Multiple sequence alignment - TraesCS7B01G190200

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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 TraesCS7B01G190200 chr7B 100.000 4981 0 0 1 4981 327267216 327272196 0.000000e+00 9199.0
1 TraesCS7B01G190200 chr7D 92.774 2823 156 22 298 3095 185130598 185133397 0.000000e+00 4039.0
2 TraesCS7B01G190200 chr7D 96.134 1164 32 7 3419 4580 185134064 185135216 0.000000e+00 1888.0
3 TraesCS7B01G190200 chr7D 94.416 394 20 2 4589 4981 185135310 185135702 5.520000e-169 604.0
4 TraesCS7B01G190200 chr7D 95.636 275 11 1 3094 3367 185133465 185133739 1.650000e-119 440.0
5 TraesCS7B01G190200 chr7D 78.972 214 32 9 4728 4937 164730446 164730242 3.130000e-27 134.0
6 TraesCS7B01G190200 chr7D 95.082 61 2 1 3617 3676 185135255 185135315 1.480000e-15 95.3
7 TraesCS7B01G190200 chr7A 90.277 2633 180 36 299 2883 192662407 192665011 0.000000e+00 3374.0
8 TraesCS7B01G190200 chr7A 85.643 1811 146 38 3094 4837 192665210 192666973 0.000000e+00 1799.0
9 TraesCS7B01G190200 chr7A 97.183 71 2 0 4866 4936 192666975 192667045 2.440000e-23 121.0
10 TraesCS7B01G190200 chr6A 82.505 1549 206 40 1000 2522 106798305 106799814 0.000000e+00 1299.0
11 TraesCS7B01G190200 chr6A 86.047 559 70 7 3470 4027 106800536 106801087 1.190000e-165 593.0
12 TraesCS7B01G190200 chr6D 82.292 1553 205 37 1000 2522 88774935 88776447 0.000000e+00 1280.0
13 TraesCS7B01G190200 chr6D 78.571 966 149 37 1087 2038 5762632 5761711 7.190000e-163 584.0
14 TraesCS7B01G190200 chr6D 85.211 426 54 8 2708 3129 88776626 88777046 3.560000e-116 429.0
15 TraesCS7B01G190200 chr6D 89.124 331 36 0 3697 4027 88777714 88778044 3.590000e-111 412.0
16 TraesCS7B01G190200 chr6D 93.878 147 9 0 149 295 394588756 394588610 6.490000e-54 222.0
17 TraesCS7B01G190200 chr6B 82.138 1534 215 37 1000 2518 169108187 169109676 0.000000e+00 1260.0
18 TraesCS7B01G190200 chr6B 85.790 563 72 5 3470 4027 169110432 169110991 1.540000e-164 590.0
19 TraesCS7B01G190200 chr6B 81.455 426 53 16 2708 3129 169109783 169110186 4.810000e-85 326.0
20 TraesCS7B01G190200 chr4B 95.238 147 7 0 149 295 483266381 483266527 3.000000e-57 233.0
21 TraesCS7B01G190200 chr4B 93.878 147 9 0 149 295 660120602 660120748 6.490000e-54 222.0
22 TraesCS7B01G190200 chr5B 94.040 151 8 1 146 295 539322720 539322870 1.390000e-55 228.0
23 TraesCS7B01G190200 chr1B 94.558 147 8 0 149 295 183877202 183877348 1.390000e-55 228.0
24 TraesCS7B01G190200 chr3B 95.105 143 7 0 149 291 183601245 183601103 5.020000e-55 226.0
25 TraesCS7B01G190200 chrUn 93.878 147 9 0 149 295 31220498 31220644 6.490000e-54 222.0
26 TraesCS7B01G190200 chr1D 93.878 147 9 0 149 295 314000481 314000335 6.490000e-54 222.0
27 TraesCS7B01G190200 chr2B 91.772 158 11 1 138 295 800062985 800062830 8.400000e-53 219.0
28 TraesCS7B01G190200 chr2B 100.000 33 0 0 1292 1324 755624730 755624698 1.500000e-05 62.1
29 TraesCS7B01G190200 chr1A 77.679 224 36 11 4720 4937 238085471 238085256 1.880000e-24 124.0


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 TraesCS7B01G190200 chr7B 327267216 327272196 4980 False 9199.000000 9199 100.000000 1 4981 1 chr7B.!!$F1 4980
1 TraesCS7B01G190200 chr7D 185130598 185135702 5104 False 1413.260000 4039 94.808400 298 4981 5 chr7D.!!$F1 4683
2 TraesCS7B01G190200 chr7A 192662407 192667045 4638 False 1764.666667 3374 91.034333 299 4936 3 chr7A.!!$F1 4637
3 TraesCS7B01G190200 chr6A 106798305 106801087 2782 False 946.000000 1299 84.276000 1000 4027 2 chr6A.!!$F1 3027
4 TraesCS7B01G190200 chr6D 88774935 88778044 3109 False 707.000000 1280 85.542333 1000 4027 3 chr6D.!!$F1 3027
5 TraesCS7B01G190200 chr6D 5761711 5762632 921 True 584.000000 584 78.571000 1087 2038 1 chr6D.!!$R1 951
6 TraesCS7B01G190200 chr6B 169108187 169110991 2804 False 725.333333 1260 83.127667 1000 4027 3 chr6B.!!$F1 3027

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
162 163 0.033405 CCTGTCTCCCTCCGTTCCTA 60.033 60.0 0.00 0.0 0.00 2.94 F
1206 1245 0.108041 GGGGCGTTTATGAGGACGAA 60.108 55.0 0.00 0.0 41.53 3.85 F
1354 1393 0.036952 CTCACTCCGGTCTGCAATGT 60.037 55.0 0.00 0.0 0.00 2.71 F
1720 1779 0.314935 GCCAGTGACATGTGTTTGGG 59.685 55.0 1.15 0.0 0.00 4.12 F
3314 3590 0.885196 TTCTGCATAACAAACGGGCC 59.115 50.0 0.00 0.0 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 1366 0.323542 GACCGGAGTGAGAGAAGGGA 60.324 60.000 9.46 0.00 0.00 4.20 R
2361 2454 0.833287 ATCGGTCTCCAACCTGATGG 59.167 55.000 0.00 0.00 46.87 3.51 R
3161 3437 0.898326 AATCACACCGGAAAAGGGGC 60.898 55.000 9.46 0.00 38.56 5.80 R
3411 3719 0.248539 CGTCTTAGACAGGGTAGCGC 60.249 60.000 13.14 0.00 32.09 5.92 R
4596 5475 1.441016 GGCGCTTGCAAGAAAGACG 60.441 57.895 30.39 22.33 41.71 4.18 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
26 27 9.515226 TTCTGCCTCACATTTTATTTACTAGTT 57.485 29.630 0.00 0.00 0.00 2.24
27 28 9.515226 TCTGCCTCACATTTTATTTACTAGTTT 57.485 29.630 0.00 0.00 0.00 2.66
28 29 9.559958 CTGCCTCACATTTTATTTACTAGTTTG 57.440 33.333 0.00 0.00 0.00 2.93
29 30 8.026607 TGCCTCACATTTTATTTACTAGTTTGC 58.973 33.333 0.00 0.00 0.00 3.68
30 31 7.488150 GCCTCACATTTTATTTACTAGTTTGCC 59.512 37.037 0.00 0.00 0.00 4.52
