Multiple sequence alignment - TraesCS1B01G209400

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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 TraesCS1B01G209400 chr1B 100.000 2034 0 0 1906 3939 380432930 380434963 0.000000e+00 3757
1 TraesCS1B01G209400 chr1B 100.000 1503 0 0 1 1503 380431025 380432527 0.000000e+00 2776
2 TraesCS1B01G209400 chr1B 89.485 485 44 5 1 482 117767999 117768479 1.210000e-169 606
3 TraesCS1B01G209400 chr1A 92.199 1564 57 30 1906 3432 351856575 351858110 0.000000e+00 2152
4 TraesCS1B01G209400 chr1A 88.935 1202 81 18 209 1377 351855076 351856258 0.000000e+00 1435
5 TraesCS1B01G209400 chr1A 93.448 580 19 7 3368 3939 351858102 351858670 0.000000e+00 843
6 TraesCS1B01G209400 chr1D 96.911 1133 33 1 1906 3038 279933214 279934344 0.000000e+00 1897
7 TraesCS1B01G209400 chr1D 91.656 815 25 22 3142 3939 279934583 279935371 0.000000e+00 1088
8 TraesCS1B01G209400 chr1D 90.358 643 37 11 843 1468 279932059 279932693 0.000000e+00 821
9 TraesCS1B01G209400 chr6B 90.269 483 40 4 1 479 274033794 274034273 3.340000e-175 625
10 TraesCS1B01G209400 chr2D 89.834 482 42 4 1 479 204551560 204552037 2.600000e-171 612
11 TraesCS1B01G209400 chr2D 89.648 483 44 3 1 479 595741178 595740698 9.360000e-171 610
12 TraesCS1B01G209400 chr5D 89.834 482 38 7 2 479 207993268 207993742 3.370000e-170 608
13 TraesCS1B01G209400 chr3A 89.770 479 42 5 3 478 218260720 218261194 1.210000e-169 606
14 TraesCS1B01G209400 chr3A 89.770 479 42 5 3 478 218310134 218310608 1.210000e-169 606
15 TraesCS1B01G209400 chr7B 89.419 482 44 4 1 479 181695156 181695633 5.630000e-168 601
16 TraesCS1B01G209400 chr7A 89.212 482 45 5 1 479 207748757 207748280 2.620000e-166 595
17 TraesCS1B01G209400 chr2A 82.550 149 20 6 761 908 551484436 551484293 4.130000e-25 126


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 TraesCS1B01G209400 chr1B 380431025 380434963 3938 False 3266.500000 3757 100.000000 1 3939 2 chr1B.!!$F2 3938
1 TraesCS1B01G209400 chr1A 351855076 351858670 3594 False 1476.666667 2152 91.527333 209 3939 3 chr1A.!!$F1 3730
2 TraesCS1B01G209400 chr1D 279932059 279935371 3312 False 1268.666667 1897 92.975000 843 3939 3 chr1D.!!$F1 3096

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
19 20 0.037232 GCACTGGCGAACTCCTAACT 60.037 55.0 0.00 0.0 0.0 2.24 F
938 966 0.179134 GGACGGATGTGAAGAGGACG 60.179 60.0 0.00 0.0 0.0 4.79 F
1201 1235 0.249447 TGTGTGTCGACCTGCTTCTG 60.249 55.0 14.12 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1115 1149 0.388649 GTACACCACGCAGTCTCTGG 60.389 60.000 0.0 0.0 41.61 3.86 R
2689 2818 0.475906 ACTGTCCTCCTTTTGCAGCT 59.524 50.000 0.0 0.0 0.00 4.24 R
2976 3105 4.579869 TGCTCCCAAGAAGAAATAGACAC 58.420 43.478 0.0 0.0 0.00 3.67 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
18 19 2.457080 GCACTGGCGAACTCCTAAC 58.543 57.895 0.00 0.00 0.00 2.34
19 20 0.037232 GCACTGGCGAACTCCTAACT 60.037 55.000 0.00 0.00 0.00 2.24
20 21 1.997669 CACTGGCGAACTCCTAACTC 58.002 55.000 0.00 0.00 0.00 3.01
21 22 0.896226 ACTGGCGAACTCCTAACTCC 59.104 55.000 0.00 0.00 0.00 3.85
22 23 1.187087 CTGGCGAACTCCTAACTCCT 58.813 55.000 0.00 0.00 0.00 3.69
23 24 1.550976 CTGGCGAACTCCTAACTCCTT 59.449 52.381 0.00 0.00 0.00 3.36
24 25 2.758979 CTGGCGAACTCCTAACTCCTTA 59.241 50.000 0.00 0.00 0.00 2.69
25 26 2.758979 TGGCGAACTCCTAACTCCTTAG 59.241 50.000 0.00 0.00 0.00 2.18
26 27 2.481622 GGCGAACTCCTAACTCCTTAGC 60.482 54.545 0.00 0.00 0.00 3.09
27 28 2.795331 GCGAACTCCTAACTCCTTAGCG 60.795 54.545 0.00 0.00 0.00 4.26
28 29 2.422832 CGAACTCCTAACTCCTTAGCGT 59.577 50.000 0.00 0.00 0.00 5.07
29 30 3.731264 CGAACTCCTAACTCCTTAGCGTG 60.731 52.174 0.00 0.00 0.00 5.34
30 31 3.083122 ACTCCTAACTCCTTAGCGTGA 57.917 47.619 0.00 0.00 0.00 4.35
31 32 2.754002 ACTCCTAACTCCTTAGCGTGAC 59.246 50.000 0.00 0.00 0.00 3.67
32 33 2.097825 TCCTAACTCCTTAGCGTGACC 58.902 52.381 0.00 0.00 0.00 4.02
33 34 1.822990 CCTAACTCCTTAGCGTGACCA 59.177 52.381 0.00 0.00 0.00 4.02
34 35 2.232941 CCTAACTCCTTAGCGTGACCAA 59.767 50.000 0.00 0.00 0.00 3.67
35 36 2.922740 AACTCCTTAGCGTGACCAAA 57.077 45.000 0.00 0.00 0.00 3.28
36 37 3.418684 AACTCCTTAGCGTGACCAAAT 57.581 42.857 0.00 0.00 0.00 2.32
37 38 3.418684 ACTCCTTAGCGTGACCAAATT 57.581 42.857 0.00 0.00 0.00 1.82
38 39 3.335579 ACTCCTTAGCGTGACCAAATTC 58.664 45.455 0.00 0.00 0.00 2.17
39 40 3.244422 ACTCCTTAGCGTGACCAAATTCA 60.244 43.478 0.00 0.00 0.00 2.57
40 41 3.941483 CTCCTTAGCGTGACCAAATTCAT 59.059 43.478 0.00 0.00 0.00 2.57
41 42 3.938963 TCCTTAGCGTGACCAAATTCATC 59.061 43.478 0.00 0.00 0.00 2.92
42 43 3.689161 CCTTAGCGTGACCAAATTCATCA 59.311 43.478 0.00 0.00 0.00 3.07
43 44 4.201851 CCTTAGCGTGACCAAATTCATCAG 60.202 45.833 0.00 0.00 0.00 2.90
44 45 1.470098 AGCGTGACCAAATTCATCAGC 59.530 47.619 0.00 0.00 0.00 4.26
45 46 1.791555 GCGTGACCAAATTCATCAGCG 60.792 52.381 0.00 0.00 0.00 5.18
46 47 1.731709 CGTGACCAAATTCATCAGCGA 59.268 47.619 0.00 0.00 0.00 4.93
47 48 2.474526 CGTGACCAAATTCATCAGCGAC 60.475 50.000 0.00 0.00 0.00 5.19
48 49 2.083774 TGACCAAATTCATCAGCGACC 58.916 47.619 0.00 0.00 0.00 4.79
