Multiple sequence alignment - TraesCS5D01G206500

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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 TraesCS5D01G206500 chr5D 100.000 7110 0 0 1 7110 312610171 312603062 0.000000e+00 13130.0
1 TraesCS5D01G206500 chr5D 75.904 166 26 8 536 688 281224293 281224129 9.890000e-09 73.1
2 TraesCS5D01G206500 chr5D 97.674 43 0 1 3948 3990 312606190 312606149 9.890000e-09 73.1
3 TraesCS5D01G206500 chr5D 97.674 43 0 1 3982 4023 312606224 312606182 9.890000e-09 73.1
4 TraesCS5D01G206500 chr5B 92.848 4027 177 44 1 3990 359315445 359311493 0.000000e+00 5738.0
5 TraesCS5D01G206500 chr5B 94.825 3092 84 29 3982 7010 359311534 359308456 0.000000e+00 4754.0
6 TraesCS5D01G206500 chr5B 94.858 914 39 5 1599 2511 648736964 648737870 0.000000e+00 1421.0
7 TraesCS5D01G206500 chr5B 96.000 100 3 1 7011 7110 359308398 359308300 2.050000e-35 161.0
8 TraesCS5D01G206500 chr5B 93.258 89 5 1 6725 6812 659987400 659987312 5.790000e-26 130.0
9 TraesCS5D01G206500 chr5B 80.833 120 20 2 543 659 681137235 681137354 2.730000e-14 91.6
10 TraesCS5D01G206500 chr5A 97.843 3014 48 11 990 3990 406672895 406669886 0.000000e+00 5190.0
11 TraesCS5D01G206500 chr5A 95.920 3162 68 19 3982 7110 406669927 406666794 0.000000e+00 5068.0
12 TraesCS5D01G206500 chr5A 95.816 478 18 1 1 478 406691929 406691454 0.000000e+00 771.0
13 TraesCS5D01G206500 chr5A 88.652 423 32 8 515 933 406673763 406673353 1.060000e-137 501.0
14 TraesCS5D01G206500 chr5A 92.632 95 4 3 6725 6818 698500938 698500846 4.470000e-27 134.0
15 TraesCS5D01G206500 chr7B 94.003 1284 68 6 1230 2511 263150378 263151654 0.000000e+00 1936.0
16 TraesCS5D01G206500 chr1B 91.179 1281 75 21 1233 2511 372098872 372097628 0.000000e+00 1705.0
17 TraesCS5D01G206500 chr1B 81.600 125 20 2 538 659 15876289 15876413 4.540000e-17 100.0
18 TraesCS5D01G206500 chr1B 80.800 125 21 1 538 659 4219451 4219327 2.110000e-15 95.3
19 TraesCS5D01G206500 chr1B 83.673 98 15 1 6912 7009 502386100 502386196 2.730000e-14 91.6
20 TraesCS5D01G206500 chr7D 95.170 911 36 5 1602 2511 513996142 513995239 0.000000e+00 1432.0
21 TraesCS5D01G206500 chr7D 79.245 159 18 6 543 688 31886210 31886054 5.870000e-16 97.1
22 TraesCS5D01G206500 chr7A 94.639 914 41 5 1599 2511 673066056 673066962 0.000000e+00 1410.0
23 TraesCS5D01G206500 chr7A 85.484 124 15 2 533 653 44824795 44824672 7.490000e-25 126.0
24 TraesCS5D01G206500 chr3D 94.639 914 41 5 1599 2511 208830981 208831887 0.000000e+00 1410.0
25 TraesCS5D01G206500 chr3D 90.625 96 7 2 6725 6820 441645674 441645581 7.490000e-25 126.0
26 TraesCS5D01G206500 chr3A 94.795 903 39 4 1610 2511 10619745 10620640 0.000000e+00 1400.0
27 TraesCS5D01G206500 chr3A 95.833 48 2 0 1230 1277 10617878 10617925 2.130000e-10 78.7
28 TraesCS5D01G206500 chr4A 83.757 708 99 12 1213 1917 654360542 654361236 0.000000e+00 656.0
29 TraesCS5D01G206500 chr4A 85.096 208 25 2 1213 1420 654249493 654249694 2.600000e-49 207.0
30 TraesCS5D01G206500 chr4A 97.561 82 2 0 6725 6806 122623770 122623851 2.670000e-29 141.0
31 TraesCS5D01G206500 chr4B 81.746 504 72 12 1371 1860 620192086 620191589 3.090000e-108 403.0
32 TraesCS5D01G206500 chr4B 80.040 506 78 13 1371 1860 620166944 620166446 3.160000e-93 353.0
33 TraesCS5D01G206500 chr1D 89.231 130 12 2 1371 1499 395811867 395811995 2.050000e-35 161.0
