Multiple sequence alignment - TraesCS5B01G158500

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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 TraesCS5B01G158500 chr5B 100.000 8872 0 0 1001 9872 292479649 292488520 0.000000e+00 16384.0
1 TraesCS5B01G158500 chr5B 100.000 564 0 0 1 564 292478649 292479212 0.000000e+00 1042.0
2 TraesCS5B01G158500 chr5D 96.171 7939 200 39 1001 8889 258249862 258257746 0.000000e+00 12881.0
3 TraesCS5B01G158500 chr5D 93.097 565 23 5 1 560 258248850 258249403 0.000000e+00 813.0
4 TraesCS5B01G158500 chr5D 86.538 416 41 11 7165 7567 511950730 511950317 2.530000e-120 444.0
5 TraesCS5B01G158500 chr5D 89.500 200 4 1 9263 9445 258258569 258258768 4.610000e-58 237.0
6 TraesCS5B01G158500 chr5D 92.000 150 10 2 9153 9302 258258423 258258570 1.000000e-49 209.0
7 TraesCS5B01G158500 chr5D 92.857 140 10 0 9015 9154 258258169 258258308 4.670000e-48 204.0
8 TraesCS5B01G158500 chr5A 97.013 7533 148 21 1001 8485 343069595 343062092 0.000000e+00 12593.0
9 TraesCS5B01G158500 chr5A 93.853 423 20 4 8513 8932 343062094 343061675 5.030000e-177 632.0
10 TraesCS5B01G158500 chr5A 83.948 461 20 17 9039 9445 343054107 343053647 9.300000e-105 392.0
11 TraesCS5B01G158500 chr5A 91.289 287 13 3 282 560 343069986 343069704 2.010000e-101 381.0
12 TraesCS5B01G158500 chr5A 91.336 277 22 2 4 280 343070358 343070084 2.600000e-100 377.0
13 TraesCS5B01G158500 chr5A 93.077 260 9 3 9622 9872 343053404 343053145 1.210000e-98 372.0
14 TraesCS5B01G158500 chr5A 88.265 196 21 2 4 198 343070859 343070665 5.960000e-57 233.0
15 TraesCS5B01G158500 chr5A 86.772 189 24 1 10 198 343071352 343071165 1.000000e-49 209.0
16 TraesCS5B01G158500 chr5A 94.118 102 4 2 9773 9872 343053425 343053324 4.770000e-33 154.0
17 TraesCS5B01G158500 chr5A 77.934 213 40 6 3973 4181 701567260 701567469 1.040000e-24 126.0
18 TraesCS5B01G158500 chr4A 76.767 1429 288 30 4295 5699 584666855 584665447 0.000000e+00 760.0
19 TraesCS5B01G158500 chr4A 79.681 502 86 11 6437 6930 584664826 584664333 2.040000e-91 348.0
20 TraesCS5B01G158500 chr4A 82.479 234 35 6 2503 2733 584668487 584668257 6.050000e-47 200.0
21 TraesCS5B01G158500 chr4A 82.927 82 11 2 9015 9093 140767205 140767286 4.950000e-08 71.3
22 TraesCS5B01G158500 chr4D 76.201 1416 298 25 4310 5699 16101969 16100567 0.000000e+00 712.0
23 TraesCS5B01G158500 chr4D 78.947 513 85 16 6437 6938 16099928 16099428 2.660000e-85 327.0
24 TraesCS5B01G158500 chr4D 82.759 232 34 6 2505 2733 16103455 16103227 1.680000e-47 202.0
25 TraesCS5B01G158500 chr3A 86.779 416 30 9 7165 7569 427763977 427763576 3.270000e-119 440.0
26 TraesCS5B01G158500 chr3A 100.000 28 0 0 385 412 403634524 403634551 1.800000e-02 52.8
27 TraesCS5B01G158500 chr2B 86.232 414 44 8 7165 7567 96104735 96104324 4.230000e-118 436.0
28 TraesCS5B01G158500 chr2B 78.748 527 92 13 6437 6954 99498845 99498330 1.590000e-87 335.0
29 TraesCS5B01G158500 chr2B 82.456 228 34 6 2509 2733 99502245 99502021 2.810000e-45 195.0
30 TraesCS5B01G158500 chr7B 85.442 419 45 11 7164 7568 384192491 384192075 1.190000e-113 422.0
31 TraesCS5B01G158500 chr6B 85.507 414 41 15 7165 7567 68294706 68295111 1.980000e-111 414.0
32 TraesCS5B01G158500 chr1B 84.988 413 42 14 7165 7564 365446848 365447253 1.540000e-107 401.0
33 TraesCS5B01G158500 chr1B 84.706 85 10 3 9012 9093 135242000 135242084 2.290000e-11 82.4
34 TraesCS5B01G158500 chr2D 84.615 416 45 10 7165 7567 61343334 61342925 7.190000e-106 396.0
35 TraesCS5B01G158500 chr2D 100.000 29 0 0 384 412 484907139 484907111 5.000000e-03 54.7
36 TraesCS5B01G158500 chr4B 83.333 234 33 6 2503 2733 27531311 27531541 2.790000e-50 211.0
37 TraesCS5B01G158500 chrUn 79.812 213 36 5 3973 4181 111043396 111043605 2.220000e-31 148.0
38 TraesCS5B01G158500 chr3B 100.000 28 0 0 385 412 398961247 398961274 1.800000e-02 52.8


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 TraesCS5B01G158500 chr5B 292478649 292488520 9871 False 8713.000000 16384 100.000000 1 9872 2 chr5B.!!$F1 9871
1 TraesCS5B01G158500 chr5D 258248850 258258768 9918 False 2868.800000 12881 92.725000 1 9445 5 chr5D.!!$F1 9444
2 TraesCS5B01G158500 chr5A 343061675 343071352 9677 True 2404.166667 12593 91.421333 4 8932 6 chr5A.!!$R2 8928
3 TraesCS5B01G158500 chr5A 343053145 343054107 962 True 306.000000 392 90.381000 9039 9872 3 chr5A.!!$R1 833
4 TraesCS5B01G158500 chr4A 584664333 584668487 4154 True 436.000000 760 79.642333 2503 6930 3 chr4A.!!$R1 4427
5 TraesCS5B01G158500 chr4D 16099428 16103455 4027 True 413.666667 712 79.302333 2505 6938 3 chr4D.!!$R1 4433
