Multiple sequence alignment - TraesCS3B01G271400

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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 TraesCS3B01G271400 chr3B 100.000 3278 0 0 1 3278 436743914 436740637 0.000000e+00 6054
1 TraesCS3B01G271400 chr3A 93.022 2780 129 16 543 3278 456779165 456776407 0.000000e+00 3999
2 TraesCS3B01G271400 chr3A 92.424 132 4 1 26 157 456782969 456782844 2.010000e-42 183
3 TraesCS3B01G271400 chr3D 92.388 1905 93 29 1406 3278 338492244 338490360 0.000000e+00 2667
4 TraesCS3B01G271400 chr3D 93.135 874 40 7 547 1414 338493133 338492274 0.000000e+00 1264
5 TraesCS3B01G271400 chr3D 84.112 321 22 13 50 356 338547082 338546777 1.930000e-72 283
6 TraesCS3B01G271400 chr3D 87.736 212 5 6 26 224 338498739 338498536 9.150000e-56 228


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G271400 chr3B 436740637 436743914 3277 True 6054.0 6054 100.0000 1 3278 1 chr3B.!!$R1 3277
1 TraesCS3B01G271400 chr3A 456776407 456782969 6562 True 2091.0 3999 92.7230 26 3278 2 chr3A.!!$R1 3252
2 TraesCS3B01G271400 chr3D 338490360 338493133 2773 True 1965.5 2667 92.7615 547 3278 2 chr3D.!!$R3 2731

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
354 383 0.038166 TGGAGTTGGAGACCATTGGC 59.962 55.0 1.54 0.0 31.53 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2302 5723 0.252742 ATCTCCCCTTGACCGACCTT 60.253 55.0 0.0 0.0 0.0 3.5 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
23 24 2.278923 GGAAGAGCCTAGCGCGAC 60.279 66.667 12.10 0.04 44.76 5.19
24 25 2.776913 GGAAGAGCCTAGCGCGACT 61.777 63.158 12.10 9.58 44.76 4.18
50 51 4.261489 GCGACAGAAGATAGATACGGGAAA 60.261 45.833 0.00 0.00 0.00 3.13
107 108 1.152204 TCCTCAACCGGTCTTCCCA 60.152 57.895 8.04 0.00 0.00 4.37
108 109 0.546747 TCCTCAACCGGTCTTCCCAT 60.547 55.000 8.04 0.00 0.00 4.00
109 110 0.328258 CCTCAACCGGTCTTCCCATT 59.672 55.000 8.04 0.00 0.00 3.16
110 111 1.557832 CCTCAACCGGTCTTCCCATTA 59.442 52.381 8.04 0.00 0.00 1.90
111 112 2.420129 CCTCAACCGGTCTTCCCATTAG 60.420 54.545 8.04 0.00 0.00 1.73
112 113 2.236395 CTCAACCGGTCTTCCCATTAGT 59.764 50.000 8.04 0.00 0.00 2.24
123 124 6.354130 GTCTTCCCATTAGTATTAGCAACCA 58.646 40.000 0.00 0.00 0.00 3.67
128 129 5.236478 CCCATTAGTATTAGCAACCAACGAG 59.764 44.000 0.00 0.00 0.00 4.18
158 159 2.124736 GGCCTCTTACGCCATGCA 60.125 61.111 0.00 0.00 46.27 3.96
159 160 2.182842 GGCCTCTTACGCCATGCAG 61.183 63.158 0.00 0.00 46.27 4.41
162 163 1.506493 CCTCTTACGCCATGCAGATC 58.494 55.000 0.00 0.00 0.00 2.75
163 164 1.069823 CCTCTTACGCCATGCAGATCT 59.930 52.381 0.00 0.00 0.00 2.75
164 165 2.402305 CTCTTACGCCATGCAGATCTC 58.598 52.381 0.00 0.00 0.00 2.75
169 175 1.783031 CGCCATGCAGATCTCCAAGC 61.783 60.000 0.00 0.00 0.00 4.01
171 177 0.106868 CCATGCAGATCTCCAAGCCA 60.107 55.000 0.00 0.00 0.00 4.75
180 186 3.201487 AGATCTCCAAGCCATGTCAATGA 59.799 43.478 0.00 0.00 35.67 2.57
181 187 2.995283 TCTCCAAGCCATGTCAATGAG 58.005 47.619 0.00 0.00 35.67 2.90
183 189 0.458669 CCAAGCCATGTCAATGAGCC 59.541 55.000 0.00 0.00 35.67 4.70
204 223 1.676967 GCACCCTCCTCTTTGCAGG 60.677 63.158 0.00 0.00 34.97 4.85
211 230 1.897802 CTCCTCTTTGCAGGCCAAAAT 59.102 47.619 5.01 0.00 42.51 1.82
218 237 1.630223 TGCAGGCCAAAATCACATGA 58.370 45.000 5.01 0.00 0.00 3.07
224 243 3.763360 AGGCCAAAATCACATGAATCGAA 59.237 39.130 5.01 0.00 0.00 3.71
225 244 4.403432 AGGCCAAAATCACATGAATCGAAT 59.597 37.500 5.01 0.00 0.00 3.34
226 245 5.105228 AGGCCAAAATCACATGAATCGAATT 60.105 36.000 5.01 0.00 0.00 2.17
227 246 5.005971 GGCCAAAATCACATGAATCGAATTG 59.994 40.000 0.00 1.47 0.00 2.32
228 247 5.806502 GCCAAAATCACATGAATCGAATTGA 59.193 36.000 0.00 0.00 0.00 2.57
229 248 6.310956 GCCAAAATCACATGAATCGAATTGAA 59.689 34.615 0.00 0.00 0.00 2.69
230 249 7.148606 GCCAAAATCACATGAATCGAATTGAAA 60.149 33.333 0.00 0.00 0.00 2.69
231 250 8.377681 CCAAAATCACATGAATCGAATTGAAAG 58.622 33.333 0.00 0.00 0.00 2.62
232 251 9.131416 CAAAATCACATGAATCGAATTGAAAGA 57.869 29.630 0.00 0.00 0.00 2.52
233 252 9.865321 AAAATCACATGAATCGAATTGAAAGAT 57.135 25.926 0.00 0.00 0.00 2.40
235 254 9.941664 AATCACATGAATCGAATTGAAAGATAC 57.058 29.630 0.00 0.00 0.00 2.24
236 255 8.722480 TCACATGAATCGAATTGAAAGATACT 57.278 30.769 0.00 0.00 0.00 2.12
237 256 8.820933 TCACATGAATCGAATTGAAAGATACTC 58.179 33.333 0.00 0.00 0.00 2.59
