Multiple sequence alignment - TraesCS6A01G274000

Loading Multiple Alignment...

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 TraesCS6A01G274000 chr6A 100.000 6021 0 0 1 6021 500087753 500081733 0.000000e+00 11119.0
1 TraesCS6A01G274000 chr6D 95.083 2827 94 16 2331 5122 358327825 358325009 0.000000e+00 4409.0
2 TraesCS6A01G274000 chr6D 89.920 1250 53 26 405 1613 358329765 358328548 0.000000e+00 1543.0
3 TraesCS6A01G274000 chr6D 86.092 719 59 20 1607 2300 358328528 358327826 0.000000e+00 736.0
4 TraesCS6A01G274000 chr6D 91.667 168 9 3 1 167 358330107 358329944 1.690000e-55 228.0
5 TraesCS6A01G274000 chr6D 86.364 198 25 2 3936 4133 334227669 334227474 1.310000e-51 215.0
6 TraesCS6A01G274000 chr6D 96.063 127 5 0 5109 5235 358324988 358324862 2.200000e-49 207.0
7 TraesCS6A01G274000 chr6D 94.958 119 5 1 214 331 358329966 358329848 1.030000e-42 185.0
8 TraesCS6A01G274000 chr6B 94.834 2613 91 14 2331 4909 539729365 539726763 0.000000e+00 4037.0
9 TraesCS6A01G274000 chr6B 90.109 1284 41 26 380 1613 539731366 539730119 0.000000e+00 1589.0
10 TraesCS6A01G274000 chr6B 85.880 517 43 12 1801 2300 539729869 539729366 1.920000e-144 523.0
11 TraesCS6A01G274000 chr6B 90.941 287 23 3 1 285 539733038 539732753 3.400000e-102 383.0
12 TraesCS6A01G274000 chr6B 93.827 162 8 1 1607 1768 539730099 539729940 6.030000e-60 243.0
13 TraesCS6A01G274000 chr6B 94.444 108 6 0 4929 5036 539726775 539726668 3.730000e-37 167.0
14 TraesCS6A01G274000 chr6B 89.024 82 5 1 1801 1878 261702425 261702344 1.380000e-16 99.0
15 TraesCS6A01G274000 chr6B 94.231 52 3 0 5143 5194 539726370 539726319 5.000000e-11 80.5
16 TraesCS6A01G274000 chr6B 100.000 39 0 0 303 341 539731399 539731361 8.370000e-09 73.1
17 TraesCS6A01G274000 chr6B 97.500 40 1 0 5092 5131 539726464 539726425 1.080000e-07 69.4
18 TraesCS6A01G274000 chr6B 97.500 40 1 0 5092 5131 539726521 539726482 1.080000e-07 69.4
19 TraesCS6A01G274000 chr1A 98.226 789 12 1 5235 6021 508893158 508893946 0.000000e+00 1378.0
20 TraesCS6A01G274000 chr1A 97.713 787 18 0 5235 6021 29004468 29005254 0.000000e+00 1354.0
21 TraesCS6A01G274000 chr7A 98.094 787 15 0 5235 6021 39060130 39059344 0.000000e+00 1371.0
22 TraesCS6A01G274000 chr7A 96.701 788 25 1 5235 6021 2977815 2978602 0.000000e+00 1310.0
23 TraesCS6A01G274000 chr7A 96.135 802 27 4 5222 6021 2979410 2980209 0.000000e+00 1306.0
24 TraesCS6A01G274000 chr4A 96.135 802 27 4 5222 6021 4573073 4573872 0.000000e+00 1306.0
25 TraesCS6A01G274000 chr5A 96.217 793 23 5 5235 6021 78132056 78131265 0.000000e+00 1291.0
26 TraesCS6A01G274000 chr5A 95.415 807 27 8 5222 6021 78130457 78129654 0.000000e+00 1277.0
27 TraesCS6A01G274000 chr2A 95.734 797 27 5 5222 6016 125338178 125337387 0.000000e+00 1277.0
28 TraesCS6A01G274000 chr2A 91.279 172 15 0 3977 4148 35976014 35976185 1.010000e-57 235.0
29 TraesCS6A01G274000 chr2A 86.500 200 27 0 3937 4136 656240941 656241140 2.820000e-53 220.0
30 TraesCS6A01G274000 chr2D 91.176 170 15 0 3977 4146 32763269 32763438 1.310000e-56 231.0
31 TraesCS6A01G274000 chr2D 87.500 200 25 0 3937 4136 512686864 512687063 1.310000e-56 231.0
32 TraesCS6A01G274000 chr2B 91.176 170 15 0 3977 4146 54440337 54440506 1.310000e-56 231.0
33 TraesCS6A01G274000 chr2B 87.000 200 26 0 3937 4136 602763475 602763674 6.070000e-55 226.0


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 TraesCS6A01G274000 chr6A 500081733 500087753 6020 True 11119.00 11119 100.000000 1 6021 1 chr6A.!!$R1 6020
1 TraesCS6A01G274000 chr6D 358324862 358330107 5245 True 1218.00 4409 92.297167 1 5235 6 chr6D.!!$R2 5234
2 TraesCS6A01G274000 chr6B 539726319 539733038 6719 True 723.44 4037 93.926600 1 5194 10 chr6B.!!$R2 5193
3 TraesCS6A01G274000 chr1A 508893158 508893946 788 False 1378.00 1378 98.226000 5235 6021 1 chr1A.!!$F2 786
4 TraesCS6A01G274000 chr1A 29004468 29005254 786 False 1354.00 1354 97.713000 5235 6021 1 chr1A.!!$F1 786
5 TraesCS6A01G274000 chr7A 39059344 39060130 786 True 1371.00 1371 98.094000 5235 6021 1 chr7A.!!$R1 786
6 TraesCS6A01G274000 chr7A 2977815 2980209 2394 False 1308.00 1310 96.418000 5222 6021 2 chr7A.!!$F1 799
7 TraesCS6A01G274000 chr4A 4573073 4573872 799 False 1306.00 1306 96.135000 5222 6021 1 chr4A.!!$F1 799
8 TraesCS6A01G274000 chr5A 78129654 78132056 2402 True 1284.00 1291 95.816000 5222 6021 2 chr5A.!!$R1 799
9 TraesCS6A01G274000 chr2A 125337387 125338178 791 True 1277.00 1277 95.734000 5222 6016 1 chr2A.!!$R1 794

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
149 150 0.035458 CGGAACACCTCTTCAGGCTT 59.965 55.000 0.00 0.00 45.05 4.35 F
347 421 0.107654 ATTCGGCAGGAGTGGTAAGC 60.108 55.000 0.00 0.00 0.00 3.09 F
349 423 0.323999 TCGGCAGGAGTGGTAAGCTA 60.324 55.000 0.00 0.00 0.00 3.32 F
799 2227 0.394488 TGGCGAGGAGACGAGAAGAT 60.394 55.000 0.00 0.00 35.09 2.40 F
1385 2844 0.463654 TGGATCTTCGATTTGCCGGG 60.464 55.000 2.18 0.00 0.00 5.73 F
1632 3121 0.512518 GGTTTGATTTGGCTTTGCGC 59.487 50.000 0.00 0.00 38.13 6.09 F
