Multiple sequence alignment - TraesCS2B01G238400

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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 TraesCS2B01G238400 chr2B 100.000 2869 0 0 1 2869 239648405 239645537 0.000000e+00 5299
1 TraesCS2B01G238400 chr2A 93.902 2050 72 20 165 2185 199033964 199031939 0.000000e+00 3044
2 TraesCS2B01G238400 chr2A 89.985 689 49 8 2185 2869 199031805 199031133 0.000000e+00 872
3 TraesCS2B01G238400 chr2D 89.474 152 8 6 175 324 186621110 186620965 4.880000e-43 185


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 TraesCS2B01G238400 chr2B 239645537 239648405 2868 True 5299 5299 100.0000 1 2869 1 chr2B.!!$R1 2868
1 TraesCS2B01G238400 chr2A 199031133 199033964 2831 True 1958 3044 91.9435 165 2869 2 chr2A.!!$R1 2704

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
67 68 0.107165 GTGGGCATCACTACCTTCCC 60.107 60.0 2.66 0.0 42.86 3.97 F
68 69 0.253160 TGGGCATCACTACCTTCCCT 60.253 55.0 0.00 0.0 34.89 4.20 F
177 178 0.719465 GACGCGTGTAATTCCCAGTG 59.281 55.0 20.70 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1165 1178 1.021390 AATTCAGAACGGGCGAGCAG 61.021 55.000 0.00 0.00 0.00 4.24 R
1331 1351 1.067516 GCAGCTGCTTTGGTTTTCTGA 59.932 47.619 31.33 0.00 38.21 3.27 R
2093 2122 1.033746 AATTCAGGGCATGCGTCAGG 61.034 55.000 12.44 3.63 0.00 3.86 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 4.988065 AGGGATGTGACAACGTCG 57.012 55.556 0.00 0.00 42.38 5.12
19 20 0.528924 TAGGGATGTGACAACGTCGG 59.471 55.000 0.00 0.00 42.38 4.79
20 21 2.388232 GGGATGTGACAACGTCGGC 61.388 63.158 0.00 0.00 42.38 5.54
21 22 1.666553 GGATGTGACAACGTCGGCA 60.667 57.895 0.00 0.00 42.38 5.69
22 23 1.626654 GGATGTGACAACGTCGGCAG 61.627 60.000 0.00 0.00 42.38 4.85
23 24 0.944311 GATGTGACAACGTCGGCAGT 60.944 55.000 0.00 0.00 34.95 4.40
24 25 1.221466 ATGTGACAACGTCGGCAGTG 61.221 55.000 0.00 0.00 34.95 3.66
25 26 2.279851 TGACAACGTCGGCAGTGG 60.280 61.111 0.00 0.00 34.95 4.00
26 27 3.041940 GACAACGTCGGCAGTGGG 61.042 66.667 0.00 0.00 0.00 4.61
28 29 4.988598 CAACGTCGGCAGTGGGCT 62.989 66.667 0.00 0.00 44.01 5.19
37 38 2.046988 CAGTGGGCTGCATCACGA 60.047 61.111 15.91 0.00 38.77 4.35
38 39 2.046892 AGTGGGCTGCATCACGAC 60.047 61.111 15.91 1.29 38.77 4.34
39 40 2.046892 GTGGGCTGCATCACGACT 60.047 61.111 0.50 0.00 0.00 4.18
40 41 1.672356 GTGGGCTGCATCACGACTT 60.672 57.895 0.50 0.00 0.00 3.01
41 42 1.672030 TGGGCTGCATCACGACTTG 60.672 57.895 0.50 0.00 0.00 3.16
42 43 2.401766 GGGCTGCATCACGACTTGG 61.402 63.158 0.50 0.00 0.00 3.61
43 44 2.482374 GCTGCATCACGACTTGGC 59.518 61.111 0.00 0.00 0.00 4.52
44 45 2.780643 CTGCATCACGACTTGGCG 59.219 61.111 0.00 0.00 37.29 5.69
45 46 3.372676 CTGCATCACGACTTGGCGC 62.373 63.158 0.00 0.00 33.86 6.53
46 47 4.505217 GCATCACGACTTGGCGCG 62.505 66.667 0.00 0.00 33.86 6.86
47 48 2.809174 CATCACGACTTGGCGCGA 60.809 61.111 12.10 0.00 33.86 5.87
48 49 2.507102 ATCACGACTTGGCGCGAG 60.507 61.111 12.10 0.00 33.86 5.03
49 50 3.282745 ATCACGACTTGGCGCGAGT 62.283 57.895 12.10 13.98 33.86 4.18
50 51 3.767230 CACGACTTGGCGCGAGTG 61.767 66.667 18.20 7.39 33.86 3.51
66 67 3.478540 GTGGGCATCACTACCTTCC 57.521 57.895 2.66 0.00 42.86 3.46
67 68 0.107165 GTGGGCATCACTACCTTCCC 60.107 60.000 2.66 0.00 42.86 3.97
68 69 0.253160 TGGGCATCACTACCTTCCCT 60.253 55.000 0.00 0.00 34.89 4.20
69 70 0.919710 GGGCATCACTACCTTCCCTT 59.080 55.000 0.00 0.00 0.00 3.95
70 71 1.408822 GGGCATCACTACCTTCCCTTG 60.409 57.143 0.00 0.00 0.00 3.61
71 72 1.282157 GGCATCACTACCTTCCCTTGT 59.718 52.381 0.00 0.00 0.00 3.16
72 73 2.633488 GCATCACTACCTTCCCTTGTC 58.367 52.381 0.00 0.00 0.00 3.18
73 74 2.893637 CATCACTACCTTCCCTTGTCG 58.106 52.381 0.00 0.00 0.00 4.35
74 75 1.263356 TCACTACCTTCCCTTGTCGG 58.737 55.000 0.00 0.00 0.00 4.79
102 103 3.324930 CTGCAGGCACAGGAGGGA 61.325 66.667 5.57 0.00 33.85 4.20
103 104 3.324930 TGCAGGCACAGGAGGGAG 61.325 66.667 0.00 0.00 0.00 4.30
104 105 4.106925 GCAGGCACAGGAGGGAGG 62.107 72.222 0.00 0.00 0.00 4.30
105 106 2.284921 CAGGCACAGGAGGGAGGA 60.285 66.667 0.00 0.00 0.00 3.71
