Multiple sequence alignment - TraesCS5A01G057900

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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 TraesCS5A01G057900 chr5A 100.000 3146 0 0 1 3146 55340587 55343732 0.000000e+00 5810
1 TraesCS5A01G057900 chr5B 93.893 2145 109 8 150 2287 74141389 74139260 0.000000e+00 3216
2 TraesCS5A01G057900 chr5B 94.412 859 47 1 2288 3146 254354881 254354024 0.000000e+00 1319
3 TraesCS5A01G057900 chr5D 93.924 1399 75 3 890 2287 67954542 67953153 0.000000e+00 2104
4 TraesCS5A01G057900 chr5D 95.412 850 39 0 2297 3146 209732143 209731294 0.000000e+00 1354
5 TraesCS5A01G057900 chr5D 91.111 360 24 3 527 886 67959091 67958740 6.100000e-132 481
6 TraesCS5A01G057900 chr7D 96.235 850 32 0 2297 3146 392390702 392389853 0.000000e+00 1393
7 TraesCS5A01G057900 chr3D 95.882 850 35 0 2297 3146 234323733 234322884 0.000000e+00 1376
8 TraesCS5A01G057900 chr3D 94.878 859 44 0 2288 3146 234309327 234310185 0.000000e+00 1343
9 TraesCS5A01G057900 chr6B 94.878 859 43 1 2288 3146 151210125 151209268 0.000000e+00 1341
10 TraesCS5A01G057900 chr6B 94.670 863 46 0 2284 3146 65109425 65110287 0.000000e+00 1339
11 TraesCS5A01G057900 chr7A 94.425 861 43 4 2288 3146 163301372 163302229 0.000000e+00 1319
12 TraesCS5A01G057900 chr7B 93.706 858 54 0 2289 3146 742418189 742419046 0.000000e+00 1286


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 TraesCS5A01G057900 chr5A 55340587 55343732 3145 False 5810 5810 100.000 1 3146 1 chr5A.!!$F1 3145
1 TraesCS5A01G057900 chr5B 74139260 74141389 2129 True 3216 3216 93.893 150 2287 1 chr5B.!!$R1 2137
2 TraesCS5A01G057900 chr5B 254354024 254354881 857 True 1319 1319 94.412 2288 3146 1 chr5B.!!$R2 858
3 TraesCS5A01G057900 chr5D 67953153 67954542 1389 True 2104 2104 93.924 890 2287 1 chr5D.!!$R1 1397
4 TraesCS5A01G057900 chr5D 209731294 209732143 849 True 1354 1354 95.412 2297 3146 1 chr5D.!!$R3 849
5 TraesCS5A01G057900 chr7D 392389853 392390702 849 True 1393 1393 96.235 2297 3146 1 chr7D.!!$R1 849
6 TraesCS5A01G057900 chr3D 234322884 234323733 849 True 1376 1376 95.882 2297 3146 1 chr3D.!!$R1 849
7 TraesCS5A01G057900 chr3D 234309327 234310185 858 False 1343 1343 94.878 2288 3146 1 chr3D.!!$F1 858
8 TraesCS5A01G057900 chr6B 151209268 151210125 857 True 1341 1341 94.878 2288 3146 1 chr6B.!!$R1 858
9 TraesCS5A01G057900 chr6B 65109425 65110287 862 False 1339 1339 94.670 2284 3146 1 chr6B.!!$F1 862
10 TraesCS5A01G057900 chr7A 163301372 163302229 857 False 1319 1319 94.425 2288 3146 1 chr7A.!!$F1 858
11 TraesCS5A01G057900 chr7B 742418189 742419046 857 False 1286 1286 93.706 2289 3146 1 chr7B.!!$F1 857

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
260 261 0.897863 CCCGGCCCAGTCAATTTTCA 60.898 55.0 0.00 0.0 0.0 2.69 F
1233 1241 0.393077 AGGCCGGACGGATATTTGAG 59.607 55.0 15.99 0.0 37.5 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 1673 0.105224 CATACACCGGGTTATCGCCA 59.895 55.0 6.32 0.0 0.00 5.69 R
3108 3120 0.041684 TCTCTCCTGAGGATGCCACA 59.958 55.0 0.00 0.0 40.58 4.17 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
26 27 9.647797 CTTCTTTTTGTAGGTTTTGTTAAAGGT 57.352 29.630 0.00 0.00 0.00 3.50
27 28 8.989653 TCTTTTTGTAGGTTTTGTTAAAGGTG 57.010 30.769 0.00 0.00 0.00 4.00
28 29 8.804204 TCTTTTTGTAGGTTTTGTTAAAGGTGA 58.196 29.630 0.00 0.00 0.00 4.02
29 30 9.425577 CTTTTTGTAGGTTTTGTTAAAGGTGAA 57.574 29.630 0.00 0.00 0.00 3.18
30 31 8.760103 TTTTGTAGGTTTTGTTAAAGGTGAAC 57.240 30.769 0.00 0.00 0.00 3.18
31 32 6.121613 TGTAGGTTTTGTTAAAGGTGAACG 57.878 37.500 0.00 0.00 0.00 3.95
32 33 5.647225 TGTAGGTTTTGTTAAAGGTGAACGT 59.353 36.000 0.00 0.00 0.00 3.99
33 34 5.648178 AGGTTTTGTTAAAGGTGAACGTT 57.352 34.783 0.00 0.00 0.00 3.99
34 35 5.404096 AGGTTTTGTTAAAGGTGAACGTTG 58.596 37.500 5.00 0.00 0.00 4.10
35 36 4.563580 GGTTTTGTTAAAGGTGAACGTTGG 59.436 41.667 5.00 0.00 0.00 3.77
36 37 5.400703 GTTTTGTTAAAGGTGAACGTTGGA 58.599 37.500 5.00 0.00 0.00 3.53
