Multiple sequence alignment - TraesCS3A01G184400

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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 TraesCS3A01G184400 chr3A 100.000 3089 0 0 1 3089 215470906 215473994 0.000000e+00 5705.0
1 TraesCS3A01G184400 chr3A 91.150 113 6 4 2811 2920 707615479 707615368 1.920000e-32 150.0
2 TraesCS3A01G184400 chr3A 90.991 111 9 1 2814 2924 330699582 330699691 6.900000e-32 148.0
3 TraesCS3A01G184400 chr3A 88.136 118 13 1 2785 2902 95472090 95472206 4.150000e-29 139.0
4 TraesCS3A01G184400 chr3A 80.214 187 15 12 4 170 610756017 610756201 1.500000e-23 121.0
5 TraesCS3A01G184400 chr3D 93.548 2294 62 31 169 2411 175400672 175402930 0.000000e+00 3338.0
6 TraesCS3A01G184400 chr3D 89.568 278 6 4 2550 2815 175403148 175403414 6.380000e-87 331.0
7 TraesCS3A01G184400 chr3D 93.750 128 4 3 2962 3089 175403588 175403711 4.070000e-44 189.0
8 TraesCS3A01G184400 chr3D 93.617 47 3 0 1604 1650 382753612 382753566 1.540000e-08 71.3
9 TraesCS3A01G184400 chr3D 93.617 47 3 0 1604 1650 383110639 383110593 1.540000e-08 71.3
10 TraesCS3A01G184400 chr3B 95.972 1862 49 11 184 2033 254767638 254769485 0.000000e+00 3000.0
11 TraesCS3A01G184400 chr3B 97.041 169 5 0 2647 2815 254774672 254774840 5.040000e-73 285.0
12 TraesCS3A01G184400 chr3B 91.209 182 10 5 2909 3089 254774854 254775030 3.080000e-60 243.0
13 TraesCS3A01G184400 chr3B 75.371 674 63 40 2029 2657 254773742 254774357 2.400000e-56 230.0
14 TraesCS3A01G184400 chr7B 100.000 87 0 0 2814 2900 731020557 731020471 8.860000e-36 161.0
15 TraesCS3A01G184400 chr5B 100.000 87 0 0 2812 2898 191035108 191035194 8.860000e-36 161.0
16 TraesCS3A01G184400 chr5B 94.845 97 4 1 2813 2909 323861086 323861181 1.920000e-32 150.0
17 TraesCS3A01G184400 chr4B 97.826 92 2 0 2814 2905 166003154 166003063 3.190000e-35 159.0
18 TraesCS3A01G184400 chr5D 95.918 98 3 1 2814 2910 49290836 49290739 1.150000e-34 158.0
19 TraesCS3A01G184400 chr5D 86.916 107 8 2 64 170 477872178 477872078 7.000000e-22 115.0
20 TraesCS3A01G184400 chr6D 92.453 106 6 2 2814 2918 248004002 248004106 1.920000e-32 150.0
21 TraesCS3A01G184400 chr6D 92.000 50 4 0 1603 1652 473103183 473103232 1.540000e-08 71.3
22 TraesCS3A01G184400 chr2D 80.105 191 17 11 3 172 104262359 104262549 4.180000e-24 122.0
23 TraesCS3A01G184400 chr2D 78.756 193 20 8 3 176 121768182 121767992 3.260000e-20 110.0
24 TraesCS3A01G184400 chr2D 93.617 47 3 0 1603 1649 599287941 599287895 1.540000e-08 71.3
25 TraesCS3A01G184400 chr1D 80.000 190 16 9 3 172 409574559 409574372 1.500000e-23 121.0
26 TraesCS3A01G184400 chr1D 80.000 190 17 7 3 172 415172456 415172268 1.500000e-23 121.0
27 TraesCS3A01G184400 chr1D 87.156 109 8 2 64 172 291083004 291083106 5.410000e-23 119.0
28 TraesCS3A01G184400 chr1D 86.239 109 8 3 64 172 291543028 291543129 9.050000e-21 111.0
29 TraesCS3A01G184400 chr2A 86.239 109 9 2 68 176 743543525 743543423 2.520000e-21 113.0
30 TraesCS3A01G184400 chr4D 80.189 106 16 5 1538 1641 84545794 84545692 1.190000e-09 75.0
31 TraesCS3A01G184400 chr4A 80.189 106 16 5 1538 1641 497440626 497440524 1.190000e-09 75.0
32 TraesCS3A01G184400 chr6B 92.157 51 2 2 1603 1652 718476178 718476227 1.540000e-08 71.3


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 TraesCS3A01G184400 chr3A 215470906 215473994 3088 False 5705.000000 5705 100.000000 1 3089 1 chr3A.!!$F2 3088
1 TraesCS3A01G184400 chr3D 175400672 175403711 3039 False 1286.000000 3338 92.288667 169 3089 3 chr3D.!!$F1 2920
2 TraesCS3A01G184400 chr3B 254767638 254769485 1847 False 3000.000000 3000 95.972000 184 2033 1 chr3B.!!$F1 1849
3 TraesCS3A01G184400 chr3B 254773742 254775030 1288 False 252.666667 285 87.873667 2029 3089 3 chr3B.!!$F2 1060

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
129 130 0.028374 AAACGGACAAAAAGCGGACG 59.972 50.0 0.00 0.00 0.00 4.79 F
147 148 0.092351 CGAAATCGACGTCCGTTTGG 59.908 55.0 10.58 8.69 43.02 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 1982 0.161024 GTCTTCACGCGCAGTTGTAC 59.839 55.0 5.73 0.0 0.0 2.90 R
2126 2166 0.808755 AAATTCGCACCGTTCCCATC 59.191 50.0 0.00 0.0 0.0 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
54 55 2.339728 TTTTTGCGCCGTCTAAATGG 57.660 45.000 4.18 0.00 34.35 3.16