106 107 2.284995 AGGCACAGGAGGGAGGAC 60.285 66.667 0.00 0.00 0.00 3.85
107 108 3.403558 GGCACAGGAGGGAGGACC 61.404 72.222 0.00 0.00 40.67 4.46
108 109 3.775654 GCACAGGAGGGAGGACCG 61.776 72.222 0.00 0.00 46.96 4.79
109 110 3.077556 CACAGGAGGGAGGACCGG 61.078 72.222 0.00 0.00 46.96 5.28
110 111 4.400251 ACAGGAGGGAGGACCGGG 62.400 72.222 6.32 0.00 46.96 5.73
111 112 4.400251 CAGGAGGGAGGACCGGGT 62.400 72.222 6.32 0.00 46.96 5.28
112 113 3.612607 AGGAGGGAGGACCGGGTT 61.613 66.667 6.32 0.00 46.96 4.11
113 114 2.609921 GGAGGGAGGACCGGGTTT 60.610 66.667 6.32 0.00 46.96 3.27
114 115 2.229203 GGAGGGAGGACCGGGTTTT 61.229 63.158 6.32 0.00 46.96 2.43
115 116 1.765727 GAGGGAGGACCGGGTTTTT 59.234 57.895 6.32 0.00 46.96 1.94
138 139 7.625498 TTTTCCCAGGAAATTATTGGAAACT 57.375 32.000 12.50 0.00 42.71 2.66
139 140 8.728596 TTTTCCCAGGAAATTATTGGAAACTA 57.271 30.769 12.50 0.00 42.71 2.24
140 141 7.954666 TTCCCAGGAAATTATTGGAAACTAG 57.045 36.000 0.00 0.00 33.76 2.57
141 142 6.431722 TCCCAGGAAATTATTGGAAACTAGG 58.568 40.000 0.00 0.00 33.76 3.02
142 143 6.218730 TCCCAGGAAATTATTGGAAACTAGGA 59.781 38.462 0.00 0.00 33.76 2.94
143 144 6.895204 CCCAGGAAATTATTGGAAACTAGGAA 59.105 38.462 0.00 0.00 33.76 3.36
144 145 7.565029 CCCAGGAAATTATTGGAAACTAGGAAT 59.435 37.037 0.00 0.00 33.76 3.01
145 146 8.981659 CCAGGAAATTATTGGAAACTAGGAATT 58.018 33.333 0.00 0.00 33.76 2.17
146 147 9.807649 CAGGAAATTATTGGAAACTAGGAATTG 57.192 33.333 0.00 0.00 0.00 2.32
147 148 8.981659 AGGAAATTATTGGAAACTAGGAATTGG 58.018 33.333 0.00 0.00 0.00 3.16
148 149 8.977412 GGAAATTATTGGAAACTAGGAATTGGA 58.023 33.333 0.00 0.00 0.00 3.53
150 151 9.547279 AAATTATTGGAAACTAGGAATTGGAGT 57.453 29.630 0.00 0.00 0.00 3.85
151 152 9.547279 AATTATTGGAAACTAGGAATTGGAGTT 57.453 29.630 0.00 0.00 0.00 3.01
152 153 6.840780 ATTGGAAACTAGGAATTGGAGTTG 57.159 37.500 0.00 0.00 0.00 3.16
153 154 5.576563 TGGAAACTAGGAATTGGAGTTGA 57.423 39.130 0.00 0.00 0.00 3.18
154 155 5.560724 TGGAAACTAGGAATTGGAGTTGAG 58.439 41.667 0.00 0.00 0.00 3.02
155 156 5.073144 TGGAAACTAGGAATTGGAGTTGAGT 59.927 40.000 0.00 0.00 0.00 3.41
156 157 6.004574 GGAAACTAGGAATTGGAGTTGAGTT 58.995 40.000 0.00 0.00 0.00 3.01
157 158 7.166167 GGAAACTAGGAATTGGAGTTGAGTTA 58.834 38.462 0.00 0.00 0.00 2.24
158 159 7.334671 GGAAACTAGGAATTGGAGTTGAGTTAG 59.665 40.741 0.00 0.00 0.00 2.34
159 160 7.554959 AACTAGGAATTGGAGTTGAGTTAGA 57.445 36.000 0.00 0.00 0.00 2.10
160 161 6.937392 ACTAGGAATTGGAGTTGAGTTAGAC 58.063 40.000 0.00 0.00 0.00 2.59
161 162 4.822026 AGGAATTGGAGTTGAGTTAGACG 58.178 43.478 0.00 0.00 0.00 4.18
162 163 3.371285 GGAATTGGAGTTGAGTTAGACGC 59.629 47.826 0.00 0.00 0.00 5.19
163 164 2.060326 TTGGAGTTGAGTTAGACGCG 57.940 50.000 3.53 3.53 0.00 6.01
164 165 0.956633 TGGAGTTGAGTTAGACGCGT 59.043 50.000 13.85 13.85 0.00 6.01
165 166 1.335597 TGGAGTTGAGTTAGACGCGTG 60.336 52.381 20.70 0.00 0.00 5.34
166 167 1.335689 GGAGTTGAGTTAGACGCGTGT 60.336 52.381 20.70 17.60 0.00 4.49
167 168 2.095567 GGAGTTGAGTTAGACGCGTGTA 60.096 50.000 20.70 16.16 0.00 2.90
168 169 3.558505 GAGTTGAGTTAGACGCGTGTAA 58.441 45.455 23.22 23.22 0.00 2.41
169 170 4.164294 GAGTTGAGTTAGACGCGTGTAAT 58.836 43.478 28.39 18.19 0.00 1.89
170 171 4.553323 AGTTGAGTTAGACGCGTGTAATT 58.447 39.130 28.39 24.85 0.00 1.40
171 172 4.620184 AGTTGAGTTAGACGCGTGTAATTC 59.380 41.667 31.52 31.52 0.00 2.17
172 173 3.504863 TGAGTTAGACGCGTGTAATTCC 58.495 45.455 33.36 23.73 28.44 3.01
173 174 2.856557 GAGTTAGACGCGTGTAATTCCC 59.143 50.000 29.51 18.83 0.00 3.97
174 175 2.231964 AGTTAGACGCGTGTAATTCCCA 59.768 45.455 28.39 5.65 0.00 4.37
177 178 0.719465 GACGCGTGTAATTCCCAGTG 59.281 55.000 20.70 0.00 0.00 3.66
181 182 1.670811 GCGTGTAATTCCCAGTGATGG 59.329 52.381 0.00 0.00 0.00 3.51
206 207 4.665833 TTCGGGATGTGGTATTAGAGTG 57.334 45.455 0.00 0.00 0.00 3.51
249 250 7.107639 TCTGTGAGAATTATAATCGACCACA 57.892 36.000 15.66 15.66 0.00 4.17
303 306 5.433051 ACCCTGGAATCCTGAGAATTGAATA 59.567 40.000 7.81 0.00 0.00 1.75
445 451 1.090052 GGCGGAACATGCTGTCCTAC 61.090 60.000 8.57 2.09 0.00 3.18
559 565 3.270839 GCTCGATGCTGGCTGCTC 61.271 66.667 17.45 10.91 43.37 4.26
