Multiple sequence alignment - TraesCS1D01G205700

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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 TraesCS1D01G205700 chr1D 100.000 4599 0 0 1 4599 291491134 291495732 0.000000e+00 8493.0
1 TraesCS1D01G205700 chr1D 95.335 493 9 1 4121 4599 315029888 315029396 0.000000e+00 771.0
2 TraesCS1D01G205700 chr1D 73.500 200 44 8 2402 2595 35920475 35920279 2.970000e-07 67.6
3 TraesCS1D01G205700 chr1B 93.490 2980 96 33 14 2937 392433623 392436560 0.000000e+00 4338.0
4 TraesCS1D01G205700 chr1B 97.955 1076 20 2 2936 4009 392436786 392437861 0.000000e+00 1864.0
5 TraesCS1D01G205700 chr1B 97.368 114 3 0 4008 4121 392438107 392438220 1.310000e-45 195.0
6 TraesCS1D01G205700 chr1A 92.890 2827 83 34 35 2797 363451380 363454152 0.000000e+00 3999.0
7 TraesCS1D01G205700 chr1A 97.260 1241 32 2 2796 4034 363454209 363455449 0.000000e+00 2102.0
8 TraesCS1D01G205700 chr1A 73.632 201 43 9 2402 2595 34881457 34881260 8.260000e-08 69.4
9 TraesCS1D01G205700 chr3D 97.280 478 13 0 4122 4599 590757806 590758283 0.000000e+00 811.0
10 TraesCS1D01G205700 chr6D 95.538 493 8 1 4121 4599 181719289 181719781 0.000000e+00 776.0
11 TraesCS1D01G205700 chr6D 80.905 199 29 8 2403 2595 327010814 327010619 1.030000e-31 148.0
12 TraesCS1D01G205700 chr7D 94.153 496 12 3 4118 4599 503001283 503001775 0.000000e+00 739.0
13 TraesCS1D01G205700 chr6B 93.983 482 23 6 4122 4599 714113388 714112909 0.000000e+00 725.0
14 TraesCS1D01G205700 chr6B 93.805 113 7 0 4122 4234 660245471 660245359 2.200000e-38 171.0
15 TraesCS1D01G205700 chr7B 93.882 474 27 2 4122 4594 714325814 714325342 0.000000e+00 713.0
16 TraesCS1D01G205700 chr7B 93.418 471 30 1 4122 4591 648049945 648050415 0.000000e+00 697.0
17 TraesCS1D01G205700 chr7B 92.373 472 33 3 4122 4591 681229367 681229837 0.000000e+00 669.0
18 TraesCS1D01G205700 chr5B 92.616 474 34 1 4122 4594 493657941 493657468 0.000000e+00 680.0
19 TraesCS1D01G205700 chr5B 92.569 471 34 1 4122 4591 358631322 358631792 0.000000e+00 675.0
20 TraesCS1D01G205700 chr6A 79.695 197 28 9 2403 2595 465611984 465611796 1.040000e-26 132.0
21 TraesCS1D01G205700 chr2A 89.796 49 4 1 2545 2592 763527375 763527423 1.380000e-05 62.1


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 TraesCS1D01G205700 chr1D 291491134 291495732 4598 False 8493.000000 8493 100.000 1 4599 1 chr1D.!!$F1 4598
1 TraesCS1D01G205700 chr1B 392433623 392438220 4597 False 2132.333333 4338 96.271 14 4121 3 chr1B.!!$F1 4107
2 TraesCS1D01G205700 chr1A 363451380 363455449 4069 False 3050.500000 3999 95.075 35 4034 2 chr1A.!!$F1 3999

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
115 122 1.134560 GGTCCAAGCAGTAGTAGACGG 59.865 57.143 0.0 0.0 0.0 4.79 F
244 267 1.228063 GCCGCAGATGGGATCACAT 60.228 57.895 11.1 11.1 0.0 3.21 F
1412 1485 0.600557 CTACTCCTGCTATCCCTGCG 59.399 60.000 0.0 0.0 0.0 5.18 F
3030 3416 0.811915 ACTCTCATCCACCTCGTTCG 59.188 55.000 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 1466 0.600557 CGCAGGGATAGCAGGAGTAG 59.399 60.0 0.0 0.0 0.0 2.57 R
1790 1863 1.559831 AGACGCTTTTTGTTTGCAGC 58.440 45.0 0.0 0.0 0.0 5.25 R
3358 3744 0.880441 CCATTGACACGGCACATTGA 59.120 50.0 0.0 0.0 0.0 2.57 R
4378 5013 0.030092 TATGGACAAGGGGGAGGAGG 60.030 60.0 0.0 0.0 0.0 4.30 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
33 34 4.278419 CGAAGGTTTCAGTTTCCCAATCTT 59.722 41.667 0.00 0.00 0.00 2.40
106 113 1.172812 GGCGAAAAGGTCCAAGCAGT 61.173 55.000 0.00 0.00 0.00 4.40
107 114 1.519408 GCGAAAAGGTCCAAGCAGTA 58.481 50.000 0.00 0.00 0.00 2.74
108 115 1.464997 GCGAAAAGGTCCAAGCAGTAG 59.535 52.381 0.00 0.00 0.00 2.57
109 116 2.767505 CGAAAAGGTCCAAGCAGTAGT 58.232 47.619 0.00 0.00 0.00 2.73
110 117 3.863400 GCGAAAAGGTCCAAGCAGTAGTA 60.863 47.826 0.00 0.00 0.00 1.82
111 118 3.927142 CGAAAAGGTCCAAGCAGTAGTAG 59.073 47.826 0.00 0.00 0.00 2.57
113 120 4.538746 AAAGGTCCAAGCAGTAGTAGAC 57.461 45.455 0.00 0.00 0.00 2.59
114 121 2.093106 AGGTCCAAGCAGTAGTAGACG 58.907 52.381 0.00 0.00 0.00 4.18
115 122 1.134560 GGTCCAAGCAGTAGTAGACGG 59.865 57.143 0.00 0.00 0.00 4.79
147 155 8.646356 CATTATTTTATGCACGCAGAAAGAAAA 58.354 29.630 11.22 8.10 38.20 2.29
244 267 1.228063 GCCGCAGATGGGATCACAT 60.228 57.895 11.10 11.10 0.00 3.21
245 268 1.233285 GCCGCAGATGGGATCACATC 61.233 60.000 27.48 27.48 45.91 3.06
367 399 2.925170 ACCTCCTGCACGCTCCTT 60.925 61.111 0.00 0.00 0.00 3.36
404 437 4.153330 TCCTCCTCCTACCCGGCC 62.153 72.222 0.00 0.00 0.00 6.13
468 510 4.814041 GCTCCTCCCTGCCTCCCT 62.814 72.222 0.00 0.00 0.00 4.20
469 511 2.767496 CTCCTCCCTGCCTCCCTG 60.767 72.222 0.00 0.00 0.00 4.45
501 543 2.158035 ACCTCCCTGATCTGATATGCCT 60.158 50.000 0.38 0.00 0.00 4.75
605 647 1.696832 GATCGTTCTTGGTCGGCTGC 61.697 60.000 0.00 0.00 0.00 5.25
624 674 2.603580 GGGGGAGGAGGGATTTGC 59.396 66.667 0.00 0.00 0.00 3.68
765 815 8.757982 ATTCTTTCCTGTTATTGATGCTATGT 57.242 30.769 0.00 0.00 0.00 2.29
771 822 6.658816 TCCTGTTATTGATGCTATGTGTGTTT 59.341 34.615 0.00 0.00 0.00 2.83
773 824 6.851609 TGTTATTGATGCTATGTGTGTTTCC 58.148 36.000 0.00 0.00 0.00 3.13
884 935 4.797471 TCAGCAATCCGAAAATGTTCTTG 58.203 39.130 0.00 0.00 0.00 3.02
902 953 4.341487 TCTTGGTCTCTAATCGTTCCTCA 58.659 43.478 0.00 0.00 0.00 3.86
959 1014 9.734620 TCTCAAATGATTTTGTTTCTTGTACTG 57.265 29.630 0.00 0.00 42.37 2.74
