Multiple sequence alignment - TraesCS3A01G385300

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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 TraesCS3A01G385300 chr3A 100.000 4379 0 0 1 4379 634934491 634938869 0.000000e+00 8087
1 TraesCS3A01G385300 chr3B 90.238 3616 193 56 503 4061 654423471 654426983 0.000000e+00 4575
2 TraesCS3A01G385300 chr3B 82.456 342 28 15 4063 4379 654427021 654427355 2.010000e-68 270
3 TraesCS3A01G385300 chr3D 88.685 3915 210 105 564 4379 495484343 495488123 0.000000e+00 4560
4 TraesCS3A01G385300 chr3D 82.322 577 76 16 2 576 495483712 495484264 1.100000e-130 477
5 TraesCS3A01G385300 chr3D 79.268 246 42 8 186 430 412076854 412076617 3.500000e-36 163
6 TraesCS3A01G385300 chr1A 81.072 1157 145 48 1123 2225 463291194 463290058 0.000000e+00 856
7 TraesCS3A01G385300 chr1D 80.722 1136 159 44 1123 2213 364065080 364063960 0.000000e+00 830
8 TraesCS3A01G385300 chr1D 83.099 213 30 6 220 430 434614660 434614868 5.780000e-44 189
9 TraesCS3A01G385300 chr1B 76.652 938 150 43 1123 2006 487496683 487495761 5.160000e-124 455
10 TraesCS3A01G385300 chr1B 92.444 225 15 2 2001 2225 487490804 487490582 1.960000e-83 320
11 TraesCS3A01G385300 chr7D 80.377 265 39 13 188 445 84247622 84247364 5.780000e-44 189
12 TraesCS3A01G385300 chr7D 78.544 261 49 5 184 441 102546326 102546582 9.740000e-37 165
13 TraesCS3A01G385300 chr4D 80.851 235 37 7 211 441 507023192 507022962 1.250000e-40 178
14 TraesCS3A01G385300 chr7A 78.731 268 39 14 186 446 43250512 43250768 3.500000e-36 163
15 TraesCS3A01G385300 chr7A 79.098 244 46 5 188 430 85603689 85603450 3.500000e-36 163
16 TraesCS3A01G385300 chr7B 78.309 272 44 12 175 437 21662532 21662797 1.260000e-35 161


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 TraesCS3A01G385300 chr3A 634934491 634938869 4378 False 8087.0 8087 100.0000 1 4379 1 chr3A.!!$F1 4378
1 TraesCS3A01G385300 chr3B 654423471 654427355 3884 False 2422.5 4575 86.3470 503 4379 2 chr3B.!!$F1 3876
2 TraesCS3A01G385300 chr3D 495483712 495488123 4411 False 2518.5 4560 85.5035 2 4379 2 chr3D.!!$F1 4377
3 TraesCS3A01G385300 chr1A 463290058 463291194 1136 True 856.0 856 81.0720 1123 2225 1 chr1A.!!$R1 1102
4 TraesCS3A01G385300 chr1D 364063960 364065080 1120 True 830.0 830 80.7220 1123 2213 1 chr1D.!!$R1 1090
5 TraesCS3A01G385300 chr1B 487495761 487496683 922 True 455.0 455 76.6520 1123 2006 1 chr1B.!!$R2 883

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
588 681 0.107848 GGCAGTAATACGCACCCACT 60.108 55.0 8.82 0.0 0.00 4.0 F
921 1015 0.254462 CCCCAAGCTTTCTCTCTCCC 59.746 60.0 0.00 0.0 0.00 4.3 F
2681 3005 0.107703 ACGTGCCATGGTGGTATCTG 60.108 55.0 14.67 0.0 40.46 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 2557 0.315886 TGCTGCAGCTGTGAAATTGG 59.684 50.0 36.61 0.0 42.66 3.16 R
2812 3136 0.457035 CCCTCGGCAATCCAACAATG 59.543 55.0 0.00 0.0 0.00 2.82 R
3635 3987 0.109723 TGCCCTACCCTCAACACAAC 59.890 55.0 0.00 0.0 0.00 3.32 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
25 26 2.812664 GCCTCCTAATTTGGCCCAG 58.187 57.895 0.00 0.00 40.71 4.45
29 30 2.369394 CTCCTAATTTGGCCCAGTGAC 58.631 52.381 0.00 0.00 0.00 3.67
30 31 1.992557 TCCTAATTTGGCCCAGTGACT 59.007 47.619 0.00 0.00 0.00 3.41
70 71 4.717313 GGCCCACCTGACCGGAAC 62.717 72.222 9.46 1.77 36.31 3.62
72 73 3.077907 CCCACCTGACCGGAACAT 58.922 61.111 9.46 0.00 36.31 2.71
75 76 0.673644 CCACCTGACCGGAACATGAC 60.674 60.000 9.46 0.00 36.31 3.06
90 91 0.537188 ATGACGTGATGAGTGACCCC 59.463 55.000 0.00 0.00 0.00 4.95
99 100 3.699134 GAGTGACCCCCAATCCGGC 62.699 68.421 0.00 0.00 34.04 6.13
101 102 3.020647 TGACCCCCAATCCGGCAT 61.021 61.111 0.00 0.00 0.00 4.40
146 147 3.334583 TTCTCCCCTCAATTTGTCGAG 57.665 47.619 0.00 0.00 0.00 4.04
162 163 2.872858 GTCGAGGAGATGGCAAAATACC 59.127 50.000 0.00 0.00 0.00 2.73
212 213 7.751047 TTTCAAACATAGTAGATACGCAGAC 57.249 36.000 0.00 0.00 0.00 3.51
213 214 6.445357 TCAAACATAGTAGATACGCAGACA 57.555 37.500 0.00 0.00 0.00 3.41
222 223 5.765677 AGTAGATACGCAGACACTCATACAT 59.234 40.000 0.00 0.00 0.00 2.29
225 226 3.066369 ACGCAGACACTCATACATACG 57.934 47.619 0.00 0.00 0.00 3.06
226 227 1.781429 CGCAGACACTCATACATACGC 59.219 52.381 0.00 0.00 0.00 4.42
227 228 2.794631 CGCAGACACTCATACATACGCA 60.795 50.000 0.00 0.00 0.00 5.24
228 229 2.535984 GCAGACACTCATACATACGCAC 59.464 50.000 0.00 0.00 0.00 5.34
229 230 3.769536 CAGACACTCATACATACGCACA 58.230 45.455 0.00 0.00 0.00 4.57
239 240 6.512297 TCATACATACGCACAATACACTCAT 58.488 36.000 0.00 0.00 0.00 2.90
241 242 4.119862 ACATACGCACAATACACTCATCC 58.880 43.478 0.00 0.00 0.00 3.51
249 250 5.237344 GCACAATACACTCATCCCTATGAAC 59.763 44.000 0.00 0.00 41.57 3.18
