Multiple sequence alignment - TraesCS1A01G260700

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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 TraesCS1A01G260700 chr1A 100.000 2738 0 0 1 2738 454532592 454535329 0.000000e+00 5057
1 TraesCS1A01G260700 chr1A 91.220 205 18 0 1 205 491270543 491270339 2.080000e-71 279
2 TraesCS1A01G260700 chr1A 91.176 204 18 0 1 204 507912010 507911807 7.470000e-71 278
3 TraesCS1A01G260700 chr1A 89.202 213 21 2 1 212 232089246 232089035 5.810000e-67 265
4 TraesCS1A01G260700 chr1D 85.595 1680 95 56 236 1858 355087323 355088912 0.000000e+00 1626
5 TraesCS1A01G260700 chr1D 90.175 458 34 3 2287 2736 355091488 355091942 1.090000e-163 586
6 TraesCS1A01G260700 chr1D 90.732 205 18 1 1 205 433907909 433907706 3.470000e-69 272
7 TraesCS1A01G260700 chr1D 90.244 205 19 1 1 205 469095865 469095662 1.620000e-67 267
8 TraesCS1A01G260700 chr1D 82.609 322 13 16 1877 2176 355089061 355089361 7.570000e-61 244
9 TraesCS1A01G260700 chr1B 87.715 1335 68 30 242 1530 476919610 476920894 0.000000e+00 1469
10 TraesCS1A01G260700 chr1B 86.640 494 22 14 1754 2221 476924662 476925137 8.750000e-140 507
11 TraesCS1A01G260700 chr3A 91.667 204 17 0 1 204 641881477 641881680 1.600000e-72 283
12 TraesCS1A01G260700 chr7D 90.732 205 17 2 1 205 565207627 565207425 3.470000e-69 272
13 TraesCS1A01G260700 chr2D 91.089 202 17 1 1 202 424710197 424709997 3.470000e-69 272
14 TraesCS1A01G260700 chr3D 90.594 202 18 1 1 202 420047963 420048163 1.620000e-67 267


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 TraesCS1A01G260700 chr1A 454532592 454535329 2737 False 5057.000000 5057 100.000000 1 2738 1 chr1A.!!$F1 2737
1 TraesCS1A01G260700 chr1D 355087323 355091942 4619 False 818.666667 1626 86.126333 236 2736 3 chr1D.!!$F1 2500
2 TraesCS1A01G260700 chr1B 476919610 476925137 5527 False 988.000000 1469 87.177500 242 2221 2 chr1B.!!$F1 1979

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
188 189 0.105964 CGTCTATTTGGATCGCCCCA 59.894 55.0 0.00 0.0 0.00 4.96 F
193 194 0.261402 ATTTGGATCGCCCCATTGGA 59.739 50.0 3.62 0.0 35.87 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1061 1090 0.325272 GAGAGGGGTTGGTGAGGAAC 59.675 60.0 0.00 0.0 0.00 3.62 R
1926 5676 0.541392 TGTGCACCCTCGCAATATCT 59.459 50.0 15.69 0.0 45.14 1.98 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
17 18 3.417601 CATGAGACATGGCCGCTG 58.582 61.111 0.00 0.00 0.00 5.18
18 19 2.184830 CATGAGACATGGCCGCTGG 61.185 63.158 9.69 0.00 0.00 4.85
68 69 6.462552 TTCAAAAGTTGAATGTGGACATGA 57.537 33.333 0.00 0.00 44.21 3.07
69 70 6.462552 TCAAAAGTTGAATGTGGACATGAA 57.537 33.333 0.00 0.00 36.59 2.57
70 71 6.871844 TCAAAAGTTGAATGTGGACATGAAA 58.128 32.000 0.00 0.00 36.59 2.69
71 72 7.499292 TCAAAAGTTGAATGTGGACATGAAAT 58.501 30.769 0.00 0.00 36.59 2.17
72 73 7.438757 TCAAAAGTTGAATGTGGACATGAAATG 59.561 33.333 0.00 0.00 43.37 2.32
81 82 2.408835 CATGAAATGGGTCGGCGC 59.591 61.111 0.00 0.00 41.79 6.53
82 83 3.202001 ATGAAATGGGTCGGCGCG 61.202 61.111 0.00 0.00 0.00 6.86
83 84 3.969250 ATGAAATGGGTCGGCGCGT 62.969 57.895 8.43 0.00 0.00 6.01
84 85 3.428282 GAAATGGGTCGGCGCGTT 61.428 61.111 8.43 5.61 38.23 4.84
85 86 3.661025 GAAATGGGTCGGCGCGTTG 62.661 63.158 12.62 0.00 36.96 4.10
104 105 3.046870 GCACATTGCCGACCCAAA 58.953 55.556 0.00 0.00 37.42 3.28
105 106 1.591183 GCACATTGCCGACCCAAAT 59.409 52.632 0.00 0.00 37.42 2.32
106 107 0.814457 GCACATTGCCGACCCAAATA 59.186 50.000 0.00 0.00 37.42 1.40
107 108 1.408702 GCACATTGCCGACCCAAATAT 59.591 47.619 0.00 0.00 37.42 1.28
108 109 2.621055 GCACATTGCCGACCCAAATATA 59.379 45.455 0.00 0.00 37.42 0.86
109 110 3.067461 GCACATTGCCGACCCAAATATAA 59.933 43.478 0.00 0.00 37.42 0.98
110 111 4.440802 GCACATTGCCGACCCAAATATAAA 60.441 41.667 0.00 0.00 37.42 1.40
111 112 5.655488 CACATTGCCGACCCAAATATAAAA 58.345 37.500 0.00 0.00 0.00 1.52
112 113 5.518487 CACATTGCCGACCCAAATATAAAAC 59.482 40.000 0.00 0.00 0.00 2.43
113 114 5.420739 ACATTGCCGACCCAAATATAAAACT 59.579 36.000 0.00 0.00 0.00 2.66
114 115 4.974368 TGCCGACCCAAATATAAAACTG 57.026 40.909 0.00 0.00 0.00 3.16
115 116 3.697045 TGCCGACCCAAATATAAAACTGG 59.303 43.478 0.00 0.00 0.00 4.00
119 120 3.726291 CCCAAATATAAAACTGGGCGG 57.274 47.619 0.00 0.00 42.10 6.13
120 121 3.292460 CCCAAATATAAAACTGGGCGGA 58.708 45.455 0.00 0.00 42.10 5.54
121 122 3.067601 CCCAAATATAAAACTGGGCGGAC 59.932 47.826 0.00 0.00 42.10 4.79
122 123 3.242936 CCAAATATAAAACTGGGCGGACG 60.243 47.826 0.00 0.00 0.00 4.79
123 124 1.589803 ATATAAAACTGGGCGGACGC 58.410 50.000 8.39 8.39 41.06 5.19
142 143 4.329545 GAACAGGCGGCTGACCCA 62.330 66.667 41.51 0.00 0.00 4.51
