Multiple sequence alignment - TraesCS2B01G605600

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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 TraesCS2B01G605600 chr2B 100.000 2449 0 0 1 2449 786812636 786815084 0 4486
1 TraesCS2B01G605600 chr2B 97.737 1944 41 3 509 2449 50469916 50471859 0 3343
2 TraesCS2B01G605600 chr2B 97.532 1945 41 6 509 2449 66031761 66029820 0 3319
3 TraesCS2B01G605600 chr2B 99.799 498 1 0 1 498 786813279 786813776 0 915
4 TraesCS2B01G605600 chr2B 97.000 500 13 2 1 498 50470051 50470550 0 839
5 TraesCS2B01G605600 chr2B 96.800 500 11 4 1 498 66031626 66031130 0 830
6 TraesCS2B01G605600 chr5B 97.941 1943 38 2 509 2449 494656361 494658303 0 3365
7 TraesCS2B01G605600 chr5B 97.787 1943 41 2 509 2449 494663603 494661661 0 3349
8 TraesCS2B01G605600 chr5B 97.788 1944 40 3 509 2449 660354239 660352296 0 3349
9 TraesCS2B01G605600 chr5B 97.685 1944 42 3 509 2449 41406359 41404416 0 3338
10 TraesCS2B01G605600 chr5B 96.994 499 14 1 1 498 660354104 660353606 0 837
11 TraesCS2B01G605600 chr5B 96.794 499 15 1 1 498 494663468 494662970 0 832
12 TraesCS2B01G605600 chr5B 96.600 500 15 2 1 498 494656496 494656995 0 828
13 TraesCS2B01G605600 chr5B 96.414 502 14 3 1 498 166662931 166663432 0 824
14 TraesCS2B01G605600 chr5B 96.400 500 16 2 1 498 537916072 537915573 0 822
15 TraesCS2B01G605600 chr4B 97.532 1945 44 4 509 2449 57125562 57123618 0 3323
16 TraesCS2B01G605600 chr4B 97.377 1944 47 4 509 2449 574590575 574592517 0 3304
17 TraesCS2B01G605600 chr4B 96.400 500 16 2 1 498 57125427 57124928 0 822
18 TraesCS2B01G605600 chr6B 97.479 1944 46 3 509 2449 663151050 663149107 0 3315
19 TraesCS2B01G605600 chr6B 96.800 500 14 2 1 498 11989069 11988570 0 833


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 TraesCS2B01G605600 chr2B 786812636 786815084 2448 False 2700.5 4486 99.8995 1 2449 2 chr2B.!!$F2 2448
1 TraesCS2B01G605600 chr2B 50469916 50471859 1943 False 2091.0 3343 97.3685 1 2449 2 chr2B.!!$F1 2448
2 TraesCS2B01G605600 chr2B 66029820 66031761 1941 True 2074.5 3319 97.1660 1 2449 2 chr2B.!!$R1 2448
3 TraesCS2B01G605600 chr5B 41404416 41406359 1943 True 3338.0 3338 97.6850 509 2449 1 chr5B.!!$R1 1940
4 TraesCS2B01G605600 chr5B 494656361 494658303 1942 False 2096.5 3365 97.2705 1 2449 2 chr5B.!!$F2 2448
5 TraesCS2B01G605600 chr5B 660352296 660354239 1943 True 2093.0 3349 97.3910 1 2449 2 chr5B.!!$R4 2448
6 TraesCS2B01G605600 chr5B 494661661 494663603 1942 True 2090.5 3349 97.2905 1 2449 2 chr5B.!!$R3 2448
7 TraesCS2B01G605600 chr5B 166662931 166663432 501 False 824.0 824 96.4140 1 498 1 chr5B.!!$F1 497
8 TraesCS2B01G605600 chr4B 574590575 574592517 1942 False 3304.0 3304 97.3770 509 2449 1 chr4B.!!$F1 1940
9 TraesCS2B01G605600 chr4B 57123618 57125562 1944 True 2072.5 3323 96.9660 1 2449 2 chr4B.!!$R1 2448
10 TraesCS2B01G605600 chr6B 663149107 663151050 1943 True 3315.0 3315 97.4790 509 2449 1 chr6B.!!$R2 1940

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
334 335 0.031857 CTGCTACTATGCGCTGCTCT 59.968 55.0 9.73 0.0 35.36 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2102 1.271163 GCACTTGGTAGCCTGGTACAA 60.271 52.381 8.58 0.0 38.7 2.41 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.038329 TCCTCGGATTGACCCCGT 59.962 61.111 0.00 0.00 46.53 5.28
18 19 2.186903 CCTCGGATTGACCCCGTG 59.813 66.667 0.00 0.00 46.53 4.94
19 20 2.186903 CTCGGATTGACCCCGTGG 59.813 66.667 0.00 0.00 46.53 4.94
20 21 4.090588 TCGGATTGACCCCGTGGC 62.091 66.667 0.00 0.00 46.53 5.01
21 22 4.402528 CGGATTGACCCCGTGGCA 62.403 66.667 0.00 0.00 41.91 4.92
22 23 2.750237 GGATTGACCCCGTGGCAC 60.750 66.667 7.79 7.79 33.59 5.01
23 24 2.033448 GATTGACCCCGTGGCACA 59.967 61.111 19.09 0.00 33.59 4.57
24 25 1.378514 GATTGACCCCGTGGCACAT 60.379 57.895 19.09 0.78 44.52 3.21
25 26 1.656818 GATTGACCCCGTGGCACATG 61.657 60.000 19.09 7.82 44.52 3.21
36 37 2.111878 GCACATGCCCGCTCCTAT 59.888 61.111 0.00 0.00 34.31 2.57
37 38 2.256591 GCACATGCCCGCTCCTATG 61.257 63.158 0.00 0.00 34.31 2.23
38 39 2.111878 ACATGCCCGCTCCTATGC 59.888 61.111 0.00 0.00 0.00 3.14
39 40 2.111669 CATGCCCGCTCCTATGCA 59.888 61.111 0.00 0.00 38.23 3.96
40 41 2.111878 ATGCCCGCTCCTATGCAC 59.888 61.111 0.00 0.00 36.41 4.57
41 42 3.814615 ATGCCCGCTCCTATGCACG 62.815 63.158 0.00 0.00 36.41 5.34
45 46 4.529219 CGCTCCTATGCACGCCCA 62.529 66.667 0.00 0.00 0.00 5.36
46 47 2.111878 GCTCCTATGCACGCCCAT 59.888 61.111 0.00 0.00 0.00 4.00
