Multiple sequence alignment - TraesCS4B01G124700

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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 TraesCS4B01G124700 chr4B 100.000 3824 0 0 1 3824 150734310 150738133 0.000000e+00 7062
1 TraesCS4B01G124700 chr4A 95.672 2611 101 6 660 3268 248836263 248833663 0.000000e+00 4185
2 TraesCS4B01G124700 chr4A 96.071 560 22 0 3265 3824 248833559 248833000 0.000000e+00 913
3 TraesCS4B01G124700 chr4D 96.603 2296 71 2 696 2991 195022589 195020301 0.000000e+00 3801
4 TraesCS4B01G124700 chr4D 97.080 822 24 0 3003 3824 195019777 195018956 0.000000e+00 1386
5 TraesCS4B01G124700 chr4D 98.901 91 1 0 479 569 42641686 42641596 3.060000e-36 163
6 TraesCS4B01G124700 chr4D 97.727 44 0 1 660 702 195023182 195023139 1.470000e-09 75
7 TraesCS4B01G124700 chr7B 94.025 318 18 1 1733 2050 279842819 279843135 7.430000e-132 481
8 TraesCS4B01G124700 chr7B 97.500 280 5 1 210 487 623810990 623811269 9.610000e-131 477
9 TraesCS4B01G124700 chr5A 97.518 282 5 1 207 486 437290803 437291084 7.430000e-132 481
10 TraesCS4B01G124700 chr5A 98.565 209 3 0 3 211 17566281 17566489 1.680000e-98 370
11 TraesCS4B01G124700 chr5A 98.565 209 3 0 3 211 320210040 320210248 1.680000e-98 370
12 TraesCS4B01G124700 chr5A 97.980 99 1 1 481 579 359981743 359981840 1.830000e-38 171
13 TraesCS4B01G124700 chr6B 97.842 278 4 1 208 483 707744118 707744395 2.670000e-131 479
14 TraesCS4B01G124700 chr6B 98.565 209 3 0 3 211 623088321 623088529 1.680000e-98 370
15 TraesCS4B01G124700 chr1B 97.842 278 4 1 208 483 593922516 593922793 2.670000e-131 479
16 TraesCS4B01G124700 chr1B 97.491 279 5 1 207 483 642731962 642732240 3.460000e-130 475
17 TraesCS4B01G124700 chr1B 100.000 94 0 0 481 574 158150180 158150087 1.410000e-39 174
18 TraesCS4B01G124700 chr5B 97.500 280 5 1 208 485 662861383 662861104 9.610000e-131 477
19 TraesCS4B01G124700 chr5B 95.270 296 10 3 193 486 455979444 455979151 2.080000e-127 466
20 TraesCS4B01G124700 chr3B 97.491 279 5 1 208 484 438378726 438378448 3.460000e-130 475
21 TraesCS4B01G124700 chr3B 98.565 209 3 0 3 211 395945787 395945995 1.680000e-98 370
22 TraesCS4B01G124700 chr3B 97.849 93 2 0 481 573 426526154 426526062 1.100000e-35 161
23 TraesCS4B01G124700 chr2B 97.163 282 6 1 208 487 27587022 27587303 3.460000e-130 475
24 TraesCS4B01G124700 chr2B 80.517 580 89 19 3 574 120237041 120236478 1.270000e-114 424
25 TraesCS4B01G124700 chr2B 96.154 104 3 1 481 584 120155532 120155430 6.570000e-38 169
26 TraesCS4B01G124700 chr2B 93.860 114 2 4 481 594 106151486 106151594 2.360000e-37 167
27 TraesCS4B01G124700 chr2B 97.849 93 2 0 478 570 91066006 91066098 1.100000e-35 161
28 TraesCS4B01G124700 chr7A 99.522 209 1 0 3 211 129265436 129265644 7.750000e-102 381
29 TraesCS4B01G124700 chr7A 99.043 209 2 0 3 211 642098478 642098686 3.610000e-100 375
30 TraesCS4B01G124700 chr7A 100.000 94 0 0 481 574 642098683 642098776 1.410000e-39 174
31 TraesCS4B01G124700 chr7A 95.283 106 3 2 466 570 24763399 24763295 2.360000e-37 167
32 TraesCS4B01G124700 chr7A 96.907 97 3 0 479 575 281041168 281041264 3.060000e-36 163
33 TraesCS4B01G124700 chr3A 99.043 209 2 0 3 211 155427146 155426938 3.610000e-100 375
34 TraesCS4B01G124700 chr3A 100.000 94 0 0 481 574 676592295 676592388 1.410000e-39 174
35 TraesCS4B01G124700 chr3A 97.959 98 2 0 477 574 621102891 621102988 1.830000e-38 171
36 TraesCS4B01G124700 chr3A 96.970 99 2 1 477 574 155965751 155965849 8.500000e-37 165
37 TraesCS4B01G124700 chr6A 99.038 208 2 0 3 210 53495627 53495420 1.300000e-99 374
38 TraesCS4B01G124700 chr1A 98.565 209 3 0 3 211 441773316 441773524 1.680000e-98 370
39 TraesCS4B01G124700 chr1A 100.000 93 0 0 481 573 441773521 441773613 5.080000e-39 172
40 TraesCS4B01G124700 chr5D 96.939 98 3 0 477 574 234728765 234728862 8.500000e-37 165


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 TraesCS4B01G124700 chr4B 150734310 150738133 3823 False 7062 7062 100.000000 1 3824 1 chr4B.!!$F1 3823
1 TraesCS4B01G124700 chr4A 248833000 248836263 3263 True 2549 4185 95.871500 660 3824 2 chr4A.!!$R1 3164
2 TraesCS4B01G124700 chr4D 195018956 195023182 4226 True 1754 3801 97.136667 660 3824 3 chr4D.!!$R2 3164
3 TraesCS4B01G124700 chr2B 120236478 120237041 563 True 424 424 80.517000 3 574 1 chr2B.!!$R2 571

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
640 644 0.177141 TTAGCACCGGTACATCCAGC 59.823 55.0 6.87 4.37 35.57 4.85 F
1546 2106 0.177373 CCAGTGCTCTGCTGATGCTA 59.823 55.0 10.32 2.10 40.09 3.49 F
2361 2921 0.343372 ATGGGCTGAAGAGGAGGGTA 59.657 55.0 0.00 0.00 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 2414 0.033090 TCTCTGCACACAGCTCAGTG 59.967 55.000 10.06 10.06 44.10 3.66 R
