Multiple sequence alignment - TraesCS6A01G181300

Loading Multiple Alignment...

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 TraesCS6A01G181300 chr6A 100.000 4722 0 0 1 4722 206343492 206348213 0.000000e+00 8720
1 TraesCS6A01G181300 chr6D 97.361 2766 62 5 1640 4404 153855963 153858718 0.000000e+00 4693
2 TraesCS6A01G181300 chr6D 92.672 1119 54 9 558 1662 153854835 153855939 0.000000e+00 1587
3 TraesCS6A01G181300 chr6D 94.833 329 9 2 4402 4722 153858920 153859248 1.520000e-139 507
4 TraesCS6A01G181300 chr6D 90.237 338 29 4 1 337 153854497 153854831 5.610000e-119 438
5 TraesCS6A01G181300 chr1D 90.104 1637 130 7 2163 3798 10549718 10548113 0.000000e+00 2097
6 TraesCS6A01G181300 chr1D 91.135 1004 76 8 2092 3088 10458004 10457007 0.000000e+00 1349
7 TraesCS6A01G181300 chr1D 92.893 197 12 1 1449 1645 254397205 254397011 7.730000e-73 285
8 TraesCS6A01G181300 chr1A 90.208 1297 102 6 2163 3459 12186279 12185008 0.000000e+00 1668
9 TraesCS6A01G181300 chr1A 84.825 659 51 18 3505 4155 12185007 12184390 6.710000e-173 617
10 TraesCS6A01G181300 chr2D 89.104 569 41 15 2953 3514 450398989 450399543 0.000000e+00 688
11 TraesCS6A01G181300 chr2D 91.361 382 13 1 1640 2021 272792754 272792393 5.450000e-139 505
12 TraesCS6A01G181300 chr2D 90.361 249 21 2 3290 3538 498869073 498868828 1.640000e-84 324
13 TraesCS6A01G181300 chr2D 91.346 208 15 2 1439 1645 272564849 272565054 1.000000e-71 281
14 TraesCS6A01G181300 chr2D 80.201 298 36 11 2941 3229 498869364 498869081 8.010000e-48 202
15 TraesCS6A01G181300 chr5A 88.752 569 40 17 2953 3514 220899654 220899103 0.000000e+00 675
16 TraesCS6A01G181300 chr5A 98.690 229 2 1 339 567 364681844 364681617 5.690000e-109 405
17 TraesCS6A01G181300 chr3B 87.986 591 43 16 2953 3538 27506509 27505942 0.000000e+00 673
18 TraesCS6A01G181300 chr3B 91.361 382 13 1 1640 2021 101912334 101912695 5.450000e-139 505
19 TraesCS6A01G181300 chr3B 90.838 382 15 1 1640 2021 700786137 700785776 1.180000e-135 494
20 TraesCS6A01G181300 chrUn 91.361 382 13 1 1640 2021 444245273 444244912 5.450000e-139 505
21 TraesCS6A01G181300 chrUn 91.099 382 14 1 1640 2021 389360294 389360655 2.540000e-137 499
22 TraesCS6A01G181300 chrUn 90.576 382 16 1 1640 2021 216517444 216517083 5.490000e-134 488
23 TraesCS6A01G181300 chrUn 91.129 372 13 1 1640 2011 93408473 93408122 1.980000e-133 486
24 TraesCS6A01G181300 chrUn 92.893 197 12 1 1449 1645 346595589 346595395 7.730000e-73 285
25 TraesCS6A01G181300 chrUn 97.849 93 2 0 1640 1732 389446195 389446287 1.360000e-35 161
26 TraesCS6A01G181300 chr4D 91.361 382 13 1 1640 2021 30386839 30386478 5.450000e-139 505
27 TraesCS6A01G181300 chr4D 92.893 197 12 1 1449 1645 30387093 30386899 7.730000e-73 285
28 TraesCS6A01G181300 chr3A 91.361 382 13 1 1640 2021 594898465 594898104 5.450000e-139 505
29 TraesCS6A01G181300 chr3A 96.396 222 8 0 336 557 531907456 531907677 2.680000e-97 366
30 TraesCS6A01G181300 chr5D 91.099 382 14 5 1640 2021 446174943 446175304 2.540000e-137 499
31 TraesCS6A01G181300 chr5D 92.893 197 12 1 1449 1645 446174689 446174883 7.730000e-73 285
32 TraesCS6A01G181300 chr5D 92.893 197 12 1 1449 1645 503277321 503277127 7.730000e-73 285
33 TraesCS6A01G181300 chr4A 91.099 382 14 1 1640 2021 73811630 73811991 2.540000e-137 499
34 TraesCS6A01G181300 chr4A 87.936 373 34 4 2963 3333 353083688 353083325 3.380000e-116 429
35 TraesCS6A01G181300 chr4A 96.347 219 8 0 339 557 640235846 640236064 1.250000e-95 361
36 TraesCS6A01G181300 chr4A 93.401 197 11 1 1449 1645 73809833 73810027 1.660000e-74 291
37 TraesCS6A01G181300 chr2B 88.946 389 22 2 1634 2021 465000077 464999709 1.200000e-125 460
38 TraesCS6A01G181300 chr7A 88.689 389 23 2 1634 2021 352180718 352180350 5.570000e-124 455
39 TraesCS6A01G181300 chr7A 96.818 220 7 0 339 558 401405161 401405380 7.470000e-98 368
40 TraesCS6A01G181300 chr7A 94.760 229 10 2 330 557 27383984 27384211 5.810000e-94 355
41 TraesCS6A01G181300 chr7A 94.372 231 10 2 339 569 129261579 129261352 7.520000e-93 351
42 TraesCS6A01G181300 chr7A 93.305 239 12 2 322 558 50272035 50272271 2.700000e-92 350
43 TraesCS6A01G181300 chr2A 95.238 231 8 2 339 569 417360230 417360457 3.470000e-96 363
44 TraesCS6A01G181300 chr2A 95.946 222 9 0 336 557 35911065 35911286 1.250000e-95 361
45 TraesCS6A01G181300 chr4B 92.929 198 12 1 1449 1646 308697376 308697571 2.150000e-73 287
46 TraesCS6A01G181300 chr1B 81.107 307 37 12 4424 4711 15459922 15459618 4.750000e-55 226
47 TraesCS6A01G181300 chr1B 81.154 260 30 11 4472 4713 15616830 15616572 1.730000e-44 191


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 TraesCS6A01G181300 chr6A 206343492 206348213 4721 False 8720.00 8720 100.00000 1 4722 1 chr6A.!!$F1 4721
