Multiple sequence alignment - TraesCS7D01G332700

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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 TraesCS7D01G332700 chr7D 100.000 2447 0 0 1 2447 423711801 423714247 0.000000e+00 4519.0
1 TraesCS7D01G332700 chr7B 92.975 1395 77 12 532 1916 440816916 440818299 0.000000e+00 2013.0
2 TraesCS7D01G332700 chr7B 93.078 549 29 3 1907 2447 440818339 440818886 0.000000e+00 795.0
3 TraesCS7D01G332700 chr7B 92.453 106 7 1 364 469 440816813 440816917 1.520000e-32 150.0
4 TraesCS7D01G332700 chr7B 95.294 85 4 0 9 93 440816731 440816815 4.240000e-28 135.0
5 TraesCS7D01G332700 chr7A 83.645 1816 163 61 681 2446 509463906 509462175 0.000000e+00 1585.0
6 TraesCS7D01G332700 chr7A 88.530 279 29 3 93 368 675874546 675874824 3.900000e-88 335.0
7 TraesCS7D01G332700 chr5D 90.511 274 24 2 93 364 162578426 162578153 6.430000e-96 361.0
8 TraesCS7D01G332700 chr5D 88.849 278 28 3 93 367 60770265 60769988 3.010000e-89 339.0
9 TraesCS7D01G332700 chr2D 89.706 272 24 4 95 362 405499879 405500150 6.480000e-91 344.0
10 TraesCS7D01G332700 chr3B 89.091 275 27 3 93 364 78846062 78845788 3.010000e-89 339.0
11 TraesCS7D01G332700 chr6D 88.889 279 24 4 93 364 145337176 145336898 1.080000e-88 337.0
12 TraesCS7D01G332700 chr1D 88.889 279 24 4 93 364 229791484 229791762 1.080000e-88 337.0
13 TraesCS7D01G332700 chr4D 88.809 277 26 4 87 360 357910643 357910917 3.900000e-88 335.0
14 TraesCS7D01G332700 chr4D 88.070 285 29 5 93 374 87667485 87667203 1.400000e-87 333.0
15 TraesCS7D01G332700 chr2A 88.406 69 7 1 466 534 288121549 288121616 5.610000e-12 82.4


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 TraesCS7D01G332700 chr7D 423711801 423714247 2446 False 4519.00 4519 100.000 1 2447 1 chr7D.!!$F1 2446
1 TraesCS7D01G332700 chr7B 440816731 440818886 2155 False 773.25 2013 93.450 9 2447 4 chr7B.!!$F1 2438
2 TraesCS7D01G332700 chr7A 509462175 509463906 1731 True 1585.00 1585 83.645 681 2446 1 chr7A.!!$R1 1765

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
674 676 0.3199 AATACGAGCCATGCGCCTAG 60.32 55.0 4.18 0.0 38.78 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2323 2416 0.316204 GACAATGCAGCCACTTTGCT 59.684 50.0 0.0 0.0 44.0 3.91 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
63 64 3.181499 GCAACTCTCCTGCATGATTTCAG 60.181 47.826 0.00 0.00 39.69 3.02
91 92 3.810812 GCTGAGCTGCAGGTGATC 58.189 61.111 25.60 6.84 45.03 2.92
92 93 1.078637 GCTGAGCTGCAGGTGATCA 60.079 57.895 25.60 14.24 45.03 2.92
93 94 1.090625 GCTGAGCTGCAGGTGATCAG 61.091 60.000 25.60 23.51 45.03 2.90
94 95 0.462225 CTGAGCTGCAGGTGATCAGG 60.462 60.000 25.60 0.00 41.07 3.86
95 96 1.818785 GAGCTGCAGGTGATCAGGC 60.819 63.158 25.60 2.56 0.00 4.85
96 97 2.254737 GAGCTGCAGGTGATCAGGCT 62.255 60.000 25.60 7.14 0.00 4.58
97 98 2.113433 GCTGCAGGTGATCAGGCTG 61.113 63.158 17.12 8.58 0.00 4.85
98 99 1.451567 CTGCAGGTGATCAGGCTGG 60.452 63.158 15.73 0.00 0.00 4.85
99 100 2.194388 CTGCAGGTGATCAGGCTGGT 62.194 60.000 15.73 7.54 0.00 4.00
100 101 1.451028 GCAGGTGATCAGGCTGGTC 60.451 63.158 20.90 20.90 0.00 4.02
101 102 1.153489 CAGGTGATCAGGCTGGTCG 60.153 63.158 22.01 4.69 27.66 4.79
102 103 1.610673 AGGTGATCAGGCTGGTCGT 60.611 57.895 22.01 7.24 27.66 4.34
103 104 0.324368 AGGTGATCAGGCTGGTCGTA 60.324 55.000 22.01 3.37 27.66 3.43
104 105 0.535335 GGTGATCAGGCTGGTCGTAA 59.465 55.000 22.01 2.60 27.66 3.18
105 106 1.139058 GGTGATCAGGCTGGTCGTAAT 59.861 52.381 22.01 3.48 27.66 1.89
106 107 2.205074 GTGATCAGGCTGGTCGTAATG 58.795 52.381 22.01 0.00 27.66 1.90
107 108 1.138859 TGATCAGGCTGGTCGTAATGG 59.861 52.381 22.01 0.00 27.66 3.16
108 109 1.139058 GATCAGGCTGGTCGTAATGGT 59.861 52.381 12.77 0.00 0.00 3.55
109 110 1.855295 TCAGGCTGGTCGTAATGGTA 58.145 50.000 15.73 0.00 0.00 3.25
110 111 2.181125 TCAGGCTGGTCGTAATGGTAA 58.819 47.619 15.73 0.00 0.00 2.85
111 112 2.769663 TCAGGCTGGTCGTAATGGTAAT 59.230 45.455 15.73 0.00 0.00 1.89
112 113 3.962063 TCAGGCTGGTCGTAATGGTAATA 59.038 43.478 15.73 0.00 0.00 0.98
113 114 4.591498 TCAGGCTGGTCGTAATGGTAATAT 59.409 41.667 15.73 0.00 0.00 1.28
114 115 4.929808 CAGGCTGGTCGTAATGGTAATATC 59.070 45.833 6.61 0.00 0.00 1.63
115 116 4.591498 AGGCTGGTCGTAATGGTAATATCA 59.409 41.667 0.00 0.00 0.00 2.15
116 117 4.689345 GGCTGGTCGTAATGGTAATATCAC 59.311 45.833 0.00 0.00 0.00 3.06
117 118 5.294356 GCTGGTCGTAATGGTAATATCACA 58.706 41.667 0.00 0.00 0.00 3.58
118 119 5.756347 GCTGGTCGTAATGGTAATATCACAA 59.244 40.000 0.00 0.00 0.00 3.33
119 120 6.073765 GCTGGTCGTAATGGTAATATCACAAG 60.074 42.308 0.00 0.00 0.00 3.16
120 121 6.285224 TGGTCGTAATGGTAATATCACAAGG 58.715 40.000 0.00 0.00 0.00 3.61
121 122 5.699458 GGTCGTAATGGTAATATCACAAGGG 59.301 44.000 0.00 0.00 0.00 3.95
122 123 5.699458 GTCGTAATGGTAATATCACAAGGGG 59.301 44.000 0.00 0.00 0.00 4.79
123 124 5.367352 TCGTAATGGTAATATCACAAGGGGT 59.633 40.000 0.00 0.00 0.00 4.95
124 125 6.554228 TCGTAATGGTAATATCACAAGGGGTA 59.446 38.462 0.00 0.00 0.00 3.69
125 126 7.236019 TCGTAATGGTAATATCACAAGGGGTAT 59.764 37.037 0.00 0.00 0.00 2.73
