Multiple sequence alignment - TraesCS7A01G221900

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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 TraesCS7A01G221900 chr7A 100.000 2937 0 0 1 2937 191215227 191212291 0.000000e+00 5424.0
1 TraesCS7A01G221900 chr7A 91.932 409 30 2 1 406 704775711 704776119 1.180000e-158 569.0
2 TraesCS7A01G221900 chr7A 91.687 409 31 2 1 406 11741608 11742016 5.500000e-157 564.0
3 TraesCS7A01G221900 chr7A 88.235 170 16 3 2209 2378 438147539 438147704 1.790000e-47 200.0
4 TraesCS7A01G221900 chr7B 94.266 1587 71 10 504 2079 147590000 147591577 0.000000e+00 2409.0
5 TraesCS7A01G221900 chr7B 90.965 819 72 2 2120 2937 147601985 147602802 0.000000e+00 1101.0
6 TraesCS7A01G221900 chr7B 92.958 142 10 0 2237 2378 382636427 382636568 1.070000e-49 207.0
7 TraesCS7A01G221900 chr7B 83.516 91 13 1 2825 2913 337028146 337028236 1.880000e-12 84.2
8 TraesCS7A01G221900 chr7B 82.609 92 13 2 2826 2915 720218124 720218034 8.730000e-11 78.7
9 TraesCS7A01G221900 chr7B 81.250 80 15 0 2671 2750 552733530 552733451 6.790000e-07 65.8
10 TraesCS7A01G221900 chr7D 96.075 1274 35 7 709 1976 180859541 180860805 0.000000e+00 2061.0
11 TraesCS7A01G221900 chr7D 84.542 524 67 8 2427 2937 180861534 180862056 9.390000e-140 507.0
12 TraesCS7A01G221900 chr7D 88.710 248 16 7 2132 2378 180861220 180861456 2.860000e-75 292.0
13 TraesCS7A01G221900 chr7D 95.489 133 5 1 1999 2131 180860862 180860993 8.250000e-51 211.0
14 TraesCS7A01G221900 chr7D 88.889 171 14 4 2209 2378 387918371 387918537 3.840000e-49 206.0
15 TraesCS7A01G221900 chr7D 75.405 309 57 10 2619 2915 71963416 71963115 6.600000e-27 132.0
16 TraesCS7A01G221900 chr7D 73.438 320 71 9 2608 2915 29136320 29136003 1.110000e-19 108.0
17 TraesCS7A01G221900 chr2A 92.824 432 28 2 1 429 754124031 754124462 8.940000e-175 623.0
18 TraesCS7A01G221900 chr2A 90.000 410 32 3 1 401 754107441 754107850 3.350000e-144 521.0
19 TraesCS7A01G221900 chr2A 82.243 107 14 4 2811 2913 662404650 662404545 1.450000e-13 87.9
20 TraesCS7A01G221900 chr1A 93.399 409 24 2 1 406 557298597 557298189 1.160000e-168 603.0
21 TraesCS7A01G221900 chr1A 92.665 409 26 3 1 406 527181773 527181366 1.170000e-163 586.0
22 TraesCS7A01G221900 chr1A 91.101 427 31 3 1 424 497335932 497336354 3.280000e-159 571.0
23 TraesCS7A01G221900 chr3A 92.421 409 28 2 1 406 7616100 7616508 5.460000e-162 580.0
24 TraesCS7A01G221900 chr2B 92.402 408 26 4 3 406 733455768 733456174 7.060000e-161 577.0
25 TraesCS7A01G221900 chr6A 91.484 411 30 3 1 406 525231737 525231327 7.110000e-156 560.0
26 TraesCS7A01G221900 chr3D 91.463 410 30 5 1 406 381293236 381292828 2.560000e-155 558.0
27 TraesCS7A01G221900 chr3D 80.825 485 78 11 2464 2936 1385449 1384968 1.660000e-97 366.0
28 TraesCS7A01G221900 chr3D 81.163 430 67 10 2518 2936 1378999 1378573 1.690000e-87 333.0
29 TraesCS7A01G221900 chr3D 81.163 430 67 10 2518 2936 1381925 1381499 1.690000e-87 333.0
30 TraesCS7A01G221900 chr4A 86.761 423 20 8 3 391 614694137 614694557 3.480000e-119 438.0
31 TraesCS7A01G221900 chrUn 80.619 485 79 11 2464 2936 384619320 384618839 7.740000e-96 361.0
32 TraesCS7A01G221900 chr4B 78.776 490 69 22 2464 2937 134656500 134656970 2.210000e-76 296.0
33 TraesCS7A01G221900 chr5B 73.871 310 65 11 2619 2915 360398767 360398461 3.090000e-20 110.0
34 TraesCS7A01G221900 chr6B 72.434 341 77 11 2589 2915 491602383 491602046 3.120000e-15 93.5


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 TraesCS7A01G221900 chr7A 191212291 191215227 2936 True 5424.00 5424 100.000000 1 2937 1 chr7A.!!$R1 2936
1 TraesCS7A01G221900 chr7B 147590000 147591577 1577 False 2409.00 2409 94.266000 504 2079 1 chr7B.!!$F1 1575
2 TraesCS7A01G221900 chr7B 147601985 147602802 817 False 1101.00 1101 90.965000 2120 2937 1 chr7B.!!$F2 817
3 TraesCS7A01G221900 chr7D 180859541 180862056 2515 False 767.75 2061 91.204000 709 2937 4 chr7D.!!$F2 2228
4 TraesCS7A01G221900 chr3D 1378573 1385449 6876 True 344.00 366 81.050333 2464 2936 3 chr3D.!!$R2 472

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
434 435 0.037326 TTTCTGGTAGTGAGCCGCAG 60.037 55.0 0.00 0.00 0.00 5.18 F
588 589 0.385473 GTGCTTCAGCGCGCTAAAAA 60.385 50.0 36.02 25.17 45.83 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1508 0.388520 CTAAGGTTTGGCAAAGCGGC 60.389 55.0 29.75 12.24 43.34 6.53 R
1971 1988 1.227999 ATGTGACGGAACTTGGCACG 61.228 55.0 0.00 0.00 32.39 5.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.280186 GGGGATCGATGACGTGGC 60.280 66.667 0.54 0.00 40.69 5.01
18 19 2.499205 GGGATCGATGACGTGGCA 59.501 61.111 0.54 0.00 40.69 4.92
19 20 1.153449 GGGATCGATGACGTGGCAA 60.153 57.895 0.54 0.00 40.69 4.52
20 21 0.742990 GGGATCGATGACGTGGCAAA 60.743 55.000 0.54 0.00 40.69 3.68
21 22 1.083489 GGATCGATGACGTGGCAAAA 58.917 50.000 0.54 0.00 40.69 2.44
22 23 1.466950 GGATCGATGACGTGGCAAAAA 59.533 47.619 0.54 0.00 40.69 1.94
23 24 2.505866 GATCGATGACGTGGCAAAAAC 58.494 47.619 0.54 0.00 40.69 2.43
24 25 0.589223 TCGATGACGTGGCAAAAACC 59.411 50.000 0.00 0.00 40.69 3.27
25 26 0.309302 CGATGACGTGGCAAAAACCA 59.691 50.000 0.00 0.00 37.38 3.67
26 27 1.068610 CGATGACGTGGCAAAAACCAT 60.069 47.619 0.00 0.00 43.01 3.55
29 30 4.671406 CGTGGCAAAAACCATGGG 57.329 55.556 18.09 0.00 43.01 4.00
30 31 1.667510 CGTGGCAAAAACCATGGGC 60.668 57.895 18.09 9.14 43.01 5.36
