Multiple sequence alignment - TraesCS3D01G141000

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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 TraesCS3D01G141000 chr3D 100.000 7895 0 0 1 7895 103361678 103353784 0.000000e+00 14580
1 TraesCS3D01G141000 chr3D 96.992 133 3 1 4830 4962 103356717 103356586 1.030000e-53 222
2 TraesCS3D01G141000 chr3D 96.992 133 3 1 4962 5093 103356849 103356717 1.030000e-53 222
3 TraesCS3D01G141000 chr3B 95.239 4663 145 29 1 4627 153965239 153960618 0.000000e+00 7310
4 TraesCS3D01G141000 chr3B 91.692 3298 165 59 4664 7895 153960614 153957360 0.000000e+00 4471
5 TraesCS3D01G141000 chr3B 95.489 133 5 1 4830 4962 153960316 153960185 2.230000e-50 211
6 TraesCS3D01G141000 chr3B 95.489 133 5 1 4962 5093 153960448 153960316 2.230000e-50 211
7 TraesCS3D01G141000 chr3A 92.099 1329 84 14 2313 3632 552782683 552783999 0.000000e+00 1853
8 TraesCS3D01G141000 chr3A 88.378 1523 118 24 739 2205 552781138 552782657 0.000000e+00 1777
9 TraesCS3D01G141000 chr3A 87.509 1449 106 44 4970 6356 552785633 552787068 0.000000e+00 1604
10 TraesCS3D01G141000 chr3A 86.374 888 60 27 3911 4768 552784117 552784973 0.000000e+00 913
11 TraesCS3D01G141000 chr3A 83.225 614 49 24 6356 6926 552787107 552787709 1.520000e-141 514
12 TraesCS3D01G141000 chr3A 81.116 233 24 7 7141 7355 552787829 552788059 1.360000e-37 169
13 TraesCS3D01G141000 chr4A 76.074 326 74 4 2884 3207 535430654 535430331 4.900000e-37 167


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 TraesCS3D01G141000 chr3D 103353784 103361678 7894 True 14580.000000 14580 100.000000 1 7895 1 chr3D.!!$R1 7894
1 TraesCS3D01G141000 chr3B 153957360 153965239 7879 True 3050.750000 7310 94.477250 1 7895 4 chr3B.!!$R1 7894
2 TraesCS3D01G141000 chr3A 552781138 552788059 6921 False 1138.333333 1853 86.450167 739 7355 6 chr3A.!!$F1 6616

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
247 249 0.955428 GTTCATGTGCGGAGGAAGCA 60.955 55.000 0.00 0.00 42.99 3.91 F
1498 1538 0.250513 GGTCTCTGCTTCGGGACATT 59.749 55.000 4.17 0.00 0.00 2.71 F
2157 2221 1.134946 CGAATTTGGTGGAGGCATTCC 59.865 52.381 0.00 0.00 46.98 3.01 F
2757 2832 1.267121 TTGACAGAGCCTCAGGTACC 58.733 55.000 2.73 2.73 0.00 3.34 F
3194 3270 1.803366 GCAAGCCTATCATGCCTGGC 61.803 60.000 12.87 12.87 45.21 4.85 F
4273 4356 2.094649 GGTCGAAGGTACTCTCAACCAG 60.095 54.545 0.00 0.00 38.49 4.00 F
4637 4738 2.414559 CGCTGTTGCCATTTTGTCCTAG 60.415 50.000 0.00 0.00 35.36 3.02 F
6339 6966 2.808906 AGGGTGACATTTTAGGAGCC 57.191 50.000 0.00 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1624 1669 1.861542 TTGCAAATCCCAAGCGTCCG 61.862 55.000 0.00 0.00 0.00 4.79 R
2757 2832 0.250467 CCCCTGCATCGGAATACCAG 60.250 60.000 1.50 0.00 35.59 4.00 R
3576 3653 1.955080 ACGCCCGAAATAACCAAACAA 59.045 42.857 0.00 0.00 0.00 2.83 R
4310 4393 1.003580 GGTCAGCAGAACCTTCATCCA 59.996 52.381 0.00 0.00 0.00 3.41 R
4916 5106 2.039084 GTGAAGAAGATCCCAGTGTGGT 59.961 50.000 0.00 0.00 35.17 4.16 R
5789 6390 0.314302 AGACGTGTTTGGAGTCTCCG 59.686 55.000 14.34 3.58 40.85 4.63 R
6481 7149 1.215647 CCGGTCGTTCTCCTTGAGG 59.784 63.158 0.00 0.00 0.00 3.86 R
7684 8522 0.038159 AAGTAGCCACTCGTGCTCAC 60.038 55.000 0.00 0.00 40.23 3.51 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
113 114 3.216800 ACACGCAATATGCTGGAATGAT 58.783 40.909 0.43 0.00 42.25 2.45
114 115 3.633525 ACACGCAATATGCTGGAATGATT 59.366 39.130 0.43 0.00 42.25 2.57
226 228 3.810941 TCTTTGTGCGTTTCCGTCTAATT 59.189 39.130 0.00 0.00 36.15 1.40
234 236 4.553429 GCGTTTCCGTCTAATTTGTTCATG 59.447 41.667 0.00 0.00 36.15 3.07
237 239 4.678509 TCCGTCTAATTTGTTCATGTGC 57.321 40.909 0.00 0.00 0.00 4.57
238 240 3.124466 TCCGTCTAATTTGTTCATGTGCG 59.876 43.478 0.00 0.00 0.00 5.34
239 241 3.416277 CGTCTAATTTGTTCATGTGCGG 58.584 45.455 0.00 0.00 0.00 5.69
240 242 3.124466 CGTCTAATTTGTTCATGTGCGGA 59.876 43.478 0.00 0.00 0.00 5.54
241 243 4.651994 GTCTAATTTGTTCATGTGCGGAG 58.348 43.478 0.00 0.00 0.00 4.63
242 244 3.689161 TCTAATTTGTTCATGTGCGGAGG 59.311 43.478 0.00 0.00 0.00 4.30
243 245 2.198827 ATTTGTTCATGTGCGGAGGA 57.801 45.000 0.00 0.00 0.00 3.71
247 249 0.955428 GTTCATGTGCGGAGGAAGCA 60.955 55.000 0.00 0.00 42.99 3.91
304 306 7.454066 TGGCCATGCATAATCCTATTATTTTGA 59.546 33.333 0.00 0.00 0.00 2.69
364 366 4.978186 TGTTTTAGACAGGTCGATACTCG 58.022 43.478 0.00 0.00 36.02 4.18
380 382 7.164498 GTCGATACTCGTTGAGTTGAAGATAAG 59.836 40.741 4.60 0.00 40.28 1.73
385 387 4.748102 TCGTTGAGTTGAAGATAAGCGTTT 59.252 37.500 0.00 0.00 0.00 3.60
448 450 3.825143 AATTTGGATGCCAACATAGCC 57.175 42.857 0.00 0.00 43.82 3.93
506 508 2.440253 TCGGATGGGTTATTGGTTAGGG 59.560 50.000 0.00 0.00 0.00 3.53
517 519 6.837048 GGTTATTGGTTAGGGGACAATTATGT 59.163 38.462 0.00 0.00 44.25 2.29
597 599 9.500864 TTGAAAAGCAAATTTAAAAGCATTGTC 57.499 25.926 11.57 8.52 32.46 3.18
632 634 8.593492 AAGAAGAAAATAACCAACATTGCTTC 57.407 30.769 0.00 0.00 32.87 3.86
670 672 4.695455 CCATTGTCGACAAATTGACCTACT 59.305 41.667 32.69 11.22 38.35 2.57
671 673 5.163854 CCATTGTCGACAAATTGACCTACTC 60.164 44.000 32.69 0.00 38.35 2.59
679 681 6.183360 CGACAAATTGACCTACTCATTGACTC 60.183 42.308 0.00 0.00 0.00 3.36
