Multiple sequence alignment - TraesCS7A01G386600

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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 TraesCS7A01G386600 chr7A 100.000 3185 0 0 1 3185 562214696 562217880 0.000000e+00 5882.0
1 TraesCS7A01G386600 chr7A 98.773 163 2 0 1 163 463720579 463720417 1.120000e-74 291.0
2 TraesCS7A01G386600 chr7D 93.534 2923 135 24 270 3185 496784813 496787688 0.000000e+00 4301.0
3 TraesCS7A01G386600 chr7B 91.754 2874 190 25 335 3184 524918636 524921486 0.000000e+00 3951.0
4 TraesCS7A01G386600 chr1D 89.156 1457 128 13 969 2398 436654306 436652853 0.000000e+00 1788.0
5 TraesCS7A01G386600 chr1A 88.522 1455 138 10 969 2398 533733799 533732349 0.000000e+00 1735.0
6 TraesCS7A01G386600 chr1A 99.387 163 1 0 1 163 177491641 177491803 2.400000e-76 296.0
7 TraesCS7A01G386600 chr1A 91.489 47 4 0 660 706 575362106 575362152 7.370000e-07 65.8
8 TraesCS7A01G386600 chr1B 88.456 1386 127 15 969 2324 591451883 591450501 0.000000e+00 1642.0
9 TraesCS7A01G386600 chr2A 99.387 163 1 0 1 163 721055629 721055791 2.400000e-76 296.0
10 TraesCS7A01G386600 chr4A 98.765 162 2 0 2 163 627942198 627942359 4.020000e-74 289.0
11 TraesCS7A01G386600 chr6A 98.171 164 3 0 1 164 13713823 13713660 1.450000e-73 287.0
12 TraesCS7A01G386600 chr5A 98.160 163 3 0 1 163 34899634 34899472 5.200000e-73 285.0
13 TraesCS7A01G386600 chr5A 98.160 163 3 0 1 163 76135802 76135964 5.200000e-73 285.0
14 TraesCS7A01G386600 chr3A 98.160 163 3 0 1 163 557654759 557654921 5.200000e-73 285.0
15 TraesCS7A01G386600 chr3A 97.590 166 4 0 1 166 716108864 716108699 5.200000e-73 285.0
16 TraesCS7A01G386600 chr2B 93.333 45 2 1 618 662 713674168 713674211 7.370000e-07 65.8


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 TraesCS7A01G386600 chr7A 562214696 562217880 3184 False 5882 5882 100.000 1 3185 1 chr7A.!!$F1 3184
1 TraesCS7A01G386600 chr7D 496784813 496787688 2875 False 4301 4301 93.534 270 3185 1 chr7D.!!$F1 2915
2 TraesCS7A01G386600 chr7B 524918636 524921486 2850 False 3951 3951 91.754 335 3184 1 chr7B.!!$F1 2849
3 TraesCS7A01G386600 chr1D 436652853 436654306 1453 True 1788 1788 89.156 969 2398 1 chr1D.!!$R1 1429
4 TraesCS7A01G386600 chr1A 533732349 533733799 1450 True 1735 1735 88.522 969 2398 1 chr1A.!!$R1 1429
5 TraesCS7A01G386600 chr1B 591450501 591451883 1382 True 1642 1642 88.456 969 2324 1 chr1B.!!$R1 1355

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
234 235 0.02811 GATCCAATGTTTCGCGAGGC 59.972 55.0 9.59 6.99 0.00 4.70 F
1299 1324 0.03496 TGTCTCCTCTGGTCTCGGAG 60.035 60.0 0.00 0.00 44.48 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1708 0.179097 GGCCCTTCTTCTGAGCTACG 60.179 60.0 0.0 0.0 0.00 3.51 R
3011 3073 0.324285 AGAGAACAGCAGGAGCAAGG 59.676 55.0 0.0 0.0 45.49 3.61 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
22 23 4.611943 CGAGATCGTGGTAGAATTCATGT 58.388 43.478 8.44 0.00 34.11 3.21
23 24 5.043903 CGAGATCGTGGTAGAATTCATGTT 58.956 41.667 8.44 0.00 34.11 2.71
24 25 5.520288 CGAGATCGTGGTAGAATTCATGTTT 59.480 40.000 8.44 0.00 34.11 2.83
25 26 6.291849 CGAGATCGTGGTAGAATTCATGTTTC 60.292 42.308 8.44 0.00 34.11 2.78
26 27 6.644347 AGATCGTGGTAGAATTCATGTTTCT 58.356 36.000 8.44 14.90 37.25 2.52
27 28 7.782049 AGATCGTGGTAGAATTCATGTTTCTA 58.218 34.615 8.44 13.40 35.19 2.10
28 29 7.923344 AGATCGTGGTAGAATTCATGTTTCTAG 59.077 37.037 16.18 8.71 36.59 2.43
29 30 6.931838 TCGTGGTAGAATTCATGTTTCTAGT 58.068 36.000 16.18 1.18 36.59 2.57
30 31 8.058667 TCGTGGTAGAATTCATGTTTCTAGTA 57.941 34.615 16.18 9.12 36.59 1.82
31 32 8.692710 TCGTGGTAGAATTCATGTTTCTAGTAT 58.307 33.333 16.18 0.65 36.59 2.12
32 33 8.755941 CGTGGTAGAATTCATGTTTCTAGTATG 58.244 37.037 16.18 11.62 36.59 2.39
33 34 9.601217 GTGGTAGAATTCATGTTTCTAGTATGT 57.399 33.333 16.18 0.00 36.59 2.29
34 35 9.599866 TGGTAGAATTCATGTTTCTAGTATGTG 57.400 33.333 16.18 0.00 36.59 3.21
35 36 8.552034 GGTAGAATTCATGTTTCTAGTATGTGC 58.448 37.037 16.18 7.25 36.59 4.57
36 37 7.559590 AGAATTCATGTTTCTAGTATGTGCC 57.440 36.000 8.44 0.00 31.75 5.01
37 38 6.543831 AGAATTCATGTTTCTAGTATGTGCCC 59.456 38.462 8.44 0.00 31.75 5.36
38 39 5.435686 TTCATGTTTCTAGTATGTGCCCT 57.564 39.130 0.00 0.00 0.00 5.19
39 40 6.553953 TTCATGTTTCTAGTATGTGCCCTA 57.446 37.500 0.00 0.00 0.00 3.53
40 41 6.161855 TCATGTTTCTAGTATGTGCCCTAG 57.838 41.667 0.00 0.00 33.46 3.02
41 42 5.897250 TCATGTTTCTAGTATGTGCCCTAGA 59.103 40.000 0.00 0.00 38.26 2.43
42 43 6.554982 TCATGTTTCTAGTATGTGCCCTAGAT 59.445 38.462 0.00 0.00 39.40 1.98
43 44 6.161855 TGTTTCTAGTATGTGCCCTAGATG 57.838 41.667 0.00 0.00 39.40 2.90
44 45 5.661312 TGTTTCTAGTATGTGCCCTAGATGT 59.339 40.000 0.00 0.00 39.40 3.06