659 665 2.378038 TCAAGAAGCCAAACAGCAACT 58.622 42.857 0.00 0.00 34.23 3.16
663 669 2.050077 GCCAAACAGCAACTCCGC 60.050 61.111 0.00 0.00 0.00 5.54
713 719 2.164338 TGCTGCAGATCTCATTTTGCA 58.836 42.857 20.43 0.46 43.62 4.08
714 720 2.758423 TGCTGCAGATCTCATTTTGCAT 59.242 40.909 20.43 0.00 44.61 3.96
715 721 3.116300 GCTGCAGATCTCATTTTGCATG 58.884 45.455 20.43 0.00 44.61 4.06
716 722 3.428999 GCTGCAGATCTCATTTTGCATGT 60.429 43.478 20.43 0.00 44.61 3.21
717 723 4.744570 CTGCAGATCTCATTTTGCATGTT 58.255 39.130 8.42 0.00 44.61 2.71
718 724 4.490743 TGCAGATCTCATTTTGCATGTTG 58.509 39.130 1.25 0.00 41.23 3.33
719 725 3.306166 GCAGATCTCATTTTGCATGTTGC 59.694 43.478 0.00 0.00 45.29 4.17
754 760 2.762887 TGCCACAAAATCAGTCCAACAA 59.237 40.909 0.00 0.00 0.00 2.83
788 794 4.701956 ATGTTGAAGAAAGGCGTAATGG 57.298 40.909 0.00 0.00 0.00 3.16
791 797 3.644966 TGAAGAAAGGCGTAATGGGAT 57.355 42.857 0.00 0.00 0.00 3.85
801 807 3.058224 GGCGTAATGGGATAGTGATTTGC 60.058 47.826 0.00 0.00 0.00 3.68
810 816 3.433615 GGATAGTGATTTGCGACCTATGC 59.566 47.826 0.00 0.00 0.00 3.14
817 823 5.180117 GTGATTTGCGACCTATGCTTATCAT 59.820 40.000 0.00 0.00 36.24 2.45
820 826 6.449635 TTTGCGACCTATGCTTATCATTTT 57.550 33.333 0.00 0.00 36.63 1.82
821 827 5.422666 TGCGACCTATGCTTATCATTTTG 57.577 39.130 0.00 0.00 36.63 2.44
822 828 4.881273 TGCGACCTATGCTTATCATTTTGT 59.119 37.500 0.00 0.00 36.63 2.83
998 1004 0.915364 AAATGGACCAGGCTCTCCTC 59.085 55.000 0.00 0.00 41.93 3.71
1080 1093 2.342354 GCATACTGTGAAAAATGTGCGC 59.658 45.455 0.00 0.00 0.00 6.09
1165 1178 1.167851 TTGCAGTACCATCAGCAAGC 58.832 50.000 0.00 0.00 41.55 4.01
1182 1195 2.048222 CTGCTCGCCCGTTCTGAA 60.048 61.111 0.00 0.00 0.00 3.02
1201 1214 3.699038 TGAATTTGGATGGGATCGAAACC 59.301 43.478 0.00 0.00 39.28 3.27
1222 1235 5.003160 ACCAGAAAATGATCGTGATTCACA 58.997 37.500 16.61 4.75 33.40 3.58
1241 1254 4.773674 TCACAATGAGGATGCTTGGAAAAT 59.226 37.500 0.00 0.00 0.00 1.82
1261 1274 3.924114 TGTACATTCAGGTGGGGTATG 57.076 47.619 0.00 0.00 0.00 2.39
1262 1275 3.455849 TGTACATTCAGGTGGGGTATGA 58.544 45.455 0.00 0.00 0.00 2.15
1273 1286 3.129813 GGTGGGGTATGAAAATTCGTTCC 59.870 47.826 3.21 3.21 34.12 3.62
1306 1322 4.857509 ACTGGGATACGATTCTAGCTTC 57.142 45.455 0.00 0.00 37.60 3.86
1309 1329 4.215908 TGGGATACGATTCTAGCTTCTGT 58.784 43.478 0.00 0.00 37.60 3.41
1317 1337 5.578727 ACGATTCTAGCTTCTGTTTCACATC 59.421 40.000 0.00 0.00 0.00 3.06
1339 1359 7.926018 ACATCTGGTGGTTATTTTTCAGAAAAC 59.074 33.333 7.89 0.00 37.56 2.43
1443 1463 0.108472 CGAAGATGAGAGTGCAGGCA 60.108 55.000 0.00 0.00 0.00 4.75
1481 1501 3.190878 GCATTGAAGGGTGCCGAG 58.809 61.111 0.00 0.00 35.35 4.63
1583 1603 1.620819 CAACCCACTCTACAGAGCACT 59.379 52.381 6.15 0.00 45.79 4.40
1607 1627 3.306433 GGAGGAAGAGGTTCAGAACAGAC 60.306 52.174 15.36 5.70 33.93 3.51
1651 1671 8.906867 GTCTGGGAATATCAAGAATTCATTTCA 58.093 33.333 8.44 1.54 36.75 2.69
1703 1723 2.421952 GGAACCAGCTAATGCATCTCCA 60.422 50.000 0.00 0.00 42.74 3.86
1772 1792 1.694133 ATCTGCTGAGGGCCTACTGC 61.694 60.000 5.73 15.90 40.92 4.40
1820 1840 0.482446 AATCCCTTGTGGCACTTCCA 59.518 50.000 19.83 0.00 44.18 3.53
1875 1895 5.945144 AATTGGCAGGAATTGAAGCTTAT 57.055 34.783 0.00 0.00 0.00 1.73
1876 1896 4.724074 TTGGCAGGAATTGAAGCTTATG 57.276 40.909 0.00 0.00 0.00 1.90
1884 1907 6.015688 CAGGAATTGAAGCTTATGTATGGCAT 60.016 38.462 4.88 4.88 41.42 4.40
1893 1916 9.994432 GAAGCTTATGTATGGCATATTTATCAC 57.006 33.333 10.92 0.00 39.56 3.06
1929 1952 9.515226 AGTATCAAACTATTAGCTTTGTCCAAA 57.485 29.630 0.00 0.00 36.36 3.28
2020 2049 4.403752 GGATTCTGCCAAGCTTCCTAATTT 59.596 41.667 0.00 0.00 0.00 1.82
2021 2050 5.105187 GGATTCTGCCAAGCTTCCTAATTTT 60.105 40.000 0.00 0.00 0.00 1.82
2022 2051 5.391312 TTCTGCCAAGCTTCCTAATTTTC 57.609 39.130 0.00 0.00 0.00 2.29
2023 2052 4.406456 TCTGCCAAGCTTCCTAATTTTCA 58.594 39.130 0.00 0.00 0.00 2.69
2024 2053 4.460382 TCTGCCAAGCTTCCTAATTTTCAG 59.540 41.667 0.00 0.00 0.00 3.02
2030 2059 6.071728 CCAAGCTTCCTAATTTTCAGTGTCAT 60.072 38.462 0.00 0.00 0.00 3.06
2032 2061 6.917533 AGCTTCCTAATTTTCAGTGTCATTG 58.082 36.000 0.00 0.00 0.00 2.82
