Multiple sequence alignment - TraesCS7D01G115500

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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 TraesCS7D01G115500 chr7D 100.000 3664 0 0 1 3664 71052377 71056040 0.000000e+00 6767
1 TraesCS7D01G115500 chr7D 93.774 3694 196 15 1 3664 71081591 71085280 0.000000e+00 5517
2 TraesCS7D01G115500 chr7D 92.245 3701 237 27 1 3664 71090181 71093868 0.000000e+00 5199
3 TraesCS7D01G115500 chr7D 94.724 2483 111 12 847 3318 71106412 71108885 0.000000e+00 3842
4 TraesCS7D01G115500 chr7D 93.040 819 55 2 1 817 71105605 71106423 0.000000e+00 1195
5 TraesCS7D01G115500 chr7D 75.945 582 93 33 3095 3664 71077401 71077947 4.700000e-64 255


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 TraesCS7D01G115500 chr7D 71052377 71056040 3663 False 6767.0 6767 100.0000 1 3664 1 chr7D.!!$F1 3663
1 TraesCS7D01G115500 chr7D 71090181 71093868 3687 False 5199.0 5199 92.2450 1 3664 1 chr7D.!!$F2 3663
2 TraesCS7D01G115500 chr7D 71077401 71085280 7879 False 2886.0 5517 84.8595 1 3664 2 chr7D.!!$F3 3663
3 TraesCS7D01G115500 chr7D 71105605 71108885 3280 False 2518.5 3842 93.8820 1 3318 2 chr7D.!!$F4 3317

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
700 4891 0.385751 ATGATACCGTCACTGCGAGG 59.614 55.000 0.00 0.00 40.28 4.63 F
992 5188 0.809385 TTCTCCTCGTCCTTAGCACG 59.191 55.000 0.00 0.00 38.67 5.34 F
1047 5243 1.226773 GCTCGTCATTGCAATGCCC 60.227 57.895 30.57 22.06 36.36 5.36 F
1680 5905 2.742053 ACATCGTGCACATCCACTAAAC 59.258 45.455 18.64 0.00 33.60 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 6038 1.437397 TGCATGGATGGGATGCTAGA 58.563 50.000 0.00 0.00 45.45 2.43 R
2043 6270 1.477558 CCACTGTCCCTCACTTTGCTT 60.478 52.381 0.00 0.00 0.00 3.91 R
2287 6514 5.644636 CAGCAACCCTTAGTTAAATTACGGA 59.355 40.000 0.00 0.00 36.18 4.69 R
3451 7683 1.659098 GCTATGCGGCCGACAATATAC 59.341 52.381 33.48 9.04 0.00 1.47 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
48 4239 8.784043 ACTTGCGAGTCACTTTAAATAGATTTT 58.216 29.630 0.00 0.00 0.00 1.82
132 4323 6.942576 AGTATGAGTTGCTCACCTTTAACAAT 59.057 34.615 0.53 0.00 43.63 2.71
134 4325 7.759489 ATGAGTTGCTCACCTTTAACAATTA 57.241 32.000 0.53 0.00 43.63 1.40
172 4363 5.943416 AGATCTAGATCACCGAACCTCATAG 59.057 44.000 29.83 0.00 40.22 2.23
194 4385 5.965922 AGTGGCCATTAAATGCTTAACTTC 58.034 37.500 9.72 0.00 29.82 3.01