55 56 0.523966 TTTTGCGCCGTCTAAATGGG 59.476 50.000 4.18 0.00 31.56 4.00
56 57 0.606944 TTTGCGCCGTCTAAATGGGT 60.607 50.000 4.18 0.00 31.56 4.51
57 58 1.022451 TTGCGCCGTCTAAATGGGTC 61.022 55.000 4.18 0.00 31.56 4.46
58 59 2.522638 GCGCCGTCTAAATGGGTCG 61.523 63.158 0.00 0.00 31.56 4.79
59 60 2.522638 CGCCGTCTAAATGGGTCGC 61.523 63.158 0.00 0.00 31.56 5.19
60 61 1.448893 GCCGTCTAAATGGGTCGCA 60.449 57.895 0.00 0.00 31.56 5.10
61 62 1.429148 GCCGTCTAAATGGGTCGCAG 61.429 60.000 0.00 0.00 31.56 5.18
62 63 0.810031 CCGTCTAAATGGGTCGCAGG 60.810 60.000 0.00 0.00 0.00 4.85
63 64 1.429148 CGTCTAAATGGGTCGCAGGC 61.429 60.000 0.00 0.00 0.00 4.85
75 76 2.751436 GCAGGCCAGAATGCGGAA 60.751 61.111 5.01 0.00 31.87 4.30
76 77 2.768492 GCAGGCCAGAATGCGGAAG 61.768 63.158 5.01 0.00 31.87 3.46
88 89 3.131478 CGGAAGCGGGCGGAAAAT 61.131 61.111 0.00 0.00 0.00 1.82
89 90 2.798689 GGAAGCGGGCGGAAAATC 59.201 61.111 0.00 0.00 0.00 2.17
90 91 2.771639 GGAAGCGGGCGGAAAATCC 61.772 63.158 0.00 0.00 0.00 3.01
100 101 3.527434 GGAAAATCCGTGTCCGTCT 57.473 52.632 0.00 0.00 0.00 4.18
101 102 1.076332 GGAAAATCCGTGTCCGTCTG 58.924 55.000 0.00 0.00 0.00 3.51
102 103 1.337447 GGAAAATCCGTGTCCGTCTGA 60.337 52.381 0.00 0.00 0.00 3.27
103 104 1.725164 GAAAATCCGTGTCCGTCTGAC 59.275 52.381 0.00 0.00 44.72 3.51
104 105 0.966920 AAATCCGTGTCCGTCTGACT 59.033 50.000 6.21 0.00 44.75 3.41
105 106 0.243907 AATCCGTGTCCGTCTGACTG 59.756 55.000 6.21 0.00 44.75 3.51
106 107 0.608308 ATCCGTGTCCGTCTGACTGA 60.608 55.000 6.21 1.70 44.75 3.41
107 108 0.608308 TCCGTGTCCGTCTGACTGAT 60.608 55.000 6.21 0.00 44.75 2.90
108 109 0.179161 CCGTGTCCGTCTGACTGATC 60.179 60.000 6.21 2.55 44.75 2.92
109 110 0.179161 CGTGTCCGTCTGACTGATCC 60.179 60.000 6.21 0.00 44.75 3.36
110 111 0.888619 GTGTCCGTCTGACTGATCCA 59.111 55.000 6.21 0.00 44.75 3.41
111 112 1.272490 GTGTCCGTCTGACTGATCCAA 59.728 52.381 6.21 0.00 44.75 3.53
112 113 1.967779 TGTCCGTCTGACTGATCCAAA 59.032 47.619 6.21 0.00 44.75 3.28
113 114 2.288825 TGTCCGTCTGACTGATCCAAAC 60.289 50.000 6.21 0.00 44.75 2.93
114 115 1.067846 TCCGTCTGACTGATCCAAACG 60.068 52.381 6.21 0.00 0.00 3.60
115 116 1.350193 CGTCTGACTGATCCAAACGG 58.650 55.000 6.21 0.00 0.00 4.44
116 117 1.067846 CGTCTGACTGATCCAAACGGA 60.068 52.381 6.21 0.00 36.85 4.69
117 118 2.338500 GTCTGACTGATCCAAACGGAC 58.662 52.381 0.00 0.00 34.62 4.79
118 119 1.967779 TCTGACTGATCCAAACGGACA 59.032 47.619 0.00 0.00 34.62 4.02
119 120 2.367241 TCTGACTGATCCAAACGGACAA 59.633 45.455 0.00 0.00 34.62 3.18
120 121 3.138304 CTGACTGATCCAAACGGACAAA 58.862 45.455 0.00 0.00 34.62 2.83
121 122 3.546724 TGACTGATCCAAACGGACAAAA 58.453 40.909 0.00 0.00 34.62 2.44
122 123 3.948473 TGACTGATCCAAACGGACAAAAA 59.052 39.130 0.00 0.00 34.62 1.94
123 124 4.036262 TGACTGATCCAAACGGACAAAAAG 59.964 41.667 0.00 0.00 34.62 2.27
124 125 3.243401 ACTGATCCAAACGGACAAAAAGC 60.243 43.478 0.00 0.00 34.62 3.51
125 126 2.287308 TGATCCAAACGGACAAAAAGCG 60.287 45.455 0.00 0.00 34.62 4.68
126 127 0.382515 TCCAAACGGACAAAAAGCGG 59.617 50.000 0.00 0.00 0.00 5.52
127 128 0.382515 CCAAACGGACAAAAAGCGGA 59.617 50.000 0.00 0.00 0.00 5.54
128 129 1.472990 CAAACGGACAAAAAGCGGAC 58.527 50.000 0.00 0.00 0.00 4.79
129 130 0.028374 AAACGGACAAAAAGCGGACG 59.972 50.000 0.00 0.00 0.00 4.79
130 131 0.810823 AACGGACAAAAAGCGGACGA 60.811 50.000 0.00 0.00 0.00 4.20
131 132 0.810823 ACGGACAAAAAGCGGACGAA 60.811 50.000 0.00 0.00 0.00 3.85
132 133 0.305313 CGGACAAAAAGCGGACGAAA 59.695 50.000 0.00 0.00 0.00 3.46
133 134 1.069500 CGGACAAAAAGCGGACGAAAT 60.069 47.619 0.00 0.00 0.00 2.17
134 135 2.581637 GGACAAAAAGCGGACGAAATC 58.418 47.619 0.00 0.00 0.00 2.17
135 136 2.230864 GACAAAAAGCGGACGAAATCG 58.769 47.619 0.48 0.48 46.33 3.34
136 137 1.868498 ACAAAAAGCGGACGAAATCGA 59.132 42.857 10.16 0.00 43.02 3.59
137 138 2.230864 CAAAAAGCGGACGAAATCGAC 58.769 47.619 10.16 3.09 43.02 4.20
138 139 0.437295 AAAAGCGGACGAAATCGACG 59.563 50.000 10.16 13.74 43.02 5.12
139 140 0.665369 AAAGCGGACGAAATCGACGT 60.665 50.000 10.16 0.00 46.58 4.34
144 145 4.950744 ACGAAATCGACGTCCGTT 57.049 50.000 10.58 1.87 43.02 4.44
145 146 3.184094 ACGAAATCGACGTCCGTTT 57.816 47.368 10.58 11.02 43.02 3.60
146 147 0.780002 ACGAAATCGACGTCCGTTTG 59.220 50.000 10.58 7.95 43.02 2.93
