Multiple sequence alignment - TraesCS3B01G405300

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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 TraesCS3B01G405300 chr3B 100.000 2591 0 0 1 2591 640666464 640669054 0.000000e+00 4785.0
1 TraesCS3B01G405300 chr3B 78.131 535 107 6 2058 2591 160150878 160151403 5.340000e-87 331.0
2 TraesCS3B01G405300 chr3B 89.286 56 3 2 229 281 747459020 747459075 1.660000e-07 67.6
3 TraesCS3B01G405300 chr3A 94.652 1496 56 12 427 1902 623222741 623224232 0.000000e+00 2298.0
4 TraesCS3B01G405300 chr3A 91.228 114 10 0 1138 1251 19895838 19895725 3.450000e-34 156.0
5 TraesCS3B01G405300 chr3A 96.000 50 2 0 1966 2015 623224233 623224282 5.940000e-12 82.4
6 TraesCS3B01G405300 chr3D 94.130 1448 59 8 829 2254 480149064 480150507 0.000000e+00 2180.0
7 TraesCS3B01G405300 chr3D 89.791 431 41 2 1 430 480127155 480127583 1.360000e-152 549.0
8 TraesCS3B01G405300 chr3D 95.865 266 3 2 574 831 480148768 480149033 8.570000e-115 424.0
9 TraesCS3B01G405300 chr3D 90.614 277 24 2 2316 2591 480150508 480150783 1.470000e-97 366.0
10 TraesCS3B01G405300 chr3D 94.904 157 8 0 428 584 480148203 480148359 1.990000e-61 246.0
11 TraesCS3B01G405300 chr3D 91.228 114 10 0 1138 1251 16887970 16888083 3.450000e-34 156.0
12 TraesCS3B01G405300 chr3D 96.970 33 1 0 1489 1521 480149073 480149041 3.600000e-04 56.5
13 TraesCS3B01G405300 chr4D 87.405 524 52 7 2069 2591 464079447 464078937 7.990000e-165 590.0
14 TraesCS3B01G405300 chr6B 81.970 538 83 10 2056 2591 113531362 113530837 6.580000e-121 444.0
15 TraesCS3B01G405300 chr6B 81.275 502 85 6 2059 2558 175334080 175334574 5.200000e-107 398.0
16 TraesCS3B01G405300 chr6B 82.143 392 59 6 2199 2589 591238576 591238957 2.490000e-85 326.0
17 TraesCS3B01G405300 chr2D 80.597 536 94 8 2058 2591 108266853 108266326 3.100000e-109 405.0
18 TraesCS3B01G405300 chr2D 79.310 116 23 1 113 227 648444228 648444113 2.140000e-11 80.5
19 TraesCS3B01G405300 chr5D 80.930 430 82 0 2069 2498 87447686 87448115 8.880000e-90 340.0
20 TraesCS3B01G405300 chr5D 91.111 45 2 1 233 275 128347714 128347758 2.780000e-05 60.2
21 TraesCS3B01G405300 chr5D 91.111 45 2 1 233 275 128379155 128379199 2.780000e-05 60.2
22 TraesCS3B01G405300 chr1D 75.992 504 106 12 2095 2591 144454498 144454993 1.990000e-61 246.0
23 TraesCS3B01G405300 chr1D 75.709 494 109 9 2101 2591 81478992 81478507 1.200000e-58 237.0
24 TraesCS3B01G405300 chr4B 77.928 222 42 7 60 279 645101853 645101637 5.820000e-27 132.0
25 TraesCS3B01G405300 chr4B 92.727 55 3 1 2537 2591 579468082 579468029 7.690000e-11 78.7
26 TraesCS3B01G405300 chr4B 97.368 38 1 0 248 285 575914984 575914947 5.980000e-07 65.8
27 TraesCS3B01G405300 chr6A 80.864 162 25 6 61 219 420845185 420845027 3.500000e-24 122.0
28 TraesCS3B01G405300 chr7B 75.771 227 41 11 61 279 545981036 545980816 4.560000e-18 102.0
29 TraesCS3B01G405300 chrUn 81.967 122 19 3 113 232 30916382 30916502 1.640000e-17 100.0
30 TraesCS3B01G405300 chr2A 77.005 187 33 9 52 232 738346862 738347044 5.900000e-17 99.0
31 TraesCS3B01G405300 chr5B 79.310 116 18 3 2477 2591 450503598 450503488 2.760000e-10 76.8
32 TraesCS3B01G405300 chr7D 83.562 73 7 5 205 275 26070822 26070891 2.150000e-06 63.9
33 TraesCS3B01G405300 chr7D 80.488 82 11 5 196 275 572436231 572436153 1.000000e-04 58.4
34 TraesCS3B01G405300 chr1A 87.500 48 5 1 233 279 139928122 139928075 1.000000e-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 TraesCS3B01G405300 chr3B 640666464 640669054 2590 False 4785.0 4785 100.00000 1 2591 1 chr3B.!!$F2 2590
1 TraesCS3B01G405300 chr3B 160150878 160151403 525 False 331.0 331 78.13100 2058 2591 1 chr3B.!!$F1 533
2 TraesCS3B01G405300 chr3A 623222741 623224282 1541 False 1190.2 2298 95.32600 427 2015 2 chr3A.!!$F1 1588
3 TraesCS3B01G405300 chr3D 480148203 480150783 2580 False 804.0 2180 93.87825 428 2591 4 chr3D.!!$F3 2163
4 TraesCS3B01G405300 chr4D 464078937 464079447 510 True 590.0 590 87.40500 2069 2591 1 chr4D.!!$R1 522
5 TraesCS3B01G405300 chr6B 113530837 113531362 525 True 444.0 444 81.97000 2056 2591 1 chr6B.!!$R1 535
6 TraesCS3B01G405300 chr2D 108266326 108266853 527 True 405.0 405 80.59700 2058 2591 1 chr2D.!!$R1 533

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
353 354 0.036875 GGCTGTAGGAGGTTGTTGCT 59.963 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 2553 0.30776 GGTTCGCACCAACTTGAGTG 59.692 55.0 0.0 6.19 43.61 3.51 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
23 24 6.252599 TCTATCCAACACCATTATTCTGCT 57.747 37.500 0.00 0.00 0.00 4.24
24 25 7.373617 TCTATCCAACACCATTATTCTGCTA 57.626 36.000 0.00 0.00 0.00 3.49
25 26 7.801104 TCTATCCAACACCATTATTCTGCTAA 58.199 34.615 0.00 0.00 0.00 3.09
26 27 6.699575 ATCCAACACCATTATTCTGCTAAC 57.300 37.500 0.00 0.00 0.00 2.34
27 28 5.565509 TCCAACACCATTATTCTGCTAACA 58.434 37.500 0.00 0.00 0.00 2.41
28 29 6.007076 TCCAACACCATTATTCTGCTAACAA 58.993 36.000 0.00 0.00 0.00 2.83
29 30 6.663093 TCCAACACCATTATTCTGCTAACAAT 59.337 34.615 0.00 0.00 0.00 2.71
30 31 6.753279 CCAACACCATTATTCTGCTAACAATG 59.247 38.462 0.00 0.00 0.00 2.82
31 32 7.315142 CAACACCATTATTCTGCTAACAATGT 58.685 34.615 3.71 0.00 0.00 2.71
