Multiple sequence alignment - TraesCS2B01G330500

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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 TraesCS2B01G330500 chr2B 100.000 2195 0 0 1 2195 474899493 474901687 0.000000e+00 4054
1 TraesCS2B01G330500 chr1A 98.524 1558 15 6 645 2195 554458262 554459818 0.000000e+00 2743
2 TraesCS2B01G330500 chr1A 99.149 235 2 0 387 621 554455920 554455686 7.240000e-115 424
3 TraesCS2B01G330500 chr1A 99.149 235 2 0 387 621 554458182 554457948 7.240000e-115 424
4 TraesCS2B01G330500 chr1A 98.723 235 3 0 387 621 554457226 554457460 3.370000e-113 418
5 TraesCS2B01G330500 chr1D 97.367 1557 30 7 645 2195 254416860 254418411 0.000000e+00 2638
6 TraesCS2B01G330500 chr1D 99.083 327 3 0 1 327 254492890 254493216 2.430000e-164 588
7 TraesCS2B01G330500 chr1D 99.083 327 2 1 1 327 254494629 254494304 8.730000e-164 586
8 TraesCS2B01G330500 chr1D 98.777 327 4 0 1 327 483917986 483918312 1.130000e-162 582
9 TraesCS2B01G330500 chr1D 97.872 235 5 0 387 621 254416780 254416546 7.300000e-110 407
10 TraesCS2B01G330500 chr6D 96.750 1569 23 12 645 2195 45511776 45510218 0.000000e+00 2590
11 TraesCS2B01G330500 chr6D 98.723 235 3 0 387 621 45511856 45512090 3.370000e-113 418
12 TraesCS2B01G330500 chr5D 96.365 1568 28 12 645 2195 6181151 6179596 0.000000e+00 2553
13 TraesCS2B01G330500 chr5D 96.768 1114 15 8 1102 2195 512416234 512415122 0.000000e+00 1838
14 TraesCS2B01G330500 chr5D 96.676 1113 16 8 1102 2195 512409297 512408187 0.000000e+00 1831
15 TraesCS2B01G330500 chr5D 99.083 327 3 0 1 327 240134322 240133996 2.430000e-164 588
16 TraesCS2B01G330500 chr5D 98.777 327 3 1 1 327 449152536 449152861 4.060000e-162 580
17 TraesCS2B01G330500 chr5D 98.442 321 5 0 5 325 6204661 6204981 1.140000e-157 566
18 TraesCS2B01G330500 chr5D 98.298 235 4 0 387 621 120799587 120799353 1.570000e-111 412
19 TraesCS2B01G330500 chr5A 96.401 1556 42 10 645 2195 607200295 607198749 0.000000e+00 2551
20 TraesCS2B01G330500 chr5A 91.414 955 52 18 1097 2029 520661594 520662540 0.000000e+00 1282
21 TraesCS2B01G330500 chr5A 97.872 235 5 0 387 621 607200375 607200609 7.300000e-110 407
22 TraesCS2B01G330500 chr7B 95.174 1554 61 11 645 2195 105256800 105255258 0.000000e+00 2442
23 TraesCS2B01G330500 chr2A 97.371 1179 20 8 1012 2182 334595896 334594721 0.000000e+00 1995
24 TraesCS2B01G330500 chr2A 96.493 998 17 7 645 1630 335830832 335829841 0.000000e+00 1633
25 TraesCS2B01G330500 chr4D 93.161 1316 62 15 895 2195 207373081 207374383 0.000000e+00 1906
26 TraesCS2B01G330500 chr4B 95.340 1030 34 9 1172 2194 308683448 308682426 0.000000e+00 1624
27 TraesCS2B01G330500 chr3D 98.777 327 4 0 1 327 21900707 21900381 1.130000e-162 582
28 TraesCS2B01G330500 chrUn 98.471 327 5 0 1 327 441827891 441828217 5.250000e-161 577
29 TraesCS2B01G330500 chr3B 97.859 327 6 1 1 327 201509745 201509420 4.090000e-157 564
30 TraesCS2B01G330500 chr3B 99.149 235 2 0 387 621 101919330 101919564 7.240000e-115 424
31 TraesCS2B01G330500 chr7A 98.723 235 3 0 387 621 109219515 109219749 3.370000e-113 418


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 TraesCS2B01G330500 chr2B 474899493 474901687 2194 False 4054.0 4054 100.0000 1 2195 1 chr2B.!!$F1 2194
1 TraesCS2B01G330500 chr1A 554457226 554459818 2592 False 1580.5 2743 98.6235 387 2195 2 chr1A.!!$F1 1808
2 TraesCS2B01G330500 chr1A 554455686 554458182 2496 True 424.0 424 99.1490 387 621 2 chr1A.!!$R1 234
3 TraesCS2B01G330500 chr1D 254416860 254418411 1551 False 2638.0 2638 97.3670 645 2195 1 chr1D.!!$F1 1550
4 TraesCS2B01G330500 chr6D 45510218 45511776 1558 True 2590.0 2590 96.7500 645 2195 1 chr6D.!!$R1 1550
5 TraesCS2B01G330500 chr5D 6179596 6181151 1555 True 2553.0 2553 96.3650 645 2195 1 chr5D.!!$R1 1550
6 TraesCS2B01G330500 chr5D 512415122 512416234 1112 True 1838.0 1838 96.7680 1102 2195 1 chr5D.!!$R5 1093
7 TraesCS2B01G330500 chr5D 512408187 512409297 1110 True 1831.0 1831 96.6760 1102 2195 1 chr5D.!!$R4 1093
8 TraesCS2B01G330500 chr5A 607198749 607200295 1546 True 2551.0 2551 96.4010 645 2195 1 chr5A.!!$R1 1550
9 TraesCS2B01G330500 chr5A 520661594 520662540 946 False 1282.0 1282 91.4140 1097 2029 1 chr5A.!!$F1 932
10 TraesCS2B01G330500 chr7B 105255258 105256800 1542 True 2442.0 2442 95.1740 645 2195 1 chr7B.!!$R1 1550
