Multiple sequence alignment - TraesCS4B01G288400

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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 TraesCS4B01G288400 chr4B 100.000 2399 0 0 1 2399 573386723 573389121 0.000000e+00 4431.0
1 TraesCS4B01G288400 chr4D 91.176 1156 63 17 628 1756 459067940 459069083 0.000000e+00 1533.0
2 TraesCS4B01G288400 chr4D 85.981 428 38 10 675 1093 459065717 459066131 2.830000e-119 438.0
3 TraesCS4B01G288400 chr4D 93.116 276 16 3 1130 1404 459066134 459066407 3.710000e-108 401.0
4 TraesCS4B01G288400 chr4D 92.748 262 13 4 2086 2347 459071992 459072247 8.100000e-100 374.0
5 TraesCS4B01G288400 chr4D 89.219 269 19 5 1750 2012 459070238 459070502 6.390000e-86 327.0
6 TraesCS4B01G288400 chr4D 81.588 277 44 6 8 280 459067382 459067655 3.100000e-54 222.0
7 TraesCS4B01G288400 chr4D 97.619 42 1 0 2014 2055 459070546 459070587 3.310000e-09 73.1
8 TraesCS4B01G288400 chr4A 86.022 1438 125 38 628 2014 9623989 9622577 0.000000e+00 1472.0
9 TraesCS4B01G288400 chr4A 86.989 538 42 11 874 1404 9626758 9626242 4.450000e-162 580.0
10 TraesCS4B01G288400 chr4A 91.282 195 14 2 2014 2208 9622539 9622348 1.830000e-66 263.0
11 TraesCS4B01G288400 chr4A 87.773 229 17 5 667 885 9627401 9627174 8.510000e-65 257.0
12 TraesCS4B01G288400 chr4A 96.875 128 4 0 502 629 16485470 16485597 5.190000e-52 215.0
13 TraesCS4B01G288400 chr4A 95.455 132 6 0 500 631 477881753 477881884 6.720000e-51 211.0
14 TraesCS4B01G288400 chr4A 93.382 136 8 1 503 637 735751903 735752038 1.450000e-47 200.0
15 TraesCS4B01G288400 chr4A 80.075 266 45 7 8 269 9628031 9627770 8.750000e-45 191.0
16 TraesCS4B01G288400 chr4A 86.620 142 16 1 1266 1404 9629222 9629081 1.150000e-33 154.0
17 TraesCS4B01G288400 chr1D 96.183 131 5 0 503 633 178459638 178459508 5.190000e-52 215.0
18 TraesCS4B01G288400 chr1B 96.875 128 4 0 503 630 409879809 409879936 5.190000e-52 215.0
19 TraesCS4B01G288400 chr1B 77.536 138 26 4 12 148 655297706 655297573 7.110000e-11 78.7
20 TraesCS4B01G288400 chr6B 93.197 147 6 4 488 630 648265355 648265501 1.870000e-51 213.0
21 TraesCS4B01G288400 chr2B 95.489 133 5 1 503 634 565052754 565052622 6.720000e-51 211.0
22 TraesCS4B01G288400 chr2D 96.094 128 5 0 503 630 592467983 592468110 2.420000e-50 209.0
23 TraesCS4B01G288400 chr3B 91.216 148 11 2 487 633 520452786 520452932 1.450000e-47 200.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G288400 chr4B 573386723 573389121 2398 False 4431.000000 4431 100.000000 1 2399 1 chr4B.!!$F1 2398
1 TraesCS4B01G288400 chr4D 459065717 459072247 6530 False 481.157143 1533 90.206714 8 2347 7 chr4D.!!$F1 2339
2 TraesCS4B01G288400 chr4A 9622348 9629222 6874 True 486.166667 1472 86.460167 8 2208 6 chr4A.!!$R1 2200

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
95 4820 0.034896 GGTTTCTCTTGGAGGTGCGA 59.965 55.0 0.0 0.0 0.0 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 8146 0.250295 CGGTCCTTCAAACCAGAGCA 60.25 55.0 0.0 0.0 36.53 4.26 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
39 4764 2.683933 GGCAGGGGTCCTCTTCGA 60.684 66.667 0.00 0.00 0.00 3.71
71 4796 2.997303 GTGTGCGTGGTACATTGATGTA 59.003 45.455 0.00 0.00 44.52 2.29
95 4820 0.034896 GGTTTCTCTTGGAGGTGCGA 59.965 55.000 0.00 0.00 0.00 5.10
104 4829 2.859165 TGGAGGTGCGATCTTTCTTT 57.141 45.000 0.00 0.00 0.00 2.52
105 4830 3.140325 TGGAGGTGCGATCTTTCTTTT 57.860 42.857 0.00 0.00 0.00 2.27
116 4841 6.815142 TGCGATCTTTCTTTTAGTTAGTACCC 59.185 38.462 0.00 0.00 0.00 3.69
119 4844 7.431668 CGATCTTTCTTTTAGTTAGTACCCTCG 59.568 40.741 0.00 0.00 0.00 4.63
142 4867 1.281867 TGCTTCTTGATAGGGTGTGGG 59.718 52.381 0.00 0.00 0.00 4.61
162 4889 3.053146 ACTCGTAAGTGGTGGAGCT 57.947 52.632 0.00 0.00 33.32 4.09
169 4896 4.222145 TCGTAAGTGGTGGAGCTAGAAAAT 59.778 41.667 0.00 0.00 39.48 1.82
175 4902 6.963322 AGTGGTGGAGCTAGAAAATTTCTAT 58.037 36.000 14.98 2.55 41.17 1.98
176 4903 7.406104 AGTGGTGGAGCTAGAAAATTTCTATT 58.594 34.615 14.98 7.57 41.17 1.73
192 4919 4.755266 TCTATTAAGGACCAAGTGCTCC 57.245 45.455 0.00 0.00 31.83 4.70
207 4934 5.514500 AGTGCTCCTAAAACTAATTGGGA 57.486 39.130 0.00 0.00 37.59 4.37
212 4939 4.606210 TCCTAAAACTAATTGGGAAGGGC 58.394 43.478 0.00 0.00 37.05 5.19
216 4943 2.231716 ACTAATTGGGAAGGGCCAAC 57.768 50.000 6.18 0.00 38.95 3.77