252 254 6.070251 ACAATACACTCATCCCTATGAACACA 60.070 38.462 0.00 0.00 41.57 3.72
256 258 3.582647 ACTCATCCCTATGAACACACACA 59.417 43.478 0.00 0.00 41.57 3.72
257 259 4.225942 ACTCATCCCTATGAACACACACAT 59.774 41.667 0.00 0.00 41.57 3.21
262 264 4.284746 TCCCTATGAACACACACATACACA 59.715 41.667 0.00 0.00 0.00 3.72
279 281 7.708322 CACATACACATTACTCTTATGAGCACT 59.292 37.037 5.57 0.00 43.85 4.40
280 282 8.260818 ACATACACATTACTCTTATGAGCACTT 58.739 33.333 5.57 0.00 43.85 3.16
288 290 4.702612 ACTCTTATGAGCACTTTCGAGAGA 59.297 41.667 10.37 0.00 43.85 3.10
291 293 3.951775 ATGAGCACTTTCGAGAGACTT 57.048 42.857 10.37 0.00 41.84 3.01
294 296 4.072839 TGAGCACTTTCGAGAGACTTAGA 58.927 43.478 10.37 0.00 41.84 2.10
317 319 3.002042 CGGCACATCATCTTGAGATTGAC 59.998 47.826 0.90 0.00 31.21 3.18
318 320 3.002042 GGCACATCATCTTGAGATTGACG 59.998 47.826 0.90 0.00 31.21 4.35
320 322 4.330894 GCACATCATCTTGAGATTGACGAA 59.669 41.667 0.00 0.00 31.21 3.85
321 323 5.502058 GCACATCATCTTGAGATTGACGAAG 60.502 44.000 0.00 0.00 31.21 3.79
339 341 0.179094 AGTCGTCGCAAACACCTTCA 60.179 50.000 0.00 0.00 0.00 3.02
342 344 2.092211 GTCGTCGCAAACACCTTCATAG 59.908 50.000 0.00 0.00 0.00 2.23
345 347 2.092211 GTCGCAAACACCTTCATAGTCG 59.908 50.000 0.00 0.00 0.00 4.18
347 349 2.930040 CGCAAACACCTTCATAGTCGAT 59.070 45.455 0.00 0.00 0.00 3.59
349 351 3.063997 GCAAACACCTTCATAGTCGATGG 59.936 47.826 0.00 0.00 36.08 3.51
379 381 4.848562 TCTCTCACTAAACACACATCGT 57.151 40.909 0.00 0.00 0.00 3.73
381 383 3.561503 TCTCACTAAACACACATCGTCG 58.438 45.455 0.00 0.00 0.00 5.12
382 384 3.251487 TCTCACTAAACACACATCGTCGA 59.749 43.478 0.00 0.00 0.00 4.20
385 387 4.804665 TCACTAAACACACATCGTCGAAAA 59.195 37.500 0.00 0.00 0.00 2.29
390 392 1.136252 CACACATCGTCGAAAAGCCTG 60.136 52.381 0.00 0.00 0.00 4.85
391 393 1.270094 ACACATCGTCGAAAAGCCTGA 60.270 47.619 0.00 0.00 0.00 3.86
397 399 5.180492 ACATCGTCGAAAAGCCTGAAATAAA 59.820 36.000 0.00 0.00 0.00 1.40
400 402 7.367159 TCGTCGAAAAGCCTGAAATAAATTA 57.633 32.000 0.00 0.00 0.00 1.40
421 423 9.840427 AAATTAAGAAAAGTACGATCACCAATG 57.160 29.630 0.00 0.00 0.00 2.82
422 424 4.946784 AGAAAAGTACGATCACCAATGC 57.053 40.909 0.00 0.00 0.00 3.56
423 425 3.370978 AGAAAAGTACGATCACCAATGCG 59.629 43.478 0.00 0.00 0.00 4.73
428 430 1.359848 ACGATCACCAATGCGAAGTC 58.640 50.000 0.00 0.00 0.00 3.01
457 459 2.667199 CCGTGACGGGTTGGTTCC 60.667 66.667 17.80 0.00 44.15 3.62
479 481 1.207089 TCACAAGGAACTAGCCATCCG 59.793 52.381 4.64 0.00 38.49 4.18
480 482 1.207089 CACAAGGAACTAGCCATCCGA 59.793 52.381 4.64 0.00 38.49 4.55
481 483 1.906574 ACAAGGAACTAGCCATCCGAA 59.093 47.619 4.64 0.00 38.49 4.30
482 484 2.280628 CAAGGAACTAGCCATCCGAAC 58.719 52.381 4.64 0.00 38.49 3.95
483 485 1.867363 AGGAACTAGCCATCCGAACT 58.133 50.000 4.64 0.00 40.78 3.01
484 486 3.028094 AGGAACTAGCCATCCGAACTA 57.972 47.619 4.64 0.00 40.78 2.24
485 487 2.694109 AGGAACTAGCCATCCGAACTAC 59.306 50.000 4.64 0.00 40.78 2.73
486 488 2.543238 GGAACTAGCCATCCGAACTACG 60.543 54.545 0.00 0.00 42.18 3.51
487 489 0.384669 ACTAGCCATCCGAACTACGC 59.615 55.000 0.00 0.00 41.07 4.42
488 490 0.669077 CTAGCCATCCGAACTACGCT 59.331 55.000 0.00 0.00 41.07 5.07
489 491 0.666913 TAGCCATCCGAACTACGCTC 59.333 55.000 0.00 0.00 41.07 5.03
499 501 1.002250 AACTACGCTCACTTCGCACG 61.002 55.000 0.00 0.00 0.00 5.34
541 543 6.042143 CCCCAAATTAGACATGTTGTATTGC 58.958 40.000 0.00 0.00 0.00 3.56
543 545 7.068103 CCCCAAATTAGACATGTTGTATTGCTA 59.932 37.037 0.00 0.00 0.00 3.49
555 557 8.908678 CATGTTGTATTGCTATGTAATCAATGC 58.091 33.333 0.00 0.00 34.74 3.56
583 676 0.179119 ACGGAGGCAGTAATACGCAC 60.179 55.000 8.82 3.68 0.00 5.34
584 677 0.874607 CGGAGGCAGTAATACGCACC 60.875 60.000 8.82 9.52 0.00 5.01
588 681 0.107848 GGCAGTAATACGCACCCACT 60.108 55.000 8.82 0.00 0.00 4.00
590 683 1.404986 GCAGTAATACGCACCCACTGA 60.405 52.381 4.31 0.00 39.13 3.41
613 706 4.530857 CCTCCGCCACCGTCCATC 62.531 72.222 0.00 0.00 0.00 3.51
664 757 4.952262 TCATCCAGCAAGAAAGAAATCG 57.048 40.909 0.00 0.00 0.00 3.34
665 758 3.127548 TCATCCAGCAAGAAAGAAATCGC 59.872 43.478 0.00 0.00 0.00 4.58
750 843 0.322008 CCACCTTCCTTGCTCTGGTC 60.322 60.000 0.00 0.00 0.00 4.02
751 844 0.322008 CACCTTCCTTGCTCTGGTCC 60.322 60.000 0.00 0.00 0.00 4.46
752 845 1.078848 CCTTCCTTGCTCTGGTCCG 60.079 63.158 0.00 0.00 0.00 4.79
753 846 1.078848 CTTCCTTGCTCTGGTCCGG 60.079 63.158 0.00 0.00 0.00 5.14
754 847 1.831652 CTTCCTTGCTCTGGTCCGGT 61.832 60.000 0.00 0.00 0.00 5.28
755 848 1.827399 TTCCTTGCTCTGGTCCGGTC 61.827 60.000 0.00 0.00 0.00 4.79
872 965 2.368011 GCCCCCGCCCTATATCTCC 61.368 68.421 0.00 0.00 0.00 3.71
920 1014 0.988063 ACCCCAAGCTTTCTCTCTCC 59.012 55.000 0.00 0.00 0.00 3.71