34 TraesCS5D01G206500 chr2A 94.565 92 3 2 6724 6814 102694791 102694881 2.670000e-29 141.0
35 TraesCS5D01G206500 chr2A 95.455 88 3 1 6719 6806 102694599 102694685 9.620000e-29 139.0
36 TraesCS5D01G206500 chr2A 97.778 45 1 0 1233 1277 37030425 37030381 2.130000e-10 78.7
37 TraesCS5D01G206500 chr3B 90.816 98 7 1 6709 6806 717035591 717035686 5.790000e-26 130.0
38 TraesCS5D01G206500 chr3B 85.526 76 10 1 6926 7001 271929188 271929114 2.130000e-10 78.7
39 TraesCS5D01G206500 chr1A 79.412 136 22 5 538 669 560464759 560464892 2.730000e-14 91.6
40 TraesCS5D01G206500 chr1A 95.833 48 2 0 1230 1277 561614310 561614357 2.130000e-10 78.7
41 TraesCS5D01G206500 chr6D 80.000 115 22 1 546 659 463857078 463856964 4.570000e-12 84.2


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 TraesCS5D01G206500 chr5D 312603062 312610171 7109 True 13130.000000 13130 100.000000 1 7110 1 chr5D.!!$R2 7109
1 TraesCS5D01G206500 chr5B 359308300 359315445 7145 True 3551.000000 5738 94.557667 1 7110 3 chr5B.!!$R2 7109
2 TraesCS5D01G206500 chr5B 648736964 648737870 906 False 1421.000000 1421 94.858000 1599 2511 1 chr5B.!!$F1 912
3 TraesCS5D01G206500 chr5A 406666794 406673763 6969 True 3586.333333 5190 94.138333 515 7110 3 chr5A.!!$R3 6595
4 TraesCS5D01G206500 chr7B 263150378 263151654 1276 False 1936.000000 1936 94.003000 1230 2511 1 chr7B.!!$F1 1281
5 TraesCS5D01G206500 chr1B 372097628 372098872 1244 True 1705.000000 1705 91.179000 1233 2511 1 chr1B.!!$R2 1278
6 TraesCS5D01G206500 chr7D 513995239 513996142 903 True 1432.000000 1432 95.170000 1602 2511 1 chr7D.!!$R2 909
7 TraesCS5D01G206500 chr7A 673066056 673066962 906 False 1410.000000 1410 94.639000 1599 2511 1 chr7A.!!$F1 912
8 TraesCS5D01G206500 chr3D 208830981 208831887 906 False 1410.000000 1410 94.639000 1599 2511 1 chr3D.!!$F1 912
9 TraesCS5D01G206500 chr3A 10617878 10620640 2762 False 739.350000 1400 95.314000 1230 2511 2 chr3A.!!$F1 1281
10 TraesCS5D01G206500 chr4A 654360542 654361236 694 False 656.000000 656 83.757000 1213 1917 1 chr4A.!!$F3 704

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
968 981 0.764752 CCTCCATCCCCTCACTACCC 60.765 65.000 0.00 0.00 0.00 3.69 F
1506 2063 0.798776 CGATCTGGTTTGTGCTGTCC 59.201 55.000 0.00 0.00 0.00 4.02 F
1524 2081 0.912486 CCGGAGACTTGGAGGGATTT 59.088 55.000 0.00 0.00 0.00 2.17 F
1962 3952 1.340114 GGAAAGCTCGGTTCATTCCCT 60.340 52.381 0.33 0.00 34.74 4.20 F
2756 4779 1.623295 CGCACGTTTGTTGCAACAC 59.377 52.632 31.17 19.52 38.92 3.32 F
2932 4957 3.058293 CAGCTAAAACGATGAAAGGCACA 60.058 43.478 0.00 0.00 0.00 4.57 F
3959 6008 4.702131 ACTTGCAACTGAAGTTTTCTGACT 59.298 37.500 0.00 0.00 35.83 3.41 F
3980 6029 3.788227 TTCTTATCTGTTGCTGTGGGT 57.212 42.857 0.00 0.00 0.00 4.51 F
5385 7436 1.063266 TCCAAGACAGCCCAAGGTTTT 60.063 47.619 0.00 0.00 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 3937 0.462759 CCTCAGGGAATGAACCGAGC 60.463 60.000 0.00 0.0 37.52 5.03 R
3218 5247 1.760613 TCGTGCTTCCCCGAAATCTAT 59.239 47.619 0.00 0.0 0.00 1.98 R
3372 5401 6.430925 TCACAATAAGAAATACTGTTGCTGCT 59.569 34.615 0.00 0.0 32.14 4.24 R
3960 6009 3.788227 ACCCACAGCAACAGATAAGAA 57.212 42.857 0.00 0.0 0.00 2.52 R
3971 6020 3.118038 AGTCAGAAAACTTACCCACAGCA 60.118 43.478 0.00 0.0 0.00 4.41 R
3972 6021 3.477530 AGTCAGAAAACTTACCCACAGC 58.522 45.455 0.00 0.0 0.00 4.40 R
