Multiple sequence alignment - TraesCS2B01G309900

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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 TraesCS2B01G309900 chr2B 100.000 4466 0 0 1 4466 442799055 442794590 0.000000e+00 8248
1 TraesCS2B01G309900 chr2B 87.288 236 16 5 3578 3812 735827464 735827242 1.590000e-64 257
2 TraesCS2B01G309900 chr2D 93.813 3669 146 29 116 3750 373228799 373225178 0.000000e+00 5443
3 TraesCS2B01G309900 chr2D 91.472 598 16 12 3889 4466 373225067 373224485 0.000000e+00 789
4 TraesCS2B01G309900 chr2A 92.701 3521 165 48 116 3611 504272218 504275671 0.000000e+00 4994
5 TraesCS2B01G309900 chr2A 92.000 600 20 5 3889 4466 504275888 504276481 0.000000e+00 817
6 TraesCS2B01G309900 chr2A 87.336 229 17 5 3578 3806 40762046 40762262 7.420000e-63 252
7 TraesCS2B01G309900 chr2A 95.200 125 2 1 3645 3769 504275673 504275793 1.270000e-45 195
8 TraesCS2B01G309900 chr4A 87.826 230 14 6 3578 3806 661951742 661951958 1.590000e-64 257
9 TraesCS2B01G309900 chr3B 87.391 230 15 4 3578 3806 456361726 456361942 7.420000e-63 252
10 TraesCS2B01G309900 chr3B 86.441 236 18 5 3578 3812 807584647 807584425 3.450000e-61 246
11 TraesCS2B01G309900 chr1B 87.391 230 15 5 3578 3806 69432280 69432496 7.420000e-63 252
12 TraesCS2B01G309900 chr6A 86.441 236 18 3 3578 3812 196920 196698 3.450000e-61 246


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 TraesCS2B01G309900 chr2B 442794590 442799055 4465 True 8248 8248 100.000000 1 4466 1 chr2B.!!$R1 4465
1 TraesCS2B01G309900 chr2D 373224485 373228799 4314 True 3116 5443 92.642500 116 4466 2 chr2D.!!$R1 4350
2 TraesCS2B01G309900 chr2A 504272218 504276481 4263 False 2002 4994 93.300333 116 4466 3 chr2A.!!$F2 4350

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
113 114 0.030092 CCTGTGGGGGAGGATAGGAA 60.030 60.0 0.0 0.0 31.48 3.36 F
226 228 0.108207 CCCTGCTCCTCATCCACATC 59.892 60.0 0.0 0.0 0.00 3.06 F
455 483 0.175531 CCCATTTTGTTCGCCCATCC 59.824 55.0 0.0 0.0 0.00 3.51 F
888 926 0.389948 GCAGACACCAACGGTCCTAG 60.390 60.0 0.0 0.0 35.89 3.02 F
2475 2530 0.678048 GGCAGAAGCAACCTACCAGG 60.678 60.0 0.0 0.0 44.61 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 1941 0.250901 ATCAGCGCCCTTCTTGTTGT 60.251 50.000 2.29 0.0 0.00 3.32 R
1921 1976 1.202348 GCCAAAATCAACTCCTTCGGG 59.798 52.381 0.00 0.0 0.00 5.14 R
2232 2287 1.281867 CCCACCAACTCAGCCAGATAA 59.718 52.381 0.00 0.0 0.00 1.75 R
2535 2590 0.958382 GCAGGCACAATTGGTCGGTA 60.958 55.000 10.83 0.0 0.00 4.02 R
3785 3842 0.179048 AGTACAGCACAACAGCAGCA 60.179 50.000 0.00 0.0 36.85 4.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.680312 CGTAGCCATAGCCATAGCAT 57.320 50.000 0.00 0.00 43.56 3.79
26 27 2.274437 CGTAGCCATAGCCATAGCATG 58.726 52.381 0.00 0.00 43.56 4.06
40 41 4.108299 CATGGGGCTGCCGTGGTA 62.108 66.667 13.40 0.00 0.00 3.25
41 42 3.797353 ATGGGGCTGCCGTGGTAG 61.797 66.667 13.40 0.00 0.00 3.18
43 44 4.162690 GGGGCTGCCGTGGTAGAG 62.163 72.222 13.40 0.00 0.00 2.43
44 45 3.075005 GGGCTGCCGTGGTAGAGA 61.075 66.667 13.40 0.00 0.00 3.10
45 46 2.496817 GGCTGCCGTGGTAGAGAG 59.503 66.667 1.35 0.00 0.00 3.20
46 47 2.052690 GGCTGCCGTGGTAGAGAGA 61.053 63.158 1.35 0.00 0.00 3.10
47 48 1.435515 GCTGCCGTGGTAGAGAGAG 59.564 63.158 8.28 0.00 0.00 3.20
48 49 1.032657 GCTGCCGTGGTAGAGAGAGA 61.033 60.000 8.28 0.00 0.00 3.10
49 50 1.464734 CTGCCGTGGTAGAGAGAGAA 58.535 55.000 0.00 0.00 0.00 2.87
50 51 1.819288 CTGCCGTGGTAGAGAGAGAAA 59.181 52.381 0.00 0.00 0.00 2.52
51 52 1.819288 TGCCGTGGTAGAGAGAGAAAG 59.181 52.381 0.00 0.00 0.00 2.62
52 53 1.135333 GCCGTGGTAGAGAGAGAAAGG 59.865 57.143 0.00 0.00 0.00 3.11
53 54 1.135333 CCGTGGTAGAGAGAGAAAGGC 59.865 57.143 0.00 0.00 0.00 4.35
54 55 1.819288 CGTGGTAGAGAGAGAAAGGCA 59.181 52.381 0.00 0.00 0.00 4.75
55 56 2.416162 CGTGGTAGAGAGAGAAAGGCAC 60.416 54.545 0.00 0.00 0.00 5.01
56 57 1.819288 TGGTAGAGAGAGAAAGGCACG 59.181 52.381 0.00 0.00 0.00 5.34
57 58 1.470112 GGTAGAGAGAGAAAGGCACGC 60.470 57.143 0.00 0.00 0.00 5.34
58 59 1.202582 GTAGAGAGAGAAAGGCACGCA 59.797 52.381 0.00 0.00 0.00 5.24
59 60 0.246086 AGAGAGAGAAAGGCACGCAG 59.754 55.000 0.00 0.00 0.00 5.18
60 61 1.357991 GAGAGAGAAAGGCACGCAGC 61.358 60.000 0.00 0.00 44.65 5.25
76 77 3.201494 GCCGCAGCTAGAGTGAGA 58.799 61.111 0.00 0.00 35.50 3.27
77 78 1.065600 GCCGCAGCTAGAGTGAGAG 59.934 63.158 0.00 0.00 35.50 3.20