31 32 7.696453 CCTCACATTTTATTTACTAGTTTGCCG 59.304 37.037 0.00 0.00 0.00 5.69
32 33 7.024768 TCACATTTTATTTACTAGTTTGCCGC 58.975 34.615 0.00 0.00 0.00 6.53
33 34 6.804295 CACATTTTATTTACTAGTTTGCCGCA 59.196 34.615 0.00 0.00 0.00 5.69
34 35 7.487829 CACATTTTATTTACTAGTTTGCCGCAT 59.512 33.333 0.00 0.00 0.00 4.73
35 36 8.032451 ACATTTTATTTACTAGTTTGCCGCATT 58.968 29.630 0.00 0.00 0.00 3.56
36 37 8.868916 CATTTTATTTACTAGTTTGCCGCATTT 58.131 29.630 0.00 0.00 0.00 2.32
37 38 8.819643 TTTTATTTACTAGTTTGCCGCATTTT 57.180 26.923 0.00 0.00 0.00 1.82
38 39 8.819643 TTTATTTACTAGTTTGCCGCATTTTT 57.180 26.923 0.00 0.00 0.00 1.94
39 40 6.704512 ATTTACTAGTTTGCCGCATTTTTG 57.295 33.333 0.00 0.00 0.00 2.44
40 41 3.025287 ACTAGTTTGCCGCATTTTTGG 57.975 42.857 0.00 0.00 0.00 3.28
45 46 2.347114 GCCGCATTTTTGGCCCTT 59.653 55.556 0.00 0.00 45.73 3.95
46 47 2.034317 GCCGCATTTTTGGCCCTTG 61.034 57.895 0.00 0.00 45.73 3.61
47 48 1.370810 CCGCATTTTTGGCCCTTGT 59.629 52.632 0.00 0.00 0.00 3.16
48 49 0.605589 CCGCATTTTTGGCCCTTGTA 59.394 50.000 0.00 0.00 0.00 2.41
49 50 1.404047 CCGCATTTTTGGCCCTTGTAG 60.404 52.381 0.00 0.00 0.00 2.74
50 51 1.272212 CGCATTTTTGGCCCTTGTAGT 59.728 47.619 0.00 0.00 0.00 2.73
51 52 2.490115 CGCATTTTTGGCCCTTGTAGTA 59.510 45.455 0.00 0.00 0.00 1.82
52 53 3.057174 CGCATTTTTGGCCCTTGTAGTAA 60.057 43.478 0.00 0.00 0.00 2.24
53 54 4.494484 GCATTTTTGGCCCTTGTAGTAAG 58.506 43.478 0.00 0.00 0.00 2.34
54 55 4.494484 CATTTTTGGCCCTTGTAGTAAGC 58.506 43.478 0.00 0.00 0.00 3.09
55 56 2.961531 TTTGGCCCTTGTAGTAAGCA 57.038 45.000 0.00 0.00 0.00 3.91
56 57 3.449746 TTTGGCCCTTGTAGTAAGCAT 57.550 42.857 0.00 0.00 0.00 3.79
57 58 4.577988 TTTGGCCCTTGTAGTAAGCATA 57.422 40.909 0.00 0.00 0.00 3.14
58 59 3.838244 TGGCCCTTGTAGTAAGCATAG 57.162 47.619 0.00 0.00 0.00 2.23
59 60 3.112263 TGGCCCTTGTAGTAAGCATAGT 58.888 45.455 0.00 0.00 0.00 2.12
60 61 3.521937 TGGCCCTTGTAGTAAGCATAGTT 59.478 43.478 0.00 0.00 0.00 2.24
61 62 4.717778 TGGCCCTTGTAGTAAGCATAGTTA 59.282 41.667 0.00 0.00 0.00 2.24
62 63 5.055144 GGCCCTTGTAGTAAGCATAGTTAC 58.945 45.833 0.00 0.00 33.72 2.50
63 64 5.163332 GGCCCTTGTAGTAAGCATAGTTACT 60.163 44.000 0.00 2.17 43.98 2.24
64 65 6.041296 GGCCCTTGTAGTAAGCATAGTTACTA 59.959 42.308 0.00 0.00 42.19 1.82
73 74 8.228035 AGTAAGCATAGTTACTACTCCTTGAG 57.772 38.462 0.00 0.00 40.71 3.02
74 75 7.835181 AGTAAGCATAGTTACTACTCCTTGAGT 59.165 37.037 0.00 1.94 40.71 3.41
75 76 9.118300 GTAAGCATAGTTACTACTCCTTGAGTA 57.882 37.037 0.00 4.09 43.23 2.59
76 77 7.571080 AGCATAGTTACTACTCCTTGAGTAC 57.429 40.000 0.00 0.00 41.51 2.73
77 78 7.348033 AGCATAGTTACTACTCCTTGAGTACT 58.652 38.462 0.00 0.00 41.51 2.73
78 79 8.492782 AGCATAGTTACTACTCCTTGAGTACTA 58.507 37.037 0.00 4.03 41.51 1.82
79 80 9.287373 GCATAGTTACTACTCCTTGAGTACTAT 57.713 37.037 0.00 9.83 41.51 2.12
116 117 8.795842 TTAAAGGGTGAAATTATCTTTAGCGA 57.204 30.769 0.00 0.00 33.34 4.93
117 118 6.927294 AAGGGTGAAATTATCTTTAGCGAG 57.073 37.500 0.00 0.00 0.00 5.03
118 119 5.990668 AGGGTGAAATTATCTTTAGCGAGT 58.009 37.500 0.00 0.00 0.00 4.18
119 120 7.120923 AGGGTGAAATTATCTTTAGCGAGTA 57.879 36.000 0.00 0.00 0.00 2.59
120 121 7.736893 AGGGTGAAATTATCTTTAGCGAGTAT 58.263 34.615 0.00 0.00 0.00 2.12
121 122 8.211629 AGGGTGAAATTATCTTTAGCGAGTATT 58.788 33.333 0.00 0.00 0.00 1.89
122 123 8.283291 GGGTGAAATTATCTTTAGCGAGTATTG 58.717 37.037 0.00 0.00 0.00 1.90
123 124 9.042008 GGTGAAATTATCTTTAGCGAGTATTGA 57.958 33.333 0.00 0.00 0.00 2.57
131 132 8.819643 ATCTTTAGCGAGTATTGATCTAAACC 57.180 34.615 0.00 0.00 0.00 3.27
132 133 7.208080 TCTTTAGCGAGTATTGATCTAAACCC 58.792 38.462 0.00 0.00 0.00 4.11
133 134 6.726490 TTAGCGAGTATTGATCTAAACCCT 57.274 37.500 0.00 0.00 0.00 4.34
134 135 5.203060 AGCGAGTATTGATCTAAACCCTC 57.797 43.478 0.00 0.00 0.00 4.30
135 136 4.896482 AGCGAGTATTGATCTAAACCCTCT 59.104 41.667 0.00 0.00 0.00 3.69
136 137 5.364157 AGCGAGTATTGATCTAAACCCTCTT 59.636 40.000 0.00 0.00 0.00 2.85
137 138 6.550108 AGCGAGTATTGATCTAAACCCTCTTA 59.450 38.462 0.00 0.00 0.00 2.10
138 139 7.233757 AGCGAGTATTGATCTAAACCCTCTTAT 59.766 37.037 0.00 0.00 0.00 1.73
139 140 8.521176 GCGAGTATTGATCTAAACCCTCTTATA 58.479 37.037 0.00 0.00 0.00 0.98
140 141 9.843334 CGAGTATTGATCTAAACCCTCTTATAC 57.157 37.037 0.00 0.00 0.00 1.47
144 145 7.613551 TTGATCTAAACCCTCTTATACTCCC 57.386 40.000 0.00 0.00 0.00 4.30
145 146 6.935036 TGATCTAAACCCTCTTATACTCCCT 58.065 40.000 0.00 0.00 0.00 4.20
146 147 6.782988 TGATCTAAACCCTCTTATACTCCCTG 59.217 42.308 0.00 0.00 0.00 4.45
147 148 6.101274 TCTAAACCCTCTTATACTCCCTGT 57.899 41.667 0.00 0.00 0.00 4.00
148 149 6.134754 TCTAAACCCTCTTATACTCCCTGTC 58.865 44.000 0.00 0.00 0.00 3.51
149 150 4.628661 AACCCTCTTATACTCCCTGTCT 57.371 45.455 0.00 0.00 0.00 3.41
150 151 4.187506 ACCCTCTTATACTCCCTGTCTC 57.812 50.000 0.00 0.00 0.00 3.36
151 152 3.117054 ACCCTCTTATACTCCCTGTCTCC 60.117 52.174 0.00 0.00 0.00 3.71
152 153 3.502356 CCTCTTATACTCCCTGTCTCCC 58.498 54.545 0.00 0.00 0.00 4.30
153 154 3.141272 CCTCTTATACTCCCTGTCTCCCT 59.859 52.174 0.00 0.00 0.00 4.20
154 155 4.403734 CTCTTATACTCCCTGTCTCCCTC 58.596 52.174 0.00 0.00 0.00 4.30