5152 7203 0.178926 TCCACGAGGGGGTAGTTTCA 60.179 55.000 0.00 0.0 37.22 2.69 R
5954 8010 2.611224 CCAGGTTAGTACGCCGTTCTTT 60.611 50.000 0.71 0.0 0.00 2.52 R
6525 8619 0.765510 AAACTGTCGCCCTCCTTCTT 59.234 50.000 0.00 0.0 0.00 2.52 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
64 65 4.464008 TGCATACTTGGGGATGATTTCTC 58.536 43.478 0.00 0.00 0.00 2.87
90 91 4.584743 TGATCATGTACCGCTCTTATGAGT 59.415 41.667 7.41 0.00 42.13 3.41
138 139 6.293955 GCCATACTTGCCAATCGTATTTACAT 60.294 38.462 0.00 0.00 0.00 2.29
142 143 5.234329 ACTTGCCAATCGTATTTACATCTCG 59.766 40.000 0.00 0.00 0.00 4.04
148 149 2.031420 TCGTATTTACATCTCGAGCCCG 60.031 50.000 7.81 0.46 37.07 6.13
177 178 3.135530 AGGCTTGGTAGACTTGATCCATC 59.864 47.826 0.00 0.00 35.73 3.51
179 180 4.445448 GGCTTGGTAGACTTGATCCATCAT 60.445 45.833 0.00 0.00 36.56 2.45
290 291 9.151177 AGCCATATGAAATTACCATTTGAATCT 57.849 29.630 3.65 4.96 32.35 2.40
291 292 9.768662 GCCATATGAAATTACCATTTGAATCTT 57.231 29.630 3.65 0.00 32.35 2.40
297 298 9.258826 TGAAATTACCATTTGAATCTTTGTGTG 57.741 29.630 0.00 0.00 32.35 3.82
298 299 9.260002 GAAATTACCATTTGAATCTTTGTGTGT 57.740 29.630 0.00 0.00 32.35 3.72
299 300 9.612066 AAATTACCATTTGAATCTTTGTGTGTT 57.388 25.926 0.00 0.00 30.89 3.32
321 322 9.683069 GTGTTTTGATATTTTCACACTGAATCT 57.317 29.630 0.00 0.00 36.11 2.40
385 386 5.396484 CCACAACTCTTGTTTATGCATCAG 58.604 41.667 0.19 0.00 43.23 2.90
543 544 5.104318 ACTCTCTTCATCCCAAAATACTCCC 60.104 44.000 0.00 0.00 0.00 4.30
547 548 3.469859 TCATCCCAAAATACTCCCTCCA 58.530 45.455 0.00 0.00 0.00 3.86
595 598 7.884816 AGATTTCAACGTGGATTATATACGG 57.115 36.000 0.00 0.00 41.74 4.02
613 616 4.096732 ACGGAGCAAAATGAGTAAATGC 57.903 40.909 0.00 0.00 37.28 3.56
616 619 3.853671 GGAGCAAAATGAGTAAATGCACG 59.146 43.478 0.00 0.00 39.42 5.34
619 622 3.301642 GCAAAATGAGTAAATGCACGCTC 59.698 43.478 0.00 0.00 37.00 5.03
620 623 4.726416 CAAAATGAGTAAATGCACGCTCT 58.274 39.130 0.00 0.00 0.00 4.09
823 833 1.377463 CCCCCGGTTAATCAACGCA 60.377 57.895 0.00 0.00 35.34 5.24
835 845 1.954146 CAACGCAGCCACACGTACT 60.954 57.895 0.00 0.00 42.68 2.73
836 846 1.663702 AACGCAGCCACACGTACTC 60.664 57.895 0.00 0.00 42.68 2.59
845 858 2.056223 ACACGTACTCCCCATCCCG 61.056 63.158 0.00 0.00 0.00 5.14
855 868 1.598130 CCCATCCCGAAAGCCGATC 60.598 63.158 0.00 0.00 41.76 3.69
939 952 1.265236 ATTTCAAAATCCCGCAGCCA 58.735 45.000 0.00 0.00 0.00 4.75
964 977 2.765807 CGCCTCCATCCCCTCACT 60.766 66.667 0.00 0.00 0.00 3.41
965 978 1.457643 CGCCTCCATCCCCTCACTA 60.458 63.158 0.00 0.00 0.00 2.74
966 979 1.749334 CGCCTCCATCCCCTCACTAC 61.749 65.000 0.00 0.00 0.00 2.73
968 981 0.764752 CCTCCATCCCCTCACTACCC 60.765 65.000 0.00 0.00 0.00 3.69
969 982 1.075525 TCCATCCCCTCACTACCCG 60.076 63.158 0.00 0.00 0.00 5.28
970 983 2.808206 CCATCCCCTCACTACCCGC 61.808 68.421 0.00 0.00 0.00 6.13
971 984 1.762460 CATCCCCTCACTACCCGCT 60.762 63.158 0.00 0.00 0.00 5.52
972 985 1.457831 ATCCCCTCACTACCCGCTC 60.458 63.158 0.00 0.00 0.00 5.03
973 986 2.948801 ATCCCCTCACTACCCGCTCC 62.949 65.000 0.00 0.00 0.00 4.70
974 987 3.155167 CCCTCACTACCCGCTCCC 61.155 72.222 0.00 0.00 0.00 4.30
975 988 3.155167 CCTCACTACCCGCTCCCC 61.155 72.222 0.00 0.00 0.00 4.81
976 989 3.155167 CTCACTACCCGCTCCCCC 61.155 72.222 0.00 0.00 0.00 5.40
1005 1420 1.921869 ATTCGATCCCACCCCACCAC 61.922 60.000 0.00 0.00 0.00 4.16