31 32 1.302431 GTGGCAAAAACCATGGGCC 60.302 57.895 18.09 18.65 43.01 5.80
32 33 3.155750 GGCAAAAACCATGGGCCA 58.844 55.556 20.47 9.61 44.01 5.36
33 34 1.003476 GGCAAAAACCATGGGCCAG 60.003 57.895 20.47 0.82 44.01 4.85
34 35 1.003476 GCAAAAACCATGGGCCAGG 60.003 57.895 18.09 12.92 0.00 4.45
35 36 1.003476 CAAAAACCATGGGCCAGGC 60.003 57.895 18.09 1.26 0.00 4.85
76 77 1.024271 CATAGAAATGCCACCCCACG 58.976 55.000 0.00 0.00 0.00 4.94
77 78 0.106719 ATAGAAATGCCACCCCACGG 60.107 55.000 0.00 0.00 0.00 4.94
101 102 2.278596 CGAACGCCACGGATCGAT 60.279 61.111 0.00 0.00 40.65 3.59
102 103 2.576893 CGAACGCCACGGATCGATG 61.577 63.158 0.54 0.00 40.65 3.84
103 104 1.226859 GAACGCCACGGATCGATGA 60.227 57.895 0.54 0.00 0.00 2.92
104 105 1.480219 GAACGCCACGGATCGATGAC 61.480 60.000 0.54 0.00 0.00 3.06
105 106 3.024609 CGCCACGGATCGATGACG 61.025 66.667 0.54 10.24 41.26 4.35
106 107 2.104331 GCCACGGATCGATGACGT 59.896 61.111 16.37 16.37 42.17 4.34
110 111 2.177044 ACGGATCGATGACGTGACA 58.823 52.632 20.02 0.00 39.64 3.58
111 112 0.098905 ACGGATCGATGACGTGACAG 59.901 55.000 20.02 1.08 39.64 3.51
112 113 1.202973 CGGATCGATGACGTGACAGC 61.203 60.000 0.54 0.00 40.69 4.40
114 115 1.802300 GATCGATGACGTGACAGCGC 61.802 60.000 0.54 0.00 46.77 5.92
115 116 3.545481 CGATGACGTGACAGCGCC 61.545 66.667 2.29 0.00 42.22 6.53
116 117 3.545481 GATGACGTGACAGCGCCG 61.545 66.667 2.29 1.74 34.88 6.46
130 131 4.925576 GCCGCGGATCGATGACGT 62.926 66.667 33.48 0.00 41.67 4.34
131 132 2.726180 CCGCGGATCGATGACGTC 60.726 66.667 24.07 9.11 41.67 4.34
139 140 3.527186 CGATGACGTCGGCATAGC 58.473 61.111 14.96 1.11 46.47 2.97
140 141 1.008424 CGATGACGTCGGCATAGCT 60.008 57.895 14.96 0.00 46.47 3.32
141 142 0.237498 CGATGACGTCGGCATAGCTA 59.763 55.000 14.96 0.00 46.47 3.32
142 143 1.135660 CGATGACGTCGGCATAGCTAT 60.136 52.381 14.96 0.00 46.47 2.97
143 144 2.254459 GATGACGTCGGCATAGCTATG 58.746 52.381 26.42 26.42 36.78 2.23
186 187 4.111016 CGTAGCCTGACGCCGTCA 62.111 66.667 20.04 20.04 40.50 4.35
187 188 2.260434 GTAGCCTGACGCCGTCAA 59.740 61.111 21.56 3.03 42.26 3.18
188 189 1.373748 GTAGCCTGACGCCGTCAAA 60.374 57.895 21.56 4.37 42.26 2.69
189 190 1.373748 TAGCCTGACGCCGTCAAAC 60.374 57.895 21.56 15.35 42.26 2.93
190 191 1.812686 TAGCCTGACGCCGTCAAACT 61.813 55.000 21.56 21.17 42.26 2.66
191 192 2.954753 GCCTGACGCCGTCAAACTG 61.955 63.158 21.56 9.24 42.26 3.16
192 193 2.551270 CTGACGCCGTCAAACTGC 59.449 61.111 21.56 0.00 42.26 4.40
193 194 2.954753 CTGACGCCGTCAAACTGCC 61.955 63.158 21.56 0.00 42.26 4.85
194 195 4.072088 GACGCCGTCAAACTGCCG 62.072 66.667 13.23 0.00 32.09 5.69
195 196 4.903010 ACGCCGTCAAACTGCCGT 62.903 61.111 0.00 0.00 0.00 5.68
196 197 4.072088 CGCCGTCAAACTGCCGTC 62.072 66.667 0.00 0.00 0.00 4.79
197 198 2.970324 GCCGTCAAACTGCCGTCA 60.970 61.111 0.00 0.00 0.00 4.35
198 199 2.935955 CCGTCAAACTGCCGTCAC 59.064 61.111 0.00 0.00 0.00 3.67
199 200 2.604174 CCGTCAAACTGCCGTCACC 61.604 63.158 0.00 0.00 0.00 4.02
200 201 2.935955 GTCAAACTGCCGTCACCG 59.064 61.111 0.00 0.00 0.00 4.94
201 202 2.970324 TCAAACTGCCGTCACCGC 60.970 61.111 0.00 0.00 0.00 5.68
202 203 4.025401 CAAACTGCCGTCACCGCC 62.025 66.667 0.00 0.00 0.00 6.13
231 232 4.961511 GCCCACGCGATATGCCGA 62.962 66.667 15.93 0.00 42.08 5.54
232 233 3.036084 CCCACGCGATATGCCGAC 61.036 66.667 15.93 0.00 42.08 4.79
233 234 3.394874 CCACGCGATATGCCGACG 61.395 66.667 15.93 0.00 42.08 5.12
234 235 3.394874 CACGCGATATGCCGACGG 61.395 66.667 15.93 10.29 42.08 4.79
244 245 3.760917 GCCGACGGCCTACTCTAT 58.239 61.111 28.74 0.00 44.06 1.98
245 246 1.286260 GCCGACGGCCTACTCTATG 59.714 63.158 28.74 0.00 44.06 2.23
246 247 1.286260 CCGACGGCCTACTCTATGC 59.714 63.158 0.00 0.00 0.00 3.14
247 248 1.286260 CGACGGCCTACTCTATGCC 59.714 63.158 0.00 0.00 41.85 4.40
251 252 1.286260 GGCCTACTCTATGCCGACG 59.714 63.158 0.00 0.00 35.08 5.12
252 253 1.286260 GCCTACTCTATGCCGACGG 59.714 63.158 10.29 10.29 0.00 4.79
267 268 3.998672 CGGCCGCCGTGGGTATAT 61.999 66.667 24.08 0.00 42.73 0.86
268 269 2.428622 GGCCGCCGTGGGTATATT 59.571 61.111 0.00 0.00 38.63 1.28
269 270 1.670083 GGCCGCCGTGGGTATATTC 60.670 63.158 0.00 0.00 38.63 1.75
270 271 1.370064 GCCGCCGTGGGTATATTCT 59.630 57.895 0.00 0.00 38.63 2.40
271 272 0.604578 GCCGCCGTGGGTATATTCTA 59.395 55.000 0.00 0.00 38.63 2.10
272 273 1.001181 GCCGCCGTGGGTATATTCTAA 59.999 52.381 0.00 0.00 38.63 2.10
273 274 2.929592 GCCGCCGTGGGTATATTCTAAG 60.930 54.545 0.00 0.00 38.63 2.18
274 275 2.334838 CGCCGTGGGTATATTCTAAGC 58.665 52.381 0.00 0.00 0.00 3.09
275 276 2.288579 CGCCGTGGGTATATTCTAAGCA 60.289 50.000 0.00 0.00 0.00 3.91
276 277 3.735591 GCCGTGGGTATATTCTAAGCAA 58.264 45.455 0.00 0.00 0.00 3.91
277 278 3.497262 GCCGTGGGTATATTCTAAGCAAC 59.503 47.826 0.00 0.00 0.00 4.17
278 279 3.739300 CCGTGGGTATATTCTAAGCAACG 59.261 47.826 0.00 0.00 39.60 4.10
279 280 3.183775 CGTGGGTATATTCTAAGCAACGC 59.816 47.826 0.00 0.00 34.22 4.84
280 281 3.497262 GTGGGTATATTCTAAGCAACGCC 59.503 47.826 0.00 0.00 0.00 5.68
281 282 2.735134 GGGTATATTCTAAGCAACGCCG 59.265 50.000 0.00 0.00 0.00 6.46
282 283 3.553508 GGGTATATTCTAAGCAACGCCGA 60.554 47.826 0.00 0.00 0.00 5.54
283 284 3.427863 GGTATATTCTAAGCAACGCCGAC 59.572 47.826 0.00 0.00 0.00 4.79
285 286 0.108992 ATTCTAAGCAACGCCGACGA 60.109 50.000 0.00 0.00 43.93 4.20
286 287 1.005294 TTCTAAGCAACGCCGACGAC 61.005 55.000 0.00 0.00 43.93 4.34
287 288 1.443872 CTAAGCAACGCCGACGACT 60.444 57.895 0.00 0.00 43.93 4.18
