Multiple sequence alignment - TraesCS3A01G373300

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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 TraesCS3A01G373300 chr3A 100.000 2894 0 0 1 2894 623361254 623364147 0.000000e+00 5345.0
1 TraesCS3A01G373300 chr3A 91.699 2313 146 18 591 2894 623354103 623356378 0.000000e+00 3166.0
2 TraesCS3A01G373300 chr3A 88.298 2068 191 25 831 2894 623229455 623231475 0.000000e+00 2431.0
3 TraesCS3A01G373300 chr3A 89.911 1348 121 8 976 2320 623340338 623341673 0.000000e+00 1722.0
4 TraesCS3A01G373300 chr3A 90.000 1340 116 7 578 1913 623389223 623390548 0.000000e+00 1716.0
5 TraesCS3A01G373300 chr3A 86.833 562 50 2 2319 2880 623341910 623342447 8.870000e-170 606.0
6 TraesCS3A01G373300 chr3B 90.316 2313 180 23 578 2880 640700287 640702565 0.000000e+00 2990.0
7 TraesCS3A01G373300 chr3B 92.340 1906 143 3 976 2880 640693494 640695397 0.000000e+00 2708.0
8 TraesCS3A01G373300 chr3B 90.148 1553 123 12 772 2320 640708111 640709637 0.000000e+00 1993.0
9 TraesCS3A01G373300 chr3B 89.925 1330 113 13 591 1913 640831858 640833173 0.000000e+00 1694.0
10 TraesCS3A01G373300 chr3B 84.655 580 47 13 2 569 753167762 753167213 9.120000e-150 540.0
11 TraesCS3A01G373300 chr3B 92.059 340 27 0 2541 2880 640766043 640766382 2.020000e-131 479.0
12 TraesCS3A01G373300 chr3B 86.711 301 35 4 1 299 460239975 460239678 2.150000e-86 329.0
13 TraesCS3A01G373300 chr3B 91.667 180 14 1 342 520 460181739 460181560 6.190000e-62 248.0
14 TraesCS3A01G373300 chr3B 81.778 225 33 7 1 221 811131367 811131587 6.370000e-42 182.0
15 TraesCS3A01G373300 chr3B 90.741 54 4 1 520 572 814628458 814628405 1.440000e-08 71.3
16 TraesCS3A01G373300 chr3D 92.192 2126 141 13 775 2894 480357787 480359893 0.000000e+00 2983.0
17 TraesCS3A01G373300 chr3D 91.649 1904 141 12 995 2894 480157923 480159812 0.000000e+00 2619.0
18 TraesCS3A01G373300 chr3D 90.265 1736 119 23 582 2312 480366335 480368025 0.000000e+00 2224.0
19 TraesCS3A01G373300 chr3D 94.095 1321 77 1 575 1895 480375396 480376715 0.000000e+00 2006.0
20 TraesCS3A01G373300 chr3D 90.104 576 54 2 2303 2878 480371386 480371958 0.000000e+00 745.0
21 TraesCS3A01G373300 chr3D 84.694 686 63 18 2201 2880 480311092 480311741 0.000000e+00 647.0
22 TraesCS3A01G373300 chr3D 85.986 421 38 8 1996 2409 480310690 480311096 5.730000e-117 431.0
23 TraesCS3A01G373300 chr3D 78.041 592 89 27 1 560 604140695 604141277 4.620000e-88 335.0
24 TraesCS3A01G373300 chr5B 84.642 586 62 17 2 570 689222811 689223385 2.520000e-155 558.0
25 TraesCS3A01G373300 chr5B 80.734 545 68 19 10 524 537501163 537501700 9.720000e-105 390.0
26 TraesCS3A01G373300 chr6B 81.450 593 71 19 10 571 712321928 712322512 1.580000e-122 449.0
27 TraesCS3A01G373300 chr6A 80.508 590 75 23 12 569 154421518 154422099 1.600000e-112 416.0
28 TraesCS3A01G373300 chr2A 76.382 597 86 38 14 572 666317890 666317311 1.320000e-68 270.0
29 TraesCS3A01G373300 chr6D 76.446 484 75 24 121 572 222660909 222661385 2.900000e-55 226.0
30 TraesCS3A01G373300 chr2D 76.446 484 74 22 121 572 606699011 606699486 2.900000e-55 226.0
31 TraesCS3A01G373300 chr5A 87.273 55 7 0 507 561 177580726 177580780 2.410000e-06 63.9


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 TraesCS3A01G373300 chr3A 623361254 623364147 2893 False 5345.000000 5345 100.000 1 2894 1 chr3A.!!$F3 2893
1 TraesCS3A01G373300 chr3A 623354103 623356378 2275 False 3166.000000 3166 91.699 591 2894 1 chr3A.!!$F2 2303
2 TraesCS3A01G373300 chr3A 623229455 623231475 2020 False 2431.000000 2431 88.298 831 2894 1 chr3A.!!$F1 2063
3 TraesCS3A01G373300 chr3A 623389223 623390548 1325 False 1716.000000 1716 90.000 578 1913 1 chr3A.!!$F4 1335
4 TraesCS3A01G373300 chr3A 623340338 623342447 2109 False 1164.000000 1722 88.372 976 2880 2 chr3A.!!$F5 1904
5 TraesCS3A01G373300 chr3B 640700287 640702565 2278 False 2990.000000 2990 90.316 578 2880 1 chr3B.!!$F2 2302
6 TraesCS3A01G373300 chr3B 640693494 640695397 1903 False 2708.000000 2708 92.340 976 2880 1 chr3B.!!$F1 1904
7 TraesCS3A01G373300 chr3B 640708111 640709637 1526 False 1993.000000 1993 90.148 772 2320 1 chr3B.!!$F3 1548
8 TraesCS3A01G373300 chr3B 640831858 640833173 1315 False 1694.000000 1694 89.925 591 1913 1 chr3B.!!$F5 1322
9 TraesCS3A01G373300 chr3B 753167213 753167762 549 True 540.000000 540 84.655 2 569 1 chr3B.!!$R3 567
10 TraesCS3A01G373300 chr3D 480357787 480359893 2106 False 2983.000000 2983 92.192 775 2894 1 chr3D.!!$F2 2119
11 TraesCS3A01G373300 chr3D 480157923 480159812 1889 False 2619.000000 2619 91.649 995 2894 1 chr3D.!!$F1 1899
12 TraesCS3A01G373300 chr3D 480366335 480376715 10380 False 1658.333333 2224 91.488 575 2878 3 chr3D.!!$F5 2303
13 TraesCS3A01G373300 chr3D 480310690 480311741 1051 False 539.000000 647 85.340 1996 2880 2 chr3D.!!$F4 884
14 TraesCS3A01G373300 chr3D 604140695 604141277 582 False 335.000000 335 78.041 1 560 1 chr3D.!!$F3 559
15 TraesCS3A01G373300 chr5B 689222811 689223385 574 False 558.000000 558 84.642 2 570 1 chr5B.!!$F2 568
16 TraesCS3A01G373300 chr5B 537501163 537501700 537 False 390.000000 390 80.734 10 524 1 chr5B.!!$F1 514
17 TraesCS3A01G373300 chr6B 712321928 712322512 584 False 449.000000 449 81.450 10 571 1 chr6B.!!$F1 561
18 TraesCS3A01G373300 chr6A 154421518 154422099 581 False 416.000000 416 80.508 12 569 1 chr6A.!!$F1 557
19 TraesCS3A01G373300 chr2A 666317311 666317890 579 True 270.000000 270 76.382 14 572 1 chr2A.!!$R1 558