45 46 5.791336 TTCTAGTATGTGCCCTAGATGTG 57.209 43.478 0.00 0.00 39.40 3.21
46 47 5.061721 TCTAGTATGTGCCCTAGATGTGA 57.938 43.478 0.00 0.00 35.82 3.58
47 48 5.645201 TCTAGTATGTGCCCTAGATGTGAT 58.355 41.667 0.00 0.00 35.82 3.06
48 49 4.881019 AGTATGTGCCCTAGATGTGATC 57.119 45.455 0.00 0.00 0.00 2.92
49 50 4.487804 AGTATGTGCCCTAGATGTGATCT 58.512 43.478 0.00 0.00 43.33 2.75
50 51 3.766068 ATGTGCCCTAGATGTGATCTG 57.234 47.619 0.00 0.00 40.51 2.90
51 52 2.470990 TGTGCCCTAGATGTGATCTGT 58.529 47.619 0.00 0.00 40.51 3.41
52 53 2.840038 TGTGCCCTAGATGTGATCTGTT 59.160 45.455 0.00 0.00 40.51 3.16
53 54 3.118629 TGTGCCCTAGATGTGATCTGTTC 60.119 47.826 0.00 0.00 40.51 3.18
54 55 3.106827 TGCCCTAGATGTGATCTGTTCA 58.893 45.455 0.00 0.00 40.51 3.18
55 56 3.713248 TGCCCTAGATGTGATCTGTTCAT 59.287 43.478 0.00 0.00 40.51 2.57
56 57 4.202295 TGCCCTAGATGTGATCTGTTCATC 60.202 45.833 0.00 3.85 40.51 2.92
57 58 4.040217 GCCCTAGATGTGATCTGTTCATCT 59.960 45.833 18.86 18.86 46.33 2.90
58 59 5.539979 CCCTAGATGTGATCTGTTCATCTG 58.460 45.833 21.42 15.19 44.95 2.90
59 60 4.989797 CCTAGATGTGATCTGTTCATCTGC 59.010 45.833 21.42 0.00 44.95 4.26
60 61 4.757019 AGATGTGATCTGTTCATCTGCT 57.243 40.909 16.24 0.00 44.08 4.24
61 62 5.866159 AGATGTGATCTGTTCATCTGCTA 57.134 39.130 16.24 0.00 44.08 3.49
62 63 6.422344 AGATGTGATCTGTTCATCTGCTAT 57.578 37.500 16.24 1.13 44.08 2.97
63 64 6.224584 AGATGTGATCTGTTCATCTGCTATG 58.775 40.000 16.24 0.00 44.08 2.23
64 65 4.124970 TGTGATCTGTTCATCTGCTATGC 58.875 43.478 0.00 0.00 36.54 3.14
65 66 4.141779 TGTGATCTGTTCATCTGCTATGCT 60.142 41.667 0.00 0.00 36.54 3.79
66 67 5.069516 TGTGATCTGTTCATCTGCTATGCTA 59.930 40.000 0.00 0.00 36.54 3.49
67 68 5.634439 GTGATCTGTTCATCTGCTATGCTAG 59.366 44.000 0.00 0.00 36.54 3.42
68 69 5.303845 TGATCTGTTCATCTGCTATGCTAGT 59.696 40.000 0.00 0.00 0.00 2.57
69 70 5.604758 TCTGTTCATCTGCTATGCTAGTT 57.395 39.130 0.00 0.00 0.00 2.24
70 71 5.595885 TCTGTTCATCTGCTATGCTAGTTC 58.404 41.667 0.00 0.00 0.00 3.01
71 72 4.363138 TGTTCATCTGCTATGCTAGTTCG 58.637 43.478 0.00 0.00 0.00 3.95
72 73 3.018598 TCATCTGCTATGCTAGTTCGC 57.981 47.619 0.00 0.00 0.00 4.70
73 74 2.362077 TCATCTGCTATGCTAGTTCGCA 59.638 45.455 0.00 0.00 45.10 5.10
86 87 7.786178 TGCTAGTTCGCATGATTAGTTTAAT 57.214 32.000 0.00 0.00 34.44 1.40
87 88 7.851508 TGCTAGTTCGCATGATTAGTTTAATC 58.148 34.615 0.00 2.61 38.95 1.75
88 89 7.710907 TGCTAGTTCGCATGATTAGTTTAATCT 59.289 33.333 0.00 0.00 39.09 2.40
89 90 8.217778 GCTAGTTCGCATGATTAGTTTAATCTC 58.782 37.037 0.00 0.79 43.79 2.75
90 91 9.469807 CTAGTTCGCATGATTAGTTTAATCTCT 57.530 33.333 0.00 0.00 43.79 3.10
92 93 9.250624 AGTTCGCATGATTAGTTTAATCTCTAC 57.749 33.333 0.00 0.00 43.79 2.59
93 94 9.250624 GTTCGCATGATTAGTTTAATCTCTACT 57.749 33.333 0.00 0.00 43.79 2.57
95 96 9.894783 TCGCATGATTAGTTTAATCTCTACTAC 57.105 33.333 0.00 0.00 43.79 2.73
96 97 9.900710 CGCATGATTAGTTTAATCTCTACTACT 57.099 33.333 0.00 0.00 43.79 2.57
147 148 8.624701 TTCGGATTAAATCTCGTAGTAACTTG 57.375 34.615 0.00 0.00 0.00 3.16
148 149 6.694411 TCGGATTAAATCTCGTAGTAACTTGC 59.306 38.462 0.00 0.00 0.00 4.01
149 150 6.696148 CGGATTAAATCTCGTAGTAACTTGCT 59.304 38.462 0.00 0.00 0.00 3.91
150 151 7.096558 CGGATTAAATCTCGTAGTAACTTGCTC 60.097 40.741 0.00 0.00 0.00 4.26
151 152 7.705325 GGATTAAATCTCGTAGTAACTTGCTCA 59.295 37.037 0.00 0.00 0.00 4.26
152 153 9.250624 GATTAAATCTCGTAGTAACTTGCTCAT 57.749 33.333 0.00 0.00 0.00 2.90
156 157 9.601217 AAATCTCGTAGTAACTTGCTCATATTT 57.399 29.630 0.00 0.00 0.00 1.40
157 158 8.804688 ATCTCGTAGTAACTTGCTCATATTTC 57.195 34.615 0.00 0.00 0.00 2.17
158 159 7.201145 TCTCGTAGTAACTTGCTCATATTTCC 58.799 38.462 0.00 0.00 0.00 3.13
159 160 6.869695 TCGTAGTAACTTGCTCATATTTCCA 58.130 36.000 0.00 0.00 0.00 3.53
160 161 7.324935 TCGTAGTAACTTGCTCATATTTCCAA 58.675 34.615 0.00 0.00 0.00 3.53
161 162 7.277098 TCGTAGTAACTTGCTCATATTTCCAAC 59.723 37.037 0.00 0.00 0.00 3.77
162 163 7.064134 CGTAGTAACTTGCTCATATTTCCAACA 59.936 37.037 0.00 0.00 0.00 3.33
163 164 7.145932 AGTAACTTGCTCATATTTCCAACAC 57.854 36.000 0.00 0.00 0.00 3.32
164 165 4.685169 ACTTGCTCATATTTCCAACACG 57.315 40.909 0.00 0.00 0.00 4.49
165 166 3.119849 ACTTGCTCATATTTCCAACACGC 60.120 43.478 0.00 0.00 0.00 5.34
166 167 1.396648 TGCTCATATTTCCAACACGCG 59.603 47.619 3.53 3.53 0.00 6.01
167 168 1.663643 GCTCATATTTCCAACACGCGA 59.336 47.619 15.93 0.00 0.00 5.87
168 169 2.536928 GCTCATATTTCCAACACGCGAC 60.537 50.000 15.93 0.00 0.00 5.19
169 170 2.004017 TCATATTTCCAACACGCGACC 58.996 47.619 15.93 0.00 0.00 4.79
170 171 2.006888 CATATTTCCAACACGCGACCT 58.993 47.619 15.93 0.00 0.00 3.85
171 172 2.172851 TATTTCCAACACGCGACCTT 57.827 45.000 15.93 0.00 0.00 3.50