49 50 2.083774 GACCAAATTCATCAGCGACCA 58.916 47.619 0.00 0.00 0.00 4.02
50 51 2.086869 ACCAAATTCATCAGCGACCAG 58.913 47.619 0.00 0.00 0.00 4.00
51 52 2.290260 ACCAAATTCATCAGCGACCAGA 60.290 45.455 0.00 0.00 0.00 3.86
52 53 2.947652 CCAAATTCATCAGCGACCAGAT 59.052 45.455 0.00 0.00 0.00 2.90
53 54 3.242969 CCAAATTCATCAGCGACCAGATG 60.243 47.826 0.00 0.00 42.25 2.90
59 60 2.299993 TCAGCGACCAGATGAACATC 57.700 50.000 6.68 6.68 43.00 3.06
60 61 1.550072 TCAGCGACCAGATGAACATCA 59.450 47.619 15.63 0.00 43.00 3.07
61 62 2.169144 TCAGCGACCAGATGAACATCAT 59.831 45.455 15.63 1.79 43.00 2.45
74 75 6.615264 ATGAACATCATCATTGTCACTAGC 57.385 37.500 0.00 0.00 36.67 3.42
75 76 5.490159 TGAACATCATCATTGTCACTAGCA 58.510 37.500 0.00 0.00 0.00 3.49
76 77 5.939296 TGAACATCATCATTGTCACTAGCAA 59.061 36.000 0.00 0.00 0.00 3.91
77 78 6.430616 TGAACATCATCATTGTCACTAGCAAA 59.569 34.615 0.00 0.00 0.00 3.68
78 79 7.121611 TGAACATCATCATTGTCACTAGCAAAT 59.878 33.333 0.00 0.00 0.00 2.32
79 80 6.792326 ACATCATCATTGTCACTAGCAAATG 58.208 36.000 0.00 0.00 0.00 2.32
80 81 5.239359 TCATCATTGTCACTAGCAAATGC 57.761 39.130 0.00 0.00 42.49 3.56
93 94 3.043635 GCAAATGCGTCAGATGTACTG 57.956 47.619 0.00 0.00 46.97 2.74
108 109 5.649831 AGATGTACTGAAGATTTCCAAAGGC 59.350 40.000 0.00 0.00 0.00 4.35
109 110 4.985538 TGTACTGAAGATTTCCAAAGGCT 58.014 39.130 0.00 0.00 0.00 4.58
110 111 5.385198 TGTACTGAAGATTTCCAAAGGCTT 58.615 37.500 0.00 0.00 0.00 4.35
111 112 5.473504 TGTACTGAAGATTTCCAAAGGCTTC 59.526 40.000 0.00 0.00 35.53 3.86
112 113 4.473444 ACTGAAGATTTCCAAAGGCTTCA 58.527 39.130 0.00 14.49 39.14 3.02
113 114 4.279420 ACTGAAGATTTCCAAAGGCTTCAC 59.721 41.667 0.00 0.00 37.85 3.18
114 115 4.473444 TGAAGATTTCCAAAGGCTTCACT 58.527 39.130 0.00 0.00 37.85 3.41
115 116 4.520492 TGAAGATTTCCAAAGGCTTCACTC 59.480 41.667 0.00 0.00 37.85 3.51
116 117 3.077359 AGATTTCCAAAGGCTTCACTCG 58.923 45.455 0.00 0.00 0.00 4.18
117 118 2.631160 TTTCCAAAGGCTTCACTCGA 57.369 45.000 0.00 0.00 0.00 4.04
118 119 2.631160 TTCCAAAGGCTTCACTCGAA 57.369 45.000 0.00 0.00 0.00 3.71
127 128 2.447244 CTTCACTCGAAGTGGCTCTT 57.553 50.000 12.89 0.67 45.94 2.85
128 129 2.064762 CTTCACTCGAAGTGGCTCTTG 58.935 52.381 6.53 0.09 45.94 3.02
129 130 1.040646 TCACTCGAAGTGGCTCTTGT 58.959 50.000 6.53 0.00 45.94 3.16
130 131 1.143305 CACTCGAAGTGGCTCTTGTG 58.857 55.000 6.53 5.34 42.35 3.33
131 132 0.753262 ACTCGAAGTGGCTCTTGTGT 59.247 50.000 6.53 4.14 36.40 3.72
132 133 1.961394 ACTCGAAGTGGCTCTTGTGTA 59.039 47.619 6.53 0.00 36.40 2.90
133 134 2.563179 ACTCGAAGTGGCTCTTGTGTAT 59.437 45.455 6.53 0.00 36.40 2.29
134 135 2.926200 CTCGAAGTGGCTCTTGTGTATG 59.074 50.000 6.53 0.00 36.40 2.39
135 136 2.002586 CGAAGTGGCTCTTGTGTATGG 58.997 52.381 6.53 0.00 36.40 2.74
136 137 2.359900 GAAGTGGCTCTTGTGTATGGG 58.640 52.381 6.53 0.00 36.40 4.00
137 138 1.362224 AGTGGCTCTTGTGTATGGGT 58.638 50.000 0.00 0.00 0.00 4.51
138 139 1.705186 AGTGGCTCTTGTGTATGGGTT 59.295 47.619 0.00 0.00 0.00 4.11
139 140 2.108250 AGTGGCTCTTGTGTATGGGTTT 59.892 45.455 0.00 0.00 0.00 3.27
140 141 2.228822 GTGGCTCTTGTGTATGGGTTTG 59.771 50.000 0.00 0.00 0.00 2.93
141 142 2.107378 TGGCTCTTGTGTATGGGTTTGA 59.893 45.455 0.00 0.00 0.00 2.69
142 143 2.749621 GGCTCTTGTGTATGGGTTTGAG 59.250 50.000 0.00 0.00 0.00 3.02
143 144 3.412386 GCTCTTGTGTATGGGTTTGAGT 58.588 45.455 0.00 0.00 0.00 3.41
144 145 4.564821 GGCTCTTGTGTATGGGTTTGAGTA 60.565 45.833 0.00 0.00 0.00 2.59
145 146 5.001232 GCTCTTGTGTATGGGTTTGAGTAA 58.999 41.667 0.00 0.00 0.00 2.24
146 147 5.122396 GCTCTTGTGTATGGGTTTGAGTAAG 59.878 44.000 0.00 0.00 0.00 2.34
147 148 6.182507 TCTTGTGTATGGGTTTGAGTAAGT 57.817 37.500 0.00 0.00 0.00 2.24
148 149 6.597562 TCTTGTGTATGGGTTTGAGTAAGTT 58.402 36.000 0.00 0.00 0.00 2.66
149 150 7.057894 TCTTGTGTATGGGTTTGAGTAAGTTT 58.942 34.615 0.00 0.00 0.00 2.66
150 151 6.627395 TGTGTATGGGTTTGAGTAAGTTTG 57.373 37.500 0.00 0.00 0.00 2.93
151 152 6.358178 TGTGTATGGGTTTGAGTAAGTTTGA 58.642 36.000 0.00 0.00 0.00 2.69
152 153 6.261381 TGTGTATGGGTTTGAGTAAGTTTGAC 59.739 38.462 0.00 0.00 0.00 3.18
153 154 5.766174 TGTATGGGTTTGAGTAAGTTTGACC 59.234 40.000 0.00 0.00 0.00 4.02
154 155 4.237976 TGGGTTTGAGTAAGTTTGACCA 57.762 40.909 0.00 0.00 0.00 4.02
155 156 4.798882 TGGGTTTGAGTAAGTTTGACCAT 58.201 39.130 0.00 0.00 0.00 3.55
156 157 4.825085 TGGGTTTGAGTAAGTTTGACCATC 59.175 41.667 0.00 0.00 0.00 3.51
157 158 4.825085 GGGTTTGAGTAAGTTTGACCATCA 59.175 41.667 0.00 0.00 0.00 3.07
158 159 5.278315 GGGTTTGAGTAAGTTTGACCATCAC 60.278 44.000 0.00 0.00 0.00 3.06
159 160 5.278315 GGTTTGAGTAAGTTTGACCATCACC 60.278 44.000 0.00 0.00 0.00 4.02
160 161 4.974645 TGAGTAAGTTTGACCATCACCT 57.025 40.909 0.00 0.00 0.00 4.00
161 162 5.304686 TGAGTAAGTTTGACCATCACCTT 57.695 39.130 0.00 0.00 0.00 3.50
162 163 5.063204 TGAGTAAGTTTGACCATCACCTTG 58.937 41.667 0.00 0.00 0.00 3.61
163 164 4.398319 AGTAAGTTTGACCATCACCTTGG 58.602 43.478 0.00 0.00 42.82 3.61
164 165 3.593442 AAGTTTGACCATCACCTTGGA 57.407 42.857 0.00 0.00 39.25 3.53
165 166 3.593442 AGTTTGACCATCACCTTGGAA 57.407 42.857 0.00 0.00 39.25 3.53
166 167 3.909732 AGTTTGACCATCACCTTGGAAA 58.090 40.909 0.00 0.00 39.25 3.13