1 TraesCS6A01G181300 chr6D 153854497 153859248 4751 False 1806.25 4693 93.77575 1 4722 4 chr6D.!!$F1 4721
2 TraesCS6A01G181300 chr1D 10548113 10549718 1605 True 2097.00 2097 90.10400 2163 3798 1 chr1D.!!$R2 1635
3 TraesCS6A01G181300 chr1D 10457007 10458004 997 True 1349.00 1349 91.13500 2092 3088 1 chr1D.!!$R1 996
4 TraesCS6A01G181300 chr1A 12184390 12186279 1889 True 1142.50 1668 87.51650 2163 4155 2 chr1A.!!$R1 1992
5 TraesCS6A01G181300 chr2D 450398989 450399543 554 False 688.00 688 89.10400 2953 3514 1 chr2D.!!$F2 561
6 TraesCS6A01G181300 chr2D 498868828 498869364 536 True 263.00 324 85.28100 2941 3538 2 chr2D.!!$R2 597
7 TraesCS6A01G181300 chr5A 220899103 220899654 551 True 675.00 675 88.75200 2953 3514 1 chr5A.!!$R1 561
8 TraesCS6A01G181300 chr3B 27505942 27506509 567 True 673.00 673 87.98600 2953 3538 1 chr3B.!!$R1 585
9 TraesCS6A01G181300 chr4D 30386478 30387093 615 True 395.00 505 92.12700 1449 2021 2 chr4D.!!$R1 572
10 TraesCS6A01G181300 chr5D 446174689 446175304 615 False 392.00 499 91.99600 1449 2021 2 chr5D.!!$F1 572
11 TraesCS6A01G181300 chr4A 73809833 73811991 2158 False 395.00 499 92.25000 1449 2021 2 chr4A.!!$F2 572

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
523 524 0.252197 AATTGACGACCTAGGGGCAC 59.748 55.0 14.81 2.61 35.63 5.01 F
767 776 0.252197 AACTACCGTCCAAGGGCATC 59.748 55.0 0.00 0.00 35.02 3.91 F
1082 1092 1.878953 CTGCAAGTGGAAGGTACGTT 58.121 50.0 0.00 0.00 0.00 3.99 F
1399 1409 2.028020 AGCCTTTTCTCGTTCACCTAGG 60.028 50.0 7.41 7.41 0.00 3.02 F
2855 4535 0.698818 AGTTGTTGGTGGAGATCCCC 59.301 55.0 0.00 0.00 34.29 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2060 3727 0.384230 GACATGTGCACCGTGTTTCG 60.384 55.000 21.36 2.80 43.41 3.46 R
2061 3728 0.944386 AGACATGTGCACCGTGTTTC 59.056 50.000 21.36 12.47 43.41 2.78 R
2721 4401 2.050077 GCCCACGCTTGCTTTCAC 60.050 61.111 0.00 0.00 0.00 3.18 R
3362 5068 6.747280 CGTCTCAATCTTTCTCTTCTCTCTTC 59.253 42.308 0.00 0.00 0.00 2.87 R
3938 5645 0.807667 CAGGCCCTGAAGAATCGTCG 60.808 60.000 4.15 0.00 32.44 5.12 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
73 74 4.301505 CAGTACGCACTGCCCAAT 57.698 55.556 2.15 0.00 45.44 3.16
75 76 0.391661 CAGTACGCACTGCCCAATCT 60.392 55.000 2.15 0.00 45.44 2.40
78 79 1.549243 TACGCACTGCCCAATCTCCA 61.549 55.000 0.00 0.00 0.00 3.86
80 81 1.442526 CGCACTGCCCAATCTCCATC 61.443 60.000 0.00 0.00 0.00 3.51
101 102 5.464588 TCCCCCAATTTCATCATTACTCA 57.535 39.130 0.00 0.00 0.00 3.41
113 114 8.877864 TTCATCATTACTCATTAGGGTTTGTT 57.122 30.769 0.00 0.00 0.00 2.83
114 115 8.279970 TCATCATTACTCATTAGGGTTTGTTG 57.720 34.615 0.00 0.00 0.00 3.33
115 116 7.888021 TCATCATTACTCATTAGGGTTTGTTGT 59.112 33.333 0.00 0.00 0.00 3.32
116 117 8.522830 CATCATTACTCATTAGGGTTTGTTGTT 58.477 33.333 0.00 0.00 0.00 2.83
117 118 8.472007 TCATTACTCATTAGGGTTTGTTGTTT 57.528 30.769 0.00 0.00 0.00 2.83
160 161 2.603075 AACATTGCCCCTGTGTATGT 57.397 45.000 0.00 0.00 0.00 2.29
161 162 2.128771 ACATTGCCCCTGTGTATGTC 57.871 50.000 0.00 0.00 0.00 3.06
187 188 0.539438 GTTGTCTGTGCCCAATCCCA 60.539 55.000 0.00 0.00 0.00 4.37
197 198 1.518774 CCAATCCCAGTTGGCATGC 59.481 57.895 9.90 9.90 41.92 4.06
245 246 2.494530 GGACCGCCCTGTTGCAAAA 61.495 57.895 0.00 0.00 0.00 2.44
246 247 1.665442 GACCGCCCTGTTGCAAAAT 59.335 52.632 0.00 0.00 0.00 1.82
254 255 3.690460 CCCTGTTGCAAAATCTAGACCT 58.310 45.455 0.00 0.00 0.00 3.85
255 256 3.441572 CCCTGTTGCAAAATCTAGACCTG 59.558 47.826 0.00 0.00 0.00 4.00
256 257 3.119708 CCTGTTGCAAAATCTAGACCTGC 60.120 47.826 0.00 13.19 0.00 4.85
264 265 1.680522 ATCTAGACCTGCCACTGCCG 61.681 60.000 0.00 0.00 36.33 5.69
277 278 1.735571 CACTGCCGGTAACAATGGTAC 59.264 52.381 1.90 0.00 0.00 3.34
280 281 3.453353 ACTGCCGGTAACAATGGTACTAT 59.547 43.478 8.47 0.00 0.00 2.12
281 282 4.650588 ACTGCCGGTAACAATGGTACTATA 59.349 41.667 8.47 0.00 0.00 1.31
286 287 5.453621 CCGGTAACAATGGTACTATAGGCAA 60.454 44.000 8.47 0.00 0.00 4.52
316 317 1.432270 GCTATTGCTGGGAGTGTCGC 61.432 60.000 0.00 0.00 36.03 5.19
323 324 2.099652 CTGGGAGTGTCGCACCTTGA 62.100 60.000 6.39 0.00 34.23 3.02
337 338 6.741358 GTCGCACCTTGATGATTAGTTTTTAC 59.259 38.462 0.00 0.00 0.00 2.01
339 340 7.820386 TCGCACCTTGATGATTAGTTTTTACTA 59.180 33.333 0.00 0.00 0.00 1.82
340 341 7.903431 CGCACCTTGATGATTAGTTTTTACTAC 59.097 37.037 0.00 0.00 0.00 2.73
341 342 8.947115 GCACCTTGATGATTAGTTTTTACTACT 58.053 33.333 0.00 0.00 0.00 2.57
348 349 9.460906 GATGATTAGTTTTTACTACTACCTCCG 57.539 37.037 0.00 0.00 0.00 4.63
349 350 8.353423 TGATTAGTTTTTACTACTACCTCCGT 57.647 34.615 0.00 0.00 0.00 4.69
350 351 8.806146 TGATTAGTTTTTACTACTACCTCCGTT 58.194 33.333 0.00 0.00 0.00 4.44
351 352 9.645059 GATTAGTTTTTACTACTACCTCCGTTT 57.355 33.333 0.00 0.00 0.00 3.60
352 353 9.645059 ATTAGTTTTTACTACTACCTCCGTTTC 57.355 33.333 0.00 0.00 0.00 2.78