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
311 333 0.033796 ATGCATCTGTCAAGGGGTGG 60.034 55.0 0.00 0.0 0.0 4.61 F
347 369 0.105039 GATGAGGAGGACGGCGAATT 59.895 55.0 16.62 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 1856 0.806868 CTTGATGAGCGGCAACACAT 59.193 50.000 1.45 2.27 0.00 3.21 R
2140 2228 4.307432 ACTAGAACCACAGTTGATTCACG 58.693 43.478 0.00 0.00 35.94 4.35 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
40 43 5.164954 GCTGGAACCGTATTAATTTTTGCA 58.835 37.500 0.00 0.00 0.00 4.08
56 60 6.523676 TTTTTGCAGGAATCGTGAATTTTC 57.476 33.333 7.17 0.00 0.00 2.29
102 108 2.197577 GCTAGGTGCTCAAGTCGATTC 58.802 52.381 0.00 0.00 38.95 2.52
116 122 2.225727 GTCGATTCGCTGGAAACCTTTT 59.774 45.455 0.00 0.00 35.40 2.27
117 123 2.882137 TCGATTCGCTGGAAACCTTTTT 59.118 40.909 0.00 0.00 35.40 1.94
118 124 2.979813 CGATTCGCTGGAAACCTTTTTG 59.020 45.455 0.00 0.00 35.40 2.44
156 163 4.934515 CCAATTTTTGGTTTTGCTGCAAT 58.065 34.783 16.77 0.00 45.93 3.56
224 232 1.961277 CAAGTGGTGCAGGTCGACC 60.961 63.158 27.67 27.67 0.00 4.79
282 304 1.738099 GAGTTGCTGCATCCGACGT 60.738 57.895 1.84 0.00 0.00 4.34
283 305 1.291877 GAGTTGCTGCATCCGACGTT 61.292 55.000 1.84 0.00 0.00 3.99
284 306 0.884704 AGTTGCTGCATCCGACGTTT 60.885 50.000 1.84 0.00 0.00 3.60
285 307 0.725784 GTTGCTGCATCCGACGTTTG 60.726 55.000 1.84 0.00 0.00 2.93
286 308 1.851021 TTGCTGCATCCGACGTTTGG 61.851 55.000 1.84 1.53 0.00 3.28
287 309 2.480555 CTGCATCCGACGTTTGGC 59.519 61.111 3.05 0.00 0.00 4.52
288 310 2.281139 TGCATCCGACGTTTGGCA 60.281 55.556 3.05 0.66 0.00 4.92
289 311 2.244436 CTGCATCCGACGTTTGGCAG 62.244 60.000 11.71 11.71 42.14 4.85
290 312 2.032634 GCATCCGACGTTTGGCAGA 61.033 57.895 3.05 0.00 0.00 4.26
291 313 1.970917 GCATCCGACGTTTGGCAGAG 61.971 60.000 3.05 0.00 0.00 3.35
292 314 0.389817 CATCCGACGTTTGGCAGAGA 60.390 55.000 3.05 0.00 0.00 3.10
293 315 0.537188 ATCCGACGTTTGGCAGAGAT 59.463 50.000 3.05 0.00 0.00 2.75
294 316 0.389817 TCCGACGTTTGGCAGAGATG 60.390 55.000 3.05 0.00 0.00 2.90
295 317 1.421485 CGACGTTTGGCAGAGATGC 59.579 57.895 0.00 0.00 0.00 3.91
296 318 1.291184 CGACGTTTGGCAGAGATGCA 61.291 55.000 2.29 0.00 36.33 3.96
297 319 1.089920 GACGTTTGGCAGAGATGCAT 58.910 50.000 0.00 0.00 36.33 3.96
298 320 1.063174 GACGTTTGGCAGAGATGCATC 59.937 52.381 19.37 19.37 36.33 3.91
299 321 1.339438 ACGTTTGGCAGAGATGCATCT 60.339 47.619 29.09 29.09 40.50 2.90
301 323 2.089980 GTTTGGCAGAGATGCATCTGT 58.910 47.619 33.33 26.66 46.93 3.41
306 328 1.941294 GCAGAGATGCATCTGTCAAGG 59.059 52.381 33.33 17.74 46.93 3.61
307 329 2.562635 CAGAGATGCATCTGTCAAGGG 58.437 52.381 33.33 13.32 41.52 3.95
308 330 1.489649 AGAGATGCATCTGTCAAGGGG 59.510 52.381 33.33 0.00 37.25 4.79
309 331 1.211457 GAGATGCATCTGTCAAGGGGT 59.789 52.381 33.33 5.65 37.25 4.95
310 332 1.064906 AGATGCATCTGTCAAGGGGTG 60.065 52.381 28.21 0.00 35.42 4.61
311 333 0.033796 ATGCATCTGTCAAGGGGTGG 60.034 55.000 0.00 0.00 0.00 4.61
312 334 1.380302 GCATCTGTCAAGGGGTGGT 59.620 57.895 0.00 0.00 0.00 4.16
313 335 0.962356 GCATCTGTCAAGGGGTGGTG 60.962 60.000 0.00 0.00 0.00 4.17
314 336 0.962356 CATCTGTCAAGGGGTGGTGC 60.962 60.000 0.00 0.00 0.00 5.01
315 337 1.136329 ATCTGTCAAGGGGTGGTGCT 61.136 55.000 0.00 0.00 0.00 4.40
316 338 1.601759 CTGTCAAGGGGTGGTGCTG 60.602 63.158 0.00 0.00 0.00 4.41
317 339 2.055689 CTGTCAAGGGGTGGTGCTGA 62.056 60.000 0.00 0.00 0.00 4.26
318 340 1.150536 GTCAAGGGGTGGTGCTGAA 59.849 57.895 0.00 0.00 0.00 3.02
319 341 0.467290 GTCAAGGGGTGGTGCTGAAA 60.467 55.000 0.00 0.00 0.00 2.69
320 342 0.467290 TCAAGGGGTGGTGCTGAAAC 60.467 55.000 0.00 0.00 0.00 2.78
321 343 1.528309 AAGGGGTGGTGCTGAAACG 60.528 57.895 0.00 0.00 0.00 3.60
322 344 1.990160 AAGGGGTGGTGCTGAAACGA 61.990 55.000 0.00 0.00 0.00 3.85
323 345 2.258726 GGGGTGGTGCTGAAACGAC 61.259 63.158 0.00 0.00 0.00 4.34
324 346 2.604174 GGGTGGTGCTGAAACGACG 61.604 63.158 0.00 0.00 30.24 5.12
325 347 2.604174 GGTGGTGCTGAAACGACGG 61.604 63.158 0.00 0.00 30.24 4.79
326 348 2.280524 TGGTGCTGAAACGACGGG 60.281 61.111 0.00 0.00 0.00 5.28
327 349 2.029964 GGTGCTGAAACGACGGGA 59.970 61.111 0.00 0.00 0.00 5.14
328 350 2.027625 GGTGCTGAAACGACGGGAG 61.028 63.158 0.00 0.00 0.00 4.30
329 351 1.006571 GTGCTGAAACGACGGGAGA 60.007 57.895 0.00 0.00 0.00 3.71
330 352 0.389948 GTGCTGAAACGACGGGAGAT 60.390 55.000 0.00 0.00 0.00 2.75
331 353 0.389817 TGCTGAAACGACGGGAGATG 60.390 55.000 0.00 0.00 0.00 2.90
332 354 0.108804 GCTGAAACGACGGGAGATGA 60.109 55.000 0.00 0.00 0.00 2.92
333 355 1.914634 CTGAAACGACGGGAGATGAG 58.085 55.000 0.00 0.00 0.00 2.90
334 356 0.530744 TGAAACGACGGGAGATGAGG 59.469 55.000 0.00 0.00 0.00 3.86
335 357 0.815734 GAAACGACGGGAGATGAGGA 59.184 55.000 0.00 0.00 0.00 3.71
336 358 0.818296 AAACGACGGGAGATGAGGAG 59.182 55.000 0.00 0.00 0.00 3.69
337 359 1.038130 AACGACGGGAGATGAGGAGG 61.038 60.000 0.00 0.00 0.00 4.30
338 360 1.152943 CGACGGGAGATGAGGAGGA 60.153 63.158 0.00 0.00 0.00 3.71
339 361 1.448922 CGACGGGAGATGAGGAGGAC 61.449 65.000 0.00 0.00 0.00 3.85
340 362 1.448922 GACGGGAGATGAGGAGGACG 61.449 65.000 0.00 0.00 0.00 4.79
341 363 2.196925 CGGGAGATGAGGAGGACGG 61.197 68.421 0.00 0.00 0.00 4.79
342 364 2.503382 GGGAGATGAGGAGGACGGC 61.503 68.421 0.00 0.00 0.00 5.68
343 365 2.725008 GAGATGAGGAGGACGGCG 59.275 66.667 4.80 4.80 0.00 6.46
344 366 1.824329 GAGATGAGGAGGACGGCGA 60.824 63.158 16.62 0.00 0.00 5.54
345 367 1.379977 AGATGAGGAGGACGGCGAA 60.380 57.895 16.62 0.00 0.00 4.70
