Multiple sequence alignment - TraesCS5D01G254100

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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 TraesCS5D01G254100 chr5D 100.000 4894 0 0 1 4894 360771400 360766507 0.000000e+00 9038.0
1 TraesCS5D01G254100 chr5D 84.542 731 107 5 1167 1891 360895216 360894486 0.000000e+00 719.0
2 TraesCS5D01G254100 chr5D 83.854 768 97 16 1153 1898 491108651 491109413 0.000000e+00 706.0
3 TraesCS5D01G254100 chr5D 81.712 257 43 4 3450 3704 360885103 360884849 1.380000e-50 211.0
4 TraesCS5D01G254100 chr5A 93.559 2127 79 21 2255 4351 461586933 461584835 0.000000e+00 3116.0
5 TraesCS5D01G254100 chr5A 93.540 1161 60 6 857 2007 461588527 461587372 0.000000e+00 1714.0
6 TraesCS5D01G254100 chr5A 84.148 757 96 18 1161 1898 613568675 613569426 0.000000e+00 712.0
7 TraesCS5D01G254100 chr5A 78.846 364 69 8 4529 4887 405038409 405038049 6.330000e-59 239.0
8 TraesCS5D01G254100 chr5A 91.453 117 6 3 729 842 461588617 461588502 1.820000e-34 158.0
9 TraesCS5D01G254100 chr5B 95.783 1162 39 4 861 2015 426134656 426133498 0.000000e+00 1866.0
10 TraesCS5D01G254100 chr5B 90.951 873 75 4 1025 1894 426366492 426365621 0.000000e+00 1171.0
11 TraesCS5D01G254100 chr5B 85.265 1113 108 30 3010 4096 426132045 426130963 0.000000e+00 1096.0
12 TraesCS5D01G254100 chr5B 84.514 762 97 15 1153 1898 605851828 605852584 0.000000e+00 734.0
13 TraesCS5D01G254100 chr5B 94.209 449 20 2 2516 2958 426133015 426132567 0.000000e+00 680.0
14 TraesCS5D01G254100 chr5B 91.522 460 27 5 2071 2529 426133481 426133033 1.500000e-174 623.0
15 TraesCS5D01G254100 chr3D 98.047 717 14 0 1 717 580342824 580342108 0.000000e+00 1247.0
16 TraesCS5D01G254100 chr3D 91.492 717 61 0 1 717 591188410 591187694 0.000000e+00 987.0
17 TraesCS5D01G254100 chr2A 90.922 683 62 0 36 718 712824102 712823420 0.000000e+00 918.0
18 TraesCS5D01G254100 chr2A 90.630 683 64 0 36 718 712835352 712834670 0.000000e+00 907.0
19 TraesCS5D01G254100 chr2A 91.439 549 40 4 4350 4894 17668126 17668671 0.000000e+00 747.0
20 TraesCS5D01G254100 chr3A 86.878 724 87 7 1 717 657224786 657225508 0.000000e+00 804.0
21 TraesCS5D01G254100 chr2B 90.500 600 57 0 118 717 54241043 54240444 0.000000e+00 793.0
22 TraesCS5D01G254100 chr2B 83.288 742 102 17 1150 1883 793881960 793882687 0.000000e+00 664.0
23 TraesCS5D01G254100 chr2B 85.599 618 84 4 107 719 631800453 631799836 1.150000e-180 643.0
24 TraesCS5D01G254100 chr2D 86.565 722 75 10 1 718 489058930 489059633 0.000000e+00 776.0
25 TraesCS5D01G254100 chr2D 84.085 377 44 13 1236 1598 513100595 513100221 2.800000e-92 350.0
26 TraesCS5D01G254100 chr7A 86.034 716 95 4 4 716 520893605 520892892 0.000000e+00 763.0
27 TraesCS5D01G254100 chr6A 75.844 563 102 25 4351 4894 610797956 610797409 6.290000e-64 255.0
28 TraesCS5D01G254100 chr4A 82.328 232 40 1 4657 4887 646321364 646321133 2.990000e-47 200.0
29 TraesCS5D01G254100 chr7B 96.364 55 2 0 4779 4833 21308365 21308419 1.880000e-14 91.6


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 TraesCS5D01G254100 chr5D 360766507 360771400 4893 True 9038.000000 9038 100.000000 1 4894 1 chr5D.!!$R1 4893
1 TraesCS5D01G254100 chr5D 360894486 360895216 730 True 719.000000 719 84.542000 1167 1891 1 chr5D.!!$R3 724
