Multiple sequence alignment - TraesCS4A01G177200

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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 TraesCS4A01G177200 chr4A 100.000 2562 0 0 1 2562 448747029 448749590 0.000000e+00 4732.0
1 TraesCS4A01G177200 chr4B 89.005 1146 63 24 512 1637 184890614 184889512 0.000000e+00 1360.0
2 TraesCS4A01G177200 chr4B 76.702 940 147 41 1644 2535 665465319 665464404 8.350000e-125 457.0
3 TraesCS4A01G177200 chr4B 90.741 54 5 0 11 64 581196167 581196114 3.540000e-09 73.1
4 TraesCS4A01G177200 chr4D 93.581 888 27 10 512 1397 121981605 121980746 0.000000e+00 1297.0
5 TraesCS4A01G177200 chr4D 88.034 234 9 4 1404 1637 121980766 121980552 2.530000e-65 259.0
6 TraesCS4A01G177200 chr6B 80.881 931 120 37 1644 2562 704048094 704048978 0.000000e+00 680.0
7 TraesCS4A01G177200 chr5D 78.879 928 145 28 1644 2535 356087183 356086271 4.750000e-162 580.0
8 TraesCS4A01G177200 chr5D 91.667 204 17 0 283 486 469246972 469247175 1.500000e-72 283.0
9 TraesCS4A01G177200 chr5D 90.476 63 6 0 2 64 445875252 445875314 1.630000e-12 84.2
10 TraesCS4A01G177200 chr3A 76.571 939 157 34 1645 2535 747671468 747670545 8.350000e-125 457.0
11 TraesCS4A01G177200 chr3A 76.508 945 143 45 1641 2535 540042192 540043107 2.340000e-120 442.0
12 TraesCS4A01G177200 chr3A 76.101 954 156 42 1644 2562 699165722 699164806 1.410000e-117 433.0
13 TraesCS4A01G177200 chr3A 91.262 206 18 0 283 488 535225726 535225521 5.400000e-72 281.0
14 TraesCS4A01G177200 chr3A 79.149 235 38 9 2280 2508 459070106 459070335 4.420000e-33 152.0
15 TraesCS4A01G177200 chr3A 80.000 195 33 5 2280 2471 459069431 459069622 3.440000e-29 139.0
16 TraesCS4A01G177200 chr3B 76.633 903 146 42 1647 2509 161826492 161825615 3.030000e-119 438.0
17 TraesCS4A01G177200 chr3B 76.368 914 153 34 1644 2510 828798622 828797725 1.410000e-117 433.0
18 TraesCS4A01G177200 chr3B 89.720 214 21 1 283 496 42088514 42088302 3.250000e-69 272.0
19 TraesCS4A01G177200 chr3B 79.817 218 36 7 2280 2493 545188666 545188879 4.420000e-33 152.0
20 TraesCS4A01G177200 chr3B 80.000 215 34 8 2283 2493 680227238 680227029 1.590000e-32 150.0
21 TraesCS4A01G177200 chr7A 76.269 906 146 40 1641 2514 665146641 665147509 3.940000e-113 418.0
22 TraesCS4A01G177200 chr7B 79.450 618 103 19 1645 2245 20389033 20388423 1.420000e-112 416.0
23 TraesCS4A01G177200 chr7B 91.176 204 18 0 285 488 724574416 724574619 6.980000e-71 278.0
24 TraesCS4A01G177200 chr2B 91.827 208 17 0 281 488 418970528 418970321 8.970000e-75 291.0
25 TraesCS4A01G177200 chr2B 79.433 141 10 9 61 183 470477629 470477768 5.880000e-12 82.4
26 TraesCS4A01G177200 chr2A 91.304 207 18 0 283 489 177665791 177665585 1.500000e-72 283.0
27 TraesCS4A01G177200 chr2A 91.304 207 18 0 283 489 258346762 258346968 1.500000e-72 283.0
28 TraesCS4A01G177200 chr1B 89.035 228 24 1 283 509 626134025 626133798 5.400000e-72 281.0
29 TraesCS4A01G177200 chr6D 89.041 219 24 0 281 499 143406456 143406238 3.250000e-69 272.0
30 TraesCS4A01G177200 chr5A 79.070 215 35 9 2283 2493 474383665 474383457 3.440000e-29 139.0
31 TraesCS4A01G177200 chr5A 81.379 145 23 4 2 144 657400910 657401052 5.790000e-22 115.0
32 TraesCS4A01G177200 chr1A 80.272 147 23 5 1 144 373349653 373349510 3.490000e-19 106.0
33 TraesCS4A01G177200 chr2D 80.128 156 13 10 70 208 378377145 378376991 1.620000e-17 100.0
34 TraesCS4A01G177200 chr1D 87.302 63 8 0 2 64 3693671 3693733 3.540000e-09 73.1
35 TraesCS4A01G177200 chr7D 88.136 59 6 1 2 60 9351944 9352001 4.570000e-08 69.4


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 TraesCS4A01G177200 chr4A 448747029 448749590 2561 False 4732 4732 100.0000 1 2562 1 chr4A.!!$F1 2561
1 TraesCS4A01G177200 chr4B 184889512 184890614 1102 True 1360 1360 89.0050 512 1637 1 chr4B.!!$R1 1125
2 TraesCS4A01G177200 chr4B 665464404 665465319 915 True 457 457 76.7020 1644 2535 1 chr4B.!!$R3 891
3 TraesCS4A01G177200 chr4D 121980552 121981605 1053 True 778 1297 90.8075 512 1637 2 chr4D.!!$R1 1125
4 TraesCS4A01G177200 chr6B 704048094 704048978 884 False 680 680 80.8810 1644 2562 1 chr6B.!!$F1 918
5 TraesCS4A01G177200 chr5D 356086271 356087183 912 True 580 580 78.8790 1644 2535 1 chr5D.!!$R1 891
6 TraesCS4A01G177200 chr3A 747670545 747671468 923 True 457 457 76.5710 1645 2535 1 chr3A.!!$R3 890
7 TraesCS4A01G177200 chr3A 540042192 540043107 915 False 442 442 76.5080 1641 2535 1 chr3A.!!$F1 894
8 TraesCS4A01G177200 chr3A 699164806 699165722 916 True 433 433 76.1010 1644 2562 1 chr3A.!!$R2 918
9 TraesCS4A01G177200 chr3B 161825615 161826492 877 True 438 438 76.6330 1647 2509 1 chr3B.!!$R2 862
10 TraesCS4A01G177200 chr3B 828797725 828798622 897 True 433 433 76.3680 1644 2510 1 chr3B.!!$R4 866
11 TraesCS4A01G177200 chr7A 665146641 665147509 868 False 418 418 76.2690 1641 2514 1 chr7A.!!$F1 873
