Multiple sequence alignment - TraesCS3B01G374700

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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 TraesCS3B01G374700 chr3B 100.000 4264 0 0 1 4264 588419065 588423328 0.000000e+00 7875
1 TraesCS3B01G374700 chr3B 91.136 1805 120 15 1596 3382 588471513 588473295 0.000000e+00 2410
2 TraesCS3B01G374700 chr3B 97.645 552 12 1 1058 1608 588470942 588471493 0.000000e+00 946
3 TraesCS3B01G374700 chr3D 90.584 1816 131 15 1585 3382 448428458 448430251 0.000000e+00 2370
4 TraesCS3B01G374700 chr3D 95.109 552 26 1 1058 1608 448427898 448428449 0.000000e+00 869
5 TraesCS3B01G374700 chr3A 91.362 1586 116 8 1586 3152 589792960 589794543 0.000000e+00 2150
6 TraesCS3B01G374700 chr3A 97.070 785 22 1 281 1064 669949854 669950638 0.000000e+00 1321
7 TraesCS3B01G374700 chr3A 96.501 543 19 0 1058 1600 589792399 589792941 0.000000e+00 898
8 TraesCS3B01G374700 chr3A 89.399 632 66 1 1749 2380 589613374 589614004 0.000000e+00 795
9 TraesCS3B01G374700 chr3A 89.964 548 53 2 1053 1599 589606268 589606814 0.000000e+00 706
10 TraesCS3B01G374700 chr3A 97.049 305 8 1 282 585 520156648 520156952 2.940000e-141 512
11 TraesCS3B01G374700 chr3A 97.794 272 6 0 793 1064 520156953 520157224 1.790000e-128 470
12 TraesCS3B01G374700 chr3A 90.805 174 15 1 3209 3382 589794544 589794716 9.220000e-57 231
13 TraesCS3B01G374700 chr3A 91.018 167 15 0 1586 1752 589606834 589607000 4.290000e-55 226
14 TraesCS3B01G374700 chr7B 95.045 888 37 4 3383 4264 607906829 607905943 0.000000e+00 1389
15 TraesCS3B01G374700 chr7B 95.028 885 37 6 3382 4264 533341977 533341098 0.000000e+00 1384
16 TraesCS3B01G374700 chr5B 94.820 888 38 7 3382 4264 315636188 315637072 0.000000e+00 1378
17 TraesCS3B01G374700 chr5B 94.582 886 41 6 3382 4262 458545474 458546357 0.000000e+00 1363
18 TraesCS3B01G374700 chr5B 96.692 786 25 1 280 1064 405508409 405509194 0.000000e+00 1306
19 TraesCS3B01G374700 chr1B 94.910 884 40 4 3382 4264 50302028 50301149 0.000000e+00 1378
20 TraesCS3B01G374700 chr2B 94.713 889 40 4 3382 4264 92479914 92480801 0.000000e+00 1375
21 TraesCS3B01G374700 chr2B 94.488 889 42 7 3380 4264 129367666 129366781 0.000000e+00 1363
22 TraesCS3B01G374700 chr2B 95.828 791 29 2 278 1064 194854917 194855707 0.000000e+00 1275
23 TraesCS3B01G374700 chr2B 80.071 1405 252 15 1586 2984 695889681 695891063 0.000000e+00 1018
24 TraesCS3B01G374700 chr4B 94.601 889 39 6 3382 4264 82099334 82098449 0.000000e+00 1367
25 TraesCS3B01G374700 chr4B 96.819 786 24 1 280 1064 659358916 659358131 0.000000e+00 1312
26 TraesCS3B01G374700 chr4B 96.315 787 28 1 279 1064 162761395 162762181 0.000000e+00 1291
27 TraesCS3B01G374700 chr2D 94.589 887 39 8 3383 4264 91728457 91729339 0.000000e+00 1363
28 TraesCS3B01G374700 chr2D 80.150 1330 232 18 1641 2966 578963668 578964969 0.000000e+00 965
29 TraesCS3B01G374700 chr4A 96.696 787 24 2 279 1064 664951971 664951186 0.000000e+00 1308
30 TraesCS3B01G374700 chr1A 96.811 784 23 2 282 1064 535320721 535319939 0.000000e+00 1308
31 TraesCS3B01G374700 chr7A 88.805 795 67 13 280 1064 492371432 492370650 0.000000e+00 955
32 TraesCS3B01G374700 chr2A 78.996 1395 254 25 1586 2966 716500051 716501420 0.000000e+00 917
33 TraesCS3B01G374700 chr2A 82.073 463 73 7 1146 1600 716499572 716500032 1.860000e-103 387


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 TraesCS3B01G374700 chr3B 588419065 588423328 4263 False 7875.0 7875 100.000000 1 4264 1 chr3B.!!$F1 4263
1 TraesCS3B01G374700 chr3B 588470942 588473295 2353 False 1678.0 2410 94.390500 1058 3382 2 chr3B.!!$F2 2324
2 TraesCS3B01G374700 chr3D 448427898 448430251 2353 False 1619.5 2370 92.846500 1058 3382 2 chr3D.!!$F1 2324
3 TraesCS3B01G374700 chr3A 669949854 669950638 784 False 1321.0 1321 97.070000 281 1064 1 chr3A.!!$F2 783
4 TraesCS3B01G374700 chr3A 589792399 589794716 2317 False 1093.0 2150 92.889333 1058 3382 3 chr3A.!!$F5 2324
5 TraesCS3B01G374700 chr3A 589613374 589614004 630 False 795.0 795 89.399000 1749 2380 1 chr3A.!!$F1 631
6 TraesCS3B01G374700 chr3A 520156648 520157224 576 False 491.0 512 97.421500 282 1064 2 chr3A.!!$F3 782
7 TraesCS3B01G374700 chr3A 589606268 589607000 732 False 466.0 706 90.491000 1053 1752 2 chr3A.!!$F4 699
8 TraesCS3B01G374700 chr7B 607905943 607906829 886 True 1389.0 1389 95.045000 3383 4264 1 chr7B.!!$R2 881
9 TraesCS3B01G374700 chr7B 533341098 533341977 879 True 1384.0 1384 95.028000 3382 4264 1 chr7B.!!$R1 882
10 TraesCS3B01G374700 chr5B 315636188 315637072 884 False 1378.0 1378 94.820000 3382 4264 1 chr5B.!!$F1 882
11 TraesCS3B01G374700 chr5B 458545474 458546357 883 False 1363.0 1363 94.582000 3382 4262 1 chr5B.!!$F3 880
12 TraesCS3B01G374700 chr5B 405508409 405509194 785 False 1306.0 1306 96.692000 280 1064 1 chr5B.!!$F2 784
13 TraesCS3B01G374700 chr1B 50301149 50302028 879 True 1378.0 1378 94.910000 3382 4264 1 chr1B.!!$R1 882
14 TraesCS3B01G374700 chr2B 92479914 92480801 887 False 1375.0 1375 94.713000 3382 4264 1 chr2B.!!$F1 882
15 TraesCS3B01G374700 chr2B 129366781 129367666 885 True 1363.0 1363 94.488000 3380 4264 1 chr2B.!!$R1 884
