Multiple sequence alignment - TraesCS5B01G146800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G146800 chr5B 100.000 2954 0 0 1 2954 275174914 275171961 0.000000e+00 5456
1 TraesCS5B01G146800 chr5B 82.353 153 23 4 412 561 706717865 706718016 2.390000e-26 130
2 TraesCS5B01G146800 chr5A 90.940 2605 102 44 413 2954 325997527 325994994 0.000000e+00 3380
3 TraesCS5B01G146800 chr5D 93.502 1262 38 8 1717 2954 231322269 231323510 0.000000e+00 1836
4 TraesCS5B01G146800 chr5D 91.951 1317 52 23 410 1703 231320928 231322213 0.000000e+00 1796
5 TraesCS5B01G146800 chr5D 85.106 141 19 2 413 551 300935370 300935230 3.070000e-30 143
6 TraesCS5B01G146800 chr7B 93.643 409 26 0 1 409 641732791 641732383 1.950000e-171 612
7 TraesCS5B01G146800 chr7B 90.465 409 38 1 1 409 659410355 659409948 3.350000e-149 538
8 TraesCS5B01G146800 chr4B 95.033 302 15 0 1380 1681 139769014 139769315 2.660000e-130 475
9 TraesCS5B01G146800 chr4D 94.702 302 16 0 1380 1681 98481761 98482062 1.240000e-128 470
10 TraesCS5B01G146800 chr4A 94.371 302 17 0 1380 1681 477834111 477833810 5.770000e-127 464
11 TraesCS5B01G146800 chr4A 86.364 132 18 0 1379 1510 477830687 477830556 8.530000e-31 145
12 TraesCS5B01G146800 chr4A 83.660 153 21 4 412 561 608187922 608187771 1.100000e-29 141
13 TraesCS5B01G146800 chr1B 82.382 403 69 2 1 402 578536551 578536150 1.680000e-92 350
14 TraesCS5B01G146800 chr2D 77.184 412 80 9 3 407 57314649 57315053 8.240000e-56 228


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 TraesCS5B01G146800 chr5B 275171961 275174914 2953 True 5456.0 5456 100.0000 1 2954 1 chr5B.!!$R1 2953
1 TraesCS5B01G146800 chr5A 325994994 325997527 2533 True 3380.0 3380 90.9400 413 2954 1 chr5A.!!$R1 2541
2 TraesCS5B01G146800 chr5D 231320928 231323510 2582 False 1816.0 1836 92.7265 410 2954 2 chr5D.!!$F1 2544
3 TraesCS5B01G146800 chr4A 477830556 477834111 3555 True 304.5 464 90.3675 1379 1681 2 chr4A.!!$R2 302

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
384 385 0.039618 GATGTGGTGGGGGATGTGTT 59.96 55.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 3083 1.607148 GGCTGTGCCGTAAAGTTTCTT 59.393 47.619 0.0 0.0 39.62 2.52 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 4.581391 GTGGGGAGGGAGAAAGGA 57.419 61.111 0.00 0.00 0.00 3.36
18 19 2.302019 GTGGGGAGGGAGAAAGGAG 58.698 63.158 0.00 0.00 0.00 3.69
19 20 1.616628 TGGGGAGGGAGAAAGGAGC 60.617 63.158 0.00 0.00 0.00 4.70
20 21 2.379459 GGGGAGGGAGAAAGGAGCC 61.379 68.421 0.00 0.00 0.00 4.70
21 22 2.379459 GGGAGGGAGAAAGGAGCCC 61.379 68.421 0.00 0.00 42.37 5.19
22 23 2.379459 GGAGGGAGAAAGGAGCCCC 61.379 68.421 0.00 0.00 43.08 5.80
23 24 2.286502 AGGGAGAAAGGAGCCCCC 60.287 66.667 0.00 0.00 43.08 5.40
31 32 4.079827 AGGAGCCCCCTTGATGAG 57.920 61.111 0.00 0.00 44.85 2.90
32 33 2.194326 GGAGCCCCCTTGATGAGC 59.806 66.667 0.00 0.00 0.00 4.26
33 34 2.381941 GGAGCCCCCTTGATGAGCT 61.382 63.158 0.00 0.00 36.25 4.09
34 35 1.611965 GAGCCCCCTTGATGAGCTT 59.388 57.895 0.00 0.00 32.97 3.74
35 36 0.750911 GAGCCCCCTTGATGAGCTTG 60.751 60.000 0.00 0.00 32.97 4.01
36 37 1.755783 GCCCCCTTGATGAGCTTGG 60.756 63.158 0.00 0.00 0.00 3.61
37 38 1.076485 CCCCCTTGATGAGCTTGGG 60.076 63.158 0.00 0.00 37.68 4.12
38 39 1.755783 CCCCTTGATGAGCTTGGGC 60.756 63.158 0.00 0.00 36.66 5.36
49 50 3.584947 GCTTGGGCTTGAAGGAGAT 57.415 52.632 0.00 0.00 35.22 2.75
50 51 1.387539 GCTTGGGCTTGAAGGAGATC 58.612 55.000 0.00 0.00 35.22 2.75
51 52 1.064832 GCTTGGGCTTGAAGGAGATCT 60.065 52.381 0.00 0.00 35.22 2.75
52 53 2.620108 GCTTGGGCTTGAAGGAGATCTT 60.620 50.000 0.00 0.00 35.35 2.40
53 54 4.488662 GCTTGGGCTTGAAGGAGATCTTC 61.489 52.174 0.00 0.00 42.40 2.87
61 62 2.345124 AAGGAGATCTTCAGCATGGC 57.655 50.000 3.21 0.00 36.16 4.40
62 63 0.473326 AGGAGATCTTCAGCATGGCC 59.527 55.000 3.21 0.00 36.16 5.36
63 64 0.182061 GGAGATCTTCAGCATGGCCA 59.818 55.000 8.56 8.56 36.16 5.36
64 65 1.202903 GGAGATCTTCAGCATGGCCAT 60.203 52.381 14.09 14.09 36.16 4.40
65 66 1.880675 GAGATCTTCAGCATGGCCATG 59.119 52.381 36.80 36.80 41.60 3.66
66 67 1.493446 AGATCTTCAGCATGGCCATGA 59.507 47.619 43.18 25.30 41.20 3.07
67 68 2.092049 AGATCTTCAGCATGGCCATGAA 60.092 45.455 43.18 29.78 41.20 2.57