346 368 0.757188 AGATGAGGAGGACGGCGAAT 60.757 55.000 16.62 0.00 0.00 3.34
347 369 0.105039 GATGAGGAGGACGGCGAATT 59.895 55.000 16.62 0.00 0.00 2.17
348 370 0.179073 ATGAGGAGGACGGCGAATTG 60.179 55.000 16.62 0.00 0.00 2.32
349 371 1.521681 GAGGAGGACGGCGAATTGG 60.522 63.158 16.62 0.00 0.00 3.16
350 372 1.956629 GAGGAGGACGGCGAATTGGA 61.957 60.000 16.62 0.00 0.00 3.53
351 373 1.521681 GGAGGACGGCGAATTGGAG 60.522 63.158 16.62 0.00 0.00 3.86
352 374 2.125106 AGGACGGCGAATTGGAGC 60.125 61.111 16.62 0.00 0.00 4.70
359 381 3.264897 CGAATTGGAGCCGCGGAG 61.265 66.667 33.48 2.86 0.00 4.63
360 382 2.186903 GAATTGGAGCCGCGGAGA 59.813 61.111 33.48 9.23 0.00 3.71
361 383 1.884926 GAATTGGAGCCGCGGAGAG 60.885 63.158 33.48 1.43 0.00 3.20
362 384 2.298158 GAATTGGAGCCGCGGAGAGA 62.298 60.000 33.48 10.48 0.00 3.10
363 385 2.303549 AATTGGAGCCGCGGAGAGAG 62.304 60.000 33.48 0.01 0.00 3.20
382 404 4.933064 CGGCGAGCGGTGGAGATC 62.933 72.222 0.00 0.00 0.00 2.75
383 405 4.593864 GGCGAGCGGTGGAGATCC 62.594 72.222 0.00 0.00 0.00 3.36
385 407 4.271816 CGAGCGGTGGAGATCCGG 62.272 72.222 0.00 0.00 46.90 5.14
386 408 4.593864 GAGCGGTGGAGATCCGGC 62.594 72.222 0.00 0.00 46.90 6.13
391 413 4.222847 GTGGAGATCCGGCGGGTC 62.223 72.222 31.31 31.31 39.43 4.46
392 414 4.770362 TGGAGATCCGGCGGGTCA 62.770 66.667 37.88 18.38 39.43 4.02
393 415 3.917760 GGAGATCCGGCGGGTCAG 61.918 72.222 37.88 7.95 33.83 3.51
394 416 3.917760 GAGATCCGGCGGGTCAGG 61.918 72.222 37.88 7.14 33.83 3.86
395 417 4.779733 AGATCCGGCGGGTCAGGT 62.780 66.667 37.88 17.73 33.83 4.00
396 418 4.222847 GATCCGGCGGGTCAGGTC 62.223 72.222 33.11 14.14 33.83 3.85
403 425 4.477975 CGGGTCAGGTCGCTCGTC 62.478 72.222 0.00 0.00 0.00 4.20
404 426 4.131088 GGGTCAGGTCGCTCGTCC 62.131 72.222 0.00 0.00 0.00 4.79
405 427 3.371063 GGTCAGGTCGCTCGTCCA 61.371 66.667 8.14 0.00 0.00 4.02
406 428 2.711922 GGTCAGGTCGCTCGTCCAT 61.712 63.158 8.14 0.00 0.00 3.41
407 429 1.517257 GTCAGGTCGCTCGTCCATG 60.517 63.158 8.14 4.23 0.00 3.66
408 430 2.202797 CAGGTCGCTCGTCCATGG 60.203 66.667 4.97 4.97 0.00 3.66
409 431 2.680352 AGGTCGCTCGTCCATGGT 60.680 61.111 12.58 0.00 0.00 3.55
410 432 2.509336 GGTCGCTCGTCCATGGTG 60.509 66.667 12.58 6.00 0.00 4.17
411 433 3.188786 GTCGCTCGTCCATGGTGC 61.189 66.667 12.58 11.10 0.00 5.01
412 434 3.381983 TCGCTCGTCCATGGTGCT 61.382 61.111 12.58 0.00 0.00 4.40
413 435 2.887568 CGCTCGTCCATGGTGCTC 60.888 66.667 12.58 0.52 0.00 4.26
414 436 2.887568 GCTCGTCCATGGTGCTCG 60.888 66.667 12.58 12.45 0.00 5.03
415 437 2.887568 CTCGTCCATGGTGCTCGC 60.888 66.667 12.58 0.00 0.00 5.03
416 438 3.647649 CTCGTCCATGGTGCTCGCA 62.648 63.158 12.58 0.00 0.00 5.10
417 439 3.490759 CGTCCATGGTGCTCGCAC 61.491 66.667 12.58 13.37 45.49 5.34
425 447 3.264897 GTGCTCGCACCCGCTATG 61.265 66.667 10.82 0.00 40.79 2.23
426 448 3.770040 TGCTCGCACCCGCTATGT 61.770 61.111 0.00 0.00 35.30 2.29
427 449 3.264897 GCTCGCACCCGCTATGTG 61.265 66.667 0.00 0.00 36.79 3.21
428 450 2.184322 CTCGCACCCGCTATGTGT 59.816 61.111 0.00 0.00 36.11 3.72
429 451 2.125713 TCGCACCCGCTATGTGTG 60.126 61.111 0.00 0.00 43.75 3.82
432 454 3.799753 CACCCGCTATGTGTGCTC 58.200 61.111 0.00 0.00 0.00 4.26
433 455 2.167219 CACCCGCTATGTGTGCTCG 61.167 63.158 0.00 0.00 0.00 5.03
434 456 3.264897 CCCGCTATGTGTGCTCGC 61.265 66.667 0.00 0.00 0.00 5.03
435 457 3.620428 CCGCTATGTGTGCTCGCG 61.620 66.667 0.00 0.00 43.08 5.87
436 458 2.880879 CGCTATGTGTGCTCGCGT 60.881 61.111 5.77 0.00 39.07 6.01
437 459 2.697425 GCTATGTGTGCTCGCGTG 59.303 61.111 5.77 4.44 0.00 5.34
438 460 1.805539 GCTATGTGTGCTCGCGTGA 60.806 57.895 13.13 0.00 0.00 4.35
439 461 1.148157 GCTATGTGTGCTCGCGTGAT 61.148 55.000 13.13 0.00 0.00 3.06
440 462 1.280982 CTATGTGTGCTCGCGTGATT 58.719 50.000 13.13 0.00 0.00 2.57
441 463 1.660607 CTATGTGTGCTCGCGTGATTT 59.339 47.619 13.13 0.00 0.00 2.17
442 464 0.166597 ATGTGTGCTCGCGTGATTTG 59.833 50.000 13.13 0.00 0.00 2.32
443 465 1.793613 GTGTGCTCGCGTGATTTGC 60.794 57.895 13.13 0.00 0.00 3.68
444 466 2.250237 TGTGCTCGCGTGATTTGCA 61.250 52.632 13.13 7.23 0.00 4.08
445 467 1.135315 GTGCTCGCGTGATTTGCAT 59.865 52.632 13.13 0.00 36.04 3.96
446 468 0.373370 GTGCTCGCGTGATTTGCATA 59.627 50.000 13.13 0.00 36.04 3.14
447 469 0.652071 TGCTCGCGTGATTTGCATAG 59.348 50.000 13.13 0.00 0.00 2.23
448 470 0.652592 GCTCGCGTGATTTGCATAGT 59.347 50.000 13.13 0.00 0.00 2.12
449 471 1.858458 GCTCGCGTGATTTGCATAGTA 59.142 47.619 13.13 0.00 0.00 1.82
450 472 2.097202 GCTCGCGTGATTTGCATAGTAG 60.097 50.000 13.13 0.00 0.00 2.57
451 473 3.372060 CTCGCGTGATTTGCATAGTAGA 58.628 45.455 5.77 0.00 0.00 2.59
452 474 3.372060 TCGCGTGATTTGCATAGTAGAG 58.628 45.455 5.77 0.00 0.00 2.43
453 475 3.066203 TCGCGTGATTTGCATAGTAGAGA 59.934 43.478 5.77 0.00 0.00 3.10
454 476 3.796717 CGCGTGATTTGCATAGTAGAGAA 59.203 43.478 0.00 0.00 0.00 2.87
455 477 4.317418 CGCGTGATTTGCATAGTAGAGAAC 60.317 45.833 0.00 0.00 0.00 3.01
456 478 4.317418 GCGTGATTTGCATAGTAGAGAACG 60.317 45.833 0.00 0.00 0.00 3.95
457 479 4.207224 CGTGATTTGCATAGTAGAGAACGG 59.793 45.833 0.00 0.00 0.00 4.44
458 480 4.025647 GTGATTTGCATAGTAGAGAACGGC 60.026 45.833 0.00 0.00 0.00 5.68
459 481 3.603158 TTTGCATAGTAGAGAACGGCA 57.397 42.857 0.00 0.00 34.30 5.69
460 482 3.819564 TTGCATAGTAGAGAACGGCAT 57.180 42.857 0.00 0.00 35.48 4.40
461 483 3.097877 TGCATAGTAGAGAACGGCATG 57.902 47.619 0.00 0.00 32.22 4.06
462 484 2.224042 TGCATAGTAGAGAACGGCATGG 60.224 50.000 0.00 0.00 32.22 3.66
