Multiple sequence alignment - TraesCS6D01G244000

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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 TraesCS6D01G244000 chr6D 100.000 2891 0 0 1 2891 346273224 346270334 0.000000e+00 5339.0
1 TraesCS6D01G244000 chr6D 92.611 203 11 3 9 208 283772255 283772054 3.640000e-74 289.0
2 TraesCS6D01G244000 chr6B 91.862 2003 88 26 289 2258 535360490 535362450 0.000000e+00 2726.0
3 TraesCS6D01G244000 chr6B 81.675 573 95 10 2317 2883 572382227 572382795 4.360000e-128 468.0
4 TraesCS6D01G244000 chr6A 94.824 1507 54 9 735 2234 497729187 497730676 0.000000e+00 2329.0
5 TraesCS6D01G244000 chr6A 89.744 390 18 9 343 711 497728808 497729196 2.020000e-131 479.0
6 TraesCS6D01G244000 chr3A 84.069 521 65 10 2376 2891 610046435 610046942 1.200000e-133 486.0
7 TraesCS6D01G244000 chr3A 84.112 107 15 2 2298 2403 15545370 15545265 5.100000e-18 102.0
8 TraesCS6D01G244000 chr2D 83.493 521 84 2 2373 2891 333980101 333980621 4.330000e-133 484.0
9 TraesCS6D01G244000 chr2D 92.344 209 13 2 2 207 518020413 518020205 7.830000e-76 294.0
10 TraesCS6D01G244000 chr5B 80.854 632 89 20 2256 2860 293243351 293243977 4.360000e-128 468.0
11 TraesCS6D01G244000 chr7D 83.015 524 76 9 2359 2880 134107412 134107924 2.030000e-126 462.0
12 TraesCS6D01G244000 chr7D 83.600 500 71 10 2397 2891 384987033 384987526 2.630000e-125 459.0
13 TraesCS6D01G244000 chr7D 93.596 203 8 4 9 207 599692254 599692053 6.060000e-77 298.0
14 TraesCS6D01G244000 chr7A 82.070 541 83 9 2355 2891 106823896 106823366 1.580000e-122 449.0
15 TraesCS6D01G244000 chr5A 82.643 507 85 3 2387 2891 556690338 556690843 2.040000e-121 446.0
16 TraesCS6D01G244000 chr7B 81.869 535 86 8 2360 2890 379495841 379495314 9.510000e-120 440.0
17 TraesCS6D01G244000 chr7B 91.509 212 14 4 3 211 635043207 635043417 3.640000e-74 289.0
18 TraesCS6D01G244000 chr5D 93.750 208 9 3 3 207 331539235 331539029 2.800000e-80 309.0
19 TraesCS6D01G244000 chr1D 92.754 207 10 4 2 205 494455999 494455795 7.830000e-76 294.0
20 TraesCS6D01G244000 chr1B 93.500 200 8 4 9 205 644218 644021 2.820000e-75 292.0
21 TraesCS6D01G244000 chr4B 91.905 210 12 4 3 208 52585548 52585756 3.640000e-74 289.0
22 TraesCS6D01G244000 chr4B 91.163 215 14 4 3 214 67507260 67507472 1.310000e-73 287.0
23 TraesCS6D01G244000 chr4B 83.696 92 15 0 2298 2389 599889117 599889208 1.430000e-13 87.9


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 TraesCS6D01G244000 chr6D 346270334 346273224 2890 True 5339 5339 100.000 1 2891 1 chr6D.!!$R2 2890
1 TraesCS6D01G244000 chr6B 535360490 535362450 1960 False 2726 2726 91.862 289 2258 1 chr6B.!!$F1 1969
2 TraesCS6D01G244000 chr6B 572382227 572382795 568 False 468 468 81.675 2317 2883 1 chr6B.!!$F2 566
3 TraesCS6D01G244000 chr6A 497728808 497730676 1868 False 1404 2329 92.284 343 2234 2 chr6A.!!$F1 1891
4 TraesCS6D01G244000 chr3A 610046435 610046942 507 False 486 486 84.069 2376 2891 1 chr3A.!!$F1 515
5 TraesCS6D01G244000 chr2D 333980101 333980621 520 False 484 484 83.493 2373 2891 1 chr2D.!!$F1 518
6 TraesCS6D01G244000 chr5B 293243351 293243977 626 False 468 468 80.854 2256 2860 1 chr5B.!!$F1 604
7 TraesCS6D01G244000 chr7D 134107412 134107924 512 False 462 462 83.015 2359 2880 1 chr7D.!!$F1 521
8 TraesCS6D01G244000 chr7A 106823366 106823896 530 True 449 449 82.070 2355 2891 1 chr7A.!!$R1 536
9 TraesCS6D01G244000 chr5A 556690338 556690843 505 False 446 446 82.643 2387 2891 1 chr5A.!!$F1 504
10 TraesCS6D01G244000 chr7B 379495314 379495841 527 True 440 440 81.869 2360 2890 1 chr7B.!!$R1 530

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
76 77 0.033208 GACAGGATGGGGCAAATGGA 60.033 55.0 0.00 0.0 43.62 3.41 F
214 215 0.035739 GAGTTGGCCTAACCGTCCAA 59.964 55.0 3.32 0.0 43.94 3.53 F
467 484 0.039437 GTGATCACGACACGACTGGT 60.039 55.0 10.69 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1168 1210 0.174162 GCCTCTCGCCAATTGCAATT 59.826 50.000 18.99 18.99 41.33 2.32 R
1202 1245 1.139654 CAGGAAGGCGATTCAGATCCA 59.860 52.381 3.10 0.00 39.91 3.41 R
2314 2365 0.037697 CGTTGAATGTCGTCCTCCCA 60.038 55.000 0.00 0.00 0.00 4.37 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.594453 TGCTGGATTAGGGCTTTGG 57.406 52.632 0.00 0.00 0.00 3.28
19 20 0.704076 TGCTGGATTAGGGCTTTGGT 59.296 50.000 0.00 0.00 0.00 3.67
20 21 1.919654 TGCTGGATTAGGGCTTTGGTA 59.080 47.619 0.00 0.00 0.00 3.25
21 22 2.513738 TGCTGGATTAGGGCTTTGGTAT 59.486 45.455 0.00 0.00 0.00 2.73
22 23 3.052944 TGCTGGATTAGGGCTTTGGTATT 60.053 43.478 0.00 0.00 0.00 1.89
23 24 3.960755 GCTGGATTAGGGCTTTGGTATTT 59.039 43.478 0.00 0.00 0.00 1.40