37 38 5.640189 TTTGTTAAAGGTGAACGTTGGAA 57.360 34.783 5.00 0.00 0.00 3.53
38 39 5.838531 TTGTTAAAGGTGAACGTTGGAAT 57.161 34.783 5.00 0.00 0.00 3.01
39 40 5.427036 TGTTAAAGGTGAACGTTGGAATC 57.573 39.130 5.00 0.00 0.00 2.52
40 41 5.127491 TGTTAAAGGTGAACGTTGGAATCT 58.873 37.500 5.00 0.00 0.00 2.40
41 42 6.289834 TGTTAAAGGTGAACGTTGGAATCTA 58.710 36.000 5.00 0.00 0.00 1.98
42 43 6.203338 TGTTAAAGGTGAACGTTGGAATCTAC 59.797 38.462 5.00 0.00 0.00 2.59
43 44 3.329929 AGGTGAACGTTGGAATCTACC 57.670 47.619 5.00 1.84 0.00 3.18
44 45 2.904434 AGGTGAACGTTGGAATCTACCT 59.096 45.455 5.00 4.18 32.74 3.08
45 46 3.000727 GGTGAACGTTGGAATCTACCTG 58.999 50.000 5.00 0.00 0.00 4.00
46 47 3.306502 GGTGAACGTTGGAATCTACCTGA 60.307 47.826 5.00 0.00 0.00 3.86
47 48 4.504858 GTGAACGTTGGAATCTACCTGAT 58.495 43.478 5.00 0.00 36.89 2.90
48 49 4.330074 GTGAACGTTGGAATCTACCTGATG 59.670 45.833 5.00 0.00 35.21 3.07
49 50 2.906354 ACGTTGGAATCTACCTGATGC 58.094 47.619 0.00 0.00 35.21 3.91
50 51 2.236146 ACGTTGGAATCTACCTGATGCA 59.764 45.455 0.00 0.00 35.21 3.96
51 52 3.270027 CGTTGGAATCTACCTGATGCAA 58.730 45.455 0.00 0.00 35.21 4.08
52 53 3.879295 CGTTGGAATCTACCTGATGCAAT 59.121 43.478 0.00 0.00 35.21 3.56
53 54 4.260907 CGTTGGAATCTACCTGATGCAATG 60.261 45.833 0.00 0.00 35.21 2.82
54 55 3.216800 TGGAATCTACCTGATGCAATGC 58.783 45.455 0.00 0.00 35.21 3.56
55 56 3.117776 TGGAATCTACCTGATGCAATGCT 60.118 43.478 6.82 0.00 35.21 3.79
56 57 4.102996 TGGAATCTACCTGATGCAATGCTA 59.897 41.667 6.82 0.00 35.21 3.49
57 58 4.453819 GGAATCTACCTGATGCAATGCTAC 59.546 45.833 6.82 0.89 35.21 3.58
58 59 4.694760 ATCTACCTGATGCAATGCTACA 57.305 40.909 6.82 5.80 33.43 2.74
59 60 4.063998 TCTACCTGATGCAATGCTACAG 57.936 45.455 19.02 19.02 34.49 2.74
60 61 1.386533 ACCTGATGCAATGCTACAGC 58.613 50.000 19.99 0.00 42.50 4.40
61 62 1.064906 ACCTGATGCAATGCTACAGCT 60.065 47.619 19.99 9.36 42.66 4.24
62 63 1.333931 CCTGATGCAATGCTACAGCTG 59.666 52.381 13.48 13.48 42.66 4.24
63 64 2.285977 CTGATGCAATGCTACAGCTGA 58.714 47.619 23.35 2.95 42.66 4.26
64 65 2.011947 TGATGCAATGCTACAGCTGAC 58.988 47.619 23.35 9.97 42.66 3.51
65 66 2.286872 GATGCAATGCTACAGCTGACT 58.713 47.619 23.35 0.27 42.66 3.41
66 67 2.189594 TGCAATGCTACAGCTGACTT 57.810 45.000 23.35 0.00 42.66 3.01
67 68 1.808343 TGCAATGCTACAGCTGACTTG 59.192 47.619 23.35 15.55 42.66 3.16
68 69 1.808945 GCAATGCTACAGCTGACTTGT 59.191 47.619 23.35 0.00 42.66 3.16
69 70 2.413765 GCAATGCTACAGCTGACTTGTG 60.414 50.000 23.35 11.69 42.66 3.33
70 71 3.069289 CAATGCTACAGCTGACTTGTGA 58.931 45.455 23.35 0.00 42.66 3.58
71 72 3.623906 ATGCTACAGCTGACTTGTGAT 57.376 42.857 23.35 0.00 42.66 3.06
72 73 4.743057 ATGCTACAGCTGACTTGTGATA 57.257 40.909 23.35 0.00 42.66 2.15
73 74 4.535526 TGCTACAGCTGACTTGTGATAA 57.464 40.909 23.35 0.00 42.66 1.75
74 75 4.245660 TGCTACAGCTGACTTGTGATAAC 58.754 43.478 23.35 0.00 42.66 1.89
75 76 4.021104 TGCTACAGCTGACTTGTGATAACT 60.021 41.667 23.35 0.00 42.66 2.24
76 77 4.932200 GCTACAGCTGACTTGTGATAACTT 59.068 41.667 23.35 0.00 38.21 2.66
77 78 6.100004 GCTACAGCTGACTTGTGATAACTTA 58.900 40.000 23.35 0.00 38.21 2.24
78 79 6.758886 GCTACAGCTGACTTGTGATAACTTAT 59.241 38.462 23.35 0.00 38.21 1.73
79 80 7.278868 GCTACAGCTGACTTGTGATAACTTATT 59.721 37.037 23.35 0.00 38.21 1.40
80 81 7.986085 ACAGCTGACTTGTGATAACTTATTT 57.014 32.000 23.35 0.00 0.00 1.40
81 82 8.396272 ACAGCTGACTTGTGATAACTTATTTT 57.604 30.769 23.35 0.00 0.00 1.82
82 83 8.507249 ACAGCTGACTTGTGATAACTTATTTTC 58.493 33.333 23.35 0.00 0.00 2.29
83 84 7.965107 CAGCTGACTTGTGATAACTTATTTTCC 59.035 37.037 8.42 0.00 0.00 3.13
84 85 7.121315 AGCTGACTTGTGATAACTTATTTTCCC 59.879 37.037 0.00 0.00 0.00 3.97
85 86 7.628580 GCTGACTTGTGATAACTTATTTTCCCC 60.629 40.741 0.00 0.00 0.00 4.81
86 87 7.235079 TGACTTGTGATAACTTATTTTCCCCA 58.765 34.615 0.00 0.00 0.00 4.96
87 88 7.393234 TGACTTGTGATAACTTATTTTCCCCAG 59.607 37.037 0.00 0.00 0.00 4.45
88 89 6.663523 ACTTGTGATAACTTATTTTCCCCAGG 59.336 38.462 0.00 0.00 0.00 4.45
