Multiple sequence alignment - TraesCS7A01G273900

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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 TraesCS7A01G273900 chr7A 100.000 2540 0 0 1 2540 287481908 287484447 0.000000e+00 4691
1 TraesCS7A01G273900 chr7A 82.101 1447 142 63 319 1708 287472089 287473475 0.000000e+00 1129
2 TraesCS7A01G273900 chr7A 83.448 1015 161 7 883 1895 287494211 287495220 0.000000e+00 937
3 TraesCS7A01G273900 chr7A 90.094 212 18 3 1704 1913 287473779 287473989 3.220000e-69 272
4 TraesCS7A01G273900 chr7A 88.038 209 11 4 2123 2323 287527551 287527753 4.220000e-58 235
5 TraesCS7A01G273900 chr7A 82.941 170 21 5 2160 2328 287493246 287493408 2.040000e-31 147
6 TraesCS7A01G273900 chr7A 94.118 85 5 0 2001 2085 287477052 287477136 2.050000e-26 130
7 TraesCS7A01G273900 chr7D 87.018 1687 132 38 359 1999 264026224 264027869 0.000000e+00 1821
8 TraesCS7A01G273900 chr7D 83.057 1328 133 45 1286 2539 264052648 264053957 0.000000e+00 1122
9 TraesCS7A01G273900 chr7D 84.641 905 128 8 940 1841 264028918 264029814 0.000000e+00 891
10 TraesCS7A01G273900 chr7D 85.392 842 115 6 940 1776 264054417 264055255 0.000000e+00 867
11 TraesCS7A01G273900 chr7D 81.471 1020 161 14 883 1894 264056338 264057337 0.000000e+00 811
12 TraesCS7A01G273900 chr7D 90.625 576 30 11 1985 2540 264027891 264028462 0.000000e+00 743
13 TraesCS7A01G273900 chr7D 83.456 272 28 7 2068 2328 264055556 264055821 1.170000e-58 237
14 TraesCS7A01G273900 chr7D 80.319 188 20 6 2153 2328 264035920 264036102 2.650000e-25 126
15 TraesCS7A01G273900 chr7B 85.426 1338 117 40 599 1901 244393728 244395022 0.000000e+00 1319
16 TraesCS7A01G273900 chr7B 84.331 919 137 5 972 1890 244396264 244397175 0.000000e+00 893
17 TraesCS7A01G273900 chr7B 84.684 901 123 11 884 1776 244404999 244405892 0.000000e+00 885
18 TraesCS7A01G273900 chr7B 90.141 355 19 8 2196 2538 244395447 244395797 4.980000e-122 448
19 TraesCS7A01G273900 chr7B 84.395 314 22 9 1925 2211 244395076 244395389 1.490000e-72 283
20 TraesCS7A01G273900 chr7B 84.191 272 25 8 2068 2328 244411145 244411409 5.430000e-62 248
21 TraesCS7A01G273900 chr7B 82.873 181 14 6 2160 2328 244406214 244406389 2.040000e-31 147


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 TraesCS7A01G273900 chr7A 287481908 287484447 2539 False 4691.000000 4691 100.00000 1 2540 1 chr7A.!!$F1 2539
1 TraesCS7A01G273900 chr7A 287493246 287495220 1974 False 542.000000 937 83.19450 883 2328 2 chr7A.!!$F4 1445
2 TraesCS7A01G273900 chr7A 287472089 287477136 5047 False 510.333333 1129 88.77100 319 2085 3 chr7A.!!$F3 1766
3 TraesCS7A01G273900 chr7D 264026224 264029814 3590 False 1151.666667 1821 87.42800 359 2540 3 chr7D.!!$F2 2181
4 TraesCS7A01G273900 chr7D 264052648 264057337 4689 False 759.250000 1122 83.34400 883 2539 4 chr7D.!!$F3 1656
5 TraesCS7A01G273900 chr7B 244393728 244397175 3447 False 735.750000 1319 86.07325 599 2538 4 chr7B.!!$F2 1939
6 TraesCS7A01G273900 chr7B 244404999 244406389 1390 False 516.000000 885 83.77850 884 2328 2 chr7B.!!$F3 1444

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
496 516 0.034089 GCTAGGGATGCCAACAACCT 60.034 55.0 5.86 0.0 38.73 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 4637 0.251077 AGGGGCTTTGCTCTTCTGTG 60.251 55.0 0.0 0.0 0.0 3.66 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.309388 GGACTCATCCATACATTCGACG 58.691 50.000 0.00 0.00 45.47 5.12
28 29 3.243434 GGACTCATCCATACATTCGACGT 60.243 47.826 0.00 0.00 45.47 4.34
29 30 3.706698 ACTCATCCATACATTCGACGTG 58.293 45.455 0.00 0.00 0.00 4.49
30 31 3.130516 ACTCATCCATACATTCGACGTGT 59.869 43.478 0.00 7.67 0.00 4.49
31 32 3.443976 TCATCCATACATTCGACGTGTG 58.556 45.455 11.76 8.07 0.00 3.82
32 33 3.119280 TCATCCATACATTCGACGTGTGT 60.119 43.478 11.76 11.37 0.00 3.72
33 34 2.601804 TCCATACATTCGACGTGTGTG 58.398 47.619 15.63 15.63 38.11 3.82
35 36 2.344441 CCATACATTCGACGTGTGTGAC 59.656 50.000 21.11 0.00 39.98 3.67
46 47 2.554806 GTGTGTGACGATACGATGGA 57.445 50.000 0.00 0.00 0.00 3.41
47 48 3.079960 GTGTGTGACGATACGATGGAT 57.920 47.619 0.00 0.00 0.00 3.41
48 49 3.444916 GTGTGTGACGATACGATGGATT 58.555 45.455 0.00 0.00 0.00 3.01
49 50 3.486108 GTGTGTGACGATACGATGGATTC 59.514 47.826 0.00 0.00 0.00 2.52
50 51 3.129638 TGTGTGACGATACGATGGATTCA 59.870 43.478 0.00 0.00 0.00 2.57
51 52 3.731216 GTGTGACGATACGATGGATTCAG 59.269 47.826 0.00 0.00 0.00 3.02
53 54 3.731216 GTGACGATACGATGGATTCAGTG 59.269 47.826 0.00 0.00 0.00 3.66
54 55 3.243401 TGACGATACGATGGATTCAGTGG 60.243 47.826 0.00 0.00 0.00 4.00
55 56 2.035961 ACGATACGATGGATTCAGTGGG 59.964 50.000 0.00 0.00 0.00 4.61
57 58 0.468226 TACGATGGATTCAGTGGGGC 59.532 55.000 0.00 0.00 0.00 5.80
58 59 1.274703 ACGATGGATTCAGTGGGGCT 61.275 55.000 0.00 0.00 0.00 5.19
59 60 0.816825 CGATGGATTCAGTGGGGCTG 60.817 60.000 0.00 0.00 46.34 4.85
61 62 2.440980 GGATTCAGTGGGGCTGGC 60.441 66.667 0.00 0.00 45.08 4.85
62 63 2.679716 GATTCAGTGGGGCTGGCT 59.320 61.111 0.00 0.00 45.08 4.75
64 65 3.951769 ATTCAGTGGGGCTGGCTGC 62.952 63.158 7.96 7.96 45.08 5.25
66 67 3.720601 CAGTGGGGCTGGCTGCTA 61.721 66.667 16.14 0.00 41.42 3.49
68 69 2.751837 GTGGGGCTGGCTGCTAAC 60.752 66.667 16.14 8.30 42.39 2.34
69 70 4.047125 TGGGGCTGGCTGCTAACC 62.047 66.667 16.14 15.24 42.39 2.85
70 71 4.047125 GGGGCTGGCTGCTAACCA 62.047 66.667 16.14 0.00 42.39 3.67