238 257 8.066595 CACATGAATCGAATTGAAAGATACTCC 58.933 37.037 0.00 0.00 0.00 3.85
239 258 7.989741 ACATGAATCGAATTGAAAGATACTCCT 59.010 33.333 0.00 0.00 0.00 3.69
240 259 7.776933 TGAATCGAATTGAAAGATACTCCTG 57.223 36.000 0.00 0.00 0.00 3.86
244 263 4.504461 CGAATTGAAAGATACTCCTGTCCG 59.496 45.833 0.00 0.00 0.00 4.79
248 267 1.777941 AAGATACTCCTGTCCGGTCC 58.222 55.000 0.00 0.00 0.00 4.46
261 280 0.972983 CCGGTCCTGATCAGACTGGT 60.973 60.000 27.96 0.00 39.77 4.00
265 284 1.895798 GTCCTGATCAGACTGGTGACA 59.104 52.381 24.62 0.00 39.59 3.58
266 285 2.300152 GTCCTGATCAGACTGGTGACAA 59.700 50.000 24.62 0.00 42.06 3.18
267 286 2.564504 TCCTGATCAGACTGGTGACAAG 59.435 50.000 24.62 2.66 42.06 3.16
272 291 1.005630 AGACTGGTGACAAGCGAGC 60.006 57.895 0.00 0.00 42.06 5.03
273 292 1.300931 GACTGGTGACAAGCGAGCA 60.301 57.895 0.00 0.00 42.06 4.26
274 293 1.287730 GACTGGTGACAAGCGAGCAG 61.288 60.000 0.00 0.00 42.06 4.24
275 294 2.031012 TGGTGACAAGCGAGCAGG 59.969 61.111 0.00 0.00 37.44 4.85
277 296 1.292223 GGTGACAAGCGAGCAGGTA 59.708 57.895 0.00 0.00 0.00 3.08
278 297 0.108138 GGTGACAAGCGAGCAGGTAT 60.108 55.000 0.00 0.00 0.00 2.73
279 298 1.281899 GTGACAAGCGAGCAGGTATC 58.718 55.000 0.00 0.00 0.00 2.24
280 299 1.134965 GTGACAAGCGAGCAGGTATCT 60.135 52.381 0.00 0.00 0.00 1.98
281 300 1.550524 TGACAAGCGAGCAGGTATCTT 59.449 47.619 0.00 0.00 0.00 2.40
282 301 2.758423 TGACAAGCGAGCAGGTATCTTA 59.242 45.455 0.00 0.00 0.00 2.10
283 302 3.181486 TGACAAGCGAGCAGGTATCTTAG 60.181 47.826 0.00 0.00 0.00 2.18
284 303 2.101582 ACAAGCGAGCAGGTATCTTAGG 59.898 50.000 0.00 0.00 0.00 2.69
285 304 0.676736 AGCGAGCAGGTATCTTAGGC 59.323 55.000 0.00 0.00 0.00 3.93
286 305 0.664767 GCGAGCAGGTATCTTAGGCG 60.665 60.000 0.00 0.00 0.00 5.52
287 306 0.952280 CGAGCAGGTATCTTAGGCGA 59.048 55.000 0.00 0.00 0.00 5.54
288 307 1.335142 CGAGCAGGTATCTTAGGCGAC 60.335 57.143 0.00 0.00 0.00 5.19
289 308 0.669077 AGCAGGTATCTTAGGCGACG 59.331 55.000 0.00 0.00 0.00 5.12
290 309 0.318784 GCAGGTATCTTAGGCGACGG 60.319 60.000 0.00 0.00 0.00 4.79
291 310 0.314302 CAGGTATCTTAGGCGACGGG 59.686 60.000 0.00 0.00 0.00 5.28
292 311 0.826672 AGGTATCTTAGGCGACGGGG 60.827 60.000 0.00 0.00 0.00 5.73
293 312 1.111715 GGTATCTTAGGCGACGGGGT 61.112 60.000 0.00 0.00 0.00 4.95
298 317 3.379865 TTAGGCGACGGGGTCATGC 62.380 63.158 0.00 0.00 32.09 4.06
300 319 4.856801 GGCGACGGGGTCATGCAT 62.857 66.667 0.00 0.00 32.09 3.96
307 326 1.609239 GGGGTCATGCATGGACTGA 59.391 57.895 25.97 4.70 35.61 3.41
310 329 1.952296 GGGTCATGCATGGACTGATTC 59.048 52.381 25.97 9.53 35.61 2.52
314 333 3.252701 GTCATGCATGGACTGATTCATCC 59.747 47.826 25.97 7.71 35.37 3.51
332 361 2.181777 GAGCATCGGACGTGCAGA 59.818 61.111 8.11 5.97 44.87 4.26
351 380 2.915604 AGACATGGAGTTGGAGACCATT 59.084 45.455 0.00 0.00 41.68 3.16
354 383 0.038166 TGGAGTTGGAGACCATTGGC 59.962 55.000 1.54 0.00 31.53 4.52
356 385 1.168714 GAGTTGGAGACCATTGGCAC 58.831 55.000 1.54 0.00 31.53 5.01
357 386 0.478072 AGTTGGAGACCATTGGCACA 59.522 50.000 1.54 0.00 31.53 4.57
360 389 0.405198 TGGAGACCATTGGCACACAT 59.595 50.000 1.54 0.00 39.29 3.21
365 394 2.297033 AGACCATTGGCACACATGTTTC 59.703 45.455 1.54 0.00 39.29 2.78
366 395 1.344114 ACCATTGGCACACATGTTTCC 59.656 47.619 1.54 0.00 39.29 3.13
367 396 1.619827 CCATTGGCACACATGTTTCCT 59.380 47.619 0.00 0.00 39.29 3.36
369 398 3.494749 CCATTGGCACACATGTTTCCTTT 60.495 43.478 0.00 0.00 39.29 3.11
370 399 3.902881 TTGGCACACATGTTTCCTTTT 57.097 38.095 0.00 0.00 39.29 2.27
371 400 3.451141 TGGCACACATGTTTCCTTTTC 57.549 42.857 0.00 0.00 0.00 2.29
372 401 2.102252 TGGCACACATGTTTCCTTTTCC 59.898 45.455 0.00 0.00 0.00 3.13
373 402 2.547855 GGCACACATGTTTCCTTTTCCC 60.548 50.000 0.00 0.00 0.00 3.97
374 403 2.547855 GCACACATGTTTCCTTTTCCCC 60.548 50.000 0.00 0.00 0.00 4.81
375 404 2.037121 CACACATGTTTCCTTTTCCCCC 59.963 50.000 0.00 0.00 0.00 5.40
376 405 2.090775 ACACATGTTTCCTTTTCCCCCT 60.091 45.455 0.00 0.00 0.00 4.79
377 406 2.972021 CACATGTTTCCTTTTCCCCCTT 59.028 45.455 0.00 0.00 0.00 3.95
378 407 3.390967 CACATGTTTCCTTTTCCCCCTTT 59.609 43.478 0.00 0.00 0.00 3.11
379 408 4.044308 ACATGTTTCCTTTTCCCCCTTTT 58.956 39.130 0.00 0.00 0.00 2.27
380 409 4.476846 ACATGTTTCCTTTTCCCCCTTTTT 59.523 37.500 0.00 0.00 0.00 1.94
381 410 4.764050 TGTTTCCTTTTCCCCCTTTTTC 57.236 40.909 0.00 0.00 0.00 2.29
