Multiple sequence alignment - TraesCS1D01G177600

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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 TraesCS1D01G177600 chr1D 100.000 2297 0 0 1 2297 252595112 252597408 0.000000e+00 4242.0
1 TraesCS1D01G177600 chr1D 89.180 305 25 7 115 412 487035628 487035325 7.750000e-100 374.0
2 TraesCS1D01G177600 chr1D 81.215 362 57 7 961 1315 252567116 252567473 4.830000e-72 281.0
3 TraesCS1D01G177600 chr1D 87.978 183 12 3 6 178 241964241 241964059 8.320000e-50 207.0
4 TraesCS1D01G177600 chr1D 89.888 89 8 1 409 496 320386741 320386829 1.870000e-21 113.0
5 TraesCS1D01G177600 chr1D 100.000 45 0 0 510 554 212433838 212433794 1.460000e-12 84.2
6 TraesCS1D01G177600 chr1D 100.000 45 0 0 510 554 351063254 351063298 1.460000e-12 84.2
7 TraesCS1D01G177600 chr1B 91.698 1048 60 12 554 1583 360364970 360363932 0.000000e+00 1428.0
8 TraesCS1D01G177600 chr1B 82.660 767 82 25 1580 2297 360363516 360362752 1.160000e-177 632.0
9 TraesCS1D01G177600 chr1B 82.561 367 56 7 961 1323 360512263 360511901 1.320000e-82 316.0
10 TraesCS1D01G177600 chr1A 92.289 843 41 3 871 1704 323961110 323961937 0.000000e+00 1175.0
11 TraesCS1D01G177600 chr1A 87.243 486 36 7 1833 2297 323968221 323968701 4.350000e-147 531.0
12 TraesCS1D01G177600 chr1A 96.154 312 12 0 562 873 323960526 323960837 5.660000e-141 510.0
13 TraesCS1D01G177600 chr1A 85.000 240 32 3 1000 1237 323895148 323895385 8.200000e-60 241.0
14 TraesCS1D01G177600 chr1A 88.571 70 8 0 1493 1562 93392941 93393010 4.070000e-13 86.1
15 TraesCS1D01G177600 chr7A 86.105 439 25 15 6 412 665827150 665826716 7.530000e-120 440.0
16 TraesCS1D01G177600 chr4A 91.275 298 25 1 115 412 504870664 504870960 2.750000e-109 405.0
17 TraesCS1D01G177600 chr3B 83.964 449 35 18 1 412 145464838 145464390 1.650000e-106 396.0
18 TraesCS1D01G177600 chr3B 86.645 307 34 6 112 412 235825619 235825314 1.320000e-87 333.0
19 TraesCS1D01G177600 chr3B 92.391 92 7 0 411 502 822221089 822221180 5.150000e-27 132.0
20 TraesCS1D01G177600 chr3B 92.391 92 7 0 411 502 822311445 822311536 5.150000e-27 132.0
21 TraesCS1D01G177600 chr2D 88.487 304 31 4 112 412 648879386 648879688 4.660000e-97 364.0
22 TraesCS1D01G177600 chr2D 88.192 271 24 7 149 412 430612224 430612493 1.320000e-82 316.0
23 TraesCS1D01G177600 chr2D 87.898 157 8 4 1 147 648879226 648879381 8.440000e-40 174.0
24 TraesCS1D01G177600 chr2D 89.011 91 10 0 408 498 87812064 87811974 1.870000e-21 113.0
25 TraesCS1D01G177600 chr2D 89.888 89 8 1 410 498 192300983 192301070 1.870000e-21 113.0
26 TraesCS1D01G177600 chr2D 100.000 46 0 0 510 555 200953122 200953167 4.070000e-13 86.1
27 TraesCS1D01G177600 chr4B 88.449 303 28 6 112 412 1756708 1757005 2.170000e-95 359.0
28 TraesCS1D01G177600 chr5A 86.688 308 34 6 112 412 589357966 589357659 3.660000e-88 335.0
29 TraesCS1D01G177600 chr7D 91.111 90 8 0 407 496 570645314 570645225 3.100000e-24 122.0
30 TraesCS1D01G177600 chr7D 86.458 96 13 0 397 492 629902174 629902269 3.120000e-19 106.0
31 TraesCS1D01G177600 chr7D 84.848 66 10 0 1491 1556 413112248 413112183 1.470000e-07 67.6
32 TraesCS1D01G177600 chr2B 89.247 93 8 2 410 501 236171130 236171221 5.190000e-22 115.0
33 TraesCS1D01G177600 chr4D 84.956 113 15 2 394 504 3260917 3261029 1.870000e-21 113.0
34 TraesCS1D01G177600 chr6B 80.741 135 18 6 1443 1572 21036867 21036736 5.220000e-17 99.0
35 TraesCS1D01G177600 chr6B 97.222 36 1 0 1491 1526 469705465 469705430 6.850000e-06 62.1
36 TraesCS1D01G177600 chrUn 100.000 45 0 0 510 554 233520269 233520313 1.460000e-12 84.2
37 TraesCS1D01G177600 chrUn 100.000 45 0 0 510 554 357881613 357881569 1.460000e-12 84.2
38 TraesCS1D01G177600 chrUn 100.000 45 0 0 510 554 387770467 387770423 1.460000e-12 84.2
39 TraesCS1D01G177600 chrUn 100.000 45 0 0 510 554 417450044 417450088 1.460000e-12 84.2
40 TraesCS1D01G177600 chrUn 100.000 45 0 0 510 554 439483028 439483072 1.460000e-12 84.2
41 TraesCS1D01G177600 chr6D 100.000 45 0 0 510 554 346830049 346830005 1.460000e-12 84.2
42 TraesCS1D01G177600 chr6D 83.784 74 11 1 1491 1564 303975192 303975120 4.090000e-08 69.4


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 TraesCS1D01G177600 chr1D 252595112 252597408 2296 False 4242.0 4242 100.0000 1 2297 1 chr1D.!!$F2 2296
1 TraesCS1D01G177600 chr1B 360362752 360364970 2218 True 1030.0 1428 87.1790 554 2297 2 chr1B.!!$R2 1743
2 TraesCS1D01G177600 chr1A 323960526 323961937 1411 False 842.5 1175 94.2215 562 1704 2 chr1A.!!$F4 1142

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
64 65 0.185175 AAGAAACCGGACTTGCCCTT 59.815 50.0 9.46 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2780 0.941463 GTCACTGCTCTCACCACACG 60.941 60.0 0.0 0.0 0.0 4.49 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
30 31 3.430333 GAGATCTCCAGTCCGAAGTTC 57.570 52.381 12.00 0.00 0.00 3.01
31 32 2.100087 GAGATCTCCAGTCCGAAGTTCC 59.900 54.545 12.00 0.00 0.00 3.62
32 33 1.137282 GATCTCCAGTCCGAAGTTCCC 59.863 57.143 0.00 0.00 0.00 3.97
33 34 1.215647 CTCCAGTCCGAAGTTCCCG 59.784 63.158 0.00 0.00 0.00 5.14
34 35 1.228644 TCCAGTCCGAAGTTCCCGA 60.229 57.895 0.00 0.00 0.00 5.14
35 36 0.828762 TCCAGTCCGAAGTTCCCGAA 60.829 55.000 0.00 0.00 0.00 4.30
36 37 0.389948 CCAGTCCGAAGTTCCCGAAG 60.390 60.000 0.00 0.00 0.00 3.79
