Multiple sequence alignment - TraesCS7D01G529100

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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 TraesCS7D01G529100 chr7D 100.000 3130 0 0 1 3130 623597017 623593888 0.000000e+00 5781.0
1 TraesCS7D01G529100 chr4D 98.023 2478 35 2 665 3130 24110110 24112585 0.000000e+00 4292.0
2 TraesCS7D01G529100 chr4D 80.515 272 33 13 525 783 24109933 24110197 1.150000e-44 191.0
3 TraesCS7D01G529100 chr4A 95.431 2517 61 11 665 3130 527957211 527959724 0.000000e+00 3962.0
4 TraesCS7D01G529100 chr4A 95.353 2518 62 10 665 3130 426664279 426661765 0.000000e+00 3951.0
5 TraesCS7D01G529100 chr4A 97.023 1478 40 3 1654 3130 112246106 112244632 0.000000e+00 2483.0
6 TraesCS7D01G529100 chr4A 91.548 1053 38 7 665 1667 112248872 112247821 0.000000e+00 1404.0
7 TraesCS7D01G529100 chr4A 96.454 141 5 0 2600 2740 426662436 426662296 1.880000e-57 233.0
8 TraesCS7D01G529100 chr7A 95.428 2187 59 8 983 3130 730253206 730251022 0.000000e+00 3446.0
9 TraesCS7D01G529100 chr7A 93.645 535 24 4 1 533 33749672 33749146 0.000000e+00 791.0
10 TraesCS7D01G529100 chr7A 93.084 535 27 4 1 533 33750918 33750392 0.000000e+00 774.0
11 TraesCS7D01G529100 chr6B 92.799 1347 83 7 1788 3130 334481852 334480516 0.000000e+00 1938.0
12 TraesCS7D01G529100 chr6B 90.851 470 36 6 1321 1789 334482474 334482011 9.530000e-175 623.0
13 TraesCS7D01G529100 chr6B 79.762 84 13 4 526 607 346565346 346565265 1.210000e-04 58.4
14 TraesCS7D01G529100 chr3D 95.527 1073 20 3 1178 2225 519300247 519301316 0.000000e+00 1690.0
15 TraesCS7D01G529100 chr3D 98.573 911 13 0 2219 3129 519301766 519302676 0.000000e+00 1611.0
16 TraesCS7D01G529100 chr3D 94.393 535 16 5 1 533 598100819 598100297 0.000000e+00 809.0
17 TraesCS7D01G529100 chr3D 94.168 463 13 2 732 1181 519299743 519300204 0.000000e+00 693.0
18 TraesCS7D01G529100 chr3D 79.923 259 35 14 537 783 519299454 519299707 1.150000e-39 174.0
19 TraesCS7D01G529100 chr3D 87.786 131 4 1 665 783 519299620 519299750 3.250000e-30 143.0
20 TraesCS7D01G529100 chr2A 95.738 962 31 3 2170 3130 20351354 20350402 0.000000e+00 1541.0
21 TraesCS7D01G529100 chr2A 93.512 709 29 5 1331 2024 20352226 20351520 0.000000e+00 1038.0
22 TraesCS7D01G529100 chr2D 91.795 780 53 7 1321 2100 254331450 254332218 0.000000e+00 1075.0
23 TraesCS7D01G529100 chr2D 94.079 456 24 2 2678 3130 164135480 164135935 0.000000e+00 689.0
24 TraesCS7D01G529100 chr2D 95.631 412 15 1 2237 2648 164135071 164135479 0.000000e+00 658.0
25 TraesCS7D01G529100 chr2D 89.084 513 55 1 2025 2536 254332289 254332801 1.220000e-178 636.0
26 TraesCS7D01G529100 chr2D 91.379 58 5 0 851 908 254331088 254331145 2.590000e-11 80.5
27 TraesCS7D01G529100 chrUn 95.140 535 17 4 1 533 114828951 114829478 0.000000e+00 835.0
28 TraesCS7D01G529100 chr5D 93.996 533 22 3 1 533 31092280 31092802 0.000000e+00 798.0
29 TraesCS7D01G529100 chr5A 92.509 534 31 4 1 533 396389260 396389785 0.000000e+00 756.0
30 TraesCS7D01G529100 chr3A 92.336 535 31 5 1 533 736939291 736938765 0.000000e+00 752.0
31 TraesCS7D01G529100 chr1A 91.963 535 34 4 1 533 384107589 384108116 0.000000e+00 741.0
32 TraesCS7D01G529100 chr1A 94.737 38 2 0 798 835 36601226 36601263 3.370000e-05 60.2
33 TraesCS7D01G529100 chr7B 91.182 533 38 6 1 531 178791228 178791753 0.000000e+00 715.0
34 TraesCS7D01G529100 chr6D 93.556 419 14 4 116 533 291621829 291622235 2.060000e-171 612.0
35 TraesCS7D01G529100 chr3B 93.023 43 3 0 798 840 272541014 272541056 2.610000e-06 63.9
36 TraesCS7D01G529100 chr3B 100.000 33 0 0 526 558 679510677 679510709 9.370000e-06 62.1
37 TraesCS7D01G529100 chr2B 92.857 42 3 0 528 569 156003062 156003103 9.370000e-06 62.1
38 TraesCS7D01G529100 chr2B 97.222 36 1 0 526 561 278802068 278802033 9.370000e-06 62.1
39 TraesCS7D01G529100 chr2B 97.222 36 1 0 526 561 278803460 278803425 9.370000e-06 62.1


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 TraesCS7D01G529100 chr7D 623593888 623597017 3129 True 5781.000000 5781 100.000000 1 3130 1 chr7D.!!$R1 3129
1 TraesCS7D01G529100 chr4D 24109933 24112585 2652 False 2241.500000 4292 89.269000 525 3130 2 chr4D.!!$F1 2605
2 TraesCS7D01G529100 chr4A 527957211 527959724 2513 False 3962.000000 3962 95.431000 665 3130 1 chr4A.!!$F1 2465
3 TraesCS7D01G529100 chr4A 426661765 426664279 2514 True 2092.000000 3951 95.903500 665 3130 2 chr4A.!!$R2 2465
4 TraesCS7D01G529100 chr4A 112244632 112248872 4240 True 1943.500000 2483 94.285500 665 3130 2 chr4A.!!$R1 2465
5 TraesCS7D01G529100 chr7A 730251022 730253206 2184 True 3446.000000 3446 95.428000 983 3130 1 chr7A.!!$R1 2147
6 TraesCS7D01G529100 chr7A 33749146 33750918 1772 True 782.500000 791 93.364500 1 533 2 chr7A.!!$R2 532
7 TraesCS7D01G529100 chr6B 334480516 334482474 1958 True 1280.500000 1938 91.825000 1321 3130 2 chr6B.!!$R2 1809