288 289 1.674611 CTAAGCAACGCCGACGACTG 61.675 60.000 0.00 0.00 43.93 3.51
289 290 2.132517 TAAGCAACGCCGACGACTGA 62.133 55.000 0.00 0.00 43.93 3.41
290 291 2.765250 AAGCAACGCCGACGACTGAT 62.765 55.000 0.00 0.00 43.93 2.90
291 292 2.789203 GCAACGCCGACGACTGATC 61.789 63.158 0.00 0.00 43.93 2.92
292 293 1.154016 CAACGCCGACGACTGATCT 60.154 57.895 0.00 0.00 43.93 2.75
293 294 0.732880 CAACGCCGACGACTGATCTT 60.733 55.000 0.00 0.00 43.93 2.40
294 295 0.038526 AACGCCGACGACTGATCTTT 60.039 50.000 0.00 0.00 43.93 2.52
295 296 0.732880 ACGCCGACGACTGATCTTTG 60.733 55.000 0.00 0.00 43.93 2.77
296 297 1.710339 GCCGACGACTGATCTTTGC 59.290 57.895 0.00 0.00 0.00 3.68
297 298 1.696832 GCCGACGACTGATCTTTGCC 61.697 60.000 0.00 0.00 0.00 4.52
298 299 1.413767 CCGACGACTGATCTTTGCCG 61.414 60.000 0.00 0.00 0.00 5.69
299 300 0.456142 CGACGACTGATCTTTGCCGA 60.456 55.000 0.00 0.00 0.00 5.54
300 301 0.992802 GACGACTGATCTTTGCCGAC 59.007 55.000 0.00 0.00 0.00 4.79
301 302 0.732880 ACGACTGATCTTTGCCGACG 60.733 55.000 0.00 0.00 0.00 5.12
302 303 1.413767 CGACTGATCTTTGCCGACGG 61.414 60.000 10.29 10.29 0.00 4.79
320 321 3.616721 CCCCCGTCGGCATAGAGG 61.617 72.222 5.50 0.00 0.00 3.69
321 322 3.616721 CCCCGTCGGCATAGAGGG 61.617 72.222 5.50 0.00 43.64 4.30
322 323 4.301027 CCCGTCGGCATAGAGGGC 62.301 72.222 5.50 0.00 42.92 5.19
329 330 4.285851 GCATAGAGGGCCATACGC 57.714 61.111 6.18 0.00 0.00 4.42
345 346 2.884207 GCCGACGGCCTTTCTACG 60.884 66.667 28.74 0.00 44.06 3.51
346 347 2.884207 CCGACGGCCTTTCTACGC 60.884 66.667 0.00 0.00 0.00 4.42
347 348 2.884207 CGACGGCCTTTCTACGCC 60.884 66.667 0.00 0.00 42.05 5.68
352 353 2.884207 GCCTTTCTACGCCGACGG 60.884 66.667 10.29 10.29 46.04 4.79
353 354 2.884207 CCTTTCTACGCCGACGGC 60.884 66.667 29.10 29.10 46.75 5.68
368 369 2.824489 GGCTTTAGCTGGGCCGTC 60.824 66.667 9.93 0.00 41.70 4.79
369 370 3.195698 GCTTTAGCTGGGCCGTCG 61.196 66.667 0.00 0.00 38.21 5.12
370 371 2.511600 CTTTAGCTGGGCCGTCGG 60.512 66.667 6.99 6.99 0.00 4.79
371 372 4.090588 TTTAGCTGGGCCGTCGGG 62.091 66.667 14.38 0.00 0.00 5.14
376 377 4.235762 CTGGGCCGTCGGGGTATG 62.236 72.222 14.38 0.00 38.44 2.39
389 390 3.159298 GGTATGCCCATCTATGCCG 57.841 57.895 0.00 0.00 0.00 5.69
390 391 0.613260 GGTATGCCCATCTATGCCGA 59.387 55.000 0.00 0.00 0.00 5.54
391 392 1.676014 GGTATGCCCATCTATGCCGAC 60.676 57.143 0.00 0.00 0.00 4.79
392 393 0.246360 TATGCCCATCTATGCCGACG 59.754 55.000 0.00 0.00 0.00 5.12
393 394 2.357517 GCCCATCTATGCCGACGG 60.358 66.667 10.29 10.29 0.00 4.79
394 395 2.343758 CCCATCTATGCCGACGGG 59.656 66.667 17.22 0.00 28.93 5.28
395 396 2.343758 CCATCTATGCCGACGGGG 59.656 66.667 17.22 1.99 39.58 5.73
396 397 2.343758 CATCTATGCCGACGGGGG 59.656 66.667 17.22 0.00 35.78 5.40
414 415 3.416490 CCGTCGGCAACACAAGTT 58.584 55.556 0.00 0.00 38.88 2.66
415 416 1.725066 CCGTCGGCAACACAAGTTT 59.275 52.632 0.00 0.00 35.28 2.66
416 417 0.099791 CCGTCGGCAACACAAGTTTT 59.900 50.000 0.00 0.00 35.28 2.43
417 418 1.468395 CCGTCGGCAACACAAGTTTTT 60.468 47.619 0.00 0.00 35.28 1.94
418 419 1.843753 CGTCGGCAACACAAGTTTTTC 59.156 47.619 0.00 0.00 35.28 2.29
419 420 2.477189 CGTCGGCAACACAAGTTTTTCT 60.477 45.455 0.00 0.00 35.28 2.52
420 421 2.851824 GTCGGCAACACAAGTTTTTCTG 59.148 45.455 0.00 0.00 35.28 3.02
421 422 2.159310 TCGGCAACACAAGTTTTTCTGG 60.159 45.455 0.00 0.00 35.28 3.86
422 423 2.416701 CGGCAACACAAGTTTTTCTGGT 60.417 45.455 0.00 0.00 35.28 4.00
423 424 3.181495 CGGCAACACAAGTTTTTCTGGTA 60.181 43.478 0.00 0.00 35.28 3.25
424 425 4.359706 GGCAACACAAGTTTTTCTGGTAG 58.640 43.478 0.00 0.00 35.28 3.18
425 426 4.142249 GGCAACACAAGTTTTTCTGGTAGT 60.142 41.667 0.00 0.00 35.28 2.73
426 427 4.798387 GCAACACAAGTTTTTCTGGTAGTG 59.202 41.667 0.00 0.00 35.28 2.74
427 428 5.392595 GCAACACAAGTTTTTCTGGTAGTGA 60.393 40.000 0.00 0.00 35.28 3.41
428 429 6.258160 CAACACAAGTTTTTCTGGTAGTGAG 58.742 40.000 0.00 0.00 35.28 3.51
429 430 4.335594 ACACAAGTTTTTCTGGTAGTGAGC 59.664 41.667 0.00 0.00 0.00 4.26
430 431 3.883489 ACAAGTTTTTCTGGTAGTGAGCC 59.117 43.478 0.00 0.00 0.00 4.70
431 432 2.767505 AGTTTTTCTGGTAGTGAGCCG 58.232 47.619 0.00 0.00 0.00 5.52
432 433 1.197036 GTTTTTCTGGTAGTGAGCCGC 59.803 52.381 0.00 0.00 0.00 6.53
433 434 0.394938 TTTTCTGGTAGTGAGCCGCA 59.605 50.000 0.00 0.00 0.00 5.69
434 435 0.037326 TTTCTGGTAGTGAGCCGCAG 60.037 55.000 0.00 0.00 0.00 5.18
435 436 2.507110 TTCTGGTAGTGAGCCGCAGC 62.507 60.000 0.00 0.00 40.32 5.25
445 446 4.541020 GCCGCAGCTGAAAAGAAC 57.459 55.556 20.43 0.00 35.50 3.01
446 447 1.952263 GCCGCAGCTGAAAAGAACT 59.048 52.632 20.43 0.00 35.50 3.01
447 448 0.386478 GCCGCAGCTGAAAAGAACTG 60.386 55.000 20.43 0.00 35.50 3.16
453 454 2.161211 CAGCTGAAAAGAACTGCTAGGC 59.839 50.000 8.42 0.00 39.72 3.93
454 455 1.470494 GCTGAAAAGAACTGCTAGGCC 59.530 52.381 0.00 0.00 0.00 5.19
455 456 2.087646 CTGAAAAGAACTGCTAGGCCC 58.912 52.381 0.00 0.00 0.00 5.80
456 457 1.705186 TGAAAAGAACTGCTAGGCCCT 59.295 47.619 0.00 0.00 0.00 5.19
457 458 2.910319 TGAAAAGAACTGCTAGGCCCTA 59.090 45.455 0.00 0.00 0.00 3.53
458 459 3.329520 TGAAAAGAACTGCTAGGCCCTAA 59.670 43.478 0.00 0.00 0.00 2.69
459 460 4.018415 TGAAAAGAACTGCTAGGCCCTAAT 60.018 41.667 0.00 0.00 0.00 1.73
460 461 3.567478 AAGAACTGCTAGGCCCTAATG 57.433 47.619 0.00 0.00 0.00 1.90
461 462 2.482494 AGAACTGCTAGGCCCTAATGT 58.518 47.619 0.00 0.00 0.00 2.71
462 463 2.846827 AGAACTGCTAGGCCCTAATGTT 59.153 45.455 0.00 0.00 0.00 2.71
