Multiple sequence alignment - TraesCS4B01G182500

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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 TraesCS4B01G182500 chr4B 100.000 3765 0 0 1 3765 400396195 400399959 0.000000e+00 6953.0
1 TraesCS4B01G182500 chr4A 89.318 2743 120 80 326 2985 152649348 152652000 0.000000e+00 3282.0
2 TraesCS4B01G182500 chr4A 97.065 511 13 1 3257 3765 152738564 152739074 0.000000e+00 859.0
3 TraesCS4B01G182500 chr4A 92.825 223 15 1 3 224 724639792 724640014 4.690000e-84 322.0
4 TraesCS4B01G182500 chr4A 95.294 85 4 0 224 308 152649202 152649286 6.560000e-28 135.0
5 TraesCS4B01G182500 chr1B 94.267 1814 73 17 980 2772 638034429 638036232 0.000000e+00 2745.0
6 TraesCS4B01G182500 chr1B 91.143 350 21 5 552 901 638034045 638034384 2.050000e-127 466.0
7 TraesCS4B01G182500 chr1B 92.694 219 16 0 1 219 262921665 262921883 2.180000e-82 316.0
8 TraesCS4B01G182500 chr1B 92.694 219 16 0 3 221 540184170 540183952 2.180000e-82 316.0
9 TraesCS4B01G182500 chr1B 87.912 91 7 3 2818 2908 638043157 638043243 1.850000e-18 104.0
10 TraesCS4B01G182500 chr4D 89.764 2120 75 60 858 2911 320213123 320211080 0.000000e+00 2582.0
11 TraesCS4B01G182500 chr4D 97.358 492 5 2 3282 3765 320210672 320210181 0.000000e+00 830.0
12 TraesCS4B01G182500 chr4D 93.590 546 22 5 326 867 320214834 320214298 0.000000e+00 802.0
13 TraesCS4B01G182500 chr4D 93.855 179 10 1 2921 3098 320211035 320210857 6.200000e-68 268.0
14 TraesCS4B01G182500 chr4D 94.521 73 4 0 3114 3186 320210772 320210700 3.070000e-21 113.0
15 TraesCS4B01G182500 chr1D 93.548 217 14 0 3 219 465541461 465541245 1.300000e-84 324.0
16 TraesCS4B01G182500 chr7B 93.151 219 15 0 1 219 705437767 705437549 4.690000e-84 322.0
17 TraesCS4B01G182500 chr7B 93.088 217 15 0 3 219 139160095 139160311 6.070000e-83 318.0
18 TraesCS4B01G182500 chr7B 92.694 219 16 0 3 221 518193623 518193841 2.180000e-82 316.0
19 TraesCS4B01G182500 chr6D 92.694 219 16 0 3 221 386833212 386832994 2.180000e-82 316.0
20 TraesCS4B01G182500 chr5B 92.661 218 16 0 3 220 323368835 323369052 7.850000e-82 315.0
21 TraesCS4B01G182500 chr7D 93.333 45 3 0 1386 1430 144147703 144147659 2.430000e-07 67.6
22 TraesCS4B01G182500 chr7A 91.667 48 4 0 1383 1430 145462193 145462240 2.430000e-07 67.6


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 TraesCS4B01G182500 chr4B 400396195 400399959 3764 False 6953.0 6953 100.0000 1 3765 1 chr4B.!!$F1 3764
1 TraesCS4B01G182500 chr4A 152649202 152652000 2798 False 1708.5 3282 92.3060 224 2985 2 chr4A.!!$F3 2761
2 TraesCS4B01G182500 chr4A 152738564 152739074 510 False 859.0 859 97.0650 3257 3765 1 chr4A.!!$F1 508
3 TraesCS4B01G182500 chr1B 638034045 638036232 2187 False 1605.5 2745 92.7050 552 2772 2 chr1B.!!$F3 2220
4 TraesCS4B01G182500 chr4D 320210181 320214834 4653 True 919.0 2582 93.8176 326 3765 5 chr4D.!!$R1 3439

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
33 34 0.034198 GGGAGAGAAGATAAGCGGGC 59.966 60.0 0.00 0.00 0.00 6.13 F
245 246 0.093705 GATTTATCGCGGCGCATCTC 59.906 55.0 32.61 14.51 0.00 2.75 F
324 335 0.174389 GTGGCAGCGATCTCTCAAGA 59.826 55.0 0.00 0.00 35.54 3.02 F
1729 3023 0.179004 TTTTTCCCCTTGAGCGCTCA 60.179 50.0 35.30 35.30 37.91 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 2775 1.736696 CGGGGCATGTTGATGAAAAGC 60.737 52.381 0.00 0.0 0.00 3.51 R
2183 3487 1.068474 CGTTCACCACCACGATCTTC 58.932 55.000 0.00 0.0 38.76 2.87 R
2417 3721 5.710513 ATATTATGGTACCGTGCGACTTA 57.289 39.130 17.34 0.0 0.00 2.24 R
3156 4621 0.322098 TGATAAGGTTGGTGGCGTGG 60.322 55.000 0.00 0.0 0.00 4.94 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
30 31 3.828875 AAAGGGGAGAGAAGATAAGCG 57.171 47.619 0.00 0.00 0.00 4.68
31 32 1.710816 AGGGGAGAGAAGATAAGCGG 58.289 55.000 0.00 0.00 0.00 5.52
32 33 0.682292 GGGGAGAGAAGATAAGCGGG 59.318 60.000 0.00 0.00 0.00 6.13
33 34 0.034198 GGGAGAGAAGATAAGCGGGC 59.966 60.000 0.00 0.00 0.00 6.13
34 35 1.044611 GGAGAGAAGATAAGCGGGCT 58.955 55.000 0.00 0.00 0.00 5.19
35 36 1.000394 GGAGAGAAGATAAGCGGGCTC 60.000 57.143 0.00 0.00 0.00 4.70
36 37 1.960689 GAGAGAAGATAAGCGGGCTCT 59.039 52.381 0.00 0.00 35.59 4.09
37 38 2.364002 GAGAGAAGATAAGCGGGCTCTT 59.636 50.000 0.00 0.00 33.26 2.85
38 39 2.364002 AGAGAAGATAAGCGGGCTCTTC 59.636 50.000 11.19 11.19 43.30 2.87
39 40 1.067821 AGAAGATAAGCGGGCTCTTCG 59.932 52.381 12.57 0.00 46.06 3.79
40 41 0.824759 AAGATAAGCGGGCTCTTCGT 59.175 50.000 0.00 0.00 0.00 3.85
41 42 0.103208 AGATAAGCGGGCTCTTCGTG 59.897 55.000 0.00 0.00 0.00 4.35