2047 2076 7.174772 TCAGTGTCATTGCTGTATGTAACATTT 59.825 33.333 0.00 0.00 37.50 2.32
2051 2080 8.022550 TGTCATTGCTGTATGTAACATTTTCAG 58.977 33.333 0.00 0.00 37.50 3.02
2060 2089 9.080283 TGTATGTAACATTTTCAGCACCAAGCA 62.080 37.037 0.00 0.00 38.47 3.91
2119 2148 1.684983 GCATGCCCTGAATTGCATAGT 59.315 47.619 6.36 0.00 45.98 2.12
2224 2387 5.754406 CACACTGAAATTTGCATCCTTTCAA 59.246 36.000 15.42 0.00 38.15 2.69
2328 2491 1.667724 CACAATTCATCTCTCGGCACC 59.332 52.381 0.00 0.00 0.00 5.01
2358 2521 3.695830 TCGGAGTTATGGGCCAATATC 57.304 47.619 11.89 6.58 0.00 1.63
2359 2522 2.976185 TCGGAGTTATGGGCCAATATCA 59.024 45.455 11.89 0.00 0.00 2.15
2360 2523 3.392947 TCGGAGTTATGGGCCAATATCAA 59.607 43.478 11.89 0.00 0.00 2.57
2364 2527 5.106157 GGAGTTATGGGCCAATATCAATTCG 60.106 44.000 11.89 0.00 0.00 3.34
2366 2529 5.707298 AGTTATGGGCCAATATCAATTCGAG 59.293 40.000 11.89 0.00 0.00 4.04
2395 2558 5.825532 TCAATATGAATGTTTGAGGTCCCA 58.174 37.500 0.00 0.00 0.00 4.37
2396 2559 6.252233 TCAATATGAATGTTTGAGGTCCCAA 58.748 36.000 0.00 0.00 0.00 4.12
2397 2560 6.377996 TCAATATGAATGTTTGAGGTCCCAAG 59.622 38.462 0.00 0.00 0.00 3.61
2398 2561 3.593442 TGAATGTTTGAGGTCCCAAGT 57.407 42.857 0.00 0.00 0.00 3.16
2399 2562 3.486383 TGAATGTTTGAGGTCCCAAGTC 58.514 45.455 0.00 0.00 0.00 3.01
2400 2563 2.586648 ATGTTTGAGGTCCCAAGTCC 57.413 50.000 0.00 0.00 0.00 3.85
2401 2564 0.476771 TGTTTGAGGTCCCAAGTCCC 59.523 55.000 0.00 0.00 0.00 4.46
2402 2565 0.476771 GTTTGAGGTCCCAAGTCCCA 59.523 55.000 0.00 0.00 0.00 4.37
2415 2578 4.459337 CCCAAGTCCCAACAGAGATTTTAC 59.541 45.833 0.00 0.00 0.00 2.01
2420 2583 6.708285 AGTCCCAACAGAGATTTTACGTATT 58.292 36.000 0.00 0.00 0.00 1.89
2426 2589 7.807907 CCAACAGAGATTTTACGTATTTGCTTT 59.192 33.333 0.00 0.00 0.00 3.51
2480 2643 6.158695 TCCTTTTGATACATAGCCTTCCTTCT 59.841 38.462 0.00 0.00 0.00 2.85
2490 2653 0.471617 CCTTCCTTCTGGCGGATGAT 59.528 55.000 10.58 0.00 0.00 2.45
2491 2654 1.590932 CTTCCTTCTGGCGGATGATG 58.409 55.000 10.58 3.43 0.00 3.07
2517 2680 3.399330 TGTGCCTTTCTTCTCCTAAACG 58.601 45.455 0.00 0.00 0.00 3.60
2518 2681 3.070446 TGTGCCTTTCTTCTCCTAAACGA 59.930 43.478 0.00 0.00 0.00 3.85
2519 2682 4.254492 GTGCCTTTCTTCTCCTAAACGAT 58.746 43.478 0.00 0.00 0.00 3.73
2520 2683 4.695928 GTGCCTTTCTTCTCCTAAACGATT 59.304 41.667 0.00 0.00 0.00 3.34
2521 2684 4.695455 TGCCTTTCTTCTCCTAAACGATTG 59.305 41.667 0.00 0.00 0.00 2.67
2527 2690 9.151471 CTTTCTTCTCCTAAACGATTGATTACA 57.849 33.333 0.00 0.00 0.00 2.41
2546 2709 9.612066 TGATTACAAAGACAACTGCATATATCA 57.388 29.630 0.00 0.00 0.00 2.15
2579 2745 2.665165 AGAGTCTATCTGTCAGGCAGG 58.335 52.381 1.12 0.00 45.08 4.85
2613 2779 8.879759 TCACCTGAAGAAAATATTACAATCGAC 58.120 33.333 0.00 0.00 0.00 4.20
2627 2793 2.907910 ATCGACATGTCAGCAAAAGC 57.092 45.000 24.93 0.00 0.00 3.51
2677 2843 2.432206 ACAACATAAGGCAAAACGGC 57.568 45.000 0.00 0.00 41.61 5.68
2684 2850 0.179062 AAGGCAAAACGGCAAATGCA 60.179 45.000 7.80 0.00 44.47 3.96
2691 2857 3.951775 AAACGGCAAATGCAGGAATTA 57.048 38.095 10.19 0.00 44.36 1.40
2727 2893 5.647658 TCCATTGCGAGTTTAACAAGATCAT 59.352 36.000 0.00 0.00 0.00 2.45
2728 2894 6.150976 TCCATTGCGAGTTTAACAAGATCATT 59.849 34.615 0.00 0.00 0.00 2.57
2730 2896 7.967854 CCATTGCGAGTTTAACAAGATCATTAA 59.032 33.333 0.00 0.00 0.00 1.40
2734 2900 8.946085 TGCGAGTTTAACAAGATCATTAAAGAT 58.054 29.630 0.00 0.00 32.39 2.40
2735 2901 9.214953 GCGAGTTTAACAAGATCATTAAAGATG 57.785 33.333 0.00 0.00 32.39 2.90
2750 2916 4.778534 AAAGATGTTGTGCTTCCATCAG 57.221 40.909 0.00 0.00 37.93 2.90
2759 2925 5.675684 TGTGCTTCCATCAGTGATTAGTA 57.324 39.130 1.86 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.292223 CCGACGTTGTCACATCCCT 59.708 57.895 1.30 0.00 32.09 4.20
2 3 2.388232 GCCGACGTTGTCACATCCC 61.388 63.158 1.30 0.00 32.09 3.85
3 4 1.626654 CTGCCGACGTTGTCACATCC 61.627 60.000 1.30 0.00 32.09 3.51
4 5 0.944311 ACTGCCGACGTTGTCACATC 60.944 55.000 1.30 0.00 32.09 3.06
5 6 1.069090 ACTGCCGACGTTGTCACAT 59.931 52.632 1.30 0.00 32.09 3.21
7 8 2.594962 CCACTGCCGACGTTGTCAC 61.595 63.158 1.30 0.00 32.09 3.67