53 54 3.116531 GGGCGACCGAAGAAACCG 61.117 66.667 0.00 0.00 43.64 4.44
61 62 1.866925 CGAAGAAACCGGACTTGCC 59.133 57.895 9.46 0.00 0.00 4.52
62 63 1.574702 CGAAGAAACCGGACTTGCCC 61.575 60.000 9.46 0.00 0.00 5.36
63 64 0.250770 GAAGAAACCGGACTTGCCCT 60.251 55.000 9.46 0.00 0.00 5.19
64 65 0.185175 AAGAAACCGGACTTGCCCTT 59.815 50.000 9.46 0.00 0.00 3.95
65 66 0.250770 AGAAACCGGACTTGCCCTTC 60.251 55.000 9.46 0.00 0.00 3.46
66 67 1.574702 GAAACCGGACTTGCCCTTCG 61.575 60.000 9.46 0.00 0.00 3.79
67 68 3.546714 AACCGGACTTGCCCTTCGG 62.547 63.158 9.46 0.00 45.42 4.30
77 78 4.187056 CCCTTCGGCGTCTTCTTC 57.813 61.111 6.85 0.00 0.00 2.87
78 79 1.805945 CCCTTCGGCGTCTTCTTCG 60.806 63.158 6.85 0.00 0.00 3.79
79 80 1.805945 CCTTCGGCGTCTTCTTCGG 60.806 63.158 6.85 0.00 0.00 4.30
85 86 2.509336 CGTCTTCTTCGGCGCCAT 60.509 61.111 28.98 0.00 0.00 4.40
86 87 2.517450 CGTCTTCTTCGGCGCCATC 61.517 63.158 28.98 0.00 0.00 3.51
87 88 2.202743 TCTTCTTCGGCGCCATCG 60.203 61.111 28.98 13.22 39.07 3.84
88 89 3.264897 CTTCTTCGGCGCCATCGG 61.265 66.667 28.98 10.38 35.95 4.18
89 90 4.830765 TTCTTCGGCGCCATCGGG 62.831 66.667 28.98 9.94 35.95 5.14
203 204 4.869440 CGGAGCAGCGCCAGAGAG 62.869 72.222 16.28 0.00 0.00 3.20
204 205 4.527583 GGAGCAGCGCCAGAGAGG 62.528 72.222 10.86 0.00 41.84 3.69
205 206 3.456365 GAGCAGCGCCAGAGAGGA 61.456 66.667 2.29 0.00 41.22 3.71
206 207 3.429080 GAGCAGCGCCAGAGAGGAG 62.429 68.421 2.29 0.00 41.22 3.69
207 208 4.527583 GCAGCGCCAGAGAGGAGG 62.528 72.222 2.29 0.00 41.22 4.30
212 213 3.844090 GCCAGAGAGGAGGCGGAC 61.844 72.222 0.00 0.00 41.70 4.79
213 214 3.522731 CCAGAGAGGAGGCGGACG 61.523 72.222 0.00 0.00 41.22 4.79
214 215 3.522731 CAGAGAGGAGGCGGACGG 61.523 72.222 0.00 0.00 0.00 4.79
215 216 3.729489 AGAGAGGAGGCGGACGGA 61.729 66.667 0.00 0.00 0.00 4.69
216 217 3.213402 GAGAGGAGGCGGACGGAG 61.213 72.222 0.00 0.00 0.00 4.63
238 239 4.554036 GCCAGGCGGAGGATGGAC 62.554 72.222 0.00 0.00 36.09 4.02
239 240 3.866582 CCAGGCGGAGGATGGACC 61.867 72.222 0.00 0.00 36.09 4.46
289 290 4.821589 GGGTCAGGGCGAGCGAAG 62.822 72.222 0.00 0.00 43.39 3.79
290 291 4.821589 GGTCAGGGCGAGCGAAGG 62.822 72.222 0.00 0.00 31.26 3.46
301 302 4.559386 GCGAAGGCGAACGCGATG 62.559 66.667 15.93 2.28 44.91 3.84
302 303 3.913573 CGAAGGCGAACGCGATGG 61.914 66.667 15.93 2.59 43.06 3.51
303 304 3.564027 GAAGGCGAACGCGATGGG 61.564 66.667 15.93 0.00 43.06 4.00
342 343 4.759205 GCCAAGGCGGGGTGGAAT 62.759 66.667 0.00 0.00 37.03 3.01
343 344 2.440247 CCAAGGCGGGGTGGAATC 60.440 66.667 0.00 0.00 37.03 2.52
344 345 2.354729 CAAGGCGGGGTGGAATCA 59.645 61.111 0.00 0.00 0.00 2.57
345 346 1.750399 CAAGGCGGGGTGGAATCAG 60.750 63.158 0.00 0.00 0.00 2.90
346 347 2.231380 AAGGCGGGGTGGAATCAGT 61.231 57.895 0.00 0.00 0.00 3.41
347 348 2.438434 GGCGGGGTGGAATCAGTG 60.438 66.667 0.00 0.00 0.00 3.66
348 349 2.438434 GCGGGGTGGAATCAGTGG 60.438 66.667 0.00 0.00 0.00 4.00
349 350 2.438434 CGGGGTGGAATCAGTGGC 60.438 66.667 0.00 0.00 0.00 5.01
350 351 2.438434 GGGGTGGAATCAGTGGCG 60.438 66.667 0.00 0.00 0.00 5.69
351 352 2.438434 GGGTGGAATCAGTGGCGG 60.438 66.667 0.00 0.00 0.00 6.13
352 353 2.438434 GGTGGAATCAGTGGCGGG 60.438 66.667 0.00 0.00 0.00 6.13
353 354 2.438434 GTGGAATCAGTGGCGGGG 60.438 66.667 0.00 0.00 0.00 5.73
354 355 3.727258 TGGAATCAGTGGCGGGGG 61.727 66.667 0.00 0.00 0.00 5.40
355 356 3.728373 GGAATCAGTGGCGGGGGT 61.728 66.667 0.00 0.00 0.00 4.95
356 357 2.124695 GAATCAGTGGCGGGGGTC 60.125 66.667 0.00 0.00 0.00 4.46
357 358 2.610859 AATCAGTGGCGGGGGTCT 60.611 61.111 0.00 0.00 0.00 3.85
358 359 2.876368 GAATCAGTGGCGGGGGTCTG 62.876 65.000 0.00 0.00 0.00 3.51
361 362 4.741239 AGTGGCGGGGGTCTGGAT 62.741 66.667 0.00 0.00 0.00 3.41
362 363 4.176752 GTGGCGGGGGTCTGGATC 62.177 72.222 0.00 0.00 0.00 3.36
363 364 4.414956 TGGCGGGGGTCTGGATCT 62.415 66.667 0.00 0.00 0.00 2.75
364 365 2.122989 GGCGGGGGTCTGGATCTA 60.123 66.667 0.00 0.00 0.00 1.98
365 366 2.508751 GGCGGGGGTCTGGATCTAC 61.509 68.421 0.00 0.00 0.00 2.59
366 367 2.857744 GCGGGGGTCTGGATCTACG 61.858 68.421 0.00 0.00 0.00 3.51
367 368 2.201022 CGGGGGTCTGGATCTACGG 61.201 68.421 0.00 0.00 0.00 4.02
368 369 2.508751 GGGGGTCTGGATCTACGGC 61.509 68.421 0.00 0.00 0.00 5.68
369 370 2.728817 GGGTCTGGATCTACGGCG 59.271 66.667 4.80 4.80 0.00 6.46
370 371 2.728817 GGTCTGGATCTACGGCGG 59.271 66.667 13.24 0.00 0.00 6.13
371 372 2.728817 GTCTGGATCTACGGCGGG 59.271 66.667 13.24 3.49 0.00 6.13
372 373 2.520982 TCTGGATCTACGGCGGGG 60.521 66.667 13.24 3.07 0.00 5.73
373 374 4.301027 CTGGATCTACGGCGGGGC 62.301 72.222 13.24 0.00 0.00 5.80
376 377 4.344474 GATCTACGGCGGGGCGAG 62.344 72.222 21.68 13.36 0.00 5.03
392 393 3.829948 GGCGAGGCCTTAAAAAGTTAAC 58.170 45.455 6.77 0.00 46.69 2.01
393 394 3.253921 GGCGAGGCCTTAAAAAGTTAACA 59.746 43.478 6.77 0.00 46.69 2.41
394 395 4.224433 GCGAGGCCTTAAAAAGTTAACAC 58.776 43.478 6.77 0.00 0.00 3.32
395 396 4.460505 CGAGGCCTTAAAAAGTTAACACG 58.539 43.478 6.77 0.00 0.00 4.49
396 397 4.024641 CGAGGCCTTAAAAAGTTAACACGT 60.025 41.667 6.77 0.00 0.00 4.49
397 398 5.177327 CGAGGCCTTAAAAAGTTAACACGTA 59.823 40.000 6.77 0.00 0.00 3.57
398 399 6.292811 CGAGGCCTTAAAAAGTTAACACGTAA 60.293 38.462 6.77 0.38 0.00 3.18
399 400 6.728200 AGGCCTTAAAAAGTTAACACGTAAC 58.272 36.000 0.00 0.00 42.22 2.50
410 411 5.803118 GTTAACACGTAACTCTTGCAAACT 58.197 37.500 0.00 0.00 39.30 2.66