960 1015 9.520204 CTCAAATGATTTTGTTTCTTGTACTGT 57.480 29.630 0.00 0.00 42.37 3.55
961 1016 9.515020 TCAAATGATTTTGTTTCTTGTACTGTC 57.485 29.630 0.00 0.00 42.37 3.51
962 1017 9.520204 CAAATGATTTTGTTTCTTGTACTGTCT 57.480 29.630 0.00 0.00 37.92 3.41
965 1020 8.909708 TGATTTTGTTTCTTGTACTGTCTTTG 57.090 30.769 0.00 0.00 0.00 2.77
966 1021 8.735315 TGATTTTGTTTCTTGTACTGTCTTTGA 58.265 29.630 0.00 0.00 0.00 2.69
967 1022 9.736023 GATTTTGTTTCTTGTACTGTCTTTGAT 57.264 29.630 0.00 0.00 0.00 2.57
968 1023 9.736023 ATTTTGTTTCTTGTACTGTCTTTGATC 57.264 29.630 0.00 0.00 0.00 2.92
969 1024 7.857734 TTGTTTCTTGTACTGTCTTTGATCA 57.142 32.000 0.00 0.00 0.00 2.92
1412 1485 0.600557 CTACTCCTGCTATCCCTGCG 59.399 60.000 0.00 0.00 0.00 5.18
1583 1656 1.843368 ATGCCACCCATTCTGACTTG 58.157 50.000 0.00 0.00 0.00 3.16
1790 1863 5.560966 ATTTGCTAGTACAATGGAAACCG 57.439 39.130 0.00 0.00 0.00 4.44
1805 1878 1.006086 AACCGCTGCAAACAAAAAGC 58.994 45.000 0.00 0.00 0.00 3.51
1921 1994 2.514458 AAACTGGGCCCTGTATTCAG 57.486 50.000 32.28 17.54 41.01 3.02
1985 2058 7.094205 CCTGGTTCTTGAGTGCAGTAATTATTT 60.094 37.037 0.00 0.00 0.00 1.40
2301 2374 6.485648 AGGTAAGTTACTAAGTTTTGGTGCTG 59.514 38.462 12.65 0.00 0.00 4.41
2600 2680 1.067295 TCCATGCCTGACTTCCAACT 58.933 50.000 0.00 0.00 0.00 3.16
3026 3412 7.554476 TCTTATGATATACTCTCATCCACCTCG 59.446 40.741 0.00 0.00 35.12 4.63
3030 3416 0.811915 ACTCTCATCCACCTCGTTCG 59.188 55.000 0.00 0.00 0.00 3.95
3178 3564 3.074538 AGAACCTTGGTGGCATAGTCTTT 59.925 43.478 0.00 0.00 40.22 2.52
3358 3744 2.291153 CCTTTGGGATGTGATGACCAGT 60.291 50.000 0.00 0.00 33.96 4.00
3505 3891 1.835927 GCTTCTCAGCAGACCCACCT 61.836 60.000 0.00 0.00 46.49 4.00
3609 3995 0.252881 AATGCCTGACCTCCCTCTCA 60.253 55.000 0.00 0.00 0.00 3.27
3628 4014 4.104738 TCTCAAAACATGTCTTCCTCCCTT 59.895 41.667 0.00 0.00 0.00 3.95
3861 4249 6.599638 GCCTTCTTATTCTGGTACAAATGACT 59.400 38.462 0.00 0.00 38.70 3.41
4003 4391 7.606349 AGAAATGAACTTTTAATCCTTGCTCC 58.394 34.615 0.00 0.00 0.00 4.70
4110 4745 4.153673 ACTGTAGTAGTACGAGGCTCAT 57.846 45.455 15.95 0.56 38.04 2.90
4121 4756 0.842635 GAGGCTCATTGATGGACCCT 59.157 55.000 10.25 0.00 0.00 4.34
4122 4757 0.549950 AGGCTCATTGATGGACCCTG 59.450 55.000 0.00 0.00 0.00 4.45
4123 4758 0.257039 GGCTCATTGATGGACCCTGT 59.743 55.000 0.00 0.00 0.00 4.00
4124 4759 1.341383 GGCTCATTGATGGACCCTGTT 60.341 52.381 0.00 0.00 0.00 3.16
4125 4760 2.092429 GGCTCATTGATGGACCCTGTTA 60.092 50.000 0.00 0.00 0.00 2.41
4126 4761 3.435601 GGCTCATTGATGGACCCTGTTAT 60.436 47.826 0.00 0.00 0.00 1.89
4127 4762 4.202461 GGCTCATTGATGGACCCTGTTATA 60.202 45.833 0.00 0.00 0.00 0.98
4128 4763 5.376625 GCTCATTGATGGACCCTGTTATAA 58.623 41.667 0.00 0.00 0.00 0.98
4129 4764 5.239525 GCTCATTGATGGACCCTGTTATAAC 59.760 44.000 8.75 8.75 0.00 1.89
4130 4765 5.690865 TCATTGATGGACCCTGTTATAACC 58.309 41.667 13.01 0.00 0.00 2.85
4131 4766 3.830744 TGATGGACCCTGTTATAACCG 57.169 47.619 13.01 6.60 0.00 4.44
4132 4767 2.436542 TGATGGACCCTGTTATAACCGG 59.563 50.000 16.85 16.85 33.58 5.28
4133 4768 1.955451 TGGACCCTGTTATAACCGGT 58.045 50.000 20.68 20.00 34.39 5.28
4134 4769 2.268107 TGGACCCTGTTATAACCGGTT 58.732 47.619 25.64 25.64 32.55 4.44
4135 4770 2.643801 TGGACCCTGTTATAACCGGTTT 59.356 45.455 27.64 15.51 32.55 3.27
4136 4771 3.011818 GGACCCTGTTATAACCGGTTTG 58.988 50.000 27.64 8.88 32.55 2.93
4137 4772 3.011818 GACCCTGTTATAACCGGTTTGG 58.988 50.000 27.64 16.61 46.41 3.28
4156 4791 3.755112 GGTCTATACCAGAAAGAGGCC 57.245 52.381 0.00 0.00 45.98 5.19
4157 4792 2.369203 GGTCTATACCAGAAAGAGGCCC 59.631 54.545 0.00 0.00 45.98 5.80
4158 4793 3.039011 GTCTATACCAGAAAGAGGCCCA 58.961 50.000 0.00 0.00 34.17 5.36
4159 4794 3.039011 TCTATACCAGAAAGAGGCCCAC 58.961 50.000 0.00 0.00 0.00 4.61
4160 4795 0.919710 ATACCAGAAAGAGGCCCACC 59.080 55.000 0.00 0.00 0.00 4.61
4161 4796 1.550130 TACCAGAAAGAGGCCCACCG 61.550 60.000 0.00 0.00 42.76 4.94
4162 4797 2.045926 CAGAAAGAGGCCCACCGG 60.046 66.667 0.00 0.00 42.76 5.28
4175 4810 3.053831 CCCACCGGGCATTAGTATTAG 57.946 52.381 6.32 0.00 35.35 1.73
4176 4811 2.290071 CCCACCGGGCATTAGTATTAGG 60.290 54.545 6.32 0.00 35.35 2.69
4177 4812 2.290071 CCACCGGGCATTAGTATTAGGG 60.290 54.545 6.32 0.00 0.00 3.53
4178 4813 1.982958 ACCGGGCATTAGTATTAGGGG 59.017 52.381 6.32 0.00 0.00 4.79
4179 4814 1.339727 CCGGGCATTAGTATTAGGGGC 60.340 57.143 0.00 0.00 0.00 5.80
4180 4815 1.628846 CGGGCATTAGTATTAGGGGCT 59.371 52.381 0.00 0.00 0.00 5.19
4181 4816 2.039879 CGGGCATTAGTATTAGGGGCTT 59.960 50.000 0.00 0.00 0.00 4.35
4182 4817 3.421844 GGGCATTAGTATTAGGGGCTTG 58.578 50.000 0.00 0.00 0.00 4.01
4183 4818 3.073946 GGGCATTAGTATTAGGGGCTTGA 59.926 47.826 0.00 0.00 0.00 3.02
4184 4819 4.072839 GGCATTAGTATTAGGGGCTTGAC 58.927 47.826 0.00 0.00 0.00 3.18
4185 4820 4.072839 GCATTAGTATTAGGGGCTTGACC 58.927 47.826 0.00 0.00 37.93 4.02
4202 4837 4.216411 TGACCCACAAGTTATCTTAGGC 57.784 45.455 0.69 0.00 32.07 3.93
4203 4838 3.585289 TGACCCACAAGTTATCTTAGGCA 59.415 43.478 0.00 0.00 32.07 4.75
4204 4839 4.042311 TGACCCACAAGTTATCTTAGGCAA 59.958 41.667 0.00 0.00 32.07 4.52
4205 4840 4.589908 ACCCACAAGTTATCTTAGGCAAG 58.410 43.478 0.00 0.00 32.07 4.01
4206 4841 4.042934 ACCCACAAGTTATCTTAGGCAAGT 59.957 41.667 0.00 0.00 33.20 3.16
4207 4842 5.010282 CCCACAAGTTATCTTAGGCAAGTT 58.990 41.667 0.00 0.00 33.20 2.66
4208 4843 6.177610 CCCACAAGTTATCTTAGGCAAGTTA 58.822 40.000 0.00 0.00 33.20 2.24