353 354 7.054491 AGTTTTTACTACTACCTCCGTTTCA 57.946 36.000 0.00 0.00 0.00 2.69
354 355 7.150640 AGTTTTTACTACTACCTCCGTTTCAG 58.849 38.462 0.00 0.00 0.00 3.02
355 356 6.655078 TTTTACTACTACCTCCGTTTCAGT 57.345 37.500 0.00 0.00 0.00 3.41
356 357 6.655078 TTTACTACTACCTCCGTTTCAGTT 57.345 37.500 0.00 0.00 0.00 3.16
357 358 6.655078 TTACTACTACCTCCGTTTCAGTTT 57.345 37.500 0.00 0.00 0.00 2.66
358 359 7.759489 TTACTACTACCTCCGTTTCAGTTTA 57.241 36.000 0.00 0.00 0.00 2.01
359 360 6.018589 ACTACTACCTCCGTTTCAGTTTAC 57.981 41.667 0.00 0.00 0.00 2.01
360 361 4.942761 ACTACCTCCGTTTCAGTTTACA 57.057 40.909 0.00 0.00 0.00 2.41
361 362 5.280654 ACTACCTCCGTTTCAGTTTACAA 57.719 39.130 0.00 0.00 0.00 2.41
362 363 5.295152 ACTACCTCCGTTTCAGTTTACAAG 58.705 41.667 0.00 0.00 0.00 3.16
363 364 4.146745 ACCTCCGTTTCAGTTTACAAGT 57.853 40.909 0.00 0.00 0.00 3.16
364 365 4.124970 ACCTCCGTTTCAGTTTACAAGTC 58.875 43.478 0.00 0.00 0.00 3.01
365 366 3.497262 CCTCCGTTTCAGTTTACAAGTCC 59.503 47.826 0.00 0.00 0.00 3.85
366 367 4.377897 CTCCGTTTCAGTTTACAAGTCCT 58.622 43.478 0.00 0.00 0.00 3.85
367 368 5.510179 CCTCCGTTTCAGTTTACAAGTCCTA 60.510 44.000 0.00 0.00 0.00 2.94
368 369 5.291971 TCCGTTTCAGTTTACAAGTCCTAC 58.708 41.667 0.00 0.00 0.00 3.18
369 370 4.149396 CCGTTTCAGTTTACAAGTCCTACG 59.851 45.833 0.00 0.00 0.00 3.51
370 371 4.375706 CGTTTCAGTTTACAAGTCCTACGC 60.376 45.833 0.00 0.00 0.00 4.42
371 372 2.937591 TCAGTTTACAAGTCCTACGCG 58.062 47.619 3.53 3.53 0.00 6.01
372 373 2.294233 TCAGTTTACAAGTCCTACGCGT 59.706 45.455 19.17 19.17 0.00 6.01
373 374 3.501828 TCAGTTTACAAGTCCTACGCGTA 59.498 43.478 19.40 19.40 0.00 4.42
374 375 4.156556 TCAGTTTACAAGTCCTACGCGTAT 59.843 41.667 20.91 5.41 0.00 3.06
375 376 5.353956 TCAGTTTACAAGTCCTACGCGTATA 59.646 40.000 20.91 8.44 0.00 1.47
376 377 5.453587 CAGTTTACAAGTCCTACGCGTATAC 59.546 44.000 20.91 19.74 0.00 1.47
377 378 4.552166 TTACAAGTCCTACGCGTATACC 57.448 45.455 20.91 10.04 0.00 2.73
378 379 2.648059 ACAAGTCCTACGCGTATACCT 58.352 47.619 20.91 12.19 0.00 3.08
379 380 3.808728 ACAAGTCCTACGCGTATACCTA 58.191 45.455 20.91 0.00 0.00 3.08
380 381 3.812053 ACAAGTCCTACGCGTATACCTAG 59.188 47.826 20.91 8.56 0.00 3.02
381 382 3.051081 AGTCCTACGCGTATACCTAGG 57.949 52.381 20.91 18.03 0.00 3.02
382 383 2.370189 AGTCCTACGCGTATACCTAGGT 59.630 50.000 20.91 20.57 0.00 3.08
383 384 3.142174 GTCCTACGCGTATACCTAGGTT 58.858 50.000 22.11 10.62 0.00 3.50
384 385 4.040461 AGTCCTACGCGTATACCTAGGTTA 59.960 45.833 22.11 9.58 0.00 2.85
385 386 4.152580 GTCCTACGCGTATACCTAGGTTAC 59.847 50.000 22.11 19.11 0.00 2.50
386 387 3.437049 CCTACGCGTATACCTAGGTTACC 59.563 52.174 22.11 13.61 0.00 2.85
387 388 2.930950 ACGCGTATACCTAGGTTACCA 58.069 47.619 22.11 1.21 0.00 3.25
388 389 3.287222 ACGCGTATACCTAGGTTACCAA 58.713 45.455 22.11 0.75 0.00 3.67
389 390 3.891366 ACGCGTATACCTAGGTTACCAAT 59.109 43.478 22.11 9.64 0.00 3.16
390 391 4.342092 ACGCGTATACCTAGGTTACCAATT 59.658 41.667 22.11 0.00 0.00 2.32
391 392 5.163416 ACGCGTATACCTAGGTTACCAATTT 60.163 40.000 22.11 0.00 0.00 1.82
392 393 5.754890 CGCGTATACCTAGGTTACCAATTTT 59.245 40.000 22.11 0.00 0.00 1.82
393 394 6.922957 CGCGTATACCTAGGTTACCAATTTTA 59.077 38.462 22.11 0.00 0.00 1.52
394 395 7.599998 CGCGTATACCTAGGTTACCAATTTTAT 59.400 37.037 22.11 5.71 0.00 1.40
395 396 8.929746 GCGTATACCTAGGTTACCAATTTTATC 58.070 37.037 22.11 0.00 0.00 1.75
396 397 9.985730 CGTATACCTAGGTTACCAATTTTATCA 57.014 33.333 22.11 0.00 0.00 2.15
452 453 8.842358 ATACGGTTTGAAAATAGAACTTCTGA 57.158 30.769 1.17 0.00 0.00 3.27
453 454 7.562454 ACGGTTTGAAAATAGAACTTCTGAA 57.438 32.000 1.17 0.00 0.00 3.02
454 455 7.639945 ACGGTTTGAAAATAGAACTTCTGAAG 58.360 34.615 15.59 15.59 0.00 3.02
455 456 7.282450 ACGGTTTGAAAATAGAACTTCTGAAGT 59.718 33.333 17.00 17.00 45.46 3.01
508 509 5.734855 CCTGTATTAGGTCGGTCAAATTG 57.265 43.478 0.00 0.00 42.00 2.32
509 510 5.424757 CCTGTATTAGGTCGGTCAAATTGA 58.575 41.667 0.00 0.00 42.00 2.57
510 511 5.293569 CCTGTATTAGGTCGGTCAAATTGAC 59.706 44.000 17.16 17.16 42.90 3.18
511 512 7.874576 CCTGTATTAGGTCGGTCAAATTGACG 61.875 46.154 18.52 13.95 43.73 4.35
512 513 9.913090 CCTGTATTAGGTCGGTCAAATTGACGA 62.913 44.444 18.52 15.76 43.73 4.20
520 521 2.629051 GTCAAATTGACGACCTAGGGG 58.371 52.381 14.81 7.16 37.67 4.79
521 522 1.065709 TCAAATTGACGACCTAGGGGC 60.066 52.381 14.81 3.61 35.63 5.80
522 523 0.988832 AAATTGACGACCTAGGGGCA 59.011 50.000 14.81 0.74 35.63 5.36
523 524 0.252197 AATTGACGACCTAGGGGCAC 59.748 55.000 14.81 2.61 35.63 5.01
524 525 1.956629 ATTGACGACCTAGGGGCACG 61.957 60.000 14.81 14.81 39.93 5.34
525 526 4.509737 GACGACCTAGGGGCACGC 62.510 72.222 14.81 6.25 43.76 5.34
539 540 4.973055 ACGCGCACGCCCTGTAAA 62.973 61.111 5.73 0.00 45.53 2.01
