Multiple sequence alignment - TraesCS3D01G126500

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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 TraesCS3D01G126500 chr3D 100.000 3859 0 0 1 3859 84566004 84562146 0.000000e+00 7127.0
1 TraesCS3D01G126500 chr3D 94.373 2346 109 6 946 3270 84498254 84495911 0.000000e+00 3579.0
2 TraesCS3D01G126500 chr3D 86.620 2728 263 47 219 2906 84501958 84499293 0.000000e+00 2922.0
3 TraesCS3D01G126500 chr3D 84.198 1734 211 37 751 2460 84505905 84504211 0.000000e+00 1626.0
4 TraesCS3D01G126500 chr3D 94.248 452 24 2 3409 3859 84495231 84494781 0.000000e+00 689.0
5 TraesCS3D01G126500 chr3D 95.522 201 9 0 8 208 527593084 527592884 4.810000e-84 322.0
6 TraesCS3D01G126500 chr3D 86.923 260 24 5 3394 3650 84495912 84495660 2.270000e-72 283.0
7 TraesCS3D01G126500 chr3B 91.358 3020 122 56 274 3270 132089065 132091968 0.000000e+00 4002.0
8 TraesCS3D01G126500 chr3B 95.578 2329 98 3 946 3270 132903285 132900958 0.000000e+00 3725.0
9 TraesCS3D01G126500 chr3B 93.817 2345 116 14 946 3270 132008502 132010837 0.000000e+00 3500.0
10 TraesCS3D01G126500 chr3B 86.961 2692 266 40 219 2879 133199481 133202118 0.000000e+00 2948.0
11 TraesCS3D01G126500 chr3B 84.538 2671 275 62 274 2906 132906899 132904329 0.000000e+00 2518.0
12 TraesCS3D01G126500 chr3B 84.774 2187 255 38 751 2906 132005317 132007456 0.000000e+00 2122.0
13 TraesCS3D01G126500 chr3B 90.756 1363 93 13 1538 2882 133204198 133205545 0.000000e+00 1788.0
14 TraesCS3D01G126500 chr3B 94.635 466 24 1 3394 3859 132900959 132900495 0.000000e+00 721.0
15 TraesCS3D01G126500 chr3B 82.345 725 79 28 572 1282 132977263 132976574 5.560000e-163 584.0
16 TraesCS3D01G126500 chr3B 89.056 466 31 3 3394 3859 132011681 132012126 9.360000e-156 560.0
17 TraesCS3D01G126500 chr3B 88.009 467 29 6 3394 3859 132092635 132093075 9.500000e-146 527.0
18 TraesCS3D01G126500 chr3B 88.077 260 21 5 3394 3650 132010836 132011088 2.250000e-77 300.0
19 TraesCS3D01G126500 chr3B 87.379 103 9 1 742 844 133203317 133203415 8.760000e-22 115.0
20 TraesCS3D01G126500 chr3B 80.000 160 20 3 740 899 132903515 132903368 1.470000e-19 108.0
21 TraesCS3D01G126500 chr3A 94.035 2347 112 14 946 3270 100843195 100840855 0.000000e+00 3533.0
22 TraesCS3D01G126500 chr3A 88.116 1969 168 29 949 2882 100879877 100877940 0.000000e+00 2279.0
23 TraesCS3D01G126500 chr3A 84.115 2260 267 49 677 2906 100883143 100880946 0.000000e+00 2100.0
24 TraesCS3D01G126500 chr3A 89.030 1340 64 21 219 1528 100845487 100844201 0.000000e+00 1583.0
25 TraesCS3D01G126500 chr3A 92.905 451 28 3 3409 3859 100840170 100839724 0.000000e+00 652.0
26 TraesCS3D01G126500 chr3A 86.165 412 30 12 3410 3811 100877532 100877138 1.660000e-113 420.0
27 TraesCS3D01G126500 chr3A 86.154 260 26 6 3394 3650 100840856 100840604 4.910000e-69 272.0
28 TraesCS3D01G126500 chr3A 81.988 161 17 3 740 900 100843425 100843277 4.050000e-25 126.0
29 TraesCS3D01G126500 chr4B 94.500 200 11 0 8 207 149001198 149000999 3.740000e-80 309.0
30 TraesCS3D01G126500 chr4B 94.000 200 12 0 8 207 149037422 149037223 1.740000e-78 303.0
31 TraesCS3D01G126500 chr4B 93.548 155 8 2 3262 3416 13408957 13409109 3.000000e-56 230.0
32 TraesCS3D01G126500 chr4B 97.037 135 3 1 3269 3403 55926031 55925898 3.880000e-55 226.0
33 TraesCS3D01G126500 chr5D 92.000 200 14 2 8 207 191930562 191930759 2.940000e-71 279.0
34 TraesCS3D01G126500 chr7A 96.403 139 5 0 3267 3405 593688624 593688486 3.000000e-56 230.0
35 TraesCS3D01G126500 chr5B 95.714 140 4 2 3256 3395 383524642 383524779 1.400000e-54 224.0
36 TraesCS3D01G126500 chr5B 93.919 148 7 2 3269 3416 545806442 545806297 5.020000e-54 222.0
37 TraesCS3D01G126500 chr2D 95.070 142 7 0 3265 3406 445188724 445188583 1.400000e-54 224.0
38 TraesCS3D01G126500 chr1B 95.683 139 6 0 3266 3404 601258840 601258978 1.400000e-54 224.0
39 TraesCS3D01G126500 chrUn 95.035 141 6 1 3255 3395 322720549 322720410 1.800000e-53 220.0
40 TraesCS3D01G126500 chrUn 92.105 38 3 0 2970 3007 291776824 291776861 2.000000e-03 54.7
41 TraesCS3D01G126500 chr2B 93.836 146 7 2 3265 3408 777524739 777524884 6.490000e-53 219.0
42 TraesCS3D01G126500 chr4A 84.848 66 10 0 2970 3035 532205268 532205203 2.490000e-07 67.6
43 TraesCS3D01G126500 chr4A 92.105 38 3 0 2970 3007 649197374 649197337 2.000000e-03 54.7
44 TraesCS3D01G126500 chr6A 93.023 43 1 1 165 207 438027181 438027221 1.160000e-05 62.1
45 TraesCS3D01G126500 chr6B 88.889 45 4 1 2963 3007 33568017 33567974 2.000000e-03 54.7


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 TraesCS3D01G126500 chr3D 84562146 84566004 3858 True 7127.000000 7127 100.000000 1 3859 1 chr3D.!!$R1 3858
1 TraesCS3D01G126500 chr3D 84494781 84505905 11124 True 1819.800000 3579 89.272400 219 3859 5 chr3D.!!$R3 3640
2 TraesCS3D01G126500 chr3B 132089065 132093075 4010 False 2264.500000 4002 89.683500 274 3859 2 chr3B.!!$F2 3585
