Multiple sequence alignment - TraesCS1D01G188800

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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 TraesCS1D01G188800 chr1D 100.000 5087 0 0 1 5087 261221093 261226179 0.000000e+00 9395
1 TraesCS1D01G188800 chr1B 88.638 3802 197 82 537 4171 350795664 350791931 0.000000e+00 4410
2 TraesCS1D01G188800 chr1B 89.105 257 15 7 315 560 350795927 350795673 1.780000e-79 307
3 TraesCS1D01G188800 chr1B 83.746 283 25 10 20 288 350797638 350797363 1.090000e-61 248
4 TraesCS1D01G188800 chr1A 87.668 1857 99 38 438 2189 338836987 338835156 0.000000e+00 2041
5 TraesCS1D01G188800 chr1A 89.171 1182 92 18 3005 4171 338834214 338833054 0.000000e+00 1441
6 TraesCS1D01G188800 chr1A 94.212 501 26 3 4382 4882 561605731 561605234 0.000000e+00 761
7 TraesCS1D01G188800 chr1A 85.366 615 32 23 2213 2784 338835162 338834563 7.340000e-163 584
8 TraesCS1D01G188800 chr1A 82.819 227 17 8 1 219 338837387 338837175 3.130000e-42 183
9 TraesCS1D01G188800 chr1A 95.918 98 4 0 4990 5087 561605200 561605103 5.270000e-35 159
10 TraesCS1D01G188800 chr3A 92.140 598 38 8 4495 5087 584738688 584738095 0.000000e+00 835
11 TraesCS1D01G188800 chr6D 93.384 529 33 2 4383 4911 100040764 100040238 0.000000e+00 782
12 TraesCS1D01G188800 chr6D 89.947 189 14 3 4904 5087 99896191 99896003 6.580000e-59 239
13 TraesCS1D01G188800 chr6A 87.745 408 43 3 4380 4787 70930813 70931213 2.140000e-128 470
14 TraesCS1D01G188800 chr3B 86.891 267 32 3 4384 4650 739909100 739908837 3.850000e-76 296
15 TraesCS1D01G188800 chr3B 85.778 225 16 7 4171 4381 790390668 790390446 1.840000e-54 224
16 TraesCS1D01G188800 chr7B 92.857 196 14 0 4381 4576 806089 805894 8.340000e-73 285
17 TraesCS1D01G188800 chr3D 88.235 102 10 2 4204 4304 571895881 571895781 2.490000e-23 121


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 TraesCS1D01G188800 chr1D 261221093 261226179 5086 False 9395.00 9395 100.000 1 5087 1 chr1D.!!$F1 5086
1 TraesCS1D01G188800 chr1B 350791931 350797638 5707 True 1655.00 4410 87.163 20 4171 3 chr1B.!!$R1 4151
2 TraesCS1D01G188800 chr1A 338833054 338837387 4333 True 1062.25 2041 86.256 1 4171 4 chr1A.!!$R1 4170
3 TraesCS1D01G188800 chr1A 561605103 561605731 628 True 460.00 761 95.065 4382 5087 2 chr1A.!!$R2 705
4 TraesCS1D01G188800 chr3A 584738095 584738688 593 True 835.00 835 92.140 4495 5087 1 chr3A.!!$R1 592
5 TraesCS1D01G188800 chr6D 100040238 100040764 526 True 782.00 782 93.384 4383 4911 1 chr6D.!!$R2 528

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
305 373 0.302890 CTGAAATCACCGCGCTGATC 59.697 55.0 16.78 7.61 30.12 2.92 F
1062 2606 0.042431 ATCTCCTGGAGCTGGACTGT 59.958 55.0 19.08 0.00 0.00 3.55 F
2258 3896 0.179034 GCCTCTGAAATCCTCCGCAT 60.179 55.0 0.00 0.00 0.00 4.73 F
3367 5242 0.038166 TCCTGCCGGAGAAAGCAAAT 59.962 50.0 5.05 0.00 38.82 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1826 3439 0.027324 GAGTATCGTCACGGTCGGAC 59.973 60.0 0.0 0.0 0.00 4.79 R
2839 4569 0.032678 CTCAGAGCAGAACACACGGT 59.967 55.0 0.0 0.0 0.00 4.83 R
3998 5899 0.030101 GATCTCACGCTCCTCTTCCG 59.970 60.0 0.0 0.0 0.00 4.30 R
4189 6100 0.032952 AGCCGTCGTGTGCTCTAAAA 59.967 50.0 0.0 0.0 30.33 1.52 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
18 19 3.475932 TGACCCTGTACAAGAGGCT 57.524 52.632 0.00 0.00 0.00 4.58
163 185 3.547813 CGAGCTGCTACTACTGTCATCAG 60.548 52.174 0.15 0.00 46.18 2.90
182 204 0.663153 GCAAGTTGACAGACACACCC 59.337 55.000 7.16 0.00 0.00 4.61
184 206 1.670811 CAAGTTGACAGACACACCCAC 59.329 52.381 0.00 0.00 0.00 4.61
232 290 5.105756 ACAAATGCCTAGTGTTATTTCTGCC 60.106 40.000 0.00 0.00 0.00 4.85
244 302 3.538634 ATTTCTGCCCGTAGAACCTAC 57.461 47.619 0.00 0.00 36.48 3.18
246 304 1.471119 TCTGCCCGTAGAACCTACAG 58.529 55.000 5.17 0.00 0.00 2.74
247 305 1.183549 CTGCCCGTAGAACCTACAGT 58.816 55.000 5.17 0.00 0.00 3.55
248 306 2.025981 TCTGCCCGTAGAACCTACAGTA 60.026 50.000 5.17 0.00 0.00 2.74
249 307 2.358267 CTGCCCGTAGAACCTACAGTAG 59.642 54.545 0.00 0.00 0.00 2.57
260 318 1.685491 CCTACAGTAGGCGTCTTCCCT 60.685 57.143 14.02 0.00 39.48 4.20
299 367 3.864686 CCGGCTGAAATCACCGCG 61.865 66.667 0.00 0.00 45.58 6.46
300 368 4.520846 CGGCTGAAATCACCGCGC 62.521 66.667 0.00 0.00 40.55 6.86
301 369 3.127533 GGCTGAAATCACCGCGCT 61.128 61.111 5.56 0.00 0.00 5.92
302 370 2.099062 GCTGAAATCACCGCGCTG 59.901 61.111 5.56 0.00 0.00 5.18
303 371 2.390599 GCTGAAATCACCGCGCTGA 61.391 57.895 6.57 6.57 0.00 4.26
304 372 1.709147 GCTGAAATCACCGCGCTGAT 61.709 55.000 11.09 11.09 31.84 2.90
305 373 0.302890 CTGAAATCACCGCGCTGATC 59.697 55.000 16.78 7.61 30.12 2.92
306 374 1.089481 TGAAATCACCGCGCTGATCC 61.089 55.000 16.78 12.17 30.12 3.36
350 1817 2.029020 GGGAAACAATTCAGCAAGGACC 60.029 50.000 0.00 0.00 37.29 4.46
367 1838 2.417651 GGACCGAATGTATCAACCGTGA 60.418 50.000 0.00 0.00 38.41 4.35
386 1857 1.601430 GAATCAATTCGCTGGGCTCTC 59.399 52.381 0.00 0.00 0.00 3.20
396 1867 0.543277 CTGGGCTCTCATGGCTACAA 59.457 55.000 0.00 0.00 0.00 2.41
