Multiple sequence alignment - TraesCS3A01G457100

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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 TraesCS3A01G457100 chr3A 100.000 2573 0 0 1 2573 694534995 694532423 0.000000e+00 4752.0
1 TraesCS3A01G457100 chr3A 91.304 69 4 1 257 325 674275193 674275259 2.730000e-15 93.5
2 TraesCS3A01G457100 chr3D 93.872 2252 83 13 317 2562 558293236 558291034 0.000000e+00 3343.0
3 TraesCS3A01G457100 chr3D 79.498 239 49 0 1157 1395 558282305 558282067 1.220000e-38 171.0
4 TraesCS3A01G457100 chrUn 95.079 1463 31 13 725 2184 40742523 40741099 0.000000e+00 2265.0
5 TraesCS3A01G457100 chrUn 95.079 1463 31 13 725 2184 40745382 40746806 0.000000e+00 2265.0
6 TraesCS3A01G457100 chrUn 95.079 1463 31 13 725 2184 303402077 303400653 0.000000e+00 2265.0
7 TraesCS3A01G457100 chrUn 94.966 437 11 3 308 733 40744048 40744484 0.000000e+00 675.0
8 TraesCS3A01G457100 chrUn 87.263 369 44 3 2195 2562 40740932 40740566 3.960000e-113 418.0
9 TraesCS3A01G457100 chrUn 87.263 369 44 3 2195 2562 40746973 40747339 3.960000e-113 418.0
10 TraesCS3A01G457100 chrUn 87.263 369 44 3 2195 2562 303400486 303400120 3.960000e-113 418.0
11 TraesCS3A01G457100 chrUn 92.308 39 1 1 166 202 70759307 70759269 1.000000e-03 54.7
12 TraesCS3A01G457100 chrUn 92.308 39 1 1 166 202 70781489 70781451 1.000000e-03 54.7
13 TraesCS3A01G457100 chr2A 83.849 291 35 10 1138 1422 603523788 603524072 1.520000e-67 267.0
14 TraesCS3A01G457100 chr2A 82.174 230 40 1 2303 2531 596151454 596151683 2.020000e-46 196.0
15 TraesCS3A01G457100 chr2A 94.828 58 3 0 257 314 81994593 81994536 9.800000e-15 91.6
16 TraesCS3A01G457100 chr2A 97.059 34 1 0 167 200 30240506 30240473 9.940000e-05 58.4
17 TraesCS3A01G457100 chr2A 97.059 34 1 0 167 200 30265414 30265381 9.940000e-05 58.4
18 TraesCS3A01G457100 chr2D 86.722 241 28 4 1138 1376 460648986 460649224 5.460000e-67 265.0
19 TraesCS3A01G457100 chr4D 81.985 272 45 3 2295 2562 7739830 7739559 7.160000e-56 228.0
20 TraesCS3A01G457100 chr6D 80.866 277 49 3 2286 2562 9373033 9373305 5.580000e-52 215.0
21 TraesCS3A01G457100 chr6D 80.597 268 45 5 2285 2549 468119005 468119268 1.560000e-47 200.0
22 TraesCS3A01G457100 chr1D 81.200 250 44 3 2295 2542 489752381 489752133 5.620000e-47 198.0
23 TraesCS3A01G457100 chr1D 100.000 29 0 0 174 202 440410489 440410517 1.000000e-03 54.7
24 TraesCS3A01G457100 chr7B 81.513 238 40 4 1141 1376 142283968 142283733 2.610000e-45 193.0
25 TraesCS3A01G457100 chr7B 81.328 241 35 9 1141 1376 143055669 143055434 1.220000e-43 187.0
26 TraesCS3A01G457100 chr7B 78.571 280 53 7 2285 2562 246619584 246619858 7.320000e-41 178.0
27 TraesCS3A01G457100 chr7B 96.875 32 1 0 169 200 481844339 481844308 1.000000e-03 54.7
28 TraesCS3A01G457100 chr5A 98.182 55 1 0 257 311 551191963 551191909 2.110000e-16 97.1
29 TraesCS3A01G457100 chr5A 94.915 59 3 0 257 315 77362720 77362662 2.730000e-15 93.5
30 TraesCS3A01G457100 chr6A 98.148 54 1 0 257 310 112998470 112998523 7.580000e-16 95.3
31 TraesCS3A01G457100 chr6A 88.000 75 4 3 257 330 615797930 615797860 1.640000e-12 84.2
32 TraesCS3A01G457100 chr4A 89.474 76 4 4 257 331 627977934 627977862 2.730000e-15 93.5
33 TraesCS3A01G457100 chr1A 96.429 56 2 0 257 312 241680298 241680243 2.730000e-15 93.5
34 TraesCS3A01G457100 chr3B 89.041 73 4 3 257 328 327862504 327862435 1.270000e-13 87.9
35 TraesCS3A01G457100 chr2B 97.059 34 1 0 167 200 45612648 45612615 9.940000e-05 58.4
36 TraesCS3A01G457100 chr5B 96.875 32 1 0 166 197 375738048 375738017 1.000000e-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 TraesCS3A01G457100 chr3A 694532423 694534995 2572 True 4752.000000 4752 100.000 1 2573 1 chr3A.!!$R1 2572
1 TraesCS3A01G457100 chr3D 558291034 558293236 2202 True 3343.000000 3343 93.872 317 2562 1 chr3D.!!$R2 2245
2 TraesCS3A01G457100 chrUn 40740566 40742523 1957 True 1341.500000 2265 91.171 725 2562 2 chrUn.!!$R3 1837
3 TraesCS3A01G457100 chrUn 303400120 303402077 1957 True 1341.500000 2265 91.171 725 2562 2 chrUn.!!$R4 1837
4 TraesCS3A01G457100 chrUn 40744048 40747339 3291 False 1119.333333 2265 92.436 308 2562 3 chrUn.!!$F1 2254

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
32 33 0.601841 TTCCTTCCCAGCGAACGTTC 60.602 55.0 18.47 18.47 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 2549 0.106369 TAGCTAGCTCTTGCGGGGTA 60.106 55.0 23.26 0.0 45.42 3.69 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 1.878953 TGTTCGCTGGAAGTTCCTTC 58.121 50.000 22.41 12.63 39.52 3.46
27 28 3.625745 GAAGTTCCTTCCCAGCGAA 57.374 52.632 0.00 0.00 34.71 4.70
28 29 1.157585 GAAGTTCCTTCCCAGCGAAC 58.842 55.000 0.00 0.00 34.71 3.95
29 30 0.602905 AAGTTCCTTCCCAGCGAACG 60.603 55.000 0.00 0.00 40.62 3.95