3 TraesCS3D01G126500 chr3B 132900495 132906899 6404 True 1768.000000 3725 88.687750 274 3859 4 chr3B.!!$R2 3585
4 TraesCS3D01G126500 chr3B 132005317 132012126 6809 False 1620.500000 3500 88.931000 751 3859 4 chr3B.!!$F1 3108
5 TraesCS3D01G126500 chr3B 133199481 133205545 6064 False 1617.000000 2948 88.365333 219 2882 3 chr3B.!!$F3 2663
6 TraesCS3D01G126500 chr3B 132976574 132977263 689 True 584.000000 584 82.345000 572 1282 1 chr3B.!!$R1 710
7 TraesCS3D01G126500 chr3A 100877138 100883143 6005 True 1599.666667 2279 86.132000 677 3811 3 chr3A.!!$R2 3134
8 TraesCS3D01G126500 chr3A 100839724 100845487 5763 True 1233.200000 3533 88.822400 219 3859 5 chr3A.!!$R1 3640

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
204 205 0.039437 ACGCGCGGGATGTTATCTAG 60.039 55.0 35.22 0.47 0.00 2.43 F
205 206 0.039437 CGCGCGGGATGTTATCTAGT 60.039 55.0 24.84 0.00 0.00 2.57 F
400 4135 0.179045 CAAAGGCCTATGAGGGACCG 60.179 60.0 5.16 0.00 35.37 4.79 F
405 4140 0.905337 GCCTATGAGGGACCGCCTAT 60.905 60.0 0.00 0.00 35.37 2.57 F
1153 4951 1.021390 GGTCAGCTTCATCACCACGG 61.021 60.0 0.00 0.00 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 12050 3.099267 ACGTCAACCAGATATAGCTGC 57.901 47.619 12.62 0.00 34.56 5.25 R
2399 12722 1.445716 GCAGGATCATGAGCTGTGGC 61.446 60.000 12.39 5.99 39.06 5.01 R
2627 12950 2.756840 TCTGCACCTCATCTCTTGTG 57.243 50.000 0.00 0.00 0.00 3.33 R
2675 13005 2.202851 ATCTCTTCTGCAGCCGCG 60.203 61.111 9.47 0.00 42.97 6.46 R
3271 13610 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 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
25 26 8.181904 TCTTGCCTATCTGAATTTCTTTTTGT 57.818 30.769 0.00 0.00 0.00 2.83
26 27 8.299570 TCTTGCCTATCTGAATTTCTTTTTGTC 58.700 33.333 0.00 0.00 0.00 3.18
29 30 7.448161 TGCCTATCTGAATTTCTTTTTGTCAGA 59.552 33.333 4.31 4.31 46.34 3.27
35 36 9.520204 TCTGAATTTCTTTTTGTCAGATTTCAC 57.480 29.630 0.00 0.00 39.73 3.18
36 37 8.647143 TGAATTTCTTTTTGTCAGATTTCACC 57.353 30.769 0.00 0.00 0.00 4.02
37 38 8.256605 TGAATTTCTTTTTGTCAGATTTCACCA 58.743 29.630 0.00 0.00 0.00 4.17
38 39 9.264719 GAATTTCTTTTTGTCAGATTTCACCAT 57.735 29.630 0.00 0.00 0.00 3.55
39 40 9.617523 AATTTCTTTTTGTCAGATTTCACCATT 57.382 25.926 0.00 0.00 0.00 3.16
40 41 8.422973 TTTCTTTTTGTCAGATTTCACCATTG 57.577 30.769 0.00 0.00 0.00 2.82
41 42 7.111247 TCTTTTTGTCAGATTTCACCATTGT 57.889 32.000 0.00 0.00 0.00 2.71
42 43 7.555087 TCTTTTTGTCAGATTTCACCATTGTT 58.445 30.769 0.00 0.00 0.00 2.83
43 44 7.492020 TCTTTTTGTCAGATTTCACCATTGTTG 59.508 33.333 0.00 0.00 0.00 3.33
44 45 6.462552 TTTGTCAGATTTCACCATTGTTGA 57.537 33.333 0.00 0.00 0.00 3.18
46 47 6.653526 TGTCAGATTTCACCATTGTTGATT 57.346 33.333 0.00 0.00 0.00 2.57
47 48 6.448852 TGTCAGATTTCACCATTGTTGATTG 58.551 36.000 0.00 0.00 0.00 2.67
50 51 6.041865 TCAGATTTCACCATTGTTGATTGGTT 59.958 34.615 0.00 0.00 43.73 3.67
51 52 6.707161 CAGATTTCACCATTGTTGATTGGTTT 59.293 34.615 0.00 0.00 43.73 3.27
54 55 9.218440 GATTTCACCATTGTTGATTGGTTTATT 57.782 29.630 0.00 0.00 43.73 1.40
55 56 8.970859 TTTCACCATTGTTGATTGGTTTATTT 57.029 26.923 0.00 0.00 43.73 1.40
56 57 8.600449 TTCACCATTGTTGATTGGTTTATTTC 57.400 30.769 0.00 0.00 43.73 2.17
57 58 7.158021 TCACCATTGTTGATTGGTTTATTTCC 58.842 34.615 0.00 0.00 43.73 3.13
58 59 6.933521 CACCATTGTTGATTGGTTTATTTCCA 59.066 34.615 0.00 0.00 43.73 3.53
59 60 7.607223 CACCATTGTTGATTGGTTTATTTCCAT 59.393 33.333 0.00 0.00 43.73 3.41
60 61 8.162746 ACCATTGTTGATTGGTTTATTTCCATT 58.837 29.630 0.00 0.00 43.73 3.16
130 131 6.716898 ACTACTATTGAACAAGTAAACCGC 57.283 37.500 0.00 0.00 0.00 5.68
132 133 6.877322 ACTACTATTGAACAAGTAAACCGCAT 59.123 34.615 0.00 0.00 0.00 4.73
133 134 5.938322 ACTATTGAACAAGTAAACCGCATG 58.062 37.500 0.00 0.00 0.00 4.06
134 135 5.703592 ACTATTGAACAAGTAAACCGCATGA 59.296 36.000 0.00 0.00 0.00 3.07
135 136 4.481930 TTGAACAAGTAAACCGCATGAG 57.518 40.909 0.00 0.00 0.00 2.90
136 137 3.472652 TGAACAAGTAAACCGCATGAGT 58.527 40.909 0.00 0.00 0.00 3.41
137 138 3.880490 TGAACAAGTAAACCGCATGAGTT 59.120 39.130 0.00 0.00 0.00 3.01
139 140 4.483476 ACAAGTAAACCGCATGAGTTTC 57.517 40.909 15.18 9.13 38.37 2.78
140 141 4.134563 ACAAGTAAACCGCATGAGTTTCT 58.865 39.130 15.18 10.70 38.37 2.52
141 142 4.213482 ACAAGTAAACCGCATGAGTTTCTC 59.787 41.667 15.18 11.00 38.37 2.87
142 143 2.993899 AGTAAACCGCATGAGTTTCTCG 59.006 45.455 15.18 0.00 38.37 4.04
143 144 2.163818 AAACCGCATGAGTTTCTCGA 57.836 45.000 0.00 0.00 31.94 4.04
144 145 2.163818 AACCGCATGAGTTTCTCGAA 57.836 45.000 0.00 0.00 32.35 3.71
145 146 2.386661 ACCGCATGAGTTTCTCGAAT 57.613 45.000 0.00 0.00 32.35 3.34
147 148 3.074412 ACCGCATGAGTTTCTCGAATTT 58.926 40.909 0.00 0.00 32.35 1.82
148 149 4.250464 ACCGCATGAGTTTCTCGAATTTA 58.750 39.130 0.00 0.00 32.35 1.40
150 151 5.163854 ACCGCATGAGTTTCTCGAATTTAAG 60.164 40.000 0.00 0.00 32.35 1.85
151 152 5.163854 CCGCATGAGTTTCTCGAATTTAAGT 60.164 40.000 0.00 0.00 32.35 2.24
152 153 6.307155 CGCATGAGTTTCTCGAATTTAAGTT 58.693 36.000 0.00 0.00 32.35 2.66