32 33 7.088589 ACACCATTATTCTGCTAACAATGTC 57.911 36.000 0.00 0.00 0.00 3.06
33 34 6.183360 ACACCATTATTCTGCTAACAATGTCG 60.183 38.462 0.00 0.00 0.00 4.35
34 35 5.296780 ACCATTATTCTGCTAACAATGTCGG 59.703 40.000 0.00 0.00 0.00 4.79
35 36 4.875544 TTATTCTGCTAACAATGTCGGC 57.124 40.909 4.11 4.11 0.00 5.54
36 37 2.177394 TTCTGCTAACAATGTCGGCA 57.823 45.000 11.41 11.41 0.00 5.69
37 38 2.401583 TCTGCTAACAATGTCGGCAT 57.598 45.000 12.11 0.00 36.80 4.40
38 39 2.279741 TCTGCTAACAATGTCGGCATC 58.720 47.619 1.37 0.00 33.50 3.91
39 40 1.331756 CTGCTAACAATGTCGGCATCC 59.668 52.381 1.37 0.00 33.50 3.51
40 41 1.065491 TGCTAACAATGTCGGCATCCT 60.065 47.619 1.37 0.00 33.50 3.24
41 42 2.017049 GCTAACAATGTCGGCATCCTT 58.983 47.619 1.37 0.00 33.50 3.36
42 43 2.032178 GCTAACAATGTCGGCATCCTTC 59.968 50.000 1.37 0.00 33.50 3.46
43 44 2.496899 AACAATGTCGGCATCCTTCT 57.503 45.000 1.37 0.00 33.50 2.85
44 45 2.029838 ACAATGTCGGCATCCTTCTC 57.970 50.000 1.37 0.00 33.50 2.87
45 46 1.278985 ACAATGTCGGCATCCTTCTCA 59.721 47.619 1.37 0.00 33.50 3.27
46 47 1.667724 CAATGTCGGCATCCTTCTCAC 59.332 52.381 1.37 0.00 33.50 3.51
47 48 0.904649 ATGTCGGCATCCTTCTCACA 59.095 50.000 0.00 0.00 0.00 3.58
48 49 0.904649 TGTCGGCATCCTTCTCACAT 59.095 50.000 0.00 0.00 0.00 3.21
49 50 1.278985 TGTCGGCATCCTTCTCACATT 59.721 47.619 0.00 0.00 0.00 2.71
50 51 1.667724 GTCGGCATCCTTCTCACATTG 59.332 52.381 0.00 0.00 0.00 2.82
51 52 1.554617 TCGGCATCCTTCTCACATTGA 59.445 47.619 0.00 0.00 0.00 2.57
52 53 1.667724 CGGCATCCTTCTCACATTGAC 59.332 52.381 0.00 0.00 0.00 3.18
53 54 2.715046 GGCATCCTTCTCACATTGACA 58.285 47.619 0.00 0.00 0.00 3.58
54 55 3.084039 GGCATCCTTCTCACATTGACAA 58.916 45.455 0.00 0.00 0.00 3.18
55 56 3.698040 GGCATCCTTCTCACATTGACAAT 59.302 43.478 0.00 0.00 0.00 2.71
56 57 4.439700 GGCATCCTTCTCACATTGACAATG 60.440 45.833 23.62 23.62 44.48 2.82
75 76 9.681692 TGACAATGTTTATGATCTGAAAAACAG 57.318 29.630 15.46 0.00 42.99 3.16
76 77 9.683069 GACAATGTTTATGATCTGAAAAACAGT 57.317 29.630 15.46 12.22 42.99 3.55
86 87 8.620116 TGATCTGAAAAACAGTATCATCAACA 57.380 30.769 0.00 0.00 45.86 3.33
87 88 9.065798 TGATCTGAAAAACAGTATCATCAACAA 57.934 29.630 0.00 0.00 45.86 2.83
96 97 9.672673 AAACAGTATCATCAACAATACTTAGCT 57.327 29.630 0.00 0.00 36.74 3.32
98 99 9.973450 ACAGTATCATCAACAATACTTAGCTAG 57.027 33.333 0.00 0.00 36.74 3.42
99 100 9.973450 CAGTATCATCAACAATACTTAGCTAGT 57.027 33.333 0.00 0.00 36.74 2.57
119 120 8.892530 AGCTAGTATTAGAGATTACACTAGGGA 58.107 37.037 0.00 0.00 37.18 4.20
120 121 9.689501 GCTAGTATTAGAGATTACACTAGGGAT 57.310 37.037 0.00 0.00 37.18 3.85
129 130 9.836179 AGAGATTACACTAGGGATCTATTTGAT 57.164 33.333 0.00 0.00 38.27 2.57
130 131 9.868277 GAGATTACACTAGGGATCTATTTGATG 57.132 37.037 0.00 0.00 35.14 3.07
131 132 9.386122 AGATTACACTAGGGATCTATTTGATGT 57.614 33.333 0.00 0.00 35.14 3.06
142 143 8.968242 GGGATCTATTTGATGTTTATTTTTCGC 58.032 33.333 0.00 0.00 35.14 4.70
143 144 8.968242 GGATCTATTTGATGTTTATTTTTCGCC 58.032 33.333 0.00 0.00 35.14 5.54
144 145 8.871686 ATCTATTTGATGTTTATTTTTCGCCC 57.128 30.769 0.00 0.00 33.43 6.13
145 146 7.831753 TCTATTTGATGTTTATTTTTCGCCCA 58.168 30.769 0.00 0.00 0.00 5.36
146 147 8.474025 TCTATTTGATGTTTATTTTTCGCCCAT 58.526 29.630 0.00 0.00 0.00 4.00
147 148 6.718454 TTTGATGTTTATTTTTCGCCCATG 57.282 33.333 0.00 0.00 0.00 3.66
148 149 4.180057 TGATGTTTATTTTTCGCCCATGC 58.820 39.130 0.00 0.00 0.00 4.06
149 150 3.667497 TGTTTATTTTTCGCCCATGCA 57.333 38.095 0.00 0.00 37.32 3.96
150 151 3.995199 TGTTTATTTTTCGCCCATGCAA 58.005 36.364 0.00 0.00 37.32 4.08
151 152 4.573900 TGTTTATTTTTCGCCCATGCAAT 58.426 34.783 0.00 0.00 37.32 3.56
152 153 4.999950 TGTTTATTTTTCGCCCATGCAATT 59.000 33.333 0.00 0.00 37.32 2.32
153 154 5.106791 TGTTTATTTTTCGCCCATGCAATTG 60.107 36.000 0.00 0.00 37.32 2.32
154 155 2.827800 TTTTTCGCCCATGCAATTGA 57.172 40.000 10.34 0.00 37.32 2.57
155 156 2.367030 TTTTCGCCCATGCAATTGAG 57.633 45.000 10.34 0.00 37.32 3.02
156 157 1.255882 TTTCGCCCATGCAATTGAGT 58.744 45.000 10.34 0.00 37.32 3.41
157 158 1.255882 TTCGCCCATGCAATTGAGTT 58.744 45.000 10.34 0.00 37.32 3.01
158 159 1.255882 TCGCCCATGCAATTGAGTTT 58.744 45.000 10.34 0.00 37.32 2.66
159 160 1.617850 TCGCCCATGCAATTGAGTTTT 59.382 42.857 10.34 0.00 37.32 2.43
160 161 1.994779 CGCCCATGCAATTGAGTTTTC 59.005 47.619 10.34 0.00 37.32 2.29
161 162 2.349590 GCCCATGCAATTGAGTTTTCC 58.650 47.619 10.34 0.00 37.47 3.13
162 163 2.027837 GCCCATGCAATTGAGTTTTCCT 60.028 45.455 10.34 0.00 37.47 3.36
163 164 3.853475 CCCATGCAATTGAGTTTTCCTC 58.147 45.455 10.34 0.00 40.89 3.71
164 165 3.512724 CCCATGCAATTGAGTTTTCCTCT 59.487 43.478 10.34 0.00 41.11 3.69
165 166 4.491676 CCATGCAATTGAGTTTTCCTCTG 58.508 43.478 10.34 0.00 41.11 3.35
166 167 4.219070 CCATGCAATTGAGTTTTCCTCTGA 59.781 41.667 10.34 0.00 41.11 3.27
167 168 5.279106 CCATGCAATTGAGTTTTCCTCTGAA 60.279 40.000 10.34 0.00 41.11 3.02
168 169 6.395629 CATGCAATTGAGTTTTCCTCTGAAT 58.604 36.000 10.34 0.00 41.11 2.57
169 170 6.017400 TGCAATTGAGTTTTCCTCTGAATC 57.983 37.500 10.34 0.00 41.11 2.52
170 171 5.771666 TGCAATTGAGTTTTCCTCTGAATCT 59.228 36.000 10.34 0.00 41.11 2.40
