Multiple sequence alignment - TraesCS4B01G353900

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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 TraesCS4B01G353900 chr4B 100.000 2333 0 0 1 2333 645456882 645459214 0.000000e+00 4309
1 TraesCS4B01G353900 chr4B 84.810 237 36 0 1088 1324 599399809 599399573 3.000000e-59 239
2 TraesCS4B01G353900 chr4B 98.198 111 2 0 1 111 660751786 660751676 6.580000e-46 195
3 TraesCS4B01G353900 chr5A 86.160 1409 125 38 935 2316 682617697 682616332 0.000000e+00 1458
4 TraesCS4B01G353900 chr5A 87.919 745 57 11 113 839 682618480 682617751 0.000000e+00 846
5 TraesCS4B01G353900 chr4D 93.121 596 29 5 939 1526 501507568 501508159 0.000000e+00 863
6 TraesCS4B01G353900 chr4D 93.774 530 23 3 319 839 501506991 501507519 0.000000e+00 787
7 TraesCS4B01G353900 chr4D 82.396 676 87 21 1658 2320 501508410 501509066 5.630000e-156 560
8 TraesCS4B01G353900 chr4D 83.636 220 25 5 109 322 501502836 501503050 1.830000e-46 196
9 TraesCS4B01G353900 chr4D 79.060 234 28 11 1088 1321 474916382 474916594 8.690000e-30 141
10 TraesCS4B01G353900 chr4D 79.703 202 31 7 1624 1819 475123936 475123739 1.120000e-28 137
11 TraesCS4B01G353900 chr2B 82.492 297 43 5 1025 1321 100024761 100025048 3.850000e-63 252
12 TraesCS4B01G353900 chr2B 97.414 116 2 1 1 116 679893824 679893710 1.830000e-46 196
13 TraesCS4B01G353900 chr2B 98.198 111 2 0 1 111 31429567 31429677 6.580000e-46 195
14 TraesCS4B01G353900 chr2B 98.198 111 2 0 1 111 793726044 793725934 6.580000e-46 195
15 TraesCS4B01G353900 chr2B 95.122 123 4 2 1 123 741715686 741715806 2.370000e-45 193
16 TraesCS4B01G353900 chr4A 85.654 237 34 0 1088 1324 681182631 681182395 1.380000e-62 250
17 TraesCS4B01G353900 chr2D 82.869 251 43 0 1074 1324 17025149 17024899 2.330000e-55 226
18 TraesCS4B01G353900 chr2A 82.845 239 31 6 1088 1321 18414211 18414444 3.040000e-49 206
19 TraesCS4B01G353900 chr6B 98.230 113 2 0 1 113 126924722 126924834 5.090000e-47 198
20 TraesCS4B01G353900 chr1B 97.436 117 2 1 1 117 3245398 3245513 5.090000e-47 198
21 TraesCS4B01G353900 chr1B 78.307 189 38 3 1663 1850 233148554 233148368 4.070000e-23 119
22 TraesCS4B01G353900 chr7B 98.198 111 2 0 1 111 142778155 142778265 6.580000e-46 195
23 TraesCS4B01G353900 chr7B 83.041 171 26 3 1680 1850 75890062 75889895 4.020000e-33 152
24 TraesCS4B01G353900 chr7A 98.198 111 2 0 1 111 6649345 6649235 6.580000e-46 195
25 TraesCS4B01G353900 chr7A 78.723 188 38 2 1663 1850 161437287 161437102 8.750000e-25 124
26 TraesCS4B01G353900 chr3D 79.253 241 39 10 1613 1850 106683393 106683161 8.630000e-35 158
27 TraesCS4B01G353900 chr3D 80.874 183 27 5 1629 1808 493038333 493038510 1.120000e-28 137
28 TraesCS4B01G353900 chr1A 82.993 147 22 3 1674 1819 50002798 50002654 1.880000e-26 130
29 TraesCS4B01G353900 chr5D 80.357 168 29 4 1690 1857 288191024 288190861 8.750000e-25 124


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 TraesCS4B01G353900 chr4B 645456882 645459214 2332 False 4309.0 4309 100.00000 1 2333 1 chr4B.!!$F1 2332
1 TraesCS4B01G353900 chr5A 682616332 682618480 2148 True 1152.0 1458 87.03950 113 2316 2 chr5A.!!$R1 2203
2 TraesCS4B01G353900 chr4D 501502836 501509066 6230 False 601.5 863 88.23175 109 2320 4 chr4D.!!$F2 2211

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
877 4845 0.099968 TGATCGTGACGTCGAATCCC 59.9 55.0 11.62 0.0 42.99 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 6162 1.394917 CTCATGACCAGCAAAGTACGC 59.605 52.381 0.0 0.0 0.0 4.42 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
27 28 9.647918 TGATATGATACTACACCTTCTCTTTCT 57.352 33.333 0.00 0.00 0.00 2.52
30 31 7.776618 TGATACTACACCTTCTCTTTCTTCA 57.223 36.000 0.00 0.00 0.00 3.02
31 32 8.367660 TGATACTACACCTTCTCTTTCTTCAT 57.632 34.615 0.00 0.00 0.00 2.57
32 33 8.816894 TGATACTACACCTTCTCTTTCTTCATT 58.183 33.333 0.00 0.00 0.00 2.57
33 34 9.660180 GATACTACACCTTCTCTTTCTTCATTT 57.340 33.333 0.00 0.00 0.00 2.32
38 39 7.597386 ACACCTTCTCTTTCTTCATTTAATGC 58.403 34.615 0.00 0.00 0.00 3.56
39 40 7.449704 ACACCTTCTCTTTCTTCATTTAATGCT 59.550 33.333 0.00 0.00 0.00 3.79
40 41 8.950210 CACCTTCTCTTTCTTCATTTAATGCTA 58.050 33.333 0.00 0.00 0.00 3.49
41 42 9.692325 ACCTTCTCTTTCTTCATTTAATGCTAT 57.308 29.630 0.00 0.00 0.00 2.97
42 43 9.947669 CCTTCTCTTTCTTCATTTAATGCTATG 57.052 33.333 0.00 0.00 0.00 2.23
45 46 9.671279 TCTCTTTCTTCATTTAATGCTATGACA 57.329 29.630 0.00 0.00 30.89 3.58
46 47 9.713740 CTCTTTCTTCATTTAATGCTATGACAC 57.286 33.333 0.00 0.00 30.89 3.67
47 48 8.677300 TCTTTCTTCATTTAATGCTATGACACC 58.323 33.333 0.00 0.00 30.89 4.16
48 49 8.579850 TTTCTTCATTTAATGCTATGACACCT 57.420 30.769 0.00 0.00 30.89 4.00
49 50 7.792374 TCTTCATTTAATGCTATGACACCTC 57.208 36.000 0.00 0.00 30.89 3.85
50 51 7.337938 TCTTCATTTAATGCTATGACACCTCA 58.662 34.615 0.00 0.00 30.89 3.86
51 52 7.994911 TCTTCATTTAATGCTATGACACCTCAT 59.005 33.333 0.00 0.00 40.47 2.90
52 53 7.734924 TCATTTAATGCTATGACACCTCATC 57.265 36.000 0.00 0.00 38.21 2.92
53 54 7.281841 TCATTTAATGCTATGACACCTCATCA 58.718 34.615 0.00 0.00 38.21 3.07
54 55 7.774625 TCATTTAATGCTATGACACCTCATCAA 59.225 33.333 0.00 0.00 38.21 2.57
