Multiple sequence alignment - TraesCS5A01G312700

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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 TraesCS5A01G312700 chr5A 100.000 3914 0 0 1 3914 524046919 524050832 0.000000e+00 7228.0
1 TraesCS5A01G312700 chr5A 100.000 36 0 0 2303 2338 524049177 524049212 2.520000e-07 67.6
2 TraesCS5A01G312700 chr5A 100.000 36 0 0 2259 2294 524049221 524049256 2.520000e-07 67.6
3 TraesCS5A01G312700 chr5B 92.165 2425 106 35 792 3183 496263310 496265683 0.000000e+00 3349.0
4 TraesCS5A01G312700 chr5B 91.270 378 21 2 3548 3914 496266012 496266388 4.510000e-139 505.0
5 TraesCS5A01G312700 chr5B 88.828 367 21 7 423 789 496262903 496263249 2.160000e-117 433.0
6 TraesCS5A01G312700 chr5B 92.271 207 12 3 3181 3383 496265742 496265948 1.380000e-74 291.0
7 TraesCS5A01G312700 chr5B 100.000 36 0 0 2303 2338 496264747 496264782 2.520000e-07 67.6
8 TraesCS5A01G312700 chr5B 100.000 36 0 0 2259 2294 496264791 496264826 2.520000e-07 67.6
9 TraesCS5A01G312700 chr5D 96.164 1147 34 7 792 1934 412307673 412308813 0.000000e+00 1866.0
10 TraesCS5A01G312700 chr5D 93.117 1235 41 23 1985 3183 412308820 412310046 0.000000e+00 1770.0
11 TraesCS5A01G312700 chr5D 88.903 793 24 20 3181 3914 412310110 412310897 0.000000e+00 918.0
12 TraesCS5A01G312700 chr5D 90.685 365 17 6 425 789 412307270 412307617 1.650000e-128 470.0
13 TraesCS5A01G312700 chr5D 88.538 253 29 0 174 426 412306988 412307240 1.370000e-79 307.0
14 TraesCS5A01G312700 chr5D 100.000 36 0 0 2303 2338 412309095 412309130 2.520000e-07 67.6
15 TraesCS5A01G312700 chr5D 100.000 36 0 0 2259 2294 412309139 412309174 2.520000e-07 67.6
16 TraesCS5A01G312700 chr7D 76.000 325 60 15 3237 3548 522865159 522865478 6.770000e-33 152.0
17 TraesCS5A01G312700 chr2A 75.789 190 40 6 3242 3429 71103041 71103226 1.500000e-14 91.6
18 TraesCS5A01G312700 chrUn 93.478 46 3 0 3251 3296 287061155 287061200 7.020000e-08 69.4
19 TraesCS5A01G312700 chr3D 93.478 46 3 0 3251 3296 570115801 570115846 7.020000e-08 69.4


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 TraesCS5A01G312700 chr5A 524046919 524050832 3913 False 2454.400000 7228 100.000000 1 3914 3 chr5A.!!$F1 3913
1 TraesCS5A01G312700 chr5B 496262903 496266388 3485 False 785.533333 3349 94.089000 423 3914 6 chr5B.!!$F1 3491
2 TraesCS5A01G312700 chr5D 412306988 412310897 3909 False 780.885714 1866 93.915286 174 3914 7 chr5D.!!$F1 3740

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
153 154 0.039035 TGCGGGATTGGCCTTAGTTT 59.961 50.0 3.32 0.00 36.66 2.66 F
750 782 0.251634 CTCAGGAGCCAGAACCTTCC 59.748 60.0 0.00 0.00 33.91 3.46 F
790 822 1.032114 GGGCGGAACAAGAATCAGGG 61.032 60.0 0.00 0.00 0.00 4.45 F
1778 1882 0.387929 ATTCGAGGGCGCTTTCGATA 59.612 50.0 27.79 20.75 44.32 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 1861 0.173935 TCGAAAGCGCCCTCGAATAA 59.826 50.0 24.20 6.4 40.89 1.40 R
1778 1882 0.904649 TCCTGTCATCGATGCCTGTT 59.095 50.0 20.81 0.0 0.00 3.16 R
1936 2041 0.968901 ATACGCACCCGGAGTTCAGA 60.969 55.0 0.73 0.0 39.22 3.27 R
3392 3619 0.035056 AGGTGCATGCTAAGGTGGTC 60.035 55.0 20.33 0.0 0.00 4.02 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
27 28 6.882610 TGTCTTGTGCATAGACAAAGAAAT 57.117 33.333 24.12 0.00 46.54 2.17
28 29 6.902341 TGTCTTGTGCATAGACAAAGAAATC 58.098 36.000 24.12 3.79 46.54 2.17
29 30 6.017933 GTCTTGTGCATAGACAAAGAAATCG 58.982 40.000 20.71 0.00 41.29 3.34
30 31 5.931724 TCTTGTGCATAGACAAAGAAATCGA 59.068 36.000 0.00 0.00 35.44 3.59
31 32 6.595326 TCTTGTGCATAGACAAAGAAATCGAT 59.405 34.615 0.00 0.00 35.44 3.59
32 33 7.763985 TCTTGTGCATAGACAAAGAAATCGATA 59.236 33.333 0.00 0.00 35.44 2.92
33 34 7.468922 TGTGCATAGACAAAGAAATCGATAG 57.531 36.000 0.00 0.00 0.00 2.08
34 35 7.041721 TGTGCATAGACAAAGAAATCGATAGT 58.958 34.615 0.00 0.00 37.40 2.12
35 36 7.010460 TGTGCATAGACAAAGAAATCGATAGTG 59.990 37.037 0.00 0.00 37.40 2.74
36 37 6.479990 TGCATAGACAAAGAAATCGATAGTGG 59.520 38.462 0.00 0.00 37.40 4.00
37 38 6.480320 GCATAGACAAAGAAATCGATAGTGGT 59.520 38.462 0.00 0.00 37.40 4.16
38 39 7.652105 GCATAGACAAAGAAATCGATAGTGGTA 59.348 37.037 0.00 0.00 37.40 3.25
39 40 8.969267 CATAGACAAAGAAATCGATAGTGGTAC 58.031 37.037 0.00 0.00 37.40 3.34
40 41 7.171630 AGACAAAGAAATCGATAGTGGTACT 57.828 36.000 0.00 0.00 37.40 2.73
41 42 7.612677 AGACAAAGAAATCGATAGTGGTACTT 58.387 34.615 0.00 0.00 37.40 2.24
42 43 7.760340 AGACAAAGAAATCGATAGTGGTACTTC 59.240 37.037 0.00 0.00 37.40 3.01
43 44 7.612677 ACAAAGAAATCGATAGTGGTACTTCT 58.387 34.615 0.00 0.00 37.40 2.85
44 45 7.760340 ACAAAGAAATCGATAGTGGTACTTCTC 59.240 37.037 0.00 0.00 37.40 2.87
45 46 6.062434 AGAAATCGATAGTGGTACTTCTCG 57.938 41.667 0.00 0.00 35.11 4.04
46 47 5.589452 AGAAATCGATAGTGGTACTTCTCGT 59.411 40.000 0.00 0.00 35.25 4.18
47 48 5.421212 AATCGATAGTGGTACTTCTCGTC 57.579 43.478 0.00 0.00 35.25 4.20
48 49 3.865446 TCGATAGTGGTACTTCTCGTCA 58.135 45.455 11.01 0.00 35.25 4.35
49 50 3.869832 TCGATAGTGGTACTTCTCGTCAG 59.130 47.826 11.01 0.00 35.25 3.51
50 51 3.869832 CGATAGTGGTACTTCTCGTCAGA 59.130 47.826 0.00 0.00 31.66 3.27