1729 3218 1.002251 CTACTCTAGCTACCGTGCAGC 60.002 57.143 0.00 0.00 39.41 5.25 F
2915 4467 0.039527 GCGGAGAAACAACGGCATTT 60.040 50.000 0.00 0.00 33.65 2.32 F
3670 5248 0.109272 CTTGGTCTGCATGCAGCTTG 60.109 55.000 37.48 22.21 45.94 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1257 2715 0.393808 GGTTTCAGGGCGATTGGCTA 60.394 55.000 6.45 0.00 42.94 3.93 R
1721 3210 0.883833 ATTTTCTGAAGGCTGCACGG 59.116 50.000 0.50 0.00 0.00 4.94 R
1948 3481 1.134401 AGCGCCTAGGTACGTACAGTA 60.134 52.381 26.02 15.59 0.00 2.74 R
2022 3561 2.029380 TGTGATCAACGACGACAGGAAT 60.029 45.455 0.00 0.00 0.00 3.01 R
2915 4467 0.465705 CTAAATCTGCCTCCGCTCCA 59.534 55.000 0.00 0.00 35.36 3.86 R
2916 4468 0.882484 GCTAAATCTGCCTCCGCTCC 60.882 60.000 0.00 0.00 35.36 4.70 R
3261 4835 1.065418 GGTGTGTTGTGCCCTAGCTAT 60.065 52.381 0.00 0.00 40.80 2.97 R
4606 6187 0.398381 GGGAGCTGATGGAGGTCTCT 60.398 60.000 0.00 0.00 45.07 3.10 R
5037 6626 1.068121 AGCCTACTCCAAACAAGCCT 58.932 50.000 0.00 0.00 0.00 4.58 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
36 37 8.798153 CAACGTTAGATCAAATCTTATTTTGCC 58.202 33.333 0.00 0.00 40.76 4.52
143 144 1.003718 CACCCCGGAACACCTCTTC 60.004 63.158 0.73 0.00 0.00 2.87
144 145 1.460689 ACCCCGGAACACCTCTTCA 60.461 57.895 0.73 0.00 0.00 3.02
147 148 1.376037 CCGGAACACCTCTTCAGGC 60.376 63.158 0.00 0.00 45.05 4.85
148 149 1.674057 CGGAACACCTCTTCAGGCT 59.326 57.895 0.00 0.00 45.05 4.58
149 150 0.035458 CGGAACACCTCTTCAGGCTT 59.965 55.000 0.00 0.00 45.05 4.35
150 151 1.543429 CGGAACACCTCTTCAGGCTTT 60.543 52.381 0.00 0.00 45.05 3.51
151 152 2.155279 GGAACACCTCTTCAGGCTTTC 58.845 52.381 0.00 0.00 45.05 2.62
152 153 1.801178 GAACACCTCTTCAGGCTTTCG 59.199 52.381 0.00 0.00 45.05 3.46
154 155 1.141053 ACACCTCTTCAGGCTTTCGTT 59.859 47.619 0.00 0.00 45.05 3.85
155 156 1.532868 CACCTCTTCAGGCTTTCGTTG 59.467 52.381 0.00 0.00 45.05 4.10
156 157 1.160137 CCTCTTCAGGCTTTCGTTGG 58.840 55.000 0.00 0.00 30.98 3.77
157 158 1.543429 CCTCTTCAGGCTTTCGTTGGT 60.543 52.381 0.00 0.00 30.98 3.67
158 159 2.222027 CTCTTCAGGCTTTCGTTGGTT 58.778 47.619 0.00 0.00 0.00 3.67
160 161 3.811083 TCTTCAGGCTTTCGTTGGTTTA 58.189 40.909 0.00 0.00 0.00 2.01
161 162 3.562557 TCTTCAGGCTTTCGTTGGTTTAC 59.437 43.478 0.00 0.00 0.00 2.01
162 163 2.920524 TCAGGCTTTCGTTGGTTTACA 58.079 42.857 0.00 0.00 0.00 2.41
164 165 2.031157 CAGGCTTTCGTTGGTTTACAGG 60.031 50.000 0.00 0.00 0.00 4.00
165 166 2.158726 AGGCTTTCGTTGGTTTACAGGA 60.159 45.455 0.00 0.00 0.00 3.86
166 167 2.619646 GGCTTTCGTTGGTTTACAGGAA 59.380 45.455 0.00 0.00 0.00 3.36
167 168 3.067040 GGCTTTCGTTGGTTTACAGGAAA 59.933 43.478 0.00 0.00 34.38 3.13
168 169 4.261867 GGCTTTCGTTGGTTTACAGGAAAT 60.262 41.667 0.00 0.00 34.77 2.17
169 170 5.048573 GGCTTTCGTTGGTTTACAGGAAATA 60.049 40.000 0.00 0.00 34.77 1.40
170 171 6.349860 GGCTTTCGTTGGTTTACAGGAAATAT 60.350 38.462 0.00 0.00 34.77 1.28
171 172 6.526674 GCTTTCGTTGGTTTACAGGAAATATG 59.473 38.462 0.00 0.00 34.77 1.78
172 173 7.574217 GCTTTCGTTGGTTTACAGGAAATATGA 60.574 37.037 0.00 0.00 34.77 2.15
174 175 7.372451 TCGTTGGTTTACAGGAAATATGAAG 57.628 36.000 0.00 0.00 0.00 3.02
177 178 8.458843 CGTTGGTTTACAGGAAATATGAAGAAT 58.541 33.333 0.00 0.00 0.00 2.40
178 179 9.788960 GTTGGTTTACAGGAAATATGAAGAATC 57.211 33.333 0.00 0.00 0.00 2.52
179 180 8.519799 TGGTTTACAGGAAATATGAAGAATCC 57.480 34.615 0.00 0.00 0.00 3.01
180 181 7.559897 TGGTTTACAGGAAATATGAAGAATCCC 59.440 37.037 0.00 0.00 0.00 3.85
181 182 7.559897 GGTTTACAGGAAATATGAAGAATCCCA 59.440 37.037 0.00 0.00 0.00 4.37
182 183 9.136323 GTTTACAGGAAATATGAAGAATCCCAT 57.864 33.333 0.00 0.00 0.00 4.00
185 186 7.465116 ACAGGAAATATGAAGAATCCCATAGG 58.535 38.462 0.00 0.00 0.00 2.57
200 201 5.756918 TCCCATAGGATAGGATTCTCGTAG 58.243 45.833 0.00 0.00 37.19 3.51
201 202 5.491439 TCCCATAGGATAGGATTCTCGTAGA 59.509 44.000 0.00 0.00 37.19 2.59
202 203 6.011893 TCCCATAGGATAGGATTCTCGTAGAA 60.012 42.308 0.79 0.79 37.19 2.10
203 204 6.663953 CCCATAGGATAGGATTCTCGTAGAAA 59.336 42.308 2.21 0.00 34.44 2.52
239 311 3.062042 GCTTTTGGTTTGCAGGAATGAG 58.938 45.455 0.00 0.00 0.00 2.90
331 405 7.929785 AGGTAATGATCAAAATTGCATCCATTC 59.070 33.333 0.00 0.00 0.00 2.67
340 414 1.153086 GCATCCATTCGGCAGGAGT 60.153 57.895 0.00 0.00 37.34 3.85
343 417 2.671070 CCATTCGGCAGGAGTGGT 59.329 61.111 9.53 0.00 45.07 4.16
347 421 0.107654 ATTCGGCAGGAGTGGTAAGC 60.108 55.000 0.00 0.00 0.00 3.09
348 422 1.192146 TTCGGCAGGAGTGGTAAGCT 61.192 55.000 0.00 0.00 0.00 3.74
349 423 0.323999 TCGGCAGGAGTGGTAAGCTA 60.324 55.000 0.00 0.00 0.00 3.32
350 424 0.753262 CGGCAGGAGTGGTAAGCTAT 59.247 55.000 0.00 0.00 0.00 2.97
351 425 1.961394 CGGCAGGAGTGGTAAGCTATA 59.039 52.381 0.00 0.00 0.00 1.31
352 426 2.364324 CGGCAGGAGTGGTAAGCTATAA 59.636 50.000 0.00 0.00 0.00 0.98
353 427 3.181469 CGGCAGGAGTGGTAAGCTATAAA 60.181 47.826 0.00 0.00 0.00 1.40
355 429 5.190677 GGCAGGAGTGGTAAGCTATAAAAA 58.809 41.667 0.00 0.00 0.00 1.94
494 1900 3.764237 TCCTACGATAAAATGAGGGCC 57.236 47.619 0.00 0.00 0.00 5.80
495 1901 3.314693 TCCTACGATAAAATGAGGGCCT 58.685 45.455 5.25 5.25 0.00 5.19