463 485 2.224066 GCATAGTAGAGAACGGCATGGT 60.224 50.000 0.00 0.00 0.00 3.55
464 486 3.384668 CATAGTAGAGAACGGCATGGTG 58.615 50.000 0.00 0.00 0.00 4.17
465 487 0.537188 AGTAGAGAACGGCATGGTGG 59.463 55.000 0.00 0.00 0.00 4.61
466 488 0.462047 GTAGAGAACGGCATGGTGGG 60.462 60.000 0.00 0.00 0.00 4.61
467 489 1.622607 TAGAGAACGGCATGGTGGGG 61.623 60.000 0.00 0.00 0.00 4.96
468 490 2.933287 AGAACGGCATGGTGGGGA 60.933 61.111 0.00 0.00 0.00 4.81
469 491 2.270874 GAGAACGGCATGGTGGGGAT 62.271 60.000 0.00 0.00 0.00 3.85
470 492 2.044053 AACGGCATGGTGGGGATG 60.044 61.111 0.00 0.00 0.00 3.51
471 493 2.550699 GAACGGCATGGTGGGGATGA 62.551 60.000 0.00 0.00 0.00 2.92
472 494 2.148723 AACGGCATGGTGGGGATGAA 62.149 55.000 0.00 0.00 0.00 2.57
473 495 1.379710 CGGCATGGTGGGGATGAAA 60.380 57.895 0.00 0.00 0.00 2.69
474 496 1.386525 CGGCATGGTGGGGATGAAAG 61.387 60.000 0.00 0.00 0.00 2.62
475 497 1.679559 GGCATGGTGGGGATGAAAGC 61.680 60.000 0.00 0.00 0.00 3.51
476 498 2.008268 GCATGGTGGGGATGAAAGCG 62.008 60.000 0.00 0.00 0.00 4.68
477 499 0.680921 CATGGTGGGGATGAAAGCGT 60.681 55.000 0.00 0.00 0.00 5.07
478 500 0.394352 ATGGTGGGGATGAAAGCGTC 60.394 55.000 0.00 0.00 0.00 5.19
487 509 4.802876 GGATGAAAGCGTCCTAAATCTG 57.197 45.455 0.00 0.00 45.15 2.90
488 510 4.442706 GGATGAAAGCGTCCTAAATCTGA 58.557 43.478 0.00 0.00 45.15 3.27
489 511 4.271291 GGATGAAAGCGTCCTAAATCTGAC 59.729 45.833 0.00 0.00 45.15 3.51
498 520 5.720261 GTCCTAAATCTGACGGCTAAAAG 57.280 43.478 0.00 0.00 0.00 2.27
499 521 5.416947 GTCCTAAATCTGACGGCTAAAAGA 58.583 41.667 0.00 0.00 0.00 2.52
500 522 5.520649 GTCCTAAATCTGACGGCTAAAAGAG 59.479 44.000 0.00 0.00 0.00 2.85
501 523 5.187186 TCCTAAATCTGACGGCTAAAAGAGT 59.813 40.000 0.00 0.00 0.00 3.24
502 524 5.875359 CCTAAATCTGACGGCTAAAAGAGTT 59.125 40.000 0.00 0.00 32.35 3.01
503 525 6.371825 CCTAAATCTGACGGCTAAAAGAGTTT 59.628 38.462 0.00 0.00 30.44 2.66
504 526 6.635030 AAATCTGACGGCTAAAAGAGTTTT 57.365 33.333 0.00 0.00 36.67 2.43
505 527 7.739498 AAATCTGACGGCTAAAAGAGTTTTA 57.261 32.000 0.00 0.00 34.19 1.52
506 528 7.739498 AATCTGACGGCTAAAAGAGTTTTAA 57.261 32.000 0.00 0.00 34.93 1.52
507 529 7.923414 ATCTGACGGCTAAAAGAGTTTTAAT 57.077 32.000 0.00 0.00 34.93 1.40
508 530 7.360575 TCTGACGGCTAAAAGAGTTTTAATC 57.639 36.000 0.00 0.00 34.93 1.75
509 531 6.932400 TCTGACGGCTAAAAGAGTTTTAATCA 59.068 34.615 0.00 0.00 34.93 2.57
510 532 7.117812 TCTGACGGCTAAAAGAGTTTTAATCAG 59.882 37.037 0.00 11.58 34.93 2.90
511 533 6.932400 TGACGGCTAAAAGAGTTTTAATCAGA 59.068 34.615 0.00 0.00 34.93 3.27
512 534 7.095355 TGACGGCTAAAAGAGTTTTAATCAGAC 60.095 37.037 0.00 0.00 34.93 3.51
513 535 6.128634 ACGGCTAAAAGAGTTTTAATCAGACG 60.129 38.462 6.41 6.41 35.48 4.18
514 536 6.128634 CGGCTAAAAGAGTTTTAATCAGACGT 60.129 38.462 0.00 0.00 34.93 4.34
515 537 7.062605 CGGCTAAAAGAGTTTTAATCAGACGTA 59.937 37.037 0.00 0.00 34.93 3.57
516 538 8.167345 GGCTAAAAGAGTTTTAATCAGACGTAC 58.833 37.037 0.00 0.00 34.93 3.67
517 539 8.706035 GCTAAAAGAGTTTTAATCAGACGTACA 58.294 33.333 0.00 0.00 34.93 2.90
519 541 7.653767 AAAGAGTTTTAATCAGACGTACAGG 57.346 36.000 0.00 0.00 0.00 4.00
520 542 5.721232 AGAGTTTTAATCAGACGTACAGGG 58.279 41.667 0.00 0.00 0.00 4.45
521 543 5.245526 AGAGTTTTAATCAGACGTACAGGGT 59.754 40.000 0.00 0.00 0.00 4.34
522 544 5.235516 AGTTTTAATCAGACGTACAGGGTG 58.764 41.667 0.00 0.00 0.00 4.61
523 545 4.877378 TTTAATCAGACGTACAGGGTGT 57.123 40.909 0.00 0.00 0.00 4.16
524 546 2.743636 AATCAGACGTACAGGGTGTG 57.256 50.000 0.00 0.00 0.00 3.82
525 547 0.895530 ATCAGACGTACAGGGTGTGG 59.104 55.000 0.00 0.00 30.32 4.17
526 548 1.374252 CAGACGTACAGGGTGTGGC 60.374 63.158 0.00 0.00 0.00 5.01
527 549 2.047560 GACGTACAGGGTGTGGCC 60.048 66.667 0.00 0.00 0.00 5.36
528 550 3.927163 GACGTACAGGGTGTGGCCG 62.927 68.421 0.00 0.00 38.44 6.13
529 551 4.752879 CGTACAGGGTGTGGCCGG 62.753 72.222 0.00 0.00 38.44 6.13
535 557 4.354162 GGGTGTGGCCGGCCTAAA 62.354 66.667 43.34 26.95 38.44 1.85
536 558 2.044352 GGTGTGGCCGGCCTAAAT 60.044 61.111 43.34 0.00 36.94 1.40
537 559 1.680989 GGTGTGGCCGGCCTAAATT 60.681 57.895 43.34 0.00 36.94 1.82
538 560 1.254975 GGTGTGGCCGGCCTAAATTT 61.255 55.000 43.34 0.00 36.94 1.82
539 561 0.108851 GTGTGGCCGGCCTAAATTTG 60.109 55.000 43.34 0.00 36.94 2.32
540 562 1.254284 TGTGGCCGGCCTAAATTTGG 61.254 55.000 43.34 0.00 36.94 3.28
541 563 1.684049 TGGCCGGCCTAAATTTGGG 60.684 57.895 43.34 15.89 36.94 4.12
547 569 2.804856 CCTAAATTTGGGCCGGCG 59.195 61.111 22.54 0.00 0.00 6.46
548 570 2.104132 CTAAATTTGGGCCGGCGC 59.896 61.111 34.64 34.64 0.00 6.53
549 571 2.676822 TAAATTTGGGCCGGCGCA 60.677 55.556 39.14 39.14 36.38 6.09
550 572 2.882402 CTAAATTTGGGCCGGCGCAC 62.882 60.000 41.97 24.75 38.61 5.34
563 585 2.277756 CGCACCGACGCCTAGTAC 60.278 66.667 0.00 0.00 0.00 2.73
564 586 2.758089 CGCACCGACGCCTAGTACT 61.758 63.158 0.00 0.00 0.00 2.73
565 587 1.226603 GCACCGACGCCTAGTACTG 60.227 63.158 5.39 0.00 0.00 2.74
566 588 1.226603 CACCGACGCCTAGTACTGC 60.227 63.158 5.39 0.00 0.00 4.40
567 589 2.412112 CCGACGCCTAGTACTGCC 59.588 66.667 5.39 0.00 0.00 4.85
568 590 2.412112 CGACGCCTAGTACTGCCC 59.588 66.667 5.39 0.00 0.00 5.36
569 591 2.119655 CGACGCCTAGTACTGCCCT 61.120 63.158 5.39 0.00 0.00 5.19
570 592 1.664321 CGACGCCTAGTACTGCCCTT 61.664 60.000 5.39 0.00 0.00 3.95
571 593 0.535797 GACGCCTAGTACTGCCCTTT 59.464 55.000 5.39 0.00 0.00 3.11
572 594 0.249398 ACGCCTAGTACTGCCCTTTG 59.751 55.000 5.39 0.00 0.00 2.77
573 595 0.462047 CGCCTAGTACTGCCCTTTGG 60.462 60.000 5.39 0.00 0.00 3.28