126 127 7.548075 CGTAATGGTAATATCACAAGGGGTATC 59.452 40.741 0.00 0.00 0.00 2.24
127 128 7.401060 AATGGTAATATCACAAGGGGTATCA 57.599 36.000 0.00 0.00 0.00 2.15
128 129 7.588866 ATGGTAATATCACAAGGGGTATCAT 57.411 36.000 0.00 0.00 0.00 2.45
129 130 6.778821 TGGTAATATCACAAGGGGTATCATG 58.221 40.000 0.00 0.00 0.00 3.07
130 131 5.648092 GGTAATATCACAAGGGGTATCATGC 59.352 44.000 0.00 0.00 0.00 4.06
131 132 4.999469 ATATCACAAGGGGTATCATGCA 57.001 40.909 0.00 0.00 0.00 3.96
132 133 3.889859 ATCACAAGGGGTATCATGCAT 57.110 42.857 0.00 0.00 0.00 3.96
133 134 2.934887 TCACAAGGGGTATCATGCATG 58.065 47.619 21.07 21.07 0.00 4.06
134 135 2.241941 TCACAAGGGGTATCATGCATGT 59.758 45.455 25.43 15.34 0.00 3.21
135 136 2.620115 CACAAGGGGTATCATGCATGTC 59.380 50.000 25.43 16.28 0.00 3.06
136 137 2.241941 ACAAGGGGTATCATGCATGTCA 59.758 45.455 25.43 12.19 0.00 3.58
137 138 3.289836 CAAGGGGTATCATGCATGTCAA 58.710 45.455 25.43 7.83 0.00 3.18
138 139 2.936202 AGGGGTATCATGCATGTCAAC 58.064 47.619 25.43 19.73 0.00 3.18
139 140 2.511218 AGGGGTATCATGCATGTCAACT 59.489 45.455 25.43 14.25 0.00 3.16
140 141 3.716353 AGGGGTATCATGCATGTCAACTA 59.284 43.478 25.43 6.27 0.00 2.24
141 142 4.067896 GGGGTATCATGCATGTCAACTAG 58.932 47.826 25.43 0.00 0.00 2.57
142 143 4.202357 GGGGTATCATGCATGTCAACTAGA 60.202 45.833 25.43 4.73 0.00 2.43
143 144 5.513788 GGGGTATCATGCATGTCAACTAGAT 60.514 44.000 25.43 11.84 0.00 1.98
144 145 6.000219 GGGTATCATGCATGTCAACTAGATT 59.000 40.000 25.43 3.00 0.00 2.40
145 146 6.488006 GGGTATCATGCATGTCAACTAGATTT 59.512 38.462 25.43 0.00 0.00 2.17
146 147 7.013655 GGGTATCATGCATGTCAACTAGATTTT 59.986 37.037 25.43 0.00 0.00 1.82
147 148 8.408601 GGTATCATGCATGTCAACTAGATTTTT 58.591 33.333 25.43 0.00 0.00 1.94
151 152 9.230122 TCATGCATGTCAACTAGATTTTTAAGA 57.770 29.630 25.43 0.00 0.00 2.10
154 155 9.230122 TGCATGTCAACTAGATTTTTAAGATGA 57.770 29.630 0.00 0.00 0.00 2.92
163 164 9.725019 ACTAGATTTTTAAGATGATGTGACACA 57.275 29.630 11.41 11.41 0.00 3.72
164 165 9.979270 CTAGATTTTTAAGATGATGTGACACAC 57.021 33.333 11.22 5.86 34.56 3.82
178 179 6.951062 TGTGACACACAATTAAATGAGGAA 57.049 33.333 3.56 0.00 41.69 3.36
179 180 7.340122 TGTGACACACAATTAAATGAGGAAA 57.660 32.000 3.56 0.00 41.69 3.13
180 181 7.424803 TGTGACACACAATTAAATGAGGAAAG 58.575 34.615 3.56 0.00 41.69 2.62
181 182 7.284261 TGTGACACACAATTAAATGAGGAAAGA 59.716 33.333 3.56 0.00 41.69 2.52
182 183 7.805071 GTGACACACAATTAAATGAGGAAAGAG 59.195 37.037 0.00 0.00 34.08 2.85
183 184 7.719193 TGACACACAATTAAATGAGGAAAGAGA 59.281 33.333 0.00 0.00 0.00 3.10
184 185 8.103948 ACACACAATTAAATGAGGAAAGAGAG 57.896 34.615 0.00 0.00 0.00 3.20
185 186 7.175641 ACACACAATTAAATGAGGAAAGAGAGG 59.824 37.037 0.00 0.00 0.00 3.69
186 187 7.391554 CACACAATTAAATGAGGAAAGAGAGGA 59.608 37.037 0.00 0.00 0.00 3.71
187 188 8.112183 ACACAATTAAATGAGGAAAGAGAGGAT 58.888 33.333 0.00 0.00 0.00 3.24
188 189 8.404000 CACAATTAAATGAGGAAAGAGAGGATG 58.596 37.037 0.00 0.00 0.00 3.51
189 190 8.112183 ACAATTAAATGAGGAAAGAGAGGATGT 58.888 33.333 0.00 0.00 0.00 3.06
190 191 8.404000 CAATTAAATGAGGAAAGAGAGGATGTG 58.596 37.037 0.00 0.00 0.00 3.21
191 192 5.768980 AAATGAGGAAAGAGAGGATGTGA 57.231 39.130 0.00 0.00 0.00 3.58
192 193 5.972327 AATGAGGAAAGAGAGGATGTGAT 57.028 39.130 0.00 0.00 0.00 3.06
193 194 7.443302 AAATGAGGAAAGAGAGGATGTGATA 57.557 36.000 0.00 0.00 0.00 2.15
194 195 7.630005 AATGAGGAAAGAGAGGATGTGATAT 57.370 36.000 0.00 0.00 0.00 1.63
195 196 6.662865 TGAGGAAAGAGAGGATGTGATATC 57.337 41.667 0.00 0.00 0.00 1.63
196 197 6.138967 TGAGGAAAGAGAGGATGTGATATCA 58.861 40.000 0.00 0.00 0.00 2.15
197 198 6.786461 TGAGGAAAGAGAGGATGTGATATCAT 59.214 38.462 9.02 0.00 0.00 2.45
198 199 7.952368 TGAGGAAAGAGAGGATGTGATATCATA 59.048 37.037 9.02 6.66 0.00 2.15
199 200 8.914213 AGGAAAGAGAGGATGTGATATCATAT 57.086 34.615 14.17 14.17 0.00 1.78
200 201 8.980596 AGGAAAGAGAGGATGTGATATCATATC 58.019 37.037 26.17 26.17 41.79 1.63
201 202 8.756927 GGAAAGAGAGGATGTGATATCATATCA 58.243 37.037 31.47 17.53 43.53 2.15
204 205 9.490083 AAGAGAGGATGTGATATCATATCATGA 57.510 33.333 31.47 0.00 43.53 3.07
244 245 8.519492 AAATGTTGTAATACTTTGTGTCATGC 57.481 30.769 0.00 0.00 0.00 4.06
245 246 6.625873 TGTTGTAATACTTTGTGTCATGCA 57.374 33.333 0.00 0.00 0.00 3.96
246 247 7.213216 TGTTGTAATACTTTGTGTCATGCAT 57.787 32.000 0.00 0.00 0.00 3.96
247 248 7.083230 TGTTGTAATACTTTGTGTCATGCATG 58.917 34.615 21.07 21.07 0.00 4.06
248 249 7.040823 TGTTGTAATACTTTGTGTCATGCATGA 60.041 33.333 25.42 25.42 0.00 3.07
249 250 7.628769 TGTAATACTTTGTGTCATGCATGAT 57.371 32.000 30.89 16.22 39.30 2.45
250 251 8.729805 TGTAATACTTTGTGTCATGCATGATA 57.270 30.769 30.89 25.85 39.30 2.15
251 252 9.171877 TGTAATACTTTGTGTCATGCATGATAA 57.828 29.630 30.89 22.04 39.30 1.75
261 262 8.298854 TGTGTCATGCATGATAATTAATAAGGC 58.701 33.333 30.89 14.22 39.30 4.35
262 263 8.298854 GTGTCATGCATGATAATTAATAAGGCA 58.701 33.333 30.89 16.52 39.30 4.75
263 264 8.858094 TGTCATGCATGATAATTAATAAGGCAA 58.142 29.630 30.89 0.53 39.30 4.52
