Multiple sequence alignment - TraesCS7B01G180200

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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 TraesCS7B01G180200 chr7B 100.000 2390 0 0 1 2390 269254535 269256924 0.000000e+00 4414
1 TraesCS7B01G180200 chr2D 91.574 1163 96 2 343 1504 106920675 106921836 0.000000e+00 1604
2 TraesCS7B01G180200 chr2D 91.041 1172 89 9 343 1500 229831525 229832694 0.000000e+00 1568
3 TraesCS7B01G180200 chr2D 86.857 350 45 1 1 349 454177206 454176857 8.010000e-105 390
4 TraesCS7B01G180200 chr2D 86.857 350 45 1 1 349 642579580 642579929 8.010000e-105 390
5 TraesCS7B01G180200 chr2D 86.286 350 47 1 1 349 431238840 431239189 1.730000e-101 379
6 TraesCS7B01G180200 chr6B 90.660 1167 101 5 343 1505 340309146 340310308 0.000000e+00 1544
7 TraesCS7B01G180200 chr6B 90.178 1069 98 5 343 1407 402311848 402310783 0.000000e+00 1386
8 TraesCS7B01G180200 chr7A 88.412 1165 128 7 343 1504 529984515 529983355 0.000000e+00 1397
9 TraesCS7B01G180200 chr7A 88.017 1160 130 8 343 1499 469330350 469329197 0.000000e+00 1363
10 TraesCS7B01G180200 chr5D 91.892 888 68 4 1504 2390 211853619 211852735 0.000000e+00 1238
11 TraesCS7B01G180200 chr7D 91.789 889 67 6 1504 2390 442339451 442338567 0.000000e+00 1232
12 TraesCS7B01G180200 chr7D 91.564 889 71 4 1504 2390 406500842 406499956 0.000000e+00 1223
13 TraesCS7B01G180200 chr7D 91.564 889 70 4 1504 2390 301952894 301953779 0.000000e+00 1221
14 TraesCS7B01G180200 chr6D 91.676 889 70 4 1504 2390 59515851 59514965 0.000000e+00 1229
15 TraesCS7B01G180200 chr6D 91.564 889 71 4 1504 2390 299467214 299468100 0.000000e+00 1223
16 TraesCS7B01G180200 chr6D 91.470 891 69 7 1504 2390 105050328 105049441 0.000000e+00 1218
17 TraesCS7B01G180200 chr6D 91.298 678 58 1 836 1513 454182444 454181768 0.000000e+00 924
18 TraesCS7B01G180200 chr6D 88.623 501 52 5 343 840 454186015 454185517 2.630000e-169 604
19 TraesCS7B01G180200 chr6D 86.000 350 48 1 1 349 217375388 217375737 8.070000e-100 374
20 TraesCS7B01G180200 chr6D 86.000 350 48 1 1 349 410368052 410367703 8.070000e-100 374
21 TraesCS7B01G180200 chr3D 91.676 889 70 4 1504 2390 175122425 175123311 0.000000e+00 1229
22 TraesCS7B01G180200 chr3D 88.148 675 76 4 829 1501 427089250 427088578 0.000000e+00 800
23 TraesCS7B01G180200 chr3D 87.320 347 42 2 5 349 336668757 336668411 1.720000e-106 396
24 TraesCS7B01G180200 chr1D 91.676 889 70 4 1504 2390 422229451 422230337 0.000000e+00 1229
25 TraesCS7B01G180200 chr3B 89.568 671 69 1 343 1012 372153802 372154472 0.000000e+00 850
26 TraesCS7B01G180200 chr3B 88.296 675 68 9 829 1500 556719552 556718886 0.000000e+00 798
27 TraesCS7B01G180200 chr3B 86.000 350 48 1 1 349 222571867 222572216 8.070000e-100 374
28 TraesCS7B01G180200 chr1B 88.869 548 59 2 343 889 271835494 271834948 0.000000e+00 673
29 TraesCS7B01G180200 chr4D 87.429 350 43 1 1 349 90155402 90155053 3.700000e-108 401
30 TraesCS7B01G180200 chr4D 86.857 350 45 1 1 349 92375887 92375538 8.010000e-105 390


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 TraesCS7B01G180200 chr7B 269254535 269256924 2389 False 4414 4414 100.0000 1 2390 1 chr7B.!!$F1 2389
1 TraesCS7B01G180200 chr2D 106920675 106921836 1161 False 1604 1604 91.5740 343 1504 1 chr2D.!!$F1 1161
2 TraesCS7B01G180200 chr2D 229831525 229832694 1169 False 1568 1568 91.0410 343 1500 1 chr2D.!!$F2 1157
3 TraesCS7B01G180200 chr6B 340309146 340310308 1162 False 1544 1544 90.6600 343 1505 1 chr6B.!!$F1 1162
4 TraesCS7B01G180200 chr6B 402310783 402311848 1065 True 1386 1386 90.1780 343 1407 1 chr6B.!!$R1 1064
5 TraesCS7B01G180200 chr7A 529983355 529984515 1160 True 1397 1397 88.4120 343 1504 1 chr7A.!!$R2 1161
6 TraesCS7B01G180200 chr7A 469329197 469330350 1153 True 1363 1363 88.0170 343 1499 1 chr7A.!!$R1 1156
7 TraesCS7B01G180200 chr5D 211852735 211853619 884 True 1238 1238 91.8920 1504 2390 1 chr5D.!!$R1 886
8 TraesCS7B01G180200 chr7D 442338567 442339451 884 True 1232 1232 91.7890 1504 2390 1 chr7D.!!$R2 886
9 TraesCS7B01G180200 chr7D 406499956 406500842 886 True 1223 1223 91.5640 1504 2390 1 chr7D.!!$R1 886
10 TraesCS7B01G180200 chr7D 301952894 301953779 885 False 1221 1221 91.5640 1504 2390 1 chr7D.!!$F1 886
11 TraesCS7B01G180200 chr6D 59514965 59515851 886 True 1229 1229 91.6760 1504 2390 1 chr6D.!!$R1 886
12 TraesCS7B01G180200 chr6D 299467214 299468100 886 False 1223 1223 91.5640 1504 2390 1 chr6D.!!$F2 886
13 TraesCS7B01G180200 chr6D 105049441 105050328 887 True 1218 1218 91.4700 1504 2390 1 chr6D.!!$R2 886
14 TraesCS7B01G180200 chr6D 454181768 454186015 4247 True 764 924 89.9605 343 1513 2 chr6D.!!$R4 1170
15 TraesCS7B01G180200 chr3D 175122425 175123311 886 False 1229 1229 91.6760 1504 2390 1 chr3D.!!$F1 886
16 TraesCS7B01G180200 chr3D 427088578 427089250 672 True 800 800 88.1480 829 1501 1 chr3D.!!$R2 672
17 TraesCS7B01G180200 chr1D 422229451 422230337 886 False 1229 1229 91.6760 1504 2390 1 chr1D.!!$F1 886
18 TraesCS7B01G180200 chr3B 372153802 372154472 670 False 850 850 89.5680 343 1012 1 chr3B.!!$F2 669
19 TraesCS7B01G180200 chr3B 556718886 556719552 666 True 798 798 88.2960 829 1500 1 chr3B.!!$R1 671
20 TraesCS7B01G180200 chr1B 271834948 271835494 546 True 673 673 88.8690 343 889 1 chr1B.!!$R1 546

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
234 235 0.105964 TGTGTCTCCCGTTTCTGTGG 59.894 55.0 0.0 0.0 0.00 4.17 F