167 168 4.482990 AGTTTGACCATCACCTTGGAAAT 58.517 39.130 0.00 0.00 39.25 2.17
168 169 4.281688 AGTTTGACCATCACCTTGGAAATG 59.718 41.667 0.00 0.00 39.25 2.32
169 170 3.524095 TGACCATCACCTTGGAAATGT 57.476 42.857 0.00 0.00 39.25 2.71
170 171 3.156293 TGACCATCACCTTGGAAATGTG 58.844 45.455 0.00 0.00 42.77 3.21
179 180 7.537596 TCACCTTGGAAATGTGAAATATGTT 57.462 32.000 0.00 0.00 46.12 2.71
180 181 7.961351 TCACCTTGGAAATGTGAAATATGTTT 58.039 30.769 0.00 0.00 46.12 2.83
181 182 8.087750 TCACCTTGGAAATGTGAAATATGTTTC 58.912 33.333 7.91 7.91 46.12 2.78
191 192 5.975693 TGAAATATGTTTCACCTTGACCC 57.024 39.130 13.03 0.00 46.49 4.46
192 193 4.770010 TGAAATATGTTTCACCTTGACCCC 59.230 41.667 13.03 0.00 46.49 4.95
193 194 2.891191 TATGTTTCACCTTGACCCCC 57.109 50.000 0.00 0.00 0.00 5.40
194 195 1.158007 ATGTTTCACCTTGACCCCCT 58.842 50.000 0.00 0.00 0.00 4.79
195 196 0.930726 TGTTTCACCTTGACCCCCTT 59.069 50.000 0.00 0.00 0.00 3.95
196 197 1.289530 TGTTTCACCTTGACCCCCTTT 59.710 47.619 0.00 0.00 0.00 3.11
197 198 1.686587 GTTTCACCTTGACCCCCTTTG 59.313 52.381 0.00 0.00 0.00 2.77
198 199 1.227249 TTCACCTTGACCCCCTTTGA 58.773 50.000 0.00 0.00 0.00 2.69
199 200 1.455822 TCACCTTGACCCCCTTTGAT 58.544 50.000 0.00 0.00 0.00 2.57
200 201 2.638325 TCACCTTGACCCCCTTTGATA 58.362 47.619 0.00 0.00 0.00 2.15
201 202 2.576191 TCACCTTGACCCCCTTTGATAG 59.424 50.000 0.00 0.00 0.00 2.08
202 203 2.308866 CACCTTGACCCCCTTTGATAGT 59.691 50.000 0.00 0.00 0.00 2.12
203 204 3.521937 CACCTTGACCCCCTTTGATAGTA 59.478 47.826 0.00 0.00 0.00 1.82
204 205 3.522343 ACCTTGACCCCCTTTGATAGTAC 59.478 47.826 0.00 0.00 0.00 2.73
205 206 3.431766 CCTTGACCCCCTTTGATAGTACG 60.432 52.174 0.00 0.00 0.00 3.67
206 207 2.112998 TGACCCCCTTTGATAGTACGG 58.887 52.381 0.00 0.00 0.00 4.02
207 208 1.415289 GACCCCCTTTGATAGTACGGG 59.585 57.143 0.00 0.00 35.06 5.28
231 232 6.210584 GGTTTTCCCATGACTCAAATAGGAAA 59.789 38.462 0.00 0.00 39.48 3.13
291 292 9.525409 CTTCAAAGTCTTCACATCAATTTCTTT 57.475 29.630 0.00 0.00 0.00 2.52
350 354 5.914898 AGAAATCCAATTTTTAGGGGTCG 57.085 39.130 0.00 0.00 31.47 4.79
357 361 4.076394 CAATTTTTAGGGGTCGTCTTCCA 58.924 43.478 0.00 0.00 0.00 3.53
376 380 5.975693 TCCATGTGTTAAACCAAATCCTC 57.024 39.130 0.00 0.00 0.00 3.71
378 382 5.835819 TCCATGTGTTAAACCAAATCCTCAA 59.164 36.000 0.00 0.00 0.00 3.02
431 435 7.687941 ACACATTAGTTCCTCAACCTATTTG 57.312 36.000 0.00 0.00 36.42 2.32
438 442 6.601332 AGTTCCTCAACCTATTTGTCTTCAA 58.399 36.000 0.00 0.00 36.49 2.69
449 453 8.793592 ACCTATTTGTCTTCAATACTCCAAAAC 58.206 33.333 0.00 0.00 33.32 2.43
460 464 2.424793 ACTCCAAAACCACTAAGGGGA 58.575 47.619 0.00 0.00 43.89 4.81
478 482 3.146066 GGGACACTTGATGCACTTACAA 58.854 45.455 0.00 0.00 0.00 2.41
485 489 2.862541 TGATGCACTTACAACCAAGCT 58.137 42.857 0.00 0.00 0.00 3.74
513 517 1.598130 GCGACCCAGACACAAGCTT 60.598 57.895 0.00 0.00 0.00 3.74
526 530 1.133482 ACAAGCTTAAGCCCAACACCT 60.133 47.619 23.71 0.00 43.38 4.00
527 531 1.270550 CAAGCTTAAGCCCAACACCTG 59.729 52.381 23.71 5.18 43.38 4.00
552 556 2.521958 CTTGGCCGGACTGGGTGTAG 62.522 65.000 9.82 0.00 38.63 2.74
583 587 2.575532 CCCCACGACCGACTACTTATA 58.424 52.381 0.00 0.00 0.00 0.98
592 596 5.609423 GACCGACTACTTATACTCTCTCCA 58.391 45.833 0.00 0.00 0.00 3.86
628 646 3.628280 GAGAAACGACTCGGCGGCT 62.628 63.158 7.21 0.00 35.12 5.52
672 690 5.895928 TCCTCTATTCGTCTCATTTCTGTG 58.104 41.667 0.00 0.00 0.00 3.66
688 706 2.894765 TCTGTGTCCCAGTTGTAATCGA 59.105 45.455 0.00 0.00 42.19 3.59
722 740 7.547019 TGCACTATTGTTAAGTGAGAGAGAATG 59.453 37.037 7.39 0.00 45.89 2.67
728 746 5.652452 TGTTAAGTGAGAGAGAATGGATCGA 59.348 40.000 0.00 0.00 0.00 3.59
750 768 1.557188 CCCCACCTTCTCCTCCCTAAA 60.557 57.143 0.00 0.00 0.00 1.85
753 771 3.561528 CCCACCTTCTCCTCCCTAAAAAC 60.562 52.174 0.00 0.00 0.00 2.43
754 772 3.561528 CCACCTTCTCCTCCCTAAAAACC 60.562 52.174 0.00 0.00 0.00 3.27
762 780 8.493787 TTCTCCTCCCTAAAAACCTATCTATC 57.506 38.462 0.00 0.00 0.00 2.08
763 781 7.838241 TCTCCTCCCTAAAAACCTATCTATCT 58.162 38.462 0.00 0.00 0.00 1.98
764 782 8.967577 TCTCCTCCCTAAAAACCTATCTATCTA 58.032 37.037 0.00 0.00 0.00 1.98
765 783 9.250246 CTCCTCCCTAAAAACCTATCTATCTAG 57.750 40.741 0.00 0.00 0.00 2.43
801 826 3.878086 ATTGCATGTAGGCGATTAACG 57.122 42.857 0.00 0.00 45.66 3.18
860 887 7.712639 CCCGATCTATATGTTTGCTATTGCTAT 59.287 37.037 0.00 0.00 40.48 2.97
870 897 7.083858 TGTTTGCTATTGCTATGTTGAAGTTC 58.916 34.615 0.00 0.00 40.48 3.01
880 907 6.972901 TGCTATGTTGAAGTTCTATCTACGTG 59.027 38.462 0.00 0.00 0.00 4.49
895 922 8.032451 TCTATCTACGTGAAAATGTTGATCACA 58.968 33.333 0.00 0.00 42.76 3.58
921 949 4.093011 CAAGGGTTGTATGAATTTGGGGA 58.907 43.478 0.00 0.00 0.00 4.81
927 955 3.550820 TGTATGAATTTGGGGACGGATG 58.449 45.455 0.00 0.00 0.00 3.51
928 956 2.826674 ATGAATTTGGGGACGGATGT 57.173 45.000 0.00 0.00 0.00 3.06
931 959 2.224892 TGAATTTGGGGACGGATGTGAA 60.225 45.455 0.00 0.00 0.00 3.18
938 966 0.179134 GGACGGATGTGAAGAGGACG 60.179 60.000 0.00 0.00 0.00 4.79
1006 1034 4.962995 TGGGTTTAAATTTGACCAGTCCAA 59.037 37.500 20.53 0.00 35.11 3.53
1007 1035 5.163395 TGGGTTTAAATTTGACCAGTCCAAC 60.163 40.000 20.53 7.74 35.11 3.77