479 1951 1.681264 GGCAGCCACCACCAATTATAC 59.319 52.381 6.55 0.00 0.00 1.47
661 2171 1.975660 TGTAACCAAAGCCTCCACAC 58.024 50.000 0.00 0.00 0.00 3.82
704 2219 0.633733 CGTGCGTGCGTCTACTTAAG 59.366 55.000 0.00 0.00 0.00 1.85
827 2351 1.951130 CACAGACTGCACGAACGCT 60.951 57.895 1.25 0.00 0.00 5.07
880 2406 1.384989 CCAGGCGAGTACGGATCAGT 61.385 60.000 3.43 3.43 40.15 3.41
916 2442 1.071987 CTGGCTGAGCACAGTGGAA 59.928 57.895 12.89 0.00 45.04 3.53
967 2505 0.453793 GCTCTCGCTTCACTCTGCTA 59.546 55.000 0.00 0.00 0.00 3.49
968 2506 1.135257 GCTCTCGCTTCACTCTGCTAA 60.135 52.381 0.00 0.00 0.00 3.09
1062 2606 0.042431 ATCTCCTGGAGCTGGACTGT 59.958 55.000 19.08 0.00 0.00 3.55
1116 2660 4.147449 CGCCATCTCTGCGTCCCA 62.147 66.667 0.00 0.00 46.59 4.37
1288 2832 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1289 2833 2.123033 GGAGGAGGAGGAGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
1480 3049 7.918076 ACTGTCCTAATCACCTTCATTTTCTA 58.082 34.615 0.00 0.00 0.00 2.10
1555 3141 3.479505 TTTGGTCCGTTGCATTATTCG 57.520 42.857 0.00 0.00 0.00 3.34
1604 3203 1.753073 AGCCCCACATACACGTAGTAC 59.247 52.381 0.00 0.00 41.61 2.73
1606 3205 2.951642 GCCCCACATACACGTAGTACTA 59.048 50.000 0.00 0.00 41.61 1.82
1607 3206 3.004106 GCCCCACATACACGTAGTACTAG 59.996 52.174 1.87 0.53 41.61 2.57
1608 3207 4.202441 CCCCACATACACGTAGTACTAGT 58.798 47.826 1.87 0.00 41.61 2.57
1609 3208 5.368145 CCCCACATACACGTAGTACTAGTA 58.632 45.833 1.87 0.00 41.61 1.82
1725 3328 1.063764 GAAGCTACGAGGGTACGACAG 59.936 57.143 0.00 0.00 37.03 3.51
1730 3333 1.542492 ACGAGGGTACGACAGTGATT 58.458 50.000 0.00 0.00 37.03 2.57
1731 3334 1.201647 ACGAGGGTACGACAGTGATTG 59.798 52.381 0.00 0.00 37.03 2.67
1762 3365 2.505557 GGTACGTGGTCCTTCGCG 60.506 66.667 0.00 0.00 44.99 5.87
1812 3425 4.142945 ACGTAGAGTAAAGTCGTGTAGCTG 60.143 45.833 0.00 0.00 33.55 4.24
1813 3426 4.142945 CGTAGAGTAAAGTCGTGTAGCTGT 60.143 45.833 0.00 0.00 0.00 4.40
1814 3427 4.162096 AGAGTAAAGTCGTGTAGCTGTG 57.838 45.455 0.00 0.00 0.00 3.66
1815 3428 3.568853 AGAGTAAAGTCGTGTAGCTGTGT 59.431 43.478 0.00 0.00 0.00 3.72
1816 3429 4.758674 AGAGTAAAGTCGTGTAGCTGTGTA 59.241 41.667 0.00 0.00 0.00 2.90
1819 3432 3.833545 AAGTCGTGTAGCTGTGTAGAG 57.166 47.619 0.00 0.00 0.00 2.43
1820 3433 2.780714 AGTCGTGTAGCTGTGTAGAGT 58.219 47.619 0.00 0.00 0.00 3.24
1821 3434 3.935315 AGTCGTGTAGCTGTGTAGAGTA 58.065 45.455 0.00 0.00 0.00 2.59
1822 3435 3.933955 AGTCGTGTAGCTGTGTAGAGTAG 59.066 47.826 0.00 0.00 0.00 2.57
1823 3436 2.676839 TCGTGTAGCTGTGTAGAGTAGC 59.323 50.000 0.00 0.00 37.71 3.58
1825 3438 3.127203 CGTGTAGCTGTGTAGAGTAGCTT 59.873 47.826 0.00 0.00 44.87 3.74
1826 3439 4.416620 GTGTAGCTGTGTAGAGTAGCTTG 58.583 47.826 0.00 0.00 44.87 4.01
1827 3440 4.079970 TGTAGCTGTGTAGAGTAGCTTGT 58.920 43.478 0.00 0.00 44.87 3.16
1872 3485 3.190118 ACGGAAAGGAACTGTCGTAGTAG 59.810 47.826 0.00 0.00 45.53 2.57
1917 3534 1.337071 CAGCTAGATTTACGGCCTCGA 59.663 52.381 0.00 0.00 40.11 4.04
1959 3577 5.479306 ACTGCATTCTTTAGTTAGAAGCGA 58.521 37.500 0.00 0.00 37.55 4.93
2016 3650 5.656480 TGATTATTGCTGCAAGTACGTAGA 58.344 37.500 20.72 0.00 35.30 2.59
2017 3651 6.280643 TGATTATTGCTGCAAGTACGTAGAT 58.719 36.000 20.72 3.01 35.30 1.98
2018 3652 6.420903 TGATTATTGCTGCAAGTACGTAGATC 59.579 38.462 20.72 13.17 35.30 2.75
2046 3680 7.544566 ACATTTGACGAGTAAAACTATGTCGAT 59.455 33.333 0.00 3.11 36.83 3.59
2112 3746 2.192664 TGCCTTGGAGTTGCGATTAA 57.807 45.000 0.00 0.00 0.00 1.40
2185 3823 5.308825 AGACAGAAGATGTTTCATCGGTTT 58.691 37.500 4.44 0.00 44.17 3.27
2195 3833 0.963225 TCATCGGTTTGGTCGTCTCA 59.037 50.000 0.00 0.00 0.00 3.27
2226 3864 6.839820 ACTGTTAGTGTTAGGTTTCTTTCG 57.160 37.500 0.00 0.00 0.00 3.46
2231 3869 4.142038 AGTGTTAGGTTTCTTTCGGCAAT 58.858 39.130 0.00 0.00 0.00 3.56
2232 3870 4.023193 AGTGTTAGGTTTCTTTCGGCAATG 60.023 41.667 0.00 0.00 0.00 2.82
2252 3890 6.743773 GCAATGAGTATAGCCTCTGAAATCCT 60.744 42.308 0.00 0.00 32.50 3.24
2254 3892 4.835615 TGAGTATAGCCTCTGAAATCCTCC 59.164 45.833 0.00 0.00 32.50 4.30
2255 3893 3.829601 AGTATAGCCTCTGAAATCCTCCG 59.170 47.826 0.00 0.00 0.00 4.63
2258 3896 0.179034 GCCTCTGAAATCCTCCGCAT 60.179 55.000 0.00 0.00 0.00 4.73
2260 3898 1.139654 CCTCTGAAATCCTCCGCATCA 59.860 52.381 0.00 0.00 0.00 3.07
2272 3910 1.300971 CCGCATCATCGGCCATAAGG 61.301 60.000 2.24 0.00 43.18 2.69
2327 3981 2.238847 TACTGCCGCTAGCTTGGTGG 62.239 60.000 13.93 7.21 44.23 4.61
2328 3982 4.408821 TGCCGCTAGCTTGGTGGG 62.409 66.667 13.93 6.43 44.23 4.61
2348 4002 1.720852 GAATTGCATGAAACGGCACAC 59.279 47.619 0.00 0.00 40.23 3.82
2359 4035 1.511887 CGGCACACGCAATTGCTAC 60.512 57.895 26.86 11.73 41.24 3.58
2403 4079 2.027561 TGTTATTCCTGTTCACTCCCGG 60.028 50.000 0.00 0.00 0.00 5.73
2489 4170 3.803082 CAGTGGTTGCCGCCGATG 61.803 66.667 0.00 0.00 33.99 3.84
2557 4247 1.372087 GGAAGCGATTGAGCCCAGTG 61.372 60.000 0.00 0.00 38.01 3.66
2558 4248 0.391661 GAAGCGATTGAGCCCAGTGA 60.392 55.000 0.00 0.00 38.01 3.41