153 154 7.412563 CCGCATGAGTTTCTCGAATTTAAGTTA 60.413 37.037 0.00 0.00 32.35 2.24
154 155 7.955324 CGCATGAGTTTCTCGAATTTAAGTTAA 59.045 33.333 0.00 0.00 32.35 2.01
155 156 9.607285 GCATGAGTTTCTCGAATTTAAGTTAAA 57.393 29.630 10.39 10.39 32.35 1.52
158 159 8.562052 TGAGTTTCTCGAATTTAAGTTAAACCC 58.438 33.333 10.20 4.83 32.35 4.11
159 160 8.454570 AGTTTCTCGAATTTAAGTTAAACCCA 57.545 30.769 10.20 0.00 0.00 4.51
160 161 9.074576 AGTTTCTCGAATTTAAGTTAAACCCAT 57.925 29.630 10.20 0.00 0.00 4.00
161 162 9.124807 GTTTCTCGAATTTAAGTTAAACCCATG 57.875 33.333 10.20 2.57 0.00 3.66
163 164 5.632959 TCGAATTTAAGTTAAACCCATGCG 58.367 37.500 10.20 5.62 0.00 4.73
165 166 5.285134 CGAATTTAAGTTAAACCCATGCGTG 59.715 40.000 10.20 0.00 0.00 5.34
166 167 3.562567 TTAAGTTAAACCCATGCGTGC 57.437 42.857 0.00 0.00 0.00 5.34
167 168 1.616159 AAGTTAAACCCATGCGTGCT 58.384 45.000 0.00 0.00 0.00 4.40
169 170 2.785562 AGTTAAACCCATGCGTGCTAA 58.214 42.857 0.00 0.00 0.00 3.09
170 171 3.150767 AGTTAAACCCATGCGTGCTAAA 58.849 40.909 0.00 0.00 0.00 1.85
171 172 3.570550 AGTTAAACCCATGCGTGCTAAAA 59.429 39.130 0.00 0.00 0.00 1.52
172 173 4.038162 AGTTAAACCCATGCGTGCTAAAAA 59.962 37.500 0.00 0.00 0.00 1.94
175 176 3.676291 ACCCATGCGTGCTAAAAATTT 57.324 38.095 0.00 0.00 0.00 1.82
177 178 2.929398 CCCATGCGTGCTAAAAATTTCC 59.071 45.455 0.00 0.00 0.00 3.13
178 179 2.929398 CCATGCGTGCTAAAAATTTCCC 59.071 45.455 0.00 0.00 0.00 3.97
180 181 0.989164 GCGTGCTAAAAATTTCCCGC 59.011 50.000 0.00 0.00 0.00 6.13
181 182 1.667467 GCGTGCTAAAAATTTCCCGCA 60.667 47.619 0.00 0.00 39.65 5.69
182 183 2.250188 CGTGCTAAAAATTTCCCGCAG 58.750 47.619 8.05 1.78 0.00 5.18
183 184 1.992667 GTGCTAAAAATTTCCCGCAGC 59.007 47.619 8.05 5.79 0.00 5.25
184 185 1.615883 TGCTAAAAATTTCCCGCAGCA 59.384 42.857 0.00 0.00 35.33 4.41
185 186 2.036475 TGCTAAAAATTTCCCGCAGCAA 59.964 40.909 8.70 0.00 34.82 3.91
187 188 1.496934 AAAAATTTCCCGCAGCAACG 58.503 45.000 0.00 0.00 0.00 4.10
188 189 0.943835 AAAATTTCCCGCAGCAACGC 60.944 50.000 0.00 0.00 0.00 4.84
199 200 3.492545 GCAACGCGCGGGATGTTA 61.493 61.111 35.22 0.00 0.00 2.41
200 201 2.819552 GCAACGCGCGGGATGTTAT 61.820 57.895 35.22 7.19 0.00 1.89
202 203 1.143183 AACGCGCGGGATGTTATCT 59.857 52.632 35.22 5.42 0.00 1.98
203 204 0.386476 AACGCGCGGGATGTTATCTA 59.614 50.000 35.22 0.00 0.00 1.98
204 205 0.039437 ACGCGCGGGATGTTATCTAG 60.039 55.000 35.22 0.47 0.00 2.43
205 206 0.039437 CGCGCGGGATGTTATCTAGT 60.039 55.000 24.84 0.00 0.00 2.57
206 207 1.602165 CGCGCGGGATGTTATCTAGTT 60.602 52.381 24.84 0.00 0.00 2.24
207 208 2.351060 CGCGCGGGATGTTATCTAGTTA 60.351 50.000 24.84 0.00 0.00 2.24
208 209 2.985139 GCGCGGGATGTTATCTAGTTAC 59.015 50.000 8.83 0.00 0.00 2.50
209 210 3.551454 GCGCGGGATGTTATCTAGTTACA 60.551 47.826 8.83 0.00 0.00 2.41
210 211 4.227538 CGCGGGATGTTATCTAGTTACAG 58.772 47.826 0.00 0.00 0.00 2.74
211 212 4.557205 GCGGGATGTTATCTAGTTACAGG 58.443 47.826 0.00 0.00 0.00 4.00
212 213 4.280174 GCGGGATGTTATCTAGTTACAGGA 59.720 45.833 0.00 0.00 0.00 3.86
213 214 5.565045 GCGGGATGTTATCTAGTTACAGGAG 60.565 48.000 0.00 0.00 0.00 3.69
214 215 5.535406 CGGGATGTTATCTAGTTACAGGAGT 59.465 44.000 0.00 0.00 0.00 3.85
215 216 6.040616 CGGGATGTTATCTAGTTACAGGAGTT 59.959 42.308 0.00 0.00 0.00 3.01
216 217 7.435305 GGGATGTTATCTAGTTACAGGAGTTC 58.565 42.308 0.00 0.00 0.00 3.01
217 218 7.288158 GGGATGTTATCTAGTTACAGGAGTTCT 59.712 40.741 0.00 0.00 0.00 3.01
285 4014 5.419542 GCAGTAAGTCCATATCAGTGTTGA 58.580 41.667 0.00 0.00 37.81 3.18
390 4125 2.290323 GCTTCTCACTTCCAAAGGCCTA 60.290 50.000 5.16 0.00 0.00 3.93
391 4126 3.623453 GCTTCTCACTTCCAAAGGCCTAT 60.623 47.826 5.16 0.00 0.00 2.57
392 4127 3.634397 TCTCACTTCCAAAGGCCTATG 57.366 47.619 5.16 0.00 0.00 2.23
393 4128 3.181329 TCTCACTTCCAAAGGCCTATGA 58.819 45.455 5.16 0.00 0.00 2.15
394 4129 3.198635 TCTCACTTCCAAAGGCCTATGAG 59.801 47.826 5.16 10.84 34.87 2.90
395 4130 2.239654 TCACTTCCAAAGGCCTATGAGG 59.760 50.000 5.16 5.97 38.80 3.86
396 4131 1.566231 ACTTCCAAAGGCCTATGAGGG 59.434 52.381 5.16 3.46 35.37 4.30
397 4132 1.846439 CTTCCAAAGGCCTATGAGGGA 59.154 52.381 5.16 6.16 35.37 4.20
398 4133 1.213296 TCCAAAGGCCTATGAGGGAC 58.787 55.000 5.16 0.00 35.37 4.46
399 4134 0.183731 CCAAAGGCCTATGAGGGACC 59.816 60.000 5.16 0.00 35.37 4.46
400 4135 0.179045 CAAAGGCCTATGAGGGACCG 60.179 60.000 5.16 0.00 35.37 4.79
401 4136 1.984288 AAAGGCCTATGAGGGACCGC 61.984 60.000 5.16 0.00 35.37 5.68
402 4137 3.942439 GGCCTATGAGGGACCGCC 61.942 72.222 0.00 0.00 35.37 6.13
403 4138 2.844839 GCCTATGAGGGACCGCCT 60.845 66.667 0.00 0.00 35.37 5.52
404 4139 1.533273 GCCTATGAGGGACCGCCTA 60.533 63.158 0.00 0.00 35.37 3.93
405 4140 0.905337 GCCTATGAGGGACCGCCTAT 60.905 60.000 0.00 0.00 35.37 2.57
477 4213 6.529829 CGAAAAACAGACAAGAAAATTCCACA 59.470 34.615 0.00 0.00 0.00 4.17
661 4409 3.111098 GCCAAATTCAGTGCATCGAATC 58.889 45.455 12.39 0.00 30.64 2.52
662 4410 3.699067 CCAAATTCAGTGCATCGAATCC 58.301 45.455 12.39 0.00 30.64 3.01