155 156 3.140519 TCTTATACTCCCTGTCTCCCTCC 59.859 52.174 0.00 0.00 0.00 4.30
156 157 0.186386 ATACTCCCTGTCTCCCTCCG 59.814 60.000 0.00 0.00 0.00 4.63
157 158 1.212934 TACTCCCTGTCTCCCTCCGT 61.213 60.000 0.00 0.00 0.00 4.69
158 159 1.305381 CTCCCTGTCTCCCTCCGTT 60.305 63.158 0.00 0.00 0.00 4.44
159 160 1.305046 TCCCTGTCTCCCTCCGTTC 60.305 63.158 0.00 0.00 0.00 3.95
160 161 2.359967 CCCTGTCTCCCTCCGTTCC 61.360 68.421 0.00 0.00 0.00 3.62
161 162 1.305381 CCTGTCTCCCTCCGTTCCT 60.305 63.158 0.00 0.00 0.00 3.36
162 163 0.033405 CCTGTCTCCCTCCGTTCCTA 60.033 60.000 0.00 0.00 0.00 2.94
163 164 1.618888 CCTGTCTCCCTCCGTTCCTAA 60.619 57.143 0.00 0.00 0.00 2.69
164 165 2.176889 CTGTCTCCCTCCGTTCCTAAA 58.823 52.381 0.00 0.00 0.00 1.85
165 166 2.766828 CTGTCTCCCTCCGTTCCTAAAT 59.233 50.000 0.00 0.00 0.00 1.40
166 167 3.958798 CTGTCTCCCTCCGTTCCTAAATA 59.041 47.826 0.00 0.00 0.00 1.40
167 168 4.553678 TGTCTCCCTCCGTTCCTAAATAT 58.446 43.478 0.00 0.00 0.00 1.28
168 169 5.708544 TGTCTCCCTCCGTTCCTAAATATA 58.291 41.667 0.00 0.00 0.00 0.86
169 170 6.138263 TGTCTCCCTCCGTTCCTAAATATAA 58.862 40.000 0.00 0.00 0.00 0.98
170 171 6.267014 TGTCTCCCTCCGTTCCTAAATATAAG 59.733 42.308 0.00 0.00 0.00 1.73
171 172 6.267242 GTCTCCCTCCGTTCCTAAATATAAGT 59.733 42.308 0.00 0.00 0.00 2.24
172 173 6.492772 TCTCCCTCCGTTCCTAAATATAAGTC 59.507 42.308 0.00 0.00 0.00 3.01
173 174 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
174 175 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
175 176 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
176 177 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
177 178 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
194 195 9.905713 AAGTCTTTGTATAGATTTTGCTATGGA 57.094 29.630 0.00 0.00 33.37 3.41
195 196 9.331282 AGTCTTTGTATAGATTTTGCTATGGAC 57.669 33.333 0.00 0.00 33.37 4.02
196 197 9.331282 GTCTTTGTATAGATTTTGCTATGGACT 57.669 33.333 0.00 0.00 33.37 3.85
203 204 8.988064 ATAGATTTTGCTATGGACTACATACG 57.012 34.615 0.00 0.00 41.03 3.06
204 205 7.050970 AGATTTTGCTATGGACTACATACGA 57.949 36.000 0.00 0.00 41.03 3.43
205 206 7.497595 AGATTTTGCTATGGACTACATACGAA 58.502 34.615 0.00 0.00 41.03 3.85
206 207 7.653713 AGATTTTGCTATGGACTACATACGAAG 59.346 37.037 0.00 0.00 41.03 3.79
207 208 4.238761 TGCTATGGACTACATACGAAGC 57.761 45.455 0.00 0.00 41.03 3.86
208 209 3.634910 TGCTATGGACTACATACGAAGCA 59.365 43.478 0.00 0.00 42.28 3.91
209 210 4.098807 TGCTATGGACTACATACGAAGCAA 59.901 41.667 0.00 0.00 41.83 3.91
210 211 5.047847 GCTATGGACTACATACGAAGCAAA 58.952 41.667 0.00 0.00 41.03 3.68
211 212 5.522460 GCTATGGACTACATACGAAGCAAAA 59.478 40.000 0.00 0.00 41.03 2.44
212 213 6.202954 GCTATGGACTACATACGAAGCAAAAT 59.797 38.462 0.00 0.00 41.03 1.82
213 214 5.794687 TGGACTACATACGAAGCAAAATG 57.205 39.130 0.00 0.00 0.00 2.32
214 215 5.483811 TGGACTACATACGAAGCAAAATGA 58.516 37.500 0.00 0.00 0.00 2.57
215 216 5.935206 TGGACTACATACGAAGCAAAATGAA 59.065 36.000 0.00 0.00 0.00 2.57
216 217 6.597672 TGGACTACATACGAAGCAAAATGAAT 59.402 34.615 0.00 0.00 0.00 2.57
217 218 6.907212 GGACTACATACGAAGCAAAATGAATG 59.093 38.462 0.00 0.00 0.00 2.67
218 219 7.201609 GGACTACATACGAAGCAAAATGAATGA 60.202 37.037 0.00 0.00 0.00 2.57
219 220 8.039603 ACTACATACGAAGCAAAATGAATGAA 57.960 30.769 0.00 0.00 0.00 2.57
220 221 8.677300 ACTACATACGAAGCAAAATGAATGAAT 58.323 29.630 0.00 0.00 0.00 2.57
221 222 7.975866 ACATACGAAGCAAAATGAATGAATC 57.024 32.000 0.00 0.00 0.00 2.52
222 223 7.765307 ACATACGAAGCAAAATGAATGAATCT 58.235 30.769 0.00 0.00 0.00 2.40
223 224 8.892723 ACATACGAAGCAAAATGAATGAATCTA 58.107 29.630 0.00 0.00 0.00 1.98
224 225 9.162793 CATACGAAGCAAAATGAATGAATCTAC 57.837 33.333 0.00 0.00 0.00 2.59
225 226 7.144722 ACGAAGCAAAATGAATGAATCTACA 57.855 32.000 0.00 0.00 0.00 2.74
226 227 7.023575 ACGAAGCAAAATGAATGAATCTACAC 58.976 34.615 0.00 0.00 0.00 2.90
227 228 7.094634 ACGAAGCAAAATGAATGAATCTACACT 60.095 33.333 0.00 0.00 0.00 3.55
228 229 7.427606 CGAAGCAAAATGAATGAATCTACACTC 59.572 37.037 0.00 0.00 0.00 3.51
229 230 7.934855 AGCAAAATGAATGAATCTACACTCT 57.065 32.000 0.00 0.00 0.00 3.24
230 231 9.453572 AAGCAAAATGAATGAATCTACACTCTA 57.546 29.630 0.00 0.00 0.00 2.43
231 232 9.453572 AGCAAAATGAATGAATCTACACTCTAA 57.546 29.630 0.00 0.00 0.00 2.10
237 238 8.791327 TGAATGAATCTACACTCTAAAATGCA 57.209 30.769 0.00 0.00 0.00 3.96
238 239 9.399797 TGAATGAATCTACACTCTAAAATGCAT 57.600 29.630 0.00 0.00 0.00 3.96
239 240 9.875675 GAATGAATCTACACTCTAAAATGCATC 57.124 33.333 0.00 0.00 0.00 3.91
240 241 9.624373 AATGAATCTACACTCTAAAATGCATCT 57.376 29.630 0.00 0.00 0.00 2.90
251 252 9.809096 ACTCTAAAATGCATCTATATACATCCG 57.191 33.333 0.00 0.00 0.00 4.18
252 253 9.809096 CTCTAAAATGCATCTATATACATCCGT 57.191 33.333 0.00 0.00 0.00 4.69
256 257 7.953158 AATGCATCTATATACATCCGTATGC 57.047 36.000 0.00 0.00 38.79 3.14
257 258 5.519722 TGCATCTATATACATCCGTATGCG 58.480 41.667 0.00 0.00 38.79 4.73
269 270 2.502213 CGTATGCGGTCCATAGTGAA 57.498 50.000 0.00 0.00 37.10 3.18
270 271 2.816689 CGTATGCGGTCCATAGTGAAA 58.183 47.619 0.00 0.00 37.10 2.69
271 272 3.390135 CGTATGCGGTCCATAGTGAAAT 58.610 45.455 0.00 0.00 37.10 2.17