47 48 2.256591 GCTCCTATGCACGCCCATG 61.257 63.158 0.00 0.00 0.00 3.66
48 49 2.203195 TCCTATGCACGCCCATGC 60.203 61.111 0.00 0.00 46.32 4.06
49 50 3.289834 CCTATGCACGCCCATGCC 61.290 66.667 0.00 0.00 45.50 4.40
50 51 3.289834 CTATGCACGCCCATGCCC 61.290 66.667 0.00 0.00 45.50 5.36
70 71 2.267324 GCCTGCCGCTCTTCTTCT 59.733 61.111 0.00 0.00 0.00 2.85
71 72 2.105466 GCCTGCCGCTCTTCTTCTG 61.105 63.158 0.00 0.00 0.00 3.02
72 73 2.105466 CCTGCCGCTCTTCTTCTGC 61.105 63.158 0.00 0.00 0.00 4.26
73 74 1.375140 CTGCCGCTCTTCTTCTGCA 60.375 57.895 0.00 0.00 0.00 4.41
74 75 1.633852 CTGCCGCTCTTCTTCTGCAC 61.634 60.000 0.00 0.00 0.00 4.57
75 76 2.394563 GCCGCTCTTCTTCTGCACC 61.395 63.158 0.00 0.00 0.00 5.01
76 77 1.743252 CCGCTCTTCTTCTGCACCC 60.743 63.158 0.00 0.00 0.00 4.61
77 78 2.097038 CGCTCTTCTTCTGCACCCG 61.097 63.158 0.00 0.00 0.00 5.28
78 79 2.394563 GCTCTTCTTCTGCACCCGC 61.395 63.158 0.00 0.00 39.24 6.13
79 80 2.048222 TCTTCTTCTGCACCCGCG 60.048 61.111 0.00 0.00 42.97 6.46
80 81 3.121030 CTTCTTCTGCACCCGCGG 61.121 66.667 21.04 21.04 46.70 6.46
81 82 4.697756 TTCTTCTGCACCCGCGGG 62.698 66.667 42.17 42.17 45.28 6.13
98 99 2.914289 GGCCACTCCCTCTCCATG 59.086 66.667 0.00 0.00 0.00 3.66
99 100 2.191641 GCCACTCCCTCTCCATGC 59.808 66.667 0.00 0.00 0.00 4.06
100 101 2.914289 CCACTCCCTCTCCATGCC 59.086 66.667 0.00 0.00 0.00 4.40
101 102 1.997311 CCACTCCCTCTCCATGCCA 60.997 63.158 0.00 0.00 0.00 4.92
102 103 1.222936 CACTCCCTCTCCATGCCAC 59.777 63.158 0.00 0.00 0.00 5.01
103 104 2.362369 ACTCCCTCTCCATGCCACG 61.362 63.158 0.00 0.00 0.00 4.94
104 105 3.746949 CTCCCTCTCCATGCCACGC 62.747 68.421 0.00 0.00 0.00 5.34
105 106 4.864334 CCCTCTCCATGCCACGCC 62.864 72.222 0.00 0.00 0.00 5.68
106 107 4.864334 CCTCTCCATGCCACGCCC 62.864 72.222 0.00 0.00 0.00 6.13
169 170 4.415150 CAGCCATCGCCCCACTGT 62.415 66.667 0.00 0.00 34.57 3.55
170 171 4.415150 AGCCATCGCCCCACTGTG 62.415 66.667 0.00 0.00 34.57 3.66
193 194 4.602259 CGCGACACACACCCTGGT 62.602 66.667 0.00 0.00 0.00 4.00
194 195 2.665185 GCGACACACACCCTGGTC 60.665 66.667 0.00 0.00 0.00 4.02
195 196 2.355837 CGACACACACCCTGGTCG 60.356 66.667 0.00 0.00 45.62 4.79
196 197 2.665185 GACACACACCCTGGTCGC 60.665 66.667 0.00 0.00 0.00 5.19
197 198 4.602259 ACACACACCCTGGTCGCG 62.602 66.667 0.00 0.00 0.00 5.87
216 217 4.385405 GCCACACTCTCGCTGGCT 62.385 66.667 3.76 0.00 46.05 4.75
217 218 2.433838 CCACACTCTCGCTGGCTG 60.434 66.667 0.00 0.00 0.00 4.85
218 219 3.117171 CACACTCTCGCTGGCTGC 61.117 66.667 6.26 6.26 38.57 5.25
263 264 4.827087 CGCGCTGCCTCCAGTCAT 62.827 66.667 5.56 0.00 41.26 3.06
264 265 3.200593 GCGCTGCCTCCAGTCATG 61.201 66.667 0.00 0.00 41.26 3.07
275 276 1.676746 CCAGTCATGGCCATCTTCTG 58.323 55.000 17.61 21.63 40.52 3.02
276 277 1.022735 CAGTCATGGCCATCTTCTGC 58.977 55.000 17.61 2.49 0.00 4.26
300 301 4.860881 CCCCCTCAGCCTCGCCTA 62.861 72.222 0.00 0.00 0.00 3.93
301 302 3.541713 CCCCTCAGCCTCGCCTAC 61.542 72.222 0.00 0.00 0.00 3.18
302 303 2.443016 CCCTCAGCCTCGCCTACT 60.443 66.667 0.00 0.00 0.00 2.57
303 304 2.790791 CCCTCAGCCTCGCCTACTG 61.791 68.421 0.00 0.00 0.00 2.74
304 305 2.105930 CTCAGCCTCGCCTACTGC 59.894 66.667 0.00 0.00 0.00 4.40
305 306 2.679996 TCAGCCTCGCCTACTGCA 60.680 61.111 0.00 0.00 41.33 4.41
306 307 2.510238 CAGCCTCGCCTACTGCAC 60.510 66.667 0.00 0.00 41.33 4.57
307 308 4.135153 AGCCTCGCCTACTGCACG 62.135 66.667 0.00 0.00 41.33 5.34
308 309 4.436998 GCCTCGCCTACTGCACGT 62.437 66.667 0.00 0.00 41.33 4.49
309 310 2.261671 CCTCGCCTACTGCACGTT 59.738 61.111 0.00 0.00 41.33 3.99
310 311 2.094659 CCTCGCCTACTGCACGTTG 61.095 63.158 0.00 0.00 41.33 4.10
311 312 2.730672 CTCGCCTACTGCACGTTGC 61.731 63.158 3.44 3.44 45.29 4.17
312 313 2.738521 CGCCTACTGCACGTTGCT 60.739 61.111 10.54 0.00 45.31 3.91
313 314 2.317609 CGCCTACTGCACGTTGCTT 61.318 57.895 10.54 2.14 45.31 3.91
314 315 1.497722 GCCTACTGCACGTTGCTTC 59.502 57.895 10.54 0.00 45.31 3.86
315 316 1.912371 GCCTACTGCACGTTGCTTCC 61.912 60.000 10.54 0.00 45.31 3.46
316 317 0.320771 CCTACTGCACGTTGCTTCCT 60.321 55.000 10.54 0.00 45.31 3.36
317 318 0.792640 CTACTGCACGTTGCTTCCTG 59.207 55.000 10.54 1.10 45.31 3.86
318 319 1.227999 TACTGCACGTTGCTTCCTGC 61.228 55.000 10.54 0.00 45.31 4.85
319 320 2.203195 TGCACGTTGCTTCCTGCT 60.203 55.556 10.54 0.00 45.31 4.24
320 321 0.950555 CTGCACGTTGCTTCCTGCTA 60.951 55.000 10.54 0.00 45.31 3.49
321 322 1.227999 TGCACGTTGCTTCCTGCTAC 61.228 55.000 10.54 0.00 45.31 3.58
322 323 0.951040 GCACGTTGCTTCCTGCTACT 60.951 55.000 0.00 0.00 43.44 2.57