172 173 1.314730 ATTTCCAACACGCGACCTTT 58.685 45.000 15.93 0.00 0.00 3.11
173 174 0.378962 TTTCCAACACGCGACCTTTG 59.621 50.000 15.93 9.84 0.00 2.77
174 175 0.745128 TTCCAACACGCGACCTTTGT 60.745 50.000 15.93 2.44 0.00 2.83
175 176 0.745128 TCCAACACGCGACCTTTGTT 60.745 50.000 15.93 10.04 33.69 2.83
176 177 0.591236 CCAACACGCGACCTTTGTTG 60.591 55.000 24.51 24.51 46.39 3.33
177 178 1.063488 AACACGCGACCTTTGTTGC 59.937 52.632 15.93 0.00 46.65 4.17
181 182 4.440214 GCGACCTTTGTTGCGATG 57.560 55.556 0.00 0.00 41.86 3.84
182 183 1.154225 GCGACCTTTGTTGCGATGG 60.154 57.895 0.00 0.00 41.86 3.51
183 184 1.852067 GCGACCTTTGTTGCGATGGT 61.852 55.000 0.00 0.00 41.86 3.55
184 185 1.434555 CGACCTTTGTTGCGATGGTA 58.565 50.000 0.00 0.00 0.00 3.25
185 186 1.801771 CGACCTTTGTTGCGATGGTAA 59.198 47.619 0.00 0.00 0.00 2.85
186 187 2.224549 CGACCTTTGTTGCGATGGTAAA 59.775 45.455 0.00 0.00 0.00 2.01
187 188 3.304123 CGACCTTTGTTGCGATGGTAAAA 60.304 43.478 0.00 0.00 0.00 1.52
188 189 4.226761 GACCTTTGTTGCGATGGTAAAAG 58.773 43.478 0.00 0.00 0.00 2.27
189 190 3.005367 ACCTTTGTTGCGATGGTAAAAGG 59.995 43.478 9.80 9.80 45.89 3.11
190 191 3.005367 CCTTTGTTGCGATGGTAAAAGGT 59.995 43.478 0.00 0.00 39.09 3.50
191 192 3.634568 TTGTTGCGATGGTAAAAGGTG 57.365 42.857 0.00 0.00 0.00 4.00
192 193 2.852449 TGTTGCGATGGTAAAAGGTGA 58.148 42.857 0.00 0.00 0.00 4.02
193 194 2.550606 TGTTGCGATGGTAAAAGGTGAC 59.449 45.455 0.00 0.00 0.00 3.67
194 195 1.434555 TGCGATGGTAAAAGGTGACG 58.565 50.000 0.00 0.00 0.00 4.35
195 196 0.096454 GCGATGGTAAAAGGTGACGC 59.904 55.000 0.00 0.00 38.23 5.19
196 197 1.722011 CGATGGTAAAAGGTGACGCT 58.278 50.000 0.00 0.00 0.00 5.07
197 198 2.073816 CGATGGTAAAAGGTGACGCTT 58.926 47.619 0.00 0.00 0.00 4.68
198 199 2.159707 CGATGGTAAAAGGTGACGCTTG 60.160 50.000 0.00 0.00 0.00 4.01
199 200 2.623878 TGGTAAAAGGTGACGCTTGA 57.376 45.000 0.00 0.00 0.00 3.02
200 201 2.215196 TGGTAAAAGGTGACGCTTGAC 58.785 47.619 0.00 0.00 0.00 3.18
201 202 1.534163 GGTAAAAGGTGACGCTTGACC 59.466 52.381 0.00 0.00 0.00 4.02
202 203 1.193874 GTAAAAGGTGACGCTTGACCG 59.806 52.381 0.00 0.00 37.32 4.79
203 204 0.463116 AAAAGGTGACGCTTGACCGT 60.463 50.000 0.00 0.00 45.30 4.83
204 205 0.463116 AAAGGTGACGCTTGACCGTT 60.463 50.000 0.00 0.00 42.24 4.44
205 206 0.878961 AAGGTGACGCTTGACCGTTC 60.879 55.000 0.00 0.00 42.24 3.95
206 207 1.593209 GGTGACGCTTGACCGTTCA 60.593 57.895 0.00 0.00 42.24 3.18
207 208 1.563173 GTGACGCTTGACCGTTCAC 59.437 57.895 0.00 0.00 42.24 3.18
208 209 0.874607 GTGACGCTTGACCGTTCACT 60.875 55.000 0.00 0.00 42.24 3.41
209 210 0.596600 TGACGCTTGACCGTTCACTC 60.597 55.000 0.00 0.00 42.24 3.51
210 211 1.282930 GACGCTTGACCGTTCACTCC 61.283 60.000 0.00 0.00 42.24 3.85
211 212 2.372690 CGCTTGACCGTTCACTCCG 61.373 63.158 0.00 0.00 0.00 4.63
212 213 2.668280 GCTTGACCGTTCACTCCGC 61.668 63.158 0.00 0.00 0.00 5.54
213 214 2.027625 CTTGACCGTTCACTCCGCC 61.028 63.158 0.00 0.00 0.00 6.13
214 215 3.524648 TTGACCGTTCACTCCGCCC 62.525 63.158 0.00 0.00 0.00 6.13
217 218 4.143333 CCGTTCACTCCGCCCGAT 62.143 66.667 0.00 0.00 0.00 4.18
218 219 2.582498 CGTTCACTCCGCCCGATC 60.582 66.667 0.00 0.00 0.00 3.69
219 220 2.202892 GTTCACTCCGCCCGATCC 60.203 66.667 0.00 0.00 0.00 3.36
220 221 2.682136 TTCACTCCGCCCGATCCA 60.682 61.111 0.00 0.00 0.00 3.41
221 222 2.287274 TTCACTCCGCCCGATCCAA 61.287 57.895 0.00 0.00 0.00 3.53
222 223 1.622607 TTCACTCCGCCCGATCCAAT 61.623 55.000 0.00 0.00 0.00 3.16
223 224 1.889105 CACTCCGCCCGATCCAATG 60.889 63.158 0.00 0.00 0.00 2.82
224 225 2.367202 ACTCCGCCCGATCCAATGT 61.367 57.895 0.00 0.00 0.00 2.71
225 226 1.153168 CTCCGCCCGATCCAATGTT 60.153 57.895 0.00 0.00 0.00 2.71
226 227 0.748005 CTCCGCCCGATCCAATGTTT 60.748 55.000 0.00 0.00 0.00 2.83
227 228 0.746563 TCCGCCCGATCCAATGTTTC 60.747 55.000 0.00 0.00 0.00 2.78
228 229 1.351707 CGCCCGATCCAATGTTTCG 59.648 57.895 0.00 0.00 0.00 3.46
229 230 1.064134 GCCCGATCCAATGTTTCGC 59.936 57.895 0.00 0.00 0.00 4.70
230 231 1.351707 CCCGATCCAATGTTTCGCG 59.648 57.895 0.00 0.00 0.00 5.87
231 232 1.087202 CCCGATCCAATGTTTCGCGA 61.087 55.000 3.71 3.71 0.00 5.87
232 233 0.301687 CCGATCCAATGTTTCGCGAG 59.698 55.000 9.59 0.00 0.00 5.03
233 234 0.301687 CGATCCAATGTTTCGCGAGG 59.698 55.000 9.59 6.15 0.00 4.63
234 235 0.028110 GATCCAATGTTTCGCGAGGC 59.972 55.000 9.59 6.99 0.00 4.70
241 242 2.340809 TTTCGCGAGGCGGAAAGA 59.659 55.556 9.59 0.00 46.98 2.52
242 243 1.079405 TTTCGCGAGGCGGAAAGAT 60.079 52.632 9.59 0.00 46.98 2.40
243 244 1.082117 TTTCGCGAGGCGGAAAGATC 61.082 55.000 9.59 0.00 46.98 2.75
244 245 3.426126 TTTCGCGAGGCGGAAAGATCT 62.426 52.381 9.59 0.00 46.98 2.75
245 246 3.711348 GCGAGGCGGAAAGATCTG 58.289 61.111 0.00 0.00 34.87 2.90