1008 1036 5.069914 GGGTTTAAATTTGACCAGTCCAACT 59.930 40.000 20.53 0.00 35.11 3.16
1038 1067 6.939730 TGCTCTCACTTGGATGTAATTTTGTA 59.060 34.615 0.00 0.00 0.00 2.41
1076 1105 0.865111 CGAGCGACATGTCAAACCAA 59.135 50.000 24.93 0.00 0.00 3.67
1101 1130 4.106925 ACAGCTAGGGCAGGCAGC 62.107 66.667 0.00 0.00 41.70 5.25
1150 1184 1.619827 TGTACCCACGAGTAAACAGGG 59.380 52.381 0.00 0.00 45.20 4.45
1151 1185 1.066645 GTACCCACGAGTAAACAGGGG 60.067 57.143 0.00 0.00 43.96 4.79
1191 1225 2.290916 GAGACAAGAGAGTGTGTGTCGA 59.709 50.000 0.00 0.00 44.08 4.20
1201 1235 0.249447 TGTGTGTCGACCTGCTTCTG 60.249 55.000 14.12 0.00 0.00 3.02
1203 1237 2.049156 TGTCGACCTGCTTCTGCG 60.049 61.111 14.12 0.00 43.34 5.18
1449 1494 2.664851 CCTCGGCGTCAACAAGCA 60.665 61.111 6.85 0.00 34.54 3.91
1473 1518 3.107017 GGAACATCCGCAAAGCAAC 57.893 52.632 0.00 0.00 0.00 4.17
1474 1519 0.729140 GGAACATCCGCAAAGCAACG 60.729 55.000 0.00 0.00 0.00 4.10
1475 1520 1.337110 GAACATCCGCAAAGCAACGC 61.337 55.000 0.00 0.00 0.00 4.84
1476 1521 2.504681 CATCCGCAAAGCAACGCC 60.505 61.111 0.00 0.00 0.00 5.68
1477 1522 4.101790 ATCCGCAAAGCAACGCCG 62.102 61.111 0.00 0.00 0.00 6.46
1945 2073 0.538746 CTAACCACAACCCCGCCTTT 60.539 55.000 0.00 0.00 0.00 3.11
1948 2076 1.606313 CCACAACCCCGCCTTTCAT 60.606 57.895 0.00 0.00 0.00 2.57
2460 2588 3.594134 GGTGGAGAGATATGTAGCATGC 58.406 50.000 10.51 10.51 0.00 4.06
2506 2634 1.142667 GACGGTAGGGAGGTAGCTACT 59.857 57.143 22.74 9.46 0.00 2.57
2567 2695 1.204941 GGTTGTAGCTCTCGACACCAT 59.795 52.381 0.00 0.00 0.00 3.55
2597 2725 1.197492 CTGTTAATTGCTGCTGTGCGA 59.803 47.619 0.00 0.00 35.36 5.10
2765 2894 3.756434 TGGCTAGGCTTGAAACATGTAAC 59.244 43.478 18.18 0.00 0.00 2.50
2854 2983 8.107095 GGTATGCCTATTCAGGGAACATAAATA 58.893 37.037 0.00 0.00 46.62 1.40
2858 2987 9.077885 TGCCTATTCAGGGAACATAAATATTTC 57.922 33.333 3.39 0.00 39.74 2.17
2859 2988 8.523658 GCCTATTCAGGGAACATAAATATTTCC 58.476 37.037 3.39 0.00 42.88 3.13
2921 3050 8.322091 GGTAACTTGTCATTATATCATAGCCCT 58.678 37.037 0.00 0.00 0.00 5.19
2976 3105 3.763360 TGAGGTTTAATGCATCAAGGGTG 59.237 43.478 0.00 0.00 0.00 4.61
3216 3481 5.948758 TCACATATCCCTTTGTTGTATGCAA 59.051 36.000 0.00 0.00 0.00 4.08
3265 3530 6.767524 AATTGTTAACTTTGGTCAGTCACA 57.232 33.333 7.22 0.00 0.00 3.58
3266 3531 6.959639 ATTGTTAACTTTGGTCAGTCACAT 57.040 33.333 7.22 0.00 0.00 3.21
3267 3532 8.458573 AATTGTTAACTTTGGTCAGTCACATA 57.541 30.769 7.22 0.00 0.00 2.29
3268 3533 8.635765 ATTGTTAACTTTGGTCAGTCACATAT 57.364 30.769 7.22 0.00 0.00 1.78
3269 3534 7.667043 TGTTAACTTTGGTCAGTCACATATC 57.333 36.000 7.22 0.00 0.00 1.63
3270 3535 6.653320 TGTTAACTTTGGTCAGTCACATATCC 59.347 38.462 7.22 0.00 0.00 2.59
3271 3536 4.222124 ACTTTGGTCAGTCACATATCCC 57.778 45.455 0.00 0.00 0.00 3.85
3272 3537 3.846588 ACTTTGGTCAGTCACATATCCCT 59.153 43.478 0.00 0.00 0.00 4.20
3273 3538 4.289672 ACTTTGGTCAGTCACATATCCCTT 59.710 41.667 0.00 0.00 0.00 3.95
3274 3539 4.927267 TTGGTCAGTCACATATCCCTTT 57.073 40.909 0.00 0.00 0.00 3.11
3275 3540 4.220693 TGGTCAGTCACATATCCCTTTG 57.779 45.455 0.00 0.00 0.00 2.77
3276 3541 3.054434 TGGTCAGTCACATATCCCTTTGG 60.054 47.826 0.00 0.00 0.00 3.28
3277 3542 3.054361 GGTCAGTCACATATCCCTTTGGT 60.054 47.826 0.00 0.00 0.00 3.67
3278 3543 4.192317 GTCAGTCACATATCCCTTTGGTC 58.808 47.826 0.00 0.00 0.00 4.02
3279 3544 3.843619 TCAGTCACATATCCCTTTGGTCA 59.156 43.478 0.00 0.00 0.00 4.02
3280 3545 4.080919 TCAGTCACATATCCCTTTGGTCAG 60.081 45.833 0.00 0.00 0.00 3.51
3281 3546 3.846588 AGTCACATATCCCTTTGGTCAGT 59.153 43.478 0.00 0.00 0.00 3.41
3282 3547 4.080863 AGTCACATATCCCTTTGGTCAGTC 60.081 45.833 0.00 0.00 0.00 3.51
3347 3612 7.445402 TGTTCTTGAAGAAGATAACCTTTCCAG 59.555 37.037 8.06 0.00 38.05 3.86
3502 3828 9.352784 GTGAATATGTAGTTATCTCTCAGATGC 57.647 37.037 0.00 0.00 35.37 3.91
3586 3914 5.635417 TCTGTCAGTTCTGATCTGTACAG 57.365 43.478 24.04 24.04 39.45 2.74
3740 4069 2.912956 AGGACATGCTTGAAGTTCCCTA 59.087 45.455 6.60 0.00 0.00 3.53
3853 4186 2.355310 CGGCCCTATTGTACCTGTGAAA 60.355 50.000 0.00 0.00 0.00 2.69
3858 4191 5.185056 GCCCTATTGTACCTGTGAAATTTGT 59.815 40.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.037232 AGTTAGGAGTTCGCCAGTGC 60.037 55.000 0.00 0.00 0.00 4.40
1 2 1.404315 GGAGTTAGGAGTTCGCCAGTG 60.404 57.143 0.00 0.00 0.00 3.66
2 3 0.896226 GGAGTTAGGAGTTCGCCAGT 59.104 55.000 0.00 0.00 0.00 4.00
3 4 1.187087 AGGAGTTAGGAGTTCGCCAG 58.813 55.000 0.00 0.00 0.00 4.85
4 5 1.640917 AAGGAGTTAGGAGTTCGCCA 58.359 50.000 0.00 0.00 0.00 5.69
5 6 2.481622 GCTAAGGAGTTAGGAGTTCGCC 60.482 54.545 0.00 0.00 36.83 5.54
6 7 2.795331 CGCTAAGGAGTTAGGAGTTCGC 60.795 54.545 0.00 0.00 36.83 4.70
7 8 2.422832 ACGCTAAGGAGTTAGGAGTTCG 59.577 50.000 0.00 0.00 36.83 3.95
8 9 3.442977 TCACGCTAAGGAGTTAGGAGTTC 59.557 47.826 0.00 0.00 36.83 3.01
9 10 3.193056 GTCACGCTAAGGAGTTAGGAGTT 59.807 47.826 0.00 0.00 36.83 3.01
10 11 2.754002 GTCACGCTAAGGAGTTAGGAGT 59.246 50.000 0.00 0.00 36.83 3.85
11 12 2.099427 GGTCACGCTAAGGAGTTAGGAG 59.901 54.545 0.00 0.00 36.83 3.69
12 13 2.097825 GGTCACGCTAAGGAGTTAGGA 58.902 52.381 0.00 0.00 36.83 2.94