68 69 2.219080 TCTTCAGCATGGCCATGAAA 57.781 45.000 43.18 30.43 41.20 2.69
69 70 2.742348 TCTTCAGCATGGCCATGAAAT 58.258 42.857 43.18 27.00 41.20 2.17
70 71 2.691526 TCTTCAGCATGGCCATGAAATC 59.308 45.455 43.18 27.35 41.20 2.17
71 72 2.447408 TCAGCATGGCCATGAAATCT 57.553 45.000 43.18 28.98 41.20 2.40
72 73 2.742348 TCAGCATGGCCATGAAATCTT 58.258 42.857 43.18 20.28 41.20 2.40
73 74 2.429250 TCAGCATGGCCATGAAATCTTG 59.571 45.455 43.18 28.08 41.20 3.02
74 75 1.760613 AGCATGGCCATGAAATCTTGG 59.239 47.619 43.18 18.56 41.20 3.61
75 76 1.483415 GCATGGCCATGAAATCTTGGT 59.517 47.619 43.18 5.46 41.65 3.67
76 77 2.482490 GCATGGCCATGAAATCTTGGTC 60.482 50.000 43.18 20.97 43.62 4.02
77 78 1.462616 TGGCCATGAAATCTTGGTCG 58.537 50.000 0.00 0.00 45.53 4.79
78 79 0.740737 GGCCATGAAATCTTGGTCGG 59.259 55.000 14.62 0.00 41.65 4.79
79 80 1.681780 GGCCATGAAATCTTGGTCGGA 60.682 52.381 14.62 0.00 41.65 4.55
80 81 1.672881 GCCATGAAATCTTGGTCGGAG 59.327 52.381 14.62 0.00 41.65 4.63
81 82 2.292267 CCATGAAATCTTGGTCGGAGG 58.708 52.381 0.00 0.00 36.67 4.30
82 83 1.672881 CATGAAATCTTGGTCGGAGGC 59.327 52.381 0.00 0.00 0.00 4.70
83 84 0.391130 TGAAATCTTGGTCGGAGGCG 60.391 55.000 0.00 0.00 0.00 5.52
84 85 0.108329 GAAATCTTGGTCGGAGGCGA 60.108 55.000 0.00 0.00 0.00 5.54
85 86 0.541863 AAATCTTGGTCGGAGGCGAT 59.458 50.000 0.00 0.00 0.00 4.58
86 87 0.105039 AATCTTGGTCGGAGGCGATC 59.895 55.000 0.00 0.00 0.00 3.69
87 88 0.757188 ATCTTGGTCGGAGGCGATCT 60.757 55.000 0.00 0.00 0.00 2.75
88 89 1.227089 CTTGGTCGGAGGCGATCTG 60.227 63.158 0.00 0.00 35.40 2.90
89 90 2.635229 CTTGGTCGGAGGCGATCTGG 62.635 65.000 0.00 0.00 34.76 3.86
90 91 3.917760 GGTCGGAGGCGATCTGGG 61.918 72.222 0.00 0.00 34.76 4.45
91 92 3.917760 GTCGGAGGCGATCTGGGG 61.918 72.222 0.00 0.00 34.76 4.96
94 95 4.247380 GGAGGCGATCTGGGGCTG 62.247 72.222 0.00 0.00 40.78 4.85
95 96 4.925861 GAGGCGATCTGGGGCTGC 62.926 72.222 0.00 0.00 40.78 5.25
99 100 3.473647 CGATCTGGGGCTGCAGGA 61.474 66.667 17.12 3.73 0.00 3.86
100 101 3.001514 GATCTGGGGCTGCAGGAA 58.998 61.111 17.12 0.00 0.00 3.36
101 102 1.304282 GATCTGGGGCTGCAGGAAA 59.696 57.895 17.12 0.00 0.00 3.13
102 103 0.750911 GATCTGGGGCTGCAGGAAAG 60.751 60.000 17.12 0.00 0.00 2.62
103 104 2.850828 ATCTGGGGCTGCAGGAAAGC 62.851 60.000 17.12 0.13 40.06 3.51
109 110 2.434185 CTGCAGGAAAGCGCGGTA 60.434 61.111 12.91 0.00 37.31 4.02
110 111 2.740714 CTGCAGGAAAGCGCGGTAC 61.741 63.158 12.91 9.17 37.31 3.34
137 138 4.223800 GCCATGCCATCGTCTTCA 57.776 55.556 0.00 0.00 0.00 3.02
138 139 2.481212 GCCATGCCATCGTCTTCAA 58.519 52.632 0.00 0.00 0.00 2.69
139 140 0.099436 GCCATGCCATCGTCTTCAAC 59.901 55.000 0.00 0.00 0.00 3.18
140 141 0.734889 CCATGCCATCGTCTTCAACC 59.265 55.000 0.00 0.00 0.00 3.77
141 142 1.679944 CCATGCCATCGTCTTCAACCT 60.680 52.381 0.00 0.00 0.00 3.50
142 143 1.399440 CATGCCATCGTCTTCAACCTG 59.601 52.381 0.00 0.00 0.00 4.00
143 144 0.321564 TGCCATCGTCTTCAACCTGG 60.322 55.000 0.00 0.00 32.67 4.45
144 145 1.648467 GCCATCGTCTTCAACCTGGC 61.648 60.000 0.00 0.00 42.61 4.85
145 146 1.026718 CCATCGTCTTCAACCTGGCC 61.027 60.000 0.00 0.00 0.00 5.36
146 147 0.321564 CATCGTCTTCAACCTGGCCA 60.322 55.000 4.71 4.71 0.00 5.36
147 148 0.321653 ATCGTCTTCAACCTGGCCAC 60.322 55.000 0.00 0.00 0.00 5.01
148 149 1.966451 CGTCTTCAACCTGGCCACC 60.966 63.158 0.00 0.00 0.00 4.61
149 150 1.456287 GTCTTCAACCTGGCCACCT 59.544 57.895 0.00 0.00 0.00 4.00
150 151 0.890996 GTCTTCAACCTGGCCACCTG 60.891 60.000 0.00 0.00 0.00 4.00
151 152 1.604593 CTTCAACCTGGCCACCTGG 60.605 63.158 0.00 4.17 46.30 4.45
179 180 3.787001 GAGTCCCGGGCCAAGGAG 61.787 72.222 18.49 8.06 31.17 3.69
207 208 2.683933 GAGGCAGGGTCCGAGGAA 60.684 66.667 0.00 0.00 0.00 3.36
208 209 2.685380 AGGCAGGGTCCGAGGAAG 60.685 66.667 0.00 0.00 0.00 3.46
209 210 2.683933 GGCAGGGTCCGAGGAAGA 60.684 66.667 0.00 0.00 0.00 2.87
210 211 2.726351 GGCAGGGTCCGAGGAAGAG 61.726 68.421 0.00 0.00 0.00 2.85
211 212 2.896443 CAGGGTCCGAGGAAGAGC 59.104 66.667 0.00 0.00 0.00 4.09
212 213 1.984570 CAGGGTCCGAGGAAGAGCA 60.985 63.158 0.00 0.00 33.37 4.26
213 214 1.985116 AGGGTCCGAGGAAGAGCAC 60.985 63.158 0.00 0.00 33.37 4.40
214 215 2.182030 GGTCCGAGGAAGAGCACG 59.818 66.667 0.00 0.00 0.00 5.34