251 252 2.897350 CGGAAAGATCTGCCGGCC 60.897 66.667 26.77 8.39 41.29 6.13
252 253 2.897350 GGAAAGATCTGCCGGCCG 60.897 66.667 26.77 21.04 0.00 6.13
253 254 2.186903 GAAAGATCTGCCGGCCGA 59.813 61.111 30.73 24.98 0.00 5.54
254 255 2.125106 AAAGATCTGCCGGCCGAC 60.125 61.111 30.73 18.13 0.00 4.79
255 256 4.514577 AAGATCTGCCGGCCGACG 62.515 66.667 30.73 12.70 43.80 5.12
311 312 9.601217 AAAGATTGGTATACTAAGTCATGTGAC 57.399 33.333 7.76 5.01 45.08 3.67
368 373 2.292016 TCGTGCAAAATGTTCAACGGAT 59.708 40.909 0.00 0.00 0.00 4.18
373 378 6.092748 GTGCAAAATGTTCAACGGATAGAAT 58.907 36.000 0.00 0.00 0.00 2.40
449 454 0.533085 TGTCCGATGAAACCAACGCA 60.533 50.000 0.00 0.00 0.00 5.24
459 464 3.508840 CCAACGCAAGGGATCGGC 61.509 66.667 0.00 0.00 46.39 5.54
602 607 2.342279 CGTCTTCTTGGGGACGCA 59.658 61.111 2.72 0.00 46.23 5.24
603 608 2.027625 CGTCTTCTTGGGGACGCAC 61.028 63.158 2.72 0.00 46.23 5.34
604 609 2.027625 GTCTTCTTGGGGACGCACG 61.028 63.158 0.00 0.00 0.00 5.34
605 610 2.030562 CTTCTTGGGGACGCACGT 59.969 61.111 0.00 0.00 0.00 4.49
606 611 2.027625 CTTCTTGGGGACGCACGTC 61.028 63.158 14.58 14.58 43.87 4.34
607 612 3.851845 TTCTTGGGGACGCACGTCG 62.852 63.158 16.19 3.23 45.41 5.12
608 613 4.351938 CTTGGGGACGCACGTCGA 62.352 66.667 16.19 1.08 45.41 4.20
688 696 3.391382 CCACCCCGTCCCAGTCTC 61.391 72.222 0.00 0.00 0.00 3.36
784 792 8.902806 TCACTTCTGTTAGTTGTTGAATCAATT 58.097 29.630 0.00 0.00 0.00 2.32
799 807 8.636213 GTTGAATCAATTGATGAATCCCACTAT 58.364 33.333 21.39 1.18 42.54 2.12
803 811 5.829391 TCAATTGATGAATCCCACTATGGTG 59.171 40.000 3.38 1.49 37.91 4.17
815 823 0.194587 CTATGGTGGGGAGAGGGGAT 59.805 60.000 0.00 0.00 0.00 3.85
821 829 0.649992 TGGGGAGAGGGGATCTTCAT 59.350 55.000 0.00 0.00 38.84 2.57
828 836 5.515710 GGGAGAGGGGATCTTCATAATTTCC 60.516 48.000 0.00 0.00 38.84 3.13
836 844 3.691575 TCTTCATAATTTCCGGGTGCAA 58.308 40.909 0.00 0.00 0.00 4.08
938 947 3.068165 TGTCATCAGCCGTTCTATCGATT 59.932 43.478 1.71 0.00 0.00 3.34
1041 1054 3.182590 TTCAGTTGGCGCTCAGGCT 62.183 57.895 7.64 3.52 46.88 4.58
1122 1147 2.604046 ACTTCGAATTGGGATCCTCG 57.396 50.000 12.58 13.10 0.00 4.63
1137 1162 1.674057 CTCGTTCCTGGGCAAGACT 59.326 57.895 0.00 0.00 0.00 3.24
1296 1321 2.051334 AGATGTCTCCTCTGGTCTCG 57.949 55.000 0.00 0.00 0.00 4.04
1299 1324 0.034960 TGTCTCCTCTGGTCTCGGAG 60.035 60.000 0.00 0.00 44.48 4.63
1305 1330 3.443925 CTGGTCTCGGAGCTGCGA 61.444 66.667 28.87 28.87 0.00 5.10
1392 1417 1.133181 TCATGGACTTCACTGGCCCA 61.133 55.000 0.00 0.00 0.00 5.36
1461 1486 1.689582 CGGGGTCCCTAGAAAGCCT 60.690 63.158 8.15 0.00 33.50 4.58
1479 1504 1.690893 CCTGGGATGACTCGTGATGAT 59.309 52.381 0.00 0.00 0.00 2.45
1683 1708 3.064207 TGTTGTCCGAGCTAACACATTC 58.936 45.455 0.00 0.00 30.06 2.67
1822 1847 2.260844 TGAGGAAACTGAACAGCTGG 57.739 50.000 19.93 1.96 44.43 4.85
2057 2082 5.139727 TGGTGTTGAGTCCATCATTTCTTT 58.860 37.500 0.00 0.00 37.89 2.52
2198 2224 2.802816 CTGTTTGAAGTGAGGAGAACGG 59.197 50.000 0.00 0.00 0.00 4.44
2324 2370 9.959749 TTTCTCAATTGTTGGTCAGTTTATTAC 57.040 29.630 5.13 0.00 0.00 1.89
2463 2515 7.159372 GGAGTTCAACTGTGGACTAATAAAGA 58.841 38.462 0.00 0.00 44.23 2.52
2489 2541 3.689161 TCTTTGATCATTACCAAGGCACG 59.311 43.478 0.00 0.00 0.00 5.34
2511 2563 3.831911 GCCATCTAGATCTGCCTCTACTT 59.168 47.826 5.18 0.00 0.00 2.24
2584 2636 4.202461 TGAGCCAGTGGGATGAATAATACC 60.202 45.833 12.15 0.00 40.22 2.73
2654 2706 7.194112 TGTACAAATCCAGGATCTGATTGTA 57.806 36.000 16.06 16.06 35.72 2.41
2656 2708 7.716560 TGTACAAATCCAGGATCTGATTGTATG 59.283 37.037 20.38 6.31 37.28 2.39
2657 2709 6.903516 ACAAATCCAGGATCTGATTGTATGA 58.096 36.000 9.99 0.00 33.98 2.15
2658 2710 7.524290 ACAAATCCAGGATCTGATTGTATGAT 58.476 34.615 9.99 0.00 33.98 2.45
2659 2711 8.663167 ACAAATCCAGGATCTGATTGTATGATA 58.337 33.333 9.99 0.00 33.98 2.15
2660 2712 9.511272 CAAATCCAGGATCTGATTGTATGATAA 57.489 33.333 1.11 0.00 32.44 1.75
2663 2715 9.902684 ATCCAGGATCTGATTGTATGATAAATC 57.097 33.333 0.00 0.00 32.44 2.17
2769 2822 6.306643 AGAAGATTATGCTATTAGGGGAGC 57.693 41.667 0.00 0.00 39.25 4.70
2810 2864 4.759693 TCATTTGTTTGCATCCGTACTCTT 59.240 37.500 0.00 0.00 0.00 2.85
2824 2878 4.814771 CCGTACTCTTGGGGAATAAATGTC 59.185 45.833 0.00 0.00 0.00 3.06
2835 2893 5.510520 GGGGAATAAATGTCTTGTTTGTGCA 60.511 40.000 0.00 0.00 0.00 4.57
2890 2948 1.755179 CAGGGACAGGCATGGTAAAG 58.245 55.000 2.31 0.00 0.00 1.85
2896 2954 2.673368 GACAGGCATGGTAAAGTTCTCG 59.327 50.000 2.31 0.00 0.00 4.04
2905 2963 5.678132 TGGTAAAGTTCTCGCCTTTTTAC 57.322 39.130 0.00 0.00 34.20 2.01
2917 2977 3.143728 GCCTTTTTACTCGTTCTTCCCA 58.856 45.455 0.00 0.00 0.00 4.37
2920 2980 5.619309 GCCTTTTTACTCGTTCTTCCCAATC 60.619 44.000 0.00 0.00 0.00 2.67