8 9 2.279851 CCACTGCCGACGTTGTCA 60.280 61.111 1.30 0.00 32.09 3.58
9 10 3.041940 CCCACTGCCGACGTTGTC 61.042 66.667 1.30 0.00 0.00 3.18
11 12 4.988598 AGCCCACTGCCGACGTTG 62.989 66.667 0.00 0.00 42.71 4.10
12 13 4.988598 CAGCCCACTGCCGACGTT 62.989 66.667 0.00 0.00 42.71 3.99
21 22 2.046892 GTCGTGATGCAGCCCACT 60.047 61.111 0.00 0.00 0.00 4.00
22 23 1.672356 AAGTCGTGATGCAGCCCAC 60.672 57.895 0.00 2.97 0.00 4.61
23 24 1.672030 CAAGTCGTGATGCAGCCCA 60.672 57.895 0.00 0.00 0.00 5.36
24 25 2.401766 CCAAGTCGTGATGCAGCCC 61.402 63.158 0.00 0.00 0.00 5.19
25 26 3.044059 GCCAAGTCGTGATGCAGCC 62.044 63.158 0.00 0.00 0.00 4.85
26 27 2.482374 GCCAAGTCGTGATGCAGC 59.518 61.111 0.00 0.00 0.00 5.25
27 28 2.780643 CGCCAAGTCGTGATGCAG 59.219 61.111 0.00 0.00 0.00 4.41
28 29 3.422303 GCGCCAAGTCGTGATGCA 61.422 61.111 0.00 0.00 0.00 3.96
29 30 4.505217 CGCGCCAAGTCGTGATGC 62.505 66.667 0.00 0.00 41.99 3.91
30 31 2.792290 CTCGCGCCAAGTCGTGATG 61.792 63.158 0.00 0.00 46.06 3.07
31 32 2.507102 CTCGCGCCAAGTCGTGAT 60.507 61.111 0.00 0.00 46.06 3.06
32 33 3.973516 ACTCGCGCCAAGTCGTGA 61.974 61.111 0.00 0.00 45.25 4.35
33 34 3.767230 CACTCGCGCCAAGTCGTG 61.767 66.667 0.00 0.00 40.91 4.35
48 49 0.107165 GGGAAGGTAGTGATGCCCAC 60.107 60.000 0.00 0.00 46.03 4.61
49 50 0.253160 AGGGAAGGTAGTGATGCCCA 60.253 55.000 0.00 0.00 38.04 5.36
50 51 0.919710 AAGGGAAGGTAGTGATGCCC 59.080 55.000 0.00 0.00 35.79 5.36
51 52 1.282157 ACAAGGGAAGGTAGTGATGCC 59.718 52.381 0.00 0.00 0.00 4.40
52 53 2.633488 GACAAGGGAAGGTAGTGATGC 58.367 52.381 0.00 0.00 0.00 3.91
53 54 2.418746 CCGACAAGGGAAGGTAGTGATG 60.419 54.545 0.00 0.00 35.97 3.07
54 55 1.831736 CCGACAAGGGAAGGTAGTGAT 59.168 52.381 0.00 0.00 35.97 3.06
55 56 1.263356 CCGACAAGGGAAGGTAGTGA 58.737 55.000 0.00 0.00 35.97 3.41
56 57 3.834732 CCGACAAGGGAAGGTAGTG 57.165 57.895 0.00 0.00 35.97 2.74
66 67 4.157120 CCTACGGCCCCGACAAGG 62.157 72.222 14.44 12.39 42.83 3.61
67 68 4.157120 CCCTACGGCCCCGACAAG 62.157 72.222 14.44 7.49 42.83 3.16
78 79 4.393155 TGTGCCTGCAGCCCTACG 62.393 66.667 8.66 0.00 42.71 3.51
79 80 2.437359 CTGTGCCTGCAGCCCTAC 60.437 66.667 8.66 4.63 42.71 3.18
80 81 3.720601 CCTGTGCCTGCAGCCCTA 61.721 66.667 8.66 0.00 42.71 3.53
85 86 3.324930 TCCCTCCTGTGCCTGCAG 61.325 66.667 6.78 6.78 36.31 4.41
86 87 3.324930 CTCCCTCCTGTGCCTGCA 61.325 66.667 0.00 0.00 0.00 4.41
87 88 4.106925 CCTCCCTCCTGTGCCTGC 62.107 72.222 0.00 0.00 0.00 4.85
88 89 2.284921 TCCTCCCTCCTGTGCCTG 60.285 66.667 0.00 0.00 0.00 4.85
89 90 2.284995 GTCCTCCCTCCTGTGCCT 60.285 66.667 0.00 0.00 0.00 4.75
90 91 3.403558 GGTCCTCCCTCCTGTGCC 61.404 72.222 0.00 0.00 0.00 5.01
91 92 3.775654 CGGTCCTCCCTCCTGTGC 61.776 72.222 0.00 0.00 0.00 4.57
92 93 3.077556 CCGGTCCTCCCTCCTGTG 61.078 72.222 0.00 0.00 0.00 3.66
93 94 4.400251 CCCGGTCCTCCCTCCTGT 62.400 72.222 0.00 0.00 0.00 4.00
94 95 3.925914 AACCCGGTCCTCCCTCCTG 62.926 68.421 0.00 0.00 0.00 3.86
95 96 2.708030 AAAACCCGGTCCTCCCTCCT 62.708 60.000 0.00 0.00 0.00 3.69
96 97 1.786407 AAAAACCCGGTCCTCCCTCC 61.786 60.000 0.00 0.00 0.00 4.30
97 98 1.765727 AAAAACCCGGTCCTCCCTC 59.234 57.895 0.00 0.00 0.00 4.30
98 99 4.013313 AAAAACCCGGTCCTCCCT 57.987 55.556 0.00 0.00 0.00 4.20
113 114 8.040002 AGTTTCCAATAATTTCCTGGGAAAAA 57.960 30.769 17.21 10.03 45.60 1.94
114 115 7.625498 AGTTTCCAATAATTTCCTGGGAAAA 57.375 32.000 17.21 4.25 45.60 2.29
115 116 7.398904 CCTAGTTTCCAATAATTTCCTGGGAAA 59.601 37.037 15.88 15.88 46.37 3.13
116 117 6.895204 CCTAGTTTCCAATAATTTCCTGGGAA 59.105 38.462 0.00 0.00 32.91 3.97
117 118 6.218730 TCCTAGTTTCCAATAATTTCCTGGGA 59.781 38.462 0.00 0.00 0.00 4.37
118 119 6.431722 TCCTAGTTTCCAATAATTTCCTGGG 58.568 40.000 0.00 0.00 0.00 4.45
119 120 7.954666 TTCCTAGTTTCCAATAATTTCCTGG 57.045 36.000 0.00 0.00 0.00 4.45
120 121 9.807649 CAATTCCTAGTTTCCAATAATTTCCTG 57.192 33.333 0.00 0.00 0.00 3.86
121 122 8.981659 CCAATTCCTAGTTTCCAATAATTTCCT 58.018 33.333 0.00 0.00 0.00 3.36
122 123 8.977412 TCCAATTCCTAGTTTCCAATAATTTCC 58.023 33.333 0.00 0.00 0.00 3.13
124 125 9.547279 ACTCCAATTCCTAGTTTCCAATAATTT 57.453 29.630 0.00 0.00 0.00 1.82