411 412 6.936374 GTTAACACGTAACTCTTGCAAACTA 58.064 36.000 0.00 0.00 39.30 2.24
412 413 5.399604 AACACGTAACTCTTGCAAACTAC 57.600 39.130 0.00 0.00 0.00 2.73
413 414 4.690122 ACACGTAACTCTTGCAAACTACT 58.310 39.130 0.00 0.00 0.00 2.57
414 415 4.743644 ACACGTAACTCTTGCAAACTACTC 59.256 41.667 0.00 0.00 0.00 2.59
415 416 4.150098 CACGTAACTCTTGCAAACTACTCC 59.850 45.833 0.00 0.00 0.00 3.85
416 417 3.678548 CGTAACTCTTGCAAACTACTCCC 59.321 47.826 0.00 0.00 0.00 4.30
417 418 4.560919 CGTAACTCTTGCAAACTACTCCCT 60.561 45.833 0.00 0.00 0.00 4.20
418 419 3.686916 ACTCTTGCAAACTACTCCCTC 57.313 47.619 0.00 0.00 0.00 4.30
419 420 3.243724 ACTCTTGCAAACTACTCCCTCT 58.756 45.455 0.00 0.00 0.00 3.69
420 421 3.007398 ACTCTTGCAAACTACTCCCTCTG 59.993 47.826 0.00 0.00 0.00 3.35
421 422 2.972713 TCTTGCAAACTACTCCCTCTGT 59.027 45.455 0.00 0.00 0.00 3.41
422 423 3.391296 TCTTGCAAACTACTCCCTCTGTT 59.609 43.478 0.00 0.00 0.00 3.16
423 424 3.402628 TGCAAACTACTCCCTCTGTTC 57.597 47.619 0.00 0.00 0.00 3.18
424 425 2.038557 TGCAAACTACTCCCTCTGTTCC 59.961 50.000 0.00 0.00 0.00 3.62
425 426 2.038557 GCAAACTACTCCCTCTGTTCCA 59.961 50.000 0.00 0.00 0.00 3.53
426 427 3.307762 GCAAACTACTCCCTCTGTTCCAT 60.308 47.826 0.00 0.00 0.00 3.41
427 428 4.081087 GCAAACTACTCCCTCTGTTCCATA 60.081 45.833 0.00 0.00 0.00 2.74
428 429 5.570844 GCAAACTACTCCCTCTGTTCCATAA 60.571 44.000 0.00 0.00 0.00 1.90
429 430 6.653989 CAAACTACTCCCTCTGTTCCATAAT 58.346 40.000 0.00 0.00 0.00 1.28
430 431 5.878406 ACTACTCCCTCTGTTCCATAATG 57.122 43.478 0.00 0.00 0.00 1.90
431 432 5.281314 ACTACTCCCTCTGTTCCATAATGT 58.719 41.667 0.00 0.00 0.00 2.71
432 433 6.441222 ACTACTCCCTCTGTTCCATAATGTA 58.559 40.000 0.00 0.00 0.00 2.29
433 434 6.901300 ACTACTCCCTCTGTTCCATAATGTAA 59.099 38.462 0.00 0.00 0.00 2.41
434 435 6.240549 ACTCCCTCTGTTCCATAATGTAAG 57.759 41.667 0.00 0.00 0.00 2.34
435 436 5.964477 ACTCCCTCTGTTCCATAATGTAAGA 59.036 40.000 0.00 0.00 0.00 2.10
436 437 6.617371 ACTCCCTCTGTTCCATAATGTAAGAT 59.383 38.462 0.00 0.00 0.00 2.40
437 438 6.830912 TCCCTCTGTTCCATAATGTAAGATG 58.169 40.000 0.00 0.00 0.00 2.90
438 439 6.386927 TCCCTCTGTTCCATAATGTAAGATGT 59.613 38.462 0.00 0.00 0.00 3.06
439 440 7.056635 CCCTCTGTTCCATAATGTAAGATGTT 58.943 38.462 0.00 0.00 0.00 2.71
440 441 7.557719 CCCTCTGTTCCATAATGTAAGATGTTT 59.442 37.037 0.00 0.00 0.00 2.83
441 442 8.960591 CCTCTGTTCCATAATGTAAGATGTTTT 58.039 33.333 0.00 0.00 0.00 2.43
468 469 8.942669 TTACATTAATGTAGTGTCAAAAAGCG 57.057 30.769 23.65 0.00 43.44 4.68
469 470 6.966021 ACATTAATGTAGTGTCAAAAAGCGT 58.034 32.000 19.51 0.00 39.68 5.07
470 471 7.075741 ACATTAATGTAGTGTCAAAAAGCGTC 58.924 34.615 19.51 0.00 39.68 5.19
471 472 6.854496 TTAATGTAGTGTCAAAAAGCGTCT 57.146 33.333 0.00 0.00 0.00 4.18
472 473 5.751243 AATGTAGTGTCAAAAAGCGTCTT 57.249 34.783 0.00 0.00 0.00 3.01
473 474 6.854496 AATGTAGTGTCAAAAAGCGTCTTA 57.146 33.333 0.00 0.00 0.00 2.10
474 475 7.435068 AATGTAGTGTCAAAAAGCGTCTTAT 57.565 32.000 0.00 0.00 0.00 1.73
475 476 8.542497 AATGTAGTGTCAAAAAGCGTCTTATA 57.458 30.769 0.00 0.00 0.00 0.98
476 477 8.718102 ATGTAGTGTCAAAAAGCGTCTTATAT 57.282 30.769 0.00 0.00 0.00 0.86
477 478 8.542497 TGTAGTGTCAAAAAGCGTCTTATATT 57.458 30.769 0.00 0.00 0.00 1.28
478 479 9.642327 TGTAGTGTCAAAAAGCGTCTTATATTA 57.358 29.630 0.00 0.00 0.00 0.98
481 482 9.378551 AGTGTCAAAAAGCGTCTTATATTATGA 57.621 29.630 0.00 0.00 0.00 2.15
482 483 9.638300 GTGTCAAAAAGCGTCTTATATTATGAG 57.362 33.333 0.00 0.00 0.00 2.90
483 484 9.594478 TGTCAAAAAGCGTCTTATATTATGAGA 57.406 29.630 0.00 0.00 0.00 3.27
484 485 9.851043 GTCAAAAAGCGTCTTATATTATGAGAC 57.149 33.333 15.28 15.28 41.11 3.36
492 493 7.090953 GTCTTATATTATGAGACGGAGGGAG 57.909 44.000 11.50 0.00 36.39 4.30
493 494 6.660094 GTCTTATATTATGAGACGGAGGGAGT 59.340 42.308 11.50 0.00 36.39 3.85
494 495 7.828223 GTCTTATATTATGAGACGGAGGGAGTA 59.172 40.741 11.50 0.00 36.39 2.59
495 496 8.558312 TCTTATATTATGAGACGGAGGGAGTAT 58.442 37.037 0.00 0.00 0.00 2.12
496 497 9.191479 CTTATATTATGAGACGGAGGGAGTATT 57.809 37.037 0.00 0.00 0.00 1.89
497 498 9.543231 TTATATTATGAGACGGAGGGAGTATTT 57.457 33.333 0.00 0.00 0.00 1.40
498 499 5.786264 TTATGAGACGGAGGGAGTATTTC 57.214 43.478 0.00 0.00 0.00 2.17
499 500 3.095912 TGAGACGGAGGGAGTATTTCA 57.904 47.619 0.00 0.00 0.00 2.69
500 501 3.437213 TGAGACGGAGGGAGTATTTCAA 58.563 45.455 0.00 0.00 0.00 2.69
501 502 3.447586 TGAGACGGAGGGAGTATTTCAAG 59.552 47.826 0.00 0.00 0.00 3.02
502 503 3.700038 GAGACGGAGGGAGTATTTCAAGA 59.300 47.826 0.00 0.00 0.00 3.02
503 504 3.702045 AGACGGAGGGAGTATTTCAAGAG 59.298 47.826 0.00 0.00 0.00 2.85
504 505 2.168728 ACGGAGGGAGTATTTCAAGAGC 59.831 50.000 0.00 0.00 0.00 4.09
505 506 2.483889 CGGAGGGAGTATTTCAAGAGCC 60.484 54.545 0.00 0.00 0.00 4.70
506 507 2.158740 GGAGGGAGTATTTCAAGAGCCC 60.159 54.545 0.00 0.00 0.00 5.19
507 508 1.486726 AGGGAGTATTTCAAGAGCCCG 59.513 52.381 0.00 0.00 39.09 6.13
508 509 1.209747 GGGAGTATTTCAAGAGCCCGT 59.790 52.381 0.00 0.00 0.00 5.28
509 510 2.280628 GGAGTATTTCAAGAGCCCGTG 58.719 52.381 0.00 0.00 0.00 4.94
510 511 2.093658 GGAGTATTTCAAGAGCCCGTGA 60.094 50.000 0.00 0.00 0.00 4.35
511 512 2.930682 GAGTATTTCAAGAGCCCGTGAC 59.069 50.000 0.00 0.00 30.70 3.67
512 513 2.567615 AGTATTTCAAGAGCCCGTGACT 59.432 45.455 0.00 0.00 30.70 3.41
513 514 2.100605 ATTTCAAGAGCCCGTGACTC 57.899 50.000 0.00 0.00 30.70 3.36
514 515 1.048601 TTTCAAGAGCCCGTGACTCT 58.951 50.000 0.00 0.00 46.45 3.24