2559 4249 0.392193 AAGCGATTGAGCCCAGTGAG 60.392 55.000 0.00 0.00 38.01 3.51
2560 4250 2.467826 GCGATTGAGCCCAGTGAGC 61.468 63.158 0.00 0.00 0.00 4.26
2674 4372 3.480133 GCCCACTGCCCTATCCGT 61.480 66.667 0.00 0.00 0.00 4.69
2793 4519 1.551430 CCCACATGCAACATGGTTCAT 59.449 47.619 11.91 0.00 0.00 2.57
2794 4520 2.417651 CCCACATGCAACATGGTTCATC 60.418 50.000 11.91 0.00 0.00 2.92
2795 4521 2.231721 CCACATGCAACATGGTTCATCA 59.768 45.455 11.91 0.00 0.00 3.07
2807 4533 2.166050 TGGTTCATCAATGGCCGAATTG 59.834 45.455 9.10 9.10 38.63 2.32
2814 4540 7.381766 TCATCAATGGCCGAATTGAATATAG 57.618 36.000 19.26 9.55 46.66 1.31
2818 4546 7.819644 TCAATGGCCGAATTGAATATAGAATG 58.180 34.615 14.47 0.00 42.22 2.67
2870 4623 5.998454 TCTGCTCTGAGACTTTTCTTTTG 57.002 39.130 9.28 0.00 29.47 2.44
2876 4663 6.076981 TCTGAGACTTTTCTTTTGATTGCC 57.923 37.500 0.00 0.00 29.47 4.52
2884 4671 5.964887 TTTCTTTTGATTGCCTTGTTTCG 57.035 34.783 0.00 0.00 0.00 3.46
2978 4830 1.632948 GGTCGGCTCGTGGCTTTAAC 61.633 60.000 9.45 2.56 41.46 2.01
2980 4832 2.396157 CGGCTCGTGGCTTTAACCC 61.396 63.158 9.45 0.00 41.46 4.11
3003 4855 1.544686 GTGGTTATGCAATTTCGCGG 58.455 50.000 6.13 0.00 33.35 6.46
3143 4995 2.579738 GCCGTGGAAGAGGAGGAC 59.420 66.667 0.00 0.00 0.00 3.85
3282 5141 1.858458 CGTTCTGCTTCTGTCGTTTGA 59.142 47.619 0.00 0.00 0.00 2.69
3283 5142 2.097202 CGTTCTGCTTCTGTCGTTTGAG 60.097 50.000 0.00 0.00 0.00 3.02
3284 5143 2.866762 GTTCTGCTTCTGTCGTTTGAGT 59.133 45.455 0.00 0.00 0.00 3.41
3285 5144 3.179443 TCTGCTTCTGTCGTTTGAGTT 57.821 42.857 0.00 0.00 0.00 3.01
3286 5145 3.531538 TCTGCTTCTGTCGTTTGAGTTT 58.468 40.909 0.00 0.00 0.00 2.66
3287 5146 3.309682 TCTGCTTCTGTCGTTTGAGTTTG 59.690 43.478 0.00 0.00 0.00 2.93
3367 5242 0.038166 TCCTGCCGGAGAAAGCAAAT 59.962 50.000 5.05 0.00 38.82 2.32
3382 5257 0.378257 CAAATTGCCCGGATCGAGTG 59.622 55.000 0.73 0.00 0.00 3.51
3481 5358 3.937062 GGCGGTTGCGCTTATCGG 61.937 66.667 9.73 2.17 44.10 4.18
3494 5377 4.454480 CGCTTATCGGTGATGGAATCGAG 61.454 52.174 0.00 0.00 39.60 4.04
3528 5411 7.069852 TGCTTAGTTCTAACTCGTACTACTG 57.930 40.000 0.00 0.00 40.37 2.74
3538 5421 4.868067 ACTCGTACTACTGTTCCTTTGTG 58.132 43.478 0.00 0.00 0.00 3.33
3745 5643 2.353607 GGAGAGTCGGCGTATGCG 60.354 66.667 6.85 0.00 44.10 4.73
3754 5652 2.185867 GCGTATGCGAAGACCCCA 59.814 61.111 7.60 0.00 41.33 4.96
3771 5669 0.951040 CCAACGAGCACAACCTCCTC 60.951 60.000 0.00 0.00 0.00 3.71
3905 5806 3.728373 GATCCAAGGCACGGGGGT 61.728 66.667 0.00 0.00 0.00 4.95
3963 5864 0.749454 GCCTTGTTGCGGAGATGGAT 60.749 55.000 0.00 0.00 0.00 3.41
4057 5958 1.803289 CTCATCGACGAGCTGGTGA 59.197 57.895 5.94 4.81 0.00 4.02
4081 5982 0.824109 CCTGGTCACGGATCTGCTTA 59.176 55.000 0.00 0.00 0.00 3.09
4147 6056 6.747659 ATGTCGAATAAAACAAAACACTGC 57.252 33.333 0.00 0.00 0.00 4.40
4156 6067 1.668751 ACAAAACACTGCAGGTACACG 59.331 47.619 19.93 4.77 0.00 4.49
4159 6070 0.466543 AACACTGCAGGTACACGGAA 59.533 50.000 19.93 0.00 0.00 4.30
4171 6082 3.181510 GGTACACGGAAATGTTCAGATGC 60.182 47.826 0.00 0.00 33.85 3.91
4172 6083 1.464608 ACACGGAAATGTTCAGATGCG 59.535 47.619 0.00 0.00 0.00 4.73
4173 6084 0.447801 ACGGAAATGTTCAGATGCGC 59.552 50.000 0.00 0.00 0.00 6.09
4174 6085 0.587242 CGGAAATGTTCAGATGCGCG 60.587 55.000 0.00 0.00 0.00 6.86
4175 6086 0.447801 GGAAATGTTCAGATGCGCGT 59.552 50.000 8.43 0.00 0.00 6.01
4176 6087 1.529826 GGAAATGTTCAGATGCGCGTC 60.530 52.381 22.11 22.11 0.00 5.19
4177 6088 0.095245 AAATGTTCAGATGCGCGTCG 59.905 50.000 23.15 17.55 0.00 5.12
4207 6118 0.863144 TTTTTAGAGCACACGACGGC 59.137 50.000 0.00 0.00 0.00 5.68
4208 6119 0.032952 TTTTAGAGCACACGACGGCT 59.967 50.000 0.00 0.00 44.48 5.52
4209 6120 0.666274 TTTAGAGCACACGACGGCTG 60.666 55.000 1.68 0.00 41.22 4.85
4210 6121 1.802337 TTAGAGCACACGACGGCTGT 61.802 55.000 0.00 0.00 41.22 4.40
4211 6122 1.802337 TAGAGCACACGACGGCTGTT 61.802 55.000 0.00 0.00 41.22 3.16
4212 6123 2.203015 AGCACACGACGGCTGTTT 60.203 55.556 0.00 0.00 39.30 2.83
4213 6124 1.772063 GAGCACACGACGGCTGTTTT 61.772 55.000 0.00 0.00 41.22 2.43
4214 6125 1.063488 GCACACGACGGCTGTTTTT 59.937 52.632 0.00 0.00 0.00 1.94
4215 6126 1.199852 GCACACGACGGCTGTTTTTG 61.200 55.000 0.00 0.00 0.00 2.44
4216 6127 1.063488 ACACGACGGCTGTTTTTGC 59.937 52.632 0.00 0.00 0.00 3.68
4217 6128 2.003443 CACGACGGCTGTTTTTGCG 61.003 57.895 0.00 0.07 0.00 4.85
4218 6129 3.091022 CGACGGCTGTTTTTGCGC 61.091 61.111 0.00 0.00 0.00 6.09
4219 6130 2.729491 GACGGCTGTTTTTGCGCC 60.729 61.111 4.18 0.00 40.40 6.53
4222 6133 2.429069 GGCTGTTTTTGCGCCGAG 60.429 61.111 4.18 0.00 33.64 4.63
4223 6134 2.331451 GCTGTTTTTGCGCCGAGT 59.669 55.556 4.18 0.00 0.00 4.18
4224 6135 1.725973 GCTGTTTTTGCGCCGAGTC 60.726 57.895 4.18 0.00 0.00 3.36
4225 6136 1.082104 CTGTTTTTGCGCCGAGTCC 60.082 57.895 4.18 0.00 0.00 3.85
4226 6137 1.507141 CTGTTTTTGCGCCGAGTCCT 61.507 55.000 4.18 0.00 0.00 3.85
4227 6138 1.206831 GTTTTTGCGCCGAGTCCTC 59.793 57.895 4.18 0.00 0.00 3.71
