Multiple sequence alignment - TraesCS1D01G197900

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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 TraesCS1D01G197900 chr1D 100.000 2409 0 0 1 2409 279098224 279100632 0.000000e+00 4449
1 TraesCS1D01G197900 chr1B 93.591 2122 85 23 325 2407 378833006 378835115 0.000000e+00 3118
2 TraesCS1D01G197900 chr1B 87.460 311 14 7 1 294 378832642 378832944 3.840000e-88 335
3 TraesCS1D01G197900 chr1A 90.664 1521 69 24 1 1465 351344208 351345711 0.000000e+00 1954
4 TraesCS1D01G197900 chr1A 93.831 616 24 7 1467 2076 351345751 351346358 0.000000e+00 915
5 TraesCS1D01G197900 chr1A 94.615 390 20 1 2019 2407 351346356 351346745 9.530000e-169 603


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 TraesCS1D01G197900 chr1D 279098224 279100632 2408 False 4449.000000 4449 100.000000 1 2409 1 chr1D.!!$F1 2408
1 TraesCS1D01G197900 chr1B 378832642 378835115 2473 False 1726.500000 3118 90.525500 1 2407 2 chr1B.!!$F1 2406
2 TraesCS1D01G197900 chr1A 351344208 351346745 2537 False 1157.333333 1954 93.036667 1 2407 3 chr1A.!!$F1 2406

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
571 644 0.036306 GGCGGAGGAGAAAAGTGGAA 59.964 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1821 0.778083 AGTTCAAACCCCTTCCTCCC 59.222 55.0 0.0 0.0 0.0 4.3 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
40 41 4.989279 AATCATGGCATGTACCTGAAAC 57.011 40.909 25.62 0.00 0.00 2.78
47 48 4.218200 TGGCATGTACCTGAAACTGATTTG 59.782 41.667 1.92 0.00 0.00 2.32
74 75 2.406596 TATGAGCAGCAGCATCACAA 57.593 45.000 3.17 0.00 45.49 3.33
147 177 5.034200 TGAACTAAAGGTGATAGCCCCTAA 58.966 41.667 0.00 0.00 0.00 2.69
305 359 9.265938 CAAACATAAACTCTTGTGATCGTATTG 57.734 33.333 0.00 0.00 0.00 1.90
308 363 5.940192 AAACTCTTGTGATCGTATTGCAA 57.060 34.783 0.00 0.00 0.00 4.08
312 367 5.106948 ACTCTTGTGATCGTATTGCAAACAG 60.107 40.000 1.71 0.00 0.00 3.16
314 369 5.929415 TCTTGTGATCGTATTGCAAACAGTA 59.071 36.000 1.71 0.00 0.00 2.74
344 407 7.090953 TCGAACAATAAACCATAATCAACCC 57.909 36.000 0.00 0.00 0.00 4.11
366 429 8.593945 ACCCTAAATTCTTATGCTCATTTTGA 57.406 30.769 0.00 0.00 0.00 2.69
407 480 1.282157 GTTGTTACCTGGCCTGGAGAT 59.718 52.381 33.43 15.03 0.00 2.75
547 620 3.125316 CAGACCAATTCGACTGCTTAACC 59.875 47.826 0.00 0.00 0.00 2.85
551 624 1.641577 ATTCGACTGCTTAACCGAGC 58.358 50.000 0.00 0.00 43.00 5.03
564 637 4.129737 CGAGCGGCGGAGGAGAAA 62.130 66.667 9.78 0.00 36.03 2.52
566 639 1.811679 GAGCGGCGGAGGAGAAAAG 60.812 63.158 9.78 0.00 0.00 2.27