264 265 9.132521 GTCATGCATGATAATTAATAAGGCAAC 57.867 33.333 30.89 9.74 39.30 4.17
265 266 8.306038 TCATGCATGATAATTAATAAGGCAACC 58.694 33.333 25.42 0.00 32.00 3.77
266 267 7.838079 TGCATGATAATTAATAAGGCAACCT 57.162 32.000 0.00 0.00 33.87 3.50
267 268 8.932434 TGCATGATAATTAATAAGGCAACCTA 57.068 30.769 0.00 0.00 31.13 3.08
268 269 9.360901 TGCATGATAATTAATAAGGCAACCTAA 57.639 29.630 0.00 0.00 31.13 2.69
269 270 9.846248 GCATGATAATTAATAAGGCAACCTAAG 57.154 33.333 0.00 0.00 31.13 2.18
274 275 9.813826 ATAATTAATAAGGCAACCTAAGATGCT 57.186 29.630 0.00 0.00 42.20 3.79
276 277 8.622948 ATTAATAAGGCAACCTAAGATGCTAC 57.377 34.615 0.00 0.00 42.20 3.58
277 278 5.896073 ATAAGGCAACCTAAGATGCTACT 57.104 39.130 0.00 0.00 42.20 2.57
278 279 6.996180 ATAAGGCAACCTAAGATGCTACTA 57.004 37.500 0.00 0.00 42.20 1.82
279 280 5.896073 AAGGCAACCTAAGATGCTACTAT 57.104 39.130 0.00 0.00 42.20 2.12
280 281 5.220710 AGGCAACCTAAGATGCTACTATG 57.779 43.478 0.00 0.00 42.20 2.23
281 282 4.901849 AGGCAACCTAAGATGCTACTATGA 59.098 41.667 0.00 0.00 42.20 2.15
282 283 5.545723 AGGCAACCTAAGATGCTACTATGAT 59.454 40.000 0.00 0.00 42.20 2.45
283 284 6.726299 AGGCAACCTAAGATGCTACTATGATA 59.274 38.462 0.00 0.00 42.20 2.15
284 285 6.814146 GGCAACCTAAGATGCTACTATGATAC 59.186 42.308 0.00 0.00 42.20 2.24
285 286 7.310113 GGCAACCTAAGATGCTACTATGATACT 60.310 40.741 0.00 0.00 42.20 2.12
286 287 8.740906 GCAACCTAAGATGCTACTATGATACTA 58.259 37.037 0.00 0.00 39.46 1.82
349 350 9.397280 TGCATGTACTAGTATATGATACTCTCC 57.603 37.037 32.20 17.75 36.98 3.71
350 351 9.397280 GCATGTACTAGTATATGATACTCTCCA 57.603 37.037 32.20 12.09 36.98 3.86
359 360 9.601810 AGTATATGATACTCTCCATTACAACCA 57.398 33.333 0.00 0.00 0.00 3.67
362 363 5.741011 TGATACTCTCCATTACAACCAACC 58.259 41.667 0.00 0.00 0.00 3.77
363 364 5.487488 TGATACTCTCCATTACAACCAACCT 59.513 40.000 0.00 0.00 0.00 3.50
383 384 5.741011 ACCTCAAGTGTGTTCTGACTTTTA 58.259 37.500 0.00 0.00 29.73 1.52
392 393 5.417580 TGTGTTCTGACTTTTAAGGTTGCTT 59.582 36.000 0.00 0.00 0.00 3.91
399 400 5.163457 TGACTTTTAAGGTTGCTTCCTTTGG 60.163 40.000 15.72 8.32 44.36 3.28
405 406 1.886542 GGTTGCTTCCTTTGGTTCGAT 59.113 47.619 0.00 0.00 0.00 3.59
410 411 1.740025 CTTCCTTTGGTTCGATGGAGC 59.260 52.381 0.00 0.00 0.00 4.70
411 412 0.391130 TCCTTTGGTTCGATGGAGCG 60.391 55.000 0.00 0.00 0.00 5.03
412 413 1.425428 CTTTGGTTCGATGGAGCGC 59.575 57.895 0.00 0.00 0.00 5.92
413 414 2.296692 CTTTGGTTCGATGGAGCGCG 62.297 60.000 0.00 0.00 0.00 6.86
416 417 2.388232 GGTTCGATGGAGCGCGTTT 61.388 57.895 8.43 0.00 0.00 3.60
417 418 1.058903 GTTCGATGGAGCGCGTTTC 59.941 57.895 8.43 0.00 0.00 2.78
418 419 1.373622 TTCGATGGAGCGCGTTTCA 60.374 52.632 6.34 6.34 0.00 2.69
419 420 1.623081 TTCGATGGAGCGCGTTTCAC 61.623 55.000 5.91 0.00 0.00 3.18
474 475 9.959721 ATGTCTGAAAATTAGTTACTACACCAT 57.040 29.630 0.00 0.00 0.00 3.55
475 476 9.431887 TGTCTGAAAATTAGTTACTACACCATC 57.568 33.333 0.00 0.00 0.00 3.51
476 477 8.880750 GTCTGAAAATTAGTTACTACACCATCC 58.119 37.037 0.00 0.00 0.00 3.51
477 478 7.762615 TCTGAAAATTAGTTACTACACCATCCG 59.237 37.037 0.00 0.00 0.00 4.18
478 479 7.388437 TGAAAATTAGTTACTACACCATCCGT 58.612 34.615 0.00 0.00 0.00 4.69
479 480 8.530311 TGAAAATTAGTTACTACACCATCCGTA 58.470 33.333 0.00 0.00 0.00 4.02
480 481 9.538508 GAAAATTAGTTACTACACCATCCGTAT 57.461 33.333 0.00 0.00 0.00 3.06
481 482 9.538508 AAAATTAGTTACTACACCATCCGTATC 57.461 33.333 0.00 0.00 0.00 2.24
482 483 7.828508 ATTAGTTACTACACCATCCGTATCA 57.171 36.000 0.00 0.00 0.00 2.15
483 484 7.643569 TTAGTTACTACACCATCCGTATCAA 57.356 36.000 0.00 0.00 0.00 2.57
484 485 6.534475 AGTTACTACACCATCCGTATCAAA 57.466 37.500 0.00 0.00 0.00 2.69
485 486 6.570692 AGTTACTACACCATCCGTATCAAAG 58.429 40.000 0.00 0.00 0.00 2.77
486 487 6.154021 AGTTACTACACCATCCGTATCAAAGT 59.846 38.462 0.00 0.00 0.00 2.66
487 488 7.340232 AGTTACTACACCATCCGTATCAAAGTA 59.660 37.037 0.00 0.00 0.00 2.24
488 489 5.899299 ACTACACCATCCGTATCAAAGTAC 58.101 41.667 0.00 0.00 0.00 2.73
489 490 5.655532 ACTACACCATCCGTATCAAAGTACT 59.344 40.000 0.00 0.00 0.00 2.73
490 491 5.416271 ACACCATCCGTATCAAAGTACTT 57.584 39.130 1.12 1.12 0.00 2.24
491 492 5.175859 ACACCATCCGTATCAAAGTACTTG 58.824 41.667 9.34 3.91 36.25 3.16
492 493 5.175859 CACCATCCGTATCAAAGTACTTGT 58.824 41.667 9.34 1.37 36.34 3.16
493 494 5.642063 CACCATCCGTATCAAAGTACTTGTT 59.358 40.000 9.34 0.00 36.34 2.83
494 495 5.642063 ACCATCCGTATCAAAGTACTTGTTG 59.358 40.000 9.34 4.87 36.34 3.33
495 496 5.642063 CCATCCGTATCAAAGTACTTGTTGT 59.358 40.000 9.34 0.00 36.34 3.32
496 497 6.148811 CCATCCGTATCAAAGTACTTGTTGTT 59.851 38.462 9.34 2.73 36.34 2.83
497 498 7.332430 CCATCCGTATCAAAGTACTTGTTGTTA 59.668 37.037 9.34 1.77 36.34 2.41
498 499 7.878477 TCCGTATCAAAGTACTTGTTGTTAG 57.122 36.000 9.34 0.00 36.34 2.34
499 500 6.869913 TCCGTATCAAAGTACTTGTTGTTAGG 59.130 38.462 9.34 9.30 36.34 2.69
500 501 6.091713 CCGTATCAAAGTACTTGTTGTTAGGG 59.908 42.308 9.34 13.72 36.34 3.53
501 502 6.091713 CGTATCAAAGTACTTGTTGTTAGGGG 59.908 42.308 9.34 0.00 36.34 4.79
