Multiple sequence alignment - TraesCS4A01G221300

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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 TraesCS4A01G221300 chr4A 100.000 3307 0 0 1 3307 527000528 527003834 0.000000e+00 6107.0
1 TraesCS4A01G221300 chr4D 93.692 2822 98 30 456 3218 71000867 70998067 0.000000e+00 4152.0
2 TraesCS4A01G221300 chr4D 94.872 273 12 1 6 278 341214819 341214549 3.050000e-115 425.0
3 TraesCS4A01G221300 chrUn 95.413 1308 39 12 725 2023 54294259 54295554 0.000000e+00 2063.0
4 TraesCS4A01G221300 chrUn 92.368 760 31 11 2039 2774 54295631 54296387 0.000000e+00 1057.0
5 TraesCS4A01G221300 chrUn 87.359 443 23 4 2848 3272 54296387 54296814 8.300000e-131 477.0
6 TraesCS4A01G221300 chrUn 90.244 287 14 6 466 739 54293914 54294199 2.430000e-96 363.0
7 TraesCS4A01G221300 chr3D 94.505 273 13 1 6 278 298241079 298241349 1.420000e-113 420.0
8 TraesCS4A01G221300 chr3A 93.863 277 15 1 6 282 592844933 592844659 1.840000e-112 416.0
9 TraesCS4A01G221300 chr3A 93.116 276 17 1 8 283 412675723 412675450 1.430000e-108 403.0
10 TraesCS4A01G221300 chr3A 80.208 96 8 9 334 420 382348412 382348319 9.910000e-06 62.1
11 TraesCS4A01G221300 chr2D 94.139 273 14 1 6 278 207639998 207639728 6.600000e-112 414.0
12 TraesCS4A01G221300 chr2A 92.806 278 18 1 6 283 262727830 262727555 5.140000e-108 401.0
13 TraesCS4A01G221300 chr2A 84.337 166 14 8 278 441 751921074 751920919 5.720000e-33 152.0
14 TraesCS4A01G221300 chr5A 93.358 271 16 1 5 275 320834717 320834449 1.850000e-107 399.0
15 TraesCS4A01G221300 chr5A 93.103 116 8 0 278 393 6529987 6529872 1.580000e-38 171.0
16 TraesCS4A01G221300 chr5A 87.970 133 16 0 1643 1775 450541450 450541582 1.230000e-34 158.0
17 TraesCS4A01G221300 chr5A 79.710 207 39 2 1646 1852 450474297 450474094 2.660000e-31 147.0
18 TraesCS4A01G221300 chr1A 92.226 283 19 3 6 287 49308537 49308817 6.650000e-107 398.0
19 TraesCS4A01G221300 chr1A 92.446 278 19 1 6 283 98875858 98876133 2.390000e-106 396.0
20 TraesCS4A01G221300 chr1A 79.085 306 41 9 3012 3295 554209168 554209472 4.360000e-44 189.0
21 TraesCS4A01G221300 chr1A 80.365 219 32 5 1638 1852 79107645 79107856 4.420000e-34 156.0
22 TraesCS4A01G221300 chr1A 78.632 234 39 5 1623 1852 78963955 78963729 9.560000e-31 145.0
23 TraesCS4A01G221300 chr3B 87.333 150 11 4 278 420 361013068 361012920 7.340000e-37 165.0
24 TraesCS4A01G221300 chr3B 83.721 172 15 9 278 441 714731652 714731486 2.060000e-32 150.0
25 TraesCS4A01G221300 chr3B 86.331 139 14 4 278 413 775072624 775072488 2.660000e-31 147.0
26 TraesCS4A01G221300 chr5D 88.806 134 10 5 278 409 97072924 97073054 3.420000e-35 159.0
27 TraesCS4A01G221300 chr5D 79.524 210 40 2 1643 1852 350220790 350220996 2.660000e-31 147.0
28 TraesCS4A01G221300 chr1D 79.909 219 41 2 1634 1852 84875903 84876118 1.230000e-34 158.0
29 TraesCS4A01G221300 chr2B 84.118 170 18 8 278 441 59983969 59984135 4.420000e-34 156.0
30 TraesCS4A01G221300 chr1B 83.529 170 19 8 278 441 109875503 109875669 2.060000e-32 150.0
31 TraesCS4A01G221300 chr4B 82.941 170 20 8 278 441 590310643 590310809 9.560000e-31 145.0
32 TraesCS4A01G221300 chr5B 86.154 130 18 0 1646 1775 410598285 410598156 1.240000e-29 141.0
33 TraesCS4A01G221300 chr6D 87.931 58 2 1 363 420 389627494 389627442 2.760000e-06 63.9


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 TraesCS4A01G221300 chr4A 527000528 527003834 3306 False 6107 6107 100.000 1 3307 1 chr4A.!!$F1 3306
1 TraesCS4A01G221300 chr4D 70998067 71000867 2800 True 4152 4152 93.692 456 3218 1 chr4D.!!$R1 2762
2 TraesCS4A01G221300 chrUn 54293914 54296814 2900 False 990 2063 91.346 466 3272 4 chrUn.!!$F1 2806

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
274 275 0.182775 GTTACCCCCACTATGGCCAG 59.817 60.0 13.05 0.00 35.79 4.85 F
1246 1344 0.179018 AGGGTGAAGAAGGTGTGCAC 60.179 55.0 10.75 10.75 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1271 1369 0.106419 GGTTGGACCTGTTGAACCCA 60.106 55.0 0.07 0.0 34.73 4.51 R
2323 2501 0.393820 CAGGTGCAGCCATTTTTGGT 59.606 50.0 13.29 0.0 40.61 3.67 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
21 22 3.136641 AGATTGGTCATAGTGGGGAGT 57.863 47.619 0.00 0.00 0.00 3.85
22 23 4.280789 AGATTGGTCATAGTGGGGAGTA 57.719 45.455 0.00 0.00 0.00 2.59
23 24 4.832492 AGATTGGTCATAGTGGGGAGTAT 58.168 43.478 0.00 0.00 0.00 2.12
24 25 4.841246 AGATTGGTCATAGTGGGGAGTATC 59.159 45.833 0.00 0.00 0.00 2.24
25 26 3.699025 TGGTCATAGTGGGGAGTATCA 57.301 47.619 0.00 0.00 36.25 2.15
26 27 4.213531 TGGTCATAGTGGGGAGTATCAT 57.786 45.455 0.00 0.00 36.25 2.45
27 28 5.348259 TGGTCATAGTGGGGAGTATCATA 57.652 43.478 0.00 0.00 36.25 2.15
28 29 5.915628 TGGTCATAGTGGGGAGTATCATAT 58.084 41.667 0.00 0.00 36.25 1.78
29 30 7.051696 TGGTCATAGTGGGGAGTATCATATA 57.948 40.000 0.00 0.00 36.25 0.86
30 31 6.895756 TGGTCATAGTGGGGAGTATCATATAC 59.104 42.308 0.00 0.00 36.25 1.47
31 32 7.126733 GGTCATAGTGGGGAGTATCATATACT 58.873 42.308 0.00 0.00 36.25 2.12
32 33 8.280084 GGTCATAGTGGGGAGTATCATATACTA 58.720 40.741 0.00 0.00 36.25 1.82
33 34 9.344772 GTCATAGTGGGGAGTATCATATACTAG 57.655 40.741 0.00 0.00 36.25 2.57
34 35 9.070210 TCATAGTGGGGAGTATCATATACTAGT 57.930 37.037 0.00 0.00 36.25 2.57
38 39 9.070210 AGTGGGGAGTATCATATACTAGTATCA 57.930 37.037 18.68 5.25 36.25 2.15
39 40 9.869667 GTGGGGAGTATCATATACTAGTATCAT 57.130 37.037 18.68 11.67 36.25 2.45
40 41 9.868160 TGGGGAGTATCATATACTAGTATCATG 57.132 37.037 18.68 17.93 36.25 3.07