42 43 0.102481 GATAAGCGGGCTCTTCGTGA 59.898 55.000 0.00 0.00 0.00 4.35
43 44 0.535335 ATAAGCGGGCTCTTCGTGAA 59.465 50.000 0.00 0.00 0.00 3.18
44 45 0.108804 TAAGCGGGCTCTTCGTGAAG 60.109 55.000 3.17 3.17 39.71 3.02
45 46 1.816863 AAGCGGGCTCTTCGTGAAGA 61.817 55.000 11.54 11.54 44.47 2.87
46 47 1.374252 GCGGGCTCTTCGTGAAGAA 60.374 57.895 12.94 0.00 45.75 2.52
47 48 1.627550 GCGGGCTCTTCGTGAAGAAC 61.628 60.000 12.94 8.80 45.75 3.01
51 52 0.793250 GCTCTTCGTGAAGAACCAGC 59.207 55.000 12.94 9.21 45.75 4.85
52 53 1.606737 GCTCTTCGTGAAGAACCAGCT 60.607 52.381 12.94 0.00 45.75 4.24
53 54 2.333014 CTCTTCGTGAAGAACCAGCTC 58.667 52.381 12.94 0.00 45.75 4.09
54 55 1.964223 TCTTCGTGAAGAACCAGCTCT 59.036 47.619 9.78 0.00 43.79 4.09
55 56 3.154710 TCTTCGTGAAGAACCAGCTCTA 58.845 45.455 9.78 0.00 43.79 2.43
56 57 3.191581 TCTTCGTGAAGAACCAGCTCTAG 59.808 47.826 9.78 0.00 43.79 2.43
57 58 1.202582 TCGTGAAGAACCAGCTCTAGC 59.797 52.381 0.00 0.00 42.49 3.42
58 59 1.067565 CGTGAAGAACCAGCTCTAGCA 60.068 52.381 4.54 0.00 45.16 3.49
59 60 2.342179 GTGAAGAACCAGCTCTAGCAC 58.658 52.381 4.54 0.00 45.16 4.40
60 61 1.067565 TGAAGAACCAGCTCTAGCACG 60.068 52.381 4.54 0.00 45.16 5.34
61 62 0.969894 AAGAACCAGCTCTAGCACGT 59.030 50.000 4.54 0.00 45.16 4.49
62 63 0.244994 AGAACCAGCTCTAGCACGTG 59.755 55.000 12.28 12.28 45.16 4.49
63 64 1.355066 GAACCAGCTCTAGCACGTGC 61.355 60.000 32.79 32.79 45.16 5.34
81 82 3.827008 TGCTCCTAGGCACTTTATGAG 57.173 47.619 2.96 0.00 41.75 2.90
82 83 3.374764 TGCTCCTAGGCACTTTATGAGA 58.625 45.455 2.96 0.00 41.75 3.27
83 84 3.774766 TGCTCCTAGGCACTTTATGAGAA 59.225 43.478 2.96 0.00 41.75 2.87
84 85 4.410228 TGCTCCTAGGCACTTTATGAGAAT 59.590 41.667 2.96 0.00 41.75 2.40
85 86 4.754114 GCTCCTAGGCACTTTATGAGAATG 59.246 45.833 2.96 0.00 41.75 2.67
86 87 5.453903 GCTCCTAGGCACTTTATGAGAATGA 60.454 44.000 2.96 0.00 41.75 2.57
87 88 6.560003 TCCTAGGCACTTTATGAGAATGAA 57.440 37.500 2.96 0.00 41.75 2.57
88 89 6.957631 TCCTAGGCACTTTATGAGAATGAAA 58.042 36.000 2.96 0.00 41.75 2.69
89 90 7.050377 TCCTAGGCACTTTATGAGAATGAAAG 58.950 38.462 2.96 0.00 41.75 2.62
90 91 6.261826 CCTAGGCACTTTATGAGAATGAAAGG 59.738 42.308 0.00 0.00 41.75 3.11
91 92 5.574188 AGGCACTTTATGAGAATGAAAGGT 58.426 37.500 0.00 0.00 27.25 3.50
92 93 5.416952 AGGCACTTTATGAGAATGAAAGGTG 59.583 40.000 0.00 0.00 27.25 4.00
93 94 5.393461 GGCACTTTATGAGAATGAAAGGTGG 60.393 44.000 0.00 0.00 0.00 4.61
94 95 5.393461 GCACTTTATGAGAATGAAAGGTGGG 60.393 44.000 0.00 0.00 0.00 4.61
95 96 4.706962 ACTTTATGAGAATGAAAGGTGGGC 59.293 41.667 0.00 0.00 0.00 5.36
96 97 2.149973 ATGAGAATGAAAGGTGGGCC 57.850 50.000 0.00 0.00 0.00 5.80
97 98 0.322456 TGAGAATGAAAGGTGGGCCG 60.322 55.000 0.00 0.00 40.50 6.13
98 99 0.322546 GAGAATGAAAGGTGGGCCGT 60.323 55.000 0.00 0.00 40.50 5.68
99 100 0.988832 AGAATGAAAGGTGGGCCGTA 59.011 50.000 0.00 0.00 40.50 4.02
100 101 1.564348 AGAATGAAAGGTGGGCCGTAT 59.436 47.619 0.00 0.00 40.50 3.06
101 102 2.775384 AGAATGAAAGGTGGGCCGTATA 59.225 45.455 0.00 0.00 40.50 1.47
102 103 3.201266 AGAATGAAAGGTGGGCCGTATAA 59.799 43.478 0.00 0.00 40.50 0.98
103 104 3.876309 ATGAAAGGTGGGCCGTATAAT 57.124 42.857 0.00 0.00 40.50 1.28
104 105 4.986054 ATGAAAGGTGGGCCGTATAATA 57.014 40.909 0.00 0.00 40.50 0.98
105 106 4.774660 TGAAAGGTGGGCCGTATAATAA 57.225 40.909 0.00 0.00 40.50 1.40
106 107 5.113446 TGAAAGGTGGGCCGTATAATAAA 57.887 39.130 0.00 0.00 40.50 1.40
107 108 5.507637 TGAAAGGTGGGCCGTATAATAAAA 58.492 37.500 0.00 0.00 40.50 1.52
108 109 5.950549 TGAAAGGTGGGCCGTATAATAAAAA 59.049 36.000 0.00 0.00 40.50 1.94
167 168 8.918116 TCTTAGCTATAAGATGGGCTGTATATG 58.082 37.037 0.00 0.00 41.98 1.78
168 169 8.838649 TTAGCTATAAGATGGGCTGTATATGA 57.161 34.615 0.00 0.00 36.40 2.15
169 170 7.118496 AGCTATAAGATGGGCTGTATATGAC 57.882 40.000 0.00 0.00 33.50 3.06
170 171 6.669591 AGCTATAAGATGGGCTGTATATGACA 59.330 38.462 0.00 0.00 36.35 3.58
171 172 7.346698 AGCTATAAGATGGGCTGTATATGACAT 59.653 37.037 0.00 0.00 37.45 3.06
172 173 7.440556 GCTATAAGATGGGCTGTATATGACATG 59.559 40.741 0.00 0.00 37.45 3.21
173 174 4.564782 AGATGGGCTGTATATGACATGG 57.435 45.455 0.00 0.00 37.45 3.66
174 175 2.566833 TGGGCTGTATATGACATGGC 57.433 50.000 0.00 0.00 37.45 4.40
175 176 1.773653 TGGGCTGTATATGACATGGCA 59.226 47.619 2.18 2.18 37.45 4.92
176 177 2.154462 GGGCTGTATATGACATGGCAC 58.846 52.381 1.45 0.00 37.45 5.01
177 178 2.224621 GGGCTGTATATGACATGGCACT 60.225 50.000 1.45 0.00 37.45 4.40
178 179 2.810274 GGCTGTATATGACATGGCACTG 59.190 50.000 1.45 0.00 37.45 3.66
179 180 2.810274 GCTGTATATGACATGGCACTGG 59.190 50.000 1.45 0.00 37.45 4.00
