Multiple sequence alignment - TraesCS6A01G159600

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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 TraesCS6A01G159600 chr6A 100.000 2625 0 0 1 2625 152032413 152029789 0.000000e+00 4848
1 TraesCS6A01G159600 chr6A 97.200 250 7 0 1 250 152054077 152053828 8.690000e-115 424
2 TraesCS6A01G159600 chr6B 95.657 1750 47 13 893 2622 225875501 225877241 0.000000e+00 2784
3 TraesCS6A01G159600 chr6D 93.764 1764 68 18 893 2625 126876494 126878246 0.000000e+00 2610
4 TraesCS6A01G159600 chr5D 90.166 661 54 8 250 901 124917771 124918429 0.000000e+00 850
5 TraesCS6A01G159600 chr5D 85.859 495 59 10 258 745 32612960 32612470 1.390000e-142 516
6 TraesCS6A01G159600 chr2B 87.801 664 66 10 250 900 768792072 768791411 0.000000e+00 763
7 TraesCS6A01G159600 chr1D 88.055 653 66 10 250 895 49665498 49664851 0.000000e+00 763
8 TraesCS6A01G159600 chr3B 85.685 496 60 9 258 745 204810517 204810025 1.800000e-141 512
9 TraesCS6A01G159600 chr3B 85.626 487 60 9 258 737 141621490 141621007 1.080000e-138 503
10 TraesCS6A01G159600 chr1B 83.877 552 74 12 264 811 389314577 389314037 1.800000e-141 512
11 TraesCS6A01G159600 chrUn 85.979 485 59 9 258 736 74556700 74557181 6.480000e-141 510
12 TraesCS6A01G159600 chr1A 85.979 485 58 10 258 736 572218735 572218255 6.480000e-141 510
13 TraesCS6A01G159600 chr1A 96.838 253 5 2 1 250 550975389 550975641 1.120000e-113 420
14 TraesCS6A01G159600 chr7A 96.813 251 6 1 1 249 602823816 602823566 4.040000e-113 418
15 TraesCS6A01G159600 chr7A 95.736 258 8 2 1 255 393226198 393225941 1.880000e-111 412
16 TraesCS6A01G159600 chr7A 96.032 252 8 1 1 250 450593187 450592936 2.430000e-110 409
17 TraesCS6A01G159600 chr7A 96.032 252 8 1 1 250 602925949 602925698 2.430000e-110 409
18 TraesCS6A01G159600 chr7A 96.032 252 6 3 1 250 628873957 628874206 8.750000e-110 407
19 TraesCS6A01G159600 chr3A 96.429 252 7 1 1 250 397387210 397386959 5.230000e-112 414
20 TraesCS6A01G159600 chr2A 96.414 251 6 2 1 249 101545100 101544851 6.760000e-111 411


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 TraesCS6A01G159600 chr6A 152029789 152032413 2624 True 4848 4848 100.000 1 2625 1 chr6A.!!$R1 2624
1 TraesCS6A01G159600 chr6B 225875501 225877241 1740 False 2784 2784 95.657 893 2622 1 chr6B.!!$F1 1729
2 TraesCS6A01G159600 chr6D 126876494 126878246 1752 False 2610 2610 93.764 893 2625 1 chr6D.!!$F1 1732
3 TraesCS6A01G159600 chr5D 124917771 124918429 658 False 850 850 90.166 250 901 1 chr5D.!!$F1 651
4 TraesCS6A01G159600 chr2B 768791411 768792072 661 True 763 763 87.801 250 900 1 chr2B.!!$R1 650
5 TraesCS6A01G159600 chr1D 49664851 49665498 647 True 763 763 88.055 250 895 1 chr1D.!!$R1 645
6 TraesCS6A01G159600 chr1B 389314037 389314577 540 True 512 512 83.877 264 811 1 chr1B.!!$R1 547

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
107 108 0.179067 TCGAAAGACCACGCCTTTGT 60.179 50.0 0.0 0.0 34.33 2.83 F
110 111 0.182775 AAAGACCACGCCTTTGTCCT 59.817 50.0 0.0 0.0 33.07 3.85 F
396 401 0.399233 ATCCACTGGTAGGGAGGAGC 60.399 60.0 0.0 0.0 36.45 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1259 1293 1.016130 CACGAAGTACAGGCCTGCAG 61.016 60.000 33.06 18.46 41.61 4.41 R
1417 1451 1.129998 CTTCGAGCAGAAAGGCACATG 59.870 52.381 0.00 0.00 38.57 3.21 R
2168 2204 4.353777 TCCCTGCTAGAACTCTACAATGT 58.646 43.478 0.00 0.00 0.00 2.71 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
19 20 2.507339 CCCACACAACATTTGTCCAC 57.493 50.000 0.00 0.00 43.23 4.02
20 21 1.753649 CCCACACAACATTTGTCCACA 59.246 47.619 0.00 0.00 43.23 4.17
21 22 2.481104 CCCACACAACATTTGTCCACAC 60.481 50.000 0.00 0.00 43.23 3.82
22 23 2.165234 CCACACAACATTTGTCCACACA 59.835 45.455 0.00 0.00 43.23 3.72
23 24 3.437428 CACACAACATTTGTCCACACAG 58.563 45.455 0.00 0.00 43.23 3.66
24 25 3.128415 CACACAACATTTGTCCACACAGA 59.872 43.478 0.00 0.00 43.23 3.41
25 26 3.128589 ACACAACATTTGTCCACACAGAC 59.871 43.478 0.00 0.00 43.23 3.51
26 27 2.687935 ACAACATTTGTCCACACAGACC 59.312 45.455 0.00 0.00 40.56 3.85
27 28 1.981256 ACATTTGTCCACACAGACCC 58.019 50.000 0.00 0.00 35.83 4.46
28 29 1.247567 CATTTGTCCACACAGACCCC 58.752 55.000 0.00 0.00 35.83 4.95
29 30 1.149101 ATTTGTCCACACAGACCCCT 58.851 50.000 0.00 0.00 35.83 4.79
30 31 0.923358 TTTGTCCACACAGACCCCTT 59.077 50.000 0.00 0.00 35.83 3.95
31 32 0.923358 TTGTCCACACAGACCCCTTT 59.077 50.000 0.00 0.00 35.83 3.11
32 33 0.923358 TGTCCACACAGACCCCTTTT 59.077 50.000 0.00 0.00 35.83 2.27
33 34 2.128535 TGTCCACACAGACCCCTTTTA 58.871 47.619 0.00 0.00 35.83 1.52
34 35 2.510382 TGTCCACACAGACCCCTTTTAA 59.490 45.455 0.00 0.00 35.83 1.52