323 324 1.671850 GCACGTTGCTTCCTGCTACTA 60.672 52.381 0.00 0.00 43.44 1.82
324 325 2.893637 CACGTTGCTTCCTGCTACTAT 58.106 47.619 0.00 0.00 43.44 2.12
325 326 2.604914 CACGTTGCTTCCTGCTACTATG 59.395 50.000 0.00 0.00 43.44 2.23
326 327 1.594862 CGTTGCTTCCTGCTACTATGC 59.405 52.381 0.00 0.00 43.44 3.14
327 328 1.594862 GTTGCTTCCTGCTACTATGCG 59.405 52.381 0.00 0.00 42.58 4.73
328 329 0.530650 TGCTTCCTGCTACTATGCGC 60.531 55.000 0.00 0.00 43.37 6.09
329 330 0.249657 GCTTCCTGCTACTATGCGCT 60.250 55.000 9.73 0.00 38.95 5.92
330 331 1.495878 CTTCCTGCTACTATGCGCTG 58.504 55.000 9.73 0.99 35.36 5.18
331 332 0.530650 TTCCTGCTACTATGCGCTGC 60.531 55.000 9.73 4.10 35.36 5.25
332 333 1.068753 CCTGCTACTATGCGCTGCT 59.931 57.895 9.73 0.00 35.36 4.24
333 334 0.943359 CCTGCTACTATGCGCTGCTC 60.943 60.000 9.73 0.00 35.36 4.26
334 335 0.031857 CTGCTACTATGCGCTGCTCT 59.968 55.000 9.73 0.00 35.36 4.09
335 336 1.268079 CTGCTACTATGCGCTGCTCTA 59.732 52.381 9.73 0.00 35.36 2.43
336 337 1.001268 TGCTACTATGCGCTGCTCTAC 60.001 52.381 9.73 0.00 35.36 2.59
337 338 1.667467 GCTACTATGCGCTGCTCTACC 60.667 57.143 9.73 0.00 0.00 3.18
338 339 0.591659 TACTATGCGCTGCTCTACCG 59.408 55.000 9.73 0.00 0.00 4.02
343 344 4.135153 CGCTGCTCTACCGCTGGT 62.135 66.667 5.58 5.58 40.16 4.00
344 345 2.771639 CGCTGCTCTACCGCTGGTA 61.772 63.158 0.00 7.15 37.09 3.25
345 346 1.227002 GCTGCTCTACCGCTGGTAC 60.227 63.158 3.72 0.00 37.09 3.34
346 347 1.064296 CTGCTCTACCGCTGGTACG 59.936 63.158 3.72 2.16 37.09 3.67
347 348 2.278661 GCTCTACCGCTGGTACGC 60.279 66.667 3.72 6.12 37.09 4.42
348 349 2.772691 GCTCTACCGCTGGTACGCT 61.773 63.158 3.72 0.00 37.09 5.07
349 350 1.064296 CTCTACCGCTGGTACGCTG 59.936 63.158 3.72 0.00 37.09 5.18
350 351 2.582498 CTACCGCTGGTACGCTGC 60.582 66.667 3.72 0.00 37.09 5.25
351 352 3.064987 CTACCGCTGGTACGCTGCT 62.065 63.158 0.00 0.00 37.09 4.24
352 353 3.350909 TACCGCTGGTACGCTGCTG 62.351 63.158 0.00 7.13 37.09 4.41
355 356 3.793144 GCTGGTACGCTGCTGCAC 61.793 66.667 16.29 6.93 39.64 4.57
356 357 3.121030 CTGGTACGCTGCTGCACC 61.121 66.667 16.29 15.90 39.64 5.01
357 358 3.881952 CTGGTACGCTGCTGCACCA 62.882 63.158 21.45 21.45 41.21 4.17
358 359 2.436646 GGTACGCTGCTGCACCAT 60.437 61.111 17.03 2.81 39.64 3.55
359 360 2.753966 GGTACGCTGCTGCACCATG 61.754 63.158 17.03 3.53 39.64 3.66
360 361 3.126879 TACGCTGCTGCACCATGC 61.127 61.111 16.29 0.00 45.29 4.06
364 365 3.138798 CTGCTGCACCATGCCCTC 61.139 66.667 0.00 0.00 44.23 4.30
366 367 4.783621 GCTGCACCATGCCCTCGA 62.784 66.667 0.00 0.00 44.23 4.04
367 368 2.821366 CTGCACCATGCCCTCGAC 60.821 66.667 0.00 0.00 44.23 4.20
368 369 3.610619 CTGCACCATGCCCTCGACA 62.611 63.158 0.00 0.00 44.23 4.35
369 370 3.127533 GCACCATGCCCTCGACAC 61.128 66.667 0.00 0.00 37.42 3.67
370 371 2.436646 CACCATGCCCTCGACACC 60.437 66.667 0.00 0.00 0.00 4.16
371 372 4.082523 ACCATGCCCTCGACACCG 62.083 66.667 0.00 0.00 37.07 4.94
377 378 4.838152 CCCTCGACACCGCCATGG 62.838 72.222 7.63 7.63 46.41 3.66
378 379 3.770040 CCTCGACACCGCCATGGA 61.770 66.667 18.40 0.00 42.00 3.41
379 380 2.509336 CTCGACACCGCCATGGAC 60.509 66.667 18.40 5.97 42.00 4.02
380 381 3.295304 CTCGACACCGCCATGGACA 62.295 63.158 18.40 0.00 42.00 4.02
381 382 2.358125 CGACACCGCCATGGACAA 60.358 61.111 18.40 0.00 42.00 3.18
382 383 1.963855 CGACACCGCCATGGACAAA 60.964 57.895 18.40 0.00 42.00 2.83
383 384 1.305219 CGACACCGCCATGGACAAAT 61.305 55.000 18.40 0.00 42.00 2.32
384 385 0.171007 GACACCGCCATGGACAAATG 59.829 55.000 18.40 8.11 42.00 2.32
385 386 0.539438 ACACCGCCATGGACAAATGT 60.539 50.000 18.40 8.78 42.00 2.71
386 387 0.109179 CACCGCCATGGACAAATGTG 60.109 55.000 18.40 8.49 42.00 3.21
387 388 1.250154 ACCGCCATGGACAAATGTGG 61.250 55.000 18.40 4.82 42.00 4.17
391 392 1.548081 CCATGGACAAATGTGGCAGA 58.452 50.000 5.56 0.00 32.51 4.26
392 393 1.475280 CCATGGACAAATGTGGCAGAG 59.525 52.381 5.56 0.00 32.51 3.35
393 394 1.475280 CATGGACAAATGTGGCAGAGG 59.525 52.381 0.00 0.00 32.51 3.69
394 395 0.251297 TGGACAAATGTGGCAGAGGG 60.251 55.000 0.00 0.00 32.51 4.30
395 396 0.038166 GGACAAATGTGGCAGAGGGA 59.962 55.000 0.00 0.00 32.51 4.20
396 397 1.341383 GGACAAATGTGGCAGAGGGAT 60.341 52.381 0.00 0.00 32.51 3.85
397 398 2.450476 GACAAATGTGGCAGAGGGATT 58.550 47.619 0.00 0.00 30.49 3.01
398 399 2.165030 GACAAATGTGGCAGAGGGATTG 59.835 50.000 0.00 0.00 30.49 2.67
399 400 2.173519 CAAATGTGGCAGAGGGATTGT 58.826 47.619 0.00 0.00 0.00 2.71
400 401 2.564062 CAAATGTGGCAGAGGGATTGTT 59.436 45.455 0.00 0.00 0.00 2.83