143 144 3.842925 GAACAGGCGGCTGACCCAA 62.843 63.158 41.51 0.00 0.00 4.12
144 145 3.429372 AACAGGCGGCTGACCCAAA 62.429 57.895 41.51 0.00 0.00 3.28
145 146 2.361610 CAGGCGGCTGACCCAAAT 60.362 61.111 33.59 0.00 0.00 2.32
146 147 2.361610 AGGCGGCTGACCCAAATG 60.362 61.111 12.25 0.00 0.00 2.32
147 148 3.451894 GGCGGCTGACCCAAATGG 61.452 66.667 0.00 0.00 41.37 3.16
148 149 2.361104 GCGGCTGACCCAAATGGA 60.361 61.111 0.00 0.00 37.39 3.41
149 150 2.700773 GCGGCTGACCCAAATGGAC 61.701 63.158 0.00 0.00 37.39 4.02
150 151 1.303236 CGGCTGACCCAAATGGACA 60.303 57.895 0.00 0.48 37.26 4.02
151 152 0.893270 CGGCTGACCCAAATGGACAA 60.893 55.000 0.00 0.00 38.35 3.18
152 153 1.337118 GGCTGACCCAAATGGACAAA 58.663 50.000 0.00 0.00 38.35 2.83
153 154 1.691434 GGCTGACCCAAATGGACAAAA 59.309 47.619 0.00 0.00 38.35 2.44
154 155 2.103941 GGCTGACCCAAATGGACAAAAA 59.896 45.455 0.00 0.00 38.35 1.94
155 156 3.392882 GCTGACCCAAATGGACAAAAAG 58.607 45.455 0.00 0.00 38.35 2.27
156 157 3.392882 CTGACCCAAATGGACAAAAAGC 58.607 45.455 0.00 0.00 38.35 3.51
157 158 2.223923 TGACCCAAATGGACAAAAAGCG 60.224 45.455 0.00 0.00 35.79 4.68
158 159 1.069978 ACCCAAATGGACAAAAAGCGG 59.930 47.619 0.00 0.00 37.39 5.52
159 160 1.342819 CCCAAATGGACAAAAAGCGGA 59.657 47.619 0.00 0.00 37.39 5.54
160 161 2.403259 CCAAATGGACAAAAAGCGGAC 58.597 47.619 0.00 0.00 37.39 4.79
161 162 2.223923 CCAAATGGACAAAAAGCGGACA 60.224 45.455 0.00 0.00 37.39 4.02
162 163 3.452474 CAAATGGACAAAAAGCGGACAA 58.548 40.909 0.00 0.00 0.00 3.18
163 164 3.810310 AATGGACAAAAAGCGGACAAA 57.190 38.095 0.00 0.00 0.00 2.83
164 165 4.335400 AATGGACAAAAAGCGGACAAAT 57.665 36.364 0.00 0.00 0.00 2.32
165 166 5.461032 AATGGACAAAAAGCGGACAAATA 57.539 34.783 0.00 0.00 0.00 1.40
166 167 4.231718 TGGACAAAAAGCGGACAAATAC 57.768 40.909 0.00 0.00 0.00 1.89
167 168 3.231160 GGACAAAAAGCGGACAAATACG 58.769 45.455 0.00 0.00 34.13 3.06
173 174 4.489249 CGGACAAATACGCCGTCT 57.511 55.556 0.00 0.00 40.17 4.18
174 175 3.628005 CGGACAAATACGCCGTCTA 57.372 52.632 0.00 0.00 40.17 2.59
175 176 2.129823 CGGACAAATACGCCGTCTAT 57.870 50.000 0.00 0.00 40.17 1.98
176 177 2.466846 CGGACAAATACGCCGTCTATT 58.533 47.619 0.00 0.00 40.17 1.73
177 178 2.861935 CGGACAAATACGCCGTCTATTT 59.138 45.455 0.00 0.00 40.17 1.40
178 179 3.302221 CGGACAAATACGCCGTCTATTTG 60.302 47.826 18.86 18.86 43.11 2.32
179 180 3.001939 GGACAAATACGCCGTCTATTTGG 59.998 47.826 22.40 10.10 42.33 3.28
180 181 3.864243 ACAAATACGCCGTCTATTTGGA 58.136 40.909 22.40 0.00 42.33 3.53
181 182 4.448210 ACAAATACGCCGTCTATTTGGAT 58.552 39.130 22.40 6.60 42.33 3.41
182 183 4.510340 ACAAATACGCCGTCTATTTGGATC 59.490 41.667 22.40 0.00 42.33 3.36
183 184 2.410785 TACGCCGTCTATTTGGATCG 57.589 50.000 0.00 0.00 0.00 3.69
184 185 0.874607 ACGCCGTCTATTTGGATCGC 60.875 55.000 0.00 0.00 0.00 4.58
185 186 1.557443 CGCCGTCTATTTGGATCGCC 61.557 60.000 0.00 0.00 0.00 5.54
186 187 1.228657 GCCGTCTATTTGGATCGCCC 61.229 60.000 0.00 0.00 0.00 6.13
187 188 0.602905 CCGTCTATTTGGATCGCCCC 60.603 60.000 0.00 0.00 0.00 5.80
188 189 0.105964 CGTCTATTTGGATCGCCCCA 59.894 55.000 0.00 0.00 0.00 4.96
189 190 1.270839 CGTCTATTTGGATCGCCCCAT 60.271 52.381 0.00 0.00 35.87 4.00
190 191 2.810400 CGTCTATTTGGATCGCCCCATT 60.810 50.000 0.00 0.00 35.87 3.16
191 192 2.554032 GTCTATTTGGATCGCCCCATTG 59.446 50.000 0.00 0.00 35.87 2.82
192 193 1.888512 CTATTTGGATCGCCCCATTGG 59.111 52.381 0.00 0.00 35.87 3.16
193 194 0.261402 ATTTGGATCGCCCCATTGGA 59.739 50.000 3.62 0.00 35.87 3.53
194 195 0.395586 TTTGGATCGCCCCATTGGAG 60.396 55.000 3.62 0.00 35.87 3.86
195 196 1.570857 TTGGATCGCCCCATTGGAGT 61.571 55.000 3.62 0.00 35.87 3.85
196 197 1.227383 GGATCGCCCCATTGGAGTT 59.773 57.895 3.62 0.00 35.07 3.01
197 198 1.103398 GGATCGCCCCATTGGAGTTG 61.103 60.000 3.62 0.00 35.07 3.16
198 199 1.728490 GATCGCCCCATTGGAGTTGC 61.728 60.000 3.62 0.53 35.07 4.17
199 200 2.215451 ATCGCCCCATTGGAGTTGCT 62.215 55.000 3.62 0.00 35.07 3.91
200 201 2.409870 CGCCCCATTGGAGTTGCTC 61.410 63.158 3.62 0.00 35.39 4.26
201 202 1.000396 GCCCCATTGGAGTTGCTCT 60.000 57.895 3.62 0.00 35.39 4.09
202 203 0.613012 GCCCCATTGGAGTTGCTCTT 60.613 55.000 3.62 0.00 35.39 2.85
203 204 1.340991 GCCCCATTGGAGTTGCTCTTA 60.341 52.381 3.62 0.00 35.39 2.10
204 205 2.648059 CCCCATTGGAGTTGCTCTTAG 58.352 52.381 3.62 0.00 35.39 2.18
205 206 2.019984 CCCATTGGAGTTGCTCTTAGC 58.980 52.381 3.62 0.00 42.82 3.09
206 207 5.770802 CCCCATTGGAGTTGCTCTTAGCA 62.771 52.174 3.62 0.00 43.45 3.49
207 208 6.996006 CCCCATTGGAGTTGCTCTTAGCAT 62.996 50.000 3.62 0.00 44.21 3.79
221 222 4.722700 GCATCTGGCACCACCGGT 62.723 66.667 0.00 0.00 46.11 5.28
222 223 2.436646 CATCTGGCACCACCGGTC 60.437 66.667 2.59 0.00 46.11 4.79