147 148 0.092351 CGAAATCGACGTCCGTTTGG 59.908 55.000 10.58 8.69 43.02 3.28
148 149 1.421382 GAAATCGACGTCCGTTTGGA 58.579 50.000 10.58 0.00 43.88 3.53
149 150 3.548823 CGAAATCGACGTCCGTTTGGAT 61.549 50.000 10.58 2.66 44.25 3.41
150 151 5.333236 CGAAATCGACGTCCGTTTGGATC 62.333 52.174 10.58 0.00 44.25 3.36
156 157 2.267642 TCCGTTTGGATCAGCCCG 59.732 61.111 0.00 0.00 40.17 6.13
157 158 2.046314 CCGTTTGGATCAGCCCGT 60.046 61.111 0.00 0.00 37.49 5.28
158 159 1.674322 CCGTTTGGATCAGCCCGTT 60.674 57.895 0.00 0.00 37.49 4.44
159 160 1.501741 CGTTTGGATCAGCCCGTTG 59.498 57.895 0.00 0.00 34.97 4.10
160 161 0.953471 CGTTTGGATCAGCCCGTTGA 60.953 55.000 0.00 0.00 34.97 3.18
161 162 1.243902 GTTTGGATCAGCCCGTTGAA 58.756 50.000 0.00 0.00 34.97 2.69
162 163 1.611491 GTTTGGATCAGCCCGTTGAAA 59.389 47.619 0.00 0.00 34.97 2.69
163 164 2.214376 TTGGATCAGCCCGTTGAAAT 57.786 45.000 0.00 0.00 34.97 2.17
164 165 2.214376 TGGATCAGCCCGTTGAAATT 57.786 45.000 0.00 0.00 34.97 1.82
165 166 1.818060 TGGATCAGCCCGTTGAAATTG 59.182 47.619 0.00 0.00 34.97 2.32
166 167 1.469767 GGATCAGCCCGTTGAAATTGC 60.470 52.381 0.00 0.00 0.00 3.56
167 168 1.474077 GATCAGCCCGTTGAAATTGCT 59.526 47.619 0.00 0.00 0.00 3.91
265 268 2.095161 GTCTGGTCCTCTGTTCGTAGTG 60.095 54.545 0.00 0.00 0.00 2.74
322 325 6.723298 AGAATATCACAACAACCAACCAAA 57.277 33.333 0.00 0.00 0.00 3.28
323 326 6.748132 AGAATATCACAACAACCAACCAAAG 58.252 36.000 0.00 0.00 0.00 2.77
354 361 5.070770 AGCTAGTCAGTCAATCAGTTCTG 57.929 43.478 0.00 0.00 0.00 3.02
583 594 8.581578 TCACCGCCTTTTTCTATCTTTTATTTT 58.418 29.630 0.00 0.00 0.00 1.82
604 615 5.752892 TTTAGAGACGGTGCAGTAGATAG 57.247 43.478 0.00 0.00 0.00 2.08
615 626 3.205507 TGCAGTAGATAGAAGAGGGGAGT 59.794 47.826 0.00 0.00 0.00 3.85
693 712 6.780706 TCTCCTTGTTACGAAGACAAATTC 57.219 37.500 0.00 0.00 36.64 2.17
844 865 5.016831 GCCTCTTCTTTTCCCTTTATTCCA 58.983 41.667 0.00 0.00 0.00 3.53
856 877 3.003689 CCTTTATTCCATGCCTAGTTGCG 59.996 47.826 0.00 0.00 0.00 4.85
858 879 1.959042 ATTCCATGCCTAGTTGCGAG 58.041 50.000 0.00 0.00 0.00 5.03
869 890 3.560896 CCTAGTTGCGAGTACTACTCCTC 59.439 52.174 10.14 4.04 42.12 3.71
870 891 2.367486 AGTTGCGAGTACTACTCCTCC 58.633 52.381 10.14 1.24 42.12 4.30
871 892 1.404748 GTTGCGAGTACTACTCCTCCC 59.595 57.143 10.14 0.00 42.12 4.30
2080 2119 1.082117 CCGGTCCAACAGCATACGAC 61.082 60.000 0.00 0.00 0.00 4.34
2083 2122 1.269166 GTCCAACAGCATACGACTCG 58.731 55.000 0.00 0.00 0.00 4.18
2126 2166 1.024579 AATGCTTAGGTGCCCGTTCG 61.025 55.000 0.00 0.00 0.00 3.95
2128 2168 1.153429 GCTTAGGTGCCCGTTCGAT 60.153 57.895 0.00 0.00 0.00 3.59
2129 2169 1.429148 GCTTAGGTGCCCGTTCGATG 61.429 60.000 0.00 0.00 0.00 3.84
2130 2170 0.810031 CTTAGGTGCCCGTTCGATGG 60.810 60.000 0.00 0.00 0.00 3.51
2139 2179 3.174788 GTTCGATGGGAACGGTGC 58.825 61.111 0.00 0.00 45.05 5.01
2144 2184 1.366111 CGATGGGAACGGTGCGAATT 61.366 55.000 0.00 0.00 0.00 2.17
2170 2210 7.861176 TTTTTCTACAATACAAAATCGTGCC 57.139 32.000 0.00 0.00 0.00 5.01
2174 2214 5.935206 TCTACAATACAAAATCGTGCCAGAA 59.065 36.000 0.00 0.00 0.00 3.02
2196 2236 6.950041 AGAATTGGATTGTTTCTCCTGATCAA 59.050 34.615 0.00 0.00 33.69 2.57
2197 2237 5.964958 TTGGATTGTTTCTCCTGATCAAC 57.035 39.130 0.00 0.00 33.69 3.18
2223 2276 4.821805 ACTGGGATTGCTATTGTTATTCCG 59.178 41.667 0.00 0.00 0.00 4.30
2277 2338 1.290955 CTGTTTGGCTGGGCATGTG 59.709 57.895 0.00 0.00 0.00 3.21
2348 2409 2.029110 CCACCCACACATGTTTGAATCC 60.029 50.000 13.59 0.00 0.00 3.01
2352 2413 0.887933 ACACATGTTTGAATCCCCGC 59.112 50.000 0.00 0.00 0.00 6.13
2353 2414 0.173255 CACATGTTTGAATCCCCGCC 59.827 55.000 0.00 0.00 0.00 6.13
2354 2415 0.970427 ACATGTTTGAATCCCCGCCC 60.970 55.000 0.00 0.00 0.00 6.13
2355 2416 1.381191 ATGTTTGAATCCCCGCCCC 60.381 57.895 0.00 0.00 0.00 5.80
2381 2442 4.329801 CCCTGCTTTTGACTTCAACAAAAC 59.670 41.667 0.00 0.00 40.63 2.43
2385 2446 4.387559 GCTTTTGACTTCAACAAAACGGTT 59.612 37.500 0.00 0.00 40.63 4.44
2387 2448 6.453265 GCTTTTGACTTCAACAAAACGGTTAC 60.453 38.462 0.00 0.00 40.63 2.50
2388 2449 5.624344 TTGACTTCAACAAAACGGTTACA 57.376 34.783 0.00 0.00 0.00 2.41
2389 2450 4.972201 TGACTTCAACAAAACGGTTACAC 58.028 39.130 0.00 0.00 0.00 2.90
2390 2451 4.696402 TGACTTCAACAAAACGGTTACACT 59.304 37.500 0.00 0.00 0.00 3.55
