Multiple sequence alignment - TraesCS2A01G183800

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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 TraesCS2A01G183800 chr2A 100.000 2528 0 0 1 2528 143728004 143725477 0 4669
1 TraesCS2A01G183800 chr2D 94.210 2556 112 11 1 2528 135605680 135603133 0 3868
2 TraesCS2A01G183800 chr2B 94.134 2557 114 10 1 2528 193395199 193392650 0 3858


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 TraesCS2A01G183800 chr2A 143725477 143728004 2527 True 4669 4669 100.000 1 2528 1 chr2A.!!$R1 2527
1 TraesCS2A01G183800 chr2D 135603133 135605680 2547 True 3868 3868 94.210 1 2528 1 chr2D.!!$R1 2527
2 TraesCS2A01G183800 chr2B 193392650 193395199 2549 True 3858 3858 94.134 1 2528 1 chr2B.!!$R1 2527

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
201 215 0.394352 TGCAGGCTAAGCTTTAGGGC 60.394 55.0 3.2 8.2 0.0 5.19 F
473 487 0.868406 AGCGAAAAAGAAGACGGCAG 59.132 50.0 0.0 0.0 0.0 4.85 F
1078 1093 0.523968 TCGCGCCGACAATAGTACAC 60.524 55.0 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1008 1023 0.321475 GCTCTTCTGCTTCAGGTGCT 60.321 55.0 0.0 0.0 31.51 4.40 R
1294 1321 0.813821 GGTTGGATGAAGGAAGCAGC 59.186 55.0 0.0 0.0 0.00 5.25 R
2504 2536 0.402121 GGAGGTGGCTTTCCAGAAGT 59.598 55.0 0.0 0.0 44.48 3.01 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
201 215 0.394352 TGCAGGCTAAGCTTTAGGGC 60.394 55.000 3.20 8.20 0.00 5.19
336 350 8.732746 ACGTTTGAACAAATAATATCTAGGCT 57.267 30.769 3.34 0.00 32.36 4.58
450 464 4.742438 TTATTGACGCTGAACAAAGTCC 57.258 40.909 0.00 0.00 33.04 3.85
473 487 0.868406 AGCGAAAAAGAAGACGGCAG 59.132 50.000 0.00 0.00 0.00 4.85
486 500 2.943653 GGCAGTTTCACCGTTCGG 59.056 61.111 9.81 9.81 0.00 4.30
507 521 1.993370 CCGTAGCAGACTTCTTTTCCG 59.007 52.381 0.00 0.00 0.00 4.30
518 532 5.123979 AGACTTCTTTTCCGCATACATTTCC 59.876 40.000 0.00 0.00 0.00 3.13
532 546 6.017109 GCATACATTTCCGAACTAATCATGGT 60.017 38.462 0.00 0.00 0.00 3.55
637 651 8.971321 GTTTTTCAAACTGTACTACGTCATAGA 58.029 33.333 0.00 0.00 34.65 1.98
638 652 8.738199 TTTTCAAACTGTACTACGTCATAGAG 57.262 34.615 0.00 0.00 34.65 2.43
662 676 3.780804 TGTACTGCAACATTGGTACCT 57.219 42.857 14.36 0.00 35.17 3.08
663 677 3.407698 TGTACTGCAACATTGGTACCTG 58.592 45.455 14.36 6.53 35.17 4.00
737 751 3.067180 CCGTAACGGGACAGTATACATGT 59.933 47.826 2.69 2.69 44.15 3.21
818 832 4.813027 TGGTACGTAAGCAAACTAGGAAG 58.187 43.478 0.00 0.00 45.62 3.46
872 886 5.382664 TCCACTTTAAACTCCTGGAAACT 57.617 39.130 0.00 0.00 0.00 2.66
926 941 4.336713 GCAGACCCTTGCTCCTTTTTATAG 59.663 45.833 0.00 0.00 40.89 1.31