4209 4844 6.828785 CCCACAAGTTATCTTAGGCAAGTTAT 59.171 38.462 0.00 0.00 33.20 1.89
4210 4845 7.012421 CCCACAAGTTATCTTAGGCAAGTTATC 59.988 40.741 0.00 0.00 33.20 1.75
4211 4846 7.770897 CCACAAGTTATCTTAGGCAAGTTATCT 59.229 37.037 0.00 0.00 33.20 1.98
4212 4847 9.167311 CACAAGTTATCTTAGGCAAGTTATCTT 57.833 33.333 0.00 0.00 31.80 2.40
4216 4851 8.151596 AGTTATCTTAGGCAAGTTATCTTAGGC 58.848 37.037 0.00 0.00 33.20 3.93
4217 4852 6.755542 ATCTTAGGCAAGTTATCTTAGGCT 57.244 37.500 12.93 12.93 39.15 4.58
4218 4853 7.857404 ATCTTAGGCAAGTTATCTTAGGCTA 57.143 36.000 11.62 11.62 38.00 3.93
4219 4854 7.670605 TCTTAGGCAAGTTATCTTAGGCTAA 57.329 36.000 19.15 19.15 41.33 3.09
4220 4855 8.086143 TCTTAGGCAAGTTATCTTAGGCTAAA 57.914 34.615 19.90 0.40 41.97 1.85
4221 4856 8.204836 TCTTAGGCAAGTTATCTTAGGCTAAAG 58.795 37.037 19.90 16.38 41.97 1.85
4222 4857 6.314899 AGGCAAGTTATCTTAGGCTAAAGT 57.685 37.500 8.54 2.64 36.60 2.66
4223 4858 6.722328 AGGCAAGTTATCTTAGGCTAAAGTT 58.278 36.000 8.54 0.00 36.60 2.66
4224 4859 7.858498 AGGCAAGTTATCTTAGGCTAAAGTTA 58.142 34.615 8.54 0.00 36.60 2.24
4225 4860 8.495260 AGGCAAGTTATCTTAGGCTAAAGTTAT 58.505 33.333 8.54 2.97 36.60 1.89
4226 4861 9.774413 GGCAAGTTATCTTAGGCTAAAGTTATA 57.226 33.333 8.54 2.09 32.07 0.98
4250 4885 9.933723 ATAAATACTAGTTGTAAGACACCGTTT 57.066 29.630 0.00 0.00 34.45 3.60
4251 4886 7.647907 AATACTAGTTGTAAGACACCGTTTG 57.352 36.000 0.00 0.00 34.45 2.93
4252 4887 5.266733 ACTAGTTGTAAGACACCGTTTGA 57.733 39.130 0.00 0.00 0.00 2.69
4253 4888 5.287226 ACTAGTTGTAAGACACCGTTTGAG 58.713 41.667 0.00 0.00 0.00 3.02
4254 4889 3.463944 AGTTGTAAGACACCGTTTGAGG 58.536 45.455 0.00 0.00 37.30 3.86
4255 4890 1.873698 TGTAAGACACCGTTTGAGGC 58.126 50.000 0.00 0.00 33.69 4.70
4256 4891 1.139256 TGTAAGACACCGTTTGAGGCA 59.861 47.619 0.00 0.00 33.69 4.75
4257 4892 2.215196 GTAAGACACCGTTTGAGGCAA 58.785 47.619 0.00 0.00 33.69 4.52
4258 4893 1.308998 AAGACACCGTTTGAGGCAAG 58.691 50.000 0.00 0.00 33.69 4.01
4259 4894 1.166531 AGACACCGTTTGAGGCAAGC 61.167 55.000 0.00 0.00 33.69 4.01
4260 4895 1.444119 GACACCGTTTGAGGCAAGCA 61.444 55.000 0.00 0.00 33.69 3.91
4261 4896 1.034838 ACACCGTTTGAGGCAAGCAA 61.035 50.000 0.00 0.00 33.69 3.91
4262 4897 0.314935 CACCGTTTGAGGCAAGCAAT 59.685 50.000 0.00 0.00 33.69 3.56
4263 4898 1.539388 CACCGTTTGAGGCAAGCAATA 59.461 47.619 0.00 0.00 33.69 1.90
4264 4899 2.030363 CACCGTTTGAGGCAAGCAATAA 60.030 45.455 0.00 0.00 33.69 1.40
4265 4900 2.625790 ACCGTTTGAGGCAAGCAATAAA 59.374 40.909 0.00 0.00 33.69 1.40
4266 4901 3.244976 CCGTTTGAGGCAAGCAATAAAG 58.755 45.455 0.00 0.00 0.00 1.85
4267 4902 3.057596 CCGTTTGAGGCAAGCAATAAAGA 60.058 43.478 0.00 0.00 0.00 2.52
4268 4903 4.380867 CCGTTTGAGGCAAGCAATAAAGAT 60.381 41.667 0.00 0.00 0.00 2.40
4269 4904 5.163663 CCGTTTGAGGCAAGCAATAAAGATA 60.164 40.000 0.00 0.00 0.00 1.98
4270 4905 6.460123 CCGTTTGAGGCAAGCAATAAAGATAT 60.460 38.462 0.00 0.00 0.00 1.63
4271 4906 6.974622 CGTTTGAGGCAAGCAATAAAGATATT 59.025 34.615 0.00 0.00 31.80 1.28
4272 4907 8.128582 CGTTTGAGGCAAGCAATAAAGATATTA 58.871 33.333 0.00 0.00 30.50 0.98
4273 4908 9.971922 GTTTGAGGCAAGCAATAAAGATATTAT 57.028 29.630 0.00 0.00 30.50 1.28
4290 4925 9.838339 AAGATATTATAATCTTCTATTGCCCGG 57.162 33.333 0.00 0.00 41.34 5.73
4291 4926 7.934120 AGATATTATAATCTTCTATTGCCCGGC 59.066 37.037 1.04 1.04 32.09 6.13
4292 4927 5.499004 TTATAATCTTCTATTGCCCGGCT 57.501 39.130 11.61 0.00 0.00 5.52
4293 4928 2.262423 AATCTTCTATTGCCCGGCTC 57.738 50.000 11.61 0.00 0.00 4.70
4294 4929 0.398318 ATCTTCTATTGCCCGGCTCC 59.602 55.000 11.61 0.00 0.00 4.70
4295 4930 1.227973 CTTCTATTGCCCGGCTCCC 60.228 63.158 11.61 0.00 0.00 4.30
4296 4931 2.682582 CTTCTATTGCCCGGCTCCCC 62.683 65.000 11.61 0.00 0.00 4.81
4297 4932 3.488569 CTATTGCCCGGCTCCCCA 61.489 66.667 11.61 0.00 0.00 4.96
4298 4933 3.018193 TATTGCCCGGCTCCCCAA 61.018 61.111 11.61 0.00 0.00 4.12
4299 4934 2.965716 CTATTGCCCGGCTCCCCAAG 62.966 65.000 11.61 0.00 0.00 3.61
4309 4944 3.495729 TCCCCAAGGAGCTGGAAC 58.504 61.111 0.00 0.00 38.96 3.62
4310 4945 2.231380 TCCCCAAGGAGCTGGAACC 61.231 63.158 0.00 0.00 38.96 3.62
4311 4946 2.356667 CCCAAGGAGCTGGAACCC 59.643 66.667 0.00 0.00 38.96 4.11
4312 4947 2.234296 CCCAAGGAGCTGGAACCCT 61.234 63.158 0.00 0.00 38.96 4.34
4313 4948 0.914417 CCCAAGGAGCTGGAACCCTA 60.914 60.000 0.00 0.00 38.96 3.53
4314 4949 0.543749 CCAAGGAGCTGGAACCCTAG 59.456 60.000 0.00 0.00 38.96 3.02
4315 4950 0.107459 CAAGGAGCTGGAACCCTAGC 60.107 60.000 0.00 0.00 40.18 3.42
4316 4951 1.275421 AAGGAGCTGGAACCCTAGCC 61.275 60.000 0.00 0.00 40.76 3.93
4317 4952 2.501610 GAGCTGGAACCCTAGCCG 59.498 66.667 0.00 0.00 40.76 5.52
4318 4953 3.741830 GAGCTGGAACCCTAGCCGC 62.742 68.421 0.00 0.00 40.76 6.53
4319 4954 4.858680 GCTGGAACCCTAGCCGCC 62.859 72.222 0.00 0.00 33.89 6.13
4320 4955 4.530857 CTGGAACCCTAGCCGCCG 62.531 72.222 0.00 0.00 0.00 6.46
4335 4970 4.796495 CCGCACCCAACCCTAGCC 62.796 72.222 0.00 0.00 0.00 3.93
4340 4975 4.832608 CCCAACCCTAGCCGCGAC 62.833 72.222 8.23 0.00 0.00 5.19
4378 5013 4.247380 CCCGCTCCAGCCCTCATC 62.247 72.222 0.00 0.00 37.91 2.92
4379 5014 4.247380 CCGCTCCAGCCCTCATCC 62.247 72.222 0.00 0.00 37.91 3.51
4380 5015 3.160047 CGCTCCAGCCCTCATCCT 61.160 66.667 0.00 0.00 37.91 3.24
4381 5016 2.828145 GCTCCAGCCCTCATCCTC 59.172 66.667 0.00 0.00 34.31 3.71
4382 5017 2.817056 GCTCCAGCCCTCATCCTCC 61.817 68.421 0.00 0.00 34.31 4.30