386 415 6.395780 TTCCTTTTCCCCCTTTTTCTTTTT 57.604 33.333 0.00 0.00 0.00 1.94
390 419 3.836365 TCCCCCTTTTTCTTTTTGCAG 57.164 42.857 0.00 0.00 0.00 4.41
396 425 3.555547 CCTTTTTCTTTTTGCAGGGTTCG 59.444 43.478 0.00 0.00 0.00 3.95
413 442 2.743538 GGGAAACCGGCCGTGTAC 60.744 66.667 26.12 17.12 43.64 2.90
414 443 2.344872 GGAAACCGGCCGTGTACT 59.655 61.111 26.12 12.07 0.00 2.73
415 444 1.591183 GGAAACCGGCCGTGTACTA 59.409 57.895 26.12 0.00 0.00 1.82
416 445 0.459063 GGAAACCGGCCGTGTACTAG 60.459 60.000 26.12 9.27 0.00 2.57
418 447 2.511545 AAACCGGCCGTGTACTAGCC 62.512 60.000 26.12 10.31 43.53 3.93
421 450 3.455469 GGCCGTGTACTAGCCGGT 61.455 66.667 1.90 0.00 43.56 5.28
423 452 2.493030 CCGTGTACTAGCCGGTGG 59.507 66.667 1.90 0.00 37.00 4.61
424 453 2.048023 CCGTGTACTAGCCGGTGGA 61.048 63.158 1.90 0.00 37.00 4.02
432 461 5.587443 GTGTACTAGCCGGTGGAAAATAAAT 59.413 40.000 1.90 0.00 0.00 1.40
440 469 5.092781 CCGGTGGAAAATAAATTTGTCTCG 58.907 41.667 0.00 0.00 0.00 4.04
442 471 4.862574 GGTGGAAAATAAATTTGTCTCGGC 59.137 41.667 0.00 0.00 0.00 5.54
444 473 5.344933 GTGGAAAATAAATTTGTCTCGGCAC 59.655 40.000 0.00 0.00 0.00 5.01
446 475 5.572896 GGAAAATAAATTTGTCTCGGCACAG 59.427 40.000 0.00 0.00 0.00 3.66
455 484 2.839486 TCTCGGCACAGAGAATTTGT 57.161 45.000 0.00 0.00 43.56 2.83
457 486 2.037121 TCTCGGCACAGAGAATTTGTGA 59.963 45.455 11.98 0.00 46.85 3.58
459 488 3.210227 TCGGCACAGAGAATTTGTGAAA 58.790 40.909 11.98 0.00 46.85 2.69
464 493 6.042143 GGCACAGAGAATTTGTGAAAAGAAA 58.958 36.000 11.98 0.00 46.85 2.52
465 494 6.703165 GGCACAGAGAATTTGTGAAAAGAAAT 59.297 34.615 11.98 0.00 46.85 2.17
466 495 7.225341 GGCACAGAGAATTTGTGAAAAGAAATT 59.775 33.333 11.98 0.00 46.85 1.82
479 518 6.754675 GTGAAAAGAAATTGAGAAAAACCCGA 59.245 34.615 0.00 0.00 0.00 5.14
480 519 6.978080 TGAAAAGAAATTGAGAAAAACCCGAG 59.022 34.615 0.00 0.00 0.00 4.63
481 520 6.465439 AAAGAAATTGAGAAAAACCCGAGT 57.535 33.333 0.00 0.00 0.00 4.18
493 532 3.286329 AACCCGAGTGTTTACCAAACT 57.714 42.857 3.68 0.00 41.90 2.66
504 543 8.647143 AGTGTTTACCAAACTGATTTCATTTG 57.353 30.769 3.68 0.00 41.90 2.32
508 547 4.622260 CCAAACTGATTTCATTTGGGGT 57.378 40.909 17.61 0.00 45.74 4.95
511 550 1.901833 ACTGATTTCATTTGGGGTGGC 59.098 47.619 0.00 0.00 0.00 5.01
521 560 0.541764 TTGGGGTGGCTCAAATGACC 60.542 55.000 0.00 0.00 0.00 4.02
526 565 1.818674 GGTGGCTCAAATGACCGAAAT 59.181 47.619 0.00 0.00 0.00 2.17
527 566 3.013921 GGTGGCTCAAATGACCGAAATA 58.986 45.455 0.00 0.00 0.00 1.40
529 568 4.097892 GGTGGCTCAAATGACCGAAATATT 59.902 41.667 0.00 0.00 0.00 1.28
530 569 5.036737 GTGGCTCAAATGACCGAAATATTG 58.963 41.667 0.00 0.00 0.00 1.90
531 570 4.097741 TGGCTCAAATGACCGAAATATTGG 59.902 41.667 0.00 0.00 36.02 3.16
532 571 4.338118 GGCTCAAATGACCGAAATATTGGA 59.662 41.667 0.00 0.00 33.82 3.53
533 572 5.163561 GGCTCAAATGACCGAAATATTGGAA 60.164 40.000 0.00 0.00 33.82 3.53
537 576 8.116651 TCAAATGACCGAAATATTGGAAGAAA 57.883 30.769 0.00 0.00 33.82 2.52
541 580 7.461182 TGACCGAAATATTGGAAGAAATTGT 57.539 32.000 0.00 0.00 33.82 2.71
544 583 9.849166 GACCGAAATATTGGAAGAAATTGTTAA 57.151 29.630 0.00 0.00 33.82 2.01
545 584 9.634163 ACCGAAATATTGGAAGAAATTGTTAAC 57.366 29.630 0.00 0.00 33.82 2.01
554 3893 3.515562 AGAAATTGTTAACCATGGCCCA 58.484 40.909 13.04 0.00 0.00 5.36
566 3905 0.392998 ATGGCCCAGCGAGTTTAGTG 60.393 55.000 0.00 0.00 0.00 2.74
574 3913 3.390135 CAGCGAGTTTAGTGGAGAAACA 58.610 45.455 0.00 0.00 38.91 2.83
667 4006 1.098712 GGAGACGCACCAACCAACAA 61.099 55.000 0.00 0.00 0.00 2.83
673 4012 0.820871 GCACCAACCAACAACCAAGA 59.179 50.000 0.00 0.00 0.00 3.02
689 4028 2.483491 CCAAGAAGAGCAAGCAGTTCTC 59.517 50.000 8.72 0.00 36.73 2.87
755 4094 0.261109 CTCCCTACCGTCCCTAACCT 59.739 60.000 0.00 0.00 0.00 3.50
987 4340 3.059352 ACCTCCACTTCAGAATTTCGG 57.941 47.619 0.00 0.00 0.00 4.30
1008 4361 2.351738 GCTTCCAGTTCACGGGATTTTG 60.352 50.000 0.00 0.00 39.87 2.44
1009 4362 1.904287 TCCAGTTCACGGGATTTTGG 58.096 50.000 6.33 6.33 35.30 3.28
1024 4377 1.747444 TTTGGCCCTCCTCTTCTTCT 58.253 50.000 0.00 0.00 0.00 2.85
1025 4378 1.280457 TTGGCCCTCCTCTTCTTCTC 58.720 55.000 0.00 0.00 0.00 2.87
1081 4434 3.936902 TTCTCGTCGGTTTGTTTCTTG 57.063 42.857 0.00 0.00 0.00 3.02
1152 4505 2.201921 AGACGACTGCTCCTTCTGTA 57.798 50.000 0.00 0.00 0.00 2.74