502 503 5.633655 TCAAAGTACTTGTTGTTAGGGGA 57.366 39.130 9.34 0.00 36.34 4.81
503 504 6.003859 TCAAAGTACTTGTTGTTAGGGGAA 57.996 37.500 9.34 0.00 36.34 3.97
504 505 6.424883 TCAAAGTACTTGTTGTTAGGGGAAA 58.575 36.000 9.34 0.00 36.34 3.13
505 506 6.319405 TCAAAGTACTTGTTGTTAGGGGAAAC 59.681 38.462 9.34 0.00 36.34 2.78
506 507 5.641789 AGTACTTGTTGTTAGGGGAAACT 57.358 39.130 0.00 0.00 0.00 2.66
507 508 6.752285 AGTACTTGTTGTTAGGGGAAACTA 57.248 37.500 0.00 0.00 0.00 2.24
508 509 6.766429 AGTACTTGTTGTTAGGGGAAACTAG 58.234 40.000 0.00 0.00 34.30 2.57
509 510 5.641789 ACTTGTTGTTAGGGGAAACTAGT 57.358 39.130 0.00 0.00 35.84 2.57
510 511 6.752285 ACTTGTTGTTAGGGGAAACTAGTA 57.248 37.500 0.00 0.00 37.85 1.82
511 512 6.528321 ACTTGTTGTTAGGGGAAACTAGTAC 58.472 40.000 0.00 0.00 37.85 2.73
512 513 6.100134 ACTTGTTGTTAGGGGAAACTAGTACA 59.900 38.462 0.00 0.00 37.85 2.90
513 514 6.497624 TGTTGTTAGGGGAAACTAGTACAA 57.502 37.500 0.00 0.00 0.00 2.41
514 515 6.897986 TGTTGTTAGGGGAAACTAGTACAAA 58.102 36.000 0.00 0.00 30.06 2.83
515 516 7.519927 TGTTGTTAGGGGAAACTAGTACAAAT 58.480 34.615 0.00 0.00 30.06 2.32
516 517 8.000127 TGTTGTTAGGGGAAACTAGTACAAATT 59.000 33.333 0.00 0.00 30.06 1.82
517 518 8.509690 GTTGTTAGGGGAAACTAGTACAAATTC 58.490 37.037 0.00 0.00 30.06 2.17
518 519 7.170277 TGTTAGGGGAAACTAGTACAAATTCC 58.830 38.462 12.95 12.95 39.03 3.01
522 523 4.925836 GGAAACTAGTACAAATTCCCCCA 58.074 43.478 10.93 0.00 34.74 4.96
523 524 5.326900 GGAAACTAGTACAAATTCCCCCAA 58.673 41.667 10.93 0.00 34.74 4.12
524 525 5.184479 GGAAACTAGTACAAATTCCCCCAAC 59.816 44.000 10.93 0.00 34.74 3.77
525 526 5.594199 AACTAGTACAAATTCCCCCAACT 57.406 39.130 0.00 0.00 0.00 3.16
526 527 6.707273 AACTAGTACAAATTCCCCCAACTA 57.293 37.500 0.00 0.00 0.00 2.24
527 528 6.903340 ACTAGTACAAATTCCCCCAACTAT 57.097 37.500 0.00 0.00 0.00 2.12
528 529 8.396619 AACTAGTACAAATTCCCCCAACTATA 57.603 34.615 0.00 0.00 0.00 1.31
529 530 8.396619 ACTAGTACAAATTCCCCCAACTATAA 57.603 34.615 0.00 0.00 0.00 0.98
530 531 8.491958 ACTAGTACAAATTCCCCCAACTATAAG 58.508 37.037 0.00 0.00 0.00 1.73
571 572 6.295688 GGTCTATCTAACAACTCCCTTCACAA 60.296 42.308 0.00 0.00 0.00 3.33
585 586 3.482786 CTTCACAAAGCGCTGATGTAAC 58.517 45.455 23.76 0.00 0.00 2.50
645 646 4.081420 AGCATAATCCCGAGCGAATAATCT 60.081 41.667 0.00 0.00 0.00 2.40
649 650 1.001706 TCCCGAGCGAATAATCTGACG 60.002 52.381 0.00 0.00 0.00 4.35
657 659 7.432545 CCGAGCGAATAATCTGACGATATAAAT 59.567 37.037 0.00 0.00 0.00 1.40
674 676 0.319900 AATACGAGCCATGCGCCTAG 60.320 55.000 4.18 0.00 38.78 3.02
675 677 1.464376 ATACGAGCCATGCGCCTAGT 61.464 55.000 4.18 3.49 38.78 2.57
676 678 2.071844 TACGAGCCATGCGCCTAGTC 62.072 60.000 4.18 0.00 38.78 2.59
677 679 2.280457 GAGCCATGCGCCTAGTCC 60.280 66.667 4.18 0.00 38.78 3.85
678 680 2.765807 AGCCATGCGCCTAGTCCT 60.766 61.111 4.18 0.00 38.78 3.85
679 681 1.457643 AGCCATGCGCCTAGTCCTA 60.458 57.895 4.18 0.00 38.78 2.94
757 763 9.231297 CTTCAAATCAGTGGAATAAAAGGAGTA 57.769 33.333 0.00 0.00 0.00 2.59
774 789 1.745489 TAGTCGCTCTCGCTGCTGA 60.745 57.895 0.00 0.00 35.26 4.26
777 792 3.628193 CGCTCTCGCTGCTGATGC 61.628 66.667 0.00 4.31 40.20 3.91
785 800 3.877357 CTGCTGATGCGGCTGCTG 61.877 66.667 20.27 3.55 43.34 4.41
788 803 2.202974 CTGATGCGGCTGCTGCTA 60.203 61.111 31.19 19.15 43.34 3.49
792 807 4.765449 TGCGGCTGCTGCTACTGG 62.765 66.667 31.19 1.81 43.34 4.00
850 865 6.442952 TCCAATTATTCAGACAAACCAAACG 58.557 36.000 0.00 0.00 0.00 3.60
863 878 6.668323 ACAAACCAAACGTAATCATCAGAAG 58.332 36.000 0.00 0.00 0.00 2.85
864 879 6.485313 ACAAACCAAACGTAATCATCAGAAGA 59.515 34.615 0.00 0.00 0.00 2.87
971 998 1.641577 GCCAGTTAGCCTACTCAACG 58.358 55.000 0.00 0.00 0.00 4.10
1046 1077 0.748729 CTCCTCCTCTTCTACGCCGT 60.749 60.000 0.00 0.00 0.00 5.68
1200 1231 3.760035 GCGTCGAGCCTTCTCCCA 61.760 66.667 0.00 0.00 40.81 4.37
1248 1282 4.681978 AGTGGCAAGGACGACGCC 62.682 66.667 0.00 0.00 46.43 5.68
1471 1505 2.309528 TCGACCATCACATAGGCAAC 57.690 50.000 0.00 0.00 0.00 4.17
1477 1511 1.089481 ATCACATAGGCAACACCGCG 61.089 55.000 0.00 0.00 46.52 6.46
1486 1520 1.571919 GCAACACCGCGAGAGATATT 58.428 50.000 8.23 0.00 0.00 1.28
1573 1612 3.000727 GCTGGTGTATAGTGTGTGAACC 58.999 50.000 0.00 0.00 0.00 3.62
1605 1644 3.446873 TGTGTTTCACTGGAGTTGCATTT 59.553 39.130 0.00 0.00 35.11 2.32
1617 1656 5.104402 TGGAGTTGCATTTGGATATCTCAGA 60.104 40.000 2.05 0.00 0.00 3.27
1639 1678 0.548031 TCAGGATCCCATGAAGGCAC 59.452 55.000 8.55 0.00 35.39 5.01
1643 1682 1.017387 GATCCCATGAAGGCACGAAC 58.983 55.000 0.00 0.00 35.39 3.95
1647 1686 0.798776 CCATGAAGGCACGAACTGAC 59.201 55.000 0.00 0.00 0.00 3.51
1662 1701 4.083324 CGAACTGACTGCCAAATTACACAT 60.083 41.667 0.00 0.00 0.00 3.21
1733 1772 3.060614 GCAGGGCAGCAGGGGAATA 62.061 63.158 0.00 0.00 0.00 1.75
1754 1793 8.023128 GGAATACATGACATAATGCCAATGTAC 58.977 37.037 0.00 0.00 37.69 2.90
1768 1807 4.201657 CCAATGTACTCATCAGGAATGCA 58.798 43.478 0.00 0.00 35.17 3.96
1796 1835 6.596309 TGAGATATTACACATAGCAGGAGG 57.404 41.667 0.00 0.00 0.00 4.30
1839 1878 6.146021 AGCAAGCCGAATAAAATGTCTTTTTG 59.854 34.615 6.69 0.00 38.03 2.44