16 TraesCS3B01G374700 chr2B 194854917 194855707 790 False 1275.0 1275 95.828000 278 1064 1 chr2B.!!$F2 786
17 TraesCS3B01G374700 chr2B 695889681 695891063 1382 False 1018.0 1018 80.071000 1586 2984 1 chr2B.!!$F3 1398
18 TraesCS3B01G374700 chr4B 82098449 82099334 885 True 1367.0 1367 94.601000 3382 4264 1 chr4B.!!$R1 882
19 TraesCS3B01G374700 chr4B 659358131 659358916 785 True 1312.0 1312 96.819000 280 1064 1 chr4B.!!$R2 784
20 TraesCS3B01G374700 chr4B 162761395 162762181 786 False 1291.0 1291 96.315000 279 1064 1 chr4B.!!$F1 785
21 TraesCS3B01G374700 chr2D 91728457 91729339 882 False 1363.0 1363 94.589000 3383 4264 1 chr2D.!!$F1 881
22 TraesCS3B01G374700 chr2D 578963668 578964969 1301 False 965.0 965 80.150000 1641 2966 1 chr2D.!!$F2 1325
23 TraesCS3B01G374700 chr4A 664951186 664951971 785 True 1308.0 1308 96.696000 279 1064 1 chr4A.!!$R1 785
24 TraesCS3B01G374700 chr1A 535319939 535320721 782 True 1308.0 1308 96.811000 282 1064 1 chr1A.!!$R1 782
25 TraesCS3B01G374700 chr7A 492370650 492371432 782 True 955.0 955 88.805000 280 1064 1 chr7A.!!$R1 784
26 TraesCS3B01G374700 chr2A 716499572 716501420 1848 False 652.0 917 80.534500 1146 2966 2 chr2A.!!$F1 1820

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
253 254 0.040425 CCGAAGAAACAACCCAAGCG 60.040 55.000 0.00 0.00 0.00 4.68 F
255 256 0.318699 GAAGAAACAACCCAAGCGCC 60.319 55.000 2.29 0.00 0.00 6.53 F
257 258 1.007387 GAAACAACCCAAGCGCCAG 60.007 57.895 2.29 0.00 0.00 4.85 F
1377 1391 1.227946 GCCTACCTCCTCTCCTCGT 59.772 63.158 0.00 0.00 0.00 4.18 F
2442 2495 0.302890 GGCTTTCGAGCATGTCATCG 59.697 55.000 9.83 9.83 40.26 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 1391 0.395862 CGGGAGTAGGAGGAGAGCAA 60.396 60.000 0.00 0.0 0.00 3.91 R
1781 1834 1.519455 GAGATCAAGGGCGTCCACG 60.519 63.158 9.71 0.0 43.27 4.94 R
2030 2083 3.939740 ATGCTCTTCCTAGGCATTTCA 57.060 42.857 2.96 0.0 43.02 2.69 R
2938 3001 0.036732 AGCATGCTCCACCTTCGAAA 59.963 50.000 16.30 0.0 0.00 3.46 R
3586 3667 0.040204 CCCTGGCCCTCATCTTTTGT 59.960 55.000 0.00 0.0 0.00 2.83 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
31 32 4.841617 TCGCTCGGGCCCTCTCAT 62.842 66.667 22.43 0.00 34.44 2.90
32 33 4.598894 CGCTCGGGCCCTCTCATG 62.599 72.222 22.43 2.32 34.44 3.07
33 34 4.925861 GCTCGGGCCCTCTCATGC 62.926 72.222 22.43 10.77 0.00 4.06
34 35 4.598894 CTCGGGCCCTCTCATGCG 62.599 72.222 22.43 3.44 0.00 4.73
38 39 4.247380 GGCCCTCTCATGCGGGAG 62.247 72.222 16.02 9.92 40.62 4.30
39 40 4.247380 GCCCTCTCATGCGGGAGG 62.247 72.222 16.02 16.50 46.22 4.30
40 41 2.765807 CCCTCTCATGCGGGAGGT 60.766 66.667 20.04 0.00 45.46 3.85
41 42 2.503061 CCTCTCATGCGGGAGGTG 59.497 66.667 16.10 0.00 42.86 4.00
42 43 2.503061 CTCTCATGCGGGAGGTGG 59.497 66.667 4.80 0.00 35.58 4.61
43 44 2.038813 TCTCATGCGGGAGGTGGA 59.961 61.111 4.80 0.00 35.58 4.02
44 45 2.025767 CTCTCATGCGGGAGGTGGAG 62.026 65.000 4.80 0.00 35.58 3.86
45 46 2.038813 TCATGCGGGAGGTGGAGA 59.961 61.111 0.00 0.00 0.00 3.71
46 47 2.187946 CATGCGGGAGGTGGAGAC 59.812 66.667 0.00 0.00 0.00 3.36
47 48 2.039624 ATGCGGGAGGTGGAGACT 59.960 61.111 0.00 0.00 0.00 3.24
48 49 2.362369 ATGCGGGAGGTGGAGACTG 61.362 63.158 0.00 0.00 0.00 3.51
49 50 3.775654 GCGGGAGGTGGAGACTGG 61.776 72.222 0.00 0.00 0.00 4.00
50 51 3.775654 CGGGAGGTGGAGACTGGC 61.776 72.222 0.00 0.00 0.00 4.85
51 52 2.284995 GGGAGGTGGAGACTGGCT 60.285 66.667 0.00 0.00 0.00 4.75
52 53 2.363172 GGGAGGTGGAGACTGGCTC 61.363 68.421 0.59 0.59 43.17 4.70
53 54 1.305718 GGAGGTGGAGACTGGCTCT 60.306 63.158 10.92 0.00 43.43 4.09
54 55 1.612395 GGAGGTGGAGACTGGCTCTG 61.612 65.000 10.92 0.00 43.43 3.35
55 56 2.237534 GAGGTGGAGACTGGCTCTGC 62.238 65.000 10.92 3.50 43.43 4.26
56 57 2.587247 GGTGGAGACTGGCTCTGCA 61.587 63.158 10.92 0.00 44.62 4.41
57 58 3.385469 TGGAGACTGGCTCTGCAG 58.615 61.111 10.92 7.63 42.13 4.41
58 59 2.288778 TGGAGACTGGCTCTGCAGG 61.289 63.158 15.13 5.82 42.13 4.85
59 60 2.125188 GAGACTGGCTCTGCAGGC 60.125 66.667 15.13 15.77 45.76 4.85
92 93 3.390521 TGCGGGTACTGGAGGCAG 61.391 66.667 0.00 0.00 33.56 4.85
93 94 4.840005 GCGGGTACTGGAGGCAGC 62.840 72.222 0.00 0.00 33.56 5.25
94 95 4.162690 CGGGTACTGGAGGCAGCC 62.163 72.222 1.84 1.84 0.00 4.85
95 96 4.162690 GGGTACTGGAGGCAGCCG 62.163 72.222 5.55 0.00 0.00 5.52
96 97 3.075005 GGTACTGGAGGCAGCCGA 61.075 66.667 5.55 0.00 0.00 5.54
97 98 2.184579 GTACTGGAGGCAGCCGAC 59.815 66.667 5.55 3.34 0.00 4.79
98 99 3.449227 TACTGGAGGCAGCCGACG 61.449 66.667 5.55 0.00 0.00 5.12
117 118 3.520862 CATGGCCATGGGACGCAC 61.521 66.667 34.31 0.00 35.24 5.34
118 119 4.820744 ATGGCCATGGGACGCACC 62.821 66.667 20.04 5.30 29.56 5.01
135 136 3.632700 CGCGGTCGGTCAAAGAAA 58.367 55.556 0.00 0.00 0.00 2.52
136 137 1.935925 CGCGGTCGGTCAAAGAAAA 59.064 52.632 0.00 0.00 0.00 2.29
137 138 0.110823 CGCGGTCGGTCAAAGAAAAG 60.111 55.000 0.00 0.00 0.00 2.27
138 139 1.223187 GCGGTCGGTCAAAGAAAAGA 58.777 50.000 0.00 0.00 0.00 2.52
139 140 1.600485 GCGGTCGGTCAAAGAAAAGAA 59.400 47.619 0.00 0.00 0.00 2.52
140 141 2.225727 GCGGTCGGTCAAAGAAAAGAAT 59.774 45.455 0.00 0.00 0.00 2.40
141 142 3.667166 GCGGTCGGTCAAAGAAAAGAATC 60.667 47.826 0.00 0.00 0.00 2.52
142 143 3.423123 CGGTCGGTCAAAGAAAAGAATCG 60.423 47.826 0.00 0.00 0.00 3.34