1307 4660 5.248870 AGTTTGTGGTTTTCTGATCACAC 57.751 39.130 5.23 5.23 39.46 3.82
1419 4816 3.427863 GCAACAAATCTCTTTCTTGCAGC 59.572 43.478 6.29 0.00 42.43 5.25
1546 4943 0.672889 TCAAAAAGCGGCAGATGCAA 59.327 45.000 7.19 0.00 44.36 4.08
1617 5033 6.723298 ATATCCGAGAGATGTTTCTGTCTT 57.277 37.500 0.00 0.00 39.53 3.01
1618 5034 4.442375 TCCGAGAGATGTTTCTGTCTTC 57.558 45.455 0.00 0.00 39.53 2.87
1619 5035 4.082845 TCCGAGAGATGTTTCTGTCTTCT 58.917 43.478 0.00 0.00 39.53 2.85
1848 5269 7.418408 CAGAAAGGTGAGAAAAACTACTTTCC 58.582 38.462 0.00 0.00 40.58 3.13
1888 5309 6.998968 TTTTGCAACCTTTTCATGTTTCAT 57.001 29.167 0.00 0.00 0.00 2.57
1889 5310 8.674263 ATTTTGCAACCTTTTCATGTTTCATA 57.326 26.923 0.00 0.00 0.00 2.15
1890 5311 7.475771 TTTGCAACCTTTTCATGTTTCATAC 57.524 32.000 0.00 0.00 0.00 2.39
1920 5341 3.736094 TCATACCTGAACCTGAATCCCT 58.264 45.455 0.00 0.00 0.00 4.20
1922 5343 4.164221 TCATACCTGAACCTGAATCCCTTC 59.836 45.833 0.00 0.00 0.00 3.46
1925 5346 2.843113 CCTGAACCTGAATCCCTTCTCT 59.157 50.000 0.00 0.00 32.29 3.10
1926 5347 4.033709 CCTGAACCTGAATCCCTTCTCTA 58.966 47.826 0.00 0.00 32.29 2.43
1927 5348 4.657969 CCTGAACCTGAATCCCTTCTCTAT 59.342 45.833 0.00 0.00 32.29 1.98
1928 5349 5.221621 CCTGAACCTGAATCCCTTCTCTATC 60.222 48.000 0.00 0.00 32.29 2.08
1929 5350 5.280499 TGAACCTGAATCCCTTCTCTATCA 58.720 41.667 0.00 0.00 32.29 2.15
1995 5416 2.819595 GGCTTCTCGGCATCGCAA 60.820 61.111 0.00 0.00 38.25 4.85
2042 5463 2.758327 TCTGGCCTCCGCACGTAT 60.758 61.111 3.32 0.00 36.38 3.06
2045 5466 2.369257 CTGGCCTCCGCACGTATCAT 62.369 60.000 3.32 0.00 36.38 2.45
2090 5511 2.686106 TGGACCGGCCTCCTTACC 60.686 66.667 12.06 2.54 37.63 2.85
2144 5565 6.194235 CCTCTTGATAGATAGGTGGAGCTAT 58.806 44.000 0.00 0.00 30.76 2.97
2174 5595 3.058160 GGACGTCTCCCGGTCGAA 61.058 66.667 16.46 0.00 42.24 3.71
2197 5618 3.664486 CAGCTAAGACCGAACGATAATCG 59.336 47.826 0.00 0.00 46.93 3.34
2251 5672 3.146066 TGGTTATGGTGCAAGAGTGAAC 58.854 45.455 0.00 0.00 31.60 3.18
2276 5697 7.453126 ACTCTCCAAATAAGAGAAGACAGAAGA 59.547 37.037 7.12 0.00 42.39 2.87
2278 5699 7.453126 TCTCCAAATAAGAGAAGACAGAAGACT 59.547 37.037 0.00 0.00 37.44 3.24
2297 5718 6.550938 AGACTGTGTGAAGATTGATGGATA 57.449 37.500 0.00 0.00 0.00 2.59
2302 5723 8.267183 ACTGTGTGAAGATTGATGGATATTGTA 58.733 33.333 0.00 0.00 0.00 2.41
2307 5728 8.778358 GTGAAGATTGATGGATATTGTAAGGTC 58.222 37.037 0.00 0.00 0.00 3.85
2344 5765 8.718656 AGATGGTAAATGCTACTAAATCCTCTT 58.281 33.333 0.00 0.00 0.00 2.85
2363 5784 5.691754 CCTCTTGTAAATTGCTTGGTTTGAC 59.308 40.000 0.00 0.00 0.00 3.18
2401 5822 9.278978 TGAACAAGATTGTACAGCTTTTATACA 57.721 29.630 9.55 0.00 41.31 2.29
2411 5832 6.500684 ACAGCTTTTATACATGTGTTGAGG 57.499 37.500 9.11 0.00 0.00 3.86
2428 5849 2.290514 TGAGGTTGCAGAGGATTGGAAG 60.291 50.000 0.00 0.00 0.00 3.46
2442 5863 3.788227 TTGGAAGCTCTGGTGTTGTAT 57.212 42.857 0.00 0.00 0.00 2.29
2489 5910 5.184864 TGTTTCAAGACACCATTTGAACAGT 59.815 36.000 0.00 0.00 41.51 3.55
2509 5930 3.327757 AGTTTGTGGGAAGCAGTCAGATA 59.672 43.478 0.00 0.00 0.00 1.98
2546 5967 6.354938 TCTGATCATCAGGGAAGAAGAAATG 58.645 40.000 14.96 0.00 44.39 2.32
2567 5988 8.908786 AAATGATCAGAAGTTTCAGAACTGTA 57.091 30.769 0.09 0.00 45.18 2.74
2585 6006 5.373222 ACTGTAGTTGAAATGCACCTGTAA 58.627 37.500 0.00 0.00 0.00 2.41
2588 6009 5.414454 TGTAGTTGAAATGCACCTGTAATCC 59.586 40.000 0.00 0.00 0.00 3.01
2598 6019 3.873952 GCACCTGTAATCCTCATGTTCTC 59.126 47.826 0.00 0.00 0.00 2.87
2600 6021 5.163405 GCACCTGTAATCCTCATGTTCTCTA 60.163 44.000 0.00 0.00 0.00 2.43
2633 6072 4.946772 TCTTCAGGTTGTCAACATTTCACA 59.053 37.500 17.29 0.00 0.00 3.58
2709 6154 6.612247 TGTGGCTAATGGATAAAACATACG 57.388 37.500 0.00 0.00 0.00 3.06
2765 6210 7.517320 ACCTACATGCTCCATATACAAATTCA 58.483 34.615 0.00 0.00 0.00 2.57
2841 6286 3.507162 TGAAAAGGCCTGAAGATGACA 57.493 42.857 5.69 0.00 0.00 3.58
2849 6294 5.006386 AGGCCTGAAGATGACAACTAAAAG 58.994 41.667 3.11 0.00 0.00 2.27
2851 6296 4.457257 GCCTGAAGATGACAACTAAAAGCT 59.543 41.667 0.00 0.00 0.00 3.74
3184 6629 2.707791 TCATTCTCTGAGCATAAGGGGG 59.292 50.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.391661 CGCTAGGCTCTTCCTTTGCA 60.392 55.000 0.00 0.00 44.75 4.08
1 2 1.710103 GCGCTAGGCTCTTCCTTTGC 61.710 60.000 0.00 0.00 44.75 3.68
2 3 1.424493 CGCGCTAGGCTCTTCCTTTG 61.424 60.000 5.56 0.00 44.75 2.77