78 79 1.380403 GCCGCAGCTAGAGTGAGAGA 61.380 60.000 0.00 0.00 35.50 3.10
79 80 0.662619 CCGCAGCTAGAGTGAGAGAG 59.337 60.000 0.00 0.00 0.00 3.20
80 81 1.662517 CGCAGCTAGAGTGAGAGAGA 58.337 55.000 0.00 0.00 0.00 3.10
81 82 1.599071 CGCAGCTAGAGTGAGAGAGAG 59.401 57.143 0.00 0.00 0.00 3.20
82 83 2.741553 CGCAGCTAGAGTGAGAGAGAGA 60.742 54.545 0.00 0.00 0.00 3.10
83 84 2.874701 GCAGCTAGAGTGAGAGAGAGAG 59.125 54.545 0.00 0.00 0.00 3.20
84 85 3.432186 GCAGCTAGAGTGAGAGAGAGAGA 60.432 52.174 0.00 0.00 0.00 3.10
85 86 4.375272 CAGCTAGAGTGAGAGAGAGAGAG 58.625 52.174 0.00 0.00 0.00 3.20
86 87 4.033709 AGCTAGAGTGAGAGAGAGAGAGT 58.966 47.826 0.00 0.00 0.00 3.24
87 88 4.122776 GCTAGAGTGAGAGAGAGAGAGTG 58.877 52.174 0.00 0.00 0.00 3.51
88 89 4.383118 GCTAGAGTGAGAGAGAGAGAGTGT 60.383 50.000 0.00 0.00 0.00 3.55
89 90 3.942829 AGAGTGAGAGAGAGAGAGTGTG 58.057 50.000 0.00 0.00 0.00 3.82
90 91 3.327757 AGAGTGAGAGAGAGAGAGTGTGT 59.672 47.826 0.00 0.00 0.00 3.72
91 92 3.411446 AGTGAGAGAGAGAGAGTGTGTG 58.589 50.000 0.00 0.00 0.00 3.82
92 93 3.072330 AGTGAGAGAGAGAGAGTGTGTGA 59.928 47.826 0.00 0.00 0.00 3.58
93 94 3.436704 GTGAGAGAGAGAGAGTGTGTGAG 59.563 52.174 0.00 0.00 0.00 3.51
94 95 2.420022 GAGAGAGAGAGAGTGTGTGAGC 59.580 54.545 0.00 0.00 0.00 4.26
95 96 1.472480 GAGAGAGAGAGTGTGTGAGCC 59.528 57.143 0.00 0.00 0.00 4.70
96 97 1.075374 AGAGAGAGAGTGTGTGAGCCT 59.925 52.381 0.00 0.00 0.00 4.58
97 98 1.202114 GAGAGAGAGTGTGTGAGCCTG 59.798 57.143 0.00 0.00 0.00 4.85
98 99 0.965439 GAGAGAGTGTGTGAGCCTGT 59.035 55.000 0.00 0.00 0.00 4.00
99 100 0.678395 AGAGAGTGTGTGAGCCTGTG 59.322 55.000 0.00 0.00 0.00 3.66
100 101 0.320247 GAGAGTGTGTGAGCCTGTGG 60.320 60.000 0.00 0.00 0.00 4.17
101 102 1.302033 GAGTGTGTGAGCCTGTGGG 60.302 63.158 0.00 0.00 0.00 4.61
102 103 2.281761 GTGTGTGAGCCTGTGGGG 60.282 66.667 0.00 0.00 38.36 4.96
103 104 3.569210 TGTGTGAGCCTGTGGGGG 61.569 66.667 0.00 0.00 35.12 5.40
104 105 3.249189 GTGTGAGCCTGTGGGGGA 61.249 66.667 0.00 0.00 35.12 4.81
105 106 2.930019 TGTGAGCCTGTGGGGGAG 60.930 66.667 0.00 0.00 35.12 4.30
106 107 3.721706 GTGAGCCTGTGGGGGAGG 61.722 72.222 0.00 0.00 35.12 4.30
107 108 3.940480 TGAGCCTGTGGGGGAGGA 61.940 66.667 0.00 0.00 35.12 3.71
108 109 2.367512 GAGCCTGTGGGGGAGGAT 60.368 66.667 0.00 0.00 35.12 3.24
109 110 1.074471 GAGCCTGTGGGGGAGGATA 60.074 63.158 0.00 0.00 35.12 2.59
110 111 1.074167 AGCCTGTGGGGGAGGATAG 60.074 63.158 0.00 0.00 35.12 2.08
111 112 2.150051 GCCTGTGGGGGAGGATAGG 61.150 68.421 0.00 0.00 35.12 2.57
112 113 1.632164 CCTGTGGGGGAGGATAGGA 59.368 63.158 0.00 0.00 31.48 2.94
113 114 0.030092 CCTGTGGGGGAGGATAGGAA 60.030 60.000 0.00 0.00 31.48 3.36
114 115 1.628043 CCTGTGGGGGAGGATAGGAAA 60.628 57.143 0.00 0.00 31.48 3.13
115 116 1.771255 CTGTGGGGGAGGATAGGAAAG 59.229 57.143 0.00 0.00 0.00 2.62
116 117 1.368203 TGTGGGGGAGGATAGGAAAGA 59.632 52.381 0.00 0.00 0.00 2.52
117 118 2.050918 GTGGGGGAGGATAGGAAAGAG 58.949 57.143 0.00 0.00 0.00 2.85
118 119 1.061346 TGGGGGAGGATAGGAAAGAGG 60.061 57.143 0.00 0.00 0.00 3.69
119 120 1.735926 GGGGAGGATAGGAAAGAGGG 58.264 60.000 0.00 0.00 0.00 4.30
120 121 1.735926 GGGAGGATAGGAAAGAGGGG 58.264 60.000 0.00 0.00 0.00 4.79
121 122 1.735926 GGAGGATAGGAAAGAGGGGG 58.264 60.000 0.00 0.00 0.00 5.40
156 157 3.006859 TCATCTCGTCTTCCTCTTTTGCA 59.993 43.478 0.00 0.00 0.00 4.08
215 217 4.168291 CGCCTCTTCCCCTGCTCC 62.168 72.222 0.00 0.00 0.00 4.70
216 218 2.690510 GCCTCTTCCCCTGCTCCT 60.691 66.667 0.00 0.00 0.00 3.69
217 219 2.741055 GCCTCTTCCCCTGCTCCTC 61.741 68.421 0.00 0.00 0.00 3.71
218 220 1.306482 CCTCTTCCCCTGCTCCTCA 60.306 63.158 0.00 0.00 0.00 3.86
219 221 0.693767 CCTCTTCCCCTGCTCCTCAT 60.694 60.000 0.00 0.00 0.00 2.90
220 222 0.758123 CTCTTCCCCTGCTCCTCATC 59.242 60.000 0.00 0.00 0.00 2.92
221 223 0.692419 TCTTCCCCTGCTCCTCATCC 60.692 60.000 0.00 0.00 0.00 3.51
222 224 0.984961 CTTCCCCTGCTCCTCATCCA 60.985 60.000 0.00 0.00 0.00 3.41
223 225 1.274703 TTCCCCTGCTCCTCATCCAC 61.275 60.000 0.00 0.00 0.00 4.02
224 226 1.997311 CCCCTGCTCCTCATCCACA 60.997 63.158 0.00 0.00 0.00 4.17
225 227 1.351080 CCCCTGCTCCTCATCCACAT 61.351 60.000 0.00 0.00 0.00 3.21
226 228 0.108207 CCCTGCTCCTCATCCACATC 59.892 60.000 0.00 0.00 0.00 3.06
227 229 1.129917 CCTGCTCCTCATCCACATCT 58.870 55.000 0.00 0.00 0.00 2.90