2610 3170 1.081892 CACGGTCCTTCTCAGCATTG 58.918 55.000 0.00 0.00 0.00 2.82 R
3684 4863 1.545651 CCAGGTTCTGTCCTTGGGTTC 60.546 57.143 0.00 0.00 35.37 3.62 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
34 35 1.150536 GTTCCAAGCACCCCTGACA 59.849 57.895 0.00 0.00 0.00 3.58
48 49 2.834549 CCCTGACAAAAGAGAGGCTAGA 59.165 50.000 0.00 0.00 0.00 2.43
68 69 6.532302 GCTAGAACTAGTCTTGAGGCTAAAAC 59.468 42.308 0.00 0.00 37.84 2.43
69 70 6.673839 AGAACTAGTCTTGAGGCTAAAACT 57.326 37.500 0.00 0.00 29.66 2.66
90 91 9.797556 AAAACTTTTTAGTCACATGAAACCTAC 57.202 29.630 0.00 0.00 0.00 3.18
129 130 5.163258 GCCCTCTCTCTCCTCATTTAATTCA 60.163 44.000 0.00 0.00 0.00 2.57
137 138 8.776119 TCTCTCCTCATTTAATTCATCTCCTTT 58.224 33.333 0.00 0.00 0.00 3.11
140 141 8.682936 TCCTCATTTAATTCATCTCCTTTAGC 57.317 34.615 0.00 0.00 0.00 3.09
141 142 8.274322 TCCTCATTTAATTCATCTCCTTTAGCA 58.726 33.333 0.00 0.00 0.00 3.49
142 143 8.348507 CCTCATTTAATTCATCTCCTTTAGCAC 58.651 37.037 0.00 0.00 0.00 4.40
143 144 8.806429 TCATTTAATTCATCTCCTTTAGCACA 57.194 30.769 0.00 0.00 0.00 4.57
144 145 9.412460 TCATTTAATTCATCTCCTTTAGCACAT 57.588 29.630 0.00 0.00 0.00 3.21
145 146 9.459640 CATTTAATTCATCTCCTTTAGCACATG 57.540 33.333 0.00 0.00 0.00 3.21
146 147 5.511234 AATTCATCTCCTTTAGCACATGC 57.489 39.130 0.00 0.00 42.49 4.06
162 163 2.092753 ACATGCGAGTTCTGGATTGGAT 60.093 45.455 0.00 0.00 0.00 3.41
193 194 9.866655 TGGAGGATAATAAATGCTCAATAACTT 57.133 29.630 8.48 0.00 38.10 2.66
219 220 8.251721 TCATTTTAGTCTCTTTAGGCTAGTCAC 58.748 37.037 0.00 0.00 40.92 3.67
226 227 1.568504 TTAGGCTAGTCACAGTGGGG 58.431 55.000 0.00 0.00 0.00 4.96
227 228 0.708209 TAGGCTAGTCACAGTGGGGA 59.292 55.000 0.00 0.00 0.00 4.81
228 229 0.616111 AGGCTAGTCACAGTGGGGAG 60.616 60.000 0.00 0.00 0.00 4.30
229 230 1.617947 GGCTAGTCACAGTGGGGAGG 61.618 65.000 0.00 0.00 0.00 4.30
231 232 1.938585 CTAGTCACAGTGGGGAGGAA 58.061 55.000 0.00 0.00 0.00 3.36
232 233 1.550976 CTAGTCACAGTGGGGAGGAAC 59.449 57.143 0.00 0.00 0.00 3.62
234 235 0.765510 GTCACAGTGGGGAGGAACTT 59.234 55.000 0.00 0.00 41.55 2.66
235 236 1.975680 GTCACAGTGGGGAGGAACTTA 59.024 52.381 0.00 0.00 41.55 2.24
237 238 1.279271 CACAGTGGGGAGGAACTTAGG 59.721 57.143 0.00 0.00 41.55 2.69
243 244 4.038633 GTGGGGAGGAACTTAGGAGTAAT 58.961 47.826 0.00 0.00 41.55 1.89
246 247 6.014413 GTGGGGAGGAACTTAGGAGTAATATC 60.014 46.154 0.00 0.00 41.55 1.63
247 248 6.082707 GGGGAGGAACTTAGGAGTAATATCA 58.917 44.000 0.00 0.00 41.55 2.15
248 249 6.014413 GGGGAGGAACTTAGGAGTAATATCAC 60.014 46.154 0.00 0.00 41.55 3.06
249 250 6.553852 GGGAGGAACTTAGGAGTAATATCACA 59.446 42.308 0.00 0.00 41.55 3.58
250 251 7.435305 GGAGGAACTTAGGAGTAATATCACAC 58.565 42.308 0.00 0.00 41.55 3.82
251 252 7.069578 GGAGGAACTTAGGAGTAATATCACACA 59.930 40.741 0.00 0.00 41.55 3.72
252 253 8.554490 AGGAACTTAGGAGTAATATCACACAT 57.446 34.615 0.00 0.00 34.21 3.21
253 254 8.993424 AGGAACTTAGGAGTAATATCACACATT 58.007 33.333 0.00 0.00 34.21 2.71
255 256 9.262358 GAACTTAGGAGTAATATCACACATTCC 57.738 37.037 0.00 0.00 34.21 3.01
256 257 8.319057 ACTTAGGAGTAATATCACACATTCCA 57.681 34.615 0.00 0.00 33.32 3.53
258 259 9.784531 CTTAGGAGTAATATCACACATTCCAAT 57.215 33.333 0.00 0.00 0.00 3.16
264 265 9.905713 AGTAATATCACACATTCCAATACAACT 57.094 29.630 0.00 0.00 0.00 3.16
268 269 5.527951 TCACACATTCCAATACAACTTTGC 58.472 37.500 0.00 0.00 0.00 3.68
270 271 5.984926 CACACATTCCAATACAACTTTGCTT 59.015 36.000 0.00 0.00 0.00 3.91
279 280 3.369546 ACAACTTTGCTTATGTGGCAC 57.630 42.857 11.55 11.55 39.55 5.01
291 292 6.094186 TGCTTATGTGGCACGTATTTAATGAA 59.906 34.615 19.55 4.06 34.56 2.57
297 298 5.006746 GTGGCACGTATTTAATGAAGAGAGG 59.993 44.000 0.00 0.00 0.00 3.69
298 299 5.116882 GGCACGTATTTAATGAAGAGAGGT 58.883 41.667 0.00 0.00 0.00 3.85
301 302 5.812642 CACGTATTTAATGAAGAGAGGTGCT 59.187 40.000 0.00 0.00 0.00 4.40
302 303 6.313905 CACGTATTTAATGAAGAGAGGTGCTT 59.686 38.462 0.00 0.00 0.00 3.91
303 304 6.313905 ACGTATTTAATGAAGAGAGGTGCTTG 59.686 38.462 0.00 0.00 0.00 4.01
305 306 5.947228 TTTAATGAAGAGAGGTGCTTGTG 57.053 39.130 0.00 0.00 0.00 3.33
311 314 2.330216 AGAGAGGTGCTTGTGGTAACT 58.670 47.619 0.00 0.00 37.61 2.24
312 315 3.507411 AGAGAGGTGCTTGTGGTAACTA 58.493 45.455 0.00 0.00 37.61 2.24
313 316 3.511934 AGAGAGGTGCTTGTGGTAACTAG 59.488 47.826 0.00 0.00 37.61 2.57
331 334 5.259832 ACTAGCTAAGTTACCGGAACATC 57.740 43.478 9.46 0.00 40.86 3.06
332 335 4.708421 ACTAGCTAAGTTACCGGAACATCA 59.292 41.667 9.46 0.00 40.86 3.07
334 337 3.259876 AGCTAAGTTACCGGAACATCACA 59.740 43.478 9.46 0.00 40.86 3.58
335 338 3.370061 GCTAAGTTACCGGAACATCACAC 59.630 47.826 9.46 0.00 40.86 3.82
