590 1073 191 22 560 1609 296679445 296680512 0.000000e+00 743
4 TraesCS5D01G126200 chr6D 79.421 1001 186 11 628 1609 472021757 472020758 0.000000e+00 689
5 TraesCS5D01G126200 chr6D 79.051 1012 187 15 628 1618 471971576 471970569 0.000000e+00 671
6 TraesCS5D01G126200 chr5B 93.002 1629 78 13 1053 2654 692223391 692225010 0.000000e+00 2344
7 TraesCS5D01G126200 chr5B 81.327 889 162 3 560 1444 444756539 444757427 0.000000e+00 719
8 TraesCS5D01G126200 chr3A 93.538 913 56 2 1744 2654 272742782 272741871 0.000000e+00 1356
9 TraesCS5D01G126200 chr3A 80.927 949 156 17 1716 2654 208399469 208400402 0.000000e+00 726
10 TraesCS5D01G126200 chr3A 86.667 285 21 6 1480 1748 272752449 272752166 1.540000e-77 300
11 TraesCS5D01G126200 chr4A 91.278 1009 59 13 1392 2373 195421922 195420916 0.000000e+00 1349
12 TraesCS5D01G126200 chr4A 78.364 550 104 11 1719 2257 163770520 163769975 2.530000e-90 342
13 TraesCS5D01G126200 chr7B 94.343 548 28 3 2109 2654 15587244 15586698 0.000000e+00 837
14 TraesCS5D01G126200 chr2B 83.669 845 134 4 1812 2654 43639140 43639982 0.000000e+00 793
15 TraesCS5D01G126200 chr7D 84.224 786 121 3 1871 2654 62679135 62679919 0.000000e+00 761
16 TraesCS5D01G126200 chr4D 81.596 902 160 5 560 1456 486782415 486781515 0.000000e+00 741
17 TraesCS5D01G126200 chr1A 82.479 839 143 4 1818 2654 550451296 550450460 0.000000e+00 732
18 TraesCS5D01G126200 chr5A 79.217 1073 195 20 560 1609 669852809 669853876 0.000000e+00 721
19 TraesCS5D01G126200 chr3B 81.938 836 143 7 1823 2654 59395327 59394496 0.000000e+00 701
20 TraesCS5D01G126200 chr3B 79.006 986 200 6 502 1482 485405707 485404724 0.000000e+00 667
21 TraesCS5D01G126200 chr3B 78.841 1035 186 28 1638 2653 828596440 828597460 0.000000e+00 667
22 TraesCS5D01G126200 chr3B 81.064 470 77 11 2191 2652 772418773 772418308 5.400000e-97 364
23 TraesCS5D01G126200 chr3B 75.445 786 148 35 1812 2570 485404358 485403591 9.100000e-90 340


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 TraesCS5D01G126200 chr5D 193136321 193138974 2653 False 4902.0 4902 100.0000 1 2654 1 chr5D.!!$F1 2653
1 TraesCS5D01G126200 chr5D 482800387 482801405 1018 False 747.0 747 80.2540 560 1560 1 chr5D.!!$F2 1000
2 TraesCS5D01G126200 chr6D 425836991 425839219 2228 False 3350.0 3350 93.9140 1 2221 1 chr6D.!!$F2 2220
3 TraesCS5D01G126200 chr6D 296679445 296680512 1067 False 743.0 743 79.5900 560 1609 1 chr6D.!!$F1 1049
4 TraesCS5D01G126200 chr6D 472020758 472021757 999 True 689.0 689 79.4210 628 1609 1 chr6D.!!$R2 981
5 TraesCS5D01G126200 chr6D 471970569 471971576 1007 True 671.0 671 79.0510 628 1618 1 chr6D.!!$R1 990
6 TraesCS5D01G126200 chr5B 692223391 692225010 1619 False 2344.0 2344 93.0020 1053 2654 1 chr5B.!!$F2 1601
7 TraesCS5D01G126200 chr5B 444756539 444757427 888 False 719.0 719 81.3270 560 1444 1 chr5B.!!$F1 884
8 TraesCS5D01G126200 chr3A 272741871 272742782 911 True 1356.0 1356 93.5380 1744 2654 1 chr3A.!!$R1 910
9 TraesCS5D01G126200 chr3A 208399469 208400402 933 False 726.0 726 80.9270 1716 2654 1 chr3A.!!$F1 938
10 TraesCS5D01G126200 chr4A 195420916 195421922 1006 True 1349.0 1349 91.2780 1392 2373 1 chr4A.!!$R2 981