55 56 7.936496 TTTAATGCTATGACACCTCATCAAA 57.064 32.000 0.00 0.00 38.21 2.69
56 57 7.936496 TTAATGCTATGACACCTCATCAAAA 57.064 32.000 0.00 0.00 38.21 2.44
57 58 8.523915 TTAATGCTATGACACCTCATCAAAAT 57.476 30.769 0.00 0.00 38.21 1.82
58 59 7.414222 AATGCTATGACACCTCATCAAAATT 57.586 32.000 0.00 0.00 38.21 1.82
59 60 6.198650 TGCTATGACACCTCATCAAAATTG 57.801 37.500 0.00 0.00 38.21 2.32
60 61 5.039333 GCTATGACACCTCATCAAAATTGC 58.961 41.667 0.00 0.00 38.21 3.56
61 62 3.940209 TGACACCTCATCAAAATTGCC 57.060 42.857 0.00 0.00 0.00 4.52
62 63 3.499338 TGACACCTCATCAAAATTGCCT 58.501 40.909 0.00 0.00 0.00 4.75
63 64 4.661222 TGACACCTCATCAAAATTGCCTA 58.339 39.130 0.00 0.00 0.00 3.93
64 65 4.701651 TGACACCTCATCAAAATTGCCTAG 59.298 41.667 0.00 0.00 0.00 3.02
65 66 4.666512 ACACCTCATCAAAATTGCCTAGT 58.333 39.130 0.00 0.00 0.00 2.57
66 67 5.079643 ACACCTCATCAAAATTGCCTAGTT 58.920 37.500 0.00 0.00 0.00 2.24
67 68 5.047802 ACACCTCATCAAAATTGCCTAGTTG 60.048 40.000 0.00 0.00 0.00 3.16
68 69 5.183713 CACCTCATCAAAATTGCCTAGTTGA 59.816 40.000 0.00 0.00 34.68 3.18
69 70 5.183904 ACCTCATCAAAATTGCCTAGTTGAC 59.816 40.000 0.00 0.00 33.09 3.18
70 71 5.183713 CCTCATCAAAATTGCCTAGTTGACA 59.816 40.000 0.00 0.00 33.09 3.58
71 72 6.127535 CCTCATCAAAATTGCCTAGTTGACAT 60.128 38.462 0.00 0.00 33.09 3.06
72 73 6.623486 TCATCAAAATTGCCTAGTTGACATG 58.377 36.000 0.00 0.00 33.09 3.21
73 74 4.808558 TCAAAATTGCCTAGTTGACATGC 58.191 39.130 0.00 0.00 0.00 4.06
74 75 4.280425 TCAAAATTGCCTAGTTGACATGCA 59.720 37.500 0.00 0.00 0.00 3.96
75 76 5.047164 TCAAAATTGCCTAGTTGACATGCAT 60.047 36.000 0.00 0.00 0.00 3.96
76 77 4.380841 AATTGCCTAGTTGACATGCATG 57.619 40.909 25.09 25.09 0.00 4.06
77 78 2.785540 TGCCTAGTTGACATGCATGA 57.214 45.000 32.75 9.00 0.00 3.07
78 79 3.286329 TGCCTAGTTGACATGCATGAT 57.714 42.857 32.75 16.80 0.00 2.45
79 80 4.420522 TGCCTAGTTGACATGCATGATA 57.579 40.909 32.75 17.43 0.00 2.15
80 81 4.129380 TGCCTAGTTGACATGCATGATAC 58.871 43.478 32.75 23.37 0.00 2.24
81 82 4.141642 TGCCTAGTTGACATGCATGATACT 60.142 41.667 32.75 27.82 0.00 2.12
82 83 5.070313 TGCCTAGTTGACATGCATGATACTA 59.930 40.000 32.75 27.51 0.00 1.82
83 84 5.636965 GCCTAGTTGACATGCATGATACTAG 59.363 44.000 32.31 32.31 36.93 2.57
84 85 5.636965 CCTAGTTGACATGCATGATACTAGC 59.363 44.000 33.00 20.01 36.48 3.42
85 86 5.287674 AGTTGACATGCATGATACTAGCT 57.712 39.130 32.75 16.16 0.00 3.32
86 87 6.410942 AGTTGACATGCATGATACTAGCTA 57.589 37.500 32.75 7.07 0.00 3.32
87 88 7.002250 AGTTGACATGCATGATACTAGCTAT 57.998 36.000 32.75 6.24 0.00 2.97
88 89 6.872547 AGTTGACATGCATGATACTAGCTATG 59.127 38.462 32.75 3.42 0.00 2.23
89 90 6.594788 TGACATGCATGATACTAGCTATGA 57.405 37.500 32.75 0.00 0.00 2.15
90 91 7.179076 TGACATGCATGATACTAGCTATGAT 57.821 36.000 32.75 4.97 0.00 2.45
91 92 8.297470 TGACATGCATGATACTAGCTATGATA 57.703 34.615 32.75 2.03 0.00 2.15
92 93 8.193438 TGACATGCATGATACTAGCTATGATAC 58.807 37.037 32.75 1.74 0.00 2.24
93 94 8.303780 ACATGCATGATACTAGCTATGATACT 57.696 34.615 32.75 0.57 0.00 2.12
94 95 9.413734 ACATGCATGATACTAGCTATGATACTA 57.586 33.333 32.75 0.00 0.00 1.82
95 96 9.676195 CATGCATGATACTAGCTATGATACTAC 57.324 37.037 22.59 0.00 0.00 2.73
96 97 8.226819 TGCATGATACTAGCTATGATACTACC 57.773 38.462 0.00 0.00 0.00 3.18
97 98 7.834181 TGCATGATACTAGCTATGATACTACCA 59.166 37.037 0.00 0.00 0.00 3.25
98 99 8.855110 GCATGATACTAGCTATGATACTACCAT 58.145 37.037 0.00 0.00 0.00 3.55
104 105 8.266392 ACTAGCTATGATACTACCATTACGAC 57.734 38.462 0.00 0.00 0.00 4.34
105 106 6.512342 AGCTATGATACTACCATTACGACC 57.488 41.667 0.00 0.00 0.00 4.79
106 107 6.008331 AGCTATGATACTACCATTACGACCA 58.992 40.000 0.00 0.00 0.00 4.02
107 108 6.151312 AGCTATGATACTACCATTACGACCAG 59.849 42.308 0.00 0.00 0.00 4.00
132 133 5.450453 CTCAAGACTTGGTCTATCCCTCTA 58.550 45.833 15.13 0.00 42.59 2.43
137 138 4.208746 ACTTGGTCTATCCCTCTAGTTCG 58.791 47.826 0.00 0.00 34.77 3.95
139 140 4.088056 TGGTCTATCCCTCTAGTTCGAG 57.912 50.000 0.00 0.00 34.77 4.04
208 209 7.256286 TGTTCGTAGTCTATTAGCTTTCCTTC 58.744 38.462 0.00 0.00 0.00 3.46
213 214 5.423886 AGTCTATTAGCTTTCCTTCAGCAC 58.576 41.667 0.00 0.00 39.99 4.40
233 234 3.188460 CACTTTTTATCTGTCGTGTGGGG 59.812 47.826 0.00 0.00 0.00 4.96
240 241 1.695242 TCTGTCGTGTGGGGTTACATT 59.305 47.619 0.00 0.00 32.43 2.71
248 249 4.204799 GTGTGGGGTTACATTCCCTATTC 58.795 47.826 0.00 0.00 44.07 1.75
253 254 4.078805 GGGGTTACATTCCCTATTCCCTTT 60.079 45.833 0.96 0.00 44.07 3.11
262 263 8.615705 ACATTCCCTATTCCCTTTATTATCCTC 58.384 37.037 0.00 0.00 0.00 3.71
266 267 6.418946 CCTATTCCCTTTATTATCCTCTGGC 58.581 44.000 0.00 0.00 0.00 4.85
269 270 4.307259 TCCCTTTATTATCCTCTGGCTGT 58.693 43.478 0.00 0.00 0.00 4.40
271 272 5.307196 TCCCTTTATTATCCTCTGGCTGTAC 59.693 44.000 0.00 0.00 0.00 2.90
307 314 2.668632 CTGCGGCCCCTGTTCTAA 59.331 61.111 0.00 0.00 0.00 2.10
308 315 1.450312 CTGCGGCCCCTGTTCTAAG 60.450 63.158 0.00 0.00 0.00 2.18
345 4296 4.944962 TTCAAGCAACCGACATAATCTG 57.055 40.909 0.00 0.00 0.00 2.90
403 4354 5.686841 TCACAATCAAGCAAAGAAATGAACG 59.313 36.000 0.00 0.00 0.00 3.95
415 4370 7.168135 GCAAAGAAATGAACGAAAGAATTGTCT 59.832 33.333 0.00 0.00 34.72 3.41
440 4395 1.826340 TACAGCTGTGCGGTGGTCAT 61.826 55.000 29.57 0.00 45.25 3.06