217 4944 1.431243 ACTAATTGGGAAGGGCCAACA 59.569 47.619 6.18 0.00 38.95 3.33
220 4947 0.116940 ATTGGGAAGGGCCAACACAT 59.883 50.000 6.18 0.00 38.95 3.21
222 4949 0.105246 TGGGAAGGGCCAACACATTT 60.105 50.000 6.18 0.00 38.95 2.32
227 4954 4.445019 GGGAAGGGCCAACACATTTAAAAA 60.445 41.667 6.18 0.00 38.95 1.94
228 4955 5.312895 GGAAGGGCCAACACATTTAAAAAT 58.687 37.500 6.18 0.00 36.34 1.82
256 4984 9.162793 GATTTTTAGCATCAAATCATCACTACG 57.837 33.333 8.75 0.00 38.67 3.51
262 4990 5.630061 CATCAAATCATCACTACGTTTGCA 58.370 37.500 0.00 0.00 31.64 4.08
265 4993 4.668576 AATCATCACTACGTTTGCACTG 57.331 40.909 0.00 0.00 0.00 3.66
270 4998 0.580104 ACTACGTTTGCACTGTTCGC 59.420 50.000 0.00 0.00 0.00 4.70
276 5064 0.941542 TTTGCACTGTTCGCTACCAC 59.058 50.000 0.00 0.00 0.00 4.16
278 5066 0.105964 TGCACTGTTCGCTACCACTT 59.894 50.000 0.00 0.00 0.00 3.16
323 5111 4.874966 CCTTTGATCTGCTTGTAAGAGGAG 59.125 45.833 0.00 0.00 36.54 3.69
329 5117 3.511934 TCTGCTTGTAAGAGGAGTTCTCC 59.488 47.826 10.57 10.57 43.44 3.71
330 5118 3.511477 TGCTTGTAAGAGGAGTTCTCCT 58.489 45.455 19.77 19.77 43.44 3.69
343 5131 4.158025 GGAGTTCTCCTCTTGTTGTATCGA 59.842 45.833 11.20 0.00 40.30 3.59
352 5140 1.149361 TGTTGTATCGATTCGGCCGC 61.149 55.000 23.51 5.56 0.00 6.53
353 5141 1.142097 TTGTATCGATTCGGCCGCA 59.858 52.632 23.51 11.40 0.00 5.69
361 5149 0.458370 GATTCGGCCGCATTGCTTTT 60.458 50.000 23.51 0.00 0.00 2.27
389 5177 3.868757 AAGCGGGATTAAAGCCTTTTC 57.131 42.857 0.00 0.00 0.00 2.29
391 5179 4.230745 AGCGGGATTAAAGCCTTTTCTA 57.769 40.909 0.00 0.00 0.00 2.10
405 5200 4.771903 CCTTTTCTAGGTTAAGAGCCTCC 58.228 47.826 0.00 0.00 39.39 4.30
424 5219 4.095483 CCTCCTTTCATGGTTTTGATCGAG 59.905 45.833 0.00 0.00 0.00 4.04
425 5220 4.651778 TCCTTTCATGGTTTTGATCGAGT 58.348 39.130 0.00 0.00 0.00 4.18
426 5221 5.070001 TCCTTTCATGGTTTTGATCGAGTT 58.930 37.500 0.00 0.00 0.00 3.01
427 5222 5.048782 TCCTTTCATGGTTTTGATCGAGTTG 60.049 40.000 0.00 0.00 0.00 3.16
429 5224 2.487762 TCATGGTTTTGATCGAGTTGGC 59.512 45.455 0.00 0.00 0.00 4.52
430 5225 1.974265 TGGTTTTGATCGAGTTGGCA 58.026 45.000 0.00 0.00 0.00 4.92
431 5226 1.606668 TGGTTTTGATCGAGTTGGCAC 59.393 47.619 0.00 0.00 0.00 5.01
433 5228 1.529438 GTTTTGATCGAGTTGGCACGA 59.471 47.619 1.03 1.03 41.47 4.35
434 5229 1.144969 TTTGATCGAGTTGGCACGAC 58.855 50.000 0.51 0.00 40.20 4.34
435 5230 1.006825 TTGATCGAGTTGGCACGACG 61.007 55.000 0.51 0.00 40.20 5.12
437 5232 1.006571 ATCGAGTTGGCACGACGTT 60.007 52.632 0.00 0.00 40.20 3.99
448 5252 2.095919 GGCACGACGTTGCTAGATTTTT 60.096 45.455 11.73 0.00 42.56 1.94
459 5263 9.167311 ACGTTGCTAGATTTTTATTTGAGAGAT 57.833 29.630 0.00 0.00 0.00 2.75
482 5286 4.977741 TTTTACGCTTGGAACTTACTCG 57.022 40.909 0.00 0.00 0.00 4.18
483 5287 2.642139 TACGCTTGGAACTTACTCGG 57.358 50.000 0.00 0.00 0.00 4.63
484 5288 0.963962 ACGCTTGGAACTTACTCGGA 59.036 50.000 0.00 0.00 0.00 4.55
485 5289 1.067776 ACGCTTGGAACTTACTCGGAG 60.068 52.381 2.83 2.83 0.00 4.63
486 5290 1.067776 CGCTTGGAACTTACTCGGAGT 60.068 52.381 15.95 15.95 0.00 3.85
487 5291 2.163010 CGCTTGGAACTTACTCGGAGTA 59.837 50.000 13.70 13.70 0.00 2.59
488 5292 3.509740 GCTTGGAACTTACTCGGAGTAC 58.490 50.000 17.11 6.21 28.93 2.73
489 5293 3.057033 GCTTGGAACTTACTCGGAGTACA 60.057 47.826 17.11 9.02 28.93 2.90
502 5306 5.244178 ACTCGGAGTACATTTCTCAGTTTCT 59.756 40.000 9.33 0.00 34.04 2.52
503 5307 6.433404 ACTCGGAGTACATTTCTCAGTTTCTA 59.567 38.462 9.33 0.00 34.04 2.10
504 5308 6.618811 TCGGAGTACATTTCTCAGTTTCTAC 58.381 40.000 0.00 0.00 34.04 2.59
505 5309 6.433404 TCGGAGTACATTTCTCAGTTTCTACT 59.567 38.462 0.00 0.00 34.04 2.57
506 5310 6.748198 CGGAGTACATTTCTCAGTTTCTACTC 59.252 42.308 0.00 0.00 34.04 2.59
507 5311 7.036829 GGAGTACATTTCTCAGTTTCTACTCC 58.963 42.308 0.00 0.00 41.73 3.85
508 5312 6.937392 AGTACATTTCTCAGTTTCTACTCCC 58.063 40.000 0.00 0.00 30.26 4.30
509 5313 6.726764 AGTACATTTCTCAGTTTCTACTCCCT 59.273 38.462 0.00 0.00 30.26 4.20
510 5314 6.043854 ACATTTCTCAGTTTCTACTCCCTC 57.956 41.667 0.00 0.00 30.26 4.30
511 5315 5.046231 ACATTTCTCAGTTTCTACTCCCTCC 60.046 44.000 0.00 0.00 30.26 4.30
512 5316 2.724454 TCTCAGTTTCTACTCCCTCCG 58.276 52.381 0.00 0.00 30.26 4.63
513 5317 2.041350 TCTCAGTTTCTACTCCCTCCGT 59.959 50.000 0.00 0.00 30.26 4.69
514 5318 2.424246 CTCAGTTTCTACTCCCTCCGTC 59.576 54.545 0.00 0.00 30.26 4.79