540 541 4.439472 CGCGCACGCCCTGTAAAC 62.439 66.667 8.75 0.00 37.98 2.01
541 542 3.047877 GCGCACGCCCTGTAAACT 61.048 61.111 0.30 0.00 34.56 2.66
542 543 2.860293 CGCACGCCCTGTAAACTG 59.140 61.111 0.00 0.00 0.00 3.16
543 544 1.666553 CGCACGCCCTGTAAACTGA 60.667 57.895 0.00 0.00 0.00 3.41
544 545 1.626654 CGCACGCCCTGTAAACTGAG 61.627 60.000 0.00 0.00 0.00 3.35
545 546 0.320421 GCACGCCCTGTAAACTGAGA 60.320 55.000 0.00 0.00 0.00 3.27
546 547 1.714794 CACGCCCTGTAAACTGAGAG 58.285 55.000 0.00 0.00 0.00 3.20
547 548 1.272490 CACGCCCTGTAAACTGAGAGA 59.728 52.381 0.00 0.00 0.00 3.10
548 549 1.546476 ACGCCCTGTAAACTGAGAGAG 59.454 52.381 0.00 0.00 0.00 3.20
549 550 1.819288 CGCCCTGTAAACTGAGAGAGA 59.181 52.381 0.00 0.00 0.00 3.10
550 551 2.159310 CGCCCTGTAAACTGAGAGAGAG 60.159 54.545 0.00 0.00 0.00 3.20
551 552 2.167487 GCCCTGTAAACTGAGAGAGAGG 59.833 54.545 0.00 0.00 0.00 3.69
552 553 3.436243 CCCTGTAAACTGAGAGAGAGGT 58.564 50.000 0.00 0.00 0.00 3.85
553 554 4.601084 CCCTGTAAACTGAGAGAGAGGTA 58.399 47.826 0.00 0.00 0.00 3.08
554 555 4.642885 CCCTGTAAACTGAGAGAGAGGTAG 59.357 50.000 0.00 0.00 0.00 3.18
555 556 5.258051 CCTGTAAACTGAGAGAGAGGTAGT 58.742 45.833 0.00 0.00 0.00 2.73
556 557 6.416415 CCTGTAAACTGAGAGAGAGGTAGTA 58.584 44.000 0.00 0.00 0.00 1.82
597 606 4.781934 AGATAACCCTGTAATGCCTTGAC 58.218 43.478 0.00 0.00 0.00 3.18
599 608 0.981183 ACCCTGTAATGCCTTGACGA 59.019 50.000 0.00 0.00 0.00 4.20
606 615 4.839121 TGTAATGCCTTGACGACCTTTAT 58.161 39.130 0.00 0.00 0.00 1.40
700 709 4.724303 CGTAAGGTGTTTTGTTGTTCACA 58.276 39.130 0.00 0.00 33.17 3.58
722 731 5.807520 ACATCTACGATAAACACAGCAAGAG 59.192 40.000 0.00 0.00 0.00 2.85
725 734 6.266323 TCTACGATAAACACAGCAAGAGATC 58.734 40.000 0.00 0.00 0.00 2.75
743 752 9.956720 CAAGAGATCACAAAGAAGTTAAACATT 57.043 29.630 0.00 0.00 0.00 2.71
756 765 8.146412 AGAAGTTAAACATTAGACAACTACCGT 58.854 33.333 0.00 0.00 0.00 4.83
767 776 0.252197 AACTACCGTCCAAGGGCATC 59.748 55.000 0.00 0.00 35.02 3.91
786 795 5.517904 GCATCTGGCATTAGACTTTTCATC 58.482 41.667 0.00 0.00 43.97 2.92
787 796 5.066893 GCATCTGGCATTAGACTTTTCATCA 59.933 40.000 0.00 0.00 43.97 3.07
788 797 6.726230 CATCTGGCATTAGACTTTTCATCAG 58.274 40.000 0.00 0.00 0.00 2.90
789 798 6.053632 TCTGGCATTAGACTTTTCATCAGA 57.946 37.500 0.00 0.00 0.00 3.27
790 799 6.111382 TCTGGCATTAGACTTTTCATCAGAG 58.889 40.000 0.00 0.00 0.00 3.35
791 800 6.053632 TGGCATTAGACTTTTCATCAGAGA 57.946 37.500 0.00 0.00 0.00 3.10
793 802 6.372659 TGGCATTAGACTTTTCATCAGAGAAC 59.627 38.462 0.00 0.00 0.00 3.01
794 803 6.597280 GGCATTAGACTTTTCATCAGAGAACT 59.403 38.462 0.00 0.00 0.00 3.01
795 804 7.201600 GGCATTAGACTTTTCATCAGAGAACTC 60.202 40.741 0.00 0.00 0.00 3.01
796 805 7.463913 GCATTAGACTTTTCATCAGAGAACTCG 60.464 40.741 0.00 0.00 34.09 4.18
797 806 4.241681 AGACTTTTCATCAGAGAACTCGC 58.758 43.478 0.00 0.00 34.09 5.03
810 820 5.345202 CAGAGAACTCGCAAATAAAGTACGT 59.655 40.000 0.00 0.00 34.09 3.57
814 824 3.676646 ACTCGCAAATAAAGTACGTGGAC 59.323 43.478 0.00 0.00 0.00 4.02
836 846 2.495084 GGACAGAAGCCGAAAAGAACT 58.505 47.619 0.00 0.00 0.00 3.01
837 847 2.224314 GGACAGAAGCCGAAAAGAACTG 59.776 50.000 0.00 0.00 0.00 3.16
840 850 3.077359 CAGAAGCCGAAAAGAACTGGAT 58.923 45.455 0.00 0.00 0.00 3.41
860 870 3.297134 TTGCAGTTTCTCAGGGTCTTT 57.703 42.857 0.00 0.00 0.00 2.52
887 897 3.184382 TCACTGAATCTGTGGGGTAGA 57.816 47.619 18.00 0.00 34.75 2.59
913 923 3.665190 CTTAAGCCGTTTCTGGAGAAGT 58.335 45.455 0.00 0.00 35.21 3.01
946 956 4.336280 AGAACTGTGCCCTAATTTCCTTC 58.664 43.478 0.00 0.00 0.00 3.46
953 963 3.053619 TGCCCTAATTTCCTTCCTCCTTC 60.054 47.826 0.00 0.00 0.00 3.46
956 966 4.724293 CCCTAATTTCCTTCCTCCTTCTCT 59.276 45.833 0.00 0.00 0.00 3.10
978 988 8.318412 TCTCTTCTGTGCAGTTTATTTATGGTA 58.682 33.333 0.00 0.00 0.00 3.25
1032 1042 5.372066 AGGGGAGAAAGATTCAGCTGATAAT 59.628 40.000 19.04 9.16 0.00 1.28
1059 1069 5.047377 GGTCTCTCCATCTGATGATAGGAAC 60.047 48.000 18.92 14.44 33.10 3.62
1082 1092 1.878953 CTGCAAGTGGAAGGTACGTT 58.121 50.000 0.00 0.00 0.00 3.99
1116 1126 2.033049 CAGAGCACATATCTGCAAAGCC 59.967 50.000 5.72 0.00 39.86 4.35
1123 1133 5.563475 GCACATATCTGCAAAGCCGAATAAT 60.563 40.000 0.00 0.00 37.11 1.28
1235 1245 9.368416 TGCAGACTTTATATCTCCATAGTTAGT 57.632 33.333 0.00 0.00 0.00 2.24
1248 1258 8.242053 TCTCCATAGTTAGTAAACAGAACTTCG 58.758 37.037 5.94 0.00 38.12 3.79
1318 1328 6.841601 TGGCATTCTACCTTATTAGCTGATT 58.158 36.000 0.00 0.00 0.00 2.57
1399 1409 2.028020 AGCCTTTTCTCGTTCACCTAGG 60.028 50.000 7.41 7.41 0.00 3.02
1440 1451 3.493176 GCTTTTCAGCAATGGGACACTTT 60.493 43.478 0.00 0.00 44.67 2.66
1809 3476 3.652869 TGAAAACACCTCTCTGGATCCTT 59.347 43.478 14.23 0.00 39.71 3.36
1890 3557 6.322456 TGATCCAATTCTATCGAGTCTGACTT 59.678 38.462 12.27 0.00 0.00 3.01