496 1902 4.485875 TCCTACGATAAAATGAGGGCCTA 58.514 43.478 5.73 0.00 0.00 3.93
497 1903 4.527038 TCCTACGATAAAATGAGGGCCTAG 59.473 45.833 5.73 0.00 0.00 3.02
790 2218 2.997315 CCACCAGTGGCGAGGAGA 60.997 66.667 9.78 0.00 44.73 3.71
791 2219 2.262915 CACCAGTGGCGAGGAGAC 59.737 66.667 9.78 0.00 0.00 3.36
792 2220 3.374402 ACCAGTGGCGAGGAGACG 61.374 66.667 9.78 0.00 0.00 4.18
793 2221 3.062466 CCAGTGGCGAGGAGACGA 61.062 66.667 0.00 0.00 35.09 4.20
794 2222 2.487428 CAGTGGCGAGGAGACGAG 59.513 66.667 0.00 0.00 35.09 4.18
795 2223 2.041115 CAGTGGCGAGGAGACGAGA 61.041 63.158 0.00 0.00 35.09 4.04
796 2224 1.303398 AGTGGCGAGGAGACGAGAA 60.303 57.895 0.00 0.00 35.09 2.87
797 2225 1.137825 GTGGCGAGGAGACGAGAAG 59.862 63.158 0.00 0.00 35.09 2.85
798 2226 1.002502 TGGCGAGGAGACGAGAAGA 60.003 57.895 0.00 0.00 35.09 2.87
799 2227 0.394488 TGGCGAGGAGACGAGAAGAT 60.394 55.000 0.00 0.00 35.09 2.40
988 2429 1.966451 CCCACACCAAGCTCGTTCC 60.966 63.158 0.00 0.00 0.00 3.62
995 2440 2.048127 AAGCTCGTTCCAGTCCGC 60.048 61.111 0.00 0.00 0.00 5.54
1097 2549 1.816835 TCTCACCAACTACCAGTAGCG 59.183 52.381 4.72 0.00 36.66 4.26
1145 2597 5.144100 TCATATCTCCTCTTCCTTCTCCAC 58.856 45.833 0.00 0.00 0.00 4.02
1149 2601 1.203237 TCCTCTTCCTTCTCCACAGCT 60.203 52.381 0.00 0.00 0.00 4.24
1167 2623 1.405391 GCTTCTCTTCTCCTGTCCAGC 60.405 57.143 0.00 0.00 0.00 4.85
1172 2628 0.820226 CTTCTCCTGTCCAGCATCGA 59.180 55.000 0.00 0.00 0.00 3.59
1225 2683 6.810911 TCATCTTCATGTTCTTCCTAGCTAC 58.189 40.000 0.00 0.00 0.00 3.58
1226 2684 6.609212 TCATCTTCATGTTCTTCCTAGCTACT 59.391 38.462 0.00 0.00 0.00 2.57
1227 2685 7.780271 TCATCTTCATGTTCTTCCTAGCTACTA 59.220 37.037 0.00 0.00 0.00 1.82
1257 2715 0.825840 CCGCCTCCTCTTAGCTAGCT 60.826 60.000 23.12 23.12 0.00 3.32
1258 2716 1.545875 CCGCCTCCTCTTAGCTAGCTA 60.546 57.143 20.67 20.67 0.00 3.32
1259 2717 1.810151 CGCCTCCTCTTAGCTAGCTAG 59.190 57.143 23.03 16.84 0.00 3.42
1374 2833 2.105006 TGAGTTGCTGCTGGATCTTC 57.895 50.000 0.00 0.00 0.00 2.87
1385 2844 0.463654 TGGATCTTCGATTTGCCGGG 60.464 55.000 2.18 0.00 0.00 5.73
1399 2858 2.495409 CCGGGGCTACGTGCATAGA 61.495 63.158 0.00 0.00 45.15 1.98
1404 2863 1.618861 GGCTACGTGCATAGATAGCG 58.381 55.000 0.00 2.98 45.15 4.26
1446 2905 1.809567 CTTTGGGGTGCCTTGACTGC 61.810 60.000 0.00 0.00 0.00 4.40
1452 2911 1.251251 GGTGCCTTGACTGCTTGATT 58.749 50.000 0.00 0.00 0.00 2.57
1632 3121 0.512518 GGTTTGATTTGGCTTTGCGC 59.487 50.000 0.00 0.00 38.13 6.09
1652 3141 3.810373 GCGATCAACGTGATTTTTGTCT 58.190 40.909 0.00 0.00 44.60 3.41
1653 3142 3.840763 GCGATCAACGTGATTTTTGTCTC 59.159 43.478 0.00 0.00 44.60 3.36
1706 3195 1.327460 CATACGCTGGTGTGTACATGC 59.673 52.381 0.00 0.00 41.27 4.06
1729 3218 1.002251 CTACTCTAGCTACCGTGCAGC 60.002 57.143 0.00 0.00 39.41 5.25
1768 3257 3.135994 TGCTTTCGTTTTCCAGTCTACC 58.864 45.455 0.00 0.00 0.00 3.18
1769 3258 2.483106 GCTTTCGTTTTCCAGTCTACCC 59.517 50.000 0.00 0.00 0.00 3.69
1770 3259 3.735591 CTTTCGTTTTCCAGTCTACCCA 58.264 45.455 0.00 0.00 0.00 4.51
1772 3261 5.484715 CTTTCGTTTTCCAGTCTACCCATA 58.515 41.667 0.00 0.00 0.00 2.74
1775 3264 6.152932 TCGTTTTCCAGTCTACCCATATAC 57.847 41.667 0.00 0.00 0.00 1.47
1777 3266 5.751990 CGTTTTCCAGTCTACCCATATACAC 59.248 44.000 0.00 0.00 0.00 2.90
1778 3267 5.524971 TTTCCAGTCTACCCATATACACG 57.475 43.478 0.00 0.00 0.00 4.49
1780 3269 4.539726 TCCAGTCTACCCATATACACGTT 58.460 43.478 0.00 0.00 0.00 3.99
1781 3270 4.340097 TCCAGTCTACCCATATACACGTTG 59.660 45.833 0.00 0.00 0.00 4.10
1782 3271 4.098960 CCAGTCTACCCATATACACGTTGT 59.901 45.833 0.00 0.00 0.00 3.32
1783 3272 5.300034 CCAGTCTACCCATATACACGTTGTA 59.700 44.000 0.00 0.00 37.24 2.41
1784 3273 6.436261 CAGTCTACCCATATACACGTTGTAG 58.564 44.000 0.00 0.00 36.14 2.74
1785 3274 5.533903 AGTCTACCCATATACACGTTGTAGG 59.466 44.000 0.00 0.00 36.14 3.18
1788 3277 5.464030 ACCCATATACACGTTGTAGGATC 57.536 43.478 0.00 0.00 36.14 3.36
1789 3278 5.145564 ACCCATATACACGTTGTAGGATCT 58.854 41.667 0.00 0.00 36.14 2.75
1790 3279 6.309357 ACCCATATACACGTTGTAGGATCTA 58.691 40.000 0.00 0.00 36.14 1.98
1791 3280 6.208204 ACCCATATACACGTTGTAGGATCTAC 59.792 42.308 0.00 0.00 36.14 2.59
1792 3281 6.208007 CCCATATACACGTTGTAGGATCTACA 59.792 42.308 3.89 3.89 36.14 2.74
1793 3282 7.093902 CCCATATACACGTTGTAGGATCTACAT 60.094 40.741 8.37 0.00 36.14 2.29
1794 3283 8.953313 CCATATACACGTTGTAGGATCTACATA 58.047 37.037 8.37 0.00 36.14 2.29
1798 3287 7.812690 ACACGTTGTAGGATCTACATATACA 57.187 36.000 8.37 0.00 0.00 2.29
1799 3288 7.872881 ACACGTTGTAGGATCTACATATACAG 58.127 38.462 8.37 3.66 0.00 2.74
1806 3333 7.988028 TGTAGGATCTACATATACAGGAGATCG 59.012 40.741 17.08 0.00 42.23 3.69
1854 3385 1.217882 AGGAAGAAACAAGCGTCACG 58.782 50.000 0.00 0.00 0.00 4.35
1912 3445 7.693969 AAAGACTGTTGGAGGAGAATTAATG 57.306 36.000 0.00 0.00 0.00 1.90
1913 3446 6.627087 AGACTGTTGGAGGAGAATTAATGA 57.373 37.500 0.00 0.00 0.00 2.57
1917 3450 6.013379 ACTGTTGGAGGAGAATTAATGACTCA 60.013 38.462 18.31 3.19 33.00 3.41
1918 3451 6.778821 TGTTGGAGGAGAATTAATGACTCAA 58.221 36.000 18.31 7.47 33.00 3.02