4228 6139 1.227704 TTTTTGCGCCGAGTCCTCA 60.228 52.632 4.18 0.00 0.00 3.86
4229 6140 1.227999 TTTTTGCGCCGAGTCCTCAG 61.228 55.000 4.18 0.00 0.00 3.35
4230 6141 2.377628 TTTTGCGCCGAGTCCTCAGT 62.378 55.000 4.18 0.00 0.00 3.41
4231 6142 2.377628 TTTGCGCCGAGTCCTCAGTT 62.378 55.000 4.18 0.00 0.00 3.16
4232 6143 2.811317 GCGCCGAGTCCTCAGTTG 60.811 66.667 0.00 0.00 0.00 3.16
4233 6144 2.811317 CGCCGAGTCCTCAGTTGC 60.811 66.667 0.00 0.00 0.00 4.17
4234 6145 2.659610 GCCGAGTCCTCAGTTGCT 59.340 61.111 0.00 0.00 0.00 3.91
4235 6146 1.004440 GCCGAGTCCTCAGTTGCTT 60.004 57.895 0.00 0.00 0.00 3.91
4236 6147 1.016653 GCCGAGTCCTCAGTTGCTTC 61.017 60.000 0.00 0.00 0.00 3.86
4237 6148 0.318441 CCGAGTCCTCAGTTGCTTCA 59.682 55.000 0.00 0.00 0.00 3.02
4238 6149 1.423395 CGAGTCCTCAGTTGCTTCAC 58.577 55.000 0.00 0.00 0.00 3.18
4239 6150 1.802069 GAGTCCTCAGTTGCTTCACC 58.198 55.000 0.00 0.00 0.00 4.02
4240 6151 1.070758 GAGTCCTCAGTTGCTTCACCA 59.929 52.381 0.00 0.00 0.00 4.17
4241 6152 1.701847 AGTCCTCAGTTGCTTCACCAT 59.298 47.619 0.00 0.00 0.00 3.55
4242 6153 1.808945 GTCCTCAGTTGCTTCACCATG 59.191 52.381 0.00 0.00 0.00 3.66
4243 6154 0.524862 CCTCAGTTGCTTCACCATGC 59.475 55.000 0.00 0.00 0.00 4.06
4244 6155 0.167470 CTCAGTTGCTTCACCATGCG 59.833 55.000 0.00 0.00 0.00 4.73
4245 6156 1.443194 CAGTTGCTTCACCATGCGC 60.443 57.895 0.00 0.00 0.00 6.09
4246 6157 1.601759 AGTTGCTTCACCATGCGCT 60.602 52.632 9.73 0.00 0.00 5.92
4247 6158 1.443194 GTTGCTTCACCATGCGCTG 60.443 57.895 9.73 4.25 0.00 5.18
4248 6159 3.271706 TTGCTTCACCATGCGCTGC 62.272 57.895 9.73 0.82 0.00 5.25
4249 6160 3.740397 GCTTCACCATGCGCTGCA 61.740 61.111 9.73 5.73 44.86 4.41
4250 6161 2.956194 CTTCACCATGCGCTGCAA 59.044 55.556 9.73 0.00 43.62 4.08
4251 6162 1.286570 CTTCACCATGCGCTGCAAA 59.713 52.632 9.73 0.00 43.62 3.68
4252 6163 0.108992 CTTCACCATGCGCTGCAAAT 60.109 50.000 9.73 0.00 43.62 2.32
4253 6164 0.317799 TTCACCATGCGCTGCAAATT 59.682 45.000 9.73 0.00 43.62 1.82
4254 6165 0.317799 TCACCATGCGCTGCAAATTT 59.682 45.000 9.73 0.00 43.62 1.82
4255 6166 1.149987 CACCATGCGCTGCAAATTTT 58.850 45.000 9.73 0.00 43.62 1.82
4256 6167 1.532007 CACCATGCGCTGCAAATTTTT 59.468 42.857 9.73 0.00 43.62 1.94
4257 6168 2.735663 CACCATGCGCTGCAAATTTTTA 59.264 40.909 9.73 0.00 43.62 1.52
4258 6169 2.995258 ACCATGCGCTGCAAATTTTTAG 59.005 40.909 9.73 0.00 43.62 1.85
4259 6170 2.222863 CCATGCGCTGCAAATTTTTAGC 60.223 45.455 9.73 11.59 43.62 3.09
4262 6173 3.836597 GCTGCAAATTTTTAGCGCG 57.163 47.368 0.00 0.00 0.00 6.86
4263 6174 0.246873 GCTGCAAATTTTTAGCGCGC 60.247 50.000 26.66 26.66 0.00 6.86
4264 6175 0.366534 CTGCAAATTTTTAGCGCGCC 59.633 50.000 30.33 10.31 0.00 6.53
4265 6176 1.340131 GCAAATTTTTAGCGCGCCG 59.660 52.632 30.33 6.10 0.00 6.46
4266 6177 1.341369 GCAAATTTTTAGCGCGCCGT 61.341 50.000 30.33 13.66 0.00 5.68
4267 6178 1.056869 CAAATTTTTAGCGCGCCGTT 58.943 45.000 30.33 12.78 0.00 4.44
4268 6179 1.056869 AAATTTTTAGCGCGCCGTTG 58.943 45.000 30.33 0.00 0.00 4.10
4269 6180 0.039888 AATTTTTAGCGCGCCGTTGT 60.040 45.000 30.33 11.88 0.00 3.32
4270 6181 0.797542 ATTTTTAGCGCGCCGTTGTA 59.202 45.000 30.33 10.64 0.00 2.41
4271 6182 0.164217 TTTTTAGCGCGCCGTTGTAG 59.836 50.000 30.33 0.00 0.00 2.74
4272 6183 2.230484 TTTTAGCGCGCCGTTGTAGC 62.230 55.000 30.33 0.00 0.00 3.58
4279 6190 2.778679 GCCGTTGTAGCGCTTCAG 59.221 61.111 18.68 6.29 0.00 3.02
4280 6191 2.778679 CCGTTGTAGCGCTTCAGC 59.221 61.111 18.68 18.64 37.78 4.26
4281 6192 2.027073 CCGTTGTAGCGCTTCAGCA 61.027 57.895 25.58 13.81 42.21 4.41
4282 6193 1.417592 CGTTGTAGCGCTTCAGCAG 59.582 57.895 25.58 16.36 42.21 4.24
4283 6194 1.790387 GTTGTAGCGCTTCAGCAGG 59.210 57.895 22.49 0.00 42.21 4.85
4284 6195 2.034879 TTGTAGCGCTTCAGCAGGC 61.035 57.895 18.68 0.00 42.21 4.85
4291 6202 2.815211 CTTCAGCAGGCGCGCTAA 60.815 61.111 32.29 14.04 45.49 3.09
4292 6203 2.358125 TTCAGCAGGCGCGCTAAA 60.358 55.556 32.29 12.99 45.49 1.85
4293 6204 1.911293 CTTCAGCAGGCGCGCTAAAA 61.911 55.000 32.29 15.06 45.49 1.52
4294 6205 1.305219 TTCAGCAGGCGCGCTAAAAT 61.305 50.000 32.29 10.84 45.49 1.82
4295 6206 0.461163 TCAGCAGGCGCGCTAAAATA 60.461 50.000 32.29 10.35 45.49 1.40
4296 6207 0.316196 CAGCAGGCGCGCTAAAATAC 60.316 55.000 32.29 12.47 45.49 1.89
4297 6208 0.742990 AGCAGGCGCGCTAAAATACA 60.743 50.000 32.29 0.00 45.49 2.29
4298 6209 0.316196 GCAGGCGCGCTAAAATACAG 60.316 55.000 32.29 10.20 0.00 2.74
4299 6210 0.316196 CAGGCGCGCTAAAATACAGC 60.316 55.000 32.29 9.98 35.61 4.40
4305 6216 3.596865 GCTAAAATACAGCGCGCAA 57.403 47.368 35.10 18.82 0.00 4.85
4306 6217 2.105323 GCTAAAATACAGCGCGCAAT 57.895 45.000 35.10 22.89 0.00 3.56
4307 6218 3.247563 GCTAAAATACAGCGCGCAATA 57.752 42.857 35.10 24.37 0.00 1.90
4308 6219 2.964768 GCTAAAATACAGCGCGCAATAC 59.035 45.455 35.10 2.51 0.00 1.89
4309 6220 3.545228 GCTAAAATACAGCGCGCAATACA 60.545 43.478 35.10 13.65 0.00 2.29
4310 6221 2.452006 AAATACAGCGCGCAATACAC 57.548 45.000 35.10 0.72 0.00 2.90
4311 6222 1.364721 AATACAGCGCGCAATACACA 58.635 45.000 35.10 10.92 0.00 3.72