4383 5018 1.074623 CTCCAGCCCTCATCCTCCT 60.075 63.158 0.00 0.00 0.00 3.69
4384 5019 1.074926 TCCAGCCCTCATCCTCCTC 60.075 63.158 0.00 0.00 0.00 3.71
4385 5020 2.146061 CCAGCCCTCATCCTCCTCC 61.146 68.421 0.00 0.00 0.00 4.30
4386 5021 2.146061 CAGCCCTCATCCTCCTCCC 61.146 68.421 0.00 0.00 0.00 4.30
4387 5022 2.851588 GCCCTCATCCTCCTCCCC 60.852 72.222 0.00 0.00 0.00 4.81
4388 5023 2.122189 CCCTCATCCTCCTCCCCC 60.122 72.222 0.00 0.00 0.00 5.40
4389 5024 2.731461 CCCTCATCCTCCTCCCCCT 61.731 68.421 0.00 0.00 0.00 4.79
4390 5025 1.319799 CCTCATCCTCCTCCCCCTT 59.680 63.158 0.00 0.00 0.00 3.95
4391 5026 1.059006 CCTCATCCTCCTCCCCCTTG 61.059 65.000 0.00 0.00 0.00 3.61
4392 5027 0.327000 CTCATCCTCCTCCCCCTTGT 60.327 60.000 0.00 0.00 0.00 3.16
4393 5028 0.326618 TCATCCTCCTCCCCCTTGTC 60.327 60.000 0.00 0.00 0.00 3.18
4394 5029 1.004891 ATCCTCCTCCCCCTTGTCC 59.995 63.158 0.00 0.00 0.00 4.02
4395 5030 1.837533 ATCCTCCTCCCCCTTGTCCA 61.838 60.000 0.00 0.00 0.00 4.02
4396 5031 1.308216 CCTCCTCCCCCTTGTCCAT 60.308 63.158 0.00 0.00 0.00 3.41
4397 5032 0.030092 CCTCCTCCCCCTTGTCCATA 60.030 60.000 0.00 0.00 0.00 2.74
4398 5033 1.132500 CTCCTCCCCCTTGTCCATAC 58.868 60.000 0.00 0.00 0.00 2.39
4399 5034 0.419865 TCCTCCCCCTTGTCCATACA 59.580 55.000 0.00 0.00 0.00 2.29
4400 5035 1.203505 TCCTCCCCCTTGTCCATACAA 60.204 52.381 0.00 0.00 43.32 2.41
4401 5036 1.852965 CCTCCCCCTTGTCCATACAAT 59.147 52.381 0.00 0.00 44.43 2.71
4402 5037 2.158608 CCTCCCCCTTGTCCATACAATC 60.159 54.545 0.00 0.00 44.43 2.67
4403 5038 2.780010 CTCCCCCTTGTCCATACAATCT 59.220 50.000 0.00 0.00 44.43 2.40
4404 5039 3.973973 CTCCCCCTTGTCCATACAATCTA 59.026 47.826 0.00 0.00 44.43 1.98
4405 5040 3.714798 TCCCCCTTGTCCATACAATCTAC 59.285 47.826 0.00 0.00 44.43 2.59
4406 5041 3.494398 CCCCCTTGTCCATACAATCTACG 60.494 52.174 0.00 0.00 44.43 3.51
4407 5042 3.131396 CCCTTGTCCATACAATCTACGC 58.869 50.000 0.00 0.00 44.43 4.42
4408 5043 3.131396 CCTTGTCCATACAATCTACGCC 58.869 50.000 0.00 0.00 44.43 5.68
4409 5044 2.502213 TGTCCATACAATCTACGCCG 57.498 50.000 0.00 0.00 30.91 6.46
4410 5045 1.067974 TGTCCATACAATCTACGCCGG 59.932 52.381 0.00 0.00 30.91 6.13
4411 5046 1.338973 GTCCATACAATCTACGCCGGA 59.661 52.381 5.05 0.00 0.00 5.14
4412 5047 1.611977 TCCATACAATCTACGCCGGAG 59.388 52.381 5.05 3.72 0.00 4.63
4426 5061 3.477346 GGAGGCCCGGTAGGAACC 61.477 72.222 0.00 0.00 42.95 3.62
4427 5062 3.477346 GAGGCCCGGTAGGAACCC 61.477 72.222 0.00 0.00 43.54 4.11
4428 5063 3.997756 GAGGCCCGGTAGGAACCCT 62.998 68.421 0.00 0.00 43.54 4.34
4429 5064 2.041612 GGCCCGGTAGGAACCCTA 60.042 66.667 0.00 0.00 43.54 3.53
4430 5065 2.138831 GGCCCGGTAGGAACCCTAG 61.139 68.421 0.00 0.00 43.54 3.02
4431 5066 1.382283 GCCCGGTAGGAACCCTAGT 60.382 63.158 0.00 0.00 43.54 2.57
4432 5067 1.398174 GCCCGGTAGGAACCCTAGTC 61.398 65.000 0.00 0.00 43.54 2.59
4433 5068 0.758310 CCCGGTAGGAACCCTAGTCC 60.758 65.000 0.00 0.00 43.54 3.85
4434 5069 0.261109 CCGGTAGGAACCCTAGTCCT 59.739 60.000 5.75 5.75 43.54 3.85
4435 5070 1.496429 CCGGTAGGAACCCTAGTCCTA 59.504 57.143 3.95 3.95 43.54 2.94
4438 5073 3.677156 GTAGGAACCCTAGTCCTACCA 57.323 52.381 20.22 0.00 46.18 3.25
4439 5074 3.986435 GTAGGAACCCTAGTCCTACCAA 58.014 50.000 20.22 0.00 46.18 3.67
4440 5075 3.797671 AGGAACCCTAGTCCTACCAAT 57.202 47.619 0.00 0.00 31.06 3.16
4441 5076 4.090027 AGGAACCCTAGTCCTACCAATT 57.910 45.455 0.00 0.00 31.06 2.32
4442 5077 4.445564 AGGAACCCTAGTCCTACCAATTT 58.554 43.478 0.00 0.00 31.06 1.82
4443 5078 4.227527 AGGAACCCTAGTCCTACCAATTTG 59.772 45.833 0.00 0.00 31.06 2.32
4444 5079 4.524053 GAACCCTAGTCCTACCAATTTGG 58.476 47.826 14.02 14.02 45.02 3.28
4445 5080 9.863898 TAGGAACCCTAGTCCTACCAATTTGGT 62.864 44.444 23.83 23.83 43.88 3.67
4446 5081 9.863898 AGGAACCCTAGTCCTACCAATTTGGTA 62.864 44.444 23.53 23.53 40.03 3.25
4458 5093 3.947834 CCAATTTGGTATCCAGAGACACC 59.052 47.826 7.31 0.00 33.81 4.16
4459 5094 4.567537 CCAATTTGGTATCCAGAGACACCA 60.568 45.833 7.31 0.00 39.27 4.17
4460 5095 3.981071 TTTGGTATCCAGAGACACCAG 57.019 47.619 0.00 0.00 41.84 4.00
4461 5096 1.866015 TGGTATCCAGAGACACCAGG 58.134 55.000 0.00 0.00 36.15 4.45
4462 5097 0.466124 GGTATCCAGAGACACCAGGC 59.534 60.000 0.00 0.00 0.00 4.85
4463 5098 0.466124 GTATCCAGAGACACCAGGCC 59.534 60.000 0.00 0.00 0.00 5.19
4464 5099 1.043116 TATCCAGAGACACCAGGCCG 61.043 60.000 0.00 0.00 0.00 6.13
4465 5100 2.805313 ATCCAGAGACACCAGGCCGA 62.805 60.000 0.00 0.00 0.00 5.54
4466 5101 2.362369 CCAGAGACACCAGGCCGAT 61.362 63.158 0.00 0.00 0.00 4.18
4467 5102 1.142748 CAGAGACACCAGGCCGATC 59.857 63.158 0.00 0.00 0.00 3.69
4468 5103 1.305297 AGAGACACCAGGCCGATCA 60.305 57.895 0.00 0.00 0.00 2.92
4469 5104 0.689080 AGAGACACCAGGCCGATCAT 60.689 55.000 0.00 0.00 0.00 2.45
4470 5105 0.531532 GAGACACCAGGCCGATCATG 60.532 60.000 0.00 0.00 0.00 3.07
4471 5106 1.221840 GACACCAGGCCGATCATGT 59.778 57.895 0.00 0.00 0.00 3.21
4472 5107 0.811616 GACACCAGGCCGATCATGTC 60.812 60.000 11.24 11.24 0.00 3.06
4481 5116 2.892305 CGATCATGTCGCTTCCTCC 58.108 57.895 5.07 0.00 44.33 4.30
4482 5117 0.103026 CGATCATGTCGCTTCCTCCA 59.897 55.000 5.07 0.00 44.33 3.86
4483 5118 1.269988 CGATCATGTCGCTTCCTCCAT 60.270 52.381 5.07 0.00 44.33 3.41
4484 5119 2.411904 GATCATGTCGCTTCCTCCATC 58.588 52.381 0.00 0.00 0.00 3.51
4485 5120 1.194218 TCATGTCGCTTCCTCCATCA 58.806 50.000 0.00 0.00 0.00 3.07
4486 5121 1.134699 TCATGTCGCTTCCTCCATCAC 60.135 52.381 0.00 0.00 0.00 3.06