51 52 4.512198 CGATAGTGGTACTTCTCGTCAGAT 59.488 45.833 0.00 0.00 31.66 2.90
52 53 5.559225 CGATAGTGGTACTTCTCGTCAGATG 60.559 48.000 0.00 0.00 31.66 2.90
53 54 3.687125 AGTGGTACTTCTCGTCAGATGA 58.313 45.455 0.00 0.00 0.00 2.92
54 55 3.692101 AGTGGTACTTCTCGTCAGATGAG 59.308 47.826 12.96 12.96 32.57 2.90
55 56 3.690139 GTGGTACTTCTCGTCAGATGAGA 59.310 47.826 17.21 17.21 38.41 3.27
56 57 4.156190 GTGGTACTTCTCGTCAGATGAGAA 59.844 45.833 26.81 26.81 45.20 2.87
57 58 4.950475 TGGTACTTCTCGTCAGATGAGAAT 59.050 41.667 28.13 21.12 45.92 2.40
58 59 5.066634 TGGTACTTCTCGTCAGATGAGAATC 59.933 44.000 28.13 21.30 45.92 2.52
59 60 5.298276 GGTACTTCTCGTCAGATGAGAATCT 59.702 44.000 28.13 20.20 45.92 2.40
60 61 5.499139 ACTTCTCGTCAGATGAGAATCTC 57.501 43.478 28.13 2.75 45.92 2.75
61 62 4.338118 ACTTCTCGTCAGATGAGAATCTCC 59.662 45.833 28.13 0.00 45.92 3.71
62 63 3.891049 TCTCGTCAGATGAGAATCTCCA 58.109 45.455 18.60 0.00 37.32 3.86
63 64 3.882288 TCTCGTCAGATGAGAATCTCCAG 59.118 47.826 18.60 0.00 37.32 3.86
64 65 2.360483 TCGTCAGATGAGAATCTCCAGC 59.640 50.000 7.91 0.00 34.92 4.85
65 66 2.361757 CGTCAGATGAGAATCTCCAGCT 59.638 50.000 7.91 1.53 34.92 4.24
66 67 3.181477 CGTCAGATGAGAATCTCCAGCTT 60.181 47.826 7.91 0.00 34.92 3.74
67 68 4.680172 CGTCAGATGAGAATCTCCAGCTTT 60.680 45.833 7.91 0.00 34.92 3.51
68 69 5.451103 CGTCAGATGAGAATCTCCAGCTTTA 60.451 44.000 7.91 0.00 34.92 1.85
69 70 6.344500 GTCAGATGAGAATCTCCAGCTTTAA 58.656 40.000 7.91 0.00 34.92 1.52
70 71 6.820656 GTCAGATGAGAATCTCCAGCTTTAAA 59.179 38.462 7.91 0.00 34.92 1.52
71 72 7.335422 GTCAGATGAGAATCTCCAGCTTTAAAA 59.665 37.037 7.91 0.00 34.92 1.52
72 73 7.551974 TCAGATGAGAATCTCCAGCTTTAAAAG 59.448 37.037 7.91 0.00 34.92 2.27
73 74 5.886960 TGAGAATCTCCAGCTTTAAAAGC 57.113 39.130 7.91 0.00 46.01 3.51
90 91 9.646427 CTTTAAAAGCTAGAGTGTACAAGAGAT 57.354 33.333 0.00 0.00 0.00 2.75
91 92 8.988064 TTAAAAGCTAGAGTGTACAAGAGATG 57.012 34.615 0.00 0.00 0.00 2.90
92 93 6.842437 AAAGCTAGAGTGTACAAGAGATGA 57.158 37.500 0.00 0.00 0.00 2.92
93 94 6.842437 AAGCTAGAGTGTACAAGAGATGAA 57.158 37.500 0.00 0.00 0.00 2.57
94 95 6.449635 AGCTAGAGTGTACAAGAGATGAAG 57.550 41.667 0.00 0.00 0.00 3.02
95 96 5.040635 GCTAGAGTGTACAAGAGATGAAGC 58.959 45.833 0.00 0.00 0.00 3.86
96 97 5.393569 GCTAGAGTGTACAAGAGATGAAGCA 60.394 44.000 0.00 0.00 0.00 3.91
97 98 5.674052 AGAGTGTACAAGAGATGAAGCAT 57.326 39.130 0.00 0.00 0.00 3.79
98 99 6.782082 AGAGTGTACAAGAGATGAAGCATA 57.218 37.500 0.00 0.00 0.00 3.14
99 100 7.175347 AGAGTGTACAAGAGATGAAGCATAA 57.825 36.000 0.00 0.00 0.00 1.90
100 101 7.615403 AGAGTGTACAAGAGATGAAGCATAAA 58.385 34.615 0.00 0.00 0.00 1.40
101 102 7.763528 AGAGTGTACAAGAGATGAAGCATAAAG 59.236 37.037 0.00 0.00 0.00 1.85
102 103 7.390027 AGTGTACAAGAGATGAAGCATAAAGT 58.610 34.615 0.00 0.00 0.00 2.66
103 104 7.332926 AGTGTACAAGAGATGAAGCATAAAGTG 59.667 37.037 0.00 0.00 0.00 3.16
104 105 6.595326 TGTACAAGAGATGAAGCATAAAGTGG 59.405 38.462 0.00 0.00 0.00 4.00
105 106 4.397417 ACAAGAGATGAAGCATAAAGTGGC 59.603 41.667 0.00 0.00 0.00 5.01
106 107 4.226427 AGAGATGAAGCATAAAGTGGCA 57.774 40.909 0.00 0.00 0.00 4.92
107 108 4.789807 AGAGATGAAGCATAAAGTGGCAT 58.210 39.130 0.00 0.00 0.00 4.40
108 109 5.933617 AGAGATGAAGCATAAAGTGGCATA 58.066 37.500 0.00 0.00 0.00 3.14
109 110 5.762218 AGAGATGAAGCATAAAGTGGCATAC 59.238 40.000 0.00 0.00 0.00 2.39
110 111 5.439721 AGATGAAGCATAAAGTGGCATACA 58.560 37.500 0.00 0.00 0.00 2.29
124 125 4.119136 TGGCATACACATGTATCAAGTCG 58.881 43.478 0.00 0.00 39.06 4.18
125 126 3.494626 GGCATACACATGTATCAAGTCGG 59.505 47.826 0.00 0.00 39.06 4.79
126 127 4.119862 GCATACACATGTATCAAGTCGGT 58.880 43.478 0.00 0.00 39.06 4.69
127 128 4.209288 GCATACACATGTATCAAGTCGGTC 59.791 45.833 0.00 0.00 39.06 4.79
128 129 3.247006 ACACATGTATCAAGTCGGTCC 57.753 47.619 0.00 0.00 0.00 4.46
129 130 2.565391 ACACATGTATCAAGTCGGTCCA 59.435 45.455 0.00 0.00 0.00 4.02
130 131 3.007506 ACACATGTATCAAGTCGGTCCAA 59.992 43.478 0.00 0.00 0.00 3.53
131 132 4.000325 CACATGTATCAAGTCGGTCCAAA 59.000 43.478 0.00 0.00 0.00 3.28
132 133 4.635765 CACATGTATCAAGTCGGTCCAAAT 59.364 41.667 0.00 0.00 0.00 2.32
133 134 5.815222 CACATGTATCAAGTCGGTCCAAATA 59.185 40.000 0.00 0.00 0.00 1.40
134 135 6.483307 CACATGTATCAAGTCGGTCCAAATAT 59.517 38.462 0.00 0.00 0.00 1.28
135 136 6.483307 ACATGTATCAAGTCGGTCCAAATATG 59.517 38.462 0.00 0.00 0.00 1.78
136 137 4.814234 TGTATCAAGTCGGTCCAAATATGC 59.186 41.667 0.00 0.00 0.00 3.14
137 138 2.276201 TCAAGTCGGTCCAAATATGCG 58.724 47.619 0.00 0.00 0.00 4.73
138 139 1.330521 CAAGTCGGTCCAAATATGCGG 59.669 52.381 0.00 0.00 0.00 5.69
139 140 0.179056 AGTCGGTCCAAATATGCGGG 60.179 55.000 0.00 0.00 0.00 6.13
140 141 0.179067 GTCGGTCCAAATATGCGGGA 60.179 55.000 0.00 0.00 0.00 5.14
141 142 0.762418 TCGGTCCAAATATGCGGGAT 59.238 50.000 0.00 0.00 32.43 3.85
142 143 1.142060 TCGGTCCAAATATGCGGGATT 59.858 47.619 0.00 0.00 32.43 3.01
143 144 1.266718 CGGTCCAAATATGCGGGATTG 59.733 52.381 0.00 0.00 32.43 2.67
144 145 1.613437 GGTCCAAATATGCGGGATTGG 59.387 52.381 5.14 5.14 42.92 3.16