1008 1023 6.833416 TCCCAACAAAGAAAGAAATGAAGAGA 59.167 34.615 0.00 0.00 0.00 3.10
1010 1025 6.640092 CCAACAAAGAAAGAAATGAAGAGAGC 59.360 38.462 0.00 0.00 0.00 4.09
1026 1041 1.275856 AGAGCACCTGAAGCAGAAGAG 59.724 52.381 0.00 0.00 32.44 2.85
1031 1046 1.696336 ACCTGAAGCAGAAGAGCAGAA 59.304 47.619 0.00 0.00 36.85 3.02
1037 1052 4.394300 TGAAGCAGAAGAGCAGAAATTAGC 59.606 41.667 0.00 0.00 36.85 3.09
1040 1055 5.358922 AGCAGAAGAGCAGAAATTAGCTAG 58.641 41.667 0.00 0.00 42.04 3.42
1041 1056 4.024977 GCAGAAGAGCAGAAATTAGCTAGC 60.025 45.833 6.62 6.62 42.04 3.42
1077 1092 1.801983 TCGCGCCGACAATAGTACA 59.198 52.632 0.00 0.00 0.00 2.90
1078 1093 0.523968 TCGCGCCGACAATAGTACAC 60.524 55.000 0.00 0.00 0.00 2.90
1080 1095 1.477030 GCGCCGACAATAGTACACCG 61.477 60.000 0.00 0.00 0.00 4.94
1119 1134 1.612726 GGCCTTGATGCACTGAGAAGT 60.613 52.381 0.00 0.00 0.00 3.01
1124 1139 4.313282 CTTGATGCACTGAGAAGTGAAGA 58.687 43.478 9.97 0.00 42.02 2.87
1125 1140 4.341366 TGATGCACTGAGAAGTGAAGAA 57.659 40.909 9.97 0.00 42.02 2.52
1294 1321 3.181471 ACTGATGATACGCTTTCCTCCAG 60.181 47.826 0.00 0.00 0.00 3.86
1350 1377 1.462283 CACTCCACAATTCTGACTGCG 59.538 52.381 0.00 0.00 0.00 5.18
1633 1660 2.428544 ACTTGTACCCACAGTTGCAA 57.571 45.000 0.00 0.00 35.67 4.08
1652 1679 3.492756 GCAAGTGAGTTCTCAGACAAGTC 59.507 47.826 2.53 0.00 0.00 3.01
1659 1686 6.313905 GTGAGTTCTCAGACAAGTCTCAAAAA 59.686 38.462 2.53 0.00 37.98 1.94
1786 1813 8.362464 TCCACCGATCAGTATTAAGCTATAAT 57.638 34.615 0.00 0.00 0.00 1.28
1814 1841 8.677148 AGATAAGAAACAAACTTTAGTCAGCA 57.323 30.769 0.00 0.00 0.00 4.41
1816 1843 5.500645 AGAAACAAACTTTAGTCAGCACC 57.499 39.130 0.00 0.00 0.00 5.01
1817 1844 4.947388 AGAAACAAACTTTAGTCAGCACCA 59.053 37.500 0.00 0.00 0.00 4.17
1819 1846 6.770785 AGAAACAAACTTTAGTCAGCACCATA 59.229 34.615 0.00 0.00 0.00 2.74
1857 1884 5.003804 TGCTCTAAGGACTCCAATTCAAAC 58.996 41.667 0.00 0.00 0.00 2.93
1887 1915 3.303990 CCTCACTTGATCACCAAACGTTG 60.304 47.826 0.00 0.00 33.76 4.10
1980 2009 4.559153 AGTTTGTTAGCAACCATGAATGC 58.441 39.130 13.00 13.00 42.87 3.56
1998 2027 0.392327 GCTCTCTGGACTTTGGAGCC 60.392 60.000 0.00 0.00 42.20 4.70
2060 2089 2.159382 GGCTAACAGCTGCAACCTTAA 58.841 47.619 15.27 0.00 41.99 1.85
2180 2209 6.716628 AGCAAAGTAATGTGGAAGAATCAGAA 59.283 34.615 0.00 0.00 0.00 3.02
2186 2215 9.525826 AGTAATGTGGAAGAATCAGAAGAAAAT 57.474 29.630 0.00 0.00 0.00 1.82
2237 2267 6.532657 GGATGCATATGTGGAAAGAACAAAAG 59.467 38.462 0.00 0.00 0.00 2.27
2238 2268 5.229423 TGCATATGTGGAAAGAACAAAAGC 58.771 37.500 4.29 0.00 0.00 3.51
