Multiple sequence alignment - TraesCS2B01G414100

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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 TraesCS2B01G414100 chr2B 100.000 4050 0 0 1 4050 591911531 591915580 0.000000e+00 7480.0
1 TraesCS2B01G414100 chr2B 90.271 442 36 6 1 438 732885817 732885379 4.540000e-159 571.0
2 TraesCS2B01G414100 chr2D 92.450 3722 114 59 431 4049 503435847 503439504 0.000000e+00 5162.0
3 TraesCS2B01G414100 chr2A 93.129 2969 95 36 443 3342 649483467 649486395 0.000000e+00 4252.0
4 TraesCS2B01G414100 chr2A 91.797 512 22 5 3369 3863 649486392 649486900 0.000000e+00 695.0
5 TraesCS2B01G414100 chr2A 89.979 469 25 8 441 894 649477880 649478341 1.620000e-163 586.0
6 TraesCS2B01G414100 chr2A 86.076 79 9 1 3923 4001 37307840 37307764 2.590000e-12 84.2
7 TraesCS2B01G414100 chr6B 85.145 1205 155 18 1326 2523 479396244 479397431 0.000000e+00 1212.0
8 TraesCS2B01G414100 chr6A 84.815 1192 158 17 1326 2511 480806546 480805372 0.000000e+00 1177.0
9 TraesCS2B01G414100 chr6A 88.939 443 42 6 1 438 286335868 286335428 1.280000e-149 540.0
10 TraesCS2B01G414100 chr6D 84.648 1192 160 17 1326 2511 341079427 341078253 0.000000e+00 1166.0
11 TraesCS2B01G414100 chr6D 88.713 443 45 4 1 440 455520998 455521438 1.660000e-148 536.0
12 TraesCS2B01G414100 chr1A 78.956 1169 207 29 1334 2493 333498735 333499873 0.000000e+00 760.0
13 TraesCS2B01G414100 chr1D 78.785 1169 209 29 1334 2493 269515939 269514801 0.000000e+00 749.0
14 TraesCS2B01G414100 chr1D 88.514 444 44 5 1 440 432633354 432632914 7.710000e-147 531.0
15 TraesCS2B01G414100 chr4D 79.796 980 165 28 1334 2298 497697196 497698157 0.000000e+00 682.0
16 TraesCS2B01G414100 chr4D 89.066 439 44 3 6 441 28419801 28420238 3.560000e-150 542.0
17 TraesCS2B01G414100 chr4B 79.472 984 161 31 1334 2298 639011470 639010509 0.000000e+00 660.0
18 TraesCS2B01G414100 chr5B 90.787 445 36 4 1 440 422109836 422109392 1.250000e-164 590.0
19 TraesCS2B01G414100 chr7B 88.636 440 46 4 1 438 533562608 533563045 2.140000e-147 532.0
20 TraesCS2B01G414100 chr7D 88.558 437 45 4 6 438 16184794 16184359 3.590000e-145 525.0
21 TraesCS2B01G414100 chr7D 88.155 439 47 5 6 442 69044972 69044537 6.000000e-143 518.0
22 TraesCS2B01G414100 chr3A 75.705 461 80 24 1885 2338 598410425 598410860 6.860000e-48 202.0


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 TraesCS2B01G414100 chr2B 591911531 591915580 4049 False 7480.0 7480 100.000 1 4050 1 chr2B.!!$F1 4049
1 TraesCS2B01G414100 chr2D 503435847 503439504 3657 False 5162.0 5162 92.450 431 4049 1 chr2D.!!$F1 3618
2 TraesCS2B01G414100 chr2A 649483467 649486900 3433 False 2473.5 4252 92.463 443 3863 2 chr2A.!!$F2 3420
3 TraesCS2B01G414100 chr6B 479396244 479397431 1187 False 1212.0 1212 85.145 1326 2523 1 chr6B.!!$F1 1197
4 TraesCS2B01G414100 chr6A 480805372 480806546 1174 True 1177.0 1177 84.815 1326 2511 1 chr6A.!!$R2 1185
5 TraesCS2B01G414100 chr6D 341078253 341079427 1174 True 1166.0 1166 84.648 1326 2511 1 chr6D.!!$R1 1185
6 TraesCS2B01G414100 chr1A 333498735 333499873 1138 False 760.0 760 78.956 1334 2493 1 chr1A.!!$F1 1159
7 TraesCS2B01G414100 chr1D 269514801 269515939 1138 True 749.0 749 78.785 1334 2493 1 chr1D.!!$R1 1159
8 TraesCS2B01G414100 chr4D 497697196 497698157 961 False 682.0 682 79.796 1334 2298 1 chr4D.!!$F2 964
9 TraesCS2B01G414100 chr4B 639010509 639011470 961 True 660.0 660 79.472 1334 2298 1 chr4B.!!$R1 964

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
238 239 0.106967 GGGGATGGAAGTTGGAGAGC 60.107 60.0 0.00 0.00 0.00 4.09 F
242 243 0.107945 ATGGAAGTTGGAGAGCGAGC 60.108 55.0 0.00 0.00 0.00 5.03 F
377 378 0.111266 GCAACTATACCGATTGCGCG 60.111 55.0 0.00 0.00 39.36 6.86 F
407 408 0.520827 TTTAATTTTACGGCGCGGCG 60.521 50.0 46.57 46.57 0.00 6.46 F
716 732 0.828022 ATTAGCGACGGGACAATGGA 59.172 50.0 0.00 0.00 0.00 3.41 F
2724 2795 0.445436 GACTGCCTGAGCGAATGTTG 59.555 55.0 0.00 0.00 44.31 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 1719 2.022129 GACGGTGAGCAGGTTGTCG 61.022 63.158 0.00 0.00 0.00 4.35 R
2561 2620 5.366186 TCAGCAATTGGGCCATTTGTATATT 59.634 36.000 30.94 15.19 30.43 1.28 R
2564 2623 3.106054 TCAGCAATTGGGCCATTTGTAT 58.894 40.909 30.94 21.64 30.43 2.29 R
2709 2780 1.668419 ATACCAACATTCGCTCAGGC 58.332 50.000 0.00 0.00 0.00 4.85 R
2830 2918 0.251653 TACAGCAGTTCCTCCTCGGT 60.252 55.000 0.00 0.00 0.00 4.69 R
