Multiple sequence alignment - TraesCS4B01G296600

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 TraesCS4B01G296600 chr4B 100.000 2277 0 0 1 2277 582147050 582144774 0.000000e+00 4205
1 TraesCS4B01G296600 chr4B 87.140 972 111 8 1306 2273 105323158 105324119 0.000000e+00 1090
2 TraesCS4B01G296600 chr4B 94.318 616 34 1 687 1302 1119968 1120582 0.000000e+00 942
3 TraesCS4B01G296600 chr4B 80.938 981 186 1 325 1305 37076051 37077030 0.000000e+00 774
4 TraesCS4B01G296600 chr4B 96.894 322 6 2 3 320 457583790 457583469 9.260000e-149 536
5 TraesCS4B01G296600 chr3D 94.411 984 53 2 320 1303 408331212 408332193 0.000000e+00 1511
6 TraesCS4B01G296600 chr3D 86.364 308 41 1 1306 1613 562514947 562515253 3.620000e-88 335
7 TraesCS4B01G296600 chr7B 93.401 985 64 1 320 1304 660722408 660721425 0.000000e+00 1458
8 TraesCS4B01G296600 chr7B 85.817 973 98 10 1306 2273 374993676 374994613 0.000000e+00 996
9 TraesCS4B01G296600 chr7B 96.262 321 10 1 1 319 633799505 633799825 2.000000e-145 525
10 TraesCS4B01G296600 chr5D 89.267 941 100 1 1306 2246 448169186 448170125 0.000000e+00 1177
11 TraesCS4B01G296600 chr5D 85.382 301 42 2 1313 1613 448942361 448942063 6.110000e-81 311
12 TraesCS4B01G296600 chr6A 85.772 991 133 5 320 1306 565318782 565317796 0.000000e+00 1042
13 TraesCS4B01G296600 chr7D 86.687 969 90 5 1306 2273 379845704 379846634 0.000000e+00 1038
14 TraesCS4B01G296600 chr7D 79.964 559 88 11 1306 1843 31940746 31941301 7.630000e-105 390
15 TraesCS4B01G296600 chr3A 85.831 981 120 10 325 1303 212135344 212134381 0.000000e+00 1024
16 TraesCS4B01G296600 chr1D 84.929 982 144 4 325 1304 53959503 53958524 0.000000e+00 990
17 TraesCS4B01G296600 chr6B 82.293 977 172 1 329 1305 563087837 563086862 0.000000e+00 845
18 TraesCS4B01G296600 chr6B 85.694 692 87 3 1582 2273 2644733 2644054 0.000000e+00 719
19 TraesCS4B01G296600 chr6B 96.296 324 8 2 1 320 674206343 674206666 1.550000e-146 529
20 TraesCS4B01G296600 chr6B 95.988 324 9 2 1 320 512636538 512636215 7.210000e-145 523
21 TraesCS4B01G296600 chr7A 81.336 943 171 5 366 1306 672039393 672040332 0.000000e+00 761
22 TraesCS4B01G296600 chr3B 96.875 320 9 1 1 319 825908772 825908453 3.330000e-148 534
23 TraesCS4B01G296600 chr3B 96.562 320 10 1 1 319 550243346 550243027 1.550000e-146 529
24 TraesCS4B01G296600 chr3B 95.988 324 9 2 1 320 573977557 573977234 7.210000e-145 523
25 TraesCS4B01G296600 chr3B 81.311 412 60 8 1306 1700 606432922 606432511 3.650000e-83 318
26 TraesCS4B01G296600 chr5B 96.562 320 10 1 1 319 563499164 563499483 1.550000e-146 529
27 TraesCS4B01G296600 chr1B 96.250 320 11 1 1 319 687670423 687670104 7.210000e-145 523
28 TraesCS4B01G296600 chr4D 81.622 555 80 7 1306 1840 281286396 281286948 7.470000e-120 440
29 TraesCS4B01G296600 chr1A 80.297 538 85 11 1306 1824 483135566 483136101 9.870000e-104 387


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 TraesCS4B01G296600 chr4B 582144774 582147050 2276 True 4205 4205 100.000 1 2277 1 chr4B.!!$R2 2276
1 TraesCS4B01G296600 chr4B 105323158 105324119 961 False 1090 1090 87.140 1306 2273 1 chr4B.!!$F3 967
2 TraesCS4B01G296600 chr4B 1119968 1120582 614 False 942 942 94.318 687 1302 1 chr4B.!!$F1 615
3 TraesCS4B01G296600 chr4B 37076051 37077030 979 False 774 774 80.938 325 1305 1 chr4B.!!$F2 980
4 TraesCS4B01G296600 chr3D 408331212 408332193 981 False 1511 1511 94.411 320 1303 1 chr3D.!!$F1 983
5 TraesCS4B01G296600 chr7B 660721425 660722408 983 True 1458 1458 93.401 320 1304 1 chr7B.!!$R1 984
6 TraesCS4B01G296600 chr7B 374993676 374994613 937 False 996 996 85.817 1306 2273 1 chr7B.!!$F1 967
7 TraesCS4B01G296600 chr5D 448169186 448170125 939 False 1177 1177 89.267 1306 2246 1 chr5D.!!$F1 940
8 TraesCS4B01G296600 chr6A 565317796 565318782 986 True 1042 1042 85.772 320 1306 1 chr6A.!!$R1 986
9 TraesCS4B01G296600 chr7D 379845704 379846634 930 False 1038 1038 86.687 1306 2273 1 chr7D.!!$F2 967
10 TraesCS4B01G296600 chr7D 31940746 31941301 555 False 390 390 79.964 1306 1843 1 chr7D.!!$F1 537
11 TraesCS4B01G296600 chr3A 212134381 212135344 963 True 1024 1024 85.831 325 1303 1 chr3A.!!$R1 978
12 TraesCS4B01G296600 chr1D 53958524 53959503 979 True 990 990 84.929 325 1304 1 chr1D.!!$R1 979
13 TraesCS4B01G296600 chr6B 563086862 563087837 975 True 845 845 82.293 329 1305 1 chr6B.!!$R3 976
14 TraesCS4B01G296600 chr6B 2644054 2644733 679 True 719 719 85.694 1582 2273 1 chr6B.!!$R1 691
15 TraesCS4B01G296600 chr7A 672039393 672040332 939 False 761 761 81.336 366 1306 1 chr7A.!!$F1 940
16 TraesCS4B01G296600 chr4D 281286396 281286948 552 False 440 440 81.622 1306 1840 1 chr4D.!!$F1 534
17 TraesCS4B01G296600 chr1A 483135566 483136101 535 False 387 387 80.297 1306 1824 1 chr1A.!!$F1 518

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
228 229 0.17668 TCATCAAGAGAGCCCGAAGC 59.823 55.0 0.0 0.0 44.25 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2236 0.03831 TTCGTGCAGAGAGGAGGAGA 59.962 55.0 0.0 0.0 33.95 3.71 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
19 20 4.371417 ACTCCTCCCACCGGCGTA 62.371 66.667 6.01 0.00 0.00 4.42
20 21 2.838225 CTCCTCCCACCGGCGTAT 60.838 66.667 6.01 0.00 0.00 3.06