89 90 6.147437 TGTGATAACTTATTTTCCCCAGGT 57.853 37.500 0.00 0.00 0.00 4.00
90 91 5.949354 TGTGATAACTTATTTTCCCCAGGTG 59.051 40.000 0.00 0.00 0.00 4.00
91 92 5.949952 GTGATAACTTATTTTCCCCAGGTGT 59.050 40.000 0.00 0.00 0.00 4.16
92 93 6.436218 GTGATAACTTATTTTCCCCAGGTGTT 59.564 38.462 0.00 0.00 0.00 3.32
93 94 7.013834 TGATAACTTATTTTCCCCAGGTGTTT 58.986 34.615 0.00 0.00 0.00 2.83
94 95 7.511028 TGATAACTTATTTTCCCCAGGTGTTTT 59.489 33.333 0.00 0.00 0.00 2.43
95 96 5.801531 ACTTATTTTCCCCAGGTGTTTTC 57.198 39.130 0.00 0.00 0.00 2.29
96 97 4.591498 ACTTATTTTCCCCAGGTGTTTTCC 59.409 41.667 0.00 0.00 0.00 3.13
97 98 2.552093 TTTTCCCCAGGTGTTTTCCA 57.448 45.000 0.00 0.00 0.00 3.53
98 99 2.785357 TTTCCCCAGGTGTTTTCCAT 57.215 45.000 0.00 0.00 0.00 3.41
99 100 2.785357 TTCCCCAGGTGTTTTCCATT 57.215 45.000 0.00 0.00 0.00 3.16
100 101 2.785357 TCCCCAGGTGTTTTCCATTT 57.215 45.000 0.00 0.00 0.00 2.32
101 102 3.053359 TCCCCAGGTGTTTTCCATTTT 57.947 42.857 0.00 0.00 0.00 1.82
102 103 2.703007 TCCCCAGGTGTTTTCCATTTTG 59.297 45.455 0.00 0.00 0.00 2.44
103 104 2.437651 CCCCAGGTGTTTTCCATTTTGT 59.562 45.455 0.00 0.00 0.00 2.83
104 105 3.118075 CCCCAGGTGTTTTCCATTTTGTT 60.118 43.478 0.00 0.00 0.00 2.83
105 106 4.522114 CCCAGGTGTTTTCCATTTTGTTT 58.478 39.130 0.00 0.00 0.00 2.83
106 107 5.396884 CCCCAGGTGTTTTCCATTTTGTTTA 60.397 40.000 0.00 0.00 0.00 2.01
107 108 5.525745 CCCAGGTGTTTTCCATTTTGTTTAC 59.474 40.000 0.00 0.00 0.00 2.01
108 109 5.525745 CCAGGTGTTTTCCATTTTGTTTACC 59.474 40.000 0.00 0.00 0.00 2.85
109 110 6.345298 CAGGTGTTTTCCATTTTGTTTACCT 58.655 36.000 0.00 0.00 35.34 3.08
110 111 7.418025 CCAGGTGTTTTCCATTTTGTTTACCTA 60.418 37.037 0.00 0.00 33.38 3.08
111 112 8.147704 CAGGTGTTTTCCATTTTGTTTACCTAT 58.852 33.333 0.00 0.00 33.38 2.57
112 113 9.369672 AGGTGTTTTCCATTTTGTTTACCTATA 57.630 29.630 0.00 0.00 33.38 1.31
113 114 9.414295 GGTGTTTTCCATTTTGTTTACCTATAC 57.586 33.333 0.00 0.00 0.00 1.47
141 142 7.602517 TTTGTTAAAGAAAACACACAATGGG 57.397 32.000 0.00 0.00 39.02 4.00
142 143 6.287589 TGTTAAAGAAAACACACAATGGGT 57.712 33.333 0.00 0.00 33.89 4.51
143 144 6.334202 TGTTAAAGAAAACACACAATGGGTC 58.666 36.000 0.00 0.00 28.95 4.46
144 145 6.153680 TGTTAAAGAAAACACACAATGGGTCT 59.846 34.615 0.00 0.00 28.95 3.85
145 146 4.918810 AAGAAAACACACAATGGGTCTC 57.081 40.909 0.00 0.00 28.95 3.36
146 147 3.897239 AGAAAACACACAATGGGTCTCA 58.103 40.909 0.00 0.00 28.95 3.27
147 148 3.885297 AGAAAACACACAATGGGTCTCAG 59.115 43.478 0.00 0.00 28.95 3.35
148 149 3.576078 AAACACACAATGGGTCTCAGA 57.424 42.857 0.00 0.00 28.95 3.27
165 166 6.238953 GGTCTCAGACGCAAAACTCCTATATA 60.239 42.308 0.00 0.00 32.65 0.86
216 217 5.456548 TTTTACTGTTTCCGATTTTCCCC 57.543 39.130 0.00 0.00 0.00 4.81
227 228 2.161713 ATTTTCCCCGATGGTGGCCA 62.162 55.000 0.00 0.00 38.19 5.36
234 235 1.375396 CGATGGTGGCCAGAAACGA 60.375 57.895 5.11 0.00 36.75 3.85
260 261 0.897863 CCCGGCCCAGTCAATTTTCA 60.898 55.000 0.00 0.00 0.00 2.69
341 342 8.514330 AACTTGTAAAACTGTCTGGTATTTCA 57.486 30.769 0.00 0.00 0.00 2.69
342 343 8.514330 ACTTGTAAAACTGTCTGGTATTTCAA 57.486 30.769 0.00 0.00 0.00 2.69
351 352 3.930848 GTCTGGTATTTCAACTACCGGTG 59.069 47.826 19.93 10.05 43.38 4.94
364 365 3.058160 CGGTGCTGGCCAGAAAGG 61.058 66.667 37.21 17.39 41.84 3.11
418 419 5.459982 AAACCCTGGCCATATTAGTTACA 57.540 39.130 5.51 0.00 0.00 2.41
423 424 6.900743 ACCCTGGCCATATTAGTTACAAAAAT 59.099 34.615 5.51 0.00 0.00 1.82
521 522 8.662781 TGGTATCTATTAATGAAAGCAGTGTC 57.337 34.615 0.00 0.00 0.00 3.67
569 570 5.065914 AGCTTGTTTTGCATGTCTCTAAGA 58.934 37.500 0.00 0.00 0.00 2.10
603 604 7.100458 ACATATTGCCTGGTGAAGTTTTATC 57.900 36.000 0.00 0.00 0.00 1.75
644 645 6.651225 GGAGAATAACATTAGGCATGGAGTAC 59.349 42.308 0.00 0.00 37.17 2.73
645 646 7.380423 AGAATAACATTAGGCATGGAGTACT 57.620 36.000 0.00 0.00 37.17 2.73
646 647 8.492415 AGAATAACATTAGGCATGGAGTACTA 57.508 34.615 0.00 0.00 37.17 1.82
659 660 6.423302 GCATGGAGTACTACTTGATTCTCATG 59.577 42.308 22.04 8.23 0.00 3.07