3648 3774 0.179158 GTTTTTGGTTGCGACGGTGT 60.179 50.000 0.00 0.00 0.00 4.16 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
28 29 9.561069 AAGTTTGAGCAATACATACCTTATAGG 57.439 33.333 0.00 0.00 42.49 2.57
29 30 7.661847 AGTTTGAGCAATACATACCTTATAGGC 59.338 37.037 0.00 0.00 39.63 3.93
30 31 6.680148 TGAGCAATACATACCTTATAGGCA 57.320 37.500 0.00 0.00 39.63 4.75
31 32 7.257790 TGAGCAATACATACCTTATAGGCAT 57.742 36.000 0.00 0.00 39.63 4.40
32 33 7.689299 TGAGCAATACATACCTTATAGGCATT 58.311 34.615 0.00 0.00 39.63 3.56
33 34 8.163408 TGAGCAATACATACCTTATAGGCATTT 58.837 33.333 0.00 0.00 39.63 2.32
34 35 8.940397 AGCAATACATACCTTATAGGCATTTT 57.060 30.769 0.00 0.00 39.63 1.82
35 36 8.796475 AGCAATACATACCTTATAGGCATTTTG 58.204 33.333 0.00 0.00 39.63 2.44
36 37 8.576442 GCAATACATACCTTATAGGCATTTTGT 58.424 33.333 0.00 0.00 39.63 2.83
38 39 6.861065 ACATACCTTATAGGCATTTTGTCG 57.139 37.500 0.00 0.00 39.63 4.35
39 40 6.588204 ACATACCTTATAGGCATTTTGTCGA 58.412 36.000 0.00 0.00 39.63 4.20
40 41 7.051623 ACATACCTTATAGGCATTTTGTCGAA 58.948 34.615 0.00 0.00 39.63 3.71
41 42 5.813080 ACCTTATAGGCATTTTGTCGAAC 57.187 39.130 0.00 0.00 39.63 3.95
42 43 5.250200 ACCTTATAGGCATTTTGTCGAACA 58.750 37.500 0.00 0.00 39.63 3.18
43 44 5.123344 ACCTTATAGGCATTTTGTCGAACAC 59.877 40.000 0.00 0.00 39.63 3.32
44 45 5.448632 CCTTATAGGCATTTTGTCGAACACC 60.449 44.000 0.00 0.00 0.00 4.16
45 46 1.981256 AGGCATTTTGTCGAACACCT 58.019 45.000 0.00 0.00 0.00 4.00
46 47 2.306847 AGGCATTTTGTCGAACACCTT 58.693 42.857 0.00 0.00 0.00 3.50
47 48 2.034558 AGGCATTTTGTCGAACACCTTG 59.965 45.455 0.00 0.00 0.00 3.61
48 49 1.786579 GCATTTTGTCGAACACCTTGC 59.213 47.619 0.00 0.00 0.00 4.01
49 50 2.043411 CATTTTGTCGAACACCTTGCG 58.957 47.619 0.00 0.00 0.00 4.85
50 51 0.378962 TTTTGTCGAACACCTTGCGG 59.621 50.000 0.00 0.00 0.00 5.69
51 52 1.440938 TTTGTCGAACACCTTGCGGG 61.441 55.000 0.00 0.00 41.89 6.13
52 53 3.723348 GTCGAACACCTTGCGGGC 61.723 66.667 0.00 0.00 39.10 6.13
82 83 4.749310 CAAGCTCTCGGGCGCTGT 62.749 66.667 7.64 0.00 36.45 4.40
83 84 4.008933 AAGCTCTCGGGCGCTGTT 62.009 61.111 7.64 0.00 36.45 3.16
84 85 3.941657 AAGCTCTCGGGCGCTGTTC 62.942 63.158 7.64 0.00 36.45 3.18
86 87 4.421479 CTCTCGGGCGCTGTTCGT 62.421 66.667 7.64 0.00 41.07 3.85
87 88 4.415332 TCTCGGGCGCTGTTCGTC 62.415 66.667 7.64 0.00 43.18 4.20
93 94 4.415332 GCGCTGTTCGTCGGAGGA 62.415 66.667 0.00 0.00 41.07 3.71
94 95 2.504244 CGCTGTTCGTCGGAGGAC 60.504 66.667 0.00 0.00 39.89 3.85
165 166 4.230002 CGCGGGAATAGCCGGGAA 62.230 66.667 2.18 0.00 43.32 3.97
166 167 2.191109 GCGGGAATAGCCGGGAAA 59.809 61.111 2.18 0.00 37.45 3.13
167 168 1.892391 GCGGGAATAGCCGGGAAAG 60.892 63.158 2.18 0.00 37.45 2.62
168 169 1.892391 CGGGAATAGCCGGGAAAGC 60.892 63.158 2.18 0.00 37.63 3.51
169 170 1.892391 GGGAATAGCCGGGAAAGCG 60.892 63.158 2.18 0.00 37.63 4.68
170 171 2.543802 GGAATAGCCGGGAAAGCGC 61.544 63.158 2.18 0.00 34.64 5.92
171 172 2.516225 AATAGCCGGGAAAGCGCC 60.516 61.111 2.29 0.00 34.64 6.53
172 173 4.910585 ATAGCCGGGAAAGCGCCG 62.911 66.667 2.29 0.00 34.64 6.46
225 226 4.935495 CGCGGGTGGATGGGGATG 62.935 72.222 0.00 0.00 0.00 3.51
226 227 4.586235 GCGGGTGGATGGGGATGG 62.586 72.222 0.00 0.00 0.00 3.51
227 228 2.772191 CGGGTGGATGGGGATGGA 60.772 66.667 0.00 0.00 0.00 3.41
228 229 2.382770 CGGGTGGATGGGGATGGAA 61.383 63.158 0.00 0.00 0.00 3.53
229 230 1.538666 GGGTGGATGGGGATGGAAG 59.461 63.158 0.00 0.00 0.00 3.46
230 231 1.289244 GGGTGGATGGGGATGGAAGT 61.289 60.000 0.00 0.00 0.00 3.01
231 232 0.631212 GGTGGATGGGGATGGAAGTT 59.369 55.000 0.00 0.00 0.00 2.66
232 233 1.686115 GGTGGATGGGGATGGAAGTTG 60.686 57.143 0.00 0.00 0.00 3.16
233 234 0.630673 TGGATGGGGATGGAAGTTGG 59.369 55.000 0.00 0.00 0.00 3.77
234 235 0.926293 GGATGGGGATGGAAGTTGGA 59.074 55.000 0.00 0.00 0.00 3.53
235 236 1.133668 GGATGGGGATGGAAGTTGGAG 60.134 57.143 0.00 0.00 0.00 3.86
236 237 1.846439 GATGGGGATGGAAGTTGGAGA 59.154 52.381 0.00 0.00 0.00 3.71
237 238 1.289160 TGGGGATGGAAGTTGGAGAG 58.711 55.000 0.00 0.00 0.00 3.20
238 239 0.106967 GGGGATGGAAGTTGGAGAGC 60.107 60.000 0.00 0.00 0.00 4.09
239 240 0.462759 GGGATGGAAGTTGGAGAGCG 60.463 60.000 0.00 0.00 0.00 5.03
240 241 0.537188 GGATGGAAGTTGGAGAGCGA 59.463 55.000 0.00 0.00 0.00 4.93
241 242 1.472376 GGATGGAAGTTGGAGAGCGAG 60.472 57.143 0.00 0.00 0.00 5.03
242 243 0.107945 ATGGAAGTTGGAGAGCGAGC 60.108 55.000 0.00 0.00 0.00 5.03