247 248 0.178767 TCTGTGGCCGAGATTCCATG 59.821 55.0 0.0 0.0 34.47 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1049 4137 0.390340 TTCCTCGTGAGCAGTGCATC 60.390 55.000 19.20 12.27 0.0 3.91 R
2172 5276 1.000717 CAACCATTTTGTCCACCGGTC 60.001 52.381 2.59 0.00 0.0 4.79 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
17 18 4.280019 AAGTCGGTTGGGTGGCCC 62.280 66.667 0.00 0.00 45.71 5.80
33 34 2.753043 CCGCCAAGCCTGCAGAAT 60.753 61.111 17.39 0.00 0.00 2.40
34 35 1.451927 CCGCCAAGCCTGCAGAATA 60.452 57.895 17.39 0.00 0.00 1.75
35 36 1.718757 CCGCCAAGCCTGCAGAATAC 61.719 60.000 17.39 1.25 0.00 1.89
36 37 1.723870 GCCAAGCCTGCAGAATACG 59.276 57.895 17.39 0.00 0.00 3.06
37 38 0.744414 GCCAAGCCTGCAGAATACGA 60.744 55.000 17.39 0.00 0.00 3.43
38 39 1.293924 CCAAGCCTGCAGAATACGAG 58.706 55.000 17.39 0.00 0.00 4.18
39 40 0.654683 CAAGCCTGCAGAATACGAGC 59.345 55.000 17.39 8.12 0.00 5.03
40 41 0.539051 AAGCCTGCAGAATACGAGCT 59.461 50.000 17.39 10.59 0.00 4.09
41 42 1.403814 AGCCTGCAGAATACGAGCTA 58.596 50.000 17.39 0.00 0.00 3.32
42 43 1.967066 AGCCTGCAGAATACGAGCTAT 59.033 47.619 17.39 0.00 0.00 2.97
43 44 2.064762 GCCTGCAGAATACGAGCTATG 58.935 52.381 17.39 0.00 0.00 2.23
44 45 2.064762 CCTGCAGAATACGAGCTATGC 58.935 52.381 17.39 0.00 0.00 3.14
45 46 2.546584 CCTGCAGAATACGAGCTATGCA 60.547 50.000 17.39 0.00 41.05 3.96
46 47 2.747436 TGCAGAATACGAGCTATGCAG 58.253 47.619 0.00 0.00 38.64 4.41
63 64 2.601664 AGCTCACTGATCCACCTCC 58.398 57.895 0.00 0.00 0.00 4.30
64 65 0.980231 AGCTCACTGATCCACCTCCC 60.980 60.000 0.00 0.00 0.00 4.30
65 66 0.980231 GCTCACTGATCCACCTCCCT 60.980 60.000 0.00 0.00 0.00 4.20
66 67 1.118838 CTCACTGATCCACCTCCCTC 58.881 60.000 0.00 0.00 0.00 4.30
67 68 0.325671 TCACTGATCCACCTCCCTCC 60.326 60.000 0.00 0.00 0.00 4.30
68 69 1.003573 ACTGATCCACCTCCCTCCC 59.996 63.158 0.00 0.00 0.00 4.30
69 70 1.003442 CTGATCCACCTCCCTCCCA 59.997 63.158 0.00 0.00 0.00 4.37
70 71 0.401105 CTGATCCACCTCCCTCCCAT 60.401 60.000 0.00 0.00 0.00 4.00
71 72 0.400525 TGATCCACCTCCCTCCCATC 60.401 60.000 0.00 0.00 0.00 3.51
72 73 0.400525 GATCCACCTCCCTCCCATCA 60.401 60.000 0.00 0.00 0.00 3.07
73 74 0.695803 ATCCACCTCCCTCCCATCAC 60.696 60.000 0.00 0.00 0.00 3.06
74 75 1.307343 CCACCTCCCTCCCATCACT 60.307 63.158 0.00 0.00 0.00 3.41
75 76 1.341156 CCACCTCCCTCCCATCACTC 61.341 65.000 0.00 0.00 0.00 3.51
76 77 1.381872 ACCTCCCTCCCATCACTCG 60.382 63.158 0.00 0.00 0.00 4.18
77 78 1.075970 CCTCCCTCCCATCACTCGA 60.076 63.158 0.00 0.00 0.00 4.04
78 79 1.395826 CCTCCCTCCCATCACTCGAC 61.396 65.000 0.00 0.00 0.00 4.20
79 80 1.729470 CTCCCTCCCATCACTCGACG 61.729 65.000 0.00 0.00 0.00 5.12
80 81 2.786495 CCCTCCCATCACTCGACGG 61.786 68.421 0.00 0.00 0.00 4.79
81 82 1.753078 CCTCCCATCACTCGACGGA 60.753 63.158 0.00 0.00 0.00 4.69
82 83 1.729470 CCTCCCATCACTCGACGGAG 61.729 65.000 0.00 0.00 46.13 4.63
83 84 2.105128 CCCATCACTCGACGGAGC 59.895 66.667 0.00 0.00 44.48 4.70
84 85 2.105128 CCATCACTCGACGGAGCC 59.895 66.667 0.00 0.00 44.48 4.70
85 86 2.710902 CCATCACTCGACGGAGCCA 61.711 63.158 0.00 0.00 44.48 4.75
86 87 1.226802 CATCACTCGACGGAGCCAG 60.227 63.158 0.00 0.00 44.48 4.85
87 88 1.679305 ATCACTCGACGGAGCCAGT 60.679 57.895 0.00 0.00 44.48 4.00
88 89 1.251527 ATCACTCGACGGAGCCAGTT 61.252 55.000 0.00 0.00 44.48 3.16
89 90 1.444553 CACTCGACGGAGCCAGTTC 60.445 63.158 0.00 0.00 44.48 3.01
90 91 2.182030 CTCGACGGAGCCAGTTCC 59.818 66.667 0.00 0.00 32.61 3.62
91 92 3.358076 CTCGACGGAGCCAGTTCCC 62.358 68.421 0.00 0.00 33.46 3.97
101 102 4.351054 CAGTTCCCGCCCCAAGCT 62.351 66.667 0.00 0.00 40.39 3.74
102 103 4.351054 AGTTCCCGCCCCAAGCTG 62.351 66.667 0.00 0.00 40.39 4.24
113 114 4.748679 CAAGCTGGCGCGCAGTTC 62.749 66.667 34.42 16.23 42.32 3.01
120 121 4.017877 GCGCGCAGTTCAGCAACT 62.018 61.111 29.10 0.00 44.26 3.16
121 122 2.171940 CGCGCAGTTCAGCAACTC 59.828 61.111 8.75 0.00 41.24 3.01
122 123 2.171940 GCGCAGTTCAGCAACTCG 59.828 61.111 0.30 0.00 41.24 4.18
123 124 2.171940 CGCAGTTCAGCAACTCGC 59.828 61.111 0.00 0.00 41.24 5.03
132 133 3.123620 GCAACTCGCTGCTCCAGG 61.124 66.667 0.00 0.00 39.34 4.45
133 134 3.123620 CAACTCGCTGCTCCAGGC 61.124 66.667 0.00 0.00 42.22 4.85
134 135 4.400961 AACTCGCTGCTCCAGGCC 62.401 66.667 0.00 0.00 40.92 5.19
136 137 4.834453 CTCGCTGCTCCAGGCCAG 62.834 72.222 5.01 0.00 40.92 4.85
140 141 3.714001 CTGCTCCAGGCCAGCTCA 61.714 66.667 14.14 0.42 40.92 4.26
141 142 3.251509 TGCTCCAGGCCAGCTCAA 61.252 61.111 14.14 0.00 40.92 3.02
142 143 2.749441 GCTCCAGGCCAGCTCAAC 60.749 66.667 5.01 0.00 33.75 3.18
143 144 2.752358 CTCCAGGCCAGCTCAACA 59.248 61.111 5.01 0.00 0.00 3.33
144 145 1.073722 CTCCAGGCCAGCTCAACAA 59.926 57.895 5.01 0.00 0.00 2.83
145 146 0.959372 CTCCAGGCCAGCTCAACAAG 60.959 60.000 5.01 0.00 0.00 3.16
146 147 1.975407 CCAGGCCAGCTCAACAAGG 60.975 63.158 5.01 0.00 0.00 3.61
147 148 1.073722 CAGGCCAGCTCAACAAGGA 59.926 57.895 5.01 0.00 0.00 3.36
148 149 0.959372 CAGGCCAGCTCAACAAGGAG 60.959 60.000 5.01 0.00 37.97 3.69
149 150 1.073897 GGCCAGCTCAACAAGGAGT 59.926 57.895 0.00 0.00 37.24 3.85
150 151 1.239968 GGCCAGCTCAACAAGGAGTG 61.240 60.000 0.00 0.00 37.24 3.51
151 152 1.239968 GCCAGCTCAACAAGGAGTGG 61.240 60.000 0.00 0.00 38.25 4.00
152 153 1.239968 CCAGCTCAACAAGGAGTGGC 61.240 60.000 0.00 0.00 37.24 5.01
153 154 0.535780 CAGCTCAACAAGGAGTGGCA 60.536 55.000 0.00 0.00 37.24 4.92
154 155 0.536006 AGCTCAACAAGGAGTGGCAC 60.536 55.000 10.29 10.29 37.24 5.01
155 156 0.819259 GCTCAACAAGGAGTGGCACA 60.819 55.000 21.41 0.00 37.24 4.57
177 178 2.180769 CGTCGTCGCTTCCATCCA 59.819 61.111 0.00 0.00 0.00 3.41
