Multiple sequence alignment - TraesCS6B01G393100

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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 TraesCS6B01G393100 chr6B 100.000 4123 0 0 1 4123 667965685 667961563 0.000000e+00 7614.0
1 TraesCS6B01G393100 chr6B 94.615 130 7 0 320 449 346808772 346808643 6.990000e-48 202.0
2 TraesCS6B01G393100 chr6D 92.652 1810 82 22 1719 3517 441917297 441915528 0.000000e+00 2558.0
3 TraesCS6B01G393100 chr6D 87.619 630 14 20 3500 4123 441915513 441914942 0.000000e+00 673.0
4 TraesCS6B01G393100 chr6D 86.239 545 38 12 872 1415 441918369 441917861 1.290000e-154 556.0
5 TraesCS6B01G393100 chr6D 82.583 333 39 11 1 323 441920232 441919909 4.060000e-70 276.0
6 TraesCS6B01G393100 chr6D 91.257 183 8 4 1480 1657 441917666 441917487 4.120000e-60 243.0
7 TraesCS6B01G393100 chr6D 90.789 152 12 1 1562 1713 441917487 441917338 6.990000e-48 202.0
8 TraesCS6B01G393100 chr6D 91.608 143 11 1 3896 4038 251262528 251262387 3.250000e-46 196.0
9 TraesCS6B01G393100 chr6D 80.702 228 11 4 3896 4123 219293590 219293396 3.320000e-31 147.0
10 TraesCS6B01G393100 chr6D 88.235 119 9 3 612 725 441919712 441919594 2.000000e-28 137.0
11 TraesCS6B01G393100 chr6D 100.000 28 0 0 3194 3221 16831170 16831143 7.000000e-03 52.8
12 TraesCS6B01G393100 chr6A 92.621 1423 76 14 1719 3140 591342184 591340790 0.000000e+00 2019.0
13 TraesCS6B01G393100 chr6A 87.378 1022 61 28 3130 4123 591339866 591338885 0.000000e+00 1110.0
14 TraesCS6B01G393100 chr6A 89.249 586 33 12 832 1415 591343305 591342748 0.000000e+00 706.0
15 TraesCS6B01G393100 chr6A 83.165 297 39 9 466 756 591343722 591343431 1.140000e-65 261.0
16 TraesCS6B01G393100 chr6A 91.257 183 8 4 1480 1657 591342553 591342374 4.120000e-60 243.0
17 TraesCS6B01G393100 chr6A 100.000 30 0 0 3174 3203 563547997 563548026 5.760000e-04 56.5
18 TraesCS6B01G393100 chr7B 93.636 330 20 1 3794 4123 597762652 597762980 3.700000e-135 492.0
19 TraesCS6B01G393100 chr7A 85.526 228 20 5 3896 4123 51996239 51996453 4.150000e-55 226.0
20 TraesCS6B01G393100 chr7A 94.203 138 8 0 321 458 625074756 625074619 1.160000e-50 211.0
21 TraesCS6B01G393100 chr7A 92.308 39 3 0 3188 3226 90475968 90475930 5.760000e-04 56.5
22 TraesCS6B01G393100 chrUn 95.556 135 6 0 315 449 297895210 297895076 2.500000e-52 217.0
23 TraesCS6B01G393100 chrUn 94.203 138 8 0 321 458 36276022 36275885 1.160000e-50 211.0
24 TraesCS6B01G393100 chrUn 93.617 141 9 0 318 458 313733999 313734139 1.160000e-50 211.0
25 TraesCS6B01G393100 chr1B 94.928 138 6 1 319 456 517899048 517899184 8.980000e-52 215.0
26 TraesCS6B01G393100 chr1A 93.706 143 8 1 317 458 485564161 485564019 3.230000e-51 213.0
27 TraesCS6B01G393100 chr1A 100.000 28 0 0 3176 3203 5494171 5494144 7.000000e-03 52.8
28 TraesCS6B01G393100 chr3B 94.203 138 8 0 321 458 5468249 5468112 1.160000e-50 211.0
29 TraesCS6B01G393100 chr3B 100.000 29 0 0 3193 3221 682119551 682119523 2.000000e-03 54.7
30 TraesCS6B01G393100 chr2B 93.617 141 9 0 318 458 160674692 160674832 1.160000e-50 211.0
31 TraesCS6B01G393100 chr2B 90.090 111 11 0 4013 4123 746389250 746389140 1.190000e-30 145.0
32 TraesCS6B01G393100 chr3D 88.172 93 10 1 4027 4118 599367958 599367866 4.360000e-20 110.0
33 TraesCS6B01G393100 chr3D 100.000 28 0 0 3176 3203 290858238 290858211 7.000000e-03 52.8
34 TraesCS6B01G393100 chr5D 91.304 46 4 0 3176 3221 319372168 319372123 3.440000e-06 63.9
35 TraesCS6B01G393100 chr5D 94.286 35 2 0 3169 3203 412263453 412263419 2.000000e-03 54.7
36 TraesCS6B01G393100 chr2D 91.304 46 4 0 3176 3221 79445970 79445925 3.440000e-06 63.9
37 TraesCS6B01G393100 chr2D 91.304 46 4 0 3176 3221 612938837 612938882 3.440000e-06 63.9
38 TraesCS6B01G393100 chr2D 94.444 36 2 0 3168 3203 547203612 547203577 5.760000e-04 56.5
39 TraesCS6B01G393100 chr7D 90.698 43 4 0 3188 3230 89286548 89286506 1.600000e-04 58.4
40 TraesCS6B01G393100 chr3A 85.965 57 5 3 3195 3250 201478332 201478278 1.600000e-04 58.4
41 TraesCS6B01G393100 chr5B 100.000 30 0 0 3193 3222 529822023 529822052 5.760000e-04 56.5
42 TraesCS6B01G393100 chr1D 90.244 41 2 2 3164 3203 59131208 59131247 7.000000e-03 52.8


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 TraesCS6B01G393100 chr6B 667961563 667965685 4122 True 7614.000000 7614 100.000 1 4123 1 chr6B.!!$R2 4122
1 TraesCS6B01G393100 chr6D 441914942 441920232 5290 True 663.571429 2558 88.482 1 4123 7 chr6D.!!$R4 4122
2 TraesCS6B01G393100 chr6A 591338885 591343722 4837 True 867.800000 2019 88.734 466 4123 5 chr6A.!!$R1 3657

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
337 348 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.0 0.00 0.00 0.00 4.12 F
1427 2626 0.036732 TGGAAGACGCTGCTTTGGAT 59.963 50.0 0.00 0.00 0.00 3.41 F
1433 2632 0.038892 ACGCTGCTTTGGATGCAAAG 60.039 50.0 29.35 29.35 43.11 2.77 F
1636 3065 0.177604 CTCTGGGCACTTGGCTCTAG 59.822 60.0 2.47 0.26 46.01 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 3642 0.108233 TCTGCACTGCACGCATCATA 60.108 50.0 6.52 0.0 39.02 2.15 R
2337 3802 0.102481 TCCTATCGTTTGGCTCTCGC 59.898 55.0 0.00 0.0 0.00 5.03 R
2954 4422 0.530870 GGGACTATTCAGCTGACGCC 60.531 60.0 18.03 12.8 36.60 5.68 R