4312 6223 1.581934 ATACAGCGCGCAATACACAT 58.418 45.000 35.10 12.81 0.00 3.21
4313 6224 2.211353 TACAGCGCGCAATACACATA 57.789 45.000 35.10 9.99 0.00 2.29
4314 6225 0.650512 ACAGCGCGCAATACACATAC 59.349 50.000 35.10 0.00 0.00 2.39
4315 6226 0.649993 CAGCGCGCAATACACATACA 59.350 50.000 35.10 0.00 0.00 2.29
4316 6227 1.261354 CAGCGCGCAATACACATACAT 59.739 47.619 35.10 3.94 0.00 2.29
4317 6228 2.474735 CAGCGCGCAATACACATACATA 59.525 45.455 35.10 0.00 0.00 2.29
4318 6229 2.475111 AGCGCGCAATACACATACATAC 59.525 45.455 35.10 0.00 0.00 2.39
4319 6230 2.219903 GCGCGCAATACACATACATACA 59.780 45.455 29.10 0.00 0.00 2.29
4320 6231 3.783377 CGCGCAATACACATACATACAC 58.217 45.455 8.75 0.00 0.00 2.90
4321 6232 3.244111 CGCGCAATACACATACATACACA 59.756 43.478 8.75 0.00 0.00 3.72
4322 6233 4.260011 CGCGCAATACACATACATACACAA 60.260 41.667 8.75 0.00 0.00 3.33
4323 6234 5.564768 GCGCAATACACATACATACACAAA 58.435 37.500 0.30 0.00 0.00 2.83
4324 6235 6.024664 GCGCAATACACATACATACACAAAA 58.975 36.000 0.30 0.00 0.00 2.44
4325 6236 6.524933 GCGCAATACACATACATACACAAAAA 59.475 34.615 0.30 0.00 0.00 1.94
4326 6237 7.460896 GCGCAATACACATACATACACAAAAAC 60.461 37.037 0.30 0.00 0.00 2.43
4327 6238 7.535599 CGCAATACACATACATACACAAAAACA 59.464 33.333 0.00 0.00 0.00 2.83
4328 6239 9.186323 GCAATACACATACATACACAAAAACAA 57.814 29.630 0.00 0.00 0.00 2.83
4468 6379 1.839994 TGTGGGATCAGAAAGCTAGGG 59.160 52.381 0.00 0.00 0.00 3.53
4477 6388 2.707791 CAGAAAGCTAGGGGGATCATCA 59.292 50.000 0.00 0.00 0.00 3.07
4543 6454 3.633986 AGAAATGTGCCAAGCTATTAGCC 59.366 43.478 12.05 0.00 43.77 3.93
4545 6456 2.806945 TGTGCCAAGCTATTAGCCTT 57.193 45.000 12.05 3.72 43.77 4.35
4591 6502 3.819368 TGAATTGACGTCATGGGCATAT 58.181 40.909 20.80 4.84 0.00 1.78
4799 6712 2.519063 CTGCCACACCTGCCACAA 60.519 61.111 0.00 0.00 0.00 3.33
4918 6831 4.265073 GCTTCTCCCATGTGTACTTCAAT 58.735 43.478 0.00 0.00 0.00 2.57
4930 6843 5.705441 TGTGTACTTCAATCCTTGGATGTTC 59.295 40.000 2.56 0.00 0.00 3.18
4953 6867 0.670854 GTCTTCTCACCGAGTTGCCC 60.671 60.000 0.00 0.00 0.00 5.36
4959 6873 0.322322 TCACCGAGTTGCCCGTTATT 59.678 50.000 0.00 0.00 0.00 1.40
4981 6895 2.601763 GCATGAATAGCAAAAGCTGTGC 59.398 45.455 13.50 13.50 42.55 4.57
5027 6941 3.244318 CCTTTGCATGCTTCCCTTCTTTT 60.244 43.478 20.33 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.347707 CCCAGACAAGCCTCTTGTACA 59.652 52.381 11.65 0.00 31.96 2.90
18 19 1.127567 CCCAGTCAGTCCCCAGACAA 61.128 60.000 0.00 0.00 46.15 3.18
163 185 0.663153 GGGTGTGTCTGTCAACTTGC 59.337 55.000 0.00 0.00 0.00 4.01
182 204 2.440409 AGCCTGCCAAAACTGATAGTG 58.560 47.619 0.00 0.00 0.00 2.74
184 206 4.009675 TGTTAGCCTGCCAAAACTGATAG 58.990 43.478 0.00 0.00 0.00 2.08
244 302 3.604875 TTTTAGGGAAGACGCCTACTG 57.395 47.619 0.00 0.00 0.00 2.74
299 367 2.288961 TTCTAACGTTCCGGATCAGC 57.711 50.000 4.15 0.00 0.00 4.26
300 368 3.068307 AGGATTCTAACGTTCCGGATCAG 59.932 47.826 4.15 1.86 34.61 2.90
301 369 3.028850 AGGATTCTAACGTTCCGGATCA 58.971 45.455 4.15 0.00 34.61 2.92
302 370 3.067742 TGAGGATTCTAACGTTCCGGATC 59.932 47.826 4.15 2.98 34.61 3.36
303 371 3.028850 TGAGGATTCTAACGTTCCGGAT 58.971 45.455 4.15 0.00 34.61 4.18
304 372 2.426024 CTGAGGATTCTAACGTTCCGGA 59.574 50.000 2.82 0.00 34.61 5.14
305 373 2.810650 CTGAGGATTCTAACGTTCCGG 58.189 52.381 2.82 0.00 34.61 5.14
306 374 2.194271 GCTGAGGATTCTAACGTTCCG 58.806 52.381 2.82 0.00 34.61 4.30
308 376 3.557595 CCATGCTGAGGATTCTAACGTTC 59.442 47.826 2.82 0.00 0.00 3.95
310 378 2.158900 CCCATGCTGAGGATTCTAACGT 60.159 50.000 0.00 0.00 0.00 3.99
312 380 3.845781 TCCCATGCTGAGGATTCTAAC 57.154 47.619 0.00 0.00 0.00 2.34
313 381 4.018506 TGTTTCCCATGCTGAGGATTCTAA 60.019 41.667 0.00 0.00 30.55 2.10
315 383 2.309755 TGTTTCCCATGCTGAGGATTCT 59.690 45.455 0.00 0.00 30.55 2.40
350 1817 5.463499 TTGATTCACGGTTGATACATTCG 57.537 39.130 0.00 0.00 0.00 3.34
367 1838 1.065199 TGAGAGCCCAGCGAATTGATT 60.065 47.619 0.00 0.00 0.00 2.57
386 1857 2.719798 GCGCTAATGTTTGTAGCCATG 58.280 47.619 0.00 0.00 40.79 3.66
396 1867 1.375396 TGGTGCTCGCGCTAATGTT 60.375 52.632 5.56 0.00 36.97 2.71
479 1951 2.546494 GGGCCGATCAATCCGCTTG 61.546 63.158 0.00 0.00 36.09 4.01
797 2321 3.344904 CAGTCTGTGCACAAAAAGGAG 57.655 47.619 21.98 7.34 0.00 3.69
827 2351 2.506217 CTTGCGCGGTAGCTTCGA 60.506 61.111 8.83 0.00 42.32 3.71
880 2406 1.067142 CAGCGGCTGTTAAGTACTCCA 60.067 52.381 21.60 0.00 0.00 3.86
916 2442 2.365586 CCACTGAGCTAGCTGGCCT 61.366 63.158 24.99 6.07 0.00 5.19
967 2505 1.214062 CTCCGCGAGCTGACTTCTT 59.786 57.895 8.23 0.00 0.00 2.52
968 2506 1.653094 CTCTCCGCGAGCTGACTTCT 61.653 60.000 8.23 0.00 31.99 2.85
1033 2577 1.045350 TCCAGGAGATCCTTCAGCCG 61.045 60.000 0.00 0.00 46.09 5.52
1357 2907 0.248539 GATTTCCTCTCGGTCGACGG 60.249 60.000 16.37 16.37 44.45 4.79
1480 3049 5.428783 ACCACCATTAATCCTAGTTACTGCT 59.571 40.000 0.00 0.00 0.00 4.24
1555 3141 0.744414 TGGCAATCCAGAGCTTACGC 60.744 55.000 0.00 0.00 37.47 4.42
1604 3203 6.513180 TCGCCAAATGAATTACTCCTACTAG 58.487 40.000 0.00 0.00 0.00 2.57