180 181 2.810274 CTGTATATGACATGGCACTGGC 59.190 50.000 1.45 0.00 37.45 4.85
181 182 2.439135 TGTATATGACATGGCACTGGCT 59.561 45.455 1.45 0.00 34.71 4.75
182 183 2.742428 ATATGACATGGCACTGGCTT 57.258 45.000 1.45 0.00 40.87 4.35
183 184 3.862877 ATATGACATGGCACTGGCTTA 57.137 42.857 1.45 0.00 40.87 3.09
184 185 2.742428 ATGACATGGCACTGGCTTAT 57.258 45.000 1.45 0.00 40.87 1.73
185 186 3.862877 ATGACATGGCACTGGCTTATA 57.137 42.857 1.45 0.00 40.87 0.98
186 187 3.198409 TGACATGGCACTGGCTTATAG 57.802 47.619 0.00 0.00 40.87 1.31
187 188 1.876156 GACATGGCACTGGCTTATAGC 59.124 52.381 3.97 0.00 41.46 2.97
196 197 3.647824 GCTTATAGCCAGCAGCCG 58.352 61.111 0.00 0.00 45.47 5.52
197 198 1.963338 GCTTATAGCCAGCAGCCGG 60.963 63.158 0.00 0.00 45.47 6.13
211 212 3.259902 GCAGCCGGCTATACTATTAACC 58.740 50.000 32.30 1.84 40.25 2.85
212 213 3.306502 GCAGCCGGCTATACTATTAACCA 60.307 47.826 32.30 0.00 40.25 3.67
213 214 4.623171 GCAGCCGGCTATACTATTAACCAT 60.623 45.833 32.30 0.00 40.25 3.55
214 215 4.870426 CAGCCGGCTATACTATTAACCATG 59.130 45.833 32.30 7.82 0.00 3.66
215 216 3.621715 GCCGGCTATACTATTAACCATGC 59.378 47.826 22.15 0.00 0.00 4.06
216 217 4.623171 GCCGGCTATACTATTAACCATGCT 60.623 45.833 22.15 0.00 0.00 3.79
217 218 5.109903 CCGGCTATACTATTAACCATGCTC 58.890 45.833 0.00 0.00 0.00 4.26
218 219 5.105310 CCGGCTATACTATTAACCATGCTCT 60.105 44.000 0.00 0.00 0.00 4.09
219 220 6.398918 CGGCTATACTATTAACCATGCTCTT 58.601 40.000 0.00 0.00 0.00 2.85
220 221 7.363530 CCGGCTATACTATTAACCATGCTCTTA 60.364 40.741 0.00 0.00 0.00 2.10
221 222 7.488471 CGGCTATACTATTAACCATGCTCTTAC 59.512 40.741 0.00 0.00 0.00 2.34
222 223 8.311836 GGCTATACTATTAACCATGCTCTTACA 58.688 37.037 0.00 0.00 0.00 2.41
226 227 7.715265 ACTATTAACCATGCTCTTACAATCG 57.285 36.000 0.00 0.00 0.00 3.34
245 246 0.093705 GATTTATCGCGGCGCATCTC 59.906 55.000 32.61 14.51 0.00 2.75
320 331 1.725557 TACCGTGGCAGCGATCTCTC 61.726 60.000 10.33 0.00 0.00 3.20
321 332 2.491621 CGTGGCAGCGATCTCTCA 59.508 61.111 3.87 0.00 0.00 3.27
323 334 1.144565 CGTGGCAGCGATCTCTCAAG 61.145 60.000 3.87 0.00 0.00 3.02
324 335 0.174389 GTGGCAGCGATCTCTCAAGA 59.826 55.000 0.00 0.00 35.54 3.02
445 490 6.037940 GCAACTGCAAAGATCTAATCTCATGA 59.962 38.462 0.00 0.00 38.81 3.07
476 521 1.510844 CCTGCCCAAAATACGGTGC 59.489 57.895 0.00 0.00 0.00 5.01
656 703 7.959651 CACAAATCTTCTCTCCTTGTTTATTCG 59.040 37.037 0.00 0.00 0.00 3.34
720 767 2.077413 TTGGATTTGTCATTTGCGGC 57.923 45.000 0.00 0.00 0.00 6.53
788 835 1.259770 GTTTTGTCGGTTCGTCTCCAC 59.740 52.381 0.00 0.00 0.00 4.02
796 843 2.096248 GGTTCGTCTCCACTCTCTCAT 58.904 52.381 0.00 0.00 0.00 2.90
805 864 5.754406 GTCTCCACTCTCTCATTCATTCATG 59.246 44.000 0.00 0.00 0.00 3.07
820 879 6.664428 TCATTCATGTACTCCATCGGATTA 57.336 37.500 0.00 0.00 0.00 1.75
837 907 2.067365 TTATGCCTCTCAGCGGAGTA 57.933 50.000 13.75 0.28 42.05 2.59
867 2121 1.739067 AGGCAAGCAACGGTTATCTC 58.261 50.000 0.00 0.00 0.00 2.75
968 2237 1.417592 GTGACATTGCTCGCTCACG 59.582 57.895 0.00 0.00 42.01 4.35
1499 2775 2.924290 GTCGAGATCCTTCTTGTTTCCG 59.076 50.000 0.00 0.00 35.22 4.30
1515 2791 2.634982 TCCGCTTTTCATCAACATGC 57.365 45.000 0.00 0.00 0.00 4.06
1659 2944 4.965119 ATTTTCAGTTCCGGCAGTAATC 57.035 40.909 0.00 0.00 0.00 1.75
1686 2980 0.314618 TGTGAAACGACGATTCCGGA 59.685 50.000 14.31 0.00 42.39 5.14
1704 2998 3.235195 CGGAAGGATAATCGCGTCTTAG 58.765 50.000 5.77 0.00 0.00 2.18
1709 3003 5.906113 AGGATAATCGCGTCTTAGATGAT 57.094 39.130 5.77 0.00 0.00 2.45
1727 3021 4.920828 TTTTTCCCCTTGAGCGCT 57.079 50.000 11.27 11.27 0.00 5.92
1729 3023 0.179004 TTTTTCCCCTTGAGCGCTCA 60.179 50.000 35.30 35.30 37.91 4.26
2076 3379 1.779724 GCCTTATTAGCTCGTTCGTCG 59.220 52.381 0.00 0.00 41.41 5.12
2078 3381 2.447250 CTTATTAGCTCGTTCGTCGCA 58.553 47.619 0.00 0.00 39.67 5.10
2110 3414 1.933181 TCACGTCAACAGCTTCAGTTG 59.067 47.619 8.70 8.70 45.82 3.16
2113 3417 1.261619 CGTCAACAGCTTCAGTTGGTC 59.738 52.381 13.64 7.93 44.84 4.02
2119 3423 1.728971 CAGCTTCAGTTGGTCGTGATC 59.271 52.381 0.00 0.00 0.00 2.92
2183 3487 3.072468 TACCTTCTGGACGCCCGG 61.072 66.667 0.00 0.00 40.31 5.73
2244 3548 1.069204 CGTACCTGAGGGACATCATGG 59.931 57.143 15.40 0.00 36.25 3.66
2436 3745 4.580167 ACTATAAGTCGCACGGTACCATAA 59.420 41.667 13.54 0.00 0.00 1.90
2437 3746 2.973694 AAGTCGCACGGTACCATAAT 57.026 45.000 13.54 0.00 0.00 1.28
2438 3747 5.710513 ATAAGTCGCACGGTACCATAATA 57.289 39.130 13.54 0.00 0.00 0.98
2439 3748 4.595762 AAGTCGCACGGTACCATAATAT 57.404 40.909 13.54 0.00 0.00 1.28
2441 3750 5.306532 AGTCGCACGGTACCATAATATAG 57.693 43.478 13.54 0.00 0.00 1.31