693 694 2.544686 AGCTATACGTCTCAGTACTGCG 59.455 50.000 18.45 17.40 35.11 5.18
775 780 7.287927 TCTCCTATACCTATGGTGAAGTTCAAG 59.712 40.741 7.25 1.05 36.19 3.02
829 834 7.686438 TGTATTGAGTGCATTAACAATGACT 57.314 32.000 15.49 4.04 41.46 3.41
841 846 7.907045 GCATTAACAATGACTAACAGATGAGTG 59.093 37.037 3.11 0.00 41.46 3.51
851 856 9.031537 TGACTAACAGATGAGTGGAGTTAATTA 57.968 33.333 0.00 0.00 0.00 1.40
866 871 7.453126 TGGAGTTAATTATGTGTTGGGTGAATT 59.547 33.333 0.00 0.00 0.00 2.17
952 960 6.127338 TGTGTTATGTCTACTGCTAGCAGATT 60.127 38.462 43.42 28.01 46.30 2.40
996 1004 3.834231 CCTTTCAATTCCCAGTGTTCCAT 59.166 43.478 0.00 0.00 0.00 3.41
1005 1013 2.651455 CCAGTGTTCCATGAGATGCAT 58.349 47.619 0.00 0.00 37.85 3.96
1045 1053 5.759763 TCAGCACATATAGCAAATGTACAGG 59.240 40.000 0.33 0.00 35.82 4.00
1143 1151 4.516698 GCCATTATGAATCTCGTCACCATT 59.483 41.667 0.00 0.00 0.00 3.16
1156 1164 1.153369 ACCATTGACAGCGGATCGG 60.153 57.895 0.00 0.00 0.00 4.18
1233 1241 0.393077 AGGCCGGACGGATATTTGAG 59.607 55.000 15.99 0.00 37.50 3.02
1238 1246 0.472471 GGACGGATATTTGAGCCCCA 59.528 55.000 0.00 0.00 0.00 4.96
1380 1388 6.322201 TGAGATATGCATCAGAAGAGTACACA 59.678 38.462 0.19 0.00 33.21 3.72
1441 1449 6.585695 ACAACTTCAGCATTGATGATTTCT 57.414 33.333 5.30 0.00 33.81 2.52
1511 1519 0.684153 ATTGGATTTGGGGGTGCGAG 60.684 55.000 0.00 0.00 0.00 5.03
1526 1534 3.306156 GGTGCGAGTTACTCCTTCTTTCT 60.306 47.826 6.80 0.00 0.00 2.52
1539 1547 4.587684 TCCTTCTTTCTTCAGGTAGTTCGT 59.412 41.667 0.00 0.00 0.00 3.85
1545 1553 4.611310 TCTTCAGGTAGTTCGTCATACG 57.389 45.455 0.00 0.00 44.19 3.06
1557 1565 2.858839 CGTCATACGAACTACACTGCA 58.141 47.619 0.00 0.00 46.05 4.41
1560 1568 4.326278 CGTCATACGAACTACACTGCATTT 59.674 41.667 0.00 0.00 46.05 2.32
1563 1571 5.929415 TCATACGAACTACACTGCATTTTCA 59.071 36.000 0.00 0.00 0.00 2.69
1582 1590 4.901197 TCACACTGCTTTCCTGGTAATA 57.099 40.909 0.00 0.00 0.00 0.98
1590 1598 9.125026 CACTGCTTTCCTGGTAATAATAGAAAT 57.875 33.333 0.00 0.00 0.00 2.17
1596 1604 7.947782 TCCTGGTAATAATAGAAATGGAGGT 57.052 36.000 0.00 0.00 0.00 3.85
1611 1619 3.380393 TGGAGGTTTTCTATCCATCGGA 58.620 45.455 0.00 0.00 38.19 4.55
1656 1664 4.570772 CAGTTCATTCCGTTGGTCGAATAT 59.429 41.667 0.00 0.00 42.86 1.28
1665 1673 0.392706 TGGTCGAATATGGCTCGCAT 59.607 50.000 0.00 0.00 36.25 4.73
1668 1676 0.950555 TCGAATATGGCTCGCATGGC 60.951 55.000 0.00 0.00 36.25 4.40
1687 1695 1.779569 CGATAACCCGGTGTATGCTC 58.220 55.000 0.00 0.00 0.00 4.26
1705 1713 0.689055 TCTTCAGCAGCTGGACATGT 59.311 50.000 22.62 0.00 31.51 3.21
1707 1715 2.302733 TCTTCAGCAGCTGGACATGTTA 59.697 45.455 22.62 0.00 31.51 2.41
1711 1719 1.625315 AGCAGCTGGACATGTTAGTCA 59.375 47.619 17.12 0.00 40.29 3.41
1741 1749 1.009389 GCTTGAAGTCGACCCGTCAG 61.009 60.000 13.01 3.51 0.00 3.51
1761 1769 2.228103 AGTCTACGCAACTCGAATGACA 59.772 45.455 2.23 0.00 41.67 3.58
1815 1823 3.862991 TCCCCGGTGTTTCGTGCA 61.863 61.111 0.00 0.00 0.00 4.57
1877 1885 1.003355 CCCGAGAAGCAGCTGGAAA 60.003 57.895 17.12 0.00 0.00 3.13
1882 1890 2.095532 CGAGAAGCAGCTGGAAAGAATG 59.904 50.000 17.12 0.00 0.00 2.67
1887 1895 4.715527 AGCAGCTGGAAAGAATGAAATC 57.284 40.909 17.12 0.00 0.00 2.17
1913 1921 2.094700 TCACGTCCACTAGTGATTCAGC 60.095 50.000 24.68 6.38 41.81 4.26
1923 1931 1.005037 TGATTCAGCGAACTGGCGT 60.005 52.632 0.00 0.00 44.59 5.68
1961 1969 7.065923 GGTGGAGATGAAATTTGTAAGGTCTAC 59.934 40.741 0.00 0.00 0.00 2.59
2040 2048 0.179129 CATTTCGGCCAGATGTTGCC 60.179 55.000 2.24 0.00 44.41 4.52
2058 2066 2.214216 CGGACTGACAGGGGTTCCA 61.214 63.158 7.51 0.00 34.83 3.53
2151 2159 0.664761 CTGGTGCTTGTTGACACAGG 59.335 55.000 0.00 0.00 38.57 4.00
2152 2160 0.034574 TGGTGCTTGTTGACACAGGT 60.035 50.000 0.00 0.00 38.57 4.00
2153 2161 0.381801 GGTGCTTGTTGACACAGGTG 59.618 55.000 0.00 0.00 38.57 4.00
2154 2162 0.381801 GTGCTTGTTGACACAGGTGG 59.618 55.000 4.24 0.00 36.77 4.61
2155 2163 0.254462 TGCTTGTTGACACAGGTGGA 59.746 50.000 4.24 0.00 33.22 4.02
2327 2336 4.746535 TGAAACAATGCTCGATACCCTA 57.253 40.909 0.00 0.00 0.00 3.53