1919 3452 7.405292 TGTTGGAGGAGAATTAATGACTCAAT 58.595 34.615 18.31 10.31 33.00 2.57
1920 3453 8.548025 TGTTGGAGGAGAATTAATGACTCAATA 58.452 33.333 18.31 6.44 33.00 1.90
1948 3481 7.372260 AGCTTCACAGATCTACCTATTTGAT 57.628 36.000 0.00 0.00 0.00 2.57
2010 3549 7.473735 TGGATCCTGATACTTGATTAGCTAG 57.526 40.000 14.23 0.00 0.00 3.42
2012 3551 7.730332 TGGATCCTGATACTTGATTAGCTAGAA 59.270 37.037 14.23 0.00 0.00 2.10
2041 3580 3.313012 AATTCCTGTCGTCGTTGATCA 57.687 42.857 0.00 0.00 0.00 2.92
2042 3581 2.060326 TTCCTGTCGTCGTTGATCAC 57.940 50.000 0.00 0.00 0.00 3.06
2085 3624 8.671921 CATATGCAAATTCTCTTAGTCAGTTGT 58.328 33.333 0.00 0.00 0.00 3.32
2092 3631 8.779354 AATTCTCTTAGTCAGTTGTGGTATTC 57.221 34.615 0.00 0.00 0.00 1.75
2105 3654 8.847196 CAGTTGTGGTATTCATACTAGCTAGTA 58.153 37.037 30.67 30.67 42.43 1.82
2106 3655 9.069082 AGTTGTGGTATTCATACTAGCTAGTAG 57.931 37.037 31.43 23.82 41.62 2.57
2107 3656 7.450124 TGTGGTATTCATACTAGCTAGTAGC 57.550 40.000 31.43 21.81 41.62 3.58
2108 3657 6.148976 TGTGGTATTCATACTAGCTAGTAGCG 59.851 42.308 31.43 25.34 41.62 4.26
2109 3658 5.123502 TGGTATTCATACTAGCTAGTAGCGC 59.876 44.000 31.43 19.52 41.62 5.92
2110 3659 5.123502 GGTATTCATACTAGCTAGTAGCGCA 59.876 44.000 31.43 19.30 41.62 6.09
2111 3660 6.183360 GGTATTCATACTAGCTAGTAGCGCAT 60.183 42.308 31.43 23.30 41.62 4.73
2121 3670 3.061139 GCTAGTAGCGCATGTAGTTTTCG 60.061 47.826 11.47 0.00 0.00 3.46
2130 3679 5.255596 CGCATGTAGTTTTCGTTGATAAGG 58.744 41.667 0.00 0.00 0.00 2.69
2137 3686 8.362639 TGTAGTTTTCGTTGATAAGGTTAGTCT 58.637 33.333 0.00 0.00 0.00 3.24
2175 3724 5.996669 AATCTTTCGTTCGTACCTTTTGT 57.003 34.783 0.00 0.00 0.00 2.83
2180 3729 4.519191 TCGTTCGTACCTTTTGTTTCAC 57.481 40.909 0.00 0.00 0.00 3.18
2181 3730 3.931468 TCGTTCGTACCTTTTGTTTCACA 59.069 39.130 0.00 0.00 0.00 3.58
2207 3756 8.280084 AGAGGTTCTAAAACTTTTCCTTTACCT 58.720 33.333 0.00 0.00 35.61 3.08
2208 3757 8.234136 AGGTTCTAAAACTTTTCCTTTACCTG 57.766 34.615 0.00 0.00 35.61 4.00
2223 3772 5.277345 CCTTTACCTGAACAGTTTTCACGAG 60.277 44.000 0.00 0.00 0.00 4.18
2224 3773 3.261981 ACCTGAACAGTTTTCACGAGT 57.738 42.857 0.00 0.00 0.00 4.18
2225 3774 4.395959 ACCTGAACAGTTTTCACGAGTA 57.604 40.909 0.00 0.00 0.00 2.59
2226 3775 4.957296 ACCTGAACAGTTTTCACGAGTAT 58.043 39.130 0.00 0.00 0.00 2.12
2232 3781 6.419710 TGAACAGTTTTCACGAGTATGTACTG 59.580 38.462 0.00 0.00 36.50 2.74
2287 3836 7.464358 TGATTTTGCTAAATCTAAGTCGCTTC 58.536 34.615 26.45 5.63 46.40 3.86
2295 3844 8.643752 GCTAAATCTAAGTCGCTTCAGATATTC 58.356 37.037 0.00 0.00 0.00 1.75
2304 3853 8.508800 AGTCGCTTCAGATATTCTTAATTACG 57.491 34.615 0.00 0.00 0.00 3.18
2305 3854 8.136165 AGTCGCTTCAGATATTCTTAATTACGT 58.864 33.333 0.00 0.00 0.00 3.57
2306 3855 8.418681 GTCGCTTCAGATATTCTTAATTACGTC 58.581 37.037 0.00 0.00 0.00 4.34
2307 3856 8.350722 TCGCTTCAGATATTCTTAATTACGTCT 58.649 33.333 0.00 0.00 0.00 4.18
2308 3857 9.608617 CGCTTCAGATATTCTTAATTACGTCTA 57.391 33.333 0.00 0.00 0.00 2.59
2317 3866 8.612233 ATTCTTAATTACGTCTAAGTCGACAC 57.388 34.615 19.50 5.98 33.54 3.67
2318 3867 6.546395 TCTTAATTACGTCTAAGTCGACACC 58.454 40.000 19.50 0.00 33.54 4.16
2319 3868 3.772060 ATTACGTCTAAGTCGACACCC 57.228 47.619 19.50 0.00 33.54 4.61
2320 3869 2.479566 TACGTCTAAGTCGACACCCT 57.520 50.000 19.50 1.44 33.54 4.34
2321 3870 2.479566 ACGTCTAAGTCGACACCCTA 57.520 50.000 19.50 2.61 33.54 3.53
2322 3871 2.783135 ACGTCTAAGTCGACACCCTAA 58.217 47.619 19.50 0.00 33.54 2.69
2323 3872 3.149196 ACGTCTAAGTCGACACCCTAAA 58.851 45.455 19.50 0.00 33.54 1.85
2324 3873 3.057946 ACGTCTAAGTCGACACCCTAAAC 60.058 47.826 19.50 5.46 33.54 2.01
2325 3874 3.058016 CGTCTAAGTCGACACCCTAAACA 60.058 47.826 19.50 0.00 33.54 2.83
2326 3875 4.483311 GTCTAAGTCGACACCCTAAACAG 58.517 47.826 19.50 1.23 34.11 3.16
2327 3876 4.022503 GTCTAAGTCGACACCCTAAACAGT 60.023 45.833 19.50 0.00 34.11 3.55
2328 3877 3.382048 AAGTCGACACCCTAAACAGTC 57.618 47.619 19.50 0.00 0.00 3.51
2329 3878 2.595238 AGTCGACACCCTAAACAGTCT 58.405 47.619 19.50 0.00 0.00 3.24
2342 3891 3.977134 AACAGTCTGATGTCTCTGCAT 57.023 42.857 6.91 0.00 31.50 3.96
2361 3910 3.367703 GCATTGAGATTTGTGGAAGGGTG 60.368 47.826 0.00 0.00 0.00 4.61
2388 3938 7.344612 AGGGGGAAACAAGATTTTATTGGATAC 59.655 37.037 0.00 0.00 31.76 2.24
2408 3958 8.613034 TGGATACCACCCTAGTTAATTTGTTTA 58.387 33.333 0.00 0.00 0.00 2.01
2430 3980 8.933807 GTTTAGACAGACCCTAGTTAATTTGTC 58.066 37.037 0.00 0.00 35.22 3.18
2434 3984 7.181125 AGACAGACCCTAGTTAATTTGTCAGAT 59.819 37.037 4.40 0.00 36.92 2.90
2459 4009 3.000684 AGTATCTACGTGAGCTGACCA 57.999 47.619 0.00 0.00 0.00 4.02
2489 4039 7.667575 ACTGTAGGAGATATGTGTGAGAAAT 57.332 36.000 0.00 0.00 0.00 2.17
2546 4096 3.383761 GTTGTTTCAGCTTTGGACCATG 58.616 45.455 0.00 0.00 0.00 3.66
2587 4137 8.789762 ACCAGTGTAAATACCACATTTTAAGAC 58.210 33.333 0.00 0.00 0.00 3.01
2591 4141 9.389570 GTGTAAATACCACATTTTAAGACACAC 57.610 33.333 0.00 0.00 31.89 3.82
2622 4172 7.995463 TTTTGTTTCCATAGCTTTGTTACAC 57.005 32.000 3.39 0.00 0.00 2.90
2768 4320 2.500098 GCTAACCAGAGACCCACATGTA 59.500 50.000 0.00 0.00 0.00 2.29