215 216 2.507324 GTCCGAGGAAGAGCACGC 60.507 66.667 0.00 0.00 0.00 5.34
216 217 3.760035 TCCGAGGAAGAGCACGCC 61.760 66.667 0.00 0.00 0.00 5.68
217 218 4.821589 CCGAGGAAGAGCACGCCC 62.822 72.222 0.00 0.00 0.00 6.13
218 219 4.069232 CGAGGAAGAGCACGCCCA 62.069 66.667 0.00 0.00 0.00 5.36
219 220 2.125350 GAGGAAGAGCACGCCCAG 60.125 66.667 0.00 0.00 0.00 4.45
220 221 4.400961 AGGAAGAGCACGCCCAGC 62.401 66.667 0.00 0.00 0.00 4.85
221 222 4.704833 GGAAGAGCACGCCCAGCA 62.705 66.667 0.00 0.00 0.00 4.41
222 223 3.426568 GAAGAGCACGCCCAGCAC 61.427 66.667 0.00 0.00 0.00 4.40
234 235 3.866582 CAGCACCGGATCCCCCTC 61.867 72.222 9.46 0.00 0.00 4.30
266 267 4.715523 CGTGCGGATGGGGGTTGT 62.716 66.667 0.00 0.00 0.00 3.32
267 268 3.061848 GTGCGGATGGGGGTTGTG 61.062 66.667 0.00 0.00 0.00 3.33
268 269 4.358841 TGCGGATGGGGGTTGTGG 62.359 66.667 0.00 0.00 0.00 4.17
269 270 4.041762 GCGGATGGGGGTTGTGGA 62.042 66.667 0.00 0.00 0.00 4.02
270 271 2.272146 CGGATGGGGGTTGTGGAG 59.728 66.667 0.00 0.00 0.00 3.86
271 272 2.683475 GGATGGGGGTTGTGGAGG 59.317 66.667 0.00 0.00 0.00 4.30
272 273 2.238701 GGATGGGGGTTGTGGAGGT 61.239 63.158 0.00 0.00 0.00 3.85
273 274 1.000896 GATGGGGGTTGTGGAGGTG 60.001 63.158 0.00 0.00 0.00 4.00
274 275 3.224007 ATGGGGGTTGTGGAGGTGC 62.224 63.158 0.00 0.00 0.00 5.01
277 278 3.948719 GGGTTGTGGAGGTGCGGA 61.949 66.667 0.00 0.00 0.00 5.54
278 279 2.668550 GGTTGTGGAGGTGCGGAC 60.669 66.667 0.00 0.00 0.00 4.79
279 280 3.041940 GTTGTGGAGGTGCGGACG 61.042 66.667 0.00 0.00 0.00 4.79
280 281 4.308458 TTGTGGAGGTGCGGACGG 62.308 66.667 0.00 0.00 0.00 4.79
307 308 4.289379 CGATCGCGCGACGTCCTA 62.289 66.667 37.37 11.87 44.19 2.94
308 309 2.425448 GATCGCGCGACGTCCTAG 60.425 66.667 37.37 0.00 44.19 3.02
309 310 2.879070 GATCGCGCGACGTCCTAGA 61.879 63.158 37.37 10.06 44.19 2.43
310 311 2.172719 GATCGCGCGACGTCCTAGAT 62.173 60.000 37.37 16.52 44.19 1.98
311 312 2.172719 ATCGCGCGACGTCCTAGATC 62.173 60.000 37.37 0.00 44.19 2.75
312 313 2.883468 CGCGCGACGTCCTAGATCT 61.883 63.158 28.94 0.00 36.87 2.75
313 314 1.082627 GCGCGACGTCCTAGATCTC 60.083 63.158 12.10 0.00 0.00 2.75
314 315 1.202072 CGCGACGTCCTAGATCTCG 59.798 63.158 10.58 0.00 0.00 4.04
315 316 1.489070 CGCGACGTCCTAGATCTCGT 61.489 60.000 10.58 6.88 39.21 4.18
316 317 0.656785 GCGACGTCCTAGATCTCGTT 59.343 55.000 10.58 0.00 36.67 3.85
317 318 1.595003 GCGACGTCCTAGATCTCGTTG 60.595 57.143 10.58 14.55 39.66 4.10
318 319 1.931841 CGACGTCCTAGATCTCGTTGA 59.068 52.381 10.58 0.00 39.21 3.18
319 320 2.544686 CGACGTCCTAGATCTCGTTGAT 59.455 50.000 10.58 0.00 39.21 2.57
328 329 1.914634 ATCTCGTTGATCAGCACGTC 58.085 50.000 17.09 0.00 0.00 4.34
329 330 0.454452 TCTCGTTGATCAGCACGTCG 60.454 55.000 17.09 11.02 0.00 5.12
330 331 1.406219 CTCGTTGATCAGCACGTCGG 61.406 60.000 17.09 7.52 0.00 4.79
331 332 2.778679 GTTGATCAGCACGTCGGC 59.221 61.111 4.47 0.00 0.00 5.54
332 333 2.809174 TTGATCAGCACGTCGGCG 60.809 61.111 8.42 8.42 44.93 6.46
362 363 3.467119 CCGTCGAAGCGGTGAACG 61.467 66.667 6.32 9.02 46.11 3.95
363 364 3.467119 CGTCGAAGCGGTGAACGG 61.467 66.667 0.00 0.00 44.51 4.44
364 365 3.774702 GTCGAAGCGGTGAACGGC 61.775 66.667 4.94 4.94 44.51 5.68
367 368 2.813908 GAAGCGGTGAACGGCGAT 60.814 61.111 16.62 0.00 45.36 4.58
368 369 3.083600 GAAGCGGTGAACGGCGATG 62.084 63.158 16.62 0.00 45.36 3.84
369 370 3.876589 AAGCGGTGAACGGCGATGT 62.877 57.895 16.62 0.00 45.36 3.06
370 371 4.147322 GCGGTGAACGGCGATGTG 62.147 66.667 16.62 0.00 44.51 3.21
371 372 3.487202 CGGTGAACGGCGATGTGG 61.487 66.667 16.62 0.00 39.42 4.17
372 373 2.358247 GGTGAACGGCGATGTGGT 60.358 61.111 16.62 0.00 0.00 4.16
373 374 2.677003 GGTGAACGGCGATGTGGTG 61.677 63.158 16.62 0.00 0.00 4.17
374 375 2.358125 TGAACGGCGATGTGGTGG 60.358 61.111 16.62 0.00 0.00 4.61
375 376 3.124921 GAACGGCGATGTGGTGGG 61.125 66.667 16.62 0.00 0.00 4.61
376 377 4.715523 AACGGCGATGTGGTGGGG 62.716 66.667 16.62 0.00 0.00 4.96
379 380 3.809013 GGCGATGTGGTGGGGGAT 61.809 66.667 0.00 0.00 0.00 3.85
380 381 2.516930 GCGATGTGGTGGGGGATG 60.517 66.667 0.00 0.00 0.00 3.51
381 382 2.998097 CGATGTGGTGGGGGATGT 59.002 61.111 0.00 0.00 0.00 3.06
382 383 1.451927 CGATGTGGTGGGGGATGTG 60.452 63.158 0.00 0.00 0.00 3.21