3628 6112 0.395724 CAATCCAACCCCCTGCCTAC 60.396 60.0 0.00 0.0 0.00 3.18 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
22 23 3.249189 AACAAGGGCTCGGAGGCA 61.249 61.111 29.49 0.00 43.44 4.75
28 29 4.416738 GGCTCGGAGGCAAAGGCT 62.417 66.667 24.86 0.00 40.97 4.58
40 41 1.600916 AAAGGCTGCCGAAGACACC 60.601 57.895 13.96 0.00 35.71 4.16
44 45 2.030562 CTGCCGAAGACACCCGTT 59.969 61.111 0.00 0.00 0.00 4.44
49 50 1.666872 CGAAGACACCCGTTCCCAC 60.667 63.158 0.00 0.00 0.00 4.61
54 55 0.673644 GACACCCGTTCCCACATCTG 60.674 60.000 0.00 0.00 0.00 2.90
80 81 4.171103 GGTAAGCCCGGGATGCGT 62.171 66.667 29.31 10.08 0.00 5.24
105 106 2.179764 GCGCATTGGAGCAAACCTA 58.820 52.632 0.30 0.00 39.87 3.08
111 112 1.448985 TTGGAGCAAACCTACGATGC 58.551 50.000 0.00 0.00 40.34 3.91
128 129 0.108472 TGCTCATGCACTCTTCGGAG 60.108 55.000 0.00 0.00 45.31 4.63
143 144 1.541672 GGAGGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
145 146 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
146 147 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
147 148 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
148 149 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
149 150 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
150 151 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
151 152 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
152 153 0.330431 AGGAGGAGGAGGAGGAGGAT 60.330 60.000 0.00 0.00 0.00 3.24
153 154 0.178935 GGAGGAGGAGGAGGAGGATG 60.179 65.000 0.00 0.00 0.00 3.51
154 155 0.856982 GAGGAGGAGGAGGAGGATGA 59.143 60.000 0.00 0.00 0.00 2.92
155 156 0.560688 AGGAGGAGGAGGAGGATGAC 59.439 60.000 0.00 0.00 0.00 3.06
156 157 0.825840 GGAGGAGGAGGAGGATGACG 60.826 65.000 0.00 0.00 0.00 4.35
167 168 3.272334 GATGACGGTGCCGCATCC 61.272 66.667 24.04 13.82 41.87 3.51
215 216 2.904866 TGCCTTGACCCGTGTTGC 60.905 61.111 0.00 0.00 0.00 4.17
222 223 2.280592 ACCCGTGTTGCGTCTTCC 60.281 61.111 0.00 0.00 39.32 3.46
232 233 4.018609 CGTCTTCCAGCGCTATGG 57.981 61.111 10.99 10.01 42.11 2.74
250 261 2.982744 GCGACAAAGAGGCAAGGGC 61.983 63.158 0.00 0.00 40.13 5.19
266 277 3.497031 GCAGCCGCGGGTAAACTC 61.497 66.667 31.92 9.33 0.00 3.01
299 310 6.893583 ACTCTAGTATTGAGAACATGCCAAT 58.106 36.000 0.00 0.75 35.66 3.16
326 337 7.450124 TTTCTAGTCCGATGATATGTACTCC 57.550 40.000 0.00 0.00 0.00 3.85
327 338 5.498393 TCTAGTCCGATGATATGTACTCCC 58.502 45.833 0.00 0.00 0.00 4.30
328 339 4.390129 AGTCCGATGATATGTACTCCCT 57.610 45.455 0.00 0.00 0.00 4.20
329 340 4.337145 AGTCCGATGATATGTACTCCCTC 58.663 47.826 0.00 0.00 0.00 4.30
330 341 3.444388 GTCCGATGATATGTACTCCCTCC 59.556 52.174 0.00 0.00 0.00 4.30
331 342 2.423892 CCGATGATATGTACTCCCTCCG 59.576 54.545 0.00 0.00 0.00 4.63
332 343 3.082548 CGATGATATGTACTCCCTCCGT 58.917 50.000 0.00 0.00 0.00 4.69
333 344 3.127203 CGATGATATGTACTCCCTCCGTC 59.873 52.174 0.00 0.00 0.00 4.79
334 345 2.872732 TGATATGTACTCCCTCCGTCC 58.127 52.381 0.00 0.00 0.00 4.79
335 346 2.169330 GATATGTACTCCCTCCGTCCC 58.831 57.143 0.00 0.00 0.00 4.46
336 347 0.928505 TATGTACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
337 348 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
338 349 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
339 350 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
340 351 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
341 352 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
342 353 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
343 354 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
344 355 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
345 356 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
346 357 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
347 358 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
348 359 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
349 360 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
350 361 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
351 362 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
352 363 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
353 364 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
354 365 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
355 366 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
356 367 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
357 368 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
358 369 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
359 370 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
360 371 9.971922 CCAAAATTCTTGTCTTAGATTTGTCTT 57.028 29.630 0.00 0.00 28.79 3.01
367 378 9.658799 TCTTGTCTTAGATTTGTCTTGATAAGG 57.341 33.333 12.58 0.00 0.00 2.69
368 379 9.658799 CTTGTCTTAGATTTGTCTTGATAAGGA 57.341 33.333 0.00 0.00 0.00 3.36
370 381 9.605275 TGTCTTAGATTTGTCTTGATAAGGATG 57.395 33.333 0.00 0.00 0.00 3.51
371 382 9.606631 GTCTTAGATTTGTCTTGATAAGGATGT 57.393 33.333 0.00 0.00 0.00 3.06
404 415 8.561738 ACTAAAAAGTGATTTGATACATCCGT 57.438 30.769 0.00 0.00 0.00 4.69
405 416 9.661563 ACTAAAAAGTGATTTGATACATCCGTA 57.338 29.630 0.00 0.00 0.00 4.02