3 4 1.153549 CGCGCTAGGCTCTTCCTTT 60.154 57.895 5.56 0.00 44.75 3.11
4 5 2.052690 TCGCGCTAGGCTCTTCCTT 61.053 57.895 5.56 0.00 44.75 3.36
6 7 2.278923 GTCGCGCTAGGCTCTTCC 60.279 66.667 5.56 0.00 40.44 3.46
7 8 1.587613 CAGTCGCGCTAGGCTCTTC 60.588 63.158 5.56 0.00 40.44 2.87
8 9 2.492090 CAGTCGCGCTAGGCTCTT 59.508 61.111 5.56 0.00 40.44 2.85
9 10 4.200283 GCAGTCGCGCTAGGCTCT 62.200 66.667 5.56 0.00 40.44 4.09
20 21 0.248094 TATCTTCTGTCGCGCAGTCG 60.248 55.000 23.32 17.11 45.23 4.18
21 22 1.064208 TCTATCTTCTGTCGCGCAGTC 59.936 52.381 23.32 6.89 45.23 3.51
22 23 1.095600 TCTATCTTCTGTCGCGCAGT 58.904 50.000 23.32 11.56 45.23 4.40
23 24 2.414058 ATCTATCTTCTGTCGCGCAG 57.586 50.000 19.99 19.99 46.34 5.18
24 25 2.349532 CGTATCTATCTTCTGTCGCGCA 60.350 50.000 8.75 1.43 0.00 6.09
50 51 0.913451 AGTGCCTCTGCCTGGAGAAT 60.913 55.000 0.00 0.00 35.52 2.40
107 108 5.293569 GTGCTCGTTGGTTGCTAATACTAAT 59.706 40.000 0.00 0.00 0.00 1.73
108 109 4.628333 GTGCTCGTTGGTTGCTAATACTAA 59.372 41.667 0.00 0.00 0.00 2.24
109 110 4.081862 AGTGCTCGTTGGTTGCTAATACTA 60.082 41.667 0.00 0.00 0.00 1.82
110 111 3.000727 GTGCTCGTTGGTTGCTAATACT 58.999 45.455 0.00 0.00 0.00 2.12
111 112 3.000727 AGTGCTCGTTGGTTGCTAATAC 58.999 45.455 0.00 0.00 0.00 1.89
112 113 3.328382 AGTGCTCGTTGGTTGCTAATA 57.672 42.857 0.00 0.00 0.00 0.98
128 129 2.747855 AGGCCGCAAAGCTAGTGC 60.748 61.111 11.42 11.42 38.68 4.40
142 143 0.533755 ATCTGCATGGCGTAAGAGGC 60.534 55.000 0.00 0.00 43.02 4.70
157 158 2.704464 TGACATGGCTTGGAGATCTG 57.296 50.000 0.00 0.00 0.00 2.90
158 159 3.201487 TCATTGACATGGCTTGGAGATCT 59.799 43.478 0.00 0.00 0.00 2.75
159 160 3.548770 TCATTGACATGGCTTGGAGATC 58.451 45.455 0.00 0.00 0.00 2.75
162 163 1.404391 GCTCATTGACATGGCTTGGAG 59.596 52.381 0.00 4.83 0.00 3.86
163 164 1.466856 GCTCATTGACATGGCTTGGA 58.533 50.000 0.00 0.00 0.00 3.53
164 165 0.458669 GGCTCATTGACATGGCTTGG 59.541 55.000 0.00 0.00 31.03 3.61
169 175 0.745486 TGCGAGGCTCATTGACATGG 60.745 55.000 15.95 0.00 0.00 3.66
171 177 0.745845 GGTGCGAGGCTCATTGACAT 60.746 55.000 15.95 0.00 0.00 3.06
180 186 3.914551 AAGAGGAGGGTGCGAGGCT 62.915 63.158 0.00 0.00 0.00 4.58
181 187 2.960688 AAAGAGGAGGGTGCGAGGC 61.961 63.158 0.00 0.00 0.00 4.70
183 189 1.743252 GCAAAGAGGAGGGTGCGAG 60.743 63.158 0.00 0.00 0.00 5.03
204 223 5.806502 TCAATTCGATTCATGTGATTTTGGC 59.193 36.000 0.00 0.00 0.00 4.52
211 230 8.722480 AGTATCTTTCAATTCGATTCATGTGA 57.278 30.769 0.00 0.00 0.00 3.58
218 237 6.763610 GGACAGGAGTATCTTTCAATTCGATT 59.236 38.462 0.00 0.00 33.73 3.34
224 243 3.775316 ACCGGACAGGAGTATCTTTCAAT 59.225 43.478 9.46 0.00 45.00 2.57
225 244 3.170717 ACCGGACAGGAGTATCTTTCAA 58.829 45.455 9.46 0.00 45.00 2.69
226 245 2.758979 GACCGGACAGGAGTATCTTTCA 59.241 50.000 9.46 0.00 45.00 2.69
227 246 2.101082 GGACCGGACAGGAGTATCTTTC 59.899 54.545 9.46 0.00 45.00 2.62
228 247 2.108970 GGACCGGACAGGAGTATCTTT 58.891 52.381 9.46 0.00 45.00 2.52
229 248 1.288335 AGGACCGGACAGGAGTATCTT 59.712 52.381 9.46 0.00 45.00 2.40
230 249 0.927767 AGGACCGGACAGGAGTATCT 59.072 55.000 9.46 0.00 45.00 1.98
231 250 1.033574 CAGGACCGGACAGGAGTATC 58.966 60.000 9.46 0.00 45.00 2.24
232 251 0.629596 TCAGGACCGGACAGGAGTAT 59.370 55.000 9.46 0.00 45.00 2.12
233 252 0.629596 ATCAGGACCGGACAGGAGTA 59.370 55.000 9.46 0.00 45.00 2.59
234 253 0.684805 GATCAGGACCGGACAGGAGT 60.685 60.000 9.46 0.00 45.00 3.85
235 254 0.684479 TGATCAGGACCGGACAGGAG 60.684 60.000 9.46 0.00 45.00 3.69
236 255 0.684479 CTGATCAGGACCGGACAGGA 60.684 60.000 15.38 3.45 45.00 3.86
238 257 0.457851 GTCTGATCAGGACCGGACAG 59.542 60.000 22.42 13.90 38.28 3.51
239 258 0.039764 AGTCTGATCAGGACCGGACA 59.960 55.000 22.42 0.00 40.25 4.02
240 259 0.457851 CAGTCTGATCAGGACCGGAC 59.542 60.000 22.42 12.09 38.59 4.79
244 263 1.205893 GTCACCAGTCTGATCAGGACC 59.794 57.143 22.42 10.79 34.56 4.46
248 267 2.344950 GCTTGTCACCAGTCTGATCAG 58.655 52.381 17.07 17.07 0.00 2.90
261 280 1.186200 AGATACCTGCTCGCTTGTCA 58.814 50.000 0.00 0.00 0.00 3.58
265 284 1.069358 GCCTAAGATACCTGCTCGCTT 59.931 52.381 0.00 0.00 0.00 4.68
266 285 0.676736 GCCTAAGATACCTGCTCGCT 59.323 55.000 0.00 0.00 0.00 4.93
267 286 0.664767 CGCCTAAGATACCTGCTCGC 60.665 60.000 0.00 0.00 0.00 5.03
272 291 0.314302 CCCGTCGCCTAAGATACCTG 59.686 60.000 0.00 0.00 0.00 4.00