683 685 9.219603 CAAATTGACCTACTCATTGACTCTTTA 57.780 33.333 0.00 0.00 0.00 1.85
697 699 9.734620 CATTGACTCTTTACATGAAAAGTCAAA 57.265 29.630 25.42 18.58 45.44 2.69
717 719 9.093458 AGTCAAAATCATAAATCCAAACTCCTT 57.907 29.630 0.00 0.00 0.00 3.36
735 737 3.264964 TCCTTCTATACGGCCAACCTTTT 59.735 43.478 2.24 0.00 0.00 2.27
736 738 4.014406 CCTTCTATACGGCCAACCTTTTT 58.986 43.478 2.24 0.00 0.00 1.94
765 773 6.038271 CCAGTAAATACACAATGTTAGAGGCC 59.962 42.308 0.00 0.00 0.00 5.19
781 789 2.755103 GAGGCCTACCCATGAAAAACTG 59.245 50.000 4.42 0.00 36.11 3.16
805 828 5.166398 CCAAAGAAGCAATCAAAGGATCAC 58.834 41.667 0.00 0.00 31.88 3.06
809 832 2.359900 AGCAATCAAAGGATCACGACC 58.640 47.619 0.00 0.00 31.88 4.79
869 892 1.000359 TCCCTCACTCATCTCGCCA 60.000 57.895 0.00 0.00 0.00 5.69
1498 1538 0.250513 GGTCTCTGCTTCGGGACATT 59.749 55.000 4.17 0.00 0.00 2.71
1553 1594 1.701847 TGCTGCCTCTCCTTTTCTTCT 59.298 47.619 0.00 0.00 0.00 2.85
1624 1669 9.846248 TCTTTATTCTTTCTTGATTGCTTTAGC 57.154 29.630 0.00 0.00 42.50 3.09
1628 1673 4.154195 TCTTTCTTGATTGCTTTAGCGGAC 59.846 41.667 0.00 0.00 45.83 4.79
1705 1753 1.623542 ATTGGTAGCTGGGGACGACC 61.624 60.000 0.00 0.00 39.11 4.79
1767 1818 4.996788 ATCTTGGATGAGAAAATGTGGC 57.003 40.909 0.00 0.00 0.00 5.01
1837 1888 5.684704 TGGAACCTGGAAATATCAGACATC 58.315 41.667 0.00 0.00 34.36 3.06
1913 1968 4.200092 GGATAGGCAAAAAGTAGACCCAG 58.800 47.826 0.00 0.00 0.00 4.45
1915 1970 3.595190 AGGCAAAAAGTAGACCCAGTT 57.405 42.857 0.00 0.00 0.00 3.16
1919 1974 4.261614 GGCAAAAAGTAGACCCAGTTTCTG 60.262 45.833 0.00 0.00 0.00 3.02
1928 1983 3.910627 AGACCCAGTTTCTGTAGGTTCAT 59.089 43.478 0.00 0.00 28.78 2.57
1955 2010 4.813750 TCTTAGTTTAGTTCCCTTCCCG 57.186 45.455 0.00 0.00 0.00 5.14
2157 2221 1.134946 CGAATTTGGTGGAGGCATTCC 59.865 52.381 0.00 0.00 46.98 3.01
2240 2305 7.332678 AGGTGAAAGCAATGCATTATTTTTCTC 59.667 33.333 26.04 23.69 36.26 2.87
2278 2343 6.036735 TGCTGTAATTAACGAGCCTGTAAATC 59.963 38.462 8.98 0.00 33.74 2.17
2348 2421 4.206477 TGTGTACATAGATGCTTGCTGT 57.794 40.909 0.00 0.00 0.00 4.40
2365 2438 5.984233 TGCTGTACTAAGTTGTCAGTTTG 57.016 39.130 0.00 0.00 0.00 2.93
2437 2512 7.982919 TCAATCATTGCTCTTTTTCCCATTATG 59.017 33.333 0.00 0.00 0.00 1.90
2494 2569 4.876107 GGTCAGGGAACATACAGTAATGTG 59.124 45.833 5.98 0.00 39.98 3.21
2608 2683 2.102578 AGGGAAATCCTCATTTTGCGG 58.897 47.619 0.00 0.00 44.06 5.69
2743 2818 7.470009 GCTTCTTTTCCTGGACTAAAATTGACA 60.470 37.037 0.00 0.00 0.00 3.58
2757 2832 1.267121 TTGACAGAGCCTCAGGTACC 58.733 55.000 2.73 2.73 0.00 3.34
3194 3270 1.803366 GCAAGCCTATCATGCCTGGC 61.803 60.000 12.87 12.87 45.21 4.85
3253 3329 3.698029 AGCAAGTGCAACAAGTTAGTG 57.302 42.857 6.00 0.00 45.16 2.74
3780 3859 7.359514 GCTTGCTTCTGATTGGATTTTTAACAC 60.360 37.037 0.00 0.00 0.00 3.32
3825 3904 4.547532 AGTTAGTTGCACTGTCTAAGACG 58.452 43.478 0.00 0.00 34.95 4.18
3847 3926 4.219919 GGTAATGAAGAGCTCCTCCTACT 58.780 47.826 10.93 0.00 0.00 2.57
3848 3927 4.651962 GGTAATGAAGAGCTCCTCCTACTT 59.348 45.833 10.93 0.00 0.00 2.24
3849 3928 5.834204 GGTAATGAAGAGCTCCTCCTACTTA 59.166 44.000 10.93 0.54 0.00 2.24
3850 3929 6.495526 GGTAATGAAGAGCTCCTCCTACTTAT 59.504 42.308 10.93 0.00 0.00 1.73
3851 3930 7.015779 GGTAATGAAGAGCTCCTCCTACTTATT 59.984 40.741 10.93 4.50 0.00 1.40
3852 3931 7.444703 AATGAAGAGCTCCTCCTACTTATTT 57.555 36.000 10.93 0.00 0.00 1.40
3857 3936 9.267084 GAAGAGCTCCTCCTACTTATTTTTATG 57.733 37.037 10.93 0.00 0.00 1.90
3860 3939 8.738645 AGCTCCTCCTACTTATTTTTATGTTG 57.261 34.615 0.00 0.00 0.00 3.33
3865 3944 9.892130 CCTCCTACTTATTTTTATGTTGTCTCT 57.108 33.333 0.00 0.00 0.00 3.10
3880 3959 4.963318 TGTCTCTGAGAGTCACCATTTT 57.037 40.909 7.80 0.00 0.00 1.82
3926 4006 5.860941 TTCTTTTAGTTGGGTGCAATTGA 57.139 34.783 10.34 0.00 0.00 2.57
4273 4356 2.094649 GGTCGAAGGTACTCTCAACCAG 60.095 54.545 0.00 0.00 38.49 4.00
4310 4393 8.535335 TGAACTGAGAACATTCTTATAGAGCTT 58.465 33.333 0.00 0.00 37.73 3.74
4378 4461 6.592607 TCATATAGAACTGGAAACACGGTTTC 59.407 38.462 16.52 16.52 39.91 2.78
4458 4541 3.557595 CCTCATCGAATGCCTAACTTGTC 59.442 47.826 0.00 0.00 0.00 3.18
4614 4715 4.142600 CCACATTTTCTTTCCTCTAAGCCG 60.143 45.833 0.00 0.00 0.00 5.52
4637 4738 2.414559 CGCTGTTGCCATTTTGTCCTAG 60.415 50.000 0.00 0.00 35.36 3.02
4641 4742 3.568007 TGTTGCCATTTTGTCCTAGTGAC 59.432 43.478 4.84 4.84 44.72 3.67
4659 4760 6.899393 AGTGACATTTATTTGTGGACACAT 57.101 33.333 5.91 0.00 41.52 3.21
4662 4765 7.014134 AGTGACATTTATTTGTGGACACATGAA 59.986 33.333 5.91 0.00 41.52 2.57
4725 4835 5.068591 TGAAATCTGATGCCAATGGAATGAG 59.931 40.000 2.05 0.67 0.00 2.90
4730 4840 5.104402 TCTGATGCCAATGGAATGAGTAAGA 60.104 40.000 6.61 0.00 0.00 2.10
4750 4860 4.887748 AGAACTTATGTGGGAGCATATCG 58.112 43.478 0.00 0.00 32.16 2.92
4942 5132 3.108376 ACTGGGATCTTCTTCACCTACC 58.892 50.000 0.00 0.00 0.00 3.18
5174 5748 6.889177 TGATCTTTCATTGCCTATGGTTTGTA 59.111 34.615 0.00 0.00 34.85 2.41
5402 5990 7.624360 TGCAGGTATAACCAACTCTTTTATG 57.376 36.000 0.00 0.00 41.95 1.90
5410 5998 6.824305 AACCAACTCTTTTATGGACATCTG 57.176 37.500 0.00 0.00 37.66 2.90
5470 6068 9.944663 TCACTGTTATTAGTGTTGTTTGAAATC 57.055 29.630 5.89 0.00 46.32 2.17
5482 6081 7.064490 GTGTTGTTTGAAATCATGTTTCCACTT 59.936 33.333 14.25 0.00 0.00 3.16
