Multiple sequence alignment - TraesCS2D01G083300

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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 TraesCS2D01G083300 chr2D 100.000 3105 0 0 1 3105 36051266 36054370 0.000000e+00 5734.0
1 TraesCS2D01G083300 chr2D 79.525 1431 238 39 698 2104 36096532 36095133 0.000000e+00 968.0
2 TraesCS2D01G083300 chr2D 78.516 1024 168 23 706 1710 35978444 35979434 2.630000e-175 625.0
3 TraesCS2D01G083300 chr2D 95.522 335 15 0 1 335 88389515 88389181 1.270000e-148 536.0
4 TraesCS2D01G083300 chr2D 93.651 189 12 0 2769 2957 36198016 36198204 1.820000e-72 283.0
5 TraesCS2D01G083300 chr2D 92.857 168 6 1 381 542 35927102 35927269 4.000000e-59 239.0
6 TraesCS2D01G083300 chr2D 87.571 177 13 5 355 528 36096806 36096636 2.440000e-46 196.0
7 TraesCS2D01G083300 chr2D 87.500 56 6 1 427 481 36051651 36051706 2.590000e-06 63.9
8 TraesCS2D01G083300 chr2A 93.042 2659 105 29 346 2957 39453411 39450786 0.000000e+00 3812.0
9 TraesCS2D01G083300 chr2A 94.454 2218 82 23 870 3061 39355087 39357289 0.000000e+00 3376.0
10 TraesCS2D01G083300 chr2A 94.221 2111 92 18 853 2957 39410724 39408638 0.000000e+00 3195.0
11 TraesCS2D01G083300 chr2A 78.537 1258 230 28 870 2104 39310857 39312097 0.000000e+00 791.0
12 TraesCS2D01G083300 chr2A 90.976 410 35 2 1551 1960 39418930 39418523 4.530000e-153 551.0
13 TraesCS2D01G083300 chr2A 96.371 248 8 1 361 608 39310506 39310752 1.040000e-109 407.0
14 TraesCS2D01G083300 chr2A 95.930 172 4 3 432 603 39354800 39354968 3.050000e-70 276.0
15 TraesCS2D01G083300 chr2A 92.000 100 6 2 340 438 39411073 39410975 4.180000e-29 139.0
16 TraesCS2D01G083300 chr2B 90.579 2558 96 51 435 2957 61476914 61474467 0.000000e+00 3254.0
17 TraesCS2D01G083300 chr2B 84.735 1284 105 40 462 1737 61366967 61368167 0.000000e+00 1201.0
18 TraesCS2D01G083300 chr2B 92.982 684 47 1 1326 2009 61311780 61312462 0.000000e+00 996.0
19 TraesCS2D01G083300 chr2B 78.494 1474 250 43 653 2105 61361825 61363252 0.000000e+00 904.0
20 TraesCS2D01G083300 chr2B 91.629 657 42 7 1724 2371 61369454 61370106 0.000000e+00 896.0
21 TraesCS2D01G083300 chr2B 92.814 167 6 3 382 542 61491921 61491755 1.440000e-58 237.0
22 TraesCS2D01G083300 chr2B 91.509 106 3 3 381 480 61491968 61491863 1.160000e-29 141.0
23 TraesCS2D01G083300 chr2B 94.366 71 4 0 349 419 61366884 61366954 3.270000e-20 110.0
24 TraesCS2D01G083300 chr2B 83.333 108 9 1 2696 2794 754143332 754143439 1.190000e-14 91.6
25 TraesCS2D01G083300 chr3D 92.703 836 51 5 1160 1994 380122973 380123799 0.000000e+00 1197.0
26 TraesCS2D01G083300 chr3D 91.447 608 39 10 1981 2584 380132158 380132756 0.000000e+00 822.0
27 TraesCS2D01G083300 chr1D 95.745 329 14 0 2 330 399186999 399187327 5.900000e-147 531.0
28 TraesCS2D01G083300 chr1D 94.864 331 17 0 1 331 321640043 321640373 4.590000e-143 518.0
29 TraesCS2D01G083300 chr1D 86.486 111 6 2 2696 2797 51831534 51831644 2.530000e-21 113.0
30 TraesCS2D01G083300 chr7D 94.529 329 18 0 1 329 236499743 236500071 2.760000e-140 508.0
31 TraesCS2D01G083300 chr3B 93.413 334 22 0 1 334 806263092 806262759 2.150000e-136 496.0
32 TraesCS2D01G083300 chr1B 93.656 331 21 0 1 331 238681769 238682099 2.150000e-136 496.0
33 TraesCS2D01G083300 chr1B 87.719 114 4 3 2694 2797 633717402 633717289 1.170000e-24 124.0
34 TraesCS2D01G083300 chr5B 93.353 331 22 0 1 331 53652566 53652236 1.000000e-134 490.0
35 TraesCS2D01G083300 chr5A 92.308 338 25 1 1 337 45752106 45751769 2.170000e-131 479.0
36 TraesCS2D01G083300 chr7B 92.749 331 23 1 1 331 41489262 41488933 7.790000e-131 477.0
37 TraesCS2D01G083300 chrUn 88.288 111 4 2 2696 2797 261568265 261568375 1.170000e-24 124.0
38 TraesCS2D01G083300 chr7A 86.364 110 7 2 2696 2797 710797023 710797132 2.530000e-21 113.0
39 TraesCS2D01G083300 chr6B 93.220 59 4 0 2696 2754 450091714 450091772 1.530000e-13 87.9


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 TraesCS2D01G083300 chr2D 36051266 36054370 3104 False 2898.95 5734 93.7500 1 3105 2 chr2D.!!$F4 3104
1 TraesCS2D01G083300 chr2D 35978444 35979434 990 False 625.00 625 78.5160 706 1710 1 chr2D.!!$F2 1004
2 TraesCS2D01G083300 chr2D 36095133 36096806 1673 True 582.00 968 83.5480 355 2104 2 chr2D.!!$R2 1749
3 TraesCS2D01G083300 chr2A 39450786 39453411 2625 True 3812.00 3812 93.0420 346 2957 1 chr2A.!!$R2 2611
4 TraesCS2D01G083300 chr2A 39354800 39357289 2489 False 1826.00 3376 95.1920 432 3061 2 chr2A.!!$F2 2629
5 TraesCS2D01G083300 chr2A 39408638 39411073 2435 True 1667.00 3195 93.1105 340 2957 2 chr2A.!!$R3 2617
6 TraesCS2D01G083300 chr2A 39310506 39312097 1591 False 599.00 791 87.4540 361 2104 2 chr2A.!!$F1 1743
7 TraesCS2D01G083300 chr2B 61474467 61476914 2447 True 3254.00 3254 90.5790 435 2957 1 chr2B.!!$R1 2522
8 TraesCS2D01G083300 chr2B 61311780 61312462 682 False 996.00 996 92.9820 1326 2009 1 chr2B.!!$F1 683
9 TraesCS2D01G083300 chr2B 61361825 61370106 8281 False 777.75 1201 87.3060 349 2371 4 chr2B.!!$F3 2022
10 TraesCS2D01G083300 chr3D 380122973 380123799 826 False 1197.00 1197 92.7030 1160 1994 1 chr3D.!!$F1 834
11 TraesCS2D01G083300 chr3D 380132158 380132756 598 False 822.00 822 91.4470 1981 2584 1 chr3D.!!$F2 603

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