145 146 1.000274 GTCCAAATATGCGGGATTGGC 60.000 52.381 6.34 0.25 41.64 4.52
146 147 0.318120 CCAAATATGCGGGATTGGCC 59.682 55.000 0.00 0.00 36.25 5.36
147 148 1.331214 CAAATATGCGGGATTGGCCT 58.669 50.000 3.32 0.00 36.66 5.19
148 149 1.688197 CAAATATGCGGGATTGGCCTT 59.312 47.619 3.32 0.00 36.66 4.35
149 150 2.890311 CAAATATGCGGGATTGGCCTTA 59.110 45.455 3.32 0.00 36.66 2.69
150 151 2.496899 ATATGCGGGATTGGCCTTAG 57.503 50.000 3.32 0.00 36.66 2.18
151 152 1.136828 TATGCGGGATTGGCCTTAGT 58.863 50.000 3.32 0.00 36.66 2.24
152 153 0.258774 ATGCGGGATTGGCCTTAGTT 59.741 50.000 3.32 0.00 36.66 2.24
153 154 0.039035 TGCGGGATTGGCCTTAGTTT 59.961 50.000 3.32 0.00 36.66 2.66
154 155 1.182667 GCGGGATTGGCCTTAGTTTT 58.817 50.000 3.32 0.00 36.66 2.43
155 156 1.135112 GCGGGATTGGCCTTAGTTTTG 60.135 52.381 3.32 0.00 36.66 2.44
156 157 1.476488 CGGGATTGGCCTTAGTTTTGG 59.524 52.381 3.32 0.00 36.66 3.28
157 158 2.536066 GGGATTGGCCTTAGTTTTGGT 58.464 47.619 3.32 0.00 36.66 3.67
158 159 2.903784 GGGATTGGCCTTAGTTTTGGTT 59.096 45.455 3.32 0.00 36.66 3.67
159 160 3.306710 GGGATTGGCCTTAGTTTTGGTTG 60.307 47.826 3.32 0.00 36.66 3.77
160 161 3.576550 GGATTGGCCTTAGTTTTGGTTGA 59.423 43.478 3.32 0.00 0.00 3.18
161 162 4.321974 GGATTGGCCTTAGTTTTGGTTGAG 60.322 45.833 3.32 0.00 0.00 3.02
162 163 3.306472 TGGCCTTAGTTTTGGTTGAGT 57.694 42.857 3.32 0.00 0.00 3.41
163 164 3.637769 TGGCCTTAGTTTTGGTTGAGTT 58.362 40.909 3.32 0.00 0.00 3.01
164 165 3.634910 TGGCCTTAGTTTTGGTTGAGTTC 59.365 43.478 3.32 0.00 0.00 3.01
165 166 3.634910 GGCCTTAGTTTTGGTTGAGTTCA 59.365 43.478 0.00 0.00 0.00 3.18
166 167 4.261614 GGCCTTAGTTTTGGTTGAGTTCAG 60.262 45.833 0.00 0.00 0.00 3.02
167 168 4.261614 GCCTTAGTTTTGGTTGAGTTCAGG 60.262 45.833 0.00 0.00 0.00 3.86
168 169 5.130350 CCTTAGTTTTGGTTGAGTTCAGGA 58.870 41.667 0.00 0.00 0.00 3.86
169 170 5.770162 CCTTAGTTTTGGTTGAGTTCAGGAT 59.230 40.000 0.00 0.00 0.00 3.24
170 171 6.294176 CCTTAGTTTTGGTTGAGTTCAGGATG 60.294 42.308 0.00 0.00 37.54 3.51
171 172 4.536765 AGTTTTGGTTGAGTTCAGGATGT 58.463 39.130 0.00 0.00 37.40 3.06
172 173 4.580580 AGTTTTGGTTGAGTTCAGGATGTC 59.419 41.667 0.00 0.00 37.40 3.06
178 179 1.613630 AGTTCAGGATGTCGGGGCT 60.614 57.895 0.00 0.00 37.40 5.19
180 181 1.918293 TTCAGGATGTCGGGGCTGT 60.918 57.895 0.00 0.00 37.40 4.40
185 186 1.745489 GATGTCGGGGCTGTTGTCC 60.745 63.158 0.00 0.00 37.19 4.02
208 209 2.745821 GACATCCGTAAACCTTCCCAAC 59.254 50.000 0.00 0.00 0.00 3.77
216 217 4.440940 CGTAAACCTTCCCAACTTTGCTTT 60.441 41.667 0.00 0.00 0.00 3.51
217 218 4.568072 AAACCTTCCCAACTTTGCTTTT 57.432 36.364 0.00 0.00 0.00 2.27
221 222 3.071457 CCTTCCCAACTTTGCTTTTGGAT 59.929 43.478 1.82 0.00 44.51 3.41
222 223 4.444733 CCTTCCCAACTTTGCTTTTGGATT 60.445 41.667 1.82 0.00 44.51 3.01
223 224 5.221621 CCTTCCCAACTTTGCTTTTGGATTA 60.222 40.000 1.82 0.00 44.51 1.75
231 232 7.637709 ACTTTGCTTTTGGATTACGAAAATC 57.362 32.000 0.00 0.00 34.36 2.17
232 233 6.362283 ACTTTGCTTTTGGATTACGAAAATCG 59.638 34.615 0.00 0.00 46.93 3.34
234 235 5.627172 TGCTTTTGGATTACGAAAATCGAG 58.373 37.500 6.78 0.00 43.74 4.04
240 241 5.416083 TGGATTACGAAAATCGAGACATGT 58.584 37.500 0.00 0.00 43.74 3.21
291 292 3.033185 CGTTGGACGTCACAAAATGTTC 58.967 45.455 18.91 5.54 36.74 3.18
310 311 3.371063 GATCGCGAGGCCCGGATA 61.371 66.667 16.66 0.00 39.04 2.59
315 316 0.320073 CGCGAGGCCCGGATATTTAA 60.320 55.000 0.73 0.00 39.04 1.52
325 326 2.129607 CGGATATTTAACGGACGGTGG 58.870 52.381 0.00 0.00 0.00 4.61
333 334 2.425143 AACGGACGGTGGTAGAGATA 57.575 50.000 0.00 0.00 0.00 1.98
337 338 1.326328 GACGGTGGTAGAGATACCCC 58.674 60.000 2.13 2.78 39.34 4.95
386 387 2.548057 ACAGTAACAATTCAGGCACACG 59.452 45.455 0.00 0.00 0.00 4.49
411 412 2.404215 CAGTCAGTCGATTTCAACGGT 58.596 47.619 0.00 0.00 0.00 4.83
419 420 1.659098 CGATTTCAACGGTCAGTAGGC 59.341 52.381 0.00 0.00 0.00 3.93
504 536 2.997315 CGGCTCCCACCACAGAGA 60.997 66.667 0.00 0.00 31.43 3.10
505 537 2.985456 GGCTCCCACCACAGAGAG 59.015 66.667 0.00 0.00 31.43 3.20
506 538 1.610673 GGCTCCCACCACAGAGAGA 60.611 63.158 0.00 0.00 31.43 3.10
507 539 1.612395 GGCTCCCACCACAGAGAGAG 61.612 65.000 0.00 0.00 31.43 3.20
508 540 1.896694 CTCCCACCACAGAGAGAGC 59.103 63.158 0.00 0.00 31.43 4.09
510 542 1.188219 TCCCACCACAGAGAGAGCAC 61.188 60.000 0.00 0.00 0.00 4.40
511 543 1.294780 CCACCACAGAGAGAGCACC 59.705 63.158 0.00 0.00 0.00 5.01
512 544 1.080230 CACCACAGAGAGAGCACCG 60.080 63.158 0.00 0.00 0.00 4.94
513 545 1.228583 ACCACAGAGAGAGCACCGA 60.229 57.895 0.00 0.00 0.00 4.69
514 546 1.247419 ACCACAGAGAGAGCACCGAG 61.247 60.000 0.00 0.00 0.00 4.63
515 547 0.962855 CCACAGAGAGAGCACCGAGA 60.963 60.000 0.00 0.00 0.00 4.04
516 548 0.451383 CACAGAGAGAGCACCGAGAG 59.549 60.000 0.00 0.00 0.00 3.20
517 549 1.312371 ACAGAGAGAGCACCGAGAGC 61.312 60.000 0.00 0.00 0.00 4.09
518 550 1.752694 AGAGAGAGCACCGAGAGCC 60.753 63.158 0.00 0.00 0.00 4.70
519 551 2.036414 AGAGAGCACCGAGAGCCA 59.964 61.111 0.00 0.00 0.00 4.75
520 552 1.599606 GAGAGAGCACCGAGAGCCAA 61.600 60.000 0.00 0.00 0.00 4.52
523 555 2.359230 AGCACCGAGAGCCAAAGC 60.359 61.111 0.00 0.00 40.32 3.51