383 384 1.691219 GATGTGGTGGGGGATGTGT 59.309 57.895 0.00 0.00 0.00 3.72
384 385 0.039618 GATGTGGTGGGGGATGTGTT 59.960 55.000 0.00 0.00 0.00 3.32
385 386 0.251742 ATGTGGTGGGGGATGTGTTG 60.252 55.000 0.00 0.00 0.00 3.33
386 387 2.117206 TGGTGGGGGATGTGTTGC 59.883 61.111 0.00 0.00 0.00 4.17
387 388 2.117206 GGTGGGGGATGTGTTGCA 59.883 61.111 0.00 0.00 0.00 4.08
388 389 1.978617 GGTGGGGGATGTGTTGCAG 60.979 63.158 0.00 0.00 0.00 4.41
389 390 2.283101 TGGGGGATGTGTTGCAGC 60.283 61.111 0.00 0.00 0.00 5.25
390 391 3.443045 GGGGGATGTGTTGCAGCG 61.443 66.667 0.00 0.00 33.59 5.18
391 392 4.120331 GGGGATGTGTTGCAGCGC 62.120 66.667 7.21 7.21 44.32 5.92
392 393 4.120331 GGGATGTGTTGCAGCGCC 62.120 66.667 11.79 2.60 40.03 6.53
393 394 3.058160 GGATGTGTTGCAGCGCCT 61.058 61.111 11.79 1.12 33.59 5.52
394 395 2.482374 GATGTGTTGCAGCGCCTC 59.518 61.111 11.79 7.61 0.00 4.70
395 396 3.372676 GATGTGTTGCAGCGCCTCG 62.373 63.158 11.79 0.00 0.00 4.63
396 397 3.881952 ATGTGTTGCAGCGCCTCGA 62.882 57.895 11.79 0.00 0.00 4.04
397 398 4.077188 GTGTTGCAGCGCCTCGAC 62.077 66.667 2.29 6.87 0.00 4.20
398 399 4.299547 TGTTGCAGCGCCTCGACT 62.300 61.111 2.29 0.00 0.00 4.18
399 400 3.044305 GTTGCAGCGCCTCGACTT 61.044 61.111 2.29 0.00 0.00 3.01
400 401 2.280797 TTGCAGCGCCTCGACTTT 60.281 55.556 2.29 0.00 0.00 2.66
401 402 2.606961 TTGCAGCGCCTCGACTTTG 61.607 57.895 2.29 0.00 0.00 2.77
402 403 3.793144 GCAGCGCCTCGACTTTGG 61.793 66.667 2.29 0.00 0.00 3.28
403 404 3.793144 CAGCGCCTCGACTTTGGC 61.793 66.667 2.29 3.38 45.25 4.52
411 412 3.137484 TCGACTTTGGCGAGGATTG 57.863 52.632 0.00 0.00 33.33 2.67
459 460 3.589654 TTGCGAGGACTCAAGGCCG 62.590 63.158 0.00 0.00 0.00 6.13
474 475 1.450312 GCCGAACTGCAGTATGGCT 60.450 57.895 36.72 18.89 42.05 4.75
504 512 3.243975 GGACCAGAGGTTGTTTTAGACGA 60.244 47.826 0.00 0.00 35.25 4.20
510 518 6.090898 CCAGAGGTTGTTTTAGACGATGTTAG 59.909 42.308 0.00 0.00 0.00 2.34
513 521 4.453136 GGTTGTTTTAGACGATGTTAGGCA 59.547 41.667 0.00 0.00 0.00 4.75
526 534 7.045416 ACGATGTTAGGCATGATTGTACTTTA 58.955 34.615 0.00 0.00 38.06 1.85
531 539 8.465999 TGTTAGGCATGATTGTACTTTAATTGG 58.534 33.333 0.00 0.00 0.00 3.16
585 601 3.491447 GGGCATGTGCATACAAAATCCTC 60.491 47.826 7.36 0.00 44.36 3.71
673 704 6.809196 TCAAATAACCCGTAAATGATTTGCAC 59.191 34.615 6.79 0.00 35.33 4.57
689 720 1.885887 TGCACAGCAAGTAATGTTCCC 59.114 47.619 0.00 0.00 34.76 3.97
690 721 1.202348 GCACAGCAAGTAATGTTCCCC 59.798 52.381 0.00 0.00 0.00 4.81
704 735 2.714250 TGTTCCCCTAACTCCACAATGT 59.286 45.455 0.00 0.00 38.99 2.71
708 739 3.199946 TCCCCTAACTCCACAATGTCATC 59.800 47.826 0.00 0.00 0.00 2.92
735 766 3.195396 TGCTTTCCACTTTCATAATGCCC 59.805 43.478 0.00 0.00 0.00 5.36
858 889 4.154015 TGCCAGTCACTTGTAATTTCGATG 59.846 41.667 0.00 0.00 0.00 3.84
873 904 2.051879 CGATGCGATAATCGGTGAGT 57.948 50.000 7.46 0.00 44.49 3.41
878 909 3.792401 TGCGATAATCGGTGAGTTTCAT 58.208 40.909 0.00 0.00 40.84 2.57
911 942 2.029221 GCTCGCCGGATTACTCCC 59.971 66.667 5.05 0.00 38.45 4.30
928 959 2.102357 CGTCATCGTACAGCGGCT 59.898 61.111 0.00 0.00 41.72 5.52
966 1001 1.066587 CGATCTTCCGCTCCTGTCC 59.933 63.158 0.00 0.00 0.00 4.02
1047 1094 3.490759 GCGCTGGTCGTGATGGTG 61.491 66.667 0.00 0.00 41.07 4.17
1048 1095 2.815211 CGCTGGTCGTGATGGTGG 60.815 66.667 0.00 0.00 0.00 4.61
1049 1096 2.347490 GCTGGTCGTGATGGTGGT 59.653 61.111 0.00 0.00 0.00 4.16
1050 1097 2.034879 GCTGGTCGTGATGGTGGTG 61.035 63.158 0.00 0.00 0.00 4.17
1051 1098 1.375908 CTGGTCGTGATGGTGGTGG 60.376 63.158 0.00 0.00 0.00 4.61
1052 1099 2.746277 GGTCGTGATGGTGGTGGC 60.746 66.667 0.00 0.00 0.00 5.01
1053 1100 3.118454 GTCGTGATGGTGGTGGCG 61.118 66.667 0.00 0.00 0.00 5.69
1054 1101 4.386951 TCGTGATGGTGGTGGCGG 62.387 66.667 0.00 0.00 0.00 6.13
1056 1103 4.722700 GTGATGGTGGTGGCGGCT 62.723 66.667 11.43 0.00 0.00 5.52
1057 1104 4.720902 TGATGGTGGTGGCGGCTG 62.721 66.667 11.43 0.00 0.00 4.85
1072 1119 4.758251 CTGCGATGGTGGTGGCGA 62.758 66.667 0.00 0.00 0.00 5.54
1228 1275 2.048222 CTCGCTTCAAGCCGTCCA 60.048 61.111 3.08 0.00 38.18 4.02
1706 1756 3.826157 CCTACCCACATTGCTCTTTTGAA 59.174 43.478 0.00 0.00 0.00 2.69
1921 2021 6.604735 ACAGTTGTGTTTCTCTGATGTTAC 57.395 37.500 0.00 0.00 30.30 2.50