272 273 3.428870 CGTATGCGGTCCATAGTGAAATC 59.571 47.826 0.00 0.00 37.10 2.17
273 274 3.845781 ATGCGGTCCATAGTGAAATCT 57.154 42.857 0.00 0.00 30.69 2.40
274 275 3.179443 TGCGGTCCATAGTGAAATCTC 57.821 47.619 0.00 0.00 0.00 2.75
275 276 2.766263 TGCGGTCCATAGTGAAATCTCT 59.234 45.455 0.00 0.00 0.00 3.10
276 277 3.958147 TGCGGTCCATAGTGAAATCTCTA 59.042 43.478 0.00 0.00 0.00 2.43
277 278 4.202121 TGCGGTCCATAGTGAAATCTCTAC 60.202 45.833 0.00 0.00 0.00 2.59
278 279 4.202121 GCGGTCCATAGTGAAATCTCTACA 60.202 45.833 0.00 0.00 0.00 2.74
279 280 5.681437 GCGGTCCATAGTGAAATCTCTACAA 60.681 44.000 0.00 0.00 0.00 2.41
280 281 6.338146 CGGTCCATAGTGAAATCTCTACAAA 58.662 40.000 0.00 0.00 0.00 2.83
281 282 6.477033 CGGTCCATAGTGAAATCTCTACAAAG 59.523 42.308 0.00 0.00 0.00 2.77
282 283 7.556844 GGTCCATAGTGAAATCTCTACAAAGA 58.443 38.462 0.00 0.00 0.00 2.52
283 284 7.492994 GGTCCATAGTGAAATCTCTACAAAGAC 59.507 40.741 0.00 0.00 0.00 3.01
284 285 8.254508 GTCCATAGTGAAATCTCTACAAAGACT 58.745 37.037 0.00 0.00 0.00 3.24
285 286 8.816894 TCCATAGTGAAATCTCTACAAAGACTT 58.183 33.333 0.00 0.00 0.00 3.01
296 297 9.661954 ATCTCTACAAAGACTTATATTGAGGGA 57.338 33.333 0.00 0.00 0.00 4.20
377 388 1.506493 CCACAACTCAGTGAGCTGAC 58.494 55.000 26.38 0.00 45.94 3.51
416 427 2.972505 CTGCGCCGGTTTCTGTGT 60.973 61.111 4.18 0.00 0.00 3.72
447 458 1.581447 CTTTGAGGTTCTTGGGCGC 59.419 57.895 0.00 0.00 0.00 6.53
541 552 2.741211 GTCTTCCCCACGCCGAAC 60.741 66.667 0.00 0.00 0.00 3.95
619 630 1.296722 GTCGTCGTCGTCCTCATCG 60.297 63.158 1.33 0.00 38.33 3.84
625 639 3.209812 TCGTCCTCATCGGCCTCG 61.210 66.667 0.00 0.00 37.82 4.63
628 642 2.833582 TCCTCATCGGCCTCGTCC 60.834 66.667 0.00 0.00 37.69 4.79
823 840 3.000041 CTGTAGCAGTGGCATTTCGTTA 59.000 45.455 0.00 0.00 44.61 3.18
839 856 1.816074 GTTATTGTGTTCAGGCCGGA 58.184 50.000 5.05 0.00 0.00 5.14
845 862 3.384532 GTTCAGGCCGGACGGGTA 61.385 66.667 7.88 0.00 38.44 3.69
1206 1245 0.108041 GGGGCGTTTATGAGGACGAA 60.108 55.000 0.00 0.00 41.53 3.85
1269 1308 2.667318 CGTCGAGTGCGCCATGTTT 61.667 57.895 4.18 0.00 37.46 2.83
1275 1314 1.213537 GTGCGCCATGTTTGCATCT 59.786 52.632 4.18 0.00 41.23 2.90
1290 1329 1.446792 ATCTGTTGCTGGTCTCGCG 60.447 57.895 0.00 0.00 0.00 5.87
1327 1366 2.362503 TCGCCATCGAGGTCCACT 60.363 61.111 0.00 0.00 40.21 4.00
1344 1383 0.323908 ACTCCCTTCTCTCACTCCGG 60.324 60.000 0.00 0.00 0.00 5.14
1354 1393 0.036952 CTCACTCCGGTCTGCAATGT 60.037 55.000 0.00 0.00 0.00 2.71
1371 1410 2.869233 TGTTGCTCTGTTTCTTTGGC 57.131 45.000 0.00 0.00 0.00 4.52
1377 1416 2.362077 GCTCTGTTTCTTTGGCCTTTCA 59.638 45.455 3.32 0.00 0.00 2.69
1382 1423 6.048509 TCTGTTTCTTTGGCCTTTCAAAATC 58.951 36.000 3.32 0.00 36.37 2.17
1427 1476 3.181487 TGAAACTGCTGTCTTCTTTTGCC 60.181 43.478 14.67 0.00 0.00 4.52
1457 1506 5.536161 AGAATTACTTCAGCTGCTTTTTCCA 59.464 36.000 9.47 0.00 33.56 3.53
1503 1552 2.708325 GAGATGGGGATTAGAAGCTGGT 59.292 50.000 0.00 0.00 0.00 4.00
1509 1558 3.071747 GGGGATTAGAAGCTGGTAGGAAG 59.928 52.174 0.00 0.00 0.00 3.46
1524 1574 3.474798 AGGAAGACCATGGTGAGTCTA 57.525 47.619 25.52 0.00 42.48 2.59
1566 1622 9.964354 TGGCATTATATAGCTTTCATGTATTCT 57.036 29.630 0.00 0.00 0.00 2.40
1720 1779 0.314935 GCCAGTGACATGTGTTTGGG 59.685 55.000 1.15 0.00 0.00 4.12
1828 1892 6.421501 GCTTCAACATCATTGTCATTGAAACA 59.578 34.615 1.73 0.00 32.51 2.83
1846 1910 5.062934 TGAAACAAACAATAGCTCCGTATCG 59.937 40.000 0.00 0.00 0.00 2.92
1857 1921 2.481185 GCTCCGTATCGTGGAACAAAAA 59.519 45.455 0.00 0.00 44.16 1.94
1897 1966 6.831976 ACCACTCAAAGAGATCAATATACCC 58.168 40.000 0.31 0.00 33.32 3.69
1898 1967 5.928839 CCACTCAAAGAGATCAATATACCCG 59.071 44.000 0.31 0.00 33.32 5.28
1955 2028 5.149973 TGCGACAGTAAGGGTTAACATTA 57.850 39.130 8.10 3.35 0.00 1.90
2019 2092 6.104146 ACTTAAGTTTTGGTGTTGTTGGTT 57.896 33.333 1.12 0.00 0.00 3.67
2088 2165 7.754851 TTAGTTTTGTATCTTCTTTGGGACC 57.245 36.000 0.00 0.00 0.00 4.46
2143 2222 9.350357 TCGTTATGACTCAGTAGATTTTTACAC 57.650 33.333 0.00 0.00 0.00 2.90
2155 2234 8.161425 AGTAGATTTTTACACTTCTTGGGCTTA 58.839 33.333 0.00 0.00 0.00 3.09
2265 2357 7.787028 TGTTGGCATATATGTCACTAACAGTA 58.213 34.615 19.45 0.00 42.90 2.74
2357 2450 4.794278 AACGTAACATTTTTCCCATCCC 57.206 40.909 0.00 0.00 0.00 3.85
2361 2454 1.571955 ACATTTTTCCCATCCCCTGC 58.428 50.000 0.00 0.00 0.00 4.85
2480 2573 6.183361 TGCTGGTGACATATGGATTACACATA 60.183 38.462 7.80 0.00 41.51 2.29
2481 2574 6.369890 GCTGGTGACATATGGATTACACATAG 59.630 42.308 7.80 10.97 41.51 2.23
2569 2664 9.480053 GGTCATGGATATTTTCATAATGTTTGG 57.520 33.333 0.00 0.00 0.00 3.28
2674 2854 6.726490 TCTTGTACACCTGTTAGATATCCC 57.274 41.667 0.00 0.00 0.00 3.85
2703 2883 6.295039 AGAATTTTCTTTGCTTGCACAATG 57.705 33.333 0.00 0.00 32.55 2.82
2761 2941 9.869757 AAATTACCAAGCAAATTATAACCAGTC 57.130 29.630 0.00 0.00 0.00 3.51
2763 2943 5.580022 ACCAAGCAAATTATAACCAGTCCT 58.420 37.500 0.00 0.00 0.00 3.85
2770 2950 9.914834 AGCAAATTATAACCAGTCCTAAACATA 57.085 29.630 0.00 0.00 0.00 2.29
2850 3030 2.807895 GCAAGCACAGCATTGCCG 60.808 61.111 4.70 0.00 44.76 5.69
2875 3055 6.908820 GGTTGGTGTTTCTTCTTAACTTTACG 59.091 38.462 0.00 0.00 0.00 3.18