8 TraesCS7D01G529100 chr3D 519299454 519302676 3222 False 862.200000 1690 91.195400 537 3129 5 chr3D.!!$F1 2592
9 TraesCS7D01G529100 chr3D 598100297 598100819 522 True 809.000000 809 94.393000 1 533 1 chr3D.!!$R1 532
10 TraesCS7D01G529100 chr2A 20350402 20352226 1824 True 1289.500000 1541 94.625000 1331 3130 2 chr2A.!!$R1 1799
11 TraesCS7D01G529100 chr2D 164135071 164135935 864 False 673.500000 689 94.855000 2237 3130 2 chr2D.!!$F1 893
12 TraesCS7D01G529100 chr2D 254331088 254332801 1713 False 597.166667 1075 90.752667 851 2536 3 chr2D.!!$F2 1685
13 TraesCS7D01G529100 chrUn 114828951 114829478 527 False 835.000000 835 95.140000 1 533 1 chrUn.!!$F1 532
14 TraesCS7D01G529100 chr5D 31092280 31092802 522 False 798.000000 798 93.996000 1 533 1 chr5D.!!$F1 532
15 TraesCS7D01G529100 chr5A 396389260 396389785 525 False 756.000000 756 92.509000 1 533 1 chr5A.!!$F1 532
16 TraesCS7D01G529100 chr3A 736938765 736939291 526 True 752.000000 752 92.336000 1 533 1 chr3A.!!$R1 532
17 TraesCS7D01G529100 chr1A 384107589 384108116 527 False 741.000000 741 91.963000 1 533 1 chr1A.!!$F2 532
18 TraesCS7D01G529100 chr7B 178791228 178791753 525 False 715.000000 715 91.182000 1 531 1 chr7B.!!$F1 530

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
457 459 0.038166 TGGAAGATGGGACTGGTTGC 59.962 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2273 6129 3.977244 GTGCGCCCCAAACACTGG 61.977 66.667 4.18 0.0 45.97 4.0 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
52 54 3.129287 CCACTGTGAGAGTTTGCAGTTTT 59.871 43.478 9.86 0.00 39.82 2.43
72 74 0.385974 GTGTGTTGATGTTGCTCGCC 60.386 55.000 0.00 0.00 0.00 5.54
83 85 2.434185 GCTCGCCGTGGTGAATGA 60.434 61.111 3.43 0.00 33.98 2.57
197 199 1.228521 CCATGGTGGCAGTGGTCAA 60.229 57.895 2.57 0.00 0.00 3.18
287 289 2.281070 CCTCAAGCACAGGCACGT 60.281 61.111 0.00 0.00 44.61 4.49
305 307 4.084745 GCACGTGAAGAAAGACGACAATAA 60.085 41.667 22.23 0.00 38.94 1.40
306 308 5.599715 CACGTGAAGAAAGACGACAATAAG 58.400 41.667 10.90 0.00 38.94 1.73
307 309 5.401376 CACGTGAAGAAAGACGACAATAAGA 59.599 40.000 10.90 0.00 38.94 2.10
308 310 6.089551 CACGTGAAGAAAGACGACAATAAGAT 59.910 38.462 10.90 0.00 38.94 2.40
309 311 6.645415 ACGTGAAGAAAGACGACAATAAGATT 59.355 34.615 0.00 0.00 38.94 2.40
310 312 6.950428 CGTGAAGAAAGACGACAATAAGATTG 59.050 38.462 0.00 0.00 37.81 2.67
311 313 7.148804 CGTGAAGAAAGACGACAATAAGATTGA 60.149 37.037 6.21 0.00 37.81 2.57
312 314 8.660373 GTGAAGAAAGACGACAATAAGATTGAT 58.340 33.333 6.21 0.00 0.00 2.57
313 315 8.873830 TGAAGAAAGACGACAATAAGATTGATC 58.126 33.333 6.21 0.00 0.00 2.92
314 316 8.777865 AAGAAAGACGACAATAAGATTGATCA 57.222 30.769 6.21 0.00 0.00 2.92
315 317 8.954950 AGAAAGACGACAATAAGATTGATCAT 57.045 30.769 6.21 0.00 0.00 2.45
318 320 7.859613 AGACGACAATAAGATTGATCATACG 57.140 36.000 6.21 0.00 0.00 3.06
319 321 6.863645 AGACGACAATAAGATTGATCATACGG 59.136 38.462 6.21 0.00 0.00 4.02
320 322 6.513180 ACGACAATAAGATTGATCATACGGT 58.487 36.000 6.21 0.00 0.00 4.83
321 323 6.984474 ACGACAATAAGATTGATCATACGGTT 59.016 34.615 6.21 0.00 0.00 4.44
322 324 7.042725 ACGACAATAAGATTGATCATACGGTTG 60.043 37.037 6.21 1.33 0.00 3.77
323 325 6.959361 ACAATAAGATTGATCATACGGTTGC 58.041 36.000 6.21 0.00 0.00 4.17
324 326 5.845985 ATAAGATTGATCATACGGTTGCG 57.154 39.130 0.00 0.00 0.00 4.85
325 327 2.483876 AGATTGATCATACGGTTGCGG 58.516 47.619 0.00 0.00 0.00 5.69
326 328 0.944386 ATTGATCATACGGTTGCGGC 59.056 50.000 0.00 0.00 0.00 6.53
327 329 0.107897 TTGATCATACGGTTGCGGCT 60.108 50.000 0.00 0.00 0.00 5.52
328 330 0.747852 TGATCATACGGTTGCGGCTA 59.252 50.000 0.00 0.00 0.00 3.93
329 331 1.137282 TGATCATACGGTTGCGGCTAA 59.863 47.619 0.00 0.00 0.00 3.09
330 332 2.206750 GATCATACGGTTGCGGCTAAA 58.793 47.619 0.00 0.00 0.00 1.85
331 333 2.096220 TCATACGGTTGCGGCTAAAA 57.904 45.000 0.00 0.00 0.00 1.52
332 334 2.004017 TCATACGGTTGCGGCTAAAAG 58.996 47.619 0.00 0.00 0.00 2.27
333 335 1.735571 CATACGGTTGCGGCTAAAAGT 59.264 47.619 0.00 0.00 0.00 2.66
334 336 1.149987 TACGGTTGCGGCTAAAAGTG 58.850 50.000 0.00 0.00 0.00 3.16
335 337 0.816421 ACGGTTGCGGCTAAAAGTGT 60.816 50.000 0.00 0.00 0.00 3.55
336 338 1.149987 CGGTTGCGGCTAAAAGTGTA 58.850 50.000 0.00 0.00 0.00 2.90
337 339 1.532007 CGGTTGCGGCTAAAAGTGTAA 59.468 47.619 0.00 0.00 0.00 2.41
338 340 2.412325 CGGTTGCGGCTAAAAGTGTAAG 60.412 50.000 0.00 0.00 0.00 2.34
339 341 2.551032 GGTTGCGGCTAAAAGTGTAAGT 59.449 45.455 0.00 0.00 0.00 2.24
340 342 3.551551 GTTGCGGCTAAAAGTGTAAGTG 58.448 45.455 0.00 0.00 0.00 3.16
341 343 2.147958 TGCGGCTAAAAGTGTAAGTGG 58.852 47.619 0.00 0.00 0.00 4.00
342 344 2.148768 GCGGCTAAAAGTGTAAGTGGT 58.851 47.619 0.00 0.00 0.00 4.16
343 345 2.159037 GCGGCTAAAAGTGTAAGTGGTC 59.841 50.000 0.00 0.00 0.00 4.02
344 346 3.395639 CGGCTAAAAGTGTAAGTGGTCA 58.604 45.455 0.00 0.00 0.00 4.02
345 347 3.432252 CGGCTAAAAGTGTAAGTGGTCAG 59.568 47.826 0.00 0.00 0.00 3.51