178 179 1.226974 CGTCGTCGCTTCCATCCAT 60.227 57.895 0.00 0.00 0.00 3.41
179 180 1.482621 CGTCGTCGCTTCCATCCATG 61.483 60.000 0.00 0.00 0.00 3.66
180 181 1.521457 TCGTCGCTTCCATCCATGC 60.521 57.895 0.00 0.00 0.00 4.06
181 182 1.815003 CGTCGCTTCCATCCATGCA 60.815 57.895 0.00 0.00 0.00 3.96
182 183 1.769098 CGTCGCTTCCATCCATGCAG 61.769 60.000 0.00 0.00 0.00 4.41
183 184 1.820906 TCGCTTCCATCCATGCAGC 60.821 57.895 0.00 0.00 32.34 5.25
184 185 2.842256 CGCTTCCATCCATGCAGCC 61.842 63.158 0.00 0.00 32.13 4.85
185 186 1.755395 GCTTCCATCCATGCAGCCA 60.755 57.895 0.00 0.00 30.53 4.75
186 187 2.012902 GCTTCCATCCATGCAGCCAC 62.013 60.000 0.00 0.00 30.53 5.01
187 188 1.380246 TTCCATCCATGCAGCCACC 60.380 57.895 0.00 0.00 0.00 4.61
188 189 1.866483 TTCCATCCATGCAGCCACCT 61.866 55.000 0.00 0.00 0.00 4.00
189 190 1.826921 CCATCCATGCAGCCACCTC 60.827 63.158 0.00 0.00 0.00 3.85
190 191 2.184830 CATCCATGCAGCCACCTCG 61.185 63.158 0.00 0.00 0.00 4.63
191 192 2.673200 ATCCATGCAGCCACCTCGT 61.673 57.895 0.00 0.00 0.00 4.18
192 193 1.337384 ATCCATGCAGCCACCTCGTA 61.337 55.000 0.00 0.00 0.00 3.43
193 194 1.815421 CCATGCAGCCACCTCGTAC 60.815 63.158 0.00 0.00 0.00 3.67
194 195 1.815421 CATGCAGCCACCTCGTACC 60.815 63.158 0.00 0.00 0.00 3.34
195 196 3.371097 ATGCAGCCACCTCGTACCG 62.371 63.158 0.00 0.00 0.00 4.02
196 197 4.065281 GCAGCCACCTCGTACCGT 62.065 66.667 0.00 0.00 0.00 4.83
197 198 2.126071 CAGCCACCTCGTACCGTG 60.126 66.667 0.00 0.00 0.00 4.94
198 199 4.065281 AGCCACCTCGTACCGTGC 62.065 66.667 0.00 0.00 0.00 5.34
200 201 3.379445 CCACCTCGTACCGTGCCT 61.379 66.667 0.00 0.00 0.00 4.75
201 202 2.181021 CACCTCGTACCGTGCCTC 59.819 66.667 0.00 0.00 0.00 4.70
202 203 3.066814 ACCTCGTACCGTGCCTCC 61.067 66.667 0.00 0.00 0.00 4.30
203 204 3.834799 CCTCGTACCGTGCCTCCC 61.835 72.222 0.00 0.00 0.00 4.30
204 205 4.189188 CTCGTACCGTGCCTCCCG 62.189 72.222 0.00 0.00 0.00 5.14
206 207 3.133464 CGTACCGTGCCTCCCGTA 61.133 66.667 0.00 0.00 0.00 4.02
207 208 2.484062 CGTACCGTGCCTCCCGTAT 61.484 63.158 0.00 0.00 0.00 3.06
208 209 1.361632 GTACCGTGCCTCCCGTATC 59.638 63.158 0.00 0.00 0.00 2.24
209 210 1.105759 GTACCGTGCCTCCCGTATCT 61.106 60.000 0.00 0.00 0.00 1.98
210 211 1.105167 TACCGTGCCTCCCGTATCTG 61.105 60.000 0.00 0.00 0.00 2.90
211 212 2.279517 CGTGCCTCCCGTATCTGC 60.280 66.667 0.00 0.00 0.00 4.26
212 213 2.279517 GTGCCTCCCGTATCTGCG 60.280 66.667 0.00 0.00 0.00 5.18
213 214 2.441348 TGCCTCCCGTATCTGCGA 60.441 61.111 0.00 0.00 0.00 5.10
214 215 2.027751 GCCTCCCGTATCTGCGAC 59.972 66.667 0.00 0.00 0.00 5.19
215 216 2.491022 GCCTCCCGTATCTGCGACT 61.491 63.158 0.00 0.00 0.00 4.18
216 217 1.360551 CCTCCCGTATCTGCGACTG 59.639 63.158 0.00 0.00 0.00 3.51
217 218 1.384989 CCTCCCGTATCTGCGACTGT 61.385 60.000 0.00 0.00 0.00 3.55
218 219 0.248661 CTCCCGTATCTGCGACTGTG 60.249 60.000 0.00 0.00 0.00 3.66
219 220 0.963856 TCCCGTATCTGCGACTGTGT 60.964 55.000 0.00 0.00 0.00 3.72
220 221 0.525668 CCCGTATCTGCGACTGTGTC 60.526 60.000 0.00 0.00 0.00 3.67
221 222 0.452184 CCGTATCTGCGACTGTGTCT 59.548 55.000 0.00 0.00 0.00 3.41
222 223 1.532090 CCGTATCTGCGACTGTGTCTC 60.532 57.143 0.00 0.00 0.00 3.36
223 224 1.532090 CGTATCTGCGACTGTGTCTCC 60.532 57.143 0.00 0.00 0.00 3.71
224 225 1.103803 TATCTGCGACTGTGTCTCCC 58.896 55.000 0.00 0.00 0.00 4.30
225 226 1.938657 ATCTGCGACTGTGTCTCCCG 61.939 60.000 0.00 0.00 0.00 5.14
226 227 2.910479 TGCGACTGTGTCTCCCGT 60.910 61.111 0.00 0.00 0.00 5.28
227 228 2.338984 GCGACTGTGTCTCCCGTT 59.661 61.111 0.00 0.00 0.00 4.44
228 229 1.300697 GCGACTGTGTCTCCCGTTT 60.301 57.895 0.00 0.00 0.00 3.60
229 230 1.282930 GCGACTGTGTCTCCCGTTTC 61.283 60.000 0.00 0.00 0.00 2.78
230 231 0.314302 CGACTGTGTCTCCCGTTTCT 59.686 55.000 0.00 0.00 0.00 2.52
231 232 1.784525 GACTGTGTCTCCCGTTTCTG 58.215 55.000 0.00 0.00 0.00 3.02
232 233 1.068741 GACTGTGTCTCCCGTTTCTGT 59.931 52.381 0.00 0.00 0.00 3.41
233 234 1.202533 ACTGTGTCTCCCGTTTCTGTG 60.203 52.381 0.00 0.00 0.00 3.66
234 235 0.105964 TGTGTCTCCCGTTTCTGTGG 59.894 55.000 0.00 0.00 0.00 4.17
235 236 1.070786 TGTCTCCCGTTTCTGTGGC 59.929 57.895 0.00 0.00 0.00 5.01
236 237 1.671379 GTCTCCCGTTTCTGTGGCC 60.671 63.158 0.00 0.00 0.00 5.36
237 238 2.742372 CTCCCGTTTCTGTGGCCG 60.742 66.667 0.00 0.00 0.00 6.13
238 239 3.234630 CTCCCGTTTCTGTGGCCGA 62.235 63.158 0.00 0.00 0.00 5.54
239 240 2.742372 CCCGTTTCTGTGGCCGAG 60.742 66.667 0.00 0.00 0.00 4.63
240 241 2.342279 CCGTTTCTGTGGCCGAGA 59.658 61.111 0.00 0.00 0.00 4.04
241 242 1.079127 CCGTTTCTGTGGCCGAGAT 60.079 57.895 5.17 0.00 0.00 2.75
242 243 0.673644 CCGTTTCTGTGGCCGAGATT 60.674 55.000 5.17 0.00 0.00 2.40
243 244 0.721718 CGTTTCTGTGGCCGAGATTC 59.278 55.000 5.17 1.97 0.00 2.52
244 245 1.087501 GTTTCTGTGGCCGAGATTCC 58.912 55.000 5.17 0.00 0.00 3.01
245 246 0.690192 TTTCTGTGGCCGAGATTCCA 59.310 50.000 5.17 0.00 0.00 3.53
246 247 0.911769 TTCTGTGGCCGAGATTCCAT 59.088 50.000 5.17 0.00 34.47 3.41
247 248 0.178767 TCTGTGGCCGAGATTCCATG 59.821 55.000 0.00 0.00 34.47 3.66
248 249 1.442526 CTGTGGCCGAGATTCCATGC 61.443 60.000 0.00 0.00 34.47 4.06
249 250 2.189499 GTGGCCGAGATTCCATGCC 61.189 63.158 0.00 0.00 42.49 4.40
250 251 2.974698 GGCCGAGATTCCATGCCG 60.975 66.667 0.00 0.00 31.55 5.69
251 252 2.974698 GCCGAGATTCCATGCCGG 60.975 66.667 0.00 0.00 42.74 6.13
252 253 2.974698 CCGAGATTCCATGCCGGC 60.975 66.667 22.73 22.73 33.47 6.13
253 254 3.341043 CGAGATTCCATGCCGGCG 61.341 66.667 23.90 8.36 33.14 6.46
254 255 2.974698 GAGATTCCATGCCGGCGG 60.975 66.667 24.35 24.35 33.14 6.13