239 240 0.034670 ATCTCTTCTGGCTGGCCAAC 60.035 55.0 15.47 0.65 46.63 3.77 F
273 274 0.038159 CAGCCGAACGGACTCTCTTT 60.038 55.0 17.63 0.00 37.50 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 6300 2.223900 TGGATCACACATCTCATCGCTC 60.224 50.000 0.0 0.0 0.0 5.03 R
2235 8392 2.618241 TGAAACATGTGACCAACTCTGC 59.382 45.455 0.0 0.0 0.0 4.26 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
23 24 3.814268 CGTTGGCCCTTGCGGATG 61.814 66.667 0.00 0.00 38.85 3.51
24 25 2.361104 GTTGGCCCTTGCGGATGA 60.361 61.111 0.00 0.00 38.85 2.92
25 26 1.754234 GTTGGCCCTTGCGGATGAT 60.754 57.895 0.00 0.00 38.85 2.45
26 27 1.453745 TTGGCCCTTGCGGATGATC 60.454 57.895 0.00 0.00 38.85 2.92
27 28 1.925285 TTGGCCCTTGCGGATGATCT 61.925 55.000 0.00 0.00 38.85 2.75
28 29 1.895707 GGCCCTTGCGGATGATCTG 60.896 63.158 0.00 0.00 38.85 2.90
37 38 2.521105 CGGATGATCTGCATGTCTCA 57.479 50.000 0.00 0.00 37.34 3.27
38 39 2.830104 CGGATGATCTGCATGTCTCAA 58.170 47.619 0.00 0.00 37.34 3.02
40 41 3.740452 CGGATGATCTGCATGTCTCAACT 60.740 47.826 0.00 0.00 37.34 3.16
41 42 4.500375 CGGATGATCTGCATGTCTCAACTA 60.500 45.833 0.00 0.00 37.34 2.24
43 44 6.571150 CGGATGATCTGCATGTCTCAACTATA 60.571 42.308 0.00 0.00 37.34 1.31
45 46 6.469782 TGATCTGCATGTCTCAACTATACA 57.530 37.500 0.00 0.00 0.00 2.29
46 47 6.877236 TGATCTGCATGTCTCAACTATACAA 58.123 36.000 0.00 0.00 0.00 2.41
47 48 6.982724 TGATCTGCATGTCTCAACTATACAAG 59.017 38.462 0.00 0.00 0.00 3.16
51 52 4.034510 GCATGTCTCAACTATACAAGTGGC 59.965 45.833 0.00 0.00 38.88 5.01
53 54 3.257375 TGTCTCAACTATACAAGTGGCGT 59.743 43.478 0.00 0.00 38.88 5.68
54 55 3.858238 GTCTCAACTATACAAGTGGCGTC 59.142 47.826 0.00 0.00 38.88 5.19
55 56 3.119245 TCTCAACTATACAAGTGGCGTCC 60.119 47.826 0.00 0.00 38.88 4.79
56 57 1.924524 CAACTATACAAGTGGCGTCCG 59.075 52.381 0.00 0.00 38.88 4.79
57 58 1.466856 ACTATACAAGTGGCGTCCGA 58.533 50.000 0.00 0.00 36.93 4.55
58 59 1.133790 ACTATACAAGTGGCGTCCGAC 59.866 52.381 0.00 0.00 36.93 4.79
59 60 1.404391 CTATACAAGTGGCGTCCGACT 59.596 52.381 0.00 0.00 0.00 4.18
60 61 0.172803 ATACAAGTGGCGTCCGACTC 59.827 55.000 0.00 0.00 0.00 3.36
61 62 1.174078 TACAAGTGGCGTCCGACTCA 61.174 55.000 0.00 0.00 0.00 3.41
62 63 1.300620 CAAGTGGCGTCCGACTCAA 60.301 57.895 0.00 0.00 0.00 3.02
63 64 0.878523 CAAGTGGCGTCCGACTCAAA 60.879 55.000 0.00 0.00 0.00 2.69
64 65 0.600255 AAGTGGCGTCCGACTCAAAG 60.600 55.000 0.00 0.00 0.00 2.77
65 66 2.027625 GTGGCGTCCGACTCAAAGG 61.028 63.158 0.00 0.00 0.00 3.11
67 68 2.027625 GGCGTCCGACTCAAAGGTG 61.028 63.158 0.00 0.00 0.00 4.00
69 70 1.366366 CGTCCGACTCAAAGGTGGT 59.634 57.895 0.00 0.00 0.00 4.16
71 72 0.602905 GTCCGACTCAAAGGTGGTGG 60.603 60.000 0.00 0.00 0.00 4.61
74 75 0.944311 CGACTCAAAGGTGGTGGTCG 60.944 60.000 0.00 0.00 36.83 4.79
76 77 0.834612 ACTCAAAGGTGGTGGTCGAA 59.165 50.000 0.00 0.00 0.00 3.71
77 78 1.202651 ACTCAAAGGTGGTGGTCGAAG 60.203 52.381 0.00 0.00 0.00 3.79
78 79 1.070134 CTCAAAGGTGGTGGTCGAAGA 59.930 52.381 0.00 0.00 0.00 2.87
92 93 3.744238 TCGAAGACATCCAAGACAACA 57.256 42.857 0.00 0.00 0.00 3.33
93 94 4.066646 TCGAAGACATCCAAGACAACAA 57.933 40.909 0.00 0.00 0.00 2.83
94 95 4.641396 TCGAAGACATCCAAGACAACAAT 58.359 39.130 0.00 0.00 0.00 2.71
97 98 4.371624 AGACATCCAAGACAACAATCCA 57.628 40.909 0.00 0.00 0.00 3.41
99 100 4.520492 AGACATCCAAGACAACAATCCAAC 59.480 41.667 0.00 0.00 0.00 3.77
100 101 4.214310 ACATCCAAGACAACAATCCAACA 58.786 39.130 0.00 0.00 0.00 3.33
101 102 4.279169 ACATCCAAGACAACAATCCAACAG 59.721 41.667 0.00 0.00 0.00 3.16
102 103 3.897239 TCCAAGACAACAATCCAACAGT 58.103 40.909 0.00 0.00 0.00 3.55
103 104 5.042463 TCCAAGACAACAATCCAACAGTA 57.958 39.130 0.00 0.00 0.00 2.74
104 105 5.630121 TCCAAGACAACAATCCAACAGTAT 58.370 37.500 0.00 0.00 0.00 2.12
107 108 7.336679 TCCAAGACAACAATCCAACAGTATATG 59.663 37.037 0.00 0.00 0.00 1.78
108 109 7.415541 CCAAGACAACAATCCAACAGTATATGG 60.416 40.741 0.00 0.00 38.09 2.74
109 110 6.721318 AGACAACAATCCAACAGTATATGGT 58.279 36.000 0.00 0.00 37.94 3.55
110 111 6.599244 AGACAACAATCCAACAGTATATGGTG 59.401 38.462 0.00 0.00 46.97 4.17
111 112 5.125417 ACAACAATCCAACAGTATATGGTGC 59.875 40.000 0.00 0.00 45.98 5.01
112 113 3.876914 ACAATCCAACAGTATATGGTGCG 59.123 43.478 0.00 0.00 45.98 5.34
113 114 4.126437 CAATCCAACAGTATATGGTGCGA 58.874 43.478 0.00 0.00 45.98 5.10
114 115 4.623932 ATCCAACAGTATATGGTGCGAT 57.376 40.909 0.00 0.00 45.98 4.58
115 116 3.990092 TCCAACAGTATATGGTGCGATC 58.010 45.455 0.00 0.00 45.98 3.69
116 117 3.386402 TCCAACAGTATATGGTGCGATCA 59.614 43.478 0.00 0.00 45.98 2.92
117 118 4.040339 TCCAACAGTATATGGTGCGATCAT 59.960 41.667 0.00 0.00 45.98 2.45
118 119 5.245075 TCCAACAGTATATGGTGCGATCATA 59.755 40.000 0.00 0.00 45.98 2.15
119 120 5.348724 CCAACAGTATATGGTGCGATCATAC 59.651 44.000 0.00 0.00 45.98 2.39
120 121 5.722021 ACAGTATATGGTGCGATCATACA 57.278 39.130 0.00 0.00 30.94 2.29
121 122 6.286240 ACAGTATATGGTGCGATCATACAT 57.714 37.500 0.00 0.00 30.94 2.29
122 123 6.101997 ACAGTATATGGTGCGATCATACATG 58.898 40.000 0.00 0.00 30.94 3.21
123 124 6.071391 ACAGTATATGGTGCGATCATACATGA 60.071 38.462 0.00 0.00 41.70 3.07
124 125 6.813152 CAGTATATGGTGCGATCATACATGAA 59.187 38.462 0.00 0.00 40.69 2.57
125 126 7.331687 CAGTATATGGTGCGATCATACATGAAA 59.668 37.037 0.00 0.00 40.69 2.69
126 127 8.043113 AGTATATGGTGCGATCATACATGAAAT 58.957 33.333 0.00 0.00 40.69 2.17