1979 3646 8.656806 TCCATTTACTTATGATACCTAGTTGGG 58.343 37.037 0.00 0.00 41.11 4.12
2060 3727 6.115446 TCCATGTATTCAGTCAAGGAATCAC 58.885 40.000 0.00 0.00 36.45 3.06
2061 3728 5.007039 CCATGTATTCAGTCAAGGAATCACG 59.993 44.000 0.00 0.00 36.45 4.35
2123 3790 4.630111 CCTTCTCTCTGCTCCATGTATTC 58.370 47.826 0.00 0.00 0.00 1.75
2125 3792 3.291584 TCTCTCTGCTCCATGTATTCGT 58.708 45.455 0.00 0.00 0.00 3.85
2451 4118 2.515523 GCATGCCAGCCAGATCGT 60.516 61.111 6.36 0.00 0.00 3.73
2721 4401 1.429927 CGGAGAGAGCTGCAGCAATG 61.430 60.000 38.24 17.37 45.16 2.82
2855 4535 0.698818 AGTTGTTGGTGGAGATCCCC 59.301 55.000 0.00 0.00 34.29 4.81
3362 5068 7.395190 TCTATTCATGGTGAGAAAACAATGG 57.605 36.000 0.00 0.00 33.04 3.16
3424 5130 7.307811 GGAGAAGTATCTGTTGTTGTTTGTACC 60.308 40.741 0.00 0.00 35.54 3.34
3739 5445 4.159693 TCTTGACCAGTACGCATAACAGAT 59.840 41.667 0.00 0.00 0.00 2.90
3741 5447 5.784578 TGACCAGTACGCATAACAGATAT 57.215 39.130 0.00 0.00 0.00 1.63
3754 5460 7.254898 CGCATAACAGATATGTGGTCAATCTTT 60.255 37.037 4.70 0.00 44.99 2.52
3816 5522 7.575414 TTTGTTGTTTGATAGCTGAGGTTAA 57.425 32.000 0.00 0.00 0.00 2.01
3839 5545 4.150897 AGTTTTGTAGGAAGACAGTGCA 57.849 40.909 0.00 0.00 0.00 4.57
3871 5577 2.107031 CCATCTTCATGTGGATAGGCCA 59.893 50.000 5.01 0.00 46.96 5.36
3891 5597 5.049405 GGCCAGATATCGGAATTTGTAACTG 60.049 44.000 15.11 0.00 0.00 3.16
3938 5645 5.932303 TGACAGCTTTACCAATGAGTCTAAC 59.068 40.000 0.00 0.00 0.00 2.34
3953 5660 3.128938 AGTCTAACGACGATTCTTCAGGG 59.871 47.826 0.00 0.00 44.93 4.45
3955 5662 0.391263 AACGACGATTCTTCAGGGCC 60.391 55.000 0.00 0.00 0.00 5.80
4008 5717 9.509956 AATGTAAACAAGCTACCTTATGTGTAA 57.490 29.630 0.00 0.00 0.00 2.41
4135 5846 6.394809 TCCTGGTTCTTGTTTGTTTTCTTTC 58.605 36.000 0.00 0.00 0.00 2.62
4263 5974 2.330231 ATTGCGTGTGAACAATTCCG 57.670 45.000 0.00 0.00 32.67 4.30
4296 6007 3.938334 GAGCTTTTCTTTTTGGGCAAACA 59.062 39.130 0.00 0.00 0.00 2.83
4301 6012 3.726291 TCTTTTTGGGCAAACAGTAGC 57.274 42.857 0.00 0.00 31.84 3.58
4302 6013 3.295973 TCTTTTTGGGCAAACAGTAGCT 58.704 40.909 0.00 0.00 31.84 3.32
4343 6055 7.531857 ACCACTATGATAGTTGATAGGTGAG 57.468 40.000 10.29 0.00 36.76 3.51
4413 6329 3.191888 ACTGGGACCATCTTACTCAGT 57.808 47.619 0.00 0.00 0.00 3.41
4434 6350 6.678568 AGTCCCTTACTGAGAATATCCATG 57.321 41.667 0.00 0.00 36.93 3.66
4483 6399 9.985730 AATTGCATATTTGATACATGTTTAGGG 57.014 29.630 2.30 0.00 0.00 3.53
4525 6441 2.290323 ACTGGGAAAATGTTCGCTAGCT 60.290 45.455 13.93 0.00 44.81 3.32
4553 6472 1.071699 TCAACAGTAGTGAACCAGCCC 59.928 52.381 4.09 0.00 0.00 5.19
4595 6514 5.950544 ACCACAAGTAGTATGGCATTCTA 57.049 39.130 4.78 7.62 36.96 2.10
4674 6593 2.762887 TGCAGTGTGGTTCCATTTCAAA 59.237 40.909 0.00 0.00 0.00 2.69
4696 6615 9.563898 TCAAATACTACAATAACTGACTACACG 57.436 33.333 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 0.320374 TACTGAAGACAACGGGCTGG 59.680 55.000 0.00 0.00 0.00 4.85
45 46 0.319211 TGCGTACTGAAGACAACGGG 60.319 55.000 0.00 0.00 35.93 5.28
73 74 2.858133 TGATGAAATTGGGGGATGGAGA 59.142 45.455 0.00 0.00 0.00 3.71
75 76 3.997726 ATGATGAAATTGGGGGATGGA 57.002 42.857 0.00 0.00 0.00 3.41
78 79 6.029492 TGAGTAATGATGAAATTGGGGGAT 57.971 37.500 0.00 0.00 0.00 3.85
80 81 6.736110 AATGAGTAATGATGAAATTGGGGG 57.264 37.500 0.00 0.00 0.00 5.40
131 132 4.837860 ACAGGGGCAATGTTTTCTCAATAA 59.162 37.500 0.00 0.00 0.00 1.40
160 161 2.027653 TGGGCACAGACAACGAATATGA 60.028 45.455 0.00 0.00 0.00 2.15
161 162 2.355197 TGGGCACAGACAACGAATATG 58.645 47.619 0.00 0.00 0.00 1.78
187 188 0.248289 GCAATTCTGGCATGCCAACT 59.752 50.000 37.47 22.70 46.63 3.16
202 203 5.163513 CCGCTAAAGAAAATTGACAGCAAT 58.836 37.500 0.00 0.00 46.35 3.56
232 233 2.164422 GGTCTAGATTTTGCAACAGGGC 59.836 50.000 0.00 0.00 0.00 5.19
236 237 2.819608 GGCAGGTCTAGATTTTGCAACA 59.180 45.455 20.52 0.00 36.53 3.33
237 238 2.819608 TGGCAGGTCTAGATTTTGCAAC 59.180 45.455 20.52 10.02 36.53 4.17
239 240 2.040278 AGTGGCAGGTCTAGATTTTGCA 59.960 45.455 20.52 9.56 36.53 4.08
240 241 2.421424 CAGTGGCAGGTCTAGATTTTGC 59.579 50.000 14.26 14.26 0.00 3.68
241 242 2.421424 GCAGTGGCAGGTCTAGATTTTG 59.579 50.000 0.00 0.00 40.72 2.44
245 246 1.680522 CGGCAGTGGCAGGTCTAGAT 61.681 60.000 17.80 0.00 43.71 1.98
246 247 2.351244 CGGCAGTGGCAGGTCTAGA 61.351 63.158 17.80 0.00 43.71 2.43
254 255 1.074072 ATTGTTACCGGCAGTGGCA 59.926 52.632 17.80 0.00 43.71 4.92
255 256 1.506262 CATTGTTACCGGCAGTGGC 59.494 57.895 6.62 6.62 40.13 5.01
256 257 0.608035 ACCATTGTTACCGGCAGTGG 60.608 55.000 16.98 16.98 45.53 4.00
264 265 7.868906 TTTTGCCTATAGTACCATTGTTACC 57.131 36.000 0.00 0.00 0.00 2.85
277 278 9.999009 CAATAGCATCACATATTTTGCCTATAG 57.001 33.333 0.00 0.00 35.71 1.31
280 281 6.491062 AGCAATAGCATCACATATTTTGCCTA 59.509 34.615 0.00 0.00 45.49 3.93
281 282 5.303589 AGCAATAGCATCACATATTTTGCCT 59.696 36.000 0.00 0.00 45.49 4.75