2391 2452 5.873712 TGACTTCAACAAAACGGTTACACTA 59.126 36.000 0.00 0.00 0.00 2.74
2405 2466 7.159372 ACGGTTACACTACATTTCTTCATCTT 58.841 34.615 0.00 0.00 0.00 2.40
2421 2497 7.106239 TCTTCATCTTTGTATCAAGAACCCTC 58.894 38.462 0.00 0.00 0.00 4.30
2422 2498 5.745227 TCATCTTTGTATCAAGAACCCTCC 58.255 41.667 0.00 0.00 0.00 4.30
2434 2510 0.108019 AACCCTCCGCGAAACTCTTT 59.892 50.000 8.23 0.00 0.00 2.52
2435 2511 0.320508 ACCCTCCGCGAAACTCTTTC 60.321 55.000 8.23 0.00 36.32 2.62
2446 2522 4.135186 GAAACTCTTTCGAAACAGGAGC 57.865 45.455 19.84 5.87 0.00 4.70
2447 2523 2.910688 ACTCTTTCGAAACAGGAGCA 57.089 45.000 19.84 0.00 0.00 4.26
2450 2526 1.067974 TCTTTCGAAACAGGAGCACGA 59.932 47.619 6.47 0.00 0.00 4.35
2452 2528 3.057104 TCTTTCGAAACAGGAGCACGATA 60.057 43.478 6.47 0.00 33.25 2.92
2453 2529 3.306917 TTCGAAACAGGAGCACGATAA 57.693 42.857 0.00 0.00 33.25 1.75
2454 2530 3.520290 TCGAAACAGGAGCACGATAAT 57.480 42.857 0.00 0.00 0.00 1.28
2493 2650 2.040278 TGACAAAAGATGCCTAGCTGGT 59.960 45.455 0.00 0.00 38.35 4.00
2500 2657 3.761897 AGATGCCTAGCTGGTCTAGTAG 58.238 50.000 0.00 0.00 42.57 2.57
2502 2659 4.351407 AGATGCCTAGCTGGTCTAGTAGTA 59.649 45.833 0.00 0.00 42.57 1.82
2503 2660 3.818180 TGCCTAGCTGGTCTAGTAGTAC 58.182 50.000 0.00 0.00 42.57 2.73
2505 2662 3.434739 GCCTAGCTGGTCTAGTAGTACCA 60.435 52.174 16.08 16.08 42.57 3.25
2507 2664 4.141436 CCTAGCTGGTCTAGTAGTACCACT 60.141 50.000 14.08 16.00 42.57 4.00
2523 2680 2.108250 ACCACTTGTCAAACTAGGGCAT 59.892 45.455 0.00 0.00 0.00 4.40
2545 2702 7.244166 CATGTTCTGCTAATAGGAAGAGTTG 57.756 40.000 0.00 0.00 0.00 3.16
2546 2703 6.605471 TGTTCTGCTAATAGGAAGAGTTGA 57.395 37.500 0.00 0.00 0.00 3.18
2547 2704 7.187824 TGTTCTGCTAATAGGAAGAGTTGAT 57.812 36.000 0.00 0.00 0.00 2.57
2548 2705 8.306313 TGTTCTGCTAATAGGAAGAGTTGATA 57.694 34.615 0.00 0.00 0.00 2.15
2601 2758 1.063942 GGATTCAGGTTAACCCAGGGG 60.064 57.143 21.30 6.87 42.03 4.79
2612 2769 1.766461 CCCAGGGGTAGGCAGTAGG 60.766 68.421 0.00 0.00 0.00 3.18
2618 2775 1.403687 GGGTAGGCAGTAGGAGGCAG 61.404 65.000 0.00 0.00 0.00 4.85
2619 2776 1.443828 GTAGGCAGTAGGAGGCAGC 59.556 63.158 0.00 0.00 0.00 5.25
2620 2777 1.045911 GTAGGCAGTAGGAGGCAGCT 61.046 60.000 0.00 0.00 0.00 4.24
2629 2786 0.758685 AGGAGGCAGCTGCTAGTAGG 60.759 60.000 35.82 0.00 41.70 3.18
2643 2800 0.969149 AGTAGGCTTTTGCTTTGGCC 59.031 50.000 0.00 0.00 46.54 5.36
2644 2801 0.678950 GTAGGCTTTTGCTTTGGCCA 59.321 50.000 0.00 0.00 46.23 5.36
2645 2802 1.276138 GTAGGCTTTTGCTTTGGCCAT 59.724 47.619 6.09 0.00 46.23 4.40
2646 2803 0.035739 AGGCTTTTGCTTTGGCCATG 59.964 50.000 6.09 3.68 46.23 3.66
2779 3277 8.177119 AGATGATGGAGTTAATCTAGTCTGAC 57.823 38.462 0.00 0.00 0.00 3.51
2780 3278 6.378710 TGATGGAGTTAATCTAGTCTGACG 57.621 41.667 1.52 0.00 0.00 4.35
2815 3313 5.392272 CCACCCGTTAAAGTTTGCCTATTAC 60.392 44.000 0.00 0.00 0.00 1.89
2816 3314 5.413523 CACCCGTTAAAGTTTGCCTATTACT 59.586 40.000 0.00 0.00 0.00 2.24
2817 3315 5.645067 ACCCGTTAAAGTTTGCCTATTACTC 59.355 40.000 0.00 0.00 0.00 2.59
2818 3316 5.065602 CCCGTTAAAGTTTGCCTATTACTCC 59.934 44.000 0.00 0.00 0.00 3.85
2819 3317 5.065602 CCGTTAAAGTTTGCCTATTACTCCC 59.934 44.000 0.00 0.00 0.00 4.30
2821 3319 6.036844 CGTTAAAGTTTGCCTATTACTCCCTC 59.963 42.308 0.00 0.00 0.00 4.30
2822 3320 4.505324 AAGTTTGCCTATTACTCCCTCC 57.495 45.455 0.00 0.00 0.00 4.30
2824 3322 2.169978 GTTTGCCTATTACTCCCTCCGT 59.830 50.000 0.00 0.00 0.00 4.69
2825 3323 3.317455 TTGCCTATTACTCCCTCCGTA 57.683 47.619 0.00 0.00 0.00 4.02
2826 3324 3.317455 TGCCTATTACTCCCTCCGTAA 57.683 47.619 0.00 0.00 0.00 3.18
2828 3326 4.228824 TGCCTATTACTCCCTCCGTAAAT 58.771 43.478 0.00 0.00 31.36 1.40
2829 3327 4.657039 TGCCTATTACTCCCTCCGTAAATT 59.343 41.667 0.00 0.00 31.36 1.82
2830 3328 5.840149 TGCCTATTACTCCCTCCGTAAATTA 59.160 40.000 0.00 0.00 31.36 1.40
2831 3329 6.327104 TGCCTATTACTCCCTCCGTAAATTAA 59.673 38.462 0.00 0.00 31.36 1.40
2832 3330 7.016858 TGCCTATTACTCCCTCCGTAAATTAAT 59.983 37.037 0.00 0.00 31.36 1.40
2833 3331 8.534496 GCCTATTACTCCCTCCGTAAATTAATA 58.466 37.037 0.00 0.00 31.36 0.98
2840 3338 8.312564 ACTCCCTCCGTAAATTAATATAAGAGC 58.687 37.037 0.00 0.00 0.00 4.09
2841 3339 7.318141 TCCCTCCGTAAATTAATATAAGAGCG 58.682 38.462 0.00 0.00 0.00 5.03