24 25 4.202151 GCTGGATTAGGGCTTTGGTATTTG 60.202 45.833 0.00 0.00 0.00 2.32
25 26 5.199982 TGGATTAGGGCTTTGGTATTTGA 57.800 39.130 0.00 0.00 0.00 2.69
26 27 5.584913 TGGATTAGGGCTTTGGTATTTGAA 58.415 37.500 0.00 0.00 0.00 2.69
27 28 6.019748 TGGATTAGGGCTTTGGTATTTGAAA 58.980 36.000 0.00 0.00 0.00 2.69
28 29 6.071051 TGGATTAGGGCTTTGGTATTTGAAAC 60.071 38.462 0.00 0.00 0.00 2.78
29 30 3.934457 AGGGCTTTGGTATTTGAAACG 57.066 42.857 0.00 0.00 0.00 3.60
30 31 3.227614 AGGGCTTTGGTATTTGAAACGT 58.772 40.909 0.00 0.00 0.00 3.99
31 32 3.639561 AGGGCTTTGGTATTTGAAACGTT 59.360 39.130 0.00 0.00 0.00 3.99
32 33 3.738791 GGGCTTTGGTATTTGAAACGTTG 59.261 43.478 0.00 0.00 0.00 4.10
33 34 3.183574 GGCTTTGGTATTTGAAACGTTGC 59.816 43.478 0.00 0.00 0.00 4.17
34 35 4.048504 GCTTTGGTATTTGAAACGTTGCT 58.951 39.130 8.00 0.00 0.00 3.91
35 36 4.506288 GCTTTGGTATTTGAAACGTTGCTT 59.494 37.500 8.00 0.00 0.00 3.91
36 37 5.006261 GCTTTGGTATTTGAAACGTTGCTTT 59.994 36.000 8.00 0.00 0.00 3.51
37 38 6.456315 GCTTTGGTATTTGAAACGTTGCTTTT 60.456 34.615 8.00 0.00 0.00 2.27
38 39 7.254151 GCTTTGGTATTTGAAACGTTGCTTTTA 60.254 33.333 8.00 0.00 0.00 1.52
39 40 7.687005 TTGGTATTTGAAACGTTGCTTTTAG 57.313 32.000 8.00 0.00 0.00 1.85
40 41 6.797454 TGGTATTTGAAACGTTGCTTTTAGT 58.203 32.000 8.00 0.00 0.00 2.24
41 42 7.259161 TGGTATTTGAAACGTTGCTTTTAGTT 58.741 30.769 8.00 0.00 0.00 2.24
42 43 7.760340 TGGTATTTGAAACGTTGCTTTTAGTTT 59.240 29.630 8.00 0.00 39.21 2.66
43 44 8.597227 GGTATTTGAAACGTTGCTTTTAGTTTT 58.403 29.630 8.00 0.00 37.00 2.43
44 45 9.961266 GTATTTGAAACGTTGCTTTTAGTTTTT 57.039 25.926 8.00 0.00 37.00 1.94
62 63 4.932268 TTTTTAAATAGACGCGGACAGG 57.068 40.909 12.47 0.00 0.00 4.00
63 64 3.872511 TTTAAATAGACGCGGACAGGA 57.127 42.857 12.47 0.00 0.00 3.86
64 65 4.395959 TTTAAATAGACGCGGACAGGAT 57.604 40.909 12.47 0.00 0.00 3.24
65 66 2.225068 AAATAGACGCGGACAGGATG 57.775 50.000 12.47 0.00 46.00 3.51
66 67 0.389391 AATAGACGCGGACAGGATGG 59.611 55.000 12.47 0.00 43.62 3.51
67 68 1.464376 ATAGACGCGGACAGGATGGG 61.464 60.000 12.47 0.00 43.62 4.00
68 69 4.530857 GACGCGGACAGGATGGGG 62.531 72.222 12.47 0.00 43.62 4.96
71 72 4.424711 GCGGACAGGATGGGGCAA 62.425 66.667 0.00 0.00 43.62 4.52
72 73 2.354729 CGGACAGGATGGGGCAAA 59.645 61.111 0.00 0.00 43.62 3.68
73 74 1.076777 CGGACAGGATGGGGCAAAT 60.077 57.895 0.00 0.00 43.62 2.32
74 75 1.386525 CGGACAGGATGGGGCAAATG 61.387 60.000 0.00 0.00 43.62 2.32
75 76 1.044790 GGACAGGATGGGGCAAATGG 61.045 60.000 0.00 0.00 43.62 3.16
76 77 0.033208 GACAGGATGGGGCAAATGGA 60.033 55.000 0.00 0.00 43.62 3.41
77 78 0.638292 ACAGGATGGGGCAAATGGAT 59.362 50.000 0.00 0.00 43.62 3.41
78 79 1.045407 CAGGATGGGGCAAATGGATG 58.955 55.000 0.00 0.00 0.00 3.51
79 80 0.761702 AGGATGGGGCAAATGGATGC 60.762 55.000 0.00 0.00 45.67 3.91
86 87 4.910722 CAAATGGATGCGGCCGCG 62.911 66.667 41.73 23.24 45.51 6.46
115 116 3.814268 CGGCCACCGCATTCCAAG 61.814 66.667 2.24 0.00 41.17 3.61
116 117 2.361104 GGCCACCGCATTCCAAGA 60.361 61.111 0.00 0.00 36.38 3.02
117 118 2.700773 GGCCACCGCATTCCAAGAC 61.701 63.158 0.00 0.00 36.38 3.01
118 119 1.971167 GCCACCGCATTCCAAGACA 60.971 57.895 0.00 0.00 34.03 3.41
119 120 1.875963 CCACCGCATTCCAAGACAC 59.124 57.895 0.00 0.00 0.00 3.67
120 121 1.497278 CACCGCATTCCAAGACACG 59.503 57.895 0.00 0.00 0.00 4.49
121 122 2.325082 ACCGCATTCCAAGACACGC 61.325 57.895 0.00 0.00 0.00 5.34
122 123 2.480555 CGCATTCCAAGACACGCC 59.519 61.111 0.00 0.00 0.00 5.68
123 124 2.877691 GCATTCCAAGACACGCCC 59.122 61.111 0.00 0.00 0.00 6.13
124 125 3.039202 GCATTCCAAGACACGCCCG 62.039 63.158 0.00 0.00 0.00 6.13
125 126 2.046314 ATTCCAAGACACGCCCGG 60.046 61.111 0.00 0.00 0.00 5.73
126 127 2.589157 ATTCCAAGACACGCCCGGA 61.589 57.895 0.73 0.00 0.00 5.14
127 128 2.798148 ATTCCAAGACACGCCCGGAC 62.798 60.000 0.73 0.00 0.00 4.79
128 129 4.308458 CCAAGACACGCCCGGACA 62.308 66.667 0.73 0.00 0.00 4.02
129 130 3.041940 CAAGACACGCCCGGACAC 61.042 66.667 0.73 0.00 0.00 3.67
130 131 4.657824 AAGACACGCCCGGACACG 62.658 66.667 0.73 6.47 40.55 4.49
138 139 3.943691 CCCGGACACGACCCCAAA 61.944 66.667 0.73 0.00 44.60 3.28
139 140 2.349755 CCGGACACGACCCCAAAT 59.650 61.111 0.00 0.00 44.60 2.32
140 141 1.743995 CCGGACACGACCCCAAATC 60.744 63.158 0.00 0.00 44.60 2.17
141 142 1.743995 CGGACACGACCCCAAATCC 60.744 63.158 0.00 0.00 44.60 3.01
142 143 1.378119 GGACACGACCCCAAATCCC 60.378 63.158 0.00 0.00 0.00 3.85
143 144 1.683441 GACACGACCCCAAATCCCT 59.317 57.895 0.00 0.00 0.00 4.20
144 145 0.906775 GACACGACCCCAAATCCCTA 59.093 55.000 0.00 0.00 0.00 3.53