263 4454 7.555554 AGAAGTTCTCAAGATAAACCATCATGG 59.444 37.037 0.54 0.54 45.02 3.66
281 4472 6.877668 TCATGGAGGTAAAAGGTACACATA 57.122 37.500 0.00 0.00 0.00 2.29
355 4546 8.026607 CCATTCCAAACGTCATATTTGTACTTT 58.973 33.333 0.00 0.00 35.65 2.66
375 4566 2.797786 TGGTTTTCCCCTTGGATTACG 58.202 47.619 0.00 0.00 41.40 3.18
378 4569 4.202545 TGGTTTTCCCCTTGGATTACGTTA 60.203 41.667 0.00 0.00 41.40 3.18
449 4640 4.395854 TGCTGCTCATGTATACAAACCAAG 59.604 41.667 10.14 6.75 0.00 3.61
471 4662 7.819900 CCAAGTAGCTCTTATGTTATATGGACC 59.180 40.741 0.00 0.00 34.66 4.46
489 4680 1.213296 CCTATGGGCCTTAGGTGTGT 58.787 55.000 28.96 0.00 33.00 3.72
530 4721 9.815936 AAATAAAATACAAAGTAGTGTACGCAC 57.184 29.630 9.48 5.16 45.57 5.34
565 4756 3.942748 GGTTGGGTAAATCATTCTACGCA 59.057 43.478 5.79 5.79 38.68 5.24
573 4764 1.075542 TCATTCTACGCAAGGCAACG 58.924 50.000 0.00 0.00 46.39 4.10
574 4765 0.796312 CATTCTACGCAAGGCAACGT 59.204 50.000 4.92 4.92 45.85 3.99
585 4776 3.305064 GCAAGGCAACGTATGAAGGAAAA 60.305 43.478 0.00 0.00 46.39 2.29
617 4808 6.949352 AATGTGTGGATTCAACATCCTATC 57.051 37.500 0.00 0.00 38.95 2.08
620 4811 4.818546 GTGTGGATTCAACATCCTATCAGG 59.181 45.833 0.00 0.00 38.95 3.86
700 4891 0.385751 ATGATACCGTCACTGCGAGG 59.614 55.000 0.00 0.00 40.28 4.63
717 4908 4.652421 TGCGAGGGTTAGTACCATTATTCT 59.348 41.667 0.00 0.00 46.96 2.40
723 4917 9.239551 GAGGGTTAGTACCATTATTCTGTTTTT 57.760 33.333 0.00 0.00 46.96 1.94
821 5016 6.072112 AGCGTAAAGTTCACATGTCAAAAT 57.928 33.333 0.00 0.00 0.00 1.82
836 5032 9.086336 ACATGTCAAAATAAAGTGTCACAAAAG 57.914 29.630 5.62 0.00 0.00 2.27
868 5064 5.186797 GGAGATCTCATGTCCAAGGTATAGG 59.813 48.000 23.85 0.00 42.05 2.57
966 5162 2.982339 TCCCCTCTACTAGCTCATCC 57.018 55.000 0.00 0.00 0.00 3.51
992 5188 0.809385 TTCTCCTCGTCCTTAGCACG 59.191 55.000 0.00 0.00 38.67 5.34
1047 5243 1.226773 GCTCGTCATTGCAATGCCC 60.227 57.895 30.57 22.06 36.36 5.36
1071 5267 3.141488 CTAGCCCTCGCCGACACT 61.141 66.667 0.00 0.00 34.57 3.55
1120 5316 3.305539 CCAAAATGAGCTTAGCTTGCACA 60.306 43.478 8.58 12.16 39.88 4.57
1153 5349 3.432046 CCAATTTGTTGCTGGTCCAAACT 60.432 43.478 7.74 0.00 31.50 2.66
1680 5905 2.742053 ACATCGTGCACATCCACTAAAC 59.258 45.455 18.64 0.00 33.60 2.01
1695 5920 8.517878 CATCCACTAAACTCATGAGAAATGTTT 58.482 33.333 29.27 19.79 35.43 2.83