35 36 3.139397 TGTCCACACAGACCCCTTTTAAT 59.861 43.478 0.00 0.00 35.83 1.40
36 37 4.351407 TGTCCACACAGACCCCTTTTAATA 59.649 41.667 0.00 0.00 35.83 0.98
37 38 4.941873 GTCCACACAGACCCCTTTTAATAG 59.058 45.833 0.00 0.00 0.00 1.73
38 39 4.600111 TCCACACAGACCCCTTTTAATAGT 59.400 41.667 0.00 0.00 0.00 2.12
39 40 4.700213 CCACACAGACCCCTTTTAATAGTG 59.300 45.833 0.00 0.00 0.00 2.74
40 41 4.156008 CACACAGACCCCTTTTAATAGTGC 59.844 45.833 0.00 0.00 0.00 4.40
41 42 3.374058 CACAGACCCCTTTTAATAGTGCG 59.626 47.826 0.00 0.00 0.00 5.34
42 43 2.943033 CAGACCCCTTTTAATAGTGCGG 59.057 50.000 0.00 0.00 0.00 5.69
43 44 2.574824 AGACCCCTTTTAATAGTGCGGT 59.425 45.455 0.00 0.00 0.00 5.68
44 45 2.941064 GACCCCTTTTAATAGTGCGGTC 59.059 50.000 7.71 7.71 32.44 4.79
45 46 2.574824 ACCCCTTTTAATAGTGCGGTCT 59.425 45.455 0.00 0.00 0.00 3.85
46 47 3.009805 ACCCCTTTTAATAGTGCGGTCTT 59.990 43.478 0.00 0.00 0.00 3.01
47 48 4.014406 CCCCTTTTAATAGTGCGGTCTTT 58.986 43.478 0.00 0.00 0.00 2.52
48 49 4.095932 CCCCTTTTAATAGTGCGGTCTTTC 59.904 45.833 0.00 0.00 0.00 2.62
49 50 4.095932 CCCTTTTAATAGTGCGGTCTTTCC 59.904 45.833 0.00 0.00 0.00 3.13
50 51 4.941873 CCTTTTAATAGTGCGGTCTTTCCT 59.058 41.667 0.00 0.00 0.00 3.36
51 52 6.110707 CCTTTTAATAGTGCGGTCTTTCCTA 58.889 40.000 0.00 0.00 0.00 2.94
52 53 6.036844 CCTTTTAATAGTGCGGTCTTTCCTAC 59.963 42.308 0.00 0.00 0.00 3.18
53 54 2.865343 ATAGTGCGGTCTTTCCTACG 57.135 50.000 0.00 0.00 0.00 3.51
54 55 1.825090 TAGTGCGGTCTTTCCTACGA 58.175 50.000 0.00 0.00 0.00 3.43
55 56 0.243095 AGTGCGGTCTTTCCTACGAC 59.757 55.000 0.00 0.00 0.00 4.34
56 57 0.243095 GTGCGGTCTTTCCTACGACT 59.757 55.000 0.00 0.00 0.00 4.18
57 58 0.524862 TGCGGTCTTTCCTACGACTC 59.475 55.000 0.00 0.00 0.00 3.36
58 59 0.524862 GCGGTCTTTCCTACGACTCA 59.475 55.000 0.00 0.00 0.00 3.41
59 60 1.068055 GCGGTCTTTCCTACGACTCAA 60.068 52.381 0.00 0.00 0.00 3.02
60 61 2.608752 GCGGTCTTTCCTACGACTCAAA 60.609 50.000 0.00 0.00 0.00 2.69
61 62 3.243336 CGGTCTTTCCTACGACTCAAAG 58.757 50.000 0.00 0.00 0.00 2.77
62 63 2.994578 GGTCTTTCCTACGACTCAAAGC 59.005 50.000 0.00 0.00 0.00 3.51
63 64 3.554337 GGTCTTTCCTACGACTCAAAGCA 60.554 47.826 0.00 0.00 0.00 3.91
64 65 4.056050 GTCTTTCCTACGACTCAAAGCAA 58.944 43.478 0.00 0.00 0.00 3.91
65 66 4.510340 GTCTTTCCTACGACTCAAAGCAAA 59.490 41.667 0.00 0.00 0.00 3.68
66 67 4.510340 TCTTTCCTACGACTCAAAGCAAAC 59.490 41.667 0.00 0.00 0.00 2.93
67 68 2.762745 TCCTACGACTCAAAGCAAACC 58.237 47.619 0.00 0.00 0.00 3.27
68 69 2.103432 TCCTACGACTCAAAGCAAACCA 59.897 45.455 0.00 0.00 0.00 3.67
69 70 2.875933 CCTACGACTCAAAGCAAACCAA 59.124 45.455 0.00 0.00 0.00 3.67
70 71 3.314080 CCTACGACTCAAAGCAAACCAAA 59.686 43.478 0.00 0.00 0.00 3.28
71 72 3.859411 ACGACTCAAAGCAAACCAAAA 57.141 38.095 0.00 0.00 0.00 2.44
72 73 3.507786 ACGACTCAAAGCAAACCAAAAC 58.492 40.909 0.00 0.00 0.00 2.43
73 74 3.192633 ACGACTCAAAGCAAACCAAAACT 59.807 39.130 0.00 0.00 0.00 2.66
74 75 4.396790 ACGACTCAAAGCAAACCAAAACTA 59.603 37.500 0.00 0.00 0.00 2.24
75 76 5.106078 ACGACTCAAAGCAAACCAAAACTAA 60.106 36.000 0.00 0.00 0.00 2.24
76 77 5.802956 CGACTCAAAGCAAACCAAAACTAAA 59.197 36.000 0.00 0.00 0.00 1.85
77 78 6.237463 CGACTCAAAGCAAACCAAAACTAAAC 60.237 38.462 0.00 0.00 0.00 2.01
78 79 5.872617 ACTCAAAGCAAACCAAAACTAAACC 59.127 36.000 0.00 0.00 0.00 3.27
79 80 6.043854 TCAAAGCAAACCAAAACTAAACCT 57.956 33.333 0.00 0.00 0.00 3.50
80 81 6.468543 TCAAAGCAAACCAAAACTAAACCTT 58.531 32.000 0.00 0.00 0.00 3.50
81 82 6.592220 TCAAAGCAAACCAAAACTAAACCTTC 59.408 34.615 0.00 0.00 0.00 3.46
82 83 4.678622 AGCAAACCAAAACTAAACCTTCG 58.321 39.130 0.00 0.00 0.00 3.79
83 84 4.399934 AGCAAACCAAAACTAAACCTTCGA 59.600 37.500 0.00 0.00 0.00 3.71
84 85 5.103687 GCAAACCAAAACTAAACCTTCGAA 58.896 37.500 0.00 0.00 0.00 3.71
85 86 5.231357 GCAAACCAAAACTAAACCTTCGAAG 59.769 40.000 18.51 18.51 0.00 3.79
86 87 4.563337 ACCAAAACTAAACCTTCGAAGC 57.437 40.909 19.99 0.00 0.00 3.86
87 88 3.002965 ACCAAAACTAAACCTTCGAAGCG 59.997 43.478 19.99 14.78 0.00 4.68
88 89 3.002965 CCAAAACTAAACCTTCGAAGCGT 59.997 43.478 19.99 15.41 0.00 5.07
89 90 4.209112 CAAAACTAAACCTTCGAAGCGTC 58.791 43.478 19.99 0.00 0.00 5.19
106 107 2.612200 TCGAAAGACCACGCCTTTG 58.388 52.632 0.00 0.00 34.33 2.77
107 108 0.179067 TCGAAAGACCACGCCTTTGT 60.179 50.000 0.00 0.00 34.33 2.83
108 109 0.234884 CGAAAGACCACGCCTTTGTC 59.765 55.000 0.00 0.00 34.33 3.18
109 110 0.591659 GAAAGACCACGCCTTTGTCC 59.408 55.000 0.00 0.00 34.33 4.02
110 111 0.182775 AAAGACCACGCCTTTGTCCT 59.817 50.000 0.00 0.00 33.07 3.85
111 112 0.182775 AAGACCACGCCTTTGTCCTT 59.817 50.000 0.00 0.00 0.00 3.36
112 113 0.182775 AGACCACGCCTTTGTCCTTT 59.817 50.000 0.00 0.00 0.00 3.11
113 114 1.029681 GACCACGCCTTTGTCCTTTT 58.970 50.000 0.00 0.00 0.00 2.27