145 146 0.616891 ACACGACCCCAAATCCCTAC 59.383 55.000 0.00 0.00 0.00 3.18
146 147 0.107361 CACGACCCCAAATCCCTACC 60.107 60.000 0.00 0.00 0.00 3.18
147 148 1.276859 ACGACCCCAAATCCCTACCC 61.277 60.000 0.00 0.00 0.00 3.69
148 149 1.276140 CGACCCCAAATCCCTACCCA 61.276 60.000 0.00 0.00 0.00 4.51
149 150 1.004436 GACCCCAAATCCCTACCCAA 58.996 55.000 0.00 0.00 0.00 4.12
150 151 1.359818 GACCCCAAATCCCTACCCAAA 59.640 52.381 0.00 0.00 0.00 3.28
151 152 2.015322 ACCCCAAATCCCTACCCAAAT 58.985 47.619 0.00 0.00 0.00 2.32
152 153 2.292851 ACCCCAAATCCCTACCCAAATG 60.293 50.000 0.00 0.00 0.00 2.32
153 154 2.397597 CCCAAATCCCTACCCAAATGG 58.602 52.381 0.00 0.00 41.37 3.16
154 155 2.023501 CCCAAATCCCTACCCAAATGGA 60.024 50.000 0.00 0.00 37.39 3.41
155 156 3.031013 CCAAATCCCTACCCAAATGGAC 58.969 50.000 0.00 0.00 37.39 4.02
156 157 3.565449 CCAAATCCCTACCCAAATGGACA 60.565 47.826 0.00 0.00 37.39 4.02
157 158 3.669939 AATCCCTACCCAAATGGACAG 57.330 47.619 0.00 0.00 37.39 3.51
158 159 1.295020 TCCCTACCCAAATGGACAGG 58.705 55.000 0.00 6.66 38.71 4.00
159 160 0.395724 CCCTACCCAAATGGACAGGC 60.396 60.000 0.00 0.00 38.08 4.85
160 161 0.395724 CCTACCCAAATGGACAGGCC 60.396 60.000 0.00 0.00 37.39 5.19
161 162 0.748005 CTACCCAAATGGACAGGCCG 60.748 60.000 0.00 0.00 40.66 6.13
162 163 2.204865 TACCCAAATGGACAGGCCGG 62.205 60.000 0.00 0.00 40.66 6.13
163 164 2.354729 CCAAATGGACAGGCCGGA 59.645 61.111 10.86 0.00 40.66 5.14
164 165 2.046285 CCAAATGGACAGGCCGGAC 61.046 63.158 10.86 0.00 40.66 4.79
165 166 1.303236 CAAATGGACAGGCCGGACA 60.303 57.895 11.69 8.74 40.66 4.02
166 167 0.893270 CAAATGGACAGGCCGGACAA 60.893 55.000 11.69 0.00 40.66 3.18
167 168 0.178975 AAATGGACAGGCCGGACAAA 60.179 50.000 11.69 0.00 40.66 2.83
168 169 0.178975 AATGGACAGGCCGGACAAAA 60.179 50.000 11.69 0.00 40.66 2.44
169 170 0.039618 ATGGACAGGCCGGACAAAAT 59.960 50.000 11.69 0.00 40.66 1.82
170 171 0.893270 TGGACAGGCCGGACAAAATG 60.893 55.000 11.69 0.00 40.66 2.32
171 172 0.608035 GGACAGGCCGGACAAAATGA 60.608 55.000 11.69 0.00 0.00 2.57
172 173 1.243902 GACAGGCCGGACAAAATGAA 58.756 50.000 11.69 0.00 0.00 2.57
173 174 0.958822 ACAGGCCGGACAAAATGAAC 59.041 50.000 11.69 0.00 0.00 3.18
174 175 0.109781 CAGGCCGGACAAAATGAACG 60.110 55.000 11.69 0.00 0.00 3.95
175 176 0.536460 AGGCCGGACAAAATGAACGT 60.536 50.000 11.69 0.00 0.00 3.99
176 177 0.109919 GGCCGGACAAAATGAACGTC 60.110 55.000 5.05 0.00 0.00 4.34
177 178 0.109919 GCCGGACAAAATGAACGTCC 60.110 55.000 5.05 0.00 44.79 4.79
181 182 3.343380 GGACAAAATGAACGTCCGTTT 57.657 42.857 6.52 0.00 39.86 3.60
182 183 3.040099 GGACAAAATGAACGTCCGTTTG 58.960 45.455 6.52 2.97 39.86 2.93
183 184 3.040099 GACAAAATGAACGTCCGTTTGG 58.960 45.455 6.52 5.78 38.60 3.28
184 185 2.223618 ACAAAATGAACGTCCGTTTGGG 60.224 45.455 6.52 4.96 38.60 4.12
185 186 1.682740 AAATGAACGTCCGTTTGGGT 58.317 45.000 6.52 0.00 38.60 4.51
186 187 1.232119 AATGAACGTCCGTTTGGGTC 58.768 50.000 6.52 0.00 38.60 4.46
205 206 4.077184 CGCGGTGGAGTTGGCCTA 62.077 66.667 3.32 0.00 0.00 3.93
206 207 2.349755 GCGGTGGAGTTGGCCTAA 59.650 61.111 3.32 0.00 0.00 2.69
207 208 2.038837 GCGGTGGAGTTGGCCTAAC 61.039 63.158 3.32 7.14 39.65 2.34
208 209 1.376812 CGGTGGAGTTGGCCTAACC 60.377 63.158 3.32 4.44 40.24 2.85
209 210 1.376812 GGTGGAGTTGGCCTAACCG 60.377 63.158 3.32 0.00 43.94 4.44
210 211 1.373812 GTGGAGTTGGCCTAACCGT 59.626 57.895 3.32 0.00 43.94 4.83
211 212 0.672711 GTGGAGTTGGCCTAACCGTC 60.673 60.000 3.32 1.93 43.94 4.79
212 213 1.078637 GGAGTTGGCCTAACCGTCC 60.079 63.158 3.32 7.35 43.94 4.79
213 214 1.675219 GAGTTGGCCTAACCGTCCA 59.325 57.895 3.32 0.00 43.94 4.02
214 215 0.035739 GAGTTGGCCTAACCGTCCAA 59.964 55.000 3.32 0.00 43.94 3.53
215 216 4.804806 TTGGCCTAACCGTCCAAC 57.195 55.556 3.32 0.00 43.94 3.77
216 217 1.073548 TTGGCCTAACCGTCCAACC 59.926 57.895 3.32 0.00 43.94 3.77
217 218 1.420532 TTGGCCTAACCGTCCAACCT 61.421 55.000 3.32 0.00 43.94 3.50
218 219 1.376812 GGCCTAACCGTCCAACCTG 60.377 63.158 0.00 0.00 0.00 4.00
219 220 2.038837 GCCTAACCGTCCAACCTGC 61.039 63.158 0.00 0.00 0.00 4.85
220 221 1.376812 CCTAACCGTCCAACCTGCC 60.377 63.158 0.00 0.00 0.00 4.85
221 222 1.677552 CTAACCGTCCAACCTGCCT 59.322 57.895 0.00 0.00 0.00 4.75
222 223 0.391263 CTAACCGTCCAACCTGCCTC 60.391 60.000 0.00 0.00 0.00 4.70
223 224 2.162338 TAACCGTCCAACCTGCCTCG 62.162 60.000 0.00 0.00 0.00 4.63
233 234 4.082523 CTGCCTCGCCGGGAAAGA 62.083 66.667 2.18 0.00 30.11 2.52
234 235 3.391665 CTGCCTCGCCGGGAAAGAT 62.392 63.158 2.18 0.00 30.11 2.40
235 236 2.589159 GCCTCGCCGGGAAAGATC 60.589 66.667 2.18 0.00 0.00 2.75
236 237 2.109181 CCTCGCCGGGAAAGATCC 59.891 66.667 2.18 0.00 45.77 3.36