346 348 3.751698 GGCTAAAAGTGTAAGTGGTCAGG 59.248 47.826 0.00 0.00 0.00 3.86
347 349 3.751698 GCTAAAAGTGTAAGTGGTCAGGG 59.248 47.826 0.00 0.00 0.00 4.45
348 350 2.951229 AAAGTGTAAGTGGTCAGGGG 57.049 50.000 0.00 0.00 0.00 4.79
349 351 1.064825 AAGTGTAAGTGGTCAGGGGG 58.935 55.000 0.00 0.00 0.00 5.40
350 352 0.192566 AGTGTAAGTGGTCAGGGGGA 59.807 55.000 0.00 0.00 0.00 4.81
351 353 0.613777 GTGTAAGTGGTCAGGGGGAG 59.386 60.000 0.00 0.00 0.00 4.30
352 354 0.546747 TGTAAGTGGTCAGGGGGAGG 60.547 60.000 0.00 0.00 0.00 4.30
353 355 1.082206 TAAGTGGTCAGGGGGAGGG 59.918 63.158 0.00 0.00 0.00 4.30
354 356 2.486410 TAAGTGGTCAGGGGGAGGGG 62.486 65.000 0.00 0.00 0.00 4.79
357 359 4.124126 GGTCAGGGGGAGGGGGAT 62.124 72.222 0.00 0.00 0.00 3.85
358 360 2.044620 GTCAGGGGGAGGGGGATT 59.955 66.667 0.00 0.00 0.00 3.01
359 361 2.044450 TCAGGGGGAGGGGGATTG 59.956 66.667 0.00 0.00 0.00 2.67
360 362 2.044450 CAGGGGGAGGGGGATTGA 59.956 66.667 0.00 0.00 0.00 2.57
361 363 2.081161 CAGGGGGAGGGGGATTGAG 61.081 68.421 0.00 0.00 0.00 3.02
362 364 2.778717 GGGGGAGGGGGATTGAGG 60.779 72.222 0.00 0.00 0.00 3.86
363 365 2.376842 GGGGAGGGGGATTGAGGA 59.623 66.667 0.00 0.00 0.00 3.71
364 366 1.772156 GGGGAGGGGGATTGAGGAG 60.772 68.421 0.00 0.00 0.00 3.69
365 367 1.318380 GGGAGGGGGATTGAGGAGA 59.682 63.158 0.00 0.00 0.00 3.71
366 368 0.766288 GGGAGGGGGATTGAGGAGAG 60.766 65.000 0.00 0.00 0.00 3.20
367 369 0.266152 GGAGGGGGATTGAGGAGAGA 59.734 60.000 0.00 0.00 0.00 3.10
368 370 1.132560 GGAGGGGGATTGAGGAGAGAT 60.133 57.143 0.00 0.00 0.00 2.75
369 371 1.977129 GAGGGGGATTGAGGAGAGATG 59.023 57.143 0.00 0.00 0.00 2.90
370 372 1.063183 GGGGGATTGAGGAGAGATGG 58.937 60.000 0.00 0.00 0.00 3.51
371 373 0.399833 GGGGATTGAGGAGAGATGGC 59.600 60.000 0.00 0.00 0.00 4.40
372 374 1.135094 GGGATTGAGGAGAGATGGCA 58.865 55.000 0.00 0.00 0.00 4.92
373 375 1.704070 GGGATTGAGGAGAGATGGCAT 59.296 52.381 0.00 0.00 0.00 4.40
374 376 2.552591 GGGATTGAGGAGAGATGGCATG 60.553 54.545 3.81 0.00 0.00 4.06
375 377 2.106166 GGATTGAGGAGAGATGGCATGT 59.894 50.000 3.81 0.00 0.00 3.21
376 378 3.326006 GGATTGAGGAGAGATGGCATGTA 59.674 47.826 3.81 0.00 0.00 2.29
377 379 4.202398 GGATTGAGGAGAGATGGCATGTAA 60.202 45.833 3.81 0.00 0.00 2.41
378 380 3.827008 TGAGGAGAGATGGCATGTAAC 57.173 47.619 3.81 0.00 0.00 2.50
379 381 3.378512 TGAGGAGAGATGGCATGTAACT 58.621 45.455 3.81 0.00 0.00 2.24
380 382 3.133542 TGAGGAGAGATGGCATGTAACTG 59.866 47.826 3.81 0.00 0.00 3.16
381 383 3.378512 AGGAGAGATGGCATGTAACTGA 58.621 45.455 3.81 0.00 0.00 3.41
382 384 3.133721 AGGAGAGATGGCATGTAACTGAC 59.866 47.826 3.81 0.00 0.00 3.51
383 385 3.462021 GAGAGATGGCATGTAACTGACC 58.538 50.000 3.81 0.00 0.00 4.02
384 386 2.840038 AGAGATGGCATGTAACTGACCA 59.160 45.455 3.81 0.00 34.28 4.02
385 387 3.264193 AGAGATGGCATGTAACTGACCAA 59.736 43.478 3.81 0.00 33.30 3.67
386 388 4.009675 GAGATGGCATGTAACTGACCAAA 58.990 43.478 3.81 0.00 33.30 3.28
387 389 4.012374 AGATGGCATGTAACTGACCAAAG 58.988 43.478 3.81 0.00 33.30 2.77
388 390 3.222173 TGGCATGTAACTGACCAAAGT 57.778 42.857 0.00 0.00 0.00 2.66
389 391 4.359434 TGGCATGTAACTGACCAAAGTA 57.641 40.909 0.00 0.00 0.00 2.24
390 392 4.720046 TGGCATGTAACTGACCAAAGTAA 58.280 39.130 0.00 0.00 0.00 2.24
391 393 5.133941 TGGCATGTAACTGACCAAAGTAAA 58.866 37.500 0.00 0.00 0.00 2.01
392 394 5.772672 TGGCATGTAACTGACCAAAGTAAAT 59.227 36.000 0.00 0.00 0.00 1.40
393 395 6.092748 GGCATGTAACTGACCAAAGTAAATG 58.907 40.000 0.00 0.00 0.00 2.32
394 396 6.092748 GCATGTAACTGACCAAAGTAAATGG 58.907 40.000 0.00 0.00 43.84 3.16
395 397 6.620678 CATGTAACTGACCAAAGTAAATGGG 58.379 40.000 0.00 0.00 42.48 4.00
396 398 5.942961 TGTAACTGACCAAAGTAAATGGGA 58.057 37.500 0.00 0.00 42.48 4.37
397 399 6.001460 TGTAACTGACCAAAGTAAATGGGAG 58.999 40.000 0.00 0.00 42.48 4.30
398 400 4.034285 ACTGACCAAAGTAAATGGGAGG 57.966 45.455 0.00 0.00 42.48 4.30
399 401 3.245264 ACTGACCAAAGTAAATGGGAGGG 60.245 47.826 0.00 0.00 42.48 4.30
400 402 2.990284 TGACCAAAGTAAATGGGAGGGA 59.010 45.455 0.00 0.00 42.48 4.20
401 403 3.399644 TGACCAAAGTAAATGGGAGGGAA 59.600 43.478 0.00 0.00 42.48 3.97
402 404 3.762288 GACCAAAGTAAATGGGAGGGAAC 59.238 47.826 0.00 0.00 42.48 3.62
403 405 3.096852 CCAAAGTAAATGGGAGGGAACC 58.903 50.000 0.00 0.00 41.26 3.62
404 406 4.433888 CCAAAGTAAATGGGAGGGAACCG 61.434 52.174 0.00 0.00 44.16 4.44
422 424 4.024984 CTGAGTGGGGGAGGGGGA 62.025 72.222 0.00 0.00 0.00 4.81
423 425 4.024984 TGAGTGGGGGAGGGGGAG 62.025 72.222 0.00 0.00 0.00 4.30
424 426 4.825679 GAGTGGGGGAGGGGGAGG 62.826 77.778 0.00 0.00 0.00 4.30
428 430 4.928520 GGGGGAGGGGGAGGGATG 62.929 77.778 0.00 0.00 0.00 3.51
430 432 4.843331 GGGAGGGGGAGGGATGCA 62.843 72.222 0.00 0.00 0.00 3.96
431 433 2.451294 GGAGGGGGAGGGATGCAT 60.451 66.667 0.00 0.00 0.00 3.96
432 434 2.533463 GGAGGGGGAGGGATGCATC 61.533 68.421 18.81 18.81 0.00 3.91
