Multiple sequence alignment - TraesCS3D01G319800

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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 TraesCS3D01G319800 chr3D 100.000 3658 0 0 1 3658 433413313 433416970 0.000000e+00 6756.0
1 TraesCS3D01G319800 chr3B 94.590 3013 119 24 410 3394 566160684 566163680 0.000000e+00 4621.0
2 TraesCS3D01G319800 chr3B 93.237 414 25 3 1 413 565854497 565854908 1.120000e-169 606.0
3 TraesCS3D01G319800 chr3B 87.823 271 28 5 3390 3658 566163714 566163981 2.740000e-81 313.0
4 TraesCS3D01G319800 chr3A 95.444 2568 70 22 861 3394 571790212 571792766 0.000000e+00 4050.0
5 TraesCS3D01G319800 chr3A 90.797 728 50 7 199 921 571789500 571790215 0.000000e+00 957.0
6 TraesCS3D01G319800 chr3A 90.775 271 21 4 3390 3658 571792800 571793068 3.470000e-95 359.0
7 TraesCS3D01G319800 chr4A 82.143 280 48 2 2012 2290 193732 193454 4.720000e-59 239.0
8 TraesCS3D01G319800 chr4A 93.333 45 3 0 2204 2248 294300211 294300255 2.360000e-07 67.6
9 TraesCS3D01G319800 chr4A 100.000 28 0 0 3444 3471 625272299 625272326 7.000000e-03 52.8
10 TraesCS3D01G319800 chr4D 81.786 280 49 2 2012 2290 464286 464008 2.200000e-57 233.0
11 TraesCS3D01G319800 chr4B 81.786 280 49 2 2012 2290 234393 234115 2.200000e-57 233.0
12 TraesCS3D01G319800 chr4B 84.496 129 20 0 2139 2267 178071960 178072088 1.070000e-25 128.0
13 TraesCS3D01G319800 chr5A 95.745 47 2 0 2207 2253 67471168 67471122 3.920000e-10 76.8
14 TraesCS3D01G319800 chr5A 82.090 67 12 0 1689 1755 697735620 697735554 1.420000e-04 58.4
15 TraesCS3D01G319800 chr2D 82.716 81 14 0 1728 1808 121704762 121704682 5.070000e-09 73.1
16 TraesCS3D01G319800 chr2D 100.000 28 0 0 3444 3471 35210445 35210418 7.000000e-03 52.8
17 TraesCS3D01G319800 chr5D 93.617 47 3 0 2207 2253 72902355 72902309 1.820000e-08 71.3
18 TraesCS3D01G319800 chr2B 81.481 81 15 0 1728 1808 174829932 174829852 2.360000e-07 67.6
19 TraesCS3D01G319800 chr1A 100.000 32 0 0 1782 1813 453074401 453074432 3.940000e-05 60.2
20 TraesCS3D01G319800 chr1A 100.000 28 0 0 1689 1716 448344226 448344199 7.000000e-03 52.8
21 TraesCS3D01G319800 chr7A 82.090 67 12 0 1689 1755 32963639 32963573 1.420000e-04 58.4
22 TraesCS3D01G319800 chr7A 80.597 67 13 0 1689 1755 115783003 115782937 7.000000e-03 52.8
23 TraesCS3D01G319800 chr6B 94.595 37 2 0 1782 1818 216356328 216356364 1.420000e-04 58.4
24 TraesCS3D01G319800 chr6A 94.595 37 2 0 1782 1818 160475787 160475823 1.420000e-04 58.4
25 TraesCS3D01G319800 chr1D 82.090 67 12 0 1689 1755 211986031 211986097 1.420000e-04 58.4
26 TraesCS3D01G319800 chr7B 96.875 32 1 0 1788 1819 713041842 713041873 2.000000e-03 54.7
27 TraesCS3D01G319800 chr1B 96.875 32 1 0 1785 1816 474835275 474835244 2.000000e-03 54.7


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 TraesCS3D01G319800 chr3D 433413313 433416970 3657 False 6756.000000 6756 100.000000 1 3658 1 chr3D.!!$F1 3657
1 TraesCS3D01G319800 chr3B 566160684 566163981 3297 False 2467.000000 4621 91.206500 410 3658 2 chr3B.!!$F2 3248
2 TraesCS3D01G319800 chr3A 571789500 571793068 3568 False 1788.666667 4050 92.338667 199 3658 3 chr3A.!!$F1 3459

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
130 131 0.030773 TCGTAGATGAGCCATGACGC 59.969 55.0 0.0 0.0 32.97 5.19 F
896 907 0.620556 AGCATTCCCGTCCACAGATT 59.379 50.0 0.0 0.0 0.00 2.40 F
912 980 0.654683 GATTCTCGTGTGCATGGCTC 59.345 55.0 0.0 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 1943 1.880340 GATCAGCCAAGCCGACGAG 60.880 63.158 0.0 0.0 0.00 4.18 R
2650 2733 2.279582 TCGGCTTCGATCTCAGAAAC 57.720 50.000 0.0 0.0 38.07 2.78 R
2672 2755 2.867368 GCTCATCTCTGCTTCATGTCAG 59.133 50.000 0.0 0.0 0.00 3.51 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
19 20 1.531423 TCGTAGAGAAGTTGCCTCGT 58.469 50.000 0.00 0.00 35.88 4.18
20 21 1.467734 TCGTAGAGAAGTTGCCTCGTC 59.532 52.381 0.00 0.00 35.88 4.20
21 22 1.790838 CGTAGAGAAGTTGCCTCGTCG 60.791 57.143 0.00 0.00 35.88 5.12
22 23 1.467734 GTAGAGAAGTTGCCTCGTCGA 59.532 52.381 0.00 0.00 35.88 4.20
23 24 0.959553 AGAGAAGTTGCCTCGTCGAA 59.040 50.000 0.00 0.00 35.88 3.71
24 25 1.068194 AGAGAAGTTGCCTCGTCGAAG 60.068 52.381 0.00 0.00 35.88 3.79
25 26 0.959553 AGAAGTTGCCTCGTCGAAGA 59.040 50.000 0.03 0.03 0.00 2.87
26 27 1.546476 AGAAGTTGCCTCGTCGAAGAT 59.454 47.619 0.35 0.00 40.67 2.40
27 28 1.921230 GAAGTTGCCTCGTCGAAGATC 59.079 52.381 0.35 0.00 40.67 2.75