1715 5940 7.812309 TGTTTCGAACACATGAGATTACTAG 57.188 36.000 0.00 0.00 36.25 2.57
1771 5996 9.726232 CATACACAAATTCTCTATGGTGATTTG 57.274 33.333 0.00 0.00 34.73 2.32
1772 5997 7.161773 ACACAAATTCTCTATGGTGATTTGG 57.838 36.000 10.65 4.90 33.37 3.28
1782 6007 3.568093 GTGATTTGGCACCACACAC 57.432 52.632 10.71 4.74 32.68 3.82
1802 6027 7.704899 CACACACCATATAGAAAACGAGATACA 59.295 37.037 0.00 0.00 0.00 2.29
1813 6038 8.928270 AGAAAACGAGATACATATTTCGAGTT 57.072 30.769 16.18 10.14 41.22 3.01
1907 6133 9.620259 GAGAAACTAATGAGGGAAGATATTGTT 57.380 33.333 0.00 0.00 0.00 2.83
1948 6174 9.708222 GCACATAGTAAGTTTGATCATTGTTAG 57.292 33.333 0.00 0.00 0.00 2.34
1967 6194 7.432148 TGTTAGGCTTCCATACATCTCTAAA 57.568 36.000 0.00 0.00 0.00 1.85
1975 6202 8.555361 GCTTCCATACATCTCTAAAATTCTGAC 58.445 37.037 0.00 0.00 0.00 3.51
2043 6270 4.431378 TCAGGTGATGGGGACTTTAACTA 58.569 43.478 0.00 0.00 0.00 2.24
2261 6488 7.067008 TCCCTTACTTTCAACTATTATGCAAGC 59.933 37.037 0.00 0.00 0.00 4.01
2311 6538 5.644636 TCCGTAATTTAACTAAGGGTTGCTG 59.355 40.000 0.00 0.00 38.75 4.41
2394 6621 9.601971 GCTAAAATGTTGTCGTTAAAGAATGTA 57.398 29.630 0.00 0.00 0.00 2.29
2588 6817 4.943705 TCATTTCCCTTTATGCAGACTCAC 59.056 41.667 0.00 0.00 0.00 3.51
3195 7425 7.880195 GGTCAATGCTATTTCTGATAGTATGGT 59.120 37.037 0.00 0.00 29.50 3.55
3236 7467 3.640967 TCCAGGGACTTTGTTTTGAATGG 59.359 43.478 0.00 0.00 34.60 3.16
3242 7473 7.550906 CAGGGACTTTGTTTTGAATGGTTTTTA 59.449 33.333 0.00 0.00 34.60 1.52
3318 7550 9.477484 GAGTAATTCTGTACTCTCTTTGTTTGA 57.523 33.333 5.34 0.00 44.45 2.69
3325 7557 9.832445 TCTGTACTCTCTTTGTTTGACTTTATT 57.168 29.630 0.00 0.00 0.00 1.40
3394 7626 4.761739 CACACCTTCATACAAACACCTCAT 59.238 41.667 0.00 0.00 0.00 2.90
3451 7683 9.321562 TCTCATAAATACCCTTTAGCGTTTTAG 57.678 33.333 0.00 0.00 0.00 1.85
3472 7705 0.321671 ATATTGTCGGCCGCATAGCT 59.678 50.000 23.51 5.09 0.00 3.32
3478 7711 0.958382 TCGGCCGCATAGCTTTGTTT 60.958 50.000 23.51 0.00 0.00 2.83
3524 7757 7.938563 AGATCTTTAGCTCGTTTATCATGAC 57.061 36.000 0.00 0.00 0.00 3.06
3527 7760 2.293677 AGCTCGTTTATCATGACGCA 57.706 45.000 0.00 0.00 39.03 5.24
3574 7807 7.389330 AGTTGGTTACGTGAACATTATTGATGA 59.611 33.333 0.00 0.00 40.09 2.92
3580 7813 9.566530 TTACGTGAACATTATTGATGATTTTGG 57.433 29.630 0.00 0.00 39.15 3.28
3583 7816 8.586273 CGTGAACATTATTGATGATTTTGGTTC 58.414 33.333 0.00 0.00 39.15 3.62