433 435 2.851102 AGGGGGAGGGATGCATCG 60.851 66.667 20.15 0.00 0.00 3.84
434 436 3.958860 GGGGGAGGGATGCATCGG 61.959 72.222 20.15 0.00 0.00 4.18
435 437 3.171388 GGGGAGGGATGCATCGGT 61.171 66.667 20.15 9.80 0.00 4.69
436 438 2.111878 GGGAGGGATGCATCGGTG 59.888 66.667 20.15 0.00 0.00 4.94
437 439 2.443394 GGGAGGGATGCATCGGTGA 61.443 63.158 20.15 0.00 0.00 4.02
438 440 1.757306 GGAGGGATGCATCGGTGAT 59.243 57.895 20.15 4.19 0.00 3.06
439 441 0.604780 GGAGGGATGCATCGGTGATG 60.605 60.000 20.15 2.45 42.37 3.07
440 442 0.604780 GAGGGATGCATCGGTGATGG 60.605 60.000 20.15 0.00 40.10 3.51
441 443 1.056125 AGGGATGCATCGGTGATGGA 61.056 55.000 20.15 6.21 43.87 3.41
442 444 0.179020 GGGATGCATCGGTGATGGAA 60.179 55.000 20.15 0.00 43.06 3.53
443 445 1.233019 GGATGCATCGGTGATGGAAG 58.767 55.000 20.15 0.00 43.06 3.46
444 446 1.202687 GGATGCATCGGTGATGGAAGA 60.203 52.381 20.15 0.00 43.06 2.87
445 447 2.551721 GGATGCATCGGTGATGGAAGAT 60.552 50.000 20.15 0.00 43.06 2.40
446 448 1.957668 TGCATCGGTGATGGAAGATG 58.042 50.000 0.00 0.42 37.44 2.90
447 449 1.233019 GCATCGGTGATGGAAGATGG 58.767 55.000 0.00 0.00 40.10 3.51
448 450 1.888215 CATCGGTGATGGAAGATGGG 58.112 55.000 0.00 0.00 36.51 4.00
449 451 1.417517 CATCGGTGATGGAAGATGGGA 59.582 52.381 0.00 0.00 36.51 4.37
450 452 0.830648 TCGGTGATGGAAGATGGGAC 59.169 55.000 0.00 0.00 0.00 4.46
451 453 0.833287 CGGTGATGGAAGATGGGACT 59.167 55.000 0.00 0.00 0.00 3.85
452 454 1.473965 CGGTGATGGAAGATGGGACTG 60.474 57.143 0.00 0.00 0.00 3.51
453 455 1.133976 GGTGATGGAAGATGGGACTGG 60.134 57.143 0.00 0.00 0.00 4.00
454 456 1.561542 GTGATGGAAGATGGGACTGGT 59.438 52.381 0.00 0.00 0.00 4.00
455 457 2.025887 GTGATGGAAGATGGGACTGGTT 60.026 50.000 0.00 0.00 0.00 3.67
456 458 2.025981 TGATGGAAGATGGGACTGGTTG 60.026 50.000 0.00 0.00 0.00 3.77
457 459 0.038166 TGGAAGATGGGACTGGTTGC 59.962 55.000 0.00 0.00 0.00 4.17
458 460 0.329596 GGAAGATGGGACTGGTTGCT 59.670 55.000 0.00 0.00 0.00 3.91
459 461 1.457346 GAAGATGGGACTGGTTGCTG 58.543 55.000 0.00 0.00 0.00 4.41
460 462 1.003580 GAAGATGGGACTGGTTGCTGA 59.996 52.381 0.00 0.00 0.00 4.26
461 463 1.067295 AGATGGGACTGGTTGCTGAA 58.933 50.000 0.00 0.00 0.00 3.02
462 464 1.637553 AGATGGGACTGGTTGCTGAAT 59.362 47.619 0.00 0.00 0.00 2.57
463 465 2.042162 AGATGGGACTGGTTGCTGAATT 59.958 45.455 0.00 0.00 0.00 2.17
464 466 3.266772 AGATGGGACTGGTTGCTGAATTA 59.733 43.478 0.00 0.00 0.00 1.40
465 467 2.790433 TGGGACTGGTTGCTGAATTAC 58.210 47.619 0.00 0.00 0.00 1.89
466 468 2.375174 TGGGACTGGTTGCTGAATTACT 59.625 45.455 0.00 0.00 0.00 2.24
467 469 3.585289 TGGGACTGGTTGCTGAATTACTA 59.415 43.478 0.00 0.00 0.00 1.82
468 470 4.192317 GGGACTGGTTGCTGAATTACTAG 58.808 47.826 0.00 0.00 0.00 2.57
469 471 3.623510 GGACTGGTTGCTGAATTACTAGC 59.376 47.826 0.00 0.00 40.29 3.42
470 472 4.508662 GACTGGTTGCTGAATTACTAGCT 58.491 43.478 9.40 0.00 40.52 3.32
471 473 5.395324 GGACTGGTTGCTGAATTACTAGCTA 60.395 44.000 9.40 0.00 40.52 3.32
472 474 5.420409 ACTGGTTGCTGAATTACTAGCTAC 58.580 41.667 11.95 11.95 42.32 3.58
473 475 4.430007 TGGTTGCTGAATTACTAGCTACG 58.570 43.478 13.17 0.00 43.40 3.51
474 476 4.158949 TGGTTGCTGAATTACTAGCTACGA 59.841 41.667 13.17 9.20 43.40 3.43
475 477 4.740695 GGTTGCTGAATTACTAGCTACGAG 59.259 45.833 13.17 0.00 43.40 4.18
476 478 5.450137 GGTTGCTGAATTACTAGCTACGAGA 60.450 44.000 13.17 0.00 43.40 4.04
477 479 5.425577 TGCTGAATTACTAGCTACGAGAG 57.574 43.478 9.40 0.00 40.52 3.20
487 489 2.594541 CTACGAGAGCAAATCGGCC 58.405 57.895 9.54 0.00 44.36 6.13
488 490 0.179111 CTACGAGAGCAAATCGGCCA 60.179 55.000 2.24 0.00 44.36 5.36
489 491 0.179111 TACGAGAGCAAATCGGCCAG 60.179 55.000 2.24 0.00 44.36 4.85
490 492 1.448540 CGAGAGCAAATCGGCCAGT 60.449 57.895 2.24 0.00 36.54 4.00
491 493 1.021390 CGAGAGCAAATCGGCCAGTT 61.021 55.000 2.24 0.00 36.54 3.16
492 494 0.449388 GAGAGCAAATCGGCCAGTTG 59.551 55.000 2.24 7.27 0.00 3.16
493 495 0.250901 AGAGCAAATCGGCCAGTTGT 60.251 50.000 2.24 0.00 0.00 3.32
494 496 0.109597 GAGCAAATCGGCCAGTTGTG 60.110 55.000 2.24 0.00 0.00 3.33
496 498 1.805428 GCAAATCGGCCAGTTGTGGT 61.805 55.000 2.24 0.00 46.96 4.16
497 499 0.673437 CAAATCGGCCAGTTGTGGTT 59.327 50.000 2.24 0.00 46.96 3.67
498 500 0.958822 AAATCGGCCAGTTGTGGTTC 59.041 50.000 2.24 0.00 46.96 3.62
499 501 0.110486 AATCGGCCAGTTGTGGTTCT 59.890 50.000 2.24 0.00 46.96 3.01
500 502 0.110486 ATCGGCCAGTTGTGGTTCTT 59.890 50.000 2.24 0.00 46.96 2.52
501 503 0.817634 TCGGCCAGTTGTGGTTCTTG 60.818 55.000 2.24 0.00 46.96 3.02
502 504 0.817634 CGGCCAGTTGTGGTTCTTGA 60.818 55.000 2.24 0.00 46.96 3.02
503 505 1.398692 GGCCAGTTGTGGTTCTTGAA 58.601 50.000 0.00 0.00 46.96 2.69
504 506 1.754226 GGCCAGTTGTGGTTCTTGAAA 59.246 47.619 0.00 0.00 46.96 2.69
505 507 2.167487 GGCCAGTTGTGGTTCTTGAAAA 59.833 45.455 0.00 0.00 46.96 2.29
506 508 3.181466 GGCCAGTTGTGGTTCTTGAAAAT 60.181 43.478 0.00 0.00 46.96 1.82