401 402 3.737559 AATGTGGCAGAGGGATTGTTA 57.262 42.857 0.00 0.00 0.00 2.41
402 403 3.737559 ATGTGGCAGAGGGATTGTTAA 57.262 42.857 0.00 0.00 0.00 2.01
403 404 3.737559 TGTGGCAGAGGGATTGTTAAT 57.262 42.857 0.00 0.00 0.00 1.40
404 405 3.355378 TGTGGCAGAGGGATTGTTAATG 58.645 45.455 0.00 0.00 0.00 1.90
405 406 2.689983 GTGGCAGAGGGATTGTTAATGG 59.310 50.000 0.00 0.00 0.00 3.16
406 407 2.580322 TGGCAGAGGGATTGTTAATGGA 59.420 45.455 0.00 0.00 0.00 3.41
407 408 3.217626 GGCAGAGGGATTGTTAATGGAG 58.782 50.000 0.00 0.00 0.00 3.86
408 409 3.372025 GGCAGAGGGATTGTTAATGGAGT 60.372 47.826 0.00 0.00 0.00 3.85
409 410 4.141482 GGCAGAGGGATTGTTAATGGAGTA 60.141 45.833 0.00 0.00 0.00 2.59
410 411 4.816925 GCAGAGGGATTGTTAATGGAGTAC 59.183 45.833 0.00 0.00 0.00 2.73
411 412 5.629133 GCAGAGGGATTGTTAATGGAGTACA 60.629 44.000 0.00 0.00 0.00 2.90
412 413 6.414732 CAGAGGGATTGTTAATGGAGTACAA 58.585 40.000 0.00 0.00 36.35 2.41
413 414 6.540189 CAGAGGGATTGTTAATGGAGTACAAG 59.460 42.308 0.00 0.00 35.48 3.16
414 415 6.443849 AGAGGGATTGTTAATGGAGTACAAGA 59.556 38.462 0.00 0.00 35.48 3.02
415 416 7.027874 AGGGATTGTTAATGGAGTACAAGAA 57.972 36.000 0.00 0.00 35.48 2.52
416 417 7.112779 AGGGATTGTTAATGGAGTACAAGAAG 58.887 38.462 0.00 0.00 35.48 2.85
417 418 6.318900 GGGATTGTTAATGGAGTACAAGAAGG 59.681 42.308 0.00 0.00 35.48 3.46
418 419 7.110155 GGATTGTTAATGGAGTACAAGAAGGA 58.890 38.462 0.00 0.00 35.48 3.36
419 420 7.281100 GGATTGTTAATGGAGTACAAGAAGGAG 59.719 40.741 0.00 0.00 35.48 3.69
420 421 6.049955 TGTTAATGGAGTACAAGAAGGAGG 57.950 41.667 0.00 0.00 0.00 4.30
421 422 5.546499 TGTTAATGGAGTACAAGAAGGAGGT 59.454 40.000 0.00 0.00 0.00 3.85
422 423 4.559862 AATGGAGTACAAGAAGGAGGTG 57.440 45.455 0.00 0.00 0.00 4.00
423 424 2.257207 TGGAGTACAAGAAGGAGGTGG 58.743 52.381 0.00 0.00 0.00 4.61
424 425 1.066071 GGAGTACAAGAAGGAGGTGGC 60.066 57.143 0.00 0.00 0.00 5.01
425 426 0.608640 AGTACAAGAAGGAGGTGGCG 59.391 55.000 0.00 0.00 0.00 5.69
426 427 0.391263 GTACAAGAAGGAGGTGGCGG 60.391 60.000 0.00 0.00 0.00 6.13
427 428 0.543410 TACAAGAAGGAGGTGGCGGA 60.543 55.000 0.00 0.00 0.00 5.54
428 429 1.078848 CAAGAAGGAGGTGGCGGAG 60.079 63.158 0.00 0.00 0.00 4.63
429 430 1.229209 AAGAAGGAGGTGGCGGAGA 60.229 57.895 0.00 0.00 0.00 3.71
430 431 0.836400 AAGAAGGAGGTGGCGGAGAA 60.836 55.000 0.00 0.00 0.00 2.87
431 432 1.219393 GAAGGAGGTGGCGGAGAAG 59.781 63.158 0.00 0.00 0.00 2.85
432 433 2.245438 GAAGGAGGTGGCGGAGAAGG 62.245 65.000 0.00 0.00 0.00 3.46
433 434 3.003763 GGAGGTGGCGGAGAAGGT 61.004 66.667 0.00 0.00 0.00 3.50
434 435 2.266055 GAGGTGGCGGAGAAGGTG 59.734 66.667 0.00 0.00 0.00 4.00
435 436 2.526873 AGGTGGCGGAGAAGGTGT 60.527 61.111 0.00 0.00 0.00 4.16
436 437 2.358737 GGTGGCGGAGAAGGTGTG 60.359 66.667 0.00 0.00 0.00 3.82
437 438 2.358737 GTGGCGGAGAAGGTGTGG 60.359 66.667 0.00 0.00 0.00 4.17
438 439 2.525629 TGGCGGAGAAGGTGTGGA 60.526 61.111 0.00 0.00 0.00 4.02
439 440 2.266055 GGCGGAGAAGGTGTGGAG 59.734 66.667 0.00 0.00 0.00 3.86
440 441 2.283529 GGCGGAGAAGGTGTGGAGA 61.284 63.158 0.00 0.00 0.00 3.71
441 442 1.216710 GCGGAGAAGGTGTGGAGAG 59.783 63.158 0.00 0.00 0.00 3.20
442 443 1.893786 CGGAGAAGGTGTGGAGAGG 59.106 63.158 0.00 0.00 0.00 3.69
443 444 1.599576 GGAGAAGGTGTGGAGAGGC 59.400 63.158 0.00 0.00 0.00 4.70
444 445 1.194781 GGAGAAGGTGTGGAGAGGCA 61.195 60.000 0.00 0.00 0.00 4.75
445 446 0.248843 GAGAAGGTGTGGAGAGGCAG 59.751 60.000 0.00 0.00 0.00 4.85
446 447 1.197430 AGAAGGTGTGGAGAGGCAGG 61.197 60.000 0.00 0.00 0.00 4.85
447 448 1.152030 AAGGTGTGGAGAGGCAGGA 60.152 57.895 0.00 0.00 0.00 3.86
448 449 1.197430 AAGGTGTGGAGAGGCAGGAG 61.197 60.000 0.00 0.00 0.00 3.69
449 450 2.664081 GGTGTGGAGAGGCAGGAGG 61.664 68.421 0.00 0.00 0.00 4.30
450 451 1.915769 GTGTGGAGAGGCAGGAGGT 60.916 63.158 0.00 0.00 0.00 3.85
451 452 1.610673 TGTGGAGAGGCAGGAGGTC 60.611 63.158 0.00 0.00 0.00 3.85
452 453 1.305718 GTGGAGAGGCAGGAGGTCT 60.306 63.158 0.00 0.00 0.00 3.85
453 454 1.305633 TGGAGAGGCAGGAGGTCTG 60.306 63.158 0.00 0.00 46.03 3.51
454 455 2.063378 GGAGAGGCAGGAGGTCTGG 61.063 68.421 0.00 0.00 43.54 3.86
455 456 2.040278 AGAGGCAGGAGGTCTGGG 59.960 66.667 0.00 0.00 43.54 4.45
456 457 3.086600 GAGGCAGGAGGTCTGGGG 61.087 72.222 0.00 0.00 43.54 4.96
463 464 4.083862 GAGGTCTGGGGCGGTGTC 62.084 72.222 0.00 0.00 0.00 3.67
464 465 4.954118 AGGTCTGGGGCGGTGTCA 62.954 66.667 0.00 0.00 0.00 3.58
465 466 4.699522 GGTCTGGGGCGGTGTCAC 62.700 72.222 0.00 0.00 0.00 3.67
466 467 4.699522 GTCTGGGGCGGTGTCACC 62.700 72.222 12.40 12.40 34.05 4.02