663 4411 3.357021 CAAATTCAGTGCATCGAATCCG 58.643 45.455 12.39 5.20 30.64 4.18
905 4696 1.059913 ATATAGCACCAGGACCAGGC 58.940 55.000 2.09 0.00 0.00 4.85
912 4706 1.115930 ACCAGGACCAGGCGCTATAG 61.116 60.000 7.64 0.00 0.00 1.31
922 4720 2.357952 CAGGCGCTATAGACACACTACA 59.642 50.000 7.64 0.00 33.62 2.74
924 4722 2.386249 GCGCTATAGACACACTACAGC 58.614 52.381 3.21 0.00 45.10 4.40
1032 4830 2.105806 GAAGCGGCTATGGGGAGAGG 62.106 65.000 1.35 0.00 0.00 3.69
1113 4911 3.365291 GACCGACATGGCACGCCTA 62.365 63.158 9.92 0.00 43.94 3.93
1153 4951 1.021390 GGTCAGCTTCATCACCACGG 61.021 60.000 0.00 0.00 0.00 4.94
1593 11882 3.868757 TTACTTCATCAGTGGACGGAG 57.131 47.619 0.00 0.00 35.97 4.63
1599 11888 3.632333 TCATCAGTGGACGGAGAACTAT 58.368 45.455 0.00 0.00 0.00 2.12
1744 12050 4.615588 TTTCATGGGCAAGTTTTTAGGG 57.384 40.909 0.00 0.00 0.00 3.53
2399 12722 1.453197 GGTCATAAGGGGTTGGGCG 60.453 63.158 0.00 0.00 0.00 6.13
2827 13165 3.127548 GCATGTGGTTCAGTGGTTGATAG 59.872 47.826 0.00 0.00 35.27 2.08
3270 13609 5.399013 GTGAAACCCACATAAAGCACATAC 58.601 41.667 0.00 0.00 45.03 2.39
3271 13610 5.183140 GTGAAACCCACATAAAGCACATACT 59.817 40.000 0.00 0.00 45.03 2.12
3272 13611 5.414454 TGAAACCCACATAAAGCACATACTC 59.586 40.000 0.00 0.00 0.00 2.59
3273 13612 3.886123 ACCCACATAAAGCACATACTCC 58.114 45.455 0.00 0.00 0.00 3.85
3274 13613 3.214328 CCCACATAAAGCACATACTCCC 58.786 50.000 0.00 0.00 0.00 4.30
3275 13614 3.117888 CCCACATAAAGCACATACTCCCT 60.118 47.826 0.00 0.00 0.00 4.20
3276 13615 4.130118 CCACATAAAGCACATACTCCCTC 58.870 47.826 0.00 0.00 0.00 4.30
3277 13616 4.130118 CACATAAAGCACATACTCCCTCC 58.870 47.826 0.00 0.00 0.00 4.30
3278 13617 3.181465 ACATAAAGCACATACTCCCTCCG 60.181 47.826 0.00 0.00 0.00 4.63
3279 13618 1.276622 AAAGCACATACTCCCTCCGT 58.723 50.000 0.00 0.00 0.00 4.69
3280 13619 0.824759 AAGCACATACTCCCTCCGTC 59.175 55.000 0.00 0.00 0.00 4.79
3281 13620 1.043673 AGCACATACTCCCTCCGTCC 61.044 60.000 0.00 0.00 0.00 4.79
3282 13621 1.734137 CACATACTCCCTCCGTCCG 59.266 63.158 0.00 0.00 0.00 4.79
3283 13622 1.455217 ACATACTCCCTCCGTCCGG 60.455 63.158 0.00 0.00 0.00 5.14
3284 13623 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
3285 13624 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
3286 13625 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
3287 13626 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3288 13627 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3289 13628 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3290 13629 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3291 13630 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3292 13631 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3293 13632 1.287425 CTCCGTCCGGAAATACTTGC 58.713 55.000 5.23 0.00 44.66 4.01
3294 13633 0.108041 TCCGTCCGGAAATACTTGCC 60.108 55.000 5.23 0.00 42.05 4.52
3295 13634 0.391927 CCGTCCGGAAATACTTGCCA 60.392 55.000 5.23 0.00 37.50 4.92
3296 13635 1.663695 CGTCCGGAAATACTTGCCAT 58.336 50.000 5.23 0.00 0.00 4.40
3297 13636 1.597663 CGTCCGGAAATACTTGCCATC 59.402 52.381 5.23 0.00 0.00 3.51
3298 13637 2.639065 GTCCGGAAATACTTGCCATCA 58.361 47.619 5.23 0.00 0.00 3.07
3299 13638 3.013921 GTCCGGAAATACTTGCCATCAA 58.986 45.455 5.23 0.00 0.00 2.57
3300 13639 3.442273 GTCCGGAAATACTTGCCATCAAA 59.558 43.478 5.23 0.00 0.00 2.69
3301 13640 4.082463 GTCCGGAAATACTTGCCATCAAAA 60.082 41.667 5.23 0.00 0.00 2.44
3302 13641 4.709397 TCCGGAAATACTTGCCATCAAAAT 59.291 37.500 0.00 0.00 0.00 1.82
3303 13642 4.805192 CCGGAAATACTTGCCATCAAAATG 59.195 41.667 0.00 0.00 0.00 2.32
3304 13643 5.394005 CCGGAAATACTTGCCATCAAAATGA 60.394 40.000 0.00 0.00 34.61 2.57
3305 13644 6.098679 CGGAAATACTTGCCATCAAAATGAA 58.901 36.000 0.00 0.00 34.61 2.57
3306 13645 6.757947 CGGAAATACTTGCCATCAAAATGAAT 59.242 34.615 0.00 0.00 34.61 2.57
3307 13646 7.920151 CGGAAATACTTGCCATCAAAATGAATA 59.080 33.333 0.00 0.00 34.61 1.75
3308 13647 9.598517 GGAAATACTTGCCATCAAAATGAATAA 57.401 29.630 0.00 0.00 34.61 1.40
3312 13651 7.910441 ACTTGCCATCAAAATGAATAAAAGG 57.090 32.000 0.00 0.00 34.61 3.11
3313 13652 6.880529 ACTTGCCATCAAAATGAATAAAAGGG 59.119 34.615 0.00 0.00 34.61 3.95
3314 13653 5.743117 TGCCATCAAAATGAATAAAAGGGG 58.257 37.500 0.00 0.00 34.61 4.79
3315 13654 5.486775 TGCCATCAAAATGAATAAAAGGGGA 59.513 36.000 0.00 0.00 34.61 4.81
3316 13655 6.158344 TGCCATCAAAATGAATAAAAGGGGAT 59.842 34.615 0.00 0.00 34.61 3.85
3317 13656 6.484308 GCCATCAAAATGAATAAAAGGGGATG 59.516 38.462 0.00 0.00 34.61 3.51
3318 13657 7.567458 CCATCAAAATGAATAAAAGGGGATGT 58.433 34.615 0.00 0.00 34.61 3.06
3319 13658 8.703743 CCATCAAAATGAATAAAAGGGGATGTA 58.296 33.333 0.00 0.00 34.61 2.29
3322 13661 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
3327 13666 7.667557 TGAATAAAAGGGGATGTATCTAGACG 58.332 38.462 0.00 0.00 0.00 4.18
3328 13667 7.289317 TGAATAAAAGGGGATGTATCTAGACGT 59.711 37.037 0.00 0.00 0.00 4.34
3329 13668 8.716674 AATAAAAGGGGATGTATCTAGACGTA 57.283 34.615 0.00 0.00 0.00 3.57