21 22 2.364579 TCCTCCCACCGGCGTATT 60.365 61.111 6.01 0.00 0.00 1.89
22 23 1.968050 CTCCTCCCACCGGCGTATTT 61.968 60.000 6.01 0.00 0.00 1.40
23 24 1.817941 CCTCCCACCGGCGTATTTG 60.818 63.158 6.01 0.00 0.00 2.32
24 25 1.817941 CTCCCACCGGCGTATTTGG 60.818 63.158 6.01 0.00 0.00 3.28
25 26 3.514362 CCCACCGGCGTATTTGGC 61.514 66.667 6.01 0.00 0.00 4.52
31 32 3.406559 GGCGTATTTGGCGAGGAC 58.593 61.111 0.00 0.00 0.00 3.85
32 33 1.153429 GGCGTATTTGGCGAGGACT 60.153 57.895 0.00 0.00 0.00 3.85
33 34 1.152383 GGCGTATTTGGCGAGGACTC 61.152 60.000 0.00 0.00 0.00 3.36
34 35 0.179108 GCGTATTTGGCGAGGACTCT 60.179 55.000 0.00 0.00 0.00 3.24
35 36 1.739371 GCGTATTTGGCGAGGACTCTT 60.739 52.381 0.00 0.00 0.00 2.85
36 37 1.927174 CGTATTTGGCGAGGACTCTTG 59.073 52.381 0.00 0.00 0.00 3.02
37 38 2.674177 CGTATTTGGCGAGGACTCTTGT 60.674 50.000 0.00 0.00 0.00 3.16
38 39 2.568623 ATTTGGCGAGGACTCTTGTT 57.431 45.000 0.00 0.00 0.00 2.83
39 40 3.695830 ATTTGGCGAGGACTCTTGTTA 57.304 42.857 0.00 0.00 0.00 2.41
40 41 3.695830 TTTGGCGAGGACTCTTGTTAT 57.304 42.857 0.00 0.00 0.00 1.89
41 42 2.961526 TGGCGAGGACTCTTGTTATC 57.038 50.000 0.00 0.00 0.00 1.75
42 43 1.480954 TGGCGAGGACTCTTGTTATCC 59.519 52.381 0.00 0.00 0.00 2.59
43 44 1.757699 GGCGAGGACTCTTGTTATCCT 59.242 52.381 0.00 0.00 45.84 3.24
44 45 2.957006 GGCGAGGACTCTTGTTATCCTA 59.043 50.000 0.00 0.00 43.12 2.94
45 46 3.004944 GGCGAGGACTCTTGTTATCCTAG 59.995 52.174 0.00 0.00 43.12 3.02
46 47 3.004944 GCGAGGACTCTTGTTATCCTAGG 59.995 52.174 0.82 0.82 43.12 3.02
47 48 3.004944 CGAGGACTCTTGTTATCCTAGGC 59.995 52.174 2.96 0.00 43.12 3.93
48 49 3.310193 AGGACTCTTGTTATCCTAGGCC 58.690 50.000 2.96 0.00 41.22 5.19
49 50 3.051727 AGGACTCTTGTTATCCTAGGCCT 60.052 47.826 11.78 11.78 41.22 5.19
50 51 3.322541 GGACTCTTGTTATCCTAGGCCTC 59.677 52.174 9.68 0.00 32.21 4.70
51 52 4.219919 GACTCTTGTTATCCTAGGCCTCT 58.780 47.826 9.68 0.00 0.00 3.69
52 53 3.964031 ACTCTTGTTATCCTAGGCCTCTG 59.036 47.826 9.68 3.03 0.00 3.35
53 54 3.309296 TCTTGTTATCCTAGGCCTCTGG 58.691 50.000 9.68 14.09 0.00 3.86
54 55 2.868964 TGTTATCCTAGGCCTCTGGT 57.131 50.000 9.68 0.00 0.00 4.00
55 56 3.985553 TGTTATCCTAGGCCTCTGGTA 57.014 47.619 9.68 0.00 0.00 3.25
56 57 3.573695 TGTTATCCTAGGCCTCTGGTAC 58.426 50.000 9.68 13.10 0.00 3.34
57 58 3.052414 TGTTATCCTAGGCCTCTGGTACA 60.052 47.826 9.68 15.30 0.00 2.90
58 59 4.161102 GTTATCCTAGGCCTCTGGTACAT 58.839 47.826 9.68 5.61 38.20 2.29
59 60 2.868964 TCCTAGGCCTCTGGTACATT 57.131 50.000 9.68 0.00 38.20 2.71
60 61 3.985553 TCCTAGGCCTCTGGTACATTA 57.014 47.619 9.68 0.00 38.20 1.90
61 62 4.487282 TCCTAGGCCTCTGGTACATTAT 57.513 45.455 9.68 0.00 38.20 1.28
62 63 5.610429 TCCTAGGCCTCTGGTACATTATA 57.390 43.478 9.68 0.00 38.20 0.98
63 64 6.167061 TCCTAGGCCTCTGGTACATTATAT 57.833 41.667 9.68 0.00 38.20 0.86
64 65 7.293326 TCCTAGGCCTCTGGTACATTATATA 57.707 40.000 9.68 0.00 38.20 0.86
65 66 7.715482 TCCTAGGCCTCTGGTACATTATATAA 58.285 38.462 9.68 0.00 38.20 0.98
66 67 8.181524 TCCTAGGCCTCTGGTACATTATATAAA 58.818 37.037 9.68 0.00 38.20 1.40
67 68 8.258708 CCTAGGCCTCTGGTACATTATATAAAC 58.741 40.741 9.68 0.00 38.20 2.01
68 69 7.017319 AGGCCTCTGGTACATTATATAAACC 57.983 40.000 0.00 7.59 38.20 3.27
69 70 5.873164 GGCCTCTGGTACATTATATAAACCG 59.127 44.000 0.00 5.75 38.20 4.44
70 71 6.295462 GGCCTCTGGTACATTATATAAACCGA 60.295 42.308 0.00 8.62 38.20 4.69
71 72 6.812160 GCCTCTGGTACATTATATAAACCGAG 59.188 42.308 18.15 18.15 38.20 4.63
72 73 7.321153 CCTCTGGTACATTATATAAACCGAGG 58.679 42.308 23.39 23.39 40.80 4.63
73 74 6.694447 TCTGGTACATTATATAAACCGAGGC 58.306 40.000 9.32 0.00 38.20 4.70
74 75 5.797051 TGGTACATTATATAAACCGAGGCC 58.203 41.667 0.00 0.00 32.69 5.19
75 76 5.307456 TGGTACATTATATAAACCGAGGCCA 59.693 40.000 5.01 5.39 32.69 5.36
76 77 5.873164 GGTACATTATATAAACCGAGGCCAG 59.127 44.000 5.01 0.00 0.00 4.85
77 78 4.906618 ACATTATATAAACCGAGGCCAGG 58.093 43.478 14.90 14.90 0.00 4.45
78 79 3.412237 TTATATAAACCGAGGCCAGGC 57.588 47.619 16.22 1.26 0.00 4.85
79 80 1.435256 ATATAAACCGAGGCCAGGCT 58.565 50.000 12.43 1.67 0.00 4.58
80 81 2.091098 TATAAACCGAGGCCAGGCTA 57.909 50.000 12.43 9.11 0.00 3.93
81 82 0.759346 ATAAACCGAGGCCAGGCTAG 59.241 55.000 12.43 2.86 0.00 3.42
82 83 0.616679 TAAACCGAGGCCAGGCTAGT 60.617 55.000 12.43 0.62 0.00 2.57
83 84 1.900545 AAACCGAGGCCAGGCTAGTC 61.901 60.000 12.43 5.17 0.00 2.59
84 85 3.905678 CCGAGGCCAGGCTAGTCG 61.906 72.222 12.43 16.62 0.00 4.18
85 86 2.829003 CGAGGCCAGGCTAGTCGA 60.829 66.667 20.52 0.00 31.67 4.20
86 87 2.196925 CGAGGCCAGGCTAGTCGAT 61.197 63.158 20.52 0.00 31.67 3.59
87 88 0.889638 CGAGGCCAGGCTAGTCGATA 60.890 60.000 20.52 0.00 31.67 2.92
88 89 0.885196 GAGGCCAGGCTAGTCGATAG 59.115 60.000 12.43 0.00 34.31 2.08
117 118 7.767250 TGACATTACTCATCATACCTCTAGG 57.233 40.000 0.00 0.00 42.17 3.02
118 119 6.721668 TGACATTACTCATCATACCTCTAGGG 59.278 42.308 0.20 0.00 40.27 3.53
141 142 7.484035 GGTTTAGACCACAACATATGATCTC 57.516 40.000 10.38 0.00 45.77 2.75
142 143 7.047891 GGTTTAGACCACAACATATGATCTCA 58.952 38.462 10.38 0.00 45.77 3.27
143 144 7.225538 GGTTTAGACCACAACATATGATCTCAG 59.774 40.741 10.38 0.00 45.77 3.35
144 145 5.287674 AGACCACAACATATGATCTCAGG 57.712 43.478 10.38 5.99 0.00 3.86
145 146 4.102210 AGACCACAACATATGATCTCAGGG 59.898 45.833 10.38 4.12 0.00 4.45