646 672 3.142174 GGACAGGAAACAGAGGAGTTTG 58.858 50.000 0.00 0.00 41.48 2.93
647 673 3.142174 GACAGGAAACAGAGGAGTTTGG 58.858 50.000 0.00 0.00 41.48 3.28
683 710 1.849219 GCGTTTGCGATTTGAACACAA 59.151 42.857 0.00 0.00 41.33 3.33
686 713 3.728221 CGTTTGCGATTTGAACACAATCA 59.272 39.130 0.00 0.00 41.33 2.57
888 923 7.957484 CGTCAAGACACTATAAAATCCAAACAG 59.043 37.037 0.72 0.00 0.00 3.16
913 948 2.032550 CCATAGCCATCAGAACGCAAAG 59.967 50.000 0.00 0.00 0.00 2.77
952 1013 2.094649 CACTAGTCTCCACCGTTTCCTC 60.095 54.545 0.00 0.00 0.00 3.71
953 1014 2.225066 ACTAGTCTCCACCGTTTCCTCT 60.225 50.000 0.00 0.00 0.00 3.69
954 1015 2.599408 AGTCTCCACCGTTTCCTCTA 57.401 50.000 0.00 0.00 0.00 2.43
955 1016 2.169330 AGTCTCCACCGTTTCCTCTAC 58.831 52.381 0.00 0.00 0.00 2.59
956 1017 2.169330 GTCTCCACCGTTTCCTCTACT 58.831 52.381 0.00 0.00 0.00 2.57
957 1018 3.009916 AGTCTCCACCGTTTCCTCTACTA 59.990 47.826 0.00 0.00 0.00 1.82
958 1019 3.377798 GTCTCCACCGTTTCCTCTACTAG 59.622 52.174 0.00 0.00 0.00 2.57
960 1021 1.136500 CCACCGTTTCCTCTACTAGGC 59.864 57.143 0.00 0.00 46.10 3.93
961 1022 2.100989 CACCGTTTCCTCTACTAGGCT 58.899 52.381 0.00 0.00 46.10 4.58
962 1023 3.285484 CACCGTTTCCTCTACTAGGCTA 58.715 50.000 0.00 0.00 46.10 3.93
963 1024 3.315749 CACCGTTTCCTCTACTAGGCTAG 59.684 52.174 19.83 19.83 46.10 3.42
964 1025 3.201708 ACCGTTTCCTCTACTAGGCTAGA 59.798 47.826 27.59 6.93 46.10 2.43
965 1026 3.565063 CCGTTTCCTCTACTAGGCTAGAC 59.435 52.174 27.59 11.47 46.10 2.59
966 1027 4.453751 CGTTTCCTCTACTAGGCTAGACT 58.546 47.826 27.59 2.16 46.10 3.24
967 1028 5.454471 CCGTTTCCTCTACTAGGCTAGACTA 60.454 48.000 27.59 4.91 46.10 2.59
968 1029 5.466393 CGTTTCCTCTACTAGGCTAGACTAC 59.534 48.000 27.59 11.70 46.10 2.73
969 1030 6.594744 GTTTCCTCTACTAGGCTAGACTACT 58.405 44.000 27.59 7.66 46.10 2.57
970 1031 6.828307 TTCCTCTACTAGGCTAGACTACTT 57.172 41.667 27.59 6.92 46.10 2.24
1040 1101 1.207791 CCCTTCCAGCTCACTACCAT 58.792 55.000 0.00 0.00 0.00 3.55
1137 1198 4.662961 CTGGCCGAGACGTGTGCA 62.663 66.667 0.00 0.00 0.00 4.57
1344 1405 3.121929 AGTTATGGCCTCTCTTCTCCA 57.878 47.619 3.32 0.00 0.00 3.86
1391 1452 1.339151 CCTCTGGAACAACTACCTGGC 60.339 57.143 0.00 0.00 38.70 4.85
1449 1510 2.357009 GCTCGATGGCATTGACTTTGAT 59.643 45.455 13.49 0.00 0.00 2.57
1955 2036 4.556942 ATTGTGTGTCTTGTGTCATGTG 57.443 40.909 0.00 0.00 0.00 3.21
2061 2146 6.588719 TTCTTTGAACCAAGTCCCATATTG 57.411 37.500 0.00 0.00 0.00 1.90
2258 2354 3.118629 TCGCCATCTTGCAACTAGAAGAT 60.119 43.478 0.00 0.00 39.09 2.40
2301 5965 6.026947 TGAACTTGAACTAGAGCTAGAACC 57.973 41.667 11.28 1.34 36.97 3.62
2365 6270 7.432148 AAGTTTTTGGAAAATACTTCCCTGT 57.568 32.000 1.18 0.00 37.79 4.00
2397 6302 3.119884 TCAATTATTCCTGTGCACTTGCG 60.120 43.478 19.41 3.83 45.83 4.85
2400 6305 3.993609 TATTCCTGTGCACTTGCGGGG 62.994 57.143 19.41 10.20 45.83 5.73
2410 6315 1.112315 ACTTGCGGGGCATCAACAAA 61.112 50.000 0.00 0.00 38.76 2.83
2462 6369 6.338937 AGACTCTAATATTTTGTGGGACGAC 58.661 40.000 0.00 0.00 0.00 4.34
2472 6379 1.677966 TGGGACGACGAAGGGAGAG 60.678 63.158 0.00 0.00 0.00 3.20
2505 6414 9.218440 GCCAGATTTATTTTCCAAAATTTCTGA 57.782 29.630 20.35 0.00 38.81 3.27
2545 6454 3.066760 ACAACTGAACTAGCCAACAAAGC 59.933 43.478 0.00 0.00 0.00 3.51
2881 6800 1.002888 AGCCATTGAGGATATGAGCGG 59.997 52.381 0.00 0.00 41.22 5.52
2884 6803 2.332104 CATTGAGGATATGAGCGGACG 58.668 52.381 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 43 5.241506 TGAAGCAAGAAAATTCACGATTCCT 59.758 36.000 0.00 0.00 30.11 3.36
102 108 4.937696 AAAAACAAAAAGGTTTCCAGCG 57.062 36.364 0.00 0.00 39.93 5.18
156 163 3.581265 AAAAAGAACTCCGGTGGGTAA 57.419 42.857 8.63 0.00 33.83 2.85
197 204 0.111061 TGCACCACTTGATTCCAGCT 59.889 50.000 0.00 0.00 0.00 4.24
208 216 3.991051 CGGTCGACCTGCACCACT 61.991 66.667 30.92 0.00 32.33 4.00
224 232 4.954680 CACAACGTTGCCGCCACG 62.955 66.667 27.61 14.88 37.70 4.94
286 308 1.941294 CCTTGACAGATGCATCTCTGC 59.059 52.381 26.44 17.59 45.37 4.26
287 309 2.562635 CCCTTGACAGATGCATCTCTG 58.437 52.381 26.44 19.94 46.59 3.35
288 310 1.489649 CCCCTTGACAGATGCATCTCT 59.510 52.381 26.44 15.73 34.22 3.10
289 311 1.211457 ACCCCTTGACAGATGCATCTC 59.789 52.381 26.44 16.71 34.22 2.75
290 312 1.064906 CACCCCTTGACAGATGCATCT 60.065 52.381 23.75 23.75 37.72 2.90
291 313 1.386533 CACCCCTTGACAGATGCATC 58.613 55.000 19.37 19.37 0.00 3.91
292 314 0.033796 CCACCCCTTGACAGATGCAT 60.034 55.000 0.00 0.00 0.00 3.96
293 315 1.379916 CCACCCCTTGACAGATGCA 59.620 57.895 0.00 0.00 0.00 3.96
294 316 0.962356 CACCACCCCTTGACAGATGC 60.962 60.000 0.00 0.00 0.00 3.91
295 317 0.962356 GCACCACCCCTTGACAGATG 60.962 60.000 0.00 0.00 0.00 2.90
296 318 1.136329 AGCACCACCCCTTGACAGAT 61.136 55.000 0.00 0.00 0.00 2.90
297 319 1.770110 AGCACCACCCCTTGACAGA 60.770 57.895 0.00 0.00 0.00 3.41
298 320 1.601759 CAGCACCACCCCTTGACAG 60.602 63.158 0.00 0.00 0.00 3.51
299 321 1.640593 TTCAGCACCACCCCTTGACA 61.641 55.000 0.00 0.00 0.00 3.58
300 322 0.467290 TTTCAGCACCACCCCTTGAC 60.467 55.000 0.00 0.00 0.00 3.18
301 323 0.467290 GTTTCAGCACCACCCCTTGA 60.467 55.000 0.00 0.00 0.00 3.02
302 324 1.795170 CGTTTCAGCACCACCCCTTG 61.795 60.000 0.00 0.00 0.00 3.61
303 325 1.528309 CGTTTCAGCACCACCCCTT 60.528 57.895 0.00 0.00 0.00 3.95
304 326 2.113139 CGTTTCAGCACCACCCCT 59.887 61.111 0.00 0.00 0.00 4.79
305 327 2.112297 TCGTTTCAGCACCACCCC 59.888 61.111 0.00 0.00 0.00 4.95
306 328 2.604174 CGTCGTTTCAGCACCACCC 61.604 63.158 0.00 0.00 0.00 4.61