1888 1928 4.458397 AGTAGGAGGTGAATGAATGCATG 58.542 43.478 0.00 0.00 34.26 4.06
1893 1933 5.068723 AGGAGGTGAATGAATGCATGAAATC 59.931 40.000 0.00 0.00 34.26 2.17
2075 2168 0.384725 CAGAAACGCGAGGCAACAAG 60.385 55.000 15.93 0.00 41.41 3.16
2160 2253 1.173913 GGCTTAAATCTGCACCGGTT 58.826 50.000 2.97 0.00 0.00 4.44
2218 2311 1.685224 GGGGATGAACTGCAGTGGA 59.315 57.895 22.49 10.53 0.00 4.02
2259 2352 5.181748 GGTTCTGCAGAGACTTGACATATT 58.818 41.667 17.43 0.00 0.00 1.28
2340 2433 2.728690 TAAGCAAAGTGGCTGCATTG 57.271 45.000 0.50 2.34 45.07 2.82
2369 2472 8.821894 GTGACTCTTGGTTATGATAATCTTGTC 58.178 37.037 0.00 1.77 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 4.458642 GCTCAGCTCCTTTTCTTCTGAAAT 59.541 41.667 0.00 0.00 41.24 2.17
63 64 1.468127 GCAGCTCAGCTCCTTTTCTTC 59.532 52.381 0.00 0.00 36.40 2.87
84 85 0.324368 TACGACCAGCCTGATCACCT 60.324 55.000 0.00 0.00 0.00 4.00
91 92 2.684001 TTACCATTACGACCAGCCTG 57.316 50.000 0.00 0.00 0.00 4.85
92 93 4.591498 TGATATTACCATTACGACCAGCCT 59.409 41.667 0.00 0.00 0.00 4.58
93 94 4.689345 GTGATATTACCATTACGACCAGCC 59.311 45.833 0.00 0.00 0.00 4.85
94 95 5.294356 TGTGATATTACCATTACGACCAGC 58.706 41.667 0.00 0.00 0.00 4.85
95 96 6.423905 CCTTGTGATATTACCATTACGACCAG 59.576 42.308 0.00 0.00 0.00 4.00
96 97 6.285224 CCTTGTGATATTACCATTACGACCA 58.715 40.000 0.00 0.00 0.00 4.02
97 98 5.699458 CCCTTGTGATATTACCATTACGACC 59.301 44.000 0.00 0.00 0.00 4.79
98 99 5.699458 CCCCTTGTGATATTACCATTACGAC 59.301 44.000 0.00 0.00 0.00 4.34
99 100 5.367352 ACCCCTTGTGATATTACCATTACGA 59.633 40.000 0.00 0.00 0.00 3.43
100 101 5.617252 ACCCCTTGTGATATTACCATTACG 58.383 41.667 0.00 0.00 0.00 3.18
101 102 8.380099 TGATACCCCTTGTGATATTACCATTAC 58.620 37.037 0.00 0.00 0.00 1.89
102 103 8.513139 TGATACCCCTTGTGATATTACCATTA 57.487 34.615 0.00 0.00 0.00 1.90
103 104 7.401060 TGATACCCCTTGTGATATTACCATT 57.599 36.000 0.00 0.00 0.00 3.16
104 105 7.405292 CATGATACCCCTTGTGATATTACCAT 58.595 38.462 0.00 0.00 0.00 3.55
105 106 6.746900 GCATGATACCCCTTGTGATATTACCA 60.747 42.308 0.00 0.00 0.00 3.25
106 107 5.648092 GCATGATACCCCTTGTGATATTACC 59.352 44.000 0.00 0.00 0.00 2.85
107 108 6.237901 TGCATGATACCCCTTGTGATATTAC 58.762 40.000 0.00 0.00 0.00 1.89
108 109 6.446909 TGCATGATACCCCTTGTGATATTA 57.553 37.500 0.00 0.00 0.00 0.98
109 110 5.323382 TGCATGATACCCCTTGTGATATT 57.677 39.130 0.00 0.00 0.00 1.28
110 111 4.999469 TGCATGATACCCCTTGTGATAT 57.001 40.909 0.00 0.00 0.00 1.63
111 112 4.104579 ACATGCATGATACCCCTTGTGATA 59.895 41.667 32.75 0.00 0.00 2.15
112 113 3.117398 ACATGCATGATACCCCTTGTGAT 60.117 43.478 32.75 2.07 0.00 3.06
113 114 2.241941 ACATGCATGATACCCCTTGTGA 59.758 45.455 32.75 0.00 0.00 3.58
114 115 2.620115 GACATGCATGATACCCCTTGTG 59.380 50.000 32.75 3.42 0.00 3.33
115 116 2.241941 TGACATGCATGATACCCCTTGT 59.758 45.455 32.75 7.91 0.00 3.16
116 117 2.934887 TGACATGCATGATACCCCTTG 58.065 47.619 32.75 4.22 0.00 3.61
117 118 3.053395 AGTTGACATGCATGATACCCCTT 60.053 43.478 32.75 7.85 0.00 3.95
118 119 2.511218 AGTTGACATGCATGATACCCCT 59.489 45.455 32.75 16.07 0.00 4.79
119 120 2.936202 AGTTGACATGCATGATACCCC 58.064 47.619 32.75 14.22 0.00 4.95
120 121 4.960938 TCTAGTTGACATGCATGATACCC 58.039 43.478 32.75 15.21 0.00 3.69
121 122 7.502120 AAATCTAGTTGACATGCATGATACC 57.498 36.000 32.75 17.46 0.00 2.73
125 126 9.230122 TCTTAAAAATCTAGTTGACATGCATGA 57.770 29.630 32.75 9.00 0.00 3.07
128 129 9.230122 TCATCTTAAAAATCTAGTTGACATGCA 57.770 29.630 0.00 0.00 0.00 3.96
137 138 9.725019 TGTGTCACATCATCTTAAAAATCTAGT 57.275 29.630 0.18 0.00 0.00 2.57
138 139 9.979270 GTGTGTCACATCATCTTAAAAATCTAG 57.021 33.333 9.31 0.00 34.08 2.43
139 140 9.500785 TGTGTGTCACATCATCTTAAAAATCTA 57.499 29.630 9.31 0.00 39.62 1.98
140 141 8.394971 TGTGTGTCACATCATCTTAAAAATCT 57.605 30.769 9.31 0.00 39.62 2.40
141 142 9.630098 ATTGTGTGTCACATCATCTTAAAAATC 57.370 29.630 9.31 0.00 44.16 2.17
142 143 9.985730 AATTGTGTGTCACATCATCTTAAAAAT 57.014 25.926 9.31 0.00 44.16 1.82
148 149 8.795513 TCATTTAATTGTGTGTCACATCATCTT 58.204 29.630 9.31 8.39 44.16 2.40
149 150 8.339344 TCATTTAATTGTGTGTCACATCATCT 57.661 30.769 9.31 2.97 44.16 2.90
150 151 7.699391 CCTCATTTAATTGTGTGTCACATCATC 59.301 37.037 9.31 0.00 44.16 2.92
151 152 7.394077 TCCTCATTTAATTGTGTGTCACATCAT 59.606 33.333 9.31 1.54 44.16 2.45
152 153 6.714356 TCCTCATTTAATTGTGTGTCACATCA 59.286 34.615 9.31 6.55 44.16 3.07
153 154 7.144722 TCCTCATTTAATTGTGTGTCACATC 57.855 36.000 9.31 3.94 44.16 3.06
154 155 7.523293 TTCCTCATTTAATTGTGTGTCACAT 57.477 32.000 9.31 0.00 44.16 3.21
155 156 6.951062 TTCCTCATTTAATTGTGTGTCACA 57.049 33.333 0.18 0.18 43.02 3.58
156 157 7.648142 TCTTTCCTCATTTAATTGTGTGTCAC 58.352 34.615 0.00 0.00 34.56 3.67
157 158 7.719193 TCTCTTTCCTCATTTAATTGTGTGTCA 59.281 33.333 0.00 0.00 0.00 3.58
158 159 8.099364 TCTCTTTCCTCATTTAATTGTGTGTC 57.901 34.615 0.00 0.00 0.00 3.67
159 160 7.175641 CCTCTCTTTCCTCATTTAATTGTGTGT 59.824 37.037 0.00 0.00 0.00 3.72
160 161 7.391554 TCCTCTCTTTCCTCATTTAATTGTGTG 59.608 37.037 0.00 0.00 0.00 3.82