2929 2989 3.555966 GTTCTTCCCAATCCACCCTATG 58.444 50.000 0.00 0.00 0.00 2.23
2962 3022 9.393249 TCTGTTAATTTAGTTTTGATTTCTGCG 57.607 29.630 0.00 0.00 0.00 5.18
2982 3042 2.168496 GGTATACATGCTCGCTCCCTA 58.832 52.381 5.01 0.00 0.00 3.53
2983 3043 2.094649 GGTATACATGCTCGCTCCCTAC 60.095 54.545 5.01 0.00 0.00 3.18
2984 3044 1.704641 ATACATGCTCGCTCCCTACA 58.295 50.000 0.00 0.00 0.00 2.74
3011 3073 0.033366 AAGAATTTGGGCCGTGTTGC 59.967 50.000 0.00 0.00 0.00 4.17
3038 3100 1.552337 CCTGCTGTTCTCTTGCTAGGA 59.448 52.381 0.00 0.00 31.49 2.94
3140 3202 8.082242 GTGAAGTTTAAGCCTTGAATGTGTTAT 58.918 33.333 0.00 0.00 0.00 1.89
3141 3203 9.290988 TGAAGTTTAAGCCTTGAATGTGTTATA 57.709 29.630 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.611943 ACATGAATTCTACCACGATCTCG 58.388 43.478 7.05 0.00 46.33 4.04
1 2 6.758886 AGAAACATGAATTCTACCACGATCTC 59.241 38.462 14.15 0.00 35.43 2.75
2 3 6.644347 AGAAACATGAATTCTACCACGATCT 58.356 36.000 14.15 0.00 35.43 2.75
3 4 6.910536 AGAAACATGAATTCTACCACGATC 57.089 37.500 14.15 0.00 35.43 3.69
4 5 7.556844 ACTAGAAACATGAATTCTACCACGAT 58.443 34.615 16.49 0.00 38.13 3.73
5 6 6.931838 ACTAGAAACATGAATTCTACCACGA 58.068 36.000 16.49 3.95 38.13 4.35
6 7 8.755941 CATACTAGAAACATGAATTCTACCACG 58.244 37.037 16.49 11.76 38.13 4.94
7 8 9.601217 ACATACTAGAAACATGAATTCTACCAC 57.399 33.333 16.49 0.00 38.13 4.16
8 9 9.599866 CACATACTAGAAACATGAATTCTACCA 57.400 33.333 16.49 10.50 38.13 3.25
9 10 8.552034 GCACATACTAGAAACATGAATTCTACC 58.448 37.037 16.49 0.00 38.13 3.18
10 11 8.552034 GGCACATACTAGAAACATGAATTCTAC 58.448 37.037 16.49 8.90 38.13 2.59
11 12 7.715249 GGGCACATACTAGAAACATGAATTCTA 59.285 37.037 18.23 18.23 38.13 2.10
12 13 6.543831 GGGCACATACTAGAAACATGAATTCT 59.456 38.462 18.00 18.00 40.18 2.40
13 14 6.543831 AGGGCACATACTAGAAACATGAATTC 59.456 38.462 0.00 3.71 0.00 2.17
14 15 6.426587 AGGGCACATACTAGAAACATGAATT 58.573 36.000 0.00 0.00 0.00 2.17
15 16 6.006275 AGGGCACATACTAGAAACATGAAT 57.994 37.500 0.00 0.00 0.00 2.57
16 17 5.435686 AGGGCACATACTAGAAACATGAA 57.564 39.130 0.00 0.00 0.00 2.57
17 18 5.897250 TCTAGGGCACATACTAGAAACATGA 59.103 40.000 0.00 0.00 41.84 3.07
18 19 6.161855 TCTAGGGCACATACTAGAAACATG 57.838 41.667 0.00 0.00 41.84 3.21
19 20 6.327626 ACATCTAGGGCACATACTAGAAACAT 59.672 38.462 0.00 0.00 46.12 2.71
20 21 5.661312 ACATCTAGGGCACATACTAGAAACA 59.339 40.000 0.00 0.00 46.12 2.83
21 22 5.986135 CACATCTAGGGCACATACTAGAAAC 59.014 44.000 0.00 0.00 46.12 2.78
22 23 5.897250 TCACATCTAGGGCACATACTAGAAA 59.103 40.000 0.00 0.00 46.12 2.52
23 24 5.454966 TCACATCTAGGGCACATACTAGAA 58.545 41.667 0.00 0.00 46.12 2.10
24 25 5.061721 TCACATCTAGGGCACATACTAGA 57.938 43.478 0.00 4.14 46.80 2.43
25 26 5.714333 AGATCACATCTAGGGCACATACTAG 59.286 44.000 0.00 0.00 38.00 2.57
26 27 5.478332 CAGATCACATCTAGGGCACATACTA 59.522 44.000 0.00 0.00 37.58 1.82
27 28 4.282957 CAGATCACATCTAGGGCACATACT 59.717 45.833 0.00 0.00 37.58 2.12
28 29 4.039730 ACAGATCACATCTAGGGCACATAC 59.960 45.833 0.00 0.00 37.58 2.39
29 30 4.226384 ACAGATCACATCTAGGGCACATA 58.774 43.478 0.00 0.00 37.58 2.29
30 31 3.044156 ACAGATCACATCTAGGGCACAT 58.956 45.455 0.00 0.00 37.58 3.21
31 32 2.470990 ACAGATCACATCTAGGGCACA 58.529 47.619 0.00 0.00 37.58 4.57
32 33 3.118629 TGAACAGATCACATCTAGGGCAC 60.119 47.826 0.00 0.00 37.58 5.01
33 34 3.106827 TGAACAGATCACATCTAGGGCA 58.893 45.455 0.00 0.00 37.58 5.36
34 35 3.827008 TGAACAGATCACATCTAGGGC 57.173 47.619 0.00 0.00 37.58 5.19
35 36 5.539979 CAGATGAACAGATCACATCTAGGG 58.460 45.833 17.55 8.08 45.61 3.53
36 37 4.989797 GCAGATGAACAGATCACATCTAGG 59.010 45.833 17.55 11.42 45.61 3.02
37 38 5.845103 AGCAGATGAACAGATCACATCTAG 58.155 41.667 17.55 14.33 45.61 2.43
38 39 5.866159 AGCAGATGAACAGATCACATCTA 57.134 39.130 17.55 0.00 45.61 1.98
40 41 5.107026 GCATAGCAGATGAACAGATCACATC 60.107 44.000 0.00 4.97 41.93 3.06
41 42 4.755629 GCATAGCAGATGAACAGATCACAT 59.244 41.667 0.00 0.00 41.93 3.21
42 43 4.124970 GCATAGCAGATGAACAGATCACA 58.875 43.478 0.00 0.00 41.93 3.58
43 44 4.378774 AGCATAGCAGATGAACAGATCAC 58.621 43.478 0.00 0.00 41.93 3.06
44 45 4.684484 AGCATAGCAGATGAACAGATCA 57.316 40.909 0.00 0.00 43.67 2.92
45 46 5.782047 ACTAGCATAGCAGATGAACAGATC 58.218 41.667 2.96 0.00 44.39 2.75
46 47 5.804944 ACTAGCATAGCAGATGAACAGAT 57.195 39.130 2.96 0.00 44.39 2.90
47 48 5.595885 GAACTAGCATAGCAGATGAACAGA 58.404 41.667 2.96 0.00 44.39 3.41
48 49 4.443725 CGAACTAGCATAGCAGATGAACAG 59.556 45.833 2.96 0.00 44.39 3.16
49 50 4.363138 CGAACTAGCATAGCAGATGAACA 58.637 43.478 2.96 0.00 44.39 3.18
50 51 3.183373 GCGAACTAGCATAGCAGATGAAC 59.817 47.826 2.96 0.00 44.39 3.18
51 52 3.181476 TGCGAACTAGCATAGCAGATGAA 60.181 43.478 2.96 0.00 44.39 2.57
