Multiple sequence alignment - TraesCS2D01G283700

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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 TraesCS2D01G283700 chr2D 100.000 2348 0 0 1 2348 357864392 357862045 0.000000e+00 4337
1 TraesCS2D01G283700 chr2D 89.155 627 60 8 1722 2343 158952310 158951687 0.000000e+00 774
2 TraesCS2D01G283700 chr3D 90.629 1430 121 9 293 1720 397920882 397922300 0.000000e+00 1886
3 TraesCS2D01G283700 chr3D 88.346 1330 148 6 402 1727 500312035 500310709 0.000000e+00 1591
4 TraesCS2D01G283700 chr3D 91.841 478 33 4 1243 1720 488576218 488575747 0.000000e+00 662
5 TraesCS2D01G283700 chr3D 91.791 268 21 1 1 268 500406012 500405746 2.850000e-99 372
6 TraesCS2D01G283700 chr3A 86.003 1729 212 24 1 1720 466100217 466098510 0.000000e+00 1825
7 TraesCS2D01G283700 chr3A 82.289 463 58 14 1262 1720 691506328 691505886 1.700000e-101 379
8 TraesCS2D01G283700 chr2A 85.644 1637 204 24 96 1720 757997247 757995630 0.000000e+00 1692
9 TraesCS2D01G283700 chr2A 84.228 894 127 12 90 978 445315483 445314599 0.000000e+00 857
10 TraesCS2D01G283700 chr2A 89.809 628 55 9 1722 2343 458830470 458831094 0.000000e+00 797
11 TraesCS2D01G283700 chr2A 84.667 750 101 12 974 1720 445307153 445306415 0.000000e+00 736
12 TraesCS2D01G283700 chr2B 83.863 1258 194 9 98 1350 748211390 748212643 0.000000e+00 1190
13 TraesCS2D01G283700 chr2B 89.372 621 57 8 1728 2344 366948402 366947787 0.000000e+00 773
14 TraesCS2D01G283700 chr2B 75.000 460 107 8 4 458 198312747 198313203 3.060000e-49 206
15 TraesCS2D01G283700 chr6B 82.198 1365 224 11 1 1350 715763263 715761903 0.000000e+00 1157
16 TraesCS2D01G283700 chr6B 89.060 777 81 4 947 1720 545331047 545330272 0.000000e+00 961
17 TraesCS2D01G283700 chr6B 77.671 1357 286 16 4 1351 695921011 695922359 0.000000e+00 811
18 TraesCS2D01G283700 chr6B 84.545 220 29 5 1504 1720 232075389 232075606 1.830000e-51 213
19 TraesCS2D01G283700 chr6B 84.444 225 26 7 1504 1723 417216937 417216717 1.830000e-51 213
20 TraesCS2D01G283700 chr6B 84.444 225 24 8 1504 1722 79246347 79246128 6.570000e-51 211
21 TraesCS2D01G283700 chr7A 79.883 1367 249 21 4 1357 717769108 717767755 0.000000e+00 977
22 TraesCS2D01G283700 chr7A 78.647 1330 269 10 26 1348 721643425 721642104 0.000000e+00 869
23 TraesCS2D01G283700 chr5D 90.287 628 54 7 1726 2348 309919351 309919976 0.000000e+00 815
24 TraesCS2D01G283700 chr6A 91.122 597 49 4 1722 2315 526308245 526307650 0.000000e+00 806
25 TraesCS2D01G283700 chr7D 89.490 628 58 7 1722 2343 277048998 277049623 0.000000e+00 787
26 TraesCS2D01G283700 chr4D 89.490 628 57 8 1722 2343 219970701 219970077 0.000000e+00 785
27 TraesCS2D01G283700 chr4D 89.013 628 62 7 1722 2343 101098720 101099346 0.000000e+00 771
28 TraesCS2D01G283700 chr6D 89.644 618 57 6 1729 2343 361368296 361368909 0.000000e+00 780
29 TraesCS2D01G283700 chr4A 73.830 470 113 10 4 468 714233719 714234183 6.670000e-41 178