6 TraesCS5B01G158500 chr2B 99498330 99502245 3915 True 265.000000 335 80.602000 2509 6954 2 chr2B.!!$R2 4445

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
90 581 0.679002 ATCAATTGGCGCAGTGCTCT 60.679 50.000 14.33 0.0 45.43 4.09 F
1055 2169 0.833287 CCATTCCTCACGATCCCAGT 59.167 55.000 0.00 0.0 0.00 4.00 F
1862 2976 0.771755 ACCCACCCAAAGTTCCTCTC 59.228 55.000 0.00 0.0 0.00 3.20 F
2813 3937 1.937191 AGTTACATTTGGGGCCCTTG 58.063 50.000 25.93 20.1 0.00 3.61 F
3528 5296 0.688487 TGTAAACACCCCGCTAAGCT 59.312 50.000 0.00 0.0 0.00 3.74 F
3704 5472 0.948678 GGCAAACCTGTTCGTGCTAA 59.051 50.000 6.64 0.0 37.17 3.09 F
5412 7225 0.464373 CCAATCCTGATGGTCCACCG 60.464 60.000 0.00 0.0 39.43 4.94 F
5724 7543 1.666011 GCTGAACTCGTGGGACTCA 59.334 57.895 0.00 0.0 0.00 3.41 F
5864 7683 1.799383 GCAGCAGCTTACTTGAGCC 59.201 57.895 0.00 0.0 43.74 4.70 F
7425 9285 0.663153 GCCACGGATACATTTCCTGC 59.337 55.000 0.00 0.0 33.30 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 2758 0.391927 CTTCGAATGGCCGGGTAACA 60.392 55.000 2.18 0.0 39.74 2.41 R
2920 4096 3.356290 AGGTGGCATAACTTGATTGACC 58.644 45.455 0.00 0.0 0.00 4.02 R
3104 4293 0.250553 CCAAACGGGCCTACAGACAA 60.251 55.000 0.84 0.0 0.00 3.18 R
4578 6376 2.158097 AGGAAGGAGCATAGCCTGGATA 60.158 50.000 0.00 0.0 35.50 2.59 R
5380 7190 0.034670 GGATTGGAAGGTGCTCTGCT 60.035 55.000 0.00 0.0 0.00 4.24 R
5630 7449 1.339631 TGGTTTGGTTATCAGCCCTCG 60.340 52.381 0.00 0.0 0.00 4.63 R
6266 8118 0.040067 GTTCAACGCAGCCTTTCTGG 60.040 55.000 0.00 0.0 43.06 3.86 R
6971 8826 1.097547 CCCGCTGTCATTTGCCCTAG 61.098 60.000 0.00 0.0 0.00 3.02 R
7633 9501 1.342374 ACCAAATGCCTGGATCCTTCC 60.342 52.381 14.23 1.2 42.94 3.46 R
8914 10793 0.038890 GCTTCTCCTCCCTGGCTTTT 59.961 55.000 0.00 0.0 35.26 2.27 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
43 534 6.458615 GGTTATGTGAAACTAAACGTTGGTGT 60.459 38.462 0.00 0.00 38.04 4.16
57 548 2.495669 GTTGGTGTTGGGTTGGATATGG 59.504 50.000 0.00 0.00 0.00 2.74
60 551 2.958355 GGTGTTGGGTTGGATATGGATG 59.042 50.000 0.00 0.00 0.00 3.51
90 581 0.679002 ATCAATTGGCGCAGTGCTCT 60.679 50.000 14.33 0.00 45.43 4.09
237 1229 5.421277 AGCAAGACTGAGATCAATTCTGAG 58.579 41.667 0.00 0.00 41.10 3.35
253 1245 1.272490 CTGAGAGCGTGGAGGTGTTTA 59.728 52.381 0.00 0.00 0.00 2.01
280 1272 5.831702 AAATTAGATGGCAGCTCTTCTTG 57.168 39.130 9.31 0.00 0.00 3.02
284 1372 2.239150 AGATGGCAGCTCTTCTTGTCAT 59.761 45.455 0.00 0.00 0.00 3.06
346 1434 5.681494 TGGATAGATTCTACCCCTAGTGT 57.319 43.478 1.38 0.00 0.00 3.55
364 1457 3.264193 AGTGTGATCATCCCAAGTAAGCA 59.736 43.478 0.00 0.00 0.00 3.91
417 1510 7.175641 AGGAGGAGATGATTGTAAAAACAACAG 59.824 37.037 0.00 0.00 31.89 3.16
418 1511 7.174946 GGAGGAGATGATTGTAAAAACAACAGA 59.825 37.037 0.00 0.00 31.89 3.41
499 1595 2.371510 CAGAGAATCCCCTCCAATCTCC 59.628 54.545 0.00 0.00 37.77 3.71
500 1596 1.702401 GAGAATCCCCTCCAATCTCCC 59.298 57.143 0.00 0.00 32.30 4.30
501 1597 1.299629 AGAATCCCCTCCAATCTCCCT 59.700 52.381 0.00 0.00 0.00 4.20
502 1598 1.702401 GAATCCCCTCCAATCTCCCTC 59.298 57.143 0.00 0.00 0.00 4.30
560 1656 1.902508 TCAGTCCACCATCACTCTTCC 59.097 52.381 0.00 0.00 0.00 3.46
561 1657 1.065854 CAGTCCACCATCACTCTTCCC 60.066 57.143 0.00 0.00 0.00 3.97
1024 2138 3.844090 GTCCTGCTCCGCTCCTCC 61.844 72.222 0.00 0.00 0.00 4.30
1055 2169 0.833287 CCATTCCTCACGATCCCAGT 59.167 55.000 0.00 0.00 0.00 4.00
1120 2234 2.678580 TCCCCGTCACGCAGATCA 60.679 61.111 0.00 0.00 0.00 2.92
1258 2372 2.683933 TCCCTGGGAGCCGAAGAC 60.684 66.667 12.53 0.00 0.00 3.01
1515 2629 2.033299 CCTTCTTCGTCTTGCTTTGCAA 59.967 45.455 0.00 0.00 46.80 4.08
1609 2723 5.300286 ACAATAGCTCCCATGTAATCAAAGC 59.700 40.000 0.00 0.00 0.00 3.51
1612 2726 3.201708 AGCTCCCATGTAATCAAAGCTCT 59.798 43.478 0.00 0.00 33.57 4.09
1789 2903 1.609208 ACTTGAGCAAAATCACGCCT 58.391 45.000 0.00 0.00 0.00 5.52
1862 2976 0.771755 ACCCACCCAAAGTTCCTCTC 59.228 55.000 0.00 0.00 0.00 3.20
1916 3030 4.690748 TCAGCTCTTTCTAAATGTTGTCCG 59.309 41.667 0.00 0.00 0.00 4.79
1997 3121 9.330063 CCTTTATTGTTCTGTATCATTCAGCTA 57.670 33.333 0.00 0.00 33.48 3.32
2327 3451 9.125026 GATGTTTGGTTATTTCAGATATCAGGT 57.875 33.333 5.32 0.00 0.00 4.00
2387 3511 2.684881 CCTTGTCACAGGCATATGGTTC 59.315 50.000 4.56 0.00 0.00 3.62
2465 3589 2.851263 AAACTGCATCCCGTACAAGA 57.149 45.000 0.00 0.00 0.00 3.02
2784 3908 7.824779 GGTCACTTGAAAGATATTCAGGTAGTT 59.175 37.037 5.76 0.00 36.75 2.24
2813 3937 1.937191 AGTTACATTTGGGGCCCTTG 58.063 50.000 25.93 20.10 0.00 3.61
2815 3939 2.044353 AGTTACATTTGGGGCCCTTGAT 59.956 45.455 25.93 12.00 0.00 2.57
2816 3940 2.837591 GTTACATTTGGGGCCCTTGATT 59.162 45.455 25.93 7.98 0.00 2.57