307 329 2.604174 CCGTCGTTTCAGCACCACC 61.604 63.158 0.00 0.00 0.00 4.61
308 330 2.604174 CCCGTCGTTTCAGCACCAC 61.604 63.158 0.00 0.00 0.00 4.16
309 331 2.280524 CCCGTCGTTTCAGCACCA 60.281 61.111 0.00 0.00 0.00 4.17
310 332 2.027625 CTCCCGTCGTTTCAGCACC 61.028 63.158 0.00 0.00 0.00 5.01
311 333 0.389948 ATCTCCCGTCGTTTCAGCAC 60.390 55.000 0.00 0.00 0.00 4.40
312 334 0.389817 CATCTCCCGTCGTTTCAGCA 60.390 55.000 0.00 0.00 0.00 4.41
313 335 0.108804 TCATCTCCCGTCGTTTCAGC 60.109 55.000 0.00 0.00 0.00 4.26
314 336 1.469940 CCTCATCTCCCGTCGTTTCAG 60.470 57.143 0.00 0.00 0.00 3.02
315 337 0.530744 CCTCATCTCCCGTCGTTTCA 59.469 55.000 0.00 0.00 0.00 2.69
316 338 0.815734 TCCTCATCTCCCGTCGTTTC 59.184 55.000 0.00 0.00 0.00 2.78
317 339 0.818296 CTCCTCATCTCCCGTCGTTT 59.182 55.000 0.00 0.00 0.00 3.60
318 340 1.038130 CCTCCTCATCTCCCGTCGTT 61.038 60.000 0.00 0.00 0.00 3.85
319 341 1.454111 CCTCCTCATCTCCCGTCGT 60.454 63.158 0.00 0.00 0.00 4.34
320 342 1.152943 TCCTCCTCATCTCCCGTCG 60.153 63.158 0.00 0.00 0.00 5.12
321 343 1.448922 CGTCCTCCTCATCTCCCGTC 61.449 65.000 0.00 0.00 0.00 4.79
322 344 1.454111 CGTCCTCCTCATCTCCCGT 60.454 63.158 0.00 0.00 0.00 5.28
323 345 2.196925 CCGTCCTCCTCATCTCCCG 61.197 68.421 0.00 0.00 0.00 5.14
324 346 2.503382 GCCGTCCTCCTCATCTCCC 61.503 68.421 0.00 0.00 0.00 4.30
325 347 2.851071 CGCCGTCCTCCTCATCTCC 61.851 68.421 0.00 0.00 0.00 3.71
326 348 1.384989 TTCGCCGTCCTCCTCATCTC 61.385 60.000 0.00 0.00 0.00 2.75
327 349 0.757188 ATTCGCCGTCCTCCTCATCT 60.757 55.000 0.00 0.00 0.00 2.90
328 350 0.105039 AATTCGCCGTCCTCCTCATC 59.895 55.000 0.00 0.00 0.00 2.92
329 351 0.179073 CAATTCGCCGTCCTCCTCAT 60.179 55.000 0.00 0.00 0.00 2.90
330 352 1.218047 CAATTCGCCGTCCTCCTCA 59.782 57.895 0.00 0.00 0.00 3.86
331 353 1.521681 CCAATTCGCCGTCCTCCTC 60.522 63.158 0.00 0.00 0.00 3.71
332 354 1.961180 CTCCAATTCGCCGTCCTCCT 61.961 60.000 0.00 0.00 0.00 3.69
333 355 1.521681 CTCCAATTCGCCGTCCTCC 60.522 63.158 0.00 0.00 0.00 4.30
334 356 2.174319 GCTCCAATTCGCCGTCCTC 61.174 63.158 0.00 0.00 0.00 3.71
335 357 2.125106 GCTCCAATTCGCCGTCCT 60.125 61.111 0.00 0.00 0.00 3.85
336 358 3.202706 GGCTCCAATTCGCCGTCC 61.203 66.667 0.00 0.00 36.45 4.79
342 364 3.264897 CTCCGCGGCTCCAATTCG 61.265 66.667 23.51 0.00 0.00 3.34
343 365 1.884926 CTCTCCGCGGCTCCAATTC 60.885 63.158 23.51 0.00 0.00 2.17
344 366 2.187946 CTCTCCGCGGCTCCAATT 59.812 61.111 23.51 0.00 0.00 2.32
345 367 2.759973 TCTCTCCGCGGCTCCAAT 60.760 61.111 23.51 0.00 0.00 3.16
346 368 3.452786 CTCTCTCCGCGGCTCCAA 61.453 66.667 23.51 0.55 0.00 3.53
365 387 4.933064 GATCTCCACCGCTCGCCG 62.933 72.222 0.00 0.00 0.00 6.46
366 388 4.593864 GGATCTCCACCGCTCGCC 62.594 72.222 0.00 0.00 35.64 5.54
367 389 4.933064 CGGATCTCCACCGCTCGC 62.933 72.222 0.00 0.00 43.74 5.03
374 396 4.222847 GACCCGCCGGATCTCCAC 62.223 72.222 5.05 0.00 35.14 4.02
375 397 4.770362 TGACCCGCCGGATCTCCA 62.770 66.667 5.05 0.00 35.14 3.86
376 398 3.917760 CTGACCCGCCGGATCTCC 61.918 72.222 5.05 0.00 0.00 3.71
377 399 3.917760 CCTGACCCGCCGGATCTC 61.918 72.222 5.05 0.00 0.00 2.75
378 400 4.779733 ACCTGACCCGCCGGATCT 62.780 66.667 5.05 0.00 0.00 2.75
379 401 4.222847 GACCTGACCCGCCGGATC 62.223 72.222 5.05 0.00 0.00 3.36
386 408 4.477975 GACGAGCGACCTGACCCG 62.478 72.222 0.00 0.00 0.00 5.28
387 409 4.131088 GGACGAGCGACCTGACCC 62.131 72.222 4.22 0.00 0.00 4.46
388 410 2.711922 ATGGACGAGCGACCTGACC 61.712 63.158 12.12 0.00 0.00 4.02
389 411 1.517257 CATGGACGAGCGACCTGAC 60.517 63.158 12.12 0.00 0.00 3.51
390 412 2.710902 CCATGGACGAGCGACCTGA 61.711 63.158 5.56 0.00 0.00 3.86
391 413 2.202797 CCATGGACGAGCGACCTG 60.203 66.667 5.56 7.96 0.00 4.00
392 414 2.680352 ACCATGGACGAGCGACCT 60.680 61.111 21.47 0.00 0.00 3.85
393 415 2.509336 CACCATGGACGAGCGACC 60.509 66.667 21.47 4.49 0.00 4.79
394 416 3.188786 GCACCATGGACGAGCGAC 61.189 66.667 21.47 0.00 0.00 5.19
395 417 3.356639 GAGCACCATGGACGAGCGA 62.357 63.158 21.47 0.00 0.00 4.93
396 418 2.887568 GAGCACCATGGACGAGCG 60.888 66.667 21.47 0.17 0.00 5.03
397 419 2.887568 CGAGCACCATGGACGAGC 60.888 66.667 21.47 16.11 0.00 5.03
398 420 2.887568 GCGAGCACCATGGACGAG 60.888 66.667 21.47 10.30 0.00 4.18
399 421 3.690280 TGCGAGCACCATGGACGA 61.690 61.111 21.47 6.19 0.00 4.20
400 422 3.490759 GTGCGAGCACCATGGACG 61.491 66.667 21.47 18.00 40.79 4.79
413 435 3.864686 GCACACATAGCGGGTGCG 61.865 66.667 3.37 0.00 46.94 5.34
415 437 2.167219 CGAGCACACATAGCGGGTG 61.167 63.158 4.27 4.27 41.95 4.61
416 438 2.184322 CGAGCACACATAGCGGGT 59.816 61.111 0.00 0.00 37.01 5.28
417 439 3.264897 GCGAGCACACATAGCGGG 61.265 66.667 0.00 0.00 37.01 6.13
418 440 3.620428 CGCGAGCACACATAGCGG 61.620 66.667 0.00 0.00 46.06 5.52
420 442 1.148157 ATCACGCGAGCACACATAGC 61.148 55.000 15.93 0.00 0.00 2.97
421 443 1.280982 AATCACGCGAGCACACATAG 58.719 50.000 15.93 0.00 0.00 2.23
422 444 1.393196 CAAATCACGCGAGCACACATA 59.607 47.619 15.93 0.00 0.00 2.29
423 445 0.166597 CAAATCACGCGAGCACACAT 59.833 50.000 15.93 0.00 0.00 3.21
424 446 1.569003 CAAATCACGCGAGCACACA 59.431 52.632 15.93 0.00 0.00 3.72
425 447 1.793613 GCAAATCACGCGAGCACAC 60.794 57.895 15.93 0.00 0.00 3.82
426 448 1.576451 ATGCAAATCACGCGAGCACA 61.576 50.000 15.93 1.31 38.12 4.57
427 449 0.373370 TATGCAAATCACGCGAGCAC 59.627 50.000 15.93 0.00 38.12 4.40
428 450 0.652071 CTATGCAAATCACGCGAGCA 59.348 50.000 15.93 13.06 39.79 4.26
429 451 0.652592 ACTATGCAAATCACGCGAGC 59.347 50.000 15.93 7.29 0.00 5.03