1606 3205 5.353394 TCGCCAAATGAATTACTCCTACT 57.647 39.130 0.00 0.00 0.00 2.57
1607 3206 5.220796 GGTTCGCCAAATGAATTACTCCTAC 60.221 44.000 0.00 0.00 37.19 3.18
1608 3207 4.879545 GGTTCGCCAAATGAATTACTCCTA 59.120 41.667 0.00 0.00 37.19 2.94
1609 3208 3.694566 GGTTCGCCAAATGAATTACTCCT 59.305 43.478 0.00 0.00 37.19 3.69
1730 3333 2.933401 TACCGCTGTTGCCTACGCA 61.933 57.895 0.00 0.00 45.49 5.24
1731 3334 2.125832 TACCGCTGTTGCCTACGC 60.126 61.111 0.00 0.00 35.36 4.42
1758 3361 1.317431 ATAGTGCAGTACCACCGCGA 61.317 55.000 8.23 0.00 36.38 5.87
1759 3362 0.459585 AATAGTGCAGTACCACCGCG 60.460 55.000 2.64 0.00 36.38 6.46
1762 3365 4.571919 TGTACAAATAGTGCAGTACCACC 58.428 43.478 2.64 0.00 37.96 4.61
1812 3425 2.159407 GGTCGGACAAGCTACTCTACAC 60.159 54.545 10.76 0.00 0.00 2.90
1813 3426 2.089980 GGTCGGACAAGCTACTCTACA 58.910 52.381 10.76 0.00 0.00 2.74
1814 3427 1.063764 CGGTCGGACAAGCTACTCTAC 59.936 57.143 10.76 0.00 0.00 2.59
1815 3428 1.339438 ACGGTCGGACAAGCTACTCTA 60.339 52.381 10.76 0.00 0.00 2.43
1816 3429 0.608582 ACGGTCGGACAAGCTACTCT 60.609 55.000 10.76 0.00 0.00 3.24
1819 3432 0.731855 GTCACGGTCGGACAAGCTAC 60.732 60.000 10.76 2.23 35.36 3.58
1820 3433 1.582968 GTCACGGTCGGACAAGCTA 59.417 57.895 10.76 0.00 35.36 3.32
1821 3434 2.338984 GTCACGGTCGGACAAGCT 59.661 61.111 10.76 0.00 35.36 3.74
1822 3435 2.814183 ATCGTCACGGTCGGACAAGC 62.814 60.000 10.76 0.00 34.97 4.01
1823 3436 0.448990 TATCGTCACGGTCGGACAAG 59.551 55.000 10.76 5.92 34.97 3.16
1824 3437 0.168788 GTATCGTCACGGTCGGACAA 59.831 55.000 10.76 0.00 34.97 3.18
1825 3438 0.674581 AGTATCGTCACGGTCGGACA 60.675 55.000 10.76 0.00 34.97 4.02
1826 3439 0.027324 GAGTATCGTCACGGTCGGAC 59.973 60.000 0.00 0.00 0.00 4.79
1827 3440 2.387309 GAGTATCGTCACGGTCGGA 58.613 57.895 0.00 0.00 0.00 4.55
1872 3485 6.238869 GGCTAGGGTATAACAGTGTACACTAC 60.239 46.154 27.48 20.39 40.20 2.73
1959 3577 3.855689 ACTACGTTATGTACCACGCTT 57.144 42.857 0.00 0.00 40.16 4.68
2001 3632 4.288670 TGTAGATCTACGTACTTGCAGC 57.711 45.455 24.32 0.74 38.85 5.25
2002 3633 6.972901 TCAAATGTAGATCTACGTACTTGCAG 59.027 38.462 24.53 11.51 38.85 4.41
2004 3635 6.075519 CGTCAAATGTAGATCTACGTACTTGC 60.076 42.308 24.53 18.78 38.85 4.01
2016 3650 9.871238 ACATAGTTTTACTCGTCAAATGTAGAT 57.129 29.630 0.00 0.00 0.00 1.98
2017 3651 9.350357 GACATAGTTTTACTCGTCAAATGTAGA 57.650 33.333 0.00 0.00 33.44 2.59
2018 3652 8.311822 CGACATAGTTTTACTCGTCAAATGTAG 58.688 37.037 0.00 0.00 33.04 2.74
2132 3766 1.812686 GCACTCCACCAGTACACCGA 61.813 60.000 0.00 0.00 32.21 4.69
2185 3823 1.632409 AGTACCTAGGTGAGACGACCA 59.368 52.381 25.33 0.00 38.63 4.02
2195 3833 5.896963 ACCTAACACTAACAGTACCTAGGT 58.103 41.667 20.57 20.57 34.23 3.08
2231 3869 4.835615 GGAGGATTTCAGAGGCTATACTCA 59.164 45.833 8.36 0.00 39.97 3.41
2232 3870 4.082463 CGGAGGATTTCAGAGGCTATACTC 60.082 50.000 0.00 0.00 37.77 2.59
2254 3892 0.320683 TCCTTATGGCCGATGATGCG 60.321 55.000 0.00 0.00 0.00 4.73
2255 3893 1.160137 GTCCTTATGGCCGATGATGC 58.840 55.000 0.00 0.00 0.00 3.91
2258 3896 1.434188 ATGGTCCTTATGGCCGATGA 58.566 50.000 0.00 0.00 33.90 2.92
2260 3898 2.305927 CCTAATGGTCCTTATGGCCGAT 59.694 50.000 0.00 0.00 33.90 4.18
2327 3981 1.336702 TGTGCCGTTTCATGCAATTCC 60.337 47.619 0.00 0.00 39.57 3.01
2328 3982 1.720852 GTGTGCCGTTTCATGCAATTC 59.279 47.619 0.00 0.00 39.57 2.17
2348 4002 1.326852 CAGAGAGCTGTAGCAATTGCG 59.673 52.381 24.02 11.43 45.16 4.85
2375 4051 0.679960 AACAGGAATAACAGGCCGGC 60.680 55.000 21.18 21.18 0.00 6.13
2403 4079 2.125673 AGTACGTCCCGCATGCAC 60.126 61.111 19.57 7.58 0.00 4.57
2489 4170 5.001232 TCGGCCTAAATACATTTATGCTCC 58.999 41.667 16.43 5.60 40.98 4.70
2560 4250 2.426183 CTCGACGGAAGCGACAACG 61.426 63.158 0.00 0.00 42.93 4.10
2622 4312 2.494918 CCATCACTCGGTCGGTCC 59.505 66.667 0.00 0.00 0.00 4.46
2793 4519 7.094248 CCATTCTATATTCAATTCGGCCATTGA 60.094 37.037 13.16 13.16 40.68 2.57
2794 4520 7.031372 CCATTCTATATTCAATTCGGCCATTG 58.969 38.462 2.24 6.50 35.73 2.82
2795 4521 6.721208 ACCATTCTATATTCAATTCGGCCATT 59.279 34.615 2.24 0.00 0.00 3.16
2839 4569 0.032678 CTCAGAGCAGAACACACGGT 59.967 55.000 0.00 0.00 0.00 4.83
2843 4573 3.827008 AAAGTCTCAGAGCAGAACACA 57.173 42.857 0.00 0.00 0.00 3.72
2845 4575 4.679373 AGAAAAGTCTCAGAGCAGAACA 57.321 40.909 0.00 0.00 0.00 3.18
2870 4623 1.725931 CGCAGACGAAACAAGGCAATC 60.726 52.381 0.00 0.00 43.93 2.67
2876 4663 2.030457 AGACAAACGCAGACGAAACAAG 59.970 45.455 0.00 0.00 43.93 3.16
2884 4671 0.307760 CCCAACAGACAAACGCAGAC 59.692 55.000 0.00 0.00 0.00 3.51
2929 4716 4.152964 GGTCCCCGCGGTAGTTCC 62.153 72.222 26.12 16.71 0.00 3.62
2961 4793 1.375013 GGTTAAAGCCACGAGCCGA 60.375 57.895 1.50 0.00 45.47 5.54
2978 4830 1.181786 AATTGCATAACCACCGTGGG 58.818 50.000 21.77 4.90 43.37 4.61
2980 4832 2.514902 CGAAATTGCATAACCACCGTG 58.485 47.619 0.00 0.00 0.00 4.94
3003 4855 0.179089 ATCGCACTCCAGTCAGCATC 60.179 55.000 0.00 0.00 0.00 3.91
