Multiple sequence alignment - TraesCS5A01G237500

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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 TraesCS5A01G237500 chr5A 100.000 2924 0 0 1 2924 453517995 453520918 0.000000e+00 5400.0
1 TraesCS5A01G237500 chr5D 92.157 2397 84 44 572 2910 352455351 352453001 0.000000e+00 3290.0
2 TraesCS5A01G237500 chr5D 97.059 34 0 1 2227 2260 352451406 352451374 4.070000e-04 56.5
3 TraesCS5A01G237500 chr5B 92.800 1986 71 25 957 2910 415128264 415126319 0.000000e+00 2809.0
4 TraesCS5A01G237500 chr5B 87.069 348 25 9 577 909 415128597 415128255 2.750000e-100 375.0
5 TraesCS5A01G237500 chr5B 88.699 292 15 9 57 335 415128971 415128685 1.000000e-89 340.0
6 TraesCS5A01G237500 chr5B 92.500 120 9 0 330 449 490757215 490757334 3.870000e-39 172.0
7 TraesCS5A01G237500 chr6A 93.724 1466 59 14 709 2156 116814021 116812571 0.000000e+00 2167.0
8 TraesCS5A01G237500 chr3A 97.071 751 15 2 1406 2156 398879899 398879156 0.000000e+00 1258.0
9 TraesCS5A01G237500 chr2B 91.021 568 32 8 731 1287 712610618 712611177 0.000000e+00 749.0
10 TraesCS5A01G237500 chr2B 96.840 443 7 2 1711 2153 712611174 712611609 0.000000e+00 734.0
11 TraesCS5A01G237500 chr2B 91.736 121 10 0 333 453 532865973 532866093 5.010000e-38 169.0
12 TraesCS5A01G237500 chr2B 90.551 127 11 1 327 453 541752449 541752574 1.800000e-37 167.0
13 TraesCS5A01G237500 chr7A 90.972 288 26 0 1501 1788 258824369 258824656 3.530000e-104 388.0
14 TraesCS5A01G237500 chr7D 90.625 288 27 0 1501 1788 243808054 243808341 1.640000e-102 383.0
15 TraesCS5A01G237500 chr7D 82.843 204 35 0 1572 1775 123219587 123219790 1.790000e-42 183.0
16 TraesCS5A01G237500 chr7D 91.129 124 9 2 333 455 214345345 214345467 1.800000e-37 167.0
17 TraesCS5A01G237500 chr7B 89.236 288 31 0 1501 1788 218976152 218975865 7.700000e-96 361.0
18 TraesCS5A01G237500 chr7B 82.075 212 34 3 1572 1781 84389122 84389331 8.330000e-41 178.0
19 TraesCS5A01G237500 chr1B 93.023 129 9 0 331 459 419879408 419879536 3.850000e-44 189.0
20 TraesCS5A01G237500 chr1B 91.736 121 10 0 330 450 362176622 362176742 5.010000e-38 169.0
21 TraesCS5A01G237500 chr6B 94.872 117 6 0 333 449 96481562 96481446 1.790000e-42 183.0
22 TraesCS5A01G237500 chr4B 93.220 118 8 0 333 450 105847563 105847446 1.080000e-39 174.0
23 TraesCS5A01G237500 chrUn 91.200 125 10 1 333 456 59911076 59911200 5.010000e-38 169.0


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 TraesCS5A01G237500 chr5A 453517995 453520918 2923 False 5400.000000 5400 100.000000 1 2924 1 chr5A.!!$F1 2923
1 TraesCS5A01G237500 chr5D 352451374 352455351 3977 True 1673.250000 3290 94.608000 572 2910 2 chr5D.!!$R1 2338
2 TraesCS5A01G237500 chr5B 415126319 415128971 2652 True 1174.666667 2809 89.522667 57 2910 3 chr5B.!!$R1 2853
3 TraesCS5A01G237500 chr6A 116812571 116814021 1450 True 2167.000000 2167 93.724000 709 2156 1 chr6A.!!$R1 1447
4 TraesCS5A01G237500 chr3A 398879156 398879899 743 True 1258.000000 1258 97.071000 1406 2156 1 chr3A.!!$R1 750
5 TraesCS5A01G237500 chr2B 712610618 712611609 991 False 741.500000 749 93.930500 731 2153 2 chr2B.!!$F3 1422

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
351 365 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.0 44.66 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2077 2119 0.179225 GCATGCGGTAACAACGACAG 60.179 55.0 0.0 0.0 0.0 3.51 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
24 25 6.959639 AAAGAACAAAGGAAGCATGTAAGA 57.040 33.333 0.00 0.00 0.00 2.10
25 26 5.948992 AGAACAAAGGAAGCATGTAAGAC 57.051 39.130 0.00 0.00 0.00 3.01
26 27 5.625150 AGAACAAAGGAAGCATGTAAGACT 58.375 37.500 0.00 0.00 0.00 3.24
27 28 6.769512 AGAACAAAGGAAGCATGTAAGACTA 58.230 36.000 0.00 0.00 0.00 2.59
28 29 6.876257 AGAACAAAGGAAGCATGTAAGACTAG 59.124 38.462 0.00 0.00 0.00 2.57
29 30 4.938226 ACAAAGGAAGCATGTAAGACTAGC 59.062 41.667 0.00 0.00 0.00 3.42
30 31 5.181748 CAAAGGAAGCATGTAAGACTAGCT 58.818 41.667 0.00 0.00 37.08 3.32
31 32 6.070767 ACAAAGGAAGCATGTAAGACTAGCTA 60.071 38.462 0.00 0.00 34.66 3.32
32 33 6.739331 AAGGAAGCATGTAAGACTAGCTAT 57.261 37.500 0.00 0.00 34.66 2.97
33 34 7.841282 AAGGAAGCATGTAAGACTAGCTATA 57.159 36.000 0.00 0.00 34.66 1.31