228 230 1.070445 CCTGCTCCTCATCCACATCTC 59.930 57.143 0.00 0.00 0.00 2.75
229 231 1.070445 CTGCTCCTCATCCACATCTCC 59.930 57.143 0.00 0.00 0.00 3.71
230 232 0.396060 GCTCCTCATCCACATCTCCC 59.604 60.000 0.00 0.00 0.00 4.30
231 233 2.039070 GCTCCTCATCCACATCTCCCT 61.039 57.143 0.00 0.00 0.00 4.20
232 234 2.406559 CTCCTCATCCACATCTCCCTT 58.593 52.381 0.00 0.00 0.00 3.95
233 235 2.104451 CTCCTCATCCACATCTCCCTTG 59.896 54.545 0.00 0.00 0.00 3.61
234 236 1.842562 CCTCATCCACATCTCCCTTGT 59.157 52.381 0.00 0.00 0.00 3.16
235 237 2.158842 CCTCATCCACATCTCCCTTGTC 60.159 54.545 0.00 0.00 0.00 3.18
236 238 1.839994 TCATCCACATCTCCCTTGTCC 59.160 52.381 0.00 0.00 0.00 4.02
237 239 1.842562 CATCCACATCTCCCTTGTCCT 59.157 52.381 0.00 0.00 0.00 3.85
238 240 2.940514 TCCACATCTCCCTTGTCCTA 57.059 50.000 0.00 0.00 0.00 2.94
239 241 2.467880 TCCACATCTCCCTTGTCCTAC 58.532 52.381 0.00 0.00 0.00 3.18
264 266 1.587043 GCCGCTCCTTCAAAACCCTC 61.587 60.000 0.00 0.00 0.00 4.30
265 267 0.960861 CCGCTCCTTCAAAACCCTCC 60.961 60.000 0.00 0.00 0.00 4.30
266 268 1.298859 CGCTCCTTCAAAACCCTCCG 61.299 60.000 0.00 0.00 0.00 4.63
310 312 3.537874 CCCTCCCGCCGGTAAGAG 61.538 72.222 1.90 6.55 0.00 2.85
393 416 5.675684 ATCTGGTTCTTCCTCTCTCTTTC 57.324 43.478 0.00 0.00 37.07 2.62
455 483 0.175531 CCCATTTTGTTCGCCCATCC 59.824 55.000 0.00 0.00 0.00 3.51
457 485 0.801836 CATTTTGTTCGCCCATCCGC 60.802 55.000 0.00 0.00 0.00 5.54
519 551 1.329906 GGATCTTGCATCAGTTCGCTG 59.670 52.381 0.00 0.00 46.29 5.18
535 567 1.082690 GCTGCGAAAAAGAGAGAGGG 58.917 55.000 0.00 0.00 0.00 4.30
631 663 3.769189 AATTTTAACTAGGGGGTGGGG 57.231 47.619 0.00 0.00 0.00 4.96
633 665 2.454708 TTTAACTAGGGGGTGGGGAA 57.545 50.000 0.00 0.00 0.00 3.97
643 675 2.757077 GTGGGGAAGGGGTGACTG 59.243 66.667 0.00 0.00 0.00 3.51
644 676 2.154074 GTGGGGAAGGGGTGACTGT 61.154 63.158 0.00 0.00 0.00 3.55
645 677 0.838987 GTGGGGAAGGGGTGACTGTA 60.839 60.000 0.00 0.00 0.00 2.74
647 679 0.546988 GGGGAAGGGGTGACTGTAGT 60.547 60.000 0.00 0.00 0.00 2.73
649 681 0.613777 GGAAGGGGTGACTGTAGTGG 59.386 60.000 0.00 0.00 0.00 4.00
650 682 1.349067 GAAGGGGTGACTGTAGTGGT 58.651 55.000 0.00 0.00 0.00 4.16
653 685 4.284178 GAAGGGGTGACTGTAGTGGTATA 58.716 47.826 0.00 0.00 0.00 1.47
654 686 3.639952 AGGGGTGACTGTAGTGGTATAC 58.360 50.000 0.00 0.00 0.00 1.47
655 687 3.012047 AGGGGTGACTGTAGTGGTATACA 59.988 47.826 5.01 0.00 34.55 2.29
656 688 3.965347 GGGGTGACTGTAGTGGTATACAT 59.035 47.826 5.01 0.00 35.21 2.29
657 689 5.103387 AGGGGTGACTGTAGTGGTATACATA 60.103 44.000 5.01 0.00 35.21 2.29
762 794 4.892934 TGCCAATAAGGTTCTTTCTTGTGT 59.107 37.500 0.00 0.00 40.61 3.72
765 797 6.568653 GCCAATAAGGTTCTTTCTTGTGTCTC 60.569 42.308 0.00 0.00 40.61 3.36
873 911 3.351740 TCTTTTGTCACCAAACTGCAGA 58.648 40.909 23.35 0.00 40.19 4.26
888 926 0.389948 GCAGACACCAACGGTCCTAG 60.390 60.000 0.00 0.00 35.89 3.02
906 949 1.154150 GCTTGAAGCGCATCACCAC 60.154 57.895 15.92 3.91 0.00 4.16
921 964 3.716195 CACCCCACCCAGATGCGA 61.716 66.667 0.00 0.00 0.00 5.10
924 967 1.526917 CCCCACCCAGATGCGATTC 60.527 63.158 0.00 0.00 0.00 2.52
930 973 0.883814 CCCAGATGCGATTCCTGCTC 60.884 60.000 0.00 0.00 0.00 4.26
956 1000 5.527951 CAGAGCTCCGTAAGTCAATACTCTA 59.472 44.000 10.93 0.00 33.75 2.43
957 1001 5.761234 AGAGCTCCGTAAGTCAATACTCTAG 59.239 44.000 10.93 0.00 33.75 2.43
970 1022 4.650972 ATACTCTAGTAGGAGGGAGCAG 57.349 50.000 0.00 0.00 37.63 4.24
973 1025 3.011934 ACTCTAGTAGGAGGGAGCAGTTT 59.988 47.826 0.00 0.00 37.63 2.66
1032 1084 1.389609 GGTGCCCGGAGATAGTCGAA 61.390 60.000 0.73 0.00 0.00 3.71
1182 1234 1.503542 CTTCAATGTGCGCACCTCC 59.496 57.895 35.72 13.65 0.00 4.30
1340 1392 2.514824 GGCCGCCATGAAGAGGAC 60.515 66.667 3.91 0.00 0.00 3.85
1428 1480 1.002087 GTGGTTCCAACAGACGAGGAT 59.998 52.381 0.00 0.00 0.00 3.24
1479 1531 1.032014 TTGCTTTGCCTGACAAGGTC 58.968 50.000 0.00 0.00 46.43 3.85
1492 1544 4.863491 TGACAAGGTCGTAGTAAGTTCAC 58.137 43.478 0.00 0.00 34.95 3.18
1494 1546 3.638160 ACAAGGTCGTAGTAAGTTCACCA 59.362 43.478 0.00 0.00 0.00 4.17
1497 1549 3.505293 AGGTCGTAGTAAGTTCACCAGTC 59.495 47.826 0.00 0.00 0.00 3.51
1510 1562 3.278574 TCACCAGTCAAGTTGGTTGAAG 58.721 45.455 2.34 0.00 46.57 3.02
1512 1564 2.357154 ACCAGTCAAGTTGGTTGAAGCT 60.357 45.455 2.34 0.00 46.57 3.74
1513 1565 3.118038 ACCAGTCAAGTTGGTTGAAGCTA 60.118 43.478 2.34 0.00 46.57 3.32