12 TraesCS4A01G177200 chr7B 20388423 20389033 610 True 416 416 79.4500 1645 2245 1 chr7B.!!$R1 600

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
292 293 0.108329 CGCCTGGTCGGTGAATAAGT 60.108 55.0 0.0 0.0 46.58 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 1873 0.107017 GGCAAGCTCATAGCCTTGGA 60.107 55.0 11.0 0.0 43.77 3.53 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 3.527427 TCCGATCATGCGCGAGGT 61.527 61.111 12.10 0.00 0.00 3.85
18 19 3.032609 CCGATCATGCGCGAGGTC 61.033 66.667 12.10 3.18 0.00 3.85
19 20 3.390017 CGATCATGCGCGAGGTCG 61.390 66.667 17.94 17.94 43.27 4.79
20 21 3.032609 GATCATGCGCGAGGTCGG 61.033 66.667 12.10 0.00 40.23 4.79
46 47 3.782443 GTAGGTGGAGGCGGGGTG 61.782 72.222 0.00 0.00 0.00 4.61
57 58 4.394712 CGGGGTGGTGGCAGAGTC 62.395 72.222 0.00 0.00 0.00 3.36
58 59 4.035102 GGGGTGGTGGCAGAGTCC 62.035 72.222 0.00 0.00 0.00 3.85
59 60 4.394712 GGGTGGTGGCAGAGTCCG 62.395 72.222 0.00 0.00 0.00 4.79
60 61 3.311110 GGTGGTGGCAGAGTCCGA 61.311 66.667 0.00 0.00 0.00 4.55
61 62 2.262915 GTGGTGGCAGAGTCCGAG 59.737 66.667 0.00 0.00 0.00 4.63
62 63 2.117423 TGGTGGCAGAGTCCGAGA 59.883 61.111 0.00 0.00 0.00 4.04
63 64 1.305297 TGGTGGCAGAGTCCGAGAT 60.305 57.895 0.00 0.00 0.00 2.75
64 65 1.323271 TGGTGGCAGAGTCCGAGATC 61.323 60.000 0.00 0.00 0.00 2.75
65 66 1.064946 GTGGCAGAGTCCGAGATCG 59.935 63.158 0.00 0.00 39.44 3.69
66 67 1.378646 TGGCAGAGTCCGAGATCGT 60.379 57.895 1.09 0.00 37.74 3.73
67 68 1.357334 GGCAGAGTCCGAGATCGTC 59.643 63.158 1.09 0.00 37.74 4.20
99 100 2.588877 GCGCACGGTGGCTATGAT 60.589 61.111 10.60 0.00 0.00 2.45
100 101 2.885676 GCGCACGGTGGCTATGATG 61.886 63.158 10.60 0.00 0.00 3.07
101 102 2.246739 CGCACGGTGGCTATGATGG 61.247 63.158 10.60 0.00 0.00 3.51
102 103 1.893808 GCACGGTGGCTATGATGGG 60.894 63.158 10.60 0.00 0.00 4.00
103 104 1.893808 CACGGTGGCTATGATGGGC 60.894 63.158 0.00 0.00 0.00 5.36
104 105 2.072487 ACGGTGGCTATGATGGGCT 61.072 57.895 3.72 0.00 0.00 5.19
105 106 1.598962 CGGTGGCTATGATGGGCTG 60.599 63.158 3.72 0.00 0.00 4.85
106 107 1.900498 GGTGGCTATGATGGGCTGC 60.900 63.158 3.72 0.00 0.00 5.25
107 108 1.900498 GTGGCTATGATGGGCTGCC 60.900 63.158 11.05 11.05 43.49 4.85
108 109 2.670934 GGCTATGATGGGCTGCCG 60.671 66.667 13.40 0.00 33.96 5.69
109 110 3.360340 GCTATGATGGGCTGCCGC 61.360 66.667 13.40 4.55 0.00 6.53
110 111 2.429058 CTATGATGGGCTGCCGCT 59.571 61.111 13.40 1.37 36.09 5.52
111 112 1.228063 CTATGATGGGCTGCCGCTT 60.228 57.895 13.40 3.99 36.09 4.68
112 113 1.512996 CTATGATGGGCTGCCGCTTG 61.513 60.000 13.40 0.00 36.09 4.01
113 114 2.963928 TATGATGGGCTGCCGCTTGG 62.964 60.000 13.40 0.00 36.09 3.61
164 165 2.408022 GCGACAGTCGGCGTAGAT 59.592 61.111 24.13 0.00 40.84 1.98
165 166 1.654743 GCGACAGTCGGCGTAGATC 60.655 63.158 24.13 1.16 40.84 2.75
166 167 1.367782 CGACAGTCGGCGTAGATCG 60.368 63.158 15.64 9.28 43.12 3.69
167 168 1.759293 CGACAGTCGGCGTAGATCGA 61.759 60.000 15.64 0.00 41.80 3.59
173 174 4.977126 GGCGTAGATCGACGGGCG 62.977 72.222 26.24 0.00 43.13 6.13
200 201 2.892425 GCAGACGGCGGATGGAAG 60.892 66.667 13.24 0.00 0.00 3.46
201 202 2.202932 CAGACGGCGGATGGAAGG 60.203 66.667 13.24 0.00 0.00 3.46
202 203 4.162690 AGACGGCGGATGGAAGGC 62.163 66.667 13.24 0.00 0.00 4.35
203 204 4.162690 GACGGCGGATGGAAGGCT 62.163 66.667 13.24 0.00 0.00 4.58
204 205 2.762459 ACGGCGGATGGAAGGCTA 60.762 61.111 13.24 0.00 0.00 3.93
205 206 2.280186 CGGCGGATGGAAGGCTAC 60.280 66.667 0.00 0.00 0.00 3.58
206 207 2.111251 GGCGGATGGAAGGCTACC 59.889 66.667 0.00 0.00 0.00 3.18
207 208 2.280186 GCGGATGGAAGGCTACCG 60.280 66.667 0.00 0.00 45.26 4.02
208 209 2.421739 CGGATGGAAGGCTACCGG 59.578 66.667 0.00 0.00 39.92 5.28
209 210 2.829592 GGATGGAAGGCTACCGGG 59.170 66.667 6.32 0.00 0.00 5.73
210 211 2.070650 GGATGGAAGGCTACCGGGT 61.071 63.158 6.32 4.46 0.00 5.28
211 212 1.446366 GATGGAAGGCTACCGGGTC 59.554 63.158 6.32 0.00 0.00 4.46
212 213 1.306654 ATGGAAGGCTACCGGGTCA 60.307 57.895 6.32 0.00 0.00 4.02
213 214 1.338136 ATGGAAGGCTACCGGGTCAG 61.338 60.000 6.32 0.21 0.00 3.51
214 215 2.732619 GGAAGGCTACCGGGTCAGG 61.733 68.421 6.32 0.00 37.30 3.86
215 216 2.687566 AAGGCTACCGGGTCAGGG 60.688 66.667 6.32 0.00 35.02 4.45
219 220 2.838225 CTACCGGGTCAGGGCGAT 60.838 66.667 6.32 0.00 35.02 4.58
220 221 3.151710 TACCGGGTCAGGGCGATG 61.152 66.667 6.32 0.00 35.02 3.84
238 239 4.221422 GGCGGGCAGATGCGTAGA 62.221 66.667 0.00 0.00 43.26 2.59
239 240 2.962253 GCGGGCAGATGCGTAGAC 60.962 66.667 0.00 0.00 43.26 2.59
240 241 2.655364 CGGGCAGATGCGTAGACG 60.655 66.667 0.00 0.00 43.26 4.18
241 242 2.805546 GGGCAGATGCGTAGACGA 59.194 61.111 6.19 0.00 43.26 4.20
242 243 1.589196 GGGCAGATGCGTAGACGAC 60.589 63.158 6.19 0.00 43.26 4.34
256 257 2.101770 CGACGACCGTTAGAGGCC 59.898 66.667 0.00 0.00 33.69 5.19