71 72 2.276740 GGGCTGGCTGCTAACCAT 59.723 61.111 16.14 0.00 42.39 3.55
72 73 1.825622 GGGCTGGCTGCTAACCATC 60.826 63.158 16.14 0.00 42.39 3.51
73 74 1.077501 GGCTGGCTGCTAACCATCA 60.078 57.895 16.14 0.00 42.39 3.07
74 75 1.099879 GGCTGGCTGCTAACCATCAG 61.100 60.000 16.14 0.00 42.39 2.90
75 76 0.107508 GCTGGCTGCTAACCATCAGA 60.108 55.000 9.31 0.00 36.36 3.27
77 78 1.483827 CTGGCTGCTAACCATCAGAGA 59.516 52.381 0.00 0.00 36.36 3.10
78 79 2.104451 CTGGCTGCTAACCATCAGAGAT 59.896 50.000 0.00 0.00 36.36 2.75
79 80 2.507058 TGGCTGCTAACCATCAGAGATT 59.493 45.455 0.00 0.00 32.26 2.40
80 81 3.137533 GGCTGCTAACCATCAGAGATTC 58.862 50.000 0.00 0.00 32.26 2.52
83 84 5.453903 GGCTGCTAACCATCAGAGATTCTTA 60.454 44.000 0.00 0.00 32.26 2.10
84 85 5.695816 GCTGCTAACCATCAGAGATTCTTAG 59.304 44.000 0.00 0.00 32.26 2.18
85 86 6.685116 GCTGCTAACCATCAGAGATTCTTAGT 60.685 42.308 0.00 0.00 32.26 2.24
86 87 7.470702 GCTGCTAACCATCAGAGATTCTTAGTA 60.471 40.741 0.00 0.00 32.26 1.82
88 89 7.014711 TGCTAACCATCAGAGATTCTTAGTAGG 59.985 40.741 0.00 0.00 0.00 3.18
90 91 6.031964 ACCATCAGAGATTCTTAGTAGGGA 57.968 41.667 0.00 0.00 0.00 4.20
91 92 6.629156 ACCATCAGAGATTCTTAGTAGGGAT 58.371 40.000 0.00 0.00 0.00 3.85
92 93 6.496565 ACCATCAGAGATTCTTAGTAGGGATG 59.503 42.308 0.00 0.00 0.00 3.51
94 95 7.234371 CCATCAGAGATTCTTAGTAGGGATGAA 59.766 40.741 0.00 0.00 32.34 2.57
95 96 8.814931 CATCAGAGATTCTTAGTAGGGATGAAT 58.185 37.037 0.00 0.00 32.34 2.57
96 97 8.187913 TCAGAGATTCTTAGTAGGGATGAATG 57.812 38.462 0.00 0.00 0.00 2.67
97 98 6.873076 CAGAGATTCTTAGTAGGGATGAATGC 59.127 42.308 0.00 0.00 0.00 3.56
98 99 6.556495 AGAGATTCTTAGTAGGGATGAATGCA 59.444 38.462 0.00 0.00 0.00 3.96
99 100 7.237263 AGAGATTCTTAGTAGGGATGAATGCAT 59.763 37.037 0.00 0.00 37.47 3.96
115 116 0.449388 GCATCAGCACAAGTACAGGC 59.551 55.000 0.00 0.00 41.58 4.85
117 118 1.736126 CATCAGCACAAGTACAGGCAG 59.264 52.381 0.00 0.00 0.00 4.85
118 119 0.035317 TCAGCACAAGTACAGGCAGG 59.965 55.000 0.00 0.00 0.00 4.85
119 120 1.302832 AGCACAAGTACAGGCAGGC 60.303 57.895 0.00 0.00 0.00 4.85
120 121 1.302832 GCACAAGTACAGGCAGGCT 60.303 57.895 0.00 0.00 0.00 4.58
121 122 1.580845 GCACAAGTACAGGCAGGCTG 61.581 60.000 22.19 22.19 0.00 4.85
122 123 1.302832 ACAAGTACAGGCAGGCTGC 60.303 57.895 30.93 30.93 44.08 5.25
124 125 1.023513 CAAGTACAGGCAGGCTGCTC 61.024 60.000 35.73 25.78 44.28 4.26
127 128 1.920325 TACAGGCAGGCTGCTCCTT 60.920 57.895 35.73 20.80 44.75 3.36
128 129 1.492133 TACAGGCAGGCTGCTCCTTT 61.492 55.000 35.73 21.48 44.75 3.11
129 130 1.605738 CAGGCAGGCTGCTCCTTTT 60.606 57.895 35.73 13.98 44.75 2.27
130 131 1.605738 AGGCAGGCTGCTCCTTTTG 60.606 57.895 35.73 0.00 44.75 2.44
132 133 2.968206 CAGGCTGCTCCTTTTGGC 59.032 61.111 0.00 0.00 44.75 4.52
134 135 1.605738 AGGCTGCTCCTTTTGGCTG 60.606 57.895 0.00 0.00 44.75 4.85
135 136 2.260743 GCTGCTCCTTTTGGCTGC 59.739 61.111 0.00 0.00 43.58 5.25
136 137 2.968206 CTGCTCCTTTTGGCTGCC 59.032 61.111 12.87 12.87 40.12 4.85
137 138 1.605738 CTGCTCCTTTTGGCTGCCT 60.606 57.895 21.03 0.00 40.12 4.75
138 139 1.152483 TGCTCCTTTTGGCTGCCTT 60.152 52.632 21.03 0.00 40.12 4.35
139 140 1.291272 GCTCCTTTTGGCTGCCTTG 59.709 57.895 21.03 6.99 40.12 3.61
140 141 1.466851 GCTCCTTTTGGCTGCCTTGT 61.467 55.000 21.03 0.00 40.12 3.16
141 142 1.043022 CTCCTTTTGGCTGCCTTGTT 58.957 50.000 21.03 0.00 40.12 2.83
142 143 0.752054 TCCTTTTGGCTGCCTTGTTG 59.248 50.000 21.03 6.02 40.12 3.33
143 144 0.249996 CCTTTTGGCTGCCTTGTTGG 60.250 55.000 21.03 11.46 39.35 3.77
144 145 0.465287 CTTTTGGCTGCCTTGTTGGT 59.535 50.000 21.03 0.00 38.35 3.67
145 146 1.686052 CTTTTGGCTGCCTTGTTGGTA 59.314 47.619 21.03 0.00 38.35 3.25
146 147 1.036707 TTTGGCTGCCTTGTTGGTAC 58.963 50.000 21.03 0.00 38.35 3.34
148 149 2.332654 GGCTGCCTTGTTGGTACGG 61.333 63.158 12.43 0.00 38.35 4.02
150 151 0.320946 GCTGCCTTGTTGGTACGGTA 60.321 55.000 0.00 0.00 38.35 4.02
152 153 1.001633 CTGCCTTGTTGGTACGGTACT 59.998 52.381 17.14 0.00 38.35 2.73
153 154 2.231964 CTGCCTTGTTGGTACGGTACTA 59.768 50.000 17.14 9.23 38.35 1.82
154 155 2.029110 TGCCTTGTTGGTACGGTACTAC 60.029 50.000 17.14 15.01 38.35 2.73
155 156 2.867429 CCTTGTTGGTACGGTACTACG 58.133 52.381 17.14 5.52 40.31 3.51
158 159 4.380867 CCTTGTTGGTACGGTACTACGAAT 60.381 45.833 17.14 0.00 37.61 3.34
159 160 4.355543 TGTTGGTACGGTACTACGAATC 57.644 45.455 17.14 0.54 37.61 2.52
161 162 4.098416 GTTGGTACGGTACTACGAATCAC 58.902 47.826 17.14 2.71 37.61 3.06
206 207 8.950210 ACTATAATTCAGGTGTTTCAGATTGTG 58.050 33.333 0.00 0.00 0.00 3.33
207 208 3.988379 TTCAGGTGTTTCAGATTGTGC 57.012 42.857 0.00 0.00 0.00 4.57
208 209 2.229792 TCAGGTGTTTCAGATTGTGCC 58.770 47.619 0.00 0.00 0.00 5.01
209 210 1.955778 CAGGTGTTTCAGATTGTGCCA 59.044 47.619 0.00 0.00 0.00 4.92
210 211 2.361757 CAGGTGTTTCAGATTGTGCCAA 59.638 45.455 0.00 0.00 0.00 4.52
211 212 3.030291 AGGTGTTTCAGATTGTGCCAAA 58.970 40.909 0.00 0.00 0.00 3.28
212 213 3.642848 AGGTGTTTCAGATTGTGCCAAAT 59.357 39.130 0.00 0.00 0.00 2.32
213 214 4.101430 AGGTGTTTCAGATTGTGCCAAATT 59.899 37.500 0.00 0.00 0.00 1.82
215 216 5.988561 GGTGTTTCAGATTGTGCCAAATTTA 59.011 36.000 0.00 0.00 0.00 1.40
216 217 6.650390 GGTGTTTCAGATTGTGCCAAATTTAT 59.350 34.615 0.00 0.00 0.00 1.40
217 218 7.816995 GGTGTTTCAGATTGTGCCAAATTTATA 59.183 33.333 0.00 0.00 0.00 0.98
219 220 8.584157 TGTTTCAGATTGTGCCAAATTTATACT 58.416 29.630 0.00 0.00 0.00 2.12