146 147 3.782523 ACCACAACATATGATCTCAGGGT 59.217 43.478 10.38 4.72 0.00 4.34
147 148 4.968719 ACCACAACATATGATCTCAGGGTA 59.031 41.667 10.38 0.00 0.00 3.69
148 149 5.070981 ACCACAACATATGATCTCAGGGTAG 59.929 44.000 10.38 0.00 0.00 3.18
149 150 5.305386 CCACAACATATGATCTCAGGGTAGA 59.695 44.000 10.38 0.00 0.00 2.59
150 151 6.013898 CCACAACATATGATCTCAGGGTAGAT 60.014 42.308 10.38 0.00 38.95 1.98
159 160 5.867903 ATCTCAGGGTAGATCAACTCTTG 57.132 43.478 0.00 0.00 35.28 3.02
160 161 4.678256 TCTCAGGGTAGATCAACTCTTGT 58.322 43.478 0.00 0.00 35.28 3.16
161 162 5.827756 TCTCAGGGTAGATCAACTCTTGTA 58.172 41.667 0.00 0.00 35.28 2.41
162 163 6.253758 TCTCAGGGTAGATCAACTCTTGTAA 58.746 40.000 0.00 0.00 35.28 2.41
163 164 6.153000 TCTCAGGGTAGATCAACTCTTGTAAC 59.847 42.308 0.00 0.00 35.28 2.50
164 165 5.187186 TCAGGGTAGATCAACTCTTGTAACC 59.813 44.000 0.00 0.00 35.28 2.85
165 166 4.470304 AGGGTAGATCAACTCTTGTAACCC 59.530 45.833 0.00 0.00 38.37 4.11
166 167 4.383880 GGGTAGATCAACTCTTGTAACCCC 60.384 50.000 0.00 0.00 35.33 4.95
167 168 4.470304 GGTAGATCAACTCTTGTAACCCCT 59.530 45.833 0.00 0.00 35.28 4.79
168 169 5.659971 GGTAGATCAACTCTTGTAACCCCTA 59.340 44.000 0.00 0.00 35.28 3.53
169 170 6.326843 GGTAGATCAACTCTTGTAACCCCTAT 59.673 42.308 0.00 0.00 35.28 2.57
170 171 7.508296 GGTAGATCAACTCTTGTAACCCCTATA 59.492 40.741 0.00 0.00 35.28 1.31
171 172 7.362802 AGATCAACTCTTGTAACCCCTATAC 57.637 40.000 0.00 0.00 0.00 1.47
172 173 7.133483 AGATCAACTCTTGTAACCCCTATACT 58.867 38.462 0.00 0.00 0.00 2.12
173 174 6.786967 TCAACTCTTGTAACCCCTATACTC 57.213 41.667 0.00 0.00 0.00 2.59
174 175 6.258354 TCAACTCTTGTAACCCCTATACTCA 58.742 40.000 0.00 0.00 0.00 3.41
175 176 6.901300 TCAACTCTTGTAACCCCTATACTCAT 59.099 38.462 0.00 0.00 0.00 2.90
176 177 7.402071 TCAACTCTTGTAACCCCTATACTCATT 59.598 37.037 0.00 0.00 0.00 2.57
177 178 8.701895 CAACTCTTGTAACCCCTATACTCATTA 58.298 37.037 0.00 0.00 0.00 1.90
178 179 8.849543 ACTCTTGTAACCCCTATACTCATTAA 57.150 34.615 0.00 0.00 0.00 1.40
179 180 9.275572 ACTCTTGTAACCCCTATACTCATTAAA 57.724 33.333 0.00 0.00 0.00 1.52
180 181 9.765795 CTCTTGTAACCCCTATACTCATTAAAG 57.234 37.037 0.00 0.00 0.00 1.85
181 182 9.275572 TCTTGTAACCCCTATACTCATTAAAGT 57.724 33.333 0.00 0.00 0.00 2.66
182 183 9.543783 CTTGTAACCCCTATACTCATTAAAGTC 57.456 37.037 0.00 0.00 0.00 3.01
183 184 8.612486 TGTAACCCCTATACTCATTAAAGTCA 57.388 34.615 0.00 0.00 0.00 3.41
184 185 9.049050 TGTAACCCCTATACTCATTAAAGTCAA 57.951 33.333 0.00 0.00 0.00 3.18
187 188 8.331931 ACCCCTATACTCATTAAAGTCAATCA 57.668 34.615 0.00 0.00 0.00 2.57
188 189 8.778059 ACCCCTATACTCATTAAAGTCAATCAA 58.222 33.333 0.00 0.00 0.00 2.57
189 190 9.277783 CCCCTATACTCATTAAAGTCAATCAAG 57.722 37.037 0.00 0.00 0.00 3.02
190 191 8.778358 CCCTATACTCATTAAAGTCAATCAAGC 58.222 37.037 0.00 0.00 0.00 4.01
191 192 9.330063 CCTATACTCATTAAAGTCAATCAAGCA 57.670 33.333 0.00 0.00 0.00 3.91
193 194 5.947443 ACTCATTAAAGTCAATCAAGCAGC 58.053 37.500 0.00 0.00 0.00 5.25
194 195 5.474532 ACTCATTAAAGTCAATCAAGCAGCA 59.525 36.000 0.00 0.00 0.00 4.41
195 196 6.152323 ACTCATTAAAGTCAATCAAGCAGCAT 59.848 34.615 0.00 0.00 0.00 3.79
196 197 6.327154 TCATTAAAGTCAATCAAGCAGCATG 58.673 36.000 0.00 0.00 40.87 4.06
197 198 5.710513 TTAAAGTCAATCAAGCAGCATGT 57.289 34.783 0.00 0.00 39.31 3.21
198 199 6.816134 TTAAAGTCAATCAAGCAGCATGTA 57.184 33.333 0.00 0.00 39.31 2.29
199 200 4.959596 AAGTCAATCAAGCAGCATGTAG 57.040 40.909 0.00 0.00 39.31 2.74
200 201 3.276857 AGTCAATCAAGCAGCATGTAGG 58.723 45.455 0.00 0.00 39.31 3.18
201 202 2.357009 GTCAATCAAGCAGCATGTAGGG 59.643 50.000 0.00 0.00 39.31 3.53
202 203 2.025981 TCAATCAAGCAGCATGTAGGGT 60.026 45.455 0.00 0.00 39.31 4.34
203 204 3.199727 TCAATCAAGCAGCATGTAGGGTA 59.800 43.478 0.00 0.00 39.31 3.69
204 205 4.139786 CAATCAAGCAGCATGTAGGGTAT 58.860 43.478 0.00 0.00 39.31 2.73
205 206 3.931907 TCAAGCAGCATGTAGGGTATT 57.068 42.857 0.00 0.00 39.31 1.89
206 207 5.567037 ATCAAGCAGCATGTAGGGTATTA 57.433 39.130 0.00 0.00 39.31 0.98
207 208 5.567037 TCAAGCAGCATGTAGGGTATTAT 57.433 39.130 0.00 0.00 39.31 1.28
208 209 5.551233 TCAAGCAGCATGTAGGGTATTATC 58.449 41.667 0.00 0.00 39.31 1.75
209 210 5.307976 TCAAGCAGCATGTAGGGTATTATCT 59.692 40.000 0.00 0.00 39.31 1.98
210 211 5.413309 AGCAGCATGTAGGGTATTATCTC 57.587 43.478 0.00 0.00 39.31 2.75
211 212 4.840680 AGCAGCATGTAGGGTATTATCTCA 59.159 41.667 0.00 0.00 39.31 3.27
212 213 5.486775 AGCAGCATGTAGGGTATTATCTCAT 59.513 40.000 0.00 0.00 39.31 2.90
213 214 5.814705 GCAGCATGTAGGGTATTATCTCATC 59.185 44.000 0.00 0.00 39.31 2.92
214 215 6.575056 GCAGCATGTAGGGTATTATCTCATCA 60.575 42.308 0.00 0.00 39.31 3.07
215 216 7.389232 CAGCATGTAGGGTATTATCTCATCAA 58.611 38.462 0.00 0.00 0.00 2.57
216 217 7.548427 CAGCATGTAGGGTATTATCTCATCAAG 59.452 40.741 0.00 0.00 0.00 3.02
217 218 7.455953 AGCATGTAGGGTATTATCTCATCAAGA 59.544 37.037 0.00 0.00 38.72 3.02
218 219 7.763528 GCATGTAGGGTATTATCTCATCAAGAG 59.236 40.741 0.00 0.00 46.14 2.85
228 229 0.176680 TCATCAAGAGAGCCCGAAGC 59.823 55.000 0.00 0.00 44.25 3.86
240 241 1.389555 CCCGAAGCTGGGTAAAATCC 58.610 55.000 0.68 0.00 44.76 3.01
241 242 2.022238 CCCGAAGCTGGGTAAAATCCC 61.022 57.143 0.68 0.00 44.76 3.85
250 251 3.775661 GGGTAAAATCCCGTGTTCATG 57.224 47.619 0.00 0.00 37.93 3.07