463 464 3.267031 AGAACTGCTAGGCCCTAATGTTT 59.733 43.478 0.00 0.00 0.00 2.83
464 465 3.004752 ACTGCTAGGCCCTAATGTTTG 57.995 47.619 0.00 0.00 0.00 2.93
465 466 2.576191 ACTGCTAGGCCCTAATGTTTGA 59.424 45.455 0.00 0.00 0.00 2.69
466 467 3.203040 ACTGCTAGGCCCTAATGTTTGAT 59.797 43.478 0.00 0.00 0.00 2.57
467 468 3.554934 TGCTAGGCCCTAATGTTTGATG 58.445 45.455 0.00 0.00 0.00 3.07
468 469 3.053693 TGCTAGGCCCTAATGTTTGATGT 60.054 43.478 0.00 0.00 0.00 3.06
469 470 3.565902 GCTAGGCCCTAATGTTTGATGTC 59.434 47.826 0.00 0.00 0.00 3.06
470 471 4.687219 GCTAGGCCCTAATGTTTGATGTCT 60.687 45.833 0.00 0.00 0.00 3.41
471 472 3.891049 AGGCCCTAATGTTTGATGTCTC 58.109 45.455 0.00 0.00 0.00 3.36
472 473 2.614057 GGCCCTAATGTTTGATGTCTCG 59.386 50.000 0.00 0.00 0.00 4.04
473 474 2.614057 GCCCTAATGTTTGATGTCTCGG 59.386 50.000 0.00 0.00 0.00 4.63
474 475 3.681594 GCCCTAATGTTTGATGTCTCGGA 60.682 47.826 0.00 0.00 0.00 4.55
475 476 4.122776 CCCTAATGTTTGATGTCTCGGAG 58.877 47.826 0.00 0.00 0.00 4.63
476 477 4.383118 CCCTAATGTTTGATGTCTCGGAGT 60.383 45.833 4.69 0.00 0.00 3.85
477 478 5.163447 CCCTAATGTTTGATGTCTCGGAGTA 60.163 44.000 4.69 0.00 0.00 2.59
478 479 6.463049 CCCTAATGTTTGATGTCTCGGAGTAT 60.463 42.308 4.69 1.28 0.00 2.12
479 480 6.986817 CCTAATGTTTGATGTCTCGGAGTATT 59.013 38.462 4.69 0.00 0.00 1.89
480 481 7.495934 CCTAATGTTTGATGTCTCGGAGTATTT 59.504 37.037 4.69 0.00 0.00 1.40
481 482 6.668541 ATGTTTGATGTCTCGGAGTATTTG 57.331 37.500 4.69 0.00 0.00 2.32
482 483 5.789521 TGTTTGATGTCTCGGAGTATTTGA 58.210 37.500 4.69 0.00 0.00 2.69
483 484 5.869344 TGTTTGATGTCTCGGAGTATTTGAG 59.131 40.000 4.69 0.00 0.00 3.02
484 485 4.655762 TGATGTCTCGGAGTATTTGAGG 57.344 45.455 4.69 0.00 0.00 3.86
485 486 4.023980 TGATGTCTCGGAGTATTTGAGGT 58.976 43.478 4.69 0.00 0.00 3.85
486 487 4.466370 TGATGTCTCGGAGTATTTGAGGTT 59.534 41.667 4.69 0.00 0.00 3.50
487 488 4.188247 TGTCTCGGAGTATTTGAGGTTG 57.812 45.455 4.69 0.00 0.00 3.77
488 489 3.830178 TGTCTCGGAGTATTTGAGGTTGA 59.170 43.478 4.69 0.00 0.00 3.18
489 490 4.082190 TGTCTCGGAGTATTTGAGGTTGAG 60.082 45.833 4.69 0.00 0.00 3.02
490 491 3.119101 TCTCGGAGTATTTGAGGTTGAGC 60.119 47.826 4.69 0.00 0.00 4.26
491 492 2.093658 TCGGAGTATTTGAGGTTGAGCC 60.094 50.000 0.00 0.00 37.58 4.70
492 493 2.644676 GGAGTATTTGAGGTTGAGCCC 58.355 52.381 0.00 0.00 38.26 5.19
493 494 2.239907 GGAGTATTTGAGGTTGAGCCCT 59.760 50.000 0.00 0.00 38.26 5.19
500 501 2.869101 GAGGTTGAGCCCTCTTTTCT 57.131 50.000 0.00 0.00 46.34 2.52
501 502 3.983044 GAGGTTGAGCCCTCTTTTCTA 57.017 47.619 0.00 0.00 46.34 2.10
502 503 4.495690 GAGGTTGAGCCCTCTTTTCTAT 57.504 45.455 0.00 0.00 46.34 1.98
503 504 4.849518 GAGGTTGAGCCCTCTTTTCTATT 58.150 43.478 0.00 0.00 46.34 1.73
504 505 5.257262 GAGGTTGAGCCCTCTTTTCTATTT 58.743 41.667 0.00 0.00 46.34 1.40
505 506 5.645201 AGGTTGAGCCCTCTTTTCTATTTT 58.355 37.500 0.00 0.00 38.26 1.82
586 587 2.860293 GTGCTTCAGCGCGCTAAA 59.140 55.556 36.02 26.55 45.83 1.85
587 588 1.206578 GTGCTTCAGCGCGCTAAAA 59.793 52.632 36.02 27.67 45.83 1.52
588 589 0.385473 GTGCTTCAGCGCGCTAAAAA 60.385 50.000 36.02 25.17 45.83 1.94
614 615 2.602933 CGCCATATTTGGACGCAATCTG 60.603 50.000 6.35 0.00 46.92 2.90
669 670 1.527433 GCCTCCCAAGCACCAAGTTC 61.527 60.000 0.00 0.00 0.00 3.01
673 674 0.804989 CCCAAGCACCAAGTTCGATC 59.195 55.000 0.00 0.00 0.00 3.69
692 693 2.143122 TCAAACTCGAGTCATGGTTGC 58.857 47.619 20.33 0.00 0.00 4.17
696 697 0.994995 CTCGAGTCATGGTTGCGAAG 59.005 55.000 3.62 0.00 0.00 3.79
773 774 1.143305 CAGTGAAGCGTCAACCTCAG 58.857 55.000 3.20 0.00 34.87 3.35
782 783 0.603975 GTCAACCTCAGCGCCTTTCT 60.604 55.000 2.29 0.00 0.00 2.52
784 785 0.954452 CAACCTCAGCGCCTTTCTTT 59.046 50.000 2.29 0.00 0.00 2.52
785 786 1.068954 CAACCTCAGCGCCTTTCTTTC 60.069 52.381 2.29 0.00 0.00 2.62
899 900 1.254975 AAACCCATAAGCAACCGGCC 61.255 55.000 0.00 0.00 46.50 6.13
901 902 3.209097 CCATAAGCAACCGGCCCG 61.209 66.667 0.00 0.00 46.50 6.13
1230 1241 2.244486 TCCTTCATCTGCTCTCCTGT 57.756 50.000 0.00 0.00 0.00 4.00
1234 1245 2.105006 TCATCTGCTCTCCTGTTTGC 57.895 50.000 0.00 0.00 0.00 3.68
1294 1305 1.067669 GTGATCTCCAGCAGTATCGCA 59.932 52.381 0.00 0.00 0.00 5.10
1500 1511 4.778143 AAGGTAGCTTGCCGGCCG 62.778 66.667 26.77 21.04 0.00 6.13
1504 1515 4.715523 TAGCTTGCCGGCCGCTTT 62.716 61.111 35.32 20.66 38.78 3.51
1579 1596 4.677584 CTCTGCAACTGATCAGGTACTAC 58.322 47.826 26.08 10.88 36.02 2.73
1729 1746 1.072173 CTGATGTGGATATTCGGGCCA 59.928 52.381 4.39 0.00 0.00 5.36
1763 1780 1.162698 CTGCTCAGTGTTCATGGTGG 58.837 55.000 0.00 0.00 0.00 4.61
1798 1815 2.431683 GACAGCAACTCCCTGCCA 59.568 61.111 0.00 0.00 43.73 4.92
1816 1833 1.476833 CCACTGCACCAGTACCAGTTT 60.477 52.381 0.00 0.00 43.43 2.66
1913 1930 6.146510 TGCGATTATCAACAACCCGATATTAC 59.853 38.462 0.00 0.00 0.00 1.89
1971 1988 2.746269 TGTTACAGAACCTGCACGTAC 58.254 47.619 0.00 0.00 34.37 3.67
1996 2013 1.800586 CAAGTTCCGTCACATGTGAGG 59.199 52.381 32.04 32.04 40.75 3.86
2049 2100 6.493166 AGTATTCCATCCCTGAAACAAATGA 58.507 36.000 0.00 0.00 0.00 2.57
2161 2438 5.220662 CGGGTTAGCATACTGATTTTGACAG 60.221 44.000 0.00 0.00 40.68 3.51
2303 2581 4.808364 AGCAGATTTCTTATTGTCTCGCTC 59.192 41.667 0.00 0.00 0.00 5.03
2319 2597 2.742053 TCGCTCCTTGTGCTTGTATTTC 59.258 45.455 0.00 0.00 0.00 2.17
2378 2656 6.638468 CCTTTCTTGTGCTTCTTGTAAATGAC 59.362 38.462 0.00 0.00 0.00 3.06
2379 2657 6.942532 TTCTTGTGCTTCTTGTAAATGACT 57.057 33.333 0.00 0.00 0.00 3.41