2 TraesCS5D01G254100 chr5D 491108651 491109413 762 False 706.000000 706 83.854000 1153 1898 1 chr5D.!!$F1 745
3 TraesCS5D01G254100 chr5A 461584835 461588617 3782 True 1662.666667 3116 92.850667 729 4351 3 chr5A.!!$R2 3622
4 TraesCS5D01G254100 chr5A 613568675 613569426 751 False 712.000000 712 84.148000 1161 1898 1 chr5A.!!$F1 737
5 TraesCS5D01G254100 chr5B 426365621 426366492 871 True 1171.000000 1171 90.951000 1025 1894 1 chr5B.!!$R1 869
6 TraesCS5D01G254100 chr5B 426130963 426134656 3693 True 1066.250000 1866 91.694750 861 4096 4 chr5B.!!$R2 3235
7 TraesCS5D01G254100 chr5B 605851828 605852584 756 False 734.000000 734 84.514000 1153 1898 1 chr5B.!!$F1 745
8 TraesCS5D01G254100 chr3D 580342108 580342824 716 True 1247.000000 1247 98.047000 1 717 1 chr3D.!!$R1 716
9 TraesCS5D01G254100 chr3D 591187694 591188410 716 True 987.000000 987 91.492000 1 717 1 chr3D.!!$R2 716
10 TraesCS5D01G254100 chr2A 712823420 712824102 682 True 918.000000 918 90.922000 36 718 1 chr2A.!!$R1 682
11 TraesCS5D01G254100 chr2A 712834670 712835352 682 True 907.000000 907 90.630000 36 718 1 chr2A.!!$R2 682
12 TraesCS5D01G254100 chr2A 17668126 17668671 545 False 747.000000 747 91.439000 4350 4894 1 chr2A.!!$F1 544
13 TraesCS5D01G254100 chr3A 657224786 657225508 722 False 804.000000 804 86.878000 1 717 1 chr3A.!!$F1 716
14 TraesCS5D01G254100 chr2B 54240444 54241043 599 True 793.000000 793 90.500000 118 717 1 chr2B.!!$R1 599
15 TraesCS5D01G254100 chr2B 793881960 793882687 727 False 664.000000 664 83.288000 1150 1883 1 chr2B.!!$F1 733
16 TraesCS5D01G254100 chr2B 631799836 631800453 617 True 643.000000 643 85.599000 107 719 1 chr2B.!!$R2 612
17 TraesCS5D01G254100 chr2D 489058930 489059633 703 False 776.000000 776 86.565000 1 718 1 chr2D.!!$F1 717
18 TraesCS5D01G254100 chr7A 520892892 520893605 713 True 763.000000 763 86.034000 4 716 1 chr7A.!!$R1 712
19 TraesCS5D01G254100 chr6A 610797409 610797956 547 True 255.000000 255 75.844000 4351 4894 1 chr6A.!!$R1 543

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
983 993 0.386858 CGGCAGTATATAGCGCACGT 60.387 55.000 11.47 0.00 0.00 4.49 F
1103 1125 1.228245 GGAGGTGGAAGCAACAGCA 60.228 57.895 7.14 0.00 38.72 4.41 F
2036 2107 0.036105 TGCATCACTCGCACCATCTT 60.036 50.000 0.00 0.00 33.55 2.40 F
2867 3195 0.108992 TGGGAAAGCTACGCGTACAG 60.109 55.000 16.41 10.06 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2088 0.036105 AAGATGGTGCGAGTGATGCA 60.036 50.0 0.00 0.0 40.70 3.96 R
2067 2138 0.249398 GTCACAGGGAGCCAACGTAT 59.751 55.0 0.00 0.0 0.00 3.06 R
3127 3942 0.610232 AGCCTGAAGGATGCACAACC 60.610 55.0 0.00 0.0 37.39 3.77 R
4067 4900 0.889994 TCCAATTCACATGCTGCACC 59.110 50.0 3.57 0.0 0.00 5.01 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
298 303 1.819903 GTATGGTCCTCCGAGATAGCC 59.180 57.143 0.00 0.00 36.30 3.93
304 309 0.470080 CCTCCGAGATAGCCAGGGAA 60.470 60.000 0.00 0.00 0.00 3.97
367 372 1.323271 TGCTCTGGAGGCGGAACTAG 61.323 60.000 0.00 0.00 0.00 2.57
665 671 5.182001 CAGAGGTCCTTGAACTTTGTAATGG 59.818 44.000 0.00 0.00 28.58 3.16
748 754 7.344352 CCCCCTTAGTTTTCCATGATTTATCAA 59.656 37.037 0.00 0.00 40.69 2.57
756 762 5.895636 TCCATGATTTATCAAAGCGTTGT 57.104 34.783 12.18 2.93 40.69 3.32