245 246 1.649267 GGAAAGATCCATTCCGCGC 59.351 57.895 0.00 0.00 45.79 6.86
246 247 1.095228 GGAAAGATCCATTCCGCGCA 61.095 55.000 8.75 0.00 45.79 6.09
247 248 0.305922 GAAAGATCCATTCCGCGCAG 59.694 55.000 8.75 0.00 0.00 5.18
366 367 3.432051 GATCCTGTCCTCCCGTGCG 62.432 68.421 0.00 0.00 0.00 5.34
390 391 3.065648 GGCGTCTCTCTCTAGATTTTCGT 59.934 47.826 0.00 0.00 0.00 3.85
405 406 7.751768 AGATTTTCGTCTTTTGGATCTTTCT 57.248 32.000 0.00 0.00 0.00 2.52
437 454 1.285023 CGATCTAGTTACCCGGCCG 59.715 63.158 21.04 21.04 0.00 6.13
467 484 0.039437 GTGATCACGACACGACTGGT 60.039 55.000 10.69 0.00 0.00 4.00
586 603 1.821216 CAGGCTTTCGGCTTTCCTAA 58.179 50.000 0.00 0.00 44.74 2.69
607 629 2.036256 CCCACCTCCCCAAGCAAG 59.964 66.667 0.00 0.00 0.00 4.01
611 633 3.983420 CCTCCCCAAGCAAGCCCA 61.983 66.667 0.00 0.00 0.00 5.36
612 634 2.677875 CTCCCCAAGCAAGCCCAC 60.678 66.667 0.00 0.00 0.00 4.61
713 735 0.548510 ATTCCTTCCTAGCCAGCCAC 59.451 55.000 0.00 0.00 0.00 5.01
750 772 1.610554 TTACCTAGGCAGCGGTCCAC 61.611 60.000 9.30 0.00 34.76 4.02
820 842 2.835895 GTCTCCCTCCTCCGCCTC 60.836 72.222 0.00 0.00 0.00 4.70
821 843 3.024356 TCTCCCTCCTCCGCCTCT 61.024 66.667 0.00 0.00 0.00 3.69
822 844 2.837291 CTCCCTCCTCCGCCTCTG 60.837 72.222 0.00 0.00 0.00 3.35
900 936 6.475402 CGCATAATTCGCCAGTATATATGTCA 59.525 38.462 0.00 0.00 0.00 3.58
903 939 5.638596 ATTCGCCAGTATATATGTCACGA 57.361 39.130 0.00 0.00 0.00 4.35
911 947 7.331934 GCCAGTATATATGTCACGAATCATTGT 59.668 37.037 0.00 0.00 0.00 2.71
913 949 8.650714 CAGTATATATGTCACGAATCATTGTGG 58.349 37.037 0.00 0.00 40.75 4.17
974 1010 3.793144 CGCAGCAGCTCGGGTTTC 61.793 66.667 0.00 0.00 39.10 2.78
975 1011 2.669569 GCAGCAGCTCGGGTTTCA 60.670 61.111 0.00 0.00 37.91 2.69
976 1012 2.684843 GCAGCAGCTCGGGTTTCAG 61.685 63.158 0.00 0.00 37.91 3.02
977 1013 2.359230 AGCAGCTCGGGTTTCAGC 60.359 61.111 0.00 0.00 35.73 4.26
979 1015 2.394563 GCAGCTCGGGTTTCAGCTC 61.395 63.158 0.00 0.00 44.47 4.09
1000 1042 3.125573 CTCGAGCTCGTCCCGTGA 61.126 66.667 33.33 13.31 40.80 4.35
1124 1166 1.376553 GCAGAGTCAAGGTCAGGCC 60.377 63.158 0.00 0.00 37.58 5.19
1166 1208 1.054348 CGCTCGTCGTGTTGCAATTG 61.054 55.000 0.59 0.00 0.00 2.32
1167 1209 1.330080 GCTCGTCGTGTTGCAATTGC 61.330 55.000 23.69 23.69 42.50 3.56
1218 1261 2.808202 CGGATTGGATCTGAATCGCCTT 60.808 50.000 10.18 0.00 37.90 4.35
1223 1266 1.224965 GATCTGAATCGCCTTCCTGC 58.775 55.000 0.00 0.00 32.49 4.85
1243 1286 1.519455 GGTTGCTCGATCAGGACGG 60.519 63.158 0.00 0.00 0.00 4.79
1282 1325 3.795041 CCTCTGCTCCCTGCCCAG 61.795 72.222 0.00 0.00 42.00 4.45
1385 1428 3.709633 ATGTGCGCCTCCAGCTCA 61.710 61.111 4.18 0.00 41.39 4.26
1459 1502 1.226974 CCCTCTCATGGTACGTGCG 60.227 63.158 0.00 0.00 0.00 5.34
1523 1571 2.096496 CGAAGCACCACATGAGAATTCC 59.904 50.000 0.00 0.00 0.00 3.01
1527 1575 1.131126 CACCACATGAGAATTCCGTGC 59.869 52.381 0.00 0.00 0.00 5.34
1757 1805 3.382832 CCTCGGCCTCACCTTCGT 61.383 66.667 0.00 0.00 35.61 3.85
1772 1820 4.676586 CGTCACCAAAACCGCGGC 62.677 66.667 28.58 3.97 0.00 6.53
1959 2007 1.753078 CCGGTGGAGAGGTCGATGA 60.753 63.158 0.00 0.00 0.00 2.92
2083 2132 1.448922 GCGATCTCGGGAGTACTGCT 61.449 60.000 14.52 0.00 40.23 4.24
2140 2189 6.706055 ATTACTGACACATTTACTGACGTG 57.294 37.500 0.00 0.00 35.48 4.49
2212 2261 4.439426 CCTCAAGGATCGTACAGAACAGAG 60.439 50.000 0.00 0.00 37.39 3.35
2225 2274 5.615289 ACAGAACAGAGCAGAAATTACACT 58.385 37.500 0.00 0.00 0.00 3.55
2227 2276 5.698089 CAGAACAGAGCAGAAATTACACTGA 59.302 40.000 0.00 0.00 36.38 3.41
2237 2286 6.088824 CAGAAATTACACTGATTTGTGCTCC 58.911 40.000 0.00 0.00 41.30 4.70
2238 2287 5.769662 AGAAATTACACTGATTTGTGCTCCA 59.230 36.000 0.00 0.00 41.30 3.86
2241 2290 2.498167 ACACTGATTTGTGCTCCACTC 58.502 47.619 0.00 0.00 41.30 3.51
2250 2299 0.890683 GTGCTCCACTCCCATTTTGG 59.109 55.000 0.00 0.00 37.25 3.28
2266 2315 0.255890 TTGGGCACTAAGGGCATCTC 59.744 55.000 0.00 0.00 34.52 2.75
2270 2319 1.340991 GGCACTAAGGGCATCTCCAAA 60.341 52.381 0.00 0.00 36.21 3.28
2272 2321 2.019984 CACTAAGGGCATCTCCAAAGC 58.980 52.381 0.00 0.00 36.21 3.51
2274 2325 2.041620 ACTAAGGGCATCTCCAAAGCAA 59.958 45.455 0.00 0.00 36.21 3.91
2276 2327 0.613012 AGGGCATCTCCAAAGCAACC 60.613 55.000 0.00 0.00 36.21 3.77
2278 2329 1.153958 GCATCTCCAAAGCAACCGC 60.154 57.895 0.00 0.00 38.99 5.68
2285 2336 2.476241 CTCCAAAGCAACCGCAAATTTC 59.524 45.455 0.00 0.00 42.27 2.17
2286 2337 2.159043 TCCAAAGCAACCGCAAATTTCA 60.159 40.909 0.00 0.00 42.27 2.69
2288 2339 3.364167 CCAAAGCAACCGCAAATTTCATG 60.364 43.478 0.00 0.00 42.27 3.07
2293 2344 2.507193 CCGCAAATTTCATGCCGCG 61.507 57.895 10.39 10.39 40.72 6.46