223 224 9.625747 TCAGATTGTGCCAAATTTATACTATCA 57.374 29.630 16.95 4.19 0.00 2.15
224 225 9.888878 CAGATTGTGCCAAATTTATACTATCAG 57.111 33.333 16.95 10.45 0.00 2.90
225 226 8.571336 AGATTGTGCCAAATTTATACTATCAGC 58.429 33.333 16.95 0.00 0.00 4.26
226 227 6.299023 TGTGCCAAATTTATACTATCAGCG 57.701 37.500 0.00 0.00 0.00 5.18
228 229 6.202762 TGTGCCAAATTTATACTATCAGCGAG 59.797 38.462 0.00 0.00 0.00 5.03
230 231 5.668866 GCCAAATTTATACTATCAGCGAGCG 60.669 44.000 0.00 0.00 0.00 5.03
231 232 5.308927 CAAATTTATACTATCAGCGAGCGC 58.691 41.667 6.78 6.78 42.33 5.92
232 233 3.636282 TTTATACTATCAGCGAGCGCA 57.364 42.857 17.68 0.00 44.88 6.09
233 234 2.902065 TATACTATCAGCGAGCGCAG 57.098 50.000 17.68 9.37 44.88 5.18
235 236 0.588737 TACTATCAGCGAGCGCAGAG 59.411 55.000 17.68 6.48 44.88 3.35
245 246 3.446570 GCGCAGAGCCAAGCCAAT 61.447 61.111 0.30 0.00 40.81 3.16
247 248 1.748122 CGCAGAGCCAAGCCAATCT 60.748 57.895 0.00 0.00 0.00 2.40
248 249 1.712977 CGCAGAGCCAAGCCAATCTC 61.713 60.000 0.00 0.00 0.00 2.75
249 250 1.712977 GCAGAGCCAAGCCAATCTCG 61.713 60.000 0.00 0.00 0.00 4.04
250 251 1.451028 AGAGCCAAGCCAATCTCGC 60.451 57.895 0.00 0.00 0.00 5.03
251 252 1.746615 GAGCCAAGCCAATCTCGCA 60.747 57.895 0.00 0.00 0.00 5.10
252 253 1.986575 GAGCCAAGCCAATCTCGCAC 61.987 60.000 0.00 0.00 0.00 5.34
253 254 2.042831 GCCAAGCCAATCTCGCACT 61.043 57.895 0.00 0.00 0.00 4.40
254 255 1.986575 GCCAAGCCAATCTCGCACTC 61.987 60.000 0.00 0.00 0.00 3.51
255 256 1.699656 CCAAGCCAATCTCGCACTCG 61.700 60.000 0.00 0.00 0.00 4.18
256 257 2.103042 AAGCCAATCTCGCACTCGC 61.103 57.895 0.00 0.00 35.26 5.03
257 258 2.786539 AAGCCAATCTCGCACTCGCA 62.787 55.000 0.00 0.00 38.40 5.10
259 260 1.446792 CCAATCTCGCACTCGCACT 60.447 57.895 0.00 0.00 38.40 4.40
261 262 1.153745 AATCTCGCACTCGCACTCC 60.154 57.895 0.00 0.00 38.40 3.85
262 263 2.564553 AATCTCGCACTCGCACTCCC 62.565 60.000 0.00 0.00 38.40 4.30
263 264 4.056125 CTCGCACTCGCACTCCCA 62.056 66.667 0.00 0.00 38.40 4.37
264 265 4.357947 TCGCACTCGCACTCCCAC 62.358 66.667 0.00 0.00 38.40 4.61
266 267 4.314440 GCACTCGCACTCCCACCA 62.314 66.667 0.00 0.00 38.36 4.17
267 268 2.047844 CACTCGCACTCCCACCAG 60.048 66.667 0.00 0.00 0.00 4.00
269 270 4.007644 CTCGCACTCCCACCAGCA 62.008 66.667 0.00 0.00 0.00 4.41
270 271 3.535629 CTCGCACTCCCACCAGCAA 62.536 63.158 0.00 0.00 0.00 3.91
271 272 2.594303 CGCACTCCCACCAGCAAA 60.594 61.111 0.00 0.00 0.00 3.68
272 273 2.192861 CGCACTCCCACCAGCAAAA 61.193 57.895 0.00 0.00 0.00 2.44
273 274 1.526575 CGCACTCCCACCAGCAAAAT 61.527 55.000 0.00 0.00 0.00 1.82
274 275 0.037975 GCACTCCCACCAGCAAAATG 60.038 55.000 0.00 0.00 0.00 2.32
275 276 1.619654 CACTCCCACCAGCAAAATGA 58.380 50.000 0.00 0.00 0.00 2.57
277 278 2.094390 CACTCCCACCAGCAAAATGATG 60.094 50.000 0.00 0.00 32.77 3.07
284 285 4.575076 GCAAAATGATGCGGCACA 57.425 50.000 4.03 6.25 36.45 4.57
286 287 2.206815 GCAAAATGATGCGGCACATA 57.793 45.000 4.03 0.00 39.84 2.29
287 288 2.121786 GCAAAATGATGCGGCACATAG 58.878 47.619 4.03 6.53 39.84 2.23
289 290 3.734597 GCAAAATGATGCGGCACATAGAA 60.735 43.478 4.03 0.00 39.84 2.10
291 292 4.924305 AAATGATGCGGCACATAGAAAT 57.076 36.364 4.03 0.00 39.84 2.17
292 293 6.207928 CAAAATGATGCGGCACATAGAAATA 58.792 36.000 4.03 0.00 39.84 1.40
293 294 5.362556 AATGATGCGGCACATAGAAATAC 57.637 39.130 4.03 0.00 39.84 1.89
294 295 4.071961 TGATGCGGCACATAGAAATACT 57.928 40.909 4.03 0.00 39.84 2.12
296 297 2.833794 TGCGGCACATAGAAATACTCC 58.166 47.619 0.00 0.00 0.00 3.85
297 298 2.434336 TGCGGCACATAGAAATACTCCT 59.566 45.455 0.00 0.00 0.00 3.69
299 300 3.988517 GCGGCACATAGAAATACTCCTAC 59.011 47.826 0.00 0.00 0.00 3.18
301 302 5.462405 CGGCACATAGAAATACTCCTACTC 58.538 45.833 0.00 0.00 0.00 2.59
302 303 5.241949 CGGCACATAGAAATACTCCTACTCT 59.758 44.000 0.00 0.00 0.00 3.24
303 304 6.430308 CGGCACATAGAAATACTCCTACTCTA 59.570 42.308 0.00 0.00 0.00 2.43
304 305 7.573469 CGGCACATAGAAATACTCCTACTCTAC 60.573 44.444 0.00 0.00 0.00 2.59
306 307 8.852135 GCACATAGAAATACTCCTACTCTACTT 58.148 37.037 0.00 0.00 0.00 2.24
308 309 9.577222 ACATAGAAATACTCCTACTCTACTTCC 57.423 37.037 0.00 0.00 0.00 3.46
309 310 9.016438 CATAGAAATACTCCTACTCTACTTCCC 57.984 40.741 0.00 0.00 0.00 3.97
310 311 7.228652 AGAAATACTCCTACTCTACTTCCCT 57.771 40.000 0.00 0.00 0.00 4.20
311 312 7.292319 AGAAATACTCCTACTCTACTTCCCTC 58.708 42.308 0.00 0.00 0.00 4.30
313 314 6.790177 ATACTCCTACTCTACTTCCCTCAT 57.210 41.667 0.00 0.00 0.00 2.90
314 315 5.056553 ACTCCTACTCTACTTCCCTCATC 57.943 47.826 0.00 0.00 0.00 2.92
315 316 4.729881 ACTCCTACTCTACTTCCCTCATCT 59.270 45.833 0.00 0.00 0.00 2.90
317 318 4.141135 TCCTACTCTACTTCCCTCATCTGG 60.141 50.000 0.00 0.00 0.00 3.86
318 319 2.393646 ACTCTACTTCCCTCATCTGGC 58.606 52.381 0.00 0.00 0.00 4.85
320 321 2.364970 CTCTACTTCCCTCATCTGGCAG 59.635 54.545 8.58 8.58 0.00 4.85
321 322 0.833287 TACTTCCCTCATCTGGCAGC 59.167 55.000 10.34 0.00 0.00 5.25
322 323 1.203441 ACTTCCCTCATCTGGCAGCA 61.203 55.000 10.34 0.00 0.00 4.41
323 324 0.034767 CTTCCCTCATCTGGCAGCAA 60.035 55.000 10.34 0.00 0.00 3.91
324 325 0.405198 TTCCCTCATCTGGCAGCAAA 59.595 50.000 10.34 0.00 0.00 3.68
375 376 0.609131 CTTTCCCTTGGACGCCACAT 60.609 55.000 0.00 0.00 30.78 3.21
378 379 0.907704 TCCCTTGGACGCCACATACT 60.908 55.000 0.00 0.00 30.78 2.12
380 381 1.472728 CCCTTGGACGCCACATACTAC 60.473 57.143 0.00 0.00 30.78 2.73
430 437 2.681976 CGAATCCCTTTCATCTGCAGGT 60.682 50.000 15.13 2.68 33.66 4.00