28 29 0.179161 AGTTGCCTCGTCGAAGATCG 60.179 55.000 0.35 0.00 40.67 3.69
37 38 2.702847 TCGAAGATCGAGCCGATGA 58.297 52.632 13.68 3.75 47.00 2.92
38 39 1.021968 TCGAAGATCGAGCCGATGAA 58.978 50.000 13.68 0.00 47.00 2.57
39 40 1.002359 TCGAAGATCGAGCCGATGAAG 60.002 52.381 13.68 4.48 47.00 3.02
40 41 1.002359 CGAAGATCGAGCCGATGAAGA 60.002 52.381 13.68 0.00 47.00 2.87
41 42 2.389998 GAAGATCGAGCCGATGAAGAC 58.610 52.381 13.68 1.20 47.00 3.01
42 43 0.671251 AGATCGAGCCGATGAAGACC 59.329 55.000 13.68 0.60 47.00 3.85
43 44 0.671251 GATCGAGCCGATGAAGACCT 59.329 55.000 13.68 0.00 47.00 3.85
44 45 1.067821 GATCGAGCCGATGAAGACCTT 59.932 52.381 13.68 0.00 47.00 3.50
45 46 0.895530 TCGAGCCGATGAAGACCTTT 59.104 50.000 0.00 0.00 0.00 3.11
46 47 1.002366 CGAGCCGATGAAGACCTTTG 58.998 55.000 0.00 0.00 0.00 2.77
47 48 0.729690 GAGCCGATGAAGACCTTTGC 59.270 55.000 0.00 0.00 0.00 3.68
48 49 0.036732 AGCCGATGAAGACCTTTGCA 59.963 50.000 0.00 0.00 0.00 4.08
49 50 1.098050 GCCGATGAAGACCTTTGCAT 58.902 50.000 0.00 0.00 0.00 3.96
50 51 1.064654 GCCGATGAAGACCTTTGCATC 59.935 52.381 0.00 0.00 35.10 3.91
53 54 3.665173 GATGAAGACCTTTGCATCGTC 57.335 47.619 0.00 0.00 0.00 4.20
54 55 1.428448 TGAAGACCTTTGCATCGTCG 58.572 50.000 0.00 0.00 0.00 5.12
55 56 1.000394 TGAAGACCTTTGCATCGTCGA 60.000 47.619 0.00 0.00 0.00 4.20
56 57 1.390463 GAAGACCTTTGCATCGTCGAC 59.610 52.381 5.18 5.18 0.00 4.20
57 58 0.317160 AGACCTTTGCATCGTCGACA 59.683 50.000 17.16 3.13 0.00 4.35
58 59 0.716108 GACCTTTGCATCGTCGACAG 59.284 55.000 17.16 8.67 0.00 3.51
59 60 0.670546 ACCTTTGCATCGTCGACAGG 60.671 55.000 17.16 14.68 0.00 4.00
60 61 1.361668 CCTTTGCATCGTCGACAGGG 61.362 60.000 17.16 4.66 0.00 4.45
61 62 1.970917 CTTTGCATCGTCGACAGGGC 61.971 60.000 17.16 15.04 0.00 5.19
62 63 2.449031 TTTGCATCGTCGACAGGGCT 62.449 55.000 17.16 0.00 0.00 5.19
63 64 2.887568 GCATCGTCGACAGGGCTG 60.888 66.667 17.16 5.97 0.00 4.85
64 65 2.887568 CATCGTCGACAGGGCTGC 60.888 66.667 17.16 0.00 0.00 5.25
65 66 3.381983 ATCGTCGACAGGGCTGCA 61.382 61.111 17.16 0.00 0.00 4.41
66 67 3.649277 ATCGTCGACAGGGCTGCAC 62.649 63.158 17.16 0.00 0.00 4.57
68 69 4.314440 GTCGACAGGGCTGCACCA 62.314 66.667 11.55 0.00 42.05 4.17
69 70 4.314440 TCGACAGGGCTGCACCAC 62.314 66.667 0.00 0.00 42.05 4.16
71 72 4.269523 GACAGGGCTGCACCACCA 62.270 66.667 0.00 0.00 42.05 4.17
72 73 3.574074 GACAGGGCTGCACCACCAT 62.574 63.158 0.00 0.00 42.05 3.55
73 74 2.753043 CAGGGCTGCACCACCATC 60.753 66.667 0.00 0.00 42.05 3.51
74 75 3.259314 AGGGCTGCACCACCATCA 61.259 61.111 0.00 0.00 42.05 3.07
75 76 2.283101 GGGCTGCACCACCATCAA 60.283 61.111 0.50 0.00 42.05 2.57
76 77 2.639327 GGGCTGCACCACCATCAAC 61.639 63.158 0.50 0.00 42.05 3.18
77 78 1.902918 GGCTGCACCACCATCAACA 60.903 57.895 0.50 0.00 38.86 3.33
78 79 1.252904 GGCTGCACCACCATCAACAT 61.253 55.000 0.50 0.00 38.86 2.71
79 80 0.604578 GCTGCACCACCATCAACATT 59.395 50.000 0.00 0.00 0.00 2.71
80 81 1.670674 GCTGCACCACCATCAACATTG 60.671 52.381 0.00 0.00 0.00 2.82
81 82 1.887854 CTGCACCACCATCAACATTGA 59.112 47.619 0.00 0.00 42.14 2.57
82 83 2.296752 CTGCACCACCATCAACATTGAA 59.703 45.455 0.00 0.00 41.13 2.69
83 84 2.035704 TGCACCACCATCAACATTGAAC 59.964 45.455 0.00 0.00 41.13 3.18
84 85 2.035704 GCACCACCATCAACATTGAACA 59.964 45.455 0.00 0.00 41.13 3.18
85 86 3.306225 GCACCACCATCAACATTGAACAT 60.306 43.478 0.00 0.00 41.13 2.71
86 87 4.082300 GCACCACCATCAACATTGAACATA 60.082 41.667 0.00 0.00 41.13 2.29
87 88 5.401550 CACCACCATCAACATTGAACATAC 58.598 41.667 0.00 0.00 41.13 2.39
88 89 5.048154 CACCACCATCAACATTGAACATACA 60.048 40.000 0.00 0.00 41.13 2.29
89 90 5.183713 ACCACCATCAACATTGAACATACAG 59.816 40.000 0.00 0.00 41.13 2.74
90 91 5.393352 CCACCATCAACATTGAACATACAGG 60.393 44.000 0.00 0.00 41.13 4.00
91 92 5.415389 CACCATCAACATTGAACATACAGGA 59.585 40.000 0.00 0.00 41.13 3.86
92 93 6.009589 ACCATCAACATTGAACATACAGGAA 58.990 36.000 0.00 0.00 41.13 3.36
93 94 6.493115 ACCATCAACATTGAACATACAGGAAA 59.507 34.615 0.00 0.00 41.13 3.13
94 95 7.015098 ACCATCAACATTGAACATACAGGAAAA 59.985 33.333 0.00 0.00 41.13 2.29
95 96 7.543172 CCATCAACATTGAACATACAGGAAAAG 59.457 37.037 0.00 0.00 41.13 2.27
96 97 7.815840 TCAACATTGAACATACAGGAAAAGA 57.184 32.000 0.00 0.00 33.55 2.52
97 98 8.408043 TCAACATTGAACATACAGGAAAAGAT 57.592 30.769 0.00 0.00 33.55 2.40
98 99 9.513906 TCAACATTGAACATACAGGAAAAGATA 57.486 29.630 0.00 0.00 33.55 1.98