412 423 9.477484 AGTGATTTGATACATCCGTATTTAGAC 57.523 33.333 0.00 0.00 38.48 2.59
413 424 9.256477 GTGATTTGATACATCCGTATTTAGACA 57.744 33.333 0.00 0.00 38.48 3.41
414 425 9.825109 TGATTTGATACATCCGTATTTAGACAA 57.175 29.630 0.00 0.00 38.48 3.18
435 446 9.546428 AGACAAATTTAAGACAAGAATTTTGGG 57.454 29.630 0.00 0.00 33.39 4.12
436 447 9.541143 GACAAATTTAAGACAAGAATTTTGGGA 57.459 29.630 0.00 0.00 33.39 4.37
437 448 9.325198 ACAAATTTAAGACAAGAATTTTGGGAC 57.675 29.630 0.00 0.00 33.39 4.46
438 449 8.487176 CAAATTTAAGACAAGAATTTTGGGACG 58.513 33.333 0.00 0.00 32.35 4.79
439 450 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79
440 451 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
441 452 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
442 453 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
443 454 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
444 455 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
445 456 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
460 471 5.602978 ACGGAGGGAGTATGATGAACTATTT 59.397 40.000 0.00 0.00 0.00 1.40
491 502 5.993748 TGTGTGTGATCTACATGACCTAA 57.006 39.130 0.00 0.00 42.24 2.69
505 516 7.524717 ACATGACCTAAGTGTGCTTATTTTT 57.475 32.000 0.00 0.00 36.68 1.94
532 543 4.940654 TGCACGAGAATGTATGGATTTGAA 59.059 37.500 0.00 0.00 0.00 2.69
533 544 5.414144 TGCACGAGAATGTATGGATTTGAAA 59.586 36.000 0.00 0.00 0.00 2.69
539 550 8.810427 CGAGAATGTATGGATTTGAAAATTTGG 58.190 33.333 0.00 0.00 0.00 3.28
553 564 7.372451 TGAAAATTTGGTACGAAGGACATAG 57.628 36.000 0.00 0.00 0.00 2.23
560 571 3.004524 GGTACGAAGGACATAGCTGTAGG 59.995 52.174 0.00 0.00 35.14 3.18
564 575 0.747255 AGGACATAGCTGTAGGCACG 59.253 55.000 0.00 0.00 44.79 5.34
565 576 0.744874 GGACATAGCTGTAGGCACGA 59.255 55.000 0.00 0.00 44.79 4.35
629 641 2.106683 GTCCGCGGATGTTTGAGGG 61.107 63.158 33.58 0.00 0.00 4.30
646 696 6.590656 TTGAGGGTGATATTTAATGGGTCT 57.409 37.500 0.00 0.00 0.00 3.85
682 732 5.898174 TCTACTATGTAATGGTGTTGGACG 58.102 41.667 0.00 0.00 38.96 4.79
689 739 2.981859 ATGGTGTTGGACGGATACTC 57.018 50.000 0.00 0.00 0.00 2.59
759 811 7.495901 TCTCTCAGAAGTGCTTATTTGGATAG 58.504 38.462 0.00 0.00 0.00 2.08
763 815 5.888161 CAGAAGTGCTTATTTGGATAGGGTT 59.112 40.000 0.00 0.00 0.00 4.11
775 1960 0.539986 ATAGGGTTGTGCCTGTACCG 59.460 55.000 0.00 0.00 37.43 4.02
779 1964 0.816421 GGTTGTGCCTGTACCGTGTT 60.816 55.000 0.00 0.00 0.00 3.32
781 1966 2.211806 GTTGTGCCTGTACCGTGTTTA 58.788 47.619 0.00 0.00 0.00 2.01
782 1967 2.613133 GTTGTGCCTGTACCGTGTTTAA 59.387 45.455 0.00 0.00 0.00 1.52
900 2098 1.401552 CATGGCGATACAACACCCAAG 59.598 52.381 0.00 0.00 0.00 3.61
915 2114 5.402630 ACACCCAAGTAAATCCCTCATTTT 58.597 37.500 0.00 0.00 36.09 1.82
916 2115 5.843969 ACACCCAAGTAAATCCCTCATTTTT 59.156 36.000 0.00 0.00 36.09 1.94
921 2120 4.620723 AGTAAATCCCTCATTTTTCCCCC 58.379 43.478 0.00 0.00 36.09 5.40
922 2121 3.576197 AAATCCCTCATTTTTCCCCCA 57.424 42.857 0.00 0.00 29.60 4.96
923 2122 2.550277 ATCCCTCATTTTTCCCCCAC 57.450 50.000 0.00 0.00 0.00 4.61
924 2123 1.162505 TCCCTCATTTTTCCCCCACA 58.837 50.000 0.00 0.00 0.00 4.17
925 2124 1.077005 TCCCTCATTTTTCCCCCACAG 59.923 52.381 0.00 0.00 0.00 3.66
926 2125 0.897621 CCTCATTTTTCCCCCACAGC 59.102 55.000 0.00 0.00 0.00 4.40
939 2138 1.376086 CACAGCCACAGATCCCACA 59.624 57.895 0.00 0.00 0.00 4.17
943 2142 0.546267 AGCCACAGATCCCACACTCT 60.546 55.000 0.00 0.00 0.00 3.24
991 2190 1.382557 AATTCCCCAAATCCGCCCC 60.383 57.895 0.00 0.00 0.00 5.80
997 2196 3.420482 CAAATCCGCCCCTCCCCT 61.420 66.667 0.00 0.00 0.00 4.79
998 2197 2.617215 AAATCCGCCCCTCCCCTT 60.617 61.111 0.00 0.00 0.00 3.95
999 2198 2.690734 AAATCCGCCCCTCCCCTTC 61.691 63.158 0.00 0.00 0.00 3.46
1005 2204 2.696504 CCCCTCCCCTTCCCCTTC 60.697 72.222 0.00 0.00 0.00 3.46
1006 2205 2.696504 CCCTCCCCTTCCCCTTCC 60.697 72.222 0.00 0.00 0.00 3.46
1007 2206 2.696504 CCTCCCCTTCCCCTTCCC 60.697 72.222 0.00 0.00 0.00 3.97
1008 2207 2.696504 CTCCCCTTCCCCTTCCCC 60.697 72.222 0.00 0.00 0.00 4.81
1171 2370 0.317479 GACCAAGAGTGTACGTGCCT 59.683 55.000 0.00 0.00 0.00 4.75
1185 2384 2.058595 TGCCTCCGAGCCCTAACTC 61.059 63.158 0.00 0.00 0.00 3.01
1224 2423 1.400494 CCGCCCGAAATCAGTTTTAGG 59.600 52.381 0.00 0.00 39.19 2.69
1227 2426 2.817844 GCCCGAAATCAGTTTTAGGTGT 59.182 45.455 3.28 0.00 38.14 4.16
1244 2443 3.009033 AGGTGTTAGATTTGTGGCTAGCA 59.991 43.478 18.24 0.00 0.00 3.49
1249 2448 3.146104 AGATTTGTGGCTAGCAACACT 57.854 42.857 24.83 15.53 38.39 3.55
1366 2565 1.538687 GCACTGCATTTCTTGGCCCT 61.539 55.000 0.00 0.00 0.00 5.19
1383 2582 3.432051 CTCGTGGCCGCCCTAAGAG 62.432 68.421 11.56 7.25 0.00 2.85
1384 2583 3.458163 CGTGGCCGCCCTAAGAGA 61.458 66.667 11.56 0.00 0.00 3.10
1389 2588 0.535328 GGCCGCCCTAAGAGATTTCC 60.535 60.000 0.00 0.00 0.00 3.13
1394 2593 2.170607 CGCCCTAAGAGATTTCCTTCCA 59.829 50.000 0.00 0.00 0.00 3.53
1395 2594 3.546724 GCCCTAAGAGATTTCCTTCCAC 58.453 50.000 0.00 0.00 0.00 4.02
1415 2614 3.876589 TTGGTCGCCGCTGGAAGAC 62.877 63.158 11.87 11.87 34.07 3.01
1421 2620 4.749310 CCGCTGGAAGACGCTGCT 62.749 66.667 0.00 0.00 34.07 4.24
1422 2621 2.740055 CGCTGGAAGACGCTGCTT 60.740 61.111 0.00 0.00 34.07 3.91