243 244 1.807573 GGAAGTTGGAGAGCGAGCG 60.808 63.158 0.00 0.00 0.00 5.03
244 245 2.433318 AAGTTGGAGAGCGAGCGC 60.433 61.111 6.78 6.78 42.33 5.92
289 290 2.951227 GCAGCAAATAAGCGGCGC 60.951 61.111 26.86 26.86 45.03 6.53
290 291 2.648724 CAGCAAATAAGCGGCGCG 60.649 61.111 27.59 12.27 40.15 6.86
307 308 4.096558 GCGATTGCGTTTCGGCCA 62.097 61.111 2.24 0.00 40.36 5.36
308 309 2.098298 CGATTGCGTTTCGGCCAG 59.902 61.111 2.24 0.00 33.05 4.85
309 310 2.202479 GATTGCGTTTCGGCCAGC 60.202 61.111 2.24 0.00 0.00 4.85
310 311 4.101790 ATTGCGTTTCGGCCAGCG 62.102 61.111 2.24 0.00 0.00 5.18
315 316 4.389576 GTTTCGGCCAGCGTGCTG 62.390 66.667 14.82 14.82 43.26 4.41
316 317 4.617520 TTTCGGCCAGCGTGCTGA 62.618 61.111 22.79 7.80 46.30 4.26
320 321 2.047274 GGCCAGCGTGCTGAACTA 60.047 61.111 22.79 0.00 46.30 2.24
321 322 2.391389 GGCCAGCGTGCTGAACTAC 61.391 63.158 22.79 6.80 46.30 2.73
322 323 1.667830 GCCAGCGTGCTGAACTACA 60.668 57.895 22.79 0.00 46.30 2.74
323 324 1.021390 GCCAGCGTGCTGAACTACAT 61.021 55.000 22.79 0.00 46.30 2.29
324 325 1.739035 GCCAGCGTGCTGAACTACATA 60.739 52.381 22.79 0.00 46.30 2.29
325 326 2.826428 CCAGCGTGCTGAACTACATAT 58.174 47.619 22.79 0.00 46.30 1.78
326 327 2.541346 CCAGCGTGCTGAACTACATATG 59.459 50.000 22.79 0.00 46.30 1.78
327 328 2.033407 CAGCGTGCTGAACTACATATGC 60.033 50.000 16.69 0.00 46.30 3.14
328 329 1.261619 GCGTGCTGAACTACATATGCC 59.738 52.381 1.58 0.00 0.00 4.40
329 330 1.522676 CGTGCTGAACTACATATGCCG 59.477 52.381 1.58 0.00 0.00 5.69
330 331 1.261619 GTGCTGAACTACATATGCCGC 59.738 52.381 1.58 0.00 0.00 6.53
331 332 0.508641 GCTGAACTACATATGCCGCG 59.491 55.000 1.58 0.00 0.00 6.46
332 333 0.508641 CTGAACTACATATGCCGCGC 59.491 55.000 0.00 0.00 0.00 6.86
333 334 1.212455 TGAACTACATATGCCGCGCG 61.212 55.000 25.67 25.67 0.00 6.86
334 335 2.480426 GAACTACATATGCCGCGCGC 62.480 60.000 27.36 23.91 38.31 6.86
335 336 3.777925 CTACATATGCCGCGCGCC 61.778 66.667 27.36 16.11 36.24 6.53
339 340 4.082523 ATATGCCGCGCGCCCTAT 62.083 61.111 27.36 14.06 36.24 2.57
340 341 3.605749 ATATGCCGCGCGCCCTATT 62.606 57.895 27.36 9.50 36.24 1.73
341 342 3.818121 TATGCCGCGCGCCCTATTT 62.818 57.895 27.36 8.34 36.24 1.40
343 344 4.187810 GCCGCGCGCCCTATTTTT 62.188 61.111 27.36 0.00 0.00 1.94
344 345 2.277884 CCGCGCGCCCTATTTTTG 60.278 61.111 27.36 7.77 0.00 2.44
345 346 2.949163 CGCGCGCCCTATTTTTGC 60.949 61.111 27.72 0.00 0.00 3.68
349 350 2.949163 CGCCCTATTTTTGCGCGC 60.949 61.111 27.26 27.26 41.95 6.86
350 351 2.582226 GCCCTATTTTTGCGCGCC 60.582 61.111 30.77 11.42 0.00 6.53
351 352 2.104132 CCCTATTTTTGCGCGCCC 59.896 61.111 30.77 1.83 0.00 6.13
352 353 2.277884 CCTATTTTTGCGCGCCCG 60.278 61.111 30.77 8.41 37.57 6.13
364 365 2.434185 CGCCCGCTGAAGCAACTA 60.434 61.111 2.79 0.00 42.21 2.24
365 366 1.815421 CGCCCGCTGAAGCAACTAT 60.815 57.895 2.79 0.00 42.21 2.12
366 367 0.529773 CGCCCGCTGAAGCAACTATA 60.530 55.000 2.79 0.00 42.21 1.31
367 368 0.938008 GCCCGCTGAAGCAACTATAC 59.062 55.000 2.79 0.00 42.21 1.47
368 369 1.583054 CCCGCTGAAGCAACTATACC 58.417 55.000 2.79 0.00 42.21 2.73
369 370 1.209128 CCGCTGAAGCAACTATACCG 58.791 55.000 2.79 0.00 42.21 4.02
370 371 1.202371 CCGCTGAAGCAACTATACCGA 60.202 52.381 2.79 0.00 42.21 4.69
371 372 2.545952 CCGCTGAAGCAACTATACCGAT 60.546 50.000 2.79 0.00 42.21 4.18
372 373 3.123804 CGCTGAAGCAACTATACCGATT 58.876 45.455 2.79 0.00 42.21 3.34
373 374 3.060272 CGCTGAAGCAACTATACCGATTG 60.060 47.826 2.79 0.00 42.21 2.67
376 377 3.729004 GCAACTATACCGATTGCGC 57.271 52.632 0.00 0.00 39.36 6.09
377 378 0.111266 GCAACTATACCGATTGCGCG 60.111 55.000 0.00 0.00 39.36 6.86
378 379 0.111266 CAACTATACCGATTGCGCGC 60.111 55.000 27.26 27.26 35.83 6.86
379 380 1.545614 AACTATACCGATTGCGCGCG 61.546 55.000 28.44 28.44 35.83 6.86
380 381 1.728074 CTATACCGATTGCGCGCGA 60.728 57.895 37.18 25.63 35.83 5.87
381 382 1.272784 CTATACCGATTGCGCGCGAA 61.273 55.000 37.18 24.32 35.83 4.70
382 383 0.870735 TATACCGATTGCGCGCGAAA 60.871 50.000 37.18 32.54 35.83 3.46
383 384 1.697772 ATACCGATTGCGCGCGAAAA 61.698 50.000 37.18 26.57 35.83 2.29
384 385 1.898459 TACCGATTGCGCGCGAAAAA 61.898 50.000 37.18 23.84 35.83 1.94
403 404 4.611984 AAAACGTTTAATTTTACGGCGC 57.388 36.364 15.03 0.00 41.81 6.53
404 405 1.868242 ACGTTTAATTTTACGGCGCG 58.132 45.000 6.90 0.00 41.81 6.86
405 406 1.173526 CGTTTAATTTTACGGCGCGG 58.826 50.000 14.03 14.03 34.30 6.46
406 407 0.909174 GTTTAATTTTACGGCGCGGC 59.091 50.000 24.49 24.49 0.00 6.53