515 516 0.318441 TTCAAGAGCCCGTGACTCTG 59.682 55.000 0.00 0.00 43.71 3.35
516 517 1.739562 CAAGAGCCCGTGACTCTGC 60.740 63.158 0.00 0.00 43.71 4.26
517 518 2.948720 AAGAGCCCGTGACTCTGCC 61.949 63.158 0.00 0.00 43.71 4.85
518 519 4.803426 GAGCCCGTGACTCTGCCG 62.803 72.222 0.00 0.00 0.00 5.69
520 521 4.803426 GCCCGTGACTCTGCCGAG 62.803 72.222 3.27 3.27 43.10 4.63
521 522 4.135153 CCCGTGACTCTGCCGAGG 62.135 72.222 10.11 0.00 41.71 4.63
522 523 4.135153 CCGTGACTCTGCCGAGGG 62.135 72.222 10.11 0.00 41.71 4.30
537 538 3.477346 GGGCTCCCCGGTAGGTTC 61.477 72.222 0.00 0.00 32.13 3.62
538 539 2.365237 GGCTCCCCGGTAGGTTCT 60.365 66.667 0.00 0.00 35.12 3.01
539 540 1.075748 GGCTCCCCGGTAGGTTCTA 60.076 63.158 0.00 0.00 35.12 2.10
540 541 1.114119 GGCTCCCCGGTAGGTTCTAG 61.114 65.000 0.00 0.00 35.12 2.43
541 542 0.396835 GCTCCCCGGTAGGTTCTAGT 60.397 60.000 0.00 0.00 35.12 2.57
542 543 1.689984 CTCCCCGGTAGGTTCTAGTC 58.310 60.000 0.00 0.00 35.12 2.59
543 544 1.214923 CTCCCCGGTAGGTTCTAGTCT 59.785 57.143 0.00 0.00 35.12 3.24
544 545 1.213926 TCCCCGGTAGGTTCTAGTCTC 59.786 57.143 0.00 0.00 35.12 3.36
545 546 1.214923 CCCCGGTAGGTTCTAGTCTCT 59.785 57.143 0.00 0.00 35.12 3.10
546 547 2.574450 CCCGGTAGGTTCTAGTCTCTC 58.426 57.143 0.00 0.00 35.12 3.20
547 548 2.173143 CCCGGTAGGTTCTAGTCTCTCT 59.827 54.545 0.00 0.00 35.12 3.10
548 549 3.371810 CCCGGTAGGTTCTAGTCTCTCTT 60.372 52.174 0.00 0.00 35.12 2.85
549 550 4.271661 CCGGTAGGTTCTAGTCTCTCTTT 58.728 47.826 0.00 0.00 0.00 2.52
550 551 5.435291 CCGGTAGGTTCTAGTCTCTCTTTA 58.565 45.833 0.00 0.00 0.00 1.85
551 552 6.063404 CCGGTAGGTTCTAGTCTCTCTTTAT 58.937 44.000 0.00 0.00 0.00 1.40
552 553 7.222872 CCGGTAGGTTCTAGTCTCTCTTTATA 58.777 42.308 0.00 0.00 0.00 0.98
553 554 7.173047 CCGGTAGGTTCTAGTCTCTCTTTATAC 59.827 44.444 0.00 0.00 0.00 1.47
554 555 7.714377 CGGTAGGTTCTAGTCTCTCTTTATACA 59.286 40.741 0.00 0.00 0.00 2.29
555 556 8.839343 GGTAGGTTCTAGTCTCTCTTTATACAC 58.161 40.741 0.00 0.00 0.00 2.90
556 557 9.617523 GTAGGTTCTAGTCTCTCTTTATACACT 57.382 37.037 0.00 0.00 0.00 3.55
557 558 8.741603 AGGTTCTAGTCTCTCTTTATACACTC 57.258 38.462 0.00 0.00 0.00 3.51
558 559 8.554011 AGGTTCTAGTCTCTCTTTATACACTCT 58.446 37.037 0.00 0.00 0.00 3.24
559 560 9.835389 GGTTCTAGTCTCTCTTTATACACTCTA 57.165 37.037 0.00 0.00 0.00 2.43
722 730 5.811190 TCCCTTTGATCCGTGAGAATTTTA 58.189 37.500 0.00 0.00 0.00 1.52
1067 1353 1.001974 TCTGTCGGCTACAAATGTGCT 59.998 47.619 0.00 0.00 37.74 4.40
1285 1571 3.761897 CACTTTCCTCCACCACCATTAA 58.238 45.455 0.00 0.00 0.00 1.40
1491 1777 8.997323 AGATGTTCTAGTTTTCTTGAATGACAG 58.003 33.333 0.00 0.00 41.78 3.51
1493 1779 8.142994 TGTTCTAGTTTTCTTGAATGACAGAC 57.857 34.615 0.00 0.00 41.78 3.51
1494 1780 7.042725 TGTTCTAGTTTTCTTGAATGACAGACG 60.043 37.037 0.00 0.00 41.78 4.18
1577 1871 7.385752 TCAAAACGTCTTACAATAGTGGTAAGG 59.614 37.037 11.18 1.34 44.88 2.69
1578 1872 4.752146 ACGTCTTACAATAGTGGTAAGGC 58.248 43.478 11.18 9.05 45.42 4.35
1585 2298 3.259876 ACAATAGTGGTAAGGCTGAACGA 59.740 43.478 0.00 0.00 0.00 3.85
1589 2302 2.028930 AGTGGTAAGGCTGAACGAAGAG 60.029 50.000 0.00 0.00 0.00 2.85
1695 2409 4.035208 ACCGTGTGTCTGAAATTTGACTTC 59.965 41.667 0.00 0.00 34.57 3.01
1702 2416 6.415867 GTGTCTGAAATTTGACTTCACACATG 59.584 38.462 0.00 0.00 35.22 3.21
1704 2418 7.013559 TGTCTGAAATTTGACTTCACACATGAT 59.986 33.333 0.00 0.00 29.98 2.45
1707 2421 7.490840 TGAAATTTGACTTCACACATGATGTT 58.509 30.769 0.00 0.00 41.87 2.71
1708 2422 8.628280 TGAAATTTGACTTCACACATGATGTTA 58.372 29.630 0.00 0.00 41.87 2.41
1709 2423 8.801715 AAATTTGACTTCACACATGATGTTAC 57.198 30.769 0.00 0.00 41.87 2.50
1710 2424 5.590104 TTGACTTCACACATGATGTTACG 57.410 39.130 0.00 0.00 41.87 3.18
1714 2441 6.751888 TGACTTCACACATGATGTTACGATAG 59.248 38.462 0.00 0.00 41.87 2.08
1754 2481 8.349245 TGTTCGAAATTTGACTTAACACATGAT 58.651 29.630 0.00 0.00 0.00 2.45
1755 2482 8.629986 GTTCGAAATTTGACTTAACACATGATG 58.370 33.333 0.00 0.00 0.00 3.07
1799 2543 7.894376 TCACGTACAAGGACTAAATTTAAGG 57.106 36.000 0.00 0.00 0.00 2.69
1864 2608 8.621126 AAGCTATCTATGAAGTATGGGATCAT 57.379 34.615 0.00 0.00 37.54 2.45
1865 2609 8.248904 AGCTATCTATGAAGTATGGGATCATC 57.751 38.462 0.00 0.00 35.53 2.92
1868 2612 6.864151 TCTATGAAGTATGGGATCATCTGG 57.136 41.667 0.00 0.00 35.53 3.86
1870 2614 2.373169 TGAAGTATGGGATCATCTGGGC 59.627 50.000 0.00 0.00 34.96 5.36
1871 2615 1.366319 AGTATGGGATCATCTGGGCC 58.634 55.000 0.00 0.00 34.96 5.80
1872 2616 0.036010 GTATGGGATCATCTGGGCCG 60.036 60.000 0.00 0.00 34.96 6.13
1922 2681 3.641437 TGTGCAAAGTGGACATAAAGC 57.359 42.857 0.00 0.00 43.78 3.51
1925 2684 3.005791 GTGCAAAGTGGACATAAAGCCTT 59.994 43.478 0.00 0.00 38.66 4.35
1928 2687 5.161358 GCAAAGTGGACATAAAGCCTTTAC 58.839 41.667 0.00 0.00 0.00 2.01
1998 2759 3.646715 GTGGGGTGGCACCAGCTA 61.647 66.667 35.69 16.40 41.02 3.32
2018 2780 2.817901 ACTCACGTGACAACTTGGTAC 58.182 47.619 15.76 0.00 0.00 3.34
2027 2789 1.207570 ACAACTTGGTACGTGTGGTGA 59.792 47.619 0.00 0.00 0.00 4.02
2031 2793 0.032952 TTGGTACGTGTGGTGAGAGC 59.967 55.000 0.00 0.00 0.00 4.09
2032 2794 1.110518 TGGTACGTGTGGTGAGAGCA 61.111 55.000 0.00 0.00 0.00 4.26
2039 2801 0.829990 TGTGGTGAGAGCAGTGACAA 59.170 50.000 0.00 0.00 0.00 3.18
2046 2808 1.127582 GAGAGCAGTGACAAACGATGC 59.872 52.381 0.00 0.00 37.15 3.91