11 TraesCS2B01G330500 chr2A 334594721 334595896 1175 True 1995.0 1995 97.3710 1012 2182 1 chr2A.!!$R1 1170
12 TraesCS2B01G330500 chr2A 335829841 335830832 991 True 1633.0 1633 96.4930 645 1630 1 chr2A.!!$R2 985
13 TraesCS2B01G330500 chr4D 207373081 207374383 1302 False 1906.0 1906 93.1610 895 2195 1 chr4D.!!$F1 1300
14 TraesCS2B01G330500 chr4B 308682426 308683448 1022 True 1624.0 1624 95.3400 1172 2194 1 chr4B.!!$R1 1022

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
344 345 0.038166 ATGGACACGATTGCCTTGGT 59.962 50.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 2790 3.840666 AGAGATGGCTGAGTGGACTAAAA 59.159 43.478 0.0 0.0 0.0 1.52 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
19 20 0.727398 GTCTGGCCCTTTCGAATTCG 59.273 55.000 21.78 21.78 41.45 3.34
37 38 9.272901 TCGAATTCGAATAAAACATCAACAATC 57.727 29.630 27.36 0.00 46.30 2.67
38 39 8.245777 CGAATTCGAATAAAACATCAACAATCG 58.754 33.333 23.29 7.80 43.02 3.34
39 40 7.969387 ATTCGAATAAAACATCAACAATCGG 57.031 32.000 9.39 0.00 0.00 4.18
40 41 6.729391 TCGAATAAAACATCAACAATCGGA 57.271 33.333 0.00 0.00 0.00 4.55
41 42 7.135089 TCGAATAAAACATCAACAATCGGAA 57.865 32.000 0.00 0.00 0.00 4.30
42 43 7.018826 TCGAATAAAACATCAACAATCGGAAC 58.981 34.615 0.00 0.00 0.00 3.62
43 44 7.021196 CGAATAAAACATCAACAATCGGAACT 58.979 34.615 0.00 0.00 0.00 3.01
44 45 7.537306 CGAATAAAACATCAACAATCGGAACTT 59.463 33.333 0.00 0.00 0.00 2.66
45 46 9.834628 GAATAAAACATCAACAATCGGAACTTA 57.165 29.630 0.00 0.00 0.00 2.24
47 48 9.840427 ATAAAACATCAACAATCGGAACTTAAG 57.160 29.630 0.00 0.00 0.00 1.85
48 49 6.877611 AACATCAACAATCGGAACTTAAGT 57.122 33.333 1.12 1.12 0.00 2.24
49 50 6.877611 ACATCAACAATCGGAACTTAAGTT 57.122 33.333 20.67 20.67 41.64 2.66
60 61 4.888038 GAACTTAAGTTCCGGTTGTTGT 57.112 40.909 30.17 2.61 46.42 3.32
61 62 5.239359 GAACTTAAGTTCCGGTTGTTGTT 57.761 39.130 30.17 2.41 46.42 2.83
62 63 5.643664 GAACTTAAGTTCCGGTTGTTGTTT 58.356 37.500 30.17 1.98 46.42 2.83
63 64 5.239359 ACTTAAGTTCCGGTTGTTGTTTC 57.761 39.130 1.12 0.00 0.00 2.78
64 65 4.945543 ACTTAAGTTCCGGTTGTTGTTTCT 59.054 37.500 1.12 0.00 0.00 2.52
65 66 5.416639 ACTTAAGTTCCGGTTGTTGTTTCTT 59.583 36.000 1.12 0.00 0.00 2.52
66 67 6.598850 ACTTAAGTTCCGGTTGTTGTTTCTTA 59.401 34.615 1.12 0.00 0.00 2.10
67 68 5.900865 AAGTTCCGGTTGTTGTTTCTTAA 57.099 34.783 0.00 0.00 0.00 1.85
68 69 5.900865 AGTTCCGGTTGTTGTTTCTTAAA 57.099 34.783 0.00 0.00 0.00 1.52
69 70 6.459670 AGTTCCGGTTGTTGTTTCTTAAAT 57.540 33.333 0.00 0.00 0.00 1.40
70 71 6.869695 AGTTCCGGTTGTTGTTTCTTAAATT 58.130 32.000 0.00 0.00 0.00 1.82
71 72 7.324935 AGTTCCGGTTGTTGTTTCTTAAATTT 58.675 30.769 0.00 0.00 0.00 1.82
72 73 7.820386 AGTTCCGGTTGTTGTTTCTTAAATTTT 59.180 29.630 0.00 0.00 0.00 1.82
73 74 7.527084 TCCGGTTGTTGTTTCTTAAATTTTG 57.473 32.000 0.00 0.00 0.00 2.44
74 75 6.535508 TCCGGTTGTTGTTTCTTAAATTTTGG 59.464 34.615 0.00 0.00 0.00 3.28
75 76 6.314152 CCGGTTGTTGTTTCTTAAATTTTGGT 59.686 34.615 0.00 0.00 0.00 3.67
76 77 7.148390 CCGGTTGTTGTTTCTTAAATTTTGGTT 60.148 33.333 0.00 0.00 0.00 3.67
77 78 7.690224 CGGTTGTTGTTTCTTAAATTTTGGTTG 59.310 33.333 0.00 0.00 0.00 3.77
78 79 8.508062 GGTTGTTGTTTCTTAAATTTTGGTTGT 58.492 29.630 0.00 0.00 0.00 3.32
79 80 9.885934 GTTGTTGTTTCTTAAATTTTGGTTGTT 57.114 25.926 0.00 0.00 0.00 2.83
80 81 9.884465 TTGTTGTTTCTTAAATTTTGGTTGTTG 57.116 25.926 0.00 0.00 0.00 3.33
81 82 9.057089 TGTTGTTTCTTAAATTTTGGTTGTTGT 57.943 25.926 0.00 0.00 0.00 3.32
82 83 9.885934 GTTGTTTCTTAAATTTTGGTTGTTGTT 57.114 25.926 0.00 0.00 0.00 2.83
94 95 7.569677 TTTGGTTGTTGTTTCTTAAGTTTCG 57.430 32.000 1.63 0.00 0.00 3.46
95 96 6.497785 TGGTTGTTGTTTCTTAAGTTTCGA 57.502 33.333 1.63 0.00 0.00 3.71
96 97 7.090953 TGGTTGTTGTTTCTTAAGTTTCGAT 57.909 32.000 1.63 0.00 0.00 3.59
97 98 7.540299 TGGTTGTTGTTTCTTAAGTTTCGATT 58.460 30.769 1.63 0.00 0.00 3.34
98 99 7.486551 TGGTTGTTGTTTCTTAAGTTTCGATTG 59.513 33.333 1.63 0.00 0.00 2.67
99 100 7.043656 GGTTGTTGTTTCTTAAGTTTCGATTGG 60.044 37.037 1.63 0.00 0.00 3.16
100 101 7.323049 TGTTGTTTCTTAAGTTTCGATTGGA 57.677 32.000 1.63 0.00 0.00 3.53
101 102 7.763356 TGTTGTTTCTTAAGTTTCGATTGGAA 58.237 30.769 1.63 0.00 0.00 3.53
102 103 8.410141 TGTTGTTTCTTAAGTTTCGATTGGAAT 58.590 29.630 1.63 0.00 33.85 3.01
103 104 9.244799 GTTGTTTCTTAAGTTTCGATTGGAATT 57.755 29.630 1.63 0.00 33.85 2.17
104 105 8.795786 TGTTTCTTAAGTTTCGATTGGAATTG 57.204 30.769 1.63 0.00 33.85 2.32