257 258 2.101770 GACGACCGTTAGAGGCCG 59.898 66.667 0.00 0.00 42.94 6.13
258 259 2.674380 ACGACCGTTAGAGGCCGT 60.674 61.111 0.00 0.00 45.30 5.68
259 260 2.101770 CGACCGTTAGAGGCCGTC 59.898 66.667 0.00 0.00 32.39 4.79
260 261 2.404995 CGACCGTTAGAGGCCGTCT 61.405 63.158 0.00 3.31 39.59 4.18
261 262 1.091771 CGACCGTTAGAGGCCGTCTA 61.092 60.000 0.00 2.22 36.64 2.59
262 263 1.316651 GACCGTTAGAGGCCGTCTAT 58.683 55.000 11.30 0.00 37.62 1.98
263 264 1.266446 GACCGTTAGAGGCCGTCTATC 59.734 57.143 11.30 9.99 37.62 2.08
264 265 0.237761 CCGTTAGAGGCCGTCTATCG 59.762 60.000 22.56 22.56 45.06 2.92
265 266 0.385723 CGTTAGAGGCCGTCTATCGC 60.386 60.000 20.08 11.09 41.64 4.58
266 267 0.385723 GTTAGAGGCCGTCTATCGCG 60.386 60.000 0.00 0.00 37.62 5.87
267 268 2.126417 TTAGAGGCCGTCTATCGCGC 62.126 60.000 0.00 0.00 37.62 6.86
268 269 4.266070 GAGGCCGTCTATCGCGCA 62.266 66.667 8.75 0.00 37.43 6.09
269 270 3.768185 GAGGCCGTCTATCGCGCAA 62.768 63.158 8.75 0.00 37.43 4.85
270 271 3.330853 GGCCGTCTATCGCGCAAG 61.331 66.667 8.75 0.27 37.43 4.01
271 272 2.278596 GCCGTCTATCGCGCAAGA 60.279 61.111 8.75 3.26 38.35 3.02
272 273 1.661821 GCCGTCTATCGCGCAAGAT 60.662 57.895 8.75 5.52 38.35 2.40
273 274 1.609840 GCCGTCTATCGCGCAAGATC 61.610 60.000 8.75 6.73 38.35 2.75
274 275 1.330779 CCGTCTATCGCGCAAGATCG 61.331 60.000 8.75 15.20 38.35 3.69
282 283 3.257561 CGCAAGATCGCCTGGTCG 61.258 66.667 0.00 0.00 43.02 4.79
283 284 2.892425 GCAAGATCGCCTGGTCGG 60.892 66.667 9.91 0.00 0.00 4.79
284 285 2.579201 CAAGATCGCCTGGTCGGT 59.421 61.111 9.91 3.67 34.25 4.69
285 286 1.811266 CAAGATCGCCTGGTCGGTG 60.811 63.158 9.91 0.00 44.95 4.94
290 291 4.924019 CGCCTGGTCGGTGAATAA 57.076 55.556 0.00 0.00 46.58 1.40
291 292 2.677971 CGCCTGGTCGGTGAATAAG 58.322 57.895 0.00 0.00 46.58 1.73
292 293 0.108329 CGCCTGGTCGGTGAATAAGT 60.108 55.000 0.00 0.00 46.58 2.24
293 294 1.653151 GCCTGGTCGGTGAATAAGTC 58.347 55.000 0.00 0.00 34.25 3.01
294 295 1.066430 GCCTGGTCGGTGAATAAGTCA 60.066 52.381 0.00 0.00 34.25 3.41
295 296 2.420129 GCCTGGTCGGTGAATAAGTCAT 60.420 50.000 0.00 0.00 38.90 3.06
296 297 3.873910 CCTGGTCGGTGAATAAGTCATT 58.126 45.455 0.00 0.00 38.90 2.57
297 298 3.871594 CCTGGTCGGTGAATAAGTCATTC 59.128 47.826 0.00 0.00 43.01 2.67
310 311 9.569167 TGAATAAGTCATTCACGTAGTTCTAAG 57.431 33.333 0.00 0.00 46.48 2.18
311 312 9.570488 GAATAAGTCATTCACGTAGTTCTAAGT 57.430 33.333 0.00 0.00 41.61 2.24
312 313 9.570488 AATAAGTCATTCACGTAGTTCTAAGTC 57.430 33.333 0.00 0.00 41.61 3.01
313 314 6.570672 AGTCATTCACGTAGTTCTAAGTCA 57.429 37.500 0.00 0.00 41.61 3.41
314 315 7.159322 AGTCATTCACGTAGTTCTAAGTCAT 57.841 36.000 0.00 0.00 41.61 3.06
315 316 7.251994 AGTCATTCACGTAGTTCTAAGTCATC 58.748 38.462 0.00 0.00 41.61 2.92
316 317 6.194876 GTCATTCACGTAGTTCTAAGTCATCG 59.805 42.308 0.00 0.00 41.61 3.84
317 318 5.868043 TTCACGTAGTTCTAAGTCATCGA 57.132 39.130 0.00 0.00 41.61 3.59
318 319 6.432607 TTCACGTAGTTCTAAGTCATCGAT 57.567 37.500 0.00 0.00 41.61 3.59
319 320 6.432607 TCACGTAGTTCTAAGTCATCGATT 57.567 37.500 0.00 0.00 41.61 3.34
320 321 6.849502 TCACGTAGTTCTAAGTCATCGATTT 58.150 36.000 0.00 0.00 41.61 2.17
321 322 6.745907 TCACGTAGTTCTAAGTCATCGATTTG 59.254 38.462 0.00 0.00 41.61 2.32
322 323 6.745907 CACGTAGTTCTAAGTCATCGATTTGA 59.254 38.462 0.00 0.00 41.61 2.69
323 324 7.432545 CACGTAGTTCTAAGTCATCGATTTGAT 59.567 37.037 0.00 0.00 41.61 2.57
450 451 9.053840 AGATAGTTAAATCGTCGATCTAGAACA 57.946 33.333 8.45 3.26 0.00 3.18
451 452 9.661187 GATAGTTAAATCGTCGATCTAGAACAA 57.339 33.333 8.45 0.00 0.00 2.83
453 454 8.341477 AGTTAAATCGTCGATCTAGAACAATG 57.659 34.615 8.45 0.00 0.00 2.82
454 455 5.643339 AAATCGTCGATCTAGAACAATGC 57.357 39.130 8.45 0.00 0.00 3.56
455 456 2.716398 TCGTCGATCTAGAACAATGCG 58.284 47.619 0.00 0.00 0.00 4.73
456 457 2.353579 TCGTCGATCTAGAACAATGCGA 59.646 45.455 0.00 0.09 0.00 5.10
457 458 3.105937 CGTCGATCTAGAACAATGCGAA 58.894 45.455 0.00 0.00 0.00 4.70
458 459 3.731216 CGTCGATCTAGAACAATGCGAAT 59.269 43.478 0.00 0.00 0.00 3.34
459 460 4.909880 CGTCGATCTAGAACAATGCGAATA 59.090 41.667 0.00 0.00 0.00 1.75
460 461 5.398416 CGTCGATCTAGAACAATGCGAATAA 59.602 40.000 0.00 0.00 0.00 1.40
461 462 6.573358 GTCGATCTAGAACAATGCGAATAAC 58.427 40.000 0.00 0.00 0.00 1.89
462 463 6.418226 GTCGATCTAGAACAATGCGAATAACT 59.582 38.462 0.00 0.00 0.00 2.24
463 464 6.978659 TCGATCTAGAACAATGCGAATAACTT 59.021 34.615 0.00 0.00 0.00 2.66
464 465 8.132995 TCGATCTAGAACAATGCGAATAACTTA 58.867 33.333 0.00 0.00 0.00 2.24
465 466 8.916654 CGATCTAGAACAATGCGAATAACTTAT 58.083 33.333 0.00 0.00 0.00 1.73
468 469 9.594478 TCTAGAACAATGCGAATAACTTATTCA 57.406 29.630 17.81 4.49 43.65 2.57
469 470 9.638300 CTAGAACAATGCGAATAACTTATTCAC 57.362 33.333 17.81 10.96 43.65 3.18
470 471 7.472543 AGAACAATGCGAATAACTTATTCACC 58.527 34.615 17.81 10.49 43.65 4.02
471 472 5.806286 ACAATGCGAATAACTTATTCACCG 58.194 37.500 17.81 8.73 43.65 4.94