2047 2809 0.867746 GAGCAGTGACAAACGATGCA 59.132 50.000 0.00 0.00 39.34 3.96
2048 2810 1.466167 GAGCAGTGACAAACGATGCAT 59.534 47.619 0.00 0.00 39.34 3.96
2055 2817 2.483877 TGACAAACGATGCATGAGGAAC 59.516 45.455 2.46 0.00 0.00 3.62
2057 2819 1.464608 CAAACGATGCATGAGGAACGT 59.535 47.619 2.46 2.98 45.71 3.99
2084 2846 2.047844 CCAGTCCACTCGGTGCAG 60.048 66.667 0.00 0.00 31.34 4.41
2086 2848 2.203640 AGTCCACTCGGTGCAGGA 60.204 61.111 0.00 0.00 31.34 3.86
2090 2852 0.036388 TCCACTCGGTGCAGGAAATC 60.036 55.000 0.00 0.00 31.34 2.17
2120 2882 6.306356 CACTTTCCATGAATTTTTGTAGAGCG 59.694 38.462 0.00 0.00 0.00 5.03
2145 2907 1.444895 CCAAGTTCTGGCATTGCGC 60.445 57.895 0.00 0.00 38.76 6.09
2169 2931 3.220110 CATGGATGGATCAAACCTCCAG 58.780 50.000 0.00 0.00 45.64 3.86
2178 2940 2.426522 TCAAACCTCCAGCTGATTTCG 58.573 47.619 17.39 0.00 0.00 3.46
2183 2945 0.095935 CTCCAGCTGATTTCGTTGCG 59.904 55.000 17.39 0.00 0.00 4.85
2197 2959 0.869730 GTTGCGGTAAACGTGGATGT 59.130 50.000 0.00 0.00 46.52 3.06
2218 2980 5.681639 TGTATCTCTCCTTAGTGATGACGA 58.318 41.667 0.00 0.00 36.77 4.20
2219 2981 6.120220 TGTATCTCTCCTTAGTGATGACGAA 58.880 40.000 0.00 0.00 36.77 3.85
2222 2984 3.079578 TCTCCTTAGTGATGACGAACGT 58.920 45.455 0.00 0.00 0.00 3.99
2230 2992 1.337728 TGATGACGAACGTGGAGCAAT 60.338 47.619 4.19 0.00 0.00 3.56
2252 3014 2.716424 AGGGGTGGTTCTCAAAGATGAA 59.284 45.455 0.00 0.00 34.49 2.57
2260 3022 6.206634 GTGGTTCTCAAAGATGAACATGGTAA 59.793 38.462 0.00 0.00 42.91 2.85
2274 3036 8.531622 TGAACATGGTAATTTTATTGTTGCTG 57.468 30.769 0.00 0.00 0.00 4.41
2275 3037 8.363390 TGAACATGGTAATTTTATTGTTGCTGA 58.637 29.630 0.00 0.00 0.00 4.26
2289 3051 3.578282 TGTTGCTGATAGAAGACCAGTCA 59.422 43.478 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.100087 GGAACTTCGGACTGGAGATCTC 59.900 54.545 14.75 14.75 0.00 2.75
11 12 2.104170 GGAACTTCGGACTGGAGATCT 58.896 52.381 0.00 0.00 0.00 2.75
12 13 1.137282 GGGAACTTCGGACTGGAGATC 59.863 57.143 0.00 0.00 0.00 2.75
13 14 1.196012 GGGAACTTCGGACTGGAGAT 58.804 55.000 0.00 0.00 0.00 2.75
14 15 1.248785 CGGGAACTTCGGACTGGAGA 61.249 60.000 0.00 0.00 0.00 3.71
15 16 1.215647 CGGGAACTTCGGACTGGAG 59.784 63.158 0.00 0.00 0.00 3.86
16 17 0.828762 TTCGGGAACTTCGGACTGGA 60.829 55.000 0.00 0.00 0.00 3.86
17 18 0.389948 CTTCGGGAACTTCGGACTGG 60.390 60.000 0.00 0.00 0.00 4.00
18 19 0.389948 CCTTCGGGAACTTCGGACTG 60.390 60.000 0.00 0.00 37.25 3.51
19 20 1.972978 CCTTCGGGAACTTCGGACT 59.027 57.895 0.00 0.00 37.25 3.85
20 21 4.592426 CCTTCGGGAACTTCGGAC 57.408 61.111 0.00 0.00 37.25 4.79
31 32 2.775032 TTTCTTCGGTCGCCCTTCGG 62.775 60.000 0.00 0.00 39.05 4.30
32 33 1.373748 TTTCTTCGGTCGCCCTTCG 60.374 57.895 0.00 0.00 40.15 3.79
33 34 1.296755 GGTTTCTTCGGTCGCCCTTC 61.297 60.000 0.00 0.00 0.00 3.46
34 35 1.302271 GGTTTCTTCGGTCGCCCTT 60.302 57.895 0.00 0.00 0.00 3.95
35 36 2.346365 GGTTTCTTCGGTCGCCCT 59.654 61.111 0.00 0.00 0.00 5.19
36 37 3.116531 CGGTTTCTTCGGTCGCCC 61.117 66.667 0.00 0.00 0.00 6.13
37 38 3.116531 CCGGTTTCTTCGGTCGCC 61.117 66.667 0.00 0.00 42.33 5.54
38 39 2.048877 TCCGGTTTCTTCGGTCGC 60.049 61.111 0.00 0.00 46.82 5.19
39 40 0.319297 AAGTCCGGTTTCTTCGGTCG 60.319 55.000 0.00 0.00 46.82 4.79
40 41 1.145803 CAAGTCCGGTTTCTTCGGTC 58.854 55.000 0.00 0.00 46.82 4.79
41 42 0.883370 GCAAGTCCGGTTTCTTCGGT 60.883 55.000 0.00 0.00 46.82 4.69
43 44 1.574702 GGGCAAGTCCGGTTTCTTCG 61.575 60.000 0.00 2.49 34.94 3.79
44 45 0.250770 AGGGCAAGTCCGGTTTCTTC 60.251 55.000 0.00 0.69 34.94 2.87
45 46 0.185175 AAGGGCAAGTCCGGTTTCTT 59.815 50.000 0.00 2.29 34.94 2.52
46 47 0.250770 GAAGGGCAAGTCCGGTTTCT 60.251 55.000 0.00 0.00 34.94 2.52
47 48 1.574702 CGAAGGGCAAGTCCGGTTTC 61.575 60.000 0.00 0.00 34.94 2.78
48 49 1.599797 CGAAGGGCAAGTCCGGTTT 60.600 57.895 0.00 0.00 34.94 3.27
49 50 2.032071 CGAAGGGCAAGTCCGGTT 59.968 61.111 0.00 0.00 34.94 4.44
62 63 2.445438 GCCGAAGAAGACGCCGAAG 61.445 63.158 0.00 0.00 0.00 3.79
63 64 2.431942 GCCGAAGAAGACGCCGAA 60.432 61.111 0.00 0.00 0.00 4.30
64 65 4.771356 CGCCGAAGAAGACGCCGA 62.771 66.667 0.00 0.00 33.71 5.54
68 69 2.509336 ATGGCGCCGAAGAAGACG 60.509 61.111 23.90 0.00 0.00 4.18
69 70 2.517450 CGATGGCGCCGAAGAAGAC 61.517 63.158 23.90 5.50 0.00 3.01
70 71 2.202743 CGATGGCGCCGAAGAAGA 60.203 61.111 23.90 1.41 0.00 2.87
71 72 3.264897 CCGATGGCGCCGAAGAAG 61.265 66.667 23.90 9.49 35.83 2.85
72 73 4.830765 CCCGATGGCGCCGAAGAA 62.831 66.667 23.90 3.26 35.83 2.52
186 187 4.869440 CTCTCTGGCGCTGCTCCG 62.869 72.222 7.64 0.00 0.00 4.63
187 188 4.527583 CCTCTCTGGCGCTGCTCC 62.528 72.222 7.64 0.71 0.00 4.70
188 189 3.429080 CTCCTCTCTGGCGCTGCTC 62.429 68.421 7.64 0.00 35.26 4.26
189 190 3.459965 CTCCTCTCTGGCGCTGCT 61.460 66.667 7.64 0.00 35.26 4.24
190 191 4.527583 CCTCCTCTCTGGCGCTGC 62.528 72.222 7.64 0.00 35.26 5.25
191 192 4.527583 GCCTCCTCTCTGGCGCTG 62.528 72.222 7.64 0.11 39.71 5.18
195 196 3.844090 GTCCGCCTCCTCTCTGGC 61.844 72.222 0.00 0.00 45.25 4.85
196 197 3.522731 CGTCCGCCTCCTCTCTGG 61.523 72.222 0.00 0.00 37.10 3.86
197 198 3.522731 CCGTCCGCCTCCTCTCTG 61.523 72.222 0.00 0.00 0.00 3.35
198 199 3.707640 CTCCGTCCGCCTCCTCTCT 62.708 68.421 0.00 0.00 0.00 3.10
199 200 3.213402 CTCCGTCCGCCTCCTCTC 61.213 72.222 0.00 0.00 0.00 3.20
221 222 4.554036 GTCCATCCTCCGCCTGGC 62.554 72.222 9.11 9.11 34.14 4.85
222 223 3.866582 GGTCCATCCTCCGCCTGG 61.867 72.222 0.00 0.00 0.00 4.45