34 35 8.429237 AAGGAAGCATGTAAGACTAGCTATAT 57.571 34.615 0.00 0.00 34.66 0.86
35 36 9.535170 AAGGAAGCATGTAAGACTAGCTATATA 57.465 33.333 0.00 0.00 34.66 0.86
36 37 8.962679 AGGAAGCATGTAAGACTAGCTATATAC 58.037 37.037 0.00 0.00 34.66 1.47
37 38 8.962679 GGAAGCATGTAAGACTAGCTATATACT 58.037 37.037 0.00 0.00 34.66 2.12
38 39 9.997482 GAAGCATGTAAGACTAGCTATATACTC 57.003 37.037 0.00 0.00 34.66 2.59
39 40 8.514330 AGCATGTAAGACTAGCTATATACTCC 57.486 38.462 0.00 0.00 33.06 3.85
40 41 7.281324 AGCATGTAAGACTAGCTATATACTCCG 59.719 40.741 0.00 0.00 33.06 4.63
41 42 7.066043 GCATGTAAGACTAGCTATATACTCCGT 59.934 40.741 0.00 0.00 0.00 4.69
42 43 8.605746 CATGTAAGACTAGCTATATACTCCGTC 58.394 40.741 0.00 0.00 0.00 4.79
43 44 7.102346 TGTAAGACTAGCTATATACTCCGTCC 58.898 42.308 0.00 0.00 0.00 4.79
44 45 4.757594 AGACTAGCTATATACTCCGTCCG 58.242 47.826 0.00 0.00 0.00 4.79
45 46 4.222588 AGACTAGCTATATACTCCGTCCGT 59.777 45.833 0.00 0.00 0.00 4.69
46 47 4.252073 ACTAGCTATATACTCCGTCCGTG 58.748 47.826 0.00 0.00 0.00 4.94
47 48 3.137446 AGCTATATACTCCGTCCGTGT 57.863 47.619 0.00 0.00 0.00 4.49
48 49 4.277515 AGCTATATACTCCGTCCGTGTA 57.722 45.455 0.00 0.00 0.00 2.90
49 50 4.841422 AGCTATATACTCCGTCCGTGTAT 58.159 43.478 0.00 7.41 0.00 2.29
50 51 5.982356 AGCTATATACTCCGTCCGTGTATA 58.018 41.667 10.16 10.16 34.81 1.47
51 52 6.590068 AGCTATATACTCCGTCCGTGTATAT 58.410 40.000 17.91 17.91 40.65 0.86
52 53 6.482641 AGCTATATACTCCGTCCGTGTATATG 59.517 42.308 20.37 15.10 39.07 1.78
53 54 6.259608 GCTATATACTCCGTCCGTGTATATGT 59.740 42.308 20.37 8.87 39.07 2.29
54 55 6.674694 ATATACTCCGTCCGTGTATATGTC 57.325 41.667 15.35 0.00 38.01 3.06
55 56 1.600957 ACTCCGTCCGTGTATATGTCG 59.399 52.381 0.00 0.00 0.00 4.35
90 94 7.165485 TGCGCCATATCCTACATATTTTTACT 58.835 34.615 4.18 0.00 0.00 2.24
103 107 8.248117 ACATATTTTTACTGTACTCAACGTCC 57.752 34.615 0.00 0.00 0.00 4.79
135 139 8.213518 ACGTATAAGTATCACGTAGGAAGAAA 57.786 34.615 0.00 0.00 46.23 2.52
148 152 4.635699 AGGAAGAAAAATCTACGGTGGT 57.364 40.909 0.00 0.00 0.00 4.16
164 168 6.212888 ACGGTGGTAACTAAAATATCGACT 57.787 37.500 0.00 0.00 37.61 4.18
165 169 7.333528 ACGGTGGTAACTAAAATATCGACTA 57.666 36.000 0.00 0.00 37.61 2.59
166 170 7.420800 ACGGTGGTAACTAAAATATCGACTAG 58.579 38.462 0.00 0.00 37.61 2.57
189 193 7.633193 AGTAGTATTTCTGAATCTCGTCAGT 57.367 36.000 2.38 0.00 44.56 3.41
195 199 9.302345 GTATTTCTGAATCTCGTCAGTTTATCA 57.698 33.333 2.38 0.00 44.56 2.15
207 211 5.408299 CGTCAGTTTATCATGTCAACCAGAA 59.592 40.000 0.00 0.00 0.00 3.02
208 212 6.401474 CGTCAGTTTATCATGTCAACCAGAAG 60.401 42.308 0.00 0.00 0.00 2.85
225 238 5.105752 CCAGAAGGTGATCGTAGAGAAAAG 58.894 45.833 0.00 0.00 43.63 2.27
236 249 4.106197 CGTAGAGAAAAGAAGATCACCCG 58.894 47.826 0.00 0.00 0.00 5.28
261 274 3.510251 CGATTCATCGCACATAACCTG 57.490 47.619 0.00 0.00 43.84 4.00
324 338 3.283751 TGTTTTCCTTTTCGAAGCCAGA 58.716 40.909 0.00 0.00 0.00 3.86
328 342 2.888594 TCCTTTTCGAAGCCAGATACG 58.111 47.619 0.00 0.00 0.00 3.06
329 343 2.232941 TCCTTTTCGAAGCCAGATACGT 59.767 45.455 0.00 0.00 0.00 3.57
330 344 3.444742 TCCTTTTCGAAGCCAGATACGTA 59.555 43.478 0.00 0.00 0.00 3.57
331 345 3.550678 CCTTTTCGAAGCCAGATACGTAC 59.449 47.826 0.00 0.00 0.00 3.67
332 346 4.421948 CTTTTCGAAGCCAGATACGTACT 58.578 43.478 0.00 0.00 0.00 2.73
333 347 5.449588 CCTTTTCGAAGCCAGATACGTACTA 60.450 44.000 0.00 0.00 0.00 1.82
334 348 4.542662 TTCGAAGCCAGATACGTACTAC 57.457 45.455 0.00 0.00 0.00 2.73
335 349 3.801698 TCGAAGCCAGATACGTACTACT 58.198 45.455 0.00 0.00 0.00 2.57
336 350 3.806521 TCGAAGCCAGATACGTACTACTC 59.193 47.826 0.00 0.00 0.00 2.59
337 351 3.059051 CGAAGCCAGATACGTACTACTCC 60.059 52.174 0.00 0.00 0.00 3.85
338 352 2.861274 AGCCAGATACGTACTACTCCC 58.139 52.381 0.00 0.00 0.00 4.30
339 353 2.442502 AGCCAGATACGTACTACTCCCT 59.557 50.000 0.00 0.00 0.00 4.20
340 354 2.813172 GCCAGATACGTACTACTCCCTC 59.187 54.545 0.00 0.00 0.00 4.30
341 355 3.410508 CCAGATACGTACTACTCCCTCC 58.589 54.545 0.00 0.00 0.00 4.30
342 356 3.065655 CAGATACGTACTACTCCCTCCG 58.934 54.545 0.00 0.00 0.00 4.63
343 357 2.703007 AGATACGTACTACTCCCTCCGT 59.297 50.000 0.00 0.00 0.00 4.69
344 358 2.604046 TACGTACTACTCCCTCCGTC 57.396 55.000 0.00 0.00 0.00 4.79
345 359 0.107459 ACGTACTACTCCCTCCGTCC 60.107 60.000 0.00 0.00 0.00 4.79