3622 7855 2.107950 TCTGTGGATGCCTTTAACGG 57.892 50.000 0.00 0.00 0.00 4.44
3646 7879 5.970317 AAAGGGGTACTACCAAAATTTCG 57.030 39.130 7.57 0.00 41.02 3.46
3652 7885 6.183360 GGGGTACTACCAAAATTTCGAGATTG 60.183 42.308 7.57 0.00 41.02 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 4200 3.059884 CTCGCAAGTCAAGTGCTTAAGA 58.940 45.455 6.67 0.00 39.95 2.10
134 4325 8.802267 GTGATCTAGATCTACAAATTAGGAGCT 58.198 37.037 28.51 0.00 38.60 4.09
172 4363 5.965922 AGAAGTTAAGCATTTAATGGCCAC 58.034 37.500 8.16 0.00 31.81 5.01
194 4385 3.059884 TCGCAAAGTCAAGCACTTAGAG 58.940 45.455 0.00 0.00 45.32 2.43
281 4472 8.696043 ACAATGCATGGTGTTAATATGTCTAT 57.304 30.769 5.74 0.00 0.00 1.98
375 4566 6.483640 CACTCTAGGGAAGCCAATATTGTAAC 59.516 42.308 14.25 3.80 0.00 2.50
378 4569 4.687219 GCACTCTAGGGAAGCCAATATTGT 60.687 45.833 14.25 0.00 0.00 2.71
471 4662 1.837439 TCACACACCTAAGGCCCATAG 59.163 52.381 0.00 2.12 0.00 2.23
585 4776 6.656693 TGTTGAATCCACACATTTTGGTTTTT 59.343 30.769 0.00 0.00 35.42 1.94
667 4858 5.849510 ACGGTATCATTGGATCGTATCAAA 58.150 37.500 0.00 0.00 33.70 2.69
676 4867 2.803133 CGCAGTGACGGTATCATTGGAT 60.803 50.000 0.00 0.00 43.52 3.41
684 4875 1.255667 AACCCTCGCAGTGACGGTAT 61.256 55.000 5.20 0.00 35.25 2.73
723 4917 9.623000 ACAGAAACTAAAGCTTTAGGAAAGTTA 57.377 29.630 37.05 10.95 43.38 2.24
780 4974 3.983988 ACGCTCGCACATATTCATTCTAG 59.016 43.478 0.00 0.00 0.00 2.43
781 4975 3.977427 ACGCTCGCACATATTCATTCTA 58.023 40.909 0.00 0.00 0.00 2.10
821 5016 8.795842 TCCTTAGAAACTTTTGTGACACTTTA 57.204 30.769 7.20 0.00 0.00 1.85
836 5032 6.227298 TGGACATGAGATCTCCTTAGAAAC 57.773 41.667 20.03 3.94 34.73 2.78
868 5064 2.033424 GTGCCTTCAAGTGGACTTCAAC 59.967 50.000 0.00 0.00 33.11 3.18
966 5162 0.037232 AGGACGAGGAGAAAAAGGCG 60.037 55.000 0.00 0.00 0.00 5.52
1008 5204 3.188254 GCAAAAACAAAATTCCCGATGGG 59.812 43.478 0.00 0.00 46.11 4.00
1047 5243 2.247437 GGCGAGGGCTAGAAATGCG 61.247 63.158 0.00 0.00 39.81 4.73
1071 5267 1.568504 GGTCACAGTATGGGTGAGGA 58.431 55.000 0.00 0.00 45.21 3.71
1120 5316 4.255833 CAACAAATTGGTGCAGGTACAT 57.744 40.909 0.00 0.00 31.63 2.29
1153 5349 0.825425 TCTTCATTGCGGTTTGGGCA 60.825 50.000 0.00 0.00 38.93 5.36
1592 5788 1.948104 TGCTTGCTTCGTTGTGTACT 58.052 45.000 0.00 0.00 0.00 2.73
1680 5905 5.989249 TGTGTTCGAAACATTTCTCATGAG 58.011 37.500 17.07 17.07 44.35 2.90