223 224 4.082523 ATCTGGCACCACCGGTCG 62.083 66.667 2.59 0.00 46.11 4.79
237 238 3.582714 CCGGTCGGGTAAGAATATACC 57.417 52.381 0.74 0.00 43.88 2.73
238 239 2.095059 CCGGTCGGGTAAGAATATACCG 60.095 54.545 0.00 0.00 45.26 4.02
239 240 2.554032 CGGTCGGGTAAGAATATACCGT 59.446 50.000 0.00 0.00 45.26 4.83
240 241 3.365364 CGGTCGGGTAAGAATATACCGTC 60.365 52.174 0.00 0.00 45.26 4.79
265 270 4.588899 CATCTGTAACCCTTCAACCATGA 58.411 43.478 0.00 0.00 0.00 3.07
266 271 4.715534 TCTGTAACCCTTCAACCATGAA 57.284 40.909 0.00 0.00 43.18 2.57
277 282 5.928264 CCTTCAACCATGAAACATTCTTTCC 59.072 40.000 0.00 0.00 44.64 3.13
278 283 5.119931 TCAACCATGAAACATTCTTTCCG 57.880 39.130 0.00 0.00 30.99 4.30
286 291 2.879103 ACATTCTTTCCGTCCACCAT 57.121 45.000 0.00 0.00 0.00 3.55
297 302 2.201732 CGTCCACCATGTGCAGTATAC 58.798 52.381 0.00 0.00 31.34 1.47
302 307 4.019771 TCCACCATGTGCAGTATACTTTCA 60.020 41.667 1.56 1.53 31.34 2.69
335 340 3.434299 AGTTCGTTTTGTAATGGTAGGCG 59.566 43.478 0.00 0.00 0.00 5.52
364 374 2.511637 AGCTAATCAAGGGGGAAGAAGG 59.488 50.000 0.00 0.00 0.00 3.46
387 397 1.471676 GGTCACTGCTTATAGTGCGCT 60.472 52.381 9.73 4.58 45.94 5.92
419 429 0.878416 GGCAAGCAACGGACATGTTA 59.122 50.000 0.00 0.00 0.00 2.41
423 433 1.651987 AGCAACGGACATGTTATCGG 58.348 50.000 17.14 5.82 0.00 4.18
458 468 3.059597 CGTCATCTGAAAGCAAAAGTCGT 60.060 43.478 0.00 0.00 0.00 4.34
461 471 1.864711 TCTGAAAGCAAAAGTCGTCCG 59.135 47.619 0.00 0.00 0.00 4.79
462 472 1.597663 CTGAAAGCAAAAGTCGTCCGT 59.402 47.619 0.00 0.00 0.00 4.69
533 543 2.668279 GCCACAGCCATTAGAAAACGTG 60.668 50.000 0.00 0.00 0.00 4.49
539 549 7.345192 CACAGCCATTAGAAAACGTGTATATC 58.655 38.462 0.00 0.00 0.00 1.63
574 584 6.354039 ACATCATCGAACCGTAAAATAACC 57.646 37.500 0.00 0.00 0.00 2.85
579 589 4.497300 TCGAACCGTAAAATAACCCAGAG 58.503 43.478 0.00 0.00 0.00 3.35
609 619 1.961277 CACGCAAAAGACTCGGGCT 60.961 57.895 0.00 0.00 0.00 5.19
610 620 1.227853 ACGCAAAAGACTCGGGCTT 60.228 52.632 0.00 0.00 0.00 4.35
712 724 4.280494 AGAAGGCGACACGTGCGT 62.280 61.111 25.33 9.46 0.00 5.24
713 725 2.429571 GAAGGCGACACGTGCGTA 60.430 61.111 25.33 0.00 0.00 4.42
714 726 1.804326 GAAGGCGACACGTGCGTAT 60.804 57.895 25.33 15.64 0.00 3.06
715 727 1.349259 GAAGGCGACACGTGCGTATT 61.349 55.000 25.33 20.82 0.00 1.89
716 728 0.947180 AAGGCGACACGTGCGTATTT 60.947 50.000 25.33 17.06 0.00 1.40
717 729 0.947180 AGGCGACACGTGCGTATTTT 60.947 50.000 25.33 3.52 0.00 1.82
718 730 0.714994 GGCGACACGTGCGTATTTTA 59.285 50.000 25.33 0.00 0.00 1.52
719 731 1.266696 GGCGACACGTGCGTATTTTAG 60.267 52.381 25.33 5.32 0.00 1.85
720 732 1.845489 GCGACACGTGCGTATTTTAGC 60.845 52.381 25.33 10.72 0.00 3.09
721 733 1.266696 CGACACGTGCGTATTTTAGCC 60.267 52.381 17.22 0.00 0.00 3.93
776 798 1.795768 TGCAACTGACGGTCTTGATC 58.204 50.000 9.88 0.00 0.00 2.92
827 852 0.652592 CGTCCGCCTGAATTGATGAC 59.347 55.000 0.00 0.00 0.00 3.06
849 878 6.011628 TGACCTTCTATTTCTTTCCCTCCAAT 60.012 38.462 0.00 0.00 0.00 3.16
952 981 0.398381 GGACTGAGGATGGAGGAGCT 60.398 60.000 0.00 0.00 0.00 4.09
953 982 1.039856 GACTGAGGATGGAGGAGCTC 58.960 60.000 4.71 4.71 0.00 4.09
954 983 0.754957 ACTGAGGATGGAGGAGCTCG 60.755 60.000 7.83 0.00 0.00 5.03
955 984 1.456518 TGAGGATGGAGGAGCTCGG 60.457 63.158 7.83 0.00 0.00 4.63
1038 1067 1.404315 GGTCAAGAGTAGGCTGAACCG 60.404 57.143 0.00 0.00 46.52 4.44
1039 1068 1.544691 GTCAAGAGTAGGCTGAACCGA 59.455 52.381 0.00 0.00 46.52 4.69
1040 1069 2.029290 GTCAAGAGTAGGCTGAACCGAA 60.029 50.000 0.00 0.00 46.52 4.30
1041 1070 2.029290 TCAAGAGTAGGCTGAACCGAAC 60.029 50.000 0.00 0.00 46.52 3.95
1042 1071 0.896226 AGAGTAGGCTGAACCGAACC 59.104 55.000 0.00 0.00 46.52 3.62
1059 1088 4.659172 CCGCCCACACACACCCAT 62.659 66.667 0.00 0.00 0.00 4.00
1060 1089 3.055719 CGCCCACACACACCCATC 61.056 66.667 0.00 0.00 0.00 3.51
1061 1090 3.055719 GCCCACACACACCCATCG 61.056 66.667 0.00 0.00 0.00 3.84
1079 1111 1.481056 CGTTCCTCACCAACCCCTCT 61.481 60.000 0.00 0.00 0.00 3.69
1080 1112 0.325272 GTTCCTCACCAACCCCTCTC 59.675 60.000 0.00 0.00 0.00 3.20
1081 1113 0.104672 TTCCTCACCAACCCCTCTCA 60.105 55.000 0.00 0.00 0.00 3.27
1082 1114 0.836400 TCCTCACCAACCCCTCTCAC 60.836 60.000 0.00 0.00 0.00 3.51
1084 1116 0.838122 CTCACCAACCCCTCTCACCT 60.838 60.000 0.00 0.00 0.00 4.00
1085 1117 0.836400 TCACCAACCCCTCTCACCTC 60.836 60.000 0.00 0.00 0.00 3.85
1086 1118 0.838122 CACCAACCCCTCTCACCTCT 60.838 60.000 0.00 0.00 0.00 3.69
1087 1119 0.545548 ACCAACCCCTCTCACCTCTC 60.546 60.000 0.00 0.00 0.00 3.20
1088 1120 1.608717 CCAACCCCTCTCACCTCTCG 61.609 65.000 0.00 0.00 0.00 4.04
1102 1142 3.344215 CTCGCGATCATGGGCAGC 61.344 66.667 10.36 0.00 0.00 5.25
1471 1537 2.494870 AGTCCGGTAGATGCGTACTTTT 59.505 45.455 0.00 0.00 0.00 2.27
