Multiple sequence alignment - TraesCS1A01G441200

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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 TraesCS1A01G441200 chr1A 100.000 3873 0 0 1 3873 589819566 589823438 0.000000e+00 7153.0
1 TraesCS1A01G441200 chr1A 84.496 129 18 2 3745 3873 42550914 42550788 4.060000e-25 126.0
2 TraesCS1A01G441200 chr1D 91.408 1641 73 30 664 2274 491803618 491805220 0.000000e+00 2187.0
3 TraesCS1A01G441200 chr1D 92.260 1460 62 20 2449 3862 491805696 491807150 0.000000e+00 2023.0
4 TraesCS1A01G441200 chr1D 81.712 257 36 4 1079 1335 480974318 480974563 1.820000e-48 204.0
5 TraesCS1A01G441200 chr1D 86.667 150 15 4 2300 2448 491805509 491805654 1.110000e-35 161.0
6 TraesCS1A01G441200 chr1B 91.098 1348 64 23 697 2025 684069568 684068258 0.000000e+00 1773.0
7 TraesCS1A01G441200 chr1B 90.806 707 37 15 3062 3743 684066895 684066192 0.000000e+00 920.0
8 TraesCS1A01G441200 chr1B 97.143 420 12 0 2449 2868 684067780 684067361 0.000000e+00 710.0
9 TraesCS1A01G441200 chr1B 92.453 212 9 3 2857 3063 684067267 684067058 2.930000e-76 296.0
10 TraesCS1A01G441200 chr1B 82.955 176 10 7 2274 2448 684067978 684067822 1.450000e-29 141.0
11 TraesCS1A01G441200 chr5B 88.141 312 35 2 1447 1756 598431886 598432197 1.700000e-98 370.0
12 TraesCS1A01G441200 chr7D 88.103 311 32 5 1452 1759 549701577 549701885 7.910000e-97 364.0
13 TraesCS1A01G441200 chr7D 97.059 34 0 1 3743 3775 544555844 544555877 5.410000e-04 56.5
14 TraesCS1A01G441200 chr2A 87.869 305 36 1 1455 1759 748681907 748682210 1.320000e-94 357.0
15 TraesCS1A01G441200 chr7A 89.494 257 27 0 1455 1711 3947846 3947590 3.730000e-85 326.0
16 TraesCS1A01G441200 chr7A 91.406 128 9 2 3746 3873 581880322 581880197 1.430000e-39 174.0
17 TraesCS1A01G441200 chr7B 82.000 250 33 4 1086 1335 736620843 736620606 6.560000e-48 202.0
18 TraesCS1A01G441200 chr7B 91.892 37 3 0 3837 3873 107564601 107564637 7.000000e-03 52.8
19 TraesCS1A01G441200 chr5D 81.959 194 29 3 1365 1552 313139339 313139146 4.010000e-35 159.0
20 TraesCS1A01G441200 chr3D 75.281 356 73 9 2500 2855 284209207 284208867 5.180000e-34 156.0
21 TraesCS1A01G441200 chr3D 80.925 173 32 1 3 175 42318391 42318220 6.750000e-28 135.0
22 TraesCS1A01G441200 chr3B 75.209 359 74 9 2497 2855 378691082 378691425 5.180000e-34 156.0
23 TraesCS1A01G441200 chr2B 88.550 131 12 2 3746 3873 604992877 604992747 5.180000e-34 156.0
24 TraesCS1A01G441200 chr4D 80.500 200 29 5 43 237 88705133 88705327 1.120000e-30 145.0
25 TraesCS1A01G441200 chr3A 74.719 356 75 8 2500 2855 371625750 371625410 1.120000e-30 145.0
26 TraesCS1A01G441200 chr3A 89.796 49 5 0 43 91 472575006 472574958 3.230000e-06 63.9
27 TraesCS1A01G441200 chr4B 81.560 141 23 3 42 182 529403449 529403312 3.160000e-21 113.0
28 TraesCS1A01G441200 chr6B 84.615 117 12 6 4 115 95484281 95484396 1.140000e-20 111.0
29 TraesCS1A01G441200 chr6B 88.333 60 5 2 44 103 682663246 682663189 1.930000e-08 71.3


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 TraesCS1A01G441200 chr1A 589819566 589823438 3872 False 7153 7153 100.000000 1 3873 1 chr1A.!!$F1 3872
1 TraesCS1A01G441200 chr1D 491803618 491807150 3532 False 1457 2187 90.111667 664 3862 3 chr1D.!!$F2 3198
2 TraesCS1A01G441200 chr1B 684066192 684069568 3376 True 768 1773 90.891000 697 3743 5 chr1B.!!$R1 3046

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
319 320 0.033601 ACAGTGGCTTGTGGTTTCCA 60.034 50.0 0.00 0.00 0.00 3.53 F
497 498 0.096976 GCGCTCGCTCATGCTAAAAA 59.903 50.0 0.00 0.00 38.26 1.94 F
1812 1831 0.704076 TTACCCCTGCAATTGCCTCT 59.296 50.0 26.94 8.01 41.18 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 1441 0.109873 CGTAGACGGCGAAGAAGTGT 60.110 55.0 16.62 0.0 35.37 3.55 R
2105 2174 0.394192 AACTAGTGCAGTGCAGAGCA 59.606 50.0 20.42 8.8 40.08 4.26 R
3278 3951 0.184933 TCAGTGGGGTGTTTTGGGAG 59.815 55.0 0.00 0.0 0.00 4.30 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
98 99 7.523293 ACATGATGAACCTTTTTCATACACA 57.477 32.000 0.00 0.00 39.08 3.72
99 100 8.125978 ACATGATGAACCTTTTTCATACACAT 57.874 30.769 0.00 0.00 39.08 3.21
100 101 8.587608 ACATGATGAACCTTTTTCATACACATT 58.412 29.630 0.00 0.00 39.08 2.71
101 102 8.865978 CATGATGAACCTTTTTCATACACATTG 58.134 33.333 0.00 0.00 39.08 2.82
102 103 7.950512 TGATGAACCTTTTTCATACACATTGT 58.049 30.769 0.00 0.00 39.08 2.71
103 104 9.072375 TGATGAACCTTTTTCATACACATTGTA 57.928 29.630 0.00 0.00 39.08 2.41
133 134 9.715123 TTCTTGTATACATTTTTCGTATGCATG 57.285 29.630 10.16 0.00 40.24 4.06
134 135 9.103861 TCTTGTATACATTTTTCGTATGCATGA 57.896 29.630 10.16 10.65 40.24 3.07
135 136 9.882996 CTTGTATACATTTTTCGTATGCATGAT 57.117 29.630 10.16 0.00 40.24 2.45
146 147 9.515020 TTTTCGTATGCATGATAAAGATTTTCC 57.485 29.630 10.16 0.00 0.00 3.13
147 148 7.800155 TCGTATGCATGATAAAGATTTTCCA 57.200 32.000 10.16 0.00 0.00 3.53
148 149 8.394971 TCGTATGCATGATAAAGATTTTCCAT 57.605 30.769 10.16 0.00 0.00 3.41
149 150 9.500785 TCGTATGCATGATAAAGATTTTCCATA 57.499 29.630 10.16 0.00 0.00 2.74
286 287 4.794248 GCAAAAGGCGAAAACAGAAAAT 57.206 36.364 0.00 0.00 0.00 1.82
287 288 4.517287 GCAAAAGGCGAAAACAGAAAATG 58.483 39.130 0.00 0.00 0.00 2.32
288 289 4.033932 GCAAAAGGCGAAAACAGAAAATGT 59.966 37.500 0.00 0.00 46.97 2.71
289 290 5.233263 GCAAAAGGCGAAAACAGAAAATGTA 59.767 36.000 0.00 0.00 43.00 2.29