30 31 1.301479 GTTCCTTCCCAGCGAACGT 60.301 57.895 0.00 0.00 0.00 3.99
31 32 0.883370 GTTCCTTCCCAGCGAACGTT 60.883 55.000 0.00 0.00 0.00 3.99
32 33 0.601841 TTCCTTCCCAGCGAACGTTC 60.602 55.000 18.47 18.47 0.00 3.95
64 65 7.321745 AGCAGTACCTAAAGAATAACAATGC 57.678 36.000 0.00 0.00 0.00 3.56
65 66 7.112779 AGCAGTACCTAAAGAATAACAATGCT 58.887 34.615 0.00 0.00 33.25 3.79
66 67 7.611855 AGCAGTACCTAAAGAATAACAATGCTT 59.388 33.333 0.00 0.00 34.33 3.91
67 68 7.910683 GCAGTACCTAAAGAATAACAATGCTTC 59.089 37.037 0.00 0.00 0.00 3.86
68 69 8.946085 CAGTACCTAAAGAATAACAATGCTTCA 58.054 33.333 0.00 0.00 0.00 3.02
69 70 9.167311 AGTACCTAAAGAATAACAATGCTTCAG 57.833 33.333 0.00 0.00 0.00 3.02
70 71 8.947115 GTACCTAAAGAATAACAATGCTTCAGT 58.053 33.333 0.00 0.00 0.00 3.41
71 72 7.820648 ACCTAAAGAATAACAATGCTTCAGTG 58.179 34.615 0.00 0.00 35.46 3.66
72 73 7.665559 ACCTAAAGAATAACAATGCTTCAGTGA 59.334 33.333 1.12 0.00 33.46 3.41
73 74 8.180267 CCTAAAGAATAACAATGCTTCAGTGAG 58.820 37.037 1.12 0.00 33.46 3.51
74 75 5.557891 AGAATAACAATGCTTCAGTGAGC 57.442 39.130 1.12 7.40 43.00 4.26
75 76 4.397417 AGAATAACAATGCTTCAGTGAGCC 59.603 41.667 10.72 0.00 42.01 4.70
76 77 1.985473 AACAATGCTTCAGTGAGCCA 58.015 45.000 10.72 5.05 42.01 4.75
77 78 1.985473 ACAATGCTTCAGTGAGCCAA 58.015 45.000 10.72 0.00 42.01 4.52
78 79 2.522185 ACAATGCTTCAGTGAGCCAAT 58.478 42.857 10.72 0.00 42.01 3.16
79 80 2.895404 ACAATGCTTCAGTGAGCCAATT 59.105 40.909 10.72 4.21 42.01 2.32
80 81 4.081406 ACAATGCTTCAGTGAGCCAATTA 58.919 39.130 10.72 0.00 42.01 1.40
81 82 4.523943 ACAATGCTTCAGTGAGCCAATTAA 59.476 37.500 10.72 0.00 42.01 1.40
82 83 4.978083 ATGCTTCAGTGAGCCAATTAAG 57.022 40.909 10.72 0.00 42.01 1.85
83 84 3.754965 TGCTTCAGTGAGCCAATTAAGT 58.245 40.909 10.72 0.00 42.01 2.24
84 85 3.503363 TGCTTCAGTGAGCCAATTAAGTG 59.497 43.478 10.72 0.00 42.01 3.16
85 86 3.671702 GCTTCAGTGAGCCAATTAAGTGC 60.672 47.826 0.00 0.00 36.66 4.40
86 87 3.423539 TCAGTGAGCCAATTAAGTGCT 57.576 42.857 0.00 0.00 38.24 4.40
87 88 4.551702 TCAGTGAGCCAATTAAGTGCTA 57.448 40.909 0.00 0.00 34.99 3.49
88 89 4.253685 TCAGTGAGCCAATTAAGTGCTAC 58.746 43.478 0.00 0.00 34.99 3.58
89 90 3.375299 CAGTGAGCCAATTAAGTGCTACC 59.625 47.826 0.00 0.00 34.99 3.18
90 91 3.009033 AGTGAGCCAATTAAGTGCTACCA 59.991 43.478 0.00 0.00 34.99 3.25
91 92 3.756434 GTGAGCCAATTAAGTGCTACCAA 59.244 43.478 0.00 0.00 34.99 3.67
92 93 4.217550 GTGAGCCAATTAAGTGCTACCAAA 59.782 41.667 0.00 0.00 34.99 3.28
93 94 5.016173 TGAGCCAATTAAGTGCTACCAAAT 58.984 37.500 0.00 0.00 34.99 2.32
94 95 5.105797 TGAGCCAATTAAGTGCTACCAAATG 60.106 40.000 0.00 0.00 34.99 2.32
95 96 3.865164 GCCAATTAAGTGCTACCAAATGC 59.135 43.478 0.00 0.00 0.00 3.56
96 97 4.432712 CCAATTAAGTGCTACCAAATGCC 58.567 43.478 0.00 0.00 0.00 4.40
97 98 4.081752 CCAATTAAGTGCTACCAAATGCCA 60.082 41.667 0.00 0.00 0.00 4.92
98 99 5.395546 CCAATTAAGTGCTACCAAATGCCAT 60.396 40.000 0.00 0.00 0.00 4.40
99 100 5.937975 ATTAAGTGCTACCAAATGCCATT 57.062 34.783 0.00 0.00 0.00 3.16
100 101 5.736951 TTAAGTGCTACCAAATGCCATTT 57.263 34.783 0.00 0.00 0.00 2.32
101 102 4.622260 AAGTGCTACCAAATGCCATTTT 57.378 36.364 0.00 0.00 0.00 1.82
102 103 4.622260 AGTGCTACCAAATGCCATTTTT 57.378 36.364 0.00 0.00 0.00 1.94
103 104 5.736951 AGTGCTACCAAATGCCATTTTTA 57.263 34.783 0.00 0.00 0.00 1.52
104 105 6.107901 AGTGCTACCAAATGCCATTTTTAA 57.892 33.333 0.00 0.00 0.00 1.52
105 106 6.165577 AGTGCTACCAAATGCCATTTTTAAG 58.834 36.000 0.00 0.00 0.00 1.85
106 107 4.934602 TGCTACCAAATGCCATTTTTAAGC 59.065 37.500 15.41 15.41 32.40 3.09
107 108 4.332543 GCTACCAAATGCCATTTTTAAGCC 59.667 41.667 12.88 1.41 0.00 4.35
108 109 3.684908 ACCAAATGCCATTTTTAAGCCC 58.315 40.909 0.00 0.00 0.00 5.19
109 110 3.330405 ACCAAATGCCATTTTTAAGCCCT 59.670 39.130 0.00 0.00 0.00 5.19
110 111 3.690628 CCAAATGCCATTTTTAAGCCCTG 59.309 43.478 0.00 0.00 0.00 4.45
111 112 3.632643 AATGCCATTTTTAAGCCCTGG 57.367 42.857 0.00 0.00 0.00 4.45
112 113 2.317371 TGCCATTTTTAAGCCCTGGA 57.683 45.000 0.00 0.00 0.00 3.86
113 114 1.899142 TGCCATTTTTAAGCCCTGGAC 59.101 47.619 0.00 0.00 0.00 4.02
114 115 1.207089 GCCATTTTTAAGCCCTGGACC 59.793 52.381 0.00 0.00 0.00 4.46
115 116 2.534990 CCATTTTTAAGCCCTGGACCA 58.465 47.619 0.00 0.00 0.00 4.02
116 117 3.106827 CCATTTTTAAGCCCTGGACCAT 58.893 45.455 0.00 0.00 0.00 3.55
117 118 3.519107 CCATTTTTAAGCCCTGGACCATT 59.481 43.478 0.00 0.00 0.00 3.16
118 119 4.383010 CCATTTTTAAGCCCTGGACCATTC 60.383 45.833 0.00 0.00 0.00 2.67
119 120 3.534357 TTTTAAGCCCTGGACCATTCA 57.466 42.857 0.00 0.00 0.00 2.57
120 121 2.806945 TTAAGCCCTGGACCATTCAG 57.193 50.000 0.00 0.00 0.00 3.02
121 122 1.668826 TAAGCCCTGGACCATTCAGT 58.331 50.000 0.00 0.00 0.00 3.41
122 123 1.668826 AAGCCCTGGACCATTCAGTA 58.331 50.000 0.00 0.00 0.00 2.74
123 124 1.668826 AGCCCTGGACCATTCAGTAA 58.331 50.000 0.00 0.00 0.00 2.24