1423 2622 2.320587 CGCTGGAAGACGCTGCTTT 61.321 57.895 0.00 0.00 34.07 3.51
1425 2624 1.871772 CTGGAAGACGCTGCTTTGG 59.128 57.895 0.00 0.00 34.07 3.28
1427 2626 0.036732 TGGAAGACGCTGCTTTGGAT 59.963 50.000 0.00 0.00 0.00 3.41
1429 2628 0.179179 GAAGACGCTGCTTTGGATGC 60.179 55.000 0.00 0.00 0.00 3.91
1430 2629 0.890542 AAGACGCTGCTTTGGATGCA 60.891 50.000 0.00 0.00 38.81 3.96
1431 2630 0.890542 AGACGCTGCTTTGGATGCAA 60.891 50.000 0.00 0.00 40.13 4.08
1432 2631 0.039256 GACGCTGCTTTGGATGCAAA 60.039 50.000 12.14 12.14 40.13 3.68
1433 2632 0.038892 ACGCTGCTTTGGATGCAAAG 60.039 50.000 29.35 29.35 43.11 2.77
1435 2634 1.199789 CGCTGCTTTGGATGCAAAGTA 59.800 47.619 32.04 28.37 42.44 2.24
1437 2636 3.674138 CGCTGCTTTGGATGCAAAGTATT 60.674 43.478 32.04 0.00 42.44 1.89
1438 2637 4.248058 GCTGCTTTGGATGCAAAGTATTT 58.752 39.130 32.04 0.00 42.44 1.40
1441 2640 6.619232 GCTGCTTTGGATGCAAAGTATTTTTC 60.619 38.462 32.04 18.51 42.44 2.29
1442 2641 5.700373 TGCTTTGGATGCAAAGTATTTTTCC 59.300 36.000 32.04 17.92 42.44 3.13
1443 2642 5.700373 GCTTTGGATGCAAAGTATTTTTCCA 59.300 36.000 32.04 0.00 42.44 3.53
1444 2643 6.128472 GCTTTGGATGCAAAGTATTTTTCCAG 60.128 38.462 32.04 11.03 39.06 3.86
1445 2644 6.418057 TTGGATGCAAAGTATTTTTCCAGT 57.582 33.333 0.00 0.00 39.06 4.00
1446 2645 6.418057 TGGATGCAAAGTATTTTTCCAGTT 57.582 33.333 0.00 0.00 35.03 3.16
1447 2646 6.825610 TGGATGCAAAGTATTTTTCCAGTTT 58.174 32.000 0.00 0.00 35.03 2.66
1448 2647 7.278875 TGGATGCAAAGTATTTTTCCAGTTTT 58.721 30.769 0.00 0.00 35.03 2.43
1449 2648 7.772757 TGGATGCAAAGTATTTTTCCAGTTTTT 59.227 29.630 0.00 0.00 35.03 1.94
1470 2669 6.561519 TTTTTGGGAATACCTTGGTTTCAA 57.438 33.333 0.00 0.00 41.11 2.69
1473 2672 6.561519 TTGGGAATACCTTGGTTTCAAAAA 57.438 33.333 0.00 0.00 41.11 1.94
1511 2840 0.251742 TCCCCAATTTGTCCTGGCAG 60.252 55.000 7.75 7.75 0.00 4.85
1513 2842 0.890683 CCCAATTTGTCCTGGCAGTC 59.109 55.000 14.43 6.86 0.00 3.51
1555 2889 5.949952 ACAGTCCACTTTTTAGGTTGAACTT 59.050 36.000 0.00 0.00 0.00 2.66
1556 2890 6.436218 ACAGTCCACTTTTTAGGTTGAACTTT 59.564 34.615 0.00 0.00 0.00 2.66
1557 2891 7.039293 ACAGTCCACTTTTTAGGTTGAACTTTT 60.039 33.333 0.00 0.00 0.00 2.27
1605 3034 9.899661 AAGGTTGTAATCTAGTGCAAATATACA 57.100 29.630 0.00 0.00 0.00 2.29
1626 3055 4.125703 CAGACATCTTATTCTCTGGGCAC 58.874 47.826 0.00 0.00 0.00 5.01
1636 3065 0.177604 CTCTGGGCACTTGGCTCTAG 59.822 60.000 2.47 0.26 46.01 2.43
1673 3102 7.644986 AACTCTCACTACGATTCTTTTGAAG 57.355 36.000 0.00 0.00 42.30 3.02
1677 3106 5.860611 TCACTACGATTCTTTTGAAGGGAA 58.139 37.500 0.00 0.00 42.30 3.97
1678 3107 5.699458 TCACTACGATTCTTTTGAAGGGAAC 59.301 40.000 0.00 0.00 42.30 3.62
1687 3116 6.001449 TCTTTTGAAGGGAACTCTCTTTCA 57.999 37.500 0.00 0.00 42.68 2.69
1693 3122 1.447945 GGAACTCTCTTTCAGCTGCC 58.552 55.000 9.47 0.00 0.00 4.85
1703 3132 3.575256 TCTTTCAGCTGCCATGTCAAAAT 59.425 39.130 9.47 0.00 0.00 1.82
1709 3138 3.057033 AGCTGCCATGTCAAAATCTGAAC 60.057 43.478 0.00 0.00 35.22 3.18
1713 3142 4.456911 TGCCATGTCAAAATCTGAACTCTC 59.543 41.667 0.00 0.00 35.22 3.20
1714 3143 4.699257 GCCATGTCAAAATCTGAACTCTCT 59.301 41.667 0.00 0.00 35.22 3.10
1716 3145 6.294397 GCCATGTCAAAATCTGAACTCTCTTT 60.294 38.462 0.00 0.00 35.22 2.52
1717 3146 7.303998 CCATGTCAAAATCTGAACTCTCTTTC 58.696 38.462 0.00 0.00 35.22 2.62
1740 3204 6.283694 TCATCATAGATGCACTGTCCTTTAC 58.716 40.000 2.19 0.00 0.00 2.01
1746 3210 5.246307 AGATGCACTGTCCTTTACCTTAAC 58.754 41.667 0.00 0.00 0.00 2.01
1787 3251 7.496920 TCAATTGCTAATCTACTGTCCTCAATG 59.503 37.037 0.00 0.00 0.00 2.82
1795 3259 7.904558 ATCTACTGTCCTCAATGAATAGTCA 57.095 36.000 0.00 0.00 38.41 3.41
1848 3312 0.456482 CAGCAGAGACTGAGAGCGTG 60.456 60.000 2.81 0.00 40.25 5.34
2103 3567 4.899502 TCTCAGGAGATTCAGGTTCAAAC 58.100 43.478 0.00 0.00 31.41 2.93
2121 3585 6.462073 TCAAACGCTATCTACTTGTTGTTC 57.538 37.500 0.00 0.00 0.00 3.18
2158 3622 0.514691 CCAAAGCAGCTTGACTCGAC 59.485 55.000 8.88 0.00 0.00 4.20
2176 3640 5.654650 ACTCGACTGATCTTCTCACCTTATT 59.345 40.000 0.00 0.00 0.00 1.40
2177 3641 6.829298 ACTCGACTGATCTTCTCACCTTATTA 59.171 38.462 0.00 0.00 0.00 0.98
2178 3642 7.504238 ACTCGACTGATCTTCTCACCTTATTAT 59.496 37.037 0.00 0.00 0.00 1.28
2213 3677 3.990469 GTGCAGAAGAACTTCATCGAGAA 59.010 43.478 15.43 0.00 41.84 2.87
2310 3775 8.840321 CCTTGACAACTCTTTATTTTTCTCTGA 58.160 33.333 0.00 0.00 0.00 3.27
2337 3802 0.320247 AAGAACTGGAGTGAGCTGCG 60.320 55.000 0.00 0.00 35.69 5.18
2341 3806 4.426112 TGGAGTGAGCTGCGCGAG 62.426 66.667 12.10 5.65 35.69 5.03
2433 3898 7.695618 CGAAATGTTTGATCTTGAATCTCCTTC 59.304 37.037 0.00 0.00 0.00 3.46
2502 3967 1.734465 GTCGACTCTCTTTTGGCATGG 59.266 52.381 8.70 0.00 0.00 3.66
2614 4079 3.381949 CAGCTATTACCGGTACTTGCTC 58.618 50.000 28.85 12.08 28.18 4.26
2641 4106 2.028112 TGACACCACAGCCATCTCTTAC 60.028 50.000 0.00 0.00 0.00 2.34
2650 4115 1.399791 GCCATCTCTTACTGCTGTTGC 59.600 52.381 0.09 0.00 40.20 4.17
2697 4165 1.200020 GTTGCAGAATCTGGAAACGGG 59.800 52.381 18.50 0.00 42.90 5.28
2782 4250 3.056536 GCTTAAGCCCCTCTTTTCCTTTG 60.057 47.826 17.00 0.00 36.25 2.77
2821 4289 4.336433 ACGGCTAATCTTTCATGTCCATTG 59.664 41.667 0.00 0.00 0.00 2.82
2954 4422 1.376424 AGCAGCATGTTGAGTCCCG 60.376 57.895 14.38 0.00 39.31 5.14