432 439 3.853355 ATCCCTTTCATCTGCAGGTAG 57.147 47.619 15.13 0.35 0.00 3.18
433 440 1.839994 TCCCTTTCATCTGCAGGTAGG 59.160 52.381 15.13 10.70 0.00 3.18
440 456 1.338337 CATCTGCAGGTAGGTACTCCG 59.662 57.143 15.13 0.00 41.75 4.63
482 502 3.745975 TGTTTCGATTTGTCACAGCTAGG 59.254 43.478 0.00 0.00 0.00 3.02
487 507 2.113860 TTTGTCACAGCTAGGGATGC 57.886 50.000 0.00 0.00 31.14 3.91
496 516 0.034089 GCTAGGGATGCCAACAACCT 60.034 55.000 5.86 0.00 38.73 3.50
511 548 1.806542 CAACCTTCCTTCCATGTGTCG 59.193 52.381 0.00 0.00 0.00 4.35
539 584 1.301423 GTTGGGTCACACAACGCTAA 58.699 50.000 7.28 0.00 38.83 3.09
633 678 1.439353 CCCCAACATGCTTCGATCGG 61.439 60.000 16.41 0.48 0.00 4.18
638 683 0.391661 ACATGCTTCGATCGGCACTT 60.392 50.000 19.12 8.12 41.39 3.16
677 725 4.142381 ACCTGTGCTGTTTTGTTTCTTCTC 60.142 41.667 0.00 0.00 0.00 2.87
682 730 5.513141 GTGCTGTTTTGTTTCTTCTCTTCAC 59.487 40.000 0.00 0.00 0.00 3.18
684 734 6.127647 TGCTGTTTTGTTTCTTCTCTTCACAT 60.128 34.615 0.00 0.00 0.00 3.21
704 754 2.859165 TCATCTGAACCCAACAGACC 57.141 50.000 0.00 0.00 45.19 3.85
730 780 1.284657 CGTGCATCTTACTCTGCTGG 58.715 55.000 0.00 0.00 39.16 4.85
732 782 0.907486 TGCATCTTACTCTGCTGGCT 59.093 50.000 0.00 0.00 39.16 4.75
733 783 1.297664 GCATCTTACTCTGCTGGCTG 58.702 55.000 0.00 0.00 35.49 4.85
768 833 3.074412 AGTTAGGAACAAACAGGATGCG 58.926 45.455 0.00 0.00 42.53 4.73
806 871 4.838046 TCGCCAACGACTGAAACA 57.162 50.000 0.00 0.00 45.12 2.83
807 872 3.299050 TCGCCAACGACTGAAACAT 57.701 47.368 0.00 0.00 45.12 2.71
808 873 0.865111 TCGCCAACGACTGAAACATG 59.135 50.000 0.00 0.00 45.12 3.21
810 875 0.387239 GCCAACGACTGAAACATGCC 60.387 55.000 0.00 0.00 0.00 4.40
861 926 5.752955 GCTTGTCTAGATGAGATTCTTGGTC 59.247 44.000 0.00 0.00 36.29 4.02
865 930 5.010617 GTCTAGATGAGATTCTTGGTCTCCC 59.989 48.000 0.00 0.00 41.08 4.30
895 1963 7.624549 TCTCTTCATCCCATATAAATACAGGC 58.375 38.462 0.00 0.00 0.00 4.85
923 1991 3.840437 GCCTTCAGCACCAACACA 58.160 55.556 0.00 0.00 42.97 3.72
924 1992 2.344535 GCCTTCAGCACCAACACAT 58.655 52.632 0.00 0.00 42.97 3.21
925 1993 0.675633 GCCTTCAGCACCAACACATT 59.324 50.000 0.00 0.00 42.97 2.71
926 1994 1.603678 GCCTTCAGCACCAACACATTG 60.604 52.381 0.00 0.00 42.97 2.82
927 1995 1.603678 CCTTCAGCACCAACACATTGC 60.604 52.381 0.00 0.00 34.17 3.56
928 1996 1.067364 CTTCAGCACCAACACATTGCA 59.933 47.619 0.00 0.00 38.81 4.08
929 1997 0.669619 TCAGCACCAACACATTGCAG 59.330 50.000 0.00 0.00 38.81 4.41
930 1998 0.942410 CAGCACCAACACATTGCAGC 60.942 55.000 0.00 0.00 38.81 5.25
931 1999 1.111116 AGCACCAACACATTGCAGCT 61.111 50.000 0.00 0.00 38.69 4.24
932 2000 0.597568 GCACCAACACATTGCAGCTA 59.402 50.000 0.00 0.00 36.22 3.32
933 2001 1.401931 GCACCAACACATTGCAGCTAG 60.402 52.381 0.00 0.00 36.22 3.42
934 2002 0.883833 ACCAACACATTGCAGCTAGC 59.116 50.000 6.62 6.62 45.96 3.42
935 2003 0.171903 CCAACACATTGCAGCTAGCC 59.828 55.000 12.13 0.00 44.83 3.93
936 2004 1.171308 CAACACATTGCAGCTAGCCT 58.829 50.000 12.13 0.00 44.83 4.58
937 2005 1.542915 CAACACATTGCAGCTAGCCTT 59.457 47.619 12.13 0.00 44.83 4.35
938 2006 1.457346 ACACATTGCAGCTAGCCTTC 58.543 50.000 12.13 0.99 44.83 3.46
953 2021 4.008916 AGCCTTCCCTACCATTCTCTTA 57.991 45.455 0.00 0.00 0.00 2.10
959 2042 7.445945 CCTTCCCTACCATTCTCTTACATTAG 58.554 42.308 0.00 0.00 0.00 1.73
978 2066 5.794687 TTAGCATACACAAGGAAACATCG 57.205 39.130 0.00 0.00 0.00 3.84
1140 2229 2.835580 CCATGTGCCATGGTTTGAAA 57.164 45.000 20.23 0.00 34.56 2.69
1168 2257 2.481854 CAGACATCTACAGCTGCATCC 58.518 52.381 15.27 0.00 0.00 3.51
1292 2381 2.872557 CAACGCCATGCAGGACAG 59.127 61.111 0.00 0.00 41.22 3.51
1546 4611 4.832248 TGTCGAAGCAAATTGAGATACCT 58.168 39.130 0.00 0.00 0.00 3.08
1572 4637 4.214332 GTGGTCTCTTGTCTCCAAAACATC 59.786 45.833 0.00 0.00 0.00 3.06
1573 4638 4.141505 TGGTCTCTTGTCTCCAAAACATCA 60.142 41.667 0.00 0.00 0.00 3.07
1589 4654 1.471684 CATCACAGAAGAGCAAAGCCC 59.528 52.381 0.00 0.00 0.00 5.19
1591 4656 0.251077 CACAGAAGAGCAAAGCCCCT 60.251 55.000 0.00 0.00 0.00 4.79
1639 4704 3.386078 TGGAGCACAGTATTGGAGATCTC 59.614 47.826 14.75 14.75 0.00 2.75
1646 4711 3.567585 CAGTATTGGAGATCTCGAGAGCA 59.432 47.826 30.48 12.00 31.88 4.26
1653 4718 0.667993 GATCTCGAGAGCAGAGTGGG 59.332 60.000 25.07 0.00 37.07 4.61
1672 4737 3.039011 GGGGCTTCTGTACAGGAGATTA 58.961 50.000 31.71 5.46 36.07 1.75
1811 5184 6.422344 TTGGTAGTATGTACACTTGTGGAA 57.578 37.500 0.00 0.00 0.00 3.53
1828 5201 4.202040 TGTGGAAATGTGCAGAAAGTTCAG 60.202 41.667 0.00 0.00 0.00 3.02
1908 5283 8.761575 ACCATTTATGCTGTTAACTGATTTTG 57.238 30.769 15.89 5.49 0.00 2.44
1913 5288 9.906660 TTTATGCTGTTAACTGATTTTGGTTAG 57.093 29.630 15.89 0.00 30.99 2.34
2009 8364 2.715749 TGGGCATTCCTGTCACATAG 57.284 50.000 0.00 0.00 36.20 2.23
2104 8459 5.652452 GTCTCAGGTAATTATTTGCCAAGGT 59.348 40.000 7.16 0.00 39.87 3.50
2111 8466 9.875708 AGGTAATTATTTGCCAAGGTTCATATA 57.124 29.630 7.16 0.00 39.87 0.86
2117 8472 7.790823 ATTTGCCAAGGTTCATATAATTTGC 57.209 32.000 0.00 0.00 0.00 3.68
2118 8473 5.275067 TGCCAAGGTTCATATAATTTGCC 57.725 39.130 0.00 0.00 0.00 4.52
2119 8474 4.713814 TGCCAAGGTTCATATAATTTGCCA 59.286 37.500 0.00 0.00 0.00 4.92
2147 8522 1.536766 TGAAACAAGCCAGCTCGAATG 59.463 47.619 0.00 0.00 0.00 2.67
2186 8561 8.795513 CCTTGTGATTATGCATTATCATTACCA 58.204 33.333 26.14 18.04 33.69 3.25
2218 8669 5.292765 ACCTAATGATGCTGATGACTAACG 58.707 41.667 0.00 0.00 0.00 3.18