171 172 6.072286 TGCAATTGAGTTTTCCTCTGAATCTC 60.072 38.462 10.34 0.00 41.11 2.75
172 173 6.072286 GCAATTGAGTTTTCCTCTGAATCTCA 60.072 38.462 10.34 0.00 41.11 3.27
173 174 7.303998 CAATTGAGTTTTCCTCTGAATCTCAC 58.696 38.462 0.00 0.00 39.37 3.51
174 175 5.551305 TGAGTTTTCCTCTGAATCTCACA 57.449 39.130 0.00 0.00 41.11 3.58
175 176 5.300752 TGAGTTTTCCTCTGAATCTCACAC 58.699 41.667 0.00 0.00 41.11 3.82
176 177 5.070981 TGAGTTTTCCTCTGAATCTCACACT 59.929 40.000 0.00 0.00 41.11 3.55
177 178 6.267699 TGAGTTTTCCTCTGAATCTCACACTA 59.732 38.462 0.00 0.00 41.11 2.74
178 179 6.459923 AGTTTTCCTCTGAATCTCACACTAC 58.540 40.000 0.00 0.00 0.00 2.73
179 180 6.042093 AGTTTTCCTCTGAATCTCACACTACA 59.958 38.462 0.00 0.00 0.00 2.74
180 181 5.651387 TTCCTCTGAATCTCACACTACAG 57.349 43.478 0.00 0.00 0.00 2.74
181 182 4.923415 TCCTCTGAATCTCACACTACAGA 58.077 43.478 0.00 0.00 34.13 3.41
182 183 5.325239 TCCTCTGAATCTCACACTACAGAA 58.675 41.667 0.00 0.00 34.71 3.02
183 184 5.954752 TCCTCTGAATCTCACACTACAGAAT 59.045 40.000 0.00 0.00 34.71 2.40
184 185 6.438741 TCCTCTGAATCTCACACTACAGAATT 59.561 38.462 0.00 0.00 34.71 2.17
185 186 7.615757 TCCTCTGAATCTCACACTACAGAATTA 59.384 37.037 0.00 0.00 34.71 1.40
186 187 8.420222 CCTCTGAATCTCACACTACAGAATTAT 58.580 37.037 0.00 0.00 34.71 1.28
187 188 9.814899 CTCTGAATCTCACACTACAGAATTATT 57.185 33.333 0.00 0.00 34.71 1.40
188 189 9.591792 TCTGAATCTCACACTACAGAATTATTG 57.408 33.333 0.00 0.00 32.66 1.90
189 190 9.376075 CTGAATCTCACACTACAGAATTATTGT 57.624 33.333 0.00 1.27 0.00 2.71
264 265 8.697507 AAATGACCTTTATTAATGCCTCTAGG 57.302 34.615 0.00 0.00 38.53 3.02
265 266 6.824958 TGACCTTTATTAATGCCTCTAGGT 57.175 37.500 0.00 0.00 37.46 3.08
266 267 6.827727 TGACCTTTATTAATGCCTCTAGGTC 58.172 40.000 16.89 16.89 46.66 3.85
267 268 6.824958 ACCTTTATTAATGCCTCTAGGTCA 57.175 37.500 0.00 0.00 37.57 4.02
268 269 7.394144 ACCTTTATTAATGCCTCTAGGTCAT 57.606 36.000 0.00 0.00 37.57 3.06
269 270 8.506196 ACCTTTATTAATGCCTCTAGGTCATA 57.494 34.615 0.00 0.00 37.57 2.15
270 271 9.117223 ACCTTTATTAATGCCTCTAGGTCATAT 57.883 33.333 0.00 0.00 37.57 1.78
271 272 9.965902 CCTTTATTAATGCCTCTAGGTCATATT 57.034 33.333 0.00 0.00 37.57 1.28
274 275 9.959721 TTATTAATGCCTCTAGGTCATATTTCC 57.040 33.333 0.00 0.00 37.57 3.13
275 276 5.912149 AATGCCTCTAGGTCATATTTCCA 57.088 39.130 0.00 0.00 37.57 3.53
276 277 5.912149 ATGCCTCTAGGTCATATTTCCAA 57.088 39.130 0.00 0.00 37.57 3.53
277 278 5.036117 TGCCTCTAGGTCATATTTCCAAC 57.964 43.478 0.00 0.00 37.57 3.77
278 279 4.473196 TGCCTCTAGGTCATATTTCCAACA 59.527 41.667 0.00 0.00 37.57 3.33
279 280 5.059833 GCCTCTAGGTCATATTTCCAACAG 58.940 45.833 0.00 0.00 37.57 3.16
280 281 5.396884 GCCTCTAGGTCATATTTCCAACAGT 60.397 44.000 0.00 0.00 37.57 3.55
281 282 6.051717 CCTCTAGGTCATATTTCCAACAGTG 58.948 44.000 0.00 0.00 0.00 3.66
283 284 3.968265 AGGTCATATTTCCAACAGTGGG 58.032 45.455 0.00 0.00 46.01 4.61
284 285 2.427095 GGTCATATTTCCAACAGTGGGC 59.573 50.000 0.00 0.00 46.01 5.36
285 286 2.097466 GTCATATTTCCAACAGTGGGCG 59.903 50.000 0.00 0.00 46.01 6.13
286 287 2.026729 TCATATTTCCAACAGTGGGCGA 60.027 45.455 0.00 0.00 46.01 5.54
287 288 2.799126 TATTTCCAACAGTGGGCGAT 57.201 45.000 0.00 0.00 46.01 4.58
288 289 1.923356 ATTTCCAACAGTGGGCGATT 58.077 45.000 0.00 0.00 46.01 3.34
289 290 0.958091 TTTCCAACAGTGGGCGATTG 59.042 50.000 0.00 0.00 46.01 2.67
290 291 0.109532 TTCCAACAGTGGGCGATTGA 59.890 50.000 0.00 0.00 46.01 2.57
291 292 0.109532 TCCAACAGTGGGCGATTGAA 59.890 50.000 0.00 0.00 46.01 2.69
292 293 0.958091 CCAACAGTGGGCGATTGAAA 59.042 50.000 0.00 0.00 41.77 2.69
293 294 1.339610 CCAACAGTGGGCGATTGAAAA 59.660 47.619 0.00 0.00 41.77 2.29
294 295 2.223923 CCAACAGTGGGCGATTGAAAAA 60.224 45.455 0.00 0.00 41.77 1.94
316 317 7.642071 AAAATGGATTTGACTCGATGTTTTG 57.358 32.000 0.00 0.00 0.00 2.44
317 318 6.573664 AATGGATTTGACTCGATGTTTTGA 57.426 33.333 0.00 0.00 0.00 2.69
318 319 5.611796 TGGATTTGACTCGATGTTTTGAG 57.388 39.130 0.00 0.00 39.05 3.02
319 320 4.083324 TGGATTTGACTCGATGTTTTGAGC 60.083 41.667 0.00 0.00 36.92 4.26
320 321 3.896648 TTTGACTCGATGTTTTGAGCC 57.103 42.857 0.00 0.00 36.92 4.70
321 322 2.839486 TGACTCGATGTTTTGAGCCT 57.161 45.000 0.00 0.00 36.92 4.58
322 323 2.416747 TGACTCGATGTTTTGAGCCTG 58.583 47.619 0.00 0.00 36.92 4.85
323 324 1.734465 GACTCGATGTTTTGAGCCTGG 59.266 52.381 0.00 0.00 36.92 4.45
324 325 1.072331 ACTCGATGTTTTGAGCCTGGT 59.928 47.619 0.00 0.00 36.92 4.00
325 326 1.466167 CTCGATGTTTTGAGCCTGGTG 59.534 52.381 0.00 0.00 0.00 4.17
326 327 0.523072 CGATGTTTTGAGCCTGGTGG 59.477 55.000 0.00 0.00 0.00 4.61
336 337 4.496336 CCTGGTGGCTAGCTGGGC 62.496 72.222 17.27 17.27 39.08 5.36
337 338 3.406200 CTGGTGGCTAGCTGGGCT 61.406 66.667 23.94 0.00 43.41 5.19
338 339 3.694058 CTGGTGGCTAGCTGGGCTG 62.694 68.421 23.94 8.37 40.10 4.85
339 340 3.721706 GGTGGCTAGCTGGGCTGT 61.722 66.667 23.94 0.00 40.10 4.40
340 341 2.367202 GGTGGCTAGCTGGGCTGTA 61.367 63.158 23.94 1.29 40.10 2.74
341 342 1.144936 GTGGCTAGCTGGGCTGTAG 59.855 63.158 23.94 0.00 40.10 2.74
342 343 2.066393 TGGCTAGCTGGGCTGTAGG 61.066 63.158 23.94 0.00 40.10 3.18
343 344 1.762460 GGCTAGCTGGGCTGTAGGA 60.762 63.158 16.84 0.00 40.10 2.94
344 345 1.745264 GCTAGCTGGGCTGTAGGAG 59.255 63.158 7.70 0.00 40.10 3.69