101 102 8.739972 ACATTGAACATACAGGAAAAGATAACC 58.260 33.333 0.00 0.00 0.00 2.85
102 103 8.960591 CATTGAACATACAGGAAAAGATAACCT 58.039 33.333 0.00 0.00 34.02 3.50
105 106 9.832445 TGAACATACAGGAAAAGATAACCTATC 57.168 33.333 0.00 0.00 35.41 2.08
106 107 9.274206 GAACATACAGGAAAAGATAACCTATCC 57.726 37.037 0.00 0.00 35.79 2.59
107 108 7.746703 ACATACAGGAAAAGATAACCTATCCC 58.253 38.462 0.00 0.00 35.79 3.85
108 109 5.291905 ACAGGAAAAGATAACCTATCCCG 57.708 43.478 0.00 0.00 35.79 5.14
109 110 4.065789 CAGGAAAAGATAACCTATCCCGC 58.934 47.826 0.00 0.00 35.79 6.13
110 111 3.974642 AGGAAAAGATAACCTATCCCGCT 59.025 43.478 0.00 0.00 35.79 5.52
111 112 4.412528 AGGAAAAGATAACCTATCCCGCTT 59.587 41.667 0.00 0.00 35.79 4.68
112 113 4.755629 GGAAAAGATAACCTATCCCGCTTC 59.244 45.833 0.00 0.00 35.79 3.86
113 114 3.662247 AAGATAACCTATCCCGCTTCG 57.338 47.619 0.00 0.00 35.79 3.79
114 115 2.595238 AGATAACCTATCCCGCTTCGT 58.405 47.619 0.00 0.00 35.79 3.85
115 116 3.759581 AGATAACCTATCCCGCTTCGTA 58.240 45.455 0.00 0.00 35.79 3.43
116 117 3.757493 AGATAACCTATCCCGCTTCGTAG 59.243 47.826 0.00 0.00 35.79 3.51
117 118 2.062971 AACCTATCCCGCTTCGTAGA 57.937 50.000 0.00 0.00 0.00 2.59
118 119 2.289592 ACCTATCCCGCTTCGTAGAT 57.710 50.000 0.00 0.00 35.04 1.98
119 120 1.887198 ACCTATCCCGCTTCGTAGATG 59.113 52.381 0.00 0.00 35.04 2.90
120 121 2.160205 CCTATCCCGCTTCGTAGATGA 58.840 52.381 0.00 0.00 35.04 2.92
121 122 2.162608 CCTATCCCGCTTCGTAGATGAG 59.837 54.545 0.00 0.00 35.04 2.90
122 123 0.315568 ATCCCGCTTCGTAGATGAGC 59.684 55.000 0.00 0.00 35.04 4.26
123 124 1.300233 CCCGCTTCGTAGATGAGCC 60.300 63.158 0.00 0.00 35.04 4.70
124 125 1.437573 CCGCTTCGTAGATGAGCCA 59.562 57.895 0.00 0.00 35.04 4.75
125 126 0.032678 CCGCTTCGTAGATGAGCCAT 59.967 55.000 0.00 0.00 35.04 4.40
126 127 1.135046 CGCTTCGTAGATGAGCCATG 58.865 55.000 0.00 0.00 35.04 3.66
127 128 1.269257 CGCTTCGTAGATGAGCCATGA 60.269 52.381 0.00 0.00 35.04 3.07
128 129 2.131183 GCTTCGTAGATGAGCCATGAC 58.869 52.381 0.00 0.00 35.04 3.06
129 130 2.389059 CTTCGTAGATGAGCCATGACG 58.611 52.381 0.00 10.45 35.04 4.35
130 131 0.030773 TCGTAGATGAGCCATGACGC 59.969 55.000 0.00 0.00 32.97 5.19
131 132 0.941463 CGTAGATGAGCCATGACGCC 60.941 60.000 0.00 0.00 0.00 5.68
132 133 0.941463 GTAGATGAGCCATGACGCCG 60.941 60.000 0.00 0.00 0.00 6.46
133 134 2.699576 TAGATGAGCCATGACGCCGC 62.700 60.000 0.00 0.00 0.00 6.53
134 135 4.166888 ATGAGCCATGACGCCGCT 62.167 61.111 0.00 0.00 34.97 5.52
135 136 3.687321 ATGAGCCATGACGCCGCTT 62.687 57.895 0.00 0.00 31.61 4.68
136 137 3.869272 GAGCCATGACGCCGCTTG 61.869 66.667 0.00 0.00 31.61 4.01
149 150 4.824166 GCTTGGCGCATGCTCACG 62.824 66.667 17.13 12.28 42.25 4.35
174 175 3.708403 ACGGAAGTAAAGGGGTTAAGG 57.292 47.619 0.00 0.00 46.88 2.69
175 176 2.306805 ACGGAAGTAAAGGGGTTAAGGG 59.693 50.000 0.00 0.00 46.88 3.95
176 177 2.573009 CGGAAGTAAAGGGGTTAAGGGA 59.427 50.000 0.00 0.00 0.00 4.20
177 178 3.620719 CGGAAGTAAAGGGGTTAAGGGAC 60.621 52.174 0.00 0.00 0.00 4.46
178 179 3.331591 GGAAGTAAAGGGGTTAAGGGACA 59.668 47.826 0.00 0.00 0.00 4.02
179 180 4.202599 GGAAGTAAAGGGGTTAAGGGACAA 60.203 45.833 0.00 0.00 0.00 3.18
180 181 5.517833 GGAAGTAAAGGGGTTAAGGGACAAT 60.518 44.000 0.00 0.00 0.00 2.71
181 182 5.610429 AGTAAAGGGGTTAAGGGACAATT 57.390 39.130 0.00 0.00 0.00 2.32
182 183 5.972698 AGTAAAGGGGTTAAGGGACAATTT 58.027 37.500 0.00 0.00 0.00 1.82
183 184 6.387127 AGTAAAGGGGTTAAGGGACAATTTT 58.613 36.000 0.00 0.00 0.00 1.82
184 185 5.560722 AAAGGGGTTAAGGGACAATTTTG 57.439 39.130 0.00 0.00 0.00 2.44
185 186 3.516586 AGGGGTTAAGGGACAATTTTGG 58.483 45.455 0.00 0.00 0.00 3.28
186 187 3.116512 AGGGGTTAAGGGACAATTTTGGT 60.117 43.478 0.00 0.00 0.00 3.67
187 188 3.649023 GGGGTTAAGGGACAATTTTGGTT 59.351 43.478 0.00 0.00 0.00 3.67
188 189 4.504165 GGGGTTAAGGGACAATTTTGGTTG 60.504 45.833 0.00 0.00 35.25 3.77
189 190 4.101898 GGGTTAAGGGACAATTTTGGTTGT 59.898 41.667 0.00 0.00 44.53 3.32
190 191 5.304871 GGGTTAAGGGACAATTTTGGTTGTA 59.695 40.000 0.00 0.00 42.08 2.41
191 192 6.183360 GGGTTAAGGGACAATTTTGGTTGTAA 60.183 38.462 0.00 0.00 42.08 2.41
192 193 6.926826 GGTTAAGGGACAATTTTGGTTGTAAG 59.073 38.462 0.00 0.00 42.08 2.34
193 194 7.201929 GGTTAAGGGACAATTTTGGTTGTAAGA 60.202 37.037 0.00 0.00 42.08 2.10
194 195 6.994421 AAGGGACAATTTTGGTTGTAAGAT 57.006 33.333 0.00 0.00 42.08 2.40
195 196 6.994421 AGGGACAATTTTGGTTGTAAGATT 57.006 33.333 0.00 0.00 42.08 2.40