114 115 1.407618 GACCACGCCTTTGTCCTTTTT 59.592 47.619 0.00 0.00 0.00 1.94
115 116 1.136110 ACCACGCCTTTGTCCTTTTTG 59.864 47.619 0.00 0.00 0.00 2.44
116 117 1.407258 CCACGCCTTTGTCCTTTTTGA 59.593 47.619 0.00 0.00 0.00 2.69
117 118 2.159170 CCACGCCTTTGTCCTTTTTGAA 60.159 45.455 0.00 0.00 0.00 2.69
118 119 3.516615 CACGCCTTTGTCCTTTTTGAAA 58.483 40.909 0.00 0.00 0.00 2.69
119 120 4.119136 CACGCCTTTGTCCTTTTTGAAAT 58.881 39.130 0.00 0.00 0.00 2.17
120 121 4.025813 CACGCCTTTGTCCTTTTTGAAATG 60.026 41.667 0.00 0.00 0.00 2.32
121 122 3.494251 CGCCTTTGTCCTTTTTGAAATGG 59.506 43.478 2.81 2.81 35.24 3.16
122 123 3.814842 GCCTTTGTCCTTTTTGAAATGGG 59.185 43.478 8.11 0.78 34.81 4.00
123 124 4.388485 CCTTTGTCCTTTTTGAAATGGGG 58.612 43.478 8.11 0.00 34.81 4.96
124 125 4.388485 CTTTGTCCTTTTTGAAATGGGGG 58.612 43.478 8.11 0.00 34.81 5.40
138 139 3.399181 GGGGGTCGCACATCTCCA 61.399 66.667 0.00 0.00 0.00 3.86
139 140 2.746375 GGGGGTCGCACATCTCCAT 61.746 63.158 0.00 0.00 0.00 3.41
140 141 1.227674 GGGGTCGCACATCTCCATC 60.228 63.158 0.00 0.00 0.00 3.51
141 142 1.592669 GGGTCGCACATCTCCATCG 60.593 63.158 0.00 0.00 0.00 3.84
142 143 2.240500 GGTCGCACATCTCCATCGC 61.241 63.158 0.00 0.00 0.00 4.58
143 144 2.278792 TCGCACATCTCCATCGCG 60.279 61.111 0.00 0.00 46.92 5.87
144 145 3.333189 CGCACATCTCCATCGCGG 61.333 66.667 6.13 0.00 42.13 6.46
145 146 2.969238 GCACATCTCCATCGCGGG 60.969 66.667 6.13 0.00 34.36 6.13
146 147 2.969238 CACATCTCCATCGCGGGC 60.969 66.667 6.13 0.00 34.36 6.13
147 148 4.592192 ACATCTCCATCGCGGGCG 62.592 66.667 6.13 6.74 41.35 6.13
148 149 4.592192 CATCTCCATCGCGGGCGT 62.592 66.667 13.21 0.00 40.74 5.68
149 150 3.849951 ATCTCCATCGCGGGCGTT 61.850 61.111 13.21 1.44 40.74 4.84
150 151 3.385749 ATCTCCATCGCGGGCGTTT 62.386 57.895 13.21 0.00 40.74 3.60
151 152 2.023414 ATCTCCATCGCGGGCGTTTA 62.023 55.000 13.21 0.00 40.74 2.01
152 153 2.202824 TCCATCGCGGGCGTTTAG 60.203 61.111 13.21 1.36 40.74 1.85
153 154 2.202824 CCATCGCGGGCGTTTAGA 60.203 61.111 13.21 0.00 40.74 2.10
154 155 1.812093 CCATCGCGGGCGTTTAGAA 60.812 57.895 13.21 0.00 40.74 2.10
155 156 1.347221 CATCGCGGGCGTTTAGAAC 59.653 57.895 13.21 0.00 40.74 3.01
156 157 1.812507 ATCGCGGGCGTTTAGAACC 60.813 57.895 13.21 0.00 40.74 3.62
157 158 2.510064 ATCGCGGGCGTTTAGAACCA 62.510 55.000 13.21 0.00 40.74 3.67
158 159 2.319096 CGCGGGCGTTTAGAACCAA 61.319 57.895 4.64 0.00 34.35 3.67
159 160 1.641123 CGCGGGCGTTTAGAACCAAT 61.641 55.000 4.64 0.00 34.35 3.16
160 161 1.371595 GCGGGCGTTTAGAACCAATA 58.628 50.000 0.00 0.00 0.00 1.90
161 162 1.738908 GCGGGCGTTTAGAACCAATAA 59.261 47.619 0.00 0.00 0.00 1.40
162 163 2.476686 GCGGGCGTTTAGAACCAATAAC 60.477 50.000 0.00 0.00 0.00 1.89
163 164 3.004862 CGGGCGTTTAGAACCAATAACT 58.995 45.455 0.00 0.00 0.00 2.24
164 165 3.437741 CGGGCGTTTAGAACCAATAACTT 59.562 43.478 0.00 0.00 0.00 2.66
165 166 4.670735 CGGGCGTTTAGAACCAATAACTTG 60.671 45.833 0.00 0.00 0.00 3.16
166 167 4.456566 GGGCGTTTAGAACCAATAACTTGA 59.543 41.667 0.00 0.00 34.04 3.02
167 168 5.391629 GGGCGTTTAGAACCAATAACTTGAG 60.392 44.000 0.00 0.00 34.04 3.02
168 169 5.410439 GGCGTTTAGAACCAATAACTTGAGA 59.590 40.000 0.00 0.00 34.04 3.27
169 170 6.093633 GGCGTTTAGAACCAATAACTTGAGAT 59.906 38.462 0.00 0.00 34.04 2.75
170 171 7.279313 GGCGTTTAGAACCAATAACTTGAGATA 59.721 37.037 0.00 0.00 34.04 1.98
171 172 8.662141 GCGTTTAGAACCAATAACTTGAGATAA 58.338 33.333 0.00 0.00 34.04 1.75
180 181 9.515226 ACCAATAACTTGAGATAAACTTTAGCA 57.485 29.630 0.00 0.00 34.04 3.49
184 185 6.481954 ACTTGAGATAAACTTTAGCAACCG 57.518 37.500 0.00 0.00 0.00 4.44
185 186 6.228258 ACTTGAGATAAACTTTAGCAACCGA 58.772 36.000 0.00 0.00 0.00 4.69
186 187 6.879458 ACTTGAGATAAACTTTAGCAACCGAT 59.121 34.615 0.00 0.00 0.00 4.18
187 188 8.038944 ACTTGAGATAAACTTTAGCAACCGATA 58.961 33.333 0.00 0.00 0.00 2.92
188 189 8.958119 TTGAGATAAACTTTAGCAACCGATAT 57.042 30.769 0.00 0.00 0.00 1.63
189 190 8.958119 TGAGATAAACTTTAGCAACCGATATT 57.042 30.769 0.00 0.00 0.00 1.28
195 196 8.556213 AAACTTTAGCAACCGATATTAGTTCA 57.444 30.769 0.00 0.00 0.00 3.18
196 197 8.556213 AACTTTAGCAACCGATATTAGTTCAA 57.444 30.769 0.00 0.00 0.00 2.69
197 198 7.971455 ACTTTAGCAACCGATATTAGTTCAAC 58.029 34.615 0.00 0.00 0.00 3.18
198 199 7.822822 ACTTTAGCAACCGATATTAGTTCAACT 59.177 33.333 0.00 0.00 0.00 3.16
199 200 9.309516 CTTTAGCAACCGATATTAGTTCAACTA 57.690 33.333 0.00 0.00 0.00 2.24
200 201 9.656040 TTTAGCAACCGATATTAGTTCAACTAA 57.344 29.630 12.46 12.46 43.95 2.24
201 202 7.535489 AGCAACCGATATTAGTTCAACTAAC 57.465 36.000 12.33 0.00 42.78 2.34
202 203 6.537660 AGCAACCGATATTAGTTCAACTAACC 59.462 38.462 12.33 4.48 42.78 2.85