507 509 4.441792 GCCAGTTGTGGTTCTTGAAAATT 58.558 39.130 0.00 0.00 46.96 1.82
508 510 4.875536 GCCAGTTGTGGTTCTTGAAAATTT 59.124 37.500 0.00 0.00 46.96 1.82
509 511 5.220643 GCCAGTTGTGGTTCTTGAAAATTTG 60.221 40.000 0.00 0.00 46.96 2.32
510 512 5.294060 CCAGTTGTGGTTCTTGAAAATTTGG 59.706 40.000 0.00 0.00 39.30 3.28
511 513 5.294060 CAGTTGTGGTTCTTGAAAATTTGGG 59.706 40.000 0.00 0.00 0.00 4.12
512 514 5.045942 AGTTGTGGTTCTTGAAAATTTGGGT 60.046 36.000 0.00 0.00 0.00 4.51
513 515 5.428184 TGTGGTTCTTGAAAATTTGGGTT 57.572 34.783 0.00 0.00 0.00 4.11
514 516 5.423886 TGTGGTTCTTGAAAATTTGGGTTC 58.576 37.500 0.00 0.00 0.00 3.62
515 517 4.506288 GTGGTTCTTGAAAATTTGGGTTCG 59.494 41.667 0.00 0.00 0.00 3.95
516 518 3.493129 GGTTCTTGAAAATTTGGGTTCGC 59.507 43.478 0.00 0.00 0.00 4.70
517 519 4.368315 GTTCTTGAAAATTTGGGTTCGCT 58.632 39.130 0.00 0.00 0.00 4.93
518 520 4.237349 TCTTGAAAATTTGGGTTCGCTC 57.763 40.909 0.00 0.00 0.00 5.03
519 521 3.005367 TCTTGAAAATTTGGGTTCGCTCC 59.995 43.478 0.00 0.00 0.00 4.70
520 522 1.268352 TGAAAATTTGGGTTCGCTCCG 59.732 47.619 0.00 0.00 0.00 4.63
521 523 1.268625 GAAAATTTGGGTTCGCTCCGT 59.731 47.619 0.00 0.00 0.00 4.69
522 524 2.188062 AAATTTGGGTTCGCTCCGTA 57.812 45.000 0.00 0.00 0.00 4.02
523 525 1.734163 AATTTGGGTTCGCTCCGTAG 58.266 50.000 0.00 0.00 0.00 3.51
524 526 0.899720 ATTTGGGTTCGCTCCGTAGA 59.100 50.000 0.00 0.00 0.00 2.59
525 527 0.680618 TTTGGGTTCGCTCCGTAGAA 59.319 50.000 0.00 0.00 0.00 2.10
526 528 0.680618 TTGGGTTCGCTCCGTAGAAA 59.319 50.000 0.00 0.00 0.00 2.52
527 529 0.680618 TGGGTTCGCTCCGTAGAAAA 59.319 50.000 0.00 0.00 0.00 2.29
528 530 1.337447 TGGGTTCGCTCCGTAGAAAAG 60.337 52.381 0.00 0.00 0.00 2.27
529 531 0.720027 GGTTCGCTCCGTAGAAAAGC 59.280 55.000 0.00 0.00 0.00 3.51
541 543 2.052782 AGAAAAGCACGGGTTGAGTT 57.947 45.000 0.00 0.00 0.00 3.01
543 545 2.099098 AGAAAAGCACGGGTTGAGTTTG 59.901 45.455 0.00 0.00 0.00 2.93
603 605 9.968743 GTCTCTTATGTTTTAGTTATTCAACCG 57.031 33.333 0.00 0.00 35.05 4.44
977 1084 1.064134 GGCAACGCCCGATTGAATC 59.936 57.895 0.00 0.00 44.06 2.52
1042 1149 2.598045 CGGCATCGTCCATCTTCAG 58.402 57.895 0.00 0.00 0.00 3.02
1070 1190 1.550524 AGGACTAGCACAATTCTCGCA 59.449 47.619 0.00 0.00 0.00 5.10
1172 1309 3.996150 TGGTACTAGGTATTAGTGCGC 57.004 47.619 0.00 0.00 43.54 6.09
1239 1422 3.118408 AGGGTGCGCTGAAATCATTAGTA 60.118 43.478 9.73 0.00 0.00 1.82
1333 1541 8.087982 TCTGAATATTTTCAATCCTATCGCAC 57.912 34.615 0.20 0.00 41.22 5.34
1781 4823 9.887862 ATATTTCCCTCCATTTCTGTATGAATT 57.112 29.630 0.00 0.00 34.24 2.17
1842 5046 4.041075 TCACTTCATGCCACTGTAAGGTTA 59.959 41.667 0.00 0.00 39.30 2.85
2273 6129 6.264841 AGTTCATTCTCTGATGAAAAAGGC 57.735 37.500 2.21 0.00 44.92 4.35
3002 6865 8.694540 TGGGTTAATAGGATTTCATTGAACATG 58.305 33.333 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 0.307453 GCGAGCAACATCAACACACA 59.693 50.000 0.00 0.00 0.00 3.72
72 74 1.399727 GCCGACTTTTCATTCACCACG 60.400 52.381 0.00 0.00 0.00 4.94
83 85 1.670083 GGCTACACGGCCGACTTTT 60.670 57.895 35.90 5.52 42.82 2.27
197 199 1.150135 TCTCTTTCCTCCTCACAGGGT 59.850 52.381 0.00 0.00 35.59 4.34
287 289 8.777865 ATCAATCTTATTGTCGTCTTTCTTCA 57.222 30.769 0.00 0.00 0.00 3.02
305 307 2.483876 CCGCAACCGTATGATCAATCT 58.516 47.619 0.00 0.00 0.00 2.40
306 308 1.069906 GCCGCAACCGTATGATCAATC 60.070 52.381 0.00 0.00 0.00 2.67
307 309 0.944386 GCCGCAACCGTATGATCAAT 59.056 50.000 0.00 0.00 0.00 2.57
308 310 0.107897 AGCCGCAACCGTATGATCAA 60.108 50.000 0.00 0.00 0.00 2.57
309 311 0.747852 TAGCCGCAACCGTATGATCA 59.252 50.000 0.00 0.00 0.00 2.92
310 312 1.860676 TTAGCCGCAACCGTATGATC 58.139 50.000 0.00 0.00 0.00 2.92
311 313 2.319136 TTTAGCCGCAACCGTATGAT 57.681 45.000 0.00 0.00 0.00 2.45
312 314 2.004017 CTTTTAGCCGCAACCGTATGA 58.996 47.619 0.00 0.00 0.00 2.15
313 315 1.735571 ACTTTTAGCCGCAACCGTATG 59.264 47.619 0.00 0.00 0.00 2.39
314 316 1.735571 CACTTTTAGCCGCAACCGTAT 59.264 47.619 0.00 0.00 0.00 3.06
315 317 1.149987 CACTTTTAGCCGCAACCGTA 58.850 50.000 0.00 0.00 0.00 4.02
316 318 0.816421 ACACTTTTAGCCGCAACCGT 60.816 50.000 0.00 0.00 0.00 4.83
317 319 1.149987 TACACTTTTAGCCGCAACCG 58.850 50.000 0.00 0.00 0.00 4.44
318 320 2.551032 ACTTACACTTTTAGCCGCAACC 59.449 45.455 0.00 0.00 0.00 3.77
319 321 3.551551 CACTTACACTTTTAGCCGCAAC 58.448 45.455 0.00 0.00 0.00 4.17
320 322 2.550606 CCACTTACACTTTTAGCCGCAA 59.449 45.455 0.00 0.00 0.00 4.85
321 323 2.147958 CCACTTACACTTTTAGCCGCA 58.852 47.619 0.00 0.00 0.00 5.69
322 324 2.148768 ACCACTTACACTTTTAGCCGC 58.851 47.619 0.00 0.00 0.00 6.53
323 325 3.395639 TGACCACTTACACTTTTAGCCG 58.604 45.455 0.00 0.00 0.00 5.52
324 326 3.751698 CCTGACCACTTACACTTTTAGCC 59.248 47.826 0.00 0.00 0.00 3.93
325 327 3.751698 CCCTGACCACTTACACTTTTAGC 59.248 47.826 0.00 0.00 0.00 3.09
326 328 4.324267 CCCCTGACCACTTACACTTTTAG 58.676 47.826 0.00 0.00 0.00 1.85
327 329 3.073356 CCCCCTGACCACTTACACTTTTA 59.927 47.826 0.00 0.00 0.00 1.52