443 4398 2.347114 CTGTGCGGTGGTCATGGA 59.653 61.111 0.00 0.00 0.00 3.41
452 4407 1.832998 GGTGGTCATGGAAAATGGCAT 59.167 47.619 0.00 0.00 0.00 4.40
586 4552 2.796651 GCAAAGAGGCGCCAGATG 59.203 61.111 31.54 21.67 0.00 2.90
587 4553 2.042831 GCAAAGAGGCGCCAGATGT 61.043 57.895 31.54 7.13 0.00 3.06
595 4561 0.249868 GGCGCCAGATGTATGCACTA 60.250 55.000 24.80 0.00 0.00 2.74
660 4626 1.005037 CAAGTACAGAGCACCGGCA 60.005 57.895 0.00 0.00 44.61 5.69
684 4652 0.180406 AACGGCCAGACTTGACAACT 59.820 50.000 2.24 0.00 0.00 3.16
697 4665 1.005630 ACAACTCTCTGCTGCGTCC 60.006 57.895 0.00 0.00 0.00 4.79
839 4807 3.677121 CCGAATAGGCAAATCATCGAGAG 59.323 47.826 0.00 0.00 32.38 3.20
840 4808 3.122613 CGAATAGGCAAATCATCGAGAGC 59.877 47.826 0.00 0.00 32.38 4.09
841 4809 3.758755 ATAGGCAAATCATCGAGAGCA 57.241 42.857 0.00 0.00 0.00 4.26
843 4811 2.219458 AGGCAAATCATCGAGAGCATG 58.781 47.619 0.00 0.00 0.00 4.06
844 4812 1.334779 GGCAAATCATCGAGAGCATGC 60.335 52.381 10.51 10.51 34.26 4.06
846 4814 2.602456 GCAAATCATCGAGAGCATGCAG 60.602 50.000 21.98 8.28 34.80 4.41
866 4834 4.492160 GTCGCCGCCTGATCGTGA 62.492 66.667 0.00 0.00 0.00 4.35
867 4835 4.492160 TCGCCGCCTGATCGTGAC 62.492 66.667 0.00 0.00 0.00 3.67
869 4837 4.796231 GCCGCCTGATCGTGACGT 62.796 66.667 4.40 0.00 0.00 4.34
870 4838 2.579787 CCGCCTGATCGTGACGTC 60.580 66.667 9.11 9.11 0.00 4.34
871 4839 2.944557 CGCCTGATCGTGACGTCG 60.945 66.667 11.62 0.00 0.00 5.12
872 4840 2.483745 GCCTGATCGTGACGTCGA 59.516 61.111 11.62 6.43 43.86 4.20
873 4841 1.154093 GCCTGATCGTGACGTCGAA 60.154 57.895 11.62 0.00 42.99 3.71
874 4842 0.525668 GCCTGATCGTGACGTCGAAT 60.526 55.000 11.62 3.91 42.99 3.34
875 4843 1.467875 CCTGATCGTGACGTCGAATC 58.532 55.000 11.62 13.30 42.99 2.52
876 4844 1.467875 CTGATCGTGACGTCGAATCC 58.532 55.000 11.62 0.67 42.99 3.01
877 4845 0.099968 TGATCGTGACGTCGAATCCC 59.900 55.000 11.62 0.00 42.99 3.85
878 4846 0.928908 GATCGTGACGTCGAATCCCG 60.929 60.000 11.62 6.19 42.99 5.14
879 4847 1.371337 ATCGTGACGTCGAATCCCGA 61.371 55.000 11.62 11.15 46.35 5.14
894 4862 1.750930 CCGATCCTAGCTGGTGCAT 59.249 57.895 0.00 0.00 42.74 3.96
896 4864 1.344438 CCGATCCTAGCTGGTGCATTA 59.656 52.381 0.00 0.00 42.74 1.90
910 4878 1.299165 CATTAGTCTACCGCGCGCT 60.299 57.895 30.48 18.28 0.00 5.92
911 4879 0.870307 CATTAGTCTACCGCGCGCTT 60.870 55.000 30.48 18.37 0.00 4.68
924 4892 3.554692 CGCTTAACGCTGGCTCCG 61.555 66.667 0.00 0.00 36.13 4.63
925 4893 3.195698 GCTTAACGCTGGCTCCGG 61.196 66.667 0.00 0.00 35.14 5.14
926 4894 3.195698 CTTAACGCTGGCTCCGGC 61.196 66.667 9.64 9.64 44.34 6.13
934 4902 3.965539 CTGGCTCCGGCACCTTGAG 62.966 68.421 13.06 0.00 40.87 3.02
948 4916 6.610741 GCACCTTGAGCCTATATAATATGC 57.389 41.667 0.00 0.00 0.00 3.14
949 4917 6.115446 GCACCTTGAGCCTATATAATATGCA 58.885 40.000 0.00 0.00 0.00 3.96
950 4918 6.037610 GCACCTTGAGCCTATATAATATGCAC 59.962 42.308 0.00 0.00 0.00 4.57
951 4919 7.105588 CACCTTGAGCCTATATAATATGCACA 58.894 38.462 0.00 0.00 0.00 4.57
952 4920 7.065085 CACCTTGAGCCTATATAATATGCACAC 59.935 40.741 0.00 0.00 0.00 3.82
953 4921 6.540189 CCTTGAGCCTATATAATATGCACACC 59.460 42.308 0.00 0.00 0.00 4.16
954 4922 5.989477 TGAGCCTATATAATATGCACACCC 58.011 41.667 0.00 0.00 0.00 4.61
955 4923 5.104527 TGAGCCTATATAATATGCACACCCC 60.105 44.000 0.00 0.00 0.00 4.95
956 4924 4.127171 GCCTATATAATATGCACACCCCG 58.873 47.826 0.00 0.00 0.00 5.73
957 4925 4.127171 CCTATATAATATGCACACCCCGC 58.873 47.826 0.00 0.00 0.00 6.13
958 4926 2.483014 TATAATATGCACACCCCGCC 57.517 50.000 0.00 0.00 0.00 6.13
959 4927 0.251165 ATAATATGCACACCCCGCCC 60.251 55.000 0.00 0.00 0.00 6.13
1008 4981 1.691434 GCTAGAGAAGGGATGTCTGGG 59.309 57.143 0.00 0.00 33.01 4.45
1242 5215 1.075970 CGACCTCATCTCCCTCCCA 60.076 63.158 0.00 0.00 0.00 4.37
1243 5216 0.687757 CGACCTCATCTCCCTCCCAA 60.688 60.000 0.00 0.00 0.00 4.12
1299 5272 1.285023 CGTCGTCCTCAAGAACCGT 59.715 57.895 0.00 0.00 0.00 4.83
1328 5301 2.412037 AAGGTCGTCGACGTCCCAAC 62.412 60.000 38.26 27.69 46.16 3.77
1374 5347 2.066262 TCAACGTCGCCTTTGATCTTC 58.934 47.619 0.00 0.00 0.00 2.87
1398 5375 4.584327 TGCGACTATGTGTGTGCTATAT 57.416 40.909 0.00 0.00 0.00 0.86
1517 5500 3.766676 TTGCAATTGTACGTGTGTGTT 57.233 38.095 7.40 0.00 0.00 3.32
1585 5730 2.758009 GCACATTTGCTGGTCATGTTT 58.242 42.857 0.00 0.00 46.17 2.83
1586 5731 3.911868 GCACATTTGCTGGTCATGTTTA 58.088 40.909 0.00 0.00 46.17 2.01
1587 5732 4.497300 GCACATTTGCTGGTCATGTTTAT 58.503 39.130 0.00 0.00 46.17 1.40
1588 5733 4.563976 GCACATTTGCTGGTCATGTTTATC 59.436 41.667 0.00 0.00 46.17 1.75
1589 5734 5.712004 CACATTTGCTGGTCATGTTTATCA 58.288 37.500 0.00 0.00 0.00 2.15
1590 5735 6.334989 CACATTTGCTGGTCATGTTTATCAT 58.665 36.000 0.00 0.00 37.22 2.45
1591 5736 6.814644 CACATTTGCTGGTCATGTTTATCATT 59.185 34.615 0.00 0.00 34.09 2.57
1592 5737 6.814644 ACATTTGCTGGTCATGTTTATCATTG 59.185 34.615 0.00 0.00 34.09 2.82
1593 5738 4.374843 TGCTGGTCATGTTTATCATTGC 57.625 40.909 0.00 0.00 34.09 3.56
1594 5739 3.762823 TGCTGGTCATGTTTATCATTGCA 59.237 39.130 0.00 0.00 34.09 4.08
1595 5740 4.220163 TGCTGGTCATGTTTATCATTGCAA 59.780 37.500 0.00 0.00 34.09 4.08