346 360 1.156645 CGTACTACTCCCTCCGTCCG 61.157 65.000 0.00 0.00 0.00 4.79
347 361 0.817229 GTACTACTCCCTCCGTCCGG 60.817 65.000 0.00 0.00 0.00 5.14
348 362 0.982852 TACTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
349 363 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
350 364 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
351 365 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
352 366 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
353 367 1.339097 CTCCCTCCGTCCGGAAATAT 58.661 55.000 5.23 0.00 44.66 1.28
354 368 1.692519 CTCCCTCCGTCCGGAAATATT 59.307 52.381 5.23 0.00 44.66 1.28
355 369 2.104281 CTCCCTCCGTCCGGAAATATTT 59.896 50.000 5.23 0.00 44.66 1.40
356 370 2.158871 TCCCTCCGTCCGGAAATATTTG 60.159 50.000 5.23 0.00 44.66 2.32
357 371 2.420967 CCCTCCGTCCGGAAATATTTGT 60.421 50.000 5.23 0.00 44.66 2.83
358 372 2.870411 CCTCCGTCCGGAAATATTTGTC 59.130 50.000 5.23 0.00 44.66 3.18
359 373 2.538449 CTCCGTCCGGAAATATTTGTCG 59.462 50.000 5.23 9.16 44.66 4.35
360 374 1.595794 CCGTCCGGAAATATTTGTCGG 59.404 52.381 23.27 23.27 41.80 4.79
361 375 2.542597 CGTCCGGAAATATTTGTCGGA 58.457 47.619 25.84 25.84 46.06 4.55
367 381 7.197071 TCCGGAAATATTTGTCGGATAAATG 57.803 36.000 25.84 9.54 43.84 2.32
368 382 6.205853 TCCGGAAATATTTGTCGGATAAATGG 59.794 38.462 25.84 12.17 43.84 3.16
369 383 6.205853 CCGGAAATATTTGTCGGATAAATGGA 59.794 38.462 24.23 4.51 42.94 3.41
370 384 7.075741 CGGAAATATTTGTCGGATAAATGGAC 58.924 38.462 19.18 9.88 0.00 4.02
371 385 7.075741 GGAAATATTTGTCGGATAAATGGACG 58.924 38.462 19.18 0.00 33.45 4.79
372 386 7.255001 GGAAATATTTGTCGGATAAATGGACGT 60.255 37.037 19.18 0.00 33.45 4.34
373 387 8.665643 AAATATTTGTCGGATAAATGGACGTA 57.334 30.769 19.18 2.66 33.45 3.57
374 388 8.842358 AATATTTGTCGGATAAATGGACGTAT 57.158 30.769 19.18 4.60 33.45 3.06
375 389 6.780706 ATTTGTCGGATAAATGGACGTATC 57.219 37.500 11.30 0.00 33.45 2.24
376 390 5.524971 TTGTCGGATAAATGGACGTATCT 57.475 39.130 0.00 0.00 33.45 1.98
377 391 6.638096 TTGTCGGATAAATGGACGTATCTA 57.362 37.500 0.00 0.00 33.45 1.98
378 392 6.250344 TGTCGGATAAATGGACGTATCTAG 57.750 41.667 0.00 0.00 33.45 2.43
379 393 5.999600 TGTCGGATAAATGGACGTATCTAGA 59.000 40.000 0.00 0.00 33.45 2.43
380 394 6.072838 TGTCGGATAAATGGACGTATCTAGAC 60.073 42.308 0.00 2.45 36.30 2.59
381 395 5.999600 TCGGATAAATGGACGTATCTAGACA 59.000 40.000 0.00 0.00 0.00 3.41
382 396 6.657966 TCGGATAAATGGACGTATCTAGACAT 59.342 38.462 0.00 0.00 0.00 3.06
383 397 7.825761 TCGGATAAATGGACGTATCTAGACATA 59.174 37.037 0.00 0.00 0.00 2.29
384 398 8.622157 CGGATAAATGGACGTATCTAGACATAT 58.378 37.037 0.00 0.00 0.00 1.78
392 406 9.128404 TGGACGTATCTAGACATATTTTAGTGT 57.872 33.333 0.00 0.00 0.00 3.55
393 407 9.962783 GGACGTATCTAGACATATTTTAGTGTT 57.037 33.333 0.00 0.00 0.00 3.32
423 437 8.786826 ACATCCATTTTTAGTCATTTCTACGA 57.213 30.769 0.00 0.00 0.00 3.43
424 438 8.665685 ACATCCATTTTTAGTCATTTCTACGAC 58.334 33.333 0.00 0.00 0.00 4.34
425 439 8.664798 CATCCATTTTTAGTCATTTCTACGACA 58.335 33.333 0.00 0.00 34.48 4.35
426 440 8.610248 TCCATTTTTAGTCATTTCTACGACAA 57.390 30.769 0.00 0.00 34.48 3.18
427 441 8.717821 TCCATTTTTAGTCATTTCTACGACAAG 58.282 33.333 0.00 0.00 34.48 3.16
428 442 8.504005 CCATTTTTAGTCATTTCTACGACAAGT 58.496 33.333 0.00 0.00 34.48 3.16
435 449 7.950236 AGTCATTTCTACGACAAGTATTTTCG 58.050 34.615 0.00 0.00 38.73 3.46
436 450 7.063074 AGTCATTTCTACGACAAGTATTTTCGG 59.937 37.037 0.00 0.00 37.07 4.30
437 451 7.062605 GTCATTTCTACGACAAGTATTTTCGGA 59.937 37.037 0.00 0.00 37.07 4.55
438 452 6.695292 TTTCTACGACAAGTATTTTCGGAC 57.305 37.500 0.00 0.00 37.07 4.79
439 453 4.406069 TCTACGACAAGTATTTTCGGACG 58.594 43.478 0.00 0.00 37.07 4.79
440 454 2.331194 ACGACAAGTATTTTCGGACGG 58.669 47.619 0.00 0.00 37.07 4.79
441 455 2.030007 ACGACAAGTATTTTCGGACGGA 60.030 45.455 0.00 0.00 37.07 4.69
442 456 2.597305 CGACAAGTATTTTCGGACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
443 457 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
444 458 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
445 459 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
446 460 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
447 461 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