273 292 0.826672 CCCCGTCGCCTAAGATACCT 60.827 60.000 0.00 0.00 0.00 3.08
274 293 1.111715 ACCCCGTCGCCTAAGATACC 61.112 60.000 0.00 0.00 0.00 2.73
275 294 0.313357 GACCCCGTCGCCTAAGATAC 59.687 60.000 0.00 0.00 0.00 2.24
277 296 0.759436 ATGACCCCGTCGCCTAAGAT 60.759 55.000 0.00 0.00 34.95 2.40
278 297 1.380785 ATGACCCCGTCGCCTAAGA 60.381 57.895 0.00 0.00 34.95 2.10
279 298 1.227263 CATGACCCCGTCGCCTAAG 60.227 63.158 0.00 0.00 34.95 2.18
280 299 2.897207 CATGACCCCGTCGCCTAA 59.103 61.111 0.00 0.00 34.95 2.69
281 300 3.845259 GCATGACCCCGTCGCCTA 61.845 66.667 0.00 0.00 34.95 3.93
283 302 4.856801 ATGCATGACCCCGTCGCC 62.857 66.667 0.00 0.00 34.95 5.54
284 303 3.576356 CATGCATGACCCCGTCGC 61.576 66.667 22.59 0.00 34.95 5.19
285 304 2.896854 CCATGCATGACCCCGTCG 60.897 66.667 28.31 4.56 34.95 5.12
286 305 1.819632 GTCCATGCATGACCCCGTC 60.820 63.158 28.31 4.90 0.00 4.79
287 306 2.272146 GTCCATGCATGACCCCGT 59.728 61.111 28.31 0.00 0.00 5.28
288 307 1.820906 CAGTCCATGCATGACCCCG 60.821 63.158 28.31 10.81 0.00 5.73
289 308 0.184451 ATCAGTCCATGCATGACCCC 59.816 55.000 28.31 11.81 0.00 4.95
290 309 1.952296 GAATCAGTCCATGCATGACCC 59.048 52.381 28.31 14.24 0.00 4.46
291 310 2.646930 TGAATCAGTCCATGCATGACC 58.353 47.619 28.31 16.71 0.00 4.02
292 311 3.252701 GGATGAATCAGTCCATGCATGAC 59.747 47.826 28.31 21.45 34.57 3.06
293 312 3.483421 GGATGAATCAGTCCATGCATGA 58.517 45.455 28.31 9.01 34.57 3.07
298 317 2.141517 GCTCGGATGAATCAGTCCATG 58.858 52.381 10.68 0.00 34.05 3.66
300 319 1.194218 TGCTCGGATGAATCAGTCCA 58.806 50.000 10.68 0.00 34.05 4.02
314 333 3.250323 CTGCACGTCCGATGCTCG 61.250 66.667 12.78 0.00 43.77 5.03
326 345 1.002430 TCTCCAACTCCATGTCTGCAC 59.998 52.381 0.00 0.00 0.00 4.57
332 361 2.291153 CCAATGGTCTCCAACTCCATGT 60.291 50.000 0.00 0.00 41.12 3.21
351 380 2.102252 GGAAAAGGAAACATGTGTGCCA 59.898 45.455 3.54 0.00 0.00 4.92
354 383 2.037121 GGGGGAAAAGGAAACATGTGTG 59.963 50.000 0.00 0.00 0.00 3.82
356 385 2.608623 AGGGGGAAAAGGAAACATGTG 58.391 47.619 0.00 0.00 0.00 3.21
357 386 3.344535 AAGGGGGAAAAGGAAACATGT 57.655 42.857 0.00 0.00 0.00 3.21
360 389 4.367166 AGAAAAAGGGGGAAAAGGAAACA 58.633 39.130 0.00 0.00 0.00 2.83
365 394 4.338118 GCAAAAAGAAAAAGGGGGAAAAGG 59.662 41.667 0.00 0.00 0.00 3.11
366 395 4.946772 TGCAAAAAGAAAAAGGGGGAAAAG 59.053 37.500 0.00 0.00 0.00 2.27
367 396 4.923415 TGCAAAAAGAAAAAGGGGGAAAA 58.077 34.783 0.00 0.00 0.00 2.29
369 398 3.118075 CCTGCAAAAAGAAAAAGGGGGAA 60.118 43.478 0.00 0.00 0.00 3.97
370 399 2.437651 CCTGCAAAAAGAAAAAGGGGGA 59.562 45.455 0.00 0.00 0.00 4.81
371 400 2.487086 CCCTGCAAAAAGAAAAAGGGGG 60.487 50.000 0.00 0.00 40.66 5.40
372 401 2.849942 CCCTGCAAAAAGAAAAAGGGG 58.150 47.619 0.00 0.00 40.66 4.79
374 403 3.555547 CGAACCCTGCAAAAAGAAAAAGG 59.444 43.478 0.00 0.00 0.00 3.11
375 404 3.555547 CCGAACCCTGCAAAAAGAAAAAG 59.444 43.478 0.00 0.00 0.00 2.27
376 405 3.526534 CCGAACCCTGCAAAAAGAAAAA 58.473 40.909 0.00 0.00 0.00 1.94
377 406 2.159028 CCCGAACCCTGCAAAAAGAAAA 60.159 45.455 0.00 0.00 0.00 2.29
378 407 1.410882 CCCGAACCCTGCAAAAAGAAA 59.589 47.619 0.00 0.00 0.00 2.52
379 408 1.036707 CCCGAACCCTGCAAAAAGAA 58.963 50.000 0.00 0.00 0.00 2.52
380 409 0.183971 TCCCGAACCCTGCAAAAAGA 59.816 50.000 0.00 0.00 0.00 2.52
381 410 1.036707 TTCCCGAACCCTGCAAAAAG 58.963 50.000 0.00 0.00 0.00 2.27
396 425 1.887344 TAGTACACGGCCGGTTTCCC 61.887 60.000 31.76 11.81 0.00 3.97
411 440 6.660094 ACAAATTTATTTTCCACCGGCTAGTA 59.340 34.615 0.00 0.00 0.00 1.82
412 441 5.479027 ACAAATTTATTTTCCACCGGCTAGT 59.521 36.000 0.00 0.00 0.00 2.57
413 442 5.961272 ACAAATTTATTTTCCACCGGCTAG 58.039 37.500 0.00 0.00 0.00 3.42
414 443 5.712917 AGACAAATTTATTTTCCACCGGCTA 59.287 36.000 0.00 0.00 0.00 3.93
415 444 4.526650 AGACAAATTTATTTTCCACCGGCT 59.473 37.500 0.00 0.00 0.00 5.52
416 445 4.816392 AGACAAATTTATTTTCCACCGGC 58.184 39.130 0.00 0.00 0.00 6.13
418 447 5.092781 CCGAGACAAATTTATTTTCCACCG 58.907 41.667 0.00 0.00 0.00 4.94
420 449 5.344933 GTGCCGAGACAAATTTATTTTCCAC 59.655 40.000 0.00 0.00 0.00 4.02
421 450 5.010112 TGTGCCGAGACAAATTTATTTTCCA 59.990 36.000 0.00 0.00 0.00 3.53
423 452 6.378582 TCTGTGCCGAGACAAATTTATTTTC 58.621 36.000 0.00 0.00 0.00 2.29
424 453 6.206634 TCTCTGTGCCGAGACAAATTTATTTT 59.793 34.615 0.00 0.00 35.23 1.82