763 769 5.554822 TTTATCAAAGCGTTGTGGTATCC 57.445 39.130 12.18 0.00 36.07 2.59
773 779 1.771565 TGTGGTATCCAGAGTACCGG 58.228 55.000 0.00 0.00 43.65 5.28
811 817 4.899239 GCACCGGATGCGCTAGCT 62.899 66.667 9.46 0.00 46.55 3.32
829 836 1.403814 CTCTCGCAGGGACCTTATCA 58.596 55.000 0.00 0.00 0.00 2.15
830 837 1.967066 CTCTCGCAGGGACCTTATCAT 59.033 52.381 0.00 0.00 0.00 2.45
831 838 1.688735 TCTCGCAGGGACCTTATCATG 59.311 52.381 0.00 0.00 0.00 3.07
832 839 1.414181 CTCGCAGGGACCTTATCATGT 59.586 52.381 0.00 0.00 0.00 3.21
833 840 1.837439 TCGCAGGGACCTTATCATGTT 59.163 47.619 0.00 0.00 0.00 2.71
834 841 2.238646 TCGCAGGGACCTTATCATGTTT 59.761 45.455 0.00 0.00 0.00 2.83
835 842 2.355756 CGCAGGGACCTTATCATGTTTG 59.644 50.000 0.00 0.00 0.00 2.93
836 843 3.356290 GCAGGGACCTTATCATGTTTGT 58.644 45.455 0.00 0.00 0.00 2.83
837 844 3.763897 GCAGGGACCTTATCATGTTTGTT 59.236 43.478 0.00 0.00 0.00 2.83
838 845 4.220602 GCAGGGACCTTATCATGTTTGTTT 59.779 41.667 0.00 0.00 0.00 2.83
839 846 5.713025 CAGGGACCTTATCATGTTTGTTTG 58.287 41.667 0.00 0.00 0.00 2.93
840 847 5.243730 CAGGGACCTTATCATGTTTGTTTGT 59.756 40.000 0.00 0.00 0.00 2.83
841 848 5.838521 AGGGACCTTATCATGTTTGTTTGTT 59.161 36.000 0.00 0.00 0.00 2.83
842 849 6.326323 AGGGACCTTATCATGTTTGTTTGTTT 59.674 34.615 0.00 0.00 0.00 2.83
843 850 6.423604 GGGACCTTATCATGTTTGTTTGTTTG 59.576 38.462 0.00 0.00 0.00 2.93
844 851 6.983890 GGACCTTATCATGTTTGTTTGTTTGT 59.016 34.615 0.00 0.00 0.00 2.83
845 852 7.494298 GGACCTTATCATGTTTGTTTGTTTGTT 59.506 33.333 0.00 0.00 0.00 2.83
846 853 8.785329 ACCTTATCATGTTTGTTTGTTTGTTT 57.215 26.923 0.00 0.00 0.00 2.83
847 854 9.225436 ACCTTATCATGTTTGTTTGTTTGTTTT 57.775 25.926 0.00 0.00 0.00 2.43
979 989 3.374330 CGCGGCAGTATATAGCGC 58.626 61.111 0.00 0.00 44.19 5.92
980 990 1.443702 CGCGGCAGTATATAGCGCA 60.444 57.895 11.47 0.00 44.19 6.09
983 993 0.386858 CGGCAGTATATAGCGCACGT 60.387 55.000 11.47 0.00 0.00 4.49
986 996 1.903139 GCAGTATATAGCGCACGTACG 59.097 52.381 15.01 15.01 0.00 3.67
987 997 2.502876 CAGTATATAGCGCACGTACGG 58.497 52.381 21.06 9.73 0.00 4.02
1007 1017 1.660264 TACTCACACTGTGCACGCG 60.660 57.895 13.13 3.53 32.98 6.01
1022 1032 3.839432 GCGCCCTCGTCCTAGCTT 61.839 66.667 0.00 0.00 38.14 3.74
1024 1034 2.501610 GCCCTCGTCCTAGCTTGG 59.498 66.667 8.03 8.03 0.00 3.61
1034 1044 3.326578 TAGCTTGGAGCCGGGCAA 61.327 61.111 23.09 5.91 43.77 4.52
1103 1125 1.228245 GGAGGTGGAAGCAACAGCA 60.228 57.895 7.14 0.00 38.72 4.41
1140 1162 3.055719 AACCATGCAAGGACGGCG 61.056 61.111 16.33 4.80 0.00 6.46
1296 1321 1.294780 CGAAAGTGGCTCTCCAGCT 59.705 57.895 0.00 0.00 46.03 4.24
1380 1414 2.250939 CGGAGCAACAAAGACGGCA 61.251 57.895 0.00 0.00 0.00 5.69
2015 2086 2.551270 CAGAACCGCGTGACTTGC 59.449 61.111 4.92 0.00 0.00 4.01
2017 2088 1.301716 AGAACCGCGTGACTTGCAT 60.302 52.632 4.92 0.00 0.00 3.96
2018 2089 1.154413 GAACCGCGTGACTTGCATG 60.154 57.895 4.92 0.00 36.56 4.06
2025 2096 0.800631 CGTGACTTGCATGCATCACT 59.199 50.000 34.51 16.38 39.45 3.41
2026 2097 1.201998 CGTGACTTGCATGCATCACTC 60.202 52.381 34.51 22.08 39.45 3.51
2028 2099 0.247974 GACTTGCATGCATCACTCGC 60.248 55.000 23.37 3.44 0.00 5.03
2031 2102 1.925415 TTGCATGCATCACTCGCACC 61.925 55.000 23.37 0.00 43.35 5.01