921 1015 0.254462 CCCCAAGCTTTCTCTCTCCC 59.746 60.000 0.00 0.00 0.00 4.30
930 1024 1.215679 TTCTCTCTCCCCCTCCGTCT 61.216 60.000 0.00 0.00 0.00 4.18
934 1028 1.619975 TCTCCCCCTCCGTCTCTCT 60.620 63.158 0.00 0.00 0.00 3.10
936 1030 2.123640 CCCCCTCCGTCTCTCTCC 60.124 72.222 0.00 0.00 0.00 3.71
943 1044 2.517402 CGTCTCTCTCCCCCTCCG 60.517 72.222 0.00 0.00 0.00 4.63
952 1053 2.123640 CCCCCTCCGTCTCTCTCC 60.124 72.222 0.00 0.00 0.00 3.71
972 1073 2.026449 CCCCTGCTCTGTCTTTCTTCAT 60.026 50.000 0.00 0.00 0.00 2.57
1227 1343 2.266055 CCGGAGAAGAAGGCGCTT 59.734 61.111 7.64 0.00 0.00 4.68
1230 1346 0.460987 CGGAGAAGAAGGCGCTTGAT 60.461 55.000 7.64 0.00 0.00 2.57
1369 1581 2.679716 CCAAGGAGGAGGCCAAGG 59.320 66.667 5.01 0.00 41.22 3.61
1578 1865 1.446272 CGAGCCAAAGACGGAGGAC 60.446 63.158 0.00 0.00 0.00 3.85
2232 2537 0.873743 CGCTTCTTCTCTCCGCCATC 60.874 60.000 0.00 0.00 0.00 3.51
2242 2547 2.797156 CTCTCCGCCATCGAATTACTTG 59.203 50.000 0.00 0.00 38.10 3.16
2243 2548 1.867233 CTCCGCCATCGAATTACTTGG 59.133 52.381 0.00 0.00 38.10 3.61
2245 2550 2.431419 TCCGCCATCGAATTACTTGGTA 59.569 45.455 2.64 0.00 38.10 3.25
2246 2551 2.800544 CCGCCATCGAATTACTTGGTAG 59.199 50.000 2.64 0.00 38.10 3.18
2247 2552 3.454375 CGCCATCGAATTACTTGGTAGT 58.546 45.455 2.64 0.00 38.10 2.73
2249 2554 5.227908 CGCCATCGAATTACTTGGTAGTAT 58.772 41.667 2.64 0.00 35.85 2.12
2251 2556 6.202188 CGCCATCGAATTACTTGGTAGTATTT 59.798 38.462 2.64 0.00 35.85 1.40
2252 2557 7.568861 CGCCATCGAATTACTTGGTAGTATTTC 60.569 40.741 2.64 0.00 40.50 2.17
2253 2558 7.307811 GCCATCGAATTACTTGGTAGTATTTCC 60.308 40.741 2.64 0.00 40.65 3.13
2254 2559 7.713507 CCATCGAATTACTTGGTAGTATTTCCA 59.286 37.037 0.00 0.00 40.65 3.53
2255 2560 9.104965 CATCGAATTACTTGGTAGTATTTCCAA 57.895 33.333 0.00 0.00 40.65 3.53
2256 2561 9.847224 ATCGAATTACTTGGTAGTATTTCCAAT 57.153 29.630 0.00 5.97 40.65 3.16
2257 2562 9.675464 TCGAATTACTTGGTAGTATTTCCAATT 57.325 29.630 0.00 0.00 40.65 2.32
2297 2602 4.401022 ACTGTGATCCAACATTGTGACAT 58.599 39.130 0.00 0.00 0.00 3.06
2300 2605 4.583907 TGTGATCCAACATTGTGACATTGT 59.416 37.500 7.25 7.25 30.67 2.71
2319 2624 4.082274 TGTGCATCGAAATTTAGCTGTG 57.918 40.909 0.00 0.69 0.00 3.66
2377 2682 3.547054 TCACAGTTTAACGTTGGGAGT 57.453 42.857 11.99 0.15 0.00 3.85
2455 2760 5.796424 ATGCTTTCAAATTTGAGTCCTGT 57.204 34.783 19.64 4.94 38.61 4.00
2456 2761 6.899393 ATGCTTTCAAATTTGAGTCCTGTA 57.101 33.333 19.64 9.99 38.61 2.74
2487 2792 2.625823 ATGTCTTTTGGCGTGGGCG 61.626 57.895 0.00 0.00 41.24 6.13
2488 2793 4.038080 GTCTTTTGGCGTGGGCGG 62.038 66.667 0.00 0.00 41.24 6.13
2509 2814 2.225019 GGCTTTGGTCATCATCATAGCG 59.775 50.000 0.00 0.00 38.32 4.26
2511 2816 1.501169 TTGGTCATCATCATAGCGCG 58.499 50.000 0.00 0.00 0.00 6.86
2534 2839 4.558226 ATTGGGGATCTTTTCCTTTTGC 57.442 40.909 0.00 0.00 44.75 3.68
2537 2842 2.164422 GGGGATCTTTTCCTTTTGCTCG 59.836 50.000 0.00 0.00 44.75 5.03
2567 2891 6.817765 TCCCAATTCTGAGTTGTAACATTC 57.182 37.500 11.28 0.00 0.00 2.67
2568 2892 6.542821 TCCCAATTCTGAGTTGTAACATTCT 58.457 36.000 11.28 0.00 0.00 2.40
2614 2938 9.908152 GTTAATTGCAGTAGTTTAAGTGGAATT 57.092 29.630 13.33 13.33 46.32 2.17
2630 2954 5.127682 AGTGGAATTGGATCATAAGTTTGGC 59.872 40.000 0.00 0.00 0.00 4.52
2644 2968 1.474077 GTTTGGCTGGATCATGGTGTC 59.526 52.381 0.00 0.00 0.00 3.67
2681 3005 0.107703 ACGTGCCATGGTGGTATCTG 60.108 55.000 14.67 0.00 40.46 2.90
2780 3104 1.411787 CCCGAGACCCTCTTCAGGTAT 60.412 57.143 0.00 0.00 37.88 2.73
2825 3151 6.258507 AGTTTCAGTTTTCATTGTTGGATTGC 59.741 34.615 0.00 0.00 0.00 3.56
2844 3179 1.539929 GCCGAGGGATCATGTTCTCAG 60.540 57.143 6.43 0.19 0.00 3.35
2862 3197 4.769488 TCTCAGCTAGTGTTCATCTTCTGT 59.231 41.667 0.00 0.00 0.00 3.41
2866 3201 6.015434 TCAGCTAGTGTTCATCTTCTGTAACA 60.015 38.462 0.00 0.00 0.00 2.41
2888 3223 1.512926 AATTCAGATACATCGCGCCC 58.487 50.000 0.00 0.00 0.00 6.13
2972 3307 0.538516 ACTCTGTCACCGAGCTCACT 60.539 55.000 15.40 0.00 31.71 3.41
2994 3329 7.120285 TCACTATCAAAGCTTCATCCAAAGAAG 59.880 37.037 0.00 0.00 44.08 2.85
3021 3356 1.006758 AGATCCCTGTCACCGAGGTTA 59.993 52.381 0.00 0.00 0.00 2.85
3024 3374 1.218316 CCTGTCACCGAGGTTAGCC 59.782 63.158 0.00 0.00 0.00 3.93
3040 3390 7.896383 AGGTTAGCCTCATTTGCATTATAAA 57.104 32.000 0.00 0.00 42.67 1.40
3041 3391 8.482852 AGGTTAGCCTCATTTGCATTATAAAT 57.517 30.769 0.00 0.00 42.67 1.40
3042 3392 8.927411 AGGTTAGCCTCATTTGCATTATAAATT 58.073 29.630 0.00 0.00 42.67 1.82
3043 3393 8.981647 GGTTAGCCTCATTTGCATTATAAATTG 58.018 33.333 0.00 0.00 0.00 2.32
3047 3397 6.985645 GCCTCATTTGCATTATAAATTGGTGA 59.014 34.615 0.00 0.00 0.00 4.02
3049 3399 9.199982 CCTCATTTGCATTATAAATTGGTGATC 57.800 33.333 0.00 0.00 0.00 2.92