2842 3340 7.039504 TCCCTCCGTAAATTAATATAAGAGCGT 60.040 37.037 0.00 0.00 0.00 5.07
2843 3341 7.601508 CCCTCCGTAAATTAATATAAGAGCGTT 59.398 37.037 0.00 0.00 0.00 4.84
2844 3342 8.985805 CCTCCGTAAATTAATATAAGAGCGTTT 58.014 33.333 0.00 0.00 0.00 3.60
2894 3392 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
2896 3394 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
2907 3405 9.411189 AGTTTACAGAGGGAGTATTAAGTAGAG 57.589 37.037 0.00 0.00 0.00 2.43
2945 3444 3.760684 AGGGTCTGCTTTTCTTATGCAAG 59.239 43.478 0.00 0.00 36.59 4.01
2992 3597 6.408858 TCTGCTACATTTCTCGATGAAAAC 57.591 37.500 12.07 3.95 46.32 2.43
3007 3612 8.025243 TCGATGAAAACGAGCTTTTATTAACT 57.975 30.769 0.00 0.00 35.75 2.24
3008 3613 8.166706 TCGATGAAAACGAGCTTTTATTAACTC 58.833 33.333 0.00 0.00 35.75 3.01
3009 3614 7.955324 CGATGAAAACGAGCTTTTATTAACTCA 59.045 33.333 0.00 0.00 31.90 3.41
3081 3686 1.817357 ATGATAGATGCATGCCACCG 58.183 50.000 16.68 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.068194 CCCATTTAGACGGCGCAAAAA 60.068 47.619 10.83 5.11 0.00 1.94
36 37 0.523966 CCCATTTAGACGGCGCAAAA 59.476 50.000 10.83 5.51 0.00 2.44
37 38 0.606944 ACCCATTTAGACGGCGCAAA 60.607 50.000 10.83 5.52 0.00 3.68
38 39 1.003112 ACCCATTTAGACGGCGCAA 60.003 52.632 10.83 0.00 0.00 4.85
39 40 1.448893 GACCCATTTAGACGGCGCA 60.449 57.895 10.83 0.00 0.00 6.09
40 41 2.522638 CGACCCATTTAGACGGCGC 61.523 63.158 6.90 0.00 0.00 6.53
41 42 2.522638 GCGACCCATTTAGACGGCG 61.523 63.158 4.80 4.80 0.00 6.46
42 43 1.429148 CTGCGACCCATTTAGACGGC 61.429 60.000 0.00 0.00 0.00 5.68
43 44 0.810031 CCTGCGACCCATTTAGACGG 60.810 60.000 0.00 0.00 0.00 4.79
44 45 1.429148 GCCTGCGACCCATTTAGACG 61.429 60.000 0.00 0.00 0.00 4.18
45 46 1.095807 GGCCTGCGACCCATTTAGAC 61.096 60.000 0.00 0.00 0.00 2.59
46 47 1.223487 GGCCTGCGACCCATTTAGA 59.777 57.895 0.00 0.00 0.00 2.10
47 48 1.077787 TGGCCTGCGACCCATTTAG 60.078 57.895 3.32 0.00 0.00 1.85
48 49 1.077787 CTGGCCTGCGACCCATTTA 60.078 57.895 3.32 0.00 0.00 1.40
49 50 2.361610 CTGGCCTGCGACCCATTT 60.362 61.111 3.32 0.00 0.00 2.32
50 51 2.215451 ATTCTGGCCTGCGACCCATT 62.215 55.000 3.32 0.00 0.00 3.16
51 52 2.683465 ATTCTGGCCTGCGACCCAT 61.683 57.895 3.32 0.00 0.00 4.00
52 53 3.329889 ATTCTGGCCTGCGACCCA 61.330 61.111 3.32 0.00 0.00 4.51
53 54 2.825836 CATTCTGGCCTGCGACCC 60.826 66.667 3.32 0.00 0.00 4.46
54 55 3.512516 GCATTCTGGCCTGCGACC 61.513 66.667 3.32 0.00 0.00 4.79
58 59 2.751436 TTCCGCATTCTGGCCTGC 60.751 61.111 3.32 4.09 35.02 4.85
59 60 2.768492 GCTTCCGCATTCTGGCCTG 61.768 63.158 3.32 2.92 35.78 4.85
60 61 2.439156 GCTTCCGCATTCTGGCCT 60.439 61.111 3.32 0.00 35.78 5.19
61 62 3.880846 CGCTTCCGCATTCTGGCC 61.881 66.667 0.00 0.00 35.30 5.36
62 63 3.880846 CCGCTTCCGCATTCTGGC 61.881 66.667 0.00 0.00 35.30 4.85
63 64 3.204827 CCCGCTTCCGCATTCTGG 61.205 66.667 0.00 0.00 35.30 3.86
64 65 3.880846 GCCCGCTTCCGCATTCTG 61.881 66.667 0.00 0.00 35.30 3.02
71 72 3.108357 GATTTTCCGCCCGCTTCCG 62.108 63.158 0.00 0.00 0.00 4.30
72 73 2.771639 GGATTTTCCGCCCGCTTCC 61.772 63.158 0.00 0.00 0.00 3.46
73 74 2.798689 GGATTTTCCGCCCGCTTC 59.201 61.111 0.00 0.00 0.00 3.86
82 83 1.076332 CAGACGGACACGGATTTTCC 58.924 55.000 0.00 0.00 46.48 3.13
83 84 1.725164 GTCAGACGGACACGGATTTTC 59.275 52.381 0.42 0.00 46.19 2.29
84 85 1.792006 GTCAGACGGACACGGATTTT 58.208 50.000 0.42 0.00 46.19 1.82
85 86 3.509388 GTCAGACGGACACGGATTT 57.491 52.632 0.42 0.00 46.19 2.17
94 95 1.067846 CGTTTGGATCAGTCAGACGGA 60.068 52.381 5.81 5.81 38.51 4.69
95 96 1.350193 CGTTTGGATCAGTCAGACGG 58.650 55.000 5.86 0.00 38.51 4.79
96 97 1.067846 TCCGTTTGGATCAGTCAGACG 60.068 52.381 6.56 6.56 40.17 4.18
97 98 2.743636 TCCGTTTGGATCAGTCAGAC 57.256 50.000 0.00 0.00 40.17 3.51
107 108 0.382515 CCGCTTTTTGTCCGTTTGGA 59.617 50.000 0.00 0.00 43.88 3.53
108 109 0.382515 TCCGCTTTTTGTCCGTTTGG 59.617 50.000 0.00 0.00 0.00 3.28
109 110 1.472990 GTCCGCTTTTTGTCCGTTTG 58.527 50.000 0.00 0.00 0.00 2.93
110 111 0.028374 CGTCCGCTTTTTGTCCGTTT 59.972 50.000 0.00 0.00 0.00 3.60
111 112 0.810823 TCGTCCGCTTTTTGTCCGTT 60.811 50.000 0.00 0.00 0.00 4.44
112 113 0.810823 TTCGTCCGCTTTTTGTCCGT 60.811 50.000 0.00 0.00 0.00 4.69
113 114 0.305313 TTTCGTCCGCTTTTTGTCCG 59.695 50.000 0.00 0.00 0.00 4.79