5613 6213 9.295825 TCAGTGCATTTTCCTCTAGATTTTTAA 57.704 29.630 0.00 0.00 0.00 1.52
5654 6255 6.930667 ATTTTGGAATGCCTAAATTCATGC 57.069 33.333 6.33 0.00 43.86 4.06
5655 6256 4.405116 TTGGAATGCCTAAATTCATGCC 57.595 40.909 0.00 0.00 38.61 4.40
5789 6390 6.258230 TCAACTCACATCATTGAATTGTCC 57.742 37.500 0.00 0.00 29.56 4.02
6121 6722 5.540337 TGGATGGAGGAGCTATTGTAAGTAG 59.460 44.000 0.00 0.00 0.00 2.57
6178 6780 8.158169 TCTTATGCCATTTCATTCATGTCTAC 57.842 34.615 0.00 0.00 0.00 2.59
6223 6825 6.581919 TCATATGTTGCACTTGTTTGAAATCG 59.418 34.615 1.90 0.00 0.00 3.34
6239 6865 4.932799 TGAAATCGAAATACCGTCACATGT 59.067 37.500 0.00 0.00 0.00 3.21
6305 6932 3.181457 ACAGACCATGATCCTAGTGCATG 60.181 47.826 0.00 8.81 39.20 4.06
6315 6942 6.288294 TGATCCTAGTGCATGGTAAATACAC 58.712 40.000 0.00 0.00 0.00 2.90
6318 6945 5.105269 TCCTAGTGCATGGTAAATACACGAA 60.105 40.000 0.00 0.00 36.38 3.85
6339 6966 2.808906 AGGGTGACATTTTAGGAGCC 57.191 50.000 0.00 0.00 0.00 4.70
6433 7101 3.173953 TCCAAAGGCAACAAGATCCAT 57.826 42.857 0.00 0.00 41.41 3.41
6481 7149 1.872679 GGGCAACGTCGACGAGATC 60.873 63.158 41.52 25.77 43.02 2.75
6514 7182 1.452108 CCGGCAAATCCAGGAGGTC 60.452 63.158 0.00 0.00 35.89 3.85
6706 7391 6.785488 TCATATAGCTTAGTGGCAAAATCG 57.215 37.500 0.00 0.00 34.17 3.34
6732 7429 3.672241 CGTTTTATTGCTTCTTTCCCCCG 60.672 47.826 0.00 0.00 0.00 5.73
6735 7432 0.967380 ATTGCTTCTTTCCCCCGCTG 60.967 55.000 0.00 0.00 0.00 5.18
6807 7505 3.253188 CCGTGTAATATTTGCCTGATGGG 59.747 47.826 0.00 0.00 38.36 4.00
6831 7534 4.098847 ACGGAGGTGAGGTGAGAC 57.901 61.111 0.00 0.00 0.00 3.36
6842 7545 3.462678 GTGAGACGGGGAGGAGGC 61.463 72.222 0.00 0.00 0.00 4.70
6928 7638 3.769536 CGTTTCAGTTTCTGGTTTGCTT 58.230 40.909 0.00 0.00 31.51 3.91
6929 7639 3.547468 CGTTTCAGTTTCTGGTTTGCTTG 59.453 43.478 0.00 0.00 31.51 4.01
6931 7641 3.781079 TCAGTTTCTGGTTTGCTTGTG 57.219 42.857 0.00 0.00 31.51 3.33
6932 7642 3.351740 TCAGTTTCTGGTTTGCTTGTGA 58.648 40.909 0.00 0.00 31.51 3.58
6944 7661 1.064758 TGCTTGTGAAGGTGGAGTGTT 60.065 47.619 0.00 0.00 0.00 3.32
6961 7678 2.030457 GTGTTCCACTCGTTCACTGTTG 59.970 50.000 0.00 0.00 0.00 3.33
6967 7684 3.123050 CACTCGTTCACTGTTGATGACA 58.877 45.455 0.00 0.00 36.65 3.58
6985 7702 3.890756 TGACACTAGAAACCGACCTGTAA 59.109 43.478 0.00 0.00 0.00 2.41
6997 7714 0.036388 ACCTGTAACTGTGATGGGCG 60.036 55.000 0.00 0.00 0.00 6.13
7025 7742 1.371558 GCCTCGGGTCAGTTTCAGT 59.628 57.895 0.00 0.00 0.00 3.41
7031 7748 2.143925 CGGGTCAGTTTCAGTTTCCTC 58.856 52.381 0.00 0.00 0.00 3.71
7052 7769 2.619849 CCTGGATCACTTTGGCTGATGT 60.620 50.000 0.00 0.00 0.00 3.06
7053 7770 3.370846 CCTGGATCACTTTGGCTGATGTA 60.371 47.826 0.00 0.00 0.00 2.29
7054 7771 4.458397 CTGGATCACTTTGGCTGATGTAT 58.542 43.478 0.00 0.00 0.00 2.29
7055 7772 5.455183 CCTGGATCACTTTGGCTGATGTATA 60.455 44.000 0.00 0.00 0.00 1.47
7056 7773 6.191657 TGGATCACTTTGGCTGATGTATAT 57.808 37.500 0.00 0.00 0.00 0.86
7057 7774 7.315066 TGGATCACTTTGGCTGATGTATATA 57.685 36.000 0.00 0.00 0.00 0.86
7058 7775 7.744733 TGGATCACTTTGGCTGATGTATATAA 58.255 34.615 0.00 0.00 0.00 0.98
7059 7776 7.879677 TGGATCACTTTGGCTGATGTATATAAG 59.120 37.037 0.00 0.00 0.00 1.73
7060 7777 7.335422 GGATCACTTTGGCTGATGTATATAAGG 59.665 40.741 0.00 0.00 0.00 2.69
7105 7893 3.559238 AAAATCAAGCGCCTAGTTGTG 57.441 42.857 2.29 0.00 0.00 3.33
7123 7911 4.886247 TGTGAACTTACGAAAAACCTGG 57.114 40.909 0.00 0.00 0.00 4.45
7145 7933 1.153329 AGACACGTCCGCAAAACCA 60.153 52.632 0.00 0.00 0.00 3.67
7146 7934 1.010462 GACACGTCCGCAAAACCAC 60.010 57.895 0.00 0.00 0.00 4.16
7168 7956 0.319986 TCACGGAACATTGCAGCGTA 60.320 50.000 0.00 0.00 0.00 4.42
7171 7969 2.543848 CACGGAACATTGCAGCGTATAT 59.456 45.455 0.00 0.00 0.00 0.86
7177 7975 1.069022 CATTGCAGCGTATATGGCACC 60.069 52.381 0.00 0.00 35.74 5.01
7207 8005 1.542030 GGCGATCGACATAGACTCCAT 59.458 52.381 21.57 0.00 0.00 3.41
7237 8045 1.751924 AGAAGAGAGCACCGGTCATAC 59.248 52.381 2.59 0.00 31.89 2.39
7257 8068 2.435805 ACTCATCACCCATCGCACTAAT 59.564 45.455 0.00 0.00 0.00 1.73
7397 8213 5.933187 TTTTCTCGTTAAATACTGCAGCA 57.067 34.783 15.27 0.00 0.00 4.41
7399 8215 3.920446 TCTCGTTAAATACTGCAGCACA 58.080 40.909 15.27 0.00 0.00 4.57
7439 8259 4.658427 TGGATCCCAGGACACACA 57.342 55.556 9.90 0.00 0.00 3.72
7440 8260 3.103236 TGGATCCCAGGACACACAT 57.897 52.632 9.90 0.00 0.00 3.21
7458 8278 3.414700 GGCGTTGCGTGTCCTCAG 61.415 66.667 0.00 0.00 0.00 3.35
7463 8283 0.032130 GTTGCGTGTCCTCAGAGACA 59.968 55.000 0.00 0.00 44.38 3.41
7481 8301 2.424956 GACAAAGGGGATAGCAAGCAAG 59.575 50.000 0.00 0.00 0.00 4.01
7482 8302 1.753073 CAAAGGGGATAGCAAGCAAGG 59.247 52.381 0.00 0.00 0.00 3.61
7483 8303 1.298953 AAGGGGATAGCAAGCAAGGA 58.701 50.000 0.00 0.00 0.00 3.36
7484 8304 1.298953 AGGGGATAGCAAGCAAGGAA 58.701 50.000 0.00 0.00 0.00 3.36
7487 8307 2.357154 GGGGATAGCAAGCAAGGAAGAA 60.357 50.000 0.00 0.00 0.00 2.52
7493 8313 3.145286 AGCAAGCAAGGAAGAAGAGAAC 58.855 45.455 0.00 0.00 0.00 3.01
7497 8317 1.195674 GCAAGGAAGAAGAGAACGCAC 59.804 52.381 0.00 0.00 0.00 5.34
7503 8323 1.371389 GAAGAGAACGCACGTCCGT 60.371 57.895 0.00 0.00 44.41 4.69
7517 8337 2.024868 TCCGTTTCATGCGTCGTGG 61.025 57.895 0.00 0.00 0.00 4.94