2414 2737 7.806180 AGTTATGGACAGAACTAATATTGGCT 58.194 34.615 10.31 0.00 40.64 4.75
2462 2785 7.891183 TGAATTTTCAGTCTACTAGCAAGTC 57.109 36.000 0.00 0.00 33.46 3.01
2467 2790 8.732746 TTTTCAGTCTACTAGCAAGTCTTTTT 57.267 30.769 0.00 0.00 37.15 1.94
2473 2796 8.613482 AGTCTACTAGCAAGTCTTTTTGAAAAC 58.387 33.333 0.00 0.00 37.15 2.43
2474 2797 8.395633 GTCTACTAGCAAGTCTTTTTGAAAACA 58.604 33.333 0.00 0.00 37.15 2.83
2492 2815 4.831613 AGGATTACCCTCGGCCTT 57.168 55.556 0.00 0.00 43.31 4.35
2501 2824 1.250154 CCCTCGGCCTTTGCATCAAA 61.250 55.000 0.00 0.00 40.13 2.69
2521 2844 7.598189 TCAAATGATGCACATAACCATTTTG 57.402 32.000 0.00 0.00 38.38 2.44
2563 6355 7.279313 ACAAAGTACGTAGTTCAACTCATGTTT 59.721 33.333 15.77 0.00 37.78 2.83
2640 6433 9.250624 GACCAGATGACTAAACACATATTCTAC 57.749 37.037 0.00 0.00 0.00 2.59
2652 9371 7.120923 ACACATATTCTACTATTGGACCGTT 57.879 36.000 0.00 0.00 0.00 4.44
2654 9373 8.139989 ACACATATTCTACTATTGGACCGTTAC 58.860 37.037 0.00 0.00 0.00 2.50
2661 9380 2.660670 ATTGGACCGTTACCCAAACA 57.339 45.000 0.00 0.00 44.60 2.83
2663 9382 0.108963 TGGACCGTTACCCAAACAGG 59.891 55.000 0.00 0.00 38.03 4.00
2691 9410 0.979665 ATCCCATGCTACCATCTCCG 59.020 55.000 0.00 0.00 0.00 4.63
2700 9419 1.338337 CTACCATCTCCGAGCGATTGT 59.662 52.381 0.00 0.00 0.00 2.71
2702 9421 1.964223 ACCATCTCCGAGCGATTGTAT 59.036 47.619 0.00 0.00 0.00 2.29
2754 9473 1.337823 GGCTGAGTAACGACCATGTGT 60.338 52.381 0.00 0.00 0.00 3.72
2775 9500 2.168496 GAATCCATCCAGATGCCATGG 58.832 52.381 7.63 7.63 38.83 3.66
2778 9503 1.906824 CATCCAGATGCCATGGCCC 60.907 63.158 33.44 23.99 41.09 5.80
2779 9504 2.397051 ATCCAGATGCCATGGCCCA 61.397 57.895 33.44 17.20 41.09 5.36
2784 9509 0.325860 AGATGCCATGGCCCACAAAT 60.326 50.000 33.44 19.11 41.09 2.32
2785 9510 0.542805 GATGCCATGGCCCACAAATT 59.457 50.000 33.44 8.13 41.09 1.82
2786 9511 0.993470 ATGCCATGGCCCACAAATTT 59.007 45.000 33.44 4.50 41.09 1.82
2788 9513 1.144503 TGCCATGGCCCACAAATTTTT 59.855 42.857 33.44 0.00 41.09 1.94
2864 9592 4.968259 AGTAATGCACACACTCCAACTTA 58.032 39.130 0.00 0.00 0.00 2.24
2883 9615 9.653287 CCAACTTAAATATGTGTCTGTCTTAGA 57.347 33.333 0.00 0.00 0.00 2.10
2899 9631 7.844779 TCTGTCTTAGACTCTACCCCATTTAAT 59.155 37.037 13.86 0.00 33.15 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.280186 GCCACGTCATCGATCCCC 60.280 66.667 0.00 0.00 40.62 4.81
1 2 0.742990 TTTGCCACGTCATCGATCCC 60.743 55.000 0.00 0.00 40.62 3.85
3 4 2.505866 GTTTTTGCCACGTCATCGATC 58.494 47.619 0.00 0.00 40.62 3.69
4 5 1.199097 GGTTTTTGCCACGTCATCGAT 59.801 47.619 0.00 0.00 40.62 3.59
5 6 0.589223 GGTTTTTGCCACGTCATCGA 59.411 50.000 0.00 0.00 40.62 3.59
6 7 0.309302 TGGTTTTTGCCACGTCATCG 59.691 50.000 0.00 0.00 43.34 3.84
7 8 2.327568 CATGGTTTTTGCCACGTCATC 58.672 47.619 0.00 0.00 41.94 2.92
8 9 1.000731 CCATGGTTTTTGCCACGTCAT 59.999 47.619 2.57 0.00 41.94 3.06
9 10 0.387202 CCATGGTTTTTGCCACGTCA 59.613 50.000 2.57 0.00 41.94 4.35
10 11 0.319469 CCCATGGTTTTTGCCACGTC 60.319 55.000 11.73 0.00 41.94 4.34
11 12 1.745264 CCCATGGTTTTTGCCACGT 59.255 52.632 11.73 0.00 41.94 4.49
12 13 1.667510 GCCCATGGTTTTTGCCACG 60.668 57.895 11.73 0.00 41.94 4.94
13 14 1.302431 GGCCCATGGTTTTTGCCAC 60.302 57.895 20.47 0.00 41.94 5.01
14 15 3.155750 GGCCCATGGTTTTTGCCA 58.844 55.556 20.47 0.00 41.76 4.92
15 16 1.003476 CTGGCCCATGGTTTTTGCC 60.003 57.895 19.05 19.05 42.49 4.52
16 17 1.003476 CCTGGCCCATGGTTTTTGC 60.003 57.895 11.73 6.16 0.00 3.68
17 18 1.003476 GCCTGGCCCATGGTTTTTG 60.003 57.895 11.73 0.00 0.00 2.44
18 19 2.223443 GGCCTGGCCCATGGTTTTT 61.223 57.895 27.77 0.00 44.06 1.94
19 20 2.607442 GGCCTGGCCCATGGTTTT 60.607 61.111 27.77 0.00 44.06 2.43
57 58 1.024271 CGTGGGGTGGCATTTCTATG 58.976 55.000 0.00 0.00 34.76 2.23
58 59 0.106719 CCGTGGGGTGGCATTTCTAT 60.107 55.000 0.00 0.00 0.00 1.98
59 60 1.301623 CCGTGGGGTGGCATTTCTA 59.698 57.895 0.00 0.00 0.00 2.10
60 61 2.035626 CCGTGGGGTGGCATTTCT 59.964 61.111 0.00 0.00 0.00 2.52
61 62 3.068064 CCCGTGGGGTGGCATTTC 61.068 66.667 0.00 0.00 38.25 2.17
62 63 3.585428 TCCCGTGGGGTGGCATTT 61.585 61.111 4.81 0.00 44.74 2.32
63 64 4.360405 GTCCCGTGGGGTGGCATT 62.360 66.667 4.81 0.00 44.74 3.56
84 85 2.278596 ATCGATCCGTGGCGTTCG 60.279 61.111 0.00 5.26 33.92 3.95
85 86 1.226859 TCATCGATCCGTGGCGTTC 60.227 57.895 0.00 0.00 0.00 3.95
86 87 1.518572 GTCATCGATCCGTGGCGTT 60.519 57.895 0.00 0.00 0.00 4.84
87 88 2.104331 GTCATCGATCCGTGGCGT 59.896 61.111 0.00 0.00 0.00 5.68
88 89 3.024609 CGTCATCGATCCGTGGCG 61.025 66.667 0.00 4.85 39.71 5.69
89 90 2.104331 ACGTCATCGATCCGTGGC 59.896 61.111 16.40 0.00 40.62 5.01
90 91 3.997561 CACGTCATCGATCCGTGG 58.002 61.111 27.39 15.55 45.97 4.94
92 93 0.098905 CTGTCACGTCATCGATCCGT 59.901 55.000 12.53 12.53 40.62 4.69
93 94 1.202973 GCTGTCACGTCATCGATCCG 61.203 60.000 11.37 11.37 40.62 4.18
94 95 1.202973 CGCTGTCACGTCATCGATCC 61.203 60.000 0.00 0.00 40.62 3.36
95 96 1.802300 GCGCTGTCACGTCATCGATC 61.802 60.000 0.00 0.00 40.62 3.69
96 97 1.874019 GCGCTGTCACGTCATCGAT 60.874 57.895 0.00 0.00 40.62 3.59
97 98 2.504026 GCGCTGTCACGTCATCGA 60.504 61.111 0.00 0.00 40.62 3.59
98 99 3.545481 GGCGCTGTCACGTCATCG 61.545 66.667 7.64 0.00 37.66 3.84
99 100 3.545481 CGGCGCTGTCACGTCATC 61.545 66.667 8.45 0.00 37.57 2.92
113 114 4.925576 ACGTCATCGATCCGCGGC 62.926 66.667 23.51 6.46 41.33 6.53
114 115 2.726180 GACGTCATCGATCCGCGG 60.726 66.667 22.12 22.12 41.33 6.46