196 197 6.993079 AGGGACAATTTTGGTTGTAAGATTC 58.007 36.000 0.00 0.00 42.08 2.52
197 198 6.553100 AGGGACAATTTTGGTTGTAAGATTCA 59.447 34.615 0.00 0.00 42.08 2.57
240 241 9.814899 ATTAAATTCATGTGTGTTCAACAAGAA 57.185 25.926 0.00 0.00 41.57 2.52
252 253 8.902806 TGTGTTCAACAAGAATCTAGTGAAATT 58.097 29.630 0.00 0.00 38.76 1.82
270 272 8.660373 AGTGAAATTTCATATTTGTCTCGAGAC 58.340 33.333 33.76 33.76 41.25 3.36
271 273 8.660373 GTGAAATTTCATATTTGTCTCGAGACT 58.340 33.333 37.63 24.51 41.35 3.24
288 290 3.087031 AGACTCCCTTGATTGCACAATG 58.913 45.455 0.00 0.00 0.00 2.82
297 300 2.488937 TGATTGCACAATGTAGGCACTG 59.511 45.455 0.00 0.00 41.52 3.66
312 315 3.066380 GGCACTGGTTTTAAATGGCAAG 58.934 45.455 7.26 0.00 35.99 4.01
319 322 6.166984 TGGTTTTAAATGGCAAGACAATCA 57.833 33.333 0.00 0.00 0.00 2.57
328 331 5.273674 TGGCAAGACAATCAAACATTTCA 57.726 34.783 0.00 0.00 0.00 2.69
333 336 2.318578 ACAATCAAACATTTCAGCGCG 58.681 42.857 0.00 0.00 0.00 6.86
336 339 0.660005 TCAAACATTTCAGCGCGTGC 60.660 50.000 14.39 14.39 43.24 5.34
340 343 3.788766 ATTTCAGCGCGTGCCGAC 61.789 61.111 19.02 0.00 44.31 4.79
376 379 2.787473 CCAGCTCCTTGGTGTCATTA 57.213 50.000 0.00 0.00 42.19 1.90
378 381 2.290260 CCAGCTCCTTGGTGTCATTACA 60.290 50.000 0.00 0.00 42.19 2.41
393 396 4.937620 GTCATTACACATTTGCTCCTCAGA 59.062 41.667 0.00 0.00 0.00 3.27
406 409 3.312890 CTCCTCAGAGTGGGATTGGTAT 58.687 50.000 0.00 0.00 35.21 2.73
412 415 4.040829 TCAGAGTGGGATTGGTATGCATAG 59.959 45.833 6.67 0.00 0.00 2.23
493 497 6.533730 AGTGTGGATAAGATCACAAGACAAA 58.466 36.000 0.00 0.00 44.19 2.83
511 516 5.069516 AGACAAAGAGTGCCAATTGTTCAAT 59.930 36.000 4.43 1.19 36.22 2.57
518 523 7.899973 AGAGTGCCAATTGTTCAATAAAAGAT 58.100 30.769 4.43 0.00 0.00 2.40
597 602 9.243105 AGTTATACAAATTTCCATGTAGTTGCT 57.757 29.630 0.00 0.00 35.64 3.91
622 627 6.784031 AGGATTAGGTATTAGGCAAATGGAG 58.216 40.000 0.00 0.00 0.00 3.86
629 634 4.931661 ATTAGGCAAATGGAGATGCAAG 57.068 40.909 0.00 0.00 44.32 4.01
642 647 4.643784 GGAGATGCAAGATGGAGTGAAAAT 59.356 41.667 0.00 0.00 0.00 1.82
646 651 7.542025 AGATGCAAGATGGAGTGAAAATTTAC 58.458 34.615 0.00 0.00 0.00 2.01
896 907 0.620556 AGCATTCCCGTCCACAGATT 59.379 50.000 0.00 0.00 0.00 2.40
899 967 2.555199 CATTCCCGTCCACAGATTCTC 58.445 52.381 0.00 0.00 0.00 2.87
912 980 0.654683 GATTCTCGTGTGCATGGCTC 59.345 55.000 0.00 0.00 0.00 4.70
1555 1624 3.059352 GGAGGTGACTACTGCAACAAT 57.941 47.619 0.00 0.00 44.43 2.71
1589 1660 5.494632 TCTGCAGCAGATTGTATCATTTG 57.505 39.130 21.85 0.00 35.39 2.32
1604 1675 7.275183 TGTATCATTTGTCCCTTCTCATGTAG 58.725 38.462 0.00 0.00 0.00 2.74
1605 1676 5.102953 TCATTTGTCCCTTCTCATGTAGG 57.897 43.478 0.00 0.00 0.00 3.18
1606 1677 4.782691 TCATTTGTCCCTTCTCATGTAGGA 59.217 41.667 11.28 1.59 33.18 2.94
1607 1678 5.250543 TCATTTGTCCCTTCTCATGTAGGAA 59.749 40.000 11.28 5.86 33.18 3.36
1608 1679 5.576563 TTTGTCCCTTCTCATGTAGGAAA 57.423 39.130 11.28 3.91 33.18 3.13
1609 1680 5.576563 TTGTCCCTTCTCATGTAGGAAAA 57.423 39.130 11.28 2.99 33.18 2.29
1868 1939 1.749634 TCGAGGTCGATTCCTTCCTTC 59.250 52.381 0.00 0.00 44.22 3.46
1869 1940 1.202428 CGAGGTCGATTCCTTCCTTCC 60.202 57.143 0.00 0.00 43.02 3.46
1870 1941 2.112190 GAGGTCGATTCCTTCCTTCCT 58.888 52.381 0.00 0.00 38.02 3.36
1871 1942 2.502130 GAGGTCGATTCCTTCCTTCCTT 59.498 50.000 0.00 0.00 38.02 3.36
1872 1943 2.502130 AGGTCGATTCCTTCCTTCCTTC 59.498 50.000 0.00 0.00 33.52 3.46
2319 2396 5.547666 TCATCCACTGGGTAAGCACATATAT 59.452 40.000 0.00 0.00 34.93 0.86
2320 2397 6.728632 TCATCCACTGGGTAAGCACATATATA 59.271 38.462 0.00 0.00 34.93 0.86
2322 2399 6.082031 TCCACTGGGTAAGCACATATATACT 58.918 40.000 0.00 0.00 34.93 2.12
2351 2428 5.303747 TCGAACGTTTAATCCAATGCAAT 57.696 34.783 0.46 0.00 0.00 3.56
2352 2429 5.328691 TCGAACGTTTAATCCAATGCAATC 58.671 37.500 0.46 0.00 0.00 2.67
2662 2745 2.169352 AGGACATGGGTTTCTGAGATCG 59.831 50.000 0.00 0.00 0.00 3.69
2981 3076 6.530019 ACATTACCATTTTCATTCTGGTCC 57.470 37.500 0.00 0.00 42.23 4.46
3025 3120 2.674747 CGCCAAGGATTTGTGGAATTGG 60.675 50.000 0.00 0.00 37.03 3.16
3144 3243 4.238761 TCTAGTCTTCGGCCGAATAATG 57.761 45.455 38.60 26.89 33.28 1.90
3174 3273 3.475566 TTGGTCTCACAAGAGTCAAGG 57.524 47.619 0.00 0.00 42.66 3.61
3372 3482 5.644636 TGATAAACACTATTTTGGGACGGAC 59.355 40.000 0.00 0.00 0.00 4.79
3378 3488 5.105595 ACACTATTTTGGGACGGACTAGTAC 60.106 44.000 0.00 0.00 0.00 2.73
3466 3616 5.821516 ACCACGACACTTATTTTGAAACA 57.178 34.783 0.00 0.00 0.00 2.83