2270 8733 7.454260 AACAAATCCACTGAAGATCCTTAAC 57.546 36.000 0.00 0.00 0.00 2.01
2295 8758 7.016153 TCTTATCATGTTGTTGTACCTTCCT 57.984 36.000 0.00 0.00 0.00 3.36
2296 8759 8.141298 TCTTATCATGTTGTTGTACCTTCCTA 57.859 34.615 0.00 0.00 0.00 2.94
2297 8760 8.598916 TCTTATCATGTTGTTGTACCTTCCTAA 58.401 33.333 0.00 0.00 0.00 2.69
2298 8761 8.556213 TTATCATGTTGTTGTACCTTCCTAAC 57.444 34.615 0.00 0.00 0.00 2.34
2316 8779 7.141758 TCCTAACTCTGCTTCCAAATGATAT 57.858 36.000 0.00 0.00 0.00 1.63
2331 8794 8.826710 TCCAAATGATATAATGAACTTCACGTC 58.173 33.333 0.00 0.00 0.00 4.34
2355 8819 7.537991 GTCTATATCGCTGTACTGGTTATGTTC 59.462 40.741 1.65 0.00 0.00 3.18
2386 8850 3.355378 TGGAAGGATGCACCATTAAGTG 58.645 45.455 7.86 0.00 42.04 3.16
2405 8869 6.432607 AAGTGATATGTGCAATCAGAAGTG 57.567 37.500 0.00 0.00 34.12 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.243434 ACGTCGAATGTATGGATGAGTCC 60.243 47.826 0.00 0.00 45.31 3.85
7 8 3.731216 CACGTCGAATGTATGGATGAGTC 59.269 47.826 0.00 0.00 0.00 3.36
8 9 3.130516 ACACGTCGAATGTATGGATGAGT 59.869 43.478 0.00 0.00 0.00 3.41
9 10 3.487207 CACACGTCGAATGTATGGATGAG 59.513 47.826 0.00 0.00 0.00 2.90
11 12 3.000222 CACACACGTCGAATGTATGGATG 60.000 47.826 0.00 0.00 0.00 3.51
14 15 2.344441 GTCACACACGTCGAATGTATGG 59.656 50.000 8.92 0.00 0.00 2.74
15 16 2.026389 CGTCACACACGTCGAATGTATG 59.974 50.000 0.00 3.45 44.07 2.39
17 18 1.677208 CGTCACACACGTCGAATGTA 58.323 50.000 0.00 0.00 44.07 2.29
18 19 2.502163 CGTCACACACGTCGAATGT 58.498 52.632 0.00 0.00 44.07 2.71
27 28 2.554806 TCCATCGTATCGTCACACAC 57.445 50.000 0.00 0.00 0.00 3.82
28 29 3.129638 TGAATCCATCGTATCGTCACACA 59.870 43.478 0.00 0.00 0.00 3.72
29 30 3.702330 TGAATCCATCGTATCGTCACAC 58.298 45.455 0.00 0.00 0.00 3.82
30 31 3.380320 ACTGAATCCATCGTATCGTCACA 59.620 43.478 0.00 0.00 0.00 3.58
31 32 3.731216 CACTGAATCCATCGTATCGTCAC 59.269 47.826 0.00 0.00 0.00 3.67
32 33 3.243401 CCACTGAATCCATCGTATCGTCA 60.243 47.826 0.00 0.00 0.00 4.35
33 34 3.309388 CCACTGAATCCATCGTATCGTC 58.691 50.000 0.00 0.00 0.00 4.20
35 36 2.610479 CCCCACTGAATCCATCGTATCG 60.610 54.545 0.00 0.00 0.00 2.92
38 39 0.468226 GCCCCACTGAATCCATCGTA 59.532 55.000 0.00 0.00 0.00 3.43
39 40 1.224592 GCCCCACTGAATCCATCGT 59.775 57.895 0.00 0.00 0.00 3.73
40 41 1.528824 AGCCCCACTGAATCCATCG 59.471 57.895 0.00 0.00 0.00 3.84
57 58 1.483827 TCTCTGATGGTTAGCAGCCAG 59.516 52.381 9.31 9.31 40.10 4.85
58 59 1.571955 TCTCTGATGGTTAGCAGCCA 58.428 50.000 0.00 0.00 40.10 4.75
59 60 2.926778 ATCTCTGATGGTTAGCAGCC 57.073 50.000 0.00 0.00 40.10 4.85
61 62 6.815089 ACTAAGAATCTCTGATGGTTAGCAG 58.185 40.000 0.00 0.00 41.62 4.24
62 63 6.798427 ACTAAGAATCTCTGATGGTTAGCA 57.202 37.500 0.00 0.00 0.00 3.49
64 65 7.726291 TCCCTACTAAGAATCTCTGATGGTTAG 59.274 40.741 0.00 0.00 0.00 2.34
65 66 7.592736 TCCCTACTAAGAATCTCTGATGGTTA 58.407 38.462 0.00 0.00 0.00 2.85
66 67 6.444704 TCCCTACTAAGAATCTCTGATGGTT 58.555 40.000 0.00 0.00 0.00 3.67
68 69 6.723515 TCATCCCTACTAAGAATCTCTGATGG 59.276 42.308 0.00 0.00 0.00 3.51
69 70 7.773489 TCATCCCTACTAAGAATCTCTGATG 57.227 40.000 0.00 0.00 0.00 3.07
70 71 8.814931 CATTCATCCCTACTAAGAATCTCTGAT 58.185 37.037 0.00 0.00 0.00 2.90
71 72 7.256119 GCATTCATCCCTACTAAGAATCTCTGA 60.256 40.741 0.00 0.00 0.00 3.27
72 73 6.873076 GCATTCATCCCTACTAAGAATCTCTG 59.127 42.308 0.00 0.00 0.00 3.35
73 74 6.556495 TGCATTCATCCCTACTAAGAATCTCT 59.444 38.462 0.00 0.00 0.00 3.10
74 75 6.763355 TGCATTCATCCCTACTAAGAATCTC 58.237 40.000 0.00 0.00 0.00 2.75
75 76 6.753913 TGCATTCATCCCTACTAAGAATCT 57.246 37.500 0.00 0.00 0.00 2.40
77 78 7.083062 TGATGCATTCATCCCTACTAAGAAT 57.917 36.000 0.00 0.00 46.60 2.40
78 79 6.499106 TGATGCATTCATCCCTACTAAGAA 57.501 37.500 0.00 0.00 46.60 2.52
79 80 5.512060 GCTGATGCATTCATCCCTACTAAGA 60.512 44.000 0.00 0.00 46.60 2.10
80 81 4.694509 GCTGATGCATTCATCCCTACTAAG 59.305 45.833 0.00 0.00 46.60 2.18
83 84 2.440627 TGCTGATGCATTCATCCCTACT 59.559 45.455 0.00 0.00 46.60 2.57
84 85 2.854963 TGCTGATGCATTCATCCCTAC 58.145 47.619 0.00 0.00 46.60 3.18
96 97 0.449388 GCCTGTACTTGTGCTGATGC 59.551 55.000 0.00 0.00 40.20 3.91
97 98 1.736126 CTGCCTGTACTTGTGCTGATG 59.264 52.381 0.00 0.00 0.00 3.07
98 99 1.339438 CCTGCCTGTACTTGTGCTGAT 60.339 52.381 0.00 0.00 0.00 2.90
99 100 0.035317 CCTGCCTGTACTTGTGCTGA 59.965 55.000 0.00 0.00 0.00 4.26
100 101 1.580845 GCCTGCCTGTACTTGTGCTG 61.581 60.000 0.00 0.00 0.00 4.41
105 106 1.002868 AGCAGCCTGCCTGTACTTG 60.003 57.895 14.25 0.00 46.52 3.16
107 108 2.664081 GGAGCAGCCTGCCTGTACT 61.664 63.158 14.25 0.00 46.52 2.73
108 109 2.124942 GGAGCAGCCTGCCTGTAC 60.125 66.667 14.25 0.00 46.52 2.90
117 118 2.968206 CAGCCAAAAGGAGCAGCC 59.032 61.111 0.00 0.00 0.00 4.85
118 119 2.260743 GCAGCCAAAAGGAGCAGC 59.739 61.111 0.00 0.00 34.28 5.25
119 120 1.183676 AAGGCAGCCAAAAGGAGCAG 61.184 55.000 15.80 0.00 0.00 4.24
120 121 1.152483 AAGGCAGCCAAAAGGAGCA 60.152 52.632 15.80 0.00 0.00 4.26
121 122 1.291272 CAAGGCAGCCAAAAGGAGC 59.709 57.895 15.80 0.00 0.00 4.70
122 123 1.043022 AACAAGGCAGCCAAAAGGAG 58.957 50.000 15.80 0.00 0.00 3.69
124 125 0.249996 CCAACAAGGCAGCCAAAAGG 60.250 55.000 15.80 4.82 0.00 3.11
126 127 1.410882 GTACCAACAAGGCAGCCAAAA 59.589 47.619 15.80 0.00 43.14 2.44
127 128 1.036707 GTACCAACAAGGCAGCCAAA 58.963 50.000 15.80 0.00 43.14 3.28
128 129 1.169661 CGTACCAACAAGGCAGCCAA 61.170 55.000 15.80 0.00 43.14 4.52