1477 1946 0.831711 AAAGCAGGTGCCGGGATTTT 60.832 50.000 2.18 0.00 43.38 1.82
1487 2044 0.805711 CCGGGATTTTGCGATTTGGC 60.806 55.000 0.00 0.00 0.00 4.52
1500 2057 2.728846 CGATTTGGCGATCTGGTTTGTG 60.729 50.000 0.00 0.00 0.00 3.33
1506 2063 0.798776 CGATCTGGTTTGTGCTGTCC 59.201 55.000 0.00 0.00 0.00 4.02
1519 2076 1.893786 CTGTCCGGAGACTTGGAGG 59.106 63.158 3.06 0.00 43.91 4.30
1520 2077 1.608717 CTGTCCGGAGACTTGGAGGG 61.609 65.000 3.06 0.00 43.91 4.30
1524 2081 0.912486 CCGGAGACTTGGAGGGATTT 59.088 55.000 0.00 0.00 0.00 2.17
1568 2946 5.423886 TGTTTGATTTTTGGTTCCAGGTTC 58.576 37.500 0.00 0.00 0.00 3.62
1617 3601 2.307098 AGAAAGCCCAAGTGAGTAGCAT 59.693 45.455 0.00 0.00 0.00 3.79
1794 3779 9.468532 TGAGTAGATGAAAGATCGATTACATTG 57.531 33.333 0.00 0.00 0.00 2.82
1941 3931 2.175069 AGGGTCTATCCAGTCGCTTCTA 59.825 50.000 0.00 0.00 38.11 2.10
1947 3937 3.810310 ATCCAGTCGCTTCTAGGAAAG 57.190 47.619 0.00 0.00 31.17 2.62
1962 3952 1.340114 GGAAAGCTCGGTTCATTCCCT 60.340 52.381 0.33 0.00 34.74 4.20
1985 3975 5.428253 TGAGGCAGTAAGTAACCATCAATC 58.572 41.667 0.00 0.00 0.00 2.67
2042 4032 8.621286 AGAGAAACTGATTCGTTGTGTATTTTT 58.379 29.630 0.00 0.00 43.15 1.94
2665 4686 5.066893 ACATTATCTTATGTTGCAGTGCCAG 59.933 40.000 13.72 0.00 35.24 4.85
2756 4779 1.623295 CGCACGTTTGTTGCAACAC 59.377 52.632 31.17 19.52 38.92 3.32
2790 4813 3.449737 AGTTATCCGCCTGCTACAACTTA 59.550 43.478 0.00 0.00 0.00 2.24
2932 4957 3.058293 CAGCTAAAACGATGAAAGGCACA 60.058 43.478 0.00 0.00 0.00 4.57
3908 5957 7.323420 TGTTGTCATATCTTTCACCTCACTAG 58.677 38.462 0.00 0.00 0.00 2.57
3949 5998 7.096477 GCATTACAAAACTACTTGCAACTGAAG 60.096 37.037 0.00 0.00 0.00 3.02
3950 5999 5.897377 ACAAAACTACTTGCAACTGAAGT 57.103 34.783 0.00 0.00 37.43 3.01
3951 6000 6.267496 ACAAAACTACTTGCAACTGAAGTT 57.733 33.333 0.00 0.11 39.12 2.66
3952 6001 6.687604 ACAAAACTACTTGCAACTGAAGTTT 58.312 32.000 13.73 13.73 38.45 2.66
3953 6002 7.151976 ACAAAACTACTTGCAACTGAAGTTTT 58.848 30.769 20.12 20.12 43.95 2.43
3954 6003 7.328493 ACAAAACTACTTGCAACTGAAGTTTTC 59.672 33.333 21.63 0.00 42.27 2.29
3955 6004 6.759497 AACTACTTGCAACTGAAGTTTTCT 57.241 33.333 0.00 0.00 35.83 2.52
3956 6005 6.124088 ACTACTTGCAACTGAAGTTTTCTG 57.876 37.500 0.00 0.00 35.83 3.02
3957 6006 5.880332 ACTACTTGCAACTGAAGTTTTCTGA 59.120 36.000 0.00 0.00 35.83 3.27
3958 6007 4.986622 ACTTGCAACTGAAGTTTTCTGAC 58.013 39.130 0.00 0.00 35.83 3.51
3959 6008 4.702131 ACTTGCAACTGAAGTTTTCTGACT 59.298 37.500 0.00 0.00 35.83 3.41
3960 6009 5.183904 ACTTGCAACTGAAGTTTTCTGACTT 59.816 36.000 0.00 0.00 42.31 3.01
3961 6010 5.643379 TGCAACTGAAGTTTTCTGACTTT 57.357 34.783 0.00 0.00 39.84 2.66
3962 6011 5.640732 TGCAACTGAAGTTTTCTGACTTTC 58.359 37.500 0.00 0.00 39.84 2.62
3963 6012 5.415701 TGCAACTGAAGTTTTCTGACTTTCT 59.584 36.000 0.00 0.00 39.84 2.52
3964 6013 6.071952 TGCAACTGAAGTTTTCTGACTTTCTT 60.072 34.615 0.00 0.00 39.84 2.52
3965 6014 7.120579 TGCAACTGAAGTTTTCTGACTTTCTTA 59.879 33.333 0.00 0.00 39.84 2.10
3966 6015 8.131731 GCAACTGAAGTTTTCTGACTTTCTTAT 58.868 33.333 0.00 0.00 39.84 1.73
3967 6016 9.657121 CAACTGAAGTTTTCTGACTTTCTTATC 57.343 33.333 0.00 0.00 39.84 1.75
3968 6017 9.620259 AACTGAAGTTTTCTGACTTTCTTATCT 57.380 29.630 3.22 0.00 39.84 1.98
3969 6018 9.050601 ACTGAAGTTTTCTGACTTTCTTATCTG 57.949 33.333 3.22 0.00 39.84 2.90