4487 5122 0.179000 ATGTCGCTTCCTCCATCACC 59.821 55.000 0.00 0.00 0.00 4.02
4488 5123 1.519455 GTCGCTTCCTCCATCACCG 60.519 63.158 0.00 0.00 0.00 4.94
4489 5124 2.892425 CGCTTCCTCCATCACCGC 60.892 66.667 0.00 0.00 0.00 5.68
4490 5125 2.514824 GCTTCCTCCATCACCGCC 60.515 66.667 0.00 0.00 0.00 6.13
4491 5126 2.202932 CTTCCTCCATCACCGCCG 60.203 66.667 0.00 0.00 0.00 6.46
4492 5127 4.467084 TTCCTCCATCACCGCCGC 62.467 66.667 0.00 0.00 0.00 6.53
4509 5144 4.864334 CCGCTGCCATCCACCTCC 62.864 72.222 0.00 0.00 0.00 4.30
4512 5147 4.864334 CTGCCATCCACCTCCGCC 62.864 72.222 0.00 0.00 0.00 6.13
4516 5151 4.489771 CATCCACCTCCGCCCCAC 62.490 72.222 0.00 0.00 0.00 4.61
4548 5183 4.899239 GCCACCTCCTCGCCGATG 62.899 72.222 0.00 0.00 0.00 3.84
4549 5184 3.147595 CCACCTCCTCGCCGATGA 61.148 66.667 0.00 0.00 0.00 2.92
4550 5185 2.105128 CACCTCCTCGCCGATGAC 59.895 66.667 0.00 0.00 0.00 3.06
4551 5186 3.518998 ACCTCCTCGCCGATGACG 61.519 66.667 0.00 0.00 39.43 4.35
4568 5203 4.867599 GGCGATCACGTCCGGGAC 62.868 72.222 17.38 17.38 41.98 4.46
4569 5204 4.867599 GCGATCACGTCCGGGACC 62.868 72.222 21.06 5.98 41.98 4.46
4570 5205 3.445687 CGATCACGTCCGGGACCA 61.446 66.667 21.06 6.11 34.56 4.02
4571 5206 2.782222 CGATCACGTCCGGGACCAT 61.782 63.158 21.06 10.67 34.56 3.55
4572 5207 1.067582 GATCACGTCCGGGACCATC 59.932 63.158 21.06 15.17 0.00 3.51
4573 5208 1.672854 GATCACGTCCGGGACCATCA 61.673 60.000 21.06 3.57 0.00 3.07
4574 5209 1.956629 ATCACGTCCGGGACCATCAC 61.957 60.000 21.06 0.00 0.00 3.06
4575 5210 3.387947 ACGTCCGGGACCATCACC 61.388 66.667 21.06 0.00 0.00 4.02
4576 5211 3.387091 CGTCCGGGACCATCACCA 61.387 66.667 21.06 0.00 0.00 4.17
4577 5212 2.267961 GTCCGGGACCATCACCAC 59.732 66.667 16.55 0.00 0.00 4.16
4578 5213 3.006728 TCCGGGACCATCACCACC 61.007 66.667 0.00 0.00 0.00 4.61
4579 5214 3.326578 CCGGGACCATCACCACCA 61.327 66.667 0.00 0.00 0.00 4.17
4580 5215 2.046314 CGGGACCATCACCACCAC 60.046 66.667 0.00 0.00 0.00 4.16
4581 5216 2.355115 GGGACCATCACCACCACC 59.645 66.667 0.00 0.00 0.00 4.61
4582 5217 2.046314 GGACCATCACCACCACCG 60.046 66.667 0.00 0.00 0.00 4.94
4583 5218 2.746277 GACCATCACCACCACCGC 60.746 66.667 0.00 0.00 0.00 5.68
4584 5219 4.697756 ACCATCACCACCACCGCG 62.698 66.667 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.618709 CTGAAACCTTCGCCAGAAAACT 59.381 45.455 0.00 0.00 35.71 2.66
1 2 2.357952 ACTGAAACCTTCGCCAGAAAAC 59.642 45.455 0.00 0.00 35.71 2.43
2 3 2.650322 ACTGAAACCTTCGCCAGAAAA 58.350 42.857 0.00 0.00 35.71 2.29
3 4 2.341846 ACTGAAACCTTCGCCAGAAA 57.658 45.000 0.00 0.00 35.71 2.52
4 5 2.341846 AACTGAAACCTTCGCCAGAA 57.658 45.000 0.00 0.00 34.76 3.02
5 6 2.218603 GAAACTGAAACCTTCGCCAGA 58.781 47.619 0.00 0.00 0.00 3.86
6 7 1.266989 GGAAACTGAAACCTTCGCCAG 59.733 52.381 0.00 0.00 0.00 4.85
7 8 1.314730 GGAAACTGAAACCTTCGCCA 58.685 50.000 0.00 0.00 0.00 5.69
8 9 0.596577 GGGAAACTGAAACCTTCGCC 59.403 55.000 0.00 0.00 0.00 5.54
9 10 1.314730 TGGGAAACTGAAACCTTCGC 58.685 50.000 0.00 0.00 33.82 4.70
10 11 3.821033 AGATTGGGAAACTGAAACCTTCG 59.179 43.478 0.00 0.00 0.00 3.79
11 12 5.301805 TCAAGATTGGGAAACTGAAACCTTC 59.698 40.000 0.00 0.00 0.00 3.46
12 13 5.208121 TCAAGATTGGGAAACTGAAACCTT 58.792 37.500 0.00 0.00 0.00 3.50
33 34 3.769300 TCTACTGCCACTGCTTCTTATCA 59.231 43.478 0.00 0.00 38.71 2.15
106 113 4.682778 AATAATGCTTGGCCGTCTACTA 57.317 40.909 0.00 0.00 0.00 1.82
107 114 3.560636 AATAATGCTTGGCCGTCTACT 57.439 42.857 0.00 0.00 0.00 2.57
108 115 4.632538 AAAATAATGCTTGGCCGTCTAC 57.367 40.909 0.00 0.00 0.00 2.59
109 116 6.312399 CATAAAATAATGCTTGGCCGTCTA 57.688 37.500 0.00 0.00 0.00 2.59
110 117 5.186996 CATAAAATAATGCTTGGCCGTCT 57.813 39.130 0.00 0.00 0.00 4.18
244 267 1.080093 GGCGAGATGGTTCGTGTGA 60.080 57.895 0.00 0.00 42.38 3.58
245 268 2.100631 GGGCGAGATGGTTCGTGTG 61.101 63.158 0.00 0.00 42.38 3.82
246 269 2.264794 GGGCGAGATGGTTCGTGT 59.735 61.111 0.00 0.00 42.38 4.49
247 270 2.885644 CGGGCGAGATGGTTCGTG 60.886 66.667 0.00 0.00 42.38 4.35
248 271 4.814294 GCGGGCGAGATGGTTCGT 62.814 66.667 0.00 0.00 42.38 3.85
273 300 1.925972 GGAGAGGGGGCTGGTCTTT 60.926 63.158 0.00 0.00 0.00 2.52
345 377 4.357947 GCGTGCAGGAGGTCGTGA 62.358 66.667 11.29 0.00 33.92 4.35
578 620 3.241995 CGACCAAGAACGATCCGATTTTC 60.242 47.826 0.00 0.00 0.00 2.29
605 647 2.368329 AAATCCCTCCTCCCCCGG 60.368 66.667 0.00 0.00 0.00 5.73
683 733 1.817941 CCAATAACCACGCCCGGAG 60.818 63.158 0.73 0.00 0.00 4.63
692 742 3.057174 GCAACGATTGGAACCAATAACCA 60.057 43.478 17.47 0.00 45.50 3.67
695 745 4.167554 GTGCAACGATTGGAACCAATAA 57.832 40.909 17.47 0.00 45.50 1.40
826 877 1.597742 CTTCCGATCGGCCATGATTT 58.402 50.000 29.62 0.00 34.68 2.17
884 935 4.722361 AAGTGAGGAACGATTAGAGACC 57.278 45.455 0.00 0.00 0.00 3.85
957 1012 4.384056 ACTCTGTTGGTGATCAAAGACAG 58.616 43.478 19.74 19.74 37.08 3.51
958 1013 4.422073 ACTCTGTTGGTGATCAAAGACA 57.578 40.909 0.00 1.52 37.08 3.41
959 1014 4.390297 GCTACTCTGTTGGTGATCAAAGAC 59.610 45.833 0.00 0.00 37.08 3.01
960 1015 4.563580 GGCTACTCTGTTGGTGATCAAAGA 60.564 45.833 0.00 0.00 37.08 2.52
961 1016 3.686726 GGCTACTCTGTTGGTGATCAAAG 59.313 47.826 0.00 0.00 37.08 2.77
962 1017 3.072330 TGGCTACTCTGTTGGTGATCAAA 59.928 43.478 0.00 0.00 37.08 2.69
963 1018 2.637382 TGGCTACTCTGTTGGTGATCAA 59.363 45.455 0.00 0.00 0.00 2.57
964 1019 2.256306 TGGCTACTCTGTTGGTGATCA 58.744 47.619 0.00 0.00 0.00 2.92