129 130 1.599518 CGTACCAACAAGGCAGCCA 60.600 57.895 15.80 0.00 43.14 4.75
130 131 2.332654 CCGTACCAACAAGGCAGCC 61.333 63.158 1.84 1.84 43.14 4.85
132 133 1.001633 AGTACCGTACCAACAAGGCAG 59.998 52.381 5.02 0.00 43.14 4.85
134 135 2.610433 GTAGTACCGTACCAACAAGGC 58.390 52.381 5.02 0.00 43.14 4.35
135 136 2.487762 TCGTAGTACCGTACCAACAAGG 59.512 50.000 5.02 0.00 45.67 3.61
136 137 3.829886 TCGTAGTACCGTACCAACAAG 57.170 47.619 5.02 0.00 0.00 3.16
137 138 4.217334 TGATTCGTAGTACCGTACCAACAA 59.783 41.667 5.02 3.25 0.00 2.83
138 139 3.755905 TGATTCGTAGTACCGTACCAACA 59.244 43.478 5.02 0.00 0.00 3.33
139 140 4.098416 GTGATTCGTAGTACCGTACCAAC 58.902 47.826 5.02 3.79 0.00 3.77
140 141 3.181511 CGTGATTCGTAGTACCGTACCAA 60.182 47.826 5.02 0.00 34.52 3.67
141 142 2.351418 CGTGATTCGTAGTACCGTACCA 59.649 50.000 5.02 0.00 34.52 3.25
142 143 2.286418 CCGTGATTCGTAGTACCGTACC 60.286 54.545 5.02 0.00 37.94 3.34
143 144 2.351726 ACCGTGATTCGTAGTACCGTAC 59.648 50.000 0.00 0.00 37.94 3.67
144 145 2.627945 ACCGTGATTCGTAGTACCGTA 58.372 47.619 0.00 0.00 37.94 4.02
145 146 1.453155 ACCGTGATTCGTAGTACCGT 58.547 50.000 0.00 0.00 37.94 4.83
146 147 2.549633 AACCGTGATTCGTAGTACCG 57.450 50.000 0.00 0.00 37.94 4.02
148 149 7.510428 TGAAAATAACCGTGATTCGTAGTAC 57.490 36.000 0.00 0.00 37.94 2.73
150 151 6.869913 TCTTGAAAATAACCGTGATTCGTAGT 59.130 34.615 0.00 0.00 37.94 2.73
152 153 7.837202 ATCTTGAAAATAACCGTGATTCGTA 57.163 32.000 0.00 0.00 37.94 3.43
153 154 6.737254 ATCTTGAAAATAACCGTGATTCGT 57.263 33.333 0.00 0.00 37.94 3.85
180 181 8.950210 CACAATCTGAAACACCTGAATTATAGT 58.050 33.333 0.00 0.00 0.00 2.12
181 182 7.912250 GCACAATCTGAAACACCTGAATTATAG 59.088 37.037 0.00 0.00 0.00 1.31
182 183 7.148086 GGCACAATCTGAAACACCTGAATTATA 60.148 37.037 0.00 0.00 0.00 0.98
185 186 4.262164 GGCACAATCTGAAACACCTGAATT 60.262 41.667 0.00 0.00 0.00 2.17
186 187 3.256631 GGCACAATCTGAAACACCTGAAT 59.743 43.478 0.00 0.00 0.00 2.57
187 188 2.622942 GGCACAATCTGAAACACCTGAA 59.377 45.455 0.00 0.00 0.00 3.02
188 189 2.229792 GGCACAATCTGAAACACCTGA 58.770 47.619 0.00 0.00 0.00 3.86
189 190 1.955778 TGGCACAATCTGAAACACCTG 59.044 47.619 0.00 0.00 31.92 4.00
203 204 6.052360 TCGCTGATAGTATAAATTTGGCACA 58.948 36.000 0.00 0.00 0.00 4.57
204 205 6.539649 TCGCTGATAGTATAAATTTGGCAC 57.460 37.500 0.00 0.00 0.00 5.01
205 206 5.179368 GCTCGCTGATAGTATAAATTTGGCA 59.821 40.000 0.00 0.00 0.00 4.92
206 207 5.622378 GCTCGCTGATAGTATAAATTTGGC 58.378 41.667 0.00 0.00 0.00 4.52
207 208 5.668866 GCGCTCGCTGATAGTATAAATTTGG 60.669 44.000 0.00 0.00 38.26 3.28
208 209 5.107491 TGCGCTCGCTGATAGTATAAATTTG 60.107 40.000 9.73 0.00 42.51 2.32
209 210 4.988540 TGCGCTCGCTGATAGTATAAATTT 59.011 37.500 9.73 0.00 42.51 1.82
210 211 4.556233 TGCGCTCGCTGATAGTATAAATT 58.444 39.130 9.73 0.00 42.51 1.82
211 212 4.082733 TCTGCGCTCGCTGATAGTATAAAT 60.083 41.667 17.55 0.00 42.61 1.40
212 213 3.252458 TCTGCGCTCGCTGATAGTATAAA 59.748 43.478 17.55 0.00 42.61 1.40
213 214 2.812011 TCTGCGCTCGCTGATAGTATAA 59.188 45.455 17.55 0.00 42.61 0.98
215 216 1.198867 CTCTGCGCTCGCTGATAGTAT 59.801 52.381 20.72 0.00 45.43 2.12
216 217 0.588737 CTCTGCGCTCGCTGATAGTA 59.411 55.000 20.72 2.62 45.43 1.82
217 218 1.358402 CTCTGCGCTCGCTGATAGT 59.642 57.895 20.72 0.00 45.43 2.12
219 220 2.026734 GCTCTGCGCTCGCTGATA 59.973 61.111 20.72 3.88 45.43 2.15
228 229 3.407046 GATTGGCTTGGCTCTGCGC 62.407 63.158 0.00 0.00 38.13 6.09
230 231 1.712977 CGAGATTGGCTTGGCTCTGC 61.713 60.000 0.00 0.00 0.00 4.26
231 232 1.712977 GCGAGATTGGCTTGGCTCTG 61.713 60.000 0.00 0.00 0.00 3.35
232 233 1.451028 GCGAGATTGGCTTGGCTCT 60.451 57.895 0.00 0.00 0.00 4.09
233 234 1.746615 TGCGAGATTGGCTTGGCTC 60.747 57.895 0.00 0.00 0.00 4.70
235 236 1.986575 GAGTGCGAGATTGGCTTGGC 61.987 60.000 0.00 0.00 0.00 4.52
237 238 1.712081 CGAGTGCGAGATTGGCTTG 59.288 57.895 0.00 0.00 40.82 4.01
238 239 2.103042 GCGAGTGCGAGATTGGCTT 61.103 57.895 0.00 0.00 40.82 4.35
239 240 2.510238 GCGAGTGCGAGATTGGCT 60.510 61.111 0.00 0.00 40.82 4.75
249 250 4.314440 TGGTGGGAGTGCGAGTGC 62.314 66.667 0.00 0.00 43.20 4.40
250 251 2.047844 CTGGTGGGAGTGCGAGTG 60.048 66.667 0.00 0.00 0.00 3.51
251 252 4.008933 GCTGGTGGGAGTGCGAGT 62.009 66.667 0.00 0.00 0.00 4.18
252 253 3.535629 TTGCTGGTGGGAGTGCGAG 62.536 63.158 0.00 0.00 0.00 5.03
253 254 2.616797 TTTTGCTGGTGGGAGTGCGA 62.617 55.000 0.00 0.00 0.00 5.10
254 255 1.526575 ATTTTGCTGGTGGGAGTGCG 61.527 55.000 0.00 0.00 0.00 5.34
255 256 0.037975 CATTTTGCTGGTGGGAGTGC 60.038 55.000 0.00 0.00 0.00 4.40
256 257 1.619654 TCATTTTGCTGGTGGGAGTG 58.380 50.000 0.00 0.00 0.00 3.51
257 258 2.173519 CATCATTTTGCTGGTGGGAGT 58.826 47.619 0.00 0.00 0.00 3.85
259 260 0.896923 GCATCATTTTGCTGGTGGGA 59.103 50.000 0.00 0.00 39.57 4.37
261 262 0.458889 CCGCATCATTTTGCTGGTGG 60.459 55.000 0.00 0.00 40.54 4.61
262 263 1.079875 GCCGCATCATTTTGCTGGTG 61.080 55.000 8.36 0.00 40.54 4.17
263 264 1.216178 GCCGCATCATTTTGCTGGT 59.784 52.632 8.36 0.00 40.54 4.00
264 265 1.079875 GTGCCGCATCATTTTGCTGG 61.080 55.000 0.00 0.00 40.54 4.85
265 266 0.388778 TGTGCCGCATCATTTTGCTG 60.389 50.000 0.00 0.00 40.54 4.41
266 267 0.533491 ATGTGCCGCATCATTTTGCT 59.467 45.000 0.00 0.00 40.54 3.91
267 268 2.121786 CTATGTGCCGCATCATTTTGC 58.878 47.619 11.88 0.00 38.94 3.68
269 270 4.717233 TTTCTATGTGCCGCATCATTTT 57.283 36.364 11.88 0.00 38.94 1.82