223 224 4.227134 CGGTCCATCCTCCGCCTG 62.227 72.222 0.00 0.00 40.28 4.85
226 227 3.917760 CTCCGGTCCATCCTCCGC 61.918 72.222 0.00 0.00 44.63 5.54
227 228 3.227276 CCTCCGGTCCATCCTCCG 61.227 72.222 0.00 0.00 45.42 4.63
228 229 3.551407 GCCTCCGGTCCATCCTCC 61.551 72.222 0.00 0.00 0.00 4.30
229 230 3.917760 CGCCTCCGGTCCATCCTC 61.918 72.222 0.00 0.00 0.00 3.71
246 247 2.833582 TCCTCTCCGGACGCATCC 60.834 66.667 0.00 0.00 42.28 3.51
247 248 2.725008 CTCCTCTCCGGACGCATC 59.275 66.667 0.00 0.00 36.69 3.91
248 249 2.835431 CCTCCTCTCCGGACGCAT 60.835 66.667 0.00 0.00 36.69 4.73
272 273 4.821589 CTTCGCTCGCCCTGACCC 62.822 72.222 0.00 0.00 0.00 4.46
273 274 4.821589 CCTTCGCTCGCCCTGACC 62.822 72.222 0.00 0.00 0.00 4.02
285 286 3.913573 CCATCGCGTTCGCCTTCG 61.914 66.667 5.77 0.00 35.26 3.79
286 287 3.564027 CCCATCGCGTTCGCCTTC 61.564 66.667 5.77 0.00 35.26 3.46
325 326 4.759205 ATTCCACCCCGCCTTGGC 62.759 66.667 0.75 0.75 35.87 4.52
326 327 2.440247 GATTCCACCCCGCCTTGG 60.440 66.667 0.00 0.00 37.55 3.61
327 328 1.750399 CTGATTCCACCCCGCCTTG 60.750 63.158 0.00 0.00 0.00 3.61
328 329 2.231380 ACTGATTCCACCCCGCCTT 61.231 57.895 0.00 0.00 0.00 4.35
329 330 2.610859 ACTGATTCCACCCCGCCT 60.611 61.111 0.00 0.00 0.00 5.52
330 331 2.438434 CACTGATTCCACCCCGCC 60.438 66.667 0.00 0.00 0.00 6.13
331 332 2.438434 CCACTGATTCCACCCCGC 60.438 66.667 0.00 0.00 0.00 6.13
332 333 2.438434 GCCACTGATTCCACCCCG 60.438 66.667 0.00 0.00 0.00 5.73
333 334 2.438434 CGCCACTGATTCCACCCC 60.438 66.667 0.00 0.00 0.00 4.95
334 335 2.438434 CCGCCACTGATTCCACCC 60.438 66.667 0.00 0.00 0.00 4.61
335 336 2.438434 CCCGCCACTGATTCCACC 60.438 66.667 0.00 0.00 0.00 4.61
336 337 2.438434 CCCCGCCACTGATTCCAC 60.438 66.667 0.00 0.00 0.00 4.02
337 338 3.727258 CCCCCGCCACTGATTCCA 61.727 66.667 0.00 0.00 0.00 3.53
338 339 3.699134 GACCCCCGCCACTGATTCC 62.699 68.421 0.00 0.00 0.00 3.01
339 340 2.124695 GACCCCCGCCACTGATTC 60.125 66.667 0.00 0.00 0.00 2.52
340 341 2.610859 AGACCCCCGCCACTGATT 60.611 61.111 0.00 0.00 0.00 2.57
341 342 3.402681 CAGACCCCCGCCACTGAT 61.403 66.667 0.00 0.00 32.90 2.90
344 345 4.741239 ATCCAGACCCCCGCCACT 62.741 66.667 0.00 0.00 0.00 4.00
345 346 4.176752 GATCCAGACCCCCGCCAC 62.177 72.222 0.00 0.00 0.00 5.01
346 347 3.016613 TAGATCCAGACCCCCGCCA 62.017 63.158 0.00 0.00 0.00 5.69
347 348 2.122989 TAGATCCAGACCCCCGCC 60.123 66.667 0.00 0.00 0.00 6.13
348 349 2.857744 CGTAGATCCAGACCCCCGC 61.858 68.421 0.00 0.00 0.00 6.13
349 350 2.201022 CCGTAGATCCAGACCCCCG 61.201 68.421 0.00 0.00 0.00 5.73
350 351 2.508751 GCCGTAGATCCAGACCCCC 61.509 68.421 0.00 0.00 0.00 5.40
351 352 2.857744 CGCCGTAGATCCAGACCCC 61.858 68.421 0.00 0.00 0.00 4.95
352 353 2.728817 CGCCGTAGATCCAGACCC 59.271 66.667 0.00 0.00 0.00 4.46
353 354 2.728817 CCGCCGTAGATCCAGACC 59.271 66.667 0.00 0.00 0.00 3.85
354 355 2.728817 CCCGCCGTAGATCCAGAC 59.271 66.667 0.00 0.00 0.00 3.51
355 356 2.520982 CCCCGCCGTAGATCCAGA 60.521 66.667 0.00 0.00 0.00 3.86
356 357 4.301027 GCCCCGCCGTAGATCCAG 62.301 72.222 0.00 0.00 0.00 3.86
359 360 4.344474 CTCGCCCCGCCGTAGATC 62.344 72.222 0.00 0.00 0.00 2.75
372 373 4.224433 GTGTTAACTTTTTAAGGCCTCGC 58.776 43.478 5.23 0.00 0.00 5.03
373 374 4.024641 ACGTGTTAACTTTTTAAGGCCTCG 60.025 41.667 5.23 1.82 0.00 4.63
374 375 5.428496 ACGTGTTAACTTTTTAAGGCCTC 57.572 39.130 5.23 0.00 0.00 4.70
375 376 6.728200 GTTACGTGTTAACTTTTTAAGGCCT 58.272 36.000 0.00 0.00 37.65 5.19
376 377 6.974677 GTTACGTGTTAACTTTTTAAGGCC 57.025 37.500 7.22 0.00 37.65 5.19
387 388 5.803118 AGTTTGCAAGAGTTACGTGTTAAC 58.197 37.500 0.00 0.00 40.57 2.01
388 389 6.757947 AGTAGTTTGCAAGAGTTACGTGTTAA 59.242 34.615 0.00 0.00 0.00 2.01
389 390 6.275335 AGTAGTTTGCAAGAGTTACGTGTTA 58.725 36.000 0.00 0.00 0.00 2.41
390 391 5.114081 AGTAGTTTGCAAGAGTTACGTGTT 58.886 37.500 0.00 0.00 0.00 3.32
391 392 4.690122 AGTAGTTTGCAAGAGTTACGTGT 58.310 39.130 0.00 0.00 0.00 4.49
392 393 4.150098 GGAGTAGTTTGCAAGAGTTACGTG 59.850 45.833 0.00 0.00 0.00 4.49
393 394 4.304939 GGAGTAGTTTGCAAGAGTTACGT 58.695 43.478 0.00 0.00 0.00 3.57
394 395 3.678548 GGGAGTAGTTTGCAAGAGTTACG 59.321 47.826 0.00 0.00 0.00 3.18
395 396 4.895961 AGGGAGTAGTTTGCAAGAGTTAC 58.104 43.478 0.00 1.82 0.00 2.50
396 397 4.838986 AGAGGGAGTAGTTTGCAAGAGTTA 59.161 41.667 0.00 0.00 0.00 2.24
397 398 3.648545 AGAGGGAGTAGTTTGCAAGAGTT 59.351 43.478 0.00 0.00 0.00 3.01
398 399 3.007398 CAGAGGGAGTAGTTTGCAAGAGT 59.993 47.826 0.00 0.00 0.00 3.24
399 400 3.007398 ACAGAGGGAGTAGTTTGCAAGAG 59.993 47.826 0.00 0.00 0.00 2.85
400 401 2.972713 ACAGAGGGAGTAGTTTGCAAGA 59.027 45.455 0.00 0.00 0.00 3.02
401 402 3.409026 ACAGAGGGAGTAGTTTGCAAG 57.591 47.619 0.00 0.00 0.00 4.01
402 403 3.496160 GGAACAGAGGGAGTAGTTTGCAA 60.496 47.826 0.00 0.00 0.00 4.08
403 404 2.038557 GGAACAGAGGGAGTAGTTTGCA 59.961 50.000 0.00 0.00 0.00 4.08
404 405 2.038557 TGGAACAGAGGGAGTAGTTTGC 59.961 50.000 0.00 0.00 0.00 3.68
442 443 9.388346 CGCTTTTTGACACTACATTAATGTAAA 57.612 29.630 24.65 15.88 42.20 2.01
443 444 8.561212 ACGCTTTTTGACACTACATTAATGTAA 58.439 29.630 24.65 11.39 42.20 2.41
444 445 8.090250 ACGCTTTTTGACACTACATTAATGTA 57.910 30.769 23.51 23.51 41.97 2.29
445 446 6.966021 ACGCTTTTTGACACTACATTAATGT 58.034 32.000 23.80 23.80 44.48 2.71
446 447 7.298122 AGACGCTTTTTGACACTACATTAATG 58.702 34.615 14.01 14.01 0.00 1.90
447 448 7.435068 AGACGCTTTTTGACACTACATTAAT 57.565 32.000 0.00 0.00 0.00 1.40