105 106 8.410141 TGTTTCTTAAGTTTCGATTGGAATTGT 58.590 29.630 1.63 0.00 33.85 2.71
106 107 9.887406 GTTTCTTAAGTTTCGATTGGAATTGTA 57.113 29.630 1.63 0.00 33.85 2.41
107 108 9.887406 TTTCTTAAGTTTCGATTGGAATTGTAC 57.113 29.630 1.63 0.00 33.85 2.90
108 109 8.842358 TCTTAAGTTTCGATTGGAATTGTACT 57.158 30.769 1.63 0.00 33.85 2.73
109 110 9.280174 TCTTAAGTTTCGATTGGAATTGTACTT 57.720 29.630 1.63 0.00 33.85 2.24
110 111 9.893305 CTTAAGTTTCGATTGGAATTGTACTTT 57.107 29.630 11.58 0.00 33.85 2.66
112 113 8.574196 AAGTTTCGATTGGAATTGTACTTTTG 57.426 30.769 0.00 0.00 33.85 2.44
113 114 6.640907 AGTTTCGATTGGAATTGTACTTTTGC 59.359 34.615 0.00 0.00 33.85 3.68
114 115 5.697473 TCGATTGGAATTGTACTTTTGCA 57.303 34.783 0.00 0.00 0.00 4.08
115 116 6.266168 TCGATTGGAATTGTACTTTTGCAT 57.734 33.333 0.00 0.00 0.00 3.96
116 117 6.686630 TCGATTGGAATTGTACTTTTGCATT 58.313 32.000 0.00 0.00 0.00 3.56
117 118 7.821652 TCGATTGGAATTGTACTTTTGCATTA 58.178 30.769 0.00 0.00 0.00 1.90
118 119 8.300286 TCGATTGGAATTGTACTTTTGCATTAA 58.700 29.630 0.00 0.00 0.00 1.40
119 120 9.086336 CGATTGGAATTGTACTTTTGCATTAAT 57.914 29.630 0.00 0.00 0.00 1.40
122 123 9.770097 TTGGAATTGTACTTTTGCATTAATTGA 57.230 25.926 0.00 0.00 0.00 2.57
123 124 9.421806 TGGAATTGTACTTTTGCATTAATTGAG 57.578 29.630 0.00 0.00 0.00 3.02
124 125 8.872845 GGAATTGTACTTTTGCATTAATTGAGG 58.127 33.333 0.00 0.00 0.00 3.86
125 126 9.638239 GAATTGTACTTTTGCATTAATTGAGGA 57.362 29.630 0.00 0.00 0.00 3.71
126 127 9.995003 AATTGTACTTTTGCATTAATTGAGGAA 57.005 25.926 0.00 0.00 0.00 3.36
132 133 9.807649 ACTTTTGCATTAATTGAGGAATATGTC 57.192 29.630 0.00 0.00 0.00 3.06
176 177 9.573133 GAACCTGTAATTATTGAAATTGACTGG 57.427 33.333 0.00 0.00 0.00 4.00
177 178 8.066612 ACCTGTAATTATTGAAATTGACTGGG 57.933 34.615 0.00 0.00 0.00 4.45
178 179 6.980397 CCTGTAATTATTGAAATTGACTGGGC 59.020 38.462 0.00 0.00 0.00 5.36
179 180 7.147846 CCTGTAATTATTGAAATTGACTGGGCT 60.148 37.037 0.00 0.00 0.00 5.19
180 181 8.133024 TGTAATTATTGAAATTGACTGGGCTT 57.867 30.769 0.00 0.00 0.00 4.35
181 182 8.034215 TGTAATTATTGAAATTGACTGGGCTTG 58.966 33.333 0.00 0.00 0.00 4.01
182 183 6.855763 ATTATTGAAATTGACTGGGCTTGA 57.144 33.333 0.00 0.00 0.00 3.02
183 184 6.662865 TTATTGAAATTGACTGGGCTTGAA 57.337 33.333 0.00 0.00 0.00 2.69
184 185 5.549742 ATTGAAATTGACTGGGCTTGAAA 57.450 34.783 0.00 0.00 0.00 2.69
185 186 5.549742 TTGAAATTGACTGGGCTTGAAAT 57.450 34.783 0.00 0.00 0.00 2.17
186 187 5.549742 TGAAATTGACTGGGCTTGAAATT 57.450 34.783 0.00 0.00 0.00 1.82
187 188 5.927819 TGAAATTGACTGGGCTTGAAATTT 58.072 33.333 0.00 0.00 31.73 1.82
188 189 5.990996 TGAAATTGACTGGGCTTGAAATTTC 59.009 36.000 11.41 11.41 41.25 2.17
189 190 5.813513 AATTGACTGGGCTTGAAATTTCT 57.186 34.783 18.64 0.00 0.00 2.52
190 191 5.813513 ATTGACTGGGCTTGAAATTTCTT 57.186 34.783 18.64 0.00 0.00 2.52
191 192 5.612725 TTGACTGGGCTTGAAATTTCTTT 57.387 34.783 18.64 0.00 0.00 2.52
192 193 5.612725 TGACTGGGCTTGAAATTTCTTTT 57.387 34.783 18.64 0.00 0.00 2.27
193 194 5.600696 TGACTGGGCTTGAAATTTCTTTTC 58.399 37.500 18.64 6.67 43.42 2.29
194 195 4.620982 ACTGGGCTTGAAATTTCTTTTCG 58.379 39.130 18.64 4.53 45.63 3.46
195 196 4.099419 ACTGGGCTTGAAATTTCTTTTCGT 59.901 37.500 18.64 5.32 45.63 3.85
196 197 5.017294 TGGGCTTGAAATTTCTTTTCGTT 57.983 34.783 18.64 0.00 45.63 3.85
197 198 5.047188 TGGGCTTGAAATTTCTTTTCGTTC 58.953 37.500 18.64 2.98 45.63 3.95
198 199 5.163457 TGGGCTTGAAATTTCTTTTCGTTCT 60.163 36.000 18.64 0.00 45.63 3.01
199 200 5.402568 GGGCTTGAAATTTCTTTTCGTTCTC 59.597 40.000 18.64 0.00 45.63 2.87
200 201 5.977129 GGCTTGAAATTTCTTTTCGTTCTCA 59.023 36.000 18.64 0.00 45.63 3.27
201 202 6.642540 GGCTTGAAATTTCTTTTCGTTCTCAT 59.357 34.615 18.64 0.00 45.63 2.90
202 203 7.807907 GGCTTGAAATTTCTTTTCGTTCTCATA 59.192 33.333 18.64 0.00 45.63 2.15
203 204 8.844690 GCTTGAAATTTCTTTTCGTTCTCATAG 58.155 33.333 18.64 0.00 45.63 2.23
204 205 9.884465 CTTGAAATTTCTTTTCGTTCTCATAGT 57.116 29.630 18.64 0.00 45.63 2.12
208 209 9.807386 AAATTTCTTTTCGTTCTCATAGTTACG 57.193 29.630 0.00 0.00 35.46 3.18
209 210 8.752766 ATTTCTTTTCGTTCTCATAGTTACGA 57.247 30.769 0.00 0.00 40.80 3.43
213 214 5.980324 TTCGTTCTCATAGTTACGAAACG 57.020 39.130 6.47 0.00 46.24 3.60
214 215 4.406069 TCGTTCTCATAGTTACGAAACGG 58.594 43.478 0.00 0.00 39.74 4.44
215 216 4.083324 TCGTTCTCATAGTTACGAAACGGT 60.083 41.667 0.00 0.00 39.74 4.83
216 217 5.121611 TCGTTCTCATAGTTACGAAACGGTA 59.878 40.000 0.00 0.00 39.74 4.02