3970 6019 8.964476 TGAAGTTTTCTGACTTTCTTATCTGT 57.036 30.769 0.00 0.00 39.84 3.41
3971 6020 9.396022 TGAAGTTTTCTGACTTTCTTATCTGTT 57.604 29.630 0.00 0.00 39.84 3.16
3972 6021 9.657121 GAAGTTTTCTGACTTTCTTATCTGTTG 57.343 33.333 0.00 0.00 39.84 3.33
3973 6022 7.643579 AGTTTTCTGACTTTCTTATCTGTTGC 58.356 34.615 0.00 0.00 0.00 4.17
3974 6023 7.500559 AGTTTTCTGACTTTCTTATCTGTTGCT 59.499 33.333 0.00 0.00 0.00 3.91
3975 6024 6.791887 TTCTGACTTTCTTATCTGTTGCTG 57.208 37.500 0.00 0.00 0.00 4.41
3976 6025 5.858381 TCTGACTTTCTTATCTGTTGCTGT 58.142 37.500 0.00 0.00 0.00 4.40
3977 6026 5.698089 TCTGACTTTCTTATCTGTTGCTGTG 59.302 40.000 0.00 0.00 0.00 3.66
3978 6027 4.756642 TGACTTTCTTATCTGTTGCTGTGG 59.243 41.667 0.00 0.00 0.00 4.17
3979 6028 4.074970 ACTTTCTTATCTGTTGCTGTGGG 58.925 43.478 0.00 0.00 0.00 4.61
3980 6029 3.788227 TTCTTATCTGTTGCTGTGGGT 57.212 42.857 0.00 0.00 0.00 4.51
3981 6030 4.901197 TTCTTATCTGTTGCTGTGGGTA 57.099 40.909 0.00 0.00 0.00 3.69
3982 6031 4.901197 TCTTATCTGTTGCTGTGGGTAA 57.099 40.909 0.00 0.00 0.00 2.85
4425 6474 5.163723 CGTGCCATTCTACACAATCTCATTT 60.164 40.000 0.00 0.00 36.57 2.32
5385 7436 1.063266 TCCAAGACAGCCCAAGGTTTT 60.063 47.619 0.00 0.00 0.00 2.43
5605 7657 7.926705 TCTGTAACCTACTCCTAAGTAAGTCT 58.073 38.462 0.00 0.00 37.53 3.24
5753 7805 1.160329 AGCAACACTCGTTCCACAGC 61.160 55.000 0.00 0.00 31.13 4.40
5983 8039 1.133790 CGTACTAACCTGGGAGAACGG 59.866 57.143 0.00 0.00 0.00 4.44
6014 8070 0.260230 TTTCCTGCCAAGGGTTGTGA 59.740 50.000 0.00 0.00 44.62 3.58
6207 8263 6.073314 AGCCAAGTAATGCAGATTATGGAAT 58.927 36.000 13.11 0.56 30.26 3.01
6236 8292 7.822713 TCGTTTGTTGATTGTTAATTTCGTTG 58.177 30.769 0.00 0.00 0.00 4.10
6238 8294 8.314635 CGTTTGTTGATTGTTAATTTCGTTGAA 58.685 29.630 0.00 0.00 0.00 2.69
6240 8296 8.918961 TTGTTGATTGTTAATTTCGTTGAAGT 57.081 26.923 0.00 0.00 0.00 3.01
6241 8297 8.918961 TGTTGATTGTTAATTTCGTTGAAGTT 57.081 26.923 0.00 0.00 0.00 2.66
6242 8298 8.802856 TGTTGATTGTTAATTTCGTTGAAGTTG 58.197 29.630 0.00 0.00 0.00 3.16
6247 8325 9.790389 ATTGTTAATTTCGTTGAAGTTGTTACA 57.210 25.926 0.00 0.00 0.00 2.41
6287 8365 3.380954 TGCAAACATGCCACTATGTATGG 59.619 43.478 0.00 0.00 40.24 2.74
6296 8374 6.493189 TGCCACTATGTATGGTCTTGATAA 57.507 37.500 0.00 0.00 39.63 1.75
6316 8394 9.814899 TTGATAATTTGATTCTCTCTCTCACTC 57.185 33.333 0.00 0.00 0.00 3.51
6321 8399 6.662865 TTGATTCTCTCTCTCACTCAAAGT 57.337 37.500 0.00 0.00 0.00 2.66
6322 8400 7.767250 TTGATTCTCTCTCTCACTCAAAGTA 57.233 36.000 0.00 0.00 0.00 2.24
6323 8401 7.953005 TGATTCTCTCTCTCACTCAAAGTAT 57.047 36.000 0.00 0.00 0.00 2.12
6324 8402 9.467796 TTGATTCTCTCTCTCACTCAAAGTATA 57.532 33.333 0.00 0.00 0.00 1.47
6325 8403 9.467796 TGATTCTCTCTCTCACTCAAAGTATAA 57.532 33.333 0.00 0.00 0.00 0.98
6405 8483 0.037877 ATCAGGGCCTGCATATGCTC 59.962 55.000 29.02 15.93 42.66 4.26
6406 8484 1.602888 CAGGGCCTGCATATGCTCC 60.603 63.158 27.13 22.60 42.66 4.70
6409 8487 0.322008 GGGCCTGCATATGCTCCTAC 60.322 60.000 27.13 13.76 42.66 3.18
6410 8488 0.397941 GGCCTGCATATGCTCCTACA 59.602 55.000 27.13 6.13 42.66 2.74
6411 8489 1.517242 GCCTGCATATGCTCCTACAC 58.483 55.000 27.13 7.34 42.66 2.90
6486 8580 0.787787 TTCTTCGTTGCGTTCATCGG 59.212 50.000 0.00 0.00 40.26 4.18
6491 8585 1.418342 CGTTGCGTTCATCGGGTAGG 61.418 60.000 0.00 0.00 40.26 3.18
6522 8616 5.180868 CACAGGAAAGAGGACAATGAGAAAG 59.819 44.000 0.00 0.00 0.00 2.62