124 125 1.992557 AGCCCTGGACCATTCAGTAAA 59.007 47.619 0.00 0.00 0.00 2.01
125 126 2.025887 AGCCCTGGACCATTCAGTAAAG 60.026 50.000 0.00 0.00 0.00 1.85
126 127 2.369394 CCCTGGACCATTCAGTAAAGC 58.631 52.381 0.00 0.00 0.00 3.51
127 128 2.290896 CCCTGGACCATTCAGTAAAGCA 60.291 50.000 0.00 0.00 0.00 3.91
128 129 3.012518 CCTGGACCATTCAGTAAAGCAG 58.987 50.000 0.00 0.00 0.00 4.24
129 130 3.560025 CCTGGACCATTCAGTAAAGCAGT 60.560 47.826 0.00 0.00 0.00 4.40
130 131 4.323485 CCTGGACCATTCAGTAAAGCAGTA 60.323 45.833 0.00 0.00 0.00 2.74
131 132 5.235850 TGGACCATTCAGTAAAGCAGTAA 57.764 39.130 0.00 0.00 0.00 2.24
132 133 5.245531 TGGACCATTCAGTAAAGCAGTAAG 58.754 41.667 0.00 0.00 0.00 2.34
133 134 5.221843 TGGACCATTCAGTAAAGCAGTAAGT 60.222 40.000 0.00 0.00 0.00 2.24
134 135 6.014070 TGGACCATTCAGTAAAGCAGTAAGTA 60.014 38.462 0.00 0.00 0.00 2.24
135 136 6.313164 GGACCATTCAGTAAAGCAGTAAGTAC 59.687 42.308 0.00 0.00 0.00 2.73
136 137 7.005709 ACCATTCAGTAAAGCAGTAAGTACT 57.994 36.000 0.00 0.00 36.90 2.73
137 138 8.130671 ACCATTCAGTAAAGCAGTAAGTACTA 57.869 34.615 0.00 0.00 34.13 1.82
138 139 8.033626 ACCATTCAGTAAAGCAGTAAGTACTAC 58.966 37.037 0.00 0.00 34.13 2.73
139 140 8.033038 CCATTCAGTAAAGCAGTAAGTACTACA 58.967 37.037 0.00 0.00 34.13 2.74
140 141 9.587772 CATTCAGTAAAGCAGTAAGTACTACAT 57.412 33.333 0.00 0.00 34.13 2.29
142 143 9.991906 TTCAGTAAAGCAGTAAGTACTACATTT 57.008 29.630 0.00 1.96 34.13 2.32
143 144 9.419297 TCAGTAAAGCAGTAAGTACTACATTTG 57.581 33.333 0.00 0.00 34.13 2.32
144 145 9.204570 CAGTAAAGCAGTAAGTACTACATTTGT 57.795 33.333 0.00 0.00 34.13 2.83
149 150 9.550406 AAGCAGTAAGTACTACATTTGTAAACA 57.450 29.630 0.00 0.00 34.13 2.83
150 151 9.550406 AGCAGTAAGTACTACATTTGTAAACAA 57.450 29.630 0.00 0.00 34.13 2.83
197 198 9.998106 TGTCTTATATTTATTTACAGAGGGAGC 57.002 33.333 0.00 0.00 0.00 4.70
198 199 9.998106 GTCTTATATTTATTTACAGAGGGAGCA 57.002 33.333 0.00 0.00 0.00 4.26
202 203 8.854614 ATATTTATTTACAGAGGGAGCATGTC 57.145 34.615 0.00 0.00 0.00 3.06
203 204 5.692115 TTATTTACAGAGGGAGCATGTCA 57.308 39.130 0.00 0.00 0.00 3.58
204 205 3.334583 TTTACAGAGGGAGCATGTCAC 57.665 47.619 0.00 0.00 0.00 3.67
205 206 1.937191 TACAGAGGGAGCATGTCACA 58.063 50.000 0.00 0.00 0.00 3.58
206 207 1.059098 ACAGAGGGAGCATGTCACAA 58.941 50.000 0.00 0.00 0.00 3.33
207 208 1.421268 ACAGAGGGAGCATGTCACAAA 59.579 47.619 0.00 0.00 0.00 2.83
208 209 2.158623 ACAGAGGGAGCATGTCACAAAA 60.159 45.455 0.00 0.00 0.00 2.44
209 210 3.087031 CAGAGGGAGCATGTCACAAAAT 58.913 45.455 0.00 0.00 0.00 1.82
210 211 4.263462 ACAGAGGGAGCATGTCACAAAATA 60.263 41.667 0.00 0.00 0.00 1.40
211 212 4.334759 CAGAGGGAGCATGTCACAAAATAG 59.665 45.833 0.00 0.00 0.00 1.73
212 213 4.225942 AGAGGGAGCATGTCACAAAATAGA 59.774 41.667 0.00 0.00 0.00 1.98
213 214 4.922206 AGGGAGCATGTCACAAAATAGAA 58.078 39.130 0.00 0.00 0.00 2.10
214 215 4.946157 AGGGAGCATGTCACAAAATAGAAG 59.054 41.667 0.00 0.00 0.00 2.85
215 216 4.943705 GGGAGCATGTCACAAAATAGAAGA 59.056 41.667 0.00 0.00 0.00 2.87
216 217 5.065731 GGGAGCATGTCACAAAATAGAAGAG 59.934 44.000 0.00 0.00 0.00 2.85
217 218 5.877012 GGAGCATGTCACAAAATAGAAGAGA 59.123 40.000 0.00 0.00 0.00 3.10
218 219 6.372659 GGAGCATGTCACAAAATAGAAGAGAA 59.627 38.462 0.00 0.00 0.00 2.87
219 220 7.094634 GGAGCATGTCACAAAATAGAAGAGAAA 60.095 37.037 0.00 0.00 0.00 2.52
220 221 7.814642 AGCATGTCACAAAATAGAAGAGAAAG 58.185 34.615 0.00 0.00 0.00 2.62
221 222 7.025963 GCATGTCACAAAATAGAAGAGAAAGG 58.974 38.462 0.00 0.00 0.00 3.11
222 223 7.533426 CATGTCACAAAATAGAAGAGAAAGGG 58.467 38.462 0.00 0.00 0.00 3.95
223 224 6.003950 TGTCACAAAATAGAAGAGAAAGGGG 58.996 40.000 0.00 0.00 0.00 4.79
224 225 5.416013 GTCACAAAATAGAAGAGAAAGGGGG 59.584 44.000 0.00 0.00 0.00 5.40
241 242 3.594603 GGGGGAAAGCTAAAGAAAAGC 57.405 47.619 0.00 0.00 40.40 3.51
242 243 2.233922 GGGGGAAAGCTAAAGAAAAGCC 59.766 50.000 0.00 0.00 41.02 4.35
243 244 2.897326 GGGGAAAGCTAAAGAAAAGCCA 59.103 45.455 0.00 0.00 41.02 4.75
244 245 3.515502 GGGGAAAGCTAAAGAAAAGCCAT 59.484 43.478 0.00 0.00 41.02 4.40
245 246 4.020218 GGGGAAAGCTAAAGAAAAGCCATT 60.020 41.667 0.00 0.00 41.02 3.16
246 247 5.186992 GGGGAAAGCTAAAGAAAAGCCATTA 59.813 40.000 0.00 0.00 41.02 1.90
247 248 6.333416 GGGAAAGCTAAAGAAAAGCCATTAG 58.667 40.000 0.00 0.00 41.02 1.73
248 249 6.333416 GGAAAGCTAAAGAAAAGCCATTAGG 58.667 40.000 0.00 0.00 41.02 2.69
249 250 6.071334 GGAAAGCTAAAGAAAAGCCATTAGGT 60.071 38.462 0.00 0.00 41.02 3.08
250 251 5.904362 AGCTAAAGAAAAGCCATTAGGTG 57.096 39.130 0.00 0.00 41.02 4.00
251 252 4.158579 AGCTAAAGAAAAGCCATTAGGTGC 59.841 41.667 0.00 0.00 41.02 5.01
252 253 4.158579 GCTAAAGAAAAGCCATTAGGTGCT 59.841 41.667 0.00 0.00 40.17 4.40
253 254 5.357032 GCTAAAGAAAAGCCATTAGGTGCTA 59.643 40.000 0.00 0.00 36.66 3.49
254 255 5.904362 AAAGAAAAGCCATTAGGTGCTAG 57.096 39.130 0.00 0.00 36.66 3.42