407 408 0.520827 TTTAATTTTACGGCGCGGCG 60.521 50.000 46.57 46.57 0.00 6.46
424 425 3.270092 GCTAGTTTAGCGCGGCCC 61.270 66.667 8.83 0.00 42.62 5.80
425 426 2.499685 CTAGTTTAGCGCGGCCCT 59.500 61.111 8.83 0.00 0.00 5.19
426 427 1.153429 CTAGTTTAGCGCGGCCCTT 60.153 57.895 8.83 0.00 0.00 3.95
427 428 1.429148 CTAGTTTAGCGCGGCCCTTG 61.429 60.000 8.83 0.00 0.00 3.61
428 429 2.862674 TAGTTTAGCGCGGCCCTTGG 62.863 60.000 8.83 0.00 0.00 3.61
429 430 4.023234 TTTAGCGCGGCCCTTGGA 62.023 61.111 8.83 0.00 0.00 3.53
446 447 4.154918 CCTTGGAGATGCTCTAACACAAAC 59.845 45.833 0.00 0.00 28.50 2.93
559 560 1.202722 TGAAGAACCTCCCACGTTTCC 60.203 52.381 0.00 0.00 0.00 3.13
649 657 5.692115 AATAAATAGGCTTTTTGGTGGGG 57.308 39.130 12.40 0.00 0.00 4.96
712 728 1.274167 ACTTGATTAGCGACGGGACAA 59.726 47.619 0.00 0.00 0.00 3.18
713 729 2.093658 ACTTGATTAGCGACGGGACAAT 60.094 45.455 0.00 0.00 0.00 2.71
714 730 1.934589 TGATTAGCGACGGGACAATG 58.065 50.000 0.00 0.00 0.00 2.82
715 731 1.217882 GATTAGCGACGGGACAATGG 58.782 55.000 0.00 0.00 0.00 3.16
716 732 0.828022 ATTAGCGACGGGACAATGGA 59.172 50.000 0.00 0.00 0.00 3.41
718 734 1.672854 TAGCGACGGGACAATGGAGG 61.673 60.000 0.00 0.00 0.00 4.30
719 735 2.511600 CGACGGGACAATGGAGGC 60.512 66.667 0.00 0.00 0.00 4.70
720 736 2.668632 GACGGGACAATGGAGGCA 59.331 61.111 0.00 0.00 0.00 4.75
721 737 1.450312 GACGGGACAATGGAGGCAG 60.450 63.158 0.00 0.00 0.00 4.85
722 738 2.825836 CGGGACAATGGAGGCAGC 60.826 66.667 0.00 0.00 0.00 5.25
723 739 2.825836 GGGACAATGGAGGCAGCG 60.826 66.667 0.00 0.00 0.00 5.18
724 740 3.512516 GGACAATGGAGGCAGCGC 61.513 66.667 0.00 0.00 0.00 5.92
725 741 2.747460 GACAATGGAGGCAGCGCA 60.747 61.111 11.47 0.00 0.00 6.09
726 742 3.044059 GACAATGGAGGCAGCGCAC 62.044 63.158 11.47 0.00 0.00 5.34
727 743 3.818787 CAATGGAGGCAGCGCACC 61.819 66.667 11.47 11.36 0.00 5.01
728 744 4.349503 AATGGAGGCAGCGCACCA 62.350 61.111 20.11 15.38 39.67 4.17
754 770 2.747686 GGCACGGGAGAAACCTCA 59.252 61.111 0.00 0.00 38.98 3.86
850 883 3.256879 ACAAGCGAAGAGAGTGAGATTGA 59.743 43.478 0.00 0.00 33.17 2.57
1004 1057 4.424867 ATACCCCAGTCCCCGCCA 62.425 66.667 0.00 0.00 0.00 5.69
1539 1598 1.766461 CCTCCGCCTTCCCCTACAT 60.766 63.158 0.00 0.00 0.00 2.29
1660 1719 1.080025 CGACACCGTCTTCTTCCCC 60.080 63.158 0.00 0.00 0.00 4.81
2558 2617 9.905713 ACTCAATTCCTTTTTCAGCATATACTA 57.094 29.630 0.00 0.00 0.00 1.82
2560 2619 9.905713 TCAATTCCTTTTTCAGCATATACTACT 57.094 29.630 0.00 0.00 0.00 2.57
2584 2643 3.547054 ATACAAATGGCCCAATTGCTG 57.453 42.857 11.48 0.00 28.34 4.41
2601 2660 9.736023 CCAATTGCTGATTAAAAAGGAGTATAC 57.264 33.333 0.00 0.00 0.00 1.47
2606 2665 9.256477 TGCTGATTAAAAAGGAGTATACATACG 57.744 33.333 5.50 0.00 38.28 3.06
2614 2673 8.644318 AAAAGGAGTATACATACGCTTAACTG 57.356 34.615 5.50 0.00 38.28 3.16
2616 2675 6.968250 AGGAGTATACATACGCTTAACTGTC 58.032 40.000 5.50 0.00 38.28 3.51
2619 2678 7.104043 AGTATACATACGCTTAACTGTCCAA 57.896 36.000 5.50 0.00 38.28 3.53
2620 2679 7.549839 AGTATACATACGCTTAACTGTCCAAA 58.450 34.615 5.50 0.00 38.28 3.28
2677 2748 3.492656 GCAATGGTAGGAGAAGCGTATCA 60.493 47.826 0.00 0.00 32.98 2.15
2709 2780 2.735134 GCGTACTAGGTTTGGTTGACTG 59.265 50.000 0.00 0.00 0.00 3.51
2724 2795 0.445436 GACTGCCTGAGCGAATGTTG 59.555 55.000 0.00 0.00 44.31 3.33
2735 2816 5.979993 TGAGCGAATGTTGGTATACCTTTA 58.020 37.500 22.41 8.95 36.82 1.85
2830 2918 1.881324 CACATGGATGTTGTGCAGTCA 59.119 47.619 0.00 0.00 39.39 3.41
3042 3134 4.501071 TGGAAGGTATAACAAACGAGAGC 58.499 43.478 0.00 0.00 0.00 4.09
3043 3135 3.869832 GGAAGGTATAACAAACGAGAGCC 59.130 47.826 0.00 0.00 0.00 4.70
3044 3136 4.382793 GGAAGGTATAACAAACGAGAGCCT 60.383 45.833 0.00 0.00 0.00 4.58
3069 3161 0.904865 TTCGGTCATCTCCTGCCTGT 60.905 55.000 0.00 0.00 0.00 4.00
3155 3250 2.525629 TGTGGCCGGACTTCCTCA 60.526 61.111 9.82 2.21 0.00 3.86
3166 3266 1.078918 CTTCCTCAGCATCGTGCCA 60.079 57.895 6.39 0.00 46.52 4.92
3192 3292 0.827507 CCCCCACAACAGTTGAAGGG 60.828 60.000 27.93 27.93 43.91 3.95
3202 3302 1.303317 GTTGAAGGGGACGTGGCAT 60.303 57.895 0.00 0.00 0.00 4.40
3344 3454 3.747976 GCGGGGTGTGATGGCAAC 61.748 66.667 0.00 0.00 0.00 4.17
3408 3518 0.465460 TGTGTGAAACTGGGTCAGCC 60.465 55.000 0.00 0.00 38.04 4.85
3409 3519 1.150536 TGTGAAACTGGGTCAGCCC 59.849 57.895 0.00 0.00 45.73 5.19
3437 3547 4.287720 GGTTTTTACTTCGTTTCTGGCAG 58.712 43.478 8.58 8.58 0.00 4.85