3073 3423 6.712095 TCGCTTATGAATTCCTCTAATGCATT 59.288 34.615 17.56 17.56 40.46 3.56
3084 3434 5.879777 TCCTCTAATGCATTGATCGTTCAAA 59.120 36.000 22.27 0.00 44.70 2.69
3090 3440 7.566858 AATGCATTGATCGTTCAAAACTTAC 57.433 32.000 12.09 1.20 44.70 2.34
3108 3458 4.816385 ACTTACATAATTGTCCATCTGCCG 59.184 41.667 0.00 0.00 37.28 5.69
3138 3488 2.868583 CTCAACGATTGTATGGGAGCTG 59.131 50.000 0.00 0.00 0.00 4.24
3159 3509 4.729918 GTGCTGGGCTGGGAGGTG 62.730 72.222 0.00 0.00 0.00 4.00
3387 3737 0.032615 AGTCCCTCTGAGGCCTACAG 60.033 60.000 18.51 20.19 32.73 2.74
3388 3738 0.324830 GTCCCTCTGAGGCCTACAGT 60.325 60.000 23.28 0.00 36.81 3.55
3389 3739 0.033011 TCCCTCTGAGGCCTACAGTC 60.033 60.000 23.28 6.98 36.81 3.51
3390 3740 1.045911 CCCTCTGAGGCCTACAGTCC 61.046 65.000 23.28 6.10 36.81 3.85
3391 3741 0.324738 CCTCTGAGGCCTACAGTCCA 60.325 60.000 23.28 9.97 36.81 4.02
3392 3742 1.690845 CCTCTGAGGCCTACAGTCCAT 60.691 57.143 23.28 0.00 36.81 3.41
3393 3743 1.411977 CTCTGAGGCCTACAGTCCATG 59.588 57.143 23.28 11.53 36.81 3.66
3394 3744 1.007118 TCTGAGGCCTACAGTCCATGA 59.993 52.381 23.28 8.14 36.81 3.07
3395 3745 1.137872 CTGAGGCCTACAGTCCATGAC 59.862 57.143 4.42 0.00 0.00 3.06
3399 3749 0.460284 GCCTACAGTCCATGACACCG 60.460 60.000 0.00 0.00 34.60 4.94
3417 3767 1.077429 GCCATTGGAGTCAGTCCCC 60.077 63.158 6.95 0.00 46.31 4.81
3530 3880 4.800993 CGCATTCCCGCATTTGTTTAATTA 59.199 37.500 0.00 0.00 0.00 1.40
3531 3881 5.289675 CGCATTCCCGCATTTGTTTAATTAA 59.710 36.000 0.00 0.00 0.00 1.40
3532 3882 6.183360 CGCATTCCCGCATTTGTTTAATTAAA 60.183 34.615 6.54 6.54 0.00 1.52
3582 3932 1.421382 TTTTGCGACGGTACAGTAGC 58.579 50.000 20.88 20.88 41.96 3.58
3600 3950 1.994463 CTGGGAGAGGAAGGTTGGG 59.006 63.158 0.00 0.00 0.00 4.12
3606 3956 2.197465 GAGAGGAAGGTTGGGTATGGT 58.803 52.381 0.00 0.00 0.00 3.55
3629 3981 6.767902 GGTATGGATGATATAATGGCATCGTT 59.232 38.462 0.00 0.00 39.36 3.85
3630 3982 7.283127 GGTATGGATGATATAATGGCATCGTTT 59.717 37.037 0.00 0.00 39.36 3.60
3631 3983 6.499234 TGGATGATATAATGGCATCGTTTG 57.501 37.500 0.00 0.00 39.36 2.93
3632 3984 6.237154 TGGATGATATAATGGCATCGTTTGA 58.763 36.000 0.00 0.00 39.36 2.69
3633 3985 6.885918 TGGATGATATAATGGCATCGTTTGAT 59.114 34.615 0.00 0.00 39.36 2.57
3690 4056 2.285977 TGATACAATCTGCTGCTGCTG 58.714 47.619 17.00 15.94 40.48 4.41
3691 4057 1.002684 GATACAATCTGCTGCTGCTGC 60.003 52.381 22.51 22.51 40.48 5.25
3692 4058 0.035725 TACAATCTGCTGCTGCTGCT 60.036 50.000 27.67 12.30 40.48 4.24
3693 4059 1.137614 CAATCTGCTGCTGCTGCTG 59.862 57.895 27.67 26.32 40.48 4.41
3722 4088 6.634837 TGTAAATTTGTCTGTACATTGTTGCG 59.365 34.615 0.00 0.00 34.97 4.85
3805 4175 5.955961 TCATCAATCCCATGTTACTCTCA 57.044 39.130 0.00 0.00 0.00 3.27
3807 4177 6.528321 TCATCAATCCCATGTTACTCTCATC 58.472 40.000 0.00 0.00 0.00 2.92
3816 4186 3.818387 TGTTACTCTCATCACGTTCGTC 58.182 45.455 0.00 0.00 0.00 4.20
3820 4191 1.128878 CTCTCATCACGTTCGTCTCGT 59.871 52.381 0.00 0.00 42.33 4.18
3824 4195 1.930908 ATCACGTTCGTCTCGTCCCC 61.931 60.000 0.00 0.00 39.55 4.81
3879 4253 3.400054 GCGCCCCCTCCTTGTACT 61.400 66.667 0.00 0.00 0.00 2.73
3880 4254 2.062177 GCGCCCCCTCCTTGTACTA 61.062 63.158 0.00 0.00 0.00 1.82
3881 4255 1.408453 GCGCCCCCTCCTTGTACTAT 61.408 60.000 0.00 0.00 0.00 2.12
3894 4268 1.228769 TACTATGCCCGGATCCGCT 60.229 57.895 29.12 14.37 38.24 5.52
3896 4270 1.669115 CTATGCCCGGATCCGCTTG 60.669 63.158 29.12 18.90 38.24 4.01
4010 4395 4.505808 TCATGCTTGCACCCAAAATTATG 58.494 39.130 0.00 0.00 0.00 1.90
4027 4412 4.668576 TTATGCTTTCTTTCACTGCTCG 57.331 40.909 0.00 0.00 0.00 5.03
4035 4420 0.881118 TTTCACTGCTCGGCATTTCC 59.119 50.000 0.00 0.00 38.13 3.13
4051 4436 4.270008 CATTTCCGGGTATGAAAAGGACT 58.730 43.478 0.00 0.00 35.52 3.85
4061 4446 6.318900 GGGTATGAAAAGGACTCCATTTGTAG 59.681 42.308 2.96 0.00 0.00 2.74
4088 4512 2.040278 AGGCTGGGGTGAGGAGAG 59.960 66.667 0.00 0.00 0.00 3.20
4156 4580 4.464947 AGAAGGAGAAGAAAGTGTTTGGG 58.535 43.478 0.00 0.00 0.00 4.12
4157 4581 3.953542 AGGAGAAGAAAGTGTTTGGGT 57.046 42.857 0.00 0.00 0.00 4.51
4158 4582 3.555966 AGGAGAAGAAAGTGTTTGGGTG 58.444 45.455 0.00 0.00 0.00 4.61
4196 4624 3.496131 CACGAAATGACGGGGGCG 61.496 66.667 0.00 0.00 37.61 6.13
4298 4749 2.585869 GCTGTCACCGTGTCGTGTG 61.586 63.158 0.00 0.00 35.18 3.82
4299 4750 1.949133 CTGTCACCGTGTCGTGTGG 60.949 63.158 0.00 0.00 35.18 4.17
4300 4751 2.105528 GTCACCGTGTCGTGTGGT 59.894 61.111 0.00 0.00 35.18 4.16
4302 4753 2.202824 CACCGTGTCGTGTGGTGT 60.203 61.111 2.51 0.00 46.36 4.16
4303 4754 2.105528 ACCGTGTCGTGTGGTGTC 59.894 61.111 0.00 0.00 33.91 3.67
4304 4755 3.028019 CCGTGTCGTGTGGTGTCG 61.028 66.667 0.00 0.00 0.00 4.35