7525 8345 3.279285 ATGCGTCGTGGATGATCTG 57.721 52.632 0.00 0.00 0.00 2.90
7526 8346 0.746659 ATGCGTCGTGGATGATCTGA 59.253 50.000 0.00 0.00 0.00 3.27
7527 8347 0.746659 TGCGTCGTGGATGATCTGAT 59.253 50.000 0.00 0.00 0.00 2.90
7528 8348 1.269257 TGCGTCGTGGATGATCTGATC 60.269 52.381 10.72 10.72 0.00 2.92
7529 8349 1.932604 GCGTCGTGGATGATCTGATCC 60.933 57.143 14.71 5.32 42.23 3.36
7530 8350 1.336332 CGTCGTGGATGATCTGATCCC 60.336 57.143 14.71 10.05 41.31 3.85
7532 8352 1.966354 TCGTGGATGATCTGATCCCAG 59.034 52.381 14.71 9.50 41.31 4.45
7544 8364 5.426689 TCTGATCCCAGATAACATATGCC 57.573 43.478 1.58 0.00 44.01 4.40
7545 8365 4.225942 TCTGATCCCAGATAACATATGCCC 59.774 45.833 1.58 0.00 44.01 5.36
7547 8367 1.003118 TCCCAGATAACATATGCCCGC 59.997 52.381 1.58 0.00 0.00 6.13
7550 8388 2.421073 CCAGATAACATATGCCCGCATG 59.579 50.000 12.42 0.58 37.82 4.06
7581 8419 3.044305 GCGTCCAGCTGCGTCTTT 61.044 61.111 8.66 0.00 44.04 2.52
7582 8420 2.607892 GCGTCCAGCTGCGTCTTTT 61.608 57.895 8.66 0.00 44.04 2.27
7606 8444 4.214327 TGCACAGTCGCACGGTCA 62.214 61.111 0.00 0.00 36.86 4.02
7624 8462 4.755123 CGGTCAGTGATCAACTTTTAACCT 59.245 41.667 3.88 0.00 36.83 3.50
7628 8466 6.935208 GTCAGTGATCAACTTTTAACCTACCT 59.065 38.462 0.00 0.00 36.83 3.08
7633 8471 8.092687 GTGATCAACTTTTAACCTACCTACTGA 58.907 37.037 0.00 0.00 0.00 3.41
7634 8472 8.653191 TGATCAACTTTTAACCTACCTACTGAA 58.347 33.333 0.00 0.00 0.00 3.02
7635 8473 8.843885 ATCAACTTTTAACCTACCTACTGAAC 57.156 34.615 0.00 0.00 0.00 3.18
7636 8474 8.026396 TCAACTTTTAACCTACCTACTGAACT 57.974 34.615 0.00 0.00 0.00 3.01
7637 8475 8.146412 TCAACTTTTAACCTACCTACTGAACTC 58.854 37.037 0.00 0.00 0.00 3.01
7638 8476 7.852550 ACTTTTAACCTACCTACTGAACTCT 57.147 36.000 0.00 0.00 0.00 3.24
7639 8477 7.668492 ACTTTTAACCTACCTACTGAACTCTG 58.332 38.462 0.00 0.00 0.00 3.35
7640 8478 5.656213 TTAACCTACCTACTGAACTCTGC 57.344 43.478 0.00 0.00 0.00 4.26
7641 8479 2.458620 ACCTACCTACTGAACTCTGCC 58.541 52.381 0.00 0.00 0.00 4.85
7642 8480 1.405821 CCTACCTACTGAACTCTGCCG 59.594 57.143 0.00 0.00 0.00 5.69
7643 8481 2.366533 CTACCTACTGAACTCTGCCGA 58.633 52.381 0.00 0.00 0.00 5.54
7644 8482 1.853963 ACCTACTGAACTCTGCCGAT 58.146 50.000 0.00 0.00 0.00 4.18
7645 8483 2.180276 ACCTACTGAACTCTGCCGATT 58.820 47.619 0.00 0.00 0.00 3.34
7646 8484 3.362706 ACCTACTGAACTCTGCCGATTA 58.637 45.455 0.00 0.00 0.00 1.75
7647 8485 3.130693 ACCTACTGAACTCTGCCGATTAC 59.869 47.826 0.00 0.00 0.00 1.89
7648 8486 2.674796 ACTGAACTCTGCCGATTACC 57.325 50.000 0.00 0.00 0.00 2.85
7649 8487 2.180276 ACTGAACTCTGCCGATTACCT 58.820 47.619 0.00 0.00 0.00 3.08
7650 8488 2.567615 ACTGAACTCTGCCGATTACCTT 59.432 45.455 0.00 0.00 0.00 3.50
7651 8489 3.190874 CTGAACTCTGCCGATTACCTTC 58.809 50.000 0.00 0.00 0.00 3.46
7654 8492 3.460857 ACTCTGCCGATTACCTTCATC 57.539 47.619 0.00 0.00 0.00 2.92
7656 8494 1.754803 TCTGCCGATTACCTTCATCGT 59.245 47.619 1.98 0.00 41.68 3.73
7657 8495 2.128035 CTGCCGATTACCTTCATCGTC 58.872 52.381 1.98 0.00 41.68 4.20
7663 8501 3.066900 CGATTACCTTCATCGTCTCCTGT 59.933 47.826 0.00 0.00 38.98 4.00
7665 8503 5.048643 CGATTACCTTCATCGTCTCCTGTAT 60.049 44.000 0.00 0.00 38.98 2.29
7670 8508 5.067936 ACCTTCATCGTCTCCTGTATGTAAG 59.932 44.000 0.00 0.00 0.00 2.34
7673 8511 2.730382 TCGTCTCCTGTATGTAAGCCA 58.270 47.619 0.00 0.00 0.00 4.75
7680 8518 4.973168 TCCTGTATGTAAGCCAATGATCC 58.027 43.478 0.00 0.00 0.00 3.36
7681 8519 4.411869 TCCTGTATGTAAGCCAATGATCCA 59.588 41.667 0.00 0.00 0.00 3.41
7682 8520 4.758674 CCTGTATGTAAGCCAATGATCCAG 59.241 45.833 0.00 0.00 0.00 3.86
7683 8521 5.371526 CTGTATGTAAGCCAATGATCCAGT 58.628 41.667 0.00 0.00 0.00 4.00
7684 8522 5.125356 TGTATGTAAGCCAATGATCCAGTG 58.875 41.667 0.00 0.00 0.00 3.66
7685 8523 3.719268 TGTAAGCCAATGATCCAGTGT 57.281 42.857 0.00 0.00 0.00 3.55
7686 8524 3.346315 TGTAAGCCAATGATCCAGTGTG 58.654 45.455 0.00 0.00 0.00 3.82
7687 8525 2.885135 AAGCCAATGATCCAGTGTGA 57.115 45.000 0.00 0.00 0.00 3.58
7699 8546 2.029666 GTGTGAGCACGAGTGGCT 59.970 61.111 5.32 2.95 46.07 4.75
7703 8550 0.038159 GTGAGCACGAGTGGCTACTT 60.038 55.000 3.47 0.00 42.78 2.24
7715 8562 2.868253 GCTACTTGCCGGAACCAAT 58.132 52.632 5.05 0.00 35.15 3.16
7727 8574 1.200020 GGAACCAATCGGAAAGTGCTG 59.800 52.381 0.00 0.00 35.59 4.41
7734 8581 1.172180 TCGGAAAGTGCTGCCCAAAG 61.172 55.000 0.00 0.00 0.00 2.77
7735 8582 1.172180 CGGAAAGTGCTGCCCAAAGA 61.172 55.000 0.00 0.00 0.00 2.52
7740 8587 2.071778 AGTGCTGCCCAAAGAAAGAA 57.928 45.000 0.00 0.00 0.00 2.52
7741 8588 2.387757 AGTGCTGCCCAAAGAAAGAAA 58.612 42.857 0.00 0.00 0.00 2.52
7743 8590 3.126073 GTGCTGCCCAAAGAAAGAAAAG 58.874 45.455 0.00 0.00 0.00 2.27
7744 8591 3.030291 TGCTGCCCAAAGAAAGAAAAGA 58.970 40.909 0.00 0.00 0.00 2.52
7746 8593 4.081198 TGCTGCCCAAAGAAAGAAAAGAAA 60.081 37.500 0.00 0.00 0.00 2.52
7747 8594 4.875536 GCTGCCCAAAGAAAGAAAAGAAAA 59.124 37.500 0.00 0.00 0.00 2.29
7748 8595 5.007039 GCTGCCCAAAGAAAGAAAAGAAAAG 59.993 40.000 0.00 0.00 0.00 2.27
7749 8596 5.427378 TGCCCAAAGAAAGAAAAGAAAAGG 58.573 37.500 0.00 0.00 0.00 3.11
7750 8597 4.273480 GCCCAAAGAAAGAAAAGAAAAGGC 59.727 41.667 0.00 0.00 0.00 4.35
7751 8598 5.674525 CCCAAAGAAAGAAAAGAAAAGGCT 58.325 37.500 0.00 0.00 0.00 4.58