2817 3941 2.043307 ACATTTGGGGCCCTTGATTT 57.957 45.000 25.93 5.20 0.00 2.17
2818 3942 2.347500 ACATTTGGGGCCCTTGATTTT 58.653 42.857 25.93 0.00 0.00 1.82
2819 3943 2.715880 ACATTTGGGGCCCTTGATTTTT 59.284 40.909 25.93 0.00 0.00 1.94
2920 4096 6.847400 TGGTGTTTACGACATTCCATATTTG 58.153 36.000 0.00 0.00 41.10 2.32
3054 4243 3.030291 TGTTGGAATTCTTGGTGTGCTT 58.970 40.909 5.23 0.00 0.00 3.91
3069 4258 5.527951 GGTGTGCTTGTTTCACATCAATAA 58.472 37.500 1.92 0.00 44.96 1.40
3104 4293 5.362430 TCCATTGGAAGTTTTTAAGTGCAGT 59.638 36.000 1.94 0.00 0.00 4.40
3250 4439 9.832445 AGACTTTTAAGTTACAGATTTCTCACA 57.168 29.630 0.00 0.00 39.88 3.58
3303 4501 4.159321 AGCTTCGTACCCTAAAACTAGGTC 59.841 45.833 0.00 0.00 35.45 3.85
3304 4502 4.679106 GCTTCGTACCCTAAAACTAGGTCC 60.679 50.000 0.00 0.00 35.45 4.46
3329 4527 4.346709 TCAGATCCACCTTGAGTTTGTACA 59.653 41.667 0.00 0.00 0.00 2.90
3330 4528 4.452455 CAGATCCACCTTGAGTTTGTACAC 59.548 45.833 0.00 0.00 0.00 2.90
3369 4570 1.799157 TAGGTTGGCCCATGCAAGGT 61.799 55.000 7.29 0.00 40.13 3.50
3395 4596 7.008021 TGTATATACCCCTTTTCCGGTAATC 57.992 40.000 10.38 0.00 38.12 1.75
3397 4598 0.986527 ACCCCTTTTCCGGTAATCGT 59.013 50.000 0.00 0.00 37.11 3.73
3521 5289 3.947910 TCTTAGTCTGTAAACACCCCG 57.052 47.619 0.00 0.00 0.00 5.73
3528 5296 0.688487 TGTAAACACCCCGCTAAGCT 59.312 50.000 0.00 0.00 0.00 3.74
3574 5342 5.995282 CCTTGTTACCAGTGATGACTTTGTA 59.005 40.000 0.00 0.00 0.00 2.41
3704 5472 0.948678 GGCAAACCTGTTCGTGCTAA 59.051 50.000 6.64 0.00 37.17 3.09
3834 5602 7.993183 CCCTATGTGGTTATGACTTTGACTTAT 59.007 37.037 0.00 0.00 0.00 1.73
3870 5638 8.954950 AATTCATCATGTTTTTGGTGTTTACA 57.045 26.923 0.00 0.00 0.00 2.41
4151 5946 2.497675 TGATACACTGCTCCTGACCTTC 59.502 50.000 0.00 0.00 0.00 3.46
4182 5977 4.093743 TGTAGAGCTAATGAACCAGGTCA 58.906 43.478 0.00 0.00 40.85 4.02
4193 5988 1.343069 ACCAGGTCAGTGTCTTCCTC 58.657 55.000 0.00 0.00 0.00 3.71
4239 6034 8.918202 TTTAAGTTTTGTATCTGACATGTCCT 57.082 30.769 22.85 10.22 38.07 3.85
4809 6607 3.532542 GAGCCCTGTTGTACTTCCATAC 58.467 50.000 0.00 0.00 0.00 2.39
4903 6704 5.049198 TCTGCAAGTAATGAAGCTGAAACTG 60.049 40.000 0.00 0.00 34.27 3.16
5380 7190 3.557898 GGAACATGAGAAGTCTGCTGGAA 60.558 47.826 0.00 0.00 0.00 3.53
5412 7225 0.464373 CCAATCCTGATGGTCCACCG 60.464 60.000 0.00 0.00 39.43 4.94
5576 7395 5.824904 AAGCTTACACAAGATGCTAATGG 57.175 39.130 0.00 0.00 33.20 3.16
5724 7543 1.666011 GCTGAACTCGTGGGACTCA 59.334 57.895 0.00 0.00 0.00 3.41
5864 7683 1.799383 GCAGCAGCTTACTTGAGCC 59.201 57.895 0.00 0.00 43.74 4.70
5918 7737 6.753180 TGCCATCTTACTCTGATAATCAGTC 58.247 40.000 0.00 0.00 44.58 3.51
6047 7872 9.218525 TCCTAGGTCATCTGAATATTCTTTTCT 57.781 33.333 16.24 7.45 0.00 2.52
6350 8202 3.710677 AGTAAGCTGGCATCTGAGAGATT 59.289 43.478 0.00 0.00 31.32 2.40
6360 8212 7.157347 TGGCATCTGAGAGATTACAATATGTC 58.843 38.462 0.00 0.00 31.32 3.06
6448 8300 3.944015 AGATGTCCTTTCTATGCAGTTGC 59.056 43.478 0.00 0.00 42.50 4.17
6888 8743 3.307059 CCCTTGTGGAAAGTAGACCAGAG 60.307 52.174 0.00 0.00 36.82 3.35
6909 8764 3.014623 GCTTTGGGGGAAGTACACATAC 58.985 50.000 0.00 0.00 0.00 2.39
7006 8862 2.592308 GGAAAGGCTCCCGCTGAT 59.408 61.111 0.00 0.00 38.44 2.90
7007 8863 1.077429 GGAAAGGCTCCCGCTGATT 60.077 57.895 0.00 0.00 38.44 2.57
7425 9285 0.663153 GCCACGGATACATTTCCTGC 59.337 55.000 0.00 0.00 33.30 4.85
7435 9295 7.134815 CGGATACATTTCCTGCTATTTTTCTG 58.865 38.462 0.00 0.00 33.30 3.02
7633 9501 2.493278 CAAAATGTGGCTACCCCTGAAG 59.507 50.000 0.00 0.00 0.00 3.02
7803 9671 3.475566 TGCTATGCTGTTGGGAGTATC 57.524 47.619 0.00 0.00 0.00 2.24
7928 9796 2.662006 TCTCAACTTGGCATCTCTCG 57.338 50.000 0.00 0.00 0.00 4.04
8005 9879 2.754552 TGGATTGTTAGATTGTGCTGCC 59.245 45.455 0.00 0.00 0.00 4.85
8172 10047 4.483243 ATAACAGGCCCGGGTGCG 62.483 66.667 24.63 13.07 0.00 5.34
8202 10077 0.109342 CTGGCACCTTCACCACTTCT 59.891 55.000 0.00 0.00 0.00 2.85
8208 10083 1.572085 CCTTCACCACTTCTGCTGCG 61.572 60.000 0.00 0.00 0.00 5.18
8520 10395 1.070601 CTTGACCTTTTTGGGCCCTTG 59.929 52.381 25.70 8.17 45.70 3.61
8571 10446 3.624777 CAAGGATGATGCAGGGTAAACT 58.375 45.455 0.00 0.00 0.00 2.66
8709 10588 6.464222 CCATGTGACTTTGTAGAGAGGTTAA 58.536 40.000 0.00 0.00 0.00 2.01
8772 10651 2.118313 TGTGATGCTTCTGGACATGG 57.882 50.000 0.00 0.00 0.00 3.66
8787 10666 4.141436 TGGACATGGATGAGATGCAATGTA 60.141 41.667 0.00 0.00 33.18 2.29
8865 10744 5.348986 CGCCCTGTGCTATATATATCGTTT 58.651 41.667 0.00 0.00 38.05 3.60
8873 10752 7.330946 TGTGCTATATATATCGTTTGGCTGTTC 59.669 37.037 0.00 0.00 0.00 3.18
8878 10757 8.902540 ATATATATCGTTTGGCTGTTCTTTGA 57.097 30.769 0.00 0.00 0.00 2.69