125 126 9.547279 AACTCCAATTCCTAGTTTCCAATAATT 57.453 29.630 0.00 0.00 29.25 1.40
126 127 8.971073 CAACTCCAATTCCTAGTTTCCAATAAT 58.029 33.333 0.00 0.00 31.21 1.28
127 128 8.167392 TCAACTCCAATTCCTAGTTTCCAATAA 58.833 33.333 0.00 0.00 31.21 1.40
128 129 7.695055 TCAACTCCAATTCCTAGTTTCCAATA 58.305 34.615 0.00 0.00 31.21 1.90
129 130 6.552008 TCAACTCCAATTCCTAGTTTCCAAT 58.448 36.000 0.00 0.00 31.21 3.16
130 131 5.947663 TCAACTCCAATTCCTAGTTTCCAA 58.052 37.500 0.00 0.00 31.21 3.53
131 132 5.073144 ACTCAACTCCAATTCCTAGTTTCCA 59.927 40.000 0.00 0.00 31.21 3.53
132 133 5.561679 ACTCAACTCCAATTCCTAGTTTCC 58.438 41.667 0.00 0.00 31.21 3.13
133 134 8.095169 TCTAACTCAACTCCAATTCCTAGTTTC 58.905 37.037 0.00 0.00 31.21 2.78
134 135 7.878644 GTCTAACTCAACTCCAATTCCTAGTTT 59.121 37.037 0.00 0.00 31.21 2.66
135 136 7.387643 GTCTAACTCAACTCCAATTCCTAGTT 58.612 38.462 0.00 0.00 33.82 2.24
136 137 6.350277 CGTCTAACTCAACTCCAATTCCTAGT 60.350 42.308 0.00 0.00 0.00 2.57
137 138 6.037098 CGTCTAACTCAACTCCAATTCCTAG 58.963 44.000 0.00 0.00 0.00 3.02
138 139 5.623824 GCGTCTAACTCAACTCCAATTCCTA 60.624 44.000 0.00 0.00 0.00 2.94
139 140 4.822026 CGTCTAACTCAACTCCAATTCCT 58.178 43.478 0.00 0.00 0.00 3.36
140 141 3.371285 GCGTCTAACTCAACTCCAATTCC 59.629 47.826 0.00 0.00 0.00 3.01
141 142 3.060895 CGCGTCTAACTCAACTCCAATTC 59.939 47.826 0.00 0.00 0.00 2.17
142 143 2.993899 CGCGTCTAACTCAACTCCAATT 59.006 45.455 0.00 0.00 0.00 2.32
143 144 2.029290 ACGCGTCTAACTCAACTCCAAT 60.029 45.455 5.58 0.00 0.00 3.16
144 145 1.338973 ACGCGTCTAACTCAACTCCAA 59.661 47.619 5.58 0.00 0.00 3.53
145 146 0.956633 ACGCGTCTAACTCAACTCCA 59.043 50.000 5.58 0.00 0.00 3.86
146 147 1.335689 ACACGCGTCTAACTCAACTCC 60.336 52.381 9.86 0.00 0.00 3.85
147 148 2.047679 ACACGCGTCTAACTCAACTC 57.952 50.000 9.86 0.00 0.00 3.01
148 149 3.631145 TTACACGCGTCTAACTCAACT 57.369 42.857 9.86 0.00 0.00 3.16
149 150 4.201561 GGAATTACACGCGTCTAACTCAAC 60.202 45.833 9.86 0.00 0.00 3.18
150 151 3.922240 GGAATTACACGCGTCTAACTCAA 59.078 43.478 9.86 0.00 0.00 3.02
151 152 3.504863 GGAATTACACGCGTCTAACTCA 58.495 45.455 9.86 0.00 0.00 3.41
152 153 2.856557 GGGAATTACACGCGTCTAACTC 59.143 50.000 9.86 8.14 0.00 3.01
153 154 2.231964 TGGGAATTACACGCGTCTAACT 59.768 45.455 9.86 0.00 0.00 2.24
154 155 2.601763 CTGGGAATTACACGCGTCTAAC 59.398 50.000 9.86 0.00 0.00 2.34
155 156 2.231964 ACTGGGAATTACACGCGTCTAA 59.768 45.455 9.86 9.59 0.00 2.10
156 157 1.820519 ACTGGGAATTACACGCGTCTA 59.179 47.619 9.86 0.00 0.00 2.59
157 158 0.606604 ACTGGGAATTACACGCGTCT 59.393 50.000 9.86 0.00 0.00 4.18
158 159 0.719465 CACTGGGAATTACACGCGTC 59.281 55.000 9.86 0.00 0.00 5.19
159 160 0.319083 TCACTGGGAATTACACGCGT 59.681 50.000 5.58 5.58 0.00 6.01
160 161 1.327460 CATCACTGGGAATTACACGCG 59.673 52.381 3.53 3.53 0.00 6.01
161 162 1.670811 CCATCACTGGGAATTACACGC 59.329 52.381 0.00 0.00 39.04 5.34
162 163 1.670811 GCCATCACTGGGAATTACACG 59.329 52.381 0.00 0.00 43.36 4.49
163 164 2.722094 TGCCATCACTGGGAATTACAC 58.278 47.619 0.00 0.00 40.37 2.90
171 172 1.386525 CCCGAAATGCCATCACTGGG 61.387 60.000 0.00 0.00 43.36 4.45
172 173 0.394216 TCCCGAAATGCCATCACTGG 60.394 55.000 0.00 0.00 46.17 4.00
173 174 1.335810 CATCCCGAAATGCCATCACTG 59.664 52.381 0.00 0.00 0.00 3.66
174 175 1.064463 ACATCCCGAAATGCCATCACT 60.064 47.619 0.00 0.00 0.00 3.41
177 178 0.670162 CCACATCCCGAAATGCCATC 59.330 55.000 0.00 0.00 0.00 3.51
181 182 4.385825 TCTAATACCACATCCCGAAATGC 58.614 43.478 0.00 0.00 0.00 3.56
249 250 9.274206 GGCTCGGAATTATCTAGTTTCTTTTAT 57.726 33.333 0.00 0.00 0.00 1.40
255 256 4.957296 TGGGCTCGGAATTATCTAGTTTC 58.043 43.478 0.00 0.00 0.00 2.78
303 306 1.356398 AGAGACGGAGAAAGAGGAGGT 59.644 52.381 0.00 0.00 0.00 3.85
402 408 1.984026 CATGGTTTGGAGGGTGGCC 60.984 63.158 0.00 0.00 0.00 5.36
433 439 1.139058 GGGTACAGGTAGGACAGCATG 59.861 57.143 0.00 0.00 46.00 4.06
434 440 1.497161 GGGTACAGGTAGGACAGCAT 58.503 55.000 0.00 0.00 0.00 3.79
445 451 2.762875 GGAGGGTCGGGGTACAGG 60.763 72.222 0.00 0.00 0.00 4.00