467 468 4.954118 TCTGGGGCGGTGTCACCT 62.954 66.667 19.82 0.00 35.66 4.00
468 469 4.704833 CTGGGGCGGTGTCACCTG 62.705 72.222 19.82 13.78 35.66 4.00
472 473 3.702048 GGCGGTGTCACCTGGCTA 61.702 66.667 23.58 0.00 35.66 3.93
473 474 2.584608 GCGGTGTCACCTGGCTAT 59.415 61.111 19.82 0.00 35.66 2.97
474 475 1.815421 GCGGTGTCACCTGGCTATG 60.815 63.158 19.82 3.58 35.66 2.23
475 476 1.153369 CGGTGTCACCTGGCTATGG 60.153 63.158 19.82 0.00 35.66 2.74
476 477 1.899437 CGGTGTCACCTGGCTATGGT 61.899 60.000 19.82 0.00 35.66 3.55
481 482 4.073201 ACCTGGCTATGGTGGAGG 57.927 61.111 0.00 0.00 36.30 4.30
482 483 1.082954 ACCTGGCTATGGTGGAGGT 59.917 57.895 0.00 0.00 36.30 3.85
483 484 1.274703 ACCTGGCTATGGTGGAGGTG 61.275 60.000 0.00 0.00 35.65 4.00
484 485 1.274703 CCTGGCTATGGTGGAGGTGT 61.275 60.000 0.00 0.00 0.00 4.16
485 486 0.620556 CTGGCTATGGTGGAGGTGTT 59.379 55.000 0.00 0.00 0.00 3.32
486 487 1.004745 CTGGCTATGGTGGAGGTGTTT 59.995 52.381 0.00 0.00 0.00 2.83
487 488 2.238646 CTGGCTATGGTGGAGGTGTTTA 59.761 50.000 0.00 0.00 0.00 2.01
488 489 2.849943 TGGCTATGGTGGAGGTGTTTAT 59.150 45.455 0.00 0.00 0.00 1.40
489 490 3.118038 TGGCTATGGTGGAGGTGTTTATC 60.118 47.826 0.00 0.00 0.00 1.75
490 491 3.477530 GCTATGGTGGAGGTGTTTATCC 58.522 50.000 0.00 0.00 36.05 2.59
491 492 2.710096 ATGGTGGAGGTGTTTATCCG 57.290 50.000 0.00 0.00 38.52 4.18
492 493 1.646912 TGGTGGAGGTGTTTATCCGA 58.353 50.000 0.00 0.00 38.52 4.55
493 494 1.276989 TGGTGGAGGTGTTTATCCGAC 59.723 52.381 0.00 0.00 38.52 4.79
494 495 1.276989 GGTGGAGGTGTTTATCCGACA 59.723 52.381 0.00 0.00 38.52 4.35
495 496 2.289819 GGTGGAGGTGTTTATCCGACAA 60.290 50.000 0.00 0.00 38.52 3.18
496 497 3.000727 GTGGAGGTGTTTATCCGACAAG 58.999 50.000 0.00 0.00 38.52 3.16
497 498 2.027561 TGGAGGTGTTTATCCGACAAGG 60.028 50.000 0.00 0.00 38.52 3.61
567 568 0.491823 TTCCCTTGTCTCCCCTCTCA 59.508 55.000 0.00 0.00 0.00 3.27
713 714 2.267324 GCCTGCCGCTCTTCTTCT 59.733 61.111 0.00 0.00 0.00 2.85
948 953 2.679996 TCAGCCTCGCCTACTGCA 60.680 61.111 0.00 0.00 41.33 4.41
963 968 1.271543 ACTGCATGTTGCTTCCTGCTA 60.272 47.619 0.75 0.00 45.31 3.49
1054 1059 5.629133 GCAGAGGGATTGTTAATGGAGTACA 60.629 44.000 0.00 0.00 0.00 2.90
1363 1371 0.034337 TCAGTACCTGCCCGTTTGTC 59.966 55.000 0.00 0.00 0.00 3.18
1382 1390 5.147330 TGTCACGTGTCTGATTAGGAAAT 57.853 39.130 16.51 0.00 0.00 2.17
1863 1873 9.487790 GACAAATTGAACCAATAAAAGGAATCA 57.512 29.630 0.00 0.00 32.43 2.57
2231 2244 8.703743 TGCCTGATGCTTTTACCATATTAAAAT 58.296 29.630 0.00 0.00 42.00 1.82
2313 2326 1.967779 GAGTCCTAGCATCTTCCTCCC 59.032 57.143 0.00 0.00 0.00 4.30
2407 2420 2.707849 GCCATCAGCACAAGCAGGG 61.708 63.158 0.00 0.00 45.49 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.750237 GTGCCACGGGGTCAATCC 60.750 66.667 5.12 0.00 36.17 3.01
6 7 1.378514 ATGTGCCACGGGGTCAATC 60.379 57.895 5.12 0.00 36.17 2.67
7 8 1.678635 CATGTGCCACGGGGTCAAT 60.679 57.895 5.12 0.00 36.17 2.57
8 9 2.282110 CATGTGCCACGGGGTCAA 60.282 61.111 5.12 0.00 36.17 3.18
19 20 2.111878 ATAGGAGCGGGCATGTGC 59.888 61.111 0.00 0.00 41.14 4.57
20 21 2.256591 GCATAGGAGCGGGCATGTG 61.257 63.158 0.00 0.00 0.00 3.21
21 22 2.111878 GCATAGGAGCGGGCATGT 59.888 61.111 0.00 0.00 0.00 3.21
22 23 2.111669 TGCATAGGAGCGGGCATG 59.888 61.111 0.00 0.00 37.31 4.06
23 24 2.111878 GTGCATAGGAGCGGGCAT 59.888 61.111 0.00 0.00 38.68 4.40
24 25 4.529219 CGTGCATAGGAGCGGGCA 62.529 66.667 0.00 0.00 37.31 5.36
28 29 3.814615 ATGGGCGTGCATAGGAGCG 62.815 63.158 0.00 0.00 37.31 5.03
29 30 2.111878 ATGGGCGTGCATAGGAGC 59.888 61.111 0.00 0.00 0.00 4.70
30 31 2.256591 GCATGGGCGTGCATAGGAG 61.257 63.158 8.40 0.00 44.43 3.69
31 32 2.203195 GCATGGGCGTGCATAGGA 60.203 61.111 8.40 0.00 44.43 2.94
32 33 3.289834 GGCATGGGCGTGCATAGG 61.290 66.667 14.18 0.00 46.81 2.57
33 34 3.289834 GGGCATGGGCGTGCATAG 61.290 66.667 14.18 0.00 46.81 2.23
53 54 2.105466 CAGAAGAAGAGCGGCAGGC 61.105 63.158 1.45 0.00 44.05 4.85
54 55 2.105466 GCAGAAGAAGAGCGGCAGG 61.105 63.158 1.45 0.00 0.00 4.85
55 56 1.375140 TGCAGAAGAAGAGCGGCAG 60.375 57.895 1.45 0.00 0.00 4.85
56 57 1.669115 GTGCAGAAGAAGAGCGGCA 60.669 57.895 1.45 0.00 0.00 5.69
57 58 2.394563 GGTGCAGAAGAAGAGCGGC 61.395 63.158 0.00 0.00 0.00 6.53
58 59 1.743252 GGGTGCAGAAGAAGAGCGG 60.743 63.158 0.00 0.00 0.00 5.52
59 60 2.097038 CGGGTGCAGAAGAAGAGCG 61.097 63.158 0.00 0.00 0.00 5.03
60 61 2.394563 GCGGGTGCAGAAGAAGAGC 61.395 63.158 0.00 0.00 42.15 4.09
61 62 2.097038 CGCGGGTGCAGAAGAAGAG 61.097 63.158 0.00 0.00 42.97 2.85
62 63 2.048222 CGCGGGTGCAGAAGAAGA 60.048 61.111 0.00 0.00 42.97 2.87