41 42 8.798402 GGGGAGTATCATATACTAGTATCATGC 58.202 40.741 18.68 12.34 36.25 4.06
42 43 9.355916 GGGAGTATCATATACTAGTATCATGCA 57.644 37.037 18.68 1.71 36.25 3.96
78 79 8.860088 AGTGTATCATACTACATCAATAGTGCA 58.140 33.333 0.00 0.00 36.09 4.57
79 80 9.645059 GTGTATCATACTACATCAATAGTGCAT 57.355 33.333 0.00 0.00 36.09 3.96
109 110 9.830186 AACATAGATTAGTATCATAGGTGGTCT 57.170 33.333 0.00 0.00 32.95 3.85
110 111 9.469097 ACATAGATTAGTATCATAGGTGGTCTC 57.531 37.037 0.00 0.00 32.95 3.36
111 112 9.467796 CATAGATTAGTATCATAGGTGGTCTCA 57.532 37.037 0.00 0.00 32.95 3.27
113 114 8.964533 AGATTAGTATCATAGGTGGTCTCATT 57.035 34.615 0.00 0.00 32.95 2.57
114 115 9.386122 AGATTAGTATCATAGGTGGTCTCATTT 57.614 33.333 0.00 0.00 32.95 2.32
119 120 7.880195 AGTATCATAGGTGGTCTCATTTATTGC 59.120 37.037 0.00 0.00 0.00 3.56
120 121 5.376625 TCATAGGTGGTCTCATTTATTGCC 58.623 41.667 0.00 0.00 0.00 4.52
121 122 3.737559 AGGTGGTCTCATTTATTGCCA 57.262 42.857 0.00 0.00 0.00 4.92
122 123 4.255510 AGGTGGTCTCATTTATTGCCAT 57.744 40.909 0.00 0.00 0.00 4.40
123 124 3.956199 AGGTGGTCTCATTTATTGCCATG 59.044 43.478 0.00 0.00 0.00 3.66
124 125 3.491447 GGTGGTCTCATTTATTGCCATGC 60.491 47.826 0.00 0.00 0.00 4.06
125 126 3.130869 GTGGTCTCATTTATTGCCATGCA 59.869 43.478 0.00 0.00 36.47 3.96
126 127 3.962063 TGGTCTCATTTATTGCCATGCAT 59.038 39.130 0.00 0.00 38.76 3.96
127 128 4.202172 TGGTCTCATTTATTGCCATGCATG 60.202 41.667 20.19 20.19 38.76 4.06
128 129 4.038282 GGTCTCATTTATTGCCATGCATGA 59.962 41.667 28.31 8.76 38.76 3.07
129 130 4.980434 GTCTCATTTATTGCCATGCATGAC 59.020 41.667 28.31 17.77 38.76 3.06
130 131 4.645588 TCTCATTTATTGCCATGCATGACA 59.354 37.500 28.31 20.53 38.76 3.58
131 132 4.684877 TCATTTATTGCCATGCATGACAC 58.315 39.130 28.31 16.49 38.76 3.67
132 133 4.159879 TCATTTATTGCCATGCATGACACA 59.840 37.500 28.31 18.81 38.76 3.72
133 134 4.739587 TTTATTGCCATGCATGACACAT 57.260 36.364 28.31 18.68 38.76 3.21
134 135 5.848833 TTTATTGCCATGCATGACACATA 57.151 34.783 28.31 17.78 38.76 2.29
135 136 5.441709 TTATTGCCATGCATGACACATAG 57.558 39.130 28.31 10.23 38.76 2.23
136 137 2.713863 TGCCATGCATGACACATAGA 57.286 45.000 28.31 0.00 31.71 1.98
137 138 3.002038 TGCCATGCATGACACATAGAA 57.998 42.857 28.31 0.40 31.71 2.10
138 139 2.946990 TGCCATGCATGACACATAGAAG 59.053 45.455 28.31 8.01 31.71 2.85
139 140 2.287427 GCCATGCATGACACATAGAAGC 60.287 50.000 28.31 14.15 0.00 3.86
140 141 2.946990 CCATGCATGACACATAGAAGCA 59.053 45.455 28.31 0.00 34.78 3.91
141 142 3.568430 CCATGCATGACACATAGAAGCAT 59.432 43.478 28.31 0.00 41.42 3.79
142 143 4.758165 CCATGCATGACACATAGAAGCATA 59.242 41.667 28.31 0.00 39.00 3.14
143 144 5.239963 CCATGCATGACACATAGAAGCATAA 59.760 40.000 28.31 0.00 39.00 1.90
144 145 6.072119 CCATGCATGACACATAGAAGCATAAT 60.072 38.462 28.31 0.00 39.00 1.28
145 146 7.120138 CCATGCATGACACATAGAAGCATAATA 59.880 37.037 28.31 0.00 39.00 0.98
146 147 8.674607 CATGCATGACACATAGAAGCATAATAT 58.325 33.333 22.59 0.00 39.00 1.28
147 148 8.625786 TGCATGACACATAGAAGCATAATATT 57.374 30.769 0.00 0.00 0.00 1.28
148 149 9.070179 TGCATGACACATAGAAGCATAATATTT 57.930 29.630 0.00 0.00 0.00 1.40
230 231 3.770263 CCACATAGGCATGTTTGTGAG 57.230 47.619 16.04 4.35 42.98 3.51
231 232 3.084039 CCACATAGGCATGTTTGTGAGT 58.916 45.455 16.04 0.00 42.98 3.41
232 233 3.127548 CCACATAGGCATGTTTGTGAGTC 59.872 47.826 16.04 0.00 42.98 3.36
233 234 3.127548 CACATAGGCATGTTTGTGAGTCC 59.872 47.826 11.53 0.00 42.98 3.85
234 235 2.489938 TAGGCATGTTTGTGAGTCCC 57.510 50.000 0.00 0.00 0.00 4.46
235 236 0.478072 AGGCATGTTTGTGAGTCCCA 59.522 50.000 0.00 0.00 0.00 4.37
236 237 1.133513 AGGCATGTTTGTGAGTCCCAA 60.134 47.619 0.00 0.00 0.00 4.12
237 238 1.270550 GGCATGTTTGTGAGTCCCAAG 59.729 52.381 0.00 0.00 0.00 3.61
238 239 1.956477 GCATGTTTGTGAGTCCCAAGT 59.044 47.619 0.00 0.00 0.00 3.16
239 240 2.287788 GCATGTTTGTGAGTCCCAAGTG 60.288 50.000 0.00 0.00 0.00 3.16
240 241 1.388547 TGTTTGTGAGTCCCAAGTGC 58.611 50.000 0.00 0.00 0.00 4.40
241 242 1.340502 TGTTTGTGAGTCCCAAGTGCA 60.341 47.619 0.00 0.00 0.00 4.57
242 243 1.956477 GTTTGTGAGTCCCAAGTGCAT 59.044 47.619 0.00 0.00 0.00 3.96
243 244 1.608055 TTGTGAGTCCCAAGTGCATG 58.392 50.000 0.00 0.00 0.00 4.06
244 245 0.764271 TGTGAGTCCCAAGTGCATGA 59.236 50.000 0.00 0.00 0.00 3.07
245 246 1.352017 TGTGAGTCCCAAGTGCATGAT 59.648 47.619 0.00 0.00 0.00 2.45
246 247 2.571202 TGTGAGTCCCAAGTGCATGATA 59.429 45.455 0.00 0.00 0.00 2.15
247 248 2.939103 GTGAGTCCCAAGTGCATGATAC 59.061 50.000 0.00 0.00 0.00 2.24
248 249 2.840038 TGAGTCCCAAGTGCATGATACT 59.160 45.455 0.00 0.00 0.00 2.12
249 250 4.030216 TGAGTCCCAAGTGCATGATACTA 58.970 43.478 0.00 0.00 0.00 1.82
250 251 4.141937 TGAGTCCCAAGTGCATGATACTAC 60.142 45.833 0.00 0.00 0.00 2.73
251 252 4.033709 AGTCCCAAGTGCATGATACTACT 58.966 43.478 0.00 0.00 0.00 2.57
252 253 4.471386 AGTCCCAAGTGCATGATACTACTT 59.529 41.667 0.00 0.00 33.94 2.24
253 254 5.661312 AGTCCCAAGTGCATGATACTACTTA 59.339 40.000 0.00 0.00 32.53 2.24
254 255 6.327626 AGTCCCAAGTGCATGATACTACTTAT 59.672 38.462 0.00 0.00 32.53 1.73
255 256 6.425114 GTCCCAAGTGCATGATACTACTTATG 59.575 42.308 0.00 0.00 32.53 1.90
256 257 6.099701 TCCCAAGTGCATGATACTACTTATGT 59.900 38.462 0.00 0.00 32.53 2.29
257 258 6.767902 CCCAAGTGCATGATACTACTTATGTT 59.232 38.462 0.00 0.00 32.53 2.71
258 259 7.931407 CCCAAGTGCATGATACTACTTATGTTA 59.069 37.037 0.00 0.00 32.53 2.41
259 260 8.765219 CCAAGTGCATGATACTACTTATGTTAC 58.235 37.037 0.00 0.00 32.53 2.50
260 261 8.765219 CAAGTGCATGATACTACTTATGTTACC 58.235 37.037 0.00 0.00 32.53 2.85