328 330 2.158519 CCCCCTGACCACTTACACTTTT 60.159 50.000 0.00 0.00 0.00 2.27
329 331 1.423921 CCCCCTGACCACTTACACTTT 59.576 52.381 0.00 0.00 0.00 2.66
330 332 1.064825 CCCCCTGACCACTTACACTT 58.935 55.000 0.00 0.00 0.00 3.16
331 333 0.192566 TCCCCCTGACCACTTACACT 59.807 55.000 0.00 0.00 0.00 3.55
332 334 0.613777 CTCCCCCTGACCACTTACAC 59.386 60.000 0.00 0.00 0.00 2.90
333 335 0.546747 CCTCCCCCTGACCACTTACA 60.547 60.000 0.00 0.00 0.00 2.41
334 336 1.272554 CCCTCCCCCTGACCACTTAC 61.273 65.000 0.00 0.00 0.00 2.34
335 337 1.082206 CCCTCCCCCTGACCACTTA 59.918 63.158 0.00 0.00 0.00 2.24
336 338 2.204151 CCCTCCCCCTGACCACTT 60.204 66.667 0.00 0.00 0.00 3.16
337 339 4.354943 CCCCTCCCCCTGACCACT 62.355 72.222 0.00 0.00 0.00 4.00
340 342 3.677689 AATCCCCCTCCCCCTGACC 62.678 68.421 0.00 0.00 0.00 4.02
341 343 2.044620 AATCCCCCTCCCCCTGAC 59.955 66.667 0.00 0.00 0.00 3.51
342 344 2.044450 CAATCCCCCTCCCCCTGA 59.956 66.667 0.00 0.00 0.00 3.86
343 345 2.044450 TCAATCCCCCTCCCCCTG 59.956 66.667 0.00 0.00 0.00 4.45
344 346 2.378522 CTCAATCCCCCTCCCCCT 59.621 66.667 0.00 0.00 0.00 4.79
345 347 2.778717 CCTCAATCCCCCTCCCCC 60.779 72.222 0.00 0.00 0.00 5.40
346 348 1.772156 CTCCTCAATCCCCCTCCCC 60.772 68.421 0.00 0.00 0.00 4.81
347 349 0.766288 CTCTCCTCAATCCCCCTCCC 60.766 65.000 0.00 0.00 0.00 4.30
348 350 0.266152 TCTCTCCTCAATCCCCCTCC 59.734 60.000 0.00 0.00 0.00 4.30
349 351 1.977129 CATCTCTCCTCAATCCCCCTC 59.023 57.143 0.00 0.00 0.00 4.30
350 352 1.415716 CCATCTCTCCTCAATCCCCCT 60.416 57.143 0.00 0.00 0.00 4.79
351 353 1.063183 CCATCTCTCCTCAATCCCCC 58.937 60.000 0.00 0.00 0.00 5.40
352 354 0.399833 GCCATCTCTCCTCAATCCCC 59.600 60.000 0.00 0.00 0.00 4.81
353 355 1.135094 TGCCATCTCTCCTCAATCCC 58.865 55.000 0.00 0.00 0.00 3.85
354 356 2.106166 ACATGCCATCTCTCCTCAATCC 59.894 50.000 0.00 0.00 0.00 3.01
355 357 3.488778 ACATGCCATCTCTCCTCAATC 57.511 47.619 0.00 0.00 0.00 2.67
356 358 4.411540 AGTTACATGCCATCTCTCCTCAAT 59.588 41.667 0.00 0.00 0.00 2.57
357 359 3.776969 AGTTACATGCCATCTCTCCTCAA 59.223 43.478 0.00 0.00 0.00 3.02
358 360 3.133542 CAGTTACATGCCATCTCTCCTCA 59.866 47.826 0.00 0.00 0.00 3.86
359 361 3.386078 TCAGTTACATGCCATCTCTCCTC 59.614 47.826 0.00 0.00 0.00 3.71
360 362 3.133721 GTCAGTTACATGCCATCTCTCCT 59.866 47.826 0.00 0.00 0.00 3.69
361 363 3.462021 GTCAGTTACATGCCATCTCTCC 58.538 50.000 0.00 0.00 0.00 3.71
362 364 3.118629 TGGTCAGTTACATGCCATCTCTC 60.119 47.826 0.00 0.00 0.00 3.20
363 365 2.840038 TGGTCAGTTACATGCCATCTCT 59.160 45.455 0.00 0.00 0.00 3.10
364 366 3.266510 TGGTCAGTTACATGCCATCTC 57.733 47.619 0.00 0.00 0.00 2.75
365 367 3.719268 TTGGTCAGTTACATGCCATCT 57.281 42.857 0.00 0.00 0.00 2.90
366 368 3.758554 ACTTTGGTCAGTTACATGCCATC 59.241 43.478 0.00 0.00 0.00 3.51
367 369 3.766545 ACTTTGGTCAGTTACATGCCAT 58.233 40.909 0.00 0.00 0.00 4.40
368 370 3.222173 ACTTTGGTCAGTTACATGCCA 57.778 42.857 0.00 0.00 0.00 4.92
369 371 5.699097 TTTACTTTGGTCAGTTACATGCC 57.301 39.130 0.00 0.00 0.00 4.40
370 372 6.092748 CCATTTACTTTGGTCAGTTACATGC 58.907 40.000 0.00 0.00 0.00 4.06
371 373 6.432783 TCCCATTTACTTTGGTCAGTTACATG 59.567 38.462 0.00 0.00 31.99 3.21
372 374 6.548321 TCCCATTTACTTTGGTCAGTTACAT 58.452 36.000 0.00 0.00 31.99 2.29
373 375 5.942961 TCCCATTTACTTTGGTCAGTTACA 58.057 37.500 0.00 0.00 31.99 2.41
374 376 5.414765 CCTCCCATTTACTTTGGTCAGTTAC 59.585 44.000 0.00 0.00 31.99 2.50
375 377 5.515886 CCCTCCCATTTACTTTGGTCAGTTA 60.516 44.000 0.00 0.00 31.99 2.24
376 378 4.407365 CCTCCCATTTACTTTGGTCAGTT 58.593 43.478 0.00 0.00 31.99 3.16
377 379 3.245264 CCCTCCCATTTACTTTGGTCAGT 60.245 47.826 0.00 0.00 31.99 3.41
378 380 3.010138 TCCCTCCCATTTACTTTGGTCAG 59.990 47.826 0.00 0.00 31.99 3.51
379 381 2.990284 TCCCTCCCATTTACTTTGGTCA 59.010 45.455 0.00 0.00 31.99 4.02
380 382 3.732048 TCCCTCCCATTTACTTTGGTC 57.268 47.619 0.00 0.00 31.99 4.02
381 383 3.501568 GGTTCCCTCCCATTTACTTTGGT 60.502 47.826 0.00 0.00 31.99 3.67
382 384 3.096852 GGTTCCCTCCCATTTACTTTGG 58.903 50.000 0.00 0.00 0.00 3.28
383 385 2.752903 CGGTTCCCTCCCATTTACTTTG 59.247 50.000 0.00 0.00 0.00 2.77
384 386 2.882643 GCGGTTCCCTCCCATTTACTTT 60.883 50.000 0.00 0.00 0.00 2.66
385 387 1.340697 GCGGTTCCCTCCCATTTACTT 60.341 52.381 0.00 0.00 0.00 2.24
386 388 0.255033 GCGGTTCCCTCCCATTTACT 59.745 55.000 0.00 0.00 0.00 2.24
387 389 0.255033 AGCGGTTCCCTCCCATTTAC 59.745 55.000 0.00 0.00 0.00 2.01
388 390 0.254747 CAGCGGTTCCCTCCCATTTA 59.745 55.000 0.00 0.00 0.00 1.40
389 391 1.000896 CAGCGGTTCCCTCCCATTT 60.001 57.895 0.00 0.00 0.00 2.32
390 392 1.915078 CTCAGCGGTTCCCTCCCATT 61.915 60.000 0.00 0.00 0.00 3.16
391 393 2.285368 TCAGCGGTTCCCTCCCAT 60.285 61.111 0.00 0.00 0.00 4.00
392 394 3.003173 CTCAGCGGTTCCCTCCCA 61.003 66.667 0.00 0.00 0.00 4.37
393 395 3.003763 ACTCAGCGGTTCCCTCCC 61.004 66.667 0.00 0.00 0.00 4.30