336 339 3.478857 AAGTTACCGGAACATCACACA 57.521 42.857 9.46 0.00 40.86 3.72
337 340 2.762745 AGTTACCGGAACATCACACAC 58.237 47.619 9.46 0.00 40.86 3.82
343 346 1.800586 CGGAACATCACACACTCCAAG 59.199 52.381 0.00 0.00 0.00 3.61
344 347 2.547855 CGGAACATCACACACTCCAAGA 60.548 50.000 0.00 0.00 0.00 3.02
345 348 3.476552 GGAACATCACACACTCCAAGAA 58.523 45.455 0.00 0.00 0.00 2.52
347 350 4.261197 GGAACATCACACACTCCAAGAAAC 60.261 45.833 0.00 0.00 0.00 2.78
358 361 6.652481 CACACTCCAAGAAACAATGAGTCTAT 59.348 38.462 0.00 0.00 34.21 1.98
361 364 8.660373 CACTCCAAGAAACAATGAGTCTATAAC 58.340 37.037 0.00 0.00 34.21 1.89
362 365 7.824779 ACTCCAAGAAACAATGAGTCTATAACC 59.175 37.037 0.00 0.00 30.81 2.85
392 395 7.812690 AATACATCATTGCATGACACTACAT 57.187 32.000 0.00 0.00 43.01 2.29
393 396 8.907222 AATACATCATTGCATGACACTACATA 57.093 30.769 0.00 0.00 43.01 2.29
394 397 6.856135 ACATCATTGCATGACACTACATAG 57.144 37.500 0.00 0.00 43.01 2.23
398 401 6.585416 TCATTGCATGACACTACATAGATGT 58.415 36.000 0.00 0.08 38.37 3.06
399 402 7.049754 TCATTGCATGACACTACATAGATGTT 58.950 34.615 0.00 0.00 36.98 2.71
400 403 6.908870 TTGCATGACACTACATAGATGTTC 57.091 37.500 0.00 0.00 41.97 3.18
413 416 5.544176 ACATAGATGTTCCTACCCACTATGG 59.456 44.000 0.81 0.00 37.90 2.74
433 436 8.795842 CTATGGAGGTAGTAACATAGTCTAGG 57.204 42.308 0.00 0.00 38.48 3.02
434 437 5.950023 TGGAGGTAGTAACATAGTCTAGGG 58.050 45.833 0.00 0.00 0.00 3.53
436 439 6.160992 TGGAGGTAGTAACATAGTCTAGGGAA 59.839 42.308 0.00 0.00 0.00 3.97
437 440 6.716173 GGAGGTAGTAACATAGTCTAGGGAAG 59.284 46.154 0.00 0.00 0.00 3.46
439 442 7.061688 AGGTAGTAACATAGTCTAGGGAAGTG 58.938 42.308 0.00 0.00 0.00 3.16
442 445 6.491383 AGTAACATAGTCTAGGGAAGTGTGA 58.509 40.000 0.00 0.00 0.00 3.58
452 456 4.538746 AGGGAAGTGTGAAGTTACTAGC 57.461 45.455 0.00 0.00 0.00 3.42
453 457 4.161102 AGGGAAGTGTGAAGTTACTAGCT 58.839 43.478 0.00 0.00 0.00 3.32
456 460 6.440965 AGGGAAGTGTGAAGTTACTAGCTTAT 59.559 38.462 0.00 0.00 0.00 1.73
460 464 8.535690 AAGTGTGAAGTTACTAGCTTATGTTC 57.464 34.615 0.00 0.00 0.00 3.18
461 465 7.897864 AGTGTGAAGTTACTAGCTTATGTTCT 58.102 34.615 0.00 0.00 0.00 3.01
463 467 8.436200 GTGTGAAGTTACTAGCTTATGTTCTTG 58.564 37.037 0.00 0.00 0.00 3.02
468 472 4.510167 ACTAGCTTATGTTCTTGCCCAT 57.490 40.909 0.00 0.00 0.00 4.00
470 474 4.641989 ACTAGCTTATGTTCTTGCCCATTG 59.358 41.667 0.00 0.00 0.00 2.82
564 568 3.373130 GGGACTAAAACGTATCCAAGCAC 59.627 47.826 0.00 0.00 32.45 4.40
565 569 3.373130 GGACTAAAACGTATCCAAGCACC 59.627 47.826 0.00 0.00 0.00 5.01
569 573 1.276622 AACGTATCCAAGCACCCTCT 58.723 50.000 0.00 0.00 0.00 3.69
574 578 3.635373 CGTATCCAAGCACCCTCTTAGTA 59.365 47.826 0.00 0.00 0.00 1.82
575 579 4.281182 CGTATCCAAGCACCCTCTTAGTAT 59.719 45.833 0.00 0.00 0.00 2.12
576 580 4.696479 ATCCAAGCACCCTCTTAGTATG 57.304 45.455 0.00 0.00 0.00 2.39
577 581 2.170607 TCCAAGCACCCTCTTAGTATGC 59.829 50.000 0.00 0.00 36.52 3.14
578 582 2.092968 CCAAGCACCCTCTTAGTATGCA 60.093 50.000 0.00 0.00 38.79 3.96
579 583 3.609853 CAAGCACCCTCTTAGTATGCAA 58.390 45.455 0.00 0.00 38.79 4.08
580 584 3.550437 AGCACCCTCTTAGTATGCAAG 57.450 47.619 0.00 0.00 38.79 4.01
581 585 2.840651 AGCACCCTCTTAGTATGCAAGT 59.159 45.455 0.00 0.00 38.79 3.16
582 586 4.030913 AGCACCCTCTTAGTATGCAAGTA 58.969 43.478 0.00 0.00 38.79 2.24
583 587 4.100189 AGCACCCTCTTAGTATGCAAGTAG 59.900 45.833 0.00 0.00 38.79 2.57
584 588 4.099573 GCACCCTCTTAGTATGCAAGTAGA 59.900 45.833 0.00 0.00 36.30 2.59
585 589 5.593010 CACCCTCTTAGTATGCAAGTAGAC 58.407 45.833 0.00 0.00 0.00 2.59
586 590 5.127194 CACCCTCTTAGTATGCAAGTAGACA 59.873 44.000 0.00 0.00 0.00 3.41
587 591 5.720041 ACCCTCTTAGTATGCAAGTAGACAA 59.280 40.000 0.00 0.00 0.00 3.18
588 592 6.384305 ACCCTCTTAGTATGCAAGTAGACAAT 59.616 38.462 0.00 0.00 0.00 2.71
589 593 6.703607 CCCTCTTAGTATGCAAGTAGACAATG 59.296 42.308 0.00 0.00 0.00 2.82
590 594 7.268586 CCTCTTAGTATGCAAGTAGACAATGT 58.731 38.462 0.00 0.00 0.00 2.71
591 595 7.223582 CCTCTTAGTATGCAAGTAGACAATGTG 59.776 40.741 0.00 0.00 0.00 3.21
592 596 6.535150 TCTTAGTATGCAAGTAGACAATGTGC 59.465 38.462 0.00 0.00 35.75 4.57
595 599 1.879380 TGCAAGTAGACAATGTGCACC 59.121 47.619 15.69 0.00 40.14 5.01
596 600 1.879380 GCAAGTAGACAATGTGCACCA 59.121 47.619 15.69 2.61 35.28 4.17
597 601 2.293122 GCAAGTAGACAATGTGCACCAA 59.707 45.455 15.69 0.00 35.28 3.67
598 602 3.057315 GCAAGTAGACAATGTGCACCAAT 60.057 43.478 15.69 0.00 35.28 3.16
599 603 4.726416 CAAGTAGACAATGTGCACCAATC 58.274 43.478 15.69 6.88 0.00 2.67
600 604 4.292186 AGTAGACAATGTGCACCAATCT 57.708 40.909 15.69 13.87 0.00 2.40
601 605 4.256920 AGTAGACAATGTGCACCAATCTC 58.743 43.478 15.69 2.52 0.00 2.75