965 1020 3.055819 TCTTGGCTACTCTGTTGGTGATC 60.056 47.826 0.00 0.00 0.00 2.92
966 1021 2.906389 TCTTGGCTACTCTGTTGGTGAT 59.094 45.455 0.00 0.00 0.00 3.06
967 1022 2.300152 CTCTTGGCTACTCTGTTGGTGA 59.700 50.000 0.00 0.00 0.00 4.02
968 1023 2.693069 CTCTTGGCTACTCTGTTGGTG 58.307 52.381 0.00 0.00 0.00 4.17
969 1024 1.002544 GCTCTTGGCTACTCTGTTGGT 59.997 52.381 0.00 0.00 38.06 3.67
1393 1466 0.600557 CGCAGGGATAGCAGGAGTAG 59.399 60.000 0.00 0.00 0.00 2.57
1412 1485 3.279875 CCATAGAAAGCGCCCGGC 61.280 66.667 2.29 0.00 44.05 6.13
1790 1863 1.559831 AGACGCTTTTTGTTTGCAGC 58.440 45.000 0.00 0.00 0.00 5.25
1805 1878 7.591057 TGTTAAAAGCATGATTCAAGAAAGACG 59.409 33.333 0.00 0.00 0.00 4.18
1921 1994 3.244345 GCAAGGCGTGGTTTTTCTTTAAC 59.756 43.478 1.91 0.00 0.00 2.01
2059 2132 4.871557 CCATCAAACACCTGCAAATTATGG 59.128 41.667 0.00 0.00 0.00 2.74
2332 2405 3.177228 ACAGGTGTCTTCTTAGGATGCT 58.823 45.455 0.00 0.00 0.00 3.79
2600 2680 7.177744 GGAAAACATTATTACAAACTCCCTCCA 59.822 37.037 0.00 0.00 0.00 3.86
2697 2798 6.134535 ACCAAGAATAACACAATACCCAGA 57.865 37.500 0.00 0.00 0.00 3.86
3026 3412 2.351726 GCAATGTCCTGTACCATCGAAC 59.648 50.000 0.00 0.00 0.00 3.95
3030 3416 3.347216 ACAAGCAATGTCCTGTACCATC 58.653 45.455 0.00 0.00 37.96 3.51
3178 3564 3.495629 GCTGACCATTGAGATAGCCATCA 60.496 47.826 0.00 0.00 33.21 3.07
3358 3744 0.880441 CCATTGACACGGCACATTGA 59.120 50.000 0.00 0.00 0.00 2.57
3609 3995 2.893489 GCAAGGGAGGAAGACATGTTTT 59.107 45.455 0.00 0.00 0.00 2.43
3628 4014 5.703592 AGATCATACAACAAAAGGTTACGCA 59.296 36.000 0.00 0.00 37.72 5.24
3838 4226 8.553459 ACAGTCATTTGTACCAGAATAAGAAG 57.447 34.615 0.00 0.00 0.00 2.85
4104 4739 0.257039 ACAGGGTCCATCAATGAGCC 59.743 55.000 0.35 0.35 36.80 4.70
4110 4745 3.118186 CCGGTTATAACAGGGTCCATCAA 60.118 47.826 22.86 0.00 40.08 2.57
4137 4772 3.039011 TGGGCCTCTTTCTGGTATAGAC 58.961 50.000 4.53 0.00 34.43 2.59
4138 4773 3.039011 GTGGGCCTCTTTCTGGTATAGA 58.961 50.000 4.53 0.00 0.00 1.98
4139 4774 2.104963 GGTGGGCCTCTTTCTGGTATAG 59.895 54.545 4.53 0.00 0.00 1.31
4140 4775 2.124411 GGTGGGCCTCTTTCTGGTATA 58.876 52.381 4.53 0.00 0.00 1.47
4141 4776 0.919710 GGTGGGCCTCTTTCTGGTAT 59.080 55.000 4.53 0.00 0.00 2.73
4142 4777 1.550130 CGGTGGGCCTCTTTCTGGTA 61.550 60.000 4.53 0.00 0.00 3.25
4143 4778 2.895424 CGGTGGGCCTCTTTCTGGT 61.895 63.158 4.53 0.00 0.00 4.00
4144 4779 2.045926 CGGTGGGCCTCTTTCTGG 60.046 66.667 4.53 0.00 0.00 3.86
4145 4780 2.045926 CCGGTGGGCCTCTTTCTG 60.046 66.667 4.53 0.00 0.00 3.02
4146 4781 3.330720 CCCGGTGGGCCTCTTTCT 61.331 66.667 4.53 0.00 35.35 2.52
4156 4791 2.290071 CCCTAATACTAATGCCCGGTGG 60.290 54.545 0.00 0.00 0.00 4.61
4157 4792 2.290071 CCCCTAATACTAATGCCCGGTG 60.290 54.545 0.00 0.00 0.00 4.94
4158 4793 1.982958 CCCCTAATACTAATGCCCGGT 59.017 52.381 0.00 0.00 0.00 5.28
4159 4794 1.339727 GCCCCTAATACTAATGCCCGG 60.340 57.143 0.00 0.00 0.00 5.73
4160 4795 1.628846 AGCCCCTAATACTAATGCCCG 59.371 52.381 0.00 0.00 0.00 6.13
4161 4796 3.073946 TCAAGCCCCTAATACTAATGCCC 59.926 47.826 0.00 0.00 0.00 5.36
4162 4797 4.072839 GTCAAGCCCCTAATACTAATGCC 58.927 47.826 0.00 0.00 0.00 4.40
4163 4798 4.072839 GGTCAAGCCCCTAATACTAATGC 58.927 47.826 0.00 0.00 0.00 3.56
4179 4814 8.962912 CTTGCCTAAGATAACTTGTGGGTCAAG 61.963 44.444 6.11 6.11 45.48 3.02
4180 4815 4.042311 TGCCTAAGATAACTTGTGGGTCAA 59.958 41.667 0.00 0.00 37.53 3.18
4181 4816 3.585289 TGCCTAAGATAACTTGTGGGTCA 59.415 43.478 0.00 0.00 37.53 4.02
4182 4817 4.216411 TGCCTAAGATAACTTGTGGGTC 57.784 45.455 0.00 0.00 37.53 4.46
4183 4818 4.042934 ACTTGCCTAAGATAACTTGTGGGT 59.957 41.667 0.00 0.00 37.36 4.51
4184 4819 4.589908 ACTTGCCTAAGATAACTTGTGGG 58.410 43.478 0.00 0.00 37.36 4.61
4185 4820 7.770897 AGATAACTTGCCTAAGATAACTTGTGG 59.229 37.037 0.00 0.00 37.36 4.17
4186 4821 8.723942 AGATAACTTGCCTAAGATAACTTGTG 57.276 34.615 0.00 0.00 37.36 3.33
4190 4825 8.151596 GCCTAAGATAACTTGCCTAAGATAACT 58.848 37.037 0.00 0.00 37.36 2.24
4191 4826 8.151596 AGCCTAAGATAACTTGCCTAAGATAAC 58.848 37.037 0.00 0.00 37.36 1.89
4192 4827 8.263854 AGCCTAAGATAACTTGCCTAAGATAA 57.736 34.615 0.00 0.00 37.36 1.75
4193 4828 7.857404 AGCCTAAGATAACTTGCCTAAGATA 57.143 36.000 0.00 0.00 37.36 1.98
4194 4829 6.755542 AGCCTAAGATAACTTGCCTAAGAT 57.244 37.500 0.00 0.00 37.36 2.40
4195 4830 7.670605 TTAGCCTAAGATAACTTGCCTAAGA 57.329 36.000 0.00 0.00 37.36 2.10
4196 4831 7.988028 ACTTTAGCCTAAGATAACTTGCCTAAG 59.012 37.037 2.69 1.76 39.86 2.18
4197 4832 7.858498 ACTTTAGCCTAAGATAACTTGCCTAA 58.142 34.615 2.69 0.00 37.53 2.69
4198 4833 7.433537 ACTTTAGCCTAAGATAACTTGCCTA 57.566 36.000 2.69 0.00 37.53 3.93
4199 4834 6.314899 ACTTTAGCCTAAGATAACTTGCCT 57.685 37.500 2.69 0.00 37.53 4.75
4200 4835 8.678593 ATAACTTTAGCCTAAGATAACTTGCC 57.321 34.615 2.69 0.00 37.53 4.52
4224 4859 9.933723 AAACGGTGTCTTACAACTAGTATTTAT 57.066 29.630 0.00 0.00 32.52 1.40
4225 4860 9.195411 CAAACGGTGTCTTACAACTAGTATTTA 57.805 33.333 0.00 0.00 32.52 1.40
4226 4861 7.927629 TCAAACGGTGTCTTACAACTAGTATTT 59.072 33.333 0.00 0.00 32.52 1.40
4227 4862 7.436118 TCAAACGGTGTCTTACAACTAGTATT 58.564 34.615 0.00 0.00 32.52 1.89
4228 4863 6.985117 TCAAACGGTGTCTTACAACTAGTAT 58.015 36.000 0.00 0.00 32.52 2.12
4229 4864 6.389830 TCAAACGGTGTCTTACAACTAGTA 57.610 37.500 0.00 0.00 32.52 1.82
4230 4865 5.266733 TCAAACGGTGTCTTACAACTAGT 57.733 39.130 0.00 0.00 32.52 2.57
4231 4866 4.684703 CCTCAAACGGTGTCTTACAACTAG 59.315 45.833 0.00 0.00 32.52 2.57
