Multiple sequence alignment - TraesCS7D01G250400

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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 TraesCS7D01G250400 chr7D 100.000 3254 0 0 1 3254 222516289 222519542 0.000000e+00 6010.0
1 TraesCS7D01G250400 chr7A 94.519 2463 100 17 800 3254 237502841 237505276 0.000000e+00 3768.0
2 TraesCS7D01G250400 chr7A 95.340 751 26 8 1 746 237389087 237389833 0.000000e+00 1184.0
3 TraesCS7D01G250400 chr7A 96.429 56 1 1 742 797 237389871 237389925 1.240000e-14 91.6
4 TraesCS7D01G250400 chr7B 94.141 1519 67 7 788 2302 174072637 174071137 0.000000e+00 2292.0
5 TraesCS7D01G250400 chr7B 95.908 953 35 4 2304 3254 174071039 174070089 0.000000e+00 1541.0
6 TraesCS7D01G250400 chr7B 96.031 655 18 5 1 654 174073620 174072973 0.000000e+00 1059.0
7 TraesCS7D01G250400 chr7B 89.362 94 2 1 652 745 174072831 174072746 9.540000e-21 111.0
8 TraesCS7D01G250400 chr7B 95.652 46 1 1 742 787 174072707 174072663 4.500000e-09 73.1


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 TraesCS7D01G250400 chr7D 222516289 222519542 3253 False 6010.00 6010 100.0000 1 3254 1 chr7D.!!$F1 3253
1 TraesCS7D01G250400 chr7A 237502841 237505276 2435 False 3768.00 3768 94.5190 800 3254 1 chr7A.!!$F1 2454
2 TraesCS7D01G250400 chr7A 237389087 237389925 838 False 637.80 1184 95.8845 1 797 2 chr7A.!!$F2 796
3 TraesCS7D01G250400 chr7B 174070089 174073620 3531 True 1015.22 2292 94.2188 1 3254 5 chr7B.!!$R1 3253