127 128 9.313118 GTATATGGTGCGATCATACATGAAATA 57.687 33.333 0.00 0.00 40.69 1.40
128 129 8.791327 ATATGGTGCGATCATACATGAAATAA 57.209 30.769 0.00 0.00 40.69 1.40
129 130 7.692460 ATGGTGCGATCATACATGAAATAAT 57.308 32.000 0.00 0.00 40.69 1.28
130 131 8.791327 ATGGTGCGATCATACATGAAATAATA 57.209 30.769 0.00 0.00 40.69 0.98
134 135 8.113062 GTGCGATCATACATGAAATAATAGAGC 58.887 37.037 0.00 0.00 40.69 4.09
135 136 7.818930 TGCGATCATACATGAAATAATAGAGCA 59.181 33.333 0.00 0.00 40.69 4.26
155 156 8.358582 AGAGCATAGATCAAATTTCCTTTTGT 57.641 30.769 0.00 0.00 37.73 2.83
156 157 8.248945 AGAGCATAGATCAAATTTCCTTTTGTG 58.751 33.333 0.00 0.00 37.73 3.33
158 159 9.023962 AGCATAGATCAAATTTCCTTTTGTGTA 57.976 29.630 0.00 0.00 37.73 2.90
159 160 9.638239 GCATAGATCAAATTTCCTTTTGTGTAA 57.362 29.630 0.00 0.00 37.73 2.41
167 168 9.018716 CAAATTTCCTTTTGTGTAATTTTTGGC 57.981 29.630 0.00 0.00 32.99 4.52
170 171 4.806247 TCCTTTTGTGTAATTTTTGGCACG 59.194 37.500 0.00 0.00 34.86 5.34
171 172 4.806247 CCTTTTGTGTAATTTTTGGCACGA 59.194 37.500 0.00 0.00 34.86 4.35
172 173 5.292101 CCTTTTGTGTAATTTTTGGCACGAA 59.708 36.000 0.00 0.00 34.54 3.85
174 175 6.910536 TTTGTGTAATTTTTGGCACGAATT 57.089 29.167 10.84 10.84 32.28 2.17
175 176 6.910536 TTGTGTAATTTTTGGCACGAATTT 57.089 29.167 11.18 4.57 34.86 1.82
176 177 8.420374 TTTGTGTAATTTTTGGCACGAATTTA 57.580 26.923 11.18 3.81 32.28 1.40
177 178 7.630470 TGTGTAATTTTTGGCACGAATTTAG 57.370 32.000 11.18 0.00 34.86 1.85
178 179 6.642950 TGTGTAATTTTTGGCACGAATTTAGG 59.357 34.615 11.18 0.00 34.86 2.69
179 180 6.864165 GTGTAATTTTTGGCACGAATTTAGGA 59.136 34.615 11.18 0.00 0.00 2.94
180 181 7.061789 GTGTAATTTTTGGCACGAATTTAGGAG 59.938 37.037 11.18 0.00 0.00 3.69
181 182 3.569250 TTTTGGCACGAATTTAGGAGC 57.431 42.857 0.00 0.00 0.00 4.70
182 183 2.489938 TTGGCACGAATTTAGGAGCT 57.510 45.000 0.00 0.00 0.00 4.09
183 184 2.024176 TGGCACGAATTTAGGAGCTC 57.976 50.000 4.71 4.71 0.00 4.09
184 185 0.931005 GGCACGAATTTAGGAGCTCG 59.069 55.000 7.83 0.00 37.33 5.03
185 186 1.470979 GGCACGAATTTAGGAGCTCGA 60.471 52.381 7.83 0.00 35.34 4.04
187 188 2.866762 GCACGAATTTAGGAGCTCGAAT 59.133 45.455 7.83 5.28 35.34 3.34
188 189 4.049186 GCACGAATTTAGGAGCTCGAATA 58.951 43.478 7.83 0.00 35.34 1.75
190 191 5.164041 GCACGAATTTAGGAGCTCGAATATC 60.164 44.000 7.83 5.33 35.34 1.63
191 192 5.059832 CACGAATTTAGGAGCTCGAATATCG 59.940 44.000 20.89 20.89 42.10 2.92
204 205 3.759086 TCGAATATCGAGGCTCATAAGCT 59.241 43.478 15.95 0.00 44.82 3.74
205 206 4.101942 CGAATATCGAGGCTCATAAGCTC 58.898 47.826 15.95 2.67 44.87 4.09
206 207 5.248200 CGAATATCGAGGCTCATAAGCTCG 61.248 50.000 15.95 10.80 44.87 5.03
229 230 5.080642 CGAAGCATGCTTTATCTCTTCTG 57.919 43.478 32.36 10.81 36.26 3.02
230 231 4.025061 CGAAGCATGCTTTATCTCTTCTGG 60.025 45.833 32.36 5.39 36.26 3.86
231 232 3.212685 AGCATGCTTTATCTCTTCTGGC 58.787 45.455 16.30 0.00 0.00 4.85
233 234 3.003482 GCATGCTTTATCTCTTCTGGCTG 59.997 47.826 11.37 0.00 0.00 4.85
234 235 3.272574 TGCTTTATCTCTTCTGGCTGG 57.727 47.619 0.00 0.00 0.00 4.85
235 236 1.946081 GCTTTATCTCTTCTGGCTGGC 59.054 52.381 0.00 0.00 0.00 4.85
236 237 2.570135 CTTTATCTCTTCTGGCTGGCC 58.430 52.381 4.43 4.43 0.00 5.36
239 240 0.034670 ATCTCTTCTGGCTGGCCAAC 60.035 55.000 15.47 0.65 46.63 3.77
240 241 1.073722 CTCTTCTGGCTGGCCAACA 59.926 57.895 15.47 8.39 46.63 3.33
242 243 0.609957 TCTTCTGGCTGGCCAACATG 60.610 55.000 15.47 4.17 46.63 3.21
243 244 0.896940 CTTCTGGCTGGCCAACATGT 60.897 55.000 15.47 0.00 46.63 3.21
244 245 0.469705 TTCTGGCTGGCCAACATGTT 60.470 50.000 15.47 4.92 46.63 2.71
246 247 0.320073 CTGGCTGGCCAACATGTTTG 60.320 55.000 15.47 6.85 46.63 2.93
247 248 1.004679 GGCTGGCCAACATGTTTGG 60.005 57.895 8.77 14.50 42.37 3.28
249 250 0.106521 GCTGGCCAACATGTTTGGTT 59.893 50.000 20.87 0.00 41.53 3.67
250 251 1.868469 CTGGCCAACATGTTTGGTTG 58.132 50.000 20.87 7.88 43.99 3.77
257 258 1.039856 ACATGTTTGGTTGGGACAGC 58.960 50.000 0.00 0.00 42.39 4.40
264 265 3.047877 GTTGGGACAGCCGAACGG 61.048 66.667 9.00 9.00 41.93 4.44
265 266 3.235481 TTGGGACAGCCGAACGGA 61.235 61.111 17.63 0.00 42.39 4.69
266 267 3.524648 TTGGGACAGCCGAACGGAC 62.525 63.158 17.63 8.31 42.39 4.79
267 268 3.692406 GGGACAGCCGAACGGACT 61.692 66.667 17.63 10.41 37.50 3.85
268 269 2.126031 GGACAGCCGAACGGACTC 60.126 66.667 17.63 7.00 37.50 3.36
269 270 2.637383 GGACAGCCGAACGGACTCT 61.637 63.158 17.63 1.81 37.50 3.24
271 272 1.587933 GACAGCCGAACGGACTCTCT 61.588 60.000 17.63 1.06 37.50 3.10
273 274 0.038159 CAGCCGAACGGACTCTCTTT 60.038 55.000 17.63 0.00 37.50 2.52
274 275 0.244178 AGCCGAACGGACTCTCTTTC 59.756 55.000 17.63 0.00 37.50 2.62
275 276 1.071567 GCCGAACGGACTCTCTTTCG 61.072 60.000 17.63 0.00 40.39 3.46
276 277 0.240411 CCGAACGGACTCTCTTTCGT 59.760 55.000 7.53 0.00 39.33 3.85
277 278 1.335689 CCGAACGGACTCTCTTTCGTT 60.336 52.381 7.53 0.00 46.45 3.85
280 281 3.662247 AACGGACTCTCTTTCGTTCAT 57.338 42.857 0.00 0.00 41.14 2.57
281 282 2.947852 ACGGACTCTCTTTCGTTCATG 58.052 47.619 0.00 0.00 31.38 3.07
282 283 2.296471 ACGGACTCTCTTTCGTTCATGT 59.704 45.455 0.00 0.00 31.38 3.21
286 287 5.164080 CGGACTCTCTTTCGTTCATGTAAAC 60.164 44.000 0.00 0.00 0.00 2.01
288 289 6.369065 GGACTCTCTTTCGTTCATGTAAACAT 59.631 38.462 0.00 0.00 36.96 2.71
290 291 7.576236 ACTCTCTTTCGTTCATGTAAACATTG 58.424 34.615 0.00 0.00 33.61 2.82