1533 1585 6.059484 AGCTAGTAAAAAGGTGCACAGTAAA 58.941 36.000 20.43 0.00 0.00 2.01
1635 1687 4.532521 AGTAATAAGTCACTGGAGGCAAGT 59.467 41.667 0.00 0.00 0.00 3.16
1889 1941 1.341156 CCCAAAACCCCAGCACCAAA 61.341 55.000 0.00 0.00 0.00 3.28
1921 1976 1.067250 GCTGATGGCTCTCTCGGTC 59.933 63.158 0.00 0.00 38.06 4.79
1969 2024 2.090775 TGCTATGTCAGTGGGATCCCTA 60.091 50.000 31.05 15.11 36.94 3.53
2058 2113 3.738281 GCATCGGTGACTATAGCACAAGT 60.738 47.826 21.15 9.19 37.99 3.16
2061 2116 4.011698 TCGGTGACTATAGCACAAGTACA 58.988 43.478 21.15 4.82 37.99 2.90
2147 2202 1.211212 TGTCAGATGGGAAGCCATGAG 59.789 52.381 0.00 0.00 0.00 2.90
2183 2238 2.482494 ACAAGGGACCCTAGGATTGAG 58.518 52.381 15.29 0.00 31.13 3.02
2211 2266 0.957362 AGCTTCTCAAACAGCTTGGC 59.043 50.000 0.00 0.00 44.28 4.52
2232 2287 3.614092 CTGTGGAGATATTGGCACTGTT 58.386 45.455 0.00 0.00 0.00 3.16
2424 2479 3.173151 TCTGTCTTGCCTAGTCATGGAA 58.827 45.455 0.00 0.00 0.00 3.53
2442 2497 2.487265 GGAATATTGTCCAGGCGGTGAT 60.487 50.000 0.00 0.00 37.65 3.06
2472 2527 2.633488 CTAAGGCAGAAGCAACCTACC 58.367 52.381 0.00 0.00 44.61 3.18
2475 2530 0.678048 GGCAGAAGCAACCTACCAGG 60.678 60.000 0.00 0.00 44.61 4.45
2510 2565 3.626217 GCCGCTGCTAGGTAAATAACTTT 59.374 43.478 0.00 0.00 33.53 2.66
2515 2570 5.820947 GCTGCTAGGTAAATAACTTTAGCCA 59.179 40.000 0.00 0.00 43.29 4.75
2520 2575 7.935210 GCTAGGTAAATAACTTTAGCCATGGTA 59.065 37.037 14.67 1.63 43.29 3.25
2535 2590 9.860650 TTAGCCATGGTATTTATGTGTTATCTT 57.139 29.630 14.67 0.00 0.00 2.40
2537 2592 9.284968 AGCCATGGTATTTATGTGTTATCTTAC 57.715 33.333 14.67 0.00 0.00 2.34
2543 2598 7.927629 GGTATTTATGTGTTATCTTACCGACCA 59.072 37.037 0.00 0.00 0.00 4.02
2548 2603 5.553123 TGTGTTATCTTACCGACCAATTGT 58.447 37.500 4.43 0.00 0.00 2.71
2549 2604 5.410132 TGTGTTATCTTACCGACCAATTGTG 59.590 40.000 4.43 0.00 0.00 3.33
2551 2606 1.816074 TCTTACCGACCAATTGTGCC 58.184 50.000 4.43 0.00 0.00 5.01
2554 2609 0.958382 TACCGACCAATTGTGCCTGC 60.958 55.000 4.43 0.00 0.00 4.85
2561 2616 2.289195 ACCAATTGTGCCTGCATTTCTG 60.289 45.455 4.43 0.00 0.00 3.02
2585 2640 6.922957 TGGCAGAAAATCATGTTTCAAGTTAC 59.077 34.615 10.43 0.00 39.52 2.50
2598 2653 8.378172 TGTTTCAAGTTACTTAACTCATCAGG 57.622 34.615 10.78 0.00 45.17 3.86
2679 2736 5.238650 GCATATGTTGGGGGTTATATATCGC 59.761 44.000 4.29 0.35 0.00 4.58
2970 3027 0.877071 CATCACTTCCGCAGCTTGTT 59.123 50.000 0.00 0.00 0.00 2.83
3000 3057 3.725895 CGACTGATGCAAGGTCAAATTCG 60.726 47.826 14.33 8.12 0.00 3.34
3006 3063 3.701241 TGCAAGGTCAAATTCGTTTGTC 58.299 40.909 0.00 0.00 33.82 3.18
3330 3387 2.044946 AACTGGGCCTTGATCCGC 60.045 61.111 4.53 0.00 0.00 5.54
3581 3638 2.122729 CAGTCCCCACTCCCCTGA 59.877 66.667 0.00 0.00 0.00 3.86
3716 3773 4.020485 CAGATATCAGATGAGCCATGGTCA 60.020 45.833 14.67 15.60 44.17 4.02
3774 3831 0.646895 GCAAGCAATTGCATTACGGC 59.353 50.000 30.89 19.39 46.60 5.68
3775 3832 1.736696 GCAAGCAATTGCATTACGGCT 60.737 47.619 30.89 5.95 46.60 5.52
3776 3833 1.921887 CAAGCAATTGCATTACGGCTG 59.078 47.619 30.89 11.19 45.16 4.85
3777 3834 0.457035 AGCAATTGCATTACGGCTGG 59.543 50.000 30.89 0.00 45.16 4.85
3778 3835 0.173255 GCAATTGCATTACGGCTGGT 59.827 50.000 25.36 0.00 41.59 4.00
3779 3836 1.403679 GCAATTGCATTACGGCTGGTA 59.596 47.619 25.36 0.00 41.59 3.25
3780 3837 2.541588 GCAATTGCATTACGGCTGGTAG 60.542 50.000 25.36 0.00 41.59 3.18
3781 3838 2.942376 CAATTGCATTACGGCTGGTAGA 59.058 45.455 0.00 0.00 31.46 2.59
3782 3839 2.309528 TTGCATTACGGCTGGTAGAG 57.690 50.000 0.00 0.00 31.46 2.43
3799 3856 2.649034 GCATGCTGCTGTTGTGCT 59.351 55.556 11.37 0.00 40.96 4.40
3800 3857 1.733041 GCATGCTGCTGTTGTGCTG 60.733 57.895 11.37 0.00 40.96 4.41
3801 3858 1.658114 CATGCTGCTGTTGTGCTGT 59.342 52.632 0.00 0.00 34.93 4.40
3802 3859 0.876399 CATGCTGCTGTTGTGCTGTA 59.124 50.000 0.00 0.00 34.93 2.74
3803 3860 0.877071 ATGCTGCTGTTGTGCTGTAC 59.123 50.000 0.00 0.00 34.93 2.90
3804 3861 0.179048 TGCTGCTGTTGTGCTGTACT 60.179 50.000 0.00 0.00 34.93 2.73
3805 3862 0.236711 GCTGCTGTTGTGCTGTACTG 59.763 55.000 0.00 0.00 34.93 2.74
3806 3863 1.586422 CTGCTGTTGTGCTGTACTGT 58.414 50.000 1.46 0.00 0.00 3.55
3807 3864 2.754472 CTGCTGTTGTGCTGTACTGTA 58.246 47.619 1.46 0.00 0.00 2.74
3808 3865 3.329386 CTGCTGTTGTGCTGTACTGTAT 58.671 45.455 1.46 0.00 0.00 2.29
3809 3866 3.066380 TGCTGTTGTGCTGTACTGTATG 58.934 45.455 1.46 0.00 0.00 2.39