2442 3751 3.855950 GTCGCACGGTACCATAATATAGC 59.144 47.826 13.54 2.59 0.00 2.97
2444 3753 3.528532 GCACGGTACCATAATATAGCCC 58.471 50.000 13.54 0.00 0.00 5.19
2448 3757 6.463897 GCACGGTACCATAATATAGCCCATAT 60.464 42.308 13.54 0.00 0.00 1.78
2474 3798 7.555306 ACATCAAGTCATCAAGAATGATCAG 57.445 36.000 0.09 0.00 45.94 2.90
2476 3800 7.993758 ACATCAAGTCATCAAGAATGATCAGAT 59.006 33.333 0.09 0.00 45.94 2.90
2477 3801 7.787725 TCAAGTCATCAAGAATGATCAGATG 57.212 36.000 13.19 13.19 45.94 2.90
2479 3803 6.496144 AGTCATCAAGAATGATCAGATGGA 57.504 37.500 17.23 5.90 45.94 3.41
2480 3804 6.526526 AGTCATCAAGAATGATCAGATGGAG 58.473 40.000 17.23 1.13 45.94 3.86
2481 3805 6.326843 AGTCATCAAGAATGATCAGATGGAGA 59.673 38.462 17.23 5.77 45.94 3.71
2482 3806 6.990939 GTCATCAAGAATGATCAGATGGAGAA 59.009 38.462 17.23 1.32 45.94 2.87
2483 3807 7.498239 GTCATCAAGAATGATCAGATGGAGAAA 59.502 37.037 17.23 1.03 45.94 2.52
2484 3808 7.498239 TCATCAAGAATGATCAGATGGAGAAAC 59.502 37.037 17.23 0.00 44.53 2.78
2485 3809 6.714278 TCAAGAATGATCAGATGGAGAAACA 58.286 36.000 0.09 0.00 0.00 2.83
2486 3810 7.170277 TCAAGAATGATCAGATGGAGAAACAA 58.830 34.615 0.09 0.00 0.00 2.83
2487 3811 7.336176 TCAAGAATGATCAGATGGAGAAACAAG 59.664 37.037 0.09 0.00 0.00 3.16
2488 3812 6.120905 AGAATGATCAGATGGAGAAACAAGG 58.879 40.000 0.09 0.00 0.00 3.61
2489 3813 4.226427 TGATCAGATGGAGAAACAAGGG 57.774 45.455 0.00 0.00 0.00 3.95
2490 3814 3.588842 TGATCAGATGGAGAAACAAGGGT 59.411 43.478 0.00 0.00 0.00 4.34
2491 3815 3.423539 TCAGATGGAGAAACAAGGGTG 57.576 47.619 0.00 0.00 0.00 4.61
2492 3816 2.711009 TCAGATGGAGAAACAAGGGTGT 59.289 45.455 0.00 0.00 40.75 4.16
2515 3840 2.502213 TATATGTGACTCGGCGTTGG 57.498 50.000 6.85 1.00 0.00 3.77
2725 4055 3.458163 GACCCGGCGGACATCTCA 61.458 66.667 30.79 0.00 0.00 3.27
2783 4113 5.177696 GCTTAGCTTGGAACCAATCGTATAG 59.822 44.000 6.74 2.58 35.20 1.31
2803 4146 4.647424 AGTGCTTACTGTATCTCAGAGC 57.353 45.455 1.79 1.05 46.27 4.09
2804 4147 4.277476 AGTGCTTACTGTATCTCAGAGCT 58.723 43.478 8.03 0.00 46.27 4.09
2805 4148 5.441500 AGTGCTTACTGTATCTCAGAGCTA 58.558 41.667 8.03 0.00 46.27 3.32
2807 4150 4.824537 TGCTTACTGTATCTCAGAGCTAGG 59.175 45.833 8.03 0.00 46.27 3.02
2809 4152 5.998981 GCTTACTGTATCTCAGAGCTAGGTA 59.001 44.000 0.00 0.00 46.27 3.08
2810 4153 6.148811 GCTTACTGTATCTCAGAGCTAGGTAG 59.851 46.154 0.00 0.00 46.27 3.18
2811 4154 5.897851 ACTGTATCTCAGAGCTAGGTAGA 57.102 43.478 0.00 0.00 46.27 2.59
2812 4155 6.255294 ACTGTATCTCAGAGCTAGGTAGAA 57.745 41.667 0.00 0.00 46.27 2.10
2813 4156 6.296026 ACTGTATCTCAGAGCTAGGTAGAAG 58.704 44.000 0.00 0.00 46.27 2.85
2814 4157 6.100569 ACTGTATCTCAGAGCTAGGTAGAAGA 59.899 42.308 0.00 0.00 46.27 2.87
2815 4158 7.085476 TGTATCTCAGAGCTAGGTAGAAGAT 57.915 40.000 13.67 13.67 0.00 2.40
2816 4159 8.208575 TGTATCTCAGAGCTAGGTAGAAGATA 57.791 38.462 12.25 12.25 0.00 1.98
2817 4160 8.318412 TGTATCTCAGAGCTAGGTAGAAGATAG 58.682 40.741 14.90 1.01 0.00 2.08
2818 4161 5.556915 TCTCAGAGCTAGGTAGAAGATAGC 58.443 45.833 0.00 0.00 41.79 2.97
2819 4162 5.072464 TCTCAGAGCTAGGTAGAAGATAGCA 59.928 44.000 0.00 0.00 43.49 3.49
2820 4163 5.312895 TCAGAGCTAGGTAGAAGATAGCAG 58.687 45.833 0.00 0.00 43.49 4.24
2821 4164 4.079253 AGAGCTAGGTAGAAGATAGCAGC 58.921 47.826 0.00 0.00 43.49 5.25
2822 4165 3.161866 AGCTAGGTAGAAGATAGCAGCC 58.838 50.000 6.25 0.00 43.49 4.85
2823 4166 3.161866 GCTAGGTAGAAGATAGCAGCCT 58.838 50.000 0.00 0.00 41.25 4.58
2824 4167 3.056891 GCTAGGTAGAAGATAGCAGCCTG 60.057 52.174 0.00 0.00 41.25 4.85
2825 4168 3.320610 AGGTAGAAGATAGCAGCCTGA 57.679 47.619 0.00 0.00 0.00 3.86
2831 4188 4.899239 ATAGCAGCCTGACCGCGC 62.899 66.667 0.00 0.00 0.00 6.86
2845 4203 3.793144 GCGCGCTGTCTTGGAAGG 61.793 66.667 26.67 0.00 0.00 3.46
2849 4207 1.016653 GCGCTGTCTTGGAAGGTCTC 61.017 60.000 0.00 0.00 0.00 3.36
2911 4269 0.244721 TCATCTGCGAGGTGTGTCTG 59.755 55.000 0.00 0.00 0.00 3.51
2913 4271 0.244994 ATCTGCGAGGTGTGTCTGTC 59.755 55.000 0.00 0.00 0.00 3.51
2914 4272 0.823769 TCTGCGAGGTGTGTCTGTCT 60.824 55.000 0.00 0.00 0.00 3.41
2916 4274 0.596577 TGCGAGGTGTGTCTGTCTAC 59.403 55.000 0.00 0.00 0.00 2.59
2919 4312 2.668834 GCGAGGTGTGTCTGTCTACTTC 60.669 54.545 0.00 0.00 0.00 3.01
2981 4377 5.496387 GTTGATGATTGCAGTATTGTCGAG 58.504 41.667 0.00 0.00 0.00 4.04
2987 4383 3.251479 TGCAGTATTGTCGAGCTCAAT 57.749 42.857 15.40 9.33 38.72 2.57
3000 4396 3.545475 CGAGCTCAATGGATAATCGATCG 59.455 47.826 15.40 9.36 35.12 3.69
3020 4416 1.882198 CGTGCGACAAATTGTGATCC 58.118 50.000 2.20 0.00 0.00 3.36