394 396 2.266055 CACTCAGCGGTTCCCTCC 59.734 66.667 0.00 0.00 0.00 4.30
395 397 2.266055 CCACTCAGCGGTTCCCTC 59.734 66.667 0.00 0.00 0.00 4.30
396 398 3.322466 CCCACTCAGCGGTTCCCT 61.322 66.667 0.00 0.00 0.00 4.20
397 399 4.410400 CCCCACTCAGCGGTTCCC 62.410 72.222 0.00 0.00 0.00 3.97
398 400 4.410400 CCCCCACTCAGCGGTTCC 62.410 72.222 0.00 0.00 0.00 3.62
399 401 3.316573 CTCCCCCACTCAGCGGTTC 62.317 68.421 0.00 0.00 0.00 3.62
400 402 3.322466 CTCCCCCACTCAGCGGTT 61.322 66.667 0.00 0.00 0.00 4.44
405 407 4.024984 TCCCCCTCCCCCACTCAG 62.025 72.222 0.00 0.00 0.00 3.35
406 408 4.024984 CTCCCCCTCCCCCACTCA 62.025 72.222 0.00 0.00 0.00 3.41
407 409 4.825679 CCTCCCCCTCCCCCACTC 62.826 77.778 0.00 0.00 0.00 3.51
411 413 4.928520 CATCCCTCCCCCTCCCCC 62.929 77.778 0.00 0.00 0.00 5.40
413 415 4.843331 TGCATCCCTCCCCCTCCC 62.843 72.222 0.00 0.00 0.00 4.30
414 416 2.451294 ATGCATCCCTCCCCCTCC 60.451 66.667 0.00 0.00 0.00 4.30
415 417 2.888447 CGATGCATCCCTCCCCCTC 61.888 68.421 20.87 0.00 0.00 4.30
416 418 2.851102 CGATGCATCCCTCCCCCT 60.851 66.667 20.87 0.00 0.00 4.79
417 419 3.958860 CCGATGCATCCCTCCCCC 61.959 72.222 20.87 0.00 0.00 5.40
418 420 3.171388 ACCGATGCATCCCTCCCC 61.171 66.667 20.87 0.00 0.00 4.81
419 421 1.772819 ATCACCGATGCATCCCTCCC 61.773 60.000 20.87 0.00 0.00 4.30
420 422 0.604780 CATCACCGATGCATCCCTCC 60.605 60.000 20.87 0.00 33.17 4.30
421 423 0.604780 CCATCACCGATGCATCCCTC 60.605 60.000 20.87 0.00 38.59 4.30
422 424 1.056125 TCCATCACCGATGCATCCCT 61.056 55.000 20.87 2.97 38.59 4.20
423 425 0.179020 TTCCATCACCGATGCATCCC 60.179 55.000 20.87 0.00 38.59 3.85
424 426 1.202687 TCTTCCATCACCGATGCATCC 60.203 52.381 20.87 3.71 38.59 3.51
425 427 2.245159 TCTTCCATCACCGATGCATC 57.755 50.000 17.10 17.10 38.59 3.91
426 428 2.501261 CATCTTCCATCACCGATGCAT 58.499 47.619 0.00 0.00 38.59 3.96
427 429 1.475571 CCATCTTCCATCACCGATGCA 60.476 52.381 0.00 0.00 38.59 3.96
428 430 1.233019 CCATCTTCCATCACCGATGC 58.767 55.000 0.00 0.00 38.59 3.91
429 431 1.417517 TCCCATCTTCCATCACCGATG 59.582 52.381 0.00 0.00 39.52 3.84
430 432 1.417890 GTCCCATCTTCCATCACCGAT 59.582 52.381 0.00 0.00 0.00 4.18
431 433 0.830648 GTCCCATCTTCCATCACCGA 59.169 55.000 0.00 0.00 0.00 4.69
432 434 0.833287 AGTCCCATCTTCCATCACCG 59.167 55.000 0.00 0.00 0.00 4.94
433 435 1.133976 CCAGTCCCATCTTCCATCACC 60.134 57.143 0.00 0.00 0.00 4.02
434 436 1.561542 ACCAGTCCCATCTTCCATCAC 59.438 52.381 0.00 0.00 0.00 3.06
435 437 1.971149 ACCAGTCCCATCTTCCATCA 58.029 50.000 0.00 0.00 0.00 3.07
436 438 2.648059 CAACCAGTCCCATCTTCCATC 58.352 52.381 0.00 0.00 0.00 3.51
437 439 1.341383 GCAACCAGTCCCATCTTCCAT 60.341 52.381 0.00 0.00 0.00 3.41
438 440 0.038166 GCAACCAGTCCCATCTTCCA 59.962 55.000 0.00 0.00 0.00 3.53
439 441 0.329596 AGCAACCAGTCCCATCTTCC 59.670 55.000 0.00 0.00 0.00 3.46
440 442 1.003580 TCAGCAACCAGTCCCATCTTC 59.996 52.381 0.00 0.00 0.00 2.87
441 443 1.067295 TCAGCAACCAGTCCCATCTT 58.933 50.000 0.00 0.00 0.00 2.40
442 444 1.067295 TTCAGCAACCAGTCCCATCT 58.933 50.000 0.00 0.00 0.00 2.90
443 445 2.134789 ATTCAGCAACCAGTCCCATC 57.865 50.000 0.00 0.00 0.00 3.51
444 446 2.610438 AATTCAGCAACCAGTCCCAT 57.390 45.000 0.00 0.00 0.00 4.00
445 447 2.375174 AGTAATTCAGCAACCAGTCCCA 59.625 45.455 0.00 0.00 0.00 4.37
446 448 3.073274 AGTAATTCAGCAACCAGTCCC 57.927 47.619 0.00 0.00 0.00 4.46
447 449 3.623510 GCTAGTAATTCAGCAACCAGTCC 59.376 47.826 0.00 0.00 37.73 3.85
448 450 4.508662 AGCTAGTAATTCAGCAACCAGTC 58.491 43.478 8.74 0.00 40.36 3.51
449 451 4.559862 AGCTAGTAATTCAGCAACCAGT 57.440 40.909 8.74 0.00 40.36 4.00
450 452 4.504461 CGTAGCTAGTAATTCAGCAACCAG 59.496 45.833 0.00 0.00 40.36 4.00
451 453 4.158949 TCGTAGCTAGTAATTCAGCAACCA 59.841 41.667 0.00 0.00 40.36 3.67
452 454 4.679662 TCGTAGCTAGTAATTCAGCAACC 58.320 43.478 0.00 0.00 40.36 3.77
453 455 5.579718 TCTCGTAGCTAGTAATTCAGCAAC 58.420 41.667 0.00 0.00 40.36 4.17
454 456 5.822278 CTCTCGTAGCTAGTAATTCAGCAA 58.178 41.667 0.00 0.00 40.36 3.91
455 457 5.425577 CTCTCGTAGCTAGTAATTCAGCA 57.574 43.478 0.00 0.00 40.36 4.41
469 471 0.179111 TGGCCGATTTGCTCTCGTAG 60.179 55.000 0.00 0.00 34.36 3.51
470 472 0.179111 CTGGCCGATTTGCTCTCGTA 60.179 55.000 0.00 0.00 34.36 3.43
471 473 1.448540 CTGGCCGATTTGCTCTCGT 60.449 57.895 0.00 0.00 34.36 4.18
472 474 1.021390 AACTGGCCGATTTGCTCTCG 61.021 55.000 0.00 0.00 35.92 4.04
473 475 0.449388 CAACTGGCCGATTTGCTCTC 59.551 55.000 0.00 0.00 0.00 3.20
474 476 0.250901 ACAACTGGCCGATTTGCTCT 60.251 50.000 9.99 0.00 0.00 4.09
475 477 0.109597 CACAACTGGCCGATTTGCTC 60.110 55.000 9.99 0.00 0.00 4.26
476 478 1.526575 CCACAACTGGCCGATTTGCT 61.527 55.000 9.99 0.00 0.00 3.91
477 479 1.080569 CCACAACTGGCCGATTTGC 60.081 57.895 9.99 0.00 0.00 3.68
478 480 0.673437 AACCACAACTGGCCGATTTG 59.327 50.000 0.00 3.55 42.08 2.32
479 481 0.958822 GAACCACAACTGGCCGATTT 59.041 50.000 0.00 0.00 42.08 2.17