1596 5741 5.105269 TGCTGGTCATGTTTATCATTGCAAT 60.105 36.000 5.99 5.99 34.09 3.56
1597 5742 5.813672 GCTGGTCATGTTTATCATTGCAATT 59.186 36.000 9.83 0.00 34.09 2.32
1615 5760 5.991606 TGCAATTCAGACAGCCATATACTAC 59.008 40.000 0.00 0.00 0.00 2.73
1616 5761 5.409826 GCAATTCAGACAGCCATATACTACC 59.590 44.000 0.00 0.00 0.00 3.18
1617 5762 6.742644 GCAATTCAGACAGCCATATACTACCT 60.743 42.308 0.00 0.00 0.00 3.08
1619 5764 5.326283 TCAGACAGCCATATACTACCTCT 57.674 43.478 0.00 0.00 0.00 3.69
1620 5765 6.449830 TCAGACAGCCATATACTACCTCTA 57.550 41.667 0.00 0.00 0.00 2.43
1621 5766 7.033782 TCAGACAGCCATATACTACCTCTAT 57.966 40.000 0.00 0.00 0.00 1.98
1622 5767 8.159229 TCAGACAGCCATATACTACCTCTATA 57.841 38.462 0.00 0.00 0.00 1.31
1629 5774 6.208994 GCCATATACTACCTCTATAATCCGGG 59.791 46.154 0.00 0.00 0.00 5.73
1636 5781 7.759607 ACTACCTCTATAATCCGGGTTTACTA 58.240 38.462 4.62 0.00 0.00 1.82
1639 5784 6.718912 ACCTCTATAATCCGGGTTTACTAGTC 59.281 42.308 4.62 0.00 0.00 2.59
1648 5793 3.431766 CGGGTTTACTAGTCCCCTCATTG 60.432 52.174 18.22 4.12 38.09 2.82
1649 5794 3.542648 GGTTTACTAGTCCCCTCATTGC 58.457 50.000 0.00 0.00 0.00 3.56
1650 5795 3.200165 GGTTTACTAGTCCCCTCATTGCT 59.800 47.826 0.00 0.00 0.00 3.91
1654 5799 4.965200 ACTAGTCCCCTCATTGCTAATC 57.035 45.455 0.00 0.00 0.00 1.75
1660 5805 7.574021 AGTCCCCTCATTGCTAATCATATTA 57.426 36.000 0.00 0.00 0.00 0.98
1661 5806 7.988937 AGTCCCCTCATTGCTAATCATATTAA 58.011 34.615 0.00 0.00 0.00 1.40
1662 5807 8.618385 AGTCCCCTCATTGCTAATCATATTAAT 58.382 33.333 0.00 0.00 0.00 1.40
1663 5808 9.247861 GTCCCCTCATTGCTAATCATATTAATT 57.752 33.333 0.00 0.00 0.00 1.40
1664 5809 9.827198 TCCCCTCATTGCTAATCATATTAATTT 57.173 29.630 0.00 0.00 0.00 1.82
1733 5878 8.846943 AATAATATCATTGGACGCTACATTCA 57.153 30.769 0.00 0.00 0.00 2.57
1734 5879 8.846943 ATAATATCATTGGACGCTACATTCAA 57.153 30.769 0.00 0.00 0.00 2.69
1735 5880 7.566760 AATATCATTGGACGCTACATTCAAA 57.433 32.000 0.00 0.00 0.00 2.69
1736 5881 7.750229 ATATCATTGGACGCTACATTCAAAT 57.250 32.000 0.00 0.00 0.00 2.32
1737 5882 5.233957 TCATTGGACGCTACATTCAAATG 57.766 39.130 1.20 1.20 42.10 2.32
1804 5949 6.509418 TTCTAGCCAAATGTATGGTCAAAC 57.491 37.500 0.00 0.00 42.75 2.93
1808 5953 6.909550 AGCCAAATGTATGGTCAAACTTTA 57.090 33.333 0.00 0.00 42.75 1.85
1819 5964 9.414295 GTATGGTCAAACTTTAACCCAAAATAC 57.586 33.333 0.00 0.00 31.78 1.89
1822 5967 5.403166 GTCAAACTTTAACCCAAAATACGGC 59.597 40.000 0.00 0.00 0.00 5.68
1824 5969 2.488937 ACTTTAACCCAAAATACGGCGG 59.511 45.455 13.24 0.00 0.00 6.13
1825 5970 0.810016 TTAACCCAAAATACGGCGGC 59.190 50.000 13.24 0.00 0.00 6.53
1826 5971 1.367599 TAACCCAAAATACGGCGGCG 61.368 55.000 31.06 31.06 0.00 6.46
1827 5972 3.883180 CCCAAAATACGGCGGCGG 61.883 66.667 35.05 17.25 0.00 6.13
1838 5983 1.525306 GGCGGCGGCTAATAAACCT 60.525 57.895 27.22 0.00 39.81 3.50
1840 5985 0.812412 GCGGCGGCTAATAAACCTGA 60.812 55.000 9.78 0.00 35.83 3.86
1844 5989 2.293399 GGCGGCTAATAAACCTGAATGG 59.707 50.000 0.00 0.00 42.93 3.16
1924 6076 9.672673 AAATGATAACAAGTCATAACTAGCACT 57.327 29.630 0.00 0.00 35.35 4.40
1940 6092 8.846423 AACTAGCACTAATAGGGATATATGCT 57.154 34.615 4.09 0.00 44.06 3.79
1970 6122 7.553504 ACATATATAGCATACTGTTGGACCA 57.446 36.000 0.00 0.00 0.00 4.02
1973 6125 2.315925 AGCATACTGTTGGACCATCG 57.684 50.000 0.00 0.00 0.00 3.84
1975 6127 1.933853 GCATACTGTTGGACCATCGTC 59.066 52.381 0.00 0.00 38.38 4.20
1976 6128 2.676750 GCATACTGTTGGACCATCGTCA 60.677 50.000 0.00 0.00 41.13 4.35
1984 6136 0.604511 GGACCATCGTCAAAACCGGT 60.605 55.000 0.00 0.00 41.13 5.28
1995 6147 3.989817 GTCAAAACCGGTTGTACGTATCT 59.010 43.478 23.08 0.00 0.00 1.98
1997 6149 2.549633 AACCGGTTGTACGTATCTCG 57.450 50.000 21.56 1.27 46.00 4.04
2023 6176 6.453643 CTATTACATAGCGTACTTTGCTGG 57.546 41.667 4.23 0.10 43.85 4.85
2029 6182 1.001974 AGCGTACTTTGCTGGTCATGA 59.998 47.619 0.00 0.00 42.14 3.07
2032 6185 3.067106 CGTACTTTGCTGGTCATGAGTT 58.933 45.455 0.00 0.00 0.00 3.01
2034 6187 3.498774 ACTTTGCTGGTCATGAGTTCT 57.501 42.857 0.00 0.00 0.00 3.01
2042 6195 5.189180 GCTGGTCATGAGTTCTCCTATTTT 58.811 41.667 0.00 0.00 0.00 1.82
2052 6205 9.915629 ATGAGTTCTCCTATTTTCATATACGTC 57.084 33.333 0.00 0.00 0.00 4.34
2111 6276 8.384607 TGTTATGCAATGCGGATTAAATAGTA 57.615 30.769 0.40 0.00 0.00 1.82
2167 6332 5.538053 TCCACTAATTTTCTTGGCATGTTCA 59.462 36.000 0.00 0.00 0.00 3.18
2186 6351 3.577667 TCAGCTTTTGATTTCCATTGCG 58.422 40.909 0.00 0.00 0.00 4.85
2191 6356 2.100216 GATTTCCATTGCGCGCGT 59.900 55.556 32.35 15.37 0.00 6.01
2192 6357 1.514014 GATTTCCATTGCGCGCGTT 60.514 52.632 32.35 13.74 0.00 4.84
2194 6359 1.343510 ATTTCCATTGCGCGCGTTTG 61.344 50.000 32.35 23.83 0.00 2.93
2241 6406 7.254151 CGGTTCTGCTAAGATAGAAGTTTAAGC 60.254 40.741 0.00 0.00 33.90 3.09
2316 6481 9.989296 ATATTAGAGCAATCCTATCAGAGTAGT 57.011 33.333 0.00 0.00 0.00 2.73
2318 6483 5.076873 AGAGCAATCCTATCAGAGTAGTCC 58.923 45.833 0.00 0.00 0.00 3.85
2319 6484 4.809193 AGCAATCCTATCAGAGTAGTCCA 58.191 43.478 0.00 0.00 0.00 4.02
2320 6485 4.586841 AGCAATCCTATCAGAGTAGTCCAC 59.413 45.833 0.00 0.00 0.00 4.02
2321 6486 4.586841 GCAATCCTATCAGAGTAGTCCACT 59.413 45.833 0.00 0.00 41.47 4.00
2322 6487 5.770663 GCAATCCTATCAGAGTAGTCCACTA 59.229 44.000 0.00 0.00 37.72 2.74