255 256 3.891049 AGAAAAGCCATTAGGTGCTAGG 58.109 45.455 0.00 0.00 36.66 3.02
256 257 2.058593 AAAGCCATTAGGTGCTAGGC 57.941 50.000 0.00 0.00 45.54 3.93
258 259 3.494850 GCCATTAGGTGCTAGGCAA 57.505 52.632 0.00 0.00 44.59 4.52
259 260 1.762708 GCCATTAGGTGCTAGGCAAA 58.237 50.000 0.00 0.00 44.59 3.68
260 261 1.678101 GCCATTAGGTGCTAGGCAAAG 59.322 52.381 0.00 0.00 44.59 2.77
261 262 2.945890 GCCATTAGGTGCTAGGCAAAGT 60.946 50.000 0.00 0.00 44.59 2.66
262 263 3.356290 CCATTAGGTGCTAGGCAAAGTT 58.644 45.455 0.00 0.00 41.47 2.66
263 264 4.523083 CCATTAGGTGCTAGGCAAAGTTA 58.477 43.478 0.00 0.00 41.47 2.24
264 265 4.576463 CCATTAGGTGCTAGGCAAAGTTAG 59.424 45.833 0.00 0.00 41.47 2.34
265 266 2.115343 AGGTGCTAGGCAAAGTTAGC 57.885 50.000 0.00 0.00 41.47 3.09
276 277 4.477302 GCAAAGTTAGCCTCGTAAAACA 57.523 40.909 0.00 0.00 0.00 2.83
277 278 4.216731 GCAAAGTTAGCCTCGTAAAACAC 58.783 43.478 0.00 0.00 0.00 3.32
278 279 4.260866 GCAAAGTTAGCCTCGTAAAACACA 60.261 41.667 0.00 0.00 0.00 3.72
279 280 5.562113 GCAAAGTTAGCCTCGTAAAACACAT 60.562 40.000 0.00 0.00 0.00 3.21
280 281 6.435428 CAAAGTTAGCCTCGTAAAACACATT 58.565 36.000 0.00 0.00 0.00 2.71
281 282 7.577979 CAAAGTTAGCCTCGTAAAACACATTA 58.422 34.615 0.00 0.00 0.00 1.90
282 283 6.963049 AGTTAGCCTCGTAAAACACATTAG 57.037 37.500 0.00 0.00 0.00 1.73
283 284 6.694447 AGTTAGCCTCGTAAAACACATTAGA 58.306 36.000 0.00 0.00 0.00 2.10
284 285 6.589139 AGTTAGCCTCGTAAAACACATTAGAC 59.411 38.462 0.00 0.00 0.00 2.59
285 286 4.251268 AGCCTCGTAAAACACATTAGACC 58.749 43.478 0.00 0.00 0.00 3.85
286 287 3.373130 GCCTCGTAAAACACATTAGACCC 59.627 47.826 0.00 0.00 0.00 4.46
287 288 4.828829 CCTCGTAAAACACATTAGACCCT 58.171 43.478 0.00 0.00 0.00 4.34
288 289 5.625197 GCCTCGTAAAACACATTAGACCCTA 60.625 44.000 0.00 0.00 0.00 3.53
289 290 6.579865 CCTCGTAAAACACATTAGACCCTAT 58.420 40.000 0.00 0.00 0.00 2.57
290 291 7.685155 GCCTCGTAAAACACATTAGACCCTATA 60.685 40.741 0.00 0.00 0.00 1.31
291 292 8.365647 CCTCGTAAAACACATTAGACCCTATAT 58.634 37.037 0.00 0.00 0.00 0.86
298 299 9.615660 AAACACATTAGACCCTATATAGATGGA 57.384 33.333 11.53 0.00 0.00 3.41
299 300 9.615660 AACACATTAGACCCTATATAGATGGAA 57.384 33.333 11.53 0.00 0.00 3.53
300 301 9.261035 ACACATTAGACCCTATATAGATGGAAG 57.739 37.037 11.53 3.88 0.00 3.46
301 302 8.700051 CACATTAGACCCTATATAGATGGAAGG 58.300 40.741 11.53 5.26 0.00 3.46
302 303 8.633724 ACATTAGACCCTATATAGATGGAAGGA 58.366 37.037 11.53 0.00 0.00 3.36
303 304 9.142014 CATTAGACCCTATATAGATGGAAGGAG 57.858 40.741 11.53 0.00 0.00 3.69
304 305 6.098716 AGACCCTATATAGATGGAAGGAGG 57.901 45.833 11.53 3.20 0.00 4.30
305 306 5.042979 AGACCCTATATAGATGGAAGGAGGG 60.043 48.000 11.53 4.91 46.66 4.30
306 307 4.870361 ACCCTATATAGATGGAAGGAGGGA 59.130 45.833 11.53 0.00 44.48 4.20
307 308 5.042979 ACCCTATATAGATGGAAGGAGGGAG 60.043 48.000 11.53 0.00 44.48 4.30
308 309 5.042979 CCCTATATAGATGGAAGGAGGGAGT 60.043 48.000 11.53 0.00 44.48 3.85
309 310 6.162420 CCCTATATAGATGGAAGGAGGGAGTA 59.838 46.154 11.53 0.00 44.48 2.59
310 311 7.064229 CCTATATAGATGGAAGGAGGGAGTAC 58.936 46.154 11.53 0.00 0.00 2.73
311 312 2.480642 AGATGGAAGGAGGGAGTACC 57.519 55.000 0.00 0.00 40.67 3.34
312 313 1.651770 AGATGGAAGGAGGGAGTACCA 59.348 52.381 0.00 0.00 43.89 3.25
403 404 1.002011 GCAGTTCCAACTCCTCCCC 60.002 63.158 0.00 0.00 37.08 4.81
960 1879 1.861982 AAAAGACGGGAGCCTAGCTA 58.138 50.000 0.00 0.00 39.88 3.32
961 1880 1.404843 AAAGACGGGAGCCTAGCTAG 58.595 55.000 14.20 14.20 39.88 3.42
962 1881 1.110518 AAGACGGGAGCCTAGCTAGC 61.111 60.000 15.74 6.62 39.88 3.42
963 1882 1.529713 GACGGGAGCCTAGCTAGCT 60.530 63.158 23.12 23.12 45.23 3.32
1407 2326 0.535797 GGTACCTCCTCAAGTTCCGG 59.464 60.000 4.06 0.00 0.00 5.14
1630 2549 3.529533 CGTCCATCTTCTTGCTTGATCT 58.470 45.455 0.00 0.00 0.00 2.75
1632 2551 4.505922 CGTCCATCTTCTTGCTTGATCTAC 59.494 45.833 0.00 0.00 0.00 2.59
1636 2555 2.168521 TCTTCTTGCTTGATCTACCCCG 59.831 50.000 0.00 0.00 0.00 5.73
1641 2560 0.178068 GCTTGATCTACCCCGCAAGA 59.822 55.000 0.00 0.00 39.97 3.02
1646 2565 1.271102 GATCTACCCCGCAAGAGCTAG 59.729 57.143 0.00 0.00 43.02 3.42
1708 2627 1.187087 GGTGACCAGCTAGCTAGTGT 58.813 55.000 20.91 15.99 0.00 3.55
1737 2657 1.682323 GGAGTAGCTGCTAGTGGGTAC 59.318 57.143 21.05 5.08 36.88 3.34
1738 2658 1.334243 GAGTAGCTGCTAGTGGGTACG 59.666 57.143 21.05 0.00 40.15 3.67
1739 2659 1.101331 GTAGCTGCTAGTGGGTACGT 58.899 55.000 10.13 0.00 0.00 3.57
1740 2660 2.092753 AGTAGCTGCTAGTGGGTACGTA 60.093 50.000 15.89 0.00 40.15 3.57
2192 3112 3.476552 TGAGTACTGACTTTTTGGGCAG 58.523 45.455 0.00 0.00 35.45 4.85
2248 3324 4.722203 TTTTTGCACGCCAATAAATGTG 57.278 36.364 0.00 0.00 32.49 3.21
2281 3358 3.806949 TTTTAGGGGAGTTCTGCACAT 57.193 42.857 0.00 0.00 0.00 3.21
2283 3360 2.787473 TAGGGGAGTTCTGCACATTG 57.213 50.000 0.00 0.00 0.00 2.82