472 473 5.583061 ACAATGCGAATAACTTATTCACCGA 59.417 36.000 17.81 3.15 43.65 4.69
473 474 5.652744 ATGCGAATAACTTATTCACCGAC 57.347 39.130 17.81 5.82 43.65 4.79
474 475 4.496360 TGCGAATAACTTATTCACCGACA 58.504 39.130 17.81 7.69 43.65 4.35
475 476 4.327898 TGCGAATAACTTATTCACCGACAC 59.672 41.667 17.81 3.26 43.65 3.67
476 477 4.547587 GCGAATAACTTATTCACCGACACG 60.548 45.833 17.81 6.52 43.65 4.49
477 478 4.794762 CGAATAACTTATTCACCGACACGA 59.205 41.667 17.81 0.00 43.65 4.35
478 479 5.286797 CGAATAACTTATTCACCGACACGAA 59.713 40.000 17.81 0.00 43.65 3.85
479 480 6.505888 CGAATAACTTATTCACCGACACGAAG 60.506 42.308 17.81 0.00 43.65 3.79
480 481 2.955614 ACTTATTCACCGACACGAAGG 58.044 47.619 0.00 0.00 0.00 3.46
481 482 2.298163 ACTTATTCACCGACACGAAGGT 59.702 45.455 0.00 0.00 42.34 3.50
482 483 3.507233 ACTTATTCACCGACACGAAGGTA 59.493 43.478 0.00 0.00 39.00 3.08
483 484 2.649331 ATTCACCGACACGAAGGTAG 57.351 50.000 0.00 0.00 39.00 3.18
484 485 1.321474 TTCACCGACACGAAGGTAGT 58.679 50.000 0.00 0.00 39.00 2.73
485 486 2.183478 TCACCGACACGAAGGTAGTA 57.817 50.000 0.00 0.00 39.00 1.82
486 487 1.806542 TCACCGACACGAAGGTAGTAC 59.193 52.381 0.00 0.00 39.00 2.73
487 488 1.808945 CACCGACACGAAGGTAGTACT 59.191 52.381 0.00 0.00 39.00 2.73
488 489 2.227388 CACCGACACGAAGGTAGTACTT 59.773 50.000 0.00 0.00 39.00 2.24
489 490 2.485814 ACCGACACGAAGGTAGTACTTC 59.514 50.000 0.00 0.00 42.63 3.01
490 491 2.746362 CCGACACGAAGGTAGTACTTCT 59.254 50.000 0.00 0.00 43.61 2.85
491 492 3.190118 CCGACACGAAGGTAGTACTTCTT 59.810 47.826 0.00 5.77 43.61 2.52
492 493 4.393062 CCGACACGAAGGTAGTACTTCTTA 59.607 45.833 0.00 0.00 43.61 2.10
493 494 5.106555 CCGACACGAAGGTAGTACTTCTTAA 60.107 44.000 0.00 0.00 43.61 1.85
494 495 6.404074 CCGACACGAAGGTAGTACTTCTTAAT 60.404 42.308 0.00 0.00 43.61 1.40
495 496 7.201644 CCGACACGAAGGTAGTACTTCTTAATA 60.202 40.741 0.00 0.00 43.61 0.98
496 497 8.341173 CGACACGAAGGTAGTACTTCTTAATAT 58.659 37.037 0.00 0.00 43.61 1.28
655 669 1.548357 ATCAGCCGTCCTTCTGCAGT 61.548 55.000 14.67 0.00 0.00 4.40
656 670 0.898326 TCAGCCGTCCTTCTGCAGTA 60.898 55.000 14.67 2.58 0.00 2.74
657 671 0.737715 CAGCCGTCCTTCTGCAGTAC 60.738 60.000 14.67 7.33 0.00 2.73
658 672 0.900647 AGCCGTCCTTCTGCAGTACT 60.901 55.000 14.67 0.00 0.00 2.73
659 673 0.737715 GCCGTCCTTCTGCAGTACTG 60.738 60.000 18.93 18.93 0.00 2.74
674 688 4.498323 GCAGTACTGTAGTAAAATCGACCG 59.502 45.833 23.44 0.00 31.52 4.79
787 805 6.219473 AGATGCTGCATCAGTAATACAGTAC 58.781 40.000 35.97 11.76 42.72 2.73
788 806 5.598416 TGCTGCATCAGTAATACAGTACT 57.402 39.130 0.00 0.00 32.14 2.73
789 807 5.592054 TGCTGCATCAGTAATACAGTACTC 58.408 41.667 0.00 0.00 32.14 2.59
790 808 5.360999 TGCTGCATCAGTAATACAGTACTCT 59.639 40.000 0.00 0.00 32.14 3.24
791 809 6.127338 TGCTGCATCAGTAATACAGTACTCTT 60.127 38.462 0.00 0.00 32.14 2.85
792 810 6.199908 GCTGCATCAGTAATACAGTACTCTTG 59.800 42.308 0.00 0.00 32.14 3.02
793 811 7.404671 TGCATCAGTAATACAGTACTCTTGA 57.595 36.000 0.00 0.00 31.78 3.02
794 812 7.484140 TGCATCAGTAATACAGTACTCTTGAG 58.516 38.462 0.00 0.00 31.78 3.02
795 813 7.122799 TGCATCAGTAATACAGTACTCTTGAGT 59.877 37.037 8.41 8.41 31.78 3.41
796 814 8.622157 GCATCAGTAATACAGTACTCTTGAGTA 58.378 37.037 6.41 6.41 31.78 2.59
885 903 3.204158 TGAGAAGAGATGCTCTCCCTACT 59.796 47.826 8.89 4.95 44.42 2.57
898 923 5.394005 GCTCTCCCTACTCTATACATGCATG 60.394 48.000 25.09 25.09 0.00 4.06
900 925 4.420206 TCCCTACTCTATACATGCATGCT 58.580 43.478 26.53 16.20 0.00 3.79
901 926 5.580022 TCCCTACTCTATACATGCATGCTA 58.420 41.667 26.53 17.14 0.00 3.49
902 927 5.654209 TCCCTACTCTATACATGCATGCTAG 59.346 44.000 26.53 23.92 0.00 3.42
903 928 5.420421 CCCTACTCTATACATGCATGCTAGT 59.580 44.000 26.53 21.34 0.00 2.57
904 929 6.603599 CCCTACTCTATACATGCATGCTAGTA 59.396 42.308 26.53 21.32 0.00 1.82
905 930 7.415765 CCCTACTCTATACATGCATGCTAGTAC 60.416 44.444 26.53 0.00 0.00 2.73
906 931 7.338196 CCTACTCTATACATGCATGCTAGTACT 59.662 40.741 26.53 7.76 0.00 2.73
907 932 7.151999 ACTCTATACATGCATGCTAGTACTC 57.848 40.000 26.53 0.00 0.00 2.59
908 933 6.151985 ACTCTATACATGCATGCTAGTACTCC 59.848 42.308 26.53 0.00 0.00 3.85
909 934 6.249192 TCTATACATGCATGCTAGTACTCCT 58.751 40.000 26.53 5.50 0.00 3.69
910 935 7.402862 TCTATACATGCATGCTAGTACTCCTA 58.597 38.462 26.53 7.64 0.00 2.94
911 936 4.862902 ACATGCATGCTAGTACTCCTAG 57.137 45.455 26.53 0.00 45.17 3.02
998 1023 3.170791 TCGGTACTAGTCCAGTAGTCG 57.829 52.381 0.00 0.00 40.48 4.18
1028 1053 2.128771 TCAGCCATAACCAAGAAGGC 57.871 50.000 0.00 0.00 45.54 4.35
1030 1055 2.106844 GCCATAACCAAGAAGGCGG 58.893 57.895 0.00 0.00 43.14 6.13
1031 1056 0.393808 GCCATAACCAAGAAGGCGGA 60.394 55.000 0.00 0.00 43.14 5.54
1032 1057 1.668419 CCATAACCAAGAAGGCGGAG 58.332 55.000 0.00 0.00 43.14 4.63
1033 1058 1.668419 CATAACCAAGAAGGCGGAGG 58.332 55.000 0.00 0.00 43.14 4.30