602 606 3.430042 AGACAATGTGCACCAATCTCT 57.570 42.857 15.69 4.92 0.00 3.10
603 607 4.558226 AGACAATGTGCACCAATCTCTA 57.442 40.909 15.69 0.00 0.00 2.43
604 608 4.910195 AGACAATGTGCACCAATCTCTAA 58.090 39.130 15.69 0.00 0.00 2.10
605 609 4.940046 AGACAATGTGCACCAATCTCTAAG 59.060 41.667 15.69 0.00 0.00 2.18
606 610 4.910195 ACAATGTGCACCAATCTCTAAGA 58.090 39.130 15.69 0.00 0.00 2.10
607 611 5.316167 ACAATGTGCACCAATCTCTAAGAA 58.684 37.500 15.69 0.00 0.00 2.52
608 612 5.948162 ACAATGTGCACCAATCTCTAAGAAT 59.052 36.000 15.69 0.00 0.00 2.40
609 613 6.435277 ACAATGTGCACCAATCTCTAAGAATT 59.565 34.615 15.69 0.00 0.00 2.17
610 614 7.039504 ACAATGTGCACCAATCTCTAAGAATTT 60.040 33.333 15.69 0.00 0.00 1.82
611 615 8.461222 CAATGTGCACCAATCTCTAAGAATTTA 58.539 33.333 15.69 0.00 0.00 1.40
612 616 7.994425 TGTGCACCAATCTCTAAGAATTTAA 57.006 32.000 15.69 0.00 0.00 1.52
613 617 8.402798 TGTGCACCAATCTCTAAGAATTTAAA 57.597 30.769 15.69 0.00 0.00 1.52
614 618 8.514594 TGTGCACCAATCTCTAAGAATTTAAAG 58.485 33.333 15.69 0.00 0.00 1.85
615 619 7.970614 GTGCACCAATCTCTAAGAATTTAAAGG 59.029 37.037 5.22 0.00 0.00 3.11
616 620 7.669722 TGCACCAATCTCTAAGAATTTAAAGGT 59.330 33.333 0.00 0.00 0.00 3.50
617 621 7.970614 GCACCAATCTCTAAGAATTTAAAGGTG 59.029 37.037 0.00 0.00 42.22 4.00
618 622 8.462016 CACCAATCTCTAAGAATTTAAAGGTGG 58.538 37.037 0.00 0.00 37.28 4.61
619 623 8.390921 ACCAATCTCTAAGAATTTAAAGGTGGA 58.609 33.333 0.00 0.00 0.00 4.02
620 624 9.413734 CCAATCTCTAAGAATTTAAAGGTGGAT 57.586 33.333 0.00 0.00 0.00 3.41
626 630 9.747898 TCTAAGAATTTAAAGGTGGATTTAGCA 57.252 29.630 0.00 0.00 0.00 3.49
627 631 9.788960 CTAAGAATTTAAAGGTGGATTTAGCAC 57.211 33.333 0.00 0.00 0.00 4.40
628 632 7.170393 AGAATTTAAAGGTGGATTTAGCACC 57.830 36.000 0.00 0.00 39.18 5.01
629 633 5.576447 ATTTAAAGGTGGATTTAGCACCG 57.424 39.130 0.00 0.00 43.35 4.94
630 634 1.834188 AAAGGTGGATTTAGCACCGG 58.166 50.000 0.00 0.00 43.35 5.28
631 635 0.696501 AAGGTGGATTTAGCACCGGT 59.303 50.000 0.00 0.00 43.35 5.28
632 636 1.575419 AGGTGGATTTAGCACCGGTA 58.425 50.000 6.87 0.00 43.35 4.02
633 637 1.208776 AGGTGGATTTAGCACCGGTAC 59.791 52.381 6.87 0.00 43.35 3.34
634 638 1.065998 GGTGGATTTAGCACCGGTACA 60.066 52.381 6.87 0.00 0.00 2.90
635 639 2.420967 GGTGGATTTAGCACCGGTACAT 60.421 50.000 6.87 0.00 0.00 2.29
636 640 2.870411 GTGGATTTAGCACCGGTACATC 59.130 50.000 6.87 0.25 0.00 3.06
637 641 2.158871 TGGATTTAGCACCGGTACATCC 60.159 50.000 6.87 11.27 40.89 3.51
638 642 2.158871 GGATTTAGCACCGGTACATCCA 60.159 50.000 6.87 0.00 40.48 3.41
639 643 2.684001 TTTAGCACCGGTACATCCAG 57.316 50.000 6.87 0.00 35.57 3.86
640 644 0.177141 TTAGCACCGGTACATCCAGC 59.823 55.000 6.87 4.37 35.57 4.85
641 645 0.973496 TAGCACCGGTACATCCAGCA 60.973 55.000 6.87 0.00 35.57 4.41
642 646 2.106683 GCACCGGTACATCCAGCAC 61.107 63.158 6.87 0.00 35.57 4.40
643 647 1.449601 CACCGGTACATCCAGCACC 60.450 63.158 6.87 0.00 35.57 5.01
644 648 1.916273 ACCGGTACATCCAGCACCA 60.916 57.895 4.49 0.00 32.77 4.17
645 649 1.153369 CCGGTACATCCAGCACCAG 60.153 63.158 0.00 0.00 32.77 4.00
646 650 1.596934 CGGTACATCCAGCACCAGT 59.403 57.895 0.00 0.00 32.77 4.00
647 651 0.821517 CGGTACATCCAGCACCAGTA 59.178 55.000 0.00 0.00 32.77 2.74
648 652 1.206132 CGGTACATCCAGCACCAGTAA 59.794 52.381 0.00 0.00 32.77 2.24
649 653 2.354303 CGGTACATCCAGCACCAGTAAA 60.354 50.000 0.00 0.00 32.77 2.01
650 654 3.681593 GGTACATCCAGCACCAGTAAAA 58.318 45.455 0.00 0.00 33.51 1.52
651 655 4.076394 GGTACATCCAGCACCAGTAAAAA 58.924 43.478 0.00 0.00 33.51 1.94
652 656 4.156008 GGTACATCCAGCACCAGTAAAAAG 59.844 45.833 0.00 0.00 33.51 2.27
653 657 4.098914 ACATCCAGCACCAGTAAAAAGA 57.901 40.909 0.00 0.00 0.00 2.52
654 658 4.074970 ACATCCAGCACCAGTAAAAAGAG 58.925 43.478 0.00 0.00 0.00 2.85
655 659 3.140325 TCCAGCACCAGTAAAAAGAGG 57.860 47.619 0.00 0.00 0.00 3.69
656 660 2.441750 TCCAGCACCAGTAAAAAGAGGT 59.558 45.455 0.00 0.00 33.91 3.85
657 661 3.117663 TCCAGCACCAGTAAAAAGAGGTT 60.118 43.478 0.00 0.00 30.44 3.50
658 662 3.636764 CCAGCACCAGTAAAAAGAGGTTT 59.363 43.478 0.00 0.00 30.44 3.27
659 663 4.499696 CCAGCACCAGTAAAAAGAGGTTTG 60.500 45.833 0.00 0.00 30.44 2.93
660 664 3.068165 AGCACCAGTAAAAAGAGGTTTGC 59.932 43.478 0.00 0.00 30.44 3.68
661 665 3.628017 CACCAGTAAAAAGAGGTTTGCG 58.372 45.455 0.00 0.00 30.44 4.85
662 666 2.034179 ACCAGTAAAAAGAGGTTTGCGC 59.966 45.455 0.00 0.00 0.00 6.09
663 667 2.307049 CAGTAAAAAGAGGTTTGCGCG 58.693 47.619 0.00 0.00 0.00 6.86
880 1440 4.657824 CTGACGGTTCGGGCACGT 62.658 66.667 8.89 0.00 44.35 4.49
881 1441 3.271706 CTGACGGTTCGGGCACGTA 62.272 63.158 8.89 0.00 41.40 3.57
917 1477 2.603560 CGGGTCAGTTTCGCTAAATCTC 59.396 50.000 0.00 0.00 0.00 2.75
