Multiple sequence alignment - TraesCS2D01G247700

Loading Multiple Alignment...

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 TraesCS2D01G247700 chr2D 100.000 2722 0 0 1 2722 291766317 291763596 0 5027
1 TraesCS2D01G247700 chrUn 97.142 2729 71 7 1 2722 189394034 189396762 0 4601
2 TraesCS2D01G247700 chr7D 97.030 2727 74 7 3 2722 203554849 203552123 0 4580
3 TraesCS2D01G247700 chr5B 96.993 2727 77 5 1 2722 679660392 679663118 0 4577
4 TraesCS2D01G247700 chr5A 96.956 2727 78 5 1 2722 16601428 16598702 0 4571
5 TraesCS2D01G247700 chr5A 96.771 2725 82 6 1 2719 300074474 300077198 0 4540
6 TraesCS2D01G247700 chr4D 96.920 2727 77 6 1 2722 123414377 123417101 0 4564
7 TraesCS2D01G247700 chr7B 96.883 2727 80 5 1 2722 743087694 743090420 0 4560
8 TraesCS2D01G247700 chr6A 96.736 2727 84 5 1 2722 289130125 289132851 0 4538
9 TraesCS2D01G247700 chr2A 96.553 2727 87 7 1 2722 735194149 735196873 0 4508


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 TraesCS2D01G247700 chr2D 291763596 291766317 2721 True 5027 5027 100.000 1 2722 1 chr2D.!!$R1 2721
1 TraesCS2D01G247700 chrUn 189394034 189396762 2728 False 4601 4601 97.142 1 2722 1 chrUn.!!$F1 2721
2 TraesCS2D01G247700 chr7D 203552123 203554849 2726 True 4580 4580 97.030 3 2722 1 chr7D.!!$R1 2719
3 TraesCS2D01G247700 chr5B 679660392 679663118 2726 False 4577 4577 96.993 1 2722 1 chr5B.!!$F1 2721
4 TraesCS2D01G247700 chr5A 16598702 16601428 2726 True 4571 4571 96.956 1 2722 1 chr5A.!!$R1 2721
5 TraesCS2D01G247700 chr5A 300074474 300077198 2724 False 4540 4540 96.771 1 2719 1 chr5A.!!$F1 2718
6 TraesCS2D01G247700 chr4D 123414377 123417101 2724 False 4564 4564 96.920 1 2722 1 chr4D.!!$F1 2721
7 TraesCS2D01G247700 chr7B 743087694 743090420 2726 False 4560 4560 96.883 1 2722 1 chr7B.!!$F1 2721
8 TraesCS2D01G247700 chr6A 289130125 289132851 2726 False 4538 4538 96.736 1 2722 1 chr6A.!!$F1 2721
9 TraesCS2D01G247700 chr2A 735194149 735196873 2724 False 4508 4508 96.553 1 2722 1 chr2A.!!$F1 2721

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
602 604 0.397564 CCCCCAAAAGCAAAGCACAT 59.602 50.0 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 1753 1.233019 CCATGGATGCTTTAGCGAGG 58.767 55.0 5.56 0.0 45.83 4.63 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
73 74 5.010719 TCACAAGACAGAGAAAGATTACCGT 59.989 40.000 0.00 0.00 0.00 4.83
198 199 1.347707 AGATCAGGGTTGAACGAAGCA 59.652 47.619 0.00 0.00 36.78 3.91
255 257 6.387465 CGATTAGAAACCAGTGACTCTACAA 58.613 40.000 0.00 0.00 0.00 2.41