448 462 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
449 463 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
450 464 1.308069 TTTCGGACGGAGGGAGTACG 61.308 60.000 0.00 0.00 46.50 3.67
451 465 2.437359 CGGACGGAGGGAGTACGT 60.437 66.667 0.00 0.00 40.75 3.57
452 466 1.153369 CGGACGGAGGGAGTACGTA 60.153 63.158 0.00 0.00 40.75 3.57
453 467 1.432270 CGGACGGAGGGAGTACGTAC 61.432 65.000 18.10 18.10 40.75 3.67
454 468 0.107459 GGACGGAGGGAGTACGTACT 60.107 60.000 27.71 27.71 41.40 2.73
455 469 1.139058 GGACGGAGGGAGTACGTACTA 59.861 57.143 27.44 0.00 41.40 1.82
456 470 2.478831 GACGGAGGGAGTACGTACTAG 58.521 57.143 27.44 16.00 41.40 2.57
457 471 1.834263 ACGGAGGGAGTACGTACTAGT 59.166 52.381 27.44 14.98 39.30 2.57
469 483 6.952935 GTACGTACTAGTACTACACAGTGT 57.047 41.667 26.36 17.48 42.58 3.55
476 490 5.832060 ACTAGTACTACACAGTGTTCCACTT 59.168 40.000 12.53 0.00 42.59 3.16
477 491 5.609533 AGTACTACACAGTGTTCCACTTT 57.390 39.130 12.53 0.00 42.59 2.66
479 493 4.481368 ACTACACAGTGTTCCACTTTCA 57.519 40.909 12.53 0.00 42.59 2.69
480 494 4.189231 ACTACACAGTGTTCCACTTTCAC 58.811 43.478 12.53 0.00 42.59 3.18
481 495 3.350219 ACACAGTGTTCCACTTTCACT 57.650 42.857 0.00 0.00 42.59 3.41
485 499 2.919228 AGTGTTCCACTTTCACTGACC 58.081 47.619 0.00 0.00 42.59 4.02
486 500 1.597663 GTGTTCCACTTTCACTGACCG 59.402 52.381 0.00 0.00 0.00 4.79
487 501 1.483004 TGTTCCACTTTCACTGACCGA 59.517 47.619 0.00 0.00 0.00 4.69
489 503 3.322541 TGTTCCACTTTCACTGACCGATA 59.677 43.478 0.00 0.00 0.00 2.92
490 504 3.587797 TCCACTTTCACTGACCGATAC 57.412 47.619 0.00 0.00 0.00 2.24
492 506 1.654105 CACTTTCACTGACCGATACGC 59.346 52.381 0.00 0.00 0.00 4.42
493 507 0.914551 CTTTCACTGACCGATACGCG 59.085 55.000 3.53 3.53 40.47 6.01
508 522 2.261671 GCGGAGAGCAACTTCGGA 59.738 61.111 12.27 0.00 46.68 4.55
531 545 3.992943 AAACGATCTCCCACATAACCA 57.007 42.857 0.00 0.00 0.00 3.67
542 556 1.658596 CACATAACCATCCACGTGTCG 59.341 52.381 15.65 0.00 0.00 4.35
566 580 4.778415 CGTGAGCTGACCCGACCG 62.778 72.222 0.00 0.00 0.00 4.79
567 581 3.681835 GTGAGCTGACCCGACCGT 61.682 66.667 0.00 0.00 0.00 4.83
568 582 3.371063 TGAGCTGACCCGACCGTC 61.371 66.667 0.00 0.00 0.00 4.79
569 583 4.131088 GAGCTGACCCGACCGTCC 62.131 72.222 0.00 0.00 31.35 4.79
570 584 4.988716 AGCTGACCCGACCGTCCA 62.989 66.667 0.00 0.00 31.35 4.02
584 598 3.766691 TCCAACCCTCGCCGCTAC 61.767 66.667 0.00 0.00 0.00 3.58
611 625 6.521151 AATCAGGTGAGGAAAAGCTTAATG 57.479 37.500 0.00 0.00 0.00 1.90
673 688 3.490890 GGCTGATCCGTGTTCTGC 58.509 61.111 0.00 0.00 37.34 4.26
726 741 7.165483 CGACGAAAGCGAAAGTTTATCTATACT 59.835 37.037 0.00 0.00 41.64 2.12
727 742 8.116624 ACGAAAGCGAAAGTTTATCTATACTG 57.883 34.615 0.00 0.00 41.64 2.74
728 743 7.222224 ACGAAAGCGAAAGTTTATCTATACTGG 59.778 37.037 0.00 0.00 41.64 4.00
729 744 6.846325 AAGCGAAAGTTTATCTATACTGGC 57.154 37.500 0.00 0.00 30.74 4.85
739 761 3.146726 TATACTGGCGCACGGGAGC 62.147 63.158 10.83 4.17 39.33 4.70
765 787 0.321671 CCAGTTTCGAGGAAGGAGCA 59.678 55.000 0.00 0.00 0.00 4.26
767 789 0.036858 AGTTTCGAGGAAGGAGCAGC 60.037 55.000 0.00 0.00 0.00 5.25
801 823 9.901172 AAGGAAAGGACGTATACAGAAATAAAT 57.099 29.630 3.32 0.00 0.00 1.40
896 930 1.739562 CAGAGGAAGCAGCGTCACC 60.740 63.158 10.71 1.25 0.00 4.02
899 933 0.603975 GAGGAAGCAGCGTCACCTTT 60.604 55.000 10.71 0.00 0.00 3.11
900 934 0.685097 AGGAAGCAGCGTCACCTTTA 59.315 50.000 10.71 0.00 0.00 1.85
904 938 2.038837 GCAGCGTCACCTTTACCCC 61.039 63.158 0.00 0.00 0.00 4.95
905 939 1.376812 CAGCGTCACCTTTACCCCC 60.377 63.158 0.00 0.00 0.00 5.40
949 983 4.453892 CCTACGGTCCCGGGTCCT 62.454 72.222 30.55 20.63 44.69 3.85
1032 1068 1.704641 AAACCTTCCTCAAACAGCCC 58.295 50.000 0.00 0.00 0.00 5.19
1075 1111 1.370587 GCGAGCTCGTAGTCCAGTCT 61.371 60.000 34.46 0.00 42.22 3.24
1076 1112 0.653636 CGAGCTCGTAGTCCAGTCTC 59.346 60.000 27.79 0.00 34.11 3.36
1158 1199 1.546323 CCATGGACTTTGACCTGCTGT 60.546 52.381 5.56 0.00 0.00 4.40
1172 1213 2.045536 CTGTTGAGCTCCAGCCCC 60.046 66.667 12.15 0.00 43.38 5.80
1205 1246 0.376152 CGCTGATGAACACCATGCTC 59.624 55.000 0.00 0.00 35.17 4.26
1211 1252 0.321919 TGAACACCATGCTCCAGCTC 60.322 55.000 0.00 0.00 42.66 4.09
1246 1287 1.153289 ACCAGTCGCTGATGATGGC 60.153 57.895 8.20 0.00 34.24 4.40