918 1478 3.676324 CGGGTCAGTTTCGCTAAATCTCT 60.676 47.826 0.00 0.00 0.00 3.10
919 1479 4.254492 GGGTCAGTTTCGCTAAATCTCTT 58.746 43.478 0.00 0.00 0.00 2.85
920 1480 4.330347 GGGTCAGTTTCGCTAAATCTCTTC 59.670 45.833 0.00 0.00 0.00 2.87
921 1481 5.172205 GGTCAGTTTCGCTAAATCTCTTCT 58.828 41.667 0.00 0.00 0.00 2.85
922 1482 5.289917 GGTCAGTTTCGCTAAATCTCTTCTC 59.710 44.000 0.00 0.00 0.00 2.87
988 1548 0.542333 GCAAACCCTAGGGAGAGACC 59.458 60.000 35.38 12.82 38.96 3.85
1063 1623 4.256180 CCCCCTCCCATGTAGCGC 62.256 72.222 0.00 0.00 0.00 5.92
1098 1658 2.046023 CAGCAGGTGGATTCGGCA 60.046 61.111 0.00 0.00 0.00 5.69
1185 1745 1.376609 AATCTGCGGCGATTCCCAAC 61.377 55.000 12.98 0.00 0.00 3.77
1546 2106 0.177373 CCAGTGCTCTGCTGATGCTA 59.823 55.000 10.32 2.10 40.09 3.49
1582 2142 3.959991 GAGCCTGTGGTCTTCCGGC 62.960 68.421 0.00 0.00 37.80 6.13
1659 2219 1.153647 CATAGCCGACGACCAGCAA 60.154 57.895 0.00 0.00 0.00 3.91
1816 2376 0.533085 TGCGTCCGAAAATGTCACCA 60.533 50.000 0.00 0.00 0.00 4.17
1854 2414 2.436824 GAACTGGCGGGGAAGAGC 60.437 66.667 0.00 0.00 0.00 4.09
1909 2469 3.756082 AGCAATTGGGGGAAATGAGTA 57.244 42.857 7.72 0.00 0.00 2.59
1935 2495 1.463831 GCTCACAGTGTCAATGCTCTG 59.536 52.381 0.00 0.00 36.42 3.35
1995 2555 2.302445 GAGCACAGAGATATGGAGGCAT 59.698 50.000 0.00 0.00 0.00 4.40
2025 2585 5.432680 AGGAGAAGCTTGATGAGAAATCA 57.567 39.130 2.10 0.00 0.00 2.57
2166 2726 4.709397 ACTAGCAAGACAGAGTTAGATGCT 59.291 41.667 0.00 0.00 44.17 3.79
2201 2761 1.782044 GAGAAGCTCCAGATCGATGC 58.218 55.000 0.54 0.00 0.00 3.91
2333 2893 3.323403 ACTGAGAAGACCAAGTTGGAGAG 59.677 47.826 28.80 13.53 40.96 3.20
2361 2921 0.343372 ATGGGCTGAAGAGGAGGGTA 59.657 55.000 0.00 0.00 0.00 3.69
2425 2985 1.485124 TCGGAAAGATGCTGAGGCTA 58.515 50.000 0.00 0.00 39.59 3.93
2470 3030 1.017177 GCTGAACGGTACCATTGCGA 61.017 55.000 13.54 0.00 0.00 5.10
2580 3140 4.577875 AGAAATCTGAAGGAGACAAGCTG 58.422 43.478 0.00 0.00 31.75 4.24
2604 3164 1.005215 CTGAACCTTGGGGAGCTTGAT 59.995 52.381 0.00 0.00 36.25 2.57
2636 3196 1.967779 TGAGAAGGACCGTGACATTGA 59.032 47.619 0.00 0.00 0.00 2.57
2640 3200 1.933021 AGGACCGTGACATTGAGGTA 58.067 50.000 0.00 0.00 37.07 3.08
2791 3351 2.202690 CGACTGTTATCGCCGCCA 60.203 61.111 0.00 0.00 34.90 5.69
2991 3551 4.815308 TGTTTGCATGTTTTCCTGGAATTG 59.185 37.500 10.45 7.29 0.00 2.32
3097 4169 6.495181 TCTGATAGGATAATGAGAACCTGTCC 59.505 42.308 0.00 0.00 39.01 4.02
3137 4209 4.804261 GCCTGTTGGATCGGCTCTATAAAT 60.804 45.833 1.67 0.00 40.62 1.40
3299 4478 7.279313 GGTTGTAGCTCGATTGGAAATAAAGTA 59.721 37.037 0.00 0.00 0.00 2.24
3336 4515 8.121305 TCACTTGTTATTTGCAACCAATAGAT 57.879 30.769 0.00 0.00 0.00 1.98
3519 4698 4.040829 TCTGAGAACTGAAATCAGAAGCCA 59.959 41.667 16.93 8.28 44.80 4.75
3551 4730 6.484308 TGTTACTGAGCTAACAAAAACCCTAC 59.516 38.462 0.00 0.00 34.38 3.18
3567 4746 3.244911 ACCCTACATGGTGGTTTCAGAAG 60.245 47.826 0.00 0.00 37.20 2.85
3684 4863 7.067494 CCAAAGAATATCCTAACCCAGTTCTTG 59.933 40.741 0.00 0.00 35.38 3.02
3795 4974 5.539955 AGCCACTACAAGATCAACCATTTTT 59.460 36.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.830991 TGCTTGGAACTTTAGCCTCTAAAAA 59.169 36.000 0.00 0.00 34.03 1.94
34 35 6.722129 TCAAGACTAGTTCTAGCCTCTCTTTT 59.278 38.462 0.00 0.00 32.51 2.27
48 49 8.521170 AAAAAGTTTTAGCCTCAAGACTAGTT 57.479 30.769 0.24 0.00 0.00 2.24
107 108 7.965718 AGATGAATTAAATGAGGAGAGAGAGG 58.034 38.462 0.00 0.00 0.00 3.69
129 130 2.169352 ACTCGCATGTGCTAAAGGAGAT 59.831 45.455 11.89 0.00 39.32 2.75
137 138 0.894835 TCCAGAACTCGCATGTGCTA 59.105 50.000 0.00 0.00 39.32 3.49
138 139 0.251354 ATCCAGAACTCGCATGTGCT 59.749 50.000 0.00 0.00 39.32 4.40
139 140 1.089920 AATCCAGAACTCGCATGTGC 58.910 50.000 0.00 0.00 37.78 4.57
140 141 1.399440 CCAATCCAGAACTCGCATGTG 59.601 52.381 0.00 0.00 0.00 3.21
141 142 1.278985 TCCAATCCAGAACTCGCATGT 59.721 47.619 0.00 0.00 0.00 3.21
142 143 2.028420 TCCAATCCAGAACTCGCATG 57.972 50.000 0.00 0.00 0.00 4.06
143 144 2.569059 CATCCAATCCAGAACTCGCAT 58.431 47.619 0.00 0.00 0.00 4.73
144 145 1.407299 CCATCCAATCCAGAACTCGCA 60.407 52.381 0.00 0.00 0.00 5.10
145 146 1.303309 CCATCCAATCCAGAACTCGC 58.697 55.000 0.00 0.00 0.00 5.03
146 147 2.698855 ACCATCCAATCCAGAACTCG 57.301 50.000 0.00 0.00 0.00 4.18
147 148 3.445096 CCAAACCATCCAATCCAGAACTC 59.555 47.826 0.00 0.00 0.00 3.01
162 163 6.430864 TGAGCATTTATTATCCTCCAAACCA 58.569 36.000 0.00 0.00 0.00 3.67
193 194 8.251721 GTGACTAGCCTAAAGAGACTAAAATGA 58.748 37.037 0.00 0.00 0.00 2.57
194 195 8.035394 TGTGACTAGCCTAAAGAGACTAAAATG 58.965 37.037 0.00 0.00 0.00 2.32
211 212 0.614979 TCCTCCCCACTGTGACTAGC 60.615 60.000 9.86 0.00 0.00 3.42
214 215 0.104934 AGTTCCTCCCCACTGTGACT 60.105 55.000 9.86 0.00 0.00 3.41