2972 4440 2.979130 GGCGTCAGCTGAATAGTCC 58.021 57.895 20.19 13.69 44.37 3.85
2978 4446 0.249073 CAGCTGAATAGTCCCCGACG 60.249 60.000 8.42 0.00 37.67 5.12
2981 4449 1.390565 CTGAATAGTCCCCGACGAGT 58.609 55.000 0.00 0.00 37.67 4.18
2999 4467 1.209504 AGTTGCAGTGTGTGTGTAGGT 59.790 47.619 0.00 0.00 0.00 3.08
3061 4530 0.941463 AAGTGCAAGCGTCTGACTCG 60.941 55.000 6.21 0.00 0.00 4.18
3075 4546 2.851824 CTGACTCGTGTTTTTGTTTGCC 59.148 45.455 0.00 0.00 0.00 4.52
3112 4583 5.880332 GGAGAACAATGGTGAATTAGTAGCA 59.120 40.000 0.00 0.00 0.00 3.49
3116 4587 8.246180 AGAACAATGGTGAATTAGTAGCATTTG 58.754 33.333 9.99 8.94 41.50 2.32
3171 5582 4.644498 TGTGCATGTATCCCTATGATGTG 58.356 43.478 0.00 0.00 34.76 3.21
3174 5585 4.531732 TGCATGTATCCCTATGATGTGCTA 59.468 41.667 0.00 0.00 37.96 3.49
3207 5621 8.358148 TCCCGAATTAGTTGTCTTAGATACATC 58.642 37.037 0.00 0.00 0.00 3.06
3268 5693 1.392589 ACCTTGTGACAACTGCTTGG 58.607 50.000 0.00 0.00 0.00 3.61
3269 5694 1.064758 ACCTTGTGACAACTGCTTGGA 60.065 47.619 6.10 0.00 0.00 3.53
3270 5695 2.023673 CCTTGTGACAACTGCTTGGAA 58.976 47.619 0.00 0.00 0.00 3.53
3274 5699 4.108699 TGTGACAACTGCTTGGAAAAAG 57.891 40.909 0.00 0.00 0.00 2.27
3340 5768 0.908198 ACTGCATCTTCCTCCTCCAC 59.092 55.000 0.00 0.00 0.00 4.02
3397 5825 2.443016 CCTCCCTCTCCTCCCACG 60.443 72.222 0.00 0.00 0.00 4.94
3456 5884 3.827898 GGGGACGACTCCTGCGAG 61.828 72.222 0.00 0.00 42.32 5.03
3457 5885 3.827898 GGGACGACTCCTGCGAGG 61.828 72.222 0.00 0.00 40.77 4.63
3458 5886 3.063084 GGACGACTCCTGCGAGGT 61.063 66.667 0.00 0.00 40.77 3.85
3459 5887 2.486042 GACGACTCCTGCGAGGTC 59.514 66.667 0.00 0.00 40.77 3.85
3460 5888 2.034376 ACGACTCCTGCGAGGTCT 59.966 61.111 0.00 0.00 40.77 3.85
3461 5889 1.587933 GACGACTCCTGCGAGGTCTT 61.588 60.000 0.00 0.00 40.77 3.01
3462 5890 1.153939 CGACTCCTGCGAGGTCTTG 60.154 63.158 0.00 0.00 40.77 3.02
3468 5896 4.680237 TGCGAGGTCTTGGCCGTG 62.680 66.667 0.00 0.00 0.00 4.94
3533 6015 9.562408 TCTACACCATAGTACATTGTTTTTGAA 57.438 29.630 0.00 0.00 0.00 2.69
3626 6110 2.060980 ACCGGATCAGAGTCAGGCC 61.061 63.158 9.46 0.00 37.01 5.19
3627 6111 2.060383 CCGGATCAGAGTCAGGCCA 61.060 63.158 5.01 0.00 0.00 5.36
3628 6112 1.440893 CGGATCAGAGTCAGGCCAG 59.559 63.158 5.01 0.00 0.00 4.85
3629 6113 1.326213 CGGATCAGAGTCAGGCCAGT 61.326 60.000 5.01 0.00 0.00 4.00
3631 6115 1.686052 GGATCAGAGTCAGGCCAGTAG 59.314 57.143 5.01 0.00 0.00 2.57
3733 6217 1.376812 AATTCAACCGGCGTCCTCC 60.377 57.895 6.01 0.00 0.00 4.30
3744 6228 2.435693 CGTCCTCCCATCAGACCCC 61.436 68.421 0.00 0.00 0.00 4.95
3745 6229 1.306997 GTCCTCCCATCAGACCCCA 60.307 63.158 0.00 0.00 0.00 4.96
3746 6230 0.695803 GTCCTCCCATCAGACCCCAT 60.696 60.000 0.00 0.00 0.00 4.00
3820 6304 1.836604 GCCCAGAAGCAAAACCCCA 60.837 57.895 0.00 0.00 0.00 4.96
3825 6309 3.551887 GAAGCAAAACCCCACCGCG 62.552 63.158 0.00 0.00 0.00 6.46
3908 6392 4.814041 AGGAGAGGCAGAGGGGGC 62.814 72.222 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.600916 GGTGTCTTCGGCAGCCTTT 60.601 57.895 10.54 0.00 0.00 3.11
28 29 2.029964 GAACGGGTGTCTTCGGCA 59.970 61.111 0.00 0.00 0.00 5.69
49 50 1.153449 TTACCGCTTCGCCCAGATG 60.153 57.895 0.00 0.00 0.00 2.90
65 66 3.395702 ACACGCATCCCGGGCTTA 61.396 61.111 18.49 0.00 46.66 3.09
87 88 0.179163 GTAGGTTTGCTCCAATGCGC 60.179 55.000 0.00 0.00 35.36 6.09
89 90 1.448985 TCGTAGGTTTGCTCCAATGC 58.551 50.000 0.00 0.00 0.00 3.56
92 93 1.003118 AGCATCGTAGGTTTGCTCCAA 59.997 47.619 8.96 0.00 42.88 3.53
111 112 0.820226 TCCTCCGAAGAGTGCATGAG 59.180 55.000 0.00 0.00 38.58 2.90
114 115 0.324738 TCCTCCTCCGAAGAGTGCAT 60.325 55.000 0.00 0.00 38.58 3.96
123 124 2.387772 CCTCCTCCTCCTCCTCCGA 61.388 68.421 0.00 0.00 0.00 4.55
128 129 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
143 144 2.501610 GCACCGTCATCCTCCTCC 59.498 66.667 0.00 0.00 0.00 4.30
145 146 3.461773 CGGCACCGTCATCCTCCT 61.462 66.667 0.00 0.00 34.35 3.69
147 148 3.740128 ATGCGGCACCGTCATCCTC 62.740 63.158 4.03 0.00 42.09 3.71
148 149 3.740128 GATGCGGCACCGTCATCCT 62.740 63.158 23.91 6.54 41.87 3.24
149 150 3.272334 GATGCGGCACCGTCATCC 61.272 66.667 23.91 13.22 41.87 3.51
150 151 3.272334 GGATGCGGCACCGTCATC 61.272 66.667 25.22 25.22 44.21 2.92
167 168 2.427245 CCTGGAGCTGTAGGGGTCG 61.427 68.421 0.00 0.00 34.90 4.79
215 216 2.240500 GCCATAGCGCTGGAAGACG 61.241 63.158 22.90 0.98 38.69 4.18
230 231 1.600636 CCTTGCCTCTTTGTCGCCA 60.601 57.895 0.00 0.00 0.00 5.69
232 233 2.982744 GCCCTTGCCTCTTTGTCGC 61.983 63.158 0.00 0.00 0.00 5.19
250 261 1.810030 GAGAGTTTACCCGCGGCTG 60.810 63.158 22.85 10.24 0.00 4.85
254 265 2.295253 ATGAAGAGAGTTTACCCGCG 57.705 50.000 0.00 0.00 0.00 6.46
304 315 5.251005 AGGGAGTACATATCATCGGACTAGA 59.749 44.000 0.00 0.00 0.00 2.43
312 323 3.444388 GGACGGAGGGAGTACATATCATC 59.556 52.174 0.00 0.00 0.00 2.92
317 328 0.928505 TGGGACGGAGGGAGTACATA 59.071 55.000 0.00 0.00 0.00 2.29
321 332 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
322 333 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
323 334 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
324 335 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
325 336 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