567 640 2.047179 GCGGCGGAGGAGAAAAGT 60.047 61.111 9.78 0.00 0.00 2.66
571 644 0.036306 GGCGGAGGAGAAAAGTGGAA 59.964 55.000 0.00 0.00 0.00 3.53
575 648 1.004862 GGAGGAGAAAAGTGGAAGGGG 59.995 57.143 0.00 0.00 0.00 4.79
582 656 1.670059 AAAGTGGAAGGGGACTAGGG 58.330 55.000 0.00 0.00 42.68 3.53
597 671 4.778143 GGGTTGCGAGGTGCCGAT 62.778 66.667 0.00 0.00 45.60 4.18
796 870 1.407656 GGGTGGTCACTGGTCAGACA 61.408 60.000 2.17 0.00 36.50 3.41
797 871 0.468226 GGTGGTCACTGGTCAGACAA 59.532 55.000 2.17 0.00 36.50 3.18
798 872 1.583054 GTGGTCACTGGTCAGACAAC 58.417 55.000 2.17 0.00 36.50 3.32
799 873 0.104120 TGGTCACTGGTCAGACAACG 59.896 55.000 2.17 0.00 36.50 4.10
860 951 0.532573 GGCTGCTACTGCACTCTGTA 59.467 55.000 0.00 0.00 45.31 2.74
861 952 1.066858 GGCTGCTACTGCACTCTGTAA 60.067 52.381 0.00 0.00 45.31 2.41
878 969 0.323629 TAAGTGGGAACTGGGAAGCG 59.676 55.000 0.00 0.00 0.00 4.68
904 995 2.573915 GTTTGTCTCTCTCCCCCATTCT 59.426 50.000 0.00 0.00 0.00 2.40
934 1025 1.109920 CGACGAGATCCATCCACCCT 61.110 60.000 0.00 0.00 0.00 4.34
1014 1108 2.514824 GAGATGGTGCGGAAGGCC 60.515 66.667 0.00 0.00 42.61 5.19
1356 1450 4.009675 TGTTTCACTGGCTGATATGGTTC 58.990 43.478 0.00 0.00 0.00 3.62
1362 1456 1.557371 TGGCTGATATGGTTCGGTTGA 59.443 47.619 0.00 0.00 0.00 3.18
1363 1457 1.940613 GGCTGATATGGTTCGGTTGAC 59.059 52.381 0.00 0.00 0.00 3.18
1454 1548 1.573108 GAATGGAGAGGTCAGGGTGA 58.427 55.000 0.00 0.00 0.00 4.02
1486 1618 0.510790 TGTACGCACGATGCAGTTTG 59.489 50.000 9.95 0.00 45.36 2.93
1596 1729 0.890683 GTTGGGAGCTTGGGAATGTG 59.109 55.000 0.00 0.00 0.00 3.21
1603 1736 3.532542 GAGCTTGGGAATGTGGTAGTAC 58.467 50.000 0.00 0.00 0.00 2.73
1659 1796 4.885907 GGTTTATAGGGGGTTTGAACTAGC 59.114 45.833 0.00 0.00 0.00 3.42
1684 1821 2.256117 AGGTTTTGTCGAGGAGTTGG 57.744 50.000 0.00 0.00 0.00 3.77
1791 1936 4.515191 TGGATTTTCCTCTTGTCGAACAAG 59.485 41.667 16.74 16.74 44.39 3.16
1929 2074 7.514721 TGGGTGAAAAGGAGATATATGGTAAC 58.485 38.462 0.00 0.00 0.00 2.50
1949 2094 1.436983 GGGCTAGCATCGTTTTCCCG 61.437 60.000 18.24 0.00 0.00 5.14
2115 2316 2.035321 GGGATGTTTTTGGTTCTTGCGA 59.965 45.455 0.00 0.00 0.00 5.10
2188 2390 5.843969 TCATCATACCTTATCTGGCCTAACA 59.156 40.000 3.32 0.00 0.00 2.41
2189 2391 6.328934 TCATCATACCTTATCTGGCCTAACAA 59.671 38.462 3.32 0.00 0.00 2.83
2216 2418 7.172019 TGAAAGGATATCATGATTCACACATCG 59.828 37.037 14.65 0.00 0.00 3.84
2229 2431 6.399639 TTCACACATCGATGCTATAACCTA 57.600 37.500 25.11 0.00 0.00 3.08
2266 2468 2.996631 AGTAAAGCTGGATTGCTGAGG 58.003 47.619 0.00 0.00 43.24 3.86