2321 3400 9.577110 ACAATACAATCAAAATTGCTCACATAG 57.423 29.630 0.00 0.00 45.16 2.23
2348 3427 1.175654 TACACTCGCCCGTATGAACA 58.824 50.000 2.06 0.00 0.00 3.18
2362 3441 0.667453 TGAACACATGCACGCACATT 59.333 45.000 0.00 0.00 0.00 2.71
2366 3445 2.358957 ACACATGCACGCACATTCTAT 58.641 42.857 0.00 0.00 0.00 1.98
2374 3453 3.803715 GCACGCACATTCTATCCCTATGT 60.804 47.826 0.00 0.00 32.98 2.29
2379 3458 3.742882 CACATTCTATCCCTATGTGCACG 59.257 47.826 13.13 0.00 41.64 5.34
2391 3470 1.324383 TGTGCACGTCCAAGAGACTA 58.676 50.000 13.13 0.00 43.91 2.59
2394 3473 1.961394 TGCACGTCCAAGAGACTAAGT 59.039 47.619 0.00 0.00 43.91 2.24
2395 3474 2.364324 TGCACGTCCAAGAGACTAAGTT 59.636 45.455 0.00 0.00 43.91 2.66
2396 3475 3.570975 TGCACGTCCAAGAGACTAAGTTA 59.429 43.478 0.00 0.00 43.91 2.24
2407 3486 6.007936 AGAGACTAAGTTAGCATAGCATCG 57.992 41.667 9.92 0.00 0.00 3.84
2437 3516 0.586802 GAAGTCACCACAAACGCCTC 59.413 55.000 0.00 0.00 0.00 4.70
2438 3517 0.107410 AAGTCACCACAAACGCCTCA 60.107 50.000 0.00 0.00 0.00 3.86
2445 3524 1.403647 CCACAAACGCCTCATAGTCGA 60.404 52.381 0.00 0.00 0.00 4.20
2449 3528 2.353607 CGCCTCATAGTCGACGGC 60.354 66.667 18.23 18.23 37.40 5.68
2498 3577 6.249035 TCGCCGAAAAGTCTGAAATAAATT 57.751 33.333 0.00 0.00 0.00 1.82
2516 3595 9.949174 AAATAAATTCAGAAAAATGCAAACACC 57.051 25.926 0.00 0.00 0.00 4.16
2519 3598 5.793026 TTCAGAAAAATGCAAACACCAAC 57.207 34.783 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.004918 CGTTCGCTGGGAAGGAACT 60.005 57.895 18.67 0.00 41.85 3.01
12 13 0.883370 AACGTTCGCTGGGAAGGAAC 60.883 55.000 26.80 8.74 41.85 3.62
13 14 0.601841 GAACGTTCGCTGGGAAGGAA 60.602 55.000 26.80 0.00 41.85 3.36
14 15 1.005394 GAACGTTCGCTGGGAAGGA 60.005 57.895 26.80 0.00 41.85 3.36
15 16 2.380410 CGAACGTTCGCTGGGAAGG 61.380 63.158 34.54 20.88 44.26 3.46
16 17 3.156334 CGAACGTTCGCTGGGAAG 58.844 61.111 34.54 9.32 44.26 3.46
38 39 8.889717 GCATTGTTATTCTTTAGGTACTGCTAA 58.110 33.333 0.00 0.00 41.52 3.09
39 40 8.265055 AGCATTGTTATTCTTTAGGTACTGCTA 58.735 33.333 0.00 0.00 41.52 3.49
40 41 7.112779 AGCATTGTTATTCTTTAGGTACTGCT 58.887 34.615 0.00 0.00 41.52 4.24
41 42 7.321745 AGCATTGTTATTCTTTAGGTACTGC 57.678 36.000 0.00 0.00 41.52 4.40
42 43 8.946085 TGAAGCATTGTTATTCTTTAGGTACTG 58.054 33.333 0.00 0.00 41.52 2.74
43 44 9.167311 CTGAAGCATTGTTATTCTTTAGGTACT 57.833 33.333 0.00 0.00 46.37 2.73
44 45 8.947115 ACTGAAGCATTGTTATTCTTTAGGTAC 58.053 33.333 0.00 0.00 29.14 3.34
45 46 8.946085 CACTGAAGCATTGTTATTCTTTAGGTA 58.054 33.333 0.00 0.00 29.14 3.08
46 47 7.665559 TCACTGAAGCATTGTTATTCTTTAGGT 59.334 33.333 0.00 0.00 29.14 3.08
47 48 8.044060 TCACTGAAGCATTGTTATTCTTTAGG 57.956 34.615 0.00 0.00 29.14 2.69
48 49 7.695618 GCTCACTGAAGCATTGTTATTCTTTAG 59.304 37.037 0.00 0.00 42.05 1.85
49 50 7.362056 GGCTCACTGAAGCATTGTTATTCTTTA 60.362 37.037 8.56 0.00 44.35 1.85
50 51 6.385033 GCTCACTGAAGCATTGTTATTCTTT 58.615 36.000 0.00 0.00 42.05 2.52
51 52 5.105997 GGCTCACTGAAGCATTGTTATTCTT 60.106 40.000 8.56 0.00 44.35 2.52
52 53 4.397417 GGCTCACTGAAGCATTGTTATTCT 59.603 41.667 8.56 0.00 44.35 2.40
53 54 4.156556 TGGCTCACTGAAGCATTGTTATTC 59.843 41.667 8.56 0.00 44.35 1.75
54 55 4.081406 TGGCTCACTGAAGCATTGTTATT 58.919 39.130 8.56 0.00 44.35 1.40
55 56 3.689347 TGGCTCACTGAAGCATTGTTAT 58.311 40.909 8.56 0.00 44.35 1.89
56 57 3.138884 TGGCTCACTGAAGCATTGTTA 57.861 42.857 8.56 0.00 44.35 2.41
57 58 1.985473 TGGCTCACTGAAGCATTGTT 58.015 45.000 8.56 0.00 44.35 2.83
58 59 1.985473 TTGGCTCACTGAAGCATTGT 58.015 45.000 8.56 0.00 44.35 2.71
59 60 3.587797 AATTGGCTCACTGAAGCATTG 57.412 42.857 8.56 0.00 44.35 2.82
60 61 4.768968 ACTTAATTGGCTCACTGAAGCATT 59.231 37.500 8.56 4.35 44.35 3.56
61 62 4.157289 CACTTAATTGGCTCACTGAAGCAT 59.843 41.667 8.56 0.00 44.35 3.79
62 63 3.503363 CACTTAATTGGCTCACTGAAGCA 59.497 43.478 8.56 0.00 44.35 3.91
63 64 3.671702 GCACTTAATTGGCTCACTGAAGC 60.672 47.826 0.00 0.00 41.73 3.86
64 65 3.755378 AGCACTTAATTGGCTCACTGAAG 59.245 43.478 0.00 0.00 30.74 3.02
65 66 3.754965 AGCACTTAATTGGCTCACTGAA 58.245 40.909 0.00 0.00 30.74 3.02
66 67 3.423539 AGCACTTAATTGGCTCACTGA 57.576 42.857 0.00 0.00 30.74 3.41
67 68 3.375299 GGTAGCACTTAATTGGCTCACTG 59.625 47.826 0.00 0.00 39.01 3.66
68 69 3.009033 TGGTAGCACTTAATTGGCTCACT 59.991 43.478 0.00 0.00 39.01 3.41
69 70 3.343617 TGGTAGCACTTAATTGGCTCAC 58.656 45.455 0.00 0.00 39.01 3.51
70 71 3.712016 TGGTAGCACTTAATTGGCTCA 57.288 42.857 0.00 0.00 39.01 4.26
71 72 5.343249 CATTTGGTAGCACTTAATTGGCTC 58.657 41.667 0.00 0.00 39.01 4.70
72 73 4.381932 GCATTTGGTAGCACTTAATTGGCT 60.382 41.667 0.00 0.00 41.51 4.75
73 74 3.865164 GCATTTGGTAGCACTTAATTGGC 59.135 43.478 0.00 0.00 0.00 4.52
74 75 4.081752 TGGCATTTGGTAGCACTTAATTGG 60.082 41.667 0.00 0.00 0.00 3.16
75 76 5.070770 TGGCATTTGGTAGCACTTAATTG 57.929 39.130 0.00 0.00 0.00 2.32