515 5319 1.477295 CAGTTTCTACTCCCTCCGTCC 59.523 57.143 0.00 0.00 30.26 4.79
516 5320 0.455005 GTTTCTACTCCCTCCGTCCG 59.545 60.000 0.00 0.00 0.00 4.79
517 5321 0.329261 TTTCTACTCCCTCCGTCCGA 59.671 55.000 0.00 0.00 0.00 4.55
518 5322 0.329261 TTCTACTCCCTCCGTCCGAA 59.671 55.000 0.00 0.00 0.00 4.30
519 5323 0.329261 TCTACTCCCTCCGTCCGAAA 59.671 55.000 0.00 0.00 0.00 3.46
520 5324 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
521 5325 1.755380 CTACTCCCTCCGTCCGAAAAT 59.245 52.381 0.00 0.00 0.00 1.82
522 5326 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
523 5327 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
524 5328 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
525 5329 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
526 5330 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
527 5331 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
528 5332 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
529 5333 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
530 5334 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
531 5335 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
532 5336 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
533 5337 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
534 5338 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
535 5339 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
536 5340 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
537 5341 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
538 5342 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
539 5343 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
540 5344 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
594 5398 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
600 5404 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
603 5407 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
604 5408 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
605 5409 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
606 5410 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
607 5411 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
608 5412 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
616 5420 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
617 5421 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
618 5422 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
619 5423 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
620 5424 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
621 5425 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
622 5426 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
623 5427 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
624 5428 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
625 5429 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
626 5430 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
649 5453 8.422566 GGAGTACATAAAAGTAGGTGCTTCTAT 58.577 37.037 0.00 0.00 37.13 1.98
650 5454 9.465985 GAGTACATAAAAGTAGGTGCTTCTATC 57.534 37.037 0.00 0.00 37.13 2.08
651 5455 9.203163 AGTACATAAAAGTAGGTGCTTCTATCT 57.797 33.333 0.00 0.00 33.88 1.98
654 5458 8.136165 ACATAAAAGTAGGTGCTTCTATCTACG 58.864 37.037 0.00 0.00 37.67 3.51
676 5481 6.062095 ACGGATAAAAGCAGCCTGTAATTAT 58.938 36.000 0.00 0.00 0.00 1.28
766 5573 0.868406 CGTCAGGTTCTCAAGTTGCC 59.132 55.000 0.00 0.00 0.00 4.52
789 5596 1.328680 CACATGGCAGACGTGATAAGC 59.671 52.381 1.13 0.00 39.46 3.09
793 5608 1.146358 GGCAGACGTGATAAGCGACC 61.146 60.000 0.00 0.00 0.00 4.79
797 5612 0.172803 GACGTGATAAGCGACCCAGT 59.827 55.000 0.00 0.00 0.00 4.00
803 5621 1.132453 GATAAGCGACCCAGTTTTGCC 59.868 52.381 0.00 0.00 0.00 4.52
819 5637 6.149308 CAGTTTTGCCAAAGAAAAAGGTTCTT 59.851 34.615 0.00 0.00 40.20 2.52
820 5638 7.333174 CAGTTTTGCCAAAGAAAAAGGTTCTTA 59.667 33.333 1.96 0.00 37.75 2.10
970 5801 1.449601 GCGACCGATCACCCACAAT 60.450 57.895 0.00 0.00 0.00 2.71
1004 5846 2.322161 CGAACCAAGCAAAGCAATGAG 58.678 47.619 0.00 0.00 0.00 2.90
1037 5879 6.047511 AGAGCCATCCTGTTGCTATATAAG 57.952 41.667 0.00 0.00 34.99 1.73
1125 5971 4.022849 GGTTCAGTTTCAGTTTCCATCTGG 60.023 45.833 0.00 0.00 34.15 3.86