4305 4756 3.688330 CGTGTCGTGTGGTGTCGC 61.688 66.667 0.00 0.00 0.00 5.19
4306 4757 3.688330 GTGTCGTGTGGTGTCGCG 61.688 66.667 0.00 0.00 41.75 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.062962 CCAAATTAGGAGGCCCATGGT 60.063 52.381 11.73 0.00 33.88 3.55
9 10 2.025887 AGTCACTGGGCCAAATTAGGAG 60.026 50.000 8.04 0.00 0.00 3.69
25 26 0.611714 ACCCCATGTCGGTTAGTCAC 59.388 55.000 0.00 0.00 0.00 3.67
29 30 0.462047 GAGCACCCCATGTCGGTTAG 60.462 60.000 0.00 0.00 0.00 2.34
30 31 1.600107 GAGCACCCCATGTCGGTTA 59.400 57.895 0.00 0.00 0.00 2.85
66 67 2.668457 GTCACTCATCACGTCATGTTCC 59.332 50.000 0.00 0.00 0.00 3.62
70 71 1.645034 GGGTCACTCATCACGTCATG 58.355 55.000 0.00 0.00 0.00 3.07
72 73 1.541310 GGGGGTCACTCATCACGTCA 61.541 60.000 0.00 0.00 0.00 4.35
75 76 0.253044 ATTGGGGGTCACTCATCACG 59.747 55.000 0.00 0.00 0.00 4.35
99 100 0.999406 CGAGCACCTTGACGGTAATG 59.001 55.000 0.00 0.00 46.94 1.90
101 102 1.290955 CCGAGCACCTTGACGGTAA 59.709 57.895 0.00 0.00 46.94 2.85
137 138 2.787473 TTGCCATCTCCTCGACAAAT 57.213 45.000 0.00 0.00 0.00 2.32
142 143 2.483013 CGGTATTTTGCCATCTCCTCGA 60.483 50.000 0.00 0.00 0.00 4.04
146 147 2.222027 CTCCGGTATTTTGCCATCTCC 58.778 52.381 0.00 0.00 0.00 3.71
151 152 3.055021 TGTGATACTCCGGTATTTTGCCA 60.055 43.478 0.00 0.00 38.60 4.92
152 153 3.537580 TGTGATACTCCGGTATTTTGCC 58.462 45.455 0.00 0.00 38.60 4.52
153 154 5.554822 TTTGTGATACTCCGGTATTTTGC 57.445 39.130 0.00 0.00 38.60 3.68
162 163 6.851222 AAATCATAGCTTTGTGATACTCCG 57.149 37.500 4.00 0.00 34.14 4.63
188 189 7.274904 GTGTCTGCGTATCTACTATGTTTGAAA 59.725 37.037 0.00 0.00 0.00 2.69
189 190 6.750501 GTGTCTGCGTATCTACTATGTTTGAA 59.249 38.462 0.00 0.00 0.00 2.69
190 191 6.095021 AGTGTCTGCGTATCTACTATGTTTGA 59.905 38.462 0.00 0.00 0.00 2.69
197 198 6.285990 TGTATGAGTGTCTGCGTATCTACTA 58.714 40.000 0.00 0.00 0.00 1.82
204 205 3.547413 GCGTATGTATGAGTGTCTGCGTA 60.547 47.826 0.00 0.00 0.00 4.42
206 207 1.781429 GCGTATGTATGAGTGTCTGCG 59.219 52.381 0.00 0.00 0.00 5.18
208 209 3.769536 TGTGCGTATGTATGAGTGTCTG 58.230 45.455 0.00 0.00 0.00 3.51
212 213 5.748630 AGTGTATTGTGCGTATGTATGAGTG 59.251 40.000 0.00 0.00 0.00 3.51
213 214 5.902681 AGTGTATTGTGCGTATGTATGAGT 58.097 37.500 0.00 0.00 0.00 3.41
222 223 2.764010 AGGGATGAGTGTATTGTGCGTA 59.236 45.455 0.00 0.00 0.00 4.42
225 226 4.960938 TCATAGGGATGAGTGTATTGTGC 58.039 43.478 0.00 0.00 37.15 4.57
226 227 6.258727 GTGTTCATAGGGATGAGTGTATTGTG 59.741 42.308 0.00 0.00 43.03 3.33
227 228 6.070251 TGTGTTCATAGGGATGAGTGTATTGT 60.070 38.462 0.00 0.00 43.03 2.71
228 229 6.258727 GTGTGTTCATAGGGATGAGTGTATTG 59.741 42.308 0.00 0.00 43.03 1.90
229 230 6.070251 TGTGTGTTCATAGGGATGAGTGTATT 60.070 38.462 0.00 0.00 43.03 1.89
239 240 4.284746 TGTGTATGTGTGTGTTCATAGGGA 59.715 41.667 0.00 0.00 0.00 4.20
241 242 6.741992 AATGTGTATGTGTGTGTTCATAGG 57.258 37.500 0.00 0.00 0.00 2.57
249 250 8.702163 TCATAAGAGTAATGTGTATGTGTGTG 57.298 34.615 0.00 0.00 0.00 3.82
252 254 7.492669 GTGCTCATAAGAGTAATGTGTATGTGT 59.507 37.037 0.00 0.00 44.00 3.72
256 258 9.319143 GAAAGTGCTCATAAGAGTAATGTGTAT 57.681 33.333 0.00 0.00 44.00 2.29
257 259 7.488150 CGAAAGTGCTCATAAGAGTAATGTGTA 59.512 37.037 0.00 0.00 44.00 2.90
262 264 7.067615 TCTCTCGAAAGTGCTCATAAGAGTAAT 59.932 37.037 0.00 0.00 44.00 1.89
279 281 2.095364 GTGCCGTCTAAGTCTCTCGAAA 60.095 50.000 0.00 0.00 0.00 3.46
280 282 1.467734 GTGCCGTCTAAGTCTCTCGAA 59.532 52.381 0.00 0.00 0.00 3.71
288 290 3.195610 TCAAGATGATGTGCCGTCTAAGT 59.804 43.478 0.00 0.00 32.48 2.24
291 293 3.023832 TCTCAAGATGATGTGCCGTCTA 58.976 45.455 0.00 0.00 32.48 2.59
294 296 2.941064 CAATCTCAAGATGATGTGCCGT 59.059 45.455 0.00 0.00 34.49 5.68
318 320 0.935196 AAGGTGTTTGCGACGACTTC 59.065 50.000 0.00 0.00 0.00 3.01
320 322 0.179094 TGAAGGTGTTTGCGACGACT 60.179 50.000 0.00 0.00 0.00 4.18
321 323 0.865769 ATGAAGGTGTTTGCGACGAC 59.134 50.000 0.00 0.00 0.00 4.34
327 329 3.063997 CCATCGACTATGAAGGTGTTTGC 59.936 47.826 0.00 0.00 37.86 3.68
333 335 4.819105 TGTTTCCATCGACTATGAAGGT 57.181 40.909 0.00 0.00 37.86 3.50
345 347 7.604164 TGTTTAGTGAGAGAAGATGTTTCCATC 59.396 37.037 0.00 0.00 46.56 3.51
347 349 6.706270 GTGTTTAGTGAGAGAAGATGTTTCCA 59.294 38.462 0.00 0.00 0.00 3.53
349 351 7.224753 TGTGTGTTTAGTGAGAGAAGATGTTTC 59.775 37.037 0.00 0.00 0.00 2.78
356 358 5.223382 ACGATGTGTGTTTAGTGAGAGAAG 58.777 41.667 0.00 0.00 0.00 2.85
362 364 3.629438 TCGACGATGTGTGTTTAGTGA 57.371 42.857 0.00 0.00 0.00 3.41
397 399 7.472543 GCATTGGTGATCGTACTTTTCTTAAT 58.527 34.615 0.00 0.00 0.00 1.40
400 402 4.142902 CGCATTGGTGATCGTACTTTTCTT 60.143 41.667 0.00 0.00 0.00 2.52
407 409 2.268298 ACTTCGCATTGGTGATCGTAC 58.732 47.619 0.00 0.00 32.68 3.67