270 271 4.924305 ATTTCTATGTGCCGCATCATTT 57.076 36.364 11.88 0.00 38.94 2.32
271 272 5.065914 AGTATTTCTATGTGCCGCATCATT 58.934 37.500 11.88 0.43 38.94 2.57
272 273 4.645535 AGTATTTCTATGTGCCGCATCAT 58.354 39.130 0.00 5.10 38.94 2.45
273 274 4.058124 GAGTATTTCTATGTGCCGCATCA 58.942 43.478 0.00 0.00 38.94 3.07
274 275 3.433615 GGAGTATTTCTATGTGCCGCATC 59.566 47.826 0.00 0.00 38.94 3.91
275 276 3.071602 AGGAGTATTTCTATGTGCCGCAT 59.928 43.478 0.00 0.00 41.42 4.73
277 278 3.113260 AGGAGTATTTCTATGTGCCGC 57.887 47.619 0.00 0.00 0.00 6.53
279 280 6.658188 AGAGTAGGAGTATTTCTATGTGCC 57.342 41.667 0.00 0.00 0.00 5.01
280 281 8.398878 AGTAGAGTAGGAGTATTTCTATGTGC 57.601 38.462 0.00 0.00 0.00 4.57
282 283 9.577222 GGAAGTAGAGTAGGAGTATTTCTATGT 57.423 37.037 0.00 0.00 0.00 2.29
283 284 9.016438 GGGAAGTAGAGTAGGAGTATTTCTATG 57.984 40.741 0.00 0.00 0.00 2.23
284 285 8.962205 AGGGAAGTAGAGTAGGAGTATTTCTAT 58.038 37.037 0.00 0.00 0.00 1.98
286 287 7.091902 TGAGGGAAGTAGAGTAGGAGTATTTCT 60.092 40.741 0.00 0.00 0.00 2.52
287 288 7.061688 TGAGGGAAGTAGAGTAGGAGTATTTC 58.938 42.308 0.00 0.00 0.00 2.17
289 290 6.593759 TGAGGGAAGTAGAGTAGGAGTATT 57.406 41.667 0.00 0.00 0.00 1.89
291 292 5.912354 AGATGAGGGAAGTAGAGTAGGAGTA 59.088 44.000 0.00 0.00 0.00 2.59
292 293 4.729881 AGATGAGGGAAGTAGAGTAGGAGT 59.270 45.833 0.00 0.00 0.00 3.85
293 294 5.070001 CAGATGAGGGAAGTAGAGTAGGAG 58.930 50.000 0.00 0.00 0.00 3.69
294 295 4.141135 CCAGATGAGGGAAGTAGAGTAGGA 60.141 50.000 0.00 0.00 0.00 2.94
296 297 3.572255 GCCAGATGAGGGAAGTAGAGTAG 59.428 52.174 0.00 0.00 0.00 2.57
297 298 3.052869 TGCCAGATGAGGGAAGTAGAGTA 60.053 47.826 0.00 0.00 0.00 2.59
299 300 2.364970 CTGCCAGATGAGGGAAGTAGAG 59.635 54.545 0.00 0.00 0.00 2.43
301 302 1.202627 GCTGCCAGATGAGGGAAGTAG 60.203 57.143 0.00 0.00 33.17 2.57
302 303 0.833287 GCTGCCAGATGAGGGAAGTA 59.167 55.000 0.00 0.00 33.17 2.24
303 304 1.203441 TGCTGCCAGATGAGGGAAGT 61.203 55.000 0.00 0.00 33.17 3.01
304 305 0.034767 TTGCTGCCAGATGAGGGAAG 60.035 55.000 0.00 0.00 33.82 3.46
306 307 0.034767 CTTTGCTGCCAGATGAGGGA 60.035 55.000 0.00 0.00 0.00 4.20
308 309 0.809385 CACTTTGCTGCCAGATGAGG 59.191 55.000 0.00 0.00 0.00 3.86
309 310 0.809385 CCACTTTGCTGCCAGATGAG 59.191 55.000 0.00 0.00 0.00 2.90
310 311 0.609957 CCCACTTTGCTGCCAGATGA 60.610 55.000 0.00 0.00 0.00 2.92
311 312 0.609957 TCCCACTTTGCTGCCAGATG 60.610 55.000 0.00 0.00 0.00 2.90
313 314 1.228245 GTCCCACTTTGCTGCCAGA 60.228 57.895 0.00 0.00 0.00 3.86
314 315 0.825010 AAGTCCCACTTTGCTGCCAG 60.825 55.000 0.00 0.00 34.11 4.85
315 316 1.108727 CAAGTCCCACTTTGCTGCCA 61.109 55.000 0.00 0.00 36.03 4.92
317 318 1.006922 GCAAGTCCCACTTTGCTGC 60.007 57.895 2.22 0.00 36.03 5.25
318 319 1.283793 CGCAAGTCCCACTTTGCTG 59.716 57.895 7.49 0.00 36.03 4.41
320 321 2.644992 CCGCAAGTCCCACTTTGC 59.355 61.111 0.00 0.00 36.03 3.68
321 322 1.455383 AAGCCGCAAGTCCCACTTTG 61.455 55.000 0.00 0.00 36.03 2.77
322 323 1.152756 AAGCCGCAAGTCCCACTTT 60.153 52.632 0.00 0.00 36.03 2.66
323 324 1.600916 GAAGCCGCAAGTCCCACTT 60.601 57.895 0.00 0.00 39.39 3.16
324 325 2.032681 GAAGCCGCAAGTCCCACT 59.967 61.111 0.00 0.00 0.00 4.00
349 350 2.427506 CGTCCAAGGGAAAGAAAGGAG 58.572 52.381 0.00 0.00 31.38 3.69
375 376 7.040340 GCTGCTGGATGAAAGATAGTAGTAGTA 60.040 40.741 0.00 0.00 0.00 1.82
378 379 5.598417 TGCTGCTGGATGAAAGATAGTAGTA 59.402 40.000 0.00 0.00 0.00 1.82
380 381 4.953667 TGCTGCTGGATGAAAGATAGTAG 58.046 43.478 0.00 0.00 0.00 2.57
430 437 2.832643 TGAATGTCCCGGAGTACCTA 57.167 50.000 0.73 0.00 0.00 3.08
432 439 2.696707 TGTATGAATGTCCCGGAGTACC 59.303 50.000 0.73 0.00 0.00 3.34
433 440 4.395959 TTGTATGAATGTCCCGGAGTAC 57.604 45.455 0.73 0.00 0.00 2.73
440 456 6.515272 AACACAGAATTGTATGAATGTCCC 57.485 37.500 0.00 0.00 35.25 4.46
482 502 1.546029 GAAGGAAGGTTGTTGGCATCC 59.454 52.381 0.00 0.00 35.27 3.51
487 507 2.297033 CACATGGAAGGAAGGTTGTTGG 59.703 50.000 0.00 0.00 0.00 3.77
496 516 1.052617 TGGACGACACATGGAAGGAA 58.947 50.000 0.00 0.00 0.00 3.36
525 562 2.621587 GACGTTTTAGCGTTGTGTGAC 58.378 47.619 0.00 0.00 45.79 3.67
584 629 1.542987 GCAGGCAAGATCAGATCCTCC 60.543 57.143 6.80 6.01 0.00 4.30
588 633 1.865970 CGAAGCAGGCAAGATCAGATC 59.134 52.381 1.64 1.64 0.00 2.75
590 635 0.107993 CCGAAGCAGGCAAGATCAGA 60.108 55.000 0.00 0.00 0.00 3.27
633 678 2.287547 TGCGTGGAAATTTCTCAAGTGC 60.288 45.455 17.42 15.99 0.00 4.40
638 683 1.879380 CAGGTGCGTGGAAATTTCTCA 59.121 47.619 17.42 10.97 0.00 3.27
677 725 4.520111 TGTTGGGTTCAGATGAATGTGAAG 59.480 41.667 3.31 0.00 40.19 3.02
682 730 3.441572 GGTCTGTTGGGTTCAGATGAATG 59.558 47.826 0.00 0.00 42.63 2.67
684 734 2.224769 GGGTCTGTTGGGTTCAGATGAA 60.225 50.000 0.00 0.00 42.63 2.57
704 754 1.929836 GAGTAAGATGCACGCTCAAGG 59.070 52.381 0.00 0.00 0.00 3.61
730 780 4.276926 CCTAACTGAAATTAGATGGCCAGC 59.723 45.833 14.72 14.72 34.59 4.85
732 782 5.708736 TCCTAACTGAAATTAGATGGCCA 57.291 39.130 8.56 8.56 34.59 5.36
733 783 5.885912 TGTTCCTAACTGAAATTAGATGGCC 59.114 40.000 0.00 0.00 34.59 5.36
798 863 0.467844 TGTGGCTGGCATGTTTCAGT 60.468 50.000 7.33 0.00 33.81 3.41
799 864 0.675083 TTGTGGCTGGCATGTTTCAG 59.325 50.000 7.33 1.65 0.00 3.02
801 866 0.388659 TGTTGTGGCTGGCATGTTTC 59.611 50.000 7.33 0.00 0.00 2.78
802 867 0.829333 TTGTTGTGGCTGGCATGTTT 59.171 45.000 7.33 0.00 0.00 2.83
803 868 0.829333 TTTGTTGTGGCTGGCATGTT 59.171 45.000 7.33 0.00 0.00 2.71