3810 3867 2.159653 GCTGTTGTGCTGTACTGTATGC 60.160 50.000 1.46 8.25 0.00 3.14
3811 3868 3.066380 CTGTTGTGCTGTACTGTATGCA 58.934 45.455 12.27 12.27 0.00 3.96
3812 3869 3.471680 TGTTGTGCTGTACTGTATGCAA 58.528 40.909 16.14 7.70 37.17 4.08
3813 3870 4.071423 TGTTGTGCTGTACTGTATGCAAT 58.929 39.130 16.14 0.00 37.17 3.56
3814 3871 4.083377 TGTTGTGCTGTACTGTATGCAATG 60.083 41.667 16.14 0.00 37.17 2.82
3828 3885 7.012327 ACTGTATGCAATGCAATAATAGTTCGT 59.988 33.333 13.45 0.00 43.62 3.85
3833 3890 2.828877 TGCAATAATAGTTCGTCCCCG 58.171 47.619 0.00 0.00 0.00 5.73
3834 3891 1.529865 GCAATAATAGTTCGTCCCCGC 59.470 52.381 0.00 0.00 0.00 6.13
3856 3913 2.490903 GTGGCATCTGAAAATGAGCTGT 59.509 45.455 0.00 0.00 0.00 4.40
3864 3921 5.793817 TCTGAAAATGAGCTGTTACTGCTA 58.206 37.500 16.35 6.35 38.70 3.49
3893 3995 8.705594 AGTAGTTGTTGCTGGATAGTATGTAAT 58.294 33.333 0.00 0.00 0.00 1.89
3947 4049 6.388619 AGGTTAGGAGCAAGGATTTAGAAA 57.611 37.500 0.00 0.00 0.00 2.52
3973 4075 1.067060 TGTCTGTCACGGACTTCACAG 59.933 52.381 17.84 0.00 40.15 3.66
3995 4097 2.362169 ATGTTATGGGTTTGCGTTGC 57.638 45.000 0.00 0.00 0.00 4.17
4003 4105 0.318955 GGTTTGCGTTGCTGAATGCT 60.319 50.000 3.02 0.00 43.51 3.79
4054 4159 4.216411 ACCATTTTATAGTGCTGACCGT 57.784 40.909 0.00 0.00 0.00 4.83
4185 4312 7.857456 TCACTGTAATATGTACAAATCCTGGT 58.143 34.615 0.00 0.00 0.00 4.00
4288 4415 7.062749 ACTTACACAATGTAGGTCTTCTTCA 57.937 36.000 0.00 0.00 38.55 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.526211 TATGGCTATGGCTACGCGAG 59.474 55.000 15.93 7.21 38.73 5.03
3 4 0.526211 CTATGGCTATGGCTACGCGA 59.474 55.000 15.93 0.00 38.73 5.87
4 5 1.078759 GCTATGGCTATGGCTACGCG 61.079 60.000 11.26 3.53 37.75 6.01
6 7 2.274437 CATGCTATGGCTATGGCTACG 58.726 52.381 18.81 4.24 41.00 3.51
9 10 3.972368 CCATGCTATGGCTATGGCT 57.028 52.632 18.81 2.61 44.70 4.75
23 24 4.108299 TACCACGGCAGCCCCATG 62.108 66.667 5.63 1.61 0.00 3.66
24 25 3.797353 CTACCACGGCAGCCCCAT 61.797 66.667 5.63 0.00 0.00 4.00
26 27 4.162690 CTCTACCACGGCAGCCCC 62.163 72.222 5.63 0.00 0.00 5.80
27 28 3.075005 TCTCTACCACGGCAGCCC 61.075 66.667 5.63 0.00 0.00 5.19
28 29 2.010582 CTCTCTCTACCACGGCAGCC 62.011 65.000 0.00 0.00 0.00 4.85
29 30 1.032657 TCTCTCTCTACCACGGCAGC 61.033 60.000 0.00 0.00 0.00 5.25
30 31 1.464734 TTCTCTCTCTACCACGGCAG 58.535 55.000 0.00 0.00 0.00 4.85
31 32 1.819288 CTTTCTCTCTCTACCACGGCA 59.181 52.381 0.00 0.00 0.00 5.69
32 33 1.135333 CCTTTCTCTCTCTACCACGGC 59.865 57.143 0.00 0.00 0.00 5.68
33 34 1.135333 GCCTTTCTCTCTCTACCACGG 59.865 57.143 0.00 0.00 0.00 4.94
34 35 1.819288 TGCCTTTCTCTCTCTACCACG 59.181 52.381 0.00 0.00 0.00 4.94
35 36 2.416162 CGTGCCTTTCTCTCTCTACCAC 60.416 54.545 0.00 0.00 0.00 4.16
36 37 1.819288 CGTGCCTTTCTCTCTCTACCA 59.181 52.381 0.00 0.00 0.00 3.25
37 38 1.470112 GCGTGCCTTTCTCTCTCTACC 60.470 57.143 0.00 0.00 0.00 3.18
38 39 1.202582 TGCGTGCCTTTCTCTCTCTAC 59.797 52.381 0.00 0.00 0.00 2.59
39 40 1.474478 CTGCGTGCCTTTCTCTCTCTA 59.526 52.381 0.00 0.00 0.00 2.43
40 41 0.246086 CTGCGTGCCTTTCTCTCTCT 59.754 55.000 0.00 0.00 0.00 3.10
41 42 1.357991 GCTGCGTGCCTTTCTCTCTC 61.358 60.000 0.00 0.00 35.15 3.20
42 43 1.375268 GCTGCGTGCCTTTCTCTCT 60.375 57.895 0.00 0.00 35.15 3.10
43 44 3.172919 GCTGCGTGCCTTTCTCTC 58.827 61.111 0.00 0.00 35.15 3.20
59 60 1.065600 CTCTCACTCTAGCTGCGGC 59.934 63.158 10.33 10.33 39.06 6.53
60 61 0.662619 CTCTCTCACTCTAGCTGCGG 59.337 60.000 0.00 0.00 0.00 5.69
61 62 1.599071 CTCTCTCTCACTCTAGCTGCG 59.401 57.143 0.00 0.00 0.00 5.18
62 63 2.874701 CTCTCTCTCTCACTCTAGCTGC 59.125 54.545 0.00 0.00 0.00 5.25
63 64 4.141846 ACTCTCTCTCTCTCACTCTAGCTG 60.142 50.000 0.00 0.00 0.00 4.24
64 65 4.033709 ACTCTCTCTCTCTCACTCTAGCT 58.966 47.826 0.00 0.00 0.00 3.32
65 66 4.122776 CACTCTCTCTCTCTCACTCTAGC 58.877 52.174 0.00 0.00 0.00 3.42
66 67 5.111989 CACACTCTCTCTCTCTCACTCTAG 58.888 50.000 0.00 0.00 0.00 2.43
67 68 4.530553 ACACACTCTCTCTCTCTCACTCTA 59.469 45.833 0.00 0.00 0.00 2.43
68 69 3.327757 ACACACTCTCTCTCTCTCACTCT 59.672 47.826 0.00 0.00 0.00 3.24
69 70 3.436704 CACACACTCTCTCTCTCTCACTC 59.563 52.174 0.00 0.00 0.00 3.51
70 71 3.072330 TCACACACTCTCTCTCTCTCACT 59.928 47.826 0.00 0.00 0.00 3.41
71 72 3.407698 TCACACACTCTCTCTCTCTCAC 58.592 50.000 0.00 0.00 0.00 3.51
72 73 3.673902 CTCACACACTCTCTCTCTCTCA 58.326 50.000 0.00 0.00 0.00 3.27