409 411 1.066858 AGACTTCGCATTGGTGATCGT 60.067 47.619 0.00 0.00 32.68 3.73
411 413 4.268884 GTCTTAGACTTCGCATTGGTGATC 59.731 45.833 4.94 0.00 32.68 2.92
413 415 3.258372 AGTCTTAGACTTCGCATTGGTGA 59.742 43.478 9.37 0.00 40.28 4.02
423 425 7.541244 CCGTCACGGTTTAAGTCTTAGACTTC 61.541 46.154 28.14 15.56 44.28 3.01
428 430 3.248266 CCCGTCACGGTTTAAGTCTTAG 58.752 50.000 16.87 0.00 46.80 2.18
437 439 1.077572 AACCAACCCGTCACGGTTT 60.078 52.632 16.87 3.66 43.88 3.27
456 458 0.320374 TGGCTAGTTCCTTGTGACGG 59.680 55.000 0.00 0.00 0.00 4.79
457 459 2.271800 GATGGCTAGTTCCTTGTGACG 58.728 52.381 0.00 0.00 0.00 4.35
472 474 1.141019 TGAGCGTAGTTCGGATGGC 59.859 57.895 0.00 0.00 42.00 4.40
479 481 0.708918 GTGCGAAGTGAGCGTAGTTC 59.291 55.000 0.00 1.97 38.58 3.01
480 482 1.002250 CGTGCGAAGTGAGCGTAGTT 61.002 55.000 0.00 0.00 37.44 2.24
481 483 1.442184 CGTGCGAAGTGAGCGTAGT 60.442 57.895 0.00 0.00 37.44 2.73
482 484 0.728129 TTCGTGCGAAGTGAGCGTAG 60.728 55.000 2.65 0.00 37.44 3.51
483 485 0.728129 CTTCGTGCGAAGTGAGCGTA 60.728 55.000 21.85 0.00 44.65 4.42
484 486 2.016704 CTTCGTGCGAAGTGAGCGT 61.017 57.895 21.85 0.00 44.65 5.07
485 487 2.765785 CTTCGTGCGAAGTGAGCG 59.234 61.111 21.85 1.24 44.65 5.03
499 501 5.852282 TGGGGCTTTAAATTCATAGCTTC 57.148 39.130 0.00 0.00 34.16 3.86
502 504 8.421002 TCTAATTTGGGGCTTTAAATTCATAGC 58.579 33.333 9.09 0.00 37.57 2.97
543 545 8.994429 TCCGTTTAAAAATGCATTGATTACAT 57.006 26.923 13.82 0.00 0.00 2.29
555 557 6.685403 CGTATTACTGCCTCCGTTTAAAAATG 59.315 38.462 0.00 0.00 0.00 2.32
561 563 2.166050 TGCGTATTACTGCCTCCGTTTA 59.834 45.455 7.75 0.00 0.00 2.01
583 676 0.034059 GCGGAGGTATCATCAGTGGG 59.966 60.000 0.00 0.00 0.00 4.61
584 677 0.034059 GGCGGAGGTATCATCAGTGG 59.966 60.000 0.00 0.00 0.00 4.00
588 681 1.744320 CGGTGGCGGAGGTATCATCA 61.744 60.000 0.00 0.00 0.00 3.07
590 683 1.745320 GACGGTGGCGGAGGTATCAT 61.745 60.000 0.00 0.00 0.00 2.45
613 706 0.036164 TGTGTCGGGGTGGAAATGAG 59.964 55.000 0.00 0.00 0.00 2.90
683 776 3.388308 TGCAACGGATTTGTTCCAATTG 58.612 40.909 0.00 0.00 45.78 2.32
751 844 1.511768 GAAGAGGAGAACCGGACCG 59.488 63.158 9.46 6.99 41.83 4.79
752 845 1.898885 GGAAGAGGAGAACCGGACC 59.101 63.158 9.46 6.01 41.83 4.46
753 846 1.511768 CGGAAGAGGAGAACCGGAC 59.488 63.158 9.46 0.99 41.41 4.79
754 847 4.013702 CGGAAGAGGAGAACCGGA 57.986 61.111 9.46 0.00 41.41 5.14
791 884 2.430244 CAGCTTTGCTTGCGGCTG 60.430 61.111 15.76 15.76 44.45 4.85
792 885 3.677648 CCAGCTTTGCTTGCGGCT 61.678 61.111 0.00 2.78 42.39 5.52
794 887 4.729856 GGCCAGCTTTGCTTGCGG 62.730 66.667 0.00 0.72 46.30 5.69
795 888 3.621892 GAGGCCAGCTTTGCTTGCG 62.622 63.158 5.01 0.00 46.30 4.85
796 889 2.260743 GAGGCCAGCTTTGCTTGC 59.739 61.111 5.01 7.03 44.92 4.01
797 890 2.643232 GGGAGGCCAGCTTTGCTTG 61.643 63.158 5.01 0.00 36.40 4.01
798 891 2.283460 GGGAGGCCAGCTTTGCTT 60.283 61.111 5.01 0.00 36.40 3.91
799 892 4.372999 GGGGAGGCCAGCTTTGCT 62.373 66.667 5.01 0.00 40.77 3.91
800 893 4.684134 TGGGGAGGCCAGCTTTGC 62.684 66.667 5.01 0.00 0.00 3.68
801 894 2.677875 GTGGGGAGGCCAGCTTTG 60.678 66.667 5.01 0.00 0.00 2.77
860 953 0.326713 GGGGAGGGGAGATATAGGGC 60.327 65.000 0.00 0.00 0.00 5.19
872 965 1.279749 GGACTAGGGTTTGGGGAGGG 61.280 65.000 0.00 0.00 0.00 4.30
920 1014 2.123640 GGGAGAGAGACGGAGGGG 60.124 72.222 0.00 0.00 0.00 4.79
921 1015 2.123640 GGGGAGAGAGACGGAGGG 60.124 72.222 0.00 0.00 0.00 4.30
930 1024 1.619975 AGAGACGGAGGGGGAGAGA 60.620 63.158 0.00 0.00 0.00 3.10
934 1028 2.691779 GGAGAGAGACGGAGGGGGA 61.692 68.421 0.00 0.00 0.00 4.81
936 1030 2.123640 GGGAGAGAGACGGAGGGG 60.124 72.222 0.00 0.00 0.00 4.79
943 1044 0.324275 ACAGAGCAGGGGAGAGAGAC 60.324 60.000 0.00 0.00 0.00 3.36
952 1053 2.847327 TGAAGAAAGACAGAGCAGGG 57.153 50.000 0.00 0.00 0.00 4.45
1227 1343 3.429960 CGATCAGCTCCTTGAACTCATCA 60.430 47.826 0.00 0.00 35.85 3.07
1230 1346 1.895798 ACGATCAGCTCCTTGAACTCA 59.104 47.619 0.00 0.00 0.00 3.41
1532 1819 4.101448 CCTCCTCGGCCTTGGGTG 62.101 72.222 0.00 0.91 0.00 4.61
1872 2177 1.219393 CTTCTCCAGCTCCGGGAAC 59.781 63.158 0.00 0.00 33.11 3.62
2242 2547 6.555315 CAGCTGTGAAATTGGAAATACTACC 58.445 40.000 5.25 0.00 0.00 3.18
2243 2548 6.030228 GCAGCTGTGAAATTGGAAATACTAC 58.970 40.000 16.64 0.00 0.00 2.73
2245 2550 4.523943 TGCAGCTGTGAAATTGGAAATACT 59.476 37.500 16.64 0.00 0.00 2.12
2246 2551 4.808558 TGCAGCTGTGAAATTGGAAATAC 58.191 39.130 16.64 0.00 0.00 1.89
2247 2552 4.618927 GCTGCAGCTGTGAAATTGGAAATA 60.619 41.667 31.33 0.00 38.21 1.40
2249 2554 2.546373 GCTGCAGCTGTGAAATTGGAAA 60.546 45.455 31.33 0.00 38.21 3.13
2251 2556 0.599558 GCTGCAGCTGTGAAATTGGA 59.400 50.000 31.33 0.00 38.21 3.53
2252 2557 0.315886 TGCTGCAGCTGTGAAATTGG 59.684 50.000 36.61 0.00 42.66 3.16