432 461 2.839486 ATTCTCTGTGCCGAGACAAA 57.161 45.000 0.00 0.00 39.62 2.83
440 469 5.186996 TCTTTTCACAAATTCTCTGTGCC 57.813 39.130 4.21 0.00 43.20 5.01
442 471 9.304731 TCAATTTCTTTTCACAAATTCTCTGTG 57.695 29.630 2.85 2.85 44.57 3.66
444 473 9.740239 TCTCAATTTCTTTTCACAAATTCTCTG 57.260 29.630 0.00 0.00 31.22 3.35
455 484 6.868622 TCGGGTTTTTCTCAATTTCTTTTCA 58.131 32.000 0.00 0.00 0.00 2.69
457 486 6.756542 CACTCGGGTTTTTCTCAATTTCTTTT 59.243 34.615 0.00 0.00 0.00 2.27
459 488 5.359860 ACACTCGGGTTTTTCTCAATTTCTT 59.640 36.000 0.00 0.00 0.00 2.52
464 493 5.009310 GGTAAACACTCGGGTTTTTCTCAAT 59.991 40.000 2.15 0.00 41.07 2.57
465 494 4.336153 GGTAAACACTCGGGTTTTTCTCAA 59.664 41.667 2.15 0.00 41.07 3.02
466 495 3.878699 GGTAAACACTCGGGTTTTTCTCA 59.121 43.478 2.15 0.00 41.07 3.27
474 513 2.171027 TCAGTTTGGTAAACACTCGGGT 59.829 45.455 7.13 0.00 43.79 5.28
479 518 7.710475 CCAAATGAAATCAGTTTGGTAAACACT 59.290 33.333 18.84 0.00 44.23 3.55
480 519 7.042119 CCCAAATGAAATCAGTTTGGTAAACAC 60.042 37.037 21.97 0.00 46.55 3.32
481 520 6.989169 CCCAAATGAAATCAGTTTGGTAAACA 59.011 34.615 21.97 0.00 46.55 2.83
493 532 2.178580 GAGCCACCCCAAATGAAATCA 58.821 47.619 0.00 0.00 0.00 2.57
504 543 2.046285 CGGTCATTTGAGCCACCCC 61.046 63.158 4.31 0.00 39.23 4.95
507 546 4.900635 ATATTTCGGTCATTTGAGCCAC 57.099 40.909 4.31 0.00 39.23 5.01
508 547 4.097741 CCAATATTTCGGTCATTTGAGCCA 59.902 41.667 4.31 0.00 39.23 4.75
511 550 7.320443 TCTTCCAATATTTCGGTCATTTGAG 57.680 36.000 0.00 0.00 0.00 3.02
521 560 9.632807 TGGTTAACAATTTCTTCCAATATTTCG 57.367 29.630 8.10 0.00 0.00 3.46
526 565 7.327214 GCCATGGTTAACAATTTCTTCCAATA 58.673 34.615 14.67 0.00 0.00 1.90
527 566 6.172630 GCCATGGTTAACAATTTCTTCCAAT 58.827 36.000 14.67 0.00 0.00 3.16
529 568 4.020662 GGCCATGGTTAACAATTTCTTCCA 60.021 41.667 14.67 0.00 0.00 3.53
530 569 4.503910 GGCCATGGTTAACAATTTCTTCC 58.496 43.478 14.67 0.00 0.00 3.46
531 570 4.020662 TGGGCCATGGTTAACAATTTCTTC 60.021 41.667 14.67 0.00 0.00 2.87
532 571 3.906846 TGGGCCATGGTTAACAATTTCTT 59.093 39.130 14.67 0.00 0.00 2.52
533 572 3.515104 CTGGGCCATGGTTAACAATTTCT 59.485 43.478 14.67 0.00 0.00 2.52
537 576 1.194218 GCTGGGCCATGGTTAACAAT 58.806 50.000 14.67 0.00 0.00 2.71
541 580 1.077787 CTCGCTGGGCCATGGTTAA 60.078 57.895 14.67 0.00 0.00 2.01
544 583 1.847798 TAAACTCGCTGGGCCATGGT 61.848 55.000 14.67 0.40 0.00 3.55
545 584 1.077787 TAAACTCGCTGGGCCATGG 60.078 57.895 6.72 7.63 0.00 3.66
554 3893 3.069729 ACTGTTTCTCCACTAAACTCGCT 59.930 43.478 0.00 0.00 37.64 4.93
566 3905 4.935885 CTGAATGCAGTACTGTTTCTCC 57.064 45.455 26.73 12.96 37.37 3.71
632 3971 2.020720 TCTCCAGCTGAAACGCAAAAA 58.979 42.857 17.39 0.00 0.00 1.94
667 4006 2.158696 AGAACTGCTTGCTCTTCTTGGT 60.159 45.455 0.00 0.00 0.00 3.67
755 4094 1.271325 GGTGGTGTGATGATGGTGTGA 60.271 52.381 0.00 0.00 0.00 3.58
987 4340 1.534729 AAATCCCGTGAACTGGAAGC 58.465 50.000 0.00 0.00 37.60 3.86
1008 4361 1.119684 GAGAGAAGAAGAGGAGGGCC 58.880 60.000 0.00 0.00 0.00 5.80
1009 4362 1.859302 TGAGAGAAGAAGAGGAGGGC 58.141 55.000 0.00 0.00 0.00 5.19
1024 4377 0.458543 GCCAGCGACGAAGAATGAGA 60.459 55.000 0.00 0.00 0.00 3.27
1025 4378 0.737367 TGCCAGCGACGAAGAATGAG 60.737 55.000 0.00 0.00 0.00 2.90
1081 4434 1.755621 GCCAATTCAATCCCTCCTCCC 60.756 57.143 0.00 0.00 0.00 4.30
1112 4465 1.002624 TCCCGGACACCAGCATTTC 60.003 57.895 0.73 0.00 0.00 2.17
1219 4572 1.317613 TGTTGCGGCTTTGATTGAGT 58.682 45.000 0.00 0.00 0.00 3.41
1307 4660 4.800993 CAGAACCAAGTATCTTAGAGTGCG 59.199 45.833 0.00 0.00 0.00 5.34
1410 4763 0.390340 CTAGGCGTCAGCTGCAAGAA 60.390 55.000 9.47 0.00 44.37 2.52
1419 4816 2.015736 AATGCTGTTCTAGGCGTCAG 57.984 50.000 0.00 0.00 0.00 3.51
1546 4943 2.568956 TGGCAATAGAAGAGCACTCTGT 59.431 45.455 0.00 0.00 40.36 3.41
1625 5041 2.601240 TGCTCCATGAAACATGGGAA 57.399 45.000 24.40 11.58 39.60 3.97
1627 5043 2.361119 CTGATGCTCCATGAAACATGGG 59.639 50.000 24.40 17.66 39.60 4.00
1628 5044 3.284617 TCTGATGCTCCATGAAACATGG 58.715 45.455 20.62 20.62 40.48 3.66
1661 5077 2.703416 TCTGCAAATTCAGTCGAGCAT 58.297 42.857 0.00 0.00 35.63 3.79
1848 5269 4.977741 CAAAATTTGCAAGGTGCTACAG 57.022 40.909 0.00 0.00 45.31 2.74
1863 5284 7.388460 TGAAACATGAAAAGGTTGCAAAATT 57.612 28.000 0.00 0.00 29.72 1.82
1864 5285 6.998968 TGAAACATGAAAAGGTTGCAAAAT 57.001 29.167 0.00 0.00 29.72 1.82