52 53 2.362077 TGCGAACTAGCATAGCAGATGA 59.638 45.455 2.96 0.00 44.39 2.92
53 54 2.747436 TGCGAACTAGCATAGCAGATG 58.253 47.619 0.68 0.00 44.39 2.90
62 63 7.710907 AGATTAAACTAATCATGCGAACTAGCA 59.289 33.333 8.66 0.00 45.41 3.49
63 64 8.077836 AGATTAAACTAATCATGCGAACTAGC 57.922 34.615 8.66 0.00 45.41 3.42
64 65 9.469807 AGAGATTAAACTAATCATGCGAACTAG 57.530 33.333 8.66 0.00 45.41 2.57
66 67 9.250624 GTAGAGATTAAACTAATCATGCGAACT 57.749 33.333 8.66 0.00 45.41 3.01
67 68 9.250624 AGTAGAGATTAAACTAATCATGCGAAC 57.749 33.333 8.66 3.53 45.41 3.95
69 70 9.894783 GTAGTAGAGATTAAACTAATCATGCGA 57.105 33.333 8.66 0.00 45.41 5.10
70 71 9.900710 AGTAGTAGAGATTAAACTAATCATGCG 57.099 33.333 8.66 0.00 45.41 4.73
121 122 9.245962 CAAGTTACTACGAGATTTAATCCGAAT 57.754 33.333 17.75 8.52 0.00 3.34
122 123 7.221452 GCAAGTTACTACGAGATTTAATCCGAA 59.779 37.037 17.75 4.27 0.00 4.30
123 124 6.694411 GCAAGTTACTACGAGATTTAATCCGA 59.306 38.462 17.75 5.77 0.00 4.55
124 125 6.696148 AGCAAGTTACTACGAGATTTAATCCG 59.304 38.462 12.00 12.00 0.00 4.18
125 126 7.705325 TGAGCAAGTTACTACGAGATTTAATCC 59.295 37.037 0.78 0.00 0.00 3.01
126 127 8.630278 TGAGCAAGTTACTACGAGATTTAATC 57.370 34.615 0.00 0.00 0.00 1.75
130 131 9.601217 AAATATGAGCAAGTTACTACGAGATTT 57.399 29.630 0.00 0.00 0.00 2.17
131 132 9.250624 GAAATATGAGCAAGTTACTACGAGATT 57.749 33.333 0.00 0.00 0.00 2.40
132 133 7.868415 GGAAATATGAGCAAGTTACTACGAGAT 59.132 37.037 0.00 0.00 0.00 2.75
133 134 7.147966 TGGAAATATGAGCAAGTTACTACGAGA 60.148 37.037 0.00 0.00 0.00 4.04
134 135 6.978659 TGGAAATATGAGCAAGTTACTACGAG 59.021 38.462 0.00 0.00 0.00 4.18
135 136 6.869695 TGGAAATATGAGCAAGTTACTACGA 58.130 36.000 0.00 0.00 0.00 3.43
136 137 7.064134 TGTTGGAAATATGAGCAAGTTACTACG 59.936 37.037 0.00 0.00 0.00 3.51
137 138 8.175716 GTGTTGGAAATATGAGCAAGTTACTAC 58.824 37.037 0.00 0.00 0.00 2.73
138 139 7.064134 CGTGTTGGAAATATGAGCAAGTTACTA 59.936 37.037 0.00 0.00 0.00 1.82
139 140 6.128282 CGTGTTGGAAATATGAGCAAGTTACT 60.128 38.462 0.00 0.00 0.00 2.24
140 141 6.021596 CGTGTTGGAAATATGAGCAAGTTAC 58.978 40.000 0.00 0.00 0.00 2.50
141 142 5.391523 GCGTGTTGGAAATATGAGCAAGTTA 60.392 40.000 0.00 0.00 0.00 2.24
142 143 4.615912 GCGTGTTGGAAATATGAGCAAGTT 60.616 41.667 0.00 0.00 0.00 2.66
143 144 3.119849 GCGTGTTGGAAATATGAGCAAGT 60.120 43.478 0.00 0.00 0.00 3.16
144 145 3.429085 GCGTGTTGGAAATATGAGCAAG 58.571 45.455 0.00 0.00 0.00 4.01
145 146 2.159585 CGCGTGTTGGAAATATGAGCAA 60.160 45.455 0.00 0.00 0.00 3.91
146 147 1.396648 CGCGTGTTGGAAATATGAGCA 59.603 47.619 0.00 0.00 0.00 4.26
147 148 1.663643 TCGCGTGTTGGAAATATGAGC 59.336 47.619 5.77 0.00 0.00 4.26
148 149 2.030457 GGTCGCGTGTTGGAAATATGAG 59.970 50.000 5.77 0.00 0.00 2.90
149 150 2.004017 GGTCGCGTGTTGGAAATATGA 58.996 47.619 5.77 0.00 0.00 2.15
150 151 2.006888 AGGTCGCGTGTTGGAAATATG 58.993 47.619 5.77 0.00 0.00 1.78
151 152 2.396590 AGGTCGCGTGTTGGAAATAT 57.603 45.000 5.77 0.00 0.00 1.28
152 153 2.172851 AAGGTCGCGTGTTGGAAATA 57.827 45.000 5.77 0.00 0.00 1.40
153 154 1.001815 CAAAGGTCGCGTGTTGGAAAT 60.002 47.619 5.77 0.00 0.00 2.17
154 155 0.378962 CAAAGGTCGCGTGTTGGAAA 59.621 50.000 5.77 0.00 0.00 3.13
155 156 0.745128 ACAAAGGTCGCGTGTTGGAA 60.745 50.000 5.77 0.00 0.00 3.53
156 157 0.745128 AACAAAGGTCGCGTGTTGGA 60.745 50.000 10.76 0.00 34.28 3.53
157 158 0.591236 CAACAAAGGTCGCGTGTTGG 60.591 55.000 24.02 10.14 45.35 3.77
158 159 2.853457 CAACAAAGGTCGCGTGTTG 58.147 52.632 20.41 20.41 44.26 3.33
159 160 1.063488 GCAACAAAGGTCGCGTGTT 59.937 52.632 5.77 6.06 35.91 3.32
160 161 2.713154 GCAACAAAGGTCGCGTGT 59.287 55.556 5.77 0.00 0.00 4.49
161 162 2.425124 CGCAACAAAGGTCGCGTG 60.425 61.111 5.77 0.00 42.66 5.34
164 165 1.154225 CCATCGCAACAAAGGTCGC 60.154 57.895 0.00 0.00 0.00 5.19
165 166 1.434555 TACCATCGCAACAAAGGTCG 58.565 50.000 0.00 0.00 33.91 4.79
166 167 3.907894 TTTACCATCGCAACAAAGGTC 57.092 42.857 0.00 0.00 33.91 3.85
167 168 3.005367 CCTTTTACCATCGCAACAAAGGT 59.995 43.478 0.00 0.00 36.86 3.50
168 169 3.005367 ACCTTTTACCATCGCAACAAAGG 59.995 43.478 6.90 6.90 43.98 3.11
169 170 3.980775 CACCTTTTACCATCGCAACAAAG 59.019 43.478 0.00 0.00 0.00 2.77
170 171 3.632604 TCACCTTTTACCATCGCAACAAA 59.367 39.130 0.00 0.00 0.00 2.83
171 172 3.003897 GTCACCTTTTACCATCGCAACAA 59.996 43.478 0.00 0.00 0.00 2.83
172 173 2.550606 GTCACCTTTTACCATCGCAACA 59.449 45.455 0.00 0.00 0.00 3.33
173 174 2.412325 CGTCACCTTTTACCATCGCAAC 60.412 50.000 0.00 0.00 0.00 4.17
174 175 1.801771 CGTCACCTTTTACCATCGCAA 59.198 47.619 0.00 0.00 0.00 4.85
175 176 1.434555 CGTCACCTTTTACCATCGCA 58.565 50.000 0.00 0.00 0.00 5.10
176 177 0.096454 GCGTCACCTTTTACCATCGC 59.904 55.000 0.00 0.00 36.06 4.58
177 178 1.722011 AGCGTCACCTTTTACCATCG 58.278 50.000 0.00 0.00 0.00 3.84