3507 3657 5.073311 AGCGAGAATTTAGCACAACTCTA 57.927 39.130 0.00 0.00 0.00 2.43
3518 3668 2.673368 GCACAACTCTAAAGACCATCGG 59.327 50.000 0.00 0.00 0.00 4.18
3522 3672 2.180276 ACTCTAAAGACCATCGGCAGT 58.820 47.619 0.00 0.00 0.00 4.40
3535 3685 3.514777 GGCAGTTCATGACAGACGA 57.485 52.632 0.00 0.00 36.67 4.20
3558 3708 3.872696 TCATCACTATCACATTTGCCGT 58.127 40.909 0.00 0.00 0.00 5.68
3559 3709 3.622612 TCATCACTATCACATTTGCCGTG 59.377 43.478 0.00 0.00 35.63 4.94
3572 3722 2.048222 CCGTGTGCATCTGACCGT 60.048 61.111 0.00 0.00 0.00 4.83
3603 3753 5.047021 GCTAGCTACCATCACCATCAAGATA 60.047 44.000 7.70 0.00 0.00 1.98
3608 3758 6.072838 GCTACCATCACCATCAAGATAACATG 60.073 42.308 0.00 0.00 0.00 3.21
3610 3760 6.607970 ACCATCACCATCAAGATAACATGAT 58.392 36.000 0.00 0.00 35.28 2.45
3616 3766 5.008019 ACCATCAAGATAACATGATTCGCAC 59.992 40.000 0.00 0.00 33.09 5.34
3617 3767 5.446709 CATCAAGATAACATGATTCGCACC 58.553 41.667 0.00 0.00 33.09 5.01
3633 3783 4.003788 CCGGAACTCGTGGTGCCT 62.004 66.667 0.00 0.00 41.61 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.801379 CGATCTTCGACGAGGCAACTTCT 62.801 52.174 1.44 0.00 46.94 2.85
7 8 3.600154 CGATCTTCGACGAGGCAACTTC 61.600 54.545 1.44 0.00 46.94 3.01
8 9 1.732732 CGATCTTCGACGAGGCAACTT 60.733 52.381 1.44 0.00 46.94 2.66
10 11 0.179171 TCGATCTTCGACGAGGCAAC 60.179 55.000 1.44 0.00 44.82 4.17
11 12 0.098905 CTCGATCTTCGACGAGGCAA 59.901 55.000 13.64 0.00 44.82 4.52
12 13 1.722082 CTCGATCTTCGACGAGGCA 59.278 57.895 13.64 0.00 44.82 4.75
13 14 4.599417 CTCGATCTTCGACGAGGC 57.401 61.111 13.64 0.80 44.82 4.70
15 16 3.049958 ATCGGCTCGATCTTCGACGAG 62.050 57.143 16.32 16.32 45.60 4.18
16 17 1.158484 ATCGGCTCGATCTTCGACGA 61.158 55.000 12.74 12.74 46.13 4.20
17 18 0.994241 CATCGGCTCGATCTTCGACG 60.994 60.000 7.06 0.00 45.19 5.12
18 19 0.308068 TCATCGGCTCGATCTTCGAC 59.692 55.000 7.06 0.00 45.19 4.20
19 20 1.002359 CTTCATCGGCTCGATCTTCGA 60.002 52.381 7.06 0.00 45.19 3.71
20 21 1.002359 TCTTCATCGGCTCGATCTTCG 60.002 52.381 7.06 0.00 45.19 3.79
21 22 2.389998 GTCTTCATCGGCTCGATCTTC 58.610 52.381 7.06 0.00 45.19 2.87
22 23 1.067821 GGTCTTCATCGGCTCGATCTT 59.932 52.381 7.06 0.00 45.19 2.40
23 24 0.671251 GGTCTTCATCGGCTCGATCT 59.329 55.000 7.06 0.00 45.19 2.75
24 25 0.671251 AGGTCTTCATCGGCTCGATC 59.329 55.000 7.06 0.00 45.19 3.69
26 27 0.895530 AAAGGTCTTCATCGGCTCGA 59.104 50.000 0.00 0.00 41.13 4.04
27 28 1.002366 CAAAGGTCTTCATCGGCTCG 58.998 55.000 0.00 0.00 0.00 5.03
28 29 0.729690 GCAAAGGTCTTCATCGGCTC 59.270 55.000 0.00 0.00 0.00 4.70
29 30 0.036732 TGCAAAGGTCTTCATCGGCT 59.963 50.000 0.00 0.00 0.00 5.52
30 31 1.064654 GATGCAAAGGTCTTCATCGGC 59.935 52.381 0.00 0.00 0.00 5.54
33 34 2.029728 CGACGATGCAAAGGTCTTCATC 59.970 50.000 11.71 0.00 33.79 2.92
34 35 2.002586 CGACGATGCAAAGGTCTTCAT 58.997 47.619 11.71 0.00 0.00 2.57
35 36 1.000394 TCGACGATGCAAAGGTCTTCA 60.000 47.619 11.71 0.00 0.00 3.02
36 37 1.390463 GTCGACGATGCAAAGGTCTTC 59.610 52.381 0.00 0.00 0.00 2.87
37 38 1.270094 TGTCGACGATGCAAAGGTCTT 60.270 47.619 11.62 0.00 0.00 3.01
38 39 0.317160 TGTCGACGATGCAAAGGTCT 59.683 50.000 11.62 0.00 0.00 3.85
39 40 0.716108 CTGTCGACGATGCAAAGGTC 59.284 55.000 11.62 0.00 0.00 3.85
40 41 0.670546 CCTGTCGACGATGCAAAGGT 60.671 55.000 11.62 0.00 0.00 3.50
41 42 1.361668 CCCTGTCGACGATGCAAAGG 61.362 60.000 11.62 9.83 0.00 3.11
42 43 1.970917 GCCCTGTCGACGATGCAAAG 61.971 60.000 11.62 0.17 0.00 2.77
43 44 2.032634 GCCCTGTCGACGATGCAAA 61.033 57.895 11.62 0.00 0.00 3.68
44 45 2.434185 GCCCTGTCGACGATGCAA 60.434 61.111 11.62 0.00 0.00 4.08
45 46 3.381983 AGCCCTGTCGACGATGCA 61.382 61.111 20.38 0.00 0.00 3.96
46 47 2.887568 CAGCCCTGTCGACGATGC 60.888 66.667 11.62 12.56 0.00 3.91
47 48 2.887568 GCAGCCCTGTCGACGATG 60.888 66.667 11.62 6.94 0.00 3.84
48 49 3.381983 TGCAGCCCTGTCGACGAT 61.382 61.111 11.62 0.00 0.00 3.73
49 50 4.357947 GTGCAGCCCTGTCGACGA 62.358 66.667 11.62 0.00 0.00 4.20
51 52 4.314440 TGGTGCAGCCCTGTCGAC 62.314 66.667 14.36 9.11 36.04 4.20
52 53 4.314440 GTGGTGCAGCCCTGTCGA 62.314 66.667 14.36 0.00 36.04 4.20
54 55 3.574074 ATGGTGGTGCAGCCCTGTC 62.574 63.158 14.36 0.00 36.04 3.51
55 56 3.574074 GATGGTGGTGCAGCCCTGT 62.574 63.158 14.36 7.39 36.04 4.00
56 57 2.753043 GATGGTGGTGCAGCCCTG 60.753 66.667 14.36 0.00 36.04 4.45
57 58 2.844195 TTGATGGTGGTGCAGCCCT 61.844 57.895 14.36 4.56 36.04 5.19
58 59 2.283101 TTGATGGTGGTGCAGCCC 60.283 61.111 14.36 14.35 36.04 5.19