63 64 3.121030 CCGCGGGTGCAGAAGAAG 61.121 66.667 20.10 0.00 42.97 2.85
64 65 4.697756 CCCGCGGGTGCAGAAGAA 62.698 66.667 36.64 0.00 42.97 2.52
81 82 2.914289 CATGGAGAGGGAGTGGCC 59.086 66.667 0.00 0.00 0.00 5.36
82 83 2.191641 GCATGGAGAGGGAGTGGC 59.808 66.667 0.00 0.00 0.00 5.01
83 84 1.997311 TGGCATGGAGAGGGAGTGG 60.997 63.158 0.00 0.00 0.00 4.00
84 85 1.222936 GTGGCATGGAGAGGGAGTG 59.777 63.158 0.00 0.00 0.00 3.51
85 86 2.362369 CGTGGCATGGAGAGGGAGT 61.362 63.158 0.00 0.00 0.00 3.85
86 87 2.503061 CGTGGCATGGAGAGGGAG 59.497 66.667 0.00 0.00 0.00 4.30
87 88 3.785859 GCGTGGCATGGAGAGGGA 61.786 66.667 9.08 0.00 0.00 4.20
88 89 4.864334 GGCGTGGCATGGAGAGGG 62.864 72.222 9.08 0.00 0.00 4.30
89 90 4.864334 GGGCGTGGCATGGAGAGG 62.864 72.222 9.08 0.00 0.00 3.69
152 153 4.415150 ACAGTGGGGCGATGGCTG 62.415 66.667 0.00 0.00 39.81 4.85
153 154 4.415150 CACAGTGGGGCGATGGCT 62.415 66.667 0.00 0.00 39.81 4.75
176 177 4.602259 ACCAGGGTGTGTGTCGCG 62.602 66.667 0.00 0.00 0.00 5.87
177 178 2.665185 GACCAGGGTGTGTGTCGC 60.665 66.667 0.00 0.00 0.00 5.19
178 179 2.355837 CGACCAGGGTGTGTGTCG 60.356 66.667 0.00 0.00 40.81 4.35
179 180 2.665185 GCGACCAGGGTGTGTGTC 60.665 66.667 0.00 0.00 0.00 3.67
180 181 4.602259 CGCGACCAGGGTGTGTGT 62.602 66.667 0.00 0.00 0.00 3.72
200 201 2.433838 CAGCCAGCGAGAGTGTGG 60.434 66.667 0.00 0.00 39.49 4.17
201 202 3.117171 GCAGCCAGCGAGAGTGTG 61.117 66.667 0.00 0.00 0.00 3.82
246 247 4.827087 ATGACTGGAGGCAGCGCG 62.827 66.667 0.00 0.00 0.00 6.86
247 248 3.200593 CATGACTGGAGGCAGCGC 61.201 66.667 0.00 0.00 0.00 5.92
248 249 2.513204 CCATGACTGGAGGCAGCG 60.513 66.667 0.00 0.00 46.37 5.18
249 250 2.827642 GCCATGACTGGAGGCAGC 60.828 66.667 0.00 0.00 46.37 5.25
252 253 1.527844 GATGGCCATGACTGGAGGC 60.528 63.158 26.56 0.35 46.37 4.70
253 254 0.549950 AAGATGGCCATGACTGGAGG 59.450 55.000 26.56 0.00 46.37 4.30
254 255 1.489649 AGAAGATGGCCATGACTGGAG 59.510 52.381 26.56 0.00 46.37 3.86
255 256 1.211212 CAGAAGATGGCCATGACTGGA 59.789 52.381 26.56 0.00 46.37 3.86
256 257 1.676746 CAGAAGATGGCCATGACTGG 58.323 55.000 26.56 5.90 46.17 4.00
257 258 1.022735 GCAGAAGATGGCCATGACTG 58.977 55.000 26.56 26.19 0.00 3.51
258 259 3.491208 GCAGAAGATGGCCATGACT 57.509 52.632 26.56 12.63 0.00 3.41
283 284 4.860881 TAGGCGAGGCTGAGGGGG 62.861 72.222 9.55 0.00 0.00 5.40
284 285 3.541713 GTAGGCGAGGCTGAGGGG 61.542 72.222 9.55 0.00 0.00 4.79
285 286 2.443016 AGTAGGCGAGGCTGAGGG 60.443 66.667 9.55 0.00 0.00 4.30
286 287 2.811101 CAGTAGGCGAGGCTGAGG 59.189 66.667 9.55 0.00 32.39 3.86
287 288 2.105930 GCAGTAGGCGAGGCTGAG 59.894 66.667 9.55 0.54 32.39 3.35
310 311 0.249657 AGCGCATAGTAGCAGGAAGC 60.250 55.000 11.47 0.00 46.19 3.86
311 312 1.495878 CAGCGCATAGTAGCAGGAAG 58.504 55.000 11.47 0.00 35.48 3.46
312 313 0.530650 GCAGCGCATAGTAGCAGGAA 60.531 55.000 11.47 0.00 35.48 3.36
313 314 1.068083 GCAGCGCATAGTAGCAGGA 59.932 57.895 11.47 0.00 35.48 3.86
314 315 0.943359 GAGCAGCGCATAGTAGCAGG 60.943 60.000 11.47 0.00 35.48 4.85
315 316 0.031857 AGAGCAGCGCATAGTAGCAG 59.968 55.000 11.47 0.00 35.48 4.24
316 317 1.001268 GTAGAGCAGCGCATAGTAGCA 60.001 52.381 11.47 0.00 35.48 3.49
317 318 1.667467 GGTAGAGCAGCGCATAGTAGC 60.667 57.143 11.47 3.34 0.00 3.58
318 319 1.400371 CGGTAGAGCAGCGCATAGTAG 60.400 57.143 11.47 0.00 41.87 2.57
319 320 0.591659 CGGTAGAGCAGCGCATAGTA 59.408 55.000 11.47 0.00 41.87 1.82
320 321 1.360551 CGGTAGAGCAGCGCATAGT 59.639 57.895 11.47 0.00 41.87 2.12
321 322 4.235065 CGGTAGAGCAGCGCATAG 57.765 61.111 11.47 0.00 41.87 2.23
327 328 1.227002 GTACCAGCGGTAGAGCAGC 60.227 63.158 7.56 0.00 39.02 5.25
328 329 1.064296 CGTACCAGCGGTAGAGCAG 59.936 63.158 7.56 0.00 39.02 4.24
329 330 3.060020 GCGTACCAGCGGTAGAGCA 62.060 63.158 19.84 0.00 39.02 4.26
330 331 2.278661 GCGTACCAGCGGTAGAGC 60.279 66.667 7.56 11.57 39.02 4.09
331 332 1.064296 CAGCGTACCAGCGGTAGAG 59.936 63.158 7.56 6.71 39.02 2.43
332 333 3.060020 GCAGCGTACCAGCGGTAGA 62.060 63.158 7.56 0.00 39.02 2.59
333 334 2.582498 GCAGCGTACCAGCGGTAG 60.582 66.667 7.56 4.53 39.02 3.18
334 335 3.066190 AGCAGCGTACCAGCGGTA 61.066 61.111 3.72 3.72 40.81 4.02
335 336 4.742201 CAGCAGCGTACCAGCGGT 62.742 66.667 5.58 5.58 43.71 5.68
338 339 3.793144 GTGCAGCAGCGTACCAGC 61.793 66.667 0.00 0.00 46.23 4.85
339 340 3.121030 GGTGCAGCAGCGTACCAG 61.121 66.667 11.86 0.00 46.23 4.00
340 341 3.252627 ATGGTGCAGCAGCGTACCA 62.253 57.895 24.45 22.28 46.84 3.25
341 342 2.436646 ATGGTGCAGCAGCGTACC 60.437 61.111 24.45 14.52 46.23 3.34