271 272 4.789075 GCCGCACCATGCAAGCAG 62.789 66.667 0.00 0.00 45.36 4.24
272 273 3.057548 CCGCACCATGCAAGCAGA 61.058 61.111 0.00 0.00 45.36 4.26
273 274 2.483745 CGCACCATGCAAGCAGAG 59.516 61.111 0.00 0.00 45.36 3.35
274 275 2.036571 CGCACCATGCAAGCAGAGA 61.037 57.895 0.00 0.00 45.36 3.10
275 276 1.505353 GCACCATGCAAGCAGAGAC 59.495 57.895 0.00 0.00 44.26 3.36
276 277 1.239296 GCACCATGCAAGCAGAGACA 61.239 55.000 0.00 0.00 44.26 3.41
277 278 0.803117 CACCATGCAAGCAGAGACAG 59.197 55.000 0.00 0.00 0.00 3.51
278 279 0.689055 ACCATGCAAGCAGAGACAGA 59.311 50.000 0.00 0.00 0.00 3.41
279 280 1.072806 ACCATGCAAGCAGAGACAGAA 59.927 47.619 0.00 0.00 0.00 3.02
280 281 1.738350 CCATGCAAGCAGAGACAGAAG 59.262 52.381 0.00 0.00 0.00 2.85
281 282 2.424557 CATGCAAGCAGAGACAGAAGT 58.575 47.619 0.00 0.00 0.00 3.01
282 283 2.627515 TGCAAGCAGAGACAGAAGTT 57.372 45.000 0.00 0.00 0.00 2.66
283 284 2.216046 TGCAAGCAGAGACAGAAGTTG 58.784 47.619 0.00 0.00 0.00 3.16
284 285 2.158914 TGCAAGCAGAGACAGAAGTTGA 60.159 45.455 0.00 0.00 0.00 3.18
285 286 2.479656 GCAAGCAGAGACAGAAGTTGAG 59.520 50.000 0.00 0.00 0.00 3.02
286 287 3.726607 CAAGCAGAGACAGAAGTTGAGT 58.273 45.455 0.00 0.00 0.00 3.41
287 288 3.383620 AGCAGAGACAGAAGTTGAGTG 57.616 47.619 0.00 0.00 0.00 3.51
288 289 1.797635 GCAGAGACAGAAGTTGAGTGC 59.202 52.381 0.00 0.00 0.00 4.40
289 290 2.804572 GCAGAGACAGAAGTTGAGTGCA 60.805 50.000 0.00 0.00 0.00 4.57
290 291 2.799412 CAGAGACAGAAGTTGAGTGCAC 59.201 50.000 9.40 9.40 0.00 4.57
291 292 1.789464 GAGACAGAAGTTGAGTGCACG 59.211 52.381 12.01 0.00 0.00 5.34
292 293 0.861837 GACAGAAGTTGAGTGCACGG 59.138 55.000 12.01 0.00 0.00 4.94
293 294 0.464036 ACAGAAGTTGAGTGCACGGA 59.536 50.000 12.01 0.00 0.00 4.69
294 295 1.143305 CAGAAGTTGAGTGCACGGAG 58.857 55.000 12.01 0.00 0.00 4.63
295 296 1.040646 AGAAGTTGAGTGCACGGAGA 58.959 50.000 12.01 0.00 0.00 3.71
296 297 1.000283 AGAAGTTGAGTGCACGGAGAG 60.000 52.381 12.01 0.00 0.00 3.20
297 298 0.601311 AAGTTGAGTGCACGGAGAGC 60.601 55.000 12.01 1.23 46.44 4.09
304 305 2.049063 GCACGGAGAGCGACAAGT 60.049 61.111 0.00 0.00 32.66 3.16
305 306 2.089349 GCACGGAGAGCGACAAGTC 61.089 63.158 0.00 0.00 32.66 3.01
315 316 2.946762 GACAAGTCGGTGGCAAGC 59.053 61.111 0.00 0.00 0.00 4.01
316 317 1.891919 GACAAGTCGGTGGCAAGCA 60.892 57.895 0.00 0.00 0.00 3.91
317 318 2.117941 GACAAGTCGGTGGCAAGCAC 62.118 60.000 0.00 0.00 0.00 4.40
318 319 2.594592 AAGTCGGTGGCAAGCACC 60.595 61.111 0.00 0.00 39.26 5.01
319 320 3.120086 AAGTCGGTGGCAAGCACCT 62.120 57.895 8.70 0.00 40.43 4.00
320 321 3.050275 GTCGGTGGCAAGCACCTC 61.050 66.667 8.70 0.00 40.43 3.85
321 322 4.329545 TCGGTGGCAAGCACCTCC 62.330 66.667 8.70 2.38 40.43 4.30
328 329 3.114616 CAAGCACCTCCGCGTCTG 61.115 66.667 4.92 0.00 36.85 3.51
332 333 4.803426 CACCTCCGCGTCTGCCTC 62.803 72.222 4.92 0.00 38.08 4.70
335 336 3.842923 CTCCGCGTCTGCCTCCAT 61.843 66.667 4.92 0.00 38.08 3.41
336 337 3.781770 CTCCGCGTCTGCCTCCATC 62.782 68.421 4.92 0.00 38.08 3.51
337 338 4.147449 CCGCGTCTGCCTCCATCA 62.147 66.667 4.92 0.00 38.08 3.07
338 339 2.887568 CGCGTCTGCCTCCATCAC 60.888 66.667 0.00 0.00 38.08 3.06
339 340 2.512515 GCGTCTGCCTCCATCACC 60.513 66.667 0.00 0.00 33.98 4.02
340 341 2.202797 CGTCTGCCTCCATCACCG 60.203 66.667 0.00 0.00 0.00 4.94
341 342 2.710902 CGTCTGCCTCCATCACCGA 61.711 63.158 0.00 0.00 0.00 4.69
387 388 2.118403 AAGGGAGGTCTTGGAGTGAA 57.882 50.000 0.00 0.00 0.00 3.18
472 473 7.099266 TGTAGATCTGCAATGGGTTAAATTG 57.901 36.000 11.44 0.00 37.94 2.32
517 518 4.385199 GGTATTGTCCCTCATGATGTTCCA 60.385 45.833 0.00 0.00 0.00 3.53
539 540 3.094484 AGTGTGGTTCTTTTTGGTGGA 57.906 42.857 0.00 0.00 0.00 4.02
540 541 3.642141 AGTGTGGTTCTTTTTGGTGGAT 58.358 40.909 0.00 0.00 0.00 3.41
635 636 5.244402 TCCATGTGGCATGATAATTGGAATC 59.756 40.000 10.34 0.00 34.44 2.52
672 674 5.844301 AAAAATTTCGCCTGCTTGTATTG 57.156 34.783 0.00 0.00 0.00 1.90
685 687 6.992123 CCTGCTTGTATTGATATACCAAGACA 59.008 38.462 3.05 3.05 43.73 3.41
718 720 6.652062 TCTCAGTTTACACGTACTATGAGACA 59.348 38.462 11.18 0.00 0.00 3.41
720 722 7.080099 TCAGTTTACACGTACTATGAGACAAC 58.920 38.462 0.00 0.00 0.00 3.32
722 724 8.232513 CAGTTTACACGTACTATGAGACAACTA 58.767 37.037 0.00 0.00 0.00 2.24
751 753 8.774546 TGAGTCTGATATTTCATCTACCTCTT 57.225 34.615 0.00 0.00 0.00 2.85
766 769 0.686112 CTCTTTCTCCCGAGCCCTCT 60.686 60.000 0.00 0.00 0.00 3.69
769 772 2.043227 CTTTCTCCCGAGCCCTCTATT 58.957 52.381 0.00 0.00 0.00 1.73
778 781 3.635373 CCGAGCCCTCTATTAGTTACACA 59.365 47.826 0.00 0.00 0.00 3.72
814 817 1.981256 ACCGCCACAAATTCTTGAGT 58.019 45.000 0.00 0.00 36.33 3.41
818 821 2.666619 CGCCACAAATTCTTGAGTCTGC 60.667 50.000 0.00 0.00 36.33 4.26
835 838 4.223700 AGTCTGCAAGTACTGATCAATGGA 59.776 41.667 0.00 0.00 33.76 3.41
906 3987 5.269189 TGTCATAGACTAATCACCTGTCCA 58.731 41.667 0.00 0.00 33.15 4.02
924 4006 3.766051 GTCCAGAGCCTTTCAAATGGATT 59.234 43.478 0.00 0.00 38.95 3.01
951 4033 6.146673 GGAAATCAAAGCTCCAAATGAAACTG 59.853 38.462 0.00 0.00 0.00 3.16
975 4057 5.009854 AGGTGTTCATGTGGTTTCTTTTG 57.990 39.130 0.00 0.00 0.00 2.44
1004 4086 1.956477 ACTGAACACAAGGAACATGCC 59.044 47.619 0.00 0.00 0.00 4.40
1049 4137 3.059597 GGAGATATTGAAACATGCGTCCG 60.060 47.826 0.00 0.00 0.00 4.79
1089 4177 6.385176 AGGAAGAGACCATTGATCACTTGATA 59.615 38.462 0.00 0.00 34.37 2.15
1122 4211 4.142049 CCTTTTAGCCAAACTTGTTGGTCA 60.142 41.667 6.95 0.00 41.53 4.02
1158 4247 0.969149 ACAACTCTGGCATCTCACGA 59.031 50.000 0.00 0.00 0.00 4.35