11 TraesCS5D01G126200 chr4A 163769975 163770520 545 True 342.0 342 78.3640 1719 2257 1 chr4A.!!$R1 538
12 TraesCS5D01G126200 chr7B 15586698 15587244 546 True 837.0 837 94.3430 2109 2654 1 chr7B.!!$R1 545
13 TraesCS5D01G126200 chr2B 43639140 43639982 842 False 793.0 793 83.6690 1812 2654 1 chr2B.!!$F1 842
14 TraesCS5D01G126200 chr7D 62679135 62679919 784 False 761.0 761 84.2240 1871 2654 1 chr7D.!!$F1 783
15 TraesCS5D01G126200 chr4D 486781515 486782415 900 True 741.0 741 81.5960 560 1456 1 chr4D.!!$R1 896
16 TraesCS5D01G126200 chr1A 550450460 550451296 836 True 732.0 732 82.4790 1818 2654 1 chr1A.!!$R1 836
17 TraesCS5D01G126200 chr5A 669852809 669853876 1067 False 721.0 721 79.2170 560 1609 1 chr5A.!!$F1 1049
18 TraesCS5D01G126200 chr3B 59394496 59395327 831 True 701.0 701 81.9380 1823 2654 1 chr3B.!!$R1 831
19 TraesCS5D01G126200 chr3B 828596440 828597460 1020 False 667.0 667 78.8410 1638 2653 1 chr3B.!!$F1 1015
20 TraesCS5D01G126200 chr3B 485403591 485405707 2116 True 503.5 667 77.2255 502 2570 2 chr3B.!!$R3 2068

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
606 607 0.673956 GAAAGCAGGGGGAAGTCGAC 60.674 60.0 7.7 7.7 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 2268 1.364269 TACCCCCGTCCACATTCTTT 58.636 50.0 0.0 0.0 0.0 2.52 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
22 23 2.965831 CGGGATTCCAAGTGAGATCCTA 59.034 50.000 4.80 0.00 0.00 2.94
40 41 5.320488 TCCTATCGGATCAGAAGGTAGAA 57.680 43.478 17.10 3.32 33.30 2.10
84 85 2.223805 GCAAGAAAACTGAGTTGGTGGG 60.224 50.000 0.00 0.00 0.00 4.61
112 113 0.680061 GTGAGGGTAATAGGGGCGAG 59.320 60.000 0.00 0.00 0.00 5.03
127 128 2.603560 GGGCGAGATTTCTTCTGTTACG 59.396 50.000 0.00 0.00 33.74 3.18
226 227 6.073222 ACGATCTTGTGATTGTTGTTAGGAAC 60.073 38.462 0.00 0.00 42.94 3.62
240 241 9.667107 TGTTGTTAGGAACAGAGGAATAATTAG 57.333 33.333 0.00 0.00 43.27 1.73
281 282 4.023291 ACGGCCTTTTCATGACCATTTAT 58.977 39.130 0.00 0.00 0.00 1.40
282 283 4.466015 ACGGCCTTTTCATGACCATTTATT 59.534 37.500 0.00 0.00 0.00 1.40
284 285 6.183360 ACGGCCTTTTCATGACCATTTATTAG 60.183 38.462 0.00 0.00 0.00 1.73
285 286 5.985530 GGCCTTTTCATGACCATTTATTAGC 59.014 40.000 0.00 0.00 0.00 3.09
286 287 5.687285 GCCTTTTCATGACCATTTATTAGCG 59.313 40.000 0.00 0.00 0.00 4.26
369 370 0.996762 TTGGGGAGGTGGTGTTCCTT 60.997 55.000 0.00 0.00 35.20 3.36
380 381 2.940410 TGGTGTTCCTTTTCGTCAGTTC 59.060 45.455 0.00 0.00 34.23 3.01
382 383 3.002348 GGTGTTCCTTTTCGTCAGTTCTG 59.998 47.826 0.00 0.00 0.00 3.02
384 385 3.869246 TGTTCCTTTTCGTCAGTTCTGTC 59.131 43.478 0.00 0.00 0.00 3.51
448 449 2.514824 GGGTCTTCCATGGCGAGC 60.515 66.667 18.96 18.96 35.00 5.03
462 463 2.610859 GAGCTGGAAGGGGGTGGA 60.611 66.667 0.00 0.00 0.00 4.02
467 468 2.125225 GGAAGGGGGTGGAGAGGT 59.875 66.667 0.00 0.00 0.00 3.85
498 499 1.305718 GTGCAGAGGGGAGAGAGGT 60.306 63.158 0.00 0.00 0.00 3.85
524 525 3.775654 GAGGGGTGGCTCAGTCCG 61.776 72.222 0.00 0.00 0.00 4.79
557 558 1.298788 CCGGTGACAACAAAACGCC 60.299 57.895 0.00 0.00 0.00 5.68
606 607 0.673956 GAAAGCAGGGGGAAGTCGAC 60.674 60.000 7.70 7.70 0.00 4.20