143 144 3.120304 GGTCGGTCAAAGAAAAGAATCGG 60.120 47.826 0.00 0.00 0.00 4.18
144 145 3.071479 TCGGTCAAAGAAAAGAATCGGG 58.929 45.455 0.00 0.00 0.00 5.14
145 146 2.812011 CGGTCAAAGAAAAGAATCGGGT 59.188 45.455 0.00 0.00 0.00 5.28
146 147 3.120304 CGGTCAAAGAAAAGAATCGGGTC 60.120 47.826 0.00 0.00 0.00 4.46
147 148 4.072839 GGTCAAAGAAAAGAATCGGGTCT 58.927 43.478 0.00 0.00 0.00 3.85
148 149 4.083271 GGTCAAAGAAAAGAATCGGGTCTG 60.083 45.833 0.00 0.00 0.00 3.51
149 150 3.502211 TCAAAGAAAAGAATCGGGTCTGC 59.498 43.478 0.00 0.00 0.00 4.26
150 151 1.726853 AGAAAAGAATCGGGTCTGCG 58.273 50.000 0.00 0.00 0.00 5.18
151 152 0.727398 GAAAAGAATCGGGTCTGCGG 59.273 55.000 0.00 0.00 0.00 5.69
152 153 1.305930 AAAAGAATCGGGTCTGCGGC 61.306 55.000 0.00 0.00 0.00 6.53
153 154 4.514577 AGAATCGGGTCTGCGGCG 62.515 66.667 0.51 0.51 0.00 6.46
154 155 4.508128 GAATCGGGTCTGCGGCGA 62.508 66.667 12.98 0.00 0.00 5.54
155 156 4.077184 AATCGGGTCTGCGGCGAA 62.077 61.111 12.98 0.00 0.00 4.70
156 157 4.514577 ATCGGGTCTGCGGCGAAG 62.515 66.667 12.98 10.94 0.00 3.79
158 159 4.735132 CGGGTCTGCGGCGAAGAA 62.735 66.667 21.24 0.38 0.00 2.52
159 160 2.358247 GGGTCTGCGGCGAAGAAA 60.358 61.111 21.24 0.00 0.00 2.52
160 161 2.391389 GGGTCTGCGGCGAAGAAAG 61.391 63.158 21.24 3.38 0.00 2.62
161 162 1.374252 GGTCTGCGGCGAAGAAAGA 60.374 57.895 21.24 5.88 0.00 2.52
162 163 0.949105 GGTCTGCGGCGAAGAAAGAA 60.949 55.000 21.24 0.00 0.00 2.52
163 164 0.440371 GTCTGCGGCGAAGAAAGAAG 59.560 55.000 21.24 0.00 0.00 2.85
164 165 0.317160 TCTGCGGCGAAGAAAGAAGA 59.683 50.000 16.86 0.00 0.00 2.87
165 166 1.148310 CTGCGGCGAAGAAAGAAGAA 58.852 50.000 10.00 0.00 0.00 2.52
166 167 1.127582 CTGCGGCGAAGAAAGAAGAAG 59.872 52.381 10.00 0.00 0.00 2.85
167 168 0.444260 GCGGCGAAGAAAGAAGAAGG 59.556 55.000 12.98 0.00 0.00 3.46
168 169 1.939838 GCGGCGAAGAAAGAAGAAGGA 60.940 52.381 12.98 0.00 0.00 3.36
169 170 2.413837 CGGCGAAGAAAGAAGAAGGAA 58.586 47.619 0.00 0.00 0.00 3.36
170 171 2.413453 CGGCGAAGAAAGAAGAAGGAAG 59.587 50.000 0.00 0.00 0.00 3.46
171 172 3.665190 GGCGAAGAAAGAAGAAGGAAGA 58.335 45.455 0.00 0.00 0.00 2.87
172 173 3.682377 GGCGAAGAAAGAAGAAGGAAGAG 59.318 47.826 0.00 0.00 0.00 2.85
173 174 4.561105 GCGAAGAAAGAAGAAGGAAGAGA 58.439 43.478 0.00 0.00 0.00 3.10
174 175 4.991687 GCGAAGAAAGAAGAAGGAAGAGAA 59.008 41.667 0.00 0.00 0.00 2.87
175 176 5.120053 GCGAAGAAAGAAGAAGGAAGAGAAG 59.880 44.000 0.00 0.00 0.00 2.85
176 177 5.637387 CGAAGAAAGAAGAAGGAAGAGAAGG 59.363 44.000 0.00 0.00 0.00 3.46
177 178 5.497464 AGAAAGAAGAAGGAAGAGAAGGG 57.503 43.478 0.00 0.00 0.00 3.95
178 179 4.288366 AGAAAGAAGAAGGAAGAGAAGGGG 59.712 45.833 0.00 0.00 0.00 4.79
179 180 3.569135 AGAAGAAGGAAGAGAAGGGGA 57.431 47.619 0.00 0.00 0.00 4.81
180 181 3.449918 AGAAGAAGGAAGAGAAGGGGAG 58.550 50.000 0.00 0.00 0.00 4.30
181 182 2.262266 AGAAGGAAGAGAAGGGGAGG 57.738 55.000 0.00 0.00 0.00 4.30
182 183 1.725182 AGAAGGAAGAGAAGGGGAGGA 59.275 52.381 0.00 0.00 0.00 3.71
183 184 2.115427 GAAGGAAGAGAAGGGGAGGAG 58.885 57.143 0.00 0.00 0.00 3.69
184 185 0.326143 AGGAAGAGAAGGGGAGGAGC 60.326 60.000 0.00 0.00 0.00 4.70
185 186 1.341913 GGAAGAGAAGGGGAGGAGCC 61.342 65.000 0.00 0.00 0.00 4.70
186 187 1.681486 GAAGAGAAGGGGAGGAGCCG 61.681 65.000 0.00 0.00 37.63 5.52
187 188 2.042843 GAGAAGGGGAGGAGCCGA 60.043 66.667 0.00 0.00 37.63 5.54
188 189 2.042435 AGAAGGGGAGGAGCCGAG 60.042 66.667 0.00 0.00 37.63 4.63
189 190 3.157949 GAAGGGGAGGAGCCGAGG 61.158 72.222 0.00 0.00 37.63 4.63
190 191 3.680920 GAAGGGGAGGAGCCGAGGA 62.681 68.421 0.00 0.00 37.63 3.71
191 192 3.687828 AAGGGGAGGAGCCGAGGAG 62.688 68.421 0.00 0.00 37.63 3.69
193 194 4.144727 GGGAGGAGCCGAGGAGGA 62.145 72.222 0.00 0.00 45.00 3.71
194 195 2.835895 GGAGGAGCCGAGGAGGAC 60.836 72.222 0.00 0.00 45.00 3.85
195 196 2.043852 GAGGAGCCGAGGAGGACA 60.044 66.667 0.00 0.00 45.00 4.02
196 197 2.363147 AGGAGCCGAGGAGGACAC 60.363 66.667 0.00 0.00 45.00 3.67
197 198 3.827898 GGAGCCGAGGAGGACACG 61.828 72.222 0.00 0.00 45.00 4.49
198 199 4.500116 GAGCCGAGGAGGACACGC 62.500 72.222 0.00 0.00 45.00 5.34
216 217 4.373116 GCTGCGGTCGGTTCCAGA 62.373 66.667 0.00 0.00 0.00 3.86
217 218 2.342279 CTGCGGTCGGTTCCAGAA 59.658 61.111 0.00 0.00 0.00 3.02
218 219 1.301401 CTGCGGTCGGTTCCAGAAA 60.301 57.895 0.00 0.00 0.00 2.52
219 220 0.882927 CTGCGGTCGGTTCCAGAAAA 60.883 55.000 0.00 0.00 0.00 2.29
220 221 0.464013 TGCGGTCGGTTCCAGAAAAA 60.464 50.000 0.00 0.00 0.00 1.94
235 236 3.785982 AAAAATGGTGGGCCGACC 58.214 55.556 28.89 28.89 37.67 4.79
236 237 2.272447 AAAAATGGTGGGCCGACCG 61.272 57.895 29.32 0.00 44.64 4.79
237 238 2.700407 AAAAATGGTGGGCCGACCGA 62.700 55.000 29.32 19.52 44.64 4.69
238 239 2.700407 AAAATGGTGGGCCGACCGAA 62.700 55.000 29.32 15.48 44.64 4.30
239 240 3.622060 AATGGTGGGCCGACCGAAG 62.622 63.158 29.32 0.00 44.64 3.79
241 242 4.011517 GGTGGGCCGACCGAAGAA 62.012 66.667 22.23 0.00 44.64 2.52
242 243 2.031465 GTGGGCCGACCGAAGAAA 59.969 61.111 6.63 0.00 44.64 2.52
243 244 2.031465 TGGGCCGACCGAAGAAAC 59.969 61.111 0.00 0.00 44.64 2.78
244 245 2.031465 GGGCCGACCGAAGAAACA 59.969 61.111 0.00 0.00 36.48 2.83
245 246 1.598685 GGGCCGACCGAAGAAACAA 60.599 57.895 0.00 0.00 36.48 2.83
246 247 1.572941 GGCCGACCGAAGAAACAAC 59.427 57.895 0.00 0.00 0.00 3.32