291 292 7.226720 ACTCTCTTTCGTTCATGTAAACATTGT 59.773 33.333 0.00 0.00 33.61 2.71
292 293 7.351981 TCTCTTTCGTTCATGTAAACATTGTG 58.648 34.615 0.00 0.00 33.61 3.33
293 294 7.225734 TCTCTTTCGTTCATGTAAACATTGTGA 59.774 33.333 0.00 0.00 33.61 3.58
295 296 5.012655 TCGTTCATGTAAACATTGTGACG 57.987 39.130 0.00 2.73 33.61 4.35
297 298 4.838642 CGTTCATGTAAACATTGTGACGTC 59.161 41.667 9.11 9.11 33.61 4.34
298 299 4.639189 TCATGTAAACATTGTGACGTCG 57.361 40.909 11.62 0.00 33.61 5.12
299 300 4.052608 TCATGTAAACATTGTGACGTCGT 58.947 39.130 11.62 0.00 33.61 4.34
301 302 5.690857 TCATGTAAACATTGTGACGTCGTAA 59.309 36.000 11.62 8.87 33.61 3.18
302 303 6.366604 TCATGTAAACATTGTGACGTCGTAAT 59.633 34.615 11.62 10.84 33.61 1.89
303 304 7.541437 TCATGTAAACATTGTGACGTCGTAATA 59.459 33.333 11.62 0.00 33.61 0.98
305 306 8.070007 TGTAAACATTGTGACGTCGTAATAAA 57.930 30.769 11.62 0.00 0.00 1.40
306 307 8.546244 TGTAAACATTGTGACGTCGTAATAAAA 58.454 29.630 11.62 0.00 0.00 1.52
307 308 9.033262 GTAAACATTGTGACGTCGTAATAAAAG 57.967 33.333 11.62 4.92 0.00 2.27
308 309 6.774354 ACATTGTGACGTCGTAATAAAAGT 57.226 33.333 11.62 5.49 0.00 2.66
309 310 7.181143 ACATTGTGACGTCGTAATAAAAGTT 57.819 32.000 11.62 0.00 0.00 2.66
310 311 7.632721 ACATTGTGACGTCGTAATAAAAGTTT 58.367 30.769 11.62 0.00 0.00 2.66
311 312 7.795272 ACATTGTGACGTCGTAATAAAAGTTTC 59.205 33.333 11.62 0.00 0.00 2.78
312 313 5.892776 TGTGACGTCGTAATAAAAGTTTCG 58.107 37.500 11.62 0.00 0.00 3.46
313 314 5.107913 TGTGACGTCGTAATAAAAGTTTCGG 60.108 40.000 11.62 0.00 0.00 4.30
314 315 5.116983 GTGACGTCGTAATAAAAGTTTCGGA 59.883 40.000 11.62 0.00 0.00 4.55
316 317 5.222631 ACGTCGTAATAAAAGTTTCGGAGT 58.777 37.500 0.00 0.00 0.00 3.85
317 318 5.691754 ACGTCGTAATAAAAGTTTCGGAGTT 59.308 36.000 0.00 0.00 0.00 3.01
318 319 6.200854 ACGTCGTAATAAAAGTTTCGGAGTTT 59.799 34.615 0.00 0.00 32.23 2.66
319 320 6.513991 CGTCGTAATAAAAGTTTCGGAGTTTG 59.486 38.462 0.00 0.00 31.32 2.93
320 321 6.301607 GTCGTAATAAAAGTTTCGGAGTTTGC 59.698 38.462 0.00 0.00 31.32 3.68
322 323 5.784578 AATAAAAGTTTCGGAGTTTGCCT 57.215 34.783 0.00 0.00 31.32 4.75
324 325 6.887626 ATAAAAGTTTCGGAGTTTGCCTAA 57.112 33.333 0.00 0.00 31.32 2.69
325 326 5.585820 AAAAGTTTCGGAGTTTGCCTAAA 57.414 34.783 0.00 0.00 31.32 1.85
326 327 5.585820 AAAGTTTCGGAGTTTGCCTAAAA 57.414 34.783 0.00 0.00 29.74 1.52
625 5344 3.762288 GGTGACCCCTATTTTCCTTTCAC 59.238 47.826 0.00 0.00 32.98 3.18
669 5389 3.097162 CCCTCCCCCAACCCTAGC 61.097 72.222 0.00 0.00 0.00 3.42
695 5415 1.618837 TGTGGCTCTCTTGTGGAGTAC 59.381 52.381 0.00 0.00 42.40 2.73
742 5491 1.227883 CCGACTCGGGCTCTAGCTA 60.228 63.158 9.85 0.00 44.15 3.32
1026 5841 2.849007 CGTCAGCACTCGCAACTG 59.151 61.111 0.00 0.00 42.27 3.16
1403 6239 2.475111 CCGGTGATACGTTGTATGCATC 59.525 50.000 0.19 0.00 0.00 3.91
1479 6315 1.826024 GGGGAGCGATGAGATGTGT 59.174 57.895 0.00 0.00 0.00 3.72
1537 6374 2.709883 CCATCGCCACCGCCATTTT 61.710 57.895 0.00 0.00 0.00 1.82
2160 8311 6.375455 CCCTGCTTTGTAATCTTGATGTAAGT 59.625 38.462 0.00 0.00 37.65 2.24
2174 8325 6.908870 TGATGTAAGTTGCTGTGATATGTC 57.091 37.500 0.00 0.00 0.00 3.06
2175 8326 6.405538 TGATGTAAGTTGCTGTGATATGTCA 58.594 36.000 0.00 0.00 0.00 3.58
2235 8392 2.982470 GCAATTTTCTTGAACCTGAGCG 59.018 45.455 0.00 0.00 0.00 5.03
2241 8398 0.320247 CTTGAACCTGAGCGCAGAGT 60.320 55.000 19.95 12.01 45.17 3.24
2327 8489 5.047802 CAGTGATTAGAAAAGGTGGTGCAAT 60.048 40.000 0.00 0.00 0.00 3.56
2416 8580 9.817809 TCATTCTTTCGCAACTAAGAGTTATAT 57.182 29.630 0.00 0.00 36.03 0.86
2423 8587 6.493802 TCGCAACTAAGAGTTATATGATCCCT 59.506 38.462 0.00 0.00 36.03 4.20
2424 8588 6.587990 CGCAACTAAGAGTTATATGATCCCTG 59.412 42.308 0.00 0.00 36.03 4.45
2427 8591 8.424918 CAACTAAGAGTTATATGATCCCTGTGT 58.575 37.037 0.00 0.00 36.03 3.72
2428 8592 8.184304 ACTAAGAGTTATATGATCCCTGTGTC 57.816 38.462 0.00 0.00 0.00 3.67
2429 8593 8.007742 ACTAAGAGTTATATGATCCCTGTGTCT 58.992 37.037 0.00 0.00 0.00 3.41
2430 8594 9.521841 CTAAGAGTTATATGATCCCTGTGTCTA 57.478 37.037 0.00 0.00 0.00 2.59
2431 8595 8.415950 AAGAGTTATATGATCCCTGTGTCTAG 57.584 38.462 0.00 0.00 0.00 2.43
2432 8596 7.531317 AGAGTTATATGATCCCTGTGTCTAGT 58.469 38.462 0.00 0.00 0.00 2.57
2433 8597 7.668052 AGAGTTATATGATCCCTGTGTCTAGTC 59.332 40.741 0.00 0.00 0.00 2.59
2434 8598 7.298374 AGTTATATGATCCCTGTGTCTAGTCA 58.702 38.462 0.00 0.00 0.00 3.41
2435 8599 7.231722 AGTTATATGATCCCTGTGTCTAGTCAC 59.768 40.741 12.51 12.51 38.63 3.67
2436 8600 3.458044 TGATCCCTGTGTCTAGTCACT 57.542 47.619 18.76 0.76 38.90 3.41
2437 8601 4.586306 TGATCCCTGTGTCTAGTCACTA 57.414 45.455 18.76 6.82 38.90 2.74
2438 8602 4.270834 TGATCCCTGTGTCTAGTCACTAC 58.729 47.826 18.76 0.00 38.90 2.73
2439 8603 3.801307 TCCCTGTGTCTAGTCACTACA 57.199 47.619 18.76 0.00 38.90 2.74
2646 8847 7.977818 ACCTTATATGTTCATGCATAAGGAGA 58.022 34.615 25.42 3.89 46.98 3.71
2658 8872 6.305272 TGCATAAGGAGATAGGATTGGATC 57.695 41.667 0.00 0.00 0.00 3.36
2778 8994 7.069826 GGCTCATATGCTCTCCTCTTATAGATT 59.930 40.741 0.00 0.00 0.00 2.40
2849 9067 3.384146 TCAAGTTGTTTGCATGACATGGT 59.616 39.130 17.03 0.00 36.70 3.55
3061 9279 0.895530 TCAGCCCGTCAAGTAAGAGG 59.104 55.000 0.00 0.00 0.00 3.69
3062 9280 0.108138 CAGCCCGTCAAGTAAGAGGG 60.108 60.000 0.00 0.00 44.72 4.30
3063 9281 0.544595 AGCCCGTCAAGTAAGAGGGT 60.545 55.000 0.52 0.00 43.82 4.34