556 588 4.740822 ATCTTGTGCACCGCCCCC 62.741 66.667 15.69 0.00 0.00 5.40
597 629 4.503910 GCAAGAACAAAACCAACTTTCCT 58.496 39.130 0.00 0.00 0.00 3.36
608 640 2.087462 AACTTTCCTTTGCGGCTGCC 62.087 55.000 16.57 9.11 41.78 4.85
628 660 1.068585 ACGGTCGTCTTCCACAACC 59.931 57.895 0.00 0.00 0.00 3.77
750 782 0.251634 CTCAGGAGCCAGAACCTTCC 59.748 60.000 0.00 0.00 33.91 3.46
789 821 1.369091 CGGGCGGAACAAGAATCAGG 61.369 60.000 0.00 0.00 0.00 3.86
790 822 1.032114 GGGCGGAACAAGAATCAGGG 61.032 60.000 0.00 0.00 0.00 4.45
1392 1488 5.878332 ATTGAAAATTTCCCCGCAATTTC 57.122 34.783 3.00 0.00 33.56 2.17
1398 1494 7.499232 TGAAAATTTCCCCGCAATTTCTTTTAA 59.501 29.630 3.00 0.00 33.56 1.52
1447 1543 9.188588 CAAATCAGTATGCCTGCAAATTAATAG 57.811 33.333 0.00 0.00 41.25 1.73
1457 1553 3.380004 TGCAAATTAATAGAACTGCGGGG 59.620 43.478 0.00 0.00 32.45 5.73
1473 1569 2.799978 GCGGGGATTTGAGTTTTGTTTG 59.200 45.455 0.00 0.00 0.00 2.93
1504 1600 5.285651 TGTTTGTGTTAATAAAGGTGCAGC 58.714 37.500 8.11 8.11 0.00 5.25
1516 1612 7.880160 ATAAAGGTGCAGCAATATGAGTTTA 57.120 32.000 19.63 11.31 0.00 2.01
1598 1694 5.927115 ACGGAGAAGTCTGATTAGTTTCAAC 59.073 40.000 0.00 0.00 32.75 3.18
1599 1695 5.061064 CGGAGAAGTCTGATTAGTTTCAACG 59.939 44.000 7.06 6.77 0.00 4.10
1600 1696 5.163943 GGAGAAGTCTGATTAGTTTCAACGC 60.164 44.000 7.06 0.00 0.00 4.84
1602 1698 2.993899 AGTCTGATTAGTTTCAACGCCG 59.006 45.455 0.00 0.00 0.00 6.46
1603 1699 2.991190 GTCTGATTAGTTTCAACGCCGA 59.009 45.455 0.00 0.00 0.00 5.54
1604 1700 3.617263 GTCTGATTAGTTTCAACGCCGAT 59.383 43.478 0.00 0.00 0.00 4.18
1757 1861 1.180029 GAGGCACCTGCATGACAATT 58.820 50.000 0.00 0.00 44.36 2.32
1778 1882 0.387929 ATTCGAGGGCGCTTTCGATA 59.612 50.000 27.79 20.75 44.32 2.92
1855 1959 5.988561 GGTGCTTTCATCAAAACCAAATACA 59.011 36.000 0.00 0.00 0.00 2.29
1934 2039 7.439157 TTTGTTTGTGGATGAGTATCTGAAG 57.561 36.000 0.00 0.00 34.92 3.02
1936 2041 6.533730 TGTTTGTGGATGAGTATCTGAAGTT 58.466 36.000 0.00 0.00 34.92 2.66
1940 2045 5.716703 TGTGGATGAGTATCTGAAGTTCTGA 59.283 40.000 14.02 14.02 34.92 3.27
1941 2046 6.211384 TGTGGATGAGTATCTGAAGTTCTGAA 59.789 38.462 15.40 0.73 34.92 3.02
1942 2047 6.533367 GTGGATGAGTATCTGAAGTTCTGAAC 59.467 42.308 15.40 12.54 34.92 3.18
1943 2048 6.438741 TGGATGAGTATCTGAAGTTCTGAACT 59.561 38.462 17.00 17.00 38.94 3.01
1944 2049 6.978080 GGATGAGTATCTGAAGTTCTGAACTC 59.022 42.308 26.31 26.31 36.95 3.01
1945 2050 6.274157 TGAGTATCTGAAGTTCTGAACTCC 57.726 41.667 27.81 11.69 36.95 3.85
1946 2051 5.106118 TGAGTATCTGAAGTTCTGAACTCCG 60.106 44.000 27.81 13.59 36.95 4.63
1947 2052 3.601443 ATCTGAAGTTCTGAACTCCGG 57.399 47.619 22.24 15.75 41.91 5.14
2010 2115 4.514781 AGTGCTCACTTGTCGTATGTTA 57.485 40.909 0.00 0.00 38.83 2.41
2011 2116 5.073311 AGTGCTCACTTGTCGTATGTTAT 57.927 39.130 0.00 0.00 38.83 1.89
2021 2126 7.490079 CACTTGTCGTATGTTATAGCCACTTAA 59.510 37.037 0.00 0.00 0.00 1.85
2022 2127 8.202137 ACTTGTCGTATGTTATAGCCACTTAAT 58.798 33.333 0.00 0.00 0.00 1.40
2023 2128 9.687210 CTTGTCGTATGTTATAGCCACTTAATA 57.313 33.333 0.00 0.00 0.00 0.98
2036 2141 9.914834 ATAGCCACTTAATAAGAACACCAAATA 57.085 29.630 7.06 0.00 0.00 1.40
2054 2159 6.490040 ACCAAATAGTGCAAACTACATCAACT 59.510 34.615 0.00 0.00 0.00 3.16
2072 2177 1.341531 ACTCTCCCTGTGTTCAACTCG 59.658 52.381 0.00 0.00 0.00 4.18
2123 2228 8.391106 AGTTAGCTTGTCTTGATAATAAAAGCG 58.609 33.333 0.00 0.00 42.50 4.68
2199 2310 1.561076 TGTGATTATCTGCAGTGGCCT 59.439 47.619 14.67 0.00 40.13 5.19
2220 2331 3.355378 TCTGAAATGTATGCCAGTTGGG 58.645 45.455 0.00 0.00 40.85 4.12
2238 2349 4.406648 TGGGACATGATAAGCAGTAGTG 57.593 45.455 0.00 0.00 0.00 2.74
2245 2356 5.877012 ACATGATAAGCAGTAGTGGTTTCTG 59.123 40.000 19.39 13.49 41.74 3.02
2375 2486 6.356977 CGACAACGCATATCCATTTCAAATAC 59.643 38.462 0.00 0.00 0.00 1.89
2376 2487 6.198687 ACAACGCATATCCATTTCAAATACG 58.801 36.000 0.00 0.00 0.00 3.06
2377 2488 5.356882 ACGCATATCCATTTCAAATACGG 57.643 39.130 0.00 0.00 0.00 4.02
2378 2489 4.819630 ACGCATATCCATTTCAAATACGGT 59.180 37.500 0.00 0.00 0.00 4.83
2379 2490 5.992829 ACGCATATCCATTTCAAATACGGTA 59.007 36.000 0.00 0.00 0.00 4.02
2383 2528 7.803189 GCATATCCATTTCAAATACGGTACAAG 59.197 37.037 0.00 0.00 0.00 3.16
2387 2532 6.072948 TCCATTTCAAATACGGTACAAGTGTG 60.073 38.462 0.00 0.00 0.00 3.82
2389 2534 5.660629 TTCAAATACGGTACAAGTGTGTG 57.339 39.130 0.00 0.00 38.82 3.82
2450 2595 5.690464 AAGAGAAGTCCTGATAAGCATGT 57.310 39.130 0.00 0.00 0.00 3.21
2486 2631 2.004583 TCCGTTCGGTTGCTTATCTG 57.995 50.000 11.04 0.00 0.00 2.90
2573 2718 5.123820 CAGCCTGTTTTTCCGAATTCATCTA 59.876 40.000 6.22 0.00 0.00 1.98
2639 2784 1.153168 CATCCATGGGTGGGACGTC 60.153 63.158 18.02 7.13 46.06 4.34
2714 2859 4.426704 AGTGTTACCTAACTGATCCAGGT 58.573 43.478 9.53 9.53 44.79 4.00
2801 2946 5.359009 CCAGTTTGCAATGGTTCAGATAGAT 59.641 40.000 10.43 0.00 0.00 1.98
2877 3022 1.657556 CTTGCGCGGAAAAAGGGAA 59.342 52.632 15.55 0.00 0.00 3.97
2882 3027 0.887387 CGCGGAAAAAGGGAACTGGA 60.887 55.000 0.00 0.00 42.68 3.86
2979 3126 3.997397 TGCTTGCGGCTGTCGGTA 61.997 61.111 3.02 0.00 42.39 4.02