114 115 2.581637 GATTTCGTCCGCTTTTTGTCC 58.418 47.619 0.00 0.00 0.00 4.02
115 116 2.096614 TCGATTTCGTCCGCTTTTTGTC 60.097 45.455 0.00 0.00 40.80 3.18
116 117 1.868498 TCGATTTCGTCCGCTTTTTGT 59.132 42.857 0.00 0.00 40.80 2.83
117 118 2.230864 GTCGATTTCGTCCGCTTTTTG 58.769 47.619 0.00 0.00 40.80 2.44
118 119 1.136446 CGTCGATTTCGTCCGCTTTTT 60.136 47.619 0.00 0.00 40.80 1.94
119 120 0.437295 CGTCGATTTCGTCCGCTTTT 59.563 50.000 0.00 0.00 40.80 2.27
120 121 0.665369 ACGTCGATTTCGTCCGCTTT 60.665 50.000 0.00 0.00 40.80 3.51
121 122 1.080974 ACGTCGATTTCGTCCGCTT 60.081 52.632 0.00 0.00 40.80 4.68
122 123 2.564975 ACGTCGATTTCGTCCGCT 59.435 55.556 0.00 1.77 40.80 5.52
127 128 0.780002 CAAACGGACGTCGATTTCGT 59.220 50.000 9.92 10.19 44.27 3.85
128 129 0.092351 CCAAACGGACGTCGATTTCG 59.908 55.000 9.92 9.50 42.43 3.46
129 130 1.421382 TCCAAACGGACGTCGATTTC 58.579 50.000 9.92 0.00 42.43 2.17
130 131 1.997606 GATCCAAACGGACGTCGATTT 59.002 47.619 9.92 9.52 42.43 2.17
131 132 1.067425 TGATCCAAACGGACGTCGATT 60.067 47.619 9.92 3.12 42.43 3.34
132 133 0.528924 TGATCCAAACGGACGTCGAT 59.471 50.000 9.92 5.26 42.43 3.59
133 134 0.109458 CTGATCCAAACGGACGTCGA 60.109 55.000 9.92 0.00 42.43 4.20
134 135 1.683790 GCTGATCCAAACGGACGTCG 61.684 60.000 9.92 7.64 45.88 5.12
135 136 1.359459 GGCTGATCCAAACGGACGTC 61.359 60.000 7.13 7.13 34.62 4.34
136 137 1.375523 GGCTGATCCAAACGGACGT 60.376 57.895 0.00 0.00 34.62 4.34
137 138 2.106683 GGGCTGATCCAAACGGACG 61.107 63.158 0.00 0.00 34.62 4.79
138 139 2.106683 CGGGCTGATCCAAACGGAC 61.107 63.158 0.00 0.00 34.62 4.79
139 140 2.119484 AACGGGCTGATCCAAACGGA 62.119 55.000 0.00 0.00 36.85 4.69
140 141 1.674322 AACGGGCTGATCCAAACGG 60.674 57.895 0.00 0.00 36.21 4.44
141 142 0.953471 TCAACGGGCTGATCCAAACG 60.953 55.000 0.00 0.00 36.21 3.60
142 143 1.243902 TTCAACGGGCTGATCCAAAC 58.756 50.000 0.00 0.00 36.21 2.93
143 144 1.988293 TTTCAACGGGCTGATCCAAA 58.012 45.000 0.00 0.00 36.21 3.28
144 145 2.214376 ATTTCAACGGGCTGATCCAA 57.786 45.000 0.00 0.00 36.21 3.53
145 146 1.818060 CAATTTCAACGGGCTGATCCA 59.182 47.619 0.00 0.00 36.21 3.41
146 147 1.469767 GCAATTTCAACGGGCTGATCC 60.470 52.381 0.00 0.00 0.00 3.36
147 148 1.474077 AGCAATTTCAACGGGCTGATC 59.526 47.619 0.00 0.00 32.76 2.92
148 149 1.474077 GAGCAATTTCAACGGGCTGAT 59.526 47.619 0.00 0.00 34.44 2.90
149 150 0.881118 GAGCAATTTCAACGGGCTGA 59.119 50.000 0.00 0.00 34.44 4.26
150 151 0.883833 AGAGCAATTTCAACGGGCTG 59.116 50.000 0.00 0.00 34.44 4.85
151 152 2.489938 TAGAGCAATTTCAACGGGCT 57.510 45.000 0.00 0.00 37.56 5.19
152 153 3.501950 CTTTAGAGCAATTTCAACGGGC 58.498 45.455 0.00 0.00 0.00 6.13
153 154 3.756434 TCCTTTAGAGCAATTTCAACGGG 59.244 43.478 0.00 0.00 0.00 5.28
154 155 4.669197 CGTCCTTTAGAGCAATTTCAACGG 60.669 45.833 0.00 0.00 0.00 4.44
155 156 4.151689 TCGTCCTTTAGAGCAATTTCAACG 59.848 41.667 0.00 0.00 0.00 4.10
156 157 5.179555 ACTCGTCCTTTAGAGCAATTTCAAC 59.820 40.000 0.00 0.00 37.99 3.18
157 158 5.179368 CACTCGTCCTTTAGAGCAATTTCAA 59.821 40.000 0.00 0.00 37.99 2.69
158 159 4.690748 CACTCGTCCTTTAGAGCAATTTCA 59.309 41.667 0.00 0.00 37.99 2.69
159 160 4.691216 ACACTCGTCCTTTAGAGCAATTTC 59.309 41.667 0.00 0.00 37.99 2.17
160 161 4.642429 ACACTCGTCCTTTAGAGCAATTT 58.358 39.130 0.00 0.00 37.99 1.82
161 162 4.273148 ACACTCGTCCTTTAGAGCAATT 57.727 40.909 0.00 0.00 37.99 2.32
162 163 3.963428 ACACTCGTCCTTTAGAGCAAT 57.037 42.857 0.00 0.00 37.99 3.56
163 164 3.746045 AACACTCGTCCTTTAGAGCAA 57.254 42.857 0.00 0.00 37.99 3.91
164 165 4.806330 CTTAACACTCGTCCTTTAGAGCA 58.194 43.478 0.00 0.00 37.99 4.26
165 166 3.613299 GCTTAACACTCGTCCTTTAGAGC 59.387 47.826 0.00 0.00 37.99 4.09
166 167 4.621886 GTGCTTAACACTCGTCCTTTAGAG 59.378 45.833 0.00 0.00 46.41 2.43
167 168 4.553323 GTGCTTAACACTCGTCCTTTAGA 58.447 43.478 0.00 0.00 46.41 2.10
265 268 1.205417 CCCAAACCTCAATCACCATGC 59.795 52.381 0.00 0.00 0.00 4.06
322 325 6.420913 TTGACTGACTAGCTTTAGGTTTCT 57.579 37.500 0.00 0.00 0.00 2.52
323 326 6.874134 TGATTGACTGACTAGCTTTAGGTTTC 59.126 38.462 0.00 0.00 0.00 2.78
354 361 3.385749 ATCACGATGTGACGGGGGC 62.386 63.158 1.11 0.00 45.65 5.80
583 594 5.032327 TCTATCTACTGCACCGTCTCTAA 57.968 43.478 0.00 0.00 0.00 2.10
585 596 3.562343 TCTATCTACTGCACCGTCTCT 57.438 47.619 0.00 0.00 0.00 3.10