247 248 1.572941 GCCGACCGAAGAAACAACC 59.427 57.895 0.00 0.00 0.00 3.77
248 249 1.848932 GCCGACCGAAGAAACAACCC 61.849 60.000 0.00 0.00 0.00 4.11
249 250 0.533308 CCGACCGAAGAAACAACCCA 60.533 55.000 0.00 0.00 0.00 4.51
250 251 1.301423 CGACCGAAGAAACAACCCAA 58.699 50.000 0.00 0.00 0.00 4.12
251 252 1.263217 CGACCGAAGAAACAACCCAAG 59.737 52.381 0.00 0.00 0.00 3.61
252 253 1.001706 GACCGAAGAAACAACCCAAGC 60.002 52.381 0.00 0.00 0.00 4.01
253 254 0.040425 CCGAAGAAACAACCCAAGCG 60.040 55.000 0.00 0.00 0.00 4.68
254 255 0.660300 CGAAGAAACAACCCAAGCGC 60.660 55.000 0.00 0.00 0.00 5.92
255 256 0.318699 GAAGAAACAACCCAAGCGCC 60.319 55.000 2.29 0.00 0.00 6.53
256 257 1.040339 AAGAAACAACCCAAGCGCCA 61.040 50.000 2.29 0.00 0.00 5.69
257 258 1.007387 GAAACAACCCAAGCGCCAG 60.007 57.895 2.29 0.00 0.00 4.85
258 259 2.420466 GAAACAACCCAAGCGCCAGG 62.420 60.000 2.29 6.20 0.00 4.45
259 260 2.920076 AAACAACCCAAGCGCCAGGA 62.920 55.000 16.62 0.00 0.00 3.86
260 261 3.058160 CAACCCAAGCGCCAGGAG 61.058 66.667 16.62 9.39 0.00 3.69
261 262 3.570212 AACCCAAGCGCCAGGAGT 61.570 61.111 16.62 9.97 0.00 3.85
262 263 3.850098 AACCCAAGCGCCAGGAGTG 62.850 63.158 16.62 3.47 0.00 3.51
263 264 4.335647 CCCAAGCGCCAGGAGTGT 62.336 66.667 16.62 0.00 0.00 3.55
264 265 3.052082 CCAAGCGCCAGGAGTGTG 61.052 66.667 10.02 0.00 0.00 3.82
265 266 2.281070 CAAGCGCCAGGAGTGTGT 60.281 61.111 2.29 0.00 0.00 3.72
266 267 2.281070 AAGCGCCAGGAGTGTGTG 60.281 61.111 2.29 0.00 0.00 3.82
267 268 4.996434 AGCGCCAGGAGTGTGTGC 62.996 66.667 2.29 0.00 33.19 4.57
275 276 3.276846 GAGTGTGTGCGCCGGTTT 61.277 61.111 4.18 0.00 0.00 3.27
276 277 3.521308 GAGTGTGTGCGCCGGTTTG 62.521 63.158 4.18 0.00 0.00 2.93
298 299 4.646945 TGCTAAGGATGTGTTTGGTTCAAA 59.353 37.500 0.00 0.00 0.00 2.69
300 301 5.009610 GCTAAGGATGTGTTTGGTTCAAAGA 59.990 40.000 0.00 0.00 33.82 2.52
349 351 3.130734 TCCAGCTGGTTAGGGATAGTT 57.869 47.619 31.58 0.00 36.34 2.24
383 385 4.574674 TGGTTGATGGATGAAGTTAGCT 57.425 40.909 0.00 0.00 0.00 3.32
477 479 4.331968 TCGGCTGATGTAGGACAAAATTT 58.668 39.130 0.00 0.00 0.00 1.82
649 652 3.279116 GCACGTCAGGCAAGCACA 61.279 61.111 0.00 0.00 0.00 4.57
722 725 2.071262 CCTCCATCTGCAGGGCTCT 61.071 63.158 15.13 0.00 0.00 4.09
844 855 4.099573 CGCCAAGTAAGAAGATAGGGAAGA 59.900 45.833 0.00 0.00 0.00 2.87
856 867 6.689109 AGATAGGGAAGAGGAGATCCATAT 57.311 41.667 0.92 0.00 43.36 1.78
979 993 3.043713 TGGCTTGCTTCGCGTCAG 61.044 61.111 5.77 4.69 0.00 3.51
1154 1168 3.188786 GCTAGTTGCACGGAGCCG 61.189 66.667 7.48 7.48 44.83 5.52
1377 1391 1.227946 GCCTACCTCCTCTCCTCGT 59.772 63.158 0.00 0.00 0.00 4.18
1670 1723 1.754226 TGCCTCATATCAGTGTACGCA 59.246 47.619 9.48 0.00 0.00 5.24
1747 1800 1.544246 TGACATCGTCTCATGGAACGT 59.456 47.619 16.68 0.00 33.15 3.99
1851 1904 3.680786 TGGAGCCAGACGTCGTGG 61.681 66.667 22.32 22.32 38.21 4.94
1883 1936 3.023949 GCTCTCCTCGTGTGCCCAT 62.024 63.158 0.00 0.00 0.00 4.00
1916 1969 1.982395 TGTAGGCCTGGGTGTCGAG 60.982 63.158 17.99 0.00 0.00 4.04
1994 2047 2.079158 CTCATCAACTTCCATGCACGT 58.921 47.619 0.00 0.00 0.00 4.49
2030 2083 2.629656 GGCACAGCGGCTGTTCAAT 61.630 57.895 31.62 8.63 42.59 2.57
2351 2404 1.229359 CTCCTCAATGCCCATGCCT 59.771 57.895 0.00 0.00 36.33 4.75
2442 2495 0.302890 GGCTTTCGAGCATGTCATCG 59.697 55.000 9.83 9.83 40.26 3.84
2482 2535 0.460311 GGCTACTACGTGCTCATGGT 59.540 55.000 0.00 0.00 0.00 3.55
2487 2540 1.618837 ACTACGTGCTCATGGTGAACT 59.381 47.619 0.00 0.00 0.00 3.01
2510 2563 0.908910 ACACAGACACAGGACAACCA 59.091 50.000 0.00 0.00 38.94 3.67
2563 2617 1.374252 GCGCGGACTCAAGAAGGAA 60.374 57.895 8.83 0.00 0.00 3.36
2593 2647 1.899814 AGCTATGTCGAACACAAGGGA 59.100 47.619 0.00 0.00 38.97 4.20
2603 2657 3.815401 CGAACACAAGGGAAGAGTTCATT 59.185 43.478 0.00 0.00 38.71 2.57
2605 2659 5.468746 CGAACACAAGGGAAGAGTTCATTTA 59.531 40.000 0.00 0.00 38.71 1.40
2641 2695 3.245229 ACCACTCACATCCATAGGCAAAA 60.245 43.478 0.00 0.00 0.00 2.44
2702 2756 4.041567 TGAAGGAGAAAACAGATGGCACTA 59.958 41.667 0.00 0.00 0.00 2.74
2707 2761 5.171339 AGAAAACAGATGGCACTACAGAT 57.829 39.130 0.00 0.00 0.00 2.90
2712 2766 4.226384 ACAGATGGCACTACAGATATGGA 58.774 43.478 0.00 0.00 0.00 3.41
2715 2769 1.341209 TGGCACTACAGATATGGAGCG 59.659 52.381 0.00 0.00 0.00 5.03
2721 2775 1.123077 ACAGATATGGAGCGAGGCAA 58.877 50.000 0.00 0.00 0.00 4.52
2735 2789 3.056328 GCAAAGTGGACGAGGGGC 61.056 66.667 0.00 0.00 0.00 5.80
2746 2800 1.374947 CGAGGGGCACTCCAAGAAA 59.625 57.895 11.97 0.00 43.57 2.52
2804 2858 0.960364 CGCTGTGGCCTTTGGTATGT 60.960 55.000 3.32 0.00 34.44 2.29
2857 2918 4.431378 TCAAGAACCTAAGGGTATGTGGA 58.569 43.478 0.00 0.00 46.67 4.02
2860 2923 4.897051 AGAACCTAAGGGTATGTGGAGAT 58.103 43.478 0.00 0.00 46.67 2.75
2865 2928 1.898863 AGGGTATGTGGAGATTGCCT 58.101 50.000 0.00 0.00 0.00 4.75
2886 2949 2.904434 TCTCTTTCCTAAAGGCGGTCTT 59.096 45.455 0.00 0.00 39.01 3.01
2913 2976 2.485122 CAACCGGGCAATTCTCGC 59.515 61.111 6.32 0.00 0.00 5.03
2993 3056 5.534207 TTTGTGAAGAATTTGGTGCTCAT 57.466 34.783 0.00 0.00 0.00 2.90
3011 3075 5.013079 TGCTCATTGTTAGGAGAAGGAAGAA 59.987 40.000 0.00 0.00 34.12 2.52
3015 3079 7.010923 CTCATTGTTAGGAGAAGGAAGAATTCG 59.989 40.741 0.00 0.00 39.18 3.34