345 346 1.753368 GCTAGCTGGGCTGTAGGAGG 61.753 65.000 7.70 0.00 40.10 4.30
346 347 0.397816 CTAGCTGGGCTGTAGGAGGT 60.398 60.000 0.00 0.00 40.10 3.85
347 348 0.042731 TAGCTGGGCTGTAGGAGGTT 59.957 55.000 0.00 0.00 40.10 3.50
348 349 1.078143 GCTGGGCTGTAGGAGGTTG 60.078 63.158 0.00 0.00 0.00 3.77
349 350 1.842381 GCTGGGCTGTAGGAGGTTGT 61.842 60.000 0.00 0.00 0.00 3.32
350 351 0.693049 CTGGGCTGTAGGAGGTTGTT 59.307 55.000 0.00 0.00 0.00 2.83
351 352 0.400213 TGGGCTGTAGGAGGTTGTTG 59.600 55.000 0.00 0.00 0.00 3.33
352 353 0.960861 GGGCTGTAGGAGGTTGTTGC 60.961 60.000 0.00 0.00 0.00 4.17
353 354 0.036875 GGCTGTAGGAGGTTGTTGCT 59.963 55.000 0.00 0.00 0.00 3.91
354 355 1.545651 GGCTGTAGGAGGTTGTTGCTT 60.546 52.381 0.00 0.00 0.00 3.91
355 356 2.230660 GCTGTAGGAGGTTGTTGCTTT 58.769 47.619 0.00 0.00 0.00 3.51
356 357 3.408634 GCTGTAGGAGGTTGTTGCTTTA 58.591 45.455 0.00 0.00 0.00 1.85
357 358 4.010349 GCTGTAGGAGGTTGTTGCTTTAT 58.990 43.478 0.00 0.00 0.00 1.40
358 359 4.095036 GCTGTAGGAGGTTGTTGCTTTATC 59.905 45.833 0.00 0.00 0.00 1.75
359 360 4.250464 TGTAGGAGGTTGTTGCTTTATCG 58.750 43.478 0.00 0.00 0.00 2.92
360 361 3.418684 AGGAGGTTGTTGCTTTATCGT 57.581 42.857 0.00 0.00 0.00 3.73
361 362 3.335579 AGGAGGTTGTTGCTTTATCGTC 58.664 45.455 0.00 0.00 0.00 4.20
362 363 2.418976 GGAGGTTGTTGCTTTATCGTCC 59.581 50.000 0.00 0.00 0.00 4.79
363 364 3.071479 GAGGTTGTTGCTTTATCGTCCA 58.929 45.455 0.00 0.00 0.00 4.02
364 365 2.812011 AGGTTGTTGCTTTATCGTCCAC 59.188 45.455 0.00 0.00 0.00 4.02
365 366 2.550606 GGTTGTTGCTTTATCGTCCACA 59.449 45.455 0.00 0.00 0.00 4.17
366 367 3.551551 GTTGTTGCTTTATCGTCCACAC 58.448 45.455 0.00 0.00 0.00 3.82
368 369 1.127951 GTTGCTTTATCGTCCACACGG 59.872 52.381 0.00 0.00 46.70 4.94
369 370 0.390603 TGCTTTATCGTCCACACGGG 60.391 55.000 0.00 0.00 46.70 5.28
370 371 0.108520 GCTTTATCGTCCACACGGGA 60.109 55.000 0.00 0.00 46.70 5.14
377 378 3.533720 TCCACACGGGATCGGATC 58.466 61.111 9.54 9.54 42.15 3.36
378 379 1.380650 TCCACACGGGATCGGATCA 60.381 57.895 18.99 0.00 42.15 2.92
379 380 1.068083 CCACACGGGATCGGATCAG 59.932 63.158 18.99 14.09 40.01 2.90
380 381 1.068083 CACACGGGATCGGATCAGG 59.932 63.158 18.99 12.07 41.39 3.86
381 382 2.029666 CACGGGATCGGATCAGGC 59.970 66.667 18.99 2.59 41.39 4.85
382 383 2.123251 ACGGGATCGGATCAGGCT 60.123 61.111 18.99 0.00 41.39 4.58
383 384 2.203771 ACGGGATCGGATCAGGCTC 61.204 63.158 18.99 1.89 41.39 4.70
384 385 1.905843 CGGGATCGGATCAGGCTCT 60.906 63.158 18.99 0.00 0.00 4.09
385 386 1.872197 CGGGATCGGATCAGGCTCTC 61.872 65.000 18.99 0.52 0.00 3.20
386 387 0.829602 GGGATCGGATCAGGCTCTCA 60.830 60.000 18.99 0.00 0.00 3.27
387 388 0.316841 GGATCGGATCAGGCTCTCAC 59.683 60.000 18.99 0.00 0.00 3.51
388 389 1.327303 GATCGGATCAGGCTCTCACT 58.673 55.000 13.02 0.00 0.00 3.41
389 390 1.686052 GATCGGATCAGGCTCTCACTT 59.314 52.381 13.02 0.00 0.00 3.16
390 391 1.107114 TCGGATCAGGCTCTCACTTC 58.893 55.000 0.00 0.00 0.00 3.01
391 392 1.110442 CGGATCAGGCTCTCACTTCT 58.890 55.000 0.00 0.00 0.00 2.85
392 393 1.066908 CGGATCAGGCTCTCACTTCTC 59.933 57.143 0.00 0.00 0.00 2.87
393 394 2.387757 GGATCAGGCTCTCACTTCTCT 58.612 52.381 0.00 0.00 0.00 3.10
394 395 2.362077 GGATCAGGCTCTCACTTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
395 396 2.897271 TCAGGCTCTCACTTCTCTCT 57.103 50.000 0.00 0.00 0.00 3.10
396 397 2.722094 TCAGGCTCTCACTTCTCTCTC 58.278 52.381 0.00 0.00 0.00 3.20
397 398 1.750778 CAGGCTCTCACTTCTCTCTCC 59.249 57.143 0.00 0.00 0.00 3.71
398 399 1.640670 AGGCTCTCACTTCTCTCTCCT 59.359 52.381 0.00 0.00 0.00 3.69
399 400 2.849943 AGGCTCTCACTTCTCTCTCCTA 59.150 50.000 0.00 0.00 0.00 2.94
400 401 3.268334 AGGCTCTCACTTCTCTCTCCTAA 59.732 47.826 0.00 0.00 0.00 2.69
401 402 3.380320 GGCTCTCACTTCTCTCTCCTAAC 59.620 52.174 0.00 0.00 0.00 2.34
402 403 4.270008 GCTCTCACTTCTCTCTCCTAACT 58.730 47.826 0.00 0.00 0.00 2.24
403 404 4.705023 GCTCTCACTTCTCTCTCCTAACTT 59.295 45.833 0.00 0.00 0.00 2.66
404 405 5.393027 GCTCTCACTTCTCTCTCCTAACTTG 60.393 48.000 0.00 0.00 0.00 3.16
405 406 4.461081 TCTCACTTCTCTCTCCTAACTTGC 59.539 45.833 0.00 0.00 0.00 4.01
406 407 4.411927 TCACTTCTCTCTCCTAACTTGCT 58.588 43.478 0.00 0.00 0.00 3.91
407 408 4.835615 TCACTTCTCTCTCCTAACTTGCTT 59.164 41.667 0.00 0.00 0.00 3.91
408 409 6.010850 TCACTTCTCTCTCCTAACTTGCTTA 58.989 40.000 0.00 0.00 0.00 3.09
409 410 6.071840 TCACTTCTCTCTCCTAACTTGCTTAC 60.072 42.308 0.00 0.00 0.00 2.34
410 411 5.775701 ACTTCTCTCTCCTAACTTGCTTACA 59.224 40.000 0.00 0.00 0.00 2.41
411 412 6.267928 ACTTCTCTCTCCTAACTTGCTTACAA 59.732 38.462 0.00 0.00 0.00 2.41
412 413 6.026947 TCTCTCTCCTAACTTGCTTACAAC 57.973 41.667 0.00 0.00 0.00 3.32
413 414 5.538813 TCTCTCTCCTAACTTGCTTACAACA 59.461 40.000 0.00 0.00 0.00 3.33
414 415 5.539048 TCTCTCCTAACTTGCTTACAACAC 58.461 41.667 0.00 0.00 0.00 3.32
415 416 5.069914 TCTCTCCTAACTTGCTTACAACACA 59.930 40.000 0.00 0.00 0.00 3.72
416 417 5.054477 TCTCCTAACTTGCTTACAACACAC 58.946 41.667 0.00 0.00 0.00 3.82
417 418 4.771903 TCCTAACTTGCTTACAACACACA 58.228 39.130 0.00 0.00 0.00 3.72
418 419 5.373222 TCCTAACTTGCTTACAACACACAT 58.627 37.500 0.00 0.00 0.00 3.21