13 14 1.822990 TGGTCACGCTAAGGAGTTAGG 59.177 52.381 0.00 0.00 36.83 2.69
14 15 3.587797 TTGGTCACGCTAAGGAGTTAG 57.412 47.619 0.00 0.00 39.04 2.34
15 16 4.546829 ATTTGGTCACGCTAAGGAGTTA 57.453 40.909 0.00 0.00 0.00 2.24
16 17 2.922740 TTTGGTCACGCTAAGGAGTT 57.077 45.000 0.00 0.00 0.00 3.01
17 18 3.244422 TGAATTTGGTCACGCTAAGGAGT 60.244 43.478 0.00 0.00 0.00 3.85
18 19 3.334691 TGAATTTGGTCACGCTAAGGAG 58.665 45.455 0.00 0.00 0.00 3.69
19 20 3.410631 TGAATTTGGTCACGCTAAGGA 57.589 42.857 0.00 0.00 0.00 3.36
20 21 3.689161 TGATGAATTTGGTCACGCTAAGG 59.311 43.478 0.00 0.00 0.00 2.69
21 22 4.728882 GCTGATGAATTTGGTCACGCTAAG 60.729 45.833 0.00 0.00 0.00 2.18
22 23 3.126858 GCTGATGAATTTGGTCACGCTAA 59.873 43.478 0.00 0.00 0.00 3.09
23 24 2.677836 GCTGATGAATTTGGTCACGCTA 59.322 45.455 0.00 0.00 0.00 4.26
24 25 1.470098 GCTGATGAATTTGGTCACGCT 59.530 47.619 0.00 0.00 0.00 5.07
25 26 1.791555 CGCTGATGAATTTGGTCACGC 60.792 52.381 0.00 0.00 0.00 5.34
26 27 1.731709 TCGCTGATGAATTTGGTCACG 59.268 47.619 0.00 0.00 0.00 4.35
27 28 2.159517 GGTCGCTGATGAATTTGGTCAC 60.160 50.000 0.00 0.00 0.00 3.67
28 29 2.083774 GGTCGCTGATGAATTTGGTCA 58.916 47.619 0.00 0.00 0.00 4.02
29 30 2.083774 TGGTCGCTGATGAATTTGGTC 58.916 47.619 0.00 0.00 0.00 4.02
30 31 2.086869 CTGGTCGCTGATGAATTTGGT 58.913 47.619 0.00 0.00 0.00 3.67
31 32 2.358957 TCTGGTCGCTGATGAATTTGG 58.641 47.619 0.00 0.00 0.00 3.28
32 33 3.624410 TCATCTGGTCGCTGATGAATTTG 59.376 43.478 9.19 0.00 43.90 2.32
33 34 3.877559 TCATCTGGTCGCTGATGAATTT 58.122 40.909 9.19 0.00 43.90 1.82
34 35 3.548745 TCATCTGGTCGCTGATGAATT 57.451 42.857 9.19 0.00 43.90 2.17
37 38 1.550072 TGTTCATCTGGTCGCTGATGA 59.450 47.619 8.01 8.01 44.79 2.92
38 39 2.014335 TGTTCATCTGGTCGCTGATG 57.986 50.000 0.00 0.00 40.82 3.07
39 40 2.169144 TGATGTTCATCTGGTCGCTGAT 59.831 45.455 12.94 0.00 0.00 2.90
40 41 1.550072 TGATGTTCATCTGGTCGCTGA 59.450 47.619 12.94 0.00 0.00 4.26
41 42 2.014335 TGATGTTCATCTGGTCGCTG 57.986 50.000 12.94 0.00 0.00 5.18
42 43 2.996249 ATGATGTTCATCTGGTCGCT 57.004 45.000 12.94 0.00 29.59 4.93
51 52 6.117488 TGCTAGTGACAATGATGATGTTCAT 58.883 36.000 0.00 0.00 40.34 2.57
52 53 5.490159 TGCTAGTGACAATGATGATGTTCA 58.510 37.500 0.00 0.00 0.00 3.18
53 54 6.426980 TTGCTAGTGACAATGATGATGTTC 57.573 37.500 0.00 0.00 0.00 3.18
54 55 6.822667 TTTGCTAGTGACAATGATGATGTT 57.177 33.333 0.00 0.00 0.00 2.71
55 56 6.679638 GCATTTGCTAGTGACAATGATGATGT 60.680 38.462 0.00 0.00 38.21 3.06
56 57 5.685954 GCATTTGCTAGTGACAATGATGATG 59.314 40.000 0.00 0.00 38.21 3.07
57 58 5.505159 CGCATTTGCTAGTGACAATGATGAT 60.505 40.000 0.51 0.00 39.32 2.45
58 59 4.201841 CGCATTTGCTAGTGACAATGATGA 60.202 41.667 0.51 0.00 39.32 2.92
59 60 4.033019 CGCATTTGCTAGTGACAATGATG 58.967 43.478 0.51 1.43 39.32 3.07
60 61 3.691118 ACGCATTTGCTAGTGACAATGAT 59.309 39.130 0.51 0.00 39.32 2.45
61 62 3.073678 ACGCATTTGCTAGTGACAATGA 58.926 40.909 0.51 0.00 39.32 2.57
62 63 3.120234 TGACGCATTTGCTAGTGACAATG 60.120 43.478 0.51 0.00 39.32 2.82
63 64 3.073678 TGACGCATTTGCTAGTGACAAT 58.926 40.909 0.51 0.00 39.32 2.71
64 65 2.480037 CTGACGCATTTGCTAGTGACAA 59.520 45.455 0.51 0.00 39.32 3.18
65 66 2.068519 CTGACGCATTTGCTAGTGACA 58.931 47.619 0.51 0.00 39.32 3.58
66 67 2.337583 TCTGACGCATTTGCTAGTGAC 58.662 47.619 0.51 0.00 39.32 3.67
67 68 2.741759 TCTGACGCATTTGCTAGTGA 57.258 45.000 0.51 0.00 39.32 3.41
68 69 2.674852 ACATCTGACGCATTTGCTAGTG 59.325 45.455 0.51 0.00 39.32 2.74
69 70 2.977914 ACATCTGACGCATTTGCTAGT 58.022 42.857 0.51 0.00 39.32 2.57
70 71 4.026228 CAGTACATCTGACGCATTTGCTAG 60.026 45.833 0.51 0.00 46.27 3.42
71 72 3.865164 CAGTACATCTGACGCATTTGCTA 59.135 43.478 0.51 0.00 46.27 3.49
72 73 2.674852 CAGTACATCTGACGCATTTGCT 59.325 45.455 0.51 0.00 46.27 3.91
73 74 2.672874 TCAGTACATCTGACGCATTTGC 59.327 45.455 0.00 0.00 46.77 3.68
83 84 6.404074 GCCTTTGGAAATCTTCAGTACATCTG 60.404 42.308 0.00 0.00 44.85 2.90
84 85 5.649831 GCCTTTGGAAATCTTCAGTACATCT 59.350 40.000 0.00 0.00 0.00 2.90
85 86 5.649831 AGCCTTTGGAAATCTTCAGTACATC 59.350 40.000 0.00 0.00 0.00 3.06
86 87 5.574188 AGCCTTTGGAAATCTTCAGTACAT 58.426 37.500 0.00 0.00 0.00 2.29
87 88 4.985538 AGCCTTTGGAAATCTTCAGTACA 58.014 39.130 0.00 0.00 0.00 2.90
88 89 5.473504 TGAAGCCTTTGGAAATCTTCAGTAC 59.526 40.000 10.47 0.00 38.43 2.73
89 90 5.473504 GTGAAGCCTTTGGAAATCTTCAGTA 59.526 40.000 13.08 0.00 42.31 2.74
90 91 4.279420 GTGAAGCCTTTGGAAATCTTCAGT 59.721 41.667 13.08 0.00 42.31 3.41
91 92 4.522022 AGTGAAGCCTTTGGAAATCTTCAG 59.478 41.667 13.08 0.00 42.31 3.02
92 93 4.473444 AGTGAAGCCTTTGGAAATCTTCA 58.527 39.130 10.47 10.47 40.28 3.02
93 94 4.378874 CGAGTGAAGCCTTTGGAAATCTTC 60.379 45.833 0.00 0.00 35.12 2.87
94 95 3.503748 CGAGTGAAGCCTTTGGAAATCTT 59.496 43.478 0.00 0.00 0.00 2.40
95 96 3.077359 CGAGTGAAGCCTTTGGAAATCT 58.923 45.455 0.00 0.00 0.00 2.40
96 97 3.074412 TCGAGTGAAGCCTTTGGAAATC 58.926 45.455 0.00 0.00 0.00 2.17
97 98 3.140325 TCGAGTGAAGCCTTTGGAAAT 57.860 42.857 0.00 0.00 0.00 2.17
98 99 2.631160 TCGAGTGAAGCCTTTGGAAA 57.369 45.000 0.00 0.00 0.00 3.13
99 100 2.494059 CTTCGAGTGAAGCCTTTGGAA 58.506 47.619 0.00 0.00 44.70 3.53