2294 2345 1.801113 CGCAAATTTCATGCCGCGT 60.801 52.632 4.92 0.00 40.72 6.01
2295 2346 1.732474 CGCAAATTTCATGCCGCGTC 61.732 55.000 4.92 0.00 40.72 5.19
2299 2350 1.977594 AATTTCATGCCGCGTCCGTC 61.978 55.000 4.92 0.00 0.00 4.79
2309 2360 2.026445 CGTCCGTCCGTGAACACA 59.974 61.111 5.80 0.00 0.00 3.72
2313 2364 1.954146 CCGTCCGTGAACACAGGTG 60.954 63.158 5.80 0.00 0.00 4.00
2328 2379 0.836400 AGGTGTGGGAGGACGACATT 60.836 55.000 0.00 0.00 40.04 2.71
2337 2388 0.949105 AGGACGACATTCAACGCCAC 60.949 55.000 0.00 0.00 0.00 5.01
2338 2389 0.949105 GGACGACATTCAACGCCACT 60.949 55.000 0.00 0.00 0.00 4.00
2345 2396 1.599071 CATTCAACGCCACTCGCATAT 59.401 47.619 0.00 0.00 43.23 1.78
2399 2472 7.703621 ACGAAATTCAATCAAACATGATGGATC 59.296 33.333 0.00 0.00 29.21 3.36
2419 2492 6.707608 TGGATCTCATCTTAAAATGACGGATG 59.292 38.462 0.00 0.00 36.21 3.51
2448 2521 3.953712 TTCACATCAACTAAGCGGAGA 57.046 42.857 0.00 0.00 0.00 3.71
2472 2545 5.614308 TCGTCCGACTAGATCTAAATGGTA 58.386 41.667 3.57 0.00 0.00 3.25
2475 2548 5.241064 GTCCGACTAGATCTAAATGGTAGCA 59.759 44.000 3.57 0.00 0.00 3.49
2488 2562 2.925706 TAGCAGGTGCCCGTTCCA 60.926 61.111 0.00 0.00 43.38 3.53
2494 2568 1.901464 GGTGCCCGTTCCACATGTT 60.901 57.895 0.00 0.00 34.94 2.71
2514 2588 1.281867 TCGGCCATGAACCAAGAGAAT 59.718 47.619 2.24 0.00 0.00 2.40
2534 2608 2.613026 TGAAGCTTCACCGTCTTCAA 57.387 45.000 25.16 0.00 42.00 2.69
2695 2769 4.821589 GGAGGAGCGACGGCCTTG 62.822 72.222 0.00 0.00 41.24 3.61
2810 2885 0.171455 GCAGACTCGACGATGTCCTT 59.829 55.000 17.92 4.51 34.02 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.704076 ACCAAAGCCCTAATCCAGCA 59.296 50.000 0.00 0.00 0.00 4.41
1 2 2.729028 TACCAAAGCCCTAATCCAGC 57.271 50.000 0.00 0.00 0.00 4.85
3 4 5.199982 TCAAATACCAAAGCCCTAATCCA 57.800 39.130 0.00 0.00 0.00 3.41
5 6 6.033966 CGTTTCAAATACCAAAGCCCTAATC 58.966 40.000 0.00 0.00 0.00 1.75
6 7 5.479027 ACGTTTCAAATACCAAAGCCCTAAT 59.521 36.000 0.00 0.00 0.00 1.73
7 8 4.828387 ACGTTTCAAATACCAAAGCCCTAA 59.172 37.500 0.00 0.00 0.00 2.69
8 9 4.400120 ACGTTTCAAATACCAAAGCCCTA 58.600 39.130 0.00 0.00 0.00 3.53
9 10 3.227614 ACGTTTCAAATACCAAAGCCCT 58.772 40.909 0.00 0.00 0.00 5.19
10 11 3.653539 ACGTTTCAAATACCAAAGCCC 57.346 42.857 0.00 0.00 0.00 5.19
11 12 3.183574 GCAACGTTTCAAATACCAAAGCC 59.816 43.478 0.00 0.00 0.00 4.35
12 13 4.048504 AGCAACGTTTCAAATACCAAAGC 58.951 39.130 0.00 0.00 0.00 3.51
13 14 6.582437 AAAGCAACGTTTCAAATACCAAAG 57.418 33.333 0.00 0.00 0.00 2.77
14 15 6.969828 AAAAGCAACGTTTCAAATACCAAA 57.030 29.167 0.00 0.00 0.00 3.28
15 16 7.259161 ACTAAAAGCAACGTTTCAAATACCAA 58.741 30.769 0.00 0.00 0.00 3.67
16 17 6.797454 ACTAAAAGCAACGTTTCAAATACCA 58.203 32.000 0.00 0.00 0.00 3.25
17 18 7.688478 AACTAAAAGCAACGTTTCAAATACC 57.312 32.000 0.00 0.00 0.00 2.73
18 19 9.961266 AAAAACTAAAAGCAACGTTTCAAATAC 57.039 25.926 0.00 0.00 0.00 1.89
41 42 4.567971 TCCTGTCCGCGTCTATTTAAAAA 58.432 39.130 4.92 0.00 0.00 1.94
42 43 4.191033 TCCTGTCCGCGTCTATTTAAAA 57.809 40.909 4.92 0.00 0.00 1.52
43 44 3.872511 TCCTGTCCGCGTCTATTTAAA 57.127 42.857 4.92 0.00 0.00 1.52
44 45 3.491964 CCATCCTGTCCGCGTCTATTTAA 60.492 47.826 4.92 0.00 0.00 1.52
45 46 2.035449 CCATCCTGTCCGCGTCTATTTA 59.965 50.000 4.92 0.00 0.00 1.40
46 47 1.202533 CCATCCTGTCCGCGTCTATTT 60.203 52.381 4.92 0.00 0.00 1.40
47 48 0.389391 CCATCCTGTCCGCGTCTATT 59.611 55.000 4.92 0.00 0.00 1.73
48 49 1.464376 CCCATCCTGTCCGCGTCTAT 61.464 60.000 4.92 0.00 0.00 1.98
49 50 2.125326 CCCATCCTGTCCGCGTCTA 61.125 63.158 4.92 0.00 0.00 2.59
50 51 3.461773 CCCATCCTGTCCGCGTCT 61.462 66.667 4.92 0.00 0.00 4.18
51 52 4.530857 CCCCATCCTGTCCGCGTC 62.531 72.222 4.92 0.00 0.00 5.19
54 55 3.936772 TTTGCCCCATCCTGTCCGC 62.937 63.158 0.00 0.00 0.00 5.54
55 56 1.076777 ATTTGCCCCATCCTGTCCG 60.077 57.895 0.00 0.00 0.00 4.79
56 57 1.044790 CCATTTGCCCCATCCTGTCC 61.045 60.000 0.00 0.00 0.00 4.02
57 58 0.033208 TCCATTTGCCCCATCCTGTC 60.033 55.000 0.00 0.00 0.00 3.51
58 59 0.638292 ATCCATTTGCCCCATCCTGT 59.362 50.000 0.00 0.00 0.00 4.00
59 60 1.045407 CATCCATTTGCCCCATCCTG 58.955 55.000 0.00 0.00 0.00 3.86
60 61 0.761702 GCATCCATTTGCCCCATCCT 60.762 55.000 0.00 0.00 36.60 3.24
61 62 1.750297 GCATCCATTTGCCCCATCC 59.250 57.895 0.00 0.00 36.60 3.51
62 63 1.364901 CGCATCCATTTGCCCCATC 59.635 57.895 0.00 0.00 39.52 3.51
63 64 2.135581 CCGCATCCATTTGCCCCAT 61.136 57.895 0.00 0.00 39.52 4.00
64 65 2.759149 CCGCATCCATTTGCCCCA 60.759 61.111 0.00 0.00 39.52 4.96
65 66 4.225703 GCCGCATCCATTTGCCCC 62.226 66.667 0.00 0.00 39.52 5.80
66 67 4.225703 GGCCGCATCCATTTGCCC 62.226 66.667 0.00 0.00 39.52 5.36