203 204 6.314400 GCAACCGATATTAGTTCAACTAACCA 59.686 38.462 12.33 4.20 42.78 3.67
204 205 7.675637 GCAACCGATATTAGTTCAACTAACCAC 60.676 40.741 12.33 5.91 42.78 4.16
205 206 6.938507 ACCGATATTAGTTCAACTAACCACA 58.061 36.000 12.33 0.00 42.78 4.17
206 207 7.562135 ACCGATATTAGTTCAACTAACCACAT 58.438 34.615 12.33 4.09 42.78 3.21
207 208 8.044908 ACCGATATTAGTTCAACTAACCACATT 58.955 33.333 12.33 0.00 42.78 2.71
208 209 8.335356 CCGATATTAGTTCAACTAACCACATTG 58.665 37.037 12.33 7.46 42.78 2.82
209 210 8.879759 CGATATTAGTTCAACTAACCACATTGT 58.120 33.333 12.33 0.00 42.78 2.71
211 212 9.733556 ATATTAGTTCAACTAACCACATTGTCA 57.266 29.630 12.33 0.00 42.78 3.58
212 213 8.635765 ATTAGTTCAACTAACCACATTGTCAT 57.364 30.769 12.33 0.00 42.78 3.06
213 214 6.560253 AGTTCAACTAACCACATTGTCATC 57.440 37.500 0.00 0.00 39.03 2.92
214 215 6.061441 AGTTCAACTAACCACATTGTCATCA 58.939 36.000 0.00 0.00 39.03 3.07
215 216 5.940192 TCAACTAACCACATTGTCATCAC 57.060 39.130 0.00 0.00 0.00 3.06
216 217 5.372373 TCAACTAACCACATTGTCATCACA 58.628 37.500 0.00 0.00 0.00 3.58
217 218 5.238432 TCAACTAACCACATTGTCATCACAC 59.762 40.000 0.00 0.00 29.76 3.82
218 219 4.072131 ACTAACCACATTGTCATCACACC 58.928 43.478 0.00 0.00 29.76 4.16
219 220 2.655090 ACCACATTGTCATCACACCA 57.345 45.000 0.00 0.00 29.76 4.17
220 221 2.942804 ACCACATTGTCATCACACCAA 58.057 42.857 0.00 0.00 29.76 3.67
221 222 3.295093 ACCACATTGTCATCACACCAAA 58.705 40.909 0.00 0.00 29.76 3.28
222 223 3.703556 ACCACATTGTCATCACACCAAAA 59.296 39.130 0.00 0.00 29.76 2.44
223 224 4.344679 ACCACATTGTCATCACACCAAAAT 59.655 37.500 0.00 0.00 29.76 1.82
224 225 5.538053 ACCACATTGTCATCACACCAAAATA 59.462 36.000 0.00 0.00 29.76 1.40
225 226 6.094719 CCACATTGTCATCACACCAAAATAG 58.905 40.000 0.00 0.00 29.76 1.73
226 227 5.574055 CACATTGTCATCACACCAAAATAGC 59.426 40.000 0.00 0.00 29.76 2.97
227 228 5.477984 ACATTGTCATCACACCAAAATAGCT 59.522 36.000 0.00 0.00 29.76 3.32
228 229 6.015180 ACATTGTCATCACACCAAAATAGCTT 60.015 34.615 0.00 0.00 29.76 3.74
229 230 7.176515 ACATTGTCATCACACCAAAATAGCTTA 59.823 33.333 0.00 0.00 29.76 3.09
230 231 7.517614 TTGTCATCACACCAAAATAGCTTAA 57.482 32.000 0.00 0.00 29.76 1.85
231 232 7.144722 TGTCATCACACCAAAATAGCTTAAG 57.855 36.000 0.00 0.00 0.00 1.85
232 233 6.714810 TGTCATCACACCAAAATAGCTTAAGT 59.285 34.615 4.02 0.00 0.00 2.24
233 234 7.023575 GTCATCACACCAAAATAGCTTAAGTG 58.976 38.462 4.02 0.00 0.00 3.16
234 235 5.371115 TCACACCAAAATAGCTTAAGTGC 57.629 39.130 4.02 0.00 0.00 4.40
235 236 4.217550 TCACACCAAAATAGCTTAAGTGCC 59.782 41.667 4.02 0.00 0.00 5.01
236 237 4.022416 CACACCAAAATAGCTTAAGTGCCA 60.022 41.667 4.02 0.00 0.00 4.92
237 238 4.772100 ACACCAAAATAGCTTAAGTGCCAT 59.228 37.500 4.02 0.00 0.00 4.40
238 239 5.245977 ACACCAAAATAGCTTAAGTGCCATT 59.754 36.000 4.02 0.00 0.00 3.16
239 240 6.435904 ACACCAAAATAGCTTAAGTGCCATTA 59.564 34.615 4.02 0.00 0.00 1.90
240 241 6.974622 CACCAAAATAGCTTAAGTGCCATTAG 59.025 38.462 4.02 0.00 0.00 1.73
241 242 5.979517 CCAAAATAGCTTAAGTGCCATTAGC 59.020 40.000 4.02 0.00 44.14 3.09
339 344 2.758130 TGCACATATCACTGGTAGGGA 58.242 47.619 0.00 0.00 28.63 4.20
396 401 0.399233 ATCCACTGGTAGGGAGGAGC 60.399 60.000 0.00 0.00 36.45 4.70
397 402 1.306141 CCACTGGTAGGGAGGAGCA 60.306 63.158 0.00 0.00 0.00 4.26
464 470 2.028203 GCACAATAGGTTGCCATGGTTT 60.028 45.455 14.67 0.00 38.96 3.27
469 475 5.777732 ACAATAGGTTGCCATGGTTTTTAGA 59.222 36.000 14.67 0.00 38.96 2.10
472 478 8.474025 CAATAGGTTGCCATGGTTTTTAGATTA 58.526 33.333 14.67 0.00 0.00 1.75
506 516 4.434545 AAGTTGGATCATGCAGCTCTAT 57.565 40.909 0.00 0.00 26.19 1.98
511 521 7.683578 AGTTGGATCATGCAGCTCTATAAATA 58.316 34.615 0.00 0.00 0.00 1.40
648 661 6.405953 GGGATCTAGTTTCAAAGATCTCGTCA 60.406 42.308 11.05 0.00 44.94 4.35
664 677 2.798283 TCGTCACGAAGAATCCAACAAC 59.202 45.455 0.00 0.00 31.06 3.32
671 684 3.493129 CGAAGAATCCAACAACGAAGACA 59.507 43.478 0.00 0.00 0.00 3.41
673 686 3.403038 AGAATCCAACAACGAAGACAGG 58.597 45.455 0.00 0.00 0.00 4.00
741 754 9.554395 AAATTTGAGAACCCAAAATAAACGAAT 57.446 25.926 0.00 0.00 39.20 3.34
750 763 9.635404 AACCCAAAATAAACGAATATGGATCTA 57.365 29.630 0.00 0.00 0.00 1.98
772 785 1.045407 TTCCCCTTCCGATATGACCG 58.955 55.000 0.00 0.00 0.00 4.79
781 794 2.963101 TCCGATATGACCGGTCTGATTT 59.037 45.455 33.39 15.80 46.53 2.17
786 799 5.573282 CGATATGACCGGTCTGATTTACATC 59.427 44.000 33.39 15.98 0.00 3.06
790 803 6.288941 TGACCGGTCTGATTTACATCTAAA 57.711 37.500 33.39 6.08 0.00 1.85
793 806 5.116180 CCGGTCTGATTTACATCTAAAGCA 58.884 41.667 0.00 0.00 36.19 3.91
806 819 4.558226 TCTAAAGCAGATGACCACATGT 57.442 40.909 0.00 0.00 36.82 3.21
814 827 4.758688 CAGATGACCACATGTACTAGCAA 58.241 43.478 0.00 0.00 36.82 3.91