286 287 5.387788 TCCCAGCAATAGCATCACATATTT 58.612 37.500 0.00 0.00 45.49 1.40
323 324 8.975295 ACGGAGGTAGTAGTAAAAACTAATCAT 58.025 33.333 0.00 0.00 31.48 2.45
337 338 6.017400 TGTAAACTGAAACGGAGGTAGTAG 57.983 41.667 0.00 0.00 0.00 2.57
339 340 4.942761 TGTAAACTGAAACGGAGGTAGT 57.057 40.909 0.00 0.00 0.00 2.73
340 341 5.295152 ACTTGTAAACTGAAACGGAGGTAG 58.705 41.667 0.00 0.00 0.00 3.18
341 342 5.280654 ACTTGTAAACTGAAACGGAGGTA 57.719 39.130 0.00 0.00 0.00 3.08
342 343 4.124970 GACTTGTAAACTGAAACGGAGGT 58.875 43.478 0.00 0.00 0.00 3.85
343 344 3.497262 GGACTTGTAAACTGAAACGGAGG 59.503 47.826 0.00 0.00 0.00 4.30
344 345 4.377897 AGGACTTGTAAACTGAAACGGAG 58.622 43.478 0.00 0.00 0.00 4.63
345 346 4.411256 AGGACTTGTAAACTGAAACGGA 57.589 40.909 0.00 0.00 0.00 4.69
346 347 4.149396 CGTAGGACTTGTAAACTGAAACGG 59.851 45.833 0.00 0.00 0.00 4.44
347 348 4.375706 GCGTAGGACTTGTAAACTGAAACG 60.376 45.833 0.00 0.00 0.00 3.60
348 349 4.375706 CGCGTAGGACTTGTAAACTGAAAC 60.376 45.833 0.00 0.00 0.00 2.78
349 350 3.737266 CGCGTAGGACTTGTAAACTGAAA 59.263 43.478 0.00 0.00 0.00 2.69
350 351 3.243501 ACGCGTAGGACTTGTAAACTGAA 60.244 43.478 11.67 0.00 0.00 3.02
351 352 2.294233 ACGCGTAGGACTTGTAAACTGA 59.706 45.455 11.67 0.00 0.00 3.41
352 353 2.669364 ACGCGTAGGACTTGTAAACTG 58.331 47.619 11.67 0.00 0.00 3.16
353 354 4.708726 ATACGCGTAGGACTTGTAAACT 57.291 40.909 24.78 0.00 0.00 2.66
354 355 4.735338 GGTATACGCGTAGGACTTGTAAAC 59.265 45.833 24.78 6.78 0.00 2.01
355 356 4.640201 AGGTATACGCGTAGGACTTGTAAA 59.360 41.667 24.78 0.00 0.00 2.01
356 357 4.199310 AGGTATACGCGTAGGACTTGTAA 58.801 43.478 24.78 0.00 0.00 2.41
357 358 3.808728 AGGTATACGCGTAGGACTTGTA 58.191 45.455 24.78 7.25 0.00 2.41
358 359 2.648059 AGGTATACGCGTAGGACTTGT 58.352 47.619 24.78 8.30 0.00 3.16
359 360 3.188048 CCTAGGTATACGCGTAGGACTTG 59.812 52.174 24.78 19.23 45.08 3.16
360 361 3.181450 ACCTAGGTATACGCGTAGGACTT 60.181 47.826 25.95 21.88 45.08 3.01
361 362 2.370189 ACCTAGGTATACGCGTAGGACT 59.630 50.000 25.95 22.11 45.08 3.85
362 363 2.772287 ACCTAGGTATACGCGTAGGAC 58.228 52.381 25.95 22.99 45.08 3.85
363 364 3.492102 AACCTAGGTATACGCGTAGGA 57.508 47.619 25.95 14.03 45.08 2.94
364 365 3.437049 GGTAACCTAGGTATACGCGTAGG 59.563 52.174 24.78 21.85 46.64 3.18
365 366 4.065088 TGGTAACCTAGGTATACGCGTAG 58.935 47.826 24.78 11.28 0.00 3.51
366 367 4.079980 TGGTAACCTAGGTATACGCGTA 57.920 45.455 22.94 22.94 0.00 4.42
367 368 2.930950 TGGTAACCTAGGTATACGCGT 58.069 47.619 19.17 19.17 0.00 6.01
368 369 3.988379 TTGGTAACCTAGGTATACGCG 57.012 47.619 16.67 3.53 0.00 6.01
369 370 8.837788 ATAAAATTGGTAACCTAGGTATACGC 57.162 34.615 16.67 13.00 0.00 4.42
370 371 9.985730 TGATAAAATTGGTAACCTAGGTATACG 57.014 33.333 16.67 0.00 0.00 3.06
426 427 9.932207 TCAGAAGTTCTATTTTCAAACCGTATA 57.068 29.630 4.74 0.00 0.00 1.47
427 428 8.842358 TCAGAAGTTCTATTTTCAAACCGTAT 57.158 30.769 4.74 0.00 0.00 3.06
428 429 8.665643 TTCAGAAGTTCTATTTTCAAACCGTA 57.334 30.769 4.74 0.00 0.00 4.02
429 430 7.282450 ACTTCAGAAGTTCTATTTTCAAACCGT 59.718 33.333 10.27 0.00 39.04 4.83
430 431 7.639945 ACTTCAGAAGTTCTATTTTCAAACCG 58.360 34.615 10.27 0.00 39.04 4.44
486 487 5.293569 GTCAATTTGACCGACCTAATACAGG 59.706 44.000 17.07 0.00 44.79 4.00
487 488 5.005394 CGTCAATTTGACCGACCTAATACAG 59.995 44.000 20.87 1.84 44.20 2.74
488 489 4.865925 CGTCAATTTGACCGACCTAATACA 59.134 41.667 20.87 0.00 44.20 2.29
489 490 5.005107 GTCGTCAATTTGACCGACCTAATAC 59.995 44.000 26.42 12.74 44.20 1.89
490 491 5.104374 GTCGTCAATTTGACCGACCTAATA 58.896 41.667 26.42 7.42 44.20 0.98
491 492 3.930848 GTCGTCAATTTGACCGACCTAAT 59.069 43.478 26.42 0.00 44.20 1.73
492 493 3.319755 GTCGTCAATTTGACCGACCTAA 58.680 45.455 26.42 8.36 44.20 2.69
493 494 2.950433 GTCGTCAATTTGACCGACCTA 58.050 47.619 26.42 8.31 44.20 3.08
494 495 1.792006 GTCGTCAATTTGACCGACCT 58.208 50.000 26.42 0.00 44.20 3.85
500 501 2.629051 CCCCTAGGTCGTCAATTTGAC 58.371 52.381 17.76 17.76 43.65 3.18
501 502 1.065709 GCCCCTAGGTCGTCAATTTGA 60.066 52.381 8.29 0.00 34.57 2.69
502 503 1.339631 TGCCCCTAGGTCGTCAATTTG 60.340 52.381 8.29 0.00 34.57 2.32
503 504 0.988832 TGCCCCTAGGTCGTCAATTT 59.011 50.000 8.29 0.00 34.57 1.82
504 505 0.252197 GTGCCCCTAGGTCGTCAATT 59.748 55.000 8.29 0.00 34.57 2.32
505 506 1.905512 GTGCCCCTAGGTCGTCAAT 59.094 57.895 8.29 0.00 34.57 2.57
506 507 2.642254 CGTGCCCCTAGGTCGTCAA 61.642 63.158 8.29 0.00 34.57 3.18
507 508 3.066190 CGTGCCCCTAGGTCGTCA 61.066 66.667 8.29 0.00 34.57 4.35
508 509 4.509737 GCGTGCCCCTAGGTCGTC 62.510 72.222 8.29 0.00 35.88 4.20
522 523 4.973055 TTTACAGGGCGTGCGCGT 62.973 61.111 22.18 2.94 43.06 6.01
523 524 4.439472 GTTTACAGGGCGTGCGCG 62.439 66.667 16.86 16.86 43.06 6.86
524 525 3.047877 AGTTTACAGGGCGTGCGC 61.048 61.111 7.17 8.17 41.06 6.09