3090 3170 3.054802 CAGCTATGAGAAAAGTGGAGGGT 60.055 47.826 0.00 0.00 0.00 4.34
3099 3179 2.887151 AAGTGGAGGGTTGGATCAAG 57.113 50.000 0.00 0.00 0.00 3.02
3103 3183 0.620556 GGAGGGTTGGATCAAGAGCA 59.379 55.000 0.00 0.00 0.00 4.26
3106 3186 0.394899 GGGTTGGATCAAGAGCAGGG 60.395 60.000 0.00 0.00 0.00 4.45
3107 3187 1.034292 GGTTGGATCAAGAGCAGGGC 61.034 60.000 0.00 0.00 0.00 5.19
3108 3188 1.034292 GTTGGATCAAGAGCAGGGCC 61.034 60.000 0.00 0.00 0.00 5.80
3109 3189 1.210204 TTGGATCAAGAGCAGGGCCT 61.210 55.000 0.00 0.00 0.00 5.19
3120 3200 1.972660 GCAGGGCCTAATGGACTCGT 61.973 60.000 5.28 0.00 42.43 4.18
3152 3232 3.942748 GACCAGTACTCTCAGATCGAACT 59.057 47.826 0.00 0.00 0.00 3.01
3153 3233 3.692101 ACCAGTACTCTCAGATCGAACTG 59.308 47.826 16.00 16.00 39.02 3.16
3154 3234 3.488384 CCAGTACTCTCAGATCGAACTGC 60.488 52.174 17.19 3.06 37.75 4.40
3155 3235 3.376859 CAGTACTCTCAGATCGAACTGCT 59.623 47.826 17.19 5.28 37.75 4.24
3156 3236 4.013728 AGTACTCTCAGATCGAACTGCTT 58.986 43.478 17.19 4.52 37.75 3.91
3157 3237 5.065346 CAGTACTCTCAGATCGAACTGCTTA 59.935 44.000 17.19 4.85 37.75 3.09
3158 3238 5.648526 AGTACTCTCAGATCGAACTGCTTAA 59.351 40.000 17.19 0.02 37.75 1.85
3159 3239 4.739195 ACTCTCAGATCGAACTGCTTAAC 58.261 43.478 17.19 0.00 37.75 2.01
3160 3240 4.461081 ACTCTCAGATCGAACTGCTTAACT 59.539 41.667 17.19 0.00 37.75 2.24
3161 3241 4.987832 TCTCAGATCGAACTGCTTAACTC 58.012 43.478 17.19 0.00 37.75 3.01
3162 3242 4.109050 CTCAGATCGAACTGCTTAACTCC 58.891 47.826 17.19 0.00 37.75 3.85
3163 3243 3.119101 TCAGATCGAACTGCTTAACTCCC 60.119 47.826 17.19 0.00 37.75 4.30
3164 3244 3.100671 AGATCGAACTGCTTAACTCCCT 58.899 45.455 0.00 0.00 0.00 4.20
3165 3245 2.743636 TCGAACTGCTTAACTCCCTG 57.256 50.000 0.00 0.00 0.00 4.45
3166 3246 2.244695 TCGAACTGCTTAACTCCCTGA 58.755 47.619 0.00 0.00 0.00 3.86
3167 3247 2.631062 TCGAACTGCTTAACTCCCTGAA 59.369 45.455 0.00 0.00 0.00 3.02
3168 3248 2.996621 CGAACTGCTTAACTCCCTGAAG 59.003 50.000 0.00 0.00 0.00 3.02
3169 3249 3.306088 CGAACTGCTTAACTCCCTGAAGA 60.306 47.826 0.00 0.00 0.00 2.87
3170 3250 4.621747 CGAACTGCTTAACTCCCTGAAGAT 60.622 45.833 0.00 0.00 0.00 2.40
3189 3269 4.934356 AGATCAGGCTCCCATTTGTTTTA 58.066 39.130 0.00 0.00 0.00 1.52
3192 3272 3.826157 TCAGGCTCCCATTTGTTTTACAG 59.174 43.478 0.00 0.00 0.00 2.74
3241 3321 2.107378 TGGTTATCCTTGTGCTGGACAA 59.893 45.455 14.10 14.10 42.55 3.18
3245 3325 0.257328 TCCTTGTGCTGGACAACCAA 59.743 50.000 10.84 0.00 46.32 3.67
3256 3336 4.037446 GCTGGACAACCAATAGAACAAACA 59.963 41.667 0.00 0.00 46.32 2.83
3257 3337 5.278957 GCTGGACAACCAATAGAACAAACAT 60.279 40.000 0.00 0.00 46.32 2.71
3269 3349 9.734620 CAATAGAACAAACATCAAACTTTCTCA 57.265 29.630 0.00 0.00 0.00 3.27
3363 3443 0.834687 ACGCCCTTGGACCTTCTACA 60.835 55.000 0.00 0.00 0.00 2.74
3364 3444 0.323629 CGCCCTTGGACCTTCTACAA 59.676 55.000 0.00 0.00 0.00 2.41
3450 3530 6.446318 TGTTTTGGACTCTAATTTGCATGAC 58.554 36.000 0.00 0.00 0.00 3.06
3469 3549 3.500680 TGACTTGAATGAAACTAACCCGC 59.499 43.478 0.00 0.00 0.00 6.13
3522 3602 6.344500 TGGTGTTGTTTATTGTGCAGAAAAT 58.656 32.000 0.00 0.00 0.00 1.82
3561 3642 5.174037 ACCTGAAAATCCACGGAGATAAA 57.826 39.130 0.00 0.00 0.00 1.40
3759 3848 3.810941 AGGAAGTTTCATCGCGTTTTACA 59.189 39.130 5.77 0.00 0.00 2.41
3893 3983 2.424601 CCAATTTCATGATGCTCACCGT 59.575 45.455 0.00 0.00 0.00 4.83
4129 4219 6.611613 TGTGAGTTCTTGATCCTATCTTGT 57.388 37.500 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.841617 ATGAGAGGGCCCGAGCGA 62.842 66.667 18.44 0.27 41.24 4.93
15 16 4.598894 CATGAGAGGGCCCGAGCG 62.599 72.222 18.44 0.00 41.24 5.03
16 17 4.925861 GCATGAGAGGGCCCGAGC 62.926 72.222 18.44 10.44 38.76 5.03
17 18 4.598894 CGCATGAGAGGGCCCGAG 62.599 72.222 18.44 4.92 0.00 4.63
25 26 2.025767 CTCCACCTCCCGCATGAGAG 62.026 65.000 0.00 0.00 34.11 3.20
26 27 2.038813 TCCACCTCCCGCATGAGA 59.961 61.111 0.00 0.00 34.11 3.27
27 28 2.060383 TCTCCACCTCCCGCATGAG 61.060 63.158 0.00 0.00 0.00 2.90
28 29 2.038813 TCTCCACCTCCCGCATGA 59.961 61.111 0.00 0.00 0.00 3.07
29 30 2.187946 GTCTCCACCTCCCGCATG 59.812 66.667 0.00 0.00 0.00 4.06
30 31 2.039624 AGTCTCCACCTCCCGCAT 59.960 61.111 0.00 0.00 0.00 4.73
31 32 2.997315 CAGTCTCCACCTCCCGCA 60.997 66.667 0.00 0.00 0.00 5.69
32 33 3.775654 CCAGTCTCCACCTCCCGC 61.776 72.222 0.00 0.00 0.00 6.13
33 34 3.775654 GCCAGTCTCCACCTCCCG 61.776 72.222 0.00 0.00 0.00 5.14
34 35 2.284995 AGCCAGTCTCCACCTCCC 60.285 66.667 0.00 0.00 0.00 4.30
35 36 1.305718 AGAGCCAGTCTCCACCTCC 60.306 63.158 0.00 0.00 42.90 4.30
36 37 1.896694 CAGAGCCAGTCTCCACCTC 59.103 63.158 0.00 0.00 42.90 3.85
37 38 2.289532 GCAGAGCCAGTCTCCACCT 61.290 63.158 0.00 0.00 42.90 4.00
38 39 2.267324 GCAGAGCCAGTCTCCACC 59.733 66.667 0.00 0.00 42.90 4.61
39 40 1.079266 CTGCAGAGCCAGTCTCCAC 60.079 63.158 8.42 0.00 42.90 4.02
40 41 2.288778 CCTGCAGAGCCAGTCTCCA 61.289 63.158 17.39 0.00 42.90 3.86
41 42 2.583520 CCTGCAGAGCCAGTCTCC 59.416 66.667 17.39 0.00 42.90 3.71
42 43 2.125188 GCCTGCAGAGCCAGTCTC 60.125 66.667 17.39 0.00 42.21 3.36
43 44 4.079850 CGCCTGCAGAGCCAGTCT 62.080 66.667 17.39 0.00 35.00 3.24
72 73 4.514577 CCTCCAGTACCCGCAGCG 62.515 72.222 8.18 8.18 0.00 5.18
73 74 4.840005 GCCTCCAGTACCCGCAGC 62.840 72.222 0.00 0.00 0.00 5.25