326 337 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
327 338 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
328 339 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
329 340 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
330 341 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
331 342 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
332 343 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
333 344 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
334 345 9.971922 AAGACAAATCTAAGACAAGAATTTTGG 57.028 29.630 0.00 0.00 33.04 3.28
341 352 9.658799 CCTTATCAAGACAAATCTAAGACAAGA 57.341 33.333 0.00 0.00 30.66 3.02
342 353 9.658799 TCCTTATCAAGACAAATCTAAGACAAG 57.341 33.333 0.00 0.00 33.57 3.16
344 355 9.605275 CATCCTTATCAAGACAAATCTAAGACA 57.395 33.333 0.00 0.00 33.57 3.41
345 356 9.606631 ACATCCTTATCAAGACAAATCTAAGAC 57.393 33.333 0.00 0.00 33.57 3.01
378 389 9.661563 ACGGATGTATCAAATCACTTTTTAGTA 57.338 29.630 0.00 0.00 0.00 1.82
379 390 8.561738 ACGGATGTATCAAATCACTTTTTAGT 57.438 30.769 0.00 0.00 0.00 2.24
386 397 9.477484 GTCTAAATACGGATGTATCAAATCACT 57.523 33.333 0.00 0.00 40.42 3.41
387 398 9.256477 TGTCTAAATACGGATGTATCAAATCAC 57.744 33.333 0.00 0.00 40.42 3.06
388 399 9.825109 TTGTCTAAATACGGATGTATCAAATCA 57.175 29.630 0.00 0.00 40.42 2.57
409 420 9.546428 CCCAAAATTCTTGTCTTAAATTTGTCT 57.454 29.630 0.00 0.00 33.95 3.41
410 421 9.541143 TCCCAAAATTCTTGTCTTAAATTTGTC 57.459 29.630 0.00 0.00 33.95 3.18
411 422 9.325198 GTCCCAAAATTCTTGTCTTAAATTTGT 57.675 29.630 0.00 0.00 33.95 2.83
412 423 8.487176 CGTCCCAAAATTCTTGTCTTAAATTTG 58.513 33.333 0.00 0.00 33.95 2.32
413 424 7.655732 CCGTCCCAAAATTCTTGTCTTAAATTT 59.344 33.333 0.00 0.00 34.86 1.82
414 425 7.014808 TCCGTCCCAAAATTCTTGTCTTAAATT 59.985 33.333 0.00 0.00 0.00 1.82
415 426 6.492087 TCCGTCCCAAAATTCTTGTCTTAAAT 59.508 34.615 0.00 0.00 0.00 1.40
416 427 5.828859 TCCGTCCCAAAATTCTTGTCTTAAA 59.171 36.000 0.00 0.00 0.00 1.52
417 428 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
418 429 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
419 430 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
420 431 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
421 432 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
422 433 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
423 434 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
424 435 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
425 436 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
426 437 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
427 438 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
428 439 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
429 440 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
430 441 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
431 442 0.337082 TCATACTCCCTCCGTCCCAA 59.663 55.000 0.00 0.00 0.00 4.12
432 443 0.561184 ATCATACTCCCTCCGTCCCA 59.439 55.000 0.00 0.00 0.00 4.37
433 444 0.969894 CATCATACTCCCTCCGTCCC 59.030 60.000 0.00 0.00 0.00 4.46
434 445 1.996798 TCATCATACTCCCTCCGTCC 58.003 55.000 0.00 0.00 0.00 4.79
435 446 2.959707 AGTTCATCATACTCCCTCCGTC 59.040 50.000 0.00 0.00 0.00 4.79
436 447 3.033659 AGTTCATCATACTCCCTCCGT 57.966 47.619 0.00 0.00 0.00 4.69
437 448 5.730296 AATAGTTCATCATACTCCCTCCG 57.270 43.478 0.00 0.00 0.00 4.63
438 449 6.831976 ACAAATAGTTCATCATACTCCCTCC 58.168 40.000 0.00 0.00 0.00 4.30
439 450 9.429359 CATACAAATAGTTCATCATACTCCCTC 57.571 37.037 0.00 0.00 0.00 4.30
440 451 7.880195 GCATACAAATAGTTCATCATACTCCCT 59.120 37.037 0.00 0.00 0.00 4.20
441 452 7.880195 AGCATACAAATAGTTCATCATACTCCC 59.120 37.037 0.00 0.00 0.00 4.30
442 453 8.839310 AGCATACAAATAGTTCATCATACTCC 57.161 34.615 0.00 0.00 0.00 3.85
460 471 6.463995 TGTAGATCACACACATAGCATACA 57.536 37.500 0.00 0.00 30.04 2.29
505 516 3.669536 TCCATACATTCTCGTGCAACAA 58.330 40.909 0.00 0.00 35.74 2.83
532 543 5.354234 CAGCTATGTCCTTCGTACCAAATTT 59.646 40.000 0.00 0.00 0.00 1.82
533 544 4.876107 CAGCTATGTCCTTCGTACCAAATT 59.124 41.667 0.00 0.00 0.00 1.82
539 550 3.550436 GCCTACAGCTATGTCCTTCGTAC 60.550 52.174 0.00 0.00 41.01 3.67
542 553 1.409064 TGCCTACAGCTATGTCCTTCG 59.591 52.381 0.00 0.00 44.23 3.79
553 564 1.804151 TCAAATGTTCGTGCCTACAGC 59.196 47.619 0.00 0.00 44.14 4.40
560 571 0.521735 GACCCCTCAAATGTTCGTGC 59.478 55.000 0.00 0.00 0.00 5.34
564 575 2.017049 CCGATGACCCCTCAAATGTTC 58.983 52.381 0.00 0.00 0.00 3.18
565 576 1.340991 CCCGATGACCCCTCAAATGTT 60.341 52.381 0.00 0.00 0.00 2.71
596 607 4.760047 GACGTGGCCGGCATGTCT 62.760 66.667 30.42 5.56 43.43 3.41
607 618 2.740826 AAACATCCGCGGACGTGG 60.741 61.111 33.75 22.06 46.45 4.94
608 619 1.955529 CTCAAACATCCGCGGACGTG 61.956 60.000 33.75 27.96 37.70 4.49
609 620 1.736645 CTCAAACATCCGCGGACGT 60.737 57.895 33.75 28.38 37.70 4.34
610 621 2.452813 CCTCAAACATCCGCGGACG 61.453 63.158 33.75 27.50 39.67 4.79
629 641 7.990886 TCTACAACCAGACCCATTAAATATCAC 59.009 37.037 0.00 0.00 0.00 3.06
663 713 4.131649 TCCGTCCAACACCATTACATAG 57.868 45.455 0.00 0.00 0.00 2.23
665 715 3.644966 ATCCGTCCAACACCATTACAT 57.355 42.857 0.00 0.00 0.00 2.29