178 179 3.071479 TCAAGCGTCACCTTTTACCATC 58.929 45.455 0.00 0.00 0.00 3.51
179 180 2.812011 GTCAAGCGTCACCTTTTACCAT 59.188 45.455 0.00 0.00 0.00 3.55
180 181 2.215196 GTCAAGCGTCACCTTTTACCA 58.785 47.619 0.00 0.00 0.00 3.25
181 182 1.534163 GGTCAAGCGTCACCTTTTACC 59.466 52.381 0.00 0.00 0.00 2.85
182 183 1.193874 CGGTCAAGCGTCACCTTTTAC 59.806 52.381 0.00 0.00 0.00 2.01
183 184 1.202557 ACGGTCAAGCGTCACCTTTTA 60.203 47.619 0.73 0.00 0.00 1.52
184 185 0.463116 ACGGTCAAGCGTCACCTTTT 60.463 50.000 0.73 0.00 0.00 2.27
185 186 0.463116 AACGGTCAAGCGTCACCTTT 60.463 50.000 7.78 0.00 0.00 3.11
186 187 0.878961 GAACGGTCAAGCGTCACCTT 60.879 55.000 7.78 0.00 0.00 3.50
187 188 1.300697 GAACGGTCAAGCGTCACCT 60.301 57.895 7.78 0.00 0.00 4.00
188 189 1.593209 TGAACGGTCAAGCGTCACC 60.593 57.895 0.00 1.94 0.00 4.02
189 190 0.874607 AGTGAACGGTCAAGCGTCAC 60.875 55.000 3.77 19.74 34.87 3.67
190 191 0.596600 GAGTGAACGGTCAAGCGTCA 60.597 55.000 3.77 5.43 34.87 4.35
191 192 1.282930 GGAGTGAACGGTCAAGCGTC 61.283 60.000 3.77 0.00 34.87 5.19
192 193 1.300697 GGAGTGAACGGTCAAGCGT 60.301 57.895 3.77 0.73 34.87 5.07
193 194 2.372690 CGGAGTGAACGGTCAAGCG 61.373 63.158 3.77 0.00 34.87 4.68
194 195 2.668280 GCGGAGTGAACGGTCAAGC 61.668 63.158 3.77 5.13 34.87 4.01
195 196 2.027625 GGCGGAGTGAACGGTCAAG 61.028 63.158 3.77 0.00 34.87 3.02
196 197 2.029964 GGCGGAGTGAACGGTCAA 59.970 61.111 3.77 0.00 34.87 3.18
197 198 3.998672 GGGCGGAGTGAACGGTCA 61.999 66.667 0.00 0.00 0.00 4.02
200 201 4.143333 ATCGGGCGGAGTGAACGG 62.143 66.667 0.20 0.00 0.00 4.44
201 202 2.582498 GATCGGGCGGAGTGAACG 60.582 66.667 0.20 0.00 0.00 3.95
202 203 2.202892 GGATCGGGCGGAGTGAAC 60.203 66.667 0.20 0.00 0.00 3.18
203 204 1.622607 ATTGGATCGGGCGGAGTGAA 61.623 55.000 0.20 0.00 0.00 3.18
204 205 2.063979 ATTGGATCGGGCGGAGTGA 61.064 57.895 0.20 0.00 0.00 3.41
205 206 1.889105 CATTGGATCGGGCGGAGTG 60.889 63.158 0.20 0.00 0.00 3.51
206 207 1.910580 AACATTGGATCGGGCGGAGT 61.911 55.000 0.20 0.00 0.00 3.85
207 208 0.748005 AAACATTGGATCGGGCGGAG 60.748 55.000 0.20 0.00 0.00 4.63
208 209 0.746563 GAAACATTGGATCGGGCGGA 60.747 55.000 0.00 0.00 0.00 5.54
209 210 1.727467 GAAACATTGGATCGGGCGG 59.273 57.895 0.00 0.00 0.00 6.13
210 211 1.351707 CGAAACATTGGATCGGGCG 59.648 57.895 5.70 0.00 33.15 6.13
211 212 1.064134 GCGAAACATTGGATCGGGC 59.936 57.895 13.04 0.00 37.08 6.13
212 213 1.087202 TCGCGAAACATTGGATCGGG 61.087 55.000 6.20 18.04 46.76 5.14
213 214 0.301687 CTCGCGAAACATTGGATCGG 59.698 55.000 11.33 0.00 37.08 4.18
214 215 0.301687 CCTCGCGAAACATTGGATCG 59.698 55.000 11.33 8.46 39.47 3.69
215 216 0.028110 GCCTCGCGAAACATTGGATC 59.972 55.000 11.33 0.00 0.00 3.36
216 217 2.098293 GCCTCGCGAAACATTGGAT 58.902 52.632 11.33 0.00 0.00 3.41
217 218 3.573558 GCCTCGCGAAACATTGGA 58.426 55.556 11.33 0.00 0.00 3.53
228 229 2.529619 GCAGATCTTTCCGCCTCGC 61.530 63.158 0.00 0.00 0.00 5.03
229 230 1.884926 GGCAGATCTTTCCGCCTCG 60.885 63.158 13.27 0.00 41.50 4.63
230 231 1.884926 CGGCAGATCTTTCCGCCTC 60.885 63.158 17.25 0.00 42.59 4.70
231 232 2.187946 CGGCAGATCTTTCCGCCT 59.812 61.111 17.25 0.00 42.59 5.52
232 233 2.897350 CCGGCAGATCTTTCCGCC 60.897 66.667 21.78 16.86 41.68 6.13
233 234 3.577313 GCCGGCAGATCTTTCCGC 61.577 66.667 24.80 15.40 41.68 5.54
234 235 2.897350 GGCCGGCAGATCTTTCCG 60.897 66.667 30.85 20.73 42.58 4.30
235 236 2.897350 CGGCCGGCAGATCTTTCC 60.897 66.667 30.85 6.07 0.00 3.13
236 237 2.174319 GTCGGCCGGCAGATCTTTC 61.174 63.158 31.70 15.11 0.00 2.62
237 238 2.125106 GTCGGCCGGCAGATCTTT 60.125 61.111 31.70 0.00 0.00 2.52
238 239 4.514577 CGTCGGCCGGCAGATCTT 62.515 66.667 31.70 0.00 0.00 2.40
248 249 3.925238 CATTGCTACGCGTCGGCC 61.925 66.667 26.37 11.68 35.02 6.13
249 250 4.575245 GCATTGCTACGCGTCGGC 62.575 66.667 18.63 22.16 0.00 5.54
250 251 2.947118 TAGGCATTGCTACGCGTCGG 62.947 60.000 18.63 11.80 0.00 4.79
251 252 1.143373 TTAGGCATTGCTACGCGTCG 61.143 55.000 18.63 11.79 0.00 5.12
252 253 1.217882 ATTAGGCATTGCTACGCGTC 58.782 50.000 18.63 1.99 0.00 5.19
253 254 1.663695 AATTAGGCATTGCTACGCGT 58.336 45.000 19.17 19.17 0.00 6.01
254 255 2.755836 AAATTAGGCATTGCTACGCG 57.244 45.000 3.53 3.53 0.00 6.01
255 256 4.545823 TGTAAATTAGGCATTGCTACGC 57.454 40.909 8.82 0.00 0.00 4.42
256 257 6.724263 TCAATGTAAATTAGGCATTGCTACG 58.276 36.000 17.51 0.00 45.19 3.51
257 258 8.925161 TTTCAATGTAAATTAGGCATTGCTAC 57.075 30.769 17.51 2.80 45.19 3.58
340 341 7.280055 CGTTGAACATTTTGCACGAATAAATT 58.720 30.769 0.00 0.00 0.00 1.82
368 373 8.474831 TCAGAGTCCGAATAATGAACAATTCTA 58.525 33.333 0.00 0.00 31.29 2.10
373 378 4.862574 CGTCAGAGTCCGAATAATGAACAA 59.137 41.667 0.00 0.00 0.00 2.83