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 TraesCS2D01G283700 chr2D 357862045 357864392 2347 True 4337 4337 100.000 1 2348 1 chr2D.!!$R2 2347
1 TraesCS2D01G283700 chr2D 158951687 158952310 623 True 774 774 89.155 1722 2343 1 chr2D.!!$R1 621
2 TraesCS2D01G283700 chr3D 397920882 397922300 1418 False 1886 1886 90.629 293 1720 1 chr3D.!!$F1 1427
3 TraesCS2D01G283700 chr3D 500310709 500312035 1326 True 1591 1591 88.346 402 1727 1 chr3D.!!$R2 1325
4 TraesCS2D01G283700 chr3A 466098510 466100217 1707 True 1825 1825 86.003 1 1720 1 chr3A.!!$R1 1719
5 TraesCS2D01G283700 chr2A 757995630 757997247 1617 True 1692 1692 85.644 96 1720 1 chr2A.!!$R3 1624
6 TraesCS2D01G283700 chr2A 445314599 445315483 884 True 857 857 84.228 90 978 1 chr2A.!!$R2 888
7 TraesCS2D01G283700 chr2A 458830470 458831094 624 False 797 797 89.809 1722 2343 1 chr2A.!!$F1 621
8 TraesCS2D01G283700 chr2A 445306415 445307153 738 True 736 736 84.667 974 1720 1 chr2A.!!$R1 746
9 TraesCS2D01G283700 chr2B 748211390 748212643 1253 False 1190 1190 83.863 98 1350 1 chr2B.!!$F2 1252
10 TraesCS2D01G283700 chr2B 366947787 366948402 615 True 773 773 89.372 1728 2344 1 chr2B.!!$R1 616
11 TraesCS2D01G283700 chr6B 715761903 715763263 1360 True 1157 1157 82.198 1 1350 1 chr6B.!!$R4 1349
12 TraesCS2D01G283700 chr6B 545330272 545331047 775 True 961 961 89.060 947 1720 1 chr6B.!!$R3 773
13 TraesCS2D01G283700 chr6B 695921011 695922359 1348 False 811 811 77.671 4 1351 1 chr6B.!!$F2 1347
14 TraesCS2D01G283700 chr7A 717767755 717769108 1353 True 977 977 79.883 4 1357 1 chr7A.!!$R1 1353
15 TraesCS2D01G283700 chr7A 721642104 721643425 1321 True 869 869 78.647 26 1348 1 chr7A.!!$R2 1322
16 TraesCS2D01G283700 chr5D 309919351 309919976 625 False 815 815 90.287 1726 2348 1 chr5D.!!$F1 622
17 TraesCS2D01G283700 chr6A 526307650 526308245 595 True 806 806 91.122 1722 2315 1 chr6A.!!$R1 593
18 TraesCS2D01G283700 chr7D 277048998 277049623 625 False 787 787 89.490 1722 2343 1 chr7D.!!$F1 621
19 TraesCS2D01G283700 chr4D 219970077 219970701 624 True 785 785 89.490 1722 2343 1 chr4D.!!$R1 621
20 TraesCS2D01G283700 chr4D 101098720 101099346 626 False 771 771 89.013 1722 2343 1 chr4D.!!$F1 621
21 TraesCS2D01G283700 chr6D 361368296 361368909 613 False 780 780 89.644 1729 2343 1 chr6D.!!$F1 614

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
474 489 1.278127 GGAGTACTACCTTGCTGGCAA 59.722 52.381 7.78 7.78 40.22 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 1378 0.318107 CACAACTGAAAAGCGCCCAG 60.318 55.0 2.29 9.48 0.0 4.45 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
29 30 6.070767 ACTCGGACTTTTTGGATGAGAGATTA 60.071 38.462 0.00 0.00 0.00 1.75
32 35 6.595716 CGGACTTTTTGGATGAGAGATTACTT 59.404 38.462 0.00 0.00 0.00 2.24
61 64 5.191727 TGTGAATCCTGGATTGGTAATGT 57.808 39.130 25.89 0.00 31.89 2.71
94 105 1.407851 GGGACGGTTGATTCCCCTAAC 60.408 57.143 0.00 0.00 45.40 2.34
109 120 3.308117 CCCCTAACTGCATCACTAACCAA 60.308 47.826 0.00 0.00 0.00 3.67