3240 5092 3.243401 GGATCCCGCATTTACAAATCCAC 60.243 47.826 0.00 0.00 33.08 4.02
3268 5122 2.032178 AGCAAACTCAAACGACAGAAGC 59.968 45.455 0.00 0.00 0.00 3.86
3298 5157 0.794473 CTTTTCTGGAACGCCCGTAC 59.206 55.000 0.00 0.00 37.93 3.67
3330 5189 1.280886 GATAGCCGCATGAGCAGTCG 61.281 60.000 10.37 0.00 42.27 4.18
3331 5190 0.948141 GGATAGCCGCATGAGCAGTC 60.948 60.000 10.37 7.36 42.27 3.51
3367 5242 1.218047 CTTCACTCGATCCGGGCAA 59.782 57.895 0.00 0.00 0.00 4.52
3382 5257 2.514824 GCCCCGTGCAGGATCTTC 60.515 66.667 8.24 0.00 45.00 2.87
3468 5345 0.304705 CCATCACCGATAAGCGCAAC 59.695 55.000 11.47 0.00 39.11 4.17
3474 5351 3.255888 TCCTCGATTCCATCACCGATAAG 59.744 47.826 0.00 0.00 0.00 1.73
3481 5358 2.166459 TGACACTCCTCGATTCCATCAC 59.834 50.000 0.00 0.00 0.00 3.06
3494 5377 6.166982 AGTTAGAACTAAGCAATGACACTCC 58.833 40.000 0.00 0.00 37.52 3.85
3528 5411 0.385390 CTGCACCACCACAAAGGAAC 59.615 55.000 0.00 0.00 41.22 3.62
3538 5421 2.736670 ATATTTCTCCCTGCACCACC 57.263 50.000 0.00 0.00 0.00 4.61
3606 5489 2.044352 TCGAGATCCACGGCTCCA 60.044 61.111 9.43 0.00 0.00 3.86
3709 5607 2.291043 GGTGACCCTCGGGACATGT 61.291 63.158 9.43 0.00 41.42 3.21
3732 5630 1.226603 GTCTTCGCATACGCCGACT 60.227 57.895 0.00 0.00 39.84 4.18
3745 5643 0.534203 TTGTGCTCGTTGGGGTCTTC 60.534 55.000 0.00 0.00 0.00 2.87
3905 5806 1.152204 TCCTTGAGACCCCACCGAA 60.152 57.895 0.00 0.00 0.00 4.30
3993 5894 4.560856 CGCTCCTCTTCCGCCTCG 62.561 72.222 0.00 0.00 0.00 4.63
3998 5899 0.030101 GATCTCACGCTCCTCTTCCG 59.970 60.000 0.00 0.00 0.00 4.30
4032 5933 1.880340 CTCGTCGATGAGCAAGCCC 60.880 63.158 21.10 0.00 0.00 5.19
4081 5982 3.359033 TGCGACACCTAGTAACCTACAT 58.641 45.455 0.00 0.00 0.00 2.29
4123 6032 7.418408 TGCAGTGTTTTGTTTTATTCGACATA 58.582 30.769 0.00 0.00 0.00 2.29
4146 6055 2.147958 TGAACATTTCCGTGTACCTGC 58.852 47.619 0.00 0.00 0.00 4.85
4147 6056 3.659786 TCTGAACATTTCCGTGTACCTG 58.340 45.455 0.00 0.00 0.00 4.00
4156 6067 0.447801 ACGCGCATCTGAACATTTCC 59.552 50.000 5.73 0.00 0.00 3.13
4159 6070 1.709760 CGACGCGCATCTGAACATT 59.290 52.632 5.73 0.00 0.00 2.71
4188 6099 0.863144 GCCGTCGTGTGCTCTAAAAA 59.137 50.000 0.00 0.00 0.00 1.94
4189 6100 0.032952 AGCCGTCGTGTGCTCTAAAA 59.967 50.000 0.00 0.00 30.33 1.52
4190 6101 0.666274 CAGCCGTCGTGTGCTCTAAA 60.666 55.000 0.00 0.00 35.12 1.85
4191 6102 1.080772 CAGCCGTCGTGTGCTCTAA 60.081 57.895 0.00 0.00 35.12 2.10
4192 6103 1.802337 AACAGCCGTCGTGTGCTCTA 61.802 55.000 0.00 0.00 35.12 2.43
4193 6104 2.644555 AAACAGCCGTCGTGTGCTCT 62.645 55.000 0.00 0.00 35.12 4.09
4194 6105 1.772063 AAAACAGCCGTCGTGTGCTC 61.772 55.000 0.00 0.00 35.12 4.26
4195 6106 1.373590 AAAAACAGCCGTCGTGTGCT 61.374 50.000 0.00 0.00 38.67 4.40
4196 6107 1.063488 AAAAACAGCCGTCGTGTGC 59.937 52.632 0.00 0.00 0.00 4.57
4197 6108 1.199852 GCAAAAACAGCCGTCGTGTG 61.200 55.000 0.00 0.00 0.00 3.82
4198 6109 1.063488 GCAAAAACAGCCGTCGTGT 59.937 52.632 0.00 0.00 0.00 4.49
4199 6110 2.003443 CGCAAAAACAGCCGTCGTG 61.003 57.895 0.00 0.00 0.00 4.35
4200 6111 2.326550 CGCAAAAACAGCCGTCGT 59.673 55.556 0.00 0.00 0.00 4.34
4201 6112 3.091022 GCGCAAAAACAGCCGTCG 61.091 61.111 0.30 0.00 0.00 5.12
4202 6113 2.729491 GGCGCAAAAACAGCCGTC 60.729 61.111 10.83 0.00 41.53 4.79
4205 6116 2.429069 CTCGGCGCAAAAACAGCC 60.429 61.111 10.83 0.00 46.88 4.85
4206 6117 1.725973 GACTCGGCGCAAAAACAGC 60.726 57.895 10.83 0.00 0.00 4.40
4207 6118 1.082104 GGACTCGGCGCAAAAACAG 60.082 57.895 10.83 0.00 0.00 3.16
4208 6119 1.503818 GAGGACTCGGCGCAAAAACA 61.504 55.000 10.83 0.00 0.00 2.83
4209 6120 1.206831 GAGGACTCGGCGCAAAAAC 59.793 57.895 10.83 0.00 0.00 2.43
4210 6121 1.227704 TGAGGACTCGGCGCAAAAA 60.228 52.632 10.83 0.00 0.00 1.94
4211 6122 1.667830 CTGAGGACTCGGCGCAAAA 60.668 57.895 10.83 0.00 0.00 2.44
4212 6123 2.048222 CTGAGGACTCGGCGCAAA 60.048 61.111 10.83 0.00 0.00 3.68
4213 6124 2.867855 AACTGAGGACTCGGCGCAA 61.868 57.895 10.83 0.00 39.55 4.85
4214 6125 3.303135 AACTGAGGACTCGGCGCA 61.303 61.111 10.83 0.00 39.55 6.09
4215 6126 2.811317 CAACTGAGGACTCGGCGC 60.811 66.667 0.00 0.00 39.55 6.53
4216 6127 2.771763 AAGCAACTGAGGACTCGGCG 62.772 60.000 0.00 0.00 39.55 6.46
4217 6128 1.004440 AAGCAACTGAGGACTCGGC 60.004 57.895 8.04 3.09 39.55 5.54
4218 6129 0.318441 TGAAGCAACTGAGGACTCGG 59.682 55.000 6.61 6.61 41.63 4.63
4219 6130 1.423395 GTGAAGCAACTGAGGACTCG 58.577 55.000 0.00 0.00 0.00 4.18
4220 6131 1.070758 TGGTGAAGCAACTGAGGACTC 59.929 52.381 0.00 0.00 0.00 3.36
4221 6132 1.131638 TGGTGAAGCAACTGAGGACT 58.868 50.000 0.00 0.00 0.00 3.85
4222 6133 1.808945 CATGGTGAAGCAACTGAGGAC 59.191 52.381 0.00 0.00 0.00 3.85
4223 6134 1.883638 GCATGGTGAAGCAACTGAGGA 60.884 52.381 0.00 0.00 0.00 3.71
4224 6135 0.524862 GCATGGTGAAGCAACTGAGG 59.475 55.000 0.00 0.00 0.00 3.86
4225 6136 0.167470 CGCATGGTGAAGCAACTGAG 59.833 55.000 0.00 0.00 0.00 3.35
4226 6137 1.855213 GCGCATGGTGAAGCAACTGA 61.855 55.000 0.30 0.00 0.00 3.41
4227 6138 1.443194 GCGCATGGTGAAGCAACTG 60.443 57.895 0.30 0.00 0.00 3.16