3087 3236 6.151985 TGTCACACCTTGTAAATTGTGAGTTT 59.848 34.615 3.57 0.00 44.51 2.66
3097 3247 7.639039 TGTAAATTGTGAGTTTGTGACAGATC 58.361 34.615 0.00 0.00 0.00 2.75
3331 3558 0.925558 TGCCACCATGTATGTCCCAT 59.074 50.000 0.00 0.00 0.00 4.00
3367 3594 7.604927 TCCTGTTAACATGTAACTATGTCAACC 59.395 37.037 9.13 0.00 38.06 3.77
3376 3603 3.634397 ACTATGTCAACCCACCATGAG 57.366 47.619 0.00 0.00 0.00 2.90
3391 3618 3.118112 ACCATGAGACTATGCAGGGAAAG 60.118 47.826 0.00 0.00 38.16 2.62
3392 3619 3.474600 CATGAGACTATGCAGGGAAAGG 58.525 50.000 0.00 0.00 0.00 3.11
3533 3778 8.282455 TGTACCGCCAATTTTCATAGAAATAA 57.718 30.769 0.00 0.00 0.00 1.40
3541 3786 8.961092 CCAATTTTCATAGAAATAACTGCATCG 58.039 33.333 0.00 0.00 0.00 3.84
3559 3853 3.559238 TCGAATTCAAAGCAAAGAGGC 57.441 42.857 6.22 0.00 0.00 4.70
3632 3926 3.801068 TTCCTTTGGGGCGTGTGGG 62.801 63.158 0.00 0.00 34.39 4.61
3781 4086 0.743688 TTGGTTGCATGACACCACAC 59.256 50.000 14.40 0.00 31.71 3.82
3852 4160 6.320418 TCAGGGAAAGAACACCTTAAACTTTC 59.680 38.462 0.00 0.00 42.86 2.62
3907 4215 2.420129 GCACAGGAATCTACACCGGATT 60.420 50.000 9.46 0.00 36.29 3.01
3909 4217 2.170607 ACAGGAATCTACACCGGATTGG 59.829 50.000 9.46 0.00 46.41 3.16
3910 4218 2.434336 CAGGAATCTACACCGGATTGGA 59.566 50.000 9.46 1.25 42.00 3.53
3911 4219 2.700897 AGGAATCTACACCGGATTGGAG 59.299 50.000 9.46 2.33 42.00 3.86
3912 4220 2.434702 GGAATCTACACCGGATTGGAGT 59.565 50.000 9.46 0.00 44.43 3.85
3913 4221 3.458189 GAATCTACACCGGATTGGAGTG 58.542 50.000 9.46 0.00 42.04 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.017933 CGATTTCTTTGTCTATGCACAAGAC 58.982 40.000 19.48 19.48 43.04 3.01
6 7 5.931724 TCGATTTCTTTGTCTATGCACAAGA 59.068 36.000 0.00 0.00 37.57 3.02
7 8 6.169419 TCGATTTCTTTGTCTATGCACAAG 57.831 37.500 0.00 0.00 37.57 3.16
8 9 6.741992 ATCGATTTCTTTGTCTATGCACAA 57.258 33.333 0.00 0.00 34.36 3.33
9 10 7.010460 CACTATCGATTTCTTTGTCTATGCACA 59.990 37.037 1.71 0.00 0.00 4.57
10 11 7.340699 CACTATCGATTTCTTTGTCTATGCAC 58.659 38.462 1.71 0.00 0.00 4.57
11 12 6.479990 CCACTATCGATTTCTTTGTCTATGCA 59.520 38.462 1.71 0.00 0.00 3.96
12 13 6.480320 ACCACTATCGATTTCTTTGTCTATGC 59.520 38.462 1.71 0.00 0.00 3.14
13 14 8.969267 GTACCACTATCGATTTCTTTGTCTATG 58.031 37.037 1.71 0.00 0.00 2.23
14 15 8.915036 AGTACCACTATCGATTTCTTTGTCTAT 58.085 33.333 1.71 0.00 0.00 1.98
15 16 8.289939 AGTACCACTATCGATTTCTTTGTCTA 57.710 34.615 1.71 0.00 0.00 2.59
16 17 7.171630 AGTACCACTATCGATTTCTTTGTCT 57.828 36.000 1.71 0.00 0.00 3.41
17 18 7.760340 AGAAGTACCACTATCGATTTCTTTGTC 59.240 37.037 1.71 0.00 0.00 3.18
18 19 7.612677 AGAAGTACCACTATCGATTTCTTTGT 58.387 34.615 1.71 0.00 0.00 2.83
19 20 7.043986 CGAGAAGTACCACTATCGATTTCTTTG 60.044 40.741 1.71 0.00 38.85 2.77
20 21 6.973474 CGAGAAGTACCACTATCGATTTCTTT 59.027 38.462 1.71 0.00 38.85 2.52
21 22 6.095160 ACGAGAAGTACCACTATCGATTTCTT 59.905 38.462 1.71 0.00 38.85 2.52
22 23 5.589452 ACGAGAAGTACCACTATCGATTTCT 59.411 40.000 1.71 3.65 38.85 2.52
23 24 5.819059 ACGAGAAGTACCACTATCGATTTC 58.181 41.667 1.71 0.00 38.85 2.17
24 25 5.356190 TGACGAGAAGTACCACTATCGATTT 59.644 40.000 1.71 0.00 38.85 2.17
25 26 4.880120 TGACGAGAAGTACCACTATCGATT 59.120 41.667 1.71 0.00 38.85 3.34
26 27 4.449131 TGACGAGAAGTACCACTATCGAT 58.551 43.478 16.23 2.16 38.85 3.59
27 28 3.865446 TGACGAGAAGTACCACTATCGA 58.135 45.455 16.23 0.00 38.85 3.59
28 29 3.869832 TCTGACGAGAAGTACCACTATCG 59.130 47.826 10.54 10.54 40.91 2.92
29 30 5.527951 TCATCTGACGAGAAGTACCACTATC 59.472 44.000 0.00 0.00 0.00 2.08
30 31 5.437946 TCATCTGACGAGAAGTACCACTAT 58.562 41.667 0.00 0.00 0.00 2.12
31 32 4.840271 TCATCTGACGAGAAGTACCACTA 58.160 43.478 0.00 0.00 0.00 2.74
32 33 3.687125 TCATCTGACGAGAAGTACCACT 58.313 45.455 0.00 0.00 0.00 4.00
33 34 3.690139 TCTCATCTGACGAGAAGTACCAC 59.310 47.826 0.21 0.00 36.59 4.16
34 35 3.951663 TCTCATCTGACGAGAAGTACCA 58.048 45.455 0.21 0.00 36.59 3.25
35 36 4.966965 TTCTCATCTGACGAGAAGTACC 57.033 45.455 11.75 0.00 42.99 3.34
41 42 3.882288 CTGGAGATTCTCATCTGACGAGA 59.118 47.826 15.36 0.00 40.14 4.04
42 43 3.550639 GCTGGAGATTCTCATCTGACGAG 60.551 52.174 15.36 0.00 40.14 4.18
43 44 2.360483 GCTGGAGATTCTCATCTGACGA 59.640 50.000 15.36 0.00 40.14 4.20
44 45 2.361757 AGCTGGAGATTCTCATCTGACG 59.638 50.000 15.36 0.00 40.14 4.35
45 46 4.405116 AAGCTGGAGATTCTCATCTGAC 57.595 45.455 15.36 0.00 40.14 3.51
46 47 6.550938 TTAAAGCTGGAGATTCTCATCTGA 57.449 37.500 15.36 0.00 40.14 3.27
47 48 7.621428 TTTTAAAGCTGGAGATTCTCATCTG 57.379 36.000 15.36 4.62 40.14 2.90
48 49 7.862512 CTTTTAAAGCTGGAGATTCTCATCT 57.137 36.000 15.36 5.99 43.03 2.90
64 65 9.646427 ATCTCTTGTACACTCTAGCTTTTAAAG 57.354 33.333 0.00 0.00 0.00 1.85
65 66 9.424319 CATCTCTTGTACACTCTAGCTTTTAAA 57.576 33.333 0.00 0.00 0.00 1.52
66 67 8.803235 TCATCTCTTGTACACTCTAGCTTTTAA 58.197 33.333 0.00 0.00 0.00 1.52
67 68 8.349568 TCATCTCTTGTACACTCTAGCTTTTA 57.650 34.615 0.00 0.00 0.00 1.52
68 69 7.233389 TCATCTCTTGTACACTCTAGCTTTT 57.767 36.000 0.00 0.00 0.00 2.27
69 70 6.842437 TCATCTCTTGTACACTCTAGCTTT 57.158 37.500 0.00 0.00 0.00 3.51