2915 4467 0.039527 GCGGAGAAACAACGGCATTT 60.040 50.000 0.00 0.00 33.65 2.32
2916 4468 1.685302 CGGAGAAACAACGGCATTTG 58.315 50.000 0.00 0.00 0.00 2.32
2939 4491 1.737838 CGGAGGCAGATTTAGCACAA 58.262 50.000 0.00 0.00 0.00 3.33
2942 4494 3.496130 CGGAGGCAGATTTAGCACAATAG 59.504 47.826 0.00 0.00 0.00 1.73
2993 4545 2.224402 GGAGACTTGGCTTGAACTCTGT 60.224 50.000 0.00 0.00 0.00 3.41
3007 4559 4.021104 TGAACTCTGTGGGTAACTCTCATG 60.021 45.833 0.00 0.00 0.00 3.07
3027 4579 8.432013 TCTCATGCTACTTATGTTCCATAATGT 58.568 33.333 0.00 2.28 0.00 2.71
3078 4630 7.065204 GGACCAAGTCTACAGAGAAAAATCATC 59.935 40.741 0.00 0.00 31.96 2.92
3111 4671 6.734137 TCTGCAACACCTAACATAACAAAAG 58.266 36.000 0.00 0.00 0.00 2.27
3117 4677 7.492352 ACACCTAACATAACAAAAGTGTCTC 57.508 36.000 0.00 0.00 36.80 3.36
3130 4690 7.907389 ACAAAAGTGTCTCAGGATGTATCTAA 58.093 34.615 0.00 0.00 31.56 2.10
3131 4691 7.819900 ACAAAAGTGTCTCAGGATGTATCTAAC 59.180 37.037 0.00 0.00 31.56 2.34
3132 4692 5.759506 AGTGTCTCAGGATGTATCTAACG 57.240 43.478 0.00 0.00 37.40 3.18
3189 4751 9.959749 TGTTTATAAACTTGTTCAATGTTCCTC 57.040 29.630 24.81 0.00 39.59 3.71
3219 4793 3.905968 TCTGTATCCACTACGAATGGGA 58.094 45.455 0.00 0.00 37.85 4.37
3236 4810 4.487714 TGGGAGGAGTAACATTCATGTC 57.512 45.455 0.00 0.00 40.80 3.06
3239 4813 4.504858 GGAGGAGTAACATTCATGTCGTT 58.495 43.478 0.00 0.00 40.80 3.85
3240 4814 4.330074 GGAGGAGTAACATTCATGTCGTTG 59.670 45.833 0.00 0.00 40.80 4.10
3250 4824 6.546395 ACATTCATGTCGTTGAATTAAGCTC 58.454 36.000 7.82 0.00 42.29 4.09
3261 4835 3.390967 TGAATTAAGCTCGGATGGGATGA 59.609 43.478 0.00 0.00 0.00 2.92
3278 4852 2.691409 TGATAGCTAGGGCACAACAC 57.309 50.000 0.00 0.00 41.70 3.32
3369 4943 9.863650 TGTATAACTAGGAACAAGCTAGACTAT 57.136 33.333 0.00 0.00 0.00 2.12
3447 5025 2.493675 TGGAGAGATCAAGACCAAGTCG 59.506 50.000 0.00 0.00 37.67 4.18
3669 5247 1.874345 GCTTGGTCTGCATGCAGCTT 61.874 55.000 37.48 0.00 45.94 3.74
3670 5248 0.109272 CTTGGTCTGCATGCAGCTTG 60.109 55.000 37.48 22.21 45.94 4.01
3671 5249 2.149803 TTGGTCTGCATGCAGCTTGC 62.150 55.000 37.48 25.93 45.94 4.01
3690 5268 2.438254 GCGACATGCATGGGACCA 60.438 61.111 29.41 0.00 45.45 4.02
3691 5269 1.825191 GCGACATGCATGGGACCAT 60.825 57.895 29.41 8.33 45.45 3.55
3791 5372 7.440556 ACAGCTAATGATGATTACAGATCACAC 59.559 37.037 0.00 0.00 33.22 3.82
4213 5794 3.052082 CAGCAGCTTCACCACGGG 61.052 66.667 0.00 0.00 0.00 5.28
4216 5797 4.680237 CAGCTTCACCACGGGCGA 62.680 66.667 0.00 0.00 0.00 5.54
4459 6040 2.104331 CTGAACGCGCTCCGGTAT 59.896 61.111 5.73 0.00 36.69 2.73
4534 6115 0.595053 CTGAGCGTGACAGTGTCGTT 60.595 55.000 18.17 6.11 34.95 3.85
4693 6274 0.987081 ATCACCATGGCTCCTCTGCT 60.987 55.000 13.04 0.00 0.00 4.24
4902 6491 1.462616 TCGATGTTTGCATCCCCTTG 58.537 50.000 0.00 0.00 46.56 3.61
4903 6492 1.176527 CGATGTTTGCATCCCCTTGT 58.823 50.000 0.00 0.00 46.56 3.16
4908 6497 2.102252 TGTTTGCATCCCCTTGTGTTTC 59.898 45.455 0.00 0.00 0.00 2.78
4912 6501 3.037549 TGCATCCCCTTGTGTTTCTTTT 58.962 40.909 0.00 0.00 0.00 2.27
5012 6601 5.457140 TGTGGTTCGATCAATTAAGTTTGC 58.543 37.500 0.00 0.00 0.00 3.68
5036 6625 3.181461 ACTCGCTGCTGCCTAAGATTTAT 60.181 43.478 10.24 0.00 35.36 1.40
5037 6626 4.039245 ACTCGCTGCTGCCTAAGATTTATA 59.961 41.667 10.24 0.00 35.36 0.98
5063 6672 3.873910 TGTTTGGAGTAGGCTAAGATGC 58.126 45.455 0.00 0.00 0.00 3.91
5122 6747 4.036262 TCGATCAATTAAATTTGAGGCCCG 59.964 41.667 0.00 0.00 38.90 6.13
5160 6942 7.816995 TCCAATACAAGCCAATTTGTACATTTC 59.183 33.333 0.00 0.00 43.93 2.17
5321 7103 8.868522 ATTATTTTCAGTTGAGTGAAGATGGA 57.131 30.769 12.38 4.63 37.72 3.41
5732 7514 2.391616 TGCAATCAGAGAAGACGCAT 57.608 45.000 0.00 0.00 0.00 4.73
5925 9321 4.828829 AGACACCCGTATCAAGTTTTAGG 58.171 43.478 0.00 0.00 0.00 2.69
5944 9340 7.834100 TTTAGGGGGATCTTTAGAAAACCTA 57.166 36.000 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.864704 TTGGACATAACAAAGGAAAGGC 57.135 40.909 0.00 0.00 0.00 4.35
36 37 8.356657 TGTTGTATTGGACATAACAAAGGAAAG 58.643 33.333 0.00 0.00 38.07 2.62
143 144 2.031157 CCTGTAAACCAACGAAAGCCTG 60.031 50.000 0.00 0.00 0.00 4.85
144 145 2.158726 TCCTGTAAACCAACGAAAGCCT 60.159 45.455 0.00 0.00 0.00 4.58
147 148 7.812648 TCATATTTCCTGTAAACCAACGAAAG 58.187 34.615 0.00 0.00 29.66 2.62
148 149 7.747155 TCATATTTCCTGTAAACCAACGAAA 57.253 32.000 0.00 0.00 0.00 3.46
149 150 7.662258 TCTTCATATTTCCTGTAAACCAACGAA 59.338 33.333 0.00 0.00 0.00 3.85
150 151 7.162761 TCTTCATATTTCCTGTAAACCAACGA 58.837 34.615 0.00 0.00 0.00 3.85
151 152 7.372451 TCTTCATATTTCCTGTAAACCAACG 57.628 36.000 0.00 0.00 0.00 4.10
152 153 9.788960 GATTCTTCATATTTCCTGTAAACCAAC 57.211 33.333 0.00 0.00 0.00 3.77
154 155 7.559897 GGGATTCTTCATATTTCCTGTAAACCA 59.440 37.037 0.00 0.00 0.00 3.67
155 156 7.559897 TGGGATTCTTCATATTTCCTGTAAACC 59.440 37.037 0.00 0.00 0.00 3.27
156 157 8.519799 TGGGATTCTTCATATTTCCTGTAAAC 57.480 34.615 0.00 0.00 0.00 2.01
160 161 7.295672 TCCTATGGGATTCTTCATATTTCCTGT 59.704 37.037 0.00 0.00 36.57 4.00
161 162 7.693132 TCCTATGGGATTCTTCATATTTCCTG 58.307 38.462 0.00 0.00 36.57 3.86