7752 8599 5.525012 CCCAAAGAAAGAAAAGAAAAGGCTG 59.475 40.000 0.00 0.00 0.00 4.85
7753 8600 6.108687 CCAAAGAAAGAAAAGAAAAGGCTGT 58.891 36.000 0.00 0.00 0.00 4.40
7755 8602 6.530019 AAGAAAGAAAAGAAAAGGCTGTCA 57.470 33.333 0.00 0.00 0.00 3.58
7756 8603 5.895928 AGAAAGAAAAGAAAAGGCTGTCAC 58.104 37.500 0.00 0.00 0.00 3.67
7757 8604 4.655762 AAGAAAAGAAAAGGCTGTCACC 57.344 40.909 0.00 0.00 0.00 4.02
7758 8605 2.959030 AGAAAAGAAAAGGCTGTCACCC 59.041 45.455 0.00 0.00 0.00 4.61
7760 8607 1.986882 AAGAAAAGGCTGTCACCCTG 58.013 50.000 0.00 0.00 31.73 4.45
7761 8608 0.538287 AGAAAAGGCTGTCACCCTGC 60.538 55.000 0.00 0.00 37.29 4.85
7762 8609 0.538287 GAAAAGGCTGTCACCCTGCT 60.538 55.000 0.00 0.00 38.06 4.24
7763 8610 0.825010 AAAAGGCTGTCACCCTGCTG 60.825 55.000 0.00 0.00 38.06 4.41
7764 8611 1.708993 AAAGGCTGTCACCCTGCTGA 61.709 55.000 0.00 0.00 38.06 4.26
7765 8612 2.359230 GGCTGTCACCCTGCTGAC 60.359 66.667 0.00 0.00 40.98 3.51
7766 8613 2.746359 GCTGTCACCCTGCTGACT 59.254 61.111 5.54 0.00 41.15 3.41
7767 8614 1.670406 GCTGTCACCCTGCTGACTG 60.670 63.158 5.54 6.00 41.15 3.51
7768 8615 2.052779 CTGTCACCCTGCTGACTGA 58.947 57.895 5.54 0.00 40.68 3.41
7769 8616 0.037512 CTGTCACCCTGCTGACTGAG 60.038 60.000 5.54 0.00 40.68 3.35
7770 8617 0.760567 TGTCACCCTGCTGACTGAGT 60.761 55.000 5.54 0.00 41.15 3.41
7771 8618 0.394565 GTCACCCTGCTGACTGAGTT 59.605 55.000 0.00 0.00 38.05 3.01
7772 8619 0.394192 TCACCCTGCTGACTGAGTTG 59.606 55.000 0.00 0.00 0.00 3.16
7773 8620 0.394192 CACCCTGCTGACTGAGTTGA 59.606 55.000 0.00 0.00 0.00 3.18
7774 8621 0.683973 ACCCTGCTGACTGAGTTGAG 59.316 55.000 0.00 0.00 0.00 3.02
7775 8622 0.673022 CCCTGCTGACTGAGTTGAGC 60.673 60.000 9.81 9.81 0.00 4.26
7776 8623 1.013005 CCTGCTGACTGAGTTGAGCG 61.013 60.000 11.44 7.39 33.97 5.03
7784 8631 2.866762 GACTGAGTTGAGCGTTTTGTCT 59.133 45.455 0.00 0.00 0.00 3.41
7791 8638 0.784778 GAGCGTTTTGTCTCCGTCTG 59.215 55.000 0.00 0.00 0.00 3.51
7859 8706 1.559682 CGGATTCTTCCTTCCTTCCCA 59.440 52.381 0.00 0.00 40.17 4.37
7861 8708 3.560105 GGATTCTTCCTTCCTTCCCATG 58.440 50.000 0.00 0.00 39.14 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.497103 TCAGGCCATGGATGAATAGTG 57.503 47.619 18.40 0.00 0.00 2.74
40 41 0.243095 AACTCGCCTAGTCAACGACC 59.757 55.000 0.00 0.00 37.50 4.79
113 114 5.289595 AGCTCGCATCGACATTAATCTTAA 58.710 37.500 0.00 0.00 0.00 1.85
114 115 4.871513 AGCTCGCATCGACATTAATCTTA 58.128 39.130 0.00 0.00 0.00 2.10
226 228 1.522668 CTTCCTCCGCACATGAACAA 58.477 50.000 0.00 0.00 0.00 2.83
234 236 0.238553 GAGTTTTGCTTCCTCCGCAC 59.761 55.000 0.00 0.00 37.07 5.34
237 239 3.990318 AAAAGAGTTTTGCTTCCTCCG 57.010 42.857 0.00 0.00 0.00 4.63
238 240 4.613850 CGCTAAAAGAGTTTTGCTTCCTCC 60.614 45.833 4.59 0.00 41.52 4.30
239 241 4.467735 CGCTAAAAGAGTTTTGCTTCCTC 58.532 43.478 4.59 0.00 41.52 3.71
240 242 3.253432 CCGCTAAAAGAGTTTTGCTTCCT 59.747 43.478 4.59 0.00 41.52 3.36
241 243 3.565516 CCGCTAAAAGAGTTTTGCTTCC 58.434 45.455 4.59 0.00 41.52 3.46
242 244 3.004419 ACCCGCTAAAAGAGTTTTGCTTC 59.996 43.478 4.59 0.00 41.52 3.86
243 245 2.956333 ACCCGCTAAAAGAGTTTTGCTT 59.044 40.909 4.59 0.00 41.52 3.91
247 249 7.336396 ACATATAGACCCGCTAAAAGAGTTTT 58.664 34.615 0.00 0.00 36.67 2.43
364 366 5.147162 CCAAACGCTTATCTTCAACTCAAC 58.853 41.667 0.00 0.00 0.00 3.18
380 382 2.650778 CTGAAAGGCCCCAAACGC 59.349 61.111 0.00 0.00 0.00 4.84
385 387 1.357420 TGAATAAGCTGAAAGGCCCCA 59.643 47.619 0.00 0.00 0.00 4.96
448 450 6.879962 ACAAAATTTTGCAATCTCATCAACG 58.120 32.000 26.94 2.11 41.79 4.10
453 455 8.895737 AGTTTGAACAAAATTTTGCAATCTCAT 58.104 25.926 26.94 5.80 41.79 2.90
454 456 8.266392 AGTTTGAACAAAATTTTGCAATCTCA 57.734 26.923 26.94 18.57 41.79 3.27
632 634 3.866651 ACAATGGTTAGCTAGAGTGCTG 58.133 45.455 0.00 0.00 43.87 4.41
642 644 4.851558 GTCAATTTGTCGACAATGGTTAGC 59.148 41.667 30.10 16.10 35.55 3.09
670 672 8.675705 TGACTTTTCATGTAAAGAGTCAATGA 57.324 30.769 25.95 2.77 39.50 2.57
671 673 9.734620 TTTGACTTTTCATGTAAAGAGTCAATG 57.265 29.630 25.95 3.94 44.05 2.82
692 694 9.358872 GAAGGAGTTTGGATTTATGATTTTGAC 57.641 33.333 0.00 0.00 0.00 3.18
737 739 9.661563 CCTCTAACATTGTGTATTTACTGGTAA 57.338 33.333 0.00 0.00 0.00 2.85
756 764 3.926058 TTTCATGGGTAGGCCTCTAAC 57.074 47.619 9.68 0.67 32.50 2.34
765 773 4.280677 TCTTTGGCAGTTTTTCATGGGTAG 59.719 41.667 0.00 0.00 0.00 3.18
781 789 3.665745 TCCTTTGATTGCTTCTTTGGC 57.334 42.857 0.00 0.00 0.00 4.52
809 832 0.829333 CCCTGAGAGTGGACCATGAG 59.171 60.000 0.00 0.00 0.00 2.90
836 859 6.039270 TGAGTGAGGGACTTGTTTGTAATTTG 59.961 38.462 0.00 0.00 41.55 2.32
869 892 0.693049 AACGGCCAGGTGAAGAAGAT 59.307 50.000 2.24 0.00 0.00 2.40
1155 1195 3.771160 GAGAGCTTCCCCGCCGAA 61.771 66.667 0.00 0.00 0.00 4.30
1278 1318 3.699894 CTCCTCACCTGGCACGCT 61.700 66.667 0.00 0.00 0.00 5.07
1498 1538 7.768120 ACAATTTTACTGATTTTTGCTGTTCCA 59.232 29.630 0.00 0.00 0.00 3.53
1553 1594 4.282449 TCCTCGTCTTGTAACAGAAATCCA 59.718 41.667 0.00 0.00 0.00 3.41
1624 1669 1.861542 TTGCAAATCCCAAGCGTCCG 61.862 55.000 0.00 0.00 0.00 4.79
1628 1673 3.458779 CAATTTTGCAAATCCCAAGCG 57.541 42.857 13.65 0.00 0.00 4.68
1678 1723 2.025321 CCCCAGCTACCAATTACCACTT 60.025 50.000 0.00 0.00 0.00 3.16
1767 1818 6.127897 ACAAGTCCAACAGAAAGAAAAGACTG 60.128 38.462 0.00 0.00 33.81 3.51