67 68 4.573950 CGGCCGCATCCATTTGCC 62.574 66.667 14.67 0.00 39.52 4.52
69 70 4.910722 CGCGGCCGCATCCATTTG 62.911 66.667 45.26 25.41 42.06 2.32
99 100 2.361104 TCTTGGAATGCGGTGGCC 60.361 61.111 0.00 0.00 38.85 5.36
100 101 1.971167 TGTCTTGGAATGCGGTGGC 60.971 57.895 0.00 0.00 40.52 5.01
101 102 1.875963 GTGTCTTGGAATGCGGTGG 59.124 57.895 0.00 0.00 0.00 4.61
102 103 1.497278 CGTGTCTTGGAATGCGGTG 59.503 57.895 0.00 0.00 0.00 4.94
103 104 2.325082 GCGTGTCTTGGAATGCGGT 61.325 57.895 0.00 0.00 0.00 5.68
104 105 2.480555 GCGTGTCTTGGAATGCGG 59.519 61.111 0.00 0.00 0.00 5.69
105 106 2.480555 GGCGTGTCTTGGAATGCG 59.519 61.111 0.00 0.00 0.00 4.73
106 107 2.877691 GGGCGTGTCTTGGAATGC 59.122 61.111 0.00 0.00 0.00 3.56
107 108 2.398554 CCGGGCGTGTCTTGGAATG 61.399 63.158 0.00 0.00 0.00 2.67
108 109 2.046314 CCGGGCGTGTCTTGGAAT 60.046 61.111 0.00 0.00 0.00 3.01
109 110 3.235481 TCCGGGCGTGTCTTGGAA 61.235 61.111 0.00 0.00 0.00 3.53
110 111 3.998672 GTCCGGGCGTGTCTTGGA 61.999 66.667 0.00 0.00 0.00 3.53
111 112 4.308458 TGTCCGGGCGTGTCTTGG 62.308 66.667 0.00 0.00 0.00 3.61
112 113 3.041940 GTGTCCGGGCGTGTCTTG 61.042 66.667 0.00 0.00 0.00 3.02
113 114 4.657824 CGTGTCCGGGCGTGTCTT 62.658 66.667 0.00 0.00 0.00 3.01
121 122 3.262448 ATTTGGGGTCGTGTCCGGG 62.262 63.158 0.00 0.00 33.95 5.73
122 123 1.743995 GATTTGGGGTCGTGTCCGG 60.744 63.158 0.00 0.00 33.95 5.14
123 124 1.743995 GGATTTGGGGTCGTGTCCG 60.744 63.158 0.00 0.00 0.00 4.79
124 125 1.378119 GGGATTTGGGGTCGTGTCC 60.378 63.158 0.00 0.00 0.00 4.02
125 126 0.906775 TAGGGATTTGGGGTCGTGTC 59.093 55.000 0.00 0.00 0.00 3.67
126 127 0.616891 GTAGGGATTTGGGGTCGTGT 59.383 55.000 0.00 0.00 0.00 4.49
127 128 0.107361 GGTAGGGATTTGGGGTCGTG 60.107 60.000 0.00 0.00 0.00 4.35
128 129 1.276859 GGGTAGGGATTTGGGGTCGT 61.277 60.000 0.00 0.00 0.00 4.34
129 130 1.276140 TGGGTAGGGATTTGGGGTCG 61.276 60.000 0.00 0.00 0.00 4.79
130 131 1.004436 TTGGGTAGGGATTTGGGGTC 58.996 55.000 0.00 0.00 0.00 4.46
131 132 1.473550 TTTGGGTAGGGATTTGGGGT 58.526 50.000 0.00 0.00 0.00 4.95
132 133 2.397597 CATTTGGGTAGGGATTTGGGG 58.602 52.381 0.00 0.00 0.00 4.96
133 134 2.023501 TCCATTTGGGTAGGGATTTGGG 60.024 50.000 0.00 0.00 38.11 4.12
134 135 3.031013 GTCCATTTGGGTAGGGATTTGG 58.969 50.000 0.00 0.00 38.11 3.28
135 136 3.701040 CTGTCCATTTGGGTAGGGATTTG 59.299 47.826 0.00 0.00 38.11 2.32
136 137 3.309848 CCTGTCCATTTGGGTAGGGATTT 60.310 47.826 10.47 0.00 37.99 2.17
137 138 2.244769 CCTGTCCATTTGGGTAGGGATT 59.755 50.000 10.47 0.00 37.99 3.01
138 139 1.852965 CCTGTCCATTTGGGTAGGGAT 59.147 52.381 10.47 0.00 37.99 3.85
139 140 1.295020 CCTGTCCATTTGGGTAGGGA 58.705 55.000 10.47 0.00 37.99 4.20
140 141 0.395724 GCCTGTCCATTTGGGTAGGG 60.396 60.000 16.62 7.77 40.33 3.53
141 142 0.395724 GGCCTGTCCATTTGGGTAGG 60.396 60.000 12.83 12.83 41.82 3.18
142 143 0.748005 CGGCCTGTCCATTTGGGTAG 60.748 60.000 0.00 0.00 38.11 3.18
143 144 1.301623 CGGCCTGTCCATTTGGGTA 59.698 57.895 0.00 0.00 38.11 3.69
144 145 2.035626 CGGCCTGTCCATTTGGGT 59.964 61.111 0.00 0.00 38.11 4.51
145 146 2.755469 CCGGCCTGTCCATTTGGG 60.755 66.667 0.00 0.00 35.41 4.12
146 147 2.046285 GTCCGGCCTGTCCATTTGG 61.046 63.158 0.00 0.00 34.01 3.28
147 148 0.893270 TTGTCCGGCCTGTCCATTTG 60.893 55.000 0.00 0.00 34.01 2.32
148 149 0.178975 TTTGTCCGGCCTGTCCATTT 60.179 50.000 0.00 0.00 34.01 2.32
149 150 0.178975 TTTTGTCCGGCCTGTCCATT 60.179 50.000 0.00 0.00 34.01 3.16
150 151 0.039618 ATTTTGTCCGGCCTGTCCAT 59.960 50.000 0.00 0.00 34.01 3.41
151 152 0.893270 CATTTTGTCCGGCCTGTCCA 60.893 55.000 0.00 0.00 34.01 4.02
152 153 0.608035 TCATTTTGTCCGGCCTGTCC 60.608 55.000 0.00 0.00 0.00 4.02
153 154 1.068541 GTTCATTTTGTCCGGCCTGTC 60.069 52.381 0.00 0.00 0.00 3.51
154 155 0.958822 GTTCATTTTGTCCGGCCTGT 59.041 50.000 0.00 0.00 0.00 4.00
155 156 0.109781 CGTTCATTTTGTCCGGCCTG 60.110 55.000 0.00 0.00 0.00 4.85
156 157 0.536460 ACGTTCATTTTGTCCGGCCT 60.536 50.000 0.00 0.00 0.00 5.19
157 158 0.109919 GACGTTCATTTTGTCCGGCC 60.110 55.000 0.00 0.00 0.00 6.13
158 159 0.109919 GGACGTTCATTTTGTCCGGC 60.110 55.000 0.00 0.00 42.42 6.13
161 162 3.040099 CAAACGGACGTTCATTTTGTCC 58.960 45.455 10.76 0.55 46.91 4.02
162 163 3.040099 CCAAACGGACGTTCATTTTGTC 58.960 45.455 10.76 0.00 37.35 3.18
163 164 2.223618 CCCAAACGGACGTTCATTTTGT 60.224 45.455 10.76 0.00 37.35 2.83
164 165 2.223618 ACCCAAACGGACGTTCATTTTG 60.224 45.455 10.76 9.91 37.35 2.44
165 166 2.025898 ACCCAAACGGACGTTCATTTT 58.974 42.857 10.76 0.00 37.35 1.82
166 167 1.605232 GACCCAAACGGACGTTCATTT 59.395 47.619 10.76 0.00 37.35 2.32
167 168 1.232119 GACCCAAACGGACGTTCATT 58.768 50.000 10.76 0.00 37.35 2.57