342 343 2.787249 CATGGTGCAGCAGCGTAC 59.213 61.111 24.45 0.00 46.23 3.67
343 344 3.126879 GCATGGTGCAGCAGCGTA 61.127 61.111 24.45 2.83 44.26 4.42
352 353 3.127533 GTGTCGAGGGCATGGTGC 61.128 66.667 0.00 0.00 44.08 5.01
353 354 2.436646 GGTGTCGAGGGCATGGTG 60.437 66.667 0.00 0.00 0.00 4.17
354 355 4.082523 CGGTGTCGAGGGCATGGT 62.083 66.667 0.00 0.00 39.00 3.55
360 361 4.838152 CCATGGCGGTGTCGAGGG 62.838 72.222 0.00 0.00 39.00 4.30
361 362 3.770040 TCCATGGCGGTGTCGAGG 61.770 66.667 6.96 0.00 39.00 4.63
362 363 2.509336 GTCCATGGCGGTGTCGAG 60.509 66.667 6.96 0.00 39.00 4.04
363 364 2.384653 TTTGTCCATGGCGGTGTCGA 62.385 55.000 6.96 0.00 39.00 4.20
364 365 1.305219 ATTTGTCCATGGCGGTGTCG 61.305 55.000 6.96 0.00 39.81 4.35
365 366 0.171007 CATTTGTCCATGGCGGTGTC 59.829 55.000 6.96 0.00 35.57 3.67
366 367 0.539438 ACATTTGTCCATGGCGGTGT 60.539 50.000 6.96 4.64 35.57 4.16
367 368 0.109179 CACATTTGTCCATGGCGGTG 60.109 55.000 6.96 4.99 35.57 4.94
368 369 1.250154 CCACATTTGTCCATGGCGGT 61.250 55.000 6.96 0.00 35.57 5.68
369 370 1.512230 CCACATTTGTCCATGGCGG 59.488 57.895 6.96 0.00 0.00 6.13
372 373 1.475280 CTCTGCCACATTTGTCCATGG 59.525 52.381 4.97 4.97 35.17 3.66
373 374 1.475280 CCTCTGCCACATTTGTCCATG 59.525 52.381 0.00 0.00 0.00 3.66
374 375 1.617804 CCCTCTGCCACATTTGTCCAT 60.618 52.381 0.00 0.00 0.00 3.41
375 376 0.251297 CCCTCTGCCACATTTGTCCA 60.251 55.000 0.00 0.00 0.00 4.02
376 377 0.038166 TCCCTCTGCCACATTTGTCC 59.962 55.000 0.00 0.00 0.00 4.02
377 378 2.134789 ATCCCTCTGCCACATTTGTC 57.865 50.000 0.00 0.00 0.00 3.18
378 379 2.173519 CAATCCCTCTGCCACATTTGT 58.826 47.619 0.00 0.00 0.00 2.83
379 380 2.173519 ACAATCCCTCTGCCACATTTG 58.826 47.619 0.00 0.00 0.00 2.32
380 381 2.610438 ACAATCCCTCTGCCACATTT 57.390 45.000 0.00 0.00 0.00 2.32
381 382 2.610438 AACAATCCCTCTGCCACATT 57.390 45.000 0.00 0.00 0.00 2.71
382 383 3.737559 TTAACAATCCCTCTGCCACAT 57.262 42.857 0.00 0.00 0.00 3.21
383 384 3.355378 CATTAACAATCCCTCTGCCACA 58.645 45.455 0.00 0.00 0.00 4.17
384 385 2.689983 CCATTAACAATCCCTCTGCCAC 59.310 50.000 0.00 0.00 0.00 5.01
385 386 2.580322 TCCATTAACAATCCCTCTGCCA 59.420 45.455 0.00 0.00 0.00 4.92
386 387 3.217626 CTCCATTAACAATCCCTCTGCC 58.782 50.000 0.00 0.00 0.00 4.85
387 388 3.891049 ACTCCATTAACAATCCCTCTGC 58.109 45.455 0.00 0.00 0.00 4.26
388 389 5.989477 TGTACTCCATTAACAATCCCTCTG 58.011 41.667 0.00 0.00 0.00 3.35
389 390 6.443849 TCTTGTACTCCATTAACAATCCCTCT 59.556 38.462 0.00 0.00 33.01 3.69
390 391 6.650120 TCTTGTACTCCATTAACAATCCCTC 58.350 40.000 0.00 0.00 33.01 4.30
391 392 6.636454 TCTTGTACTCCATTAACAATCCCT 57.364 37.500 0.00 0.00 33.01 4.20
392 393 6.318900 CCTTCTTGTACTCCATTAACAATCCC 59.681 42.308 0.00 0.00 33.01 3.85
393 394 7.110155 TCCTTCTTGTACTCCATTAACAATCC 58.890 38.462 0.00 0.00 33.01 3.01
394 395 7.281100 CCTCCTTCTTGTACTCCATTAACAATC 59.719 40.741 0.00 0.00 33.01 2.67
395 396 7.112779 CCTCCTTCTTGTACTCCATTAACAAT 58.887 38.462 0.00 0.00 33.01 2.71
396 397 6.043938 ACCTCCTTCTTGTACTCCATTAACAA 59.956 38.462 0.00 0.00 0.00 2.83
397 398 5.546499 ACCTCCTTCTTGTACTCCATTAACA 59.454 40.000 0.00 0.00 0.00 2.41
398 399 5.875359 CACCTCCTTCTTGTACTCCATTAAC 59.125 44.000 0.00 0.00 0.00 2.01
399 400 5.045869 CCACCTCCTTCTTGTACTCCATTAA 60.046 44.000 0.00 0.00 0.00 1.40
400 401 4.469945 CCACCTCCTTCTTGTACTCCATTA 59.530 45.833 0.00 0.00 0.00 1.90
401 402 3.264450 CCACCTCCTTCTTGTACTCCATT 59.736 47.826 0.00 0.00 0.00 3.16
402 403 2.840651 CCACCTCCTTCTTGTACTCCAT 59.159 50.000 0.00 0.00 0.00 3.41
403 404 2.257207 CCACCTCCTTCTTGTACTCCA 58.743 52.381 0.00 0.00 0.00 3.86
404 405 1.066071 GCCACCTCCTTCTTGTACTCC 60.066 57.143 0.00 0.00 0.00 3.85
405 406 1.404315 CGCCACCTCCTTCTTGTACTC 60.404 57.143 0.00 0.00 0.00 2.59
406 407 0.608640 CGCCACCTCCTTCTTGTACT 59.391 55.000 0.00 0.00 0.00 2.73
407 408 0.391263 CCGCCACCTCCTTCTTGTAC 60.391 60.000 0.00 0.00 0.00 2.90
408 409 0.543410 TCCGCCACCTCCTTCTTGTA 60.543 55.000 0.00 0.00 0.00 2.41
409 410 1.831652 CTCCGCCACCTCCTTCTTGT 61.832 60.000 0.00 0.00 0.00 3.16
410 411 1.078848 CTCCGCCACCTCCTTCTTG 60.079 63.158 0.00 0.00 0.00 3.02
411 412 0.836400 TTCTCCGCCACCTCCTTCTT 60.836 55.000 0.00 0.00 0.00 2.52
412 413 1.229209 TTCTCCGCCACCTCCTTCT 60.229 57.895 0.00 0.00 0.00 2.85
413 414 1.219393 CTTCTCCGCCACCTCCTTC 59.781 63.158 0.00 0.00 0.00 3.46
414 415 2.294078 CCTTCTCCGCCACCTCCTT 61.294 63.158 0.00 0.00 0.00 3.36
415 416 2.685380 CCTTCTCCGCCACCTCCT 60.685 66.667 0.00 0.00 0.00 3.69