1473 1539 1.931172 CCGGTAGATGCGTACTTTTGG 59.069 52.381 0.00 0.00 0.00 3.28
1498 1564 0.459489 GCTTTGTGGGTCAAGTGCAA 59.541 50.000 0.00 0.00 37.32 4.08
1503 1569 2.503331 TGTGGGTCAAGTGCAATAGTG 58.497 47.619 0.00 0.00 0.00 2.74
1504 1570 2.158682 TGTGGGTCAAGTGCAATAGTGT 60.159 45.455 0.00 0.00 0.00 3.55
1568 2217 2.479566 TGACTGGAGTTGGAGATTGC 57.520 50.000 0.00 0.00 0.00 3.56
1600 2249 7.078228 ACAGATACTTCTCGTTTCAATTTTGC 58.922 34.615 0.00 0.00 0.00 3.68
1636 2291 4.510340 CGTGTTATTCTTATAGCCACCACC 59.490 45.833 0.00 0.00 0.00 4.61
1647 3609 1.765314 AGCCACCACCTAGCTTGATAG 59.235 52.381 0.00 0.00 31.27 2.08
1681 3643 8.758829 AGAAAGGTTTATCTTTTCTGTTGGTTT 58.241 29.630 4.61 0.00 46.05 3.27
1733 3695 7.288810 TCCAACCAAAATATATTGCTGGATC 57.711 36.000 24.08 0.00 36.58 3.36
1734 3696 6.016360 TCCAACCAAAATATATTGCTGGATCG 60.016 38.462 24.08 11.89 36.58 3.69
1747 3709 2.726241 GCTGGATCGTTGTTGCTTTTTC 59.274 45.455 0.00 0.00 0.00 2.29
1748 3710 3.550842 GCTGGATCGTTGTTGCTTTTTCT 60.551 43.478 0.00 0.00 0.00 2.52
1751 3713 5.516090 TGGATCGTTGTTGCTTTTTCTTAC 58.484 37.500 0.00 0.00 0.00 2.34
1752 3714 5.066634 TGGATCGTTGTTGCTTTTTCTTACA 59.933 36.000 0.00 0.00 0.00 2.41
1810 5430 6.935741 TTAAAAGAATGATACGGACCATGG 57.064 37.500 11.19 11.19 0.00 3.66
1824 5444 2.358898 GACCATGGCATAACAAGCGAAT 59.641 45.455 13.04 0.00 0.00 3.34
1829 5449 5.388111 CATGGCATAACAAGCGAATATCAG 58.612 41.667 0.00 0.00 0.00 2.90
1890 5640 1.965414 TCCTCCACAAGCCTGGATTA 58.035 50.000 0.00 0.00 39.72 1.75
1917 5667 9.377312 TGAATTTATTCGTGTGATTCTCATGTA 57.623 29.630 7.58 0.07 39.62 2.29
1918 5668 9.638300 GAATTTATTCGTGTGATTCTCATGTAC 57.362 33.333 7.58 0.00 0.00 2.90
1919 5669 6.806120 TTATTCGTGTGATTCTCATGTACG 57.194 37.500 7.58 0.00 34.64 3.67
1920 5670 3.842732 TCGTGTGATTCTCATGTACGT 57.157 42.857 7.58 0.00 34.80 3.57
1979 5740 9.748708 CAAAACATGAAGAGATTTTCCAGTTTA 57.251 29.630 0.00 0.00 34.67 2.01
2151 5964 1.004745 ACATCGGCCCACTTTCTTCAT 59.995 47.619 0.00 0.00 0.00 2.57
2162 5975 7.378181 GCCCACTTTCTTCATTATCAAGAAAA 58.622 34.615 5.59 0.00 45.08 2.29
2171 5984 8.397906 TCTTCATTATCAAGAAAATGCCTAACG 58.602 33.333 0.00 0.00 33.91 3.18
2183 5996 2.660802 CTAACGAGGCCAACGGGT 59.339 61.111 22.33 13.96 36.17 5.28
2221 6034 7.595604 ACGGAAAATGTATGGTAAACGATTTT 58.404 30.769 0.00 0.00 0.00 1.82
2222 6035 7.539366 ACGGAAAATGTATGGTAAACGATTTTG 59.461 33.333 0.00 0.00 0.00 2.44
2223 6036 7.539366 CGGAAAATGTATGGTAAACGATTTTGT 59.461 33.333 0.00 0.00 0.00 2.83
2224 6037 8.856247 GGAAAATGTATGGTAAACGATTTTGTC 58.144 33.333 0.00 0.00 0.00 3.18
2225 6038 9.620660 GAAAATGTATGGTAAACGATTTTGTCT 57.379 29.630 0.00 0.00 0.00 3.41
2262 8066 4.571984 GGTAAACAATTAAGTACGCCCGAT 59.428 41.667 0.00 0.00 0.00 4.18
2339 8189 2.366590 AGAGAACACTGCACATCTCACA 59.633 45.455 12.96 0.00 40.57 3.58
2340 8190 2.478134 GAGAACACTGCACATCTCACAC 59.522 50.000 7.90 0.00 38.51 3.82
2370 8220 0.249657 CTTGCGGTCCTCTCCATAGC 60.250 60.000 0.00 0.00 0.00 2.97
2374 8224 2.134287 GGTCCTCTCCATAGCCGCA 61.134 63.158 0.00 0.00 0.00 5.69
2379 8229 1.971505 CTCTCCATAGCCGCACCCAA 61.972 60.000 0.00 0.00 0.00 4.12
2410 8260 5.510520 GCCTCTCTCCTACCACTCATATTTG 60.511 48.000 0.00 0.00 0.00 2.32
2414 8264 3.035363 TCCTACCACTCATATTTGCCGA 58.965 45.455 0.00 0.00 0.00 5.54
2423 8273 0.662619 ATATTTGCCGATGGTGTGCG 59.337 50.000 0.00 0.00 0.00 5.34
2428 8278 2.202797 CCGATGGTGTGCGAGAGG 60.203 66.667 0.00 0.00 0.00 3.69
2522 8372 1.661341 CCCTATGCTGTTGAGAGTGC 58.339 55.000 0.00 0.00 0.00 4.40
2528 8378 1.571460 CTGTTGAGAGTGCCGTTGC 59.429 57.895 0.00 0.00 38.26 4.17
2557 8407 4.778415 GAGTTGCGAGGCGAGCGA 62.778 66.667 0.00 0.00 37.44 4.93
2573 8423 1.972198 CGACAGGAGGGCTGTAACA 59.028 57.895 0.00 0.00 34.88 2.41
2577 8427 1.021390 CAGGAGGGCTGTAACAAGCG 61.021 60.000 0.00 0.00 44.52 4.68
2581 8431 2.561373 GGCTGTAACAAGCGTGGC 59.439 61.111 4.26 0.00 44.52 5.01
2657 8507 2.047274 CCAACCATCGTCGGTGCT 60.047 61.111 0.00 0.00 39.95 4.40
2676 8526 2.149803 TACAACCGACGGCCAGTGAG 62.150 60.000 15.39 0.00 0.00 3.51
2683 8533 2.749044 CGGCCAGTGAGCTGCAAT 60.749 61.111 2.24 0.00 41.26 3.56
2686 8536 1.246056 GGCCAGTGAGCTGCAATTGA 61.246 55.000 10.34 0.00 41.26 2.57
2704 8554 2.125310 CATCGGGCGGTGCTACAA 60.125 61.111 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.184830 CCAGCGGCCATGTCTCATG 61.185 63.158 2.24 3.11 0.00 3.07
1 2 2.191375 CCAGCGGCCATGTCTCAT 59.809 61.111 2.24 0.00 0.00 2.90
2 3 4.783621 GCCAGCGGCCATGTCTCA 62.784 66.667 2.24 0.00 44.06 3.27
46 47 6.462552 TTCATGTCCACATTCAACTTTTGA 57.537 33.333 0.00 0.00 38.04 2.69
47 48 7.307514 CCATTTCATGTCCACATTCAACTTTTG 60.308 37.037 0.00 0.00 33.61 2.44