1922 2022 5.234329 ACAGTTGTGTTTCTCTGATGTTACG 59.766 40.000 0.00 0.00 30.30 3.18
1954 2062 0.953727 TGCAGCATTGACACCTTGAC 59.046 50.000 0.00 0.00 0.00 3.18
1955 2063 0.953727 GCAGCATTGACACCTTGACA 59.046 50.000 0.00 0.00 0.00 3.58
2061 2169 4.638865 TGAATTCAGATGCAGTCATGAAGG 59.361 41.667 3.38 0.00 31.96 3.46
2062 2170 2.704464 TCAGATGCAGTCATGAAGGG 57.296 50.000 0.00 0.00 31.96 3.95
2124 2232 4.844349 ACCAACTTACCATACAGCTGAT 57.156 40.909 23.35 6.78 0.00 2.90
2181 2289 8.697507 AGAGATGTACTTTTCCATTGAAAACT 57.302 30.769 0.73 0.00 43.68 2.66
2182 2290 9.793259 AGAGATGTACTTTTCCATTGAAAACTA 57.207 29.630 0.73 0.00 43.68 2.24
2223 2367 8.097038 AGAGCAGATTGTATTTAAGTGTTCAGA 58.903 33.333 0.00 0.00 0.00 3.27
2233 2377 9.314501 GTATTTAAGTGTTCAGATTTCAACGAC 57.685 33.333 0.00 0.00 0.00 4.34
2297 2876 2.880963 AAAGCTTAACCGCAGCAAAA 57.119 40.000 0.00 0.00 39.99 2.44
2298 2877 2.880963 AAGCTTAACCGCAGCAAAAA 57.119 40.000 0.00 0.00 39.99 1.94
2337 3043 5.912528 AGTTTAACACTAAGATTTCGTGCG 58.087 37.500 0.00 0.00 31.97 5.34
2347 3053 7.006210 CACTAAGATTTCGTGCGAATACAAAAC 59.994 37.037 7.87 0.00 33.79 2.43
2376 3082 8.788806 ACTTTATTTCATCCGTGAATGTAACAA 58.211 29.630 0.00 0.00 43.49 2.83
2377 3083 9.619316 CTTTATTTCATCCGTGAATGTAACAAA 57.381 29.630 0.00 0.00 43.49 2.83
2493 4154 7.392953 TCTGTTGCCATCAATGACTAAATACAA 59.607 33.333 0.00 0.00 34.29 2.41
2778 4457 9.000486 GGTCTATCATATAGCAAAAGTTTACCC 58.000 37.037 0.00 0.00 0.00 3.69
2828 4507 7.631717 AAAAGAACATAAGAGTAGGAATGGC 57.368 36.000 0.00 0.00 0.00 4.40
2844 4523 2.877097 TGGCATACATTGGAGTGTGT 57.123 45.000 0.00 0.00 33.71 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.916206 GCTCCTTTCTCCCTCCCCAC 61.916 65.000 0.00 0.00 0.00 4.61
3 4 2.379459 GGGCTCCTTTCTCCCTCCC 61.379 68.421 0.00 0.00 37.08 4.30
5 6 2.379459 GGGGGCTCCTTTCTCCCTC 61.379 68.421 0.52 0.00 39.95 4.30
6 7 2.286502 GGGGGCTCCTTTCTCCCT 60.287 66.667 0.52 0.00 39.95 4.20
15 16 1.931007 AAGCTCATCAAGGGGGCTCC 61.931 60.000 0.00 0.00 32.46 4.70
16 17 0.750911 CAAGCTCATCAAGGGGGCTC 60.751 60.000 0.00 0.00 32.46 4.70
17 18 1.305623 CAAGCTCATCAAGGGGGCT 59.694 57.895 0.00 0.00 34.52 5.19
18 19 1.755783 CCAAGCTCATCAAGGGGGC 60.756 63.158 0.00 0.00 0.00 5.80
19 20 1.076485 CCCAAGCTCATCAAGGGGG 60.076 63.158 0.00 0.00 35.83 5.40
20 21 1.755783 GCCCAAGCTCATCAAGGGG 60.756 63.158 0.00 0.00 39.96 4.79
21 22 3.930504 GCCCAAGCTCATCAAGGG 58.069 61.111 0.00 0.00 42.55 3.95
31 32 1.064832 AGATCTCCTTCAAGCCCAAGC 60.065 52.381 0.00 0.00 40.32 4.01
32 33 3.362870 AAGATCTCCTTCAAGCCCAAG 57.637 47.619 0.00 0.00 0.00 3.61
42 43 1.133853 GGCCATGCTGAAGATCTCCTT 60.134 52.381 0.00 0.00 37.93 3.36
43 44 0.473326 GGCCATGCTGAAGATCTCCT 59.527 55.000 0.00 0.00 0.00 3.69
44 45 0.182061 TGGCCATGCTGAAGATCTCC 59.818 55.000 0.00 0.00 0.00 3.71
45 46 1.880675 CATGGCCATGCTGAAGATCTC 59.119 52.381 31.95 0.00 31.39 2.75
46 47 1.493446 TCATGGCCATGCTGAAGATCT 59.507 47.619 36.47 0.27 38.65 2.75
47 48 1.977056 TCATGGCCATGCTGAAGATC 58.023 50.000 36.47 0.00 38.65 2.75
48 49 2.447408 TTCATGGCCATGCTGAAGAT 57.553 45.000 36.47 1.74 38.65 2.40
49 50 2.219080 TTTCATGGCCATGCTGAAGA 57.781 45.000 36.47 18.67 38.65 2.87
50 51 2.693591 AGATTTCATGGCCATGCTGAAG 59.306 45.455 36.47 15.96 38.65 3.02
51 52 2.742348 AGATTTCATGGCCATGCTGAA 58.258 42.857 36.47 28.53 38.65 3.02
52 53 2.429250 CAAGATTTCATGGCCATGCTGA 59.571 45.455 36.47 24.81 38.65 4.26
53 54 2.483013 CCAAGATTTCATGGCCATGCTG 60.483 50.000 36.47 23.87 38.65 4.41
54 55 1.760613 CCAAGATTTCATGGCCATGCT 59.239 47.619 36.47 25.55 38.65 3.79
55 56 1.483415 ACCAAGATTTCATGGCCATGC 59.517 47.619 36.47 23.83 38.21 4.06
56 57 2.223641 CGACCAAGATTTCATGGCCATG 60.224 50.000 35.76 35.76 38.21 3.66
57 58 2.026641 CGACCAAGATTTCATGGCCAT 58.973 47.619 14.09 14.09 38.21 4.40
58 59 1.462616 CGACCAAGATTTCATGGCCA 58.537 50.000 8.56 8.56 38.21 5.36
59 60 0.740737 CCGACCAAGATTTCATGGCC 59.259 55.000 0.00 0.00 38.21 5.36
60 61 1.672881 CTCCGACCAAGATTTCATGGC 59.327 52.381 1.85 0.00 38.21 4.40
61 62 2.292267 CCTCCGACCAAGATTTCATGG 58.708 52.381 0.42 0.42 40.34 3.66
62 63 1.672881 GCCTCCGACCAAGATTTCATG 59.327 52.381 0.00 0.00 0.00 3.07