6525 8619 4.520492 GGAAAGAGGACAATGAGAAAGCAA 59.480 41.667 0.00 0.00 0.00 3.91
6567 8662 6.569179 TCAATACAAAAGTCCTGTTTAGGC 57.431 37.500 0.00 0.00 44.22 3.93
6578 8673 0.813184 TGTTTAGGCGAGGGAGTACG 59.187 55.000 0.00 0.00 0.00 3.67
6764 8861 8.625651 TGTATTGCTTAGTCTCTTCTATCAGAC 58.374 37.037 0.00 0.00 39.58 3.51
6883 8986 3.443588 GCAAGTCTTTTGCCCGGT 58.556 55.556 0.00 0.00 39.38 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.960938 TCGAGAAATCATCCCCAAGTATG 58.039 43.478 0.00 0.00 0.00 2.39
52 53 5.243981 ACATGATCATCGAGAAATCATCCC 58.756 41.667 4.86 0.00 37.90 3.85
64 65 2.713895 AGAGCGGTACATGATCATCG 57.286 50.000 4.86 7.68 0.00 3.84
90 91 3.458118 CCACCATATTACTTGGGGACTCA 59.542 47.826 0.00 0.00 40.29 3.41
128 129 2.287427 ACGGGCTCGAGATGTAAATACG 60.287 50.000 15.95 8.35 40.11 3.06
138 139 1.886313 CTAGCGTACGGGCTCGAGA 60.886 63.158 15.95 0.00 43.54 4.04
148 149 2.022934 AGTCTACCAAGCCTAGCGTAC 58.977 52.381 0.00 0.00 0.00 3.67
177 178 3.631046 GCCCGCTCCCCTCCTATG 61.631 72.222 0.00 0.00 0.00 2.23
204 205 7.715686 AGAATTTAGGGTGGATCTAATTTCGTC 59.284 37.037 0.00 0.00 39.50 4.20
237 238 8.694540 ACATATTTGCTTAGTATTCCATTGCAA 58.305 29.630 0.00 0.00 37.20 4.08
238 239 8.236585 ACATATTTGCTTAGTATTCCATTGCA 57.763 30.769 0.00 0.00 0.00 4.08
294 295 9.462174 GATTCAGTGTGAAAATATCAAAACACA 57.538 29.630 6.53 0.00 40.12 3.72
295 296 9.683069 AGATTCAGTGTGAAAATATCAAAACAC 57.317 29.630 0.00 0.00 40.12 3.32
314 315 8.689061 TCACATTTCAATTTCCCATAGATTCAG 58.311 33.333 0.00 0.00 0.00 3.02
360 361 2.954989 TGCATAAACAAGAGTTGTGGCA 59.045 40.909 0.00 0.00 44.59 4.92
420 421 6.763135 TGAGAAAGTAGACATGGATAATGCAC 59.237 38.462 0.00 0.00 40.22 4.57
429 430 3.308053 CGCATGTGAGAAAGTAGACATGG 59.692 47.826 0.00 0.82 43.86 3.66
589 592 6.540551 TGCATTTACTCATTTTGCTCCGTATA 59.459 34.615 0.00 0.00 34.47 1.47
595 598 3.301642 GCGTGCATTTACTCATTTTGCTC 59.698 43.478 0.00 0.00 34.47 4.26
613 616 9.283420 CAGATGTATATAGACATTTAGAGCGTG 57.717 37.037 13.94 0.43 40.18 5.34
679 689 5.499004 AAATCAGCCACACTTACTTCCTA 57.501 39.130 0.00 0.00 0.00 2.94
681 691 5.246307 ACTAAATCAGCCACACTTACTTCC 58.754 41.667 0.00 0.00 0.00 3.46
686 696 6.553953 TCCATACTAAATCAGCCACACTTA 57.446 37.500 0.00 0.00 0.00 2.24
765 775 2.358247 GAACGGGTGCCACGTCAT 60.358 61.111 2.94 0.00 44.83 3.06
823 833 1.612442 ATGGGGAGTACGTGTGGCT 60.612 57.895 0.00 0.00 0.00 4.75
835 845 3.792736 CGGCTTTCGGGATGGGGA 61.793 66.667 0.00 0.00 34.75 4.81
836 846 3.120086 ATCGGCTTTCGGGATGGGG 62.120 63.158 0.00 0.00 39.77 4.96
918 931 2.038295 TGGCTGCGGGATTTTGAAATTT 59.962 40.909 0.00 0.00 0.00 1.82
939 952 4.537433 GATGGAGGCGCCGCTCTT 62.537 66.667 29.50 16.88 40.66 2.85
958 971 3.155167 GGGGAGCGGGTAGTGAGG 61.155 72.222 0.00 0.00 0.00 3.86
1101 1527 4.143333 AGATCGTGGAACCCGGCG 62.143 66.667 0.00 0.00 0.00 6.46
1102 1528 2.511600 CAGATCGTGGAACCCGGC 60.512 66.667 0.00 0.00 0.00 6.13
1103 1529 0.739813 GAACAGATCGTGGAACCCGG 60.740 60.000 0.00 0.00 0.00 5.73
1104 1530 1.076533 CGAACAGATCGTGGAACCCG 61.077 60.000 0.00 0.00 46.52 5.28
1105 1531 2.750815 CGAACAGATCGTGGAACCC 58.249 57.895 0.00 0.00 46.52 4.11
1477 1946 0.676466 AACCAGATCGCCAAATCGCA 60.676 50.000 0.00 0.00 0.00 5.10
1487 2044 0.798776 GGACAGCACAAACCAGATCG 59.201 55.000 0.00 0.00 0.00 3.69
1500 2057 1.216710 CTCCAAGTCTCCGGACAGC 59.783 63.158 0.00 0.00 44.36 4.40