817 830 4.617253 TGACCACATGTACTAGCAAACT 57.383 40.909 0.00 0.00 0.00 2.66
870 883 1.497991 CGCTTGTTCTCTCCAACGAA 58.502 50.000 0.00 0.00 0.00 3.85
872 885 2.210116 GCTTGTTCTCTCCAACGAACA 58.790 47.619 0.00 0.00 45.41 3.18
891 906 5.454232 CGAACACGTGCACTTTTAAGATTTT 59.546 36.000 17.22 0.00 0.00 1.82
1055 1085 2.758497 CGCAGCACATCATCTGTCA 58.242 52.632 0.00 0.00 35.29 3.58
1218 1252 4.710167 TCCGTCTCCGCGTCCTCA 62.710 66.667 4.92 0.00 0.00 3.86
1259 1293 1.493950 CGATCTGATGGTTGCCGCTC 61.494 60.000 0.00 0.00 0.00 5.03
1416 1450 0.391263 GAGGTGAAAGGGCGTGTAGG 60.391 60.000 0.00 0.00 0.00 3.18
1417 1451 2.038837 GGTGAAAGGGCGTGTAGGC 61.039 63.158 0.00 0.00 45.91 3.93
1625 1661 8.125978 AGTTGGAAAATTCAGATTATGCTTCA 57.874 30.769 0.00 0.00 0.00 3.02
1643 1679 3.394674 TCATTTCGTAACTGTGGCTCA 57.605 42.857 0.00 0.00 0.00 4.26
1785 1821 6.594159 CGAGTTCCTGTATTTTCCATACTGTT 59.406 38.462 0.00 0.00 0.00 3.16
1935 1971 4.686091 TCAGTGAGCACTACATTCTTTTCG 59.314 41.667 2.36 0.00 40.20 3.46
1941 1977 3.058224 GCACTACATTCTTTTCGTGCCTT 60.058 43.478 0.00 0.00 41.19 4.35
2064 2100 5.222130 GGAATAGTCCACCAACCCATCATAT 60.222 44.000 3.85 0.00 44.26 1.78
2074 2110 4.831155 CCAACCCATCATATGCTGATTTCT 59.169 41.667 8.13 0.00 42.07 2.52
2168 2204 5.124457 GCATGCTTGAATCCTTTTCTGTCTA 59.876 40.000 11.37 0.00 0.00 2.59
2269 2315 6.554334 TTGGTAATCAACTTAGTGCTGAAC 57.446 37.500 0.00 0.00 0.00 3.18
2270 2316 5.865085 TGGTAATCAACTTAGTGCTGAACT 58.135 37.500 0.00 0.00 43.40 3.01
2271 2317 5.700832 TGGTAATCAACTTAGTGCTGAACTG 59.299 40.000 0.00 0.00 40.26 3.16
2272 2318 4.756084 AATCAACTTAGTGCTGAACTGC 57.244 40.909 0.00 0.00 40.26 4.40
2433 2482 7.004691 ACTTTAAGAATAAGTTCCTGGCAGTT 58.995 34.615 14.43 3.45 32.06 3.16
2435 2484 8.561738 TTTAAGAATAAGTTCCTGGCAGTTAG 57.438 34.615 14.43 0.00 34.81 2.34
2451 2500 4.822026 CAGTTAGTACTTTGGCTAGTGCT 58.178 43.478 0.00 13.29 42.58 4.40
2546 2595 7.962964 TCTACCAATTTAGAGAATAATGGCG 57.037 36.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.753649 TGTGGACAAATGTTGTGTGGG 59.246 47.619 0.00 0.00 45.52 4.61
1 2 2.165234 TGTGTGGACAAATGTTGTGTGG 59.835 45.455 0.00 0.00 45.52 4.17
2 3 3.128415 TCTGTGTGGACAAATGTTGTGTG 59.872 43.478 0.00 0.00 45.52 3.82
4 5 3.489059 GGTCTGTGTGGACAAATGTTGTG 60.489 47.826 0.00 0.00 45.52 3.33
6 7 2.034558 GGGTCTGTGTGGACAAATGTTG 59.965 50.000 0.00 0.00 37.91 3.33
7 8 2.306847 GGGTCTGTGTGGACAAATGTT 58.693 47.619 0.00 0.00 37.91 2.71
8 9 1.478654 GGGGTCTGTGTGGACAAATGT 60.479 52.381 0.00 0.00 37.91 2.71
9 10 1.202927 AGGGGTCTGTGTGGACAAATG 60.203 52.381 0.00 0.00 37.91 2.32
10 11 1.149101 AGGGGTCTGTGTGGACAAAT 58.851 50.000 0.00 0.00 37.91 2.32
11 12 0.923358 AAGGGGTCTGTGTGGACAAA 59.077 50.000 0.00 0.00 37.91 2.83
12 13 0.923358 AAAGGGGTCTGTGTGGACAA 59.077 50.000 0.00 0.00 37.91 3.18
13 14 0.923358 AAAAGGGGTCTGTGTGGACA 59.077 50.000 0.00 0.00 37.91 4.02
14 15 2.943036 TAAAAGGGGTCTGTGTGGAC 57.057 50.000 0.00 0.00 35.66 4.02
15 16 4.600111 ACTATTAAAAGGGGTCTGTGTGGA 59.400 41.667 0.00 0.00 0.00 4.02
16 17 4.700213 CACTATTAAAAGGGGTCTGTGTGG 59.300 45.833 0.00 0.00 0.00 4.17
17 18 4.156008 GCACTATTAAAAGGGGTCTGTGTG 59.844 45.833 0.00 0.00 0.00 3.82
18 19 4.332828 GCACTATTAAAAGGGGTCTGTGT 58.667 43.478 0.00 0.00 0.00 3.72
19 20 3.374058 CGCACTATTAAAAGGGGTCTGTG 59.626 47.826 0.00 0.00 0.00 3.66
20 21 3.606687 CGCACTATTAAAAGGGGTCTGT 58.393 45.455 0.00 0.00 0.00 3.41
21 22 2.943033 CCGCACTATTAAAAGGGGTCTG 59.057 50.000 0.00 0.00 0.00 3.51
22 23 2.574824 ACCGCACTATTAAAAGGGGTCT 59.425 45.455 0.00 0.00 42.80 3.85
23 24 2.995283 ACCGCACTATTAAAAGGGGTC 58.005 47.619 0.00 0.00 42.80 4.46
25 26 3.277142 AGACCGCACTATTAAAAGGGG 57.723 47.619 0.00 0.00 39.70 4.79
26 27 4.095932 GGAAAGACCGCACTATTAAAAGGG 59.904 45.833 0.00 0.00 0.00 3.95
27 28 4.941873 AGGAAAGACCGCACTATTAAAAGG 59.058 41.667 0.00 0.00 44.74 3.11
28 29 6.237755 CGTAGGAAAGACCGCACTATTAAAAG 60.238 42.308 0.00 0.00 44.74 2.27
29 30 5.577945 CGTAGGAAAGACCGCACTATTAAAA 59.422 40.000 0.00 0.00 44.74 1.52
30 31 5.104374 CGTAGGAAAGACCGCACTATTAAA 58.896 41.667 0.00 0.00 44.74 1.52
31 32 4.398988 TCGTAGGAAAGACCGCACTATTAA 59.601 41.667 0.00 0.00 44.74 1.40
32 33 3.947196 TCGTAGGAAAGACCGCACTATTA 59.053 43.478 0.00 0.00 44.74 0.98
33 34 2.756760 TCGTAGGAAAGACCGCACTATT 59.243 45.455 0.00 0.00 44.74 1.73
34 35 2.098770 GTCGTAGGAAAGACCGCACTAT 59.901 50.000 0.00 0.00 44.74 2.12
35 36 1.470098 GTCGTAGGAAAGACCGCACTA 59.530 52.381 0.00 0.00 44.74 2.74
36 37 0.243095 GTCGTAGGAAAGACCGCACT 59.757 55.000 0.00 0.00 44.74 4.40
37 38 0.243095 AGTCGTAGGAAAGACCGCAC 59.757 55.000 0.00 0.00 44.74 5.34
38 39 0.524862 GAGTCGTAGGAAAGACCGCA 59.475 55.000 0.00 0.00 44.74 5.69