219 220 1.834263 CTCCTAAGTTCCTCCCCACTG 59.166 57.143 0.00 0.00 0.00 3.66
226 227 8.008513 TGTGTGATATTACTCCTAAGTTCCTC 57.991 38.462 0.00 0.00 36.92 3.71
227 228 7.973048 TGTGTGATATTACTCCTAAGTTCCT 57.027 36.000 0.00 0.00 36.92 3.36
228 229 9.262358 GAATGTGTGATATTACTCCTAAGTTCC 57.738 37.037 0.00 0.00 36.92 3.62
229 230 9.262358 GGAATGTGTGATATTACTCCTAAGTTC 57.738 37.037 0.00 0.00 36.92 3.01
231 232 8.319057 TGGAATGTGTGATATTACTCCTAAGT 57.681 34.615 0.00 0.00 39.66 2.24
232 233 9.784531 ATTGGAATGTGTGATATTACTCCTAAG 57.215 33.333 0.00 0.00 0.00 2.18
235 236 8.713971 TGTATTGGAATGTGTGATATTACTCCT 58.286 33.333 0.00 0.00 0.00 3.69
243 244 7.176515 AGCAAAGTTGTATTGGAATGTGTGATA 59.823 33.333 0.00 0.00 0.00 2.15
246 247 5.531634 AGCAAAGTTGTATTGGAATGTGTG 58.468 37.500 0.00 0.00 0.00 3.82
247 248 5.789643 AGCAAAGTTGTATTGGAATGTGT 57.210 34.783 0.00 0.00 0.00 3.72
248 249 7.814107 ACATAAGCAAAGTTGTATTGGAATGTG 59.186 33.333 0.00 0.00 0.00 3.21
249 250 7.814107 CACATAAGCAAAGTTGTATTGGAATGT 59.186 33.333 0.00 0.00 0.00 2.71
250 251 7.276218 CCACATAAGCAAAGTTGTATTGGAATG 59.724 37.037 0.00 0.00 0.00 2.67
251 252 7.322664 CCACATAAGCAAAGTTGTATTGGAAT 58.677 34.615 0.00 0.00 0.00 3.01
252 253 6.686630 CCACATAAGCAAAGTTGTATTGGAA 58.313 36.000 0.00 0.00 0.00 3.53
253 254 5.336372 GCCACATAAGCAAAGTTGTATTGGA 60.336 40.000 0.00 0.00 0.00 3.53
255 256 5.345741 GTGCCACATAAGCAAAGTTGTATTG 59.654 40.000 0.00 0.00 43.02 1.90
256 257 5.469479 GTGCCACATAAGCAAAGTTGTATT 58.531 37.500 0.00 0.00 43.02 1.89
258 259 3.058570 CGTGCCACATAAGCAAAGTTGTA 60.059 43.478 0.00 0.00 43.02 2.41
259 260 2.287547 CGTGCCACATAAGCAAAGTTGT 60.288 45.455 0.00 0.00 43.02 3.32
263 264 4.355543 AATACGTGCCACATAAGCAAAG 57.644 40.909 0.00 0.00 43.02 2.77
264 265 4.775058 AAATACGTGCCACATAAGCAAA 57.225 36.364 0.00 0.00 43.02 3.68
265 266 5.881777 TTAAATACGTGCCACATAAGCAA 57.118 34.783 0.00 0.00 43.02 3.91
268 269 7.915508 TCTTCATTAAATACGTGCCACATAAG 58.084 34.615 0.00 0.00 0.00 1.73
270 271 7.269316 TCTCTTCATTAAATACGTGCCACATA 58.731 34.615 0.00 0.00 0.00 2.29
279 280 6.313905 ACAAGCACCTCTCTTCATTAAATACG 59.686 38.462 0.00 0.00 0.00 3.06
291 292 2.330216 AGTTACCACAAGCACCTCTCT 58.670 47.619 0.00 0.00 0.00 3.10
297 298 4.566987 ACTTAGCTAGTTACCACAAGCAC 58.433 43.478 0.00 0.00 37.44 4.40
298 299 4.884668 ACTTAGCTAGTTACCACAAGCA 57.115 40.909 0.00 0.00 37.44 3.91
311 314 4.463539 TGTGATGTTCCGGTAACTTAGCTA 59.536 41.667 0.00 0.00 38.99 3.32
312 315 3.259876 TGTGATGTTCCGGTAACTTAGCT 59.740 43.478 0.00 0.00 38.99 3.32
313 316 3.370061 GTGTGATGTTCCGGTAACTTAGC 59.630 47.826 0.00 0.00 38.99 3.09
314 317 4.387862 GTGTGTGATGTTCCGGTAACTTAG 59.612 45.833 0.00 0.00 38.99 2.18
317 320 2.367567 AGTGTGTGATGTTCCGGTAACT 59.632 45.455 0.00 0.00 38.99 2.24
324 327 3.126001 TCTTGGAGTGTGTGATGTTCC 57.874 47.619 0.00 0.00 0.00 3.62
325 328 4.335315 TGTTTCTTGGAGTGTGTGATGTTC 59.665 41.667 0.00 0.00 0.00 3.18
326 329 4.269183 TGTTTCTTGGAGTGTGTGATGTT 58.731 39.130 0.00 0.00 0.00 2.71
331 334 4.336433 ACTCATTGTTTCTTGGAGTGTGTG 59.664 41.667 0.00 0.00 37.43 3.82
332 335 4.526970 ACTCATTGTTTCTTGGAGTGTGT 58.473 39.130 0.00 0.00 37.43 3.72
334 337 5.041191 AGACTCATTGTTTCTTGGAGTGT 57.959 39.130 0.00 0.00 38.82 3.55
335 338 8.660373 GTTATAGACTCATTGTTTCTTGGAGTG 58.340 37.037 0.00 0.00 38.82 3.51
336 339 7.824779 GGTTATAGACTCATTGTTTCTTGGAGT 59.175 37.037 0.00 0.00 41.22 3.85
337 340 8.043710 AGGTTATAGACTCATTGTTTCTTGGAG 58.956 37.037 0.00 0.00 0.00 3.86
374 377 6.585416 ACATCTATGTAGTGTCATGCAATGA 58.415 36.000 0.00 0.00 45.34 2.57
375 378 6.856135 ACATCTATGTAGTGTCATGCAATG 57.144 37.500 0.00 0.00 42.25 2.82
376 379 6.484643 GGAACATCTATGTAGTGTCATGCAAT 59.515 38.462 0.00 0.00 40.80 3.56
377 380 5.817296 GGAACATCTATGTAGTGTCATGCAA 59.183 40.000 0.00 0.00 40.80 4.08
378 381 5.129320 AGGAACATCTATGTAGTGTCATGCA 59.871 40.000 0.00 0.00 40.80 3.96
379 382 5.605534 AGGAACATCTATGTAGTGTCATGC 58.394 41.667 0.00 0.00 40.80 4.06
380 383 7.148641 GGTAGGAACATCTATGTAGTGTCATG 58.851 42.308 0.00 0.00 40.80 3.07
384 387 5.363005 GTGGGTAGGAACATCTATGTAGTGT 59.637 44.000 0.00 0.00 40.80 3.55
385 388 5.598830 AGTGGGTAGGAACATCTATGTAGTG 59.401 44.000 0.00 0.00 40.80 2.74
388 391 6.724441 CCATAGTGGGTAGGAACATCTATGTA 59.276 42.308 0.00 0.00 35.14 2.29
392 395 5.394738 CTCCATAGTGGGTAGGAACATCTA 58.605 45.833 0.00 0.00 38.32 1.98
393 396 4.227197 CTCCATAGTGGGTAGGAACATCT 58.773 47.826 0.00 0.00 38.32 2.90
394 397 3.325135 CCTCCATAGTGGGTAGGAACATC 59.675 52.174 0.00 0.00 38.32 3.06
398 401 4.194678 CTACCTCCATAGTGGGTAGGAA 57.805 50.000 9.90 0.00 45.09 3.36
399 402 3.897657 CTACCTCCATAGTGGGTAGGA 57.102 52.381 9.90 0.00 45.09 2.94