805 870 1.219646 GTTTTGTTGTGGCTGGCATG 58.780 50.000 7.33 0.00 0.00 4.06
806 871 0.829333 TGTTTTGTTGTGGCTGGCAT 59.171 45.000 7.33 0.00 0.00 4.40
807 872 0.175302 CTGTTTTGTTGTGGCTGGCA 59.825 50.000 0.00 0.00 0.00 4.92
808 873 0.459489 TCTGTTTTGTTGTGGCTGGC 59.541 50.000 0.00 0.00 0.00 4.85
810 875 3.983344 GCTTATCTGTTTTGTTGTGGCTG 59.017 43.478 0.00 0.00 0.00 4.85
861 926 0.758123 GGATGAAGAGAGCAGGGGAG 59.242 60.000 0.00 0.00 0.00 4.30
865 930 5.752036 TTATATGGGATGAAGAGAGCAGG 57.248 43.478 0.00 0.00 0.00 4.85
907 1975 1.603678 GCAATGTGTTGGTGCTGAAGG 60.604 52.381 0.00 0.00 35.83 3.46
923 1991 1.141858 GTAGGGAAGGCTAGCTGCAAT 59.858 52.381 15.72 0.00 45.15 3.56
924 1992 0.541863 GTAGGGAAGGCTAGCTGCAA 59.458 55.000 15.72 0.00 45.15 4.08
925 1993 1.338136 GGTAGGGAAGGCTAGCTGCA 61.338 60.000 15.72 0.00 45.15 4.41
926 1994 1.338136 TGGTAGGGAAGGCTAGCTGC 61.338 60.000 15.72 0.09 41.94 5.25
927 1995 1.428869 ATGGTAGGGAAGGCTAGCTG 58.571 55.000 15.72 0.00 0.00 4.24
928 1996 2.050918 GAATGGTAGGGAAGGCTAGCT 58.949 52.381 15.72 0.00 0.00 3.32
929 1997 2.037902 GAGAATGGTAGGGAAGGCTAGC 59.962 54.545 6.04 6.04 0.00 3.42
930 1998 3.582164 AGAGAATGGTAGGGAAGGCTAG 58.418 50.000 0.00 0.00 0.00 3.42
931 1999 3.708236 AGAGAATGGTAGGGAAGGCTA 57.292 47.619 0.00 0.00 0.00 3.93
932 2000 2.577772 AGAGAATGGTAGGGAAGGCT 57.422 50.000 0.00 0.00 0.00 4.58
933 2001 3.454812 TGTAAGAGAATGGTAGGGAAGGC 59.545 47.826 0.00 0.00 0.00 4.35
934 2002 5.896073 ATGTAAGAGAATGGTAGGGAAGG 57.104 43.478 0.00 0.00 0.00 3.46
935 2003 6.931840 GCTAATGTAAGAGAATGGTAGGGAAG 59.068 42.308 0.00 0.00 0.00 3.46
936 2004 6.385759 TGCTAATGTAAGAGAATGGTAGGGAA 59.614 38.462 0.00 0.00 0.00 3.97
937 2005 5.903010 TGCTAATGTAAGAGAATGGTAGGGA 59.097 40.000 0.00 0.00 0.00 4.20
938 2006 6.174720 TGCTAATGTAAGAGAATGGTAGGG 57.825 41.667 0.00 0.00 0.00 3.53
953 2021 6.183360 CGATGTTTCCTTGTGTATGCTAATGT 60.183 38.462 0.00 0.00 0.00 2.71
959 2042 2.477863 GGCGATGTTTCCTTGTGTATGC 60.478 50.000 0.00 0.00 0.00 3.14
978 2066 0.469144 TTGGGGACTGAAGGTTTGGC 60.469 55.000 0.00 0.00 0.00 4.52
1110 2199 3.941704 TGGCACATGGTATTGATGGTA 57.058 42.857 0.00 0.00 0.00 3.25
1139 2228 1.630369 TGTAGATGTCTGCCAGCCTTT 59.370 47.619 0.00 0.00 0.00 3.11
1140 2229 1.209019 CTGTAGATGTCTGCCAGCCTT 59.791 52.381 0.00 0.00 0.00 4.35
1168 2257 1.881324 TGGTGTGCACATCATGTTCTG 59.119 47.619 28.65 0.00 30.91 3.02
1350 4415 3.832171 CTTGAGCAGACGCGTCGC 61.832 66.667 33.27 33.27 45.49 5.19
1382 4447 0.609131 TGTGCTTTCTTGGCTAGCCC 60.609 55.000 30.81 13.83 34.03 5.19
1572 4637 0.251077 AGGGGCTTTGCTCTTCTGTG 60.251 55.000 0.00 0.00 0.00 3.66
1573 4638 0.480252 AAGGGGCTTTGCTCTTCTGT 59.520 50.000 0.00 0.00 0.00 3.41
1595 4660 1.559219 TGCCTGCAGTTGCTCCTAATA 59.441 47.619 13.81 0.00 42.66 0.98
1597 4662 0.606401 GTGCCTGCAGTTGCTCCTAA 60.606 55.000 13.81 0.00 42.66 2.69
1598 4663 1.003355 GTGCCTGCAGTTGCTCCTA 60.003 57.895 13.81 0.00 42.66 2.94
1639 4704 2.570582 GAAGCCCCACTCTGCTCTCG 62.571 65.000 0.00 0.00 36.66 4.04
1646 4711 1.270907 CTGTACAGAAGCCCCACTCT 58.729 55.000 18.45 0.00 0.00 3.24
1653 4718 5.163301 TGGATTAATCTCCTGTACAGAAGCC 60.163 44.000 24.68 19.67 36.20 4.35
1781 5154 7.229707 ACAAGTGTACATACTACCAAAATTGCA 59.770 33.333 0.00 0.00 0.00 4.08
1811 5184 5.505654 CGGTTAACTGAACTTTCTGCACATT 60.506 40.000 8.90 0.00 38.21 2.71
1828 5201 7.242914 TGTTTCTCTTCTCTTTTCGGTTAAC 57.757 36.000 0.00 0.00 0.00 2.01
1913 5288 7.870445 AGAGAGATCTTTTGTTAGACACTTGTC 59.130 37.037 0.00 0.77 45.08 3.18
1966 5379 9.054922 CCAAAATTCCATGTTATTGTTCTGTTT 57.945 29.630 0.00 0.00 0.00 2.83
1990 5403 2.195727 TCTATGTGACAGGAATGCCCA 58.804 47.619 0.00 0.00 37.41 5.36
2050 8405 4.816925 GCCATTAGAGACACCATTACTTCC 59.183 45.833 0.00 0.00 0.00 3.46
2104 8459 5.986741 CAGCATGCTTGGCAAATTATATGAA 59.013 36.000 19.98 0.00 43.62 2.57
2111 8466 2.809696 GTTTCAGCATGCTTGGCAAATT 59.190 40.909 19.98 0.00 43.62 1.82
2113 8468 1.138464 TGTTTCAGCATGCTTGGCAAA 59.862 42.857 19.98 11.71 43.62 3.68
2117 8472 1.425412 GCTTGTTTCAGCATGCTTGG 58.575 50.000 19.98 8.26 39.83 3.61
2118 8473 1.269883 TGGCTTGTTTCAGCATGCTTG 60.270 47.619 19.98 13.88 42.10 4.01
2119 8474 1.000506 CTGGCTTGTTTCAGCATGCTT 59.999 47.619 19.98 0.00 42.10 3.91
2147 8522 3.241067 TCACAAGGTTATAGGTCGTGC 57.759 47.619 0.00 0.00 0.00 5.34
2186 8561 4.665009 TCAGCATCATTAGGTATTCCCCTT 59.335 41.667 0.00 0.00 35.97 3.95
2270 8733 7.106239 AGGAAGGTACAACAACATGATAAGAG 58.894 38.462 0.00 0.00 0.00 2.85
2296 8759 8.985315 TCATTATATCATTTGGAAGCAGAGTT 57.015 30.769 0.00 0.00 0.00 3.01
2297 8760 8.844244 GTTCATTATATCATTTGGAAGCAGAGT 58.156 33.333 0.00 0.00 0.00 3.24
2298 8761 9.064706 AGTTCATTATATCATTTGGAAGCAGAG 57.935 33.333 0.00 0.00 0.00 3.35
2316 8779 6.856426 CAGCGATATAGACGTGAAGTTCATTA 59.144 38.462 9.18 0.90 0.00 1.90
2331 8794 7.368059 TGAACATAACCAGTACAGCGATATAG 58.632 38.462 0.00 0.00 0.00 1.31
2333 8796 6.156748 TGAACATAACCAGTACAGCGATAT 57.843 37.500 0.00 0.00 0.00 1.63
2363 8827 4.220382 CACTTAATGGTGCATCCTTCCAAA 59.780 41.667 0.00 0.00 37.07 3.28
2364 8828 3.763360 CACTTAATGGTGCATCCTTCCAA 59.237 43.478 0.00 0.00 37.07 3.53
2371 8835 5.008911 TGCACATATCACTTAATGGTGCATC 59.991 40.000 11.95 0.00 36.32 3.91
2386 8850 4.274459 GGTCCACTTCTGATTGCACATATC 59.726 45.833 0.00 0.00 0.00 1.63
2405 8869 1.064952 CAAGTGACGTTGGTTTGGTCC 59.935 52.381 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.