123 124 2.254459 CATAGCTATGCCGACGTCATC 58.746 52.381 20.37 6.73 0.00 2.92
124 125 2.354109 CATAGCTATGCCGACGTCAT 57.646 50.000 20.37 4.86 0.00 3.06
125 126 3.865700 CATAGCTATGCCGACGTCA 57.134 52.632 20.37 0.00 0.00 4.35
151 152 4.807039 CCGACGGGCTAACGGTGG 62.807 72.222 5.81 0.00 41.47 4.61
169 170 3.620300 TTGACGGCGTCAGGCTACG 62.620 63.158 36.94 10.73 43.69 3.51
170 171 1.373748 TTTGACGGCGTCAGGCTAC 60.374 57.895 36.94 13.88 43.69 3.58
171 172 1.373748 GTTTGACGGCGTCAGGCTA 60.374 57.895 36.94 23.35 43.69 3.93
172 173 2.665185 GTTTGACGGCGTCAGGCT 60.665 61.111 36.94 3.60 43.69 4.58
173 174 2.665185 AGTTTGACGGCGTCAGGC 60.665 61.111 36.94 31.30 43.69 4.85
174 175 2.954753 GCAGTTTGACGGCGTCAGG 61.955 63.158 36.94 27.86 43.69 3.86
175 176 2.551270 GCAGTTTGACGGCGTCAG 59.449 61.111 36.94 27.64 43.69 3.51
176 177 2.970324 GGCAGTTTGACGGCGTCA 60.970 61.111 36.29 36.29 40.24 4.35
209 210 4.295119 ATATCGCGTGGGCCCGTC 62.295 66.667 19.37 12.21 35.02 4.79
210 211 4.602259 CATATCGCGTGGGCCCGT 62.602 66.667 19.37 0.80 35.02 5.28
214 215 4.961511 TCGGCATATCGCGTGGGC 62.962 66.667 5.77 6.12 43.84 5.36
215 216 3.036084 GTCGGCATATCGCGTGGG 61.036 66.667 5.77 0.00 43.84 4.61
216 217 3.394874 CGTCGGCATATCGCGTGG 61.395 66.667 5.77 0.00 43.84 4.94
217 218 3.394874 CCGTCGGCATATCGCGTG 61.395 66.667 5.77 0.00 43.84 5.34
228 229 1.286260 GCATAGAGTAGGCCGTCGG 59.714 63.158 6.99 6.99 0.00 4.79
229 230 1.286260 GGCATAGAGTAGGCCGTCG 59.714 63.158 0.00 0.00 46.38 5.12
234 235 1.286260 CCGTCGGCATAGAGTAGGC 59.714 63.158 0.00 0.00 34.16 3.93
251 252 1.670083 GAATATACCCACGGCGGCC 60.670 63.158 13.24 9.54 0.00 6.13
252 253 0.604578 TAGAATATACCCACGGCGGC 59.395 55.000 13.24 0.00 0.00 6.53
253 254 2.929592 GCTTAGAATATACCCACGGCGG 60.930 54.545 13.24 0.00 0.00 6.13
254 255 2.288579 TGCTTAGAATATACCCACGGCG 60.289 50.000 4.80 4.80 0.00 6.46
255 256 3.396260 TGCTTAGAATATACCCACGGC 57.604 47.619 0.00 0.00 0.00 5.68
256 257 3.739300 CGTTGCTTAGAATATACCCACGG 59.261 47.826 0.00 0.00 0.00 4.94
257 258 3.183775 GCGTTGCTTAGAATATACCCACG 59.816 47.826 0.00 0.00 0.00 4.94
258 259 3.497262 GGCGTTGCTTAGAATATACCCAC 59.503 47.826 0.00 0.00 0.00 4.61
259 260 3.735591 GGCGTTGCTTAGAATATACCCA 58.264 45.455 0.00 0.00 0.00 4.51
260 261 2.735134 CGGCGTTGCTTAGAATATACCC 59.265 50.000 0.00 0.00 0.00 3.69
261 262 3.427863 GTCGGCGTTGCTTAGAATATACC 59.572 47.826 6.85 0.00 0.00 2.73
262 263 3.119136 CGTCGGCGTTGCTTAGAATATAC 59.881 47.826 6.85 0.00 0.00 1.47
263 264 3.003585 TCGTCGGCGTTGCTTAGAATATA 59.996 43.478 10.18 0.00 39.49 0.86
264 265 2.124903 CGTCGGCGTTGCTTAGAATAT 58.875 47.619 6.85 0.00 0.00 1.28
265 266 1.132834 TCGTCGGCGTTGCTTAGAATA 59.867 47.619 10.18 0.00 39.49 1.75
266 267 0.108992 TCGTCGGCGTTGCTTAGAAT 60.109 50.000 10.18 0.00 39.49 2.40
267 268 1.005294 GTCGTCGGCGTTGCTTAGAA 61.005 55.000 10.18 0.00 39.49 2.10
268 269 1.443194 GTCGTCGGCGTTGCTTAGA 60.443 57.895 10.18 0.00 39.49 2.10
269 270 1.443872 AGTCGTCGGCGTTGCTTAG 60.444 57.895 10.18 0.00 39.49 2.18
270 271 1.731613 CAGTCGTCGGCGTTGCTTA 60.732 57.895 10.18 0.00 39.49 3.09
271 272 2.765250 ATCAGTCGTCGGCGTTGCTT 62.765 55.000 10.18 0.00 39.49 3.91
272 273 3.282745 ATCAGTCGTCGGCGTTGCT 62.283 57.895 10.18 3.50 39.49 3.91
273 274 2.789203 GATCAGTCGTCGGCGTTGC 61.789 63.158 10.18 0.81 39.49 4.17
274 275 0.732880 AAGATCAGTCGTCGGCGTTG 60.733 55.000 10.18 9.90 39.49 4.10
275 276 0.038526 AAAGATCAGTCGTCGGCGTT 60.039 50.000 10.18 0.00 39.49 4.84
276 277 0.732880 CAAAGATCAGTCGTCGGCGT 60.733 55.000 10.18 0.00 39.49 5.68
277 278 1.991430 CAAAGATCAGTCGTCGGCG 59.009 57.895 1.15 1.15 39.92 6.46
278 279 1.696832 GGCAAAGATCAGTCGTCGGC 61.697 60.000 0.00 0.00 0.00 5.54
279 280 1.413767 CGGCAAAGATCAGTCGTCGG 61.414 60.000 0.00 0.00 0.00 4.79
280 281 0.456142 TCGGCAAAGATCAGTCGTCG 60.456 55.000 6.70 0.39 33.97 5.12
281 282 0.992802 GTCGGCAAAGATCAGTCGTC 59.007 55.000 6.70 0.00 33.97 4.20
282 283 0.732880 CGTCGGCAAAGATCAGTCGT 60.733 55.000 6.70 0.00 33.97 4.34
283 284 1.413767 CCGTCGGCAAAGATCAGTCG 61.414 60.000 0.00 0.00 0.00 4.18
284 285 2.373938 CCGTCGGCAAAGATCAGTC 58.626 57.895 0.00 0.00 0.00 3.51
285 286 4.598257 CCGTCGGCAAAGATCAGT 57.402 55.556 0.00 0.00 0.00 3.41
303 304 3.616721 CCTCTATGCCGACGGGGG 61.617 72.222 17.22 0.00 35.78 5.40
304 305 3.616721 CCCTCTATGCCGACGGGG 61.617 72.222 17.22 6.83 39.58 5.73
305 306 4.301027 GCCCTCTATGCCGACGGG 62.301 72.222 17.22 0.00 37.97 5.28
306 307 4.301027 GGCCCTCTATGCCGACGG 62.301 72.222 10.29 10.29 39.48 4.79
312 313 4.285851 GCGTATGGCCCTCTATGC 57.714 61.111 0.00 2.73 34.80 3.14
329 330 2.884207 GCGTAGAAAGGCCGTCGG 60.884 66.667 6.99 6.99 0.00 4.79
330 331 2.884207 GGCGTAGAAAGGCCGTCG 60.884 66.667 0.00 0.00 45.99 5.12
335 336 2.884207 CCGTCGGCGTAGAAAGGC 60.884 66.667 9.28 0.00 36.15 4.35
336 337 2.884207 GCCGTCGGCGTAGAAAGG 60.884 66.667 22.50 0.00 39.62 3.11
346 347 2.511600 CCCAGCTAAAGCCGTCGG 60.512 66.667 6.99 6.99 43.38 4.79
347 348 3.195698 GCCCAGCTAAAGCCGTCG 61.196 66.667 0.00 0.00 43.38 5.12
348 349 2.824489 GGCCCAGCTAAAGCCGTC 60.824 66.667 5.19 0.00 43.38 4.79
351 352 2.824489 GACGGCCCAGCTAAAGCC 60.824 66.667 10.13 10.13 43.38 4.35
352 353 3.195698 CGACGGCCCAGCTAAAGC 61.196 66.667 0.00 0.00 42.49 3.51
353 354 2.511600 CCGACGGCCCAGCTAAAG 60.512 66.667 0.00 0.00 0.00 1.85
354 355 4.090588 CCCGACGGCCCAGCTAAA 62.091 66.667 8.86 0.00 0.00 1.85