449 454 2.231380 AACCACTGGCCGATCCCTT 61.231 57.895 0.00 0.00 0.00 3.95
586 591 2.027625 CGTGCGTCCCCAAGAAGAC 61.028 63.158 0.00 0.00 0.00 3.01
587 592 2.342279 CGTGCGTCCCCAAGAAGA 59.658 61.111 0.00 0.00 0.00 2.87
622 630 3.246880 AAGAAGGGGAACGGCGGT 61.247 61.111 13.24 3.35 0.00 5.68
740 748 1.303561 ATGCTGCGCTGGAGGAAAA 60.304 52.632 16.47 0.00 0.00 2.29
745 753 1.703438 GAAGTGATGCTGCGCTGGAG 61.703 60.000 16.47 2.29 0.00 3.86
799 807 1.837533 AAGATCCCCTCTCCCCACCA 61.838 60.000 0.00 0.00 31.03 4.17
803 811 2.723530 TATGAAGATCCCCTCTCCCC 57.276 55.000 0.00 0.00 31.03 4.81
809 817 3.074538 CCCGGAAATTATGAAGATCCCCT 59.925 47.826 0.73 0.00 0.00 4.79
815 823 3.358111 TGCACCCGGAAATTATGAAGA 57.642 42.857 0.73 0.00 0.00 2.87
821 829 4.874459 CCAGGTTTTGCACCCGGAAATTA 61.874 47.826 0.73 0.00 45.55 1.40
836 844 3.421844 GATCTAGTTGGTTGCCAGGTTT 58.578 45.455 0.00 0.00 33.81 3.27
841 849 0.392461 GCGGATCTAGTTGGTTGCCA 60.392 55.000 0.00 0.00 0.00 4.92
1041 1054 1.682854 CTTGGCTTTGAAACCAGAGCA 59.317 47.619 9.59 0.00 41.85 4.26
1122 1147 1.303643 CCCAGTCTTGCCCAGGAAC 60.304 63.158 0.00 0.00 0.00 3.62
1137 1162 1.306141 AGATGCCCGAAGAGACCCA 60.306 57.895 0.00 0.00 0.00 4.51
1176 1201 2.747855 GCCCCAGACTTCGCCTTG 60.748 66.667 0.00 0.00 0.00 3.61
1270 1295 3.705579 ACCAGAGGAGACATCTTGATCAG 59.294 47.826 0.00 0.00 0.00 2.90
1296 1321 0.661552 TATCGTACAGTCGCAGCTCC 59.338 55.000 0.00 0.00 0.00 4.70
1299 1324 1.190323 GCAATATCGTACAGTCGCAGC 59.810 52.381 0.00 0.00 0.00 5.25
1305 1330 6.183360 CCTTGACATTTGCAATATCGTACAGT 60.183 38.462 0.00 0.00 0.00 3.55
1392 1417 1.821332 GCAGCTGGCTAATTCCGCT 60.821 57.895 17.12 0.00 40.25 5.52
1452 1477 1.757118 CGAGTCATCCCAGGCTTTCTA 59.243 52.381 0.00 0.00 0.00 2.10
1461 1486 2.670939 AGATCATCACGAGTCATCCCA 58.329 47.619 0.00 0.00 0.00 4.37
1479 1504 2.352617 GCCCGCATTGATGTTGAAAAGA 60.353 45.455 0.00 0.00 0.00 2.52
1683 1708 0.179097 GGCCCTTCTTCTGAGCTACG 60.179 60.000 0.00 0.00 0.00 3.51
1822 1847 1.201343 GCGTTCTGTATCCTCTTCGC 58.799 55.000 0.00 0.00 36.06 4.70
2057 2082 2.196595 CAGTTATTCCCTCCAGGTCCA 58.803 52.381 0.00 0.00 36.75 4.02
2198 2224 3.053455 CCTTCTCTTCGTATGGAATCGC 58.947 50.000 0.00 0.00 33.26 4.58
2324 2370 2.614057 GCCCTCATGTAAACTGGAATCG 59.386 50.000 0.00 0.00 0.00 3.34
2463 2515 5.716228 TGCCTTGGTAATGATCAAAGATGTT 59.284 36.000 0.00 0.00 0.00 2.71
2489 2541 3.430453 AGTAGAGGCAGATCTAGATGGC 58.570 50.000 10.74 13.21 41.98 4.40
2511 2563 6.712276 TGACACCATACAATATGTTACCACA 58.288 36.000 0.00 0.00 37.31 4.17
2584 2636 2.730069 TGCACGAAAATCTTGCACAAG 58.270 42.857 7.35 3.94 44.96 3.16
2656 2708 8.655092 GCAAGCTGTATGATACTCAGATTTATC 58.345 37.037 4.03 0.00 36.00 1.75
2657 2709 8.152898 TGCAAGCTGTATGATACTCAGATTTAT 58.847 33.333 4.03 0.00 36.00 1.40
2658 2710 7.500141 TGCAAGCTGTATGATACTCAGATTTA 58.500 34.615 4.03 0.00 36.00 1.40
2659 2711 6.351711 TGCAAGCTGTATGATACTCAGATTT 58.648 36.000 4.03 0.00 36.00 2.17
2660 2712 5.922053 TGCAAGCTGTATGATACTCAGATT 58.078 37.500 4.03 0.00 38.13 2.40
2661 2713 5.541953 TGCAAGCTGTATGATACTCAGAT 57.458 39.130 4.03 0.00 0.00 2.90
2662 2714 5.069516 TGATGCAAGCTGTATGATACTCAGA 59.930 40.000 4.03 0.00 0.00 3.27
2663 2715 5.295152 TGATGCAAGCTGTATGATACTCAG 58.705 41.667 4.03 0.00 0.00 3.35
2810 2864 5.510520 GCACAAACAAGACATTTATTCCCCA 60.511 40.000 0.00 0.00 0.00 4.96
2824 2878 5.125900 TGATCCCAGATTATGCACAAACAAG 59.874 40.000 0.00 0.00 0.00 3.16
2835 2893 3.723681 TCAGGGCTTTGATCCCAGATTAT 59.276 43.478 0.48 0.00 46.36 1.28
2857 2915 0.700564 TCCCTGCCTTCTGAAAGCAT 59.299 50.000 13.59 0.00 0.00 3.79
2890 2948 3.739810 AGAACGAGTAAAAAGGCGAGAAC 59.260 43.478 0.00 0.00 0.00 3.01
2896 2954 3.143728 TGGGAAGAACGAGTAAAAAGGC 58.856 45.455 0.00 0.00 0.00 4.35
2905 2963 1.679032 GGGTGGATTGGGAAGAACGAG 60.679 57.143 0.00 0.00 0.00 4.18
2917 2977 5.892348 ACAGAGAAAAACATAGGGTGGATT 58.108 37.500 0.00 0.00 0.00 3.01
2920 2980 7.703058 ATTAACAGAGAAAAACATAGGGTGG 57.297 36.000 0.00 0.00 0.00 4.61
2960 3020 1.009389 GGAGCGAGCATGTATACCGC 61.009 60.000 13.45 13.45 45.39 5.68
2962 3022 0.969894 AGGGAGCGAGCATGTATACC 59.030 55.000 0.00 0.00 0.00 2.73
2982 3042 4.340950 CGGCCCAAATTCTTTATACCATGT 59.659 41.667 0.00 0.00 0.00 3.21
2983 3043 4.340950 ACGGCCCAAATTCTTTATACCATG 59.659 41.667 0.00 0.00 0.00 3.66
2984 3044 4.340950 CACGGCCCAAATTCTTTATACCAT 59.659 41.667 0.00 0.00 0.00 3.55
3011 3073 0.324285 AGAGAACAGCAGGAGCAAGG 59.676 55.000 0.00 0.00 45.49 3.61
3016 3078 2.418471 CCTAGCAAGAGAACAGCAGGAG 60.418 54.545 0.00 0.00 32.16 3.69
3038 3100 2.853077 CCCCTAATCCTTCCAGGTTTCT 59.147 50.000 0.00 0.00 36.53 2.52


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

AutoCloner maintained by Alex Coulton.