73 74 2.420022 GCTCACACACTCTCTCTCTCTC 59.580 54.545 0.00 0.00 0.00 3.20
74 75 2.436417 GCTCACACACTCTCTCTCTCT 58.564 52.381 0.00 0.00 0.00 3.10
75 76 1.472480 GGCTCACACACTCTCTCTCTC 59.528 57.143 0.00 0.00 0.00 3.20
76 77 1.075374 AGGCTCACACACTCTCTCTCT 59.925 52.381 0.00 0.00 0.00 3.10
77 78 1.202114 CAGGCTCACACACTCTCTCTC 59.798 57.143 0.00 0.00 0.00 3.20
78 79 1.255882 CAGGCTCACACACTCTCTCT 58.744 55.000 0.00 0.00 0.00 3.10
79 80 0.965439 ACAGGCTCACACACTCTCTC 59.035 55.000 0.00 0.00 0.00 3.20
80 81 0.678395 CACAGGCTCACACACTCTCT 59.322 55.000 0.00 0.00 0.00 3.10
81 82 0.320247 CCACAGGCTCACACACTCTC 60.320 60.000 0.00 0.00 0.00 3.20
82 83 1.750930 CCACAGGCTCACACACTCT 59.249 57.895 0.00 0.00 0.00 3.24
83 84 1.302033 CCCACAGGCTCACACACTC 60.302 63.158 0.00 0.00 0.00 3.51
84 85 2.822637 CCCCACAGGCTCACACACT 61.823 63.158 0.00 0.00 0.00 3.55
85 86 2.281761 CCCCACAGGCTCACACAC 60.282 66.667 0.00 0.00 0.00 3.82
86 87 3.569210 CCCCCACAGGCTCACACA 61.569 66.667 0.00 0.00 0.00 3.72
87 88 3.249189 TCCCCCACAGGCTCACAC 61.249 66.667 0.00 0.00 0.00 3.82
88 89 2.930019 CTCCCCCACAGGCTCACA 60.930 66.667 0.00 0.00 0.00 3.58
89 90 3.721706 CCTCCCCCACAGGCTCAC 61.722 72.222 0.00 0.00 0.00 3.51
90 91 1.897037 TATCCTCCCCCACAGGCTCA 61.897 60.000 0.00 0.00 0.00 4.26
91 92 1.074471 TATCCTCCCCCACAGGCTC 60.074 63.158 0.00 0.00 0.00 4.70
92 93 1.074167 CTATCCTCCCCCACAGGCT 60.074 63.158 0.00 0.00 0.00 4.58
93 94 2.150051 CCTATCCTCCCCCACAGGC 61.150 68.421 0.00 0.00 0.00 4.85
94 95 0.030092 TTCCTATCCTCCCCCACAGG 60.030 60.000 0.00 0.00 0.00 4.00
95 96 1.771255 CTTTCCTATCCTCCCCCACAG 59.229 57.143 0.00 0.00 0.00 3.66
96 97 1.368203 TCTTTCCTATCCTCCCCCACA 59.632 52.381 0.00 0.00 0.00 4.17
97 98 2.050918 CTCTTTCCTATCCTCCCCCAC 58.949 57.143 0.00 0.00 0.00 4.61
98 99 1.061346 CCTCTTTCCTATCCTCCCCCA 60.061 57.143 0.00 0.00 0.00 4.96
99 100 1.735926 CCTCTTTCCTATCCTCCCCC 58.264 60.000 0.00 0.00 0.00 5.40
100 101 1.735926 CCCTCTTTCCTATCCTCCCC 58.264 60.000 0.00 0.00 0.00 4.81
101 102 1.735926 CCCCTCTTTCCTATCCTCCC 58.264 60.000 0.00 0.00 0.00 4.30
102 103 1.735926 CCCCCTCTTTCCTATCCTCC 58.264 60.000 0.00 0.00 0.00 4.30
126 127 2.010582 AAGACGAGATGAGAGCGGCC 62.011 60.000 0.00 0.00 32.38 6.13
138 139 2.675348 GGATGCAAAAGAGGAAGACGAG 59.325 50.000 0.00 0.00 0.00 4.18
187 188 3.308014 AAGAGGCGGCAGTCAGCTC 62.308 63.158 13.08 0.00 44.79 4.09
215 217 2.158842 GGACAAGGGAGATGTGGATGAG 60.159 54.545 0.00 0.00 0.00 2.90
216 218 1.839994 GGACAAGGGAGATGTGGATGA 59.160 52.381 0.00 0.00 0.00 2.92
217 219 1.842562 AGGACAAGGGAGATGTGGATG 59.157 52.381 0.00 0.00 0.00 3.51
218 220 2.277008 AGGACAAGGGAGATGTGGAT 57.723 50.000 0.00 0.00 0.00 3.41
219 221 2.044492 AGTAGGACAAGGGAGATGTGGA 59.956 50.000 0.00 0.00 0.00 4.02
220 222 2.432510 GAGTAGGACAAGGGAGATGTGG 59.567 54.545 0.00 0.00 0.00 4.17
221 223 2.099921 CGAGTAGGACAAGGGAGATGTG 59.900 54.545 0.00 0.00 0.00 3.21
222 224 2.379972 CGAGTAGGACAAGGGAGATGT 58.620 52.381 0.00 0.00 0.00 3.06
223 225 1.067821 GCGAGTAGGACAAGGGAGATG 59.932 57.143 0.00 0.00 0.00 2.90
224 226 1.404843 GCGAGTAGGACAAGGGAGAT 58.595 55.000 0.00 0.00 0.00 2.75
225 227 0.683504 GGCGAGTAGGACAAGGGAGA 60.684 60.000 0.00 0.00 0.00 3.71
226 228 1.817209 GGCGAGTAGGACAAGGGAG 59.183 63.158 0.00 0.00 0.00 4.30
227 229 2.050350 CGGCGAGTAGGACAAGGGA 61.050 63.158 0.00 0.00 0.00 4.20
228 230 2.494918 CGGCGAGTAGGACAAGGG 59.505 66.667 0.00 0.00 0.00 3.95
229 231 2.202756 GCGGCGAGTAGGACAAGG 60.203 66.667 12.98 0.00 0.00 3.61
230 232 2.202756 GGCGGCGAGTAGGACAAG 60.203 66.667 12.98 0.00 0.00 3.16
231 233 4.124351 CGGCGGCGAGTAGGACAA 62.124 66.667 29.19 0.00 0.00 3.18
251 253 1.809684 GAGACGGAGGGTTTTGAAGG 58.190 55.000 0.00 0.00 0.00 3.46
256 258 2.168666 GAGGCGAGACGGAGGGTTTT 62.169 60.000 0.00 0.00 0.00 2.43
293 295 3.537874 CTCTTACCGGCGGGAGGG 61.538 72.222 31.78 22.85 36.97 4.30
310 312 0.035439 TGGATTTTGGAGCGGGAGAC 60.035 55.000 0.00 0.00 0.00 3.36
393 416 0.383491 CACAAACGCGCAGAGTCAAG 60.383 55.000 5.73 0.00 41.76 3.02
457 485 0.514691 GGACAAGAAGACGCAAGCAG 59.485 55.000 0.00 0.00 45.62 4.24
519 551 1.550976 TCTCCCCTCTCTCTTTTTCGC 59.449 52.381 0.00 0.00 0.00 4.70
528 560 0.973496 GGTTTCGCTCTCCCCTCTCT 60.973 60.000 0.00 0.00 0.00 3.10
535 567 2.046217 GGTGGGGTTTCGCTCTCC 60.046 66.667 0.00 0.00 0.00 3.71