669 719 3.261981 GAGTATCCGTCCAACACCATT 57.738 47.619 0.00 0.00 0.00 3.16
759 811 1.964373 CACGGTACAGGCACAACCC 60.964 63.158 0.00 0.00 40.58 4.11
763 815 2.616634 TTAAACACGGTACAGGCACA 57.383 45.000 0.00 0.00 0.00 4.57
813 1998 2.972267 CCGCATGGCAACCAATGT 59.028 55.556 0.00 0.00 36.95 2.71
827 2012 3.512516 GAGAGCCCATGTTGCCGC 61.513 66.667 1.17 0.00 0.00 6.53
866 2064 4.265206 CATGAGGCCCATGGTTCC 57.735 61.111 20.58 11.50 46.85 3.62
886 2084 5.506708 AGGGATTTACTTGGGTGTTGTATC 58.493 41.667 0.00 0.00 0.00 2.24
893 2091 6.358974 AAAAATGAGGGATTTACTTGGGTG 57.641 37.500 0.00 0.00 32.76 4.61
900 2098 4.161565 GTGGGGGAAAAATGAGGGATTTAC 59.838 45.833 0.00 0.00 32.76 2.01
915 2114 1.852157 ATCTGTGGCTGTGGGGGAA 60.852 57.895 0.00 0.00 0.00 3.97
916 2115 2.204136 ATCTGTGGCTGTGGGGGA 60.204 61.111 0.00 0.00 0.00 4.81
921 2120 0.957395 GTGTGGGATCTGTGGCTGTG 60.957 60.000 0.00 0.00 0.00 3.66
922 2121 1.130054 AGTGTGGGATCTGTGGCTGT 61.130 55.000 0.00 0.00 0.00 4.40
923 2122 0.392193 GAGTGTGGGATCTGTGGCTG 60.392 60.000 0.00 0.00 0.00 4.85
924 2123 0.546267 AGAGTGTGGGATCTGTGGCT 60.546 55.000 0.00 0.00 0.00 4.75
925 2124 0.107945 GAGAGTGTGGGATCTGTGGC 60.108 60.000 0.00 0.00 0.00 5.01
926 2125 0.539051 GGAGAGTGTGGGATCTGTGG 59.461 60.000 0.00 0.00 0.00 4.17
939 2138 1.814248 GCTTGGTTTGAACGGGAGAGT 60.814 52.381 0.00 0.00 0.00 3.24
943 2142 0.536460 GGAGCTTGGTTTGAACGGGA 60.536 55.000 0.00 0.00 0.00 5.14
991 2190 2.696504 GGGGAAGGGGAAGGGGAG 60.697 72.222 0.00 0.00 0.00 4.30
997 2196 2.612746 CGGGAAGGGGAAGGGGAA 60.613 66.667 0.00 0.00 0.00 3.97
998 2197 3.937372 GACGGGAAGGGGAAGGGGA 62.937 68.421 0.00 0.00 0.00 4.81
999 2198 3.408853 GACGGGAAGGGGAAGGGG 61.409 72.222 0.00 0.00 0.00 4.79
1000 2199 2.198304 CTTGACGGGAAGGGGAAGGG 62.198 65.000 0.00 0.00 0.00 3.95
1001 2200 1.299976 CTTGACGGGAAGGGGAAGG 59.700 63.158 0.00 0.00 0.00 3.46
1002 2201 1.377333 GCTTGACGGGAAGGGGAAG 60.377 63.158 0.00 0.00 0.00 3.46
1003 2202 2.754375 GCTTGACGGGAAGGGGAA 59.246 61.111 0.00 0.00 0.00 3.97
1004 2203 3.327404 GGCTTGACGGGAAGGGGA 61.327 66.667 0.00 0.00 0.00 4.81
1005 2204 4.426313 GGGCTTGACGGGAAGGGG 62.426 72.222 0.00 0.00 0.00 4.79
1006 2205 4.778143 CGGGCTTGACGGGAAGGG 62.778 72.222 0.00 0.00 0.00 3.95
1171 2370 2.042230 GGGGAGTTAGGGCTCGGA 60.042 66.667 0.00 0.00 36.41 4.55
1224 2423 4.215399 TGTTGCTAGCCACAAATCTAACAC 59.785 41.667 18.59 0.00 0.00 3.32
1227 2426 4.651778 AGTGTTGCTAGCCACAAATCTAA 58.348 39.130 22.03 0.00 33.99 2.10
1236 2435 1.347707 ACTGCTTAGTGTTGCTAGCCA 59.652 47.619 13.29 0.00 0.00 4.75
1244 2443 0.736325 CGCGCCTACTGCTTAGTGTT 60.736 55.000 0.00 0.00 38.05 3.32
1249 2448 3.845259 CCCCGCGCCTACTGCTTA 61.845 66.667 0.00 0.00 38.05 3.09
1366 2565 3.458163 CTCTTAGGGCGGCCACGA 61.458 66.667 31.59 20.46 44.60 4.35
1373 2572 2.170607 TGGAAGGAAATCTCTTAGGGCG 59.829 50.000 0.00 0.00 0.00 6.13
1377 2576 4.631813 CCAACGTGGAAGGAAATCTCTTAG 59.368 45.833 0.00 0.00 40.96 2.18
1380 2579 2.372172 ACCAACGTGGAAGGAAATCTCT 59.628 45.455 10.46 0.00 40.96 3.10
1383 2582 1.463444 CGACCAACGTGGAAGGAAATC 59.537 52.381 10.46 0.00 40.96 2.17
1384 2583 1.519408 CGACCAACGTGGAAGGAAAT 58.481 50.000 10.46 0.00 40.96 2.17
1389 2588 3.411351 CGGCGACCAACGTGGAAG 61.411 66.667 0.00 5.47 40.96 3.46
1407 2606 0.603707 TCCAAAGCAGCGTCTTCCAG 60.604 55.000 0.00 0.00 0.00 3.86
1415 2614 4.970392 TTTGCATCCAAAGCAGCG 57.030 50.000 0.00 0.00 43.75 5.18
1421 2620 6.825610 ACTGGAAAAATACTTTGCATCCAAA 58.174 32.000 1.86 0.00 38.56 3.28
1422 2621 6.418057 ACTGGAAAAATACTTTGCATCCAA 57.582 33.333 1.86 0.00 33.26 3.53
1423 2622 6.418057 AACTGGAAAAATACTTTGCATCCA 57.582 33.333 0.34 0.34 32.90 3.41
1447 2646 6.561519 TTGAAACCAAGGTATTCCCAAAAA 57.438 33.333 0.00 0.00 34.66 1.94
1448 2647 6.561519 TTTGAAACCAAGGTATTCCCAAAA 57.438 33.333 0.00 0.00 34.66 2.44
1449 2648 6.561519 TTTTGAAACCAAGGTATTCCCAAA 57.438 33.333 0.00 0.00 34.66 3.28
1450 2649 6.561519 TTTTTGAAACCAAGGTATTCCCAA 57.438 33.333 0.00 0.00 34.66 4.12
1511 2840 5.764192 ACTGTATCCTACATTCCTACTCGAC 59.236 44.000 0.00 0.00 38.15 4.20
1513 2842 6.243811 GACTGTATCCTACATTCCTACTCG 57.756 45.833 0.00 0.00 38.15 4.18
1557 2891 9.753674 ACCTTCCTATTGACATTAGATTTCAAA 57.246 29.630 6.04 0.00 33.13 2.69
1576 2910 5.499004 TTGCACTAGATTACAACCTTCCT 57.501 39.130 0.00 0.00 0.00 3.36
1577 2911 6.759497 ATTTGCACTAGATTACAACCTTCC 57.241 37.500 0.00 0.00 0.00 3.46
1605 3034 4.036518 AGTGCCCAGAGAATAAGATGTCT 58.963 43.478 0.00 0.00 0.00 3.41
1621 3050 1.099879 CATGCTAGAGCCAAGTGCCC 61.100 60.000 0.00 0.00 42.71 5.36
1636 3065 2.097142 GTGAGAGTTTGATCAGGCATGC 59.903 50.000 9.90 9.90 0.00 4.06
1673 3102 1.447945 GCAGCTGAAAGAGAGTTCCC 58.552 55.000 20.43 0.00 34.07 3.97
1677 3106 1.350351 ACATGGCAGCTGAAAGAGAGT 59.650 47.619 20.43 2.76 34.07 3.24
1678 3107 2.008329 GACATGGCAGCTGAAAGAGAG 58.992 52.381 20.43 2.09 34.07 3.20
1679 3108 1.348696 TGACATGGCAGCTGAAAGAGA 59.651 47.619 20.43 0.00 34.07 3.10
1687 3116 2.799017 TCAGATTTTGACATGGCAGCT 58.201 42.857 0.00 0.00 0.00 4.24
1693 3122 7.868775 TGAAAGAGAGTTCAGATTTTGACATG 58.131 34.615 0.00 0.00 34.94 3.21
1703 3132 7.147776 TGCATCTATGATGAAAGAGAGTTCAGA 60.148 37.037 11.25 0.00 40.72 3.27