1142 5988 1.263217 CTGGTTCGAGTGGTTTTTCGG 59.737 52.381 0.00 0.00 37.42 4.30
1146 5992 1.203313 CGAGTGGTTTTTCGGTCGC 59.797 57.895 0.00 0.00 33.39 5.19
1273 6119 3.952628 GAGAACTTCGGGGCCGTGG 62.953 68.421 0.00 0.00 40.74 4.94
1377 6226 3.064324 GTCGCCATGGCAGCCTTT 61.064 61.111 34.93 0.00 42.06 3.11
1410 6259 9.988815 TTATTCTCTGCTTAATTAGTCATCTCC 57.011 33.333 0.00 0.00 0.00 3.71
1458 6309 3.778629 GAGGAGTTTTACCTGTATCCCCA 59.221 47.826 0.00 0.00 37.93 4.96
1460 6311 3.522343 GGAGTTTTACCTGTATCCCCACT 59.478 47.826 0.00 0.00 0.00 4.00
1491 6342 6.069440 TCCCCTGAGTCAATTTCAGTATTGAT 60.069 38.462 5.20 0.00 44.01 2.57
1493 6344 7.201767 CCCCTGAGTCAATTTCAGTATTGATTC 60.202 40.741 12.25 12.25 44.76 2.52
1504 6355 8.771920 TTTCAGTATTGATTCGTCACTTGTAT 57.228 30.769 0.00 0.00 32.27 2.29
1536 6404 8.853345 CATGATGTAGTTTACTGAATTGCAAAC 58.147 33.333 1.71 1.21 0.00 2.93
1548 6416 4.443725 TGAATTGCAAACATTTGTACTGCG 59.556 37.500 1.71 0.00 38.87 5.18
1587 6455 6.098409 TGGGGCACTTTTACTGTTCAATTTAA 59.902 34.615 0.00 0.00 0.00 1.52
1588 6456 7.158697 GGGGCACTTTTACTGTTCAATTTAAT 58.841 34.615 0.00 0.00 0.00 1.40
1589 6457 7.659799 GGGGCACTTTTACTGTTCAATTTAATT 59.340 33.333 0.00 0.00 0.00 1.40
1590 6458 9.699703 GGGCACTTTTACTGTTCAATTTAATTA 57.300 29.630 0.00 0.00 0.00 1.40
1632 6507 3.253677 ACAAACAAACAACAAGACGGTCA 59.746 39.130 11.27 0.00 0.00 4.02
1705 6580 6.878317 AGCTGCATGTACTCTACTTCATTAA 58.122 36.000 1.02 0.00 0.00 1.40
1717 6592 8.794553 ACTCTACTTCATTAAAGAAGAGAACGA 58.205 33.333 23.42 11.96 46.18 3.85
1719 6594 9.627395 TCTACTTCATTAAAGAAGAGAACGAAG 57.373 33.333 23.42 10.52 46.18 3.79
1748 6623 1.648116 TGGTACAGGGTAACAGGTCC 58.352 55.000 0.00 0.00 39.74 4.46
1756 6631 3.134804 CAGGGTAACAGGTCCATCTAAGG 59.865 52.174 0.00 0.00 39.74 2.69
1757 6632 2.158798 GGGTAACAGGTCCATCTAAGGC 60.159 54.545 0.00 0.00 39.74 4.35
1758 6633 2.158798 GGTAACAGGTCCATCTAAGGCC 60.159 54.545 0.00 0.00 0.00 5.19
1759 6634 1.668826 AACAGGTCCATCTAAGGCCA 58.331 50.000 5.01 0.00 0.00 5.36
1760 6635 1.668826 ACAGGTCCATCTAAGGCCAA 58.331 50.000 5.01 0.00 0.00 4.52
1761 6636 1.282157 ACAGGTCCATCTAAGGCCAAC 59.718 52.381 5.01 0.00 0.00 3.77
1763 6638 0.623723 GGTCCATCTAAGGCCAACCA 59.376 55.000 5.01 0.00 39.06 3.67
1764 6639 1.005450 GGTCCATCTAAGGCCAACCAA 59.995 52.381 5.01 0.00 39.06 3.67
1814 7849 1.439679 GGAAGCTAAACGGTGACCAG 58.560 55.000 1.11 0.00 0.00 4.00
1820 7855 2.140717 CTAAACGGTGACCAGAACCAC 58.859 52.381 1.11 0.00 37.57 4.16
1822 7857 1.678598 AACGGTGACCAGAACCACGA 61.679 55.000 1.11 0.00 37.57 4.35
1825 7860 1.301479 GTGACCAGAACCACGACCC 60.301 63.158 0.00 0.00 0.00 4.46
1827 7862 1.004918 GACCAGAACCACGACCCTG 60.005 63.158 0.00 0.00 0.00 4.45
1923 7964 3.935203 TGAGCTTCTCAATCGTGGATTTC 59.065 43.478 0.00 0.00 37.57 2.17
1938 7979 2.158900 GGATTTCAAGGGAGATCGCTCA 60.159 50.000 0.00 0.00 43.14 4.26
1966 8007 7.530010 TCTTTTCAATTCTCTTGGAATAAGCG 58.470 34.615 0.00 0.00 43.17 4.68
1969 8010 6.817765 TCAATTCTCTTGGAATAAGCGTTT 57.182 33.333 0.00 0.00 43.17 3.60
1993 8034 5.889853 TGTCTCGCTTTCTAGATAACCCTTA 59.110 40.000 0.00 0.00 0.00 2.69
2048 8133 2.640332 GGGAAGAGAAGAAGTGGAGGTT 59.360 50.000 0.00 0.00 0.00 3.50
2126 9585 1.437573 GACGATCGTGGGATGCTCA 59.562 57.895 28.12 0.00 31.51 4.26
2165 9624 5.511377 GTGTGATTTTGCGGTATGTATGTTG 59.489 40.000 0.00 0.00 0.00 3.33
2210 9669 7.812648 TGAATTCTTGTGGTAAAGTTATTCCG 58.187 34.615 7.05 0.00 33.41 4.30
2292 9751 7.875554 GGAAGTTTACCTTGCCATATTCAAAAA 59.124 33.333 0.00 0.00 35.61 1.94
2322 9781 4.603131 ACTAGGTGTACTCGTTGGGATAA 58.397 43.478 0.00 0.00 0.00 1.75
2328 9787 7.893658 AGGTGTACTCGTTGGGATAATATAAG 58.106 38.462 0.00 0.00 0.00 1.73
2366 9825 9.740710 AGGTTATTATATATCAAACTCCCAAGC 57.259 33.333 0.00 0.00 0.00 4.01
2367 9826 9.740710 GGTTATTATATATCAAACTCCCAAGCT 57.259 33.333 0.00 0.00 0.00 3.74
2371 9830 9.965902 ATTATATATCAAACTCCCAAGCTAAGG 57.034 33.333 0.00 0.00 0.00 2.69
2372 9831 2.200373 TCAAACTCCCAAGCTAAGGC 57.800 50.000 0.00 0.00 39.06 4.35
2373 9832 1.423541 TCAAACTCCCAAGCTAAGGCA 59.576 47.619 0.00 0.00 41.70 4.75
2374 9833 2.158534 TCAAACTCCCAAGCTAAGGCAA 60.159 45.455 0.00 0.00 41.70 4.52
2375 9834 1.911057 AACTCCCAAGCTAAGGCAAC 58.089 50.000 0.00 0.00 41.70 4.17
2376 9835 0.038310 ACTCCCAAGCTAAGGCAACC 59.962 55.000 0.00 0.00 41.70 3.77