2454 2465 9.003658 CAATCTTAACTATGTCCTGAAACACTT 57.996 33.333 0.00 0.00 30.55 3.16
2549 2560 5.917447 GCTGATCCTTTGAAGAAACAAACTC 59.083 40.000 0.00 0.00 36.11 3.01
2555 2566 7.214381 TCCTTTGAAGAAACAAACTCGATCTA 58.786 34.615 0.00 0.00 36.11 1.98
2558 2569 9.716507 CTTTGAAGAAACAAACTCGATCTAAAA 57.283 29.630 0.00 0.00 36.11 1.52
2654 2666 5.065914 CGGATTGGATGAAAGATATGTGGT 58.934 41.667 0.00 0.00 0.00 4.16
2826 2838 1.303561 AGCTTGCCAGGCGATCAAA 60.304 52.632 7.03 0.00 34.52 2.69
2841 2853 5.067805 GGCGATCAAATTAGGTCCAAAGAAT 59.932 40.000 0.00 0.00 0.00 2.40
2981 2993 0.652071 CGAACATAGCGCAAGATGCA 59.348 50.000 11.47 0.00 45.36 3.96
3108 3120 5.338381 CCCACCAACAATACTGTGATACTCT 60.338 44.000 0.00 0.00 35.37 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.647797 ACCTTTAACAAAACCTACAAAAAGAAG 57.352 29.630 0.00 0.00 0.00 2.85
1 2 9.425577 CACCTTTAACAAAACCTACAAAAAGAA 57.574 29.630 0.00 0.00 0.00 2.52
2 3 8.804204 TCACCTTTAACAAAACCTACAAAAAGA 58.196 29.630 0.00 0.00 0.00 2.52
3 4 8.989653 TCACCTTTAACAAAACCTACAAAAAG 57.010 30.769 0.00 0.00 0.00 2.27
4 5 9.205719 GTTCACCTTTAACAAAACCTACAAAAA 57.794 29.630 0.00 0.00 0.00 1.94
5 6 7.541437 CGTTCACCTTTAACAAAACCTACAAAA 59.459 33.333 0.00 0.00 0.00 2.44
6 7 7.028361 CGTTCACCTTTAACAAAACCTACAAA 58.972 34.615 0.00 0.00 0.00 2.83
7 8 6.150809 ACGTTCACCTTTAACAAAACCTACAA 59.849 34.615 0.00 0.00 0.00 2.41
8 9 5.647225 ACGTTCACCTTTAACAAAACCTACA 59.353 36.000 0.00 0.00 0.00 2.74
9 10 6.122850 ACGTTCACCTTTAACAAAACCTAC 57.877 37.500 0.00 0.00 0.00 3.18
10 11 6.404513 CCAACGTTCACCTTTAACAAAACCTA 60.405 38.462 0.00 0.00 0.00 3.08
11 12 5.404096 CAACGTTCACCTTTAACAAAACCT 58.596 37.500 0.00 0.00 0.00 3.50
12 13 4.563580 CCAACGTTCACCTTTAACAAAACC 59.436 41.667 0.00 0.00 0.00 3.27
13 14 5.400703 TCCAACGTTCACCTTTAACAAAAC 58.599 37.500 0.00 0.00 0.00 2.43
14 15 5.640189 TCCAACGTTCACCTTTAACAAAA 57.360 34.783 0.00 0.00 0.00 2.44
15 16 5.640189 TTCCAACGTTCACCTTTAACAAA 57.360 34.783 0.00 0.00 0.00 2.83
16 17 5.591067 AGATTCCAACGTTCACCTTTAACAA 59.409 36.000 0.00 0.00 0.00 2.83
17 18 5.127491 AGATTCCAACGTTCACCTTTAACA 58.873 37.500 0.00 0.00 0.00 2.41
18 19 5.684550 AGATTCCAACGTTCACCTTTAAC 57.315 39.130 0.00 0.00 0.00 2.01
19 20 5.702209 GGTAGATTCCAACGTTCACCTTTAA 59.298 40.000 0.00 0.00 0.00 1.52
20 21 5.012354 AGGTAGATTCCAACGTTCACCTTTA 59.988 40.000 0.00 0.00 31.10 1.85
21 22 4.070009 GGTAGATTCCAACGTTCACCTTT 58.930 43.478 0.00 0.00 0.00 3.11
22 23 3.326880 AGGTAGATTCCAACGTTCACCTT 59.673 43.478 0.00 0.00 31.10 3.50
23 24 2.904434 AGGTAGATTCCAACGTTCACCT 59.096 45.455 0.00 0.48 0.00 4.00
24 25 3.000727 CAGGTAGATTCCAACGTTCACC 58.999 50.000 0.00 0.00 0.00 4.02
25 26 3.921677 TCAGGTAGATTCCAACGTTCAC 58.078 45.455 0.00 0.00 0.00 3.18
26 27 4.503910 CATCAGGTAGATTCCAACGTTCA 58.496 43.478 0.00 0.00 33.72 3.18
27 28 3.309954 GCATCAGGTAGATTCCAACGTTC 59.690 47.826 0.00 0.00 33.72 3.95
28 29 3.270877 GCATCAGGTAGATTCCAACGTT 58.729 45.455 0.00 0.00 33.72 3.99
29 30 2.236146 TGCATCAGGTAGATTCCAACGT 59.764 45.455 0.00 0.00 33.72 3.99
30 31 2.905075 TGCATCAGGTAGATTCCAACG 58.095 47.619 0.00 0.00 33.72 4.10
31 32 4.498682 GCATTGCATCAGGTAGATTCCAAC 60.499 45.833 3.15 0.00 33.72 3.77
32 33 3.633525 GCATTGCATCAGGTAGATTCCAA 59.366 43.478 3.15 0.00 33.72 3.53
33 34 3.117776 AGCATTGCATCAGGTAGATTCCA 60.118 43.478 11.91 0.00 33.72 3.53
34 35 3.484407 AGCATTGCATCAGGTAGATTCC 58.516 45.455 11.91 0.00 33.72 3.01
35 36 5.059161 TGTAGCATTGCATCAGGTAGATTC 58.941 41.667 11.91 0.00 33.72 2.52
36 37 5.039920 TGTAGCATTGCATCAGGTAGATT 57.960 39.130 11.91 0.00 33.72 2.40
37 38 4.639334 CTGTAGCATTGCATCAGGTAGAT 58.361 43.478 18.74 0.00 37.48 1.98
38 39 3.742327 GCTGTAGCATTGCATCAGGTAGA 60.742 47.826 23.94 3.62 41.59 2.59
39 40 2.547211 GCTGTAGCATTGCATCAGGTAG 59.453 50.000 23.94 10.19 41.59 3.18
40 41 2.171237 AGCTGTAGCATTGCATCAGGTA 59.829 45.455 24.91 3.25 45.16 3.08
41 42 1.064906 AGCTGTAGCATTGCATCAGGT 60.065 47.619 22.47 22.47 45.16 4.00