2032 2103 2.400962 GCATGCATCACTCGCACCA 61.401 57.895 14.21 0.00 43.35 4.17
2033 2104 1.721664 GCATGCATCACTCGCACCAT 61.722 55.000 14.21 0.00 43.35 3.55
2034 2105 0.306840 CATGCATCACTCGCACCATC 59.693 55.000 0.00 0.00 43.35 3.51
2035 2106 0.179702 ATGCATCACTCGCACCATCT 59.820 50.000 0.00 0.00 43.35 2.90
2036 2107 0.036105 TGCATCACTCGCACCATCTT 60.036 50.000 0.00 0.00 33.55 2.40
2039 2110 2.349590 CATCACTCGCACCATCTTTCA 58.650 47.619 0.00 0.00 0.00 2.69
2040 2111 2.768253 TCACTCGCACCATCTTTCAT 57.232 45.000 0.00 0.00 0.00 2.57
2041 2112 2.349590 TCACTCGCACCATCTTTCATG 58.650 47.619 0.00 0.00 0.00 3.07
2042 2113 1.399440 CACTCGCACCATCTTTCATGG 59.601 52.381 0.00 0.00 44.54 3.66
2043 2114 1.019673 CTCGCACCATCTTTCATGGG 58.980 55.000 5.62 0.00 43.32 4.00
2044 2115 0.617935 TCGCACCATCTTTCATGGGA 59.382 50.000 5.62 0.00 43.32 4.37
2045 2116 1.004161 TCGCACCATCTTTCATGGGAA 59.996 47.619 5.62 0.00 43.32 3.97
2046 2117 1.402968 CGCACCATCTTTCATGGGAAG 59.597 52.381 5.62 0.00 43.32 3.46
2047 2118 1.753073 GCACCATCTTTCATGGGAAGG 59.247 52.381 5.62 6.85 43.32 3.46
2048 2119 1.753073 CACCATCTTTCATGGGAAGGC 59.247 52.381 5.62 0.00 43.32 4.35
2050 2121 1.753073 CCATCTTTCATGGGAAGGCAC 59.247 52.381 9.06 0.00 35.58 5.01
2051 2122 1.753073 CATCTTTCATGGGAAGGCACC 59.247 52.381 9.06 0.00 33.82 5.01
2052 2123 0.776810 TCTTTCATGGGAAGGCACCA 59.223 50.000 9.06 0.86 43.22 4.17
2055 2126 1.559368 TTCATGGGAAGGCACCATTG 58.441 50.000 5.76 1.96 46.25 2.82
2057 2128 0.974010 CATGGGAAGGCACCATTGCT 60.974 55.000 5.76 0.00 46.25 3.91
2058 2129 0.974010 ATGGGAAGGCACCATTGCTG 60.974 55.000 2.98 0.00 46.25 4.41
2085 2156 0.249120 CATACGTTGGCTCCCTGTGA 59.751 55.000 0.00 0.00 0.00 3.58
2127 2372 1.928868 CCCATCTTGGCTTCCAGTTT 58.071 50.000 0.00 0.00 35.79 2.66
2139 2384 1.966451 CCAGTTTCACCGACTGCCC 60.966 63.158 0.00 0.00 42.42 5.36
2226 2517 9.198475 TCTACTAACTTTAGTAAATAGCAGGCT 57.802 33.333 9.58 0.00 43.47 4.58
2246 2537 4.991687 GGCTCCTCCGATCTAAAATAAGTG 59.008 45.833 0.00 0.00 0.00 3.16
2261 2552 6.767524 AAATAAGTGTATCGCCCATTTTCA 57.232 33.333 0.00 0.00 0.00 2.69
2292 2583 7.094162 TGTTCACAACAAAGTTACCATTTCTGA 60.094 33.333 0.00 0.00 38.72 3.27
2601 2923 7.013655 ACCATAAATGCCAGTGATGTAGATTTC 59.986 37.037 0.00 0.00 0.00 2.17
2622 2944 0.261696 ACCTTCCCTTGGCAAGTTGT 59.738 50.000 24.57 11.48 0.00 3.32
2867 3195 0.108992 TGGGAAAGCTACGCGTACAG 60.109 55.000 16.41 10.06 0.00 2.74
2971 3782 4.553330 TTCATGGACCTAACCTCACTTC 57.447 45.455 0.00 0.00 0.00 3.01
3002 3813 6.992123 ACTTCACAACTCACATAGTTCATCAA 59.008 34.615 0.00 0.00 45.64 2.57
3088 3900 5.646467 TTTTCTTCTTACGTTTCAGTCGG 57.354 39.130 0.00 0.00 0.00 4.79
3090 3902 2.295349 TCTTCTTACGTTTCAGTCGGCT 59.705 45.455 0.00 0.00 0.00 5.52
3127 3942 6.645827 TGATTTGATTTTGTGGCATGTACAAG 59.354 34.615 14.39 0.00 39.03 3.16
3276 4092 5.551760 AGCCGATTGTGACTTAGATTTTG 57.448 39.130 0.00 0.00 0.00 2.44
3279 4095 5.795441 GCCGATTGTGACTTAGATTTTGTTC 59.205 40.000 0.00 0.00 0.00 3.18
3355 4186 9.433317 CAATGAAGATACATAATTTTAACGCGT 57.567 29.630 5.58 5.58 0.00 6.01
3660 4491 1.372087 GATCCGAGCCAAGGCACAAG 61.372 60.000 14.40 1.68 44.88 3.16
3713 4544 6.823286 TTGGACCCTTAGATGATCATACAA 57.177 37.500 8.54 4.82 0.00 2.41