251 252 3.086282 GGGTAAAATCCCGTGTTCATGT 58.914 45.455 0.00 0.00 37.93 3.21
252 253 3.508402 GGGTAAAATCCCGTGTTCATGTT 59.492 43.478 0.00 0.00 37.93 2.71
253 254 4.701171 GGGTAAAATCCCGTGTTCATGTTA 59.299 41.667 0.00 0.00 37.93 2.41
254 255 5.392272 GGGTAAAATCCCGTGTTCATGTTAC 60.392 44.000 0.00 0.00 37.93 2.50
255 256 4.776795 AAAATCCCGTGTTCATGTTACC 57.223 40.909 0.00 0.00 0.00 2.85
256 257 3.426787 AATCCCGTGTTCATGTTACCA 57.573 42.857 0.00 0.00 0.00 3.25
257 258 3.644966 ATCCCGTGTTCATGTTACCAT 57.355 42.857 0.00 0.00 0.00 3.55
258 259 3.426787 TCCCGTGTTCATGTTACCATT 57.573 42.857 0.00 0.00 0.00 3.16
259 260 3.078097 TCCCGTGTTCATGTTACCATTG 58.922 45.455 0.00 0.00 0.00 2.82
260 261 3.078097 CCCGTGTTCATGTTACCATTGA 58.922 45.455 0.00 0.00 0.00 2.57
261 262 3.694072 CCCGTGTTCATGTTACCATTGAT 59.306 43.478 0.00 0.00 0.00 2.57
262 263 4.201910 CCCGTGTTCATGTTACCATTGATC 60.202 45.833 0.00 0.00 0.00 2.92
263 264 4.201910 CCGTGTTCATGTTACCATTGATCC 60.202 45.833 0.00 0.00 0.00 3.36
264 265 4.635765 CGTGTTCATGTTACCATTGATCCT 59.364 41.667 0.00 0.00 0.00 3.24
265 266 5.815222 CGTGTTCATGTTACCATTGATCCTA 59.185 40.000 0.00 0.00 0.00 2.94
266 267 6.315144 CGTGTTCATGTTACCATTGATCCTAA 59.685 38.462 0.00 0.00 0.00 2.69
267 268 7.465916 CGTGTTCATGTTACCATTGATCCTAAG 60.466 40.741 0.00 0.00 0.00 2.18
268 269 7.552687 GTGTTCATGTTACCATTGATCCTAAGA 59.447 37.037 0.00 0.00 0.00 2.10
269 270 7.552687 TGTTCATGTTACCATTGATCCTAAGAC 59.447 37.037 0.00 0.00 0.00 3.01
270 271 6.280643 TCATGTTACCATTGATCCTAAGACG 58.719 40.000 0.00 0.00 0.00 4.18
271 272 4.439057 TGTTACCATTGATCCTAAGACGC 58.561 43.478 0.00 0.00 0.00 5.19
272 273 4.081365 TGTTACCATTGATCCTAAGACGCA 60.081 41.667 0.00 0.00 0.00 5.24
273 274 2.906354 ACCATTGATCCTAAGACGCAC 58.094 47.619 0.00 0.00 0.00 5.34
274 275 2.213499 CCATTGATCCTAAGACGCACC 58.787 52.381 0.00 0.00 0.00 5.01
275 276 1.860950 CATTGATCCTAAGACGCACCG 59.139 52.381 0.00 0.00 0.00 4.94
276 277 0.459585 TTGATCCTAAGACGCACCGC 60.460 55.000 0.00 0.00 0.00 5.68
277 278 1.320344 TGATCCTAAGACGCACCGCT 61.320 55.000 0.00 0.00 0.00 5.52
278 279 0.179108 GATCCTAAGACGCACCGCTT 60.179 55.000 0.00 0.00 0.00 4.68
279 280 0.460284 ATCCTAAGACGCACCGCTTG 60.460 55.000 0.00 0.00 0.00 4.01
280 281 2.100631 CCTAAGACGCACCGCTTGG 61.101 63.158 0.00 0.00 39.35 3.61
281 282 2.047655 TAAGACGCACCGCTTGGG 60.048 61.111 0.00 0.00 43.87 4.12
282 283 2.501223 CTAAGACGCACCGCTTGGGA 62.501 60.000 6.29 0.00 40.70 4.37
283 284 2.775032 TAAGACGCACCGCTTGGGAC 62.775 60.000 6.29 0.91 40.70 4.46
289 290 4.342086 ACCGCTTGGGACCCCCTA 62.342 66.667 8.45 0.00 45.70 3.53
290 291 3.793888 CCGCTTGGGACCCCCTAC 61.794 72.222 8.45 0.00 45.70 3.18
291 292 3.793888 CGCTTGGGACCCCCTACC 61.794 72.222 8.45 0.00 45.70 3.18
292 293 3.417779 GCTTGGGACCCCCTACCC 61.418 72.222 8.45 0.00 45.70 3.69
296 297 3.759101 GGGACCCCCTACCCGAGA 61.759 72.222 0.00 0.00 41.34 4.04
297 298 2.613421 GGACCCCCTACCCGAGAT 59.387 66.667 0.00 0.00 0.00 2.75
298 299 1.533513 GGACCCCCTACCCGAGATC 60.534 68.421 0.00 0.00 0.00 2.75
299 300 1.542679 GACCCCCTACCCGAGATCT 59.457 63.158 0.00 0.00 0.00 2.75
300 301 0.828343 GACCCCCTACCCGAGATCTG 60.828 65.000 0.00 0.00 0.00 2.90
301 302 2.210711 CCCCCTACCCGAGATCTGC 61.211 68.421 0.00 0.00 0.00 4.26
302 303 2.210711 CCCCTACCCGAGATCTGCC 61.211 68.421 0.00 0.00 0.00 4.85
303 304 2.565645 CCCTACCCGAGATCTGCCG 61.566 68.421 0.00 0.00 0.00 5.69
304 305 2.565645 CCTACCCGAGATCTGCCGG 61.566 68.421 14.42 14.42 44.94 6.13
305 306 1.828660 CTACCCGAGATCTGCCGGT 60.829 63.158 18.55 13.92 43.93 5.28
306 307 1.380785 TACCCGAGATCTGCCGGTT 60.381 57.895 18.55 9.56 43.93 4.44
307 308 0.974010 TACCCGAGATCTGCCGGTTT 60.974 55.000 18.55 9.73 43.93 3.27
308 309 1.078426 CCCGAGATCTGCCGGTTTT 60.078 57.895 18.55 0.00 43.93 2.43
309 310 1.369091 CCCGAGATCTGCCGGTTTTG 61.369 60.000 18.55 3.10 43.93 2.44
310 311 0.391130 CCGAGATCTGCCGGTTTTGA 60.391 55.000 13.39 0.00 40.78 2.69
311 312 0.721718 CGAGATCTGCCGGTTTTGAC 59.278 55.000 0.00 0.00 0.00 3.18
312 313 1.808411 GAGATCTGCCGGTTTTGACA 58.192 50.000 0.00 0.00 0.00 3.58
313 314 1.464997 GAGATCTGCCGGTTTTGACAC 59.535 52.381 0.00 0.00 0.00 3.67
314 315 0.521735 GATCTGCCGGTTTTGACACC 59.478 55.000 1.90 0.00 0.00 4.16
315 316 0.179004 ATCTGCCGGTTTTGACACCA 60.179 50.000 1.90 0.00 36.49 4.17
316 317 0.394488 TCTGCCGGTTTTGACACCAA 60.394 50.000 1.90 0.00 36.49 3.67
317 318 0.248866 CTGCCGGTTTTGACACCAAC 60.249 55.000 1.90 0.00 36.49 3.77
318 319 0.965866 TGCCGGTTTTGACACCAACA 60.966 50.000 1.90 0.00 36.49 3.33
380 381 1.691195 TTCTGGTGGCGAGTTGTCCA 61.691 55.000 0.00 0.00 0.00 4.02
424 426 1.440518 CTCCGGCGTCGTCATATCG 60.441 63.158 9.28 0.00 33.95 2.92
471 475 3.256879 GTCTTGCGATGGATGAGGATCTA 59.743 47.826 0.00 0.00 34.92 1.98
484 488 6.432162 GGATGAGGATCTAATGCATGCTTTAA 59.568 38.462 22.09 15.08 34.92 1.52
535 539 2.810274 GAGCAAGCACATGAGTTCTTCA 59.190 45.455 0.00 0.00 40.85 3.02
595 600 7.227156 GTCTCAGGATATTTTATGTGATGGGT 58.773 38.462 0.00 0.00 0.00 4.51
626 631 2.230992 ACAGTGAGAGAGCTGTGATGAC 59.769 50.000 0.00 0.00 43.45 3.06
684 689 4.405680 AGGGTTACTCATGACGATGATCAA 59.594 41.667 0.00 0.00 37.97 2.57
745 750 1.843206 TGGCACTGCTTGATATACCCA 59.157 47.619 0.00 0.00 0.00 4.51