419 420 5.825679 TCCTAACTTGCTTACAACACACATT 59.174 36.000 0.00 0.00 0.00 2.71
420 421 6.017440 TCCTAACTTGCTTACAACACACATTC 60.017 38.462 0.00 0.00 0.00 2.67
421 422 5.835113 AACTTGCTTACAACACACATTCT 57.165 34.783 0.00 0.00 0.00 2.40
422 423 5.424121 ACTTGCTTACAACACACATTCTC 57.576 39.130 0.00 0.00 0.00 2.87
423 424 5.126067 ACTTGCTTACAACACACATTCTCT 58.874 37.500 0.00 0.00 0.00 3.10
424 425 6.288294 ACTTGCTTACAACACACATTCTCTA 58.712 36.000 0.00 0.00 0.00 2.43
425 426 6.936900 ACTTGCTTACAACACACATTCTCTAT 59.063 34.615 0.00 0.00 0.00 1.98
597 1019 1.135315 GTACGTCCTACTTGCGCGA 59.865 57.895 12.10 0.00 0.00 5.87
635 1057 2.668250 TGTCACCATCTACAAACGACG 58.332 47.619 0.00 0.00 0.00 5.12
827 1256 2.501723 TCACCTACCTCCAATCTTGCTC 59.498 50.000 0.00 0.00 0.00 4.26
835 1299 1.298116 CAATCTTGCTCGGCATGCG 60.298 57.895 12.44 7.41 38.76 4.73
836 1300 3.117175 AATCTTGCTCGGCATGCGC 62.117 57.895 12.44 10.44 38.76 6.09
892 1356 0.523072 CATTTTCTCCGTGCAGGTGG 59.477 55.000 5.57 0.00 41.99 4.61
950 1414 2.429571 TCGTGCGTCGCTAACACC 60.430 61.111 19.50 0.00 39.67 4.16
986 1450 2.118313 TACGTGTCACCTAGCTAGCA 57.882 50.000 18.83 4.97 0.00 3.49
1024 1488 1.518572 GACATACGGTGCGACCAGG 60.519 63.158 6.21 0.00 38.47 4.45
1587 2060 2.123248 TTGCTCCGGCCACTTCATCA 62.123 55.000 2.24 0.00 37.74 3.07
1710 2183 6.801718 TCGTTCTCTTGGGAATCCTATTAA 57.198 37.500 0.00 0.00 0.00 1.40
1753 2226 1.368641 TCATGCGAAGAAATGACCGG 58.631 50.000 0.00 0.00 29.28 5.28
1756 2229 0.034198 TGCGAAGAAATGACCGGTGA 59.966 50.000 14.63 2.52 0.00 4.02
1902 2378 9.935682 AATCGTGATGACATTGTTAACAATATC 57.064 29.630 28.64 27.16 44.10 1.63
2019 2495 9.868160 ATTAATCCATAAGAAAAGGAGGTTAGG 57.132 33.333 0.00 0.00 34.40 2.69
2032 2508 3.559384 GGAGGTTAGGTTTCCCACTTCAG 60.559 52.174 0.00 0.00 0.00 3.02
2169 2660 0.313043 ACTAGTGGGTGTTGTCGTCG 59.687 55.000 0.00 0.00 0.00 5.12
2223 2714 1.616159 ACTGGATGGGTTGGTTTTCG 58.384 50.000 0.00 0.00 0.00 3.46
2308 2799 2.500098 TGAAGGGATTCGACGATTCCTT 59.500 45.455 28.48 24.09 33.91 3.36
2327 2818 2.417339 TGAGGAAACAAGTCGAGTCG 57.583 50.000 6.09 6.09 0.00 4.18
2340 2831 3.064820 AGTCGAGTCGTTTGTGCAAAAAT 59.935 39.130 13.12 0.00 31.33 1.82
2389 2880 5.947228 GACACATGTCATTCTTTCCAGAA 57.053 39.130 7.15 0.00 44.18 3.02
2439 2930 6.422100 CCTGATGTATCCTATCTTGTTCAACG 59.578 42.308 0.00 0.00 0.00 4.10
2454 2945 2.821546 TCAACGTAGTGGCAGATATGC 58.178 47.619 3.01 3.01 45.00 3.14
2535 3028 2.375173 GGATGGGGTGGAGGGGTA 59.625 66.667 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.498900 TGTTAGCAGAATAATGGTGTTGGATAG 59.501 37.037 0.00 0.00 32.19 2.08
3 4 6.186957 TGTTAGCAGAATAATGGTGTTGGAT 58.813 36.000 0.00 0.00 32.19 3.41
4 5 5.565509 TGTTAGCAGAATAATGGTGTTGGA 58.434 37.500 0.00 0.00 32.19 3.53
5 6 5.895636 TGTTAGCAGAATAATGGTGTTGG 57.104 39.130 0.00 0.00 32.19 3.77
6 7 7.315142 ACATTGTTAGCAGAATAATGGTGTTG 58.685 34.615 18.53 2.48 34.40 3.33
7 8 7.466746 ACATTGTTAGCAGAATAATGGTGTT 57.533 32.000 18.53 2.70 34.40 3.32
8 9 6.183360 CGACATTGTTAGCAGAATAATGGTGT 60.183 38.462 18.53 5.88 34.40 4.16
9 10 6.194463 CGACATTGTTAGCAGAATAATGGTG 58.806 40.000 18.53 10.53 34.40 4.17
10 11 5.296780 CCGACATTGTTAGCAGAATAATGGT 59.703 40.000 18.53 9.14 34.40 3.55
11 12 5.751680 CCGACATTGTTAGCAGAATAATGG 58.248 41.667 18.53 7.46 34.40 3.16
12 13 5.207768 GCCGACATTGTTAGCAGAATAATG 58.792 41.667 14.99 14.99 35.65 1.90
13 14 4.881273 TGCCGACATTGTTAGCAGAATAAT 59.119 37.500 9.78 0.00 0.00 1.28
14 15 4.257731 TGCCGACATTGTTAGCAGAATAA 58.742 39.130 9.78 0.00 0.00 1.40
15 16 3.867857 TGCCGACATTGTTAGCAGAATA 58.132 40.909 9.78 0.00 0.00 1.75
16 17 2.710377 TGCCGACATTGTTAGCAGAAT 58.290 42.857 9.78 0.00 0.00 2.40
17 18 2.177394 TGCCGACATTGTTAGCAGAA 57.823 45.000 9.78 0.00 0.00 3.02
18 19 2.279741 GATGCCGACATTGTTAGCAGA 58.720 47.619 16.56 0.00 36.35 4.26
19 20 1.331756 GGATGCCGACATTGTTAGCAG 59.668 52.381 16.56 0.00 36.35 4.24
20 21 1.065491 AGGATGCCGACATTGTTAGCA 60.065 47.619 14.60 14.60 36.35 3.49
21 22 1.668419 AGGATGCCGACATTGTTAGC 58.332 50.000 5.34 5.34 36.35 3.09
22 23 3.535561 AGAAGGATGCCGACATTGTTAG 58.464 45.455 0.00 0.00 36.35 2.34
23 24 3.055458 TGAGAAGGATGCCGACATTGTTA 60.055 43.478 0.00 0.00 36.35 2.41
24 25 2.290260 TGAGAAGGATGCCGACATTGTT 60.290 45.455 0.00 0.00 36.35 2.83
25 26 1.278985 TGAGAAGGATGCCGACATTGT 59.721 47.619 0.00 0.00 36.35 2.71
26 27 1.667724 GTGAGAAGGATGCCGACATTG 59.332 52.381 0.00 0.00 36.35 2.82
27 28 1.278985 TGTGAGAAGGATGCCGACATT 59.721 47.619 0.00 0.00 36.35 2.71
28 29 0.904649 TGTGAGAAGGATGCCGACAT 59.095 50.000 0.00 0.00 39.98 3.06
29 30 0.904649 ATGTGAGAAGGATGCCGACA 59.095 50.000 0.00 0.00 0.00 4.35
30 31 1.667724 CAATGTGAGAAGGATGCCGAC 59.332 52.381 0.00 0.00 0.00 4.79
31 32 1.554617 TCAATGTGAGAAGGATGCCGA 59.445 47.619 0.00 0.00 0.00 5.54
32 33 1.667724 GTCAATGTGAGAAGGATGCCG 59.332 52.381 0.00 0.00 0.00 5.69
33 34 2.715046 TGTCAATGTGAGAAGGATGCC 58.285 47.619 0.00 0.00 0.00 4.40
34 35 4.669318 CATTGTCAATGTGAGAAGGATGC 58.331 43.478 16.15 0.00 34.00 3.91
49 50 9.681692 CTGTTTTTCAGATCATAAACATTGTCA 57.318 29.630 12.14 0.00 46.27 3.58
50 51 9.683069 ACTGTTTTTCAGATCATAAACATTGTC 57.317 29.630 12.14 0.00 46.27 3.18