8914 10793 0.405198 TGGAGGCCAAAATCAGCAGA 59.595 50.000 5.01 0.00 0.00 4.26
8917 10796 2.299867 GGAGGCCAAAATCAGCAGAAAA 59.700 45.455 5.01 0.00 0.00 2.29
8927 10806 0.964358 CAGCAGAAAAGCCAGGGAGG 60.964 60.000 0.00 0.00 41.84 4.30
8932 10811 1.632920 AGAAAAGCCAGGGAGGAGAAG 59.367 52.381 0.00 0.00 41.22 2.85
8933 10812 0.038890 AAAAGCCAGGGAGGAGAAGC 59.961 55.000 0.00 0.00 41.22 3.86
8935 10814 1.560866 AAGCCAGGGAGGAGAAGCAG 61.561 60.000 0.00 0.00 41.22 4.24
8936 10815 3.041469 GCCAGGGAGGAGAAGCAGG 62.041 68.421 0.00 0.00 41.22 4.85
8938 10817 3.080121 AGGGAGGAGAAGCAGGCG 61.080 66.667 0.00 0.00 0.00 5.52
8956 10835 4.476410 CTCGCGTGCTGCCGTAGA 62.476 66.667 5.77 9.96 42.08 2.59
8958 10837 4.778415 CGCGTGCTGCCGTAGACT 62.778 66.667 0.00 0.00 42.08 3.24
8959 10838 2.432628 GCGTGCTGCCGTAGACTT 60.433 61.111 11.14 0.00 37.76 3.01
8960 10839 1.153901 GCGTGCTGCCGTAGACTTA 60.154 57.895 11.14 0.00 37.76 2.24
8961 10840 1.411493 GCGTGCTGCCGTAGACTTAC 61.411 60.000 11.14 0.00 37.76 2.34
8962 10841 0.801067 CGTGCTGCCGTAGACTTACC 60.801 60.000 0.00 0.00 0.00 2.85
8963 10842 0.801067 GTGCTGCCGTAGACTTACCG 60.801 60.000 0.00 0.00 0.00 4.02
8965 10844 1.585521 CTGCCGTAGACTTACCGCG 60.586 63.158 0.00 0.00 36.99 6.46
8966 10845 2.953303 GCCGTAGACTTACCGCGC 60.953 66.667 0.00 0.00 0.00 6.86
8967 10846 2.649975 CCGTAGACTTACCGCGCG 60.650 66.667 25.67 25.67 0.00 6.86
8968 10847 2.099062 CGTAGACTTACCGCGCGT 59.901 61.111 29.95 18.85 0.00 6.01
8970 10849 1.870901 GTAGACTTACCGCGCGTGG 60.871 63.158 35.76 35.76 0.00 4.94
8971 10850 3.688475 TAGACTTACCGCGCGTGGC 62.688 63.158 37.13 20.94 38.69 5.01
8980 10859 4.228097 GCGCGTGGCTGTGCTATG 62.228 66.667 8.43 0.00 42.01 2.23
8981 10860 4.228097 CGCGTGGCTGTGCTATGC 62.228 66.667 9.53 9.53 46.11 3.14
8983 10862 1.521457 GCGTGGCTGTGCTATGCTA 60.521 57.895 11.82 0.00 46.09 3.49
8985 10864 0.179100 CGTGGCTGTGCTATGCTAGT 60.179 55.000 0.00 0.00 0.00 2.57
8987 10866 1.667724 GTGGCTGTGCTATGCTAGTTG 59.332 52.381 0.00 0.00 0.00 3.16
8989 10868 2.290260 TGGCTGTGCTATGCTAGTTGTT 60.290 45.455 0.00 0.00 0.00 2.83
8990 10869 2.096496 GGCTGTGCTATGCTAGTTGTTG 59.904 50.000 0.00 0.00 0.00 3.33
8993 10872 4.715896 CTGTGCTATGCTAGTTGTTGTTG 58.284 43.478 0.00 0.00 0.00 3.33
8994 10873 3.058293 TGTGCTATGCTAGTTGTTGTTGC 60.058 43.478 0.00 0.00 0.00 4.17
8995 10874 2.487762 TGCTATGCTAGTTGTTGTTGCC 59.512 45.455 0.00 0.00 0.00 4.52
8996 10875 2.749621 GCTATGCTAGTTGTTGTTGCCT 59.250 45.455 0.00 0.00 0.00 4.75
8998 10877 3.648339 ATGCTAGTTGTTGTTGCCTTG 57.352 42.857 0.00 0.00 0.00 3.61
8999 10878 2.374184 TGCTAGTTGTTGTTGCCTTGT 58.626 42.857 0.00 0.00 0.00 3.16
9000 10879 2.757868 TGCTAGTTGTTGTTGCCTTGTT 59.242 40.909 0.00 0.00 0.00 2.83
9001 10880 3.181491 TGCTAGTTGTTGTTGCCTTGTTC 60.181 43.478 0.00 0.00 0.00 3.18
9002 10881 2.959507 AGTTGTTGTTGCCTTGTTCC 57.040 45.000 0.00 0.00 0.00 3.62
9003 10882 2.456577 AGTTGTTGTTGCCTTGTTCCT 58.543 42.857 0.00 0.00 0.00 3.36
9007 10886 1.136891 GTTGTTGCCTTGTTCCTGCTT 59.863 47.619 0.00 0.00 0.00 3.91
9010 10889 2.622942 TGTTGCCTTGTTCCTGCTTAAG 59.377 45.455 0.00 0.00 0.00 1.85
9011 10890 2.623416 GTTGCCTTGTTCCTGCTTAAGT 59.377 45.455 4.02 0.00 0.00 2.24
9013 10892 1.541588 GCCTTGTTCCTGCTTAAGTGG 59.458 52.381 4.02 7.27 0.00 4.00
9072 11248 0.584396 TCGTTGCTTTGTGTTAGGCG 59.416 50.000 0.00 0.00 0.00 5.52
9176 11466 1.739466 CCATGCGTGTGCTTCAACTAT 59.261 47.619 4.96 0.00 43.34 2.12
9254 11544 4.012374 TCATTGTTTCTCCCTGATGCTTC 58.988 43.478 0.00 0.00 0.00 3.86
9259 11549 4.187694 GTTTCTCCCTGATGCTTCTACTG 58.812 47.826 0.88 0.00 0.00 2.74
9440 11793 3.365868 GCATGACTTTGTCGGCATACAAA 60.366 43.478 13.29 13.29 44.81 2.83
9445 11798 2.645730 TTGTCGGCATACAAAATGGC 57.354 45.000 0.00 1.73 36.45 4.40
9446 11799 1.832883 TGTCGGCATACAAAATGGCT 58.167 45.000 9.47 0.00 41.72 4.75
9447 11800 2.166829 TGTCGGCATACAAAATGGCTT 58.833 42.857 9.47 0.00 41.72 4.35
9448 11801 2.163412 TGTCGGCATACAAAATGGCTTC 59.837 45.455 9.47 3.80 41.72 3.86
9449 11802 2.163412 GTCGGCATACAAAATGGCTTCA 59.837 45.455 9.47 0.00 41.72 3.02
9450 11803 3.023119 TCGGCATACAAAATGGCTTCAT 58.977 40.909 9.47 0.00 41.72 2.57
9471 11848 1.211457 GGTCCTCTCAATGGATGCACT 59.789 52.381 0.00 0.00 35.87 4.40
9473 11850 1.487976 TCCTCTCAATGGATGCACTCC 59.512 52.381 7.90 7.90 45.19 3.85
9474 11851 1.476471 CCTCTCAATGGATGCACTCCC 60.476 57.143 11.25 4.14 44.23 4.30
9475 11852 1.489649 CTCTCAATGGATGCACTCCCT 59.510 52.381 11.25 1.25 44.23 4.20
9476 11853 1.487976 TCTCAATGGATGCACTCCCTC 59.512 52.381 11.25 0.00 44.23 4.30