3064 9282 0.391263 GCCCGTCAAGTAAGAGGGTG 60.391 60.000 0.52 0.00 43.82 4.61
3065 9283 0.249398 CCCGTCAAGTAAGAGGGTGG 59.751 60.000 0.00 0.00 40.95 4.61
3066 9284 1.263356 CCGTCAAGTAAGAGGGTGGA 58.737 55.000 0.00 0.00 38.44 4.02
3067 9285 1.204941 CCGTCAAGTAAGAGGGTGGAG 59.795 57.143 0.00 0.00 38.44 3.86
3068 9286 2.168496 CGTCAAGTAAGAGGGTGGAGA 58.832 52.381 0.00 0.00 0.00 3.71
3069 9287 2.761208 CGTCAAGTAAGAGGGTGGAGAT 59.239 50.000 0.00 0.00 0.00 2.75
3070 9288 3.429547 CGTCAAGTAAGAGGGTGGAGATG 60.430 52.174 0.00 0.00 0.00 2.90
3071 9289 3.515901 GTCAAGTAAGAGGGTGGAGATGT 59.484 47.826 0.00 0.00 0.00 3.06
3072 9290 3.515502 TCAAGTAAGAGGGTGGAGATGTG 59.484 47.826 0.00 0.00 0.00 3.21
3073 9291 2.472029 AGTAAGAGGGTGGAGATGTGG 58.528 52.381 0.00 0.00 0.00 4.17
3074 9292 2.188817 GTAAGAGGGTGGAGATGTGGT 58.811 52.381 0.00 0.00 0.00 4.16
3075 9293 2.642171 AAGAGGGTGGAGATGTGGTA 57.358 50.000 0.00 0.00 0.00 3.25
3076 9294 1.867363 AGAGGGTGGAGATGTGGTAC 58.133 55.000 0.00 0.00 0.00 3.34
3077 9295 1.362932 AGAGGGTGGAGATGTGGTACT 59.637 52.381 0.00 0.00 0.00 2.73
3078 9296 2.188817 GAGGGTGGAGATGTGGTACTT 58.811 52.381 0.00 0.00 0.00 2.24
3079 9297 2.572104 GAGGGTGGAGATGTGGTACTTT 59.428 50.000 0.00 0.00 0.00 2.66
3080 9298 3.773119 GAGGGTGGAGATGTGGTACTTTA 59.227 47.826 0.00 0.00 0.00 1.85
3081 9299 4.172807 AGGGTGGAGATGTGGTACTTTAA 58.827 43.478 0.00 0.00 0.00 1.52
3082 9300 4.019591 AGGGTGGAGATGTGGTACTTTAAC 60.020 45.833 0.00 0.00 0.00 2.01
3083 9301 4.263156 GGGTGGAGATGTGGTACTTTAACA 60.263 45.833 0.00 0.00 0.00 2.41
3084 9302 4.694037 GGTGGAGATGTGGTACTTTAACAC 59.306 45.833 0.00 0.00 46.44 3.32
3085 9303 4.694037 GTGGAGATGTGGTACTTTAACACC 59.306 45.833 0.00 0.00 45.69 4.16
3086 9304 4.595781 TGGAGATGTGGTACTTTAACACCT 59.404 41.667 0.00 0.00 45.69 4.00
3087 9305 5.781306 TGGAGATGTGGTACTTTAACACCTA 59.219 40.000 0.00 0.00 45.69 3.08
3088 9306 6.442564 TGGAGATGTGGTACTTTAACACCTAT 59.557 38.462 0.00 0.00 45.69 2.57
3089 9307 6.761714 GGAGATGTGGTACTTTAACACCTATG 59.238 42.308 0.00 0.00 45.69 2.23
3090 9308 6.650120 AGATGTGGTACTTTAACACCTATGG 58.350 40.000 0.00 0.00 45.69 2.74
3091 9309 4.581868 TGTGGTACTTTAACACCTATGGC 58.418 43.478 0.00 0.00 45.69 4.40
3092 9310 4.287585 TGTGGTACTTTAACACCTATGGCT 59.712 41.667 0.00 0.00 45.69 4.75
3093 9311 5.221966 TGTGGTACTTTAACACCTATGGCTT 60.222 40.000 0.00 0.00 45.69 4.35
3094 9312 5.708697 GTGGTACTTTAACACCTATGGCTTT 59.291 40.000 0.00 0.00 40.48 3.51
3095 9313 5.708230 TGGTACTTTAACACCTATGGCTTTG 59.292 40.000 0.00 0.00 35.73 2.77
3096 9314 5.941647 GGTACTTTAACACCTATGGCTTTGA 59.058 40.000 0.00 0.00 0.00 2.69
3097 9315 6.602009 GGTACTTTAACACCTATGGCTTTGAT 59.398 38.462 0.00 0.00 0.00 2.57
3098 9316 7.122204 GGTACTTTAACACCTATGGCTTTGATT 59.878 37.037 0.00 0.00 0.00 2.57
3099 9317 6.924111 ACTTTAACACCTATGGCTTTGATTG 58.076 36.000 0.00 0.00 0.00 2.67
3100 9318 3.874392 AACACCTATGGCTTTGATTGC 57.126 42.857 0.00 0.00 0.00 3.56
3101 9319 2.806434 ACACCTATGGCTTTGATTGCA 58.194 42.857 0.00 0.00 0.00 4.08
3102 9320 2.756760 ACACCTATGGCTTTGATTGCAG 59.243 45.455 0.00 0.00 0.00 4.41
3103 9321 3.018856 CACCTATGGCTTTGATTGCAGA 58.981 45.455 0.00 0.00 0.00 4.26
3104 9322 3.635373 CACCTATGGCTTTGATTGCAGAT 59.365 43.478 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.263484 GACATGCAGATCATCCGCAAG 59.737 52.381 0.00 0.00 39.48 4.01
15 16 1.134310 AGACATGCAGATCATCCGCAA 60.134 47.619 0.00 0.00 39.48 4.85
16 17 0.466963 AGACATGCAGATCATCCGCA 59.533 50.000 0.00 0.00 40.50 5.69
17 18 1.146637 GAGACATGCAGATCATCCGC 58.853 55.000 0.00 0.00 31.79 5.54
18 19 2.521105 TGAGACATGCAGATCATCCG 57.479 50.000 0.00 0.00 31.79 4.18
19 20 3.806380 AGTTGAGACATGCAGATCATCC 58.194 45.455 0.00 0.00 31.79 3.51
20 21 7.150640 TGTATAGTTGAGACATGCAGATCATC 58.849 38.462 0.00 0.00 31.79 2.92
21 22 7.059202 TGTATAGTTGAGACATGCAGATCAT 57.941 36.000 0.00 0.00 35.31 2.45
23 24 6.983307 ACTTGTATAGTTGAGACATGCAGATC 59.017 38.462 0.00 0.00 31.29 2.75
24 25 6.760298 CACTTGTATAGTTGAGACATGCAGAT 59.240 38.462 0.00 0.00 33.85 2.90
25 26 6.101997 CACTTGTATAGTTGAGACATGCAGA 58.898 40.000 0.00 0.00 33.85 4.26
26 27 5.292834 CCACTTGTATAGTTGAGACATGCAG 59.707 44.000 0.00 0.00 33.85 4.41
27 28 5.178061 CCACTTGTATAGTTGAGACATGCA 58.822 41.667 0.00 0.00 33.85 3.96
28 29 4.034510 GCCACTTGTATAGTTGAGACATGC 59.965 45.833 0.00 0.00 33.85 4.06
29 30 4.268644 CGCCACTTGTATAGTTGAGACATG 59.731 45.833 0.00 0.00 33.85 3.21
30 31 4.081642 ACGCCACTTGTATAGTTGAGACAT 60.082 41.667 0.00 0.00 33.85 3.06
31 32 3.257375 ACGCCACTTGTATAGTTGAGACA 59.743 43.478 0.00 0.00 33.85 3.41
32 33 3.846360 ACGCCACTTGTATAGTTGAGAC 58.154 45.455 0.00 0.00 33.85 3.36
33 34 3.119245 GGACGCCACTTGTATAGTTGAGA 60.119 47.826 0.00 0.00 33.85 3.27
34 35 3.187700 GGACGCCACTTGTATAGTTGAG 58.812 50.000 0.00 0.00 33.85 3.02
35 36 2.416296 CGGACGCCACTTGTATAGTTGA 60.416 50.000 0.00 0.00 33.85 3.18
36 37 1.924524 CGGACGCCACTTGTATAGTTG 59.075 52.381 0.00 0.00 33.85 3.16
37 38 1.820519 TCGGACGCCACTTGTATAGTT 59.179 47.619 0.00 0.00 33.85 2.24
38 39 1.133790 GTCGGACGCCACTTGTATAGT 59.866 52.381 0.00 0.00 37.68 2.12
40 41 1.402968 GAGTCGGACGCCACTTGTATA 59.597 52.381 1.89 0.00 0.00 1.47
41 42 0.172803 GAGTCGGACGCCACTTGTAT 59.827 55.000 1.89 0.00 0.00 2.29