217 218 5.794945 CGTTCTCATAGTTACGAAACGGTAA 59.205 40.000 0.00 0.00 40.73 2.85
218 219 6.021939 CGTTCTCATAGTTACGAAACGGTAAG 60.022 42.308 0.00 0.00 40.73 2.34
219 220 6.741992 TCTCATAGTTACGAAACGGTAAGA 57.258 37.500 0.00 0.00 40.73 2.10
220 221 7.144722 TCTCATAGTTACGAAACGGTAAGAA 57.855 36.000 0.00 0.00 40.73 2.52
221 222 7.592938 TCTCATAGTTACGAAACGGTAAGAAA 58.407 34.615 0.00 0.00 40.73 2.52
222 223 7.752239 TCTCATAGTTACGAAACGGTAAGAAAG 59.248 37.037 0.00 0.00 40.73 2.62
223 224 7.592938 TCATAGTTACGAAACGGTAAGAAAGA 58.407 34.615 0.00 0.00 40.73 2.52
224 225 8.246180 TCATAGTTACGAAACGGTAAGAAAGAT 58.754 33.333 0.00 0.00 40.73 2.40
225 226 9.507280 CATAGTTACGAAACGGTAAGAAAGATA 57.493 33.333 0.00 0.00 40.73 1.98
227 228 8.816640 AGTTACGAAACGGTAAGAAAGATAAA 57.183 30.769 0.00 0.00 40.73 1.40
228 229 9.260002 AGTTACGAAACGGTAAGAAAGATAAAA 57.740 29.630 0.00 0.00 40.73 1.52
232 233 8.375465 ACGAAACGGTAAGAAAGATAAAATACG 58.625 33.333 0.00 0.00 0.00 3.06
233 234 8.586273 CGAAACGGTAAGAAAGATAAAATACGA 58.414 33.333 0.00 0.00 0.00 3.43
234 235 9.897349 GAAACGGTAAGAAAGATAAAATACGAG 57.103 33.333 0.00 0.00 0.00 4.18
235 236 7.460751 ACGGTAAGAAAGATAAAATACGAGC 57.539 36.000 0.00 0.00 0.00 5.03
236 237 6.478016 ACGGTAAGAAAGATAAAATACGAGCC 59.522 38.462 0.00 0.00 0.00 4.70
237 238 6.700520 CGGTAAGAAAGATAAAATACGAGCCT 59.299 38.462 0.00 0.00 0.00 4.58
238 239 7.306632 CGGTAAGAAAGATAAAATACGAGCCTG 60.307 40.741 0.00 0.00 0.00 4.85
239 240 7.494952 GGTAAGAAAGATAAAATACGAGCCTGT 59.505 37.037 0.00 0.00 0.00 4.00
240 241 7.923414 AAGAAAGATAAAATACGAGCCTGTT 57.077 32.000 0.00 0.00 0.00 3.16
241 242 7.923414 AGAAAGATAAAATACGAGCCTGTTT 57.077 32.000 0.00 0.00 0.00 2.83
242 243 8.336801 AGAAAGATAAAATACGAGCCTGTTTT 57.663 30.769 0.00 0.00 0.00 2.43
243 244 9.444600 AGAAAGATAAAATACGAGCCTGTTTTA 57.555 29.630 0.00 0.00 32.53 1.52
251 252 9.444600 AAAATACGAGCCTGTTTTATAGAAAGA 57.555 29.630 0.00 0.00 0.00 2.52
252 253 8.649973 AATACGAGCCTGTTTTATAGAAAGAG 57.350 34.615 0.00 0.00 0.00 2.85
253 254 6.038997 ACGAGCCTGTTTTATAGAAAGAGT 57.961 37.500 0.00 0.00 0.00 3.24
254 255 7.166691 ACGAGCCTGTTTTATAGAAAGAGTA 57.833 36.000 0.00 0.00 0.00 2.59
255 256 7.609056 ACGAGCCTGTTTTATAGAAAGAGTAA 58.391 34.615 0.00 0.00 0.00 2.24
256 257 8.258708 ACGAGCCTGTTTTATAGAAAGAGTAAT 58.741 33.333 0.00 0.00 0.00 1.89
257 258 9.099454 CGAGCCTGTTTTATAGAAAGAGTAATT 57.901 33.333 0.00 0.00 0.00 1.40
275 276 9.878599 AGAGTAATTAATCGTTGTTGTTTCAAG 57.121 29.630 7.24 0.00 0.00 3.02
276 277 9.113876 GAGTAATTAATCGTTGTTGTTTCAAGG 57.886 33.333 0.00 0.00 35.41 3.61
277 278 8.626526 AGTAATTAATCGTTGTTGTTTCAAGGT 58.373 29.630 0.00 0.00 35.54 3.50
278 279 9.240159 GTAATTAATCGTTGTTGTTTCAAGGTT 57.760 29.630 0.00 0.00 35.54 3.50
280 281 9.804758 AATTAATCGTTGTTGTTTCAAGGTTAA 57.195 25.926 0.00 0.00 35.54 2.01
281 282 9.974980 ATTAATCGTTGTTGTTTCAAGGTTAAT 57.025 25.926 0.00 0.00 35.54 1.40
282 283 7.924103 AATCGTTGTTGTTTCAAGGTTAATC 57.076 32.000 0.00 0.00 35.54 1.75
283 284 6.687081 TCGTTGTTGTTTCAAGGTTAATCT 57.313 33.333 0.00 0.00 35.54 2.40
284 285 7.789273 TCGTTGTTGTTTCAAGGTTAATCTA 57.211 32.000 0.00 0.00 35.54 1.98
285 286 8.385898 TCGTTGTTGTTTCAAGGTTAATCTAT 57.614 30.769 0.00 0.00 35.54 1.98
286 287 8.842280 TCGTTGTTGTTTCAAGGTTAATCTATT 58.158 29.630 0.00 0.00 35.54 1.73
287 288 9.458374 CGTTGTTGTTTCAAGGTTAATCTATTT 57.542 29.630 0.00 0.00 0.00 1.40
297 298 9.459640 TCAAGGTTAATCTATTTATTCGTCTCG 57.540 33.333 0.00 0.00 0.00 4.04
298 299 9.459640 CAAGGTTAATCTATTTATTCGTCTCGA 57.540 33.333 0.00 0.00 0.00 4.04
314 315 8.712285 TTCGTCTCGATAATATTTTTCCTTGT 57.288 30.769 0.00 0.00 35.23 3.16
315 316 8.712285 TCGTCTCGATAATATTTTTCCTTGTT 57.288 30.769 0.00 0.00 0.00 2.83
316 317 8.814235 TCGTCTCGATAATATTTTTCCTTGTTC 58.186 33.333 0.00 0.00 0.00 3.18
317 318 8.600625 CGTCTCGATAATATTTTTCCTTGTTCA 58.399 33.333 0.00 0.00 0.00 3.18
318 319 9.704098 GTCTCGATAATATTTTTCCTTGTTCAC 57.296 33.333 0.00 0.00 0.00 3.18
319 320 9.667107 TCTCGATAATATTTTTCCTTGTTCACT 57.333 29.630 0.00 0.00 0.00 3.41
330 331 9.974980 TTTTTCCTTGTTCACTAATAAATGGAC 57.025 29.630 0.00 0.00 0.00 4.02
331 332 8.698973 TTTCCTTGTTCACTAATAAATGGACA 57.301 30.769 0.00 0.00 32.29 4.02
332 333 7.681939 TCCTTGTTCACTAATAAATGGACAC 57.318 36.000 0.00 0.00 33.96 3.67
333 334 6.370442 TCCTTGTTCACTAATAAATGGACACG 59.630 38.462 0.00 0.00 33.96 4.49