2323 6488 6.435904 GCAATCCTATCAGAGTAGTCCACTAT 59.564 42.308 0.00 0.00 37.72 2.12
2324 6489 7.612244 GCAATCCTATCAGAGTAGTCCACTATA 59.388 40.741 0.00 0.00 37.72 1.31
2325 6490 9.521841 CAATCCTATCAGAGTAGTCCACTATAA 57.478 37.037 0.00 0.00 37.72 0.98
2326 6491 9.747898 AATCCTATCAGAGTAGTCCACTATAAG 57.252 37.037 0.00 0.00 37.72 1.73
2327 6492 8.507582 TCCTATCAGAGTAGTCCACTATAAGA 57.492 38.462 0.00 0.00 37.72 2.10
2328 6493 8.946248 TCCTATCAGAGTAGTCCACTATAAGAA 58.054 37.037 0.00 0.00 37.72 2.52
2329 6494 9.747898 CCTATCAGAGTAGTCCACTATAAGAAT 57.252 37.037 0.00 0.00 37.72 2.40
2332 6497 8.824756 TCAGAGTAGTCCACTATAAGAATTGT 57.175 34.615 0.00 0.00 37.72 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.647918 AGAAAGAGAAGGTGTAGTATCATATCA 57.352 33.333 0.00 0.00 0.00 2.15
4 5 9.475620 TGAAGAAAGAGAAGGTGTAGTATCATA 57.524 33.333 0.00 0.00 0.00 2.15
5 6 8.367660 TGAAGAAAGAGAAGGTGTAGTATCAT 57.632 34.615 0.00 0.00 0.00 2.45
6 7 7.776618 TGAAGAAAGAGAAGGTGTAGTATCA 57.223 36.000 0.00 0.00 0.00 2.15
7 8 9.660180 AAATGAAGAAAGAGAAGGTGTAGTATC 57.340 33.333 0.00 0.00 0.00 2.24
12 13 8.730680 GCATTAAATGAAGAAAGAGAAGGTGTA 58.269 33.333 0.00 0.00 0.00 2.90
13 14 7.449704 AGCATTAAATGAAGAAAGAGAAGGTGT 59.550 33.333 0.00 0.00 0.00 4.16
14 15 7.824672 AGCATTAAATGAAGAAAGAGAAGGTG 58.175 34.615 0.00 0.00 0.00 4.00
15 16 9.692325 ATAGCATTAAATGAAGAAAGAGAAGGT 57.308 29.630 0.00 0.00 0.00 3.50
16 17 9.947669 CATAGCATTAAATGAAGAAAGAGAAGG 57.052 33.333 0.00 0.00 0.00 3.46
19 20 9.671279 TGTCATAGCATTAAATGAAGAAAGAGA 57.329 29.630 0.00 0.00 34.06 3.10
20 21 9.713740 GTGTCATAGCATTAAATGAAGAAAGAG 57.286 33.333 0.00 0.00 34.06 2.85
21 22 8.677300 GGTGTCATAGCATTAAATGAAGAAAGA 58.323 33.333 0.00 0.00 34.06 2.52
22 23 8.680903 AGGTGTCATAGCATTAAATGAAGAAAG 58.319 33.333 0.00 0.00 34.06 2.62
23 24 8.579850 AGGTGTCATAGCATTAAATGAAGAAA 57.420 30.769 0.00 0.00 34.06 2.52
24 25 7.828717 TGAGGTGTCATAGCATTAAATGAAGAA 59.171 33.333 0.00 0.00 34.06 2.52
25 26 7.337938 TGAGGTGTCATAGCATTAAATGAAGA 58.662 34.615 0.00 0.00 34.06 2.87
26 27 7.558161 TGAGGTGTCATAGCATTAAATGAAG 57.442 36.000 0.00 0.00 34.06 3.02
27 28 7.774625 TGATGAGGTGTCATAGCATTAAATGAA 59.225 33.333 0.00 0.00 43.92 2.57
28 29 7.281841 TGATGAGGTGTCATAGCATTAAATGA 58.718 34.615 0.00 0.00 43.92 2.57
29 30 7.500720 TGATGAGGTGTCATAGCATTAAATG 57.499 36.000 0.00 0.00 43.92 2.32
30 31 8.523915 TTTGATGAGGTGTCATAGCATTAAAT 57.476 30.769 0.00 0.00 43.92 1.40
31 32 7.936496 TTTGATGAGGTGTCATAGCATTAAA 57.064 32.000 0.00 0.00 43.92 1.52
32 33 7.936496 TTTTGATGAGGTGTCATAGCATTAA 57.064 32.000 0.00 0.00 43.92 1.40
33 34 8.407832 CAATTTTGATGAGGTGTCATAGCATTA 58.592 33.333 0.00 0.00 43.92 1.90
34 35 7.262772 CAATTTTGATGAGGTGTCATAGCATT 58.737 34.615 0.00 0.00 43.92 3.56
35 36 6.682113 GCAATTTTGATGAGGTGTCATAGCAT 60.682 38.462 0.00 0.00 43.92 3.79
36 37 5.393352 GCAATTTTGATGAGGTGTCATAGCA 60.393 40.000 0.00 0.00 43.92 3.49
37 38 5.039333 GCAATTTTGATGAGGTGTCATAGC 58.961 41.667 0.00 0.00 43.92 2.97
38 39 5.359009 AGGCAATTTTGATGAGGTGTCATAG 59.641 40.000 0.00 0.00 43.92 2.23
39 40 5.263599 AGGCAATTTTGATGAGGTGTCATA 58.736 37.500 0.00 0.00 43.92 2.15
40 41 4.091549 AGGCAATTTTGATGAGGTGTCAT 58.908 39.130 0.00 0.00 46.75 3.06
41 42 3.499338 AGGCAATTTTGATGAGGTGTCA 58.501 40.909 0.00 0.00 37.02 3.58
42 43 4.702131 ACTAGGCAATTTTGATGAGGTGTC 59.298 41.667 0.00 0.00 0.00 3.67
43 44 4.666512 ACTAGGCAATTTTGATGAGGTGT 58.333 39.130 0.00 0.00 0.00 4.16
44 45 5.183713 TCAACTAGGCAATTTTGATGAGGTG 59.816 40.000 0.00 0.00 0.00 4.00
45 46 5.183904 GTCAACTAGGCAATTTTGATGAGGT 59.816 40.000 0.00 0.00 30.96 3.85
46 47 5.183713 TGTCAACTAGGCAATTTTGATGAGG 59.816 40.000 0.00 0.00 30.96 3.86
47 48 6.258230 TGTCAACTAGGCAATTTTGATGAG 57.742 37.500 0.00 0.00 30.96 2.90
48 49 6.623486 CATGTCAACTAGGCAATTTTGATGA 58.377 36.000 0.00 0.00 34.09 2.92
49 50 5.290158 GCATGTCAACTAGGCAATTTTGATG 59.710 40.000 0.00 0.00 34.09 3.07
50 51 5.047164 TGCATGTCAACTAGGCAATTTTGAT 60.047 36.000 0.00 0.00 34.09 2.57
51 52 4.280425 TGCATGTCAACTAGGCAATTTTGA 59.720 37.500 0.00 0.00 34.09 2.69
52 53 4.558178 TGCATGTCAACTAGGCAATTTTG 58.442 39.130 0.00 0.00 34.09 2.44
53 54 4.870123 TGCATGTCAACTAGGCAATTTT 57.130 36.364 0.00 0.00 34.09 1.82
54 55 4.463539 TCATGCATGTCAACTAGGCAATTT 59.536 37.500 25.43 0.00 38.08 1.82
55 56 4.018490 TCATGCATGTCAACTAGGCAATT 58.982 39.130 25.43 0.00 38.08 2.32
56 57 3.623703 TCATGCATGTCAACTAGGCAAT 58.376 40.909 25.43 0.00 38.08 3.56
57 58 3.070476 TCATGCATGTCAACTAGGCAA 57.930 42.857 25.43 0.00 38.08 4.52
58 59 2.785540 TCATGCATGTCAACTAGGCA 57.214 45.000 25.43 0.00 39.03 4.75
59 60 4.384056 AGTATCATGCATGTCAACTAGGC 58.616 43.478 25.43 7.61 0.00 3.93
60 61 5.636965 GCTAGTATCATGCATGTCAACTAGG 59.363 44.000 34.82 26.24 36.77 3.02
61 62 6.453943 AGCTAGTATCATGCATGTCAACTAG 58.546 40.000 32.98 32.98 37.84 2.57
62 63 6.410942 AGCTAGTATCATGCATGTCAACTA 57.589 37.500 25.43 24.50 0.00 2.24
63 64 5.287674 AGCTAGTATCATGCATGTCAACT 57.712 39.130 25.43 24.67 0.00 3.16
64 65 6.870439 TCATAGCTAGTATCATGCATGTCAAC 59.130 38.462 25.43 19.94 0.00 3.18
65 66 6.996509 TCATAGCTAGTATCATGCATGTCAA 58.003 36.000 25.43 7.83 0.00 3.18