216 227 3.689649 GCAAGAACATGAGGGTCGTAAAT 59.310 43.478 0.00 0.00 0.00 1.40
250 261 4.462483 GGTGAAATGGTCTAGAATTTGCCA 59.538 41.667 7.05 4.54 0.00 4.92
281 294 4.696805 GGGGCCTGGGGGTGAAAC 62.697 72.222 0.84 0.00 34.45 2.78
417 432 8.192110 GGTTGTATTGGTGAAAACTAAGTTTGA 58.808 33.333 0.00 0.00 35.80 2.69
474 489 1.278127 GGAGTACTACCTTGCTGGCAA 59.722 52.381 7.78 7.78 40.22 4.52
476 491 2.742589 GAGTACTACCTTGCTGGCAAAC 59.257 50.000 9.32 3.88 40.22 2.93
516 531 3.432326 GGTAATCTTGCTAGAGTGTGGGG 60.432 52.174 8.38 0.00 32.92 4.96
549 564 5.376625 TGATGATAAACCTCCCTTATGCAC 58.623 41.667 0.00 0.00 0.00 4.57
585 600 4.666176 GCTATACAACATTTGCAACGATCG 59.334 41.667 14.88 14.88 0.00 3.69
607 622 5.805486 TCGAGAGATCACGGTAGAAAATTTG 59.195 40.000 0.00 0.00 33.31 2.32
639 654 4.997395 TGTGGATGACAGCTTCTTTAGAAC 59.003 41.667 0.00 0.00 0.00 3.01
641 656 5.645497 GTGGATGACAGCTTCTTTAGAACAT 59.355 40.000 0.00 0.00 0.00 2.71
695 712 1.786937 AATGCAAAGTGTTGTGGGGA 58.213 45.000 0.00 0.00 37.06 4.81
825 845 6.602009 GCTGGGTGTAACTATAAGTGGATTTT 59.398 38.462 0.00 0.00 36.74 1.82
889 910 6.704050 GGCAACTATTTCAGGACTCTATCTTC 59.296 42.308 0.00 0.00 0.00 2.87
1021 1043 1.064758 TGTGGAGAACTGTTGGCTGTT 60.065 47.619 0.00 0.00 39.06 3.16
1035 1057 0.676782 GCTGTTTACTGGGCACGGAT 60.677 55.000 0.00 0.00 0.00 4.18
1064 1086 4.034626 TCCGAACAACATACGGCAATATTG 59.965 41.667 11.27 11.27 45.25 1.90
1356 1378 3.350833 AGGGATGAACTGAAGAACATGC 58.649 45.455 0.00 0.00 0.00 4.06
1372 1394 1.181098 ATGCTGGGCGCTTTTCAGTT 61.181 50.000 7.64 0.70 40.11 3.16
1399 1422 1.341679 TGGCCTTCTCTACTTCGCCTA 60.342 52.381 3.32 0.00 37.29 3.93
1400 1423 1.964933 GGCCTTCTCTACTTCGCCTAT 59.035 52.381 0.00 0.00 33.50 2.57
1402 1425 2.288518 GCCTTCTCTACTTCGCCTATGG 60.289 54.545 0.00 0.00 0.00 2.74
1486 1514 2.238353 GCATGAGCACTTGTCGTGT 58.762 52.632 0.00 0.00 45.57 4.49
1490 1519 1.324383 TGAGCACTTGTCGTGTCCTA 58.676 50.000 0.00 0.00 45.57 2.94
1626 1659 5.221441 GGTTTCCCAGTTATGCTTTGAACTT 60.221 40.000 0.00 0.00 33.60 2.66
1746 1780 7.875971 AGAGCATAGTTTGTTAGTTTTCAAGG 58.124 34.615 0.00 0.00 0.00 3.61
1798 1832 8.834465 GTGAATAGCTTGTTACTTGATCATGAT 58.166 33.333 8.25 8.25 0.00 2.45
1946 1983 0.457851 CTACTCGAGGACAAGCAGGG 59.542 60.000 18.41 0.00 0.00 4.45
2117 2158 9.133627 GGTGTTGTTTTTGTGCAAAAATAAAAT 57.866 25.926 23.64 0.00 43.69 1.82
2148 2189 7.475840 GGAACGAGCTGAAAATTTATGAAGAT 58.524 34.615 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.109359 AGTAATCTCTCATCCAAAAAGTCCG 58.891 40.000 0.00 0.00 0.00 4.79
29 30 5.304686 TCCAGGATTCACAACACTTAAGT 57.695 39.130 1.12 1.12 0.00 2.24
32 35 5.009631 CCAATCCAGGATTCACAACACTTA 58.990 41.667 12.23 0.00 28.87 2.24
88 99 3.627395 TGGTTAGTGATGCAGTTAGGG 57.373 47.619 0.00 0.00 0.00 3.53
94 105 6.500684 AAACTATGTTGGTTAGTGATGCAG 57.499 37.500 0.00 0.00 30.46 4.41
145 156 6.264518 GTCTAGTTTCCCAATCACCTTTTTCA 59.735 38.462 0.00 0.00 0.00 2.69
250 261 0.405973 GGCCCCTTTCTCTTTGGAGT 59.594 55.000 0.00 0.00 40.29 3.85