3330 13669 8.896722 ATAAAAGGGGATGTATCTAGACGTAT 57.103 34.615 0.00 0.00 0.00 3.06
3331 13670 7.613551 AAAAGGGGATGTATCTAGACGTATT 57.386 36.000 0.00 0.00 0.00 1.89
3332 13671 7.613551 AAAGGGGATGTATCTAGACGTATTT 57.386 36.000 0.00 0.00 0.00 1.40
3333 13672 7.613551 AAGGGGATGTATCTAGACGTATTTT 57.386 36.000 0.00 0.00 0.00 1.82
3334 13673 8.716674 AAGGGGATGTATCTAGACGTATTTTA 57.283 34.615 0.00 0.00 0.00 1.52
3335 13674 8.350852 AGGGGATGTATCTAGACGTATTTTAG 57.649 38.462 0.00 0.00 0.00 1.85
3336 13675 7.949006 AGGGGATGTATCTAGACGTATTTTAGT 59.051 37.037 0.00 0.00 0.00 2.24
3337 13676 8.583296 GGGGATGTATCTAGACGTATTTTAGTT 58.417 37.037 0.00 0.00 0.00 2.24
3338 13677 9.623350 GGGATGTATCTAGACGTATTTTAGTTC 57.377 37.037 0.00 0.00 0.00 3.01
3350 13689 9.623350 GACGTATTTTAGTTCTAGATACATCCC 57.377 37.037 0.00 0.00 0.00 3.85
3351 13690 9.364653 ACGTATTTTAGTTCTAGATACATCCCT 57.635 33.333 0.00 0.00 0.00 4.20
3360 13699 9.225682 AGTTCTAGATACATCCCTTTTTATCCA 57.774 33.333 0.00 0.00 0.00 3.41
3366 13705 9.713684 AGATACATCCCTTTTTATCCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
3369 13708 8.378115 ACATCCCTTTTTATCCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
3370 13709 8.260114 ACATCCCTTTTTATCCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
3371 13710 7.789202 TCCCTTTTTATCCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
3372 13711 8.200024 TCCCTTTTTATCCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
3373 13712 8.313292 TCCCTTTTTATCCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
3374 13713 8.096414 CCCTTTTTATCCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
3381 13720 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
3382 13721 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
3383 13722 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
3384 13723 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
3385 13724 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
3386 13725 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
3387 13726 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
3388 13727 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
3389 13728 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3390 13729 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3391 13730 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
3392 13731 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
3393 13732 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
3394 13733 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
3407 13746 6.583562 ACGGAGGGAGTATGAATTTAGAAAG 58.416 40.000 0.00 0.00 0.00 2.62
3546 14741 2.489722 GCTAAAGGGTCAAAGCTCAAGG 59.510 50.000 0.00 0.00 32.18 3.61
3625 14830 3.188460 TCAATCTAAACCTGCACTTTCGC 59.812 43.478 0.00 0.00 0.00 4.70
3699 14905 6.348050 GCACAAAGAGGAGTGAATAAGTTCAG 60.348 42.308 0.00 0.00 44.58 3.02
3816 15022 9.937175 GTCAAATGTTCTATATTCAAAGTAGGC 57.063 33.333 0.00 0.00 0.00 3.93
3818 15024 7.730364 AATGTTCTATATTCAAAGTAGGCCG 57.270 36.000 0.00 0.00 0.00 6.13
3819 15025 6.474140 TGTTCTATATTCAAAGTAGGCCGA 57.526 37.500 0.00 0.00 0.00 5.54
3836 15042 2.673368 GCCGATGTGTTGAGTTCCTTAG 59.327 50.000 0.00 0.00 0.00 2.18
3840 15046 5.643777 CCGATGTGTTGAGTTCCTTAGAAAT 59.356 40.000 0.00 0.00 32.58 2.17
3843 15049 6.539649 TGTGTTGAGTTCCTTAGAAATTCG 57.460 37.500 0.00 0.00 32.58 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.181904 ACAAAAAGAAATTCAGATAGGCAAGA 57.818 30.769 0.00 0.00 0.00 3.02
1 2 8.084073 TGACAAAAAGAAATTCAGATAGGCAAG 58.916 33.333 0.00 0.00 0.00 4.01
2 3 7.950512 TGACAAAAAGAAATTCAGATAGGCAA 58.049 30.769 0.00 0.00 0.00 4.52
3 4 7.448161 TCTGACAAAAAGAAATTCAGATAGGCA 59.552 33.333 0.00 0.00 38.20 4.75
11 12 8.256605 TGGTGAAATCTGACAAAAAGAAATTCA 58.743 29.630 0.00 0.00 34.15 2.57
12 13 8.647143 TGGTGAAATCTGACAAAAAGAAATTC 57.353 30.769 0.00 0.00 0.00 2.17
13 14 9.617523 AATGGTGAAATCTGACAAAAAGAAATT 57.382 25.926 0.00 0.00 0.00 1.82
14 15 9.048446 CAATGGTGAAATCTGACAAAAAGAAAT 57.952 29.630 0.00 0.00 0.00 2.17
15 16 8.040132 ACAATGGTGAAATCTGACAAAAAGAAA 58.960 29.630 0.00 0.00 0.00 2.52
16 17 7.555087 ACAATGGTGAAATCTGACAAAAAGAA 58.445 30.769 0.00 0.00 0.00 2.52
17 18 7.111247 ACAATGGTGAAATCTGACAAAAAGA 57.889 32.000 0.00 0.00 0.00 2.52
18 19 7.492020 TCAACAATGGTGAAATCTGACAAAAAG 59.508 33.333 0.00 0.00 0.00 2.27
19 20 7.326454 TCAACAATGGTGAAATCTGACAAAAA 58.674 30.769 0.00 0.00 0.00 1.94
20 21 6.871844 TCAACAATGGTGAAATCTGACAAAA 58.128 32.000 0.00 0.00 0.00 2.44
21 22 6.462552 TCAACAATGGTGAAATCTGACAAA 57.537 33.333 0.00 0.00 0.00 2.83
23 24 6.448852 CAATCAACAATGGTGAAATCTGACA 58.551 36.000 4.61 0.00 0.00 3.58
24 25 5.865552 CCAATCAACAATGGTGAAATCTGAC 59.134 40.000 4.61 0.00 31.84 3.51
25 26 6.028146 CCAATCAACAATGGTGAAATCTGA 57.972 37.500 4.61 0.00 31.84 3.27
35 36 8.564509 AATGGAAATAAACCAATCAACAATGG 57.435 30.769 0.00 0.00 40.93 3.16