448 449 6.854496 AGACGCTTTTTGACACTACATTAA 57.146 33.333 0.00 0.00 0.00 1.40
449 450 6.854496 AAGACGCTTTTTGACACTACATTA 57.146 33.333 0.00 0.00 0.00 1.90
450 451 5.751243 AAGACGCTTTTTGACACTACATT 57.249 34.783 0.00 0.00 0.00 2.71
451 452 8.718102 ATATAAGACGCTTTTTGACACTACAT 57.282 30.769 0.00 0.00 0.00 2.29
452 453 8.542497 AATATAAGACGCTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
455 456 9.378551 TCATAATATAAGACGCTTTTTGACACT 57.621 29.630 0.00 0.00 0.00 3.55
456 457 9.638300 CTCATAATATAAGACGCTTTTTGACAC 57.362 33.333 0.00 0.00 0.00 3.67
457 458 9.594478 TCTCATAATATAAGACGCTTTTTGACA 57.406 29.630 0.00 0.00 0.00 3.58
458 459 9.851043 GTCTCATAATATAAGACGCTTTTTGAC 57.149 33.333 0.00 0.00 31.01 3.18
468 469 6.660094 ACTCCCTCCGTCTCATAATATAAGAC 59.340 42.308 0.00 0.00 36.82 3.01
469 470 6.791371 ACTCCCTCCGTCTCATAATATAAGA 58.209 40.000 0.00 0.00 0.00 2.10
470 471 8.754991 ATACTCCCTCCGTCTCATAATATAAG 57.245 38.462 0.00 0.00 0.00 1.73
471 472 9.543231 AAATACTCCCTCCGTCTCATAATATAA 57.457 33.333 0.00 0.00 0.00 0.98
472 473 9.186837 GAAATACTCCCTCCGTCTCATAATATA 57.813 37.037 0.00 0.00 0.00 0.86
473 474 7.674348 TGAAATACTCCCTCCGTCTCATAATAT 59.326 37.037 0.00 0.00 0.00 1.28
474 475 7.008332 TGAAATACTCCCTCCGTCTCATAATA 58.992 38.462 0.00 0.00 0.00 0.98
475 476 5.839063 TGAAATACTCCCTCCGTCTCATAAT 59.161 40.000 0.00 0.00 0.00 1.28
476 477 5.205821 TGAAATACTCCCTCCGTCTCATAA 58.794 41.667 0.00 0.00 0.00 1.90
477 478 4.800023 TGAAATACTCCCTCCGTCTCATA 58.200 43.478 0.00 0.00 0.00 2.15
478 479 3.643237 TGAAATACTCCCTCCGTCTCAT 58.357 45.455 0.00 0.00 0.00 2.90
479 480 3.095912 TGAAATACTCCCTCCGTCTCA 57.904 47.619 0.00 0.00 0.00 3.27
480 481 3.700038 TCTTGAAATACTCCCTCCGTCTC 59.300 47.826 0.00 0.00 0.00 3.36
481 482 3.702045 CTCTTGAAATACTCCCTCCGTCT 59.298 47.826 0.00 0.00 0.00 4.18
482 483 3.738590 GCTCTTGAAATACTCCCTCCGTC 60.739 52.174 0.00 0.00 0.00 4.79
483 484 2.168728 GCTCTTGAAATACTCCCTCCGT 59.831 50.000 0.00 0.00 0.00 4.69
484 485 2.483889 GGCTCTTGAAATACTCCCTCCG 60.484 54.545 0.00 0.00 0.00 4.63
485 486 2.158740 GGGCTCTTGAAATACTCCCTCC 60.159 54.545 0.00 0.00 0.00 4.30
486 487 2.483889 CGGGCTCTTGAAATACTCCCTC 60.484 54.545 0.00 0.00 0.00 4.30
487 488 1.486726 CGGGCTCTTGAAATACTCCCT 59.513 52.381 0.00 0.00 0.00 4.20
488 489 1.209747 ACGGGCTCTTGAAATACTCCC 59.790 52.381 0.00 0.00 0.00 4.30
489 490 2.093658 TCACGGGCTCTTGAAATACTCC 60.094 50.000 0.00 0.00 0.00 3.85
490 491 2.930682 GTCACGGGCTCTTGAAATACTC 59.069 50.000 0.00 0.00 0.00 2.59
491 492 2.567615 AGTCACGGGCTCTTGAAATACT 59.432 45.455 0.00 0.00 0.00 2.12
492 493 2.930682 GAGTCACGGGCTCTTGAAATAC 59.069 50.000 0.00 0.00 0.00 1.89
493 494 2.832129 AGAGTCACGGGCTCTTGAAATA 59.168 45.455 5.89 0.00 40.08 1.40
494 495 1.625818 AGAGTCACGGGCTCTTGAAAT 59.374 47.619 5.89 0.00 40.08 2.17
495 496 1.048601 AGAGTCACGGGCTCTTGAAA 58.951 50.000 5.89 0.00 40.08 2.69
496 497 0.318441 CAGAGTCACGGGCTCTTGAA 59.682 55.000 8.63 0.00 40.97 2.69
497 498 1.967535 CAGAGTCACGGGCTCTTGA 59.032 57.895 8.63 0.00 40.97 3.02
498 499 1.739562 GCAGAGTCACGGGCTCTTG 60.740 63.158 8.63 6.56 40.97 3.02
499 500 2.659610 GCAGAGTCACGGGCTCTT 59.340 61.111 8.63 0.00 40.97 2.85
500 501 3.386237 GGCAGAGTCACGGGCTCT 61.386 66.667 5.89 5.89 43.43 4.09
501 502 4.803426 CGGCAGAGTCACGGGCTC 62.803 72.222 1.40 1.40 37.14 4.70
503 504 4.803426 CTCGGCAGAGTCACGGGC 62.803 72.222 5.61 0.00 39.60 6.13
504 505 4.135153 CCTCGGCAGAGTCACGGG 62.135 72.222 13.02 0.00 42.86 5.28
505 506 4.135153 CCCTCGGCAGAGTCACGG 62.135 72.222 13.02 2.95 42.86 4.94
518 519 3.997756 AACCTACCGGGGAGCCCTC 62.998 68.421 6.32 0.00 42.67 4.30
519 520 3.997756 GAACCTACCGGGGAGCCCT 62.998 68.421 6.32 0.00 42.67 5.19
520 521 2.594365 TAGAACCTACCGGGGAGCCC 62.594 65.000 6.32 0.00 41.09 5.19
521 522 1.075748 TAGAACCTACCGGGGAGCC 60.076 63.158 6.32 0.00 40.03 4.70
522 523 0.396835 ACTAGAACCTACCGGGGAGC 60.397 60.000 6.32 0.00 40.03 4.70
523 524 1.214923 AGACTAGAACCTACCGGGGAG 59.785 57.143 6.32 0.00 40.03 4.30
524 525 1.213926 GAGACTAGAACCTACCGGGGA 59.786 57.143 6.32 0.00 40.03 4.81
525 526 1.214923 AGAGACTAGAACCTACCGGGG 59.785 57.143 6.32 0.00 40.03 5.73
526 527 2.173143 AGAGAGACTAGAACCTACCGGG 59.827 54.545 6.32 0.00 41.89 5.73
527 528 3.564053 AGAGAGACTAGAACCTACCGG 57.436 52.381 0.00 0.00 0.00 5.28
528 529 7.714377 TGTATAAAGAGAGACTAGAACCTACCG 59.286 40.741 0.00 0.00 0.00 4.02
529 530 8.839343 GTGTATAAAGAGAGACTAGAACCTACC 58.161 40.741 0.00 0.00 0.00 3.18
530 531 9.617523 AGTGTATAAAGAGAGACTAGAACCTAC 57.382 37.037 0.00 0.00 0.00 3.18
531 532 9.835389 GAGTGTATAAAGAGAGACTAGAACCTA 57.165 37.037 0.00 0.00 0.00 3.08
532 533 8.554011 AGAGTGTATAAAGAGAGACTAGAACCT 58.446 37.037 0.00 0.00 0.00 3.50
533 534 8.741603 AGAGTGTATAAAGAGAGACTAGAACC 57.258 38.462 0.00 0.00 0.00 3.62
552 553 8.766476 TGATACTACTGGTAACTAGTAGAGTGT 58.234 37.037 22.61 7.44 44.31 3.55
553 554 9.044150 GTGATACTACTGGTAACTAGTAGAGTG 57.956 40.741 22.61 3.81 44.31 3.51
554 555 7.925483 CGTGATACTACTGGTAACTAGTAGAGT 59.075 40.741 22.61 13.09 44.31 3.24
555 556 7.925483 ACGTGATACTACTGGTAACTAGTAGAG 59.075 40.741 22.61 6.03 44.31 2.43
556 557 7.708322 CACGTGATACTACTGGTAACTAGTAGA 59.292 40.741 22.61 10.72 44.31 2.59
557 558 7.042187 CCACGTGATACTACTGGTAACTAGTAG 60.042 44.444 19.30 16.68 45.66 2.57