66 67 6.594788 TCATAGCTAGTATCATGCATGTCA 57.405 37.500 25.43 12.19 0.00 3.58
67 68 8.412456 AGTATCATAGCTAGTATCATGCATGTC 58.588 37.037 25.43 16.49 0.00 3.06
68 69 8.303780 AGTATCATAGCTAGTATCATGCATGT 57.696 34.615 25.43 15.34 0.00 3.21
69 70 9.676195 GTAGTATCATAGCTAGTATCATGCATG 57.324 37.037 21.07 21.07 0.00 4.06
70 71 8.855110 GGTAGTATCATAGCTAGTATCATGCAT 58.145 37.037 0.00 0.00 0.00 3.96
71 72 7.834181 TGGTAGTATCATAGCTAGTATCATGCA 59.166 37.037 0.00 0.00 0.00 3.96
72 73 8.226819 TGGTAGTATCATAGCTAGTATCATGC 57.773 38.462 0.00 0.00 0.00 4.06
78 79 9.376075 GTCGTAATGGTAGTATCATAGCTAGTA 57.624 37.037 0.00 0.00 0.00 1.82
79 80 7.336427 GGTCGTAATGGTAGTATCATAGCTAGT 59.664 40.741 0.00 0.00 0.00 2.57
80 81 7.336176 TGGTCGTAATGGTAGTATCATAGCTAG 59.664 40.741 0.00 0.00 0.00 3.42
81 82 7.170277 TGGTCGTAATGGTAGTATCATAGCTA 58.830 38.462 0.00 0.00 0.00 3.32
82 83 6.008331 TGGTCGTAATGGTAGTATCATAGCT 58.992 40.000 0.00 0.00 0.00 3.32
83 84 6.263516 TGGTCGTAATGGTAGTATCATAGC 57.736 41.667 0.00 0.00 0.00 2.97
84 85 6.323266 GCTGGTCGTAATGGTAGTATCATAG 58.677 44.000 0.00 0.00 0.00 2.23
85 86 5.184479 GGCTGGTCGTAATGGTAGTATCATA 59.816 44.000 0.00 0.00 0.00 2.15
86 87 4.021368 GGCTGGTCGTAATGGTAGTATCAT 60.021 45.833 0.00 0.00 0.00 2.45
87 88 3.319972 GGCTGGTCGTAATGGTAGTATCA 59.680 47.826 0.00 0.00 0.00 2.15
88 89 3.573110 AGGCTGGTCGTAATGGTAGTATC 59.427 47.826 0.00 0.00 0.00 2.24
89 90 3.573110 GAGGCTGGTCGTAATGGTAGTAT 59.427 47.826 0.00 0.00 0.00 2.12
90 91 2.954318 GAGGCTGGTCGTAATGGTAGTA 59.046 50.000 0.00 0.00 0.00 1.82
91 92 1.755380 GAGGCTGGTCGTAATGGTAGT 59.245 52.381 0.00 0.00 0.00 2.73
92 93 1.754803 TGAGGCTGGTCGTAATGGTAG 59.245 52.381 0.00 0.00 0.00 3.18
93 94 1.855295 TGAGGCTGGTCGTAATGGTA 58.145 50.000 0.00 0.00 0.00 3.25
94 95 0.981183 TTGAGGCTGGTCGTAATGGT 59.019 50.000 0.00 0.00 0.00 3.55
95 96 1.207089 TCTTGAGGCTGGTCGTAATGG 59.793 52.381 0.00 0.00 0.00 3.16
96 97 2.093973 AGTCTTGAGGCTGGTCGTAATG 60.094 50.000 0.00 0.00 0.00 1.90
97 98 2.180276 AGTCTTGAGGCTGGTCGTAAT 58.820 47.619 0.00 0.00 0.00 1.89
98 99 1.629043 AGTCTTGAGGCTGGTCGTAA 58.371 50.000 0.00 0.00 0.00 3.18
99 100 1.272490 CAAGTCTTGAGGCTGGTCGTA 59.728 52.381 6.76 0.00 0.00 3.43
100 101 0.034059 CAAGTCTTGAGGCTGGTCGT 59.966 55.000 6.76 0.00 0.00 4.34
101 102 0.671781 CCAAGTCTTGAGGCTGGTCG 60.672 60.000 14.42 0.00 0.00 4.79
102 103 0.398318 ACCAAGTCTTGAGGCTGGTC 59.602 55.000 14.42 0.00 0.00 4.02
103 104 0.398318 GACCAAGTCTTGAGGCTGGT 59.602 55.000 14.42 2.56 0.00 4.00
104 105 0.689623 AGACCAAGTCTTGAGGCTGG 59.310 55.000 14.42 0.00 40.28 4.85
105 106 3.431486 GGATAGACCAAGTCTTGAGGCTG 60.431 52.174 14.42 0.00 40.28 4.85
106 107 2.769095 GGATAGACCAAGTCTTGAGGCT 59.231 50.000 14.42 13.22 40.28 4.58
107 108 2.158885 GGGATAGACCAAGTCTTGAGGC 60.159 54.545 14.42 6.49 40.28 4.70
132 133 2.034879 CCACCAATGCGCTCGAACT 61.035 57.895 9.73 0.00 0.00 3.01
137 138 2.434185 TCGACCACCAATGCGCTC 60.434 61.111 9.73 0.00 0.00 5.03
139 140 3.499737 CCTCGACCACCAATGCGC 61.500 66.667 0.00 0.00 0.00 6.09
208 209 4.457810 CACACGACAGATAAAAAGTGCTG 58.542 43.478 0.00 0.00 33.36 4.41
213 214 3.408634 ACCCCACACGACAGATAAAAAG 58.591 45.455 0.00 0.00 0.00 2.27
240 241 6.735704 CCAGAGGATAATAAAGGGAATAGGGA 59.264 42.308 0.00 0.00 0.00 4.20
248 249 4.713792 ACAGCCAGAGGATAATAAAGGG 57.286 45.455 0.00 0.00 0.00 3.95
253 254 6.464322 CCACAATGTACAGCCAGAGGATAATA 60.464 42.308 0.33 0.00 0.00 0.98
260 261 2.479566 ACCACAATGTACAGCCAGAG 57.520 50.000 0.33 0.00 0.00 3.35
262 263 1.541147 CCAACCACAATGTACAGCCAG 59.459 52.381 0.33 0.00 0.00 4.85
266 267 2.744202 GAGAGCCAACCACAATGTACAG 59.256 50.000 0.33 0.00 0.00 2.74
269 270 2.093306 CGAGAGCCAACCACAATGTA 57.907 50.000 0.00 0.00 0.00 2.29
292 299 0.322187 TTTCTTAGAACAGGGGCCGC 60.322 55.000 12.88 12.88 0.00 6.53
345 4296 4.392138 ACAGCTACGCTATTCCAAACTTTC 59.608 41.667 0.00 0.00 36.40 2.62
369 4320 6.492007 TTGCTTGATTGTGAGAGATCTTTC 57.508 37.500 6.31 6.31 0.00 2.62
389 4340 7.165427 ACAATTCTTTCGTTCATTTCTTTGC 57.835 32.000 0.00 0.00 0.00 3.68
415 4370 1.535028 CACCGCACAGCTGTATCAAAA 59.465 47.619 21.20 0.00 0.00 2.44
421 4376 1.826340 ATGACCACCGCACAGCTGTA 61.826 55.000 21.20 0.00 0.00 2.74
440 4395 1.079956 GTGCGCATGCCATTTTCCA 60.080 52.632 15.91 0.00 41.78 3.53
443 4398 2.125991 CGGTGCGCATGCCATTTT 60.126 55.556 15.91 0.00 41.78 1.82
586 4552 0.572590 CGCAAGTCGCTAGTGCATAC 59.427 55.000 0.00 0.00 38.19 2.39
587 4553 0.454196 TCGCAAGTCGCTAGTGCATA 59.546 50.000 0.00 0.00 38.19 3.14
595 4561 2.432456 TCGCAATCGCAAGTCGCT 60.432 55.556 0.00 0.00 39.08 4.93
660 4626 1.071471 CAAGTCTGGCCGTTGAGGT 59.929 57.895 0.00 0.00 43.70 3.85
684 4652 3.443925 CTCCGGACGCAGCAGAGA 61.444 66.667 0.00 0.00 0.00 3.10
849 4817 4.492160 TCACGATCAGGCGGCGAC 62.492 66.667 12.98 8.50 35.12 5.19
850 4818 4.492160 GTCACGATCAGGCGGCGA 62.492 66.667 12.98 4.50 35.12 5.54
852 4820 4.796231 ACGTCACGATCAGGCGGC 62.796 66.667 2.91 0.00 35.12 6.53
853 4821 2.579787 GACGTCACGATCAGGCGG 60.580 66.667 11.55 0.00 35.12 6.13
854 4822 2.844224 TTCGACGTCACGATCAGGCG 62.844 60.000 17.16 7.52 41.82 5.52
855 4823 0.525668 ATTCGACGTCACGATCAGGC 60.526 55.000 17.16 0.00 41.82 4.85