2377 9836 0.681243 CTCCCAAGCTAAGGCAACCC 60.681 60.000 0.00 0.00 41.70 4.11
2378 9837 1.140134 TCCCAAGCTAAGGCAACCCT 61.140 55.000 0.00 0.00 45.77 4.34
2389 9848 3.751479 AGGCAACCCTTGTTTGAATTC 57.249 42.857 0.00 0.00 38.74 2.17
2390 9849 3.308401 AGGCAACCCTTGTTTGAATTCT 58.692 40.909 7.05 0.00 38.74 2.40
2391 9850 3.070015 AGGCAACCCTTGTTTGAATTCTG 59.930 43.478 7.05 0.00 38.74 3.02
2392 9851 3.181466 GGCAACCCTTGTTTGAATTCTGT 60.181 43.478 7.05 0.00 30.42 3.41
2393 9852 4.038642 GGCAACCCTTGTTTGAATTCTGTA 59.961 41.667 7.05 0.00 30.42 2.74
2394 9853 5.452636 GGCAACCCTTGTTTGAATTCTGTAA 60.453 40.000 7.05 0.00 30.42 2.41
2395 9854 5.691754 GCAACCCTTGTTTGAATTCTGTAAG 59.308 40.000 7.05 6.25 30.42 2.34
2396 9855 6.682861 GCAACCCTTGTTTGAATTCTGTAAGT 60.683 38.462 7.05 0.00 29.99 2.24
2397 9856 6.635030 ACCCTTGTTTGAATTCTGTAAGTC 57.365 37.500 7.05 0.00 33.76 3.01
2398 9857 6.365520 ACCCTTGTTTGAATTCTGTAAGTCT 58.634 36.000 7.05 0.00 31.03 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 4740 4.787280 AGGACCCCTGCCCTCTCG 62.787 72.222 0.00 0.00 29.57 4.04
31 4755 1.269621 ACCAAGTTGTCGTCGAAGAGG 60.270 52.381 0.00 0.80 44.69 3.69
39 4764 1.448893 ACGCACACCAAGTTGTCGT 60.449 52.632 1.45 0.99 32.25 4.34
71 4796 1.978580 ACCTCCAAGAGAAACCATCGT 59.021 47.619 0.00 0.00 0.00 3.73
72 4797 2.350522 CACCTCCAAGAGAAACCATCG 58.649 52.381 0.00 0.00 0.00 3.84
74 4799 1.611673 CGCACCTCCAAGAGAAACCAT 60.612 52.381 0.00 0.00 0.00 3.55
95 4820 7.040494 GCGAGGGTACTAACTAAAAGAAAGAT 58.960 38.462 0.00 0.00 0.00 2.40
104 4829 1.133025 GCACGCGAGGGTACTAACTAA 59.867 52.381 15.93 0.00 36.38 2.24
105 4830 0.734889 GCACGCGAGGGTACTAACTA 59.265 55.000 15.93 0.00 36.38 2.24
116 4841 1.203928 CCTATCAAGAAGCACGCGAG 58.796 55.000 15.93 5.97 0.00 5.03
119 4844 1.009829 CACCCTATCAAGAAGCACGC 58.990 55.000 0.00 0.00 0.00 5.34
150 4877 5.635120 AGAAATTTTCTAGCTCCACCACTT 58.365 37.500 9.92 0.00 38.49 3.16
156 4883 9.614792 GTCCTTAATAGAAATTTTCTAGCTCCA 57.385 33.333 20.35 2.93 44.80 3.86
192 4919 4.349365 TGGCCCTTCCCAATTAGTTTTAG 58.651 43.478 0.00 0.00 30.32 1.85
207 4934 7.309770 TCTATTTTTAAATGTGTTGGCCCTT 57.690 32.000 0.00 0.00 0.00 3.95
238 4966 4.496895 GCAAACGTAGTGATGATTTGATGC 59.503 41.667 3.45 0.00 45.00 3.91
241 4969 4.754618 AGTGCAAACGTAGTGATGATTTGA 59.245 37.500 3.45 0.00 45.00 2.69
255 4983 0.110823 GGTAGCGAACAGTGCAAACG 60.111 55.000 0.00 0.00 33.85 3.60
256 4984 0.941542 TGGTAGCGAACAGTGCAAAC 59.058 50.000 0.00 0.00 33.85 2.93
262 4990 3.155501 AGAGTAAGTGGTAGCGAACAGT 58.844 45.455 0.00 0.00 0.00 3.55
265 4993 3.910648 ACAAGAGTAAGTGGTAGCGAAC 58.089 45.455 0.00 0.00 0.00 3.95
297 5085 6.013725 TCCTCTTACAAGCAGATCAAAGGTAA 60.014 38.462 0.00 0.00 0.00 2.85
299 5087 4.287067 TCCTCTTACAAGCAGATCAAAGGT 59.713 41.667 0.00 0.00 0.00 3.50
300 5088 4.836825 TCCTCTTACAAGCAGATCAAAGG 58.163 43.478 0.00 0.00 0.00 3.11
301 5089 5.486526 ACTCCTCTTACAAGCAGATCAAAG 58.513 41.667 0.00 0.00 0.00 2.77
303 5091 5.247110 AGAACTCCTCTTACAAGCAGATCAA 59.753 40.000 0.00 0.00 0.00 2.57
304 5092 4.774726 AGAACTCCTCTTACAAGCAGATCA 59.225 41.667 0.00 0.00 0.00 2.92
305 5093 5.337578 AGAACTCCTCTTACAAGCAGATC 57.662 43.478 0.00 0.00 0.00 2.75
306 5094 4.161377 GGAGAACTCCTCTTACAAGCAGAT 59.839 45.833 12.98 0.00 46.16 2.90
308 5096 3.855858 GGAGAACTCCTCTTACAAGCAG 58.144 50.000 12.98 0.00 46.16 4.24
309 5097 3.963428 GGAGAACTCCTCTTACAAGCA 57.037 47.619 12.98 0.00 46.16 3.91
323 5111 5.230306 CGAATCGATACAACAAGAGGAGAAC 59.770 44.000 0.00 0.00 0.00 3.01
329 5117 2.540101 GGCCGAATCGATACAACAAGAG 59.460 50.000 3.36 0.00 0.00 2.85
330 5118 2.546778 GGCCGAATCGATACAACAAGA 58.453 47.619 3.36 0.00 0.00 3.02
332 5120 1.282817 CGGCCGAATCGATACAACAA 58.717 50.000 24.07 0.00 0.00 2.83
333 5121 1.149361 GCGGCCGAATCGATACAACA 61.149 55.000 33.48 0.00 0.00 3.33
334 5122 1.149361 TGCGGCCGAATCGATACAAC 61.149 55.000 33.48 6.69 0.00 3.32
343 5131 0.814457 TAAAAGCAATGCGGCCGAAT 59.186 45.000 33.48 24.55 0.00 3.34
361 5149 9.969001 AAAGGCTTTAATCCCGCTTTATATATA 57.031 29.630 11.52 0.00 0.00 0.86
389 5177 5.363939 CATGAAAGGAGGCTCTTAACCTAG 58.636 45.833 15.23 0.00 37.77 3.02
391 5179 3.054065 CCATGAAAGGAGGCTCTTAACCT 60.054 47.826 15.23 0.00 41.41 3.50
405 5200 5.156355 CCAACTCGATCAAAACCATGAAAG 58.844 41.667 0.00 0.00 32.06 2.62