334 335 6.370442 CCTTGTTCACTAATAAATGGACACGA 59.630 38.462 0.00 0.00 33.96 4.35
335 336 7.065803 CCTTGTTCACTAATAAATGGACACGAT 59.934 37.037 0.00 0.00 33.96 3.73
336 337 7.915293 TGTTCACTAATAAATGGACACGATT 57.085 32.000 0.00 0.00 28.99 3.34
337 338 7.747888 TGTTCACTAATAAATGGACACGATTG 58.252 34.615 0.00 0.00 28.99 2.67
338 339 6.358118 TCACTAATAAATGGACACGATTGC 57.642 37.500 0.00 0.00 0.00 3.56
339 340 5.295787 TCACTAATAAATGGACACGATTGCC 59.704 40.000 0.00 0.00 0.00 4.52
340 341 5.296780 CACTAATAAATGGACACGATTGCCT 59.703 40.000 0.00 0.00 0.00 4.75
341 342 5.885912 ACTAATAAATGGACACGATTGCCTT 59.114 36.000 0.00 0.00 0.00 4.35
342 343 4.637483 ATAAATGGACACGATTGCCTTG 57.363 40.909 0.00 0.00 0.00 3.61
343 344 1.176527 AATGGACACGATTGCCTTGG 58.823 50.000 0.00 0.00 0.00 3.61
344 345 0.038166 ATGGACACGATTGCCTTGGT 59.962 50.000 0.00 0.00 0.00 3.67
345 346 0.687920 TGGACACGATTGCCTTGGTA 59.312 50.000 0.00 0.00 0.00 3.25
346 347 1.280710 TGGACACGATTGCCTTGGTAT 59.719 47.619 0.00 0.00 0.00 2.73
347 348 1.940613 GGACACGATTGCCTTGGTATC 59.059 52.381 0.00 0.00 0.00 2.24
348 349 1.940613 GACACGATTGCCTTGGTATCC 59.059 52.381 0.00 0.00 0.00 2.59
349 350 1.308998 CACGATTGCCTTGGTATCCC 58.691 55.000 0.00 0.00 0.00 3.85
350 351 0.916086 ACGATTGCCTTGGTATCCCA 59.084 50.000 0.00 0.00 39.65 4.37
351 352 1.494721 ACGATTGCCTTGGTATCCCAT 59.505 47.619 0.00 0.00 41.49 4.00
352 353 1.881973 CGATTGCCTTGGTATCCCATG 59.118 52.381 0.00 0.00 41.49 3.66
353 354 2.487086 CGATTGCCTTGGTATCCCATGA 60.487 50.000 0.00 0.00 41.49 3.07
354 355 3.565307 GATTGCCTTGGTATCCCATGAA 58.435 45.455 0.00 0.00 41.49 2.57
355 356 3.464720 TTGCCTTGGTATCCCATGAAA 57.535 42.857 0.00 0.00 41.49 2.69
356 357 3.464720 TGCCTTGGTATCCCATGAAAA 57.535 42.857 0.00 0.00 41.49 2.29
357 358 3.992999 TGCCTTGGTATCCCATGAAAAT 58.007 40.909 0.00 0.00 41.49 1.82
358 359 5.136068 TGCCTTGGTATCCCATGAAAATA 57.864 39.130 0.00 0.00 41.49 1.40
359 360 5.523588 TGCCTTGGTATCCCATGAAAATAA 58.476 37.500 0.00 0.00 41.49 1.40
360 361 5.960811 TGCCTTGGTATCCCATGAAAATAAA 59.039 36.000 0.00 0.00 41.49 1.40
361 362 6.127196 TGCCTTGGTATCCCATGAAAATAAAC 60.127 38.462 0.00 0.00 41.49 2.01
362 363 6.127196 GCCTTGGTATCCCATGAAAATAAACA 60.127 38.462 0.00 0.00 41.49 2.83
363 364 7.418942 GCCTTGGTATCCCATGAAAATAAACAT 60.419 37.037 0.00 0.00 41.49 2.71
364 365 9.142014 CCTTGGTATCCCATGAAAATAAACATA 57.858 33.333 0.00 0.00 41.49 2.29
624 625 8.842280 AGAAGTACGAGAATTCTATAACTGAGG 58.158 37.037 8.25 0.00 31.63 3.86
629 1258 8.012957 ACGAGAATTCTATAACTGAGGTTGAT 57.987 34.615 8.25 0.00 36.92 2.57
633 1262 8.552296 AGAATTCTATAACTGAGGTTGATTGGT 58.448 33.333 6.06 0.00 36.92 3.67
634 1263 8.511604 AATTCTATAACTGAGGTTGATTGGTG 57.488 34.615 0.00 0.00 36.92 4.17
641 1270 5.690865 ACTGAGGTTGATTGGTGTTAAGAA 58.309 37.500 0.00 0.00 0.00 2.52
642 1271 6.126409 ACTGAGGTTGATTGGTGTTAAGAAA 58.874 36.000 0.00 0.00 0.00 2.52
643 1272 6.605594 ACTGAGGTTGATTGGTGTTAAGAAAA 59.394 34.615 0.00 0.00 0.00 2.29
647 1434 6.382859 AGGTTGATTGGTGTTAAGAAAAACCT 59.617 34.615 0.00 0.00 42.77 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.727398 CGAATTCGAAAGGGCCAGAC 59.273 55.000 23.29 0.00 43.02 3.51
1 2 0.611200 TCGAATTCGAAAGGGCCAGA 59.389 50.000 27.36 1.08 46.30 3.86
2 3 3.153024 TCGAATTCGAAAGGGCCAG 57.847 52.632 27.36 0.00 46.30 4.85
12 13 8.245777 CGATTGTTGATGTTTTATTCGAATTCG 58.754 33.333 21.78 21.78 41.45 3.34
13 14 8.523464 CCGATTGTTGATGTTTTATTCGAATTC 58.477 33.333 17.19 7.13 0.00 2.17
14 15 8.240682 TCCGATTGTTGATGTTTTATTCGAATT 58.759 29.630 17.19 0.00 0.00 2.17
15 16 7.757526 TCCGATTGTTGATGTTTTATTCGAAT 58.242 30.769 16.15 16.15 0.00 3.34
16 17 7.135089 TCCGATTGTTGATGTTTTATTCGAA 57.865 32.000 0.00 0.00 0.00 3.71
17 18 6.729391 TCCGATTGTTGATGTTTTATTCGA 57.271 33.333 0.00 0.00 0.00 3.71
18 19 7.021196 AGTTCCGATTGTTGATGTTTTATTCG 58.979 34.615 0.00 0.00 0.00 3.34
19 20 8.742554 AAGTTCCGATTGTTGATGTTTTATTC 57.257 30.769 0.00 0.00 0.00 1.75
21 22 9.840427 CTTAAGTTCCGATTGTTGATGTTTTAT 57.160 29.630 0.00 0.00 0.00 1.40
22 23 8.842280 ACTTAAGTTCCGATTGTTGATGTTTTA 58.158 29.630 1.12 0.00 0.00 1.52
23 24 7.712797 ACTTAAGTTCCGATTGTTGATGTTTT 58.287 30.769 1.12 0.00 0.00 2.43
24 25 7.272037 ACTTAAGTTCCGATTGTTGATGTTT 57.728 32.000 1.12 0.00 0.00 2.83
25 26 6.877611 ACTTAAGTTCCGATTGTTGATGTT 57.122 33.333 1.12 0.00 0.00 2.71