842 847 0.674895 GCTTTGAGCATGGAGTCGGT 60.675 55.000 0.00 0.00 41.89 4.69
1028 1034 2.096496 CCGATTGCTTGGAGATTGTGAC 59.904 50.000 0.00 0.00 0.00 3.67
1110 1117 4.285775 AGAGAGCTAGCTTCCTTGTTTTCT 59.714 41.667 20.42 7.11 0.00 2.52
1236 1243 0.401738 CCCTCTTTCCTGCTCACCAA 59.598 55.000 0.00 0.00 0.00 3.67
1352 1359 3.566261 CAAGCATTGTCGTCGCCT 58.434 55.556 0.00 0.00 42.34 5.52
1353 1360 1.868997 CAAGCATTGTCGTCGCCTT 59.131 52.632 0.00 0.00 42.34 4.35
1408 1415 4.039124 AGACCGAATTTCCAAAACAATGCT 59.961 37.500 0.00 0.00 0.00 3.79
1474 1481 3.088532 TGGATTTTCACCCTGGAAATCG 58.911 45.455 9.06 0.00 36.71 3.34
1521 1528 1.059098 AAGATGCAGTCCACCTGTGA 58.941 50.000 0.00 0.00 43.55 3.58
1529 1536 1.847506 TCCACCTGTGATGCCACCT 60.848 57.895 0.00 0.00 42.53 4.00
1530 1537 1.075482 CCACCTGTGATGCCACCTT 59.925 57.895 0.00 0.00 42.53 3.50
1531 1538 1.246056 CCACCTGTGATGCCACCTTG 61.246 60.000 0.00 0.00 42.53 3.61
1644 1674 0.251634 TCGCAGCCACCATGACATTA 59.748 50.000 0.00 0.00 0.00 1.90
1671 1701 6.351711 CAACTCTGTCAGATCCATGGAAATA 58.648 40.000 20.67 1.64 0.00 1.40
1688 1718 9.645059 CATGGAAATATATACGAAGACATGTCT 57.355 33.333 22.89 22.89 42.75 3.41
1760 1805 4.345337 GACCGCATCGATTCCTCC 57.655 61.111 0.00 0.00 0.00 4.30
1843 1888 2.107953 GGCAGCCAGATCGAGGAC 59.892 66.667 6.55 3.28 0.00 3.85
1930 1975 4.155733 CCACGCTACCGGCCATCA 62.156 66.667 0.00 0.00 39.22 3.07
1931 1976 2.125310 CACGCTACCGGCCATCAA 60.125 61.111 0.00 0.00 39.22 2.57
2042 2087 3.991536 GAAGAGCACGAGACGGCCC 62.992 68.421 0.00 0.00 0.00 5.80
2121 2167 4.473520 CACCGCCTTGATCCGCCT 62.474 66.667 0.00 0.00 0.00 5.52
2150 2196 4.697756 CAAGAACCCGCCGCCTCA 62.698 66.667 0.00 0.00 0.00 3.86
2184 2230 2.534019 CGCCAAACTGTGTGCGACT 61.534 57.895 11.81 0.00 44.66 4.18
2190 2236 2.462456 AACTGTGTGCGACTCATCAT 57.538 45.000 0.00 0.00 0.00 2.45
2221 2267 3.993081 CTCTGCACGAAGAAGAAGAACAT 59.007 43.478 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.674050 ATACGCCGGTGGGAGGAGT 62.674 63.158 21.14 0.00 43.94 3.85
4 5 1.991167 AAATACGCCGGTGGGAGGA 60.991 57.895 21.14 0.00 37.45 3.71
5 6 1.817941 CAAATACGCCGGTGGGAGG 60.818 63.158 21.14 0.52 37.45 4.30
6 7 1.817941 CCAAATACGCCGGTGGGAG 60.818 63.158 21.14 4.14 39.33 4.30
7 8 2.269562 CCAAATACGCCGGTGGGA 59.730 61.111 21.14 7.19 34.06 4.37
8 9 3.514362 GCCAAATACGCCGGTGGG 61.514 66.667 21.14 11.45 0.00 4.61
9 10 3.871574 CGCCAAATACGCCGGTGG 61.872 66.667 21.14 11.24 0.00 4.61
10 11 2.808958 CTCGCCAAATACGCCGGTG 61.809 63.158 14.93 14.93 0.00 4.94
11 12 2.510691 CTCGCCAAATACGCCGGT 60.511 61.111 1.90 0.00 0.00 5.28
12 13 3.269347 CCTCGCCAAATACGCCGG 61.269 66.667 0.00 0.00 0.00 6.13
13 14 2.202824 TCCTCGCCAAATACGCCG 60.203 61.111 0.00 0.00 0.00 6.46
14 15 1.152383 GAGTCCTCGCCAAATACGCC 61.152 60.000 0.00 0.00 0.00 5.68
15 16 0.179108 AGAGTCCTCGCCAAATACGC 60.179 55.000 0.00 0.00 34.09 4.42
16 17 1.927174 CAAGAGTCCTCGCCAAATACG 59.073 52.381 0.00 0.00 34.09 3.06
17 18 2.973945 ACAAGAGTCCTCGCCAAATAC 58.026 47.619 0.00 0.00 34.09 1.89
18 19 3.695830 AACAAGAGTCCTCGCCAAATA 57.304 42.857 0.00 0.00 34.09 1.40
19 20 2.568623 AACAAGAGTCCTCGCCAAAT 57.431 45.000 0.00 0.00 34.09 2.32
20 21 3.596214 GATAACAAGAGTCCTCGCCAAA 58.404 45.455 0.00 0.00 34.09 3.28
21 22 2.093658 GGATAACAAGAGTCCTCGCCAA 60.094 50.000 0.00 0.00 34.09 4.52
22 23 1.480954 GGATAACAAGAGTCCTCGCCA 59.519 52.381 0.00 0.00 34.09 5.69
23 24 1.757699 AGGATAACAAGAGTCCTCGCC 59.242 52.381 0.00 0.00 37.88 5.54
24 25 3.004944 CCTAGGATAACAAGAGTCCTCGC 59.995 52.174 1.05 0.00 41.34 5.03
25 26 3.004944 GCCTAGGATAACAAGAGTCCTCG 59.995 52.174 14.75 0.00 41.34 4.63
26 27 3.322541 GGCCTAGGATAACAAGAGTCCTC 59.677 52.174 14.75 0.00 41.34 3.71
27 28 3.051727 AGGCCTAGGATAACAAGAGTCCT 60.052 47.826 14.75 1.21 44.31 3.85
28 29 3.310193 AGGCCTAGGATAACAAGAGTCC 58.690 50.000 14.75 0.00 0.00 3.85
29 30 4.038642 CAGAGGCCTAGGATAACAAGAGTC 59.961 50.000 14.75 0.00 0.00 3.36
30 31 3.964031 CAGAGGCCTAGGATAACAAGAGT 59.036 47.826 14.75 0.00 0.00 3.24
31 32 3.323403 CCAGAGGCCTAGGATAACAAGAG 59.677 52.174 14.75 0.00 0.00 2.85
32 33 3.309296 CCAGAGGCCTAGGATAACAAGA 58.691 50.000 14.75 0.00 0.00 3.02
33 34 3.041946 ACCAGAGGCCTAGGATAACAAG 58.958 50.000 26.29 2.53 0.00 3.16
34 35 3.130734 ACCAGAGGCCTAGGATAACAA 57.869 47.619 26.29 0.00 0.00 2.83
35 36 2.868964 ACCAGAGGCCTAGGATAACA 57.131 50.000 26.29 0.00 0.00 2.41
36 37 3.573695 TGTACCAGAGGCCTAGGATAAC 58.426 50.000 26.29 19.89 0.00 1.89
37 38 3.985553 TGTACCAGAGGCCTAGGATAA 57.014 47.619 26.29 11.10 0.00 1.75
38 39 4.487282 AATGTACCAGAGGCCTAGGATA 57.513 45.455 26.29 13.79 0.00 2.59
39 40 3.352611 AATGTACCAGAGGCCTAGGAT 57.647 47.619 26.29 14.62 0.00 3.24
40 41 2.868964 AATGTACCAGAGGCCTAGGA 57.131 50.000 26.29 8.15 0.00 2.94
41 42 7.973048 TTATATAATGTACCAGAGGCCTAGG 57.027 40.000 19.66 19.66 0.00 3.02
42 43 8.258708 GGTTTATATAATGTACCAGAGGCCTAG 58.741 40.741 4.42 0.20 0.00 3.02
43 44 7.093640 CGGTTTATATAATGTACCAGAGGCCTA 60.094 40.741 4.42 0.00 0.00 3.93
44 45 6.295688 CGGTTTATATAATGTACCAGAGGCCT 60.296 42.308 3.86 3.86 0.00 5.19
45 46 5.873164 CGGTTTATATAATGTACCAGAGGCC 59.127 44.000 13.00 0.00 0.00 5.19
46 47 6.694447 TCGGTTTATATAATGTACCAGAGGC 58.306 40.000 13.00 0.00 0.00 4.70