48 49 6.707161 CCATTTCATGTCCACATTCAACTTTT 59.293 34.615 0.00 0.00 33.61 2.27
49 50 6.225318 CCATTTCATGTCCACATTCAACTTT 58.775 36.000 0.00 0.00 33.61 2.66
50 51 5.279607 CCCATTTCATGTCCACATTCAACTT 60.280 40.000 0.00 0.00 33.61 2.66
51 52 4.221262 CCCATTTCATGTCCACATTCAACT 59.779 41.667 0.00 0.00 33.61 3.16
52 53 4.021192 ACCCATTTCATGTCCACATTCAAC 60.021 41.667 0.00 0.00 33.61 3.18
53 54 4.158786 ACCCATTTCATGTCCACATTCAA 58.841 39.130 0.00 0.00 33.61 2.69
54 55 3.763360 GACCCATTTCATGTCCACATTCA 59.237 43.478 0.00 0.00 33.61 2.57
55 56 3.181497 CGACCCATTTCATGTCCACATTC 60.181 47.826 0.00 0.00 33.61 2.67
56 57 2.754552 CGACCCATTTCATGTCCACATT 59.245 45.455 0.00 0.00 33.61 2.71
57 58 2.368439 CGACCCATTTCATGTCCACAT 58.632 47.619 0.00 0.00 36.96 3.21
58 59 1.612991 CCGACCCATTTCATGTCCACA 60.613 52.381 0.00 0.00 0.00 4.17
59 60 1.094785 CCGACCCATTTCATGTCCAC 58.905 55.000 0.00 0.00 0.00 4.02
60 61 0.679640 GCCGACCCATTTCATGTCCA 60.680 55.000 0.00 0.00 0.00 4.02
61 62 1.714899 CGCCGACCCATTTCATGTCC 61.715 60.000 0.00 0.00 0.00 4.02
62 63 1.721487 CGCCGACCCATTTCATGTC 59.279 57.895 0.00 0.00 0.00 3.06
63 64 2.406616 GCGCCGACCCATTTCATGT 61.407 57.895 0.00 0.00 0.00 3.21
64 65 2.408835 GCGCCGACCCATTTCATG 59.591 61.111 0.00 0.00 0.00 3.07
65 66 3.202001 CGCGCCGACCCATTTCAT 61.202 61.111 0.00 0.00 0.00 2.57
66 67 4.690719 ACGCGCCGACCCATTTCA 62.691 61.111 5.73 0.00 0.00 2.69
67 68 3.428282 AACGCGCCGACCCATTTC 61.428 61.111 5.73 0.00 0.00 2.17
68 69 3.732892 CAACGCGCCGACCCATTT 61.733 61.111 5.73 0.00 0.00 2.32
87 88 0.814457 TATTTGGGTCGGCAATGTGC 59.186 50.000 0.00 0.00 44.08 4.57
88 89 4.909696 TTATATTTGGGTCGGCAATGTG 57.090 40.909 0.00 0.00 0.00 3.21
89 90 5.420739 AGTTTTATATTTGGGTCGGCAATGT 59.579 36.000 0.00 0.00 0.00 2.71
90 91 5.748152 CAGTTTTATATTTGGGTCGGCAATG 59.252 40.000 0.00 0.00 0.00 2.82
91 92 5.163457 CCAGTTTTATATTTGGGTCGGCAAT 60.163 40.000 0.00 0.00 0.00 3.56
92 93 4.158764 CCAGTTTTATATTTGGGTCGGCAA 59.841 41.667 0.00 0.00 0.00 4.52
93 94 3.697045 CCAGTTTTATATTTGGGTCGGCA 59.303 43.478 0.00 0.00 0.00 5.69
94 95 3.067601 CCCAGTTTTATATTTGGGTCGGC 59.932 47.826 0.19 0.00 44.27 5.54
95 96 4.911514 CCCAGTTTTATATTTGGGTCGG 57.088 45.455 0.19 0.00 44.27 4.79
100 101 3.242936 CGTCCGCCCAGTTTTATATTTGG 60.243 47.826 0.00 0.00 0.00 3.28
101 102 3.790789 GCGTCCGCCCAGTTTTATATTTG 60.791 47.826 0.00 0.00 34.56 2.32
102 103 2.356695 GCGTCCGCCCAGTTTTATATTT 59.643 45.455 0.00 0.00 34.56 1.40
103 104 1.944709 GCGTCCGCCCAGTTTTATATT 59.055 47.619 0.00 0.00 34.56 1.28
104 105 1.589803 GCGTCCGCCCAGTTTTATAT 58.410 50.000 0.00 0.00 34.56 0.86
105 106 3.068574 GCGTCCGCCCAGTTTTATA 57.931 52.632 0.00 0.00 34.56 0.98
106 107 3.899395 GCGTCCGCCCAGTTTTAT 58.101 55.556 0.00 0.00 34.56 1.40
125 126 3.842925 TTGGGTCAGCCGCCTGTTC 62.843 63.158 0.00 0.00 40.09 3.18
126 127 2.713531 ATTTGGGTCAGCCGCCTGTT 62.714 55.000 0.00 0.00 40.09 3.16
127 128 3.210012 ATTTGGGTCAGCCGCCTGT 62.210 57.895 0.00 0.00 40.09 4.00
128 129 2.361610 ATTTGGGTCAGCCGCCTG 60.362 61.111 0.00 0.00 40.54 4.85
129 130 2.361610 CATTTGGGTCAGCCGCCT 60.362 61.111 0.00 0.00 34.97 5.52
130 131 3.451894 CCATTTGGGTCAGCCGCC 61.452 66.667 0.00 0.00 34.97 6.13
131 132 2.361104 TCCATTTGGGTCAGCCGC 60.361 61.111 0.00 0.00 38.11 6.53
132 133 0.893270 TTGTCCATTTGGGTCAGCCG 60.893 55.000 0.00 0.00 36.07 5.52
133 134 1.337118 TTTGTCCATTTGGGTCAGCC 58.663 50.000 0.00 0.00 36.07 4.85
134 135 3.392882 CTTTTTGTCCATTTGGGTCAGC 58.607 45.455 0.00 0.00 36.07 4.26
135 136 3.392882 GCTTTTTGTCCATTTGGGTCAG 58.607 45.455 0.00 0.00 36.07 3.51
136 137 2.223923 CGCTTTTTGTCCATTTGGGTCA 60.224 45.455 0.00 0.00 38.11 4.02
137 138 2.403259 CGCTTTTTGTCCATTTGGGTC 58.597 47.619 0.00 0.00 38.11 4.46
138 139 1.069978 CCGCTTTTTGTCCATTTGGGT 59.930 47.619 0.00 0.00 38.11 4.51
139 140 1.342819 TCCGCTTTTTGTCCATTTGGG 59.657 47.619 0.00 0.00 35.41 4.12
140 141 2.223923 TGTCCGCTTTTTGTCCATTTGG 60.224 45.455 0.00 0.00 0.00 3.28
141 142 3.090952 TGTCCGCTTTTTGTCCATTTG 57.909 42.857 0.00 0.00 0.00 2.32
142 143 3.810310 TTGTCCGCTTTTTGTCCATTT 57.190 38.095 0.00 0.00 0.00 2.32
143 144 3.810310 TTTGTCCGCTTTTTGTCCATT 57.190 38.095 0.00 0.00 0.00 3.16
144 145 4.614993 CGTATTTGTCCGCTTTTTGTCCAT 60.615 41.667 0.00 0.00 0.00 3.41
145 146 3.304123 CGTATTTGTCCGCTTTTTGTCCA 60.304 43.478 0.00 0.00 0.00 4.02
146 147 3.231160 CGTATTTGTCCGCTTTTTGTCC 58.769 45.455 0.00 0.00 0.00 4.02
147 148 2.655001 GCGTATTTGTCCGCTTTTTGTC 59.345 45.455 0.00 0.00 0.00 3.18
148 149 2.606065 GGCGTATTTGTCCGCTTTTTGT 60.606 45.455 3.96 0.00 0.00 2.83
149 150 1.982913 GGCGTATTTGTCCGCTTTTTG 59.017 47.619 3.96 0.00 0.00 2.44