2253 2558 1.698165 CTGCTGCAGCTGTGAAATTG 58.302 50.000 36.61 12.99 42.66 2.32
2297 2602 4.475028 CACAGCTAAATTTCGATGCACAA 58.525 39.130 7.77 0.00 0.00 3.33
2300 2605 2.159393 GCCACAGCTAAATTTCGATGCA 60.159 45.455 7.77 0.00 35.50 3.96
2319 2624 1.234615 TTCGGCACAAACAGCTAGCC 61.235 55.000 12.13 0.00 41.86 3.93
2377 2682 1.473677 CGCTTTGGGCTCAATCATTCA 59.526 47.619 0.00 0.00 39.13 2.57
2397 2702 1.008538 CGCAGTGCCCAAAGAACAC 60.009 57.895 10.11 0.00 34.48 3.32
2424 2729 7.869429 ACTCAAATTTGAAAGCATAAAGGTCTG 59.131 33.333 20.82 6.82 36.64 3.51
2487 2792 2.555757 GCTATGATGATGACCAAAGCCC 59.444 50.000 0.00 0.00 0.00 5.19
2488 2793 2.225019 CGCTATGATGATGACCAAAGCC 59.775 50.000 0.00 0.00 0.00 4.35
2489 2794 2.350197 GCGCTATGATGATGACCAAAGC 60.350 50.000 0.00 0.00 0.00 3.51
2490 2795 2.096565 CGCGCTATGATGATGACCAAAG 60.097 50.000 5.56 0.00 0.00 2.77
2497 2802 2.159612 CCCAATTCGCGCTATGATGATG 60.160 50.000 5.56 0.00 0.00 3.07
2509 2814 2.871182 GGAAAAGATCCCCAATTCGC 57.129 50.000 0.00 0.00 43.00 4.70
2534 2839 5.238583 ACTCAGAATTGGGAAAAGTACGAG 58.761 41.667 0.00 0.00 0.00 4.18
2537 2842 6.635030 ACAACTCAGAATTGGGAAAAGTAC 57.365 37.500 0.00 0.00 0.00 2.73
2577 2901 6.877322 ACTACTGCAATTAACTACGAATTGGT 59.123 34.615 9.46 0.00 42.20 3.67
2582 2906 9.480053 ACTTAAACTACTGCAATTAACTACGAA 57.520 29.630 0.00 0.00 0.00 3.85
2584 2908 8.166706 CCACTTAAACTACTGCAATTAACTACG 58.833 37.037 0.00 0.00 0.00 3.51
2595 2919 6.374333 TGATCCAATTCCACTTAAACTACTGC 59.626 38.462 0.00 0.00 0.00 4.40
2614 2938 4.079844 TGATCCAGCCAAACTTATGATCCA 60.080 41.667 0.00 0.00 29.90 3.41
2630 2954 3.400255 CTGCATAGACACCATGATCCAG 58.600 50.000 0.00 0.00 0.00 3.86
2644 2968 3.002791 ACGTTGATGAACACCTGCATAG 58.997 45.455 0.00 0.00 31.78 2.23
2681 3005 2.613691 CTCATCATTTTGTTGGCAGCC 58.386 47.619 3.66 3.66 0.00 4.85
2798 3122 9.311916 CAATCCAACAATGAAAACTGAAACTTA 57.688 29.630 0.00 0.00 0.00 2.24
2801 3125 6.421405 GCAATCCAACAATGAAAACTGAAAC 58.579 36.000 0.00 0.00 0.00 2.78
2802 3126 5.526846 GGCAATCCAACAATGAAAACTGAAA 59.473 36.000 0.00 0.00 0.00 2.69
2806 3130 3.320541 TCGGCAATCCAACAATGAAAACT 59.679 39.130 0.00 0.00 0.00 2.66
2812 3136 0.457035 CCCTCGGCAATCCAACAATG 59.543 55.000 0.00 0.00 0.00 2.82
2823 3149 0.465705 GAGAACATGATCCCTCGGCA 59.534 55.000 0.00 0.00 0.00 5.69
2825 3151 1.539929 GCTGAGAACATGATCCCTCGG 60.540 57.143 0.00 6.32 35.66 4.63
2844 3179 7.421530 TTTGTTACAGAAGATGAACACTAGC 57.578 36.000 0.00 0.00 32.38 3.42
2862 3197 5.963004 GCGCGATGTATCTGAATTTTTGTTA 59.037 36.000 12.10 0.00 0.00 2.41
2866 3201 3.243068 GGGCGCGATGTATCTGAATTTTT 60.243 43.478 12.10 0.00 0.00 1.94
2888 3223 2.521958 ATTGGACGGGGACTTGCTCG 62.522 60.000 0.00 0.00 0.00 5.03
2994 3329 0.249657 GTGACAGGGATCTCGATGGC 60.250 60.000 0.00 0.00 0.00 4.40
2999 3334 1.729470 CCTCGGTGACAGGGATCTCG 61.729 65.000 0.00 0.00 0.00 4.04
3021 3356 6.987992 CACCAATTTATAATGCAAATGAGGCT 59.012 34.615 0.00 0.00 30.34 4.58
3024 3374 8.908678 CGATCACCAATTTATAATGCAAATGAG 58.091 33.333 0.00 0.00 0.00 2.90
3029 3379 6.389830 AGCGATCACCAATTTATAATGCAA 57.610 33.333 0.00 0.00 0.00 4.08
3030 3380 6.389830 AAGCGATCACCAATTTATAATGCA 57.610 33.333 0.00 0.00 0.00 3.96
3031 3381 8.236586 TCATAAGCGATCACCAATTTATAATGC 58.763 33.333 0.00 0.00 0.00 3.56
3036 3386 8.299570 GGAATTCATAAGCGATCACCAATTTAT 58.700 33.333 7.93 0.00 0.00 1.40
3037 3387 7.502226 AGGAATTCATAAGCGATCACCAATTTA 59.498 33.333 7.93 0.00 0.00 1.40
3038 3388 6.322201 AGGAATTCATAAGCGATCACCAATTT 59.678 34.615 7.93 0.00 0.00 1.82
3039 3389 5.829924 AGGAATTCATAAGCGATCACCAATT 59.170 36.000 7.93 0.00 0.00 2.32
3040 3390 5.380043 AGGAATTCATAAGCGATCACCAAT 58.620 37.500 7.93 0.00 0.00 3.16
3041 3391 4.780815 AGGAATTCATAAGCGATCACCAA 58.219 39.130 7.93 0.00 0.00 3.67
3042 3392 4.101585 AGAGGAATTCATAAGCGATCACCA 59.898 41.667 7.93 0.00 0.00 4.17
3043 3393 4.636249 AGAGGAATTCATAAGCGATCACC 58.364 43.478 7.93 0.00 0.00 4.02
3047 3397 6.233434 TGCATTAGAGGAATTCATAAGCGAT 58.767 36.000 7.93 0.00 0.00 4.58
3049 3399 5.929697 TGCATTAGAGGAATTCATAAGCG 57.070 39.130 7.93 1.28 0.00 4.68
3073 3423 9.820229 GACAATTATGTAAGTTTTGAACGATCA 57.180 29.630 0.00 0.00 40.74 2.92
3084 3434 5.296780 CGGCAGATGGACAATTATGTAAGTT 59.703 40.000 0.00 0.00 40.74 2.66
3090 3440 3.378112 ACAACGGCAGATGGACAATTATG 59.622 43.478 0.00 0.00 0.00 1.90
3108 3458 6.183360 CCCATACAATCGTTGAGTTCTACAAC 60.183 42.308 0.00 0.00 42.54 3.32
3207 3557 0.452184 TCCTCGTCTTCTGCACGATC 59.548 55.000 0.00 0.00 44.90 3.69
3373 3723 1.411977 CATGGACTGTAGGCCTCAGAG 59.588 57.143 28.29 17.85 36.81 3.35
3387 3737 1.656818 CCAATGGCGGTGTCATGGAC 61.657 60.000 0.00 0.00 0.00 4.02