42 43 1.333931 CAGCTGTAGCATTGCATCAGG 59.666 52.381 23.94 11.95 45.16 3.86
43 44 2.031807 GTCAGCTGTAGCATTGCATCAG 59.968 50.000 14.67 20.82 45.16 2.90
44 45 2.011947 GTCAGCTGTAGCATTGCATCA 58.988 47.619 14.67 8.33 45.16 3.07
45 46 2.286872 AGTCAGCTGTAGCATTGCATC 58.713 47.619 14.67 3.89 45.16 3.91
46 47 2.414994 AGTCAGCTGTAGCATTGCAT 57.585 45.000 14.67 0.00 45.16 3.96
47 48 1.808343 CAAGTCAGCTGTAGCATTGCA 59.192 47.619 14.67 0.00 45.16 4.08
48 49 1.808945 ACAAGTCAGCTGTAGCATTGC 59.191 47.619 14.67 0.00 45.16 3.56
49 50 3.069289 TCACAAGTCAGCTGTAGCATTG 58.931 45.455 14.67 13.93 45.16 2.82
50 51 3.407424 TCACAAGTCAGCTGTAGCATT 57.593 42.857 14.67 0.00 45.16 3.56
51 52 3.623906 ATCACAAGTCAGCTGTAGCAT 57.376 42.857 14.67 0.00 45.16 3.79
52 53 4.021104 AGTTATCACAAGTCAGCTGTAGCA 60.021 41.667 14.67 0.00 45.16 3.49
53 54 4.499183 AGTTATCACAAGTCAGCTGTAGC 58.501 43.478 14.67 5.62 42.49 3.58
54 55 8.709386 AATAAGTTATCACAAGTCAGCTGTAG 57.291 34.615 14.67 4.84 0.00 2.74
55 56 9.502091 AAAATAAGTTATCACAAGTCAGCTGTA 57.498 29.630 14.67 0.00 0.00 2.74
56 57 7.986085 AAATAAGTTATCACAAGTCAGCTGT 57.014 32.000 14.67 0.00 0.00 4.40
57 58 7.965107 GGAAAATAAGTTATCACAAGTCAGCTG 59.035 37.037 7.63 7.63 0.00 4.24
58 59 7.121315 GGGAAAATAAGTTATCACAAGTCAGCT 59.879 37.037 0.00 0.00 0.00 4.24
59 60 7.251281 GGGAAAATAAGTTATCACAAGTCAGC 58.749 38.462 0.00 0.00 0.00 4.26
60 61 7.393234 TGGGGAAAATAAGTTATCACAAGTCAG 59.607 37.037 0.00 0.00 0.00 3.51
61 62 7.235079 TGGGGAAAATAAGTTATCACAAGTCA 58.765 34.615 0.00 0.00 0.00 3.41
62 63 7.148069 CCTGGGGAAAATAAGTTATCACAAGTC 60.148 40.741 0.00 0.00 0.00 3.01
63 64 6.663523 CCTGGGGAAAATAAGTTATCACAAGT 59.336 38.462 0.00 0.00 0.00 3.16
64 65 6.663523 ACCTGGGGAAAATAAGTTATCACAAG 59.336 38.462 0.00 0.00 0.00 3.16
65 66 6.435904 CACCTGGGGAAAATAAGTTATCACAA 59.564 38.462 0.00 0.00 0.00 3.33
66 67 5.949354 CACCTGGGGAAAATAAGTTATCACA 59.051 40.000 0.00 0.00 0.00 3.58
67 68 5.949952 ACACCTGGGGAAAATAAGTTATCAC 59.050 40.000 1.10 0.00 0.00 3.06
68 69 6.147437 ACACCTGGGGAAAATAAGTTATCA 57.853 37.500 1.10 0.00 0.00 2.15
69 70 7.476540 AAACACCTGGGGAAAATAAGTTATC 57.523 36.000 1.10 0.00 0.00 1.75
70 71 7.038587 GGAAAACACCTGGGGAAAATAAGTTAT 60.039 37.037 1.10 0.00 0.00 1.89
71 72 6.268158 GGAAAACACCTGGGGAAAATAAGTTA 59.732 38.462 1.10 0.00 0.00 2.24
72 73 5.071250 GGAAAACACCTGGGGAAAATAAGTT 59.929 40.000 1.10 0.00 0.00 2.66
73 74 4.591498 GGAAAACACCTGGGGAAAATAAGT 59.409 41.667 1.10 0.00 0.00 2.24
74 75 4.591072 TGGAAAACACCTGGGGAAAATAAG 59.409 41.667 1.10 0.00 0.00 1.73
75 76 4.557705 TGGAAAACACCTGGGGAAAATAA 58.442 39.130 1.10 0.00 0.00 1.40
76 77 4.200447 TGGAAAACACCTGGGGAAAATA 57.800 40.909 1.10 0.00 0.00 1.40
77 78 3.053359 TGGAAAACACCTGGGGAAAAT 57.947 42.857 1.10 0.00 0.00 1.82
78 79 2.552093 TGGAAAACACCTGGGGAAAA 57.448 45.000 1.10 0.00 0.00 2.29
79 80 2.785357 ATGGAAAACACCTGGGGAAA 57.215 45.000 1.10 0.00 0.00 3.13
80 81 2.785357 AATGGAAAACACCTGGGGAA 57.215 45.000 1.10 0.00 0.00 3.97
81 82 2.703007 CAAAATGGAAAACACCTGGGGA 59.297 45.455 1.10 0.00 0.00 4.81
82 83 2.437651 ACAAAATGGAAAACACCTGGGG 59.562 45.455 0.00 0.00 0.00 4.96
83 84 3.836365 ACAAAATGGAAAACACCTGGG 57.164 42.857 0.00 0.00 0.00 4.45
84 85 5.525745 GGTAAACAAAATGGAAAACACCTGG 59.474 40.000 0.00 0.00 0.00 4.45
85 86 6.345298 AGGTAAACAAAATGGAAAACACCTG 58.655 36.000 0.00 0.00 31.64 4.00
86 87 6.553953 AGGTAAACAAAATGGAAAACACCT 57.446 33.333 0.00 0.00 0.00 4.00
87 88 9.414295 GTATAGGTAAACAAAATGGAAAACACC 57.586 33.333 0.00 0.00 0.00 4.16
115 116 9.319143 CCCATTGTGTGTTTTCTTTAACAAATA 57.681 29.630 0.00 0.00 39.54 1.40
116 117 7.826744 ACCCATTGTGTGTTTTCTTTAACAAAT 59.173 29.630 0.00 0.00 39.54 2.32
117 118 7.162082 ACCCATTGTGTGTTTTCTTTAACAAA 58.838 30.769 0.00 0.00 39.54 2.83
118 119 6.702329 ACCCATTGTGTGTTTTCTTTAACAA 58.298 32.000 0.00 0.00 39.54 2.83
119 120 6.153680 AGACCCATTGTGTGTTTTCTTTAACA 59.846 34.615 0.00 0.00 35.75 2.41
120 121 6.569780 AGACCCATTGTGTGTTTTCTTTAAC 58.430 36.000 0.00 0.00 0.00 2.01