4228 6139 1.601759 AGCGCATGGTGAAGCAACT 60.602 52.632 11.47 0.00 0.00 3.16
4229 6140 1.443194 CAGCGCATGGTGAAGCAAC 60.443 57.895 11.47 0.00 46.53 4.17
4230 6141 2.956194 CAGCGCATGGTGAAGCAA 59.044 55.556 11.47 0.00 46.53 3.91
4231 6142 3.740397 GCAGCGCATGGTGAAGCA 61.740 61.111 11.47 0.00 46.53 3.91
4232 6143 2.752322 TTTGCAGCGCATGGTGAAGC 62.752 55.000 11.47 0.51 46.53 3.86
4233 6144 0.108992 ATTTGCAGCGCATGGTGAAG 60.109 50.000 11.47 0.00 46.53 3.02
4234 6145 0.317799 AATTTGCAGCGCATGGTGAA 59.682 45.000 11.47 0.00 46.53 3.18
4235 6146 0.317799 AAATTTGCAGCGCATGGTGA 59.682 45.000 11.47 0.00 46.53 4.02
4236 6147 1.149987 AAAATTTGCAGCGCATGGTG 58.850 45.000 11.47 0.00 46.34 4.17
4237 6148 1.881591 AAAAATTTGCAGCGCATGGT 58.118 40.000 11.47 0.00 38.76 3.55
4238 6149 2.222863 GCTAAAAATTTGCAGCGCATGG 60.223 45.455 11.47 0.00 38.76 3.66
4239 6150 3.029167 GCTAAAAATTTGCAGCGCATG 57.971 42.857 11.47 6.31 38.76 4.06
4244 6155 0.246873 GCGCGCTAAAAATTTGCAGC 60.247 50.000 26.67 12.22 0.00 5.25
4245 6156 0.366534 GGCGCGCTAAAAATTTGCAG 59.633 50.000 32.29 0.00 0.00 4.41
4246 6157 1.340657 CGGCGCGCTAAAAATTTGCA 61.341 50.000 32.29 0.00 0.00 4.08
4247 6158 1.340131 CGGCGCGCTAAAAATTTGC 59.660 52.632 32.29 8.93 0.00 3.68
4248 6159 1.056869 AACGGCGCGCTAAAAATTTG 58.943 45.000 32.29 11.51 0.00 2.32
4249 6160 1.056869 CAACGGCGCGCTAAAAATTT 58.943 45.000 32.29 10.45 0.00 1.82
4250 6161 0.039888 ACAACGGCGCGCTAAAAATT 60.040 45.000 32.29 13.05 0.00 1.82
4251 6162 0.797542 TACAACGGCGCGCTAAAAAT 59.202 45.000 32.29 14.74 0.00 1.82
4252 6163 0.164217 CTACAACGGCGCGCTAAAAA 59.836 50.000 32.29 11.49 0.00 1.94
4253 6164 1.782807 CTACAACGGCGCGCTAAAA 59.217 52.632 32.29 10.92 0.00 1.52
4254 6165 2.732670 GCTACAACGGCGCGCTAAA 61.733 57.895 32.29 9.81 0.00 1.85
4255 6166 3.183323 GCTACAACGGCGCGCTAA 61.183 61.111 32.29 9.08 0.00 3.09
4262 6173 2.778679 CTGAAGCGCTACAACGGC 59.221 61.111 12.05 0.00 0.00 5.68
4263 6174 1.959899 CTGCTGAAGCGCTACAACGG 61.960 60.000 12.05 9.25 45.83 4.44
4264 6175 1.417592 CTGCTGAAGCGCTACAACG 59.582 57.895 12.05 0.00 45.83 4.10
4265 6176 1.790387 CCTGCTGAAGCGCTACAAC 59.210 57.895 12.05 1.22 45.83 3.32
4266 6177 2.034879 GCCTGCTGAAGCGCTACAA 61.035 57.895 12.05 0.00 45.83 2.41
4267 6178 2.434884 GCCTGCTGAAGCGCTACA 60.435 61.111 12.05 6.24 45.83 2.74
4268 6179 3.558411 CGCCTGCTGAAGCGCTAC 61.558 66.667 12.05 0.79 46.50 3.58
4274 6185 1.911293 TTTTAGCGCGCCTGCTGAAG 61.911 55.000 30.33 0.00 46.70 3.02
4275 6186 1.305219 ATTTTAGCGCGCCTGCTGAA 61.305 50.000 30.33 14.04 46.70 3.02
4276 6187 0.461163 TATTTTAGCGCGCCTGCTGA 60.461 50.000 30.33 9.86 46.70 4.26
4277 6188 0.316196 GTATTTTAGCGCGCCTGCTG 60.316 55.000 30.33 0.00 46.70 4.41
4279 6190 0.316196 CTGTATTTTAGCGCGCCTGC 60.316 55.000 30.33 11.62 37.91 4.85
4280 6191 0.316196 GCTGTATTTTAGCGCGCCTG 60.316 55.000 30.33 15.16 0.00 4.85
4281 6192 2.014594 GCTGTATTTTAGCGCGCCT 58.985 52.632 30.33 17.79 0.00 5.52
4282 6193 4.589967 GCTGTATTTTAGCGCGCC 57.410 55.556 30.33 11.28 0.00 6.53
4287 6198 2.105323 ATTGCGCGCTGTATTTTAGC 57.895 45.000 33.29 0.00 37.80 3.09
4288 6199 3.960002 GTGTATTGCGCGCTGTATTTTAG 59.040 43.478 33.29 0.00 0.00 1.85
4289 6200 3.371285 TGTGTATTGCGCGCTGTATTTTA 59.629 39.130 33.29 5.92 0.00 1.52
4290 6201 2.160615 TGTGTATTGCGCGCTGTATTTT 59.839 40.909 33.29 10.99 0.00 1.82
4291 6202 1.735018 TGTGTATTGCGCGCTGTATTT 59.265 42.857 33.29 12.40 0.00 1.40
4292 6203 1.364721 TGTGTATTGCGCGCTGTATT 58.635 45.000 33.29 14.19 0.00 1.89
4293 6204 1.581934 ATGTGTATTGCGCGCTGTAT 58.418 45.000 33.29 23.13 0.00 2.29
4294 6205 1.855978 GTATGTGTATTGCGCGCTGTA 59.144 47.619 33.29 21.10 0.00 2.74
4295 6206 0.650512 GTATGTGTATTGCGCGCTGT 59.349 50.000 33.29 22.20 0.00 4.40
4296 6207 0.649993 TGTATGTGTATTGCGCGCTG 59.350 50.000 33.29 0.00 0.00 5.18
4297 6208 1.581934 ATGTATGTGTATTGCGCGCT 58.418 45.000 33.29 16.10 0.00 5.92
4298 6209 2.219903 TGTATGTATGTGTATTGCGCGC 59.780 45.455 27.26 27.26 0.00 6.86
4299 6210 3.244111 TGTGTATGTATGTGTATTGCGCG 59.756 43.478 0.00 0.00 0.00 6.86
4300 6211 4.787381 TGTGTATGTATGTGTATTGCGC 57.213 40.909 0.00 0.00 0.00 6.09
4301 6212 7.535599 TGTTTTTGTGTATGTATGTGTATTGCG 59.464 33.333 0.00 0.00 0.00 4.85
4302 6213 8.735303 TGTTTTTGTGTATGTATGTGTATTGC 57.265 30.769 0.00 0.00 0.00 3.56
4389 6300 3.308401 AGTGCCAAGTGATTTTCCCTTT 58.692 40.909 0.00 0.00 0.00 3.11
4543 6454 0.538057 TTCAGCACTGCCCAAGGAAG 60.538 55.000 0.00 0.00 0.00 3.46
4545 6456 0.106268 TTTTCAGCACTGCCCAAGGA 60.106 50.000 0.00 0.00 0.00 3.36
4799 6712 3.418995 TGCGTAACTACAGAGGAGAAGT 58.581 45.455 0.00 0.00 0.00 3.01
4918 6831 0.546747 AGACCGGGAACATCCAAGGA 60.547 55.000 6.32 0.00 38.64 3.36
4976 6890 1.698506 TAAACCCCCAAACAGCACAG 58.301 50.000 0.00 0.00 0.00 3.66
4981 6895 4.893524 AGAAAGAGTTAAACCCCCAAACAG 59.106 41.667 0.00 0.00 0.00 3.16
5027 6941 0.951525 CGCGTGGTACATTTGGTGGA 60.952 55.000 0.00 0.00 44.52 4.02


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

AutoCloner maintained by Alex Coulton.