261 262 7.442656 AGTGCATGATACTACTTATGTTACCC 58.557 38.462 0.00 0.00 0.00 3.69
262 263 6.649557 GTGCATGATACTACTTATGTTACCCC 59.350 42.308 0.00 0.00 0.00 4.95
263 264 6.171213 GCATGATACTACTTATGTTACCCCC 58.829 44.000 0.00 0.00 0.00 5.40
264 265 6.239772 GCATGATACTACTTATGTTACCCCCA 60.240 42.308 0.00 0.00 0.00 4.96
265 266 6.736110 TGATACTACTTATGTTACCCCCAC 57.264 41.667 0.00 0.00 0.00 4.61
266 267 6.446451 TGATACTACTTATGTTACCCCCACT 58.554 40.000 0.00 0.00 0.00 4.00
267 268 7.594570 TGATACTACTTATGTTACCCCCACTA 58.405 38.462 0.00 0.00 0.00 2.74
268 269 8.236643 TGATACTACTTATGTTACCCCCACTAT 58.763 37.037 0.00 0.00 0.00 2.12
269 270 6.742559 ACTACTTATGTTACCCCCACTATG 57.257 41.667 0.00 0.00 0.00 2.23
270 271 5.605488 ACTACTTATGTTACCCCCACTATGG 59.395 44.000 0.00 0.00 37.25 2.74
271 272 3.137728 ACTTATGTTACCCCCACTATGGC 59.862 47.826 0.00 0.00 35.79 4.40
272 273 0.850784 ATGTTACCCCCACTATGGCC 59.149 55.000 0.00 0.00 35.79 5.36
273 274 0.550393 TGTTACCCCCACTATGGCCA 60.550 55.000 8.56 8.56 35.79 5.36
274 275 0.182775 GTTACCCCCACTATGGCCAG 59.817 60.000 13.05 0.00 35.79 4.85
275 276 1.641552 TTACCCCCACTATGGCCAGC 61.642 60.000 13.05 0.00 35.79 4.85
276 277 4.209866 CCCCCACTATGGCCAGCC 62.210 72.222 13.05 0.38 35.79 4.85
277 278 3.099170 CCCCACTATGGCCAGCCT 61.099 66.667 13.05 0.00 35.79 4.58
278 279 2.512896 CCCACTATGGCCAGCCTC 59.487 66.667 13.05 0.00 35.79 4.70
279 280 2.377810 CCCACTATGGCCAGCCTCA 61.378 63.158 13.05 0.00 35.79 3.86
280 281 1.713005 CCCACTATGGCCAGCCTCAT 61.713 60.000 13.05 0.00 35.79 2.90
281 282 1.059098 CCACTATGGCCAGCCTCATA 58.941 55.000 13.05 0.00 36.94 2.15
282 283 1.632409 CCACTATGGCCAGCCTCATAT 59.368 52.381 13.05 0.00 36.94 1.78
283 284 2.355513 CCACTATGGCCAGCCTCATATC 60.356 54.545 13.05 0.00 36.94 1.63
284 285 2.303890 CACTATGGCCAGCCTCATATCA 59.696 50.000 13.05 0.00 36.94 2.15
285 286 3.054582 CACTATGGCCAGCCTCATATCAT 60.055 47.826 13.05 0.00 36.94 2.45
286 287 2.509166 ATGGCCAGCCTCATATCATG 57.491 50.000 13.05 0.00 36.94 3.07
287 288 1.437397 TGGCCAGCCTCATATCATGA 58.563 50.000 0.00 0.00 37.76 3.07
288 289 1.990327 TGGCCAGCCTCATATCATGAT 59.010 47.619 13.81 13.81 38.85 2.45
289 290 3.183801 TGGCCAGCCTCATATCATGATA 58.816 45.455 17.56 17.56 38.85 2.15
290 291 3.054875 TGGCCAGCCTCATATCATGATAC 60.055 47.826 17.60 4.98 38.85 2.24
291 292 3.199508 GGCCAGCCTCATATCATGATACT 59.800 47.826 17.60 7.21 38.85 2.12
292 293 4.190001 GCCAGCCTCATATCATGATACTG 58.810 47.826 17.60 17.47 39.71 2.74
293 294 4.323333 GCCAGCCTCATATCATGATACTGT 60.323 45.833 17.60 0.00 39.00 3.55
294 295 5.105187 GCCAGCCTCATATCATGATACTGTA 60.105 44.000 17.60 0.00 39.00 2.74
295 296 6.407865 GCCAGCCTCATATCATGATACTGTAT 60.408 42.308 17.60 0.00 39.00 2.29
296 297 7.208777 CCAGCCTCATATCATGATACTGTATC 58.791 42.308 17.60 18.64 39.00 2.24
324 325 8.936070 AATAAATGTTACGCTACTATGTGTCA 57.064 30.769 0.00 0.00 32.52 3.58
325 326 9.542462 AATAAATGTTACGCTACTATGTGTCAT 57.458 29.630 0.00 0.00 32.52 3.06
326 327 6.828502 AATGTTACGCTACTATGTGTCATG 57.171 37.500 0.00 0.00 32.52 3.07
327 328 4.109766 TGTTACGCTACTATGTGTCATGC 58.890 43.478 0.00 0.00 32.52 4.06
328 329 2.959507 ACGCTACTATGTGTCATGCA 57.040 45.000 0.00 0.00 0.00 3.96
329 330 3.459232 ACGCTACTATGTGTCATGCAT 57.541 42.857 0.00 0.00 0.00 3.96
330 331 4.584327 ACGCTACTATGTGTCATGCATA 57.416 40.909 0.00 0.00 0.00 3.14
331 332 4.550422 ACGCTACTATGTGTCATGCATAG 58.450 43.478 13.99 13.99 46.67 2.23
384 385 8.976353 AGTCTATGATACTATGCATTAGGAAGG 58.024 37.037 3.54 0.00 31.68 3.46
385 386 8.754080 GTCTATGATACTATGCATTAGGAAGGT 58.246 37.037 3.54 0.00 31.68 3.50
386 387 9.990868 TCTATGATACTATGCATTAGGAAGGTA 57.009 33.333 3.54 0.00 31.68 3.08
388 389 8.671987 ATGATACTATGCATTAGGAAGGTAGT 57.328 34.615 3.54 0.88 31.68 2.73
389 390 9.769677 ATGATACTATGCATTAGGAAGGTAGTA 57.230 33.333 3.54 3.44 31.68 1.82
390 391 9.769677 TGATACTATGCATTAGGAAGGTAGTAT 57.230 33.333 3.54 8.56 36.89 2.12
392 393 9.769677 ATACTATGCATTAGGAAGGTAGTATCA 57.230 33.333 3.54 0.00 31.70 2.15
393 394 7.897864 ACTATGCATTAGGAAGGTAGTATCAC 58.102 38.462 3.54 0.00 31.68 3.06
394 395 6.747414 ATGCATTAGGAAGGTAGTATCACA 57.253 37.500 0.00 0.00 0.00 3.58
395 396 6.747414 TGCATTAGGAAGGTAGTATCACAT 57.253 37.500 0.00 0.00 0.00 3.21
396 397 6.759272 TGCATTAGGAAGGTAGTATCACATC 58.241 40.000 0.00 0.00 0.00 3.06
397 398 6.326323 TGCATTAGGAAGGTAGTATCACATCA 59.674 38.462 0.00 0.00 0.00 3.07
398 399 7.016563 TGCATTAGGAAGGTAGTATCACATCAT 59.983 37.037 0.00 0.00 0.00 2.45
399 400 8.531982 GCATTAGGAAGGTAGTATCACATCATA 58.468 37.037 0.00 0.00 0.00 2.15
402 403 9.601810 TTAGGAAGGTAGTATCACATCATATGT 57.398 33.333 1.90 0.00 46.22 2.29
404 405 9.775539 AGGAAGGTAGTATCACATCATATGTAT 57.224 33.333 1.90 0.00 42.70 2.29
405 406 9.809096 GGAAGGTAGTATCACATCATATGTATG 57.191 37.037 1.90 7.90 42.70 2.39
429 430 9.811995 ATGATACTAACTTACGAATTACAAGCA 57.188 29.630 0.00 0.00 0.00 3.91
430 431 9.297586 TGATACTAACTTACGAATTACAAGCAG 57.702 33.333 0.00 0.00 0.00 4.24
431 432 6.404712 ACTAACTTACGAATTACAAGCAGC 57.595 37.500 0.00 0.00 0.00 5.25
432 433 4.680171 AACTTACGAATTACAAGCAGCC 57.320 40.909 0.00 0.00 0.00 4.85
433 434 2.671396 ACTTACGAATTACAAGCAGCCG 59.329 45.455 0.00 0.00 0.00 5.52
434 435 2.373540 TACGAATTACAAGCAGCCGT 57.626 45.000 0.00 0.00 0.00 5.68
435 436 2.373540 ACGAATTACAAGCAGCCGTA 57.626 45.000 0.00 0.00 0.00 4.02
436 437 2.901249 ACGAATTACAAGCAGCCGTAT 58.099 42.857 0.00 0.00 0.00 3.06