1506 2063 1.279271 ACAAATCCCTCCAAGTCTCCG 59.721 52.381 0.00 0.00 0.00 4.63
1519 2076 5.420739 AGGAGAGAGTTAGTCTGACAAATCC 59.579 44.000 10.88 5.80 34.71 3.01
1520 2077 6.524101 AGGAGAGAGTTAGTCTGACAAATC 57.476 41.667 10.88 10.55 34.71 2.17
1524 2081 5.141182 ACAAAGGAGAGAGTTAGTCTGACA 58.859 41.667 10.88 0.00 34.71 3.58
1568 2946 1.811266 CGTTGGTGCTCCCGATCAG 60.811 63.158 1.59 0.00 35.15 2.90
1941 3931 1.340114 GGGAATGAACCGAGCTTTCCT 60.340 52.381 10.19 0.00 38.75 3.36
1947 3937 0.462759 CCTCAGGGAATGAACCGAGC 60.463 60.000 0.00 0.00 37.52 5.03
1962 3952 4.901197 TTGATGGTTACTTACTGCCTCA 57.099 40.909 0.00 0.00 0.00 3.86
1985 3975 2.988493 CAAATCACAGAAAACCGCATGG 59.012 45.455 0.00 0.00 42.84 3.66
2042 4032 9.976776 CCTAGTATACTTCCTAATGACCTGATA 57.023 37.037 11.40 0.00 0.00 2.15
2756 4779 6.037172 GCAGGCGGATAACTTATATACAATGG 59.963 42.308 0.00 0.00 0.00 3.16
2932 4957 2.156098 AGGTGCCATCCAGTGTGGT 61.156 57.895 2.04 0.00 39.03 4.16
3218 5247 1.760613 TCGTGCTTCCCCGAAATCTAT 59.239 47.619 0.00 0.00 0.00 1.98
3372 5401 6.430925 TCACAATAAGAAATACTGTTGCTGCT 59.569 34.615 0.00 0.00 32.14 4.24
3373 5402 6.611381 TCACAATAAGAAATACTGTTGCTGC 58.389 36.000 0.00 0.00 32.14 5.25
3374 5403 8.032952 TCTCACAATAAGAAATACTGTTGCTG 57.967 34.615 0.00 0.00 32.14 4.41
3375 5404 8.798859 ATCTCACAATAAGAAATACTGTTGCT 57.201 30.769 0.00 0.00 32.14 3.91
3949 5998 7.589221 CAGCAACAGATAAGAAAGTCAGAAAAC 59.411 37.037 0.00 0.00 0.00 2.43
3950 5999 7.283127 ACAGCAACAGATAAGAAAGTCAGAAAA 59.717 33.333 0.00 0.00 0.00 2.29
3951 6000 6.767902 ACAGCAACAGATAAGAAAGTCAGAAA 59.232 34.615 0.00 0.00 0.00 2.52
3952 6001 6.203530 CACAGCAACAGATAAGAAAGTCAGAA 59.796 38.462 0.00 0.00 0.00 3.02
3953 6002 5.698089 CACAGCAACAGATAAGAAAGTCAGA 59.302 40.000 0.00 0.00 0.00 3.27
3954 6003 5.106791 CCACAGCAACAGATAAGAAAGTCAG 60.107 44.000 0.00 0.00 0.00 3.51
3955 6004 4.756642 CCACAGCAACAGATAAGAAAGTCA 59.243 41.667 0.00 0.00 0.00 3.41
3956 6005 4.154918 CCCACAGCAACAGATAAGAAAGTC 59.845 45.833 0.00 0.00 0.00 3.01
3957 6006 4.074970 CCCACAGCAACAGATAAGAAAGT 58.925 43.478 0.00 0.00 0.00 2.66
3958 6007 4.074970 ACCCACAGCAACAGATAAGAAAG 58.925 43.478 0.00 0.00 0.00 2.62
3959 6008 4.098914 ACCCACAGCAACAGATAAGAAA 57.901 40.909 0.00 0.00 0.00 2.52
3960 6009 3.788227 ACCCACAGCAACAGATAAGAA 57.212 42.857 0.00 0.00 0.00 2.52
3961 6010 4.286032 ACTTACCCACAGCAACAGATAAGA 59.714 41.667 0.00 0.00 0.00 2.10
3962 6011 4.579869 ACTTACCCACAGCAACAGATAAG 58.420 43.478 0.00 0.00 0.00 1.73
3963 6012 4.634012 ACTTACCCACAGCAACAGATAA 57.366 40.909 0.00 0.00 0.00 1.75
3964 6013 4.634012 AACTTACCCACAGCAACAGATA 57.366 40.909 0.00 0.00 0.00 1.98
3965 6014 3.508845 AACTTACCCACAGCAACAGAT 57.491 42.857 0.00 0.00 0.00 2.90
3966 6015 3.290948 AAACTTACCCACAGCAACAGA 57.709 42.857 0.00 0.00 0.00 3.41
3967 6016 3.632145 AGAAAACTTACCCACAGCAACAG 59.368 43.478 0.00 0.00 0.00 3.16
3968 6017 3.380004 CAGAAAACTTACCCACAGCAACA 59.620 43.478 0.00 0.00 0.00 3.33
3969 6018 3.630312 TCAGAAAACTTACCCACAGCAAC 59.370 43.478 0.00 0.00 0.00 4.17
3970 6019 3.630312 GTCAGAAAACTTACCCACAGCAA 59.370 43.478 0.00 0.00 0.00 3.91
3971 6020 3.118038 AGTCAGAAAACTTACCCACAGCA 60.118 43.478 0.00 0.00 0.00 4.41
3972 6021 3.477530 AGTCAGAAAACTTACCCACAGC 58.522 45.455 0.00 0.00 0.00 4.40
3973 6022 5.823045 AGAAAGTCAGAAAACTTACCCACAG 59.177 40.000 0.00 0.00 38.52 3.66