4067 4900 3.616219 TCTGTTAATGAATGGTTCCCCG 58.384 45.455 0.00 0.00 0.00 5.73
4093 4926 4.096833 GCAGCATGTGAATTGGATTAGACA 59.903 41.667 0.00 0.00 39.31 3.41
4095 4928 6.682113 GCAGCATGTGAATTGGATTAGACAAT 60.682 38.462 0.00 0.00 38.16 2.71
4097 4930 7.762615 CAGCATGTGAATTGGATTAGACAATTT 59.237 33.333 5.06 0.00 45.60 1.82
4098 4931 8.316214 AGCATGTGAATTGGATTAGACAATTTT 58.684 29.630 5.06 0.00 45.60 1.82
4099 4932 8.938906 GCATGTGAATTGGATTAGACAATTTTT 58.061 29.630 5.06 0.00 45.60 1.94
4203 5040 3.814268 CGGAATGGGTTGCGCCAG 61.814 66.667 4.18 0.00 42.10 4.85
4246 5084 1.773635 CCCCAGGTGGATTTGGTCA 59.226 57.895 0.00 0.00 37.39 4.02
4332 5172 2.392662 TGCAACAAGGGAAATGGTTGA 58.607 42.857 7.48 0.00 42.34 3.18
4334 5174 3.390639 TGCAACAAGGGAAATGGTTGATT 59.609 39.130 7.48 0.00 42.34 2.57
4342 5182 6.803587 AGGGAAATGGTTGATTATCCCTAT 57.196 37.500 9.37 0.00 43.21 2.57
4385 5225 5.571251 CGGTAAACCCCCTCTAAACACATTA 60.571 44.000 0.00 0.00 0.00 1.90
4392 5232 5.398581 CCCCCTCTAAACACATTAATGGCTA 60.399 44.000 19.37 4.58 0.00 3.93
4412 5252 5.783875 GGCTAAGATTACTCCATACCCCTTA 59.216 44.000 0.00 0.00 0.00 2.69
4413 5253 6.271624 GGCTAAGATTACTCCATACCCCTTAA 59.728 42.308 0.00 0.00 0.00 1.85
4414 5254 7.037514 GGCTAAGATTACTCCATACCCCTTAAT 60.038 40.741 0.00 0.00 0.00 1.40
4415 5255 9.043548 GCTAAGATTACTCCATACCCCTTAATA 57.956 37.037 0.00 0.00 0.00 0.98
4443 5283 5.712152 AAAGGACATGATGGTCTTTGTTC 57.288 39.130 12.21 0.00 37.20 3.18
4444 5284 4.371624 AGGACATGATGGTCTTTGTTCA 57.628 40.909 0.00 0.00 37.91 3.18
4445 5285 4.927049 AGGACATGATGGTCTTTGTTCAT 58.073 39.130 0.00 0.00 37.91 2.57
4477 5317 1.605457 CGTGCTAAGAACTCTGGCACA 60.605 52.381 24.58 4.33 46.71 4.57
4581 5436 4.321899 CCTTTCAATGGGAGAAAAATCGCA 60.322 41.667 0.00 0.00 44.96 5.10
4585 5440 6.791028 TTTCAATGGGAGAAAAATCGCAAGAG 60.791 38.462 0.00 0.00 44.19 2.85
4616 5471 1.133025 CAATGGGAATCGAACCTGCAC 59.867 52.381 10.93 0.00 0.00 4.57
4634 5489 2.546665 CACGTTCGAGTTAAAAGCACG 58.453 47.619 0.00 0.00 0.00 5.34
4637 5493 2.717893 CGTTCGAGTTAAAAGCACGCTC 60.718 50.000 0.00 0.00 0.00 5.03
4648 5504 2.813908 CACGCTCCGCTAACCACC 60.814 66.667 0.00 0.00 0.00 4.61
4676 5532 4.558178 TGCCAATTTGCTGTGTTAGATTG 58.442 39.130 2.90 0.00 0.00 2.67
4732 5588 7.684489 CGCGACAAAATTTAAAACAAAAGTTCA 59.316 29.630 0.00 0.00 0.00 3.18
4776 5632 3.633525 TGTGCAATAGGGATCAAATCAGC 59.366 43.478 0.00 0.00 0.00 4.26
4833 5692 6.672657 ACTATACTAACTGGGATTTGGTGTCT 59.327 38.462 0.00 0.00 0.00 3.41
4863 5724 5.174395 GCAGCCAGTCTATATGAACCATAG 58.826 45.833 0.00 0.00 29.42 2.23
4879 5740 6.153680 TGAACCATAGGCCGTGAAATTATTTT 59.846 34.615 12.15 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 4.810191 TGCAACAACCTGTTTACCTTTT 57.190 36.364 0.00 0.00 38.77 2.27
298 303 9.053840 GCATGATGTATATATGATCTTTCCCTG 57.946 37.037 0.00 0.00 0.00 4.45
304 309 8.328055 TCCCTGCATGATGTATATATGATCTT 57.672 34.615 0.00 0.00 0.00 2.40
367 372 0.839946 AGACCCTCCATACATGCACC 59.160 55.000 0.00 0.00 0.00 5.01
504 509 5.087323 AGACTCCTCAGGTACTTGATTTCA 58.913 41.667 8.28 0.00 34.60 2.69
719 725 3.537337 TCATGGAAAACTAAGGGGGAGA 58.463 45.455 0.00 0.00 0.00 3.71
720 726 4.526438 ATCATGGAAAACTAAGGGGGAG 57.474 45.455 0.00 0.00 0.00 4.30