70 71 6.627065 GCTTCATCTCTTGTACACTCTAGCTT 60.627 42.308 0.00 0.00 0.00 3.74
71 72 5.163561 GCTTCATCTCTTGTACACTCTAGCT 60.164 44.000 0.00 0.00 0.00 3.32
72 73 5.040635 GCTTCATCTCTTGTACACTCTAGC 58.959 45.833 0.00 0.00 0.00 3.42
73 74 6.201226 TGCTTCATCTCTTGTACACTCTAG 57.799 41.667 0.00 0.00 0.00 2.43
74 75 6.782082 ATGCTTCATCTCTTGTACACTCTA 57.218 37.500 0.00 0.00 0.00 2.43
75 76 5.674052 ATGCTTCATCTCTTGTACACTCT 57.326 39.130 0.00 0.00 0.00 3.24
76 77 7.547370 ACTTTATGCTTCATCTCTTGTACACTC 59.453 37.037 0.00 0.00 0.00 3.51
77 78 7.332926 CACTTTATGCTTCATCTCTTGTACACT 59.667 37.037 0.00 0.00 0.00 3.55
78 79 7.413438 CCACTTTATGCTTCATCTCTTGTACAC 60.413 40.741 0.00 0.00 0.00 2.90
79 80 6.595326 CCACTTTATGCTTCATCTCTTGTACA 59.405 38.462 0.00 0.00 0.00 2.90
80 81 6.457528 GCCACTTTATGCTTCATCTCTTGTAC 60.458 42.308 0.00 0.00 0.00 2.90
81 82 5.586243 GCCACTTTATGCTTCATCTCTTGTA 59.414 40.000 0.00 0.00 0.00 2.41
82 83 4.397417 GCCACTTTATGCTTCATCTCTTGT 59.603 41.667 0.00 0.00 0.00 3.16
83 84 4.397103 TGCCACTTTATGCTTCATCTCTTG 59.603 41.667 0.00 0.00 0.00 3.02
84 85 4.592942 TGCCACTTTATGCTTCATCTCTT 58.407 39.130 0.00 0.00 0.00 2.85
85 86 4.226427 TGCCACTTTATGCTTCATCTCT 57.774 40.909 0.00 0.00 0.00 3.10
86 87 5.528690 TGTATGCCACTTTATGCTTCATCTC 59.471 40.000 0.00 0.00 0.00 2.75
87 88 5.297776 GTGTATGCCACTTTATGCTTCATCT 59.702 40.000 0.00 0.00 41.11 2.90
88 89 5.066375 TGTGTATGCCACTTTATGCTTCATC 59.934 40.000 0.00 0.00 44.81 2.92
89 90 4.949238 TGTGTATGCCACTTTATGCTTCAT 59.051 37.500 0.00 0.00 44.81 2.57
90 91 4.331108 TGTGTATGCCACTTTATGCTTCA 58.669 39.130 0.00 0.00 44.81 3.02
91 92 4.963276 TGTGTATGCCACTTTATGCTTC 57.037 40.909 0.00 0.00 44.81 3.86
92 93 4.706476 ACATGTGTATGCCACTTTATGCTT 59.294 37.500 0.00 0.00 44.81 3.91
93 94 4.272489 ACATGTGTATGCCACTTTATGCT 58.728 39.130 0.00 0.00 44.81 3.79
94 95 4.637483 ACATGTGTATGCCACTTTATGC 57.363 40.909 0.00 0.00 44.81 3.14
95 96 7.495135 TGATACATGTGTATGCCACTTTATG 57.505 36.000 9.11 0.00 44.81 1.90
96 97 7.775093 ACTTGATACATGTGTATGCCACTTTAT 59.225 33.333 9.11 0.00 44.81 1.40
97 98 7.109501 ACTTGATACATGTGTATGCCACTTTA 58.890 34.615 9.11 0.00 44.81 1.85
98 99 5.945784 ACTTGATACATGTGTATGCCACTTT 59.054 36.000 9.11 0.00 44.81 2.66
99 100 5.500234 ACTTGATACATGTGTATGCCACTT 58.500 37.500 9.11 0.00 44.81 3.16
100 101 5.102953 ACTTGATACATGTGTATGCCACT 57.897 39.130 9.11 0.00 44.81 4.00
101 102 4.025730 CGACTTGATACATGTGTATGCCAC 60.026 45.833 9.11 0.00 40.99 5.01
102 103 4.119136 CGACTTGATACATGTGTATGCCA 58.881 43.478 9.11 1.19 40.99 4.92
103 104 3.494626 CCGACTTGATACATGTGTATGCC 59.505 47.826 9.11 0.00 40.99 4.40
104 105 4.119862 ACCGACTTGATACATGTGTATGC 58.880 43.478 9.11 3.79 40.99 3.14
105 106 4.745125 GGACCGACTTGATACATGTGTATG 59.255 45.833 9.11 0.00 40.99 2.39
106 107 4.404394 TGGACCGACTTGATACATGTGTAT 59.596 41.667 9.11 5.40 43.38 2.29
107 108 3.764972 TGGACCGACTTGATACATGTGTA 59.235 43.478 9.11 0.00 34.67 2.90
108 109 2.565391 TGGACCGACTTGATACATGTGT 59.435 45.455 9.11 0.10 0.00 3.72
109 110 3.245518 TGGACCGACTTGATACATGTG 57.754 47.619 9.11 0.00 0.00 3.21
110 111 3.973206 TTGGACCGACTTGATACATGT 57.027 42.857 2.69 2.69 0.00 3.21
111 112 6.566564 GCATATTTGGACCGACTTGATACATG 60.567 42.308 0.00 0.00 0.00 3.21
112 113 5.470098 GCATATTTGGACCGACTTGATACAT 59.530 40.000 0.00 0.00 0.00 2.29
113 114 4.814234 GCATATTTGGACCGACTTGATACA 59.186 41.667 0.00 0.00 0.00 2.29
114 115 4.084537 CGCATATTTGGACCGACTTGATAC 60.085 45.833 0.00 0.00 0.00 2.24
115 116 4.055360 CGCATATTTGGACCGACTTGATA 58.945 43.478 0.00 0.00 0.00 2.15
116 117 2.872245 CGCATATTTGGACCGACTTGAT 59.128 45.455 0.00 0.00 0.00 2.57
117 118 2.276201 CGCATATTTGGACCGACTTGA 58.724 47.619 0.00 0.00 0.00 3.02
118 119 1.330521 CCGCATATTTGGACCGACTTG 59.669 52.381 0.00 0.00 0.00 3.16
119 120 1.663695 CCGCATATTTGGACCGACTT 58.336 50.000 0.00 0.00 0.00 3.01
120 121 0.179056 CCCGCATATTTGGACCGACT 60.179 55.000 0.00 0.00 0.00 4.18
121 122 0.179067 TCCCGCATATTTGGACCGAC 60.179 55.000 0.00 0.00 0.00 4.79
122 123 0.762418 ATCCCGCATATTTGGACCGA 59.238 50.000 0.00 0.00 0.00 4.69
123 124 1.266718 CAATCCCGCATATTTGGACCG 59.733 52.381 0.00 0.00 0.00 4.79
124 125 1.613437 CCAATCCCGCATATTTGGACC 59.387 52.381 0.00 0.00 40.89 4.46
125 126 1.000274 GCCAATCCCGCATATTTGGAC 60.000 52.381 5.89 0.00 40.89 4.02
126 127 1.327303 GCCAATCCCGCATATTTGGA 58.673 50.000 5.89 0.00 40.89 3.53
127 128 0.318120 GGCCAATCCCGCATATTTGG 59.682 55.000 0.00 0.00 41.26 3.28
128 129 1.331214 AGGCCAATCCCGCATATTTG 58.669 50.000 5.01 0.00 34.51 2.32
129 130 2.086610 AAGGCCAATCCCGCATATTT 57.913 45.000 5.01 0.00 34.51 1.40
130 131 2.108250 ACTAAGGCCAATCCCGCATATT 59.892 45.455 5.01 0.00 34.51 1.28
131 132 1.705186 ACTAAGGCCAATCCCGCATAT 59.295 47.619 5.01 0.00 34.51 1.78
132 133 1.136828 ACTAAGGCCAATCCCGCATA 58.863 50.000 5.01 0.00 34.51 3.14
133 134 0.258774 AACTAAGGCCAATCCCGCAT 59.741 50.000 5.01 0.00 34.51 4.73
134 135 0.039035 AAACTAAGGCCAATCCCGCA 59.961 50.000 5.01 0.00 34.51 5.69
135 136 1.135112 CAAAACTAAGGCCAATCCCGC 60.135 52.381 5.01 0.00 34.51 6.13