3974 6023 5.751586 AGAAAGTCAGAAAACTTACCCACA 58.248 37.500 0.00 0.00 38.52 4.17
3975 6024 6.694877 AAGAAAGTCAGAAAACTTACCCAC 57.305 37.500 0.00 0.00 38.52 4.61
3976 6025 8.437575 AGATAAGAAAGTCAGAAAACTTACCCA 58.562 33.333 0.00 0.00 38.52 4.51
3977 6026 8.722394 CAGATAAGAAAGTCAGAAAACTTACCC 58.278 37.037 0.00 0.00 38.52 3.69
3978 6027 9.274206 ACAGATAAGAAAGTCAGAAAACTTACC 57.726 33.333 0.00 0.00 38.52 2.85
3981 6030 8.131731 GCAACAGATAAGAAAGTCAGAAAACTT 58.868 33.333 0.00 0.00 41.20 2.66
3982 6031 7.500559 AGCAACAGATAAGAAAGTCAGAAAACT 59.499 33.333 0.00 0.00 0.00 2.66
4425 6474 8.539770 TGCAGTGTCATAAAAAGAAAACAAAA 57.460 26.923 0.00 0.00 0.00 2.44
5152 7203 0.178926 TCCACGAGGGGGTAGTTTCA 60.179 55.000 0.00 0.00 37.22 2.69
5372 7423 4.157840 GGTATGTAAGAAAACCTTGGGCTG 59.842 45.833 0.00 0.00 36.34 4.85
5385 7436 5.419788 TCGAAGCAAGGTTAGGTATGTAAGA 59.580 40.000 0.00 0.00 0.00 2.10
5753 7805 4.713806 CACTGTATAGCTATCTTCGGTCG 58.286 47.826 10.16 5.41 0.00 4.79
5954 8010 2.611224 CCAGGTTAGTACGCCGTTCTTT 60.611 50.000 0.71 0.00 0.00 2.52
6014 8070 3.494251 GCACCGCAAAGAATGAAAAATGT 59.506 39.130 0.00 0.00 0.00 2.71
6233 8289 4.342772 CTGCACAGTGTAACAACTTCAAC 58.657 43.478 1.61 0.00 41.43 3.18
6236 8292 2.614057 AGCTGCACAGTGTAACAACTTC 59.386 45.455 1.02 0.00 41.43 3.01
6238 8294 1.942657 CAGCTGCACAGTGTAACAACT 59.057 47.619 0.00 0.00 41.43 3.16
6240 8296 2.036958 ACAGCTGCACAGTGTAACAA 57.963 45.000 15.27 0.00 41.43 2.83
6241 8297 2.900716 TACAGCTGCACAGTGTAACA 57.099 45.000 15.27 0.00 41.43 2.41
6242 8298 4.929808 AGTATTACAGCTGCACAGTGTAAC 59.070 41.667 15.27 12.81 37.54 2.50
6267 8345 4.883585 AGACCATACATAGTGGCATGTTTG 59.116 41.667 0.00 0.91 40.49 2.93
6287 8365 9.814899 TGAGAGAGAGAATCAAATTATCAAGAC 57.185 33.333 0.00 0.00 37.82 3.01
6296 8374 7.678837 ACTTTGAGTGAGAGAGAGAATCAAAT 58.321 34.615 0.00 0.00 37.82 2.32
6405 8483 5.215160 GTTTCTTCAGCAATGTTGTGTAGG 58.785 41.667 0.00 0.00 0.00 3.18
6406 8484 4.905866 CGTTTCTTCAGCAATGTTGTGTAG 59.094 41.667 0.00 0.00 0.00 2.74
6409 8487 3.694734 ACGTTTCTTCAGCAATGTTGTG 58.305 40.909 0.00 0.00 0.00 3.33
6410 8488 4.370364 AACGTTTCTTCAGCAATGTTGT 57.630 36.364 0.00 0.00 31.17 3.32
6411 8489 6.804534 TTAAACGTTTCTTCAGCAATGTTG 57.195 33.333 18.42 0.00 32.36 3.33
6472 8566 1.418342 CCTACCCGATGAACGCAACG 61.418 60.000 0.00 0.00 39.64 4.10
6477 8571 1.227263 CCTGCCTACCCGATGAACG 60.227 63.158 0.00 0.00 42.18 3.95
6486 8580 1.204146 TTCCTGTGATCCTGCCTACC 58.796 55.000 0.00 0.00 0.00 3.18
6491 8585 1.556911 TCCTCTTTCCTGTGATCCTGC 59.443 52.381 0.00 0.00 0.00 4.85
6522 8616 1.301677 CTGTCGCCCTCCTTCTTTGC 61.302 60.000 0.00 0.00 0.00 3.68
6525 8619 0.765510 AAACTGTCGCCCTCCTTCTT 59.234 50.000 0.00 0.00 0.00 2.52
6567 8662 1.396996 CCATTTTTGCGTACTCCCTCG 59.603 52.381 0.00 0.00 0.00 4.63
6578 8673 4.612943 TCAAGTCGTTAACCCATTTTTGC 58.387 39.130 0.00 0.00 0.00 3.68
6579 8674 6.067263 TCTCAAGTCGTTAACCCATTTTTG 57.933 37.500 0.00 0.00 0.00 2.44
6637 8733 4.894784 TCTTGTACAAGGACTTGGATGAC 58.105 43.478 30.35 8.70 44.45 3.06
6764 8861 1.605202 CCAATGCAACCAAAAGACCGG 60.605 52.381 0.00 0.00 0.00 5.28
7037 9210 6.380274 TGTGTTTTTGTTTAGTGTGGGGATTA 59.620 34.615 0.00 0.00 0.00 1.75
7044 9217 7.066505 GTGGTTTTGTGTTTTTGTTTAGTGTG 58.933 34.615 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.