721 727 4.965283 AATCATGGAAAACTAAGGGGGA 57.035 40.909 0.00 0.00 0.00 4.81
722 728 6.838612 TGATAAATCATGGAAAACTAAGGGGG 59.161 38.462 0.00 0.00 0.00 5.40
723 729 7.896383 TGATAAATCATGGAAAACTAAGGGG 57.104 36.000 0.00 0.00 0.00 4.79
724 730 9.807649 CTTTGATAAATCATGGAAAACTAAGGG 57.192 33.333 0.00 0.00 36.56 3.95
725 731 9.305925 GCTTTGATAAATCATGGAAAACTAAGG 57.694 33.333 0.00 0.00 36.56 2.69
726 732 9.013490 CGCTTTGATAAATCATGGAAAACTAAG 57.987 33.333 0.00 0.00 36.56 2.18
727 733 8.519526 ACGCTTTGATAAATCATGGAAAACTAA 58.480 29.630 0.00 0.00 36.56 2.24
748 754 1.623811 ACTCTGGATACCACAACGCTT 59.376 47.619 0.00 0.00 0.00 4.68
756 762 0.632835 ACCCGGTACTCTGGATACCA 59.367 55.000 0.00 0.00 42.03 3.25
763 769 2.126071 CGTGCACCCGGTACTCTG 60.126 66.667 12.15 0.00 0.00 3.35
773 779 2.896801 CTGTGTCCTTGCGTGCACC 61.897 63.158 12.15 4.74 0.00 5.01
811 817 1.688735 CATGATAAGGTCCCTGCGAGA 59.311 52.381 0.00 0.00 0.00 4.04
846 853 7.466804 ACATGATAAGGTCCCTCAAGTAAAAA 58.533 34.615 0.00 0.00 0.00 1.94
847 854 7.027874 ACATGATAAGGTCCCTCAAGTAAAA 57.972 36.000 0.00 0.00 0.00 1.52
848 855 6.636454 ACATGATAAGGTCCCTCAAGTAAA 57.364 37.500 0.00 0.00 0.00 2.01
849 856 6.214615 TCAACATGATAAGGTCCCTCAAGTAA 59.785 38.462 0.00 0.00 0.00 2.24
850 857 5.724370 TCAACATGATAAGGTCCCTCAAGTA 59.276 40.000 0.00 0.00 0.00 2.24
851 858 4.536090 TCAACATGATAAGGTCCCTCAAGT 59.464 41.667 0.00 0.00 0.00 3.16
852 859 5.102953 TCAACATGATAAGGTCCCTCAAG 57.897 43.478 0.00 0.00 0.00 3.02
853 860 5.715439 ATCAACATGATAAGGTCCCTCAA 57.285 39.130 0.00 0.00 34.88 3.02
854 861 5.044919 ACAATCAACATGATAAGGTCCCTCA 60.045 40.000 0.00 0.00 35.76 3.86
855 862 5.440610 ACAATCAACATGATAAGGTCCCTC 58.559 41.667 0.00 0.00 35.76 4.30
856 863 5.456921 ACAATCAACATGATAAGGTCCCT 57.543 39.130 0.00 0.00 35.76 4.20
857 864 5.888161 AGAACAATCAACATGATAAGGTCCC 59.112 40.000 0.00 0.00 35.76 4.46
858 865 7.987458 TCTAGAACAATCAACATGATAAGGTCC 59.013 37.037 0.00 0.00 35.76 4.46
859 866 8.948631 TCTAGAACAATCAACATGATAAGGTC 57.051 34.615 0.00 0.00 35.76 3.85
978 988 0.730494 GTGTGAGTACCCGTACGTGC 60.730 60.000 15.21 0.00 40.80 5.34
979 989 0.877071 AGTGTGAGTACCCGTACGTG 59.123 55.000 15.21 5.13 40.80 4.49
980 990 0.877071 CAGTGTGAGTACCCGTACGT 59.123 55.000 15.21 0.00 40.80 3.57
983 993 0.599558 GCACAGTGTGAGTACCCGTA 59.400 55.000 27.37 0.00 35.23 4.02
986 996 0.944311 CGTGCACAGTGTGAGTACCC 60.944 60.000 27.37 8.34 35.23 3.69
987 997 1.557443 GCGTGCACAGTGTGAGTACC 61.557 60.000 27.37 9.08 35.23 3.34
1007 1017 2.022240 CTCCAAGCTAGGACGAGGGC 62.022 65.000 0.00 0.00 33.19 5.19
1022 1032 4.344865 GGAAGTTGCCCGGCTCCA 62.345 66.667 11.61 0.00 0.00 3.86
1034 1044 1.140772 GGTTTGGGAGGGAGGGAAGT 61.141 60.000 0.00 0.00 0.00 3.01
1798 1869 0.749049 CTGCATCTCCATGACGAGGA 59.251 55.000 0.00 0.00 30.57 3.71
2015 2086 0.306840 GATGGTGCGAGTGATGCATG 59.693 55.000 2.46 0.00 45.34 4.06
2017 2088 0.036105 AAGATGGTGCGAGTGATGCA 60.036 50.000 0.00 0.00 40.70 3.96
2018 2089 1.063174 GAAAGATGGTGCGAGTGATGC 59.937 52.381 0.00 0.00 0.00 3.91
2019 2090 2.349590 TGAAAGATGGTGCGAGTGATG 58.650 47.619 0.00 0.00 0.00 3.07
2020 2091 2.768253 TGAAAGATGGTGCGAGTGAT 57.232 45.000 0.00 0.00 0.00 3.06
2021 2092 2.349590 CATGAAAGATGGTGCGAGTGA 58.650 47.619 0.00 0.00 0.00 3.41