39 40 0.524862 TGAGTCGTAGGAAAGACCGC 59.475 55.000 0.00 0.00 44.74 5.68
40 41 3.243336 CTTTGAGTCGTAGGAAAGACCG 58.757 50.000 0.00 0.00 44.74 4.79
41 42 2.994578 GCTTTGAGTCGTAGGAAAGACC 59.005 50.000 4.53 0.00 38.08 3.85
42 43 3.650139 TGCTTTGAGTCGTAGGAAAGAC 58.350 45.455 4.53 0.00 37.63 3.01
43 44 4.330944 TTGCTTTGAGTCGTAGGAAAGA 57.669 40.909 4.53 0.00 0.00 2.52
44 45 4.319549 GGTTTGCTTTGAGTCGTAGGAAAG 60.320 45.833 10.04 4.06 31.31 2.62
45 46 3.562557 GGTTTGCTTTGAGTCGTAGGAAA 59.437 43.478 6.82 6.82 0.00 3.13
46 47 3.135994 GGTTTGCTTTGAGTCGTAGGAA 58.864 45.455 0.00 0.00 0.00 3.36
47 48 2.103432 TGGTTTGCTTTGAGTCGTAGGA 59.897 45.455 0.00 0.00 0.00 2.94
48 49 2.489971 TGGTTTGCTTTGAGTCGTAGG 58.510 47.619 0.00 0.00 0.00 3.18
49 50 4.545823 TTTGGTTTGCTTTGAGTCGTAG 57.454 40.909 0.00 0.00 0.00 3.51
50 51 4.396790 AGTTTTGGTTTGCTTTGAGTCGTA 59.603 37.500 0.00 0.00 0.00 3.43
51 52 3.192633 AGTTTTGGTTTGCTTTGAGTCGT 59.807 39.130 0.00 0.00 0.00 4.34
52 53 3.769536 AGTTTTGGTTTGCTTTGAGTCG 58.230 40.909 0.00 0.00 0.00 4.18
53 54 6.035650 GGTTTAGTTTTGGTTTGCTTTGAGTC 59.964 38.462 0.00 0.00 0.00 3.36
54 55 5.872617 GGTTTAGTTTTGGTTTGCTTTGAGT 59.127 36.000 0.00 0.00 0.00 3.41
55 56 6.106003 AGGTTTAGTTTTGGTTTGCTTTGAG 58.894 36.000 0.00 0.00 0.00 3.02
56 57 6.043854 AGGTTTAGTTTTGGTTTGCTTTGA 57.956 33.333 0.00 0.00 0.00 2.69
57 58 6.454981 CGAAGGTTTAGTTTTGGTTTGCTTTG 60.455 38.462 0.00 0.00 0.00 2.77
58 59 5.579119 CGAAGGTTTAGTTTTGGTTTGCTTT 59.421 36.000 0.00 0.00 0.00 3.51
59 60 5.105675 TCGAAGGTTTAGTTTTGGTTTGCTT 60.106 36.000 0.00 0.00 0.00 3.91
60 61 4.399934 TCGAAGGTTTAGTTTTGGTTTGCT 59.600 37.500 0.00 0.00 0.00 3.91
61 62 4.674475 TCGAAGGTTTAGTTTTGGTTTGC 58.326 39.130 0.00 0.00 0.00 3.68
62 63 5.231357 GCTTCGAAGGTTTAGTTTTGGTTTG 59.769 40.000 25.77 0.00 0.00 2.93
63 64 5.345702 GCTTCGAAGGTTTAGTTTTGGTTT 58.654 37.500 25.77 0.00 0.00 3.27
64 65 4.496840 CGCTTCGAAGGTTTAGTTTTGGTT 60.497 41.667 25.77 0.00 0.00 3.67
65 66 3.002965 CGCTTCGAAGGTTTAGTTTTGGT 59.997 43.478 25.77 0.00 0.00 3.67
66 67 3.002965 ACGCTTCGAAGGTTTAGTTTTGG 59.997 43.478 25.77 0.00 0.00 3.28
67 68 4.205323 ACGCTTCGAAGGTTTAGTTTTG 57.795 40.909 25.77 0.00 0.00 2.44
68 69 4.463515 GACGCTTCGAAGGTTTAGTTTT 57.536 40.909 25.77 0.00 0.00 2.43
82 83 1.773496 CGTGGTCTTTCGACGCTTC 59.227 57.895 0.00 0.00 40.80 3.86
83 84 3.932289 CGTGGTCTTTCGACGCTT 58.068 55.556 0.00 0.00 40.80 4.68
87 88 0.234884 CAAAGGCGTGGTCTTTCGAC 59.765 55.000 0.00 0.00 35.12 4.20
88 89 0.179067 ACAAAGGCGTGGTCTTTCGA 60.179 50.000 0.00 0.00 35.12 3.71
89 90 0.234884 GACAAAGGCGTGGTCTTTCG 59.765 55.000 0.26 0.00 35.12 3.46
90 91 0.591659 GGACAAAGGCGTGGTCTTTC 59.408 55.000 7.88 0.00 35.12 2.62
91 92 0.182775 AGGACAAAGGCGTGGTCTTT 59.817 50.000 7.88 0.00 38.03 2.52
92 93 0.182775 AAGGACAAAGGCGTGGTCTT 59.817 50.000 7.88 0.00 0.00 3.01
93 94 0.182775 AAAGGACAAAGGCGTGGTCT 59.817 50.000 7.88 0.00 0.00 3.85
94 95 1.029681 AAAAGGACAAAGGCGTGGTC 58.970 50.000 0.00 0.00 0.00 4.02
95 96 1.136110 CAAAAAGGACAAAGGCGTGGT 59.864 47.619 0.00 0.00 0.00 4.16
96 97 1.407258 TCAAAAAGGACAAAGGCGTGG 59.593 47.619 0.00 0.00 0.00 4.94
97 98 2.861462 TCAAAAAGGACAAAGGCGTG 57.139 45.000 0.00 0.00 0.00 5.34
98 99 3.878160 TTTCAAAAAGGACAAAGGCGT 57.122 38.095 0.00 0.00 0.00 5.68
99 100 3.494251 CCATTTCAAAAAGGACAAAGGCG 59.506 43.478 0.00 0.00 0.00 5.52
100 101 3.814842 CCCATTTCAAAAAGGACAAAGGC 59.185 43.478 0.00 0.00 0.00 4.35
101 102 4.388485 CCCCATTTCAAAAAGGACAAAGG 58.612 43.478 0.00 0.00 0.00 3.11
102 103 4.388485 CCCCCATTTCAAAAAGGACAAAG 58.612 43.478 0.00 0.00 0.00 2.77
103 104 4.429854 CCCCCATTTCAAAAAGGACAAA 57.570 40.909 0.00 0.00 0.00 2.83
121 122 2.666596 GATGGAGATGTGCGACCCCC 62.667 65.000 0.00 0.00 0.00 5.40
122 123 1.227674 GATGGAGATGTGCGACCCC 60.228 63.158 0.00 0.00 0.00 4.95
123 124 1.592669 CGATGGAGATGTGCGACCC 60.593 63.158 0.00 0.00 0.00 4.46
124 125 2.240500 GCGATGGAGATGTGCGACC 61.241 63.158 0.00 0.00 0.00 4.79
125 126 3.313750 GCGATGGAGATGTGCGAC 58.686 61.111 0.00 0.00 0.00 5.19
128 129 2.969238 CCCGCGATGGAGATGTGC 60.969 66.667 8.23 0.00 42.00 4.57
129 130 2.969238 GCCCGCGATGGAGATGTG 60.969 66.667 8.23 0.00 42.00 3.21
130 131 4.592192 CGCCCGCGATGGAGATGT 62.592 66.667 8.23 0.00 42.00 3.06
131 132 4.592192 ACGCCCGCGATGGAGATG 62.592 66.667 17.16 0.00 42.00 2.90
132 133 2.023414 TAAACGCCCGCGATGGAGAT 62.023 55.000 17.16 0.00 42.00 2.75
133 134 2.622903 CTAAACGCCCGCGATGGAGA 62.623 60.000 17.16 0.00 42.00 3.71
134 135 2.202824 TAAACGCCCGCGATGGAG 60.203 61.111 17.16 5.47 42.00 3.86
135 136 2.202824 CTAAACGCCCGCGATGGA 60.203 61.111 17.16 0.00 42.00 3.41