2276 2478 0.689055 ATTGCTGAGGTGTGCTCTGA 59.311 50.000 0.00 0.00 0.00 3.27
2355 2557 3.046390 CGAGGAGTATCTTTGCTAAGCG 58.954 50.000 2.75 0.00 33.73 4.68
2372 2575 4.380841 AAGCGATTTGTCATTGCATCAT 57.619 36.364 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.458989 TCAAATCAGTTTCAGGTACATGCC 59.541 41.667 1.79 0.00 0.00 4.40
40 41 5.798934 GCTGCTCATAACTTGTTCAAATCAG 59.201 40.000 0.00 0.00 0.00 2.90
47 48 2.485426 TGCTGCTGCTCATAACTTGTTC 59.515 45.455 17.00 0.00 40.48 3.18
74 75 7.149202 TGCTAGGATATTTAAGTGACCCAAT 57.851 36.000 0.00 0.00 0.00 3.16
147 177 1.203441 TTCCATCCAGGCTGTGCTCT 61.203 55.000 14.43 0.00 37.29 4.09
305 359 8.667987 TTATTGTTCGAATTGATACTGTTTGC 57.332 30.769 0.00 0.00 0.00 3.68
308 363 8.788806 TGGTTTATTGTTCGAATTGATACTGTT 58.211 29.630 0.00 0.00 0.00 3.16
349 412 9.414295 CACTCAAATTCAAAATGAGCATAAGAA 57.586 29.630 4.36 0.00 43.41 2.52
366 429 8.181904 ACAACACCATAAATCTCACTCAAATT 57.818 30.769 0.00 0.00 0.00 1.82
407 480 2.268920 GCTCCCGCATCAACCTCA 59.731 61.111 0.00 0.00 35.78 3.86
515 588 2.087646 GAATTGGTCTGGCTGGTCTTC 58.912 52.381 0.00 0.00 0.00 2.87
516 589 1.611673 CGAATTGGTCTGGCTGGTCTT 60.612 52.381 0.00 0.00 0.00 3.01
517 590 0.036010 CGAATTGGTCTGGCTGGTCT 60.036 55.000 0.00 0.00 0.00 3.85
518 591 0.036388 TCGAATTGGTCTGGCTGGTC 60.036 55.000 0.00 0.00 0.00 4.02
524 597 1.813513 AAGCAGTCGAATTGGTCTGG 58.186 50.000 14.43 0.30 0.00 3.86
547 620 3.642778 TTTTCTCCTCCGCCGCTCG 62.643 63.158 0.00 0.00 38.08 5.03
551 624 1.741770 CCACTTTTCTCCTCCGCCG 60.742 63.158 0.00 0.00 0.00 6.46
554 627 1.339151 CCCTTCCACTTTTCTCCTCCG 60.339 57.143 0.00 0.00 0.00 4.63
561 634 2.026169 CCCTAGTCCCCTTCCACTTTTC 60.026 54.545 0.00 0.00 0.00 2.29
563 636 1.132168 ACCCTAGTCCCCTTCCACTTT 60.132 52.381 0.00 0.00 0.00 2.66
564 637 0.496841 ACCCTAGTCCCCTTCCACTT 59.503 55.000 0.00 0.00 0.00 3.16
566 639 0.618981 CAACCCTAGTCCCCTTCCAC 59.381 60.000 0.00 0.00 0.00 4.02
567 640 1.205460 GCAACCCTAGTCCCCTTCCA 61.205 60.000 0.00 0.00 0.00 3.53
571 644 1.686110 CTCGCAACCCTAGTCCCCT 60.686 63.158 0.00 0.00 0.00 4.79
575 648 1.448013 GCACCTCGCAACCCTAGTC 60.448 63.158 0.00 0.00 41.79 2.59
582 656 3.499737 CCATCGGCACCTCGCAAC 61.500 66.667 0.00 0.00 45.17 4.17
597 671 1.525077 GCCGGTAAATCCATCGCCA 60.525 57.895 1.90 0.00 35.57 5.69
600 674 0.874390 CATGGCCGGTAAATCCATCG 59.126 55.000 7.51 1.57 38.46 3.84
796 870 1.071228 GCGGGGTCCTATAATTCCGTT 59.929 52.381 0.00 0.00 39.64 4.44
797 871 0.683412 GCGGGGTCCTATAATTCCGT 59.317 55.000 0.00 0.00 39.64 4.69