4232 4867 4.624015 CCTCAAACGGTGTCTTACAACTA 58.376 43.478 0.00 0.00 32.52 2.24
4233 4868 3.463944 CCTCAAACGGTGTCTTACAACT 58.536 45.455 0.00 0.00 32.52 3.16
4234 4869 2.032290 GCCTCAAACGGTGTCTTACAAC 60.032 50.000 0.00 0.00 31.00 3.32
4235 4870 2.215196 GCCTCAAACGGTGTCTTACAA 58.785 47.619 0.00 0.00 0.00 2.41
4236 4871 1.139256 TGCCTCAAACGGTGTCTTACA 59.861 47.619 0.00 0.00 0.00 2.41
4237 4872 1.873698 TGCCTCAAACGGTGTCTTAC 58.126 50.000 0.00 0.00 0.00 2.34
4238 4873 2.489971 CTTGCCTCAAACGGTGTCTTA 58.510 47.619 0.00 0.00 0.00 2.10
4239 4874 1.308998 CTTGCCTCAAACGGTGTCTT 58.691 50.000 0.00 0.00 0.00 3.01
4240 4875 1.166531 GCTTGCCTCAAACGGTGTCT 61.167 55.000 0.00 0.00 0.00 3.41
4241 4876 1.282875 GCTTGCCTCAAACGGTGTC 59.717 57.895 0.00 0.00 0.00 3.67
4242 4877 1.034838 TTGCTTGCCTCAAACGGTGT 61.035 50.000 0.00 0.00 0.00 4.16
4243 4878 0.314935 ATTGCTTGCCTCAAACGGTG 59.685 50.000 0.00 0.00 0.00 4.94
4244 4879 1.904287 TATTGCTTGCCTCAAACGGT 58.096 45.000 0.00 0.00 0.00 4.83
4245 4880 3.057596 TCTTTATTGCTTGCCTCAAACGG 60.058 43.478 0.00 0.00 0.00 4.44
4246 4881 4.159377 TCTTTATTGCTTGCCTCAAACG 57.841 40.909 0.00 0.00 0.00 3.60
4247 4882 9.971922 ATAATATCTTTATTGCTTGCCTCAAAC 57.028 29.630 0.00 0.00 30.64 2.93
4264 4899 9.838339 CCGGGCAATAGAAGATTATAATATCTT 57.162 33.333 14.96 9.09 45.20 2.40
4265 4900 7.934120 GCCGGGCAATAGAAGATTATAATATCT 59.066 37.037 15.62 14.42 36.44 1.98
4266 4901 7.934120 AGCCGGGCAATAGAAGATTATAATATC 59.066 37.037 23.09 0.64 0.00 1.63
4267 4902 7.806180 AGCCGGGCAATAGAAGATTATAATAT 58.194 34.615 23.09 0.00 0.00 1.28
4268 4903 7.195374 AGCCGGGCAATAGAAGATTATAATA 57.805 36.000 23.09 0.00 0.00 0.98
4269 4904 6.067217 AGCCGGGCAATAGAAGATTATAAT 57.933 37.500 23.09 0.00 0.00 1.28
4270 4905 5.488341 GAGCCGGGCAATAGAAGATTATAA 58.512 41.667 23.09 0.00 0.00 0.98
4271 4906 4.081087 GGAGCCGGGCAATAGAAGATTATA 60.081 45.833 23.09 0.00 0.00 0.98
4272 4907 3.307762 GGAGCCGGGCAATAGAAGATTAT 60.308 47.826 23.09 0.00 0.00 1.28
4273 4908 2.038557 GGAGCCGGGCAATAGAAGATTA 59.961 50.000 23.09 0.00 0.00 1.75
4274 4909 1.202818 GGAGCCGGGCAATAGAAGATT 60.203 52.381 23.09 0.00 0.00 2.40
4275 4910 0.398318 GGAGCCGGGCAATAGAAGAT 59.602 55.000 23.09 0.00 0.00 2.40
4276 4911 1.696097 GGGAGCCGGGCAATAGAAGA 61.696 60.000 23.09 0.00 0.00 2.87
4277 4912 1.227973 GGGAGCCGGGCAATAGAAG 60.228 63.158 23.09 0.00 0.00 2.85
4278 4913 2.752807 GGGGAGCCGGGCAATAGAA 61.753 63.158 23.09 0.00 0.00 2.10
4279 4914 3.168528 GGGGAGCCGGGCAATAGA 61.169 66.667 23.09 0.00 0.00 1.98
4280 4915 2.965716 CTTGGGGAGCCGGGCAATAG 62.966 65.000 23.09 5.56 0.00 1.73
4281 4916 3.018193 TTGGGGAGCCGGGCAATA 61.018 61.111 23.09 0.00 0.00 1.90
4282 4917 4.447342 CTTGGGGAGCCGGGCAAT 62.447 66.667 23.09 0.00 0.00 3.56
4292 4927 2.231380 GGTTCCAGCTCCTTGGGGA 61.231 63.158 0.00 0.00 38.81 4.81
4293 4928 2.356667 GGTTCCAGCTCCTTGGGG 59.643 66.667 0.00 0.00 38.81 4.96
4294 4929 0.914417 TAGGGTTCCAGCTCCTTGGG 60.914 60.000 0.00 0.00 38.81 4.12
4295 4930 0.543749 CTAGGGTTCCAGCTCCTTGG 59.456 60.000 0.00 0.00 39.70 3.61
4296 4931 0.107459 GCTAGGGTTCCAGCTCCTTG 60.107 60.000 0.00 0.00 34.86 3.61
4297 4932 1.275421 GGCTAGGGTTCCAGCTCCTT 61.275 60.000 0.00 0.00 37.91 3.36
4298 4933 1.690985 GGCTAGGGTTCCAGCTCCT 60.691 63.158 0.00 0.00 37.91 3.69
4299 4934 2.911928 GGCTAGGGTTCCAGCTCC 59.088 66.667 0.00 0.00 37.91 4.70
4300 4935 2.501610 CGGCTAGGGTTCCAGCTC 59.498 66.667 0.00 0.00 37.91 4.09
4301 4936 3.787001 GCGGCTAGGGTTCCAGCT 61.787 66.667 0.00 0.00 37.91 4.24
4302 4937 4.858680 GGCGGCTAGGGTTCCAGC 62.859 72.222 0.00 0.00 37.05 4.85
4303 4938 4.530857 CGGCGGCTAGGGTTCCAG 62.531 72.222 7.61 0.00 0.00 3.86
4318 4953 4.796495 GGCTAGGGTTGGGTGCGG 62.796 72.222 0.00 0.00 0.00 5.69
4323 4958 4.832608 GTCGCGGCTAGGGTTGGG 62.833 72.222 1.90 0.00 0.00 4.12
4361 4996 4.247380 GATGAGGGCTGGAGCGGG 62.247 72.222 0.00 0.00 43.26 6.13
4362 4997 4.247380 GGATGAGGGCTGGAGCGG 62.247 72.222 0.00 0.00 43.26 5.52
4363 4998 3.160047 AGGATGAGGGCTGGAGCG 61.160 66.667 0.00 0.00 43.26 5.03
4364 4999 2.817056 GGAGGATGAGGGCTGGAGC 61.817 68.421 0.00 0.00 41.14 4.70
4365 5000 1.074623 AGGAGGATGAGGGCTGGAG 60.075 63.158 0.00 0.00 0.00 3.86
4366 5001 1.074926 GAGGAGGATGAGGGCTGGA 60.075 63.158 0.00 0.00 0.00 3.86
4367 5002 2.146061 GGAGGAGGATGAGGGCTGG 61.146 68.421 0.00 0.00 0.00 4.85
4368 5003 2.146061 GGGAGGAGGATGAGGGCTG 61.146 68.421 0.00 0.00 0.00 4.85
4369 5004 2.288643 GGGAGGAGGATGAGGGCT 59.711 66.667 0.00 0.00 0.00 5.19
4370 5005 2.851588 GGGGAGGAGGATGAGGGC 60.852 72.222 0.00 0.00 0.00 5.19
4371 5006 2.122189 GGGGGAGGAGGATGAGGG 60.122 72.222 0.00 0.00 0.00 4.30
4372 5007 1.059006 CAAGGGGGAGGAGGATGAGG 61.059 65.000 0.00 0.00 0.00 3.86
4373 5008 0.327000 ACAAGGGGGAGGAGGATGAG 60.327 60.000 0.00 0.00 0.00 2.90
4374 5009 0.326618 GACAAGGGGGAGGAGGATGA 60.327 60.000 0.00 0.00 0.00 2.92
4375 5010 1.348775 GGACAAGGGGGAGGAGGATG 61.349 65.000 0.00 0.00 0.00 3.51
4376 5011 1.004891 GGACAAGGGGGAGGAGGAT 59.995 63.158 0.00 0.00 0.00 3.24
4377 5012 1.837533 ATGGACAAGGGGGAGGAGGA 61.838 60.000 0.00 0.00 0.00 3.71
4378 5013 0.030092 TATGGACAAGGGGGAGGAGG 60.030 60.000 0.00 0.00 0.00 4.30
4379 5014 1.132500 GTATGGACAAGGGGGAGGAG 58.868 60.000 0.00 0.00 0.00 3.69
4380 5015 0.419865 TGTATGGACAAGGGGGAGGA 59.580 55.000 0.00 0.00 30.68 3.71
4381 5016 1.295020 TTGTATGGACAAGGGGGAGG 58.705 55.000 0.00 0.00 40.72 4.30