437 438 4.049546 ACGAATTACAAGCAGCCGTATA 57.950 40.909 0.00 0.00 0.00 1.47
438 439 3.800506 ACGAATTACAAGCAGCCGTATAC 59.199 43.478 0.00 0.00 0.00 1.47
439 440 4.049186 CGAATTACAAGCAGCCGTATACT 58.951 43.478 0.56 0.00 0.00 2.12
440 441 5.217393 CGAATTACAAGCAGCCGTATACTA 58.783 41.667 0.56 0.00 0.00 1.82
441 442 5.862323 CGAATTACAAGCAGCCGTATACTAT 59.138 40.000 0.56 0.00 0.00 2.12
442 443 6.183359 CGAATTACAAGCAGCCGTATACTATG 60.183 42.308 0.56 0.00 0.00 2.23
443 444 5.777850 TTACAAGCAGCCGTATACTATGA 57.222 39.130 0.56 0.00 0.00 2.15
444 445 4.873746 ACAAGCAGCCGTATACTATGAT 57.126 40.909 0.56 0.00 0.00 2.45
445 446 5.977489 ACAAGCAGCCGTATACTATGATA 57.023 39.130 0.56 0.00 0.00 2.15
446 447 5.710984 ACAAGCAGCCGTATACTATGATAC 58.289 41.667 0.56 0.00 0.00 2.24
447 448 5.477291 ACAAGCAGCCGTATACTATGATACT 59.523 40.000 0.56 0.00 31.24 2.12
448 449 6.657966 ACAAGCAGCCGTATACTATGATACTA 59.342 38.462 0.56 0.00 31.24 1.82
449 450 6.928979 AGCAGCCGTATACTATGATACTAG 57.071 41.667 0.56 0.00 31.24 2.57
450 451 5.297278 AGCAGCCGTATACTATGATACTAGC 59.703 44.000 0.56 0.00 33.06 3.42
451 452 5.066117 GCAGCCGTATACTATGATACTAGCA 59.934 44.000 0.56 0.00 34.29 3.49
452 453 6.487960 CAGCCGTATACTATGATACTAGCAC 58.512 44.000 0.56 0.00 34.29 4.40
453 454 5.293814 AGCCGTATACTATGATACTAGCACG 59.706 44.000 0.56 0.00 34.29 5.34
454 455 5.292834 GCCGTATACTATGATACTAGCACGA 59.707 44.000 0.56 0.00 33.10 4.35
455 456 6.703857 CCGTATACTATGATACTAGCACGAC 58.296 44.000 0.56 0.00 31.24 4.34
456 457 6.312180 CCGTATACTATGATACTAGCACGACA 59.688 42.308 0.56 0.00 31.24 4.35
457 458 7.172095 CGTATACTATGATACTAGCACGACAC 58.828 42.308 0.56 0.00 31.24 3.67
458 459 7.063191 CGTATACTATGATACTAGCACGACACT 59.937 40.741 0.56 0.00 31.24 3.55
459 460 5.676532 ACTATGATACTAGCACGACACTC 57.323 43.478 0.00 0.00 0.00 3.51
460 461 3.610786 ATGATACTAGCACGACACTCG 57.389 47.619 0.00 0.00 46.93 4.18
535 536 8.856247 AGAACGACAAAAATGAAGTAACAAAAC 58.144 29.630 0.00 0.00 0.00 2.43
536 537 8.522178 AACGACAAAAATGAAGTAACAAAACA 57.478 26.923 0.00 0.00 0.00 2.83
599 600 3.737850 GCTCTATAATTGAGGTGCAGCT 58.262 45.455 20.31 20.31 32.57 4.24
622 633 2.033424 CAGCTGCAGACATGATGAATGG 59.967 50.000 20.43 0.00 40.94 3.16
623 634 1.337071 GCTGCAGACATGATGAATGGG 59.663 52.381 20.43 0.00 40.94 4.00
682 693 7.095649 GCAACACATTTCTTTAATCCCAAGAAC 60.096 37.037 0.00 0.00 39.47 3.01
964 1055 4.381292 CCTTCCAATTTCCAGAGTCATTGC 60.381 45.833 0.00 0.00 0.00 3.56
989 1084 2.736347 AGCTACCTAATCGACACACCT 58.264 47.619 0.00 0.00 0.00 4.00
1151 1249 2.170166 GAGGTTCAACAATGGATGCCA 58.830 47.619 0.00 0.00 38.19 4.92
1246 1344 0.179018 AGGGTGAAGAAGGTGTGCAC 60.179 55.000 10.75 10.75 0.00 4.57
1271 1369 1.227089 CTACAAGCTGCGCGAGGAT 60.227 57.895 12.10 0.00 0.00 3.24
1281 1379 1.375396 CGCGAGGATGGGTTCAACA 60.375 57.895 0.00 0.00 0.00 3.33
1453 1551 3.113191 AGTGAGGGACAGATGATCAGT 57.887 47.619 0.09 0.00 0.00 3.41
1454 1552 3.030291 AGTGAGGGACAGATGATCAGTC 58.970 50.000 9.22 9.22 32.87 3.51
1456 1554 3.029570 TGAGGGACAGATGATCAGTCAG 58.970 50.000 17.84 6.12 37.87 3.51
1457 1555 3.295093 GAGGGACAGATGATCAGTCAGA 58.705 50.000 17.84 0.00 37.87 3.27
1458 1556 3.896888 GAGGGACAGATGATCAGTCAGAT 59.103 47.826 17.84 4.80 37.87 2.90
1459 1557 3.642377 AGGGACAGATGATCAGTCAGATG 59.358 47.826 17.84 0.00 37.87 2.90
1460 1558 3.391965 GGACAGATGATCAGTCAGATGC 58.608 50.000 17.84 0.00 37.87 3.91
1493 1591 0.450482 GTGGCGTTTGTTGATCGTCG 60.450 55.000 0.00 0.00 31.65 5.12
1556 1654 0.247736 GAAGAAGCTGGCGGAGAAGA 59.752 55.000 0.00 0.00 0.00 2.87
1633 1731 1.446272 CTCCAAGGACGGCGACTTC 60.446 63.158 16.62 0.00 0.00 3.01
1846 1944 1.671054 CAACACCGGCGACCAGATT 60.671 57.895 9.30 0.00 0.00 2.40
1853 1951 0.527817 CGGCGACCAGATTGAGGTAC 60.528 60.000 0.00 0.00 40.09 3.34
1864 1962 5.356190 CCAGATTGAGGTACGTTGAGTAGTA 59.644 44.000 0.00 0.00 35.72 1.82
1865 1963 6.256686 CAGATTGAGGTACGTTGAGTAGTAC 58.743 44.000 0.00 0.00 41.64 2.73
1944 2043 3.935315 TCTTGCTTTGTGATCTGGAGAG 58.065 45.455 0.00 0.00 0.00 3.20
1978 2081 1.748493 TGAGCAGTCAACCCAACAAAC 59.252 47.619 0.00 0.00 0.00 2.93
2323 2501 1.077930 GATCAGCCTGAGCCAGCAA 60.078 57.895 0.00 0.00 41.25 3.91
2326 2504 3.573229 AGCCTGAGCCAGCAACCA 61.573 61.111 0.00 0.00 41.25 3.67
2428 2619 7.562135 ACAGATTGGTACGATAAATAGGTTGT 58.438 34.615 0.00 0.00 0.00 3.32
2500 2692 7.120716 TGCAAATATATGGTGGCATATGAGAT 58.879 34.615 6.97 0.00 0.00 2.75
2552 2744 3.125316 CGGAGTGATTTGTAGCTTGGAAC 59.875 47.826 0.00 0.00 0.00 3.62
2577 2769 6.299141 GGCATCTCTCTATGGGTTTCAAATA 58.701 40.000 0.00 0.00 0.00 1.40
2602 2794 3.042682 TCTTCTGTTTGGGTGTGAGGTA 58.957 45.455 0.00 0.00 0.00 3.08
2656 2848 3.244561 GGAGATGTGAGGACTGTGGAAAA 60.245 47.826 0.00 0.00 0.00 2.29
2706 2898 3.424433 GGTTGCTTACGATGCAGTGTTAC 60.424 47.826 0.00 0.00 41.71 2.50
2708 2900 1.990563 GCTTACGATGCAGTGTTACGT 59.009 47.619 12.97 12.97 40.23 3.57
2709 2901 2.410730 GCTTACGATGCAGTGTTACGTT 59.589 45.455 13.44 2.52 38.18 3.99
2727 2919 2.221981 CGTTTTTCAGTCTGGAGTCTGC 59.778 50.000 0.00 0.00 32.53 4.26
2817 3013 7.517614 TTGACTGGCAAAACTATATTGTGAA 57.482 32.000 0.00 0.00 32.46 3.18
2820 3016 8.584157 TGACTGGCAAAACTATATTGTGAAAAT 58.416 29.630 0.00 0.00 0.00 1.82
2866 3062 5.534207 ACAATTTGTGCCTGAAGATTGAA 57.466 34.783 0.15 0.00 0.00 2.69
2879 3075 6.365247 CCTGAAGATTGAAAAATTGACTGCAG 59.635 38.462 13.48 13.48 31.59 4.41
2882 3078 6.645790 AGATTGAAAAATTGACTGCAGTCT 57.354 33.333 38.81 23.17 44.99 3.24
2930 3126 5.528043 TTTTTGAGCCAACTTGAGCATTA 57.472 34.783 5.41 0.00 0.00 1.90