26 27 6.877611 AACTTAAGTTCCGATTGTTGATGT 57.122 33.333 15.22 0.00 31.64 3.06
40 41 5.416639 AGAAACAACAACCGGAACTTAAGTT 59.583 36.000 20.67 20.67 41.64 2.66
41 42 4.945543 AGAAACAACAACCGGAACTTAAGT 59.054 37.500 9.46 1.12 0.00 2.24
42 43 5.494632 AGAAACAACAACCGGAACTTAAG 57.505 39.130 9.46 0.00 0.00 1.85
43 44 5.900865 AAGAAACAACAACCGGAACTTAA 57.099 34.783 9.46 0.00 0.00 1.85
44 45 6.998968 TTAAGAAACAACAACCGGAACTTA 57.001 33.333 9.46 1.69 0.00 2.24
45 46 5.900865 TTAAGAAACAACAACCGGAACTT 57.099 34.783 9.46 2.62 0.00 2.66
46 47 5.900865 TTTAAGAAACAACAACCGGAACT 57.099 34.783 9.46 0.00 0.00 3.01
47 48 7.528481 AAATTTAAGAAACAACAACCGGAAC 57.472 32.000 9.46 0.00 0.00 3.62
48 49 7.064728 CCAAAATTTAAGAAACAACAACCGGAA 59.935 33.333 9.46 0.00 0.00 4.30
49 50 6.535508 CCAAAATTTAAGAAACAACAACCGGA 59.464 34.615 9.46 0.00 0.00 5.14
50 51 6.314152 ACCAAAATTTAAGAAACAACAACCGG 59.686 34.615 0.00 0.00 0.00 5.28
51 52 7.297229 ACCAAAATTTAAGAAACAACAACCG 57.703 32.000 0.00 0.00 0.00 4.44
52 53 8.508062 ACAACCAAAATTTAAGAAACAACAACC 58.492 29.630 0.00 0.00 0.00 3.77
53 54 9.885934 AACAACCAAAATTTAAGAAACAACAAC 57.114 25.926 0.00 0.00 0.00 3.32
54 55 9.884465 CAACAACCAAAATTTAAGAAACAACAA 57.116 25.926 0.00 0.00 0.00 2.83
55 56 9.057089 ACAACAACCAAAATTTAAGAAACAACA 57.943 25.926 0.00 0.00 0.00 3.33
56 57 9.885934 AACAACAACCAAAATTTAAGAAACAAC 57.114 25.926 0.00 0.00 0.00 3.32
68 69 8.652463 CGAAACTTAAGAAACAACAACCAAAAT 58.348 29.630 10.09 0.00 0.00 1.82
69 70 7.866393 TCGAAACTTAAGAAACAACAACCAAAA 59.134 29.630 10.09 0.00 0.00 2.44
70 71 7.368833 TCGAAACTTAAGAAACAACAACCAAA 58.631 30.769 10.09 0.00 0.00 3.28
71 72 6.910995 TCGAAACTTAAGAAACAACAACCAA 58.089 32.000 10.09 0.00 0.00 3.67
72 73 6.497785 TCGAAACTTAAGAAACAACAACCA 57.502 33.333 10.09 0.00 0.00 3.67
73 74 7.043656 CCAATCGAAACTTAAGAAACAACAACC 60.044 37.037 10.09 0.00 0.00 3.77
74 75 7.698970 TCCAATCGAAACTTAAGAAACAACAAC 59.301 33.333 10.09 0.00 0.00 3.32
75 76 7.763356 TCCAATCGAAACTTAAGAAACAACAA 58.237 30.769 10.09 0.00 0.00 2.83
76 77 7.323049 TCCAATCGAAACTTAAGAAACAACA 57.677 32.000 10.09 0.00 0.00 3.33
77 78 8.797266 ATTCCAATCGAAACTTAAGAAACAAC 57.203 30.769 10.09 0.00 33.08 3.32
78 79 9.243637 CAATTCCAATCGAAACTTAAGAAACAA 57.756 29.630 10.09 0.00 33.08 2.83
79 80 8.410141 ACAATTCCAATCGAAACTTAAGAAACA 58.590 29.630 10.09 0.00 33.08 2.83
80 81 8.797266 ACAATTCCAATCGAAACTTAAGAAAC 57.203 30.769 10.09 0.00 33.08 2.78
81 82 9.887406 GTACAATTCCAATCGAAACTTAAGAAA 57.113 29.630 10.09 0.00 33.08 2.52
82 83 9.280174 AGTACAATTCCAATCGAAACTTAAGAA 57.720 29.630 10.09 0.00 33.08 2.52
83 84 8.842358 AGTACAATTCCAATCGAAACTTAAGA 57.158 30.769 10.09 0.00 33.08 2.10
84 85 9.893305 AAAGTACAATTCCAATCGAAACTTAAG 57.107 29.630 0.00 0.00 30.15 1.85
86 87 9.672086 CAAAAGTACAATTCCAATCGAAACTTA 57.328 29.630 0.00 0.00 30.15 2.24
87 88 7.169140 GCAAAAGTACAATTCCAATCGAAACTT 59.831 33.333 0.00 0.00 31.89 2.66
88 89 6.640907 GCAAAAGTACAATTCCAATCGAAACT 59.359 34.615 0.00 0.00 33.08 2.66
89 90 6.419413 TGCAAAAGTACAATTCCAATCGAAAC 59.581 34.615 0.00 0.00 33.08 2.78
90 91 6.507900 TGCAAAAGTACAATTCCAATCGAAA 58.492 32.000 0.00 0.00 33.08 3.46
91 92 6.078202 TGCAAAAGTACAATTCCAATCGAA 57.922 33.333 0.00 0.00 34.14 3.71
92 93 5.697473 TGCAAAAGTACAATTCCAATCGA 57.303 34.783 0.00 0.00 0.00 3.59
93 94 6.949578 AATGCAAAAGTACAATTCCAATCG 57.050 33.333 0.00 0.00 0.00 3.34
96 97 9.770097 TCAATTAATGCAAAAGTACAATTCCAA 57.230 25.926 0.00 0.00 0.00 3.53
97 98 9.421806 CTCAATTAATGCAAAAGTACAATTCCA 57.578 29.630 0.00 0.00 0.00 3.53
98 99 8.872845 CCTCAATTAATGCAAAAGTACAATTCC 58.127 33.333 0.00 0.00 0.00 3.01
99 100 9.638239 TCCTCAATTAATGCAAAAGTACAATTC 57.362 29.630 0.00 0.00 0.00 2.17
100 101 9.995003 TTCCTCAATTAATGCAAAAGTACAATT 57.005 25.926 0.00 0.00 0.00 2.32
106 107 9.807649 GACATATTCCTCAATTAATGCAAAAGT 57.192 29.630 0.00 0.00 0.00 2.66
150 151 9.573133 CCAGTCAATTTCAATAATTACAGGTTC 57.427 33.333 0.00 0.00 0.00 3.62
151 152 8.531146 CCCAGTCAATTTCAATAATTACAGGTT 58.469 33.333 0.00 0.00 0.00 3.50
152 153 7.363793 GCCCAGTCAATTTCAATAATTACAGGT 60.364 37.037 0.00 0.00 0.00 4.00
153 154 6.980397 GCCCAGTCAATTTCAATAATTACAGG 59.020 38.462 0.00 0.00 0.00 4.00
154 155 7.775120 AGCCCAGTCAATTTCAATAATTACAG 58.225 34.615 0.00 0.00 0.00 2.74
155 156 7.716799 AGCCCAGTCAATTTCAATAATTACA 57.283 32.000 0.00 0.00 0.00 2.41
156 157 8.250332 TCAAGCCCAGTCAATTTCAATAATTAC 58.750 33.333 0.00 0.00 0.00 1.89