3505 3630 3.064324 GCGACAGGGCTTGGCATT 61.064 61.111 2.46 0.00 32.77 3.56
3558 3684 1.544825 CCCATCCGCCCGAGACATAT 61.545 60.000 0.00 0.00 0.00 1.78
3577 3703 6.058183 ACATATTTAAGGTGATGTGGAGAGC 58.942 40.000 0.00 0.00 31.41 4.09
3603 3729 3.712016 TTCATTCCTCCGAACCATCAA 57.288 42.857 0.00 0.00 0.00 2.57
3634 3760 1.955495 TAAATGCTCGCTGAGGCCGA 61.955 55.000 0.00 0.00 34.44 5.54
3648 3774 1.971167 GCCGATTCAACAGGTGGCA 60.971 57.895 0.00 0.00 42.03 4.92
3706 3832 0.108041 GCACATGGCCATGAAAAGGG 60.108 55.000 44.72 27.07 41.20 3.95
3714 3840 1.256812 CCATGAAAAGGGGGTCACAC 58.743 55.000 0.00 0.00 0.00 3.82
3865 3992 6.957150 ACAGTGTCAATCGTATACTAGTAGC 58.043 40.000 8.85 3.26 0.00 3.58
3868 3995 5.852229 GTGTCAATCGTATACTAGTAGCAGC 59.148 44.000 8.85 0.00 0.00 5.25
3869 3996 5.080731 GTCAATCGTATACTAGTAGCAGCG 58.919 45.833 8.85 9.63 0.00 5.18
3870 3997 4.992951 TCAATCGTATACTAGTAGCAGCGA 59.007 41.667 17.07 17.07 0.00 4.93
3871 3998 5.642491 TCAATCGTATACTAGTAGCAGCGAT 59.358 40.000 19.01 19.01 39.11 4.58
3872 3999 6.815142 TCAATCGTATACTAGTAGCAGCGATA 59.185 38.462 22.17 12.53 36.93 2.92
3873 4000 7.494952 TCAATCGTATACTAGTAGCAGCGATAT 59.505 37.037 22.17 14.78 36.93 1.63
3874 4001 8.762426 CAATCGTATACTAGTAGCAGCGATATA 58.238 37.037 22.17 4.04 36.93 0.86
3875 4002 9.491675 AATCGTATACTAGTAGCAGCGATATAT 57.508 33.333 22.17 12.09 36.93 0.86
3918 4048 3.053544 TGTTTAGGGTCTGTTTGGTTCCA 60.054 43.478 0.00 0.00 0.00 3.53
3937 4077 2.642129 CCAAACATTGGTCGCGCA 59.358 55.556 8.75 0.00 45.93 6.09
3943 4083 0.109319 ACATTGGTCGCGCAAAATCC 60.109 50.000 8.75 2.14 0.00 3.01
3944 4084 0.109365 CATTGGTCGCGCAAAATCCA 60.109 50.000 8.75 5.03 0.00 3.41
3946 4086 0.600557 TTGGTCGCGCAAAATCCATT 59.399 45.000 8.75 0.00 0.00 3.16
4015 4155 5.696270 GTCCTTTGTTAAATCTTTGGCCAAG 59.304 40.000 19.48 12.99 0.00 3.61
4031 4173 2.606587 AAGCCTGGCGGTGGAATCT 61.607 57.895 13.96 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.561069 CCTATAAGGTATGTATTGCTCAAACTT 57.439 33.333 0.00 0.00 0.00 2.66
3 4 7.661847 GCCTATAAGGTATGTATTGCTCAAACT 59.338 37.037 0.00 0.00 37.80 2.66
4 5 7.444183 TGCCTATAAGGTATGTATTGCTCAAAC 59.556 37.037 0.00 0.00 37.80 2.93
5 6 7.513856 TGCCTATAAGGTATGTATTGCTCAAA 58.486 34.615 0.00 0.00 37.80 2.69
6 7 7.073457 TGCCTATAAGGTATGTATTGCTCAA 57.927 36.000 0.00 0.00 37.80 3.02
7 8 6.680148 TGCCTATAAGGTATGTATTGCTCA 57.320 37.500 0.00 0.00 37.80 4.26
8 9 8.567285 AAATGCCTATAAGGTATGTATTGCTC 57.433 34.615 0.00 0.00 39.94 4.26
9 10 8.796475 CAAAATGCCTATAAGGTATGTATTGCT 58.204 33.333 0.00 0.00 39.94 3.91
10 11 8.576442 ACAAAATGCCTATAAGGTATGTATTGC 58.424 33.333 12.85 0.00 39.94 3.56
12 13 8.999431 CGACAAAATGCCTATAAGGTATGTATT 58.001 33.333 0.00 0.00 39.94 1.89
13 14 8.372459 TCGACAAAATGCCTATAAGGTATGTAT 58.628 33.333 0.00 0.00 39.94 2.29
14 15 7.728148 TCGACAAAATGCCTATAAGGTATGTA 58.272 34.615 0.00 0.00 39.94 2.29
15 16 6.588204 TCGACAAAATGCCTATAAGGTATGT 58.412 36.000 0.00 0.00 39.94 2.29
16 17 7.011950 TGTTCGACAAAATGCCTATAAGGTATG 59.988 37.037 0.00 0.00 39.94 2.39
17 18 7.012044 GTGTTCGACAAAATGCCTATAAGGTAT 59.988 37.037 0.00 0.00 42.81 2.73
18 19 6.314400 GTGTTCGACAAAATGCCTATAAGGTA 59.686 38.462 0.00 0.00 37.80 3.08
19 20 5.123344 GTGTTCGACAAAATGCCTATAAGGT 59.877 40.000 0.00 0.00 37.80 3.50
20 21 5.448632 GGTGTTCGACAAAATGCCTATAAGG 60.449 44.000 0.00 0.00 38.80 2.69
21 22 5.354234 AGGTGTTCGACAAAATGCCTATAAG 59.646 40.000 0.00 0.00 0.00 1.73
22 23 5.250200 AGGTGTTCGACAAAATGCCTATAA 58.750 37.500 0.00 0.00 0.00 0.98
23 24 4.839121 AGGTGTTCGACAAAATGCCTATA 58.161 39.130 0.00 0.00 0.00 1.31
24 25 3.686016 AGGTGTTCGACAAAATGCCTAT 58.314 40.909 0.00 0.00 0.00 2.57
25 26 3.134574 AGGTGTTCGACAAAATGCCTA 57.865 42.857 0.00 0.00 0.00 3.93
26 27 1.981256 AGGTGTTCGACAAAATGCCT 58.019 45.000 0.00 0.00 0.00 4.75
27 28 2.393764 CAAGGTGTTCGACAAAATGCC 58.606 47.619 0.00 0.00 0.00 4.40
28 29 1.786579 GCAAGGTGTTCGACAAAATGC 59.213 47.619 0.00 0.00 0.00 3.56
29 30 2.043411 CGCAAGGTGTTCGACAAAATG 58.957 47.619 0.00 0.00 0.00 2.32
30 31 2.399396 CGCAAGGTGTTCGACAAAAT 57.601 45.000 0.00 0.00 0.00 1.82
31 32 3.907927 CGCAAGGTGTTCGACAAAA 57.092 47.368 0.00 0.00 0.00 2.44
69 70 4.421479 ACGAACAGCGCCCGAGAG 62.421 66.667 2.29 0.00 46.04 3.20
70 71 4.415332 GACGAACAGCGCCCGAGA 62.415 66.667 2.29 0.00 46.04 4.04
76 77 4.415332 TCCTCCGACGAACAGCGC 62.415 66.667 0.00 0.00 46.04 5.92