76 77 5.937975 ATGGCATTTGGTAGCACTTAATT 57.062 34.783 0.00 0.00 0.00 1.40
77 78 5.937975 AATGGCATTTGGTAGCACTTAAT 57.062 34.783 6.96 0.00 0.00 1.40
78 79 5.736951 AAATGGCATTTGGTAGCACTTAA 57.263 34.783 23.80 0.00 0.00 1.85
79 80 5.736951 AAAATGGCATTTGGTAGCACTTA 57.263 34.783 24.96 0.00 31.77 2.24
80 81 4.622260 AAAATGGCATTTGGTAGCACTT 57.378 36.364 24.96 4.30 31.77 3.16
81 82 4.622260 AAAAATGGCATTTGGTAGCACT 57.378 36.364 24.96 5.02 31.77 4.40
82 83 5.163864 GCTTAAAAATGGCATTTGGTAGCAC 60.164 40.000 29.12 15.39 33.46 4.40
83 84 4.934602 GCTTAAAAATGGCATTTGGTAGCA 59.065 37.500 29.12 13.65 33.46 3.49
84 85 4.332543 GGCTTAAAAATGGCATTTGGTAGC 59.667 41.667 27.68 27.68 32.95 3.58
85 86 4.875536 GGGCTTAAAAATGGCATTTGGTAG 59.124 41.667 24.96 20.35 31.77 3.18
86 87 4.534103 AGGGCTTAAAAATGGCATTTGGTA 59.466 37.500 24.96 16.98 31.77 3.25
87 88 3.330405 AGGGCTTAAAAATGGCATTTGGT 59.670 39.130 24.96 17.91 31.77 3.67
88 89 3.690628 CAGGGCTTAAAAATGGCATTTGG 59.309 43.478 24.96 15.84 31.77 3.28
89 90 3.690628 CCAGGGCTTAAAAATGGCATTTG 59.309 43.478 24.96 13.85 31.77 2.32
90 91 3.586618 TCCAGGGCTTAAAAATGGCATTT 59.413 39.130 19.39 19.39 0.00 2.32
91 92 3.055167 GTCCAGGGCTTAAAAATGGCATT 60.055 43.478 6.96 6.96 0.00 3.56
92 93 2.501316 GTCCAGGGCTTAAAAATGGCAT 59.499 45.455 0.00 0.00 0.00 4.40
93 94 1.899142 GTCCAGGGCTTAAAAATGGCA 59.101 47.619 0.00 0.00 0.00 4.92
94 95 1.207089 GGTCCAGGGCTTAAAAATGGC 59.793 52.381 0.00 0.00 0.00 4.40
95 96 2.534990 TGGTCCAGGGCTTAAAAATGG 58.465 47.619 0.00 0.00 0.00 3.16
96 97 4.222588 TGAATGGTCCAGGGCTTAAAAATG 59.777 41.667 0.00 0.00 0.00 2.32
97 98 4.424842 TGAATGGTCCAGGGCTTAAAAAT 58.575 39.130 0.00 0.00 0.00 1.82
98 99 3.831911 CTGAATGGTCCAGGGCTTAAAAA 59.168 43.478 0.00 0.00 0.00 1.94
99 100 3.181423 ACTGAATGGTCCAGGGCTTAAAA 60.181 43.478 0.00 0.00 36.03 1.52
100 101 2.378547 ACTGAATGGTCCAGGGCTTAAA 59.621 45.455 0.00 0.00 36.03 1.52
101 102 1.992557 ACTGAATGGTCCAGGGCTTAA 59.007 47.619 0.00 0.00 36.03 1.85
102 103 1.668826 ACTGAATGGTCCAGGGCTTA 58.331 50.000 0.00 0.00 36.03 3.09
103 104 1.668826 TACTGAATGGTCCAGGGCTT 58.331 50.000 0.00 0.00 36.03 4.35
104 105 1.668826 TTACTGAATGGTCCAGGGCT 58.331 50.000 0.00 0.00 36.03 5.19
105 106 2.369394 CTTTACTGAATGGTCCAGGGC 58.631 52.381 0.00 0.00 36.03 5.19
106 107 2.290896 TGCTTTACTGAATGGTCCAGGG 60.291 50.000 0.00 0.00 36.03 4.45
107 108 3.012518 CTGCTTTACTGAATGGTCCAGG 58.987 50.000 0.00 0.00 36.03 4.45
108 109 3.679389 ACTGCTTTACTGAATGGTCCAG 58.321 45.455 0.00 0.00 37.64 3.86
109 110 3.788227 ACTGCTTTACTGAATGGTCCA 57.212 42.857 0.00 0.00 0.00 4.02
110 111 5.246307 ACTTACTGCTTTACTGAATGGTCC 58.754 41.667 0.00 0.00 0.00 4.46
111 112 7.097834 AGTACTTACTGCTTTACTGAATGGTC 58.902 38.462 0.00 0.00 34.72 4.02
112 113 7.005709 AGTACTTACTGCTTTACTGAATGGT 57.994 36.000 0.00 0.00 34.72 3.55
113 114 8.033038 TGTAGTACTTACTGCTTTACTGAATGG 58.967 37.037 0.00 0.00 39.30 3.16
114 115 8.981724 TGTAGTACTTACTGCTTTACTGAATG 57.018 34.615 0.00 0.00 39.30 2.67
116 117 9.991906 AAATGTAGTACTTACTGCTTTACTGAA 57.008 29.630 0.00 0.00 39.30 3.02
117 118 9.419297 CAAATGTAGTACTTACTGCTTTACTGA 57.581 33.333 0.00 0.00 39.30 3.41
118 119 9.204570 ACAAATGTAGTACTTACTGCTTTACTG 57.795 33.333 0.00 5.24 39.30 2.74
123 124 9.550406 TGTTTACAAATGTAGTACTTACTGCTT 57.450 29.630 0.00 0.00 39.30 3.91
124 125 9.550406 TTGTTTACAAATGTAGTACTTACTGCT 57.450 29.630 0.00 0.00 35.21 4.24
171 172 9.998106 GCTCCCTCTGTAAATAAATATAAGACA 57.002 33.333 0.00 0.00 0.00 3.41
172 173 9.998106 TGCTCCCTCTGTAAATAAATATAAGAC 57.002 33.333 0.00 0.00 0.00 3.01
176 177 9.944376 GACATGCTCCCTCTGTAAATAAATATA 57.056 33.333 0.00 0.00 0.00 0.86
177 178 8.439971 TGACATGCTCCCTCTGTAAATAAATAT 58.560 33.333 0.00 0.00 0.00 1.28
178 179 7.715249 GTGACATGCTCCCTCTGTAAATAAATA 59.285 37.037 0.00 0.00 0.00 1.40
179 180 6.543831 GTGACATGCTCCCTCTGTAAATAAAT 59.456 38.462 0.00 0.00 0.00 1.40
180 181 5.880332 GTGACATGCTCCCTCTGTAAATAAA 59.120 40.000 0.00 0.00 0.00 1.40
181 182 5.045942 TGTGACATGCTCCCTCTGTAAATAA 60.046 40.000 0.00 0.00 0.00 1.40
182 183 4.469586 TGTGACATGCTCCCTCTGTAAATA 59.530 41.667 0.00 0.00 0.00 1.40
183 184 3.264193 TGTGACATGCTCCCTCTGTAAAT 59.736 43.478 0.00 0.00 0.00 1.40
184 185 2.637382 TGTGACATGCTCCCTCTGTAAA 59.363 45.455 0.00 0.00 0.00 2.01
185 186 2.256306 TGTGACATGCTCCCTCTGTAA 58.744 47.619 0.00 0.00 0.00 2.41
186 187 1.937191 TGTGACATGCTCCCTCTGTA 58.063 50.000 0.00 0.00 0.00 2.74
187 188 1.059098 TTGTGACATGCTCCCTCTGT 58.941 50.000 0.00 0.00 0.00 3.41
188 189 2.189594 TTTGTGACATGCTCCCTCTG 57.810 50.000 0.00 0.00 0.00 3.35
189 190 2.957402 TTTTGTGACATGCTCCCTCT 57.043 45.000 0.00 0.00 0.00 3.69
190 191 4.517285 TCTATTTTGTGACATGCTCCCTC 58.483 43.478 0.00 0.00 0.00 4.30