63 64 1.743772 CGCCTCCGACCAAGATTTCAT 60.744 52.381 0.00 0.00 36.29 2.57
64 65 0.391130 CGCCTCCGACCAAGATTTCA 60.391 55.000 0.00 0.00 36.29 2.69
65 66 0.108329 TCGCCTCCGACCAAGATTTC 60.108 55.000 0.00 0.00 38.82 2.17
66 67 1.980052 TCGCCTCCGACCAAGATTT 59.020 52.632 0.00 0.00 38.82 2.17
67 68 3.708210 TCGCCTCCGACCAAGATT 58.292 55.556 0.00 0.00 38.82 2.40
77 78 4.247380 CAGCCCCAGATCGCCTCC 62.247 72.222 0.00 0.00 0.00 4.30
78 79 4.925861 GCAGCCCCAGATCGCCTC 62.926 72.222 0.00 0.00 0.00 4.70
82 83 2.541547 TTTCCTGCAGCCCCAGATCG 62.542 60.000 8.66 0.00 34.77 3.69
83 84 0.750911 CTTTCCTGCAGCCCCAGATC 60.751 60.000 8.66 0.00 34.77 2.75
84 85 1.305623 CTTTCCTGCAGCCCCAGAT 59.694 57.895 8.66 0.00 34.77 2.90
85 86 2.759114 CTTTCCTGCAGCCCCAGA 59.241 61.111 8.66 0.00 34.77 3.86
86 87 3.066814 GCTTTCCTGCAGCCCCAG 61.067 66.667 8.66 2.08 0.00 4.45
92 93 2.434185 TACCGCGCTTTCCTGCAG 60.434 61.111 6.78 6.78 0.00 4.41
93 94 2.740826 GTACCGCGCTTTCCTGCA 60.741 61.111 5.56 0.00 0.00 4.41
94 95 3.849953 CGTACCGCGCTTTCCTGC 61.850 66.667 5.56 0.00 0.00 4.85
120 121 0.099436 GTTGAAGACGATGGCATGGC 59.901 55.000 13.29 13.29 0.00 4.40
121 122 0.734889 GGTTGAAGACGATGGCATGG 59.265 55.000 3.81 6.26 0.00 3.66
122 123 1.399440 CAGGTTGAAGACGATGGCATG 59.601 52.381 3.81 0.00 0.00 4.06
123 124 1.679944 CCAGGTTGAAGACGATGGCAT 60.680 52.381 0.00 0.00 31.52 4.40
124 125 0.321564 CCAGGTTGAAGACGATGGCA 60.322 55.000 0.00 0.00 31.52 4.92
125 126 2.471255 CCAGGTTGAAGACGATGGC 58.529 57.895 0.00 0.00 31.52 4.40
126 127 1.026718 GGCCAGGTTGAAGACGATGG 61.027 60.000 0.00 0.00 38.29 3.51
127 128 0.321564 TGGCCAGGTTGAAGACGATG 60.322 55.000 0.00 0.00 0.00 3.84
128 129 0.321653 GTGGCCAGGTTGAAGACGAT 60.322 55.000 5.11 0.00 0.00 3.73
129 130 1.070786 GTGGCCAGGTTGAAGACGA 59.929 57.895 5.11 0.00 0.00 4.20
130 131 1.966451 GGTGGCCAGGTTGAAGACG 60.966 63.158 5.11 0.00 0.00 4.18
131 132 0.890996 CAGGTGGCCAGGTTGAAGAC 60.891 60.000 5.11 0.00 0.00 3.01
132 133 1.455849 CAGGTGGCCAGGTTGAAGA 59.544 57.895 5.11 0.00 0.00 2.87
133 134 1.604593 CCAGGTGGCCAGGTTGAAG 60.605 63.158 5.11 0.00 0.00 3.02
134 135 2.391130 ACCAGGTGGCCAGGTTGAA 61.391 57.895 5.11 0.00 40.64 2.69
135 136 2.776526 ACCAGGTGGCCAGGTTGA 60.777 61.111 5.11 0.00 40.64 3.18
136 137 2.598394 CACCAGGTGGCCAGGTTG 60.598 66.667 12.37 8.11 40.64 3.77
137 138 4.603535 GCACCAGGTGGCCAGGTT 62.604 66.667 21.77 0.00 40.64 3.50
162 163 3.787001 CTCCTTGGCCCGGGACTC 61.787 72.222 30.93 15.00 0.00 3.36
190 191 2.683933 TTCCTCGGACCCTGCCTC 60.684 66.667 0.00 0.00 0.00 4.70
191 192 2.685380 CTTCCTCGGACCCTGCCT 60.685 66.667 0.00 0.00 0.00 4.75
192 193 2.683933 TCTTCCTCGGACCCTGCC 60.684 66.667 0.00 0.00 0.00 4.85
193 194 2.896443 CTCTTCCTCGGACCCTGC 59.104 66.667 0.00 0.00 0.00 4.85
194 195 1.984570 TGCTCTTCCTCGGACCCTG 60.985 63.158 0.00 0.00 0.00 4.45
195 196 1.985116 GTGCTCTTCCTCGGACCCT 60.985 63.158 0.00 0.00 0.00 4.34
196 197 2.579738 GTGCTCTTCCTCGGACCC 59.420 66.667 0.00 0.00 0.00 4.46
197 198 2.182030 CGTGCTCTTCCTCGGACC 59.818 66.667 0.00 0.00 0.00 4.46
198 199 2.507324 GCGTGCTCTTCCTCGGAC 60.507 66.667 0.00 0.00 0.00 4.79
199 200 3.760035 GGCGTGCTCTTCCTCGGA 61.760 66.667 0.00 0.00 0.00 4.55
200 201 4.821589 GGGCGTGCTCTTCCTCGG 62.822 72.222 0.00 0.00 0.00 4.63
201 202 3.997064 CTGGGCGTGCTCTTCCTCG 62.997 68.421 0.00 0.00 0.00 4.63
202 203 2.125350 CTGGGCGTGCTCTTCCTC 60.125 66.667 0.00 0.00 0.00 3.71
203 204 4.400961 GCTGGGCGTGCTCTTCCT 62.401 66.667 0.00 0.00 0.00 3.36
204 205 4.704833 TGCTGGGCGTGCTCTTCC 62.705 66.667 0.00 0.00 0.00 3.46
205 206 3.426568 GTGCTGGGCGTGCTCTTC 61.427 66.667 0.00 0.00 0.00 2.87
217 218 3.866582 GAGGGGGATCCGGTGCTG 61.867 72.222 5.45 0.00 41.52 4.41
249 250 4.715523 ACAACCCCCATCCGCACG 62.716 66.667 0.00 0.00 0.00 5.34
250 251 3.061848 CACAACCCCCATCCGCAC 61.062 66.667 0.00 0.00 0.00 5.34
251 252 4.358841 CCACAACCCCCATCCGCA 62.359 66.667 0.00 0.00 0.00 5.69
252 253 3.995506 CTCCACAACCCCCATCCGC 62.996 68.421 0.00 0.00 0.00 5.54
253 254 2.272146 CTCCACAACCCCCATCCG 59.728 66.667 0.00 0.00 0.00 4.18
254 255 2.238701 ACCTCCACAACCCCCATCC 61.239 63.158 0.00 0.00 0.00 3.51
255 256 1.000896 CACCTCCACAACCCCCATC 60.001 63.158 0.00 0.00 0.00 3.51