4390 5025 1.067974 CCGGCGTAGATTGTATGGACA 59.932 52.381 6.01 0.00 0.00 4.02
4391 5026 1.338973 TCCGGCGTAGATTGTATGGAC 59.661 52.381 6.01 0.00 0.00 4.02
4392 5027 1.611977 CTCCGGCGTAGATTGTATGGA 59.388 52.381 6.01 0.00 0.00 3.41
4393 5028 1.336887 CCTCCGGCGTAGATTGTATGG 60.337 57.143 6.01 0.00 0.00 2.74
4394 5029 1.935300 GCCTCCGGCGTAGATTGTATG 60.935 57.143 6.01 0.00 39.62 2.39
4395 5030 0.317479 GCCTCCGGCGTAGATTGTAT 59.683 55.000 6.01 0.00 39.62 2.29
4396 5031 1.737816 GCCTCCGGCGTAGATTGTA 59.262 57.895 6.01 0.00 39.62 2.41
4397 5032 2.499685 GCCTCCGGCGTAGATTGT 59.500 61.111 6.01 0.00 39.62 2.71
4409 5044 3.477346 GGTTCCTACCGGGCCTCC 61.477 72.222 6.32 0.00 34.01 4.30
4410 5045 2.594365 TAGGGTTCCTACCGGGCCTC 62.594 65.000 6.32 0.00 46.04 4.70
4411 5046 2.600735 CTAGGGTTCCTACCGGGCCT 62.601 65.000 6.32 0.00 46.04 5.19
4412 5047 2.041612 TAGGGTTCCTACCGGGCC 60.042 66.667 6.32 0.00 46.04 5.80
4413 5048 1.382283 ACTAGGGTTCCTACCGGGC 60.382 63.158 6.32 0.00 46.04 6.13
4414 5049 0.758310 GGACTAGGGTTCCTACCGGG 60.758 65.000 6.32 0.00 46.04 5.73
4415 5050 0.261109 AGGACTAGGGTTCCTACCGG 59.739 60.000 0.00 0.00 46.04 5.28
4416 5051 2.580962 GTAGGACTAGGGTTCCTACCG 58.419 57.143 20.22 0.00 46.18 4.02
4419 5054 4.913154 ATTGGTAGGACTAGGGTTCCTA 57.087 45.455 3.95 3.95 34.61 2.94
4420 5055 3.797671 ATTGGTAGGACTAGGGTTCCT 57.202 47.619 5.75 5.75 37.71 3.36
4421 5056 4.524053 CAAATTGGTAGGACTAGGGTTCC 58.476 47.826 0.00 0.00 0.00 3.62
4422 5057 4.524053 CCAAATTGGTAGGACTAGGGTTC 58.476 47.826 3.34 0.00 31.35 3.62
4423 5058 4.586306 CCAAATTGGTAGGACTAGGGTT 57.414 45.455 3.34 0.00 31.35 4.11
4444 5079 0.466124 GGCCTGGTGTCTCTGGATAC 59.534 60.000 0.00 0.00 33.63 2.24
4445 5080 1.043116 CGGCCTGGTGTCTCTGGATA 61.043 60.000 0.00 0.00 0.00 2.59
4446 5081 2.362369 CGGCCTGGTGTCTCTGGAT 61.362 63.158 0.00 0.00 0.00 3.41
4447 5082 2.805313 ATCGGCCTGGTGTCTCTGGA 62.805 60.000 0.00 0.00 0.00 3.86
4448 5083 2.303549 GATCGGCCTGGTGTCTCTGG 62.304 65.000 0.00 0.00 0.00 3.86
4449 5084 1.142748 GATCGGCCTGGTGTCTCTG 59.857 63.158 0.00 0.00 0.00 3.35
4450 5085 0.689080 ATGATCGGCCTGGTGTCTCT 60.689 55.000 0.00 0.00 0.00 3.10
4451 5086 0.531532 CATGATCGGCCTGGTGTCTC 60.532 60.000 0.00 0.00 0.00 3.36
4452 5087 1.267574 ACATGATCGGCCTGGTGTCT 61.268 55.000 0.00 0.00 0.00 3.41
4453 5088 0.811616 GACATGATCGGCCTGGTGTC 60.812 60.000 0.00 4.57 0.00 3.67
4454 5089 1.221840 GACATGATCGGCCTGGTGT 59.778 57.895 0.00 0.00 0.00 4.16
4455 5090 4.131376 GACATGATCGGCCTGGTG 57.869 61.111 0.00 0.00 0.00 4.17
4464 5099 2.224137 TGATGGAGGAAGCGACATGATC 60.224 50.000 0.00 0.00 0.00 2.92
4465 5100 1.764723 TGATGGAGGAAGCGACATGAT 59.235 47.619 0.00 0.00 0.00 2.45
4466 5101 1.134699 GTGATGGAGGAAGCGACATGA 60.135 52.381 0.00 0.00 0.00 3.07
4467 5102 1.293924 GTGATGGAGGAAGCGACATG 58.706 55.000 0.00 0.00 0.00 3.21
4468 5103 0.179000 GGTGATGGAGGAAGCGACAT 59.821 55.000 0.00 0.00 0.00 3.06
4469 5104 1.596934 GGTGATGGAGGAAGCGACA 59.403 57.895 0.00 0.00 0.00 4.35
4470 5105 1.519455 CGGTGATGGAGGAAGCGAC 60.519 63.158 0.00 0.00 36.98 5.19
4471 5106 2.892640 CGGTGATGGAGGAAGCGA 59.107 61.111 0.00 0.00 36.98 4.93
4472 5107 2.892425 GCGGTGATGGAGGAAGCG 60.892 66.667 0.00 0.00 37.83 4.68
4473 5108 2.514824 GGCGGTGATGGAGGAAGC 60.515 66.667 0.00 0.00 0.00 3.86
4474 5109 2.202932 CGGCGGTGATGGAGGAAG 60.203 66.667 0.00 0.00 0.00 3.46
4475 5110 4.467084 GCGGCGGTGATGGAGGAA 62.467 66.667 9.78 0.00 0.00 3.36
4492 5127 4.864334 GGAGGTGGATGGCAGCGG 62.864 72.222 0.00 0.00 0.00 5.52
4495 5130 4.864334 GGCGGAGGTGGATGGCAG 62.864 72.222 0.00 0.00 0.00 4.85
4499 5134 4.489771 GTGGGGCGGAGGTGGATG 62.490 72.222 0.00 0.00 0.00 3.51
4531 5166 4.899239 CATCGGCGAGGAGGTGGC 62.899 72.222 17.69 0.00 0.00 5.01
4532 5167 3.147595 TCATCGGCGAGGAGGTGG 61.148 66.667 21.27 0.96 0.00 4.61
4533 5168 2.105128 GTCATCGGCGAGGAGGTG 59.895 66.667 25.61 12.94 0.00 4.00
4534 5169 3.518998 CGTCATCGGCGAGGAGGT 61.519 66.667 29.13 5.09 0.00 3.85
4544 5179 2.277949 ACGTGATCGCCGTCATCG 60.278 61.111 0.00 0.00 41.18 3.84
4551 5186 4.867599 GTCCCGGACGTGATCGCC 62.868 72.222 0.73 0.00 41.18 5.54
4552 5187 4.867599 GGTCCCGGACGTGATCGC 62.868 72.222 11.55 0.00 41.18 4.58
4553 5188 2.679132 GATGGTCCCGGACGTGATCG 62.679 65.000 11.55 0.00 43.34 3.69
4554 5189 1.067582 GATGGTCCCGGACGTGATC 59.932 63.158 11.55 8.86 32.65 2.92
4555 5190 1.684391 TGATGGTCCCGGACGTGAT 60.684 57.895 11.55 3.50 32.65 3.06
4556 5191 2.283316 TGATGGTCCCGGACGTGA 60.283 61.111 11.55 0.00 32.65 4.35
4557 5192 2.125673 GTGATGGTCCCGGACGTG 60.126 66.667 11.55 0.00 32.65 4.49
4558 5193 3.387947 GGTGATGGTCCCGGACGT 61.388 66.667 11.55 2.65 32.65 4.34
4559 5194 3.387091 TGGTGATGGTCCCGGACG 61.387 66.667 11.55 0.00 32.65 4.79
4560 5195 2.267961 GTGGTGATGGTCCCGGAC 59.732 66.667 9.30 9.30 0.00 4.79
4561 5196 3.006728 GGTGGTGATGGTCCCGGA 61.007 66.667 0.73 0.00 0.00 5.14
4562 5197 3.326578 TGGTGGTGATGGTCCCGG 61.327 66.667 0.00 0.00 0.00 5.73
4563 5198 2.046314 GTGGTGGTGATGGTCCCG 60.046 66.667 0.00 0.00 0.00 5.14
4564 5199 2.355115 GGTGGTGGTGATGGTCCC 59.645 66.667 0.00 0.00 0.00 4.46
4565 5200 2.046314 CGGTGGTGGTGATGGTCC 60.046 66.667 0.00 0.00 0.00 4.46
4566 5201 2.746277 GCGGTGGTGGTGATGGTC 60.746 66.667 0.00 0.00 0.00 4.02
4567 5202 4.697756 CGCGGTGGTGGTGATGGT 62.698 66.667 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.