136 137 1.476488 CCAAAACTAAGGCCAATCCCG 59.524 52.381 5.01 0.00 34.51 5.14
137 138 2.536066 ACCAAAACTAAGGCCAATCCC 58.464 47.619 5.01 0.00 34.51 3.85
138 139 3.576550 TCAACCAAAACTAAGGCCAATCC 59.423 43.478 5.01 0.00 0.00 3.01
139 140 4.280929 ACTCAACCAAAACTAAGGCCAATC 59.719 41.667 5.01 0.00 0.00 2.67
140 141 4.223144 ACTCAACCAAAACTAAGGCCAAT 58.777 39.130 5.01 0.00 0.00 3.16
141 142 3.637769 ACTCAACCAAAACTAAGGCCAA 58.362 40.909 5.01 0.00 0.00 4.52
142 143 3.306472 ACTCAACCAAAACTAAGGCCA 57.694 42.857 5.01 0.00 0.00 5.36
143 144 3.634910 TGAACTCAACCAAAACTAAGGCC 59.365 43.478 0.00 0.00 0.00 5.19
144 145 4.261614 CCTGAACTCAACCAAAACTAAGGC 60.262 45.833 0.00 0.00 0.00 4.35
145 146 5.130350 TCCTGAACTCAACCAAAACTAAGG 58.870 41.667 0.00 0.00 0.00 2.69
146 147 6.263168 ACATCCTGAACTCAACCAAAACTAAG 59.737 38.462 0.00 0.00 0.00 2.18
147 148 6.126409 ACATCCTGAACTCAACCAAAACTAA 58.874 36.000 0.00 0.00 0.00 2.24
148 149 5.690865 ACATCCTGAACTCAACCAAAACTA 58.309 37.500 0.00 0.00 0.00 2.24
149 150 4.536765 ACATCCTGAACTCAACCAAAACT 58.463 39.130 0.00 0.00 0.00 2.66
150 151 4.554723 CGACATCCTGAACTCAACCAAAAC 60.555 45.833 0.00 0.00 0.00 2.43
151 152 3.563808 CGACATCCTGAACTCAACCAAAA 59.436 43.478 0.00 0.00 0.00 2.44
152 153 3.138304 CGACATCCTGAACTCAACCAAA 58.862 45.455 0.00 0.00 0.00 3.28
153 154 2.549992 CCGACATCCTGAACTCAACCAA 60.550 50.000 0.00 0.00 0.00 3.67
154 155 1.001974 CCGACATCCTGAACTCAACCA 59.998 52.381 0.00 0.00 0.00 3.67
155 156 1.676014 CCCGACATCCTGAACTCAACC 60.676 57.143 0.00 0.00 0.00 3.77
156 157 1.676014 CCCCGACATCCTGAACTCAAC 60.676 57.143 0.00 0.00 0.00 3.18
157 158 0.613260 CCCCGACATCCTGAACTCAA 59.387 55.000 0.00 0.00 0.00 3.02
158 159 1.899437 GCCCCGACATCCTGAACTCA 61.899 60.000 0.00 0.00 0.00 3.41
159 160 1.153349 GCCCCGACATCCTGAACTC 60.153 63.158 0.00 0.00 0.00 3.01
160 161 1.613630 AGCCCCGACATCCTGAACT 60.614 57.895 0.00 0.00 0.00 3.01
161 162 1.450312 CAGCCCCGACATCCTGAAC 60.450 63.158 0.00 0.00 0.00 3.18
162 163 1.488705 AACAGCCCCGACATCCTGAA 61.489 55.000 0.00 0.00 0.00 3.02
163 164 1.918293 AACAGCCCCGACATCCTGA 60.918 57.895 0.00 0.00 0.00 3.86
164 165 1.746615 CAACAGCCCCGACATCCTG 60.747 63.158 0.00 0.00 0.00 3.86
165 166 2.185310 GACAACAGCCCCGACATCCT 62.185 60.000 0.00 0.00 0.00 3.24
166 167 1.745489 GACAACAGCCCCGACATCC 60.745 63.158 0.00 0.00 0.00 3.51
167 168 1.745489 GGACAACAGCCCCGACATC 60.745 63.158 0.00 0.00 0.00 3.06
168 169 2.351276 GGACAACAGCCCCGACAT 59.649 61.111 0.00 0.00 0.00 3.06
169 170 4.308458 CGGACAACAGCCCCGACA 62.308 66.667 0.00 0.00 45.58 4.35
195 196 5.423886 CAAAAGCAAAGTTGGGAAGGTTTA 58.576 37.500 0.00 0.00 30.70 2.01
201 202 4.769345 AATCCAAAAGCAAAGTTGGGAA 57.231 36.364 2.77 0.00 43.82 3.97
208 209 6.580791 TCGATTTTCGTAATCCAAAAGCAAAG 59.419 34.615 7.21 0.00 41.35 2.77
216 217 5.872617 ACATGTCTCGATTTTCGTAATCCAA 59.127 36.000 0.00 0.00 41.35 3.53
217 218 5.416083 ACATGTCTCGATTTTCGTAATCCA 58.584 37.500 0.00 1.91 41.35 3.41
221 222 5.742453 GCTCTACATGTCTCGATTTTCGTAA 59.258 40.000 0.00 0.00 41.35 3.18
222 223 5.163693 TGCTCTACATGTCTCGATTTTCGTA 60.164 40.000 0.00 0.00 41.35 3.43
223 224 4.106197 GCTCTACATGTCTCGATTTTCGT 58.894 43.478 0.00 0.00 41.35 3.85
231 232 0.743688 AGGCTGCTCTACATGTCTCG 59.256 55.000 0.00 0.00 0.00 4.04
232 233 1.805871 GCAGGCTGCTCTACATGTCTC 60.806 57.143 31.37 0.00 40.96 3.36
234 235 1.150567 CGCAGGCTGCTCTACATGTC 61.151 60.000 34.17 4.69 42.25 3.06
283 284 1.398390 GCCTCGCGATCTGAACATTTT 59.602 47.619 10.36 0.00 0.00 1.82
309 310 4.269183 TCTCTACCACCGTCCGTTAAATA 58.731 43.478 0.00 0.00 0.00 1.40
310 311 3.091545 TCTCTACCACCGTCCGTTAAAT 58.908 45.455 0.00 0.00 0.00 1.40
315 316 1.673168 GTATCTCTACCACCGTCCGT 58.327 55.000 0.00 0.00 0.00 4.69
325 326 5.469760 GTCTACTTTCTCGGGGTATCTCTAC 59.530 48.000 0.00 0.00 0.00 2.59
333 334 2.322339 AAGGTCTACTTTCTCGGGGT 57.678 50.000 0.00 0.00 35.35 4.95
386 387 4.027295 CGTTGAAATCGACTGACTGCTATC 60.027 45.833 0.00 0.00 0.00 2.08
411 412 2.697761 GCTGTCCGTCGCCTACTGA 61.698 63.158 0.00 0.00 0.00 3.41
460 492 2.594592 AGGTGGTTCCGTGCTTGC 60.595 61.111 0.00 0.00 41.99 4.01
469 501 3.103911 CGTGTCGCGAGGTGGTTC 61.104 66.667 10.24 0.00 44.77 3.62
504 536 1.294780 CTTTGGCTCTCGGTGCTCT 59.705 57.895 0.00 0.00 0.00 4.09
505 537 2.394563 GCTTTGGCTCTCGGTGCTC 61.395 63.158 0.00 0.00 35.22 4.26
506 538 2.359230 GCTTTGGCTCTCGGTGCT 60.359 61.111 0.00 0.00 35.22 4.40
507 539 3.793144 CGCTTTGGCTCTCGGTGC 61.793 66.667 0.00 0.00 36.09 5.01
508 540 3.121030 CCGCTTTGGCTCTCGGTG 61.121 66.667 0.00 0.00 37.33 4.94
510 542 1.234615 TTTTCCGCTTTGGCTCTCGG 61.235 55.000 0.00 0.00 42.96 4.63
511 543 0.591170 TTTTTCCGCTTTGGCTCTCG 59.409 50.000 0.00 0.00 37.80 4.04
531 563 1.611673 CGGTGCACAAGATTTCTCCCT 60.612 52.381 20.43 0.00 0.00 4.20
608 640 1.068417 TTGTGGAAGACGACCGTGG 59.932 57.895 0.00 0.00 0.00 4.94
628 660 3.997064 CTGCGCGAAGGGAGTGGAG 62.997 68.421 12.10 0.00 46.37 3.86
704 736 1.358725 TATGCGCTCGGTTGCTTGAC 61.359 55.000 9.73 0.00 0.00 3.18
750 782 1.226802 CTGTGGCTGGTCGATCGAG 60.227 63.158 20.09 8.37 0.00 4.04