136 137 1.812093 TTCTAAACGCCCGCGATGG 60.812 57.895 17.16 1.15 42.83 3.51
137 138 1.347221 GTTCTAAACGCCCGCGATG 59.653 57.895 17.16 0.00 42.83 3.84
138 139 1.812507 GGTTCTAAACGCCCGCGAT 60.813 57.895 17.16 0.00 42.83 4.58
139 140 2.432972 GGTTCTAAACGCCCGCGA 60.433 61.111 17.16 0.00 42.83 5.87
140 141 1.641123 ATTGGTTCTAAACGCCCGCG 61.641 55.000 7.69 7.69 46.03 6.46
141 142 1.371595 TATTGGTTCTAAACGCCCGC 58.628 50.000 0.00 0.00 0.00 6.13
142 143 3.004862 AGTTATTGGTTCTAAACGCCCG 58.995 45.455 0.00 0.00 0.00 6.13
143 144 4.456566 TCAAGTTATTGGTTCTAAACGCCC 59.543 41.667 0.00 0.00 37.02 6.13
144 145 5.410439 TCTCAAGTTATTGGTTCTAAACGCC 59.590 40.000 0.00 0.00 37.02 5.68
145 146 6.476243 TCTCAAGTTATTGGTTCTAAACGC 57.524 37.500 0.00 0.00 37.02 4.84
154 155 9.515226 TGCTAAAGTTTATCTCAAGTTATTGGT 57.485 29.630 0.00 0.00 37.02 3.67
158 159 8.665685 CGGTTGCTAAAGTTTATCTCAAGTTAT 58.334 33.333 0.00 0.00 0.00 1.89
159 160 7.874016 TCGGTTGCTAAAGTTTATCTCAAGTTA 59.126 33.333 0.00 0.00 0.00 2.24
160 161 6.708949 TCGGTTGCTAAAGTTTATCTCAAGTT 59.291 34.615 0.00 0.00 0.00 2.66
161 162 6.228258 TCGGTTGCTAAAGTTTATCTCAAGT 58.772 36.000 0.00 0.00 0.00 3.16
162 163 6.721571 TCGGTTGCTAAAGTTTATCTCAAG 57.278 37.500 0.00 0.00 0.00 3.02
163 164 8.958119 ATATCGGTTGCTAAAGTTTATCTCAA 57.042 30.769 0.00 0.00 0.00 3.02
164 165 8.958119 AATATCGGTTGCTAAAGTTTATCTCA 57.042 30.769 0.00 0.00 0.00 3.27
169 170 9.656040 TGAACTAATATCGGTTGCTAAAGTTTA 57.344 29.630 0.00 0.00 0.00 2.01
170 171 8.556213 TGAACTAATATCGGTTGCTAAAGTTT 57.444 30.769 0.00 0.00 0.00 2.66
171 172 8.448615 GTTGAACTAATATCGGTTGCTAAAGTT 58.551 33.333 0.00 0.00 0.00 2.66
172 173 7.822822 AGTTGAACTAATATCGGTTGCTAAAGT 59.177 33.333 0.00 0.00 0.00 2.66
173 174 8.197988 AGTTGAACTAATATCGGTTGCTAAAG 57.802 34.615 0.00 0.00 0.00 1.85
174 175 9.656040 TTAGTTGAACTAATATCGGTTGCTAAA 57.344 29.630 13.39 0.00 35.89 1.85
175 176 9.090692 GTTAGTTGAACTAATATCGGTTGCTAA 57.909 33.333 19.48 0.00 42.06 3.09
176 177 7.707893 GGTTAGTTGAACTAATATCGGTTGCTA 59.292 37.037 19.48 0.00 42.06 3.49
177 178 6.537660 GGTTAGTTGAACTAATATCGGTTGCT 59.462 38.462 19.48 0.00 42.06 3.91
178 179 6.314400 TGGTTAGTTGAACTAATATCGGTTGC 59.686 38.462 19.48 4.87 42.06 4.17
179 180 7.332430 TGTGGTTAGTTGAACTAATATCGGTTG 59.668 37.037 19.48 0.00 42.06 3.77
180 181 7.388437 TGTGGTTAGTTGAACTAATATCGGTT 58.612 34.615 19.48 0.00 42.06 4.44
181 182 6.938507 TGTGGTTAGTTGAACTAATATCGGT 58.061 36.000 19.48 0.00 42.06 4.69
182 183 8.335356 CAATGTGGTTAGTTGAACTAATATCGG 58.665 37.037 19.48 4.88 42.06 4.18
183 184 8.879759 ACAATGTGGTTAGTTGAACTAATATCG 58.120 33.333 19.48 8.52 42.06 2.92
185 186 9.733556 TGACAATGTGGTTAGTTGAACTAATAT 57.266 29.630 19.48 10.05 42.06 1.28
186 187 9.733556 ATGACAATGTGGTTAGTTGAACTAATA 57.266 29.630 19.48 10.20 42.06 0.98
187 188 8.635765 ATGACAATGTGGTTAGTTGAACTAAT 57.364 30.769 19.48 2.53 42.06 1.73
188 189 7.717436 TGATGACAATGTGGTTAGTTGAACTAA 59.283 33.333 13.39 13.39 38.28 2.24
189 190 7.172532 GTGATGACAATGTGGTTAGTTGAACTA 59.827 37.037 0.00 0.00 38.21 2.24
190 191 6.017109 GTGATGACAATGTGGTTAGTTGAACT 60.017 38.462 2.37 2.37 38.21 3.01
191 192 6.142817 GTGATGACAATGTGGTTAGTTGAAC 58.857 40.000 0.00 0.00 37.31 3.18
192 193 5.825151 TGTGATGACAATGTGGTTAGTTGAA 59.175 36.000 0.00 0.00 0.00 2.69
193 194 5.238432 GTGTGATGACAATGTGGTTAGTTGA 59.762 40.000 0.00 0.00 32.49 3.18
194 195 5.451908 GTGTGATGACAATGTGGTTAGTTG 58.548 41.667 0.00 0.00 32.49 3.16
195 196 4.518970 GGTGTGATGACAATGTGGTTAGTT 59.481 41.667 0.00 0.00 32.49 2.24
196 197 4.072131 GGTGTGATGACAATGTGGTTAGT 58.928 43.478 0.00 0.00 32.49 2.24
197 198 4.071423 TGGTGTGATGACAATGTGGTTAG 58.929 43.478 0.00 0.00 32.49 2.34
198 199 4.092116 TGGTGTGATGACAATGTGGTTA 57.908 40.909 0.00 0.00 32.49 2.85
199 200 2.942804 TGGTGTGATGACAATGTGGTT 58.057 42.857 0.00 0.00 32.49 3.67
200 201 2.655090 TGGTGTGATGACAATGTGGT 57.345 45.000 0.00 0.00 32.49 4.16
201 202 4.319139 TTTTGGTGTGATGACAATGTGG 57.681 40.909 0.00 0.00 32.49 4.17
202 203 5.574055 GCTATTTTGGTGTGATGACAATGTG 59.426 40.000 0.00 0.00 32.49 3.21
203 204 5.477984 AGCTATTTTGGTGTGATGACAATGT 59.522 36.000 0.00 0.00 32.49 2.71
204 205 5.957798 AGCTATTTTGGTGTGATGACAATG 58.042 37.500 0.00 0.00 32.49 2.82
205 206 6.594788 AAGCTATTTTGGTGTGATGACAAT 57.405 33.333 0.00 0.00 32.49 2.71
206 207 7.230510 ACTTAAGCTATTTTGGTGTGATGACAA 59.769 33.333 1.29 0.00 32.49 3.18
207 208 6.714810 ACTTAAGCTATTTTGGTGTGATGACA 59.285 34.615 1.29 0.00 0.00 3.58
208 209 7.023575 CACTTAAGCTATTTTGGTGTGATGAC 58.976 38.462 1.29 0.00 0.00 3.06
209 210 6.349280 GCACTTAAGCTATTTTGGTGTGATGA 60.349 38.462 1.29 0.00 0.00 2.92
210 211 5.801947 GCACTTAAGCTATTTTGGTGTGATG 59.198 40.000 1.29 0.00 0.00 3.07