653 654 3.740115 TCGTCTCTGGTCATCGATATGA 58.260 45.455 0.00 0.00 39.87 2.15
724 726 1.454539 CCCTTCCAAGTGAACCCGT 59.545 57.895 0.00 0.00 0.00 5.28
735 737 1.066143 GTGAACCCGTGGATCATCACT 60.066 52.381 6.26 0.00 36.89 3.41
741 743 2.159156 CCCGTGGATCATCACTAACGAA 60.159 50.000 0.00 0.00 35.63 3.85
803 805 1.523258 CTCAAGATCTGGCCAGCGG 60.523 63.158 28.91 14.33 0.00 5.52
1463 1468 1.888018 CTACCATGACGACGGGTGT 59.112 57.895 10.40 0.00 36.14 4.16
1520 1540 2.675371 GGGTACTTGTGGCTCCCC 59.325 66.667 0.00 0.00 32.66 4.81
1633 1667 2.202395 GGCCTGGAGCTGTGCAAAA 61.202 57.895 0.00 0.00 43.05 2.44
2174 2281 8.928270 AGTAGAAACTATAAAGAATGTGGACG 57.072 34.615 0.00 0.00 32.84 4.79
2434 2555 7.967854 CACTTGAATAAATGTAAAGCCGATGAA 59.032 33.333 0.00 0.00 0.00 2.57
2482 2604 2.941453 TGATTGTAGTGGAGAGCGAC 57.059 50.000 0.00 0.00 0.00 5.19
2600 2723 0.099436 GATTCTGTGCATTGGCGGTC 59.901 55.000 0.00 0.00 45.35 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.322349 CGATAGGATCTCACTTGGAATCCC 60.322 50.000 0.00 0.0 35.50 3.85
22 23 3.235200 CCCTTCTACCTTCTGATCCGAT 58.765 50.000 0.00 0.0 0.00 4.18
40 41 2.257409 AATTGATGCGAGCCGACCCT 62.257 55.000 0.00 0.0 0.00 4.34
84 85 3.118000 CCTATTACCCTCACTGGAAACCC 60.118 52.174 0.00 0.0 38.35 4.11
127 128 3.330267 CATAGATAGCGCCTTTCTTCCC 58.670 50.000 2.29 0.0 0.00 3.97
226 227 7.227512 AGGAAAATCACGCTAATTATTCCTCTG 59.772 37.037 6.84 0.0 41.00 3.35
281 282 5.825679 AGCAATTGTCATAATAACCCGCTAA 59.174 36.000 7.40 0.0 0.00 3.09
282 283 5.373222 AGCAATTGTCATAATAACCCGCTA 58.627 37.500 7.40 0.0 0.00 4.26
284 285 4.568152 AGCAATTGTCATAATAACCCGC 57.432 40.909 7.40 0.0 0.00 6.13
285 286 5.507315 GGGAAGCAATTGTCATAATAACCCG 60.507 44.000 7.40 0.0 0.00 5.28
286 287 5.507315 CGGGAAGCAATTGTCATAATAACCC 60.507 44.000 7.40 0.0 0.00 4.11
369 370 3.067601 TGCTACAGACAGAACTGACGAAA 59.932 43.478 8.87 0.0 40.63 3.46
380 381 1.824230 AGGCTTCTCTGCTACAGACAG 59.176 52.381 0.00 0.0 35.39 3.51
382 383 3.020984 AGTAGGCTTCTCTGCTACAGAC 58.979 50.000 0.00 0.0 35.39 3.51
384 385 2.360801 GGAGTAGGCTTCTCTGCTACAG 59.639 54.545 18.85 0.0 31.69 2.74
444 445 4.101448 CCACCCCCTTCCAGCTCG 62.101 72.222 0.00 0.0 0.00 5.03
448 449 1.997874 CCTCTCCACCCCCTTCCAG 60.998 68.421 0.00 0.0 0.00 3.86
724 726 3.181490 CGGAGTTCGTTAGTGATGATCCA 60.181 47.826 0.00 0.0 0.00 3.41
803 805 2.908796 GGACGAACCTCCCATCCC 59.091 66.667 0.00 0.0 35.41 3.85
929 931 1.179152 TAACGCAAGATCGACCTCCA 58.821 50.000 0.00 0.0 43.62 3.86
1502 1522 2.675371 GGGAGCCACAAGTACCCC 59.325 66.667 0.00 0.0 35.00 4.95
1633 1667 3.547787 AAGACCCTCCTGGCCGAGT 62.548 63.158 0.00 0.0 37.83 4.18
2161 2268 1.364269 TACCCCCGTCCACATTCTTT 58.636 50.000 0.00 0.0 0.00 2.52
2174 2281 2.572290 GCTACATGTGTGATTACCCCC 58.428 52.381 9.11 0.0 0.00 5.40
2286 2406 1.662438 GATTTTCATTCGGCCCGGCA 61.662 55.000 12.58 0.0 0.00 5.69
2295 2415 6.335777 CAGTTCCATCCAAGGATTTTCATTC 58.664 40.000 0.00 0.0 37.56 2.67
2600 2723 1.676006 GATGACCATAAAAGCCCGTGG 59.324 52.381 0.00 0.0 37.74 4.94


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

AutoCloner maintained by Alex Coulton.