168 169 0.947180 CGACCCAAACGGACGTTCAT 60.947 55.000 10.76 0.00 43.65 2.57
169 170 1.592131 CGACCCAAACGGACGTTCA 60.592 57.895 10.76 0.00 43.65 3.18
170 171 3.237290 CGACCCAAACGGACGTTC 58.763 61.111 10.76 0.00 43.65 3.95
188 189 3.599285 TTAGGCCAACTCCACCGCG 62.599 63.158 5.01 0.00 0.00 6.46
189 190 2.038837 GTTAGGCCAACTCCACCGC 61.039 63.158 5.01 0.00 34.06 5.68
190 191 1.376812 GGTTAGGCCAACTCCACCG 60.377 63.158 5.01 0.00 37.30 4.94
191 192 1.376812 CGGTTAGGCCAACTCCACC 60.377 63.158 5.01 0.00 37.30 4.61
192 193 0.672711 GACGGTTAGGCCAACTCCAC 60.673 60.000 5.01 0.00 37.30 4.02
193 194 1.675219 GACGGTTAGGCCAACTCCA 59.325 57.895 5.01 0.00 37.30 3.86
194 195 4.611961 GACGGTTAGGCCAACTCC 57.388 61.111 5.01 0.31 37.30 3.85
201 202 2.038837 GCAGGTTGGACGGTTAGGC 61.039 63.158 0.00 0.00 0.00 3.93
202 203 1.376812 GGCAGGTTGGACGGTTAGG 60.377 63.158 0.00 0.00 0.00 2.69
203 204 0.391263 GAGGCAGGTTGGACGGTTAG 60.391 60.000 0.00 0.00 0.00 2.34
204 205 1.675219 GAGGCAGGTTGGACGGTTA 59.325 57.895 0.00 0.00 0.00 2.85
205 206 2.430367 GAGGCAGGTTGGACGGTT 59.570 61.111 0.00 0.00 0.00 4.44
206 207 4.003788 CGAGGCAGGTTGGACGGT 62.004 66.667 0.00 0.00 0.00 4.83
216 217 3.391665 ATCTTTCCCGGCGAGGCAG 62.392 63.158 9.30 7.68 39.21 4.85
217 218 3.385749 GATCTTTCCCGGCGAGGCA 62.386 63.158 9.30 0.00 39.21 4.75
218 219 2.589159 GATCTTTCCCGGCGAGGC 60.589 66.667 9.30 0.00 39.21 4.70
219 220 2.044806 ATGGATCTTTCCCGGCGAGG 62.045 60.000 9.30 8.47 41.83 4.63
220 221 0.179045 AATGGATCTTTCCCGGCGAG 60.179 55.000 9.30 0.00 41.83 5.03
221 222 0.179056 GAATGGATCTTTCCCGGCGA 60.179 55.000 9.30 0.00 41.83 5.54
222 223 1.166531 GGAATGGATCTTTCCCGGCG 61.167 60.000 13.83 0.00 41.83 6.46
223 224 1.166531 CGGAATGGATCTTTCCCGGC 61.167 60.000 17.13 0.00 41.83 6.13
224 225 1.166531 GCGGAATGGATCTTTCCCGG 61.167 60.000 17.13 0.00 41.83 5.73
225 226 1.498865 CGCGGAATGGATCTTTCCCG 61.499 60.000 17.13 16.63 41.83 5.14
226 227 1.786049 GCGCGGAATGGATCTTTCCC 61.786 60.000 8.83 11.44 41.83 3.97
227 228 1.095228 TGCGCGGAATGGATCTTTCC 61.095 55.000 8.83 14.47 42.94 3.13
228 229 0.305922 CTGCGCGGAATGGATCTTTC 59.694 55.000 11.90 0.00 0.00 2.62
229 230 1.718757 GCTGCGCGGAATGGATCTTT 61.719 55.000 23.20 0.00 0.00 2.52
230 231 2.182842 GCTGCGCGGAATGGATCTT 61.183 57.895 23.20 0.00 0.00 2.40
231 232 2.590007 GCTGCGCGGAATGGATCT 60.590 61.111 23.20 0.00 0.00 2.75
276 277 2.720758 CTCTGGCTTCGCGTGTTCG 61.721 63.158 5.77 0.00 40.37 3.95
277 278 1.372997 TCTCTGGCTTCGCGTGTTC 60.373 57.895 5.77 0.00 0.00 3.18
278 279 1.664965 GTCTCTGGCTTCGCGTGTT 60.665 57.895 5.77 0.00 0.00 3.32
279 280 2.049063 GTCTCTGGCTTCGCGTGT 60.049 61.111 5.77 0.00 0.00 4.49
280 281 2.049156 TGTCTCTGGCTTCGCGTG 60.049 61.111 5.77 1.17 0.00 5.34
281 282 2.259818 CTGTCTCTGGCTTCGCGT 59.740 61.111 5.77 0.00 0.00 6.01
282 283 1.803519 GACTGTCTCTGGCTTCGCG 60.804 63.158 0.00 0.00 0.00 5.87
283 284 1.803519 CGACTGTCTCTGGCTTCGC 60.804 63.158 6.21 0.00 0.00 4.70
284 285 0.179176 CTCGACTGTCTCTGGCTTCG 60.179 60.000 6.21 0.00 0.00 3.79
285 286 0.885196 ACTCGACTGTCTCTGGCTTC 59.115 55.000 6.21 0.00 0.00 3.86
286 287 0.600557 CACTCGACTGTCTCTGGCTT 59.399 55.000 6.21 0.00 0.00 4.35
287 288 1.872197 GCACTCGACTGTCTCTGGCT 61.872 60.000 6.21 0.00 0.00 4.75
288 289 1.445238 GCACTCGACTGTCTCTGGC 60.445 63.158 6.21 1.34 0.00 4.85
289 290 0.315251 TTGCACTCGACTGTCTCTGG 59.685 55.000 6.21 0.00 0.00 3.86
290 291 2.057316 CTTTGCACTCGACTGTCTCTG 58.943 52.381 6.21 0.00 0.00 3.35
291 292 1.683917 ACTTTGCACTCGACTGTCTCT 59.316 47.619 6.21 0.00 0.00 3.10
292 293 2.055100 GACTTTGCACTCGACTGTCTC 58.945 52.381 6.21 0.00 0.00 3.36
293 294 1.600663 CGACTTTGCACTCGACTGTCT 60.601 52.381 6.21 0.00 31.24 3.41
294 295 0.778815 CGACTTTGCACTCGACTGTC 59.221 55.000 0.00 0.00 31.24 3.51
295 296 1.215655 GCGACTTTGCACTCGACTGT 61.216 55.000 10.93 0.00 34.15 3.55
366 367 1.989706 AATCTAGAGAGAGACGCCCC 58.010 55.000 0.00 0.00 34.35 5.80
390 391 3.498397 GTGCGTGAGAAAGATCCAAAAGA 59.502 43.478 0.00 0.00 0.00 2.52
421 422 1.134610 CAAACGGCCGGGTAACTAGAT 60.135 52.381 31.76 0.00 0.00 1.98
424 425 1.296068 CCAAACGGCCGGGTAACTA 59.704 57.895 31.76 0.00 0.00 2.24
425 426 2.032987 CCAAACGGCCGGGTAACT 59.967 61.111 31.76 3.35 0.00 2.24
426 427 3.057548 CCCAAACGGCCGGGTAAC 61.058 66.667 31.76 0.00 37.70 2.50
437 454 1.579429 GTGATCACGCCACCCAAAC 59.421 57.895 10.69 0.00 0.00 2.93
467 484 4.954092 TGTTTACATGCATGCGTGATAA 57.046 36.364 39.42 28.83 36.80 1.75
507 524 1.660560 TTGTCCTAGTCGGCCTACGC 61.661 60.000 0.00 0.00 43.86 4.42
586 603 2.612115 CTTGGGGAGGTGGGAGCT 60.612 66.667 0.00 0.00 0.00 4.09