413 416 7.229106 CACTTCCCTAGACTATGTTACTACCTC 59.771 44.444 0.00 0.00 0.00 3.85
428 431 5.418209 GCTAGTAACTTCACACTTCCCTAGA 59.582 44.000 0.00 0.00 0.00 2.43
433 436 7.097834 ACATAAGCTAGTAACTTCACACTTCC 58.902 38.462 0.00 0.00 0.00 3.46
434 437 8.535690 AACATAAGCTAGTAACTTCACACTTC 57.464 34.615 0.00 0.00 0.00 3.01
436 439 7.897864 AGAACATAAGCTAGTAACTTCACACT 58.102 34.615 0.00 0.00 0.00 3.55
437 440 8.436200 CAAGAACATAAGCTAGTAACTTCACAC 58.564 37.037 0.00 0.00 0.00 3.82
439 442 7.413109 GGCAAGAACATAAGCTAGTAACTTCAC 60.413 40.741 0.00 0.00 0.00 3.18
442 445 5.880887 GGGCAAGAACATAAGCTAGTAACTT 59.119 40.000 0.00 0.00 0.00 2.66
452 456 4.380867 GGTCACAATGGGCAAGAACATAAG 60.381 45.833 0.00 0.00 0.00 1.73
453 457 3.509575 GGTCACAATGGGCAAGAACATAA 59.490 43.478 0.00 0.00 0.00 1.90
456 460 1.327303 GGTCACAATGGGCAAGAACA 58.673 50.000 0.00 0.00 0.00 3.18
460 464 1.588082 GCTGGTCACAATGGGCAAG 59.412 57.895 0.00 0.00 0.00 4.01
461 465 1.907807 GGCTGGTCACAATGGGCAA 60.908 57.895 0.00 0.00 0.00 4.52
463 467 0.323360 TAAGGCTGGTCACAATGGGC 60.323 55.000 0.00 0.00 0.00 5.36
468 472 4.042311 TCCAAATACTAAGGCTGGTCACAA 59.958 41.667 0.00 0.00 0.00 3.33
470 474 4.216411 TCCAAATACTAAGGCTGGTCAC 57.784 45.455 0.00 0.00 0.00 3.67
508 512 3.676093 AGTGGGACTAAAACTTGCTAGC 58.324 45.455 8.10 8.10 0.00 3.42
564 568 5.854010 TGTCTACTTGCATACTAAGAGGG 57.146 43.478 0.00 0.00 0.00 4.30
565 569 7.223582 CACATTGTCTACTTGCATACTAAGAGG 59.776 40.741 0.00 0.00 0.00 3.69
569 573 6.092122 GTGCACATTGTCTACTTGCATACTAA 59.908 38.462 13.17 0.00 44.53 2.24
574 578 2.489329 GGTGCACATTGTCTACTTGCAT 59.511 45.455 20.43 0.00 44.53 3.96
575 579 1.879380 GGTGCACATTGTCTACTTGCA 59.121 47.619 20.43 0.00 40.81 4.08
576 580 1.879380 TGGTGCACATTGTCTACTTGC 59.121 47.619 20.43 0.00 0.00 4.01
577 581 4.456911 AGATTGGTGCACATTGTCTACTTG 59.543 41.667 20.43 0.00 0.00 3.16
578 582 4.655963 AGATTGGTGCACATTGTCTACTT 58.344 39.130 20.43 0.00 0.00 2.24
579 583 4.019860 AGAGATTGGTGCACATTGTCTACT 60.020 41.667 20.43 11.39 33.06 2.57
580 584 4.256920 AGAGATTGGTGCACATTGTCTAC 58.743 43.478 20.43 9.65 33.06 2.59
581 585 4.558226 AGAGATTGGTGCACATTGTCTA 57.442 40.909 20.43 0.00 33.06 2.59
582 586 3.430042 AGAGATTGGTGCACATTGTCT 57.570 42.857 20.43 15.14 30.80 3.41
583 587 4.937620 TCTTAGAGATTGGTGCACATTGTC 59.062 41.667 20.43 10.24 0.00 3.18
584 588 4.910195 TCTTAGAGATTGGTGCACATTGT 58.090 39.130 20.43 0.27 0.00 2.71
585 589 5.885230 TTCTTAGAGATTGGTGCACATTG 57.115 39.130 20.43 0.00 0.00 2.82
586 590 7.472334 AAATTCTTAGAGATTGGTGCACATT 57.528 32.000 20.43 1.66 0.00 2.71
587 591 8.579850 TTAAATTCTTAGAGATTGGTGCACAT 57.420 30.769 20.43 3.94 0.00 3.21
588 592 7.994425 TTAAATTCTTAGAGATTGGTGCACA 57.006 32.000 20.43 0.00 0.00 4.57
589 593 7.970614 CCTTTAAATTCTTAGAGATTGGTGCAC 59.029 37.037 8.80 8.80 0.00 4.57
590 594 7.669722 ACCTTTAAATTCTTAGAGATTGGTGCA 59.330 33.333 0.00 0.00 0.00 4.57
591 595 7.970614 CACCTTTAAATTCTTAGAGATTGGTGC 59.029 37.037 0.00 0.00 0.00 5.01
592 596 8.462016 CCACCTTTAAATTCTTAGAGATTGGTG 58.538 37.037 0.00 0.00 0.00 4.17
593 597 8.390921 TCCACCTTTAAATTCTTAGAGATTGGT 58.609 33.333 0.00 0.00 31.17 3.67
594 598 8.807948 TCCACCTTTAAATTCTTAGAGATTGG 57.192 34.615 0.00 0.00 30.80 3.16
600 604 9.747898 TGCTAAATCCACCTTTAAATTCTTAGA 57.252 29.630 0.00 0.00 0.00 2.10
601 605 9.788960 GTGCTAAATCCACCTTTAAATTCTTAG 57.211 33.333 0.00 0.00 0.00 2.18
615 619 2.389962 TGTACCGGTGCTAAATCCAC 57.610 50.000 23.67 7.81 0.00 4.02
616 620 2.158871 GGATGTACCGGTGCTAAATCCA 60.159 50.000 25.87 7.25 33.73 3.41
617 621 2.158871 TGGATGTACCGGTGCTAAATCC 60.159 50.000 24.77 24.77 42.61 3.01
618 622 3.131396 CTGGATGTACCGGTGCTAAATC 58.869 50.000 23.67 16.94 42.61 2.17
619 623 2.745152 GCTGGATGTACCGGTGCTAAAT 60.745 50.000 23.67 8.98 46.24 1.40
620 624 1.406341 GCTGGATGTACCGGTGCTAAA 60.406 52.381 23.67 3.75 46.24 1.85
621 625 0.177141 GCTGGATGTACCGGTGCTAA 59.823 55.000 23.67 4.55 46.24 3.09
622 626 0.973496 TGCTGGATGTACCGGTGCTA 60.973 55.000 23.67 10.49 46.24 3.49
623 627 2.290287 TGCTGGATGTACCGGTGCT 61.290 57.895 23.67 9.20 46.24 4.40
624 628 2.106683 GTGCTGGATGTACCGGTGC 61.107 63.158 19.93 18.21 46.24 5.01
625 629 1.449601 GGTGCTGGATGTACCGGTG 60.450 63.158 19.93 0.00 46.24 4.94
626 630 2.987125 GGTGCTGGATGTACCGGT 59.013 61.111 13.98 13.98 46.24 5.28
630 634 5.001232 TCTTTTTACTGGTGCTGGATGTAC 58.999 41.667 0.00 0.00 0.00 2.90
631 635 5.235850 TCTTTTTACTGGTGCTGGATGTA 57.764 39.130 0.00 0.00 0.00 2.29
632 636 4.074970 CTCTTTTTACTGGTGCTGGATGT 58.925 43.478 0.00 0.00 0.00 3.06
633 637 3.441572 CCTCTTTTTACTGGTGCTGGATG 59.558 47.826 0.00 0.00 0.00 3.51