9479 11856 0.467384 AATGGATGCACTCCCTCTCG 59.533 55.000 11.25 0.00 44.23 4.04
9480 11857 0.689080 ATGGATGCACTCCCTCTCGT 60.689 55.000 11.25 0.00 44.23 4.18
9481 11858 1.142748 GGATGCACTCCCTCTCGTG 59.857 63.158 0.00 0.00 38.19 4.35
9485 11862 2.888863 CACTCCCTCTCGTGCTCC 59.111 66.667 0.00 0.00 0.00 4.70
9488 11865 2.680352 TCCCTCTCGTGCTCCACC 60.680 66.667 0.00 0.00 0.00 4.61
9489 11866 2.997315 CCCTCTCGTGCTCCACCA 60.997 66.667 0.00 0.00 0.00 4.17
9490 11867 2.362369 CCCTCTCGTGCTCCACCAT 61.362 63.158 0.00 0.00 0.00 3.55
9492 11869 0.742281 CCTCTCGTGCTCCACCATTG 60.742 60.000 0.00 0.00 0.00 2.82
9513 11890 2.784596 GCATCAGCGCTGCGTAAA 59.215 55.556 32.44 15.66 0.00 2.01
9514 11891 1.581147 GCATCAGCGCTGCGTAAAC 60.581 57.895 32.44 13.89 0.00 2.01
9515 11892 1.787215 CATCAGCGCTGCGTAAACA 59.213 52.632 32.44 14.05 0.00 2.83
9516 11893 0.374758 CATCAGCGCTGCGTAAACAT 59.625 50.000 32.44 15.83 0.00 2.71
9517 11894 1.592543 CATCAGCGCTGCGTAAACATA 59.407 47.619 32.44 12.44 0.00 2.29
9519 11896 2.070028 TCAGCGCTGCGTAAACATAAA 58.930 42.857 32.44 7.78 0.00 1.40
9523 11900 5.007234 TCAGCGCTGCGTAAACATAAATAAT 59.993 36.000 32.44 0.00 0.00 1.28
9524 11901 5.336990 CAGCGCTGCGTAAACATAAATAATC 59.663 40.000 26.68 0.40 0.00 1.75
9525 11902 5.007234 AGCGCTGCGTAAACATAAATAATCA 59.993 36.000 24.04 0.00 0.00 2.57
9527 11904 5.619607 CGCTGCGTAAACATAAATAATCACC 59.380 40.000 14.93 0.00 0.00 4.02
9528 11905 5.619607 GCTGCGTAAACATAAATAATCACCG 59.380 40.000 0.00 0.00 0.00 4.94
9529 11906 6.510478 GCTGCGTAAACATAAATAATCACCGA 60.510 38.462 0.00 0.00 0.00 4.69
9530 11907 7.485418 TGCGTAAACATAAATAATCACCGAT 57.515 32.000 0.00 0.00 0.00 4.18
9531 11908 7.348956 TGCGTAAACATAAATAATCACCGATG 58.651 34.615 0.00 0.00 0.00 3.84
9532 11909 6.795114 GCGTAAACATAAATAATCACCGATGG 59.205 38.462 0.00 0.00 0.00 3.51
9533 11910 7.307514 GCGTAAACATAAATAATCACCGATGGA 60.308 37.037 0.00 0.00 0.00 3.41
9534 11911 8.552865 CGTAAACATAAATAATCACCGATGGAA 58.447 33.333 0.00 0.00 0.00 3.53
9557 11934 4.314740 TTTTTGGTAGTGCTTTGCGATT 57.685 36.364 0.00 0.00 0.00 3.34
9558 11935 5.440234 TTTTTGGTAGTGCTTTGCGATTA 57.560 34.783 0.00 0.00 0.00 1.75
9559 11936 4.413495 TTTGGTAGTGCTTTGCGATTAC 57.587 40.909 0.00 0.00 0.00 1.89
9579 11956 6.757897 TTACCATCGAAGAAAATTCTGCAT 57.242 33.333 2.21 0.00 43.58 3.96
9581 11958 6.029346 ACCATCGAAGAAAATTCTGCATTT 57.971 33.333 2.21 0.00 43.58 2.32
9584 11961 7.542130 ACCATCGAAGAAAATTCTGCATTTAAC 59.458 33.333 2.21 0.00 43.58 2.01
9585 11962 7.253420 CCATCGAAGAAAATTCTGCATTTAACG 60.253 37.037 2.21 0.00 43.58 3.18
9586 11963 6.893759 TCGAAGAAAATTCTGCATTTAACGA 58.106 32.000 2.21 0.00 37.65 3.85
9588 11965 7.858382 TCGAAGAAAATTCTGCATTTAACGAAA 59.142 29.630 2.21 0.00 37.65 3.46
9592 11969 9.528018 AGAAAATTCTGCATTTAACGAAAGAAA 57.472 25.926 0.00 0.00 33.60 2.52
9595 11972 9.474920 AAATTCTGCATTTAACGAAAGAAATGA 57.525 25.926 10.66 0.00 42.95 2.57
9596 11973 9.643693 AATTCTGCATTTAACGAAAGAAATGAT 57.356 25.926 10.66 0.00 42.95 2.45
9597 11974 9.643693 ATTCTGCATTTAACGAAAGAAATGATT 57.356 25.926 10.66 0.00 42.95 2.57
9598 11975 8.673626 TCTGCATTTAACGAAAGAAATGATTC 57.326 30.769 10.66 0.00 42.95 2.52
9599 11976 7.481483 TCTGCATTTAACGAAAGAAATGATTCG 59.519 33.333 10.66 6.38 42.95 3.34
9605 11982 5.456192 ACGAAAGAAATGATTCGTAGCTG 57.544 39.130 11.34 0.00 46.55 4.24
9606 11983 5.168569 ACGAAAGAAATGATTCGTAGCTGA 58.831 37.500 11.34 0.00 46.55 4.26
9607 11984 5.637810 ACGAAAGAAATGATTCGTAGCTGAA 59.362 36.000 11.34 0.00 46.55 3.02
9610 11987 8.328146 CGAAAGAAATGATTCGTAGCTGAAATA 58.672 33.333 0.00 0.00 40.63 1.40
9611 11988 9.988350 GAAAGAAATGATTCGTAGCTGAAATAA 57.012 29.630 0.00 0.00 40.63 1.40
9722 12182 9.950680 ATATACAAGCAAATTCTCCATTTAACG 57.049 29.630 0.00 0.00 32.90 3.18
9744 12204 3.317149 GGAAGCAATGATTCATAGCTGCA 59.683 43.478 19.00 0.00 35.42 4.41
9777 12237 5.331902 CGCCTTGTCATTCGAAATAAACAT 58.668 37.500 0.00 0.00 0.00 2.71
9864 12324 2.357009 GCATCGTCATGATTTGGAAGCT 59.643 45.455 0.00 0.00 34.13 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 508 5.589452 ACCAACGTTTAGTTTCACATAACCA 59.411 36.000 0.00 0.00 42.02 3.67
19 510 6.488817 ACACCAACGTTTAGTTTCACATAAC 58.511 36.000 0.00 0.00 42.02 1.89
43 534 2.244510 AGTGCATCCATATCCAACCCAA 59.755 45.455 0.00 0.00 0.00 4.12
57 548 4.303086 CAATTGATCCCTCAAGTGCATC 57.697 45.455 0.00 0.00 46.58 3.91
90 581 4.111255 TGAACTTCCAATTGTGATCCCA 57.889 40.909 4.43 0.00 0.00 4.37
237 1229 3.974871 TTTTTAAACACCTCCACGCTC 57.025 42.857 0.00 0.00 0.00 5.03
346 1434 8.439971 AGTAATATTGCTTACTTGGGATGATCA 58.560 33.333 0.00 0.00 38.49 2.92
499 1595 1.772156 GGGGAAGATGGGGGAGAGG 60.772 68.421 0.00 0.00 0.00 3.69