60 61 9.234827 TGTTGATGATACTGTTTTTCAGATCAT 57.765 29.630 15.35 15.35 46.27 2.45
61 62 8.620116 TGTTGATGATACTGTTTTTCAGATCA 57.380 30.769 0.00 7.01 46.27 2.92
70 71 9.672673 AGCTAAGTATTGTTGATGATACTGTTT 57.327 29.630 0.00 0.00 38.66 2.83
72 73 9.973450 CTAGCTAAGTATTGTTGATGATACTGT 57.027 33.333 0.00 0.00 38.66 3.55
73 74 9.973450 ACTAGCTAAGTATTGTTGATGATACTG 57.027 33.333 0.00 0.00 38.66 2.74
93 94 8.892530 TCCCTAGTGTAATCTCTAATACTAGCT 58.107 37.037 0.00 0.00 37.40 3.32
94 95 9.689501 ATCCCTAGTGTAATCTCTAATACTAGC 57.310 37.037 0.00 0.00 37.40 3.42
103 104 9.836179 ATCAAATAGATCCCTAGTGTAATCTCT 57.164 33.333 0.00 0.00 28.20 3.10
104 105 9.868277 CATCAAATAGATCCCTAGTGTAATCTC 57.132 37.037 0.00 0.00 33.72 2.75
105 106 9.386122 ACATCAAATAGATCCCTAGTGTAATCT 57.614 33.333 0.00 0.00 33.72 2.40
116 117 8.968242 GCGAAAAATAAACATCAAATAGATCCC 58.032 33.333 0.00 0.00 33.72 3.85
117 118 8.968242 GGCGAAAAATAAACATCAAATAGATCC 58.032 33.333 0.00 0.00 33.72 3.36
118 119 8.968242 GGGCGAAAAATAAACATCAAATAGATC 58.032 33.333 0.00 0.00 33.72 2.75
119 120 8.474025 TGGGCGAAAAATAAACATCAAATAGAT 58.526 29.630 0.00 0.00 37.48 1.98
120 121 7.831753 TGGGCGAAAAATAAACATCAAATAGA 58.168 30.769 0.00 0.00 0.00 1.98
121 122 8.542132 CATGGGCGAAAAATAAACATCAAATAG 58.458 33.333 0.00 0.00 0.00 1.73
122 123 7.010923 GCATGGGCGAAAAATAAACATCAAATA 59.989 33.333 0.00 0.00 0.00 1.40
123 124 6.183360 GCATGGGCGAAAAATAAACATCAAAT 60.183 34.615 0.00 0.00 0.00 2.32
124 125 5.121454 GCATGGGCGAAAAATAAACATCAAA 59.879 36.000 0.00 0.00 0.00 2.69
125 126 4.629200 GCATGGGCGAAAAATAAACATCAA 59.371 37.500 0.00 0.00 0.00 2.57
126 127 4.180057 GCATGGGCGAAAAATAAACATCA 58.820 39.130 0.00 0.00 0.00 3.07
127 128 4.180057 TGCATGGGCGAAAAATAAACATC 58.820 39.130 0.00 0.00 45.35 3.06
128 129 4.199432 TGCATGGGCGAAAAATAAACAT 57.801 36.364 0.00 0.00 45.35 2.71
129 130 3.667497 TGCATGGGCGAAAAATAAACA 57.333 38.095 0.00 0.00 45.35 2.83
130 131 5.121454 TCAATTGCATGGGCGAAAAATAAAC 59.879 36.000 0.00 0.00 45.35 2.01
131 132 5.240891 TCAATTGCATGGGCGAAAAATAAA 58.759 33.333 0.00 0.00 45.35 1.40
132 133 4.825422 TCAATTGCATGGGCGAAAAATAA 58.175 34.783 0.00 0.00 45.35 1.40
133 134 4.081752 ACTCAATTGCATGGGCGAAAAATA 60.082 37.500 0.00 0.00 45.35 1.40
134 135 3.264104 CTCAATTGCATGGGCGAAAAAT 58.736 40.909 0.00 0.00 45.35 1.82
135 136 2.036992 ACTCAATTGCATGGGCGAAAAA 59.963 40.909 0.00 0.00 45.35 1.94
136 137 1.617850 ACTCAATTGCATGGGCGAAAA 59.382 42.857 0.00 0.00 45.35 2.29
137 138 1.255882 ACTCAATTGCATGGGCGAAA 58.744 45.000 0.00 0.00 45.35 3.46
138 139 1.255882 AACTCAATTGCATGGGCGAA 58.744 45.000 0.00 0.00 45.35 4.70
139 140 1.255882 AAACTCAATTGCATGGGCGA 58.744 45.000 0.00 0.00 45.35 5.54
140 141 1.994779 GAAAACTCAATTGCATGGGCG 59.005 47.619 0.00 0.00 45.35 6.13
141 142 2.027837 AGGAAAACTCAATTGCATGGGC 60.028 45.455 0.00 0.00 41.68 5.36
142 143 3.853475 GAGGAAAACTCAATTGCATGGG 58.147 45.455 0.00 0.00 45.85 4.00
153 154 5.546526 AGTGTGAGATTCAGAGGAAAACTC 58.453 41.667 0.00 0.00 46.98 3.01
154 155 5.559148 AGTGTGAGATTCAGAGGAAAACT 57.441 39.130 0.00 0.00 36.43 2.66
155 156 6.223852 TGTAGTGTGAGATTCAGAGGAAAAC 58.776 40.000 0.00 0.00 36.43 2.43
156 157 6.267699 TCTGTAGTGTGAGATTCAGAGGAAAA 59.732 38.462 0.00 0.00 36.43 2.29
157 158 5.775195 TCTGTAGTGTGAGATTCAGAGGAAA 59.225 40.000 0.00 0.00 36.43 3.13
158 159 5.325239 TCTGTAGTGTGAGATTCAGAGGAA 58.675 41.667 0.00 0.00 37.45 3.36
159 160 4.923415 TCTGTAGTGTGAGATTCAGAGGA 58.077 43.478 0.00 0.00 0.00 3.71
160 161 5.651387 TTCTGTAGTGTGAGATTCAGAGG 57.349 43.478 0.00 0.00 34.28 3.69
161 162 9.814899 AATAATTCTGTAGTGTGAGATTCAGAG 57.185 33.333 0.00 0.00 34.28 3.35
162 163 9.591792 CAATAATTCTGTAGTGTGAGATTCAGA 57.408 33.333 0.00 0.00 0.00 3.27
163 164 9.376075 ACAATAATTCTGTAGTGTGAGATTCAG 57.624 33.333 0.00 0.00 31.46 3.02
238 239 9.136323 CCTAGAGGCATTAATAAAGGTCATTTT 57.864 33.333 0.00 0.00 32.01 1.82
239 240 8.282256 ACCTAGAGGCATTAATAAAGGTCATTT 58.718 33.333 0.00 0.00 39.32 2.32
240 241 7.816411 ACCTAGAGGCATTAATAAAGGTCATT 58.184 34.615 0.00 0.00 39.32 2.57
241 242 7.394144 ACCTAGAGGCATTAATAAAGGTCAT 57.606 36.000 0.00 0.00 39.32 3.06
242 243 6.824958 ACCTAGAGGCATTAATAAAGGTCA 57.175 37.500 0.00 0.00 39.32 4.02
244 245 6.824958 TGACCTAGAGGCATTAATAAAGGT 57.175 37.500 0.00 0.00 38.77 3.50
245 246 9.965902 AATATGACCTAGAGGCATTAATAAAGG 57.034 33.333 5.06 0.00 39.32 3.11
248 249 9.959721 GGAAATATGACCTAGAGGCATTAATAA 57.040 33.333 5.06 0.00 39.32 1.40
249 250 9.111519 TGGAAATATGACCTAGAGGCATTAATA 57.888 33.333 5.06 0.00 39.32 0.98
250 251 7.988937 TGGAAATATGACCTAGAGGCATTAAT 58.011 34.615 5.06 0.00 39.32 1.40
251 252 7.387265 TGGAAATATGACCTAGAGGCATTAA 57.613 36.000 5.06 0.00 39.32 1.40
252 253 7.147391 TGTTGGAAATATGACCTAGAGGCATTA 60.147 37.037 5.06 0.00 39.32 1.90
253 254 5.912149 TGGAAATATGACCTAGAGGCATT 57.088 39.130 5.06 0.00 39.32 3.56
254 255 5.132648 TGTTGGAAATATGACCTAGAGGCAT 59.867 40.000 5.11 5.11 39.32 4.40
255 256 4.473196 TGTTGGAAATATGACCTAGAGGCA 59.527 41.667 0.00 0.00 39.32 4.75
256 257 5.036117 TGTTGGAAATATGACCTAGAGGC 57.964 43.478 0.00 0.00 39.32 4.70
257 258 6.051717 CACTGTTGGAAATATGACCTAGAGG 58.948 44.000 0.00 0.00 42.17 3.69