1367 1408 3.737559 TTTTACCATCAGGACCTGCAT 57.262 42.857 17.33 8.45 38.69 3.96
1490 1531 2.714991 GGGTTACTCGTCCCCGTCC 61.715 68.421 0.00 0.00 37.89 4.79
1829 1870 4.169696 TTCGCCTACCCCGCCATG 62.170 66.667 0.00 0.00 0.00 3.66
1893 1934 2.287608 CGACGCTTCAGCTACCATGATA 60.288 50.000 0.00 0.00 39.32 2.15
1894 1935 3.312828 GACGCTTCAGCTACCATGATAG 58.687 50.000 0.00 0.00 39.32 2.08
1895 1936 2.064762 CGCTTCAGCTACCATGATAGC 58.935 52.381 11.50 11.50 46.74 2.97
2164 2209 3.176578 CGTCCATGCGCGTACGTT 61.177 61.111 17.90 0.00 42.83 3.99
2165 2210 1.868692 CGTCCATGCGCGTACGTTA 60.869 57.895 17.90 3.90 42.83 3.18
2166 2211 1.627424 GTCCATGCGCGTACGTTAC 59.373 57.895 17.90 7.23 42.83 2.50
2167 2212 1.516821 TCCATGCGCGTACGTTACC 60.517 57.895 17.90 3.57 42.83 2.85
2168 2213 1.517694 CCATGCGCGTACGTTACCT 60.518 57.895 17.90 0.00 42.83 3.08
2169 2214 0.248580 CCATGCGCGTACGTTACCTA 60.249 55.000 17.90 0.00 42.83 3.08
2170 2215 0.841984 CATGCGCGTACGTTACCTAC 59.158 55.000 17.90 0.00 42.83 3.18
2184 2229 6.025707 CGTTACCTACGTACTAGTGTACTG 57.974 45.833 5.39 0.00 44.97 2.74
2201 2246 2.111384 ACTGCTACCACTAGGGATGTG 58.889 52.381 0.00 0.00 41.15 3.21
2205 2250 1.139058 CTACCACTAGGGATGTGCACC 59.861 57.143 15.69 0.00 41.15 5.01
2209 2254 2.359900 CACTAGGGATGTGCACCTTTC 58.640 52.381 15.69 8.63 38.30 2.62
2210 2255 2.026822 CACTAGGGATGTGCACCTTTCT 60.027 50.000 15.69 9.50 38.30 2.52
2211 2256 2.644798 ACTAGGGATGTGCACCTTTCTT 59.355 45.455 15.69 0.00 38.30 2.52
2212 2257 2.683211 AGGGATGTGCACCTTTCTTT 57.317 45.000 15.69 0.00 31.68 2.52
2213 2258 2.962859 AGGGATGTGCACCTTTCTTTT 58.037 42.857 15.69 0.00 31.68 2.27
2337 2386 4.308899 TCTCTCCTTCGCTACATTTAGC 57.691 45.455 0.49 0.49 46.51 3.09
2416 2465 2.953648 TCATCAATGGCAATGGCAGTAG 59.046 45.455 16.10 7.54 42.43 2.57
2417 2466 1.105457 TCAATGGCAATGGCAGTAGC 58.895 50.000 16.10 0.00 42.43 3.58
2423 2472 0.373716 GCAATGGCAGTAGCACGTAC 59.626 55.000 0.00 0.00 44.61 3.67
2467 2539 1.092348 GAAATGTCAGTAACCGGGCC 58.908 55.000 6.32 0.00 0.00 5.80
2483 2555 1.444895 GCCGTGCCTTTGCTGATTG 60.445 57.895 0.00 0.00 38.71 2.67
2655 2738 4.137872 GTACGCACGCAGGGCCTA 62.138 66.667 5.28 0.00 0.00 3.93
2656 2739 3.833645 TACGCACGCAGGGCCTAG 61.834 66.667 5.28 6.13 0.00 3.02
2703 2786 2.434185 CGGAAGCTAGGCACGCAA 60.434 61.111 0.00 0.00 0.00 4.85
2910 2998 2.259818 GCCGCCTGATCGATCGAT 59.740 61.111 29.76 29.76 37.59 3.59
2922 3010 1.663074 GATCGATCGACCTGCCTGC 60.663 63.158 22.06 0.00 0.00 4.85
2923 3011 2.081425 GATCGATCGACCTGCCTGCT 62.081 60.000 22.06 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.068716 AGTCTTACATGCTTCCTTTGTTCTTTT 59.931 33.333 0.00 0.00 0.00 2.27
1 2 6.547510 AGTCTTACATGCTTCCTTTGTTCTTT 59.452 34.615 0.00 0.00 0.00 2.52
2 3 6.064717 AGTCTTACATGCTTCCTTTGTTCTT 58.935 36.000 0.00 0.00 0.00 2.52
3 4 5.625150 AGTCTTACATGCTTCCTTTGTTCT 58.375 37.500 0.00 0.00 0.00 3.01
4 5 5.948992 AGTCTTACATGCTTCCTTTGTTC 57.051 39.130 0.00 0.00 0.00 3.18
5 6 5.412904 GCTAGTCTTACATGCTTCCTTTGTT 59.587 40.000 0.00 0.00 0.00 2.83
6 7 4.938226 GCTAGTCTTACATGCTTCCTTTGT 59.062 41.667 0.00 0.00 0.00 2.83
7 8 5.181748 AGCTAGTCTTACATGCTTCCTTTG 58.818 41.667 0.00 0.00 0.00 2.77
8 9 5.428184 AGCTAGTCTTACATGCTTCCTTT 57.572 39.130 0.00 0.00 0.00 3.11
9 10 6.739331 ATAGCTAGTCTTACATGCTTCCTT 57.261 37.500 0.00 0.00 32.81 3.36
10 11 8.962679 GTATATAGCTAGTCTTACATGCTTCCT 58.037 37.037 0.00 0.00 32.81 3.36
11 12 8.962679 AGTATATAGCTAGTCTTACATGCTTCC 58.037 37.037 0.00 0.00 32.81 3.46
12 13 9.997482 GAGTATATAGCTAGTCTTACATGCTTC 57.003 37.037 0.00 0.00 32.81 3.86
13 14 8.962679 GGAGTATATAGCTAGTCTTACATGCTT 58.037 37.037 0.00 0.00 32.81 3.91
14 15 7.281324 CGGAGTATATAGCTAGTCTTACATGCT 59.719 40.741 0.00 0.00 34.42 3.79
15 16 7.066043 ACGGAGTATATAGCTAGTCTTACATGC 59.934 40.741 0.00 0.00 41.94 4.06
16 17 8.495361 ACGGAGTATATAGCTAGTCTTACATG 57.505 38.462 0.00 0.00 41.94 3.21
36 37 1.600957 ACGACATATACACGGACGGAG 59.399 52.381 0.00 0.00 0.00 4.63
37 38 1.667236 ACGACATATACACGGACGGA 58.333 50.000 0.00 0.00 0.00 4.69
38 39 2.480224 AACGACATATACACGGACGG 57.520 50.000 0.00 0.00 0.00 4.79
39 40 4.828291 AAAAACGACATATACACGGACG 57.172 40.909 0.00 0.00 0.00 4.79
90 94 3.433274 CGTAGTACTGGACGTTGAGTACA 59.567 47.826 26.91 16.54 44.74 2.90