798 872 0.036671 GGCGGGGTCCTATAATTCCG 60.037 60.000 0.00 0.00 40.33 4.30
799 873 1.061546 TGGCGGGGTCCTATAATTCC 58.938 55.000 0.00 0.00 0.00 3.01
860 951 1.073199 CGCTTCCCAGTTCCCACTT 59.927 57.895 0.00 0.00 0.00 3.16
861 952 1.201429 ATCGCTTCCCAGTTCCCACT 61.201 55.000 0.00 0.00 0.00 4.00
864 955 1.153147 GGATCGCTTCCCAGTTCCC 60.153 63.158 0.00 0.00 38.75 3.97
865 956 1.521681 CGGATCGCTTCCCAGTTCC 60.522 63.158 0.00 0.00 42.06 3.62
866 957 0.391263 AACGGATCGCTTCCCAGTTC 60.391 55.000 0.00 0.00 42.06 3.01
869 960 0.673644 ACAAACGGATCGCTTCCCAG 60.674 55.000 0.00 0.00 42.06 4.45
878 969 1.137282 GGGGAGAGAGACAAACGGATC 59.863 57.143 0.00 0.00 0.00 3.36
886 977 1.343478 GGAGAATGGGGGAGAGAGACA 60.343 57.143 0.00 0.00 0.00 3.41
904 995 0.686441 ATCTCGTCGTGGGGATTGGA 60.686 55.000 0.00 0.00 0.00 3.53
934 1025 2.044492 TCCCTTCTCTTCTTGGCCTCTA 59.956 50.000 3.32 0.00 0.00 2.43
1294 1388 0.831307 GGCAGAGTTAGGATTCGGGT 59.169 55.000 0.00 0.00 0.00 5.28
1356 1450 3.403057 CGCGACACCAGTCAACCG 61.403 66.667 0.00 0.00 45.23 4.44
1428 1522 2.776536 CTGACCTCTCCATTCCAGGAAT 59.223 50.000 9.12 9.12 37.20 3.01
1454 1548 7.564128 CATCGTGCGTACATAATAACAAGAAT 58.436 34.615 4.09 0.00 0.00 2.40
1486 1618 4.309099 ACAAATCATGTGCATTTCACCAC 58.691 39.130 0.00 0.00 45.03 4.16
1596 1729 5.470777 TGCTAATGTTTGGTGTTGTACTACC 59.529 40.000 4.98 6.33 37.48 3.18
1603 1736 3.068024 ACCAGTGCTAATGTTTGGTGTTG 59.932 43.478 0.00 0.00 40.47 3.33
1684 1821 0.778083 AGTTCAAACCCCTTCCTCCC 59.222 55.000 0.00 0.00 0.00 4.30
1791 1936 2.677836 TCCGCATGACAAGCAGTATTTC 59.322 45.455 3.27 0.00 0.00 2.17
1929 2074 1.436983 GGGAAAACGATGCTAGCCCG 61.437 60.000 20.46 20.46 0.00 6.13
1949 2094 2.579207 TAGCAGCGAGGTAACACATC 57.421 50.000 0.00 0.00 41.41 3.06
2094 2295 2.403259 CGCAAGAACCAAAAACATCCC 58.597 47.619 0.00 0.00 43.02 3.85
2115 2316 8.174757 TCATGATTTGATCCAGGGAAATATGAT 58.825 33.333 0.00 0.00 0.00 2.45
2188 2390 8.756486 TGTGTGAATCATGATATCCTTTCATT 57.244 30.769 9.04 0.00 31.50 2.57
2189 2391 8.935614 ATGTGTGAATCATGATATCCTTTCAT 57.064 30.769 9.04 5.90 34.15 2.57
2216 2418 6.406692 TGAGGTGAACTAGGTTATAGCATC 57.593 41.667 0.00 0.00 0.00 3.91
2229 2431 6.998673 AGCTTTACTAACAATTGAGGTGAACT 59.001 34.615 13.59 7.74 0.00 3.01
2276 2478 1.120530 CGTTACCTGGGCCTGAGTAT 58.879 55.000 12.58 0.00 0.00 2.12
2355 2557 4.931661 AGGGATGATGCAATGACAAATC 57.068 40.909 0.00 0.00 0.00 2.17
2372 2575 2.038863 TAGCTCACTCCCAAAAGGGA 57.961 50.000 2.82 2.82 40.01 4.20


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

AutoCloner maintained by Alex Coulton.