273 274 0.958091 TTTCAATCGCCCACTGTTGG 59.042 50.000 0.00 0.00 43.50 3.77
274 275 2.791383 TTTTCAATCGCCCACTGTTG 57.209 45.000 0.00 0.00 0.00 3.33
291 292 7.925483 TCAAAACATCGAGTCAAATCCATTTTT 59.075 29.630 0.00 0.00 0.00 1.94
292 293 7.432869 TCAAAACATCGAGTCAAATCCATTTT 58.567 30.769 0.00 0.00 0.00 1.82
293 294 6.980593 TCAAAACATCGAGTCAAATCCATTT 58.019 32.000 0.00 0.00 0.00 2.32
294 295 6.573664 TCAAAACATCGAGTCAAATCCATT 57.426 33.333 0.00 0.00 0.00 3.16
295 296 5.392380 GCTCAAAACATCGAGTCAAATCCAT 60.392 40.000 0.00 0.00 0.00 3.41
296 297 4.083324 GCTCAAAACATCGAGTCAAATCCA 60.083 41.667 0.00 0.00 0.00 3.41
297 298 4.406943 GCTCAAAACATCGAGTCAAATCC 58.593 43.478 0.00 0.00 0.00 3.01
298 299 4.154918 AGGCTCAAAACATCGAGTCAAATC 59.845 41.667 0.00 0.00 36.30 2.17
299 300 4.074970 AGGCTCAAAACATCGAGTCAAAT 58.925 39.130 0.00 0.00 36.30 2.32
300 301 3.250762 CAGGCTCAAAACATCGAGTCAAA 59.749 43.478 0.00 0.00 36.30 2.69
301 302 2.807967 CAGGCTCAAAACATCGAGTCAA 59.192 45.455 0.00 0.00 36.30 3.18
302 303 2.416747 CAGGCTCAAAACATCGAGTCA 58.583 47.619 0.00 0.00 36.30 3.41
303 304 1.734465 CCAGGCTCAAAACATCGAGTC 59.266 52.381 0.00 0.00 33.97 3.36
304 305 1.072331 ACCAGGCTCAAAACATCGAGT 59.928 47.619 0.00 0.00 0.00 4.18
305 306 1.466167 CACCAGGCTCAAAACATCGAG 59.534 52.381 0.00 0.00 0.00 4.04
306 307 1.522668 CACCAGGCTCAAAACATCGA 58.477 50.000 0.00 0.00 0.00 3.59
307 308 0.523072 CCACCAGGCTCAAAACATCG 59.477 55.000 0.00 0.00 0.00 3.84
319 320 4.496336 GCCCAGCTAGCCACCAGG 62.496 72.222 12.13 6.42 38.23 4.45
320 321 3.406200 AGCCCAGCTAGCCACCAG 61.406 66.667 12.13 0.00 36.99 4.00
321 322 3.720601 CAGCCCAGCTAGCCACCA 61.721 66.667 12.13 0.00 36.40 4.17
322 323 2.317149 CTACAGCCCAGCTAGCCACC 62.317 65.000 12.13 0.00 36.40 4.61
323 324 1.144936 CTACAGCCCAGCTAGCCAC 59.855 63.158 12.13 0.00 36.40 5.01
324 325 2.066393 CCTACAGCCCAGCTAGCCA 61.066 63.158 12.13 0.00 36.40 4.75
325 326 1.753368 CTCCTACAGCCCAGCTAGCC 61.753 65.000 12.13 0.00 36.40 3.93
326 327 1.745264 CTCCTACAGCCCAGCTAGC 59.255 63.158 6.62 6.62 36.40 3.42
327 328 0.397816 ACCTCCTACAGCCCAGCTAG 60.398 60.000 0.00 0.00 36.40 3.42
328 329 0.042731 AACCTCCTACAGCCCAGCTA 59.957 55.000 0.00 0.00 36.40 3.32
329 330 1.229658 AACCTCCTACAGCCCAGCT 60.230 57.895 0.00 0.00 40.77 4.24
330 331 1.078143 CAACCTCCTACAGCCCAGC 60.078 63.158 0.00 0.00 0.00 4.85
331 332 0.693049 AACAACCTCCTACAGCCCAG 59.307 55.000 0.00 0.00 0.00 4.45
332 333 0.400213 CAACAACCTCCTACAGCCCA 59.600 55.000 0.00 0.00 0.00 5.36
333 334 0.960861 GCAACAACCTCCTACAGCCC 60.961 60.000 0.00 0.00 0.00 5.19
334 335 0.036875 AGCAACAACCTCCTACAGCC 59.963 55.000 0.00 0.00 0.00 4.85
335 336 1.897560 AAGCAACAACCTCCTACAGC 58.102 50.000 0.00 0.00 0.00 4.40
336 337 4.330074 CGATAAAGCAACAACCTCCTACAG 59.670 45.833 0.00 0.00 0.00 2.74
337 338 4.250464 CGATAAAGCAACAACCTCCTACA 58.750 43.478 0.00 0.00 0.00 2.74
338 339 4.251268 ACGATAAAGCAACAACCTCCTAC 58.749 43.478 0.00 0.00 0.00 3.18
339 340 4.501071 GACGATAAAGCAACAACCTCCTA 58.499 43.478 0.00 0.00 0.00 2.94
340 341 3.335579 GACGATAAAGCAACAACCTCCT 58.664 45.455 0.00 0.00 0.00 3.69
341 342 2.418976 GGACGATAAAGCAACAACCTCC 59.581 50.000 0.00 0.00 0.00 4.30
342 343 3.071479 TGGACGATAAAGCAACAACCTC 58.929 45.455 0.00 0.00 0.00 3.85
343 344 2.812011 GTGGACGATAAAGCAACAACCT 59.188 45.455 0.00 0.00 0.00 3.50
344 345 2.550606 TGTGGACGATAAAGCAACAACC 59.449 45.455 0.00 0.00 0.00 3.77
345 346 3.551551 GTGTGGACGATAAAGCAACAAC 58.448 45.455 0.00 0.00 0.00 3.32
346 347 3.889196 GTGTGGACGATAAAGCAACAA 57.111 42.857 0.00 0.00 0.00 2.83
361 362 1.068083 CTGATCCGATCCCGTGTGG 59.932 63.158 5.91 0.00 0.00 4.17
362 363 1.068083 CCTGATCCGATCCCGTGTG 59.932 63.158 5.91 0.00 0.00 3.82
363 364 2.797278 GCCTGATCCGATCCCGTGT 61.797 63.158 5.91 0.00 0.00 4.49
364 365 2.029666 GCCTGATCCGATCCCGTG 59.970 66.667 5.91 0.00 0.00 4.94
365 366 2.123251 AGCCTGATCCGATCCCGT 60.123 61.111 5.91 0.00 0.00 5.28
366 367 1.872197 GAGAGCCTGATCCGATCCCG 61.872 65.000 5.91 0.00 0.00 5.14
367 368 0.829602 TGAGAGCCTGATCCGATCCC 60.830 60.000 5.91 0.00 0.00 3.85
368 369 0.316841 GTGAGAGCCTGATCCGATCC 59.683 60.000 5.91 0.00 0.00 3.36
369 370 1.327303 AGTGAGAGCCTGATCCGATC 58.673 55.000 1.01 1.01 0.00 3.69
370 371 1.686052 GAAGTGAGAGCCTGATCCGAT 59.314 52.381 0.00 0.00 0.00 4.18
371 372 1.107114 GAAGTGAGAGCCTGATCCGA 58.893 55.000 0.00 0.00 0.00 4.55
372 373 1.066908 GAGAAGTGAGAGCCTGATCCG 59.933 57.143 0.00 0.00 0.00 4.18
373 374 2.362077 GAGAGAAGTGAGAGCCTGATCC 59.638 54.545 0.00 0.00 0.00 3.36
374 375 3.290710 AGAGAGAAGTGAGAGCCTGATC 58.709 50.000 0.00 0.00 0.00 2.92
375 376 3.290710 GAGAGAGAAGTGAGAGCCTGAT 58.709 50.000 0.00 0.00 0.00 2.90
376 377 2.620367 GGAGAGAGAAGTGAGAGCCTGA 60.620 54.545 0.00 0.00 0.00 3.86
377 378 1.750778 GGAGAGAGAAGTGAGAGCCTG 59.249 57.143 0.00 0.00 0.00 4.85
378 379 1.640670 AGGAGAGAGAAGTGAGAGCCT 59.359 52.381 0.00 0.00 0.00 4.58
379 380 2.143876 AGGAGAGAGAAGTGAGAGCC 57.856 55.000 0.00 0.00 0.00 4.70
380 381 4.270008 AGTTAGGAGAGAGAAGTGAGAGC 58.730 47.826 0.00 0.00 0.00 4.09
381 382 5.393027 GCAAGTTAGGAGAGAGAAGTGAGAG 60.393 48.000 0.00 0.00 0.00 3.20
382 383 4.461081 GCAAGTTAGGAGAGAGAAGTGAGA 59.539 45.833 0.00 0.00 0.00 3.27