968 1058 1.139947 GCTCGACCGAGAAGAAGGG 59.860 63.158 21.91 0.00 44.53 3.95
971 1061 3.976758 TCGCTCGACCGAGAAGAA 58.023 55.556 21.91 2.18 44.53 2.52
1257 1350 1.352156 GCGCGTACACCTCCTTCTTG 61.352 60.000 8.43 0.00 0.00 3.02
1398 1494 7.856145 TGCACAAGGTTTTGTCATAAATTTT 57.144 28.000 0.00 0.00 45.53 1.82
1447 1543 1.534729 AACTCAAATCCCCGCAGTTC 58.465 50.000 0.00 0.00 0.00 3.01
1457 1553 4.415881 ACCCCCAAACAAAACTCAAATC 57.584 40.909 0.00 0.00 0.00 2.17
1473 1569 7.038870 ACCTTTATTAACACAAACAATACCCCC 60.039 37.037 0.00 0.00 0.00 5.40
1504 1600 8.531146 ACTTCACCCCAAAATAAACTCATATTG 58.469 33.333 0.00 0.00 0.00 1.90
1516 1612 4.835284 AACACAAACTTCACCCCAAAAT 57.165 36.364 0.00 0.00 0.00 1.82
1598 1694 3.747099 AGTTCATCTTCAAAATCGGCG 57.253 42.857 0.00 0.00 0.00 6.46
1599 1695 4.798574 ACAAGTTCATCTTCAAAATCGGC 58.201 39.130 0.00 0.00 33.63 5.54
1600 1696 6.917477 TCAAACAAGTTCATCTTCAAAATCGG 59.083 34.615 0.00 0.00 33.63 4.18
1629 1725 9.533253 CAGTAATTCAAGGAAAACAGAACAAAT 57.467 29.630 0.00 0.00 0.00 2.32
1757 1861 0.173935 TCGAAAGCGCCCTCGAATAA 59.826 50.000 24.20 6.40 40.89 1.40
1778 1882 0.904649 TCCTGTCATCGATGCCTGTT 59.095 50.000 20.81 0.00 0.00 3.16
1855 1959 3.951563 TGAGGCCCATTATAAGCTGTT 57.048 42.857 0.00 0.00 0.00 3.16
1868 1972 6.515696 GCATGAAGTTTCTATTAATGAGGCCC 60.516 42.308 0.00 0.00 0.00 5.80
1934 2039 2.027625 CGCACCCGGAGTTCAGAAC 61.028 63.158 0.73 5.00 0.00 3.01
1936 2041 0.968901 ATACGCACCCGGAGTTCAGA 60.969 55.000 0.73 0.00 39.22 3.27
1940 2045 2.493030 CGATACGCACCCGGAGTT 59.507 61.111 0.73 0.00 39.22 3.01
2010 2115 8.823220 ATTTGGTGTTCTTATTAAGTGGCTAT 57.177 30.769 3.45 0.00 0.00 2.97
2011 2116 9.391006 CTATTTGGTGTTCTTATTAAGTGGCTA 57.609 33.333 3.45 0.00 0.00 3.93
2021 2126 7.524717 AGTTTGCACTATTTGGTGTTCTTAT 57.475 32.000 0.00 0.00 39.21 1.73
2022 2127 6.952773 AGTTTGCACTATTTGGTGTTCTTA 57.047 33.333 0.00 0.00 39.21 2.10
2023 2128 5.852282 AGTTTGCACTATTTGGTGTTCTT 57.148 34.783 0.00 0.00 39.21 2.52
2024 2129 5.825679 TGTAGTTTGCACTATTTGGTGTTCT 59.174 36.000 0.00 0.00 37.83 3.01
2029 2134 6.490040 AGTTGATGTAGTTTGCACTATTTGGT 59.510 34.615 0.00 0.00 37.83 3.67
2036 2141 4.319177 GGAGAGTTGATGTAGTTTGCACT 58.681 43.478 0.00 0.00 36.99 4.40
2054 2159 1.068588 CACGAGTTGAACACAGGGAGA 59.931 52.381 0.00 0.00 0.00 3.71
2072 2177 4.142687 ACTGTCAGTTGCAACTTGTAACAC 60.143 41.667 29.23 17.42 43.89 3.32
2123 2228 2.159382 TCACAATCCCGCCTTCTTTTC 58.841 47.619 0.00 0.00 0.00 2.29
2199 2310 3.010027 TCCCAACTGGCATACATTTCAGA 59.990 43.478 0.00 0.00 0.00 3.27
2220 2331 6.036517 CAGAAACCACTACTGCTTATCATGTC 59.963 42.308 0.00 0.00 0.00 3.06
2238 2349 3.777478 CACCAATGCATCATCAGAAACC 58.223 45.455 0.00 0.00 0.00 3.27
2348 2459 3.687212 TGAAATGGATATGCGTTGTCGTT 59.313 39.130 2.07 0.00 39.49 3.85
2375 2486 1.658994 AACCACACACACTTGTACCG 58.341 50.000 0.00 0.00 33.30 4.02
2376 2487 5.786311 TCTATAACCACACACACTTGTACC 58.214 41.667 0.00 0.00 33.30 3.34
2377 2488 5.347907 GCTCTATAACCACACACACTTGTAC 59.652 44.000 0.00 0.00 33.30 2.90
2378 2489 5.475719 GCTCTATAACCACACACACTTGTA 58.524 41.667 0.00 0.00 33.30 2.41
2379 2490 4.315803 GCTCTATAACCACACACACTTGT 58.684 43.478 0.00 0.00 35.84 3.16
2383 2528 3.328382 TGGCTCTATAACCACACACAC 57.672 47.619 0.00 0.00 0.00 3.82
2450 2595 1.066908 CGGAACCTGCAGAAAAAGCAA 59.933 47.619 17.39 0.00 42.17 3.91
2486 2631 1.606668 TCAAACCACCAGATTTGCGAC 59.393 47.619 0.00 0.00 36.06 5.19
2714 2859 4.219288 CCGACATGATGATAGATCCAGACA 59.781 45.833 0.00 0.00 0.00 3.41
2801 2946 1.476085 CCTCCTTTTGTGTGTGTGCAA 59.524 47.619 0.00 0.00 0.00 4.08
2877 3022 9.256228 TCACTAAATCTACTCATAACTTCCAGT 57.744 33.333 0.00 0.00 0.00 4.00
2882 3027 8.531982 TGTGCTCACTAAATCTACTCATAACTT 58.468 33.333 1.47 0.00 0.00 2.66
2932 3077 6.053005 CGGAGGAAGTAAGCAAAACCATATA 58.947 40.000 0.00 0.00 0.00 0.86
3087 3236 4.002982 GGCAAACATGTAGATCTGTCACA 58.997 43.478 5.18 1.91 0.00 3.58
3097 3247 5.314923 ACATAGCAAAGGCAAACATGTAG 57.685 39.130 0.00 0.00 44.61 2.74
3268 3490 9.665719 TGCATGTTAAGATAATTGAGTTAGTGA 57.334 29.630 0.00 0.00 0.00 3.41
3367 3594 1.202734 CCCTGCATAGTCTCATGGTGG 60.203 57.143 0.00 0.00 0.00 4.61
3376 3603 1.559682 TGGTCCTTTCCCTGCATAGTC 59.440 52.381 0.00 0.00 0.00 2.59
3391 3618 1.032114 GGTGCATGCTAAGGTGGTCC 61.032 60.000 20.33 3.88 0.00 4.46
3392 3619 0.035056 AGGTGCATGCTAAGGTGGTC 60.035 55.000 20.33 0.00 0.00 4.02
3533 3778 3.921119 TTGCTTTGAATTCGATGCAGT 57.079 38.095 26.41 0.00 40.21 4.40
3541 3786 2.564504 AGGGCCTCTTTGCTTTGAATTC 59.435 45.455 0.00 0.00 0.00 2.17
3559 3853 5.236263 GGTGTTTTTGTTTTGCTATTCAGGG 59.764 40.000 0.00 0.00 0.00 4.45
3632 3926 3.645268 GAGCACACCCCATCCCCAC 62.645 68.421 0.00 0.00 0.00 4.61
3781 4086 7.013464 TGGTTGTATAAAGTTGTAAAGTGTGGG 59.987 37.037 0.00 0.00 0.00 4.61
3825 4133 6.373759 AGTTTAAGGTGTTCTTTCCCTGATT 58.626 36.000 0.00 0.00 36.93 2.57
3841 4149 9.780413 GCATCTCATCTTTTAGAAAGTTTAAGG 57.220 33.333 0.00 0.00 0.00 2.69
3852 4160 6.748333 TCTTGTTGGCATCTCATCTTTTAG 57.252 37.500 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.