74 75 3.376935 CTGCCTCCAGTACCCGCAG 62.377 68.421 0.00 0.00 40.81 5.18
75 76 3.390521 CTGCCTCCAGTACCCGCA 61.391 66.667 0.00 0.00 34.31 5.69
76 77 4.840005 GCTGCCTCCAGTACCCGC 62.840 72.222 0.00 0.00 41.26 6.13
77 78 4.162690 GGCTGCCTCCAGTACCCG 62.163 72.222 12.43 0.00 41.26 5.28
78 79 4.162690 CGGCTGCCTCCAGTACCC 62.163 72.222 17.92 0.00 41.26 3.69
79 80 3.075005 TCGGCTGCCTCCAGTACC 61.075 66.667 17.92 0.00 41.26 3.34
80 81 2.184579 GTCGGCTGCCTCCAGTAC 59.815 66.667 17.92 1.61 41.26 2.73
81 82 3.449227 CGTCGGCTGCCTCCAGTA 61.449 66.667 17.92 0.00 41.26 2.74
100 101 3.520862 GTGCGTCCCATGGCCATG 61.521 66.667 34.82 34.82 38.51 3.66
101 102 4.820744 GGTGCGTCCCATGGCCAT 62.821 66.667 14.09 14.09 0.00 4.40
118 119 0.110823 CTTTTCTTTGACCGACCGCG 60.111 55.000 0.00 0.00 37.24 6.46
119 120 1.223187 TCTTTTCTTTGACCGACCGC 58.777 50.000 0.00 0.00 0.00 5.68
120 121 3.423123 CGATTCTTTTCTTTGACCGACCG 60.423 47.826 0.00 0.00 0.00 4.79
121 122 3.120304 CCGATTCTTTTCTTTGACCGACC 60.120 47.826 0.00 0.00 0.00 4.79
122 123 3.120304 CCCGATTCTTTTCTTTGACCGAC 60.120 47.826 0.00 0.00 0.00 4.79
123 124 3.071479 CCCGATTCTTTTCTTTGACCGA 58.929 45.455 0.00 0.00 0.00 4.69
124 125 2.812011 ACCCGATTCTTTTCTTTGACCG 59.188 45.455 0.00 0.00 0.00 4.79
125 126 4.072839 AGACCCGATTCTTTTCTTTGACC 58.927 43.478 0.00 0.00 0.00 4.02
126 127 4.613850 GCAGACCCGATTCTTTTCTTTGAC 60.614 45.833 0.00 0.00 0.00 3.18
127 128 3.502211 GCAGACCCGATTCTTTTCTTTGA 59.498 43.478 0.00 0.00 0.00 2.69
128 129 3.667960 CGCAGACCCGATTCTTTTCTTTG 60.668 47.826 0.00 0.00 0.00 2.77
129 130 2.484264 CGCAGACCCGATTCTTTTCTTT 59.516 45.455 0.00 0.00 0.00 2.52
130 131 2.076863 CGCAGACCCGATTCTTTTCTT 58.923 47.619 0.00 0.00 0.00 2.52
131 132 1.676014 CCGCAGACCCGATTCTTTTCT 60.676 52.381 0.00 0.00 0.00 2.52
132 133 0.727398 CCGCAGACCCGATTCTTTTC 59.273 55.000 0.00 0.00 0.00 2.29
133 134 1.305930 GCCGCAGACCCGATTCTTTT 61.306 55.000 0.00 0.00 0.00 2.27
134 135 1.745489 GCCGCAGACCCGATTCTTT 60.745 57.895 0.00 0.00 0.00 2.52
135 136 2.125106 GCCGCAGACCCGATTCTT 60.125 61.111 0.00 0.00 0.00 2.52
136 137 4.514577 CGCCGCAGACCCGATTCT 62.515 66.667 0.00 0.00 0.00 2.40
137 138 4.508128 TCGCCGCAGACCCGATTC 62.508 66.667 0.00 0.00 0.00 2.52
138 139 4.077184 TTCGCCGCAGACCCGATT 62.077 61.111 0.00 0.00 0.00 3.34
139 140 4.514577 CTTCGCCGCAGACCCGAT 62.515 66.667 0.00 0.00 0.00 4.18
141 142 4.735132 TTCTTCGCCGCAGACCCG 62.735 66.667 0.00 0.00 0.00 5.28
142 143 2.358247 TTTCTTCGCCGCAGACCC 60.358 61.111 0.00 0.00 0.00 4.46
143 144 0.949105 TTCTTTCTTCGCCGCAGACC 60.949 55.000 0.00 0.00 0.00 3.85
144 145 0.440371 CTTCTTTCTTCGCCGCAGAC 59.560 55.000 0.00 0.00 0.00 3.51
145 146 0.317160 TCTTCTTTCTTCGCCGCAGA 59.683 50.000 0.00 0.00 0.00 4.26
146 147 1.127582 CTTCTTCTTTCTTCGCCGCAG 59.872 52.381 0.00 0.00 0.00 5.18
147 148 1.148310 CTTCTTCTTTCTTCGCCGCA 58.852 50.000 0.00 0.00 0.00 5.69
148 149 0.444260 CCTTCTTCTTTCTTCGCCGC 59.556 55.000 0.00 0.00 0.00 6.53
149 150 2.080286 TCCTTCTTCTTTCTTCGCCG 57.920 50.000 0.00 0.00 0.00 6.46
150 151 3.665190 TCTTCCTTCTTCTTTCTTCGCC 58.335 45.455 0.00 0.00 0.00 5.54
151 152 4.561105 TCTCTTCCTTCTTCTTTCTTCGC 58.439 43.478 0.00 0.00 0.00 4.70
152 153 5.637387 CCTTCTCTTCCTTCTTCTTTCTTCG 59.363 44.000 0.00 0.00 0.00 3.79
153 154 5.937540 CCCTTCTCTTCCTTCTTCTTTCTTC 59.062 44.000 0.00 0.00 0.00 2.87
154 155 5.222027 CCCCTTCTCTTCCTTCTTCTTTCTT 60.222 44.000 0.00 0.00 0.00 2.52
155 156 4.288366 CCCCTTCTCTTCCTTCTTCTTTCT 59.712 45.833 0.00 0.00 0.00 2.52
156 157 4.287326 TCCCCTTCTCTTCCTTCTTCTTTC 59.713 45.833 0.00 0.00 0.00 2.62
157 158 4.243643 TCCCCTTCTCTTCCTTCTTCTTT 58.756 43.478 0.00 0.00 0.00 2.52
158 159 3.843619 CTCCCCTTCTCTTCCTTCTTCTT 59.156 47.826 0.00 0.00 0.00 2.52
159 160 3.449918 CTCCCCTTCTCTTCCTTCTTCT 58.550 50.000 0.00 0.00 0.00 2.85
160 161 2.503765 CCTCCCCTTCTCTTCCTTCTTC 59.496 54.545 0.00 0.00 0.00 2.87
161 162 2.114506 TCCTCCCCTTCTCTTCCTTCTT 59.885 50.000 0.00 0.00 0.00 2.52
162 163 1.725182 TCCTCCCCTTCTCTTCCTTCT 59.275 52.381 0.00 0.00 0.00 2.85
163 164 2.115427 CTCCTCCCCTTCTCTTCCTTC 58.885 57.143 0.00 0.00 0.00 3.46
164 165 1.903955 GCTCCTCCCCTTCTCTTCCTT 60.904 57.143 0.00 0.00 0.00 3.36
165 166 0.326143 GCTCCTCCCCTTCTCTTCCT 60.326 60.000 0.00 0.00 0.00 3.36
166 167 1.341913 GGCTCCTCCCCTTCTCTTCC 61.342 65.000 0.00 0.00 0.00 3.46
167 168 1.681486 CGGCTCCTCCCCTTCTCTTC 61.681 65.000 0.00 0.00 0.00 2.87
168 169 1.687493 CGGCTCCTCCCCTTCTCTT 60.687 63.158 0.00 0.00 0.00 2.85
169 170 2.042435 CGGCTCCTCCCCTTCTCT 60.042 66.667 0.00 0.00 0.00 3.10
170 171 2.042843 TCGGCTCCTCCCCTTCTC 60.043 66.667 0.00 0.00 0.00 2.87
171 172 2.042435 CTCGGCTCCTCCCCTTCT 60.042 66.667 0.00 0.00 0.00 2.85
172 173 3.157949 CCTCGGCTCCTCCCCTTC 61.158 72.222 0.00 0.00 0.00 3.46
173 174 3.684628 TCCTCGGCTCCTCCCCTT 61.685 66.667 0.00 0.00 0.00 3.95
174 175 4.150454 CTCCTCGGCTCCTCCCCT 62.150 72.222 0.00 0.00 0.00 4.79
176 177 4.144727 TCCTCCTCGGCTCCTCCC 62.145 72.222 0.00 0.00 0.00 4.30
177 178 2.835895 GTCCTCCTCGGCTCCTCC 60.836 72.222 0.00 0.00 0.00 4.30
178 179 2.043852 TGTCCTCCTCGGCTCCTC 60.044 66.667 0.00 0.00 0.00 3.71
179 180 2.363147 GTGTCCTCCTCGGCTCCT 60.363 66.667 0.00 0.00 0.00 3.69