3023 4419 2.095853 GTGCGACAAATTGTGATCCGAT 59.904 45.455 2.20 0.00 0.00 4.18
3039 4435 1.342555 CGATGAAGACGTGCGGTTTA 58.657 50.000 0.00 0.00 0.00 2.01
3069 4465 1.299544 CGGCGTTTCCAACCAAACC 60.300 57.895 0.00 0.00 33.37 3.27
3074 4470 2.800273 GCGTTTCCAACCAAACCGAAAT 60.800 45.455 0.00 0.00 33.37 2.17
3110 4516 8.628630 TTTGTTTTGTTTTGAGGGAAAGAAAT 57.371 26.923 0.00 0.00 33.54 2.17
3111 4517 7.841915 TGTTTTGTTTTGAGGGAAAGAAATC 57.158 32.000 0.00 0.00 33.54 2.17
3112 4518 7.390027 TGTTTTGTTTTGAGGGAAAGAAATCA 58.610 30.769 0.00 0.00 33.54 2.57
3119 4584 6.935240 TTGAGGGAAAGAAATCAGAGTAGA 57.065 37.500 0.00 0.00 0.00 2.59
3156 4621 0.165944 GGCACGTAACTGACACATGC 59.834 55.000 0.00 0.00 32.71 4.06
3161 4626 0.165944 GTAACTGACACATGCCACGC 59.834 55.000 0.00 0.00 0.00 5.34
3180 4645 1.282157 GCCACCAACCTTATCAGTCCT 59.718 52.381 0.00 0.00 0.00 3.85
3181 4646 2.290960 GCCACCAACCTTATCAGTCCTT 60.291 50.000 0.00 0.00 0.00 3.36
3182 4647 3.814316 GCCACCAACCTTATCAGTCCTTT 60.814 47.826 0.00 0.00 0.00 3.11
3183 4648 4.407365 CCACCAACCTTATCAGTCCTTTT 58.593 43.478 0.00 0.00 0.00 2.27
3184 4649 4.832823 CCACCAACCTTATCAGTCCTTTTT 59.167 41.667 0.00 0.00 0.00 1.94
3246 4711 4.577834 TCCGGAGAAAACAAAAACATCC 57.422 40.909 0.00 0.00 0.00 3.51
3252 4717 6.636850 CGGAGAAAACAAAAACATCCAAGTAG 59.363 38.462 0.00 0.00 0.00 2.57
3253 4718 6.420903 GGAGAAAACAAAAACATCCAAGTAGC 59.579 38.462 0.00 0.00 0.00 3.58
3254 4719 6.872920 AGAAAACAAAAACATCCAAGTAGCA 58.127 32.000 0.00 0.00 0.00 3.49
3255 4720 6.756542 AGAAAACAAAAACATCCAAGTAGCAC 59.243 34.615 0.00 0.00 0.00 4.40
3280 4745 2.691409 TTTATCAGAACCGCCCTGAG 57.309 50.000 0.00 0.00 43.07 3.35
3315 4780 2.778659 CAGCACTTCGCAATTTAGAGC 58.221 47.619 0.00 0.00 46.13 4.09
3365 4838 1.764571 AAGCACACGGTCCCAAGCTA 61.765 55.000 0.00 0.00 0.00 3.32
3404 4877 0.179108 AGACGCTAGCCCGATTTCAC 60.179 55.000 9.66 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.518249 CGCTTATCTTCTCTCCCCTTTTT 58.482 43.478 0.00 0.00 0.00 1.94
9 10 3.118223 CCGCTTATCTTCTCTCCCCTTTT 60.118 47.826 0.00 0.00 0.00 2.27
10 11 2.436173 CCGCTTATCTTCTCTCCCCTTT 59.564 50.000 0.00 0.00 0.00 3.11
11 12 2.043227 CCGCTTATCTTCTCTCCCCTT 58.957 52.381 0.00 0.00 0.00 3.95
12 13 1.710816 CCGCTTATCTTCTCTCCCCT 58.289 55.000 0.00 0.00 0.00 4.79
13 14 0.682292 CCCGCTTATCTTCTCTCCCC 59.318 60.000 0.00 0.00 0.00 4.81
14 15 0.034198 GCCCGCTTATCTTCTCTCCC 59.966 60.000 0.00 0.00 0.00 4.30
15 16 1.000394 GAGCCCGCTTATCTTCTCTCC 60.000 57.143 0.00 0.00 0.00 3.71
16 17 1.960689 AGAGCCCGCTTATCTTCTCTC 59.039 52.381 0.00 0.00 0.00 3.20
17 18 2.080654 AGAGCCCGCTTATCTTCTCT 57.919 50.000 0.00 0.00 0.00 3.10
18 19 2.749776 GAAGAGCCCGCTTATCTTCTC 58.250 52.381 8.96 0.00 43.57 2.87
19 20 1.067821 CGAAGAGCCCGCTTATCTTCT 59.932 52.381 12.57 0.00 44.34 2.85
20 21 1.202428 ACGAAGAGCCCGCTTATCTTC 60.202 52.381 6.96 6.96 43.51 2.87
21 22 0.824759 ACGAAGAGCCCGCTTATCTT 59.175 50.000 0.00 0.00 36.02 2.40
22 23 0.103208 CACGAAGAGCCCGCTTATCT 59.897 55.000 0.00 0.00 0.00 1.98
23 24 0.102481 TCACGAAGAGCCCGCTTATC 59.898 55.000 0.00 0.00 0.00 1.75
24 25 0.535335 TTCACGAAGAGCCCGCTTAT 59.465 50.000 0.00 0.00 0.00 1.73
25 26 0.108804 CTTCACGAAGAGCCCGCTTA 60.109 55.000 0.20 0.00 40.79 3.09
26 27 1.374758 CTTCACGAAGAGCCCGCTT 60.375 57.895 0.20 0.00 40.79 4.68
27 28 1.816863 TTCTTCACGAAGAGCCCGCT 61.817 55.000 9.32 0.00 46.80 5.52
28 29 1.374252 TTCTTCACGAAGAGCCCGC 60.374 57.895 9.32 0.00 46.80 6.13
29 30 2.446341 GTTCTTCACGAAGAGCCCG 58.554 57.895 11.38 0.00 46.80 6.13
32 33 0.793250 GCTGGTTCTTCACGAAGAGC 59.207 55.000 13.46 13.46 46.80 4.09
33 34 2.029470 AGAGCTGGTTCTTCACGAAGAG 60.029 50.000 9.32 0.42 46.80 2.85
34 35 1.964223 AGAGCTGGTTCTTCACGAAGA 59.036 47.619 5.38 5.38 44.94 2.87
35 36 2.447244 AGAGCTGGTTCTTCACGAAG 57.553 50.000 0.00 0.08 39.71 3.79
36 37 2.352814 GCTAGAGCTGGTTCTTCACGAA 60.353 50.000 0.00 0.00 38.21 3.85
37 38 1.202582 GCTAGAGCTGGTTCTTCACGA 59.797 52.381 0.00 0.00 38.21 4.35
38 39 1.067565 TGCTAGAGCTGGTTCTTCACG 60.068 52.381 2.72 0.00 42.66 4.35
39 40 2.342179 GTGCTAGAGCTGGTTCTTCAC 58.658 52.381 2.72 0.00 42.66 3.18
40 41 1.067565 CGTGCTAGAGCTGGTTCTTCA 60.068 52.381 2.72 0.00 42.66 3.02
41 42 1.067495 ACGTGCTAGAGCTGGTTCTTC 60.067 52.381 2.72 0.00 42.66 2.87
42 43 0.969894 ACGTGCTAGAGCTGGTTCTT 59.030 50.000 2.72 0.00 42.66 2.52
43 44 0.244994 CACGTGCTAGAGCTGGTTCT 59.755 55.000 0.82 0.00 42.66 3.01
44 45 1.355066 GCACGTGCTAGAGCTGGTTC 61.355 60.000 32.55 0.00 42.66 3.62
45 46 1.374758 GCACGTGCTAGAGCTGGTT 60.375 57.895 32.55 0.00 42.66 3.67