3104 3301 6.816136 AGGATTTAACCAACTCCAGTTTTTG 58.184 36.000 0.00 0.00 36.24 2.44
3211 3409 6.970484 TGAGACACTTTAAAATCTGCCTTTC 58.030 36.000 1.98 0.00 0.00 2.62
3272 3487 5.028549 TCTCTGAATCCAAATACTCCAGC 57.971 43.478 0.00 0.00 0.00 4.85
3273 3488 4.471025 TCTCTGAATCCAAATACTCCAGCA 59.529 41.667 0.00 0.00 0.00 4.41
3274 3489 5.131642 TCTCTGAATCCAAATACTCCAGCAT 59.868 40.000 0.00 0.00 0.00 3.79
3275 3490 5.371526 TCTGAATCCAAATACTCCAGCATC 58.628 41.667 0.00 0.00 0.00 3.91
3276 3491 4.464008 TGAATCCAAATACTCCAGCATCC 58.536 43.478 0.00 0.00 0.00 3.51
3277 3492 3.515602 ATCCAAATACTCCAGCATCCC 57.484 47.619 0.00 0.00 0.00 3.85
3278 3493 2.204463 TCCAAATACTCCAGCATCCCA 58.796 47.619 0.00 0.00 0.00 4.37
3279 3494 2.580322 TCCAAATACTCCAGCATCCCAA 59.420 45.455 0.00 0.00 0.00 4.12
3280 3495 2.689983 CCAAATACTCCAGCATCCCAAC 59.310 50.000 0.00 0.00 0.00 3.77
3281 3496 3.355378 CAAATACTCCAGCATCCCAACA 58.645 45.455 0.00 0.00 0.00 3.33
3282 3497 3.956199 CAAATACTCCAGCATCCCAACAT 59.044 43.478 0.00 0.00 0.00 2.71
3283 3498 2.715749 TACTCCAGCATCCCAACATG 57.284 50.000 0.00 0.00 0.00 3.21
3284 3499 0.994247 ACTCCAGCATCCCAACATGA 59.006 50.000 0.00 0.00 0.00 3.07
3285 3500 1.340405 ACTCCAGCATCCCAACATGAC 60.340 52.381 0.00 0.00 0.00 3.06
3286 3501 0.994247 TCCAGCATCCCAACATGACT 59.006 50.000 0.00 0.00 0.00 3.41
3287 3502 2.171237 CTCCAGCATCCCAACATGACTA 59.829 50.000 0.00 0.00 0.00 2.59
3288 3503 2.779430 TCCAGCATCCCAACATGACTAT 59.221 45.455 0.00 0.00 0.00 2.12
3289 3504 3.202818 TCCAGCATCCCAACATGACTATT 59.797 43.478 0.00 0.00 0.00 1.73
3290 3505 3.956199 CCAGCATCCCAACATGACTATTT 59.044 43.478 0.00 0.00 0.00 1.40
3291 3506 4.037208 CCAGCATCCCAACATGACTATTTC 59.963 45.833 0.00 0.00 0.00 2.17
3292 3507 4.037208 CAGCATCCCAACATGACTATTTCC 59.963 45.833 0.00 0.00 0.00 3.13
3293 3508 3.953612 GCATCCCAACATGACTATTTCCA 59.046 43.478 0.00 0.00 0.00 3.53
3294 3509 4.586001 GCATCCCAACATGACTATTTCCAT 59.414 41.667 0.00 0.00 0.00 3.41
3295 3510 5.769662 GCATCCCAACATGACTATTTCCATA 59.230 40.000 0.00 0.00 0.00 2.74
3296 3511 6.435277 GCATCCCAACATGACTATTTCCATAT 59.565 38.462 0.00 0.00 0.00 1.78
3297 3512 7.362401 GCATCCCAACATGACTATTTCCATATC 60.362 40.741 0.00 0.00 0.00 1.63
3298 3513 7.392766 TCCCAACATGACTATTTCCATATCT 57.607 36.000 0.00 0.00 0.00 1.98
3299 3514 7.453393 TCCCAACATGACTATTTCCATATCTC 58.547 38.462 0.00 0.00 0.00 2.75
3300 3515 7.293299 TCCCAACATGACTATTTCCATATCTCT 59.707 37.037 0.00 0.00 0.00 3.10
3301 3516 7.389884 CCCAACATGACTATTTCCATATCTCTG 59.610 40.741 0.00 0.00 0.00 3.35
3302 3517 7.094890 CCAACATGACTATTTCCATATCTCTGC 60.095 40.741 0.00 0.00 0.00 4.26
3303 3518 7.313740 ACATGACTATTTCCATATCTCTGCT 57.686 36.000 0.00 0.00 0.00 4.24
3304 3519 7.160049 ACATGACTATTTCCATATCTCTGCTG 58.840 38.462 0.00 0.00 0.00 4.41
3305 3520 6.737720 TGACTATTTCCATATCTCTGCTGT 57.262 37.500 0.00 0.00 0.00 4.40
3306 3521 7.129457 TGACTATTTCCATATCTCTGCTGTT 57.871 36.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.464828 ACTCCCCACTATGACCAATCTT 58.535 45.455 0.00 0.00 0.00 2.40
2 3 4.593206 TGATACTCCCCACTATGACCAATC 59.407 45.833 0.00 0.00 0.00 2.67
3 4 4.566837 TGATACTCCCCACTATGACCAAT 58.433 43.478 0.00 0.00 0.00 3.16
4 5 4.002256 TGATACTCCCCACTATGACCAA 57.998 45.455 0.00 0.00 0.00 3.67
5 6 3.699025 TGATACTCCCCACTATGACCA 57.301 47.619 0.00 0.00 0.00 4.02
6 7 7.126733 AGTATATGATACTCCCCACTATGACC 58.873 42.308 0.00 0.00 0.00 4.02
7 8 9.344772 CTAGTATATGATACTCCCCACTATGAC 57.655 40.741 2.44 0.00 0.00 3.06
8 9 9.070210 ACTAGTATATGATACTCCCCACTATGA 57.930 37.037 0.00 0.00 0.00 2.15
12 13 9.070210 TGATACTAGTATATGATACTCCCCACT 57.930 37.037 15.42 0.00 0.00 4.00
13 14 9.869667 ATGATACTAGTATATGATACTCCCCAC 57.130 37.037 15.42 0.00 0.00 4.61
14 15 9.868160 CATGATACTAGTATATGATACTCCCCA 57.132 37.037 15.42 5.35 0.00 4.96
15 16 8.798402 GCATGATACTAGTATATGATACTCCCC 58.202 40.741 22.89 8.64 0.00 4.81
16 17 9.355916 TGCATGATACTAGTATATGATACTCCC 57.644 37.037 22.89 9.00 0.00 4.30
52 53 8.860088 TGCACTATTGATGTAGTATGATACACT 58.140 33.333 5.28 0.00 38.43 3.55
53 54 9.645059 ATGCACTATTGATGTAGTATGATACAC 57.355 33.333 5.28 2.36 38.43 2.90
83 84 9.830186 AGACCACCTATGATACTAATCTATGTT 57.170 33.333 0.00 0.00 32.93 2.71
84 85 9.469097 GAGACCACCTATGATACTAATCTATGT 57.531 37.037 0.00 0.00 32.93 2.29
85 86 9.467796 TGAGACCACCTATGATACTAATCTATG 57.532 37.037 0.00 0.00 32.93 2.23
88 89 8.964533 AATGAGACCACCTATGATACTAATCT 57.035 34.615 0.00 0.00 32.93 2.40
93 94 7.880195 GCAATAAATGAGACCACCTATGATACT 59.120 37.037 0.00 0.00 0.00 2.12
94 95 7.119846 GGCAATAAATGAGACCACCTATGATAC 59.880 40.741 0.00 0.00 0.00 2.24
95 96 7.168219 GGCAATAAATGAGACCACCTATGATA 58.832 38.462 0.00 0.00 0.00 2.15
96 97 6.006449 GGCAATAAATGAGACCACCTATGAT 58.994 40.000 0.00 0.00 0.00 2.45
97 98 5.104151 TGGCAATAAATGAGACCACCTATGA 60.104 40.000 0.00 0.00 0.00 2.15
98 99 5.132502 TGGCAATAAATGAGACCACCTATG 58.867 41.667 0.00 0.00 0.00 2.23
99 100 5.387113 TGGCAATAAATGAGACCACCTAT 57.613 39.130 0.00 0.00 0.00 2.57
100 101 4.853468 TGGCAATAAATGAGACCACCTA 57.147 40.909 0.00 0.00 0.00 3.08
101 102 3.737559 TGGCAATAAATGAGACCACCT 57.262 42.857 0.00 0.00 0.00 4.00
102 103 3.491447 GCATGGCAATAAATGAGACCACC 60.491 47.826 0.00 0.00 0.00 4.61
103 104 3.130869 TGCATGGCAATAAATGAGACCAC 59.869 43.478 0.00 0.00 34.76 4.16
104 105 3.363627 TGCATGGCAATAAATGAGACCA 58.636 40.909 0.00 0.00 34.76 4.02
105 106 4.038282 TCATGCATGGCAATAAATGAGACC 59.962 41.667 25.97 0.00 43.62 3.85