480 482 0.110486 AGAACCACAACTGGCCGATT 59.890 50.000 0.00 0.00 42.08 3.34
481 483 0.110486 AAGAACCACAACTGGCCGAT 59.890 50.000 0.00 0.00 42.08 4.18
482 484 0.817634 CAAGAACCACAACTGGCCGA 60.818 55.000 0.00 0.00 42.08 5.54
483 485 0.817634 TCAAGAACCACAACTGGCCG 60.818 55.000 0.00 0.00 42.08 6.13
484 486 1.398692 TTCAAGAACCACAACTGGCC 58.601 50.000 0.00 0.00 42.08 5.36
485 487 3.518634 TTTTCAAGAACCACAACTGGC 57.481 42.857 0.00 0.00 42.08 4.85
486 488 5.294060 CCAAATTTTCAAGAACCACAACTGG 59.706 40.000 0.00 0.00 44.26 4.00
487 489 5.294060 CCCAAATTTTCAAGAACCACAACTG 59.706 40.000 0.00 0.00 0.00 3.16
488 490 5.045942 ACCCAAATTTTCAAGAACCACAACT 60.046 36.000 0.00 0.00 0.00 3.16
489 491 5.182487 ACCCAAATTTTCAAGAACCACAAC 58.818 37.500 0.00 0.00 0.00 3.32
490 492 5.428184 ACCCAAATTTTCAAGAACCACAA 57.572 34.783 0.00 0.00 0.00 3.33
491 493 5.423886 GAACCCAAATTTTCAAGAACCACA 58.576 37.500 0.00 0.00 0.00 4.17
492 494 4.506288 CGAACCCAAATTTTCAAGAACCAC 59.494 41.667 0.00 0.00 0.00 4.16
493 495 4.688021 CGAACCCAAATTTTCAAGAACCA 58.312 39.130 0.00 0.00 0.00 3.67
494 496 3.493129 GCGAACCCAAATTTTCAAGAACC 59.507 43.478 0.00 0.00 0.00 3.62
495 497 4.368315 AGCGAACCCAAATTTTCAAGAAC 58.632 39.130 0.00 0.00 0.00 3.01
496 498 4.500716 GGAGCGAACCCAAATTTTCAAGAA 60.501 41.667 0.00 0.00 0.00 2.52
497 499 3.005367 GGAGCGAACCCAAATTTTCAAGA 59.995 43.478 0.00 0.00 0.00 3.02
498 500 3.317150 GGAGCGAACCCAAATTTTCAAG 58.683 45.455 0.00 0.00 0.00 3.02
499 501 2.287909 CGGAGCGAACCCAAATTTTCAA 60.288 45.455 0.00 0.00 0.00 2.69
500 502 1.268352 CGGAGCGAACCCAAATTTTCA 59.732 47.619 0.00 0.00 0.00 2.69
501 503 1.268625 ACGGAGCGAACCCAAATTTTC 59.731 47.619 0.00 0.00 0.00 2.29
502 504 1.324383 ACGGAGCGAACCCAAATTTT 58.676 45.000 0.00 0.00 0.00 1.82
503 505 2.081462 CTACGGAGCGAACCCAAATTT 58.919 47.619 0.00 0.00 0.00 1.82
504 506 1.276989 TCTACGGAGCGAACCCAAATT 59.723 47.619 0.00 0.00 0.00 1.82
505 507 0.899720 TCTACGGAGCGAACCCAAAT 59.100 50.000 0.00 0.00 0.00 2.32
506 508 0.680618 TTCTACGGAGCGAACCCAAA 59.319 50.000 0.00 0.00 0.00 3.28
507 509 0.680618 TTTCTACGGAGCGAACCCAA 59.319 50.000 0.00 0.00 0.00 4.12
508 510 0.680618 TTTTCTACGGAGCGAACCCA 59.319 50.000 0.00 0.00 0.00 4.51
509 511 1.356938 CTTTTCTACGGAGCGAACCC 58.643 55.000 0.00 0.00 0.00 4.11
510 512 0.720027 GCTTTTCTACGGAGCGAACC 59.280 55.000 0.00 0.00 0.00 3.62
511 513 1.126296 GTGCTTTTCTACGGAGCGAAC 59.874 52.381 0.00 0.00 39.23 3.95
512 514 1.425412 GTGCTTTTCTACGGAGCGAA 58.575 50.000 0.00 0.00 39.23 4.70
513 515 0.731514 CGTGCTTTTCTACGGAGCGA 60.732 55.000 0.00 0.00 39.23 4.93
514 516 1.702299 CGTGCTTTTCTACGGAGCG 59.298 57.895 0.00 0.00 39.23 5.03
519 521 1.459592 CTCAACCCGTGCTTTTCTACG 59.540 52.381 0.00 0.00 39.83 3.51
520 522 2.490991 ACTCAACCCGTGCTTTTCTAC 58.509 47.619 0.00 0.00 0.00 2.59
521 523 2.922740 ACTCAACCCGTGCTTTTCTA 57.077 45.000 0.00 0.00 0.00 2.10
522 524 2.052782 AACTCAACCCGTGCTTTTCT 57.947 45.000 0.00 0.00 0.00 2.52
523 525 2.159296 ACAAACTCAACCCGTGCTTTTC 60.159 45.455 0.00 0.00 0.00 2.29
524 526 1.822371 ACAAACTCAACCCGTGCTTTT 59.178 42.857 0.00 0.00 0.00 2.27
525 527 1.404035 GACAAACTCAACCCGTGCTTT 59.596 47.619 0.00 0.00 0.00 3.51
526 528 1.021968 GACAAACTCAACCCGTGCTT 58.978 50.000 0.00 0.00 0.00 3.91
527 529 1.157870 CGACAAACTCAACCCGTGCT 61.158 55.000 0.00 0.00 0.00 4.40
528 530 1.278637 CGACAAACTCAACCCGTGC 59.721 57.895 0.00 0.00 0.00 5.34
529 531 1.503818 CCCGACAAACTCAACCCGTG 61.504 60.000 0.00 0.00 0.00 4.94
534 536 1.332686 GGTGAACCCGACAAACTCAAC 59.667 52.381 0.00 0.00 0.00 3.18
580 582 7.390996 TGCCGGTTGAATAACTAAAACATAAGA 59.609 33.333 1.90 0.00 36.99 2.10
603 605 2.030805 GCCAGATTAACGATGGATTGCC 60.031 50.000 6.61 0.00 36.09 4.52
662 664 1.527370 GGGAATAGCTCGGCCTGTT 59.473 57.895 0.00 0.00 0.00 3.16
663 665 2.444256 GGGGAATAGCTCGGCCTGT 61.444 63.158 0.00 0.00 0.00 4.00
977 1084 1.136147 GCAGATCTTGGCAGCAACG 59.864 57.895 0.00 0.00 0.00 4.10
1026 1133 1.216122 GAGCTGAAGATGGACGATGC 58.784 55.000 0.00 0.00 0.00 3.91
1034 1141 1.523258 CCTGCCGGAGCTGAAGATG 60.523 63.158 5.05 0.00 40.18 2.90
1042 1149 3.461773 TGCTAGTCCTGCCGGAGC 61.462 66.667 5.05 3.29 40.84 4.70
1070 1190 4.353788 AGATGAGAGTAGAGGATACCAGCT 59.646 45.833 0.00 0.00 37.17 4.24
1172 1309 4.093998 CACTGGCTGATTAACTACTTGCTG 59.906 45.833 0.00 0.00 0.00 4.41
1239 1422 4.638304 ACTCGTACCAGTTTAGCACAATT 58.362 39.130 0.00 0.00 0.00 2.32
1333 1541 5.489249 AGAGATGCAGAATATACATGCCAG 58.511 41.667 0.00 0.00 39.22 4.85
1781 4823 9.419297 GCATGTTATTGTAACGATCTAGGATTA 57.581 33.333 0.00 0.00 0.00 1.75
2273 6129 3.977244 GTGCGCCCCAAACACTGG 61.977 66.667 4.18 0.00 45.97 4.00
2589 6449 4.429108 GAGCGAGCTATCTTTGAAAGAGT 58.571 43.478 13.56 4.76 41.61 3.24
3002 6865 2.151202 TCCCTGTGCAGAACGAAATTC 58.849 47.619 0.02 0.00 37.62 2.17


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

AutoCloner maintained by Alex Coulton.