500 1596 2.143419 CGGGGAAGATGGGGGAGAG 61.143 68.421 0.00 0.00 0.00 3.20
501 1597 2.040884 CGGGGAAGATGGGGGAGA 60.041 66.667 0.00 0.00 0.00 3.71
502 1598 2.040884 TCGGGGAAGATGGGGGAG 60.041 66.667 0.00 0.00 0.00 4.30
1029 2143 2.124695 GTGAGGAATGGCGGGGAC 60.125 66.667 0.00 0.00 0.00 4.46
1120 2234 2.428890 GCACTAGACTAGCACATCCAGT 59.571 50.000 9.52 0.00 0.00 4.00
1515 2629 5.479306 TCGCTAGAGCTGTTTGAATAACTT 58.521 37.500 0.00 0.00 39.32 2.66
1644 2758 0.391927 CTTCGAATGGCCGGGTAACA 60.392 55.000 2.18 0.00 39.74 2.41
1970 3094 7.284034 AGCTGAATGATACAGAACAATAAAGGG 59.716 37.037 0.00 0.00 37.54 3.95
1997 3121 4.621460 CCGTAGAACGAATTCGATGCATAT 59.379 41.667 33.05 13.14 46.05 1.78
2327 3451 4.841246 ACAAGGTTAAACCCCATTGCAATA 59.159 37.500 12.53 0.00 39.75 1.90
2456 3580 5.941948 ATTTGAGAAGGTTTCTTGTACGG 57.058 39.130 0.00 0.00 40.87 4.02
2465 3589 5.298276 TGCACGTAAGAATTTGAGAAGGTTT 59.702 36.000 0.00 0.00 43.62 3.27
2729 3853 6.343703 ACAAGAAACACGGAAAGTACTTACT 58.656 36.000 8.92 0.00 38.39 2.24
2784 3908 4.221703 CCCCAAATGTAACTAATGCACCAA 59.778 41.667 0.00 0.00 0.00 3.67
2820 3944 9.567776 TGATATGGAACTGAAGACAAGTTTAAA 57.432 29.630 0.00 0.00 0.00 1.52
2821 3945 9.567776 TTGATATGGAACTGAAGACAAGTTTAA 57.432 29.630 0.00 0.00 0.00 1.52
2920 4096 3.356290 AGGTGGCATAACTTGATTGACC 58.644 45.455 0.00 0.00 0.00 4.02
3104 4293 0.250553 CCAAACGGGCCTACAGACAA 60.251 55.000 0.84 0.00 0.00 3.18
3303 4501 1.577736 ACTCAAGGTGGATCTGAGGG 58.422 55.000 12.14 0.00 0.00 4.30
3304 4502 3.244700 ACAAACTCAAGGTGGATCTGAGG 60.245 47.826 12.14 0.03 0.00 3.86
3329 4527 3.629087 AGACTAACAGGCCTATACACGT 58.371 45.455 3.98 0.00 0.00 4.49
3330 4528 4.215827 CCTAGACTAACAGGCCTATACACG 59.784 50.000 3.98 0.00 0.00 4.49
3369 4570 5.713760 ACCGGAAAAGGGGTATATACAAA 57.286 39.130 9.46 0.00 33.95 2.83
3395 4596 5.276868 GCTGTTCACAAGTATATGCCTAACG 60.277 44.000 0.00 0.00 0.00 3.18
3397 4598 5.584649 GTGCTGTTCACAAGTATATGCCTAA 59.415 40.000 0.00 0.00 44.98 2.69
3521 5289 8.684520 TCGGGATCTAAACTTATATAGCTTAGC 58.315 37.037 0.00 0.00 34.11 3.09
3528 5296 9.021807 CAAGGACTCGGGATCTAAACTTATATA 57.978 37.037 0.00 0.00 0.00 0.86
3574 5342 7.195374 ACAAACCACACCAGTATATCATACT 57.805 36.000 0.00 0.00 0.00 2.12
3834 5602 5.183530 ACATGATGAATTTCCAGACCTCA 57.816 39.130 0.00 0.00 0.00 3.86
4151 5946 6.037610 GGTTCATTAGCTCTACAACATCTTGG 59.962 42.308 0.00 0.00 0.00 3.61
4182 5977 4.083565 GGAACTACAGAGAGGAAGACACT 58.916 47.826 0.00 0.00 0.00 3.55
4578 6376 2.158097 AGGAAGGAGCATAGCCTGGATA 60.158 50.000 0.00 0.00 35.50 2.59
4809 6607 8.425577 AACATGAAATTAGGACGATAAGAGTG 57.574 34.615 0.00 0.00 0.00 3.51
4903 6704 3.445450 TGAGAGTGCATAGAGAACTCCAC 59.555 47.826 0.00 0.48 41.02 4.02
4932 6733 0.618458 GGTGAGTACTGCCCAATGGA 59.382 55.000 0.00 0.00 0.00 3.41
5380 7190 0.034670 GGATTGGAAGGTGCTCTGCT 60.035 55.000 0.00 0.00 0.00 4.24
5412 7225 2.567615 TCCCCTGCTGAAAGTAAGAGAC 59.432 50.000 0.00 0.00 35.30 3.36
5576 7395 8.761497 GTCCAAGCAAAAAGTTATACCTTTTTC 58.239 33.333 15.51 11.41 46.44 2.29
5630 7449 1.339631 TGGTTTGGTTATCAGCCCTCG 60.340 52.381 0.00 0.00 0.00 4.63
5706 7525 0.033504 TTGAGTCCCACGAGTTCAGC 59.966 55.000 0.00 0.00 0.00 4.26
5724 7543 4.081642 CGGATATCCTTATCACGGGACATT 60.082 45.833 19.61 0.00 36.68 2.71
5918 7737 5.417811 CATGAATAGTAGCAGGCTGATAGG 58.582 45.833 20.86 0.00 0.00 2.57
6047 7872 6.591001 TGCATAACAGGATCAGCATAGTTAA 58.409 36.000 0.00 0.00 0.00 2.01
6266 8118 0.040067 GTTCAACGCAGCCTTTCTGG 60.040 55.000 0.00 0.00 43.06 3.86
6350 8202 2.543031 GCTGCCGACTCGACATATTGTA 60.543 50.000 0.00 0.00 0.00 2.41
6360 8212 4.803426 GACCTGGCTGCCGACTCG 62.803 72.222 14.98 1.53 0.00 4.18
6448 8300 4.274950 GGATGTATTGTTGGGGTTCATACG 59.725 45.833 0.00 0.00 0.00 3.06
6888 8743 2.215942 ATGTGTACTTCCCCCAAAGC 57.784 50.000 0.00 0.00 0.00 3.51
6909 8764 1.269621 ACCTGAAGACGGTTCAGAACG 60.270 52.381 24.04 13.81 46.57 3.95
6971 8826 1.097547 CCCGCTGTCATTTGCCCTAG 61.098 60.000 0.00 0.00 0.00 3.02
7243 9101 7.601705 TTCATATCCCAAAATCCCAGATTTC 57.398 36.000 3.20 0.00 0.00 2.17
7324 9182 4.155826 TCTTTGTCTTTTATGCCACGGATG 59.844 41.667 0.00 0.00 0.00 3.51
7425 9285 7.962918 CCCGTATGAAGTTTCACAGAAAAATAG 59.037 37.037 0.00 0.00 40.49 1.73
7435 9295 5.320549 TCTACTCCCGTATGAAGTTTCAC 57.679 43.478 0.00 0.00 40.49 3.18
7633 9501 1.342374 ACCAAATGCCTGGATCCTTCC 60.342 52.381 14.23 1.20 42.94 3.46
7648 9516 4.009675 GCTACATGGATGAGTCAACCAAA 58.990 43.478 24.21 12.72 39.62 3.28
7803 9671 5.125900 TGGGTCACTTTATTTGCATCATCAG 59.874 40.000 0.00 0.00 0.00 2.90
7970 9844 7.112122 TCTAACAATCCAATACAACTGAGCAT 58.888 34.615 0.00 0.00 0.00 3.79