290 291 6.636443 CAAAAGGCGAAAACAGAAAATGTAC 58.364 36.000 0.00 0.00 43.00 2.90
291 292 5.508200 AAGGCGAAAACAGAAAATGTACA 57.492 34.783 0.00 0.00 43.00 2.90
292 293 5.705609 AGGCGAAAACAGAAAATGTACAT 57.294 34.783 1.41 1.41 43.00 2.29
293 294 6.811253 AGGCGAAAACAGAAAATGTACATA 57.189 33.333 9.21 0.00 43.00 2.29
294 295 7.209471 AGGCGAAAACAGAAAATGTACATAA 57.791 32.000 9.21 0.00 43.00 1.90
295 296 7.653647 AGGCGAAAACAGAAAATGTACATAAA 58.346 30.769 9.21 0.00 43.00 1.40
296 297 8.138712 AGGCGAAAACAGAAAATGTACATAAAA 58.861 29.630 9.21 0.00 43.00 1.52
297 298 8.756864 GGCGAAAACAGAAAATGTACATAAAAA 58.243 29.630 9.21 0.00 43.00 1.94
298 299 9.562752 GCGAAAACAGAAAATGTACATAAAAAC 57.437 29.630 9.21 0.08 43.00 2.43
299 300 9.758470 CGAAAACAGAAAATGTACATAAAAACG 57.242 29.630 9.21 0.00 43.00 3.60
302 303 9.790389 AAACAGAAAATGTACATAAAAACGACA 57.210 25.926 9.21 0.00 43.00 4.35
303 304 9.445786 AACAGAAAATGTACATAAAAACGACAG 57.554 29.630 9.21 0.00 43.00 3.51
304 305 8.617809 ACAGAAAATGTACATAAAAACGACAGT 58.382 29.630 9.21 0.00 41.60 3.55
305 306 8.891928 CAGAAAATGTACATAAAAACGACAGTG 58.108 33.333 9.21 0.00 0.00 3.66
306 307 8.073768 AGAAAATGTACATAAAAACGACAGTGG 58.926 33.333 9.21 0.00 0.00 4.00
307 308 4.735662 TGTACATAAAAACGACAGTGGC 57.264 40.909 0.00 0.00 0.00 5.01
308 309 4.382291 TGTACATAAAAACGACAGTGGCT 58.618 39.130 0.00 0.00 0.00 4.75
309 310 4.817464 TGTACATAAAAACGACAGTGGCTT 59.183 37.500 0.00 0.00 0.00 4.35
310 311 4.223320 ACATAAAAACGACAGTGGCTTG 57.777 40.909 0.00 0.00 0.00 4.01
311 312 3.630312 ACATAAAAACGACAGTGGCTTGT 59.370 39.130 0.00 0.00 0.00 3.16
312 313 2.559998 AAAAACGACAGTGGCTTGTG 57.440 45.000 0.00 0.00 0.00 3.33
313 314 0.738389 AAAACGACAGTGGCTTGTGG 59.262 50.000 0.00 2.20 33.60 4.17
314 315 0.393808 AAACGACAGTGGCTTGTGGT 60.394 50.000 0.00 4.98 41.00 4.16
315 316 0.393808 AACGACAGTGGCTTGTGGTT 60.394 50.000 13.91 13.91 42.63 3.67
316 317 0.393808 ACGACAGTGGCTTGTGGTTT 60.394 50.000 0.00 0.00 36.77 3.27
317 318 0.307760 CGACAGTGGCTTGTGGTTTC 59.692 55.000 0.00 0.00 0.00 2.78
318 319 0.668535 GACAGTGGCTTGTGGTTTCC 59.331 55.000 0.00 0.00 0.00 3.13
319 320 0.033601 ACAGTGGCTTGTGGTTTCCA 60.034 50.000 0.00 0.00 0.00 3.53
320 321 0.670162 CAGTGGCTTGTGGTTTCCAG 59.330 55.000 0.00 0.00 32.34 3.86
321 322 1.109323 AGTGGCTTGTGGTTTCCAGC 61.109 55.000 0.00 0.00 32.34 4.85
322 323 2.192861 TGGCTTGTGGTTTCCAGCG 61.193 57.895 0.00 0.00 32.34 5.18
323 324 2.193536 GGCTTGTGGTTTCCAGCGT 61.194 57.895 0.00 0.00 32.34 5.07
324 325 1.008538 GCTTGTGGTTTCCAGCGTG 60.009 57.895 0.00 0.00 32.34 5.34
325 326 1.008538 CTTGTGGTTTCCAGCGTGC 60.009 57.895 0.00 0.00 32.34 5.34
326 327 2.406452 CTTGTGGTTTCCAGCGTGCC 62.406 60.000 0.00 0.00 32.34 5.01
327 328 4.025401 GTGGTTTCCAGCGTGCCG 62.025 66.667 0.00 0.00 32.34 5.69
338 339 3.849951 CGTGCCGGGCCAGTCTAT 61.850 66.667 17.97 0.00 0.00 1.98
339 340 2.590092 GTGCCGGGCCAGTCTATT 59.410 61.111 17.97 0.00 0.00 1.73
340 341 1.077716 GTGCCGGGCCAGTCTATTT 60.078 57.895 17.97 0.00 0.00 1.40
341 342 0.179468 GTGCCGGGCCAGTCTATTTA 59.821 55.000 17.97 0.00 0.00 1.40
342 343 0.468226 TGCCGGGCCAGTCTATTTAG 59.532 55.000 17.97 0.00 0.00 1.85
343 344 0.468648 GCCGGGCCAGTCTATTTAGT 59.531 55.000 8.12 0.00 0.00 2.24
344 345 1.810412 GCCGGGCCAGTCTATTTAGTG 60.810 57.143 8.12 0.00 0.00 2.74
345 346 1.760613 CCGGGCCAGTCTATTTAGTGA 59.239 52.381 4.39 0.00 0.00 3.41
346 347 2.224066 CCGGGCCAGTCTATTTAGTGAG 60.224 54.545 4.39 0.00 0.00 3.51
347 348 2.224066 CGGGCCAGTCTATTTAGTGAGG 60.224 54.545 4.39 0.00 0.00 3.86
348 349 2.485657 GGGCCAGTCTATTTAGTGAGGC 60.486 54.545 4.39 0.00 40.08 4.70
349 350 2.474816 GCCAGTCTATTTAGTGAGGCG 58.525 52.381 0.00 0.00 0.00 5.52
350 351 2.159085 GCCAGTCTATTTAGTGAGGCGT 60.159 50.000 0.00 0.00 0.00 5.68
351 352 3.707793 CCAGTCTATTTAGTGAGGCGTC 58.292 50.000 0.00 0.00 0.00 5.19
352 353 3.381908 CCAGTCTATTTAGTGAGGCGTCT 59.618 47.826 8.06 0.00 0.00 4.18
353 354 4.355437 CAGTCTATTTAGTGAGGCGTCTG 58.645 47.826 8.06 0.00 0.00 3.51
354 355 4.096532 CAGTCTATTTAGTGAGGCGTCTGA 59.903 45.833 8.06 0.00 0.00 3.27
355 356 4.890581 AGTCTATTTAGTGAGGCGTCTGAT 59.109 41.667 8.06 0.00 0.00 2.90
356 357 4.979197 GTCTATTTAGTGAGGCGTCTGATG 59.021 45.833 8.06 0.00 0.00 3.07
357 358 2.010145 TTTAGTGAGGCGTCTGATGC 57.990 50.000 13.40 13.40 0.00 3.91
358 359 0.179137 TTAGTGAGGCGTCTGATGCG 60.179 55.000 15.13 0.00 0.00 4.73
359 360 1.029947 TAGTGAGGCGTCTGATGCGA 61.030 55.000 15.13 0.00 0.00 5.10
360 361 1.875813 GTGAGGCGTCTGATGCGAG 60.876 63.158 15.13 0.00 0.00 5.03
361 362 2.959071 GAGGCGTCTGATGCGAGC 60.959 66.667 15.13 2.44 0.00 5.03
362 363 4.862092 AGGCGTCTGATGCGAGCG 62.862 66.667 15.13 0.00 0.00 5.03
374 375 4.135153 CGAGCGCACCCTACAGCT 62.135 66.667 11.47 0.00 43.33 4.24
375 376 2.266055 GAGCGCACCCTACAGCTT 59.734 61.111 11.47 0.00 40.39 3.74
376 377 2.046892 AGCGCACCCTACAGCTTG 60.047 61.111 11.47 0.00 36.41 4.01
377 378 3.804193 GCGCACCCTACAGCTTGC 61.804 66.667 0.30 0.00 0.00 4.01
378 379 2.046892 CGCACCCTACAGCTTGCT 60.047 61.111 4.44 0.00 32.56 3.91
379 380 1.218047 CGCACCCTACAGCTTGCTA 59.782 57.895 4.44 0.00 32.56 3.49
380 381 0.391130 CGCACCCTACAGCTTGCTAA 60.391 55.000 4.44 0.00 32.56 3.09
381 382 1.087501 GCACCCTACAGCTTGCTAAC 58.912 55.000 0.00 0.00 32.00 2.34
382 383 1.610624 GCACCCTACAGCTTGCTAACA 60.611 52.381 0.00 0.00 32.00 2.41