46 47 2.262915 GCACGTGCTAGAGCTGGT 59.737 61.111 32.55 0.00 42.66 4.00
61 62 3.374764 TCTCATAAAGTGCCTAGGAGCA 58.625 45.455 14.75 0.22 41.46 4.26
62 63 4.408182 TTCTCATAAAGTGCCTAGGAGC 57.592 45.455 14.75 3.68 29.37 4.70
63 64 6.166984 TCATTCTCATAAAGTGCCTAGGAG 57.833 41.667 14.75 0.00 0.00 3.69
64 65 6.560003 TTCATTCTCATAAAGTGCCTAGGA 57.440 37.500 14.75 0.00 0.00 2.94
65 66 6.261826 CCTTTCATTCTCATAAAGTGCCTAGG 59.738 42.308 3.67 3.67 0.00 3.02
66 67 6.825721 ACCTTTCATTCTCATAAAGTGCCTAG 59.174 38.462 0.00 0.00 0.00 3.02
67 68 6.599244 CACCTTTCATTCTCATAAAGTGCCTA 59.401 38.462 0.00 0.00 0.00 3.93
68 69 5.416952 CACCTTTCATTCTCATAAAGTGCCT 59.583 40.000 0.00 0.00 0.00 4.75
69 70 5.393461 CCACCTTTCATTCTCATAAAGTGCC 60.393 44.000 0.00 0.00 0.00 5.01
70 71 5.393461 CCCACCTTTCATTCTCATAAAGTGC 60.393 44.000 0.00 0.00 0.00 4.40
71 72 5.393461 GCCCACCTTTCATTCTCATAAAGTG 60.393 44.000 0.00 0.00 0.00 3.16
72 73 4.706962 GCCCACCTTTCATTCTCATAAAGT 59.293 41.667 0.00 0.00 0.00 2.66
73 74 4.098501 GGCCCACCTTTCATTCTCATAAAG 59.901 45.833 0.00 0.00 0.00 1.85
74 75 4.023291 GGCCCACCTTTCATTCTCATAAA 58.977 43.478 0.00 0.00 0.00 1.40
75 76 3.631250 GGCCCACCTTTCATTCTCATAA 58.369 45.455 0.00 0.00 0.00 1.90
76 77 2.421388 CGGCCCACCTTTCATTCTCATA 60.421 50.000 0.00 0.00 0.00 2.15
77 78 1.683011 CGGCCCACCTTTCATTCTCAT 60.683 52.381 0.00 0.00 0.00 2.90
78 79 0.322456 CGGCCCACCTTTCATTCTCA 60.322 55.000 0.00 0.00 0.00 3.27
79 80 0.322546 ACGGCCCACCTTTCATTCTC 60.323 55.000 0.00 0.00 0.00 2.87
80 81 0.988832 TACGGCCCACCTTTCATTCT 59.011 50.000 0.00 0.00 0.00 2.40
81 82 2.052782 ATACGGCCCACCTTTCATTC 57.947 50.000 0.00 0.00 0.00 2.67
82 83 3.655615 TTATACGGCCCACCTTTCATT 57.344 42.857 0.00 0.00 0.00 2.57
83 84 3.876309 ATTATACGGCCCACCTTTCAT 57.124 42.857 0.00 0.00 0.00 2.57
84 85 4.774660 TTATTATACGGCCCACCTTTCA 57.225 40.909 0.00 0.00 0.00 2.69
85 86 6.453926 TTTTTATTATACGGCCCACCTTTC 57.546 37.500 0.00 0.00 0.00 2.62
141 142 8.918116 CATATACAGCCCATCTTATAGCTAAGA 58.082 37.037 0.00 0.00 45.61 2.10
142 143 8.918116 TCATATACAGCCCATCTTATAGCTAAG 58.082 37.037 0.00 0.00 36.46 2.18
143 144 8.696374 GTCATATACAGCCCATCTTATAGCTAA 58.304 37.037 0.00 0.00 33.33 3.09
144 145 7.839200 TGTCATATACAGCCCATCTTATAGCTA 59.161 37.037 0.00 0.00 33.33 3.32
145 146 6.669591 TGTCATATACAGCCCATCTTATAGCT 59.330 38.462 0.00 0.00 35.52 3.32
146 147 6.878317 TGTCATATACAGCCCATCTTATAGC 58.122 40.000 0.00 0.00 33.01 2.97
147 148 7.930325 CCATGTCATATACAGCCCATCTTATAG 59.070 40.741 0.00 0.00 42.70 1.31
148 149 7.635750 GCCATGTCATATACAGCCCATCTTATA 60.636 40.741 0.00 0.00 42.70 0.98
149 150 6.656902 CCATGTCATATACAGCCCATCTTAT 58.343 40.000 0.00 0.00 42.70 1.73
150 151 5.571454 GCCATGTCATATACAGCCCATCTTA 60.571 44.000 0.00 0.00 42.70 2.10
151 152 4.808665 GCCATGTCATATACAGCCCATCTT 60.809 45.833 0.00 0.00 42.70 2.40
152 153 3.307975 GCCATGTCATATACAGCCCATCT 60.308 47.826 0.00 0.00 42.70 2.90
153 154 3.012518 GCCATGTCATATACAGCCCATC 58.987 50.000 0.00 0.00 42.70 3.51
154 155 2.376181 TGCCATGTCATATACAGCCCAT 59.624 45.455 0.00 0.00 42.70 4.00
155 156 1.773653 TGCCATGTCATATACAGCCCA 59.226 47.619 0.00 0.00 42.70 5.36
156 157 2.154462 GTGCCATGTCATATACAGCCC 58.846 52.381 0.00 0.00 42.70 5.19
157 158 2.810274 CAGTGCCATGTCATATACAGCC 59.190 50.000 0.00 0.00 42.70 4.85
158 159 2.810274 CCAGTGCCATGTCATATACAGC 59.190 50.000 0.00 0.00 42.70 4.40
159 160 2.810274 GCCAGTGCCATGTCATATACAG 59.190 50.000 0.00 0.00 42.70 2.74
160 161 2.439135 AGCCAGTGCCATGTCATATACA 59.561 45.455 0.00 0.00 39.74 2.29
161 162 3.131709 AGCCAGTGCCATGTCATATAC 57.868 47.619 0.00 0.00 38.69 1.47
162 163 3.862877 AAGCCAGTGCCATGTCATATA 57.137 42.857 0.00 0.00 38.69 0.86
163 164 2.742428 AAGCCAGTGCCATGTCATAT 57.258 45.000 0.00 0.00 38.69 1.78
164 165 3.862877 ATAAGCCAGTGCCATGTCATA 57.137 42.857 0.00 0.00 38.69 2.15
165 166 2.742428 ATAAGCCAGTGCCATGTCAT 57.258 45.000 0.00 0.00 38.69 3.06
166 167 2.746142 GCTATAAGCCAGTGCCATGTCA 60.746 50.000 0.00 0.00 38.69 3.58
167 168 1.876156 GCTATAAGCCAGTGCCATGTC 59.124 52.381 0.00 0.00 38.69 3.06
168 169 1.972872 GCTATAAGCCAGTGCCATGT 58.027 50.000 0.00 0.00 38.69 3.21
179 180 1.963338 CCGGCTGCTGGCTATAAGC 60.963 63.158 15.72 0.00 41.46 3.09
180 181 4.368391 CCGGCTGCTGGCTATAAG 57.632 61.111 15.72 0.00 41.46 1.73
190 191 3.259902 GGTTAATAGTATAGCCGGCTGC 58.740 50.000 38.98 26.31 41.71 5.25
191 192 4.530710 TGGTTAATAGTATAGCCGGCTG 57.469 45.455 38.98 0.00 0.00 4.85
192 193 4.623171 GCATGGTTAATAGTATAGCCGGCT 60.623 45.833 34.85 34.85 31.18 5.52