180 181 3.827898 CGTGTCCTCCTCGGCTCC 61.828 72.222 0.00 0.00 0.00 4.70
181 182 4.500116 GCGTGTCCTCCTCGGCTC 62.500 72.222 0.00 0.00 0.00 4.70
199 200 3.876589 TTCTGGAACCGACCGCAGC 62.877 63.158 0.00 0.00 0.00 5.25
200 201 0.882927 TTTTCTGGAACCGACCGCAG 60.883 55.000 0.00 0.00 0.00 5.18
201 202 0.464013 TTTTTCTGGAACCGACCGCA 60.464 50.000 0.00 0.00 0.00 5.69
202 203 2.323213 TTTTTCTGGAACCGACCGC 58.677 52.632 0.00 0.00 0.00 5.68
218 219 2.272447 CGGTCGGCCCACCATTTTT 61.272 57.895 20.40 0.00 36.01 1.94
219 220 2.675075 CGGTCGGCCCACCATTTT 60.675 61.111 20.40 0.00 36.01 1.82
220 221 3.198953 TTCGGTCGGCCCACCATTT 62.199 57.895 20.40 0.00 36.01 2.32
221 222 3.622060 CTTCGGTCGGCCCACCATT 62.622 63.158 20.40 0.00 36.01 3.16
222 223 4.096003 CTTCGGTCGGCCCACCAT 62.096 66.667 20.40 0.00 36.01 3.55
224 225 3.540367 TTTCTTCGGTCGGCCCACC 62.540 63.158 9.94 9.94 0.00 4.61
225 226 2.031465 TTTCTTCGGTCGGCCCAC 59.969 61.111 0.00 0.00 0.00 4.61
226 227 2.031465 GTTTCTTCGGTCGGCCCA 59.969 61.111 0.00 0.00 0.00 5.36
227 228 1.598685 TTGTTTCTTCGGTCGGCCC 60.599 57.895 0.00 0.00 0.00 5.80
228 229 1.572941 GTTGTTTCTTCGGTCGGCC 59.427 57.895 0.00 0.00 0.00 6.13
229 230 1.572941 GGTTGTTTCTTCGGTCGGC 59.427 57.895 0.00 0.00 0.00 5.54
230 231 0.533308 TGGGTTGTTTCTTCGGTCGG 60.533 55.000 0.00 0.00 0.00 4.79
231 232 1.263217 CTTGGGTTGTTTCTTCGGTCG 59.737 52.381 0.00 0.00 0.00 4.79
232 233 1.001706 GCTTGGGTTGTTTCTTCGGTC 60.002 52.381 0.00 0.00 0.00 4.79
233 234 1.029681 GCTTGGGTTGTTTCTTCGGT 58.970 50.000 0.00 0.00 0.00 4.69
234 235 0.040425 CGCTTGGGTTGTTTCTTCGG 60.040 55.000 0.00 0.00 0.00 4.30
235 236 0.660300 GCGCTTGGGTTGTTTCTTCG 60.660 55.000 0.00 0.00 0.00 3.79
236 237 0.318699 GGCGCTTGGGTTGTTTCTTC 60.319 55.000 7.64 0.00 0.00 2.87
237 238 1.040339 TGGCGCTTGGGTTGTTTCTT 61.040 50.000 7.64 0.00 0.00 2.52
238 239 1.454847 TGGCGCTTGGGTTGTTTCT 60.455 52.632 7.64 0.00 0.00 2.52
239 240 1.007387 CTGGCGCTTGGGTTGTTTC 60.007 57.895 7.64 0.00 0.00 2.78
240 241 2.498056 CCTGGCGCTTGGGTTGTTT 61.498 57.895 7.64 0.00 0.00 2.83
241 242 2.912025 CCTGGCGCTTGGGTTGTT 60.912 61.111 7.64 0.00 0.00 2.83
242 243 3.850098 CTCCTGGCGCTTGGGTTGT 62.850 63.158 7.64 0.00 0.00 3.32
243 244 3.058160 CTCCTGGCGCTTGGGTTG 61.058 66.667 7.64 0.98 0.00 3.77
244 245 3.570212 ACTCCTGGCGCTTGGGTT 61.570 61.111 7.64 0.00 0.00 4.11
245 246 4.335647 CACTCCTGGCGCTTGGGT 62.336 66.667 7.64 7.35 0.00 4.51
246 247 4.335647 ACACTCCTGGCGCTTGGG 62.336 66.667 7.64 7.46 0.00 4.12
247 248 3.052082 CACACTCCTGGCGCTTGG 61.052 66.667 7.64 10.29 0.00 3.61
248 249 2.281070 ACACACTCCTGGCGCTTG 60.281 61.111 7.64 0.00 0.00 4.01
249 250 2.281070 CACACACTCCTGGCGCTT 60.281 61.111 7.64 0.00 0.00 4.68
250 251 4.996434 GCACACACTCCTGGCGCT 62.996 66.667 7.64 0.00 0.00 5.92
258 259 3.276846 AAACCGGCGCACACACTC 61.277 61.111 10.83 0.00 0.00 3.51
259 260 3.582120 CAAACCGGCGCACACACT 61.582 61.111 10.83 0.00 0.00 3.55
262 263 2.780149 CTTAGCAAACCGGCGCACAC 62.780 60.000 10.83 0.00 39.27 3.82
263 264 2.592001 TTAGCAAACCGGCGCACA 60.592 55.556 10.83 0.00 39.27 4.57
264 265 2.175811 CTTAGCAAACCGGCGCAC 59.824 61.111 10.83 0.00 39.27 5.34
265 266 2.813226 ATCCTTAGCAAACCGGCGCA 62.813 55.000 10.83 0.00 39.27 6.09
266 267 2.112815 ATCCTTAGCAAACCGGCGC 61.113 57.895 0.00 0.00 39.27 6.53
267 268 1.024579 ACATCCTTAGCAAACCGGCG 61.025 55.000 0.00 0.00 39.27 6.46
268 269 0.451783 CACATCCTTAGCAAACCGGC 59.548 55.000 0.00 0.00 0.00 6.13
269 270 1.821216 ACACATCCTTAGCAAACCGG 58.179 50.000 0.00 0.00 0.00 5.28
270 271 3.564511 CAAACACATCCTTAGCAAACCG 58.435 45.455 0.00 0.00 0.00 4.44
271 272 3.320826 ACCAAACACATCCTTAGCAAACC 59.679 43.478 0.00 0.00 0.00 3.27
272 273 4.584327 ACCAAACACATCCTTAGCAAAC 57.416 40.909 0.00 0.00 0.00 2.93
273 274 4.646945 TGAACCAAACACATCCTTAGCAAA 59.353 37.500 0.00 0.00 0.00 3.68
274 275 4.211125 TGAACCAAACACATCCTTAGCAA 58.789 39.130 0.00 0.00 0.00 3.91
275 276 3.826524 TGAACCAAACACATCCTTAGCA 58.173 40.909 0.00 0.00 0.00 3.49
276 277 4.846779 TTGAACCAAACACATCCTTAGC 57.153 40.909 0.00 0.00 0.00 3.09
277 278 6.633500 TCTTTGAACCAAACACATCCTTAG 57.367 37.500 0.00 0.00 0.00 2.18
298 299 2.324541 CTAGCCACCCTAGCATCTTCT 58.675 52.381 0.00 0.00 37.34 2.85
300 301 1.428869 CCTAGCCACCCTAGCATCTT 58.571 55.000 0.00 0.00 41.87 2.40
400 402 9.965902 CTATCCTAACCATGCTTTATCCTTTAT 57.034 33.333 0.00 0.00 0.00 1.40
402 404 6.717084 GCTATCCTAACCATGCTTTATCCTTT 59.283 38.462 0.00 0.00 0.00 3.11
477 479 6.795590 TCCCCAAAATACTGGTTCTTTGATA 58.204 36.000 8.04 0.00 34.33 2.15
761 772 0.957395 GCTGAGCTGCAACCTAGCAA 60.957 55.000 1.02 0.00 45.13 3.91
844 855 1.893786 GCGGCGATATGGATCTCCT 59.106 57.895 12.98 0.00 35.15 3.69
856 867 4.854784 GAGATCAGTGCGCGGCGA 62.855 66.667 28.54 8.58 0.00 5.54
1377 1391 0.395862 CGGGAGTAGGAGGAGAGCAA 60.396 60.000 0.00 0.00 0.00 3.91
1419 1433 1.993370 CATTTCGTCGAGGAGTTGGTC 59.007 52.381 7.98 0.00 0.00 4.02
1528 1542 4.083862 GGCGGAAGAGGGCGAAGT 62.084 66.667 0.00 0.00 0.00 3.01
1577 1597 2.125912 AGCGTCATGAGCGTGACC 60.126 61.111 15.13 9.29 44.37 4.02
1628 1681 3.723348 GCCACGTTTGTCTCGGCC 61.723 66.667 0.00 0.00 36.73 6.13
1781 1834 1.519455 GAGATCAAGGGCGTCCACG 60.519 63.158 9.71 0.00 43.27 4.94