606 638 5.544562 CCCACCCCCTAGTTAAAATTTGAAA 59.455 40.000 0.00 0.00 0.00 2.69
626 658 0.838987 TACAGTCACCCCTTCCCCAC 60.839 60.000 0.00 0.00 0.00 4.61
627 659 0.546747 CTACAGTCACCCCTTCCCCA 60.547 60.000 0.00 0.00 0.00 4.96
631 663 1.349067 ACCACTACAGTCACCCCTTC 58.651 55.000 0.00 0.00 0.00 3.46
633 665 2.942604 ATACCACTACAGTCACCCCT 57.057 50.000 0.00 0.00 0.00 4.79
649 681 9.938280 TGCCCTTGTACTCATTATTATGTATAC 57.062 33.333 0.00 0.00 33.34 1.47
650 682 9.938280 GTGCCCTTGTACTCATTATTATGTATA 57.062 33.333 0.00 0.00 33.34 1.47
653 685 6.062095 GGTGCCCTTGTACTCATTATTATGT 58.938 40.000 0.00 0.00 33.34 2.29
654 686 6.061441 TGGTGCCCTTGTACTCATTATTATG 58.939 40.000 0.00 0.00 0.00 1.90
655 687 6.260700 TGGTGCCCTTGTACTCATTATTAT 57.739 37.500 0.00 0.00 0.00 1.28
656 688 5.702065 TGGTGCCCTTGTACTCATTATTA 57.298 39.130 0.00 0.00 0.00 0.98
657 689 4.584638 TGGTGCCCTTGTACTCATTATT 57.415 40.909 0.00 0.00 0.00 1.40
762 794 2.026729 TGGTGCGGGTATTCATTTGAGA 60.027 45.455 0.00 0.00 0.00 3.27
765 797 2.951642 AGATGGTGCGGGTATTCATTTG 59.048 45.455 0.00 0.00 0.00 2.32
873 911 0.034896 CAAGCTAGGACCGTTGGTGT 59.965 55.000 0.00 0.00 35.25 4.16
888 926 1.154150 GTGGTGATGCGCTTCAAGC 60.154 57.895 25.49 18.64 38.02 4.01
906 949 1.526917 GAATCGCATCTGGGTGGGG 60.527 63.158 0.00 0.00 33.32 4.96
930 973 6.503261 AGTATTGACTTACGGAGCTCTGCG 62.503 50.000 22.80 16.14 40.95 5.18
942 985 7.692289 GCTCCCTCCTACTAGAGTATTGACTTA 60.692 44.444 0.00 0.00 35.45 2.24
956 1000 1.630878 CCAAAACTGCTCCCTCCTACT 59.369 52.381 0.00 0.00 0.00 2.57
957 1001 1.628846 TCCAAAACTGCTCCCTCCTAC 59.371 52.381 0.00 0.00 0.00 3.18
970 1022 1.971695 CTCCCACCGCCTCCAAAAC 60.972 63.158 0.00 0.00 0.00 2.43
973 1025 3.636231 CACTCCCACCGCCTCCAA 61.636 66.667 0.00 0.00 0.00 3.53
1032 1084 2.039084 GTCTTTGGTCTCATCCACCAGT 59.961 50.000 0.00 0.00 44.89 4.00
1364 1416 1.051812 CGCCCCAGATTCAGGAGTAT 58.948 55.000 0.00 0.00 0.00 2.12
1428 1480 1.988107 ACCTTGCTCTTCCCATCTTGA 59.012 47.619 0.00 0.00 0.00 3.02
1479 1531 4.868067 ACTTGACTGGTGAACTTACTACG 58.132 43.478 0.00 0.00 0.00 3.51
1492 1544 2.301346 AGCTTCAACCAACTTGACTGG 58.699 47.619 0.00 0.00 38.70 4.00
1494 1546 4.423625 ACTAGCTTCAACCAACTTGACT 57.576 40.909 0.00 0.00 38.70 3.41
1497 1549 6.918022 CCTTTTTACTAGCTTCAACCAACTTG 59.082 38.462 0.00 0.00 0.00 3.16
1510 1562 5.934935 TTACTGTGCACCTTTTTACTAGC 57.065 39.130 15.69 0.00 0.00 3.42
1512 1564 6.358991 ACCTTTACTGTGCACCTTTTTACTA 58.641 36.000 15.69 0.00 0.00 1.82
1513 1565 5.198207 ACCTTTACTGTGCACCTTTTTACT 58.802 37.500 15.69 0.00 0.00 2.24
1635 1687 1.836166 CTTCCAGCAGAGGGATCTTCA 59.164 52.381 0.00 0.00 33.63 3.02
1889 1941 0.250901 ATCAGCGCCCTTCTTGTTGT 60.251 50.000 2.29 0.00 0.00 3.32
1921 1976 1.202348 GCCAAAATCAACTCCTTCGGG 59.798 52.381 0.00 0.00 0.00 5.14
2058 2113 7.928167 CCATAACTATCTTCACTGATGCTTGTA 59.072 37.037 0.00 0.00 0.00 2.41
2061 2116 6.893583 ACCATAACTATCTTCACTGATGCTT 58.106 36.000 0.00 0.00 0.00 3.91
2183 2238 4.791088 GCTGTTTGAGAAGCTTGAAGTTCC 60.791 45.833 2.10 0.00 36.47 3.62
2211 2266 3.272574 ACAGTGCCAATATCTCCACAG 57.727 47.619 0.00 0.00 0.00 3.66
2232 2287 1.281867 CCCACCAACTCAGCCAGATAA 59.718 52.381 0.00 0.00 0.00 1.75
2274 2329 5.745227 AGGTACTCAATGTCCATAACCTTG 58.255 41.667 0.00 0.00 35.50 3.61
2418 2473 1.881973 CCGCCTGGACAATATTCCATG 59.118 52.381 0.00 0.00 44.97 3.66
2424 2479 2.050144 AGATCACCGCCTGGACAATAT 58.950 47.619 0.00 0.00 39.21 1.28
2472 2527 1.600413 GCGGCTTCTGAAAAACACCTG 60.600 52.381 0.00 0.00 0.00 4.00
2475 2530 1.758783 CAGCGGCTTCTGAAAAACAC 58.241 50.000 0.00 0.00 36.19 3.32
2503 2558 9.640952 ACACATAAATACCATGGCTAAAGTTAT 57.359 29.630 13.04 7.65 0.00 1.89
2515 2570 9.485206 GTCGGTAAGATAACACATAAATACCAT 57.515 33.333 0.00 0.00 0.00 3.55
2520 2575 8.974060 ATTGGTCGGTAAGATAACACATAAAT 57.026 30.769 0.00 0.00 0.00 1.40
2535 2590 0.958382 GCAGGCACAATTGGTCGGTA 60.958 55.000 10.83 0.00 0.00 4.02
2537 2592 1.597797 ATGCAGGCACAATTGGTCGG 61.598 55.000 10.83 2.59 0.00 4.79
2543 2598 2.754946 CCAGAAATGCAGGCACAATT 57.245 45.000 0.00 0.00 0.00 2.32
2554 2609 6.647481 TGAAACATGATTTTCTGCCAGAAATG 59.353 34.615 19.86 16.59 43.06 2.32
2561 2616 7.147976 AGTAACTTGAAACATGATTTTCTGCC 58.852 34.615 0.00 0.00 36.58 4.85
2585 2640 9.829507 AAAGAGACATAATCCTGATGAGTTAAG 57.170 33.333 0.00 0.00 0.00 1.85