211 212 5.105756 GGCACTTAAGCTATTTTGGTGTGAT 60.106 40.000 1.29 0.00 34.17 3.06
212 213 4.217550 GGCACTTAAGCTATTTTGGTGTGA 59.782 41.667 1.29 0.00 34.17 3.58
213 214 4.022416 TGGCACTTAAGCTATTTTGGTGTG 60.022 41.667 1.29 0.00 34.17 3.82
214 215 4.148838 TGGCACTTAAGCTATTTTGGTGT 58.851 39.130 1.29 0.00 34.17 4.16
215 216 4.782019 TGGCACTTAAGCTATTTTGGTG 57.218 40.909 1.29 0.00 34.17 4.17
216 217 6.405842 GCTAATGGCACTTAAGCTATTTTGGT 60.406 38.462 1.29 0.00 42.08 3.67
217 218 5.979517 GCTAATGGCACTTAAGCTATTTTGG 59.020 40.000 1.29 0.00 42.08 3.28
233 234 2.989422 ACGTTGAAAGTGCTAATGGC 57.011 45.000 0.00 0.00 42.22 4.40
234 235 4.634004 TGGATACGTTGAAAGTGCTAATGG 59.366 41.667 0.00 0.00 42.51 3.16
235 236 5.121611 TGTGGATACGTTGAAAGTGCTAATG 59.878 40.000 0.00 0.00 42.51 1.90
236 237 5.242434 TGTGGATACGTTGAAAGTGCTAAT 58.758 37.500 0.00 0.00 42.51 1.73
237 238 4.633175 TGTGGATACGTTGAAAGTGCTAA 58.367 39.130 0.00 0.00 42.51 3.09
238 239 4.260139 TGTGGATACGTTGAAAGTGCTA 57.740 40.909 0.00 0.00 42.51 3.49
239 240 3.120321 TGTGGATACGTTGAAAGTGCT 57.880 42.857 0.00 0.00 42.51 4.40
240 241 3.364964 CCTTGTGGATACGTTGAAAGTGC 60.365 47.826 0.00 0.00 42.51 4.40
241 242 4.062293 TCCTTGTGGATACGTTGAAAGTG 58.938 43.478 0.00 0.00 37.46 3.16
242 243 4.315803 CTCCTTGTGGATACGTTGAAAGT 58.684 43.478 0.00 0.00 42.29 2.66
243 244 3.684788 CCTCCTTGTGGATACGTTGAAAG 59.315 47.826 0.00 0.00 42.29 2.62
244 245 3.558321 CCCTCCTTGTGGATACGTTGAAA 60.558 47.826 0.00 0.00 42.29 2.69
245 246 2.027561 CCCTCCTTGTGGATACGTTGAA 60.028 50.000 0.00 0.00 42.29 2.69
246 247 1.553248 CCCTCCTTGTGGATACGTTGA 59.447 52.381 0.00 0.00 42.29 3.18
247 248 1.406887 CCCCTCCTTGTGGATACGTTG 60.407 57.143 0.00 0.00 42.29 4.10
248 249 0.909623 CCCCTCCTTGTGGATACGTT 59.090 55.000 0.00 0.00 42.29 3.99
327 332 2.158219 TCCTCACTTTCCCTACCAGTGA 60.158 50.000 0.00 1.53 43.71 3.41
339 344 0.178990 GGCACACCCTTCCTCACTTT 60.179 55.000 0.00 0.00 0.00 2.66
345 350 0.779997 AATCTTGGCACACCCTTCCT 59.220 50.000 0.00 0.00 39.29 3.36
396 401 6.266323 ACTACTAGTAGTCGATGTGCAAATG 58.734 40.000 26.61 1.92 42.30 2.32
397 402 6.452494 ACTACTAGTAGTCGATGTGCAAAT 57.548 37.500 26.61 2.73 42.30 2.32
469 475 8.328758 TGATCCAACTTTCTATGAGGTTGTAAT 58.671 33.333 0.00 0.00 37.80 1.89
472 478 6.126863 TGATCCAACTTTCTATGAGGTTGT 57.873 37.500 0.00 0.00 37.80 3.32
551 563 5.309638 TGGTGCAACTTTAGTACTGCATTA 58.690 37.500 5.39 3.31 41.83 1.90
648 661 3.493503 GTCTTCGTTGTTGGATTCTTCGT 59.506 43.478 0.00 0.00 0.00 3.85
664 677 4.511454 TGTCAAAATTCAGACCTGTCTTCG 59.489 41.667 0.00 0.00 37.98 3.79
671 684 1.531149 CGCGTGTCAAAATTCAGACCT 59.469 47.619 0.00 0.00 33.89 3.85
673 686 1.263217 ACCGCGTGTCAAAATTCAGAC 59.737 47.619 4.92 3.88 35.37 3.51
723 736 8.630037 AGATCCATATTCGTTTATTTTGGGTTC 58.370 33.333 0.00 0.00 0.00 3.62
741 754 5.159637 TCGGAAGGGGAAAATAGATCCATA 58.840 41.667 0.00 0.00 38.80 2.74
750 763 3.496160 CGGTCATATCGGAAGGGGAAAAT 60.496 47.826 0.00 0.00 0.00 1.82
786 799 5.423015 AGTACATGTGGTCATCTGCTTTAG 58.577 41.667 9.11 0.00 31.15 1.85
790 803 3.181471 GCTAGTACATGTGGTCATCTGCT 60.181 47.826 9.11 0.00 31.15 4.24
793 806 5.046304 AGTTTGCTAGTACATGTGGTCATCT 60.046 40.000 9.11 0.29 31.15 2.90
848 861 0.603975 GTTGGAGAGAACAAGCGGCT 60.604 55.000 0.00 0.00 0.00 5.52
870 883 6.261381 TCCTAAAATCTTAAAAGTGCACGTGT 59.739 34.615 18.38 5.84 0.00 4.49
872 885 6.870971 TCCTAAAATCTTAAAAGTGCACGT 57.129 33.333 12.01 5.01 0.00 4.49
1259 1293 1.016130 CACGAAGTACAGGCCTGCAG 61.016 60.000 33.06 18.46 41.61 4.41
1416 1450 1.136147 CGAGCAGAAAGGCACATGC 59.864 57.895 0.00 0.00 38.97 4.06
1417 1451 1.129998 CTTCGAGCAGAAAGGCACATG 59.870 52.381 0.00 0.00 38.57 3.21
1625 1661 5.488341 ACTTATGAGCCACAGTTACGAAAT 58.512 37.500 0.00 0.00 0.00 2.17
1643 1679 5.497474 ACCCAACAAGCTCGATAAACTTAT 58.503 37.500 0.00 0.00 0.00 1.73
1760 1796 6.106673 ACAGTATGGAAAATACAGGAACTCG 58.893 40.000 0.00 0.00 43.62 4.18
1864 1900 6.139679 TGATCATCTCCTGGTTTACCTTTT 57.860 37.500 0.00 0.00 36.82 2.27
1875 1911 8.733458 TGTTCATTTTAAGTTGATCATCTCCTG 58.267 33.333 6.75 2.04 0.00 3.86
2168 2204 4.353777 TCCCTGCTAGAACTCTACAATGT 58.646 43.478 0.00 0.00 0.00 2.71
2265 2311 8.515695 AAATCATGAATCTAATCAGCAGTTCA 57.484 30.769 0.00 0.00 31.76 3.18
2266 2312 9.798994 AAAAATCATGAATCTAATCAGCAGTTC 57.201 29.630 0.00 0.00 31.76 3.01
2433 2482 5.419542 CATGAAGCACTAGCCAAAGTACTA 58.580 41.667 0.00 0.00 43.56 1.82
2435 2484 3.375299 CCATGAAGCACTAGCCAAAGTAC 59.625 47.826 0.00 0.00 43.56 2.73
2546 2595 2.611292 GTGATGCATTGAGGCTGTAGAC 59.389 50.000 0.00 0.00 34.04 2.59


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

AutoCloner maintained by Alex Coulton.