104 105 8.876790 GCGGTTTACTTGTTCAATAGTAGTAAT 58.123 33.333 0.00 0.00 32.97 1.89
105 106 7.871973 TGCGGTTTACTTGTTCAATAGTAGTAA 59.128 33.333 0.00 0.00 31.48 2.24
106 107 7.377398 TGCGGTTTACTTGTTCAATAGTAGTA 58.623 34.615 0.00 0.00 0.00 1.82
107 108 6.225318 TGCGGTTTACTTGTTCAATAGTAGT 58.775 36.000 0.00 0.00 0.00 2.73
108 109 6.715344 TGCGGTTTACTTGTTCAATAGTAG 57.285 37.500 0.00 0.00 0.00 2.57
109 110 6.874664 TCATGCGGTTTACTTGTTCAATAGTA 59.125 34.615 0.00 0.00 0.00 1.82
110 111 5.703592 TCATGCGGTTTACTTGTTCAATAGT 59.296 36.000 0.00 0.00 0.00 2.12
113 114 4.518970 ACTCATGCGGTTTACTTGTTCAAT 59.481 37.500 0.00 0.00 0.00 2.57
114 115 3.880490 ACTCATGCGGTTTACTTGTTCAA 59.120 39.130 0.00 0.00 0.00 2.69
116 117 4.483476 AACTCATGCGGTTTACTTGTTC 57.517 40.909 0.00 0.00 0.00 3.18
118 119 4.134563 AGAAACTCATGCGGTTTACTTGT 58.865 39.130 13.74 0.00 37.07 3.16
120 121 3.432252 CGAGAAACTCATGCGGTTTACTT 59.568 43.478 13.74 6.07 37.07 2.24
121 122 2.993899 CGAGAAACTCATGCGGTTTACT 59.006 45.455 13.74 12.48 37.07 2.24
124 125 2.163818 TCGAGAAACTCATGCGGTTT 57.836 45.000 13.67 13.67 39.25 3.27
126 127 2.386661 ATTCGAGAAACTCATGCGGT 57.613 45.000 0.00 0.00 0.00 5.68
128 129 5.858475 ACTTAAATTCGAGAAACTCATGCG 58.142 37.500 0.00 0.00 0.00 4.73
129 130 9.607285 TTTAACTTAAATTCGAGAAACTCATGC 57.393 29.630 0.00 0.00 0.00 4.06
132 133 8.562052 GGGTTTAACTTAAATTCGAGAAACTCA 58.438 33.333 0.00 0.00 0.00 3.41
133 134 8.562052 TGGGTTTAACTTAAATTCGAGAAACTC 58.438 33.333 0.00 0.00 0.00 3.01
134 135 8.454570 TGGGTTTAACTTAAATTCGAGAAACT 57.545 30.769 0.00 0.00 0.00 2.66
135 136 9.124807 CATGGGTTTAACTTAAATTCGAGAAAC 57.875 33.333 0.00 0.00 0.00 2.78
136 137 7.810759 GCATGGGTTTAACTTAAATTCGAGAAA 59.189 33.333 0.00 0.00 0.00 2.52
137 138 7.309920 GCATGGGTTTAACTTAAATTCGAGAA 58.690 34.615 0.00 0.00 0.00 2.87
139 140 5.737290 CGCATGGGTTTAACTTAAATTCGAG 59.263 40.000 0.68 0.00 0.00 4.04
140 141 5.181622 ACGCATGGGTTTAACTTAAATTCGA 59.818 36.000 10.03 0.00 0.00 3.71
141 142 5.285134 CACGCATGGGTTTAACTTAAATTCG 59.715 40.000 13.50 0.00 0.00 3.34
142 143 5.061684 GCACGCATGGGTTTAACTTAAATTC 59.938 40.000 13.50 0.00 0.00 2.17
143 144 4.926832 GCACGCATGGGTTTAACTTAAATT 59.073 37.500 13.50 0.00 0.00 1.82
144 145 4.219725 AGCACGCATGGGTTTAACTTAAAT 59.780 37.500 13.50 0.00 0.00 1.40
145 146 3.570550 AGCACGCATGGGTTTAACTTAAA 59.429 39.130 13.50 0.00 0.00 1.52
147 148 2.785562 AGCACGCATGGGTTTAACTTA 58.214 42.857 13.50 0.00 0.00 2.24
148 149 1.616159 AGCACGCATGGGTTTAACTT 58.384 45.000 13.50 0.00 0.00 2.66
150 151 3.562567 TTTAGCACGCATGGGTTTAAC 57.437 42.857 13.50 3.44 0.00 2.01
151 152 4.585955 TTTTTAGCACGCATGGGTTTAA 57.414 36.364 13.50 11.78 0.00 1.52
152 153 4.792521 ATTTTTAGCACGCATGGGTTTA 57.207 36.364 13.50 6.26 0.00 2.01
153 154 3.676291 ATTTTTAGCACGCATGGGTTT 57.324 38.095 13.50 7.26 0.00 3.27
154 155 3.676291 AATTTTTAGCACGCATGGGTT 57.324 38.095 13.50 2.26 0.00 4.11
155 156 3.584834 GAAATTTTTAGCACGCATGGGT 58.415 40.909 10.03 10.03 0.00 4.51
156 157 2.929398 GGAAATTTTTAGCACGCATGGG 59.071 45.455 8.44 8.44 0.00 4.00
157 158 2.929398 GGGAAATTTTTAGCACGCATGG 59.071 45.455 0.00 0.00 0.00 3.66
158 159 2.598192 CGGGAAATTTTTAGCACGCATG 59.402 45.455 0.00 0.00 0.00 4.06
159 160 2.874849 CGGGAAATTTTTAGCACGCAT 58.125 42.857 0.00 0.00 0.00 4.73
160 161 1.667467 GCGGGAAATTTTTAGCACGCA 60.667 47.619 16.61 0.00 44.52 5.24
161 162 0.989164 GCGGGAAATTTTTAGCACGC 59.011 50.000 8.26 8.26 38.94 5.34
163 164 1.992667 GCTGCGGGAAATTTTTAGCAC 59.007 47.619 10.10 5.83 0.00 4.40
165 166 2.362169 TGCTGCGGGAAATTTTTAGC 57.638 45.000 0.00 0.00 0.00 3.09
166 167 2.661195 CGTTGCTGCGGGAAATTTTTAG 59.339 45.455 0.00 0.00 0.00 1.85
167 168 2.667137 CGTTGCTGCGGGAAATTTTTA 58.333 42.857 0.00 0.00 0.00 1.52
169 170 0.943835 GCGTTGCTGCGGGAAATTTT 60.944 50.000 0.00 0.00 0.00 1.82
170 171 1.372872 GCGTTGCTGCGGGAAATTT 60.373 52.632 0.00 0.00 0.00 1.82
171 172 2.258286 GCGTTGCTGCGGGAAATT 59.742 55.556 0.00 0.00 0.00 1.82
181 182 3.943479 TAACATCCCGCGCGTTGCT 62.943 57.895 29.95 16.19 43.27 3.91
182 183 2.695712 GATAACATCCCGCGCGTTGC 62.696 60.000 29.95 8.80 41.47 4.17
183 184 1.151777 AGATAACATCCCGCGCGTTG 61.152 55.000 29.95 23.61 0.00 4.10
184 185 0.386476 TAGATAACATCCCGCGCGTT 59.614 50.000 29.95 18.17 0.00 4.84
185 186 0.039437 CTAGATAACATCCCGCGCGT 60.039 55.000 29.95 11.67 0.00 6.01
187 188 2.150397 AACTAGATAACATCCCGCGC 57.850 50.000 0.00 0.00 0.00 6.86
188 189 4.227538 CTGTAACTAGATAACATCCCGCG 58.772 47.826 0.00 0.00 0.00 6.46
189 190 4.280174 TCCTGTAACTAGATAACATCCCGC 59.720 45.833 0.00 0.00 0.00 6.13
190 191 5.535406 ACTCCTGTAACTAGATAACATCCCG 59.465 44.000 0.00 0.00 0.00 5.14
191 192 6.980416 ACTCCTGTAACTAGATAACATCCC 57.020 41.667 0.00 0.00 0.00 3.85
194 195 9.696572 TGTAGAACTCCTGTAACTAGATAACAT 57.303 33.333 0.00 0.00 0.00 2.71
195 196 9.524496 TTGTAGAACTCCTGTAACTAGATAACA 57.476 33.333 0.00 0.00 0.00 2.41
199 200 8.027771 CGTTTTGTAGAACTCCTGTAACTAGAT 58.972 37.037 0.00 0.00 0.00 1.98