1913 1968 9.482627 CTAAGATCCATATGAACCTACAGAAAC 57.517 37.037 3.65 0.00 0.00 2.78
1915 1970 8.783660 ACTAAGATCCATATGAACCTACAGAA 57.216 34.615 3.65 0.00 0.00 3.02
1928 1983 7.072076 GGGAAGGGAACTAAACTAAGATCCATA 59.928 40.741 3.08 0.00 42.68 2.74
1955 2010 7.498239 AAGGGAATAAGCGTAATTCCTTTAGAC 59.502 37.037 20.21 8.51 45.67 2.59
2157 2221 2.282555 CGTATCAACAGCATGGAAGACG 59.717 50.000 0.00 0.00 43.62 4.18
2161 2225 4.188462 CCTAACGTATCAACAGCATGGAA 58.812 43.478 0.00 0.00 43.62 3.53
2200 2264 5.889289 TGCTTTCACCTGTTACTAACCTTTT 59.111 36.000 0.00 0.00 0.00 2.27
2268 2333 5.879237 TCATTGATGAAACGATTTACAGGC 58.121 37.500 0.00 0.00 33.08 4.85
2317 2382 5.580691 GCATCTATGTACACAAGTTACAGCA 59.419 40.000 0.00 0.00 0.00 4.41
2348 2421 3.459145 TGCGCAAACTGACAACTTAGTA 58.541 40.909 8.16 0.00 0.00 1.82
2365 2438 5.880054 AACCAGGTGATATTTATATGCGC 57.120 39.130 0.00 0.00 0.00 6.09
2449 2524 8.690884 TGACCAATCTGAATACAAAAGAACAAA 58.309 29.630 0.00 0.00 0.00 2.83
2494 2569 3.766676 TCAAGATCACGAGCTCTGTAC 57.233 47.619 12.85 7.84 0.00 2.90
2608 2683 4.510038 AATATTTGGATGATCAAGCCGC 57.490 40.909 0.00 0.00 0.00 6.53
2743 2818 1.008403 TACCAGGTACCTGAGGCTCT 58.992 55.000 38.35 16.84 46.30 4.09
2757 2832 0.250467 CCCCTGCATCGGAATACCAG 60.250 60.000 1.50 0.00 35.59 4.00
2823 2899 9.614269 ACCATAAGGGGTTATAAATTATTGCAT 57.386 29.630 0.00 0.00 42.91 3.96
3194 3270 4.749099 GCTTGATAGCATACCTCTGTTCTG 59.251 45.833 0.00 0.00 46.95 3.02
3230 3306 3.694072 ACTAACTTGTTGCACTTGCTTCA 59.306 39.130 2.33 0.00 42.66 3.02
3576 3653 1.955080 ACGCCCGAAATAACCAAACAA 59.045 42.857 0.00 0.00 0.00 2.83
3634 3713 4.705991 ACGGTGAAAAAGTAAGTTGGGAAA 59.294 37.500 0.00 0.00 0.00 3.13
3673 3752 4.385825 ACGGTTCAAGCTTCAATCACTAA 58.614 39.130 0.00 0.00 0.00 2.24
3825 3904 4.219919 AGTAGGAGGAGCTCTTCATTACC 58.780 47.826 25.32 10.00 0.00 2.85
3847 3926 9.996554 TGACTCTCAGAGACAACATAAAAATAA 57.003 29.630 9.27 0.00 32.27 1.40
3848 3927 9.424319 GTGACTCTCAGAGACAACATAAAAATA 57.576 33.333 9.27 0.00 36.31 1.40
3849 3928 7.389053 GGTGACTCTCAGAGACAACATAAAAAT 59.611 37.037 16.26 0.00 40.57 1.82
3850 3929 6.706270 GGTGACTCTCAGAGACAACATAAAAA 59.294 38.462 16.26 0.00 40.57 1.94
3851 3930 6.183360 TGGTGACTCTCAGAGACAACATAAAA 60.183 38.462 19.39 0.00 44.12 1.52
3852 3931 5.304357 TGGTGACTCTCAGAGACAACATAAA 59.696 40.000 19.39 0.00 44.12 1.40
3857 3936 3.951775 ATGGTGACTCTCAGAGACAAC 57.048 47.619 14.55 14.55 41.07 3.32
3860 3939 5.146010 AGAAAATGGTGACTCTCAGAGAC 57.854 43.478 9.27 2.22 33.32 3.36
3865 3944 7.540474 ACTAAGTAGAAAATGGTGACTCTCA 57.460 36.000 0.00 0.00 0.00 3.27
3926 4006 9.490379 GTTTATAACTATCGTCCTTGATCCAAT 57.510 33.333 0.00 0.00 0.00 3.16
4310 4393 1.003580 GGTCAGCAGAACCTTCATCCA 59.996 52.381 0.00 0.00 0.00 3.41
4378 4461 7.275341 TGAATAAACAGCCTTATTTTCATTGCG 59.725 33.333 0.00 0.00 32.77 4.85
4458 4541 4.518970 ACCAAAGCAAATATATGGGCTACG 59.481 41.667 10.75 6.28 35.11 3.51
4637 4738 6.676950 TCATGTGTCCACAAATAAATGTCAC 58.323 36.000 3.95 0.00 45.41 3.67
4641 4742 7.652909 ACTGTTTCATGTGTCCACAAATAAATG 59.347 33.333 3.95 0.00 45.41 2.32
4659 4760 6.516527 GCCATGACTATTTTTCCACTGTTTCA 60.517 38.462 0.00 0.00 0.00 2.69
4662 4765 4.220602 GGCCATGACTATTTTTCCACTGTT 59.779 41.667 0.00 0.00 0.00 3.16
4725 4835 6.366332 CGATATGCTCCCACATAAGTTCTTAC 59.634 42.308 0.00 0.00 36.17 2.34
4730 4840 4.380531 CACGATATGCTCCCACATAAGTT 58.619 43.478 0.00 0.00 36.17 2.66
4750 4860 6.765989 TCCCACATAATAACTATCAGTTGCAC 59.234 38.462 1.84 0.00 39.11 4.57
4916 5106 2.039084 GTGAAGAAGATCCCAGTGTGGT 59.961 50.000 0.00 0.00 35.17 4.16
4942 5132 8.674607 CCAGCCAACTATACCTACTTTTTAAAG 58.325 37.037 0.80 0.80 41.73 1.85
5402 5990 7.651304 CACAAGACTATATTCAGTCAGATGTCC 59.349 40.741 8.09 0.00 46.15 4.02
5410 5998 7.602644 TCAACAACCACAAGACTATATTCAGTC 59.397 37.037 0.00 0.00 44.44 3.51
5654 6255 3.126000 GCCTCTTCTGAAAATGAAGACGG 59.874 47.826 2.51 8.88 43.19 4.79
5655 6256 3.748048 TGCCTCTTCTGAAAATGAAGACG 59.252 43.478 2.51 1.38 43.19 4.18
5789 6390 0.314302 AGACGTGTTTGGAGTCTCCG 59.686 55.000 14.34 3.58 40.85 4.63
6140 6742 3.250744 GGCATAAGAAAACTTTTCGCCC 58.749 45.455 15.09 7.37 0.00 6.13
6178 6780 5.840243 TGATATTTGAAGGAACCATGCAG 57.160 39.130 0.00 0.00 0.00 4.41
6223 6825 4.510571 ACCCTAACATGTGACGGTATTTC 58.489 43.478 0.00 0.00 0.00 2.17
6239 6865 6.828788 TGGATACGCACAAATTATACCCTAA 58.171 36.000 0.00 0.00 42.51 2.69
6305 6932 5.663456 TGTCACCCTATTCGTGTATTTACC 58.337 41.667 0.00 0.00 32.86 2.85
6315 6942 4.511826 GCTCCTAAAATGTCACCCTATTCG 59.488 45.833 0.00 0.00 0.00 3.34
6318 6945 4.047883 AGGCTCCTAAAATGTCACCCTAT 58.952 43.478 0.00 0.00 0.00 2.57
6433 7101 2.367202 GGTCAGAGGCCCGGAATGA 61.367 63.158 0.73 0.00 0.00 2.57
6481 7149 1.215647 CCGGTCGTTCTCCTTGAGG 59.784 63.158 0.00 0.00 0.00 3.86
6706 7391 4.166523 GGAAAGAAGCAATAAAACGGAGC 58.833 43.478 0.00 0.00 0.00 4.70
6732 7429 3.326900 TCCCCCGGGAATTACAGC 58.673 61.111 26.32 0.00 42.05 4.40
6766 7464 1.433534 GCCGAGTCTTTTCTCCTGTG 58.566 55.000 0.00 0.00 0.00 3.66
6776 7474 3.814005 AATATTACACGGCCGAGTCTT 57.186 42.857 35.90 22.22 0.00 3.01
6823 7526 2.360980 CTCCTCCCCGTCTCACCT 59.639 66.667 0.00 0.00 0.00 4.00