47 48 7.321153 CCTCGGTTTATATAATGTACCAGAGG 58.679 42.308 23.39 23.39 40.13 3.69
48 49 6.812160 GCCTCGGTTTATATAATGTACCAGAG 59.188 42.308 18.15 18.15 33.44 3.35
49 50 6.295462 GGCCTCGGTTTATATAATGTACCAGA 60.295 42.308 13.00 10.26 0.00 3.86
50 51 5.873164 GGCCTCGGTTTATATAATGTACCAG 59.127 44.000 13.00 9.66 0.00 4.00
51 52 5.307456 TGGCCTCGGTTTATATAATGTACCA 59.693 40.000 3.32 5.68 0.00 3.25
52 53 5.797051 TGGCCTCGGTTTATATAATGTACC 58.203 41.667 3.32 5.15 0.00 3.34
53 54 5.873164 CCTGGCCTCGGTTTATATAATGTAC 59.127 44.000 3.32 0.00 0.00 2.90
54 55 5.570034 GCCTGGCCTCGGTTTATATAATGTA 60.570 44.000 7.66 0.00 0.00 2.29
55 56 4.806286 GCCTGGCCTCGGTTTATATAATGT 60.806 45.833 7.66 0.00 0.00 2.71
56 57 3.689649 GCCTGGCCTCGGTTTATATAATG 59.310 47.826 7.66 0.00 0.00 1.90
57 58 3.587506 AGCCTGGCCTCGGTTTATATAAT 59.412 43.478 16.57 0.00 0.00 1.28
58 59 2.976882 AGCCTGGCCTCGGTTTATATAA 59.023 45.455 16.57 0.00 0.00 0.98
59 60 2.616524 AGCCTGGCCTCGGTTTATATA 58.383 47.619 16.57 0.00 0.00 0.86
60 61 1.435256 AGCCTGGCCTCGGTTTATAT 58.565 50.000 16.57 0.00 0.00 0.86
61 62 1.968493 CTAGCCTGGCCTCGGTTTATA 59.032 52.381 16.57 0.00 0.00 0.98
62 63 0.759346 CTAGCCTGGCCTCGGTTTAT 59.241 55.000 16.57 0.00 0.00 1.40
63 64 0.616679 ACTAGCCTGGCCTCGGTTTA 60.617 55.000 16.57 0.00 0.00 2.01
64 65 1.900545 GACTAGCCTGGCCTCGGTTT 61.901 60.000 16.57 0.00 0.00 3.27
65 66 2.284699 ACTAGCCTGGCCTCGGTT 60.285 61.111 16.57 5.19 0.00 4.44
66 67 2.760385 GACTAGCCTGGCCTCGGT 60.760 66.667 16.57 9.04 0.00 4.69
67 68 3.905678 CGACTAGCCTGGCCTCGG 61.906 72.222 16.57 5.70 0.00 4.63
68 69 0.889638 TATCGACTAGCCTGGCCTCG 60.890 60.000 16.57 18.41 0.00 4.63
69 70 0.885196 CTATCGACTAGCCTGGCCTC 59.115 60.000 16.57 6.80 0.00 4.70
70 71 0.478942 TCTATCGACTAGCCTGGCCT 59.521 55.000 16.57 5.44 0.00 5.19
71 72 1.203523 CATCTATCGACTAGCCTGGCC 59.796 57.143 16.57 0.00 0.00 5.36
72 73 2.163509 TCATCTATCGACTAGCCTGGC 58.836 52.381 11.65 11.65 0.00 4.85
73 74 4.013050 TCATCATCTATCGACTAGCCTGG 58.987 47.826 0.00 0.00 0.00 4.45
74 75 4.457257 TGTCATCATCTATCGACTAGCCTG 59.543 45.833 0.00 0.00 0.00 4.85
75 76 4.657013 TGTCATCATCTATCGACTAGCCT 58.343 43.478 0.00 0.00 0.00 4.58
76 77 5.574891 ATGTCATCATCTATCGACTAGCC 57.425 43.478 0.00 0.00 0.00 3.93
77 78 7.757526 AGTAATGTCATCATCTATCGACTAGC 58.242 38.462 0.00 0.00 32.56 3.42
78 79 8.940952 TGAGTAATGTCATCATCTATCGACTAG 58.059 37.037 0.00 0.00 32.56 2.57
79 80 8.848474 TGAGTAATGTCATCATCTATCGACTA 57.152 34.615 0.00 0.00 32.56 2.59
80 81 7.751768 TGAGTAATGTCATCATCTATCGACT 57.248 36.000 0.00 0.00 32.56 4.18
92 93 7.398618 CCCTAGAGGTATGATGAGTAATGTCAT 59.601 40.741 0.00 0.00 40.00 3.06
93 94 6.721668 CCCTAGAGGTATGATGAGTAATGTCA 59.278 42.308 0.00 0.00 0.00 3.58
94 95 7.164230 CCCTAGAGGTATGATGAGTAATGTC 57.836 44.000 0.00 0.00 0.00 3.06
110 111 3.581332 TGTTGTGGTCTAAACCCTAGAGG 59.419 47.826 0.00 0.00 45.83 3.69
111 112 4.884668 TGTTGTGGTCTAAACCCTAGAG 57.115 45.455 0.00 0.00 45.83 2.43
112 113 6.670464 TCATATGTTGTGGTCTAAACCCTAGA 59.330 38.462 1.90 0.00 45.83 2.43
113 114 6.884832 TCATATGTTGTGGTCTAAACCCTAG 58.115 40.000 1.90 0.00 45.83 3.02
114 115 6.877668 TCATATGTTGTGGTCTAAACCCTA 57.122 37.500 1.90 0.00 45.83 3.53
115 116 5.772393 TCATATGTTGTGGTCTAAACCCT 57.228 39.130 1.90 0.00 45.83 4.34
116 117 6.357367 AGATCATATGTTGTGGTCTAAACCC 58.643 40.000 1.90 0.00 45.83 4.11
117 118 7.047891 TGAGATCATATGTTGTGGTCTAAACC 58.952 38.462 1.90 0.00 46.66 3.27
118 119 7.225538 CCTGAGATCATATGTTGTGGTCTAAAC 59.774 40.741 1.90 0.00 0.00 2.01
119 120 7.275183 CCTGAGATCATATGTTGTGGTCTAAA 58.725 38.462 1.90 0.00 0.00 1.85
120 121 6.183361 CCCTGAGATCATATGTTGTGGTCTAA 60.183 42.308 1.90 0.00 0.00 2.10
121 122 5.305386 CCCTGAGATCATATGTTGTGGTCTA 59.695 44.000 1.90 0.00 0.00 2.59
122 123 4.102210 CCCTGAGATCATATGTTGTGGTCT 59.898 45.833 1.90 0.00 0.00 3.85
123 124 4.141620 ACCCTGAGATCATATGTTGTGGTC 60.142 45.833 1.90 0.00 0.00 4.02
124 125 3.782523 ACCCTGAGATCATATGTTGTGGT 59.217 43.478 1.90 0.00 0.00 4.16
125 126 4.428294 ACCCTGAGATCATATGTTGTGG 57.572 45.455 1.90 0.00 0.00 4.17
126 127 6.410942 TCTACCCTGAGATCATATGTTGTG 57.589 41.667 1.90 0.00 0.00 3.33
137 138 5.276440 ACAAGAGTTGATCTACCCTGAGAT 58.724 41.667 3.54 0.00 37.23 2.75
138 139 4.678256 ACAAGAGTTGATCTACCCTGAGA 58.322 43.478 3.54 0.00 37.23 3.27
139 140 6.334202 GTTACAAGAGTTGATCTACCCTGAG 58.666 44.000 3.54 0.00 37.23 3.35
140 141 5.187186 GGTTACAAGAGTTGATCTACCCTGA 59.813 44.000 3.54 0.00 37.23 3.86
141 142 5.420409 GGTTACAAGAGTTGATCTACCCTG 58.580 45.833 3.54 2.20 37.23 4.45
142 143 4.470304 GGGTTACAAGAGTTGATCTACCCT 59.530 45.833 3.54 0.00 37.23 4.34
143 144 4.383880 GGGGTTACAAGAGTTGATCTACCC 60.384 50.000 3.54 0.00 37.23 3.69
144 145 4.470304 AGGGGTTACAAGAGTTGATCTACC 59.530 45.833 3.54 0.00 37.23 3.18
145 146 5.678955 AGGGGTTACAAGAGTTGATCTAC 57.321 43.478 0.00 0.00 37.23 2.59
146 147 8.287350 AGTATAGGGGTTACAAGAGTTGATCTA 58.713 37.037 0.00 0.00 37.23 1.98
147 148 7.133483 AGTATAGGGGTTACAAGAGTTGATCT 58.867 38.462 0.00 0.00 41.27 2.75
148 149 7.069578 TGAGTATAGGGGTTACAAGAGTTGATC 59.930 40.741 0.00 0.00 0.00 2.92
149 150 6.901300 TGAGTATAGGGGTTACAAGAGTTGAT 59.099 38.462 0.00 0.00 0.00 2.57
150 151 6.258354 TGAGTATAGGGGTTACAAGAGTTGA 58.742 40.000 0.00 0.00 0.00 3.18