525 526 1.626654 CTCAGTTTACAGGGCGTGCG 61.627 60.000 7.17 0.00 0.00 5.34
526 527 0.320421 TCTCAGTTTACAGGGCGTGC 60.320 55.000 7.17 0.00 0.00 5.34
527 528 1.272490 TCTCTCAGTTTACAGGGCGTG 59.728 52.381 5.50 5.50 0.00 5.34
528 529 1.546476 CTCTCTCAGTTTACAGGGCGT 59.454 52.381 0.00 0.00 0.00 5.68
529 530 1.819288 TCTCTCTCAGTTTACAGGGCG 59.181 52.381 0.00 0.00 0.00 6.13
530 531 2.167487 CCTCTCTCTCAGTTTACAGGGC 59.833 54.545 0.00 0.00 0.00 5.19
531 532 3.436243 ACCTCTCTCTCAGTTTACAGGG 58.564 50.000 0.00 0.00 0.00 4.45
532 533 5.258051 ACTACCTCTCTCTCAGTTTACAGG 58.742 45.833 0.00 0.00 0.00 4.00
533 534 7.771361 TCATACTACCTCTCTCTCAGTTTACAG 59.229 40.741 0.00 0.00 0.00 2.74
534 535 7.553402 GTCATACTACCTCTCTCTCAGTTTACA 59.447 40.741 0.00 0.00 0.00 2.41
535 536 7.771826 AGTCATACTACCTCTCTCTCAGTTTAC 59.228 40.741 0.00 0.00 0.00 2.01
536 537 7.771361 CAGTCATACTACCTCTCTCTCAGTTTA 59.229 40.741 0.00 0.00 0.00 2.01
537 538 6.601613 CAGTCATACTACCTCTCTCTCAGTTT 59.398 42.308 0.00 0.00 0.00 2.66
538 539 6.069905 TCAGTCATACTACCTCTCTCTCAGTT 60.070 42.308 0.00 0.00 0.00 3.16
539 540 5.427157 TCAGTCATACTACCTCTCTCTCAGT 59.573 44.000 0.00 0.00 0.00 3.41
540 541 5.924356 TCAGTCATACTACCTCTCTCTCAG 58.076 45.833 0.00 0.00 0.00 3.35
541 542 5.959583 TCAGTCATACTACCTCTCTCTCA 57.040 43.478 0.00 0.00 0.00 3.27
542 543 7.817418 AATTCAGTCATACTACCTCTCTCTC 57.183 40.000 0.00 0.00 0.00 3.20
543 544 7.617723 ACAAATTCAGTCATACTACCTCTCTCT 59.382 37.037 0.00 0.00 0.00 3.10
544 545 7.777095 ACAAATTCAGTCATACTACCTCTCTC 58.223 38.462 0.00 0.00 0.00 3.20
545 546 7.726033 ACAAATTCAGTCATACTACCTCTCT 57.274 36.000 0.00 0.00 0.00 3.10
546 547 7.278868 CCAACAAATTCAGTCATACTACCTCTC 59.721 40.741 0.00 0.00 0.00 3.20
547 548 7.106239 CCAACAAATTCAGTCATACTACCTCT 58.894 38.462 0.00 0.00 0.00 3.69
548 549 6.316390 CCCAACAAATTCAGTCATACTACCTC 59.684 42.308 0.00 0.00 0.00 3.85
549 550 6.012858 TCCCAACAAATTCAGTCATACTACCT 60.013 38.462 0.00 0.00 0.00 3.08
550 551 6.177610 TCCCAACAAATTCAGTCATACTACC 58.822 40.000 0.00 0.00 0.00 3.18
551 552 7.606456 TCTTCCCAACAAATTCAGTCATACTAC 59.394 37.037 0.00 0.00 0.00 2.73
552 553 7.685481 TCTTCCCAACAAATTCAGTCATACTA 58.315 34.615 0.00 0.00 0.00 1.82
553 554 6.542821 TCTTCCCAACAAATTCAGTCATACT 58.457 36.000 0.00 0.00 0.00 2.12
554 555 6.817765 TCTTCCCAACAAATTCAGTCATAC 57.182 37.500 0.00 0.00 0.00 2.39
555 556 8.956426 GTTATCTTCCCAACAAATTCAGTCATA 58.044 33.333 0.00 0.00 0.00 2.15
556 557 7.093771 GGTTATCTTCCCAACAAATTCAGTCAT 60.094 37.037 0.00 0.00 0.00 3.06
597 606 9.893305 AGAACAAGTCAAATAAAATAAAGGTCG 57.107 29.630 0.00 0.00 0.00 4.79
677 686 4.099824 GTGAACAACAAAACACCTTACGG 58.900 43.478 0.00 0.00 0.00 4.02
678 687 4.724303 TGTGAACAACAAAACACCTTACG 58.276 39.130 0.00 0.00 35.24 3.18
679 688 6.560711 AGATGTGAACAACAAAACACCTTAC 58.439 36.000 0.00 0.00 43.61 2.34
681 690 5.659440 AGATGTGAACAACAAAACACCTT 57.341 34.783 0.00 0.00 43.61 3.50
682 691 5.220777 CGTAGATGTGAACAACAAAACACCT 60.221 40.000 0.00 0.00 43.61 4.00
683 692 4.967575 CGTAGATGTGAACAACAAAACACC 59.032 41.667 0.00 0.00 43.61 4.16
684 693 5.802064 TCGTAGATGTGAACAACAAAACAC 58.198 37.500 0.00 0.00 43.61 3.32
689 698 7.224949 TGTGTTTATCGTAGATGTGAACAACAA 59.775 33.333 8.74 0.61 45.12 2.83
690 699 6.702282 TGTGTTTATCGTAGATGTGAACAACA 59.298 34.615 8.74 0.00 45.12 3.33
691 700 7.112528 TGTGTTTATCGTAGATGTGAACAAC 57.887 36.000 8.74 0.00 45.12 3.32
693 702 5.347635 GCTGTGTTTATCGTAGATGTGAACA 59.652 40.000 0.00 0.00 45.12 3.18
694 703 5.347635 TGCTGTGTTTATCGTAGATGTGAAC 59.652 40.000 0.00 0.00 45.12 3.18
695 704 5.474825 TGCTGTGTTTATCGTAGATGTGAA 58.525 37.500 0.00 0.00 45.12 3.18
696 705 5.066968 TGCTGTGTTTATCGTAGATGTGA 57.933 39.130 0.00 0.00 45.12 3.58
697 706 5.576774 TCTTGCTGTGTTTATCGTAGATGTG 59.423 40.000 0.00 0.00 45.12 3.21
698 707 5.720202 TCTTGCTGTGTTTATCGTAGATGT 58.280 37.500 0.00 0.00 45.12 3.06
699 708 6.036470 TCTCTTGCTGTGTTTATCGTAGATG 58.964 40.000 0.00 0.00 45.12 2.90
700 709 6.208988 TCTCTTGCTGTGTTTATCGTAGAT 57.791 37.500 0.00 0.00 45.12 1.98
743 752 2.173519 CCCTTGGACGGTAGTTGTCTA 58.826 52.381 0.00 0.00 36.58 2.59
745 754 0.672711 GCCCTTGGACGGTAGTTGTC 60.673 60.000 0.00 0.00 35.60 3.18
754 763 2.825836 GCCAGATGCCCTTGGACG 60.826 66.667 2.00 0.00 0.00 4.79
756 765 0.925558 TAATGCCAGATGCCCTTGGA 59.074 50.000 2.00 0.00 40.16 3.53
767 776 6.111382 TCTCTGATGAAAAGTCTAATGCCAG 58.889 40.000 0.00 0.00 0.00 4.85
786 795 5.345202 ACGTACTTTATTTGCGAGTTCTCTG 59.655 40.000 0.00 0.00 0.00 3.35
787 796 5.345202 CACGTACTTTATTTGCGAGTTCTCT 59.655 40.000 0.00 0.00 0.00 3.10
788 797 5.444218 CCACGTACTTTATTTGCGAGTTCTC 60.444 44.000 0.00 0.00 0.00 2.87
789 798 4.387862 CCACGTACTTTATTTGCGAGTTCT 59.612 41.667 0.00 0.00 0.00 3.01
790 799 4.386652 TCCACGTACTTTATTTGCGAGTTC 59.613 41.667 0.00 0.00 0.00 3.01