193 194 3.621715 GCATGGTTAATAGTATAGCCGGC 59.378 47.826 21.89 21.89 0.00 6.13
194 195 5.086104 AGCATGGTTAATAGTATAGCCGG 57.914 43.478 0.00 0.00 0.00 6.13
195 196 5.967088 AGAGCATGGTTAATAGTATAGCCG 58.033 41.667 0.00 0.00 0.00 5.52
196 197 8.311836 TGTAAGAGCATGGTTAATAGTATAGCC 58.688 37.037 0.00 0.00 0.00 3.93
197 198 9.706691 TTGTAAGAGCATGGTTAATAGTATAGC 57.293 33.333 0.00 0.00 0.00 2.97
200 201 9.424319 CGATTGTAAGAGCATGGTTAATAGTAT 57.576 33.333 0.00 0.00 0.00 2.12
201 202 8.635328 TCGATTGTAAGAGCATGGTTAATAGTA 58.365 33.333 0.00 0.00 0.00 1.82
202 203 7.497595 TCGATTGTAAGAGCATGGTTAATAGT 58.502 34.615 0.00 0.00 0.00 2.12
203 204 7.946655 TCGATTGTAAGAGCATGGTTAATAG 57.053 36.000 0.00 0.00 0.00 1.73
204 205 8.902540 AATCGATTGTAAGAGCATGGTTAATA 57.097 30.769 10.50 0.00 0.00 0.98
205 206 7.807977 AATCGATTGTAAGAGCATGGTTAAT 57.192 32.000 10.50 0.00 0.00 1.40
206 207 7.624360 AAATCGATTGTAAGAGCATGGTTAA 57.376 32.000 12.25 0.00 0.00 2.01
207 208 8.902540 ATAAATCGATTGTAAGAGCATGGTTA 57.097 30.769 12.25 0.00 0.00 2.85
208 209 7.807977 ATAAATCGATTGTAAGAGCATGGTT 57.192 32.000 12.25 0.00 0.00 3.67
209 210 7.426929 GATAAATCGATTGTAAGAGCATGGT 57.573 36.000 12.25 0.00 0.00 3.55
226 227 0.093705 GAGATGCGCCGCGATAAATC 59.906 55.000 18.91 12.69 0.00 2.17
249 250 0.245539 GGTCCCGTCTCGTGATTTCA 59.754 55.000 0.00 0.00 0.00 2.69
264 265 0.743097 GCATGAGGCTTGATTGGTCC 59.257 55.000 0.00 0.00 40.25 4.46
320 331 3.059352 ACCCTCGGAACTCAAATCTTG 57.941 47.619 0.00 0.00 0.00 3.02
321 332 4.094476 TCTACCCTCGGAACTCAAATCTT 58.906 43.478 0.00 0.00 0.00 2.40
323 334 3.181474 CCTCTACCCTCGGAACTCAAATC 60.181 52.174 0.00 0.00 0.00 2.17
324 335 2.766828 CCTCTACCCTCGGAACTCAAAT 59.233 50.000 0.00 0.00 0.00 2.32
436 481 4.999950 GGGTTCAGCGAATATCATGAGATT 59.000 41.667 15.23 15.23 35.67 2.40
445 490 0.179018 GGGCAGGGTTCAGCGAATAT 60.179 55.000 0.00 0.00 0.00 1.28
537 582 2.159393 GCAATGAATGGCTGCTCGTTTA 60.159 45.455 0.00 0.00 33.20 2.01
626 673 3.064900 AGGAGAGAAGATTTGTGTGGC 57.935 47.619 0.00 0.00 0.00 5.01
634 681 7.162082 ACACGAATAAACAAGGAGAGAAGATT 58.838 34.615 0.00 0.00 0.00 2.40
656 703 3.304057 CGAGAAGAAAGGGCAAGAAACAC 60.304 47.826 0.00 0.00 0.00 3.32
788 835 6.814043 TGGAGTACATGAATGAATGAGAGAG 58.186 40.000 0.00 0.00 0.00 3.20
796 843 5.551305 ATCCGATGGAGTACATGAATGAA 57.449 39.130 0.00 0.00 40.72 2.57
805 864 3.511934 AGAGGCATAATCCGATGGAGTAC 59.488 47.826 0.00 0.00 35.06 2.73
820 879 0.396417 ACTACTCCGCTGAGAGGCAT 60.396 55.000 12.54 0.00 41.42 4.40
837 907 5.650703 ACCGTTGCTTGCCTTTTTATATACT 59.349 36.000 0.00 0.00 0.00 2.12
867 2121 0.820891 CAATTGAGGATGGCGAGGGG 60.821 60.000 0.00 0.00 0.00 4.79
901 2155 2.311124 AAATCCTACGGCAGCAGTAC 57.689 50.000 0.64 0.00 0.00 2.73
902 2156 3.343941 AAAAATCCTACGGCAGCAGTA 57.656 42.857 5.23 5.23 0.00 2.74
935 2204 0.664224 GTCACGCTAGGACTAGGAGC 59.336 60.000 8.33 0.00 33.87 4.70
968 2237 2.187946 CGTGTGAGGGGCTCATCC 59.812 66.667 0.00 0.00 42.73 3.51
978 2247 0.720027 CTGATTGCAGCTCGTGTGAG 59.280 55.000 0.00 0.00 45.49 3.51
1499 2775 1.736696 CGGGGCATGTTGATGAAAAGC 60.737 52.381 0.00 0.00 0.00 3.51
1610 2887 3.125146 TCAACTATGAAATGTGCTGCGAC 59.875 43.478 0.00 0.00 30.99 5.19
1659 2944 4.974103 ATCGTCGTTTCACAAAAGAGAG 57.026 40.909 0.00 0.00 29.67 3.20
1686 2980 5.707242 TCATCTAAGACGCGATTATCCTT 57.293 39.130 15.93 8.33 0.00 3.36
1719 3013 2.232756 TGTTGTACTTGAGCGCTCAA 57.767 45.000 41.28 41.28 46.27 3.02
1720 3014 2.232756 TTGTTGTACTTGAGCGCTCA 57.767 45.000 35.30 35.30 37.91 4.26
1721 3015 3.289076 GTTTTGTTGTACTTGAGCGCTC 58.711 45.455 30.42 30.42 0.00 5.03
1722 3016 2.286184 CGTTTTGTTGTACTTGAGCGCT 60.286 45.455 11.27 11.27 0.00 5.92
1723 3017 2.034076 CGTTTTGTTGTACTTGAGCGC 58.966 47.619 0.00 0.00 0.00 5.92
1724 3018 2.034076 GCGTTTTGTTGTACTTGAGCG 58.966 47.619 0.00 0.00 0.00 5.03
1725 3019 3.059634 TGCGTTTTGTTGTACTTGAGC 57.940 42.857 0.00 0.00 0.00 4.26
1726 3020 4.035017 CCTTGCGTTTTGTTGTACTTGAG 58.965 43.478 0.00 0.00 0.00 3.02
1727 3021 3.440872 ACCTTGCGTTTTGTTGTACTTGA 59.559 39.130 0.00 0.00 0.00 3.02
1729 3023 3.692593 AGACCTTGCGTTTTGTTGTACTT 59.307 39.130 0.00 0.00 0.00 2.24
1735 3037 4.973663 CGATAAAAGACCTTGCGTTTTGTT 59.026 37.500 0.00 0.00 0.00 2.83
1842 3145 2.741985 CCCGCGCTGTGTCATCAA 60.742 61.111 5.56 0.00 0.00 2.57
1904 3207 1.745489 GTCGTTGGAGCCCATGGTC 60.745 63.158 11.73 0.00 38.29 4.02
2078 3381 1.670791 TGACGTGATCATGCATGCAT 58.329 45.000 27.46 27.46 37.08 3.96
2110 3414 7.640240 GCAAACTCTAATTAATTGATCACGACC 59.360 37.037 11.05 0.00 0.00 4.79
2183 3487 1.068474 CGTTCACCACCACGATCTTC 58.932 55.000 0.00 0.00 38.76 2.87