2894 3074 7.921214 ACTTTACGTGATGTCTAATATGACTGG 59.079 37.037 0.00 0.00 37.79 4.00
3019 3217 7.568349 TGATAGGCCCACATAATATCTGAATC 58.432 38.462 0.00 0.00 0.00 2.52
3073 3271 6.936335 AGCCTGCTTTGCTAATAACAAAATTT 59.064 30.769 0.00 0.00 37.28 1.82
3159 3435 3.558931 TTTCGCCCAGTGATCATGTAT 57.441 42.857 0.00 0.00 0.00 2.29
3161 3437 1.000274 TCGCCCAGTGATCATGTATCG 60.000 52.381 0.00 0.99 37.42 2.92
3305 3581 5.862323 TCAGACTTAGTCGTTTCTGCATAAC 59.138 40.000 6.73 0.00 37.67 1.89
3314 3590 0.885196 TTCTGCATAACAAACGGGCC 59.115 50.000 0.00 0.00 0.00 5.80
3347 3632 1.628340 AGCCCAACACATGCTACACTA 59.372 47.619 0.00 0.00 32.56 2.74
3348 3633 2.239654 AGCCCAACACATGCTACACTAT 59.760 45.455 0.00 0.00 32.56 2.12
3359 3644 5.190925 ACATGCTACACTATCCCCACTTTTA 59.809 40.000 0.00 0.00 0.00 1.52
3360 3645 5.353394 TGCTACACTATCCCCACTTTTAG 57.647 43.478 0.00 0.00 0.00 1.85
3362 3647 5.128827 TGCTACACTATCCCCACTTTTAGAG 59.871 44.000 0.00 0.00 0.00 2.43
3363 3648 4.489306 ACACTATCCCCACTTTTAGAGC 57.511 45.455 0.00 0.00 0.00 4.09
3364 3649 4.104831 ACACTATCCCCACTTTTAGAGCT 58.895 43.478 0.00 0.00 0.00 4.09
3366 3651 5.724854 ACACTATCCCCACTTTTAGAGCTTA 59.275 40.000 0.00 0.00 0.00 3.09
3370 3678 2.356844 CCCCACTTTTAGAGCTTACCCC 60.357 54.545 0.00 0.00 0.00 4.95
3437 3997 0.109873 CCTGTCTAAGACGCGTCGTT 60.110 55.000 31.31 25.62 41.37 3.85
3465 4025 1.303309 CGGATCATTTCCAGCTGACC 58.697 55.000 17.39 4.46 45.78 4.02
3493 4053 8.773404 TGTGCTACTCTTATTTTTAGTCCTTC 57.227 34.615 0.00 0.00 0.00 3.46
3803 4567 6.763610 CACTGGTAATTTTTAACCTGCCAAAA 59.236 34.615 2.78 0.00 38.03 2.44
3966 4730 2.274645 CCACGATGGCTGGGCAAAA 61.275 57.895 0.12 0.00 0.00 2.44
4007 4771 5.594317 GGTAGAATGCCACCATACTCATTTT 59.406 40.000 0.00 0.00 42.29 1.82
4051 4815 5.113502 ACTGAACTTGCAGCATTTTAGTC 57.886 39.130 0.00 0.00 39.51 2.59
4074 4838 2.215942 ACTTACAAATGCTCCCCCAC 57.784 50.000 0.00 0.00 0.00 4.61
4105 4869 3.361158 CCGGCGTGGCAATTGTGA 61.361 61.111 6.01 0.00 0.00 3.58
4308 5083 7.308408 GCATTCTCTTAACCTTTTCCGTTAACT 60.308 37.037 3.71 0.00 33.34 2.24
4309 5084 9.211485 CATTCTCTTAACCTTTTCCGTTAACTA 57.789 33.333 3.71 0.00 33.34 2.24
4341 5118 0.629058 TTTGGGGGCATTACTCCCTC 59.371 55.000 1.61 0.00 44.80 4.30
4363 5140 6.763610 CCTCCATCTCAAAATGTAAGTCCTAC 59.236 42.308 0.00 0.00 0.00 3.18
4411 5188 5.863935 GCTTAAGTTTGATTTTCGGCATTCT 59.136 36.000 4.02 0.00 0.00 2.40
4596 5475 6.564125 GCTTAGCGACATGGTTTATACATGAC 60.564 42.308 11.87 5.31 46.60 3.06
4644 5523 0.608308 GGCGGAGTTTAGGGCAACTT 60.608 55.000 0.00 0.00 37.11 2.66
4682 5561 2.566824 GACGGCACCAAATGTCCAT 58.433 52.632 0.00 0.00 0.00 3.41
4687 5566 1.549203 GCACCAAATGTCCATGGACT 58.451 50.000 37.92 24.07 44.80 3.85
4751 5630 2.627699 CCAACTGTAGGCACCAAATGTT 59.372 45.455 0.00 0.00 0.00 2.71
4944 5824 6.152154 TCAACTTATTCGGACACAGATACTCA 59.848 38.462 0.00 0.00 0.00 3.41
4956 5836 8.986847 GGACACAGATACTCAATCAGATAATTG 58.013 37.037 0.00 0.00 37.03 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.515226 AACTAGTAAATAAAATGTGAGGCAGAA 57.485 29.630 0.00 0.00 0.00 3.02
1 2 9.515226 AAACTAGTAAATAAAATGTGAGGCAGA 57.485 29.630 0.00 0.00 0.00 4.26
2 3 9.559958 CAAACTAGTAAATAAAATGTGAGGCAG 57.440 33.333 0.00 0.00 0.00 4.85
3 4 8.026607 GCAAACTAGTAAATAAAATGTGAGGCA 58.973 33.333 0.00 0.00 0.00 4.75
4 5 7.488150 GGCAAACTAGTAAATAAAATGTGAGGC 59.512 37.037 0.00 0.00 0.00 4.70
5 6 7.696453 CGGCAAACTAGTAAATAAAATGTGAGG 59.304 37.037 0.00 0.00 0.00 3.86
6 7 7.218204 GCGGCAAACTAGTAAATAAAATGTGAG 59.782 37.037 0.00 0.00 0.00 3.51
7 8 7.024768 GCGGCAAACTAGTAAATAAAATGTGA 58.975 34.615 0.00 0.00 0.00 3.58
8 9 6.804295 TGCGGCAAACTAGTAAATAAAATGTG 59.196 34.615 0.00 0.00 0.00 3.21
9 10 6.915349 TGCGGCAAACTAGTAAATAAAATGT 58.085 32.000 0.00 0.00 0.00 2.71
10 11 7.985634 ATGCGGCAAACTAGTAAATAAAATG 57.014 32.000 6.82 0.00 0.00 2.32
11 12 8.996024 AAATGCGGCAAACTAGTAAATAAAAT 57.004 26.923 6.82 0.00 0.00 1.82
12 13 8.819643 AAAATGCGGCAAACTAGTAAATAAAA 57.180 26.923 6.82 0.00 0.00 1.52
13 14 8.704234 CAAAAATGCGGCAAACTAGTAAATAAA 58.296 29.630 6.82 0.00 0.00 1.40
14 15 7.329717 CCAAAAATGCGGCAAACTAGTAAATAA 59.670 33.333 6.82 0.00 0.00 1.40
15 16 6.809196 CCAAAAATGCGGCAAACTAGTAAATA 59.191 34.615 6.82 0.00 0.00 1.40
16 17 5.637387 CCAAAAATGCGGCAAACTAGTAAAT 59.363 36.000 6.82 0.00 0.00 1.40
17 18 4.985409 CCAAAAATGCGGCAAACTAGTAAA 59.015 37.500 6.82 0.00 0.00 2.01
18 19 4.551388 CCAAAAATGCGGCAAACTAGTAA 58.449 39.130 6.82 0.00 0.00 2.24
19 20 4.167554 CCAAAAATGCGGCAAACTAGTA 57.832 40.909 6.82 0.00 0.00 1.82
20 21 3.025287 CCAAAAATGCGGCAAACTAGT 57.975 42.857 6.82 0.00 0.00 2.57
29 30 0.605589 TACAAGGGCCAAAAATGCGG 59.394 50.000 6.18 0.00 0.00 5.69
30 31 1.272212 ACTACAAGGGCCAAAAATGCG 59.728 47.619 6.18 0.00 0.00 4.73
31 32 4.494484 CTTACTACAAGGGCCAAAAATGC 58.506 43.478 6.18 0.00 0.00 3.56
32 33 4.021544 TGCTTACTACAAGGGCCAAAAATG 60.022 41.667 6.18 0.00 0.00 2.32
33 34 4.156477 TGCTTACTACAAGGGCCAAAAAT 58.844 39.130 6.18 0.00 0.00 1.82
34 35 3.567397 TGCTTACTACAAGGGCCAAAAA 58.433 40.909 6.18 0.00 0.00 1.94
35 36 3.231207 TGCTTACTACAAGGGCCAAAA 57.769 42.857 6.18 0.00 0.00 2.44