1219 4310 7.861630 TGGTAGACTTTTCTTTGAAATCTTCG 58.138 34.615 2.76 0.00 32.75 3.79
1304 4395 5.876651 TCATATAGAGCTTGGCTTGAGAA 57.123 39.130 0.00 0.00 39.88 2.87
1307 4398 6.765036 TCATATAGAGCTTGGCTTGAGAAAAG 59.235 38.462 0.00 0.00 39.88 2.27
1314 4405 2.514803 TGGCTTGAGAAAAGTAAGGCC 58.485 47.619 0.00 0.00 43.80 5.19
1359 4450 1.403679 GTGTCCTCTGATCTCGGTGAG 59.596 57.143 0.00 0.00 0.00 3.51
1364 4455 4.693566 GTCCTCTGATCTCGGTGAGTATAG 59.306 50.000 0.00 0.00 0.00 1.31
1407 4500 7.551262 TCACTTTAGACTCTGCTTGTTTGTTTA 59.449 33.333 0.00 0.00 0.00 2.01
1443 4537 7.208064 ACTTTCCTCCTAGCCATGTAAATAA 57.792 36.000 0.00 0.00 0.00 1.40
1625 4726 1.681264 CCTTTTGTTGCGAGGACCTTT 59.319 47.619 0.00 0.00 32.11 3.11
1633 4734 1.663739 CGAGGACCTTTGTCGACCA 59.336 57.895 14.12 0.00 42.73 4.02
1672 4773 1.925972 GGAGAAGCCCCCTTCCACT 60.926 63.158 0.17 0.00 46.97 4.00
1681 4782 2.224646 GCCCCCTTCCACTATCATCTTC 60.225 54.545 0.00 0.00 0.00 2.87
1837 4938 5.313712 CGACCATTTAGGCCAGGTATTATT 58.686 41.667 5.01 0.00 43.14 1.40
1865 4966 1.684450 TGTTGTCGAGAACTAGCACCA 59.316 47.619 23.92 1.47 0.00 4.17
1886 4987 8.647226 GCACCATTTAGTTGATTTGAATGTAAC 58.353 33.333 0.00 0.00 0.00 2.50
1992 5095 4.464069 TTTTTCTGGTTGGTTGAGTTGG 57.536 40.909 0.00 0.00 0.00 3.77
2114 5218 0.032130 GTGTGAGCTCGTCTCCAACA 59.968 55.000 9.64 2.79 41.18 3.33
2123 5227 1.809619 GTCTCCAACATGCGCGCTA 60.810 57.895 33.29 19.04 0.00 4.26
2172 5276 0.523072 CGTTCATCAGTGGCAAAGGG 59.477 55.000 0.00 0.00 0.00 3.95
2187 5291 0.481128 AAGGGACCGGTGGACAAAAT 59.519 50.000 14.63 0.00 0.00 1.82
2226 5330 1.076044 CCCCGGGCAAGATCCAAAT 60.076 57.895 17.73 0.00 0.00 2.32
2232 5336 2.371658 GGCAAGATCCAAATAGCCCT 57.628 50.000 0.00 0.00 36.17 5.19
2238 5342 5.694995 CAAGATCCAAATAGCCCTTCCTAA 58.305 41.667 0.00 0.00 0.00 2.69
2258 5362 5.648092 CCTAACAGATTCAAATCCCTCGTTT 59.352 40.000 0.00 0.00 36.04 3.60
2263 5367 1.243902 TCAAATCCCTCGTTTGCCAC 58.756 50.000 0.00 0.00 36.69 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.280019 GGGCCACCCAACCGACTT 62.280 66.667 4.39 0.00 44.65 3.01
15 16 2.891941 TATTCTGCAGGCTTGGCGGG 62.892 60.000 15.13 0.00 38.20 6.13
16 17 1.451927 TATTCTGCAGGCTTGGCGG 60.452 57.895 15.13 0.00 39.01 6.13
17 18 1.723870 GTATTCTGCAGGCTTGGCG 59.276 57.895 15.13 0.00 0.00 5.69
18 19 0.744414 TCGTATTCTGCAGGCTTGGC 60.744 55.000 15.13 0.00 0.00 4.52
19 20 1.293924 CTCGTATTCTGCAGGCTTGG 58.706 55.000 15.13 1.17 0.00 3.61
20 21 0.654683 GCTCGTATTCTGCAGGCTTG 59.345 55.000 15.13 0.62 0.00 4.01
21 22 0.539051 AGCTCGTATTCTGCAGGCTT 59.461 50.000 15.13 1.39 0.00 4.35
22 23 1.403814 TAGCTCGTATTCTGCAGGCT 58.596 50.000 15.13 14.71 0.00 4.58
23 24 2.064762 CATAGCTCGTATTCTGCAGGC 58.935 52.381 15.13 7.35 0.00 4.85
24 25 2.064762 GCATAGCTCGTATTCTGCAGG 58.935 52.381 15.13 0.00 0.00 4.85
25 26 2.747436 TGCATAGCTCGTATTCTGCAG 58.253 47.619 7.63 7.63 34.92 4.41
26 27 2.747436 CTGCATAGCTCGTATTCTGCA 58.253 47.619 0.00 0.00 37.93 4.41
27 28 1.458827 GCTGCATAGCTCGTATTCTGC 59.541 52.381 0.00 0.00 46.57 4.26
39 40 2.481854 GTGGATCAGTGAGCTGCATAG 58.518 52.381 8.52 0.00 42.29 2.23
40 41 1.139654 GGTGGATCAGTGAGCTGCATA 59.860 52.381 8.52 0.00 42.29 3.14
41 42 0.107312 GGTGGATCAGTGAGCTGCAT 60.107 55.000 8.52 0.00 42.29 3.96
42 43 1.196766 AGGTGGATCAGTGAGCTGCA 61.197 55.000 8.52 0.00 42.29 4.41
43 44 0.461693 GAGGTGGATCAGTGAGCTGC 60.462 60.000 8.52 1.48 42.29 5.25
44 45 0.177604 GGAGGTGGATCAGTGAGCTG 59.822 60.000 8.52 0.00 43.87 4.24
45 46 0.980231 GGGAGGTGGATCAGTGAGCT 60.980 60.000 8.52 0.00 0.00 4.09
46 47 0.980231 AGGGAGGTGGATCAGTGAGC 60.980 60.000 0.00 0.00 0.00 4.26
47 48 1.118838 GAGGGAGGTGGATCAGTGAG 58.881 60.000 0.00 0.00 0.00 3.51
48 49 0.325671 GGAGGGAGGTGGATCAGTGA 60.326 60.000 0.00 0.00 0.00 3.41
49 50 1.341156 GGGAGGGAGGTGGATCAGTG 61.341 65.000 0.00 0.00 0.00 3.66
50 51 1.003573 GGGAGGGAGGTGGATCAGT 59.996 63.158 0.00 0.00 0.00 3.41
51 52 0.401105 ATGGGAGGGAGGTGGATCAG 60.401 60.000 0.00 0.00 0.00 2.90
52 53 0.400525 GATGGGAGGGAGGTGGATCA 60.401 60.000 0.00 0.00 0.00 2.92
53 54 0.400525 TGATGGGAGGGAGGTGGATC 60.401 60.000 0.00 0.00 0.00 3.36
54 55 0.695803 GTGATGGGAGGGAGGTGGAT 60.696 60.000 0.00 0.00 0.00 3.41
55 56 1.306997 GTGATGGGAGGGAGGTGGA 60.307 63.158 0.00 0.00 0.00 4.02
56 57 1.307343 AGTGATGGGAGGGAGGTGG 60.307 63.158 0.00 0.00 0.00 4.61
57 58 1.680522 CGAGTGATGGGAGGGAGGTG 61.681 65.000 0.00 0.00 0.00 4.00
58 59 1.381872 CGAGTGATGGGAGGGAGGT 60.382 63.158 0.00 0.00 0.00 3.85
59 60 1.075970 TCGAGTGATGGGAGGGAGG 60.076 63.158 0.00 0.00 0.00 4.30
60 61 1.729470 CGTCGAGTGATGGGAGGGAG 61.729 65.000 0.00 0.00 0.00 4.30
61 62 1.753078 CGTCGAGTGATGGGAGGGA 60.753 63.158 0.00 0.00 0.00 4.20
62 63 2.786495 CCGTCGAGTGATGGGAGGG 61.786 68.421 0.00 0.00 45.96 4.30
63 64 2.808315 CCGTCGAGTGATGGGAGG 59.192 66.667 0.00 0.00 45.96 4.30
68 69 1.226802 CTGGCTCCGTCGAGTGATG 60.227 63.158 0.00 0.00 38.49 3.07
69 70 1.251527 AACTGGCTCCGTCGAGTGAT 61.252 55.000 0.00 0.00 38.49 3.06
70 71 1.863662 GAACTGGCTCCGTCGAGTGA 61.864 60.000 0.00 0.00 38.49 3.41
71 72 1.444553 GAACTGGCTCCGTCGAGTG 60.445 63.158 0.00 0.00 38.49 3.51
72 73 2.637383 GGAACTGGCTCCGTCGAGT 61.637 63.158 0.00 0.00 38.49 4.18
73 74 2.182030 GGAACTGGCTCCGTCGAG 59.818 66.667 0.00 0.00 39.33 4.04
74 75 3.379445 GGGAACTGGCTCCGTCGA 61.379 66.667 0.00 0.00 36.21 4.20
75 76 4.796231 CGGGAACTGGCTCCGTCG 62.796 72.222 0.00 0.00 39.04 5.12
96 97 4.748679 GAACTGCGCGCCAGCTTG 62.749 66.667 30.77 13.60 45.78 4.01
103 104 3.918114 GAGTTGCTGAACTGCGCGC 62.918 63.158 27.26 27.26 42.80 6.86