135 139 9.252962 CGATATTTTAGTTACCACCGTAGATTT 57.747 33.333 0.00 0.00 0.00 2.17
159 163 7.710044 ACGAGATTCAGAAATACTACTAGTCGA 59.290 37.037 0.00 0.00 0.00 4.20
164 168 8.734218 ACTGACGAGATTCAGAAATACTACTA 57.266 34.615 7.68 0.00 45.19 1.82
165 169 7.633193 ACTGACGAGATTCAGAAATACTACT 57.367 36.000 7.68 0.00 45.19 2.57
166 170 8.690680 AAACTGACGAGATTCAGAAATACTAC 57.309 34.615 7.68 0.00 45.19 2.73
189 193 5.875224 TCACCTTCTGGTTGACATGATAAA 58.125 37.500 0.00 0.00 46.05 1.40
195 199 2.303022 ACGATCACCTTCTGGTTGACAT 59.697 45.455 0.00 0.00 46.05 3.06
207 211 6.378564 TGATCTTCTTTTCTCTACGATCACCT 59.621 38.462 0.00 0.00 33.11 4.00
208 212 6.474102 GTGATCTTCTTTTCTCTACGATCACC 59.526 42.308 15.04 2.40 45.00 4.02
243 256 2.642427 TGCAGGTTATGTGCGATGAAT 58.358 42.857 0.00 0.00 44.35 2.57
256 269 1.079819 CGTCGGACTGATGCAGGTT 60.080 57.895 6.57 0.00 35.51 3.50
261 274 1.517257 CTCCACGTCGGACTGATGC 60.517 63.158 6.57 0.00 39.64 3.91
294 308 3.392882 GAAAAGGAAAACATGCAGTGGG 58.607 45.455 0.00 0.00 0.00 4.61
324 338 2.224402 GGACGGAGGGAGTAGTACGTAT 60.224 54.545 0.00 0.00 34.43 3.06
328 342 0.817229 CCGGACGGAGGGAGTAGTAC 60.817 65.000 4.40 0.00 37.50 2.73
329 343 0.982852 TCCGGACGGAGGGAGTAGTA 60.983 60.000 9.76 0.00 39.76 1.82
330 344 1.856539 TTCCGGACGGAGGGAGTAGT 61.857 60.000 13.64 0.00 46.06 2.73
331 345 0.682209 TTTCCGGACGGAGGGAGTAG 60.682 60.000 13.64 0.00 46.06 2.57
332 346 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
333 347 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
334 348 1.339097 ATATTTCCGGACGGAGGGAG 58.661 55.000 13.64 0.00 46.06 4.30
335 349 1.797320 AATATTTCCGGACGGAGGGA 58.203 50.000 13.64 4.95 46.06 4.20
336 350 2.218603 CAAATATTTCCGGACGGAGGG 58.781 52.381 13.64 0.00 46.06 4.30
337 351 2.870411 GACAAATATTTCCGGACGGAGG 59.130 50.000 13.64 0.00 46.06 4.30
338 352 2.538449 CGACAAATATTTCCGGACGGAG 59.462 50.000 13.64 3.15 46.06 4.63
339 353 2.542597 CGACAAATATTTCCGGACGGA 58.457 47.619 1.83 9.76 43.52 4.69
340 354 1.595794 CCGACAAATATTTCCGGACGG 59.404 52.381 23.90 17.76 42.49 4.79
341 355 2.542597 TCCGACAAATATTTCCGGACG 58.457 47.619 25.56 15.23 43.47 4.79
344 358 6.205853 TCCATTTATCCGACAAATATTTCCGG 59.794 38.462 22.93 22.93 41.36 5.14
345 359 7.075741 GTCCATTTATCCGACAAATATTTCCG 58.924 38.462 0.00 5.26 0.00 4.30
346 360 7.075741 CGTCCATTTATCCGACAAATATTTCC 58.924 38.462 0.00 0.00 0.00 3.13
347 361 7.636326 ACGTCCATTTATCCGACAAATATTTC 58.364 34.615 0.00 0.00 0.00 2.17
348 362 7.562454 ACGTCCATTTATCCGACAAATATTT 57.438 32.000 0.00 0.00 0.00 1.40
349 363 8.842358 ATACGTCCATTTATCCGACAAATATT 57.158 30.769 0.00 0.00 0.00 1.28
350 364 8.311836 AGATACGTCCATTTATCCGACAAATAT 58.688 33.333 0.00 0.00 0.00 1.28
351 365 7.663827 AGATACGTCCATTTATCCGACAAATA 58.336 34.615 0.00 0.00 0.00 1.40
352 366 6.522054 AGATACGTCCATTTATCCGACAAAT 58.478 36.000 0.00 0.00 0.00 2.32
353 367 5.909477 AGATACGTCCATTTATCCGACAAA 58.091 37.500 0.00 0.00 0.00 2.83
354 368 5.524971 AGATACGTCCATTTATCCGACAA 57.475 39.130 0.00 0.00 0.00 3.18
355 369 5.999600 TCTAGATACGTCCATTTATCCGACA 59.000 40.000 0.00 0.00 0.00 4.35
356 370 6.072838 TGTCTAGATACGTCCATTTATCCGAC 60.073 42.308 0.00 0.00 32.06 4.79
357 371 5.999600 TGTCTAGATACGTCCATTTATCCGA 59.000 40.000 0.00 0.00 0.00 4.55
358 372 6.250344 TGTCTAGATACGTCCATTTATCCG 57.750 41.667 0.00 0.00 0.00 4.18
366 380 9.128404 ACACTAAAATATGTCTAGATACGTCCA 57.872 33.333 0.00 0.00 0.00 4.02
367 381 9.962783 AACACTAAAATATGTCTAGATACGTCC 57.037 33.333 0.00 0.00 0.00 4.79
397 411 9.878667 TCGTAGAAATGACTAAAAATGGATGTA 57.121 29.630 0.00 0.00 0.00 2.29
398 412 8.665685 GTCGTAGAAATGACTAAAAATGGATGT 58.334 33.333 0.00 0.00 39.69 3.06
399 413 8.664798 TGTCGTAGAAATGACTAAAAATGGATG 58.335 33.333 0.00 0.00 41.46 3.51
400 414 8.786826 TGTCGTAGAAATGACTAAAAATGGAT 57.213 30.769 0.00 0.00 41.46 3.41
401 415 8.610248 TTGTCGTAGAAATGACTAAAAATGGA 57.390 30.769 0.00 0.00 41.46 3.41
402 416 8.504005 ACTTGTCGTAGAAATGACTAAAAATGG 58.496 33.333 0.00 0.00 41.46 3.16
409 423 9.069078 CGAAAATACTTGTCGTAGAAATGACTA 57.931 33.333 0.00 0.00 41.46 2.59
410 424 7.063074 CCGAAAATACTTGTCGTAGAAATGACT 59.937 37.037 0.00 0.00 41.46 3.41
411 425 7.062605 TCCGAAAATACTTGTCGTAGAAATGAC 59.937 37.037 0.00 0.00 39.69 3.06