162 163 7.895144 TCCTATGGGATTCTTCATATTTCCT 57.105 36.000 0.00 0.00 36.57 3.36
177 178 4.676799 ACGAGAATCCTATCCTATGGGA 57.323 45.455 0.00 0.00 44.51 4.37
178 179 5.756918 TCTACGAGAATCCTATCCTATGGG 58.243 45.833 0.00 0.00 0.00 4.00
179 180 7.704578 TTTCTACGAGAATCCTATCCTATGG 57.295 40.000 0.00 0.00 33.67 2.74
208 209 7.039082 TCCTGCAAACCAAAAGCTCTAAAATAT 60.039 33.333 0.00 0.00 0.00 1.28
211 212 4.404073 TCCTGCAAACCAAAAGCTCTAAAA 59.596 37.500 0.00 0.00 0.00 1.52
212 213 3.957497 TCCTGCAAACCAAAAGCTCTAAA 59.043 39.130 0.00 0.00 0.00 1.85
252 325 7.969536 ACGAAGGATATGAATTATTCCTGTG 57.030 36.000 2.22 0.00 0.00 3.66
331 405 0.753262 ATAGCTTACCACTCCTGCCG 59.247 55.000 0.00 0.00 0.00 5.69
497 1903 2.203042 CTGCAGCTGGAGCCTAGC 60.203 66.667 22.98 1.38 43.38 3.42
661 2077 3.849951 CCCCATCGACCTCACCCG 61.850 72.222 0.00 0.00 0.00 5.28
665 2081 0.106369 ACGTATCCCCATCGACCTCA 60.106 55.000 0.00 0.00 0.00 3.86
668 2084 0.243095 GCTACGTATCCCCATCGACC 59.757 60.000 0.00 0.00 0.00 4.79
787 2215 0.248702 GACGGCCATCTTCTCGTCTC 60.249 60.000 2.24 0.00 45.61 3.36
788 2216 1.810532 GACGGCCATCTTCTCGTCT 59.189 57.895 2.24 0.00 45.61 4.18
789 2217 4.403976 GACGGCCATCTTCTCGTC 57.596 61.111 2.24 0.00 43.62 4.20
790 2218 2.277858 AAGACGGCCATCTTCTCGT 58.722 52.632 8.61 0.00 33.50 4.18
795 2223 2.680370 GGGGGAAGACGGCCATCTT 61.680 63.158 15.20 15.20 41.74 2.40
796 2224 3.090532 GGGGGAAGACGGCCATCT 61.091 66.667 2.24 0.00 0.00 2.90
797 2225 3.407967 TGGGGGAAGACGGCCATC 61.408 66.667 2.24 0.00 0.00 3.51
798 2226 3.728373 GTGGGGGAAGACGGCCAT 61.728 66.667 2.24 0.00 0.00 4.40
988 2429 4.227134 CGGATGGAGGGCGGACTG 62.227 72.222 0.00 0.00 0.00 3.51
1120 2572 4.220602 GGAGAAGGAAGAGGAGATATGAGC 59.779 50.000 0.00 0.00 0.00 4.26
1145 2597 1.898472 TGGACAGGAGAAGAGAAGCTG 59.102 52.381 0.00 0.00 0.00 4.24
1149 2601 2.015456 TGCTGGACAGGAGAAGAGAA 57.985 50.000 1.01 0.00 0.00 2.87
1184 2640 4.658786 AAGAGGAGGGCGGGGTGT 62.659 66.667 0.00 0.00 0.00 4.16
1257 2715 0.393808 GGTTTCAGGGCGATTGGCTA 60.394 55.000 6.45 0.00 42.94 3.93
1258 2716 1.678970 GGTTTCAGGGCGATTGGCT 60.679 57.895 6.45 0.00 42.94 4.75
1259 2717 2.710902 GGGTTTCAGGGCGATTGGC 61.711 63.158 0.00 0.00 42.51 4.52
1260 2718 2.406616 CGGGTTTCAGGGCGATTGG 61.407 63.158 0.00 0.00 0.00 3.16
1374 2833 3.269347 CGTAGCCCCGGCAAATCG 61.269 66.667 8.74 3.30 44.88 3.34
1385 2844 1.618861 CGCTATCTATGCACGTAGCC 58.381 55.000 12.88 0.00 44.83 3.93
1399 2858 2.503061 CTCACTGCCAGCCGCTAT 59.497 61.111 0.00 0.00 38.78 2.97
1404 2863 3.368571 GCAACCTCACTGCCAGCC 61.369 66.667 0.00 0.00 33.51 4.85
1446 2905 1.754234 CCCGGGCTTCCCAATCAAG 60.754 63.158 8.08 0.00 45.83 3.02
1549 3012 7.276218 TGTTAATTACAAGCACGATAGGTGTAC 59.724 37.037 0.00 0.00 40.42 2.90
1550 3013 7.321908 TGTTAATTACAAGCACGATAGGTGTA 58.678 34.615 0.00 0.00 40.42 2.90
1551 3014 6.167685 TGTTAATTACAAGCACGATAGGTGT 58.832 36.000 0.00 0.00 40.42 4.16
1552 3015 6.656314 TGTTAATTACAAGCACGATAGGTG 57.344 37.500 0.00 0.00 40.90 4.00
1588 3051 3.125146 GTGCTAGTTGATCACGCAAATCA 59.875 43.478 0.00 0.00 31.77 2.57
1632 3121 4.084066 TGGAGACAAAAATCACGTTGATCG 60.084 41.667 0.00 0.00 41.24 3.69
1721 3210 0.883833 ATTTTCTGAAGGCTGCACGG 59.116 50.000 0.50 0.00 0.00 4.94
1723 3212 3.255642 TGGTTATTTTCTGAAGGCTGCAC 59.744 43.478 0.50 0.00 0.00 4.57
1729 3218 5.712152 AAGCAGTGGTTATTTTCTGAAGG 57.288 39.130 5.60 0.00 0.00 3.46
1768 3257 7.210718 TGTAGATCCTACAACGTGTATATGG 57.789 40.000 4.50 0.00 31.66 2.74
1772 3261 9.511272 TGTATATGTAGATCCTACAACGTGTAT 57.489 33.333 10.40 6.65 31.66 2.29
1775 3264 7.174426 TCCTGTATATGTAGATCCTACAACGTG 59.826 40.741 10.40 3.44 0.00 4.49
1777 3266 7.606839 TCTCCTGTATATGTAGATCCTACAACG 59.393 40.741 10.40 3.13 0.00 4.10
1778 3267 8.865420 TCTCCTGTATATGTAGATCCTACAAC 57.135 38.462 10.40 5.89 0.00 3.32
1780 3269 7.988028 CGATCTCCTGTATATGTAGATCCTACA 59.012 40.741 8.98 8.98 39.48 2.74
1781 3270 8.205512 TCGATCTCCTGTATATGTAGATCCTAC 58.794 40.741 0.00 0.00 39.48 3.18
1782 3271 8.320338 TCGATCTCCTGTATATGTAGATCCTA 57.680 38.462 0.00 0.00 39.48 2.94
1783 3272 7.201702 TCGATCTCCTGTATATGTAGATCCT 57.798 40.000 0.00 0.00 39.48 3.24
1784 3273 7.554835 ACTTCGATCTCCTGTATATGTAGATCC 59.445 40.741 0.00 0.00 39.48 3.36
1785 3274 8.500753 ACTTCGATCTCCTGTATATGTAGATC 57.499 38.462 0.00 0.00 39.33 2.75
1788 3277 7.805542 CACAACTTCGATCTCCTGTATATGTAG 59.194 40.741 0.00 0.00 0.00 2.74
1789 3278 7.501225 TCACAACTTCGATCTCCTGTATATGTA 59.499 37.037 0.00 0.00 0.00 2.29
1790 3279 6.321435 TCACAACTTCGATCTCCTGTATATGT 59.679 38.462 0.00 0.00 0.00 2.29
1791 3280 6.739112 TCACAACTTCGATCTCCTGTATATG 58.261 40.000 0.00 0.00 0.00 1.78
1792 3281 6.961360 TCACAACTTCGATCTCCTGTATAT 57.039 37.500 0.00 0.00 0.00 0.86
1793 3282 6.961360 ATCACAACTTCGATCTCCTGTATA 57.039 37.500 0.00 0.00 0.00 1.47
1794 3283 5.860941 ATCACAACTTCGATCTCCTGTAT 57.139 39.130 0.00 0.00 0.00 2.29
1797 3286 7.278646 TCAATTAATCACAACTTCGATCTCCTG 59.721 37.037 0.00 0.00 0.00 3.86
1798 3287 7.278868 GTCAATTAATCACAACTTCGATCTCCT 59.721 37.037 0.00 0.00 0.00 3.69