383 384 4.462483 AGCAAGTTAGGAGAGAGAAGTGAG 59.538 45.833 0.00 0.00 0.00 3.51
384 385 4.411927 AGCAAGTTAGGAGAGAGAAGTGA 58.588 43.478 0.00 0.00 0.00 3.41
385 386 4.799564 AGCAAGTTAGGAGAGAGAAGTG 57.200 45.455 0.00 0.00 0.00 3.16
386 387 5.775701 TGTAAGCAAGTTAGGAGAGAGAAGT 59.224 40.000 0.00 0.00 0.00 3.01
387 388 6.274157 TGTAAGCAAGTTAGGAGAGAGAAG 57.726 41.667 0.00 0.00 0.00 2.85
388 389 6.041637 TGTTGTAAGCAAGTTAGGAGAGAGAA 59.958 38.462 0.00 0.00 34.94 2.87
389 390 5.538813 TGTTGTAAGCAAGTTAGGAGAGAGA 59.461 40.000 0.00 0.00 34.94 3.10
390 391 5.635700 GTGTTGTAAGCAAGTTAGGAGAGAG 59.364 44.000 0.00 0.00 34.94 3.20
391 392 5.069914 TGTGTTGTAAGCAAGTTAGGAGAGA 59.930 40.000 0.00 0.00 34.94 3.10
392 393 5.177696 GTGTGTTGTAAGCAAGTTAGGAGAG 59.822 44.000 0.00 0.00 34.94 3.20
393 394 5.054477 GTGTGTTGTAAGCAAGTTAGGAGA 58.946 41.667 0.00 0.00 34.94 3.71
394 395 4.814234 TGTGTGTTGTAAGCAAGTTAGGAG 59.186 41.667 0.00 0.00 34.94 3.69
395 396 4.771903 TGTGTGTTGTAAGCAAGTTAGGA 58.228 39.130 0.00 0.00 34.94 2.94
396 397 5.689383 ATGTGTGTTGTAAGCAAGTTAGG 57.311 39.130 0.00 0.00 34.94 2.69
397 398 6.959361 AGAATGTGTGTTGTAAGCAAGTTAG 58.041 36.000 0.00 0.00 34.94 2.34
398 399 6.765989 AGAGAATGTGTGTTGTAAGCAAGTTA 59.234 34.615 0.00 0.00 34.94 2.24
399 400 5.590259 AGAGAATGTGTGTTGTAAGCAAGTT 59.410 36.000 0.00 0.00 34.94 2.66
400 401 5.126067 AGAGAATGTGTGTTGTAAGCAAGT 58.874 37.500 0.00 0.00 34.94 3.16
401 402 5.679734 AGAGAATGTGTGTTGTAAGCAAG 57.320 39.130 0.00 0.00 34.94 4.01
402 403 6.371548 GGATAGAGAATGTGTGTTGTAAGCAA 59.628 38.462 0.00 0.00 0.00 3.91
403 404 5.874810 GGATAGAGAATGTGTGTTGTAAGCA 59.125 40.000 0.00 0.00 0.00 3.91
404 405 5.294552 GGGATAGAGAATGTGTGTTGTAAGC 59.705 44.000 0.00 0.00 0.00 3.09
405 406 6.406370 TGGGATAGAGAATGTGTGTTGTAAG 58.594 40.000 0.00 0.00 0.00 2.34
406 407 6.212589 TCTGGGATAGAGAATGTGTGTTGTAA 59.787 38.462 0.00 0.00 0.00 2.41
407 408 5.719563 TCTGGGATAGAGAATGTGTGTTGTA 59.280 40.000 0.00 0.00 0.00 2.41
408 409 4.532126 TCTGGGATAGAGAATGTGTGTTGT 59.468 41.667 0.00 0.00 0.00 3.32
409 410 5.089970 TCTGGGATAGAGAATGTGTGTTG 57.910 43.478 0.00 0.00 0.00 3.33
421 422 7.649702 TCTTCCTATTAGTCTCTGGGATAGA 57.350 40.000 0.00 0.00 0.00 1.98
422 423 7.093945 GCTTCTTCCTATTAGTCTCTGGGATAG 60.094 44.444 0.00 0.00 0.00 2.08
423 424 6.722129 GCTTCTTCCTATTAGTCTCTGGGATA 59.278 42.308 0.00 0.00 0.00 2.59
424 425 5.542251 GCTTCTTCCTATTAGTCTCTGGGAT 59.458 44.000 0.00 0.00 0.00 3.85
425 426 4.896482 GCTTCTTCCTATTAGTCTCTGGGA 59.104 45.833 0.00 0.00 0.00 4.37
441 442 9.967346 AAAAGTTAAGAATAGGTTTGCTTCTTC 57.033 29.630 0.43 0.00 39.34 2.87
597 1019 4.520492 GTGACATGAAGGTTCCATGAGTTT 59.480 41.667 0.00 0.00 42.89 2.66
635 1057 6.630443 GTGTGAATGACATCTTTATCGATTGC 59.370 38.462 1.71 0.00 36.78 3.56
827 1256 3.945434 GAGGACATGCGCATGCCG 61.945 66.667 42.18 24.84 42.39 5.69
835 1299 1.943340 GGAAGAAATCGGAGGACATGC 59.057 52.381 0.00 0.00 0.00 4.06
836 1300 2.565841 GGGAAGAAATCGGAGGACATG 58.434 52.381 0.00 0.00 0.00 3.21
892 1356 3.471806 GGGAGCGGAGGGAAGTCC 61.472 72.222 0.00 0.00 0.00 3.85
950 1414 1.071605 GTAAGTGTTGAGGCGCTCAG 58.928 55.000 7.64 0.00 41.75 3.35
982 1446 3.307269 GCCATGGATGATCTAGCTTGCTA 60.307 47.826 18.40 2.19 0.00 3.49
986 1450 1.002888 CCGCCATGGATGATCTAGCTT 59.997 52.381 18.40 0.00 42.00 3.74
1024 1488 2.486966 GCTTGGCGTCATCTTGGC 59.513 61.111 0.00 0.00 0.00 4.52
1048 1515 0.470080 TAGCCGAAGATCCTGAGGGG 60.470 60.000 0.00 0.00 0.00 4.79
1053 1520 0.317103 CGTCGTAGCCGAAGATCCTG 60.317 60.000 0.00 0.00 46.26 3.86
1348 1818 2.331805 CGCGAGGTAGACCCATCG 59.668 66.667 0.00 6.10 37.11 3.84
1441 1911 2.671682 GCAGTCCCTTGGGTCCTC 59.328 66.667 5.51 0.00 0.00 3.71
1710 2183 3.260475 TCCGAATGAATGGACAACGAT 57.740 42.857 0.00 0.00 0.00 3.73
1866 2342 5.984233 TGTCATCACGATTTACTTATGGC 57.016 39.130 0.00 0.00 0.00 4.40
1924 2400 9.875691 CTATGCCTAGTATGTGCTCAAATATAA 57.124 33.333 0.00 0.00 0.00 0.98
2032 2508 6.870971 TGGTTTCAAGTCCAATAGTTACAC 57.129 37.500 0.00 0.00 0.00 2.90
2063 2553 0.307760 GGTTCGCACCAACTTGAGTG 59.692 55.000 0.00 6.19 43.61 3.51
2067 2558 1.157870 AGTCGGTTCGCACCAACTTG 61.158 55.000 4.79 0.00 36.92 3.16
2076 2567 0.807667 ATCTGCATCAGTCGGTTCGC 60.808 55.000 0.00 0.00 32.61 4.70
2169 2660 7.271223 GTGCATTTCATGTAGTGTTTCATGTAC 59.729 37.037 0.00 0.00 41.22 2.90
2223 2714 2.162008 ACGCCTTCTCGAAGTCTACTTC 59.838 50.000 11.98 11.98 46.63 3.01
2308 2799 1.679680 ACGACTCGACTTGTTTCCTCA 59.320 47.619 5.20 0.00 0.00 3.86
2327 2818 3.382015 ACGTTGCATTTTTGCACAAAC 57.618 38.095 0.00 0.00 45.32 2.93
2340 2831 4.274602 TCACTTTAATCCCTACGTTGCA 57.725 40.909 0.00 0.00 0.00 4.08
2344 2835 6.761714 GTCATCATTCACTTTAATCCCTACGT 59.238 38.462 0.00 0.00 0.00 3.57
2389 2880 1.272147 CCTGTCTTAGGCCCTTTTGCT 60.272 52.381 0.00 0.00 40.38 3.91
2416 2907 6.873997 ACGTTGAACAAGATAGGATACATCA 58.126 36.000 0.00 0.00 41.41 3.07
2422 2913 5.661458 CCACTACGTTGAACAAGATAGGAT 58.339 41.667 3.44 0.00 0.00 3.24
2454 2945 5.066593 GGCCCTACCAATAAGAATTCTCAG 58.933 45.833 8.78 0.00 38.86 3.35
2535 3028 4.404394 TCGTCAGTGTATTGTGGTATGGAT 59.596 41.667 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.