1099 1124 0.250467 TGGAGGAGAACAAGCAGCAC 60.250 55.000 0.00 0.00 0.00 4.40
1101 1126 1.612726 GGAGGAGAACAAGCAGCACAT 60.613 52.381 0.00 0.00 0.00 3.21
1146 1171 4.078516 GTACAAGGACGGCCGGCT 62.079 66.667 33.64 14.39 39.96 5.52
1172 1197 0.320421 CAAGGAGACGCCGGAGAAAA 60.320 55.000 13.83 0.00 43.43 2.29
1291 1316 3.250323 CGTCGCTGCGTCTCCATG 61.250 66.667 22.48 3.63 0.00 3.66
1303 1328 0.034089 TCTCCATGCTCGTCTCCTCA 60.034 55.000 0.00 0.00 0.00 3.86
1328 1353 5.885912 TGCTGGAAGAACTACCCATAAATTC 59.114 40.000 0.00 0.00 34.07 2.17
1429 1456 2.708861 TCTGGACTTTCCTTTGCCACTA 59.291 45.455 0.00 0.00 37.46 2.74
1430 1457 2.814336 CTGGACTTTCCTTTGCCACTAC 59.186 50.000 0.00 0.00 37.46 2.73
1550 1578 6.522165 CGCCTCGTTCCTTTCTTTTTATTTAC 59.478 38.462 0.00 0.00 0.00 2.01
1554 1582 8.680039 TCGTTCCTTTCTTTTTATTTACTGGA 57.320 30.769 0.00 0.00 0.00 3.86
1594 1622 1.133216 GAAGCGCAAAGAGGAAATCCC 59.867 52.381 11.47 0.00 36.42 3.85
1598 1626 1.202336 CGCAAAGAGGAAATCCCATGC 60.202 52.381 0.00 1.67 37.41 4.06
1617 1645 3.469863 AAAACGACCGCTGGCCTCA 62.470 57.895 3.32 0.00 0.00 3.86
1637 1665 5.222079 TCACTCCATTGTTGTTACTAGCA 57.778 39.130 0.00 0.00 0.00 3.49
1638 1666 5.616270 TCACTCCATTGTTGTTACTAGCAA 58.384 37.500 0.00 0.00 0.00 3.91
1639 1667 6.058833 TCACTCCATTGTTGTTACTAGCAAA 58.941 36.000 0.00 0.00 0.00 3.68
1642 1670 8.677300 CACTCCATTGTTGTTACTAGCAAATAT 58.323 33.333 0.00 0.00 0.00 1.28
1657 1685 6.720112 AGCAAATATCAAATATGCCTGTGT 57.280 33.333 0.00 0.00 37.73 3.72
1723 1752 8.466617 AAGTATGACTCAGTACCCTTACATAG 57.533 38.462 0.00 0.00 0.00 2.23
1745 1774 5.010282 AGGAGCGTCCTCAATTTTAACATT 58.990 37.500 1.23 0.00 45.66 2.71
1747 1776 4.485163 AGCGTCCTCAATTTTAACATTGC 58.515 39.130 9.10 0.00 34.58 3.56
1839 1873 8.994429 TTAAAATGCATTCGATGTGGTAAATT 57.006 26.923 13.38 0.96 0.00 1.82
1862 1896 1.500474 AGGCTATGAGCTTGCCACTA 58.500 50.000 18.49 0.00 46.90 2.74
1873 1907 2.280524 GCCACTACACGCCACACA 60.281 61.111 0.00 0.00 0.00 3.72
1886 1920 3.505680 ACGCCACACATGTCATTATGTTT 59.494 39.130 0.00 0.00 39.17 2.83
1985 2021 9.378551 AGACTTTTGAAAAACTAAACAAATCCC 57.621 29.630 0.00 0.00 33.38 3.85
2016 2052 9.829507 ATAAATGACTTTTGAATTGGTGAACAA 57.170 25.926 0.00 0.00 44.54 2.83
2132 2176 9.142515 GCATGAACAACTTATGAAATCATGAAA 57.857 29.630 14.93 0.00 43.10 2.69
2297 2388 8.335532 TGTCATTTGATTTTATTTCTCGACCT 57.664 30.769 0.00 0.00 0.00 3.85
2362 2458 8.375717 GTTTTGCAAAACCACTAACATTTTTC 57.624 30.769 34.76 11.82 41.77 2.29
2447 2560 7.903995 TTCTTGAGCATGTTTTTGAAAACTT 57.096 28.000 17.33 10.31 46.37 2.66
2552 2680 4.482952 AAAAGTTATGGAGTCTACCCCG 57.517 45.455 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.484742 GACCTCGCGCATGATCGGA 62.485 63.158 8.75 0.00 0.00 4.55
1 2 3.032609 GACCTCGCGCATGATCGG 61.033 66.667 8.75 0.00 0.00 4.18
2 3 3.390017 CGACCTCGCGCATGATCG 61.390 66.667 8.75 7.51 0.00 3.69
3 4 3.032609 CCGACCTCGCGCATGATC 61.033 66.667 8.75 0.00 38.18 2.92
4 5 4.592192 CCCGACCTCGCGCATGAT 62.592 66.667 8.75 0.00 38.18 2.45
21 22 3.834799 CTCCACCTACCGGCGTCC 61.835 72.222 6.01 0.00 0.00 4.79
22 23 3.834799 CCTCCACCTACCGGCGTC 61.835 72.222 6.01 0.00 0.00 5.19
29 30 3.782443 CACCCCGCCTCCACCTAC 61.782 72.222 0.00 0.00 0.00 3.18
40 41 4.394712 GACTCTGCCACCACCCCG 62.395 72.222 0.00 0.00 0.00 5.73
41 42 4.035102 GGACTCTGCCACCACCCC 62.035 72.222 0.00 0.00 0.00 4.95
42 43 4.394712 CGGACTCTGCCACCACCC 62.395 72.222 0.00 0.00 0.00 4.61
43 44 3.302347 CTCGGACTCTGCCACCACC 62.302 68.421 0.00 0.00 0.00 4.61
44 45 1.608717 ATCTCGGACTCTGCCACCAC 61.609 60.000 0.00 0.00 0.00 4.16
45 46 1.305297 ATCTCGGACTCTGCCACCA 60.305 57.895 0.00 0.00 0.00 4.17
46 47 1.439644 GATCTCGGACTCTGCCACC 59.560 63.158 0.00 0.00 0.00 4.61
47 48 1.064946 CGATCTCGGACTCTGCCAC 59.935 63.158 0.00 0.00 35.37 5.01
48 49 1.377366 GACGATCTCGGACTCTGCCA 61.377 60.000 4.44 0.00 44.95 4.92
49 50 1.357334 GACGATCTCGGACTCTGCC 59.643 63.158 4.44 0.00 44.95 4.85
50 51 1.010574 CGACGATCTCGGACTCTGC 60.011 63.158 4.44 0.00 44.95 4.26
82 83 2.588877 ATCATAGCCACCGTGCGC 60.589 61.111 0.00 0.00 36.02 6.09
83 84 2.246739 CCATCATAGCCACCGTGCG 61.247 63.158 0.00 0.00 36.02 5.34
84 85 1.893808 CCCATCATAGCCACCGTGC 60.894 63.158 0.00 0.00 0.00 5.34
85 86 1.893808 GCCCATCATAGCCACCGTG 60.894 63.158 0.00 0.00 0.00 4.94
86 87 2.072487 AGCCCATCATAGCCACCGT 61.072 57.895 0.00 0.00 0.00 4.83
87 88 1.598962 CAGCCCATCATAGCCACCG 60.599 63.158 0.00 0.00 0.00 4.94
88 89 1.900498 GCAGCCCATCATAGCCACC 60.900 63.158 0.00 0.00 0.00 4.61
89 90 1.900498 GGCAGCCCATCATAGCCAC 60.900 63.158 0.00 0.00 44.59 5.01
90 91 2.517414 GGCAGCCCATCATAGCCA 59.483 61.111 0.00 0.00 44.59 4.75
91 92 2.670934 CGGCAGCCCATCATAGCC 60.671 66.667 5.63 0.00 41.86 3.93
92 93 3.360340 GCGGCAGCCCATCATAGC 61.360 66.667 5.63 0.00 37.42 2.97