791 800 4.151157 GTCCACGTACTTTATTTGCGAGTT 59.849 41.667 0.00 0.00 0.00 3.01
793 802 3.241552 CGTCCACGTACTTTATTTGCGAG 60.242 47.826 0.00 0.00 34.11 5.03
794 803 2.662637 CGTCCACGTACTTTATTTGCGA 59.337 45.455 0.00 0.00 34.11 5.10
795 804 2.222640 CCGTCCACGTACTTTATTTGCG 60.223 50.000 0.00 0.00 37.74 4.85
796 805 2.094734 CCCGTCCACGTACTTTATTTGC 59.905 50.000 0.00 0.00 37.74 3.68
797 806 3.368843 GTCCCGTCCACGTACTTTATTTG 59.631 47.826 0.00 0.00 37.74 2.32
810 820 3.691342 CGGCTTCTGTCCCGTCCA 61.691 66.667 0.00 0.00 39.67 4.02
814 824 0.320421 TCTTTTCGGCTTCTGTCCCG 60.320 55.000 0.00 0.00 45.64 5.14
836 846 1.425066 ACCCTGAGAAACTGCAATCCA 59.575 47.619 0.00 0.00 0.00 3.41
837 847 2.087646 GACCCTGAGAAACTGCAATCC 58.912 52.381 0.00 0.00 0.00 3.01
840 850 3.297134 AAAGACCCTGAGAAACTGCAA 57.703 42.857 0.00 0.00 0.00 4.08
860 870 4.081406 CCCACAGATTCAGTGATGGAAAA 58.919 43.478 10.70 0.00 39.30 2.29
880 890 2.367894 ACGGCTTAAGCTTATCTACCCC 59.632 50.000 25.88 5.29 41.70 4.95
887 897 4.081087 TCTCCAGAAACGGCTTAAGCTTAT 60.081 41.667 25.88 8.23 41.70 1.73
913 923 1.871039 GCACAGTTCTTTACGCTGGAA 59.129 47.619 0.00 0.00 34.79 3.53
929 939 2.025321 GGAGGAAGGAAATTAGGGCACA 60.025 50.000 0.00 0.00 0.00 4.57
946 956 1.622811 ACTGCACAGAAGAGAAGGAGG 59.377 52.381 4.31 0.00 0.00 4.30
953 963 7.383102 ACCATAAATAAACTGCACAGAAGAG 57.617 36.000 4.31 0.00 0.00 2.85
956 966 8.630054 AAGTACCATAAATAAACTGCACAGAA 57.370 30.769 4.31 0.00 0.00 3.02
978 988 6.663523 CCATTTAACTGAGGTGGGAAATAAGT 59.336 38.462 0.00 0.00 0.00 2.24
1059 1069 0.037326 TACCTTCCACTTGCAGCTCG 60.037 55.000 0.00 0.00 0.00 5.03
1082 1092 5.970317 ATGTGCTCTGACAAATTCAATGA 57.030 34.783 0.00 0.00 32.21 2.57
1123 1133 8.709272 TTGGATGAGAATAAATATGCATCCAA 57.291 30.769 23.59 23.59 40.74 3.53
1154 1164 9.729281 ATTTCCAATTTACTGATTTCATTTGCT 57.271 25.926 0.00 0.00 0.00 3.91
1229 1239 6.803642 ACTCACGAAGTTCTGTTTACTAACT 58.196 36.000 0.56 0.00 41.61 2.24
1296 1306 9.273016 TGTTAATCAGCTAATAAGGTAGAATGC 57.727 33.333 0.00 0.00 0.00 3.56
1399 1409 4.599047 AGCTATACAGAGATGCAAGGTC 57.401 45.455 0.00 0.00 0.00 3.85
1430 1441 5.359009 CGTAGTAGGATAGAAAAGTGTCCCA 59.641 44.000 0.00 0.00 0.00 4.37
1483 1496 2.023984 TGGAACTCAGAGCATAGGAGGA 60.024 50.000 0.00 0.00 32.98 3.71
1809 3476 8.094284 TCCCTCTCAATCTATCTTTCAATTCA 57.906 34.615 0.00 0.00 0.00 2.57
1947 3614 6.500751 AGGTATCATAAGTAAATGGATCCCGT 59.499 38.462 9.90 0.00 0.00 5.28
2060 3727 0.384230 GACATGTGCACCGTGTTTCG 60.384 55.000 21.36 2.80 43.41 3.46
2061 3728 0.944386 AGACATGTGCACCGTGTTTC 59.056 50.000 21.36 12.47 43.41 2.78
2123 3790 4.568152 AGGTGTTTTGATTCCTTGAACG 57.432 40.909 0.00 0.00 0.00 3.95
2721 4401 2.050077 GCCCACGCTTGCTTTCAC 60.050 61.111 0.00 0.00 0.00 3.18
2855 4535 8.557592 TCAATTCTATATATTTGCTGAGCCAG 57.442 34.615 0.23 0.00 34.12 4.85
3362 5068 6.747280 CGTCTCAATCTTTCTCTTCTCTCTTC 59.253 42.308 0.00 0.00 0.00 2.87
3424 5130 4.388499 CCACGTCCCAAGACCCCG 62.388 72.222 0.00 0.00 40.12 5.73
3741 5447 9.906660 GTTGTCATATTAAAAAGATTGACCACA 57.093 29.630 0.00 0.00 32.85 4.17
3754 5460 9.542462 GGTAGAGCATACAGTTGTCATATTAAA 57.458 33.333 2.07 0.00 0.00 1.52
3775 5481 5.120399 CAACAAAGCCATATAACCGGTAGA 58.880 41.667 8.00 0.00 0.00 2.59
3816 5522 4.947388 TGCACTGTCTTCCTACAAAACTTT 59.053 37.500 0.00 0.00 0.00 2.66
3839 5545 4.021229 ACATGAAGATGGATGCACAACAT 58.979 39.130 0.00 0.00 35.80 2.71
3858 5564 2.768527 CCGATATCTGGCCTATCCACAT 59.231 50.000 3.32 0.00 40.72 3.21
3871 5577 6.582636 TCAGCAGTTACAAATTCCGATATCT 58.417 36.000 0.34 0.00 0.00 1.98
3891 5597 6.039717 TCAAGGAAGTTGCCATATATTTCAGC 59.960 38.462 0.00 0.00 35.94 4.26
3938 5645 0.807667 CAGGCCCTGAAGAATCGTCG 60.808 60.000 4.15 0.00 32.44 5.12
3953 5660 5.585390 CATAAATTGATTCCAGACACAGGC 58.415 41.667 0.00 0.00 0.00 4.85
3955 5662 6.094464 TCTGCATAAATTGATTCCAGACACAG 59.906 38.462 0.00 0.00 0.00 3.66
4135 5846 8.600668 TCCCTAATTCAGATAATCCAGAATCAG 58.399 37.037 0.00 0.00 30.87 2.90
4249 5960 5.924825 ACTACTCTTACGGAATTGTTCACAC 59.075 40.000 0.00 0.00 0.00 3.82
4263 5974 8.070769 CCAAAAAGAAAAGCTCACTACTCTTAC 58.929 37.037 0.00 0.00 30.54 2.34
4343 6055 3.306703 CCATTAAATTGTGCGTTGATGCC 59.693 43.478 0.00 0.00 0.00 4.40
4351 6063 5.407995 ACAAAATGGACCATTAAATTGTGCG 59.592 36.000 25.01 8.46 33.72 5.34
4413 6329 7.878621 AATCATGGATATTCTCAGTAAGGGA 57.121 36.000 0.00 0.00 0.00 4.20
4459 6375 8.759481 TCCCTAAACATGTATCAAATATGCAA 57.241 30.769 0.00 0.00 0.00 4.08
4525 6441 6.822442 TGGTTCACTACTGTTGAACTATTGA 58.178 36.000 19.27 1.03 41.00 2.57
4595 6514 6.186957 TGTGCTTGTGGAAGGATGTTTATAT 58.813 36.000 0.00 0.00 31.41 0.86
4674 6593 9.918630 AAAACGTGTAGTCAGTTATTGTAGTAT 57.081 29.630 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.