104 105 2.171940 GAGTTGCTGAACTGCGCG 59.828 61.111 0.00 0.00 42.80 6.86
105 106 2.171940 CGAGTTGCTGAACTGCGC 59.828 61.111 0.00 0.00 42.80 6.09
106 107 2.171940 GCGAGTTGCTGAACTGCG 59.828 61.111 0.00 0.53 42.80 5.18
115 116 3.123620 CCTGGAGCAGCGAGTTGC 61.124 66.667 3.69 3.69 44.41 4.17
116 117 3.123620 GCCTGGAGCAGCGAGTTG 61.124 66.667 0.00 0.00 42.97 3.16
117 118 4.400961 GGCCTGGAGCAGCGAGTT 62.401 66.667 0.00 0.00 46.50 3.01
119 120 4.834453 CTGGCCTGGAGCAGCGAG 62.834 72.222 3.32 0.00 46.50 5.03
123 124 3.263859 TTGAGCTGGCCTGGAGCAG 62.264 63.158 15.36 0.00 46.50 4.24
124 125 3.251509 TTGAGCTGGCCTGGAGCA 61.252 61.111 15.36 0.00 46.50 4.26
125 126 2.749441 GTTGAGCTGGCCTGGAGC 60.749 66.667 12.06 8.69 42.60 4.70
126 127 0.959372 CTTGTTGAGCTGGCCTGGAG 60.959 60.000 12.06 0.00 0.00 3.86
127 128 1.073722 CTTGTTGAGCTGGCCTGGA 59.926 57.895 12.06 0.00 0.00 3.86
128 129 1.975407 CCTTGTTGAGCTGGCCTGG 60.975 63.158 12.06 1.66 0.00 4.45
129 130 0.959372 CTCCTTGTTGAGCTGGCCTG 60.959 60.000 3.32 4.26 0.00 4.85
130 131 1.377994 CTCCTTGTTGAGCTGGCCT 59.622 57.895 3.32 0.00 0.00 5.19
131 132 1.073897 ACTCCTTGTTGAGCTGGCC 59.926 57.895 0.00 0.00 35.72 5.36
132 133 1.239968 CCACTCCTTGTTGAGCTGGC 61.240 60.000 0.00 0.00 35.72 4.85
133 134 1.239968 GCCACTCCTTGTTGAGCTGG 61.240 60.000 0.00 0.00 36.98 4.85
134 135 0.535780 TGCCACTCCTTGTTGAGCTG 60.536 55.000 0.00 0.00 35.72 4.24
135 136 0.536006 GTGCCACTCCTTGTTGAGCT 60.536 55.000 0.00 0.00 35.72 4.09
136 137 0.819259 TGTGCCACTCCTTGTTGAGC 60.819 55.000 0.00 0.00 35.72 4.26
137 138 0.947244 GTGTGCCACTCCTTGTTGAG 59.053 55.000 0.00 0.00 38.37 3.02
138 139 0.254462 TGTGTGCCACTCCTTGTTGA 59.746 50.000 0.00 0.00 35.11 3.18
139 140 0.664761 CTGTGTGCCACTCCTTGTTG 59.335 55.000 0.00 0.00 35.11 3.33
140 141 0.466189 CCTGTGTGCCACTCCTTGTT 60.466 55.000 0.00 0.00 35.11 2.83
141 142 1.149174 CCTGTGTGCCACTCCTTGT 59.851 57.895 0.00 0.00 35.11 3.16
142 143 2.263741 GCCTGTGTGCCACTCCTTG 61.264 63.158 0.00 0.00 35.11 3.61
143 144 2.113986 GCCTGTGTGCCACTCCTT 59.886 61.111 0.00 0.00 35.11 3.36
144 145 4.320456 CGCCTGTGTGCCACTCCT 62.320 66.667 0.00 0.00 35.11 3.69
145 146 4.626081 ACGCCTGTGTGCCACTCC 62.626 66.667 0.00 0.00 35.11 3.85
146 147 3.044305 GACGCCTGTGTGCCACTC 61.044 66.667 0.00 0.00 35.11 3.51
147 148 4.969196 CGACGCCTGTGTGCCACT 62.969 66.667 0.00 0.00 35.11 4.00
149 150 4.961511 GACGACGCCTGTGTGCCA 62.962 66.667 0.00 0.00 0.00 4.92
160 161 1.226974 ATGGATGGAAGCGACGACG 60.227 57.895 2.12 2.12 42.93 5.12
161 162 1.766143 GCATGGATGGAAGCGACGAC 61.766 60.000 0.00 0.00 0.00 4.34
162 163 1.521457 GCATGGATGGAAGCGACGA 60.521 57.895 0.00 0.00 0.00 4.20
163 164 1.769098 CTGCATGGATGGAAGCGACG 61.769 60.000 0.00 0.00 0.00 5.12
164 165 2.020131 CTGCATGGATGGAAGCGAC 58.980 57.895 0.00 0.00 0.00 5.19
165 166 1.820906 GCTGCATGGATGGAAGCGA 60.821 57.895 0.00 0.00 0.00 4.93
166 167 2.719979 GCTGCATGGATGGAAGCG 59.280 61.111 0.00 0.00 0.00 4.68
167 168 1.755395 TGGCTGCATGGATGGAAGC 60.755 57.895 0.50 0.00 0.00 3.86
168 169 1.389609 GGTGGCTGCATGGATGGAAG 61.390 60.000 0.50 0.00 0.00 3.46
169 170 1.380246 GGTGGCTGCATGGATGGAA 60.380 57.895 0.50 0.00 0.00 3.53
170 171 2.274948 GAGGTGGCTGCATGGATGGA 62.275 60.000 0.50 0.00 0.00 3.41
171 172 1.826921 GAGGTGGCTGCATGGATGG 60.827 63.158 0.50 0.00 0.00 3.51
172 173 2.184830 CGAGGTGGCTGCATGGATG 61.185 63.158 0.50 0.00 0.00 3.51
173 174 1.337384 TACGAGGTGGCTGCATGGAT 61.337 55.000 0.50 0.00 0.00 3.41
174 175 1.987306 TACGAGGTGGCTGCATGGA 60.987 57.895 0.50 0.00 0.00 3.41
175 176 1.815421 GTACGAGGTGGCTGCATGG 60.815 63.158 0.50 0.00 0.00 3.66
176 177 1.815421 GGTACGAGGTGGCTGCATG 60.815 63.158 0.50 0.00 0.00 4.06
177 178 2.584608 GGTACGAGGTGGCTGCAT 59.415 61.111 0.50 0.00 0.00 3.96
190 191 1.105759 AGATACGGGAGGCACGGTAC 61.106 60.000 0.00 0.00 35.23 3.34
191 192 1.105167 CAGATACGGGAGGCACGGTA 61.105 60.000 0.00 2.39 35.23 4.02
192 193 2.043248 AGATACGGGAGGCACGGT 60.043 61.111 0.00 0.29 35.23 4.83
193 194 2.417516 CAGATACGGGAGGCACGG 59.582 66.667 0.00 0.00 35.23 4.94
194 195 2.279517 GCAGATACGGGAGGCACG 60.280 66.667 0.00 0.00 37.36 5.34
195 196 2.279517 CGCAGATACGGGAGGCAC 60.280 66.667 0.00 0.00 0.00 5.01
196 197 2.441348 TCGCAGATACGGGAGGCA 60.441 61.111 0.00 0.00 0.00 4.75
197 198 2.027751 GTCGCAGATACGGGAGGC 59.972 66.667 0.00 0.00 40.67 4.70
198 199 1.360551 CAGTCGCAGATACGGGAGG 59.639 63.158 0.00 0.00 40.67 4.30
199 200 0.248661 CACAGTCGCAGATACGGGAG 60.249 60.000 0.00 0.00 40.67 4.30
200 201 0.963856 ACACAGTCGCAGATACGGGA 60.964 55.000 0.00 0.00 40.67 5.14
201 202 0.525668 GACACAGTCGCAGATACGGG 60.526 60.000 0.00 0.00 40.67 5.28
202 203 0.452184 AGACACAGTCGCAGATACGG 59.548 55.000 0.00 0.00 40.67 4.02
203 204 1.532090 GGAGACACAGTCGCAGATACG 60.532 57.143 3.47 0.00 40.67 3.06
204 205 1.202313 GGGAGACACAGTCGCAGATAC 60.202 57.143 3.47 0.00 40.67 2.24
205 206 1.103803 GGGAGACACAGTCGCAGATA 58.896 55.000 3.47 0.00 40.67 1.98
206 207 1.893786 GGGAGACACAGTCGCAGAT 59.106 57.895 3.47 0.00 40.67 2.90
207 208 2.626780 CGGGAGACACAGTCGCAGA 61.627 63.158 3.47 0.00 37.67 4.26
208 209 2.126307 CGGGAGACACAGTCGCAG 60.126 66.667 3.47 0.00 37.67 5.18
209 210 2.023414 AAACGGGAGACACAGTCGCA 62.023 55.000 3.47 0.00 37.67 5.10
210 211 1.282930 GAAACGGGAGACACAGTCGC 61.283 60.000 0.00 0.00 37.67 5.19
211 212 0.314302 AGAAACGGGAGACACAGTCG 59.686 55.000 0.00 0.00 37.67 4.18
212 213 1.068741 ACAGAAACGGGAGACACAGTC 59.931 52.381 0.00 0.00 0.00 3.51