36 37 2.961531 TGCTTACTACAAGGGCCAAA 57.038 45.000 6.18 0.00 0.00 3.28
37 38 3.521937 ACTATGCTTACTACAAGGGCCAA 59.478 43.478 6.18 0.00 0.00 4.52
38 39 3.112263 ACTATGCTTACTACAAGGGCCA 58.888 45.455 6.18 0.00 0.00 5.36
39 40 3.840124 ACTATGCTTACTACAAGGGCC 57.160 47.619 0.00 0.00 0.00 5.80
40 41 5.915175 AGTAACTATGCTTACTACAAGGGC 58.085 41.667 0.00 0.00 35.57 5.19
47 48 9.339850 CTCAAGGAGTAGTAACTATGCTTACTA 57.660 37.037 0.47 0.47 37.92 1.82
48 49 7.835181 ACTCAAGGAGTAGTAACTATGCTTACT 59.165 37.037 0.00 2.17 41.51 2.24
49 50 7.998580 ACTCAAGGAGTAGTAACTATGCTTAC 58.001 38.462 0.00 0.00 41.51 2.34
50 51 9.118300 GTACTCAAGGAGTAGTAACTATGCTTA 57.882 37.037 6.36 0.00 44.42 3.09
51 52 7.835181 AGTACTCAAGGAGTAGTAACTATGCTT 59.165 37.037 11.08 0.00 44.13 3.91
52 53 7.348033 AGTACTCAAGGAGTAGTAACTATGCT 58.652 38.462 11.08 0.00 44.13 3.79
53 54 7.571080 AGTACTCAAGGAGTAGTAACTATGC 57.429 40.000 11.08 0.00 44.13 3.14
90 91 9.233649 TCGCTAAAGATAATTTCACCCTTTAAA 57.766 29.630 0.00 0.00 31.47 1.52
91 92 8.795842 TCGCTAAAGATAATTTCACCCTTTAA 57.204 30.769 0.00 0.00 31.47 1.52
92 93 8.044908 ACTCGCTAAAGATAATTTCACCCTTTA 58.955 33.333 0.00 0.00 0.00 1.85
93 94 6.884836 ACTCGCTAAAGATAATTTCACCCTTT 59.115 34.615 0.00 0.00 0.00 3.11
94 95 6.415573 ACTCGCTAAAGATAATTTCACCCTT 58.584 36.000 0.00 0.00 0.00 3.95
95 96 5.990668 ACTCGCTAAAGATAATTTCACCCT 58.009 37.500 0.00 0.00 0.00 4.34
96 97 7.964604 ATACTCGCTAAAGATAATTTCACCC 57.035 36.000 0.00 0.00 0.00 4.61
97 98 9.042008 TCAATACTCGCTAAAGATAATTTCACC 57.958 33.333 0.00 0.00 0.00 4.02
105 106 9.909644 GGTTTAGATCAATACTCGCTAAAGATA 57.090 33.333 0.00 0.00 33.29 1.98
106 107 7.873505 GGGTTTAGATCAATACTCGCTAAAGAT 59.126 37.037 0.00 0.00 33.29 2.40
107 108 7.069578 AGGGTTTAGATCAATACTCGCTAAAGA 59.930 37.037 0.00 0.00 33.29 2.52
108 109 7.210873 AGGGTTTAGATCAATACTCGCTAAAG 58.789 38.462 0.00 0.00 33.29 1.85
109 110 7.069578 AGAGGGTTTAGATCAATACTCGCTAAA 59.930 37.037 0.00 0.00 0.00 1.85
110 111 6.550108 AGAGGGTTTAGATCAATACTCGCTAA 59.450 38.462 0.00 0.00 0.00 3.09
111 112 6.069331 AGAGGGTTTAGATCAATACTCGCTA 58.931 40.000 0.00 0.00 0.00 4.26
112 113 4.896482 AGAGGGTTTAGATCAATACTCGCT 59.104 41.667 0.00 0.00 0.00 4.93
113 114 5.203060 AGAGGGTTTAGATCAATACTCGC 57.797 43.478 0.00 0.00 0.00 5.03
114 115 9.843334 GTATAAGAGGGTTTAGATCAATACTCG 57.157 37.037 0.00 0.00 0.00 4.18
118 119 9.322769 GGGAGTATAAGAGGGTTTAGATCAATA 57.677 37.037 0.00 0.00 0.00 1.90
119 120 8.019652 AGGGAGTATAAGAGGGTTTAGATCAAT 58.980 37.037 0.00 0.00 0.00 2.57
120 121 7.290248 CAGGGAGTATAAGAGGGTTTAGATCAA 59.710 40.741 0.00 0.00 0.00 2.57
121 122 6.782988 CAGGGAGTATAAGAGGGTTTAGATCA 59.217 42.308 0.00 0.00 0.00 2.92
122 123 6.783482 ACAGGGAGTATAAGAGGGTTTAGATC 59.217 42.308 0.00 0.00 0.00 2.75
123 124 6.694611 ACAGGGAGTATAAGAGGGTTTAGAT 58.305 40.000 0.00 0.00 0.00 1.98
124 125 6.068379 AGACAGGGAGTATAAGAGGGTTTAGA 60.068 42.308 0.00 0.00 0.00 2.10
125 126 6.137559 AGACAGGGAGTATAAGAGGGTTTAG 58.862 44.000 0.00 0.00 0.00 1.85
126 127 6.101274 AGACAGGGAGTATAAGAGGGTTTA 57.899 41.667 0.00 0.00 0.00 2.01
127 128 4.961585 AGACAGGGAGTATAAGAGGGTTT 58.038 43.478 0.00 0.00 0.00 3.27
128 129 4.548669 GAGACAGGGAGTATAAGAGGGTT 58.451 47.826 0.00 0.00 0.00 4.11
129 130 3.117054 GGAGACAGGGAGTATAAGAGGGT 60.117 52.174 0.00 0.00 0.00 4.34
130 131 3.502356 GGAGACAGGGAGTATAAGAGGG 58.498 54.545 0.00 0.00 0.00 4.30
131 132 3.141272 AGGGAGACAGGGAGTATAAGAGG 59.859 52.174 0.00 0.00 0.00 3.69
132 133 4.403734 GAGGGAGACAGGGAGTATAAGAG 58.596 52.174 0.00 0.00 0.00 2.85
133 134 3.140519 GGAGGGAGACAGGGAGTATAAGA 59.859 52.174 0.00 0.00 0.00 2.10
134 135 3.502356 GGAGGGAGACAGGGAGTATAAG 58.498 54.545 0.00 0.00 0.00 1.73
135 136 2.158505 CGGAGGGAGACAGGGAGTATAA 60.159 54.545 0.00 0.00 0.00 0.98
136 137 1.424302 CGGAGGGAGACAGGGAGTATA 59.576 57.143 0.00 0.00 0.00 1.47
137 138 0.186386 CGGAGGGAGACAGGGAGTAT 59.814 60.000 0.00 0.00 0.00 2.12
138 139 1.212934 ACGGAGGGAGACAGGGAGTA 61.213 60.000 0.00 0.00 0.00 2.59
139 140 2.095438 AACGGAGGGAGACAGGGAGT 62.095 60.000 0.00 0.00 0.00 3.85
140 141 1.305381 AACGGAGGGAGACAGGGAG 60.305 63.158 0.00 0.00 0.00 4.30
141 142 1.305046 GAACGGAGGGAGACAGGGA 60.305 63.158 0.00 0.00 0.00 4.20
142 143 2.359967 GGAACGGAGGGAGACAGGG 61.360 68.421 0.00 0.00 0.00 4.45
143 144 0.033405 TAGGAACGGAGGGAGACAGG 60.033 60.000 0.00 0.00 0.00 4.00
144 145 1.848652 TTAGGAACGGAGGGAGACAG 58.151 55.000 0.00 0.00 0.00 3.51
145 146 2.314071 TTTAGGAACGGAGGGAGACA 57.686 50.000 0.00 0.00 0.00 3.41
146 147 6.267242 ACTTATATTTAGGAACGGAGGGAGAC 59.733 42.308 0.00 0.00 0.00 3.36
147 148 6.379579 ACTTATATTTAGGAACGGAGGGAGA 58.620 40.000 0.00 0.00 0.00 3.71
148 149 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
149 150 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
150 151 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
151 152 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
152 153 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
168 169 9.905713 TCCATAGCAAAATCTATACAAAGACTT 57.094 29.630 0.00 0.00 0.00 3.01
169 170 9.331282 GTCCATAGCAAAATCTATACAAAGACT 57.669 33.333 0.00 0.00 0.00 3.24