121 122 6.378564 TGAGACCCATTGTGTGTTTTCTTTAA 59.621 34.615 0.00 0.00 0.00 1.52
122 123 5.888724 TGAGACCCATTGTGTGTTTTCTTTA 59.111 36.000 0.00 0.00 0.00 1.85
123 124 4.709397 TGAGACCCATTGTGTGTTTTCTTT 59.291 37.500 0.00 0.00 0.00 2.52
124 125 4.277476 TGAGACCCATTGTGTGTTTTCTT 58.723 39.130 0.00 0.00 0.00 2.52
125 126 3.885297 CTGAGACCCATTGTGTGTTTTCT 59.115 43.478 0.00 0.00 0.00 2.52
126 127 3.882888 TCTGAGACCCATTGTGTGTTTTC 59.117 43.478 0.00 0.00 0.00 2.29
127 128 3.632145 GTCTGAGACCCATTGTGTGTTTT 59.368 43.478 0.00 0.00 0.00 2.43
128 129 3.214328 GTCTGAGACCCATTGTGTGTTT 58.786 45.455 0.00 0.00 0.00 2.83
129 130 2.806745 CGTCTGAGACCCATTGTGTGTT 60.807 50.000 7.07 0.00 0.00 3.32
130 131 1.270305 CGTCTGAGACCCATTGTGTGT 60.270 52.381 7.07 0.00 0.00 3.72
131 132 1.432514 CGTCTGAGACCCATTGTGTG 58.567 55.000 7.07 0.00 0.00 3.82
132 133 0.320771 GCGTCTGAGACCCATTGTGT 60.321 55.000 7.07 0.00 0.00 3.72
133 134 0.320683 TGCGTCTGAGACCCATTGTG 60.321 55.000 7.07 0.00 0.00 3.33
134 135 0.396435 TTGCGTCTGAGACCCATTGT 59.604 50.000 7.07 0.00 0.00 2.71
135 136 1.522668 TTTGCGTCTGAGACCCATTG 58.477 50.000 7.07 0.00 0.00 2.82
136 137 1.880027 GTTTTGCGTCTGAGACCCATT 59.120 47.619 7.07 0.00 0.00 3.16
137 138 1.072331 AGTTTTGCGTCTGAGACCCAT 59.928 47.619 7.07 0.00 0.00 4.00
138 139 0.468226 AGTTTTGCGTCTGAGACCCA 59.532 50.000 7.07 0.66 0.00 4.51
139 140 1.149148 GAGTTTTGCGTCTGAGACCC 58.851 55.000 7.07 0.00 0.00 4.46
140 141 1.149148 GGAGTTTTGCGTCTGAGACC 58.851 55.000 7.07 0.60 0.00 3.85
141 142 2.156343 AGGAGTTTTGCGTCTGAGAC 57.844 50.000 1.65 1.65 0.00 3.36
142 143 5.854010 ATATAGGAGTTTTGCGTCTGAGA 57.146 39.130 0.00 0.00 0.00 3.27
143 144 8.594881 ATTTATATAGGAGTTTTGCGTCTGAG 57.405 34.615 0.00 0.00 0.00 3.35
144 145 8.958119 AATTTATATAGGAGTTTTGCGTCTGA 57.042 30.769 0.00 0.00 0.00 3.27
146 147 9.269453 GGTAATTTATATAGGAGTTTTGCGTCT 57.731 33.333 0.00 0.00 0.00 4.18
147 148 9.269453 AGGTAATTTATATAGGAGTTTTGCGTC 57.731 33.333 0.00 0.00 0.00 5.19
148 149 9.623000 AAGGTAATTTATATAGGAGTTTTGCGT 57.377 29.630 0.00 0.00 0.00 5.24
191 192 6.461927 GGGGAAAATCGGAAACAGTAAAAAGT 60.462 38.462 0.00 0.00 0.00 2.66
200 201 2.088423 CATCGGGGAAAATCGGAAACA 58.912 47.619 0.00 0.00 0.00 2.83
216 217 1.375396 TCGTTTCTGGCCACCATCG 60.375 57.895 0.00 5.26 30.82 3.84
245 246 3.959535 TTGGATGAAAATTGACTGGGC 57.040 42.857 0.00 0.00 0.00 5.36
246 247 6.465948 TGATTTTGGATGAAAATTGACTGGG 58.534 36.000 0.00 0.00 43.12 4.45
247 248 8.556213 AATGATTTTGGATGAAAATTGACTGG 57.444 30.769 0.00 0.00 43.12 4.00
248 249 9.820229 CAAATGATTTTGGATGAAAATTGACTG 57.180 29.630 0.00 0.00 43.12 3.51
249 250 9.781633 TCAAATGATTTTGGATGAAAATTGACT 57.218 25.926 0.00 0.00 43.12 3.41
318 319 8.621286 AGTTGAAATACCAGACAGTTTTACAAG 58.379 33.333 0.00 0.00 0.00 3.16
341 342 3.246112 TGGCCAGCACCGGTAGTT 61.246 61.111 6.87 0.00 0.00 2.24
342 343 3.706373 CTGGCCAGCACCGGTAGT 61.706 66.667 22.33 0.00 0.00 2.73
449 450 4.162131 GCATGGAAAATGTTATTGGGACCT 59.838 41.667 0.00 0.00 0.00 3.85
497 498 8.662781 TGACACTGCTTTCATTAATAGATACC 57.337 34.615 0.00 0.00 0.00 2.73
508 509 3.354948 TGCCTATGACACTGCTTTCAT 57.645 42.857 0.00 0.00 36.43 2.57
509 510 2.857186 TGCCTATGACACTGCTTTCA 57.143 45.000 0.00 0.00 0.00 2.69
511 512 3.354948 TCATGCCTATGACACTGCTTT 57.645 42.857 0.00 0.00 38.37 3.51
521 522 2.050144 ACCTACCCAGTCATGCCTATG 58.950 52.381 0.00 0.00 35.57 2.23
569 570 6.156256 TCACCAGGCAATATGTACTCTAGTTT 59.844 38.462 0.00 0.00 0.00 2.66
775 780 8.911247 ATTTAGAAAACTCACAGAACACAAAC 57.089 30.769 0.00 0.00 0.00 2.93
829 834 9.599866 CACATAATTAACTCCACTCATCTGTTA 57.400 33.333 0.00 0.00 0.00 2.41
841 846 6.827586 TTCACCCAACACATAATTAACTCC 57.172 37.500 0.00 0.00 0.00 3.85
952 960 0.953471 CCATCGCCGTTCTGACCAAA 60.953 55.000 0.00 0.00 0.00 3.28
1025 1033 7.984391 TGTTTCCTGTACATTTGCTATATGTG 58.016 34.615 0.00 0.00 36.89 3.21
1119 1127 2.476619 GGTGACGAGATTCATAATGGCG 59.523 50.000 0.00 0.00 0.00 5.69