334 336 3.334691 TCTGTAGCCAGTTTCAATTCCG 58.665 45.455 0.00 0.00 39.82 4.30
450 452 1.066573 CAGGTCAGAGCTTGTGGTAGG 60.067 57.143 0.00 0.00 0.00 3.18
489 491 3.181471 CGCAGATCCACTCAACTAGGAAT 60.181 47.826 0.00 0.00 34.62 3.01
529 531 3.585862 TGACTGTTTGAACGATCCTAGC 58.414 45.455 0.00 0.00 0.00 3.42
602 604 0.397564 CCCCCAAAAGCAAAGCACAT 59.602 50.000 0.00 0.00 0.00 3.21
823 825 3.139077 GGGCCCGTATAGAAAGTCAATG 58.861 50.000 5.69 0.00 0.00 2.82
827 829 4.260784 GCCCGTATAGAAAGTCAATGCTTG 60.261 45.833 0.00 0.00 0.00 4.01
904 906 2.017049 CTAAGCAAGGGGAATTCCGTG 58.983 52.381 18.30 15.92 38.92 4.94
986 988 4.016444 TCTTTCTTGTTCCACTTGCAAGT 58.984 39.130 26.36 26.36 40.14 3.16
1078 1081 3.549625 GCAAATTCTCATTGGATCTCGGC 60.550 47.826 0.00 0.00 0.00 5.54
1135 1138 2.116238 GGGTAGCACCACCAGATCTTA 58.884 52.381 0.00 0.00 41.02 2.10
1177 1180 7.929159 TCGTATTTCGTATGTACATGTTCCTA 58.071 34.615 18.81 0.00 40.80 2.94
1230 1233 7.324935 TCGTGACAGCTATAAACAATTCCTTA 58.675 34.615 0.00 0.00 0.00 2.69
1250 1253 8.657387 TCCTTATTCCCATTAACAAAACATCA 57.343 30.769 0.00 0.00 0.00 3.07
1293 1296 0.808755 CCGGTACAGAAATTGGTGCC 59.191 55.000 0.00 3.25 36.56 5.01
1320 1324 7.698836 TTCTACTTTGTTTACGTTAGTGACC 57.301 36.000 0.00 0.00 0.00 4.02
1325 1329 0.037419 TTTACGTTAGTGACCGGGGC 60.037 55.000 6.32 0.00 0.00 5.80
1327 1331 3.751246 CGTTAGTGACCGGGGCGA 61.751 66.667 6.32 0.00 0.00 5.54
1384 1388 4.020928 TGTGGGATGCTCGTTTAACTTCTA 60.021 41.667 0.00 0.00 0.00 2.10
1419 1423 4.105577 TCCTTATTTACCTGGGTGCACTA 58.894 43.478 17.98 5.47 0.00 2.74
1421 1425 4.323945 CCTTATTTACCTGGGTGCACTACA 60.324 45.833 17.98 14.95 0.00 2.74
1438 1442 6.264292 TGCACTACATTTTCAAAAGCTTCCTA 59.736 34.615 0.00 0.00 0.00 2.94
1446 1450 4.280436 TCAAAAGCTTCCTATCGAACCA 57.720 40.909 0.00 0.00 0.00 3.67
1447 1451 4.647611 TCAAAAGCTTCCTATCGAACCAA 58.352 39.130 0.00 0.00 0.00 3.67
1467 1471 2.919228 ACTCCTATTTCAATCCGTGCC 58.081 47.619 0.00 0.00 0.00 5.01
1583 1588 2.948115 TGTTCCTATGCCCATCCAATG 58.052 47.619 0.00 0.00 0.00 2.82
1601 1606 7.202016 TCCAATGTTGTCTAACTTTGCTAAG 57.798 36.000 6.35 6.35 44.36 2.18
1628 1633 4.161754 CCCTTCTCTACCCGTATCTTGTTT 59.838 45.833 0.00 0.00 0.00 2.83
1641 1646 6.293955 CCGTATCTTGTTTGTTCTGGAAACAT 60.294 38.462 0.00 0.00 41.66 2.71
1747 1752 8.715088 GTTCGCTCTCAAATAAAAACCTAGTTA 58.285 33.333 0.00 0.00 0.00 2.24
1748 1753 8.248117 TCGCTCTCAAATAAAAACCTAGTTAC 57.752 34.615 0.00 0.00 0.00 2.50
2009 2016 3.778954 AGTCACTAGGCAAGAAAGCTT 57.221 42.857 0.00 0.00 33.74 3.74