383 384 2.350522 CACCCTACAGCTTGCTAACAG 58.649 52.381 0.00 0.00 0.00 3.16
384 385 1.339151 ACCCTACAGCTTGCTAACAGC 60.339 52.381 0.00 0.00 42.82 4.40
396 397 1.594862 GCTAACAGCAAGACATAGGCG 59.405 52.381 0.00 0.00 41.89 5.52
397 398 1.594862 CTAACAGCAAGACATAGGCGC 59.405 52.381 0.00 0.00 0.00 6.53
398 399 1.361668 AACAGCAAGACATAGGCGCG 61.362 55.000 0.00 0.00 0.00 6.86
399 400 2.892425 AGCAAGACATAGGCGCGC 60.892 61.111 25.94 25.94 0.00 6.86
400 401 3.941836 GCAAGACATAGGCGCGCC 61.942 66.667 42.34 42.34 0.00 6.53
401 402 3.272334 CAAGACATAGGCGCGCCC 61.272 66.667 44.47 29.27 36.58 6.13
402 403 3.781307 AAGACATAGGCGCGCCCA 61.781 61.111 44.47 34.90 36.58 5.36
403 404 3.106986 AAGACATAGGCGCGCCCAT 62.107 57.895 44.47 35.54 36.58 4.00
404 405 2.591715 GACATAGGCGCGCCCATT 60.592 61.111 44.47 29.86 36.58 3.16
405 406 1.301401 GACATAGGCGCGCCCATTA 60.301 57.895 44.47 31.03 36.58 1.90
406 407 0.882927 GACATAGGCGCGCCCATTAA 60.883 55.000 44.47 25.67 36.58 1.40
407 408 0.884704 ACATAGGCGCGCCCATTAAG 60.885 55.000 44.47 28.68 36.58 1.85
408 409 0.602638 CATAGGCGCGCCCATTAAGA 60.603 55.000 44.47 21.94 36.58 2.10
409 410 0.320771 ATAGGCGCGCCCATTAAGAG 60.321 55.000 44.47 0.00 36.58 2.85
410 411 2.377628 TAGGCGCGCCCATTAAGAGG 62.378 60.000 44.47 0.00 36.58 3.69
417 418 1.227973 CCCATTAAGAGGGCTCCGC 60.228 63.158 3.04 0.00 39.96 5.54
418 419 1.526887 CCATTAAGAGGGCTCCGCA 59.473 57.895 0.00 0.00 0.00 5.69
419 420 0.533755 CCATTAAGAGGGCTCCGCAG 60.534 60.000 0.00 0.00 0.00 5.18
434 435 3.114616 CAGGCGTCTGAGCGGTTG 61.115 66.667 12.86 0.00 43.49 3.77
446 447 3.422303 CGGTTGCTAGCGCTTGCA 61.422 61.111 36.58 36.58 42.66 4.08
447 448 2.176792 GGTTGCTAGCGCTTGCAC 59.823 61.111 39.19 31.32 40.70 4.57
448 449 2.202222 GTTGCTAGCGCTTGCACG 60.202 61.111 39.19 14.63 40.70 5.34
449 450 2.356913 TTGCTAGCGCTTGCACGA 60.357 55.556 39.19 26.39 40.70 4.35
450 451 1.741401 TTGCTAGCGCTTGCACGAT 60.741 52.632 39.19 6.38 40.70 3.73
451 452 1.969809 TTGCTAGCGCTTGCACGATG 61.970 55.000 39.19 11.46 40.70 3.84
452 453 2.322422 CTAGCGCTTGCACGATGC 59.678 61.111 18.68 0.33 45.29 3.91
453 454 2.125552 TAGCGCTTGCACGATGCT 60.126 55.556 18.68 13.45 45.31 3.79
454 455 0.871592 CTAGCGCTTGCACGATGCTA 60.872 55.000 18.68 14.10 45.31 3.49
455 456 0.871592 TAGCGCTTGCACGATGCTAG 60.872 55.000 18.68 13.75 46.39 3.42
459 460 1.717937 CTTGCACGATGCTAGCACC 59.282 57.895 22.07 10.03 45.31 5.01
460 461 1.003959 TTGCACGATGCTAGCACCA 60.004 52.632 22.07 9.48 45.31 4.17
461 462 1.298157 TTGCACGATGCTAGCACCAC 61.298 55.000 22.07 13.44 45.31 4.16
462 463 2.464459 GCACGATGCTAGCACCACC 61.464 63.158 22.07 8.77 40.96 4.61
463 464 2.167219 CACGATGCTAGCACCACCG 61.167 63.158 22.07 21.55 0.00 4.94
464 465 2.184322 CGATGCTAGCACCACCGT 59.816 61.111 22.07 1.92 0.00 4.83
465 466 2.167219 CGATGCTAGCACCACCGTG 61.167 63.158 22.07 0.88 43.35 4.94
466 467 1.815421 GATGCTAGCACCACCGTGG 60.815 63.158 22.07 16.47 45.02 4.94
475 476 4.489249 CCACCGTGGTCGATGTAC 57.511 61.111 9.64 0.00 39.71 2.90
476 477 1.515519 CCACCGTGGTCGATGTACG 60.516 63.158 9.64 10.76 44.09 3.67
477 478 2.156446 CACCGTGGTCGATGTACGC 61.156 63.158 11.86 0.00 42.26 4.42
478 479 2.947621 CCGTGGTCGATGTACGCG 60.948 66.667 3.53 3.53 42.26 6.01
479 480 3.604202 CGTGGTCGATGTACGCGC 61.604 66.667 5.73 0.00 42.26 6.86
480 481 3.604202 GTGGTCGATGTACGCGCG 61.604 66.667 30.96 30.96 42.26 6.86
483 484 3.669446 GTCGATGTACGCGCGCTC 61.669 66.667 32.58 23.02 42.26 5.03
494 495 2.956439 CGCGCTCGCTCATGCTAA 60.956 61.111 5.56 0.00 39.32 3.09
495 496 2.516589 CGCGCTCGCTCATGCTAAA 61.517 57.895 5.56 0.00 39.32 1.85
496 497 1.715585 GCGCTCGCTCATGCTAAAA 59.284 52.632 0.00 0.00 38.26 1.52
497 498 0.096976 GCGCTCGCTCATGCTAAAAA 59.903 50.000 0.00 0.00 38.26 1.94
614 615 7.816945 AAAATGTCTGTGAACTCAAAAGTTG 57.183 32.000 0.00 0.00 45.80 3.16
615 616 6.515272 AATGTCTGTGAACTCAAAAGTTGT 57.485 33.333 0.00 0.00 45.80 3.32
616 617 5.957842 TGTCTGTGAACTCAAAAGTTGTT 57.042 34.783 0.00 0.00 45.80 2.83
617 618 5.938322 TGTCTGTGAACTCAAAAGTTGTTC 58.062 37.500 0.00 0.00 45.80 3.18
618 619 5.471797 TGTCTGTGAACTCAAAAGTTGTTCA 59.528 36.000 0.00 0.00 45.80 3.18
622 623 5.713792 TGAACTCAAAAGTTGTTCACCAA 57.286 34.783 0.00 0.00 45.80 3.67
623 624 6.090483 TGAACTCAAAAGTTGTTCACCAAA 57.910 33.333 0.00 0.00 45.80 3.28
624 625 6.696411 TGAACTCAAAAGTTGTTCACCAAAT 58.304 32.000 0.00 0.00 45.80 2.32
625 626 7.158021 TGAACTCAAAAGTTGTTCACCAAATT 58.842 30.769 0.00 0.00 45.80 1.82
636 637 9.758651 AGTTGTTCACCAAATTTTTAACTATCC 57.241 29.630 0.00 0.00 34.07 2.59
637 638 9.535878 GTTGTTCACCAAATTTTTAACTATCCA 57.464 29.630 0.00 0.00 34.07 3.41
654 655 8.814038 AACTATCCATATATTTCAGAATGCCC 57.186 34.615 0.00 0.00 34.76 5.36
655 656 7.932134 ACTATCCATATATTTCAGAATGCCCA 58.068 34.615 0.00 0.00 34.76 5.36
656 657 8.563502 ACTATCCATATATTTCAGAATGCCCAT 58.436 33.333 0.00 0.00 34.76 4.00
659 660 8.756486 TCCATATATTTCAGAATGCCCATATG 57.244 34.615 0.00 0.00 34.76 1.78
660 661 8.338493 TCCATATATTTCAGAATGCCCATATGT 58.662 33.333 1.24 0.00 34.76 2.29
661 662 8.410912 CCATATATTTCAGAATGCCCATATGTG 58.589 37.037 1.24 0.00 34.76 3.21
662 663 9.181061 CATATATTTCAGAATGCCCATATGTGA 57.819 33.333 1.24 0.00 34.76 3.58
865 866 4.812476 TTGCCTCCGTCGCCATCG 62.812 66.667 0.00 0.00 0.00 3.84