359 360 4.235762 CATACCCCGACGGCCCAG 62.236 72.222 8.86 0.00 33.26 4.45
371 372 0.613260 TCGGCATAGATGGGCATACC 59.387 55.000 0.00 0.00 40.81 2.73
372 373 1.726853 GTCGGCATAGATGGGCATAC 58.273 55.000 0.00 0.00 0.00 2.39
373 374 0.246360 CGTCGGCATAGATGGGCATA 59.754 55.000 0.00 0.00 0.00 3.14
374 375 1.004560 CGTCGGCATAGATGGGCAT 60.005 57.895 0.00 0.00 0.00 4.40
375 376 2.421314 CGTCGGCATAGATGGGCA 59.579 61.111 0.00 0.00 0.00 5.36
376 377 2.357517 CCGTCGGCATAGATGGGC 60.358 66.667 0.00 0.00 42.22 5.36
378 379 2.343758 CCCCGTCGGCATAGATGG 59.656 66.667 5.50 7.19 44.79 3.51
379 380 2.343758 CCCCCGTCGGCATAGATG 59.656 66.667 5.50 0.00 0.00 2.90
397 398 0.099791 AAAACTTGTGTTGCCGACGG 59.900 50.000 10.29 10.29 36.39 4.79
398 399 1.843753 GAAAAACTTGTGTTGCCGACG 59.156 47.619 0.00 0.00 36.39 5.12
399 400 2.851824 CAGAAAAACTTGTGTTGCCGAC 59.148 45.455 0.00 0.00 36.39 4.79
400 401 2.159310 CCAGAAAAACTTGTGTTGCCGA 60.159 45.455 0.00 0.00 36.39 5.54
401 402 2.192624 CCAGAAAAACTTGTGTTGCCG 58.807 47.619 0.00 0.00 36.39 5.69
402 403 3.245518 ACCAGAAAAACTTGTGTTGCC 57.754 42.857 0.00 0.00 36.39 4.52
403 404 4.798387 CACTACCAGAAAAACTTGTGTTGC 59.202 41.667 0.00 0.00 36.39 4.17
404 405 6.189677 TCACTACCAGAAAAACTTGTGTTG 57.810 37.500 0.00 0.00 36.39 3.33
405 406 5.163652 GCTCACTACCAGAAAAACTTGTGTT 60.164 40.000 0.00 0.00 38.16 3.32
406 407 4.335594 GCTCACTACCAGAAAAACTTGTGT 59.664 41.667 0.00 0.00 0.00 3.72
407 408 4.261197 GGCTCACTACCAGAAAAACTTGTG 60.261 45.833 0.00 0.00 0.00 3.33
408 409 3.883489 GGCTCACTACCAGAAAAACTTGT 59.117 43.478 0.00 0.00 0.00 3.16
409 410 3.058914 CGGCTCACTACCAGAAAAACTTG 60.059 47.826 0.00 0.00 0.00 3.16
410 411 3.139077 CGGCTCACTACCAGAAAAACTT 58.861 45.455 0.00 0.00 0.00 2.66
411 412 2.767505 CGGCTCACTACCAGAAAAACT 58.232 47.619 0.00 0.00 0.00 2.66
412 413 1.197036 GCGGCTCACTACCAGAAAAAC 59.803 52.381 0.00 0.00 0.00 2.43
413 414 1.202710 TGCGGCTCACTACCAGAAAAA 60.203 47.619 0.00 0.00 0.00 1.94
414 415 0.394938 TGCGGCTCACTACCAGAAAA 59.605 50.000 0.00 0.00 0.00 2.29
415 416 0.037326 CTGCGGCTCACTACCAGAAA 60.037 55.000 0.00 0.00 0.00 2.52
416 417 1.591703 CTGCGGCTCACTACCAGAA 59.408 57.895 0.00 0.00 0.00 3.02
417 418 3.006756 GCTGCGGCTCACTACCAGA 62.007 63.158 11.21 0.00 35.22 3.86
418 419 2.510238 GCTGCGGCTCACTACCAG 60.510 66.667 11.21 0.00 35.22 4.00
428 429 0.386478 CAGTTCTTTTCAGCTGCGGC 60.386 55.000 10.33 10.33 39.06 6.53
429 430 0.386478 GCAGTTCTTTTCAGCTGCGG 60.386 55.000 9.47 0.00 43.60 5.69
430 431 3.083213 GCAGTTCTTTTCAGCTGCG 57.917 52.632 9.47 0.00 43.60 5.18
432 433 2.161211 GCCTAGCAGTTCTTTTCAGCTG 59.839 50.000 7.63 7.63 36.80 4.24
433 434 2.431454 GCCTAGCAGTTCTTTTCAGCT 58.569 47.619 0.00 0.00 39.22 4.24
434 435 1.470494 GGCCTAGCAGTTCTTTTCAGC 59.530 52.381 0.00 0.00 0.00 4.26
435 436 2.087646 GGGCCTAGCAGTTCTTTTCAG 58.912 52.381 0.84 0.00 0.00 3.02
436 437 1.705186 AGGGCCTAGCAGTTCTTTTCA 59.295 47.619 2.82 0.00 0.00 2.69
437 438 2.498644 AGGGCCTAGCAGTTCTTTTC 57.501 50.000 2.82 0.00 0.00 2.29
438 439 4.263949 ACATTAGGGCCTAGCAGTTCTTTT 60.264 41.667 13.99 0.00 0.00 2.27
439 440 3.267031 ACATTAGGGCCTAGCAGTTCTTT 59.733 43.478 13.99 0.00 0.00 2.52
440 441 2.846827 ACATTAGGGCCTAGCAGTTCTT 59.153 45.455 13.99 0.00 0.00 2.52
441 442 2.482494 ACATTAGGGCCTAGCAGTTCT 58.518 47.619 13.99 0.00 0.00 3.01
442 443 3.283259 AACATTAGGGCCTAGCAGTTC 57.717 47.619 13.99 0.00 0.00 3.01
443 444 3.010138 TCAAACATTAGGGCCTAGCAGTT 59.990 43.478 13.99 15.68 0.00 3.16
444 445 2.576191 TCAAACATTAGGGCCTAGCAGT 59.424 45.455 13.99 10.68 0.00 4.40
445 446 3.281727 TCAAACATTAGGGCCTAGCAG 57.718 47.619 13.99 10.05 0.00 4.24
446 447 3.053693 ACATCAAACATTAGGGCCTAGCA 60.054 43.478 13.99 0.00 0.00 3.49
447 448 3.555966 ACATCAAACATTAGGGCCTAGC 58.444 45.455 13.99 0.00 0.00 3.42
448 449 5.041191 AGACATCAAACATTAGGGCCTAG 57.959 43.478 13.99 5.79 0.00 3.02
449 450 4.442893 CGAGACATCAAACATTAGGGCCTA 60.443 45.833 9.81 9.81 0.00 3.93
450 451 3.682718 CGAGACATCAAACATTAGGGCCT 60.683 47.826 12.58 12.58 0.00 5.19
451 452 2.614057 CGAGACATCAAACATTAGGGCC 59.386 50.000 0.00 0.00 0.00 5.80
452 453 2.614057 CCGAGACATCAAACATTAGGGC 59.386 50.000 0.00 0.00 0.00 5.19
453 454 4.122776 CTCCGAGACATCAAACATTAGGG 58.877 47.826 0.00 0.00 0.00 3.53
454 455 4.759782 ACTCCGAGACATCAAACATTAGG 58.240 43.478 1.33 0.00 0.00 2.69
455 456 8.331022 CAAATACTCCGAGACATCAAACATTAG 58.669 37.037 1.33 0.00 0.00 1.73
456 457 8.038351 TCAAATACTCCGAGACATCAAACATTA 58.962 33.333 1.33 0.00 0.00 1.90
457 458 6.878923 TCAAATACTCCGAGACATCAAACATT 59.121 34.615 1.33 0.00 0.00 2.71
458 459 6.406370 TCAAATACTCCGAGACATCAAACAT 58.594 36.000 1.33 0.00 0.00 2.71
459 460 5.789521 TCAAATACTCCGAGACATCAAACA 58.210 37.500 1.33 0.00 0.00 2.83
460 461 5.292101 CCTCAAATACTCCGAGACATCAAAC 59.708 44.000 1.33 0.00 0.00 2.93
461 462 5.046591 ACCTCAAATACTCCGAGACATCAAA 60.047 40.000 1.33 0.00 0.00 2.69
462 463 4.466370 ACCTCAAATACTCCGAGACATCAA 59.534 41.667 1.33 0.00 0.00 2.57
463 464 4.023980 ACCTCAAATACTCCGAGACATCA 58.976 43.478 1.33 0.00 0.00 3.07
464 465 4.657436 ACCTCAAATACTCCGAGACATC 57.343 45.455 1.33 0.00 0.00 3.06
465 466 4.466370 TCAACCTCAAATACTCCGAGACAT 59.534 41.667 1.33 0.00 0.00 3.06
466 467 3.830178 TCAACCTCAAATACTCCGAGACA 59.170 43.478 1.33 0.00 0.00 3.41
467 468 4.425520 CTCAACCTCAAATACTCCGAGAC 58.574 47.826 1.33 0.00 0.00 3.36