6825 7528 3.462678 GCCTCCTCCCCGTCTCAC 61.463 72.222 0.00 0.00 0.00 3.51
6827 7530 4.816984 TCGCCTCCTCCCCGTCTC 62.817 72.222 0.00 0.00 0.00 3.36
6828 7531 3.680920 AATCGCCTCCTCCCCGTCT 62.681 63.158 0.00 0.00 0.00 4.18
6829 7532 2.732619 AAATCGCCTCCTCCCCGTC 61.733 63.158 0.00 0.00 0.00 4.79
6830 7533 2.687566 AAATCGCCTCCTCCCCGT 60.688 61.111 0.00 0.00 0.00 5.28
6831 7534 2.203070 CAAATCGCCTCCTCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
6842 7545 3.505680 TCACCTCCCAATCAAACAAATCG 59.494 43.478 0.00 0.00 0.00 3.34
6944 7661 2.364002 TCATCAACAGTGAACGAGTGGA 59.636 45.455 0.00 0.00 37.30 4.02
6956 7673 4.386049 GTCGGTTTCTAGTGTCATCAACAG 59.614 45.833 0.00 0.00 38.97 3.16
6961 7678 3.056749 ACAGGTCGGTTTCTAGTGTCATC 60.057 47.826 0.00 0.00 0.00 2.92
6967 7684 3.893813 ACAGTTACAGGTCGGTTTCTAGT 59.106 43.478 0.00 0.00 0.00 2.57
7015 7732 3.045634 TCCAGGAGGAAACTGAAACTGA 58.954 45.455 0.00 0.00 44.43 3.41
7016 7733 3.492102 TCCAGGAGGAAACTGAAACTG 57.508 47.619 0.00 0.00 44.43 3.16
7031 7748 2.022195 CATCAGCCAAAGTGATCCAGG 58.978 52.381 0.00 0.00 32.06 4.45
7055 7772 9.856162 TTCCTTACAAAAACAAGTAGTCCTTAT 57.144 29.630 0.00 0.00 0.00 1.73
7056 7773 9.683870 TTTCCTTACAAAAACAAGTAGTCCTTA 57.316 29.630 0.00 0.00 0.00 2.69
7057 7774 8.584063 TTTCCTTACAAAAACAAGTAGTCCTT 57.416 30.769 0.00 0.00 0.00 3.36
7058 7775 8.584063 TTTTCCTTACAAAAACAAGTAGTCCT 57.416 30.769 0.00 0.00 0.00 3.85
7102 7890 3.065648 GCCAGGTTTTTCGTAAGTTCACA 59.934 43.478 0.00 0.00 39.48 3.58
7105 7893 3.065648 TGTGCCAGGTTTTTCGTAAGTTC 59.934 43.478 0.00 0.00 39.48 3.01
7123 7911 2.042520 TTTTGCGGACGTGTCTGTGC 62.043 55.000 10.33 7.80 38.23 4.57
7145 7933 1.167851 CTGCAATGTTCCGTGATGGT 58.832 50.000 0.00 0.00 39.52 3.55
7146 7934 0.179156 GCTGCAATGTTCCGTGATGG 60.179 55.000 0.00 0.00 40.09 3.51
7207 8005 0.811915 GCTCTCTTCTCTACCGTGCA 59.188 55.000 0.00 0.00 0.00 4.57
7237 8045 2.602257 TTAGTGCGATGGGTGATGAG 57.398 50.000 0.00 0.00 0.00 2.90
7257 8068 2.029020 CGTGAGGTCAGAGTCAATGGAA 60.029 50.000 0.00 0.00 0.00 3.53
7399 8215 2.029073 CCCAACACGTCTCTGCGT 59.971 61.111 0.00 0.00 46.88 5.24
7428 8248 1.600636 AACGCCATGTGTGTCCTGG 60.601 57.895 0.00 0.00 36.45 4.45
7438 8258 3.027170 GAGGACACGCAACGCCATG 62.027 63.158 0.00 0.00 0.00 3.66
7439 8259 2.742372 GAGGACACGCAACGCCAT 60.742 61.111 0.00 0.00 0.00 4.40
7440 8260 4.228567 TGAGGACACGCAACGCCA 62.229 61.111 0.00 0.00 0.00 5.69
7458 8278 2.293170 GCTTGCTATCCCCTTTGTCTC 58.707 52.381 0.00 0.00 0.00 3.36
7463 8283 1.640670 TCCTTGCTTGCTATCCCCTTT 59.359 47.619 0.00 0.00 0.00 3.11
7481 8301 1.061485 GACGTGCGTTCTCTTCTTCC 58.939 55.000 0.00 0.00 0.00 3.46
7482 8302 1.061485 GGACGTGCGTTCTCTTCTTC 58.939 55.000 0.00 0.00 0.00 2.87
7483 8303 0.663568 CGGACGTGCGTTCTCTTCTT 60.664 55.000 22.12 0.00 0.00 2.52
7484 8304 1.081376 CGGACGTGCGTTCTCTTCT 60.081 57.895 22.12 0.00 0.00 2.85
7487 8307 0.938168 GAAACGGACGTGCGTTCTCT 60.938 55.000 40.62 28.80 0.00 3.10
7493 8313 2.202171 GCATGAAACGGACGTGCG 60.202 61.111 28.33 28.33 39.78 5.34
7497 8317 2.369629 ACGACGCATGAAACGGACG 61.370 57.895 0.00 4.40 39.15 4.79
7503 8323 1.933181 GATCATCCACGACGCATGAAA 59.067 47.619 0.00 0.00 30.43 2.69
7523 8343 4.521146 GGGCATATGTTATCTGGGATCAG 58.479 47.826 4.29 0.00 42.21 2.90
7524 8344 3.055167 CGGGCATATGTTATCTGGGATCA 60.055 47.826 4.29 0.00 0.00 2.92
7525 8345 3.535561 CGGGCATATGTTATCTGGGATC 58.464 50.000 4.29 0.00 0.00 3.36
7526 8346 2.356125 GCGGGCATATGTTATCTGGGAT 60.356 50.000 4.29 0.00 0.00 3.85
7527 8347 1.003118 GCGGGCATATGTTATCTGGGA 59.997 52.381 4.29 0.00 0.00 4.37
7528 8348 1.271325 TGCGGGCATATGTTATCTGGG 60.271 52.381 4.29 0.00 0.00 4.45
7529 8349 2.183478 TGCGGGCATATGTTATCTGG 57.817 50.000 4.29 0.00 0.00 3.86
7530 8350 3.076621 ACATGCGGGCATATGTTATCTG 58.923 45.455 5.74 0.00 34.00 2.90
7532 8352 2.813754 ACACATGCGGGCATATGTTATC 59.186 45.455 11.51 0.00 40.69 1.75
7534 8354 1.946081 CACACATGCGGGCATATGTTA 59.054 47.619 14.38 0.00 40.69 2.41
7535 8355 0.740149 CACACATGCGGGCATATGTT 59.260 50.000 14.38 0.00 40.69 2.71
7536 8356 1.727511 GCACACATGCGGGCATATGT 61.728 55.000 11.51 11.51 43.85 2.29
7537 8357 1.008194 GCACACATGCGGGCATATG 60.008 57.895 10.17 10.17 43.33 1.78
7538 8358 3.435590 GCACACATGCGGGCATAT 58.564 55.556 2.32 0.00 43.33 1.78
7547 8367 2.253154 CACACGCAGGCACACATG 59.747 61.111 0.00 0.00 0.00 3.21
7568 8406 1.799258 AAGGCAAAAGACGCAGCTGG 61.799 55.000 17.12 8.27 0.00 4.85
7569 8407 0.662374 CAAGGCAAAAGACGCAGCTG 60.662 55.000 10.11 10.11 0.00 4.24
7572 8410 0.936297 GCACAAGGCAAAAGACGCAG 60.936 55.000 0.00 0.00 43.97 5.18
7593 8431 1.073216 GATCACTGACCGTGCGACTG 61.073 60.000 0.00 0.00 43.46 3.51
7598 8436 1.512926 AAGTTGATCACTGACCGTGC 58.487 50.000 0.00 0.00 43.46 5.34
7604 8442 7.074653 AGGTAGGTTAAAAGTTGATCACTGA 57.925 36.000 0.00 0.00 35.12 3.41
7606 8444 8.095169 CAGTAGGTAGGTTAAAAGTTGATCACT 58.905 37.037 0.00 0.00 37.30 3.41
7621 8459 2.458620 GGCAGAGTTCAGTAGGTAGGT 58.541 52.381 0.00 0.00 0.00 3.08
7624 8462 2.502142 TCGGCAGAGTTCAGTAGGTA 57.498 50.000 0.00 0.00 0.00 3.08
7628 8466 3.362706 AGGTAATCGGCAGAGTTCAGTA 58.637 45.455 0.00 0.00 0.00 2.74
7633 8471 3.738281 CGATGAAGGTAATCGGCAGAGTT 60.738 47.826 0.00 0.00 42.47 3.01