424 5219 0.942410 TCTAGCAACGTCGTGCCAAC 60.942 55.000 8.57 0.00 46.14 3.77
425 5220 0.037697 ATCTAGCAACGTCGTGCCAA 60.038 50.000 8.57 0.00 46.14 4.52
426 5221 0.037697 AATCTAGCAACGTCGTGCCA 60.038 50.000 8.57 0.00 46.14 4.92
427 5222 1.076332 AAATCTAGCAACGTCGTGCC 58.924 50.000 8.57 2.54 46.14 5.01
429 5224 7.012943 TCAAATAAAAATCTAGCAACGTCGTG 58.987 34.615 0.00 0.00 0.00 4.35
430 5225 7.117236 TCTCAAATAAAAATCTAGCAACGTCGT 59.883 33.333 0.00 0.00 0.00 4.34
431 5226 7.453034 TCTCAAATAAAAATCTAGCAACGTCG 58.547 34.615 0.00 0.00 0.00 5.12
433 5228 8.547967 TCTCTCAAATAAAAATCTAGCAACGT 57.452 30.769 0.00 0.00 0.00 3.99
434 5229 9.994432 AATCTCTCAAATAAAAATCTAGCAACG 57.006 29.630 0.00 0.00 0.00 4.10
467 5271 2.745515 ACTCCGAGTAAGTTCCAAGC 57.254 50.000 0.00 0.00 0.00 4.01
481 5285 6.622549 AGTAGAAACTGAGAAATGTACTCCG 58.377 40.000 0.00 0.00 33.57 4.63
482 5286 7.036829 GGAGTAGAAACTGAGAAATGTACTCC 58.963 42.308 17.12 17.12 44.81 3.85
483 5287 7.036829 GGGAGTAGAAACTGAGAAATGTACTC 58.963 42.308 10.35 10.35 35.56 2.59
484 5288 6.726764 AGGGAGTAGAAACTGAGAAATGTACT 59.273 38.462 0.00 0.00 35.56 2.73
485 5289 6.937392 AGGGAGTAGAAACTGAGAAATGTAC 58.063 40.000 0.00 0.00 35.56 2.90
486 5290 6.154706 GGAGGGAGTAGAAACTGAGAAATGTA 59.845 42.308 0.00 0.00 35.56 2.29
487 5291 5.046231 GGAGGGAGTAGAAACTGAGAAATGT 60.046 44.000 0.00 0.00 35.56 2.71
488 5292 5.423886 GGAGGGAGTAGAAACTGAGAAATG 58.576 45.833 0.00 0.00 35.56 2.32
489 5293 4.160626 CGGAGGGAGTAGAAACTGAGAAAT 59.839 45.833 0.00 0.00 35.56 2.17
502 5306 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
503 5307 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
504 5308 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
505 5309 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
506 5310 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
507 5311 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
508 5312 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
509 5313 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
510 5314 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
511 5315 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
512 5316 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
513 5317 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
514 5318 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
568 5372 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
574 5378 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
577 5381 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
578 5382 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
579 5383 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
580 5384 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
581 5385 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
582 5386 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
590 5394 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
591 5395 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
592 5396 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
593 5397 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
594 5398 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
595 5399 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
596 5400 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
597 5401 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
598 5402 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
599 5403 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
600 5404 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
601 5405 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
602 5406 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
603 5407 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
604 5408 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
605 5409 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
606 5410 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
607 5411 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
608 5412 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
609 5413 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
610 5414 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
611 5415 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