875 876 4.812476 CGCCATCGCCGTCTCCAA 62.812 66.667 0.00 0.00 0.00 3.53
982 1001 5.163195 CCTTAGGCTTAGGCTTATTCTTGGA 60.163 44.000 14.80 0.00 39.70 3.53
1287 1306 2.043450 CTCTGGGGGCTCGAGTCT 60.043 66.667 17.97 0.00 0.00 3.24
1290 1309 1.379977 CTGGGGGCTCGAGTCTGTA 60.380 63.158 17.97 2.30 0.00 2.74
1495 1514 4.329545 GGGACAAGCTCCACGCCA 62.330 66.667 0.00 0.00 41.63 5.69
1500 1519 4.626081 AAGCTCCACGCCACGCTT 62.626 61.111 0.00 0.00 40.39 4.68
1503 1522 2.972505 CTCCACGCCACGCTTGTT 60.973 61.111 0.00 0.00 0.00 2.83
1611 1630 3.782244 GACTGCTTCTGCCGCGTG 61.782 66.667 4.92 0.00 38.71 5.34
1750 1769 2.042831 GCGCCATTGCCACTCTCTT 61.043 57.895 0.00 0.00 0.00 2.85
1752 1771 1.737838 CGCCATTGCCACTCTCTTTA 58.262 50.000 0.00 0.00 0.00 1.85
1765 1784 5.338381 CCACTCTCTTTAGACCATAAGGCAA 60.338 44.000 0.00 0.00 39.06 4.52
1766 1785 5.582665 CACTCTCTTTAGACCATAAGGCAAC 59.417 44.000 0.00 0.00 39.06 4.17
1771 1790 5.880332 TCTTTAGACCATAAGGCAACATCAC 59.120 40.000 0.00 0.00 39.06 3.06
1774 1793 3.053395 AGACCATAAGGCAACATCACCAT 60.053 43.478 0.00 0.00 39.06 3.55
1775 1794 3.701040 GACCATAAGGCAACATCACCATT 59.299 43.478 0.00 0.00 39.06 3.16
1792 1811 5.010820 TCACCATTTTCATCACATTTGCTCA 59.989 36.000 0.00 0.00 0.00 4.26
1812 1831 0.704076 TTACCCCTGCAATTGCCTCT 59.296 50.000 26.94 8.01 41.18 3.69
1817 1836 0.809385 CCTGCAATTGCCTCTGAGTG 59.191 55.000 26.94 8.07 41.18 3.51
2085 2154 7.534282 ACTTTAGGTAGCGAGTTTCTAGTAAC 58.466 38.462 4.17 4.17 0.00 2.50
2087 2156 4.006319 AGGTAGCGAGTTTCTAGTAACGT 58.994 43.478 6.59 0.00 33.26 3.99
2102 2171 5.684550 AGTAACGTTGTCAAGGAAAATCC 57.315 39.130 11.99 0.00 36.58 3.01
2121 2190 1.516161 CTTTGCTCTGCACTGCACTA 58.484 50.000 8.21 0.63 38.71 2.74
2140 2209 5.233988 CACTAGTTCTTCTCTGTTCTTGGG 58.766 45.833 0.00 0.00 0.00 4.12
2145 2214 6.368805 AGTTCTTCTCTGTTCTTGGGAAAAT 58.631 36.000 0.00 0.00 32.81 1.82
2165 2236 9.657419 GGAAAATTGTTGGTGATATCTGAATTT 57.343 29.630 3.98 3.55 0.00 1.82
2170 2241 9.643693 ATTGTTGGTGATATCTGAATTTTTGAC 57.356 29.630 3.98 0.00 0.00 3.18
2171 2242 8.175925 TGTTGGTGATATCTGAATTTTTGACA 57.824 30.769 3.98 0.00 0.00 3.58
2172 2243 8.805175 TGTTGGTGATATCTGAATTTTTGACAT 58.195 29.630 3.98 0.00 0.00 3.06
2175 2246 9.685276 TGGTGATATCTGAATTTTTGACATAGT 57.315 29.630 3.98 0.00 0.00 2.12
2193 2264 9.546428 TGACATAGTAATTGTTGGTGATATCTG 57.454 33.333 3.98 0.00 0.00 2.90
2194 2265 9.764363 GACATAGTAATTGTTGGTGATATCTGA 57.236 33.333 3.98 0.00 0.00 3.27
2219 2290 3.054878 GCTGGCAAAAGTTTCATGACTG 58.945 45.455 0.00 0.00 0.00 3.51
2266 2338 6.240894 AGTTAGTGATCATTTGTGTGATGGT 58.759 36.000 0.00 0.00 38.88 3.55
2270 2342 5.771666 AGTGATCATTTGTGTGATGGTCTTT 59.228 36.000 0.00 0.00 38.88 2.52
2303 2637 7.118390 GTGGGCTAGCATAGATAACAAATACTG 59.882 40.741 18.24 0.00 42.77 2.74
2338 2673 7.017645 CACAAACTGATGATTACTAACACTGC 58.982 38.462 0.00 0.00 0.00 4.40
2348 2683 3.469008 ACTAACACTGCACAAGTAGCA 57.531 42.857 0.00 0.00 36.83 3.49
2356 2691 1.001974 TGCACAAGTAGCAGGGTGTAG 59.998 52.381 0.00 0.00 37.02 2.74
2363 2698 2.689073 AGCAGGGTGTAGTCATGCT 58.311 52.632 0.00 0.00 42.18 3.79
2381 2716 4.568072 TGCTTGCTTACTAAGGAATGGA 57.432 40.909 3.46 0.00 38.20 3.41
2386 2721 6.936900 GCTTGCTTACTAAGGAATGGATCATA 59.063 38.462 3.46 0.00 38.20 2.15
2403 2738 5.359009 GGATCATATTCCCATGCTTGTATGG 59.641 44.000 10.20 10.20 45.83 2.74
2407 2742 3.737559 TTCCCATGCTTGTATGGTCTT 57.262 42.857 14.81 0.00 44.98 3.01
2480 2856 6.069440 TCTGAACTGGATTCCTGGTTATGATT 60.069 38.462 13.49 0.00 36.36 2.57
2539 2915 1.335145 CGTACATAATCCCGGTCCCT 58.665 55.000 0.00 0.00 0.00 4.20
2773 3149 1.413077 GCCGAGTACCTATCCAAGCTT 59.587 52.381 0.00 0.00 0.00 3.74
2929 3412 2.415512 CTGATGACAGTGACAGTGCATG 59.584 50.000 18.74 7.37 39.11 4.06
3056 3544 2.416547 CCTTGCACATACACTGCAGTAC 59.583 50.000 21.20 3.90 45.21 2.73
3114 3766 6.272318 TGTCAATGTTCAAAATGTCACCTTC 58.728 36.000 0.00 0.00 0.00 3.46
3130 3782 1.406069 CCTTCTCATGTCGTCCCCTTG 60.406 57.143 0.00 0.00 0.00 3.61
3133 3785 0.391661 CTCATGTCGTCCCCTTGGTG 60.392 60.000 0.00 0.00 0.00 4.17
3137 3789 2.203182 TCGTCCCCTTGGTGTCCT 59.797 61.111 0.00 0.00 0.00 3.85
3157 3809 5.286558 GTCCTTATCTTTCTTCGTCTTGTCG 59.713 44.000 0.00 0.00 0.00 4.35
3169 3821 0.699399 TCTTGTCGACCTCCTCTCCT 59.301 55.000 14.12 0.00 0.00 3.69
3215 3888 0.392998 CAACGACCCTCCCATCCTTG 60.393 60.000 0.00 0.00 0.00 3.61
3278 3951 1.205893 AGCTCTCAATCGAAGGTGTCC 59.794 52.381 0.00 0.00 0.00 4.02
3283 3956 0.613260 CAATCGAAGGTGTCCTCCCA 59.387 55.000 0.00 0.00 30.89 4.37
3374 4047 0.950555 GGACAGTGCGATGACAAGCA 60.951 55.000 5.04 5.04 41.55 3.91
3418 4093 6.358974 TTGATCCACTACATCAACAGAAGA 57.641 37.500 0.00 0.00 35.71 2.87
3438 4113 3.177487 GACAACCGTCGGACTAATCTTC 58.823 50.000 20.51 0.00 31.07 2.87
3494 4169 6.782082 TCTACACTTCTGCTAGATGAATGT 57.218 37.500 0.00 6.29 0.00 2.71
3497 4172 3.937079 CACTTCTGCTAGATGAATGTGCA 59.063 43.478 0.00 0.00 0.00 4.57
3700 4395 4.452455 GCACGGAATGGAGATATACCTTTG 59.548 45.833 0.00 0.00 0.00 2.77
3733 4429 6.893020 AGGGGAAAATGTTCTACTAGATGT 57.107 37.500 0.00 0.00 33.92 3.06
3734 4430 7.989947 AGGGGAAAATGTTCTACTAGATGTA 57.010 36.000 0.00 0.00 33.92 2.29
3736 4432 9.004231 AGGGGAAAATGTTCTACTAGATGTAAT 57.996 33.333 0.00 0.00 33.92 1.89
3737 4433 9.057089 GGGGAAAATGTTCTACTAGATGTAATG 57.943 37.037 0.00 0.00 33.92 1.90