59 60 1.252904 ATGTTGATGGTGGTGCAGCC 61.253 55.000 14.36 5.89 37.90 4.85
60 61 0.604578 AATGTTGATGGTGGTGCAGC 59.395 50.000 9.47 9.47 0.00 5.25
61 62 1.887854 TCAATGTTGATGGTGGTGCAG 59.112 47.619 0.00 0.00 31.01 4.41
62 63 1.992538 TCAATGTTGATGGTGGTGCA 58.007 45.000 0.00 0.00 31.01 4.57
63 64 2.035704 TGTTCAATGTTGATGGTGGTGC 59.964 45.455 0.00 0.00 37.00 5.01
64 65 4.524316 ATGTTCAATGTTGATGGTGGTG 57.476 40.909 0.00 0.00 37.00 4.17
65 66 5.076182 TGTATGTTCAATGTTGATGGTGGT 58.924 37.500 0.00 0.00 37.00 4.16
66 67 5.393352 CCTGTATGTTCAATGTTGATGGTGG 60.393 44.000 0.00 0.00 37.00 4.61
67 68 5.415389 TCCTGTATGTTCAATGTTGATGGTG 59.585 40.000 0.00 0.00 37.00 4.17
68 69 5.569355 TCCTGTATGTTCAATGTTGATGGT 58.431 37.500 0.00 0.00 37.00 3.55
69 70 6.513806 TTCCTGTATGTTCAATGTTGATGG 57.486 37.500 0.00 0.00 37.00 3.51
70 71 8.298854 TCTTTTCCTGTATGTTCAATGTTGATG 58.701 33.333 0.00 0.00 37.00 3.07
71 72 8.408043 TCTTTTCCTGTATGTTCAATGTTGAT 57.592 30.769 0.00 0.00 37.00 2.57
72 73 7.815840 TCTTTTCCTGTATGTTCAATGTTGA 57.184 32.000 0.00 0.00 34.92 3.18
75 76 8.739972 GGTTATCTTTTCCTGTATGTTCAATGT 58.260 33.333 0.00 0.00 0.00 2.71
76 77 8.960591 AGGTTATCTTTTCCTGTATGTTCAATG 58.039 33.333 0.00 0.00 0.00 2.82
79 80 9.832445 GATAGGTTATCTTTTCCTGTATGTTCA 57.168 33.333 0.00 0.00 33.34 3.18
80 81 9.274206 GGATAGGTTATCTTTTCCTGTATGTTC 57.726 37.037 0.00 0.00 35.52 3.18
81 82 8.218488 GGGATAGGTTATCTTTTCCTGTATGTT 58.782 37.037 0.00 0.00 35.52 2.71
82 83 7.472945 CGGGATAGGTTATCTTTTCCTGTATGT 60.473 40.741 0.00 0.00 35.52 2.29
83 84 6.874134 CGGGATAGGTTATCTTTTCCTGTATG 59.126 42.308 0.00 0.00 35.52 2.39
84 85 6.520231 GCGGGATAGGTTATCTTTTCCTGTAT 60.520 42.308 5.33 0.00 36.28 2.29
85 86 5.221581 GCGGGATAGGTTATCTTTTCCTGTA 60.222 44.000 5.33 0.00 36.28 2.74
86 87 4.444449 GCGGGATAGGTTATCTTTTCCTGT 60.444 45.833 5.33 0.00 36.28 4.00
87 88 4.065789 GCGGGATAGGTTATCTTTTCCTG 58.934 47.826 0.00 0.00 36.65 3.86
88 89 3.974642 AGCGGGATAGGTTATCTTTTCCT 59.025 43.478 0.00 0.00 35.52 3.36
89 90 4.353383 AGCGGGATAGGTTATCTTTTCC 57.647 45.455 0.00 0.00 35.52 3.13
90 91 4.448060 CGAAGCGGGATAGGTTATCTTTTC 59.552 45.833 0.00 0.00 35.52 2.29
91 92 4.141779 ACGAAGCGGGATAGGTTATCTTTT 60.142 41.667 0.00 0.00 35.52 2.27
92 93 3.387050 ACGAAGCGGGATAGGTTATCTTT 59.613 43.478 0.00 0.00 35.52 2.52
93 94 2.963782 ACGAAGCGGGATAGGTTATCTT 59.036 45.455 0.00 0.00 35.52 2.40
94 95 2.595238 ACGAAGCGGGATAGGTTATCT 58.405 47.619 0.00 0.00 35.52 1.98
95 96 3.755378 TCTACGAAGCGGGATAGGTTATC 59.245 47.826 0.00 0.00 31.35 1.75
96 97 3.759581 TCTACGAAGCGGGATAGGTTAT 58.240 45.455 0.00 0.00 31.35 1.89
97 98 3.213206 TCTACGAAGCGGGATAGGTTA 57.787 47.619 0.00 0.00 31.35 2.85
98 99 2.062971 TCTACGAAGCGGGATAGGTT 57.937 50.000 0.00 0.00 34.19 3.50
99 100 1.887198 CATCTACGAAGCGGGATAGGT 59.113 52.381 0.00 0.00 0.00 3.08
100 101 2.160205 TCATCTACGAAGCGGGATAGG 58.840 52.381 0.00 0.00 0.00 2.57
101 102 2.414824 GCTCATCTACGAAGCGGGATAG 60.415 54.545 0.00 0.00 0.00 2.08
102 103 1.540267 GCTCATCTACGAAGCGGGATA 59.460 52.381 0.00 0.00 0.00 2.59
103 104 0.315568 GCTCATCTACGAAGCGGGAT 59.684 55.000 0.00 0.00 0.00 3.85
104 105 1.734137 GCTCATCTACGAAGCGGGA 59.266 57.895 0.00 0.00 0.00 5.14
105 106 1.300233 GGCTCATCTACGAAGCGGG 60.300 63.158 0.00 0.00 0.00 6.13
106 107 0.032678 ATGGCTCATCTACGAAGCGG 59.967 55.000 0.00 0.00 0.00 5.52
107 108 1.135046 CATGGCTCATCTACGAAGCG 58.865 55.000 0.00 0.00 0.00 4.68
108 109 2.131183 GTCATGGCTCATCTACGAAGC 58.869 52.381 0.00 0.00 0.00 3.86
109 110 2.389059 CGTCATGGCTCATCTACGAAG 58.611 52.381 0.00 0.00 34.34 3.79
110 111 1.536072 GCGTCATGGCTCATCTACGAA 60.536 52.381 16.75 0.00 34.34 3.85
111 112 0.030773 GCGTCATGGCTCATCTACGA 59.969 55.000 16.75 0.00 34.34 3.43
112 113 0.941463 GGCGTCATGGCTCATCTACG 60.941 60.000 0.00 11.80 40.72 3.51
113 114 0.941463 CGGCGTCATGGCTCATCTAC 60.941 60.000 0.00 0.00 42.02 2.59
114 115 1.363807 CGGCGTCATGGCTCATCTA 59.636 57.895 0.00 0.00 42.02 1.98
115 116 2.107750 CGGCGTCATGGCTCATCT 59.892 61.111 0.00 0.00 42.02 2.90
116 117 3.643978 GCGGCGTCATGGCTCATC 61.644 66.667 9.37 0.00 42.02 2.92
117 118 3.687321 AAGCGGCGTCATGGCTCAT 62.687 57.895 9.37 0.00 42.02 2.90
118 119 4.393155 AAGCGGCGTCATGGCTCA 62.393 61.111 9.37 0.00 42.02 4.26
119 120 3.869272 CAAGCGGCGTCATGGCTC 61.869 66.667 9.37 0.00 42.02 4.70
144 145 0.386352 TTACTTCCGTGTCGCGTGAG 60.386 55.000 5.77 4.75 39.32 3.51