612 5416 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
613 5417 0.839277 TATGTACTCCCTCCGTCCGA 59.161 55.000 0.00 0.00 0.00 4.55
614 5418 1.683943 TTATGTACTCCCTCCGTCCG 58.316 55.000 0.00 0.00 0.00 4.79
615 5419 3.450096 ACTTTTATGTACTCCCTCCGTCC 59.550 47.826 0.00 0.00 0.00 4.79
616 5420 4.732672 ACTTTTATGTACTCCCTCCGTC 57.267 45.455 0.00 0.00 0.00 4.79
617 5421 4.648307 CCTACTTTTATGTACTCCCTCCGT 59.352 45.833 0.00 0.00 0.00 4.69
618 5422 4.648307 ACCTACTTTTATGTACTCCCTCCG 59.352 45.833 0.00 0.00 0.00 4.63
619 5423 5.684291 GCACCTACTTTTATGTACTCCCTCC 60.684 48.000 0.00 0.00 0.00 4.30
620 5424 5.128991 AGCACCTACTTTTATGTACTCCCTC 59.871 44.000 0.00 0.00 0.00 4.30
621 5425 5.030820 AGCACCTACTTTTATGTACTCCCT 58.969 41.667 0.00 0.00 0.00 4.20
622 5426 5.354842 AGCACCTACTTTTATGTACTCCC 57.645 43.478 0.00 0.00 0.00 4.30
623 5427 6.641474 AGAAGCACCTACTTTTATGTACTCC 58.359 40.000 0.00 0.00 0.00 3.85
624 5428 9.465985 GATAGAAGCACCTACTTTTATGTACTC 57.534 37.037 0.00 0.00 29.69 2.59
625 5429 9.203163 AGATAGAAGCACCTACTTTTATGTACT 57.797 33.333 0.00 0.00 29.69 2.73
649 5453 2.500098 ACAGGCTGCTTTTATCCGTAGA 59.500 45.455 15.89 0.00 0.00 2.59
650 5454 2.906354 ACAGGCTGCTTTTATCCGTAG 58.094 47.619 15.89 0.00 0.00 3.51
651 5455 4.475051 TTACAGGCTGCTTTTATCCGTA 57.525 40.909 15.89 0.00 0.00 4.02
652 5456 3.343941 TTACAGGCTGCTTTTATCCGT 57.656 42.857 15.89 0.00 0.00 4.69
653 5457 4.900635 AATTACAGGCTGCTTTTATCCG 57.099 40.909 15.89 0.00 0.00 4.18
654 5458 8.848474 TCTATAATTACAGGCTGCTTTTATCC 57.152 34.615 15.89 0.00 0.00 2.59
766 5573 0.674581 ATCACGTCTGCCATGTGGTG 60.675 55.000 0.35 0.00 41.80 4.17
789 5596 1.028905 TCTTTGGCAAAACTGGGTCG 58.971 50.000 14.43 0.00 0.00 4.79
793 5608 4.260985 ACCTTTTTCTTTGGCAAAACTGG 58.739 39.130 14.43 11.94 0.00 4.00
797 5612 7.335673 CCTTAAGAACCTTTTTCTTTGGCAAAA 59.664 33.333 14.43 2.64 39.30 2.44
803 5621 7.010460 CAGCAACCTTAAGAACCTTTTTCTTTG 59.990 37.037 3.36 0.00 39.30 2.77
912 5743 1.323235 GTGCCGTTTGCTTGTTTTGTC 59.677 47.619 0.00 0.00 42.00 3.18
970 5801 1.120530 GGTTCGGATAAGCCTCTCCA 58.879 55.000 0.00 0.00 0.00 3.86
1011 5853 1.817099 GCAACAGGATGGCTCTCGG 60.817 63.158 0.00 0.00 43.62 4.63
1125 5971 1.071041 CGACCGAAAAACCACTCGAAC 60.071 52.381 0.00 0.00 37.23 3.95
1377 6226 4.465632 TTAAGCAGAGAATAAGCCGTCA 57.534 40.909 0.00 0.00 0.00 4.35
1386 6235 8.261349 AGGAGATGACTAATTAAGCAGAGAAT 57.739 34.615 0.00 0.00 0.00 2.40
1409 6258 9.415544 CAAATTAACTCCATTTCAGAAAGAAGG 57.584 33.333 1.28 3.93 37.57 3.46
1410 6259 9.415544 CCAAATTAACTCCATTTCAGAAAGAAG 57.584 33.333 1.28 1.74 37.57 2.85
1458 6309 1.149782 TGACTCAGGGGAGGAGGAGT 61.150 60.000 0.00 0.00 45.81 3.85
1460 6311 0.719015 ATTGACTCAGGGGAGGAGGA 59.281 55.000 0.00 0.00 45.81 3.71
1491 6342 6.718522 TCATGGGTATATACAAGTGACGAA 57.281 37.500 14.70 0.00 0.00 3.85
1493 6344 6.455647 ACATCATGGGTATATACAAGTGACG 58.544 40.000 14.70 9.39 0.00 4.35
1508 6359 6.095300 TGCAATTCAGTAAACTACATCATGGG 59.905 38.462 0.00 0.00 0.00 4.00
1528 6379 2.730928 GCGCAGTACAAATGTTTGCAAT 59.269 40.909 0.30 0.00 41.79 3.56
1536 6404 5.868257 TCAGAAATAAGCGCAGTACAAATG 58.132 37.500 11.47 0.00 0.00 2.32
1548 6416 3.448660 AGTGCCCCAATTCAGAAATAAGC 59.551 43.478 0.00 0.00 0.00 3.09
1587 6455 8.398878 TGTTTGGACTAAATTTCGAAGGTAAT 57.601 30.769 0.00 0.00 0.00 1.89
1588 6456 7.804843 TGTTTGGACTAAATTTCGAAGGTAA 57.195 32.000 0.00 0.00 0.00 2.85
1589 6457 7.804843 TTGTTTGGACTAAATTTCGAAGGTA 57.195 32.000 0.00 0.00 0.00 3.08
1590 6458 6.702716 TTGTTTGGACTAAATTTCGAAGGT 57.297 33.333 0.00 0.00 0.00 3.50
1632 6507 2.680913 GCTGAGCAATCGCGGTGTT 61.681 57.895 6.13 2.52 45.49 3.32
1705 6580 7.278868 CCATATAACTTGCTTCGTTCTCTTCTT 59.721 37.037 0.00 0.00 0.00 2.52
1717 6592 5.710409 ACCCTGTACCATATAACTTGCTT 57.290 39.130 0.00 0.00 0.00 3.91
1719 6594 6.350906 TGTTACCCTGTACCATATAACTTGC 58.649 40.000 0.00 0.00 0.00 4.01
1746 6621 3.534357 TTTTGGTTGGCCTTAGATGGA 57.466 42.857 3.32 0.00 35.27 3.41
1748 6623 4.599047 TGTTTTTGGTTGGCCTTAGATG 57.401 40.909 3.32 0.00 35.27 2.90
1756 6631 1.731720 TGCAGTTGTTTTTGGTTGGC 58.268 45.000 0.00 0.00 0.00 4.52
1757 6632 3.750652 AGTTTGCAGTTGTTTTTGGTTGG 59.249 39.130 0.00 0.00 0.00 3.77
1758 6633 4.450419 TCAGTTTGCAGTTGTTTTTGGTTG 59.550 37.500 0.00 0.00 0.00 3.77