3738 4434 9.614792 GGGAAAATGTTCTACTAGATGTAATGT 57.385 33.333 0.00 0.00 33.92 2.71
3862 4559 4.885907 AGAAGGTGATGTTCTATTGGCATG 59.114 41.667 0.00 0.00 32.29 4.06
3863 4560 4.240881 AGGTGATGTTCTATTGGCATGT 57.759 40.909 0.00 0.00 0.00 3.21
3864 4561 3.949754 AGGTGATGTTCTATTGGCATGTG 59.050 43.478 0.00 0.00 0.00 3.21
3865 4562 3.947196 GGTGATGTTCTATTGGCATGTGA 59.053 43.478 0.00 0.00 0.00 3.58
3866 4563 4.398988 GGTGATGTTCTATTGGCATGTGAA 59.601 41.667 0.00 0.00 0.00 3.18
3867 4564 5.105797 GGTGATGTTCTATTGGCATGTGAAA 60.106 40.000 0.00 0.00 0.00 2.69
3868 4565 6.406177 GGTGATGTTCTATTGGCATGTGAAAT 60.406 38.462 0.00 0.00 0.00 2.17
3869 4566 7.037438 GTGATGTTCTATTGGCATGTGAAATT 58.963 34.615 0.00 0.00 0.00 1.82
3870 4567 7.546667 GTGATGTTCTATTGGCATGTGAAATTT 59.453 33.333 0.00 0.00 0.00 1.82
3871 4568 7.760794 TGATGTTCTATTGGCATGTGAAATTTC 59.239 33.333 11.41 11.41 0.00 2.17
3872 4569 6.990798 TGTTCTATTGGCATGTGAAATTTCA 58.009 32.000 16.91 16.91 34.20 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 9.241919 TGTGTATGAAAAAGGTTCATCATGTAT 57.758 29.630 4.90 0.00 39.59 2.29
73 74 8.628630 TGTGTATGAAAAAGGTTCATCATGTA 57.371 30.769 4.90 0.00 39.59 2.29
74 75 7.523293 TGTGTATGAAAAAGGTTCATCATGT 57.477 32.000 4.90 0.00 39.59 3.21
75 76 8.865978 CAATGTGTATGAAAAAGGTTCATCATG 58.134 33.333 4.90 0.00 39.59 3.07
76 77 8.587608 ACAATGTGTATGAAAAAGGTTCATCAT 58.412 29.630 4.90 1.48 39.59 2.45
77 78 7.950512 ACAATGTGTATGAAAAAGGTTCATCA 58.049 30.769 4.90 0.00 39.59 3.07
107 108 9.715123 CATGCATACGAAAAATGTATACAAGAA 57.285 29.630 10.14 0.00 31.33 2.52
108 109 9.103861 TCATGCATACGAAAAATGTATACAAGA 57.896 29.630 10.14 0.00 31.33 3.02
109 110 9.882996 ATCATGCATACGAAAAATGTATACAAG 57.117 29.630 10.14 0.63 31.33 3.16
120 121 9.515020 GGAAAATCTTTATCATGCATACGAAAA 57.485 29.630 0.00 0.00 0.00 2.29
121 122 8.681806 TGGAAAATCTTTATCATGCATACGAAA 58.318 29.630 0.00 0.00 0.00 3.46
122 123 8.219546 TGGAAAATCTTTATCATGCATACGAA 57.780 30.769 0.00 0.00 0.00 3.85
123 124 7.800155 TGGAAAATCTTTATCATGCATACGA 57.200 32.000 0.00 0.00 0.00 3.43
253 254 9.658475 GTTTTCGCCTTTTGCTTTTTATTTTAT 57.342 25.926 0.00 0.00 38.05 1.40
254 255 8.665685 TGTTTTCGCCTTTTGCTTTTTATTTTA 58.334 25.926 0.00 0.00 38.05 1.52
255 256 7.530863 TGTTTTCGCCTTTTGCTTTTTATTTT 58.469 26.923 0.00 0.00 38.05 1.82
256 257 7.065204 TCTGTTTTCGCCTTTTGCTTTTTATTT 59.935 29.630 0.00 0.00 38.05 1.40
257 258 6.536941 TCTGTTTTCGCCTTTTGCTTTTTATT 59.463 30.769 0.00 0.00 38.05 1.40
258 259 6.045955 TCTGTTTTCGCCTTTTGCTTTTTAT 58.954 32.000 0.00 0.00 38.05 1.40
259 260 5.411781 TCTGTTTTCGCCTTTTGCTTTTTA 58.588 33.333 0.00 0.00 38.05 1.52
260 261 4.249661 TCTGTTTTCGCCTTTTGCTTTTT 58.750 34.783 0.00 0.00 38.05 1.94
261 262 3.855858 TCTGTTTTCGCCTTTTGCTTTT 58.144 36.364 0.00 0.00 38.05 2.27
262 263 3.518634 TCTGTTTTCGCCTTTTGCTTT 57.481 38.095 0.00 0.00 38.05 3.51
263 264 3.518634 TTCTGTTTTCGCCTTTTGCTT 57.481 38.095 0.00 0.00 38.05 3.91
264 265 3.518634 TTTCTGTTTTCGCCTTTTGCT 57.481 38.095 0.00 0.00 38.05 3.91
265 266 4.033932 ACATTTTCTGTTTTCGCCTTTTGC 59.966 37.500 0.00 0.00 32.90 3.68
266 267 5.717038 ACATTTTCTGTTTTCGCCTTTTG 57.283 34.783 0.00 0.00 32.90 2.44
267 268 6.334202 TGTACATTTTCTGTTTTCGCCTTTT 58.666 32.000 0.00 0.00 39.39 2.27
268 269 5.897050 TGTACATTTTCTGTTTTCGCCTTT 58.103 33.333 0.00 0.00 39.39 3.11
269 270 5.508200 TGTACATTTTCTGTTTTCGCCTT 57.492 34.783 0.00 0.00 39.39 4.35
270 271 5.705609 ATGTACATTTTCTGTTTTCGCCT 57.294 34.783 1.41 0.00 39.39 5.52
271 272 7.861176 TTTATGTACATTTTCTGTTTTCGCC 57.139 32.000 14.77 0.00 39.39 5.54
272 273 9.562752 GTTTTTATGTACATTTTCTGTTTTCGC 57.437 29.630 14.77 0.00 39.39 4.70
273 274 9.758470 CGTTTTTATGTACATTTTCTGTTTTCG 57.242 29.630 14.77 3.44 39.39 3.46
276 277 9.790389 TGTCGTTTTTATGTACATTTTCTGTTT 57.210 25.926 14.77 0.00 39.39 2.83
277 278 9.445786 CTGTCGTTTTTATGTACATTTTCTGTT 57.554 29.630 14.77 0.00 39.39 3.16
278 279 8.617809 ACTGTCGTTTTTATGTACATTTTCTGT 58.382 29.630 14.77 4.50 42.13 3.41
279 280 8.891928 CACTGTCGTTTTTATGTACATTTTCTG 58.108 33.333 14.77 0.81 0.00 3.02
280 281 8.073768 CCACTGTCGTTTTTATGTACATTTTCT 58.926 33.333 14.77 0.00 0.00 2.52
281 282 7.149031 GCCACTGTCGTTTTTATGTACATTTTC 60.149 37.037 14.77 0.56 0.00 2.29
282 283 6.639279 GCCACTGTCGTTTTTATGTACATTTT 59.361 34.615 14.77 0.00 0.00 1.82
283 284 6.016610 AGCCACTGTCGTTTTTATGTACATTT 60.017 34.615 14.77 0.00 0.00 2.32
284 285 5.472137 AGCCACTGTCGTTTTTATGTACATT 59.528 36.000 14.77 0.00 0.00 2.71
285 286 5.001232 AGCCACTGTCGTTTTTATGTACAT 58.999 37.500 13.93 13.93 0.00 2.29
286 287 4.382291 AGCCACTGTCGTTTTTATGTACA 58.618 39.130 0.00 0.00 0.00 2.90
287 288 5.144359 CAAGCCACTGTCGTTTTTATGTAC 58.856 41.667 0.00 0.00 0.00 2.90
288 289 4.817464 ACAAGCCACTGTCGTTTTTATGTA 59.183 37.500 0.00 0.00 0.00 2.29
289 290 3.630312 ACAAGCCACTGTCGTTTTTATGT 59.370 39.130 0.00 0.00 0.00 2.29
290 291 3.974401 CACAAGCCACTGTCGTTTTTATG 59.026 43.478 0.00 0.00 0.00 1.90
291 292 3.004315 CCACAAGCCACTGTCGTTTTTAT 59.996 43.478 0.00 0.00 0.00 1.40
292 293 2.356382 CCACAAGCCACTGTCGTTTTTA 59.644 45.455 0.00 0.00 0.00 1.52
293 294 1.134175 CCACAAGCCACTGTCGTTTTT 59.866 47.619 0.00 0.00 0.00 1.94
294 295 0.738389 CCACAAGCCACTGTCGTTTT 59.262 50.000 0.00 0.00 0.00 2.43
295 296 0.393808 ACCACAAGCCACTGTCGTTT 60.394 50.000 0.00 0.00 0.00 3.60