2022 2093 1.399440 CCATGAAAGATGGTGCGAGTG 59.601 52.381 0.00 0.00 34.56 3.51
2023 2094 1.679944 CCCATGAAAGATGGTGCGAGT 60.680 52.381 0.00 0.00 37.48 4.18
2025 2096 0.617935 TCCCATGAAAGATGGTGCGA 59.382 50.000 0.00 0.00 37.48 5.10
2026 2097 1.402968 CTTCCCATGAAAGATGGTGCG 59.597 52.381 0.00 0.00 37.48 5.34
2028 2099 1.753073 GCCTTCCCATGAAAGATGGTG 59.247 52.381 8.81 0.00 37.48 4.17
2031 2102 1.753073 GGTGCCTTCCCATGAAAGATG 59.247 52.381 8.81 0.00 0.00 2.90
2032 2103 1.358787 TGGTGCCTTCCCATGAAAGAT 59.641 47.619 8.81 0.00 0.00 2.40
2033 2104 0.776810 TGGTGCCTTCCCATGAAAGA 59.223 50.000 8.81 0.00 0.00 2.52
2034 2105 1.856629 ATGGTGCCTTCCCATGAAAG 58.143 50.000 0.00 0.00 41.17 2.62
2035 2106 1.901159 CAATGGTGCCTTCCCATGAAA 59.099 47.619 0.00 0.00 41.87 2.69
2036 2107 1.559368 CAATGGTGCCTTCCCATGAA 58.441 50.000 0.00 0.00 41.87 2.57
2039 2110 4.039042 GCAATGGTGCCTTCCCAT 57.961 55.556 0.00 0.00 45.68 4.00
2048 2119 1.805254 GCTAGTGCCAGCAATGGTG 59.195 57.895 5.31 5.31 41.40 4.17
2055 2126 0.652592 CAACGTATGCTAGTGCCAGC 59.347 55.000 0.00 0.00 42.15 4.85
2057 2128 0.742990 GCCAACGTATGCTAGTGCCA 60.743 55.000 0.00 0.00 38.71 4.92
2058 2129 0.462047 AGCCAACGTATGCTAGTGCC 60.462 55.000 9.76 0.00 35.69 5.01
2060 2131 1.571919 GGAGCCAACGTATGCTAGTG 58.428 55.000 11.29 0.00 38.11 2.74
2063 2134 0.464036 CAGGGAGCCAACGTATGCTA 59.536 55.000 11.29 0.00 38.11 3.49
2064 2135 1.221840 CAGGGAGCCAACGTATGCT 59.778 57.895 11.14 11.14 41.42 3.79
2067 2138 0.249398 GTCACAGGGAGCCAACGTAT 59.751 55.000 0.00 0.00 0.00 3.06
2068 2139 1.669440 GTCACAGGGAGCCAACGTA 59.331 57.895 0.00 0.00 0.00 3.57
2069 2140 2.426023 GTCACAGGGAGCCAACGT 59.574 61.111 0.00 0.00 0.00 3.99
2085 2156 1.683441 GATCGGAAAGGGTGGTGGT 59.317 57.895 0.00 0.00 0.00 4.16
2139 2384 2.280628 CGCTAGTTTTAGAAGCTGGGG 58.719 52.381 0.00 0.00 34.03 4.96
2178 2469 9.751542 GTAGAGTTATAGTTGCTGTTACATGAT 57.248 33.333 0.00 0.00 0.00 2.45
2179 2470 8.967918 AGTAGAGTTATAGTTGCTGTTACATGA 58.032 33.333 0.00 0.00 0.00 3.07
2223 2514 4.991687 CACTTATTTTAGATCGGAGGAGCC 59.008 45.833 0.00 0.00 0.00 4.70
2224 2515 5.602628 ACACTTATTTTAGATCGGAGGAGC 58.397 41.667 0.00 0.00 0.00 4.70
2226 2517 7.591165 CGATACACTTATTTTAGATCGGAGGA 58.409 38.462 0.00 0.00 33.00 3.71
2246 2537 4.805219 ACAAGTTTGAAAATGGGCGATAC 58.195 39.130 0.00 0.00 0.00 2.24
2278 2569 6.156256 TGCTGTACCTATCAGAAATGGTAACT 59.844 38.462 0.00 0.00 36.89 2.24
2292 2583 5.305386 TCTGTTCATGCTATGCTGTACCTAT 59.695 40.000 0.00 0.00 0.00 2.57
2601 2923 1.069049 CAACTTGCCAAGGGAAGGTTG 59.931 52.381 21.93 18.13 40.58 3.77
2622 2944 1.516161 ACAGTCTAGTACACGTCGCA 58.484 50.000 0.00 0.00 0.00 5.10
2782 3109 4.450419 CACTCTATGCTATGCAAAGCTACC 59.550 45.833 0.00 0.00 43.62 3.18
3002 3813 5.789643 AAAGAATAACTTGCACCACATGT 57.210 34.783 0.00 0.00 38.98 3.21
3076 3888 2.049433 CGGAGCCGACTGAAACGT 60.049 61.111 2.00 0.00 42.83 3.99
3077 3889 1.801913 CTCGGAGCCGACTGAAACG 60.802 63.158 7.66 0.00 44.01 3.60
3078 3890 2.095252 GCTCGGAGCCGACTGAAAC 61.095 63.158 19.20 0.00 44.01 2.78
3079 3891 2.261671 GCTCGGAGCCGACTGAAA 59.738 61.111 19.20 0.00 44.01 2.69
3080 3892 2.989253 TGCTCGGAGCCGACTGAA 60.989 61.111 26.00 3.64 44.01 3.02