1143 1151 2.449031 AAAGTGCCGATCCGCTGTCA 62.449 55.000 7.56 0.00 0.00 3.58
1148 1156 2.125106 AGGAAAGTGCCGATCCGC 60.125 61.111 0.00 0.00 38.31 5.54
1152 1160 0.322546 GAACCCAGGAAAGTGCCGAT 60.323 55.000 0.00 0.00 0.00 4.18
1156 1164 0.954452 CACTGAACCCAGGAAAGTGC 59.046 55.000 0.00 0.00 44.60 4.40
1233 1241 0.329596 AAGTTGAGGACTGATGGGGC 59.670 55.000 0.00 0.00 39.00 5.80
1238 1246 4.327680 GCTTTGGTAAGTTGAGGACTGAT 58.672 43.478 0.00 0.00 39.00 2.90
1394 1402 3.077359 CCTAAAGTGAGCTTGTCCTTGG 58.923 50.000 0.00 0.00 34.71 3.61
1441 1449 0.106769 TCTCCACTGCAGCCAAACAA 60.107 50.000 15.27 0.00 0.00 2.83
1511 1519 6.995364 ACTACCTGAAGAAAGAAGGAGTAAC 58.005 40.000 0.00 0.00 34.97 2.50
1539 1547 5.929415 TGAAAATGCAGTGTAGTTCGTATGA 59.071 36.000 0.00 0.00 0.00 2.15
1545 1553 5.207768 CAGTGTGAAAATGCAGTGTAGTTC 58.792 41.667 0.00 0.00 32.91 3.01
1554 1562 2.694628 AGGAAAGCAGTGTGAAAATGCA 59.305 40.909 0.00 0.00 42.45 3.96
1557 1565 3.299503 ACCAGGAAAGCAGTGTGAAAAT 58.700 40.909 0.00 0.00 0.00 1.82
1560 1568 3.569194 TTACCAGGAAAGCAGTGTGAA 57.431 42.857 0.00 0.00 0.00 3.18
1563 1571 7.195374 TCTATTATTACCAGGAAAGCAGTGT 57.805 36.000 0.00 0.00 0.00 3.55
1590 1598 3.134081 GTCCGATGGATAGAAAACCTCCA 59.866 47.826 0.00 0.00 42.95 3.86
1596 1604 4.585581 TCATACGGTCCGATGGATAGAAAA 59.414 41.667 20.51 0.00 32.73 2.29
1625 1633 5.533154 ACCAACGGAATGAACTGTAAATTGA 59.467 36.000 0.00 0.00 0.00 2.57
1665 1673 0.105224 CATACACCGGGTTATCGCCA 59.895 55.000 6.32 0.00 0.00 5.69
1668 1676 1.340248 AGAGCATACACCGGGTTATCG 59.660 52.381 6.32 0.00 0.00 2.92
1687 1695 1.531423 AACATGTCCAGCTGCTGAAG 58.469 50.000 30.10 14.85 32.44 3.02
1705 1713 1.477553 AGCCGTATCCCGTTGACTAA 58.522 50.000 0.00 0.00 33.66 2.24
1707 1715 0.108329 CAAGCCGTATCCCGTTGACT 60.108 55.000 0.00 0.00 33.66 3.41
1711 1719 0.611714 ACTTCAAGCCGTATCCCGTT 59.388 50.000 0.00 0.00 33.66 4.44
1741 1749 2.592194 TGTCATTCGAGTTGCGTAGAC 58.408 47.619 0.00 0.00 41.80 2.59
1761 1769 3.733337 GATCGTGCCAGAATCCAGTATT 58.267 45.455 0.00 0.00 0.00 1.89
1815 1823 1.470098 GCTGTGATCGCCTTGTCAAAT 59.530 47.619 3.31 0.00 0.00 2.32
1882 1890 4.989168 ACTAGTGGACGTGAAACAGATTTC 59.011 41.667 0.00 0.00 43.96 2.17
1887 1895 3.364889 TCACTAGTGGACGTGAAACAG 57.635 47.619 22.48 0.00 37.23 3.16
1913 1921 2.476051 GCATGTCACGCCAGTTCG 59.524 61.111 0.00 0.00 0.00 3.95
1923 1931 1.302431 CTCCACCGTTGGCATGTCA 60.302 57.895 0.00 0.00 43.56 3.58
1961 1969 0.108424 CTCTGACGGGAGCTTCAAGG 60.108 60.000 0.00 0.00 0.00 3.61
2040 2048 1.764571 TTGGAACCCCTGTCAGTCCG 61.765 60.000 0.00 0.00 0.00 4.79
2058 2066 0.486879 TTGCCCTGTTCCCCAGAATT 59.513 50.000 0.00 0.00 44.49 2.17
2151 2159 1.139058 CCAGGTAGCCATGTACTCCAC 59.861 57.143 0.00 0.00 0.00 4.02
2152 2160 1.007842 TCCAGGTAGCCATGTACTCCA 59.992 52.381 0.00 0.00 0.00 3.86
2153 2161 1.689273 CTCCAGGTAGCCATGTACTCC 59.311 57.143 0.00 0.00 0.00 3.85
2154 2162 1.069358 GCTCCAGGTAGCCATGTACTC 59.931 57.143 0.00 0.00 36.45 2.59
2155 2163 1.123928 GCTCCAGGTAGCCATGTACT 58.876 55.000 0.00 0.00 36.45 2.73
2294 2303 6.348950 CGAGCATTGTTTCAAACCCTAATACA 60.349 38.462 0.00 0.00 0.00 2.29
2327 2336 0.260816 TATGACAGCCGTACCCTCCT 59.739 55.000 0.00 0.00 0.00 3.69
2412 2423 5.983333 AAGATTGAGGGATGGTGTTAGAT 57.017 39.130 0.00 0.00 0.00 1.98
2422 2433 6.846505 TCAGGACATAGTTAAGATTGAGGGAT 59.153 38.462 0.00 0.00 0.00 3.85
2454 2465 4.082625 TGTCGACGCAATCTTAACCTTCTA 60.083 41.667 11.62 0.00 0.00 2.10
2490 2501 0.608130 CTAAACCTTTGCCCTTGCCC 59.392 55.000 0.00 0.00 36.33 5.36
2654 2666 2.912690 TTGGTGTGACAACATCGGTA 57.087 45.000 3.26 0.00 40.59 4.02
2826 2838 7.339466 GGACATGTTGTATTCTTTGGACCTAAT 59.661 37.037 0.00 0.00 0.00 1.73
2981 2993 1.000955 CTCACTGGTCCGCTGTTAAGT 59.999 52.381 0.00 0.00 0.00 2.24
3056 3068 1.338973 ACTTGCTCGTTACTCGACCAA 59.661 47.619 0.00 0.00 44.01 3.67
3108 3120 0.041684 TCTCTCCTGAGGATGCCACA 59.958 55.000 0.00 0.00 40.58 4.17


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

AutoCloner maintained by Alex Coulton.