148 149 3.743534 TTTCCCGGCTATTCCCGCG 62.744 63.158 0.00 0.00 46.77 6.46
149 150 1.892391 CTTTCCCGGCTATTCCCGC 60.892 63.158 0.00 0.00 46.77 6.13
151 152 1.892391 CGCTTTCCCGGCTATTCCC 60.892 63.158 0.00 0.00 0.00 3.97
152 153 2.543802 GCGCTTTCCCGGCTATTCC 61.544 63.158 0.00 0.00 0.00 3.01
153 154 3.023118 GCGCTTTCCCGGCTATTC 58.977 61.111 0.00 0.00 0.00 1.75
162 163 2.810012 GATCGTTCCGGCGCTTTCC 61.810 63.158 7.64 0.00 0.00 3.13
163 164 2.701606 GATCGTTCCGGCGCTTTC 59.298 61.111 7.64 0.00 0.00 2.62
164 165 3.186047 CGATCGTTCCGGCGCTTT 61.186 61.111 7.64 0.00 0.00 3.51
208 209 4.935495 CATCCCCATCCACCCGCG 62.935 72.222 0.00 0.00 0.00 6.46
209 210 4.586235 CCATCCCCATCCACCCGC 62.586 72.222 0.00 0.00 0.00 6.13
210 211 2.343475 CTTCCATCCCCATCCACCCG 62.343 65.000 0.00 0.00 0.00 5.28
211 212 1.289244 ACTTCCATCCCCATCCACCC 61.289 60.000 0.00 0.00 0.00 4.61
212 213 0.631212 AACTTCCATCCCCATCCACC 59.369 55.000 0.00 0.00 0.00 4.61
213 214 1.686115 CCAACTTCCATCCCCATCCAC 60.686 57.143 0.00 0.00 0.00 4.02
214 215 0.630673 CCAACTTCCATCCCCATCCA 59.369 55.000 0.00 0.00 0.00 3.41
215 216 0.926293 TCCAACTTCCATCCCCATCC 59.074 55.000 0.00 0.00 0.00 3.51
216 217 1.846439 TCTCCAACTTCCATCCCCATC 59.154 52.381 0.00 0.00 0.00 3.51
217 218 1.849039 CTCTCCAACTTCCATCCCCAT 59.151 52.381 0.00 0.00 0.00 4.00
218 219 1.289160 CTCTCCAACTTCCATCCCCA 58.711 55.000 0.00 0.00 0.00 4.96
219 220 0.106967 GCTCTCCAACTTCCATCCCC 60.107 60.000 0.00 0.00 0.00 4.81
220 221 0.462759 CGCTCTCCAACTTCCATCCC 60.463 60.000 0.00 0.00 0.00 3.85
221 222 0.537188 TCGCTCTCCAACTTCCATCC 59.463 55.000 0.00 0.00 0.00 3.51
222 223 1.933247 CTCGCTCTCCAACTTCCATC 58.067 55.000 0.00 0.00 0.00 3.51
223 224 0.107945 GCTCGCTCTCCAACTTCCAT 60.108 55.000 0.00 0.00 0.00 3.41
224 225 1.293498 GCTCGCTCTCCAACTTCCA 59.707 57.895 0.00 0.00 0.00 3.53
225 226 1.807573 CGCTCGCTCTCCAACTTCC 60.808 63.158 0.00 0.00 0.00 3.46
226 227 2.448705 GCGCTCGCTCTCCAACTTC 61.449 63.158 0.00 0.00 38.26 3.01
227 228 2.433318 GCGCTCGCTCTCCAACTT 60.433 61.111 0.00 0.00 38.26 2.66
228 229 4.785512 CGCGCTCGCTCTCCAACT 62.786 66.667 5.56 0.00 39.32 3.16
264 265 2.652893 CTTATTTGCTGCGCCCGCTC 62.653 60.000 17.83 6.41 42.51 5.03
265 266 2.749839 TTATTTGCTGCGCCCGCT 60.750 55.556 17.83 2.93 42.51 5.52
266 267 2.278142 CTTATTTGCTGCGCCCGC 60.278 61.111 4.18 8.60 42.35 6.13
267 268 2.278142 GCTTATTTGCTGCGCCCG 60.278 61.111 4.18 0.00 0.00 6.13
268 269 2.278142 CGCTTATTTGCTGCGCCC 60.278 61.111 4.18 0.00 43.08 6.13
272 273 2.951227 GCGCCGCTTATTTGCTGC 60.951 61.111 0.00 0.00 39.28 5.25
273 274 2.648724 CGCGCCGCTTATTTGCTG 60.649 61.111 7.78 0.00 0.00 4.41
290 291 4.096558 TGGCCGAAACGCAATCGC 62.097 61.111 0.00 0.00 38.93 4.58
291 292 2.098298 CTGGCCGAAACGCAATCG 59.902 61.111 0.00 0.00 42.43 3.34
292 293 2.202479 GCTGGCCGAAACGCAATC 60.202 61.111 0.00 0.00 0.00 2.67
293 294 4.101790 CGCTGGCCGAAACGCAAT 62.102 61.111 0.00 0.00 40.02 3.56
298 299 4.389576 CAGCACGCTGGCCGAAAC 62.390 66.667 11.29 0.00 40.17 2.78
299 300 4.617520 TCAGCACGCTGGCCGAAA 62.618 61.111 18.47 0.00 43.75 3.46
300 301 4.617520 TTCAGCACGCTGGCCGAA 62.618 61.111 18.47 3.17 43.75 4.30
302 303 3.932580 TAGTTCAGCACGCTGGCCG 62.933 63.158 18.47 0.00 43.75 6.13
303 304 2.047274 TAGTTCAGCACGCTGGCC 60.047 61.111 18.47 9.50 43.75 5.36
304 305 1.021390 ATGTAGTTCAGCACGCTGGC 61.021 55.000 18.47 11.79 43.75 4.85
305 306 2.293677 TATGTAGTTCAGCACGCTGG 57.706 50.000 18.47 1.04 43.75 4.85
306 307 2.033407 GCATATGTAGTTCAGCACGCTG 60.033 50.000 12.91 12.91 44.86 5.18
307 308 2.205074 GCATATGTAGTTCAGCACGCT 58.795 47.619 4.29 0.00 0.00 5.07
308 309 1.261619 GGCATATGTAGTTCAGCACGC 59.738 52.381 4.29 0.00 0.00 5.34
309 310 1.522676 CGGCATATGTAGTTCAGCACG 59.477 52.381 4.29 0.00 0.00 5.34
310 311 1.261619 GCGGCATATGTAGTTCAGCAC 59.738 52.381 4.29 0.00 0.00 4.40
311 312 1.581934 GCGGCATATGTAGTTCAGCA 58.418 50.000 4.29 0.00 0.00 4.41
312 313 0.508641 CGCGGCATATGTAGTTCAGC 59.491 55.000 4.29 0.00 0.00 4.26
313 314 0.508641 GCGCGGCATATGTAGTTCAG 59.491 55.000 8.83 0.00 0.00 3.02
314 315 1.212455 CGCGCGGCATATGTAGTTCA 61.212 55.000 24.84 0.00 0.00 3.18
315 316 1.487231 CGCGCGGCATATGTAGTTC 59.513 57.895 24.84 0.00 0.00 3.01
316 317 2.594962 GCGCGCGGCATATGTAGTT 61.595 57.895 33.06 0.00 42.87 2.24
317 318 3.036084 GCGCGCGGCATATGTAGT 61.036 61.111 33.06 0.00 42.87 2.73
318 319 3.777925 GGCGCGCGGCATATGTAG 61.778 66.667 45.39 9.50 46.16 2.74