586 597 3.878103 TCTTCTATCTACTGCACCGTCTC 59.122 47.826 0.00 0.00 0.00 3.36
604 615 1.552792 CTTCCTCACACTCCCCTCTTC 59.447 57.143 0.00 0.00 0.00 2.87
615 626 1.261480 GTCTCTGCCTCTTCCTCACA 58.739 55.000 0.00 0.00 0.00 3.58
693 712 4.712476 CTTGGTCTCCTAAAGGATGATGG 58.288 47.826 0.00 0.00 44.46 3.51
844 865 3.288964 AGTAGTACTCGCAACTAGGCAT 58.711 45.455 0.00 0.00 30.26 4.40
856 877 2.025898 GCAGTGGGAGGAGTAGTACTC 58.974 57.143 20.24 20.24 44.32 2.59
858 879 2.146920 AGCAGTGGGAGGAGTAGTAC 57.853 55.000 0.00 0.00 0.00 2.73
932 955 0.318120 GGTTCTTGGTGGTGCAATGG 59.682 55.000 0.00 0.00 0.00 3.16
933 956 0.318120 GGGTTCTTGGTGGTGCAATG 59.682 55.000 0.00 0.00 0.00 2.82
934 957 1.178534 CGGGTTCTTGGTGGTGCAAT 61.179 55.000 0.00 0.00 0.00 3.56
1536 1559 3.479203 CCCATAGTGCCAGCCGGA 61.479 66.667 5.05 0.00 0.00 5.14
1957 1982 0.161024 GTCTTCACGCGCAGTTGTAC 59.839 55.000 5.73 0.00 0.00 2.90
2060 2085 1.813753 CGTATGCTGTTGGACCGGG 60.814 63.158 6.32 0.00 0.00 5.73
2061 2086 1.082117 GTCGTATGCTGTTGGACCGG 61.082 60.000 0.00 0.00 0.00 5.28
2080 2119 2.045280 CTGGGTCAGCCTATCCGAG 58.955 63.158 0.00 0.00 34.45 4.63
2126 2166 0.808755 AAATTCGCACCGTTCCCATC 59.191 50.000 0.00 0.00 0.00 3.51
2128 2168 1.033574 AAAAATTCGCACCGTTCCCA 58.966 45.000 0.00 0.00 0.00 4.37
2129 2169 3.877874 AAAAATTCGCACCGTTCCC 57.122 47.368 0.00 0.00 0.00 3.97
2157 2197 4.075682 TCCAATTCTGGCACGATTTTGTA 58.924 39.130 0.00 0.00 43.17 2.41
2158 2198 2.890311 TCCAATTCTGGCACGATTTTGT 59.110 40.909 0.00 0.00 43.17 2.83
2160 2200 4.021192 ACAATCCAATTCTGGCACGATTTT 60.021 37.500 0.00 0.00 43.17 1.82
2161 2201 3.511146 ACAATCCAATTCTGGCACGATTT 59.489 39.130 0.00 0.00 43.17 2.17
2162 2202 3.091545 ACAATCCAATTCTGGCACGATT 58.908 40.909 0.00 0.00 43.17 3.34
2163 2203 2.726821 ACAATCCAATTCTGGCACGAT 58.273 42.857 0.00 0.00 43.17 3.73
2164 2204 2.198827 ACAATCCAATTCTGGCACGA 57.801 45.000 0.00 0.00 43.17 4.35
2165 2205 3.057315 AGAAACAATCCAATTCTGGCACG 60.057 43.478 0.00 0.00 43.17 5.34
2166 2206 4.488879 GAGAAACAATCCAATTCTGGCAC 58.511 43.478 0.00 0.00 43.17 5.01
2167 2207 3.511146 GGAGAAACAATCCAATTCTGGCA 59.489 43.478 0.00 0.00 43.17 4.92
2168 2208 3.766051 AGGAGAAACAATCCAATTCTGGC 59.234 43.478 0.00 0.00 43.17 4.85
2169 2209 5.012239 TCAGGAGAAACAATCCAATTCTGG 58.988 41.667 0.00 0.00 45.08 3.86
2170 2210 6.376299 TGATCAGGAGAAACAATCCAATTCTG 59.624 38.462 0.00 0.00 39.47 3.02
2174 2214 6.251471 AGTTGATCAGGAGAAACAATCCAAT 58.749 36.000 0.00 0.00 39.47 3.16
2187 2227 4.626287 GCAATCCCAGTAAGTTGATCAGGA 60.626 45.833 0.00 0.00 0.00 3.86
2189 2229 4.521146 AGCAATCCCAGTAAGTTGATCAG 58.479 43.478 0.00 0.00 0.00 2.90
2196 2236 7.502561 GGAATAACAATAGCAATCCCAGTAAGT 59.497 37.037 0.00 0.00 0.00 2.24
2197 2237 7.307989 CGGAATAACAATAGCAATCCCAGTAAG 60.308 40.741 0.00 0.00 0.00 2.34
2248 2309 4.889409 CCCAGCCAAACAGTCATACATTAT 59.111 41.667 0.00 0.00 0.00 1.28
2266 2327 1.434696 GTGTATGCACATGCCCAGC 59.565 57.895 9.26 0.00 44.64 4.85
2277 2338 5.156355 CAAATTCCAAGACAGTGTGTATGC 58.844 41.667 0.00 0.00 0.00 3.14
2358 2419 3.799281 TTGTTGAAGTCAAAAGCAGGG 57.201 42.857 0.00 0.00 37.63 4.45
2363 2424 6.583050 TGTAACCGTTTTGTTGAAGTCAAAAG 59.417 34.615 4.44 0.00 42.68 2.27
2373 2434 7.190871 AGAAATGTAGTGTAACCGTTTTGTTG 58.809 34.615 0.00 0.00 37.80 3.33
2381 2442 7.596749 AAGATGAAGAAATGTAGTGTAACCG 57.403 36.000 0.00 0.00 37.80 4.44
2405 2466 1.404986 CGCGGAGGGTTCTTGATACAA 60.405 52.381 0.00 0.00 34.98 2.41
2411 2472 0.602905 AGTTTCGCGGAGGGTTCTTG 60.603 55.000 6.13 0.00 42.82 3.02
2434 2510 3.520290 ATTATCGTGCTCCTGTTTCGA 57.480 42.857 0.00 0.00 35.14 3.71
2435 2511 4.360563 ACTATTATCGTGCTCCTGTTTCG 58.639 43.478 0.00 0.00 0.00 3.46
2436 2512 7.438459 ACAATACTATTATCGTGCTCCTGTTTC 59.562 37.037 0.00 0.00 0.00 2.78
2440 2516 7.715265 AAACAATACTATTATCGTGCTCCTG 57.285 36.000 0.00 0.00 0.00 3.86
2441 2517 8.612619 CAAAAACAATACTATTATCGTGCTCCT 58.387 33.333 0.00 0.00 0.00 3.69
2444 2520 8.726988 ACACAAAAACAATACTATTATCGTGCT 58.273 29.630 0.00 0.00 0.00 4.40
2445 2521 8.785101 CACACAAAAACAATACTATTATCGTGC 58.215 33.333 0.00 0.00 0.00 5.34
2446 2522 9.820229 ACACACAAAAACAATACTATTATCGTG 57.180 29.630 0.00 0.00 0.00 4.35
2447 2523 9.820229 CACACACAAAAACAATACTATTATCGT 57.180 29.630 0.00 0.00 0.00 3.73