2595 2650 4.521146 ACCTGCAAAGAGACATAATCCTG 58.479 43.478 0.00 0.00 0.00 3.86
2598 2653 6.961554 CGTAAAACCTGCAAAGAGACATAATC 59.038 38.462 0.00 0.00 0.00 1.75
2607 2664 1.262151 GCGACGTAAAACCTGCAAAGA 59.738 47.619 0.00 0.00 0.00 2.52
2679 2736 2.662006 TGTTCTCAGGCTTCAGATCG 57.338 50.000 0.00 0.00 0.00 3.69
2979 3036 3.189287 ACGAATTTGACCTTGCATCAGTC 59.811 43.478 0.00 0.00 0.00 3.51
3000 3057 1.834188 ATTCATGGGTCCCGACAAAC 58.166 50.000 2.65 0.00 0.00 2.93
3006 3063 1.967319 CAAGGTATTCATGGGTCCCG 58.033 55.000 2.65 0.00 0.00 5.14
3132 3189 4.418013 TGTAAGTGTTTCATCATTGCCG 57.582 40.909 0.00 0.00 0.00 5.69
3637 3694 2.559668 CACCCGACCTTACTCAGTTACA 59.440 50.000 0.00 0.00 0.00 2.41
3716 3773 6.680874 TTCAAAAGAAAAATGCTTGCACAT 57.319 29.167 0.00 0.00 0.00 3.21
3744 3801 1.636148 ATTGCTTGCAAGACCATGGT 58.364 45.000 30.39 19.89 0.00 3.55
3783 3840 0.876399 TACAGCACAACAGCAGCATG 59.124 50.000 0.00 0.00 40.87 4.06
3784 3841 0.877071 GTACAGCACAACAGCAGCAT 59.123 50.000 0.00 0.00 36.85 3.79
3785 3842 0.179048 AGTACAGCACAACAGCAGCA 60.179 50.000 0.00 0.00 36.85 4.41
3786 3843 0.236711 CAGTACAGCACAACAGCAGC 59.763 55.000 0.00 0.00 36.85 5.25
3787 3844 1.586422 ACAGTACAGCACAACAGCAG 58.414 50.000 0.00 0.00 36.85 4.24
3788 3845 2.900716 TACAGTACAGCACAACAGCA 57.099 45.000 0.00 0.00 36.85 4.41
3789 3846 2.159653 GCATACAGTACAGCACAACAGC 60.160 50.000 0.00 0.00 0.00 4.40
3790 3847 3.066380 TGCATACAGTACAGCACAACAG 58.934 45.455 5.61 0.00 31.05 3.16
3791 3848 3.118905 TGCATACAGTACAGCACAACA 57.881 42.857 5.61 0.00 31.05 3.33
3792 3849 4.406069 CATTGCATACAGTACAGCACAAC 58.594 43.478 8.65 0.00 36.62 3.32
3793 3850 3.119884 GCATTGCATACAGTACAGCACAA 60.120 43.478 3.15 0.00 36.62 3.33
3794 3851 2.419673 GCATTGCATACAGTACAGCACA 59.580 45.455 3.15 2.94 36.62 4.57
3795 3852 2.419673 TGCATTGCATACAGTACAGCAC 59.580 45.455 7.38 0.69 36.62 4.40
3796 3853 2.709213 TGCATTGCATACAGTACAGCA 58.291 42.857 7.38 5.61 31.71 4.41
3797 3854 3.763097 TTGCATTGCATACAGTACAGC 57.237 42.857 12.95 0.77 38.76 4.40
3798 3855 8.777413 ACTATTATTGCATTGCATACAGTACAG 58.223 33.333 12.95 5.50 38.76 2.74
3799 3856 8.675705 ACTATTATTGCATTGCATACAGTACA 57.324 30.769 12.95 0.00 38.76 2.90
3800 3857 9.599322 GAACTATTATTGCATTGCATACAGTAC 57.401 33.333 12.95 0.00 38.76 2.73
3801 3858 8.495148 CGAACTATTATTGCATTGCATACAGTA 58.505 33.333 12.95 0.00 38.76 2.74
3802 3859 7.012327 ACGAACTATTATTGCATTGCATACAGT 59.988 33.333 12.95 8.76 38.76 3.55
3803 3860 7.355017 ACGAACTATTATTGCATTGCATACAG 58.645 34.615 12.95 8.17 38.76 2.74
3804 3861 7.258022 ACGAACTATTATTGCATTGCATACA 57.742 32.000 12.95 0.00 38.76 2.29
3805 3862 6.797033 GGACGAACTATTATTGCATTGCATAC 59.203 38.462 12.95 0.00 38.76 2.39
3806 3863 6.072728 GGGACGAACTATTATTGCATTGCATA 60.073 38.462 12.95 4.15 38.76 3.14
3807 3864 5.278463 GGGACGAACTATTATTGCATTGCAT 60.278 40.000 12.95 5.57 38.76 3.96
3808 3865 4.036262 GGGACGAACTATTATTGCATTGCA 59.964 41.667 7.38 7.38 36.47 4.08
3809 3866 4.537015 GGGACGAACTATTATTGCATTGC 58.463 43.478 0.46 0.46 0.00 3.56
3810 3867 5.108385 GGGGACGAACTATTATTGCATTG 57.892 43.478 0.00 0.00 0.00 2.82
3833 3890 1.796617 GCTCATTTTCAGATGCCACGC 60.797 52.381 0.00 0.00 0.00 5.34
3834 3891 1.741706 AGCTCATTTTCAGATGCCACG 59.258 47.619 0.00 0.00 0.00 4.94
3926 4028 7.865706 TGATTTCTAAATCCTTGCTCCTAAC 57.134 36.000 11.82 0.00 43.19 2.34
3973 4075 3.610677 GCAACGCAAACCCATAACATAAC 59.389 43.478 0.00 0.00 0.00 1.89
3995 4097 2.879026 CTGATGTCCCATCAGCATTCAG 59.121 50.000 18.27 0.00 39.03 3.02
4003 4105 4.508551 AGCAATTACTGATGTCCCATCA 57.491 40.909 6.72 6.72 0.00 3.07
4054 4159 4.872124 CAGATGCACAGTTATGCTACTCAA 59.128 41.667 0.00 0.00 46.28 3.02
4212 4339 6.286240 TCATAGATGTAGCAGTGTTCAGTT 57.714 37.500 0.00 0.00 0.00 3.16
4213 4340 5.921962 TCATAGATGTAGCAGTGTTCAGT 57.078 39.130 0.00 0.00 0.00 3.41
4214 4341 5.521735 GGTTCATAGATGTAGCAGTGTTCAG 59.478 44.000 0.00 0.00 0.00 3.02
4215 4342 5.419542 GGTTCATAGATGTAGCAGTGTTCA 58.580 41.667 0.00 0.00 0.00 3.18
4216 4343 4.811557 GGGTTCATAGATGTAGCAGTGTTC 59.188 45.833 0.00 0.00 0.00 3.18
4217 4344 4.384208 GGGGTTCATAGATGTAGCAGTGTT 60.384 45.833 0.00 0.00 0.00 3.32
4220 4347 2.706190 GGGGGTTCATAGATGTAGCAGT 59.294 50.000 1.60 0.00 0.00 4.40
4221 4348 3.409026 GGGGGTTCATAGATGTAGCAG 57.591 52.381 1.60 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.