1695 5920 6.374613 AGACACTAGTAATCTCATGTGTTCGA 59.625 38.462 0.00 0.00 38.52 3.71
1715 5940 8.954350 TCTATAGTAAAGTGTGTTCCTAGACAC 58.046 37.037 7.58 7.58 46.05 3.67
1744 5969 9.685276 AAATCACCATAGAGAATTTGTGTATGA 57.315 29.630 11.04 0.00 0.00 2.15
1771 5996 3.275617 TTCTATATGGTGTGTGGTGCC 57.724 47.619 0.00 0.00 0.00 5.01
1772 5997 4.436852 CGTTTTCTATATGGTGTGTGGTGC 60.437 45.833 0.00 0.00 0.00 5.01
1802 6027 5.808366 TGGGATGCTAGAACTCGAAATAT 57.192 39.130 0.00 0.00 0.00 1.28
1809 6034 3.672808 CATGGATGGGATGCTAGAACTC 58.327 50.000 0.00 0.00 0.00 3.01
1812 6037 1.776063 TGCATGGATGGGATGCTAGAA 59.224 47.619 0.00 0.00 45.45 2.10
1813 6038 1.437397 TGCATGGATGGGATGCTAGA 58.563 50.000 0.00 0.00 45.45 2.43
1948 6174 7.716998 TCAGAATTTTAGAGATGTATGGAAGCC 59.283 37.037 0.00 0.00 0.00 4.35
1949 6175 8.555361 GTCAGAATTTTAGAGATGTATGGAAGC 58.445 37.037 0.00 0.00 0.00 3.86
1967 6194 7.170965 AGGGCATATCAAATATCGTCAGAATT 58.829 34.615 0.00 0.00 0.00 2.17
1975 6202 5.065602 CACATGGAGGGCATATCAAATATCG 59.934 44.000 0.00 0.00 0.00 2.92
2043 6270 1.477558 CCACTGTCCCTCACTTTGCTT 60.478 52.381 0.00 0.00 0.00 3.91
2287 6514 5.644636 CAGCAACCCTTAGTTAAATTACGGA 59.355 40.000 0.00 0.00 36.18 4.69
2311 6538 8.139989 TGAAACTTTATCCTAATAGAGTACGGC 58.860 37.037 0.00 0.00 33.01 5.68
2357 6584 6.638063 CGACAACATTTTAGCCATATCCATTG 59.362 38.462 0.00 0.00 0.00 2.82
2424 6651 8.944029 CACTTTCTTCTATGAAATGTGACTCAT 58.056 33.333 0.00 0.00 37.31 2.90
2454 6683 9.231297 TGCTAGAAATTGTAGCTTCAGTTTTAT 57.769 29.630 20.38 9.22 42.94 1.40
3394 7626 6.946583 AGTTACTAGTGGAAGTGTGAGTGATA 59.053 38.462 5.39 0.00 0.00 2.15
3436 7668 7.306983 CCGACAATATACTAAAACGCTAAAGGG 60.307 40.741 0.00 0.00 0.00 3.95
3451 7683 1.659098 GCTATGCGGCCGACAATATAC 59.341 52.381 33.48 9.04 0.00 1.47
3472 7705 5.581479 TGCTCGTACTACACAAGAAAACAAA 59.419 36.000 0.00 0.00 0.00 2.83
3478 7711 4.514781 ACATGCTCGTACTACACAAGAA 57.485 40.909 0.00 0.00 0.00 2.52
3524 7757 5.927030 ACACAACTAAAGTCACAATATGCG 58.073 37.500 0.00 0.00 0.00 4.73
3527 7760 8.999431 CCAACTACACAACTAAAGTCACAATAT 58.001 33.333 0.00 0.00 0.00 1.28
3622 7855 6.207221 TCGAAATTTTGGTAGTACCCCTTTTC 59.793 38.462 16.91 16.66 37.50 2.29
3632 7865 9.280174 TCTAAACAATCTCGAAATTTTGGTAGT 57.720 29.630 5.58 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.