161 162 7.461749 TCCTCTCTTTCCTCATTTAATTGTGT 58.538 34.615 0.00 0.00 0.00 3.72
162 163 7.928307 TCCTCTCTTTCCTCATTTAATTGTG 57.072 36.000 0.00 0.00 0.00 3.33
163 164 8.112183 ACATCCTCTCTTTCCTCATTTAATTGT 58.888 33.333 0.00 0.00 0.00 2.71
164 165 8.404000 CACATCCTCTCTTTCCTCATTTAATTG 58.596 37.037 0.00 0.00 0.00 2.32
165 166 8.331740 TCACATCCTCTCTTTCCTCATTTAATT 58.668 33.333 0.00 0.00 0.00 1.40
166 167 7.865820 TCACATCCTCTCTTTCCTCATTTAAT 58.134 34.615 0.00 0.00 0.00 1.40
167 168 7.257790 TCACATCCTCTCTTTCCTCATTTAA 57.742 36.000 0.00 0.00 0.00 1.52
168 169 6.874278 TCACATCCTCTCTTTCCTCATTTA 57.126 37.500 0.00 0.00 0.00 1.40
169 170 5.768980 TCACATCCTCTCTTTCCTCATTT 57.231 39.130 0.00 0.00 0.00 2.32
170 171 5.972327 ATCACATCCTCTCTTTCCTCATT 57.028 39.130 0.00 0.00 0.00 2.57
171 172 6.786461 TGATATCACATCCTCTCTTTCCTCAT 59.214 38.462 0.00 0.00 0.00 2.90
172 173 6.138967 TGATATCACATCCTCTCTTTCCTCA 58.861 40.000 0.00 0.00 0.00 3.86
173 174 6.662865 TGATATCACATCCTCTCTTTCCTC 57.337 41.667 0.00 0.00 0.00 3.71
174 175 8.914213 ATATGATATCACATCCTCTCTTTCCT 57.086 34.615 7.78 0.00 0.00 3.36
175 176 8.756927 TGATATGATATCACATCCTCTCTTTCC 58.243 37.037 18.97 0.00 29.04 3.13
178 179 9.490083 TCATGATATGATATCACATCCTCTCTT 57.510 33.333 18.97 0.00 33.59 2.85
218 219 9.619316 GCATGACACAAAGTATTACAACATTTA 57.381 29.630 0.00 0.00 0.00 1.40
219 220 8.140628 TGCATGACACAAAGTATTACAACATTT 58.859 29.630 0.00 0.00 0.00 2.32
220 221 7.656412 TGCATGACACAAAGTATTACAACATT 58.344 30.769 0.00 0.00 0.00 2.71
221 222 7.213216 TGCATGACACAAAGTATTACAACAT 57.787 32.000 0.00 0.00 0.00 2.71
222 223 6.625873 TGCATGACACAAAGTATTACAACA 57.374 33.333 0.00 0.00 0.00 3.33
223 224 7.304735 TCATGCATGACACAAAGTATTACAAC 58.695 34.615 25.42 0.00 0.00 3.32
224 225 7.446001 TCATGCATGACACAAAGTATTACAA 57.554 32.000 25.42 0.00 0.00 2.41
225 226 7.628769 ATCATGCATGACACAAAGTATTACA 57.371 32.000 30.92 3.74 40.03 2.41
235 236 8.298854 GCCTTATTAATTATCATGCATGACACA 58.701 33.333 30.92 17.76 40.03 3.72
236 237 8.298854 TGCCTTATTAATTATCATGCATGACAC 58.701 33.333 30.92 4.80 40.03 3.67
237 238 8.406730 TGCCTTATTAATTATCATGCATGACA 57.593 30.769 30.92 18.55 40.03 3.58
238 239 9.132521 GTTGCCTTATTAATTATCATGCATGAC 57.867 33.333 30.92 13.88 40.03 3.06
239 240 8.306038 GGTTGCCTTATTAATTATCATGCATGA 58.694 33.333 30.47 30.47 41.70 3.07
240 241 8.308931 AGGTTGCCTTATTAATTATCATGCATG 58.691 33.333 21.07 21.07 0.00 4.06
241 242 8.426569 AGGTTGCCTTATTAATTATCATGCAT 57.573 30.769 0.00 0.00 0.00 3.96
242 243 7.838079 AGGTTGCCTTATTAATTATCATGCA 57.162 32.000 0.00 0.00 0.00 3.96
243 244 9.846248 CTTAGGTTGCCTTATTAATTATCATGC 57.154 33.333 0.00 0.00 34.61 4.06
248 249 9.813826 AGCATCTTAGGTTGCCTTATTAATTAT 57.186 29.630 4.41 0.00 38.52 1.28
250 251 9.067986 GTAGCATCTTAGGTTGCCTTATTAATT 57.932 33.333 4.41 0.00 38.52 1.40
251 252 8.440771 AGTAGCATCTTAGGTTGCCTTATTAAT 58.559 33.333 4.41 0.00 38.52 1.40
252 253 7.802117 AGTAGCATCTTAGGTTGCCTTATTAA 58.198 34.615 4.41 0.00 38.52 1.40
253 254 7.374975 AGTAGCATCTTAGGTTGCCTTATTA 57.625 36.000 4.41 0.00 38.52 0.98
254 255 6.253946 AGTAGCATCTTAGGTTGCCTTATT 57.746 37.500 4.41 0.00 38.52 1.40
255 256 5.896073 AGTAGCATCTTAGGTTGCCTTAT 57.104 39.130 4.41 0.00 38.52 1.73
256 257 6.553476 TCATAGTAGCATCTTAGGTTGCCTTA 59.447 38.462 4.41 0.00 38.52 2.69
257 258 5.366768 TCATAGTAGCATCTTAGGTTGCCTT 59.633 40.000 4.41 0.00 38.52 4.35
258 259 4.901849 TCATAGTAGCATCTTAGGTTGCCT 59.098 41.667 4.41 0.00 38.52 4.75
259 260 5.215252 TCATAGTAGCATCTTAGGTTGCC 57.785 43.478 4.41 0.00 38.52 4.52
260 261 7.607250 AGTATCATAGTAGCATCTTAGGTTGC 58.393 38.462 0.00 0.00 38.16 4.17
323 324 9.397280 GGAGAGTATCATATACTAGTACATGCA 57.603 37.037 15.09 6.14 37.82 3.96
324 325 9.397280 TGGAGAGTATCATATACTAGTACATGC 57.603 37.037 15.09 3.29 37.82 4.06
333 334 9.601810 TGGTTGTAATGGAGAGTATCATATACT 57.398 33.333 0.00 0.00 37.82 2.12
336 337 8.157476 GGTTGGTTGTAATGGAGAGTATCATAT 58.843 37.037 0.00 0.00 37.82 1.78
337 338 7.347222 AGGTTGGTTGTAATGGAGAGTATCATA 59.653 37.037 0.00 0.00 37.82 2.15
338 339 6.158695 AGGTTGGTTGTAATGGAGAGTATCAT 59.841 38.462 0.00 0.00 37.82 2.45
339 340 5.487488 AGGTTGGTTGTAATGGAGAGTATCA 59.513 40.000 0.00 0.00 37.82 2.15
340 341 5.990668 AGGTTGGTTGTAATGGAGAGTATC 58.009 41.667 0.00 0.00 0.00 2.24
341 342 5.487488 TGAGGTTGGTTGTAATGGAGAGTAT 59.513 40.000 0.00 0.00 0.00 2.12
342 343 4.841813 TGAGGTTGGTTGTAATGGAGAGTA 59.158 41.667 0.00 0.00 0.00 2.59
343 344 3.650942 TGAGGTTGGTTGTAATGGAGAGT 59.349 43.478 0.00 0.00 0.00 3.24
344 345 4.286297 TGAGGTTGGTTGTAATGGAGAG 57.714 45.455 0.00 0.00 0.00 3.20
345 346 4.104102 ACTTGAGGTTGGTTGTAATGGAGA 59.896 41.667 0.00 0.00 0.00 3.71
346 347 4.216257 CACTTGAGGTTGGTTGTAATGGAG 59.784 45.833 0.00 0.00 0.00 3.86
347 348 4.141287 CACTTGAGGTTGGTTGTAATGGA 58.859 43.478 0.00 0.00 0.00 3.41
348 349 3.888930 ACACTTGAGGTTGGTTGTAATGG 59.111 43.478 0.00 0.00 0.00 3.16
349 350 4.338118 ACACACTTGAGGTTGGTTGTAATG 59.662 41.667 0.00 0.00 0.00 1.90