1799 3288 7.402640 GTCAATTAATCACAACTTCGATCTCC 58.597 38.462 0.00 0.00 0.00 3.71
1806 3333 7.377766 TGCTAGGTCAATTAATCACAACTTC 57.622 36.000 0.00 0.00 0.00 3.01
1854 3385 4.039245 TGGATGCAGAATACACCTACTAGC 59.961 45.833 0.00 0.00 0.00 3.42
1858 3389 5.822519 TGATTTGGATGCAGAATACACCTAC 59.177 40.000 0.00 0.00 0.00 3.18
1923 3456 7.898014 TCAAATAGGTAGATCTGTGAAGCTA 57.102 36.000 5.18 5.05 0.00 3.32
1925 3458 8.364142 AGTATCAAATAGGTAGATCTGTGAAGC 58.636 37.037 5.18 0.00 0.00 3.86
1931 3464 8.784994 ACGTACAGTATCAAATAGGTAGATCTG 58.215 37.037 5.18 0.00 0.00 2.90
1945 3478 3.133691 CGCCTAGGTACGTACAGTATCA 58.866 50.000 26.02 4.38 38.90 2.15
1948 3481 1.134401 AGCGCCTAGGTACGTACAGTA 60.134 52.381 26.02 15.59 0.00 2.74
2020 3559 3.432252 GTGATCAACGACGACAGGAATTT 59.568 43.478 0.00 0.00 0.00 1.82
2022 3561 2.029380 TGTGATCAACGACGACAGGAAT 60.029 45.455 0.00 0.00 0.00 3.01
2041 3580 6.983890 TGCATATGTTCGTTCATACTACATGT 59.016 34.615 2.69 2.69 33.87 3.21
2042 3581 7.406799 TGCATATGTTCGTTCATACTACATG 57.593 36.000 4.29 0.00 33.87 3.21
2085 3624 5.123502 GCGCTACTAGCTAGTATGAATACCA 59.876 44.000 29.24 10.04 39.60 3.25
2092 3631 4.427096 ACATGCGCTACTAGCTAGTATG 57.573 45.455 29.24 25.87 39.60 2.39
2105 3654 2.139917 TCAACGAAAACTACATGCGCT 58.860 42.857 9.73 0.00 0.00 5.92
2106 3655 2.587612 TCAACGAAAACTACATGCGC 57.412 45.000 0.00 0.00 0.00 6.09
2107 3656 5.163893 ACCTTATCAACGAAAACTACATGCG 60.164 40.000 0.00 0.00 0.00 4.73
2108 3657 6.178239 ACCTTATCAACGAAAACTACATGC 57.822 37.500 0.00 0.00 0.00 4.06
2109 3658 8.932791 ACTAACCTTATCAACGAAAACTACATG 58.067 33.333 0.00 0.00 0.00 3.21
2110 3659 9.148104 GACTAACCTTATCAACGAAAACTACAT 57.852 33.333 0.00 0.00 0.00 2.29
2111 3660 8.362639 AGACTAACCTTATCAACGAAAACTACA 58.637 33.333 0.00 0.00 0.00 2.74
2113 3662 8.362639 ACAGACTAACCTTATCAACGAAAACTA 58.637 33.333 0.00 0.00 0.00 2.24
2114 3663 7.215085 ACAGACTAACCTTATCAACGAAAACT 58.785 34.615 0.00 0.00 0.00 2.66
2115 3664 7.417496 ACAGACTAACCTTATCAACGAAAAC 57.583 36.000 0.00 0.00 0.00 2.43
2116 3665 9.715121 AATACAGACTAACCTTATCAACGAAAA 57.285 29.630 0.00 0.00 0.00 2.29
2150 3699 7.252708 ACAAAAGGTACGAACGAAAGATTTTT 58.747 30.769 0.14 0.00 0.00 1.94
2151 3700 6.788243 ACAAAAGGTACGAACGAAAGATTTT 58.212 32.000 0.14 0.00 0.00 1.82
2152 3701 6.367686 ACAAAAGGTACGAACGAAAGATTT 57.632 33.333 0.14 0.00 0.00 2.17
2153 3702 5.996669 ACAAAAGGTACGAACGAAAGATT 57.003 34.783 0.14 0.00 0.00 2.40
2154 3703 5.996669 AACAAAAGGTACGAACGAAAGAT 57.003 34.783 0.14 0.00 0.00 2.40
2175 3724 7.614192 AGGAAAAGTTTTAGAACCTCTGTGAAA 59.386 33.333 0.00 0.00 36.39 2.69
2180 3729 8.350722 GGTAAAGGAAAAGTTTTAGAACCTCTG 58.649 37.037 0.00 0.00 36.39 3.35
2181 3730 8.280084 AGGTAAAGGAAAAGTTTTAGAACCTCT 58.720 33.333 0.00 0.00 36.39 3.69
2207 3756 6.419710 CAGTACATACTCGTGAAAACTGTTCA 59.580 38.462 0.00 0.00 33.46 3.18
2208 3757 6.615839 GCAGTACATACTCGTGAAAACTGTTC 60.616 42.308 0.00 0.00 33.46 3.18
2223 3772 4.386867 TGCTCTTACCAGCAGTACATAC 57.613 45.455 0.00 0.00 44.73 2.39
2232 3781 7.736447 ATAATTAAGTGATGCTCTTACCAGC 57.264 36.000 0.00 0.00 40.13 4.85
2295 3844 5.741040 GGGTGTCGACTTAGACGTAATTAAG 59.259 44.000 17.92 10.66 43.70 1.85
2300 3849 2.783135 AGGGTGTCGACTTAGACGTAA 58.217 47.619 17.92 0.00 43.70 3.18
2301 3850 2.479566 AGGGTGTCGACTTAGACGTA 57.520 50.000 17.92 0.00 43.70 3.57
2302 3851 2.479566 TAGGGTGTCGACTTAGACGT 57.520 50.000 17.92 6.55 43.70 4.34
2303 3852 3.058016 TGTTTAGGGTGTCGACTTAGACG 60.058 47.826 17.92 0.00 43.70 4.18
2304 3853 4.022503 ACTGTTTAGGGTGTCGACTTAGAC 60.023 45.833 17.92 6.15 41.30 2.59
2305 3854 4.147321 ACTGTTTAGGGTGTCGACTTAGA 58.853 43.478 17.92 0.00 0.00 2.10
2306 3855 4.217983 AGACTGTTTAGGGTGTCGACTTAG 59.782 45.833 17.92 4.46 34.92 2.18
2307 3856 4.022589 CAGACTGTTTAGGGTGTCGACTTA 60.023 45.833 17.92 1.58 34.92 2.24
2308 3857 2.963782 AGACTGTTTAGGGTGTCGACTT 59.036 45.455 17.92 2.56 34.92 3.01
2309 3858 2.296471 CAGACTGTTTAGGGTGTCGACT 59.704 50.000 17.92 0.00 34.92 4.18
2310 3859 2.295349 TCAGACTGTTTAGGGTGTCGAC 59.705 50.000 9.11 9.11 34.92 4.20
2311 3860 2.589720 TCAGACTGTTTAGGGTGTCGA 58.410 47.619 1.59 0.00 34.92 4.20
2312 3861 3.254060 CATCAGACTGTTTAGGGTGTCG 58.746 50.000 1.59 0.00 34.92 4.35
2313 3862 4.021016 AGACATCAGACTGTTTAGGGTGTC 60.021 45.833 1.59 0.00 35.05 3.67
2314 3863 3.904339 AGACATCAGACTGTTTAGGGTGT 59.096 43.478 1.59 0.00 0.00 4.16
2315 3864 4.221703 AGAGACATCAGACTGTTTAGGGTG 59.778 45.833 1.59 0.00 0.00 4.61
2316 3865 4.221703 CAGAGACATCAGACTGTTTAGGGT 59.778 45.833 1.59 0.00 0.00 4.34
2317 3866 4.753233 CAGAGACATCAGACTGTTTAGGG 58.247 47.826 1.59 0.00 0.00 3.53
2318 3867 4.180057 GCAGAGACATCAGACTGTTTAGG 58.820 47.826 1.59 0.00 33.57 2.69
2319 3868 4.814147 TGCAGAGACATCAGACTGTTTAG 58.186 43.478 1.59 0.00 33.57 1.85
2320 3869 4.871933 TGCAGAGACATCAGACTGTTTA 57.128 40.909 1.59 0.00 33.57 2.01
2321 3870 3.758755 TGCAGAGACATCAGACTGTTT 57.241 42.857 1.59 0.00 33.57 2.83
2322 3871 3.977134 ATGCAGAGACATCAGACTGTT 57.023 42.857 1.59 0.00 33.57 3.16