296 297 0.393808 AACCACAAGCCACTGTCGTT 60.394 50.000 0.00 0.00 0.00 3.85
297 298 0.393808 AAACCACAAGCCACTGTCGT 60.394 50.000 0.00 0.00 0.00 4.34
298 299 0.307760 GAAACCACAAGCCACTGTCG 59.692 55.000 0.00 0.00 0.00 4.35
299 300 0.668535 GGAAACCACAAGCCACTGTC 59.331 55.000 0.00 0.00 0.00 3.51
300 301 0.033601 TGGAAACCACAAGCCACTGT 60.034 50.000 0.00 0.00 0.00 3.55
301 302 0.670162 CTGGAAACCACAAGCCACTG 59.330 55.000 0.00 0.00 0.00 3.66
302 303 1.109323 GCTGGAAACCACAAGCCACT 61.109 55.000 0.00 0.00 0.00 4.00
303 304 1.363807 GCTGGAAACCACAAGCCAC 59.636 57.895 0.00 0.00 0.00 5.01
304 305 2.192861 CGCTGGAAACCACAAGCCA 61.193 57.895 0.00 0.00 0.00 4.75
305 306 2.193536 ACGCTGGAAACCACAAGCC 61.194 57.895 0.00 0.00 0.00 4.35
306 307 1.008538 CACGCTGGAAACCACAAGC 60.009 57.895 0.00 0.00 0.00 4.01
307 308 1.008538 GCACGCTGGAAACCACAAG 60.009 57.895 0.00 0.00 0.00 3.16
308 309 2.485795 GGCACGCTGGAAACCACAA 61.486 57.895 0.00 0.00 0.00 3.33
309 310 2.904866 GGCACGCTGGAAACCACA 60.905 61.111 0.00 0.00 0.00 4.17
322 323 0.179468 TAAATAGACTGGCCCGGCAC 59.821 55.000 12.58 1.03 0.00 5.01
323 324 0.468226 CTAAATAGACTGGCCCGGCA 59.532 55.000 12.58 0.00 0.00 5.69
324 325 0.468648 ACTAAATAGACTGGCCCGGC 59.531 55.000 0.00 0.00 0.00 6.13
325 326 1.760613 TCACTAAATAGACTGGCCCGG 59.239 52.381 0.00 0.00 0.00 5.73
326 327 2.224066 CCTCACTAAATAGACTGGCCCG 60.224 54.545 0.00 0.00 0.00 6.13
327 328 2.485657 GCCTCACTAAATAGACTGGCCC 60.486 54.545 0.00 0.00 33.15 5.80
328 329 2.803492 CGCCTCACTAAATAGACTGGCC 60.803 54.545 0.00 0.00 34.50 5.36
329 330 2.159085 ACGCCTCACTAAATAGACTGGC 60.159 50.000 0.00 0.00 34.58 4.85
330 331 3.381908 AGACGCCTCACTAAATAGACTGG 59.618 47.826 0.00 0.00 0.00 4.00
331 332 4.096532 TCAGACGCCTCACTAAATAGACTG 59.903 45.833 0.00 0.00 0.00 3.51
332 333 4.270834 TCAGACGCCTCACTAAATAGACT 58.729 43.478 0.00 0.00 0.00 3.24
333 334 4.634184 TCAGACGCCTCACTAAATAGAC 57.366 45.455 0.00 0.00 0.00 2.59
334 335 4.499865 GCATCAGACGCCTCACTAAATAGA 60.500 45.833 0.00 0.00 0.00 1.98
335 336 3.738282 GCATCAGACGCCTCACTAAATAG 59.262 47.826 0.00 0.00 0.00 1.73
336 337 3.717707 GCATCAGACGCCTCACTAAATA 58.282 45.455 0.00 0.00 0.00 1.40
337 338 2.555199 GCATCAGACGCCTCACTAAAT 58.445 47.619 0.00 0.00 0.00 1.40
338 339 1.735700 CGCATCAGACGCCTCACTAAA 60.736 52.381 0.00 0.00 0.00 1.85
339 340 0.179137 CGCATCAGACGCCTCACTAA 60.179 55.000 0.00 0.00 0.00 2.24
340 341 1.029947 TCGCATCAGACGCCTCACTA 61.030 55.000 0.00 0.00 0.00 2.74
341 342 2.182791 CGCATCAGACGCCTCACT 59.817 61.111 0.00 0.00 0.00 3.41
342 343 1.875813 CTCGCATCAGACGCCTCAC 60.876 63.158 0.00 0.00 0.00 3.51
343 344 2.491621 CTCGCATCAGACGCCTCA 59.508 61.111 0.00 0.00 0.00 3.86
344 345 2.959071 GCTCGCATCAGACGCCTC 60.959 66.667 0.00 0.00 0.00 4.70
345 346 4.862092 CGCTCGCATCAGACGCCT 62.862 66.667 0.00 0.00 0.00 5.52
357 358 3.649277 AAGCTGTAGGGTGCGCTCG 62.649 63.158 9.73 0.00 31.30 5.03
358 359 2.103042 CAAGCTGTAGGGTGCGCTC 61.103 63.158 9.73 4.47 31.30 5.03
359 360 2.046892 CAAGCTGTAGGGTGCGCT 60.047 61.111 9.73 0.00 0.00 5.92
360 361 2.852495 TAGCAAGCTGTAGGGTGCGC 62.852 60.000 0.00 0.00 0.00 6.09
361 362 0.391130 TTAGCAAGCTGTAGGGTGCG 60.391 55.000 4.53 0.00 0.00 5.34
362 363 1.087501 GTTAGCAAGCTGTAGGGTGC 58.912 55.000 4.53 0.00 0.00 5.01
363 364 2.350522 CTGTTAGCAAGCTGTAGGGTG 58.649 52.381 4.53 0.00 0.00 4.61
364 365 1.339151 GCTGTTAGCAAGCTGTAGGGT 60.339 52.381 4.53 0.00 41.89 4.34
365 366 1.373570 GCTGTTAGCAAGCTGTAGGG 58.626 55.000 4.53 0.00 41.89 3.53
376 377 1.594862 CGCCTATGTCTTGCTGTTAGC 59.405 52.381 0.00 0.00 42.82 3.09
377 378 1.594862 GCGCCTATGTCTTGCTGTTAG 59.405 52.381 0.00 0.00 0.00 2.34
378 379 1.651987 GCGCCTATGTCTTGCTGTTA 58.348 50.000 0.00 0.00 0.00 2.41
379 380 1.361668 CGCGCCTATGTCTTGCTGTT 61.362 55.000 0.00 0.00 0.00 3.16
380 381 1.811266 CGCGCCTATGTCTTGCTGT 60.811 57.895 0.00 0.00 0.00 4.40
381 382 3.009140 CGCGCCTATGTCTTGCTG 58.991 61.111 0.00 0.00 0.00 4.41
382 383 2.892425 GCGCGCCTATGTCTTGCT 60.892 61.111 23.24 0.00 0.00 3.91
383 384 3.941836 GGCGCGCCTATGTCTTGC 61.942 66.667 41.71 12.20 0.00 4.01
384 385 3.272334 GGGCGCGCCTATGTCTTG 61.272 66.667 45.23 0.00 36.10 3.02
385 386 2.608970 AATGGGCGCGCCTATGTCTT 62.609 55.000 43.69 28.99 37.37 3.01
386 387 1.754380 TAATGGGCGCGCCTATGTCT 61.754 55.000 43.69 31.78 37.37 3.41
387 388 0.882927 TTAATGGGCGCGCCTATGTC 60.883 55.000 43.69 29.79 37.37 3.06
388 389 0.884704 CTTAATGGGCGCGCCTATGT 60.885 55.000 43.69 33.13 37.37 2.29
389 390 0.602638 TCTTAATGGGCGCGCCTATG 60.603 55.000 43.69 32.01 37.37 2.23
390 391 0.320771 CTCTTAATGGGCGCGCCTAT 60.321 55.000 45.23 42.34 39.04 2.57
391 392 1.069090 CTCTTAATGGGCGCGCCTA 59.931 57.895 45.23 42.13 36.10 3.93
392 393 2.203070 CTCTTAATGGGCGCGCCT 60.203 61.111 45.23 30.73 36.10 5.52
393 394 3.279875 CCTCTTAATGGGCGCGCC 61.280 66.667 41.63 41.63 0.00 6.53
394 395 3.279875 CCCTCTTAATGGGCGCGC 61.280 66.667 25.94 25.94 37.99 6.86
417 418 3.114616 CAACCGCTCAGACGCCTG 61.115 66.667 0.00 0.00 41.74 4.85
434 435 2.322422 CATCGTGCAAGCGCTAGC 59.678 61.111 12.05 4.06 45.58 3.42
435 436 2.322422 GCATCGTGCAAGCGCTAG 59.678 61.111 12.05 0.00 44.26 3.42
444 445 2.464459 GGTGGTGCTAGCATCGTGC 61.464 63.158 22.51 13.98 45.46 5.34
445 446 2.167219 CGGTGGTGCTAGCATCGTG 61.167 63.158 22.51 10.09 44.30 4.35