7634 8472 2.223829 CGATGAAGGTAATCGGCAGAGT 60.224 50.000 0.00 0.00 42.47 3.24
7635 8473 2.398498 CGATGAAGGTAATCGGCAGAG 58.602 52.381 0.00 0.00 42.47 3.35
7636 8474 2.509052 CGATGAAGGTAATCGGCAGA 57.491 50.000 0.00 0.00 42.47 4.26
7642 8480 4.657436 ACAGGAGACGATGAAGGTAATC 57.343 45.455 0.00 0.00 0.00 1.75
7643 8481 5.598830 ACATACAGGAGACGATGAAGGTAAT 59.401 40.000 0.00 0.00 0.00 1.89
7644 8482 4.954202 ACATACAGGAGACGATGAAGGTAA 59.046 41.667 0.00 0.00 0.00 2.85
7645 8483 4.533815 ACATACAGGAGACGATGAAGGTA 58.466 43.478 0.00 0.00 0.00 3.08
7646 8484 3.366396 ACATACAGGAGACGATGAAGGT 58.634 45.455 0.00 0.00 0.00 3.50
7647 8485 5.515797 TTACATACAGGAGACGATGAAGG 57.484 43.478 0.00 0.00 0.00 3.46
7648 8486 4.979197 GCTTACATACAGGAGACGATGAAG 59.021 45.833 0.00 0.00 0.00 3.02
7649 8487 4.202121 GGCTTACATACAGGAGACGATGAA 60.202 45.833 0.00 0.00 0.00 2.57
7650 8488 3.318275 GGCTTACATACAGGAGACGATGA 59.682 47.826 0.00 0.00 0.00 2.92
7651 8489 3.068165 TGGCTTACATACAGGAGACGATG 59.932 47.826 0.00 0.00 0.00 3.84
7654 8492 3.520290 TTGGCTTACATACAGGAGACG 57.480 47.619 0.00 0.00 0.00 4.18
7656 8494 5.221722 GGATCATTGGCTTACATACAGGAGA 60.222 44.000 0.00 0.00 0.00 3.71
7657 8495 4.999950 GGATCATTGGCTTACATACAGGAG 59.000 45.833 0.00 0.00 0.00 3.69
7663 8501 5.104569 TCACACTGGATCATTGGCTTACATA 60.105 40.000 0.00 0.00 0.00 2.29
7665 8503 3.008923 TCACACTGGATCATTGGCTTACA 59.991 43.478 0.00 0.00 0.00 2.41
7670 8508 0.737219 GCTCACACTGGATCATTGGC 59.263 55.000 0.00 0.00 0.00 4.52
7673 8511 1.276138 TCGTGCTCACACTGGATCATT 59.724 47.619 0.00 0.00 45.10 2.57
7680 8518 2.313172 GCCACTCGTGCTCACACTG 61.313 63.158 0.69 0.00 45.10 3.66
7681 8519 1.179174 TAGCCACTCGTGCTCACACT 61.179 55.000 0.69 0.00 45.10 3.55
7682 8520 1.009389 GTAGCCACTCGTGCTCACAC 61.009 60.000 0.69 0.00 43.76 3.82
7683 8521 1.179174 AGTAGCCACTCGTGCTCACA 61.179 55.000 0.69 0.00 40.23 3.58
7684 8522 0.038159 AAGTAGCCACTCGTGCTCAC 60.038 55.000 0.00 0.00 40.23 3.51
7685 8523 0.038251 CAAGTAGCCACTCGTGCTCA 60.038 55.000 0.00 0.00 40.23 4.26
7686 8524 1.355066 GCAAGTAGCCACTCGTGCTC 61.355 60.000 2.20 0.00 40.23 4.26
7687 8525 1.374758 GCAAGTAGCCACTCGTGCT 60.375 57.895 2.20 0.00 42.81 4.40
7699 8546 0.391927 CCGATTGGTTCCGGCAAGTA 60.392 55.000 0.00 0.00 39.22 2.24
7703 8550 0.958382 CTTTCCGATTGGTTCCGGCA 60.958 55.000 0.00 0.00 44.96 5.69
7715 8562 1.152860 TTTGGGCAGCACTTTCCGA 60.153 52.632 0.00 0.00 0.00 4.55
7727 8574 4.273480 GCCTTTTCTTTTCTTTCTTTGGGC 59.727 41.667 0.00 0.00 0.00 5.36
7734 8581 5.043903 GGTGACAGCCTTTTCTTTTCTTTC 58.956 41.667 0.00 0.00 0.00 2.62
7735 8582 4.141937 GGGTGACAGCCTTTTCTTTTCTTT 60.142 41.667 16.60 0.00 31.81 2.52
7740 8587 2.310538 CAGGGTGACAGCCTTTTCTTT 58.689 47.619 23.62 0.00 45.25 2.52
7741 8588 1.986882 CAGGGTGACAGCCTTTTCTT 58.013 50.000 23.62 0.00 45.25 2.52
7743 8590 0.538287 AGCAGGGTGACAGCCTTTTC 60.538 55.000 23.62 14.87 45.25 2.29
7744 8591 0.825010 CAGCAGGGTGACAGCCTTTT 60.825 55.000 23.62 11.76 45.25 2.27
7746 8593 2.149383 TCAGCAGGGTGACAGCCTT 61.149 57.895 23.62 7.80 45.25 4.35
7748 8595 2.359230 GTCAGCAGGGTGACAGCC 60.359 66.667 22.62 16.14 45.34 4.85
7752 8599 0.394565 AACTCAGTCAGCAGGGTGAC 59.605 55.000 20.66 20.66 46.22 3.67
7753 8600 0.394192 CAACTCAGTCAGCAGGGTGA 59.606 55.000 0.00 0.00 0.00 4.02
7755 8602 0.683973 CTCAACTCAGTCAGCAGGGT 59.316 55.000 0.00 0.00 0.00 4.34
7756 8603 0.673022 GCTCAACTCAGTCAGCAGGG 60.673 60.000 4.15 0.00 0.00 4.45
7757 8604 1.013005 CGCTCAACTCAGTCAGCAGG 61.013 60.000 8.98 0.00 0.00 4.85
7758 8605 0.319383 ACGCTCAACTCAGTCAGCAG 60.319 55.000 8.98 4.88 0.00 4.24
7760 8607 1.221414 AAACGCTCAACTCAGTCAGC 58.779 50.000 0.00 0.00 0.00 4.26
7761 8608 2.609459 ACAAAACGCTCAACTCAGTCAG 59.391 45.455 0.00 0.00 0.00 3.51
7762 8609 2.607635 GACAAAACGCTCAACTCAGTCA 59.392 45.455 0.00 0.00 0.00 3.41
7763 8610 2.866762 AGACAAAACGCTCAACTCAGTC 59.133 45.455 0.00 0.00 0.00 3.51
7764 8611 2.866762 GAGACAAAACGCTCAACTCAGT 59.133 45.455 0.00 0.00 0.00 3.41
7765 8612 2.221981 GGAGACAAAACGCTCAACTCAG 59.778 50.000 0.00 0.00 32.83 3.35
7766 8613 2.210116 GGAGACAAAACGCTCAACTCA 58.790 47.619 0.00 0.00 32.83 3.41
7767 8614 1.192534 CGGAGACAAAACGCTCAACTC 59.807 52.381 0.00 0.00 32.83 3.01
7768 8615 1.217882 CGGAGACAAAACGCTCAACT 58.782 50.000 0.00 0.00 32.83 3.16
7769 8616 0.935196 ACGGAGACAAAACGCTCAAC 59.065 50.000 0.00 0.00 32.83 3.18
7770 8617 1.202486 AGACGGAGACAAAACGCTCAA 60.202 47.619 0.00 0.00 32.83 3.02
7771 8618 0.387929 AGACGGAGACAAAACGCTCA 59.612 50.000 0.00 0.00 32.83 4.26
7772 8619 0.784778 CAGACGGAGACAAAACGCTC 59.215 55.000 0.00 0.00 0.00 5.03
7773 8620 0.600255 CCAGACGGAGACAAAACGCT 60.600 55.000 0.00 0.00 0.00 5.07
7774 8621 1.860078 CCAGACGGAGACAAAACGC 59.140 57.895 0.00 0.00 0.00 4.84
7775 8622 1.566018 GGCCAGACGGAGACAAAACG 61.566 60.000 0.00 0.00 0.00 3.60
7776 8623 1.566018 CGGCCAGACGGAGACAAAAC 61.566 60.000 2.24 0.00 0.00 2.43
7859 8706 3.881952 TTGCTGTCGCCTGTCGCAT 62.882 57.895 0.00 0.00 37.30 4.73
7861 8708 4.077188 GTTGCTGTCGCCTGTCGC 62.077 66.667 0.00 0.00 38.27 5.19


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

AutoCloner maintained by Alex Coulton.