8005 9879 4.604114 TGCCTCTGCATTCTCACG 57.396 55.556 0.00 0.00 44.23 4.35
8202 10077 1.153765 CGTCTCCAAGATCGCAGCA 60.154 57.895 0.00 0.00 0.00 4.41
8208 10083 3.712187 GTCCTTGATCGTCTCCAAGATC 58.288 50.000 0.00 0.00 41.56 2.75
8375 10250 9.192642 ACCCTACAAAACAAGTAAAAACATACT 57.807 29.630 0.00 0.00 37.73 2.12
8498 10373 0.471022 GGGCCCAAAAAGGTCAAGGA 60.471 55.000 19.95 0.00 30.99 3.36
8571 10446 2.179764 GCTCAGGCGGCAAAACATA 58.820 52.632 13.08 0.00 0.00 2.29
8732 10611 4.280425 ACATTAACCATGCACATGTCAACA 59.720 37.500 9.63 0.00 36.14 3.33
8733 10612 4.622313 CACATTAACCATGCACATGTCAAC 59.378 41.667 9.63 0.00 36.14 3.18
8772 10651 5.925397 CAGGACTAGTACATTGCATCTCATC 59.075 44.000 8.10 0.00 0.00 2.92
8865 10744 2.542020 TCATCGTCAAAGAACAGCCA 57.458 45.000 0.00 0.00 0.00 4.75
8873 10752 4.319115 CACGAAGCAAATTCATCGTCAAAG 59.681 41.667 0.00 0.00 45.78 2.77
8914 10793 0.038890 GCTTCTCCTCCCTGGCTTTT 59.961 55.000 0.00 0.00 35.26 2.27
8917 10796 1.994507 CTGCTTCTCCTCCCTGGCT 60.995 63.158 0.00 0.00 35.26 4.75
8940 10819 4.771356 GTCTACGGCAGCACGCGA 62.771 66.667 15.93 0.00 43.84 5.87
8941 10820 2.860690 TAAGTCTACGGCAGCACGCG 62.861 60.000 3.53 3.53 43.84 6.01
8942 10821 1.153901 TAAGTCTACGGCAGCACGC 60.154 57.895 0.00 0.00 41.28 5.34
8946 10825 4.396854 CGGTAAGTCTACGGCAGC 57.603 61.111 0.00 0.00 0.00 5.25
8949 10828 2.953303 GCGCGGTAAGTCTACGGC 60.953 66.667 8.83 5.12 45.91 5.68
8950 10829 2.649975 CGCGCGGTAAGTCTACGG 60.650 66.667 24.84 0.00 0.00 4.02
8952 10831 1.870901 CCACGCGCGGTAAGTCTAC 60.871 63.158 35.22 0.00 0.00 2.59
8953 10832 2.486504 CCACGCGCGGTAAGTCTA 59.513 61.111 35.22 0.00 0.00 2.59
8963 10842 4.228097 CATAGCACAGCCACGCGC 62.228 66.667 5.73 0.00 37.98 6.86
8965 10844 1.493950 CTAGCATAGCACAGCCACGC 61.494 60.000 0.00 0.00 0.00 5.34
8966 10845 0.179100 ACTAGCATAGCACAGCCACG 60.179 55.000 0.00 0.00 44.39 4.94
8967 10846 1.667724 CAACTAGCATAGCACAGCCAC 59.332 52.381 0.00 0.00 44.39 5.01
8968 10847 1.278985 ACAACTAGCATAGCACAGCCA 59.721 47.619 0.00 0.00 44.39 4.75
8970 10849 2.744202 ACAACAACTAGCATAGCACAGC 59.256 45.455 0.00 0.00 44.39 4.40
8971 10850 4.715896 CAACAACAACTAGCATAGCACAG 58.284 43.478 0.00 0.00 44.39 3.66
8974 10853 2.487762 GGCAACAACAACTAGCATAGCA 59.512 45.455 0.00 0.00 44.39 3.49
8975 10854 2.749621 AGGCAACAACAACTAGCATAGC 59.250 45.455 0.00 0.00 40.90 2.97
8978 10857 2.958355 ACAAGGCAACAACAACTAGCAT 59.042 40.909 0.00 0.00 41.41 3.79
8979 10858 2.374184 ACAAGGCAACAACAACTAGCA 58.626 42.857 0.00 0.00 41.41 3.49
8980 10859 3.372060 GAACAAGGCAACAACAACTAGC 58.628 45.455 0.00 0.00 41.41 3.42
8981 10860 3.632145 AGGAACAAGGCAACAACAACTAG 59.368 43.478 0.00 0.00 41.41 2.57
8983 10862 2.166254 CAGGAACAAGGCAACAACAACT 59.834 45.455 0.00 0.00 41.41 3.16
8985 10864 1.134848 GCAGGAACAAGGCAACAACAA 60.135 47.619 0.00 0.00 41.41 2.83
8987 10866 0.746659 AGCAGGAACAAGGCAACAAC 59.253 50.000 0.00 0.00 41.41 3.32
8989 10868 2.356665 TAAGCAGGAACAAGGCAACA 57.643 45.000 0.00 0.00 41.41 3.33
8990 10869 2.623416 ACTTAAGCAGGAACAAGGCAAC 59.377 45.455 1.29 0.00 0.00 4.17
8993 10872 1.541588 CCACTTAAGCAGGAACAAGGC 59.458 52.381 8.51 0.00 0.00 4.35
8994 10873 3.140325 TCCACTTAAGCAGGAACAAGG 57.860 47.619 13.32 0.00 0.00 3.61
8995 10874 4.761739 TGATTCCACTTAAGCAGGAACAAG 59.238 41.667 24.40 0.00 43.60 3.16
8996 10875 4.724399 TGATTCCACTTAAGCAGGAACAA 58.276 39.130 24.40 16.06 43.60 2.83
8998 10877 5.705609 TTTGATTCCACTTAAGCAGGAAC 57.294 39.130 24.40 19.22 43.60 3.62
8999 10878 6.916360 AATTTGATTCCACTTAAGCAGGAA 57.084 33.333 24.22 24.22 44.77 3.36
9000 10879 6.721208 AGAAATTTGATTCCACTTAAGCAGGA 59.279 34.615 12.02 12.02 0.00 3.86
9001 10880 6.928520 AGAAATTTGATTCCACTTAAGCAGG 58.071 36.000 1.29 5.28 0.00 4.85
9002 10881 9.512435 CATAGAAATTTGATTCCACTTAAGCAG 57.488 33.333 1.29 0.00 0.00 4.24
9003 10882 7.975616 GCATAGAAATTTGATTCCACTTAAGCA 59.024 33.333 1.29 0.00 0.00 3.91
9007 10886 9.466497 AGAAGCATAGAAATTTGATTCCACTTA 57.534 29.630 0.00 0.00 38.65 2.24
9010 10889 8.897752 ACTAGAAGCATAGAAATTTGATTCCAC 58.102 33.333 0.00 0.00 38.65 4.02
9011 10890 8.896744 CACTAGAAGCATAGAAATTTGATTCCA 58.103 33.333 0.00 0.00 38.65 3.53
9013 10892 8.400947 TGCACTAGAAGCATAGAAATTTGATTC 58.599 33.333 9.91 0.00 38.26 2.52
9044 11220 2.409378 CACAAAGCAACGATTTGATGCC 59.591 45.455 11.30 0.00 46.76 4.40
9072 11248 6.319141 ACAAGAAATCAAAGTAGGAAGCAC 57.681 37.500 0.00 0.00 0.00 4.40
9154 11330 1.528076 TTGAAGCACACGCATGGGT 60.528 52.632 10.03 10.03 42.27 4.51
9155 11331 1.081242 GTTGAAGCACACGCATGGG 60.081 57.895 8.44 8.44 42.27 4.00