150 151 1.400500 CGGCGTATTTGTCCGCTTTTT 60.400 47.619 0.00 0.00 36.53 1.94
151 152 0.167251 CGGCGTATTTGTCCGCTTTT 59.833 50.000 0.00 0.00 36.53 2.27
152 153 0.952010 ACGGCGTATTTGTCCGCTTT 60.952 50.000 12.58 0.00 46.49 3.51
153 154 1.356527 GACGGCGTATTTGTCCGCTT 61.357 55.000 14.74 0.00 46.49 4.68
154 155 1.808390 GACGGCGTATTTGTCCGCT 60.808 57.895 14.74 0.00 46.49 5.52
155 156 0.526096 TAGACGGCGTATTTGTCCGC 60.526 55.000 14.74 0.00 46.49 5.54
156 157 6.295935 CCAAATAGACGGCGTATTTGTCCG 62.296 50.000 30.74 19.76 42.56 4.79
157 158 3.001939 CCAAATAGACGGCGTATTTGTCC 59.998 47.826 30.74 13.92 42.56 4.02
158 159 3.866910 TCCAAATAGACGGCGTATTTGTC 59.133 43.478 30.74 14.53 42.56 3.18
159 160 3.864243 TCCAAATAGACGGCGTATTTGT 58.136 40.909 30.74 13.19 42.56 2.83
160 161 4.376008 CGATCCAAATAGACGGCGTATTTG 60.376 45.833 28.50 28.50 43.24 2.32
161 162 3.739300 CGATCCAAATAGACGGCGTATTT 59.261 43.478 14.74 13.93 31.54 1.40
162 163 3.314553 CGATCCAAATAGACGGCGTATT 58.685 45.455 14.74 7.48 0.00 1.89
163 164 2.925306 GCGATCCAAATAGACGGCGTAT 60.925 50.000 14.74 13.91 0.00 3.06
164 165 1.601162 GCGATCCAAATAGACGGCGTA 60.601 52.381 14.74 0.00 0.00 4.42
165 166 0.874607 GCGATCCAAATAGACGGCGT 60.875 55.000 14.65 14.65 0.00 5.68
166 167 1.557443 GGCGATCCAAATAGACGGCG 61.557 60.000 4.80 4.80 39.35 6.46
167 168 1.228657 GGGCGATCCAAATAGACGGC 61.229 60.000 0.00 0.00 45.83 5.68
168 169 0.602905 GGGGCGATCCAAATAGACGG 60.603 60.000 0.00 0.00 37.22 4.79
169 170 0.105964 TGGGGCGATCCAAATAGACG 59.894 55.000 0.00 0.00 37.22 4.18
170 171 2.554032 CAATGGGGCGATCCAAATAGAC 59.446 50.000 1.33 0.00 40.62 2.59
171 172 2.488891 CCAATGGGGCGATCCAAATAGA 60.489 50.000 0.00 0.00 40.62 1.98
172 173 1.888512 CCAATGGGGCGATCCAAATAG 59.111 52.381 0.00 0.00 40.62 1.73
173 174 1.496857 TCCAATGGGGCGATCCAAATA 59.503 47.619 0.00 0.00 40.62 1.40
174 175 0.261402 TCCAATGGGGCGATCCAAAT 59.739 50.000 0.00 0.00 40.62 2.32
175 176 0.395586 CTCCAATGGGGCGATCCAAA 60.396 55.000 0.00 0.00 40.62 3.28
176 177 1.227102 CTCCAATGGGGCGATCCAA 59.773 57.895 0.00 0.00 40.62 3.53
177 178 1.570857 AACTCCAATGGGGCGATCCA 61.571 55.000 0.00 0.00 41.60 3.41
178 179 1.103398 CAACTCCAATGGGGCGATCC 61.103 60.000 0.00 0.00 36.21 3.36
179 180 1.728490 GCAACTCCAATGGGGCGATC 61.728 60.000 0.00 0.00 36.21 3.69
180 181 1.754234 GCAACTCCAATGGGGCGAT 60.754 57.895 0.00 0.00 36.21 4.58
181 182 2.361104 GCAACTCCAATGGGGCGA 60.361 61.111 0.00 0.00 36.21 5.54
182 183 2.361610 AGCAACTCCAATGGGGCG 60.362 61.111 0.00 0.00 36.21 6.13
183 184 0.613012 AAGAGCAACTCCAATGGGGC 60.613 55.000 0.00 0.00 36.21 5.80
184 185 2.648059 CTAAGAGCAACTCCAATGGGG 58.352 52.381 0.00 0.00 38.37 4.96
185 186 2.019984 GCTAAGAGCAACTCCAATGGG 58.980 52.381 0.00 0.00 41.89 4.00
197 198 0.107508 TGGTGCCAGATGCTAAGAGC 60.108 55.000 0.00 0.00 42.82 4.09
198 199 1.661341 GTGGTGCCAGATGCTAAGAG 58.339 55.000 0.00 0.00 42.00 2.85
199 200 0.253044 GGTGGTGCCAGATGCTAAGA 59.747 55.000 0.00 0.00 42.00 2.10
200 201 1.091771 CGGTGGTGCCAGATGCTAAG 61.092 60.000 0.00 0.00 42.00 2.18
201 202 1.078497 CGGTGGTGCCAGATGCTAA 60.078 57.895 0.00 0.00 42.00 3.09
202 203 2.584064 CGGTGGTGCCAGATGCTA 59.416 61.111 0.00 0.00 42.00 3.49
203 204 4.415150 CCGGTGGTGCCAGATGCT 62.415 66.667 0.00 0.00 42.00 3.79
204 205 4.722700 ACCGGTGGTGCCAGATGC 62.723 66.667 6.12 0.00 41.77 3.91
205 206 2.436646 GACCGGTGGTGCCAGATG 60.437 66.667 14.63 0.00 35.25 2.90
206 207 4.082523 CGACCGGTGGTGCCAGAT 62.083 66.667 14.63 0.00 35.25 2.90
217 218 2.095059 CGGTATATTCTTACCCGACCGG 60.095 54.545 0.00 0.00 43.51 5.28
218 219 3.207474 CGGTATATTCTTACCCGACCG 57.793 52.381 0.00 0.00 41.96 4.79
219 220 3.569701 TGACGGTATATTCTTACCCGACC 59.430 47.826 3.10 0.00 38.77 4.79
220 221 4.791974 CTGACGGTATATTCTTACCCGAC 58.208 47.826 3.10 0.00 38.77 4.79
221 222 3.254166 GCTGACGGTATATTCTTACCCGA 59.746 47.826 3.10 0.00 38.77 5.14
222 223 3.005050 TGCTGACGGTATATTCTTACCCG 59.995 47.826 0.00 0.00 38.77 5.28
223 224 4.595762 TGCTGACGGTATATTCTTACCC 57.404 45.455 0.00 0.00 38.77 3.69
224 225 5.864474 CAGATGCTGACGGTATATTCTTACC 59.136 44.000 0.00 0.00 34.94 2.85
225 226 6.448006 ACAGATGCTGACGGTATATTCTTAC 58.552 40.000 0.82 0.00 35.18 2.34
226 227 6.650427 ACAGATGCTGACGGTATATTCTTA 57.350 37.500 0.82 0.00 35.18 2.10
227 228 5.537300 ACAGATGCTGACGGTATATTCTT 57.463 39.130 0.82 0.00 35.18 2.52
228 229 6.448006 GTTACAGATGCTGACGGTATATTCT 58.552 40.000 0.82 0.00 35.18 2.40
229 230 5.634020 GGTTACAGATGCTGACGGTATATTC 59.366 44.000 0.82 0.00 35.18 1.75
230 231 5.510861 GGGTTACAGATGCTGACGGTATATT 60.511 44.000 0.82 0.00 35.18 1.28
231 232 4.021368 GGGTTACAGATGCTGACGGTATAT 60.021 45.833 0.82 0.00 35.18 0.86