856 4824 1.467875 GATTCGACGTCACGATCAGG 58.532 55.000 17.16 0.00 41.82 3.86
857 4825 1.467875 GGATTCGACGTCACGATCAG 58.532 55.000 17.16 0.00 41.82 2.90
858 4826 0.099968 GGGATTCGACGTCACGATCA 59.900 55.000 17.16 0.00 41.82 2.92
859 4827 0.928908 CGGGATTCGACGTCACGATC 60.929 60.000 17.16 14.08 44.94 3.69
860 4828 1.063649 CGGGATTCGACGTCACGAT 59.936 57.895 17.16 5.69 44.94 3.73
861 4829 2.481919 CGGGATTCGACGTCACGA 59.518 61.111 17.16 5.73 44.94 4.35
862 4830 2.481919 TCGGGATTCGACGTCACG 59.518 61.111 17.16 13.83 43.74 4.35
869 4837 4.739348 ACCAGCTAGGATCGGGATTCGA 62.739 54.545 8.91 0.00 46.61 3.71
870 4838 0.244994 CCAGCTAGGATCGGGATTCG 59.755 60.000 0.00 0.00 41.22 3.34
871 4839 1.001406 CACCAGCTAGGATCGGGATTC 59.999 57.143 8.91 0.00 41.22 2.52
872 4840 1.051812 CACCAGCTAGGATCGGGATT 58.948 55.000 8.91 0.00 41.22 3.01
873 4841 1.476007 GCACCAGCTAGGATCGGGAT 61.476 60.000 8.91 0.00 41.22 3.85
874 4842 2.134287 GCACCAGCTAGGATCGGGA 61.134 63.158 8.91 0.00 41.22 5.14
875 4843 1.762522 ATGCACCAGCTAGGATCGGG 61.763 60.000 8.91 0.00 42.74 5.14
876 4844 0.107456 AATGCACCAGCTAGGATCGG 59.893 55.000 8.91 0.00 42.74 4.18
877 4845 2.036475 ACTAATGCACCAGCTAGGATCG 59.964 50.000 8.91 0.00 42.74 3.69
878 4846 3.323403 AGACTAATGCACCAGCTAGGATC 59.677 47.826 8.91 0.00 42.74 3.36
879 4847 3.312890 AGACTAATGCACCAGCTAGGAT 58.687 45.455 8.91 0.00 42.74 3.24
880 4848 2.752030 AGACTAATGCACCAGCTAGGA 58.248 47.619 8.91 0.00 42.74 2.94
886 4854 1.571919 GCGGTAGACTAATGCACCAG 58.428 55.000 0.00 0.00 0.00 4.00
894 4862 0.451383 TTAAGCGCGCGGTAGACTAA 59.549 50.000 36.14 25.29 0.00 2.24
896 4864 1.515736 GTTAAGCGCGCGGTAGACT 60.516 57.895 36.14 21.96 0.00 3.24
910 4878 4.010224 TGCCGGAGCCAGCGTTAA 62.010 61.111 5.05 0.00 38.69 2.01
911 4879 4.752879 GTGCCGGAGCCAGCGTTA 62.753 66.667 5.05 0.00 38.69 3.18
925 4893 6.037610 GTGCATATTATATAGGCTCAAGGTGC 59.962 42.308 0.00 0.00 0.00 5.01
926 4894 7.065085 GTGTGCATATTATATAGGCTCAAGGTG 59.935 40.741 8.91 0.00 30.97 4.00
928 4896 6.540189 GGTGTGCATATTATATAGGCTCAAGG 59.460 42.308 8.91 0.00 30.97 3.61
929 4897 6.540189 GGGTGTGCATATTATATAGGCTCAAG 59.460 42.308 8.91 0.00 30.97 3.02
931 4899 5.104527 GGGGTGTGCATATTATATAGGCTCA 60.105 44.000 0.00 4.85 0.00 4.26
932 4900 5.368989 GGGGTGTGCATATTATATAGGCTC 58.631 45.833 0.00 2.57 0.00 4.70
934 4902 4.127171 CGGGGTGTGCATATTATATAGGC 58.873 47.826 0.00 0.00 0.00 3.93
936 4904 4.127171 GGCGGGGTGTGCATATTATATAG 58.873 47.826 0.00 0.00 0.00 1.31
937 4905 3.118186 GGGCGGGGTGTGCATATTATATA 60.118 47.826 0.00 0.00 0.00 0.86
938 4906 2.356741 GGGCGGGGTGTGCATATTATAT 60.357 50.000 0.00 0.00 0.00 0.86
939 4907 1.003812 GGGCGGGGTGTGCATATTATA 59.996 52.381 0.00 0.00 0.00 0.98
940 4908 0.251165 GGGCGGGGTGTGCATATTAT 60.251 55.000 0.00 0.00 0.00 1.28
942 4910 2.123897 GGGCGGGGTGTGCATATT 60.124 61.111 0.00 0.00 0.00 1.28
943 4911 4.562425 CGGGCGGGGTGTGCATAT 62.562 66.667 0.00 0.00 0.00 1.78
950 4918 3.282745 CTATCGATCGGGCGGGGTG 62.283 68.421 16.41 0.00 0.00 4.61
951 4919 2.989824 CTATCGATCGGGCGGGGT 60.990 66.667 16.41 0.00 0.00 4.95
952 4920 4.436998 GCTATCGATCGGGCGGGG 62.437 72.222 16.41 1.56 0.00 5.73
953 4921 4.778415 CGCTATCGATCGGGCGGG 62.778 72.222 28.71 17.06 43.25 6.13
957 4925 2.801162 CGCACGCTATCGATCGGG 60.801 66.667 16.41 11.76 39.41 5.14
958 4926 3.461982 GCGCACGCTATCGATCGG 61.462 66.667 16.41 0.47 39.41 4.18
959 4927 2.725815 TGCGCACGCTATCGATCG 60.726 61.111 16.77 9.36 42.51 3.69
1242 5215 1.202770 CGGAACTTGGTGAAGTCCCTT 60.203 52.381 0.00 0.00 41.87 3.95
1243 5216 0.396811 CGGAACTTGGTGAAGTCCCT 59.603 55.000 0.00 0.00 41.87 4.20
1299 5272 0.318699 CGACGACCTTGAAGCTGTCA 60.319 55.000 9.30 0.00 0.00 3.58
1328 5301 5.677319 TGGAGTGGAGTAGGTCAATTAAG 57.323 43.478 0.00 0.00 0.00 1.85
1374 5347 2.814269 AGCACACACATAGTCGCATAG 58.186 47.619 0.00 0.00 0.00 2.23
1398 5375 5.188948 TGCAAAAGCACTTAGGAGGAGTATA 59.811 40.000 0.00 0.00 0.00 1.47
1472 5451 0.319641 TACGGCACACACGTAATGCA 60.320 50.000 16.75 0.00 43.03 3.96
1473 5452 0.368907 CTACGGCACACACGTAATGC 59.631 55.000 8.86 8.86 44.96 3.56
1474 5453 1.705256 ACTACGGCACACACGTAATG 58.295 50.000 0.00 0.00 44.96 1.90
1475 5454 3.574284 TTACTACGGCACACACGTAAT 57.426 42.857 0.00 0.00 44.96 1.89
1517 5500 0.324738 TTCAGGCCCACACAAACCAA 60.325 50.000 0.00 0.00 0.00 3.67
1582 5727 5.517770 GGCTGTCTGAATTGCAATGATAAAC 59.482 40.000 13.82 8.71 0.00 2.01
1585 5730 4.271661 TGGCTGTCTGAATTGCAATGATA 58.728 39.130 13.82 3.71 0.00 2.15
1586 5731 3.093814 TGGCTGTCTGAATTGCAATGAT 58.906 40.909 13.82 0.00 0.00 2.45
1587 5732 2.516906 TGGCTGTCTGAATTGCAATGA 58.483 42.857 13.82 3.03 0.00 2.57
1588 5733 3.520290 ATGGCTGTCTGAATTGCAATG 57.480 42.857 13.82 0.24 0.00 2.82
1589 5734 6.066690 AGTATATGGCTGTCTGAATTGCAAT 58.933 36.000 5.99 5.99 0.00 3.56
1590 5735 5.439721 AGTATATGGCTGTCTGAATTGCAA 58.560 37.500 0.00 0.00 0.00 4.08
1591 5736 5.039920 AGTATATGGCTGTCTGAATTGCA 57.960 39.130 0.00 0.00 0.00 4.08
1592 5737 5.409826 GGTAGTATATGGCTGTCTGAATTGC 59.590 44.000 0.00 0.00 0.00 3.56
1593 5738 6.763355 AGGTAGTATATGGCTGTCTGAATTG 58.237 40.000 0.00 0.00 0.00 2.32
1594 5739 6.784969 AGAGGTAGTATATGGCTGTCTGAATT 59.215 38.462 0.00 0.00 0.00 2.17