256 257 3.180282 CACCTCCACAACCCCCAT 58.820 61.111 0.00 0.00 0.00 4.00
257 258 3.897122 GCACCTCCACAACCCCCA 61.897 66.667 0.00 0.00 0.00 4.96
260 261 3.948719 TCCGCACCTCCACAACCC 61.949 66.667 0.00 0.00 0.00 4.11
261 262 2.668550 GTCCGCACCTCCACAACC 60.669 66.667 0.00 0.00 0.00 3.77
262 263 3.041940 CGTCCGCACCTCCACAAC 61.042 66.667 0.00 0.00 0.00 3.32
263 264 4.308458 CCGTCCGCACCTCCACAA 62.308 66.667 0.00 0.00 0.00 3.33
290 291 4.289379 TAGGACGTCGCGCGATCG 62.289 66.667 35.33 35.33 44.77 3.69
291 292 2.172719 ATCTAGGACGTCGCGCGATC 62.173 60.000 37.03 28.66 44.77 3.69
292 293 2.172719 GATCTAGGACGTCGCGCGAT 62.173 60.000 37.03 22.09 44.77 4.58
293 294 2.879070 GATCTAGGACGTCGCGCGA 61.879 63.158 31.40 31.40 44.77 5.87
295 296 1.082627 GAGATCTAGGACGTCGCGC 60.083 63.158 9.92 0.00 0.00 6.86
296 297 1.202072 CGAGATCTAGGACGTCGCG 59.798 63.158 9.92 0.00 0.00 5.87
297 298 0.656785 AACGAGATCTAGGACGTCGC 59.343 55.000 9.92 2.53 38.00 5.19
298 299 1.931841 TCAACGAGATCTAGGACGTCG 59.068 52.381 9.92 2.42 38.00 5.12
309 310 1.795525 CGACGTGCTGATCAACGAGAT 60.796 52.381 23.06 4.40 40.48 2.75
310 311 0.454452 CGACGTGCTGATCAACGAGA 60.454 55.000 23.06 0.00 0.00 4.04
311 312 1.406219 CCGACGTGCTGATCAACGAG 61.406 60.000 23.06 16.14 0.00 4.18
312 313 1.443702 CCGACGTGCTGATCAACGA 60.444 57.895 23.06 0.00 0.00 3.85
313 314 3.071459 GCCGACGTGCTGATCAACG 62.071 63.158 16.40 16.40 0.00 4.10
314 315 2.778679 GCCGACGTGCTGATCAAC 59.221 61.111 0.00 0.00 0.00 3.18
315 316 2.809174 CGCCGACGTGCTGATCAA 60.809 61.111 0.00 0.00 33.53 2.57
346 347 3.467119 CCGTTCACCGCTTCGACG 61.467 66.667 0.00 0.00 34.38 5.12
347 348 3.774702 GCCGTTCACCGCTTCGAC 61.775 66.667 0.00 0.00 34.38 4.20
350 351 2.813908 ATCGCCGTTCACCGCTTC 60.814 61.111 0.00 0.00 34.38 3.86
351 352 3.118454 CATCGCCGTTCACCGCTT 61.118 61.111 0.00 0.00 34.38 4.68
352 353 4.373116 ACATCGCCGTTCACCGCT 62.373 61.111 0.00 0.00 34.38 5.52
353 354 4.147322 CACATCGCCGTTCACCGC 62.147 66.667 0.00 0.00 34.38 5.68
354 355 3.487202 CCACATCGCCGTTCACCG 61.487 66.667 0.00 0.00 0.00 4.94
355 356 2.358247 ACCACATCGCCGTTCACC 60.358 61.111 0.00 0.00 0.00 4.02
356 357 2.677003 CCACCACATCGCCGTTCAC 61.677 63.158 0.00 0.00 0.00 3.18
357 358 2.358125 CCACCACATCGCCGTTCA 60.358 61.111 0.00 0.00 0.00 3.18
358 359 3.124921 CCCACCACATCGCCGTTC 61.125 66.667 0.00 0.00 0.00 3.95
359 360 4.715523 CCCCACCACATCGCCGTT 62.716 66.667 0.00 0.00 0.00 4.44
362 363 3.809013 ATCCCCCACCACATCGCC 61.809 66.667 0.00 0.00 0.00 5.54
363 364 2.516930 CATCCCCCACCACATCGC 60.517 66.667 0.00 0.00 0.00 4.58
364 365 1.451927 CACATCCCCCACCACATCG 60.452 63.158 0.00 0.00 0.00 3.84
365 366 0.039618 AACACATCCCCCACCACATC 59.960 55.000 0.00 0.00 0.00 3.06
366 367 0.251742 CAACACATCCCCCACCACAT 60.252 55.000 0.00 0.00 0.00 3.21
367 368 1.152599 CAACACATCCCCCACCACA 59.847 57.895 0.00 0.00 0.00 4.17
368 369 2.275380 GCAACACATCCCCCACCAC 61.275 63.158 0.00 0.00 0.00 4.16
369 370 2.117206 GCAACACATCCCCCACCA 59.883 61.111 0.00 0.00 0.00 4.17
370 371 1.978617 CTGCAACACATCCCCCACC 60.979 63.158 0.00 0.00 0.00 4.61
371 372 2.639327 GCTGCAACACATCCCCCAC 61.639 63.158 0.00 0.00 0.00 4.61
372 373 2.283101 GCTGCAACACATCCCCCA 60.283 61.111 0.00 0.00 0.00 4.96
373 374 3.443045 CGCTGCAACACATCCCCC 61.443 66.667 0.00 0.00 0.00 5.40
374 375 4.120331 GCGCTGCAACACATCCCC 62.120 66.667 0.00 0.00 0.00 4.81
375 376 4.120331 GGCGCTGCAACACATCCC 62.120 66.667 7.64 0.00 0.00 3.85
376 377 3.044059 GAGGCGCTGCAACACATCC 62.044 63.158 7.64 0.00 0.00 3.51
377 378 2.482374 GAGGCGCTGCAACACATC 59.518 61.111 7.64 0.00 0.00 3.06
378 379 3.425713 CGAGGCGCTGCAACACAT 61.426 61.111 7.64 0.00 0.00 3.21
379 380 4.600576 TCGAGGCGCTGCAACACA 62.601 61.111 7.64 0.00 0.00 3.72
380 381 4.077188 GTCGAGGCGCTGCAACAC 62.077 66.667 7.64 0.00 0.00 3.32
381 382 3.807631 AAGTCGAGGCGCTGCAACA 62.808 57.895 7.64 0.00 0.00 3.33
382 383 2.607892 AAAGTCGAGGCGCTGCAAC 61.608 57.895 7.64 1.03 0.00 4.17
383 384 2.280797 AAAGTCGAGGCGCTGCAA 60.281 55.556 7.64 0.00 0.00 4.08
384 385 3.043713 CAAAGTCGAGGCGCTGCA 61.044 61.111 7.64 0.00 0.00 4.41
385 386 3.793144 CCAAAGTCGAGGCGCTGC 61.793 66.667 7.64 0.00 0.00 5.25