93 94 1.228063 AAGCGGCAGCCCATCATAG 60.228 57.895 5.63 0.00 46.67 2.23
94 95 1.526686 CAAGCGGCAGCCCATCATA 60.527 57.895 5.63 0.00 46.67 2.15
95 96 2.831742 CAAGCGGCAGCCCATCAT 60.832 61.111 5.63 0.00 46.67 2.45
146 147 2.985486 GATCTACGCCGACTGTCGCC 62.985 65.000 23.87 13.08 38.82 5.54
147 148 1.654743 GATCTACGCCGACTGTCGC 60.655 63.158 23.87 17.41 38.82 5.19
148 149 1.367782 CGATCTACGCCGACTGTCG 60.368 63.158 22.49 22.49 40.07 4.35
149 150 2.012237 TCGATCTACGCCGACTGTC 58.988 57.895 0.00 0.00 42.26 3.51
150 151 2.033328 CGTCGATCTACGCCGACTGT 62.033 60.000 6.86 0.00 46.15 3.55
151 152 1.367782 CGTCGATCTACGCCGACTG 60.368 63.158 6.86 3.69 46.15 3.51
152 153 2.532256 CCGTCGATCTACGCCGACT 61.532 63.158 13.89 0.00 46.15 4.18
153 154 2.052414 CCGTCGATCTACGCCGAC 60.052 66.667 13.89 3.42 46.15 4.79
154 155 3.274586 CCCGTCGATCTACGCCGA 61.275 66.667 13.89 0.00 46.15 5.54
155 156 4.977126 GCCCGTCGATCTACGCCG 62.977 72.222 13.89 7.36 42.94 6.46
156 157 4.977126 CGCCCGTCGATCTACGCC 62.977 72.222 13.89 6.45 41.51 5.68
157 158 3.945434 TCGCCCGTCGATCTACGC 61.945 66.667 13.89 1.15 43.16 4.42
183 184 2.892425 CTTCCATCCGCCGTCTGC 60.892 66.667 0.00 0.00 0.00 4.26
184 185 2.202932 CCTTCCATCCGCCGTCTG 60.203 66.667 0.00 0.00 0.00 3.51
185 186 4.162690 GCCTTCCATCCGCCGTCT 62.163 66.667 0.00 0.00 0.00 4.18
186 187 2.792947 TAGCCTTCCATCCGCCGTC 61.793 63.158 0.00 0.00 0.00 4.79
187 188 2.762459 TAGCCTTCCATCCGCCGT 60.762 61.111 0.00 0.00 0.00 5.68
188 189 2.280186 GTAGCCTTCCATCCGCCG 60.280 66.667 0.00 0.00 0.00 6.46
189 190 2.111251 GGTAGCCTTCCATCCGCC 59.889 66.667 0.00 0.00 0.00 6.13
190 191 2.280186 CGGTAGCCTTCCATCCGC 60.280 66.667 0.00 0.00 35.01 5.54
191 192 2.421739 CCGGTAGCCTTCCATCCG 59.578 66.667 0.00 0.00 40.72 4.18
192 193 2.041206 GACCCGGTAGCCTTCCATCC 62.041 65.000 0.00 0.00 0.00 3.51
193 194 1.335132 TGACCCGGTAGCCTTCCATC 61.335 60.000 0.00 0.00 0.00 3.51
194 195 1.306654 TGACCCGGTAGCCTTCCAT 60.307 57.895 0.00 0.00 0.00 3.41
195 196 1.987855 CTGACCCGGTAGCCTTCCA 60.988 63.158 0.00 0.00 0.00 3.53
196 197 2.732619 CCTGACCCGGTAGCCTTCC 61.733 68.421 0.00 0.00 0.00 3.46
197 198 2.732619 CCCTGACCCGGTAGCCTTC 61.733 68.421 0.00 0.00 0.00 3.46
198 199 2.687566 CCCTGACCCGGTAGCCTT 60.688 66.667 0.00 0.00 0.00 4.35
202 203 2.838225 ATCGCCCTGACCCGGTAG 60.838 66.667 0.00 0.00 0.00 3.18
203 204 3.151710 CATCGCCCTGACCCGGTA 61.152 66.667 0.00 0.00 0.00 4.02
221 222 4.221422 TCTACGCATCTGCCCGCC 62.221 66.667 0.00 0.00 37.91 6.13
222 223 2.962253 GTCTACGCATCTGCCCGC 60.962 66.667 0.00 0.00 37.91 6.13
223 224 2.655364 CGTCTACGCATCTGCCCG 60.655 66.667 0.00 0.00 37.91 6.13
224 225 1.589196 GTCGTCTACGCATCTGCCC 60.589 63.158 0.00 0.00 39.60 5.36
225 226 1.939785 CGTCGTCTACGCATCTGCC 60.940 63.158 0.00 0.00 46.10 4.85
226 227 3.589982 CGTCGTCTACGCATCTGC 58.410 61.111 0.00 0.00 46.10 4.26
239 240 2.101770 GGCCTCTAACGGTCGTCG 59.898 66.667 0.00 0.00 45.88 5.12
240 241 2.101770 CGGCCTCTAACGGTCGTC 59.898 66.667 0.00 0.00 46.53 4.20
243 244 1.266446 GATAGACGGCCTCTAACGGTC 59.734 57.143 13.69 6.35 34.99 4.79
244 245 1.316651 GATAGACGGCCTCTAACGGT 58.683 55.000 13.69 0.00 34.99 4.83
245 246 0.237761 CGATAGACGGCCTCTAACGG 59.762 60.000 22.54 11.75 41.67 4.44
246 247 0.385723 GCGATAGACGGCCTCTAACG 60.386 60.000 24.35 24.35 45.81 3.18
247 248 0.385723 CGCGATAGACGGCCTCTAAC 60.386 60.000 0.00 10.95 42.83 2.34
248 249 1.947013 CGCGATAGACGGCCTCTAA 59.053 57.895 0.00 1.77 42.83 2.10
249 250 2.614446 GCGCGATAGACGGCCTCTA 61.614 63.158 12.10 12.51 42.83 2.43
250 251 3.967335 GCGCGATAGACGGCCTCT 61.967 66.667 12.10 5.53 42.83 3.69
251 252 3.768185 TTGCGCGATAGACGGCCTC 62.768 63.158 12.10 0.00 42.83 4.70
252 253 3.774959 CTTGCGCGATAGACGGCCT 62.775 63.158 12.10 0.00 42.83 5.19
253 254 3.330853 CTTGCGCGATAGACGGCC 61.331 66.667 12.10 0.00 42.83 6.13
254 255 1.609840 GATCTTGCGCGATAGACGGC 61.610 60.000 12.10 1.14 42.83 5.68
255 256 1.330779 CGATCTTGCGCGATAGACGG 61.331 60.000 12.10 3.07 42.83 4.79
256 257 2.046923 CGATCTTGCGCGATAGACG 58.953 57.895 12.10 13.15 45.66 4.18
265 266 3.257561 CGACCAGGCGATCTTGCG 61.258 66.667 0.00 0.00 35.06 4.85
266 267 2.892425 CCGACCAGGCGATCTTGC 60.892 66.667 0.00 0.00 0.00 4.01
267 268 1.811266 CACCGACCAGGCGATCTTG 60.811 63.158 0.00 0.00 46.52 3.02
268 269 1.541310 TTCACCGACCAGGCGATCTT 61.541 55.000 0.00 0.00 46.52 2.40
269 270 1.330655 ATTCACCGACCAGGCGATCT 61.331 55.000 0.00 0.00 46.52 2.75
270 271 0.387929 TATTCACCGACCAGGCGATC 59.612 55.000 0.00 0.00 46.52 3.69
271 272 0.828022 TTATTCACCGACCAGGCGAT 59.172 50.000 0.00 0.00 46.52 4.58
272 273 0.174845 CTTATTCACCGACCAGGCGA 59.825 55.000 0.00 0.00 46.52 5.54
273 274 0.108329 ACTTATTCACCGACCAGGCG 60.108 55.000 0.00 0.00 46.52 5.52
274 275 1.066430 TGACTTATTCACCGACCAGGC 60.066 52.381 0.00 0.00 46.52 4.85