170 171 9.331282 AGTCCATAGCAAAATCTATACAAAGAC 57.669 33.333 0.00 0.00 0.00 3.01
178 179 8.803235 TCGTATGTAGTCCATAGCAAAATCTAT 58.197 33.333 0.00 0.00 36.71 1.98
179 180 8.173542 TCGTATGTAGTCCATAGCAAAATCTA 57.826 34.615 0.00 0.00 36.71 1.98
180 181 7.050970 TCGTATGTAGTCCATAGCAAAATCT 57.949 36.000 0.00 0.00 36.71 2.40
181 182 7.569591 GCTTCGTATGTAGTCCATAGCAAAATC 60.570 40.741 0.00 0.00 36.71 2.17
182 183 6.202954 GCTTCGTATGTAGTCCATAGCAAAAT 59.797 38.462 0.00 0.00 36.71 1.82
183 184 5.522460 GCTTCGTATGTAGTCCATAGCAAAA 59.478 40.000 0.00 0.00 36.71 2.44
184 185 5.047847 GCTTCGTATGTAGTCCATAGCAAA 58.952 41.667 0.00 0.00 36.71 3.68
185 186 4.098807 TGCTTCGTATGTAGTCCATAGCAA 59.901 41.667 0.00 0.00 38.08 3.91
186 187 3.634910 TGCTTCGTATGTAGTCCATAGCA 59.365 43.478 0.00 0.00 38.49 3.49
187 188 4.238761 TGCTTCGTATGTAGTCCATAGC 57.761 45.455 0.00 0.00 36.71 2.97
188 189 7.438160 TCATTTTGCTTCGTATGTAGTCCATAG 59.562 37.037 0.00 0.00 36.71 2.23
189 190 7.269316 TCATTTTGCTTCGTATGTAGTCCATA 58.731 34.615 0.00 0.00 34.86 2.74
190 191 6.112734 TCATTTTGCTTCGTATGTAGTCCAT 58.887 36.000 0.00 0.00 37.58 3.41
191 192 5.483811 TCATTTTGCTTCGTATGTAGTCCA 58.516 37.500 0.00 0.00 0.00 4.02
192 193 6.417191 TTCATTTTGCTTCGTATGTAGTCC 57.583 37.500 0.00 0.00 0.00 3.85
193 194 7.684670 TCATTCATTTTGCTTCGTATGTAGTC 58.315 34.615 0.00 0.00 0.00 2.59
194 195 7.609760 TCATTCATTTTGCTTCGTATGTAGT 57.390 32.000 0.00 0.00 0.00 2.73
195 196 9.162793 GATTCATTCATTTTGCTTCGTATGTAG 57.837 33.333 0.00 0.00 0.00 2.74
196 197 8.892723 AGATTCATTCATTTTGCTTCGTATGTA 58.107 29.630 0.00 0.00 0.00 2.29
197 198 7.765307 AGATTCATTCATTTTGCTTCGTATGT 58.235 30.769 0.00 0.00 0.00 2.29
198 199 9.162793 GTAGATTCATTCATTTTGCTTCGTATG 57.837 33.333 0.00 0.00 0.00 2.39
199 200 8.892723 TGTAGATTCATTCATTTTGCTTCGTAT 58.107 29.630 0.00 0.00 0.00 3.06
200 201 8.175069 GTGTAGATTCATTCATTTTGCTTCGTA 58.825 33.333 0.00 0.00 0.00 3.43
201 202 7.023575 GTGTAGATTCATTCATTTTGCTTCGT 58.976 34.615 0.00 0.00 0.00 3.85
202 203 7.246311 AGTGTAGATTCATTCATTTTGCTTCG 58.754 34.615 0.00 0.00 0.00 3.79
203 204 8.457261 AGAGTGTAGATTCATTCATTTTGCTTC 58.543 33.333 0.00 0.00 0.00 3.86
204 205 8.345724 AGAGTGTAGATTCATTCATTTTGCTT 57.654 30.769 0.00 0.00 0.00 3.91
205 206 7.934855 AGAGTGTAGATTCATTCATTTTGCT 57.065 32.000 0.00 0.00 0.00 3.91
211 212 9.399797 TGCATTTTAGAGTGTAGATTCATTCAT 57.600 29.630 0.00 0.00 0.00 2.57
212 213 8.791327 TGCATTTTAGAGTGTAGATTCATTCA 57.209 30.769 0.00 0.00 0.00 2.57
213 214 9.875675 GATGCATTTTAGAGTGTAGATTCATTC 57.124 33.333 0.00 0.00 0.00 2.67
214 215 9.624373 AGATGCATTTTAGAGTGTAGATTCATT 57.376 29.630 0.00 0.00 0.00 2.57
225 226 9.809096 CGGATGTATATAGATGCATTTTAGAGT 57.191 33.333 11.19 0.00 38.38 3.24
226 227 9.809096 ACGGATGTATATAGATGCATTTTAGAG 57.191 33.333 11.19 0.00 38.38 2.43
230 231 8.830580 GCATACGGATGTATATAGATGCATTTT 58.169 33.333 9.90 0.00 38.38 1.82
231 232 7.169813 CGCATACGGATGTATATAGATGCATTT 59.830 37.037 9.90 0.00 38.38 2.32
232 233 6.642540 CGCATACGGATGTATATAGATGCATT 59.357 38.462 9.90 1.23 38.38 3.56
233 234 6.152379 CGCATACGGATGTATATAGATGCAT 58.848 40.000 9.90 0.00 40.68 3.96
234 235 5.519722 CGCATACGGATGTATATAGATGCA 58.480 41.667 9.90 0.00 39.28 3.96
250 251 2.502213 TTCACTATGGACCGCATACG 57.498 50.000 0.00 0.00 39.67 3.06
251 252 4.632153 AGATTTCACTATGGACCGCATAC 58.368 43.478 0.00 0.00 0.00 2.39
252 253 4.588951 AGAGATTTCACTATGGACCGCATA 59.411 41.667 0.00 0.00 0.00 3.14
253 254 3.389329 AGAGATTTCACTATGGACCGCAT 59.611 43.478 0.00 0.00 0.00 4.73
254 255 2.766263 AGAGATTTCACTATGGACCGCA 59.234 45.455 0.00 0.00 0.00 5.69
255 256 3.460857 AGAGATTTCACTATGGACCGC 57.539 47.619 0.00 0.00 0.00 5.68
256 257 5.515797 TGTAGAGATTTCACTATGGACCG 57.484 43.478 0.00 0.00 0.00 4.79
257 258 7.492994 GTCTTTGTAGAGATTTCACTATGGACC 59.507 40.741 0.00 0.00 0.00 4.46
258 259 8.254508 AGTCTTTGTAGAGATTTCACTATGGAC 58.745 37.037 0.00 0.00 0.00 4.02
259 260 8.367660 AGTCTTTGTAGAGATTTCACTATGGA 57.632 34.615 0.00 0.00 0.00 3.41
270 271 9.661954 TCCCTCAATATAAGTCTTTGTAGAGAT 57.338 33.333 0.00 0.00 0.00 2.75
271 272 9.137459 CTCCCTCAATATAAGTCTTTGTAGAGA 57.863 37.037 0.00 0.00 0.00 3.10
272 273 8.919145 ACTCCCTCAATATAAGTCTTTGTAGAG 58.081 37.037 0.00 0.00 0.00 2.43
273 274 8.840200 ACTCCCTCAATATAAGTCTTTGTAGA 57.160 34.615 0.00 0.00 0.00 2.59
293 294 9.503399 CCACAGGAATATTAGTAAATTACTCCC 57.497 37.037 9.17 3.42 40.14 4.30
318 319 9.379791 AGCATAAAACTAATACTACAGTGTTCC 57.620 33.333 0.00 0.00 31.76 3.62
365 368 3.649793 GCGTTCTCGTCAGCTCACTGA 62.650 57.143 0.00 0.00 43.00 3.41
377 388 1.377366 TAGCTCCCTCTGCGTTCTCG 61.377 60.000 0.00 0.00 40.37 4.04
429 440 1.172180 TGCGCCCAAGAACCTCAAAG 61.172 55.000 4.18 0.00 0.00 2.77
447 458 1.226211 CGCAAGAGCAAATCGGCTG 60.226 57.895 0.00 0.00 45.99 4.85
619 630 4.176851 GACGACGAGGACGAGGCC 62.177 72.222 0.00 0.00 42.66 5.19
805 822 4.006989 ACAATAACGAAATGCCACTGCTA 58.993 39.130 0.00 0.00 38.71 3.49
823 840 1.671054 CGTCCGGCCTGAACACAAT 60.671 57.895 0.00 0.00 0.00 2.71
839 856 4.011517 CCACCGTGGCTTACCCGT 62.012 66.667 4.16 0.00 35.87 5.28
857 874 1.676529 TCTCGCGGTGATAAGAGGAAG 59.323 52.381 6.13 0.00 0.00 3.46