151 152 6.540438 TGAGTATAGGGGTTACAAGAGTTG 57.460 41.667 0.00 0.00 0.00 3.16
152 153 7.750947 AATGAGTATAGGGGTTACAAGAGTT 57.249 36.000 0.00 0.00 0.00 3.01
153 154 8.849543 TTAATGAGTATAGGGGTTACAAGAGT 57.150 34.615 0.00 0.00 0.00 3.24
154 155 9.765795 CTTTAATGAGTATAGGGGTTACAAGAG 57.234 37.037 0.00 0.00 0.00 2.85
155 156 9.275572 ACTTTAATGAGTATAGGGGTTACAAGA 57.724 33.333 0.00 0.00 0.00 3.02
156 157 9.543783 GACTTTAATGAGTATAGGGGTTACAAG 57.456 37.037 0.00 0.00 0.00 3.16
157 158 9.049050 TGACTTTAATGAGTATAGGGGTTACAA 57.951 33.333 0.00 0.00 0.00 2.41
158 159 8.612486 TGACTTTAATGAGTATAGGGGTTACA 57.388 34.615 0.00 0.00 0.00 2.41
161 162 8.778059 TGATTGACTTTAATGAGTATAGGGGTT 58.222 33.333 0.00 0.00 0.00 4.11
162 163 8.331931 TGATTGACTTTAATGAGTATAGGGGT 57.668 34.615 0.00 0.00 0.00 4.95
163 164 9.277783 CTTGATTGACTTTAATGAGTATAGGGG 57.722 37.037 0.00 0.00 0.00 4.79
164 165 8.778358 GCTTGATTGACTTTAATGAGTATAGGG 58.222 37.037 0.00 0.00 0.00 3.53
165 166 9.330063 TGCTTGATTGACTTTAATGAGTATAGG 57.670 33.333 0.00 0.00 0.00 2.57
167 168 8.830580 GCTGCTTGATTGACTTTAATGAGTATA 58.169 33.333 0.00 0.00 0.00 1.47
168 169 7.337689 TGCTGCTTGATTGACTTTAATGAGTAT 59.662 33.333 0.00 0.00 0.00 2.12
169 170 6.654582 TGCTGCTTGATTGACTTTAATGAGTA 59.345 34.615 0.00 0.00 0.00 2.59
170 171 5.474532 TGCTGCTTGATTGACTTTAATGAGT 59.525 36.000 0.00 0.00 0.00 3.41
171 172 5.946298 TGCTGCTTGATTGACTTTAATGAG 58.054 37.500 0.00 0.00 0.00 2.90
172 173 5.963176 TGCTGCTTGATTGACTTTAATGA 57.037 34.783 0.00 0.00 0.00 2.57
173 174 6.097356 ACATGCTGCTTGATTGACTTTAATG 58.903 36.000 20.66 4.21 0.00 1.90
174 175 6.276832 ACATGCTGCTTGATTGACTTTAAT 57.723 33.333 20.66 0.00 0.00 1.40
175 176 5.710513 ACATGCTGCTTGATTGACTTTAA 57.289 34.783 20.66 0.00 0.00 1.52
176 177 5.355071 CCTACATGCTGCTTGATTGACTTTA 59.645 40.000 20.66 1.30 0.00 1.85
177 178 4.157289 CCTACATGCTGCTTGATTGACTTT 59.843 41.667 20.66 0.20 0.00 2.66
178 179 3.693085 CCTACATGCTGCTTGATTGACTT 59.307 43.478 20.66 0.87 0.00 3.01
179 180 3.276857 CCTACATGCTGCTTGATTGACT 58.723 45.455 20.66 1.53 0.00 3.41
180 181 2.357009 CCCTACATGCTGCTTGATTGAC 59.643 50.000 20.66 0.00 0.00 3.18
181 182 2.025981 ACCCTACATGCTGCTTGATTGA 60.026 45.455 20.66 3.95 0.00 2.57
182 183 2.372264 ACCCTACATGCTGCTTGATTG 58.628 47.619 20.66 10.20 0.00 2.67
183 184 2.814805 ACCCTACATGCTGCTTGATT 57.185 45.000 20.66 3.55 0.00 2.57
184 185 4.443978 AATACCCTACATGCTGCTTGAT 57.556 40.909 20.66 8.67 0.00 2.57
185 186 3.931907 AATACCCTACATGCTGCTTGA 57.068 42.857 20.66 5.30 0.00 3.02
186 187 5.555017 AGATAATACCCTACATGCTGCTTG 58.445 41.667 13.31 13.31 0.00 4.01
187 188 5.307976 TGAGATAATACCCTACATGCTGCTT 59.692 40.000 0.00 0.00 0.00 3.91
188 189 4.840680 TGAGATAATACCCTACATGCTGCT 59.159 41.667 0.00 0.00 0.00 4.24
189 190 5.152623 TGAGATAATACCCTACATGCTGC 57.847 43.478 0.00 0.00 0.00 5.25
190 191 6.939622 TGATGAGATAATACCCTACATGCTG 58.060 40.000 0.00 0.00 0.00 4.41
191 192 7.455953 TCTTGATGAGATAATACCCTACATGCT 59.544 37.037 0.00 0.00 0.00 3.79
192 193 7.615403 TCTTGATGAGATAATACCCTACATGC 58.385 38.462 0.00 0.00 0.00 4.06
193 194 9.029368 TCTCTTGATGAGATAATACCCTACATG 57.971 37.037 0.00 0.00 46.03 3.21
208 209 1.805871 GCTTCGGGCTCTCTTGATGAG 60.806 57.143 0.00 0.00 43.96 2.90
209 210 0.176680 GCTTCGGGCTCTCTTGATGA 59.823 55.000 0.00 0.00 38.06 2.92
210 211 2.687842 GCTTCGGGCTCTCTTGATG 58.312 57.895 0.00 0.00 38.06 3.07
230 231 3.086282 ACATGAACACGGGATTTTACCC 58.914 45.455 0.00 0.00 45.92 3.69
231 232 4.776795 AACATGAACACGGGATTTTACC 57.223 40.909 0.00 0.00 0.00 2.85
232 233 5.181622 TGGTAACATGAACACGGGATTTTAC 59.818 40.000 0.00 0.00 46.17 2.01
233 234 5.314529 TGGTAACATGAACACGGGATTTTA 58.685 37.500 0.00 0.00 46.17 1.52
234 235 4.145807 TGGTAACATGAACACGGGATTTT 58.854 39.130 0.00 0.00 46.17 1.82
235 236 3.757270 TGGTAACATGAACACGGGATTT 58.243 40.909 0.00 0.00 46.17 2.17
236 237 3.426787 TGGTAACATGAACACGGGATT 57.573 42.857 0.00 0.00 46.17 3.01
250 251 4.270325 GTGCGTCTTAGGATCAATGGTAAC 59.730 45.833 0.00 0.00 0.00 2.50
251 252 4.439057 GTGCGTCTTAGGATCAATGGTAA 58.561 43.478 0.00 0.00 0.00 2.85
252 253 3.181469 GGTGCGTCTTAGGATCAATGGTA 60.181 47.826 0.00 0.00 0.00 3.25
253 254 2.420129 GGTGCGTCTTAGGATCAATGGT 60.420 50.000 0.00 0.00 0.00 3.55
254 255 2.213499 GGTGCGTCTTAGGATCAATGG 58.787 52.381 0.00 0.00 0.00 3.16
255 256 1.860950 CGGTGCGTCTTAGGATCAATG 59.139 52.381 0.00 0.00 0.00 2.82
256 257 1.806623 GCGGTGCGTCTTAGGATCAAT 60.807 52.381 0.00 0.00 0.00 2.57
257 258 0.459585 GCGGTGCGTCTTAGGATCAA 60.460 55.000 0.00 0.00 0.00 2.57
258 259 1.141019 GCGGTGCGTCTTAGGATCA 59.859 57.895 0.00 0.00 0.00 2.92
259 260 0.179108 AAGCGGTGCGTCTTAGGATC 60.179 55.000 0.00 0.00 0.00 3.36
260 261 0.460284 CAAGCGGTGCGTCTTAGGAT 60.460 55.000 0.00 0.00 0.00 3.24
261 262 1.080093 CAAGCGGTGCGTCTTAGGA 60.080 57.895 0.00 0.00 0.00 2.94
262 263 2.100631 CCAAGCGGTGCGTCTTAGG 61.101 63.158 0.00 0.00 0.00 2.69
263 264 2.100631 CCCAAGCGGTGCGTCTTAG 61.101 63.158 0.00 0.00 0.00 2.18
264 265 2.047655 CCCAAGCGGTGCGTCTTA 60.048 61.111 0.00 0.00 0.00 2.10
265 266 3.936203 TCCCAAGCGGTGCGTCTT 61.936 61.111 0.00 0.00 0.00 3.01
266 267 4.681978 GTCCCAAGCGGTGCGTCT 62.682 66.667 0.00 0.00 0.00 4.18