275 276 3.871594 GAATGACTTATTCACCGACCAGG 59.128 47.826 0.00 0.00 43.79 4.45
285 286 9.570488 ACTTAGAACTACGTGAATGACTTATTC 57.430 33.333 0.00 0.00 44.45 1.75
286 287 9.570488 GACTTAGAACTACGTGAATGACTTATT 57.430 33.333 0.00 0.00 0.00 1.40
287 288 8.737175 TGACTTAGAACTACGTGAATGACTTAT 58.263 33.333 0.00 0.00 0.00 1.73
288 289 8.102800 TGACTTAGAACTACGTGAATGACTTA 57.897 34.615 0.00 0.00 0.00 2.24
289 290 6.978338 TGACTTAGAACTACGTGAATGACTT 58.022 36.000 0.00 0.00 0.00 3.01
290 291 6.570672 TGACTTAGAACTACGTGAATGACT 57.429 37.500 0.00 0.00 0.00 3.41
291 292 6.194876 CGATGACTTAGAACTACGTGAATGAC 59.805 42.308 0.00 0.00 0.00 3.06
292 293 6.093082 TCGATGACTTAGAACTACGTGAATGA 59.907 38.462 0.00 0.00 0.00 2.57
293 294 6.255950 TCGATGACTTAGAACTACGTGAATG 58.744 40.000 0.00 0.00 0.00 2.67
294 295 6.432607 TCGATGACTTAGAACTACGTGAAT 57.567 37.500 0.00 0.00 0.00 2.57
295 296 5.868043 TCGATGACTTAGAACTACGTGAA 57.132 39.130 0.00 0.00 0.00 3.18
296 297 6.432607 AATCGATGACTTAGAACTACGTGA 57.567 37.500 0.00 0.00 0.00 4.35
297 298 6.745907 TCAAATCGATGACTTAGAACTACGTG 59.254 38.462 0.00 0.00 0.00 4.49
298 299 6.849502 TCAAATCGATGACTTAGAACTACGT 58.150 36.000 0.00 0.00 0.00 3.57
299 300 7.916128 ATCAAATCGATGACTTAGAACTACG 57.084 36.000 0.00 0.00 31.20 3.51
424 425 9.053840 TGTTCTAGATCGACGATTTAACTATCT 57.946 33.333 12.40 5.24 0.00 1.98
425 426 9.661187 TTGTTCTAGATCGACGATTTAACTATC 57.339 33.333 12.40 0.00 0.00 2.08
427 428 9.447040 CATTGTTCTAGATCGACGATTTAACTA 57.553 33.333 12.40 7.69 0.00 2.24
428 429 7.043325 GCATTGTTCTAGATCGACGATTTAACT 60.043 37.037 12.40 6.89 0.00 2.24
429 430 7.058005 GCATTGTTCTAGATCGACGATTTAAC 58.942 38.462 12.40 13.34 0.00 2.01
430 431 6.075046 CGCATTGTTCTAGATCGACGATTTAA 60.075 38.462 12.40 1.84 0.00 1.52
431 432 5.398416 CGCATTGTTCTAGATCGACGATTTA 59.602 40.000 12.40 9.78 0.00 1.40
432 433 4.207224 CGCATTGTTCTAGATCGACGATTT 59.793 41.667 12.40 9.05 0.00 2.17
433 434 3.731216 CGCATTGTTCTAGATCGACGATT 59.269 43.478 12.40 4.93 0.00 3.34
434 435 3.003378 TCGCATTGTTCTAGATCGACGAT 59.997 43.478 10.78 10.78 0.00 3.73
435 436 2.353579 TCGCATTGTTCTAGATCGACGA 59.646 45.455 0.00 0.00 0.00 4.20
436 437 2.716398 TCGCATTGTTCTAGATCGACG 58.284 47.619 0.00 0.00 0.00 5.12
437 438 6.418226 AGTTATTCGCATTGTTCTAGATCGAC 59.582 38.462 0.00 0.00 0.00 4.20
438 439 6.504398 AGTTATTCGCATTGTTCTAGATCGA 58.496 36.000 0.00 0.00 0.00 3.59
439 440 6.755461 AGTTATTCGCATTGTTCTAGATCG 57.245 37.500 0.00 0.00 0.00 3.69
442 443 9.594478 TGAATAAGTTATTCGCATTGTTCTAGA 57.406 29.630 23.98 5.57 45.82 2.43
454 455 4.794762 TCGTGTCGGTGAATAAGTTATTCG 59.205 41.667 23.98 16.22 45.82 3.34
455 456 6.237755 CCTTCGTGTCGGTGAATAAGTTATTC 60.238 42.308 23.28 23.28 43.73 1.75
456 457 5.579511 CCTTCGTGTCGGTGAATAAGTTATT 59.420 40.000 7.87 7.87 0.00 1.40
457 458 5.107133 CCTTCGTGTCGGTGAATAAGTTAT 58.893 41.667 0.00 0.00 0.00 1.89
458 459 4.022068 ACCTTCGTGTCGGTGAATAAGTTA 60.022 41.667 0.00 0.00 30.90 2.24
459 460 3.243975 ACCTTCGTGTCGGTGAATAAGTT 60.244 43.478 0.00 0.00 30.90 2.66
460 461 2.298163 ACCTTCGTGTCGGTGAATAAGT 59.702 45.455 0.00 0.00 30.90 2.24
461 462 2.955614 ACCTTCGTGTCGGTGAATAAG 58.044 47.619 0.00 0.00 30.90 1.73
462 463 3.507233 ACTACCTTCGTGTCGGTGAATAA 59.493 43.478 0.00 0.00 34.76 1.40
463 464 3.084039 ACTACCTTCGTGTCGGTGAATA 58.916 45.455 0.00 0.00 34.76 1.75
464 465 1.891150 ACTACCTTCGTGTCGGTGAAT 59.109 47.619 0.00 0.00 34.76 2.57
465 466 1.321474 ACTACCTTCGTGTCGGTGAA 58.679 50.000 0.00 0.00 34.76 3.18
466 467 1.806542 GTACTACCTTCGTGTCGGTGA 59.193 52.381 0.00 0.00 34.76 4.02
467 468 1.808945 AGTACTACCTTCGTGTCGGTG 59.191 52.381 0.00 0.00 34.76 4.94
468 469 2.191128 AGTACTACCTTCGTGTCGGT 57.809 50.000 0.00 0.00 37.31 4.69
469 470 2.746362 AGAAGTACTACCTTCGTGTCGG 59.254 50.000 0.00 0.00 44.46 4.79
470 471 4.416505 AAGAAGTACTACCTTCGTGTCG 57.583 45.455 0.00 0.00 44.46 4.35
500 501 9.817809 GTCCAACAATCTAATCTGTCAAGTATA 57.182 33.333 0.00 0.00 0.00 1.47
501 502 8.321353 TGTCCAACAATCTAATCTGTCAAGTAT 58.679 33.333 0.00 0.00 0.00 2.12
502 503 7.602644 GTGTCCAACAATCTAATCTGTCAAGTA 59.397 37.037 0.00 0.00 0.00 2.24
503 504 6.428159 GTGTCCAACAATCTAATCTGTCAAGT 59.572 38.462 0.00 0.00 0.00 3.16
504 505 6.401474 CGTGTCCAACAATCTAATCTGTCAAG 60.401 42.308 0.00 0.00 0.00 3.02
505 506 5.408299 CGTGTCCAACAATCTAATCTGTCAA 59.592 40.000 0.00 0.00 0.00 3.18
506 507 4.929211 CGTGTCCAACAATCTAATCTGTCA 59.071 41.667 0.00 0.00 0.00 3.58
507 508 4.929808 ACGTGTCCAACAATCTAATCTGTC 59.070 41.667 0.00 0.00 0.00 3.51
508 509 4.894784 ACGTGTCCAACAATCTAATCTGT 58.105 39.130 0.00 0.00 0.00 3.41
509 510 5.291128 GGTACGTGTCCAACAATCTAATCTG 59.709 44.000 0.00 0.00 0.00 2.90
510 511 5.416947 GGTACGTGTCCAACAATCTAATCT 58.583 41.667 0.00 0.00 0.00 2.40
655 669 4.395854 TGCTCGGTCGATTTTACTACAGTA 59.604 41.667 0.00 0.00 0.00 2.74