100 101 2.169832 CTTCGAGTGAAGCCTTTGGA 57.830 50.000 0.00 0.00 44.70 3.53
111 112 1.143305 CACAAGAGCCACTTCGAGTG 58.857 55.000 7.72 7.72 45.53 3.51
112 113 0.753262 ACACAAGAGCCACTTCGAGT 59.247 50.000 0.00 0.00 36.61 4.18
113 114 2.724977 TACACAAGAGCCACTTCGAG 57.275 50.000 0.00 0.00 36.61 4.04
114 115 2.353704 CCATACACAAGAGCCACTTCGA 60.354 50.000 0.00 0.00 36.61 3.71
115 116 2.002586 CCATACACAAGAGCCACTTCG 58.997 52.381 0.00 0.00 36.61 3.79
116 117 2.290323 ACCCATACACAAGAGCCACTTC 60.290 50.000 0.00 0.00 36.61 3.01
117 118 1.705186 ACCCATACACAAGAGCCACTT 59.295 47.619 0.00 0.00 39.70 3.16
118 119 1.362224 ACCCATACACAAGAGCCACT 58.638 50.000 0.00 0.00 0.00 4.00
119 120 2.200373 AACCCATACACAAGAGCCAC 57.800 50.000 0.00 0.00 0.00 5.01
120 121 2.107378 TCAAACCCATACACAAGAGCCA 59.893 45.455 0.00 0.00 0.00 4.75
121 122 2.749621 CTCAAACCCATACACAAGAGCC 59.250 50.000 0.00 0.00 0.00 4.70
122 123 3.412386 ACTCAAACCCATACACAAGAGC 58.588 45.455 0.00 0.00 0.00 4.09
123 124 6.231211 ACTTACTCAAACCCATACACAAGAG 58.769 40.000 0.00 0.00 0.00 2.85
124 125 6.182507 ACTTACTCAAACCCATACACAAGA 57.817 37.500 0.00 0.00 0.00 3.02
125 126 6.877611 AACTTACTCAAACCCATACACAAG 57.122 37.500 0.00 0.00 0.00 3.16
126 127 6.829298 TCAAACTTACTCAAACCCATACACAA 59.171 34.615 0.00 0.00 0.00 3.33
127 128 6.261381 GTCAAACTTACTCAAACCCATACACA 59.739 38.462 0.00 0.00 0.00 3.72
128 129 6.293790 GGTCAAACTTACTCAAACCCATACAC 60.294 42.308 0.00 0.00 0.00 2.90
129 130 5.766174 GGTCAAACTTACTCAAACCCATACA 59.234 40.000 0.00 0.00 0.00 2.29
130 131 5.766174 TGGTCAAACTTACTCAAACCCATAC 59.234 40.000 0.00 0.00 0.00 2.39
131 132 5.942961 TGGTCAAACTTACTCAAACCCATA 58.057 37.500 0.00 0.00 0.00 2.74
132 133 4.798882 TGGTCAAACTTACTCAAACCCAT 58.201 39.130 0.00 0.00 0.00 4.00
133 134 4.237976 TGGTCAAACTTACTCAAACCCA 57.762 40.909 0.00 0.00 0.00 4.51
134 135 4.825085 TGATGGTCAAACTTACTCAAACCC 59.175 41.667 0.00 0.00 0.00 4.11
135 136 5.278315 GGTGATGGTCAAACTTACTCAAACC 60.278 44.000 0.00 0.00 0.00 3.27
136 137 5.531287 AGGTGATGGTCAAACTTACTCAAAC 59.469 40.000 0.00 0.00 0.00 2.93
137 138 5.690865 AGGTGATGGTCAAACTTACTCAAA 58.309 37.500 0.00 0.00 0.00 2.69
138 139 5.304686 AGGTGATGGTCAAACTTACTCAA 57.695 39.130 0.00 0.00 0.00 3.02
139 140 4.974645 AGGTGATGGTCAAACTTACTCA 57.025 40.909 0.00 0.00 0.00 3.41
140 141 4.455877 CCAAGGTGATGGTCAAACTTACTC 59.544 45.833 0.00 0.00 35.65 2.59
141 142 4.104102 TCCAAGGTGATGGTCAAACTTACT 59.896 41.667 0.00 0.00 41.46 2.24
142 143 4.394729 TCCAAGGTGATGGTCAAACTTAC 58.605 43.478 0.00 0.00 41.46 2.34
143 144 4.715534 TCCAAGGTGATGGTCAAACTTA 57.284 40.909 0.00 0.00 41.46 2.24
144 145 3.593442 TCCAAGGTGATGGTCAAACTT 57.407 42.857 0.00 0.00 41.46 2.66
145 146 3.593442 TTCCAAGGTGATGGTCAAACT 57.407 42.857 0.00 0.00 41.46 2.66
146 147 4.039124 ACATTTCCAAGGTGATGGTCAAAC 59.961 41.667 8.51 0.00 41.46 2.93
147 148 4.039004 CACATTTCCAAGGTGATGGTCAAA 59.961 41.667 0.00 0.00 45.40 2.69
148 149 3.573538 CACATTTCCAAGGTGATGGTCAA 59.426 43.478 0.00 0.00 45.40 3.18
149 150 3.156293 CACATTTCCAAGGTGATGGTCA 58.844 45.455 0.00 0.00 45.40 4.02
150 151 3.420893 TCACATTTCCAAGGTGATGGTC 58.579 45.455 0.00 0.00 46.01 4.02
151 152 3.524095 TCACATTTCCAAGGTGATGGT 57.476 42.857 0.00 0.00 46.01 3.55
156 157 8.243289 GAAACATATTTCACATTTCCAAGGTG 57.757 34.615 0.00 0.00 43.29 4.00
170 171 4.159693 GGGGGTCAAGGTGAAACATATTTC 59.840 45.833 0.00 0.00 43.96 2.17
171 172 4.093743 GGGGGTCAAGGTGAAACATATTT 58.906 43.478 0.00 0.00 39.98 1.40
172 173 3.336694 AGGGGGTCAAGGTGAAACATATT 59.663 43.478 0.00 0.00 39.98 1.28
173 174 2.926329 AGGGGGTCAAGGTGAAACATAT 59.074 45.455 0.00 0.00 39.98 1.78
174 175 2.354328 AGGGGGTCAAGGTGAAACATA 58.646 47.619 0.00 0.00 39.98 2.29
175 176 1.158007 AGGGGGTCAAGGTGAAACAT 58.842 50.000 0.00 0.00 39.98 2.71
176 177 0.930726 AAGGGGGTCAAGGTGAAACA 59.069 50.000 0.00 0.00 39.98 2.83
177 178 1.686587 CAAAGGGGGTCAAGGTGAAAC 59.313 52.381 0.00 0.00 0.00 2.78
178 179 1.571457 TCAAAGGGGGTCAAGGTGAAA 59.429 47.619 0.00 0.00 0.00 2.69
179 180 1.227249 TCAAAGGGGGTCAAGGTGAA 58.773 50.000 0.00 0.00 0.00 3.18
180 181 1.455822 ATCAAAGGGGGTCAAGGTGA 58.544 50.000 0.00 0.00 0.00 4.02
181 182 2.308866 ACTATCAAAGGGGGTCAAGGTG 59.691 50.000 0.00 0.00 0.00 4.00
182 183 2.644151 ACTATCAAAGGGGGTCAAGGT 58.356 47.619 0.00 0.00 0.00 3.50
183 184 3.431766 CGTACTATCAAAGGGGGTCAAGG 60.432 52.174 0.00 0.00 0.00 3.61
184 185 3.431766 CCGTACTATCAAAGGGGGTCAAG 60.432 52.174 0.00 0.00 0.00 3.02
185 186 2.502538 CCGTACTATCAAAGGGGGTCAA 59.497 50.000 0.00 0.00 0.00 3.18
186 187 2.112998 CCGTACTATCAAAGGGGGTCA 58.887 52.381 0.00 0.00 0.00 4.02
187 188 1.415289 CCCGTACTATCAAAGGGGGTC 59.585 57.143 0.00 0.00 37.19 4.46
188 189 1.274011 ACCCGTACTATCAAAGGGGGT 60.274 52.381 3.73 1.22 46.10 4.95
189 190 1.503800 ACCCGTACTATCAAAGGGGG 58.496 55.000 3.73 0.63 46.10 5.40
190 191 3.639672 AAACCCGTACTATCAAAGGGG 57.360 47.619 3.73 1.29 46.10 4.79
192 193 3.943381 GGGAAAACCCGTACTATCAAAGG 59.057 47.826 0.00 0.00 35.07 3.11
193 194 4.581868 TGGGAAAACCCGTACTATCAAAG 58.418 43.478 0.00 0.00 39.07 2.77
194 195 4.637387 TGGGAAAACCCGTACTATCAAA 57.363 40.909 0.00 0.00 39.07 2.69