468 469 3.119101 GCTCAACCTCAAATACTCCGAGA 60.119 47.826 1.33 0.00 0.00 4.04
469 470 3.190874 GCTCAACCTCAAATACTCCGAG 58.809 50.000 0.00 0.00 0.00 4.63
470 471 2.093658 GGCTCAACCTCAAATACTCCGA 60.094 50.000 0.00 0.00 34.51 4.55
471 472 2.280628 GGCTCAACCTCAAATACTCCG 58.719 52.381 0.00 0.00 34.51 4.63
472 473 2.239907 AGGGCTCAACCTCAAATACTCC 59.760 50.000 0.00 0.00 35.43 3.85
473 474 3.636153 AGGGCTCAACCTCAAATACTC 57.364 47.619 0.00 0.00 35.43 2.59
482 483 4.936685 AATAGAAAAGAGGGCTCAACCT 57.063 40.909 0.00 0.00 45.57 3.50
483 484 5.984695 AAAATAGAAAAGAGGGCTCAACC 57.015 39.130 0.00 0.00 37.93 3.77
518 519 2.416547 TCCCGTACTAAAAGAGTCGTCG 59.583 50.000 0.00 0.00 39.81 5.12
519 520 4.629251 ATCCCGTACTAAAAGAGTCGTC 57.371 45.455 0.00 0.00 39.81 4.20
521 522 6.501781 ACAATATCCCGTACTAAAAGAGTCG 58.498 40.000 0.00 0.00 39.81 4.18
549 550 5.994054 AGCACGCAACATTATATTGAGAGAT 59.006 36.000 1.71 0.00 31.99 2.75
602 603 1.375908 GCCTCACAGATTGCGTCCA 60.376 57.895 0.00 0.00 0.00 4.02
614 615 3.756963 GGAATTTATAATCCCCGCCTCAC 59.243 47.826 0.00 0.00 0.00 3.51
655 656 1.522668 TGATCGAACTTGGTGCTTGG 58.477 50.000 0.00 0.00 0.00 3.61
669 670 2.881074 ACCATGACTCGAGTTTGATCG 58.119 47.619 21.08 10.29 44.07 3.69
673 674 1.136252 CGCAACCATGACTCGAGTTTG 60.136 52.381 21.08 19.44 0.00 2.93
692 693 2.667199 AACGTTTCCCCGGCTTCG 60.667 61.111 0.00 0.00 0.00 3.79
696 697 2.404186 GGATCAACGTTTCCCCGGC 61.404 63.158 7.66 0.00 0.00 6.13
697 698 1.003112 TGGATCAACGTTTCCCCGG 60.003 57.895 14.90 0.00 0.00 5.73
699 700 1.313091 GCCTGGATCAACGTTTCCCC 61.313 60.000 14.90 9.08 0.00 4.81
753 754 0.880278 TGAGGTTGACGCTTCACTGC 60.880 55.000 0.00 0.00 0.00 4.40
773 774 1.788886 CTTTGCTTGAAAGAAAGGCGC 59.211 47.619 0.00 0.00 43.50 6.53
782 783 1.282570 CGGCGAGCTTTGCTTGAAA 59.717 52.632 0.00 0.00 42.27 2.69
784 785 3.049674 CCGGCGAGCTTTGCTTGA 61.050 61.111 9.30 0.00 42.27 3.02
785 786 3.031964 CTCCGGCGAGCTTTGCTTG 62.032 63.158 9.30 2.63 39.88 4.01
973 983 4.240323 TCCTCTTCCCTTACCTCACTTTT 58.760 43.478 0.00 0.00 0.00 2.27
982 992 5.741673 GCATCATCTTCTCCTCTTCCCTTAC 60.742 48.000 0.00 0.00 0.00 2.34
1051 1061 2.205074 GTGGTAGCCGAACATGATGAG 58.795 52.381 0.00 0.00 0.00 2.90
1294 1305 4.681978 GCCAGGTTCGTGGACGCT 62.682 66.667 14.54 0.00 40.44 5.07
1497 1508 0.388520 CTAAGGTTTGGCAAAGCGGC 60.389 55.000 29.75 12.24 43.34 6.53
1498 1509 1.243902 TCTAAGGTTTGGCAAAGCGG 58.756 50.000 29.75 23.69 43.34 5.52
1500 1511 6.093404 GTCTTAATCTAAGGTTTGGCAAAGC 58.907 40.000 29.40 29.40 39.10 3.51
1501 1512 6.621613 GGTCTTAATCTAAGGTTTGGCAAAG 58.378 40.000 13.94 0.69 36.45 2.77
1502 1513 5.182380 CGGTCTTAATCTAAGGTTTGGCAAA 59.818 40.000 8.93 8.93 36.45 3.68
1503 1514 4.698304 CGGTCTTAATCTAAGGTTTGGCAA 59.302 41.667 0.00 0.00 36.45 4.52
1504 1515 4.020039 TCGGTCTTAATCTAAGGTTTGGCA 60.020 41.667 0.00 0.00 36.45 4.92
1505 1516 4.510571 TCGGTCTTAATCTAAGGTTTGGC 58.489 43.478 0.00 0.00 36.45 4.52
1579 1596 2.037136 CAGGAAGCTGGCTTGGACG 61.037 63.158 12.79 0.00 36.26 4.79
1729 1746 2.165641 TGAGCAGACGAACATCGGTATT 59.834 45.455 4.66 0.00 45.59 1.89
1763 1780 2.093500 TGTCCAGCATGTGTAGGATGAC 60.093 50.000 0.00 0.00 31.91 3.06
1816 1833 2.754648 AGGCCGTTTCCTGACTGTA 58.245 52.632 0.00 0.00 34.56 2.74
1913 1930 2.699954 ACTGAAGAATGTTACAGGCGG 58.300 47.619 0.00 0.00 35.08 6.13
1971 1988 1.227999 ATGTGACGGAACTTGGCACG 61.228 55.000 0.00 0.00 32.39 5.34
1996 2013 4.397103 TGAGAATTGTGTGGCTGATCATTC 59.603 41.667 0.00 0.00 0.00 2.67
2049 2100 4.412796 TGATTCCGATTTCTCTGCATCT 57.587 40.909 0.00 0.00 0.00 2.90
2161 2438 4.278419 CGATAGGAATTTTGGATGGAACCC 59.722 45.833 0.00 0.00 0.00 4.11
2349 2627 3.118542 CAAGAAGCACAAGAAAGGTTGC 58.881 45.455 0.00 0.00 0.00 4.17
2378 2656 6.656632 TCTGTCCATAACTAGCTTCCATAG 57.343 41.667 0.00 0.00 0.00 2.23
2379 2657 6.611642 AGTTCTGTCCATAACTAGCTTCCATA 59.388 38.462 0.00 0.00 34.23 2.74
2414 2737 2.811410 TCCTTAGTCTAACGCCTCCAA 58.189 47.619 0.00 0.00 0.00 3.53
2501 2824 7.278424 GCTTAACAAAATGGTTATGTGCATCAT 59.722 33.333 0.00 0.00 40.25 2.45
2511 2834 8.116651 TGCTATCTTGCTTAACAAAATGGTTA 57.883 30.769 0.00 0.00 37.96 2.85
2521 2844 6.736853 CGTACTTTGTTGCTATCTTGCTTAAC 59.263 38.462 0.00 0.00 0.00 2.01
2563 6355 4.536065 CTTTACATTCGAGTTTGCTTGCA 58.464 39.130 0.00 0.00 0.00 4.08
2579 6371 8.908903 ACTGTTGTGTCATTTTATTCCTTTACA 58.091 29.630 0.00 0.00 0.00 2.41
2596 6388 6.597562 TCTGGTCCTATTTTAACTGTTGTGT 58.402 36.000 2.69 0.00 0.00 3.72
2640 6433 3.677190 TGTTTGGGTAACGGTCCAATAG 58.323 45.455 0.00 0.00 41.96 1.73
2652 9371 4.322650 GGATACGTACAACCTGTTTGGGTA 60.323 45.833 0.00 0.00 39.84 3.69
2654 9373 3.004862 GGATACGTACAACCTGTTTGGG 58.995 50.000 0.00 0.00 39.84 4.12
2661 9380 2.116238 AGCATGGGATACGTACAACCT 58.884 47.619 0.00 0.00 37.60 3.50
2663 9382 3.181473 TGGTAGCATGGGATACGTACAAC 60.181 47.826 0.00 0.00 36.76 3.32
2700 9419 4.474651 CAGGGAACATATGGCCTATGGATA 59.525 45.833 19.84 5.01 41.41 2.59
2702 9421 2.644299 CAGGGAACATATGGCCTATGGA 59.356 50.000 19.84 0.00 41.41 3.41
2754 9473 2.490168 CCATGGCATCTGGATGGATTCA 60.490 50.000 0.00 0.00 39.29 2.57
2788 9513 9.644993 CGTTATATTTAATCGAAGCATCACAAA 57.355 29.630 0.00 0.00 0.00 2.83
2883 9615 5.163088 GGGACATGATTAAATGGGGTAGAGT 60.163 44.000 0.00 0.00 31.46 3.24
2899 9631 5.512942 TCTCCAGTTTATTTGGGACATGA 57.487 39.130 0.00 0.00 39.30 3.07


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

AutoCloner maintained by Alex Coulton.