412 426 7.062605 GTCCGAAAATACTTGTCGTAGAAATGA 59.937 37.037 0.00 0.00 39.69 2.57
413 427 7.171434 GTCCGAAAATACTTGTCGTAGAAATG 58.829 38.462 0.00 0.00 39.69 2.32
414 428 6.034256 CGTCCGAAAATACTTGTCGTAGAAAT 59.966 38.462 0.00 0.00 39.69 2.17
415 429 5.343058 CGTCCGAAAATACTTGTCGTAGAAA 59.657 40.000 0.00 0.00 39.69 2.52
416 430 4.853196 CGTCCGAAAATACTTGTCGTAGAA 59.147 41.667 0.00 0.00 39.69 2.10
417 431 4.406069 CGTCCGAAAATACTTGTCGTAGA 58.594 43.478 0.00 0.00 32.93 2.59
418 432 3.545078 CCGTCCGAAAATACTTGTCGTAG 59.455 47.826 0.00 0.00 32.93 3.51
419 433 3.190327 TCCGTCCGAAAATACTTGTCGTA 59.810 43.478 0.00 0.00 32.93 3.43
420 434 2.030007 TCCGTCCGAAAATACTTGTCGT 60.030 45.455 0.00 0.00 32.93 4.34
421 435 2.597305 CTCCGTCCGAAAATACTTGTCG 59.403 50.000 0.00 0.00 34.58 4.35
422 436 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
423 437 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
424 438 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
425 439 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
426 440 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
427 441 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
428 442 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
429 443 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
430 444 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
431 445 1.308069 CGTACTCCCTCCGTCCGAAA 61.308 60.000 0.00 0.00 0.00 3.46
432 446 1.746615 CGTACTCCCTCCGTCCGAA 60.747 63.158 0.00 0.00 0.00 4.30
433 447 1.613317 TACGTACTCCCTCCGTCCGA 61.613 60.000 0.00 0.00 36.12 4.55
434 448 1.153369 TACGTACTCCCTCCGTCCG 60.153 63.158 0.00 0.00 36.12 4.79
435 449 0.107459 AGTACGTACTCCCTCCGTCC 60.107 60.000 22.45 0.00 36.12 4.79
436 450 2.159028 ACTAGTACGTACTCCCTCCGTC 60.159 54.545 30.53 0.00 37.73 4.79
437 451 1.834263 ACTAGTACGTACTCCCTCCGT 59.166 52.381 30.53 15.70 37.73 4.69
438 452 2.611225 ACTAGTACGTACTCCCTCCG 57.389 55.000 30.53 15.13 37.73 4.63
439 453 4.681074 AGTACTAGTACGTACTCCCTCC 57.319 50.000 30.53 15.80 45.05 4.30
440 454 5.980715 GTGTAGTACTAGTACGTACTCCCTC 59.019 48.000 30.53 18.79 45.05 4.30
441 455 5.422331 TGTGTAGTACTAGTACGTACTCCCT 59.578 44.000 30.53 21.65 45.05 4.20
442 456 5.661458 TGTGTAGTACTAGTACGTACTCCC 58.339 45.833 30.53 16.45 45.05 4.30
443 457 6.254589 CACTGTGTAGTACTAGTACGTACTCC 59.745 46.154 30.53 16.77 45.05 3.85
444 458 6.809196 ACACTGTGTAGTACTAGTACGTACTC 59.191 42.308 30.53 22.66 45.05 2.59
446 460 6.952935 ACACTGTGTAGTACTAGTACGTAC 57.047 41.667 23.87 23.09 40.80 3.67
447 461 6.590292 GGAACACTGTGTAGTACTAGTACGTA 59.410 42.308 23.87 15.00 40.80 3.57
448 462 5.409826 GGAACACTGTGTAGTACTAGTACGT 59.590 44.000 23.87 15.86 40.80 3.57
449 463 5.409520 TGGAACACTGTGTAGTACTAGTACG 59.590 44.000 23.87 13.05 40.80 3.67
450 464 6.808008 TGGAACACTGTGTAGTACTAGTAC 57.192 41.667 23.03 23.03 34.74 2.73
469 483 3.613193 CGTATCGGTCAGTGAAAGTGGAA 60.613 47.826 0.00 0.00 38.01 3.53
476 490 4.777781 CGCGTATCGGTCAGTGAA 57.222 55.556 0.00 0.00 33.78 3.18
485 499 0.525668 AAGTTGCTCTCCGCGTATCG 60.526 55.000 4.92 0.00 43.27 2.92
486 500 1.201343 GAAGTTGCTCTCCGCGTATC 58.799 55.000 4.92 0.00 43.27 2.24
487 501 0.525668 CGAAGTTGCTCTCCGCGTAT 60.526 55.000 4.92 0.00 43.27 3.06
489 503 2.430921 CGAAGTTGCTCTCCGCGT 60.431 61.111 4.92 0.00 43.27 6.01
490 504 3.181967 CCGAAGTTGCTCTCCGCG 61.182 66.667 0.00 0.00 43.27 6.46
492 506 1.508632 TTTTCCGAAGTTGCTCTCCG 58.491 50.000 0.00 0.00 0.00 4.63
513 527 2.368875 GGATGGTTATGTGGGAGATCGT 59.631 50.000 0.00 0.00 0.00 3.73
517 531 1.484653 CGTGGATGGTTATGTGGGAGA 59.515 52.381 0.00 0.00 0.00 3.71
519 533 1.065782 CACGTGGATGGTTATGTGGGA 60.066 52.381 7.95 0.00 31.75 4.37
549 563 4.778415 CGGTCGGGTCAGCTCACG 62.778 72.222 0.00 0.00 0.00 4.35
554 568 3.998672 TTGGACGGTCGGGTCAGC 61.999 66.667 1.43 0.00 38.70 4.26
562 576 4.754667 GGCGAGGGTTGGACGGTC 62.755 72.222 0.00 0.00 0.00 4.79
566 580 3.766691 TAGCGGCGAGGGTTGGAC 61.767 66.667 12.98 0.00 0.00 4.02
567 581 3.766691 GTAGCGGCGAGGGTTGGA 61.767 66.667 12.98 0.00 0.00 3.53
568 582 4.832608 GGTAGCGGCGAGGGTTGG 62.833 72.222 12.98 0.00 0.00 3.77
569 583 4.832608 GGGTAGCGGCGAGGGTTG 62.833 72.222 12.98 0.00 0.00 3.77
570 584 3.667217 TAGGGTAGCGGCGAGGGTT 62.667 63.158 12.98 0.00 0.00 4.11