1595 5740 6.318913 AGAGGTAGTATATGGCTGTCTGAAT 58.681 40.000 0.00 0.00 0.00 2.57
1596 5741 5.706447 AGAGGTAGTATATGGCTGTCTGAA 58.294 41.667 0.00 0.00 0.00 3.02
1597 5742 5.326283 AGAGGTAGTATATGGCTGTCTGA 57.674 43.478 0.00 0.00 0.00 3.27
1615 5760 6.152492 GGACTAGTAAACCCGGATTATAGAGG 59.848 46.154 0.73 0.00 0.00 3.69
1616 5761 6.152492 GGGACTAGTAAACCCGGATTATAGAG 59.848 46.154 0.73 4.02 34.03 2.43
1617 5762 6.012745 GGGACTAGTAAACCCGGATTATAGA 58.987 44.000 0.73 0.00 34.03 1.98
1619 5764 5.086621 GGGGACTAGTAAACCCGGATTATA 58.913 45.833 0.73 0.00 44.09 0.98
1620 5765 3.906218 GGGGACTAGTAAACCCGGATTAT 59.094 47.826 0.73 0.00 44.09 1.28
1621 5766 3.308401 GGGGACTAGTAAACCCGGATTA 58.692 50.000 0.73 0.00 44.09 1.75
1622 5767 2.121948 GGGGACTAGTAAACCCGGATT 58.878 52.381 0.73 0.00 44.09 3.01
1629 5774 4.489306 AGCAATGAGGGGACTAGTAAAC 57.511 45.455 0.00 0.00 44.43 2.01
1709 5854 8.846943 TTGAATGTAGCGTCCAATGATATTAT 57.153 30.769 0.00 0.00 0.00 1.28
1724 5869 5.572511 TGTTTGATTCGCATTTGAATGTAGC 59.427 36.000 5.68 0.00 38.65 3.58
1727 5872 8.706492 ATATTGTTTGATTCGCATTTGAATGT 57.294 26.923 5.68 0.00 38.65 2.71
1793 5938 9.414295 GTATTTTGGGTTAAAGTTTGACCATAC 57.586 33.333 25.83 20.20 35.11 2.39
1795 5940 7.149307 CGTATTTTGGGTTAAAGTTTGACCAT 58.851 34.615 25.83 15.43 35.11 3.55
1804 5949 2.732912 GCCGCCGTATTTTGGGTTAAAG 60.733 50.000 0.00 0.00 0.00 1.85
1808 5953 2.692766 CGCCGCCGTATTTTGGGTT 61.693 57.895 0.00 0.00 0.00 4.11
1819 5964 2.629763 GTTTATTAGCCGCCGCCG 59.370 61.111 0.00 0.00 34.57 6.46
1822 5967 1.658994 TTCAGGTTTATTAGCCGCCG 58.341 50.000 0.00 0.00 0.00 6.46
1824 5969 3.211045 TCCATTCAGGTTTATTAGCCGC 58.789 45.455 0.00 0.00 39.02 6.53
1825 5970 3.815401 CCTCCATTCAGGTTTATTAGCCG 59.185 47.826 0.00 0.00 39.02 5.52
1826 5971 4.793201 ACCTCCATTCAGGTTTATTAGCC 58.207 43.478 0.00 0.00 45.24 3.93
1827 5972 8.465273 AAATACCTCCATTCAGGTTTATTAGC 57.535 34.615 0.00 0.00 45.24 3.09
1857 6005 7.506114 TGTTGAATACTGGTAGTTCTGAACTT 58.494 34.615 26.33 11.92 42.81 2.66
1867 6015 9.577110 TCGTACTTTAATGTTGAATACTGGTAG 57.423 33.333 0.00 0.00 0.00 3.18
1870 6020 8.246908 TGTCGTACTTTAATGTTGAATACTGG 57.753 34.615 0.00 0.00 0.00 4.00
1919 6071 8.609617 TGTAAGCATATATCCCTATTAGTGCT 57.390 34.615 0.00 0.00 42.87 4.40
1951 6103 4.587262 ACGATGGTCCAACAGTATGCTATA 59.413 41.667 0.00 0.00 42.53 1.31
1952 6104 3.388024 ACGATGGTCCAACAGTATGCTAT 59.612 43.478 0.00 0.00 42.53 2.97
1953 6105 2.764010 ACGATGGTCCAACAGTATGCTA 59.236 45.455 0.00 0.00 42.53 3.49
1954 6106 1.555075 ACGATGGTCCAACAGTATGCT 59.445 47.619 0.00 0.00 42.53 3.79
1957 6109 3.973206 TTGACGATGGTCCAACAGTAT 57.027 42.857 5.33 0.00 42.73 2.12
1960 6112 2.031157 GGTTTTGACGATGGTCCAACAG 60.031 50.000 16.70 0.00 42.73 3.16
1970 6122 1.794116 CGTACAACCGGTTTTGACGAT 59.206 47.619 28.64 9.86 34.63 3.73
1973 6125 3.989817 AGATACGTACAACCGGTTTTGAC 59.010 43.478 19.55 14.48 0.00 3.18
1975 6127 3.059834 CGAGATACGTACAACCGGTTTTG 59.940 47.826 19.55 11.43 37.22 2.44
1976 6128 3.244976 CGAGATACGTACAACCGGTTTT 58.755 45.455 19.55 15.10 37.22 2.43
1984 6136 8.225777 CTATGTAATAGCACGAGATACGTACAA 58.774 37.037 0.00 0.00 46.17 2.41
2003 6155 4.178540 GACCAGCAAAGTACGCTATGTAA 58.821 43.478 0.00 0.00 37.72 2.41
2004 6156 3.193903 TGACCAGCAAAGTACGCTATGTA 59.806 43.478 0.00 0.00 37.72 2.29
2010 6162 1.394917 CTCATGACCAGCAAAGTACGC 59.605 52.381 0.00 0.00 0.00 4.42
2012 6164 4.319177 AGAACTCATGACCAGCAAAGTAC 58.681 43.478 0.00 0.00 0.00 2.73
2029 6182 8.162878 TCGACGTATATGAAAATAGGAGAACT 57.837 34.615 0.00 0.00 0.00 3.01
2032 6185 8.331730 TGATCGACGTATATGAAAATAGGAGA 57.668 34.615 0.00 0.00 0.00 3.71
2034 6187 9.923143 ATTTGATCGACGTATATGAAAATAGGA 57.077 29.630 0.00 0.00 0.00 2.94
2042 6195 9.908152 AGTTAATCATTTGATCGACGTATATGA 57.092 29.630 0.00 0.00 32.75 2.15
2077 6241 5.994668 TCCGCATTGCATAACATAGATGTAA 59.005 36.000 9.69 0.00 40.80 2.41
2080 6244 5.556355 ATCCGCATTGCATAACATAGATG 57.444 39.130 9.69 0.00 0.00 2.90
2138 6303 7.938490 ACATGCCAAGAAAATTAGTGGAAAATT 59.062 29.630 0.00 0.00 32.54 1.82
2139 6304 7.452562 ACATGCCAAGAAAATTAGTGGAAAAT 58.547 30.769 0.00 0.00 32.54 1.82
2140 6305 6.825610 ACATGCCAAGAAAATTAGTGGAAAA 58.174 32.000 0.00 0.00 32.54 2.29
2141 6306 6.418057 ACATGCCAAGAAAATTAGTGGAAA 57.582 33.333 0.00 0.00 32.54 3.13
2142 6307 6.041409 TGAACATGCCAAGAAAATTAGTGGAA 59.959 34.615 0.00 0.00 32.54 3.53
2143 6308 5.538053 TGAACATGCCAAGAAAATTAGTGGA 59.462 36.000 0.00 0.00 32.54 4.02
2157 6322 4.309099 GAAATCAAAAGCTGAACATGCCA 58.691 39.130 0.00 0.00 37.67 4.92
2167 6332 2.340337 GCGCAATGGAAATCAAAAGCT 58.660 42.857 0.30 0.00 0.00 3.74
2191 6356 2.760477 CATGGTCGGGGTCCCAAA 59.240 61.111 10.98 0.00 33.66 3.28
2192 6357 3.334891 CCATGGTCGGGGTCCCAA 61.335 66.667 10.98 0.00 33.66 4.12
2211 6376 3.982475 TCTATCTTAGCAGAACCGCATG 58.018 45.455 0.00 0.00 30.76 4.06
2212 6377 4.100189 ACTTCTATCTTAGCAGAACCGCAT 59.900 41.667 0.00 0.00 30.76 4.73
2241 6406 9.961265 TTTGAAGGAGTAACAGTATATCATACG 57.039 33.333 0.00 0.00 0.00 3.06
2292 6457 7.396055 GGACTACTCTGATAGGATTGCTCTAAT 59.604 40.741 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.