2024 2031 6.594744 AAGAAAGCTTGATGGGAACAAAAAT 58.405 32.000 0.00 0.00 37.04 1.82
2257 2268 2.355209 GGGAGGAGTAGCTCTTGGTTTG 60.355 54.545 0.00 0.00 0.00 2.93
2266 2277 4.313277 AGCTCTTGGTTTGAAGAAAAGC 57.687 40.909 0.00 0.00 44.81 3.51
2276 2287 3.961480 TGAAGAAAAGCGAGGAGATGA 57.039 42.857 0.00 0.00 0.00 2.92
2278 2289 3.997021 TGAAGAAAAGCGAGGAGATGAAC 59.003 43.478 0.00 0.00 0.00 3.18
2310 2321 8.355169 TCAGTCTTTTTCCTTTCTTTGATGATG 58.645 33.333 0.00 0.00 0.00 3.07
2377 2388 3.576078 TGGAGAAAAACCTCTTGAGCA 57.424 42.857 0.00 0.00 33.79 4.26
2428 2439 3.252554 TGGGACCTGCCTTTTTAATGT 57.747 42.857 0.00 0.00 36.66 2.71
2545 2556 2.079158 AGGTCAGCATCACATGAAACG 58.921 47.619 0.00 0.00 0.00 3.60
2557 2568 4.814234 TCACATGAAACGTTTAGCACTTCT 59.186 37.500 14.65 0.00 0.00 2.85
2567 2578 5.515626 ACGTTTAGCACTTCTGTTCGATATC 59.484 40.000 0.00 0.00 0.00 1.63
2568 2579 5.515270 CGTTTAGCACTTCTGTTCGATATCA 59.485 40.000 3.12 0.00 0.00 2.15
2576 2587 4.511617 TCTGTTCGATATCAGATGGAGC 57.488 45.455 3.12 0.00 36.04 4.70
2583 2594 3.131755 CGATATCAGATGGAGCATGGCTA 59.868 47.826 3.12 0.00 39.88 3.93
2590 2601 1.289160 TGGAGCATGGCTAGAAGGTT 58.711 50.000 0.00 0.00 39.88 3.50
2614 2625 3.066900 GCCTAGCTAGTCTTGTCAATCGA 59.933 47.826 19.31 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 7.721409 TCTGATCAAATTGGATTGGATGAAA 57.279 32.000 0.00 0.00 33.11 2.69
334 336 1.469917 CGCATGTCGGCAAATGATTC 58.530 50.000 0.00 0.00 33.78 2.52
450 452 3.280920 CGTAGCAGAGCCCAATCTC 57.719 57.895 0.00 0.00 0.00 2.75
489 491 2.068519 CAGTCAGCAATGCGTACTTCA 58.931 47.619 11.77 0.00 0.00 3.02
529 531 8.671384 ACTCTGACTTGATTAGCTACTAGTAG 57.329 38.462 23.25 23.25 36.29 2.57
602 604 0.321919 ACGCGTGGGTGAGTAGAGTA 60.322 55.000 12.93 0.00 0.00 2.59
699 701 1.265454 CGGCCTCCTTAGTCACCCTT 61.265 60.000 0.00 0.00 0.00 3.95
763 765 6.763135 CCTAACTAACAATTATGCTGCTCTCA 59.237 38.462 0.00 0.00 0.00 3.27
823 825 2.450160 CGGCATATCGGAAAAACAAGC 58.550 47.619 0.00 0.00 0.00 4.01
827 829 1.002792 GGAGCGGCATATCGGAAAAAC 60.003 52.381 1.45 0.00 0.00 2.43
879 881 4.021456 CGGAATTCCCCTTGCTTAGTTTTT 60.021 41.667 19.01 0.00 0.00 1.94
986 988 9.226606 ACGATACTGACATTTTATTTTCCTTGA 57.773 29.630 0.00 0.00 0.00 3.02
1050 1053 5.475909 AGATCCAATGAGAATTTGCGCATAT 59.524 36.000 12.75 9.80 0.00 1.78
1053 1056 3.018856 AGATCCAATGAGAATTTGCGCA 58.981 40.909 5.66 5.66 0.00 6.09
1135 1138 6.894339 AATACGAGAATTTCCACCTTGTTT 57.106 33.333 0.00 0.00 0.00 2.83
1208 1211 9.120538 GGAATAAGGAATTGTTTATAGCTGTCA 57.879 33.333 0.00 0.00 0.00 3.58