625 639 3.001330 CAGAATTAAGAATGCCGACGACC 59.999 47.826 0.00 0.00 0.00 4.79
670 685 3.301906 CGTCTCTACAAAATGTCTCGCAG 59.698 47.826 0.00 0.00 0.00 5.18
673 688 3.852536 GGACGTCTCTACAAAATGTCTCG 59.147 47.826 16.46 0.00 0.00 4.04
739 761 3.617263 CCTTCCTCGAAACTGGAATTACG 59.383 47.826 4.49 0.00 40.98 3.18
765 787 1.688735 GTCCTTTCCTTTTGCCTTGCT 59.311 47.619 0.00 0.00 0.00 3.91
767 789 1.681264 ACGTCCTTTCCTTTTGCCTTG 59.319 47.619 0.00 0.00 0.00 3.61
802 824 9.573166 CCCCCTTTTTCTAATTTTTCTGATTTT 57.427 29.630 0.00 0.00 0.00 1.82
817 839 8.944138 TCTTTTCAATTATTTCCCCCTTTTTCT 58.056 29.630 0.00 0.00 0.00 2.52
818 840 9.567776 TTCTTTTCAATTATTTCCCCCTTTTTC 57.432 29.630 0.00 0.00 0.00 2.29
819 841 9.573166 CTTCTTTTCAATTATTTCCCCCTTTTT 57.427 29.630 0.00 0.00 0.00 1.94
820 842 8.944138 TCTTCTTTTCAATTATTTCCCCCTTTT 58.056 29.630 0.00 0.00 0.00 2.27
855 881 0.738762 CATCAGCGCACACTAGCAGT 60.739 55.000 11.47 0.00 35.48 4.40
896 930 2.271173 GGACTGGCGGGGGTAAAG 59.729 66.667 0.00 0.00 0.00 1.85
899 933 4.326227 AGTGGACTGGCGGGGGTA 62.326 66.667 0.00 0.00 0.00 3.69
904 938 1.966451 GTTTGGAGTGGACTGGCGG 60.966 63.158 0.00 0.00 0.00 6.13
905 939 1.966451 GGTTTGGAGTGGACTGGCG 60.966 63.158 0.00 0.00 0.00 5.69
945 979 1.675720 GCAGAGGCAGAGGAGAGGAC 61.676 65.000 0.00 0.00 40.72 3.85
948 982 0.106268 TAGGCAGAGGCAGAGGAGAG 60.106 60.000 0.00 0.00 43.71 3.20
949 983 0.560193 ATAGGCAGAGGCAGAGGAGA 59.440 55.000 0.00 0.00 43.71 3.71
1032 1068 3.485431 CGAGCTTGCTGGCGAGTG 61.485 66.667 10.98 0.00 37.29 3.51
1088 1124 0.815095 TCAGTGAGACGTGTGTGTGT 59.185 50.000 0.00 0.00 0.00 3.72
1158 1199 3.393970 CTCGGGGCTGGAGCTCAA 61.394 66.667 17.19 2.44 45.20 3.02
1236 1277 2.664185 CGCCTCCGCCATCATCAG 60.664 66.667 0.00 0.00 0.00 2.90
1418 1459 3.078836 CCCGGGGACACCACGTAT 61.079 66.667 14.71 0.00 40.22 3.06
1851 1892 1.520342 GAGCCGTGCTGATGAGGAC 60.520 63.158 2.98 0.00 39.88 3.85
1893 1934 6.011122 AGGAAGGATTATTGAATCACTGCT 57.989 37.500 0.51 0.00 42.95 4.24
1894 1935 6.238869 GGAAGGAAGGATTATTGAATCACTGC 60.239 42.308 0.51 0.00 42.95 4.40
1895 1936 6.017605 CGGAAGGAAGGATTATTGAATCACTG 60.018 42.308 0.51 0.00 42.95 3.66
2033 2075 7.903145 TCCTACTACACATCTTTACACACATT 58.097 34.615 0.00 0.00 0.00 2.71
2077 2119 0.179225 GCATGCGGTAACAACGACAG 60.179 55.000 0.00 0.00 0.00 3.51
2171 2216 9.475170 TCCCTAGTGGTAGCAGTACACTAGTAC 62.475 48.148 23.81 0.00 42.15 2.73
2172 2217 5.397221 CCCTAGTGGTAGCAGTACACTAGTA 60.397 48.000 23.81 5.12 38.12 1.82
2173 2218 4.525024 CCTAGTGGTAGCAGTACACTAGT 58.475 47.826 23.81 0.00 38.12 2.57
2174 2219 3.884091 CCCTAGTGGTAGCAGTACACTAG 59.116 52.174 21.21 21.21 38.70 2.57
2175 2220 3.524789 TCCCTAGTGGTAGCAGTACACTA 59.475 47.826 5.35 0.00 34.77 2.74
2176 2221 2.310945 TCCCTAGTGGTAGCAGTACACT 59.689 50.000 5.35 0.00 34.77 3.55
2177 2222 2.731572 TCCCTAGTGGTAGCAGTACAC 58.268 52.381 5.35 0.00 34.77 2.90
2178 2223 3.296854 CATCCCTAGTGGTAGCAGTACA 58.703 50.000 5.35 0.00 34.77 2.90
2179 2224 3.068307 CACATCCCTAGTGGTAGCAGTAC 59.932 52.174 5.35 0.00 33.43 2.73
2184 2229 0.830648 TGCACATCCCTAGTGGTAGC 59.169 55.000 0.00 0.00 37.46 3.58
2201 2246 6.531594 GCATTGATAAGGTAAAAGAAAGGTGC 59.468 38.462 0.00 0.00 0.00 5.01
2359 2408 1.102222 ACTAGTCAGGTCGATCGGCC 61.102 60.000 31.20 31.20 40.91 6.13
2448 2520 1.092348 GGCCCGGTTACTGACATTTC 58.908 55.000 0.00 0.00 0.00 2.17
2467 2539 4.157817 GCAATCAGCAAAGGCACG 57.842 55.556 0.00 0.00 44.61 5.34
2653 2736 2.288458 GGTGAGTCACGTAGCTAGCTAG 59.712 54.545 24.78 16.84 34.83 3.42
2654 2737 2.286872 GGTGAGTCACGTAGCTAGCTA 58.713 52.381 20.67 20.67 34.83 3.32
2655 2738 1.096416 GGTGAGTCACGTAGCTAGCT 58.904 55.000 23.12 23.12 34.83 3.32
2656 2739 0.100861 GGGTGAGTCACGTAGCTAGC 59.899 60.000 16.89 6.62 34.83 3.42
2692 2775 3.364964 CCAAAGTTAACTTGCGTGCCTAG 60.365 47.826 21.22 0.82 36.12 3.02
2693 2776 2.550606 CCAAAGTTAACTTGCGTGCCTA 59.449 45.455 21.22 0.00 36.12 3.93
2694 2777 1.336755 CCAAAGTTAACTTGCGTGCCT 59.663 47.619 21.22 1.11 36.12 4.75
2695 2778 1.766069 CCAAAGTTAACTTGCGTGCC 58.234 50.000 21.22 0.00 36.12 5.01
2703 2786 0.313987 GCCGCTTGCCAAAGTTAACT 59.686 50.000 1.12 1.12 35.69 2.24


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

AutoCloner maintained by Alex Coulton.