43 44 2.023414 TTGAGTCGGACGCCACTTGT 62.023 55.000 9.41 0.00 0.00 3.16
45 46 0.600255 CTTTGAGTCGGACGCCACTT 60.600 55.000 9.41 0.00 0.00 3.16
46 47 1.006102 CTTTGAGTCGGACGCCACT 60.006 57.895 9.41 0.00 0.00 4.00
47 48 2.027625 CCTTTGAGTCGGACGCCAC 61.028 63.158 9.41 0.88 0.00 5.01
51 52 0.944311 CACCACCTTTGAGTCGGACG 60.944 60.000 1.89 0.00 0.00 4.79
53 54 1.052124 ACCACCACCTTTGAGTCGGA 61.052 55.000 0.00 0.00 0.00 4.55
54 55 0.602905 GACCACCACCTTTGAGTCGG 60.603 60.000 0.00 0.00 0.00 4.79
55 56 0.944311 CGACCACCACCTTTGAGTCG 60.944 60.000 0.00 0.00 0.00 4.18
56 57 0.391597 TCGACCACCACCTTTGAGTC 59.608 55.000 0.00 0.00 0.00 3.36
57 58 0.834612 TTCGACCACCACCTTTGAGT 59.165 50.000 0.00 0.00 0.00 3.41
58 59 1.070134 TCTTCGACCACCACCTTTGAG 59.930 52.381 0.00 0.00 0.00 3.02
59 60 1.124780 TCTTCGACCACCACCTTTGA 58.875 50.000 0.00 0.00 0.00 2.69
60 61 1.226746 GTCTTCGACCACCACCTTTG 58.773 55.000 0.00 0.00 0.00 2.77
61 62 0.834612 TGTCTTCGACCACCACCTTT 59.165 50.000 0.00 0.00 0.00 3.11
62 63 1.002087 GATGTCTTCGACCACCACCTT 59.998 52.381 0.00 0.00 0.00 3.50
63 64 0.608640 GATGTCTTCGACCACCACCT 59.391 55.000 0.00 0.00 0.00 4.00
64 65 0.391263 GGATGTCTTCGACCACCACC 60.391 60.000 0.00 0.00 31.13 4.61
65 66 0.320374 TGGATGTCTTCGACCACCAC 59.680 55.000 0.00 0.00 34.13 4.16
67 68 1.275291 TCTTGGATGTCTTCGACCACC 59.725 52.381 0.00 0.00 31.87 4.61
69 70 1.967779 TGTCTTGGATGTCTTCGACCA 59.032 47.619 0.00 0.00 0.00 4.02
71 72 3.390135 TGTTGTCTTGGATGTCTTCGAC 58.610 45.455 0.00 0.00 0.00 4.20
74 75 4.761739 TGGATTGTTGTCTTGGATGTCTTC 59.238 41.667 0.00 0.00 0.00 2.87
76 77 4.371624 TGGATTGTTGTCTTGGATGTCT 57.628 40.909 0.00 0.00 0.00 3.41
77 78 4.278170 TGTTGGATTGTTGTCTTGGATGTC 59.722 41.667 0.00 0.00 0.00 3.06
78 79 4.214310 TGTTGGATTGTTGTCTTGGATGT 58.786 39.130 0.00 0.00 0.00 3.06
79 80 4.279169 ACTGTTGGATTGTTGTCTTGGATG 59.721 41.667 0.00 0.00 0.00 3.51
80 81 4.473444 ACTGTTGGATTGTTGTCTTGGAT 58.527 39.130 0.00 0.00 0.00 3.41
81 82 3.897239 ACTGTTGGATTGTTGTCTTGGA 58.103 40.909 0.00 0.00 0.00 3.53
82 83 5.964958 ATACTGTTGGATTGTTGTCTTGG 57.035 39.130 0.00 0.00 0.00 3.61
83 84 7.121168 ACCATATACTGTTGGATTGTTGTCTTG 59.879 37.037 4.09 0.00 36.79 3.02
84 85 7.121168 CACCATATACTGTTGGATTGTTGTCTT 59.879 37.037 4.09 0.00 36.79 3.01
85 86 6.599244 CACCATATACTGTTGGATTGTTGTCT 59.401 38.462 4.09 0.00 36.79 3.41
86 87 6.677920 GCACCATATACTGTTGGATTGTTGTC 60.678 42.308 4.09 0.00 36.79 3.18
87 88 5.125417 GCACCATATACTGTTGGATTGTTGT 59.875 40.000 4.09 0.00 36.79 3.32
88 89 5.581605 GCACCATATACTGTTGGATTGTTG 58.418 41.667 4.09 0.00 36.79 3.33
89 90 4.335315 CGCACCATATACTGTTGGATTGTT 59.665 41.667 4.09 0.00 36.79 2.83
91 92 4.126437 TCGCACCATATACTGTTGGATTG 58.874 43.478 4.09 0.00 36.79 2.67
92 93 4.415881 TCGCACCATATACTGTTGGATT 57.584 40.909 4.09 0.00 36.79 3.01
93 94 4.040339 TGATCGCACCATATACTGTTGGAT 59.960 41.667 4.09 0.00 36.79 3.41
94 95 3.386402 TGATCGCACCATATACTGTTGGA 59.614 43.478 4.09 0.00 36.79 3.53
97 98 6.096673 TGTATGATCGCACCATATACTGTT 57.903 37.500 0.00 0.00 0.00 3.16
99 100 6.332630 TCATGTATGATCGCACCATATACTG 58.667 40.000 0.00 0.00 0.00 2.74
100 101 6.530019 TCATGTATGATCGCACCATATACT 57.470 37.500 0.00 0.00 0.00 2.12
101 102 7.595311 TTTCATGTATGATCGCACCATATAC 57.405 36.000 0.00 0.00 36.56 1.47
102 103 9.883142 TTATTTCATGTATGATCGCACCATATA 57.117 29.630 0.00 0.00 36.56 0.86
103 104 8.791327 TTATTTCATGTATGATCGCACCATAT 57.209 30.769 0.00 0.00 36.56 1.78
104 105 8.791327 ATTATTTCATGTATGATCGCACCATA 57.209 30.769 0.00 0.00 36.56 2.74
107 108 8.479313 TCTATTATTTCATGTATGATCGCACC 57.521 34.615 0.00 0.00 36.56 5.01
108 109 8.113062 GCTCTATTATTTCATGTATGATCGCAC 58.887 37.037 0.00 0.00 36.56 5.34
109 110 7.818930 TGCTCTATTATTTCATGTATGATCGCA 59.181 33.333 0.00 0.00 36.56 5.10
110 111 8.189709 TGCTCTATTATTTCATGTATGATCGC 57.810 34.615 0.00 0.00 36.56 4.58
129 130 9.466497 ACAAAAGGAAATTTGATCTATGCTCTA 57.534 29.630 0.00 0.00 41.73 2.43
130 131 8.248945 CACAAAAGGAAATTTGATCTATGCTCT 58.751 33.333 0.00 0.00 41.73 4.09
142 143 8.743714 TGCCAAAAATTACACAAAAGGAAATTT 58.256 25.926 0.00 0.00 32.61 1.82
143 144 8.187480 GTGCCAAAAATTACACAAAAGGAAATT 58.813 29.630 0.00 0.00 33.23 1.82
144 145 7.466590 CGTGCCAAAAATTACACAAAAGGAAAT 60.467 33.333 0.00 0.00 33.23 2.17
146 147 5.292101 CGTGCCAAAAATTACACAAAAGGAA 59.708 36.000 0.00 0.00 33.23 3.36
147 148 4.806247 CGTGCCAAAAATTACACAAAAGGA 59.194 37.500 0.00 0.00 33.23 3.36
148 149 4.806247 TCGTGCCAAAAATTACACAAAAGG 59.194 37.500 0.00 0.00 33.23 3.11
149 150 5.957910 TCGTGCCAAAAATTACACAAAAG 57.042 34.783 0.00 0.00 33.23 2.27
150 151 6.910536 ATTCGTGCCAAAAATTACACAAAA 57.089 29.167 0.00 0.00 33.23 2.44
151 152 6.910536 AATTCGTGCCAAAAATTACACAAA 57.089 29.167 0.00 0.00 33.23 2.83
153 154 6.642950 CCTAAATTCGTGCCAAAAATTACACA 59.357 34.615 0.00 0.00 33.23 3.72
154 155 6.864165 TCCTAAATTCGTGCCAAAAATTACAC 59.136 34.615 0.00 0.00 0.00 2.90
155 156 6.982852 TCCTAAATTCGTGCCAAAAATTACA 58.017 32.000 0.00 0.00 0.00 2.41
156 157 6.034577 GCTCCTAAATTCGTGCCAAAAATTAC 59.965 38.462 0.00 0.00 0.00 1.89
158 159 4.929211 GCTCCTAAATTCGTGCCAAAAATT 59.071 37.500 0.00 0.00 0.00 1.82
159 160 4.220602 AGCTCCTAAATTCGTGCCAAAAAT 59.779 37.500 0.00 0.00 0.00 1.82
160 161 3.572255 AGCTCCTAAATTCGTGCCAAAAA 59.428 39.130 0.00 0.00 0.00 1.94