1230 1233 6.933514 AGGTGATGTTTTGTTAATGGGAAT 57.066 33.333 0.00 0.00 0.00 3.01
1250 1253 2.143925 CGGAAGAGCGAAGAAAAAGGT 58.856 47.619 0.00 0.00 0.00 3.50
1293 1296 9.628983 GTCACTAACGTAAACAAAGTAGAAAAG 57.371 33.333 0.00 0.00 0.00 2.27
1320 1324 4.910585 CTTCCCCGAATCGCCCCG 62.911 72.222 0.00 0.00 0.00 5.73
1325 1329 0.320771 CATAGGCCTTCCCCGAATCG 60.321 60.000 12.58 0.00 0.00 3.34
1327 1331 0.474184 CACATAGGCCTTCCCCGAAT 59.526 55.000 12.58 0.00 0.00 3.34
1419 1423 6.817765 TCGATAGGAAGCTTTTGAAAATGT 57.182 33.333 0.00 0.00 0.00 2.71
1421 1425 6.621613 GGTTCGATAGGAAGCTTTTGAAAAT 58.378 36.000 0.00 0.00 46.96 1.82
1438 1442 5.823045 GGATTGAAATAGGAGTTGGTTCGAT 59.177 40.000 0.00 0.00 0.00 3.59
1446 1450 3.279434 GGCACGGATTGAAATAGGAGTT 58.721 45.455 0.00 0.00 0.00 3.01
1447 1451 2.919228 GGCACGGATTGAAATAGGAGT 58.081 47.619 0.00 0.00 0.00 3.85
1467 1471 3.777465 ATTGGTATATCGATCGGTCCG 57.223 47.619 16.41 4.39 0.00 4.79
1601 1606 2.149973 TACGGGTAGAGAAGGGGAAC 57.850 55.000 0.00 0.00 0.00 3.62
1628 1633 4.437682 AGGAAGACATGTTTCCAGAACA 57.562 40.909 27.17 0.00 45.28 3.18
1641 1646 5.629133 CGGGAAAAGATGGAATAGGAAGACA 60.629 44.000 0.00 0.00 0.00 3.41
1747 1752 1.475751 CCATGGATGCTTTAGCGAGGT 60.476 52.381 5.56 0.00 45.83 3.85
1748 1753 1.233019 CCATGGATGCTTTAGCGAGG 58.767 55.000 5.56 0.00 45.83 4.63
1842 1848 5.680619 TCTGTTTCTGTCTTTAAGAGGCAA 58.319 37.500 0.00 0.00 40.04 4.52
2055 2064 6.148315 CCATTCCTTCTTTCCTTTGAAATTGC 59.852 38.462 0.00 0.00 39.65 3.56
2257 2268 3.372514 GGTTCATCTCCTCGCTTTTCTTC 59.627 47.826 0.00 0.00 0.00 2.87
2266 2277 3.119291 CTGAATTCGGTTCATCTCCTCG 58.881 50.000 6.08 0.00 45.36 4.63
2276 2287 6.321435 AGAAAGGAAAAAGACTGAATTCGGTT 59.679 34.615 20.71 4.82 35.19 4.44
2278 2289 6.319141 AGAAAGGAAAAAGACTGAATTCGG 57.681 37.500 12.91 12.91 0.00 4.30
2310 2321 7.756722 CAGGGAATTCAAATAGATGTGTTGAAC 59.243 37.037 7.93 0.00 42.36 3.18
2405 2416 4.709886 ACATTAAAAAGGCAGGTCCCATAC 59.290 41.667 0.00 0.00 34.51 2.39
2428 2439 2.350895 CCTGTTGCCGGGATGTCA 59.649 61.111 2.18 0.00 39.78 3.58
2545 2556 6.752351 TCTGATATCGAACAGAAGTGCTAAAC 59.248 38.462 14.69 0.00 39.68 2.01
2557 2568 4.562143 CCATGCTCCATCTGATATCGAACA 60.562 45.833 0.00 0.00 0.00 3.18
2567 2578 2.550423 CCTTCTAGCCATGCTCCATCTG 60.550 54.545 0.00 0.00 40.44 2.90
2568 2579 1.698532 CCTTCTAGCCATGCTCCATCT 59.301 52.381 0.00 0.00 40.44 2.90
2590 2601 4.276183 CGATTGACAAGACTAGCTAGGCTA 59.724 45.833 29.49 14.03 41.95 3.93
2614 2625 0.406361 AGGAGAAGACGAGTCAGGGT 59.594 55.000 5.99 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.