1194 1233 2.477357 CGCGTCTTCTTCGTCCTCATAA 60.477 50.000 0.00 0.00 0.00 1.90
1195 1234 1.063616 CGCGTCTTCTTCGTCCTCATA 59.936 52.381 0.00 0.00 0.00 2.15
1206 1245 2.282958 TCCAGGTCCGCGTCTTCT 60.283 61.111 4.92 0.00 0.00 2.85
1275 1314 1.372499 GTACGCGAGACCAGCAACA 60.372 57.895 15.93 0.00 34.19 3.33
1290 1329 1.903183 AGGGAGTTGCTGAGGAAGTAC 59.097 52.381 0.00 0.00 0.00 2.73
1325 1364 0.323908 CCGGAGTGAGAGAAGGGAGT 60.324 60.000 0.00 0.00 0.00 3.85
1327 1366 0.323542 GACCGGAGTGAGAGAAGGGA 60.324 60.000 9.46 0.00 0.00 4.20
1354 1393 2.071778 AGGCCAAAGAAACAGAGCAA 57.928 45.000 5.01 0.00 0.00 3.91
1369 1408 5.939296 TCAAATGAATGGATTTTGAAAGGCC 59.061 36.000 0.00 0.00 36.66 5.19
1371 1410 7.658575 ACAGTCAAATGAATGGATTTTGAAAGG 59.341 33.333 14.48 0.00 43.65 3.11
1377 1416 7.118680 GCATCAACAGTCAAATGAATGGATTTT 59.881 33.333 14.48 0.00 43.65 1.82
1382 1423 4.811908 TGCATCAACAGTCAAATGAATGG 58.188 39.130 14.48 0.00 43.65 3.16
1427 1476 3.545624 GCAGCTGAAGTAATTCTGCATCG 60.546 47.826 28.51 19.64 46.64 3.84
1457 1506 3.007398 GGAGGAGATGACTATCGGCAATT 59.993 47.826 0.00 0.00 38.38 2.32
1503 1552 3.474798 AGACTCACCATGGTCTTCCTA 57.525 47.619 16.53 0.00 39.44 2.94
1509 1558 5.220931 GCATTTGATTAGACTCACCATGGTC 60.221 44.000 16.53 3.39 0.00 4.02
1564 1620 7.978975 GCAATGCCATAAATAAACTAAACCAGA 59.021 33.333 0.00 0.00 0.00 3.86
1565 1621 8.130307 GCAATGCCATAAATAAACTAAACCAG 57.870 34.615 0.00 0.00 0.00 4.00
1594 1651 3.746492 CAGTAAAACAGTAGCCACCTGAC 59.254 47.826 2.24 0.00 34.04 3.51
1695 1754 1.301716 ACATGTCACTGGCACGACC 60.302 57.895 9.23 0.00 39.84 4.79
1698 1757 0.662619 AAACACATGTCACTGGCACG 59.337 50.000 0.00 0.00 0.00 5.34
1720 1779 6.273071 AGTTGCCAACTTTAAATGTTCTGAC 58.727 36.000 3.74 0.00 39.04 3.51
1828 1892 3.131577 TCCACGATACGGAGCTATTGTTT 59.868 43.478 0.00 0.00 0.00 2.83
1857 1921 5.730550 TGAGTGGTAAGATACGCTGATTTT 58.269 37.500 0.00 0.00 0.00 1.82
1955 2028 7.554118 AGGAATACTGTTGTTCGATGATTGATT 59.446 33.333 0.00 0.00 0.00 2.57
1990 2063 9.281075 CAACAACACCAAAACTTAAGTACTAAC 57.719 33.333 8.92 0.00 0.00 2.34
2019 2092 7.381789 AAAGCAAAGGGAAAAAGGGTAAATA 57.618 32.000 0.00 0.00 0.00 1.40
2088 2165 7.203255 ACGAAGGGTTCTTTTAATCTTTCAG 57.797 36.000 0.00 0.00 32.52 3.02
2143 2222 3.511146 TGCAGGAAAATAAGCCCAAGAAG 59.489 43.478 0.00 0.00 0.00 2.85
2361 2454 0.833287 ATCGGTCTCCAACCTGATGG 59.167 55.000 0.00 0.00 46.87 3.51
2460 2553 6.467677 AGGCTATGTGTAATCCATATGTCAC 58.532 40.000 1.24 4.15 0.00 3.67
2480 2573 1.071385 CCGATCCAAAGCTATGAGGCT 59.929 52.381 0.00 0.00 45.30 4.58
2481 2574 1.070758 TCCGATCCAAAGCTATGAGGC 59.929 52.381 0.00 0.00 0.00 4.70
2674 2854 5.524646 TGCAAGCAAAGAAAATTCTTCCAAG 59.475 36.000 8.74 2.22 46.22 3.61
2703 2883 2.305052 ACTAGCACAAAGGTAACCCTCC 59.695 50.000 0.00 0.00 41.56 4.30
2793 2973 8.638685 ATTGCAATTTGCTACTTCATATGTTC 57.361 30.769 21.19 0.00 45.31 3.18
2850 3030 6.908820 CGTAAAGTTAAGAAGAAACACCAACC 59.091 38.462 0.00 0.00 0.00 3.77
2875 3055 6.073327 TCGTCCAGTCATATTAGACATCAC 57.927 41.667 0.00 0.00 40.98 3.06
2894 3074 7.040473 TCTCCTATTATGAGGAAGTTTCGTC 57.960 40.000 7.44 7.44 45.20 4.20
2962 3158 1.552337 TCTCCAAGGACACATGAGCTC 59.448 52.381 6.82 6.82 0.00 4.09
3129 3405 3.322541 TCACTGGGCGAAATTCCGATATA 59.677 43.478 0.00 0.00 0.00 0.86
3159 3435 3.562232 ACACCGGAAAAGGGGCGA 61.562 61.111 9.46 0.00 38.56 5.54
3161 3437 0.898326 AATCACACCGGAAAAGGGGC 60.898 55.000 9.46 0.00 38.56 5.80
3347 3632 3.202373 GGGTAAGCTCTAAAAGTGGGGAT 59.798 47.826 0.00 0.00 0.00 3.85
3348 3633 2.574824 GGGTAAGCTCTAAAAGTGGGGA 59.425 50.000 0.00 0.00 0.00 4.81
3411 3719 0.248539 CGTCTTAGACAGGGTAGCGC 60.249 60.000 13.14 0.00 32.09 5.92
3416 3724 1.881602 GACGCGTCTTAGACAGGGT 59.118 57.895 31.12 19.68 36.05 4.34
3437 3997 0.657312 GAAATGATCCGTCATGCGCA 59.343 50.000 14.96 14.96 44.20 6.09
3465 4025 9.220767 AGGACTAAAAATAAGAGTAGCACAAAG 57.779 33.333 0.00 0.00 0.00 2.77
3803 4567 6.669591 TGAACTGGCTCATGCTATAGGTATAT 59.330 38.462 1.04 0.00 39.59 0.86
4007 4771 0.955905 GGGCGCAAACCTTCAACTAA 59.044 50.000 10.83 0.00 0.00 2.24
4051 4815 2.231235 GGGGGAGCATTTGTAAGTTGTG 59.769 50.000 0.00 0.00 0.00 3.33
4280 5055 5.010282 ACGGAAAAGGTTAAGAGAATGCAT 58.990 37.500 0.00 0.00 0.00 3.96
4341 5118 7.331026 TGAGTAGGACTTACATTTTGAGATGG 58.669 38.462 0.00 0.00 34.56 3.51
4363 5140 6.237915 GCAAGTTTGAGTTTGGACAAAATGAG 60.238 38.462 2.21 0.00 37.66 2.90
4411 5188 9.689501 CCTATGGTTAACAGAAAAGGGTTAATA 57.310 33.333 8.10 0.00 40.41 0.98
4538 5332 1.941377 TGGAAGGCATGCAAAAGGAT 58.059 45.000 21.36 0.00 0.00 3.24
4596 5475 1.441016 GGCGCTTGCAAGAAAGACG 60.441 57.895 30.39 22.33 41.71 4.18
4628 5507 2.225727 CGTTGAAGTTGCCCTAAACTCC 59.774 50.000 0.00 0.00 39.48 3.85
4644 5523 1.561717 CGTTTGGTGATCCGCGTTGA 61.562 55.000 4.92 0.00 36.30 3.18
4682 5561 2.093394 TGAACACGTCCAAAAGAGTCCA 60.093 45.455 0.00 0.00 0.00 4.02
4906 5786 9.624697 TCCGAATAAGTTGAATTCAAATTTGAG 57.375 29.630 31.53 21.33 40.67 3.02
4956 5836 7.601073 TTCATTGACATGTCAGTCTTATCAC 57.399 36.000 26.48 0.00 41.13 3.06


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

AutoCloner maintained by Alex Coulton.