322 323 3.605749 AATAGGGCGCGCGGCATAT 62.606 57.895 43.96 43.96 46.76 1.78
326 327 4.187810 AAAAATAGGGCGCGCGGC 62.188 61.111 43.74 43.74 42.51 6.53
327 328 2.277884 CAAAAATAGGGCGCGCGG 60.278 61.111 33.06 13.66 0.00 6.46
328 329 2.949163 GCAAAAATAGGGCGCGCG 60.949 61.111 28.44 28.44 0.00 6.86
329 330 2.949163 CGCAAAAATAGGGCGCGC 60.949 61.111 25.94 25.94 44.49 6.86
333 334 2.582226 GGCGCGCAAAAATAGGGC 60.582 61.111 34.42 7.22 42.10 5.19
334 335 2.104132 GGGCGCGCAAAAATAGGG 59.896 61.111 34.42 0.00 0.00 3.53
335 336 2.277884 CGGGCGCGCAAAAATAGG 60.278 61.111 34.42 7.95 0.00 2.57
336 337 2.949163 GCGGGCGCGCAAAAATAG 60.949 61.111 38.74 15.43 34.62 1.73
347 348 0.529773 TATAGTTGCTTCAGCGGGCG 60.530 55.000 0.00 0.00 45.83 6.13
348 349 0.938008 GTATAGTTGCTTCAGCGGGC 59.062 55.000 0.00 0.00 45.83 6.13
349 350 1.583054 GGTATAGTTGCTTCAGCGGG 58.417 55.000 0.00 0.00 45.83 6.13
350 351 1.202371 TCGGTATAGTTGCTTCAGCGG 60.202 52.381 0.00 0.00 45.83 5.52
351 352 2.203800 TCGGTATAGTTGCTTCAGCG 57.796 50.000 0.00 0.00 45.83 5.18
352 353 3.303395 GCAATCGGTATAGTTGCTTCAGC 60.303 47.826 2.36 0.00 43.56 4.26
353 354 3.060272 CGCAATCGGTATAGTTGCTTCAG 60.060 47.826 7.58 0.00 44.44 3.02
354 355 2.863740 CGCAATCGGTATAGTTGCTTCA 59.136 45.455 7.58 0.00 44.44 3.02
355 356 2.348591 GCGCAATCGGTATAGTTGCTTC 60.349 50.000 0.30 0.00 44.44 3.86
356 357 1.597663 GCGCAATCGGTATAGTTGCTT 59.402 47.619 0.30 0.00 44.44 3.91
357 358 1.217882 GCGCAATCGGTATAGTTGCT 58.782 50.000 0.30 0.00 44.44 3.91
358 359 0.111266 CGCGCAATCGGTATAGTTGC 60.111 55.000 8.75 0.00 43.49 4.17
359 360 0.111266 GCGCGCAATCGGTATAGTTG 60.111 55.000 29.10 0.00 35.95 3.16
360 361 1.545614 CGCGCGCAATCGGTATAGTT 61.546 55.000 32.61 0.00 35.95 2.24
361 362 2.014554 CGCGCGCAATCGGTATAGT 61.015 57.895 32.61 0.00 35.95 2.12
362 363 1.272784 TTCGCGCGCAATCGGTATAG 61.273 55.000 32.61 10.59 35.95 1.31
363 364 0.870735 TTTCGCGCGCAATCGGTATA 60.871 50.000 32.61 0.00 35.95 1.47
364 365 1.697772 TTTTCGCGCGCAATCGGTAT 61.698 50.000 32.61 0.00 35.95 2.73
365 366 1.898459 TTTTTCGCGCGCAATCGGTA 61.898 50.000 32.61 1.29 35.95 4.02
366 367 3.243274 TTTTTCGCGCGCAATCGGT 62.243 52.632 32.61 0.00 35.95 4.69
367 368 2.500795 TTTTTCGCGCGCAATCGG 60.501 55.556 32.61 14.68 35.95 4.18
381 382 4.373815 CGCGCCGTAAAATTAAACGTTTTT 60.374 37.500 20.19 9.79 37.40 1.94
382 383 3.117669 CGCGCCGTAAAATTAAACGTTTT 59.882 39.130 20.19 2.88 37.40 2.43
383 384 2.651234 CGCGCCGTAAAATTAAACGTTT 59.349 40.909 18.90 18.90 37.40 3.60
384 385 2.232524 CGCGCCGTAAAATTAAACGTT 58.767 42.857 0.00 0.00 37.40 3.99
385 386 1.463858 CCGCGCCGTAAAATTAAACGT 60.464 47.619 0.00 0.00 37.40 3.99
386 387 1.173526 CCGCGCCGTAAAATTAAACG 58.826 50.000 0.00 5.70 38.80 3.60
387 388 0.909174 GCCGCGCCGTAAAATTAAAC 59.091 50.000 0.00 0.00 0.00 2.01
388 389 0.520827 CGCCGCGCCGTAAAATTAAA 60.521 50.000 0.00 0.00 0.00 1.52
389 390 1.060622 CGCCGCGCCGTAAAATTAA 59.939 52.632 0.00 0.00 0.00 1.40
390 391 2.702206 CGCCGCGCCGTAAAATTA 59.298 55.556 0.00 0.00 0.00 1.40
408 409 1.153429 AAGGGCCGCGCTAAACTAG 60.153 57.895 10.79 0.00 0.00 2.57
409 410 1.448893 CAAGGGCCGCGCTAAACTA 60.449 57.895 10.79 0.00 0.00 2.24
410 411 2.746277 CAAGGGCCGCGCTAAACT 60.746 61.111 10.79 0.00 0.00 2.66
411 412 3.810896 CCAAGGGCCGCGCTAAAC 61.811 66.667 10.79 0.00 0.00 2.01
412 413 3.969250 CTCCAAGGGCCGCGCTAAA 62.969 63.158 10.79 0.00 0.00 1.85
413 414 4.467084 CTCCAAGGGCCGCGCTAA 62.467 66.667 10.79 0.00 0.00 3.09
418 419 4.496336 AGCATCTCCAAGGGCCGC 62.496 66.667 0.00 0.00 0.00 6.53
419 420 2.203126 GAGCATCTCCAAGGGCCG 60.203 66.667 0.00 0.00 0.00 6.13
432 433 3.000041 CGGCTATGTTTGTGTTAGAGCA 59.000 45.455 0.00 0.00 0.00 4.26
529 530 4.527816 TGGGAGGTTCTTCAATTGATTTGG 59.472 41.667 9.40 0.86 35.92 3.28
559 560 1.144969 TGACGCTGGCTTCTTTTACG 58.855 50.000 1.14 0.00 0.00 3.18
677 685 9.340695 CGCTAATCAAGTTCACATTTATTTTCA 57.659 29.630 0.00 0.00 0.00 2.69
678 686 9.554724 TCGCTAATCAAGTTCACATTTATTTTC 57.445 29.630 0.00 0.00 0.00 2.29
712 728 4.790962 CTGGTGCGCTGCCTCCAT 62.791 66.667 19.25 0.00 33.09 3.41
754 770 3.230990 GTGGGGCGGCACCTTTTT 61.231 61.111 23.89 0.00 39.10 1.94
850 883 1.141657 TGTTGCTCTGCTTCTGGTTCT 59.858 47.619 0.00 0.00 0.00 3.01
1004 1057 1.448540 CTCGCAATGCCTCGTCCTT 60.449 57.895 0.00 0.00 0.00 3.36
1009 1062 3.257561 CGACCTCGCAATGCCTCG 61.258 66.667 0.00 0.00 0.00 4.63