558 559 6.763135 CCACGTGATACTACTGGTAACTAGTA 59.237 42.308 19.30 0.00 35.17 1.82
559 560 5.587844 CCACGTGATACTACTGGTAACTAGT 59.412 44.000 19.30 0.00 33.74 2.57
560 561 5.587844 ACCACGTGATACTACTGGTAACTAG 59.412 44.000 19.30 0.00 33.39 2.57
563 564 4.708726 ACCACGTGATACTACTGGTAAC 57.291 45.455 19.30 0.00 33.39 2.50
567 568 3.587797 ACAACCACGTGATACTACTGG 57.412 47.619 19.30 0.00 0.00 4.00
722 730 3.838244 ATATATCAACACGTGCTGGGT 57.162 42.857 17.22 9.05 0.00 4.51
1067 1353 1.817520 CACACACCAACTGGCGACA 60.818 57.895 0.00 0.00 39.32 4.35
1098 1384 3.394836 GAAGGTGGCGCTCTCCCT 61.395 66.667 7.64 4.52 0.00 4.20
1285 1571 6.016943 GTCGAAACATAGATCTAGTAGCACCT 60.017 42.308 8.70 0.00 0.00 4.00
1483 1769 7.347508 ACACACTAAAATACGTCTGTCATTC 57.652 36.000 0.00 0.00 0.00 2.67
1491 1777 9.361712 GAGTAAACAAACACACTAAAATACGTC 57.638 33.333 0.00 0.00 0.00 4.34
1493 1779 9.872757 ATGAGTAAACAAACACACTAAAATACG 57.127 29.630 0.00 0.00 0.00 3.06
1564 1858 3.857052 TCGTTCAGCCTTACCACTATTG 58.143 45.455 0.00 0.00 0.00 1.90
1572 1866 3.579335 ACTCTCTTCGTTCAGCCTTAC 57.421 47.619 0.00 0.00 0.00 2.34
1577 1871 4.238514 ACAATGTACTCTCTTCGTTCAGC 58.761 43.478 0.00 0.00 0.00 4.26
1578 1872 7.044641 CGATTACAATGTACTCTCTTCGTTCAG 60.045 40.741 8.72 0.00 0.00 3.02
1585 2298 9.871238 AAACATACGATTACAATGTACTCTCTT 57.129 29.630 8.72 0.00 33.59 2.85
1658 2371 1.802960 ACACGGTGTCTACTGTCGTAG 59.197 52.381 8.21 0.00 44.49 3.51
1675 2388 5.739161 GTGTGAAGTCAAATTTCAGACACAC 59.261 40.000 19.35 19.35 44.01 3.82
1676 2389 5.879237 GTGTGAAGTCAAATTTCAGACACA 58.121 37.500 10.33 9.74 44.01 3.72
1682 2396 7.041635 ACATCATGTGTGAAGTCAAATTTCA 57.958 32.000 0.00 0.00 40.28 2.69
1683 2397 7.935338 AACATCATGTGTGAAGTCAAATTTC 57.065 32.000 0.00 0.00 41.14 2.17
1695 2409 7.165977 GTGTCTACTATCGTAACATCATGTGTG 59.834 40.741 0.00 0.00 41.14 3.82
1702 2416 7.127042 CACTGAGTGTCTACTATCGTAACATC 58.873 42.308 4.01 0.00 37.25 3.06
1704 2418 5.936372 ACACTGAGTGTCTACTATCGTAACA 59.064 40.000 13.33 0.00 43.92 2.41
1708 2422 4.948608 CACACTGAGTGTCTACTATCGT 57.051 45.455 16.50 0.00 43.92 3.73
1724 2451 6.964934 GTGTTAAGTCAAATTTCGAACACACT 59.035 34.615 17.17 0.00 42.85 3.55
1731 2458 7.802720 CACATCATGTGTTAAGTCAAATTTCGA 59.197 33.333 9.87 0.00 43.08 3.71
1754 2481 7.266939 GTGAAAAACGTTCAATTACAACACA 57.733 32.000 0.00 0.00 0.00 3.72
1858 2602 2.284515 AAACCCGGCCCAGATGATCC 62.285 60.000 0.00 0.00 0.00 3.36
1864 2608 2.528127 TCTGAAACCCGGCCCAGA 60.528 61.111 0.00 0.00 33.72 3.86
1865 2609 2.045926 CTCTGAAACCCGGCCCAG 60.046 66.667 0.00 0.00 0.00 4.45
1868 2612 2.269241 CCTCTCTGAAACCCGGCC 59.731 66.667 0.00 0.00 0.00 6.13
1870 2614 1.069358 GATAGCCTCTCTGAAACCCGG 59.931 57.143 0.00 0.00 0.00 5.73
1871 2615 2.035632 AGATAGCCTCTCTGAAACCCG 58.964 52.381 0.00 0.00 0.00 5.28
1872 2616 4.835615 TCATAGATAGCCTCTCTGAAACCC 59.164 45.833 0.98 0.00 34.99 4.11
1902 2661 2.295909 GGCTTTATGTCCACTTTGCACA 59.704 45.455 0.00 0.00 0.00 4.57
1918 2677 8.896320 AATAAAATTTCCAACGTAAAGGCTTT 57.104 26.923 17.76 17.76 0.00 3.51
1919 2678 7.601130 GGAATAAAATTTCCAACGTAAAGGCTT 59.399 33.333 0.00 0.00 43.92 4.35
1922 2681 6.034150 GCGGAATAAAATTTCCAACGTAAAGG 59.966 38.462 4.29 0.00 44.58 3.11
1925 2684 5.087397 CGCGGAATAAAATTTCCAACGTAA 58.913 37.500 0.00 0.00 44.58 3.18
1928 2687 2.849473 CCGCGGAATAAAATTTCCAACG 59.151 45.455 24.07 6.40 44.58 4.10
2002 2763 1.135024 ACACGTACCAAGTTGTCACGT 60.135 47.619 20.28 20.28 45.87 4.49
2018 2780 0.941463 GTCACTGCTCTCACCACACG 60.941 60.000 0.00 0.00 0.00 4.49
2027 2789 1.151668 GCATCGTTTGTCACTGCTCT 58.848 50.000 0.00 0.00 0.00 4.09
2031 2793 2.159612 CCTCATGCATCGTTTGTCACTG 60.160 50.000 0.00 0.00 0.00 3.66
2032 2794 2.079158 CCTCATGCATCGTTTGTCACT 58.921 47.619 0.00 0.00 0.00 3.41
2039 2801 1.078709 CACGTTCCTCATGCATCGTT 58.921 50.000 6.16 0.00 0.00 3.85
2046 2808 1.021390 GCCTGGACACGTTCCTCATG 61.021 60.000 14.95 0.00 46.10 3.07
2047 2809 1.296715 GCCTGGACACGTTCCTCAT 59.703 57.895 14.95 0.00 46.10 2.90
2048 2810 2.741092 GCCTGGACACGTTCCTCA 59.259 61.111 14.95 0.00 46.10 3.86
2068 2830 2.047844 CCTGCACCGAGTGGACTG 60.048 66.667 6.23 0.00 39.21 3.51
2084 2846 5.596362 TTCATGGAAAGTGCCAGGATTTCC 61.596 45.833 18.21 18.21 46.76 3.13
2086 2848 3.173953 TCATGGAAAGTGCCAGGATTT 57.826 42.857 0.00 0.00 43.16 2.17
2090 2852 3.967332 AAATTCATGGAAAGTGCCAGG 57.033 42.857 0.00 0.00 42.15 4.45
2096 2858 6.206634 TCGCTCTACAAAAATTCATGGAAAGT 59.793 34.615 0.00 0.00 0.00 2.66
2145 2907 2.874701 GAGGTTTGATCCATCCATGTCG 59.125 50.000 0.00 0.00 0.00 4.35
2169 2931 2.239201 GTTTACCGCAACGAAATCAGC 58.761 47.619 0.00 0.00 0.00 4.26
2178 2940 0.869730 ACATCCACGTTTACCGCAAC 59.130 50.000 0.00 0.00 41.42 4.17
2183 2945 4.341520 AGGAGAGATACATCCACGTTTACC 59.658 45.833 0.00 0.00 38.12 2.85
2190 2952 6.491745 TCATCACTAAGGAGAGATACATCCAC 59.508 42.308 0.00 0.00 38.12 4.02
2197 2959 5.236695 CGTTCGTCATCACTAAGGAGAGATA 59.763 44.000 0.00 0.00 31.92 1.98
2218 2980 0.035439 CACCCCTATTGCTCCACGTT 60.035 55.000 0.00 0.00 0.00 3.99
2219 2981 1.602237 CACCCCTATTGCTCCACGT 59.398 57.895 0.00 0.00 0.00 4.49
2222 2984 0.623723 GAACCACCCCTATTGCTCCA 59.376 55.000 0.00 0.00 0.00 3.86
2230 2992 3.526899 TCATCTTTGAGAACCACCCCTA 58.473 45.455 0.00 0.00 0.00 3.53
2260 3022 8.579850 TGGTCTTCTATCAGCAACAATAAAAT 57.420 30.769 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.