9156 11332 1.155889 TAGTTGAAGCACACGCATGG 58.844 50.000 0.00 0.00 42.27 3.66
9157 11333 3.165890 CAATAGTTGAAGCACACGCATG 58.834 45.455 0.00 0.00 42.27 4.06
9176 11466 0.318869 CAATGAAGCAACGCCAGCAA 60.319 50.000 0.00 0.00 0.00 3.91
9254 11544 7.360101 GGTTGTAGCACAAAATCTGTACAGTAG 60.360 40.741 21.99 10.98 40.15 2.57
9259 11549 4.378046 CGGGTTGTAGCACAAAATCTGTAC 60.378 45.833 3.74 0.00 40.15 2.90
9425 11778 2.560542 AGCCATTTTGTATGCCGACAAA 59.439 40.909 8.70 8.70 45.29 2.83
9440 11793 1.918262 TGAGAGGACCATGAAGCCATT 59.082 47.619 0.00 0.00 0.00 3.16
9445 11798 3.920231 TCCATTGAGAGGACCATGAAG 57.080 47.619 0.00 0.00 0.00 3.02
9446 11799 3.686405 GCATCCATTGAGAGGACCATGAA 60.686 47.826 0.00 0.00 38.13 2.57
9447 11800 2.158711 GCATCCATTGAGAGGACCATGA 60.159 50.000 0.00 0.00 38.13 3.07
9448 11801 2.228059 GCATCCATTGAGAGGACCATG 58.772 52.381 0.00 0.00 38.13 3.66
9449 11802 1.848388 TGCATCCATTGAGAGGACCAT 59.152 47.619 0.00 0.00 38.13 3.55
9450 11803 1.065199 GTGCATCCATTGAGAGGACCA 60.065 52.381 0.00 0.00 38.13 4.02
9471 11848 2.680352 GGTGGAGCACGAGAGGGA 60.680 66.667 0.00 0.00 35.60 4.20
9473 11850 0.742281 CAATGGTGGAGCACGAGAGG 60.742 60.000 0.00 0.00 34.83 3.69
9474 11851 2.759783 CAATGGTGGAGCACGAGAG 58.240 57.895 0.00 0.00 34.83 3.20
9484 11861 0.458669 GCTGATGCTTCCAATGGTGG 59.541 55.000 0.00 0.00 40.35 4.61
9485 11862 0.099968 CGCTGATGCTTCCAATGGTG 59.900 55.000 0.00 0.00 36.97 4.17
9488 11865 0.248498 CAGCGCTGATGCTTCCAATG 60.248 55.000 33.66 0.00 44.46 2.82
9489 11866 2.001361 GCAGCGCTGATGCTTCCAAT 62.001 55.000 40.21 0.00 44.46 3.16
9490 11867 2.693762 GCAGCGCTGATGCTTCCAA 61.694 57.895 40.21 0.00 44.46 3.53
9492 11869 4.233635 CGCAGCGCTGATGCTTCC 62.234 66.667 40.21 19.35 44.46 3.46
9494 11871 1.298157 TTTACGCAGCGCTGATGCTT 61.298 50.000 40.21 21.77 44.46 3.91
9496 11873 1.581147 GTTTACGCAGCGCTGATGC 60.581 57.895 40.21 24.97 41.89 3.91
9497 11874 0.374758 ATGTTTACGCAGCGCTGATG 59.625 50.000 40.21 30.86 0.00 3.07
9498 11875 1.934589 TATGTTTACGCAGCGCTGAT 58.065 45.000 40.21 27.86 0.00 2.90
9499 11876 1.715993 TTATGTTTACGCAGCGCTGA 58.284 45.000 40.21 17.93 0.00 4.26
9500 11877 2.519002 TTTATGTTTACGCAGCGCTG 57.481 45.000 32.83 32.83 0.00 5.18
9501 11878 4.868450 TTATTTATGTTTACGCAGCGCT 57.132 36.364 16.61 2.64 0.00 5.92
9503 11880 5.619607 GGTGATTATTTATGTTTACGCAGCG 59.380 40.000 14.82 14.82 0.00 5.18
9505 11882 6.939627 TCGGTGATTATTTATGTTTACGCAG 58.060 36.000 0.00 0.00 0.00 5.18
9506 11883 6.905544 TCGGTGATTATTTATGTTTACGCA 57.094 33.333 0.00 0.00 0.00 5.24
9507 11884 6.795114 CCATCGGTGATTATTTATGTTTACGC 59.205 38.462 0.00 0.00 0.00 4.42
9508 11885 8.078959 TCCATCGGTGATTATTTATGTTTACG 57.921 34.615 0.00 0.00 0.00 3.18
9536 11913 4.314740 AATCGCAAAGCACTACCAAAAA 57.685 36.364 0.00 0.00 0.00 1.94
9537 11914 4.320641 GGTAATCGCAAAGCACTACCAAAA 60.321 41.667 0.00 0.00 31.33 2.44
9538 11915 3.189702 GGTAATCGCAAAGCACTACCAAA 59.810 43.478 0.00 0.00 31.33 3.28
9539 11916 2.745281 GGTAATCGCAAAGCACTACCAA 59.255 45.455 0.00 0.00 31.33 3.67
9540 11917 2.289756 TGGTAATCGCAAAGCACTACCA 60.290 45.455 8.79 8.79 35.64 3.25
9541 11918 2.352388 TGGTAATCGCAAAGCACTACC 58.648 47.619 0.00 0.00 31.51 3.18
9542 11919 4.197107 GATGGTAATCGCAAAGCACTAC 57.803 45.455 0.00 0.00 0.00 2.73
9550 11927 7.886830 CAGAATTTTCTTCGATGGTAATCGCAA 60.887 37.037 3.30 0.00 44.45 4.85
9551 11928 6.456853 CAGAATTTTCTTCGATGGTAATCGCA 60.457 38.462 3.30 0.00 44.45 5.10
9552 11929 5.904080 CAGAATTTTCTTCGATGGTAATCGC 59.096 40.000 3.30 0.00 44.45 4.58
9553 11930 5.904080 GCAGAATTTTCTTCGATGGTAATCG 59.096 40.000 1.75 1.75 45.31 3.34
9554 11931 6.785191 TGCAGAATTTTCTTCGATGGTAATC 58.215 36.000 0.00 0.00 34.74 1.75
9555 11932 6.757897 TGCAGAATTTTCTTCGATGGTAAT 57.242 33.333 0.00 0.00 34.74 1.89
9556 11933 6.757897 ATGCAGAATTTTCTTCGATGGTAA 57.242 33.333 0.00 0.00 34.74 2.85
9557 11934 6.757897 AATGCAGAATTTTCTTCGATGGTA 57.242 33.333 0.00 0.00 34.74 3.25
9558 11935 5.649782 AATGCAGAATTTTCTTCGATGGT 57.350 34.783 0.00 0.00 34.74 3.55
9559 11936 7.253420 CGTTAAATGCAGAATTTTCTTCGATGG 60.253 37.037 0.00 0.00 39.29 3.51
9565 11942 9.528018 TTCTTTCGTTAAATGCAGAATTTTCTT 57.472 25.926 0.00 0.00 39.29 2.52
9566 11943 9.528018 TTTCTTTCGTTAAATGCAGAATTTTCT 57.472 25.926 0.00 0.00 39.29 2.52
9585 11962 9.988350 TTATTTCAGCTACGAATCATTTCTTTC 57.012 29.630 0.00 0.00 0.00 2.62
9722 12182 3.317149 TGCAGCTATGAATCATTGCTTCC 59.683 43.478 25.09 19.42 46.90 3.46
9744 12204 1.904287 TGACAAGGCGGTATGCTTTT 58.096 45.000 0.00 0.00 40.44 2.27


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

AutoCloner maintained by Alex Coulton.