163 164 2.356135 GAGCTCCTAAATTCGTGCCAA 58.644 47.619 0.87 0.00 0.00 4.52
164 165 1.739035 CGAGCTCCTAAATTCGTGCCA 60.739 52.381 8.47 0.00 0.00 4.92
165 166 0.931005 CGAGCTCCTAAATTCGTGCC 59.069 55.000 8.47 0.00 0.00 5.01
166 167 1.922570 TCGAGCTCCTAAATTCGTGC 58.077 50.000 8.47 0.00 34.83 5.34
167 168 5.059832 CGATATTCGAGCTCCTAAATTCGTG 59.940 44.000 8.47 0.00 43.74 4.35
182 183 4.098055 GCTTATGAGCCTCGATATTCGA 57.902 45.455 0.00 0.00 44.03 3.71
204 205 1.860950 GAGATAAAGCATGCTTCGCGA 59.139 47.619 32.01 18.06 34.84 5.87
205 206 1.863454 AGAGATAAAGCATGCTTCGCG 59.137 47.619 32.01 0.00 34.84 5.87
206 207 3.559242 AGAAGAGATAAAGCATGCTTCGC 59.441 43.478 32.01 21.30 37.43 4.70
207 208 4.025061 CCAGAAGAGATAAAGCATGCTTCG 60.025 45.833 32.01 13.19 37.43 3.79
209 210 3.631227 GCCAGAAGAGATAAAGCATGCTT 59.369 43.478 27.21 27.21 37.98 3.91
210 211 3.117963 AGCCAGAAGAGATAAAGCATGCT 60.118 43.478 16.30 16.30 0.00 3.79
211 212 3.003482 CAGCCAGAAGAGATAAAGCATGC 59.997 47.826 10.51 10.51 0.00 4.06
212 213 3.564644 CCAGCCAGAAGAGATAAAGCATG 59.435 47.826 0.00 0.00 0.00 4.06
213 214 3.818180 CCAGCCAGAAGAGATAAAGCAT 58.182 45.455 0.00 0.00 0.00 3.79
215 216 1.946081 GCCAGCCAGAAGAGATAAAGC 59.054 52.381 0.00 0.00 0.00 3.51
217 218 1.915489 TGGCCAGCCAGAAGAGATAAA 59.085 47.619 7.43 0.00 41.89 1.40
219 220 3.322501 TGGCCAGCCAGAAGAGATA 57.677 52.632 7.43 0.00 41.89 1.98
220 221 4.159099 TGGCCAGCCAGAAGAGAT 57.841 55.556 7.43 0.00 41.89 2.75
229 230 1.004679 CCAAACATGTTGGCCAGCC 60.005 57.895 17.83 7.35 32.18 4.85
230 231 0.106521 AACCAAACATGTTGGCCAGC 59.893 50.000 12.82 13.50 43.23 4.85
231 232 1.868469 CAACCAAACATGTTGGCCAG 58.132 50.000 12.82 0.00 43.23 4.85
236 237 2.802774 GCTGTCCCAACCAAACATGTTG 60.803 50.000 12.82 2.87 42.11 3.33
239 240 0.318120 GGCTGTCCCAACCAAACATG 59.682 55.000 0.00 0.00 0.00 3.21
240 241 1.178534 CGGCTGTCCCAACCAAACAT 61.179 55.000 0.00 0.00 0.00 2.71
242 243 1.104577 TTCGGCTGTCCCAACCAAAC 61.105 55.000 0.00 0.00 0.00 2.93
243 244 1.104577 GTTCGGCTGTCCCAACCAAA 61.105 55.000 0.00 0.00 0.00 3.28
244 245 1.527380 GTTCGGCTGTCCCAACCAA 60.527 57.895 0.00 0.00 0.00 3.67
246 247 3.047877 CGTTCGGCTGTCCCAACC 61.048 66.667 0.00 0.00 0.00 3.77
247 248 3.047877 CCGTTCGGCTGTCCCAAC 61.048 66.667 0.00 0.00 0.00 3.77
249 250 3.998672 GTCCGTTCGGCTGTCCCA 61.999 66.667 6.35 0.00 0.00 4.37
250 251 3.644399 GAGTCCGTTCGGCTGTCCC 62.644 68.421 6.35 0.00 0.00 4.46
252 253 1.153997 GAGAGTCCGTTCGGCTGTC 60.154 63.158 6.35 10.69 0.00 3.51
255 256 0.244178 GAAAGAGAGTCCGTTCGGCT 59.756 55.000 6.35 7.08 0.00 5.52
257 258 0.240411 ACGAAAGAGAGTCCGTTCGG 59.760 55.000 22.73 4.74 46.75 4.30
261 262 2.296471 ACATGAACGAAAGAGAGTCCGT 59.704 45.455 0.00 0.00 36.77 4.69
263 264 5.694910 TGTTTACATGAACGAAAGAGAGTCC 59.305 40.000 0.00 0.00 32.18 3.85
264 265 6.764877 TGTTTACATGAACGAAAGAGAGTC 57.235 37.500 0.00 0.00 32.18 3.36
265 266 7.226720 ACAATGTTTACATGAACGAAAGAGAGT 59.773 33.333 0.00 0.00 36.56 3.24
266 267 7.531871 CACAATGTTTACATGAACGAAAGAGAG 59.468 37.037 0.00 0.00 36.56 3.20
267 268 7.225734 TCACAATGTTTACATGAACGAAAGAGA 59.774 33.333 0.00 0.00 36.56 3.10
268 269 7.321271 GTCACAATGTTTACATGAACGAAAGAG 59.679 37.037 0.00 0.00 36.56 2.85
269 270 7.129622 GTCACAATGTTTACATGAACGAAAGA 58.870 34.615 0.00 0.00 36.56 2.52
271 272 5.904630 CGTCACAATGTTTACATGAACGAAA 59.095 36.000 0.00 0.00 36.56 3.46
273 274 4.508492 ACGTCACAATGTTTACATGAACGA 59.492 37.500 18.11 4.53 36.56 3.85
274 275 4.768145 ACGTCACAATGTTTACATGAACG 58.232 39.130 0.00 13.31 36.56 3.95
275 276 4.838642 CGACGTCACAATGTTTACATGAAC 59.161 41.667 17.16 0.00 36.56 3.18
276 277 4.508492 ACGACGTCACAATGTTTACATGAA 59.492 37.500 17.16 0.00 36.56 2.57
277 278 4.052608 ACGACGTCACAATGTTTACATGA 58.947 39.130 17.16 0.00 36.56 3.07
278 279 4.383774 ACGACGTCACAATGTTTACATG 57.616 40.909 17.16 0.00 36.56 3.21
280 281 7.634809 TTATTACGACGTCACAATGTTTACA 57.365 32.000 17.16 0.00 0.00 2.41
281 282 8.916657 TTTTATTACGACGTCACAATGTTTAC 57.083 30.769 17.16 0.00 0.00 2.01
282 283 8.763356 ACTTTTATTACGACGTCACAATGTTTA 58.237 29.630 17.16 0.00 0.00 2.01
286 287 7.004980 CGAAACTTTTATTACGACGTCACAATG 59.995 37.037 17.16 0.66 0.00 2.82
288 289 6.346339 CGAAACTTTTATTACGACGTCACAA 58.654 36.000 17.16 8.81 0.00 3.33
290 291 5.116983 TCCGAAACTTTTATTACGACGTCAC 59.883 40.000 17.16 0.00 0.00 3.67
291 292 5.218885 TCCGAAACTTTTATTACGACGTCA 58.781 37.500 17.16 0.00 0.00 4.35
292 293 5.343325 ACTCCGAAACTTTTATTACGACGTC 59.657 40.000 2.43 5.18 0.00 4.34
293 294 5.222631 ACTCCGAAACTTTTATTACGACGT 58.777 37.500 5.52 5.52 0.00 4.34
295 296 6.301607 GCAAACTCCGAAACTTTTATTACGAC 59.698 38.462 0.00 0.00 0.00 4.34
297 298 5.566395 GGCAAACTCCGAAACTTTTATTACG 59.434 40.000 0.00 0.00 0.00 3.18
298 299 6.675026 AGGCAAACTCCGAAACTTTTATTAC 58.325 36.000 0.00 0.00 0.00 1.89
299 300 6.887626 AGGCAAACTCCGAAACTTTTATTA 57.112 33.333 0.00 0.00 0.00 0.98
301 302 6.887626 TTAGGCAAACTCCGAAACTTTTAT 57.112 33.333 0.00 0.00 0.00 1.40
302 303 6.696441 TTTAGGCAAACTCCGAAACTTTTA 57.304 33.333 0.00 0.00 0.00 1.52
303 304 5.585820 TTTAGGCAAACTCCGAAACTTTT 57.414 34.783 0.00 0.00 0.00 2.27
305 306 5.585820 TTTTTAGGCAAACTCCGAAACTT 57.414 34.783 0.00 0.00 31.86 2.66
333 334 4.690748 CGTCTGTTATTCTCTTTCAGGCAA 59.309 41.667 0.00 0.00 31.34 4.52