2323 3872 3.260128 TCAATGCAGAGACATCAGACTGT 59.740 43.478 1.59 0.00 33.57 3.55
2324 3873 3.858247 TCAATGCAGAGACATCAGACTG 58.142 45.455 0.00 0.00 0.00 3.51
2325 3874 3.768215 TCTCAATGCAGAGACATCAGACT 59.232 43.478 1.67 0.00 39.62 3.24
2326 3875 4.120792 TCTCAATGCAGAGACATCAGAC 57.879 45.455 1.67 0.00 39.62 3.51
2327 3876 5.354842 AATCTCAATGCAGAGACATCAGA 57.645 39.130 7.75 0.00 46.58 3.27
2328 3877 5.354513 ACAAATCTCAATGCAGAGACATCAG 59.645 40.000 7.75 1.04 46.58 2.90
2329 3878 5.123344 CACAAATCTCAATGCAGAGACATCA 59.877 40.000 7.75 0.00 46.58 3.07
2342 3891 3.498481 CCTCACCCTTCCACAAATCTCAA 60.498 47.826 0.00 0.00 0.00 3.02
2361 3910 5.719563 TCCAATAAAATCTTGTTTCCCCCTC 59.280 40.000 0.00 0.00 0.00 4.30
2388 3938 7.881232 TCTGTCTAAACAAATTAACTAGGGTGG 59.119 37.037 0.00 0.00 34.24 4.61
2408 3958 6.497259 TCTGACAAATTAACTAGGGTCTGTCT 59.503 38.462 0.00 0.00 34.44 3.41
2430 3980 4.703424 CTCACGTAGATACTACGCATCTG 58.297 47.826 24.48 17.29 43.97 2.90
2434 3984 2.287103 CAGCTCACGTAGATACTACGCA 59.713 50.000 24.48 14.17 43.97 5.24
2448 3998 5.122396 CCTACAGTAAATTTGGTCAGCTCAC 59.878 44.000 0.00 0.00 0.00 3.51
2459 4009 9.823647 CTCACACATATCTCCTACAGTAAATTT 57.176 33.333 0.00 0.00 0.00 1.82
2546 4096 8.506168 TTTACACTGGTGAGAAATATCCATTC 57.494 34.615 7.78 0.00 0.00 2.67
2622 4172 9.541724 GCTTGTTTTCCTTTTAAAGTTTCTTTG 57.458 29.630 3.91 0.00 0.00 2.77
2842 4394 8.981647 GCAGAATTTATGTCATGTTCAAAAGTT 58.018 29.630 0.00 0.00 0.00 2.66
2915 4467 0.465705 CTAAATCTGCCTCCGCTCCA 59.534 55.000 0.00 0.00 35.36 3.86
2916 4468 0.882484 GCTAAATCTGCCTCCGCTCC 60.882 60.000 0.00 0.00 35.36 4.70
2971 4523 2.038295 CAGAGTTCAAGCCAAGTCTCCT 59.962 50.000 0.00 0.00 34.36 3.69
2993 4545 5.661312 ACATAAGTAGCATGAGAGTTACCCA 59.339 40.000 0.00 0.00 0.00 4.51
3050 4602 4.602340 TTTCTCTGTAGACTTGGTCCAC 57.398 45.455 0.00 0.00 32.18 4.02
3052 4604 6.231211 TGATTTTTCTCTGTAGACTTGGTCC 58.769 40.000 0.00 0.00 32.18 4.46
3105 4658 6.365970 AGATACATCCTGAGACACTTTTGT 57.634 37.500 0.00 0.00 39.32 2.83
3106 4659 7.009631 CGTTAGATACATCCTGAGACACTTTTG 59.990 40.741 0.00 0.00 0.00 2.44
3111 4671 5.752892 TCGTTAGATACATCCTGAGACAC 57.247 43.478 0.00 0.00 0.00 3.67
3201 4775 3.228453 TCCTCCCATTCGTAGTGGATAC 58.772 50.000 5.30 0.00 39.12 2.24
3219 4793 5.147330 TCAACGACATGAATGTTACTCCT 57.853 39.130 0.00 0.00 41.95 3.69
3236 4810 2.287915 CCCATCCGAGCTTAATTCAACG 59.712 50.000 0.00 0.00 0.00 4.10
3239 4813 3.390967 TCATCCCATCCGAGCTTAATTCA 59.609 43.478 0.00 0.00 0.00 2.57
3240 4814 4.008074 TCATCCCATCCGAGCTTAATTC 57.992 45.455 0.00 0.00 0.00 2.17
3250 4824 1.759445 CCCTAGCTATCATCCCATCCG 59.241 57.143 0.00 0.00 0.00 4.18
3261 4835 1.065418 GGTGTGTTGTGCCCTAGCTAT 60.065 52.381 0.00 0.00 40.80 2.97
3278 4852 2.838386 GCAGACTGTATGCATTGGTG 57.162 50.000 21.37 0.00 43.31 4.17
3447 5025 2.199236 GCCATACGTAGTGTACTTGGC 58.801 52.381 15.99 15.99 46.46 4.52
3611 5189 4.120331 GCTTGCGACACCCATGGC 62.120 66.667 6.09 0.00 0.00 4.40
3733 5314 2.010497 GAAGAATGGAAGCCTCGGAAC 58.990 52.381 0.00 0.00 0.00 3.62
3791 5372 2.546321 GTCAGCACGTTGTCGCAG 59.454 61.111 0.00 0.00 41.18 5.18
3888 5469 1.067084 CACGCGATGATCAGCTCCT 59.933 57.895 15.93 0.00 0.00 3.69
4170 5751 2.125310 AAATCGGCGGCGTGATGA 60.125 55.556 31.06 12.11 0.00 2.92
4175 5756 2.971428 ATCATCGAAATCGGCGGCGT 62.971 55.000 31.06 15.68 40.29 5.68
4213 5794 2.103042 GGTCTCTGCCATGTGTCGC 61.103 63.158 0.00 0.00 0.00 5.19
4216 5797 1.913262 TCCGGTCTCTGCCATGTGT 60.913 57.895 0.00 0.00 0.00 3.72
4492 6073 3.419759 GACGTCGCGCCACCAAAT 61.420 61.111 0.00 0.00 0.00 2.32
4534 6115 4.081185 TGCGGCTTCATCTCGGCA 62.081 61.111 0.00 0.00 36.42 5.69
4606 6187 0.398381 GGGAGCTGATGGAGGTCTCT 60.398 60.000 0.00 0.00 45.07 3.10
4693 6274 2.125552 CGCCTCGTTCAGATGGCA 60.126 61.111 0.00 0.00 40.71 4.92
4918 6507 7.775561 ACTTGAAACATAAGGGGATGATTACTC 59.224 37.037 0.00 0.00 0.00 2.59
4919 6508 7.557719 CACTTGAAACATAAGGGGATGATTACT 59.442 37.037 0.00 0.00 0.00 2.24
4924 6513 5.255397 ACACTTGAAACATAAGGGGATGA 57.745 39.130 0.00 0.00 32.86 2.92
5012 6601 1.875813 CTTAGGCAGCAGCGAGTCG 60.876 63.158 8.54 8.54 43.41 4.18
5036 6625 2.266279 AGCCTACTCCAAACAAGCCTA 58.734 47.619 0.00 0.00 0.00 3.93
5037 6626 1.068121 AGCCTACTCCAAACAAGCCT 58.932 50.000 0.00 0.00 0.00 4.58
5122 6747 6.071952 TGGCTTGTATTGGAATCTTGACTTTC 60.072 38.462 0.00 0.00 0.00 2.62
5160 6942 6.262944 TGCTCATAGGGCTGTTAATTTGTATG 59.737 38.462 0.00 0.00 0.00 2.39
5195 6977 3.278574 TGGTGTTCCAAGACAGTTTCAG 58.721 45.455 0.00 0.00 41.25 3.02
5201 6983 1.202687 TGCTCTGGTGTTCCAAGACAG 60.203 52.381 0.00 0.00 43.81 3.51
5321 7103 4.078537 TGTTCAATGATTTGACCACCGAT 58.921 39.130 0.00 0.00 41.50 4.18
5732 7514 7.514721 AGGAAACTAATTCTGTTGTAGGTTCA 58.485 34.615 9.28 0.00 41.40 3.18
5798 7581 4.278170 CCATCTAACTTGAGCAACAAACCA 59.722 41.667 0.00 0.00 38.08 3.67
5925 9321 6.424032 ACACATAGGTTTTCTAAAGATCCCC 58.576 40.000 0.00 0.00 0.00 4.81
5944 9340 5.940192 TCTACAAAGAAATCGCAACACAT 57.060 34.783 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.