106 107 4.980434 GTCATGCATGGCAATAAATGAGAC 59.020 41.667 26.04 8.36 43.62 3.36
107 108 4.645588 TGTCATGCATGGCAATAAATGAGA 59.354 37.500 30.82 3.91 43.62 3.27
108 109 4.743151 GTGTCATGCATGGCAATAAATGAG 59.257 41.667 34.01 0.13 44.94 2.90
109 110 4.159879 TGTGTCATGCATGGCAATAAATGA 59.840 37.500 34.01 7.61 44.94 2.57
110 111 4.434520 TGTGTCATGCATGGCAATAAATG 58.565 39.130 34.01 2.58 44.94 2.32
111 112 4.739587 TGTGTCATGCATGGCAATAAAT 57.260 36.364 34.01 0.00 44.94 1.40
112 113 4.739587 ATGTGTCATGCATGGCAATAAA 57.260 36.364 34.01 20.14 44.94 1.40
113 114 5.131784 TCTATGTGTCATGCATGGCAATAA 58.868 37.500 34.01 22.53 44.94 1.40
114 115 4.716794 TCTATGTGTCATGCATGGCAATA 58.283 39.130 34.01 27.05 44.94 1.90
115 116 3.558033 TCTATGTGTCATGCATGGCAAT 58.442 40.909 34.01 27.34 44.94 3.56
116 117 3.002038 TCTATGTGTCATGCATGGCAA 57.998 42.857 34.01 23.37 44.94 4.52
117 118 2.713863 TCTATGTGTCATGCATGGCA 57.286 45.000 29.45 29.45 44.86 4.92
118 119 2.287427 GCTTCTATGTGTCATGCATGGC 60.287 50.000 24.40 24.40 0.00 4.40
119 120 2.946990 TGCTTCTATGTGTCATGCATGG 59.053 45.455 25.97 8.58 0.00 3.66
120 121 4.830826 ATGCTTCTATGTGTCATGCATG 57.169 40.909 21.07 21.07 38.10 4.06
121 122 8.803397 ATATTATGCTTCTATGTGTCATGCAT 57.197 30.769 0.00 0.00 41.60 3.96
122 123 8.625786 AATATTATGCTTCTATGTGTCATGCA 57.374 30.769 0.00 0.00 0.00 3.96
210 211 3.084039 ACTCACAAACATGCCTATGTGG 58.916 45.455 16.08 11.33 46.54 4.17
211 212 3.127548 GGACTCACAAACATGCCTATGTG 59.872 47.826 12.13 12.13 46.54 3.21
213 214 2.684881 GGGACTCACAAACATGCCTATG 59.315 50.000 0.00 0.00 40.24 2.23
214 215 2.308570 TGGGACTCACAAACATGCCTAT 59.691 45.455 0.00 0.00 0.00 2.57
215 216 1.702401 TGGGACTCACAAACATGCCTA 59.298 47.619 0.00 0.00 0.00 3.93
216 217 0.478072 TGGGACTCACAAACATGCCT 59.522 50.000 0.00 0.00 0.00 4.75
217 218 1.270550 CTTGGGACTCACAAACATGCC 59.729 52.381 0.00 0.00 0.00 4.40
218 219 1.956477 ACTTGGGACTCACAAACATGC 59.044 47.619 0.00 0.00 0.00 4.06
219 220 2.287788 GCACTTGGGACTCACAAACATG 60.288 50.000 0.00 0.00 0.00 3.21
220 221 1.956477 GCACTTGGGACTCACAAACAT 59.044 47.619 0.00 0.00 0.00 2.71
221 222 1.340502 TGCACTTGGGACTCACAAACA 60.341 47.619 0.00 0.00 0.00 2.83
222 223 1.388547 TGCACTTGGGACTCACAAAC 58.611 50.000 0.00 0.00 0.00 2.93
223 224 1.955778 CATGCACTTGGGACTCACAAA 59.044 47.619 0.00 0.00 0.00 2.83
224 225 1.142667 TCATGCACTTGGGACTCACAA 59.857 47.619 0.00 0.00 0.00 3.33
225 226 0.764271 TCATGCACTTGGGACTCACA 59.236 50.000 0.00 0.00 0.00 3.58
226 227 2.119801 ATCATGCACTTGGGACTCAC 57.880 50.000 0.00 0.00 0.00 3.51
227 228 2.840038 AGTATCATGCACTTGGGACTCA 59.160 45.455 0.00 0.00 0.00 3.41
228 229 3.550437 AGTATCATGCACTTGGGACTC 57.450 47.619 0.00 0.00 0.00 3.36
229 230 4.033709 AGTAGTATCATGCACTTGGGACT 58.966 43.478 5.29 0.00 0.00 3.85
230 231 4.408182 AGTAGTATCATGCACTTGGGAC 57.592 45.455 5.29 0.00 0.00 4.46
231 232 6.099701 ACATAAGTAGTATCATGCACTTGGGA 59.900 38.462 5.29 0.00 33.47 4.37
232 233 6.291377 ACATAAGTAGTATCATGCACTTGGG 58.709 40.000 5.29 2.16 33.47 4.12
233 234 7.792374 AACATAAGTAGTATCATGCACTTGG 57.208 36.000 5.29 2.42 33.47 3.61
234 235 8.765219 GGTAACATAAGTAGTATCATGCACTTG 58.235 37.037 5.29 0.00 33.47 3.16
235 236 7.931948 GGGTAACATAAGTAGTATCATGCACTT 59.068 37.037 5.29 4.15 39.74 3.16
236 237 7.442656 GGGTAACATAAGTAGTATCATGCACT 58.557 38.462 0.00 5.31 39.74 4.40
237 238 6.649557 GGGGTAACATAAGTAGTATCATGCAC 59.350 42.308 0.00 0.00 39.74 4.57
238 239 6.239772 GGGGGTAACATAAGTAGTATCATGCA 60.240 42.308 0.00 0.00 39.74 3.96
239 240 6.171213 GGGGGTAACATAAGTAGTATCATGC 58.829 44.000 0.00 0.00 39.74 4.06
240 241 7.016268 AGTGGGGGTAACATAAGTAGTATCATG 59.984 40.741 0.00 0.00 39.74 3.07
241 242 7.080353 AGTGGGGGTAACATAAGTAGTATCAT 58.920 38.462 0.00 0.00 39.74 2.45
242 243 6.446451 AGTGGGGGTAACATAAGTAGTATCA 58.554 40.000 0.00 0.00 39.74 2.15
243 244 6.990908 AGTGGGGGTAACATAAGTAGTATC 57.009 41.667 0.00 0.00 39.74 2.24
244 245 7.456902 CCATAGTGGGGGTAACATAAGTAGTAT 59.543 40.741 0.00 0.00 39.74 2.12
245 246 6.783977 CCATAGTGGGGGTAACATAAGTAGTA 59.216 42.308 0.00 0.00 39.74 1.82
246 247 5.605488 CCATAGTGGGGGTAACATAAGTAGT 59.395 44.000 0.00 0.00 39.74 2.73
247 248 5.512576 GCCATAGTGGGGGTAACATAAGTAG 60.513 48.000 0.00 0.00 38.19 2.57
248 249 4.348754 GCCATAGTGGGGGTAACATAAGTA 59.651 45.833 0.00 0.00 38.19 2.24
249 250 3.137728 GCCATAGTGGGGGTAACATAAGT 59.862 47.826 0.00 0.00 38.19 2.24
250 251 3.497942 GGCCATAGTGGGGGTAACATAAG 60.498 52.174 0.00 0.00 38.19 1.73
251 252 2.444010 GGCCATAGTGGGGGTAACATAA 59.556 50.000 0.00 0.00 38.19 1.90
252 253 2.059490 GGCCATAGTGGGGGTAACATA 58.941 52.381 0.00 0.00 38.19 2.29
253 254 0.850784 GGCCATAGTGGGGGTAACAT 59.149 55.000 0.00 0.00 38.19 2.71
254 255 0.550393 TGGCCATAGTGGGGGTAACA 60.550 55.000 0.00 0.00 38.19 2.41
255 256 0.182775 CTGGCCATAGTGGGGGTAAC 59.817 60.000 5.51 0.00 38.19 2.50
256 257 1.641552 GCTGGCCATAGTGGGGGTAA 61.642 60.000 5.51 0.00 38.19 2.85
257 258 2.076184 GCTGGCCATAGTGGGGGTA 61.076 63.158 5.51 0.00 38.19 3.69
258 259 3.420482 GCTGGCCATAGTGGGGGT 61.420 66.667 5.51 0.00 38.19 4.95
259 260 4.209866 GGCTGGCCATAGTGGGGG 62.210 72.222 5.51 0.00 38.19 5.40
260 261 3.099170 AGGCTGGCCATAGTGGGG 61.099 66.667 5.51 0.00 38.19 4.96
261 262 1.713005 ATGAGGCTGGCCATAGTGGG 61.713 60.000 5.51 0.00 38.19 4.61
262 263 1.059098 TATGAGGCTGGCCATAGTGG 58.941 55.000 5.51 0.00 41.55 4.00
263 264 2.303890 TGATATGAGGCTGGCCATAGTG 59.696 50.000 5.51 0.00 38.92 2.74