213 214 1.120530 ACAGAAACGGGAGACACAGT 58.879 50.000 0.00 0.00 0.00 3.55
214 215 1.502231 CACAGAAACGGGAGACACAG 58.498 55.000 0.00 0.00 0.00 3.66
215 216 0.105964 CCACAGAAACGGGAGACACA 59.894 55.000 0.00 0.00 0.00 3.72
216 217 1.228657 GCCACAGAAACGGGAGACAC 61.229 60.000 0.00 0.00 0.00 3.67
217 218 1.070786 GCCACAGAAACGGGAGACA 59.929 57.895 0.00 0.00 0.00 3.41
218 219 1.671379 GGCCACAGAAACGGGAGAC 60.671 63.158 0.00 0.00 0.00 3.36
219 220 2.747686 GGCCACAGAAACGGGAGA 59.252 61.111 0.00 0.00 0.00 3.71
220 221 2.742372 CGGCCACAGAAACGGGAG 60.742 66.667 2.24 0.00 0.00 4.30
221 222 3.234630 CTCGGCCACAGAAACGGGA 62.235 63.158 2.24 0.00 0.00 5.14
222 223 2.521958 ATCTCGGCCACAGAAACGGG 62.522 60.000 2.24 0.00 0.00 5.28
223 224 0.673644 AATCTCGGCCACAGAAACGG 60.674 55.000 2.24 0.00 0.00 4.44
224 225 0.721718 GAATCTCGGCCACAGAAACG 59.278 55.000 2.24 0.00 0.00 3.60
225 226 1.087501 GGAATCTCGGCCACAGAAAC 58.912 55.000 2.24 2.09 0.00 2.78
226 227 0.690192 TGGAATCTCGGCCACAGAAA 59.310 50.000 2.24 0.00 0.00 2.52
227 228 0.911769 ATGGAATCTCGGCCACAGAA 59.088 50.000 2.24 0.00 36.92 3.02
228 229 0.178767 CATGGAATCTCGGCCACAGA 59.821 55.000 2.24 3.20 36.92 3.41
229 230 1.442526 GCATGGAATCTCGGCCACAG 61.443 60.000 2.24 0.00 36.92 3.66
230 231 1.451927 GCATGGAATCTCGGCCACA 60.452 57.895 2.24 0.00 36.92 4.17
231 232 2.189499 GGCATGGAATCTCGGCCAC 61.189 63.158 2.24 0.00 44.01 5.01
232 233 2.192979 GGCATGGAATCTCGGCCA 59.807 61.111 2.24 0.00 44.01 5.36
233 234 2.974698 CGGCATGGAATCTCGGCC 60.975 66.667 0.00 0.00 41.20 6.13
234 235 2.974698 CCGGCATGGAATCTCGGC 60.975 66.667 0.00 0.00 42.00 5.54
235 236 2.974698 GCCGGCATGGAATCTCGG 60.975 66.667 24.80 0.00 42.00 4.63
236 237 3.341043 CGCCGGCATGGAATCTCG 61.341 66.667 28.98 0.98 42.00 4.04
237 238 2.974698 CCGCCGGCATGGAATCTC 60.975 66.667 28.98 0.00 42.00 2.75
257 258 1.239296 TGTCTCTGCTTGCATGGTGC 61.239 55.000 1.34 0.00 45.29 5.01
258 259 0.803117 CTGTCTCTGCTTGCATGGTG 59.197 55.000 1.34 0.00 0.00 4.17
259 260 0.689055 TCTGTCTCTGCTTGCATGGT 59.311 50.000 1.34 0.00 0.00 3.55
260 261 1.738350 CTTCTGTCTCTGCTTGCATGG 59.262 52.381 1.34 0.00 0.00 3.66
261 262 2.424557 ACTTCTGTCTCTGCTTGCATG 58.575 47.619 0.00 0.00 0.00 4.06
262 263 2.812591 CAACTTCTGTCTCTGCTTGCAT 59.187 45.455 0.00 0.00 0.00 3.96
263 264 2.158914 TCAACTTCTGTCTCTGCTTGCA 60.159 45.455 0.00 0.00 0.00 4.08
264 265 2.479656 CTCAACTTCTGTCTCTGCTTGC 59.520 50.000 0.00 0.00 0.00 4.01
265 266 3.493877 CACTCAACTTCTGTCTCTGCTTG 59.506 47.826 0.00 0.00 0.00 4.01
266 267 3.726607 CACTCAACTTCTGTCTCTGCTT 58.273 45.455 0.00 0.00 0.00 3.91
267 268 2.547642 GCACTCAACTTCTGTCTCTGCT 60.548 50.000 0.00 0.00 0.00 4.24
268 269 1.797635 GCACTCAACTTCTGTCTCTGC 59.202 52.381 0.00 0.00 0.00 4.26
269 270 2.799412 GTGCACTCAACTTCTGTCTCTG 59.201 50.000 10.32 0.00 0.00 3.35
270 271 2.544694 CGTGCACTCAACTTCTGTCTCT 60.545 50.000 16.19 0.00 0.00 3.10
271 272 1.789464 CGTGCACTCAACTTCTGTCTC 59.211 52.381 16.19 0.00 0.00 3.36
272 273 1.539065 CCGTGCACTCAACTTCTGTCT 60.539 52.381 16.19 0.00 0.00 3.41
273 274 0.861837 CCGTGCACTCAACTTCTGTC 59.138 55.000 16.19 0.00 0.00 3.51
274 275 0.464036 TCCGTGCACTCAACTTCTGT 59.536 50.000 16.19 0.00 0.00 3.41
275 276 1.143305 CTCCGTGCACTCAACTTCTG 58.857 55.000 16.19 0.00 0.00 3.02
276 277 1.000283 CTCTCCGTGCACTCAACTTCT 60.000 52.381 16.19 0.00 0.00 2.85
277 278 1.423395 CTCTCCGTGCACTCAACTTC 58.577 55.000 16.19 0.00 0.00 3.01
278 279 0.601311 GCTCTCCGTGCACTCAACTT 60.601 55.000 16.19 0.00 0.00 2.66
279 280 1.005630 GCTCTCCGTGCACTCAACT 60.006 57.895 16.19 0.00 0.00 3.16
280 281 2.375766 CGCTCTCCGTGCACTCAAC 61.376 63.158 16.19 0.00 0.00 3.18
281 282 2.049156 CGCTCTCCGTGCACTCAA 60.049 61.111 16.19 0.00 0.00 3.02
282 283 2.983592 TCGCTCTCCGTGCACTCA 60.984 61.111 16.19 0.00 38.35 3.41
283 284 2.505118 GTCGCTCTCCGTGCACTC 60.505 66.667 16.19 0.00 38.35 3.51
284 285 2.755542 CTTGTCGCTCTCCGTGCACT 62.756 60.000 16.19 0.00 38.35 4.40
285 286 2.355837 TTGTCGCTCTCCGTGCAC 60.356 61.111 6.82 6.82 38.35 4.57
286 287 2.049156 CTTGTCGCTCTCCGTGCA 60.049 61.111 0.00 0.00 38.35 4.57
287 288 2.049063 ACTTGTCGCTCTCCGTGC 60.049 61.111 0.00 0.00 38.35 5.34
288 289 1.797933 CGACTTGTCGCTCTCCGTG 60.798 63.158 10.23 0.00 38.35 4.94
289 290 2.561885 CGACTTGTCGCTCTCCGT 59.438 61.111 10.23 0.00 38.35 4.69
290 291 2.202492 CCGACTTGTCGCTCTCCG 60.202 66.667 16.59 0.00 38.61 4.63
291 292 1.444553 CACCGACTTGTCGCTCTCC 60.445 63.158 16.59 0.00 0.00 3.71
292 293 1.444553 CCACCGACTTGTCGCTCTC 60.445 63.158 16.59 0.00 0.00 3.20
293 294 2.651361 CCACCGACTTGTCGCTCT 59.349 61.111 16.59 0.00 0.00 4.09
294 295 3.112709 GCCACCGACTTGTCGCTC 61.113 66.667 16.59 2.88 0.00 5.03
295 296 3.454587 TTGCCACCGACTTGTCGCT 62.455 57.895 16.59 1.43 0.00 4.93
296 297 2.954753 CTTGCCACCGACTTGTCGC 61.955 63.158 16.59 4.79 0.00 5.19
297 298 2.954753 GCTTGCCACCGACTTGTCG 61.955 63.158 15.28 15.28 0.00 4.35
298 299 1.891919 TGCTTGCCACCGACTTGTC 60.892 57.895 0.00 0.00 0.00 3.18
299 300 2.186826 GTGCTTGCCACCGACTTGT 61.187 57.895 0.00 0.00 38.55 3.16
300 301 2.639286 GTGCTTGCCACCGACTTG 59.361 61.111 0.00 0.00 38.55 3.16
311 312 3.114616 CAGACGCGGAGGTGCTTG 61.115 66.667 12.47 0.00 0.00 4.01
315 316 4.803426 GAGGCAGACGCGGAGGTG 62.803 72.222 12.47 2.69 39.92 4.00
318 319 3.781770 GATGGAGGCAGACGCGGAG 62.782 68.421 12.47 0.00 39.92 4.63
319 320 3.838271 GATGGAGGCAGACGCGGA 61.838 66.667 12.47 0.00 39.92 5.54
320 321 4.147449 TGATGGAGGCAGACGCGG 62.147 66.667 12.47 0.00 39.92 6.46