232 233 3.319972 GGGTTACAGATGCTGACGGTATA 59.680 47.826 0.82 0.00 35.18 1.47
233 234 2.102588 GGGTTACAGATGCTGACGGTAT 59.897 50.000 0.82 0.00 35.18 2.73
234 235 1.479323 GGGTTACAGATGCTGACGGTA 59.521 52.381 0.82 0.00 35.18 4.02
235 236 0.249398 GGGTTACAGATGCTGACGGT 59.751 55.000 0.82 0.00 35.18 4.83
236 237 0.537188 AGGGTTACAGATGCTGACGG 59.463 55.000 0.82 0.00 35.18 4.79
237 238 2.271800 GAAGGGTTACAGATGCTGACG 58.728 52.381 0.82 0.00 35.18 4.35
238 239 3.334583 TGAAGGGTTACAGATGCTGAC 57.665 47.619 0.82 0.00 35.18 3.51
239 240 3.559171 GGTTGAAGGGTTACAGATGCTGA 60.559 47.826 0.82 0.00 35.18 4.26
240 241 2.749621 GGTTGAAGGGTTACAGATGCTG 59.250 50.000 0.00 0.00 37.52 4.41
265 270 2.938838 TGGTGGACGGAAAGAATGTTT 58.061 42.857 0.00 0.00 0.00 2.83
266 271 2.649531 TGGTGGACGGAAAGAATGTT 57.350 45.000 0.00 0.00 0.00 2.71
277 282 2.159099 AGTATACTGCACATGGTGGACG 60.159 50.000 4.10 0.00 33.64 4.79
278 283 3.543680 AGTATACTGCACATGGTGGAC 57.456 47.619 4.10 0.00 33.64 4.02
297 302 2.218759 CGAACTGGTCGTCAACTGAAAG 59.781 50.000 7.00 0.00 45.09 2.62
373 383 2.167693 AGGTTACAGCGCACTATAAGCA 59.832 45.455 11.47 0.00 36.06 3.91
419 429 1.153168 CGTCTTGGGATTGGCCGAT 60.153 57.895 4.69 4.69 37.63 4.18
423 433 1.017387 GATGACGTCTTGGGATTGGC 58.983 55.000 17.92 0.00 0.00 4.52
458 468 0.913924 GGGGTAGGAATTTGGACGGA 59.086 55.000 0.00 0.00 0.00 4.69
461 471 0.913924 TCCGGGGTAGGAATTTGGAC 59.086 55.000 0.00 0.00 37.36 4.02
462 472 0.913924 GTCCGGGGTAGGAATTTGGA 59.086 55.000 0.00 0.00 42.77 3.53
533 543 3.870723 TGTTGCGATTTGGCGATATAC 57.129 42.857 0.00 0.00 35.06 1.47
539 549 1.469917 GATGATGTTGCGATTTGGCG 58.530 50.000 0.00 0.00 35.06 5.69
717 729 9.730705 CAATGAATGATCTCCTAAAATAGGCTA 57.269 33.333 0.00 0.00 45.82 3.93
718 730 7.668886 CCAATGAATGATCTCCTAAAATAGGCT 59.331 37.037 0.00 0.00 45.82 4.58
719 731 7.667219 TCCAATGAATGATCTCCTAAAATAGGC 59.333 37.037 0.00 0.00 45.82 3.93
827 852 6.097412 CCAATTGGAGGGAAAGAAATAGAAGG 59.903 42.308 20.50 0.00 37.39 3.46
869 898 7.787725 ATGGTAAGCAATTAGTAGTAGTTGC 57.212 36.000 23.34 23.34 46.90 4.17
871 900 9.953565 TGAAATGGTAAGCAATTAGTAGTAGTT 57.046 29.630 0.00 0.00 0.00 2.24
875 904 8.903820 GGATTGAAATGGTAAGCAATTAGTAGT 58.096 33.333 0.00 0.00 31.65 2.73
876 905 8.070171 CGGATTGAAATGGTAAGCAATTAGTAG 58.930 37.037 0.00 0.00 31.65 2.57
877 906 7.468084 GCGGATTGAAATGGTAAGCAATTAGTA 60.468 37.037 0.00 0.00 31.65 1.82
878 907 6.680378 GCGGATTGAAATGGTAAGCAATTAGT 60.680 38.462 0.00 0.00 31.65 2.24
879 908 5.687285 GCGGATTGAAATGGTAAGCAATTAG 59.313 40.000 0.00 0.00 31.65 1.73
880 909 5.587289 GCGGATTGAAATGGTAAGCAATTA 58.413 37.500 0.00 0.00 31.65 1.40
881 910 4.432712 GCGGATTGAAATGGTAAGCAATT 58.567 39.130 0.00 0.00 31.65 2.32
882 911 3.489059 CGCGGATTGAAATGGTAAGCAAT 60.489 43.478 0.00 0.00 33.97 3.56
883 912 2.159448 CGCGGATTGAAATGGTAAGCAA 60.159 45.455 0.00 0.00 0.00 3.91
921 950 1.153127 TCAGTCCCACGCGGTTTTT 60.153 52.632 12.47 0.00 0.00 1.94
922 951 1.597027 CTCAGTCCCACGCGGTTTT 60.597 57.895 12.47 0.00 0.00 2.43
923 952 2.030562 CTCAGTCCCACGCGGTTT 59.969 61.111 12.47 0.00 0.00 3.27
924 953 4.003788 CCTCAGTCCCACGCGGTT 62.004 66.667 12.47 0.00 0.00 4.44
925 954 4.988716 TCCTCAGTCCCACGCGGT 62.989 66.667 12.47 0.00 0.00 5.68
926 955 3.461773 ATCCTCAGTCCCACGCGG 61.462 66.667 12.47 0.00 0.00 6.46
927 956 2.202797 CATCCTCAGTCCCACGCG 60.203 66.667 3.53 3.53 0.00 6.01
928 957 2.187946 CCATCCTCAGTCCCACGC 59.812 66.667 0.00 0.00 0.00 5.34
929 958 1.680522 CCTCCATCCTCAGTCCCACG 61.681 65.000 0.00 0.00 0.00 4.94
930 959 0.325671 TCCTCCATCCTCAGTCCCAC 60.326 60.000 0.00 0.00 0.00 4.61
931 960 0.031716 CTCCTCCATCCTCAGTCCCA 60.032 60.000 0.00 0.00 0.00 4.37
932 961 1.406860 GCTCCTCCATCCTCAGTCCC 61.407 65.000 0.00 0.00 0.00 4.46
933 962 0.398381 AGCTCCTCCATCCTCAGTCC 60.398 60.000 0.00 0.00 0.00 3.85
934 963 1.039856 GAGCTCCTCCATCCTCAGTC 58.960 60.000 0.87 0.00 0.00 3.51
935 964 0.754957 CGAGCTCCTCCATCCTCAGT 60.755 60.000 8.47 0.00 0.00 3.41
952 981 2.223782 CCATTTTATACCGACCGACCGA 60.224 50.000 0.00 0.00 0.00 4.69
953 982 2.129607 CCATTTTATACCGACCGACCG 58.870 52.381 0.00 0.00 0.00 4.79
954 983 1.869132 GCCATTTTATACCGACCGACC 59.131 52.381 0.00 0.00 0.00 4.79
955 984 1.869132 GGCCATTTTATACCGACCGAC 59.131 52.381 0.00 0.00 0.00 4.79
1038 1067 3.284449 GTGTGTGTGGGCGGGTTC 61.284 66.667 0.00 0.00 0.00 3.62
1039 1068 4.887190 GGTGTGTGTGGGCGGGTT 62.887 66.667 0.00 0.00 0.00 4.11
1042 1071 4.659172 ATGGGTGTGTGTGGGCGG 62.659 66.667 0.00 0.00 0.00 6.13
1059 1088 1.460689 AGGGGTTGGTGAGGAACGA 60.461 57.895 0.00 0.00 0.00 3.85
1060 1089 1.003718 GAGGGGTTGGTGAGGAACG 60.004 63.158 0.00 0.00 0.00 3.95
1061 1090 0.325272 GAGAGGGGTTGGTGAGGAAC 59.675 60.000 0.00 0.00 0.00 3.62