157 158 8.359875 TCAAGCCCAGTCAATTTCAATAATTA 57.640 30.769 0.00 0.00 0.00 1.40
158 159 7.243604 TCAAGCCCAGTCAATTTCAATAATT 57.756 32.000 0.00 0.00 0.00 1.40
159 160 6.855763 TCAAGCCCAGTCAATTTCAATAAT 57.144 33.333 0.00 0.00 0.00 1.28
160 161 6.662865 TTCAAGCCCAGTCAATTTCAATAA 57.337 33.333 0.00 0.00 0.00 1.40
161 162 6.662865 TTTCAAGCCCAGTCAATTTCAATA 57.337 33.333 0.00 0.00 0.00 1.90
162 163 5.549742 TTTCAAGCCCAGTCAATTTCAAT 57.450 34.783 0.00 0.00 0.00 2.57
163 164 5.549742 ATTTCAAGCCCAGTCAATTTCAA 57.450 34.783 0.00 0.00 0.00 2.69
164 165 5.549742 AATTTCAAGCCCAGTCAATTTCA 57.450 34.783 0.00 0.00 0.00 2.69
165 166 6.226052 AGAAATTTCAAGCCCAGTCAATTTC 58.774 36.000 19.99 6.95 39.39 2.17
166 167 6.178607 AGAAATTTCAAGCCCAGTCAATTT 57.821 33.333 19.99 0.00 0.00 1.82
167 168 5.813513 AGAAATTTCAAGCCCAGTCAATT 57.186 34.783 19.99 0.00 0.00 2.32
168 169 5.813513 AAGAAATTTCAAGCCCAGTCAAT 57.186 34.783 19.99 0.00 0.00 2.57
169 170 5.612725 AAAGAAATTTCAAGCCCAGTCAA 57.387 34.783 19.99 0.00 0.00 3.18
170 171 5.600696 GAAAAGAAATTTCAAGCCCAGTCA 58.399 37.500 19.99 0.00 45.58 3.41
171 172 4.681483 CGAAAAGAAATTTCAAGCCCAGTC 59.319 41.667 19.99 5.14 46.42 3.51
172 173 4.099419 ACGAAAAGAAATTTCAAGCCCAGT 59.901 37.500 19.99 8.11 46.42 4.00
173 174 4.620982 ACGAAAAGAAATTTCAAGCCCAG 58.379 39.130 19.99 7.55 46.42 4.45
174 175 4.664150 ACGAAAAGAAATTTCAAGCCCA 57.336 36.364 19.99 0.00 46.42 5.36
175 176 5.289595 AGAACGAAAAGAAATTTCAAGCCC 58.710 37.500 19.99 4.62 46.42 5.19
176 177 5.977129 TGAGAACGAAAAGAAATTTCAAGCC 59.023 36.000 19.99 5.90 46.42 4.35
177 178 7.629027 ATGAGAACGAAAAGAAATTTCAAGC 57.371 32.000 19.99 5.77 46.42 4.01
178 179 9.884465 ACTATGAGAACGAAAAGAAATTTCAAG 57.116 29.630 19.99 8.48 46.42 3.02
182 183 9.807386 CGTAACTATGAGAACGAAAAGAAATTT 57.193 29.630 0.00 0.00 37.53 1.82
183 184 9.199982 TCGTAACTATGAGAACGAAAAGAAATT 57.800 29.630 0.00 0.00 41.01 1.82
184 185 8.752766 TCGTAACTATGAGAACGAAAAGAAAT 57.247 30.769 0.00 0.00 41.01 2.17
192 193 4.083324 ACCGTTTCGTAACTATGAGAACGA 60.083 41.667 17.94 0.00 42.12 3.85
193 194 4.161333 ACCGTTTCGTAACTATGAGAACG 58.839 43.478 3.36 13.53 36.56 3.95
194 195 7.023575 TCTTACCGTTTCGTAACTATGAGAAC 58.976 38.462 3.36 0.00 31.89 3.01
195 196 7.144722 TCTTACCGTTTCGTAACTATGAGAA 57.855 36.000 3.36 0.00 31.89 2.87
196 197 6.741992 TCTTACCGTTTCGTAACTATGAGA 57.258 37.500 3.36 0.66 31.89 3.27
197 198 7.752239 TCTTTCTTACCGTTTCGTAACTATGAG 59.248 37.037 3.36 0.00 31.89 2.90
198 199 7.592938 TCTTTCTTACCGTTTCGTAACTATGA 58.407 34.615 3.36 0.00 31.89 2.15
199 200 7.801547 TCTTTCTTACCGTTTCGTAACTATG 57.198 36.000 3.36 0.00 31.89 2.23
201 202 9.906660 TTTATCTTTCTTACCGTTTCGTAACTA 57.093 29.630 3.36 0.00 31.89 2.24
202 203 8.816640 TTTATCTTTCTTACCGTTTCGTAACT 57.183 30.769 3.36 0.00 31.89 2.24
206 207 8.375465 CGTATTTTATCTTTCTTACCGTTTCGT 58.625 33.333 0.00 0.00 0.00 3.85
207 208 8.586273 TCGTATTTTATCTTTCTTACCGTTTCG 58.414 33.333 0.00 0.00 0.00 3.46
208 209 9.897349 CTCGTATTTTATCTTTCTTACCGTTTC 57.103 33.333 0.00 0.00 0.00 2.78
209 210 8.385858 GCTCGTATTTTATCTTTCTTACCGTTT 58.614 33.333 0.00 0.00 0.00 3.60
210 211 7.010830 GGCTCGTATTTTATCTTTCTTACCGTT 59.989 37.037 0.00 0.00 0.00 4.44
211 212 6.478016 GGCTCGTATTTTATCTTTCTTACCGT 59.522 38.462 0.00 0.00 0.00 4.83
212 213 6.700520 AGGCTCGTATTTTATCTTTCTTACCG 59.299 38.462 0.00 0.00 0.00 4.02
213 214 7.494952 ACAGGCTCGTATTTTATCTTTCTTACC 59.505 37.037 0.00 0.00 0.00 2.85
214 215 8.421673 ACAGGCTCGTATTTTATCTTTCTTAC 57.578 34.615 0.00 0.00 0.00 2.34
215 216 9.444600 AAACAGGCTCGTATTTTATCTTTCTTA 57.555 29.630 0.00 0.00 0.00 2.10
216 217 7.923414 AACAGGCTCGTATTTTATCTTTCTT 57.077 32.000 0.00 0.00 0.00 2.52
217 218 7.923414 AAACAGGCTCGTATTTTATCTTTCT 57.077 32.000 0.00 0.00 0.00 2.52
225 226 9.444600 TCTTTCTATAAAACAGGCTCGTATTTT 57.555 29.630 0.00 0.00 0.00 1.82
226 227 9.099454 CTCTTTCTATAAAACAGGCTCGTATTT 57.901 33.333 0.00 0.00 0.00 1.40
227 228 8.258708 ACTCTTTCTATAAAACAGGCTCGTATT 58.741 33.333 0.00 0.00 0.00 1.89
228 229 7.783042 ACTCTTTCTATAAAACAGGCTCGTAT 58.217 34.615 0.00 0.00 0.00 3.06
229 230 7.166691 ACTCTTTCTATAAAACAGGCTCGTA 57.833 36.000 0.00 0.00 0.00 3.43
230 231 6.038997 ACTCTTTCTATAAAACAGGCTCGT 57.961 37.500 0.00 0.00 0.00 4.18
231 232 8.649973 ATTACTCTTTCTATAAAACAGGCTCG 57.350 34.615 0.00 0.00 0.00 5.03