191 192 4.574674 TCTATTTTGTGACATGCTCCCT 57.425 40.909 0.00 0.00 0.00 4.20
192 193 4.943705 TCTTCTATTTTGTGACATGCTCCC 59.056 41.667 0.00 0.00 0.00 4.30
193 194 5.877012 TCTCTTCTATTTTGTGACATGCTCC 59.123 40.000 0.00 0.00 0.00 4.70
194 195 6.974932 TCTCTTCTATTTTGTGACATGCTC 57.025 37.500 0.00 0.00 0.00 4.26
195 196 7.094463 CCTTTCTCTTCTATTTTGTGACATGCT 60.094 37.037 0.00 0.00 0.00 3.79
196 197 7.025963 CCTTTCTCTTCTATTTTGTGACATGC 58.974 38.462 0.00 0.00 0.00 4.06
197 198 7.362401 CCCCTTTCTCTTCTATTTTGTGACATG 60.362 40.741 0.00 0.00 0.00 3.21
198 199 6.660949 CCCCTTTCTCTTCTATTTTGTGACAT 59.339 38.462 0.00 0.00 0.00 3.06
199 200 6.003950 CCCCTTTCTCTTCTATTTTGTGACA 58.996 40.000 0.00 0.00 0.00 3.58
200 201 5.416013 CCCCCTTTCTCTTCTATTTTGTGAC 59.584 44.000 0.00 0.00 0.00 3.67
201 202 5.570320 CCCCCTTTCTCTTCTATTTTGTGA 58.430 41.667 0.00 0.00 0.00 3.58
202 203 5.904362 CCCCCTTTCTCTTCTATTTTGTG 57.096 43.478 0.00 0.00 0.00 3.33
221 222 2.233922 GGCTTTTCTTTAGCTTTCCCCC 59.766 50.000 0.00 0.00 38.67 5.40
222 223 2.897326 TGGCTTTTCTTTAGCTTTCCCC 59.103 45.455 0.00 0.00 38.67 4.81
223 224 4.808414 ATGGCTTTTCTTTAGCTTTCCC 57.192 40.909 0.00 0.00 38.67 3.97
224 225 6.071334 ACCTAATGGCTTTTCTTTAGCTTTCC 60.071 38.462 0.00 0.00 38.67 3.13
225 226 6.808704 CACCTAATGGCTTTTCTTTAGCTTTC 59.191 38.462 0.00 0.00 38.67 2.62
226 227 6.691508 CACCTAATGGCTTTTCTTTAGCTTT 58.308 36.000 0.00 0.00 38.67 3.51
227 228 5.336770 GCACCTAATGGCTTTTCTTTAGCTT 60.337 40.000 0.00 0.00 38.67 3.74
228 229 4.158579 GCACCTAATGGCTTTTCTTTAGCT 59.841 41.667 0.00 0.00 38.67 3.32
229 230 4.158579 AGCACCTAATGGCTTTTCTTTAGC 59.841 41.667 0.00 0.00 36.92 3.09
230 231 5.904362 AGCACCTAATGGCTTTTCTTTAG 57.096 39.130 0.00 0.00 36.92 1.85
231 232 5.885912 CCTAGCACCTAATGGCTTTTCTTTA 59.114 40.000 0.00 0.00 41.41 1.85
232 233 4.706962 CCTAGCACCTAATGGCTTTTCTTT 59.293 41.667 0.00 0.00 41.41 2.52
233 234 4.273318 CCTAGCACCTAATGGCTTTTCTT 58.727 43.478 0.00 0.00 41.41 2.52
234 235 3.891049 CCTAGCACCTAATGGCTTTTCT 58.109 45.455 0.00 0.00 41.41 2.52
235 236 2.359214 GCCTAGCACCTAATGGCTTTTC 59.641 50.000 0.00 0.00 41.41 2.29
236 237 2.291540 TGCCTAGCACCTAATGGCTTTT 60.292 45.455 0.00 0.00 43.57 2.27
237 238 1.284785 TGCCTAGCACCTAATGGCTTT 59.715 47.619 0.00 0.00 43.57 3.51
238 239 0.918983 TGCCTAGCACCTAATGGCTT 59.081 50.000 0.00 0.00 43.57 4.35
239 240 0.918983 TTGCCTAGCACCTAATGGCT 59.081 50.000 0.00 0.00 43.57 4.75
240 241 1.678101 CTTTGCCTAGCACCTAATGGC 59.322 52.381 0.00 0.00 38.71 4.40
241 242 3.004752 ACTTTGCCTAGCACCTAATGG 57.995 47.619 0.00 0.00 38.71 3.16
242 243 4.035675 GCTAACTTTGCCTAGCACCTAATG 59.964 45.833 0.00 0.00 38.71 1.90
243 244 4.200092 GCTAACTTTGCCTAGCACCTAAT 58.800 43.478 0.00 0.00 38.71 1.73
244 245 3.606687 GCTAACTTTGCCTAGCACCTAA 58.393 45.455 0.00 0.00 38.71 2.69
245 246 2.093128 GGCTAACTTTGCCTAGCACCTA 60.093 50.000 6.96 0.00 46.38 3.08
246 247 1.340114 GGCTAACTTTGCCTAGCACCT 60.340 52.381 6.96 0.00 46.38 4.00
247 248 1.095600 GGCTAACTTTGCCTAGCACC 58.904 55.000 6.96 0.00 46.38 5.01
255 256 4.216731 GTGTTTTACGAGGCTAACTTTGC 58.783 43.478 0.00 0.00 0.00 3.68
256 257 5.412526 TGTGTTTTACGAGGCTAACTTTG 57.587 39.130 0.00 0.00 0.00 2.77
257 258 6.628919 AATGTGTTTTACGAGGCTAACTTT 57.371 33.333 0.00 0.00 0.00 2.66
258 259 7.117379 GTCTAATGTGTTTTACGAGGCTAACTT 59.883 37.037 0.00 0.00 0.00 2.66
259 260 6.589139 GTCTAATGTGTTTTACGAGGCTAACT 59.411 38.462 0.00 0.00 0.00 2.24
260 261 6.183360 GGTCTAATGTGTTTTACGAGGCTAAC 60.183 42.308 0.00 0.00 0.00 2.34
261 262 5.870978 GGTCTAATGTGTTTTACGAGGCTAA 59.129 40.000 0.00 0.00 0.00 3.09
262 263 5.413499 GGTCTAATGTGTTTTACGAGGCTA 58.587 41.667 0.00 0.00 0.00 3.93
263 264 4.251268 GGTCTAATGTGTTTTACGAGGCT 58.749 43.478 0.00 0.00 0.00 4.58
264 265 3.373130 GGGTCTAATGTGTTTTACGAGGC 59.627 47.826 0.00 0.00 0.00 4.70
265 266 4.828829 AGGGTCTAATGTGTTTTACGAGG 58.171 43.478 0.00 0.00 0.00 4.63
272 273 9.615660 TCCATCTATATAGGGTCTAATGTGTTT 57.384 33.333 9.89 0.00 0.00 2.83
273 274 9.615660 TTCCATCTATATAGGGTCTAATGTGTT 57.384 33.333 9.89 0.00 0.00 3.32
274 275 9.261035 CTTCCATCTATATAGGGTCTAATGTGT 57.739 37.037 9.89 0.00 0.00 3.72
275 276 8.700051 CCTTCCATCTATATAGGGTCTAATGTG 58.300 40.741 9.89 1.15 0.00 3.21
276 277 8.633724 TCCTTCCATCTATATAGGGTCTAATGT 58.366 37.037 9.89 0.00 0.00 2.71
277 278 9.142014 CTCCTTCCATCTATATAGGGTCTAATG 57.858 40.741 9.89 5.15 0.00 1.90
278 279 8.293216 CCTCCTTCCATCTATATAGGGTCTAAT 58.707 40.741 9.89 0.00 0.00 1.73
279 280 7.313276 CCCTCCTTCCATCTATATAGGGTCTAA 60.313 44.444 9.89 0.00 38.09 2.10
280 281 6.162420 CCCTCCTTCCATCTATATAGGGTCTA 59.838 46.154 9.89 0.00 38.09 2.59
281 282 5.042979 CCCTCCTTCCATCTATATAGGGTCT 60.043 48.000 9.89 0.00 38.09 3.85
282 283 5.043281 TCCCTCCTTCCATCTATATAGGGTC 60.043 48.000 9.89 0.00 42.58 4.46