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
783 972 1.135575 GGCTGAAGGATTGCAGTTTCG 60.136 52.381 0.0 0.0 34.66 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2752 3087 1.909302 TCCAAGGAGAAGCCGAATCTT 59.091 47.619 0.0 0.0 43.43 2.4 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
45 46 2.487086 CCGATTGCCTCATATCAACCCA 60.487 50.000 0.00 0.00 0.00 4.51
280 281 9.597681 CAACTAGTATATAGGGTTAAAGGAGGA 57.402 37.037 0.00 0.00 0.00 3.71
448 449 8.800370 TCATTGCTGTACTATTGACCAATTTA 57.200 30.769 0.17 0.00 32.50 1.40
569 570 2.179517 CTGAGGACTGTCGTCGGC 59.820 66.667 21.99 4.02 41.16 5.54
570 571 3.343788 CTGAGGACTGTCGTCGGCC 62.344 68.421 21.99 0.00 41.16 6.13
588 589 2.679716 CTGGGGGAGAAAGCTGGG 59.320 66.667 0.00 0.00 0.00 4.45
593 594 1.717032 GGGGAGAAAGCTGGGTTTTT 58.283 50.000 0.00 0.00 0.00 1.94
674 822 1.683365 AGGTGCCAATGCCATGACC 60.683 57.895 0.00 0.00 36.33 4.02
783 972 1.135575 GGCTGAAGGATTGCAGTTTCG 60.136 52.381 0.00 0.00 34.66 3.46
843 1058 7.225931 TCCTCGATTCTTTAATATTTGAACCGG 59.774 37.037 0.00 0.00 0.00 5.28
897 1112 6.690194 AAGCTACAAATAGGATTTGAGCTG 57.310 37.500 23.84 12.32 39.91 4.24
925 1140 7.442364 TCTTGTGAAAACTACTCTTGGATCAAG 59.558 37.037 0.00 1.53 42.25 3.02
987 1202 3.459232 TCTTACGATGGCTCCATGAAG 57.541 47.619 6.07 7.17 36.70 3.02
1128 1343 1.645704 CCTCGTCTCATCACGTCCGT 61.646 60.000 0.00 0.00 40.79 4.69
1182 1397 1.616865 CGTCTCACCCAAACTGACCTA 59.383 52.381 0.00 0.00 0.00 3.08
1242 1460 2.150719 TCCAAGAACTGCCCCGGAA 61.151 57.895 0.73 0.00 0.00 4.30
1540 1758 4.864334 CCGTGCAGGAGATGGCCC 62.864 72.222 8.24 0.00 45.00 5.80
2147 2382 3.706373 CCACACCACCTCCGAGGG 61.706 72.222 18.99 7.56 40.58 4.30
2260 2495 7.913674 ATCTTTTGGAACTACTGATCTTCAC 57.086 36.000 0.00 0.00 0.00 3.18
2265 2500 5.330233 TGGAACTACTGATCTTCACCAGTA 58.670 41.667 0.00 0.00 42.86 2.74
2383 2717 7.311092 TGGAACTATGGAAGAGTCTTTGTAA 57.689 36.000 6.88 0.00 0.00 2.41
2467 2802 1.739466 TCGCTGATTCTGAAATGCCAC 59.261 47.619 0.00 0.00 0.00 5.01
2485 2820 3.947834 GCCACCTGCTACAAATCTACAAT 59.052 43.478 0.00 0.00 36.87 2.71
2578 2913 3.213506 CCACTCCATGTGTCACTGAAAA 58.786 45.455 4.27 0.00 44.81 2.29
2752 3087 1.226859 CGGCGCGATGAACCTTAGA 60.227 57.895 12.10 0.00 0.00 2.10
2830 3165 3.214328 ACTCAGGAACTTTGCGATGTTT 58.786 40.909 6.67 0.00 34.60 2.83
2914 3249 0.402121 GAACCTCCAAGCCTTCAGGT 59.598 55.000 0.00 0.00 41.27 4.00
3081 3416 3.118592 AGCAGGGTCAGCATAGTTTAGAC 60.119 47.826 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 5.892160 CCATTGCTATGGGTTGATATGAG 57.108 43.478 18.33 0.00 46.43 2.90
275 276 1.401905 CGCTACAAATGCCTTTCCTCC 59.598 52.381 0.00 0.00 0.00 4.30
277 278 0.811281 GCGCTACAAATGCCTTTCCT 59.189 50.000 0.00 0.00 0.00 3.36
278 279 0.811281 AGCGCTACAAATGCCTTTCC 59.189 50.000 8.99 0.00 0.00 3.13
280 281 1.470098 CTGAGCGCTACAAATGCCTTT 59.530 47.619 11.50 0.00 0.00 3.11
310 311 1.708993 AAGGTCAGGTCAGGCTTGCA 61.709 55.000 0.00 0.00 0.00 4.08
448 449 1.420138 ACCCAACGAAATCAGACCAGT 59.580 47.619 0.00 0.00 0.00 4.00
569 570 2.679716 CAGCTTTCTCCCCCAGGG 59.320 66.667 0.00 0.00 46.11 4.45
570 571 2.679716 CCAGCTTTCTCCCCCAGG 59.320 66.667 0.00 0.00 0.00 4.45
596 597 9.874205 CAACCAAACCACAGATGATATAAAATT 57.126 29.630 0.00 0.00 0.00 1.82
597 598 8.477256 CCAACCAAACCACAGATGATATAAAAT 58.523 33.333 0.00 0.00 0.00 1.82
602 603 5.191727 TCCAACCAAACCACAGATGATAT 57.808 39.130 0.00 0.00 0.00 1.63
674 822 4.084641 GCTCAGCAGCTGATAATAAACTCG 60.085 45.833 25.59 10.70 43.09 4.18
783 972 4.894784 TCCAAACAGACTCATTGTACTCC 58.105 43.478 0.00 0.00 0.00 3.85
841 1056 1.666888 GCAGAAATTTCACACCAGCCG 60.667 52.381 19.99 0.00 0.00 5.52
843 1058 1.266718 TCGCAGAAATTTCACACCAGC 59.733 47.619 19.99 11.80 0.00 4.85
897 1112 6.920569 TCCAAGAGTAGTTTTCACAAGAAC 57.079 37.500 0.00 0.00 32.39 3.01
963 1178 7.793398 CCTTCATGGAGCCATCGTAAGAAAAA 61.793 42.308 13.42 0.00 45.60 1.94
987 1202 2.040412 GGAACCCATATCACCTCATCCC 59.960 54.545 0.00 0.00 0.00 3.85
1101 1316 0.464013 GATGAGACGAGGAGGACGGA 60.464 60.000 0.00 0.00 34.93 4.69
1104 1319 0.378962 CGTGATGAGACGAGGAGGAC 59.621 60.000 0.00 0.00 42.10 3.85
1128 1343 1.289530 GAAGAAGAGGGAGGAGGGAGA 59.710 57.143 0.00 0.00 0.00 3.71
1395 1613 1.812922 GAGGACCTCGTCGTAGCGA 60.813 63.158 5.55 0.00 39.22 4.93
1705 1935 2.094854 CGAGCTTGTAGTACTTCCGGTT 60.095 50.000 0.00 0.00 0.00 4.44
2435 2770 2.463553 ATCAGCGAACAATTGATGCG 57.536 45.000 13.59 12.91 30.76 4.73
2467 2802 6.108687 TGTCAGATTGTAGATTTGTAGCAGG 58.891 40.000 0.00 0.00 0.00 4.85
2485 2820 4.803452 AGGTTTTCTTTGGGATTGTCAGA 58.197 39.130 0.00 0.00 0.00 3.27
2686 3021 7.956315 AGCTGGAATATAATGTCTTCCTACCTA 59.044 37.037 4.19 0.00 39.36 3.08
2752 3087 1.909302 TCCAAGGAGAAGCCGAATCTT 59.091 47.619 0.00 0.00 43.43 2.40
2914 3249 0.613260 AACCATACAAGCTGAGGCGA 59.387 50.000 0.00 0.00 44.37 5.54


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

AutoCloner maintained by Alex Coulton.