264 265 2.624495 TGATATGAGGCTGGCCATAGT 58.376 47.619 5.51 0.00 38.92 2.12
265 266 3.199289 TCATGATATGAGGCTGGCCATAG 59.801 47.826 5.51 0.00 38.92 2.23
266 267 3.183801 TCATGATATGAGGCTGGCCATA 58.816 45.455 5.51 12.34 38.92 2.74
267 268 1.990327 TCATGATATGAGGCTGGCCAT 59.010 47.619 5.51 8.81 38.92 4.40
268 269 1.437397 TCATGATATGAGGCTGGCCA 58.563 50.000 14.39 4.71 38.92 5.36
269 270 2.803030 ATCATGATATGAGGCTGGCC 57.197 50.000 6.36 3.00 43.53 5.36
270 271 4.190001 CAGTATCATGATATGAGGCTGGC 58.810 47.826 18.18 2.79 43.53 4.85
271 272 5.417754 ACAGTATCATGATATGAGGCTGG 57.582 43.478 23.63 12.59 43.29 4.85
272 273 7.779073 TGATACAGTATCATGATATGAGGCTG 58.221 38.462 17.93 19.61 43.53 4.85
273 274 7.968014 TGATACAGTATCATGATATGAGGCT 57.032 36.000 17.93 7.71 43.53 4.58
299 300 8.936070 TGACACATAGTAGCGTAACATTTATT 57.064 30.769 0.00 0.00 0.00 1.40
300 301 8.978539 CATGACACATAGTAGCGTAACATTTAT 58.021 33.333 0.00 0.00 0.00 1.40
301 302 7.042992 GCATGACACATAGTAGCGTAACATTTA 60.043 37.037 0.00 0.00 0.00 1.40
302 303 6.238103 GCATGACACATAGTAGCGTAACATTT 60.238 38.462 0.00 0.00 0.00 2.32
303 304 5.234329 GCATGACACATAGTAGCGTAACATT 59.766 40.000 0.00 0.00 0.00 2.71
304 305 4.745125 GCATGACACATAGTAGCGTAACAT 59.255 41.667 0.00 0.00 0.00 2.71
305 306 4.109766 GCATGACACATAGTAGCGTAACA 58.890 43.478 0.00 0.00 0.00 2.41
306 307 4.109766 TGCATGACACATAGTAGCGTAAC 58.890 43.478 0.00 0.00 0.00 2.50
307 308 4.379339 TGCATGACACATAGTAGCGTAA 57.621 40.909 0.00 0.00 0.00 3.18
308 309 4.584327 ATGCATGACACATAGTAGCGTA 57.416 40.909 0.00 0.00 0.00 4.42
309 310 2.959507 TGCATGACACATAGTAGCGT 57.040 45.000 0.00 0.00 0.00 5.07
358 359 8.976353 CCTTCCTAATGCATAGTATCATAGACT 58.024 37.037 0.00 0.00 0.00 3.24
359 360 8.754080 ACCTTCCTAATGCATAGTATCATAGAC 58.246 37.037 0.00 0.00 0.00 2.59
360 361 8.901472 ACCTTCCTAATGCATAGTATCATAGA 57.099 34.615 0.00 0.00 0.00 1.98
362 363 9.769677 ACTACCTTCCTAATGCATAGTATCATA 57.230 33.333 0.00 0.00 0.00 2.15
363 364 8.671987 ACTACCTTCCTAATGCATAGTATCAT 57.328 34.615 0.00 0.00 0.00 2.45
364 365 9.769677 ATACTACCTTCCTAATGCATAGTATCA 57.230 33.333 0.00 0.00 31.76 2.15
366 367 9.769677 TGATACTACCTTCCTAATGCATAGTAT 57.230 33.333 11.08 11.08 37.18 2.12
367 368 9.021807 GTGATACTACCTTCCTAATGCATAGTA 57.978 37.037 0.00 0.81 0.00 1.82
368 369 7.509318 TGTGATACTACCTTCCTAATGCATAGT 59.491 37.037 0.00 0.00 0.00 2.12
369 370 7.896811 TGTGATACTACCTTCCTAATGCATAG 58.103 38.462 0.00 0.00 0.00 2.23
370 371 7.849322 TGTGATACTACCTTCCTAATGCATA 57.151 36.000 0.00 0.00 0.00 3.14
371 372 6.747414 TGTGATACTACCTTCCTAATGCAT 57.253 37.500 0.00 0.00 0.00 3.96
372 373 6.326323 TGATGTGATACTACCTTCCTAATGCA 59.674 38.462 0.00 0.00 0.00 3.96
373 374 6.759272 TGATGTGATACTACCTTCCTAATGC 58.241 40.000 0.00 0.00 0.00 3.56
376 377 9.601810 ACATATGATGTGATACTACCTTCCTAA 57.398 33.333 10.38 0.00 43.01 2.69
378 379 9.775539 ATACATATGATGTGATACTACCTTCCT 57.224 33.333 10.38 0.00 44.60 3.36
379 380 9.809096 CATACATATGATGTGATACTACCTTCC 57.191 37.037 10.38 0.00 44.60 3.46
403 404 9.811995 TGCTTGTAATTCGTAAGTTAGTATCAT 57.188 29.630 0.00 0.00 39.48 2.45
404 405 9.297586 CTGCTTGTAATTCGTAAGTTAGTATCA 57.702 33.333 0.00 0.00 39.48 2.15
405 406 8.267367 GCTGCTTGTAATTCGTAAGTTAGTATC 58.733 37.037 0.00 0.00 39.48 2.24
406 407 7.224167 GGCTGCTTGTAATTCGTAAGTTAGTAT 59.776 37.037 0.00 0.00 39.48 2.12
407 408 6.532657 GGCTGCTTGTAATTCGTAAGTTAGTA 59.467 38.462 0.00 0.00 39.48 1.82
408 409 5.350640 GGCTGCTTGTAATTCGTAAGTTAGT 59.649 40.000 0.00 0.00 39.48 2.24
409 410 5.500290 CGGCTGCTTGTAATTCGTAAGTTAG 60.500 44.000 0.00 0.00 39.48 2.34
410 411 4.327898 CGGCTGCTTGTAATTCGTAAGTTA 59.672 41.667 0.00 0.00 39.48 2.24
411 412 3.124636 CGGCTGCTTGTAATTCGTAAGTT 59.875 43.478 0.00 0.00 39.48 2.66
412 413 2.671396 CGGCTGCTTGTAATTCGTAAGT 59.329 45.455 0.00 0.00 39.48 2.24
413 414 2.671396 ACGGCTGCTTGTAATTCGTAAG 59.329 45.455 0.00 0.00 0.00 2.34
414 415 2.690786 ACGGCTGCTTGTAATTCGTAA 58.309 42.857 0.00 0.00 0.00 3.18
415 416 2.373540 ACGGCTGCTTGTAATTCGTA 57.626 45.000 0.00 0.00 0.00 3.43
416 417 2.373540 TACGGCTGCTTGTAATTCGT 57.626 45.000 0.00 0.35 0.00 3.85
417 418 4.049186 AGTATACGGCTGCTTGTAATTCG 58.951 43.478 0.00 0.00 0.00 3.34
418 419 6.866770 TCATAGTATACGGCTGCTTGTAATTC 59.133 38.462 0.00 0.00 0.00 2.17
419 420 6.755206 TCATAGTATACGGCTGCTTGTAATT 58.245 36.000 0.00 0.00 0.00 1.40
420 421 6.340962 TCATAGTATACGGCTGCTTGTAAT 57.659 37.500 0.00 0.00 0.00 1.89
421 422 5.777850 TCATAGTATACGGCTGCTTGTAA 57.222 39.130 0.00 0.00 0.00 2.41
422 423 5.977489 ATCATAGTATACGGCTGCTTGTA 57.023 39.130 0.00 3.67 0.00 2.41
423 424 4.873746 ATCATAGTATACGGCTGCTTGT 57.126 40.909 0.00 1.23 0.00 3.16
424 425 5.955488 AGTATCATAGTATACGGCTGCTTG 58.045 41.667 0.00 0.00 37.41 4.01
425 426 6.183360 GCTAGTATCATAGTATACGGCTGCTT 60.183 42.308 0.00 0.00 37.41 3.91
426 427 5.297278 GCTAGTATCATAGTATACGGCTGCT 59.703 44.000 0.00 0.00 37.41 4.24
427 428 5.066117 TGCTAGTATCATAGTATACGGCTGC 59.934 44.000 0.00 0.00 37.41 5.25
428 429 6.487960 GTGCTAGTATCATAGTATACGGCTG 58.512 44.000 0.00 0.00 37.41 4.85
429 430 5.293814 CGTGCTAGTATCATAGTATACGGCT 59.706 44.000 0.00 0.00 37.41 5.52
430 431 5.292834 TCGTGCTAGTATCATAGTATACGGC 59.707 44.000 12.79 0.00 37.41 5.68
431 432 6.312180 TGTCGTGCTAGTATCATAGTATACGG 59.688 42.308 12.79 0.00 37.41 4.02
432 433 7.063191 AGTGTCGTGCTAGTATCATAGTATACG 59.937 40.741 8.91 8.91 37.41 3.06
433 434 8.254178 AGTGTCGTGCTAGTATCATAGTATAC 57.746 38.462 0.00 0.00 33.33 1.47