416 417 3.003763 ACCTTCTCCGCCACCTCC 61.004 66.667 0.00 0.00 0.00 4.30
417 418 2.266055 CACCTTCTCCGCCACCTC 59.734 66.667 0.00 0.00 0.00 3.85
418 419 2.526873 ACACCTTCTCCGCCACCT 60.527 61.111 0.00 0.00 0.00 4.00
419 420 2.358737 CACACCTTCTCCGCCACC 60.359 66.667 0.00 0.00 0.00 4.61
420 421 2.358737 CCACACCTTCTCCGCCAC 60.359 66.667 0.00 0.00 0.00 5.01
421 422 2.525629 TCCACACCTTCTCCGCCA 60.526 61.111 0.00 0.00 0.00 5.69
422 423 2.232298 CTCTCCACACCTTCTCCGCC 62.232 65.000 0.00 0.00 0.00 6.13
423 424 1.216710 CTCTCCACACCTTCTCCGC 59.783 63.158 0.00 0.00 0.00 5.54
424 425 1.893786 CCTCTCCACACCTTCTCCG 59.106 63.158 0.00 0.00 0.00 4.63
425 426 1.194781 TGCCTCTCCACACCTTCTCC 61.195 60.000 0.00 0.00 0.00 3.71
426 427 0.248843 CTGCCTCTCCACACCTTCTC 59.751 60.000 0.00 0.00 0.00 2.87
427 428 1.197430 CCTGCCTCTCCACACCTTCT 61.197 60.000 0.00 0.00 0.00 2.85
428 429 1.194781 TCCTGCCTCTCCACACCTTC 61.195 60.000 0.00 0.00 0.00 3.46
429 430 1.152030 TCCTGCCTCTCCACACCTT 60.152 57.895 0.00 0.00 0.00 3.50
430 431 1.611851 CTCCTGCCTCTCCACACCT 60.612 63.158 0.00 0.00 0.00 4.00
431 432 2.664081 CCTCCTGCCTCTCCACACC 61.664 68.421 0.00 0.00 0.00 4.16
432 433 1.893919 GACCTCCTGCCTCTCCACAC 61.894 65.000 0.00 0.00 0.00 3.82
433 434 1.610673 GACCTCCTGCCTCTCCACA 60.611 63.158 0.00 0.00 0.00 4.17
434 435 1.305718 AGACCTCCTGCCTCTCCAC 60.306 63.158 0.00 0.00 0.00 4.02
435 436 1.305633 CAGACCTCCTGCCTCTCCA 60.306 63.158 0.00 0.00 35.89 3.86
436 437 2.063378 CCAGACCTCCTGCCTCTCC 61.063 68.421 0.00 0.00 41.57 3.71
437 438 2.063378 CCCAGACCTCCTGCCTCTC 61.063 68.421 0.00 0.00 41.57 3.20
438 439 2.040278 CCCAGACCTCCTGCCTCT 59.960 66.667 0.00 0.00 41.57 3.69
439 440 3.086600 CCCCAGACCTCCTGCCTC 61.087 72.222 0.00 0.00 41.57 4.70
446 447 4.083862 GACACCGCCCCAGACCTC 62.084 72.222 0.00 0.00 0.00 3.85
447 448 4.954118 TGACACCGCCCCAGACCT 62.954 66.667 0.00 0.00 0.00 3.85
448 449 4.699522 GTGACACCGCCCCAGACC 62.700 72.222 0.00 0.00 0.00 3.85
449 450 4.699522 GGTGACACCGCCCCAGAC 62.700 72.222 9.33 0.00 36.97 3.51
450 451 4.954118 AGGTGACACCGCCCCAGA 62.954 66.667 18.93 0.00 44.90 3.86
451 452 4.704833 CAGGTGACACCGCCCCAG 62.705 72.222 18.93 2.84 44.90 4.45
455 456 3.031417 ATAGCCAGGTGACACCGCC 62.031 63.158 18.93 10.97 44.90 6.13
456 457 1.815421 CATAGCCAGGTGACACCGC 60.815 63.158 18.93 16.60 44.90 5.68
457 458 1.153369 CCATAGCCAGGTGACACCG 60.153 63.158 18.93 13.28 44.90 4.94
458 459 1.991230 ACCATAGCCAGGTGACACC 59.009 57.895 17.43 17.43 38.13 4.16
464 465 1.082954 ACCTCCACCATAGCCAGGT 59.917 57.895 0.00 0.00 40.85 4.00
465 466 1.274703 ACACCTCCACCATAGCCAGG 61.275 60.000 0.00 0.00 0.00 4.45
466 467 0.620556 AACACCTCCACCATAGCCAG 59.379 55.000 0.00 0.00 0.00 4.85
467 468 1.072266 AAACACCTCCACCATAGCCA 58.928 50.000 0.00 0.00 0.00 4.75
468 469 3.477530 GATAAACACCTCCACCATAGCC 58.522 50.000 0.00 0.00 0.00 3.93
469 470 3.477530 GGATAAACACCTCCACCATAGC 58.522 50.000 0.00 0.00 0.00 2.97
470 471 3.386726 TCGGATAAACACCTCCACCATAG 59.613 47.826 0.00 0.00 0.00 2.23
471 472 3.133362 GTCGGATAAACACCTCCACCATA 59.867 47.826 0.00 0.00 0.00 2.74
472 473 2.093128 GTCGGATAAACACCTCCACCAT 60.093 50.000 0.00 0.00 0.00 3.55
473 474 1.276989 GTCGGATAAACACCTCCACCA 59.723 52.381 0.00 0.00 0.00 4.17
474 475 1.276989 TGTCGGATAAACACCTCCACC 59.723 52.381 0.00 0.00 0.00 4.61
475 476 2.754946 TGTCGGATAAACACCTCCAC 57.245 50.000 0.00 0.00 0.00 4.02
476 477 2.027561 CCTTGTCGGATAAACACCTCCA 60.028 50.000 0.00 0.00 33.16 3.86
477 478 2.629051 CCTTGTCGGATAAACACCTCC 58.371 52.381 0.00 0.00 33.16 4.30
567 568 4.270325 GCGAAATACCTAACGAGAGCAAAT 59.730 41.667 0.00 0.00 0.00 2.32
963 968 1.360551 CGGTAGAGCAGCGCATAGT 59.639 57.895 11.47 0.00 41.87 2.12
1017 1022 1.617804 CCCTCTGCCACATTTGTCCAT 60.618 52.381 0.00 0.00 0.00 3.41
1054 1059 0.836400 TTCTCCGCCACCTCCTTCTT 60.836 55.000 0.00 0.00 0.00 2.52
1231 1238 8.125728 ACAACAAACATTTTCTATGTTTTCCG 57.874 30.769 11.90 5.70 46.45 4.30
1363 1371 5.569059 GCAAAATTTCCTAATCAGACACGTG 59.431 40.000 15.48 15.48 0.00 4.49
1514 1522 9.447040 GTTCAATTTGTCTTAGGAAACAAGTAC 57.553 33.333 0.00 0.00 36.78 2.73
1517 1525 7.488322 TGGTTCAATTTGTCTTAGGAAACAAG 58.512 34.615 0.00 0.00 36.78 3.16
2089 2102 1.271163 GCACTTGGTAGCCTGGTACAA 60.271 52.381 8.58 0.00 38.70 2.41
2231 2244 9.767684 CGTATTTCTTTTCTAATGCATGTGTTA 57.232 29.630 0.00 0.00 0.00 2.41
2407 2420 8.504005 ACAAATGTATGCTTACTAAGACAACAC 58.496 33.333 10.74 2.33 0.00 3.32


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

AutoCloner maintained by Alex Coulton.