200 201 7.365741 CGTTTTGTAGAACTCCTGTAACTAGA 58.634 38.462 0.00 0.00 0.00 2.43
202 203 6.265196 TCCGTTTTGTAGAACTCCTGTAACTA 59.735 38.462 0.00 0.00 0.00 2.24
203 204 5.069516 TCCGTTTTGTAGAACTCCTGTAACT 59.930 40.000 0.00 0.00 0.00 2.24
204 205 5.291971 TCCGTTTTGTAGAACTCCTGTAAC 58.708 41.667 0.00 0.00 0.00 2.50
205 206 5.534207 TCCGTTTTGTAGAACTCCTGTAA 57.466 39.130 0.00 0.00 0.00 2.41
206 207 5.534207 TTCCGTTTTGTAGAACTCCTGTA 57.466 39.130 0.00 0.00 0.00 2.74
207 208 4.411256 TTCCGTTTTGTAGAACTCCTGT 57.589 40.909 0.00 0.00 0.00 4.00
208 209 5.277828 CCTTTTCCGTTTTGTAGAACTCCTG 60.278 44.000 0.00 0.00 0.00 3.86
209 210 4.820173 CCTTTTCCGTTTTGTAGAACTCCT 59.180 41.667 0.00 0.00 0.00 3.69
210 211 4.818005 TCCTTTTCCGTTTTGTAGAACTCC 59.182 41.667 0.00 0.00 0.00 3.85
211 212 5.049612 CCTCCTTTTCCGTTTTGTAGAACTC 60.050 44.000 0.00 0.00 0.00 3.01
212 213 4.820173 CCTCCTTTTCCGTTTTGTAGAACT 59.180 41.667 0.00 0.00 0.00 3.01
213 214 4.818005 TCCTCCTTTTCCGTTTTGTAGAAC 59.182 41.667 0.00 0.00 0.00 3.01
214 215 5.038651 TCCTCCTTTTCCGTTTTGTAGAA 57.961 39.130 0.00 0.00 0.00 2.10
215 216 4.504340 CCTCCTCCTTTTCCGTTTTGTAGA 60.504 45.833 0.00 0.00 0.00 2.59
216 217 3.751698 CCTCCTCCTTTTCCGTTTTGTAG 59.248 47.826 0.00 0.00 0.00 2.74
217 218 3.746940 CCTCCTCCTTTTCCGTTTTGTA 58.253 45.455 0.00 0.00 0.00 2.41
390 4125 0.833834 CCTCATAGGCGGTCCCTCAT 60.834 60.000 0.00 0.00 44.96 2.90
391 4126 1.457643 CCTCATAGGCGGTCCCTCA 60.458 63.158 0.00 0.00 44.96 3.86
392 4127 0.543174 ATCCTCATAGGCGGTCCCTC 60.543 60.000 0.00 0.00 44.96 4.30
394 4129 0.896226 GTATCCTCATAGGCGGTCCC 59.104 60.000 0.00 0.00 34.61 4.46
395 4130 1.546476 CTGTATCCTCATAGGCGGTCC 59.454 57.143 0.00 0.00 34.61 4.46
396 4131 2.229302 GTCTGTATCCTCATAGGCGGTC 59.771 54.545 0.00 0.00 34.61 4.79
397 4132 2.240279 GTCTGTATCCTCATAGGCGGT 58.760 52.381 0.00 0.00 34.61 5.68
398 4133 1.546476 GGTCTGTATCCTCATAGGCGG 59.454 57.143 0.00 0.00 34.61 6.13
399 4134 2.239400 TGGTCTGTATCCTCATAGGCG 58.761 52.381 0.00 0.00 34.61 5.52
400 4135 4.772624 TGTATGGTCTGTATCCTCATAGGC 59.227 45.833 0.00 0.00 34.61 3.93
401 4136 6.249192 TCTGTATGGTCTGTATCCTCATAGG 58.751 44.000 0.00 0.00 36.46 2.57
402 4137 6.945435 ACTCTGTATGGTCTGTATCCTCATAG 59.055 42.308 0.00 0.00 0.00 2.23
403 4138 6.853490 ACTCTGTATGGTCTGTATCCTCATA 58.147 40.000 0.00 0.00 0.00 2.15
404 4139 5.710646 ACTCTGTATGGTCTGTATCCTCAT 58.289 41.667 0.00 0.00 0.00 2.90
405 4140 5.130705 ACTCTGTATGGTCTGTATCCTCA 57.869 43.478 0.00 0.00 0.00 3.86
477 4213 1.029681 TCAGTGTACTGTGACAGCGT 58.970 50.000 13.37 0.00 44.12 5.07
661 4409 0.537371 GATTAATCCCTGGCACCCGG 60.537 60.000 3.92 0.00 0.00 5.73
662 4410 0.474184 AGATTAATCCCTGGCACCCG 59.526 55.000 11.92 0.00 0.00 5.28
663 4411 1.986882 CAGATTAATCCCTGGCACCC 58.013 55.000 11.92 0.00 0.00 4.61
797 4575 2.735444 GCTAGTGACGCATGCTCTAACA 60.735 50.000 17.13 5.66 0.00 2.41
912 4706 1.466167 CAATGGCAGCTGTAGTGTGTC 59.534 52.381 16.64 0.00 0.00 3.67
997 4795 0.036010 CTTCCTGCGAAGGTCATGGT 60.036 55.000 9.98 0.00 41.66 3.55
1593 11882 6.823689 TCTCTGGAGGCAATTTACAATAGTTC 59.176 38.462 0.00 0.00 0.00 3.01
1599 11888 4.908601 TCTCTCTGGAGGCAATTTACAA 57.091 40.909 0.00 0.00 39.86 2.41
1744 12050 3.099267 ACGTCAACCAGATATAGCTGC 57.901 47.619 12.62 0.00 34.56 5.25
2399 12722 1.445716 GCAGGATCATGAGCTGTGGC 61.446 60.000 12.39 5.99 39.06 5.01
2627 12950 2.756840 TCTGCACCTCATCTCTTGTG 57.243 50.000 0.00 0.00 0.00 3.33
2675 13005 2.202851 ATCTCTTCTGCAGCCGCG 60.203 61.111 9.47 0.00 42.97 6.46
3270 13609 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
3271 13610 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3272 13611 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3273 13612 1.935933 CAAGTATTTCCGGACGGAGG 58.064 55.000 13.64 0.00 46.06 4.30
3274 13613 1.287425 GCAAGTATTTCCGGACGGAG 58.713 55.000 13.64 1.75 46.06 4.63
3275 13614 0.108041 GGCAAGTATTTCCGGACGGA 60.108 55.000 1.83 9.76 43.52 4.69
3276 13615 0.391927 TGGCAAGTATTTCCGGACGG 60.392 55.000 1.83 3.96 0.00 4.79
3277 13616 1.597663 GATGGCAAGTATTTCCGGACG 59.402 52.381 1.83 0.00 0.00 4.79
3278 13617 2.639065 TGATGGCAAGTATTTCCGGAC 58.361 47.619 1.83 0.00 0.00 4.79
3279 13618 3.358111 TTGATGGCAAGTATTTCCGGA 57.642 42.857 0.00 0.00 0.00 5.14
3280 13619 4.448537 TTTTGATGGCAAGTATTTCCGG 57.551 40.909 0.00 0.00 35.04 5.14
3281 13620 5.649557 TCATTTTGATGGCAAGTATTTCCG 58.350 37.500 0.00 0.00 35.04 4.30
3282 13621 9.598517 TTATTCATTTTGATGGCAAGTATTTCC 57.401 29.630 0.00 0.00 35.04 3.13
3286 13625 9.603921 CCTTTTATTCATTTTGATGGCAAGTAT 57.396 29.630 0.00 0.00 35.04 2.12
3287 13626 8.040132 CCCTTTTATTCATTTTGATGGCAAGTA 58.960 33.333 0.00 0.00 35.04 2.24
3288 13627 6.880529 CCCTTTTATTCATTTTGATGGCAAGT 59.119 34.615 0.00 0.00 35.04 3.16
3289 13628 6.316890 CCCCTTTTATTCATTTTGATGGCAAG 59.683 38.462 0.00 0.00 35.04 4.01
3290 13629 6.013032 TCCCCTTTTATTCATTTTGATGGCAA 60.013 34.615 0.00 0.00 0.00 4.52