446 447 2.184322 CGGTGGTGCTAGCATCGT 59.816 61.111 22.51 0.00 44.30 3.73
448 449 1.815421 CCACGGTGGTGCTAGCATC 60.815 63.158 22.51 21.98 43.00 3.91
449 450 2.268920 CCACGGTGGTGCTAGCAT 59.731 61.111 22.51 0.00 43.00 3.79
460 461 2.180017 GCGTACATCGACCACGGT 59.820 61.111 14.67 0.00 42.86 4.83
461 462 2.947621 CGCGTACATCGACCACGG 60.948 66.667 14.67 4.27 42.86 4.94
462 463 3.604202 GCGCGTACATCGACCACG 61.604 66.667 8.43 10.07 42.86 4.94
463 464 3.604202 CGCGCGTACATCGACCAC 61.604 66.667 24.19 0.00 42.86 4.16
466 467 3.669446 GAGCGCGCGTACATCGAC 61.669 66.667 32.35 11.90 42.86 4.20
588 589 9.352784 CAACTTTTGAGTTCACAGACATTTTTA 57.647 29.630 0.00 0.00 0.00 1.52
589 590 7.872483 ACAACTTTTGAGTTCACAGACATTTTT 59.128 29.630 0.00 0.00 0.00 1.94
590 591 7.378181 ACAACTTTTGAGTTCACAGACATTTT 58.622 30.769 0.00 0.00 0.00 1.82
591 592 6.924111 ACAACTTTTGAGTTCACAGACATTT 58.076 32.000 0.00 0.00 0.00 2.32
592 593 6.515272 ACAACTTTTGAGTTCACAGACATT 57.485 33.333 0.00 0.00 0.00 2.71
593 594 6.150976 TGAACAACTTTTGAGTTCACAGACAT 59.849 34.615 0.00 0.00 44.60 3.06
594 595 5.471797 TGAACAACTTTTGAGTTCACAGACA 59.528 36.000 0.00 0.00 44.60 3.41
595 596 5.938322 TGAACAACTTTTGAGTTCACAGAC 58.062 37.500 0.00 0.00 44.60 3.51
600 601 5.713792 TTGGTGAACAACTTTTGAGTTCA 57.286 34.783 0.00 0.00 46.53 3.18
601 602 7.595311 AATTTGGTGAACAACTTTTGAGTTC 57.405 32.000 0.00 0.00 39.19 3.01
602 603 7.977789 AAATTTGGTGAACAACTTTTGAGTT 57.022 28.000 0.00 0.00 38.36 3.01
603 604 7.977789 AAAATTTGGTGAACAACTTTTGAGT 57.022 28.000 9.99 0.00 44.89 3.41
610 611 9.758651 GGATAGTTAAAAATTTGGTGAACAACT 57.241 29.630 0.00 0.00 39.19 3.16
611 612 9.535878 TGGATAGTTAAAAATTTGGTGAACAAC 57.464 29.630 0.00 0.00 39.19 3.32
628 629 9.905713 GGGCATTCTGAAATATATGGATAGTTA 57.094 33.333 0.00 0.00 0.00 2.24
629 630 8.393259 TGGGCATTCTGAAATATATGGATAGTT 58.607 33.333 0.00 0.00 0.00 2.24
630 631 7.932134 TGGGCATTCTGAAATATATGGATAGT 58.068 34.615 0.00 0.00 0.00 2.12
631 632 8.991783 ATGGGCATTCTGAAATATATGGATAG 57.008 34.615 0.00 0.00 0.00 2.08
633 634 9.363401 CATATGGGCATTCTGAAATATATGGAT 57.637 33.333 0.00 0.00 0.00 3.41
634 635 8.338493 ACATATGGGCATTCTGAAATATATGGA 58.662 33.333 7.80 0.00 30.80 3.41
635 636 8.410912 CACATATGGGCATTCTGAAATATATGG 58.589 37.037 7.80 9.40 30.80 2.74
636 637 9.181061 TCACATATGGGCATTCTGAAATATATG 57.819 33.333 7.80 7.43 31.84 1.78
637 638 9.758021 TTCACATATGGGCATTCTGAAATATAT 57.242 29.630 7.80 0.00 0.00 0.86
638 639 9.585369 TTTCACATATGGGCATTCTGAAATATA 57.415 29.630 7.80 0.00 0.00 0.86
639 640 8.481492 TTTCACATATGGGCATTCTGAAATAT 57.519 30.769 7.80 0.00 0.00 1.28
640 641 7.894753 TTTCACATATGGGCATTCTGAAATA 57.105 32.000 7.80 0.00 0.00 1.40
641 642 6.795144 TTTCACATATGGGCATTCTGAAAT 57.205 33.333 7.80 0.00 0.00 2.17
642 643 6.602410 TTTTCACATATGGGCATTCTGAAA 57.398 33.333 7.80 9.11 0.00 2.69
643 644 6.602410 TTTTTCACATATGGGCATTCTGAA 57.398 33.333 7.80 3.30 0.00 3.02
822 823 1.056660 GAAGGGAGTGAGTGGTTGGA 58.943 55.000 0.00 0.00 0.00 3.53
865 866 1.153349 GGATGGAGTTGGAGACGGC 60.153 63.158 0.00 0.00 0.00 5.68
875 876 2.402564 CTGGGTAGTCATGGATGGAGT 58.597 52.381 0.00 0.00 0.00 3.85
1422 1441 0.109873 CGTAGACGGCGAAGAAGTGT 60.110 55.000 16.62 0.00 35.37 3.55
1495 1514 1.835483 CGCAGCTCTTCAACAAGCGT 61.835 55.000 0.00 0.00 43.37 5.07
1539 1558 2.202544 GAGCTGAGGTCGTCGCAG 60.203 66.667 0.00 7.58 44.58 5.18
1662 1681 2.282251 TGGGACGAGCAGACGACT 60.282 61.111 5.12 0.00 37.03 4.18
1750 1769 4.018870 TGGTGATGTTGCCTTATGGTCTAA 60.019 41.667 0.00 0.00 35.27 2.10
1752 1771 2.308570 TGGTGATGTTGCCTTATGGTCT 59.691 45.455 0.00 0.00 35.27 3.85
1765 1784 5.640357 GCAAATGTGATGAAAATGGTGATGT 59.360 36.000 0.00 0.00 0.00 3.06
1766 1785 5.872617 AGCAAATGTGATGAAAATGGTGATG 59.127 36.000 0.00 0.00 0.00 3.07
1771 1790 6.978343 AATGAGCAAATGTGATGAAAATGG 57.022 33.333 0.00 0.00 0.00 3.16
1774 1793 6.397272 GGGTAATGAGCAAATGTGATGAAAA 58.603 36.000 0.00 0.00 0.00 2.29
1775 1794 5.105392 GGGGTAATGAGCAAATGTGATGAAA 60.105 40.000 0.00 0.00 0.00 2.69
1792 1811 1.288932 AGAGGCAATTGCAGGGGTAAT 59.711 47.619 30.32 6.56 44.36 1.89
1812 1831 4.548451 ATCTGATGAACTCAAGCACTCA 57.452 40.909 0.00 0.00 32.14 3.41
1817 1836 5.174395 ACAGTGTATCTGATGAACTCAAGC 58.826 41.667 0.00 0.00 46.27 4.01
1982 2005 9.750125 GAAATATTCAGGAGCGGAAAATAAAAT 57.250 29.630 0.00 0.00 0.00 1.82
1983 2006 8.744652 TGAAATATTCAGGAGCGGAAAATAAAA 58.255 29.630 0.00 0.00 34.08 1.52
1984 2007 8.287439 TGAAATATTCAGGAGCGGAAAATAAA 57.713 30.769 0.00 0.00 34.08 1.40
1985 2008 7.873719 TGAAATATTCAGGAGCGGAAAATAA 57.126 32.000 0.00 0.00 34.08 1.40
2027 2078 4.080863 ACCTCAATGAGATTGGAGGTACAC 60.081 45.833 12.53 0.00 43.01 2.90
2102 2171 1.463831 CTAGTGCAGTGCAGAGCAAAG 59.536 52.381 20.42 10.85 43.20 2.77
2105 2174 0.394192 AACTAGTGCAGTGCAGAGCA 59.606 50.000 20.42 8.80 40.08 4.26
2106 2175 1.074752 GAACTAGTGCAGTGCAGAGC 58.925 55.000 20.42 7.12 40.08 4.09
2107 2176 2.739885 AGAACTAGTGCAGTGCAGAG 57.260 50.000 20.42 20.45 40.08 3.35
2108 2177 2.630098 AGAAGAACTAGTGCAGTGCAGA 59.370 45.455 20.42 8.87 40.08 4.26
2109 2178 2.992543 GAGAAGAACTAGTGCAGTGCAG 59.007 50.000 20.42 9.88 40.08 4.41
2110 2179 2.630098 AGAGAAGAACTAGTGCAGTGCA 59.370 45.455 15.37 15.37 37.63 4.57
2111 2180 2.992543 CAGAGAAGAACTAGTGCAGTGC 59.007 50.000 8.58 8.58 37.63 4.40