283 284 4.870361 TCCCTCCTTCCATCTATATAGGGT 59.130 45.833 9.89 0.00 42.58 4.34
284 285 5.042979 ACTCCCTCCTTCCATCTATATAGGG 60.043 48.000 9.89 4.49 43.23 3.53
285 286 6.098716 ACTCCCTCCTTCCATCTATATAGG 57.901 45.833 9.89 0.00 0.00 2.57
286 287 7.064229 GGTACTCCCTCCTTCCATCTATATAG 58.936 46.154 3.10 3.10 0.00 1.31
287 288 6.511445 TGGTACTCCCTCCTTCCATCTATATA 59.489 42.308 0.00 0.00 0.00 0.86
288 289 5.318889 TGGTACTCCCTCCTTCCATCTATAT 59.681 44.000 0.00 0.00 0.00 0.86
289 290 4.673132 TGGTACTCCCTCCTTCCATCTATA 59.327 45.833 0.00 0.00 0.00 1.31
290 291 3.471306 TGGTACTCCCTCCTTCCATCTAT 59.529 47.826 0.00 0.00 0.00 1.98
291 292 2.863238 TGGTACTCCCTCCTTCCATCTA 59.137 50.000 0.00 0.00 0.00 1.98
292 293 1.651770 TGGTACTCCCTCCTTCCATCT 59.348 52.381 0.00 0.00 0.00 2.90
293 294 2.176247 TGGTACTCCCTCCTTCCATC 57.824 55.000 0.00 0.00 0.00 3.51
294 295 2.412591 CATGGTACTCCCTCCTTCCAT 58.587 52.381 0.00 0.00 36.30 3.41
295 296 1.879575 CATGGTACTCCCTCCTTCCA 58.120 55.000 0.00 0.00 0.00 3.53
296 297 0.470341 GCATGGTACTCCCTCCTTCC 59.530 60.000 0.00 0.00 0.00 3.46
297 298 1.204146 TGCATGGTACTCCCTCCTTC 58.796 55.000 0.00 0.00 0.00 3.46
298 299 1.898863 ATGCATGGTACTCCCTCCTT 58.101 50.000 0.00 0.00 0.00 3.36
299 300 1.898863 AATGCATGGTACTCCCTCCT 58.101 50.000 0.00 0.00 0.00 3.69
300 301 2.092429 TGAAATGCATGGTACTCCCTCC 60.092 50.000 0.00 0.00 0.00 4.30
301 302 2.945668 GTGAAATGCATGGTACTCCCTC 59.054 50.000 0.00 0.00 0.00 4.30
302 303 2.578021 AGTGAAATGCATGGTACTCCCT 59.422 45.455 0.00 0.00 0.00 4.20
303 304 2.945668 GAGTGAAATGCATGGTACTCCC 59.054 50.000 19.18 4.33 30.93 4.30
304 305 3.878778 AGAGTGAAATGCATGGTACTCC 58.121 45.455 23.18 12.44 36.18 3.85
305 306 5.886960 AAAGAGTGAAATGCATGGTACTC 57.113 39.130 21.00 21.00 35.88 2.59
306 307 6.655078 AAAAAGAGTGAAATGCATGGTACT 57.345 33.333 0.00 4.74 0.00 2.73
307 308 7.816640 TCTAAAAAGAGTGAAATGCATGGTAC 58.183 34.615 0.00 0.00 0.00 3.34
308 309 7.994425 TCTAAAAAGAGTGAAATGCATGGTA 57.006 32.000 0.00 0.00 0.00 3.25
309 310 6.899393 TCTAAAAAGAGTGAAATGCATGGT 57.101 33.333 0.00 0.00 0.00 3.55
310 311 7.373493 ACTTCTAAAAAGAGTGAAATGCATGG 58.627 34.615 0.00 0.00 0.00 3.66
338 339 4.399004 TGTTGTTTGTTTCCAGGATTGG 57.601 40.909 0.00 0.00 46.49 3.16
961 1880 2.317149 ATCTTGGGTCGCTGGCTAGC 62.317 60.000 12.81 12.81 46.62 3.42
962 1881 0.249657 GATCTTGGGTCGCTGGCTAG 60.250 60.000 0.00 0.00 0.00 3.42
963 1882 1.823295 GATCTTGGGTCGCTGGCTA 59.177 57.895 0.00 0.00 0.00 3.93
1134 2053 1.686325 GCCGGTCCTGCTCCTTGATA 61.686 60.000 1.90 0.00 0.00 2.15
1630 2549 0.106369 TAGCTAGCTCTTGCGGGGTA 60.106 55.000 23.26 0.00 45.42 3.69
1632 2551 1.365633 CTAGCTAGCTCTTGCGGGG 59.634 63.158 23.26 0.00 45.42 5.73
1646 2565 7.279750 AGAGAGTAATTAAGGTGTAGCTAGC 57.720 40.000 6.62 6.62 0.00 3.42
1708 2627 2.667470 AGCAGCTACTCCTAATTCCGA 58.333 47.619 0.00 0.00 0.00 4.55
1737 2657 5.352016 ACAACTACTCTTCTCTGCTACTACG 59.648 44.000 0.00 0.00 0.00 3.51
1738 2658 6.746745 ACAACTACTCTTCTCTGCTACTAC 57.253 41.667 0.00 0.00 0.00 2.73
1739 2659 7.169591 AGAACAACTACTCTTCTCTGCTACTA 58.830 38.462 0.00 0.00 0.00 1.82
1740 2660 6.007703 AGAACAACTACTCTTCTCTGCTACT 58.992 40.000 0.00 0.00 0.00 2.57
2037 2957 5.975693 AAGGCACCTCGATAAATTGAAAA 57.024 34.783 0.00 0.00 0.00 2.29
2052 2972 1.138859 AGCAGGAAAAACAAAGGCACC 59.861 47.619 0.00 0.00 0.00 5.01
2166 3086 5.278022 GCCCAAAAAGTCAGTACTCAGAAAG 60.278 44.000 0.00 0.00 33.75 2.62
2298 3375 8.124823 CGTCTATGTGAGCAATTTTGATTGTAT 58.875 33.333 0.00 0.00 34.21 2.29
2336 3415 0.098728 GTGCATGTGTTCATACGGGC 59.901 55.000 0.00 0.00 32.47 6.13
2340 3419 1.196581 TGTGCGTGCATGTGTTCATAC 59.803 47.619 7.93 0.00 32.47 2.39
2348 3427 1.942657 GGATAGAATGTGCGTGCATGT 59.057 47.619 7.93 0.00 0.00 3.21
2362 3441 1.961394 GGACGTGCACATAGGGATAGA 59.039 52.381 18.64 0.00 0.00 1.98
2366 3445 0.249120 CTTGGACGTGCACATAGGGA 59.751 55.000 18.64 0.00 0.00 4.20
2379 3458 5.980715 GCTATGCTAACTTAGTCTCTTGGAC 59.019 44.000 0.00 0.00 44.80 4.02
2391 3470 7.169982 GTCAATCTTACGATGCTATGCTAACTT 59.830 37.037 0.00 0.00 0.00 2.66
2394 3473 5.629435 CGTCAATCTTACGATGCTATGCTAA 59.371 40.000 0.00 0.00 42.90 3.09
2395 3474 5.048991 TCGTCAATCTTACGATGCTATGCTA 60.049 40.000 0.00 0.00 43.90 3.49
2396 3475 3.983988 CGTCAATCTTACGATGCTATGCT 59.016 43.478 0.00 0.00 42.90 3.79
2407 3486 4.304110 TGTGGTGACTTCGTCAATCTTAC 58.696 43.478 0.00 0.00 44.49 2.34
2437 3516 4.470876 ACGTTGCCGTCGACTATG 57.529 55.556 14.70 3.10 46.28 2.23
2449 3528 0.679505 TTCAGTGGGAGGAGACGTTG 59.320 55.000 0.00 0.00 0.00 4.10
2455 3534 0.679505 TGTTCGTTCAGTGGGAGGAG 59.320 55.000 0.00 0.00 0.00 3.69
2498 3577 3.862267 CGTTGGTGTTTGCATTTTTCTGA 59.138 39.130 0.00 0.00 0.00 3.27
2551 3630 0.841961 GGTTAGGTGGTGGTATCCCC 59.158 60.000 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.