559 565 3.403038 AGAAATTCAACACCGGAGACAG 58.597 45.455 9.46 0.00 0.00 3.51
622 628 0.392461 TGATTTGTCCCTAGTGGCGC 60.392 55.000 0.00 0.00 0.00 6.53
663 669 0.803768 CTGATGACTCACGCCTTCCG 60.804 60.000 0.00 0.00 44.21 4.30
670 676 2.360483 AGAGCATACCTGATGACTCACG 59.640 50.000 9.85 0.00 39.35 4.35
672 678 4.021632 GCATAGAGCATACCTGATGACTCA 60.022 45.833 9.85 0.00 44.79 3.41
734 740 3.451141 TTGTTGGACTGATTTTGTGGC 57.549 42.857 0.00 0.00 0.00 5.01
735 741 3.742369 GCATTGTTGGACTGATTTTGTGG 59.258 43.478 0.00 0.00 0.00 4.17
754 760 5.988310 TCTTCAACATTGAATCTTGGCAT 57.012 34.783 7.48 0.00 45.26 4.40
780 786 3.363970 CGCAAATCACTATCCCATTACGC 60.364 47.826 0.00 0.00 0.00 4.42
788 794 3.433615 GCATAGGTCGCAAATCACTATCC 59.566 47.826 0.00 0.00 0.00 2.59
791 797 3.819564 AGCATAGGTCGCAAATCACTA 57.180 42.857 0.00 0.00 0.00 2.74
801 807 8.687824 AAAAACAAAATGATAAGCATAGGTCG 57.312 30.769 0.00 0.00 35.78 4.79
821 827 9.561270 GCTTTGGATACTCTTAAGATGAAAAAC 57.439 33.333 5.44 0.00 37.61 2.43
822 828 9.520515 AGCTTTGGATACTCTTAAGATGAAAAA 57.479 29.630 5.44 2.58 37.61 1.94
833 839 6.500589 TGGCTATAAGCTTTGGATACTCTT 57.499 37.500 3.20 0.00 41.99 2.85
836 842 7.017056 AGAGATTGGCTATAAGCTTTGGATACT 59.983 37.037 3.20 0.00 41.99 2.12
837 843 7.118971 CAGAGATTGGCTATAAGCTTTGGATAC 59.881 40.741 3.20 0.00 41.99 2.24
839 845 6.002704 CAGAGATTGGCTATAAGCTTTGGAT 58.997 40.000 3.20 0.00 41.99 3.41
998 1004 2.986842 GATGCTCGACAAGAACATCG 57.013 50.000 0.00 0.00 41.05 3.84
1080 1093 2.084610 TCTCCACATTGCACTTCTCG 57.915 50.000 0.00 0.00 0.00 4.04
1104 1117 1.517257 CGACAGCACGTGATCCCTC 60.517 63.158 22.23 6.16 0.00 4.30
1165 1178 1.021390 AATTCAGAACGGGCGAGCAG 61.021 55.000 0.00 0.00 0.00 4.24
1182 1195 3.053693 TCTGGTTTCGATCCCATCCAAAT 60.054 43.478 4.22 0.00 0.00 2.32
1201 1214 7.245604 TCATTGTGAATCACGATCATTTTCTG 58.754 34.615 12.93 2.19 36.44 3.02
1222 1235 5.716228 TGTACATTTTCCAAGCATCCTCATT 59.284 36.000 0.00 0.00 0.00 2.57
1241 1254 3.455849 TCATACCCCACCTGAATGTACA 58.544 45.455 0.00 0.00 0.00 2.90
1262 1275 9.893305 CAGTAAGAAACAATAGGAACGAATTTT 57.107 29.630 0.00 0.00 0.00 1.82
1273 1286 8.888579 AATCGTATCCCAGTAAGAAACAATAG 57.111 34.615 0.00 0.00 0.00 1.73
1317 1337 6.578023 TGGTTTTCTGAAAAATAACCACCAG 58.422 36.000 16.47 0.00 36.77 4.00
1323 1343 7.011389 AGCTGCTTTGGTTTTCTGAAAAATAAC 59.989 33.333 16.47 5.74 36.77 1.89
1331 1351 1.067516 GCAGCTGCTTTGGTTTTCTGA 59.932 47.619 31.33 0.00 38.21 3.27
1360 1380 9.143631 CATCCCAATTCTTGATAACTTTGTTTC 57.856 33.333 0.00 0.00 0.00 2.78
1443 1463 3.094572 CCATTTCTTGGGCATTCTCAGT 58.905 45.455 0.00 0.00 42.33 3.41
1478 1498 1.107538 TAAGCTCCCGGACATCCTCG 61.108 60.000 0.73 0.00 0.00 4.63
1481 1501 1.416401 TGAATAAGCTCCCGGACATCC 59.584 52.381 0.73 0.00 0.00 3.51
1583 1603 4.090090 CTGTTCTGAACCTCTTCCTCCTA 58.910 47.826 17.26 0.00 0.00 2.94
1651 1671 7.753630 AGGTTCATTTGGCTTCATAGATATCT 58.246 34.615 10.73 10.73 0.00 1.98
1660 1680 2.038426 TCTCGAGGTTCATTTGGCTTCA 59.962 45.455 13.56 0.00 0.00 3.02
1691 1711 7.722949 AAAGATTTCCTTTGGAGATGCATTA 57.277 32.000 0.00 0.00 43.10 1.90
1703 1723 1.963515 AGTGCCGCAAAGATTTCCTTT 59.036 42.857 0.00 0.00 45.48 3.11
1772 1792 1.565305 GGTCGCTGCTAGTGAGAATG 58.435 55.000 0.00 0.00 35.09 2.67
1820 1840 3.270433 ACCAATCCTTCCTCATGTCCATT 59.730 43.478 0.00 0.00 0.00 3.16
1826 1846 4.275810 ACATCAACCAATCCTTCCTCATG 58.724 43.478 0.00 0.00 0.00 3.07
1875 1895 9.710900 CAAGACTAGTGATAAATATGCCATACA 57.289 33.333 0.00 0.00 0.00 2.29
1876 1896 9.712305 ACAAGACTAGTGATAAATATGCCATAC 57.288 33.333 0.00 0.00 0.00 2.39
1915 1938 8.802267 AGTAGCAAATATTTTGGACAAAGCTAA 58.198 29.630 11.82 0.00 32.35 3.09
1916 1939 8.243426 CAGTAGCAAATATTTTGGACAAAGCTA 58.757 33.333 0.00 3.54 30.50 3.32
1917 1940 7.092716 CAGTAGCAAATATTTTGGACAAAGCT 58.907 34.615 0.00 4.49 31.97 3.74
1982 2011 2.616842 AGAATCCAAAACACGCGACTTT 59.383 40.909 15.93 6.52 0.00 2.66
2020 2049 5.994668 TGTTACATACAGCAATGACACTGAA 59.005 36.000 0.00 0.00 37.35 3.02
2021 2050 5.546526 TGTTACATACAGCAATGACACTGA 58.453 37.500 0.00 0.00 37.35 3.41
2022 2051 5.861222 TGTTACATACAGCAATGACACTG 57.139 39.130 1.26 0.00 39.86 3.66