334 335 4.245660 CGTCTGTTATTCTCTTTCAGGCA 58.754 43.478 0.00 0.00 31.34 4.75
335 336 3.062774 GCGTCTGTTATTCTCTTTCAGGC 59.937 47.826 0.00 0.00 0.00 4.85
336 337 3.304559 CGCGTCTGTTATTCTCTTTCAGG 59.695 47.826 0.00 0.00 0.00 3.86
337 338 3.241804 GCGCGTCTGTTATTCTCTTTCAG 60.242 47.826 8.43 0.00 0.00 3.02
339 340 2.666508 TGCGCGTCTGTTATTCTCTTTC 59.333 45.455 8.43 0.00 0.00 2.62
340 341 2.683968 TGCGCGTCTGTTATTCTCTTT 58.316 42.857 8.43 0.00 0.00 2.52
344 345 2.683968 TCTTTGCGCGTCTGTTATTCT 58.316 42.857 8.43 0.00 0.00 2.40
441 5154 1.234615 CGCCGAAATCTTGGTGTGGT 61.235 55.000 0.00 0.00 0.00 4.16
625 5344 4.033358 CGAATCAAGAGTGAAATCGGGAAG 59.967 45.833 7.15 0.00 40.62 3.46
669 5389 2.082231 CACAAGAGAGCCACAATGGAG 58.918 52.381 0.00 0.00 40.96 3.86
740 5489 1.765314 AGGCAATGGCAGAGTACCTAG 59.235 52.381 10.05 0.00 43.71 3.02
742 5491 1.879575 TAGGCAATGGCAGAGTACCT 58.120 50.000 10.05 0.00 43.71 3.08
1464 6300 2.223900 TGGATCACACATCTCATCGCTC 60.224 50.000 0.00 0.00 0.00 5.03
1479 6315 3.410628 ATGGCTGGCCGTGGATCA 61.411 61.111 5.44 0.00 39.42 2.92
1537 6374 7.036154 AGAGGAAATTATATCATCCATGGCA 57.964 36.000 6.96 0.00 34.30 4.92
2142 8293 7.443879 TCACAGCAACTTACATCAAGATTACAA 59.556 33.333 0.00 0.00 37.71 2.41
2174 8325 7.884816 TCTTTTTATTTCTCCTCGTAGTGTG 57.115 36.000 0.00 0.00 0.00 3.82
2175 8326 8.148999 ACTTCTTTTTATTTCTCCTCGTAGTGT 58.851 33.333 0.00 0.00 0.00 3.55
2235 8392 2.618241 TGAAACATGTGACCAACTCTGC 59.382 45.455 0.00 0.00 0.00 4.26
2241 8398 6.353323 TCTAGTTCTTGAAACATGTGACCAA 58.647 36.000 0.00 3.45 0.00 3.67
2306 8468 7.531857 TTAATTGCACCACCTTTTCTAATCA 57.468 32.000 0.00 0.00 0.00 2.57
2416 8580 3.458044 AGTGACTAGACACAGGGATCA 57.542 47.619 23.90 0.00 42.45 2.92
2423 8587 6.650427 AACAAGATGTAGTGACTAGACACA 57.350 37.500 23.90 9.91 42.45 3.72
2424 8588 7.145985 TGAAACAAGATGTAGTGACTAGACAC 58.854 38.462 16.23 16.23 40.60 3.67
2427 8591 6.719829 TCCTGAAACAAGATGTAGTGACTAGA 59.280 38.462 0.00 0.00 0.00 2.43
2428 8592 6.925211 TCCTGAAACAAGATGTAGTGACTAG 58.075 40.000 0.00 0.00 0.00 2.57
2429 8593 6.911250 TCCTGAAACAAGATGTAGTGACTA 57.089 37.500 0.00 0.00 0.00 2.59
2430 8594 5.808366 TCCTGAAACAAGATGTAGTGACT 57.192 39.130 0.00 0.00 0.00 3.41
2431 8595 7.819900 ACTAATCCTGAAACAAGATGTAGTGAC 59.180 37.037 0.00 0.00 0.00 3.67
2432 8596 7.819415 CACTAATCCTGAAACAAGATGTAGTGA 59.181 37.037 16.38 0.00 35.89 3.41
2433 8597 7.065085 CCACTAATCCTGAAACAAGATGTAGTG 59.935 40.741 15.51 15.51 34.99 2.74
2434 8598 7.106239 CCACTAATCCTGAAACAAGATGTAGT 58.894 38.462 0.00 0.00 0.00 2.73
2435 8599 6.037610 GCCACTAATCCTGAAACAAGATGTAG 59.962 42.308 0.00 0.00 0.00 2.74
2436 8600 5.880332 GCCACTAATCCTGAAACAAGATGTA 59.120 40.000 0.00 0.00 0.00 2.29
2437 8601 4.702131 GCCACTAATCCTGAAACAAGATGT 59.298 41.667 0.00 0.00 0.00 3.06
2438 8602 4.701651 TGCCACTAATCCTGAAACAAGATG 59.298 41.667 0.00 0.00 0.00 2.90
2439 8603 4.922206 TGCCACTAATCCTGAAACAAGAT 58.078 39.130 0.00 0.00 0.00 2.40
2646 8847 3.496870 GCTTGGGTTCGATCCAATCCTAT 60.497 47.826 17.49 0.00 42.63 2.57
2658 8872 1.613437 ACATTGGAAAGCTTGGGTTCG 59.387 47.619 0.00 0.00 0.00 3.95
2754 8970 8.415553 CCAATCTATAAGAGGAGAGCATATGAG 58.584 40.741 6.97 0.00 0.00 2.90
2778 8994 4.170256 GCTTTTTGTTCTTTGTTCGTCCA 58.830 39.130 0.00 0.00 0.00 4.02
2966 9184 5.428457 TGGTGTGTGATTCTATCTTATGGGT 59.572 40.000 0.00 0.00 0.00 4.51
2981 9199 5.590663 TGCTGTTATAACTTTTGGTGTGTGA 59.409 36.000 16.33 0.00 0.00 3.58
3061 9279 4.694037 GTGTTAAAGTACCACATCTCCACC 59.306 45.833 0.00 0.00 0.00 4.61
3062 9280 4.694037 GGTGTTAAAGTACCACATCTCCAC 59.306 45.833 2.33 0.00 36.94 4.02
3063 9281 4.595781 AGGTGTTAAAGTACCACATCTCCA 59.404 41.667 7.35 0.00 39.46 3.86
3064 9282 5.161943 AGGTGTTAAAGTACCACATCTCC 57.838 43.478 7.35 0.00 39.46 3.71
3065 9283 6.761714 CCATAGGTGTTAAAGTACCACATCTC 59.238 42.308 7.35 0.00 39.46 2.75
3066 9284 6.650120 CCATAGGTGTTAAAGTACCACATCT 58.350 40.000 7.35 4.00 39.46 2.90
3067 9285 5.296035 GCCATAGGTGTTAAAGTACCACATC 59.704 44.000 7.35 0.00 39.46 3.06
3068 9286 5.045140 AGCCATAGGTGTTAAAGTACCACAT 60.045 40.000 7.35 0.00 39.46 3.21
3069 9287 4.287585 AGCCATAGGTGTTAAAGTACCACA 59.712 41.667 7.35 0.00 39.46 4.17
3070 9288 4.840271 AGCCATAGGTGTTAAAGTACCAC 58.160 43.478 7.35 0.00 39.46 4.16
3071 9289 5.508280 AAGCCATAGGTGTTAAAGTACCA 57.492 39.130 7.35 0.00 39.46 3.25
3072 9290 5.941647 TCAAAGCCATAGGTGTTAAAGTACC 59.058 40.000 0.00 0.00 37.23 3.34
3073 9291 7.625828 ATCAAAGCCATAGGTGTTAAAGTAC 57.374 36.000 0.00 0.00 0.00 2.73
3074 9292 7.362574 GCAATCAAAGCCATAGGTGTTAAAGTA 60.363 37.037 0.00 0.00 0.00 2.24
3075 9293 6.572314 GCAATCAAAGCCATAGGTGTTAAAGT 60.572 38.462 0.00 0.00 0.00 2.66
3076 9294 5.807011 GCAATCAAAGCCATAGGTGTTAAAG 59.193 40.000 0.00 0.00 0.00 1.85
3077 9295 5.244851 TGCAATCAAAGCCATAGGTGTTAAA 59.755 36.000 0.00 0.00 0.00 1.52
3078 9296 4.769488 TGCAATCAAAGCCATAGGTGTTAA 59.231 37.500 0.00 0.00 0.00 2.01
3079 9297 4.339748 TGCAATCAAAGCCATAGGTGTTA 58.660 39.130 0.00 0.00 0.00 2.41
3080 9298 3.164268 TGCAATCAAAGCCATAGGTGTT 58.836 40.909 0.00 0.00 0.00 3.32
3081 9299 2.756760 CTGCAATCAAAGCCATAGGTGT 59.243 45.455 0.00 0.00 0.00 4.16
3082 9300 3.018856 TCTGCAATCAAAGCCATAGGTG 58.981 45.455 0.00 0.00 0.00 4.00
3083 9301 3.370840 TCTGCAATCAAAGCCATAGGT 57.629 42.857 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.