1709 3138 6.282167 ACAGTGCATCTATGATGAAAGAGAG 58.718 40.000 11.25 0.00 0.00 3.20
1713 3142 5.366460 AGGACAGTGCATCTATGATGAAAG 58.634 41.667 11.25 0.83 0.00 2.62
1714 3143 5.363562 AGGACAGTGCATCTATGATGAAA 57.636 39.130 11.25 0.00 0.00 2.69
1716 3145 5.363562 AAAGGACAGTGCATCTATGATGA 57.636 39.130 11.25 0.00 0.00 2.92
1717 3146 5.468072 GGTAAAGGACAGTGCATCTATGATG 59.532 44.000 0.00 3.42 0.00 3.07
1726 3190 3.181463 ACGTTAAGGTAAAGGACAGTGCA 60.181 43.478 0.00 0.00 0.00 4.57
1787 3251 4.441415 CAGCTTTCCGACGTATGACTATTC 59.559 45.833 0.00 0.00 0.00 1.75
1795 3259 0.178068 ATGGCAGCTTTCCGACGTAT 59.822 50.000 0.00 0.00 0.00 3.06
1862 3326 2.604046 AATGTAGGATCGCACCAGAC 57.396 50.000 0.00 0.00 0.00 3.51
2103 3567 6.752351 AGTACATGAACAACAAGTAGATAGCG 59.248 38.462 0.00 0.00 34.15 4.26
2121 3585 6.127758 TGCTTTGGTGCCTATAAAAGTACATG 60.128 38.462 0.00 0.00 33.21 3.21
2176 3640 2.137523 CTGCACTGCACGCATCATATA 58.862 47.619 6.52 0.00 39.02 0.86
2177 3641 0.942252 CTGCACTGCACGCATCATAT 59.058 50.000 6.52 0.00 39.02 1.78
2178 3642 0.108233 TCTGCACTGCACGCATCATA 60.108 50.000 6.52 0.00 39.02 2.15
2262 3726 6.365520 AGGGTACAGAAAAATCATCCCATAC 58.634 40.000 0.00 0.00 36.45 2.39
2310 3775 4.805609 GCTCACTCCAGTTCTTCAAAGGAT 60.806 45.833 0.00 0.00 0.00 3.24
2337 3802 0.102481 TCCTATCGTTTGGCTCTCGC 59.898 55.000 0.00 0.00 0.00 5.03
2341 3806 1.291132 GTGCTCCTATCGTTTGGCTC 58.709 55.000 0.00 0.00 0.00 4.70
2502 3967 3.120304 GGTTGTCTTACTGATTTCGGTGC 60.120 47.826 2.24 0.00 36.70 5.01
2614 4079 2.740055 GCTGTGGTGTCAGGAGCG 60.740 66.667 0.00 0.00 36.12 5.03
2641 4106 2.031333 GTCAGAAAGGAAGCAACAGCAG 60.031 50.000 0.00 0.00 0.00 4.24
2650 4115 3.955650 TCCCGTTAGTCAGAAAGGAAG 57.044 47.619 0.00 0.00 30.23 3.46
2724 4192 5.961396 ACTACTACTACTATTGATGGCCG 57.039 43.478 0.00 0.00 0.00 6.13
2782 4250 0.807667 CCGTGAGCTAGTGGATGTGC 60.808 60.000 0.00 0.00 0.00 4.57
2821 4289 2.824489 GGCCGGTTAAGCTCCTGC 60.824 66.667 1.90 0.00 40.05 4.85
2892 4360 1.079127 AGCTTCGATTGGTGTCCCG 60.079 57.895 0.00 0.00 0.00 5.14
2944 4412 2.432628 CTGACGCCGGGACTCAAC 60.433 66.667 2.18 0.00 0.00 3.18
2954 4422 0.530870 GGGACTATTCAGCTGACGCC 60.531 60.000 18.03 12.80 36.60 5.68
2966 4434 0.968901 TGCAACTCGTCGGGGACTAT 60.969 55.000 0.00 0.00 0.00 2.12
2967 4435 1.592400 CTGCAACTCGTCGGGGACTA 61.592 60.000 0.00 0.00 0.00 2.59
2972 4440 2.029073 ACACTGCAACTCGTCGGG 59.971 61.111 0.00 0.00 0.00 5.14
2978 4446 1.867233 CCTACACACACACTGCAACTC 59.133 52.381 0.00 0.00 0.00 3.01
2981 4449 2.411628 AACCTACACACACACTGCAA 57.588 45.000 0.00 0.00 0.00 4.08
3023 4491 4.207635 CACTTGCAACACATCAAACATGAC 59.792 41.667 0.00 0.00 0.00 3.06
3052 4520 3.542310 GCAAACAAAAACACGAGTCAGAC 59.458 43.478 0.00 0.00 0.00 3.51
3075 4546 6.097270 ACCATTGTTCTCCATGGTATGATTTG 59.903 38.462 12.58 4.01 44.78 2.32
3112 4583 4.485163 GAGTTACGATTGGCAAAGCAAAT 58.515 39.130 3.01 0.00 34.53 2.32
3116 4587 1.730064 TCGAGTTACGATTGGCAAAGC 59.270 47.619 3.01 0.00 46.45 3.51
3128 5539 4.561606 ACATGCGTGAAATACTCGAGTTAC 59.438 41.667 25.44 13.63 37.64 2.50
3207 5621 5.301045 TCCCACATTACTTGTCTAGATACGG 59.699 44.000 0.00 0.00 36.00 4.02
3218 5632 3.721087 ACCTCCTTCCCACATTACTTG 57.279 47.619 0.00 0.00 0.00 3.16
3221 5635 6.243216 TGTATTACCTCCTTCCCACATTAC 57.757 41.667 0.00 0.00 0.00 1.89
3226 5651 6.544931 GGTATTTTGTATTACCTCCTTCCCAC 59.455 42.308 0.00 0.00 35.89 4.61
3255 5680 4.704540 TCTTCTTTTTCCAAGCAGTTGTCA 59.295 37.500 0.00 0.00 30.95 3.58
3297 5725 2.672874 CAGCCGTCGAATTTCAATCAGA 59.327 45.455 0.00 0.00 0.00 3.27
3340 5768 2.567985 GACTAGAGGAGAAGACTCGGG 58.432 57.143 0.00 0.00 43.44 5.14
3448 5876 3.706373 GGCCAAGACCTCGCAGGA 61.706 66.667 0.00 0.00 37.67 3.86
3450 5878 4.379243 ACGGCCAAGACCTCGCAG 62.379 66.667 2.24 0.00 0.00 5.18
3451 5879 4.680237 CACGGCCAAGACCTCGCA 62.680 66.667 2.24 0.00 0.00 5.10
3452 5880 4.681978 ACACGGCCAAGACCTCGC 62.682 66.667 2.24 0.00 0.00 5.03
3453 5881 2.030562 AACACGGCCAAGACCTCG 59.969 61.111 2.24 0.00 0.00 4.63
3454 5882 2.617274 GCAACACGGCCAAGACCTC 61.617 63.158 2.24 0.00 0.00 3.85
3455 5883 2.594592 GCAACACGGCCAAGACCT 60.595 61.111 2.24 0.00 0.00 3.85
3571 6055 4.919168 GGTTCGGTTTACAAAACCATTAGC 59.081 41.667 18.81 10.22 40.70 3.09
3626 6110 1.281925 ATCCAACCCCCTGCCTACTG 61.282 60.000 0.00 0.00 0.00 2.74
3627 6111 0.552615 AATCCAACCCCCTGCCTACT 60.553 55.000 0.00 0.00 0.00 2.57
3628 6112 0.395724 CAATCCAACCCCCTGCCTAC 60.396 60.000 0.00 0.00 0.00 3.18
3629 6113 1.580066 CCAATCCAACCCCCTGCCTA 61.580 60.000 0.00 0.00 0.00 3.93
3631 6115 2.364186 CCAATCCAACCCCCTGCC 60.364 66.667 0.00 0.00 0.00 4.85
3686 6170 4.821589 GAAGGAGGCTGGACCGCG 62.822 72.222 0.00 0.00 46.52 6.46
3687 6171 3.378399 GAGAAGGAGGCTGGACCGC 62.378 68.421 0.00 0.32 46.52 5.68
3688 6172 1.261238 AAGAGAAGGAGGCTGGACCG 61.261 60.000 0.00 0.00 46.52 4.79
3689 6173 0.539518 GAAGAGAAGGAGGCTGGACC 59.460 60.000 0.00 0.00 39.61 4.46
3733 6217 1.051008 TCGATGATGGGGTCTGATGG 58.949 55.000 0.00 0.00 0.00 3.51
3744 6228 2.091112 GCGGAGGCGATCGATGATG 61.091 63.158 21.57 6.00 0.00 3.07
3745 6229 2.259818 GCGGAGGCGATCGATGAT 59.740 61.111 21.57 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.