434 435 7.275123 CGAGTGTCGTGCTAGTATCATAGTATA 59.725 40.741 0.00 0.00 34.72 1.47
435 436 6.091034 CGAGTGTCGTGCTAGTATCATAGTAT 59.909 42.308 0.00 0.00 34.72 2.12
436 437 5.404667 CGAGTGTCGTGCTAGTATCATAGTA 59.595 44.000 0.00 0.00 34.72 1.82
437 438 4.211584 CGAGTGTCGTGCTAGTATCATAGT 59.788 45.833 0.00 0.00 34.72 2.12
438 439 4.703424 CGAGTGTCGTGCTAGTATCATAG 58.297 47.826 0.00 0.00 34.72 2.23
439 440 4.727235 CGAGTGTCGTGCTAGTATCATA 57.273 45.455 0.00 0.00 34.72 2.15
440 441 3.610786 CGAGTGTCGTGCTAGTATCAT 57.389 47.619 0.00 0.00 34.72 2.45
491 492 3.788227 TCTCAACTGCCAAATGTAGGT 57.212 42.857 0.00 0.00 0.00 3.08
535 536 7.382218 AGCTCGTGGAAACTTTATTTTGATTTG 59.618 33.333 0.00 0.00 0.00 2.32
536 537 7.433680 AGCTCGTGGAAACTTTATTTTGATTT 58.566 30.769 0.00 0.00 0.00 2.17
575 576 3.717707 TGCACCTCAATTATAGAGCGAC 58.282 45.455 0.00 0.00 0.00 5.19
602 603 2.298610 CCATTCATCATGTCTGCAGCT 58.701 47.619 9.47 0.00 0.00 4.24
605 606 1.064240 AGCCCATTCATCATGTCTGCA 60.064 47.619 0.00 0.00 0.00 4.41
622 633 1.899142 GGGGAGAGTCAGATGATAGCC 59.101 57.143 0.00 0.00 0.00 3.93
623 634 1.899142 GGGGGAGAGTCAGATGATAGC 59.101 57.143 0.00 0.00 0.00 2.97
682 693 2.267642 TCGATGGCGAGTTTGGGG 59.732 61.111 0.00 0.00 42.51 4.96
989 1084 1.079197 ATCGCCATTGCACGTCTCA 60.079 52.632 0.00 0.00 37.32 3.27
1246 1344 2.447887 CGCAGCTTGTAGCAGTCGG 61.448 63.158 1.09 0.00 45.56 4.79
1271 1369 0.106419 GGTTGGACCTGTTGAACCCA 60.106 55.000 0.07 0.00 34.73 4.51
1453 1551 2.364970 CCAACAAAAACTGGGCATCTGA 59.635 45.455 0.00 0.00 0.00 3.27
1454 1552 2.102925 ACCAACAAAAACTGGGCATCTG 59.897 45.455 0.00 0.00 37.00 2.90
1456 1554 2.482864 CACCAACAAAAACTGGGCATC 58.517 47.619 0.00 0.00 37.00 3.91
1457 1555 1.140652 CCACCAACAAAAACTGGGCAT 59.859 47.619 0.00 0.00 37.00 4.40
1458 1556 0.539051 CCACCAACAAAAACTGGGCA 59.461 50.000 0.00 0.00 37.00 5.36
1459 1557 0.813610 GCCACCAACAAAAACTGGGC 60.814 55.000 0.00 0.00 37.00 5.36
1460 1558 0.529555 CGCCACCAACAAAAACTGGG 60.530 55.000 0.00 0.00 37.00 4.45
1556 1654 2.191375 CTCCATGACGCCCAGCAT 59.809 61.111 0.00 0.00 0.00 3.79
1639 1737 0.759959 TCACCTTGGTGCCGTAGAAA 59.240 50.000 14.49 0.00 0.00 2.52
1735 1833 2.341101 GCGGTCGTCCTGGAAGAGA 61.341 63.158 12.75 3.26 34.07 3.10
1846 1944 4.645535 ACTGTACTACTCAACGTACCTCA 58.354 43.478 0.00 0.00 36.13 3.86
1864 1962 6.325028 AGACCAGCATGATAGTACAATACTGT 59.675 38.462 0.00 0.00 39.69 3.55
1865 1963 6.753180 AGACCAGCATGATAGTACAATACTG 58.247 40.000 0.00 0.00 39.69 2.74
1919 2017 4.851843 TCCAGATCACAAAGCAAGATGAT 58.148 39.130 0.00 0.00 34.50 2.45
2276 2454 1.928706 TATTTTTGGTCGCCGCAGCC 61.929 55.000 0.00 0.00 34.57 4.85
2279 2457 0.453793 CCATATTTTTGGTCGCCGCA 59.546 50.000 0.00 0.00 31.74 5.69
2287 2465 5.450965 GCTGATCAGTCCACCATATTTTTGG 60.451 44.000 23.38 0.00 42.82 3.28
2323 2501 0.393820 CAGGTGCAGCCATTTTTGGT 59.606 50.000 13.29 0.00 40.61 3.67
2428 2619 4.498513 CGGCACCGATACATCTGTACTTAA 60.499 45.833 2.01 0.00 42.83 1.85
2458 2650 1.303309 GCATGTATGGCTGTGAGACC 58.697 55.000 0.00 0.00 0.00 3.85
2500 2692 2.221169 GACCACAGCACATTCTGACAA 58.779 47.619 0.00 0.00 37.51 3.18
2552 2744 2.103094 TGAAACCCATAGAGAGATGCCG 59.897 50.000 0.00 0.00 0.00 5.69
2577 2769 4.342092 CCTCACACCCAAACAGAAGAAAAT 59.658 41.667 0.00 0.00 0.00 1.82
2602 2794 3.886505 ACATTTACAAACCACACGGACAT 59.113 39.130 0.00 0.00 35.59 3.06
2706 2898 2.221981 GCAGACTCCAGACTGAAAAACG 59.778 50.000 3.32 0.00 39.55 3.60
2708 2900 3.206150 GTGCAGACTCCAGACTGAAAAA 58.794 45.455 3.32 0.00 39.55 1.94
2709 2901 2.485479 GGTGCAGACTCCAGACTGAAAA 60.485 50.000 3.32 0.00 39.55 2.29
2850 3046 5.984926 GTCAATTTTTCAATCTTCAGGCACA 59.015 36.000 0.00 0.00 0.00 4.57
2879 3075 8.549338 AAAGGAAAAATAGTACTGCAGTAGAC 57.451 34.615 26.70 18.55 0.00 2.59
2882 3078 9.569122 AAGAAAAGGAAAAATAGTACTGCAGTA 57.431 29.630 22.67 22.67 0.00 2.74
2911 3107 3.754965 ACTAATGCTCAAGTTGGCTCAA 58.245 40.909 14.71 0.00 0.00 3.02
2917 3113 7.038048 TCAGTGATCTACTAATGCTCAAGTTG 58.962 38.462 0.00 0.00 37.60 3.16
2928 3124 4.038522 GCCAGCAGATCAGTGATCTACTAA 59.961 45.833 30.54 0.00 46.25 2.24
2930 3126 2.364970 GCCAGCAGATCAGTGATCTACT 59.635 50.000 30.54 27.44 46.25 2.57
2958 3155 1.272490 TCTACCGTGTGAGGCTTCAAG 59.728 52.381 0.00 0.00 34.49 3.02
2961 3158 1.000506 TGTTCTACCGTGTGAGGCTTC 59.999 52.381 0.00 0.00 33.69 3.86
3012 3209 4.705023 CCTCCCCACTTTTTAACATACTGG 59.295 45.833 0.00 0.00 0.00 4.00
3070 3267 9.070179 GGAGTTGGTTAAATCCTTAAACTGTTA 57.930 33.333 0.00 0.00 45.28 2.41
3211 3409 1.800805 ACATTCAGCCAACTCACTCG 58.199 50.000 0.00 0.00 0.00 4.18
3272 3487 7.886970 AGATATGGAAATAGTCATGTTGGGATG 59.113 37.037 0.00 0.00 0.00 3.51
3273 3488 7.993416 AGATATGGAAATAGTCATGTTGGGAT 58.007 34.615 0.00 0.00 0.00 3.85
3274 3489 7.293299 AGAGATATGGAAATAGTCATGTTGGGA 59.707 37.037 0.00 0.00 0.00 4.37
3275 3490 7.389884 CAGAGATATGGAAATAGTCATGTTGGG 59.610 40.741 0.00 0.00 0.00 4.12
3276 3491 7.094890 GCAGAGATATGGAAATAGTCATGTTGG 60.095 40.741 0.00 0.00 0.00 3.77
3277 3492 7.660617 AGCAGAGATATGGAAATAGTCATGTTG 59.339 37.037 0.00 0.00 0.00 3.33
3278 3493 7.660617 CAGCAGAGATATGGAAATAGTCATGTT 59.339 37.037 0.00 0.00 0.00 2.71
3279 3494 7.160049 CAGCAGAGATATGGAAATAGTCATGT 58.840 38.462 0.00 0.00 0.00 3.21
3280 3495 7.160049 ACAGCAGAGATATGGAAATAGTCATG 58.840 38.462 0.00 0.00 0.00 3.07
3281 3496 7.313740 ACAGCAGAGATATGGAAATAGTCAT 57.686 36.000 0.00 0.00 0.00 3.06
3282 3497 6.737720 ACAGCAGAGATATGGAAATAGTCA 57.262 37.500 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.