145 146 0.030504 TTTACTTCCGTGTCGCGTGA 59.969 50.000 5.77 0.00 39.32 4.35
146 147 0.433492 CTTTACTTCCGTGTCGCGTG 59.567 55.000 5.77 0.00 39.32 5.34
147 148 0.665369 CCTTTACTTCCGTGTCGCGT 60.665 55.000 5.77 0.00 39.32 6.01
148 149 1.349259 CCCTTTACTTCCGTGTCGCG 61.349 60.000 0.00 0.00 40.95 5.87
149 150 1.017701 CCCCTTTACTTCCGTGTCGC 61.018 60.000 0.00 0.00 0.00 5.19
150 151 0.319405 ACCCCTTTACTTCCGTGTCG 59.681 55.000 0.00 0.00 0.00 4.35
151 152 2.556144 AACCCCTTTACTTCCGTGTC 57.444 50.000 0.00 0.00 0.00 3.67
152 153 3.244665 CCTTAACCCCTTTACTTCCGTGT 60.245 47.826 0.00 0.00 0.00 4.49
153 154 3.340928 CCTTAACCCCTTTACTTCCGTG 58.659 50.000 0.00 0.00 0.00 4.94
154 155 2.306805 CCCTTAACCCCTTTACTTCCGT 59.693 50.000 0.00 0.00 0.00 4.69
155 156 2.573009 TCCCTTAACCCCTTTACTTCCG 59.427 50.000 0.00 0.00 0.00 4.30
156 157 3.331591 TGTCCCTTAACCCCTTTACTTCC 59.668 47.826 0.00 0.00 0.00 3.46
157 158 4.645863 TGTCCCTTAACCCCTTTACTTC 57.354 45.455 0.00 0.00 0.00 3.01
158 159 5.610429 ATTGTCCCTTAACCCCTTTACTT 57.390 39.130 0.00 0.00 0.00 2.24
159 160 5.610429 AATTGTCCCTTAACCCCTTTACT 57.390 39.130 0.00 0.00 0.00 2.24
160 161 6.460781 CAAAATTGTCCCTTAACCCCTTTAC 58.539 40.000 0.00 0.00 0.00 2.01
161 162 5.544562 CCAAAATTGTCCCTTAACCCCTTTA 59.455 40.000 0.00 0.00 0.00 1.85
162 163 4.349636 CCAAAATTGTCCCTTAACCCCTTT 59.650 41.667 0.00 0.00 0.00 3.11
163 164 3.907474 CCAAAATTGTCCCTTAACCCCTT 59.093 43.478 0.00 0.00 0.00 3.95
164 165 3.116512 ACCAAAATTGTCCCTTAACCCCT 60.117 43.478 0.00 0.00 0.00 4.79
165 166 3.244582 ACCAAAATTGTCCCTTAACCCC 58.755 45.455 0.00 0.00 0.00 4.95
166 167 4.101898 ACAACCAAAATTGTCCCTTAACCC 59.898 41.667 0.00 0.00 38.44 4.11
167 168 5.284861 ACAACCAAAATTGTCCCTTAACC 57.715 39.130 0.00 0.00 38.44 2.85
168 169 7.718525 TCTTACAACCAAAATTGTCCCTTAAC 58.281 34.615 0.00 0.00 41.89 2.01
169 170 7.899648 TCTTACAACCAAAATTGTCCCTTAA 57.100 32.000 0.00 0.00 41.89 1.85
170 171 8.485578 AATCTTACAACCAAAATTGTCCCTTA 57.514 30.769 0.00 0.00 41.89 2.69
171 172 6.994421 ATCTTACAACCAAAATTGTCCCTT 57.006 33.333 0.00 0.00 41.89 3.95
172 173 6.553100 TGAATCTTACAACCAAAATTGTCCCT 59.447 34.615 0.00 0.00 41.89 4.20
173 174 6.754193 TGAATCTTACAACCAAAATTGTCCC 58.246 36.000 0.00 0.00 41.89 4.46
174 175 8.655651 TTTGAATCTTACAACCAAAATTGTCC 57.344 30.769 0.00 0.00 41.89 4.02
270 272 3.379372 CCTACATTGTGCAATCAAGGGAG 59.621 47.826 6.90 6.90 39.05 4.30
271 273 3.355378 CCTACATTGTGCAATCAAGGGA 58.645 45.455 6.65 0.00 34.11 4.20
288 290 3.257127 TGCCATTTAAAACCAGTGCCTAC 59.743 43.478 0.00 0.00 0.00 3.18
297 300 7.011857 TGTTTGATTGTCTTGCCATTTAAAACC 59.988 33.333 0.00 0.00 0.00 3.27
312 315 2.339400 CGCGCTGAAATGTTTGATTGTC 59.661 45.455 5.56 0.00 0.00 3.18
319 322 1.371635 GGCACGCGCTGAAATGTTT 60.372 52.632 5.73 0.00 38.60 2.83
333 336 0.928451 GACAACAAAAGCGTCGGCAC 60.928 55.000 0.00 0.00 43.41 5.01
336 339 0.378962 TTGGACAACAAAAGCGTCGG 59.621 50.000 0.00 0.00 35.79 4.79
369 372 4.650734 TGAGGAGCAAATGTGTAATGACA 58.349 39.130 0.00 0.00 0.00 3.58
376 379 2.551721 CCACTCTGAGGAGCAAATGTGT 60.552 50.000 9.85 0.00 42.98 3.72
378 381 1.004044 CCCACTCTGAGGAGCAAATGT 59.996 52.381 9.85 0.00 42.98 2.71
393 396 3.326521 TCCTATGCATACCAATCCCACT 58.673 45.455 1.16 0.00 0.00 4.00
406 409 1.555075 GAATATCCGGCCTCCTATGCA 59.445 52.381 0.00 0.00 0.00 3.96
412 415 1.416401 TCACAAGAATATCCGGCCTCC 59.584 52.381 0.00 0.00 0.00 4.30
493 497 7.288810 TCTTTTATTGAACAATTGGCACTCT 57.711 32.000 10.83 0.00 32.50 3.24
511 516 5.860941 TGGGCACAAAGTTGAATCTTTTA 57.139 34.783 0.00 0.00 35.77 1.52
518 523 7.256756 CAATTAAATTGGGCACAAAGTTGAA 57.743 32.000 4.97 0.00 40.55 2.69
592 597 6.110411 TGCCTAATACCTAATCCTAGCAAC 57.890 41.667 0.00 0.00 0.00 4.17
597 602 7.737607 TCTCCATTTGCCTAATACCTAATCCTA 59.262 37.037 0.00 0.00 0.00 2.94
622 627 6.753744 GGTAAATTTTCACTCCATCTTGCATC 59.246 38.462 0.00 0.00 0.00 3.91
629 634 9.710900 ATTCTTTTGGTAAATTTTCACTCCATC 57.289 29.630 0.00 0.00 0.00 3.51
642 647 9.454859 ACAAATGTTTTCCATTCTTTTGGTAAA 57.545 25.926 0.00 0.00 43.04 2.01
646 651 7.220491 GCAAACAAATGTTTTCCATTCTTTTGG 59.780 33.333 8.73 0.00 45.07 3.28
813 824 0.179045 AAGTGTGCGCTCTTGGTTCT 60.179 50.000 13.42 0.00 0.00 3.01
896 907 0.390340 GAAGAGCCATGCACACGAGA 60.390 55.000 0.00 0.00 0.00 4.04
899 967 0.167470 CTTGAAGAGCCATGCACACG 59.833 55.000 0.00 0.00 0.00 4.49
912 980 8.648097 CGAATTCGTTGGGATATATACTTGAAG 58.352 37.037 19.67 0.00 34.11 3.02