386 387 3.793144 GCCAAAGTCGAGGCGCTG 61.793 66.667 7.64 0.00 41.70 5.18
393 394 0.320374 ACAATCCTCGCCAAAGTCGA 59.680 50.000 0.00 0.00 34.52 4.20
394 395 2.004583 TACAATCCTCGCCAAAGTCG 57.995 50.000 0.00 0.00 0.00 4.18
395 396 4.636206 AGAATTACAATCCTCGCCAAAGTC 59.364 41.667 0.00 0.00 0.00 3.01
396 397 4.589908 AGAATTACAATCCTCGCCAAAGT 58.410 39.130 0.00 0.00 0.00 2.66
397 398 5.355350 AGAAGAATTACAATCCTCGCCAAAG 59.645 40.000 0.00 0.00 0.00 2.77
398 399 5.253330 AGAAGAATTACAATCCTCGCCAAA 58.747 37.500 0.00 0.00 0.00 3.28
399 400 4.843728 AGAAGAATTACAATCCTCGCCAA 58.156 39.130 0.00 0.00 0.00 4.52
400 401 4.487714 AGAAGAATTACAATCCTCGCCA 57.512 40.909 0.00 0.00 0.00 5.69
401 402 5.602628 ACTAGAAGAATTACAATCCTCGCC 58.397 41.667 0.00 0.00 0.00 5.54
402 403 6.273825 TGACTAGAAGAATTACAATCCTCGC 58.726 40.000 0.00 0.00 0.00 5.03
403 404 7.923344 ACATGACTAGAAGAATTACAATCCTCG 59.077 37.037 0.00 0.00 0.00 4.63
404 405 9.606631 AACATGACTAGAAGAATTACAATCCTC 57.393 33.333 0.00 0.00 0.00 3.71
405 406 9.965902 AAACATGACTAGAAGAATTACAATCCT 57.034 29.630 0.00 0.00 0.00 3.24
409 410 8.296713 GCCAAAACATGACTAGAAGAATTACAA 58.703 33.333 0.00 0.00 0.00 2.41
410 411 7.446931 TGCCAAAACATGACTAGAAGAATTACA 59.553 33.333 0.00 0.00 0.00 2.41
411 412 7.816640 TGCCAAAACATGACTAGAAGAATTAC 58.183 34.615 0.00 0.00 0.00 1.89
444 445 1.446272 GTTCGGCCTTGAGTCCTCG 60.446 63.158 0.00 0.00 0.00 4.63
445 446 0.390472 CAGTTCGGCCTTGAGTCCTC 60.390 60.000 0.00 0.00 0.00 3.71
459 460 1.098050 CCCAAGCCATACTGCAGTTC 58.902 55.000 27.06 11.91 0.00 3.01
510 518 6.220726 ACCCAATTAAAGTACAATCATGCC 57.779 37.500 0.00 0.00 0.00 4.40
529 537 9.535170 TTGTGGAATTAATTCTTGTATTACCCA 57.465 29.630 23.85 10.16 37.00 4.51
645 676 8.713271 GCAAATCATTTACGGGTTATTTGAAAA 58.287 29.630 9.18 0.00 36.77 2.29
646 677 7.872993 TGCAAATCATTTACGGGTTATTTGAAA 59.127 29.630 9.18 0.00 36.77 2.69
647 678 7.329717 GTGCAAATCATTTACGGGTTATTTGAA 59.670 33.333 9.18 0.00 36.77 2.69
648 679 6.809196 GTGCAAATCATTTACGGGTTATTTGA 59.191 34.615 9.18 0.00 36.77 2.69
673 704 4.589908 AGTTAGGGGAACATTACTTGCTG 58.410 43.478 0.00 0.00 40.86 4.41
689 720 3.941483 GTGGATGACATTGTGGAGTTAGG 59.059 47.826 0.00 0.00 0.00 2.69
690 721 3.941483 GGTGGATGACATTGTGGAGTTAG 59.059 47.826 0.00 0.00 0.00 2.34
704 735 1.067295 AGTGGAAAGCAGGTGGATGA 58.933 50.000 0.00 0.00 0.00 2.92
708 739 1.691196 TGAAAGTGGAAAGCAGGTGG 58.309 50.000 0.00 0.00 0.00 4.61
858 889 3.604772 GCATGAAACTCACCGATTATCGC 60.605 47.826 9.34 0.00 38.82 4.58
873 904 7.413475 GAGCTTCTCGATTTATAGCATGAAA 57.587 36.000 0.00 0.00 34.37 2.69
928 959 0.965866 AGCTACACTGGCTAGTCGCA 60.966 55.000 15.01 0.00 41.67 5.10
1055 1102 4.758251 TCGCCACCACCATCGCAG 62.758 66.667 0.00 0.00 0.00 5.18
1267 1314 2.635229 CTAGCACTAGCAGCGGGTGG 62.635 65.000 18.03 0.00 45.49 4.61
1802 1894 2.359169 TGGCGTCATCCAGGAGTCC 61.359 63.158 0.00 0.00 0.00 3.85
1921 2021 2.730069 TGCTGCATGAAAAACAAGACG 58.270 42.857 0.00 0.00 0.00 4.18
1922 2022 4.746115 TCAATGCTGCATGAAAAACAAGAC 59.254 37.500 17.00 0.00 0.00 3.01
1954 2062 1.746615 CTGGTCCGGTTGGCATCTG 60.747 63.158 0.00 0.00 34.14 2.90
1955 2063 2.671070 CTGGTCCGGTTGGCATCT 59.329 61.111 0.00 0.00 34.14 2.90
2124 2232 4.162888 ACATGATGCACTGACCAATCTAGA 59.837 41.667 0.00 0.00 0.00 2.43
2223 2367 5.056480 TGATCACACTCTTGTCGTTGAAAT 58.944 37.500 0.00 0.00 31.66 2.17
2233 2377 3.396560 TGTCAGCTTGATCACACTCTTG 58.603 45.455 0.00 0.00 0.00 3.02
2297 2876 9.893305 GTGTTAAACTATGCTGATAGTGTTTTT 57.107 29.630 0.00 0.00 43.46 1.94
2298 2877 9.284968 AGTGTTAAACTATGCTGATAGTGTTTT 57.715 29.630 0.00 0.00 43.46 2.43
2299 2878 8.848474 AGTGTTAAACTATGCTGATAGTGTTT 57.152 30.769 0.00 0.00 43.46 2.83
2376 3082 2.034179 GGCTGTGCCGTAAAGTTTCTTT 59.966 45.455 0.00 0.59 39.62 2.52
2377 3083 1.607148 GGCTGTGCCGTAAAGTTTCTT 59.393 47.619 0.00 0.00 39.62 2.52
2493 4154 4.014406 GTTGTTCCGGGAATATTGGTTCT 58.986 43.478 13.48 0.00 0.00 3.01
2778 4457 4.087892 CAGCTGGACAGGGGACGG 62.088 72.222 5.57 0.00 0.00 4.79
2827 4506 3.081061 TGGAACACACTCCAATGTATGC 58.919 45.455 0.00 0.00 42.69 3.14
2844 4523 7.442969 ACGTGTTCTTTATTGTCAGTTATGGAA 59.557 33.333 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.