350 351 4.532834 ACACACTTGAGGTTGGTTGTAAT 58.467 39.130 0.00 0.00 0.00 1.89
351 352 3.958018 ACACACTTGAGGTTGGTTGTAA 58.042 40.909 0.00 0.00 0.00 2.41
352 353 3.637911 ACACACTTGAGGTTGGTTGTA 57.362 42.857 0.00 0.00 0.00 2.41
353 354 2.507407 ACACACTTGAGGTTGGTTGT 57.493 45.000 0.00 0.00 0.00 3.32
354 355 3.016736 AGAACACACTTGAGGTTGGTTG 58.983 45.455 0.00 0.00 0.00 3.77
355 356 3.016736 CAGAACACACTTGAGGTTGGTT 58.983 45.455 0.00 0.00 0.00 3.67
356 357 2.238646 TCAGAACACACTTGAGGTTGGT 59.761 45.455 0.00 0.00 0.00 3.67
357 358 2.614057 GTCAGAACACACTTGAGGTTGG 59.386 50.000 0.00 0.00 0.00 3.77
358 359 3.535561 AGTCAGAACACACTTGAGGTTG 58.464 45.455 0.00 0.00 0.00 3.77
359 360 3.914426 AGTCAGAACACACTTGAGGTT 57.086 42.857 0.00 0.00 0.00 3.50
360 361 3.914426 AAGTCAGAACACACTTGAGGT 57.086 42.857 0.00 0.00 31.42 3.85
361 362 6.238484 CCTTAAAAGTCAGAACACACTTGAGG 60.238 42.308 0.00 0.00 33.01 3.86
362 363 6.316390 ACCTTAAAAGTCAGAACACACTTGAG 59.684 38.462 0.00 0.00 33.01 3.02
363 364 6.177610 ACCTTAAAAGTCAGAACACACTTGA 58.822 36.000 0.00 0.00 33.01 3.02
392 393 0.391130 CGCTCCATCGAACCAAAGGA 60.391 55.000 0.00 0.00 0.00 3.36
399 400 1.058903 GAAACGCGCTCCATCGAAC 59.941 57.895 5.73 0.00 0.00 3.95
405 406 1.959226 GGAAGTGAAACGCGCTCCA 60.959 57.895 5.73 0.00 45.86 3.86
410 411 1.278637 GTGTGGGAAGTGAAACGCG 59.721 57.895 3.53 3.53 45.86 6.01
411 412 1.652563 GGTGTGGGAAGTGAAACGC 59.347 57.895 0.00 0.00 45.86 4.84
412 413 0.531090 TCGGTGTGGGAAGTGAAACG 60.531 55.000 0.00 0.00 45.86 3.60
413 414 1.226746 CTCGGTGTGGGAAGTGAAAC 58.773 55.000 0.00 0.00 0.00 2.78
416 417 0.761323 TTCCTCGGTGTGGGAAGTGA 60.761 55.000 0.00 0.00 36.78 3.41
417 418 0.324943 ATTCCTCGGTGTGGGAAGTG 59.675 55.000 0.00 0.00 43.64 3.16
418 419 1.553704 GTATTCCTCGGTGTGGGAAGT 59.446 52.381 0.00 0.00 43.64 3.01
419 420 1.553248 TGTATTCCTCGGTGTGGGAAG 59.447 52.381 0.00 0.00 43.64 3.46
459 460 7.643569 TTGATACGGATGGTGTAGTAACTAA 57.356 36.000 0.00 0.00 0.00 2.24
462 463 6.335777 ACTTTGATACGGATGGTGTAGTAAC 58.664 40.000 0.00 0.00 0.00 2.50
467 468 6.071221 ACAAGTACTTTGATACGGATGGTGTA 60.071 38.462 5.07 0.00 39.21 2.90
468 469 5.175859 CAAGTACTTTGATACGGATGGTGT 58.824 41.667 5.07 0.00 39.21 4.16
469 470 5.175859 ACAAGTACTTTGATACGGATGGTG 58.824 41.667 5.07 0.00 39.21 4.17
470 471 5.416271 ACAAGTACTTTGATACGGATGGT 57.584 39.130 5.07 0.00 39.21 3.55
471 472 5.642063 ACAACAAGTACTTTGATACGGATGG 59.358 40.000 13.09 0.00 39.21 3.51
472 473 6.721571 ACAACAAGTACTTTGATACGGATG 57.278 37.500 13.09 5.27 39.21 3.51
473 474 7.548075 CCTAACAACAAGTACTTTGATACGGAT 59.452 37.037 13.09 0.00 39.21 4.18
474 475 6.869913 CCTAACAACAAGTACTTTGATACGGA 59.130 38.462 13.09 0.00 39.21 4.69
475 476 6.091713 CCCTAACAACAAGTACTTTGATACGG 59.908 42.308 13.09 6.36 39.21 4.02
476 477 6.091713 CCCCTAACAACAAGTACTTTGATACG 59.908 42.308 13.09 1.16 39.21 3.06
477 478 7.163441 TCCCCTAACAACAAGTACTTTGATAC 58.837 38.462 13.09 0.00 39.21 2.24
478 479 7.319052 TCCCCTAACAACAAGTACTTTGATA 57.681 36.000 13.09 5.89 39.21 2.15
479 480 6.195600 TCCCCTAACAACAAGTACTTTGAT 57.804 37.500 13.09 5.09 39.21 2.57
480 481 5.633655 TCCCCTAACAACAAGTACTTTGA 57.366 39.130 13.09 0.00 39.21 2.69
481 482 6.320418 AGTTTCCCCTAACAACAAGTACTTTG 59.680 38.462 5.07 5.54 42.68 2.77
482 483 6.429151 AGTTTCCCCTAACAACAAGTACTTT 58.571 36.000 5.07 0.00 0.00 2.66
483 484 6.009908 AGTTTCCCCTAACAACAAGTACTT 57.990 37.500 1.12 1.12 0.00 2.24
484 485 5.641789 AGTTTCCCCTAACAACAAGTACT 57.358 39.130 0.00 0.00 0.00 2.73
485 486 6.528321 ACTAGTTTCCCCTAACAACAAGTAC 58.472 40.000 0.00 0.00 0.00 2.73
486 487 6.752285 ACTAGTTTCCCCTAACAACAAGTA 57.248 37.500 0.00 0.00 0.00 2.24
487 488 5.641789 ACTAGTTTCCCCTAACAACAAGT 57.358 39.130 0.00 0.00 0.00 3.16
488 489 6.527423 TGTACTAGTTTCCCCTAACAACAAG 58.473 40.000 0.00 0.00 0.00 3.16
489 490 6.497624 TGTACTAGTTTCCCCTAACAACAA 57.502 37.500 0.00 0.00 0.00 2.83
490 491 6.497624 TTGTACTAGTTTCCCCTAACAACA 57.502 37.500 0.00 0.00 0.00 3.33
491 492 7.991084 ATTTGTACTAGTTTCCCCTAACAAC 57.009 36.000 0.00 0.00 0.00 3.32
492 493 7.666804 GGAATTTGTACTAGTTTCCCCTAACAA 59.333 37.037 10.93 5.90 31.60 2.83
493 494 7.170277 GGAATTTGTACTAGTTTCCCCTAACA 58.830 38.462 10.93 0.14 31.60 2.41
494 495 6.600822 GGGAATTTGTACTAGTTTCCCCTAAC 59.399 42.308 23.74 6.21 46.53 2.34
495 496 6.724351 GGGAATTTGTACTAGTTTCCCCTAA 58.276 40.000 23.74 4.18 46.53 2.69
496 497 6.317663 GGGAATTTGTACTAGTTTCCCCTA 57.682 41.667 23.74 0.00 46.53 3.53
497 498 5.188988 GGGAATTTGTACTAGTTTCCCCT 57.811 43.478 23.74 0.00 46.53 4.79
500 501 4.925836 TGGGGGAATTTGTACTAGTTTCC 58.074 43.478 12.95 12.95 36.04 3.13
501 502 6.008331 AGTTGGGGGAATTTGTACTAGTTTC 58.992 40.000 0.00 0.00 0.00 2.78
502 503 5.960704 AGTTGGGGGAATTTGTACTAGTTT 58.039 37.500 0.00 0.00 0.00 2.66
503 504 5.594199 AGTTGGGGGAATTTGTACTAGTT 57.406 39.130 0.00 0.00 0.00 2.24
504 505 6.903340 ATAGTTGGGGGAATTTGTACTAGT 57.097 37.500 0.00 0.00 0.00 2.57
505 506 8.491958 ACTTATAGTTGGGGGAATTTGTACTAG 58.508 37.037 0.00 0.00 0.00 2.57