591 608 2.677875 GCTTGCTTGGGGAGGTGG 60.678 66.667 0.00 0.00 0.00 4.61
607 629 1.092348 GTCAAAACCGGATAGTGGGC 58.908 55.000 9.46 0.00 0.00 5.36
727 749 1.523938 CCGCTGCCTAGGTAAAGCC 60.524 63.158 20.71 8.94 37.58 4.35
750 772 1.089481 CATGGATTCGTCCACCCGTG 61.089 60.000 0.00 0.00 43.37 4.94
820 842 2.811317 GACGACGGAAGCAGGCAG 60.811 66.667 0.00 0.00 0.00 4.85
821 843 3.282745 GAGACGACGGAAGCAGGCA 62.283 63.158 0.00 0.00 0.00 4.75
822 844 2.507324 GAGACGACGGAAGCAGGC 60.507 66.667 0.00 0.00 0.00 4.85
823 845 2.182030 GGAGACGACGGAAGCAGG 59.818 66.667 0.00 0.00 0.00 4.85
900 936 3.129287 GGAATTCAGCCACAATGATTCGT 59.871 43.478 7.93 0.00 0.00 3.85
903 939 2.428171 CGGGAATTCAGCCACAATGATT 59.572 45.455 7.93 0.00 0.00 2.57
911 947 1.302949 CCTTCCGGGAATTCAGCCA 59.697 57.895 10.44 0.00 37.23 4.75
1166 1208 1.274596 CTCTCGCCAATTGCAATTGC 58.725 50.000 36.20 29.76 43.38 3.56
1167 1209 1.917273 CCTCTCGCCAATTGCAATTG 58.083 50.000 35.14 35.14 44.12 2.32
1168 1210 0.174162 GCCTCTCGCCAATTGCAATT 59.826 50.000 18.99 18.99 41.33 2.32
1202 1245 1.139654 CAGGAAGGCGATTCAGATCCA 59.860 52.381 3.10 0.00 39.91 3.41
1223 1266 1.519455 GTCCTGATCGAGCAACCGG 60.519 63.158 4.32 0.00 0.00 5.28
1243 1286 1.450312 CCGTCCAGCTTCATGTCCC 60.450 63.158 0.00 0.00 0.00 4.46
1459 1502 3.502191 TGGTCGTATTACACCGTAACC 57.498 47.619 9.44 0.00 35.15 2.85
2001 2049 4.042684 AGACCAAAAGGAGAAGAAGATGCT 59.957 41.667 0.00 0.00 0.00 3.79
2083 2132 2.237965 CCTCCCATCCAACCCACCA 61.238 63.158 0.00 0.00 0.00 4.17
2140 2189 1.268352 TCATTTACACTTTGCACGGCC 59.732 47.619 0.00 0.00 0.00 6.13
2151 2200 5.864986 CCAGTTCGGTAATGTCATTTACAC 58.135 41.667 2.79 0.00 42.09 2.90
2212 2261 5.464168 AGCACAAATCAGTGTAATTTCTGC 58.536 37.500 8.55 8.55 41.52 4.26
2225 2274 0.770499 TGGGAGTGGAGCACAAATCA 59.230 50.000 0.00 0.00 36.74 2.57
2227 2276 2.610438 AATGGGAGTGGAGCACAAAT 57.390 45.000 0.00 0.00 36.74 2.32
2250 2299 0.255890 TTGGAGATGCCCTTAGTGCC 59.744 55.000 0.00 0.00 34.97 5.01
2266 2315 2.208431 TGAAATTTGCGGTTGCTTTGG 58.792 42.857 0.00 0.00 43.34 3.28
2270 2319 1.431496 GCATGAAATTTGCGGTTGCT 58.569 45.000 0.00 0.00 43.34 3.91
2272 2321 0.714994 CGGCATGAAATTTGCGGTTG 59.285 50.000 0.00 0.00 41.07 3.77
2274 2325 1.445926 GCGGCATGAAATTTGCGGT 60.446 52.632 0.00 0.00 41.08 5.68
2276 2327 2.989162 CGCGGCATGAAATTTGCG 59.011 55.556 0.00 0.00 41.07 4.85
2278 2329 1.133363 CGGACGCGGCATGAAATTTG 61.133 55.000 17.00 0.00 0.00 2.32
2293 2344 1.663702 CCTGTGTTCACGGACGGAC 60.664 63.158 12.65 0.00 0.00 4.79
2294 2345 2.129146 ACCTGTGTTCACGGACGGA 61.129 57.895 12.65 0.00 0.00 4.69
2295 2346 1.954146 CACCTGTGTTCACGGACGG 60.954 63.158 12.65 6.20 0.00 4.79
2299 2350 1.891919 CCCACACCTGTGTTCACGG 60.892 63.158 0.00 4.93 42.83 4.94
2300 2351 0.880278 CTCCCACACCTGTGTTCACG 60.880 60.000 0.00 0.00 42.83 4.35
2302 2353 0.692756 TCCTCCCACACCTGTGTTCA 60.693 55.000 0.00 0.00 42.83 3.18
2303 2354 0.250338 GTCCTCCCACACCTGTGTTC 60.250 60.000 0.00 0.00 42.83 3.18
2304 2355 1.837090 GTCCTCCCACACCTGTGTT 59.163 57.895 0.00 0.00 42.83 3.32
2309 2360 0.836400 AATGTCGTCCTCCCACACCT 60.836 55.000 0.00 0.00 0.00 4.00
2313 2364 1.439679 GTTGAATGTCGTCCTCCCAC 58.560 55.000 0.00 0.00 0.00 4.61
2314 2365 0.037697 CGTTGAATGTCGTCCTCCCA 60.038 55.000 0.00 0.00 0.00 4.37
2321 2372 1.282248 CGAGTGGCGTTGAATGTCGT 61.282 55.000 0.00 0.00 34.64 4.34
2337 2388 8.839947 TGAATTGTTGTCAAAATATATGCGAG 57.160 30.769 0.00 0.00 37.11 5.03
2338 2389 9.631452 TTTGAATTGTTGTCAAAATATATGCGA 57.369 25.926 0.00 0.00 40.96 5.10
2345 2396 8.963130 CGCTTAGTTTGAATTGTTGTCAAAATA 58.037 29.630 1.42 2.64 44.35 1.40
2369 2420 3.560503 TGTTTGATTGAATTTCGTCCGC 58.439 40.909 0.00 0.00 0.00 5.54
2419 2492 6.901887 CGCTTAGTTGATGTGAATGTAATGAC 59.098 38.462 0.00 0.00 0.00 3.06
2448 2521 5.071370 ACCATTTAGATCTAGTCGGACGAT 58.929 41.667 16.25 0.31 0.00 3.73
2488 2562 0.251121 TGGTTCATGGCCGAACATGT 60.251 50.000 20.78 0.00 45.82 3.21
2494 2568 0.690192 TTCTCTTGGTTCATGGCCGA 59.310 50.000 0.00 0.00 0.00 5.54
2514 2588 2.613026 TGAAGACGGTGAAGCTTCAA 57.387 45.000 29.99 12.23 43.41 2.69
2640 2714 0.037975 CTTGGTGGGCTCAACATTGC 60.038 55.000 4.39 0.00 40.73 3.56
2687 2761 3.953775 CTGGTCCCACAAGGCCGT 61.954 66.667 0.00 0.00 35.27 5.68
2695 2769 4.767255 CCGCTGCTCTGGTCCCAC 62.767 72.222 0.00 0.00 0.00 4.61
2800 2875 1.770294 GAGGAGGAGAAGGACATCGT 58.230 55.000 0.00 0.00 0.00 3.73
2810 2885 1.221293 GAGACCGACGAGGAGGAGA 59.779 63.158 8.56 0.00 45.00 3.71


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

AutoCloner maintained by Alex Coulton.