1085 1117 3.344215 GCTGCCCATGATCGCGAG 61.344 66.667 16.66 0.00 0.00 5.03
1086 1118 3.797225 GAGCTGCCCATGATCGCGA 62.797 63.158 13.09 13.09 0.00 5.87
1087 1119 3.344215 GAGCTGCCCATGATCGCG 61.344 66.667 0.00 0.00 0.00 5.87
1088 1120 2.203112 TGAGCTGCCCATGATCGC 60.203 61.111 0.00 0.00 0.00 4.58
1102 1142 3.316573 GAGGCCTTCCACCCGTGAG 62.317 68.421 6.77 0.00 33.74 3.51
1197 1237 2.987547 GGTCCACGTCGTCCTCCA 60.988 66.667 0.00 0.00 0.00 3.86
1471 1537 1.327303 GACCCACAAAGCATGAACCA 58.673 50.000 0.00 0.00 0.00 3.67
1473 1539 2.362077 ACTTGACCCACAAAGCATGAAC 59.638 45.455 0.00 0.00 38.08 3.18
1498 1564 6.546034 ACAGCTTCAACCAAAACTTACACTAT 59.454 34.615 0.00 0.00 0.00 2.12
1503 1569 3.796717 GCACAGCTTCAACCAAAACTTAC 59.203 43.478 0.00 0.00 0.00 2.34
1504 1570 3.445450 TGCACAGCTTCAACCAAAACTTA 59.555 39.130 0.00 0.00 0.00 2.24
1543 2183 6.203723 GCAATCTCCAACTCCAGTCATATAAC 59.796 42.308 0.00 0.00 0.00 1.89
1544 2184 6.126796 TGCAATCTCCAACTCCAGTCATATAA 60.127 38.462 0.00 0.00 0.00 0.98
1553 2202 2.238521 GGTTTGCAATCTCCAACTCCA 58.761 47.619 0.00 0.00 0.00 3.86
1568 2217 5.924475 AACGAGAAGTATCTGTTGGTTTG 57.076 39.130 0.00 0.00 35.54 2.93
1600 2249 6.727824 AGAATAACACGAGGATTTGTGAAG 57.272 37.500 2.10 0.00 40.57 3.02
1636 2291 6.424509 CCTTTCTCAGCAATCTATCAAGCTAG 59.575 42.308 0.00 0.00 35.19 3.42
1647 3609 8.518702 AGAAAAGATAAACCTTTCTCAGCAATC 58.481 33.333 0.00 0.00 35.50 2.67
1718 3680 5.532406 AGCAACAACGATCCAGCAATATATT 59.468 36.000 0.00 0.00 0.00 1.28
1733 3695 7.642194 TCATAAGTGTAAGAAAAAGCAACAACG 59.358 33.333 0.00 0.00 0.00 4.10
1734 3696 8.850454 TCATAAGTGTAAGAAAAAGCAACAAC 57.150 30.769 0.00 0.00 0.00 3.32
1810 5430 4.752101 AGGTCTGATATTCGCTTGTTATGC 59.248 41.667 0.00 0.00 0.00 3.14
1829 5449 8.766151 CCGAAGAAGAAGCTAATTAATTAGGTC 58.234 37.037 30.28 23.87 46.80 3.85
1863 5566 1.983224 CTTGTGGAGGATCACGGGT 59.017 57.895 0.00 0.00 40.31 5.28
1917 5667 3.252701 CCCTCGCAATATCTGTACTACGT 59.747 47.826 0.00 0.00 0.00 3.57
1918 5668 3.252701 ACCCTCGCAATATCTGTACTACG 59.747 47.826 0.00 0.00 0.00 3.51
1919 5669 4.547532 CACCCTCGCAATATCTGTACTAC 58.452 47.826 0.00 0.00 0.00 2.73
1920 5670 3.005472 GCACCCTCGCAATATCTGTACTA 59.995 47.826 0.00 0.00 0.00 1.82
1926 5676 0.541392 TGTGCACCCTCGCAATATCT 59.459 50.000 15.69 0.00 45.14 1.98
2151 5964 6.677781 CCTCGTTAGGCATTTTCTTGATAA 57.322 37.500 0.00 0.00 35.64 1.75
2183 5996 4.279671 ACATTTTCCGTTACATTTGCCTCA 59.720 37.500 0.00 0.00 0.00 3.86
2231 6044 8.453320 GCGTACTTAATTGTTTACCATACCTTT 58.547 33.333 0.00 0.00 0.00 3.11
2232 6045 7.066163 GGCGTACTTAATTGTTTACCATACCTT 59.934 37.037 0.00 0.00 0.00 3.50
2233 6046 6.539826 GGCGTACTTAATTGTTTACCATACCT 59.460 38.462 0.00 0.00 0.00 3.08
2246 8050 2.144482 CCGATCGGGCGTACTTAATT 57.856 50.000 26.95 0.00 0.00 1.40
2279 8083 4.080863 GGATAAGGAAAGAGAGAGCAACCA 60.081 45.833 0.00 0.00 0.00 3.67
2283 8087 6.380079 AAAAGGATAAGGAAAGAGAGAGCA 57.620 37.500 0.00 0.00 0.00 4.26
2323 8173 0.250467 GGGTGTGAGATGTGCAGTGT 60.250 55.000 0.00 0.00 0.00 3.55
2327 8177 1.841302 GAGGGGGTGTGAGATGTGCA 61.841 60.000 0.00 0.00 0.00 4.57
2353 8203 2.134287 GGCTATGGAGAGGACCGCA 61.134 63.158 0.00 0.00 0.00 5.69
2374 8224 3.628646 GAGAGGCGCATGGTTGGGT 62.629 63.158 10.83 0.00 38.05 4.51
2379 8229 1.075970 TAGGAGAGAGGCGCATGGT 60.076 57.895 10.83 0.00 0.00 3.55
2410 8260 2.887568 CTCTCGCACACCATCGGC 60.888 66.667 0.00 0.00 0.00 5.54
2414 8264 2.267006 CTGCCTCTCGCACACCAT 59.733 61.111 0.00 0.00 44.64 3.55
2423 8273 1.444553 CAACGACGGTCTGCCTCTC 60.445 63.158 6.57 0.00 0.00 3.20
2428 8278 0.669318 TGAATCCAACGACGGTCTGC 60.669 55.000 6.57 0.00 0.00 4.26
2497 8347 1.754234 CAACAGCATAGGGGGTGGC 60.754 63.158 0.00 0.00 40.47 5.01
2507 8357 0.250467 AACGGCACTCTCAACAGCAT 60.250 50.000 0.00 0.00 0.00 3.79
2510 8360 1.571460 GCAACGGCACTCTCAACAG 59.429 57.895 0.00 0.00 40.72 3.16
2528 8378 3.197790 CAACTCGCCATGGCCTCG 61.198 66.667 30.79 20.26 37.98 4.63
2566 8416 1.491563 GTCGCCACGCTTGTTACAG 59.508 57.895 0.00 0.00 0.00 2.74
2577 8427 4.030452 GTTGCAGCAGGTCGCCAC 62.030 66.667 0.00 0.00 44.04 5.01
2602 8452 2.874694 CGATTCCAGCACGCCATCG 61.875 63.158 0.00 0.00 42.43 3.84
2612 8462 1.971481 TCAATGATGGCCGATTCCAG 58.029 50.000 0.00 0.00 39.89 3.86
2657 8507 2.149803 CTCACTGGCCGTCGGTTGTA 62.150 60.000 13.94 0.00 31.34 2.41
2676 8526 1.226773 GCCCGATGTCAATTGCAGC 60.227 57.895 0.00 4.40 0.00 5.25
2679 8529 2.406616 ACCGCCCGATGTCAATTGC 61.407 57.895 0.00 0.00 0.00 3.56
2683 8533 2.651105 TAGCACCGCCCGATGTCAA 61.651 57.895 0.00 0.00 0.00 3.18
2686 8536 2.949909 TTGTAGCACCGCCCGATGT 61.950 57.895 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.