2239 2269 4.627035 GCATATGTGGAAAGAACAAAAGCC 59.373 41.667 4.29 0.00 0.00 4.35
2255 2285 9.377312 GAACAAAAGCCCATTATTTTAATGCTA 57.623 29.630 2.40 0.00 0.00 3.49
2398 2429 4.458989 CCACAACTGTTGGCTACAATGTAT 59.541 41.667 23.15 0.00 39.13 2.29
2420 2451 8.590204 TGTATACTACAAACTTCCATGAGAACA 58.410 33.333 4.17 0.00 35.38 3.18
2430 2462 2.367241 TCCATGAGAACACTTCCAACGA 59.633 45.455 0.00 0.00 0.00 3.85
2523 2555 0.402121 ACTTCTGGAAAGCCACCTCC 59.598 55.000 0.00 0.00 39.92 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 3.752747 CCACTCACAGCACAATGATTGTA 59.247 43.478 10.89 0.00 43.23 2.41
113 114 0.389426 CACTCCCCGAGGTAAACACG 60.389 60.000 0.00 0.00 33.35 4.49
201 215 2.673610 GCGCCTGGCATTCTCTATCTAG 60.674 54.545 20.29 0.00 42.87 2.43
227 241 0.540454 TCTCTTGAGGCTCAGGCATG 59.460 55.000 20.77 13.14 40.87 4.06
450 464 1.398960 CCGTCTTCTTTTTCGCTGCTG 60.399 52.381 0.00 0.00 0.00 4.41
473 487 1.620413 CTACGGCCGAACGGTGAAAC 61.620 60.000 35.90 0.00 38.39 2.78
486 500 1.732809 GGAAAAGAAGTCTGCTACGGC 59.267 52.381 0.00 0.00 39.26 5.68
507 521 6.017109 ACCATGATTAGTTCGGAAATGTATGC 60.017 38.462 0.20 0.00 0.00 3.14
637 651 6.055588 GGTACCAATGTTGCAGTACATATCT 58.944 40.000 7.15 0.00 37.76 1.98
638 652 6.017934 CAGGTACCAATGTTGCAGTACATATC 60.018 42.308 15.94 0.00 37.76 1.63
662 676 5.045359 CCTGATCAGATATGGGCCTATTTCA 60.045 44.000 24.62 1.73 0.00 2.69
663 677 5.190528 TCCTGATCAGATATGGGCCTATTTC 59.809 44.000 24.62 9.37 0.00 2.17
818 832 5.240891 TGCTAGTTTGCATGCCTATCTATC 58.759 41.667 16.68 8.76 38.12 2.08
872 886 6.237154 CAATAATTCAGGGGAAAAGGCAAAA 58.763 36.000 0.00 0.00 36.43 2.44
926 941 0.461961 ATGGTAGTCCTCTCGCTTGC 59.538 55.000 0.00 0.00 34.23 4.01
930 945 3.318275 TGTTATGATGGTAGTCCTCTCGC 59.682 47.826 0.00 0.00 34.23 5.03
932 947 5.854010 TGTGTTATGATGGTAGTCCTCTC 57.146 43.478 0.00 0.00 34.23 3.20
977 992 3.287222 TCTTTCTTTGTTGGGAGTGGTG 58.713 45.455 0.00 0.00 0.00 4.17
978 993 3.662759 TCTTTCTTTGTTGGGAGTGGT 57.337 42.857 0.00 0.00 0.00 4.16
1008 1023 0.321475 GCTCTTCTGCTTCAGGTGCT 60.321 55.000 0.00 0.00 31.51 4.40
1010 1025 1.001746 TCTGCTCTTCTGCTTCAGGTG 59.998 52.381 0.00 0.00 31.51 4.00
1026 1041 3.065925 CACCTTGGCTAGCTAATTTCTGC 59.934 47.826 14.42 0.00 0.00 4.26
1031 1046 4.778213 TCATCACCTTGGCTAGCTAATT 57.222 40.909 14.42 1.62 0.00 1.40
1037 1052 2.286872 CAGCTTCATCACCTTGGCTAG 58.713 52.381 0.00 0.00 0.00 3.42
1040 1055 0.610232 ACCAGCTTCATCACCTTGGC 60.610 55.000 0.00 0.00 0.00 4.52
1041 1056 1.457346 GACCAGCTTCATCACCTTGG 58.543 55.000 0.00 0.00 0.00 3.61
1068 1083 3.194861 CCATGGTGTCGGTGTACTATTG 58.805 50.000 2.57 0.00 0.00 1.90