430 452 3.372060 TCTACTATGCAAATCACGCGAG 58.628 45.455 15.93 4.59 0.00 5.03
431 453 3.066203 TCTCTACTATGCAAATCACGCGA 59.934 43.478 15.93 0.00 0.00 5.87
432 454 3.372060 TCTCTACTATGCAAATCACGCG 58.628 45.455 3.53 3.53 0.00 6.01
433 455 4.317418 CGTTCTCTACTATGCAAATCACGC 60.317 45.833 0.00 0.00 0.00 5.34
434 456 4.207224 CCGTTCTCTACTATGCAAATCACG 59.793 45.833 0.00 0.00 0.00 4.35
435 457 4.025647 GCCGTTCTCTACTATGCAAATCAC 60.026 45.833 0.00 0.00 0.00 3.06
436 458 4.119862 GCCGTTCTCTACTATGCAAATCA 58.880 43.478 0.00 0.00 0.00 2.57
437 459 4.119862 TGCCGTTCTCTACTATGCAAATC 58.880 43.478 0.00 0.00 0.00 2.17
438 460 4.137116 TGCCGTTCTCTACTATGCAAAT 57.863 40.909 0.00 0.00 0.00 2.32
439 461 3.603158 TGCCGTTCTCTACTATGCAAA 57.397 42.857 0.00 0.00 0.00 3.68
440 462 3.457234 CATGCCGTTCTCTACTATGCAA 58.543 45.455 0.00 0.00 30.69 4.08
441 463 2.224042 CCATGCCGTTCTCTACTATGCA 60.224 50.000 0.00 0.00 0.00 3.96
442 464 2.224066 ACCATGCCGTTCTCTACTATGC 60.224 50.000 0.00 0.00 0.00 3.14
443 465 3.384668 CACCATGCCGTTCTCTACTATG 58.615 50.000 0.00 0.00 0.00 2.23
444 466 2.365617 CCACCATGCCGTTCTCTACTAT 59.634 50.000 0.00 0.00 0.00 2.12
445 467 1.754803 CCACCATGCCGTTCTCTACTA 59.245 52.381 0.00 0.00 0.00 1.82
446 468 0.537188 CCACCATGCCGTTCTCTACT 59.463 55.000 0.00 0.00 0.00 2.57
447 469 0.462047 CCCACCATGCCGTTCTCTAC 60.462 60.000 0.00 0.00 0.00 2.59
448 470 1.622607 CCCCACCATGCCGTTCTCTA 61.623 60.000 0.00 0.00 0.00 2.43
449 471 2.671070 CCCACCATGCCGTTCTCT 59.329 61.111 0.00 0.00 0.00 3.10
450 472 2.270874 ATCCCCACCATGCCGTTCTC 62.271 60.000 0.00 0.00 0.00 2.87
451 473 2.308722 ATCCCCACCATGCCGTTCT 61.309 57.895 0.00 0.00 0.00 3.01
452 474 2.120909 CATCCCCACCATGCCGTTC 61.121 63.158 0.00 0.00 0.00 3.95
453 475 2.044053 CATCCCCACCATGCCGTT 60.044 61.111 0.00 0.00 0.00 4.44
454 476 2.148723 TTTCATCCCCACCATGCCGT 62.149 55.000 0.00 0.00 0.00 5.68
455 477 1.379710 TTTCATCCCCACCATGCCG 60.380 57.895 0.00 0.00 0.00 5.69
456 478 1.679559 GCTTTCATCCCCACCATGCC 61.680 60.000 0.00 0.00 0.00 4.40
457 479 1.818555 GCTTTCATCCCCACCATGC 59.181 57.895 0.00 0.00 0.00 4.06
458 480 0.680921 ACGCTTTCATCCCCACCATG 60.681 55.000 0.00 0.00 0.00 3.66
459 481 0.394352 GACGCTTTCATCCCCACCAT 60.394 55.000 0.00 0.00 0.00 3.55
460 482 1.002624 GACGCTTTCATCCCCACCA 60.003 57.895 0.00 0.00 0.00 4.17
461 483 1.749258 GGACGCTTTCATCCCCACC 60.749 63.158 0.00 0.00 0.00 4.61
462 484 0.539986 TAGGACGCTTTCATCCCCAC 59.460 55.000 0.00 0.00 35.38 4.61
463 485 1.281419 TTAGGACGCTTTCATCCCCA 58.719 50.000 0.00 0.00 35.38 4.96
464 486 2.413310 TTTAGGACGCTTTCATCCCC 57.587 50.000 0.00 0.00 35.38 4.81
465 487 3.561725 CAGATTTAGGACGCTTTCATCCC 59.438 47.826 0.00 0.00 35.38 3.85
466 488 4.271291 GTCAGATTTAGGACGCTTTCATCC 59.729 45.833 0.00 0.00 34.98 3.51
467 489 5.396750 GTCAGATTTAGGACGCTTTCATC 57.603 43.478 0.00 0.00 0.00 2.92
476 498 5.416947 TCTTTTAGCCGTCAGATTTAGGAC 58.583 41.667 0.00 0.00 0.00 3.85
477 499 5.187186 ACTCTTTTAGCCGTCAGATTTAGGA 59.813 40.000 0.00 0.00 0.00 2.94
478 500 5.420409 ACTCTTTTAGCCGTCAGATTTAGG 58.580 41.667 0.00 0.00 0.00 2.69
479 501 6.969828 AACTCTTTTAGCCGTCAGATTTAG 57.030 37.500 0.00 0.00 0.00 1.85
480 502 7.739498 AAAACTCTTTTAGCCGTCAGATTTA 57.261 32.000 0.00 0.00 0.00 1.40
481 503 6.635030 AAAACTCTTTTAGCCGTCAGATTT 57.365 33.333 0.00 0.00 0.00 2.17
482 504 7.739498 TTAAAACTCTTTTAGCCGTCAGATT 57.261 32.000 0.00 0.00 36.56 2.40
483 505 7.606456 TGATTAAAACTCTTTTAGCCGTCAGAT 59.394 33.333 0.00 0.00 36.56 2.90
484 506 6.932400 TGATTAAAACTCTTTTAGCCGTCAGA 59.068 34.615 0.00 0.00 36.56 3.27
485 507 7.117812 TCTGATTAAAACTCTTTTAGCCGTCAG 59.882 37.037 0.00 0.00 36.56 3.51
486 508 6.932400 TCTGATTAAAACTCTTTTAGCCGTCA 59.068 34.615 0.00 0.00 36.56 4.35
487 509 7.235080 GTCTGATTAAAACTCTTTTAGCCGTC 58.765 38.462 0.00 0.00 36.56 4.79
488 510 6.128634 CGTCTGATTAAAACTCTTTTAGCCGT 60.129 38.462 0.00 0.00 36.56 5.68
489 511 6.128634 ACGTCTGATTAAAACTCTTTTAGCCG 60.129 38.462 0.00 0.00 36.56 5.52
490 512 7.130303 ACGTCTGATTAAAACTCTTTTAGCC 57.870 36.000 0.00 0.00 36.56 3.93
491 513 8.706035 TGTACGTCTGATTAAAACTCTTTTAGC 58.294 33.333 0.00 0.00 36.56 3.09
493 515 9.199982 CCTGTACGTCTGATTAAAACTCTTTTA 57.800 33.333 0.00 0.00 34.19 1.52
494 516 7.172703 CCCTGTACGTCTGATTAAAACTCTTTT 59.827 37.037 0.00 0.00 36.67 2.27
495 517 6.649557 CCCTGTACGTCTGATTAAAACTCTTT 59.350 38.462 0.00 0.00 0.00 2.52
496 518 6.164176 CCCTGTACGTCTGATTAAAACTCTT 58.836 40.000 0.00 0.00 0.00 2.85
497 519 5.245526 ACCCTGTACGTCTGATTAAAACTCT 59.754 40.000 0.00 0.00 0.00 3.24
498 520 5.347907 CACCCTGTACGTCTGATTAAAACTC 59.652 44.000 0.00 0.00 0.00 3.01
499 521 5.221581 ACACCCTGTACGTCTGATTAAAACT 60.222 40.000 0.00 0.00 0.00 2.66
500 522 4.992951 ACACCCTGTACGTCTGATTAAAAC 59.007 41.667 0.00 0.00 0.00 2.43
501 523 4.992319 CACACCCTGTACGTCTGATTAAAA 59.008 41.667 0.00 0.00 0.00 1.52
502 524 4.561938 CCACACCCTGTACGTCTGATTAAA 60.562 45.833 0.00 0.00 0.00 1.52
503 525 3.056393 CCACACCCTGTACGTCTGATTAA 60.056 47.826 0.00 0.00 0.00 1.40
504 526 2.494471 CCACACCCTGTACGTCTGATTA 59.506 50.000 0.00 0.00 0.00 1.75
505 527 1.275291 CCACACCCTGTACGTCTGATT 59.725 52.381 0.00 0.00 0.00 2.57
506 528 0.895530 CCACACCCTGTACGTCTGAT 59.104 55.000 0.00 0.00 0.00 2.90
507 529 1.812686 GCCACACCCTGTACGTCTGA 61.813 60.000 0.00 0.00 0.00 3.27
508 530 1.374252 GCCACACCCTGTACGTCTG 60.374 63.158 0.00 0.00 0.00 3.51
509 531 2.580601 GGCCACACCCTGTACGTCT 61.581 63.158 0.00 0.00 0.00 4.18