1865 5286 6.998968 ATGAAACATGAAAAGGTTGCAAAA 57.001 29.167 0.00 0.00 36.21 2.44
1866 5287 7.271511 AGTATGAAACATGAAAAGGTTGCAAA 58.728 30.769 0.00 0.00 36.21 3.68
1867 5288 6.815089 AGTATGAAACATGAAAAGGTTGCAA 58.185 32.000 0.00 0.00 36.21 4.08
1868 5289 6.403866 AGTATGAAACATGAAAAGGTTGCA 57.596 33.333 0.00 0.00 36.99 4.08
1869 5290 7.367285 TGTAGTATGAAACATGAAAAGGTTGC 58.633 34.615 0.00 0.00 0.00 4.17
1870 5291 9.743057 TTTGTAGTATGAAACATGAAAAGGTTG 57.257 29.630 0.00 0.00 0.00 3.77
1871 5292 9.965824 CTTTGTAGTATGAAACATGAAAAGGTT 57.034 29.630 0.00 0.00 0.00 3.50
1872 5293 9.131791 ACTTTGTAGTATGAAACATGAAAAGGT 57.868 29.630 0.00 0.00 31.21 3.50
1920 5341 7.350382 ACACCTCTGTAGAGATTGATAGAGAA 58.650 38.462 10.40 0.00 44.74 2.87
1922 5343 6.770303 TGACACCTCTGTAGAGATTGATAGAG 59.230 42.308 10.40 0.00 44.74 2.43
1925 5346 6.322456 CCTTGACACCTCTGTAGAGATTGATA 59.678 42.308 10.40 0.80 44.74 2.15
1926 5347 5.128499 CCTTGACACCTCTGTAGAGATTGAT 59.872 44.000 10.40 0.00 44.74 2.57
1927 5348 4.464244 CCTTGACACCTCTGTAGAGATTGA 59.536 45.833 10.40 0.00 44.74 2.57
1928 5349 4.382470 CCCTTGACACCTCTGTAGAGATTG 60.382 50.000 10.40 9.11 44.74 2.67
1929 5350 3.772025 CCCTTGACACCTCTGTAGAGATT 59.228 47.826 10.40 0.00 44.74 2.40
2042 5463 1.205655 CTCTTGGCGGTTCTCTCATGA 59.794 52.381 0.00 0.00 0.00 3.07
2045 5466 1.293498 GCTCTTGGCGGTTCTCTCA 59.707 57.895 0.00 0.00 0.00 3.27
2072 5493 2.582978 GTAAGGAGGCCGGTCCAC 59.417 66.667 13.29 8.57 39.34 4.02
2090 5511 2.955660 AGCTAGGAAGGAGATCTCAACG 59.044 50.000 23.85 6.13 0.00 4.10
2144 5565 3.181475 GGAGACGTCCTTGCTTGATCATA 60.181 47.826 13.01 0.00 40.17 2.15
2174 5595 4.608951 GATTATCGTTCGGTCTTAGCTGT 58.391 43.478 0.00 0.00 0.00 4.40
2251 5672 7.759433 GTCTTCTGTCTTCTCTTATTTGGAGAG 59.241 40.741 0.00 0.00 40.35 3.20
2255 5676 7.593875 CAGTCTTCTGTCTTCTCTTATTTGG 57.406 40.000 0.00 0.00 36.97 3.28
2276 5697 7.114754 ACAATATCCATCAATCTTCACACAGT 58.885 34.615 0.00 0.00 0.00 3.55
2278 5699 9.112725 CTTACAATATCCATCAATCTTCACACA 57.887 33.333 0.00 0.00 0.00 3.72
2297 5718 1.280998 CCCCTTGACCGACCTTACAAT 59.719 52.381 0.00 0.00 0.00 2.71
2302 5723 0.252742 ATCTCCCCTTGACCGACCTT 60.253 55.000 0.00 0.00 0.00 3.50
2307 5728 1.200519 TTACCATCTCCCCTTGACCG 58.799 55.000 0.00 0.00 0.00 4.79
2344 5765 5.809562 CACTTGTCAAACCAAGCAATTTACA 59.190 36.000 1.04 0.00 44.55 2.41
2349 5770 3.784338 CACACTTGTCAAACCAAGCAAT 58.216 40.909 1.04 0.00 44.55 3.56
2363 5784 3.129852 TCTTGTTCAAACGCACACTTG 57.870 42.857 0.00 0.00 0.00 3.16
2401 5822 1.421268 TCCTCTGCAACCTCAACACAT 59.579 47.619 0.00 0.00 0.00 3.21
2411 5832 1.742268 GAGCTTCCAATCCTCTGCAAC 59.258 52.381 0.00 0.00 0.00 4.17
2428 5849 4.193826 TCTCAAGATACAACACCAGAGC 57.806 45.455 0.00 0.00 0.00 4.09
2442 5863 9.784531 AACAAGATCTAAAATCACTTCTCAAGA 57.215 29.630 0.00 0.00 0.00 3.02
2489 5910 2.957402 ATCTGACTGCTTCCCACAAA 57.043 45.000 0.00 0.00 0.00 2.83
2546 5967 7.653713 TCAACTACAGTTCTGAAACTTCTGATC 59.346 37.037 11.35 0.00 43.28 2.92
2567 5988 4.666512 AGGATTACAGGTGCATTTCAACT 58.333 39.130 0.00 0.00 45.42 3.16
2585 6006 5.363562 TGTTGCATAGAGAACATGAGGAT 57.636 39.130 0.00 0.00 0.00 3.24
2588 6009 7.317842 AGAAATGTTGCATAGAGAACATGAG 57.682 36.000 0.00 0.00 41.00 2.90
2598 6019 6.017400 ACAACCTGAAGAAATGTTGCATAG 57.983 37.500 0.00 0.00 41.28 2.23
2600 6021 4.341806 TGACAACCTGAAGAAATGTTGCAT 59.658 37.500 0.00 0.00 41.28 3.96
2652 6091 8.607713 TCATATTAAACTCAACAAGGAGGGTAA 58.392 33.333 0.00 0.00 39.27 2.85
2653 6092 8.153221 TCATATTAAACTCAACAAGGAGGGTA 57.847 34.615 0.00 0.00 39.27 3.69
2709 6154 5.163683 CCATTAAGCAGCAGATATGGCATAC 60.164 44.000 9.83 4.30 0.00 2.39
2829 6274 6.429385 AGAAGCTTTTAGTTGTCATCTTCAGG 59.571 38.462 0.00 0.00 33.23 3.86
2841 6286 6.015180 TGCCATGAATCAAGAAGCTTTTAGTT 60.015 34.615 0.00 0.00 0.00 2.24
2849 6294 3.734293 GCTCTTGCCATGAATCAAGAAGC 60.734 47.826 18.68 18.46 45.36 3.86
2851 6296 3.442625 CAGCTCTTGCCATGAATCAAGAA 59.557 43.478 18.68 8.84 45.36 2.52
2891 6336 3.653539 TCGCCATTTTAGCTATCGCTA 57.346 42.857 0.00 0.00 46.79 4.26
3123 6568 1.003839 GCTCACCACCATCCGTGAA 60.004 57.895 0.00 0.00 46.20 3.18
3135 6580 2.258726 GGAAACCCGTGTGCTCACC 61.259 63.158 13.00 0.00 41.09 4.02
3184 6629 9.098355 TCTCATTGATAACTAACAGCATTACAC 57.902 33.333 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.