634 638 3.074538 ACCTCTTTTTACTGGTGCTGGAT 59.925 43.478 0.00 0.00 0.00 3.41
635 639 2.441750 ACCTCTTTTTACTGGTGCTGGA 59.558 45.455 0.00 0.00 0.00 3.86
636 640 2.863809 ACCTCTTTTTACTGGTGCTGG 58.136 47.619 0.00 0.00 0.00 4.85
637 641 4.610945 CAAACCTCTTTTTACTGGTGCTG 58.389 43.478 0.00 0.00 32.53 4.41
638 642 3.068165 GCAAACCTCTTTTTACTGGTGCT 59.932 43.478 0.00 0.00 32.53 4.40
639 643 3.381045 GCAAACCTCTTTTTACTGGTGC 58.619 45.455 0.00 0.00 32.53 5.01
640 644 3.628017 CGCAAACCTCTTTTTACTGGTG 58.372 45.455 0.00 0.00 32.53 4.17
641 645 2.034179 GCGCAAACCTCTTTTTACTGGT 59.966 45.455 0.30 0.00 0.00 4.00
642 646 2.661594 GCGCAAACCTCTTTTTACTGG 58.338 47.619 0.30 0.00 0.00 4.00
643 647 2.307049 CGCGCAAACCTCTTTTTACTG 58.693 47.619 8.75 0.00 0.00 2.74
644 648 1.265905 CCGCGCAAACCTCTTTTTACT 59.734 47.619 8.75 0.00 0.00 2.24
645 649 1.681825 CCGCGCAAACCTCTTTTTAC 58.318 50.000 8.75 0.00 0.00 2.01
646 650 0.039888 GCCGCGCAAACCTCTTTTTA 60.040 50.000 8.75 0.00 0.00 1.52
647 651 1.299850 GCCGCGCAAACCTCTTTTT 60.300 52.632 8.75 0.00 0.00 1.94
648 652 2.335011 GCCGCGCAAACCTCTTTT 59.665 55.556 8.75 0.00 0.00 2.27
649 653 4.025401 CGCCGCGCAAACCTCTTT 62.025 61.111 8.75 0.00 0.00 2.52
650 654 4.980805 TCGCCGCGCAAACCTCTT 62.981 61.111 8.75 0.00 0.00 2.85
880 1440 3.697747 CGTGGGTCGGGGCAAGTA 61.698 66.667 0.00 0.00 35.71 2.24
917 1477 5.177696 GGCGTGCTTATTAATACAGGAGAAG 59.822 44.000 8.97 0.44 0.00 2.85
918 1478 5.054477 GGCGTGCTTATTAATACAGGAGAA 58.946 41.667 8.97 0.00 0.00 2.87
919 1479 4.502604 GGGCGTGCTTATTAATACAGGAGA 60.503 45.833 8.97 0.00 0.00 3.71
920 1480 3.746492 GGGCGTGCTTATTAATACAGGAG 59.254 47.826 8.97 0.39 0.00 3.69
921 1481 3.134985 TGGGCGTGCTTATTAATACAGGA 59.865 43.478 8.97 3.57 0.00 3.86
922 1482 3.472652 TGGGCGTGCTTATTAATACAGG 58.527 45.455 0.00 0.00 0.00 4.00
988 1548 2.279517 GCCCATCGCTAGGTGTCG 60.280 66.667 0.00 0.00 0.00 4.35
1013 1573 2.614520 GGCGCCTTCTTCTTCTTATTCC 59.385 50.000 22.15 0.00 0.00 3.01
1136 1696 1.686325 CTCATCGTCCCCAACCGGAT 61.686 60.000 9.46 0.00 33.48 4.18
1229 1789 0.898789 AGAATCCACCGGTGACTCGT 60.899 55.000 36.07 15.47 0.00 4.18
1371 1931 1.079127 CGACCCCGTCTTTGCTGAT 60.079 57.895 0.00 0.00 0.00 2.90
1405 1965 2.756283 CGAGTCCCGCCTCTCCTT 60.756 66.667 0.00 0.00 0.00 3.36
1558 2118 0.617413 AAGACCACAGGCTCCAGATG 59.383 55.000 0.00 0.00 0.00 2.90
1816 2376 2.629617 CACCAACAGAGGCTTCCAATTT 59.370 45.455 0.00 0.00 0.00 1.82
1854 2414 0.033090 TCTCTGCACACAGCTCAGTG 59.967 55.000 10.06 10.06 44.10 3.66
1909 2469 1.966901 TTGACACTGTGAGCCGTGGT 61.967 55.000 15.86 0.00 35.51 4.16
1935 2495 0.693049 TTCCCTCCACTTCTGCCTTC 59.307 55.000 0.00 0.00 0.00 3.46
1995 2555 5.563592 TCATCAAGCTTCTCCTTCATTTCA 58.436 37.500 0.00 0.00 0.00 2.69
2025 2585 0.183492 TCAGGCTGTCCAACTGCTTT 59.817 50.000 15.27 0.00 41.90 3.51
2091 2651 2.282180 TGGGCCACCGAAAGCTTC 60.282 61.111 0.00 0.00 40.75 3.86
2097 2657 3.399181 CTAGCCTGGGCCACCGAA 61.399 66.667 0.00 0.00 43.17 4.30
2102 2662 2.204074 TGTTCCTAGCCTGGGCCA 60.204 61.111 5.85 5.85 43.17 5.36
2166 2726 2.922503 TCCACCTCCTTCTGCGCA 60.923 61.111 10.98 10.98 0.00 6.09
2333 2893 0.394899 CTTCAGCCCATCCAGTTCCC 60.395 60.000 0.00 0.00 0.00 3.97
2408 2968 2.698855 TGTAGCCTCAGCATCTTTCC 57.301 50.000 0.00 0.00 43.56 3.13
2470 3030 4.126437 TCATCACAGTGAACACGTTGATT 58.874 39.130 7.50 0.00 36.32 2.57
2604 3164 3.133003 GGTCCTTCTCAGCATTGTAGCTA 59.867 47.826 0.00 0.00 44.54 3.32
2610 3170 1.081892 CACGGTCCTTCTCAGCATTG 58.918 55.000 0.00 0.00 0.00 2.82
2636 3196 2.307098 AGTGCTTCTGCCTTCAATACCT 59.693 45.455 0.00 0.00 38.71 3.08
2640 3200 4.144297 TGTTTAGTGCTTCTGCCTTCAAT 58.856 39.130 0.00 0.00 38.71 2.57
2791 3351 1.344763 AGCAGCGTAGACAAAGGAAGT 59.655 47.619 0.00 0.00 0.00 3.01
2869 3429 6.723977 TGGAAGCCTGGTTATTCTTATTTGTT 59.276 34.615 0.00 0.00 0.00 2.83
2991 3551 3.817647 AGACATTGAACAAAGACCAGCTC 59.182 43.478 0.00 0.00 0.00 4.09
3097 4169 5.023533 ACAGGCATGTAAGGTATGTACAG 57.976 43.478 0.06 0.00 38.09 2.74
3253 4325 7.895759 ACAACCATTGTAAGAAGTGCATAATT 58.104 30.769 0.00 0.00 43.27 1.40
3299 4478 3.498774 AACAAGTGAGCCACAAGATCT 57.501 42.857 7.86 0.00 36.74 2.75
3336 4515 4.886489 TGCATAGCAGCAATACAATTACCA 59.114 37.500 0.00 0.00 42.46 3.25
3396 4575 6.588348 AAAAGTCTGCAACAAATTTACAGC 57.412 33.333 0.00 0.00 0.00 4.40
3515 4694 8.210946 TGTTAGCTCAGTAACATTTATATGGCT 58.789 33.333 0.00 0.00 37.86 4.75
3531 4710 5.106157 CCATGTAGGGTTTTTGTTAGCTCAG 60.106 44.000 0.00 0.00 0.00 3.35
3684 4863 1.545651 CCAGGTTCTGTCCTTGGGTTC 60.546 57.143 0.00 0.00 35.37 3.62
3741 4920 8.233190 GCGTTCTTAAGTACTAGTCTTGTTCTA 58.767 37.037 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.