3081 3893 3.749064 GTGCTCGGAGCCGACTGA 61.749 66.667 26.00 4.40 44.01 3.41
3082 3894 4.803426 GGTGCTCGGAGCCGACTG 62.803 72.222 26.00 0.48 44.01 3.51
3084 3896 3.665675 AATGGTGCTCGGAGCCGAC 62.666 63.158 26.00 18.05 44.01 4.79
3085 3897 3.390521 AATGGTGCTCGGAGCCGA 61.391 61.111 26.00 15.02 46.87 5.54
3086 3898 2.930385 ATCAATGGTGCTCGGAGCCG 62.930 60.000 26.00 1.74 41.51 5.52
3087 3899 0.749454 AATCAATGGTGCTCGGAGCC 60.749 55.000 26.00 16.91 41.51 4.70
3088 3900 1.098050 AAATCAATGGTGCTCGGAGC 58.902 50.000 22.78 22.78 42.82 4.70
3090 3902 2.488204 TCAAATCAATGGTGCTCGGA 57.512 45.000 0.00 0.00 0.00 4.55
3127 3942 0.610232 AGCCTGAAGGATGCACAACC 60.610 55.000 0.00 0.00 37.39 3.77
3238 4054 6.431234 ACAATCGGCTAAGATTTCAAGTCTTT 59.569 34.615 0.00 0.00 38.66 2.52
3355 4186 3.588396 TGGGATAGCCTGCATATGATTCA 59.412 43.478 6.97 0.00 0.00 2.57
3660 4491 5.163854 CCGTATTCAATGGTTTGTCAGAGTC 60.164 44.000 0.00 0.00 34.32 3.36
3871 4703 3.149196 CTGGAGCAACCACTTTATGTGT 58.851 45.455 0.00 0.00 44.64 3.72
4067 4900 0.889994 TCCAATTCACATGCTGCACC 59.110 50.000 3.57 0.00 0.00 5.01
4101 4934 9.747898 ACTATTTGTCTAATCCAATTGTGGTAA 57.252 29.630 4.43 0.00 46.11 2.85
4103 4936 9.920946 ATACTATTTGTCTAATCCAATTGTGGT 57.079 29.630 4.43 0.00 46.11 4.16
4129 4962 5.104527 CCATGACAACTACAATTCCTCCCTA 60.105 44.000 0.00 0.00 0.00 3.53
4134 4967 5.241403 TGACCATGACAACTACAATTCCT 57.759 39.130 0.00 0.00 0.00 3.36
4203 5040 2.808906 AGATGCACTTTTAGACCCCC 57.191 50.000 0.00 0.00 0.00 5.40
4280 5118 7.147141 TGGGACCTAATATCAAATGGACTTGAT 60.147 37.037 4.41 4.41 45.71 2.57
4282 5120 6.364701 TGGGACCTAATATCAAATGGACTTG 58.635 40.000 0.00 0.00 0.00 3.16
4358 5198 3.393941 TGTTTAGAGGGGGTTTACCGAAA 59.606 43.478 0.00 0.00 41.60 3.46
4366 5206 5.269189 CCATTAATGTGTTTAGAGGGGGTT 58.731 41.667 14.25 0.00 0.00 4.11
4385 5225 5.014228 GGGGTATGGAGTAATCTTAGCCATT 59.986 44.000 17.40 0.00 39.81 3.16
4415 5255 9.479549 ACAAAGACCATCATGTCCTTTATTATT 57.520 29.630 0.00 0.00 35.83 1.40
4426 5266 6.535150 CGTACTATGAACAAAGACCATCATGT 59.465 38.462 0.00 0.00 34.54 3.21
4463 5303 2.952714 GCCATGTGCCAGAGTTCTT 58.047 52.632 0.00 0.00 0.00 2.52
4477 5317 1.007734 CGTATCGTACGCAGGCCAT 60.008 57.895 11.24 0.00 45.81 4.40
4579 5434 3.518590 CATTGCCCTCATTTTCTCTTGC 58.481 45.455 0.00 0.00 0.00 4.01
4581 5436 3.102204 CCCATTGCCCTCATTTTCTCTT 58.898 45.455 0.00 0.00 0.00 2.85
4585 5440 3.491447 CGATTCCCATTGCCCTCATTTTC 60.491 47.826 0.00 0.00 0.00 2.29
4616 5471 1.191647 AGCGTGCTTTTAACTCGAACG 59.808 47.619 0.00 0.00 0.00 3.95
4621 5476 3.949313 CGGAGCGTGCTTTTAACTC 57.051 52.632 0.00 0.00 0.00 3.01
4648 5504 1.735198 CAGCAAATTGGCAGTGGCG 60.735 57.895 12.58 0.00 42.47 5.69
4650 5506 3.204505 CACAGCAAATTGGCAGTGG 57.795 52.632 19.81 4.39 44.57 4.00
4676 5532 5.573146 AGTTTCTTAATCATTTGCGCTAGC 58.427 37.500 9.73 4.06 45.41 3.42
4732 5588 9.040939 GCACACTTTGGTTTATCTTTATTTTGT 57.959 29.630 0.00 0.00 0.00 2.83
4739 5595 7.378181 CCTATTGCACACTTTGGTTTATCTTT 58.622 34.615 0.00 0.00 0.00 2.52
4776 5632 2.032894 GTGGTTGACTGTTGTGATGTCG 60.033 50.000 0.00 0.00 33.81 4.35
4833 5692 4.164030 TCATATAGACTGGCTGCCTTTTCA 59.836 41.667 21.03 2.75 0.00 2.69


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

AutoCloner maintained by Alex Coulton.