656 670 3.192001 TGCTCGGTCGATTTTACTACAGT 59.808 43.478 0.00 0.00 0.00 3.55
657 671 3.766151 TGCTCGGTCGATTTTACTACAG 58.234 45.455 0.00 0.00 0.00 2.74
658 672 3.853831 TGCTCGGTCGATTTTACTACA 57.146 42.857 0.00 0.00 0.00 2.74
659 673 4.492085 GCTTTGCTCGGTCGATTTTACTAC 60.492 45.833 0.00 0.00 0.00 2.73
700 714 0.904649 TCGACTGGTCTGCATGGAAT 59.095 50.000 0.00 0.00 0.00 3.01
701 715 0.037326 GTCGACTGGTCTGCATGGAA 60.037 55.000 8.70 0.00 0.00 3.53
787 805 5.755861 GGCCTGCTAAAACTATACTCAAGAG 59.244 44.000 0.00 0.00 0.00 2.85
788 806 5.188948 TGGCCTGCTAAAACTATACTCAAGA 59.811 40.000 3.32 0.00 0.00 3.02
789 807 5.428253 TGGCCTGCTAAAACTATACTCAAG 58.572 41.667 3.32 0.00 0.00 3.02
790 808 5.429681 TGGCCTGCTAAAACTATACTCAA 57.570 39.130 3.32 0.00 0.00 3.02
791 809 5.188948 TCTTGGCCTGCTAAAACTATACTCA 59.811 40.000 3.32 0.00 0.00 3.41
792 810 5.671493 TCTTGGCCTGCTAAAACTATACTC 58.329 41.667 3.32 0.00 0.00 2.59
793 811 5.693769 TCTTGGCCTGCTAAAACTATACT 57.306 39.130 3.32 0.00 0.00 2.12
794 812 5.297029 CCTTCTTGGCCTGCTAAAACTATAC 59.703 44.000 3.32 0.00 0.00 1.47
795 813 5.437060 CCTTCTTGGCCTGCTAAAACTATA 58.563 41.667 3.32 0.00 0.00 1.31
796 814 4.273318 CCTTCTTGGCCTGCTAAAACTAT 58.727 43.478 3.32 0.00 0.00 2.12
885 903 6.249192 AGGAGTACTAGCATGCATGTATAGA 58.751 40.000 31.10 19.35 0.00 1.98
998 1023 1.939974 TATGGCTGATCAACTCGTGC 58.060 50.000 0.00 0.00 0.00 5.34
1028 1053 2.197324 CCTCCTCCTCCTCCTCCG 59.803 72.222 0.00 0.00 0.00 4.63
1029 1054 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1030 1055 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1031 1056 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1032 1057 0.996762 TCTCCTCCTCCTCCTCCTCC 60.997 65.000 0.00 0.00 0.00 4.30
1033 1058 1.075536 GATCTCCTCCTCCTCCTCCTC 59.924 61.905 0.00 0.00 0.00 3.71
1076 1101 2.354259 CTGCTTGTTCTCCTCCATGTC 58.646 52.381 0.00 0.00 0.00 3.06
1101 1126 3.071457 TGCAGTTGACATCTTCTTCCAGA 59.929 43.478 0.00 0.00 0.00 3.86
1156 1181 0.458716 CTCTTTTCTCCGGCGTCTCC 60.459 60.000 6.01 0.00 0.00 3.71
1291 1316 1.227205 CCAGCATGAGGAGACGAGC 60.227 63.158 0.00 0.00 39.69 5.03
1303 1328 5.450818 TTTATGGGTAGTTCTTCCAGCAT 57.549 39.130 0.00 0.00 33.68 3.79
1328 1353 1.612726 CCAGGCCCAGAAACAGAAGAG 60.613 57.143 0.00 0.00 0.00 2.85
1404 1431 3.772025 TGGCAAAGGAAAGTCCAGAAAAA 59.228 39.130 0.00 0.00 39.61 1.94
1429 1456 1.847506 TCACCAGGGCCATCTGTGT 60.848 57.895 6.18 6.83 33.14 3.72
1430 1457 1.377725 GTCACCAGGGCCATCTGTG 60.378 63.158 6.18 7.75 33.14 3.66
1565 1593 3.799420 CCTCTTTGCGCTTCTATACACTC 59.201 47.826 9.73 0.00 0.00 3.51
1594 1622 1.442520 CCAGCGGTCGTTTTGCATG 60.443 57.895 0.00 0.00 0.00 4.06
1598 1626 2.966309 GAGGCCAGCGGTCGTTTTG 61.966 63.158 5.01 0.00 29.39 2.44
1617 1645 8.807948 ATATTTGCTAGTAACAACAATGGAGT 57.192 30.769 0.00 0.00 0.00 3.85
1637 1665 6.757947 GCAACACACAGGCATATTTGATATTT 59.242 34.615 0.00 0.00 0.00 1.40
1638 1666 6.127394 TGCAACACACAGGCATATTTGATATT 60.127 34.615 0.00 0.00 31.58 1.28
1639 1667 5.360429 TGCAACACACAGGCATATTTGATAT 59.640 36.000 0.00 0.00 31.58 1.63
1642 1670 2.889678 TGCAACACACAGGCATATTTGA 59.110 40.909 0.00 0.00 31.58 2.69
1657 1685 3.577649 TTTTTGTCTTCCGTTGCAACA 57.422 38.095 28.01 7.99 0.00 3.33
1686 1715 7.620880 ACTGAGTCATACTTATTTGGCTTACA 58.379 34.615 0.00 0.00 0.00 2.41
1688 1717 8.202137 GGTACTGAGTCATACTTATTTGGCTTA 58.798 37.037 0.00 0.00 0.00 3.09
1723 1752 4.965119 ATGTTAAAATTGAGGACGCTCC 57.035 40.909 0.00 0.00 36.58 4.70
1745 1774 3.364441 GCAACATGGTGAGCCGCA 61.364 61.111 16.85 0.00 37.67 5.69
1747 1776 2.672651 TGGCAACATGGTGAGCCG 60.673 61.111 16.85 0.00 46.17 5.52
1839 1873 0.107017 GGCAAGCTCATAGCCTTGGA 60.107 55.000 11.00 0.00 43.77 3.53
1873 1907 4.269183 TCCCTTGCGAAACATAATGACAT 58.731 39.130 0.00 0.00 0.00 3.06
1886 1920 5.523438 AAGTTTTAAACAATCCCTTGCGA 57.477 34.783 10.60 0.00 35.69 5.10
1926 1962 1.012486 CGTTGGGAGTAGTTCGTGCC 61.012 60.000 0.00 0.00 0.00 5.01
1927 1963 1.623973 GCGTTGGGAGTAGTTCGTGC 61.624 60.000 0.00 0.00 0.00 5.34
2099 2143 8.883954 TTTCATAAGTTGTTCATGCATTTCAA 57.116 26.923 0.00 0.00 0.00 2.69
2100 2144 9.142515 GATTTCATAAGTTGTTCATGCATTTCA 57.857 29.630 0.00 0.00 0.00 2.69
2101 2145 9.142515 TGATTTCATAAGTTGTTCATGCATTTC 57.857 29.630 0.00 0.00 0.00 2.17
2250 2323 8.100164 TGACAGTGTATCCAAAACATATTCTGA 58.900 33.333 0.00 0.00 0.00 3.27
2252 2325 9.466497 AATGACAGTGTATCCAAAACATATTCT 57.534 29.630 0.00 0.00 0.00 2.40
2272 2345 8.335532 AGGTCGAGAAATAAAATCAAATGACA 57.664 30.769 0.00 0.00 0.00 3.58
2447 2560 8.511604 TGGATTTCCAAAATTTAAAAGTTGCA 57.488 26.923 0.00 0.00 44.35 4.08
2535 2663 1.117150 TGCGGGGTAGACTCCATAAC 58.883 55.000 0.00 0.00 0.00 1.89
2537 2665 0.757935 GGTGCGGGGTAGACTCCATA 60.758 60.000 0.00 0.00 0.00 2.74
2539 2667 2.682494 GGTGCGGGGTAGACTCCA 60.682 66.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.