2112 2181 4.250116 ACAGAGAAGAACTAGTGCAGTG 57.750 45.455 3.69 0.00 37.63 3.66
2121 2190 5.373812 TTTCCCAAGAACAGAGAAGAACT 57.626 39.130 0.00 0.00 0.00 3.01
2145 2214 8.637099 TGTCAAAAATTCAGATATCACCAACAA 58.363 29.630 5.32 0.00 0.00 2.83
2167 2238 9.546428 CAGATATCACCAACAATTACTATGTCA 57.454 33.333 5.32 0.00 0.00 3.58
2168 2239 9.764363 TCAGATATCACCAACAATTACTATGTC 57.236 33.333 5.32 0.00 0.00 3.06
2173 2244 8.408601 GCAATTCAGATATCACCAACAATTACT 58.591 33.333 5.32 0.00 0.00 2.24
2175 2246 8.407832 CAGCAATTCAGATATCACCAACAATTA 58.592 33.333 5.32 0.00 0.00 1.40
2176 2247 7.262772 CAGCAATTCAGATATCACCAACAATT 58.737 34.615 5.32 0.00 0.00 2.32
2177 2248 6.183360 CCAGCAATTCAGATATCACCAACAAT 60.183 38.462 5.32 0.00 0.00 2.71
2178 2249 5.125900 CCAGCAATTCAGATATCACCAACAA 59.874 40.000 5.32 0.00 0.00 2.83
2179 2250 4.641541 CCAGCAATTCAGATATCACCAACA 59.358 41.667 5.32 0.00 0.00 3.33
2181 2252 3.633525 GCCAGCAATTCAGATATCACCAA 59.366 43.478 5.32 0.00 0.00 3.67
2182 2253 3.216800 GCCAGCAATTCAGATATCACCA 58.783 45.455 5.32 0.00 0.00 4.17
2183 2254 3.216800 TGCCAGCAATTCAGATATCACC 58.783 45.455 5.32 0.00 0.00 4.02
2184 2255 4.906065 TTGCCAGCAATTCAGATATCAC 57.094 40.909 5.32 0.00 0.00 3.06
2185 2256 5.419788 ACTTTTGCCAGCAATTCAGATATCA 59.580 36.000 5.80 0.00 35.70 2.15
2186 2257 5.899299 ACTTTTGCCAGCAATTCAGATATC 58.101 37.500 5.80 0.00 35.70 1.63
2187 2258 5.927281 ACTTTTGCCAGCAATTCAGATAT 57.073 34.783 5.80 0.00 35.70 1.63
2189 2260 4.612264 AACTTTTGCCAGCAATTCAGAT 57.388 36.364 5.80 0.00 35.70 2.90
2191 2262 4.121317 TGAAACTTTTGCCAGCAATTCAG 58.879 39.130 12.68 9.12 35.70 3.02
2193 2264 4.751098 TCATGAAACTTTTGCCAGCAATTC 59.249 37.500 5.80 7.57 35.70 2.17
2194 2265 4.512571 GTCATGAAACTTTTGCCAGCAATT 59.487 37.500 5.80 0.00 35.70 2.32
2195 2266 4.060205 GTCATGAAACTTTTGCCAGCAAT 58.940 39.130 5.80 0.00 35.70 3.56
2196 2267 3.132646 AGTCATGAAACTTTTGCCAGCAA 59.867 39.130 0.00 0.00 0.00 3.91
2197 2268 2.694628 AGTCATGAAACTTTTGCCAGCA 59.305 40.909 0.00 0.00 0.00 4.41
2240 2312 7.231317 ACCATCACACAAATGATCACTAACTTT 59.769 33.333 0.00 0.00 37.20 2.66
2285 2385 7.011389 TGTGTGAGCAGTATTTGTTATCTATGC 59.989 37.037 0.00 0.00 0.00 3.14
2328 2662 3.469008 TGCTACTTGTGCAGTGTTAGT 57.531 42.857 0.00 0.00 35.97 2.24
2338 2673 2.299013 TGACTACACCCTGCTACTTGTG 59.701 50.000 0.00 0.00 34.92 3.33
2348 2683 0.987294 AGCAAGCATGACTACACCCT 59.013 50.000 0.00 0.00 0.00 4.34
2356 2691 5.220931 CCATTCCTTAGTAAGCAAGCATGAC 60.221 44.000 4.22 0.00 0.00 3.06
2363 2698 9.507329 GAATATGATCCATTCCTTAGTAAGCAA 57.493 33.333 4.22 0.00 0.00 3.91
2403 2738 7.809806 CACTGAATAATTTGTTGAGGGAAAGAC 59.190 37.037 0.00 0.00 0.00 3.01
2407 2742 7.004086 AGTCACTGAATAATTTGTTGAGGGAA 58.996 34.615 0.00 0.00 0.00 3.97
2441 2776 5.760253 TCCAGTTCAGAAGTTCAGTCAAATC 59.240 40.000 5.50 0.00 0.00 2.17
2480 2856 3.814842 CCTGCAAGTAGATCAACAACACA 59.185 43.478 0.00 0.00 0.00 3.72
2539 2915 2.028484 GCAACGACCGTCACCTCA 59.972 61.111 0.00 0.00 0.00 3.86
2560 2936 1.299014 GCACTCATCCTCTCTCGCG 60.299 63.158 0.00 0.00 0.00 5.87
3114 3766 0.391661 CACCAAGGGGACGACATGAG 60.392 60.000 0.00 0.00 38.05 2.90
3130 3782 5.074584 AGACGAAGAAAGATAAGGACACC 57.925 43.478 0.00 0.00 0.00 4.16
3133 3785 5.286558 CGACAAGACGAAGAAAGATAAGGAC 59.713 44.000 0.00 0.00 35.09 3.85
3157 3809 2.716017 CGGTGCAGGAGAGGAGGTC 61.716 68.421 0.00 0.00 0.00 3.85
3278 3951 0.184933 TCAGTGGGGTGTTTTGGGAG 59.815 55.000 0.00 0.00 0.00 4.30
3283 3956 3.876309 ATGTAGTCAGTGGGGTGTTTT 57.124 42.857 0.00 0.00 0.00 2.43
3418 4093 2.415090 CGAAGATTAGTCCGACGGTTGT 60.415 50.000 14.79 2.17 0.00 3.32
3427 4102 0.876342 CGGCCAGCGAAGATTAGTCC 60.876 60.000 2.24 0.00 0.00 3.85
3456 4131 9.813080 CAGAAGTGTAGAAATAAAGCAAAGTAC 57.187 33.333 0.00 0.00 0.00 2.73
3457 4132 8.504005 GCAGAAGTGTAGAAATAAAGCAAAGTA 58.496 33.333 0.00 0.00 0.00 2.24
3458 4133 7.229506 AGCAGAAGTGTAGAAATAAAGCAAAGT 59.770 33.333 0.00 0.00 0.00 2.66
3459 4134 7.588512 AGCAGAAGTGTAGAAATAAAGCAAAG 58.411 34.615 0.00 0.00 0.00 2.77
3492 4167 4.027674 ACATATTACAACCCAGTGCACA 57.972 40.909 21.04 0.00 0.00 4.57
3494 4169 4.657013 TCAACATATTACAACCCAGTGCA 58.343 39.130 0.00 0.00 0.00 4.57
3497 4172 9.528489 AAAAGTATCAACATATTACAACCCAGT 57.472 29.630 0.00 0.00 0.00 4.00
3527 4202 9.066892 ACATGAGATTCTAACAGCAAAGTAAAA 57.933 29.630 0.00 0.00 0.00 1.52
3562 4254 4.508376 CAAAACGTGCCCAACTTTAAAC 57.492 40.909 0.00 0.00 0.00 2.01
3630 4325 5.069516 CCAGGAAAAGGGAACATATGATTGG 59.930 44.000 10.38 0.00 0.00 3.16
3674 4369 3.244422 GGTATATCTCCATTCCGTGCCAA 60.244 47.826 0.00 0.00 0.00 4.52
3680 4375 4.899502 AGCAAAGGTATATCTCCATTCCG 58.100 43.478 0.00 0.00 0.00 4.30
3711 4406 9.057089 CATTACATCTAGTAGAACATTTTCCCC 57.943 37.037 3.45 0.00 33.43 4.81
3733 4429 8.504811 TGTGATATTCTCTCCCCAATACATTA 57.495 34.615 0.00 0.00 0.00 1.90
3734 4430 7.392766 TGTGATATTCTCTCCCCAATACATT 57.607 36.000 0.00 0.00 0.00 2.71
3736 4432 6.239973 CCATGTGATATTCTCTCCCCAATACA 60.240 42.308 0.00 0.00 0.00 2.29
3737 4433 6.013379 TCCATGTGATATTCTCTCCCCAATAC 60.013 42.308 0.00 0.00 0.00 1.89
3738 4434 6.090870 TCCATGTGATATTCTCTCCCCAATA 58.909 40.000 0.00 0.00 0.00 1.90
3833 4530 9.120538 GCCAATAGAACATCACCTTCTTAATAA 57.879 33.333 0.00 0.00 0.00 1.40
3835 4532 7.118723 TGCCAATAGAACATCACCTTCTTAAT 58.881 34.615 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.