2023 2052 7.452880 AAATGTTACATACAGCAATGACACT 57.547 32.000 0.00 0.00 40.83 3.55
2024 2053 7.807433 TGAAAATGTTACATACAGCAATGACAC 59.193 33.333 0.00 0.00 40.83 3.67
2032 2061 5.095490 GGTGCTGAAAATGTTACATACAGC 58.905 41.667 27.55 27.55 45.92 4.40
2060 2089 2.221169 CACACACAGTTGTATGCACCT 58.779 47.619 0.00 0.00 33.30 4.00
2093 2122 1.033746 AATTCAGGGCATGCGTCAGG 61.034 55.000 12.44 3.63 0.00 3.86
2096 2125 1.226773 GCAATTCAGGGCATGCGTC 60.227 57.895 12.44 6.58 0.00 5.19
2119 2148 1.538950 TGCAATGTCGCTGTATTTGCA 59.461 42.857 4.66 4.66 0.00 4.08
2210 2373 9.352784 CGATATTAAAAGTTGAAAGGATGCAAA 57.647 29.630 0.00 0.00 0.00 3.68
2212 2375 6.972328 GCGATATTAAAAGTTGAAAGGATGCA 59.028 34.615 0.00 0.00 0.00 3.96
2224 2387 6.882678 AGTTTGTGTAGGGCGATATTAAAAGT 59.117 34.615 0.00 0.00 0.00 2.66
2235 2398 2.736144 TGTAGAGTTTGTGTAGGGCG 57.264 50.000 0.00 0.00 0.00 6.13
2277 2440 3.967332 ACATTTCCAGGCCAATTTCAG 57.033 42.857 5.01 0.00 0.00 3.02
2308 2471 1.667724 GGTGCCGAGAGATGAATTGTG 59.332 52.381 0.00 0.00 0.00 3.33
2336 2499 2.348411 ATTGGCCCATAACTCCGAAG 57.652 50.000 0.00 0.00 0.00 3.79
2337 2500 3.392947 TGATATTGGCCCATAACTCCGAA 59.607 43.478 0.00 0.00 0.00 4.30
2340 2503 5.106157 CGAATTGATATTGGCCCATAACTCC 60.106 44.000 0.00 0.00 0.00 3.85
2385 2548 0.476771 GTTGGGACTTGGGACCTCAA 59.523 55.000 0.00 0.00 0.00 3.02
2395 2558 4.969484 ACGTAAAATCTCTGTTGGGACTT 58.031 39.130 0.00 0.00 0.00 3.01
2396 2559 4.618920 ACGTAAAATCTCTGTTGGGACT 57.381 40.909 0.00 0.00 0.00 3.85
2397 2560 6.980051 AATACGTAAAATCTCTGTTGGGAC 57.020 37.500 0.00 0.00 0.00 4.46
2398 2561 6.128117 GCAAATACGTAAAATCTCTGTTGGGA 60.128 38.462 0.00 0.00 0.00 4.37
2399 2562 6.027749 GCAAATACGTAAAATCTCTGTTGGG 58.972 40.000 0.00 0.00 0.00 4.12
2400 2563 6.842163 AGCAAATACGTAAAATCTCTGTTGG 58.158 36.000 0.00 0.00 0.00 3.77
2401 2564 8.728088 AAAGCAAATACGTAAAATCTCTGTTG 57.272 30.769 0.00 0.00 0.00 3.33
2402 2565 8.784043 AGAAAGCAAATACGTAAAATCTCTGTT 58.216 29.630 0.00 0.00 0.00 3.16
2426 2589 7.974504 GGGGGAACTTGAATACTTGATATAGA 58.025 38.462 0.00 0.00 0.00 1.98
2453 2616 5.066593 GGAAGGCTATGTATCAAAAGGAGG 58.933 45.833 0.00 0.00 0.00 4.30
2480 2643 1.957668 CACATCTTCATCATCCGCCA 58.042 50.000 0.00 0.00 0.00 5.69
2486 2649 5.831702 GAAGAAAGGCACATCTTCATCAT 57.168 39.130 16.93 0.00 46.07 2.45
2491 2654 3.949132 AGGAGAAGAAAGGCACATCTTC 58.051 45.455 15.08 15.08 46.69 2.87
2520 2683 9.612066 TGATATATGCAGTTGTCTTTGTAATCA 57.388 29.630 0.00 0.00 0.00 2.57
2527 2690 7.578310 AAGCATGATATATGCAGTTGTCTTT 57.422 32.000 13.60 0.00 46.77 2.52
2595 2761 8.338259 GCTGACATGTCGATTGTAATATTTTCT 58.662 33.333 20.54 0.00 0.00 2.52
2599 2765 7.552458 TTGCTGACATGTCGATTGTAATATT 57.448 32.000 20.54 0.00 0.00 1.28
2604 2770 4.378356 GCTTTTGCTGACATGTCGATTGTA 60.378 41.667 20.54 7.80 43.35 2.41
2652 2818 6.403855 GCCGTTTTGCCTTATGTTGTATAGAA 60.404 38.462 0.00 0.00 0.00 2.10
2655 2821 4.700692 TGCCGTTTTGCCTTATGTTGTATA 59.299 37.500 0.00 0.00 0.00 1.47
2656 2822 3.508012 TGCCGTTTTGCCTTATGTTGTAT 59.492 39.130 0.00 0.00 0.00 2.29
2674 2840 3.508744 ACTTAATTCCTGCATTTGCCG 57.491 42.857 0.00 0.00 41.18 5.69
2677 2843 6.071391 AGGTTGGTACTTAATTCCTGCATTTG 60.071 38.462 0.00 0.00 0.00 2.32
2684 2850 5.853572 TGGAAGGTTGGTACTTAATTCCT 57.146 39.130 14.20 4.08 36.52 3.36
2691 2857 2.159382 CGCAATGGAAGGTTGGTACTT 58.841 47.619 0.00 0.00 0.00 2.24
2727 2893 5.769662 ACTGATGGAAGCACAACATCTTTAA 59.230 36.000 0.00 0.00 41.12 1.52
2728 2894 5.181811 CACTGATGGAAGCACAACATCTTTA 59.818 40.000 0.00 0.00 41.12 1.85
2730 2896 3.504906 CACTGATGGAAGCACAACATCTT 59.495 43.478 0.00 0.00 41.12 2.40
2734 2900 2.636647 TCACTGATGGAAGCACAACA 57.363 45.000 0.00 0.00 0.00 3.33
2735 2901 4.697352 ACTAATCACTGATGGAAGCACAAC 59.303 41.667 0.00 0.00 0.00 3.32
2759 2925 6.359480 GCGTAGGCAATTTAGATACAAGTT 57.641 37.500 1.75 0.00 39.62 2.66
2780 2946 1.278637 GAAACACACGAGGGTTGCG 59.721 57.895 0.00 0.00 0.00 4.85
2789 2955 8.817100 TCAGCTTTAAGATATATGAAACACACG 58.183 33.333 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.