1069 1084 2.419574 GCCATGGTGTCGGTGTACTATT 60.420 50.000 14.67 0.00 0.00 1.73
1071 1086 0.533491 GCCATGGTGTCGGTGTACTA 59.467 55.000 14.67 0.00 0.00 1.82
1073 1088 0.533491 TAGCCATGGTGTCGGTGTAC 59.467 55.000 14.67 0.00 0.00 2.90
1077 1092 0.676782 GCTTTAGCCATGGTGTCGGT 60.677 55.000 14.67 0.00 34.31 4.69
1078 1093 0.392998 AGCTTTAGCCATGGTGTCGG 60.393 55.000 14.67 2.82 43.38 4.79
1080 1095 1.098050 CCAGCTTTAGCCATGGTGTC 58.902 55.000 14.67 0.00 43.38 3.67
1119 1134 2.499289 CTCTGGAGGCTTAGCTTCTTCA 59.501 50.000 15.68 5.80 34.98 3.02
1209 1236 1.902918 GTGTGCATTCTGGTGCCCA 60.903 57.895 0.00 0.00 44.43 5.36
1294 1321 0.813821 GGTTGGATGAAGGAAGCAGC 59.186 55.000 0.00 0.00 0.00 5.25
1350 1377 4.056125 GCGGCCCTTTCACCTTGC 62.056 66.667 0.00 0.00 0.00 4.01
1633 1660 4.211125 TGAGACTTGTCTGAGAACTCACT 58.789 43.478 8.11 0.00 35.46 3.41
1721 1748 9.986157 TCCTACTTCCTAGTAACTAGATTGAAA 57.014 33.333 0.00 0.00 36.26 2.69
1738 1765 6.935208 GGATTGTATGTATGGTTCCTACTTCC 59.065 42.308 0.00 0.00 0.00 3.46
1816 1843 5.292765 AGAGCAACGATAATCACCACTATG 58.707 41.667 0.00 0.00 0.00 2.23
1817 1844 5.537300 AGAGCAACGATAATCACCACTAT 57.463 39.130 0.00 0.00 0.00 2.12
1819 1846 3.895232 AGAGCAACGATAATCACCACT 57.105 42.857 0.00 0.00 0.00 4.00
1830 1857 1.919240 TGGAGTCCTTAGAGCAACGA 58.081 50.000 11.33 0.00 0.00 3.85
1857 1884 3.624861 GGTGATCAAGTGAGGCACATAAG 59.375 47.826 14.99 0.00 36.74 1.73
1887 1915 9.243637 TGTTGCATGTAGTTTATCTTTTGAAAC 57.756 29.630 0.00 0.00 36.08 2.78
1946 1975 8.026607 GGTTGCTAACAAACTTCTAATGCATAA 58.973 33.333 0.00 0.00 40.54 1.90
1955 1984 6.449698 CATTCATGGTTGCTAACAAACTTCT 58.550 36.000 0.00 0.00 44.28 2.85
1980 2009 1.274712 AGGCTCCAAAGTCCAGAGAG 58.725 55.000 0.00 0.00 0.00 3.20
1981 2010 2.623418 TAGGCTCCAAAGTCCAGAGA 57.377 50.000 0.00 0.00 0.00 3.10
2029 2058 5.471116 TGCAGCTGTTAGCCTTTATATGATG 59.529 40.000 16.64 0.00 43.77 3.07
2047 2076 3.582714 GCAATCTTTAAGGTTGCAGCT 57.417 42.857 30.77 0.00 45.57 4.24
2237 2267 6.785488 GCCTTTAGCATTAAAATAATGGGC 57.215 37.500 11.02 10.36 42.97 5.36
2255 2285 1.479323 CTATGCCATGCACTTGCCTTT 59.521 47.619 0.00 0.00 43.04 3.11
2371 2402 1.602377 GTAGCCAACAGTTGTGGTCAC 59.398 52.381 12.42 5.59 0.00 3.67
2398 2429 7.062749 AGTGTTCTCATGGAAGTTTGTAGTA 57.937 36.000 0.00 0.00 34.23 1.82
2420 2451 6.479001 GCATATACAGTGTAATCGTTGGAAGT 59.521 38.462 7.16 0.00 0.00 3.01
2504 2536 0.402121 GGAGGTGGCTTTCCAGAAGT 59.598 55.000 0.00 0.00 44.48 3.01


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

AutoCloner maintained by Alex Coulton.