1853 1906 4.803426 GAGAGCACGCCCACGAGG 62.803 72.222 0.00 0.00 43.93 4.63
2030 2083 3.939740 ATGCTCTTCCTAGGCATTTCA 57.060 42.857 2.96 0.00 43.02 2.69
2100 2153 5.416952 CCTGGAAGAGATTTACAGCAACATT 59.583 40.000 0.00 0.00 34.07 2.71
2482 2535 5.303333 TGTCCTGTGTCTGTGTATAAGTTCA 59.697 40.000 0.00 0.00 0.00 3.18
2487 2540 4.345547 TGGTTGTCCTGTGTCTGTGTATAA 59.654 41.667 0.00 0.00 34.23 0.98
2510 2563 1.975327 CACCCTCACGACACCATCT 59.025 57.895 0.00 0.00 0.00 2.90
2533 2586 4.240103 CCGCGCCCCTCATCATCA 62.240 66.667 0.00 0.00 0.00 3.07
2593 2647 6.183360 CGTCAGCCATGAATAAATGAACTCTT 60.183 38.462 0.00 0.00 37.14 2.85
2603 2657 2.236146 AGTGGTCGTCAGCCATGAATAA 59.764 45.455 0.00 0.00 37.14 1.40
2605 2659 0.615331 AGTGGTCGTCAGCCATGAAT 59.385 50.000 0.00 0.00 37.14 2.57
2641 2695 6.183360 GCTTAATCACAAGCTCGTAAATCCTT 60.183 38.462 0.70 0.00 46.04 3.36
2678 2732 3.760684 GTGCCATCTGTTTTCTCCTTCAT 59.239 43.478 0.00 0.00 0.00 2.57
2702 2756 1.123077 TTGCCTCGCTCCATATCTGT 58.877 50.000 0.00 0.00 0.00 3.41
2707 2761 0.107703 CCACTTTGCCTCGCTCCATA 60.108 55.000 0.00 0.00 0.00 2.74
2712 2766 2.357517 CGTCCACTTTGCCTCGCT 60.358 61.111 0.00 0.00 0.00 4.93
2715 2769 1.376037 CCCTCGTCCACTTTGCCTC 60.376 63.158 0.00 0.00 0.00 4.70
2721 2775 2.526873 AGTGCCCCTCGTCCACTT 60.527 61.111 0.00 0.00 36.48 3.16
2735 2789 1.401931 CGCAGCCATTTTCTTGGAGTG 60.402 52.381 0.00 0.00 39.25 3.51
2804 2858 6.487668 ACAATCTCAATGTCATCAGTGTTCAA 59.512 34.615 0.00 0.00 40.07 2.69
2857 2918 5.109500 CCTTTAGGAAAGAGAGGCAATCT 57.891 43.478 0.47 0.00 41.02 2.40
2865 2928 2.537143 AGACCGCCTTTAGGAAAGAGA 58.463 47.619 0.00 0.00 41.02 3.10
2875 2938 1.873486 GCAATTGCAAAGACCGCCTTT 60.873 47.619 25.36 0.00 45.48 3.11
2886 2949 2.739784 CCCGGTTGGCAATTGCAA 59.260 55.556 30.32 18.83 44.36 4.08
2938 3001 0.036732 AGCATGCTCCACCTTCGAAA 59.963 50.000 16.30 0.00 0.00 3.46
2966 3029 7.446931 TGAGCACCAAATTCTTCACAAATAGTA 59.553 33.333 0.00 0.00 0.00 1.82
2971 3034 4.998671 TGAGCACCAAATTCTTCACAAA 57.001 36.364 0.00 0.00 0.00 2.83
2973 3036 4.341806 ACAATGAGCACCAAATTCTTCACA 59.658 37.500 0.00 0.00 0.00 3.58
2993 3056 4.935808 GCGAATTCTTCCTTCTCCTAACAA 59.064 41.667 3.52 0.00 0.00 2.83
3011 3075 2.741228 GCACTGAAGATCTGGAGCGAAT 60.741 50.000 0.00 0.00 0.00 3.34
3015 3079 1.206610 TGAGCACTGAAGATCTGGAGC 59.793 52.381 0.00 0.54 0.00 4.70
3039 3103 0.460284 CATAGTCACCACGCCTGTCC 60.460 60.000 0.00 0.00 0.00 4.02
3040 3104 1.084370 GCATAGTCACCACGCCTGTC 61.084 60.000 0.00 0.00 0.00 3.51
3090 3170 1.210204 AGGCCCTGCTCTTGATCCAA 61.210 55.000 0.00 0.00 0.00 3.53
3099 3179 0.107643 GAGTCCATTAGGCCCTGCTC 59.892 60.000 0.00 0.00 33.74 4.26
3103 3183 0.541863 CAACGAGTCCATTAGGCCCT 59.458 55.000 0.00 0.00 33.74 5.19
3106 3186 3.195661 CCTAACAACGAGTCCATTAGGC 58.804 50.000 0.00 0.00 36.49 3.93
3107 3187 4.467198 ACCTAACAACGAGTCCATTAGG 57.533 45.455 13.86 13.86 44.99 2.69
3108 3188 5.347907 GTCAACCTAACAACGAGTCCATTAG 59.652 44.000 0.00 0.00 0.00 1.73
3109 3189 5.232463 GTCAACCTAACAACGAGTCCATTA 58.768 41.667 0.00 0.00 0.00 1.90
3120 3200 4.897076 TGAGAGTACTGGTCAACCTAACAA 59.103 41.667 0.00 0.00 36.82 2.83
3152 3232 4.478206 CTGATCTTCAGGGAGTTAAGCA 57.522 45.455 0.00 0.00 40.71 3.91
3163 3243 2.950309 CAAATGGGAGCCTGATCTTCAG 59.050 50.000 0.00 0.00 43.91 3.02
3164 3244 2.309755 ACAAATGGGAGCCTGATCTTCA 59.690 45.455 0.00 0.00 0.00 3.02
3165 3245 3.010200 ACAAATGGGAGCCTGATCTTC 57.990 47.619 0.00 0.00 0.00 2.87
3166 3246 3.463048 AACAAATGGGAGCCTGATCTT 57.537 42.857 0.00 0.00 0.00 2.40
3167 3247 3.463048 AAACAAATGGGAGCCTGATCT 57.537 42.857 0.00 0.00 0.00 2.75
3168 3248 4.462483 TGTAAAACAAATGGGAGCCTGATC 59.538 41.667 0.00 0.00 0.00 2.92
3169 3249 4.415596 TGTAAAACAAATGGGAGCCTGAT 58.584 39.130 0.00 0.00 0.00 2.90
3170 3250 3.826157 CTGTAAAACAAATGGGAGCCTGA 59.174 43.478 0.00 0.00 0.00 3.86
3230 3310 3.146066 GTTCTATTGGTTGTCCAGCACA 58.854 45.455 0.00 0.00 45.22 4.57
3241 3321 8.695456 AGAAAGTTTGATGTTTGTTCTATTGGT 58.305 29.630 0.00 0.00 0.00 3.67
3245 3325 9.956720 CTTGAGAAAGTTTGATGTTTGTTCTAT 57.043 29.630 0.00 0.00 0.00 1.98
3256 3336 3.638160 TGCAAGCCTTGAGAAAGTTTGAT 59.362 39.130 9.04 0.00 0.00 2.57
3257 3337 3.023119 TGCAAGCCTTGAGAAAGTTTGA 58.977 40.909 9.04 0.00 0.00 2.69
3269 3349 2.573462 TCAGGAGTAGAATGCAAGCCTT 59.427 45.455 0.00 0.00 0.00 4.35
3363 3443 2.381961 TCAAGGGCCAGGTAATTCCTTT 59.618 45.455 6.18 0.00 45.67 3.11
3364 3444 2.000048 TCAAGGGCCAGGTAATTCCTT 59.000 47.619 6.18 0.00 45.67 3.36
3375 3455 0.616395 TGGAGACGTATCAAGGGCCA 60.616 55.000 12.92 0.00 0.00 5.36
3450 3530 3.502211 AGTGCGGGTTAGTTTCATTCAAG 59.498 43.478 0.00 0.00 0.00 3.02
3469 3549 3.444657 GCTGAAAACAGCGTCAGTG 57.555 52.632 6.46 0.00 42.72 3.66
3522 3602 8.746052 TTTTCAGGTCATTCTGAGAACTTTTA 57.254 30.769 0.00 0.00 43.64 1.52
3586 3667 0.040204 CCCTGGCCCTCATCTTTTGT 59.960 55.000 0.00 0.00 0.00 2.83
3759 3848 3.414136 TTGGCGGCGGCTCCATATT 62.414 57.895 33.21 0.00 39.81 1.28
3893 3983 2.536365 GATGGAATTACTCACGCACGA 58.464 47.619 0.00 0.00 0.00 4.35
3985 4075 5.394738 TCAGAACATAGTGGATACTAGGGG 58.605 45.833 0.00 0.00 43.56 4.79


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

AutoCloner maintained by Alex Coulton.