1284 1343 2.188469 GGGCGGCCTTATTGTCGA 59.812 61.111 22.87 0.00 0.00 4.20
1660 1719 2.022129 GACGGTGAGCAGGTTGTCG 61.022 63.158 0.00 0.00 0.00 4.35
2558 2617 6.554605 AGCAATTGGGCCATTTGTATATTAGT 59.445 34.615 30.94 11.64 30.43 2.24
2559 2618 6.869913 CAGCAATTGGGCCATTTGTATATTAG 59.130 38.462 30.94 15.75 30.43 1.73
2560 2619 6.552725 TCAGCAATTGGGCCATTTGTATATTA 59.447 34.615 30.94 15.26 30.43 0.98
2561 2620 5.366186 TCAGCAATTGGGCCATTTGTATATT 59.634 36.000 30.94 15.19 30.43 1.28
2562 2621 4.900652 TCAGCAATTGGGCCATTTGTATAT 59.099 37.500 30.94 17.92 30.43 0.86
2563 2622 4.285020 TCAGCAATTGGGCCATTTGTATA 58.715 39.130 30.94 18.91 30.43 1.47
2564 2623 3.106054 TCAGCAATTGGGCCATTTGTAT 58.894 40.909 30.94 21.64 30.43 2.29
2601 2660 7.067532 TGTATTTTGGACAGTTAAGCGTATG 57.932 36.000 0.00 0.00 0.00 2.39
2606 2665 6.644592 TGCAATTGTATTTTGGACAGTTAAGC 59.355 34.615 7.40 0.00 0.00 3.09
2614 2673 6.478344 TCTTGTGTTGCAATTGTATTTTGGAC 59.522 34.615 0.59 0.00 36.36 4.02
2616 2675 6.841443 TCTTGTGTTGCAATTGTATTTTGG 57.159 33.333 0.59 0.00 36.36 3.28
2677 2748 4.813750 ACCTAGTACGCAATTACCAGTT 57.186 40.909 0.00 0.00 0.00 3.16
2709 2780 1.668419 ATACCAACATTCGCTCAGGC 58.332 50.000 0.00 0.00 0.00 4.85
2735 2816 9.253832 TCCACACACATCATTAATCCTTTATTT 57.746 29.630 0.00 0.00 0.00 1.40
2747 2828 6.899393 AGTAATGTTTCCACACACATCATT 57.101 33.333 0.00 0.00 35.03 2.57
2748 2829 6.899393 AAGTAATGTTTCCACACACATCAT 57.101 33.333 0.00 0.00 35.03 2.45
2759 2840 8.871686 CCAAAGGCAATATAAGTAATGTTTCC 57.128 34.615 0.00 0.00 0.00 3.13
2786 2871 6.714810 TGAGCCATACATCAGTAAACAAACTT 59.285 34.615 0.00 0.00 33.13 2.66
2830 2918 0.251653 TACAGCAGTTCCTCCTCGGT 60.252 55.000 0.00 0.00 0.00 4.69
3042 3134 0.382515 GAGATGACCGAACGAGGAGG 59.617 60.000 0.00 0.00 34.73 4.30
3043 3135 0.382515 GGAGATGACCGAACGAGGAG 59.617 60.000 0.00 0.00 34.73 3.69
3044 3136 0.034380 AGGAGATGACCGAACGAGGA 60.034 55.000 0.00 0.00 34.73 3.71
3069 3161 1.589630 CAGCAGCACGGTAGGTACA 59.410 57.895 0.00 0.00 0.00 2.90
3139 3234 2.266055 CTGAGGAAGTCCGGCCAC 59.734 66.667 2.24 0.00 42.08 5.01
3166 3266 3.797507 CTGTTGTGGGGGCAGCAGT 62.798 63.158 0.00 0.00 41.00 4.40
3222 3322 0.521735 CCTTTTAGCACAGCGAACCC 59.478 55.000 0.00 0.00 0.00 4.11
3340 3450 1.228245 TCCTCCTGTTGGCTGTTGC 60.228 57.895 0.00 0.00 38.76 4.17
3341 3451 1.239968 GCTCCTCCTGTTGGCTGTTG 61.240 60.000 0.00 0.00 0.00 3.33
3342 3452 1.073897 GCTCCTCCTGTTGGCTGTT 59.926 57.895 0.00 0.00 0.00 3.16
3343 3453 2.149383 TGCTCCTCCTGTTGGCTGT 61.149 57.895 0.00 0.00 0.00 4.40
3344 3454 1.673665 GTGCTCCTCCTGTTGGCTG 60.674 63.158 0.00 0.00 0.00 4.85
3345 3455 2.753029 GTGCTCCTCCTGTTGGCT 59.247 61.111 0.00 0.00 0.00 4.75
3346 3456 2.743928 CGTGCTCCTCCTGTTGGC 60.744 66.667 0.00 0.00 0.00 4.52
3347 3457 2.046892 CCGTGCTCCTCCTGTTGG 60.047 66.667 0.00 0.00 0.00 3.77
3373 3483 3.959975 CACAAACACACGCCCCCG 61.960 66.667 0.00 0.00 41.14 5.73
3409 3519 0.503961 ACGAAGTAAAAACCGACGCG 59.496 50.000 3.53 3.53 41.94 6.01
3475 3585 4.072088 GTCGCCGGACGTGCTTTG 62.072 66.667 5.05 0.00 44.19 2.77
3505 3630 0.250295 CGTCCCTGTTGCCAGAAAGA 60.250 55.000 0.00 0.00 41.50 2.52
3558 3684 2.301870 ACGCTCTCCACATCACCTTAAA 59.698 45.455 0.00 0.00 0.00 1.52
3577 3703 2.351726 GGTTCGGAGGAATGAATGAACG 59.648 50.000 0.00 0.00 37.24 3.95
3648 3774 0.179158 GTTTTTGGTTGCGACGGTGT 60.179 50.000 0.00 0.00 0.00 4.16
3654 3780 4.113354 GTGTAAATGGTTTTTGGTTGCGA 58.887 39.130 0.00 0.00 0.00 5.10
3714 3840 3.411351 CACGGGAGAACGTTGGCG 61.411 66.667 5.00 0.00 46.25 5.69
3865 3992 6.469275 TCGCTCGATAAAAGAATATATCGCTG 59.531 38.462 9.61 6.87 46.42 5.18
3869 3996 7.950108 TCGTCGCTCGATAAAAGAATATATC 57.050 36.000 0.00 0.00 44.01 1.63
3921 4051 1.203928 TTTTGCGCGACCAATGTTTG 58.796 45.000 12.10 0.00 0.00 2.93
3937 4077 5.908341 ACCAAACAACGTACAATGGATTTT 58.092 33.333 14.90 0.00 0.00 1.82
3943 4083 5.722592 GCAACAAACCAAACAACGTACAATG 60.723 40.000 0.00 0.00 0.00 2.82
3944 4084 4.327627 GCAACAAACCAAACAACGTACAAT 59.672 37.500 0.00 0.00 0.00 2.71
3946 4086 3.243336 GCAACAAACCAAACAACGTACA 58.757 40.909 0.00 0.00 0.00 2.90
3973 4113 2.017049 GACTCGTTGGCAGCCAAATAT 58.983 47.619 29.04 14.31 45.73 1.28
3974 4114 1.448985 GACTCGTTGGCAGCCAAATA 58.551 50.000 29.04 17.79 45.73 1.40
4015 4155 2.514824 GAGATTCCACCGCCAGGC 60.515 66.667 0.00 0.00 42.76 4.85
4018 4158 2.892640 CGAGAGATTCCACCGCCA 59.107 61.111 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.