2417 3721 5.710513 ATATTATGGTACCGTGCGACTTA 57.289 39.130 17.34 0.00 0.00 2.24
2466 3775 5.198965 CCCTTGTTTCTCCATCTGATCATT 58.801 41.667 0.00 0.00 0.00 2.57
2470 3794 3.331889 ACACCCTTGTTTCTCCATCTGAT 59.668 43.478 0.00 0.00 28.43 2.90
2471 3795 2.711009 ACACCCTTGTTTCTCCATCTGA 59.289 45.455 0.00 0.00 28.43 3.27
2472 3796 3.146104 ACACCCTTGTTTCTCCATCTG 57.854 47.619 0.00 0.00 28.43 2.90
2483 3807 6.984474 CGAGTCACATATATAAACACCCTTGT 59.016 38.462 0.00 0.00 37.67 3.16
2484 3808 6.423905 CCGAGTCACATATATAAACACCCTTG 59.576 42.308 0.00 0.00 0.00 3.61
2485 3809 6.522054 CCGAGTCACATATATAAACACCCTT 58.478 40.000 0.00 0.00 0.00 3.95
2486 3810 5.510861 GCCGAGTCACATATATAAACACCCT 60.511 44.000 0.00 0.00 0.00 4.34
2487 3811 4.689345 GCCGAGTCACATATATAAACACCC 59.311 45.833 0.00 0.00 0.00 4.61
2488 3812 4.384846 CGCCGAGTCACATATATAAACACC 59.615 45.833 0.00 0.00 0.00 4.16
2489 3813 4.980434 ACGCCGAGTCACATATATAAACAC 59.020 41.667 0.00 0.00 0.00 3.32
2490 3814 5.190992 ACGCCGAGTCACATATATAAACA 57.809 39.130 0.00 0.00 0.00 2.83
2491 3815 5.107607 CCAACGCCGAGTCACATATATAAAC 60.108 44.000 0.00 0.00 0.00 2.01
2492 3816 4.986034 CCAACGCCGAGTCACATATATAAA 59.014 41.667 0.00 0.00 0.00 1.40
2493 3817 4.552355 CCAACGCCGAGTCACATATATAA 58.448 43.478 0.00 0.00 0.00 0.98
2494 3818 3.057104 CCCAACGCCGAGTCACATATATA 60.057 47.826 0.00 0.00 0.00 0.86
2495 3819 2.288825 CCCAACGCCGAGTCACATATAT 60.289 50.000 0.00 0.00 0.00 0.86
2515 3840 3.074412 CCCTACACACAGACAATCAACC 58.926 50.000 0.00 0.00 0.00 3.77
2602 3932 2.991076 GCAGTAGCTCGACGTGGGT 61.991 63.158 0.00 0.00 37.91 4.51
2719 4049 0.792640 GCACGTTGACAGGTGAGATG 59.207 55.000 11.60 0.00 40.64 2.90
2725 4055 4.539083 TGGCGCACGTTGACAGGT 62.539 61.111 10.83 0.00 0.00 4.00
2783 4113 4.647424 AGCTCTGAGATACAGTAAGCAC 57.353 45.455 9.28 0.00 44.04 4.40
2803 4146 4.217550 GTCAGGCTGCTATCTTCTACCTAG 59.782 50.000 10.34 0.00 0.00 3.02
2804 4147 4.145807 GTCAGGCTGCTATCTTCTACCTA 58.854 47.826 10.34 0.00 0.00 3.08
2805 4148 2.962421 GTCAGGCTGCTATCTTCTACCT 59.038 50.000 10.34 0.00 0.00 3.08
2807 4150 2.287909 CGGTCAGGCTGCTATCTTCTAC 60.288 54.545 10.34 0.00 0.00 2.59
2809 4152 0.749649 CGGTCAGGCTGCTATCTTCT 59.250 55.000 10.34 0.00 0.00 2.85
2810 4153 0.878086 GCGGTCAGGCTGCTATCTTC 60.878 60.000 10.34 0.00 45.76 2.87
2811 4154 1.144936 GCGGTCAGGCTGCTATCTT 59.855 57.895 10.34 0.00 45.76 2.40
2812 4155 2.818132 GCGGTCAGGCTGCTATCT 59.182 61.111 10.34 0.00 45.76 1.98
2831 4188 0.734253 CGAGACCTTCCAAGACAGCG 60.734 60.000 0.00 0.00 0.00 5.18
2837 4195 1.848652 TAGGACCGAGACCTTCCAAG 58.151 55.000 0.00 0.00 38.76 3.61
2845 4203 4.189639 ACTGAACAAATAGGACCGAGAC 57.810 45.455 0.00 0.00 0.00 3.36
2849 4207 3.365969 GGCAAACTGAACAAATAGGACCG 60.366 47.826 0.00 0.00 0.00 4.79
2981 4377 2.028523 CGCGATCGATTATCCATTGAGC 59.971 50.000 21.57 0.00 38.10 4.26
2987 4383 1.001745 CGCACGCGATCGATTATCCA 61.002 55.000 21.57 0.00 42.83 3.41
3000 4396 1.250476 GATCACAATTTGTCGCACGC 58.750 50.000 0.00 0.00 0.00 5.34
3010 4406 3.618594 CACGTCTTCATCGGATCACAATT 59.381 43.478 0.00 0.00 0.00 2.32
3020 4416 1.320555 CTAAACCGCACGTCTTCATCG 59.679 52.381 0.00 0.00 0.00 3.84
3023 4419 0.947180 GCCTAAACCGCACGTCTTCA 60.947 55.000 0.00 0.00 0.00 3.02
3069 4465 7.014702 ACAAAACAAAAAGAACTGCAATTTCG 58.985 30.769 0.00 0.00 0.00 3.46
3074 4470 7.697691 TCAAAACAAAACAAAAAGAACTGCAA 58.302 26.923 0.00 0.00 0.00 4.08
3110 4516 4.438336 CGTATGGTTTCGCTTCTACTCTGA 60.438 45.833 0.00 0.00 0.00 3.27
3111 4517 3.791887 CGTATGGTTTCGCTTCTACTCTG 59.208 47.826 0.00 0.00 0.00 3.35
3112 4518 4.030134 CGTATGGTTTCGCTTCTACTCT 57.970 45.455 0.00 0.00 0.00 3.24
3156 4621 0.322098 TGATAAGGTTGGTGGCGTGG 60.322 55.000 0.00 0.00 0.00 4.94
3161 4626 3.721087 AAGGACTGATAAGGTTGGTGG 57.279 47.619 0.00 0.00 0.00 4.61
3246 4711 9.250624 GGTTCTGATAAATACTAGTGCTACTTG 57.749 37.037 5.39 0.00 0.00 3.16
3252 4717 4.448060 GGCGGTTCTGATAAATACTAGTGC 59.552 45.833 5.39 0.00 0.00 4.40
3253 4718 4.989168 GGGCGGTTCTGATAAATACTAGTG 59.011 45.833 5.39 0.00 0.00 2.74
3254 4719 4.900054 AGGGCGGTTCTGATAAATACTAGT 59.100 41.667 0.00 0.00 0.00 2.57
3255 4720 5.010719 TCAGGGCGGTTCTGATAAATACTAG 59.989 44.000 0.00 0.00 36.46 2.57
3280 4745 0.880278 TGCTGCACCGAACTGAAGAC 60.880 55.000 0.00 0.00 0.00 3.01
3315 4780 5.266242 CGACCTTTTGACTTTTGAGAACTG 58.734 41.667 0.00 0.00 0.00 3.16
3365 4838 0.999406 CGATTTGGTTGAGCGATCGT 59.001 50.000 17.81 3.24 35.98 3.73


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

AutoCloner maintained by Alex Coulton.