506 507 8.396619 ACTTATAGTTGGGGGAATTTGTACTA 57.603 34.615 0.00 0.00 0.00 1.82
507 508 7.280044 ACTTATAGTTGGGGGAATTTGTACT 57.720 36.000 0.00 0.00 0.00 2.73
517 518 9.862149 ACTCAAATTTATACTTATAGTTGGGGG 57.138 33.333 0.00 0.00 0.00 5.40
544 545 5.783360 TGAAGGGAGTTGTTAGATAGACCAA 59.217 40.000 0.00 0.00 0.00 3.67
545 546 5.187186 GTGAAGGGAGTTGTTAGATAGACCA 59.813 44.000 0.00 0.00 0.00 4.02
557 558 0.040067 GCGCTTTGTGAAGGGAGTTG 60.040 55.000 0.00 0.00 45.78 3.16
559 560 0.886490 CAGCGCTTTGTGAAGGGAGT 60.886 55.000 7.50 0.00 45.78 3.85
571 572 2.113860 ATGTGGTTACATCAGCGCTT 57.886 45.000 7.50 0.00 44.00 4.68
585 586 5.065914 CAGGGACTACATATTTGGATGTGG 58.934 45.833 0.00 0.00 42.35 4.17
596 597 3.111484 TGCCATTGACAGGGACTACATA 58.889 45.455 0.00 0.00 36.02 2.29
645 646 4.862574 GCATGGCTCGTATTTATATCGTCA 59.137 41.667 0.00 0.00 0.00 4.35
649 650 3.001330 GGCGCATGGCTCGTATTTATATC 59.999 47.826 10.83 0.00 42.94 1.63
674 676 3.873952 GAGATCCTTGTGTGCATTAGGAC 59.126 47.826 10.14 6.22 39.47 3.85
675 677 3.776969 AGAGATCCTTGTGTGCATTAGGA 59.223 43.478 10.29 10.29 40.82 2.94
676 678 4.148128 AGAGATCCTTGTGTGCATTAGG 57.852 45.455 0.00 0.00 0.00 2.69
677 679 5.181009 TGAAGAGATCCTTGTGTGCATTAG 58.819 41.667 0.00 0.00 34.68 1.73
678 680 5.164620 TGAAGAGATCCTTGTGTGCATTA 57.835 39.130 0.00 0.00 34.68 1.90
679 681 4.025040 TGAAGAGATCCTTGTGTGCATT 57.975 40.909 0.00 0.00 34.68 3.56
774 789 2.513204 CAGTAGCAGCAGCCGCAT 60.513 61.111 2.79 0.00 43.56 4.73
777 792 0.877649 CATACCAGTAGCAGCAGCCG 60.878 60.000 0.00 0.00 43.56 5.52
778 793 0.179000 ACATACCAGTAGCAGCAGCC 59.821 55.000 0.00 0.00 43.56 4.85
779 794 2.029838 AACATACCAGTAGCAGCAGC 57.970 50.000 0.00 0.00 42.56 5.25
780 795 3.871594 GGTTAACATACCAGTAGCAGCAG 59.128 47.826 8.10 0.00 38.12 4.24
781 796 3.262151 TGGTTAACATACCAGTAGCAGCA 59.738 43.478 8.10 0.00 43.14 4.41
782 797 3.869065 TGGTTAACATACCAGTAGCAGC 58.131 45.455 8.10 0.00 43.14 5.25
792 807 3.617263 CGCTTCTCTGGTGGTTAACATAC 59.383 47.826 8.10 5.86 0.00 2.39
850 865 6.634805 TGAAGTGGACTCTTCTGATGATTAC 58.365 40.000 13.32 0.00 42.76 1.89
863 878 2.440539 TTTCGAGCTGAAGTGGACTC 57.559 50.000 0.00 0.00 37.99 3.36
864 879 2.103263 AGTTTTCGAGCTGAAGTGGACT 59.897 45.455 0.00 0.00 37.99 3.85
1160 1191 4.136511 TAATCACGGCGAGCGGCA 62.137 61.111 16.62 0.00 46.16 5.69
1200 1231 0.952010 GCCGGTTGTACATGAACGGT 60.952 55.000 21.80 0.00 42.98 4.83
1471 1505 3.702330 TGTACAAATATCTCTCGCGGTG 58.298 45.455 6.13 0.00 0.00 4.94
1550 1585 4.253685 GTTCACACACTATACACCAGCAT 58.746 43.478 0.00 0.00 0.00 3.79
1551 1586 3.556213 GGTTCACACACTATACACCAGCA 60.556 47.826 0.00 0.00 0.00 4.41
1552 1587 3.000727 GGTTCACACACTATACACCAGC 58.999 50.000 0.00 0.00 0.00 4.85
1553 1588 3.250744 CGGTTCACACACTATACACCAG 58.749 50.000 0.00 0.00 0.00 4.00
1554 1589 2.629137 ACGGTTCACACACTATACACCA 59.371 45.455 0.00 0.00 0.00 4.17
1555 1590 3.308438 ACGGTTCACACACTATACACC 57.692 47.619 0.00 0.00 0.00 4.16
1605 1644 3.577805 TCCTGACGTCTGAGATATCCA 57.422 47.619 22.46 0.00 0.00 3.41
1617 1656 0.833287 CCTTCATGGGATCCTGACGT 59.167 55.000 12.58 0.00 0.00 4.34
1639 1678 3.249799 TGTGTAATTTGGCAGTCAGTTCG 59.750 43.478 0.00 0.00 0.00 3.95
1643 1682 5.163513 GGAAATGTGTAATTTGGCAGTCAG 58.836 41.667 0.00 0.00 0.00 3.51
1647 1686 4.925054 CACTGGAAATGTGTAATTTGGCAG 59.075 41.667 0.00 0.00 0.00 4.85
1662 1701 3.876914 GTCTCACATGTTGACACTGGAAA 59.123 43.478 18.57 0.00 0.00 3.13
1733 1772 6.121590 TGAGTACATTGGCATTATGTCATGT 58.878 36.000 8.03 15.15 37.42 3.21
1754 1793 7.689446 ATCTCATTATTGCATTCCTGATGAG 57.311 36.000 12.79 12.79 40.00 2.90
1796 1835 6.471198 GGCTTGCTTCCGTTTTATGTATTTAC 59.529 38.462 0.00 0.00 0.00 2.01
1860 1899 6.406370 CATTCATTCACCTCCTACTACAACA 58.594 40.000 0.00 0.00 0.00 3.33
1861 1900 5.294552 GCATTCATTCACCTCCTACTACAAC 59.705 44.000 0.00 0.00 0.00 3.32
1862 1901 5.045942 TGCATTCATTCACCTCCTACTACAA 60.046 40.000 0.00 0.00 0.00 2.41
1864 1903 5.023533 TGCATTCATTCACCTCCTACTAC 57.976 43.478 0.00 0.00 0.00 2.73
1865 1904 5.366477 TCATGCATTCATTCACCTCCTACTA 59.634 40.000 0.00 0.00 0.00 1.82
1925 2014 1.764054 CTCTCGGATGCCTCCCCTT 60.764 63.158 2.04 0.00 38.45 3.95
1926 2015 2.123077 CTCTCGGATGCCTCCCCT 60.123 66.667 2.04 0.00 38.45 4.79
2005 2097 8.712363 GCGTGTCATGTATATGATCAACTATTT 58.288 33.333 5.38 0.00 44.62 1.40
2075 2168 5.409520 TGCATGTCTCTGTCTGTAACATTTC 59.590 40.000 0.00 0.00 37.23 2.17
2160 2253 2.775384 AGGAATAACAACCTATGGCCGA 59.225 45.455 0.00 0.00 34.47 5.54
2163 2256 4.523083 TCACAGGAATAACAACCTATGGC 58.477 43.478 0.00 0.00 32.30 4.40
2218 2311 5.714806 CAGAACCATTAACCCCATACTTGTT 59.285 40.000 0.00 0.00 0.00 2.83
2323 2416 0.316204 GACAATGCAGCCACTTTGCT 59.684 50.000 0.00 0.00 44.00 3.91
2340 2433 7.203910 AGATTATCATAACCAAGAGTCACGAC 58.796 38.462 0.00 0.00 0.00 4.34
2369 2472 6.747280 CCAAATATCTAAAAACAGCTTCACCG 59.253 38.462 0.00 0.00 0.00 4.94
2414 2519 6.258507 CCTTTTTGAAACTGGGTCATGAAAAG 59.741 38.462 0.00 0.00 35.00 2.27


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

AutoCloner maintained by Alex Coulton.