321 322 2.887568 GTGATGGAGGCAGACGCG 60.888 66.667 3.53 3.53 39.92 6.01
322 323 2.512515 GGTGATGGAGGCAGACGC 60.513 66.667 0.00 0.00 37.44 5.19
323 324 2.202797 CGGTGATGGAGGCAGACG 60.203 66.667 0.00 0.00 0.00 4.18
324 325 1.142748 CTCGGTGATGGAGGCAGAC 59.857 63.158 0.00 0.00 0.00 3.51
325 326 2.060383 CCTCGGTGATGGAGGCAGA 61.060 63.158 0.00 0.00 44.18 4.26
326 327 2.503061 CCTCGGTGATGGAGGCAG 59.497 66.667 0.00 0.00 44.18 4.85
331 332 1.006043 ACTCTTCTCCTCGGTGATGGA 59.994 52.381 0.00 0.00 0.00 3.41
332 333 1.135915 CACTCTTCTCCTCGGTGATGG 59.864 57.143 0.00 0.00 0.00 3.51
333 334 1.821753 ACACTCTTCTCCTCGGTGATG 59.178 52.381 0.00 0.00 0.00 3.07
334 335 1.821753 CACACTCTTCTCCTCGGTGAT 59.178 52.381 0.00 0.00 0.00 3.06
335 336 1.248486 CACACTCTTCTCCTCGGTGA 58.752 55.000 0.00 0.00 0.00 4.02
336 337 0.962489 ACACACTCTTCTCCTCGGTG 59.038 55.000 0.00 0.00 0.00 4.94
337 338 1.341531 CAACACACTCTTCTCCTCGGT 59.658 52.381 0.00 0.00 0.00 4.69
338 339 1.341531 ACAACACACTCTTCTCCTCGG 59.658 52.381 0.00 0.00 0.00 4.63
339 340 2.608261 GGACAACACACTCTTCTCCTCG 60.608 54.545 0.00 0.00 0.00 4.63
340 341 2.289133 GGGACAACACACTCTTCTCCTC 60.289 54.545 0.00 0.00 0.00 3.71
341 342 1.694696 GGGACAACACACTCTTCTCCT 59.305 52.381 0.00 0.00 0.00 3.69
387 388 9.730420 GTGTTTGATTATGAACTTTAGTGTTGT 57.270 29.630 0.00 0.00 0.00 3.32
410 411 5.843019 TCCAAGAATTTTAGGAGGAGTGT 57.157 39.130 0.00 0.00 0.00 3.55
472 473 5.070580 ACCAGTATAGTATGACTCCCAAAGC 59.929 44.000 0.00 0.00 0.00 3.51
517 518 3.835395 TCCACCAAAAAGAACCACACTTT 59.165 39.130 0.00 0.00 38.91 2.66
529 530 3.182887 ACCATAGGCATCCACCAAAAA 57.817 42.857 0.00 0.00 0.00 1.94
539 540 5.705400 AGGCATAAGTTTAACCATAGGCAT 58.295 37.500 13.98 6.89 0.00 4.40
540 541 5.124036 AGGCATAAGTTTAACCATAGGCA 57.876 39.130 13.98 0.00 0.00 4.75
635 636 6.020520 GCGAAATTTTTAGAGAGGACTAGACG 60.021 42.308 0.00 0.00 0.00 4.18
685 687 8.508883 AGTACGTGTAAACTGAGATATCTTCT 57.491 34.615 6.70 0.00 37.41 2.85
743 745 0.747852 GGCTCGGGAGAAAGAGGTAG 59.252 60.000 0.00 0.00 39.18 3.18
751 753 2.177233 ACTAATAGAGGGCTCGGGAGAA 59.823 50.000 0.00 0.00 39.18 2.87
766 769 8.818622 AGACTGTCTATGGTGTGTAACTAATA 57.181 34.615 8.91 0.00 38.04 0.98
769 772 8.640063 TTTAGACTGTCTATGGTGTGTAACTA 57.360 34.615 17.60 0.00 38.04 2.24
778 781 3.369157 GGCGGTTTTAGACTGTCTATGGT 60.369 47.826 17.60 0.00 36.29 3.55
814 817 4.020307 TGTCCATTGATCAGTACTTGCAGA 60.020 41.667 0.00 0.00 0.00 4.26
818 821 5.760253 GGGTATGTCCATTGATCAGTACTTG 59.240 44.000 0.00 0.00 38.11 3.16
876 3957 7.283354 CAGGTGATTAGTCTATGACAGTGACTA 59.717 40.741 13.22 13.22 40.86 2.59
878 3959 6.127591 ACAGGTGATTAGTCTATGACAGTGAC 60.128 42.308 0.00 0.00 34.60 3.67
893 3974 2.254152 AGGCTCTGGACAGGTGATTA 57.746 50.000 0.00 0.00 0.00 1.75
924 4006 5.804944 TCATTTGGAGCTTTGATTTCCAA 57.195 34.783 1.27 1.27 46.33 3.53
951 4033 4.918810 AAGAAACCACATGAACACCTTC 57.081 40.909 0.00 0.00 0.00 3.46
975 4057 3.055819 TCCTTGTGTTCAGTCTATCAGCC 60.056 47.826 0.00 0.00 0.00 4.85
1004 4086 6.917477 TCCAACATGAAAATGTCTTCTTTTCG 59.083 34.615 0.00 0.00 42.72 3.46
1049 4137 0.390340 TTCCTCGTGAGCAGTGCATC 60.390 55.000 19.20 12.27 0.00 3.91
1089 4177 9.271828 CAAGTTTGGCTAAAAGGACAATTAAAT 57.728 29.630 0.00 0.00 33.89 1.40
1122 4211 7.989741 CCAGAGTTGTATGAGATACCAATCTTT 59.010 37.037 0.00 0.00 42.73 2.52
1158 4247 1.856629 CCCTGATTGTGGCCTCAATT 58.143 50.000 28.68 15.75 38.03 2.32
1219 4310 5.068987 TCCAAATATTCCAAGCAGTAATGGC 59.931 40.000 0.00 0.00 36.62 4.40
1304 4395 3.118371 CCAGGTAAGATCGGCCTTACTTT 60.118 47.826 19.63 10.90 44.74 2.66
1307 4398 1.540580 GCCAGGTAAGATCGGCCTTAC 60.541 57.143 15.07 15.07 44.67 2.34
1314 4405 7.554835 ACTCTATATCTAAGCCAGGTAAGATCG 59.445 40.741 4.19 0.00 31.38 3.69
1354 4445 7.900782 TTACAAAAGAAGTGCTATACTCACC 57.099 36.000 0.00 0.00 39.18 4.02
1364 4455 9.730420 TCTAAAGTGAATTTACAAAAGAAGTGC 57.270 29.630 2.93 0.00 32.01 4.40
1407 4500 1.147191 GAGGAAAGTCCCCCAAAAGGT 59.853 52.381 0.00 0.00 37.19 3.50
1710 4811 4.388499 GACGGCTCGCTTCCCCAA 62.388 66.667 0.00 0.00 0.00 4.12
1781 4882 3.576078 TTTGTGTTCCTCATGTCTGGT 57.424 42.857 0.00 0.00 0.00 4.00
1784 4885 4.371624 TCCATTTGTGTTCCTCATGTCT 57.628 40.909 0.00 0.00 0.00 3.41
1837 4938 5.163683 GCTAGTTCTCGACAACACAGGTATA 60.164 44.000 6.33 0.00 0.00 1.47
1892 4993 6.152661 ACCGGATTTTCATACAAACATGACAT 59.847 34.615 9.46 0.00 34.69 3.06
1893 4994 5.475220 ACCGGATTTTCATACAAACATGACA 59.525 36.000 9.46 0.00 34.69 3.58
1992 5095 1.207593 GCCGCACACATTCTGACAC 59.792 57.895 0.00 0.00 0.00 3.67
2064 5167 1.519751 TTTTTGTCCATCCACGCCGG 61.520 55.000 0.00 0.00 0.00 6.13
2091 5195 1.579084 GGAGACGAGCTCACACGAGT 61.579 60.000 15.40 1.49 45.81 4.18
2114 5218 2.356793 GCATCCTCTAGCGCGCAT 60.357 61.111 35.10 20.44 0.00 4.73
2145 5249 1.667724 CCACTGATGAACGAGGAATGC 59.332 52.381 0.00 0.00 0.00 3.56
2172 5276 1.000717 CAACCATTTTGTCCACCGGTC 60.001 52.381 2.59 0.00 0.00 4.79
2226 5330 5.772393 TTTGAATCTGTTAGGAAGGGCTA 57.228 39.130 0.00 0.00 0.00 3.93
2232 5336 5.045869 ACGAGGGATTTGAATCTGTTAGGAA 60.046 40.000 3.94 0.00 35.73 3.36
2238 5342 3.191371 GCAAACGAGGGATTTGAATCTGT 59.809 43.478 1.76 0.00 39.01 3.41
2258 5362 3.181471 ACACATGGAAAAATTTCGTGGCA 60.181 39.130 13.32 0.00 38.06 4.92
2263 5367 7.459486 TGAAAACAACACATGGAAAAATTTCG 58.541 30.769 0.00 0.00 38.06 3.46
2353 5457 2.104967 CCTGCATGGGTCAATCACAAT 58.895 47.619 0.00 0.00 31.12 2.71


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

AutoCloner maintained by Alex Coulton.