3291 13630 5.486775 TCCCCTTTTATTCATTTTGATGGCA 59.513 36.000 0.00 0.00 0.00 4.92
3292 13631 5.988287 TCCCCTTTTATTCATTTTGATGGC 58.012 37.500 0.00 0.00 0.00 4.40
3293 13632 7.567458 ACATCCCCTTTTATTCATTTTGATGG 58.433 34.615 0.00 0.00 32.31 3.51
3296 13635 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
3301 13640 8.314751 CGTCTAGATACATCCCCTTTTATTCAT 58.685 37.037 0.00 0.00 0.00 2.57
3302 13641 7.289317 ACGTCTAGATACATCCCCTTTTATTCA 59.711 37.037 0.00 0.00 0.00 2.57
3303 13642 7.668492 ACGTCTAGATACATCCCCTTTTATTC 58.332 38.462 0.00 0.00 0.00 1.75
3304 13643 7.613551 ACGTCTAGATACATCCCCTTTTATT 57.386 36.000 0.00 0.00 0.00 1.40
3305 13644 8.896722 ATACGTCTAGATACATCCCCTTTTAT 57.103 34.615 0.00 0.00 0.00 1.40
3306 13645 8.716674 AATACGTCTAGATACATCCCCTTTTA 57.283 34.615 0.00 0.00 0.00 1.52
3307 13646 7.613551 AATACGTCTAGATACATCCCCTTTT 57.386 36.000 0.00 0.00 0.00 2.27
3308 13647 7.613551 AAATACGTCTAGATACATCCCCTTT 57.386 36.000 0.00 0.00 0.00 3.11
3309 13648 7.613551 AAAATACGTCTAGATACATCCCCTT 57.386 36.000 0.00 0.00 0.00 3.95
3310 13649 7.949006 ACTAAAATACGTCTAGATACATCCCCT 59.051 37.037 0.00 0.00 0.00 4.79
3311 13650 8.120140 ACTAAAATACGTCTAGATACATCCCC 57.880 38.462 0.00 0.00 0.00 4.81
3312 13651 9.623350 GAACTAAAATACGTCTAGATACATCCC 57.377 37.037 0.00 0.00 0.00 3.85
3324 13663 9.623350 GGGATGTATCTAGAACTAAAATACGTC 57.377 37.037 17.13 17.13 37.78 4.34
3325 13664 9.364653 AGGGATGTATCTAGAACTAAAATACGT 57.635 33.333 0.00 0.00 0.00 3.57
3334 13673 9.225682 TGGATAAAAAGGGATGTATCTAGAACT 57.774 33.333 0.00 0.00 0.00 3.01
3340 13679 9.713684 TCAAAATGGATAAAAAGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
3343 13682 9.486123 TCATCAAAATGGATAAAAAGGGATGTA 57.514 29.630 0.00 0.00 33.42 2.29
3344 13683 8.260114 GTCATCAAAATGGATAAAAAGGGATGT 58.740 33.333 0.00 0.00 33.42 3.06
3345 13684 8.259411 TGTCATCAAAATGGATAAAAAGGGATG 58.741 33.333 0.00 0.00 33.42 3.51
3346 13685 8.378115 TGTCATCAAAATGGATAAAAAGGGAT 57.622 30.769 0.00 0.00 33.42 3.85
3347 13686 7.789202 TGTCATCAAAATGGATAAAAAGGGA 57.211 32.000 0.00 0.00 33.42 4.20
3348 13687 8.096414 ACTTGTCATCAAAATGGATAAAAAGGG 58.904 33.333 0.00 0.00 33.42 3.95
3356 13695 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
3357 13696 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
3358 13697 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
3359 13698 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
3360 13699 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
3361 13700 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
3362 13701 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
3363 13702 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
3364 13703 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
3365 13704 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
3366 13705 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
3367 13706 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3368 13707 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3369 13708 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3370 13709 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3371 13710 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
3372 13711 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
3373 13712 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
3374 13713 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
3375 13714 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
3376 13715 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
3377 13716 1.108776 CATACTCCCTCCGTCCGAAA 58.891 55.000 0.00 0.00 0.00 3.46
3378 13717 0.256752 TCATACTCCCTCCGTCCGAA 59.743 55.000 0.00 0.00 0.00 4.30
3379 13718 0.256752 TTCATACTCCCTCCGTCCGA 59.743 55.000 0.00 0.00 0.00 4.55
3380 13719 1.329256 ATTCATACTCCCTCCGTCCG 58.671 55.000 0.00 0.00 0.00 4.79
3381 13720 3.840124 AAATTCATACTCCCTCCGTCC 57.160 47.619 0.00 0.00 0.00 4.79
3382 13721 5.786264 TCTAAATTCATACTCCCTCCGTC 57.214 43.478 0.00 0.00 0.00 4.79
3383 13722 6.156429 ACTTTCTAAATTCATACTCCCTCCGT 59.844 38.462 0.00 0.00 0.00 4.69
3384 13723 6.583562 ACTTTCTAAATTCATACTCCCTCCG 58.416 40.000 0.00 0.00 0.00 4.63
3407 13746 4.994852 TCACACTGCTAGGTCAAACATAAC 59.005 41.667 0.00 0.00 0.00 1.89
3419 13758 5.422666 TTTCATGTTTGTCACACTGCTAG 57.577 39.130 0.00 0.00 38.61 3.42
3546 14741 4.708726 AACAATAGATTTGCTCACTGGC 57.291 40.909 0.00 0.00 0.00 4.85
3699 14905 9.083080 GCTTTTATTATTACACCATGGTTTCAC 57.917 33.333 16.84 0.00 0.00 3.18
3700 14906 8.807118 TGCTTTTATTATTACACCATGGTTTCA 58.193 29.630 16.84 0.00 0.00 2.69
3816 15022 4.188247 TCTAAGGAACTCAACACATCGG 57.812 45.455 0.00 0.00 38.49 4.18
3818 15024 7.117812 TCGAATTTCTAAGGAACTCAACACATC 59.882 37.037 0.00 0.00 38.49 3.06
3819 15025 6.934645 TCGAATTTCTAAGGAACTCAACACAT 59.065 34.615 0.00 0.00 38.49 3.21


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

AutoCloner maintained by Alex Coulton.