510 532 2.047560 GGCCACACCCTGTACGTC 60.048 66.667 0.00 0.00 0.00 4.34
511 533 3.998672 CGGCCACACCCTGTACGT 61.999 66.667 2.24 0.00 33.26 3.57
512 534 4.752879 CCGGCCACACCCTGTACG 62.753 72.222 2.24 0.00 33.26 3.67
518 540 3.655350 ATTTAGGCCGGCCACACCC 62.655 63.158 45.13 19.46 38.92 4.61
519 541 1.254975 AAATTTAGGCCGGCCACACC 61.255 55.000 45.13 20.27 38.92 4.16
520 542 0.108851 CAAATTTAGGCCGGCCACAC 60.109 55.000 45.13 20.70 38.92 3.82
521 543 1.254284 CCAAATTTAGGCCGGCCACA 61.254 55.000 45.13 30.53 38.92 4.17
522 544 1.515487 CCAAATTTAGGCCGGCCAC 59.485 57.895 45.13 21.93 38.92 5.01
523 545 1.684049 CCCAAATTTAGGCCGGCCA 60.684 57.895 45.13 28.81 38.92 5.36
524 546 3.088941 GCCCAAATTTAGGCCGGCC 62.089 63.158 39.29 39.29 43.76 6.13
525 547 2.499205 GCCCAAATTTAGGCCGGC 59.501 61.111 21.18 21.18 43.76 6.13
530 552 2.804856 CGCCGGCCCAAATTTAGG 59.195 61.111 23.46 0.00 0.00 2.69
531 553 2.104132 GCGCCGGCCCAAATTTAG 59.896 61.111 23.46 4.03 0.00 1.85
532 554 2.676822 TGCGCCGGCCCAAATTTA 60.677 55.556 23.46 0.00 38.85 1.40
533 555 4.371590 GTGCGCCGGCCCAAATTT 62.372 61.111 23.46 0.00 38.85 1.82
546 568 2.277756 GTACTAGGCGTCGGTGCG 60.278 66.667 0.00 0.00 35.06 5.34
547 569 1.226603 CAGTACTAGGCGTCGGTGC 60.227 63.158 0.00 0.00 0.00 5.01
548 570 1.226603 GCAGTACTAGGCGTCGGTG 60.227 63.158 0.00 0.00 0.00 4.94
549 571 2.413142 GGCAGTACTAGGCGTCGGT 61.413 63.158 0.00 0.00 0.00 4.69
550 572 2.412112 GGCAGTACTAGGCGTCGG 59.588 66.667 0.00 0.00 0.00 4.79
551 573 1.664321 AAGGGCAGTACTAGGCGTCG 61.664 60.000 12.09 0.00 0.00 5.12
552 574 0.535797 AAAGGGCAGTACTAGGCGTC 59.464 55.000 12.09 3.10 0.00 5.19
553 575 0.249398 CAAAGGGCAGTACTAGGCGT 59.751 55.000 0.00 1.73 0.00 5.68
554 576 0.462047 CCAAAGGGCAGTACTAGGCG 60.462 60.000 0.00 0.00 0.00 5.52
555 577 0.107165 CCCAAAGGGCAGTACTAGGC 60.107 60.000 0.00 2.62 35.35 3.93
567 589 2.045926 CCCTCGACTGCCCAAAGG 60.046 66.667 0.00 0.00 0.00 3.11
568 590 1.672356 CACCCTCGACTGCCCAAAG 60.672 63.158 0.00 0.00 0.00 2.77
569 591 2.429930 CACCCTCGACTGCCCAAA 59.570 61.111 0.00 0.00 0.00 3.28
570 592 4.329545 GCACCCTCGACTGCCCAA 62.330 66.667 0.00 0.00 0.00 4.12
572 594 3.959991 GAAGCACCCTCGACTGCCC 62.960 68.421 2.14 0.00 33.57 5.36
573 595 2.435059 GAAGCACCCTCGACTGCC 60.435 66.667 2.14 0.00 33.57 4.85
574 596 1.294659 CTTGAAGCACCCTCGACTGC 61.295 60.000 0.00 0.00 0.00 4.40
575 597 1.294659 GCTTGAAGCACCCTCGACTG 61.295 60.000 13.09 0.00 41.89 3.51
576 598 1.004440 GCTTGAAGCACCCTCGACT 60.004 57.895 13.09 0.00 41.89 4.18
646 672 2.033194 GCTGCACCGTACTCAACCC 61.033 63.158 0.00 0.00 0.00 4.11
647 673 2.380410 CGCTGCACCGTACTCAACC 61.380 63.158 0.00 0.00 0.00 3.77
743 770 7.119407 GGTTAAGTAAAGCTGAGGGTAGAAAAG 59.881 40.741 0.00 0.00 32.65 2.27
857 891 4.794278 TTTATAGTGTCTTGACGGAGCA 57.206 40.909 0.00 0.00 0.00 4.26
904 939 0.658536 GTGCTCTGTGCTTTGCGTTC 60.659 55.000 3.20 0.00 43.37 3.95
913 948 1.445238 GAGGAGACGTGCTCTGTGC 60.445 63.158 0.00 0.00 43.43 4.57
952 1013 4.882427 TGTGCAAGTAGTCTAGCCTAGTAG 59.118 45.833 0.00 0.00 0.00 2.57
953 1014 4.851843 TGTGCAAGTAGTCTAGCCTAGTA 58.148 43.478 0.00 0.00 0.00 1.82
954 1015 3.697045 CTGTGCAAGTAGTCTAGCCTAGT 59.303 47.826 0.00 0.00 0.00 2.57
955 1016 3.067461 CCTGTGCAAGTAGTCTAGCCTAG 59.933 52.174 0.00 0.00 0.00 3.02
956 1017 3.024547 CCTGTGCAAGTAGTCTAGCCTA 58.975 50.000 0.00 0.00 0.00 3.93
957 1018 1.827969 CCTGTGCAAGTAGTCTAGCCT 59.172 52.381 0.00 0.00 0.00 4.58
958 1019 1.740718 GCCTGTGCAAGTAGTCTAGCC 60.741 57.143 0.00 0.00 37.47 3.93
959 1020 1.066858 TGCCTGTGCAAGTAGTCTAGC 60.067 52.381 0.00 0.00 46.66 3.42
1040 1101 2.461695 CAAGGAGTGCTAGGAAGAGGA 58.538 52.381 0.00 0.00 0.00 3.71
1137 1198 5.762179 TGACAAACTCATAGTTCCCAGAT 57.238 39.130 0.00 0.00 37.47 2.90
1203 1264 0.838122 AGTGGCTGGCTAGGTTCAGT 60.838 55.000 0.00 0.00 33.81 3.41
1391 1452 4.873129 CGGACGAGGATGCACCGG 62.873 72.222 0.00 0.00 44.74 5.28
1449 1510 2.586079 GCGCTGCCTTGCTCGATA 60.586 61.111 0.00 0.00 0.00 2.92
1480 1541 4.640771 TCTTTAGGTCAGTGGCAAGATT 57.359 40.909 0.00 0.00 0.00 2.40
1784 1856 0.806868 CTTGATGAGCGGCAACACAT 59.193 50.000 1.45 2.27 0.00 3.21
1955 2036 6.903883 ACAATTAACACACGATCCTATGAC 57.096 37.500 0.00 0.00 0.00 3.06
2090 2176 5.242393 AGAATCAAAAGCAGTGTAGTGCATT 59.758 36.000 13.62 5.50 46.60 3.56
2129 2217 8.397906 CCACAGTTGATTCACGAAATATTGTAT 58.602 33.333 0.00 0.00 0.00 2.29
2140 2228 4.307432 ACTAGAACCACAGTTGATTCACG 58.693 43.478 0.00 0.00 35.94 4.35
2274 2568 6.448006 TCTAGCTCTAGTTCAAGTTCAACAC 58.552 40.000 0.00 0.00 34.84 3.32
2284 2578 5.326069 AGTTCTGGTTCTAGCTCTAGTTCA 58.674 41.667 0.00 1.78 34.84 3.18
2397 6302 2.679336 GCAAATGATTTGTTGATGCCCC 59.321 45.455 18.12 0.00 42.56 5.80
2400 6305 7.436970 TGAGATATGCAAATGATTTGTTGATGC 59.563 33.333 18.12 5.17 42.56 3.91
2410 6315 8.515695 TTTGTCTCTTGAGATATGCAAATGAT 57.484 30.769 3.50 0.00 0.00 2.45
2462 6369 2.125512 CCGGTTGCTCTCCCTTCG 60.126 66.667 0.00 0.00 0.00 3.79
2472 6379 2.959507 AAATAAATCTGGCCGGTTGC 57.040 45.000 12.43 0.00 40.16 4.17
2516 6425 7.165485 TGTTGGCTAGTTCAGTTGTATTGTAT 58.835 34.615 0.00 0.00 0.00 2.29
2545 6454 7.784633 ATTGTTGTTTGAATAGTGTTTTGGG 57.215 32.000 0.00 0.00 0.00 4.12
2629 6541 6.426980 TTTTGTCTGTGCTATGCAGATAAG 57.573 37.500 0.00 0.00 42.20 1.73
2634 6546 4.637534 ACCTATTTTGTCTGTGCTATGCAG 59.362 41.667 0.00 0.00 40.08 4.41


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

AutoCloner maintained by Alex Coulton.