279 280 3.097429 ATCTCGGGTAGGGGGTCCC 62.097 68.421 0.00 0.00 45.90 4.46
280 281 1.533513 GATCTCGGGTAGGGGGTCC 60.534 68.421 0.00 0.00 0.00 4.46
281 282 0.828343 CAGATCTCGGGTAGGGGGTC 60.828 65.000 0.00 0.00 0.00 4.46
282 283 1.233369 CAGATCTCGGGTAGGGGGT 59.767 63.158 0.00 0.00 0.00 4.95
283 284 2.210711 GCAGATCTCGGGTAGGGGG 61.211 68.421 0.00 0.00 0.00 5.40
284 285 2.210711 GGCAGATCTCGGGTAGGGG 61.211 68.421 0.00 0.00 0.00 4.79
285 286 2.565645 CGGCAGATCTCGGGTAGGG 61.566 68.421 0.00 0.00 0.00 3.53
286 287 2.565645 CCGGCAGATCTCGGGTAGG 61.566 68.421 13.71 0.00 42.32 3.18
287 288 1.392710 AACCGGCAGATCTCGGGTAG 61.393 60.000 22.66 0.00 45.54 3.18
288 289 0.974010 AAACCGGCAGATCTCGGGTA 60.974 55.000 22.66 0.00 46.82 3.69
292 293 0.721718 GTCAAAACCGGCAGATCTCG 59.278 55.000 0.00 0.00 0.00 4.04
293 294 1.464997 GTGTCAAAACCGGCAGATCTC 59.535 52.381 0.00 0.00 0.00 2.75
294 295 1.523758 GTGTCAAAACCGGCAGATCT 58.476 50.000 0.00 0.00 0.00 2.75
295 296 0.521735 GGTGTCAAAACCGGCAGATC 59.478 55.000 0.00 0.00 0.00 2.75
296 297 0.179004 TGGTGTCAAAACCGGCAGAT 60.179 50.000 0.00 0.00 43.73 2.90
297 298 0.394488 TTGGTGTCAAAACCGGCAGA 60.394 50.000 0.00 0.00 43.73 4.26
298 299 0.248866 GTTGGTGTCAAAACCGGCAG 60.249 55.000 0.00 0.00 43.73 4.85
299 300 0.965866 TGTTGGTGTCAAAACCGGCA 60.966 50.000 0.00 0.00 43.73 5.69
300 301 0.173708 TTGTTGGTGTCAAAACCGGC 59.826 50.000 0.00 0.00 43.73 6.13
301 302 2.164624 TCTTTGTTGGTGTCAAAACCGG 59.835 45.455 0.00 0.00 43.73 5.28
302 303 3.175929 GTCTTTGTTGGTGTCAAAACCG 58.824 45.455 0.00 0.00 43.73 4.44
303 304 3.924073 GTGTCTTTGTTGGTGTCAAAACC 59.076 43.478 0.00 0.00 40.94 3.27
304 305 4.805219 AGTGTCTTTGTTGGTGTCAAAAC 58.195 39.130 0.00 0.00 34.96 2.43
305 306 6.405286 CCATAGTGTCTTTGTTGGTGTCAAAA 60.405 38.462 0.00 0.00 34.96 2.44
306 307 5.067153 CCATAGTGTCTTTGTTGGTGTCAAA 59.933 40.000 0.00 0.00 34.28 2.69
307 308 4.578516 CCATAGTGTCTTTGTTGGTGTCAA 59.421 41.667 0.00 0.00 0.00 3.18
308 309 4.133820 CCATAGTGTCTTTGTTGGTGTCA 58.866 43.478 0.00 0.00 0.00 3.58
309 310 4.385825 TCCATAGTGTCTTTGTTGGTGTC 58.614 43.478 0.00 0.00 0.00 3.67
310 311 4.431416 TCCATAGTGTCTTTGTTGGTGT 57.569 40.909 0.00 0.00 0.00 4.16
311 312 4.320494 GCTTCCATAGTGTCTTTGTTGGTG 60.320 45.833 0.00 0.00 0.00 4.17
312 313 3.821033 GCTTCCATAGTGTCTTTGTTGGT 59.179 43.478 0.00 0.00 0.00 3.67
313 314 4.074970 AGCTTCCATAGTGTCTTTGTTGG 58.925 43.478 0.00 0.00 0.00 3.77
314 315 4.756642 TGAGCTTCCATAGTGTCTTTGTTG 59.243 41.667 0.00 0.00 0.00 3.33
315 316 4.973168 TGAGCTTCCATAGTGTCTTTGTT 58.027 39.130 0.00 0.00 0.00 2.83
316 317 4.623932 TGAGCTTCCATAGTGTCTTTGT 57.376 40.909 0.00 0.00 0.00 2.83
317 318 4.394300 CCTTGAGCTTCCATAGTGTCTTTG 59.606 45.833 0.00 0.00 0.00 2.77
318 319 4.042187 ACCTTGAGCTTCCATAGTGTCTTT 59.958 41.667 0.00 0.00 0.00 2.52
360 361 1.228657 GGACAACTCGCCACCAGAAC 61.229 60.000 0.00 0.00 0.00 3.01
433 435 3.870007 CAAGACATACATTGCATCGAGC 58.130 45.455 0.00 0.00 45.96 5.03
484 488 1.409064 CTTGGCATGAGAGCAATGCAT 59.591 47.619 8.35 0.00 42.65 3.96
516 520 2.551459 ACTGAAGAACTCATGTGCTTGC 59.449 45.455 0.00 0.00 41.92 4.01
535 539 2.483188 GCAATCGGGGTCTTCGAATACT 60.483 50.000 12.72 0.00 40.15 2.12
595 600 6.661377 ACAGCTCTCTCACTGTTAGAGAATTA 59.339 38.462 19.16 1.71 46.65 1.40
626 631 4.645535 CCATATGGACCACATAACAGAGG 58.354 47.826 17.49 0.00 44.75 3.69
684 689 1.420138 ACCGAAGTGAATGGGTCAAGT 59.580 47.619 0.00 0.00 38.23 3.16
745 750 6.305272 TGGAAGAATAGAAGCATGAGACTT 57.695 37.500 0.00 0.00 0.00 3.01
842 847 4.399395 CTCCTGCGCCAGCCTTGA 62.399 66.667 4.18 0.00 44.33 3.02
1028 1034 5.895928 TGTAATGACGAGATTTCCAGAGAG 58.104 41.667 0.00 0.00 0.00 3.20
1236 1243 1.211212 TGGCATCATCAGCTAGCAAGT 59.789 47.619 18.83 0.00 0.00 3.16
1352 1359 4.755123 GTGAAAACCCAAGATCTTCGAGAA 59.245 41.667 4.57 0.00 0.00 2.87
1353 1360 4.315803 GTGAAAACCCAAGATCTTCGAGA 58.684 43.478 4.57 0.00 0.00 4.04
1392 1399 6.998968 TGTTGAAAGCATTGTTTTGGAAAT 57.001 29.167 3.02 0.00 0.00 2.17
1425 1432 2.554344 GGCCTTCATTGGTTGTACCTGA 60.554 50.000 0.00 0.00 39.58 3.86
1547 1554 3.857854 GCATGGCGACTCACAGCG 61.858 66.667 0.00 0.00 0.00 5.18
1552 1559 4.758251 CGGGTGCATGGCGACTCA 62.758 66.667 0.00 0.00 0.00 3.41
1644 1674 3.136077 CCATGGATCTGACAGAGTTGGAT 59.864 47.826 5.56 0.00 0.00 3.41
1671 1701 8.462811 GGTGATATGAGACATGTCTTCGTATAT 58.537 37.037 28.46 24.54 40.61 0.86
1688 1718 2.882761 CCTCTACCGTTCGGTGATATGA 59.117 50.000 24.37 13.60 39.14 2.15
1760 1805 7.142306 CACATGATGCTATTGGAGATTTAGG 57.858 40.000 0.00 0.00 0.00 2.69
1892 1937 1.822615 GCTGTTGGCCAGGTTTTGT 59.177 52.632 5.11 0.00 41.81 2.83
1953 1998 2.437359 CTTCCTTCTGCCGGCCTG 60.437 66.667 26.77 17.37 0.00 4.85
2009 2054 2.666190 TTCTCCACTGCAGCGTGC 60.666 61.111 15.27 3.44 45.29 5.34
2111 2157 1.612146 TGGTGGAGAGGCGGATCAA 60.612 57.895 0.00 0.00 0.00 2.57
2112 2158 2.038813 TGGTGGAGAGGCGGATCA 59.961 61.111 0.00 0.00 0.00 2.92
2121 2167 1.070786 GTTCTTGCGGTGGTGGAGA 59.929 57.895 0.00 0.00 0.00 3.71
2184 2230 2.091444 TGCAGAGAGGAGGAGATGATGA 60.091 50.000 0.00 0.00 0.00 2.92
2190 2236 0.038310 TTCGTGCAGAGAGGAGGAGA 59.962 55.000 0.00 0.00 33.95 3.71


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

AutoCloner maintained by Alex Coulton.