955 1024 1.732308 GACACCCTCGTACCGATCC 59.268 63.158 0.00 0.00 34.61 3.36
1359 1428 2.536365 CGCGTACATGTGACTGGTAAT 58.464 47.619 9.11 0.00 0.00 1.89
1555 1624 3.070015 TCTGCTGCAGATTATTGATCGGA 59.930 43.478 27.35 3.62 39.85 4.55
1587 1656 5.576563 TTTTCCTACATGAGAAGGGACAA 57.423 39.130 0.00 0.00 33.40 3.18
1588 1657 5.313712 GTTTTTCCTACATGAGAAGGGACA 58.686 41.667 0.00 0.00 33.40 4.02
1589 1660 4.392138 CGTTTTTCCTACATGAGAAGGGAC 59.608 45.833 0.00 1.24 33.40 4.46
1604 1675 5.875359 AGATAAGACTCATCCACGTTTTTCC 59.125 40.000 0.00 0.00 0.00 3.13
1605 1676 6.969828 AGATAAGACTCATCCACGTTTTTC 57.030 37.500 0.00 0.00 0.00 2.29
1606 1677 7.228706 ACAAAGATAAGACTCATCCACGTTTTT 59.771 33.333 0.00 0.00 0.00 1.94
1607 1678 6.710744 ACAAAGATAAGACTCATCCACGTTTT 59.289 34.615 0.00 0.00 0.00 2.43
1608 1679 6.231211 ACAAAGATAAGACTCATCCACGTTT 58.769 36.000 0.00 0.00 0.00 3.60
1609 1680 5.794894 ACAAAGATAAGACTCATCCACGTT 58.205 37.500 0.00 0.00 0.00 3.99
1868 1939 2.815647 GCCAAGCCGACGAGAAGG 60.816 66.667 0.00 0.00 0.00 3.46
1869 1940 2.097038 CAGCCAAGCCGACGAGAAG 61.097 63.158 0.00 0.00 0.00 2.85
1870 1941 1.888436 ATCAGCCAAGCCGACGAGAA 61.888 55.000 0.00 0.00 0.00 2.87
1871 1942 2.284798 GATCAGCCAAGCCGACGAGA 62.285 60.000 0.00 0.00 0.00 4.04
1872 1943 1.880340 GATCAGCCAAGCCGACGAG 60.880 63.158 0.00 0.00 0.00 4.18
2319 2396 6.038356 GGATTAAACGTTCGATTGGAGAGTA 58.962 40.000 0.00 0.00 0.00 2.59
2320 2397 4.868734 GGATTAAACGTTCGATTGGAGAGT 59.131 41.667 0.00 0.00 0.00 3.24
2322 2399 4.823157 TGGATTAAACGTTCGATTGGAGA 58.177 39.130 0.00 0.00 0.00 3.71
2351 2428 2.295349 GTGGTCTCGGTCTTGTTAGTGA 59.705 50.000 0.00 0.00 0.00 3.41
2352 2429 2.609737 GGTGGTCTCGGTCTTGTTAGTG 60.610 54.545 0.00 0.00 0.00 2.74
2650 2733 2.279582 TCGGCTTCGATCTCAGAAAC 57.720 50.000 0.00 0.00 38.07 2.78
2672 2755 2.867368 GCTCATCTCTGCTTCATGTCAG 59.133 50.000 0.00 0.00 0.00 3.51
2981 3076 6.455646 GCGGGATAGATTTTAGATTACATGCG 60.456 42.308 0.00 0.00 0.00 4.73
3025 3120 9.525409 TGTTTTTGAGTGTTCTACTAGAGTTAC 57.475 33.333 0.00 0.00 40.53 2.50
3131 3229 2.030185 GCTCTCTACATTATTCGGCCGA 60.030 50.000 27.28 27.28 0.00 5.54
3132 3230 2.288213 TGCTCTCTACATTATTCGGCCG 60.288 50.000 22.12 22.12 0.00 6.13
3133 3231 3.386768 TGCTCTCTACATTATTCGGCC 57.613 47.619 0.00 0.00 0.00 6.13
3144 3243 3.876274 TGTGAGACCAATGCTCTCTAC 57.124 47.619 7.06 4.77 35.99 2.59
3163 3262 5.567138 AAGTTTGTGAACCTTGACTCTTG 57.433 39.130 0.00 0.00 36.39 3.02
3174 3273 7.860872 CCATAAACCTAGTCAAAGTTTGTGAAC 59.139 37.037 15.08 6.65 42.03 3.18
3192 3291 6.771267 AGGTCGGATAATTTTCTCCATAAACC 59.229 38.462 0.00 0.00 0.00 3.27
3347 3455 5.644636 TCCGTCCCAAAATAGTGTTTATCAC 59.355 40.000 0.00 0.00 46.46 3.06
3349 3457 5.878669 AGTCCGTCCCAAAATAGTGTTTATC 59.121 40.000 0.00 0.00 0.00 1.75
3350 3458 5.812286 AGTCCGTCCCAAAATAGTGTTTAT 58.188 37.500 0.00 0.00 0.00 1.40
3351 3459 5.231702 AGTCCGTCCCAAAATAGTGTTTA 57.768 39.130 0.00 0.00 0.00 2.01
3353 3461 3.782656 AGTCCGTCCCAAAATAGTGTT 57.217 42.857 0.00 0.00 0.00 3.32
3396 3506 9.834628 TGTAAAATTTCAGTCGCTTTAAATAGG 57.165 29.630 0.00 0.00 0.00 2.57
3416 3566 6.442541 TTGGAAGTGAGGGAGTATGTAAAA 57.557 37.500 0.00 0.00 0.00 1.52
3466 3616 8.466617 TCTCGCTCTTATTAAATACTTCCTCT 57.533 34.615 0.00 0.00 0.00 3.69
3479 3629 6.595716 AGTTGTGCTAAATTCTCGCTCTTATT 59.404 34.615 0.00 0.00 0.00 1.40
3507 3657 2.086869 CATGAACTGCCGATGGTCTTT 58.913 47.619 0.00 0.00 0.00 2.52
3518 3668 1.989165 GAGTCGTCTGTCATGAACTGC 59.011 52.381 0.00 0.00 0.00 4.40
3522 3672 3.507622 AGTGATGAGTCGTCTGTCATGAA 59.492 43.478 13.45 0.00 33.43 2.57
3535 3685 3.873361 CGGCAAATGTGATAGTGATGAGT 59.127 43.478 0.00 0.00 0.00 3.41
3558 3708 2.358615 GGCACGGTCAGATGCACA 60.359 61.111 0.00 0.00 43.93 4.57
3559 3709 2.046892 AGGCACGGTCAGATGCAC 60.047 61.111 0.00 0.00 43.93 4.57
3572 3722 1.457643 ATGGTAGCTAGCGGAGGCA 60.458 57.895 17.59 0.00 43.41 4.75
3603 3753 0.802494 GTTCCGGTGCGAATCATGTT 59.198 50.000 0.00 0.00 0.00 2.71
3608 3758 1.445582 ACGAGTTCCGGTGCGAATC 60.446 57.895 0.00 0.00 43.93 2.52
3610 3760 2.355363 CACGAGTTCCGGTGCGAA 60.355 61.111 0.00 0.00 43.93 4.70
3616 3766 2.642254 TAGGCACCACGAGTTCCGG 61.642 63.158 0.00 0.00 43.93 5.14
3617 3767 1.445582 GTAGGCACCACGAGTTCCG 60.446 63.158 0.00 0.00 36.79 4.30


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

AutoCloner maintained by Alex Coulton.