249 250 9.878599 CTTGAAACAACAACGATTAATTACTCT 57.121 29.630 0.00 0.00 0.00 3.24
250 251 9.113876 CCTTGAAACAACAACGATTAATTACTC 57.886 33.333 0.00 0.00 0.00 2.59
251 252 8.626526 ACCTTGAAACAACAACGATTAATTACT 58.373 29.630 0.00 0.00 0.00 2.24
252 253 8.791355 ACCTTGAAACAACAACGATTAATTAC 57.209 30.769 0.00 0.00 0.00 1.89
254 255 9.804758 TTAACCTTGAAACAACAACGATTAATT 57.195 25.926 0.00 0.00 0.00 1.40
255 256 9.974980 ATTAACCTTGAAACAACAACGATTAAT 57.025 25.926 0.00 0.00 0.00 1.40
256 257 9.453325 GATTAACCTTGAAACAACAACGATTAA 57.547 29.630 0.00 0.00 0.00 1.40
257 258 8.842280 AGATTAACCTTGAAACAACAACGATTA 58.158 29.630 0.00 0.00 0.00 1.75
258 259 7.712797 AGATTAACCTTGAAACAACAACGATT 58.287 30.769 0.00 0.00 0.00 3.34
259 260 7.272037 AGATTAACCTTGAAACAACAACGAT 57.728 32.000 0.00 0.00 0.00 3.73
260 261 6.687081 AGATTAACCTTGAAACAACAACGA 57.313 33.333 0.00 0.00 0.00 3.85
261 262 9.458374 AAATAGATTAACCTTGAAACAACAACG 57.542 29.630 0.00 0.00 0.00 4.10
271 272 9.459640 CGAGACGAATAAATAGATTAACCTTGA 57.540 33.333 0.00 0.00 0.00 3.02
272 273 9.459640 TCGAGACGAATAAATAGATTAACCTTG 57.540 33.333 0.00 0.00 31.06 3.61
288 289 9.326413 ACAAGGAAAAATATTATCGAGACGAAT 57.674 29.630 0.00 0.00 39.99 3.34
289 290 8.712285 ACAAGGAAAAATATTATCGAGACGAA 57.288 30.769 0.00 0.00 39.99 3.85
290 291 8.712285 AACAAGGAAAAATATTATCGAGACGA 57.288 30.769 0.00 0.00 41.13 4.20
291 292 8.600625 TGAACAAGGAAAAATATTATCGAGACG 58.399 33.333 0.00 0.00 0.00 4.18
292 293 9.704098 GTGAACAAGGAAAAATATTATCGAGAC 57.296 33.333 0.00 0.00 0.00 3.36
293 294 9.667107 AGTGAACAAGGAAAAATATTATCGAGA 57.333 29.630 0.00 0.00 0.00 4.04
304 305 9.974980 GTCCATTTATTAGTGAACAAGGAAAAA 57.025 29.630 0.00 0.00 0.00 1.94
305 306 9.137459 TGTCCATTTATTAGTGAACAAGGAAAA 57.863 29.630 0.00 0.00 0.00 2.29
306 307 8.573035 GTGTCCATTTATTAGTGAACAAGGAAA 58.427 33.333 0.00 0.00 0.00 3.13
307 308 7.094975 CGTGTCCATTTATTAGTGAACAAGGAA 60.095 37.037 0.00 0.00 0.00 3.36
308 309 6.370442 CGTGTCCATTTATTAGTGAACAAGGA 59.630 38.462 0.00 0.00 0.00 3.36
309 310 6.370442 TCGTGTCCATTTATTAGTGAACAAGG 59.630 38.462 0.00 0.00 0.00 3.61
310 311 7.359262 TCGTGTCCATTTATTAGTGAACAAG 57.641 36.000 0.00 0.00 0.00 3.16
311 312 7.915293 ATCGTGTCCATTTATTAGTGAACAA 57.085 32.000 0.00 0.00 0.00 2.83
312 313 7.625395 GCAATCGTGTCCATTTATTAGTGAACA 60.625 37.037 0.00 0.00 0.00 3.18
313 314 6.687105 GCAATCGTGTCCATTTATTAGTGAAC 59.313 38.462 0.00 0.00 0.00 3.18
314 315 6.183360 GGCAATCGTGTCCATTTATTAGTGAA 60.183 38.462 0.00 0.00 0.00 3.18
315 316 5.295787 GGCAATCGTGTCCATTTATTAGTGA 59.704 40.000 0.00 0.00 0.00 3.41
316 317 5.296780 AGGCAATCGTGTCCATTTATTAGTG 59.703 40.000 0.00 0.00 0.00 2.74
317 318 5.437060 AGGCAATCGTGTCCATTTATTAGT 58.563 37.500 0.00 0.00 0.00 2.24
318 319 6.201517 CAAGGCAATCGTGTCCATTTATTAG 58.798 40.000 0.00 0.00 0.00 1.73
319 320 5.067153 CCAAGGCAATCGTGTCCATTTATTA 59.933 40.000 0.00 0.00 0.00 0.98
320 321 4.142182 CCAAGGCAATCGTGTCCATTTATT 60.142 41.667 0.00 0.00 0.00 1.40
321 322 3.381272 CCAAGGCAATCGTGTCCATTTAT 59.619 43.478 0.00 0.00 0.00 1.40
322 323 2.752354 CCAAGGCAATCGTGTCCATTTA 59.248 45.455 0.00 0.00 0.00 1.40
323 324 1.545582 CCAAGGCAATCGTGTCCATTT 59.454 47.619 0.00 0.00 0.00 2.32
324 325 1.176527 CCAAGGCAATCGTGTCCATT 58.823 50.000 0.00 0.00 0.00 3.16
325 326 0.038166 ACCAAGGCAATCGTGTCCAT 59.962 50.000 0.00 0.00 0.00 3.41
326 327 0.687920 TACCAAGGCAATCGTGTCCA 59.312 50.000 0.00 0.00 0.00 4.02
327 328 1.940613 GATACCAAGGCAATCGTGTCC 59.059 52.381 0.00 0.00 0.00 4.02
328 329 1.940613 GGATACCAAGGCAATCGTGTC 59.059 52.381 0.00 0.00 0.00 3.67
329 330 2.038387 GGATACCAAGGCAATCGTGT 57.962 50.000 0.00 0.00 0.00 4.49
621 622 6.700081 GGTTTTTCTTAACACCAATCAACCTC 59.300 38.462 0.00 0.00 34.79 3.85
622 623 6.382859 AGGTTTTTCTTAACACCAATCAACCT 59.617 34.615 0.00 0.00 36.70 3.50
623 624 6.578944 AGGTTTTTCTTAACACCAATCAACC 58.421 36.000 0.00 0.00 36.70 3.77
624 625 7.489160 AGAGGTTTTTCTTAACACCAATCAAC 58.511 34.615 0.00 0.00 36.70 3.18
629 1258 5.394773 GCCAAGAGGTTTTTCTTAACACCAA 60.395 40.000 0.00 0.00 36.70 3.67
633 1262 4.098807 GTGGCCAAGAGGTTTTTCTTAACA 59.901 41.667 7.24 0.00 35.70 2.41
634 1263 4.617959 GTGGCCAAGAGGTTTTTCTTAAC 58.382 43.478 7.24 0.00 35.70 2.01
641 1270 3.443588 GCGTGGCCAAGAGGTTTT 58.556 55.556 23.82 0.00 37.19 2.43
1863 2790 3.840666 AGAGATGGCTGAGTGGACTAAAA 59.159 43.478 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.