2493 2650 7.392673 CCTAGTTTGACAAGTGGTACTACTAGA 59.607 40.741 12.76 0.00 36.58 2.43
2500 2657 3.072211 GCCCTAGTTTGACAAGTGGTAC 58.928 50.000 0.00 0.00 0.00 3.34
2502 2659 1.493022 TGCCCTAGTTTGACAAGTGGT 59.507 47.619 0.00 0.00 0.00 4.16
2503 2660 2.270352 TGCCCTAGTTTGACAAGTGG 57.730 50.000 0.00 0.00 0.00 4.00
2505 2662 3.508845 ACATGCCCTAGTTTGACAAGT 57.491 42.857 0.00 0.00 0.00 3.16
2507 2664 3.820467 CAGAACATGCCCTAGTTTGACAA 59.180 43.478 0.00 0.00 0.00 3.18
2523 2680 6.605471 TCAACTCTTCCTATTAGCAGAACA 57.395 37.500 0.00 0.00 0.00 3.18
2532 2689 6.183361 CCAGCTTCCTATCAACTCTTCCTATT 60.183 42.308 0.00 0.00 0.00 1.73
2533 2690 5.306678 CCAGCTTCCTATCAACTCTTCCTAT 59.693 44.000 0.00 0.00 0.00 2.57
2534 2691 4.651503 CCAGCTTCCTATCAACTCTTCCTA 59.348 45.833 0.00 0.00 0.00 2.94
2535 2692 3.454082 CCAGCTTCCTATCAACTCTTCCT 59.546 47.826 0.00 0.00 0.00 3.36
2536 2693 3.432890 CCCAGCTTCCTATCAACTCTTCC 60.433 52.174 0.00 0.00 0.00 3.46
2537 2694 3.452627 TCCCAGCTTCCTATCAACTCTTC 59.547 47.826 0.00 0.00 0.00 2.87
2538 2695 3.454858 TCCCAGCTTCCTATCAACTCTT 58.545 45.455 0.00 0.00 0.00 2.85
2539 2696 3.121929 TCCCAGCTTCCTATCAACTCT 57.878 47.619 0.00 0.00 0.00 3.24
2540 2697 3.914426 TTCCCAGCTTCCTATCAACTC 57.086 47.619 0.00 0.00 0.00 3.01
2541 2698 4.870021 ATTTCCCAGCTTCCTATCAACT 57.130 40.909 0.00 0.00 0.00 3.16
2542 2699 4.098501 CCAATTTCCCAGCTTCCTATCAAC 59.901 45.833 0.00 0.00 0.00 3.18
2543 2700 4.280819 CCAATTTCCCAGCTTCCTATCAA 58.719 43.478 0.00 0.00 0.00 2.57
2544 2701 3.373001 CCCAATTTCCCAGCTTCCTATCA 60.373 47.826 0.00 0.00 0.00 2.15
2545 2702 3.225940 CCCAATTTCCCAGCTTCCTATC 58.774 50.000 0.00 0.00 0.00 2.08
2546 2703 2.690936 GCCCAATTTCCCAGCTTCCTAT 60.691 50.000 0.00 0.00 0.00 2.57
2547 2704 1.341976 GCCCAATTTCCCAGCTTCCTA 60.342 52.381 0.00 0.00 0.00 2.94
2548 2705 0.615827 GCCCAATTTCCCAGCTTCCT 60.616 55.000 0.00 0.00 0.00 3.36
2601 2758 1.045911 AGCTGCCTCCTACTGCCTAC 61.046 60.000 0.00 0.00 32.91 3.18
2603 2760 2.040278 AGCTGCCTCCTACTGCCT 59.960 61.111 0.00 0.00 32.91 4.75
2612 2769 1.068921 GCCTACTAGCAGCTGCCTC 59.931 63.158 34.39 8.53 43.38 4.70
2618 2775 1.743996 AGCAAAAGCCTACTAGCAGC 58.256 50.000 0.00 0.00 34.23 5.25
2619 2776 3.119708 CCAAAGCAAAAGCCTACTAGCAG 60.120 47.826 0.00 0.00 34.23 4.24
2620 2777 2.819608 CCAAAGCAAAAGCCTACTAGCA 59.180 45.455 0.00 0.00 34.23 3.49
2629 2786 0.885596 TGCATGGCCAAAGCAAAAGC 60.886 50.000 27.91 14.41 42.56 3.51
2643 2800 4.801330 AATAATGGCCATCTCATGCATG 57.199 40.909 21.08 21.07 0.00 4.06
2644 2801 5.547465 CAAAATAATGGCCATCTCATGCAT 58.453 37.500 21.08 2.67 0.00 3.96
2645 2802 4.741235 GCAAAATAATGGCCATCTCATGCA 60.741 41.667 25.91 0.00 0.00 3.96
2646 2803 3.744426 GCAAAATAATGGCCATCTCATGC 59.256 43.478 21.08 20.72 0.00 4.06
2815 3313 7.488471 CGCTCTTATATTAATTTACGGAGGGAG 59.512 40.741 17.02 0.00 34.63 4.30
2816 3314 7.039504 ACGCTCTTATATTAATTTACGGAGGGA 60.040 37.037 22.59 0.00 35.94 4.20
2817 3315 7.095270 ACGCTCTTATATTAATTTACGGAGGG 58.905 38.462 18.58 18.58 37.30 4.30
2818 3316 8.530269 AACGCTCTTATATTAATTTACGGAGG 57.470 34.615 0.00 0.00 0.00 4.30
2868 3366 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
2870 3368 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
2881 3379 9.411189 CTCTACTTAATACTCCCTCTGTAAACT 57.589 37.037 0.00 0.00 0.00 2.66
2882 3380 9.187996 ACTCTACTTAATACTCCCTCTGTAAAC 57.812 37.037 0.00 0.00 0.00 2.01
2901 3399 9.998752 ACCCTCAGCAATATTATATACTCTACT 57.001 33.333 0.00 0.00 0.00 2.57
2904 3402 8.976353 CAGACCCTCAGCAATATTATATACTCT 58.024 37.037 0.00 0.00 0.00 3.24
2905 3403 7.708752 GCAGACCCTCAGCAATATTATATACTC 59.291 40.741 0.00 0.00 0.00 2.59
2906 3404 7.401493 AGCAGACCCTCAGCAATATTATATACT 59.599 37.037 0.00 0.00 30.69 2.12
2907 3405 7.560368 AGCAGACCCTCAGCAATATTATATAC 58.440 38.462 0.00 0.00 30.69 1.47
2917 3415 1.143684 AGAAAAGCAGACCCTCAGCAA 59.856 47.619 0.00 0.00 30.69 3.91
2945 3444 9.521503 AGAAAATTGTAAGAAAGAGAAAGCAAC 57.478 29.630 0.00 0.00 0.00 4.17
2992 3597 6.849305 ACGTTTTGTGAGTTAATAAAAGCTCG 59.151 34.615 0.00 0.00 0.00 5.03
2996 3601 7.847166 GGGACGTTTTGTGAGTTAATAAAAG 57.153 36.000 0.00 0.00 0.00 2.27
3028 3633 2.086054 ATCTCTTGTCAGTTGCGTCC 57.914 50.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.