195 196 4.225492 TCATGGGAAAACCCGTACTATCAA 59.775 41.667 0.00 0.00 39.07 2.57
196 197 3.775866 TCATGGGAAAACCCGTACTATCA 59.224 43.478 0.00 0.00 39.07 2.15
197 198 4.124970 GTCATGGGAAAACCCGTACTATC 58.875 47.826 0.00 0.00 39.07 2.08
198 199 3.778629 AGTCATGGGAAAACCCGTACTAT 59.221 43.478 0.00 0.00 39.07 2.12
199 200 3.175594 AGTCATGGGAAAACCCGTACTA 58.824 45.455 0.00 0.00 39.07 1.82
200 201 1.982958 AGTCATGGGAAAACCCGTACT 59.017 47.619 0.00 0.00 39.07 2.73
201 202 2.289819 TGAGTCATGGGAAAACCCGTAC 60.290 50.000 0.00 0.00 39.07 3.67
202 203 1.979308 TGAGTCATGGGAAAACCCGTA 59.021 47.619 0.00 0.00 39.07 4.02
203 204 0.768622 TGAGTCATGGGAAAACCCGT 59.231 50.000 0.00 0.00 39.07 5.28
204 205 1.904287 TTGAGTCATGGGAAAACCCG 58.096 50.000 0.00 0.00 39.07 5.28
205 206 4.402474 CCTATTTGAGTCATGGGAAAACCC 59.598 45.833 0.00 0.00 39.07 4.11
206 207 5.261216 TCCTATTTGAGTCATGGGAAAACC 58.739 41.667 0.00 0.00 40.81 3.27
207 208 6.834168 TTCCTATTTGAGTCATGGGAAAAC 57.166 37.500 8.65 0.00 38.10 2.43
238 239 9.834628 CTTGAAGACTTTTGTTTGTGTAGTTTA 57.165 29.630 0.00 0.00 0.00 2.01
240 241 6.806739 GCTTGAAGACTTTTGTTTGTGTAGTT 59.193 34.615 0.00 0.00 0.00 2.24
241 242 6.151144 AGCTTGAAGACTTTTGTTTGTGTAGT 59.849 34.615 0.00 0.00 0.00 2.73
242 243 6.555315 AGCTTGAAGACTTTTGTTTGTGTAG 58.445 36.000 0.00 0.00 0.00 2.74
244 245 5.391312 AGCTTGAAGACTTTTGTTTGTGT 57.609 34.783 0.00 0.00 0.00 3.72
245 246 5.863397 TGAAGCTTGAAGACTTTTGTTTGTG 59.137 36.000 2.10 0.00 0.00 3.33
247 248 6.949578 TTGAAGCTTGAAGACTTTTGTTTG 57.050 33.333 2.10 0.00 0.00 2.93
249 250 6.691508 ACTTTGAAGCTTGAAGACTTTTGTT 58.308 32.000 20.36 0.00 0.00 2.83
251 252 6.558909 AGACTTTGAAGCTTGAAGACTTTTG 58.441 36.000 20.36 2.44 0.00 2.44
252 253 6.765915 AGACTTTGAAGCTTGAAGACTTTT 57.234 33.333 20.36 3.56 0.00 2.27
253 254 6.375455 TGAAGACTTTGAAGCTTGAAGACTTT 59.625 34.615 24.06 15.61 36.21 2.66
299 303 7.954835 AGTGAAGAATTTGGTGATGAAATTGA 58.045 30.769 0.00 0.00 34.00 2.57
342 346 1.191535 CACATGGAAGACGACCCCTA 58.808 55.000 0.00 0.00 0.00 3.53
350 354 6.015434 AGGATTTGGTTTAACACATGGAAGAC 60.015 38.462 0.00 0.00 0.00 3.01
357 361 6.074648 TCCTTGAGGATTTGGTTTAACACAT 58.925 36.000 0.00 0.00 39.78 3.21
376 380 8.110860 AGTATACACAGGAAACAAAATCCTTG 57.889 34.615 5.50 0.00 45.06 3.61
431 435 7.094762 CCTTAGTGGTTTTGGAGTATTGAAGAC 60.095 40.741 0.00 0.00 0.00 3.01
438 442 4.018688 GTCCCCTTAGTGGTTTTGGAGTAT 60.019 45.833 0.00 0.00 0.00 2.12
449 453 2.941415 GCATCAAGTGTCCCCTTAGTGG 60.941 54.545 0.00 0.00 0.00 4.00
460 464 3.550820 TGGTTGTAAGTGCATCAAGTGT 58.449 40.909 0.00 0.00 0.00 3.55
478 482 2.261671 CACCGCGTCTAGCTTGGT 59.738 61.111 4.92 0.00 45.59 3.67
502 506 2.230660 GTTGGGCTTAAGCTTGTGTCT 58.769 47.619 25.88 0.00 41.70 3.41
513 517 0.179004 CCACACAGGTGTTGGGCTTA 60.179 55.000 1.58 0.00 42.83 3.09
535 539 3.000819 CTACACCCAGTCCGGCCA 61.001 66.667 2.24 0.00 0.00 5.36
540 544 1.597461 GCCTCACTACACCCAGTCC 59.403 63.158 0.00 0.00 0.00 3.85
568 572 4.685628 GGAGAGAGTATAAGTAGTCGGTCG 59.314 50.000 0.00 0.00 35.76 4.79
571 575 4.453136 GCTGGAGAGAGTATAAGTAGTCGG 59.547 50.000 0.00 0.00 35.76 4.79
574 578 7.717875 CACTTAGCTGGAGAGAGTATAAGTAGT 59.282 40.741 0.00 0.00 31.68 2.73
583 587 5.279556 GGTTTTACACTTAGCTGGAGAGAGT 60.280 44.000 0.00 0.00 0.00 3.24
592 596 2.901839 TCTCCGGGTTTTACACTTAGCT 59.098 45.455 0.00 0.00 0.00 3.32
628 646 2.022722 AGGAAGGGGATTAGGGTTCGTA 60.023 50.000 0.00 0.00 0.00 3.43
672 690 3.870633 AGTCTCGATTACAACTGGGAC 57.129 47.619 0.00 0.00 0.00 4.46
688 706 7.161404 TCACTTAACAATAGTGCATCAAGTCT 58.839 34.615 0.00 0.00 42.12 3.24
722 740 0.682292 GAGAAGGTGGGGATCGATCC 59.318 60.000 32.57 32.57 46.41 3.36
728 746 1.004891 GGGAGGAGAAGGTGGGGAT 59.995 63.158 0.00 0.00 0.00 3.85
769 787 6.072728 CGCCTACATGCAATAAAGCCTAAATA 60.073 38.462 0.00 0.00 0.00 1.40
770 788 5.278463 CGCCTACATGCAATAAAGCCTAAAT 60.278 40.000 0.00 0.00 0.00 1.40
771 789 4.036262 CGCCTACATGCAATAAAGCCTAAA 59.964 41.667 0.00 0.00 0.00 1.85
772 790 3.563808 CGCCTACATGCAATAAAGCCTAA 59.436 43.478 0.00 0.00 0.00 2.69
774 792 1.949525 CGCCTACATGCAATAAAGCCT 59.050 47.619 0.00 0.00 0.00 4.58
775 793 1.946768 TCGCCTACATGCAATAAAGCC 59.053 47.619 0.00 0.00 0.00 4.35
783 808 2.303163 ACGTTAATCGCCTACATGCA 57.697 45.000 0.00 0.00 44.19 3.96
801 826 8.806177 AGTTTTTATACAAATCGGACCAAAAC 57.194 30.769 0.00 0.00 33.66 2.43
860 887 8.708742 CATTTTCACGTAGATAGAACTTCAACA 58.291 33.333 0.00 0.00 0.00 3.33
870 897 8.185003 TGTGATCAACATTTTCACGTAGATAG 57.815 34.615 0.00 0.00 42.07 2.08
895 922 5.490159 CCAAATTCATACAACCCTTGCAAT 58.510 37.500 0.00 0.00 0.00 3.56
921 949 0.811915 CTCGTCCTCTTCACATCCGT 59.188 55.000 0.00 0.00 0.00 4.69
927 955 0.959553 TCCACACTCGTCCTCTTCAC 59.040 55.000 0.00 0.00 0.00 3.18
928 956 1.613925 CTTCCACACTCGTCCTCTTCA 59.386 52.381 0.00 0.00 0.00 3.02
931 959 0.827925 TGCTTCCACACTCGTCCTCT 60.828 55.000 0.00 0.00 0.00 3.69
938 966 1.815003 CATTTCCCTGCTTCCACACTC 59.185 52.381 0.00 0.00 0.00 3.51
982 1010 4.342665 TGGACTGGTCAAATTTAAACCCAC 59.657 41.667 15.70 9.10 31.78 4.61