1759 6634 4.636249 TCAGTTTGCAGTTGTTTTTGGTT 58.364 34.783 0.00 0.00 0.00 3.67
1760 6635 4.264460 TCAGTTTGCAGTTGTTTTTGGT 57.736 36.364 0.00 0.00 0.00 3.67
1761 6636 5.407995 TCTTTCAGTTTGCAGTTGTTTTTGG 59.592 36.000 0.00 0.00 0.00 3.28
1763 6638 6.454795 TCTCTTTCAGTTTGCAGTTGTTTTT 58.545 32.000 0.00 0.00 0.00 1.94
1764 6639 6.024552 TCTCTTTCAGTTTGCAGTTGTTTT 57.975 33.333 0.00 0.00 0.00 2.43
1808 7843 1.458777 AGGGTCGTGGTTCTGGTCA 60.459 57.895 0.00 0.00 0.00 4.02
1814 7849 3.524648 TTCGGCAGGGTCGTGGTTC 62.525 63.158 0.00 0.00 30.45 3.62
1820 7855 2.432628 GTCAGTTCGGCAGGGTCG 60.433 66.667 0.00 0.00 0.00 4.79
1822 7857 0.535102 CTTTGTCAGTTCGGCAGGGT 60.535 55.000 0.00 0.00 0.00 4.34
1825 7860 0.868406 GTCCTTTGTCAGTTCGGCAG 59.132 55.000 0.00 0.00 0.00 4.85
1827 7862 1.002792 GTTGTCCTTTGTCAGTTCGGC 60.003 52.381 0.00 0.00 0.00 5.54
1923 7964 1.480137 AGAACTGAGCGATCTCCCTTG 59.520 52.381 0.90 0.00 38.58 3.61
1966 8007 5.291371 GGGTTATCTAGAAAGCGAGACAAAC 59.709 44.000 0.00 0.00 30.73 2.93
1969 8010 4.279145 AGGGTTATCTAGAAAGCGAGACA 58.721 43.478 0.00 0.00 0.00 3.41
1980 8021 6.759272 TGTGCTTAGCATAAGGGTTATCTAG 58.241 40.000 11.03 0.00 41.91 2.43
2059 8144 0.877743 GTCCTTCAAACCAGAGCAGC 59.122 55.000 0.00 0.00 0.00 5.25
2060 8145 1.528129 GGTCCTTCAAACCAGAGCAG 58.472 55.000 0.00 0.00 36.75 4.24
2061 8146 0.250295 CGGTCCTTCAAACCAGAGCA 60.250 55.000 0.00 0.00 36.53 4.26
2062 8147 1.578206 GCGGTCCTTCAAACCAGAGC 61.578 60.000 0.00 0.00 36.53 4.09
2165 9624 3.932710 TCAAATCGAGGTTCATACTGTGC 59.067 43.478 0.00 0.00 0.00 4.57
2210 9669 3.507233 TCCATTGCACAATTCCAGAAGAC 59.493 43.478 0.00 0.00 0.00 3.01
2224 9683 8.995027 AGAAAATAATACCTATGTCCATTGCA 57.005 30.769 0.00 0.00 0.00 4.08
2253 9712 5.897250 AGGTAAACTTCCATCTTTTGGTTGT 59.103 36.000 0.00 0.00 46.52 3.32
2292 9751 8.800332 CCCAACGAGTACACCTAGTATAATAAT 58.200 37.037 0.00 0.00 34.67 1.28
2295 9754 6.367983 TCCCAACGAGTACACCTAGTATAAT 58.632 40.000 0.00 0.00 34.67 1.28
2347 9806 7.017155 TGCCTTAGCTTGGGAGTTTGATATATA 59.983 37.037 8.58 0.00 40.80 0.86
2348 9807 6.183361 TGCCTTAGCTTGGGAGTTTGATATAT 60.183 38.462 8.58 0.00 40.80 0.86
2349 9808 5.131977 TGCCTTAGCTTGGGAGTTTGATATA 59.868 40.000 8.58 0.00 40.80 0.86
2350 9809 4.079787 TGCCTTAGCTTGGGAGTTTGATAT 60.080 41.667 8.58 0.00 40.80 1.63
2351 9810 3.265737 TGCCTTAGCTTGGGAGTTTGATA 59.734 43.478 8.58 0.00 40.80 2.15
2352 9811 2.041620 TGCCTTAGCTTGGGAGTTTGAT 59.958 45.455 8.58 0.00 40.80 2.57
2353 9812 1.423541 TGCCTTAGCTTGGGAGTTTGA 59.576 47.619 8.58 0.00 40.80 2.69
2354 9813 1.909700 TGCCTTAGCTTGGGAGTTTG 58.090 50.000 8.58 0.00 40.80 2.93
2355 9814 2.239400 GTTGCCTTAGCTTGGGAGTTT 58.761 47.619 8.58 0.00 40.80 2.66
2356 9815 1.547901 GGTTGCCTTAGCTTGGGAGTT 60.548 52.381 8.58 0.00 40.80 3.01
2357 9816 0.038310 GGTTGCCTTAGCTTGGGAGT 59.962 55.000 8.58 0.00 40.80 3.85
2358 9817 0.681243 GGGTTGCCTTAGCTTGGGAG 60.681 60.000 8.58 0.00 40.80 4.30
2359 9818 1.140134 AGGGTTGCCTTAGCTTGGGA 61.140 55.000 8.58 2.49 40.80 4.37
2360 9819 0.251787 AAGGGTTGCCTTAGCTTGGG 60.252 55.000 0.00 0.00 40.80 4.12
2361 9820 0.890683 CAAGGGTTGCCTTAGCTTGG 59.109 55.000 0.00 0.00 40.80 3.61
2362 9821 1.620822 ACAAGGGTTGCCTTAGCTTG 58.379 50.000 0.00 0.00 40.80 4.01
2363 9822 2.365293 CAAACAAGGGTTGCCTTAGCTT 59.635 45.455 0.00 0.00 40.80 3.74
2364 9823 1.963515 CAAACAAGGGTTGCCTTAGCT 59.036 47.619 0.00 0.00 40.80 3.32
2365 9824 1.960689 TCAAACAAGGGTTGCCTTAGC 59.039 47.619 0.00 0.00 37.30 3.09
2366 9825 4.871933 ATTCAAACAAGGGTTGCCTTAG 57.128 40.909 0.00 0.00 37.30 2.18
2367 9826 4.898861 AGAATTCAAACAAGGGTTGCCTTA 59.101 37.500 8.44 0.00 37.30 2.69
2368 9827 3.711190 AGAATTCAAACAAGGGTTGCCTT 59.289 39.130 8.44 0.00 37.30 4.35
2369 9828 3.070015 CAGAATTCAAACAAGGGTTGCCT 59.930 43.478 8.44 0.00 37.30 4.75
2370 9829 3.181466 ACAGAATTCAAACAAGGGTTGCC 60.181 43.478 8.44 0.00 37.30 4.52
2371 9830 4.058721 ACAGAATTCAAACAAGGGTTGC 57.941 40.909 8.44 0.00 37.30 4.17
2372 9831 6.805713 ACTTACAGAATTCAAACAAGGGTTG 58.194 36.000 8.44 0.00 37.30 3.77
2373 9832 6.833933 AGACTTACAGAATTCAAACAAGGGTT 59.166 34.615 8.44 0.00 39.43 4.11
2374 9833 6.365520 AGACTTACAGAATTCAAACAAGGGT 58.634 36.000 8.44 0.00 0.00 4.34
2375 9834 6.884280 AGACTTACAGAATTCAAACAAGGG 57.116 37.500 8.44 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.