385 400 5.833131 AGTTTTCACCAATACAACCATGTCT 59.167 36.000 0.00 0.00 41.05 3.41
390 405 7.648039 AACTTAGTTTTCACCAATACAACCA 57.352 32.000 0.00 0.00 0.00 3.67
417 432 3.897505 GGATTTCCAAATCGGGGAATCAT 59.102 43.478 13.67 0.00 43.57 2.45
474 489 2.037772 CCAGACTTCAGCACTACCTGTT 59.962 50.000 0.00 0.00 34.47 3.16
476 491 1.620819 ACCAGACTTCAGCACTACCTG 59.379 52.381 0.00 0.00 0.00 4.00
516 531 6.931840 GGGAGGTTTATCATCAATAGAGTCAC 59.068 42.308 0.00 0.00 0.00 3.67
549 564 5.185454 TGTTGTATAGCACAGGGAATTGAG 58.815 41.667 0.00 0.00 38.72 3.02
585 600 7.596749 TTCAAATTTTCTACCGTGATCTCTC 57.403 36.000 0.00 0.00 0.00 3.20
600 615 6.866248 GTCATCCACACCGTTATTCAAATTTT 59.134 34.615 0.00 0.00 0.00 1.82
607 622 2.351726 GCTGTCATCCACACCGTTATTC 59.648 50.000 0.00 0.00 0.00 1.75
639 654 2.027377 AGCAAAGGAGAGTGGAGACATG 60.027 50.000 0.00 0.00 46.14 3.21
641 656 1.345741 CAGCAAAGGAGAGTGGAGACA 59.654 52.381 0.00 0.00 38.70 3.41
695 712 7.520798 TCAGGTTCATTAGATATCAGCCAAAT 58.479 34.615 5.32 0.00 0.00 2.32
729 746 2.957474 TCTTTTTCCCCAAGGACCAAG 58.043 47.619 0.00 0.00 43.90 3.61
825 845 4.550395 GCGGAATTTTTGCTCGCA 57.450 50.000 0.00 0.00 44.87 5.10
889 910 5.689514 CCGCTTCTTCATTACATCTCTAGTG 59.310 44.000 0.00 0.00 0.00 2.74
909 930 0.041090 ATTCCCCAACCATTTCCGCT 59.959 50.000 0.00 0.00 0.00 5.52
1021 1043 2.364324 GACATAGATCCGTGCCCAGTAA 59.636 50.000 0.00 0.00 0.00 2.24
1035 1057 3.735820 GCCGTATGTTGTTCGGACATAGA 60.736 47.826 0.00 0.00 46.05 1.98
1054 1076 2.164219 AGCACCAAGAACAATATTGCCG 59.836 45.455 15.48 0.00 0.00 5.69
1064 1086 5.163884 GGAAGAAACGTATAGCACCAAGAAC 60.164 44.000 0.00 0.00 0.00 3.01
1356 1378 0.318107 CACAACTGAAAAGCGCCCAG 60.318 55.000 2.29 9.48 0.00 4.45
1372 1394 2.540383 AGTAGAGAAGGCCACATCACA 58.460 47.619 5.01 0.00 0.00 3.58
1412 1435 2.949447 ACTCCAAAAGCAACAGGACAT 58.051 42.857 0.00 0.00 0.00 3.06
1486 1514 7.676683 ATCCAAAGCAAGTATCTAAGTAGGA 57.323 36.000 0.00 0.00 0.00 2.94
1490 1519 6.100424 AGGCTATCCAAAGCAAGTATCTAAGT 59.900 38.462 0.00 0.00 44.64 2.24
1626 1659 4.141018 AGGAAACTAAGAAAGGGGAAAGCA 60.141 41.667 0.00 0.00 40.61 3.91
1720 1754 8.999431 CCTTGAAAACTAACAAACTATGCTCTA 58.001 33.333 0.00 0.00 0.00 2.43
1724 1758 8.135529 ACTTCCTTGAAAACTAACAAACTATGC 58.864 33.333 0.00 0.00 0.00 3.14
1746 1780 9.722056 CATGTTAAAGCATAGACCATAAACTTC 57.278 33.333 0.00 0.00 0.00 3.01
1835 1870 8.679288 AATTTCAATCACTTTTTCTAGCATCG 57.321 30.769 0.00 0.00 0.00 3.84
1920 1957 4.222145 TGCTTGTCCTCGAGTAGGTAAATT 59.778 41.667 12.31 0.00 46.62 1.82
1946 1983 2.936202 TCAGCATCCCCAAGCTTAATC 58.064 47.619 0.00 0.00 39.50 1.75
2058 2095 1.939934 CTGAAAACAGCGTCAGTCCAA 59.060 47.619 0.00 0.00 37.16 3.53
2079 2117 2.994186 ACAACACCACGGTAGTTCTT 57.006 45.000 0.00 0.00 0.00 2.52
2169 2210 6.349300 TCTGGTATCTTTTTGCTCCAGTATC 58.651 40.000 8.52 0.00 41.88 2.24
2274 2321 1.774894 CGGGGACAAGTCAAGGGGAA 61.775 60.000 2.29 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.