987 1015 8.754991 TCTAAGTTGGACTGGTCAAATTTAAA 57.245 30.769 3.10 0.00 34.80 1.52
1038 1067 1.609208 GTTGGACAATCACACCAGCT 58.391 50.000 0.00 0.00 35.08 4.24
1076 1105 2.315176 CTGCCCTAGCTGTCTCACTAT 58.685 52.381 0.00 0.00 40.80 2.12
1115 1149 0.388649 GTACACCACGCAGTCTCTGG 60.389 60.000 0.00 0.00 41.61 3.86
1150 1184 1.204312 GCTGAGTGCGTTTTCGTCC 59.796 57.895 0.00 0.00 46.03 4.79
1151 1185 1.204312 GGCTGAGTGCGTTTTCGTC 59.796 57.895 0.00 0.00 46.03 4.20
1191 1225 2.032681 GGGAACGCAGAAGCAGGT 59.967 61.111 0.00 0.00 42.27 4.00
1377 1422 3.963687 CTGCTGCTGCGGTCCATCA 62.964 63.158 15.76 0.00 43.34 3.07
1418 1463 2.668550 GAGGTGCGGGTTGTGTCC 60.669 66.667 0.00 0.00 0.00 4.02
1419 1464 3.041940 CGAGGTGCGGGTTGTGTC 61.042 66.667 0.00 0.00 36.03 3.67
1966 2094 2.043652 GGAGGCATGGGCATGTGT 60.044 61.111 0.00 0.00 43.71 3.72
2137 2265 2.666596 GATAAGGGTGCTGCGGAGGG 62.667 65.000 5.93 0.00 0.00 4.30
2266 2394 2.983879 CGGAGGGGGTTGCTGGAAT 61.984 63.158 0.00 0.00 0.00 3.01
2469 2597 1.530323 GTCAAATGTTACAGGGGCGT 58.470 50.000 0.00 0.00 0.00 5.68
2506 2634 3.364549 GGATGAACCAATTCCCATCACA 58.635 45.455 0.00 0.00 37.67 3.58
2567 2695 6.145858 CAGCAGCAATTAACAGCAACAAATAA 59.854 34.615 0.00 0.00 0.00 1.40
2597 2725 5.363939 GAAGCCTTACAGACTGATGCTAAT 58.636 41.667 10.08 0.00 0.00 1.73
2689 2818 0.475906 ACTGTCCTCCTTTTGCAGCT 59.524 50.000 0.00 0.00 0.00 4.24
2792 2921 7.433708 TGAGCGAAATATTTGTCAGAAAGAA 57.566 32.000 5.17 0.00 0.00 2.52
2860 2989 7.361799 CGAAAATACAAGTAGAAGAAAAGGGGG 60.362 40.741 0.00 0.00 0.00 5.40
2921 3050 7.953005 TGGATTGTTAATTTCCAGATAAGCA 57.047 32.000 0.00 0.00 34.65 3.91
2976 3105 4.579869 TGCTCCCAAGAAGAAATAGACAC 58.420 43.478 0.00 0.00 0.00 3.67
3058 3292 5.335583 CGAAGTGAATAAACATTCAGGCCAA 60.336 40.000 5.01 0.00 40.77 4.52
3097 3331 9.276590 CTACTGCCTATCATGACATTAAATTGA 57.723 33.333 0.00 0.00 0.00 2.57
3106 3340 4.895889 ACTAAGCTACTGCCTATCATGACA 59.104 41.667 0.00 0.00 40.80 3.58
3145 3410 5.179368 CGATCTGCTTCAAAACACTAAAGGA 59.821 40.000 0.00 0.00 0.00 3.36
3244 3509 7.174253 GGATATGTGACTGACCAAAGTTAACAA 59.826 37.037 8.61 0.00 33.44 2.83
3245 3510 6.653320 GGATATGTGACTGACCAAAGTTAACA 59.347 38.462 8.61 0.00 33.92 2.41
3246 3511 6.093633 GGGATATGTGACTGACCAAAGTTAAC 59.906 42.308 0.00 0.00 0.00 2.01
3248 3513 5.487488 AGGGATATGTGACTGACCAAAGTTA 59.513 40.000 0.00 0.00 0.00 2.24
3249 3514 4.289672 AGGGATATGTGACTGACCAAAGTT 59.710 41.667 0.00 0.00 0.00 2.66
3254 3519 3.054434 CCAAAGGGATATGTGACTGACCA 60.054 47.826 0.00 0.00 35.59 4.02
3255 3520 3.054361 ACCAAAGGGATATGTGACTGACC 60.054 47.826 0.00 0.00 38.05 4.02
3256 3521 4.192317 GACCAAAGGGATATGTGACTGAC 58.808 47.826 0.00 0.00 38.05 3.51
3258 3523 4.194640 CTGACCAAAGGGATATGTGACTG 58.805 47.826 0.00 0.00 38.05 3.51
3259 3524 3.846588 ACTGACCAAAGGGATATGTGACT 59.153 43.478 0.00 0.00 38.05 3.41
3260 3525 4.192317 GACTGACCAAAGGGATATGTGAC 58.808 47.826 0.00 0.00 38.05 3.67
3261 3526 3.843619 TGACTGACCAAAGGGATATGTGA 59.156 43.478 0.00 0.00 38.05 3.58
3262 3527 3.941483 GTGACTGACCAAAGGGATATGTG 59.059 47.826 0.00 0.00 38.05 3.21
3263 3528 3.846588 AGTGACTGACCAAAGGGATATGT 59.153 43.478 0.00 0.00 38.05 2.29
3264 3529 4.494091 AGTGACTGACCAAAGGGATATG 57.506 45.455 0.00 0.00 38.05 1.78
3265 3530 6.636454 TTAAGTGACTGACCAAAGGGATAT 57.364 37.500 0.00 0.00 38.05 1.63
3266 3531 6.235664 GTTTAAGTGACTGACCAAAGGGATA 58.764 40.000 0.00 0.00 38.05 2.59
3267 3532 4.993705 TTAAGTGACTGACCAAAGGGAT 57.006 40.909 0.00 0.00 38.05 3.85
3268 3533 4.457466 GTTTAAGTGACTGACCAAAGGGA 58.543 43.478 0.00 0.00 38.05 4.20
3269 3534 3.568430 GGTTTAAGTGACTGACCAAAGGG 59.432 47.826 7.82 0.00 41.29 3.95
3270 3535 4.461198 AGGTTTAAGTGACTGACCAAAGG 58.539 43.478 13.31 0.00 32.81 3.11
3271 3536 5.123227 TGAGGTTTAAGTGACTGACCAAAG 58.877 41.667 13.31 0.00 32.81 2.77
3272 3537 5.105567 TGAGGTTTAAGTGACTGACCAAA 57.894 39.130 13.31 1.52 32.81 3.28
3273 3538 4.163458 ACTGAGGTTTAAGTGACTGACCAA 59.837 41.667 13.31 3.38 32.81 3.67
3274 3539 3.709653 ACTGAGGTTTAAGTGACTGACCA 59.290 43.478 13.31 0.00 32.81 4.02
3275 3540 4.058817 CACTGAGGTTTAAGTGACTGACC 58.941 47.826 5.26 5.26 45.43 4.02
3276 3541 3.495001 GCACTGAGGTTTAAGTGACTGAC 59.505 47.826 6.98 0.00 45.43 3.51
3277 3542 3.133901 TGCACTGAGGTTTAAGTGACTGA 59.866 43.478 6.98 0.00 45.43 3.41
3278 3543 3.466836 TGCACTGAGGTTTAAGTGACTG 58.533 45.455 6.98 0.00 45.43 3.51
3279 3544 3.838244 TGCACTGAGGTTTAAGTGACT 57.162 42.857 6.98 0.00 45.43 3.41
3280 3545 3.189287 CCATGCACTGAGGTTTAAGTGAC 59.811 47.826 6.98 0.00 45.43 3.67
3281 3546 3.181445 ACCATGCACTGAGGTTTAAGTGA 60.181 43.478 6.98 0.00 45.43 3.41
3282 3547 3.149196 ACCATGCACTGAGGTTTAAGTG 58.851 45.455 0.00 0.00 45.37 3.16
3347 3612 8.492748 TGAACACGTATTTGACTGATAAAGTTC 58.507 33.333 0.00 0.00 40.07 3.01
3436 3762 1.308069 CCAATGGGCAGAACGGTCAG 61.308 60.000 1.87 0.00 0.00 3.51
3526 3852 2.497273 TGCTACTCTATTGCAGCAGTGA 59.503 45.455 0.00 0.00 39.03 3.41
3551 3877 6.426025 CAGAACTGACAGATTGTTGATCAGAA 59.574 38.462 10.08 0.00 39.33 3.02
3740 4069 2.304761 ACGGTCCCACACATTAATCTGT 59.695 45.455 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.