3388 3738 1.378382 CCAATGGCGGTGTCATGGA 60.378 57.895 0.00 0.00 0.00 3.41
3389 3739 1.378382 TCCAATGGCGGTGTCATGG 60.378 57.895 0.00 0.00 0.00 3.66
3390 3740 0.677731 ACTCCAATGGCGGTGTCATG 60.678 55.000 0.00 0.00 0.00 3.07
3391 3741 0.392998 GACTCCAATGGCGGTGTCAT 60.393 55.000 0.00 0.00 45.04 3.06
3392 3742 1.003839 GACTCCAATGGCGGTGTCA 60.004 57.895 0.00 0.00 45.04 3.58
3393 3743 1.003839 TGACTCCAATGGCGGTGTC 60.004 57.895 0.00 5.44 45.62 3.67
3394 3744 1.003355 CTGACTCCAATGGCGGTGT 60.003 57.895 0.00 0.00 35.50 4.16
3395 3745 1.003355 ACTGACTCCAATGGCGGTG 60.003 57.895 0.00 0.00 0.00 4.94
3399 3749 1.077429 GGGGACTGACTCCAATGGC 60.077 63.158 0.00 0.00 41.63 4.40
3417 3767 9.184062 CTTCTTCTTCTTCTTCTATCATCATCG 57.816 37.037 0.00 0.00 0.00 3.84
3471 3821 7.307101 CCACAAAACCAATGGAATTAAAGAACG 60.307 37.037 6.16 0.00 32.46 3.95
3582 3932 0.842467 ACCCAACCTTCCTCTCCCAG 60.842 60.000 0.00 0.00 0.00 4.45
3600 3950 9.224267 GATGCCATTATATCATCCATACCATAC 57.776 37.037 0.00 0.00 32.60 2.39
3606 3956 8.046107 TCAAACGATGCCATTATATCATCCATA 58.954 33.333 0.00 0.00 34.63 2.74
3629 3981 2.746279 ACCCTCAACACAACCATCAA 57.254 45.000 0.00 0.00 0.00 2.57
3630 3982 2.039746 CCTACCCTCAACACAACCATCA 59.960 50.000 0.00 0.00 0.00 3.07
3631 3983 2.618045 CCCTACCCTCAACACAACCATC 60.618 54.545 0.00 0.00 0.00 3.51
3632 3984 1.354368 CCCTACCCTCAACACAACCAT 59.646 52.381 0.00 0.00 0.00 3.55
3633 3985 0.768622 CCCTACCCTCAACACAACCA 59.231 55.000 0.00 0.00 0.00 3.67
3634 3986 0.608308 GCCCTACCCTCAACACAACC 60.608 60.000 0.00 0.00 0.00 3.77
3635 3987 0.109723 TGCCCTACCCTCAACACAAC 59.890 55.000 0.00 0.00 0.00 3.32
3636 3988 0.400213 CTGCCCTACCCTCAACACAA 59.600 55.000 0.00 0.00 0.00 3.33
3637 3989 0.472925 TCTGCCCTACCCTCAACACA 60.473 55.000 0.00 0.00 0.00 3.72
3638 3990 0.250513 CTCTGCCCTACCCTCAACAC 59.749 60.000 0.00 0.00 0.00 3.32
3690 4056 4.756084 ACAGACAAATTTACAGAGCAGC 57.244 40.909 0.00 0.00 0.00 5.25
3691 4057 6.785488 TGTACAGACAAATTTACAGAGCAG 57.215 37.500 0.00 0.00 30.68 4.24
3692 4058 7.228507 ACAATGTACAGACAAATTTACAGAGCA 59.771 33.333 0.33 0.00 39.59 4.26
3693 4059 7.584987 ACAATGTACAGACAAATTTACAGAGC 58.415 34.615 0.33 0.00 39.59 4.09
3694 4060 9.385902 CAACAATGTACAGACAAATTTACAGAG 57.614 33.333 0.33 0.00 39.59 3.35
3695 4061 7.860373 GCAACAATGTACAGACAAATTTACAGA 59.140 33.333 0.33 0.00 39.59 3.41
3805 4175 1.505353 GGGACGAGACGAACGTGAT 59.495 57.895 4.19 0.00 43.97 3.06
3807 4177 2.126580 GGGGACGAGACGAACGTG 60.127 66.667 4.19 0.00 43.97 4.49
3816 4186 2.513897 GCGGAAATGGGGGACGAG 60.514 66.667 0.00 0.00 0.00 4.18
3820 4191 4.440829 GGCAGCGGAAATGGGGGA 62.441 66.667 0.00 0.00 0.00 4.81
3824 4195 0.962356 ACAAGAGGCAGCGGAAATGG 60.962 55.000 0.00 0.00 0.00 3.16
3879 4253 2.425592 CAAGCGGATCCGGGCATA 59.574 61.111 33.98 0.00 40.19 3.14
3880 4254 4.569180 CCAAGCGGATCCGGGCAT 62.569 66.667 33.98 9.94 40.19 4.40
3894 4268 1.193462 CCTTGCTGGAAATGGGCCAA 61.193 55.000 11.89 0.00 38.35 4.52
3896 4270 3.022710 GCCTTGCTGGAAATGGGCC 62.023 63.158 0.00 0.00 38.35 5.80
3924 4298 0.381089 AACTTCGCTACCGATCCTCG 59.619 55.000 0.00 0.00 43.97 4.63
3929 4303 3.118884 ACACCAATAACTTCGCTACCGAT 60.119 43.478 0.00 0.00 43.97 4.18
3934 4308 2.027561 AGCCACACCAATAACTTCGCTA 60.028 45.455 0.00 0.00 0.00 4.26
4010 4395 0.110010 GCCGAGCAGTGAAAGAAAGC 60.110 55.000 0.00 0.00 0.00 3.51
4027 4412 2.100749 CCTTTTCATACCCGGAAATGCC 59.899 50.000 0.73 0.00 34.50 4.40
4035 4420 3.560636 ATGGAGTCCTTTTCATACCCG 57.439 47.619 11.33 0.00 0.00 5.28
4039 4424 8.044908 GGTACTACAAATGGAGTCCTTTTCATA 58.955 37.037 17.83 12.87 30.10 2.15
4051 4436 2.238646 CTGCCCAGGTACTACAAATGGA 59.761 50.000 0.00 0.00 36.02 3.41
4073 4497 1.194781 TGTTCTCTCCTCACCCCAGC 61.195 60.000 0.00 0.00 0.00 4.85
4079 4503 1.016653 GCCGCTTGTTCTCTCCTCAC 61.017 60.000 0.00 0.00 0.00 3.51
4088 4512 3.314388 CTCTTGCCGCCGCTTGTTC 62.314 63.158 0.00 0.00 35.36 3.18
4115 4539 0.748005 TTAATTCCGCCTGCAGCCTC 60.748 55.000 8.66 0.00 38.78 4.70
4127 4551 7.987750 ACACTTTCTTCTCCTTCTTAATTCC 57.012 36.000 0.00 0.00 0.00 3.01
4156 4580 2.592993 TACAGTGGCAGGGGAGCAC 61.593 63.158 0.00 0.00 35.83 4.40
4157 4581 2.203922 TACAGTGGCAGGGGAGCA 60.204 61.111 0.00 0.00 35.83 4.26
4158 4582 2.269241 GTACAGTGGCAGGGGAGC 59.731 66.667 0.00 0.00 0.00 4.70
4189 4617 0.179103 ACGATTAGTTTACGCCCCCG 60.179 55.000 0.00 0.00 41.14 5.73
4196 4624 3.615224 TCCCACCCACGATTAGTTTAC 57.385 47.619 0.00 0.00 0.00 2.01
4300 4751 4.912485 TTGTTTCGGGGCGCGACA 62.912 61.111 26.78 19.32 0.00 4.35
4301 4752 4.379143 GTTGTTTCGGGGCGCGAC 62.379 66.667 26.78 16.85 0.00 5.19


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

AutoCloner maintained by Alex Coulton.